Computes and plots combined effects and quantiles for effects of time independent predictors on subject level parameters of a ctStanFit object.
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 = 50, filter = NA, plot = FALSE, ...)fit object from ctStanFit
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.
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.
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.
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.
Logical. If TRUE (default), the ctStanParMatrices function
is used to return an expanded range of possible matrices of interest.
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.
Positive integer specifying the maximum number of saved iterations to use. Character string 'all' can also be used.
positive numeric indicating time interval to use for discrete time parameter matrices,
if parmatrices=TRUE.
Positive integer specifying the number of subjects to compute values for. Character string 'all' can also be used. Time taken is a function of nsubjects*niterations.
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).
Logical. If TRUE, nothing is returned but instead ctPlotArray
is used to plot the output instead.
arguments to pass to ctPlotArray for plotting.
Either a three dimensional array of predictor effects, or nothing with a plot generated.
# NOT RUN {
#samples reduced here for speed
ctStanTIpredeffects(ctstantestfit,plot=TRUE,whichpars='CINT',nsamples=10,nsubjects=10)
# }
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