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

Depends on dependencies of plot_GDM.Rmd, until section preparation (needs maxsplines from given model)

#TODO : make independent from plot_GDM.Rmd

Overviewbar without correlated groups

# run for each desired model.

#######
# Here : EFdistance
restab <- create_restab0()

#######
# See script `GDM_multifun_thresholds.Rmd` for loading restab.
#
# for EFtrheshold weighted average :
# model_name <- "EFturnover_WEIGTHED_mean_across_thresholds"
model_name <- "EFnestedness_WEIGTHED_mean_across_thresholds"
#
# restab <- readRDS(paste(pathtodata, "/analysis/output_datasets/weighted_avg_over_all_thresholds_EFturnover.Rds", sep = ""))
restab <- readRDS(paste(pathtodata, "/analysis/output_datasets/weighted_avg_over_all_thresholds_EFnestedness.Rds", sep = ""))
setnames(restab, old = c("wres"), new = c("maxsplines")) #TODO : this line is maybe not needed any more
restab <- merge(restab, nicenames[, .(names, correlated, lui_ground, lui_ground_nicenames, lui_component)], by = "names")


#######
# create overviewbars
# exclude correlated drivers
ov_list <- create_overviewbar_restab(restab = restab[correlated != "yes", ])

# above- below
df <- data.frame(ov_list$`above-below`)
ov1 <- create_overview_above_below_abiotic_barplot()

df <- data.frame(ov_list$`turnover-nestedness`)
ov2 <- create_overview_turnover_nestedness_abiotic_barplot()

plot_grid(NULL, ov1, ov2, NULL,  nrow = 4, align = T, labels = model_name)

# saved as : "sensitivity_small_extras_overviewbar_without_correlated_gdm_EFdistance_LUI.pdf" A5
#            "sensitivity_small_extras_overviewbar_without_correlated_EFnestedness_WEIGTHED_mean_across_thresholds.pdf"

Overviewbar summing effects

dependencies : needs maxsplines from given model, and variable called restab. Run from script plot_GDM.Rmd.

# create categories : biotic, LUI, abiotic
restab[lui_component %in% c("nestedness", "turnover"), lui_component := "bio"]
sumtab <- aggregate(maxsplines ~ lui_component, restab, sum)
ggplot(sumtab, aes(x = lui_component, y = maxsplines)) +
  geom_bar(stat = "identity") + ggtitle("Summed contributions of EFnestedness0.7")

allanecology/multiFunBetadivLuiGDM documentation built on Nov. 12, 2023, 6:16 a.m.