Description Usage Arguments Details Value Note Author(s) References See Also Examples
This function calculates the transition probability matrix between any two values s and t and then prints it. The function also calculates and prints the cov(P(s,t)) matrix if the user specifies. Values are returned invisibly.
1 |
object |
An msSurv object. |
s |
The lower time. Default is 0. |
t |
The highter time. Default is "last" which is the highest (or "last") event time. |
deci |
Numeric argument specifying number of decimal places for estimates. Default is 4. |
covar |
Logical argument to determine if var(P(s,t)) is computed. Default is FALSE. |
Computation of P(s,t) and var(P(s,t)) for multistate models are described in Andersen et al. (1993).
Returned invisibly:
The transition probability matrix between two times s and t.
Covariance matrix for the transition probability matrix
between two times s and t (if covar==TRUE
).
If s = 0 and all subjects begin in the initial state at time 0, then the top row of P(0,t) yields the state occupation probabilities at time t. Data are assumed to follow a Markovian model.
Nicole Ferguson <nicole.ferguson@kennesaw.edu>, Guy Brock <guy.brock@louisville.edu>, Somnath Datta <somnath.datta@louisville.edu>
Nicole Ferguson, Somnath Datta, Guy Brock (2012). msSurv: An R Package for Nonparametric Estimation of Multistate Models. Journal of Statistical Software, 50(14), 1-24. URL http://www.jstatsoft.org/v50/i14/.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## Row elements of data
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")
## Running msSurv
ans1 <- msSurv(ex1,treeobj)
Pst(ans1, s=0.25, t=2.5)
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