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‎tests/testthat/_snaps/table_ratet01.md

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Original file line numberDiff line numberDiff line change
@@ -3,32 +3,46 @@
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Code
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res
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Output
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B: Placebo A: Drug X C: Combination
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(N=134) (N=134) (N=132)
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———————————————————————————————————————————————————————————————————————————————————————————————————
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Number of exacerbations per patient
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0 10 (7.46%) 6 (4.48%) 11 (8.33%)
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1 25 (18.66%) 21 (15.67%) 14 (10.61%)
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2 38 (28.36%) 41 (30.60%) 33 (25.00%)
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3 22 (16.42%) 26 (19.40%) 21 (15.91%)
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4 13 (9.70%) 18 (13.43%) 30 (22.73%)
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5 11 (8.21%) 10 (7.46%) 12 (9.09%)
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6 10 (7.46%) 7 (5.22%) 7 (5.30%)
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7 3 (2.24%) 4 (2.99%) 3 (2.27%)
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8 1 (0.75%) 1 (0.75%) 1 (0.76%)
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9 1 (0.75%) 0 (0.00%) 0 (0.00%)
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Unadjusted exacerbation rate (per year)
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Rate 7.2364 8.2148 9.8131
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Adjusted (QP) exacerbation rate (per year)
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Rate 2.4550 2.8514 3.4304
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Rate CI (1.6194, 3.7219) (1.8974, 4.2850) (2.2946, 5.1284)
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Rate Ratio 1.1615 1.3973
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Rate Ratio CI (0.6462, 2.0877) (0.7789, 2.5067)
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p-value 0.6169 0.2619
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Adjusted (NB) exacerbation rate (per year)
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Rate 2.7374 2.8150 2.9789
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Rate CI (2.3932, 3.1311) (2.4681, 3.2106) (2.6152, 3.3932)
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Rate Ratio 1.0283 1.0882
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Rate Ratio CI (0.8856, 1.1941) (0.9381, 1.2624)
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p-value 0.7140 0.2643
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B: Placebo A: Drug X C: Combination
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(N=134) (N=134) (N=132)
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—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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Number of exacerbations per patient
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0 10 (7.46%) 6 (4.48%) 11 (8.33%)
11+
1 25 (18.66%) 21 (15.67%) 14 (10.61%)
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2 38 (28.36%) 41 (30.60%) 33 (25.00%)
13+
3 22 (16.42%) 26 (19.40%) 21 (15.91%)
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4 13 (9.70%) 18 (13.43%) 30 (22.73%)
15+
5 11 (8.21%) 10 (7.46%) 12 (9.09%)
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6 10 (7.46%) 7 (5.22%) 7 (5.30%)
17+
7 3 (2.24%) 4 (2.99%) 3 (2.27%)
18+
8 1 (0.75%) 1 (0.75%) 1 (0.76%)
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9 1 (0.75%) 0 (0.00%) 0 (0.00%)
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Unadjusted exacerbation rate (per year) with offset
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Rate 7.2364 8.2148 9.8131
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Unadjusted exacerbation rate (per year)
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Rate 2.7761 2.8433 2.9848
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Adjusted (QP) exacerbation rate (per year) with offset
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Rate 2.4550 2.8514 3.4304
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Rate CI (1.6194, 3.7219) (1.8974, 4.2850) (2.2946, 5.1284)
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Rate Ratio 1.1615 1.3973
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Rate Ratio CI (0.6462, 2.0877) (0.7789, 2.5067)
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p-value 0.6169 0.2619
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Adjusted (QP) exacerbation rate (per year)
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Rate 2.7380 2.8161 2.9771
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Rate CI (2.3920, 3.1339) (2.4676, 3.2137) (2.6125, 3.3926)
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Rate Ratio 1.0285 1.0873
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Rate Ratio CI (0.8849, 1.1954) (0.9366, 1.2624)
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p-value 0.7140 0.2714
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Adjusted (NB) exacerbation rate (per year) with offset
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Rate 18.4450 28.0582 23.9304
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Rate CI (13.9015, 24.4736) (21.3288, 36.9108) (18.1382, 31.5722)
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Rate Ratio 1.5212 1.2974
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Rate Ratio CI (1.1166, 2.0724) (0.9505, 1.7708)
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p-value 0.0078 0.1009
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Adjusted (NB) exacerbation rate (per year)
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Rate 2.7374 2.8150 2.9789
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Rate CI (2.3932, 3.1311) (2.4681, 3.2106) (2.6152, 3.3932)
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Rate Ratio 1.0283 1.0882
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Rate Ratio CI (0.8856, 1.1941) (0.9381, 1.2624)
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p-value 0.7140 0.2643
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‎tests/testthat/test-table_ratet01.R

Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,17 @@ testthat::test_that("RATET01 is produced correctly", {
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conf_level = 0.95,
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distribution = "poisson",
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rate_mean_method = "emmeans",
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var_labels = "Unadjusted exacerbation rate (per year) with offset",
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table_names = "unadj-offest",
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.stats = c("rate"),
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.labels = c(rate = "Rate")
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) %>%
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summarize_glm_count(
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vars = "AVAL",
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variables = list(arm = "ARM", covariates = NULL),
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conf_level = 0.95,
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distribution = "poisson",
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rate_mean_method = "emmeans",
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var_labels = "Unadjusted exacerbation rate (per year)",
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table_names = "unadj",
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.stats = c("rate"),
@@ -34,6 +45,20 @@ testthat::test_that("RATET01 is produced correctly", {
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conf_level = 0.95,
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distribution = "quasipoisson",
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rate_mean_method = "ppmeans",
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var_labels = "Adjusted (QP) exacerbation rate (per year) with offset",
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table_names = "adj-qp-offest",
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.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
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.labels = c(
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rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
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rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
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)
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) %>%
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summarize_glm_count(
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vars = "AVAL",
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variables = list(arm = "ARM", covariates = c("REGION1")),
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conf_level = 0.95,
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distribution = "quasipoisson",
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rate_mean_method = "emmeans",
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var_labels = "Adjusted (QP) exacerbation rate (per year)",
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table_names = "adj-qp",
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.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
@@ -48,6 +73,20 @@ testthat::test_that("RATET01 is produced correctly", {
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conf_level = 0.95,
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distribution = "negbin",
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rate_mean_method = "emmeans",
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var_labels = "Adjusted (NB) exacerbation rate (per year) with offset",
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table_names = "adj-nb-offest",
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.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
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.labels = c(
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rate = "Rate", rate_ci = "Rate CI", rate_ratio = "Rate Ratio",
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rate_ratio_ci = "Rate Ratio CI", pval = "p-value"
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)
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) %>%
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summarize_glm_count(
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vars = "AVAL",
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variables = list(arm = "ARM", covariates = c("REGION1")),
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conf_level = 0.95,
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distribution = "negbin",
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rate_mean_method = "emmeans",
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var_labels = "Adjusted (NB) exacerbation rate (per year)",
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table_names = "adj-nb",
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.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),

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