DOI: 10.6084/m9.figshare.3563841.v1
title: Supplement 1. R script and data files used for diversity partitioning, and to bootstrap confidence intervals for diversity metrics described in the main text.

description: File List ESM_data.rda (MD5: af1874078a6c7ca8fa855c446e82da01) ESM_FUNCTIONS.R (MD5: c7afecca8cc52d0aa275c981b720be28) ESM_calculate_pcnm.R (MD5: 37be4482aa5c2d7fde6333cdb5ec7fde) ESM_ENV_varselect_and_varpart.R (MD5: 5927c0784a36542dce8bd0e23f82bf36) ESM_diversity_partitioning_boot.R (MD5: 452b039642b1fd29d0f1ea1386ceb66e) ESM_dbRDA_varselect_and_varpart.R (MD5: ba09da2389c99fd051fa5ae3e11ab206) ESM_dbRDA_model_and_varpart_for_CYARISA_finescale.R (MD5: 6c56def49cba3845d88a4b446dee6129) ESM_dbRDA_model_and_varpart_for_CYARISA.R (MD5: 452622aef26fa3b9d819dccaf0eeff52) ESM_dbRDA_model_and_varpart_for_BACT_finescale.R (MD5: c20fe9a98db643613627f25623113fae) ESM_dbRDA_model_and_varpart_for_BACT.R (MD5: 475377a5657b41145c2c471c70f09ba6) All files at once: Rcode.zip (MD5: 27e0fed325b02999ced46bd10c128d16) Description These supplemental files include R script necessary to recreate the analyses described by Sokol et al. in <b>“Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains.” </b>The script files load the properly formatted data set stored in the ESM_data.rda file, and use the functions available in the ESM_FUNCTIONS.R source code. All files must be in the same directory to work properly. Contact Eric R. Sokol at sokole@vt.edu or sokole@gmail.com with any questions. ESM_data.rda – Data object to be loaded in R. Includes correctly formatted data frames and variables used in the analysis. ESM_FUNCTIONS.R – Source code with functions used in the analyses in Sokol et al., other R script files call this source code. ESM_calculate_pcnm.R – R script to calculate spatial variables (PCNM eigenvectors) ESM_ENV_varselect_and_varpart.R – R script for model selection used to select spatial variables (PCNM eigenvectors) associated with different environmental variables (univariate analysis) and overall environmental variation (multivariate analysis using redundancy analysis). ESM_diversity_partitioning_boot.R – R script for diversity partitioning and calculating 95% CIs using bootstrap resampling. ESM_dbRDA_varselect_and_varpart.R – Source code that is called by other script files for distance-based redundancy analysis (dbRDA) model selection and variation partitioning. ESM_dbRDA_model_and_varpart_for_CYARISA_finescale.R – R script for variation partitioning for cyanobacterial ARISA profiles using only fine scale spatial filters (PCNM&gt;8), calls the source code in ESM_dbRDA_varselect_and_varpart.R ESM_dbRDA_model_and_varpart_for_CYARISA.R – R script for variation partitioning for cyanobacterial ARISA profiles, calls the source code in ESM_dbRDA_varselect_and_varpart.R ESM_dbRDA_model_and_varpart_for_BACT_finescale.R – R script for variation partitioning for bacterial tRFLP profiles using only fine scale spatial filters (PCNM&gt;8), calls the source code in ESM_dbRDA_varselect_and_varpart.R ESM_dbRDA_model_and_varpart_for_BACT.R – R script for variation partitioning for bacterial tRFLP profiles, calls the source code in ESM_dbRDA_varselect_and_varpart.R