summarize_num_patients {tern} | R Documentation |
Count number of patients
Description
The analyze function analyze_num_patients()
creates a layout element to count total numbers of unique or
non-unique patients. The primary analysis variable vars
is used to uniquely identify patients.
The count_by
variable can be used to identify non-unique patients such that the number of patients with a unique
combination of values in vars
and count_by
will be returned instead as the nonunique
statistic. The required
variable can be used to specify a variable required to be non-missing for the record to be included in the counts.
The summarize function summarize_num_patients()
performs the same function as analyze_num_patients()
except it
creates content rows, not data rows, to summarize the current table row/column context and operates on the level of
the latest row split or the root of the table if no row splits have occurred.
Usage
analyze_num_patients(
lyt,
vars,
required = NULL,
count_by = NULL,
unique_count_suffix = TRUE,
na_str = default_na_str(),
nested = TRUE,
.stats = NULL,
.formats = NULL,
.labels = c(unique = "Number of patients with at least one event", nonunique =
"Number of events"),
show_labels = c("default", "visible", "hidden"),
.indent_mods = 0L,
riskdiff = FALSE,
...
)
summarize_num_patients(
lyt,
var,
required = NULL,
count_by = NULL,
unique_count_suffix = TRUE,
na_str = default_na_str(),
.stats = NULL,
.formats = NULL,
.labels = c(unique = "Number of patients with at least one event", nonunique =
"Number of events"),
.indent_mods = 0L,
riskdiff = FALSE,
...
)
s_num_patients(
x,
labelstr,
.N_col,
count_by = NULL,
unique_count_suffix = TRUE
)
s_num_patients_content(
df,
labelstr = "",
.N_col,
.var,
required = NULL,
count_by = NULL,
unique_count_suffix = TRUE
)
Arguments
lyt |
( |
vars |
( |
required |
( |
count_by |
( |
unique_count_suffix |
( |
na_str |
( |
nested |
( |
.stats |
( |
.formats |
(named |
.labels |
(named |
show_labels |
( |
.indent_mods |
(named |
riskdiff |
( |
... |
additional arguments for the lower level functions. |
x |
( |
labelstr |
( |
.N_col |
( |
df |
( |
.var , var |
( |
Details
In general, functions that starts with analyze*
are expected to
work like rtables::analyze()
, while functions that starts with summarize*
are based upon rtables::summarize_row_groups()
. The latter provides a
value for each dividing split in the row and column space, but, being it
bound to the fundamental splits, it is repeated by design in every page
when pagination is involved.
Value
-
analyze_num_patients()
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_num_patients_content()
to the table layout.
-
summarize_num_patients()
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_num_patients_content()
to the table layout.
-
s_num_patients()
returns a namedlist
of 3 statistics:-
unique
: Vector of counts and percentages. -
nonunique
: Vector of counts. -
unique_count
: Counts.
-
-
s_num_patients_content()
returns the same values ass_num_patients()
.
Functions
-
analyze_num_patients()
: Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper forrtables::analyze()
. -
summarize_num_patients()
: Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper forrtables::summarize_row_groups()
. -
s_num_patients()
: Statistics function which counts the number of unique patients, the corresponding percentage taken with respect to the total number of patients, and the number of non-unique patients. -
s_num_patients_content()
: Statistics function which counts the number of unique patients in a column (variable), the corresponding percentage taken with respect to the total number of patients, and the number of non-unique patients in the column.
Note
As opposed to summarize_num_patients()
, this function does not repeat the produced rows.
Examples
df <- data.frame(
USUBJID = as.character(c(1, 2, 1, 4, NA, 6, 6, 8, 9)),
ARM = c("A", "A", "A", "A", "A", "B", "B", "B", "B"),
AGE = c(10, 15, 10, 17, 8, 11, 11, 19, 17),
SEX = c("M", "M", "M", "F", "F", "F", "M", "F", "M")
)
# analyze_num_patients
tbl <- basic_table() %>%
split_cols_by("ARM") %>%
add_colcounts() %>%
analyze_num_patients("USUBJID", .stats = c("unique")) %>%
build_table(df)
tbl
# summarize_num_patients
tbl <- basic_table() %>%
split_cols_by("ARM") %>%
split_rows_by("SEX") %>%
summarize_num_patients("USUBJID", .stats = "unique_count") %>%
build_table(df)
tbl
# Use the statistics function to count number of unique and nonunique patients.
s_num_patients(x = as.character(c(1, 1, 1, 2, 4, NA)), labelstr = "", .N_col = 6L)
s_num_patients(
x = as.character(c(1, 1, 1, 2, 4, NA)),
labelstr = "",
.N_col = 6L,
count_by = c(1, 1, 2, 1, 1, 1)
)
# Count number of unique and non-unique patients.
df <- data.frame(
USUBJID = as.character(c(1, 2, 1, 4, NA)),
EVENT = as.character(c(10, 15, 10, 17, 8))
)
s_num_patients_content(df, .N_col = 5, .var = "USUBJID")
df_by_event <- data.frame(
USUBJID = as.character(c(1, 2, 1, 4, NA)),
EVENT = c(10, 15, 10, 17, 8)
)
s_num_patients_content(df_by_event, .N_col = 5, .var = "USUBJID", count_by = "EVENT")