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address CRAN feedback
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8 changes: 4 additions & 4 deletions DESCRIPTION
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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")),
Expand All @@ -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)
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2 changes: 1 addition & 1 deletion NEWS.md
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# micronutr 0.1.0
# micronutr 0.1.1

This is the first CRAN release of the `micronutr` package.

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7 changes: 4 additions & 3 deletions R/micronutr.R
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################################################################################
#
#'
#' 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
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39 changes: 26 additions & 13 deletions README.Rmd
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Expand Up @@ -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)
Expand All @@ -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:
Expand All @@ -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.
Expand All @@ -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.
71 changes: 47 additions & 24 deletions README.md
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@@ -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 -->

Expand All @@ -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?

Expand All @@ -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
Expand Down Expand Up @@ -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},
#> }
Expand All @@ -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.
8 changes: 8 additions & 0 deletions cran-comments.md
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## 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
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4 changes: 2 additions & 2 deletions inst/CITATION
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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"
)
7 changes: 7 additions & 0 deletions inst/WORDLIST
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Expand Up @@ -7,9 +7,14 @@ CRP
Clewes
CodeFactor
Codecov
EPG
IGO
Kupka
Lifecycle
Mei
NC
NHD
NMH
ORCID
Raiten
Rawat
Expand All @@ -22,6 +27,7 @@ Zenodo
agp
ajcn
crp
cutoffs
doi
haemoglobinaemia
hb
Expand All @@ -32,5 +38,6 @@ org
psu
tibble
u
urinaryiodine
µg
α
7 changes: 4 additions & 3 deletions man/micronutr.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 4 additions & 0 deletions vignettes/haemoglobinaemia.Rmd
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Expand Up @@ -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/>
4 changes: 4 additions & 0 deletions vignettes/inflammation.Rmd
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Expand Up @@ -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/>
4 changes: 4 additions & 0 deletions vignettes/iodine-deficiency.Rmd
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Expand Up @@ -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/>
4 changes: 4 additions & 0 deletions vignettes/iron-deficiency.Rmd
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Expand Up @@ -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/>

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