Discrete binning only smooths: fitting
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-09-discrete-bin-age.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_51_test.fst"))Define formula for our model
form_mu <- born_weight ~ marital_status + race + s(age_bin)
form <- form_muRun the model of interest and save results
{
sink(path_modelled_sink)
bamlss_model <- bamlss(
form, data = bwdata_model, binning = TRUE,
n.iter = 1000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 317041.7 logPost -270258. logLik -158512. edf 8.7495 eps 0.4705 iteration 1"
#> [2] "AICc 302009.1 logPost -156229. logLik -150995. edf 8.9683 eps 0.1038 iteration 2"
#> [3] "AICc 291838.0 logPost -146780. logLik -145908. edf 10.767 eps 0.0552 iteration 3"
#> [4] "AICc 286793.8 logPost -143774. logLik -143383. edf 13.570 eps 0.0356 iteration 4"
#> [5] "AICc 285488.7 logPost -142950. logLik -142728. edf 15.506 eps 0.0167 iteration 5"
#> [6] "AICc 285131.7 logPost -142712. logLik -142549. edf 15.949 eps 0.0033 iteration 6"
#> [7] "AICc 284834.3 logPost -142563. logLik -142401. edf 15.988 eps 0.0012 iteration 7"
#> [8] "AICc 284563.6 logPost -142427. logLik -142265. edf 15.987 eps 0.0011 iteration 8"
#> [9] "AICc 284317.2 logPost -142304. logLik -142142. edf 15.986 eps 0.0019 iteration 9"
#> [10] "AICc 284093.3 logPost -142191. logLik -142030. edf 15.985 eps 0.0017 iteration 10"
#> [11] "AICc 283890.0 logPost -142089. logLik -141929. edf 15.984 eps 0.0008 iteration 11"
#> [12] "AICc 283705.6 logPost -141997. logLik -141836. edf 15.982 eps 0.0011 iteration 12"
#> [13] "AICc 283538.5 logPost -141913. logLik -141753. edf 15.980 eps 0.0007 iteration 13"
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#> [20] "AICc 282740.6 logPost -141510. logLik -141354. edf 15.964 eps 0.0005 iteration 20"
#> [21] "AICc 282666.5 logPost -141473. logLik -141317. edf 15.961 eps 0.0004 iteration 21"
#> [22] "AICc 282599.6 logPost -141439. logLik -141283. edf 15.957 eps 0.0003 iteration 22"
#> [23] "AICc 282539.4 logPost -141409. logLik -141253. edf 15.954 eps 0.0003 iteration 23"
#> [24] "AICc 282485.2 logPost -141381. logLik -141226. edf 15.949 eps 0.0003 iteration 24"
#> [25] "AICc 282436.4 logPost -141356. logLik -141202. edf 15.945 eps 0.0008 iteration 25"
#> [26] "AICc 282392.4 logPost -141334. logLik -141180. edf 15.940 eps 0.0002 iteration 26"
#> [27] "AICc 282352.9 logPost -141314. logLik -141160. edf 15.935 eps 0.0002 iteration 27"
#> [28] "AICc 282317.3 logPost -141295. logLik -141142. edf 15.929 eps 0.0002 iteration 28"
#> [29] "AICc 282285.2 logPost -141279. logLik -141126. edf 15.923 eps 0.0002 iteration 29"
#> [30] "AICc 282256.4 logPost -141264. logLik -141112. edf 15.916 eps 0.0001 iteration 30"
#> [31] "AICc 282230.5 logPost -141251. logLik -141099. edf 15.909 eps 0.0002 iteration 31"
#> [32] "AICc 282207.2 logPost -141239. logLik -141087. edf 15.901 eps 0.0004 iteration 32"
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#> [41] "AICc 282088.3 logPost -141176. logLik -141028. edf 15.818 eps 0.0000 iteration 40"
#> [42] "elapsed time: 3.29sec"
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#> [134] "|********************| 100% 0.00sec 26.92sec"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 0.108 0.001 0.108saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 113.902 0.939 33.706