About
Last updated: 2021-02-23
Checks: 7 0
Knit directory: globalIRmap/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200414) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version eb09752. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | eb09752 | messamat | 2021-02-23 | wflow_publish(“analysis/About.Rmd”) |
| Rmd | 772154a | messamat | 2021-02-23 | Update gauging stations page and app |
| html | 772154a | messamat | 2021-02-23 | Update gauging stations page and app |
| html | 9b48bde | messamat | 2021-01-06 | Build site. |
| Rmd | f1d9dcf | messamat | 2021-01-06 | Start building up workflowr website, start incorporating mandrake (but wait as very unstable still), plan gauge selection documentation |
| html | f1d9dcf | messamat | 2021-01-06 | Start building up workflowr website, start incorporating mandrake (but wait as very unstable still), plan gauge selection documentation |
| html | a77a5ae | Mathis Loïc Messager | 2020-04-16 | Build site. |
| html | 4797458 | Mathis Loïc Messager | 2020-04-16 | Build site. |
| html | 28d8bfd | Mathis Loïc Messager | 2020-04-16 | Build site. |
| html | 80008f7 | Mathis Loïc Messager | 2020-04-14 | Build site. |
| Rmd | ce60469 | Mathis Loïc Messager | 2020-04-14 | First publication |
| Rmd | b8ce7d1 | unknown | 2020-04-14 | change to workflowr project structure |
| Rmd | b206686 | Mathis Loïc Messager | 2020-04-14 | Start workflowr project. |
Global prevalence of non-perennial rivers and streams
Manuscript under review
!!This research compendium is still under development!!
Authors
Mathis Loïc Messager (mathis.messager@mail.mcgill.ca) 
Bernhard Lehner (bernhard.lehner@mcgill.ca)
Charlotte Cockburn
Nicolas Lamouroux
Hervé Pella
Ton Snelder
Klement Tockner
Tim Trautmann
Caitlin Watt
Thibault Datry (thibault.datry@inrae.fr)
Contents
This repository contains the research compendium for: [citation] - Paper - link to be added - Appendices - link to be added
How to use
Read the code, access the data
See the code directory on GitHub for the source code that generated the figures and statistical results contained in the manuscript. The raw data is stored on Repository link to be added and HydroSHEDS and will be downloaded when starting the analysis.
Install the R package
This repository is organized as an R package, providing documented functions to reproduce and extend the analysis reported in the publication. Note that this package has been written explicitly for this project and may not be suitable for general use.
This project is setup with a drake workflow, ensuring reproducibility. Intermediate targets/objects will be stored in a hidden .drake directory.
The R library of this project is managed by renv. This makes sure that the exact same package versions are used when recreating the project. When calling renv::restore(), all required packages will be installed with their specific version.
Please note that this project was built with R version 4.0.3 on a Windows 10 operating system. The renv packages from this project are not compatible with R versions prior to version 3.6.0.
To copy (i.e., clone) this repository to your local machine (for Windows only, please contact author for guidance on other platforms).
In Git Bash, the following commands illustrate the procedure to make a local copy of the Github repository in a newly created directory at C://test_globalIRmap :
Mathis@DESKTOP MINGW64 /c/temp
$ cd /c/
Mathis@DESKTOP MINGW64 /c
$ mkdir test_globalIRmap
Mathis@DESKTOP MINGW64 /c
$ cd /c/test_globalIRmap
Mathis@DESKTOP MINGW64 /c/test_globalIRmap
$ git clone https://github.com/messamat/globalIRmap.git
Cloning into 'globalIRmap'...
remote: Enumerating objects: 116, done.
remote: Counting objects: 100% (116/116), done.
remote: Compressing objects: 100% (89/89), done.
remote: Total 7363 (delta 48), reused 75 (delta 19), pack-reused 7247
Receiving objects: 100% (7363/7363), 1.91 GiB | 3.78 MiB/s, done.
Resolving deltas: 100% (925/925), done.In R Studio for Windows, the following procedure can be used:
- Click on “File” in the menu ribbon
- Select “New project…”
- Choose the “Version control” option in the New Project Wizard window.
- Then, select “Git” in the next window.
- In the next window, fill the fields as follows:
- Repository URL: https://github.com/messamat/globalIRmap
- Project directory name: [will autofill as “globalIRmap”]
- Create project as subdirectory of: [choose the directory, e.g., C://test_globalIRmap]
- Repository URL: https://github.com/messamat/globalIRmap
- Tick “Open in new session” and then click “Create project”.
Then open this project in R and run:
Structure of the analysis
In the drake philosophy, every R object is a “target” with dependencies. This repository contains more targets than actually needed to replicate the associated publication. Future task: create a simplified workflow to strictly reproduce main results
If you want to replicate the publication, you need to build the following targets: - - - -
Other practical notes
Notes and resources
The issues tracker is the place to report problems or ask questions
See the repository history for a fine-grained view of progress and changes.
The structure of this compendium is based on the work of Patrick Schratz, Carl Boettiger, Ben Marwick, and the workflowr package.
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 rstudioapi_0.11 whisker_0.4 knitr_1.29
[5] magrittr_1.5 R6_2.4.1 rlang_0.4.10 stringr_1.4.0
[9] tools_4.0.2 xfun_0.17 git2r_0.27.1 htmltools_0.5.0
[13] ellipsis_0.3.0 rprojroot_1.3-2 yaml_2.2.1 digest_0.6.25
[17] tibble_3.0.1 lifecycle_0.2.0 crayon_1.3.4 later_1.0.0
[21] vctrs_0.3.4 promises_1.1.0 fs_1.5.0 glue_1.4.0
[25] evaluate_0.14 rmarkdown_2.6 stringi_1.4.6 compiler_4.0.2
[29] pillar_1.4.4 backports_1.1.10 httpuv_1.5.4 renv_0.9.3
[33] pkgconfig_2.0.3