# MPI - Project Management in R ## Link to collaborative doc https://hackmd.io/@drmowinckels/2023-11-21-MPI ## Share code, ideas and questions by writing in this document we can have a collaborative document throughout the course. I have setup a "skeleton" based on the various sections of today to help us be organised. ## Introduction Let's get a little aquianted! Write in this list your name, your field of study, and your favourite ice-cream flavour. - Athanasia Mowinckel - Research Software Engineering - Lemon sorbet - Emil Stobbe - Sounds of the Environment, Pistachio - Florian Bolenz - Cognitive Psychology - Stracciatella - Michael Krause - Research IT - salted caramel - Maike Hille - PhD student in Neuroscience - vanilla - Anne Klimesch - Clinical Neuroscience - Vegan Almond Magnum - Linda Kerbl - Psychology - pistacchio - Marlene Hecht - Psychology - Pistachio - Moana Beyer - PhD Student in Neuroscience - Pistachio - Neele Engelmann - Psychology - Vanilla - Lisa Oswald - Political Psychology / Data Science - Pistachio - Maike Kleemeyer - RDM - chocolate fudge brownie - Annika Werwach - Early cognitive development - Yogurt - Stefan Herzog - cognitive science/judgment and decision making - bourbon whiskey pecan - Lou Haux - comparative and developmental psychology - yoghurt - Elahe Keramati - Philosophy - pistacchio - Monalisa Chikezie - Msc student - Cognitive Neuroscience - Vanilla Add notes from this section here ```r # Run in R install.packages(c( "remotes", # installing packages from GitHub "rmarkdown", # rendering reports "fs", # file system operations "here", # navigating paths "usethis", # for course materials "tidyverse" # data-wrangling )) ``` ### Exercise Explore your R installation ```r install.packages("usethis") library(usethis) # saves project on desktop by default for most users use_course("rstats-wtf/wtf-explore-libraries") # use_course("rstats-wtf/wtf-explore-libraries", destdir = "my/new/location") # can alternatively download from # https://github.com/rstats-wtf/wtf-explore-libraries ``` ## Project Oriented Workflow Pretty code fonts: monospaced ligatures. Mo uses Fira Code Retina https://betterwebtype.com/5-free-monospaced-fonts-with-coding-ligatures/ #### About R and long file paths > Despite the long path support in Windows [since Win10 1607 from 2016] and efforts like this [changes to R outlined in the post], it will take “at least” very long before one could reliably rely on paths longer than 260 characters on Windows. https://blog.r-project.org/2023/03/07/path-length-limit-on-windows/ IIUC the changes to R to support long paths on Windows were release with R 4.3. The corresponding [RStudio issue](https://github.com/rstudio/rstudio/issues/12806) (if that's the IDE used in this case) is still open. Other developers also suggest that this might also more likley occur on symlinked institutional paths, where the location _seems_ to not be that long, but actually is a pointer to a path that ##### Python path issues https://stackoverflow.com/questions/74894455/what-does-error-in-file-existspythonpath-file-name-conversion-problem-na ### Exercise ```r library(usethis) # saves project on desktop by default for most users use_course("rstats-wtf/wtf-fix-paths") # use_course("rstats-wtf/wtf-fix-paths", destdir = "my/new/location") # can alternatively download from # https://github.com/rstats-wtf/wtf-fix-paths ``` ## Naming files Add notes from this section here ## Project Structure Add notes from this section here ### Exercise Create a report that adheres to project organization strategies. ```r library(usethis) # saves project on desktop by default for most users use_course("rstats-wtf/wtf-packages-report") # use_course("rstats-wtf/wtf-packages-report", destdir = "my/new/location") # can alternatively download from # https://github.com/rstats-wtf/wtf-packages-report ``` ## Package Management Add notes from this section here ### Exercise Explore the changes {renv} makes to a project. ```r library(usethis) # saves project on desktop by default for most users use_course("capro-uio/wtf-explore-renv") # use_course("capro-uio/wtf-explore-renv", destdir = "my/new/location") # can alternatively download from # https://github.com/capro-uio/wtf-explore-renv ``` # the targets pacakge https://www.joelnitta.com/posts/2021-11-16_r-bioinfo-flow/