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update rate01 test #174

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Dec 3, 2024
Merged

update rate01 test #174

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67b5828
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shajoezhu Nov 28, 2024
c98d57c
update
shajoezhu Nov 29, 2024
cfed3ee
test
shajoezhu Nov 29, 2024
7ba8d63
update
shajoezhu Nov 29, 2024
e4f82fd
test not using remotes for pak
shajoezhu Nov 29, 2024
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1 change: 0 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,6 @@ Suggests:
VignetteBuilder:
knitr
Remotes:
insightsengineering/tern@main,
pharmaverse/pharmaverseadam@main
biocViews:
Config/Needs/website: insightsengineering/nesttemplate
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70 changes: 42 additions & 28 deletions tests/testthat/_snaps/table_ratet01.md
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Expand Up @@ -3,32 +3,46 @@
Code
res
Output
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————————
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 2.7374 2.8150 2.9789
Rate CI (2.3932, 3.1311) (2.4681, 3.2106) (2.6152, 3.3932)
Rate Ratio 1.0283 1.0882
Rate Ratio CI (0.8856, 1.1941) (0.9381, 1.2624)
p-value 0.7140 0.2643
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
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) with offset
Rate 7.2364 8.2148 9.8131
Unadjusted exacerbation rate (per year)
Rate 2.7761 2.8433 2.9848
Adjusted (QP) exacerbation rate (per year) with offset
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 (QP) exacerbation rate (per year)
Rate 2.7380 2.8161 2.9771
Rate CI (2.3920, 3.1339) (2.4676, 3.2137) (2.6125, 3.3926)
Rate Ratio 1.0285 1.0873
Rate Ratio CI (0.8849, 1.1954) (0.9366, 1.2624)
p-value 0.7140 0.2714
Adjusted (NB) exacerbation rate (per year) with offset
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
Adjusted (NB) exacerbation rate (per year)
Rate 2.7374 2.8150 2.9789
Rate CI (2.3932, 3.1311) (2.4681, 3.2106) (2.6152, 3.3932)
Rate Ratio 1.0283 1.0882
Rate Ratio CI (0.8856, 1.1941) (0.9381, 1.2624)
p-value 0.7140 0.2643

39 changes: 39 additions & 0 deletions tests/testthat/test-table_ratet01.R
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Expand Up @@ -23,6 +23,17 @@ testthat::test_that("RATET01 is produced correctly", {
conf_level = 0.95,
distribution = "poisson",
rate_mean_method = "emmeans",
var_labels = "Unadjusted exacerbation rate (per year) with offset",
table_names = "unadj-offest",
.stats = c("rate"),
.labels = c(rate = "Rate")
) %>%
summarize_glm_count(
vars = "AVAL",
variables = list(arm = "ARM", 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"),
Expand All @@ -34,6 +45,20 @@ testthat::test_that("RATET01 is produced correctly", {
conf_level = 0.95,
distribution = "quasipoisson",
rate_mean_method = "ppmeans",
var_labels = "Adjusted (QP) exacerbation rate (per year) with offset",
table_names = "adj-qp-offest",
.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", covariates = c("REGION1")),
conf_level = 0.95,
distribution = "quasipoisson",
rate_mean_method = "emmeans",
var_labels = "Adjusted (QP) exacerbation rate (per year)",
table_names = "adj-qp",
.stats = c("rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
Expand All @@ -48,6 +73,20 @@ testthat::test_that("RATET01 is produced correctly", {
conf_level = 0.95,
distribution = "negbin",
rate_mean_method = "emmeans",
var_labels = "Adjusted (NB) exacerbation rate (per year) with offset",
table_names = "adj-nb-offest",
.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", 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"),
Expand Down
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