vignettes/analysis_nonpublic.R
In allanecology/BetaDivMultifun: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality
# This is the nonpublic file for the data assembly and analysis
# Usage :
# - in header of each script, the variables needed to be loaded are specified (elements of vector sections_to_be_loaded)
# (is done automatically) : source analysis_nonpublic.R with this specified vector in order to load the needed variables
# - **Important note** about transferring RDS files from linux to windows systems : can not be done using copy-paste.
# need to state that it is a binary file. Can be avoided using .csv files. For Rds, no solution was currently found.
# https://stackoverflow.com/questions/30892505/trouble-unzipping-file-under-windows
#TODO user : connect to planteco and nsch to get input files
# Explanation of name:
# Was historically thought to not be public because contains file paths, but decided to keep it close to all code.
# # please specify the vector of wanted datasets. The following vector will load all datasets.
# sections_to_be_loaded <- c("assemble_covariates",
# "assemble_functions",
# "imputed_functions",
# "functions_dissimilarity",
# "prepared_covariates",
# "raw_diversity",
# "betadiversity",
# "raw_lui",
# "LUI",
# "additional",
# "master_diversity_alpha_beta_gamma",
# "to_be_specified", #TODO check if needed
# "plotting",
# "results",
# "gdminput",
# "gdmoutput")
if(!exists("sections_to_be_loaded")){
sections_to_be_loaded <- c()
}
# PACKAGE
# load functions and small helper datasets from the package in case not already loaded
if(!"BetaDivMultifun" %in% (.packages())){
devtools::load_all()
}
# LOCAL ABSOLUTE PATHS
# note : for IPS Computer : "/run/user/1001/...", but for laptop : "/run/user/1000/..."
pathtoexplosynthesis <- "/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Data"
pathtodata <- "/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun"
pathtoout <- "~/Documents/github/BetaDivMultifun/vignettes/out"
# GENERAL
# is the updated version of plotNAset, selection based on diversity AND functions
# first version constructed in calc_betadiversities.Rmd, second version in function_imputation.Rmd
plotNAset <- readRDS(paste(pathtodata, "/data_assembly/helper_data/plotNAset.rds", sep = ""))
info_data <- data.table::fread(paste(pathtodata, "/data_assembly/helper_data/info_data.csv", sep = ""), header=T)
usedforBetadivMultifun <- info_data[`used for BetadivMultiFun` == "yes", ColumnName]
data("colorder_gdm_input")
data("usefulplotids")
data("model_names")
data("nicenames")
# settings for plotting
suppressPackageStartupMessages(require(ggplot2))
suppressPackageStartupMessages(require(cowplot))
theme_set(theme_half_open())
######################
# CONSTRUCTION OF ASSEMBLED DATA FROM RAW
######################
if("assemble_covariates" %in% sections_to_be_loaded){
# COVARIATES
small_glsoil <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/BE env covariates.txt", sep=""))
main_glsoil <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/Grassland EP soil descriptors.txt", sep=""))
glsoil <- fread(paste0(pathtodata, "/data_assembly/output_data/intermediate_glsoil.csv"))
names_gl <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/20826_plotNames.txt", sep=""))
plt.sur <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/18148_landscape.txt", sep=""))
geodist <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/20907.txt", sep=""))
landscape <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/31018_5_Dataset/31018_5_data.csv", sep=""))
landscape2 <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/LandUse-31319_31369/LandUse/LandscapeMetrics_acrossYears_acrossScales_Long_UpdatedOct22.csv", sep=""))
}
if("assemble_functions" %in% sections_to_be_loaded){
# FUNCTIONS
# prerequisite : store raw grassland functions for gapfilling
# download dataset 27087 version 24 and run bexis_to_wide_format.R
# create output .csv and use as input for here.
raw_grlfuns <- data.table::fread(paste(pathtoexplosynthesis, "/Grassland_functions/31621_grassland_functions_bexis/31621_9_Dataset/bexis_to_wide_format_output.csv", sep = ""), header=T)
# selection of required functions for gapfilling
selection <- info_data[`used for Gapfilling` == "yes", ColumnName]
raw_grlfuns <- raw_grlfuns[, ..selection]
rm(selection)
}
######################
# ASSEMBLED DATA INPUT FOR ANALYSIS
######################
if("imputed_functions" %in% sections_to_be_loaded){
# IMPUTED FUNCTIONS
imputed_grlfuns <- readRDS(paste(pathtodata, "/data_assembly/output_data/imputed_function_values.rds", sep = ""))
}
if("functions_dissimilarity" %in% sections_to_be_loaded){
# FUNCTIONS DISSIMILARITY
if(!exists("model_names_selection") | model_names_selection$model_class == "multifun"){
# if no specific class of EFmaster is selected, or the multifunctionality models are selected.
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFmaster.rds", sep = ""))
} else if(model_names_selection$model_class == "singlefun"){
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/singleEFdist.rds", sep = "")) # single functions, already scaled
} else {
stop("Error : unclear which Functions input should be read, please indicate in model_names_selection.
In case EFbeta or EFbeta abundance was intented, please run by hand or implement, the automatic running
of these response variables is deprecated.")
}
# EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFbeta_abund.rds", sep = "")) # EFbeta abund
# EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFquantile_median.rds", sep = "")) # EFbeta abund
}
if("prepared_covariates" %in% sections_to_be_loaded){
## PREPARED COVARIATES
predictors <- readRDS(paste(pathtodata, "/data_assembly/output_data/predictors.rds", sep = ""))
predictors_soil <- readRDS(paste(pathtodata, "/data_assembly/output_data/predictors_soil.rds", sep = ""))
}
if("raw_diversity" %in% sections_to_be_loaded){
# DIVERSITY
#Note 28.9.23 : used updated diversity dataset. (errors were corrected.) Will delete the outdated diversity dataset
#TODO delete 2 rows below, AND delete old dataset in rawdata
# spdiv <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/201124_EP_species_diversity_GRL.txt", sep=""))
# spinfo <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/210112_EP_species_info_GRL.txt", sep=""))
spdiv <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/221102_EP_species_diversity_GRL_Patch22.txt", sep=""))
spinfo <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/221102_EP_species_info_GRL_patch22.txt", sep=""))
# new arthropod data
arthro <- fread(paste0(pathtodata, "/data_assembly/raw_data/21969_4_data.txt")) # temporal arthropod dataset
arth_tr <- fread(paste0(pathtodata, "/data_assembly/raw_data/Temporal_arth_trophicGroups_withNAs.csv"))
arth_remove <- fread(paste0(pathtodata, "/data_assembly/raw_data/26008_2_data.txt"))
# new fungal symbionts data
lt <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27686_3_data.txt")) #lookout table
a11 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27687_3_data.txt")) #2011
a14 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27689_3_data.txt")) #2014
a17 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27691_3_data.txt")) #2017
# run script to add arthropod and AMF data to synthesis dataset
source("vignettes/diversity_dataset_update.R")
names_trlevel <- data.table::fread(paste(pathtodata, "/data_assembly/helper_data/trophic_level_renaming.csv", sep = ""))
#TODO names_trlevel is currently not used any more --> probably delete
}
if("betadiversity" %in% sections_to_be_loaded){
# BETADIVERSITY
trlevels <- readRDS(paste(pathtodata, "/data_assembly/output_data/trlevels_vector.rds", sep = ""))
masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_incl_poll_and_tertcons.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_no_bats_with_birds.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_abundance.rds", sep = "")) # note: needs some special modifications in scripts
}
if("raw_lui" %in% sections_to_be_loaded){
# LUI
rawlui <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/25086_Input Data for LUI Calculation Tool of all grassland plots since 2006 - revised 2019_1.1.0/25086.txt", sep = ""), header=T)
}
if("LUI" %in% sections_to_be_loaded){
# LUI
LUI <- readRDS(paste(pathtodata, "/data_assembly/output_data/LUI.rds", sep = ""))
distLUI <- readRDS(paste(pathtodata, "/data_assembly/output_data/distLUI.rds", sep = ""))
}
if("additional" %in% sections_to_be_loaded){
if("master_diversity_alpha_beta_gamma" %in% sections_to_be_loaded){
masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta_gamma.rds", sep = ""))
}
if("to_be_specified" %in% sections_to_be_loaded){
# ADDITIONAL
# masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta.rds", sep = ""))
masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta_gamma.rds", sep = ""))
# note that for the above masterdiv : 2 columns with plot names are given, so is alphadiv given in 2 columns.
# master_alpha <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_alpha.rds", sep = ""))
# master_gamma <- ... "master_gamma.rds"
}
}
if("gdminput" %in% sections_to_be_loaded){
# gdminput
# if not specified differently, will read in the results from the GDM model EFturnover 0.7 with LUI
if(!exists("model_names_selection")){
print("model selection is not given, default is EFturnover_0.7")
model_names_selection <- model_names[which(model_names$modelname == "gdm_EFturnover_0.7_LUI"), ]
}
# modelname <- model_names_selection$modelname
# model_name <- modelname #TODO delete soon (Nov 2022) just left to see if I will miss this
gdminput <- readRDS(paste(pathtodata, paste("/analysis/output_datasets/gdm",
model_names_selection$funs,
model_names_selection$lui, "input.Rds", sep = "_"), sep = ""))
}
if("gdmoutput" %in% sections_to_be_loaded){
if(!exists("model_names_selection")){
print("model selection is not given, default is EFturnover_0.7")
model_names_selection <- model_names[which(model_names$modelname == "gdm_EFturnover_0.7_LUI"), ]
}
# model_name <- paste("gdm", funs, lui, sep = "_") #TODO delete soon if realise that not needed (Nov 2022)
gdmoutput <- readRDS(paste_gdm_input_path_together(pathtoout = pathtodata,
name = paste("gdm_", model_names_selection$funs,
"_", model_names_selection$lui,
sep = "")))
model_specs <- data.table::fread(paste(pathtodata, "/analysis/output_datasets/",
model_names_selection$modelname, "_GDM_model_specs.csv", sep = ""))
# overviewbar_data <- readRDS(paste(pathtodata, "/analysis/output_datasets/",
# model_names_selection$modelname, "_overviewbar_data.RDS", sep = ""))
}
if("thresholds" %in% sections_to_be_loaded){
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFmaster_all_thresholds.rds", sep = ""))
# note : overwrites current EFmaster in case "functions_dissimilarity" is also loaded
# deviance explained of all models
devexpl <- readRDS(paste(pathtodata, "/analysis/output_datasets/devexpl_all_models.RDS", sep = ""))
# note : previously called model_results.csv and read in by "results" section of analysis_nonpublic.R.
# isplines of all models
isplines_all_models <- readRDS(paste(pathtodata, "/analysis/output_datasets/isplines_all_threshold_models.RDS", sep = ""))
# #
# ispline uncertainty of all threshold models
threshold_model_names <- c(paste("gdm_EFturnover_", seq(0.1, 0.9, 0.1), sep = ""),
paste("gdm_EFnestedness_", seq(0.1, 0.9, 0.1), sep = ""))
# create vector with all paths of the expected models
threshold_model_paths <- paste(pathtodata, "/analysis/output_datasets/uncertainty_calc/", threshold_model_names, "_LUI_uncertainty.Rds",sep = "")
# edit start ---
# ispline_uncertainty_all_thresholds <- lapply(X = threshold_model_paths,FUN = function(x) readRDS(x)) # read all threshold files in a list
# in case the above line does not work (random readRDS error)
EFturn01 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.1_LUI_uncertainty.Rds")
EFturn02 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.2_LUI_uncertainty.Rds")
EFturn03 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.3_LUI_uncertainty.Rds")
EFturn04 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.4_LUI_uncertainty.Rds")
EFturn05 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.5_LUI_uncertainty.Rds")
EFturn06 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.6_LUI_uncertainty.Rds")
EFturn07 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.7_LUI_uncertainty.Rds")
EFturn08 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.8_LUI_uncertainty.Rds")
EFturn09 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.9_LUI_uncertainty.Rds")
EFnes01 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.1_LUI_uncertainty.Rds")
EFnes02 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.2_LUI_uncertainty.Rds")
EFnes03 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.3_LUI_uncertainty.Rds")
EFnes04 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.4_LUI_uncertainty.Rds")
EFnes05 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.5_LUI_uncertainty.Rds")
EFnes06 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.6_LUI_uncertainty.Rds")
EFnes07 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.7_LUI_uncertainty.Rds")
EFnes08 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.8_LUI_uncertainty.Rds")
EFnes09 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.9_LUI_uncertainty.Rds")
ispline_uncertainty_all_thresholds <- list(EFturn01, EFturn02, EFturn03,
EFturn04, EFturn05, EFturn06,
EFturn07, EFturn08, EFturn09,
EFnes01, EFnes02, EFnes03,
EFnes04, EFnes05, EFnes06,
EFnes07, EFnes08, EFnes09
)
# -- edit end
names(ispline_uncertainty_all_thresholds) <- threshold_model_names
rm(threshold_model_names, threshold_model_paths)
rm(EFturn01, EFturn02, EFturn03,
EFturn04, EFturn05, EFturn06,
EFturn07, EFturn08, EFturn09,
EFnes01, EFnes02, EFnes03,
EFnes04, EFnes05, EFnes06,
EFnes07, EFnes08, EFnes09)
}
allanecology/BetaDivMultifun documentation built on Nov. 9, 2023, 8:47 p.m.
R Package Documentation
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# This is the nonpublic file for the data assembly and analysis
# Usage :
# - in header of each script, the variables needed to be loaded are specified (elements of vector sections_to_be_loaded)
# (is done automatically) : source analysis_nonpublic.R with this specified vector in order to load the needed variables
# - **Important note** about transferring RDS files from linux to windows systems : can not be done using copy-paste.
# need to state that it is a binary file. Can be avoided using .csv files. For Rds, no solution was currently found.
# https://stackoverflow.com/questions/30892505/trouble-unzipping-file-under-windows
#TODO user : connect to planteco and nsch to get input files
# Explanation of name:
# Was historically thought to not be public because contains file paths, but decided to keep it close to all code.
# # please specify the vector of wanted datasets. The following vector will load all datasets.
# sections_to_be_loaded <- c("assemble_covariates",
# "assemble_functions",
# "imputed_functions",
# "functions_dissimilarity",
# "prepared_covariates",
# "raw_diversity",
# "betadiversity",
# "raw_lui",
# "LUI",
# "additional",
# "master_diversity_alpha_beta_gamma",
# "to_be_specified", #TODO check if needed
# "plotting",
# "results",
# "gdminput",
# "gdmoutput")
if(!exists("sections_to_be_loaded")){
sections_to_be_loaded <- c()
}
# PACKAGE
# load functions and small helper datasets from the package in case not already loaded
if(!"BetaDivMultifun" %in% (.packages())){
devtools::load_all()
}
# LOCAL ABSOLUTE PATHS
# note : for IPS Computer : "/run/user/1001/...", but for laptop : "/run/user/1000/..."
pathtoexplosynthesis <- "/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Data"
pathtodata <- "/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun"
pathtoout <- "~/Documents/github/BetaDivMultifun/vignettes/out"
# GENERAL
# is the updated version of plotNAset, selection based on diversity AND functions
# first version constructed in calc_betadiversities.Rmd, second version in function_imputation.Rmd
plotNAset <- readRDS(paste(pathtodata, "/data_assembly/helper_data/plotNAset.rds", sep = ""))
info_data <- data.table::fread(paste(pathtodata, "/data_assembly/helper_data/info_data.csv", sep = ""), header=T)
usedforBetadivMultifun <- info_data[`used for BetadivMultiFun` == "yes", ColumnName]
data("colorder_gdm_input")
data("usefulplotids")
data("model_names")
data("nicenames")
# settings for plotting
suppressPackageStartupMessages(require(ggplot2))
suppressPackageStartupMessages(require(cowplot))
theme_set(theme_half_open())
######################
# CONSTRUCTION OF ASSEMBLED DATA FROM RAW
######################
if("assemble_covariates" %in% sections_to_be_loaded){
# COVARIATES
small_glsoil <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/BE env covariates.txt", sep=""))
main_glsoil <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/Grassland EP soil descriptors.txt", sep=""))
glsoil <- fread(paste0(pathtodata, "/data_assembly/output_data/intermediate_glsoil.csv"))
names_gl <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/20826_plotNames.txt", sep=""))
plt.sur <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/18148_landscape.txt", sep=""))
geodist <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/20907.txt", sep=""))
landscape <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/31018_5_Dataset/31018_5_data.csv", sep=""))
landscape2 <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/LandUse-31319_31369/LandUse/LandscapeMetrics_acrossYears_acrossScales_Long_UpdatedOct22.csv", sep=""))
}
if("assemble_functions" %in% sections_to_be_loaded){
# FUNCTIONS
# prerequisite : store raw grassland functions for gapfilling
# download dataset 27087 version 24 and run bexis_to_wide_format.R
# create output .csv and use as input for here.
raw_grlfuns <- data.table::fread(paste(pathtoexplosynthesis, "/Grassland_functions/31621_grassland_functions_bexis/31621_9_Dataset/bexis_to_wide_format_output.csv", sep = ""), header=T)
# selection of required functions for gapfilling
selection <- info_data[`used for Gapfilling` == "yes", ColumnName]
raw_grlfuns <- raw_grlfuns[, ..selection]
rm(selection)
}
######################
# ASSEMBLED DATA INPUT FOR ANALYSIS
######################
if("imputed_functions" %in% sections_to_be_loaded){
# IMPUTED FUNCTIONS
imputed_grlfuns <- readRDS(paste(pathtodata, "/data_assembly/output_data/imputed_function_values.rds", sep = ""))
}
if("functions_dissimilarity" %in% sections_to_be_loaded){
# FUNCTIONS DISSIMILARITY
if(!exists("model_names_selection") | model_names_selection$model_class == "multifun"){
# if no specific class of EFmaster is selected, or the multifunctionality models are selected.
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFmaster.rds", sep = ""))
} else if(model_names_selection$model_class == "singlefun"){
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/singleEFdist.rds", sep = "")) # single functions, already scaled
} else {
stop("Error : unclear which Functions input should be read, please indicate in model_names_selection.
In case EFbeta or EFbeta abundance was intented, please run by hand or implement, the automatic running
of these response variables is deprecated.")
}
# EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFbeta_abund.rds", sep = "")) # EFbeta abund
# EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFquantile_median.rds", sep = "")) # EFbeta abund
}
if("prepared_covariates" %in% sections_to_be_loaded){
## PREPARED COVARIATES
predictors <- readRDS(paste(pathtodata, "/data_assembly/output_data/predictors.rds", sep = ""))
predictors_soil <- readRDS(paste(pathtodata, "/data_assembly/output_data/predictors_soil.rds", sep = ""))
}
if("raw_diversity" %in% sections_to_be_loaded){
# DIVERSITY
#Note 28.9.23 : used updated diversity dataset. (errors were corrected.) Will delete the outdated diversity dataset
#TODO delete 2 rows below, AND delete old dataset in rawdata
# spdiv <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/201124_EP_species_diversity_GRL.txt", sep=""))
# spinfo <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/210112_EP_species_info_GRL.txt", sep=""))
spdiv <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/221102_EP_species_diversity_GRL_Patch22.txt", sep=""))
spinfo <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/221102_EP_species_info_GRL_patch22.txt", sep=""))
# new arthropod data
arthro <- fread(paste0(pathtodata, "/data_assembly/raw_data/21969_4_data.txt")) # temporal arthropod dataset
arth_tr <- fread(paste0(pathtodata, "/data_assembly/raw_data/Temporal_arth_trophicGroups_withNAs.csv"))
arth_remove <- fread(paste0(pathtodata, "/data_assembly/raw_data/26008_2_data.txt"))
# new fungal symbionts data
lt <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27686_3_data.txt")) #lookout table
a11 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27687_3_data.txt")) #2011
a14 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27689_3_data.txt")) #2014
a17 <- fread(paste0(pathtodata, "/data_assembly/raw_data/AMF2023/27691_3_data.txt")) #2017
# run script to add arthropod and AMF data to synthesis dataset
source("vignettes/diversity_dataset_update.R")
names_trlevel <- data.table::fread(paste(pathtodata, "/data_assembly/helper_data/trophic_level_renaming.csv", sep = ""))
#TODO names_trlevel is currently not used any more --> probably delete
}
if("betadiversity" %in% sections_to_be_loaded){
# BETADIVERSITY
trlevels <- readRDS(paste(pathtodata, "/data_assembly/output_data/trlevels_vector.rds", sep = ""))
masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_incl_poll_and_tertcons.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_no_bats_with_birds.rds", sep = ""))
# masterbeta <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_beta_abundance.rds", sep = "")) # note: needs some special modifications in scripts
}
if("raw_lui" %in% sections_to_be_loaded){
# LUI
rawlui <- data.table::fread(paste(pathtodata, "/data_assembly/raw_data/25086_Input Data for LUI Calculation Tool of all grassland plots since 2006 - revised 2019_1.1.0/25086.txt", sep = ""), header=T)
}
if("LUI" %in% sections_to_be_loaded){
# LUI
LUI <- readRDS(paste(pathtodata, "/data_assembly/output_data/LUI.rds", sep = ""))
distLUI <- readRDS(paste(pathtodata, "/data_assembly/output_data/distLUI.rds", sep = ""))
}
if("additional" %in% sections_to_be_loaded){
if("master_diversity_alpha_beta_gamma" %in% sections_to_be_loaded){
masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta_gamma.rds", sep = ""))
}
if("to_be_specified" %in% sections_to_be_loaded){
# ADDITIONAL
# masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta.rds", sep = ""))
masterdiversity <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_diversity_alpha_beta_gamma.rds", sep = ""))
# note that for the above masterdiv : 2 columns with plot names are given, so is alphadiv given in 2 columns.
# master_alpha <- readRDS(paste(pathtodata, "/data_assembly/output_data/master_alpha.rds", sep = ""))
# master_gamma <- ... "master_gamma.rds"
}
}
if("gdminput" %in% sections_to_be_loaded){
# gdminput
# if not specified differently, will read in the results from the GDM model EFturnover 0.7 with LUI
if(!exists("model_names_selection")){
print("model selection is not given, default is EFturnover_0.7")
model_names_selection <- model_names[which(model_names$modelname == "gdm_EFturnover_0.7_LUI"), ]
}
# modelname <- model_names_selection$modelname
# model_name <- modelname #TODO delete soon (Nov 2022) just left to see if I will miss this
gdminput <- readRDS(paste(pathtodata, paste("/analysis/output_datasets/gdm",
model_names_selection$funs,
model_names_selection$lui, "input.Rds", sep = "_"), sep = ""))
}
if("gdmoutput" %in% sections_to_be_loaded){
if(!exists("model_names_selection")){
print("model selection is not given, default is EFturnover_0.7")
model_names_selection <- model_names[which(model_names$modelname == "gdm_EFturnover_0.7_LUI"), ]
}
# model_name <- paste("gdm", funs, lui, sep = "_") #TODO delete soon if realise that not needed (Nov 2022)
gdmoutput <- readRDS(paste_gdm_input_path_together(pathtoout = pathtodata,
name = paste("gdm_", model_names_selection$funs,
"_", model_names_selection$lui,
sep = "")))
model_specs <- data.table::fread(paste(pathtodata, "/analysis/output_datasets/",
model_names_selection$modelname, "_GDM_model_specs.csv", sep = ""))
# overviewbar_data <- readRDS(paste(pathtodata, "/analysis/output_datasets/",
# model_names_selection$modelname, "_overviewbar_data.RDS", sep = ""))
}
if("thresholds" %in% sections_to_be_loaded){
EFmaster <- readRDS(paste(pathtodata, "/data_assembly/output_data/EFmaster_all_thresholds.rds", sep = ""))
# note : overwrites current EFmaster in case "functions_dissimilarity" is also loaded
# deviance explained of all models
devexpl <- readRDS(paste(pathtodata, "/analysis/output_datasets/devexpl_all_models.RDS", sep = ""))
# note : previously called model_results.csv and read in by "results" section of analysis_nonpublic.R.
# isplines of all models
isplines_all_models <- readRDS(paste(pathtodata, "/analysis/output_datasets/isplines_all_threshold_models.RDS", sep = ""))
# #
# ispline uncertainty of all threshold models
threshold_model_names <- c(paste("gdm_EFturnover_", seq(0.1, 0.9, 0.1), sep = ""),
paste("gdm_EFnestedness_", seq(0.1, 0.9, 0.1), sep = ""))
# create vector with all paths of the expected models
threshold_model_paths <- paste(pathtodata, "/analysis/output_datasets/uncertainty_calc/", threshold_model_names, "_LUI_uncertainty.Rds",sep = "")
# edit start ---
# ispline_uncertainty_all_thresholds <- lapply(X = threshold_model_paths,FUN = function(x) readRDS(x)) # read all threshold files in a list
# in case the above line does not work (random readRDS error)
EFturn01 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.1_LUI_uncertainty.Rds")
EFturn02 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.2_LUI_uncertainty.Rds")
EFturn03 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.3_LUI_uncertainty.Rds")
EFturn04 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.4_LUI_uncertainty.Rds")
EFturn05 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.5_LUI_uncertainty.Rds")
EFturn06 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.6_LUI_uncertainty.Rds")
EFturn07 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.7_LUI_uncertainty.Rds")
EFturn08 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.8_LUI_uncertainty.Rds")
EFturn09 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFturnover_0.9_LUI_uncertainty.Rds")
EFnes01 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.1_LUI_uncertainty.Rds")
EFnes02 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.2_LUI_uncertainty.Rds")
EFnes03 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.3_LUI_uncertainty.Rds")
EFnes04 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.4_LUI_uncertainty.Rds")
EFnes05 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.5_LUI_uncertainty.Rds")
EFnes06 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.6_LUI_uncertainty.Rds")
EFnes07 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.7_LUI_uncertainty.Rds")
EFnes08 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.8_LUI_uncertainty.Rds")
EFnes09 <- readRDS("/run/user/1000/gvfs/smb-share:server=nas-ips,share=ips/groups/planteco/PROJECTS/Exploratories Synthesis/Research Projects/BetaDivMultifun/analysis/output_datasets/uncertainty_calc/gdm_EFnestedness_0.9_LUI_uncertainty.Rds")
ispline_uncertainty_all_thresholds <- list(EFturn01, EFturn02, EFturn03,
EFturn04, EFturn05, EFturn06,
EFturn07, EFturn08, EFturn09,
EFnes01, EFnes02, EFnes03,
EFnes04, EFnes05, EFnes06,
EFnes07, EFnes08, EFnes09
)
# -- edit end
names(ispline_uncertainty_all_thresholds) <- threshold_model_names
rm(threshold_model_names, threshold_model_paths)
rm(EFturn01, EFturn02, EFturn03,
EFturn04, EFturn05, EFturn06,
EFturn07, EFturn08, EFturn09,
EFnes01, EFnes02, EFnes03,
EFnes04, EFnes05, EFnes06,
EFnes07, EFnes08, EFnes09)
}
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