Processing of Strata without Events
Source:vignettes/ep_spec_strata_w_events.Rmd
ep_spec_strata_w_events.RmdOverview
The only_strata_with_events endpoint parameter specifies
whether the output data will include all strata levels or only those
levels that contain events. By default, all levels will be included in
the endpoint
Note: If there is a minimum of one event present in any treatment arm within a specific strata level, that level will be incorporated into the endpoint for all treatment arms regardsless of whether one of the treatment arms has no events in that stratum.
This functionality is useful in cases where the endpoint
specification contains groups and strata that result in many 100s or
1000s of combinations and where only the combinations with events are of
interest. In this case only_strata_with_events can be set
to TRUE to remove the irrelevant combinations and save
computation time.
Examples
Ex 7.1
Let us consider the following endpoint specification, where
mk_adae is defined as in the Quick
Start, and grouping is performed on SOC (System Organ Class) and
stratification is performed on race. By default, all strata levels are
included, i.e. only_strata_with_events = FALSE.
ep_spec_ex7_1 <- chef::mk_endpoint_str(
data_prepare = mk_adae,
study_metadata = list(),
pop_var = "SAFFL",
pop_value = "Y",
custom_pop_filter = "TRT01A %in% c('Placebo', 'Xanomeline High Dose') & !is.na(AESOC)",
treatment_var = "TRT01A",
treatment_refval = "Xanomeline High Dose",
group_by = list(list(AESOC = c())),
stratify_by = list(c("RACE")),
stat_by_strata_by_trt = list(N = chefStats::n_subj, n = chefStats::n_subj_event),
endpoint_label = "AESOC: <AESOC>",
only_strata_with_events = FALSE
)In this setup we note:
-
TRT01Ahas 2 treatment arms in the analysis data due tocustom_pop_filter -
group_by:AESOChas 23 levels -
stratify_by:RACEhas 4 levels -
stat_by_strata_by_trt: 2 statistics per combination of group level and strata level
For each SOC this implies:
- Strata =
TOTAL: 2 treatment arms x 2 statistics = 4 combinations - Strata =
RACE: 2 treatment arms x 3 races x 2 statistics = 12 combinations
Thus we have 23 SOCs x (4 + 12) = 368 combinations, i.e. 368 rows in the output data.
Specifically, let us consider the SOC “Eye Disorder” and print the
the subset of the output data that covers that SOC (see below). As
expected 4 + 12 = 16 rows are provided. We also notice that two of the
strata levels for RACE has no event (n = 0),
which leads to the next example.
ep_stat[endpoint_label == "AESOC: EYE DISORDERS", c("stat_filter", "fn_name", "stat_result_value")]
#> stat_filter
#> <char>
#> 1: TOTAL_ == "total" & TRT01A == "Placebo"
#> 2: TOTAL_ == "total" & TRT01A == "Placebo"
#> 3: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
#> 4: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
#> 5: RACE == "WHITE" & TRT01A == "Placebo"
#> 6: RACE == "WHITE" & TRT01A == "Placebo"
#> 7: RACE == "BLACK OR AFRICAN AMERICAN" & TRT01A == "Placebo"
#> 8: RACE == "BLACK OR AFRICAN AMERICAN" & TRT01A == "Placebo"
#> 9: RACE == "AMERICAN INDIAN OR ALASKA NATIVE" & TRT01A == "Placebo"
#> 10: RACE == "AMERICAN INDIAN OR ALASKA NATIVE" & TRT01A == "Placebo"
#> 11: RACE == "WHITE" & TRT01A == "Xanomeline High Dose"
#> 12: RACE == "WHITE" & TRT01A == "Xanomeline High Dose"
#> 13: RACE == "BLACK OR AFRICAN AMERICAN" & TRT01A == "Xanomeline High Dose"
#> 14: RACE == "BLACK OR AFRICAN AMERICAN" & TRT01A == "Xanomeline High Dose"
#> 15: RACE == "AMERICAN INDIAN OR ALASKA NATIVE" & TRT01A == "Xanomeline High Dose"
#> 16: RACE == "AMERICAN INDIAN OR ALASKA NATIVE" & TRT01A == "Xanomeline High Dose"
#> fn_name stat_result_value
#> <char> <num>
#> 1: N 69
#> 2: n 4
#> 3: N 70
#> 4: n 1
#> 5: N 63
#> 6: n 4
#> 7: N 6
#> 8: n 0
#> 9: N 0
#> 10: n 0
#> 11: N 61
#> 12: n 1
#> 13: N 8
#> 14: n 0
#> 15: N 1
#> 16: n 0Ex 7.2
Suppose that we are only interested in the combinations of group
levels and strata levels in example 7.1 that have events. To accomplish
this we may specify only_strata_with_events = TRUE.
ep_spec_ex7_2 <- chef::mk_endpoint_str(
data_prepare = mk_adae,
study_metadata = list(),
pop_var = "SAFFL",
pop_value = "Y",
custom_pop_filter = "TRT01A %in% c('Placebo', 'Xanomeline High Dose') & !is.na(AESOC)",
treatment_var = "TRT01A",
treatment_refval = "Xanomeline High Dose",
group_by = list(list(AESOC = c())),
stratify_by = list(c("RACE")),
stat_by_strata_by_trt = list(N = chefStats::n_subj, n = chefStats::n_subj_event),
endpoint_label = "AESOC: <AESOC>",
only_strata_with_events = TRUE
)Now the number of combination in the output has been reduced to 256.
Let us revisit the SOC “Eye Disorder” and print all rows in the
output that relate to that SOC (see below). We notice that 2 strata
levels for RACE are not present anymore (“BLACK OR AFRICAN
AMERICAN”, “AMERICAN INDIAN OR ALASKA NATIVE”) since they have no events
c.f. example 7.1., which effectively reduces the number of
rows/combinations to 8 for this SOC.
ep_stat[endpoint_label == "AESOC: EYE DISORDERS", c("stat_filter", "fn_name", "stat_result_value")]
#> stat_filter fn_name
#> <char> <char>
#> 1: TOTAL_ == "total" & TRT01A == "Placebo" N
#> 2: TOTAL_ == "total" & TRT01A == "Placebo" n
#> 3: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose" N
#> 4: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose" n
#> 5: RACE == "WHITE" & TRT01A == "Placebo" N
#> 6: RACE == "WHITE" & TRT01A == "Placebo" n
#> 7: RACE == "WHITE" & TRT01A == "Xanomeline High Dose" N
#> 8: RACE == "WHITE" & TRT01A == "Xanomeline High Dose" n
#> stat_result_value
#> <num>
#> 1: 69
#> 2: 4
#> 3: 70
#> 4: 1
#> 5: 63
#> 6: 4
#> 7: 61
#> 8: 1Similarly, the number of combinations for many of the other 22 SOCs are also less than the full 16 combinations:
table(ep_stat$endpoint_label)
#>
#> AESOC: CARDIAC DISORDERS
#> 12
#> AESOC: CONGENITAL, FAMILIAL AND GENETIC DISORDERS
#> 12
#> AESOC: EAR AND LABYRINTH DISORDERS
#> 12
#> AESOC: EYE DISORDERS
#> 8
#> AESOC: GASTROINTESTINAL DISORDERS
#> 16
#> AESOC: GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS
#> 12
#> AESOC: HEPATOBILIARY DISORDERS
#> 8
#> AESOC: IMMUNE SYSTEM DISORDERS
#> 8
#> AESOC: INFECTIONS AND INFESTATIONS
#> 12
#> AESOC: INJURY, POISONING AND PROCEDURAL COMPLICATIONS
#> 12
#> AESOC: INVESTIGATIONS
#> 8
#> AESOC: METABOLISM AND NUTRITION DISORDERS
#> 12
#> AESOC: MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS
#> 12
#> AESOC: NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)
#> 8
#> AESOC: NERVOUS SYSTEM DISORDERS
#> 16
#> AESOC: PSYCHIATRIC DISORDERS
#> 12
#> AESOC: RENAL AND URINARY DISORDERS
#> 8
#> AESOC: REPRODUCTIVE SYSTEM AND BREAST DISORDERS
#> 8
#> AESOC: RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS
#> 16
#> AESOC: SKIN AND SUBCUTANEOUS TISSUE DISORDERS
#> 16
#> AESOC: SOCIAL CIRCUMSTANCES
#> 8
#> AESOC: SURGICAL AND MEDICAL PROCEDURES
#> 12
#> AESOC: VASCULAR DISORDERS
#> 8