TikiWiki Mod details : wikiplugins-r

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This public repository lists the mods packages available from tikiwiki.org server. It's used by tikiwiki admins to update features that are not included in the public release of Tikiwiki. see TikiMods page on tw.o

wikiplugins : r

authorXavier de Pedro Puente (xavi)
changelog0.1 initial package
0.2 Graphs also allowed inside wiki pages, as png images. Removed the need for StatWiki.r file.
0.3 Png can be loaded in pages (allowed by local .htaccess file in ./temp folder)
0.4 Security checking enabled by default and many new optional params: security, wikisyntax and other graph params. Thanks LPH for your help. Params Filtered.
0.5 parsing xml files fixed. Wrap param added (and enabled by default). Since 0.5.1, calls to the r plugin don't require admin validation, and in addition, can't execute dangerous commands. A new sister plugin is added (rr) which allows executing potentially dangerous commands. Since 0.52, icon is added, and textarea box to allow inserting R code from the plugin helper is added.
0.60 Added basic codemirror css and js file for rsplus (so far, only copied from the Python ones). Further improvements to the highlighter for rsplus to come.
0.61 Removed codemirror css and js files since they are now part of Tiki 7. Plugin made compatible again with Tiki <7. Carriage returns allowed inside R code in pretty trackers through wiki page templates, because PluginR removes all br p /p tags from the content to be parsed by R. Thanks Jonnyb for tips.
0.62 Ported to work with Tiki7.x also (thanks jonnyb), and minor issue fixed with servers where R has no X11 support.
0.70 Added optional generation of SVG and/or PDF files from each plot, in order to allow producing high quality vectorial plots which can be enlarged or edited without loosing quality. Also minor enhancement added for better display of png images when inside tiki slideshows in Tiki 6.5+ and 7.2+.
0.71 Same value pairs for onefile param as with otehr params. Added language files (they work in Tiki8+).
0.72 Added the ability to create and display several png's when the R call wants to generate new graphs from any command and the user writes "# newgraph" before the new graph so that pluginR opens up the required new graphic device.
0.73 Creation of folders for temp only if they are missing (therefore removing the harmless but annoying warning when they exist already)
0.74 R icon shown also in Tiki9. Empty lines above figures from googleVis package removed (thanks RobertPlummer)
0.75 svg generation works again with this small change and r43765 to clean svn code (thanks changi and jyhem)
0.76 Fixing bug introduced in r41927 removing new lines with \n for way too many cases. New param added as removen, to allow the user to choose when to have them removed (like in charts created through googleVis R package)
0.77 Adding biocLite and shiny commands to Run apps in different ways in the list of monitored commands
0.78 File .RData created in the right folder in all cases. Clearing Tiki caches finally cleans also folders from PluginR under temp/cache. Param echo added to show an echo of the commands introduced. New params (and code) added also borrowed from PluginCode to let the user customize the echo output (caption, wrap, colors, ln).
0.79 Some minor refactoring, and better defaults when just param echo is set to 1 (defaults then: ln enabled, colors set to r, and caption as R code or RR code, depending on the type of plugin call). Reset the list of basic and advanced params for easier use.
0.80 Caching implemented for html results when no change in plugin call, parameters from tracker item data, nor files attached to the tracker item to be processed. Complex runs that took 2 minutes to be generated did load subsequent times in just 2 seconds to display results when no change in input values (!)
0.81 Added message and icon to indicate when cached R content is displayed and how to force content refresh. The plugin currently avoids cached content when it detects some change in the tracker item (last Modif) associated in the run (via pretty tracker type of runs). Thanks Moises for bug reporting and jonnyb for code tips
0.82 Cleaner indication of Cached R content, showing just an icon and some descriptive message on mouseover. Clearing R cache after clicking on that button fixed.
0.83 Fixed for Tiki11+ the iframed wiki pages to include some html files produced server side by R packages (such as RCharts)
0.84 Param removen improved a bit to match again some of the extra blank lines added for granted in charts from googleVis package
0.85 Multiuser Cache added: split apart cached files from different users for the same page or itemId
0.86 Multiuser .RData added: split apart .RData files from different users for the same page or itemId
0.87 Allow the display of pdf files generated by PluginRR on disk. Param echo accepts also y/n or yes/no as values, as well as 1/0. Param customoutput added (thanks Jyhem and joelobrecht ).
0.88 Cached files stored by default in folder with page id instead of page name to fix issues with pagenames with special characters (thanks Jyhem). New param cacheby (pageid | pagename) added, which defaults to pageid to be futureproof with people using it in other languages with special characters in pagenames, but allowing to respect previous behavior when choosing the other option pagename which matches current wiki argument variable page for advanced custom R scripts in wiki pages.
0.89 .htaccess in temp allows js and css files, so that scripts for the R clickme package can be much shorter reusing getwd() for the output path.
0.89.1 Concatenation character for the url to refresh cache fixed for some SEFURL cases.
0.89.2 Param parse_body added to allow parsing wiki plugin calls such as trackerlist with csv output inside plugin R. Additional debug output has been added when echodebug is set to '1' (commited on behalf of geoff and jonnyb: thanks!).
0.89.3 Update plugin to display as expected with Tiki 13 onwards. Only show refresh icon to users with permission to edit pages and only when they do not show the page version for printing (tiki-print.php). Display icon to refresh in fontawesome icons to match tiki's theme.
0.89.4 Harden restriction of file types allowed under temp (extension name allowed only at the end of the filename).
contributorxavi
descriptionAllows using R syntax for statistics, scientific computing & graphs (see http://www.r-project.org). In wiki syntax, type {R()}{R} or with some params, as reported at the documentation. This same version works for Tiki3 up to Tiki12.
devurlhttps://dev.tiki.org/PluginR
docurlhttps://doc.tiki.org/PluginR
fileslib/wiki-plugins/wikiplugin_r.php
lib/wiki-plugins/wikiplugin_rr.php
temp/.htaccess
lang/en/language_r.php
lang/ca/language_r.php
lang/es/language_r.php
pics/icons/r.png
img/icons/r.png
lastmodif2017-01-23 00:06:30 +0100 (Mon, 23 Jan 2017)
licenceGNU/GPL
modnamewikiplugins-r
namer
revision0.89.4
typewikiplugins
version9