From 7d645675efca68fef4cc1e79aae9d547836ef168 Mon Sep 17 00:00:00 2001 From: Ernest Guevarra Date: Mon, 8 Apr 2024 21:57:32 +0100 Subject: [PATCH] address CRAN feedback --- DESCRIPTION | 8 ++-- NEWS.md | 2 +- R/micronutr.R | 7 ++-- README.Rmd | 39 ++++++++++++------ README.md | 71 ++++++++++++++++++++++----------- cran-comments.md | 8 ++++ inst/CITATION | 4 +- inst/WORDLIST | 7 ++++ man/micronutr.Rd | 7 ++-- vignettes/haemoglobinaemia.Rmd | 4 ++ vignettes/inflammation.Rmd | 4 ++ vignettes/iodine-deficiency.Rmd | 4 ++ vignettes/iron-deficiency.Rmd | 4 ++ 13 files changed, 119 insertions(+), 50 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b79c0ea..0518ed8 100644 --- a/DESCRIPTION +++ b/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 = "ernest@guevarra.io", 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 + . License: GPL (>= 3) Depends: R (>= 2.10) diff --git a/NEWS.md b/NEWS.md index 3897037..959d3ff 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# micronutr 0.1.0 +# micronutr 0.1.1 This is the first CRAN release of the `micronutr` package. diff --git a/R/micronutr.R b/R/micronutr.R index bd1144d..4e9241c 100644 --- a/R/micronutr.R +++ b/R/micronutr.R @@ -1,8 +1,7 @@ ################################################################################ # #' -#' 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 @@ -10,7 +9,9 @@ #' 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 +#' . #' #' @docType package #' @keywords internal diff --git a/README.Rmd b/README.Rmd index de6126b..d9e6843 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( library(micronutr) ``` -# micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations +# micronutr: Determining Vitamin and Mineral Status of Populations [![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. diff --git a/README.md b/README.md index 0cc7359..bfcd900 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# micronutr: Utilities for Calculating Indicators of Vitamin and Mineral Status of Populations +# micronutr: Determining Vitamin and Mineral Status of Populations @@ -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 , -#> R package version 0.1.0, . +#> R package version 0.1.1, . #> #> 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. diff --git a/cran-comments.md b/cran-comments.md index 2893d8b..286c79b 100644 --- a/cran-comments.md +++ b/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 diff --git a/inst/CITATION b/inst/CITATION index c9c8005..9fc2d3e 100644 --- a/inst/CITATION +++ b/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" ) diff --git a/inst/WORDLIST b/inst/WORDLIST index 72f1145..54d1272 100644 --- a/inst/WORDLIST +++ b/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 diff --git a/man/micronutr.Rd b/man/micronutr.Rd index db139dc..e732839 100644 --- a/man/micronutr.Rd +++ b/man/micronutr.Rd @@ -4,8 +4,7 @@ \name{micronutr} \alias{micronutr-package} \alias{micronutr} -\title{Utilities for Calculating Indicators of Vitamin and Mineral Status of -Populations} +\title{Determining Vitamin and Mineral Status of Populations} \description{ Vitamin and mineral deficiencies continue to be a significant public health problem. This is particularly critical in developing countries where @@ -13,7 +12,9 @@ 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 +\url{https://www.who.int/teams/nutrition-and-food-safety/databases/vitamin-and-mineral-nutrition-information-system}. } \seealso{ Useful links: diff --git a/vignettes/haemoglobinaemia.Rmd b/vignettes/haemoglobinaemia.Rmd index d79cafa..2d510ea 100644 --- a/vignettes/haemoglobinaemia.Rmd +++ b/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. +

diff --git a/vignettes/inflammation.Rmd b/vignettes/inflammation.Rmd index 67f4ae5..7eb2297 100644 --- a/vignettes/inflammation.Rmd +++ b/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. +

diff --git a/vignettes/iodine-deficiency.Rmd b/vignettes/iodine-deficiency.Rmd index b70690d..5167612 100644 --- a/vignettes/iodine-deficiency.Rmd +++ b/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. +

diff --git a/vignettes/iron-deficiency.Rmd b/vignettes/iron-deficiency.Rmd index c865d22..70f4a4f 100644 --- a/vignettes/iron-deficiency.Rmd +++ b/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. +