Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence

R and Mathematica scripts for "Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence"

This respository contains code accompanying the manuscript "Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence" by Pajares-Murgó et al.  The file *data.csv* contains the data obtained in the experiment of PSF. The dataset is divided by columns: Tray indicates each 15-cell plastic tray, ISO (individual soil sources) indicates the soil beneath 6 adult individuals of each species, ISE (individual seed sources) indicates the seeds collected from 5 adult individual of each species, CANOPY_soil and RECRUIT indicate the plant species, and success is the binomial variable that indicates the the proportion of experimental cells with soil of species j containing a seedling of species i at the end of the experiment.  The file *recruitment_density.csv* contains the data on the recruitment of plant species observed in the field. The dataset is divided by columns: CANOPY and RECRUIT indicate the plant species, Fij indicates the frequency of recruitment between pairs of species, Eij indicates the efficiency of recruitment between pairs of species (estimated as the number of saplings of species i recruiting under species j divided by the cover of the canopy and recruit species), cover_can indicates the cover of canopy species and cover_rec indicates the cover of recruit species.  The files *1. Testing for species-specific PSFs*, *2. Field crossvalidation*, *Pairwise-level feedback* and *Community-level feedback* contain an implementation of the models described in the Main Text, suitable for numerical integration, along with other useful functions for generating figures and analysis in the Main Text and figures and tables in the Supplementary Information.   Please email [e-mail] or [e-mail] with any questions.