DOI: 10.5281/zenodo.7343389
title: Nitrogen enrichment and foliar fungal pathogens affect the mechanisms of multispecies plant coexistence

description: This is the data and code repository for the manuscript entitled "Nitrogen enrichment and foliar fungal pathogens affect the mechanisms of multispecies plant coexistence". DATA: <strong>data.txt</strong> Dataset collected in the PaNDiv experiment, a large field experiment in Münchenbuchsee (near Bern) which investigates the mechanisms by which nitrogen enrichment affects ecosystem functioning. The dataset is composed by the following elements: <em>year </em>--- 2017 or 2018 <em>block </em>--- experimental block in the PaNDiv experiment (1, 2, 3 or 4) <em>plot </em>--- experimental plot in the PaNDiv experiment (from 1 to 336) <em>nitrogen </em>--- addition of nitrogen to the soil (0 = no, 1 = yes) <em>fungicide </em>--- application of fungicide to the vegetation (0 = no, 1 = yes) <em>treatment</em> --- control, nitrogen addition, fungicide application, and their combined effect <em>number</em> --- replicate number of the focal species; numbers are repeated because it restarts with each target focal-neighbour species combination (not shown) <em>focal_sp</em> --- 8 possible species: tar_off = <em>Taraxacum officinale</em> cre_bie = <em>Crepis biennis</em> rum_ace = <em>Rumex acetosa</em> dac_glo = <em>Dactylis glomerata</em> ant_odo = <em>Anthoxanthum odoratum</em> cen_jac = <em>Centaurea jacea</em> sal_pra = <em>Salvia pratensis</em> pla_med = <em>Plantago media</em> <em>biomass_i </em>--- initial biomass of the focal plant (start of the growing season; February/March) <em>biomass_f</em> --- final biomass of the focal plant (end of the growing season; June) <em>tar_off</em> --- visually estimated cover for this species as a neighbour <em>cre_bie</em> --- visually estimated cover for this species as a neighbour <em>rum_ace</em> --- visually estimated cover for this species as a neighbour <em>dac_glo</em> --- visually estimated cover for this species as a neighbour <em>ant_odo</em> --- visually estimated cover for this species as a neighbour <em>cen_jac</em> --- visually estimated cover for this species as a neighbour <em>sal_pra</em> --- visually estimated cover for this species as a neighbour <em>pla_med</em> --- visually estimated cover for this species as a neighbour <em>herbs </em>--- visually estimated cover for non-target herb species in the PaNDiv experiment <em>grasses </em>--- visually estimated cover for non-target grass species in the PaNDiv experiment <em>legumes </em>--- visually estimated cover for non-target legume species in the PaNDiv experiment CODE: <strong>001-optimx.R</strong> Code that uses maximum likelihood to fit population models to the data. Produces several datasets with model coefficients and AIC values. <strong>002-model_sel_coefs.R</strong> Code to select the coefficients based on the best model and add the size effect of the focal plants when needed. Creates all interaction matrices and intrinsic growth rate vectors. <strong>003-final_matrices.R</strong> Code to adjust the matrices for coexistence computing. <strong>004-coexistence.R</strong> Computes structural coexistence outputs. Provides a clean dataset with structural niche differences, structural fitness differences, and other multispecies coexistence metrics.