Convert scripts that use the palmerpenguins
package to use the versions of the penguins and
penguins_raw datasets that are available in R ≥ 4.5.0.
The Palmer Penguins datasets have become very
popular in the R community, especially in educational contexts, and
as an alternative
to the iris dataset. Now that penguins and
penguins_raw are in datasets (R ≥ 4.5.0),
they are more widely available and easier to get started with,
especially for new R users and for use in teaching.
The version of penguins in datasets (R
≥ 4.5.0) has some shorter variable names than the
palmerpenguins equivalent (e.g. bill_len
instead of bill_length_mm), for more compact code and data
display. It does mean, however, that for those wanting to use R’s
version of penguins, it isn’t simply a case of removing the
call to library(palmerpenguins) or replacing
palmerpenguins with datasets in
data("penguins", package = "palmerpenguins") and the script
still running. The basepenguins package takes care of
converting files by removing the call to palmerpenguins
and making the necessary conversions to variable names, ensuring that
the resulting scripts still run using the datasets
versions of penguins and penguins_raw.
basepenguins is available on CRAN:
install.packages("basepenguins")Or get the development version from R-universe:
install.packages("basepenguins", repos = "https://ellakaye.r-universe.dev")If a file is ‘convertible’, i.e. it contains
library(palmerpenguins) or
data("penguins", package = "palmerpenguins") (with any
style of quotes), and has one of a specified set of extensions (by
default "R", "r", "qmd",
"rmd", "Rmd"), then converting it will do the
following:
library(palmerpenguins) (or same with
palmerpenguins in quotes) with the empty
string""data("penguins", package = "palmerpenguins")
(with any style of quotes) with
data("penguins", package = "datasets")bill_length_mm -> bill_lenbill_depth_mm -> bill_depflipper_length_mm -> flipper_lenbody_mass_g -> body_massends_with("_mm") with
starts_with("flipper_"), starts_with("bill_")Here, we simply show the ‘before-and-after’ when converting a single
file. For a more extensive guide to using the package, see the Get
Started vignette, vignette("basepenguins").
library(basepenguins)Get and see an example file provided by the package (adapted from a section of the palmerpenguins Get Started vignette):
penguins_file <- example_files("penguins.R")
cat(readLines(penguins_file), sep = "\n")
#> library(palmerpenguins)
#> library(ggplot2)
#> library(dplyr)
#>
#> # exploring scatterplots
#> penguins |>
#> select(body_mass_g, ends_with("_mm")) |>
#> ggplot(aes(x = flipper_length_mm, y = body_mass_g)) +
#> geom_point(aes(color = species, shape = species), size = 2) +
#> scale_color_manual(values = c("darkorange", "darkorchid", "cyan4"))Then, convert the file (saving it to a new file) and see the new script:
convert_files(penguins_file, "penguins_converted.R")
#> - ends_with("_mm") replaced on line 7 in penguins_converted.R
#> - Please check the changed output files.cat(readLines("penguins_converted.R"), sep = "\n")
#>
#> library(ggplot2)
#> library(dplyr)
#>
#> # exploring scatterplots
#> penguins |>
#> select(body_mass, starts_with("flipper_"), starts_with("bill_")) |>
#> ggplot(aes(x = flipper_len, y = body_mass)) +
#> geom_point(aes(color = species, shape = species), size = 2) +
#> scale_color_manual(values = c("darkorange", "darkorchid", "cyan4"))There are four functions in basepenguins to convert
mulitple files. In each case, the default extensions
(i.e. file types to convert) are "R", "r",
"qmd", "rmd", "Rmd". If
input contains non-convertible files (i.e. without the
specified extensions or without reference to
palmerpenguins), they will be copied unmodified to their
new output location in convert_files() and
convert_dir(), or left untouched by
convert_files_inplace() and
convert_dir_inplace().
convert_files(input, output, extensions) |
convert an input vector of files to new
output locations |
convert_files_inplace(input, extensions) |
convert a vector of files by overwriting them |
convert_dir(input, output, extensions) |
convert all files in input directory into a new
output directory (preserving nesting structure) |
convert_dir_inplace(input, extensions) |
convert all files in a directory by overwriting them |