R statistics/Installation: Difference between revisions

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R and many of its packages are pre-built and distributed through the CRAN network of mirrors. In addition many Linux distributions pre-package R and a number of the most popular libraries.
R and many of its packages are pre-built and distributed through the CRAN network of mirrors. In addition many Linux distributions pre-package R and a number of the most popular libraries.


==== Status of "rgrass" packages ====
=== Status of rgrass package ===


See overview here: https://cran.r-project.org/web/packages/rgrass/index.html
See the overview here: https://cran.r-project.org/web/packages/rgrass/index.html


==== Source packages ====
=== Installation ===
 
From the R console first pick a local mirror:
chooseCRANmirror()
 
you can then see which repos has been picked with
options("repos")
 
To permanently save the mirror site add it to <tt>~/.Rprofile</tt>. For example:
options(repos=c(CRAN="<nowiki>http://cran.stat.auckland.ac.nz</nowiki>"))
 
and then run <tt>install.packages()</tt> as in the Quick Start section above.
 
For more information see http://cran.r-project.org/doc/manuals/R-admin.html


==== Linux ====
==== Linux ====
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Once those are installed start "<tt>R</tt>" at the command prompt and install the <tt>rgrass</tt> library:
Once those are installed start "<tt>R</tt>" at the command prompt and install the <tt>rgrass</tt> library:


install.packages("rgrass", dependencies = TRUE)
<source lang="bash">
install.packages("rgrass", dependencies = TRUE)
install.packages("terra")
</source>


* [https://cran.r-project.org/bin/linux/debian/ Debian] and [https://cran.r-project.org/bin/linux/ubuntu/ Ubuntu] specific help is also available from the R-project website.
* [https://cran.r-project.org/bin/linux/debian/ Debian] and [https://cran.r-project.org/bin/linux/ubuntu/ Ubuntu] specific help is also available from the R-project website.
Line 38: Line 28:
===== RPM based =====
===== RPM based =====


* '''RedHat, Fedora, openSuse, ...''' and similar distros: take the latest '''''R''''' RPM and install it
* '''RedHat, Fedora, openSuse, ...''' and similar distros:  
 
''R'' and a number of pre-build cran packages are already present in the main repositories. Start with:


  # sudo dnf install R-core R-core-devel R-XML
  # sudo dnf install R


Once those are installed, start "<tt>R</tt>" at the command prompt and install the <tt>rgrass</tt> library:
This R RPM is a meta-package. It has no content but ensures that the following components are installed: R-core, R-core-devel, R-java, R-java-devel, libRmath, libRmath-devel. Once those are installed, start "<tt>R</tt>" and install the <tt>rgrass</tt> library:


<source lang="bash">
<source lang="bash">
R
install.packages("rgrass", dependencies = TRUE)
install.packages("rgrass", dependencies = TRUE)
install.packages("terra")
</source>
</source>
'''Usage:''' You have the best user experience if you launch R or RStudio within a running GRASS GIS session (then R automatically recognizes the current settings of the [[Computational region]] and "sees" the GRASS maps).


==== Mac OSX ====
==== Mac OSX ====


Start an R session, then
Start an R session and try:


* for install.packages() you might have to rely on building packages from source code. try:
<source lang="bash">
<source lang="bash">
R
install.packages("rgrass", type="source", dependencies = TRUE)
install.packages("rgrass", type="source", dependencies = TRUE)
</source>
</source>
Line 67: Line 49:
'''Startup of GRASS from within R:'''
'''Startup of GRASS from within R:'''


First you need to find the path to the GRASS binaries: Control-click on the GRASS.app and you'll get a popup menu; select "Show Package Contents" - this opens you to the directory structure. Go to Contents->MacOS which would be "GISBASE"; So, in my case, the "gisBase" parameter is "/HD/Applications/Grass-8.2.app/Contents/MacOS". If you Command-click at the top of the window on the folder icon beside "MacOS" (from the line above this one), you can see the full path.
First you need to find the path to the GRASS binaries: Control-click on the GRASS.app and you'll get a popup menu; select "Show Package Contents" - this opens you to the directory structure. Go to Contents->Resources which would be "GISBASE"; So, in my case, the "gisBase" parameter is "/HD/Applications/Grass-8.2.app/Contents/Resources". If you Command-click at the top of the window on the folder icon beside "Resources" (from the line above this one), you can see the full path.


Now we can run GRASS from within a R session:
Now we can run GRASS from within a R session:
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<source lang="bash">
<source lang="bash">
library(rgrass)
library(rgrass)
initGRASS(gisBase ='/Applications/GRASS/GRASS-8.2.app/Contents/MacOS',  
initGRASS(gisBase ='/Applications/GRASS-8.2.app/Contents/Resources',  
           location = 'geostat2012_ll', mapset = 'user1',  
           location = 'nc_spm_08_grass7',  
           gisDbase = '/Users/Lars/Documents/Biologi/grassdata', override = TRUE)
          mapset = 'user1',  
           gisDbase = '/Users/carol/Documents/grassdata',  
          override = TRUE)
</source>
</source>


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or install Task View 'Spatial' - Analysis of Spatial Data
or install Task View 'Spatial' - Analysis of Spatial Data
  install.packages("ctv")
  install.packages("ctv")
  library("ctv")
  library(ctv)
  install.views("Spatial")
  install.views("Spatial")


Line 103: Line 87:
In winGRASS ([https://grass.osgeo.org/download/windows/#standalone-installers standalone installer] and [https://grass.osgeo.org/download/windows/#OSGeo4W OSGeo4W]) the installation path of R and RStudio are dynamically loaded into PATH.
In winGRASS ([https://grass.osgeo.org/download/windows/#standalone-installers standalone installer] and [https://grass.osgeo.org/download/windows/#OSGeo4W OSGeo4W]) the installation path of R and RStudio are dynamically loaded into PATH.


* Start winGRASS, bring the winGRASS-windows console in front and type ''R'' for opening a R-session (command line mode) inside a GRASS-session.
* Start winGRASS, bring the winGRASS-windows console in front and type ''R'' for opening an R session (command line mode) inside a GRASS session.
* Start winGRASS, bring the winGRASS-windows console in front and type ''RGui'' for opening a R-session (GUI mode) inside a GRASS-session.
* Start winGRASS, bring the winGRASS-windows console in front and type ''RGui'' for opening an R session (GUI mode) inside a GRASS session.


[[Category:Installation]]
[[Category:Installation]]

Latest revision as of 11:46, 18 March 2024

First of all you need to install R in your system.

R and many of its packages are pre-built and distributed through the CRAN network of mirrors. In addition many Linux distributions pre-package R and a number of the most popular libraries.

Status of rgrass package

See the overview here: https://cran.r-project.org/web/packages/rgrass/index.html

Installation

Linux

Debian and Ubuntu

R and a number of pre-build cran packages are already present in the main repositories. Start with: 

# apt-get install r-base r-cran-vr r-cran-rodbc r-cran-xml

Once those are installed start "R" at the command prompt and install the rgrass library: 

install.packages("rgrass", dependencies = TRUE)
install.packages("terra")
  • Debian and Ubuntu specific help is also available from the R-project website.
RPM based
  • RedHat, Fedora, openSuse, ... and similar distros:
# sudo dnf install R

This R RPM is a meta-package. It has no content but ensures that the following components are installed: R-core, R-core-devel, R-java, R-java-devel, libRmath, libRmath-devel. Once those are installed, start "R" and install the rgrass library: 

install.packages("rgrass", dependencies = TRUE)
install.packages("terra")

Mac OSX

Start an R session and try: 

install.packages("rgrass", type="source", dependencies = TRUE)

Startup of GRASS from within R:

First you need to find the path to the GRASS binaries: Control-click on the GRASS.app and you'll get a popup menu; select "Show Package Contents" - this opens you to the directory structure. Go to Contents->Resources which would be "GISBASE"; So, in my case, the "gisBase" parameter is "/HD/Applications/Grass-8.2.app/Contents/Resources". If you Command-click at the top of the window on the folder icon beside "Resources" (from the line above this one), you can see the full path.

Now we can run GRASS from within a R session: 

library(rgrass)
initGRASS(gisBase ='/Applications/GRASS-8.2.app/Contents/Resources', 
          location = 'nc_spm_08_grass7', 
          mapset = 'user1', 
          gisDbase = '/Users/carol/Documents/grassdata', 
          override = TRUE)
Troubleshooting

If you get an error message when trying to call GRASS from R containing this line: dyld: Library not loaded: /usr/local/lib/libintl.8.dylib you need to establish a link from /Applications/Grass/GRASS-8.2.app/Contents/MacOS/lib/libintl.8.dylib to /usr/local/lib. This can be done through Terminal with the command: 

sudo ln -s /Applications/Grass/GRASS-8.2.app/Contents/MacOS/lib/libintl.8.dylib /usr/local/lib/

Note: The path to the GRASS-x.x.app and the version number in libintl.X.dylib must reflect your own configuration.

MS Windows

Installation

Run: 

install.packages("rgrass", dependencies = TRUE)

or install Task View 'Spatial' - Analysis of Spatial Data 

install.packages("ctv")
library(ctv)
install.views("Spatial")
Usage

In winGRASS (standalone installer and OSGeo4W) the installation path of R and RStudio are dynamically loaded into PATH.

  • Start winGRASS, bring the winGRASS-windows console in front and type R for opening an R session (command line mode) inside a GRASS session.
  • Start winGRASS, bring the winGRASS-windows console in front and type RGui for opening an R session (GUI mode) inside a GRASS session.
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