Data and scripts for "The role of stochasticity in fungal community assembly – explaining apparent stochasticity with field experiments" (Q11579)

The results presented in the manuscript The role of stochasticity in fungal community assembly explaining apparent stochasticity by field experiments can be reproduced by the data and scripts provided in this repository. Concerning the analysis of observational data: The file ObservationalData.RData includes all data: XData is the dataframe including the predictors, and t is the vector of responses (F. rosea occurrences). The script O1_model_observational_data.R defines the models, fits the models, and computes model fits based on cross-validation. The results are saved into a file. The script O2_show_results_observational_data.R loads the results saved by the previous script, and outputs the results reported in the manuscript. Concerning the analysis of experimental data: The file ExperimentalData.RData includes all data: the dataframe meta includes the relevant predictors, otu.table the matrix of samples x OTU read counts, and the dataframe taxonomy the taxonomic placement of those OTUs. The script E1_compute_model_based_ordinations.R precomputes the gllvm-ordinations needed both for the colonization success model as well as the community divergence model. The precomputed ordinations are saved into a file. The script E2_model_colonization_success.R defines the colonization success model, fits the model, and computes model fit based on cross-validation. The results are saved into a file. The script E3_show_colonization_model_results.R loads the results saved by the previous script, and outputs the results reported in the manuscript. The script E4_model_community_divergence defines the community divergence model and fits the model. The results are saved into a file. The script E5_show_community_divergence_model_results.R loads the results saved by the previous scripts, and outputs the results reported in the manuscript, including Table 1 and Figure 2.