knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(annotater)
annotater
came to be while teaching workshops or helping peers and realizing that many issues relate to package installation failures and dependency issues for packages that were not even used in a problematic script. Scripts get passed around, code is copied and pasted, and we might not know what certain packages are for. Additionally, it is often useful to specify a package's source and version within a script, for reproducibility purposes and to keep a record of where any of the packages can be obtained.
This package works around a suite of functions that match package load calls (i.e. library
and require
) in a character string with one line per element, and replace them with annotated versions. As of version 0.2.0, loading packages with pacman::p_load
is also supported.
First, match_pkg_names
produces a tibble of package load calls and package names.
pkgs_string <- c("library(boot)\nrequire(Matrix)") match_pkg_names(pkgs_string)
The values in this tabular output are then passed to
utils::packageDescription
, which parses and returns the 'DESCRIPTION' file of an installed package. Fields of interest from these descriptions are then used to build the annotations.
The 'Title' field from a package's description makes for a good summary of what it does, so annotate_pkg_calls
uses it to build annotations. These titles are inserted after each package load call, separated by a commenting symbol.
pkgs_string <- c("library(boot)\nrequire(tools)") annotate_pkg_calls(pkgs_string)
A similar approach is used by annotate_repo_source
to paste the repository source and version number.
pkgs_string <- c("library(boot)\nrequire(lattice)") annotate_repo_source(pkgs_string)
Titles, repositories and version numbers can be annotated together in the output from annotate_repostitle
.
pkgs_string <- c("library(boot)\nrequire(lattice)") annotate_repostitle(pkgs_string)
To annotate which functions are being called from each loaded package, use annotate_fun_calls
.
testcode <- c('library(purrr) x <- list("a", 1, c("bo","bi","bu")) pluck(x, 1) map(x, pluck, 2)') annotate_fun_calls(testcode)
To annotate which datasets are being called from each loaded package, use annotate_pkg_datasets
.
testcode <- c('library(tidyr) summary(household) plot(fish_encounters)') annotate_pkg_datasets(testcode)
tidyverse
and other metapackagesThe tidyverse
package is a meta-package with few exported functions of its own, so the annotation tools provided here (annotate_fun_calls
) will not match the functions from the various individual packages (such as dplyr
or readr
) that get attached when loading tidyverse
. As of version 0.2.2, load calls for metapackages can be replaced with separate calls to each of the core metapackage components as defined by their respective attach.R
files.
These main package functions can be called through their respective RStudio addins, written to work on the active .R or .Rmd file open in the Source pane.
Describes the packages being loaded by calling annotate_pkg_calls
.
Adds the source and version by calling annotate_repo_source
. This addin aligns the commenting symbols vertically for aesthetic purposes.
Adds titles, sources, and versions by calling annotate_repostitles
.
Adds all the unique functions being called by each loaded package, calls annotate_fun_calls
.
Adds all the datasets being called by each loaded package, calls annotate_pkg_datasets
. Works for lazy loaded data, namespaced data, or objects called with data
.
Replace a call to a metapackage with multiple calls to each of its core components.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.