Bruno Rodrigues, head of the statistics and data strategy departments at the Ministry of Higher Education and Research of Luxembourg
Slides available online at https://is.gd/raps_reprotea
Here are the 4 main things influencing an analysis’ reproducibility:
Source: Peng, Roger D. 2011. “Reproducible Research in Computational Science.” Science 334 (6060): 1226–27
R < 3.6 (set.seed(1234))
[1] 2 6 5 8 9R >= 3.6 (set.seed(1234))
[1] 10 6 5 4 1Real impact on papers published with R < 3.6! (ongoing research project)
{stringr} < 1.5.0:
{stringr} >= 1.5.0:
(Actually a good change, but if you rely on that old behaviour for your script…)
Rarely an issue, but Neupane, et al. 2019:
While preparing a manuscript, to our surprise, attempts by team members to replicate these results produced different calculated NMR chemical shifts despite using the same Gaussian files and the same procedure outlined by Willoughby et al. […] these conclusions were based on chemical shifts that appeared to depend on the computer system on which step 15 of that protocol was performed.
Works on my machine!
We’ll ship your computer then.
vente-maison-2010-2021.xlsx in the data folderscripts/project_start folder):
We need to answer these questions
{renv}Create a renv.lock file in 2 steps!
renv::init() and check the folder for renv.lock(renv::init() will take some time to run the first time)
renv.lock filerenv.lock file{
"R": {
"Version": "4.2.2",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://packagemanager.rstudio.com/all/latest"
}
]
},
"Packages": {
"MASS": {
"Package": "MASS",
"Version": "7.3-58.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "762e1804143a332333c054759f89a706",
"Requirements": []
},
"Matrix": {
"Package": "Matrix",
"Version": "1.5-1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "539dc0c0c05636812f1080f473d2c177",
"Requirements": [
"lattice"
]
***and many more packages***renv.lock filerenv.lock file not just a recordscripts/renv_restorerenv::restore() (answer Y to active the project when asked){renv} conclusionShortcomings:
but… :
renv.lock file is “free”{targets}scripts/targets_pipeline_final/ folder_targets.R scripttargets::tar_visnetwork()_targets.R provides a clear view of what’s happening (beyond documentation)renv::init()Remember the problem: works on my machine?
Turns out we will ship the whole computer to solve the issue using Docker.
scripts/Docker/hello_docker/Dockerfile)docker build -t hello .docker run --rm --name hello_container hello--rm: remove the container after running--name some_name: name your container some_name
renv.lock file)targets::tar_make()RUN statementsCMD, gets executedLook at the Dockerfile here.
RUN do?COPY do?scripts/Docker/dockerized_projectrenv.lock file_targets.Ranalyse_data.Rmdfunctions/ folderBuild the image docker build -t housing_image .
/path/to/shared_folder to the one you made: docker run --rm --name housing_container -v /path/to/shared_folder:/home/housing/shared_folder:rw housing_imagerenv.lock file{targets}: not only good for reproducibility, but also an amazing tool all aroundContact me if you have questions:
Thank you!