Scripts to tidy trait and allometry data bases. These scripts are intended to work particularly the TRY data base, but it provides a framework to incorporate data from additional sources.
For additional details on these scripts (the "knitted" R Markdown), check the documentation here.
- TidyTraitAllomDB.Rmd – This This (mostly) R Markdown script takes data downloaded from the TRY data base (plus additional sources) and apply tidy data standards. In a tidy data set, each row represents one observation, each column represents a variable, and each cell represents a value. In addition, categorical traits are also harmonised into consistent categories and species taxonomy is standardised to the best extent possible (likely with some user input).
- Make sure to download the Fortran code SplitAuthor.f90 to the main working directory. Also, make sure to download the directory RUtils containing multiple ancillary functions.
- Data downloaded directly from the TRY data base should go to the directory defined in variable
orig_path. - The csv files provided in InputLists are examples. One should be able to add/remove traits according to their needs, however, new traits without standardised values and units will require code development, specifically in files RUtils/TRY_Harmonise_Utils.r and RUtils/TRY_Fix_OrigValue_Str.r.
- Data sets other than TRY can be provided, but users ought to format the data in tidy format, using variable names consistent to those defined in InputLists. Brief examples of additional data sets from different data bases are provided in AdditionalData.
Important notes.
- These scripts are (permanently?) under development. Contributions, suggestions, and pull requests with bug fixes are always welcome!