ctsem (version 3.2.1)

ctStanDiscreteParsPlot: ctStanDiscreteParsPlot

Description

Plots model implied regression strengths at specified times for continuous time models fit with ctStanFit.

Usage

ctStanDiscreteParsPlot(
  x,
  indices = "all",
  add = FALSE,
  legend = TRUE,
  polygon = TRUE,
  gg = TRUE,
  plot = TRUE,
  quantiles = c(0.025, 0.5, 0.975),
  times = seq(0, 10, 0.1),
  latentNames = "auto",
  lwdvec = "auto",
  colvec = "auto",
  ltyvec = "auto",
  plotcontrol = list(ylab = "Value", xlab = "Time interval", main =
    "Regression coefficients", type = "l", xaxs = "i"),
  grid = FALSE,
  legendcontrol = list(x = "topright", bg = "white"),
  polygonalpha = 0.1,
  polygoncontrol = list(steps = 20)
)

Arguments

x

list object returned from ctStanDiscretePars.

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.

add

Logical. If FALSE, a new plot is generated, if TRUE, specified plot/s are overlayed on existing plot.

legend

Logical. If TRUE, generates a legend.

polygon

Logical. If TRUE, fills a polygon between the first and last specified quantiles.

gg

Logical -- use GGplot2 or not? if TRUE, other graphical parameters are ignored, and the ggplot object is returned and may be modified further.

plot

Logical. Only relevant with gg=TRUE.

quantiles

numeric vector of length 3, with values between 0 and 1, specifying which quantiles to plot. The default of c(.05,.5,.95) plots 95% credible intervals and the posterior median at 50%.

times

Numeric vector of positive values, discrete time parameters will be calculated for each.

latentNames

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

lwdvec

Either 'auto', or a vector of positive integers denoting line widths for each quantile. 'auto' specifies c(1,3,1) if there are 3 quantiles to be plotted (default), otherwise simply 3.

colvec

Either 'auto', or a vector of color values denoting colors for each index to be plotted. 'auto' generates colors using the grDevices::rainbow function.

ltyvec

Either 'auto', or a vector of line type integers (as for the lty parameter normally) denoting line types for each quantile. 'auto' specifies c(3, 1, 3) if there are 3 quantiles to be plotted (default), otherwise simply 1.

plotcontrol

list of arguments to pass to plot function. The following arguments are ignored: ylim,lwd,lty,col,x,y.

grid

Logical. Plot with a grid?

legendcontrol

list of arguments to pass to legend function. 'legend=' and 'text.col=' arguments will be ignored.

polygonalpha

Numeric between 0 and 1 to multiply the alpha (transparency) of colvec by for the fill polygon.

polygoncontrol

list of arguments to pass to ctPoly function (if polygon=TRUE). x,y, and col arguments will be ignored. Steps specifies the number of polygons to overlay to create a graduated transparency. Set to 1 for a flat looking plot.

Examples

# NOT RUN {
if (!exists("ctstantestfit")) example(ctstantestfit)
x <- ctStanDiscretePars(ctstantestfit)
ctStanDiscreteParsPlot(x, indices='CR')

#to modify plot:
g <- ctStanDiscreteParsPlot(x, indices='CR',plot=FALSE) + 
 ggplot2::labs(title='My ggplot modification')
print(g)
# }
# NOT RUN {
# }