Figures and data analysis used in the manuscript are summarized in :
- SummarySporeTraitAnalysis.RMD
That RMD file already loads the three datasets used for those figures:
a) output/Spore_Database_Fungi.csv: Spore size and shape data assembled after extracting data from Mycobank Descriptions + other sources (More details on "AssemblingDataSources.R)
b) output/FungalTaxanomy_col.csv: Fungal taxonomy as in the Catalogue of Life
c) output/GuildData.csv: Fungal functional groups, which inlcudes FungGuild + Lichens + Ectomycorrhiza + Insect pathogens + AMF + Plant pathogens.
The three datasets are already uploaded to this repo. Further details on those datasets and the r packages used can be found in "MatchingSpore_FunctionData.R"
The algorithm for spore extraction was developed by @Franz Krah (the original code can be found here). The algorithm takes text from downloaded Mycobank descriptions that roughly follows the format "... *Spore ... d x d um ... ". The algorithm then extracts the spore name and associated quantities from the text and gathers the results in a table with rows representing each species name. This original code allows extractions for all spore types at once. @Carlos Aguilar and @Jeff Powell later seperated and modified the code to enhance extraction accuracy for different spore types, which follow slightly differnt notation conventions(these modified codes can be found in the folder AlgorithmSporeExtraction.