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tools:rtools

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The R tools can be used for postprocessing experiments: loading data, computing prediction scores, indices or calibrate experiments as well as plotting, formating data and saving data. Furthermore, by dividing the data in chunks, you can speed your execution by using startR.

You can join the Earth RTools mailing list to receive the latest updates about news.

A quarterly meeting is taking place in the department to discuss about the plans and priorities of the R tools (or any other topic we need to discuss). Here you can find a document were the minutes are being gathered:

2020

2019

Please, see specific information for each tool:

R Tips

General R solutions which are useful in the department but doesn't belong exclusively to an in-house R package will be listed here.

1. How to change a CDO version in your open R session

> system('module load CDO/1.5.3-foss-2015a')
The following have been reloaded with a version change:
1) CDO/1.6.3-foss-2015a => CDO/1.5.3-foss-2015a

In this case, CDO version has been changed from a newer to an older version.

Remember that you can see the full list of CDO version by running:

  module av CDO

in your terminal

2. How to load dependencies of R package sf

This package could be used by loading the following modules in this specific order:

  module load R/3.6.1-foss-2015a-bare    
  module load GDAL/2.2.1-foss-2015a-GEOS-3.8.0
  module load PROJ/6.1.1-foss-2015a
  module load GEOS/3.8.0-foss-2015a

Note: Avoid to include them in your bashrc, just load them when it is a requirement.

3. How to load dependencies of R package rgdal

This package could be used by loading the following modules in this specific order:

- for R 3.2.0:

  module load R/3.2.0-foss-2015a-bare
  module load GDAL/2.1.3-foss-2015a
  module load PROJ/4.8.0-foss-2015a

- for R 3.6.1:

  module load R/3.6.1-foss-2015a-bare
  module load GDAL/2.2.1-foss-2015a-GEOS-3.8.0

Note: Avoid to include them in your bashrc, just load them when it is a requirement.

4. How to avoid Load error in R 3.6.1: cdo -griddes core dumped

To avoid an error of Load because of the command CDO -griddes, a different version of HDF5 is required:

  module load HDF5/1.8.14-foss-2015a
tools/rtools.txt · Last modified: 2020/03/23 17:37 by nperez