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pkgdev.Rmd
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pkgdev.Rmd
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---
title: "pkgdev"
author: "Alexander Kirchmair"
---
```{r setup, include=FALSE}
library(devtools)
library(usethis)
library(testthat)
library(SummarizedExperiment)
library(BiocGenerics)
```
```{r initial setup}
use_mit_license()
use_readme_rmd()
use_pipe()
```
```{r}
use_package("ggplot2")
use_package("dplyr")
use_package("BiocGenerics")
use_package("SummarizedExperiment")
use_package("methods")
use_package("IsoCorrectoR")
use_package("crayon")
use_package("rlang")
use_package("matrixStats")
use_package("multcomp", type = "Suggests")
use_package("glmmTMB", type = "Suggests")
use_package("limma", type = "Suggests")
use_package("nlme", type = "Suggests")
use_package("missForest", type = "Suggests")
use_package("betareg", type = "Suggests")
use_package("contrast", type = "Suggests")
```
R functions
```{r}
use_r("AllClasses")
use_r("AllGenerics")
use_r("AllMethods")
use_r("AllImports")
use_r("r-data-functions")
use_r("r-preprocessing-functions")
use_r("r-normalization-functions")
use_r("r-imputation-functions")
use_r("r-difftest-functions")
use_r("r-plotting-functions")
use_r("r-isocorrection-functions")
use_r("r-testing-functions")
```
Element data
```{r}
isocomp <- getElementCompositions()
use_data(isocomp, internal = TRUE) # include data in package
```
```{r}
load_all()
```
Update documentation
Code > Insert Roxygen Skeleton
```{r}
document()
```
Unit tests
```{r}
lapply(list.files("R/", pattern = ".R"), use_test)
```
Test/check
```{r check}
check()
```
```{r}
usethis::use_build_ignore("pkgdev.Rmd")
usethis::use_build_ignore("desktop.ini")
usethis::use_git_ignore("desktop.ini")
```
```{r}
devtools::build_readme()
```
Install the package
```{r}
install()
```