Last updated: 2021-01-06

Checks: 6 1

Knit directory: globalIRmap/analysis/

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.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

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.

Seed: set.seed(12345)

The command set.seed(12345) 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.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 6d566e5

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 6d566e5. 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:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .drake/config/
    Ignored:    .drake/data/
    Ignored:    .drake/drake/
    Ignored:    .drake/keys/
    Ignored:    .drake/scratch/
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  .Rbuildignore
    Untracked:  Compare_models_20201026.Rmd
    Untracked:  analysis/methods_refdisdat.Rmd
    Untracked:  analysis/results_diagnostics.Rmd
    Untracked:  figtabres.docx
    Untracked:  figtabres_20201220_1.docx
    Untracked:  log/
    Untracked:  removeGSIMper.R
    Untracked:  schema.ini

Unstaged changes:
    Modified:   IntermittentAnalysis_MasterScript_reproduced.R
    Deleted:    _workflowr.yml
    Modified:   analysis/_site.yml
    Modified:   analysis/about.Rmd
    Deleted:    analysis/diagnostics.Rmd
    Deleted:    analysis/figure/figtabres.Rmd/basic map-1.png
    Modified:   analysis/license.Rmd
    Modified:   drake_cache.csv
    Modified:   globalIRmap.Rproj
    Modified:   interactive.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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
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)

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.git

Then start R in this directory and run

packrat::restore() # restores all R packages with their specific version
r_make() # recreates the analysis

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.

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 utils     datasets  methods   base     

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     workflowr_1.6.2  R6_2.4.1         rlang_0.4.7     
 [9] stringr_1.4.0    tools_4.0.2      xfun_0.17        git2r_0.27.1    
[13] htmltools_0.4.0  ellipsis_0.3.0   yaml_2.2.1       digest_0.6.25   
[17] rprojroot_1.3-2  tibble_3.0.1     lifecycle_0.2.0  crayon_1.3.4    
[21] later_1.0.0      vctrs_0.3.4      promises_1.1.0   fs_1.5.0        
[25] glue_1.4.0       evaluate_0.14    rmarkdown_2.3    stringi_1.4.6   
[29] compiler_4.0.2   pillar_1.4.4     backports_1.1.10 httpuv_1.5.4    
[33] pkgconfig_2.0.3

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