NOTE: find all instances of
NOTEand make sure to overwrite with the appropriate text
This repository holds all supplementary source code needed to reproduce the calculations and plots of the following publication: NOTE: AUTHORS. NOTE: TITLE. <<NOTE: add journal citation, doi and link>>. doi:???.
The fully compiled analysis files are available as [HTML reports](NOTE: ADDRESS). For the easiest way to run the source R Markdown (.Rmd) files that produce these HTML reports along with the data figures in PDF and PNG format and the data tables in XLSX format, please follow the instructions below.
R Markdown is a so-called "literate programming" format that enables easy creation of dynamic documents with the R language. HTML and PDF reports can be generated from R Markdown files using knitr and pandoc, which can be installed automatically with RStudio, and are fully integrated into this cross-platform IDE. All software used for these reports (R, RStudio, etc.) is freely available and completely open-source.
The quickest and easiest way is to use RStudio.
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Download and install R for your operating system
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Download and install RStudio for your operating system
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Download a [zip file of this repository](NOTE: https://github.com/ORGANIZATION/REPOSITORY/archive/master.zip) and unpack it in an easy to find directory on your computer
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Start RStudio and select File --> New Project from the menu, select the "Existing Directory" option and browse to the repository folder from the zip file in the "Project working directory" field, then select "Create Project"
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Install the required libraries by running the following command in the Console in RStudio: install.packages(NOTE: c("tidyverse", "readxl", "openxlsx", "knitr", "latex2exp", "boot", "broom")) or by installing them manually in the RStudio's Packages manager.
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Open any of the R Markdown (.Rmd) files in the file browser
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To generate an HTML report ("knit HTML"), select File --> Knit from the menu. The HTML report will be displayed upon successful completion (it might take a minute or two for files with more complex calculations or figures) and is saved as a standalone file in the same directory (these are the files made [available online](NOTE: https://ADDRESS/) and linked in the SI). All generated data figures are saved as PDF and PNG in the figures/ sub-directory. All generated data tables are saved as XLSX in the tables/ sub-directory.
We hope that this code, or any part of it, might prove useful to other members of the scientific community interested in the subject matter. All code is completely open-access and can be modified and repurposed in every way. If significant portions are reused in a scientific publication, please consider citing our work. Please make sure to cite this work if re-using any of our data.
The R Markdown files in this repository make use of various R modules for data processing, plotting and modelling. All of these should be installed automatically when the first R Markdown file is knitted (if the knitting fails because of a missing package, please install it manually, an error will indicate which package could not be installed).