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Remove obsolete survfit helpers #324

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merged 1 commit into from
Jun 10, 2024
Merged

Remove obsolete survfit helpers #324

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105 changes: 0 additions & 105 deletions R/aaa_survival_prob.R
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Original file line number Diff line number Diff line change
Expand Up @@ -116,111 +116,6 @@ available_survfit_summary_elements <- function(object) {
)
}

survfit_summary_patch_infinite_time <- function(object, eval_time) {
time_neg_inf <- is.infinite(eval_time) & (eval_time < 0)
time_inf <- is.infinite(eval_time) & (eval_time > 0)

patch_neg_inf <- function(x, value, n_patch) {
rbind(
matrix(value, nrow = n_patch, ncol = ncol(x)),
x
)
}
patch_inf <- function(x, value, n_patch) {
rbind(
x,
matrix(value, nrow = n_patch, ncol = ncol(x))
)
}

# glmnet does not provide standard errors etc
has_std_error <- "std.err" %in% names(object)

if (any(time_neg_inf)) {
object$surv <- patch_neg_inf(
object$surv,
value = 1,
n_patch = sum(time_neg_inf)
)
object$cumhaz <- patch_neg_inf(
object$cumhaz,
value = 0,
n_patch = sum(time_neg_inf)
)
if (has_std_error) {
object$std.err <- patch_neg_inf(
object$std.err,
value = NA_real_,
n_patch = sum(time_neg_inf)
)
object$lower <- patch_neg_inf(
object$lower,
value = NA_real_,
n_patch = sum(time_neg_inf)
)
object$upper <- patch_neg_inf(
object$upper,
value = NA_real_,
n_patch = sum(time_neg_inf)
)
object$std.chaz <- patch_neg_inf(
object$std.chaz,
value = NA_real_,
n_patch = sum(time_neg_inf)
)
}
}
if (any(time_inf)) {
object$surv <- patch_inf(object$surv, value = 0, n_patch = sum(time_inf))
object$cumhaz <- patch_inf(
object$cumhaz,
value = 1,
n_patch = sum(time_inf)
)
if (has_std_error) {
object$std.err <- patch_inf(
object$std.err,
value = NA_real_,
n_patch = sum(time_inf)
)
object$lower <- patch_inf(
object$lower,
value = NA_real_,
n_patch = sum(time_inf)
)
object$upper <- patch_inf(
object$upper,
value = NA_real_,
n_patch = sum(time_inf)
)
object$std.chaz <- patch_inf(
object$std.chaz,
value = NA_real_,
n_patch = sum(time_inf)
)
}
}

object
}

survfit_summary_restore_time_order <- function(object, eval_time) {
# preserve original order of `eval_time` because `summary()` returns a result for
# an ordered vector of finite time
# Note that this requires a survfit summary object which has already been
# patched for infinite time points
original_order_time <- match(eval_time, sort(eval_time))

elements <- available_survfit_summary_elements(object)

# restore original order of prediction time points
for (i in elements) {
object[[i]] <- object[[i]][original_order_time, , drop = FALSE]
}

object
}

survfit_summary_patch_missings <- function(object, index_missing, eval_time, n_obs) {
if (is.null(index_missing)) {
return(object)
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