transfer from old repo
This commit is contained in:
parent
cfa4a5f9cc
commit
277e2b8cf3
1111 changed files with 83736 additions and 0 deletions
172
2 Longterm/260315/last_sensitivity.R
Executable file
172
2 Longterm/260315/last_sensitivity.R
Executable file
|
|
@ -0,0 +1,172 @@
|
|||
targets::tar_read("df_all_data_formatted") |>
|
||||
events_ready() |>
|
||||
dplyr::filter(!is.na(pase_0), !is.na(pase_4)) |>
|
||||
(\(data){
|
||||
c("pase_0", "pase_4") |>
|
||||
purrr::map(\(exp){
|
||||
list(
|
||||
"Univariable" = cox_regression(data = data, all.vars = FALSE, use.strata = FALSE, outcome.var = exp),
|
||||
"Multivariable" = cox_regression(data = data, all.vars = TRUE, use.strata = FALSE, outcome.var = exp)
|
||||
) |>
|
||||
purrr::map(\(.x){
|
||||
.x |>
|
||||
gtsummary::tbl_regression(exponentiate = TRUE) |>
|
||||
fix_labels()
|
||||
}) |>
|
||||
tbl_merged_named()
|
||||
})
|
||||
})() |>
|
||||
gtsummary::tbl_stack()
|
||||
|
||||
|
||||
targets::tar_read("df_all_data_formatted") |>
|
||||
pase_cutter(drop.nas = TRUE) |>
|
||||
events_ready(v.groups = c("clin", "lifestyle.events", "ses", "assess.events", "quartiles")) |>
|
||||
dplyr::select(-dplyr::any_of(c("pase_0", "pase_4", "pase_change"))) |>
|
||||
(\(data){
|
||||
c("pase_0_quartile", "pase_4_quartile") |>
|
||||
purrr::map(\(exp){
|
||||
list(
|
||||
"Univariable" = cox_regression(data = data, all.vars = FALSE, use.strata = FALSE, outcome.var = exp),
|
||||
"Multivariable" = cox_regression(data = data, all.vars = TRUE, use.strata = FALSE, outcome.var = exp)
|
||||
) |>
|
||||
purrr::map(\(.x){
|
||||
.x |>
|
||||
gtsummary::tbl_regression(exponentiate = TRUE) |>
|
||||
fix_labels()
|
||||
}) |>
|
||||
tbl_merged_named()
|
||||
})
|
||||
})() |>
|
||||
gtsummary::tbl_stack()
|
||||
|
||||
|
||||
targets::tar_read("df_all_data_formatted") |>
|
||||
pase_cutter(drop.nas = TRUE) |>
|
||||
get_vars(vars.groups = c("clin", "lifestyle.events", "ses", "assess.events", "quartiles"), vars.vec = c("inc_time")) |>
|
||||
dplyr::mutate(time = time + inc_time / 365) |>
|
||||
dplyr::select(-dplyr::any_of(c("pase_0", "pase_4", "pase_change", "inc_time", "event.include", "pase_4_quartile"))) |>
|
||||
(\(data){
|
||||
list(
|
||||
"Univariable" = cox_regression(data = data, all.vars = FALSE, use.strata = FALSE, outcome.var = "pase_0_quartile"),
|
||||
"Multivariable" = cox_regression(data = data, all.vars = TRUE, use.strata = FALSE, outcome.var = "pase_0_quartile")
|
||||
) |>
|
||||
purrr::map(\(.x){
|
||||
.x |>
|
||||
gtsummary::tbl_regression(exponentiate = TRUE) |>
|
||||
fix_labels()
|
||||
}) |>
|
||||
tbl_merged_named()
|
||||
})()
|
||||
|
||||
ls_sens <- list(
|
||||
pase_0_all_quartile = list(
|
||||
data = targets::tar_read("df_all_data_formatted") |>
|
||||
pase_cutter(drop.nas = FALSE) |>
|
||||
get_vars(vars.groups = c("clin", "lifestyle.events", "ses", "assess.pred", "quartiles"), vars.vec = c("inc_time",
|
||||
"time",
|
||||
"status")) |>
|
||||
dplyr::mutate(time = time + inc_time / 365) |>
|
||||
dplyr::select(-dplyr::any_of(c("pase_0", "pase_4", "pase_change", "inc_time", "event.include", "pase_4_quartile"))),
|
||||
main.exp = "pase_0_quartile"
|
||||
),
|
||||
# pase_0_all_contin = list(
|
||||
# data = targets::tar_read("df_all_data_formatted") |>
|
||||
# get_vars(vars.groups = c("clin", "lifestyle.events", "ses", "assess.pred", "quartiles"), vars.vec = c("inc_time",
|
||||
# "time",
|
||||
# "status")) |>
|
||||
# dplyr::mutate(time = time + inc_time / 365) |>
|
||||
# dplyr::select(-dplyr::any_of(c("pase_4", "pase_change", "inc_time", "event.include", "pase_0_quartile", "pase_4_quartile"))),
|
||||
# main.exp = "pase_0"
|
||||
# ),
|
||||
pase_0_excl_quartile = list(
|
||||
data = targets::tar_read("df_all_data_formatted") |>
|
||||
pase_cutter(drop.nas = TRUE,drop.pase = FALSE) |>
|
||||
events_ready(v.groups = c("clin", "lifestyle.events", "ses", "assess.pred", "quartiles"), vars.vec = c("inc_time",
|
||||
"time",
|
||||
"status")) |>
|
||||
dplyr::select(-dplyr::any_of(c("pase_0","pase_4", "pase_change", "inc_time", "event.include", "pase_4_quartile"))),
|
||||
main.exp = "pase_0_quartile"
|
||||
),
|
||||
# pase_0_excl_contin = list(
|
||||
# data = targets::tar_read("df_all_data_formatted") |>
|
||||
# events_ready(v.groups = c("clin", "lifestyle.events", "ses", "assess.pred", "quartiles"), vars.vec = c("inc_time",
|
||||
# "time",
|
||||
# "status")) |>
|
||||
# dplyr::filter(!is.na(pase_0), !is.na(pase_4)) |>
|
||||
# dplyr::select(-pase_4),
|
||||
# main.exp = "pase_0"
|
||||
# ),
|
||||
pase_4_quartile = list(
|
||||
data = targets::tar_read("df_all_data_formatted") |>
|
||||
dplyr::mutate(pase_4_quartile=cut(x = pase_4, breaks = quantile(pase_4, na.rm = TRUE), labels = 1:4, include.lowest = TRUE)) |>
|
||||
get_vars(vars.groups = c("clin", "lifestyle.events", "ses", "assess.events", "quartiles"))|>
|
||||
dplyr::filter(!is.na(pase_4_quartile),event.include) |>
|
||||
dplyr::select(-dplyr::any_of(c("pase_0","pase_4", "pase_change", "inc_time", "event.include", "pase_0_quartile"))),
|
||||
main.exp = "pase_4_quartile"
|
||||
),
|
||||
# pase_4_contin = list(
|
||||
# data = targets::tar_read("df_all_data_formatted") |>
|
||||
# events_ready() |>
|
||||
# dplyr::filter(!is.na(pase_0), !is.na(pase_4)) |>
|
||||
# dplyr::select(-pase_0),
|
||||
# main.exp = "pase_4"
|
||||
# ),
|
||||
pase_4_change_late_cut = list(
|
||||
data = targets::tar_read("df_all_data_formatted") |>
|
||||
events_ready() |>
|
||||
dplyr::filter(!is.na(pase_0), !is.na(pase_4)) |>
|
||||
pase_cutter(drop.pase = TRUE),
|
||||
main.exp = "pase_change"
|
||||
# ),
|
||||
# pase_4_change_earliest_cut = list(
|
||||
# data = targets::tar_read("df_all_data_formatted") |>
|
||||
# pase_cutter(drop.pase = TRUE)|>
|
||||
# events_ready(vars.vec = c("pase_change")) |>
|
||||
# dplyr::filter(!is.na(pase_change)) ,
|
||||
# main.exp = "pase_change"
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
|
||||
f <- function(data, main.exp, ...) {
|
||||
set.seed(3023)
|
||||
imp <- fun_impute(data = data, ignore = main.exp)
|
||||
|
||||
list(
|
||||
"Univariable" = cox_regression(data = data, all.vars = FALSE, use.strata = FALSE, outcome.var = main.exp),
|
||||
"Multivariable" = cox_regression(data = data, all.vars = TRUE, use.strata = FALSE, outcome.var = main.exp),
|
||||
"Multivariable Imputed" = cox_regression(data = imp, all.vars = TRUE, use.strata = FALSE, outcome.var = main.exp)
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
ls_out <- purrr::map(ls_sens, \(.x){
|
||||
do.call(f, .x)
|
||||
})
|
||||
|
||||
ls_stack <- ls_out |>
|
||||
purrr::imap(\(.x, .i){
|
||||
list(
|
||||
"Group counts" = ls_sens[[.i]][["data"]] |>
|
||||
dplyr::select(ls_sens[[.i]][["main.exp"]]) |>
|
||||
gtsummary::tbl_summary(statistic = list(gtsummary::all_continuous() ~ "{N_nonmiss} ({p_nonmiss}%)", gtsummary::all_categorical() ~ "{n} ({p}%)")) |>
|
||||
fix_labels(),
|
||||
.x |>
|
||||
lapply(\(.y){
|
||||
.y |>
|
||||
tbl_regression_standard() |>
|
||||
# gtsummary::modify_table_styling(columns = tidyselect::starts_with("p.value"), hide = TRUE) |>
|
||||
gtsummary::remove_row_type(variables = -dplyr::any_of(ls_sens[[.i]][["main.exp"]]), type = "all") |>
|
||||
gtsummary::bold_p()
|
||||
})
|
||||
) |>
|
||||
purrr::list_flatten() |>
|
||||
tbl_merged_named()
|
||||
}) |>
|
||||
tbl_stack_named()
|
||||
|
||||
ls_stack <- ls_stack|> gtsummary::as_gt() |> gt::tab_style(style = gt::cell_text(weight="bold"),locations = gt::cells_row_groups(dplyr::everything()))
|
||||
|
||||
ls_stack |> gt::gtsave(filename = here::here("out/pase_extra_cox2.docx"))
|
||||
Loading…
Reference in a new issue