Nitrogen enrichment and foliar fungal pathogens affect the mechanisms of multispecies plant coexistence

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:

data.txt

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:

• year --- 2017 or 2018
• block --- experimental block in the PaNDiv experiment (1, 2, 3 or 4)
• plot --- experimental plot in the PaNDiv experiment (from 1 to 336)
• nitrogen --- addition of nitrogen to the soil (0 = no, 1 = yes)
• fungicide --- application of fungicide to the vegetation (0 = no, 1 = yes)
• treatment --- control, nitrogen addition, fungicide application, and their combined effect
• number --- replicate number of the focal species; numbers are repeated because it restarts with each target focal-neighbour species combination (not shown)
• focal_sp --- 8 possible species:
  • tar_off = Taraxacum officinale
  • cre_bie = Crepis biennis
  • rum_ace = Rumex acetosa
  • dac_glo = Dactylis glomerata
  • ant_odo = Anthoxanthum odoratum
  • cen_jac = Centaurea jacea
  • sal_pra = Salvia pratensis
  • pla_med = Plantago media
• biomass_i --- initial biomass of the focal plant (start of the growing season; February/March)
• biomass_f --- final biomass of the focal plant (end of the growing season; June)
• tar_off --- visually estimated cover for this species as a neighbour
• cre_bie --- visually estimated cover for this species as a neighbour
• rum_ace --- visually estimated cover for this species as a neighbour
• dac_glo --- visually estimated cover for this species as a neighbour
• ant_odo --- visually estimated cover for this species as a neighbour
• cen_jac --- visually estimated cover for this species as a neighbour
• sal_pra --- visually estimated cover for this species as a neighbour
• pla_med --- visually estimated cover for this species as a neighbour
• herbs --- visually estimated cover for non-target herb species in the PaNDiv experiment
• grasses --- visually estimated cover for non-target grass species in the PaNDiv experiment
• legumes --- visually estimated cover for non-target legume species in the PaNDiv experiment

CODE:

001-optimx.R

Code that uses maximum likelihood to fit population models to the data. Produces several datasets with model coefficients and AIC values.

002-model_sel_coefs.R

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.

003-final_matrices.R

Code to adjust the matrices for coexistence computing.

004-coexistence.R

Computes structural coexistence outputs. Provides a clean dataset with structural niche differences, structural fitness differences, and other multispecies coexistence metrics.