this includes all scripts, analyses, and results of our re-analysis of Zanne et al. 2014 Nature 506: 89-92
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dryad
figures
handling_climate_data
intermediate_results
README.md
R_source_custom_functions.R
annotated_analyses_script.R
annotated_analyses_script_v1.1.R
cleanGbifCoords.1.0.py
results_ClimateScoringSensitivity.txt

README.md

Description of files (representing data, scripts, and results) associated with a critique of Zanne AE et al. (2014) Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89–92.

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The folder in which the README is located contains the following files:

  • README.md : This very file
  • annotated_analyses_script.R : The file with all annotated R scripts to repeat our analyses. It demonstrates the implementation of our analyses, but running them serially takes very long. Therefore, we actually executed them on the OSCAR computer cluster at the Centre for Computation and Visualization at Brown University. To facilitate following all our steps, we provide saves of intermediate results after each section of the script.
  • annotated_analyses_script_v1.1.R : This file is a slightly updated set of analyses -- the only changes are due to new figures, at the request of reviewers
  • R_source_custom_functions.R : This file contains custom R functions which we wrote to facilitate the analyses. It is read from the R script.
  • cleanGbifCoords.1.0.py : This is a general-use version of a portion of the script that we developed to clean the Zanne et al. climate data. Specifially, this script will remove political centroids and locations of major herbaria from a collection of latitudes/longitudes. If used, please cite our BCA: Edwards EJ, J de Vos, MJ Donoghue. 2015. Brief Communications Arising: Doubtful pathways to cold tolerance in plants. Nature doi:10.1038/nature14393.
  • results_ClimateScoringSensitivity.txt : This is a tab-delimited file containing the results of analyses that differed in the handling of the climate data (annotated_analyses_script.R contains the relevant annotations). It contains the following elements indicated by headers: file, treetype treename : descriptors of the analysis ntaxa : number of taxa in the tree n00 : number of taxa freezing unexposed without freezing-adaptated trait n01 : number of taxa freezing unexposed with freezing-adaptated trait n10 : number of taxa freezing exposed without freezing-adaptated trait n11 : number of taxa freezing exposed with freezing-adaptated trait groom : imprecise and doubtful coordinates from GbIF data excluded? minclimdat : minimum number of coordinates required for including a species perc : percentile threshold to score a species as freezingExposed trait : vessel, phenology, or woodiness data set ratemat : were simultaneous transitions ok (simultOK) or not (NULL) loglik : log likelihood AICc : AICc score trans_00.01 : transition rate from state 00 to state 01 ... trans_11.10 : transition rate from state 11 to state 10 traitfirst : % contribution of trait-first pathway simult : % contribution of simultaneous pathway climfirst : % contribution of climate-first pathway climratesum : sum of all climate-state transition rates traitratesum : sum of all trait-state transition rates clim_vs_trait_labil : persistence00 : persistence times state 00 ... persistence11 : persistence times state 11 diagnosis : did the analyses execute correctly? analysis : analysis identifier dAIC : delta-AIC score for preference of the model used

And it contains the following subfolders:

  • ./dryad/ : Contains the data as provided by Zanne et al.
  • ./handling_climate_data/ : Contains data, scripts, and results, pertaining to summarizing gbif localities into a single minimum-temperature value per species
  • ./intermediate_results/ : Contains intermediate results, that is, results generated and processed in R at 11 intermediate stages of the analyses.
  • ./figures/ : Contains additional figures generated using the R script. annotated_analyses_script_v1.1.R

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The subfolder "./dryad/" contains 5 files, that are copied unaltered from the datadryad digital repository where Zanne et al. uploaded their data

  • GlobalLeafPhenologyDatabase.csv : leaf phenology data (abbreviated "phenol")
  • GlobalVessel_A_data.txt : conduit size data (abbreviated "vessel")
  • GlobalWoodinessDatabase.csv : woodiness data (abbreviated "woody")
  • MinimumFreezingExposure.csv : climate data as handled by Zanne et al.
  • Vascular_Plants_rooted.dated.tre : Zanne et al.'s phylogeny

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The subfolder "./handling_climate_data/" contains

  • getTminPerSpecies.py : An annotated phython script to pars the gbif locality data as we received it from Zanne et al. and summarize it as one minimal value per species.
  • allHerbaria_ADM1_badCoords.txt : The coordinates that represent the corners of the 0.01° x 0.01° gridcells that contain centroids of major political areas and herbaria that house > 1,500,000 specimens. See annotation in phython script for details.
  • gbif_cords_tmin_species-summ.txt : The extensive output file of the python script.
    It contains more information that just for the R analyses.
  • errors.out : The error outfile containing the lines in the gbif locality data file that needed to be excluded due to presence of NA.
  • climate_data_grooming_levels_JdV.txt : The slimmed version of the file gbif_cords_tmin_species-summ.txt, containing only those columns that contain data analyzed in the downstream analyses. NB: the file with the actual gbif coordinate data is not provided because it is 2.25 GB in size. We received from Zanne et al.

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The subfolder "./intermediate_results/" contains intermediate results, listed and named in order of appearance in the R script.

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The subfolder "./figures/" contains three figures generated by the R script. Two are Figure 1A, 1B in the main manuscript, and the third illustrates the influence of additional cleansing of the GBIF data, and enforcing minimum sample sizes.