abnormal_by_baseline {tern}R Documentation

Count patients with abnormal analysis range values by baseline status

Description

[Stable]

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:

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 = NULL,
  .formats = NULL,
  .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,
  .var,
  abnormal,
  na_str = "<Missing>",
  variables = list(id = "USUBJID", baseline = "BNRIND")
)

Arguments

lyt

(PreDataTableLayouts)
layout that analyses will be added to.

abnormal

(character)
values identifying the abnormal range level(s) in .var.

variables

(named list of string)
list of additional analysis variables.

na_str

(string)
the explicit na_level argument you used in the pre-processing steps (maybe with df_explicit_na()). The default is "<Missing>".

nested

(flag)
whether this layout instruction should be applied within the existing layout structure _if possible (TRUE, the default) or as a new top-level element (FALSE). Ignored if it would nest a split. underneath analyses, which is not allowed.

...

additional arguments for the lower level functions.

table_names

(character)
this can be customized in the case that the same vars are analyzed multiple times, to avoid warnings from rtables.

.stats

(character)
statistics to select for the table. Run get_stats("abnormal_by_baseline") to see available statistics for this function.

.formats

(named character or list)
formats for the statistics. See Details in analyze_vars for more information on the "auto" setting.

.labels

(named character)
labels for the statistics (without indent).

.indent_mods

(named integer)
indent modifiers for the labels. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.

df

(data.frame)
data set containing all analysis variables.

.var, var

(string)
single variable name that is passed by rtables when requested by a statistics function.

Value

Functions

Note

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)


[Package tern version 0.9.6 Index]