Cumulative Counts with Thresholds

Usage

s_count_cumulative(
  x,
  thresholds,
  lower_tail = TRUE,
  include_eq = TRUE,
  .N_col,
  ...
)

a_count_cumulative(
  x,
  thresholds,
  lower_tail = TRUE,
  include_eq = TRUE,
  .N_col,
  ...
)

count_cumulative(
  lyt,
  vars,
  var_labels = vars,
  show_labels = "visible",
  ...,
  table_names = vars,
  .stats = NULL,
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

Arguments

x

(numeric)
vector of numbers we want to analyze.

thresholds

(numeric)
vector of cutoff value for the counts.

lower_tail

(logical)
whether to count lower tail, default is TRUE.

include_eq

(logical)
whether to include value equal to the threshold in count, default is TRUE.

.N_col

(count)
denominator for fraction calculation.

...

additional arguments for the lower level functions.

lyt

(layout)
input layout where analyses will be added to.

vars

(character)
variable names for the primary analysis variable to be iterated over.

var_labels

character for label.

show_labels

label visibility: one of "default", "visible" and "hidden".

table_names

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

.stats

(character)
statistics to select for the table.

.formats

(named character or list)
formats for the statistics.

.labels

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

.indent_mods

(named integer)
indent modifiers for the labels.

Value

A named list of count_fractions: a list with each thresholds value as a component, each component contains a vector for the count and fraction.

a_count_cumulative() returns the corresponding list with formatted rtables::CellValue().

Functions

• s_count_cumulative(): Statistics function that produces a named lists given a numeric vector of thresholds.

• a_count_cumulative(): Formatted Analysis function which can be further customized by calling rtables::make_afun() on it. It is used as afun in rtables::analyze().

• count_cumulative(): Layout creating function which can be be used for creating summary tables for cumulative counts of a variable. The ellipsis (...) conveys arguments to s_count_cumulative(), for instance lower_tail = FALSE if upper tail should be accounted for.

See also

Examples

# Internal function - s_count_cumulative
if (FALSE) {
set.seed(1, kind = "Mersenne-Twister")
x <- c(sample(1:10, 10), NA)
.N_col <- length(x)
s_count_cumulative(x, thresholds = c(0, 5, 11), .N_col = .N_col)
s_count_cumulative(x, thresholds = c(0, 5, 11), include_eq = FALSE, na.rm = FALSE, .N_col = .N_col)
}

# Internal function - a_count_cumulative
if (FALSE) {
# Use the Formatted Analysis function for `analyze()`. We need to ungroup `count_fraction` first
# so that the `rtables` formatting function `format_count_fraction()` can be applied correctly.
afun <- make_afun(a_count_cumulative, .ungroup_stats = "count_fraction")
afun(x, thresholds = c(0, 5, 11), .N_col = .N_col)
}

basic_table() %>%
  split_cols_by("ARM") %>%
  add_colcounts() %>%
  count_cumulative(
    vars = "AGE",
    thresholds = c(40, 60)
  ) %>%
  build_table(tern_ex_adsl)
#>           A: Drug X    B: Placebo   C: Combination
#>             (N=69)       (N=73)         (N=58)    
#> ——————————————————————————————————————————————————
#> AGE                                               
#>   <= 40   52 (75.4%)   58 (79.5%)     41 (70.7%)  
#>   <= 60   69 (100%)    73 (100%)      58 (100%)