pkgdoc

Dataframe the documentation of available packages, and reference objects across multiple packages by package or concept. Combined with krittr::kable() or DT::datatable(), pkgdoc allows you to reference functions by package or concept across multiple packages and to provide links to each topic’s help file (similar to the Reference section of a pkgdown website but not limited to a single package).

• Reference and tutorial
• pkgdoc in action

Installation

# install.packages("devtools")
devtools::install_github("maurolepore/pkgdoc")

Example

library(pkgdoc)

search_docs() creates a dataframe of documentation available to you.

# Documentation of all installed packages
search_docs()
#> # A tibble: 71,919 x 11
#>    package libpath id    name  title topic encoding type  alias keyword
#>    <chr>   <chr>   <chr> <chr> <chr> <chr> <chr>    <chr> <chr> <chr>  
#>  1 acepack C:/Use~ 1/1   ace   Alte~ ace   ""       help  ace   models 
#>  2 acepack C:/Use~ 1/2   avas  Addi~ avas  ""       help  avas  models 
#>  3 acepack C:/Use~ 1/2   avas  Addi~ avas  ""       help  avas~ models 
#>  4 addine~ C:/Use~ 2/1   addi~ RStu~ addi~ ""       help  addi~ <NA>   
#>  5 addine~ C:/Use~ 2/1   addi~ RStu~ addi~ ""       help  addi~ <NA>   
#>  6 addine~ C:/Use~ 2/2   find~ Find~ find~ ""       help  find~ <NA>   
#>  7 addine~ C:/Use~ 2/3   inse~ Inse~ inse~ ""       help  inse~ <NA>   
#>  8 addine~ C:/Use~ 2/4   refo~ Refo~ refo~ ""       help  refo~ <NA>   
#>  9 addine~ C:/Use~ 2/5   subs~ Subs~ subs~ ""       help  subs~ <NA>   
#> 10 AGBflu~ C:/Use~ 3/1   AGBf~ AGBf~ AGBf~ UTF-8    help  AGBf~ intern~
#> # ... with 71,909 more rows, and 1 more variable: concept <chr>

some_packages <- c("utils", "base")
search_docs(some_packages)
#> # A tibble: 5,935 x 11
#>    package libpath id    name  title topic encoding type  alias keyword
#>    <chr>   <chr>   <chr> <chr> <chr> <chr> <chr>    <chr> <chr> <chr>  
#>  1 base    C:/Use~ 10/1  abbr~ Abbr~ abbr~ ""       help  abbr~ charac~
#>  2 base    C:/Use~ 10/2  agrep Appr~ agrep ""       help  agrep charac~
#>  3 base    C:/Use~ 10/2  agrep Appr~ agrep ""       help  agre~ charac~
#>  4 base    C:/Use~ 10/2  agrep Appr~ agrep ""       help  fuzz~ charac~
#>  5 base    C:/Use~ 10/2  agrep Appr~ agrep ""       help  .ama~ charac~
#>  6 base    C:/Use~ 10/2  agrep Appr~ agrep ""       help  .ama~ charac~
#>  7 base    C:/Use~ 10/3  all.~ Test~ all.~ ""       help  all.~ progra~
#>  8 base    C:/Use~ 10/3  all.~ Test~ all.~ ""       help  all.~ progra~
#>  9 base    C:/Use~ 10/3  all.~ Test~ all.~ ""       help  all.~ progra~
#> 10 base    C:/Use~ 10/3  all.~ Test~ all.~ ""       help  all.~ progra~
#> # ... with 5,925 more rows, and 1 more variable: concept <chr>

reference_package() and reference_concept() allow you to pick specific documentation.

reference_package(c("stats", "MASS"))
#> Warning:   All packages should be attached `strip_s3class` to work properly.
#>   Not attached: MASS
#> # A tibble: 970 x 5
#>    topic     alias            title                   concept       package
#>    <chr>     <chr>            <chr>                   <chr>         <chr>  
#>  1 .checkMF~ .checkMFClasses~ Functions to Check the~ Utilities     stats  
#>  2 .preform~ .preformat.ts, ~ Printing and Formattin~ Time Series   stats  
#>  3 abbey     abbey            Determinations of Nick~ Datasets ava~ MASS   
#>  4 accdeaths accdeaths        Accidental Deaths in t~ Datasets ava~ MASS   
#>  5 acf       acf, ccf, pacf,~ Auto- and Cross- Covar~ Time Series   stats  
#>  6 acf2AR    acf2AR           Compute an AR Process ~ Time Series   stats  
#>  7 add.scope add.scope, drop~ Compute Allowed Change~ Statistical ~ stats  
#>  8 add1      add1, drop1      Add or Drop All Possib~ Statistical ~ stats  
#>  9 addmargi~ addmargins       Puts Arbitrary Margins~ totals        stats  
#> 10 addmargi~ addmargins       Puts Arbitrary Margins~ margins       stats  
#> # ... with 960 more rows

reference_concept(c("combine strings", "files", "PCA"))
#> # A tibble: 4 x 5
#>   topic     alias                    title              concept     package
#>   <chr>     <chr>                    <chr>              <chr>       <chr>  
#> 1 find.pac~ find.package, path.pack~ Find Packages      files       base   
#> 2 paste     paste, paste0            Concatenate Strin~ combine st~ base   
#> 3 prcomp    prcomp, plot, predict, ~ Principal Compone~ PCA         stats  
#> 4 princomp  princomp, plot, print, ~ Principal Compone~ PCA         stats

Use knittr::kable() or DT::datatable() for the links to become clickable.

library(fgeo)
#> -- Attaching packages ------------------------------------------------------- fgeo 0.0.0.9002 --
#> v fgeo.analyze 0.0.0.9003     v fgeo.tool    0.0.0.9005
#> v fgeo.plot    0.0.0.9402     v fgeo.x       0.0.0.9000
#> -- Conflicts --------------------------------------------------------------- fgeo_conflicts() --
#> x fgeo.tool::filter() masks stats::filter()

reference_concept(
  c("datasets", "plot functions"),
  url = "https://forestgeo.github.io/",
  ) %>% 
  arrange(concept) %>%
  head() %>% 
  knitr::kable()

topic	alias	title	concept	package
?	datasets, elevation, habitat, stem5, stem6, taxa, tree5, tree6, vft_4quad, tree6_3species	Datasets from Luquillo, Puerto Rico.	datasets	fgeo.x
?	download_data	Download data from fgeo.data.	datasets	fgeo.x
?	example_path	Path to directory containing example data.	datasets	fgeo.x
?	autoplot	Quick habitat plots.	plot functions	fgeo.plot
?	autoplot	Quick plot of species distribution and/or topography.	plot functions	fgeo.plot
?	autoplot_by_species	List plots of species distribution and topography (good for pdf output).	plot functions	fgeo.plot