msmtools (version 1.3)

survplot: Plot and get survival data from a multi-state model

Description

Plot a Kaplan-Meier curve and compare it with the fitted survival probability computed from a msm model. Fast builds and returns the associated datasets.

Usage

survplot(x, from = 1, to = NULL, range = NULL, covariates = "mean",
  exacttimes = TRUE, times, grid = 100L, km = FALSE, return.all = FALSE,
  return.km = NULL, return.p = NULL, convert = FALSE, add = FALSE,
  ci = c("none", "normal", "bootstrap"), interp = c("start", "midpoint"),
  B = 100L, legend.pos = "topright", xlab = "Time",
  ylab = "Survival Probability", main = NULL, lty.fit = 1, lwd.fit = 1,
  col.fit = "red", lty.ci.fit = 3, lwd.ci.fit = 1, col.ci.fit = col.fit,
  mark.time = FALSE, lty.km = 5, lwd.km = 1, col.km = "darkblue",
  do.plot = TRUE, plot.width = 7, plot.height = 7, devnew = TRUE,
  verbose = TRUE)

Arguments

x

A msm object.

from

State from which to compute the estimated survival. Default to state 1.

to

The absorbing state to which compute the estimated survival. Default to the highest state found by absorbing.msm.

range

A numeric vector of two elements which gives the time range of the plot.

covariates

Covariate values for which to evaluate the expected probabilities. These can either be: the string "mean", denoting the means of the covariates in the data (this is the default), the number 0, indicating that all the covariates should be set to zero, or a list of values, with optional names. For example: list (75, 1) where the order of the list follows the order of the covariates originally given in the model formula, or a named list: list (age = 75, gender = "M").

exacttimes

If TRUE (default) then transition times are known and exact. This is inherited from msm and should be set the same way.

times

An optional numeric vector giving the times at which to compute the fitted survival.

grid

An integer which tells at how many points to compute the fitted survival (see 'Details'). If times is passed, grid is ignored. It has a default of 100 points.

km

If TRUE, then the Kaplan-Meier curve is shown. Default is FALSE.

return.all

If TRUE, then all the datasets used to draw the plot will be return to the environment. This argument saves you some typing time since you do not have to pass neither return.km nor return.p. Default is FALSE (see 'Details').

return.km

If TRUE, then the dataset used for building the Kaplan-Meier is returned as an object of class data.table unless convert is set to TRUE (see convert). Default is FALSE. survplot must be assigned to an object in order to get the data in the environment (see 'Details').

return.p

If TRUE, then the dataset used for building the fitted survival curve is returned as an object of class data.table unless convert is set to TRUE (see convert). Default is FALSE. survplot must be assigned to an object in order to get the data in the environment (see 'Details').

convert

If TRUE, then any returned object is automatically converted to the class data.frame. This is done in place and comes at very low cost both from running time and memory consumption (see setDF).

add

If TRUE, then a new layer is added to the current plot. Default is FALSE.

ci

If "none" (the default), then no confidence intervals are plotted. If "normal" or "bootstrap", confidence intervals are plotted based on the respective method in pmatrix.msm. This is very computationally-intensive, since intervals must be computed at a series of times.

interp

If "start" (the default), then the entry time into the absorbing state is assumed to be the time it is first observed in the data. If "midpoint", then the entry time into the absorbing state is assumed to be halfway between the time it is first observed and the previous observation time. This is generally more reasonable for "progressive" models with observations at arbitrary times.

B

Number of bootstrap or normal replicates for the confidence interval. The default is 100 rather than the usual 1000, since these plots are for rough diagnostic purposes.

legend.pos

Where to position the legend. Default is "topright", but x and y coordinate can be passed. If NULL, then legend is not shown.

xlab

x axis label.

ylab

y axis label.

main

The main title of the plot(s) as character. Default is NULL.

lty.fit

Line type for the fitted curve. See par.

lwd.fit

Line width for the fitted curve. See par.

col.fit

Line color for the fitted curve. See par.

lty.ci.fit

Line type for the fitted curve confidence limits. See par.

lwd.ci.fit

Line width for the fitted curve confidence limits. See par.

col.ci.fit

Line color for the fitted curve confidence limits. See par.

mark.time

Mark the empirical survival curve at each censoring point. See lines.survfit.

lty.km

Line type for the Kaplan-Meier passed to lines.survfit. See par.

lwd.km

Line width for the Kaplan-Meier passed to lines.survfit. See par.

col.km

Line color for the Kaplan-Meier passed to lines.survfit. See par.

do.plot

If FALSE, then no plot is shown at all. Default is TRUE.

plot.width

Width of new graphical device. Default is 7. See par.

plot.height

Height of new graphical device. Default is 7. See par.

devnew

Set the graphical device where to plot. By default, survplot plots on a new device by setting dev.new. If FALSE, then a plot is drawn onto the current device as specified by dev.cur. If FALSE and no external devices are opened, then a plot is drawn using internal graphics. See dev.

verbose

If FALSE, all information produced by print, cat and message are suppressed. Default is TRUE.

Value

If return.all is set to TRUE, then survplot returns a named list with $km and $fitted as data.table or as data.frame when convert = TRUE. To save them in the working environment, assign survplot to an object (see 'Examples').

$km contains up to 4 columns:

subject

The ordered subject ID as passed in the msm function.

mintime

The times at which to compute the fitted survival.

mintime_exact

If exacttimes is TRUE, then the relative timing is reported.

anystate

State of transition to compute the Kaplan-Meier.

------

$fitted contains 2 columns:

time

Times at which to compute the fitted survival.

probs

The corresponding values of the fitted survival.

Details

The function is a wrapper of plot.survfit.msm and does more things. survplot manages correctly the plot of a fitted survival in an exact times framework (when exacttimes = TRUE) by just resetting the time scale and looking at the follow-up time. It can fastly build and return to the user the datasets used to compute the Kaplan-Meier and the fitted survival by setting return.all = TRUE. When this is TRUE, setting return.km or return.p to FALSE produces an error and survplot does not conclude the job. If these are set to TRUE, a warning is raised but the job is taken to the end. For more details about how survplot returns objects, please refer to the vignette with vignette("msmtools").

The user can defined custom times (through times) or let survplot choose them on its own (through grid). In the latter case, survplot looks for the follow-up time and divides it by grid. The higher it is, the finer the grid will be so that computing the fitted survival will take longer, but will be more precise.

References

Titman, A. and Sharples, L.D. (2010). Model diagnostics for multi-state models, Statistical Methods in Medical Research, 19, 621-651.

Titman, A. and Sharples, L.D. (2008). A general goodness-of-fit test for Markov and hidden Markov models, Statistics in Medicine, 27, 2177-2195.

Jackson, C.H. (2011). Multi-State Models for Panel Data: The msm Package for R. Journal of Statistical Software, 38(8), 1-29. URL http://www.jstatsoft.org/v38/i08/.

See Also

plot.survfit.msm msm, pmatrix.msm, setDF

Examples

# NOT RUN {
data( hosp )

# augmenting the data
hosp_augmented = augment( data = hosp, data_key = subj, n_events = adm_number,
                          pattern = label_3, t_start = dateIN, t_end = dateOUT,
                          t_cens = dateCENS )

# let's define the initial transition matrix for our model
Qmat = matrix( data = 0, nrow = 3, ncol = 3, byrow = TRUE )
Qmat[ 1, 1:3 ] = 1
Qmat[ 2, 1:3 ] = 1
colnames( Qmat ) = c( 'IN', 'OUT', 'DEAD' )
rownames( Qmat ) = c( 'IN', 'OUT', 'DEAD' )

# attaching the msm package and running the model using
# gender and age as covariates
library( msm )
msm_model = msm( status_num ~ augmented_int, subject = subj,
                 data = hosp_augmented, covariates = ~ gender + age,
                 exacttimes = TRUE, gen.inits = TRUE, qmatrix = Qmat,
                 method = 'BFGS', control = list( fnscale = 6e+05, trace = 0,
                 REPORT = 1, maxit = 10000 ) )

# plotting the fitted and empirical survival from state = 1
survplot( msm_model, km = TRUE, ci = 'none',
          verbose = FALSE )

# plotting the fitted and empirical survival from state = 2 and
# adding it to the previous plot
survplot( msm_model, from = 2, km = TRUE, ci = 'none', add = TRUE,
          verbose = FALSE )

# returning fitted and empirical data
all_data = survplot( msm_model, ci = 'none', return.all = TRUE,
                     verbose = FALSE, do.plot = FALSE )

# saving them separately
km_data = all_data[[ 1 ]]
fitted_data = all_data[[ 2 ]]
# }
# NOT RUN {
# }