Cleanup gtcrosstabs #31
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aspina7
commented
Apr 17, 2023
| y = {{case}}, | ||
| include = {{exposure}}, | ||
| method.args = list(family = poisson, | ||
| offset = log({{obstime}})), |
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chucking an error with {{obstime}} - cant figure out how to just feed all of this in to method.args clean - this would allow to specify up top and only need one call to gtsummary::tbl_uvregression
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note to self: create a temp var which is log ostime, then can just pass all as a char!
|
hey @zkamvar - can I bug you for a sec? They are all now in tbl_univariate_stratified_internal.R (realise now I should probably rename this for clarity)...
None of the documentation is up to scratch just yet (sorry) - and the code is still very repeaty ineffecienty.... 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) |
|
sorry @aspina7, I had missed this when you tagged me TWO YEARS ago 😭. If it's any consolation, I was in the final stretch for an end of a project for my old job (https://carpentries.org/blog/2023/04/dovetail-17/) and was planning to come back to this, but then my workload tripled unexpectedly.... |
|
haha no worries at all @zkamvar - a valid consolation! Have got it all working - just gonna remove mess, add tests and then will get one of the guys to clean up the grittier code bits later .... least it works |
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I also dont get how its been two years .... feel like the grey men have been at my time again |
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starting a new function for adding cross tabulations to a gtsummary tbl_uvregression