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

knitr::opts_chunk$set(echo = TRUE)

Documentation of cleaning

This is a documenation of the cleaning round in October 2022 - summer 2023. Mainly serves to create a searchable commit. But also to keep track of changes.

next step

• TODO HERE go on with plotting things : currently : plot_modelwise_GDM and plot_unique_GDM . Need to create input for average over threshold plots, and either move to separate script or include in plot_modelwise_GDM.

  • Add description in the powerpoint readme about plot_modelwise_GDM which iterates over model_names, and plot_unique which is only runned once.

• TODO HERE GDM_multifun_thresholds : almost finished runningt he plotUncertainty. Need 2 more, and TODO TODO TODO important **GDM_multifun_thresholds.Rmd** : check if there is an error in the plotting function of gdm. Why do x values vary??

  • Run the missing 2 models by hand TODO TODO TODODELIDU

• merge scripts alpha_plots.Rmd and introductory_plots.Rmd

• [x] DONE address package error of a map-related package

Major topics of scripts

• data assembly (create input data) ok
• analysis (create output data)
• visualisation and summarising (create summaries and plots from output data)

Documentation of cleaning

• Added documentation of datasets

• plot_GDM.Rmd :

  • removed automaticrun variable : all runs are automatic from now.

  • chosing model from model_names.

  • 3 functions for the same job, just different dataset : create_bio_aboveground_barplot, create_bio_belowground_barplot, create_abio_barplot. Lession learned for future project : do a common function for the same types of plots

  • reading in LUI input : before I gave the variable compon_lui by hand, now this is called lui and taken from model_names_selecton$lui.

  • renamed to plot_modelwise_GDM. Only contains plots which are produced for each model indivdually. All other plots (that only need to be runned once = unique run) are in plot_unique_GDM

small datasets

small datasets that are stored in /vignettes are transferred to /data

usethis::use_data(\<nameofdataset\>) if necessary with overwrite = T to overwrite existing dataset

No loading is needed, because R packages use "lazy-loading", i.e. only load data when necessary.

model_names

will be used uniquely to select the current model to run, or to run all of them.

names need to be cleaned!

• model_names column "name" renamed to "modelname"

• added columns : funs, lui containing more info about the selected model --> reduce the amount of hand-filled input

• model_names column luiinput will not be used in the future any more : there will not be a model with all 3 components together, but only with individual ones. (because LUI components are correlated.)

thresholds

• Dec 22 Implemented new calculation of average over all threshold : NEW is that the avearage is not only calcluated for the maximum values, but across all 200 values of each predictor. Therefore, the function plotUncertainty_sd has been deprecated, and a new function plotUncertainty_slim was implemented.

  • all models have to be re-runned on the cluster. (including updater of the cluster scripts documentation.

Problematic scripts

• GDM_multifun_thresholds

prepare_and_run_GDM.Rmd

implement the use of the model_names table. Select used models with model_names_selection.

• funs needs to be changed to model_names_selection$funs

• compon_luli is deprecated: use lui instead

• replaced modelname with model_names_selection$modelname

Sequence of analysis steps

• is in file the_analysis_hive.Rmd now. (hive-drone wording is used here)

Files

• [ ] alpha_plots.Rmd
• [x] 0 analysis_nonpublic.R betadiversity_imputation.R betadiversity_imputation.Rmd
• [x] 2 calc_betadiversities.Rmd (calc_betadiversities.html)
• [x] 1b calc_covariates.Rmd
• [x] calc_LUI.Rmd
• [x] 4b calc_multifun_from_imputed_additional_sensitivity.R
• [x] 4 calc_multifun_from_imputed.Rmd
• [ ] check_GDM_input_GAM.Rmd
• [ ] check_GDM_input.Rmd
• [x] 1a clean_and_load_soil_covariates.Rmd
• [ ] cluster_scripts_documentation.Rmd
• [ ] detect_GDM_effect_shape.Rmd
• [ ] explore_functions_dataset.Rmd
• [ ] filenames.txt
• [x] 3 function_imputation.Rmd
• [ ] gdm_model_diagnostics_overview.pdf
• [ ] GDM_multifun_thresholds.Rmd
• [ ] GDM_predictions.Rmd
• [ ] GDM_pvalues_test.R
• [ ] GDM_sensitivity_indirect_beta_effects.Rmd
• [ ] introductory_plots.Rmd
• [ ] package_testing.Rmd
• [ ] plot_GDM.Rmd
• [x] prepare_and_run_GDM.Rmd
• [ ] quick_singlefunctions_plot.R
• [ ] README_how-to-use-this-package.html (README_how-to-use-this-package.Rmd)
• [ ] result_GDM_model_diagnostics_plots.Rmd
• [ ] sensitivity_GDM_variable_sequence_does_not_matter.R
• [ ] sensitivity_small_extras.Rmd
• [ ] single_functions_effect_on_multifunctionality.Rmd
• [ ] suppl_analysis_differences_in_richness.Rmd
• [ ] THEORY_simulate_betadiversity.R

helper_datasets

from vignettes/

• [x] nicenames.csv (added to /data)
• [x] nicenames_old_may2021.csv (added to /old)
• [x] helper_model_names.csv (added to /data)

from data_assembly/helper_data and analysis/helper_data

• usefulplotids added to /data

• colorder_gdm_input added to /data

clean

Evaluate if useful content is in there, think about what to do later.

• [ ] GDM_multifun_betadiv_lui_analysis.Rmd

Re-Analysis

Take care that the following points are included in re-analysis :

• %var expl. plot is re-done. Seems there was an error in manually entering the values in a large table. New : use the small tables extracted for each model and rbind them to a full table of model specs.

• Implement permutations in plot_GDM.Rmd.

Future todos

• document data

• screen through all scripts and solve remaining #TODO

• remove sections_to-be_loaded in the end of every script!

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