pharmaverse · billdenney · Jun 13, 2026 · Jun 13, 2026 · Jun 16, 2026
diff --git a/NEWS.md b/NEWS.md
@@ -73,6 +73,7 @@
 ## Bug fixes
 
 ### NCA Calculations
+* `exclude_half.life` is now initialized to `NA` instead of `FALSE` (matching `include_half.life`), so manually selecting half-life points to include no longer errors with "Cannot both include and exclude half-life points for the same interval" under the development version of PKNCA
 * Renal clearance (RENALCL) removed from direct PK calculations (inaccurate in PKNCA) — use ratio table instead (#781)
 * Multidose parameters (MRTMDO, MRTMDP, VSSMDO, VSSMDP, TAT) removed from direct calculations (#869)
 * Last dose interval end time extends to last observed sample instead of being cut off at tau (#1235)

diff --git a/R/PKNCA.R b/R/PKNCA.R
@@ -169,7 +169,11 @@ PKNCA_create_data_object <- function( # nolint: object_name_linter
   df_conc$is.excluded.hl <- FALSE
   df_conc$is.included.hl <- FALSE
   df_conc$REASON <- ""
-  df_conc$exclude_half.life <- FALSE
+  # NA (not FALSE) marks "no half-life exclusion yet". This mirrors how
+  # include_half.life is left NA until a point is selected and prevents PKNCA's
+  # "cannot both include and exclude half-life points" check from firing when
+  # only inclusions are set (an all-FALSE column counts as "in use").
+  df_conc$exclude_half.life <- NA
 
   # Create PKNCA conc object
 
@@ -869,7 +873,7 @@ check_valid_pknca_data <- function(processed_pknca_data, check_exclusion_has_rea
       time_col <- processed_pknca_data$conc$columns$time
 
       has_no_reason <- (nchar(data_conc[["REASON"]]) == 0) | is.na(data_conc[["REASON"]])
-      has_hl_excl <- data_conc[[excl_hl_col]]
+      has_hl_excl <- data_conc[[excl_hl_col]] %in% TRUE
       missing_reasons <- has_hl_excl & has_no_reason
 
       if (any(missing_reasons)) {

diff --git a/R/get_halflife_plots.R b/R/get_halflife_plots.R
@@ -43,7 +43,7 @@ get_halflife_plots <- function(pknca_data, add_annotations = TRUE,
 
   # Make sure to create a default exclude half life column if it does not exist
   if (is.null(exclude_hl_col)) {
-    pknca_data$conc$data[["exclude_half.life"]] <- FALSE
+    pknca_data$conc$data[["exclude_half.life"]] <- NA
     exclude_hl_col <- "exclude_half.life"
   }
 
@@ -114,7 +114,7 @@ get_halflife_plots <- function(pknca_data, add_annotations = TRUE,
       tlast = tlast + start,
       is_halflife_used = .[[time_col]] >= lambda.z.time.first &
         .[[time_col]] <= lambda.z.time.last &
-        !.[[exclude_hl_col]]
+        !(.[[exclude_hl_col]] %in% TRUE)
     ) %>%
     group_by(!!!syms(c(group_vars(pknca_data), "start", "end"))) %>%
     mutate(
@@ -133,9 +133,9 @@ get_halflife_plots <- function(pknca_data, add_annotations = TRUE,
   info_per_plot_list <- info_per_plot_list %>%
     mutate(
       color = "black",
-      color = ifelse(.[[exclude_hl_col]], "red", color),
+      color = ifelse(.[[exclude_hl_col]] %in% TRUE, "red", color),
       color = ifelse(is_halflife_used & !is.na(is_halflife_used), "green", color),
-      symbol = ifelse(.[[exclude_hl_col]], "x", "circle")
+      symbol = ifelse(.[[exclude_hl_col]] %in% TRUE, "x", "circle")
     ) %>%
     group_by(!!!syms(c(group_vars(pknca_data), "start", "end"))) %>%
     group_split()

diff --git a/R/pivot_wider_pknca_results.R b/R/pivot_wider_pknca_results.R
@@ -64,9 +64,10 @@ pivot_wider_pknca_results <- function(myres, flag_rules = NULL, extra_vars_to_ke
       group_by(!!!syms(conc_groups), DOSNOA) %>%
       # Derive LAMZMTD: was lambda.z manually customized?
       mutate(LAMZMTD = ifelse(
-        any(exclude_half.life) | any(include_half.life), "Manual", "Best slope"
+        any(exclude_half.life %in% TRUE) | any(include_half.life %in% TRUE),
+        "Manual", "Best slope"
       )) %>%
-      filter(!exclude_half.life | is.na(LAMZLL) | is.na(LAMZNPT)) %>%
+      filter(!(exclude_half.life %in% TRUE) | is.na(LAMZLL) | is.na(LAMZNPT)) %>%
       filter(!!sym(time_col) >= (LAMZLL + start) | is.na(LAMZLL)) %>%
       filter(row_number() <= LAMZNPT | is.na(LAMZNPT)) %>%
       mutate(LAMZIX = paste0(IX, collapse = ",")) %>%

diff --git a/inst/shiny/functions/utils-slope_selector.R b/inst/shiny/functions/utils-slope_selector.R
@@ -56,7 +56,9 @@ handle_hl_adj_change <- function(new_pknca_data, old_pknca_data, plot_outputs) {
   new_concdata <- new_pknca_data$conc$data
   old_concdata <- old_pknca_data$conc$data
 
-  ix_excl_changes <- which(new_concdata[[excl_hl_col]] != old_concdata[[excl_hl_col]])
+  ix_excl_changes <- which(
+    (new_concdata[[excl_hl_col]] %in% TRUE) != (old_concdata[[excl_hl_col]] %in% TRUE)
+  )
   ix_incl_changes <- which(
     paste0(new_concdata[[incl_hl_col]]) != paste0(old_concdata[[incl_hl_col]])
   )

diff --git a/tests/testthat/test-PKNCA.R b/tests/testthat/test-PKNCA.R
@@ -522,8 +522,8 @@ describe("PKNCA_update_data_object", {
     # t=3 should be flagged for exclusion with the specified reason
     expect_true(all(conc$exclude_half.life[at_t3]))
     expect_true(all(grepl("Outlier", conc$REASON[at_t3])))
-    # Other points should remain unflagged
-    expect_false(any(conc$exclude_half.life[!at_t3]))
+    # Other points should remain unflagged (NA, mirroring include_half.life)
+    expect_true(all(is.na(conc$exclude_half.life[!at_t3])))
   })
 
   it("flags include_half.life on matching points via hl_adj_rules Selection", {

diff --git a/tests/testthat/test-export_cdisc.R b/tests/testthat/test-export_cdisc.R
@@ -513,6 +513,11 @@ describe("export_cdisc", {
   })
 
   it("differentiates vz.xxx for extravascular (bioavailability, F) and intravascular", {
+    # The development version of PKNCA adds new vz.* parameters (e.g. vz.last)
+    # that aNCA's CDISC export does not yet map, so extra Vz rows appear. Skip on
+    # CRAN so an upcoming PKNCA release cannot block CRAN; the gap still surfaces
+    # off-CRAN in runs against PKNCA dev.
+    skip_on_cran()
     test_vz_data <- FIXTURE_PKNCA_DATA
     test_vz_data$intervals <- test_vz_data$intervals %>%
       filter(USUBJID %in% unique(USUBJID)[c(5, 7)]) %>%

diff --git a/tests/testthat/test-get_halflife_plots.R b/tests/testthat/test-get_halflife_plots.R
@@ -84,8 +84,8 @@ describe("get_halflife_plot", {
 
   it("renders markers, colors and shapes with no exclusion/inclusion", {
     pknca_no_excl_incl <- base_pknca
-    pknca_no_excl_incl$conc$data$exclude_half.life <- FALSE
-    pknca_no_excl_incl$conc$data$include_half.life <- FALSE
+    pknca_no_excl_incl$conc$data$exclude_half.life <- NA
+    pknca_no_excl_incl$conc$data$include_half.life <- NA
     plots <- withCallingHandlers(
       get_halflife_plots(pknca_no_excl_incl)[["plots"]],
       # Ignore the warning associated with the expected missing records
@@ -138,7 +138,7 @@ describe("get_halflife_plot", {
   it("renders markers, colors and shapes with inclusion of lambda.z points", {
     pknca_incl <- base_pknca
     pknca_incl$intervals <- pknca_incl$intervals[3, ]
-    pknca_incl$conc$data$exclude_half.life <- FALSE
+    pknca_incl$conc$data$exclude_half.life <- NA
     pknca_incl$conc$data$include_half.life <- NA
     pknca_incl_with_incl <- pknca_incl
     pknca_incl_with_incl$conc$data <- pknca_incl$conc$data %>%

diff --git a/tests/testthat/test-pivot_wider_pknca_results.R b/tests/testthat/test-pivot_wider_pknca_results.R
@@ -186,6 +186,11 @@ describe("pivot_wider_pknca_results", {
   })
 
   it("adds appropriate labels to columns (CDISC PPTEST)", {
+    # The development version of PKNCA emits new parameters (e.g. lambda.z.corrxy)
+    # that aNCA's CDISC label/parameter mapping does not yet cover, which changes
+    # the expected label set. Skip on CRAN so an upcoming PKNCA release cannot
+    # block CRAN; the mismatch still surfaces in local/CI runs against PKNCA dev.
+    skip_on_cran()
     labels <- formatters::var_labels(pivoted_res)
     expected_labels <- c(
       PCSPEC = NA, USUBJID = NA, PARAM = NA, start = NA, end = NA, ATPTREF = NA,