survival_timepoint {tern} | R Documentation |
Survival time point analysis
Description
Summarize patients' survival rate and difference of survival rates between groups at a time point.
Usage
surv_timepoint(
lyt,
vars,
time_point,
is_event,
control = control_surv_timepoint(),
method = c("surv", "surv_diff", "both"),
na_str = default_na_str(),
nested = TRUE,
...,
table_names_suffix = "",
var_labels = "Time",
show_labels = "visible",
.stats = c("pt_at_risk", "event_free_rate", "rate_ci", "rate_diff", "rate_diff_ci",
"ztest_pval"),
.formats = NULL,
.labels = NULL,
.indent_mods = if (method == "both") {
c(rate_diff = 1L, rate_diff_ci = 2L,
ztest_pval = 2L)
} else {
c(rate_diff_ci = 1L, ztest_pval = 1L)
}
)
s_surv_timepoint(
df,
.var,
time_point,
is_event,
control = control_surv_timepoint()
)
a_surv_timepoint(
df,
.var,
time_point,
is_event,
control = control_surv_timepoint()
)
s_surv_timepoint_diff(
df,
.var,
.ref_group,
.in_ref_col,
time_point,
control = control_surv_timepoint(),
...
)
a_surv_timepoint_diff(
df,
.var,
.ref_group,
.in_ref_col,
time_point,
control = control_surv_timepoint(),
...
)
Arguments
lyt |
( |
vars |
( |
time_point |
( |
is_event |
( |
control |
(
|
method |
( |
na_str |
( |
nested |
( |
... |
additional arguments for the lower level functions. |
table_names_suffix |
( |
var_labels |
( |
show_labels |
( |
.stats |
( |
.formats |
(named |
.labels |
(named |
.indent_mods |
(named |
df |
( |
.var |
( |
.ref_group |
( |
.in_ref_col |
( |
Value
-
surv_timepoint()
returns a layout object suitable for passing to further layouting functions, or tortables::build_table()
. Adding this function to anrtable
layout will add formatted rows containing the statistics froms_surv_timepoint()
and/ors_surv_timepoint_diff()
to the table layout depending on the value ofmethod
.
-
s_surv_timepoint()
returns the statistics:-
pt_at_risk
: Patients remaining at risk. -
event_free_rate
: Event-free rate (%). -
rate_se
: Standard error of event free rate. -
rate_ci
: Confidence interval for event free rate.
-
-
a_surv_timepoint()
returns the corresponding list with formattedrtables::CellValue()
.
-
s_surv_timepoint_diff()
returns the statistics:-
rate_diff
: Event-free rate difference between two groups. -
rate_diff_ci
: Confidence interval for the difference. -
ztest_pval
: p-value to test the difference is 0.
-
-
a_surv_timepoint_diff()
returns the corresponding list with formattedrtables::CellValue()
.
Functions
-
surv_timepoint()
: Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper forrtables::analyze()
. -
s_surv_timepoint()
: Statistics function which analyzes survival rate. -
a_surv_timepoint()
: Formatted analysis function which is used asafun
insurv_timepoint()
whenmethod = "surv"
. -
s_surv_timepoint_diff()
: Statistics function which analyzes difference between two survival rates. -
a_surv_timepoint_diff()
: Formatted analysis function which is used asafun
insurv_timepoint()
whenmethod = "surv_diff"
.
Examples
library(dplyr)
adtte_f <- tern_ex_adtte %>%
filter(PARAMCD == "OS") %>%
mutate(
AVAL = day2month(AVAL),
is_event = CNSR == 0
)
# Survival at given time points.
basic_table() %>%
split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
add_colcounts() %>%
surv_timepoint(
vars = "AVAL",
var_labels = "Months",
is_event = "is_event",
time_point = 7
) %>%
build_table(df = adtte_f)
# Difference in survival at given time points.
basic_table() %>%
split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
add_colcounts() %>%
surv_timepoint(
vars = "AVAL",
var_labels = "Months",
is_event = "is_event",
time_point = 9,
method = "surv_diff",
.indent_mods = c("rate_diff" = 0L, "rate_diff_ci" = 2L, "ztest_pval" = 2L)
) %>%
build_table(df = adtte_f)
# Survival and difference in survival at given time points.
basic_table() %>%
split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
add_colcounts() %>%
surv_timepoint(
vars = "AVAL",
var_labels = "Months",
is_event = "is_event",
time_point = 9,
method = "both"
) %>%
build_table(df = adtte_f)