Full model without rainfall: fitting
Prematurity 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, "pre-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 <- premature ~ 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 171382.6 logPost -85885.4 logLik -85609.9 edf 81.365 eps 0.5494 iteration 1"
#> [2] "AICc 162371.6 logPost -81370.2 logLik -81100.5 edf 85.282 eps 0.1913 iteration 2"
#> [3] "AICc 161244.9 logPost -80856.5 logLik -80536.1 edf 86.241 eps 0.0598 iteration 3"
#> [4] "AICc 161037.1 logPost -80718.3 logLik -80432.4 edf 86.039 eps 0.0236 iteration 4"
#> [5] "AICc 160996.8 logPost -80690.3 logLik -80412.5 edf 85.835 eps 0.0103 iteration 5"
#> [6] "AICc 160988.9 logPost -80686.2 logLik -80408.7 edf 85.754 eps 0.0046 iteration 6"
#> [7] "AICc 160987.4 logPost -80685.4 logLik -80407.9 edf 85.720 eps 0.0020 iteration 7"
#> [8] "AICc 160987.1 logPost -80685.3 logLik -80407.8 edf 85.706 eps 0.0009 iteration 8"
#> [9] "AICc 160987.1 logPost -80685.3 logLik -80407.8 edf 85.699 eps 0.0004 iteration 9"
#> [10] "AICc 160987.1 logPost -80685.2 logLik -80407.8 edf 85.696 eps 0.0001 iteration 10"
#> [11] "AICc 160987.1 logPost -80685.2 logLik -80407.8 edf 85.695 eps 0.0000 iteration 11"
#> [12] "AICc 160987.1 logPost -80685.2 logLik -80407.8 edf 85.695 eps 0.0000 iteration 11"
#> [13] "elapsed time: 51.03sec"
#> [14] "Starting the sampler...Starting the sampler..."
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#> [105] "|********************| 100% 0.00sec 169.17min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 4.570 0.016 4.586saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 40699.438 23.087 10240.537