RWsearch stands for « Search in R packages, task views, CRAN and in the Web ».
RWsearch is a management tool that serves several purposes:
Compare to other packages (packagefinder, websearchr) or web services (RDocumentation, rdrr) with similar objectives, the search options of RWsearch are more sophisticated and allow for a finer search. RWsearch also addresses a much larger number of web search engines. Non-standard evaluation (or evaluation of non-standard content) makes it user friendly.
This vignette deals with points 5 and 6. Points 1 to 4 and 7 to 8 are discussed in other vignettes.
For the rest of this vignette, crandb must be loaded in .GlobalEnv as well as one vector and one list of selected packages. Read in Vignette 1 the function used to download a fresh version of crandb. Here, we use the small file of 50 packages provided in RWsearch/data.
crandb_load(system.file("data", "zcrandb.rda", package = "RWsearch")) # $newfile # crandb loaded. 50 packages listed between 2013-08-04 and 2019-02-10 vec <- s_crandb(find, select = "P") ; vec #  "findR" "packagefinder" "wfindr" lst <- s_crandb_list(thermodynamic, "chemical reaction", select = "PT") ; lst # $thermodynamic #  "aiRthermo" "CHNOSZ" # # $`chemical reaction` #  "bioPN" "RxnSim" "sbioPN" ls() #  "crandb" "lst" "vec"
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.
|CRAN||pdf in browser||
|crandb||text||txt file, pager||
|crandb||text||md file, pager||
|crandb||text||tex + pdf files||
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
p_archive() opens the
p_check() opens the
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
p_html2() opens the local help pages of each packages. The urls start by
file:///C:/ (on Windows).
p_vig() opens one html page that lists the vignettes of the selected packages. The url starts by
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
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.
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_table7pdf() and their variants rely on the automatic scaling tools of html and pdf files to display more columns in a readable manner.
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_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.
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 <firstname.lastname@example.org> # 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@example.com> # 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.pdf
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 <firstname.lastname@example.org> # 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
By default, pdf files
pkgstext_chemicalreaction.pdf are automatically generated in the current directory rom the tex files. The beginning of the “pkgstext_thermodynamic.pdf” file looks like:
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.