Full model without rainfall: fitting
Low birthweight model including covariates at municipality level with linear effects.
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, "lbw-15-full-no-rain.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 <- lbw ~ sex + born_race + birth_place +
marital_status + study_years + consult_num + s(age) +
s(wk_ini) + s(rivwk_conception, bs = "cc") +
remoteness + prop_tap_toilet + s(res_muni, bs = "re")Run the model of interest and save results
{
sink(path_modelled_sink)
bamlss_model <- bamlss(
form, family = "binomial", data = bwdata_model,
n.iter = 8000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 139282.9 logPost -69882.8 logLik -69566.2 edf 75.229 eps 0.5483 iteration 1"
#> [2] "AICc 130130.0 logPost -65998.2 logLik -64985.7 edf 79.241 eps 0.2211 iteration 2"
#> [3] "AICc 129803.7 logPost -70325.5 logLik -64822.0 edf 79.845 eps 0.0367 iteration 3"
#> [4] "AICc 129789.0 logPost -76962.0 logLik -64814.5 edf 79.985 eps 0.0067 iteration 4"
#> [5] "AICc 129787.8 logPost -78702.7 logLik -64813.9 edf 79.928 eps 0.0020 iteration 5"
#> [6] "AICc 129787.8 logPost -78905.3 logLik -64813.9 edf 79.907 eps 0.0007 iteration 6"
#> [7] "AICc 129787.8 logPost -78925.9 logLik -64814.0 edf 79.899 eps 0.0002 iteration 7"
#> [8] "AICc 129787.9 logPost -78927.9 logLik -64814.0 edf 79.896 eps 0.0000 iteration 8"
#> [9] "AICc 129787.9 logPost -78927.9 logLik -64814.0 edf 79.896 eps 0.0000 iteration 8"
#> [10] "elapsed time: 41.67sec"
#> [11] "Starting the sampler...Starting the sampler..."
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#> [102] "|********************| 100% 0.00sec 169.55min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 4.503 0.007 4.549saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 40751.926 27.022 10254.004