Merge pull request #82 from nutriverse:dev

create post-stratification estimator; fix #71; fix #81

.Rbuildignore

@@ -14,3 +14,4 @@
 ^README\.html$
 ^LICENSE\.md$
 ^vignettes/articles$
+^CITATION\.cff$

CITATION.cff

@@ -0,0 +1,217 @@
+# --------------------------------------------
+# CITATION file created with {cffr} R package
+# See also: https://docs.ropensci.org/cffr/
+# --------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "sleacr" in publications use:'
+type: software
+license: GPL-3.0-or-later
+title: 'sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and
+  Coverage (SLEAC) Tools'
+version: 0.1.0.9000
+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. SLEAC, which stands for
+  Simplified Lot Quality Assurance Sampling 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. SLEAC is designed
+  to complement the Semi-quantitative Evaluation of Access and Coverage (SQUEAC) method.
+  This package provides functions for use in conducting a SLEAC assessment.
+authors:
+- family-names: Guevarra
+  given-names: Ernest
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-4887-4415
+- family-names: Myatt
+  given-names: Mark
+  email: [email protected]
+  orcid: https://orcid.org/0000-0003-1119-1474
+preferred-citation:
+  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
+  url: https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf
+repository-code: https://github.com/nutriverse/sleacr
+url: https://nutriverse.io/sleacr/
+contact:
+- family-names: Guevarra
+  given-names: Ernest
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-4887-4415
+keywords:
+- cmam
+- coverage
+- rstats
+- sleac
+references:
+- 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: '2025'
+  version: '>= 4.1.0'
+- type: software
+  title: parallel
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  institution:
+    name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2025'
+- type: software
+  title: parallelly
+  abstract: 'parallelly: Enhancing the ''parallel'' Package'
+  notes: Imports
+  url: https://parallelly.futureverse.org
+  repository: https://CRAN.R-project.org/package=parallelly
+  authors:
+  - family-names: Bengtsson
+    given-names: Henrik
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-7579-5165
+  year: '2025'
+  doi: 10.32614/CRAN.package.parallelly
+- 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: [email protected]
+  year: '2025'
+  doi: 10.32614/CRAN.package.covr
+- 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: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  year: '2025'
+  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: [email protected]
+  - family-names: Xie
+    given-names: Yihui
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Dervieux
+    given-names: Christophe
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4474-2498
+  - family-names: McPherson
+    given-names: Jonathan
+    email: [email protected]
+  - family-names: Luraschi
+    given-names: Javier
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Atkins
+    given-names: Aron
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Cheng
+    given-names: Joe
+    email: [email protected]
+  - family-names: Chang
+    given-names: Winston
+    email: [email protected]
+  - family-names: Iannone
+    given-names: Richard
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-3925-190X
+  year: '2025'
+  doi: 10.32614/CRAN.package.rmarkdown
+- 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: [email protected]
+    orcid: https://orcid.org/0000-0002-4035-0289
+  - family-names: Hester
+    given-names: Jim
+    email: [email protected]
+  year: '2025'
+  identifiers:
+  - type: url
+    value: https://docs.ropensci.org/spelling/
+  doi: 10.32614/CRAN.package.spelling
+- 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: [email protected]
+  year: '2025'
+  doi: 10.32614/CRAN.package.testthat
+  version: '>= 3.0.0'
+- type: software
+  title: tibble
+  abstract: 'tibble: Simple Data Frames'
+  notes: Suggests
+  url: https://tibble.tidyverse.org/
+  repository: https://CRAN.R-project.org/package=tibble
+  authors:
+  - family-names: Müller
+    given-names: Kirill
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-1416-3412
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2025'
+  doi: 10.32614/CRAN.package.tibble
+

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sleacr
 Type: Package
 Title: Simplified Lot Quality Assurance Sampling Evaluation of Access and 
     Coverage (SLEAC) Tools
-Version: 0.0.0.9000
+Version: 0.1.0.9000
 Authors@R: c(
     person("Ernest", "Guevarra", 
            comment = c(ORCID = "0000-0002-4887-4415"), 
@@ -12,29 +12,36 @@ Authors@R: c(
            comment = c(ORCID = "0000-0003-1119-1474"),
            email = "[email protected]", 
            role = c("aut", "cph")))
-Description: 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. SLEAC, which stands for Simplified Lot Quality 
-    Assurance Sampling 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. SLEAC is designed to complement the Semi-quantitative Evaluation 
-    of Access and Coverage (SQUEAC) method. This package provides functions for 
+Description: 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. SLEAC, which stands for Simplified Lot Quality
+    Assurance Sampling 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. SLEAC is designed to complement the Semi-quantitative Evaluation
+    of Access and Coverage (SQUEAC) method. This package provides functions for
     use in conducting a SLEAC assessment.
 License: GPL (>= 3)
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1.0)
+Imports: 
+    cli,
+    parallel,
+    parallelly,
+    squeacr
 Suggests: 
     covr,
     knitr,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0),
     tibble
+Remotes:
+    rapidsurveys/squeacr
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
@@ -44,6 +51,3 @@ URL: https://nutriverse.io/sleacr/,https://github.com/nutriverse/sleacr
 BugReports: https://github.com/nutriverse/sleacr/issues
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Imports: 
-    parallel,
-    parallelly

NAMESPACE

@@ -2,6 +2,8 @@
 
 S3method(plot,lqasSim)
 S3method(print,lqasClass)
+export(estimate_coverage)
+export(estimate_coverage_overall)
 export(get_n_cases)
 export(get_n_clusters)
 export(get_sample_d)
@@ -16,6 +18,7 @@ export(lqas_simulate_population)
 export(lqas_simulate_run)
 export(lqas_simulate_runs)
 export(lqas_simulate_test)
+importFrom(cli,cli_abort)
 importFrom(graphics,abline)
 importFrom(graphics,legend)
 importFrom(graphics,lines)

R/03-classify_coverage.R

@@ -23,7 +23,10 @@
 #'
 #' @examples
 #' lqas_classify_coverage(n = 6, n_total = 40)
-#' with(survey_data, lqas_classify_coverage(n = in_cases, n_total = n))
+#' with(
+#'   survey_data,
+#'   lqas_classify_coverage(n = cases_in, n_total = cases_total)
+#' )
 #'
 #' @export
 #' @rdname lqas_classify

R/04-test_classifier.R

@@ -181,7 +181,7 @@ lqas_simulate_runs <- function(pop,
     dUpper = dUpper,
     mc.cores = cores
   ) |>
-    (\(x) do.call(rbind, x))()
+    do.call(rbind, args = _)
 
   ## Return result ----
   result
@@ -218,7 +218,7 @@ lqas_simulate_test <- function(pop,
     dUpper = dUpper,
     mc.cores = cores
   ) |>
-    (\(x) do.call(rbind, x))()
+    do.call(rbind, args = _)
 
   ## concatenate parameters and results
   x <- list(x, dLower, dUpper, pLower = pLower, pUpper = pUpper)