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tools:rtools [2024/04/04 12:21]
vagudets 		tools:rtools [2024/05/02 14:43] (current)
vagudets [R Tips]
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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. +At BSC-ES there is a collaborative effort to share resources for data analysis in R and develop some in-houseR tools that are maintained by the R developer team. 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 will find more information about our in-house packages further down, in the 'In-house Packages' section.
  
 You can join the [[http://mailman3.bsc.es/postorius/lists/earth-rtools.bsc.es/|Earth RTools mailing list]] to receive the latest updates about news. Check the list of R tips below to learn about **BSC-ES infrastructure** and other R tips. You can join the [[http://mailman3.bsc.es/postorius/lists/earth-rtools.bsc.es/|Earth RTools mailing list]] to receive the latest updates about news. Check the list of R tips below to learn about **BSC-ES infrastructure** and other R tips.
  
-The list of R packages installed in the latest maintained R modules (as of 2024-02-02) can be found {{ :tools:r_modules_and_packages_20240202.ods |here}}, and a list of functions in each department R package (as of 2021-01-18) can be found [[https://docs.google.com/spreadsheets/d/1gA-O1WkgH50VnyxOz9gbec_DsyvWMkyF-9SlFANXLqI/edit#gid=1328408011| here]].+===== Getting started: using R at BSC-ES =====
  
-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:+==== Environment Modules ==== 
 + 
 +The Workstations, the BSC-ES Hub and the HPC machines use [[https://earth.bsc.es/wiki/doku.php?id=library:environment_modules | environment modules]], which are maintained by our IT team. Each module contains a set of software packages that can only be used if the module has been loaded in the environment.  
 + 
 +For example, to load CDO and R in the workstation, you should load the corresponding modules with the 'module load' command: 
 +    module load CDO/1.9.8-foss-2015a 
 +    module load R/4.1.2-foss-2015a-bare 
 + 
 +The currently maintained R module versions are: 
 + 
 +  * Workstations: R/4.1.2-foss-2015a-bare (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:workstations| Computing - Workstations]]) 
 +  * BSC-ES Hub: R/4.2.1-foss-2021b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:bsceshub|Computing - Bsceshub (Testing phase)]]) 
 +  * Nord3v2: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:nord3-v2|Computing - Nord3v2]]) 
 +  * CTE-AMD: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:amd|Computing - AMD]]) 
 + 
 +Check the wiki page for each machine to see if you need to follow any additional steps to be able to load the correct modules. 
 + 
 +==== R packages ==== 
 + 
 +The R modules contain the latest released version of our in-house R packages, as well as many other R packages that may be used by people in the department. 
 +There is no need to install any packages locally by yourself; you can load the corresponding module and check if the R package is already installed. If it is not installed, you may open an issue in the Requests GitLab project (https://earth.bsc.es/gitlab/es/requests/-/issues) and tag Stamen Miroslavov Minkov (@smirosla) to ask him to install it in the machines. 
 + 
 +Some packages may require additional modules; see the ‘R tips’ section below. 
 + 
 +The list of R packages installed in the latest maintained R modules (as of 2024-02-02) can be found {{ :tools:r_modules_and_packages_20240202.ods |here}}, and a list of functions in each department R package (as of 2021-01-18) can be found [[https://docs.google.com/spreadsheets/d/1gA-O1WkgH50VnyxOz9gbec_DsyvWMkyF-9SlFANXLqI/edit#gid=1328408011| here]] or in the documentation for each package on CRAN. 
 + 
 +==== Where to run R ==== 
 + 
 +  * To open an R session in the terminal, simply type ‘R’ after loading the R module.  
 +  * RStudio Server is available on the Workstations and Nord3v2. See the section ‘RStudio Server’ below. RStudio Server is not yet available on the Hub, but you can use VSCode. See the ‘R tips’ section below.  
 +  * To use Jupyter Notebooks in the BSC-ES Hub, see the [[https://earth.bsc.es/wiki/doku.php?id=computing:howto:jupyter_notebooks#r_experimental | Jupyter Notebook wiki page]]. For the workstations, the up-to-date R version is not working with Jupyter Notebooks. 
 + 
 +===== R User Meeting ===== 
 + 
 +A monthly meeting takes 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:
   * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing&s|Minutes until June 2022]]   * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing&s|Minutes until June 2022]]
   * [[https://docs.google.com/document/d/1mdLCS7SC5-8NwAB_gAzUsEnJN4yYEYmAlVys0qT8Edk/edit?usp=sharing|Minutes since July 2022]]   * [[https://docs.google.com/document/d/1mdLCS7SC5-8NwAB_gAzUsEnJN4yYEYmAlVys0qT8Edk/edit?usp=sharing|Minutes since July 2022]]
  
-===== R User Meeting ===== 
 ====2024==== ====2024====
-  * R tools user meeting (Mix Mode, 01/02/2024){{ :tools:r_user_meeting_20240201.pdf | Slides}} +  * R tools user meeting (Hybrid Mode, 01/02/2024){{ :tools:r_user_meeting_20240201.pdf | Slides}} 
-  * R tools user meeting (Mix Mode, 04/04/2024){{ :tools:r_user_meeting_20240404.pdf | Slides}}+  * R tools user meeting (Hybrid Mode, 04/04/2024){{ :tools:r_user_meeting_20240404.pdf | Slides}} 
 +  * R tools user meeting (Hybrid Mode, 02/05/2024){{ :tools:r_user_meeting_20240502.pdf | Slides}}
 ====2023==== ====2023====
   * R tools user meeting (Mix Mode, 14/12/2023){{ :tools:r_user_meeting_20231214.pdf | Slides}}   * R tools user meeting (Mix Mode, 14/12/2023){{ :tools:r_user_meeting_20231214.pdf | Slides}}
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   * R tools user meeting (BSC, 07/11/2019) {{ :tools:rtools_user_meeting_20191107.pdf |Slides}}{{ :tools:rtools_user_meeting_minutes_20191107.pdf |minutes}}   * R tools user meeting (BSC, 07/11/2019) {{ :tools:rtools_user_meeting_20191107.pdf |Slides}}{{ :tools:rtools_user_meeting_minutes_20191107.pdf |minutes}}
      
-===== Packages =====+===== In-house Packages =====
  
 Brief Summary and links to in-house packages: {{ :tools:package_summary.pdf | Package Summary}} Brief Summary and links to in-house packages: {{ :tools:package_summary.pdf | Package Summary}}
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-How to access, what you will find (servers, machines, partitions, modules) and how to open RStudio: check the slides and share them with your colleagues. {{ :tools:what_do_we_know_about_bsc-es_infrastructure_.pdf |slides}}+How to access, what you will find (servers, machines, partitions, modules) and how to open RStudio: check the slides and share them with your colleagues. {{ :tools:what_do_we_know_about_bsc-es_infrastructure.pdf |slides}}
  
 How to access BSC Hub and run R from the terminal and using VSCode: {{ :tools:ghr_-_bschub_demo.pdf |}}  How to access BSC Hub and run R from the terminal and using VSCode: {{ :tools:ghr_-_bschub_demo.pdf |}} 
tools/rtools.1712233270.txt.gz · Last modified: 2024/04/04 12:21 by vagudets

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