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README.Rmd
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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, echo = FALSE}
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
error = FALSE,
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
library(nipnTK)
```
# nipnTK: National Information Platforms for Nutrition (NiPN) Data Quality Toolkit <img src="man/figures/logo.png" width="200px" align="right" display="none" />
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://cran.r-project.org/package=nipnTK)
[](https://cran.r-project.org/web/checks/check_results_nipnTK.html)
[](https://CRAN.R-project.org/package=nipnTK)
[](https://cran.r-project.org/package=nipnTK)
[](https://cran.r-project.org/package=nipnTK)
[](https://github.com/nutriverse/nipnTK/actions/workflows/R-CMD-check.yaml)
[](https://github.com/nutriverse/nipnTK/actions/workflows/test-coverage.yaml)
[](https://app.codecov.io/gh/nutriverse/nipnTK?branch=main)
[](https://www.codefactor.io/repository/github/nutriverse/nipntk)
[](https://zenodo.org/badge/latestdoi/118171028)
<!-- badges: end -->
[National Information Platforms for Nutrition (NiPN)](https://www.nipn-nutrition-platforms.org) is an initiative of the European Commission to provide support to countries to strengthen their information systems for nutrition and to improve the analysis of data so as to better inform the strategic decisions they are faced with to prevent malnutrition and its consequences.
As part of this mandate, [NiPN](https://www.nipn-nutrition-platforms.org) has commissioned work on the development of a toolkit to assess the quality of various nutrition-specific and nutrition-related data. This is a companion R package to the toolkit of practical analytical methods that can be applied to variables in datasets to assess their quality.
The focus of the toolkit is on data required to assess anthropometric status such as measurements of weight, height or length, MUAC, sex and age. The focus is on anthropometric status but many of presented methods could be applied to other types of data. [NiPN](https://www.nipn-nutrition-platforms.org) may commission additional toolkits to examine other variables or other types of variables.
## Installation
You can install `nipnTK` from [CRAN](https://cran.r-project.org):
```{r install_cran, echo = TRUE, eval = FALSE}
install.packages("nipnTK")
```
You can install the development version of `nipnTK` from [GitHub](https://github.com/nutriverse/nipnTK) with:
```{r gh-installation, eval = FALSE}
if(!require(remotes)) install.packages("remotes")
remotes::install_github("nutriverse/nipnTK")
```
## Usage
Data quality is assessed by:
1. Range checks and value checks to identify *univariate* outliers - [guide](https://nutriverse.io/nipnTK/articles/rl.html)
2. Scatterplots and statistical methods to identify *bivariate* outliers - [guide](https://nutriverse.io/nipnTK/articles/sp.html)
3. Use of flags to identify outliers in anthropometric indices - [guide](https://nutriverse.io/nipnTK/articles/flagging.html)
4. Examining the distribution and the statistics of the distribution of measurements and anthropometric indices - [guide](https://nutriverse.io/nipnTK/articles/ad.html)
5. Assessing the extent of digit preference in recorded measurements - [guide](https://nutriverse.io/nipnTK/articles/dp.html)
6. Assessing the extent of age heaping in recorded ages - [guide](https://nutriverse.io/nipnTK/articles/ah.html)
7. Examining the sex ratio - [guide](https://nutriverse.io/nipnTK/articles/sr.html)
8. Examining age distributions and age by sex distributions - [guide](https://nutriverse.io/nipnTK/articles/as.html)
These activities and a proposed order in which they should be performed are shown below:
```{r, echo = FALSE, eval = TRUE}
knitr::include_graphics("man/figures/nipnWorkflow.png")
```
## Citation
If you find the `nipnTK` package useful, please cite using the suggested citation provided by a call to the `citation` function as follows:
```{r cite}
citation("nipnTK")
```
## Community guidelines
Feedback, bug reports and feature requests are welcome; file issues or seek support [here](https://github.com/nutriverse/nipnTK/issues). If you would like to contribute to the package, please see our [contributing guidelines](https://nutriverse.io/nipnTK/CONTRIBUTING.html).
This project is released with a [Contributor Code of Conduct](https://nutriverse.io/nipnTK/CODE_OF_CONDUCT.html). By participating in this project you agree to abide by its terms.