arkhe/README.Rmd at main · tesselle/arkhe · GitHub

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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 = NULL
)
Sys.setenv(LANGUAGE = "en") # Force locale
```

# arkhe <img width=120px src="man/figures/logo.png" align="right" />

<!-- badges: start -->
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[![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)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3526659.svg)](https://doi.org/10.5281/zenodo.3526659)
<!-- badges: end -->

## Overview

A dependency-free collection of simple functions for cleaning rectangular data. This package allows to detect, count and replace values or discard rows/columns using a predicate function. In addition, it provides tools to check conditions and return informative error messages.

---

```{r citation, echo=FALSE, comment='', results='asis'}
cite <- utils::citation("arkhe")
print(cite, bibtex = FALSE)
```

## Installation

You can install the released version of **arkhe** from [CRAN](https://CRAN.R-project.org) with:

```{r cran-installation, eval=FALSE}
install.packages("arkhe")
```

And the development version from [Codeberg](https://codeberg.org/) with:

```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_git("https://codeberg.org/tesselle/arkhe")
```

## Usage

```{r}
## Load the package
library(arkhe)

## Set seed for reproductibility
set.seed(12345)

## Create a matrix
X <- matrix(sample(1:10, 25, TRUE), nrow = 5, ncol = 5)

## Add NA
k <- sample(1:25, 3, FALSE)
X[k] <- NA
X

## Count missing values in rows
count(X, f = is.na, margin = 1)

## Count non-missing values in columns
count(X, f = is.na, margin = 2, negate = TRUE)

## Find row with NA
detect(X, f = is.na, margin = 1)

## Find column without any NA
detect(X, f = is.na, margin = 2, negate = TRUE, all = TRUE)

## Remove row with any NA
discard(X, f = is.na, margin = 1, all = FALSE)

## Remove column with any NA
discard(X, f = is.na, margin = 2, all = FALSE)

## Replace NA with zeros
replace_NA(X, value = 0)
```

## Translation

This package provides translations of user-facing communications, like messages, warnings and errors. The preferred language is by default taken from the locale. This can be overridden by setting of the environment variable `LANGUAGE` (you only need to do this once per session):

``` r
Sys.setenv(LANGUAGE = "<language code>")
```

Languages currently available are English (`en`), French (`fr`) and Spanish (`es`).

## Contributing

Please note that the **arkhe** project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project, you agree to abide by its terms.

```{r metadata, include=FALSE}
## Update codemeta.json
codemetar::write_codemeta(verbose = FALSE)

## Update CITATION.cff
cff_keys <- list(
  identifiers = list(
    list(description = "The concept DOI.",
         type = "doi",
         value = "10.5281/zenodo.3526659"),
    list(description = "The versioned DOI for version 0.1.0.",
         type = "doi",
         value = "10.5281/zenodo.3526660"),
    list(description = "The versioned DOI for version 0.2.0.",
         type = "doi",
         value = "10.5281/zenodo.3583089"),
    list(description = "The versioned DOI for version 0.2.1.",
         type = "doi",
         value = "10.5281/zenodo.3668868"),
    list(description = "The versioned DOI for version 0.2.2.",
         type = "doi",
         value = "10.5281/zenodo.3724463"),
    list(description = "The versioned DOI for version 0.3.0.",
         type = "doi",
         value = "10.5281/zenodo.4675724"),
    list(description = "The versioned DOI for version 0.3.1.",
         type = "doi",
         value = "10.5281/zenodo.4761928"),
    list(description = "The versioned DOI for version 0.4.0.",
         type = "doi",
         value = "10.5281/zenodo.5515470"),
    list(description = "The versioned DOI for version 0.5.0.",
         type = "doi",
         value = "10.5281/zenodo.6647041"),
    list(description = "The versioned DOI for version 1.0.0.",
         type = "doi",
         value = "10.5281/zenodo.7261616"),
    list(description = "The versioned DOI for version 1.1.0.",
         type = "doi",
         value = "10.5281/zenodo.7546749"),
    list(description = "The versioned DOI for version 1.2.0.",
         type = "doi",
         value = "10.5281/zenodo.7925529"),
    list(description = "The versioned DOI for version 1.3.0.",
         type = "doi",
         value = "10.5281/zenodo.8308598"),
    list(description = "The versioned DOI for version 1.4.0.",
         type = "doi",
         value = "10.5281/zenodo.10148702"),
    list(description = "The versioned DOI for version 1.5.0.",
         type = "doi",
         value = "10.5281/zenodo.10534310"),
    list(description = "The versioned DOI for version 1.6.0.",
         type = "doi",
         value = "10.5281/zenodo.10694357"),
    list(description = "The versioned DOI for version 1.7.0.",
         type = "doi",
         value = "10.5281/zenodo.13121710"),
    list(description = "The versioned DOI for version 1.8.0.",
         type = "doi",
         value = "10.5281/zenodo.14054350"),
    list(description = "The versioned DOI for version 1.9.0.",
         type = "doi",
         value = "10.5281/zenodo.14355274"),
    list(description = "The versioned DOI for version 1.10.0.",
         type = "doi",
         value = "10.5281/zenodo.14926270"),
    list(description = "The versioned DOI for version 1.11.0.",
         type = "doi",
         value = "10.5281/zenodo.15390837"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.arkhe")
  )
)
cff <- cffr::cff_create("DESCRIPTION", keys = cff_keys)
if (cffr::cff_validate(cff)) cffr::cff_write(cff, outfile = "CITATION.cff")
```