mstate: plot.MarkovTest – R documentation

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plot.MarkovTest

Plot method for a MarkovTest object

Description

Plot method for an object of class 'MarkovTest'. It plots the trace of the log-rank statistics provided by MarkovTest.

Usage

## S3 method for class 'MarkovTest'
plot(
  x,
  y,
  what = c("states", "overall"),
  idx = NULL,
  quantiles = TRUE,
  qsup,
  states,
  xlab,
  ylab,
  main,
  ...
)

Arguments

`x`	Object of class 'MarkovTest'
`y`	The grid at which `MarkovTest` was calculated
`what`	Choose "states" for plotting state-specific traces, and "overall" for the overall chi-squared trace
`idx`	Vector of indices of wild bootstrap traces to plot
`quantiles`	Boolean whether or not to plot the 2.5 and 97.5 percent quantiles, default is `TRUE`
`qsup`	The index of the function in either `fn` (when plotting state-specific) or `fn2` (when plotting overall) to plot along with the traces; when missing this line is not included
`states`	Number of the qualifying state(s) to plot trace for
`xlab`	Text for x-axis label
`ylab`	Text for y-axis label
`main`	Text for title (main)
`...`	Further arguments to plot

Value

No return value

Author(s)

Hein Putter H.Putter@lumc.nl

Examples

## Not run: 
# Example provided by the prothrombin data
data("prothr")
# Apply Markov test to grid of monthly time points over the first 7.5 years
year <- 365.25
month <- year / 12
grid <- month * (1:90)
# Markov test for transition 1 (wild bootstrap based on 100 replications)
MT <- MarkovTest(prothr, id = "id", transition = 1,
                 grid = grid, B = 100)

plot(MT, grid, what="states", idx=1:50, states=rownames(attr(prothr, "trans")),
     xlab="Days since randomisation", ylab="Log-rank test statistic",
     main="Transition Normal -> Low")

plot(MT, grid,what="overall", idx=1:50,
     xlab="Days since randomisation", ylab="Chi-square test statistic",
     main="Transition Normal -> Low")

plot(MT, grid, what="states", quantiles=FALSE) # only trace
plot(MT, grid, what="states") # trace plus quantiles (default)
plot(MT, grid, what="states", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces
 
plot(MT, grid, what="overall", quantiles=FALSE) # only trace
plot(MT, grid, what="overall") # trace plus quantiles (default)
plot(MT, grid, what="overall", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces


## End(Not run)

mstate

Data Preparation, Estimation and Prediction in Multi-State Models

v0.3.1

GPL (>= 2)

Authors

Hein Putter [aut, cre], Liesbeth C. de Wreede [aut], Marta Fiocco [aut], Ronald B. Geskus [ctb], Edouard F. Bonneville [ctb], Damjan Manevski [ctb]

Initial release

2020-12-17