icmstate (version 0.2.0)

plot_probtrans: Plot the transition probabilities for a fitted npmsm model

Description

For a fitted npmsm model plot the transition probabilities from a certain state for all possible (direct and indirect) transitions.

Usage

plot_probtrans(
  npmsmlist,
  from = NULL,
  to = NULL,
  transitions = NULL,
  landmark,
  interpolate = TRUE,
  facet = TRUE,
  times_interpol = NULL,
  c.legend = TRUE,
  c.names = NULL
)

Value

A plot will be produced in the plotting window. When assigning the output to an object, the underlying data frame used for plotting and a 'ggplot' object will be returned in a list.

Arguments

npmsmlist

An "npmsm" object or a list containing multiple "npmsm" objects

from

A numeric value indicating the state from which we consider the transition probabilities. Default is NULL, meaning we consider transition probabilities from all states from which a direct transition is possible.

to

A numeric vector indicating to which states we consider the transition probabilities. Only states that can be reached from the "from" state are considered.

transitions

A numeric vector indicating which transitions to consider (plot). Can only be used if "from" is not specified, as it only works for direct transitions.

landmark

A landmark time indicating from which time on survival should be determined. If missing, the smallest between the time in the first "npmsm" object or 0 will be used.

interpolate

Should the cumulative hazard be linearly interpolated before determining transition probabilities? Default is TRUE.

facet

Should the resulting plot be faceted (one panel per transition)? Default is TRUE.

times_interpol

At which times should the cumulative hazard be interpolated? Only necessary to specify if interpolate = TRUE.

c.legend

Should legend be displayed for colour (different entries in npmsmlist)? Default is TRUE.

c.names

A character vector indicating the names to display in the legend. These names should represent the entries in npmsmlist.. Default = NULL.

Examples

require(mstate)
require(ggplot2)
#Generate from an illness-death model with exponential transitions with 
#rates 1/2, 1/10 and 1 for 10 subjects over a time grid.
gd <- sim_weibmsm(tmat = trans.illdeath(), shape = c(1,1,1),
                  scale = c(2, 10, 1), n_subj = 10, obs_pars = c(2, 0.5, 20), 
                  startprobs = c(0.9, 0.1, 0))
#Fit 2 models: 1 with at most 4 iterations and 1 with at most 20
mod1 <- npmsm(gd, trans.illdeath(), maxit = 4)
mod2 <- npmsm(gd, trans.illdeath(), maxit = 20)

#Plot the transition probabilities from state 1, without interpolating 
#the cumulative hazard for the npmsm runs with max 4 and 20 iterations.
plot_probtrans(list(mod1, mod2), from = 1, interpolate = FALSE,
               c.names = c("4 iterations", "20 iterations"))