Only covariates: fitting
Birthweight model including covariates at municipality level
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-muni-00-covs.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
Now we define the same models as in the previous study.
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,
n.iter = 1000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 4458377. logPost -2229229 logLik -2229184 edf 4.2021 eps 0.0299 iteration 1"
#> [2] "AICc 4458249. logPost -2229206 logLik -2229119 edf 5.3771 eps 0.0007 iteration 2"
#> [3] "AICc 4458121. logPost -2229167 logLik -2229052 edf 8.1029 eps 0.0007 iteration 3"
#> [4] "AICc 4457879. logPost -2229090 logLik -2228927 edf 12.443 eps 0.0007 iteration 4"
#> [5] "AICc 4457558. logPost -2228948 logLik -2228762 edf 17.218 eps 0.0013 iteration 5"
#> [6] "AICc 4457450. logPost -2228874 logLik -2228705 edf 19.531 eps 0.0008 iteration 6"
#> [7] "AICc 4457423. logPost -2228862 logLik -2228691 edf 19.797 eps 0.0003 iteration 7"
#> [8] "AICc 4457417. logPost -2228859 logLik -2228688 edf 19.770 eps 0.0001 iteration 8"
#> [9] "AICc 4457416. logPost -2228859 logLik -2228688 edf 19.757 eps 0.0000 iteration 9"
#> [10] "AICc 4457416. logPost -2228859 logLik -2228688 edf 19.757 eps 0.0000 iteration 9"
#> [11] "elapsed time: 22.54sec"
#> [12] "Starting the sampler..."
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#> [103] "|********************| 100% 0.00sec 10.64min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 0.116 0.000 0.116saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 2626.596 2.224 684.595