VRE #1676

Project Activity #1544: ICES training course, Training course in the R Environment

ICES Training Course in the R Environment (TCRE)

Added by Mike Drew over 3 years ago. Updated over 3 years ago.

Status:ReleasedStart date:Dec 03, 2015
Priority:NormalDue date:Jan 11, 2016
Assignee:Mike Drew% Done:

100%

Sprint:WP08
VRE_Policy:Restricted Invite_Policy:VRE_Manager
Milestones:
Duration: 28

Description

The development of a new or use of existing VRE(s) for the R Environment course (see attached course proposal). Integration of course specific datasets, extractions and tools into the VRE(s).

R environment proposal.docx (17.2 KB) Mike Drew, Dec 03, 2015 11:53 AM


Related issues

Related to BlueBRIDGE - Incident #1840: ICES_TCRE VRE: Missing "geospatial" Resources? Closed Dec 17, 2015
Related to BlueBRIDGE - Incident #1841: ICES_TCRE VRE: TabMan is not working Closed Dec 17, 2015
Related to BlueBRIDGE - Project Task #631: T4.2 VREs Creation and Deployment [Months: 1-30] Closed Feb 02, 2016 Nov 10, 2017

History

#1 Updated by Mike Drew over 3 years ago

  • Parent task set to #1544

#2 Updated by Mike Drew over 3 years ago

  • % Done changed from 0 to 10

As discussed in our telephone correspondence today, please set up a VRE for the R course. Please refer to the attached proposal document for the relevant add-ons required for the environment.

#3 Updated by Leonardo Candela over 3 years ago

Please, have a look at https://support.d4science.org/projects/bluebridge/wiki/VREs_Deployment_and_Operation for the procudure for asking for a new VRE.

The request should be a bit more focused on the VRE per se rather than on the course, i.e. please focus in dataset and facilities. In the specific case, a detailed list of R packages is needed.

#4 Updated by Pasquale Pagano over 3 years ago

  • Invite_Policy set to VRE_Manager
  • VRE_Policy set to Restricted
  • Tracker changed from Task to VRE

#5 Updated by Gianpaolo Coro over 3 years ago

According to the call of this morning, this is going to be a first VRE for a training course, to be also evaluated by trainers. Trainers will try to use the Workspace and the online RStudio environment first. No preparatory R-package is required on the RStudio machine (they can be installed by the users themselves). Rather, the following applications should be provided (I list also those available by default):

 - Workspace
 - Social Networking
 - TabMan with RStudio
 - Species Product Discovery
 - GeoExplorer
 - StatMan with the following Algorithms: DBScan, KMeans, LOF, XMeans, Most Observed Species, Most Observed Taxa, Species Observations per Area, CMSY, SGVM Interpolation, Generic Charts, GEO Charts, Species Observation Lme Area Per Year, Species Observation Meow Area Per Year, Species Observations Trend Per Year, Taxonomy Observations Trend Per Year, Occurrence Enrichment, BiOnym Local, Time Series Analysis, Feed Forward Ann, Feed Forward ANN Distribution

This VRE is going to be tested by people who teach in the biodiversity and stock assessment domains.

#6 Updated by Gianpaolo Coro over 3 years ago

Here is a proposal for a name and description of this VRE:
Name: ICES TCRE

Description: A Virtual Research Environment that supports the "ICES Training Course in the R Environment" (TCRE). The objective of the course is to provide participants with a solid foundation in efficient use of the R environment using various typical and familiar fisheries data sets (landings data, catch data, survey data and tagging data) as case examples. Emphasis is put on data munging and literate programming starting with "raw" data (individual stations, individual fish measurements) and culminating with deliverance of publishable output produced from a single coded document file.

This VRE provides access to processing as well as to data preparation and sharing facilities, including: an online R development environment (RStudio), data mining algorithms, a tabular data management application, GIS maps of environmental and biological data, access to biodiversity occurrence records and taxonomic data from major data providers (e.g. OBIS, GBIF, WoRMS, Catalog of Life), state-of-the-art stock assessment models and sharing tools (Workspace, Social Networking).

#7 Updated by Gianpaolo Coro over 3 years ago

  • Assignee changed from Gianpaolo Coro to Leonardo Candela

#8 Updated by Gianpaolo Coro over 3 years ago

  • Due date changed from Feb 01, 2016 to Jan 11, 2016

#9 Updated by Leonardo Candela over 3 years ago

  • % Done changed from 10 to 80
  • Status changed from New to Planned

The VRE is almost ready https://i-marine.d4science.org/group/ices_tcre/ices_tcre

There is one issue issue with the GeoExplorer we are going to fix.

As soon as it is fixed I'll change the Status.

#10 Updated by Leonardo Candela over 3 years ago

  • Status changed from Planned to Available

#11 Updated by Leonardo Candela over 3 years ago

  • Related to Incident #1840: ICES_TCRE VRE: Missing "geospatial" Resources? added

#12 Updated by Leonardo Candela over 3 years ago

  • Related to Incident #1841: ICES_TCRE VRE: TabMan is not working added

#13 Updated by Leonardo Candela over 3 years ago

  • % Done changed from 80 to 100

#14 Updated by Leonardo Candela over 3 years ago

  • Assignee changed from Leonardo Candela to Mike Drew

#15 Updated by Leonardo Candela over 3 years ago

  • Related to Project Task #631: T4.2 VREs Creation and Deployment [Months: 1-30] added

#16 Updated by Leonardo Candela over 3 years ago

  • Status changed from Available to Released

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