Only covariates with binning: fitting
Birthweight model including covariates at municipality level with binning option.
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.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-muni-01-covs-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_41_model.fst"))Define formula for our model
form_sigma <- sigma ~ 1
form_mu <- born_weight ~ s(remoteness) + s(prop_tap_toilet)
form <- list(form_mu, form_sigma)Run 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 4873071. logPost -2582651 logLik -2436526 edf 9.3467 eps 0.1928 iteration 1"
#> [2] "AICc 4598169. logPost -2299275 logLik -2299074 edf 9.8623 eps 0.1272 iteration 2"
#> [3] "AICc 4486998. logPost -2243656 logLik -2243482 edf 16.524 eps 0.0336 iteration 3"
#> [4] "AICc 4459259. logPost -2229780 logLik -2229610 edf 19.637 eps 0.0176 iteration 4"
#> [5] "AICc 4457573. logPost -2228938 logLik -2228767 edf 19.775 eps 0.0049 iteration 5"
#> [6] "AICc 4457465. logPost -2228884 logLik -2228712 edf 19.776 eps 0.0008 iteration 6"
#> [7] "AICc 4457432. logPost -2228867 logLik -2228696 edf 19.763 eps 0.0003 iteration 7"
#> [8] "AICc 4457421. logPost -2228862 logLik -2228691 edf 19.756 eps 0.0001 iteration 8"
#> [9] "AICc 4457418. logPost -2228860 logLik -2228689 edf 19.753 eps 0.0001 iteration 9"
#> [10] "AICc 4457418. logPost -2228860 logLik -2228689 edf 19.753 eps 0.0001 iteration 9"
#> [11] "elapsed time: 14.76sec"
#> [12] "Starting the sampler..."
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#> [103] "|********************| 100% 0.00sec 10.90min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 0.355 0.004 0.359saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 2652.596 1.833 684.350