Code
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM", ref_group = "B: Placebo", split_fun = ref_group_position("first")) %>%
analyze_vars(
"AVAL_f",
var_labels = "Number of exacerbations per patient",
.stats = c("count_fraction"),
.formats = c("count_fraction" = "xx (xx.xx%)"),
.labels = c("Number of exacerbations per patient")
) %>%
summarize_glm_count(
vars = "AVAL",
variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = NULL),
conf_level = 0.95,
distribution = "poisson",
rate_mean_method = "emmeans",
var_labels = "Unadjusted exacerbation rate (per year)",
table_names = "unadj",
.stats = c("rate"),
.labels = c(rate = "Rate")
) %>%
summarize_glm_count(
vars = "AVAL",
variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = c("REGION1")),
conf_level = 0.95,
distribution = "quasipoisson",
rate_mean_method = "ppmeans",
var_labels = "Adjusted (QP) exacerbation rate (per year)",
table_names = "adj-qp",
.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
.labels = c(
rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
)
) %>%
summarize_glm_count(
vars = "AVAL",
variables = list(arm = "ARM", offset = "lgTMATRSK", covariates = c("REGION1")),
conf_level = 0.95,
distribution = "negbin",
rate_mean_method = "emmeans",
var_labels = "Adjusted (NB) exacerbation rate (per year)",
table_names = "adj-nb",
.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
.labels = c(
rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
)
)
result <- build_table(
lyt = lyt,
df = anl
)
result B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
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Number of exacerbations per patient
0 10 (7.46%) 6 (4.48%) 11 (8.33%)
1 25 (18.66%) 21 (15.67%) 14 (10.61%)
2 38 (28.36%) 41 (30.60%) 33 (25.00%)
3 22 (16.42%) 26 (19.40%) 21 (15.91%)
4 13 (9.70%) 18 (13.43%) 30 (22.73%)
5 11 (8.21%) 10 (7.46%) 12 (9.09%)
6 10 (7.46%) 7 (5.22%) 7 (5.30%)
7 3 (2.24%) 4 (2.99%) 3 (2.27%)
8 1 (0.75%) 1 (0.75%) 1 (0.76%)
9 1 (0.75%) 0 (0.00%) 0 (0.00%)
Unadjusted exacerbation rate (per year)
Rate 7.2364 8.2148 9.8131
Adjusted (QP) exacerbation rate (per year)
Rate 2.4550 2.8514 3.4304
Rate CI (1.6194, 3.7219) (1.8974, 4.2850) (2.2946, 5.1284)
Rate Ratio 1.1615 1.3973
Rate Ratio CI (0.6462, 2.0877) (0.7789, 2.5067)
p-value 0.6169 0.2619
Adjusted (NB) exacerbation rate (per year)
Rate 18.4450 28.0582 23.9304
Rate CI (13.9015, 24.4736) (21.3288, 36.9108) (18.1382, 31.5722)
Rate Ratio 1.5212 1.2974
Rate Ratio CI (1.1166, 2.0724) (0.9505, 1.7708)
p-value 0.0078 0.1009