ctStanTIpredeffects: Get time independent predictor effect estimates

In ctsem: Continuous Time Structural Equation Modelling

Get time independent predictor effect estimates

Description

Computes and plots combined effects and quantiles for effects of time independent predictors on subject level parameters of a ctStanFit object.

Usage

ctStanTIpredeffects(
  fit,
  returndifference = FALSE,
  probs = c(0.025, 0.5, 0.975),
  includeMeanUncertainty = FALSE,
  whichTIpreds = 1,
  parmatrices = TRUE,
  whichpars = "all",
  nsamples = 100,
  timeinterval = 1,
  nsubjects = 20,
  filter = NA,
  plot = FALSE
)

Arguments

fit	fit object from ctStanFit
returndifference	logical. If FALSE, absolute parameter values are returned. If TRUE, only the effect of the covariate (i.e. without the average value of the parameter) are returned. The former can be easier to interpret, but the latter are more likely to fit multiple plots together. Not used if parmatrices=TRUE.
probs	numeric vector of quantile probabilities from 0 to 1. Specify 3 values if plotting, the 2nd will be drawn as a line with uncertainty polygon based on 1st and 3rd.
includeMeanUncertainty	if TRUE, output includes sampling variation in the mean parameters. If FALSE, mean parameters are fixed at their median, only uncertainty in time independent predictor effects is included.
whichTIpreds	integer vector specifying which of the tipreds in the fit object you want to use to calculate effects. Unless quadratic / higher order versions of predictors have been included, selecting more than one probably doesn't make sense. If for instance a squared predictor has been included, then you can specify both the linear and squared version. The x axis of the plot (if generated) will be based off the first indexed predictor. To check what predictors are in the model, run fit$ctstanmodel$TIpredNames.
parmatrices	Logical. If TRUE (default), system matrices rather than specific parameters are referenced – e.g. 'DRIFT' instead of a parameter name like drift12.
whichpars	if parmatrices==TRUE, character vector specifying which matrices, and potentially which indices of the matrices, to plot. c('dtDRIFT[2,1]', 'DRIFT') would output for row 2 and column 1 of the discrete time drift matrix, as well as all indices of the continuous time drift matrix. If parmatrices==FALSE, integer vector specifying which of the subject level parameters to compute effects on. The integers corresponding to certain parameters can be found in the param column of the fit$setup$matsetup object. In either case 'all' uses all available parameters.
nsamples	Positive integer specifying the maximum number of saved iterations to use. Character string 'all' can also be used.
timeinterval	positive numeric indicating time interval to use for discrete time parameter matrices, if parmatrices=TRUE.
nsubjects	Positive integer specifying the number of subjects to compute values for. When only one TIpred is used, this specifies the number of points along the curve. Character string 'all' can also be used. Time taken for plotting is a function of nsubjects*niterations.
filter	either NA, or a length 2 vector, where the first element contains the time independent predictor index to filter by, and the second contains the comparison operator in string form (e.g. "< 3", to only calculate effects for subjects where the tipreds of the denoted index are less than 3).
plot	Logical. If TRUE, nothing is returned but instead ctPlotArray is used to plot the output instead.

Value

Either a three dimensional array of predictor effects, or nothing with a plot generated.

Examples

ctStanTIpredeffects(ctstantestfit,
 whichpars=c('CINT','dtDIFFUSION[2,2]'), plot=TRUE)

ctsem documentation built on Sept. 11, 2024, 9:06 p.m.