Full model: 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-10-full-re.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_aux <- 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")
form <- update(form_aux, . ~ . +
s(neg_mbsi_mean_1wk, pos_mbsi_mean_1wk, k = 70) +
s(neg_mckee_mean_8wk, pos_mckee_mean_8wk, k = 70) +
s(neg_ext_mbsi_mean_8wk, pos_ext_mbsi_mean_8wk, k = 70))Run the model of interest and save results
{
sink(path_modelled_sink)
bamlss_model <- bamlss(
form, family = "binomial", data = bwdata_model,
n.iter = 3000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 139298.7 logPost -69468.9 logLik -69507.4 edf 141.88 eps 0.5483 iteration 1"
#> [2] "AICc 129929.2 logPost -65763.4 logLik -64781.3 edf 183.17 eps 0.2223 iteration 2"
#> [3] "AICc 129565.2 logPost -65044.3 logLik -64572.1 edf 210.29 eps 0.0380 iteration 3"
#> [4] "AICc 129537.6 logPost -64994.8 logLik -64550.5 edf 218.13 eps 0.0079 iteration 4"
#> [5] "AICc 129531.4 logPost -65029.6 logLik -64545.1 edf 220.39 eps 0.0029 iteration 5"
#> [6] "AICc 129529.0 logPost -65062.6 logLik -64543.1 edf 221.17 eps 0.0014 iteration 6"
#> [7] "AICc 129527.8 logPost -65075.5 logLik -64542.2 edf 221.48 eps 0.0008 iteration 7"
#> [8] "AICc 129527.2 logPost -65073.9 logLik -64541.8 edf 221.62 eps 0.0005 iteration 8"
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#> [11] "AICc 129526.3 logPost -65053.5 logLik -64541.2 edf 221.73 eps 0.0002 iteration 11"
#> [12] "AICc 129526.2 logPost -65048.7 logLik -64541.2 edf 221.74 eps 0.0001 iteration 12"
#> [13] "AICc 129526.2 logPost -65045.0 logLik -64541.1 edf 221.75 eps 0.0001 iteration 13"
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#> [15] "AICc 129526.1 logPost -65039.5 logLik -64541.1 edf 221.76 eps 0.0001 iteration 15"
#> [16] "AICc 129526.1 logPost -65039.5 logLik -64541.1 edf 221.76 eps 0.0001 iteration 15"
#> [17] "elapsed time: 10.11min"
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#> [109] "|********************| 100% 0.00sec 175.46min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 4.998 0.024 5.082saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 42919.275 20.108 11256.108