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5_Convergence_Checks.R
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5_Convergence_Checks.R
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# Convergence Checks for all real data examples ---------------------------
library(cmdstanr)
library(tidyverse)
convergence_all <- NULL
time_all <- vector("list",length = 11)
# Shorebirds --------------------------------------------------------------
sp_data <- "Shorebird"
model <- "gamye"
model_variant <- "spatial"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[1]] <- fit$time()$total/3600
names(time_all)[1] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary() %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "hier"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[2]] <- fit$time()$total/3600
names(time_all)[2] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary()%>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
# CBC --------------------------------------------------------------
sp_data <- "CBC"
model <- "gamye"
model_variant <- "spatial"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[3]] <- fit$time()$total/3600
names(time_all)[3] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary() %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "hier"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[4]] <- fit$time()$total/3600
names(time_all)[4] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary()%>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model <- "first_diff"
model_variant <- "spatial"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[5]] <- fit$time()$total/3600
names(time_all)[5] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary() %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "hier"
fit <- readRDS(paste0(paste("output/fit",sp_data,model_variant,model,
sep = "_"),".rds"))
time_all[[6]] <- fit$time()$total/3600
names(time_all)[6] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- fit$summary()%>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
# BBS --------------------------------------------------------------
sp_data <- "BBS"
species <- "Eastern Whip-poor-will"
model <- "gamye"
model_variant <- "spatial"
fit <- readRDS(paste0(paste("output/",species,"_",model,"_",model_variant,
sep = ""),".rds"))
time_all[[7]] <- fit$model_fit$time()$total/3600
names(time_all)[7] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- readRDS(paste0("output/",paste(model,model_variant,
sep = "_"),"_param_summary.rds"))
conv_tmp <- conv_tmp %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "hier"
fit <- readRDS(paste0(paste("output/",species,"_",model,"_",model_variant,
sep = ""),".rds"))
time_all[[8]] <- fit$model_fit$time()$total/3600
names(time_all)[8] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- readRDS(paste0("output/",paste(model,model_variant,
sep = "_"),"_param_summary.rds"))
conv_tmp <- conv_tmp %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model <- "first_diff"
model_variant <- "spatial"
fit <- readRDS(paste0(paste("output/",species,"_",model,"_",model_variant,
sep = ""),".rds"))
time_all[[9]] <- fit$model_fit$time()$total/3600
names(time_all)[9] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- readRDS(paste0("output/",paste(model,model_variant,
sep = "_"),"_param_summary.rds"))
conv_tmp <- conv_tmp %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "hier"
fit <- readRDS(paste0(paste("output/",species,"_",model,"_",model_variant,
sep = ""),".rds"))
time_all[[10]] <- fit$model_fit$time()$total/3600
names(time_all)[10] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- readRDS(paste0("output/",paste(model,model_variant,
sep = "_"),"_param_summary.rds"))
conv_tmp <- conv_tmp %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
model_variant <- "nonhier"
fit <- readRDS(paste0(paste("output/",species,"_",model,"_",model_variant,
sep = ""),".rds"))
time_all[[11]] <- fit$model_fit$time()$total/3600
names(time_all)[11] <- paste(sp_data,model,model_variant,sep = "_")
conv_tmp <- readRDS(paste0("output/",paste(model,model_variant,
sep = "_"),"_param_summary.rds"))
conv_tmp <- conv_tmp %>%
mutate(species = sp_data,
model = model,
model_variant = model_variant)
convergence_all <- bind_rows(convergence_all,conv_tmp)
convergence_all <- convergence_all %>%
mutate(variable_type = stringr::str_extract(variable, "^\\w+"))
saveRDS(convergence_all,
file = "output/convergence_all_real_data.rds")
saveRDS(time_all,
file = "output/fit_time_all_real_data.rds")
ess_fail <- convergence_all %>%
filter(ess_bulk < 400)
rhat_fail <- convergence_all %>%
filter(rhat > 1.02 )
convergence_summary <- convergence_all %>%
filter(is.finite(rhat),
is.finite(ess_bulk)) %>%
group_by(species,model,model_variant,variable_type) %>%
summarise(max_rhat = max(rhat,na.rm = TRUE),
min_ess_bulk = min(ess_bulk,na.rm = TRUE),
.groups = "keep")