count_patients_with_flags {tern} | R Documentation |
Count the number of patients with particular flags
Description
The primary analysis variable .var
denotes the unique patient identifier.
Usage
count_patients_with_flags(
lyt,
var,
flag_variables,
flag_labels = NULL,
var_labels = var,
show_labels = "hidden",
riskdiff = FALSE,
na_str = default_na_str(),
nested = TRUE,
...,
table_names = paste0("tbl_flags_", var),
.stats = "count_fraction",
.formats = NULL,
.indent_mods = NULL
)
s_count_patients_with_flags(
df,
.var,
flag_variables,
flag_labels = NULL,
.N_col,
.N_row,
denom = c("n", "N_row", "N_col")
)
a_count_patients_with_flags(
df,
.var,
flag_variables,
flag_labels = NULL,
.N_col,
.N_row,
denom = c("n", "N_row", "N_col")
)
Arguments
lyt |
( |
var |
( |
flag_variables |
( |
flag_labels |
( |
var_labels |
( |
show_labels |
( |
riskdiff |
( |
na_str |
( |
nested |
( |
... |
additional arguments for the lower level functions. |
table_names |
( |
.stats |
( |
.formats |
(named |
.indent_mods |
(named |
df |
( |
.var |
( |
.N_col |
( |
.N_row |
( |
denom |
(
|
Value
-
count_patients_with_flags()
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_count_patients_with_flags()
to the table layout.
-
s_count_patients_with_flags()
returns the count and the fraction of unique identifiers with each particular flag as a list of statisticsn
,count
,count_fraction
, andn_blq
, with one element per flag.
-
a_count_patients_with_flags()
returns the corresponding list with formattedrtables::CellValue()
.
Functions
-
count_patients_with_flags()
: Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper forrtables::analyze()
. -
s_count_patients_with_flags()
: Statistics function which counts the number of patients for which a particular flag variable isTRUE
. -
a_count_patients_with_flags()
: Formatted analysis function which is used asafun
incount_patients_with_flags()
.
Note
If flag_labels
is not specified, variables labels will be extracted from df
. If variables are not
labeled, variable names will be used instead. Alternatively, a named vector
can be supplied to
flag_variables
such that within each name-value pair the name corresponds to the variable name and the value is
the label to use for this variable.
See Also
Examples
library(dplyr)
# Add labelled flag variables to analysis dataset.
adae <- tern_ex_adae %>%
mutate(
fl1 = TRUE %>% with_label("Total AEs"),
fl2 = (TRTEMFL == "Y") %>%
with_label("Total number of patients with at least one adverse event"),
fl3 = (TRTEMFL == "Y" & AEOUT == "FATAL") %>%
with_label("Total number of patients with fatal AEs"),
fl4 = (TRTEMFL == "Y" & AEOUT == "FATAL" & AEREL == "Y") %>%
with_label("Total number of patients with related fatal AEs")
)
# `count_patients_with_flags()`
lyt2 <- basic_table() %>%
split_cols_by("ARM") %>%
add_colcounts() %>%
count_patients_with_flags(
"SUBJID",
flag_variables = c("fl1", "fl2", "fl3", "fl4"),
denom = "N_col"
)
build_table(lyt2, adae, alt_counts_df = tern_ex_adsl)
# `s_count_patients_with_flags()`
s_count_patients_with_flags(
adae,
"SUBJID",
flag_variables = c("fl1", "fl2", "fl3", "fl4"),
denom = "N_col",
.N_col = 1000
)
# We need to ungroup `count_fraction` first so that the `rtables` formatting
# function `format_count_fraction()` can be applied correctly.
# `a_count_patients_with_flags()`
afun <- make_afun(a_count_patients_with_flags,
.stats = "count_fraction",
.ungroup_stats = "count_fraction"
)
afun(
adae,
.N_col = 10L,
.N_row = 10L,
.var = "USUBJID",
flag_variables = c("fl1", "fl2", "fl3", "fl4")
)