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-04-inter-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)
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 285998.8 logPost -163704. logLik -142989. edf 9.5175 eps 0.0392 iteration 1"
#> [2] "AICc 280893.6 logPost -141836. logLik -140424. edf 22.231 eps 0.0214 iteration 2"
#> [3] "AICc 271838.7 logPost -137318. logLik -135875. edf 43.830 eps 0.0358 iteration 3"
#> [4] "AICc 268758.8 logPost -134989. logLik -134329. edf 50.228 eps 0.0199 iteration 4"
#> [5] "AICc 268607.3 logPost -134664. logLik -134250. edf 53.378 eps 0.0030 iteration 5"
#> [6] "AICc 268602.2 logPost -134635. logLik -134245. edf 55.096 eps 0.0003 iteration 6"
#> [7] "AICc 268602.2 logPost -134635. logLik -134245. edf 55.098 eps 0.0000 iteration 7"
#> [8] "AICc 268602.2 logPost -134635. logLik -134245. edf 55.098 eps 0.0000 iteration 7"
#> [9] "elapsed time: 1.44sec"
#> [10] "Starting the sampler..."
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#> [101] "|********************| 100% 0.00sec 39.77sec"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 0.204 0.004 0.208saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 164.048 1.011 45.468