History: r_test

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Source of version: 119 (current)

^
R_test seeks to be an easy way of testing __PluginR__ ([https://doc.tiki.org/PluginR]) on basic and advanced usage.
{DIV(float="right")}{img src="http://www.r-project.org/Rlogo.jpg" thumb="y" button="y"}{DIV}
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 [http://en.wikipedia.org/wiki/Web_2.0|Web 2.0] GUI:
* __Welcome to Plugin R__ page: tests if R & PluginR are installed successfully already.
* __Test1_simple_test__. Testing simple R commands to test that the installation went fine
** Simple Text output
** Simple graphical output
* __Test2_params__. Testing several other commands
** Tiki Dynamic variable usage
** Parsing html code
** Wikisyntax param
* __Test3_interface__. Testing the process of working with datasets for a script to use them as parameters. The interface is organized in 4 tabas:
## Listing raw datasets
*** This first tab uses the standard output of [https://doc.tiki.org/PluginTrackerList|Plugin TrackerList] to display the data stored in the database of datasets  ("Tracker" or items, in Tiki terms).
## Showing the results after the dataset is run
*** This part uses a [https://doc.tiki.org/Pretty+Tracker|Pretty Tracker] with the (smarty) template in a wiki page, instead of just the standard output of [https://doc.tiki.org/PluginTrackerList|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 [https://doc.tiki.org/Wysiwyg|Wysiwyg] editor in Tiki.
## 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 [https://doc.tiki.org/PluginTracker|Plugin Tracker] to preload a previous item when requested (itemId value must be assigned in the url).
## Inserting new datasets
*** This last tab allows to insert new items, by means of using [https://doc.tiki.org/PluginTracker|Plugin Tracker], despite the fact that the page has already loaded a previous item or not.
* __Test4_export__. Testing the production of a basic image with svg and pdf export. (in the future, extended with the help of other R packages)
* __Test5_wordcloud__. Testing some nice graphs from R. You might need some  extra packages for R:
** Word-cloud art
* __Test6_googleVis__. Testing some nice interactive graphs
** Created through the googleVis package. You might need some  extra R packages.
* __Test7_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.
* __Test8_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.
* __Test9_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. 
* __Test10_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.
* __Test11_animation__. Showing a way to produce a self-moving chart with data from different decades using the -+ggplot2+- and -+__animation__+- packages.
* __Test12_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.

This menu will be created also: ((Profile_r_test_menupage))

__Requirements__:
* A Tiki site on a server :-). See [https://doc.tiki.org/Requirements|Requirements] and [https://doc.tiki.org/Installation|Installation] if needed. 
* [https://doc.tiki.org/PluginR|PluginR] , 
+ downloadable as a Mod from [http://mods.tiki.org/details.php?type=wikiplugins&mod=r|http://mods.tiki.org]
+ or installable as a mod from the tiki mods interface: tiki-mods.php
* [http://r-project.org|R project] installed in the same server as Tiki
* Understand how to apply a profile into your own Tiki site :-)
+ See the page ((Welcome to Tiki Profiles))
^

__New since August 2011__:
* See related profile ((R_HeatMaps)), as shown in:
+ http://ueb.vhir.org/User+2011

{maketoc}

These pages will be created:
~~lightgrey:''(listed properly only when shown here: http://profiles.tiki.org/r_test , not when you are at profile installation in your remote tiki site)''~~
{TITLESEARCH(search="r_test",exclude="r_test",noheader="1")}{TITLESEARCH}

!! Trackers

{CODE(caption=>YAML,wrap=>1)}
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_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
{CODE}

!! Groups & Permissions

{CODE(caption=>YAML, wrap=1)}
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
 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
{CODE}


!! Sample data

{CODE(caption=>YAML,wrap=>1)}
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]

{CODE}

!! Modules
{CODE(caption=>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
{CODE}


!! Wiki pages

{CODE(caption=>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_test01_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_test02_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_test03_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_test03_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_test04_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_test05_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_test06_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_test07_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_test08_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_test09_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_test09_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_test09_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_test09_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_test09_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_test09_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_test09_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_test09_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_test09_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_test10_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_test11_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_test12_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
{CODE}

!! Content Templates for pre-defined reports

{CODE(caption=>YAML,wrap="1")}
objects:
 -
  type: template
  ref: content_template_report_01
  data:
   name: Report 01
   content: wikicontent:Profile_r_test_ContentTemplate_Report_01
   sections: [ wiki ]
{CODE}

!! Useful navigational aid
!!! Wiki Page for the Menu
This will add the page ((Profile_r_test_menupage)) as the menu content

{CODE(caption=>YAML,wrap="1")}
objects:
  -
    type: wiki_page
    ref: r_test_menupage_include
    data:
      name: Menu for R tests
      description: Collaborative simple menu
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_test_menupage
{CODE}

!!! Module wiki side menu
{CODE(caption=>YAML,wrap=>1)}
objects:
 -
  type: module
  ref: module_menupage
  data:
   name: menupage
   position: right
   groups: [ Anonymous, Registered ]
   order: 2
   params:
    pagemenu: Menu for R tests
{CODE}

!!! Extra features enabled for this profile
Add smileys for an easy way to add icons for bullets in the wiki page menu, without making them too much on the right. 
{CODE(caption=>YAML,wrap="1")}
preferences:
 feature_smileys: y
 feature_search_fulltext: y
 feature_wiki_argvariable: y
 feature_syntax_highlighter: y
 wiki_dynvar_style: double
 wikiplugin_div: y
 wikiplugin_group: y
 wikiplugin_iframe: y
 wikiplugin_img: y
 wikiplugin_pluginmanager: 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_listpages: y
 wikiplugininline_titlesearch: y
{CODE}

-=Links=-
* [https://doc.tiki.org/PluginR]
* [https://dev.tiki.org/PluginR]
* [http://r-project.org]
* [http://mods.tiki.org/details.php?type=wikiplugins&mod=r]
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History: r_test

Source of version: 119 (current)

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History: r_test

Source of version: 119 (current)

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