About
Last updated: 2021-01-06
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.
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Unstaged changes:
Modified: IntermittentAnalysis_MasterScript_reproduced.R
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Modified: globalIRmap.Rproj
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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 | 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 clone the project, a working installation of git is required. Open a terminal in the directory of your choice and execute:
git clone git@github.com:messamat/globalIRmap.gitThen start R in this directory and run
packrat::restore() # restores all R packages with their specific version
r_make() # recreates the analysisStructure 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.
sessionInfo()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_0.4.7 stringr_1.4.0
[9] tools_4.0.2 xfun_0.17 git2r_0.27.1 htmltools_0.4.0
[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_2.3 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