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This shows you the differences between two versions of the page.

--- tools:rtools [2021/12/02 14:53]
nperez
+++ tools:rtools [2024/04/04 12:21] (current)
vagudets
@@ Line 3: / Line 3: @@
 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 functions in each department R package and the R modules with library versions can be found [[https://docs.google.com/spreadsheets/d/1gA-O1WkgH50VnyxOz9gbec_DsyvWMkyF-9SlFANXLqI/edit#gid=1328408011| here]].
+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]].
 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:
-  * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing&s|Minutes]]
+  * [[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]]
+===== R User Meeting =====
+====2024====
+  * R tools user meeting (Mix 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}}
+====2023====
+  * R tools user meeting (Mix Mode, 14/12/2023){{ :tools:r_user_meeting_20231214.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 02/11/2023){{ :tools:r_user_meeting_20231102.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 05/10/2023){{ :tools:r_user_meeting_20231005.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 07/09/2023){{ :tools:r_user_meeting_20230907.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 06/07/2023){{ :tools:r_user_meeting_20230706.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 01/06/2023){{ :tools:r_user_meeting_20230601.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 04/05/2023){{ :tools:r_user_meeting_20230504.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 06/04/2023){{ :tools:r_user_meeting_20230406.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 02/03/2023){{ :tools:r_user_meeting_20230302.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 02/02/2023){{ :tools:r_user_meeting_20230202.pdf | Slides}}
+====2022====
+  * R tools user meeting (Mix Mode, 01/12/2022){{ :tools:r_user_meeting_20221201.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 03/11/2022){{ :tools:r_user_meeting_20221103.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 06/10/2022){{ :tools:r_user_meeting_06102022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 01/09/2022){{ :tools:r_user_meeting_01092022.pdf | Slides}} [[https://rpubs.com/aho/936896|Quarto html]]
+  * R tools user meeting (Mix Mode, 07/07/2022){{ :tools:r_user_meeting_07072022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 02/06/2022){{ :tools:r_user_meeting_02062022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 05/05/2022){{ :tools:r_user_meeting_05052022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 07/04/2022){{ :tools:r_user_meeting_07042022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 03/03/2022){{ :tools:r_user_meeting_03032022.pdf | Slides}}
+  * R tools user meeting (Mix Mode, 03/02/2022){{ :tools:r_user_meeting_03022022.pdf | Slides}}
 ====2021====
@@ Line 29: / Line 58: @@
   * R tools user meeting (BSC, 07/11/2019) {{ :tools:rtools_user_meeting_20191107.pdf |Slides}}{{ :tools:rtools_user_meeting_minutes_20191107.pdf |minutes}}
-Please, see specific information for each tool:
+===== Packages =====
+Brief Summary and links to in-house packages: {{ :tools:package_summary.pdf | Package Summary}}
+See specific information for each tool:
   * [[https://earth.bsc.es/wiki/doku.php?id=tools:startR&s[]=startR|startR]]
@@ Line 39: / Line 72: @@
   * [[https://earth.bsc.es/wiki/doku.php?id=tools:s2dverification&s[]=s2dverification|s2dverification]] //[deprecated 04/09/2020]//
-==== Presentations ====
-  * {{ :tools:training_introductiontothedeptrtools.pdf | Training: Introduction to the department tools (2021-01-26)}}
+===== Presentations =====
+  * {{ :tools:r_tool_roadmap_2024.pdf |R Tools Roadmap 2024}}
+  * {{ :tools:day2_04_handson_r_tools.pdf | BSC Training (PATC) 2023 - Climate Forecast Analysis hands-on tutorial: R tools}}
+  * {{ :tools:create_r_package_in_bsc-es.pdf | Create R Package in BSC-ES}} (2023-05-26)
+  * {{ :tools:r_tool_roadmap_2023.pdf | R Tools Roadmap 2023}}
+  * {{ :tools:patc2022_r_handson.pdf | PATC2022 - Climate Forecast Analysis hands-on tutorial: R tools}}
+  * {{ :tools:training_introductiontothedeptrtools.pdf | Training: Introduction to the department tools }} (2021-01-26)
   * [[https://docs.google.com/presentation/d/1AfVKHxSDbMw0HD5yDCZ6evx2PpbsFG9_gsRDxMNFhU8/edit#slide=id.g60506b0e68_0_432|General scheme of the department R tools]]
   * {{ :tools:18nov2020-ivmw-o.pdf |Overview Development and Maintenance}}
-====How to cite====
+===== How to report an issue =====
+We use issues to identify and address bugs and propose new developments in the codebase. If you find a problem in our tools, please read this document to see if you should and how to report an issue. [[https://docs.google.com/document/d/1zRlmsRwFDJctDB94x6HGf6ezu3HFHhEjaBu0hVcrwTI/edit?usp=sharing|Guidelines for R-related questions in Earth Sciences]]
-If you are using any of the R packages being developed at the department, you can include a citation in your research items.
-  * **startR**
+===== How to source a function from GitLab repository =====
-  BSC-CNS and Nicolau Manubens (2021). startR: Automatically Retrieve Multidimensional Distributed Data Sets. R package version 2.1.0. https://earth.bsc.es/gitlab/es/startR/
+If we want to test a developing function from GitLab, sourcing the file on GitLab is very useful. Of course, you can save the file and source it locally, but when the file is updated, you need to manually update the local file, which is not convenient.
+If the repository is **public**, you can follow these two ways.
+. If you have the git repo cloned under your personal directory:
+  - git checkout to the branch where the function is.
+  - Open an R session, source the function from the git repo. Source the depended packages as well. You can modify the following lines for your package.
+  path <- "/home/Earth/aho/s2dv/R/"  # the git repo path
+  ff <- lapply(list.files(path), function(x) paste0(path, x))
+  invisible(lapply(ff, source))
+  # load all the depended packages
+  lib <- c('parallel', 'abind', 'bigmemory', 'future', 'multiApply', 'PCICt', 'ClimProjDiags', 'ncdf4', 'plyr', 'easyNCDF')
+  invisible(lapply(lib, library, character.only = TRUE))
+. If you don't have a local git repo:
+ Source the file by raw file URL. E.g.,
+  source("https://earth.bsc.es/gitlab/external/cstools/-/raw/master/R/s2dv_cube.R")
+Remember that you need to use the raw URL, which can be found in the upper-right corner of the file.
+Note that you may need to load other packages or source other functions used in the sourced function. In contrast, by the first method above, all the possible needs are taken care of already.
+If the repository is **not public**, see {{ :tools:source_functions_from_non-public_gitlab_repo.pdf | this slide}}
+===== How to cite R Tools =====
+If you use any R packages, both developed in or outside of the department, you can include a citation in your research items.
+//Reference//: https://ropensci.org/blog/2021/11/16/how-to-cite-r-and-r-packages/
+==== Cite R package ====
+To get the most updated citation text, you can simply use R function "citation". For example,
+    > citation("s2dv")
+    To cite package 's2dv' in publications use:
+      BSC-CNS, An-Chi Ho and Nuria Perez-Zanon (2023). s2dv: A Set of
+      Common Tools for Seasonal to Decadal Verification. R package version
+.0.0. https://CRAN.R-project.org/package=s2dv
+    A BibTeX entry for LaTeX users is
+      @Manual{,
+        title = {s2dv: A Set of Common Tools for Seasonal to Decadal Verification},
+        author = {{BSC-CNS} and An-Chi Ho and Nuria Perez-Zanon},
+        year = {2023},
+        note = {R package version 2.0.0},
+        url = {https://CRAN.R-project.org/package=s2dv},
+      }
+Notice that you may want to change the version number in case the research is done with a previous version.
+==== Cite R ====
+To cite R software along with its base packages, type citation(). The year varies with the R version you use.
+    > citation()
+    To cite R in publications use:
+      R Core Team (2021). R: A language and environment for statistical
+      computing. R Foundation for Statistical Computing, Vienna, Austria.
+      URL https://www.R-project.org/.
+    A BibTeX entry for LaTeX users is
+      @Manual{,
+        title = {R: A Language and Environment for Statistical Computing},
+        author = {{R Core Team}},
+        organization = {R Foundation for Statistical Computing},
+        address = {Vienna, Austria},
+        year = {2021},
+        url = {https://www.R-project.org/},
+      }
+    We have invested a lot of time and effort in creating R, please cite it
+    when using it for data analysis. See also ‘citation("pkgname")’ for
+    citing R packages.
+==== Package publication ====
+Some packages have their own publication, which can also be considered being included.
-  * **ClimProjDiags**
-  N. Pérez-Zanón, and A. Hunter, 2020: ClimProjDiags: Set of tools to compute various climate indices, version 0.1.0. Barcelona Supercomputing Center, R package, https://CRAN.R-project.org/package=ClimProjDiags
   * **CSTools**
-  Núria Pérez-Zanón, Louis-Philippe Caron, Carmen Alvarez-Castro, Lauriane Batte, Jost von Hardenberg, Llorenç LLedó, Nicolau Manubens, Eroteida Sánchez-Garcia, Bert van Schaeybroeck, Verónica Torralba and Deborah Verfaillie (2021). CSTools: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales. R package version 4.0.0. https://CRAN.R-project.org/package=CSTools
+  Pérez-Zanón, N., Caron, L.-P., Terzago, S., Van Schaeybroeck, B., Lledó, L., Manubens, N., Roulin, E., Alvarez-Castro, M. C., Batté, L., Bretonnière, P.-A., Corti, S., Delgado-Torres, C., Domínguez, M., Fabiano, F., Giuntoli, I., von Hardenberg, J., Sánchez-García, E., Torralba, V., and Verfaillie, D.: Climate Services Toolbox (CSTools) v4.0: from climate forecasts to climate forecast information, Geosci. Model Dev., 15, 6115–6142, https://doi.org/10.5194/gmd-15-6115-2022, 2022.
   * **CSIndicators**
-  Pérez-Zanón, N., Chihchung, C. and Lledó, L.: CSIndicators: Sectoral Indicators for Climate Services Based on Sub-Seasonal to Decadal Climate Predictions, CRAN [online] Available from: https://cran.r-project.org/package=CSIndicators, 2021.
+  Pérez-Zanón, N., Ho, A. Chou, C., Lledó, L., Marcos-Matamoros, R., Rifà, E. and González-Reviriego, N. (2023). CSIndicators: Get tailored climate indicators for applications in your sector. Climate Services. https://doi.org/10.1016/j.cliser.2023.100393
   * **s2dverification**
   Nicolau Manubens, Louis-Philippe Caron, Alasdair Hunter, Omar Bellprat, Eleftheria Exarchou, Neven S. Fučkar, Javier Garcia-Serrano, François Massonnet, Martin Ménégoz, Valentina Sicardi, Lauriane Batté, Chloé Prodhomme, Verónica Torralba, Nicola Cortesi, Oriol Mula-Valls, Kim Serradell, Virginie Guemas, Francisco J. Doblas-Reyes, An R package for climate forecast verification, Environmental Modelling & Software, Volume 103, 2018, Pages 29-42, ISSN 1364-8152,https://doi.org/10.1016/j.envsoft.2018.01.018.
-  * **s2dv**
-  BSC-CNS, An-Chi Ho and Núria Pérez-Zanón (2020). s2dv: A Set of Common Tools for Seasonal to Decadal Verification. R package version 0.1.0. https://CRAN.R-project.org/package=s2dv
-  * Given that these packages are using **R environment**, you can also include:
-  R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
-//**Note** that the version of R and packages can be updated, you can check the latest reference by open a terminal and running `citation()` for the R version and `citation("packageName") for each package. We are also working on a manuscript about CSTools.//
+==== Acknowlegement ====
-Finally, it is recommended to add a sentence in **Acknowledgements** section of your manuscripts where readers can check the full list of software used. Here is an example from [[https://journals.ametsoc.org/view/journals/clim/aop/jcliD200138/jcliD200138.xml | 'How Reliable Are Decadal Climate Predictions of Near-Surface Air Temperature?']] (Verfaille et al, 2020):
+You can also choose to put the packages in the acknowledgment section. Here is an example from [[https://journals.ametsoc.org/view/journals/clim/aop/jcliD200138/jcliD200138.xml | 'How Reliable Are Decadal Climate Predictions of Near-Surface Air Temperature?']] (Verfaille et al, 2020):
 //We acknowledge the use of the s2dverification (Manubens et al. 2018), startR (BSC/CNS and Manubens 2020), SpecsVerification (Siegert 2017), CSTools (Pérez-Zanón et al. 2019), ClimProjDiags (BSC/CNS et al. 2020), and boot (Davison and Hinkley 1997; Canty and Ripley 2020) R (R Core Team 2013) software packages.//
-====R Tips====
+==== Manuscript ====
+It is recommended to add some sentences in the manuscripts where readers can check the full list of software used. For example,
+//All analyses were performed using R Statistical Software (v4.1.2; R Core Team 2021). Temperature data was processed via the R packages: startR (v2.3.0; BSC-CNS etc. 2023), s2dv (v2.0.0; BSC-CNS etc. 2023). The indices were calculated using the R package: CSIndicators (v1.0.1; N. Perez etc. 2023).//
+===== RStudio-server =====
+You can launch RStudio-server on workstation or on Nord3v2. It opens RStudio IDE as a webpage. Please follow the instruction:
+  * [[https://earth.bsc.es/wiki/doku.php?id=computing:workstations#using_rstudio-server_in_ws|On workstation]]
+  * [[https://earth.bsc.es/wiki/doku.php?id=computing:nord3-v2#using_rstudio-server_in_nord3-v2|On Nord3v2]]
+===== R Tips =====
 General R solutions that are useful in the department but doesn't belong exclusively to an in-house R package will be listed here.
-**1. BSC-ES infrastructure
-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}}
+**1. BSC-ES infrastructure**
+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 |}}
 **2. How to change a CDO version in your open R session**
@@ Line 101: / Line 233: @@
 in your terminal
-**3. How to load dependencies of R package sf**
+**3. How to load dependencies of R package sf, terra, and mapview**
-This package could be used by loading the following modules in this specific order:
+This package could be used by loading the following modules (note that order may affect):
-    module load R/3.6.1-foss-2015a-bare
+(on workstation)
-    module load GDAL/2.2.1-foss-2015a-GEOS-3.8.0
+    module load R/4.1.2-foss-2015a-bare
-    module load PROJ/6.1.1-foss-2015a
+    module load GDAL/2.2.1-foss-2015a
-    module load GEOS/3.8.0-foss-2015a
+    module load PROJ/4.8.0-foss-2015a
+    module load GEOS/3.7.2-foss-2015a-Python-2.7.9
+(on nord3v2)
+    module load R/4.1.2-foss-2019b
+    module load GDAL/3.3.2-foss-2019b-Python-3.7.4
+    module load PROJ/7.2.1-foss-2019b
+    module load GEOS/3.7.2-foss-2019b-Python-3.7.4
+(on hub)
+    module load R/4.2.1-foss-2021b
+    module load GDAL/3.5.2-foss-2021b-Python-3.9.6
+    module load PROJ/9.1.0-foss-2021b
+    module load GEOS/3.11.0-GCC-11.2.0
+Note: Avoid to include them in your bashrc, just load them when it is a requirement.
-Note: Avoid to include them in your bashrc, just load them when it is a requirement.
 Note2: to use library RNetCDF `module load HDF5/1.10.5-foss-2015a` is required.
@@ Line 116: / Line 262: @@
 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
-    # if necessary add: module load PROJ/5.0.1-foss-2015a
+    # if necessary add: module load PROJ/6.1.1-foss-2015a
+ - for R 4.1.2:
+    module load R/4.1.2-foss-2015a-bare
+    module load GDAL/2.2.1-foss-2015a
+    # if necessary add: module load PROJ/6.1.1-foss-2015a
-Note: Avoid to include them in your bashrc, just load them when it is a requirement.
+Note: Avoid including them in your bashrc, just load them when it is a requirement.
 **5. How to avoid Load error in R 3.6.1:  cdo -griddes core dumped**
@@ Line 137: / Line 283: @@
 The same requirement also applies to s2dv::CDORemap and startR::CDORemapper.
-**6. How to use 'rmapshaper' library in Nord3**
+**6. How to use 'rmapshaper' library in workstation and Nord3v2**
-To correctly use the R library rmapshaper in Nord3, you need to load the following modules in advance:
+To correctly use the R library rmapshaper,  you need to load the following modules:
-    module load R protobuf/3.7.1-GCCcore-8.3.0 jq/1.5-GCCcore-8.3.0 nodejs/10.21.0-GCCcore-8.3.0
+ - On workstation:
+    module load R/4.1.2-foss-2015a-bare
+    module load libprotobuf/3.5.1-foss-2015a libjq/1.5.-foss-2015a nodejs/10.21.0-foss-2015a
+ - On Nord3v2:
+    module load R/4.1.2-foss-2019b
+    module load protobuf/3.7.1-GCCcore-8.3.0 jq/1.5-GCCcore-8.3.0 nodejs/10.21.0-GCCcore-8.3.0
@@ Line 174: / Line 326: @@
 If the error persists, **check your code with a smaller data sample** to discard a problem with your code since this error message indicates that you are requesting more memory than the available.
+**9. Special characters **
+In case of problems with accents or special characters, try to change the R session language to the most convenient: `Sys.setlocale("LC_ALL","en_US.UTF-8")`.
+**10. Test the development on Git**
+There are several ways to source the functions under development. Depending on the attributes of the function and the use case, the most suitable way can vary. Check the slides: {{ :tools:source_git_function.pdf | source_git_function.pdf}}
+**11. How to load dependencies of R package RNetCDF**
+This package could be used by loading the following modules (note that order may affect):
+(on workstation)
+    module load R/4.1.2-foss-2015a-bare
+    module load HDF5/1.10.5-foss-2015a
+(on nord3v2)
+    module load R/4.1.2-foss-2019b
+    module load HDF5/1.10.5-gompi-2019b

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