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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
library(micronutr)
```
# micronutr: Determining Vitamin and Mineral Status of Populations <img src="man/figures/logo.png" width="200px" align="right" />
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://CRAN.R-project.org/package=micronutr)
[](https://cran.r-project.org/web/checks/check_results_micronutr.html)
[](https://CRAN.R-project.org/package=micronutr)
[](https://cran.r-project.org/package=micronutr)
[](https://cran.r-project.org/package=micronutr)
[](https://github.com/nutriverse/micronutr/actions/workflows/R-CMD-check.yaml)
[](https://github.com/nutriverse/micronutr/actions/workflows/test-coverage.yaml)
[](https://app.codecov.io/gh/nutriverse/micronutr?branch=main)
[](https://www.codefactor.io/repository/github/nutriverse/micronutr)
[](https://zenodo.org/badge/latestdoi/584725138)
<!-- badges: end -->
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:
```{r install-cran, echo = TRUE, eval = FALSE}
install.packages("micronutr")
```
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(
"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 package for the purposes described above.
* [Detecting **haemoglobinaemia**](https://nutriverse.io/micronutr/articles/haemoglobinaemia.html)
* [Detecting **inflammation**](https://nutriverse.io/micronutr/articles/inflammation.html)
* [Detecting **iron deficiency**](https://nutriverse.io/micronutr/articles/iron-deficiency.html)
* [Detecting **iodine deficiency**](https://nutriverse.io/micronutr/articles/iodine-deficiency.html)
## Citation
If you find the `micronutr` package useful, please cite using the suggested citation provided by a call to the `citation` function as follows:
```{r citation, echo = TRUE, eval = TRUE}
citation("micronutr")
```
## Community guidelines
Feedback, bug reports, and feature requests are welcome; file issues or seek support [here](https://github.com/nutriverse/micronutr/issues). If you would like to contribute to the package, please see our [contributing 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.