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.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")

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..."                                                                   
#>  [13] "Starting the sampler..."                                                                   
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#>  [15] ""                                                                                          
#>  [16] ""                                                                                          
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#>  [23] ""                                                                                          
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#>  [31] ""                                                                                          
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#>  [35] ""                                                                                          
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#>  [39] ""                                                                                          
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#>  [43] ""                                                                                          
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#>  [47] ""                                                                                          
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#>  [98] ""                                                                                          
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system.time(saveRDS(bamlss_model, file = path_modelled_data))
#>    user  system elapsed 
#>   0.355   0.004   0.359
saveRDS(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