Growth model without rainfall: dic

Load packages, read data and source custom scripts

rm(list = ls())
library(bamlss)

#> Loading required package: coda

#> Loading required package: colorspace

#> Loading required package: mgcv

#> Loading required package: nlme

#> This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.

#> 
#> Attaching package: 'bamlss'

#> The following object is masked from 'package:mgcv':
#> 
#>     smooth.construct

library(gamlss.dist)

#> Loading required package: MASS

library(sf)

#> Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1

library(ggplot2)

path_proj <- day2day::git_path()
path_data <- file.path(path_proj, "data")
path_processed <- file.path(path_data, "processed")
path_modelled <- file.path(path_data, "modelled")

source(file.path(path_proj, "src", "51-bamlss.R"))

bwdata_file <- file.path(path_processed, "bwdata_41_model.fst")
model_file <- file.path(path_modelled, "lbw-25-growth-no-rain.rds")
form_file <- gsub("(\\.rds)$", "-form\\1", model_file)
model_file_burned <- gsub("(\\.rds)$", "-burned\\1", model_file)

bwdata_model <- fst::read_fst(bwdata_file)
form <- readRDS(form_file)
model <- readRDS(model_file_burned)

Diagnostics

frame <- bamlss.frame(form, family = "binomial", data = bwdata_model,
                      model.matrix = FALSE, smooth.construct = FALSE)
model$y <- frame$y

par(mar = c(4, 4, 3, 1), mfrow = c(1, 2))
plot(model, which = "qq-resid", spar = FALSE)
plot(model, which = "hist-resid", spar = FALSE)

DIC

system.time(dic <- DIC(model))

#>    user  system elapsed 
#> 707.796 196.936 905.074

dic

#>       DIC       pd
#>  120464.6 80.21149

Time to execute the task

Only useful when executed with Rscript.

proc.time()

#>     user   system  elapsed 
#> 1868.794  519.167 2388.719