Merge pull request #42 from nutriverse/dev

tidy up package

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools in R <img src="man/figures/logo.png" width="200px" align="right" />
 
 <!-- badges: start -->
-[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 [![R-CMD-check](https://github.com/nutriverse/sleacr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/sleacr/actions/workflows/R-CMD-check.yaml)
 [![test-coverage](https://github.com/nutriverse/sleacr/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/nutriverse/sleacr/actions/workflows/test-coverage.yaml)
@@ -27,9 +27,19 @@ knitr::opts_chunk$set(
 
 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. This package provides functions for use in conducting a SLEAC assessment.
 
+## What does the package do?
+
+The `{sleacr}` package provides functions that facilitate the design, sampling, data collection, and data analysis of a SLEAC survey. The current version of the `{sleacr}` package currently provides the following:
+
+* Functions to calculate the sample size needed for a SLEAC survey;
+
+* Functions to draw a stage 1 sample for a SLEAC survey;
+
+* Functions to determine the performance of chosen classifier cut-offs for analysis of SLEAC survey data.
+
 ## Installation
 
-The `sleacr` package is not yet available on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R Universe](https://nutriverse.r-universe.dev) as follows:
+The `{sleacr}` package is not yet available on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R Universe](https://nutriverse.r-universe.dev) as follows:
 
 ```{r install, echo = TRUE, eval = FALSE}
 install.packages(
@@ -38,19 +48,9 @@ install.packages(
 )
 ```
 
-## What does `sleacr` do?
-
-The `sleacr` package provides functions that facilitate the design, sampling, data collection, and data analysis of a SLEAC survey. The current version of the `sleacr` package currently provides the following:
-
-* Functions to calculate the sample size needed for a SLEAC survey;
-
-* Functions to draw a stage 1 sample for a SLEAC survey;
-
-* Functions to determine the performance of chosen classifier cut-offs for analysis of SLEAC survey data.
-
 ## Citation
 
-If you find the `sleacr` package useful, please cite using the suggested citation provided by a call to the `citation` function as follows:
+If you use `{sleacr}` in your work, please cite using the suggested citation provided by a call to the `citation` function as follows:
 
 ```{r cite}
 citation("sleacr")

README.md

@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-[![Project Status: WIP – Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
-public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 [![R-CMD-check](https://github.com/nutriverse/sleacr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/sleacr/actions/workflows/R-CMD-check.yaml)
@@ -31,9 +31,23 @@ 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 SLEAC assessment.
 
+## What does the package do?
+
+The `{sleacr}` package provides functions that facilitate the design,
+sampling, data collection, and data analysis of a SLEAC survey. The
+current version of the `{sleacr}` package currently provides the
+following:
+
+  - Functions to calculate the sample size needed for a SLEAC survey;
+
+  - Functions to draw a stage 1 sample for a SLEAC survey;
+
+  - Functions to determine the performance of chosen classifier cut-offs
+    for analysis of SLEAC survey data.
+
 ## Installation
 
-The `sleacr` package is not yet available on
+The `{sleacr}` package is not yet available on
 [CRAN](https://cran.r-project.org) but can be installed from the
 [nutriverse R Universe](https://nutriverse.r-universe.dev) as follows:
 
@@ -44,43 +58,32 @@ install.packages(
 )
 ```
 
-## What does `sleacr` do?
-
-The `sleacr` package provides functions that facilitate the design,
-sampling, data collection, and data analysis of a SLEAC survey. The
-current version of the `sleacr` package currently provides the
-following:
-
-  - Functions to calculate the sample size needed for a SLEAC survey;
-
-  - Functions to draw a stage 1 sample for a SLEAC survey;
-
-  - Functions to determine the performance of chosen classifier cut-offs
-    for analysis of SLEAC survey data.
-
 ## Citation
 
-If you find the `sleacr` package useful, please cite using the suggested
+If you use `{sleacr}` in your work, please cite using the suggested
 citation provided by a call to the `citation` function as follows:
 
 ``` r
 citation("sleacr")
 #> To cite sleacr in publications use:
 #> 
-#>   Ernest Guevarra (2023). sleacr: Simplified Lot Quality
+#>   Mark Myatt, Ernest Guevarra, Lionella Fieschi, Allison
+#>   Norris, Saul Guerrero, Lilly Schofield, Daniel Jones, Ephrem
+#>   Emru, Kate Sadler (2012). _Semi-Quantitative Evaluation of
+#>   Access and Coverage (SQUEAC)/Simplified Lot Quality
 #>   Assurance Sampling Evaluation of Access and Coverage (SLEAC)
-#>   Tools in R R package version 0.0.0.9000 URL
-#>   https://nutriverse.io/sleacr/ DOI 10.5281/zenodo.7510932
+#>   Technical Reference_.
+#>   <https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools in R},
-#>     author = {{Ernest Guevarra}},
-#>     year = {2023},
-#>     note = {R package version 0.0.0.9000},
-#>     url = {https://nutriverse.io/sleacr/},
-#>     doi = {10.5281/zenodo.7510932},
+#>     title = {Semi-Quantitative Evaluation of Access and Coverage ({SQUEAC})/Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage ({SLEAC}) Technical Reference},
+#>     author = {{Mark Myatt} and {Ernest Guevarra} and {Lionella Fieschi} and {Allison Norris} and {Saul Guerrero} and {Lilly Schofield} and {Daniel Jones} and {Ephrem Emru} and {Kate Sadler}},
+#>     year = {2012},
+#>     publisher = {FHI 360/FANTA},
+#>     location = {Washington, DC},
+#>     url = {https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf},
 #>   }
 ```
 

inst/CITATION

@@ -1,18 +1,10 @@
-citHeader("To cite sleacr in publications use:")
-
-citEntry(
-  entry    = "Manual",
-  title    = "sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools in R",
-  author   = person("Ernest Guevarra"),
-  year     = "2023",
-  note     = "R package version 0.0.0.9000",
-  url      = "https://nutriverse.io/sleacr/",
-  doi      = "10.5281/zenodo.7510932",
-  textVersion = paste(
-    "Ernest Guevarra (2023).",
-    "sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools in R",
-    "R package version 0.0.0.9000",
-    "URL https://nutriverse.io/sleacr/",
-    "DOI 10.5281/zenodo.7510932"
-  )
-)
+bibentry(
+  bibtype   = "Manual",
+  header    = "To cite sleacr in publications use:",
+	title     = "Semi-Quantitative Evaluation of Access and Coverage ({SQUEAC})/Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage ({SLEAC}) Technical Reference",
+	author    = c(person("Mark Myatt"), person("Ernest Guevarra"), person("Lionella Fieschi"), person("Allison Norris"), person("Saul Guerrero"), person("Lilly Schofield"), person("Daniel Jones"), person("Ephrem Emru"), person("Kate Sadler")),
+  year      = "2012",
+  publisher = "FHI 360/FANTA",
+  location  = "Washington, DC",
+	url       = "https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf"
+)

vignettes/sleacr.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Introduction"
+title: "Introduction to sleacr"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Introduction}