prop_diff: Proportion difference estimation

In tern: Create Common TLGs Used in Clinical Trials

Proportion difference estimation

Description

The analysis function estimate_proportion_diff() creates a layout element to estimate the difference in proportion of responders within a studied population. The primary analysis variable, vars, is a logical variable indicating whether a response has occurred for each record. See the method parameter for options of methods to use when constructing the confidence interval of the proportion difference. A stratification variable can be supplied via the strata element of the variables argument.

Usage

estimate_proportion_diff(
  lyt,
  vars,
  variables = list(strata = NULL),
  conf_level = 0.95,
  method = c("waldcc", "wald", "cmh", "ha", "newcombe", "newcombecc", "strat_newcombe",
    "strat_newcombecc"),
  weights_method = "cmh",
  na_str = default_na_str(),
  nested = TRUE,
  ...,
  var_labels = vars,
  show_labels = "hidden",
  table_names = vars,
  .stats = NULL,
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

s_proportion_diff(
  df,
  .var,
  .ref_group,
  .in_ref_col,
  variables = list(strata = NULL),
  conf_level = 0.95,
  method = c("waldcc", "wald", "cmh", "ha", "newcombe", "newcombecc", "strat_newcombe",
    "strat_newcombecc"),
  weights_method = "cmh"
)

a_proportion_diff(
  df,
  .var,
  .ref_group,
  .in_ref_col,
  variables = list(strata = NULL),
  conf_level = 0.95,
  method = c("waldcc", "wald", "cmh", "ha", "newcombe", "newcombecc", "strat_newcombe",
    "strat_newcombecc"),
  weights_method = "cmh"
)

Arguments

lyt	(PreDataTableLayouts) layout that analyses will be added to.
vars	(character) variable names for the primary analysis variable to be iterated over.
variables	(named list of string) list of additional analysis variables.
conf_level	(proportion) confidence level of the interval.
method	(string) the method used for the confidence interval estimation.
weights_method	(string) weights method. Can be either "cmh" or "heuristic" and directs the way weights are estimated.
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.
...	additional arguments for the lower level functions.
var_labels	(character) variable labels.
show_labels	(string) label visibility: one of "default", "visible" and "hidden".
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("estimate_proportion_diff") 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	(string) single variable name that is passed by rtables when requested by a statistics function.
.ref_group	(data.frame or vector) the data corresponding to the reference group.
.in_ref_col	(flag) TRUE when working with the reference level, FALSE otherwise.

Value

• estimate_proportion_diff() 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_proportion_diff() to the table layout.

• s_proportion_diff() returns a named list of elements diff and diff_ci.

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

Functions

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

• s_proportion_diff(): Statistics function estimating the difference in terms of responder proportion.

• a_proportion_diff(): Formatted analysis function which is used as afun in estimate_proportion_diff().

Note

When performing an unstratified analysis, methods "cmh", "strat_newcombe", and "strat_newcombecc" are not permitted.

See Also

d_proportion_diff()

Examples

## "Mid" case: 4/4 respond in group A, 1/2 respond in group B.
nex <- 100 # Number of example rows
dta <- data.frame(
  "rsp" = sample(c(TRUE, FALSE), nex, TRUE),
  "grp" = sample(c("A", "B"), nex, TRUE),
  "f1" = sample(c("a1", "a2"), nex, TRUE),
  "f2" = sample(c("x", "y", "z"), nex, TRUE),
  stringsAsFactors = TRUE
)

l <- basic_table() %>%
  split_cols_by(var = "grp", ref_group = "B") %>%
  estimate_proportion_diff(
    vars = "rsp",
    conf_level = 0.90,
    method = "ha"
  )

build_table(l, df = dta)

s_proportion_diff(
  df = subset(dta, grp == "A"),
  .var = "rsp",
  .ref_group = subset(dta, grp == "B"),
  .in_ref_col = FALSE,
  conf_level = 0.90,
  method = "ha"
)

# CMH example with strata
s_proportion_diff(
  df = subset(dta, grp == "A"),
  .var = "rsp",
  .ref_group = subset(dta, grp == "B"),
  .in_ref_col = FALSE,
  variables = list(strata = c("f1", "f2")),
  conf_level = 0.90,
  method = "cmh"
)

a_proportion_diff(
  df = subset(dta, grp == "A"),
  .var = "rsp",
  .ref_group = subset(dta, grp == "B"),
  .in_ref_col = FALSE,
  conf_level = 0.90,
  method = "ha"
)

tern documentation built on Sept. 24, 2024, 9:06 a.m.