26. Creating this package

Nathan Brouwer

2018-12-10

Introduction

The following code outlines the key steps I did, principally using the usethis package.

Packages

I use these packages for setting things up

library(devtools)
library(usethis)
library(here)

Create repository

I create a shroom git repo then cloned into it by hand by creating an RStudio Project.

Set up package with usethis

I then used create_package() within my project directory to build the basic package infrastructure This overights the initial project (after a handy prompt in the console).

create_package(path = getwd())

Create vignette infrastructure

Create a vignette infrastructure and dummy vignette

usethis::use_vignette("Results-model-equation")

Create “readme” and “news” files

use_readme_rmd()
use_news_md()

Create git ignore

Am not sure how to use this properly yet

use_git_ignore(".pdf", directory = ".")

Add required packages

use_package("dplyr", "Imports")
use_package("tidyr", "Imports")
use_package("ggplot2", "Imports")
use_package("nlme", "Imports")
use_package("lme4", "Imports")
use_package("bbmle", "Imports") #bbmle
use_package("RCurl", "Imports")
use_package("GGally", "Imports")
use_package("broom", "Imports")
use_package("arm", "Imports")
use_package("psych", "Imports")
devtools::use_package("stringi", "Imports")
devtools::use_package("stringr", "Imports")
devtools::use_package("ggpubr", "Imports")
devtools::use_package("plotrix", "Imports")
devtools::use_package("here", "Imports")

devtools::use_package("cowplot", "Imports")



devtools::use_package("data.tree", "Imports")
devtools::use_package("treemap", "Imports")
#use_package("igraph", "Imports")

devtools::use_package("PRISMAstatement",
                      "Imports")


devtools::use_package("sjPlot", "Imports")
devtools::use_package("sjlabelled", "Imports")
devtools::use_package("sjmisc", "Imports")

devtools::use_package("visreg", "Imports")

Don’t save/load user workspace between sessions

use_blank_slate()

Use roxygen for documentation

use_roxygen_md()

Package-level documents

“Adds a dummy .R file that will prompt roxygen to generate basic package-level documentation.”

use_package_doc()

Use pkgdown

For making front end website

use_pkgdown()

Set up data

dir.create(here("/inst"))
dir.create(here("/inst/extdata"))

Look at data in my extdata file

External data is stored in “/inst/extdata”

list.files(here::here("/inst/extdata"))

Raw data

milk_raw <- read.csv(here::here("/inst/extdata",
                    "skibiel_mammalsmilk_raw.csv"))

use_data(milk_raw)
use_r("milk_raw")

Other data data

Just the fat column

milk <- read.csv(here::here("/inst/extdata",
                    "skibiel_mammalsmilk.csv"))

use_data(milk)
use_r("milk")

Just the primates and relatives rows

milk_primates <- read.csv(here::here("/inst/extdata",
                    "skibiel_primate_fat.csv"))

use_data(milk_primates)
use_r("milk_primates")

Just the fat column

milk_fat <- read.csv(here::here("/inst/extdata",
                    "skibiel_fat.csv"))

use_data(milk_fat)
use_r("milk_fat")

License

http://kbroman.org/pkg_primer/pages/licenses.html

usethis::use_mit_license(name = "Nathan Brouwer")

#use_data_raw()

Spell check

use_spell_check

Other potentially useful usethis functions

use_r() #Create or edit a .R file

use_build_ignore() Add files to .Rbuildignore

use_version() use_dev_version() Increment package version

edit_r_profile() edit_r_environ() edit_r_makevars() edit_rstudio_snippets() edit_git_config() edit_git_ignore()

use_directory() Use a directory

devtools functions

“Builds package vignettes using the same algorithm that R CMD build does”

devtools::build_vignettes()

“This uses a fairly rudimentary algorithm where any files in ‘inst/doc’ with a name that exists in ‘vignettes’ are removed.”

clean_vignettes() 

pckgdown functions

pkgdown::build_site()

check_failures

Rcmd.exe

“Clean and rebuild” ==> Rcmd.exe INSTALL –preclean –no-multiarch –with-keep.source mammalsmilk

“Install restart” ==> Rcmd.exe INSTALL –no-multiarch –with-keep.source mammalsmilk

Devtools function

## "Document"
devtools::document(roclets=c('rd', 'collate', 'namespace'))

## "Load all"
devtools::load_all(".")

## devtools::build_vignettes()

## "Check"
devtools::check()