CompositeReady: An constructor function for the S4 CompositeReady class

In pscore: Standardizing Physiological Composite Risk Endpoints

An constructor function for the S4 CompositeReady class

Description

An constructor function for the S4 CompositeReady class

Usage

CompositeReady(
  data,
  covmat,
  sigma,
  standardize,
  use.prethreshold,
  distances,
  distanceDensity,
  winsorizedValues,
  better,
  rawdata,
  groups,
  thresholds,
  higherisbetter,
  k,
  rawtrans
)

Arguments

data	A data frame of the ready to use data
covmat	A covariance matrix of the data
sigma	A vector of the standard deviations of each variable
standardize	A logical whether the data were standardized or not
use.prethreshold	A logical value whether to calculate covariance matrix based on the data after winsorizing, but before applying the threshold. Defaults to FALSE, so that covariances are calculated after thresholds (if any) are applied.
distances	A data frame of the distance scores
distanceDensity	A ggplot2 graph of the densities of each distance score. If not passed, generated automatically from the data.
winsorizedValues	A data frame indicating the values used (if any) for winsorization. Should have one row for each variable in the dataset.
better	A logical vector the same length as the number of columns in the distance scores indicating whether higher or lower values are better for each.
rawdata	A data frame with at least one row and column
groups	an optional character vector. If omitted defaults to a character vector of all “one”s.
thresholds	an optional named list where names match the names in groups. If using defaults for groups, should name it “a”.
higherisbetter	an optional logical vector
k	an optional integer, the number of columns in the raw data
rawtrans	A list of functions to transform the raw data (and thresholds).

Value

An S4 object of class “CompositeReady”

Examples

#make me!

pscore documentation built on May 14, 2022, 1:06 a.m.