• Creating this package
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    1. Creating this package

    Nathan Brouwer

    2018-11-27

    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("z-updating_package")

    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("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")

    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