Merge pull request #46 from nutriverse/dev

refactor tests; fix #43; fix #44; fix #45

.Rbuildignore

@@ -11,3 +11,4 @@
 ^_pkgdown\.yml$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^README\.html$

.gitignore

@@ -5,3 +5,5 @@
 .DS_Store
 inst/doc
 docs
+
+README.html

DESCRIPTION

@@ -28,7 +28,7 @@ Suggests:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 URL: https://nutriverse.io/micronutr/, https://github.com/nutriverse/micronutr
 BugReports: https://github.com/nutriverse/micronutr/issues

NEWS.md

@@ -1,5 +1,15 @@
 # micronutr 0.1.1.9000
 
+This is a GitHub-only and R Universe-only development release. In this release:
+
+## Bug fixes
+
+* refactor tests for haemoglobin correction functions to resolve warning messages.
+
+## General updates
+
+* update `_pkgdown.yml` website template to match nutriverse theme.
+
 
 # micronutr 0.1.1
 

README.Rmd

@@ -56,7 +56,7 @@ You can install `micronutr` from [CRAN](https://cran.r-project.org) with:
 install.packages("micronutr")
 ```
 
-You can install the development version of `micronutr` from [nutriverse r-universe](https://nutriverse.r-universe.dev) with:
+You can install the development version of `micronutr` from [nutriverse R Universe](https://nutriverse.r-universe.dev) with:
 
 ```{r install-r-universe, echo = TRUE, eval = FALSE}
 install.packages(

README.md

@@ -42,17 +42,17 @@ The `micronutr` package provides tools for determining select vitamin
 and mineral deficiencies using R. Currently, `micronutr` has functions
 for:
 
-- Detecting **haemoglobinaemia** or anaemia based on an individual’s
-  *serum haemoglobin* level;
+  - Detecting **haemoglobinaemia** or anaemia based on an individual’s
+    *serum haemoglobin* level;
 
-- Detecting **inflammation** status based on *c-reactive protein (CRP)*
-  and *alpha(1)-acid-glycoprotein (AGP)*;
+  - Detecting **inflammation** status based on *c-reactive protein
+    (CRP)* and *alpha(1)-acid-glycoprotein (AGP)*;
 
-- Detecting **iron deficiency** status based on an individual’s *serum
-  ferritin* level;
+  - Detecting **iron deficiency** status based on an individual’s *serum
+    ferritin* level;
 
-- Detecting **iodine deficiency** status based on a population’s mean
-  urinary iodine concentration.
+  - Detecting **iodine deficiency** status based on a population’s mean
+    urinary iodine concentration.
 
 ## Installation
 
@@ -64,7 +64,7 @@ install.packages("micronutr")
 ```
 
 You can install the development version of `micronutr` from [nutriverse
-r-universe](https://nutriverse.r-universe.dev) with:
+R Universe](https://nutriverse.r-universe.dev) with:
 
 ``` r
 install.packages(
@@ -78,17 +78,17 @@ install.packages(
 `micronutr` comes packaged with vignettes that show how to use the
 package for the purposes described above.
 
-- [Detecting
-  **haemoglobinaemia**](https://nutriverse.io/micronutr/articles/haemoglobinaemia.html)
+  - [Detecting
+    **haemoglobinaemia**](https://nutriverse.io/micronutr/articles/haemoglobinaemia.html)
 
-- [Detecting
-  **inflammation**](https://nutriverse.io/micronutr/articles/inflammation.html)
+  - [Detecting
+    **inflammation**](https://nutriverse.io/micronutr/articles/inflammation.html)
 
-- [Detecting **iron
-  deficiency**](https://nutriverse.io/micronutr/articles/iron-deficiency.html)
+  - [Detecting **iron
+    deficiency**](https://nutriverse.io/micronutr/articles/iron-deficiency.html)
 
-- [Detecting **iodine
-  deficiency**](https://nutriverse.io/micronutr/articles/iodine-deficiency.html)
+  - [Detecting **iodine
+    deficiency**](https://nutriverse.io/micronutr/articles/iodine-deficiency.html)
 
 ## Citation
 
@@ -102,8 +102,9 @@ citation("micronutr")
 #> 
 #>   Ernest Guevarra, Nicholus Tint Zaw (2024). _micronutr: Determining
 #>   Vitamin and Mineral Status of Populations_.
-#>   doi:10.5281/zenodo.7503846 <https://doi.org/10.5281/zenodo.7503846>,
-#>   R package version 0.1.1, <https://nutriverse.io/micronutr/>.
+#>   doi:10.5281/zenodo.7503846
+#>   <https://doi.org/10.5281/zenodo.7503846>, R package version 0.1.1,
+#>   <https://nutriverse.io/micronutr/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 

pkgdown/_pkgdown.yml

@@ -7,16 +7,18 @@ development:
 
 template:
   bootstrap: 5
-  bootswatch: cosmo
-  theme: haddock
-  ganalytics: #
+  bootswatch: pulse
+  theme: breeze-light
+  ganalytics: G-1V9EDVDNEZ
+  bslib:
+    pkgdown-nav-height: 100px
 
 navbar:
   bg: success
   type: light
   structure:
     left:  [home, reference, articles, news]
-    right: [mastodon, linkedin, github]
+    right: [mastodon, github]
 
   components:
     articles:
@@ -32,10 +34,7 @@ navbar:
         href: articles/iodine-deficiency.html
     mastodon:
       icon: "fab fa-mastodon fa-lg"
-      href: https://fosstodon.org/@katilingban
-    linkedin:
-      icon: "fab fa-linkedin fa-lg"
-      href: https://www.linkedin.com/company/katilingban
+      href: https://fosstodon.org/@nutriverse
 
 home:
   #links:

pkgdown/favicon/site.webmanifest

@@ -0,0 +1,21 @@
+{
+  "name": "",
+  "short_name": "",
+  "icons": [
+    {
+      "src": "/web-app-manifest-192x192.png",
+      "sizes": "192x192",
+      "type": "image/png",
+      "purpose": "maskable"
+    },
+    {
+      "src": "/web-app-manifest-512x512.png",
+      "sizes": "512x512",
+      "type": "image/png",
+      "purpose": "maskable"
+    }
+  ],
+  "theme_color": "#ffffff",
+  "background_color": "#ffffff",
+  "display": "standalone"
+}

tests/testthat/test-01-correct_haemoglobin.R

@@ -41,12 +41,8 @@ test_that("correction factor for altitude errors", {
 
 
 test_that("correct haemoglobin output is correct", {
-  expect_type(
-    correct_hb(hb = mnData$hb[1]), "double"
-  )
-  expect_type(
-    correct_hb(hb = mnData$hb[1], alt = mnData$altitude[1]), "double"
-  )
+  expect_warning(correct_hb(hb = mnData$hb[1]))
+  expect_warning(correct_hb(hb = mnData$hb[1], alt = mnData$altitude[1]))
   expect_type(
     correct_hb(hb = mnData$hb[1], alt = mnData$altitude[1], smoke = 0),
     "double"