package-code.Rmd

---
title: "R Notebook"
output: html_notebook
---

This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 

Try executing this chunk by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Cmd+Shift+Enter*. 

```{r}
#Tutorial for making R package using devtools

#https://tinyheero.github.io/jekyll/update/2015/07/26/making-your-first-R-package.html
#https://r-pkgs.org/description.html
```


```{r}
library(roxygen2)
library(devtools)
```

```{r}
#Create framework of the R package
#devtools::create("BIGr")

#Will need to edit the DESCRIPTION file with the correct information
```

```{r}
##Function to extract read count data from MADC file
```

```{r}
#Functions are added either to individual .R files, or lumped together in .R files with common theme (such as a diversity .R file with all genomic diversity analyses)
```

```{r}
#Testing the R functions
#https://r-pkgs.org/testing-basics.html
devtools::load_all()
```


```{r}
setwd("/Users/ams866/Library/CloudStorage/Box-Box/AS_Projects/Pipelines/R_packge/BIGr")
#Each time you add new documentation to your R function, you need to run devtools::document() again to re-generate the .Rd files.
devtools::document()
```
```{r}
#Making the citation file
usethis::use_citation()
```


```{r}
#Make a vignette(s) to provide examples for using the package

usethat::use_vignette("introduction")
```

```{r}
#Make the pdf manual
setwd("/Users/ams866/Library/CloudStorage/Box-Box/AS_Projects/Pipelines/R_packge/BIGr")
devtools::build_manual()
```

```{r}
#Adding needed packages to description
usethis::use_package("dplyr") # Default is "Imports"
usethis::use_package("foreach")
usethis::use_package("doParallel")
#usethis::use_package("kinship2", min_version = "1.9.6.1")

#If wanting to add specific minimum versions
# exact version
usethis::use_package("Rdpack", min_version = "0.7")

# min version = currently installed version
usethis::use_package("tidyr", min_version = TRUE)
usethis::use_package("readr", min_version = TRUE)
```


```{r}
#Test install
devtools::install_github("alex-sandercock/BIGr")
```

```{r}
#library(BIGr)

dosage2vcf(dart.report = "/Users/ams866/Library/CloudStorage/Box-Box/AS_Projects/Strawberry/Report_DSt21-8501/DSt23-8501_Allele_Dose_Report.csv",
           dart.counts = "/Users/ams866/Library/CloudStorage/Box-Box/AS_Projects/Strawberry/Report_DSt21-8501/Report_DSt23-8501_Counts.csv",
           ploidy=2,
           output.file = "Test")
```
```{r}
install.packages("devtools") #If not already installed
library(devtools)
devtools::install_github("Breeding-Insight/BIGr")
library("BIGr")
```