diff --git a/.Rbuildignore b/.Rbuildignore
index 9ce61f7..e9e993d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -11,6 +11,7 @@ codemeta.json
^README_files$
^LICENSE\.md$
^examples$
+^\.claude$
^\.github$
^doc$
^Meta$
diff --git a/.gitignore b/.gitignore
index da1ad62..4063398 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,9 @@
Rproj.user
.Rproj.user
.Rhistory
+README.html
+.claude/settings.local.json
+
# C++
.o
@@ -21,4 +24,3 @@ revdep/
# Mac
.DS_Store
-README.html
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
deleted file mode 100644
index 18f2611..0000000
--- a/CRAN-SUBMISSION
+++ /dev/null
@@ -1,3 +0,0 @@
-Version: 0.3.1
-Date: 2024-03-22 07:38:26 UTC
-SHA: 26301b740b0063b5ac98dd1061d8bd11e37077b3
diff --git a/DESCRIPTION b/DESCRIPTION
index ca18cd0..cfed481 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: mobsim
Type: Package
Title: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes
-Version: 0.3.2
+Version: 0.3.3
Authors@R: c(
person("Felix", "May", email = "felix.may@fu-berlin.de",
role = c("aut", "cre","cph"),
@@ -9,7 +9,7 @@ Authors@R: c(
person("Alban", "Sagouis", email = "alban.sagouis@idiv.de",
role = "aut",
comment = c(ORCID = "0000-0002-3827-1063")),
- person("German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig",
+ person("German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig",
role = "fnd", comment = c(ROR = "01jty7g66")),
person("Freie Universität Berlin",
role = "fnd", comment = c(ROR = "046ak2485"))
@@ -24,7 +24,7 @@ Description: Simulation, analysis and sampling of spatial
decay of similarity.
License: GPL (>= 3)
Depends:
- R (>= 4.0.0)
+ R (>= 4.1.0)
Imports:
Rcpp,
vegan,
@@ -33,10 +33,11 @@ Imports:
utils,
graphics,
stats,
+ spatstat.geom,
+ spatstat.explore,
methods
Suggests:
quarto,
- spatstat.geom,
spatstat.random,
testthat (>= 3.0.0),
mockery,
@@ -44,9 +45,10 @@ Suggests:
LinkingTo: Rcpp
Config/testthat/edition: 3
Config/testthat/parallel: false
+Config/testthat/start-first: *utils*, *create_motherpoints*, *simulation*, *sampling*
VignetteBuilder: quarto
Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
Language: en-GB
Encoding: UTF-8
URL: https://github.com/MoBiodiv/mobsim
diff --git a/NAMESPACE b/NAMESPACE
index 2274fae..0482202 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,20 +3,35 @@
S3method(plot,community)
S3method(plot,dist_decay)
S3method(plot,divar)
+S3method(plot,mother_map)
S3method(plot,sad)
S3method(plot,spec_sample_curve)
S3method(summary,community)
S3method(summary,sad)
+S3method(torusify,community)
+S3method(torusify,data.frame)
+S3method(torusify,mother_map)
+S3method(torusify,numeric)
export(abund_rect)
export(community)
+export(community2ppp)
export(community_to_sad)
+export(create_motherpoints)
+export(create_random_ID)
export(dist_decay)
export(dist_decay_quadrats)
export(div_rand_rect)
export(div_rect)
export(divar)
+export(drift_x_motherpoints)
+export(drift_x_species)
+export(drift_y_motherpoints)
+export(drift_y_species)
+export(jitter_motherpoints)
+export(jitter_species)
export(rThomas_rcpp)
export(rare_curve)
+export(replace_individuals)
export(sample_quadrats)
export(sampling_grids)
export(sampling_one_quadrat)
@@ -31,7 +46,11 @@ export(sim_thomas_community)
export(sim_thomas_coords)
export(spec_sample)
export(spec_sample_curve)
+export(torusify)
importFrom(Rcpp,sourceCpp)
importFrom(methods,is)
importFrom(sads,rsad)
+importFrom(spatstat.explore,marktable)
+importFrom(spatstat.geom,owin)
+importFrom(spatstat.geom,ppp)
useDynLib(mobsim, .registration = TRUE)
diff --git a/R/Diversity_Area_Relationships.R b/R/Diversity_Area_Relationships.R
index 9681a0d..e8a16d2 100644
--- a/R/Diversity_Area_Relationships.R
+++ b/R/Diversity_Area_Relationships.R
@@ -118,8 +118,8 @@ div_rand_rect <- function(
n_rect = 100,
exclude_zeros = FALSE
) {
- dx_plot <- comm$x_min_max[2] - comm$x_min_max[1]
- dy_plot <- comm$y_min_max[2] - comm$y_min_max[1]
+ dx_plot <- comm$x_min_max[[2]] - comm$x_min_max[[1]]
+ dy_plot <- comm$y_min_max[[2]] - comm$y_min_max[[1]]
area <- dx_plot * dy_plot * prop_area
square_size <- sqrt(area)
@@ -139,13 +139,13 @@ div_rand_rect <- function(
xpos <- stats::runif(
n_rect,
- min = comm$x_min_max[1],
- max = comm$x_min_max[2] - dx_rect
+ min = comm$x_min_max[[1]],
+ max = comm$x_min_max[[2]] - dx_rect
)
ypos <- stats::runif(
n_rect,
- min = comm$y_min_max[1],
- max = comm$y_min_max[2] - dy_rect
+ min = comm$y_min_max[[1]],
+ max = comm$y_min_max[[2]] - dy_rect
)
div_plots <- mapply(
@@ -154,7 +154,7 @@ div_rand_rect <- function(
ypos,
MoreArgs = list(xsize = dx_rect, ysize = dy_rect, comm = comm)
)
- if (exclude_zeros == TRUE)
+ if (isTRUE(exclude_zeros))
div_plots <- div_plots[, div_plots["n_species", ] > 0]
return(c(
@@ -220,8 +220,8 @@ divar <- function(
stop("DiVAR requires a community object as input. See ?community.")
n_scales <- length(prop_area)
- dx_plot <- comm$x_min_max[2] - comm$x_min_max[1]
- dy_plot <- comm$y_min_max[2] - comm$y_min_max[1]
+ dx_plot <- comm$x_min_max[[2]] - comm$x_min_max[[1]]
+ dy_plot <- comm$y_min_max[[2]] - comm$y_min_max[[1]]
div_area <- sapply(
prop_area,
@@ -314,11 +314,11 @@ abund_rect <- function(x0, y0, xsize, ysize, comm) {
x <- comm$census$x
y <- comm$census$y
- # logical vector which trees are in the sampling rectangle
- in_rect <- (x >= x0 & x < (x0 + xsize) & y >= y0 & y < (y0 + ysize))
+ # logical vector which trees are in the sampling rectangle
+ in_rect <- (x >= x0 & x < (x0 + xsize) & y >= y0 & y < (y0 + ysize))
- abund <- table(comm$census$species[in_rect])
- return(abund)
+ abund <- table(comm$census$species[in_rect])
+ return(abund)
}
#' Distance decay of similarity
@@ -345,6 +345,7 @@ abund_rect <- function(x0, y0, xsize, ysize, comm) {
#'@export
#'
dist_decay <- function(
+ comm,
prop_area = 0.005,
n_samples = 20,
method = "bray",
@@ -354,12 +355,12 @@ dist_decay <- function(
if (length(prop_area) != 1L) stop("prop_area has to be of length 1")
- if (!is(comm, "community"))
- stop("dist_decay requires a community object as input. See ?community.")
+ if (!is(comm, "community"))
+ stop("dist_decay requires a community object as input. See ?community.")
- dx_plot <- comm$x_min_max[2] - comm$x_min_max[1]
- dy_plot <- comm$y_min_max[2] - comm$y_min_max[1]
- area <- dx_plot * dy_plot * prop_area
+ dx_plot <- comm$x_min_max[[2]] - comm$x_min_max[[1]]
+ dy_plot <- comm$y_min_max[[2]] - comm$y_min_max[[1]]
+ area <- dx_plot * dy_plot * prop_area
samples1 <- sample_quadrats(
comm,
@@ -379,12 +380,12 @@ dist_decay <- function(
similarity = as.numeric(similarity)
)
- # order by increasing distance
- dat_out <- dat_out[order(dat_out$distance), ]
+ # order by increasing distance
+ dat_out <- dat_out[order(dat_out$distance), ]
- class(dat_out) <- c("dist_decay", "data.frame")
+ class(dat_out) <- c("dist_decay", "data.frame")
- return(dat_out)
+ return(dat_out)
}
#' Distance decay of similarity with user-defined quadrats
@@ -424,12 +425,12 @@ dist_decay_quadrats <- function(samples, method = "bray", binary = FALSE) {
similarity = as.numeric(similarity)
)
- # order by increasing distance
- dat_out <- dat_out[order(dat_out$distance), ]
+ # order by increasing distance
+ dat_out <- dat_out[order(dat_out$distance), ]
- class(dat_out) <- c("dist_decay", "data.frame")
+ class(dat_out) <- c("dist_decay", "data.frame")
- return(dat_out)
+ return(dat_out)
}
@@ -503,4 +504,3 @@ plot.dist_decay <- function(x, ...) {
#
# return(abund.plots[,1])
# }
-#
diff --git a/R/Sample_quadrats.R b/R/Sample_quadrats.R
index ff2b145..a6189a1 100644
--- a/R/Sample_quadrats.R
+++ b/R/Sample_quadrats.R
@@ -57,18 +57,18 @@ sample_quadrats <- function(
quadrat_size <- sqrt(quadrat_area)
- community_size <- (comm$x_min_max[2] - comm$x_min_max[1]) *
- (comm$y_min_max[2] - comm$y_min_max[1])
+ community_size <- (comm$x_min_max[[2]] - comm$x_min_max[[1]]) *
+ (comm$y_min_max[[2]] - comm$y_min_max[[1]])
if (quadrat_size < community_size) {
# This works as long as we use square quadrats
if (n_quadrats == 1L) {
xy_dat <- sampling_one_quadrat(
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2] - quadrat_size,
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2] - quadrat_size,
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]] - quadrat_size,
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]] - quadrat_size,
seed = seed
)
} else {
@@ -80,20 +80,20 @@ sample_quadrats <- function(
xy_dat <- sampling_random_spatstat(
n_quadrats = n_quadrats,
min_dist = min_dist,
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2] - quadrat_size,
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2] - quadrat_size,
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]] - quadrat_size,
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]] - quadrat_size,
seed = seed
)
} else {
xy_dat <- sampling_random_bruteforce(
n_quadrats = n_quadrats,
min_dist = min_dist,
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2] - quadrat_size,
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2] - quadrat_size,
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]] - quadrat_size,
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]] - quadrat_size,
seed = seed
)
} # end of no spatstat
@@ -102,10 +102,10 @@ sample_quadrats <- function(
xy_dat <- sampling_random_overlap(
n_quadrats = n_quadrats,
min_dist = min_dist,
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2] - quadrat_size,
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2] - quadrat_size,
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]] - quadrat_size,
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]] - quadrat_size,
seed = seed
)
}
@@ -114,10 +114,10 @@ sample_quadrats <- function(
if (method == "transect") {
xy_dat <- sampling_transects(
n_quadrats = n_quadrats,
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2],
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2],
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]],
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]],
x0 = x0,
y0 = y0,
delta_x = delta_x,
@@ -129,10 +129,10 @@ sample_quadrats <- function(
if (method == "grid") {
xy_dat <- sampling_grids(
n_quadrats = n_quadrats,
- xmin = comm$x_min_max[1],
- xmax = comm$x_min_max[2],
- ymin = comm$y_min_max[1],
- ymax = comm$y_min_max[2],
+ xmin = comm$x_min_max[[1]],
+ xmax = comm$x_min_max[[2]],
+ ymin = comm$y_min_max[[1]],
+ ymax = comm$y_min_max[[2]],
x0 = x0,
y0 = y0,
delta_x = delta_x,
@@ -156,8 +156,8 @@ sample_quadrats <- function(
comm_tab <- table(comm$census$species)
xy_dat <- data.frame(
- x = comm$x_min_max[1],
- y = comm$y_min_max[1]
+ x = comm$x_min_max[[1]],
+ y = comm$y_min_max[[1]]
)
rownames(xy_dat) <- "site1"
@@ -171,13 +171,13 @@ sample_quadrats <- function(
}
# plot sampling design
- if (plot == TRUE) {
+ if (isTRUE(plot)) {
plot(comm)
graphics::rect(
- xy_dat$x,
- xy_dat$y,
- xy_dat$x + quadrat_size,
- xy_dat$y + quadrat_size,
+ xleft = xy_dat$x,
+ ybottom = xy_dat$y,
+ xright = xy_dat$x + quadrat_size,
+ ytop = xy_dat$y + quadrat_size,
lwd = 2,
col = grDevices::adjustcolor("white", alpha.f = 0.6)
)
@@ -243,7 +243,7 @@ sampling_random_spatstat <- function(
#' Creates coordinates (lower left corner of a quadrat) randomly distributed but without overlapping each
#' other
#'
-#' This function works without having the \code{spatstat.random} package install.
+#' This function works without having the \code{spatstat.random} package installed.
#'
#' @inheritParams sampling_random_spatstat
#'
diff --git a/R/Sim_Community.R b/R/Sim_Community.R
index 5b5d0ee..497a515 100644
--- a/R/Sim_Community.R
+++ b/R/Sim_Community.R
@@ -266,7 +266,7 @@ sim_sad <- function(
abund_local <- table(sample_vec)
s_local <- sum(abund_local > 0L)
- if (fix_s_sim == TRUE && s_local < s_pool) {
+ if (isTRUE(fix_s_sim) && s_local < s_pool) {
s_diff <- s_pool - s_local
abund_local[abund_local == 0L] <- 1L
N <- sum(abund_local)
@@ -333,6 +333,7 @@ summary.sad <- function(object, ...) {
#' species abundance rank on the x-axis (descending) and species abundance on
#' the y-axis (Hubbell 2001).
#'
+#'
#' @return This function is called for its side effects and has no return value.
#'
#' @references
@@ -655,6 +656,8 @@ sim_poisson_community <- function(
yrange = c(0, 1),
seed = NULL
) {
+ base::stopifnot("n_sim has to be >= to s_pool" = n_sim >= s_pool)
+
abund_vec <- sim_sad(
s_pool = s_pool,
n_sim = n_sim,
@@ -1144,6 +1147,7 @@ sim_thomas_community <- function(
yrange = c(0, 1),
seed = NULL
) {
+ base::stopifnot("n_sim has to be >= to s_pool" = n_sim >= s_pool)
abund_vec <- sim_sad(
s_pool = s_pool,
n_sim = n_sim,
diff --git a/R/create_motherpoints.R b/R/create_motherpoints.R
new file mode 100644
index 0000000..3c1943d
--- /dev/null
+++ b/R/create_motherpoints.R
@@ -0,0 +1,137 @@
+#' Creates a random number of mother points for a given number of species
+#'
+#' @param s_local (integer) Species number.
+#' @param n_motherpoints_range (integer vector) Vector of integer values for the number of motherpoints a species can get.
+#' @param xrange (numeric vector) Extent of the community in x-direction.
+#' @param yrange (numeric vector) Extent of the community in y-direction.
+#' @param seed (integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.
+#'
+#' @returns A named list of class \code{mother_map} with three elements:
+#' \enumerate{
+#' \item \code{n_mother_points} a vector of integers giving the number of mother points per species
+#' \item \code{xmother} List of length equal to the number of species. Each list element
+#' is a vector of x coordinates for every mother point. If one element is \code{numeric(0)}, the
+#' corresponding species has no mother point and is not clustered.
+#' \item \code{ymother} List of length equal to the number of species. Each list element
+#' is a vector of y coordinates for every mother point. If one element is \code{numeric(0)}, the
+#' corresponding species has no mother point and is not clustered.
+#' }
+#'
+#' @details For each species, the function first draws a random number of
+#' mother points in the given \code{n_motherpoints_range}. Then the function
+#' places as many mother points as needed in the window given by \code{xrange}
+#' and \code{yrange}.
+#' @author Alban Sagouis
+#'
+#'
+#' @examples
+#' # Default behaviour
+#' mpcoords <- create_motherpoints(s_local = 10L)
+#'
+#' # With more variability for the number of motherpoints
+#' mpcoords <- create_motherpoints(s_local = 10L, n_motherpoints_range = 1L:100L)
+#'
+#' # Allowing no clustering at all
+#' mpcoords <- create_motherpoints(s_local = 10L, n_motherpoints_range = 0L:5L)
+#'
+#' # Fixing the seed
+#' mpcoords <- create_motherpoints(10L, seed = 42L)
+#'
+#' # Integration with mobsim::sim_thomas_coords()
+#' abund_vec <- 11L:100L # a community with 90 species
+#' s_local <- length(abund_vec)
+#' mpcoords <- create_motherpoints(s_local, seed = 42L)
+#' simdat <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' # Integration with mobsim::sim_thomas_coords() without clustering
+#' abund_vec <- 20L:25L
+#' s_local <- length(abund_vec)
+#' mpcoords <- create_motherpoints(s_local, n_motherpoints_range = 0L:1L, seed = 42L)
+#' simdat <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' plot(simdat)
+#'
+#' @export
+
+create_motherpoints <- function(
+ s_local,
+ n_motherpoints_range = 1:4,
+ xrange = c(0, 1),
+ yrange = c(0, 1),
+ seed = NULL
+) {
+ if (!is.null(seed)) set.seed(seed)
+
+ n_mother_points <- sample(
+ x = n_motherpoints_range,
+ size = s_local,
+ replace = TRUE
+ )
+ xmother <- lapply(
+ n_mother_points,
+ stats::runif,
+ min = xrange[[1L]],
+ max = xrange[[2L]]
+ )
+ ymother <- lapply(
+ n_mother_points,
+ stats::runif,
+ min = yrange[[1L]],
+ max = yrange[[2L]]
+ )
+
+ mpcoords <- list(
+ n_mother_points = n_mother_points,
+ xmother = xmother,
+ ymother = ymother,
+ x_min_max = xrange,
+ y_min_max = yrange
+ )
+ class(mpcoords) <- c("mother_map", "list")
+
+ return(mpcoords)
+}
+
+
+#' Plot mother_map object object
+#'
+#' Plot positions and species identities of all mother points created by
+#' \code{\link{create_motherpoints}} or \code{\link{jitter_motherpoints}}.
+#'
+#' @param x mother_map object
+#' @param col Colour vector to mark species identities
+#' @param pch Plotting character to mark species identities.
+#' pch 16 is advised for large data sets.
+#' @param ... Other parameters to \code{\link[graphics:plot.default]{graphics::plot}}
+#'
+#' @rdname create_motherpoints
+#'
+#' @examples
+#' mpcoords <- create_motherpoints(10L)
+#' plot(mpcoords)
+#'
+#' @export
+#'
+plot.mother_map <- function(x, col = NULL, pch = NULL, ...) {
+ nspec <- length(x$n_mother_points)
+ if (is.null(col)) col <- grDevices::rainbow(nspec, alpha = 1)
+ if (is.null(pch)) pch <- 16
+
+ graphics::plot(
+ x = unlist(x$xmother),
+ y = unlist(x$ymother),
+ xlim = x$x_min_max,
+ ylim = x$y_min_max,
+ col = rep(x = seq_along(x$n_mother_points), times = x$n_mother_points),
+ xlab = "X",
+ ylab = "Y",
+ pch = pch,
+ las = 1,
+ asp = 1,
+ ...
+ )
+}
diff --git a/R/drift_motherpoints.R b/R/drift_motherpoints.R
new file mode 100644
index 0000000..fadcca3
--- /dev/null
+++ b/R/drift_motherpoints.R
@@ -0,0 +1,79 @@
+#' Adds a fixed drift movement to mother points x coordinates
+#'
+#' @param drift (numeric) Amount of spatial drift
+#' @inheritParams jitter_motherpoints
+#' @rdname drift_motherpoints
+#'
+#' @returns A named list of class \code{mother_map} with three elements:
+#' \enumerate{
+#' \item \code{n_mother_points} a vector of integers giving the number of
+#' mother points per species
+#' \item \code{xmother} List of length equal to the number of species. Each
+#' list element is a vector of x coordinates for every mother points. If one
+#' element is NA, the the corresponding species is not clustered.
+#' \item \code{ymother} List of length equal to the number of species. Each
+#' list element is a vector of y coordinates for every mother points. If one
+#' element is NA, the the corresponding species is not clustered.
+#' }
+#'
+#' @details The function takes a \code{mother_map} object and adds a fixed
+#' drift value to either the x or y coordinates. In a 1 by 1 landscape, a drift
+#' of 0.5 means moving over half the map.
+#'
+#' @author Alban Sagouis
+#'
+#'
+#' @examples
+#' # Default behaviour
+#' mpcoords <- create_motherpoints(s_local = 10L)
+#' mpcoordsD <- drift_x_motherpoints(mpcoords, 0.1)
+#' par(mfrow = c(1L, 2L))
+#' plot(mpcoords)
+#' plot(mpcoordsD)
+#'
+#' # With more distance for the movements of motherpoints
+#' mpcoordsD <- mpcoords |>
+#' drift_x_motherpoints(drift = 0.5) |>
+#' drift_y_motherpoints(drift = 0.5)
+#'
+#' # Integration with mobsim::sim_thomas_coords()
+#' abund_vec <- 11L:100L # a community with 90 species
+#' s_local <- length(abund_vec)
+#' mpcoords <- create_motherpoints(s_local, seed = 42L)
+#' simdat <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' ## computing biodiversity metrics
+#' div1 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat,
+#' n_rect = 10L, exclude_zeros = TRUE)
+#'
+#' ## moving motherpoints slightly
+#' mpcoordsD <- drift_x_motherpoints(mpcoords, 0.01) |>
+#' drift_y_motherpoints(drift = 0.01)
+#' simdat2 <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' ## computing biodiversity metrics
+#' div2 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat2,
+#' n_rect = 10L, exclude_zeros = TRUE)
+#'
+#' @export
+
+drift_x_motherpoints <- function(mpcoords, drift) {
+ mpcoords$xmother <- lapply(mpcoords$xmother, function(x) x + drift)
+
+ return(mpcoords)
+}
+
+#' Adds a fixed drift movement to mother points y coordinates
+#' @inherit drift_x_motherpoints
+#' @rdname drift_motherpoints
+#' @export
+
+drift_y_motherpoints <- function(mpcoords, drift) {
+ mpcoords$ymother <- lapply(mpcoords$ymother, function(x) x + drift)
+
+ return(mpcoords)
+}
diff --git a/R/drift_species.R b/R/drift_species.R
new file mode 100644
index 0000000..0f92d0a
--- /dev/null
+++ b/R/drift_species.R
@@ -0,0 +1,47 @@
+#' Adds the same fixed movement to all individuals of a species on x
+#'
+#' @param drift (numeric) A single value added to the x or y coordinates.
+#' @inheritParams jitter_species
+#' @rdname drift_species
+#'
+#' @returns A named list of class \code{community} as described in
+#' \code{\link[mobsim]{community}}
+#'
+#' @details The function takes a \code{community} object and adds a fixed
+#' drift value to either x or y coordinate per species. In a 1 by 1 landscape, a
+#' drift of 0.5 means moving over half the map.
+#' @seealso drift_motherpoints
+#' @author Alban Sagouis
+#'
+#'
+#' @examples
+#' # Default behaviour
+#' simdat <- mobsim::sim_thomas_community(s_pool = 5L, n_sim = 100L,
+#' mother_points = 1L)
+#' simdatD <- simdat |>
+#' drift_x_species(0.1) |>
+#' drift_y_species(-0.2)
+#' par(mfrow = c(1L, 2L))
+#' plot(simdat)
+#' plot(simdatD)
+#'
+#' @export
+#'
+
+drift_x_species <- function(comm, drift) {
+ comm$census$x <- comm$census$x + drift
+
+ return(comm)
+}
+
+#' Adds the same fixed movement to all individuals of a species on y
+#' @inherit drift_x_species
+#' @rdname drift_species
+#' @export
+#'
+
+drift_y_species <- function(comm, drift) {
+ comm$census$y <- comm$census$y + drift
+
+ return(comm)
+}
diff --git a/R/jitter_motherpoints.R b/R/jitter_motherpoints.R
new file mode 100644
index 0000000..f603694
--- /dev/null
+++ b/R/jitter_motherpoints.R
@@ -0,0 +1,89 @@
+#' Adds a random movement to mother point coordinates
+#'
+#' @param mpcoords (mother_map) List of class \code{mother_map}.
+#' @param sd (numeric) Standard deviation for the \code{\link[stats]{rnorm}}.
+#' @inheritParams create_motherpoints
+#'
+#' @returns A named list of class \code{mother_map} with three elements:
+#' \enumerate{
+#' \item \code{n_mother_points} a vector of integers giving the number of mother points per species
+#' \item \code{xmother} List of length equal to the number of species. Each list element
+#' is a vector of x coordinates for every mother points. If one element is NA, the
+#' the corresponding species is not clustered.
+#' \item \code{ymother} List of length equal to the number of species. Each list element
+#' is a vector of y coordinates for every mother points. If one element is NA, the
+#' the corresponding species is not clustered.
+#' }
+#'
+#' @details The function takes a \code{mother_map} object and adds a random
+#' jitter value to each coordinate. The jitter follows a normal probability
+#' distribution of \code{mean} = 0 and \code{sd} specified by the used with
+#' argument \code{sd}.
+#'
+#' @author Alban Sagouis
+#'
+#'
+#' @examples
+#' # Default behaviour
+#' mpcoords <- create_motherpoints(s_local = 10L)
+#' mpcoordsJ <- jitter_motherpoints(mpcoords)
+#' par(mfrow = c(1L, 2L))
+#' plot(mpcoords)
+#' plot(mpcoordsJ)
+#'
+#' # With more variability for the movements of motherpoints
+#' mpcoordsJ <- jitter_motherpoints(mpcoords, sd = 2)
+#'
+#' # Fixing the seed
+#' mpcoordsJ <- jitter_motherpoints(mpcoords, seed = 42L)
+#'
+#' # Integration with mobsim::sim_thomas_coords()
+#' abund_vec <- 11L:100L # a community with 90 species
+#' s_local <- length(abund_vec)
+#' mpcoords <- create_motherpoints(s_local, seed = 42L)
+#' simdat <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' ## computing biodiversity metrics
+#' div1 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat, n_rect = 10L, exclude_zeros = TRUE)
+#'
+#' ## moving motherpoints slightly
+#' mpcoordsJ <- jitter_motherpoints(mpcoords)
+#' simdat2 <- mobsim::sim_thomas_coords(abund_vec,
+#' xmother = mpcoords$xmother, # list of vectors
+#' ymother = mpcoords$ymother # list of vectors
+#' )
+#' ## computing biodiversity metrics
+#' div2 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat2,
+#' n_rect = 10L, exclude_zeros = TRUE)
+#'
+#' @export
+
+jitter_motherpoints <- function(mpcoords, sd = 0.01, seed = NULL) {
+ if (!is.null(seed)) set.seed(seed)
+
+ mpcoords$xmother <- lapply(
+ mpcoords$xmother,
+ function(x)
+ x +
+ stats::rnorm(
+ n = length(x),
+ mean = 0,
+ sd = sd
+ )
+ )
+
+ mpcoords$ymother <- lapply(
+ mpcoords$ymother,
+ function(y)
+ y +
+ stats::rnorm(
+ n = length(y),
+ mean = 0,
+ sd = sd
+ )
+ )
+
+ return(mpcoords)
+}
diff --git a/R/jitter_species.R b/R/jitter_species.R
new file mode 100644
index 0000000..d7e106f
--- /dev/null
+++ b/R/jitter_species.R
@@ -0,0 +1,48 @@
+#' Adds the same random movement to all individuals of a species
+#'
+#' @param comm (community) List of class \code{community}.
+#' @inheritParams jitter_motherpoints
+#'
+#' @returns A named list of class \code{community} as described in
+#' \code{\link[mobsim]{community}}
+#'
+#' @details The function takes a \code{community} object and adds a random
+#' jitter value to each coordinate per species. The jitter follows a normal
+#' probability distribution of \code{mean} = 0 and \code{sd} specified by the
+#' used with argument \code{sd}.
+#' @seealso jitter_motherpoints
+#' @author Alban Sagouis
+#'
+#'
+#' @examples
+#' # Default behaviour
+#' simdat <- mobsim::sim_thomas_community(s_pool = 5L, n_sim = 100L,
+#' mother_points = 1L)
+#' simdatJ <- jitter_species(simdat)
+#' par(mfrow = c(1L, 2L))
+#' plot(simdat)
+#' plot(simdatJ)
+#'
+#' # With more variability for the movement of individuals
+#' simdatJ <- jitter_species(simdat, sd = 2)
+#'
+#' # Fixing the seed
+#' simdatJ <- jitter_species(simdat, seed = 42L)
+#'
+#' @export
+
+jitter_species <- function(comm, sd = 0.01, seed = NULL) {
+ if (!is.null(seed)) set.seed(seed)
+
+ sp <- unique(comm$census$species)
+ x_shift <- stats::setNames(
+ stats::rnorm(n = length(sp), mean = 0L, sd = sd), nm = sp
+ )
+ y_shift <- stats::setNames(
+ stats::rnorm(n = length(sp), mean = 0L, sd = sd), nm = sp
+ )
+ comm$census$x <- comm$census$x + x_shift[comm$census$species]
+ comm$census$y <- comm$census$y + y_shift[comm$census$species]
+
+ return(comm)
+}
diff --git a/R/mobsim_package.R b/R/mobsim_package.R
index dc08bc3..0810814 100644
--- a/R/mobsim_package.R
+++ b/R/mobsim_package.R
@@ -1,3 +1,12 @@
+## usethis namespace: start
+#' @importFrom Rcpp sourceCpp
+## usethis namespace: end
+NULL
+
+#' @useDynLib mobsim, .registration = TRUE
+#' @details
+#' `r lifecycle::badge("stable")`
+#'
#' mobsim: A package for spatial analysis of scale-dependent biodiversity changes.
#'
#' @description
@@ -5,11 +14,4 @@
#' as well as for the analysis of spatially-explicit data, where each individual
#' is described by its xy-coordinates and a species identity label.
#'
-#' @keywords internal
-#'
"_PACKAGE"
-NULL
-
-#' @useDynLib mobsim, .registration = TRUE
-#' @importFrom Rcpp sourceCpp
-NULL
diff --git a/R/reproduction.R b/R/reproduction.R
new file mode 100644
index 0000000..3338770
--- /dev/null
+++ b/R/reproduction.R
@@ -0,0 +1,45 @@
+#' Takes an object of class \code{\link[mobsim]{community}} and replaces
+#' individual species identities based on the neighbours
+#'
+#' @param comm Community object
+#' @importFrom spatstat.explore marktable
+#' @inheritParams spatstat.explore::marktable
+#' @inheritParams create_motherpoints
+#'
+#' @details For each individual, the function first identifies neighbours'
+#' identity using the \code{\link[spatstat.explore]{marktable}} function,
+#' computes relative abundances and uses these relative abundances as random
+#' drawing probabilities in \code{\link[base]{sample}}.
+#' The neighbourhood community of an individual is restricted by parameter N
+#' (number of individual) or R (radius).
+#' @author Alban Sagouis
+#'
+#' @examples
+#' # Integrated between mobsim::sim_thomas_coords() and the analysis of
+#' # biodiversity
+#' simdat <- mobsim::sim_thomas_coords(11L:100L)
+#' mobsim::div_rand_rect(comm = simdat, prop_area = 0.01, n_rect = 20L)
+#' simdat2 <- replace_individuals(simdat, N = 10L)
+#' mobsim::div_rand_rect(comm = simdat2, prop_area = 0.01, n_rect = 20L)
+#'
+#' @export
+
+replace_individuals <- function(comm, N = NULL, R = NULL, seed = NULL) {
+ if (is.null(N) && is.null(R))
+ stop("At least one of 'N' or 'R' must be specified.")
+ if (!is.null(seed)) set.seed(seed)
+
+ spatial_comm <- community2ppp(comm)
+
+ contingency_table <- spatstat.explore::marktable(spatial_comm, N = N, R = R)
+ S <- ncol(contingency_table)
+ comm$census$species <- factor(
+ apply(
+ X = contingency_table,
+ MARGIN = 1L,
+ FUN = function(ind)
+ names(ind)[[sample.int(n = S, size = 1L, prob = ind / sum(ind))]]
+ )
+ )
+ return(comm)
+}
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..5c0f5d4
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,249 @@
+# Utilities
+
+## torusify() ----
+#' Rounds coordinates around like on a torus
+#'
+#' @param mpcoords Can be either a data.frame with columns \code{xmother} and
+#' \code{ymother} or an object of class \code{mother_map} or a \code{numeric}
+#' vector.
+#' @param ... Kept for future uses.
+#'
+#' @details \code{torusify()} is a generic function that calls functions adapted
+#' to the class of argument \code{mapcoords}. Classes \code{data.frame},
+#' \code{numeric} and \code{mother_map} are accepted at the moment.
+#'
+#' \code{torusify()} takes coordinates and makes sure that all
+#' coordinates actually inside the window specified
+#' in \code{x_min_max} and \code{y_min_max}.
+#'
+#' @returns Object returned depends on the object given. For an object of class
+#' \code{mother_map} as given by \code{\link{create_motherpoints}}, see
+#' \code{\link{torusify.mother_map}}. For a \code{data.frame}, see
+#' \code{\link{torusify.data.frame}} and for a \code{numeric} vector, see
+#' \code{\link{torusify.numeric}}.
+#'
+#' @examples
+#' # Default behaviour
+#' mpcoords <- create_motherpoints(s_local = 10L)
+#' mpcoordsJ <- jitter_motherpoints(mpcoords)
+#' mcoordsT <- torusify(mpcoordsJ)
+#' @export
+
+torusify <- function(mpcoords, ...) {
+ UseMethod("torusify", mpcoords)
+}
+
+
+#' Rounds coordinates around like on a torus
+#'
+#' @param mpcoords A named list of class \code{mother_map} with three elements:
+#' \enumerate{
+#' \item \code{n_mother_points} a vector of integers giving the number of
+#' mother points per species \item \code{xmother} List of length equal to the
+#' number of species. Each list element is a vector of x coordinates for
+#' every mother points. If one element is NA, the the corresponding species
+#' is not clustered.
+#' \item \code{ymother} List of length equal to the number of species. Each
+#' list element is a vector of y coordinates for every mother points. If one
+#' element is NA, the the corresponding species is not clustered.
+#' }
+#' @param ... Kept for future uses.
+#'
+#' @returns An object of class \code{mother_map} of the same dimensions as the
+#' one provided to the function.
+#' @details The function takes a \code{mother_map} object and makes sure that
+#' all coordinates that were just jittered are actually inside the window
+#' specified in the \code{x_min_max} and \code{y_min_max} elements of the
+#' \code{mother_map} object.
+#'
+#' @author Alban Sagouis
+#'
+#' @examples
+#' # Default behaviour
+#' mpcoords <- create_motherpoints(s_local = 10L)
+#' mpcoordsJ <- jitter_motherpoints(mpcoords)
+#' mcoordsT <- torusify(mpcoordsJ)
+#'
+#' @rdname torusify
+#' @export
+
+torusify.mother_map <- function(mpcoords, ...) {
+ mpcoords$xmother <- lapply(
+ X = mpcoords$xmother,
+ FUN = function(MPs)
+ (MPs %% diff(mpcoords$x_min_max)) + mpcoords$x_min_max[1L]
+ )
+ mpcoords$ymother <- lapply(
+ X = mpcoords$ymother,
+ FUN = function(MPs)
+ (MPs %% diff(mpcoords$y_min_max)) + mpcoords$y_min_max[1L]
+ )
+
+ return(mpcoords)
+}
+
+
+#' Rounds coordinates around like on a torus
+#'
+#' @param mpcoords A list of class \code{\link[mobsim]{community}}
+#' @param ... Kept for future uses.
+#'
+#' @returns A list of class \code{community} of same dimension as
+#' \code{mpcoords}.
+#'
+#' @details The function takes a \code{community} and makes sure that all
+#' individual coordinates are actually inside the window specified by the
+#' \code{x_min_max} and \code{y_min_max} elements of the \code{community}
+#' object.
+#'
+#' @author Alban Sagouis
+#'
+#' @examples
+#' simdat <- mobsim::sim_thomas_community(10L, 100L, mother_points = 1)
+#' simdatJ <- jitter_species(simdat, sd = 1)
+#' simdatJ <- torusify(simdatJ)
+#'
+#' @rdname torusify
+#' @export
+
+torusify.community <- function(mpcoords, ...) {
+ mpcoords$census$x <- mpcoords$census$x %%
+ diff(mpcoords$x_min_max) +
+ mpcoords$x_min_max[1L]
+ mpcoords$census$y <- mpcoords$census$y %%
+ diff(mpcoords$y_min_max) +
+ mpcoords$y_min_max[1L]
+ return(mpcoords)
+}
+
+
+#' Rounds coordinates around like on a torus
+#'
+#' @param mpcoords A data.frame with two columns \code{xmother} and \code{ymother}
+#' @param x_min_max vector of 2 values describing the window on the x axis
+#' @param y_min_max vector of 2 values describing the window on the y axis
+#' @param ... Kept for future uses.
+#'
+#' @returns A \code{data.frame} of same dimension as \code{mpcoords}.
+#'
+#' @details The function takes a \code{data.frame} and makes sure that all
+#' coordinates are actually inside the window specified
+#' by the \code{x_min_max} and \code{y_min_max} arguments.
+#'
+#' @author Alban Sagouis
+#'
+#' @examples
+#' x_min_max <- c(0, 1)
+#' y_min_max <- c(0, 1)
+#' mpcoords <- data.frame(xmother = stats::runif(100L),
+#' ymother = stats::runif(100L))
+#' mcoordsT <- torusify(mpcoords, x_min_max, y_min_max)
+#'
+#' @rdname torusify
+#' @export
+
+torusify.data.frame <- function(mpcoords, x_min_max, y_min_max, ...) {
+ if (!all(is.element(c("xmother", "ymother"), colnames(mpcoords))))
+ stop("mpcoords must have columns named 'xmother' and 'ymother'")
+ mpcoords$xmother <- mpcoords$xmother %% diff(x_min_max) + x_min_max[1L]
+ mpcoords$ymother <- mpcoords$ymother %% diff(y_min_max) + y_min_max[1L]
+ return(mpcoords)
+}
+
+
+#' Rounds coordinates around like on a torus
+#'
+#' @param mpcoords A vector of class \code{numeric}.
+#' @param range vector of 2 values describing the window.
+#' @param ... Kept for future uses.
+#'
+#' @returns A \code{numeric} vector of same length as \code{mpcoords}.
+#'
+#' @details The function takes a \code{numeric} vector and makes sure that all
+#' values are actually inside the window specified
+#' by the \code{range} argument.
+#'
+#' @author Alban Sagouis
+#'
+#' @examples
+#' mpcoords <- stats::runif(10L, min = -1, max = 2)
+#' torusify(mpcoords, range = c(0, 1))
+#'
+#' @rdname torusify
+#' @export
+
+torusify.numeric <- function(mpcoords, range, ...) {
+ return(mpcoords %% diff(range) + range[1L])
+}
+
+
+## community2ppp() ----
+#' Converts an object of class \code{\link[mobsim]{community}} into an object of
+#' class \code{\link[spatstat.geom]{ppp}}.
+#'
+#' @param comm Community object
+#'
+#' @importFrom spatstat.geom ppp
+#' @importFrom spatstat.geom owin
+#'
+#' @details Extracts x and y coordinates and species marks from \code{comm} and
+#' builds a marked planar point pattern (\code{\link[spatstat.geom]{ppp}}) with
+#' an observation window derived from the \code{x_min_max} and \code{y_min_max}
+#' elements of the \code{community} object.
+#' @author Alban Sagouis
+#'
+#' @examples
+#' # Integrated between mobsim::sim_thomas_coords() and spatstat.explore::marktable()
+#' simdat <- mobsim::sim_thomas_coords(abund_vec = 11L:100L)
+#' simdat <- community2ppp(comm = simdat)
+#' spatstat.explore::marktable(X = simdat, N = 10L)
+#'
+#' @export
+
+community2ppp <- function(comm) {
+ spatstat.geom::ppp(
+ x = comm$census$x,
+ y = comm$census$y,
+ marks = comm$census$species,
+ window = spatstat.geom::owin(
+ xrange = comm$x_min_max,
+ yrange = comm$y_min_max
+ )
+ )
+}
+
+## create_random_ID() ----
+#' Creates a random string.
+#'
+#' @param n (integer) number of random strings to create. Default is 1.
+#' @inheritParams jitter_motherpoints
+#'
+#' @returns A character vector of length \code{n}. Each string is composed of
+#' five uppercase letters, a zero-padded four-digit integer, and one uppercase
+#' letter (e.g. \code{"QEAYJ1252R"}).
+#'
+#' @export
+#'
+
+create_random_ID <- function(n = 1L, seed = NULL) {
+ if (exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) {
+ oldseed <- get(".Random.seed", envir = .GlobalEnv, inherits = FALSE)
+ on.exit(
+ assign(".Random.seed", oldseed, envir = .GlobalEnv),
+ add = TRUE
+ )
+ }
+ if (!is.null(seed)) set.seed(seed) else set.seed(Sys.time())
+
+ a <- do.call(
+ paste0,
+ replicate(5L, sample(LETTERS, n, replace = TRUE), simplify = FALSE)
+ )
+ return(
+ paste0(
+ a,
+ sprintf(fmt = "%04d", sample(9999L, n, replace = TRUE)),
+ sample(LETTERS, n, replace = TRUE)
+ )
+ )
+}
diff --git a/README.md b/README.md
index a983293..4884d36 100644
--- a/README.md
+++ b/README.md
@@ -74,7 +74,8 @@ abundance distribution and the same total number of individuals.
``` r
library(mobsim)
comm_rand <- sim_poisson_community(s_pool = 30, n_sim = 300)
-comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300, sigma = 0.05, mother_points = 1)
+comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300,
+ sigma = 0.05, mother_points = 1)
```
``` r
@@ -109,7 +110,7 @@ plot(m_species ~ prop_area, data = sar_rand, type = "b", log = "xy",
xlab = "Proportion of area sampled", ylab = "No. of species",
ylim = c(3,30))
lines(m_species ~ prop_area, data = sar_agg, type = "b", col = 2)
-legend("bottomright", c("Random","Aggregated"), col = 1:2, lwd = 2)
+legend("bottomright", c("Random", "Aggregated"), col = 1:2, lwd = 2)
```
@@ -140,3 +141,32 @@ id="fig-sampling" />
Figure 3
+
+### Dynamic communities
+
+This is a basic example which shows you how to make a community move in
+space:
+
+``` r
+simdat <- sim_thomas_community(s_pool = 5L, n_sim = 100L, mother_points = 1L)
+simdatJ <- jitter_species(simdat, sd = 0.05) |>
+ drift_x_species(drift = 0.01) |>
+ drift_y_species(drift = -0.02) |>
+ torusify()
+par(mfrow = c(1L, 2L))
+plot(simdat, las = 1, main = "T0")
+plot(simdatJ, las = 1, main = "T1")
+```
+
+
+
+

+
+Figure 4
+
+
+
+And now several steps with species movement in-between each step:
+
+
diff --git a/README.qmd b/README.qmd
index c09e821..9a91dc3 100644
--- a/README.qmd
+++ b/README.qmd
@@ -82,7 +82,8 @@ and the same total number of individuals.
#| label: example
library(mobsim)
comm_rand <- sim_poisson_community(s_pool = 30, n_sim = 300)
-comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300, sigma = 0.05, mother_points = 1)
+comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300,
+ sigma = 0.05, mother_points = 1)
```
```{r}
#| label: fig-map
@@ -111,7 +112,7 @@ plot(m_species ~ prop_area, data = sar_rand, type = "b", log = "xy",
xlab = "Proportion of area sampled", ylab = "No. of species",
ylim = c(3,30))
lines(m_species ~ prop_area, data = sar_agg, type = "b", col = 2)
-legend("bottomright", c("Random","Aggregated"), col = 1:2, lwd = 2)
+legend("bottomright", c("Random", "Aggregated"), col = 1:2, lwd = 2)
```
### Sampling of communities
@@ -126,3 +127,23 @@ par(mfrow = c(1,2))
samples_rand <- sample_quadrats(comm_rand, avoid_overlap = TRUE)
samples_agg <- sample_quadrats(comm_agg, avoid_overlap = TRUE)
```
+
+### Dynamic communities
+This is a basic example which shows you how to make a community move in space:
+
+```{r}
+#| label: fig-dynamic
+
+simdat <- sim_thomas_community(s_pool = 5L, n_sim = 100L, mother_points = 1L)
+simdatJ <- jitter_species(simdat, sd = 0.05) |>
+ drift_x_species(drift = 0.01) |>
+ drift_y_species(drift = -0.02) |>
+ torusify()
+par(mfrow = c(1L, 2L))
+plot(simdat, las = 1, main = "T0")
+plot(simdatJ, las = 1, main = "T1")
+```
+
+And now several steps with species movement in-between each step:
+
+
diff --git a/README_files/figure-commonmark/fig-dynamic-1.png b/README_files/figure-commonmark/fig-dynamic-1.png
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index b4bfef1..92177d5 100644
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diff --git a/README_files/figure-commonmark/fig-sampling-1.png b/README_files/figure-commonmark/fig-sampling-1.png
index e806847..c9559b8 100644
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diff --git a/README_files/figure-commonmark/fig-sar-1.png b/README_files/figure-commonmark/fig-sar-1.png
index 59835ef..0dd2e64 100644
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diff --git a/codemeta.json b/codemeta.json
index 25bea7a..8fcc9de 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -7,13 +7,13 @@
"codeRepository": "https://github.com/MoBiodiv/mobsim",
"issueTracker": "https://github.com/MoBiodiv/mobsim/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
- "version": "0.3.2",
+ "version": "0.3.3",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
"url": "https://r-project.org"
},
- "runtimePlatform": "R version 4.5.0 (2025-04-11)",
+ "runtimePlatform": "R version 4.5.2 (2025-10-31)",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
@@ -48,7 +48,7 @@
"funder": [
{
"@type": "Organization",
- "name": "German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig"
+ "name": "German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig"
},
{
"@type": "Organization",
@@ -77,18 +77,6 @@
},
"sameAs": "https://CRAN.R-project.org/package=quarto"
},
- {
- "@type": "SoftwareApplication",
- "identifier": "spatstat.geom",
- "name": "spatstat.geom",
- "provider": {
- "@id": "https://cran.r-project.org",
- "@type": "Organization",
- "name": "Comprehensive R Archive Network (CRAN)",
- "url": "https://cran.r-project.org"
- },
- "sameAs": "https://CRAN.R-project.org/package=spatstat.geom"
- },
{
"@type": "SoftwareApplication",
"identifier": "spatstat.random",
@@ -144,7 +132,7 @@
"@type": "SoftwareApplication",
"identifier": "R",
"name": "R",
- "version": ">= 4.0.0"
+ "version": ">= 4.1.0"
},
"2": {
"@type": "SoftwareApplication",
@@ -204,13 +192,37 @@
"name": "stats"
},
"9": {
+ "@type": "SoftwareApplication",
+ "identifier": "spatstat.geom",
+ "name": "spatstat.geom",
+ "provider": {
+ "@id": "https://cran.r-project.org",
+ "@type": "Organization",
+ "name": "Comprehensive R Archive Network (CRAN)",
+ "url": "https://cran.r-project.org"
+ },
+ "sameAs": "https://CRAN.R-project.org/package=spatstat.geom"
+ },
+ "10": {
+ "@type": "SoftwareApplication",
+ "identifier": "spatstat.explore",
+ "name": "spatstat.explore",
+ "provider": {
+ "@id": "https://cran.r-project.org",
+ "@type": "Organization",
+ "name": "Comprehensive R Archive Network (CRAN)",
+ "url": "https://cran.r-project.org"
+ },
+ "sameAs": "https://CRAN.R-project.org/package=spatstat.explore"
+ },
+ "11": {
"@type": "SoftwareApplication",
"identifier": "methods",
"name": "methods"
},
"SystemRequirements": null
},
- "fileSize": "2425.796KB",
+ "fileSize": "3781.327KB",
"citation": [
{
"@type": "ScholarlyArticle",
@@ -262,6 +274,5 @@
"readme": "https://github.com/MoBiodiv/mobsim/blob/master/README.md",
"contIntegration": "https://github.com/MoBiodiv/mobsim/actions/workflows/R-CMD-check.yaml",
"developmentStatus": "https://www.repostatus.org/",
- "keywords": ["species", "simulation", "biodiversity", "macroecology", "rarefaction", "point-pattern-analysis", "species-abundance-distributions", "r", "r-package", "rstats"],
- "relatedLink": "https://CRAN.R-project.org/package=mobsim"
+ "keywords": ["species", "simulation", "biodiversity", "macroecology", "rarefaction", "point-pattern-analysis", "species-abundance-distributions", "r", "r-package", "rstats"]
}
diff --git a/inst/LNFUA1284L_jittering.gif b/inst/LNFUA1284L_jittering.gif
new file mode 100755
index 0000000..48f3a55
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diff --git a/man/community2ppp.Rd b/man/community2ppp.Rd
new file mode 100644
index 0000000..2ee5ee0
--- /dev/null
+++ b/man/community2ppp.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{community2ppp}
+\alias{community2ppp}
+\title{Converts an object of class \code{\link[mobsim]{community}} into an object of
+class \code{\link[spatstat.geom]{ppp}}.}
+\usage{
+community2ppp(comm)
+}
+\arguments{
+\item{comm}{Community object}
+}
+\description{
+Converts an object of class \code{\link[mobsim]{community}} into an object of
+class \code{\link[spatstat.geom]{ppp}}.
+}
+\details{
+Extracts x and y coordinates and species marks from \code{comm} and
+builds a marked planar point pattern (\code{\link[spatstat.geom]{ppp}}) with
+an observation window derived from the \code{x_min_max} and \code{y_min_max}
+elements of the \code{community} object.
+}
+\examples{
+# Integrated between mobsim::sim_thomas_coords() and spatstat.explore::marktable()
+simdat <- mobsim::sim_thomas_coords(abund_vec = 11L:100L)
+simdat <- community2ppp(comm = simdat)
+spatstat.explore::marktable(X = simdat, N = 10L)
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/create_motherpoints.Rd b/man/create_motherpoints.Rd
new file mode 100644
index 0000000..e7180f7
--- /dev/null
+++ b/man/create_motherpoints.Rd
@@ -0,0 +1,97 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_motherpoints.R
+\name{create_motherpoints}
+\alias{create_motherpoints}
+\alias{plot.mother_map}
+\title{Creates a random number of mother points for a given number of species}
+\usage{
+create_motherpoints(
+ s_local,
+ n_motherpoints_range = 1:4,
+ xrange = c(0, 1),
+ yrange = c(0, 1),
+ seed = NULL
+)
+
+\method{plot}{mother_map}(x, col = NULL, pch = NULL, ...)
+}
+\arguments{
+\item{s_local}{(integer) Species number.}
+
+\item{n_motherpoints_range}{(integer vector) Vector of integer values for the number of motherpoints a species can get.}
+
+\item{xrange}{(numeric vector) Extent of the community in x-direction.}
+
+\item{yrange}{(numeric vector) Extent of the community in y-direction.}
+
+\item{seed}{(integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.}
+
+\item{x}{mother_map object}
+
+\item{col}{Colour vector to mark species identities}
+
+\item{pch}{Plotting character to mark species identities.
+pch 16 is advised for large data sets.}
+
+\item{...}{Other parameters to \code{\link[graphics:plot.default]{graphics::plot}}}
+}
+\value{
+A named list of class \code{mother_map} with three elements:
+\enumerate{
+\item \code{n_mother_points} a vector of integers giving the number of mother points per species
+\item \code{xmother} List of length equal to the number of species. Each list element
+is a vector of x coordinates for every mother point. If one element is \code{numeric(0)}, the
+corresponding species has no mother point and is not clustered.
+\item \code{ymother} List of length equal to the number of species. Each list element
+is a vector of y coordinates for every mother point. If one element is \code{numeric(0)}, the
+corresponding species has no mother point and is not clustered.
+}
+}
+\description{
+Plot positions and species identities of all mother points created by
+\code{\link{create_motherpoints}} or \code{\link{jitter_motherpoints}}.
+}
+\details{
+For each species, the function first draws a random number of
+mother points in the given \code{n_motherpoints_range}. Then the function
+places as many mother points as needed in the window given by \code{xrange}
+and \code{yrange}.
+}
+\examples{
+# Default behaviour
+mpcoords <- create_motherpoints(s_local = 10L)
+
+# With more variability for the number of motherpoints
+mpcoords <- create_motherpoints(s_local = 10L, n_motherpoints_range = 1L:100L)
+
+# Allowing no clustering at all
+mpcoords <- create_motherpoints(s_local = 10L, n_motherpoints_range = 0L:5L)
+
+# Fixing the seed
+mpcoords <- create_motherpoints(10L, seed = 42L)
+
+# Integration with mobsim::sim_thomas_coords()
+abund_vec <- 11L:100L # a community with 90 species
+s_local <- length(abund_vec)
+mpcoords <- create_motherpoints(s_local, seed = 42L)
+simdat <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+# Integration with mobsim::sim_thomas_coords() without clustering
+abund_vec <- 20L:25L
+s_local <- length(abund_vec)
+mpcoords <- create_motherpoints(s_local, n_motherpoints_range = 0L:1L, seed = 42L)
+simdat <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+plot(simdat)
+
+mpcoords <- create_motherpoints(10L)
+plot(mpcoords)
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/create_random_ID.Rd b/man/create_random_ID.Rd
new file mode 100644
index 0000000..15ffccf
--- /dev/null
+++ b/man/create_random_ID.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{create_random_ID}
+\alias{create_random_ID}
+\title{Creates a random string.}
+\usage{
+create_random_ID(n = 1L, seed = NULL)
+}
+\arguments{
+\item{n}{(integer) number of random strings to create. Default is 1.}
+
+\item{seed}{(integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.}
+}
+\value{
+A character vector of length \code{n}. Each string is composed of
+five uppercase letters, a zero-padded four-digit integer, and one uppercase
+letter (e.g. \code{"QEAYJ1252R"}).
+}
+\description{
+Creates a random string.
+}
diff --git a/man/drift_motherpoints.Rd b/man/drift_motherpoints.Rd
new file mode 100644
index 0000000..ea22aa0
--- /dev/null
+++ b/man/drift_motherpoints.Rd
@@ -0,0 +1,79 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/drift_motherpoints.R
+\name{drift_x_motherpoints}
+\alias{drift_x_motherpoints}
+\alias{drift_y_motherpoints}
+\title{Adds a fixed drift movement to mother points x coordinates}
+\usage{
+drift_x_motherpoints(mpcoords, drift)
+
+drift_y_motherpoints(mpcoords, drift)
+}
+\arguments{
+\item{mpcoords}{(mother_map) List of class \code{mother_map}.}
+
+\item{drift}{(numeric) Amount of spatial drift}
+}
+\value{
+A named list of class \code{mother_map} with three elements:
+\enumerate{
+\item \code{n_mother_points} a vector of integers giving the number of
+mother points per species
+\item \code{xmother} List of length equal to the number of species. Each
+list element is a vector of x coordinates for every mother points. If one
+element is NA, the the corresponding species is not clustered.
+\item \code{ymother} List of length equal to the number of species. Each
+list element is a vector of y coordinates for every mother points. If one
+element is NA, the the corresponding species is not clustered.
+}
+}
+\description{
+Adds a fixed drift movement to mother points x coordinates
+
+Adds a fixed drift movement to mother points y coordinates
+}
+\details{
+The function takes a \code{mother_map} object and adds a fixed
+drift value to either the x or y coordinates. In a 1 by 1 landscape, a drift
+of 0.5 means moving over half the map.
+}
+\examples{
+# Default behaviour
+mpcoords <- create_motherpoints(s_local = 10L)
+mpcoordsD <- drift_x_motherpoints(mpcoords, 0.1)
+par(mfrow = c(1L, 2L))
+plot(mpcoords)
+plot(mpcoordsD)
+
+# With more distance for the movements of motherpoints
+mpcoordsD <- mpcoords |>
+ drift_x_motherpoints(drift = 0.5) |>
+ drift_y_motherpoints(drift = 0.5)
+
+# Integration with mobsim::sim_thomas_coords()
+abund_vec <- 11L:100L # a community with 90 species
+s_local <- length(abund_vec)
+mpcoords <- create_motherpoints(s_local, seed = 42L)
+simdat <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+## computing biodiversity metrics
+div1 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat,
+ n_rect = 10L, exclude_zeros = TRUE)
+
+## moving motherpoints slightly
+mpcoordsD <- drift_x_motherpoints(mpcoords, 0.01) |>
+ drift_y_motherpoints(drift = 0.01)
+simdat2 <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+## computing biodiversity metrics
+div2 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat2,
+ n_rect = 10L, exclude_zeros = TRUE)
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/drift_species.Rd b/man/drift_species.Rd
new file mode 100644
index 0000000..ec30c60
--- /dev/null
+++ b/man/drift_species.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/drift_species.R
+\name{drift_x_species}
+\alias{drift_x_species}
+\alias{drift_y_species}
+\title{Adds the same fixed movement to all individuals of a species on x}
+\usage{
+drift_x_species(comm, drift)
+
+drift_y_species(comm, drift)
+}
+\arguments{
+\item{comm}{(community) List of class \code{community}.}
+
+\item{drift}{(numeric) A single value added to the x or y coordinates.}
+}
+\value{
+A named list of class \code{community} as described in
+\code{\link[mobsim]{community}}
+}
+\description{
+Adds the same fixed movement to all individuals of a species on x
+
+Adds the same fixed movement to all individuals of a species on y
+}
+\details{
+The function takes a \code{community} object and adds a fixed
+drift value to either x or y coordinate per species. In a 1 by 1 landscape, a
+drift of 0.5 means moving over half the map.
+}
+\examples{
+# Default behaviour
+simdat <- mobsim::sim_thomas_community(s_pool = 5L, n_sim = 100L,
+ mother_points = 1L)
+simdatD <- simdat |>
+ drift_x_species(0.1) |>
+ drift_y_species(-0.2)
+par(mfrow = c(1L, 2L))
+plot(simdat)
+plot(simdatD)
+
+}
+\seealso{
+drift_motherpoints
+}
+\author{
+Alban Sagouis
+}
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diff --git a/man/jitter_motherpoints.Rd b/man/jitter_motherpoints.Rd
new file mode 100644
index 0000000..4f59209
--- /dev/null
+++ b/man/jitter_motherpoints.Rd
@@ -0,0 +1,75 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/jitter_motherpoints.R
+\name{jitter_motherpoints}
+\alias{jitter_motherpoints}
+\title{Adds a random movement to mother point coordinates}
+\usage{
+jitter_motherpoints(mpcoords, sd = 0.01, seed = NULL)
+}
+\arguments{
+\item{mpcoords}{(mother_map) List of class \code{mother_map}.}
+
+\item{sd}{(numeric) Standard deviation for the \code{\link[stats]{rnorm}}.}
+
+\item{seed}{(integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.}
+}
+\value{
+A named list of class \code{mother_map} with three elements:
+\enumerate{
+\item \code{n_mother_points} a vector of integers giving the number of mother points per species
+\item \code{xmother} List of length equal to the number of species. Each list element
+is a vector of x coordinates for every mother points. If one element is NA, the
+the corresponding species is not clustered.
+\item \code{ymother} List of length equal to the number of species. Each list element
+is a vector of y coordinates for every mother points. If one element is NA, the
+the corresponding species is not clustered.
+}
+}
+\description{
+Adds a random movement to mother point coordinates
+}
+\details{
+The function takes a \code{mother_map} object and adds a random
+jitter value to each coordinate. The jitter follows a normal probability
+distribution of \code{mean} = 0 and \code{sd} specified by the used with
+argument \code{sd}.
+}
+\examples{
+# Default behaviour
+mpcoords <- create_motherpoints(s_local = 10L)
+mpcoordsJ <- jitter_motherpoints(mpcoords)
+par(mfrow = c(1L, 2L))
+plot(mpcoords)
+plot(mpcoordsJ)
+
+# With more variability for the movements of motherpoints
+mpcoordsJ <- jitter_motherpoints(mpcoords, sd = 2)
+
+# Fixing the seed
+mpcoordsJ <- jitter_motherpoints(mpcoords, seed = 42L)
+
+# Integration with mobsim::sim_thomas_coords()
+abund_vec <- 11L:100L # a community with 90 species
+s_local <- length(abund_vec)
+mpcoords <- create_motherpoints(s_local, seed = 42L)
+simdat <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+## computing biodiversity metrics
+div1 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat, n_rect = 10L, exclude_zeros = TRUE)
+
+## moving motherpoints slightly
+mpcoordsJ <- jitter_motherpoints(mpcoords)
+simdat2 <- mobsim::sim_thomas_coords(abund_vec,
+ xmother = mpcoords$xmother, # list of vectors
+ ymother = mpcoords$ymother # list of vectors
+)
+## computing biodiversity metrics
+div2 <- mobsim::div_rand_rect(prop_area = 0.01, comm = simdat2,
+ n_rect = 10L, exclude_zeros = TRUE)
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/jitter_species.Rd b/man/jitter_species.Rd
new file mode 100644
index 0000000..aa2eeb6
--- /dev/null
+++ b/man/jitter_species.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/jitter_species.R
+\name{jitter_species}
+\alias{jitter_species}
+\title{Adds the same random movement to all individuals of a species}
+\usage{
+jitter_species(comm, sd = 0.01, seed = NULL)
+}
+\arguments{
+\item{comm}{(community) List of class \code{community}.}
+
+\item{sd}{(numeric) Standard deviation for the \code{\link[stats]{rnorm}}.}
+
+\item{seed}{(integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.}
+}
+\value{
+A named list of class \code{community} as described in
+\code{\link[mobsim]{community}}
+}
+\description{
+Adds the same random movement to all individuals of a species
+}
+\details{
+The function takes a \code{community} object and adds a random
+jitter value to each coordinate per species. The jitter follows a normal
+probability distribution of \code{mean} = 0 and \code{sd} specified by the
+used with argument \code{sd}.
+}
+\examples{
+# Default behaviour
+simdat <- mobsim::sim_thomas_community(s_pool = 5L, n_sim = 100L,
+ mother_points = 1L)
+simdatJ <- jitter_species(simdat)
+par(mfrow = c(1L, 2L))
+plot(simdat)
+plot(simdatJ)
+
+# With more variability for the movement of individuals
+simdatJ <- jitter_species(simdat, sd = 2)
+
+# Fixing the seed
+simdatJ <- jitter_species(simdat, seed = 42L)
+
+}
+\seealso{
+jitter_motherpoints
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/mobsim-package.Rd b/man/mobsim-package.Rd
index cd23f51..d2f80c4 100644
--- a/man/mobsim-package.Rd
+++ b/man/mobsim-package.Rd
@@ -4,12 +4,17 @@
\name{mobsim-package}
\alias{mobsim}
\alias{mobsim-package}
-\title{mobsim: A package for spatial analysis of scale-dependent biodiversity changes.}
+\title{mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes}
\description{
The package includes functions to simulate species distributions in space
as well as for the analysis of spatially-explicit data, where each individual
is described by its xy-coordinates and a species identity label.
}
+\details{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+
+mobsim: A package for spatial analysis of scale-dependent biodiversity changes.
+}
\seealso{
Useful links:
\itemize{
@@ -28,9 +33,8 @@ Authors:
Other contributors:
\itemize{
- \item German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (01jty7g66) [funder]
- \item Freie Universität Berlin (046ak2485) [funder]
+ \item German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (\href{https://ror.org/01jty7g66}{ROR}) [funder]
+ \item Freie Universität Berlin (\href{https://ror.org/046ak2485}{ROR}) [funder]
}
}
-\keyword{internal}
diff --git a/man/replace_individuals.Rd b/man/replace_individuals.Rd
new file mode 100644
index 0000000..ca5bde6
--- /dev/null
+++ b/man/replace_individuals.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reproduction.R
+\name{replace_individuals}
+\alias{replace_individuals}
+\title{Takes an object of class \code{\link[mobsim]{community}} and replaces
+individual species identities based on the neighbours}
+\usage{
+replace_individuals(comm, N = NULL, R = NULL, seed = NULL)
+}
+\arguments{
+\item{comm}{Community object}
+
+\item{N}{
+ Number of neighbours of each point. Incompatible with \code{R}.
+ }
+
+\item{R}{
+ Neighbourhood radius. Incompatible with \code{N}.
+ }
+
+\item{seed}{(integer) Any integer passed to \code{\link[base]{set.seed}} for reproducibility.}
+}
+\description{
+Takes an object of class \code{\link[mobsim]{community}} and replaces
+individual species identities based on the neighbours
+}
+\details{
+For each individual, the function first identifies neighbours'
+identity using the \code{\link[spatstat.explore]{marktable}} function,
+computes relative abundances and uses these relative abundances as random
+drawing probabilities in \code{\link[base]{sample}}.
+The neighbourhood community of an individual is restricted by parameter N
+(number of individual) or R (radius).
+}
+\examples{
+# Integrated between mobsim::sim_thomas_coords() and the analysis of
+# biodiversity
+simdat <- mobsim::sim_thomas_coords(11L:100L)
+mobsim::div_rand_rect(comm = simdat, prop_area = 0.01, n_rect = 20L)
+simdat2 <- replace_individuals(simdat, N = 10L)
+mobsim::div_rand_rect(comm = simdat2, prop_area = 0.01, n_rect = 20L)
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/man/sampling_random_bruteforce.Rd b/man/sampling_random_bruteforce.Rd
index 3a312c2..a798e46 100644
--- a/man/sampling_random_bruteforce.Rd
+++ b/man/sampling_random_bruteforce.Rd
@@ -36,5 +36,5 @@ a data.frame with 2 columns x and y giving the coordinates of the
lower left corner of the square quadrats.
}
\description{
-This function works without having the \code{spatstat.random} package install.
+This function works without having the \code{spatstat.random} package installed.
}
diff --git a/man/torusify.Rd b/man/torusify.Rd
new file mode 100644
index 0000000..9cb3f16
--- /dev/null
+++ b/man/torusify.Rd
@@ -0,0 +1,113 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{torusify}
+\alias{torusify}
+\alias{torusify.mother_map}
+\alias{torusify.community}
+\alias{torusify.data.frame}
+\alias{torusify.numeric}
+\title{Rounds coordinates around like on a torus}
+\usage{
+torusify(mpcoords, ...)
+
+\method{torusify}{mother_map}(mpcoords, ...)
+
+\method{torusify}{community}(mpcoords, ...)
+
+\method{torusify}{data.frame}(mpcoords, x_min_max, y_min_max, ...)
+
+\method{torusify}{numeric}(mpcoords, range, ...)
+}
+\arguments{
+\item{mpcoords}{A vector of class \code{numeric}.}
+
+\item{...}{Kept for future uses.}
+
+\item{x_min_max}{vector of 2 values describing the window on the x axis}
+
+\item{y_min_max}{vector of 2 values describing the window on the y axis}
+
+\item{range}{vector of 2 values describing the window.}
+}
+\value{
+Object returned depends on the object given. For an object of class
+\code{mother_map} as given by \code{\link{create_motherpoints}}, see
+\code{\link{torusify.mother_map}}. For a \code{data.frame}, see
+\code{\link{torusify.data.frame}} and for a \code{numeric} vector, see
+\code{\link{torusify.numeric}}.
+
+An object of class \code{mother_map} of the same dimensions as the
+one provided to the function.
+
+A list of class \code{community} of same dimension as
+\code{mpcoords}.
+
+A \code{data.frame} of same dimension as \code{mpcoords}.
+
+A \code{numeric} vector of same length as \code{mpcoords}.
+}
+\description{
+Rounds coordinates around like on a torus
+
+Rounds coordinates around like on a torus
+
+Rounds coordinates around like on a torus
+
+Rounds coordinates around like on a torus
+
+Rounds coordinates around like on a torus
+}
+\details{
+\code{torusify()} is a generic function that calls functions adapted
+to the class of argument \code{mapcoords}. Classes \code{data.frame},
+\code{numeric} and \code{mother_map} are accepted at the moment.
+
+\code{torusify()} takes coordinates and makes sure that all
+coordinates actually inside the window specified
+in \code{x_min_max} and \code{y_min_max}.
+
+The function takes a \code{mother_map} object and makes sure that
+all coordinates that were just jittered are actually inside the window
+specified in the \code{x_min_max} and \code{y_min_max} elements of the
+\code{mother_map} object.
+
+The function takes a \code{community} and makes sure that all
+individual coordinates are actually inside the window specified by the
+\code{x_min_max} and \code{y_min_max} elements of the \code{community}
+object.
+
+The function takes a \code{data.frame} and makes sure that all
+coordinates are actually inside the window specified
+by the \code{x_min_max} and \code{y_min_max} arguments.
+
+The function takes a \code{numeric} vector and makes sure that all
+values are actually inside the window specified
+by the \code{range} argument.
+}
+\examples{
+# Default behaviour
+mpcoords <- create_motherpoints(s_local = 10L)
+mpcoordsJ <- jitter_motherpoints(mpcoords)
+mcoordsT <- torusify(mpcoordsJ)
+# Default behaviour
+mpcoords <- create_motherpoints(s_local = 10L)
+mpcoordsJ <- jitter_motherpoints(mpcoords)
+mcoordsT <- torusify(mpcoordsJ)
+
+simdat <- mobsim::sim_thomas_community(10L, 100L, mother_points = 1)
+simdatJ <- jitter_species(simdat, sd = 1)
+simdatJ <- torusify(simdatJ)
+
+x_min_max <- c(0, 1)
+y_min_max <- c(0, 1)
+mpcoords <- data.frame(xmother = stats::runif(100L),
+ ymother = stats::runif(100L))
+mcoordsT <- torusify(mpcoords, x_min_max, y_min_max)
+
+mpcoords <- stats::runif(10L, min = -1, max = 2)
+torusify(mpcoords, range = c(0, 1))
+
+}
+\author{
+Alban Sagouis
+}
diff --git a/mobsim.Rproj b/mobsim.Rproj
index 4d263d7..07b3123 100644
--- a/mobsim.Rproj
+++ b/mobsim.Rproj
@@ -1,4 +1,5 @@
Version: 1.0
+ProjectId: 812660be-c7f9-4549-8ca6-c035076de98e
RestoreWorkspace: Default
SaveWorkspace: Default
@@ -17,4 +18,5 @@ AutoAppendNewline: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/tests/testthat.R b/tests/testthat.R
index a6e8024..1cd8cac 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,6 +1,4 @@
library(testthat)
-library(mobsim)
test_check("mobsim")
# test_package("mobsim", reporter="summary")
-# test_dir("./tests/testthat", reporter="summary")
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
index 865fdf7..bb64008 100644
Binary files a/tests/testthat/Rplots.pdf and b/tests/testthat/Rplots.pdf differ
diff --git a/tests/testthat/_snaps/create_motherpoints.md b/tests/testthat/_snaps/create_motherpoints.md
new file mode 100644
index 0000000..821d71d
--- /dev/null
+++ b/tests/testthat/_snaps/create_motherpoints.md
@@ -0,0 +1,1873 @@
+# snapshot test with clustering
+
+ Code
+ create_motherpoints(s_local = 100L, seed = 42L)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2 3 3 1 1 3 4 1 3 1 1 4 2 4 4 3 2 1
+ [38] 2 4 2 3 3 2 2 4 4 4 2 2 1 4 1 4 2 4 2 3 4 3 1 1 2 2 2 2 2 4 3 2 1 2 3 2 2
+ [75] 2 4 1 1 1 3 4 1 2 1 1 4 4 1 3 3 1 4 1 4 4 2 1 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.6262453
+
+ $xmother[[2]]
+ [1] 0.2171577
+
+ $xmother[[3]]
+ [1] 0.2165673
+
+ $xmother[[4]]
+ [1] 0.388945
+
+ $xmother[[5]]
+ [1] 0.9424557 0.9626080
+
+ $xmother[[6]]
+ [1] 0.739855279 0.733245906 0.535761290 0.002272966
+
+ $xmother[[7]]
+ [1] 0.6089375 0.8368016
+
+ $xmother[[8]]
+ [1] 0.7515226 0.4527316
+
+ $xmother[[9]]
+ [1] 0.53579
+
+ $xmother[[10]]
+ [1] 0.537376695 0.001380844 0.355665954 0.612133090
+
+ $xmother[[11]]
+ [1] 0.8289421 0.3567220 0.4106351
+
+ $xmother[[12]]
+ [1] 0.5734759 0.5896783 0.7196573 0.3949730
+
+ $xmother[[13]]
+ [1] 0.9192039 0.9625703 0.2335235
+
+ $xmother[[14]]
+ [1] 0.7244976 0.9036345 0.6034741 0.6315073
+
+ $xmother[[15]]
+ [1] 0.9373858
+
+ $xmother[[16]]
+ [1] 0.8504828
+
+ $xmother[[17]]
+ [1] 0.5798209 0.8214039
+
+ $xmother[[18]]
+ [1] 0.1137186 0.7645078 0.6236135 0.1484466
+
+ $xmother[[19]]
+ [1] 0.08026447 0.46406955
+
+ $xmother[[20]]
+ [1] 0.7793682 0.7335280
+
+ $xmother[[21]]
+ [1] 0.8172304 0.1701625 0.9447203
+
+ $xmother[[22]]
+ [1] 0.2936238 0.1490721 0.7193786
+
+ $xmother[[23]]
+ [1] 0.324086
+
+ $xmother[[24]]
+ [1] 0.7788095
+
+ $xmother[[25]]
+ [1] 0.3944410 0.6785929 0.7758250
+
+ $xmother[[26]]
+ [1] 0.18786904 0.02908582 0.13571380 0.68016418
+
+ $xmother[[27]]
+ [1] 0.934823
+
+ $xmother[[28]]
+ [1] 0.5504941 0.6017662 0.1969945
+
+ $xmother[[29]]
+ [1] 0.5352366
+
+ $xmother[[30]]
+ [1] 0.1795557
+
+ $xmother[[31]]
+ [1] 0.4518865 0.3170534 0.1161747 0.1861022
+
+ $xmother[[32]]
+ [1] 0.7297301 0.4118721
+
+ $xmother[[33]]
+ [1] 0.4140497 0.4803101 0.4274945 0.1364904
+
+ $xmother[[34]]
+ [1] 0.8246794 0.5923042 0.7943970 0.7690324
+
+ $xmother[[35]]
+ [1] 0.9180564 0.8626298 0.3169752
+
+ $xmother[[36]]
+ [1] 0.2592606 0.7422665
+
+ $xmother[[37]]
+ [1] 0.7473611
+
+ $xmother[[38]]
+ [1] 0.9179040 0.7931912
+
+ $xmother[[39]]
+ [1] 0.1333296 0.2877498 0.1946761 0.7841094
+
+ $xmother[[40]]
+ [1] 0.1288722 0.1290893
+
+ $xmother[[41]]
+ [1] 0.07225311 0.05312948 0.53187444
+
+ $xmother[[42]]
+ [1] 0.1123082 0.7431877 0.7313155
+
+ $xmother[[43]]
+ [1] 0.8851177 0.5171111
+
+ $xmother[[44]]
+ [1] 0.8519310 0.4427963
+
+ $xmother[[45]]
+ [1] 0.1578801 0.4423246 0.9677337 0.4845879
+
+ $xmother[[46]]
+ [1] 0.2524584 0.2596900 0.5420159 0.6498758
+
+ $xmother[[47]]
+ [1] 0.33641913 0.06094975 0.45131085 0.83875503
+
+ $xmother[[48]]
+ [1] 0.5746373 0.3533504
+
+ $xmother[[49]]
+ [1] 0.5474261 0.8927186
+
+ $xmother[[50]]
+ [1] 0.4899906
+
+ $xmother[[51]]
+ [1] 0.1716321 0.5430310 0.9614677 0.3136838
+
+ $xmother[[52]]
+ [1] 0.8205145
+
+ $xmother[[53]]
+ [1] 0.30705440 0.18545358 0.04834678 0.24567415
+
+ $xmother[[54]]
+ [1] 0.3511069 0.1590224
+
+ $xmother[[55]]
+ [1] 0.30409800 0.01754832 0.99655268 0.80439331
+
+ $xmother[[56]]
+ [1] 0.0865806 0.8699333
+
+ $xmother[[57]]
+ [1] 0.55458586 0.42137842 0.06763682
+
+ $xmother[[58]]
+ [1] 0.56143796 0.07072189 0.21139194 0.54962041
+
+ $xmother[[59]]
+ [1] 0.4819814 0.1594699 0.1495790
+
+ $xmother[[60]]
+ [1] 0.4992729
+
+ $xmother[[61]]
+ [1] 0.9405649
+
+ $xmother[[62]]
+ [1] 0.3342313 0.1884343
+
+ $xmother[[63]]
+ [1] 0.2697162 0.5307441
+
+ $xmother[[64]]
+ [1] 0.02145023 0.79876031
+
+ $xmother[[65]]
+ [1] 0.1103351 0.5397983
+
+ $xmother[[66]]
+ [1] 0.5712339 0.6189515
+
+ $xmother[[67]]
+ [1] 0.7148537 0.1233006 0.3110496 0.9457392
+
+ $xmother[[68]]
+ [1] 0.5000251 0.1352305 0.8692578
+
+ $xmother[[69]]
+ [1] 0.2050496 0.9250459
+
+ $xmother[[70]]
+ [1] 0.8867536
+
+ $xmother[[71]]
+ [1] 0.1362958 0.7853494
+
+ $xmother[[72]]
+ [1] 0.4533034 0.1357424 0.8852210
+
+ $xmother[[73]]
+ [1] 0.3367135 0.3192741
+
+ $xmother[[74]]
+ [1] 0.4037828 0.4790773
+
+ $xmother[[75]]
+ [1] 0.3679018 0.4656906
+
+ $xmother[[76]]
+ [1] 0.04989215 0.18735671 0.98265941 0.32827407
+
+ $xmother[[77]]
+ [1] 0.1709964
+
+ $xmother[[78]]
+ [1] 0.4882549
+
+ $xmother[[79]]
+ [1] 0.01868741
+
+ $xmother[[80]]
+ [1] 0.33948508 0.02966338 0.86722866
+
+ $xmother[[81]]
+ [1] 0.7317076 0.3152608 0.3864540 0.3324460
+
+ $xmother[[82]]
+ [1] 0.08977797
+
+ $xmother[[83]]
+ [1] 0.7570556 0.6029685
+
+ $xmother[[84]]
+ [1] 0.1454
+
+ $xmother[[85]]
+ [1] 0.03251748
+
+ $xmother[[86]]
+ [1] 0.48376814 0.44456953 0.06038559 0.32750602
+
+ $xmother[[87]]
+ [1] 0.8784290 0.9306049 0.3921785 0.1588468
+
+ $xmother[[88]]
+ [1] 0.3199476
+
+ $xmother[[89]]
+ [1] 0.3069656 0.1078113 0.9793343
+
+ $xmother[[90]]
+ [1] 0.49690343 0.09307467 0.21177366
+
+ $xmother[[91]]
+ [1] 0.9305007
+
+ $xmother[[92]]
+ [1] 0.2968464 0.6532182 0.9010705 0.9907958
+
+ $xmother[[93]]
+ [1] 0.4303332
+
+ $xmother[[94]]
+ [1] 0.3937769 0.1419089 0.2798067 0.5648222
+
+ $xmother[[95]]
+ [1] 0.9351395 0.3584001 0.8420072 0.7224092
+
+ $xmother[[96]]
+ [1] 0.7507360 0.9239885
+
+ $xmother[[97]]
+ [1] 0.002378107
+
+ $xmother[[98]]
+ [1] 0.1604299 0.3992730 0.6753196 0.4803720
+
+ $xmother[[99]]
+ [1] 0.5338288 0.3169502
+
+ $xmother[[100]]
+ [1] 0.8147576 0.2922195
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.4091321
+
+ $ymother[[2]]
+ [1] 0.09091831
+
+ $ymother[[3]]
+ [1] 0.7985966
+
+ $ymother[[4]]
+ [1] 0.3597852
+
+ $ymother[[5]]
+ [1] 0.04048758 0.04108634
+
+ $ymother[[6]]
+ [1] 0.9544342 0.3733412 0.8064197 0.9100590
+
+ $ymother[[7]]
+ [1] 0.4400762 0.5763365
+
+ $ymother[[8]]
+ [1] 0.0736678 0.1646274
+
+ $ymother[[9]]
+ [1] 0.7398908
+
+ $ymother[[10]]
+ [1] 0.4757110 0.6855210 0.9515149 0.4974645
+
+ $ymother[[11]]
+ [1] 0.4705006 0.5601920 0.6525101
+
+ $ymother[[12]]
+ [1] 0.2795735 0.9799076 0.6438641 0.5825784
+
+ $ymother[[13]]
+ [1] 0.6158710 0.9251403 0.3900229
+
+ $ymother[[14]]
+ [1] 0.28791969 0.09073596 0.32203390 0.75827011
+
+ $ymother[[15]]
+ [1] 0.1044129
+
+ $ymother[[16]]
+ [1] 0.7102779
+
+ $ymother[[17]]
+ [1] 0.9664774 0.2014912
+
+ $ymother[[18]]
+ [1] 0.10848865 0.05540218 0.82972352 0.58119776
+
+ $ymother[[19]]
+ [1] 0.4700924 0.3650141
+
+ $ymother[[20]]
+ [1] 0.2801246 0.5997159
+
+ $ymother[[21]]
+ [1] 0.81856961 0.09783228 0.96368953
+
+ $ymother[[22]]
+ [1] 0.16873644 0.08608341 0.86121070
+
+ $ymother[[23]]
+ [1] 0.5247906
+
+ $ymother[[24]]
+ [1] 0.6568109
+
+ $ymother[[25]]
+ [1] 0.2295194 0.7212260 0.4907504
+
+ $ymother[[26]]
+ [1] 0.9652556 0.9069425 0.5512505 0.0755991
+
+ $ymother[[27]]
+ [1] 0.02270001
+
+ $ymother[[28]]
+ [1] 0.5132395 0.6307262 0.4187716
+
+ $ymother[[29]]
+ [1] 0.8792659
+
+ $ymother[[30]]
+ [1] 0.1079871
+
+ $ymother[[31]]
+ [1] 0.98027870 0.26496663 0.08427752 0.38590718
+
+ $ymother[[32]]
+ [1] 0.1248958 0.5815542
+
+ $ymother[[33]]
+ [1] 0.2401496 0.7218879 0.1459287 0.1528388
+
+ $ymother[[34]]
+ [1] 0.25922267 0.77788626 0.42646630 0.06004834
+
+ $ymother[[35]]
+ [1] 0.1148325 0.4827569 0.9791736
+
+ $ymother[[36]]
+ [1] 0.8115168 0.5429128
+
+ $ymother[[37]]
+ [1] 0.07236709
+
+ $ymother[[38]]
+ [1] 0.4664852 0.3399056
+
+ $ymother[[39]]
+ [1] 0.6899186 0.5141574 0.5149230 0.5455144
+
+ $ymother[[40]]
+ [1] 0.44745733 0.08388484
+
+ $ymother[[41]]
+ [1] 0.93013369 0.01644819 0.41409240
+
+ $ymother[[42]]
+ [1] 0.22697609 0.09964059 0.48292388
+
+ $ymother[[43]]
+ [1] 0.6501287 0.9213298
+
+ $ymother[[44]]
+ [1] 0.3626018 0.8551350
+
+ $ymother[[45]]
+ [1] 0.3009062 0.4656624 0.1427307 0.8077190
+
+ $ymother[[46]]
+ [1] 0.66580763 0.06194098 0.43092557 0.39685508
+
+ $ymother[[47]]
+ [1] 0.6969568 0.6593197 0.4073507 0.3069202
+
+ $ymother[[48]]
+ [1] 0.2551073 0.6725682
+
+ $ymother[[49]]
+ [1] 0.8943934 0.8457362
+
+ $ymother[[50]]
+ [1] 0.3929019
+
+ $ymother[[51]]
+ [1] 0.07905054 0.82842306 0.07289182 0.11476268
+
+ $ymother[[52]]
+ [1] 0.6399843
+
+ $ymother[[53]]
+ [1] 0.3205662 0.1887495 0.3938296 0.8620260
+
+ $ymother[[54]]
+ [1] 0.347911407 0.001433898
+
+ $ymother[[55]]
+ [1] 0.9112845 0.9517234 0.4909190 0.4636517
+
+ $ymother[[56]]
+ [1] 0.596472 0.906051
+
+ $ymother[[57]]
+ [1] 0.1730012 0.7858811 0.2329344
+
+ $ymother[[58]]
+ [1] 0.5770482 0.8408770 0.1322038 0.8958912
+
+ $ymother[[59]]
+ [1] 0.4501373 0.8941425 0.2485452
+
+ $ymother[[60]]
+ [1] 0.08369529
+
+ $ymother[[61]]
+ [1] 0.04864107
+
+ $ymother[[62]]
+ [1] 0.9798159 0.4841677
+
+ $ymother[[63]]
+ [1] 0.8453930 0.4162936
+
+ $ymother[[64]]
+ [1] 0.4893425 0.1832878
+
+ $ymother[[65]]
+ [1] 0.7591615 0.3051433
+
+ $ymother[[66]]
+ [1] 0.16567825 0.03280914
+
+ $ymother[[67]]
+ [1] 0.1365052 0.1771364 0.5195605 0.8111208
+
+ $ymother[[68]]
+ [1] 0.1153620 0.8934218 0.5753529
+
+ $ymother[[69]]
+ [1] 0.1465724 0.9028058
+
+ $ymother[[70]]
+ [1] 0.2530025
+
+ $ymother[[71]]
+ [1] 0.1505976 0.7685472
+
+ $ymother[[72]]
+ [1] 0.2301233 0.3053993 0.5185696
+
+ $ymother[[73]]
+ [1] 0.3345997 0.1544350
+
+ $ymother[[74]]
+ [1] 0.2663696 0.3507546
+
+ $ymother[[75]]
+ [1] 0.5784584 0.8086018
+
+ $ymother[[76]]
+ [1] 0.9332703 0.8338633 0.1270028 0.6494540
+
+ $ymother[[77]]
+ [1] 0.6903517
+
+ $ymother[[78]]
+ [1] 0.03204482
+
+ $ymother[[79]]
+ [1] 0.9204891
+
+ $ymother[[80]]
+ [1] 0.4784689 0.2665206 0.8565107
+
+ $ymother[[81]]
+ [1] 0.2291465 0.7919469 0.6467749 0.4243347
+
+ $ymother[[82]]
+ [1] 0.09506827
+
+ $ymother[[83]]
+ [1] 0.003467704 0.531133669
+
+ $ymother[[84]]
+ [1] 0.5243071
+
+ $ymother[[85]]
+ [1] 0.2131856
+
+ $ymother[[86]]
+ [1] 0.7169321 0.9613436 0.5182666 0.1745280
+
+ $ymother[[87]]
+ [1] 0.5625401 0.7592582 0.6669713 0.2248729
+
+ $ymother[[88]]
+ [1] 0.3458498
+
+ $ymother[[89]]
+ [1] 0.3198318 0.9048984 0.1991984
+
+ $ymother[[90]]
+ [1] 0.6809630 0.1375178 0.1069947
+
+ $ymother[[91]]
+ [1] 0.0928594
+
+ $ymother[[92]]
+ [1] 0.9164490 0.2770604 0.8857939 0.7728646
+
+ $ymother[[93]]
+ [1] 0.7950512
+
+ $ymother[[94]]
+ [1] 0.20567359 0.04819332 0.03881593 0.28457413
+
+ $ymother[[95]]
+ [1] 0.3488098 0.7374533 0.2516636 0.5174370
+
+ $ymother[[96]]
+ [1] 0.7594447 0.6360845
+
+ $ymother[[97]]
+ [1] 0.2039407
+
+ $ymother[[98]]
+ [1] 0.9930452821 0.0004050434 0.2065700251 0.6340280906
+
+ $ymother[[99]]
+ [1] 0.01729183 0.02673547
+
+ $ymother[[100]]
+ [1] 0.6078406 0.5705414
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test with clustering - no range
+
+ Code
+ create_motherpoints(s_local = 100L, n_motherpoints_range = 1L, seed = 42L)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+ [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.6262453
+
+ $xmother[[2]]
+ [1] 0.2171577
+
+ $xmother[[3]]
+ [1] 0.2165673
+
+ $xmother[[4]]
+ [1] 0.388945
+
+ $xmother[[5]]
+ [1] 0.9424557
+
+ $xmother[[6]]
+ [1] 0.962608
+
+ $xmother[[7]]
+ [1] 0.7398553
+
+ $xmother[[8]]
+ [1] 0.7332459
+
+ $xmother[[9]]
+ [1] 0.5357613
+
+ $xmother[[10]]
+ [1] 0.002272966
+
+ $xmother[[11]]
+ [1] 0.6089375
+
+ $xmother[[12]]
+ [1] 0.8368016
+
+ $xmother[[13]]
+ [1] 0.7515226
+
+ $xmother[[14]]
+ [1] 0.4527316
+
+ $xmother[[15]]
+ [1] 0.53579
+
+ $xmother[[16]]
+ [1] 0.5373767
+
+ $xmother[[17]]
+ [1] 0.001380844
+
+ $xmother[[18]]
+ [1] 0.355666
+
+ $xmother[[19]]
+ [1] 0.6121331
+
+ $xmother[[20]]
+ [1] 0.8289421
+
+ $xmother[[21]]
+ [1] 0.356722
+
+ $xmother[[22]]
+ [1] 0.4106351
+
+ $xmother[[23]]
+ [1] 0.5734759
+
+ $xmother[[24]]
+ [1] 0.5896783
+
+ $xmother[[25]]
+ [1] 0.7196573
+
+ $xmother[[26]]
+ [1] 0.394973
+
+ $xmother[[27]]
+ [1] 0.9192039
+
+ $xmother[[28]]
+ [1] 0.9625703
+
+ $xmother[[29]]
+ [1] 0.2335235
+
+ $xmother[[30]]
+ [1] 0.7244976
+
+ $xmother[[31]]
+ [1] 0.9036345
+
+ $xmother[[32]]
+ [1] 0.6034741
+
+ $xmother[[33]]
+ [1] 0.6315073
+
+ $xmother[[34]]
+ [1] 0.9373858
+
+ $xmother[[35]]
+ [1] 0.8504828
+
+ $xmother[[36]]
+ [1] 0.5798209
+
+ $xmother[[37]]
+ [1] 0.8214039
+
+ $xmother[[38]]
+ [1] 0.1137186
+
+ $xmother[[39]]
+ [1] 0.7645078
+
+ $xmother[[40]]
+ [1] 0.6236135
+
+ $xmother[[41]]
+ [1] 0.1484466
+
+ $xmother[[42]]
+ [1] 0.08026447
+
+ $xmother[[43]]
+ [1] 0.4640696
+
+ $xmother[[44]]
+ [1] 0.7793682
+
+ $xmother[[45]]
+ [1] 0.733528
+
+ $xmother[[46]]
+ [1] 0.8172304
+
+ $xmother[[47]]
+ [1] 0.1701625
+
+ $xmother[[48]]
+ [1] 0.9447203
+
+ $xmother[[49]]
+ [1] 0.2936238
+
+ $xmother[[50]]
+ [1] 0.1490721
+
+ $xmother[[51]]
+ [1] 0.7193786
+
+ $xmother[[52]]
+ [1] 0.324086
+
+ $xmother[[53]]
+ [1] 0.7788095
+
+ $xmother[[54]]
+ [1] 0.394441
+
+ $xmother[[55]]
+ [1] 0.6785929
+
+ $xmother[[56]]
+ [1] 0.775825
+
+ $xmother[[57]]
+ [1] 0.187869
+
+ $xmother[[58]]
+ [1] 0.02908582
+
+ $xmother[[59]]
+ [1] 0.1357138
+
+ $xmother[[60]]
+ [1] 0.6801642
+
+ $xmother[[61]]
+ [1] 0.934823
+
+ $xmother[[62]]
+ [1] 0.5504941
+
+ $xmother[[63]]
+ [1] 0.6017662
+
+ $xmother[[64]]
+ [1] 0.1969945
+
+ $xmother[[65]]
+ [1] 0.5352366
+
+ $xmother[[66]]
+ [1] 0.1795557
+
+ $xmother[[67]]
+ [1] 0.4518865
+
+ $xmother[[68]]
+ [1] 0.3170534
+
+ $xmother[[69]]
+ [1] 0.1161747
+
+ $xmother[[70]]
+ [1] 0.1861022
+
+ $xmother[[71]]
+ [1] 0.7297301
+
+ $xmother[[72]]
+ [1] 0.4118721
+
+ $xmother[[73]]
+ [1] 0.4140497
+
+ $xmother[[74]]
+ [1] 0.4803101
+
+ $xmother[[75]]
+ [1] 0.4274945
+
+ $xmother[[76]]
+ [1] 0.1364904
+
+ $xmother[[77]]
+ [1] 0.8246794
+
+ $xmother[[78]]
+ [1] 0.5923042
+
+ $xmother[[79]]
+ [1] 0.794397
+
+ $xmother[[80]]
+ [1] 0.7690324
+
+ $xmother[[81]]
+ [1] 0.9180564
+
+ $xmother[[82]]
+ [1] 0.8626298
+
+ $xmother[[83]]
+ [1] 0.3169752
+
+ $xmother[[84]]
+ [1] 0.2592606
+
+ $xmother[[85]]
+ [1] 0.7422665
+
+ $xmother[[86]]
+ [1] 0.7473611
+
+ $xmother[[87]]
+ [1] 0.917904
+
+ $xmother[[88]]
+ [1] 0.7931912
+
+ $xmother[[89]]
+ [1] 0.1333296
+
+ $xmother[[90]]
+ [1] 0.2877498
+
+ $xmother[[91]]
+ [1] 0.1946761
+
+ $xmother[[92]]
+ [1] 0.7841094
+
+ $xmother[[93]]
+ [1] 0.1288722
+
+ $xmother[[94]]
+ [1] 0.1290893
+
+ $xmother[[95]]
+ [1] 0.07225311
+
+ $xmother[[96]]
+ [1] 0.05312948
+
+ $xmother[[97]]
+ [1] 0.5318744
+
+ $xmother[[98]]
+ [1] 0.1123082
+
+ $xmother[[99]]
+ [1] 0.7431877
+
+ $xmother[[100]]
+ [1] 0.7313155
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.8851177
+
+ $ymother[[2]]
+ [1] 0.5171111
+
+ $ymother[[3]]
+ [1] 0.851931
+
+ $ymother[[4]]
+ [1] 0.4427963
+
+ $ymother[[5]]
+ [1] 0.1578801
+
+ $ymother[[6]]
+ [1] 0.4423246
+
+ $ymother[[7]]
+ [1] 0.9677337
+
+ $ymother[[8]]
+ [1] 0.4845879
+
+ $ymother[[9]]
+ [1] 0.2524584
+
+ $ymother[[10]]
+ [1] 0.25969
+
+ $ymother[[11]]
+ [1] 0.5420159
+
+ $ymother[[12]]
+ [1] 0.6498758
+
+ $ymother[[13]]
+ [1] 0.3364191
+
+ $ymother[[14]]
+ [1] 0.06094975
+
+ $ymother[[15]]
+ [1] 0.4513109
+
+ $ymother[[16]]
+ [1] 0.838755
+
+ $ymother[[17]]
+ [1] 0.5746373
+
+ $ymother[[18]]
+ [1] 0.3533504
+
+ $ymother[[19]]
+ [1] 0.5474261
+
+ $ymother[[20]]
+ [1] 0.8927186
+
+ $ymother[[21]]
+ [1] 0.4899906
+
+ $ymother[[22]]
+ [1] 0.1716321
+
+ $ymother[[23]]
+ [1] 0.543031
+
+ $ymother[[24]]
+ [1] 0.9614677
+
+ $ymother[[25]]
+ [1] 0.3136838
+
+ $ymother[[26]]
+ [1] 0.8205145
+
+ $ymother[[27]]
+ [1] 0.3070544
+
+ $ymother[[28]]
+ [1] 0.1854536
+
+ $ymother[[29]]
+ [1] 0.04834678
+
+ $ymother[[30]]
+ [1] 0.2456741
+
+ $ymother[[31]]
+ [1] 0.3511069
+
+ $ymother[[32]]
+ [1] 0.1590224
+
+ $ymother[[33]]
+ [1] 0.304098
+
+ $ymother[[34]]
+ [1] 0.01754832
+
+ $ymother[[35]]
+ [1] 0.9965527
+
+ $ymother[[36]]
+ [1] 0.8043933
+
+ $ymother[[37]]
+ [1] 0.0865806
+
+ $ymother[[38]]
+ [1] 0.8699333
+
+ $ymother[[39]]
+ [1] 0.5545859
+
+ $ymother[[40]]
+ [1] 0.4213784
+
+ $ymother[[41]]
+ [1] 0.06763682
+
+ $ymother[[42]]
+ [1] 0.561438
+
+ $ymother[[43]]
+ [1] 0.07072189
+
+ $ymother[[44]]
+ [1] 0.2113919
+
+ $ymother[[45]]
+ [1] 0.5496204
+
+ $ymother[[46]]
+ [1] 0.4819814
+
+ $ymother[[47]]
+ [1] 0.1594699
+
+ $ymother[[48]]
+ [1] 0.149579
+
+ $ymother[[49]]
+ [1] 0.4992729
+
+ $ymother[[50]]
+ [1] 0.9405649
+
+ $ymother[[51]]
+ [1] 0.3342313
+
+ $ymother[[52]]
+ [1] 0.1884343
+
+ $ymother[[53]]
+ [1] 0.2697162
+
+ $ymother[[54]]
+ [1] 0.5307441
+
+ $ymother[[55]]
+ [1] 0.02145023
+
+ $ymother[[56]]
+ [1] 0.7987603
+
+ $ymother[[57]]
+ [1] 0.1103351
+
+ $ymother[[58]]
+ [1] 0.5397983
+
+ $ymother[[59]]
+ [1] 0.5712339
+
+ $ymother[[60]]
+ [1] 0.6189515
+
+ $ymother[[61]]
+ [1] 0.7148537
+
+ $ymother[[62]]
+ [1] 0.1233006
+
+ $ymother[[63]]
+ [1] 0.3110496
+
+ $ymother[[64]]
+ [1] 0.9457392
+
+ $ymother[[65]]
+ [1] 0.5000251
+
+ $ymother[[66]]
+ [1] 0.1352305
+
+ $ymother[[67]]
+ [1] 0.8692578
+
+ $ymother[[68]]
+ [1] 0.2050496
+
+ $ymother[[69]]
+ [1] 0.9250459
+
+ $ymother[[70]]
+ [1] 0.8867536
+
+ $ymother[[71]]
+ [1] 0.1362958
+
+ $ymother[[72]]
+ [1] 0.7853494
+
+ $ymother[[73]]
+ [1] 0.4533034
+
+ $ymother[[74]]
+ [1] 0.1357424
+
+ $ymother[[75]]
+ [1] 0.885221
+
+ $ymother[[76]]
+ [1] 0.3367135
+
+ $ymother[[77]]
+ [1] 0.3192741
+
+ $ymother[[78]]
+ [1] 0.4037828
+
+ $ymother[[79]]
+ [1] 0.4790773
+
+ $ymother[[80]]
+ [1] 0.3679018
+
+ $ymother[[81]]
+ [1] 0.4656906
+
+ $ymother[[82]]
+ [1] 0.04989215
+
+ $ymother[[83]]
+ [1] 0.1873567
+
+ $ymother[[84]]
+ [1] 0.9826594
+
+ $ymother[[85]]
+ [1] 0.3282741
+
+ $ymother[[86]]
+ [1] 0.1709964
+
+ $ymother[[87]]
+ [1] 0.4882549
+
+ $ymother[[88]]
+ [1] 0.01868741
+
+ $ymother[[89]]
+ [1] 0.3394851
+
+ $ymother[[90]]
+ [1] 0.02966338
+
+ $ymother[[91]]
+ [1] 0.8672287
+
+ $ymother[[92]]
+ [1] 0.7317076
+
+ $ymother[[93]]
+ [1] 0.3152608
+
+ $ymother[[94]]
+ [1] 0.386454
+
+ $ymother[[95]]
+ [1] 0.332446
+
+ $ymother[[96]]
+ [1] 0.08977797
+
+ $ymother[[97]]
+ [1] 0.7570556
+
+ $ymother[[98]]
+ [1] 0.6029685
+
+ $ymother[[99]]
+ [1] 0.1454
+
+ $ymother[[100]]
+ [1] 0.03251748
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test without clustering
+
+ Code
+ create_motherpoints(s_local = 100L, n_motherpoints_range = 0L:1L, seed = 42L)
+ Output
+ $n_mother_points
+ [1] 0 0 0 0 1 1 1 1 0 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 1 0
+ [38] 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 0 0 0 1 1 1 1 1 1 0 1 0 1 0 1 1
+ [75] 1 1 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 1 0 1 1 1 0 1 1 1
+
+ $xmother
+ $xmother[[1]]
+ numeric(0)
+
+ $xmother[[2]]
+ numeric(0)
+
+ $xmother[[3]]
+ numeric(0)
+
+ $xmother[[4]]
+ numeric(0)
+
+ $xmother[[5]]
+ [1] 0.6262453
+
+ $xmother[[6]]
+ [1] 0.2171577
+
+ $xmother[[7]]
+ [1] 0.2165673
+
+ $xmother[[8]]
+ [1] 0.388945
+
+ $xmother[[9]]
+ numeric(0)
+
+ $xmother[[10]]
+ [1] 0.9424557
+
+ $xmother[[11]]
+ numeric(0)
+
+ $xmother[[12]]
+ [1] 0.962608
+
+ $xmother[[13]]
+ numeric(0)
+
+ $xmother[[14]]
+ [1] 0.7398553
+
+ $xmother[[15]]
+ numeric(0)
+
+ $xmother[[16]]
+ numeric(0)
+
+ $xmother[[17]]
+ [1] 0.7332459
+
+ $xmother[[18]]
+ [1] 0.5357613
+
+ $xmother[[19]]
+ [1] 0.002272966
+
+ $xmother[[20]]
+ [1] 0.6089375
+
+ $xmother[[21]]
+ numeric(0)
+
+ $xmother[[22]]
+ numeric(0)
+
+ $xmother[[23]]
+ numeric(0)
+
+ $xmother[[24]]
+ numeric(0)
+
+ $xmother[[25]]
+ numeric(0)
+
+ $xmother[[26]]
+ [1] 0.8368016
+
+ $xmother[[27]]
+ numeric(0)
+
+ $xmother[[28]]
+ numeric(0)
+
+ $xmother[[29]]
+ numeric(0)
+
+ $xmother[[30]]
+ numeric(0)
+
+ $xmother[[31]]
+ [1] 0.7515226
+
+ $xmother[[32]]
+ [1] 0.4527316
+
+ $xmother[[33]]
+ [1] 0.53579
+
+ $xmother[[34]]
+ [1] 0.5373767
+
+ $xmother[[35]]
+ numeric(0)
+
+ $xmother[[36]]
+ [1] 0.001380844
+
+ $xmother[[37]]
+ numeric(0)
+
+ $xmother[[38]]
+ [1] 0.355666
+
+ $xmother[[39]]
+ [1] 0.6121331
+
+ $xmother[[40]]
+ [1] 0.8289421
+
+ $xmother[[41]]
+ numeric(0)
+
+ $xmother[[42]]
+ numeric(0)
+
+ $xmother[[43]]
+ [1] 0.356722
+
+ $xmother[[44]]
+ [1] 0.4106351
+
+ $xmother[[45]]
+ [1] 0.5734759
+
+ $xmother[[46]]
+ [1] 0.5896783
+
+ $xmother[[47]]
+ [1] 0.7196573
+
+ $xmother[[48]]
+ [1] 0.394973
+
+ $xmother[[49]]
+ [1] 0.9192039
+
+ $xmother[[50]]
+ numeric(0)
+
+ $xmother[[51]]
+ [1] 0.9625703
+
+ $xmother[[52]]
+ numeric(0)
+
+ $xmother[[53]]
+ [1] 0.2335235
+
+ $xmother[[54]]
+ [1] 0.7244976
+
+ $xmother[[55]]
+ [1] 0.9036345
+
+ $xmother[[56]]
+ [1] 0.6034741
+
+ $xmother[[57]]
+ numeric(0)
+
+ $xmother[[58]]
+ [1] 0.6315073
+
+ $xmother[[59]]
+ numeric(0)
+
+ $xmother[[60]]
+ numeric(0)
+
+ $xmother[[61]]
+ numeric(0)
+
+ $xmother[[62]]
+ [1] 0.9373858
+
+ $xmother[[63]]
+ [1] 0.8504828
+
+ $xmother[[64]]
+ [1] 0.5798209
+
+ $xmother[[65]]
+ [1] 0.8214039
+
+ $xmother[[66]]
+ [1] 0.1137186
+
+ $xmother[[67]]
+ [1] 0.7645078
+
+ $xmother[[68]]
+ numeric(0)
+
+ $xmother[[69]]
+ [1] 0.6236135
+
+ $xmother[[70]]
+ numeric(0)
+
+ $xmother[[71]]
+ [1] 0.1484466
+
+ $xmother[[72]]
+ numeric(0)
+
+ $xmother[[73]]
+ [1] 0.08026447
+
+ $xmother[[74]]
+ [1] 0.4640696
+
+ $xmother[[75]]
+ [1] 0.7793682
+
+ $xmother[[76]]
+ [1] 0.733528
+
+ $xmother[[77]]
+ numeric(0)
+
+ $xmother[[78]]
+ numeric(0)
+
+ $xmother[[79]]
+ numeric(0)
+
+ $xmother[[80]]
+ numeric(0)
+
+ $xmother[[81]]
+ [1] 0.8172304
+
+ $xmother[[82]]
+ numeric(0)
+
+ $xmother[[83]]
+ [1] 0.1701625
+
+ $xmother[[84]]
+ numeric(0)
+
+ $xmother[[85]]
+ numeric(0)
+
+ $xmother[[86]]
+ [1] 0.9447203
+
+ $xmother[[87]]
+ [1] 0.2936238
+
+ $xmother[[88]]
+ numeric(0)
+
+ $xmother[[89]]
+ numeric(0)
+
+ $xmother[[90]]
+ numeric(0)
+
+ $xmother[[91]]
+ numeric(0)
+
+ $xmother[[92]]
+ [1] 0.1490721
+
+ $xmother[[93]]
+ numeric(0)
+
+ $xmother[[94]]
+ [1] 0.7193786
+
+ $xmother[[95]]
+ [1] 0.324086
+
+ $xmother[[96]]
+ [1] 0.7788095
+
+ $xmother[[97]]
+ numeric(0)
+
+ $xmother[[98]]
+ [1] 0.394441
+
+ $xmother[[99]]
+ [1] 0.6785929
+
+ $xmother[[100]]
+ [1] 0.775825
+
+
+ $ymother
+ $ymother[[1]]
+ numeric(0)
+
+ $ymother[[2]]
+ numeric(0)
+
+ $ymother[[3]]
+ numeric(0)
+
+ $ymother[[4]]
+ numeric(0)
+
+ $ymother[[5]]
+ [1] 0.187869
+
+ $ymother[[6]]
+ [1] 0.02908582
+
+ $ymother[[7]]
+ [1] 0.1357138
+
+ $ymother[[8]]
+ [1] 0.6801642
+
+ $ymother[[9]]
+ numeric(0)
+
+ $ymother[[10]]
+ [1] 0.934823
+
+ $ymother[[11]]
+ numeric(0)
+
+ $ymother[[12]]
+ [1] 0.5504941
+
+ $ymother[[13]]
+ numeric(0)
+
+ $ymother[[14]]
+ [1] 0.6017662
+
+ $ymother[[15]]
+ numeric(0)
+
+ $ymother[[16]]
+ numeric(0)
+
+ $ymother[[17]]
+ [1] 0.1969945
+
+ $ymother[[18]]
+ [1] 0.5352366
+
+ $ymother[[19]]
+ [1] 0.1795557
+
+ $ymother[[20]]
+ [1] 0.4518865
+
+ $ymother[[21]]
+ numeric(0)
+
+ $ymother[[22]]
+ numeric(0)
+
+ $ymother[[23]]
+ numeric(0)
+
+ $ymother[[24]]
+ numeric(0)
+
+ $ymother[[25]]
+ numeric(0)
+
+ $ymother[[26]]
+ [1] 0.3170534
+
+ $ymother[[27]]
+ numeric(0)
+
+ $ymother[[28]]
+ numeric(0)
+
+ $ymother[[29]]
+ numeric(0)
+
+ $ymother[[30]]
+ numeric(0)
+
+ $ymother[[31]]
+ [1] 0.1161747
+
+ $ymother[[32]]
+ [1] 0.1861022
+
+ $ymother[[33]]
+ [1] 0.7297301
+
+ $ymother[[34]]
+ [1] 0.4118721
+
+ $ymother[[35]]
+ numeric(0)
+
+ $ymother[[36]]
+ [1] 0.4140497
+
+ $ymother[[37]]
+ numeric(0)
+
+ $ymother[[38]]
+ [1] 0.4803101
+
+ $ymother[[39]]
+ [1] 0.4274945
+
+ $ymother[[40]]
+ [1] 0.1364904
+
+ $ymother[[41]]
+ numeric(0)
+
+ $ymother[[42]]
+ numeric(0)
+
+ $ymother[[43]]
+ [1] 0.8246794
+
+ $ymother[[44]]
+ [1] 0.5923042
+
+ $ymother[[45]]
+ [1] 0.794397
+
+ $ymother[[46]]
+ [1] 0.7690324
+
+ $ymother[[47]]
+ [1] 0.9180564
+
+ $ymother[[48]]
+ [1] 0.8626298
+
+ $ymother[[49]]
+ [1] 0.3169752
+
+ $ymother[[50]]
+ numeric(0)
+
+ $ymother[[51]]
+ [1] 0.2592606
+
+ $ymother[[52]]
+ numeric(0)
+
+ $ymother[[53]]
+ [1] 0.7422665
+
+ $ymother[[54]]
+ [1] 0.7473611
+
+ $ymother[[55]]
+ [1] 0.917904
+
+ $ymother[[56]]
+ [1] 0.7931912
+
+ $ymother[[57]]
+ numeric(0)
+
+ $ymother[[58]]
+ [1] 0.1333296
+
+ $ymother[[59]]
+ numeric(0)
+
+ $ymother[[60]]
+ numeric(0)
+
+ $ymother[[61]]
+ numeric(0)
+
+ $ymother[[62]]
+ [1] 0.2877498
+
+ $ymother[[63]]
+ [1] 0.1946761
+
+ $ymother[[64]]
+ [1] 0.7841094
+
+ $ymother[[65]]
+ [1] 0.1288722
+
+ $ymother[[66]]
+ [1] 0.1290893
+
+ $ymother[[67]]
+ [1] 0.07225311
+
+ $ymother[[68]]
+ numeric(0)
+
+ $ymother[[69]]
+ [1] 0.05312948
+
+ $ymother[[70]]
+ numeric(0)
+
+ $ymother[[71]]
+ [1] 0.5318744
+
+ $ymother[[72]]
+ numeric(0)
+
+ $ymother[[73]]
+ [1] 0.1123082
+
+ $ymother[[74]]
+ [1] 0.7431877
+
+ $ymother[[75]]
+ [1] 0.7313155
+
+ $ymother[[76]]
+ [1] 0.8851177
+
+ $ymother[[77]]
+ numeric(0)
+
+ $ymother[[78]]
+ numeric(0)
+
+ $ymother[[79]]
+ numeric(0)
+
+ $ymother[[80]]
+ numeric(0)
+
+ $ymother[[81]]
+ [1] 0.5171111
+
+ $ymother[[82]]
+ numeric(0)
+
+ $ymother[[83]]
+ [1] 0.851931
+
+ $ymother[[84]]
+ numeric(0)
+
+ $ymother[[85]]
+ numeric(0)
+
+ $ymother[[86]]
+ [1] 0.4427963
+
+ $ymother[[87]]
+ [1] 0.1578801
+
+ $ymother[[88]]
+ numeric(0)
+
+ $ymother[[89]]
+ numeric(0)
+
+ $ymother[[90]]
+ numeric(0)
+
+ $ymother[[91]]
+ numeric(0)
+
+ $ymother[[92]]
+ [1] 0.4423246
+
+ $ymother[[93]]
+ numeric(0)
+
+ $ymother[[94]]
+ [1] 0.9677337
+
+ $ymother[[95]]
+ [1] 0.4845879
+
+ $ymother[[96]]
+ [1] 0.2524584
+
+ $ymother[[97]]
+ numeric(0)
+
+ $ymother[[98]]
+ [1] 0.25969
+
+ $ymother[[99]]
+ [1] 0.5420159
+
+ $ymother[[100]]
+ [1] 0.6498758
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test plotting method for mother_map class
+
+
+
diff --git a/tests/testthat/_snaps/drift_motherpoints.md b/tests/testthat/_snaps/drift_motherpoints.md
new file mode 100644
index 0000000..2f0945a
--- /dev/null
+++ b/tests/testthat/_snaps/drift_motherpoints.md
@@ -0,0 +1,2492 @@
+# snapshot test drift_x with clustering
+
+ Code
+ drift_x_motherpoints(mpcoords, drift = 0.1)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2 3 3 1 1 3 4 1 3 1 1 4 2 4 4 3 2 1
+ [38] 2 4 2 3 3 2 2 4 4 4 2 2 1 4 1 4 2 4 2 3 4 3 1 1 2 2 2 2 2 4 3 2 1 2 3 2 2
+ [75] 2 4 1 1 1 3 4 1 2 1 1 4 4 1 3 3 1 4 1 4 4 2 1 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.7262453
+
+ $xmother[[2]]
+ [1] 0.3171577
+
+ $xmother[[3]]
+ [1] 0.3165673
+
+ $xmother[[4]]
+ [1] 0.488945
+
+ $xmother[[5]]
+ [1] 1.042456 1.062608
+
+ $xmother[[6]]
+ [1] 0.8398553 0.8332459 0.6357613 0.1022730
+
+ $xmother[[7]]
+ [1] 0.7089375 0.9368016
+
+ $xmother[[8]]
+ [1] 0.8515226 0.5527316
+
+ $xmother[[9]]
+ [1] 0.63579
+
+ $xmother[[10]]
+ [1] 0.6373767 0.1013808 0.4556660 0.7121331
+
+ $xmother[[11]]
+ [1] 0.9289421 0.4567220 0.5106351
+
+ $xmother[[12]]
+ [1] 0.6734759 0.6896783 0.8196573 0.4949730
+
+ $xmother[[13]]
+ [1] 1.0192039 1.0625703 0.3335235
+
+ $xmother[[14]]
+ [1] 0.8244976 1.0036345 0.7034741 0.7315073
+
+ $xmother[[15]]
+ [1] 1.037386
+
+ $xmother[[16]]
+ [1] 0.9504828
+
+ $xmother[[17]]
+ [1] 0.6798209 0.9214039
+
+ $xmother[[18]]
+ [1] 0.2137186 0.8645078 0.7236135 0.2484466
+
+ $xmother[[19]]
+ [1] 0.1802645 0.5640696
+
+ $xmother[[20]]
+ [1] 0.8793682 0.8335280
+
+ $xmother[[21]]
+ [1] 0.9172304 0.2701625 1.0447203
+
+ $xmother[[22]]
+ [1] 0.3936238 0.2490721 0.8193786
+
+ $xmother[[23]]
+ [1] 0.424086
+
+ $xmother[[24]]
+ [1] 0.8788095
+
+ $xmother[[25]]
+ [1] 0.4944410 0.7785929 0.8758250
+
+ $xmother[[26]]
+ [1] 0.2878690 0.1290858 0.2357138 0.7801642
+
+ $xmother[[27]]
+ [1] 1.034823
+
+ $xmother[[28]]
+ [1] 0.6504941 0.7017662 0.2969945
+
+ $xmother[[29]]
+ [1] 0.6352366
+
+ $xmother[[30]]
+ [1] 0.2795557
+
+ $xmother[[31]]
+ [1] 0.5518865 0.4170534 0.2161747 0.2861022
+
+ $xmother[[32]]
+ [1] 0.8297301 0.5118721
+
+ $xmother[[33]]
+ [1] 0.5140497 0.5803101 0.5274945 0.2364904
+
+ $xmother[[34]]
+ [1] 0.9246794 0.6923042 0.8943970 0.8690324
+
+ $xmother[[35]]
+ [1] 1.0180564 0.9626298 0.4169752
+
+ $xmother[[36]]
+ [1] 0.3592606 0.8422665
+
+ $xmother[[37]]
+ [1] 0.8473611
+
+ $xmother[[38]]
+ [1] 1.0179040 0.8931912
+
+ $xmother[[39]]
+ [1] 0.2333296 0.3877498 0.2946761 0.8841094
+
+ $xmother[[40]]
+ [1] 0.2288722 0.2290893
+
+ $xmother[[41]]
+ [1] 0.1722531 0.1531295 0.6318744
+
+ $xmother[[42]]
+ [1] 0.2123082 0.8431877 0.8313155
+
+ $xmother[[43]]
+ [1] 0.9851177 0.6171111
+
+ $xmother[[44]]
+ [1] 0.9519310 0.5427963
+
+ $xmother[[45]]
+ [1] 0.2578801 0.5423246 1.0677337 0.5845879
+
+ $xmother[[46]]
+ [1] 0.3524584 0.3596900 0.6420159 0.7498758
+
+ $xmother[[47]]
+ [1] 0.4364191 0.1609497 0.5513109 0.9387550
+
+ $xmother[[48]]
+ [1] 0.6746373 0.4533504
+
+ $xmother[[49]]
+ [1] 0.6474261 0.9927186
+
+ $xmother[[50]]
+ [1] 0.5899906
+
+ $xmother[[51]]
+ [1] 0.2716321 0.6430310 1.0614677 0.4136838
+
+ $xmother[[52]]
+ [1] 0.9205145
+
+ $xmother[[53]]
+ [1] 0.4070544 0.2854536 0.1483468 0.3456741
+
+ $xmother[[54]]
+ [1] 0.4511069 0.2590224
+
+ $xmother[[55]]
+ [1] 0.4040980 0.1175483 1.0965527 0.9043933
+
+ $xmother[[56]]
+ [1] 0.1865806 0.9699333
+
+ $xmother[[57]]
+ [1] 0.6545859 0.5213784 0.1676368
+
+ $xmother[[58]]
+ [1] 0.6614380 0.1707219 0.3113919 0.6496204
+
+ $xmother[[59]]
+ [1] 0.5819814 0.2594699 0.2495790
+
+ $xmother[[60]]
+ [1] 0.5992729
+
+ $xmother[[61]]
+ [1] 1.040565
+
+ $xmother[[62]]
+ [1] 0.4342313 0.2884343
+
+ $xmother[[63]]
+ [1] 0.3697162 0.6307441
+
+ $xmother[[64]]
+ [1] 0.1214502 0.8987603
+
+ $xmother[[65]]
+ [1] 0.2103351 0.6397983
+
+ $xmother[[66]]
+ [1] 0.6712339 0.7189515
+
+ $xmother[[67]]
+ [1] 0.8148537 0.2233006 0.4110496 1.0457392
+
+ $xmother[[68]]
+ [1] 0.6000251 0.2352305 0.9692578
+
+ $xmother[[69]]
+ [1] 0.3050496 1.0250459
+
+ $xmother[[70]]
+ [1] 0.9867536
+
+ $xmother[[71]]
+ [1] 0.2362958 0.8853494
+
+ $xmother[[72]]
+ [1] 0.5533034 0.2357424 0.9852210
+
+ $xmother[[73]]
+ [1] 0.4367135 0.4192741
+
+ $xmother[[74]]
+ [1] 0.5037828 0.5790773
+
+ $xmother[[75]]
+ [1] 0.4679018 0.5656906
+
+ $xmother[[76]]
+ [1] 0.1498922 0.2873567 1.0826594 0.4282741
+
+ $xmother[[77]]
+ [1] 0.2709964
+
+ $xmother[[78]]
+ [1] 0.5882549
+
+ $xmother[[79]]
+ [1] 0.1186874
+
+ $xmother[[80]]
+ [1] 0.4394851 0.1296634 0.9672287
+
+ $xmother[[81]]
+ [1] 0.8317076 0.4152608 0.4864540 0.4324460
+
+ $xmother[[82]]
+ [1] 0.189778
+
+ $xmother[[83]]
+ [1] 0.8570556 0.7029685
+
+ $xmother[[84]]
+ [1] 0.2454
+
+ $xmother[[85]]
+ [1] 0.1325175
+
+ $xmother[[86]]
+ [1] 0.5837681 0.5445695 0.1603856 0.4275060
+
+ $xmother[[87]]
+ [1] 0.9784290 1.0306049 0.4921785 0.2588468
+
+ $xmother[[88]]
+ [1] 0.4199476
+
+ $xmother[[89]]
+ [1] 0.4069656 0.2078113 1.0793343
+
+ $xmother[[90]]
+ [1] 0.5969034 0.1930747 0.3117737
+
+ $xmother[[91]]
+ [1] 1.030501
+
+ $xmother[[92]]
+ [1] 0.3968464 0.7532182 1.0010705 1.0907958
+
+ $xmother[[93]]
+ [1] 0.5303332
+
+ $xmother[[94]]
+ [1] 0.4937769 0.2419089 0.3798067 0.6648222
+
+ $xmother[[95]]
+ [1] 1.0351395 0.4584001 0.9420072 0.8224092
+
+ $xmother[[96]]
+ [1] 0.850736 1.023988
+
+ $xmother[[97]]
+ [1] 0.1023781
+
+ $xmother[[98]]
+ [1] 0.2604299 0.4992730 0.7753196 0.5803720
+
+ $xmother[[99]]
+ [1] 0.6338288 0.4169502
+
+ $xmother[[100]]
+ [1] 0.9147576 0.3922195
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.4091321
+
+ $ymother[[2]]
+ [1] 0.09091831
+
+ $ymother[[3]]
+ [1] 0.7985966
+
+ $ymother[[4]]
+ [1] 0.3597852
+
+ $ymother[[5]]
+ [1] 0.04048758 0.04108634
+
+ $ymother[[6]]
+ [1] 0.9544342 0.3733412 0.8064197 0.9100590
+
+ $ymother[[7]]
+ [1] 0.4400762 0.5763365
+
+ $ymother[[8]]
+ [1] 0.0736678 0.1646274
+
+ $ymother[[9]]
+ [1] 0.7398908
+
+ $ymother[[10]]
+ [1] 0.4757110 0.6855210 0.9515149 0.4974645
+
+ $ymother[[11]]
+ [1] 0.4705006 0.5601920 0.6525101
+
+ $ymother[[12]]
+ [1] 0.2795735 0.9799076 0.6438641 0.5825784
+
+ $ymother[[13]]
+ [1] 0.6158710 0.9251403 0.3900229
+
+ $ymother[[14]]
+ [1] 0.28791969 0.09073596 0.32203390 0.75827011
+
+ $ymother[[15]]
+ [1] 0.1044129
+
+ $ymother[[16]]
+ [1] 0.7102779
+
+ $ymother[[17]]
+ [1] 0.9664774 0.2014912
+
+ $ymother[[18]]
+ [1] 0.10848865 0.05540218 0.82972352 0.58119776
+
+ $ymother[[19]]
+ [1] 0.4700924 0.3650141
+
+ $ymother[[20]]
+ [1] 0.2801246 0.5997159
+
+ $ymother[[21]]
+ [1] 0.81856961 0.09783228 0.96368953
+
+ $ymother[[22]]
+ [1] 0.16873644 0.08608341 0.86121070
+
+ $ymother[[23]]
+ [1] 0.5247906
+
+ $ymother[[24]]
+ [1] 0.6568109
+
+ $ymother[[25]]
+ [1] 0.2295194 0.7212260 0.4907504
+
+ $ymother[[26]]
+ [1] 0.9652556 0.9069425 0.5512505 0.0755991
+
+ $ymother[[27]]
+ [1] 0.02270001
+
+ $ymother[[28]]
+ [1] 0.5132395 0.6307262 0.4187716
+
+ $ymother[[29]]
+ [1] 0.8792659
+
+ $ymother[[30]]
+ [1] 0.1079871
+
+ $ymother[[31]]
+ [1] 0.98027870 0.26496663 0.08427752 0.38590718
+
+ $ymother[[32]]
+ [1] 0.1248958 0.5815542
+
+ $ymother[[33]]
+ [1] 0.2401496 0.7218879 0.1459287 0.1528388
+
+ $ymother[[34]]
+ [1] 0.25922267 0.77788626 0.42646630 0.06004834
+
+ $ymother[[35]]
+ [1] 0.1148325 0.4827569 0.9791736
+
+ $ymother[[36]]
+ [1] 0.8115168 0.5429128
+
+ $ymother[[37]]
+ [1] 0.07236709
+
+ $ymother[[38]]
+ [1] 0.4664852 0.3399056
+
+ $ymother[[39]]
+ [1] 0.6899186 0.5141574 0.5149230 0.5455144
+
+ $ymother[[40]]
+ [1] 0.44745733 0.08388484
+
+ $ymother[[41]]
+ [1] 0.93013369 0.01644819 0.41409240
+
+ $ymother[[42]]
+ [1] 0.22697609 0.09964059 0.48292388
+
+ $ymother[[43]]
+ [1] 0.6501287 0.9213298
+
+ $ymother[[44]]
+ [1] 0.3626018 0.8551350
+
+ $ymother[[45]]
+ [1] 0.3009062 0.4656624 0.1427307 0.8077190
+
+ $ymother[[46]]
+ [1] 0.66580763 0.06194098 0.43092557 0.39685508
+
+ $ymother[[47]]
+ [1] 0.6969568 0.6593197 0.4073507 0.3069202
+
+ $ymother[[48]]
+ [1] 0.2551073 0.6725682
+
+ $ymother[[49]]
+ [1] 0.8943934 0.8457362
+
+ $ymother[[50]]
+ [1] 0.3929019
+
+ $ymother[[51]]
+ [1] 0.07905054 0.82842306 0.07289182 0.11476268
+
+ $ymother[[52]]
+ [1] 0.6399843
+
+ $ymother[[53]]
+ [1] 0.3205662 0.1887495 0.3938296 0.8620260
+
+ $ymother[[54]]
+ [1] 0.347911407 0.001433898
+
+ $ymother[[55]]
+ [1] 0.9112845 0.9517234 0.4909190 0.4636517
+
+ $ymother[[56]]
+ [1] 0.596472 0.906051
+
+ $ymother[[57]]
+ [1] 0.1730012 0.7858811 0.2329344
+
+ $ymother[[58]]
+ [1] 0.5770482 0.8408770 0.1322038 0.8958912
+
+ $ymother[[59]]
+ [1] 0.4501373 0.8941425 0.2485452
+
+ $ymother[[60]]
+ [1] 0.08369529
+
+ $ymother[[61]]
+ [1] 0.04864107
+
+ $ymother[[62]]
+ [1] 0.9798159 0.4841677
+
+ $ymother[[63]]
+ [1] 0.8453930 0.4162936
+
+ $ymother[[64]]
+ [1] 0.4893425 0.1832878
+
+ $ymother[[65]]
+ [1] 0.7591615 0.3051433
+
+ $ymother[[66]]
+ [1] 0.16567825 0.03280914
+
+ $ymother[[67]]
+ [1] 0.1365052 0.1771364 0.5195605 0.8111208
+
+ $ymother[[68]]
+ [1] 0.1153620 0.8934218 0.5753529
+
+ $ymother[[69]]
+ [1] 0.1465724 0.9028058
+
+ $ymother[[70]]
+ [1] 0.2530025
+
+ $ymother[[71]]
+ [1] 0.1505976 0.7685472
+
+ $ymother[[72]]
+ [1] 0.2301233 0.3053993 0.5185696
+
+ $ymother[[73]]
+ [1] 0.3345997 0.1544350
+
+ $ymother[[74]]
+ [1] 0.2663696 0.3507546
+
+ $ymother[[75]]
+ [1] 0.5784584 0.8086018
+
+ $ymother[[76]]
+ [1] 0.9332703 0.8338633 0.1270028 0.6494540
+
+ $ymother[[77]]
+ [1] 0.6903517
+
+ $ymother[[78]]
+ [1] 0.03204482
+
+ $ymother[[79]]
+ [1] 0.9204891
+
+ $ymother[[80]]
+ [1] 0.4784689 0.2665206 0.8565107
+
+ $ymother[[81]]
+ [1] 0.2291465 0.7919469 0.6467749 0.4243347
+
+ $ymother[[82]]
+ [1] 0.09506827
+
+ $ymother[[83]]
+ [1] 0.003467704 0.531133669
+
+ $ymother[[84]]
+ [1] 0.5243071
+
+ $ymother[[85]]
+ [1] 0.2131856
+
+ $ymother[[86]]
+ [1] 0.7169321 0.9613436 0.5182666 0.1745280
+
+ $ymother[[87]]
+ [1] 0.5625401 0.7592582 0.6669713 0.2248729
+
+ $ymother[[88]]
+ [1] 0.3458498
+
+ $ymother[[89]]
+ [1] 0.3198318 0.9048984 0.1991984
+
+ $ymother[[90]]
+ [1] 0.6809630 0.1375178 0.1069947
+
+ $ymother[[91]]
+ [1] 0.0928594
+
+ $ymother[[92]]
+ [1] 0.9164490 0.2770604 0.8857939 0.7728646
+
+ $ymother[[93]]
+ [1] 0.7950512
+
+ $ymother[[94]]
+ [1] 0.20567359 0.04819332 0.03881593 0.28457413
+
+ $ymother[[95]]
+ [1] 0.3488098 0.7374533 0.2516636 0.5174370
+
+ $ymother[[96]]
+ [1] 0.7594447 0.6360845
+
+ $ymother[[97]]
+ [1] 0.2039407
+
+ $ymother[[98]]
+ [1] 0.9930452821 0.0004050434 0.2065700251 0.6340280906
+
+ $ymother[[99]]
+ [1] 0.01729183 0.02673547
+
+ $ymother[[100]]
+ [1] 0.6078406 0.5705414
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test drift_x without clustering
+
+ Code
+ drift_x_motherpoints(mpcoords, drift = 0.1)
+ Output
+ $n_mother_points
+ [1] 0 0 0 0 1 1 1 1 0 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 1 0
+ [38] 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 0 0 0 1 1 1 1 1 1 0 1 0 1 0 1 1
+ [75] 1 1 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 1 0 1 1 1 0 1 1 1
+
+ $xmother
+ $xmother[[1]]
+ numeric(0)
+
+ $xmother[[2]]
+ numeric(0)
+
+ $xmother[[3]]
+ numeric(0)
+
+ $xmother[[4]]
+ numeric(0)
+
+ $xmother[[5]]
+ [1] 0.7262453
+
+ $xmother[[6]]
+ [1] 0.3171577
+
+ $xmother[[7]]
+ [1] 0.3165673
+
+ $xmother[[8]]
+ [1] 0.488945
+
+ $xmother[[9]]
+ numeric(0)
+
+ $xmother[[10]]
+ [1] 1.042456
+
+ $xmother[[11]]
+ numeric(0)
+
+ $xmother[[12]]
+ [1] 1.062608
+
+ $xmother[[13]]
+ numeric(0)
+
+ $xmother[[14]]
+ [1] 0.8398553
+
+ $xmother[[15]]
+ numeric(0)
+
+ $xmother[[16]]
+ numeric(0)
+
+ $xmother[[17]]
+ [1] 0.8332459
+
+ $xmother[[18]]
+ [1] 0.6357613
+
+ $xmother[[19]]
+ [1] 0.102273
+
+ $xmother[[20]]
+ [1] 0.7089375
+
+ $xmother[[21]]
+ numeric(0)
+
+ $xmother[[22]]
+ numeric(0)
+
+ $xmother[[23]]
+ numeric(0)
+
+ $xmother[[24]]
+ numeric(0)
+
+ $xmother[[25]]
+ numeric(0)
+
+ $xmother[[26]]
+ [1] 0.9368016
+
+ $xmother[[27]]
+ numeric(0)
+
+ $xmother[[28]]
+ numeric(0)
+
+ $xmother[[29]]
+ numeric(0)
+
+ $xmother[[30]]
+ numeric(0)
+
+ $xmother[[31]]
+ [1] 0.8515226
+
+ $xmother[[32]]
+ [1] 0.5527316
+
+ $xmother[[33]]
+ [1] 0.63579
+
+ $xmother[[34]]
+ [1] 0.6373767
+
+ $xmother[[35]]
+ numeric(0)
+
+ $xmother[[36]]
+ [1] 0.1013808
+
+ $xmother[[37]]
+ numeric(0)
+
+ $xmother[[38]]
+ [1] 0.455666
+
+ $xmother[[39]]
+ [1] 0.7121331
+
+ $xmother[[40]]
+ [1] 0.9289421
+
+ $xmother[[41]]
+ numeric(0)
+
+ $xmother[[42]]
+ numeric(0)
+
+ $xmother[[43]]
+ [1] 0.456722
+
+ $xmother[[44]]
+ [1] 0.5106351
+
+ $xmother[[45]]
+ [1] 0.6734759
+
+ $xmother[[46]]
+ [1] 0.6896783
+
+ $xmother[[47]]
+ [1] 0.8196573
+
+ $xmother[[48]]
+ [1] 0.494973
+
+ $xmother[[49]]
+ [1] 1.019204
+
+ $xmother[[50]]
+ numeric(0)
+
+ $xmother[[51]]
+ [1] 1.06257
+
+ $xmother[[52]]
+ numeric(0)
+
+ $xmother[[53]]
+ [1] 0.3335235
+
+ $xmother[[54]]
+ [1] 0.8244976
+
+ $xmother[[55]]
+ [1] 1.003635
+
+ $xmother[[56]]
+ [1] 0.7034741
+
+ $xmother[[57]]
+ numeric(0)
+
+ $xmother[[58]]
+ [1] 0.7315073
+
+ $xmother[[59]]
+ numeric(0)
+
+ $xmother[[60]]
+ numeric(0)
+
+ $xmother[[61]]
+ numeric(0)
+
+ $xmother[[62]]
+ [1] 1.037386
+
+ $xmother[[63]]
+ [1] 0.9504828
+
+ $xmother[[64]]
+ [1] 0.6798209
+
+ $xmother[[65]]
+ [1] 0.9214039
+
+ $xmother[[66]]
+ [1] 0.2137186
+
+ $xmother[[67]]
+ [1] 0.8645078
+
+ $xmother[[68]]
+ numeric(0)
+
+ $xmother[[69]]
+ [1] 0.7236135
+
+ $xmother[[70]]
+ numeric(0)
+
+ $xmother[[71]]
+ [1] 0.2484466
+
+ $xmother[[72]]
+ numeric(0)
+
+ $xmother[[73]]
+ [1] 0.1802645
+
+ $xmother[[74]]
+ [1] 0.5640696
+
+ $xmother[[75]]
+ [1] 0.8793682
+
+ $xmother[[76]]
+ [1] 0.833528
+
+ $xmother[[77]]
+ numeric(0)
+
+ $xmother[[78]]
+ numeric(0)
+
+ $xmother[[79]]
+ numeric(0)
+
+ $xmother[[80]]
+ numeric(0)
+
+ $xmother[[81]]
+ [1] 0.9172304
+
+ $xmother[[82]]
+ numeric(0)
+
+ $xmother[[83]]
+ [1] 0.2701625
+
+ $xmother[[84]]
+ numeric(0)
+
+ $xmother[[85]]
+ numeric(0)
+
+ $xmother[[86]]
+ [1] 1.04472
+
+ $xmother[[87]]
+ [1] 0.3936238
+
+ $xmother[[88]]
+ numeric(0)
+
+ $xmother[[89]]
+ numeric(0)
+
+ $xmother[[90]]
+ numeric(0)
+
+ $xmother[[91]]
+ numeric(0)
+
+ $xmother[[92]]
+ [1] 0.2490721
+
+ $xmother[[93]]
+ numeric(0)
+
+ $xmother[[94]]
+ [1] 0.8193786
+
+ $xmother[[95]]
+ [1] 0.424086
+
+ $xmother[[96]]
+ [1] 0.8788095
+
+ $xmother[[97]]
+ numeric(0)
+
+ $xmother[[98]]
+ [1] 0.494441
+
+ $xmother[[99]]
+ [1] 0.7785929
+
+ $xmother[[100]]
+ [1] 0.875825
+
+
+ $ymother
+ $ymother[[1]]
+ numeric(0)
+
+ $ymother[[2]]
+ numeric(0)
+
+ $ymother[[3]]
+ numeric(0)
+
+ $ymother[[4]]
+ numeric(0)
+
+ $ymother[[5]]
+ [1] 0.187869
+
+ $ymother[[6]]
+ [1] 0.02908582
+
+ $ymother[[7]]
+ [1] 0.1357138
+
+ $ymother[[8]]
+ [1] 0.6801642
+
+ $ymother[[9]]
+ numeric(0)
+
+ $ymother[[10]]
+ [1] 0.934823
+
+ $ymother[[11]]
+ numeric(0)
+
+ $ymother[[12]]
+ [1] 0.5504941
+
+ $ymother[[13]]
+ numeric(0)
+
+ $ymother[[14]]
+ [1] 0.6017662
+
+ $ymother[[15]]
+ numeric(0)
+
+ $ymother[[16]]
+ numeric(0)
+
+ $ymother[[17]]
+ [1] 0.1969945
+
+ $ymother[[18]]
+ [1] 0.5352366
+
+ $ymother[[19]]
+ [1] 0.1795557
+
+ $ymother[[20]]
+ [1] 0.4518865
+
+ $ymother[[21]]
+ numeric(0)
+
+ $ymother[[22]]
+ numeric(0)
+
+ $ymother[[23]]
+ numeric(0)
+
+ $ymother[[24]]
+ numeric(0)
+
+ $ymother[[25]]
+ numeric(0)
+
+ $ymother[[26]]
+ [1] 0.3170534
+
+ $ymother[[27]]
+ numeric(0)
+
+ $ymother[[28]]
+ numeric(0)
+
+ $ymother[[29]]
+ numeric(0)
+
+ $ymother[[30]]
+ numeric(0)
+
+ $ymother[[31]]
+ [1] 0.1161747
+
+ $ymother[[32]]
+ [1] 0.1861022
+
+ $ymother[[33]]
+ [1] 0.7297301
+
+ $ymother[[34]]
+ [1] 0.4118721
+
+ $ymother[[35]]
+ numeric(0)
+
+ $ymother[[36]]
+ [1] 0.4140497
+
+ $ymother[[37]]
+ numeric(0)
+
+ $ymother[[38]]
+ [1] 0.4803101
+
+ $ymother[[39]]
+ [1] 0.4274945
+
+ $ymother[[40]]
+ [1] 0.1364904
+
+ $ymother[[41]]
+ numeric(0)
+
+ $ymother[[42]]
+ numeric(0)
+
+ $ymother[[43]]
+ [1] 0.8246794
+
+ $ymother[[44]]
+ [1] 0.5923042
+
+ $ymother[[45]]
+ [1] 0.794397
+
+ $ymother[[46]]
+ [1] 0.7690324
+
+ $ymother[[47]]
+ [1] 0.9180564
+
+ $ymother[[48]]
+ [1] 0.8626298
+
+ $ymother[[49]]
+ [1] 0.3169752
+
+ $ymother[[50]]
+ numeric(0)
+
+ $ymother[[51]]
+ [1] 0.2592606
+
+ $ymother[[52]]
+ numeric(0)
+
+ $ymother[[53]]
+ [1] 0.7422665
+
+ $ymother[[54]]
+ [1] 0.7473611
+
+ $ymother[[55]]
+ [1] 0.917904
+
+ $ymother[[56]]
+ [1] 0.7931912
+
+ $ymother[[57]]
+ numeric(0)
+
+ $ymother[[58]]
+ [1] 0.1333296
+
+ $ymother[[59]]
+ numeric(0)
+
+ $ymother[[60]]
+ numeric(0)
+
+ $ymother[[61]]
+ numeric(0)
+
+ $ymother[[62]]
+ [1] 0.2877498
+
+ $ymother[[63]]
+ [1] 0.1946761
+
+ $ymother[[64]]
+ [1] 0.7841094
+
+ $ymother[[65]]
+ [1] 0.1288722
+
+ $ymother[[66]]
+ [1] 0.1290893
+
+ $ymother[[67]]
+ [1] 0.07225311
+
+ $ymother[[68]]
+ numeric(0)
+
+ $ymother[[69]]
+ [1] 0.05312948
+
+ $ymother[[70]]
+ numeric(0)
+
+ $ymother[[71]]
+ [1] 0.5318744
+
+ $ymother[[72]]
+ numeric(0)
+
+ $ymother[[73]]
+ [1] 0.1123082
+
+ $ymother[[74]]
+ [1] 0.7431877
+
+ $ymother[[75]]
+ [1] 0.7313155
+
+ $ymother[[76]]
+ [1] 0.8851177
+
+ $ymother[[77]]
+ numeric(0)
+
+ $ymother[[78]]
+ numeric(0)
+
+ $ymother[[79]]
+ numeric(0)
+
+ $ymother[[80]]
+ numeric(0)
+
+ $ymother[[81]]
+ [1] 0.5171111
+
+ $ymother[[82]]
+ numeric(0)
+
+ $ymother[[83]]
+ [1] 0.851931
+
+ $ymother[[84]]
+ numeric(0)
+
+ $ymother[[85]]
+ numeric(0)
+
+ $ymother[[86]]
+ [1] 0.4427963
+
+ $ymother[[87]]
+ [1] 0.1578801
+
+ $ymother[[88]]
+ numeric(0)
+
+ $ymother[[89]]
+ numeric(0)
+
+ $ymother[[90]]
+ numeric(0)
+
+ $ymother[[91]]
+ numeric(0)
+
+ $ymother[[92]]
+ [1] 0.4423246
+
+ $ymother[[93]]
+ numeric(0)
+
+ $ymother[[94]]
+ [1] 0.9677337
+
+ $ymother[[95]]
+ [1] 0.4845879
+
+ $ymother[[96]]
+ [1] 0.2524584
+
+ $ymother[[97]]
+ numeric(0)
+
+ $ymother[[98]]
+ [1] 0.25969
+
+ $ymother[[99]]
+ [1] 0.5420159
+
+ $ymother[[100]]
+ [1] 0.6498758
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test drift_y with clustering
+
+ Code
+ drift_y_motherpoints(mpcoords, drift = 0.1)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2 3 3 1 1 3 4 1 3 1 1 4 2 4 4 3 2 1
+ [38] 2 4 2 3 3 2 2 4 4 4 2 2 1 4 1 4 2 4 2 3 4 3 1 1 2 2 2 2 2 4 3 2 1 2 3 2 2
+ [75] 2 4 1 1 1 3 4 1 2 1 1 4 4 1 3 3 1 4 1 4 4 2 1 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.6262453
+
+ $xmother[[2]]
+ [1] 0.2171577
+
+ $xmother[[3]]
+ [1] 0.2165673
+
+ $xmother[[4]]
+ [1] 0.388945
+
+ $xmother[[5]]
+ [1] 0.9424557 0.9626080
+
+ $xmother[[6]]
+ [1] 0.739855279 0.733245906 0.535761290 0.002272966
+
+ $xmother[[7]]
+ [1] 0.6089375 0.8368016
+
+ $xmother[[8]]
+ [1] 0.7515226 0.4527316
+
+ $xmother[[9]]
+ [1] 0.53579
+
+ $xmother[[10]]
+ [1] 0.537376695 0.001380844 0.355665954 0.612133090
+
+ $xmother[[11]]
+ [1] 0.8289421 0.3567220 0.4106351
+
+ $xmother[[12]]
+ [1] 0.5734759 0.5896783 0.7196573 0.3949730
+
+ $xmother[[13]]
+ [1] 0.9192039 0.9625703 0.2335235
+
+ $xmother[[14]]
+ [1] 0.7244976 0.9036345 0.6034741 0.6315073
+
+ $xmother[[15]]
+ [1] 0.9373858
+
+ $xmother[[16]]
+ [1] 0.8504828
+
+ $xmother[[17]]
+ [1] 0.5798209 0.8214039
+
+ $xmother[[18]]
+ [1] 0.1137186 0.7645078 0.6236135 0.1484466
+
+ $xmother[[19]]
+ [1] 0.08026447 0.46406955
+
+ $xmother[[20]]
+ [1] 0.7793682 0.7335280
+
+ $xmother[[21]]
+ [1] 0.8172304 0.1701625 0.9447203
+
+ $xmother[[22]]
+ [1] 0.2936238 0.1490721 0.7193786
+
+ $xmother[[23]]
+ [1] 0.324086
+
+ $xmother[[24]]
+ [1] 0.7788095
+
+ $xmother[[25]]
+ [1] 0.3944410 0.6785929 0.7758250
+
+ $xmother[[26]]
+ [1] 0.18786904 0.02908582 0.13571380 0.68016418
+
+ $xmother[[27]]
+ [1] 0.934823
+
+ $xmother[[28]]
+ [1] 0.5504941 0.6017662 0.1969945
+
+ $xmother[[29]]
+ [1] 0.5352366
+
+ $xmother[[30]]
+ [1] 0.1795557
+
+ $xmother[[31]]
+ [1] 0.4518865 0.3170534 0.1161747 0.1861022
+
+ $xmother[[32]]
+ [1] 0.7297301 0.4118721
+
+ $xmother[[33]]
+ [1] 0.4140497 0.4803101 0.4274945 0.1364904
+
+ $xmother[[34]]
+ [1] 0.8246794 0.5923042 0.7943970 0.7690324
+
+ $xmother[[35]]
+ [1] 0.9180564 0.8626298 0.3169752
+
+ $xmother[[36]]
+ [1] 0.2592606 0.7422665
+
+ $xmother[[37]]
+ [1] 0.7473611
+
+ $xmother[[38]]
+ [1] 0.9179040 0.7931912
+
+ $xmother[[39]]
+ [1] 0.1333296 0.2877498 0.1946761 0.7841094
+
+ $xmother[[40]]
+ [1] 0.1288722 0.1290893
+
+ $xmother[[41]]
+ [1] 0.07225311 0.05312948 0.53187444
+
+ $xmother[[42]]
+ [1] 0.1123082 0.7431877 0.7313155
+
+ $xmother[[43]]
+ [1] 0.8851177 0.5171111
+
+ $xmother[[44]]
+ [1] 0.8519310 0.4427963
+
+ $xmother[[45]]
+ [1] 0.1578801 0.4423246 0.9677337 0.4845879
+
+ $xmother[[46]]
+ [1] 0.2524584 0.2596900 0.5420159 0.6498758
+
+ $xmother[[47]]
+ [1] 0.33641913 0.06094975 0.45131085 0.83875503
+
+ $xmother[[48]]
+ [1] 0.5746373 0.3533504
+
+ $xmother[[49]]
+ [1] 0.5474261 0.8927186
+
+ $xmother[[50]]
+ [1] 0.4899906
+
+ $xmother[[51]]
+ [1] 0.1716321 0.5430310 0.9614677 0.3136838
+
+ $xmother[[52]]
+ [1] 0.8205145
+
+ $xmother[[53]]
+ [1] 0.30705440 0.18545358 0.04834678 0.24567415
+
+ $xmother[[54]]
+ [1] 0.3511069 0.1590224
+
+ $xmother[[55]]
+ [1] 0.30409800 0.01754832 0.99655268 0.80439331
+
+ $xmother[[56]]
+ [1] 0.0865806 0.8699333
+
+ $xmother[[57]]
+ [1] 0.55458586 0.42137842 0.06763682
+
+ $xmother[[58]]
+ [1] 0.56143796 0.07072189 0.21139194 0.54962041
+
+ $xmother[[59]]
+ [1] 0.4819814 0.1594699 0.1495790
+
+ $xmother[[60]]
+ [1] 0.4992729
+
+ $xmother[[61]]
+ [1] 0.9405649
+
+ $xmother[[62]]
+ [1] 0.3342313 0.1884343
+
+ $xmother[[63]]
+ [1] 0.2697162 0.5307441
+
+ $xmother[[64]]
+ [1] 0.02145023 0.79876031
+
+ $xmother[[65]]
+ [1] 0.1103351 0.5397983
+
+ $xmother[[66]]
+ [1] 0.5712339 0.6189515
+
+ $xmother[[67]]
+ [1] 0.7148537 0.1233006 0.3110496 0.9457392
+
+ $xmother[[68]]
+ [1] 0.5000251 0.1352305 0.8692578
+
+ $xmother[[69]]
+ [1] 0.2050496 0.9250459
+
+ $xmother[[70]]
+ [1] 0.8867536
+
+ $xmother[[71]]
+ [1] 0.1362958 0.7853494
+
+ $xmother[[72]]
+ [1] 0.4533034 0.1357424 0.8852210
+
+ $xmother[[73]]
+ [1] 0.3367135 0.3192741
+
+ $xmother[[74]]
+ [1] 0.4037828 0.4790773
+
+ $xmother[[75]]
+ [1] 0.3679018 0.4656906
+
+ $xmother[[76]]
+ [1] 0.04989215 0.18735671 0.98265941 0.32827407
+
+ $xmother[[77]]
+ [1] 0.1709964
+
+ $xmother[[78]]
+ [1] 0.4882549
+
+ $xmother[[79]]
+ [1] 0.01868741
+
+ $xmother[[80]]
+ [1] 0.33948508 0.02966338 0.86722866
+
+ $xmother[[81]]
+ [1] 0.7317076 0.3152608 0.3864540 0.3324460
+
+ $xmother[[82]]
+ [1] 0.08977797
+
+ $xmother[[83]]
+ [1] 0.7570556 0.6029685
+
+ $xmother[[84]]
+ [1] 0.1454
+
+ $xmother[[85]]
+ [1] 0.03251748
+
+ $xmother[[86]]
+ [1] 0.48376814 0.44456953 0.06038559 0.32750602
+
+ $xmother[[87]]
+ [1] 0.8784290 0.9306049 0.3921785 0.1588468
+
+ $xmother[[88]]
+ [1] 0.3199476
+
+ $xmother[[89]]
+ [1] 0.3069656 0.1078113 0.9793343
+
+ $xmother[[90]]
+ [1] 0.49690343 0.09307467 0.21177366
+
+ $xmother[[91]]
+ [1] 0.9305007
+
+ $xmother[[92]]
+ [1] 0.2968464 0.6532182 0.9010705 0.9907958
+
+ $xmother[[93]]
+ [1] 0.4303332
+
+ $xmother[[94]]
+ [1] 0.3937769 0.1419089 0.2798067 0.5648222
+
+ $xmother[[95]]
+ [1] 0.9351395 0.3584001 0.8420072 0.7224092
+
+ $xmother[[96]]
+ [1] 0.7507360 0.9239885
+
+ $xmother[[97]]
+ [1] 0.002378107
+
+ $xmother[[98]]
+ [1] 0.1604299 0.3992730 0.6753196 0.4803720
+
+ $xmother[[99]]
+ [1] 0.5338288 0.3169502
+
+ $xmother[[100]]
+ [1] 0.8147576 0.2922195
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.5091321
+
+ $ymother[[2]]
+ [1] 0.1909183
+
+ $ymother[[3]]
+ [1] 0.8985966
+
+ $ymother[[4]]
+ [1] 0.4597852
+
+ $ymother[[5]]
+ [1] 0.1404876 0.1410863
+
+ $ymother[[6]]
+ [1] 1.0544342 0.4733412 0.9064197 1.0100590
+
+ $ymother[[7]]
+ [1] 0.5400762 0.6763365
+
+ $ymother[[8]]
+ [1] 0.1736678 0.2646274
+
+ $ymother[[9]]
+ [1] 0.8398908
+
+ $ymother[[10]]
+ [1] 0.5757110 0.7855210 1.0515149 0.5974645
+
+ $ymother[[11]]
+ [1] 0.5705006 0.6601920 0.7525101
+
+ $ymother[[12]]
+ [1] 0.3795735 1.0799076 0.7438641 0.6825784
+
+ $ymother[[13]]
+ [1] 0.7158710 1.0251403 0.4900229
+
+ $ymother[[14]]
+ [1] 0.3879197 0.1907360 0.4220339 0.8582701
+
+ $ymother[[15]]
+ [1] 0.2044129
+
+ $ymother[[16]]
+ [1] 0.8102779
+
+ $ymother[[17]]
+ [1] 1.0664774 0.3014912
+
+ $ymother[[18]]
+ [1] 0.2084887 0.1554022 0.9297235 0.6811978
+
+ $ymother[[19]]
+ [1] 0.5700924 0.4650141
+
+ $ymother[[20]]
+ [1] 0.3801246 0.6997159
+
+ $ymother[[21]]
+ [1] 0.9185696 0.1978323 1.0636895
+
+ $ymother[[22]]
+ [1] 0.2687364 0.1860834 0.9612107
+
+ $ymother[[23]]
+ [1] 0.6247906
+
+ $ymother[[24]]
+ [1] 0.7568109
+
+ $ymother[[25]]
+ [1] 0.3295194 0.8212260 0.5907504
+
+ $ymother[[26]]
+ [1] 1.0652556 1.0069425 0.6512505 0.1755991
+
+ $ymother[[27]]
+ [1] 0.1227
+
+ $ymother[[28]]
+ [1] 0.6132395 0.7307262 0.5187716
+
+ $ymother[[29]]
+ [1] 0.9792659
+
+ $ymother[[30]]
+ [1] 0.2079871
+
+ $ymother[[31]]
+ [1] 1.0802787 0.3649666 0.1842775 0.4859072
+
+ $ymother[[32]]
+ [1] 0.2248958 0.6815542
+
+ $ymother[[33]]
+ [1] 0.3401496 0.8218879 0.2459287 0.2528388
+
+ $ymother[[34]]
+ [1] 0.3592227 0.8778863 0.5264663 0.1600483
+
+ $ymother[[35]]
+ [1] 0.2148325 0.5827569 1.0791736
+
+ $ymother[[36]]
+ [1] 0.9115168 0.6429128
+
+ $ymother[[37]]
+ [1] 0.1723671
+
+ $ymother[[38]]
+ [1] 0.5664852 0.4399056
+
+ $ymother[[39]]
+ [1] 0.7899186 0.6141574 0.6149230 0.6455144
+
+ $ymother[[40]]
+ [1] 0.5474573 0.1838848
+
+ $ymother[[41]]
+ [1] 1.0301337 0.1164482 0.5140924
+
+ $ymother[[42]]
+ [1] 0.3269761 0.1996406 0.5829239
+
+ $ymother[[43]]
+ [1] 0.7501287 1.0213298
+
+ $ymother[[44]]
+ [1] 0.4626018 0.9551350
+
+ $ymother[[45]]
+ [1] 0.4009062 0.5656624 0.2427307 0.9077190
+
+ $ymother[[46]]
+ [1] 0.7658076 0.1619410 0.5309256 0.4968551
+
+ $ymother[[47]]
+ [1] 0.7969568 0.7593197 0.5073507 0.4069202
+
+ $ymother[[48]]
+ [1] 0.3551073 0.7725682
+
+ $ymother[[49]]
+ [1] 0.9943934 0.9457362
+
+ $ymother[[50]]
+ [1] 0.4929019
+
+ $ymother[[51]]
+ [1] 0.1790505 0.9284231 0.1728918 0.2147627
+
+ $ymother[[52]]
+ [1] 0.7399843
+
+ $ymother[[53]]
+ [1] 0.4205662 0.2887495 0.4938296 0.9620260
+
+ $ymother[[54]]
+ [1] 0.4479114 0.1014339
+
+ $ymother[[55]]
+ [1] 1.0112845 1.0517234 0.5909190 0.5636517
+
+ $ymother[[56]]
+ [1] 0.696472 1.006051
+
+ $ymother[[57]]
+ [1] 0.2730012 0.8858811 0.3329344
+
+ $ymother[[58]]
+ [1] 0.6770482 0.9408770 0.2322038 0.9958912
+
+ $ymother[[59]]
+ [1] 0.5501373 0.9941425 0.3485452
+
+ $ymother[[60]]
+ [1] 0.1836953
+
+ $ymother[[61]]
+ [1] 0.1486411
+
+ $ymother[[62]]
+ [1] 1.0798159 0.5841677
+
+ $ymother[[63]]
+ [1] 0.9453930 0.5162936
+
+ $ymother[[64]]
+ [1] 0.5893425 0.2832878
+
+ $ymother[[65]]
+ [1] 0.8591615 0.4051433
+
+ $ymother[[66]]
+ [1] 0.2656782 0.1328091
+
+ $ymother[[67]]
+ [1] 0.2365052 0.2771364 0.6195605 0.9111208
+
+ $ymother[[68]]
+ [1] 0.2153620 0.9934218 0.6753529
+
+ $ymother[[69]]
+ [1] 0.2465724 1.0028058
+
+ $ymother[[70]]
+ [1] 0.3530025
+
+ $ymother[[71]]
+ [1] 0.2505976 0.8685472
+
+ $ymother[[72]]
+ [1] 0.3301233 0.4053993 0.6185696
+
+ $ymother[[73]]
+ [1] 0.4345997 0.2544350
+
+ $ymother[[74]]
+ [1] 0.3663696 0.4507546
+
+ $ymother[[75]]
+ [1] 0.6784584 0.9086018
+
+ $ymother[[76]]
+ [1] 1.0332703 0.9338633 0.2270028 0.7494540
+
+ $ymother[[77]]
+ [1] 0.7903517
+
+ $ymother[[78]]
+ [1] 0.1320448
+
+ $ymother[[79]]
+ [1] 1.020489
+
+ $ymother[[80]]
+ [1] 0.5784689 0.3665206 0.9565107
+
+ $ymother[[81]]
+ [1] 0.3291465 0.8919469 0.7467749 0.5243347
+
+ $ymother[[82]]
+ [1] 0.1950683
+
+ $ymother[[83]]
+ [1] 0.1034677 0.6311337
+
+ $ymother[[84]]
+ [1] 0.6243071
+
+ $ymother[[85]]
+ [1] 0.3131856
+
+ $ymother[[86]]
+ [1] 0.8169321 1.0613436 0.6182666 0.2745280
+
+ $ymother[[87]]
+ [1] 0.6625401 0.8592582 0.7669713 0.3248729
+
+ $ymother[[88]]
+ [1] 0.4458498
+
+ $ymother[[89]]
+ [1] 0.4198318 1.0048984 0.2991984
+
+ $ymother[[90]]
+ [1] 0.7809630 0.2375178 0.2069947
+
+ $ymother[[91]]
+ [1] 0.1928594
+
+ $ymother[[92]]
+ [1] 1.0164490 0.3770604 0.9857939 0.8728646
+
+ $ymother[[93]]
+ [1] 0.8950512
+
+ $ymother[[94]]
+ [1] 0.3056736 0.1481933 0.1388159 0.3845741
+
+ $ymother[[95]]
+ [1] 0.4488098 0.8374533 0.3516636 0.6174370
+
+ $ymother[[96]]
+ [1] 0.8594447 0.7360845
+
+ $ymother[[97]]
+ [1] 0.3039407
+
+ $ymother[[98]]
+ [1] 1.0930453 0.1004050 0.3065700 0.7340281
+
+ $ymother[[99]]
+ [1] 0.1172918 0.1267355
+
+ $ymother[[100]]
+ [1] 0.7078406 0.6705414
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test drift_y without clustering
+
+ Code
+ drift_y_motherpoints(mpcoords, drift = 0.1)
+ Output
+ $n_mother_points
+ [1] 0 0 0 0 1 1 1 1 0 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 1 0
+ [38] 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 0 0 0 1 1 1 1 1 1 0 1 0 1 0 1 1
+ [75] 1 1 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 1 0 1 1 1 0 1 1 1
+
+ $xmother
+ $xmother[[1]]
+ numeric(0)
+
+ $xmother[[2]]
+ numeric(0)
+
+ $xmother[[3]]
+ numeric(0)
+
+ $xmother[[4]]
+ numeric(0)
+
+ $xmother[[5]]
+ [1] 0.6262453
+
+ $xmother[[6]]
+ [1] 0.2171577
+
+ $xmother[[7]]
+ [1] 0.2165673
+
+ $xmother[[8]]
+ [1] 0.388945
+
+ $xmother[[9]]
+ numeric(0)
+
+ $xmother[[10]]
+ [1] 0.9424557
+
+ $xmother[[11]]
+ numeric(0)
+
+ $xmother[[12]]
+ [1] 0.962608
+
+ $xmother[[13]]
+ numeric(0)
+
+ $xmother[[14]]
+ [1] 0.7398553
+
+ $xmother[[15]]
+ numeric(0)
+
+ $xmother[[16]]
+ numeric(0)
+
+ $xmother[[17]]
+ [1] 0.7332459
+
+ $xmother[[18]]
+ [1] 0.5357613
+
+ $xmother[[19]]
+ [1] 0.002272966
+
+ $xmother[[20]]
+ [1] 0.6089375
+
+ $xmother[[21]]
+ numeric(0)
+
+ $xmother[[22]]
+ numeric(0)
+
+ $xmother[[23]]
+ numeric(0)
+
+ $xmother[[24]]
+ numeric(0)
+
+ $xmother[[25]]
+ numeric(0)
+
+ $xmother[[26]]
+ [1] 0.8368016
+
+ $xmother[[27]]
+ numeric(0)
+
+ $xmother[[28]]
+ numeric(0)
+
+ $xmother[[29]]
+ numeric(0)
+
+ $xmother[[30]]
+ numeric(0)
+
+ $xmother[[31]]
+ [1] 0.7515226
+
+ $xmother[[32]]
+ [1] 0.4527316
+
+ $xmother[[33]]
+ [1] 0.53579
+
+ $xmother[[34]]
+ [1] 0.5373767
+
+ $xmother[[35]]
+ numeric(0)
+
+ $xmother[[36]]
+ [1] 0.001380844
+
+ $xmother[[37]]
+ numeric(0)
+
+ $xmother[[38]]
+ [1] 0.355666
+
+ $xmother[[39]]
+ [1] 0.6121331
+
+ $xmother[[40]]
+ [1] 0.8289421
+
+ $xmother[[41]]
+ numeric(0)
+
+ $xmother[[42]]
+ numeric(0)
+
+ $xmother[[43]]
+ [1] 0.356722
+
+ $xmother[[44]]
+ [1] 0.4106351
+
+ $xmother[[45]]
+ [1] 0.5734759
+
+ $xmother[[46]]
+ [1] 0.5896783
+
+ $xmother[[47]]
+ [1] 0.7196573
+
+ $xmother[[48]]
+ [1] 0.394973
+
+ $xmother[[49]]
+ [1] 0.9192039
+
+ $xmother[[50]]
+ numeric(0)
+
+ $xmother[[51]]
+ [1] 0.9625703
+
+ $xmother[[52]]
+ numeric(0)
+
+ $xmother[[53]]
+ [1] 0.2335235
+
+ $xmother[[54]]
+ [1] 0.7244976
+
+ $xmother[[55]]
+ [1] 0.9036345
+
+ $xmother[[56]]
+ [1] 0.6034741
+
+ $xmother[[57]]
+ numeric(0)
+
+ $xmother[[58]]
+ [1] 0.6315073
+
+ $xmother[[59]]
+ numeric(0)
+
+ $xmother[[60]]
+ numeric(0)
+
+ $xmother[[61]]
+ numeric(0)
+
+ $xmother[[62]]
+ [1] 0.9373858
+
+ $xmother[[63]]
+ [1] 0.8504828
+
+ $xmother[[64]]
+ [1] 0.5798209
+
+ $xmother[[65]]
+ [1] 0.8214039
+
+ $xmother[[66]]
+ [1] 0.1137186
+
+ $xmother[[67]]
+ [1] 0.7645078
+
+ $xmother[[68]]
+ numeric(0)
+
+ $xmother[[69]]
+ [1] 0.6236135
+
+ $xmother[[70]]
+ numeric(0)
+
+ $xmother[[71]]
+ [1] 0.1484466
+
+ $xmother[[72]]
+ numeric(0)
+
+ $xmother[[73]]
+ [1] 0.08026447
+
+ $xmother[[74]]
+ [1] 0.4640696
+
+ $xmother[[75]]
+ [1] 0.7793682
+
+ $xmother[[76]]
+ [1] 0.733528
+
+ $xmother[[77]]
+ numeric(0)
+
+ $xmother[[78]]
+ numeric(0)
+
+ $xmother[[79]]
+ numeric(0)
+
+ $xmother[[80]]
+ numeric(0)
+
+ $xmother[[81]]
+ [1] 0.8172304
+
+ $xmother[[82]]
+ numeric(0)
+
+ $xmother[[83]]
+ [1] 0.1701625
+
+ $xmother[[84]]
+ numeric(0)
+
+ $xmother[[85]]
+ numeric(0)
+
+ $xmother[[86]]
+ [1] 0.9447203
+
+ $xmother[[87]]
+ [1] 0.2936238
+
+ $xmother[[88]]
+ numeric(0)
+
+ $xmother[[89]]
+ numeric(0)
+
+ $xmother[[90]]
+ numeric(0)
+
+ $xmother[[91]]
+ numeric(0)
+
+ $xmother[[92]]
+ [1] 0.1490721
+
+ $xmother[[93]]
+ numeric(0)
+
+ $xmother[[94]]
+ [1] 0.7193786
+
+ $xmother[[95]]
+ [1] 0.324086
+
+ $xmother[[96]]
+ [1] 0.7788095
+
+ $xmother[[97]]
+ numeric(0)
+
+ $xmother[[98]]
+ [1] 0.394441
+
+ $xmother[[99]]
+ [1] 0.6785929
+
+ $xmother[[100]]
+ [1] 0.775825
+
+
+ $ymother
+ $ymother[[1]]
+ numeric(0)
+
+ $ymother[[2]]
+ numeric(0)
+
+ $ymother[[3]]
+ numeric(0)
+
+ $ymother[[4]]
+ numeric(0)
+
+ $ymother[[5]]
+ [1] 0.287869
+
+ $ymother[[6]]
+ [1] 0.1290858
+
+ $ymother[[7]]
+ [1] 0.2357138
+
+ $ymother[[8]]
+ [1] 0.7801642
+
+ $ymother[[9]]
+ numeric(0)
+
+ $ymother[[10]]
+ [1] 1.034823
+
+ $ymother[[11]]
+ numeric(0)
+
+ $ymother[[12]]
+ [1] 0.6504941
+
+ $ymother[[13]]
+ numeric(0)
+
+ $ymother[[14]]
+ [1] 0.7017662
+
+ $ymother[[15]]
+ numeric(0)
+
+ $ymother[[16]]
+ numeric(0)
+
+ $ymother[[17]]
+ [1] 0.2969945
+
+ $ymother[[18]]
+ [1] 0.6352366
+
+ $ymother[[19]]
+ [1] 0.2795557
+
+ $ymother[[20]]
+ [1] 0.5518865
+
+ $ymother[[21]]
+ numeric(0)
+
+ $ymother[[22]]
+ numeric(0)
+
+ $ymother[[23]]
+ numeric(0)
+
+ $ymother[[24]]
+ numeric(0)
+
+ $ymother[[25]]
+ numeric(0)
+
+ $ymother[[26]]
+ [1] 0.4170534
+
+ $ymother[[27]]
+ numeric(0)
+
+ $ymother[[28]]
+ numeric(0)
+
+ $ymother[[29]]
+ numeric(0)
+
+ $ymother[[30]]
+ numeric(0)
+
+ $ymother[[31]]
+ [1] 0.2161747
+
+ $ymother[[32]]
+ [1] 0.2861022
+
+ $ymother[[33]]
+ [1] 0.8297301
+
+ $ymother[[34]]
+ [1] 0.5118721
+
+ $ymother[[35]]
+ numeric(0)
+
+ $ymother[[36]]
+ [1] 0.5140497
+
+ $ymother[[37]]
+ numeric(0)
+
+ $ymother[[38]]
+ [1] 0.5803101
+
+ $ymother[[39]]
+ [1] 0.5274945
+
+ $ymother[[40]]
+ [1] 0.2364904
+
+ $ymother[[41]]
+ numeric(0)
+
+ $ymother[[42]]
+ numeric(0)
+
+ $ymother[[43]]
+ [1] 0.9246794
+
+ $ymother[[44]]
+ [1] 0.6923042
+
+ $ymother[[45]]
+ [1] 0.894397
+
+ $ymother[[46]]
+ [1] 0.8690324
+
+ $ymother[[47]]
+ [1] 1.018056
+
+ $ymother[[48]]
+ [1] 0.9626298
+
+ $ymother[[49]]
+ [1] 0.4169752
+
+ $ymother[[50]]
+ numeric(0)
+
+ $ymother[[51]]
+ [1] 0.3592606
+
+ $ymother[[52]]
+ numeric(0)
+
+ $ymother[[53]]
+ [1] 0.8422665
+
+ $ymother[[54]]
+ [1] 0.8473611
+
+ $ymother[[55]]
+ [1] 1.017904
+
+ $ymother[[56]]
+ [1] 0.8931912
+
+ $ymother[[57]]
+ numeric(0)
+
+ $ymother[[58]]
+ [1] 0.2333296
+
+ $ymother[[59]]
+ numeric(0)
+
+ $ymother[[60]]
+ numeric(0)
+
+ $ymother[[61]]
+ numeric(0)
+
+ $ymother[[62]]
+ [1] 0.3877498
+
+ $ymother[[63]]
+ [1] 0.2946761
+
+ $ymother[[64]]
+ [1] 0.8841094
+
+ $ymother[[65]]
+ [1] 0.2288722
+
+ $ymother[[66]]
+ [1] 0.2290893
+
+ $ymother[[67]]
+ [1] 0.1722531
+
+ $ymother[[68]]
+ numeric(0)
+
+ $ymother[[69]]
+ [1] 0.1531295
+
+ $ymother[[70]]
+ numeric(0)
+
+ $ymother[[71]]
+ [1] 0.6318744
+
+ $ymother[[72]]
+ numeric(0)
+
+ $ymother[[73]]
+ [1] 0.2123082
+
+ $ymother[[74]]
+ [1] 0.8431877
+
+ $ymother[[75]]
+ [1] 0.8313155
+
+ $ymother[[76]]
+ [1] 0.9851177
+
+ $ymother[[77]]
+ numeric(0)
+
+ $ymother[[78]]
+ numeric(0)
+
+ $ymother[[79]]
+ numeric(0)
+
+ $ymother[[80]]
+ numeric(0)
+
+ $ymother[[81]]
+ [1] 0.6171111
+
+ $ymother[[82]]
+ numeric(0)
+
+ $ymother[[83]]
+ [1] 0.951931
+
+ $ymother[[84]]
+ numeric(0)
+
+ $ymother[[85]]
+ numeric(0)
+
+ $ymother[[86]]
+ [1] 0.5427963
+
+ $ymother[[87]]
+ [1] 0.2578801
+
+ $ymother[[88]]
+ numeric(0)
+
+ $ymother[[89]]
+ numeric(0)
+
+ $ymother[[90]]
+ numeric(0)
+
+ $ymother[[91]]
+ numeric(0)
+
+ $ymother[[92]]
+ [1] 0.5423246
+
+ $ymother[[93]]
+ numeric(0)
+
+ $ymother[[94]]
+ [1] 1.067734
+
+ $ymother[[95]]
+ [1] 0.5845879
+
+ $ymother[[96]]
+ [1] 0.3524584
+
+ $ymother[[97]]
+ numeric(0)
+
+ $ymother[[98]]
+ [1] 0.35969
+
+ $ymother[[99]]
+ [1] 0.6420159
+
+ $ymother[[100]]
+ [1] 0.7498758
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
diff --git a/tests/testthat/_snaps/drift_species.md b/tests/testthat/_snaps/drift_species.md
new file mode 100644
index 0000000..86a0f0d
--- /dev/null
+++ b/tests/testthat/_snaps/drift_species.md
@@ -0,0 +1,54 @@
+# snapshot test with drift
+
+ Code
+ drift_x_species(simdat, drift = 0.1)
+ Output
+ $census
+ x y species
+ 1 1.0148060 0.4577418 species_01
+ 2 1.0370754 0.7191123 species_02
+ 3 0.3861395 0.9346722 species_03
+ 4 0.9304476 0.2554288 species_04
+ 5 0.7417455 0.4622928 species_05
+ 6 0.6190959 0.9400145 species_06
+ 7 0.8365883 0.9782264 species_07
+ 8 0.2346666 0.1174874 species_08
+ 9 0.7569923 0.4749971 species_09
+ 10 0.8050648 0.5603327 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
+---
+
+ Code
+ drift_y_species(simdat, drift = 0.1)
+ Output
+ $census
+ x y species
+ 1 0.9148060 0.5577418 species_01
+ 2 0.9370754 0.8191123 species_02
+ 3 0.2861395 1.0346722 species_03
+ 4 0.8304476 0.3554288 species_04
+ 5 0.6417455 0.5622928 species_05
+ 6 0.5190959 1.0400145 species_06
+ 7 0.7365883 1.0782264 species_07
+ 8 0.1346666 0.2174874 species_08
+ 9 0.6569923 0.5749971 species_09
+ 10 0.7050648 0.6603327 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
diff --git a/tests/testthat/_snaps/jitter_motherpoints.md b/tests/testthat/_snaps/jitter_motherpoints.md
new file mode 100644
index 0000000..220601e
--- /dev/null
+++ b/tests/testthat/_snaps/jitter_motherpoints.md
@@ -0,0 +1,1246 @@
+# snapshot test with clustering
+
+ Code
+ jitter_motherpoints(mpcoords, seed = 42L)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2 3 3 1 1 3 4 1 3 1 1 4 2 4 4 3 2 1
+ [38] 2 4 2 3 3 2 2 4 4 4 2 2 1 4 1 4 2 4 2 3 4 3 1 1 2 2 2 2 2 4 3 2 1 2 3 2 2
+ [75] 2 4 1 1 1 3 4 1 2 1 1 4 4 1 3 3 1 4 1 4 4 2 1 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.6399549
+
+ $xmother[[2]]
+ [1] 0.2115107
+
+ $xmother[[3]]
+ [1] 0.2201986
+
+ $xmother[[4]]
+ [1] 0.3952737
+
+ $xmother[[5]]
+ [1] 0.9464984 0.9615468
+
+ $xmother[[6]]
+ [1] 0.754970499 0.732299315 0.555945527 0.001645825
+
+ $xmother[[7]]
+ [1] 0.6219861 0.8596680
+
+ $xmother[[8]]
+ [1] 0.7376340 0.4499437
+
+ $xmother[[9]]
+ [1] 0.5344568
+
+ $xmother[[10]]
+ [1] 0.543736199 -0.001461686 0.329101400 0.587728421
+
+ $xmother[[11]]
+ [1] 0.8421433 0.3536556 0.3928220
+
+ $xmother[[12]]
+ [1] 0.5717567 0.6018251 0.7386092 0.3906684
+
+ $xmother[[13]]
+ [1] 0.9166312 0.9449387 0.2381245
+
+ $xmother[[14]]
+ [1] 0.7180977 0.9081890 0.6105225 0.6418583
+
+ $xmother[[15]]
+ [1] 0.9312966
+
+ $xmother[[16]]
+ [1] 0.8555323
+
+ $xmother[[17]]
+ [1] 0.5626508 0.8135593
+
+ $xmother[[18]]
+ [1] 0.1052095 0.7403657 0.6239747 0.1505066
+
+ $xmother[[19]]
+ [1] 0.07665389 0.47165118
+
+ $xmother[[20]]
+ [1] 0.7721011 0.7198451
+
+ $xmother[[21]]
+ [1] 0.8215586 0.1620485 0.9591613
+
+ $xmother[[22]]
+ [1] 0.2893094 0.1556285 0.7225978
+
+ $xmother[[23]]
+ [1] 0.3162476
+
+ $xmother[[24]]
+ [1] 0.7945668
+
+ $xmother[[25]]
+ [1] 0.4008700 0.6794905 0.7785906
+
+ $xmother[[26]]
+ [1] 0.19466193 0.02998415 0.10578290 0.68301301
+
+ $xmother[[27]]
+ [1] 0.9311506
+
+ $xmother[[28]]
+ [1] 0.5523464 0.6075845 0.2109919
+
+ $xmother[[29]]
+ [1] 0.5279637
+
+ $xmother[[30]]
+ [1] 0.1925812
+
+ $xmother[[31]]
+ [1] 0.4552450 0.3274384 0.1253820 0.1933109
+
+ $xmother[[32]]
+ [1] 0.7192989 0.4109702
+
+ $xmother[[33]]
+ [1] 0.4202849 0.4707749 0.4220662 0.1423003
+
+ $xmother[[34]]
+ [1] 0.8323612 0.5969419 0.7855392 0.7580346
+
+ $xmother[[35]]
+ [1] 0.9331835 0.8652090 0.3178596
+
+ $xmother[[36]]
+ [1] 0.2580516 0.7303232
+
+ $xmother[[37]]
+ [1] 0.7534811
+
+ $xmother[[38]]
+ [1] 0.9157326 0.7913636
+
+ $xmother[[39]]
+ [1] 0.1426631 0.2959675 0.2085973 0.7793476
+
+ $xmother[[40]]
+ [1] 0.1353756 0.1430004
+
+ $xmother[[41]]
+ [1] 0.06114522 0.04452156 0.52055705
+
+ $xmother[[42]]
+ [1] 0.0977161 0.7439875 0.7378475
+
+ $xmother[[43]]
+ [1] 0.8971273 0.5275586
+
+ $xmother[[44]]
+ [1] 0.8418989 0.4612811
+
+ $xmother[[45]]
+ [1] 0.1512124 0.4433798 0.9635111 0.4833644
+
+ $xmother[[46]]
+ [1] 0.2543404 0.2608816 0.5417650 0.6509566
+
+ $xmother[[47]]
+ [1] 0.33156478 0.05590757 0.43469986 0.83493170
+
+ $xmother[[48]]
+ [1] 0.5695108 0.3803693
+
+ $xmother[[49]]
+ [1] 0.5338049 0.8940912
+
+ $xmother[[50]]
+ [1] 0.4750543
+
+ $xmother[[51]]
+ [1] 0.1569278 0.5442780 0.9515013 0.3136656
+
+ $xmother[[52]]
+ [1] 0.816232
+
+ $xmother[[53]]
+ [1] 0.3009177 0.1652068 0.0360993 0.2474693
+
+ $xmother[[54]]
+ [1] 0.3567831 0.1540936
+
+ $xmother[[55]]
+ [1] 0.30409863 0.02877722 1.01095124 0.79342217
+
+ $xmother[[56]]
+ [1] 0.08540741 0.88194825
+
+ $xmother[[57]]
+ [1] 0.54988857 0.42085373 0.06677575
+
+ $xmother[[58]]
+ [1] 0.55256117 0.06627505 0.21109749 0.54548172
+
+ $xmother[[59]]
+ [1] 0.4931153 0.1546599 0.1452473
+
+ $xmother[[60]]
+ [1] 0.5062415
+
+ $xmother[[61]]
+ [1] 0.9300012
+
+ $xmother[[62]]
+ [1] 0.3338243 0.1729189
+
+ $xmother[[63]]
+ [1] 0.2813879 0.5280076
+
+ $xmother[[64]]
+ [1] 0.01677178 0.78637778
+
+ $xmother[[65]]
+ [1] 0.1102575 0.5317955
+
+ $xmother[[66]]
+ [1] 0.5658990 0.6318283
+
+ $xmother[[67]]
+ [1] 0.7130984 0.1125828 0.3126817 0.9421118
+
+ $xmother[[68]]
+ [1] 0.5059252 0.1495547 0.8593309
+
+ $xmother[[69]]
+ [1] 0.2095961 0.9258949
+
+ $xmother[[70]]
+ [1] 0.8957093
+
+ $xmother[[71]]
+ [1] 0.1339980 0.7937156
+
+ $xmother[[72]]
+ [1] 0.4358529 0.1526370 0.8938688
+
+ $xmother[[73]]
+ [1] 0.3352058 0.3047840
+
+ $xmother[[74]]
+ [1] 0.4102129 0.4839092
+
+ $xmother[[75]]
+ [1] 0.3678383 0.4672051
+
+ $xmother[[76]]
+ [1] 0.04405106 0.19104478 0.98560596 0.32548148
+
+ $xmother[[77]]
+ [1] 0.157634
+
+ $xmother[[78]]
+ [1] 0.4952624
+
+ $xmother[[79]]
+ [1] 0.02422938
+
+ $xmother[[80]]
+ [1] 0.33112202 0.01371749 0.86927825
+
+ $xmother[[81]]
+ [1] 0.7282567 0.3177869 0.3735140 0.3228543
+
+ $xmother[[82]]
+ [1] 0.1006357
+
+ $xmother[[83]]
+ [1] 0.7610934 0.6088334
+
+ $xmother[[84]]
+ [1] 0.1635523
+
+ $xmother[[85]]
+ [1] 0.0338057
+
+ $xmother[[86]]
+ [1] 0.46375885 0.44790730 0.07209884 0.34810141
+
+ $xmother[[87]]
+ [1] 0.8646604 0.9190963 0.3851202 0.1483062
+
+ $xmother[[88]]
+ [1] 0.3134902
+
+ $xmother[[89]]
+ [1] 0.30511184 0.09579903 0.99970403
+
+ $xmother[[90]]
+ [1] 0.49798118 0.09223359 0.21672985
+
+ $xmother[[91]]
+ [1] 0.9308749
+
+ $xmother[[92]]
+ [1] 0.2955255 0.6679861 0.8989002 0.9779598
+
+ $xmother[[93]]
+ [1] 0.4341899
+
+ $xmother[[94]]
+ [1] 0.3902618 0.1366909 0.2691254 0.5691059
+
+ $xmother[[95]]
+ [1] 0.9333993 0.3635568 0.8396635 0.7158242
+
+ $xmother[[96]]
+ [1] 0.7632384 0.9212708
+
+ $xmother[[97]]
+ [1] 0.01185763
+
+ $xmother[[98]]
+ [1] 0.1484141 0.3946118 0.6726261 0.4764624
+
+ $xmother[[99]]
+ [1] 0.5473159 0.3167225
+
+ $xmother[[100]]
+ [1] 0.8171998 0.2827958
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.4018399
+
+ $ymother[[2]]
+ [1] 0.100899
+
+ $ymother[[3]]
+ [1] 0.8111815
+
+ $ymother[[4]]
+ [1] 0.3722739
+
+ $ymother[[5]]
+ [1] 0.02668121 0.06158595
+
+ $ymother[[6]]
+ [1] 0.9646030 0.3730741 0.8134557 0.9003452
+
+ $ymother[[7]]
+ [1] 0.4291147 0.5768270
+
+ $ymother[[8]]
+ [1] 0.06168284 0.16652758
+
+ $ymother[[9]]
+ [1] 0.7528678
+
+ $ymother[[10]]
+ [1] 0.4653723 0.6781365 0.9519806 0.4872885
+
+ $ymother[[11]]
+ [1] 0.4666678 0.5689195 0.6622056
+
+ $ymother[[12]]
+ [1] 0.2834120 0.9613920 0.6433241 0.5932262
+
+ $ymother[[13]]
+ [1] 0.6240030 0.9232321 0.3630236
+
+ $ymother[[14]]
+ [1] 0.28852935 0.09647348 0.32249194 0.75984424
+
+ $ymother[[15]]
+ [1] 0.1087286
+
+ $ymother[[16]]
+ [1] 0.7063124
+
+ $ymother[[17]]
+ [1] 0.9795772 0.2061952
+
+ $ymother[[18]]
+ [1] 0.09606195 0.06921793 0.84176810 0.58943850
+
+ $ymother[[19]]
+ [1] 0.4534661 0.3593211
+
+ $ymother[[20]]
+ [1] 0.2864798 0.6001531
+
+ $ymother[[21]]
+ [1] 0.8220497 0.1224282 0.9555057
+
+ $ymother[[22]]
+ [1] 0.14760444 0.08882036 0.85433473
+
+ $ymother[[23]]
+ [1] 0.529251
+
+ $ymother[[24]]
+ [1] 0.648687
+
+ $ymother[[25]]
+ [1] 0.2516399 0.7199890 0.4859770
+
+ $ymother[[26]]
+ [1] 0.96359298 0.91556811 0.55222393 0.05934293
+
+ $ymother[[27]]
+ [1] 0.0226538
+
+ $ymother[[28]]
+ [1] 0.5208419 0.6311161 0.4261223
+
+ $ymother[[29]]
+ [1] 0.8778012
+
+ $ymother[[30]]
+ [1] 0.1074082
+
+ $ymother[[31]]
+ [1] 0.98510239 0.27489607 0.07181357 0.38557230
+
+ $ymother[[32]]
+ [1] 0.1241862 0.5739650
+
+ $ymother[[33]]
+ [1] 0.2298060 0.7155806 0.1517968 0.1486755
+
+ $ymother[[34]]
+ [1] 0.25137379 0.77952042 0.41409916 0.07050707
+
+ $ymother[[35]]
+ [1] 0.1099866 0.4846482 0.9796836
+
+ $ymother[[36]]
+ [1] 0.8115144 0.5610066
+
+ $ymother[[37]]
+ [1] 0.06411381
+
+ $ymother[[38]]
+ [1] 0.4779400 0.3402214
+
+ $ymother[[39]]
+ [1] 0.6815665 0.5134697 0.5223907 0.5412592
+
+ $ymother[[40]]
+ [1] 0.43973651 0.08541248
+
+ $ymother[[41]]
+ [1] 0.9400197 0.0157136 0.4002221
+
+ $ymother[[42]]
+ [1] 0.21390933 0.09195663 0.47765279
+
+ $ymother[[43]]
+ [1] 0.6499144 0.9280348
+
+ $ymother[[44]]
+ [1] 0.3582556 0.8439962
+
+ $ymother[[45]]
+ [1] 0.3069772 0.4684170 0.1543041 0.7908942
+
+ $ymother[[46]]
+ [1] 0.6666808 0.0754746 0.4381673 0.3885296
+
+ $ymother[[47]]
+ [1] 0.7042820 0.6506004 0.4028167 0.3187956
+
+ $ymother[[48]]
+ [1] 0.2522059 0.6808536
+
+ $ymother[[49]]
+ [1] 0.8914812 0.8299725
+
+ $ymother[[50]]
+ [1] 0.3844137
+
+ $ymother[[51]]
+ [1] 0.06816534 0.82358015 0.06952871 0.11322910
+
+ $ymother[[52]]
+ [1] 0.6375518
+
+ $ymother[[53]]
+ [1] 0.3394882 0.1748895 0.3896814 0.8655168
+
+ $ymother[[54]]
+ [1] 0.364195829 0.002319117
+
+ $ymother[[55]]
+ [1] 0.9236760 0.9352779 0.5053825 0.4567461
+
+ $ymother[[56]]
+ [1] 0.5937077 0.8949568
+
+ $ymother[[57]]
+ [1] 0.1743399 0.8037345 0.2571560
+
+ $ymother[[58]]
+ [1] 0.5662799 0.8457364 0.1460890 0.8939346
+
+ $ymother[[59]]
+ [1] 0.4479556 0.8910948 0.2545235
+
+ $ymother[[60]]
+ [1] 0.09766959
+
+ $ymother[[61]]
+ [1] 0.05551727
+
+ $ymother[[62]]
+ [1] 0.9830177 0.4811490
+
+ $ymother[[63]]
+ [1] 0.8503765 0.4107982
+
+ $ymother[[64]]
+ [1] 0.486550 0.194253
+
+ $ymother[[65]]
+ [1] 0.7635816 0.3075535
+
+ $ymother[[66]]
+ [1] 0.16312217 0.04211947
+
+ $ymother[[67]]
+ [1] 0.1498543 0.1684437 0.5201153 0.8116115
+
+ $ymother[[68]]
+ [1] 0.1095785 0.8834344 0.5753286
+
+ $ymother[[69]]
+ [1] 0.1531275 0.9175742
+
+ $ymother[[70]]
+ [1] 0.2339109
+
+ $ymother[[71]]
+ [1] 0.1435732 0.7654329
+
+ $ymother[[72]]
+ [1] 0.2134918 0.2978940 0.5107961
+
+ $ymother[[73]]
+ [1] 0.3273740 0.1325466
+
+ $ymother[[74]]
+ [1] 0.2685038 0.3444354
+
+ $ymother[[75]]
+ [1] 0.5936633 0.8165614
+
+ $ymother[[76]]
+ [1] 0.9187350 0.8348473 0.1210651 0.6583368
+
+ $ymother[[77]]
+ [1] 0.6908824
+
+ $ymother[[78]]
+ [1] 0.02647459
+
+ $ymother[[79]]
+ [1] 0.9248731
+
+ $ymother[[80]]
+ [1] 0.4799950 0.2648744 0.8767096
+
+ $ymother[[81]]
+ [1] 0.2238526 0.7872390 0.6313155 0.4239294
+
+ $ymother[[82]]
+ [1] 0.1039718
+
+ $ymother[[83]]
+ [1] -0.01724617 0.52863302
+
+ $ymother[[84]]
+ [1] 0.5124906
+
+ $ymother[[85]]
+ [1] 0.2276049
+
+ $ymother[[86]]
+ [1] 0.7305110 0.9646886 0.5325600 0.1658548
+
+ $ymother[[87]]
+ [1] 0.5720467 0.7534081 0.6701809 0.2218790
+
+ $ymother[[88]]
+ [1] 0.3430643
+
+ $ymother[[89]]
+ [1] 0.3252929 0.8918602 0.1966892
+
+ $ymother[[90]]
+ [1] 0.6826731 0.1334831 0.1080413
+
+ $ymother[[91]]
+ [1] 0.08967059
+
+ $ymother[[92]]
+ [1] 0.9326324 0.2842023 0.9154525 0.7649139
+
+ $ymother[[93]]
+ [1] 0.8031949
+
+ $ymother[[94]]
+ [1] 0.22665390 0.05120312 0.02798518 0.27451090
+
+ $ymother[[95]]
+ [1] 0.3484557 0.7505446 0.2591676 0.4960533
+
+ $ymother[[96]]
+ [1] 0.7524412 0.6359940
+
+ $ymother[[97]]
+ [1] 0.1893594
+
+ $ymother[[98]]
+ [1] 0.99999058 -0.02420831 0.20800292 0.63011587
+
+ $ymother[[99]]
+ [1] 0.01238018 0.02389900
+
+ $ymother[[100]]
+ [1] 0.6109885 0.5745046
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# snapshot test without clustering
+
+ Code
+ jitter_motherpoints(mpcoords, seed = 42L)
+ Output
+ $n_mother_points
+ [1] 0 0 0 0 1 1 1 1 0 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 1 0
+ [38] 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 0 0 0 1 1 1 1 1 1 0 1 0 1 0 1 1
+ [75] 1 1 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 1 0 1 1 1 0 1 1 1
+
+ $xmother
+ $xmother[[1]]
+ numeric(0)
+
+ $xmother[[2]]
+ numeric(0)
+
+ $xmother[[3]]
+ numeric(0)
+
+ $xmother[[4]]
+ numeric(0)
+
+ $xmother[[5]]
+ [1] 0.6399549
+
+ $xmother[[6]]
+ [1] 0.2115107
+
+ $xmother[[7]]
+ [1] 0.2201986
+
+ $xmother[[8]]
+ [1] 0.3952737
+
+ $xmother[[9]]
+ numeric(0)
+
+ $xmother[[10]]
+ [1] 0.9464984
+
+ $xmother[[11]]
+ numeric(0)
+
+ $xmother[[12]]
+ [1] 0.9615468
+
+ $xmother[[13]]
+ numeric(0)
+
+ $xmother[[14]]
+ [1] 0.7549705
+
+ $xmother[[15]]
+ numeric(0)
+
+ $xmother[[16]]
+ numeric(0)
+
+ $xmother[[17]]
+ [1] 0.7322993
+
+ $xmother[[18]]
+ [1] 0.5559455
+
+ $xmother[[19]]
+ [1] 0.001645825
+
+ $xmother[[20]]
+ [1] 0.6219861
+
+ $xmother[[21]]
+ numeric(0)
+
+ $xmother[[22]]
+ numeric(0)
+
+ $xmother[[23]]
+ numeric(0)
+
+ $xmother[[24]]
+ numeric(0)
+
+ $xmother[[25]]
+ numeric(0)
+
+ $xmother[[26]]
+ [1] 0.859668
+
+ $xmother[[27]]
+ numeric(0)
+
+ $xmother[[28]]
+ numeric(0)
+
+ $xmother[[29]]
+ numeric(0)
+
+ $xmother[[30]]
+ numeric(0)
+
+ $xmother[[31]]
+ [1] 0.737634
+
+ $xmother[[32]]
+ [1] 0.4499437
+
+ $xmother[[33]]
+ [1] 0.5344568
+
+ $xmother[[34]]
+ [1] 0.5437362
+
+ $xmother[[35]]
+ numeric(0)
+
+ $xmother[[36]]
+ [1] -0.001461686
+
+ $xmother[[37]]
+ numeric(0)
+
+ $xmother[[38]]
+ [1] 0.3291014
+
+ $xmother[[39]]
+ [1] 0.5877284
+
+ $xmother[[40]]
+ [1] 0.8421433
+
+ $xmother[[41]]
+ numeric(0)
+
+ $xmother[[42]]
+ numeric(0)
+
+ $xmother[[43]]
+ [1] 0.3536556
+
+ $xmother[[44]]
+ [1] 0.392822
+
+ $xmother[[45]]
+ [1] 0.5717567
+
+ $xmother[[46]]
+ [1] 0.6018251
+
+ $xmother[[47]]
+ [1] 0.7386092
+
+ $xmother[[48]]
+ [1] 0.3906684
+
+ $xmother[[49]]
+ [1] 0.9166312
+
+ $xmother[[50]]
+ numeric(0)
+
+ $xmother[[51]]
+ [1] 0.9449387
+
+ $xmother[[52]]
+ numeric(0)
+
+ $xmother[[53]]
+ [1] 0.2381245
+
+ $xmother[[54]]
+ [1] 0.7180977
+
+ $xmother[[55]]
+ [1] 0.908189
+
+ $xmother[[56]]
+ [1] 0.6105225
+
+ $xmother[[57]]
+ numeric(0)
+
+ $xmother[[58]]
+ [1] 0.6418583
+
+ $xmother[[59]]
+ numeric(0)
+
+ $xmother[[60]]
+ numeric(0)
+
+ $xmother[[61]]
+ numeric(0)
+
+ $xmother[[62]]
+ [1] 0.9312966
+
+ $xmother[[63]]
+ [1] 0.8555323
+
+ $xmother[[64]]
+ [1] 0.5626508
+
+ $xmother[[65]]
+ [1] 0.8135593
+
+ $xmother[[66]]
+ [1] 0.1052095
+
+ $xmother[[67]]
+ [1] 0.7403657
+
+ $xmother[[68]]
+ numeric(0)
+
+ $xmother[[69]]
+ [1] 0.6239747
+
+ $xmother[[70]]
+ numeric(0)
+
+ $xmother[[71]]
+ [1] 0.1505066
+
+ $xmother[[72]]
+ numeric(0)
+
+ $xmother[[73]]
+ [1] 0.07665389
+
+ $xmother[[74]]
+ [1] 0.4716512
+
+ $xmother[[75]]
+ [1] 0.7721011
+
+ $xmother[[76]]
+ [1] 0.7198451
+
+ $xmother[[77]]
+ numeric(0)
+
+ $xmother[[78]]
+ numeric(0)
+
+ $xmother[[79]]
+ numeric(0)
+
+ $xmother[[80]]
+ numeric(0)
+
+ $xmother[[81]]
+ [1] 0.8215586
+
+ $xmother[[82]]
+ numeric(0)
+
+ $xmother[[83]]
+ [1] 0.1620485
+
+ $xmother[[84]]
+ numeric(0)
+
+ $xmother[[85]]
+ numeric(0)
+
+ $xmother[[86]]
+ [1] 0.9591613
+
+ $xmother[[87]]
+ [1] 0.2893094
+
+ $xmother[[88]]
+ numeric(0)
+
+ $xmother[[89]]
+ numeric(0)
+
+ $xmother[[90]]
+ numeric(0)
+
+ $xmother[[91]]
+ numeric(0)
+
+ $xmother[[92]]
+ [1] 0.1556285
+
+ $xmother[[93]]
+ numeric(0)
+
+ $xmother[[94]]
+ [1] 0.7225978
+
+ $xmother[[95]]
+ [1] 0.3162476
+
+ $xmother[[96]]
+ [1] 0.7945668
+
+ $xmother[[97]]
+ numeric(0)
+
+ $xmother[[98]]
+ [1] 0.40087
+
+ $xmother[[99]]
+ [1] 0.6794905
+
+ $xmother[[100]]
+ [1] 0.7785906
+
+
+ $ymother
+ $ymother[[1]]
+ numeric(0)
+
+ $ymother[[2]]
+ numeric(0)
+
+ $ymother[[3]]
+ numeric(0)
+
+ $ymother[[4]]
+ numeric(0)
+
+ $ymother[[5]]
+ [1] 0.1946619
+
+ $ymother[[6]]
+ [1] 0.02998415
+
+ $ymother[[7]]
+ [1] 0.1057829
+
+ $ymother[[8]]
+ [1] 0.683013
+
+ $ymother[[9]]
+ numeric(0)
+
+ $ymother[[10]]
+ [1] 0.9311506
+
+ $ymother[[11]]
+ numeric(0)
+
+ $ymother[[12]]
+ [1] 0.5523464
+
+ $ymother[[13]]
+ numeric(0)
+
+ $ymother[[14]]
+ [1] 0.6075845
+
+ $ymother[[15]]
+ numeric(0)
+
+ $ymother[[16]]
+ numeric(0)
+
+ $ymother[[17]]
+ [1] 0.2109919
+
+ $ymother[[18]]
+ [1] 0.5279637
+
+ $ymother[[19]]
+ [1] 0.1925812
+
+ $ymother[[20]]
+ [1] 0.455245
+
+ $ymother[[21]]
+ numeric(0)
+
+ $ymother[[22]]
+ numeric(0)
+
+ $ymother[[23]]
+ numeric(0)
+
+ $ymother[[24]]
+ numeric(0)
+
+ $ymother[[25]]
+ numeric(0)
+
+ $ymother[[26]]
+ [1] 0.3274384
+
+ $ymother[[27]]
+ numeric(0)
+
+ $ymother[[28]]
+ numeric(0)
+
+ $ymother[[29]]
+ numeric(0)
+
+ $ymother[[30]]
+ numeric(0)
+
+ $ymother[[31]]
+ [1] 0.125382
+
+ $ymother[[32]]
+ [1] 0.1933109
+
+ $ymother[[33]]
+ [1] 0.7192989
+
+ $ymother[[34]]
+ [1] 0.4109702
+
+ $ymother[[35]]
+ numeric(0)
+
+ $ymother[[36]]
+ [1] 0.4202849
+
+ $ymother[[37]]
+ numeric(0)
+
+ $ymother[[38]]
+ [1] 0.4707749
+
+ $ymother[[39]]
+ [1] 0.4220662
+
+ $ymother[[40]]
+ [1] 0.1423003
+
+ $ymother[[41]]
+ numeric(0)
+
+ $ymother[[42]]
+ numeric(0)
+
+ $ymother[[43]]
+ [1] 0.8323612
+
+ $ymother[[44]]
+ [1] 0.5969419
+
+ $ymother[[45]]
+ [1] 0.7855392
+
+ $ymother[[46]]
+ [1] 0.7580346
+
+ $ymother[[47]]
+ [1] 0.9331835
+
+ $ymother[[48]]
+ [1] 0.865209
+
+ $ymother[[49]]
+ [1] 0.3178596
+
+ $ymother[[50]]
+ numeric(0)
+
+ $ymother[[51]]
+ [1] 0.2580516
+
+ $ymother[[52]]
+ numeric(0)
+
+ $ymother[[53]]
+ [1] 0.7303232
+
+ $ymother[[54]]
+ [1] 0.7534811
+
+ $ymother[[55]]
+ [1] 0.9157326
+
+ $ymother[[56]]
+ [1] 0.7913636
+
+ $ymother[[57]]
+ numeric(0)
+
+ $ymother[[58]]
+ [1] 0.1426631
+
+ $ymother[[59]]
+ numeric(0)
+
+ $ymother[[60]]
+ numeric(0)
+
+ $ymother[[61]]
+ numeric(0)
+
+ $ymother[[62]]
+ [1] 0.2959675
+
+ $ymother[[63]]
+ [1] 0.2085973
+
+ $ymother[[64]]
+ [1] 0.7793476
+
+ $ymother[[65]]
+ [1] 0.1353756
+
+ $ymother[[66]]
+ [1] 0.1430004
+
+ $ymother[[67]]
+ [1] 0.06114522
+
+ $ymother[[68]]
+ numeric(0)
+
+ $ymother[[69]]
+ [1] 0.04452156
+
+ $ymother[[70]]
+ numeric(0)
+
+ $ymother[[71]]
+ [1] 0.520557
+
+ $ymother[[72]]
+ numeric(0)
+
+ $ymother[[73]]
+ [1] 0.0977161
+
+ $ymother[[74]]
+ [1] 0.7439875
+
+ $ymother[[75]]
+ [1] 0.7378475
+
+ $ymother[[76]]
+ [1] 0.8971273
+
+ $ymother[[77]]
+ numeric(0)
+
+ $ymother[[78]]
+ numeric(0)
+
+ $ymother[[79]]
+ numeric(0)
+
+ $ymother[[80]]
+ numeric(0)
+
+ $ymother[[81]]
+ [1] 0.5275586
+
+ $ymother[[82]]
+ numeric(0)
+
+ $ymother[[83]]
+ [1] 0.8418989
+
+ $ymother[[84]]
+ numeric(0)
+
+ $ymother[[85]]
+ numeric(0)
+
+ $ymother[[86]]
+ [1] 0.4612811
+
+ $ymother[[87]]
+ [1] 0.1512124
+
+ $ymother[[88]]
+ numeric(0)
+
+ $ymother[[89]]
+ numeric(0)
+
+ $ymother[[90]]
+ numeric(0)
+
+ $ymother[[91]]
+ numeric(0)
+
+ $ymother[[92]]
+ [1] 0.4433798
+
+ $ymother[[93]]
+ numeric(0)
+
+ $ymother[[94]]
+ [1] 0.9635111
+
+ $ymother[[95]]
+ [1] 0.4833644
+
+ $ymother[[96]]
+ [1] 0.2543404
+
+ $ymother[[97]]
+ numeric(0)
+
+ $ymother[[98]]
+ [1] 0.2608816
+
+ $ymother[[99]]
+ [1] 0.541765
+
+ $ymother[[100]]
+ [1] 0.6509566
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
diff --git a/tests/testthat/_snaps/jitter_species.md b/tests/testthat/_snaps/jitter_species.md
new file mode 100644
index 0000000..4309e3f
--- /dev/null
+++ b/tests/testthat/_snaps/jitter_species.md
@@ -0,0 +1,108 @@
+# snapshot test with Thoms process
+
+ Code
+ jitter_species(simdat, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 0.70562431 0.7492636 species_01
+ 2 0.66944759 0.4828926 species_01
+ 3 0.93533619 0.4812669 species_02
+ 4 0.96695333 0.1083010 species_02
+ 5 0.91843733 0.6411184 species_03
+ 6 0.94340404 0.5321446 species_07
+ 7 0.06576721 0.4925216 species_08
+ 8 0.43193198 1.0121692 species_08
+ 9 0.28507829 0.7226997 species_09
+ 10 0.84556285 0.1318787 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
+# snapshot test with Poisson process
+
+ Code
+ jitter_species(simdat, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 0.9285156 0.4567952 species_01
+ 2 0.9507850 0.7181657 species_01
+ 3 0.2804926 0.9548565 species_02
+ 4 0.8248006 0.2756131 species_02
+ 5 0.6453768 0.4616657 species_03
+ 6 0.5254246 0.9530632 species_07
+ 7 0.7406310 1.0010929 species_08
+ 8 0.1387093 0.1403538 species_08
+ 9 0.6559310 0.4611085 species_09
+ 10 0.7201800 0.5575449 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
+# snapshot test wide jitter
+
+ Code
+ jitter_species(simdat, sd = 3, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 4.80479007 0.4662330 species_01
+ 2 4.76861335 0.1998621 species_01
+ 3 -0.75311134 6.5163538 species_02
+ 4 -0.72149420 6.1433879 species_02
+ 5 2.00419128 0.4536032 species_03
+ 6 2.83566323 4.4337049 species_07
+ 7 1.27452950 7.3295913 species_08
+ 8 1.64069426 7.8492389 species_08
+ 9 -0.03223401 -3.4299938 species_09
+ 10 5.36501362 -0.7016997 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
+# snapshot test with singletons only
+
+ Code
+ jitter_species(simdat, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 0.9285156 0.47079047 species_01
+ 2 0.9314284 0.74197871 species_02
+ 3 0.2897708 0.92078364 species_03
+ 4 0.8367763 0.25264094 species_04
+ 5 0.6457882 0.46095961 species_05
+ 6 0.5180347 0.94637403 species_06
+ 7 0.7517035 0.97538390 species_07
+ 8 0.1337200 0.09092281 species_08
+ 9 0.6771765 0.45059241 species_09
+ 10 0.7044376 0.57353388 species_10
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
diff --git a/tests/testthat/_snaps/reproduction.md b/tests/testthat/_snaps/reproduction.md
new file mode 100644
index 0000000..4a27427
--- /dev/null
+++ b/tests/testthat/_snaps/reproduction.md
@@ -0,0 +1,10024 @@
+# replace_individuals() default snapshot with N specified
+
+ Code
+ replace_individuals(simdat, N = 10L, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 0.2969200108 0.7481924411 species_84
+ 2 0.9351822325 0.5594644234 species_01
+ 3 0.9401116716 0.4973732976 species_79
+ 4 0.8026704120 0.1290908219 species_01
+ 5 0.9566387638 0.5367317737 species_61
+ 6 0.2330104264 0.6877789761 species_84
+ 7 0.8361267822 0.1314326243 species_80
+ 8 0.8270092790 0.1589600912 species_58
+ 9 0.8364962446 0.1267843071 species_85
+ 10 0.7951843644 0.1438685443 species_49
+ 11 0.9377981281 0.5614110614 species_88
+ 12 0.5507992439 0.8111403334 species_26
+ 13 0.5601414737 0.7690868892 species_48
+ 14 0.5592672781 0.8433217500 species_02
+ 15 0.5396709233 0.8179694827 species_45
+ 16 0.5502605606 0.8570405105 species_80
+ 17 0.8504450614 0.6992702883 species_50
+ 18 0.5508116453 0.8596730356 species_59
+ 19 0.2019271289 0.1837934778 species_70
+ 20 0.2848723910 0.0447854538 species_86
+ 21 0.5590870665 0.8471583480 species_80
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+ 24 0.9165234709 0.1119148814 species_03
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+ 4995 0.2625249166 0.2217573983 species_31
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
+# replace_individuals() default snapshot with R specified
+
+ Code
+ replace_individuals(simdat, R = 0.1, seed = 42L)
+ Output
+ $census
+ x y species
+ 1 0.2969200108 0.7481924411 species_29
+ 2 0.9351822325 0.5594644234 species_67
+ 3 0.9401116716 0.4973732976 species_64
+ 4 0.8026704120 0.1290908219 species_34
+ 5 0.9566387638 0.5367317737 species_90
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+ 7 0.8361267822 0.1314326243 species_01
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+ 11 0.9377981281 0.5614110614 species_82
+ 12 0.5507992439 0.8111403334 species_48
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+ 14 0.5592672781 0.8433217500 species_59
+ 15 0.5396709233 0.8179694827 species_59
+ 16 0.5502605606 0.8570405105 species_27
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+ 18 0.5508116453 0.8596730356 species_80
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+ 22 0.8533943299 0.7048412949 species_50
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+ 4870 0.4687760573 0.8588070310 species_83
+ 4871 0.4844199506 0.7336379153 species_30
+ 4872 0.8500715033 0.0116499864 species_56
+ 4873 0.3003389485 0.6918187476 species_75
+ 4874 0.0075579538 0.2022520597 species_51
+ 4875 0.1172226097 0.6991771917 species_71
+ 4876 0.5089746142 0.8255056932 species_68
+ 4877 0.4904532547 0.8776364910 species_59
+ 4878 0.1517532183 0.4333774794 species_37
+ 4879 0.4468119121 0.2570977515 species_14
+ 4880 0.3460130011 0.7429168319 species_65
+ 4881 0.3352851156 0.7441458982 species_43
+ 4882 0.4591529488 0.8711100528 species_56
+ 4883 0.4511705204 0.2438326757 species_73
+ 4884 0.8338911163 0.5294766941 species_84
+ 4885 0.8537184870 0.4849977097 species_13
+ 4886 0.4774420471 0.7492843505 species_42
+ 4887 0.1520675979 0.4703975977 species_76
+ 4888 0.4691394164 0.7627849565 species_83
+ 4889 0.3993239187 0.2315410643 species_58
+ 4890 0.8574015750 0.0053623387 species_58
+ 4891 0.4458648728 0.7469039101 species_23
+ 4892 0.4355516441 0.7232859917 species_53
+ 4893 0.0985933488 0.7227304850 species_51
+ 4894 0.2583537212 0.8893635005 species_67
+ 4895 0.2611827809 0.9045254697 species_33
+ 4896 0.2942042083 0.5035304883 species_61
+ 4897 0.3306926341 0.1202935879 species_54
+ 4898 0.6467473030 0.8111325297 species_49
+ 4899 0.0761346913 0.1647611324 species_06
+ 4900 0.2999457455 0.1332269282 species_31
+ 4901 0.0798212481 0.1586031319 species_51
+ 4902 0.6715358004 0.7959809471 species_03
+ 4903 0.3142501920 0.1280544721 species_73
+ 4904 0.2987239700 0.4932051866 species_83
+ 4905 0.0461551674 0.1462355621 species_51
+ 4906 0.6705125316 0.8198885742 species_17
+ 4907 0.2614750400 0.1999924973 species_68
+ 4908 0.8416561796 0.7943182217 species_12
+ 4909 0.2609605077 0.1886325960 species_31
+ 4910 0.6746440188 0.7944136617 species_27
+ 4911 0.6020167007 0.9786310797 species_33
+ 4912 0.2958081144 0.1192414777 species_60
+ 4913 0.0400543500 0.1788476469 species_89
+ 4914 0.7389131754 0.3517302414 species_65
+ 4915 0.8475078495 0.7903152851 species_71
+ 4916 0.6075819215 0.9616495357 species_26
+ 4917 0.2678528475 0.1623697271 species_90
+ 4918 0.6448298190 0.9764160521 species_64
+ 4919 0.7988607403 0.8156553479 species_87
+ 4920 0.3277517784 0.1378311326 species_63
+ 4921 0.3312668806 0.0836721296 species_55
+ 4922 0.7679036026 0.3622615116 species_70
+ 4923 0.7313977694 0.3409549363 species_65
+ 4924 0.9776423115 0.5298375108 species_79
+ 4925 0.6330312951 0.7679313574 species_55
+ 4926 0.5952439742 0.9535764299 species_70
+ 4927 0.0670152525 0.1850098573 species_40
+ 4928 0.9535751905 0.5281156826 species_64
+ 4929 0.6780021473 0.7951865819 species_90
+ 4930 0.0565551159 0.1929737681 species_90
+ 4931 0.6099637487 0.8087342306 species_44
+ 4932 0.6266052979 0.9913139071 species_80
+ 4933 0.6381961158 0.9677598264 species_51
+ 4934 0.3207260146 0.1256333094 species_24
+ 4935 0.6359829063 0.7983340895 species_87
+ 4936 0.3490975402 0.1629658036 species_63
+ 4937 0.6449653050 0.8110528473 species_90
+ 4938 0.7107940856 0.3286739576 species_46
+ 4939 0.7084982801 0.3229845026 species_46
+ 4940 0.0455311743 0.1896744025 species_82
+ 4941 0.2531280264 0.1879968422 species_24
+ 4942 0.6054224433 0.9574510879 species_26
+ 4943 0.2849525927 0.2131949997 species_47
+ 4944 0.5704560662 0.9686480482 species_39
+ 4945 0.7246157065 0.3354868678 species_80
+ 4946 0.7268167409 0.3592763299 species_74
+ 4947 0.3522362822 0.1207342527 species_31
+ 4948 0.6149131265 0.9838885677 species_21
+ 4949 0.7311658587 0.3370954483 species_70
+ 4950 0.0540245830 0.1627777645 species_85
+ 4951 0.6299664743 0.7981167296 species_90
+ 4952 0.8209356038 0.7840630524 species_27
+ 4953 0.3717560711 0.4998677538 species_63
+ 4954 0.8205328875 0.7695292218 species_30
+ 4955 0.3069336217 0.0888907103 species_85
+ 4956 0.9931009086 0.5447366957 species_90
+ 4957 0.3102976931 0.5135420638 species_61
+ 4958 0.3417751717 0.1270468253 species_66
+ 4959 0.0194114811 0.1970475724 species_63
+ 4960 0.6203933494 0.8107641476 species_33
+ 4961 0.6973385338 0.2941499904 species_70
+ 4962 0.3534032605 0.5160226165 species_63
+ 4963 0.6072932351 0.9591799117 species_90
+ 4964 0.6598747818 0.8104010776 species_30
+ 4965 0.8867973587 0.8124071478 species_31
+ 4966 0.2461717219 0.2025446789 species_65
+ 4967 0.6127831966 0.9722704776 species_21
+ 4968 0.3180955339 0.5031254263 species_78
+ 4969 0.6372193785 0.7885450232 species_90
+ 4970 0.3661467328 0.5077545250 species_84
+ 4971 0.0422365410 0.1852774584 species_46
+ 4972 0.0795615071 0.1813230998 species_68
+ 4973 0.3367323389 0.1103545570 species_65
+ 4974 0.3269774257 0.4910904900 species_59
+ 4975 0.7258972468 0.3518937173 species_70
+ 4976 0.6132203605 0.9755872623 species_90
+ 4977 0.0340150275 0.1781533077 species_76
+ 4978 0.2905893194 0.4803525224 species_16
+ 4979 0.0281275268 0.2020961499 species_89
+ 4980 0.8161481099 0.7443268177 species_30
+ 4981 0.3227988171 0.5341615921 species_76
+ 4982 0.7084229771 0.3258959018 species_81
+ 4983 0.6731626807 0.8104390603 species_27
+ 4984 0.8267994460 0.7757042358 species_14
+ 4985 0.6020221775 0.9647005339 species_80
+ 4986 0.0530238549 0.1582421851 species_76
+ 4987 0.2940143238 0.5289281953 species_38
+ 4988 0.0661308028 0.1698739900 species_40
+ 4989 0.0499866422 0.1641458929 species_67
+ 4990 0.6089288516 0.7959831477 species_59
+ 4991 0.0544366492 0.1370206182 species_82
+ 4992 0.3452479540 0.1076716388 species_55
+ 4993 0.9813637427 0.5490995993 species_82
+ 4994 0.7408132785 0.2958430596 species_34
+ 4995 0.2625249166 0.2217573983 species_82
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "community"
+
diff --git a/tests/testthat/_snaps/sampling-sample_quadrats().md b/tests/testthat/_snaps/sampling-sample_quadrats.md
similarity index 100%
rename from tests/testthat/_snaps/sampling-sample_quadrats().md
rename to tests/testthat/_snaps/sampling-sample_quadrats.md
diff --git a/tests/testthat/_snaps/simulation_functions-sim_sad().md b/tests/testthat/_snaps/simulation_functions-sim_sad.md
similarity index 100%
rename from tests/testthat/_snaps/simulation_functions-sim_sad().md
rename to tests/testthat/_snaps/simulation_functions-sim_sad.md
diff --git a/tests/testthat/_snaps/utils.md b/tests/testthat/_snaps/utils.md
new file mode 100644
index 0000000..985b84d
--- /dev/null
+++ b/tests/testthat/_snaps/utils.md
@@ -0,0 +1,366 @@
+# torusify() - mother_map method - default snapshot 0-1 range
+
+ Code
+ torusify(mpcoordsJ)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 0.01690673
+
+ $xmother[[2]]
+ [1] 0.4446157
+
+ $xmother[[3]]
+ [1] 0.07827696
+
+ $xmother[[4]]
+ [1] 0.845256
+
+ $xmother[[5]]
+ [1] 0.2952425 0.1958382
+
+ $xmother[[6]]
+ [1] 0.9247695 0.6217610 0.5022408 0.6478620
+
+ $xmother[[7]]
+ [1] 0.6522046 0.6709913
+
+ $xmother[[8]]
+ [1] 0.2215262 0.8488034
+
+ $xmother[[9]]
+ [1] 0.6039843
+
+ $xmother[[10]]
+ [1] 0.7407673 0.1545754 0.2382927 0.5852006
+
+ $xmother[[11]]
+ [1] 0.57211868 0.45964346 0.09184628
+
+ $xmother[[12]]
+ [1] 0.5216790 0.6175640 0.1173316 0.6661692
+
+ $xmother[[13]]
+ [1] 0.1159468 0.3504895 0.3512587
+
+ $xmother[[14]]
+ [1] 0.6988536 0.6997776 0.4612603 0.5037960
+
+ $xmother[[15]]
+ [1] 0.9579136
+
+ $xmother[[16]]
+ [1] 0.5538019
+
+ $xmother[[17]]
+ [1] 0.5977693 0.3238998
+
+ $xmother[[18]]
+ [1] 0.61854155 0.01846501 0.62278076 0.29360308
+
+ $xmother[[19]]
+ [1] 0.89964530 0.03403397
+
+ $xmother[[20]]
+ [1] 0.3863739 0.7448466
+
+
+ $ymother
+ $ymother[[1]]
+ [1] 0.487928
+
+ $ymother[[2]]
+ [1] 0.8371071
+
+ $ymother[[3]]
+ [1] 0.1604623
+
+ $ymother[[4]]
+ [1] 0.3988662
+
+ $ymother[[5]]
+ [1] 0.207488390 0.008764592
+
+ $ymother[[6]]
+ [1] 0.7889623 0.9435680 0.4080965 0.4666923
+
+ $ymother[[7]]
+ [1] 0.54900808 0.04575119
+
+ $ymother[[8]]
+ [1] 0.6449886 0.5351375
+
+ $ymother[[9]]
+ [1] 0.8562194
+
+ $ymother[[10]]
+ [1] 0.4799001 0.7135969 0.1044995 0.8448424
+
+ $ymother[[11]]
+ [1] 0.5939472 0.4712747 0.2412478
+
+ $ymother[[12]]
+ [1] 0.2054988 0.8477978 0.4678529 0.5380697
+
+ $ymother[[13]]
+ [1] 0.72967974 0.07912444 0.07246405
+
+ $ymother[[14]]
+ [1] 0.2971583 0.4770838 0.6376082 0.9063661
+
+ $ymother[[15]]
+ [1] 0.08664575
+
+ $ymother[[16]]
+ [1] 0.3198165
+
+ $ymother[[17]]
+ [1] 0.1643664 0.9909220
+
+ $ymother[[18]]
+ [1] 0.48188800 0.02625542 0.35946901 0.79859871
+
+ $ymother[[19]]
+ [1] 0.08843574 0.18497579
+
+ $ymother[[20]]
+ [1] 0.3358003 0.4675923
+
+
+ $x_min_max
+ [1] 0 1
+
+ $y_min_max
+ [1] 0 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# torusify() - mother_map method - wild range snapshot
+
+ Code
+ torusify(mpcoordsJ)
+ Output
+ $n_mother_points
+ [1] 1 1 1 1 2 4 2 2 1 4 3 4 3 4 1 1 2 4 2 2
+
+ $xmother
+ $xmother[[1]]
+ [1] 9.920938
+
+ $xmother[[2]]
+ [1] 8.583326
+
+ $xmother[[3]]
+ [1] 9.067169
+
+ $xmother[[4]]
+ [1] 9.791924
+
+ $xmother[[5]]
+ [1] 9.37768 8.71005
+
+ $xmother[[6]]
+ [1] 9.314973 9.527499 8.949210 9.483866
+
+ $xmother[[7]]
+ [1] 9.389800 8.482046
+
+ $xmother[[8]]
+ [1] 8.609634 8.533973
+
+ $xmother[[9]]
+ [1] 9.607933
+
+ $xmother[[10]]
+ [1] 9.573683 9.161910 8.445952 8.491802
+
+ $xmother[[11]]
+ [1] 9.183897 9.839203 9.527618
+
+ $xmother[[12]]
+ [1] 9.559110 9.591104 8.549083 8.623746
+
+ $xmother[[13]]
+ [1] 9.003702 9.990468 9.322225
+
+ $xmother[[14]]
+ [1] 9.317692 8.033205 8.808009 9.902281
+
+ $xmother[[15]]
+ [1] 9.742606
+
+ $xmother[[16]]
+ [1] 9.592738
+
+ $xmother[[17]]
+ [1] 8.346565 9.001177
+
+ $xmother[[18]]
+ [1] 9.789806 9.279553 9.137194 9.969210
+
+ $xmother[[19]]
+ [1] 8.882463 9.793578
+
+ $xmother[[20]]
+ [1] 8.952862 9.594536
+
+
+ $ymother
+ $ymother[[1]]
+ [1] -0.3225981
+
+ $ymother[[2]]
+ [1] 0.1083937
+
+ $ymother[[3]]
+ [1] -0.01137924
+
+ $ymother[[4]]
+ [1] 0.09207103
+
+ $ymother[[5]]
+ [1] 0.4480331 -0.9482466
+
+ $ymother[[6]]
+ [1] -0.07055863 -0.84004661 0.88749505 0.66410262
+
+ $ymother[[7]]
+ [1] 0.26836392 0.05363593
+
+ $ymother[[8]]
+ [1] -0.97952141 0.04954517
+
+ $ymother[[9]]
+ [1] 0.85779
+
+ $ymother[[10]]
+ [1] 0.06150408 0.87150211 0.46352779 -0.50952576
+
+ $ymother[[11]]
+ [1] -0.6302295 -0.9650784 -0.5250488
+
+ $ymother[[12]]
+ [1] -0.7045207 0.9334098 0.7730712 0.2054962
+
+ $ymother[[13]]
+ [1] -0.2700814 0.2876944 -0.9945018
+
+ $ymother[[14]]
+ [1] 0.2228031 -0.7888219 0.9706802 0.4214294
+
+ $ymother[[15]]
+ [1] 0.8306204
+
+ $ymother[[16]]
+ [1] -0.06102422
+
+ $ymother[[17]]
+ [1] -0.2093883 -0.7919203
+
+ $ymother[[18]]
+ [1] 0.6984553 0.4152004 0.3019247 -0.2387933
+
+ $ymother[[19]]
+ [1] 0.8282910 0.9182217
+
+ $ymother[[20]]
+ [1] -0.1284384 0.4698653
+
+
+ $x_min_max
+ [1] 8 10
+
+ $y_min_max
+ [1] -1 1
+
+ attr(,"class")
+ [1] "mother_map" "list"
+
+# torusify() - community method - wild range snapshot
+
+ Code
+ torusify(simdatJ)
+ Output
+ $census
+ x y species
+ 1 9.509855 -0.8146547 species_01
+ 2 9.425606 0.6576038 species_01
+ 3 8.193557 -0.9694344 species_02
+ 4 8.267398 0.2258254 species_02
+ 5 8.918997 -0.9046513 species_03
+ 6 9.772739 0.9528009 species_07
+ 7 9.311961 -0.2386575 species_08
+ 8 8.076466 0.8227788 species_08
+ 9 8.253906 -0.6934055 species_09
+ 10 8.195461 -0.5670331 species_10
+
+ $x_min_max
+ [1] 8 10
+
+ $y_min_max
+ [1] -1 1
+
+ attr(,"class")
+ [1] "community"
+
+# torusify() - data.frame method - wild range snapshot
+
+ Code
+ torusify(mpcoords, x_min_max, y_min_max)
+ Output
+ xmother ymother
+ 1 8.659224 0.61612555
+ 2 8.748302 -0.44515933
+ 3 8.144558 0.95556692
+ 4 8.321791 0.78667293
+ 5 9.566982 -0.67024977
+ 6 9.076384 -0.94315286
+ 7 9.946353 0.56081387
+ 8 9.538666 0.62295252
+ 9 9.627969 0.78787851
+ 10 9.820259 0.34401704
+ 11 8.830967 -0.04961753
+ 12 9.876449 0.24422057
+ 13 8.738689 0.55243313
+ 14 8.021715 -0.25932108
+ 15 8.849171 -0.98420664
+ 16 8.760058 0.33166432
+ 17 8.912906 -0.97066341
+ 18 9.469949 -0.16936411
+ 19 8.899988 0.62640563
+ 20 9.241331 -0.55288543
+
+# torudify() - numeric method - wild range snapshot
+
+ Code
+ torusify(mpcoords, range = c(0, 1))
+ Output
+ [1] 0.6592242 0.7483017 0.1445581 0.3217905 0.5669821 0.0763838 0.9463533
+ [8] 0.5386664 0.6279692 0.8202591
+
+# community2ppp() default behaviour snapshot
+
+ Code
+ community2ppp(simdat)
+ Output
+ Marked planar point pattern: 4995 points
+ Multitype, with levels =
+ species_01 species_02 species_03 species_04 species_05 species_06 species_07
+ species_08 species_09 species_10 species_11 species_12 species_13 species_14
+ species_15 species_16 species_17 species_18 species_19 species_20 species_21
+ species_22 species_23 species_24 species_25 species_26 species_27 species_28
+ species_29 species_30 species_31 species_32 species_33 species_34 species_35
+ species_36 species_37 species_38 species_39 species_40 species_41 species_42
+ species_43 species_44 species_45 species_46 species_47 species_48 species_49
+ species_50 species_51 species_52 species_53 species_54 species_55 species_56
+ species_57 species_58 species_59 species_60 species_61 species_62 species_63
+ species_64 species_65 species_66 species_67 species_68 species_69 species_70
+ species_71 species_72 species_73 species_74 species_75 species_76 species_77
+ species_78 species_79 species_80 species_81 species_82 species_83 species_84
+ species_85 species_86 species_87 species_88 species_89 species_90
+ window: rectangle = [0, 1] x [0, 1] units
+
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
new file mode 100644
index 0000000..98f28b3
--- /dev/null
+++ b/tests/testthat/setup.R
@@ -0,0 +1,6 @@
+base::options(digits = 7)
+suppressWarnings({
+ suppressMessages({
+ if (isTRUE(require(paint))) paint::unmask_print()
+ })
+})
diff --git a/tests/testthat/test-create_motherpoints.R b/tests/testthat/test-create_motherpoints.R
new file mode 100644
index 0000000..e21c29d
--- /dev/null
+++ b/tests/testthat/test-create_motherpoints.R
@@ -0,0 +1,103 @@
+## structure ----
+test_that("create_motherpoints() output is class mother_map", {
+ result <- create_motherpoints(s_local = 10L, seed = 1L)
+ expect_s3_class(result, "mother_map")
+ expect_true(all(is.element(
+ c("n_mother_points", "xmother", "ymother", "x_min_max", "y_min_max"),
+ names(result)
+ )))
+})
+
+test_that("create_motherpoints() xmother and ymother are always lists", {
+ # Default range — sapply would have given a list anyway, confirm list
+ r1 <- create_motherpoints(s_local = 10L, seed = 1L)
+ expect_type(r1$xmother, "list")
+ expect_type(r1$ymother, "list")
+
+ # Uniform count (n_motherpoints_range = 1L) — previously collapsed to vector
+ r2 <- create_motherpoints(s_local = 10L, n_motherpoints_range = 1L, seed = 1L)
+ expect_type(r2$xmother, "list")
+ expect_type(r2$ymother, "list")
+
+ # Uniform count > 1 — previously collapsed to matrix
+ r3 <- create_motherpoints(s_local = 10L, n_motherpoints_range = 2L, seed = 1L)
+ expect_type(r3$xmother, "list")
+ expect_type(r3$ymother, "list")
+})
+
+test_that("create_motherpoints() list lengths match s_local", {
+ s <- 15L
+ result <- create_motherpoints(s_local = s, seed = 1L)
+ expect_length(result$xmother, s)
+ expect_length(result$ymother, s)
+ expect_length(result$n_mother_points, s)
+})
+
+## invariants ----
+test_that("create_motherpoints() coordinates stay within xrange/yrange", {
+ xr <- c(2, 5)
+ yr <- c(-1, 3)
+ result <- create_motherpoints(
+ s_local = 20L,
+ xrange = xr,
+ yrange = yr,
+ seed = 1L
+ )
+ all_x <- unlist(result$xmother)
+ all_y <- unlist(result$ymother)
+ expect_true(all(all_x >= xr[[1L]] & all_x <= xr[[2L]]))
+ expect_true(all(all_y >= yr[[1L]] & all_y <= yr[[2L]]))
+})
+
+test_that("create_motherpoints() n_mother_points values are within n_motherpoints_range", {
+ rng <- 1L:5L
+ result <- create_motherpoints(s_local = 50L, n_motherpoints_range = rng, seed = 1L)
+ expect_true(all(is.element(result$n_mother_points, rng)))
+})
+
+## reproducibility ----
+test_that("create_motherpoints() seed produces identical results", {
+ r1 <- create_motherpoints(s_local = 20L, seed = 99L)
+ r2 <- create_motherpoints(s_local = 20L, seed = 99L)
+ expect_equal(r1$n_mother_points, r2$n_mother_points)
+ expect_equal(r1$xmother, r2$xmother)
+ expect_equal(r1$ymother, r2$ymother)
+})
+
+test_that("create_motherpoints() stores xrange and yrange correctly", {
+ xr <- c(2, 5)
+ yr <- c(-1, 3)
+ result <- create_motherpoints(s_local = 5L, xrange = xr, yrange = yr, seed = 1L)
+ expect_equal(result$x_min_max, xr)
+ expect_equal(result$y_min_max, yr)
+})
+
+## snapshots ----
+test_that("snapshot test with clustering", {
+ expect_snapshot(create_motherpoints(s_local = 100L, seed = 42L))
+})
+
+test_that("snapshot test with clustering - no range", {
+ expect_snapshot(create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 1L,
+ seed = 42L
+ ))
+})
+
+test_that("snapshot test without clustering", {
+ expect_snapshot(create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 0L:1L,
+ seed = 42L
+ ))
+})
+
+test_that("snapshot test plotting method for mother_map class", {
+ mpcoords <- create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 0L:1L,
+ seed = 42L
+ )
+ expect_snapshot_output(plot(mpcoords))
+})
diff --git a/tests/testthat/test-drift_motherpoints.R b/tests/testthat/test-drift_motherpoints.R
new file mode 100644
index 0000000..8bd4ece
--- /dev/null
+++ b/tests/testthat/test-drift_motherpoints.R
@@ -0,0 +1,90 @@
+## invariants ----
+test_that("drift_x_motherpoints() shifts all x by exactly drift", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ d <- 0.15
+ result <- drift_x_motherpoints(mpcoords, drift = d)
+ expect_equal(
+ mapply(FUN = function(r, o) all(r == o + d), result$xmother, mpcoords$xmother),
+ rep(TRUE, length(mpcoords$xmother))
+ )
+})
+
+test_that("drift_y_motherpoints() shifts all y by exactly drift", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ d <- -0.3
+ result <- drift_y_motherpoints(mpcoords, drift = d)
+ expect_equal(
+ mapply(FUN = function(r, o) all(r == o + d), result$ymother, mpcoords$ymother),
+ rep(TRUE, length(mpcoords$ymother))
+ )
+})
+
+test_that("drift_x_motherpoints() does not change y coordinates", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- drift_x_motherpoints(mpcoords, drift = 0.1)
+ expect_equal(result$ymother, mpcoords$ymother)
+})
+
+test_that("drift_y_motherpoints() does not change x coordinates", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- drift_y_motherpoints(mpcoords, drift = 0.1)
+ expect_equal(result$xmother, mpcoords$xmother)
+})
+
+test_that("drift_x_motherpoints() preserves mother_map class", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- drift_x_motherpoints(mpcoords, drift = 0.1)
+ expect_s3_class(result, "mother_map")
+})
+
+test_that("drift_y_motherpoints() preserves mother_map class", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- drift_y_motherpoints(mpcoords, drift = 0.1)
+ expect_s3_class(result, "mother_map")
+})
+
+## edge cases ----
+test_that("drift_x_motherpoints() errors when drift is not provided", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ expect_error(drift_x_motherpoints(mpcoords))
+})
+
+test_that("drift_y_motherpoints() errors when drift is not provided", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ expect_error(drift_y_motherpoints(mpcoords))
+})
+
+test_that("drift_x_motherpoints() with zero drift leaves x unchanged", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- drift_x_motherpoints(mpcoords, drift = 0)
+ expect_equal(result$xmother, mpcoords$xmother)
+})
+
+## snapshots ----
+test_that("snapshot test drift_x with clustering", {
+ mpcoords <- create_motherpoints(s_local = 100L, seed = 42L)
+ expect_snapshot(drift_x_motherpoints(mpcoords, drift = 0.1))
+})
+
+test_that("snapshot test drift_x without clustering", {
+ mpcoords <- create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 0:1,
+ seed = 42L
+ )
+ expect_snapshot(drift_x_motherpoints(mpcoords, drift = 0.1))
+})
+
+test_that("snapshot test drift_y with clustering", {
+ mpcoords <- create_motherpoints(s_local = 100L, seed = 42L)
+ expect_snapshot(drift_y_motherpoints(mpcoords, drift = 0.1))
+})
+
+test_that("snapshot test drift_y without clustering", {
+ mpcoords <- create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 0:1,
+ seed = 42L
+ )
+ expect_snapshot(drift_y_motherpoints(mpcoords, drift = 0.1))
+})
diff --git a/tests/testthat/test-drift_species.R b/tests/testthat/test-drift_species.R
new file mode 100644
index 0000000..f7efbd5
--- /dev/null
+++ b/tests/testthat/test-drift_species.R
@@ -0,0 +1,70 @@
+## invariants ----
+test_that("drift_x_species() shifts all x by exactly drift", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ d <- 0.15
+ result <- drift_x_species(simdat, drift = d)
+ expect_equal(result$census$x, simdat$census$x + d)
+})
+
+test_that("drift_y_species() shifts all y by exactly drift", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ d <- -0.3
+ result <- drift_y_species(simdat, drift = d)
+ expect_equal(result$census$y, simdat$census$y + d)
+})
+
+test_that("drift_x_species() does not change y coordinates or species", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_x_species(simdat, drift = 0.1)
+ expect_equal(result$census$y, simdat$census$y)
+ expect_equal(as.character(result$census$species), as.character(simdat$census$species))
+})
+
+test_that("drift_y_species() does not change x coordinates or species", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_y_species(simdat, drift = 0.1)
+ expect_equal(result$census$x, simdat$census$x)
+ expect_equal(as.character(result$census$species), as.character(simdat$census$species))
+})
+
+test_that("drift_x_species() preserves community class", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_x_species(simdat, drift = 0.1)
+ expect_s3_class(result, "community")
+})
+
+test_that("drift_y_species() preserves community class", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_y_species(simdat, drift = 0.1)
+ expect_s3_class(result, "community")
+})
+
+## edge cases ----
+test_that("drift_x_species() with zero drift leaves coordinates unchanged", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_x_species(simdat, drift = 0)
+ expect_equal(result$census$x, simdat$census$x)
+})
+
+test_that("drift_y_species() with zero drift leaves coordinates unchanged", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- drift_y_species(simdat, drift = 0)
+ expect_equal(result$census$y, simdat$census$y)
+})
+
+test_that("drift_x_species() errors when drift is not provided", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ expect_error(drift_x_species(simdat))
+})
+
+test_that("drift_y_species() errors when drift is not provided", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ expect_error(drift_y_species(simdat))
+})
+
+## snapshots ----
+test_that("snapshot test with drift", {
+ simdat <- sim_thomas_community(10L, 10L, fix_s_sim = TRUE, seed = 42L)
+ expect_snapshot(drift_x_species(simdat, drift = 0.1))
+ expect_snapshot(drift_y_species(simdat, drift = 0.1))
+})
diff --git a/tests/testthat/test-jitter_motherpoints.R b/tests/testthat/test-jitter_motherpoints.R
new file mode 100644
index 0000000..8c8a515
--- /dev/null
+++ b/tests/testthat/test-jitter_motherpoints.R
@@ -0,0 +1,72 @@
+## structure ----
+test_that("jitter_motherpoints() returns a mother_map object", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- jitter_motherpoints(mpcoords, seed = 1L)
+ expect_s3_class(result, "mother_map")
+ expect_true(all(is.element(
+ c("n_mother_points", "xmother", "ymother", "x_min_max", "y_min_max"),
+ names(result)
+ )))
+})
+
+test_that("jitter_motherpoints() preserves list lengths", {
+ s <- 15L
+ mpcoords <- create_motherpoints(s_local = s, seed = 42L)
+ result <- jitter_motherpoints(mpcoords, seed = 1L)
+ expect_length(result$xmother, s)
+ expect_length(result$ymother, s)
+ expect_length(result$n_mother_points, s)
+})
+
+test_that("jitter_motherpoints() preserves n_mother_points", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- jitter_motherpoints(mpcoords, seed = 1L)
+ expect_equal(result$n_mother_points, mpcoords$n_mother_points)
+})
+
+## invariants ----
+test_that("jitter_motherpoints() coordinates actually change", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ result <- jitter_motherpoints(mpcoords, sd = 0.1, seed = 1L)
+ expect_false(isTRUE(all.equal(unlist(result$xmother), unlist(mpcoords$xmother))))
+})
+
+test_that("jitter_motherpoints() species with 0 mother points are unaffected", {
+ mpcoords <- create_motherpoints(
+ s_local = 20L,
+ n_motherpoints_range = 0L:3L,
+ seed = 42L
+ )
+ zero_idx <- which(mpcoords$n_mother_points == 0L)
+ if (length(zero_idx) > 0L) {
+ result <- jitter_motherpoints(mpcoords, sd = 1, seed = 1L)
+ for (i in zero_idx) {
+ expect_length(result$xmother[[i]], 0L)
+ expect_length(result$ymother[[i]], 0L)
+ }
+ }
+})
+
+## reproducibility ----
+test_that("jitter_motherpoints() seed produces identical results", {
+ mpcoords <- create_motherpoints(s_local = 10L, seed = 42L)
+ r1 <- jitter_motherpoints(mpcoords, seed = 7L)
+ r2 <- jitter_motherpoints(mpcoords, seed = 7L)
+ expect_equal(r1$xmother, r2$xmother)
+ expect_equal(r1$ymother, r2$ymother)
+})
+
+## snapshots ----
+test_that("snapshot test with clustering", {
+ mpcoords <- create_motherpoints(s_local = 100L, seed = 42L)
+ expect_snapshot(jitter_motherpoints(mpcoords, seed = 42L))
+})
+
+test_that("snapshot test without clustering", {
+ mpcoords <- create_motherpoints(
+ s_local = 100L,
+ n_motherpoints_range = 0:1,
+ seed = 42L
+ )
+ expect_snapshot(jitter_motherpoints(mpcoords, seed = 42L))
+})
diff --git a/tests/testthat/test-jitter_species.R b/tests/testthat/test-jitter_species.R
new file mode 100644
index 0000000..36d989d
--- /dev/null
+++ b/tests/testthat/test-jitter_species.R
@@ -0,0 +1,88 @@
+## structure ----
+test_that("jitter_species() returns a community object", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- jitter_species(simdat, seed = 1L)
+ expect_s3_class(result, "community")
+ expect_true(all(is.element(c("census", "x_min_max", "y_min_max"), names(result))))
+})
+
+test_that("jitter_species() preserves row count", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ expect_equal(nrow(jitter_species(simdat, seed = 1L)$census), nrow(simdat$census))
+})
+
+## invariants ----
+test_that("jitter_species() preserves species column order", {
+ # Use an interleaved census so the bug would have been visible
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ # Shuffle rows to interleave species
+ set.seed(1L)
+ idx <- sample.int(nrow(simdat$census))
+ simdat$census <- simdat$census[idx, ]
+ rownames(simdat$census) <- NULL
+
+ result <- jitter_species(simdat, sd = 0.1, seed = 1L)
+ expect_equal(
+ as.character(result$census$species),
+ as.character(simdat$census$species)
+ )
+})
+
+test_that("jitter_species() applies the same x/y shift to all individuals of a species", {
+ simdat <- sim_thomas_community(3L, 30L, fix_s_sim = TRUE, seed = 42L)
+ result <- jitter_species(simdat, sd = 0.05, seed = 1L)
+
+ for (sp in levels(simdat$census$species)) {
+ idx <- simdat$census$species == sp
+ if (sum(idx) < 2L) next
+ x_diffs <- result$census$x[idx] - simdat$census$x[idx]
+ y_diffs <- result$census$y[idx] - simdat$census$y[idx]
+ expect_true(all(abs(x_diffs - x_diffs[[1L]]) < 1e-12),
+ label = paste0("x shift uniform within species ", sp))
+ expect_true(all(abs(y_diffs - y_diffs[[1L]]) < 1e-12),
+ label = paste0("y shift uniform within species ", sp))
+ }
+})
+
+test_that("jitter_species() coordinates actually change", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- jitter_species(simdat, sd = 0.1, seed = 1L)
+ expect_false(isTRUE(all.equal(result$census$x, simdat$census$x)))
+})
+
+test_that("jitter_species() with sd = 0 leaves coordinates unchanged", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ result <- jitter_species(simdat, sd = 0, seed = 1L)
+ expect_equal(result$census$x, simdat$census$x)
+ expect_equal(result$census$y, simdat$census$y)
+})
+
+## reproducibility ----
+test_that("jitter_species() seed produces identical results", {
+ simdat <- sim_thomas_community(5L, 20L, seed = 42L)
+ r1 <- jitter_species(simdat, seed = 7L)
+ r2 <- jitter_species(simdat, seed = 7L)
+ expect_equal(r1$census$x, r2$census$x)
+ expect_equal(r1$census$y, r2$census$y)
+})
+
+## snapshots ----
+test_that("snapshot test with Thoms process", {
+ simdat <- sim_thomas_community(10L, 10L, seed = 42L)
+ expect_snapshot(jitter_species(simdat, seed = 42L))
+})
+
+test_that("snapshot test with Poisson process", {
+ simdat <- sim_poisson_community(10L, 10L, seed = 42L)
+ expect_snapshot(jitter_species(simdat, seed = 42L))
+})
+
+test_that("snapshot test wide jitter", {
+ simdat <- sim_thomas_community(10L, 10L, seed = 42L)
+ expect_snapshot(jitter_species(simdat, sd = 3, seed = 42L))
+})
+
+test_that("snapshot test with singletons only", {
+ simdat <- sim_thomas_community(10L, 10L, fix_s_sim = TRUE, seed = 42L)
+ expect_snapshot(jitter_species(simdat, seed = 42L))
+})
diff --git a/tests/testthat/test_patterns_of_biodiversity_functions.R b/tests/testthat/test-patterns_of_biodiversity_functions.R
similarity index 100%
rename from tests/testthat/test_patterns_of_biodiversity_functions.R
rename to tests/testthat/test-patterns_of_biodiversity_functions.R
diff --git a/tests/testthat/test-reproduction.R b/tests/testthat/test-reproduction.R
new file mode 100644
index 0000000..f5e4094
--- /dev/null
+++ b/tests/testthat/test-reproduction.R
@@ -0,0 +1,61 @@
+# Reproduction functions
+
+## edge cases ----
+test_that("replace_individuals() errors when both N and R are NULL", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ expect_error(replace_individuals(simdat), regexp = "N.*R|R.*N", ignore.case = TRUE)
+})
+
+## structure ----
+test_that("replace_individuals() output is class community", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- replace_individuals(simdat, N = 5L, seed = 42L)
+ expect_s3_class(result, "community")
+})
+
+test_that("replace_individuals() preserves individual count", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- replace_individuals(simdat, N = 5L, seed = 42L)
+ expect_equal(nrow(result$census), nrow(simdat$census))
+})
+
+test_that("replace_individuals() species column is a factor", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- replace_individuals(simdat, N = 5L, seed = 42L)
+ expect_true(is.factor(result$census$species))
+})
+
+test_that("replace_individuals() x and y coordinates are unchanged", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- replace_individuals(simdat, N = 5L, seed = 42L)
+ expect_equal(result$census$x, simdat$census$x)
+ expect_equal(result$census$y, simdat$census$y)
+})
+
+## invariants ----
+test_that("replace_individuals() only assigns existing species", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- replace_individuals(simdat, N = 5L, seed = 42L)
+ original_species <- levels(simdat$census$species)
+ result_species <- levels(result$census$species)
+ expect_true(all(is.element(result_species, original_species)))
+})
+
+## reproducibility ----
+test_that("replace_individuals() seed produces identical results", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ r1 <- replace_individuals(simdat, N = 5L, seed = 7L)
+ r2 <- replace_individuals(simdat, N = 5L, seed = 7L)
+ expect_equal(as.character(r1$census$species), as.character(r2$census$species))
+})
+
+## snapshots ----
+test_that("replace_individuals() default snapshot with N specified", {
+ simdat <- sim_thomas_coords(11L:100L, seed = 42L)
+ expect_snapshot(replace_individuals(simdat, N = 10L, seed = 42L))
+})
+
+test_that("replace_individuals() default snapshot with R specified", {
+ simdat <- sim_thomas_coords(11L:100L, seed = 42L)
+ expect_snapshot(replace_individuals(simdat, R = 0.1, seed = 42L))
+})
diff --git a/tests/testthat/test_sampling-sample_quadrats().R b/tests/testthat/test-sampling-sample_quadrats.R
similarity index 100%
rename from tests/testthat/test_sampling-sample_quadrats().R
rename to tests/testthat/test-sampling-sample_quadrats.R
diff --git a/tests/testthat/test_sampling-sampling_grids().R b/tests/testthat/test-sampling-sampling_grids.R
similarity index 100%
rename from tests/testthat/test_sampling-sampling_grids().R
rename to tests/testthat/test-sampling-sampling_grids.R
diff --git a/tests/testthat/test_sampling-sampling_random_with_overlap.R b/tests/testthat/test-sampling-sampling_random_with_overlap.R
similarity index 100%
rename from tests/testthat/test_sampling-sampling_random_with_overlap.R
rename to tests/testthat/test-sampling-sampling_random_with_overlap.R
diff --git a/tests/testthat/test_sampling-sampling_random_without_overlap_bruteforce.R b/tests/testthat/test-sampling-sampling_random_without_overlap_bruteforce.R
similarity index 100%
rename from tests/testthat/test_sampling-sampling_random_without_overlap_bruteforce.R
rename to tests/testthat/test-sampling-sampling_random_without_overlap_bruteforce.R
diff --git a/tests/testthat/test_sampling-sampling_random_without_overlap_spatstat.R b/tests/testthat/test-sampling-sampling_random_without_overlap_spatstat.R
similarity index 100%
rename from tests/testthat/test_sampling-sampling_random_without_overlap_spatstat.R
rename to tests/testthat/test-sampling-sampling_random_without_overlap_spatstat.R
diff --git a/tests/testthat/test_sampling-sampling_transects().R b/tests/testthat/test-sampling-sampling_transects.R
similarity index 100%
rename from tests/testthat/test_sampling-sampling_transects().R
rename to tests/testthat/test-sampling-sampling_transects.R
diff --git a/tests/testthat/test_simulation_functions-classes.R b/tests/testthat/test-simulation_functions-classes.R
similarity index 100%
rename from tests/testthat/test_simulation_functions-classes.R
rename to tests/testthat/test-simulation_functions-classes.R
diff --git a/tests/testthat/test_simulation_functions-poisson_process.r b/tests/testthat/test-simulation_functions-poisson_process.r
similarity index 100%
rename from tests/testthat/test_simulation_functions-poisson_process.r
rename to tests/testthat/test-simulation_functions-poisson_process.r
diff --git a/tests/testthat/test_simulation_functions-sim_sad().R b/tests/testthat/test-simulation_functions-sim_sad.R
similarity index 100%
rename from tests/testthat/test_simulation_functions-sim_sad().R
rename to tests/testthat/test-simulation_functions-sim_sad.R
diff --git a/tests/testthat/test_simulation_functions-thomas_process.r b/tests/testthat/test-simulation_functions-thomas_process.r
similarity index 100%
rename from tests/testthat/test_simulation_functions-thomas_process.r
rename to tests/testthat/test-simulation_functions-thomas_process.r
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
new file mode 100644
index 0000000..6697337
--- /dev/null
+++ b/tests/testthat/test-utils.R
@@ -0,0 +1,172 @@
+# tests utility functions
+## torusify() — invariants ----
+test_that("torusify.mother_map() output stays within x_min_max and y_min_max", {
+ mpcoords <- create_motherpoints(s_local = 20L, seed = 42L)
+ mpcoordsJ <- jitter_motherpoints(mpcoords, sd = 5, seed = 1L)
+ result <- torusify(mpcoordsJ)
+ all_x <- unlist(result$xmother)
+ all_y <- unlist(result$ymother)
+ expect_true(all(all_x >= result$x_min_max[[1L]] & all_x < result$x_min_max[[2L]]))
+ expect_true(all(all_y >= result$y_min_max[[1L]] & all_y < result$y_min_max[[2L]]))
+})
+
+test_that("torusify.community() output stays within x_min_max and y_min_max", {
+ simdat <- sim_thomas_community(5L, 50L, seed = 42L)
+ simdatJ <- jitter_species(simdat, sd = 5, seed = 1L)
+ result <- torusify(simdatJ)
+ expect_true(all(
+ result$census$x >= result$x_min_max[[1L]] &
+ result$census$x < result$x_min_max[[2L]]
+ ))
+ expect_true(all(
+ result$census$y >= result$y_min_max[[1L]] &
+ result$census$y < result$y_min_max[[2L]]
+ ))
+})
+
+test_that("torusify.numeric() output stays within range", {
+ vals <- stats::runif(50L, min = -3, max = 3)
+ result <- torusify(vals, range = c(0, 1))
+ expect_true(all(result >= 0 & result < 1))
+})
+
+## torusify.data.frame() — invariants ----
+test_that("torusify.data.frame() output stays within x_min_max and y_min_max", {
+ set.seed(1L)
+ x_min_max <- c(0, 1)
+ y_min_max <- c(0, 1)
+ df <- data.frame(
+ xmother = stats::runif(30L, min = -1, max = 2),
+ ymother = stats::runif(30L, min = -1, max = 2)
+ )
+ result <- torusify(df, x_min_max = x_min_max, y_min_max = y_min_max)
+ expect_true(all(result$xmother >= x_min_max[[1L]] & result$xmother < x_min_max[[2L]]))
+ expect_true(all(result$ymother >= y_min_max[[1L]] & result$ymother < y_min_max[[2L]]))
+})
+
+## torusify.data.frame() — edge cases ----
+test_that("torusify.data.frame() errors when xmother column is missing", {
+ df <- data.frame(ymother = stats::runif(10L))
+ expect_error(
+ torusify(df, x_min_max = c(0, 1), y_min_max = c(0, 1)),
+ "xmother"
+ )
+})
+
+test_that("torusify.data.frame() errors when ymother column is missing", {
+ df <- data.frame(xmother = stats::runif(10L))
+ expect_error(
+ torusify(df, x_min_max = c(0, 1), y_min_max = c(0, 1)),
+ "ymother"
+ )
+})
+
+## community2ppp() — structure ----
+test_that("community2ppp() output is class ppp", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- community2ppp(simdat)
+ expect_s3_class(result, "ppp")
+})
+
+test_that("community2ppp() point count matches community individual count", {
+ simdat <- sim_thomas_coords(11L:30L, seed = 42L)
+ result <- community2ppp(simdat)
+ expect_equal(result$n, nrow(simdat$census))
+})
+
+## create_random_ID() — seed and structure ----
+test_that("create_random_ID() works in a fresh-seed context (no prior RNG)", {
+ # Simulate a fresh session by removing .Random.seed temporarily
+ old_seed <- if (exists(".Random.seed")) .Random.seed else NULL
+ on.exit({
+ if (!is.null(old_seed)) assign(".Random.seed", old_seed, envir = .GlobalEnv)
+ })
+ rm(".Random.seed", envir = .GlobalEnv)
+ expect_no_error(create_random_ID(seed = 1L))
+})
+
+test_that("create_random_ID() n > 1 returns correct length and format", {
+ result <- create_random_ID(n = 5L, seed = 1L)
+ expect_length(result, 5L)
+ expect_true(all(nchar(result) == 10L))
+ expect_true(all(grepl(pattern = "^[A-Z]{5}[0-9]{4}[A-Z]$", x = result)))
+})
+
+## torusify() — snapshots ----
+test_that("torusify() - mother_map method - default snapshot 0-1 range", {
+ mpcoords <- create_motherpoints(s_local = 20L, seed = 42L)
+ mpcoordsJ <- jitter_motherpoints(mpcoords, sd = 3, seed = 42L)
+ expect_snapshot(torusify(mpcoordsJ))
+})
+
+test_that("torusify() - mother_map method - wild range snapshot", {
+ mpcoords <- create_motherpoints(
+ s_local = 20L,
+ xrange = c(8, 10),
+ yrange = c(-1, 1),
+ seed = 42L
+ )
+ mpcoordsJ <- jitter_motherpoints(mpcoords, sd = 3, seed = 42L)
+ expect_snapshot(torusify(mpcoordsJ))
+})
+
+test_that("torusify() - community method - wild range snapshot", {
+ simdat <- sim_thomas_community(
+ 10L,
+ 10L,
+ xrange = c(8, 10),
+ yrange = c(-1, 1),
+ seed = 42L
+ )
+ simdatJ <- jitter_species(simdat, sd = 3, seed = 42L)
+ expect_snapshot(torusify(simdatJ))
+})
+
+test_that("torusify() - data.frame method - wild range snapshot", {
+ set.seed(42L)
+ x_min_max <- c(8, 10)
+ y_min_max <- c(-1, 1)
+ mpcoords <- data.frame(
+ xmother = stats::runif(
+ 20L,
+ min = x_min_max[1L] - 1,
+ max = x_min_max[2L] + 1
+ ),
+ ymother = stats::runif(
+ 20L,
+ min = y_min_max[1L] - 1,
+ max = y_min_max[2L] + 1
+ )
+ )
+ expect_snapshot(torusify(mpcoords, x_min_max, y_min_max))
+})
+
+test_that("torudify() - numeric method - wild range snapshot", {
+ set.seed(42L)
+ mpcoords <- stats::runif(10L, min = -2, max = 2)
+ expect_snapshot(torusify(mpcoords, range = c(0, 1)))
+})
+
+
+## community2ppp() ----
+test_that("community2ppp() default behaviour snapshot", {
+ simdat <- sim_thomas_coords(11L:100L)
+ expect_snapshot(community2ppp(simdat))
+})
+
+## create_random_ID() ----
+test_that("create_random_ID() default behaviour", {
+ expect_equal(create_random_ID(seed = 42L), "QEAYJ1252R")
+})
+
+test_that("create_random_ID() is not affected by global seed", {
+ set.seed(84L)
+ expect_false(create_random_ID() == create_random_ID(seed = 84L))
+})
+
+test_that("create_random_ID() does not affect global seed", {
+ set.seed(84L)
+ reference84 <- .Random.seed
+ create_random_ID(seed = 42L)
+ expect_equal(reference84, .Random.seed)
+})
diff --git a/vignettes/Biodiversity_Changes.qmd b/vignettes/Biodiversity_Changes.qmd
index b2de657..81bc9a2 100644
--- a/vignettes/Biodiversity_Changes.qmd
+++ b/vignettes/Biodiversity_Changes.qmd
@@ -6,6 +6,10 @@ output:
html_document:
number_sections: true
toc: true
+knitr:
+ opts_chunk:
+ dpi: 72
+ fig.retina: 1
vignette: >
%\VignetteIndexEntry{Changes of biodiversity components}
%\VignetteEngine{quarto::html}
diff --git a/vignettes/Biodiversity_Patterns.qmd b/vignettes/Biodiversity_Patterns.qmd
index 0772671..6779412 100644
--- a/vignettes/Biodiversity_Patterns.qmd
+++ b/vignettes/Biodiversity_Patterns.qmd
@@ -9,6 +9,10 @@ output:
collapse: true
fig-width: 5
fig-height: 5
+knitr:
+ opts_chunk:
+ dpi: 72
+ fig.retina: 1
vignette: >
%\VignetteIndexEntry{Analysis of biodiversity patterns}
%\VignetteEngine{quarto::html}
diff --git a/vignettes/Introduction_mobsim.qmd b/vignettes/Introduction_mobsim.qmd
index 14be88b..bbe18aa 100644
--- a/vignettes/Introduction_mobsim.qmd
+++ b/vignettes/Introduction_mobsim.qmd
@@ -9,6 +9,10 @@ output:
collapse: true
fig-width: 5
fig-height: 5
+knitr:
+ opts_chunk:
+ dpi: 72
+ fig.retina: 1
vignette: >
%\VignetteIndexEntry{Introduction to mobsim}
%\VignetteEngine{quarto::html}
diff --git a/vignettes/Sampling_communities.qmd b/vignettes/Sampling_communities.qmd
index 8c0e0fc..51bccfe 100644
--- a/vignettes/Sampling_communities.qmd
+++ b/vignettes/Sampling_communities.qmd
@@ -9,6 +9,10 @@ output:
collapse: true
fig-width: 4.4
fig-height: 5
+knitr:
+ opts_chunk:
+ dpi: 72
+ fig.retina: 1
vignette: >
%\VignetteIndexEntry{Sampling communities with mobsim}
%\VignetteEngine{quarto::html}
diff --git a/vignettes/Simulating_communities.qmd b/vignettes/Simulating_communities.qmd
index cb46933..1fe248d 100644
--- a/vignettes/Simulating_communities.qmd
+++ b/vignettes/Simulating_communities.qmd
@@ -9,6 +9,10 @@ output:
collapse: true
fig-height: 4
fig-width: 3.5
+knitr:
+ opts_chunk:
+ dpi: 72
+ fig.retina: 1
vignette: >
%\VignetteIndexEntry{Simulating communities with mobsim}
%\VignetteEngine{quarto::html}