Linear tap water with random effects: fitting
Birthweight model including covariates at municipality level with linear effects.
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-muni-14-water-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
Now we define the same models as in the previous study.
form_sigma <- sigma ~ 1
form_mu <- born_weight ~ prop_tap_toilet + s(res_muni, bs = "re")
form <- list(form_mu, form_sigma)Run the model of interest and save results
{
sink(path_modelled_sink)
bamlss_model <- bamlss(
form, data = bwdata_model,
n.iter = 1000, burnin = 0, cores = 4, combine = FALSE, light = TRUE
)
sink()
}
readLines(path_modelled_sink)#> [1] "AICc 4465554. logPost -2455057 logLik -2232773 edf 4.0881 eps 0.0322 iteration 1"
#> [2] "AICc 4458520. logPost -2231484 logLik -2229248 edf 11.674 eps 0.0076 iteration 2"
#> [3] "AICc 4456619. logPost -2228826 logLik -2228277 edf 32.192 eps 0.0040 iteration 3"
#> [4] "AICc 4456381. logPost -2228409 logLik -2228146 edf 43.877 eps 0.0016 iteration 4"
#> [5] "AICc 4456379. logPost -2228388 logLik -2228144 edf 45.376 eps 0.0001 iteration 5"
#> [6] "AICc 4456379. logPost -2228387 logLik -2228144 edf 45.371 eps 0.0000 iteration 6"
#> [7] "AICc 4456379. logPost -2228387 logLik -2228144 edf 45.371 eps 0.0000 iteration 6"
#> [8] "elapsed time: 9.62sec"
#> [9] "Starting the sampler...Starting the sampler..."
#> [10] ""
#> [11] "Starting the sampler..."
#> [12] "Starting the sampler..."
#> [13] ""
#> [14] ""
#> [15] "|| | 0% | 0% 12.80min12.80min"
#> [16] "| | 0% 12.79min"
#> [17] "| | 0% 12.83min"
#> [18] "|* | 5% 11.73min 37.05sec"
#> [19] "|* | 5% 11.85min 37.41sec"
#> [20] "|* | 5% 11.85min 37.41sec"
#> [21] "|* | 5% 12.03min 37.98sec"
#> [22] "|** | 10% 11.08min 1.23min"
#> [23] "|** | 10% 11.10min 1.23min"
#> [24] "|** | 10% 11.14min 1.24min"
#> [25] "|** | 10% 11.20min 1.24min"
#> [26] "|*** | 15% 10.65min 1.88min"
#> [27] "|*** | 15% 10.65min 1.88min"
#> [28] "|*** | 15% 10.70min 1.89min"
#> [29] "|*** | 15% 10.75min 1.90min"
#> [30] "|**** | 20% 10.12min 2.53min"
#> [31] "|**** | 20% 10.12min 2.53min"
#> [32] "|**** | 20% 10.15min 2.54min"
#> [33] "|**** | 20% 10.24min 2.56min"
#> [34] "|***** | 25% 9.83min 3.28min"
#> [35] "|***** | 25% 9.82min 3.27min"
#> [36] "|***** | 25% 9.83min 3.28min"
#> [37] "|***** | 25% 9.91min 3.30min"
#> [38] "|****** | 30% 9.21min 3.95min"
#> [39] "|****** | 30% 9.20min 3.94min"
#> [40] "|****** | 30% 9.23min 3.96min"
#> [41] "|****** | 30% 9.28min 3.98min"
#> [42] "|******* | 35% 8.62min 4.64min"
#> [43] "|******* | 35% 8.62min 4.64min"
#> [44] "|******* | 35% 8.65min 4.66min"
#> [45] "|******* | 35% 8.69min 4.68min"
#> [46] "|******** | 40% 7.96min 5.31min"
#> [47] "|******** | 40% 7.97min 5.31min"
#> [48] "|******** | 40% 8.00min 5.33min"
#> [49] "|******** | 40% 8.02min 5.34min"
#> [50] "|********* | 45% 7.28min 5.95min"
#> [51] "|********* | 45% 7.29min 5.97min"
#> [52] "|********* | 45% 7.31min 5.98min"
#> [53] "|********* | 45% 7.33min 5.99min"
#> [54] "|********** | 50% 6.57min 6.57min"
#> [55] "|********** | 50% 6.59min 6.59min"
#> [56] "|********** | 50% 6.60min 6.60min"
#> [57] "|********** | 50% 6.62min 6.62min"
#> [58] "|*********** | 55% 5.90min 7.22min"
#> [59] "|*********** | 55% 5.91min 7.23min"
#> [60] "|*********** | 55% 5.93min 7.24min"
#> [61] "|*********** | 55% 5.94min 7.26min"
#> [62] "|************ | 60% 5.23min 7.84min"
#> [63] "|************ | 60% 5.23min 7.85min"
#> [64] "|************ | 60% 5.24min 7.87min"
#> [65] "|************ | 60% 5.25min 7.88min"
#> [66] "|************* | 65% 4.56min 8.47min"
#> [67] "|************* | 65% 4.57min 8.48min"
#> [68] "|************* | 65% 4.57min 8.50min"
#> [69] "|************* | 65% 4.58min 8.51min"
#> [70] "|************** | 70% 3.89min 9.08min"
#> [71] "|************** | 70% 3.90min 9.09min"
#> [72] "|************** | 70% 3.90min 9.11min"
#> [73] "|************** | 70% 3.91min 9.12min"
#> [74] "|*************** | 75% 3.23min 9.69min"
#> [75] "|*************** | 75% 3.24min 9.71min"
#> [76] "|*************** | 75% 3.24min 9.73min"
#> [77] "|*************** | 75% 3.25min 9.76min"
#> [78] "|**************** | 80% 2.58min 10.31min"
#> [79] "|**************** | 80% 2.58min 10.33min"
#> [80] "|**************** | 80% 2.59min 10.35min"
#> [81] "|**************** | 80% 2.59min 10.37min"
#> [82] "|***************** | 85% 1.93min 10.93min"
#> [83] "|***************** | 85% 1.93min 10.95min"
#> [84] "|***************** | 85% 1.94min 10.97min"
#> [85] "|***************** | 85% 1.94min 10.99min"
#> [86] "|****************** | 90% 1.28min 11.55min"
#> [87] "|****************** | 90% 1.28min 11.56min"
#> [88] "|****************** | 90% 1.29min 11.58min"
#> [89] "|****************** | 90% 1.29min 11.61min"
#> [90] "|******************* | 95% 38.45sec 12.18min"
#> [91] "|******************* | 95% 38.49sec 12.19min"
#> [92] "|******************* | 95% 38.56sec 12.21min"
#> [93] "|******************* | 95% 38.64sec 12.24min"
#> [94] "|********************| 100% 0.00sec 12.79min"
#> [95] ""
#> [96] "|********************| 100% 0.00sec 12.80min"
#> [97] ""
#> [98] "|********************| 100% 0.00sec 12.82min"
#> [99] ""
#> [100] "|********************| 100% 0.00sec 12.83min"system.time(saveRDS(bamlss_model, file = path_modelled_data))#> user system elapsed
#> 2.21 0.00 2.21saveRDS(form, file = path_modelled_form)Time to execute the task
Only useful when executed with Rscript.
proc.time()#> user system elapsed
#> 3130.705 9.988 804.350