Skip to contents

Cumulative Counts with Thresholds

Source: R/count_cumulative.R
count_cumulative.Rd

[Stable]

Summarize cumulative counts of a (numeric) vector that is less than, less or equal to, greater than, or greater or equal to user-specific 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",
  na_str = NA_character_,
  nested = TRUE,
  ...,
  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)
character for label.

show_labels

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

na_str

(string)
string used to replace all NA or empty values in the output.

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.

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. 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.

Value

  • s_count_cumulative() returns a named list of count_fractions: a list with each thresholds value as a component, each component containing a vector for the count and fraction.

  • count_cumulative() returns a layout object suitable for passing to further layouting functions, or to rtables::build_table(). Adding this function to an rtable layout will add formatted rows containing the statistics from s_count_cumulative() to the table layout.

Functions

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

  • a_count_cumulative(): Formatted analysis function which is used as afun in count_cumulative().

  • count_cumulative(): Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper for rtables::analyze().

See also

Relevant helper function h_count_cumulative(), and descriptive function d_count_cumulative().

Examples

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%)