Strong stabilization promotes the persistence of rare species - Data chapter
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Birds
Fish
Herps
Invertebrates
Mammals
Plants
.RData
.Rhistory
.gitattributes
.gitignore
AllPattern.xlsx
AllPattern_in.csv
AllPattern_out.csv
AllResults.csv
AllResults.xlsx
GompertzFuns.r
Patterndiagram.R
Portalnull.csv
Portalrates.csv
PortalrelA.csv
README.md
RareStabilizationData.Rproj
Sim_data.jpeg
Sim_scenarios.jpeg
Watkinson_fd_bias.R
background.csv
background_function.R
background_run.R
birdpattern.csv
birdras.csv
birdresults.csv
birds_results.R
dd_bias.r
densityD.txt
dissim_figures.R
dissim_results.R
dissimilarity.R
dissimilarity.csv
fd_bias.R
finalfigures.R
findv_function.R
fish_results.R
fishpattern.csv
fishras.csv
fishresults.csv
growth.R
growth2.R
herppattern.csv
herpras.csv
herpresults.csv
immigration.R
immigration2.R
immigration_simulations.R
invertebrate_results.R
invertpattern.csv
invertras.csv
invertresults.csv
mammal_results.R
mammalpattern.csv
mammalras.csv
mammalresults.csv
nonlinearpattern.csv
nonlinearpattern_in.csv
nonlinearpattern_out.csv
nonlinearresults.csv
null_function.R
null_function_cor.R
plantpattern.csv
plantras.csv
plantresults.csv
plants_results.R
ra_func.R
rawfigures.R
re_done.RData
reptiles_results.R
run_data.r
run_dataINLA.R
run_results.R
samplingfunction.R
simulations.R
stabil_function.r
stabil_function_INLA.r
stabil_function_cor.R
stabil_function_nonlin.R
stabil_function_raw.R
state space model.R
supplementary_figures.R
testgrowth.R
unbiasedNFD_function.R

README.md

Do persistent rare species experience stronger negative frequency dependence than common species? Glenda Yenni, Peter B. Adler, S. K. Morgan Ernest

Code and data used in publication and supplements, as well as some exploratory code not used in the final publication.

##Main files:

*stabil_funtion - The main analysis *null_function - Shuffling to achieve the 'null' results *simulations - Function used in the simulations in Appendix 3 *immigration - Function used in the immigration simulations in Appendix 4 *supplementary_figures - Production of figures in Appendix 5 *stabil_function_nonlin - Function discussed in Appendix 6

Subfolders contain the data used for that taxonomic group. Files named with 'results' or 'pattern' are the overall results from this data.

The file stabil_function is the function used in the main analysis. Other files with similar names are other attempts, not used in the manuscript. Similarly for the null, simulation, and immigration functions, other files with similar names represent exploratory models not used in the manuscript.