Discrete binning: fitting
Load packages, read data and source custom scripts
Paths are defined relative to the git repository location.
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.constructlibrary(gamlss.dist)#> Loading required package: MASSpath_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")
path_modelled_data <- file.path(path_modelled, "bw-08-discrete-bin.rds")
path_modelled_sink <- gsub("\\.rds$", "\\.txt", path_modelled_data)
path_modelled_form <- gsub("(\\.rds)$", "-form\\1", path_modelled_data)
bwdata_model <- fst::read_fst(file.path(path_processed, "bwdata_51_test.fst"))Define formula for our model
form_mu <- born_weight ~ marital_status + race + s(municipality, bs = "re") +
s(age_bin)
form <- form_muRun the model of interest and save results
{
sink(path_modelled_sink)
bamlss_model <- bamlss(
form, data = bwdata_model, binning = TRUE,
n.iter = 1000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 314201.0 logPost -281319. logLik -157090. edf 10.260 eps 0.2655 iteration 1"
#> [2] "AICc 301662.7 logPost -157024. logLik -150818. edf 12.461 eps 0.0958 iteration 2"
#> [3] "AICc 287480.9 logPost -145229. logLik -143703. edf 36.826 eps 0.0634 iteration 3"
#> [4] "AICc 278765.8 logPost -140087. logLik -139330. edf 52.671 eps 0.0478 iteration 4"
#> [5] "AICc 276084.6 logPost -138484. logLik -137986. edf 55.438 eps 0.0205 iteration 5"
#> [6] "AICc 275371.7 logPost -138045. logLik -137629. edf 55.839 eps 0.0058 iteration 6"
#> [7] "AICc 274781.1 logPost -137748. logLik -137334. edf 55.877 eps 0.0026 iteration 7"
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#> [11] "AICc 272843.9 logPost -136778. logLik -136365. edf 55.887 eps 0.0015 iteration 11"
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#> [29] "AICc 269297.5 logPost -134996. logLik -134592. edf 55.875 eps 0.0003 iteration 29"
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#> [46] "elapsed time: 5.81sec"
#> [47] "Starting the sampler..."
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#> [138] "|********************| 100% 0.00sec 37.19sec"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 0.197 0.007 0.205saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 157.708 1.137 46.570