https://doi.org/10.5061/dryad.18931zd5j

These code and data files reproduce analyses in the above-named manuscript. Code files are enumerated and named below. In this README, each code file additionally contains a bullet point list of what it does. Each bullet point begins with a key verb (Reads, Sources, Loads, Saves, Creates). With the exception of "Creates", these verbs refer to typical R functions ("load", "read_csv", etc.). "Creates" typically refers to the creation of a figure or statistic(s), but occasionally to a data product used on the fly or for inspection. Further details can be obtained from annotated code chunks within the files. Some code chunks can take a long time to run. In these cases, we supply an alternate code chunk (immediately following) that loads the data product as an R data file (.Rda). All required Rda files are included. 

1. dataPrep

• reads in GMPD ("gmpd_main.csv")
• reads in PanTHERIA ("PanTHERIA_1-0_WR05_Aug2008.txt")
• reads in mammal phylogeny ("WR_2005_ST.txt")
• GMPD metadata available here: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.1799
• PanTHERIA metadata available here: https://esajournals.onlinelibrary.wiley.com/doi/10.1890/08-1494.1
• Mammal phylogeny available here: https://doi.org/10.1038/nature05634
• creates check that no HP combos refer to intermediate (ungulate) hosts
• creates theta
• creates nri (i.e. "get_nri.Rda", which is loaded in other files)

2. g1

• sources dataPrep
• creates figS1

3. compCorr

• sources dataPrep
• creates figS2 [correlations of abund/components]

4. makeTaxTreePara

• sources dataPrep
• saves get_txInfo
• saves get_taxTree

5. abundPhylo

• sources dataPrep
• creates abund
• loads get_txInfo
• creates abouheif.moran test
• reads "PhyloRetained2.csv", a hand-typed text file that designates which parasite species from the taxonomic analysis are retained in the phylogenetic analysis (used to annotate fig1)
• creates fig1

6. predGlobAbund

• reads "GMPD_main.csv" (see 1. for metadata)
• reads ecoregions (described in, and available via, https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2) via file "wwf_terr_ecos.shp" (note these standard ESRI shapefiles require supporting files with same name and extensions dbf, htm, lyr, prj, sbn, sbx, shp.xml, shx
• sources dataPrep
• saves get_nEcos
• creates abund [also done in abundPhylo]
• loads get_txInfo
• creates fig2
• creates pgls stat test [globAbun~nEco+nHost+z]

7. bestHost

• sources dataPrep
• creates best
• saves get_bestHost
• loads get_taxTree
• creates fig3
• creates figS3
• creates pgls stat tests [best~z]

8. fitnessDecay

• sources dataPrep
• loads get_txInfo
• creates figS4
• creates pgls stat test [evenness~z]

9. dietSim

• sources dataPrep
• reads EltonTraits (metadata available at: https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1) via "EltonTraits.csv"
• saves get_dietSim

10. geogOverlap

• sources dataPrep
• reads IUCN layers (metadata available at: https://www.iucnredlist.org/resources/spatial-data-download)
• creates areaOverlap for species pairs
• saves get_Olaps
• loads get_Olaps

11. bodyMassSim

• sources dataPrep
• reads Pantheria (see 1. for metadata)
• saves get_delBM
• saves get_delBMLog

12. abundOverHostSet

• sources dataPrep
• reads in mammal phylogeny (see 1. for details)
• loads get_dietSim
• loads get_Olaps
• loads get_delBM
• loads get_delBMLog
• creates pdw (i.e. saves as "get_pdw.Rda")
• creates pdw.best.worst.pi (i.e. saves as "get_pdwBestWorstPi.Rda")
• creates fig4
• creates lm stat tests [delZpi~pd|olap|diet|bm]

13. phylogenetic_abundPhylo

• sources dataPrep
• reads phyloRetained (list of parasite species typed manually that are retained from taxonomic analysis in the phylogenetic analysis)
• reads ultrametric.newick (Regular Newick file format of parasite phylogenetic tree explained in supplementary material)

14. phylogenetic_predGlobAbundance

• sources dataPrep
• reads wwf_terr_ecos.shp
• reads ultrametric.newick (Regular Newick file format of parasite phylogenetic tree explained in supplementary material)
• creates fig S6

15. phylogenetic_bestHost

• sources dataPrep
• reads ultrametric.newick (Regular Newick file format of parasite phylogenetic tree explained in supplementary material)
• creates figs S7 & S8

16. phylogenetic_fitnessDecay

• sources dataPrep
• reads ultrametric.newick (Regular Newick file format of parasite phylogenetic tree explained in supplementary material)
• creates fig S9