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Run model on cluster

this script runs a model on our scientific computing cluster This restricts the model to one historical Swedish region, Skellefteå

library(dplyr); library(brms)
setwd("/usr/users/rarslan/updated_data/")

args = commandArgs()
dataset = args[6]
uptobyear = args[7]

load(paste0(dataset, ".rdata"))

model_data = get(paste0(dataset, ".1")) %>% tbl_df %>% 
    filter(byear < uptobyear) %>%   
    filter(region == "Skelleftea") %>%
    select(children, birth_cohort, male, maternalage.factor, paternalage.mean, paternalage, paternal_loss, maternal_loss, older_siblings, nr.siblings, last_born, idParents) %>% 
    na.omit()

model = brm(    bf(
    children ~ paternalage + birth_cohort + male + maternalage.factor + paternalage.mean + paternal_loss + maternal_loss + older_siblings + nr.siblings + last_born + (1 | idParents), 
    hu ~ paternalage + birth_cohort + male + maternalage.factor + paternalage.mean + paternal_loss + maternal_loss + older_siblings + nr.siblings + last_born + (1 | idParents)
),
prior = c(set_prior("normal(0,5)", class = "b"),
                    set_prior("normal(0,5)", class = "b", nlpar = "hu"),
                    set_prior("student_t(3, 0, 5)", class = "sd")), 
family = hurdle_poisson(), data = model_data, 
chains = 6, iter = 800, warmup = 300, cores = 6, ranef = FALSE)

summary(model)

saveRDS(model,file = paste0("coefs/", dataset, "/r16_restrict_to_skelleftea.rds"))