Dataset and code for the manuscript "Plant indirect interactions reduce species richness but increase phylogenetic diversity"

This Zenodo repository contains the original data set and code for replicating the result published in the paper "Plant indirect interactions reduce species richness but increase phylogenetic diversity"

The "BD.xlsx" data frame contains the original data. The first column, "ID," is an ID for each one of the patches (i.e., vegetation units containing one or more individuals for the same or different species separated from other patches by bare ground). The second and third columns, "localidad" and "suelo", inform about the location where patches are found. The "species" column identifies the different species present at each patch.
 The "Comb1.xlsx" data frame contains the possible combination of 4 species for each ID (concatenation of "localidad" and "suelo") for all the species found in the sampling. Besides "ID", there is one column for each of the species included in interactions ("spA", "spB", "spC", "spD") that contains the name of the species.
The "phylo.xlsx" data frame contains the taxonomic information of the species found during the sampling. For each species recorded in column "species" we assign its genus (column "genus") and family (column "family")
  "ALL_IN.xlsx" is a data frame containing for each "ID" (proxy of location), the species involved in interactions ("spA", "spB", "spC" & "spD"), the "interaction sign" indicating if a given interaction is positive or negative (results based on simulation) and "Order" indicating the number of species involved in the interactions(from two to four).
"Code.R" provides the R code necessary to obtain the results. As statistics is based on simulation, every run can provide slightly different results, although differences do not affect interpretation. Please note that running time can be elevated depending on the computer used.