abnormal_by_baseline {tern} | R Documentation |
Count patients with abnormal analysis range values by baseline status
Description
The analyze function count_abnormal_by_baseline()
creates a layout element to count patients with abnormal
analysis range values, categorized by baseline status.
This function analyzes primary analysis variable var
which indicates abnormal range results. Additional
analysis variables that can be supplied as a list via the variables
parameter are id
(defaults to
USUBJID
), a variable to indicate unique subject identifiers, and baseline
(defaults to BNRIND
), a
variable to indicate baseline reference ranges.
For each direction specified via the abnormal
parameter (e.g. High or Low), we condition on baseline
range result and count patients in the numerator and denominator as follows for each of the following
categories:
-
Not <abnormality>
-
num
: The number of patients without abnormality at baseline (excluding those with missing baseline) and with at least one abnormality post-baseline. -
denom
: The number of patients without abnormality at baseline (excluding those with missing baseline).
-
-
<Abnormality>
-
num
: The number of patients with abnormality as baseline and at least one abnormality post-baseline. -
denom
: The number of patients with abnormality at baseline.
-
-
Total
-
num
: The number of patients with at least one post-baseline record and at least one abnormality post-baseline. -
denom
: The number of patients with at least one post-baseline record.
-
This function assumes that df
has been filtered to only include post-baseline records.
Usage
count_abnormal_by_baseline(
lyt,
var,
abnormal,
variables = list(id = "USUBJID", baseline = "BNRIND"),
na_str = "<Missing>",
nested = TRUE,
...,
table_names = abnormal,
.stats = "fraction",
.stat_names = NULL,
.formats = list(fraction = format_fraction),
.labels = NULL,
.indent_mods = NULL
)
s_count_abnormal_by_baseline(
df,
.var,
abnormal,
na_str = "<Missing>",
variables = list(id = "USUBJID", baseline = "BNRIND"),
...
)
a_count_abnormal_by_baseline(
df,
...,
.stats = NULL,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL
)
Arguments
lyt |
( |
abnormal |
( |
variables |
(named |
na_str |
( |
nested |
( |
... |
additional arguments for the lower level functions. |
table_names |
( |
.stats |
( Options are: |
.stat_names |
( |
.formats |
(named |
.labels |
(named |
.indent_mods |
(named |
df |
( |
.var , var |
( |
Value
-
count_abnormal_by_baseline()
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_abnormal_by_baseline()
to the table layout.
-
s_count_abnormal_by_baseline()
returns statisticfraction
which is a named list with 3 labeled elements:not_abnormal
,abnormal
, andtotal
. Each element contains a vector withnum
anddenom
patient counts.
-
a_count_abnormal_by_baseline()
returns the corresponding list with formattedrtables::CellValue()
.
Functions
-
count_abnormal_by_baseline()
: Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper forrtables::analyze()
. -
s_count_abnormal_by_baseline()
: Statistics function for a singleabnormal
level. -
a_count_abnormal_by_baseline()
: Formatted analysis function which is used asafun
incount_abnormal_by_baseline()
.
Note
-
df
should be filtered to include only post-baseline records. If the baseline variable or analysis variable contains
NA
records, it is expected thatdf
has been pre-processed usingdf_explicit_na()
orexplicit_na()
.
See Also
Relevant description function d_count_abnormal_by_baseline()
.
Examples
df <- data.frame(
USUBJID = as.character(c(1:6)),
ANRIND = factor(c(rep("LOW", 4), "NORMAL", "HIGH")),
BNRIND = factor(c("LOW", "NORMAL", "HIGH", NA, "LOW", "NORMAL"))
)
df <- df_explicit_na(df)
# Layout creating function.
basic_table() %>%
count_abnormal_by_baseline(var = "ANRIND", abnormal = c(High = "HIGH")) %>%
build_table(df)
# Passing of statistics function and formatting arguments.
df2 <- data.frame(
ID = as.character(c(1, 2, 3, 4)),
RANGE = factor(c("NORMAL", "LOW", "HIGH", "HIGH")),
BLRANGE = factor(c("LOW", "HIGH", "HIGH", "NORMAL"))
)
basic_table() %>%
count_abnormal_by_baseline(
var = "RANGE",
abnormal = c(Low = "LOW"),
variables = list(id = "ID", baseline = "BLRANGE"),
.formats = c(fraction = "xx / xx"),
.indent_mods = c(fraction = 2L)
) %>%
build_table(df2)