V2: Display and download the documentation
Introduction
RWsearch stands for « Search in R packages, task views, CRAN and in the Web ».
This vignette introduces the following features cited in the README file:
.5. Display the results as a list or as a table in the console or in the browser and save them as txt, md, html, tex or pdf files.
.6. In one instruction, download in one directory the whole documentation and the tar.gz files related to one or several packages. This is the perfect tool to read the documentation off-line and study the source code of a package.
(Down)Load crandb and extract packages
In this vignette, crandb must be loaded in
.GlobalEnv. This can be done either by downloading a fresh
version of crandb or by loading a file. Read Vignette 1 and the
details about crandb_down(). Here, we use
the small file of 94 packages saved in RWsearch/data.
or
crandb_load(system.file("data", "zcrandb.rda", package = "RWsearch"))
# $newfile
# crandb loaded. 94 packages listed between 2016-02-11 and 2024-09-20"
vec <- s_crandb(find, select = "P") ; vec
# [1] "findR" "packagefinder" "wfindr"
lst <- s_crandb_list(thermodynamic, "chemical reaction", select = "PT") ; lst
# $thermodynamic
# [1] "aiRthermo" "CHNOSZ"
#
# $`chemical reaction`
# [1] "RxnSim"
ls()
# [1] "crandb" "lst" "vec" Explore the selected packages
RWsearch can print the information related to the selected packages in the console, in the pager, in txt, md, tex and pdf files and in html pages.
The source of information can be R itself, crandb or your local CRAN.
The information provided by R or your local CRAN is usually in html or pdf format. The information extracted from crandb can be presented in a table or in a classical text with sections and sub-sections.
| Source | Format | Output | Functions |
|---|---|---|---|
| CRAN | html | browser | p_page(),
p_archive(),
p_check(),
e_check() |
| R | html | browser | p_html(),
p_html2(),
p_man(),
p_vig(),
p_vig_all() |
| CRAN | pdf in browser | p_pdfweb() |
|
| R | pdf viewer | p_pdf() |
|
| crandb | table | console | p_table(),
p_table2(),
p_table5(),
p_table7(),
p_vers(),
p_deps() |
| crandb | table | browser | p_display(),
p_display5(),
p_display7() |
| crandb | table | pdf file | table2pdf(),
p_table2pdf() |
p_table3pdf(),
p_table5pdf(),
p_table7pdf() |
|||
| crandb | text | txt file, pager | p_text() |
| crandb | text | md file, pager | p_text2md() |
| crandb | text | tex + pdf files | p_text2pdf() |
HTML and PDF formats
A simple but useful feature is to launch the html pages directly from R.
Local pdf pages are opened in the pdf viewer.
Remote pdf pages are opened in the pdf application provided by the browser.
p_page() opens the
yourCRAN/packagespkg/index.html pages
p_archive() opens the
https://cran.r-project.org/src/contrib/Archive/pkg
pages.
p_check() opens the
yourCRAN/checks/check.results.pkg.html pages.
e_check() opens the
yourCRAN/checks/check.results.emailadresse.html
pages (the check page of each maintainer identified by the maintainer
email addresses)
p_html() opens the local help pages of
each packages. The urls start by http://127.0.0.1:.
p_html2() opens the local help pages of
each packages. The urls start by file:///C:/ (on
Windows).
p_man() opens the CRAN help pages of
each packages. The urls start by
https://search.r-project.org/.
p_vig() opens one html page that lists
the vignettes of the selected packages. The url starts by
http://127.0.0.1:.
p_vig_all() opens one html page that
lists the vignettes of all installed packages. This can be a huge list.
The url starts by http://127.0.0.1:.
p_pdf() opens the manual(s) of the
selected packages in the pdf viewer. If the manuals do not exist, they
are created on the fly by Texlive or Miktex.
p_pdfweb() opens the pdf file
yourCRAN/packages/pkg/pkg.pdf in the pdf
application provided by the browser.
Table format
The generic function is p_table() which
has an argument columns to select any (combination of)
column(s) in crandb. The default value prints
3 columns (Package name + Title + Description). Other predefined
functions print 2 columns (Package name + Title), 5 columns (3 columns +
Author + Maintainer), 7 columns (5 columns + Version + Published). In
the console, the width is limited and the most interesting function is
p_table2(); It displays the package name
and package title.
p_deps(),
p_vers() and
p_vers() print the package dependencies
and the package versions installed on the computer (version) and the
binary version and the source version available on CRAN.
p_display7(),
p_table7pdf() and their variants rely on
the automatic scaling tools of html and pdf files to display more
columns in a readable manner.
p_table2() prints in the console
p_deps() prints in the console
p_vers() prints in the console
p_vers_deps() prints in the console
p_vers_deps(vec)
# nsloaded version binary crandb difvb difbc compare gcc tdeps ndeps
# magrittr TRUE 2.0.3 2.0.3 2.0.3 0 0 0 yes 0 0
# curl FALSE 5.2.3 5.2.3 5.2.3 0 0 0 yes 0 0
# sys FALSE 3.4.3 3.4.3 3.4.3 0 0 0 yes 0 0
# rstudioapi FALSE 0.16.0 0.16.0 0.16.0 0 0 0 no 0 0
# R6 FALSE 2.5.1 2.5.1 2.5.1 0 0 0 no 0 0
# sourcetools FALSE 0.1.7-1 0.1.7-1 0.1.7-1 0 0 0 yes 0 0
# fastmap TRUE 1.2.0 1.2.0 1.2.0 0 0 0 yes 0 0
# commonmark FALSE 1.9.2 1.9.2 1.9.2 0 0 0 yes 0 0
# cpp11 FALSE 0.5.0 0.5.0 0.5.0 0 0 0 no 0 0
# base64enc FALSE 0.1-3 0.1-3 0.1-3 0 0 0 yes 0 0
# backports FALSE 1.5.0 1.5.0 1.5.0 0 0 0 yes 0 0
# yaml TRUE 2.3.10 2.3.10 2.3.10 0 0 0 yes 0 0
# utf8 FALSE 1.2.4 1.2.4 1.2.4 0 0 0 yes 0 0
# rappdirs FALSE 0.3.3 0.3.3 0.3.3 0 0 0 yes 0 0
# evaluate FALSE 1.0.0 1.0.0 1.0.1 0 -1 -1 no 0 0
# cli TRUE 3.6.3 3.6.3 3.6.3 0 0 0 yes 1 0
# glue FALSE 1.8.0 1.8.0 1.8.0 0 0 0 yes 1 0
# rlang TRUE 1.1.4 1.1.4 1.1.4 0 0 0 yes 1 0
# jsonlite FALSE 1.8.9 1.8.9 1.8.9 0 0 0 yes 1 0
# clipr FALSE 0.8.0 0.8.0 0.8.0 0 0 0 no 1 0
# mime FALSE 0.12 0.12 0.12 0 0 0 yes 1 0
# generics FALSE 0.1.3 0.1.3 0.1.3 0 0 0 no 1 0
# pkgconfig TRUE 2.0.3 2.0.3 2.0.3 0 0 0 no 1 0
# fs FALSE 1.6.4 1.6.4 1.6.4 0 0 0 yes 1 0
# digest TRUE 0.6.36 0.6.37 0.6.37 -1 0 -1 yes 1 0
# textutils FALSE <NA> 0.4-1 0.4-1 -2 0 -2 no 1 0
# Rcpp FALSE 1.0.13 1.0.13 1.0.13 0 0 0 yes 2 0
# xtable FALSE 1.8-4 1.8-4 1.8-4 0 0 0 no 2 0
# withr FALSE 3.0.1 3.0.1 3.0.1 0 0 0 no 2 0
# fansi FALSE 1.0.6 1.0.6 1.0.6 0 0 0 yes 2 0
# stringi FALSE 1.8.4 1.8.4 1.8.4 0 0 0 yes 3 0
# crayon FALSE 1.5.3 1.5.3 1.5.3 0 0 0 no 3 0
# xfun FALSE 0.48 0.48 0.48 0 0 0 yes 3 0
# askpass FALSE 1.2.1 1.2.1 1.2.1 0 0 0 yes 1 1
# timechange FALSE 0.3.0 0.3.0 0.3.0 0 0 0 yes 1 1
# checkmate FALSE 2.3.2 2.3.2 2.3.2 0 0 0 yes 2 1
# highr FALSE 0.11 0.11 0.11 0 0 0 no 4 1
# tinytex FALSE 0.53 0.53 0.53 0 0 0 no 4 1
# openssl FALSE 2.2.2 2.2.2 2.2.2 0 0 0 yes 2 2
# cachem FALSE 1.1.0 1.1.0 1.1.0 0 0 0 yes 3 2
# later FALSE 1.3.2 1.3.2 1.3.2 0 0 0 yes 4 2
# pander FALSE <NA> 0.6.5 0.6.5 -2 0 -2 yes 8 2
# lubridate FALSE 1.9.3 1.9.3 1.9.3 0 0 0 yes 4 3
# memoise FALSE 2.0.1 2.0.1 2.0.1 0 0 0 no 4 3
# lifecycle TRUE 1.0.4 1.0.4 1.0.4 0 0 0 no 5 3
# qpdf FALSE 1.3.4 1.3.4 1.3.4 0 0 0 yes 6 4
# vctrs FALSE 0.6.5 0.6.5 0.6.5 0 0 0 yes 6 4
# htmltools TRUE 0.5.8.1 0.5.8.1 0.5.8.1 0 0 0 yes 6 4
# knitr FALSE 1.48 1.48 1.48 0 0 0 no 8 4
# pdftools FALSE 3.4.1 3.4.1 3.4.1 0 0 0 yes 7 5
# reactR FALSE 0.6.1 0.6.1 0.6.1 0 0 0 no 7 5
# fontawesome FALSE 0.5.2 0.5.2 0.5.2 0 0 0 no 7 5
# jquerylib FALSE 0.1.4 0.1.4 0.1.4 0 0 0 no 7 5
# purrr FALSE 1.0.2 1.0.2 1.0.2 0 0 0 yes 8 6
# promises FALSE 1.3.0 1.3.0 1.3.0 0 0 0 yes 9 6
# tidyselect FALSE 1.2.1 1.2.1 1.2.1 0 0 0 yes 10 6
# httr FALSE 1.4.7 1.4.7 1.4.7 0 0 0 no 9 7
# httpuv FALSE 1.6.15 1.6.15 1.6.15 0 0 0 yes 10 7
# pillar FALSE 1.9.0 1.9.0 1.9.0 0 0 0 no 10 7
# stringr FALSE 1.5.1 1.5.1 1.5.1 0 0 0 no 11 7
# sass FALSE 0.4.9 0.4.9 0.4.9 0 0 0 yes 11 8
# tibble FALSE 3.2.1 3.2.1 3.2.1 0 0 0 yes 13 10
# findR FALSE 0.2.1 0.2.1 0.2.1 0 0 0 no 18 14
# dplyr FALSE 1.1.4 1.1.4 1.1.4 0 0 0 yes 19 15
# wfindr FALSE <NA> 0.1.0 0.1.0 -2 0 -2 no 20 16
# bslib FALSE 0.8.0 0.8.0 0.8.0 0 0 0 no 21 17
# tidyr FALSE 1.3.1 1.3.1 1.3.1 0 0 0 yes 26 20
# rmarkdown FALSE 2.28 2.28 2.28 0 0 0 no 30 25
# htmlwidgets TRUE 1.6.4 1.6.4 1.6.4 0 0 0 no 31 26
# formattable FALSE 0.2.1 0.2.1 0.2.1 0 0 0 no 32 27
# reactable FALSE 0.4.4 0.4.4 0.4.4 0 0 0 no 33 28
# shiny FALSE 1.9.1 1.9.1 1.9.1 0 0 0 no 35 29
# shinyjs FALSE 2.1.0 2.1.0 2.1.0 0 0 0 no 36 30
# htmlTable FALSE 2.4.3 2.4.3 2.4.3 0 0 0 no 39 34
# shinybusy FALSE 0.3.3 0.3.3 0.3.3 0 0 0 no 44 38
# packagefinder FALSE <NA> 0.3.5 0.3.5 -2 0 -2 no 77 71 
Text format
More information can be printed with texts in classical format than in tables as the page width is usually not a constraint.
RWsearch has 3 functions:
p_text(),
p_text2md(),
p_text2pdf() to produce files in classical
UTF-8 text, UTF-8 markdown and pdf format. The level of information
extracted from crandb is controlled by the
arguments beforetext, f_maintext, aftertext.
Any column of crandb can be selected as well
as the links to the main files in CRAN. An internet connexion is
required as many queries are sent to CRAN to find the NEWS and README
urls.
p_text() prints in a txt file
The following text appears in the “pkgstext_thermodynamic.txt” file:
# == aiRthermo ==
# aiRthermo: Atmospheric Thermodynamics and Visualization
# Deals with many computations related to the thermodynamics of atmospheric processes. It includes many functions designed to consider the density of air with varying degrees of water vapour in it, saturation pressures and mixing ratios, conversion of moisture indices, computation of atmospheric states of parcels subject to dry or pseudoadiabatic vertical evolutions and atmospheric instability indices that are routinely used for operational weather forecasts or meteorological diagnostics.
# Depends: NA
# Imports: NA
# Suggests: NA
# Version: 1.2.1
# Published: 2018-09-16
# Maintainer: Santos J. González-Rojí <[email protected]>
# https://cran.univ-paris1.fr/web/packages/aiRthermo/index.html
# https://cran.univ-paris1.fr/web/packages/aiRthermo/aiRthermo.pdf
# https://cran.univ-paris1.fr/web/packages/aiRthermo/news/news.html
# == CHNOSZ ==
# CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry
# An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.
# Depends: R (>= 3.1.0)
# Imports: grDevices, graphics, stats, utils
# Suggests: limSolve, testthat, knitr, rmarkdown, tufte
# Version: 1.2.0
# Published: 2019-02-10
# Maintainer: Jeffrey Dick <[email protected]>
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/index.html
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/CHNOSZ.pdf
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/NEWS
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/vignettes/anintro.html
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/vignettes/eos-regress.html
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/vignettes/obigt.html
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/vignettes/equilibrium.pdf
# https://cran.univ-paris1.fr/web/packages/CHNOSZ/vignettes/hotspring.pdfp_text2md() prints in a txt file with md extension
The first part of the “pkgstext_thermodynamic.md” file is:
# ---
# title: TITLE
# author: AUTHOR
# date: 2019-02-24
# output:
# pdf_document:
# keep_tex: false
# toc: false
# number_sections: true
# fontsize: 10pt
# papersize: a4paper
# geometry: margin=1in
# ---
#
#
# # aiRthermo
# aiRthermo: Atmospheric Thermodynamics and Visualization
# Deals with many computations related to the thermodynamics of atmospheric processes. It includes many functions designed to consider the density of air with varying degrees of water vapour in it, saturation pressures and mixing ratios, conversion of moisture indices, computation of atmospheric states of parcels subject to dry or pseudoadiabatic vertical evolutions and atmospheric instability indices that are routinely used for operational weather forecasts or meteorological diagnostics.
# Depends: NA
# Imports: NA
# Suggests: NA
# Version: 1.2.1
# Published: 2018-09-16
# Maintainer: Santos J. González-Rojí <[email protected]>
# https://cran.univ-paris1.fr/web/packages/aiRthermo/index.html
# https://cran.univ-paris1.fr/web/packages/aiRthermo/aiRthermo.pdf
# https://cran.univ-paris1.fr/web/packages/aiRthermo/news/news.html p_text2pdf() prints in a pdf file (article style)
By default, pdf files pkgstext_thermodynamic.pdf and
pkgstext_chemicalreaction.pdf are automatically generated
in the current directory rom the tex files. The beginning of the
“pkgstext_thermodynamic.pdf” file looks like:
Download the documentation
p_down() is a smart function designed
for people who need to work offline. It downloads all R package
documentation with just one line of code. The pictures speak by
themselves: 35 files were downloaded in 11 seconds (on one SSD disk and
with a standard ADSL line). Package vectors are downloaded in the
current directory. Package lists are downloaded in sub-directories.
p_down()
p_down(vec, NEWS = TRUE, ChangeLog = TRUE, targz = TRUE)
p_down(lst, NEWS = TRUE, ChangeLog = TRUE, targz = TRUE)
p_down0()
p_down0() has been recently added to
download one or two documents or download the tar.gz package and
decompress it on the fly.