In allanecology/BetaDivMultifun: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality

knitr::opts_chunk$set(echo = TRUE)

Aim

The analysis consists of various small (drone) scripts. The order is indicated, but instead of calling them by hand, giving the model names as inputs, this script does this job for you, as the hive does the coordination job for the drones. (source for hive-drone terminology).

The conductor script here calls the drone scripts of the analysis in order to run the full analysis from one place.

Requirements

The script vignettes/analysis_nonpublic.R loads the necessary requirements, specifying the specific requirements by variable sections_to_be_loaded. Each section includes an option to load the requirements.

Requires access to the Plant Ecology Group (Fischer) drive "planteco" at the IPS Bern. See header of the analysis_nonpublic.R file.

Sequence of analysis

Prepare data

ksource("vignettes/clean_and_load_soil_covariates.Rmd")
ksource("vignettes/calc_covariates.Rmd")
ksouce("vignettes/calc_betadiversities.Rmd")
ksource("vignettes/function_imputation.Rmd")
# Note : plotNAset is created here.
# potentially need to re-run calc_betadiversities.Rmd
#    again with the correct number of plots!!
# ksouce("vignettes/calc_betadiversities.Rmd")

#TODO add early scripts

Fit models

Scripts depending on output of each other, need to run per model.

Requirements

if(!exists("model_names")){
  sections_to_be_loaded <- c()
  source("vignettes/analysis_nonpublic.R")
}

single model

Chose model by hand

# select a given model
model_names_selection <- model_names[which(model_names$modelname == "gdm_EFturnover_0.7_LUI"), ]
#
# run analysis and create results
ksource("vignettes/prepare_and_run_GDM.Rmd") # default model : EF turnover 0.7 LUI
ksource("vignettes/check_GDM_input.Rmd") # produce nice plots/ results about correlations among input variables
ksource("vignettes/plot_modelwise_GDM.Rmd") # produce bar and line plots of the current model

all models

Loop through all models. Dont forget to transfer the output from vignettes/out to pathtodata.

source("vignettes/analysis_nonpublic.R")

# run all single function and multifunctionality models
for(mod in model_names[model_class %in% c("multifun", "singlefun") & lui == "LUI", modelname]){
  model_names_selection <- model_names[which(model_names$modelname == mod), ]
  # run analysis and create results
  ksource("vignettes/prepare_and_run_GDM.Rmd") 
  ksource("vignettes/check_GDM_input.Rmd") # produce nice plots/ results about correlations among input variables
  ksource("vignettes/plot_modelwise_GDM.Rmd") # produce bar and line plots of the current model
}

Permutations

Run on cluster

# run cluster_scripts by hand on cluster!
print("run cluster_scripts_documentation.Rmd by hand on cluster!")

Model output

Note : the below scripts only need to be run once, after the above scripts have been run for all models.

ksource("vignettes/check_GDM_diagnostics.Rmd") # 1 script for all model diagnostics
ksource("vignettes/plot_unique_GDM.Rmd") # plot single EF models 
ksource("vignettes/summarise_GDM_results.Rmd") # create summary tables of all model results (deviance explained and isplines)

Threshold overview

calculate sd

In order to calculate a summary model over all thresholds over all x values (not just maximum x, but a full line), the sd needs to be calculated everywhere.

Run the thresholds part of cluster_scripts_documentation.Rmd on the cluster. If no cluster is available : create a script "gdm_uncertainty.R". Copy paste the part from cluster_scripts_documentation.Rmd in this file. Run it through all nestedness and turnover tresholds with LUI. Note that this script calculates sd for 1 model. In order to run through all, the input has been changed manually (you find code to change automatically in cluster_scripts_documentation.Rmd).

source("gdm_uncertainty.R")

The output are 18 .Rds files for thresholds 0.1 - 0.9 for turnover and nestedness. E.g. "analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.8_LUI_uncertainty.Rds"

ksource("vignettes/GDM_multifun_thresholds.Rmd") # calcluate models and generate plots (line and barplots)
# could be added : a script plotting barplots with se

allanecology/BetaDivMultifun documentation built on Nov. 9, 2023, 8:47 p.m.