refresh repository in preparation for CRAN submission

.Rbuildignore

@@ -12,3 +12,4 @@
 ^pkgdown$
 ^CODE_OF_CONDUCT\.md$
 ^README\.html$
+^CITATION\.cff$

.github/FUNDING.yml

@@ -3,7 +3,7 @@
 github: ernestguevarra
 patreon: # ernestguevarra
 open_collective: # Replace with a single Open Collective username
-ko_fi: # Replace with a single Ko-fi username
+ko_fi: ernestguevarra
 tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
 community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
 liberapay: # Replace with a single Liberapay username

.github/workflows/mirror-codeberg.yaml

@@ -0,0 +1,19 @@
+name: Mirror to other git server
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+jobs:
+  mirror:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: yesolutions/mirror-action@master
+        with:
+          REMOTE: https://codeberg.org/nutriverse/squeacr
+          GIT_USERNAME: ${{ secrets.CODEBERG_USERNAME }}
+          GIT_PASSWORD: ${{ secrets.CODEBERG_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -34,15 +34,16 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
-          file: ./cobertura.xml
-          plugin: noop
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
 

CITATION.cff

@@ -0,0 +1,259 @@
+# --------------------------------------------
+# CITATION file created with {cffr} R package
+# See also: https://docs.ropensci.org/cffr/
+# --------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "squeacr" in publications use:'
+type: software
+license: GPL-3.0-only
+title: 'squeacr: Semi-Quantitative Evaluation of Access and Coverage (SQUEAC) Tools'
+version: 0.1.1
+doi: 10.5281/zenodo.7509665
+abstract: In the recent past, measurement of coverage has been mainly through two-stage
+  cluster sampled surveys either as part of a nutrition assessment or through a specific
+  coverage survey known as Centric Systematic Area Sampling (CSAS). However, such
+  methods are resource intensive and often only used for final programme evaluation
+  meaning results arrive too late for programme adaptation. SQUEAC, which stands for
+  Semi-Quantitative Evaluation of Access and Coverage, is a low resource method designed
+  specifically to address this limitation and is used regularly for monitoring, planning
+  and importantly, timely improvement to programme quality, both for agency and Ministry
+  of Health (MoH) led programmes. This package provides functions for use in conducting
+  a SQUEAC investigation.
+authors:
+- family-names: Guevarra
+  given-names: Ernest
+  email: ernest@guevarra.io
+  orcid: https://orcid.org/0000-0002-4887-4415
+preferred-citation:
+  type: manual
+  title: 'squeacr: Semi-Quantitative Evaluation of Access and Coverage (SQUEAC) Tools'
+  authors:
+  - name: Ernest Guevarra
+  - name: Mark Myatt
+  year: '2026'
+  notes: R package version 0.1.1
+  url: https://nutriverse.io/squeacr/
+  doi: 10.5281/zenodo.7509665
+repository-code: https://github.com/nutriverse/squeacr
+url: https://nutriverse.io/squeacr/
+contact:
+- family-names: Guevarra
+  given-names: Ernest
+  email: ernest@guevarra.io
+  orcid: https://orcid.org/0000-0002-4887-4415
+keywords:
+- acute-malnutrition
+- cmam
+- coverage
+- rstats
+- squeac
+- survey
+- wasting
+references:
+- type: book
+  title: Semi-Quantitative Evaluation of Access and Coverage (SQUEAC)/Simplified Lot
+    Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Technical
+    Reference
+  authors:
+  - name: Mark Myatt
+  - name: Ernest Guevarra
+  - name: Lionella Fieschi
+  - name: Allison Norris
+  - name: Saul Guerrero
+  - name: Lilly Schofield
+  - name: Daniel Jones
+  - name: Ephrem Emru
+  - name: Kate Sadler
+  year: '2012'
+  publisher:
+    name: FHI 360/FANTA
+    address: Washington, DC
+- type: software
+  title: 'R: A Language and Environment for Statistical Computing'
+  notes: Depends
+  url: https://www.R-project.org/
+  authors:
+  - name: R Core Team
+  institution:
+    name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2026'
+  version: '>= 2.10'
+- type: software
+  title: tibble
+  abstract: 'tibble: Simple Data Frames'
+  notes: Imports
+  url: https://tibble.tidyverse.org/
+  repository: https://CRAN.R-project.org/package=tibble
+  authors:
+  - family-names: Müller
+    given-names: Kirill
+    email: kirill@cynkra.com
+    orcid: https://orcid.org/0000-0002-1416-3412
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.tibble
+- type: software
+  title: zoo
+  abstract: 'zoo: S3 Infrastructure for Regular and Irregular Time Series (Z''s Ordered
+    Observations)'
+  notes: Imports
+  url: https://zoo.R-Forge.R-project.org/
+  repository: https://CRAN.R-project.org/package=zoo
+  authors:
+  - family-names: Zeileis
+    given-names: Achim
+    email: Achim.Zeileis@R-project.org
+    orcid: https://orcid.org/0000-0003-0918-3766
+  - family-names: Grothendieck
+    given-names: Gabor
+    email: ggrothendieck@gmail.com
+  - family-names: Ryan
+    given-names: Jeffrey A.
+    email: jeff.a.ryan@gmail.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.zoo
+- type: software
+  title: knitr
+  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
+  notes: Suggests
+  url: https://yihui.org/knitr/
+  repository: https://CRAN.R-project.org/package=knitr
+  authors:
+  - family-names: Xie
+    given-names: Yihui
+    email: xie@yihui.name
+    orcid: https://orcid.org/0000-0003-0645-5666
+  year: '2026'
+  doi: 10.32614/CRAN.package.knitr
+- type: software
+  title: rmarkdown
+  abstract: 'rmarkdown: Dynamic Documents for R'
+  notes: Suggests
+  url: https://pkgs.rstudio.com/rmarkdown/
+  repository: https://CRAN.R-project.org/package=rmarkdown
+  authors:
+  - family-names: Allaire
+    given-names: JJ
+    email: jj@posit.co
+  - family-names: Xie
+    given-names: Yihui
+    email: xie@yihui.name
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Dervieux
+    given-names: Christophe
+    email: cderv@posit.co
+    orcid: https://orcid.org/0000-0003-4474-2498
+  - family-names: McPherson
+    given-names: Jonathan
+    email: jonathan@posit.co
+  - family-names: Luraschi
+    given-names: Javier
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevin@posit.co
+  - family-names: Atkins
+    given-names: Aron
+    email: aron@posit.co
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Cheng
+    given-names: Joe
+    email: joe@posit.co
+  - family-names: Chang
+    given-names: Winston
+    email: winston@posit.co
+  - family-names: Iannone
+    given-names: Richard
+    email: rich@posit.co
+    orcid: https://orcid.org/0000-0003-3925-190X
+  year: '2026'
+  doi: 10.32614/CRAN.package.rmarkdown
+- type: software
+  title: testthat
+  abstract: 'testthat: Unit Testing for R'
+  notes: Suggests
+  url: https://testthat.r-lib.org
+  repository: https://CRAN.R-project.org/package=testthat
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  year: '2026'
+  doi: 10.32614/CRAN.package.testthat
+  version: '>= 3.0.0'
+- type: software
+  title: covr
+  abstract: 'covr: Test Coverage for Packages'
+  notes: Suggests
+  url: https://covr.r-lib.org
+  repository: https://CRAN.R-project.org/package=covr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+    email: james.f.hester@gmail.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.covr
+- type: software
+  title: spelling
+  abstract: 'spelling: Tools for Spell Checking in R'
+  notes: Suggests
+  url: https://ropensci.r-universe.dev/spelling
+  repository: https://CRAN.R-project.org/package=spelling
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroenooms@gmail.com
+    orcid: https://orcid.org/0000-0002-4035-0289
+  - family-names: Hester
+    given-names: Jim
+    email: james.hester@rstudio.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.spelling
+- type: software
+  title: readxl
+  abstract: 'readxl: Read Excel Files'
+  notes: Suggests
+  url: https://readxl.tidyverse.org
+  repository: https://CRAN.R-project.org/package=readxl
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+    orcid: https://orcid.org/0000-0003-4757-117X
+  - family-names: Bryan
+    given-names: Jennifer
+    email: jenny@posit.co
+    orcid: https://orcid.org/0000-0002-6983-2759
+  year: '2026'
+  doi: 10.32614/CRAN.package.readxl
+- type: software
+  title: dplyr
+  abstract: 'dplyr: A Grammar of Data Manipulation'
+  notes: Suggests
+  url: https://dplyr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=dplyr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+    orcid: https://orcid.org/0000-0003-4757-117X
+  - family-names: François
+    given-names: Romain
+    orcid: https://orcid.org/0000-0002-2444-4226
+  - family-names: Henry
+    given-names: Lionel
+  - family-names: Müller
+    given-names: Kirill
+    orcid: https://orcid.org/0000-0002-1416-3412
+  - family-names: Vaughan
+    given-names: Davis
+    email: davis@posit.co
+    orcid: https://orcid.org/0000-0003-4777-038X
+  year: '2026'
+  doi: 10.32614/CRAN.package.dplyr
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: squeacr
 Type: Package
 Title: Semi-Quantitative Evaluation of Access and Coverage (SQUEAC) Tools
-Version: 0.1.0.9000
+Version: 0.1.1
 Authors@R: person(given = "Ernest", 
                   family = "Guevarra", 
                   comment = c(ORCID = "0000-0002-4887-4415"), 
@@ -36,7 +36,7 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 URL: https://nutriverse.io/squeacr/, https://github.com/nutriverse/squeacr
 BugReports: https://github.com/nutriverse/squeacr/issues