Code and data description to reproduce Tietje et al. (in prep) Drivers of global plant diversity
We provide here a final dataset (processed_data/shp_object_fin_analysis.RDS) which contains measures on the botanical country level for species richness, diversification rates and environmental variables, as well as scripts to process figures, the SEM and to build this data set.
All files used and produced throughout each step are described here, however due to the large size and data ownership requirements, the source data needs to be downloaded (e.g. CRU TS, wordclim, soil data, WCVP) from the respective sources. Version number and information how to obtain data is listed in the description part below.
Scripts are described in master_analysis.R, and also source some scripts. More information about system requirements and descriptions of each script can be found there.
Primary data includes files obtained online / from collaborators. Processed data is the final datafile used for analysis.
| File | Description |
|---|---|
| checklist_names.txt | Text file containing World Checklist of Vascular Plants taxonomy, taxon status, unique ID and synonyms |
| checklist_distribution.txt | Text file containing World Checklist of Vascular Plants taxon presence data in botanical countries, provided by collaborators (publication in prep) |
| ALLMB.tre | Phylogeny with GenBank and Open Tree of Life taxa with a backbone provided by Magallón et al. (2015). From Smith & Brown 2018 |
| GBMB.tre | Phylogeny with GenBank taxa with a backbone provided by Magallón et al. (2015). From Smith & Brown 2018. Used to identify taxa with molecular information |
| ott.rds | Open Tree of Life taxonomy file (.rds version of taxonomy.tsv, Version: 3.0. Available on https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0). Used to identify source for tip label name (NCBI or GBIF) |
| fin_species_match_NCBI.rds | List with taxonomy matching results for NCBI phylogeny tip labels with WCVP IDs |
| gbif_all.rds | Download of taxonomic information from GBIF for GBIF phylogeny tip labels |
| fern_list.txt | List of fern and fern allies families (Pteridophytes), available on theplantlist.org/browse |
| soil_raster_layer_000832.tif | Soil raster layer with most probable soil types, available on https://files.isric.org/soilgrids/latest/data/wrb/MostProbable.vrt and saved as geotiff with lower resolution for reasonable computation time |
| shapefile_biomes/wwf_terr_ecos.* | Shapefile with terrestrial ecoregions of the world (biomes). Available on https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world |
| shapefile_bot_countries/level3.* | Shapefile with polygons for all 369 TDWG level 3 units |
| wc2.1_30s_elev.tif | WorldClim elevation data, available on https://biogeo.ucdavis.edu/data/worldclim/v2.1/base/wc2.1_30s_elev.zip |
| cru_ts4.04.1901.2019.pet.dat.nc | CRU TS v. 4.04, available on https://catalogue.ceda.ac.uk/uuid/89e1e34ec3554dc98594a5732622bce9. Free account required for download. |
| cru_ts4.04.1901.2019.tmp.dat.nc | See above |
| cru_ts4.04.1901.2019.pre.dat.nc | See above |
| tczti_mat_ann_fsy1.nc | Miocene mean annual temperature from https://www.paleo.bristol.ac.uk/ummodel/users/Bradshaw_et_al_2012/new2/ |
| tczti_precip_ann_fsy1.nc | Miocene annual precipitation, source as above |
| tcztk-tczti_mat_ann_fsy1.nc | Miocene mean annual temperature anomaly |
| tcztk-tczti_precip_ann_fsy1.nc | Miocene annual precipitation anomaly |
| CHELSA_cur_V1_2B_r10m/10min/bio_1.tif | CHELSA Last Glacial Maxiumum Bioclims, Version 1.2, 5/29/2018, obrtained via paleoclim.org |
| CHELSA_cur_V1_2B_r10m/10min/bio_12.tif | see above |
| chelsa_LGM_v1_2B_r10m/10min/bio_1.tif | see above |
| chelsa_LGM_v1_2B_r10m/10min/bio_12.tif | see above |
| Islands_TDWG_AllData.txt | Island classifications from http://dx.doi.org/10.1111/j.1466-8238.2011.00728.x |
Files to make figures and inspect final SEM (scripts 17-19).
| File | Description |
|---|---|
| sem_input_data.RDS | Data.frame to feed to the Structural Equation Model selection process, including full names for each geographic unit (botanical country) |
| shp_object_fin_analysis.RDS | Spatial object including all data in sem_input_data.rds |
| best_model.RDATA | Best SEM lavaan model object |
