x) Creating data objects for an R Package • biodata

For overview read https://r-pkgs.org/data.html

Preliminaries

library(usethis)
library(here)

Create /data-raw

This creates the folder /data-raw and adds a file DATASET.R

usethis::use_data_raw()

Create data processing scripts

Create script file

usethis::use_data_raw(name = "human_gene_lengths")

Get the data

In this case I’m using data from Whitlock and Schulter’s 2nd edition of Analysis of Biological Data, downloaded from the book’s website https://whitlockschluter.zoology.ubc.ca/

human_gene_lengths <- read.csv(url("http://whitlockschluter.zoology.ubc.ca/wp-content/data/chapter04/chap04e1HumanGeneLengths.csv"))

names(human_gene_lengths) <- "gene_length"

Create the .RData file

This converts and R object into a .RData file that can be loaded with data().

If necessary it creates a data/ folder for the package.

usethis::use_data(human_gene_lengths, 
                  overwrite = TRUE)

Create documentation file for the data

All datasets need a .R file the goes in the R/ folder, along with any .R files that define functions.

usethis::use_r(name = "human_gene_lengths", open = T)

This is an opportunity though to provide full documentation for the dataset. A minimal helpfile could look like this:

#' Dataset helpfile header . . .
#'
#' Short description of data . . .
#'
#' @format A data frame with x rows and y column(s)
#' \describe{
#'   \item{column1}{Describe column here . . .}
#'   \item{column2}{Describe column here . . .}
#'  ...
#' }
#' @source \url{http://www.whereyougotthedata.com/"}
#'
"dataset_name"

You can also add additional things that appear in R help files such as full citation information and examples.

For other examples see https://github.com/hadley/babynames/blob/master/R/data.R

The function defined below can be used to build this helpfile template automatically. It is also found in my biodata package.

# Function to build template for dataset helpf file
make_dateset_helpfile <- function(dataset,
                                  dataset_name  = "temp"){
  library(here)

  dataset <- human_gene_lengths
  dataset_name <- "human_gene_lengths"
  to_sink <- paste(dataset_name,"R",sep = ".")
  to_sink_with_dir <- here::here("R",to_sink)

  sink(to_sink_with_dir)
  cat("#' Dataset helpfile header . . .\n")
  cat("#'\n")
  cat("#' Short description of data . . . \n")
  cat("#'\n")
  cat("#' @format A data frame with ", dim(dataset)[1], " rows and ",dim(dataset)[2]," column(s)\n", sep = "")
  cat("#' \\describe{\n", sep = "")

  for(i in 1:ncol(dataset)){
    colname.i <- names(dataset)[i]
    cat("#'   \\item{",colname.i,"}{Describe column ",colname.i, " here . . .}\n",sep = "")
  }

  cat("#' }\n")
  cat("#' @source \\url{http://www.whereyougotthedata.com/}\n")
  cat("#'\n")
  cat("'",dataset_name,"'", sep = "")
  sink()
}