Eric R. Sokol, Craig W. Herbold, Charles K. Lee, S. Craig Cary, and J. E. Barrett. 2013. Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains. Ecosphere 4:136. http://dx.doi.org/10.1890/es13-00136.1


Supplement

R script and data files used for diversity partitioning, and to bootstrap confidence intervals for diversity metrics described in the main text.
Ecological Archives C004-014-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Eric R. Sokol1,†, Craig Herbold2,3,4, Charles K. Lee2,3, S. Craig Cary2,3,4, and John E. Barrett1

1 Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060 USA

2 Department of Biological Sciences, University of Waikato, Hamilton, New Zealand

3 International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand

4 College of Earth and Ocean Sciences, University of Delaware, Newark, DE 19716 USA

†E-mail: sokole@vt.edu


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 “Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains.” 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>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>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