In brouwern/shroom: Example Analyses for Cell and Molecular Biology

knitr::opts_chunk$set(echo = TRUE, eval = FALSE)

Introduction

The following code outlines the key steps I did, principally using the usethis package, to set up a this package for containing code relate to this paper:

Skibiel et al 2013. The evolution of the nutrient composition of mammalian milks. Journal of Animal Ecology 82: 1254-1264. https://doi.org/10.1111/1365-2656.12095

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("temp")

Create "readme" and "news" files

use_readme_md()
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("ggpubr", "Imports")

use_package("nlme", "Imports")
use_package("lme4", "Imports")
use_package("bbmle", "Imports")
use_package("RCurl", "Imports")
use_package("GGally", "Imports")
use_package("broom", "Imports")

use_package("arm", "Imports")

devtools::use_package("data.table", "Imports")
devtools::use_package("car", "Imports")
devtools::use_package("lawstat", "Imports")
devtools::use_package("effsize", "Imports")
devtools::use_package("here", "Imports")
devtools::use_package("metafor", "Imports")
devtools::use_package("Formula", "Imports")
devtools::use_package("data.tree", "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

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

brouwern/shroom documentation built on May 24, 2019, 7:54 a.m.