## ----echo=FALSE-------------------------------------------
options(width=60,digits=3)
options(prompt="R> ")
library(knitr)
opts_chunk$set(fig.path="multistate-", linewidth=80)

hook_output = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
    # this hook is used only when the linewidth option is not NULL
    if (!is.null(n <- options$linewidth)) {
        x = knitr:::split_lines(x)
        # any lines wider than n should be wrapped
        if (any(nchar(x) > n)) 
            x = strwrap(x, width = n)
        x = paste(x, collapse = "\n")
    }
    hook_output(x, options)
})


## ---------------------------------------------------------
if (!require("msm"))
    stop("The `msm` package should be installed
to run code in this vignette") 
Qind <- rbind(c(0, 1, 0, 0),
              c(0, 0, 1, 0),
              c(0, 0, 0, 1),
              c(0, 0, 0, 0))
psor.wide.msm <- msm(state ~ months, subject=ptnum, data=psor, 
                     qmatrix = Qind,  gen.inits=TRUE,
                     covariates = ~ollwsdrt+hieffusn)
psor.wide.msm

## ---------------------------------------------------------
inds <- rbind(
    c(1,1,1,0,0,0,0,0,0),
    c(1,1,1,0,0,0,0,0,1),
    c(1,1,1,0,0,0,0,1,1),
    c(1,1,1,0,0,0,1,1,1),
    c(1,1,1,0,0,1,1,1,1),
    c(1,1,1,0,1,1,1,1,1),
    c(1,1,1,1,1,1,1,1,1)
)

## ---------------------------------------------------------
totlos.msm(psor.wide.msm, covariates=0, tot=10)

## ---------------------------------------------------------
focus_tlos <- function(par){
    x.new <- updatepars.msm(psor.wide.msm, par)
    totlos.msm(x.new, covariates=0, tot=10)["State 4"]
}

## ---------------------------------------------------------
library(fic)
fic(wide=psor.wide.msm, inds=inds, focus=focus_tlos)