Merge pull request #12 from OxfordIHTM/dev

spell check and create utils functions

Author: ernestguevarra

.github/CONTRIBUTING.md

@@ -0,0 +1,35 @@
+# Contributing
+
+## Bugs
+
+* Submit an issue on the [issues page](https://github.com/OxfordIHTM/codeditr/issues)
+
+## Code contributions
+
+* Fork this repository to your Github account
+
+* Clone your version on your account down to your machine from your account 
+
+```
+git clone https://github.com/<yourgithubusername>/codeditr.git
+```
+
+* Make sure to track progress upstream i.e., on our version of `codeditr` 
+at `OxfordIHTM/codeditr`, by doing 
+
+```
+git remote add upstream https://github.com/OxfordIHTM/codeditr.git
+```
+
+* Before making changes make sure to pull changes in from `upstream` by doing 
+either `git fetch upstream` then merge later or `git pull upstream` to fetch 
+and merge in one step
+
+* Make your changes on a new feature branch
+
+* Please write a test or tests for your changes if they affect code and not just 
+documentation
+
+* Push up changes to your account
+
+* Submit a pull request at `OxfordIHTM/codeditr`

.github/workflows/R-CMD-check.yaml

@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -39,7 +39,7 @@ jobs:
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results

DESCRIPTION

@@ -1,27 +1,31 @@
 Package: codeditr
 Type: Package
-Title: Implementing Basic Checks on Cause-of-Death Data Based on World Health 
-    Organization's CoDEdit Tool 
+Title: Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool 
 Version: 0.0.0.9000
 Authors@R: c(
-    person("Anita", "Makori", email = "mark@brixtonhealth.com",
-           role = c("aut", "cph")),
+    person("Anita", "Makori", role = c("aut", "cph")),
     person("Ernest", "Guevarra", 
            comment = c(ORCID = "0000-0002-4887-4415"), 
-           email = "ernest@guevarra.io", role = c("aut", "cre", "cph")))
+           email = "ernest@guevarra.io", role = c("aut", "cre", "cph")),
+    person("Sanjeev", "Pugazhendhi", role = c("ths", "rev")),
+    person("Williams", "Udoh Ituen-Umanah", role = "rev"),
+    person("Proochista", "Ariana", role = c("rev", "cph")))
 Description: The World Health Organization's CoDEdit electronic tool is intended 
     to help producers of cause-of-death statistics in strengthening their 
     capacity to perform routine checks on their data. This package ports the
-    original tool built using Microsoft Acess into R so as to leverage the
+    original tool built using Microsoft Access into R so as to leverage the
     utility and function of the original tool into a usable application
     program interface that can be used for building more universal tools or for
     creating programmatic scientific workflows aimed at routine, automated, and
     large-scale monitoring of cause-of-death data.
 License: GPL (>= 3)
 Depends: 
     R (>= 2.10)
+Suggests:
+    covr,
+    spelling
 Encoding: UTF-8
+Language: en-GB
 LazyData: true
-RoxygenNote: 7.2.3
-Suggests: 
-    covr
+RoxygenNote: 7.3.1
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,2 +1,3 @@
 # Generated by roxygen2: do not edit by hand
 
+export(get_age_values)

R/codeditr-package.R

@@ -0,0 +1,17 @@
+#'
+#' Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool
+#'
+#' The World Health Organization's CoDEdit electronic tool is intended to help
+#' producers of cause-of-death statistics in strengthening their capacity to
+#' perform routine checks on their data. This package ports the original tool
+#' built using Microsoft Access into R so as to leverage the utility and
+#' function of the original tool into a usable application program interface
+#' that can be used for building more universal tools or for creating
+#' programmatic scientific workflows aimed at routine, automated, and
+#' large-scale monitoring of cause-of-death data quality.
+#'
+#' @docType package
+#' @keywords internal
+#' @name codeditr
+#'
+"_PACKAGE"

R/codeditr.R

@@ -0,0 +1,53 @@
+#'
+#' Get various age values for all three age types
+#'
+#' @param age_value An integer value for the age
+#' @param age_type The age type of the specified age value. Can be either
+#'   *"D"* for day, *"M"* for month, or *"Y"* for year.
+#'
+#' @returns A named list of age values in days, months, and years.
+#'
+#' @examples
+#' get_age_values(1, "Y")
+#'
+#' @rdname get_age
+#' @export
+#'
+
+get_age_values <- function(age_value, age_type = c("D", "M", "Y")) {
+  if (age_value > 100 & age_type == "Y")
+    warning(
+      "Age value of greater than 100 for age type `year` has been provided. Please double check that these are correct inputs."
+    )
+
+  if (age_value > 31 & age_type == "D")
+    warning(
+      "Age value of greater than 31 for age type `day` has been provided. Please double check that these are correct inputs."
+    )
+
+  if (age_value > 12 & age_type == "M")
+    warning(
+      "Age value of greater than 12 for age type `month` has been provided. Please double check that these are correct inputs."
+    )
+
+  if (age_type == "D")
+    list(
+      days = age_value,
+      months = age_value / (365.25 / 12),
+      years = age_value / 365.25
+    )
+
+  if (age_type == "M")
+    list(
+      days = age_value * (365.25 / 12),
+      months = age_value,
+      years = age_value / 12
+    )
+
+  if (age_type == "Y")
+    list(
+      days = age_value * 365.25,
+      months = age_value * 12,
+      years = age_value
+    )
+}

R/utils.R

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# codeditr: Implementing Basic Checks on Cause-of-Death Data Based on World Health Organization's CoDEdit Tool <img src='man/figures/logo.png' width='200px' align='right' />
+# codeditr: Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool <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)
@@ -22,23 +22,23 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/OxfordIHTM/codeditr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codeditr?branch=main)
 <!-- badges: end -->
 
-The [World Health Organization](https://www.who.int/)'s [CoDEdit electronic tool](https://www.who.int/standards/classifications/classification-of-diseases/services/codedit-tool) is intended to help producers of cause-of-death statistics in strengthening their capacity to perform routine checks on their data. This package ports the original tool built using Microsoft Acess into R so as to leverage the utility and function of the original tool into a usable application program interface that can be used for building more universal tools or for creating programmatic scientific workflows aimed at routine, automated, and large-scale monitoring of cause-of-death data.
+The [World Health Organization](https://www.who.int/)'s [CoDEdit electronic tool](https://www.who.int/standards/classifications/classification-of-diseases/services/codedit-tool) is intended to help producers of cause-of-death statistics in strengthening their capacity to perform routine checks on their data. This package ports the original tool built using Microsoft Access into R so as to leverage the utility and function of the original tool into a usable application program interface that can be used for building more universal tools or for creating programmatic scientific workflows aimed at routine, automated, and large-scale monitoring of cause-of-death data.
 
 ## What does `codeditr` do?
 
-The `codeditr` package provides functions for implementing data quality checks on cause-of-death records. It is built upon the same heuristics and algorithms that the WHO CodEdit v2.0 electronic tool uses to evaluate quality of cause-of-death data produced and used by country level statisticians in charge of mortality reporting.
+The `codeditr` package provides functions for implementing data quality checks on cause-of-death records. It is built upon the same heuristics and algorithms that the WHO CoDEdit v2.0 electronic tool uses to evaluate quality of cause-of-death data produced and used by country level statisticians in charge of mortality reporting.
 
 Through this package, end users will have the ability to programmatically create scientific workflows for research on cause-of-death data and their quality or build more open tools or applications for routine monitoring of cause-of-death data.
 
 ## Installation
 
-`coeditr` is not yet on CRAN.
+`coeditr` is not yet on CRAN but can be installed through the [Oxford IHTM R-universe](https://oxfordihtm.r-universe.dev) with:
 
-You can install the development version of `codeditr` from [GitHub](https://github.com/OxfordIHTM/codeditr) with:
-
-```{r gh-installation1, eval = FALSE}
-if(!require(remotes)) install.packages("remotes")
-remotes::install_github("OxfordIHTM/codeditr")
+```{r install, eval = FALSE}
+install.packages(
+  "codeditr",
+  repos = c("https://oxfordihtm.r-universe.dev", "https://cloud.r-project.org")
+)
 ```
 
 then load `codeditr`
@@ -52,7 +52,7 @@ library(codeditr)
 
 ## Citation
 
-If you find the `codeitr` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows:
+If you find the `codeditr` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows:
 
 ```{r citation}
 citation("codeditr")

README.Rmd

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# codeditr: Implementing Basic Checks on Cause-of-Death Data Based on World Health Organization’s CoDEdit Tool <img src='man/figures/logo.png' width='200px' align='right' />
+# codeditr: Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool <img src='man/figures/logo.png' width='200px' align='right' />
 
 <!-- badges: start -->
 
@@ -20,7 +20,7 @@ electronic
 tool](https://www.who.int/standards/classifications/classification-of-diseases/services/codedit-tool)
 is intended to help producers of cause-of-death statistics in
 strengthening their capacity to perform routine checks on their data.
-This package ports the original tool built using Microsoft Acess into R
+This package ports the original tool built using Microsoft Access into R
 so as to leverage the utility and function of the original tool into a
 usable application program interface that can be used for building more
 universal tools or for creating programmatic scientific workflows aimed
@@ -31,7 +31,7 @@ data.
 
 The `codeditr` package provides functions for implementing data quality
 checks on cause-of-death records. It is built upon the same heuristics
-and algorithms that the WHO CodEdit v2.0 electronic tool uses to
+and algorithms that the WHO CoDEdit v2.0 electronic tool uses to
 evaluate quality of cause-of-death data produced and used by country
 level statisticians in charge of mortality reporting.
 
@@ -42,14 +42,14 @@ applications for routine monitoring of cause-of-death data.
 
 ## Installation
 
-`coeditr` is not yet on CRAN.
-
-You can install the development version of `codeditr` from
-[GitHub](https://github.com/OxfordIHTM/codeditr) with:
+`coeditr` is not yet on CRAN but can be installed through the [Oxford
+IHTM R-universe](https://oxfordihtm.r-universe.dev) with:
 
 ``` r
-if(!require(remotes)) install.packages("remotes")
-remotes::install_github("OxfordIHTM/codeditr")
+install.packages(
+  "codeditr",
+  repos = c("https://oxfordihtm.r-universe.dev", "https://cloud.r-project.org")
+)
 ```
 
 then load `codeditr`
@@ -63,8 +63,9 @@ library(codeditr)
 
 ## Citation
 
-If you find the `codeitr` package useful please cite using the suggested
-citation provided by a call to the `citation()` function as follows:
+If you find the `codeditr` package useful please cite using the
+suggested citation provided by a call to the `citation()` function as
+follows:
 
 ``` r
 citation("codeditr")

README.md

@@ -1,16 +1,9 @@
-citHeader("To cite codeditr in publications use:")
-
-citEntry(
-  entry    = "Manual",
-  title    = "codeditr: Implementing Basic Checks on Cause-of-Death Data Based on World Health Organization's CoDEdit Tool",
+bibentry(
+  bibtype  = "Manual",
+  header   = "To cite codeditr in publications use:",
+  title    = "codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool",
   author   = c(person("Anita Makori"),  person("Ernest Guevarra")),
   year     = "2024",
   note     = "R package version 0.0.9000",
-  url      = "https://oxford-ihtm.io/codeditr/",
-  textVersion = paste(
-    paste("Anita Makori and Ernest Guevarra (2024).",
-          "codeditr: Implementing Basic Checks on Cause-of-Death Data Based on World Health Organization's CoDEdit Tool.",
-          "R package version 0.0.9000.",
-          "URL https://oxford-ihtm.io/codeditr/")
-  )
+  url      = "https://oxford-ihtm.io/codeditr/"
 )

inst/CITATION

@@ -0,0 +1,16 @@
+CMD
+CoDEdit
+Codecov
+FreeId
+ICD
+IHTM
+Ituen
+Lifecycle
+ORCID
+Udoh
+Umanah
+WIP
+codedit
+int
+www
+’s