aspina7
commented
1 year ago hey @zkamvar - can I bug you for a sec? I managed to pull apart your two_by_two_functions so that they now work in gtsummary and for categorical variables too!
They are all now in tbl_univariate_stratified_internal.R (realise now I should probably rename this for clarity)...
tbl_cmh_internal()pulls all the bits together for stratified tableadd_crosstabs()returns the appropriate counts for a tbl_cmh or a gtsummary::tbl_uvregression.
None of the documentation is up to scratch just yet (sorry) - and the code is still very repeaty ineffecienty.... One thing that would make it all cleaner is if I could pass arguments to the gtsummary regression call (see comment above) but I cant get it to cooperate. Any chance you could take a quick peak please? Copying a dataframe below that can use to mess .... Thanks! Oh the brightside is that I can probably re-use most of the tests! And it also means we can retire most of our old table functions
linelist_cleaned <- tibble::tribble(
~DIED, ~fever_bin, ~age_group, ~obstime,
FALSE, FALSE, "45+", 4L,
TRUE, FALSE, "15-29", 12L,
TRUE, FALSE, "15-29", 20L,
TRUE, FALSE, "3-14", 16L,
FALSE, TRUE, "45+", 23L,
TRUE, FALSE, "30-44", 21L,
TRUE, TRUE, "15-29", 30L,
TRUE, TRUE, "45+", 30L,
FALSE, FALSE, "3-14", 13L,
FALSE, TRUE, "3-14", 27L,
TRUE, FALSE, "15-29", 6L,
FALSE, TRUE, "3-14", 19L,
FALSE, FALSE, "30-44", 10L,
FALSE, TRUE, "45+", 4L,
FALSE, TRUE, "45+", 18L,
FALSE, FALSE, "45+", 19L,
FALSE, TRUE, "45+", 21L,
FALSE, FALSE, "3-14", 27L,
FALSE, FALSE, "45+", 29L,
TRUE, FALSE, "30-44", 10L,
TRUE, TRUE, "15-29", 6L,
TRUE, FALSE, "30-44", 10L,
TRUE, FALSE, "15-29", 17L,
FALSE, FALSE, "15-29", 25L,
FALSE, TRUE, "45+", 25L,
TRUE, TRUE, "45+", 18L,
FALSE, TRUE, "15-29", 1L,
FALSE, TRUE, "15-29", 23L,
FALSE, FALSE, "45+", 8L,
FALSE, FALSE, "3-14", 28L,
FALSE, TRUE, "45+", 21L,
FALSE, FALSE, "15-29", 28L,
FALSE, TRUE, "0-2", 19L,
FALSE, TRUE, "45+", 11L,
FALSE, FALSE, "3-14", 25L,
FALSE, TRUE, "0-2", 26L,
FALSE, TRUE, "3-14", 15L,
FALSE, FALSE, "45+", 10L,
FALSE, TRUE, "3-14", 15L,
TRUE, FALSE, "15-29", 1L,
FALSE, TRUE, "15-29", 20L,
FALSE, TRUE, "15-29", 29L,
FALSE, TRUE, "3-14", 6L,
FALSE, TRUE, "30-44", 7L,
TRUE, FALSE, "30-44", 20L,
FALSE, FALSE, "45+", 21L,
FALSE, TRUE, "45+", 26L,
FALSE, TRUE, "30-44", 16L,
TRUE, FALSE, "30-44", 16L,
TRUE, TRUE, "3-14", 30L,
FALSE, FALSE, "15-29", 22L,
FALSE, FALSE, "15-29", 18L,
TRUE, FALSE, "45+", 14L,
TRUE, FALSE, "15-29", 25L,
TRUE, FALSE, "3-14", 9L,
FALSE, TRUE, "30-44", 15L,
FALSE, TRUE, "30-44", 8L,
FALSE, TRUE, "0-2", 1L,
TRUE, TRUE, "15-29", 20L,
FALSE, TRUE, "3-14", 8L,
FALSE, FALSE, "45+", 20L,
FALSE, TRUE, "15-29", 15L,
FALSE, TRUE, "30-44", 25L,
FALSE, FALSE, "15-29", 5L,
FALSE, FALSE, "3-14", 2L,
FALSE, FALSE, "0-2", 22L,
TRUE, FALSE, "3-14", 1L,
FALSE, FALSE, "45+", 3L,
FALSE, TRUE, "45+", 29L,
TRUE, TRUE, "45+", 12L,
TRUE, FALSE, "45+", 23L,
FALSE, FALSE, "15-29", 20L,
FALSE, TRUE, "45+", 3L,
FALSE, TRUE, "45+", 14L,
FALSE, TRUE, "15-29", 10L,
FALSE, FALSE, "45+", 16L,
FALSE, TRUE, "15-29", 3L,
TRUE, FALSE, "45+", 9L,
FALSE, TRUE, "45+", 5L,
FALSE, TRUE, "15-29", 10L,
FALSE, TRUE, "45+", 20L,
FALSE, FALSE, "15-29", 1L,
FALSE, FALSE, "30-44", 10L,
TRUE, TRUE, "15-29", 18L,
FALSE, TRUE, "15-29", 20L,
FALSE, FALSE, "0-2", 25L,
FALSE, FALSE, "45+", 14L,
FALSE, TRUE, "45+", 16L,
FALSE, FALSE, "3-14", 27L,
FALSE, FALSE, "45+", 15L,
TRUE, FALSE, "3-14", 25L,
TRUE, FALSE, "15-29", 1L,
TRUE, TRUE, "0-2", 2L,
FALSE, FALSE, "0-2", 19L,
FALSE, TRUE, "15-29", 15L,
FALSE, TRUE, "30-44", 18L,
FALSE, TRUE, "45+", 18L,
TRUE, TRUE, "45+", 16L,
FALSE, FALSE, "15-29", 18L,
FALSE, FALSE, "0-2", 6L,
FALSE, TRUE, "30-44", 12L,
FALSE, FALSE, "3-14", 29L,
FALSE, FALSE, "15-29", 1L,
FALSE, FALSE, "30-44", 16L,
FALSE, FALSE, "0-2", 30L,
TRUE, TRUE, "30-44", 23L,
TRUE, TRUE, "15-29", 12L,
TRUE, FALSE, "45+", 24L,
FALSE, FALSE, "45+", 7L,
FALSE, TRUE, "30-44", 28L,
TRUE, FALSE, "30-44", 9L,
FALSE, TRUE, "30-44", 8L,
FALSE, TRUE, "45+", 14L,
FALSE, FALSE, "45+", 25L,
FALSE, TRUE, "30-44", 9L,
TRUE, FALSE, "30-44", 26L,
FALSE, FALSE, "45+", 8L,
FALSE, FALSE, "15-29", 8L,
TRUE, FALSE, "45+", 18L,
TRUE, FALSE, "15-29", 8L,
FALSE, FALSE, "3-14", 23L,
TRUE, FALSE, "3-14", 19L,
FALSE, TRUE, "15-29", 1L,
FALSE, FALSE, "0-2", 17L,
FALSE, TRUE, "3-14", 2L,
FALSE, TRUE, "3-14", 18L,
FALSE, FALSE, "3-14", 8L,
FALSE, TRUE, "30-44", 19L,
TRUE, TRUE, "0-2", 6L,
FALSE, TRUE, "30-44", 13L,
TRUE, TRUE, "15-29", 16L,
FALSE, FALSE, "0-2", 25L,
FALSE, TRUE, "3-14", 28L,
TRUE, FALSE, "15-29", 12L,
FALSE, FALSE, "45+", 24L,
FALSE, FALSE, "3-14", 3L,
TRUE, FALSE, "45+", 5L,
FALSE, FALSE, "45+", 15L,
FALSE, FALSE, "45+", 3L,
FALSE, FALSE, "15-29", 20L,
FALSE, FALSE, "15-29", 23L,
FALSE, TRUE, "30-44", 1L,
TRUE, FALSE, "45+", 12L,
TRUE, TRUE, "15-29", 13L,
TRUE, TRUE, "3-14", 21L,
FALSE, FALSE, "45+", 22L,
TRUE, FALSE, "0-2", 23L,
TRUE, TRUE, "45+", 12L,
FALSE, TRUE, "15-29", 16L,
FALSE, TRUE, "3-14", 24L,
TRUE, FALSE, "30-44", 15L,
FALSE, TRUE, "15-29", 4L,
TRUE, TRUE, "45+", 11L,
FALSE, TRUE, "15-29", 16L,
FALSE, TRUE, "45+", 6L,
FALSE, TRUE, "15-29", 17L,
FALSE, TRUE, "45+", 10L,
FALSE, FALSE, "45+", 11L,
FALSE, FALSE, "30-44", 6L,
TRUE, TRUE, "30-44", 7L,
TRUE, FALSE, "45+", 8L,
TRUE, FALSE, "30-44", 29L,
FALSE, FALSE, "45+", 29L,
TRUE, TRUE, "45+", 22L,
TRUE, FALSE, "0-2", 18L,
TRUE, TRUE, "45+", 2L,
FALSE, TRUE, "30-44", 12L,
FALSE, FALSE, "45+", 17L,
FALSE, TRUE, "45+", 25L,
FALSE, FALSE, "15-29", 5L,
FALSE, TRUE, "3-14", 25L,
FALSE, TRUE, "30-44", 29L,
FALSE, TRUE, "30-44", 27L,
FALSE, TRUE, "3-14", 27L,
FALSE, FALSE, "45+", 12L,
TRUE, TRUE, "45+", 1L,
TRUE, TRUE, "3-14", 30L,
FALSE, TRUE, "15-29", 25L,
FALSE, FALSE, "3-14", 11L,
TRUE, FALSE, "15-29", 13L,
FALSE, TRUE, "45+", 24L,
FALSE, FALSE, "15-29", 5L,
FALSE, TRUE, "3-14", 24L,
FALSE, FALSE, "30-44", 8L,
FALSE, FALSE, "3-14", 11L,
FALSE, TRUE, "15-29", 17L,
FALSE, FALSE, "15-29", 17L,
TRUE, TRUE, "30-44", 11L,
FALSE, FALSE, "45+", 20L,
FALSE, TRUE, "0-2", 11L,
TRUE, TRUE, "3-14", 9L,
FALSE, TRUE, "0-2", 7L,
TRUE, TRUE, "45+", 7L,
TRUE, FALSE, "45+", 19L,
TRUE, FALSE, "30-44", 25L,
FALSE, FALSE, "15-29", 3L,
FALSE, FALSE, "3-14", 24L,
FALSE, TRUE, "45+", 29L,
FALSE, FALSE, "15-29", 29L,
TRUE, FALSE, "30-44", 13L,
FALSE, FALSE, "3-14", 15L,
FALSE, FALSE, "15-29", 7L,
TRUE, TRUE, "45+", 23L,
TRUE, TRUE, "3-14", 1L,
FALSE, FALSE, "0-2", 27L,
TRUE, FALSE, "0-2", 20L,
FALSE, TRUE, "15-29", 22L,
TRUE, TRUE, "45+", 7L,
FALSE, TRUE, "30-44", 15L,
FALSE, FALSE, "0-2", 15L,
FALSE, FALSE, "15-29", 29L,
TRUE, FALSE, "45+", 21L,
FALSE, TRUE, "3-14", 1L
)
el_tablo <- tbl_cmh_internal(linelist_cleaned,
DIED,
fever_bin,
age_group,
measure = "OR")
add_crosstabs(el_tablo)
starting a new function for adding cross tabulations to a gtsummary tbl_uvregression