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Fix bug preventing control_riskdiff(format) from being recognized #1434

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Merged
edelarua merged 1 commit into from
Aug 27, 2025
Merged

Fix bug preventing control_riskdiff(format) from being recognized #1434

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3 changes: 3 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
# tern 0.9.9.9001

### Bug Fixes
* Fixed bug in `tabulate_rsp_subgroups()` and `tabulate_survival_subgroups()` preventing risk difference column format specified via `control_riskdiff()` from being applied.

# tern 0.9.9

### Enhancements
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1 change: 1 addition & 0 deletions R/response_subgroups.R
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Expand Up @@ -312,6 +312,7 @@ tabulate_rsp_subgroups <- function(lyt,
colvars_or$vars <- c(colvars_or$vars, "riskdiff")
colvars_or$labels <- c(colvars_or$labels, riskdiff = riskdiff$col_label)
arm_cols <- paste(rep(c("n_rsp", "n_rsp", "n", "n")), c(riskdiff$arm_x, riskdiff$arm_y), sep = "_")
extra_args[[".formats"]] <- c(extra_args[[".formats"]], list(riskdiff = riskdiff$format))

df_prop_diff <- df$prop %>%
dplyr::select(-"prop") %>%
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1 change: 1 addition & 0 deletions R/survival_duration_subgroups.R
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Expand Up @@ -318,6 +318,7 @@ tabulate_survival_subgroups <- function(lyt,
colvars_hr$vars <- c(colvars_hr$vars, "riskdiff")
colvars_hr$labels <- c(colvars_hr$labels, riskdiff = riskdiff$col_label)
arm_cols <- paste(rep(c("n_events", "n_events", "n", "n")), c(riskdiff$arm_x, riskdiff$arm_y), sep = "_")
extra_args[[".formats"]] <- c(extra_args[[".formats"]], list(riskdiff = riskdiff$format))

df_prop_diff <- df$survtime %>%
dplyr::select(-"median") %>%
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22 changes: 11 additions & 11 deletions tests/testthat/_snaps/response_subgroups.md
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Expand Up @@ -279,15 +279,15 @@
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test) (95% CI)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164 -17.0 (-30.5 - -3.5)
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006 -32.2 (-48.8 - -15.6)
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852 1.6 (-19.7 - 22.8)
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801 -16.6 (-35.2 - 2.0)
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181 -16.7 (-36.6 - 3.3)
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test) (95% CI)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164 -17 (-31 - -4)
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006 -32 (-49 - -16)
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852 2 (-20 - 23)
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801 -17 (-35 - 2)
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181 -17 (-37 - 3)

24 changes: 12 additions & 12 deletions tests/testthat/_snaps/survival_duration_subgroups.md
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Expand Up @@ -265,16 +265,16 @@
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI (95% CI)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06) 14.3 (-0.5 - 29.1)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96) 14.3 (-5.7 - 34.4)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65) 14.3 (-7.6 - 36.1)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51) 29.8 (6.7 - 53.0)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61) -4.5 (-31.6 - 22.5)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36) 14.0 (-11.7 - 39.7)
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI (95% CI)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06) 14 (-0 - 29)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96) 14 (-6 - 34)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65) 14 (-8 - 36)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51) 30 (7 - 53)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61) -5 (-32 - 23)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36) 14 (-12 - 40)

3 changes: 2 additions & 1 deletion tests/testthat/test-response_subgroups.R
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Expand Up @@ -301,7 +301,8 @@ testthat::test_that("tabulate_rsp_subgroups riskdiff argument works as expected"
riskdiff = control_riskdiff(
arm_x = levels(df$prop$arm)[1],
arm_y = levels(df$prop$arm)[2],
col_label = "Prop. Diff\n(95% CI)"
col_label = "Prop. Diff\n(95% CI)",
format = "xx. (xx. - xx.)"
)
)

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3 changes: 2 additions & 1 deletion tests/testthat/test-survival_duration_subgroups.R
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Expand Up @@ -281,7 +281,8 @@ testthat::test_that("tabulate_survival_subgroups riskdiff argument works as expe
df,
time_unit = adtte$AVALU[1],
riskdiff = control_riskdiff(
col_label = "Prop. Diff\n(95% CI)"
col_label = "Prop. Diff\n(95% CI)",
format = "xx. (xx. - xx.)"
)
)

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