diff --git a/R/analyze_variables.R b/R/analyze_variables.R index d54aa0bac0..b2dccab158 100644 --- a/R/analyze_variables.R +++ b/R/analyze_variables.R @@ -188,8 +188,8 @@ s_summary.numeric <- function(x, mean_sdi <- y$mean[[1]] + c(-1, 1) * stats::sd(x, na.rm = FALSE) names(mean_sdi) <- c("mean_sdi_lwr", "mean_sdi_upr") y$mean_sdi <- formatters::with_label(mean_sdi, "Mean -/+ 1xSD") - mean_long <- c(y$mean, y$mean_ci) - y$mean_long <- formatters::with_label(mean_long, paste0("Mean (", f_conf_level(control$conf_level), ")")) + mean_ci_3d <- c(y$mean, y$mean_ci) + y$mean_ci_3d <- formatters::with_label(mean_ci_3d, paste0("Mean (", f_conf_level(control$conf_level), ")")) mean_pval <- stat_mean_pval(x, test_mean = control$test_mean, na.rm = FALSE, n_min = 2) y$mean_pval <- formatters::with_label(mean_pval, paste("Mean", f_pval(control$test_mean))) @@ -201,8 +201,8 @@ s_summary.numeric <- function(x, median_ci <- stat_median_ci(x, conf_level = control$conf_level, na.rm = FALSE, gg_helper = FALSE) y$median_ci <- formatters::with_label(median_ci, paste("Median", f_conf_level(control$conf_level))) - median_long <- c(y$median, median_ci) - y$median_long <- formatters::with_label(median_long, paste0("Median (", f_conf_level(control$conf_level), ")")) + median_ci_3d <- c(y$median, median_ci) + y$median_ci_3d <- formatters::with_label(median_ci_3d, paste0("Median (", f_conf_level(control$conf_level), ")")) q <- control$quantiles if (any(is.na(x))) { @@ -236,8 +236,8 @@ s_summary.numeric <- function(x, y$geom_cv <- c("geom_cv" = sqrt(exp(stats::sd(log(x_no_negative_vals), na.rm = FALSE) ^ 2) - 1) * 100) # styler: off - geom_mean_long <- c(y$geom_mean, y$geom_mean_ci) - y$geom_mean_long <- formatters::with_label(geom_mean_long, paste0("Geometric Mean (", f_conf_level(control$conf_level), ")")) + geom_mean_ci_3d <- c(y$geom_mean, y$geom_mean_ci) + y$geom_mean_ci_3d <- formatters::with_label(geom_mean_ci_3d, paste0("Geometric Mean (", f_conf_level(control$conf_level), ")")) y } diff --git a/R/survival_coxph_pairwise.R b/R/survival_coxph_pairwise.R index 15b056e8be..98b0fedfd2 100644 --- a/R/survival_coxph_pairwise.R +++ b/R/survival_coxph_pairwise.R @@ -65,7 +65,7 @@ s_coxph_pairwise <- function(df, pvalue = formatters::with_label("", paste0("p-value (", pval_method, ")")), hr = formatters::with_label("", "Hazard Ratio"), hr_ci = formatters::with_label("", f_conf_level(conf_level)), - hr_long = formatters::with_label("", paste0("Hazard Ratio (", f_conf_level(conf_level), ")")), + hr_ci_3d = formatters::with_label("", paste0("Hazard Ratio (", f_conf_level(conf_level), ")")), n_tot = formatters::with_label("", "Total n"), n_tot_events = formatters::with_label("", "Total events") ) @@ -112,7 +112,7 @@ s_coxph_pairwise <- function(df, pvalue = formatters::with_label(unname(pval), paste0("p-value (", pval_method, ")")), hr = formatters::with_label(sum_cox$conf.int[1, 1], "Hazard Ratio"), hr_ci = formatters::with_label(unname(sum_cox$conf.int[1, 3:4]), f_conf_level(conf_level)), - hr_long = formatters::with_label( + hr_ci_3d = formatters::with_label( c(sum_cox$conf.int[1, 1], unname(sum_cox$conf.int[1, 3:4])), paste0("Hazard Ratio (", f_conf_level(conf_level), ")") ), @@ -129,12 +129,12 @@ s_coxph_pairwise <- function(df, #' @keywords internal a_coxph_pairwise <- make_afun( s_coxph_pairwise, - .indent_mods = c(pvalue = 0L, hr = 0L, hr_ci = 1L, n_tot = 0L, n_tot_events = 0L, hr_long = 0L), + .indent_mods = c(pvalue = 0L, hr = 0L, hr_ci = 1L, n_tot = 0L, n_tot_events = 0L, hr_ci_3d = 0L), .formats = c( pvalue = "x.xxxx | (<0.0001)", hr = "xx.xx", hr_ci = "(xx.xx, xx.xx)", - hr_long = "xx.xx (xx.xx - xx.xx)", + hr_ci_3d = "xx.xx (xx.xx - xx.xx)", n_tot = "xx.xx", n_tot_events = "xx.xx" ) diff --git a/R/survival_time.R b/R/survival_time.R index 7acd6bf368..6865d956ef 100644 --- a/R/survival_time.R +++ b/R/survival_time.R @@ -43,7 +43,7 @@ NULL #' * `s_surv_time()` returns the statistics: #' * `median`: Median survival time. #' * `median_ci`: Confidence interval for median time. -#' * `median_long`: Median with confidence interval for median time. +#' * `median_ci_3d`: Median with confidence interval for median time. #' * `quantiles`: Survival time for two specified quantiles. #' * `quantiles_lower`: quantile with confidence interval for the first specified quantile. #' * `quantiles_upper`: quantile with confidence interval for the second specified quantile. @@ -102,7 +102,7 @@ s_surv_time <- function(df, range_censor = formatters::with_label(range_censor, "Range (censored)"), range_event = formatters::with_label(range_event, "Range (event)"), range = formatters::with_label(range, "Range"), - median_long = formatters::with_label( + median_ci_3d = formatters::with_label( c( unname(srv_tab["median"]), unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))]) @@ -153,12 +153,12 @@ a_surv_time <- function(df, # Use method-specific defaults fmts <- c( median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x", - median_long = "xx.x (xx.x - xx.x)", + median_ci_3d = "xx.x (xx.x - xx.x)", quantiles_lower = "xx.x (xx.x - xx.x)", quantiles_upper = "xx.x (xx.x - xx.x)" ) lbls <- c( median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)", - median_long = "Median (95% CI)", + median_ci_3d = "Median (95% CI)", quantiles_lower = "25%-ile (95% CI)", quantiles_upper = "75%-ile (95% CI)" ) diff --git a/R/survival_timepoint.R b/R/survival_timepoint.R index 95190fcbd8..f266837104 100644 --- a/R/survival_timepoint.R +++ b/R/survival_timepoint.R @@ -39,7 +39,7 @@ NULL #' * `event_free_rate`: Event-free rate (%). #' * `rate_se`: Standard error of event free rate. #' * `rate_ci`: Confidence interval for event free rate. -#' * `event_free_rate_long`: Event-free rate (%) with Confidence interval. +#' * `event_free_rate_3d`: Event-free rate (%) with Confidence interval. #' #' @keywords internal s_surv_timepoint <- function(df, @@ -74,14 +74,14 @@ s_surv_timepoint <- function(df, rate_se <- df_srv_fit$std.err rate_ci <- c(df_srv_fit$lower, df_srv_fit$upper) } - event_free_rate_long <- c(event_free_rate, rate_ci) + event_free_rate_3d <- c(event_free_rate, rate_ci) list( pt_at_risk = formatters::with_label(pt_at_risk, "Patients remaining at risk"), event_free_rate = formatters::with_label(event_free_rate * 100, "Event Free Rate (%)"), rate_se = formatters::with_label(rate_se * 100, "Standard Error of Event Free Rate"), rate_ci = formatters::with_label(rate_ci * 100, f_conf_level(conf_level)), - event_free_rate_long = formatters::with_label( - event_free_rate_long * 100, paste0("Event Free Rate (", f_conf_level(conf_level), ")") + event_free_rate_3d = formatters::with_label( + event_free_rate_3d * 100, paste0("Event Free Rate (", f_conf_level(conf_level), ")") ) ) } @@ -115,7 +115,7 @@ a_surv_timepoint <- make_afun( #' * `s_surv_timepoint_diff()` returns the statistics: #' * `rate_diff`: Event-free rate difference between two groups. #' * `rate_diff_ci`: Confidence interval for the difference. -#' * `rate_diff_long`: Event-free rate difference and confidence interval between two groups. +#' * `rate_diff_ci_3d`: Event-free rate difference and confidence interval between two groups. #' * `ztest_pval`: p-value to test the difference is 0. #' #' @keywords internal @@ -131,7 +131,7 @@ s_surv_timepoint_diff <- function(df, list( rate_diff = formatters::with_label("", "Difference in Event Free Rate"), rate_diff_ci = formatters::with_label("", f_conf_level(control$conf_level)), - rate_diff_long = formatters::with_label( + rate_diff_ci_3d = formatters::with_label( "", paste0("Difference in Event Free Rate", f_conf_level(control$conf_level)) ), ztest_pval = formatters::with_label("", "p-value (Z-test)") @@ -151,7 +151,7 @@ s_surv_timepoint_diff <- function(df, qs <- c(-1, 1) * stats::qnorm(1 - (1 - control$conf_level) / 2) rate_diff_ci <- rate_diff + qs * se_diff - rate_diff_long <- c(rate_diff, rate_diff_ci) + rate_diff_ci_3d <- c(rate_diff, rate_diff_ci) ztest_pval <- if (is.na(rate_diff)) { NA } else { @@ -160,8 +160,8 @@ s_surv_timepoint_diff <- function(df, list( rate_diff = formatters::with_label(rate_diff, "Difference in Event Free Rate"), rate_diff_ci = formatters::with_label(rate_diff_ci, f_conf_level(control$conf_level)), - rate_diff_long = formatters::with_label( - rate_diff_long, paste0("Difference in Event Free Rate", f_conf_level(control$conf_level)) + rate_diff_ci_3d = formatters::with_label( + rate_diff_ci_3d, paste0("Difference in Event Free Rate", f_conf_level(control$conf_level)) ), ztest_pval = formatters::with_label(ztest_pval, "p-value (Z-test)") ) @@ -179,7 +179,7 @@ a_surv_timepoint_diff <- make_afun( .formats = c( rate_diff = "xx.xx", rate_diff_ci = "(xx.xx, xx.xx)", - rate_diff_long = format_xx("xx.xx (xx.xx, xx.xx)"), + rate_diff_ci_3d = format_xx("xx.xx (xx.xx, xx.xx)"), ztest_pval = "x.xxxx | (<0.0001)" ) ) @@ -273,8 +273,8 @@ surv_timepoint <- function(lyt, extra_args <- list(time_point = time_point, is_event = is_event, control = control, ...) f <- list( - surv = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "event_free_rate_long"), - surv_diff = c("rate_diff", "rate_diff_ci", "ztest_pval", "rate_diff_long") + surv = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "event_free_rate_3d"), + surv_diff = c("rate_diff", "rate_diff_ci", "ztest_pval", "rate_diff_ci_3d") ) .stats <- h_split_param(.stats, .stats, f = f) .formats <- h_split_param(.formats, names(.formats), f = f) diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R index 0411e32251..b5b64ba378 100644 --- a/R/utils_default_stats_formats_labels.R +++ b/R/utils_default_stats_formats_labels.R @@ -387,8 +387,8 @@ tern_default_stats <- list( "n", "sum", "mean", "sd", "se", "mean_sd", "mean_se", "mean_ci", "mean_sei", "mean_sdi", "mean_pval", "median", "mad", "median_ci", "quantiles", "iqr", "range", "min", "max", "median_range", "cv", "geom_mean", "geom_mean_ci", "geom_cv", - "median_long", - "mean_long", "geom_mean_long" + "median_ci_3d", + "mean_ci_3d", "geom_mean_ci_3d" ), count_cumulative = c("count_fraction", "count_fraction_fixed_dp"), count_missed_doses = c("n", "count_fraction", "count_fraction_fixed_dp"), @@ -409,12 +409,12 @@ tern_default_stats <- list( summarize_num_patients = c("unique", "nonunique", "unique_count"), summarize_patients_events_in_cols = c("unique", "all"), surv_time = c( - "median", "median_ci", "median_long", "quantiles", + "median", "median_ci", "median_ci_3d", "quantiles", "quantiles_lower", "quantiles_upper", "range_censor", "range_event", "range" ), surv_timepoint = c( "pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "rate_diff", "rate_diff_ci", "ztest_pval", - "event_free_rate_long" + "event_free_rate_3d" ), tabulate_rsp_biomarkers = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"), tabulate_rsp_subgroups = c("n", "n_rsp", "prop", "n_tot", "or", "ci", "pval"), @@ -450,11 +450,11 @@ tern_default_formats <- c( mean_sei = "(xx.xx, xx.xx)", mean_sdi = "(xx.xx, xx.xx)", mean_pval = "x.xxxx | (<0.0001)", - mean_long = "xx.xx (xx.xx - xx.xx)", + mean_ci_3d = "xx.xx (xx.xx - xx.xx)", median = "xx.x", mad = "xx.x", median_ci = "(xx.xx, xx.xx)", - median_long = "xx.xx (xx.xx - xx.xx)", + median_ci_3d = "xx.xx (xx.xx - xx.xx)", quantiles = "xx.x - xx.x", quantiles_lower = "xx.xx (xx.xx - xx.xx)", quantiles_upper = "xx.xx (xx.xx - xx.xx)", @@ -466,7 +466,7 @@ tern_default_formats <- c( cv = "xx.x", geom_mean = "xx.x", geom_mean_ci = "(xx.xx, xx.xx)", - geom_mean_long = "xx.xx (xx.xx - xx.xx)", + geom_mean_ci_3d = "xx.xx (xx.xx - xx.xx)", geom_cv = "xx.x", pval = "x.xxxx | (<0.0001)", pval_counts = "x.xxxx | (<0.0001)", @@ -504,11 +504,11 @@ tern_default_labels <- c( mean_sei = "Mean -/+ 1xSE", mean_sdi = "Mean -/+ 1xSD", mean_pval = "Mean p-value (H0: mean = 0)", - mean_long = "Mean (95% CI)", + mean_ci_3d = "Mean (95% CI)", median = "Median", mad = "Median Absolute Deviation", median_ci = "Median 95% CI", - median_long = "Median (95% CI)", + median_ci_3d = "Median (95% CI)", quantiles = "25% and 75%-ile", quantiles_lower = "25%-ile (95% CI)", quantiles_upper = "75%-ile (95% CI)", @@ -520,7 +520,7 @@ tern_default_labels <- c( cv = "CV (%)", geom_mean = "Geometric Mean", geom_mean_ci = "Geometric Mean 95% CI", - geom_mean_long = "Geometric Mean (95% CI)", + geom_mean_ci_3d = "Geometric Mean (95% CI)", geom_cv = "CV % Geometric Mean", pval = "p-value (t-test)", # Default for numeric pval_counts = "p-value (chi-squared test)", # Default for counts diff --git a/tests/testthat/_snaps/analyze_variables.md b/tests/testthat/_snaps/analyze_variables.md index dc064755f7..8c10718bdf 100644 --- a/tests/testthat/_snaps/analyze_variables.md +++ b/tests/testthat/_snaps/analyze_variables.md @@ -49,7 +49,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr NA NA NA attr(,"label") @@ -77,7 +77,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr NA NA NA attr(,"label") @@ -129,7 +129,7 @@ geom_cv NA - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr NaN NA NA attr(,"label") @@ -187,7 +187,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr 1 NA NA attr(,"label") @@ -215,7 +215,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr 1 NA NA attr(,"label") @@ -267,7 +267,7 @@ geom_cv NA - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr 1 NA NA attr(,"label") @@ -325,7 +325,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr NA NA NA attr(,"label") @@ -353,7 +353,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr NA NA NA attr(,"label") @@ -405,7 +405,7 @@ geom_cv NA - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr NA NA NA attr(,"label") @@ -463,7 +463,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr 1.500000 -4.853102 7.853102 attr(,"label") @@ -491,7 +491,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr 1.5 NA NA attr(,"label") @@ -543,7 +543,7 @@ geom_cv 52.10922 - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr 1.41421356 0.01729978 115.60839614 attr(,"label") @@ -601,7 +601,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr 6.000000 3.318768 8.681232 attr(,"label") @@ -629,7 +629,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr 6.5 1.0 10.0 attr(,"label") @@ -681,7 +681,7 @@ geom_cv 96.61307 - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr 4.842534 2.456211 9.547283 attr(,"label") diff --git a/tests/testthat/_snaps/compare_variables.md b/tests/testthat/_snaps/compare_variables.md index 0cacb94c3c..6c98b121bb 100644 --- a/tests/testthat/_snaps/compare_variables.md +++ b/tests/testthat/_snaps/compare_variables.md @@ -3,13 +3,13 @@ Code res Output - [1] "n" "sum" "mean" "sd" - [5] "se" "mean_sd" "mean_se" "mean_ci" - [9] "mean_sei" "mean_sdi" "mean_long" "mean_pval" - [13] "median" "mad" "median_ci" "median_long" - [17] "quantiles" "iqr" "range" "min" - [21] "max" "median_range" "cv" "geom_mean" - [25] "geom_mean_ci" "geom_cv" "geom_mean_long" "pval" + [1] "n" "sum" "mean" "sd" + [5] "se" "mean_sd" "mean_se" "mean_ci" + [9] "mean_sei" "mean_sdi" "mean_ci_3d" "mean_pval" + [13] "median" "mad" "median_ci" "median_ci_3d" + [17] "quantiles" "iqr" "range" "min" + [21] "max" "median_range" "cv" "geom_mean" + [25] "geom_mean_ci" "geom_cv" "geom_mean_ci_3d" "pval" # s_compare for numeric does not give p-value when not at least 2 values in each group diff --git a/tests/testthat/_snaps/summarize_change.md b/tests/testthat/_snaps/summarize_change.md index f46df79af1..6b127938a7 100644 --- a/tests/testthat/_snaps/summarize_change.md +++ b/tests/testthat/_snaps/summarize_change.md @@ -49,7 +49,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr NA NA NA attr(,"label") @@ -77,7 +77,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr NA NA NA attr(,"label") @@ -129,7 +129,7 @@ geom_cv NA - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr NaN NA NA attr(,"label") @@ -187,7 +187,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $mean_long + $mean_ci_3d mean mean_ci_lwr mean_ci_upr 3.000000 -4.452413 10.452413 attr(,"label") @@ -215,7 +215,7 @@ attr(,"label") [1] "Median 95% CI" - $median_long + $median_ci_3d median median_ci_lwr median_ci_upr 3 NA NA attr(,"label") @@ -267,7 +267,7 @@ geom_cv NA - $geom_mean_long + $geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr NA NA NA attr(,"label") @@ -326,7 +326,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $`FALSE`$mean_long + $`FALSE`$mean_ci_3d mean mean_ci_lwr mean_ci_upr 1.500000 -4.853102 7.853102 attr(,"label") @@ -354,7 +354,7 @@ attr(,"label") [1] "Median 95% CI" - $`FALSE`$median_long + $`FALSE`$median_ci_3d median median_ci_lwr median_ci_upr 1.5 NA NA attr(,"label") @@ -406,7 +406,7 @@ geom_cv 52.10922 - $`FALSE`$geom_mean_long + $`FALSE`$geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr 1.41421356 0.01729978 115.60839614 attr(,"label") @@ -460,7 +460,7 @@ attr(,"label") [1] "Mean -/+ 1xSD" - $`TRUE`$mean_long + $`TRUE`$mean_ci_3d mean mean_ci_lwr mean_ci_upr 2.50000 -16.55931 21.55931 attr(,"label") @@ -488,7 +488,7 @@ attr(,"label") [1] "Median 95% CI" - $`TRUE`$median_long + $`TRUE`$median_ci_3d median median_ci_lwr median_ci_upr 2.5 NA NA attr(,"label") @@ -540,7 +540,7 @@ geom_cv 127.0458 - $`TRUE`$geom_mean_long + $`TRUE`$geom_mean_ci_3d geom_mean mean_ci_lwr mean_ci_upr 2.000000e+00 2.992824e-04 1.336530e+04 attr(,"label") diff --git a/tests/testthat/_snaps/survival_coxph_pairwise.md b/tests/testthat/_snaps/survival_coxph_pairwise.md index 3c81dbda37..a309f01b0a 100644 --- a/tests/testthat/_snaps/survival_coxph_pairwise.md +++ b/tests/testthat/_snaps/survival_coxph_pairwise.md @@ -18,7 +18,7 @@ attr(,"label") [1] "95% CI" - $hr_long + $hr_ci_3d [1] 0.7108557 0.4779138 1.0573368 attr(,"label") [1] "Hazard Ratio (95% CI)" @@ -54,7 +54,7 @@ attr(,"label") [1] "90% CI" - $hr_long + $hr_ci_3d [1] 0.7108557 0.5094153 0.9919525 attr(,"label") [1] "Hazard Ratio (90% CI)" @@ -90,7 +90,7 @@ attr(,"label") [1] "95% CI" - $hr_long + $hr_ci_3d [1] 0.6251817 0.4014842 0.9735181 attr(,"label") [1] "Hazard Ratio (95% CI)" @@ -126,7 +126,7 @@ attr(,"label") [1] "90% CI" - $hr_long + $hr_ci_3d [1] 0.6251817 0.4311132 0.9066115 attr(,"label") [1] "Hazard Ratio (90% CI)" diff --git a/tests/testthat/_snaps/survival_time.md b/tests/testthat/_snaps/survival_time.md index dad2784e94..10d0453dce 100644 --- a/tests/testthat/_snaps/survival_time.md +++ b/tests/testthat/_snaps/survival_time.md @@ -33,7 +33,7 @@ attr(,"label") [1] "Range" - $median_long + $median_ci_3d [1] 23.91143 18.25878 32.85945 attr(,"label") [1] "Median (95% CI)" @@ -84,7 +84,7 @@ attr(,"label") [1] "Range" - $median_long + $median_ci_3d [1] 23.91143 13.59124 37.97055 attr(,"label") [1] "Median (99% CI)" diff --git a/tests/testthat/_snaps/survival_timepoint.md b/tests/testthat/_snaps/survival_timepoint.md index 1ca511c166..18e7f1f433 100644 --- a/tests/testthat/_snaps/survival_timepoint.md +++ b/tests/testthat/_snaps/survival_timepoint.md @@ -23,7 +23,7 @@ attr(,"label") [1] "95% CI" - $event_free_rate_long + $event_free_rate_3d [1] 82.19178 73.41549 90.96807 attr(,"label") [1] "Event Free Rate (95% CI)" @@ -54,7 +54,7 @@ attr(,"label") [1] "99% CI" - $event_free_rate_long + $event_free_rate_3d [1] 75.49797 62.15793 91.70097 attr(,"label") [1] "Event Free Rate (99% CI)" @@ -85,7 +85,7 @@ attr(,"label") [1] "95% CI" - $event_free_rate_long + $event_free_rate_3d [1] NA NA NA attr(,"label") [1] "Event Free Rate (95% CI)" @@ -130,7 +130,7 @@ attr(,"label") [1] "95% CI" - $rate_diff_long + $rate_diff_ci_3d [1] 4.269100 -7.767371 16.305570 attr(,"label") [1] "Difference in Event Free Rate95% CI" @@ -156,7 +156,7 @@ attr(,"label") [1] "90% CI" - $rate_diff_long + $rate_diff_ci_3d [1] 9.640872 -1.404177 20.685921 attr(,"label") [1] "Difference in Event Free Rate90% CI" diff --git a/tests/testthat/_snaps/utils_default_stats_formats_labels.md b/tests/testthat/_snaps/utils_default_stats_formats_labels.md index ea57d3c8a2..87115adb62 100644 --- a/tests/testthat/_snaps/utils_default_stats_formats_labels.md +++ b/tests/testthat/_snaps/utils_default_stats_formats_labels.md @@ -33,7 +33,7 @@ [13] "mad" "median_ci" "quantiles" "iqr" [17] "range" "min" "max" "median_range" [21] "cv" "geom_mean" "geom_mean_ci" "geom_cv" - [25] "median_long" "mean_long" "geom_mean_long" + [25] "median_ci_3d" "mean_ci_3d" "geom_mean_ci_3d" # get_labels_from_stats works as expected @@ -100,7 +100,7 @@ "xx.x" "xx.x (xx.x - xx.x)" "xx.x" geom_mean geom_mean_ci geom_cv "xx.x" "(xx.xx, xx.xx)" "xx.x" - median_long mean_long geom_mean_long + median_ci_3d mean_ci_3d geom_mean_ci_3d "xx.xx (xx.xx - xx.xx)" "xx.xx (xx.xx - xx.xx)" "xx.xx (xx.xx - xx.xx)" # summary_labels works as expected @@ -132,9 +132,9 @@ "CV (%)" "Geometric Mean" geom_mean_ci geom_cv "Geometric Mean 95% CI" "CV % Geometric Mean" - median_long mean_long + median_ci_3d mean_ci_3d "Median (95% CI)" "Mean (95% CI)" - geom_mean_long + geom_mean_ci_3d "Geometric Mean (95% CI)" ---