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.construct
library(gamlss.dist)
#> Loading required package: MASS
path_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..."                                                                 
#>  [15] ""                                                                                                               
#>  [16] "Starting the sampler..."                                                                                        
#>  [17] "Starting the sampler..."                                                                                        
#>  [18] ""                                                                                                               
#>  [19] ""                                                                                                               
#>  [20] ""                                                                                                               
#>  [21] "||          |                                             |   0% |   0%  169.80min169.72min    |   0% 169.61min"
#>  [22] "|                    |   0% 169.92min"                                                                          
#>  [23] "|*                   |   5% 159.55min  8.40min"                                                                 
#>  [24] ""                                                                                                               
#>  [25] "|*                   |   5% |*                   |   5%159.94min  159.94min 8.42min  8.42min"                   
#>  [26] "|*                   |   5% 159.94min  8.42min"                                                                 
#>  [27] "|**                  |  10% 151.15min 16.79min"                                                                 
#>  [28] "|**                  |  10% 151.15min 16.79min"                                                                 
#>  [29] "|**                  |  10% 151.33min 16.81min"                                                                 
#>  [30] "|**                  |  10% 151.33min 16.81min"                                                                 
#>  [31] "|***                 |  15% 142.85min 25.21min"                                                                 
#>  [32] "|***                 |  15% 142.95min 25.23min"                                                                 
#>  [33] "|***                 |  15% 143.04min 25.24min"                                                                 
#>  [34] "|***                 |  15% 143.05min 25.24min"                                                                 
#>  [35] "|****                |  20% 134.41min 33.60min"                                                                 
#>  [36] "|****                |  20% 134.50min 33.63min"                                                                 
#>  [37] "|****                |  20% 134.57min 33.64min"                                                                 
#>  [38] "|****                |  20% 134.58min 33.65min"                                                                 
#>  [39] "|*****               |  25% 126.06min 42.02min"                                                                 
#>  [40] "|*****               |  25% 126.25min 42.08min"                                                                 
#>  [41] "|*****               |  25% 126.29min 42.10min"                                                                 
#>  [42] "|*****               |  25% 126.31min 42.10min"                                                                 
#>  [43] "|******              |  30% 117.78min 50.48min"                                                                 
#>  [44] "|******              |  30% 117.95min 50.55min"                                                                 
#>  [45] "|******              |  30% 117.98min 50.56min"                                                                 
#>  [46] "|******              |  30% 118.00min 50.57min"                                                                 
#>  [47] "|*******             |  35% 109.40min 58.91min"                                                                 
#>  [48] "|*******             |  35% 109.59min 59.01min"                                                                 
#>  [49] "|*******             |  35% 109.59min 59.01min"                                                                 
#>  [50] "|*******             |  35% 109.63min 59.03min"                                                                 
#>  [51] "|********            |  40% 100.99min 67.33min"                                                                 
#>  [52] ""                                                                                                               
#>  [53] "|********            |  40% 101.18min 67.45min|********            |  40% 101.18min 67.45min"                   
#>  [54] "|********            |  40% 101.21min 67.47min"                                                                 
#>  [55] "|*********           |  45% 92.55min 75.72min"                                                                  
#>  [56] "|*********           |  45% 92.70min 75.84min"                                                                  
#>  [57] "|*********           |  45% 92.71min 75.85min"                                                                  
#>  [58] "|*********           |  45% 92.73min 75.87min"                                                                  
#>  [59] "|**********          |  50% 84.24min 84.24min"                                                                  
#>  [60] "|**********          |  50% 84.36min 84.36min"                                                                  
#>  [61] "|**********          |  50% 84.37min 84.37min"                                                                  
#>  [62] "|**********          |  50% 84.39min 84.39min"                                                                  
#>  [63] "|***********         |  55% 75.86min 92.72min"                                                                  
#>  [64] "|***********         |  55% 75.96min 92.84min"                                                                  
#>  [65] "|***********         |  55% 75.98min 92.86min"                                                                  
#>  [66] "|***********         |  55% 75.99min 92.88min"                                                                  
#>  [67] "|************        |  60% 67.47min 101.20min"                                                                 
#>  [68] "|************        |  60% 67.54min 101.31min"                                                                 
#>  [69] "|************        |  60% 67.56min 101.34min"                                                                 
#>  [70] "|************        |  60% 67.58min 101.37min"                                                                 
#>  [71] "|*************       |  65% 59.05min 109.66min"                                                                 
#>  [72] "|*************       |  65% 59.10min 109.76min"                                                                 
#>  [73] "|*************       |  65% 59.13min 109.81min"                                                                 
#>  [74] "|*************       |  65% 59.15min 109.85min"                                                                 
#>  [75] "|**************      |  70% 50.63min 118.14min"                                                                 
#>  [76] "|**************      |  70% 50.68min 118.25min"                                                                 
#>  [77] "|**************      |  70% 50.70min 118.30min"                                                                 
#>  [78] "|**************      |  70% 50.71min 118.33min"                                                                 
#>  [79] "|***************     |  75% 42.20min 126.61min"                                                                 
#>  [80] "|***************     |  75% 42.24min 126.73min"                                                                 
#>  [81] "|***************     |  75% 42.27min 126.81min"                                                                 
#>  [82] "|***************     |  75% 42.28min 126.83min"                                                                 
#>  [83] "|****************    |  80% 33.77min 135.08min"                                                                 
#>  [84] "|****************    |  80% 33.80min 135.21min"                                                                 
#>  [85] "|****************    |  80% 33.82min 135.30min"                                                                 
#>  [86] "|****************    |  80% 33.83min 135.31min"                                                                 
#>  [87] "|*****************   |  85% 25.33min 143.55min"                                                                 
#>  [88] "|*****************   |  85% 25.36min 143.69min"                                                                 
#>  [89] "|*****************   |  85% 25.37min 143.78min"                                                                 
#>  [90] "|*****************   |  85% 25.37min 143.78min"                                                                 
#>  [91] "|******************  |  90% 16.90min 152.06min"                                                                 
#>  [92] "|******************  |  90% 16.91min 152.18min"                                                                 
#>  [93] "|******************  |  90% 16.92min 152.28min"                                                                 
#>  [94] "|******************  |  90% 16.92min 152.29min"                                                                 
#>  [95] "|******************* |  95%  8.45min 160.53min"                                                                 
#>  [96] "|******************* |  95%  8.46min 160.65min"                                                                 
#>  [97] "|******************* |  95%  8.46min 160.76min"                                                                 
#>  [98] "|******************* |  95%  8.46min 160.78min"                                                                 
#>  [99] "|********************| 100%  0.00sec 168.96min"                                                                 
#> [100] ""                                                                                                               
#> [101] "|********************| 100%  0.00sec 169.05min"                                                                 
#> [102] ""                                                                                                               
#> [103] "|********************| 100%  0.00sec 169.15min"                                                                 
#> [104] ""                                                                                                               
#> [105] "|********************| 100%  0.00sec 169.17min"
system.time(saveRDS(bamlss_model, file = path_modelled_data))
#>    user  system elapsed 
#>   4.570   0.016   4.586
saveRDS(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