edelarua
commented
2 months ago Example with similar structure to AET02_PTYR created using refactored function:
library(tern)
adsl <- random.cdisc.data::cadsl %>% df_explicit_na()
adaette <- random.cdisc.data::cadaette %>% df_explicit_na()
anl <- adaette %>%
dplyr::filter(PARAM == "Time to first occurrence of any adverse event") %>%
dplyr::mutate(n_events = 1 - CNSR)
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
estimate_incidence_rate(
vars = "AVAL",
n_events = "n_events",
.stats = c("person_years", "n_events", "rate")
) %>%
split_rows_by("SEX", child_labels = "visible") %>%
estimate_incidence_rate(
vars = "AVAL",
n_events = "n_events",
.stats = c("n_unique", "n_rate"),
summarize = TRUE,
label_fmt = "%.labels"
) %>%
split_rows_by("STRATA1") %>%
estimate_incidence_rate(
vars = "AVAL",
n_events = "n_events",
.stats = "n_rate",
summarize = TRUE,
label_fmt = "%s"
)
result <- lyt %>% build_table(anl, alt_counts_df = adsl)
result A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total patient-years at risk 162.4 103.9 172.6
Number of adverse events observed 78 104 67
AE rate per 100 patient-years 48.03 100.14 38.82
F
Total number of patients with at least one adverse event 45 63 36
Number of adverse events observed (AE rate per 100 patient-years) 45 (46.7) 63 (97.5) 36 (42.9)
A 12 (49.0) 18 (69.3) 9 (31.0)
B 15 (50.6) 23 (113.5) 14 (58.6)
C 18 (42.6) 22 (119.4) 13 (42.0)
M
Total number of patients with at least one adverse event 33 41 31
Number of adverse events observed (AE rate per 100 patient-years) 33 (50.0) 41 (104.6) 31 (35.0)
A 9 (40.4) 13 (83.6) 10 (33.7)
B 16 (80.4) 15 (165.6) 10 (34.4)
C 8 (33.6) 13 (89.0) 11 (36.8) 
github-actions[bot]
shajoezhu
Pull Request
Fixes #1299