DOI: 10.5061/dryad.5qfttdzcz
title: ClimateAnalyzer: set of scripts to delimit regions based on bioclimatic variables

description: Habitat stability is important for maintaining biodiversity by preventing
 species extinction, but this stability is being challenged by climate
 change. The tropical alpine ecosystem is currently one of the ecosystems
 most threatened by global warming, and the flora close to the permanent
 snow line is at high risk of extinction. The tropical alpine ecosystem,
 found in South and Central America, Malesia and Papuasia, Africa, and
 Hawaii, is of relatively young evolutionary age, and it has been exposed
 to changing climates since its origin, particularly during the
 Pleistocene. Estimating habitat loss and gain between the Last Glacial
 Maximum (LGM) and the present allows us to relate current biodiversity to
 past changes in climate and habitat stability. In order to do so, 1) we
 developed a unifying climate-based delimitation of tropical alpine regions
 across continents, and 2) we used this delimitation to assess the degree
 of habitat stability, i.e. the overlap of suitable areas between the LGM
 and the present, in different tropical alpine regions. Finally, we discuss
 the link between habitat stability and tropical alpine plant diversity.
 Our climate-based delimitation approach can be easily applied to other
 ecosystems using our developed code, facilitating macro-comparative
 studies of habitat dynamics through time.
description: The dataset consists of a set of script developed for the
 corresponding publication using CHELSA v.1.2 (https://chelsa-climate.org/downloads/) to delimit tropical alpine regions based on bioclimatic variables. Using the scripts and setting the limits of the respective bioclimatic variables, will result in the GIS shapefiles with the delimitied region. Here, we provide the corresponding GIS shapefiles and figures for the above mentioned publication, that were the outcome of running the R scripts. The shapefiles and figures are based on the mean temperature of the coldest and warmest quarter (bioclim 10 and bioclim 11) of -3 to +10/+18°C respectively, plus a restriction to the tropics based on bioclim 3, the ratio of diurnal variation to annual variation in temperatures, ranging from 50 to 300 °C/10.
description: # ClimateAnalyzer 
 ClimateAnalyzer is a set of script written in R to delimit areas based on
 bioclimatic variables. The scripts have been developed to delimit tropical
 alpine areas based on bioclimatic variables from CHELSA
 (). The work has been
 presented in Kandziora et al (under review) "The ghost of past
 climate acting on present-day plant diversity: lessons from a
 climate-based delimitation of the tropical alpine ecosystem". ##
 Description of the data and file structure The uploaded GIS shapefiles and
 figures are based on a delimitation based on the mean temperature of the
 coldest and warmest quarter (bioclim 10 and bioclim 11) of -3 to +10 °C,
 plus a restriction to the tropics based on bioclim 3, the ratio of diurnal
 variation to annual variation in temperatures, ranging from 50 to
 300 °C/10. The delimitation was done for current climatic conditions as
 well as two reconstructions of the climate during the last glacial
 maximum, based on MPI-M_MPI-ESM-P (abbreviated to MPI) and MIROC_MIROC-ESM
 (abbreviated as MIROC). ## Sharing/Access information All scripts and
 files are licenced under CC0 v.1 ## Code/Software In order to repeat the
 analysis users have to rerun script 01 and 02. Script 01 is delimiting the
 areas based on the bioclimatic variables and script 02 compares different
 delimitations with each other. The scripts can also be adapted to any
 other region, or use of different bioclimatic variables to delimit certain
 areas. Getting started * download the bioclimatic raster layers
 (000_download_data.sh) * install all needed packages (check
 000_install_packages.R and adapt 'path_to_libraries' and working
 directory) * load all packages (00_set_stage_ondemand.R) * load
 00_set_variables.R - here the different bioclimatic limits are being
 defined, elevation, resolution and projection are set * make sure that the
 climate data is downloaded (see 000_download_data.sh) and that the path to
 the raster layers is correctly provided (function
 'get_path_data' in 00_set_your_data.R) * run 01_set_analyses.R
 to get the areas delimited by the bioclimatic variables * run
 02_run_all_postanalyses.R to compare different areas to each other * run
 03_get_climatespace.R to do a PCA and get the niche space per area In case
 you want to analyze your own climatic delimitation/region, adapt regional
 limits and names within the function 'get_extent_area'
 (00_set_your_data.R) ## Shapefiles The uploaded shapefiles are the result
 of running the scripts to delimit the tropical alpine ecosystem as
 described in the corresponding publication.