From 98642b7c431613b8f65761381610e4915fc98ae7 Mon Sep 17 00:00:00 2001 From: Aariq Date: Thu, 25 Jun 2020 15:14:53 -0400 Subject: [PATCH] updated reproducibility instructions. --- README.md | 3 ++- session_info.txt | 20 -------------------- 2 files changed, 2 insertions(+), 21 deletions(-) delete mode 100644 session_info.txt diff --git a/README.md b/README.md index 9f85633..2407452 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,10 @@ [![DOI](https://zenodo.org/badge/139384786.svg)](https://zenodo.org/badge/latestdoi/139384786) -This repository contains the R scripts (.R and .Rmd files) necessary to reproduce results from this paper. Datasets generated by these scripts are found in the "data" directory. To run scripts "1-muir-data-wrangling.R" and "2-muir-analys.Rmd", you will need to download the dataset from Muir et al (2017), from [Data Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.1r8c2). Unzip the download and place the contents inside "data/muir/". Session info is provided in `session_info.txt`. +This repository contains the R scripts (.R and .Rmd files) necessary to reproduce results from this paper. Datasets generated by these scripts are found in the "data" directory. To run scripts "1-muir-data-wrangling.R" and "2-muir-analys.Rmd", you will need to download the dataset from Muir et al (2017), from [Data Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.1r8c2). Unzip the download and place the contents inside "data/muir/". Figures and tables generated by the analysis are found in the "out" directory. +This project uses [renv](https://rstudio.github.io/renv/articles/renv.html) to manage package dependencies. After downloading this (or forking it via GitHub), open the .Rproj file. After installing and loading the `renv` package, simply run `restore()` to install the exact configuration of R packages originally used in this analysis. ### References Muir CD, Conesa MÀ, Roldán EJ, et al (2017) Weak coordination between leaf structure and function among closely related tomato species. New Phytol 213:1642–1653. doi: 10.1111/nph.14285 \ No newline at end of file diff --git a/session_info.txt b/session_info.txt deleted file mode 100644 index 15d06f5..0000000 --- a/session_info.txt +++ /dev/null @@ -1,20 +0,0 @@ -R version 4.0.0 (2020-04-24) -Platform: x86_64-apple-darwin17.0 (64-bit) -Running under: macOS Mojave 10.14.6 - -Matrix products: default -BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib -LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib - -locale: -[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 - -attached base packages: -[1] stats graphics grDevices datasets utils methods base - -other attached packages: -[1] BiocManager_1.30.10 renv_0.10.0-42 - -loaded via a namespace (and not attached): - [1] compiler_4.0.0 htmltools_0.4.0 tools_4.0.0 yaml_2.2.1 Rcpp_1.0.4.6 rmarkdown_2.1 knitr_1.28 - [8] xfun_0.14 digest_0.6.25 rlang_0.4.6 evaluate_0.14