`"msSurv"`

contains nonparametric estimates
for multistate models subject to right censoring and possibly left
truncation by calling `msSurv`

.`new("msSurv", ...)`

.
"msSurv" objects are also returned from function `msSurv`

`tree`

:- Object of class
`"graphNEL"`

. A`graphNEL`

object with nodes corresponding to the states in the multistate model and the edges corresponding to the allowed transitions. `ns`

:- Object of class
`"numeric"`

. The number of unique states in the multistate model. `et`

:- Object of class
`"numeric"`

. The event times. `pos.trans`

:- Object of class
`"character"`

. Possible transtitions between states. `nt.states`

:- Object of class
`"character"`

. The non-terminal states in the multistate model. `dNs`

:- Object of class
`"array"`

. A matrix containing the differential of the counting processes for the event times. `Ys`

:- Object of class
`"array"`

. A matrix containing the at risk sets for the event times. `sum_dNs`

:- Object of class
`"array"`

. A matrix containing the differential for the counting process for total transitions out of each state, at each event time. `dNs.K`

:- Object of class
`"array"`

. A matrix containing the differential of the weighted counting process described in Datta and Satten (2001). `Ys.K`

:- Object of class
`"array"`

. A matrix containing the weighted at risk sets described in Datta and Satten (2001). `sum_dNs.K`

:- Object of class
`"array"`

. A matrix containing the differential of the weighted counting process for total transitions out of each state, at each event time. `ps`

:- Object of class
`"array"`

. A matrix with state occupation probabilities for each state at each event time. `AJs`

:- Object of class
`"array"`

. An array containing matrices of Aalen-Johansen estimates (transition probabilities) at each event time. `I.dA`

:- Object of class
`"array"`

. A matrix containing the I+dA transition matrices for Aalen-Johansen computation. `cov.AJs`

:- Object of class
`"array"`

. An array containing the variance-covariance matrices for transition probabilities at each event time. `var.sop`

:- Object of class
`"array"`

. A matrix containing covariance estimates for the state occupation probabilities. `cov.dA`

:- Object of class
`"array"`

. A matrix containing the covariance of dA matrices used for computation of cov(P(s,t)). `Fnorm`

:- Object of class
`"array"`

. A matrix containing normalized state entry distributions. Note: "NA" is recorded for`Fnorm`

at the initial state(s) (node(s)). `Fsub`

:- Object of class
`"array"`

. A matrix containing unnormalized (subdistribution) state entry distributions. Note: "NA" is recorded for`Fsub`

at the initial state(s) (node(s)). `Gnorm`

:- Object of class
`"array"`

. A matrix containing normalized state exit distributions. Note: "NA" is recorded for`Gnorm`

at the terminal state(s) (node(s)). `Gsub`

:- Object of class
`"array"`

. A matrix containing unnormalized (subdistribution) state exit distributions. Note: "NA" is recorded for`Gsub`

at the terminal state(s) (node(s)). `Fnorm.var`

:- Object of class
`"array or NULL"`

. A matrix containing variance estimates for the normalized state entry distributions. Will be`NULL`

if the user does not specify`bs=TRUE`

. `Fsub.var`

:- Object of class
`"array or NULL"`

. A matrix containing variance estimates for the unnormalized (subdistribution) state entry distributions. Will be`NULL`

if the user does not specify`bs=TRUE`

. `Gnorm.var`

:- Object of class
`"array or NULL"`

. A matrix containing variance estimates for the normalized state exit distributions. Will be`NULL`

if the user does not specify`bs=TRUE`

. `Gsub.var`

:- Object of class
`"array or NULL"`

. A matrix containing variance estimates for the unnormalized (subdistribution) state exit distributions. Will be`NULL`

if the user does not specify`bs=TRUE`

.

- ACCESSOR FUNCTIONS
`signature(object = "msSurv")`

: Accessor functions are defined for each of the slots in an`msSurv`

object, e.g.`tree`

,`ns`

,`et`

, etc. The accessor functions all have the same name as the corresponding slot name, and all have the same signature.`signature(x = "msSurv")`

: Print method for "msSurv" objects.- show
`signature(object = "msSurv")`

: Show method for "msSurv" objects.- summary
`signature(object = "msSurv")`

: Summary function for "msSurv" objects. Additional arguements:`digits=3`

- The number of significant digits to use for estimates. Defalt is 3.
`all=FALSE`

- Logical argument to determine whether
summary information should be displayed for all event times or
only for the key percentile time points (IQR). Default is FALSE
where
`all=FALSE`

corresponds to only the IQR of event times being displayed in the summary output. `times=NULL`

- Numeric vector of time-points at which to
present summary information. Overrides
`all`

if supplied. `ci.fun="linear"`

- Transformation applied to confidence intervals. Possible choices are "linear", "log", "log-log", and "cloglog". Default is "linear".
`ci.level=0.95`

- Confidence level. Default is 0.95.
`stateocc=TRUE`

- Logical argument specifying whether
state occupation probabilities should be displayed. Default is
`TRUE`

. `trans.pr=TRUE`

- Logical argument specifying whether
state transition probabilities should be displayed. Default is
`TRUE`

. `dist=TRUE`

- Logical argument specifying whether
state entry / exit distributions should be displayed. Default is
`TRUE`

. `DS=FALSE`

- Logical argument specifying whether
Datta-Satten weighted counting processes.
Default is
`FALSE`

.

- plot
`signature(x = "msSurv", y = "missing")`

: Plotting method for "msSurv" objects. Additional arguments:`states="ALL"`

- States in the multistate model to be plotted. Default is all states in the system. User may specify individual states or multiple states to plot.
`trans="ALL"`

- Transitions in the multistate model to be plotted. Default is all transitions. Transitions should be entered with a space between the two states, e.g.: "1 1".
`CI=TRUE`

- A logical argument to specify whether
pointwise confidence intervals should be plotted. If the
user specifies
`CI=FALSE`

, only the estimates are plotted. If the user specifies`CI=TRUE`

, plots of each estimate and its corresponding confidence intervals are created (if appropriate variances are available). The default is`TRUE`

. `ci.level=0.95`

- Confidence level. Default is 0.95.
`ci.trans="linear"`

- Transformation applied to confidence intervals. Possible choices are "linear", "log", "log-log", and "cloglog". Default is "linear".
`plot.type="stateocc"`

- Determines the type of estimate to be plotted. User may specify "transprob" for transition probability plots, "stateocc" for state occupation probability plots, "entry.norm" / "entry.sub" for normalized / unnormalized state entry time distributions, or "exit.norm" / "exit.sub" for normalized / unnormalized state exit time distributions. "stateocc" is the default.
`...`

- Further arguments passed to
`xyplot`

Andersen, P.K., Borgan, O., Gill, R.D. and Keiding, N. (1993). Statistical models based on counting processes. Springer Series in Statistics. New York, NY: Springer.

Datta, S. and Satten G.A. (2001). Validity of the Aalen-Johansen estimators of stage occupation probabilities and Nelson-Aalen estimators of integrated transition hazards for non-Markov models. Statistics and Probability Letters, 55(4): 403-411.

Datta S, Satten GA (2002). Estimation of Integrated Transition Hazards and Stage Occupation Probabilities for Non-Markov Systems under Dependent Censoring. Biometrics, 58(4), 792-802.

`'msSurv'`

see `msSurv`

.## 3-state illness-death multistate model (no left-truncation) ## Row data for 3 individuals ## Data in the form "id", "start", "stop", "start.stage", "end.stage" p1 <- c(1,0,0.21,1,3) p2 <- c(2,0,0.799,1,2) p22 <- c(2,0.799,1.577,2,3) p3 <- c(3,0,0.199,1,0) ## Combining data into a matrix ex1 <- rbind(p1,p2,p22,p3) colnames(ex1) <- c("id", "start", "stop", "start.stage", "end.stage") ex1 <- data.frame(id=ex1[,1], start=ex1[,2], stop=ex1[,3], start.stage=ex1[,4], end.stage=ex1[,5]) ## Inputting nodes & edges of the tree structure Nodes <- c("1","2","3") # states in MSM Edges <- list("1"=list(edges=c("2","3")),"2"=list(edges=c("3")), "3"=list(edges=NULL)) ## allowed transitions between states ## edges=NULL implies terminal node ## Specifying tree treeobj <- new("graphNEL", nodes=Nodes, edgeL=Edges, edgemode="directed") ans1 <- msSurv(ex1, treeobj) print(ans1) ## same as 'show(ans1)' summary(ans1) ## prints IQR for ans1 summary(ans1, all=TRUE) ## prints all event times for ans1 ## prints only state occupation probability info for all event times summary(ans1, all=TRUE, trans.pr=FALSE, dist=FALSE) plot(ans1) ## plots state occupation probability plot(ans1, states="1") plot(ans1, states=c("1", "2")) plot(ans1, plot.type="transprob") ## plots for transition probability plot(ans1, plot.type="transprob", trans=c("1 2", "1 3"))