mfd_overview

This repo generates statistics and plots to summarize the Microflora Danica project and reproduces the results from "Section I: The Microflora Danica data set" and Supplementary Figures 1 and 2 of the MFD manuscripts.

Please download the input data from the Zenodo repo and the metadata repo in the /data folder and amend the /scripts/R_scripts/<NAME>.Rmd files under the "Load data" section if required by new releases of the data. The files will generally have the form of <RELEASE_DATE>. and "RELEASE_DATE" will have to match the one from the download.

Scripts

Breakdown of the scripts contained in this repo and what they were used for:

• '/scripts/scripts_R/MFD_colors.R' is a utility script to re-create the same color palette for the MFD ontology habitats;
• '/scripts/scripts_R/mfd_table_map.Rmd' generates Figure 1a and Figure 1b;
• '/scripts/scripts_R/sankey_plot.Rmd' generates Figure 1c and Supplementary Figure 1;
• '/scripts/scripts_R/reference_DK_grid.Rmd' generates Supplementary Figure 2;