Growth model with t-distribution: continue mcmc

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

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", "43-mcmc-continue-light.R"))
source(file.path(path_proj, "src", "45-mcmc-reshape.R"))
source(file.path(path_proj, "src", "46-mcmc-last-sample.R"))

bwdata_model <- fst::read_fst(file.path(path_processed, "bwdata_41_model.fst"))

path_modelled_data <- file.path(path_modelled, "bw-20-growth-re-t.rds")
path_modelled_form <- gsub("(\\.rds)$", "-form\\1", path_modelled_data)
path_modelled_continue <- gsub("(\\.rds)$", "-continue\\1", path_modelled_data)
path_modelled_sink <- gsub("\\.rds$", "\\.txt", path_modelled_continue)

bamlss_model <- readRDS(path_modelled_data)
form <- readRDS(path_modelled_form)

Continue with sampling

starting_value <- last_sample(bamlss_model)
{
    sink(path_modelled_sink)
    bamlss_model <- bamlss(
        form, family = TF, data = bwdata_model,
        start = starting_value, optimizer = FALSE,
        n.iter = 4000, burnin = 0, cores = 3, combine = FALSE, light = TRUE
    )
    sink()
}
readLines(path_modelled_sink)

#>  [1] "Starting the sampler..."                        
#>  [2] "Starting the sampler...Starting the sampler..." 
#>  [3] ""                                               
#>  [4] ""                                               
#>  [5] "|                    |   0% 613.16min"          
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#>  [8] "|*                   |   5% 557.10min 29.32min" 
#>  [9] "|*                   |   5% 557.61min 29.35min" 
#> [10] "|*                   |   5% 557.61min 29.35min" 
#> [11] "|**                  |  10% 519.84min 57.76min" 
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#> [14] "|***                 |  15% 487.50min 86.03min" 
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#> [66] ""                                               
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#> [68] ""                                               
#> [69] "|********************| 100%  0.00sec 571.30min"

system.time(saveRDS(bamlss_model, file = path_modelled_continue))

#>    user  system elapsed 
#>   9.523   0.038   9.607

Time to execute the task

Only useful when executed with Rscript.

proc.time()

#>       user     system    elapsed 
#> 103003.346     20.949  34402.574