address CRAN feedback

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: micronutr
 Type: Package
-Title: Utilities for Calculating Indicators of Vitamin and Mineral Status of
-    Populations
-Version: 0.1.0
+Title: Determining Vitamin and Mineral Status of Populations
+Version: 0.1.1
 Authors@R: c(
     person("Ernest", "Guevarra", comment = c(ORCID = "0000-0002-4887-4415"), 
            email = "[email protected]", role = c("aut", "cre", "cph")),
@@ -15,7 +14,8 @@ Description: Vitamin and mineral deficiencies continue to be a significant
     answering questions related to the magnitude and distribution of
     deficiencies of selected vitamins and minerals. This package provides tools
     for calculating and determining select vitamin and mineral deficiencies
-    using R.
+    based on World Health Organization (WHO) guidelines found at
+    <https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system>.
 License: GPL (>= 3)
 Depends: 
     R (>= 2.10)

NEWS.md

@@ -1,4 +1,4 @@
-# micronutr 0.1.0
+# micronutr 0.1.1
 
 This is the first CRAN release of the `micronutr` package.
 

R/micronutr.R

@@ -1,16 +1,17 @@
 ################################################################################
 #
 #'
-#' Utilities for Calculating Indicators of Vitamin and Mineral Status of
-#' Populations
+#' Determining Vitamin and Mineral Status of Populations
 #'
 #' Vitamin and mineral deficiencies continue to be a significant public health
 #' problem. This is particularly critical in developing countries where
 #' deficiencies to Vitamin A, iron, iodine, and other micronutrients lead to
 #' adverse health consequences. Cross-sectional surveys are helpful in answering
 #' questions related to the magnitude and distribution of deficiencies of
 #' selected vitamins and minerals. This package provides tools for
-#' calculating and determining select vitamin and mineral deficiencies using R.
+#' calculating and determining select vitamin and mineral deficiencies based on
+#' World Health Organization (WHO) guidelines found at
+#' <https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system>.
 #'
 #' @docType package
 #' @keywords internal

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 library(micronutr)
 ```
 
-# micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations <img src="man/figures/logo.png" width="200px" align="right" />
+# micronutr: Determining Vitamin and Mineral Status of Populations <img src="man/figures/logo.png" width="200px" align="right" />
 
 <!-- badges: start -->
 [![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)
@@ -30,6 +30,20 @@ library(micronutr)
 
 Vitamin and mineral deficiencies continue to be a significant public health problem. This is particularly critical in developing countries where deficiencies to vitamin A, iron, iodine, and other micronutrients lead to adverse health consequences. Cross-sectional surveys are helpful in answering questions related to the magnitude and distribution of deficiencies of selected vitamins and minerals.
 
+This package provides tools for determining select vitamin and mineral deficiencies based on World Health Organization (WHO) guidelines found [here](https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system).
+
+## What does `micronutr` do?
+
+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 **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 **iodine deficiency** status based on a population's mean urinary iodine concentration.
+
 ## Installation
 
 You can install `micronutr` from [CRAN](https://cran.r-project.org) with:
@@ -47,18 +61,6 @@ install.packages(
 )
 ```
 
-## What does `micronutr` do?
-
-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 **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 **iodine deficiency** status based on a population's mean urinary iodine concentration.
-
 ## Usage
 
 `micronutr` comes packaged with vignettes that show how to use the package for the purposes described above.
@@ -85,3 +87,14 @@ Feedback, bug reports, and feature requests are welcome; file issues or seek sup
 
 This project is released with a [Contributor Code of Conduct](https://nutriverse.io/micronutr/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
+## References
+
+1. Guideline on haemoglobin cutoffs to define anaemia in individuals and populations. Geneva: World
+Health Organization; 2024. Licence: CC BY-NC-SA 3.0 IGO.
+
+2. Serum ferritin concentrations for the assessment of iron status in individuals and populations: technical brief. Geneva: World Health Organization; 2020. License: CC BY-NC-SA 3.0 IGO.
+
+3. C-reactive protein concentrations as a marker of inflammation or infection for interpreting biomarkers of micronutrient status. Vitamin and Mineral Nutrition Information System. Geneva: World Health Organization; 2014.
+
+4. Urinary iodine concentrations for determining iodine status deficiency in populations. Vitamin and Mineral
+Nutrition Information System. Geneva: World Health Organization; 2013.

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations <img src="man/figures/logo.png" width="200px" align="right" />
+# micronutr: Determining Vitamin and Mineral Status of Populations <img src="man/figures/logo.png" width="200px" align="right" />
 
 <!-- badges: start -->
 
@@ -27,24 +27,9 @@ lead to adverse health consequences. Cross-sectional surveys are helpful
 in answering questions related to the magnitude and distribution of
 deficiencies of selected vitamins and minerals.
 
-## Installation
-
-You can install `micronutr` from [CRAN](https://cran.r-project.org)
-with:
-
-``` r
-install.packages("micronutr")
-```
-
-You can install the development version of `micronutr` from [nutriverse
-r-universe](https://nutriverse.r-universe.dev) with:
-
-``` r
-install.packages(
-  "micronutr", 
-  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
-)
-```
+This package provides tools for determining select vitamin and mineral
+deficiencies based on World Health Organization (WHO) guidelines found
+[here](https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system).
 
 ## What does `micronutr` do?
 
@@ -64,6 +49,25 @@ for:
 - Detecting **iodine deficiency** status based on a population’s mean
   urinary iodine concentration.
 
+## Installation
+
+You can install `micronutr` from [CRAN](https://cran.r-project.org)
+with:
+
+``` r
+install.packages("micronutr")
+```
+
+You can install the development version of `micronutr` from [nutriverse
+r-universe](https://nutriverse.r-universe.dev) with:
+
+``` r
+install.packages(
+  "micronutr", 
+  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
+)
+```
+
 ## Usage
 
 `micronutr` comes packaged with vignettes that show how to use the
@@ -91,18 +95,18 @@ follows:
 citation("micronutr")
 #> To cite micronutr in publications use:
 #> 
-#>   Ernest Guevarra, Nicholus Tint Zaw (2024). _micronutr: Utilities for
-#>   Calculating Indicators of Vitamin and Mineral Status of Populations_.
+#>   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 0.1.0, <https://nutriverse.io/micronutr/>.
+#>   R package version 0.1.1, <https://nutriverse.io/micronutr/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations},
+#>     title = {micronutr: Determining Vitamin and Mineral Status of Populations},
 #>     author = {{Ernest Guevarra} and {Nicholus Tint Zaw}},
 #>     year = {2024},
-#>     note = {R package version 0.1.0},
+#>     note = {R package version 0.1.1},
 #>     url = {https://nutriverse.io/micronutr/},
 #>     doi = {10.5281/zenodo.7503846},
 #>   }
@@ -119,3 +123,22 @@ guidelines](https://nutriverse.io/micronutr/CONTRIBUTING.html).
 This project is released with a [Contributor Code of
 Conduct](https://nutriverse.io/micronutr/CODE_OF_CONDUCT.html). By
 contributing to this project, you agree to abide by its terms.
+
+## References
+
+1.  Guideline on haemoglobin cutoffs to define anaemia in individuals
+    and populations. Geneva: World Health Organization; 2024. Licence:
+    CC BY-NC-SA 3.0 IGO.
+
+2.  Serum ferritin concentrations for the assessment of iron status in
+    individuals and populations: technical brief. Geneva: World Health
+    Organization; 2020. License: CC BY-NC-SA 3.0 IGO.
+
+3.  C-reactive protein concentrations as a marker of inflammation or
+    infection for interpreting biomarkers of micronutrient status.
+    Vitamin and Mineral Nutrition Information System. Geneva: World
+    Health Organization; 2014.
+
+4.  Urinary iodine concentrations for determining iodine status
+    deficiency in populations. Vitamin and Mineral Nutrition Information
+    System. Geneva: World Health Organization; 2013.

cran-comments.md

@@ -1,3 +1,11 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Shortened the package title to less than 65 characters.
+
+* Added a URL link in angle brackets in the DESCRIPTION file for the WHO
+guidelines I used as reference for the methods in this package.
+
 ## Test environments
 * local ubuntu 22.04 install, R 4.3.3
 * macos-latest (on GitHub Actions), release

inst/CITATION

@@ -1,10 +1,10 @@
 bibentry(
   bibtype  = "Manual",
   header   = "To cite micronutr in publications use:",
-  title    = "micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations",
+  title    = "micronutr: Determining Vitamin and Mineral Status of Populations",
   author   = c(person("Ernest Guevarra"), person("Nicholus Tint Zaw")),
   year     = "2024",
-  note     = "R package version 0.1.0",
+  note     = "R package version 0.1.1",
   url      = "https://nutriverse.io/micronutr/",
   doi      = "10.5281/zenodo.7503846"
 )

inst/WORDLIST

@@ -7,9 +7,14 @@ CRP
 Clewes
 CodeFactor
 Codecov
+EPG
+IGO
 Kupka
 Lifecycle
 Mei
+NC
+NHD
+NMH
 ORCID
 Raiten
 Rawat
@@ -22,6 +27,7 @@ Zenodo
 agp
 ajcn
 crp
+cutoffs
 doi
 haemoglobinaemia
 hb
@@ -32,5 +38,6 @@ org
 psu
 tibble
 u
+urinaryiodine
 µg
 α

vignettes/haemoglobinaemia.Rmd

@@ -109,5 +109,9 @@ correct_hb(hb = 105, alt = 1400, smoke = 1.5)
 
 This individual will have a corrected haemoglobin of 102.5 g/L.
 
+## References
+
+Guideline on haemoglobin cutoffs to define anaemia in individuals and populations. Geneva: World Health Organization; 2024. Licence: CC BY-NC-SA 3.0 IGO.
+
 <br/>
 <br/>

vignettes/inflammation.Rmd

@@ -97,5 +97,9 @@ detect_inflammation(crp = 2)
 
 we get the same result as using the `detect_inflammation_crp()`.
 
+## References
+
+C-reactive protein concentrations as a marker of inflammation or infection for interpreting biomarkers of micronutrient status. Vitamin and Mineral Nutrition Information System. Geneva: World Health Organization; 2014.
+
 <br/>
 <br/>

vignettes/iodine-deficiency.Rmd

@@ -50,5 +50,9 @@ The following table presents the median urinary iodine concentration (UIC) that
 It is important to note that only population-level assessments of iodine status are possible from the survey methodology of casual, spot urine sample collection. Iodine status estimates based on the methodology of casual spot urine sample collection cannot be used to classify individual status and should not be presented as a prevalence of deficiency or adequacy. The information provided in the table above is frequently misinterpreted to reflect the situation of individuals. The correct interpretation is that populations with a median urinary iodine <20 microgram/L have **“severe”** iodine deficiency, populations with a median urinary iodine 20-49 microgram/L have **“moderate”** iodine deficiency, and populations with a median urinary iodine 50-99 microgram/L have **“mild”** iodine deficiency.
 
 
+## References
+
+Urinary iodine concentrations for determining iodine status deficiency in populations. Vitamin and Mineral Nutrition Information System. Geneva: World Health Organization; 2013.
+
 <br/>
 <br/>

vignettes/iron-deficiency.Rmd

@@ -134,5 +134,9 @@ and for a person with serum ferritin of 11.3 microgram/L and an AGP of 2, we use
 correct_ferritin(agp = 2, ferritin = 11.3)
 ```
 
+## References
+
+Serum ferritin concentrations for the assessment of iron status in individuals and populations: technical brief. Geneva: World Health Organization; 2020. License: CC BY-NC-SA 3.0 IGO.
+
 <br/>
 <br/>