The Optimal Species Richness Environments for Human Populations

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