nutriverse · ernestguevarra · Dec 24, 2020 · Aug 8, 2022 · Aug 8, 2022 · Aug 8, 2022
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: zscorer
 Type: Package
-Title: Child Anthropometry z-Score Calculator
+Title: Child Anthropometry Z-Score Calculator
 Version: 0.3.1.9000
 Authors@R: c(
     person("Mark", "Myatt", email = "mark@brixtonhealth.com",
@@ -9,11 +9,11 @@ Authors@R: c(
     person("Ernest", "Guevarra", 
            comment = c(ORCID = "0000-0002-4887-4415"), 
            email = "ernestgmd@gmail.com", role = c("aut", "cre")))
-Description: A tool for calculating z-scores and centiles for weight-for-age, 
-    length/height-for-age, weight-for-length/height, BMI-for-age, 
-    head circumference-for-age, age circumference-for-age, 
-    subscapular skinfold-for-age, triceps skinfold-for-age based on the 
-    WHO Child Growth Standards. 
+Description: A tool for calculating z-scores for weight-for-age, 
+    length/height-for-age, weight-for-length/height, BMI-for-age, head 
+    circumference-for-age, age circumference-for-age, subscapular 
+    skinfold-for-age, triceps skinfold-for-age based on various growth
+    standards. 
 Depends: R (>= 2.10)
 Imports: 
    shiny
@@ -28,8 +28,8 @@ License: AGPL-3
 Encoding: UTF-8
 LazyData: true
 Language: en-GB
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)
-URL: https://nutriverse/zscorer/, https://github.com/nutriverse/zscorer
+URL: https://nutriverse.io/zscorer/, https://github.com/nutriverse/zscorer
 BugReports: https://github.com/nutriverse/zscorer/issues
 VignetteBuilder: knitr
diff --git a/README.Rmd b/README.Rmd
@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
   fig.path = "man/figures/README-")
 ```
 
-# zscorer: Anthropometric z-score Calculator <img src="man/figures/logo.png" width="200" align="right" />
+# zscorer: Anthropometric Z-Score Calculator <img src="man/figures/logo.png" width="200" align="right" />
 
 <!-- badges: start -->
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
@@ -22,14 +22,14 @@ knitr::opts_chunk$set(
 [![CRAN](https://img.shields.io/cran/l/zscorer.svg)](https://CRAN.R-project.org/package=zscorer)
 [![CRAN](http://cranlogs.r-pkg.org/badges/zscorer)](https://CRAN.R-project.org/package=zscorer)
 [![CRAN](http://cranlogs.r-pkg.org/badges/grand-total/zscorer)](https://CRAN.R-project.org/package=zscorer)
-[![R-CMD-check](https://github.com/nutriverse/zscorer/workflows/R-CMD-check/badge.svg)](https://github.com/nutriverse/zscorer/actions)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/nutriverse/zscorer?branch=master&svg=true)](https://ci.appveyor.com/project/nutriverse/zscorer)
+[![R-CMD-check](https://github.com/nutriverse/zscorer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/zscorer/actions/workflows/R-CMD-check.yaml)
 [![test-coverage](https://github.com/nutriverse/zscorer/workflows/test-coverage/badge.svg)](https://github.com/nutriverse/zscorer/actions)
 [![Codecov test coverage](https://codecov.io/gh/nutriverse/zscorer/branch/master/graph/badge.svg)](https://codecov.io/gh/nutriverse/zscorer?branch=master)
 [![DOI](https://zenodo.org/badge/119683584.svg)](https://zenodo.org/badge/latestdoi/119683584)
 [![CodeFactor](https://www.codefactor.io/repository/github/nutriverse/zscorer/badge)](https://www.codefactor.io/repository/github/nutriverse/zscorer)
 <!-- badges: end -->
 
+Nutritional status, especially in children, has been widely assessed using anthropometric measures in both developing and developed countries. Once a childs' anthropometry has been correctly measured and their age has been recorded, their growth and nutritional status can be assessed using a standardised age- and sex-specific growth reference to calculate z-scores. These z-scores express anthropometric measurements as several standard deviations (SDs) below or above the reference mean or median value. The calculation of anthropometric z-scores is one of the most widely-used analytical technique used in nutrition surveys and nutrition research.
 
 ## What does `zscorer` do?
 

diff --git a/README.md b/README.md
@@ -1,62 +1,71 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# zscorer: Anthropometric z-score Calculator <img src="man/figures/logo.png" width="200" align="right" />
+# zscorer: Anthropometric Z-Score Calculator <img src="man/figures/logo.png" width="200" align="right" />
 
 <!-- badges: start -->
 
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/zscorer)](https://cran.r-project.org/package=zscorer)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/zscorer)](https://cran.r-project.org/package=zscorer)
 [![CRAN](https://img.shields.io/cran/l/zscorer.svg)](https://CRAN.R-project.org/package=zscorer)
 [![CRAN](http://cranlogs.r-pkg.org/badges/zscorer)](https://CRAN.R-project.org/package=zscorer)
 [![CRAN](http://cranlogs.r-pkg.org/badges/grand-total/zscorer)](https://CRAN.R-project.org/package=zscorer)
-[![R-CMD-check](https://github.com/nutriverse/zscorer/workflows/R-CMD-check/badge.svg)](https://github.com/nutriverse/zscorer/actions)
-[![AppVeyor Build
-Status](https://ci.appveyor.com/api/projects/status/github/nutriverse/zscorer?branch=master&svg=true)](https://ci.appveyor.com/project/nutriverse/zscorer)
+[![R-CMD-check](https://github.com/nutriverse/zscorer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/zscorer/actions/workflows/R-CMD-check.yaml)
 [![test-coverage](https://github.com/nutriverse/zscorer/workflows/test-coverage/badge.svg)](https://github.com/nutriverse/zscorer/actions)
 [![Codecov test
 coverage](https://codecov.io/gh/nutriverse/zscorer/branch/master/graph/badge.svg)](https://codecov.io/gh/nutriverse/zscorer?branch=master)
 [![DOI](https://zenodo.org/badge/119683584.svg)](https://zenodo.org/badge/latestdoi/119683584)
 [![CodeFactor](https://www.codefactor.io/repository/github/nutriverse/zscorer/badge)](https://www.codefactor.io/repository/github/nutriverse/zscorer)
 <!-- badges: end -->
 
+Nutritional status, especially in children, has been widely assessed
+using anthropometric measures in both developing and developed
+countries. Once a childs’ anthropometry has been correctly measured and
+their age has been recorded, their growth and nutritional status can be
+assessed using a standardised age- and sex-specific growth reference to
+calculate z-scores. These z-scores express anthropometric measurements
+as several standard deviations (SDs) below or above the reference mean
+or median value. The calculation of anthropometric z-scores is one of
+the most widely-used analytical technique used in nutrition surveys and
+nutrition research.
+
 ## What does `zscorer` do?
 
 The `zscorer` packages facilitates the calculation of a range of
 anthropometric *z-scores* (i.e. the number of standard deviations from
 the mean) and adds them to survey data:
 
-  - **Weight-for-length (wfl)** z-scores for children with lengths
+-   **Weight-for-length (wfl)** z-scores for children with lengths
     between 45 and 110 cm
 
-  - **Weight-for-height (wfh)** z-scores for children with heights
+-   **Weight-for-height (wfh)** z-scores for children with heights
     between 65 and 120 cm
 
-  - **Length-for-age (lfa)** z-scores for children aged less than 24
+-   **Length-for-age (lfa)** z-scores for children aged less than 24
     months
 
-  - **Height-for-age (hfa)** z-scores for children aged between 24 and
+-   **Height-for-age (hfa)** z-scores for children aged between 24 and
     228 months
 
-  - **Weight-for-age (wfa)** z-scores for children aged between zero and
+-   **Weight-for-age (wfa)** z-scores for children aged between zero and
     120 months
 
-  - **Body mass index-for-age (bfa)** z-scores for children aged between
+-   **Body mass index-for-age (bfa)** z-scores for children aged between
     zero and 228 months
 
-  - **MUAC-for-age (mfa)** z-scores for children aged between 3 and 228
+-   **MUAC-for-age (mfa)** z-scores for children aged between 3 and 228
     months
 
-  - **Triceps skinfold-for-age (tsa)** z-scores for children aged
+-   **Triceps skinfold-for-age (tsa)** z-scores for children aged
     between 3 and 60 months
 
-  - **Sub-scapular skinfold-for-age (ssa)** z-scores for children aged
+-   **Sub-scapular skinfold-for-age (ssa)** z-scores for children aged
     between 3 and 60 months
 
-  - **Head circumference-for-age (hca)** z-scores for children aged
+-   **Head circumference-for-age (hca)** z-scores for children aged
     between zero and 60 months
 
 The *z-scores* are calculated using the **WHO Child Growth
@@ -164,7 +173,7 @@ z-scores. These rules are described in the table below.
 
 
 | **index**  | **standing** | **age**     | **height**       | **Action**                           |
-| ---------- | ------------ | ----------- | ---------------- | ------------------------------------ |
+|------------|--------------|-------------|------------------|--------------------------------------|
 | hfa or lfa | standing     | \< 731 days |                  | index = lfa height = height + 0.7 cm |
 | hfa or lfa | supine       | \< 731 days |                  | index = lfa                          |
 | hfa or lfa | unknown      | \< 731 days |                  | index = lfa                          |
@@ -190,7 +199,7 @@ Error conditions are listed in the table below.
 
 
 | **Error condition**                               | **Action**                                                                 |
-| ------------------------------------------------- | -------------------------------------------------------------------------- |
+|---------------------------------------------------|----------------------------------------------------------------------------|
 | Missing or nonsense value in `standing` parameter | Set `standing` to `3` (unknown) and apply appropriate height or age rules. |
 | Unknown `index` specified                         | Return **NA** for z-score.                                                 |
 | Missing `sex`                                     | Return **NA** for z-score.                                                 |
@@ -522,7 +531,7 @@ run_zscorer()
 This will initiate the Shiny app using the installed web browser in your
 current device as shown below:
 
-<img src="man/figures/zscorerApp.png" width="2450" />
+![](man/figures/zscorerApp.png)<!-- -->
 
 ## Citation
 
@@ -534,16 +543,18 @@ citation("zscorer")
 #> 
 #> To cite package 'zscorer' in publications use:
 #> 
-#>   Mark Myatt and Ernest Guevarra (NA). zscorer: Child Anthropometry
-#>   z-Score Calculator. https://nutriverse/zscorer/,
-#>   https://github.com/nutriverse/zscorer.
+#>   Myatt M, Guevarra E (2019). _zscorer: Child Anthropometry z-Score
+#>   Calculator_. R package version 0.3.1,
+#>   <https://CRAN.R-project.org/package=zscorer>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {zscorer: Child Anthropometry z-Score Calculator},
 #>     author = {Mark Myatt and Ernest Guevarra},
-#>     note = {https://nutriverse/zscorer/, https://github.com/nutriverse/zscorer},
+#>     year = {2019},
+#>     note = {R package version 0.3.1},
+#>     url = {https://CRAN.R-project.org/package=zscorer},
 #>   }
 ```
 

diff --git a/appveyor.yml b/appveyor.yml