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R_demo


R_demo demonstrates common uses of R to produce advanced and/or interactive graphs and reports in web pages within a full Wiki CMS/Groupware site, through the usage of PluginR (https://doc.tiki.org/PluginR).

There are a few sets of pages already created to show off some possibilities, as well as to allow quick starting new users into customizing their more complex interfaces to run their R scripts and packages through a nice Web 2.0 GUI:
  • Demo1_simple_test. Testing simple R commands to test that the installation went fine
    • Simple Text output
    • Simple graphical output
  • Demo2_params. Testing several other commands
    • Tiki Dynamic variable usage
    • Parsing html code
    • Wikisyntax param
  • Demo3_interface. Testing the process of working with datasets for a script to use them as parameters. The interface is organized in 4 tabas:
    1. Listing raw datasets
      • This first tab uses the standard output of Plugin TrackerList to display the data stored in the database of datasets ("Tracker" or items, in Tiki terms).
    2. Showing the results after the dataset is run
      • This part uses a Pretty Tracker with the (smarty) template in a wiki page, instead of just the standard output of Plugin TrackerList used in the first tab. Thus, the display is controlled by the (smarty) template "r_test3_template01", and it can be much more customized with the Wysiwyg editor in Tiki.
    3. Dataset edition (provided that a dataset is selected in the first tab)
      • This third tab allows the user to edit the parameters for the graph generated by the R script, by means of using Plugin Tracker to preload a previous item when requested (itemId value must be assigned in the url).
    4. Inserting new datasets
      • This last tab allows to insert new items, by means of using Plugin Tracker, despite the fact that the page has already loaded a previous item or not.
  • Demo4_export. Testing the production of a basic image with svg and pdf export. (in the future, extended with the help of other R packages)
  • Demo5_wordcloud. Testing some nice graphs from R. You might need some extra packages for R:
    • Word-cloud art
  • Demo6_googleVis. Testing some nice interactive graphs
    • Created through the googleVis package. You might need some extra R packages.
  • Demo7_plot.ly. Testing Plot.ly (see https://plot.ly/ ). The Plotly R graphing library allows you to create and share interactive, publication-quality plots in your browser. Plotly is also built for working together, and makes it easy to post graphs and data publicly with a URL or privately to collaborators.
  • Demo8_customoutput. Testing the customoutput parameter.
    • Introduced in PluginR v0.87, customoutput produces no hardcoded graphical output from PluginR, but leaves the R script inside the plugin to manage chart generation. In a later step, image is displayed with either img for images, or mediaplayer for pdf's, videos, etc.
  • Demo9_rcharts. Testing a series of examples of nice charts using rCharts and the corresponding javascript library used in each case. rCharts is an R package to create, customize and publish interactive javascript visualizations from R using a familiar lattice style plotting interface.
  • Demo10_clickme. Testing the clickme package from Nacho Caballero. Clickme is an R package that lets you create interactive visualizations in the browser directly from your R session.
  • Demo11_animation. Showing a way to produce a self-moving chart with data from different decades using the ggplot2 and animation packages.
  • Demo12_ecoengine. Testing the ecoengine package from rOpenSci, which is a collaborative effort to develop R-based tools for facilitating Open Science. Some distribution maps is generated for a species using LeafletJS, as well as a photo gallery created from a queried species for demostration purposes.
  • Demo13_parse_body. Testing the parse_body param from PluginR v 0.81.2+, which facilitates a better communication between data collected in trackers andits usage in R
  • Demo14_webshot. Testing the webshot package. Webshot makes it easy to take screenshots of web pages (all or sections defined by css selectors) from R, and save them as png or pdf. (requires PhantomJS, installable from within the webshot R package).
  • Demo15_pivottables. Testing the rpivotTable package, which is an R htmlwidget built around the pivottable library. PivotTable.js is a Javascript Pivot Table library with drag'n'drop functionality built on top of jQuery/jQueryUI and written in CoffeeScript by Nicolas Kruchten at Datacratic. It is available under an MIT license.

This menu will be created also: Profile_r_demo_menupage

Requirements:


New since August 2011:



These pages will be created:
(listed properly only when shown here: http://profiles.tiki.org/R_demo , not when you are at profile installation in your remote tiki site)




Trackers


YAML
preferences: feature_trackers: y trackerfield_file: y trackerfield_files: y trackerfield_dropdownother: y feature_user_watches: y feature_view_tpl: n feature_edit_templates: y feature_wiki_templates: y feature_jquery_media: y wikiplugin_r: y wikiplugin_rr: y wikiplugin_aname: y feature_smileys: y feature_search_fulltext: y feature_wiki_argvariable: y feature_syntax_highlighter: y feature_syntax_highlighter_theme: default wiki_dynvar_style: double wikiplugin_div: y wikiplugin_group: y wikiplugin_iframe: y wikiplugin_img: y wikiplugin_pluginmanager: y wikiplugin_list: y wikiplugin_listpages: y wikiplugin_titlesearch: y wikiplugininline_div: y wikiplugininline_group: y wikiplugininline_iframe: y wikiplugininline_img: y wikiplugininline_fade: y wikiplugininline_remarksbox: y wikiplugininline_pluginmanager: y wikiplugininline_list: y wikiplugininline_listpages: y wikiplugininline_titlesearch: y feature_multilingual: y lang_use_db: y instructions: Welcome to Plugin R objects: - type: tracker ref: r_test_tracker1 data: name: Datasets description: Files with data (like csv) to be processed by R scripts through tracker plugin calls default_status: open show: [ status, creation_date, modification_date, list_modification_date ] allow: [ comments, one_item_per_user, attachments ] - type: tracker_field ref: r_test_summary data: name: Summary tracker: $r_test_tracker1 type: text_field flags: [ searchable, public, list, mandatory, link ] order: 10 - type: tracker_field ref: r_test_description data: name: Description tracker: $r_test_tracker1 type: text_area options: 1 flags: [ public ] order: 20 - type: tracker_field ref: r_test_from data: name: From user tracker: $r_test_tracker1 type: user options: 1 flags: [ searchable, public, list ] order: 30 - type: tracker_field ref: r_test_attachment data: name: Dataset file tracker: $r_test_tracker1 type: attachment flags: [ searchable, public, list ] order: 40 - type: tracker_field ref: r_test_xmin data: name: Minimum value for axis X tracker: $r_test_tracker1 type: text_field flags: [ searchable, public, list ] order: 50 - type: tracker_field ref: r_test_xmax data: name: Maximum value for axis X tracker: $r_test_tracker1 type: text_field flags: [ searchable, public, list ] order: 60


Groups & Permissions


YAML
permissions: Anonymous: allow: view deny: [ ] Registered: description: Will be ignored because group is already created allow: - create_tracker_items - list_trackers - view_trackers - watch_trackers deny: [ ] objects: - type: wiki_page id: r_test3_template01 allow: use_as_template - type: wiki_page id: r_test13_template01 allow: use_as_template Editors: description: Trusted users allow: - modify_tracker_items - trust_input - view_templates - edit_templates - use_content_templates - edit_content_templates - admin_content_templates - use_as_template Admins: description: Have all rights allow: - admin - trust_input



Sample data


YAML
objects: - type: tracker_item ref: dataset_001 data: tracker: $r_test_tracker1 status: open values: - [ $r_test_summary, Sample dataset ] - [ $r_test_from, admin ] - [ $r_test_description, "This dataset was created as part of the sample data for r_test." ] - [ $r_test_attachment, ''] - [ $r_test_xmin, 1] - [ $r_test_xmax, 10] - type: tracker_item ref: dataset_002 data: tracker: $r_test_tracker1 status: pending values: - [ $r_test_summary, We are working on this dataset ] - [ $r_test_from, admin ] - [ $r_test_description, "This will soon be changed" ] - [ $r_test_attachment, ''] - [ $r_test_xmin, 21] - [ $r_test_xmax, 30] - type: tracker_item ref: dataset_003 data: tracker: $r_test_tracker1 status: closed values: - [ $r_test_summary, A really old dataset ] - [ $r_test_from, admin ] - [ $r_test_description, "This dataset is outdated." ] - [ $r_test_attachment, ''] - [ $r_test_xmin, 100] - [ $r_test_xmax, 110]


Modules

YAML
objects: - type: module ref: module_last_modif_tracker_items data: name: last_modif_tracker_items groups: [ Anonymous, Registered ] position: right order: 5 params: trackerId: $r_test_tracker1 name: Summary



Wiki pages


YAML
preferences: enable: [ feature_wiki ] objects: - type: wiki_page ref: r_test_instructions_page data: name: Welcome to Plugin R description: Basic intructions of PluginR and this profile lang: en mode: create_or_update content: wikicontent:Profile_r_test_instructions - type: wiki_page ref: r_test1_page data: name: r_demo01_simple_test description: Interface to send datasets lang: en mode: create_or_update content: wikicontent:Profile_r_test1_simple_test - type: wiki_page ref: r_test2_page data: name: r_demo02_params description: Interface to test several things lang: en mode: create_or_update content: wikicontent:Profile_r_test2_params - type: wiki_page ref: r_test3_page data: name: r_demo03_interface description: Interface to change graph params and display png lang: en mode: create_or_update content: wikicontent:Profile_r_test3_interface - type: wiki_page ref: r_test3_template01_page data: name: r_demo03_template01 description: Template for wiki page lang: en mode: create_or_update content: wikicontent:Profile_r_test3_template01 - type: wiki_page ref: r_test4_page data: name: r_demo04_export description: Interface to test some export options for figures lang: en mode: create_or_update content: wikicontent:Profile_r_test4_export - type: wiki_page ref: r_test5_page data: name: r_demo05_wordcloud description: Some examples of neat Cloud-art graphs to dogfood Tiki information lang: en mode: create_or_update content: wikicontent:Profile_r_test5_wordcloud - type: wiki_page ref: r_test6_page data: name: r_demo06_googleVis description: Some examples of neat usage of RGoogleVis package lang: en mode: create_or_update content: wikicontent:Profile_r_test6_googleVis - type: wiki_page ref: r_test7_page data: name: r_demo07_plot.ly description: Some examples of using Plot.ly lang: en mode: create_or_update content: wikicontent:Profile_r_test7_plot.ly - type: wiki_page ref: r_test8_page data: name: r_demo08_customoutput description: Some examples of the usage of parameter customoutput producing either custom png or custom pdf displayed embedded within the same wiki page lang: en mode: create_or_update content: wikicontent:Profile_r_test8_customoutput - type: wiki_page ref: r_test9_page0 data: name: r_demo09_rcharts description: series of examples of nice charts using the R package rCharts and the corresponding javascript library used in each case. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts - type: wiki_page ref: r_test9_page1 data: name: r_demo09_rcharts_highcharts description: an example of nice charts using the R package rCharts and the corresponding javascript library HighCharts. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_highcharts - type: wiki_page ref: r_test9_page2 data: name: r_demo09_rcharts_leaflet description: an example of nice charts using the R package rCharts and the corresponding javascript library Leaflet. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_leaflet - type: wiki_page ref: r_test9_page3 data: name: r_demo09_rcharts_morris description: an example of nice charts using the R package rCharts and the corresponding javascript library MorrisJS. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_morris - type: wiki_page ref: r_test9_page4 data: name: r_demo09_rcharts_nvd3 description: an example of nice charts using the R package rCharts and the corresponding javascript library NVD3. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_nvd3 - type: wiki_page ref: r_test9_page5 data: name: r_demo09_rcharts_polychart description: an example of nice charts using the R package rCharts and the corresponding javascript library Polychart. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_polychart - type: wiki_page ref: r_test9_page6 data: name: r_demo09_rcharts_rickshaw description: an example of nice charts using the R package rCharts and the corresponding javascript library RickShaw. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_rickshaw - type: wiki_page ref: r_test9_page7 data: name: r_demo09_rcharts_xcharts description: an example of nice charts using the R package rCharts and the corresponding javascript library XCharts. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_xcharts - type: wiki_page ref: r_test9_page8 data: name: r_demo09_rcharts_512paths description: an example of nice charts using the R package rCharts and some js functions to produce an awesome chart from NY Times 512 Paths to the White House. lang: en mode: create_or_update content: wikicontent:Profile_r_test9_rcharts_512paths - type: wiki_page ref: r_test10_page data: name: r_demo10_clickme description: Some examples with the Clickme R package that lets you create interactive visualizations in the browser directly from your R session lang: en mode: create_or_update content: wikicontent:Profile_r_test10_clickme - type: wiki_page ref: r_test11_page data: name: r_demo11_animation description: An example of chart showing choropleths of different decades using R packages ggplot2 and animation lang: en mode: create_or_update content: wikicontent:Profile_r_test11_animation - type: wiki_page ref: r_test12_page data: name: r_demo12_ecoengine description: Some distribution maps is generated for a species using LeafletJS, as well as a photo gallery created from a queried species for demostration purposes. lang: en mode: create_or_update content: wikicontent:Profile_r_test12_ecoengine - type: wiki_page ref: r_test13_page data: name: r_demo13_parse_body description: Demostration of the usage of parameter parse_body lang: en mode: create_or_update content: wikicontent:Profile_r_test13_parse_body - type: wiki_page ref: r_test13_template01_page data: name: r_demo13_template01 description: Template for wiki page lang: en mode: create_or_update content: wikicontent:Profile_r_test3_template - type: wiki_page ref: r_test14_page data: name: r_demo14_webshot description: Demostration of the usage of the Webshot R package lang: en mode: create_or_update content: wikicontent:Profile_r_test14_webshot - type: wiki_page ref: r_test15_page data: name: r_demo15_pivottables description: Demostration of the usage of the rpivotTable R package (which uses PivotTable.js - a Javascript Pivot Table library with drag and drop functionality built on top of jQuery/jQueryUI and written in CoffeeScript by Nicolas Kruchten at Datacratic) lang: en mode: create_or_update content: wikicontent:Profile_r_test15_pivottables


Content Templates for pre-defined reports


YAML
objects: - type: template ref: content_template_report_01 data: name: Report 01 content: wikicontent:Profile_r_test_ContentTemplate_Report_01 sections: [ wiki ]


Useful navigational aid

Wiki Page for the Menu

This will add the page Profile_r_test_menupage as the menu content

YAML
objects: - type: wiki_page ref: r_test_menupage_include data: name: Menu for R demo description: Collaborative simple menu lang: en mode: create_or_update content: wikicontent:Profile_r_demo_menupage


Module wiki side menu

YAML
objects: - type: module ref: module_menupage data: name: menupage position: right groups: [ Anonymous, Registered ] order: 2 params: pagemenu: Menu for R demo



Links