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1301 feature request add confidence intervals for quantiles in surv time #1306

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1301 feature request add confidence intervals for quantiles in surv time #1306

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c35948a
add 3 new stats to surv_time
iaugusty Sep 9, 2024
56b5f29
update test snapshot for survival_time
iaugusty Sep 9, 2024
3bc7d42
[skip style] [skip vbump] Restyle files
github-actions[bot] Sep 9, 2024
d6e8f4b
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
iaugusty Sep 9, 2024
a65114a
fix lint checks
iaugusty Sep 9, 2024
7806a15
fix lint checks + merge from main
iaugusty Sep 9, 2024
881f5e7
[skip style] [skip vbump] Restyle files
github-actions[bot] Sep 9, 2024
98ff6c8
renaming stats per review suggestion
iaugusty Sep 10, 2024
4ea5147
typo
iaugusty Sep 10, 2024
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github-actions[bot] Sep 10, 2024
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dependabot-preview[bot] Sep 10, 2024
f3187a9
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
Melkiades Sep 16, 2024
761954d
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
shajoezhu Sep 24, 2024
bcc0cbd
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
Melkiades Sep 24, 2024
4976bb5
updates for snapshots + add long version of stats (mean, median, geom…
iaugusty Sep 27, 2024
e7bfd91
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
Melkiades Oct 1, 2024
620f068
update name of new stats according to suggestion median_long into med…
iaugusty Oct 14, 2024
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45 changes: 40 additions & 5 deletions R/survival_time.R
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Original file line number Diff line number Diff line change
Expand Up @@ -70,10 +70,24 @@ s_surv_time <- function(df,
conf.type = conf_type
)
srv_tab <- summary(srv_fit, extend = TRUE)$table
srv_qt_tab <- stats::quantile(srv_fit, probs = quantiles)$quantile
srv_qt_tab_pre <- stats::quantile(srv_fit, probs = quantiles)
srv_qt_tab <- srv_qt_tab_pre$quantile
range_censor <- range_noinf(df[[.var]][!df[[is_event]]], na.rm = TRUE)
range_event <- range_noinf(df[[.var]][df[[is_event]]], na.rm = TRUE)
range <- range_noinf(df[[.var]], na.rm = TRUE)

names(quantiles) <- as.character(100 * quantiles)
srv_qt_tab_pre <- unlist(srv_qt_tab_pre)
srv_qt_ci <- lapply(quantiles, function(x) {
name <- as.character(100 * x)

c(
srv_qt_tab_pre[[paste0("quantile.", name)]],
srv_qt_tab_pre[[paste0("lower.", name)]],
srv_qt_tab_pre[[paste0("upper.", name)]]
)
})

list(
median = formatters::with_label(unname(srv_tab["median"]), "Median"),
median_ci = formatters::with_label(
Expand All @@ -84,7 +98,20 @@ 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")
range = formatters::with_label(range, "Range"),
median_ci_1_line = formatters::with_label(
c(
unname(srv_tab["median"]),
unname(srv_tab[paste0(srv_fit$conf.int, c("LCL", "UCL"))])
),
paste0("Median ", f_conf_level(conf_level))
),
quantiles_ci_1 = formatters::with_label(
unname(srv_qt_ci[[1]]), paste0(quantiles[1] * 100, "%-ile with ", f_conf_level(conf_level))
),
quantiles_ci_2 = formatters::with_label(
unname(srv_qt_ci[[2]]), paste0(quantiles[2] * 100, "%-ile with ", f_conf_level(conf_level))
)
)
}

Expand Down Expand Up @@ -121,8 +148,17 @@ a_surv_time <- function(df,
rng_censor_upr <- x_stats[["range_censor"]][2]

# Use method-specific defaults
fmts <- c(median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x")
lbls <- c(median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)")
fmts <- c(
median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x",
median_ci_1_line = "xx.x (xx.x - xx.x)",
quantiles_ci_1 = "xx.x (xx.x - xx.x)", quantiles_ci_2 = "xx.x (xx.x - xx.x)"
)
lbls <- c(
median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)",
median_ci_1_line = "Median 95% CI",
quantiles_ci_1 = "25%-ile with 95% CI",
quantiles_ci_2 = "75%-ile with 95% CI"
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)
lbls_custom <- .labels
.formats <- c(.formats, fmts[setdiff(names(fmts), names(.formats))])
.labels <- c(.labels, lbls[setdiff(names(lbls), names(lbls_custom))])
Expand Down Expand Up @@ -209,7 +245,6 @@ surv_time <- function(lyt,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names,
na_str = na_str,
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why not?

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it is already passed as extra_args into the analysis function . If the na_str is passed as a named list (to be able to show the formatted value as "NA (NA, NA)" when a stat is all missing), having na_str as extra_args and inside analyze gave an error.

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@Melkiades Melkiades Sep 9, 2024 •
edited
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I see! good catch! thanks :)

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I think this may also be present elsewhere. Can you add an issue regarding this please?

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after looking at it again, it might be more easy to remove na_str from extra_args and keep it in analyze only. Then it is much easier to accomplish "NA (NA, NA)", and there would not be the need for a named list to na_str to accomplish this.
Would it be ok to remove it from in_rows call and keep it only in analyze?

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The use of na_str seems a bit duplicated. It is more straightforward to modify it from the analyze function instead of sending it down. Yet the statistical functions may be used and tested externally from the decided analyze. For simplicity, I would keep only the na_str on the top level. If users want to use custom analyze functions can provide their own NA handling directly there

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Sounds fine to me!

nested = nested,
extra_args = extra_args
)
Expand Down
25 changes: 24 additions & 1 deletion R/utils_default_stats_formats_labels.R
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Original file line number Diff line number Diff line change
Expand Up @@ -344,6 +344,20 @@ labels_use_control <- function(labels_default, control, labels_custom = NULL) {
labels_default["quantiles"]
)
}
if ("quantiles" %in% names(control) && "quantiles_ci_1" %in% names(labels_default) &&
!"quantiles_ci_1" %in% names(labels_custom)) { # nolint
labels_default["quantiles_ci_1"] <- gsub(
"[0-9]+%-ile", paste0(control[["quantiles"]][1] * 100, "%-ile", ""),
labels_default["quantiles_ci_1"]
)
}
if ("quantiles" %in% names(control) && "quantiles_ci_2" %in% names(labels_default) &&
!"quantiles_ci_2" %in% names(labels_custom)) { # nolint
labels_default["quantiles_ci_2"] <- gsub(
"[0-9]+%-ile", paste0(control[["quantiles"]][2] * 100, "%-ile", ""),
labels_default["quantiles_ci_2"]
)
}
if ("test_mean" %in% names(control) && "mean_pval" %in% names(labels_default) &&
!"mean_pval" %in% names(labels_custom)) { # nolint
labels_default["mean_pval"] <- gsub(
Expand Down Expand Up @@ -392,7 +406,10 @@ tern_default_stats <- list(
summarize_glm_count = c("n", "rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
summarize_num_patients = c("unique", "nonunique", "unique_count"),
summarize_patients_events_in_cols = c("unique", "all"),
surv_time = c("median", "median_ci", "quantiles", "range_censor", "range_event", "range"),
surv_time = c(
"median", "median_ci", "median_ci_1_line", "quantiles",
"quantiles_ci_1", "quantiles_ci_2", "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"),
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"),
Expand Down Expand Up @@ -431,7 +448,10 @@ tern_default_formats <- c(
median = "xx.x",
mad = "xx.x",
median_ci = "(xx.xx, xx.xx)",
median_ci_1_line = "xx.xx (xx.xx, xx.xx)",
quantiles = "xx.x - xx.x",
quantiles_ci_1 = "xx.xx (xx.xx, xx.xx)",
quantiles_ci_2 = "xx.xx (xx.xx, xx.xx)",
iqr = "xx.x",
range = "xx.x - xx.x",
min = "xx.x",
Expand Down Expand Up @@ -480,7 +500,10 @@ tern_default_labels <- c(
median = "Median",
mad = "Median Absolute Deviation",
median_ci = "Median 95% CI",
median_ci_1_line = "Median 95% CI",
quantiles = "25% and 75%-ile",
quantiles_ci_1 = "25%-ile 95% CI",
quantiles_ci_2 = "75%-ile 95% CI",
iqr = "IQR",
range = "Min - Max",
min = "Minimum",
Expand Down
68 changes: 52 additions & 16 deletions tests/testthat/_snaps/survival_time.md
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,21 @@
attr(,"label")
[1] "Range"

$median_ci_1_line
[1] 23.91143 18.25878 32.85945
attr(,"label")
[1] "Median 95% CI"

$quantiles_ci_1
[1] 9.822926 5.628823 16.690121
attr(,"label")
[1] "25%-ile with 95% CI"

$quantiles_ci_2
[1] 41.98181 32.85945 53.41445
attr(,"label")
[1] "75%-ile with 95% CI"


# s_surv_time works with customized arguments

Expand Down Expand Up @@ -69,6 +84,21 @@
attr(,"label")
[1] "Range"

$median_ci_1_line
[1] 23.91143 13.59124 37.97055
attr(,"label")
[1] "Median 99% CI"

$quantiles_ci_1
[1] 6.649204 1.887860 12.771697
attr(,"label")
[1] "20%-ile with 99% CI"

$quantiles_ci_2
[1] 51.09487 37.97055 NA
attr(,"label")
[1] "80%-ile with 99% CI"


# a_surv_time works with default arguments

Expand All @@ -77,13 +107,16 @@
Output
RowsVerticalSection (in_rows) object print method:
----------------------------
row_name formatted_cell indent_mod row_label
1 Median 24.8 0 Median
2 95% CI (21.1, 31.3) 0 95% CI
3 25% and 75%-ile 10.8, 47.6 0 25% and 75%-ile
4 Range (censored) 0.8 to 78.9 0 Range (censored)
5 Range (event) 0.1 to 155.5 0 Range (event)
6 Range 0.1 to 155.5 0 Range
row_name formatted_cell indent_mod row_label
1 Median 24.8 0 Median
2 95% CI (21.1, 31.3) 0 95% CI
3 Median 95% CI 24.8 (21.1 - 31.3) 0 Median 95% CI
4 25% and 75%-ile 10.8, 47.6 0 25% and 75%-ile
5 25%-ile with 95% CI 10.8 (6.6 - 13.4) 0 25%-ile with 95% CI
6 75%-ile with 95% CI 47.6 (39.3 - 57.8) 0 75%-ile with 95% CI
7 Range (censored) 0.8 to 78.9 0 Range (censored)
8 Range (event) 0.1 to 155.5 0 Range (event)
9 Range 0.1 to 155.5 0 Range

# a_surv_time works with customized arguments

Expand Down Expand Up @@ -115,15 +148,18 @@
Code
res
Output
ARM A ARM B ARM C
———————————————————————————————————————————————————————————————————
Survival Time (Months)
Median 32.0 23.9 20.8
90% CI (25.6, 49.3) (18.9, 32.1) (13.0, 26.0)
40% and 60%-ile 25.6, 46.5 18.3, 29.2 13.0, 25.7
Range (censored) 0.8 to 63.5 6.2 to 78.9 3.4 to 52.4
Range (event) 0.3 to 155.5 0.1 to 154.1 0.6 to 80.7
Range 0.3 to 155.5 0.1 to 154.1 0.6 to 80.7
ARM A ARM B ARM C
—————————————————————————————————————————————————————————————————————————————————————
Survival Time (Months)
Median 32.0 23.9 20.8
90% CI (25.6, 49.3) (18.9, 32.1) (13.0, 26.0)
Median 90% CI 32.0 (25.6 - 49.3) 23.9 (18.9 - 32.1) 20.8 (13.0 - 26.0)
40% and 60%-ile 25.6, 46.5 18.3, 29.2 13.0, 25.7
40%-ile with 90% CI 25.6 (20.7 - 33.4) 18.3 (12.8 - 23.9) 13.0 (10.1 - 24.8)
60%-ile with 90% CI 46.5 (32.0 - 57.8) 29.2 (23.9 - 41.3) 25.7 (20.8 - 37.1)
Range (censored) 0.8 to 63.5 6.2 to 78.9 3.4 to 52.4
Range (event) 0.3 to 155.5 0.1 to 154.1 0.6 to 80.7
Range 0.3 to 155.5 0.1 to 154.1 0.6 to 80.7

# surv_time works with referential footnotes

Expand Down
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