Merge pull request #24 from OxfordIHTM/dev

add tests for recode sex and recode age type
OxfordIHTM · Apr 28, 2024 · 2a370a2 · 2a370a2
2 parents b2e53e9 + 138544c
commit 2a370a2
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diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,9 +28,11 @@ Imports:
     tibble
 Suggests:
     covr,
-    spelling
+    spelling,
+    testthat (>= 3.0.0)
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
+Config/testthat/edition: 3
diff --git a/R/cod_recode_sex.R b/R/cod_recode_sex.R
@@ -23,7 +23,7 @@
 #' @export
 #'
 
-cod_recode_sex <- function(sex_value, sex_code = c(1, 2), codedit = TRUE) {
+cod_recode_sex <- function(sex_value, sex_code = c(1L, 2L), codedit = TRUE) {
   if (codedit) {
     sex_value[!sex_value %in% sex_code] <- 9L
   } else {

diff --git a/README.Rmd b/README.Rmd
@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/OxfordIHTM/codeditr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OxfordIHTM/codeditr/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/OxfordIHTM/codeditr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codeditr?branch=main)
+[![CodeFactor](https://www.codefactor.io/repository/github/OxfordIHTM/codeditr/badge)](https://www.codefactor.io/repository/github/OxfordIHTM/codeditr)
 <!-- 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 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.

diff --git a/README.md b/README.md
@@ -13,6 +13,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 [![R-CMD-check](https://github.com/OxfordIHTM/codeditr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OxfordIHTM/codeditr/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/OxfordIHTM/codeditr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OxfordIHTM/codeditr?branch=main)
+[![CodeFactor](https://www.codefactor.io/repository/github/OxfordIHTM/codeditr/badge)](https://www.codefactor.io/repository/github/OxfordIHTM/codeditr)
 <!-- badges: end -->
 
 The [World Health Organization](https://www.who.int/)’s [CoDEdit
@@ -69,17 +70,17 @@ follows:
 
 ``` r
 citation("codeditr")
-#> To cite zscorer in publications use:
+#> To cite codeditr in publications use:
 #> 
-#>   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/
+#>   Anita Makori, Ernest Guevarra (2024). _codeditr: Implementing
+#>   Cause-of-Death Data Checks Based on World Health Organization's
+#>   CoDEdit Tool_. R package version 0.0.9000,
+#>   <https://oxford-ihtm.io/codeditr/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {codeditr: Implementing Basic Checks on Cause-of-Death Data Based on World Health Organization's CoDEdit Tool},
+#>     title = {codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool},
 #>     author = {{Anita Makori} and {Ernest Guevarra}},
 #>     year = {2024},
 #>     note = {R package version 0.0.9000},

diff --git a/man/cod_recode_sex.Rd b/man/cod_recode_sex.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(codeditr)
+
+test_check("codeditr")
diff --git a/tests/testthat/test-cod_recode_age_type.R b/tests/testthat/test-cod_recode_age_type.R
@@ -0,0 +1,97 @@
+# Tests for recode age type ----------------------------------------------------
+
+age_type       <- c(rep("D", 3), rep("M", 2), rep("Y", 3))
+
+age_type1      <- c(rep("d", 3), rep("m", 2), rep("y", 3))
+age_type_code1 <- c("d", "m", "y")
+
+age_type2      <- c(rep("days", 3), rep("months", 2), rep("years", 3))
+age_type_code2 <- c("days", "months", "years")
+
+age_type3      <- c(rep(1L, 3), rep(2L, 2), rep(3L, 3))
+age_type_code3 <- c(1L, 2L, 3L)
+
+age_type4      <- c(rep("d", 3), "m", NA_character_, rep("y", 3))
+age_type_code4 <- c("d", "m", "y")
+
+age_type5      <- c(rep(1L, 3), 2L, NA_integer_, rep(3L, 3))
+age_type_code5 <- c(1L, 2L, 3L)
+
+expected    <- c(rep("D", 3), rep("M", 2), rep("Y", 3))
+expected_na <- c(rep("D", 3), "M", NA_character_, rep("Y", 3))
+
+
+testthat::test_that(
+  "output of recode age type is as expected", {
+    expect_vector(
+      cod_recode_age_type(age_type = age_type),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type),
+      expected
+    )
+
+    ## input is different characters ----
+    expect_vector(
+      cod_recode_age_type(age_type = age_type1, age_type_code = age_type_code1),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type1, age_type_code = age_type_code1),
+      expected
+    )
+
+    ## input is different characters ----
+    expect_vector(
+      cod_recode_age_type(age_type = age_type2, age_type_code = age_type_code2),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type2, age_type_code = age_type_code2),
+      expected
+    )
+
+    ## input is integer ----
+    expect_vector(
+      cod_recode_age_type(age_type = age_type3, age_type_code = age_type_code3),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type3, age_type_code = age_type_code3),
+      expected
+    )
+
+    ## input has NA ----
+    expect_vector(
+      cod_recode_age_type(age_type = age_type4, age_type_code = age_type_code4),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type4, age_type_code = age_type_code4),
+      expected_na
+    )
+
+    ## input has NA ----
+    expect_vector(
+      cod_recode_age_type(age_type = age_type5, age_type_code = age_type_code5),
+      ptype = character(),
+      size = 8
+    )
+
+    expect_equal(
+      cod_recode_age_type(age_type = age_type5, age_type_code = age_type_code5),
+      expected_na
+    )
+  }
+)
diff --git a/tests/testthat/test-cod_recode_sex.R b/tests/testthat/test-cod_recode_sex.R
@@ -0,0 +1,47 @@
+# Tests for recode sex ---------------------------------------------------------
+
+sex_value  <- c(rep(1L, 2), rep(2L, 3), NA_integer_)
+
+sex_value1 <- c(rep("m", 2), rep("f", 3), NA_character_)
+sex_code1  <- c("m", "f")
+
+expected <- c(1L, 1L, 2L, 2L, 2L, NA_integer_)
+expected_codedit <- c(1L, 1L, 2L, 2L, 2L, 9L)
+
+testthat::test_that(
+  "output of recode sex is as expected", {
+    expect_vector(
+      cod_recode_sex(sex_value = sex_value), ptype = integer(), size = 6
+    )
+
+    expect_equal(cod_recode_sex(sex_value = sex_value), expected_codedit)
+
+    expect_vector(
+      cod_recode_sex(
+        sex_value = sex_value1, sex_code = sex_code1, codedit = FALSE
+      ),
+      ptype = integer(),
+      size = 6
+    )
+
+    expect_equal(
+      cod_recode_sex(
+        sex_value = sex_value1, sex_code = sex_code1, codedit = FALSE
+      ),
+      expected
+    )
+
+    expect_vector(
+      cod_recode_sex(sex_value = sex_value1, sex_code = sex_code1),
+      ptype = integer(),
+      size = 6
+    )
+
+    expect_equal(
+      cod_recode_sex(
+        sex_value = sex_value1, sex_code = sex_code1, codedit = TRUE
+      ),
+      expected_codedit
+    )
+  }
+)