More small changes with prior specs.

R/crwPostIS.R

@@ -145,7 +145,8 @@
   }  else {
     colnames(out$sim) <- apply(expand.grid(c("mu","nu"), c("x","y")), 1, paste, collapse=".")
   }
-  isw <- ifelse(is.null(object.sim$thetaSampList) & fullPost==TRUE, out$ll - object.sim$loglik - dens, 0)
+  ln.prior = ifelse(!is.null(object.sim$prior), object.sim$prior(par[eInd]), 0)
+  isw <- ifelse(is.null(object.sim$thetaSampList) & fullPost==TRUE, out$ll - object.sim$loglik - dens, 0) + ln.prior
   samp <- list(alpha.sim=out$sim,
                predType=object.sim$predType, Time=object.sim$Time,
                loglik=out$lly+out$llx, par=par, log.isw = isw)

R/crwSamplePar.R

@@ -124,10 +124,11 @@ crwSamplePar <- function(object.sim, method="IS", size=1000, df=Inf, grid.eps=1,
       par[eInd] <- parMLE[eInd] + eps
       if(df==Inf) dens <- dmvnorm(eps, sigma=scale*Cmat, log=TRUE) - dmvnorm(0.0*eps, sigma=scale*Cmat, log=TRUE)
       else dens <- dmvt(eps, sigma=scale*Cmat, df=df, log=TRUE) - dmvt(0.0*eps, sigma=scale*Cmat, df=df, log=TRUE)
+      ln.prior = ifelse(!is.null(prior), prior(par[eInd]), 0)
       n2ll.val <- crwN2ll(par[eInd], fixPar, y, noObs, delta, a,
                           P, mov.mf, err.mfX, err.mfY, rho=rho, activity=activity,
                           n.errX, n.errY, n.mov, driftMod, prior, need.hess=FALSE, 
-                          constr=list(lower=lower, upper=upper)) + prior(par[is.na(fixPar)])
+                          constr=list(lower=lower, upper=upper)) + ln.prior
       thetaMat[i,] <- c(-n2ll.val/2 - dens, -n2ll.val/2, dens, par)
     }
     thetaMat[size,] <- c(object.sim$loglik, object.sim$loglik, 0, object.sim$par)

man/crwMLE.Rd

@@ -50,7 +50,8 @@ are vectors the same length as theta giving the box constraints for the
 parameters}
 
 \item{prior}{A function returning the log-density function of the parameter
-prior specification}
+prior distribution. THIS MUST BE A FUNCTION OF ONLY THE FREE PARAMETERS. Any
+fixed parameters should not be included.}
 
 \item{need.hess}{A logical value which decides whether or not to evaluate
 the Hessian for parameter standard errors}
@@ -156,17 +157,10 @@ longitude mdoel.
 The \code{inital.state} is a list with the following elemets (with the exact
 names):
 
-\code{a1.y} A vector with initial state values for the \dQuote{latitude}
-coordinate. It have 2 elemets (location at time 1, velocity at time 1) for
-non-drift models and 3 elemets for drift models (location at time 1,
-velocity at time 1, drift velocity at time 1) for driftmodels,
-
-\code{P1.y} Covarince matrix for the state at time 1 (measure of uncertainty
-for your inital state) \code{a1.y},
-
-\code{a1.x} Same as \code{a1.y}, but in the \dQuote{longitude} coordinate,
-
-\code{P1.x} Same as \code{P1.y}, but in the \dQuote{longitude} coordinate.
+\code{a} A vector with initial state values. It has 4 elemets (x location at time 1, x velocity at time 1, y location at time 1,
+y velocity at time 1) for
+non-drift models and 6 elemets for drift models (x location at time 1,
+x velocity at time 1, x drift velocity at time 1, etc...).
 
 \code{theta} and \code{fixPar} are vectors with the appropriate number or
 parameters. \code{theta} contains only those paraemters which are to be