Full model with flexible prior: 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-11-full-re-p1.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
hyper <- list(a = 5, b = 1000)
form_aux <- lbw ~ sex + born_race + birth_place +
marital_status + study_years + consult_num + s(age, xt = hyper) +
s(wk_ini, xt = hyper) + s(rivwk_conception, bs = "cc", xt = hyper) +
remoteness + prop_tap_toilet + s(res_muni, bs = "re", xt = hyper)
form <- update(form_aux, . ~ . +
s(neg_mbsi_mean_1wk, pos_mbsi_mean_1wk, k = 70, xt = hyper) +
s(neg_mckee_mean_8wk, pos_mckee_mean_8wk, k = 70, xt = hyper) +
s(neg_ext_mbsi_mean_8wk, pos_ext_mbsi_mean_8wk, k = 70, xt = hyper))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 139298.7 logPost -8377857 logLik -69507.4 edf 141.88 eps 0.5483 iteration 1"
#> [2] "AICc 129929.2 logPost -7939268 logLik -64781.3 edf 183.17 eps 0.2223 iteration 2"
#> [3] "AICc 129565.2 logPost -8992485 logLik -64572.1 edf 210.29 eps 0.0380 iteration 3"
#> [4] "AICc 129537.6 logPost -6947691 logLik -64550.5 edf 218.13 eps 0.0079 iteration 4"
#> [5] "AICc 129531.4 logPost -1047376 logLik -64545.1 edf 220.39 eps 0.0029 iteration 5"
#> [6] "AICc 129529.0 logPost -1379598 logLik -64543.1 edf 221.17 eps 0.0014 iteration 6"
#> [7] "AICc 129527.8 logPost -1508622 logLik -64542.2 edf 221.48 eps 0.0008 iteration 7"
#> [8] "AICc 129527.2 logPost -1490440 logLik -64541.8 edf 221.62 eps 0.0005 iteration 8"
#> [9] "AICc 129526.8 logPost -1419587 logLik -64541.5 edf 221.68 eps 0.0003 iteration 9"
#> [10] "AICc 129526.5 logPost -1344386 logLik -64541.3 edf 221.71 eps 0.0003 iteration 10"
#> [11] "AICc 129526.3 logPost -1280304 logLik -64541.2 edf 221.73 eps 0.0002 iteration 11"
#> [12] "AICc 129526.2 logPost -1231166 logLik -64541.2 edf 221.74 eps 0.0001 iteration 12"
#> [13] "AICc 129526.2 logPost -1193967 logLik -64541.1 edf 221.75 eps 0.0001 iteration 13"
#> [14] "AICc 129526.1 logPost -1159101 logLik -64541.1 edf 221.75 eps 0.0001 iteration 14"
#> [15] "AICc 129526.1 logPost -1137510 logLik -64541.1 edf 221.76 eps 0.0001 iteration 15"
#> [16] "AICc 129526.1 logPost -1137510 logLik -64541.1 edf 221.76 eps 0.0001 iteration 15"
#> [17] "elapsed time: 10.18min"
#> [18] "Starting the sampler..."
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#> [109] "|********************| 100% 0.00sec 455.79min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 6.596 0.040 6.655saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 110184.76 35.36 28081.39