One-term models: smooths

Load packages, read data and source custom scripts

rm(list = ls())
library(dplyr)

#> 
#> Attaching package: 'dplyr'

#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag

#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

library(mgcv)

#> Loading required package: nlme

#> 
#> Attaching package: 'nlme'

#> The following object is masked from 'package:dplyr':
#> 
#>     collapse

#> This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.

library(purrr)

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_out_model_data <- file.path(path_modelled,  "lbw-explore-smooths.rds")

bwdata_model <- fst::read_fst(file.path(path_processed, "bwdata_41_model.fst"))

Exploratory models of low birthweight with covariates

terms <- list(
    ~ s(age),
    ~ s(wk_ini),
    ~ s(rivwk_conception, bs = "cc"),
    ~ s(remoteness),
    ~ s(rur_prop),
    ~ s(prop_tap_toilet),
    ~ s(longitud, latitud)
    )

data_model <- tibble::tibble(
    formula = map(terms, ~ update(., lbw ~ .))
)

data_model <- data_model %>%
    mutate(model = map(formula, ~ gam(.x, "binomial", data = bwdata_model)))

saveRDS(data_model, file = path_out_model_data)

Time to execute the task

Only useful when executed with Rscript.

proc.time()

#>    user  system elapsed 
#>  60.961   2.947  64.005