ctsem (version 3.11.0)

ctDiscreteParsPlot: ctDiscreteParsPlot

Description

Plots the output from ctDiscretePars, for model implied regression strengths at specified times for continuous time models fit with ctStanFit.

Usage

ctDiscreteParsPlot(
  x,
  indices = "all",
  quantiles = c(0.025, 0.5, 0.975),
  latentNames = "auto",
  ylab = "Coefficient",
  xlab = "Time interval",
  ylim = NA,
  facets = NA,
  splitSubjects = TRUE,
  colour = "Effect",
  title = "auto",
  polygonalpha = 0.1,
  ggcode = FALSE
)
ctStanDiscreteParsPlot(
  x,
  indices = "all",
  quantiles = c(0.025, 0.5, 0.975),
  latentNames = "auto",
  ylab = "Coefficient",
  xlab = "Time interval",
  ylim = NA,
  facets = NA,
  splitSubjects = TRUE,
  colour = "Effect",
  title = "auto",
  polygonalpha = 0.1,
  ggcode = FALSE
)

Value

A ggplot2 object. This can be modified by the various ggplot2 functions, or displayed using print(x).

Arguments

x

list object returned from ctDiscretePars.

indices

Either a string specifying type of plot to create, or an n by 2 matrix specifying which indices of the output matrix to plot. 'AR' specifies all diagonals, for discrete time autoregression parameters. 'CR' specifies all off-diagonals,for discrete time cross regression parameters. 'all' plots all AR and CR effects at once.

quantiles

numeric vector of length 3, with values between 0 and 1, specifying which quantiles to plot. The default plots 95% credible intervals and the posterior median at 50%.

latentNames

Vector of character strings denoting names for the latent variables. 'auto' just uses eta1 eta2 etc.

ylab

y label.

xlab

x label.

ylim

Custom ylim.

facets

May be 'Subject' or 'Effect'.

splitSubjects

if TRUE, subjects are plotted separately, if FALSE they are combined.

colour

Character string denoting how colour varies. 'Effect' or 'Subject'.

title

Character string. 'auto' generates automatically, NULL can be used to disable title.

polygonalpha

Numeric between 0 and 1 to multiply the alpha of the fill.

ggcode

if TRUE, returns a list containing the data.table to plot, and a character string that can be evaluated (with the necessary arguments such as ylab etc filled in). For modifying plots.

Examples

data.table::setDTthreads(1) #ignore this line
x <- ctDiscretePars(ctstantestfit)
ctDiscreteParsPlot(x, indices='CR')

#to modify plot:
g <- ctDiscreteParsPlot(x, indices='CR') +
 ggplot2::labs(title='My ggplot modification')
print(g)