The Optimal Species Richness Environments for Human Populations

This supporting document should allow one to recreate the analysis performed as part of “The optimal species richness environments for human populations, ” By Freeman et al. 2018 Submitted to PNAS July 2018. The annotated scripts in this directory (RichnessSIScripts.pdf) contain code to replicate the analysis, as well as code for additional analyses not included in the main paper or supplemental information. To replicate the analysis, one can either analyze the data files provided or build their own data set. As discussed in the main body of the text, we built three data sets following the procedures outlined by Tallavaara et al. (2017) for linking species richness values, net primary productivity and pathogen stress to each ethnographic case. We do not replicate the scripts provided by Tallavaara et al.(2017) as these are available, clear and should be cited when used.To replicate our analysis, one needs to set their working directory in R to the file location that contains the data files. There are 11 files that follow the naming convention “name.csv.” The 11 files are “MainFinal.csv”. “AGPOP3Eco.csv”, “HGFEM4R.csv”, “AGPOPClass.csv”, “CountryMeansEco2.csv”, “AGPOP3EcoH.csv”, “AGPOP3EcoL.csv”, “HiHG.csv”, “LowHG,csv”, “CountryMeansEco2H.csv”, and “CountryMeansEco2L.csv”. The first five files are the main files, the second six files are divided into high and low species richness environments by economy type for convenience. In each file, the variables are defined as follows: 1. Group/Country–name of the ethnographic society of country 2. Latitude–the latitude at the geographic center of a group’s territory or a country’s territory. 3. Longitude–the longitude at the geographic center of a group’s territory or a country’s territory. 4. Class–an ordinal ranking of wealth and status differentiation among the hunter-gatherer and agriculturalists societies (see main text for more details) 5. Class2–an binary ranking of wealth and status differentiation among the hunter-gatherer and agriculturalists societies (see main text for more details). 6. ECI–The average economic complexity index since 1973 as measured among modern countries. 7. DENSITY–Population density in people per square kilometer. This is a point in time estimatefor hunter-gatherer and agricultural groups and an average density since 1973 among nation states. 8. LnDENSITY–The natural log of population density 9. npp–net primary productivity estimated at the center of each group’s territory 10. npp2-Net primary productivity squared 11. biodiv–Standardized estimate of species richness at the center of each group’s range. 12. biodiv2–Species richness *100 ad squared. 13. pathos–Index of pathogen stress at the center of a group’s territory. 14. DivDiff–The absolute value of species richness-the species richness value of peak population density (values identified in Fig. 2 of the main manuscript).1 5. ID–A nominal variable that denotes economy type. HG=hunter-gatherer, AG=subsistence agriculturalist, IND=modern nation state Tallavaara, M., J. T. Eronen, and M. Luoto2017. Supporting data and script for ”productivity, biodiversity, and pathogens influence the global hunter-gatherer population density” (Tallavaara et al. pnas 2018).https://doi.org/10.5281/zenodo.1167852