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tools:rtools [2023/11/08 09:00] erifarov |
tools:rtools [2024/09/12 12:27] (current) vagudets [2024] |
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- | The R tools can be used for postprocessing experiments: | + | 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: |
You can join the [[http:// | You can join the [[http:// | ||
- | The list of functions in each department R package and the R modules with library versions can be found [[https:// | + | ===== Getting started: using R at BSC-ES ===== |
- | A quarterly meeting is taking place in the department to discuss about the plans and priorities | + | ==== Environment Modules ==== |
- | * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing& | + | |
- | * [[https:// | + | The Workstations, |
+ | |||
+ | For example, to load CDO and R in the workstation, | ||
+ | module load CDO/ | ||
+ | module load R/ | ||
+ | |||
+ | The currently maintained R module versions | ||
+ | |||
+ | * Workstations: | ||
+ | * BSC-ES Hub: R/4.2.1-foss-2021b (See: [[https:// | ||
+ | * Nord3v2: R/ | ||
+ | * CTE-AMD: R/ | ||
+ | |||
+ | 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:// | ||
+ | |||
+ | 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 {{ : | ||
+ | |||
+ | ==== 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:// | ||
===== R User Meeting ===== | ===== 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:// | ||
+ | * [[https:// | ||
+ | |||
+ | ====2024==== | ||
+ | * R tools user meeting (Hybrid Mode, 01/ | ||
+ | * R tools user meeting (Hybrid Mode, 04/ | ||
+ | * R tools user meeting (Hybrid Mode, 02/ | ||
+ | * R tools user meeting (Hybrid Mode, 01/ | ||
+ | * R tools user meeting (Hybrid Mode, 04/ | ||
+ | * R tools user meeting (Hybrid Mode, 09/ | ||
====2023==== | ====2023==== | ||
+ | * R tools user meeting (Mix Mode, 14/ | ||
* R tools user meeting (Mix Mode, 02/ | * R tools user meeting (Mix Mode, 02/ | ||
* R tools user meeting (Mix Mode, 05/ | * R tools user meeting (Mix Mode, 05/ | ||
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* R tools user meeting (BSC, 07/11/2019) {{ : | * R tools user meeting (BSC, 07/11/2019) {{ : | ||
| | ||
- | ===== Packages ===== | + | ===== In-house |
Brief Summary and links to in-house packages: {{ : | Brief Summary and links to in-house packages: {{ : | ||
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===== Presentations ===== | ===== Presentations ===== | ||
+ | * {{ : | ||
* {{ : | * {{ : | ||
* {{ : | * {{ : | ||
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If the repository is **not public**, see {{ : | If the repository is **not public**, see {{ : | ||
- | ===== How to cite ===== | + | ===== How to cite R Tools ===== |
- | If you are using any of the R packages | + | If you use any R packages, both developed |
- | * **startR** | + | // |
- | BSC-CNS and Nicolau Manubens | + | |
+ | ==== Cite R package ==== | ||
+ | To get the most updated citation text, you can simply use R function " | ||
+ | |||
+ | > citation(" | ||
+ | To cite package ' | ||
+ | | ||
+ | BSC-CNS, An-Chi Ho and Nuria Perez-Zanon | ||
+ | Common Tools for Seasonal to Decadal Verification. R package version | ||
+ | | ||
+ | |||
+ | 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:// | ||
+ | |||
+ | 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:// | ||
+ | } | ||
+ | |||
+ | We have invested a lot of time and effort in creating R, please cite it | ||
+ | when using it for data analysis. See also ‘citation(" | ||
+ | citing R packages. | ||
+ | |||
+ | |||
+ | ==== Package publication ==== | ||
+ | |||
+ | Some packages have their own publication, | ||
- | * **ClimProjDiags** | ||
- | N. Pérez-Zanón, | ||
* **CSTools** | * **CSTools** | ||
Pérez-Zanón, | Pérez-Zanón, | ||
- | | ||
- | Núria Pérez-Zanón, | ||
* **CSIndicators** | * **CSIndicators** | ||
Pérez-Zanón, | Pérez-Zanón, | ||
- | Pérez-Zanón, | ||
- | |||
* **s2dverification** | * **s2dverification** | ||
Nicolau Manubens, Louis-Philippe Caron, Alasdair Hunter, Omar Bellprat, Eleftheria Exarchou, Neven S. Fučkar, Javier Garcia-Serrano, | Nicolau Manubens, Louis-Philippe Caron, Alasdair Hunter, Omar Bellprat, Eleftheria Exarchou, Neven S. Fučkar, Javier Garcia-Serrano, | ||
- | * **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:// | ||
- | |||
- | * Given that these packages are using **R environment**, | ||
- | R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https:// | ||
- | //**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(" | + | ==== Acknowlegement ==== |
- | Finally, it is recommended | + | You can also choose |
//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.// | //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.// | ||
+ | |||
+ | ==== 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 ===== | ===== RStudio-server ===== | ||
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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. {{ : | + | 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. {{ : |
+ | |||
+ | How to access BSC Hub and run R from the terminal and using VSCode: {{ : | ||