R_test seeks to be an easy way of testing
PluginR (
https://doc.tiki.org/PluginR) on basic and advanced usage.
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:
- 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 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 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.
- 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).
- 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.
- 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:
- 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:
:
These pages will be created:
(listed properly only when shown here: http://profiles.tiki.org/r_test , not when you are at profile installation in your remote tiki site)
Trackers
YAML
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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
Groups & Permissions
YAML
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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
Sample data
YAML
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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
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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
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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
Content Templates for pre-defined reports
YAML
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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
This will add the page
Profile_r_test_menupage as the menu content
YAML
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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
YAML
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objects:
-
type: module
ref: module_menupage
data:
name: menupage
position: right
groups: [ Anonymous, Registered ]
order: 2
params:
pagemenu: Menu for R tests
Add smileys for an easy way to add icons for bullets in the wiki page menu, without making them too much on the right.
YAML
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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
Links