Nothing

```
################################################################
## Copyright 2014 Tracy Holsclaw.
## This file is part of NHMM.
## NHMM is free software: you can redistribute it and/or modify it under
## the terms of the GNU General Public License as published by the Free Software
## Foundation, either version 3 of the License, or any later version.
## NHMM is distributed in the hope that it will be useful, but WITHOUT ANY
## WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
## A PARTICULAR PURPOSE. See the GNU General Public License for more details.
## You should have received a copy of the GNU General Public License along with
## NHMM. If not, see <http://www.gnu.org/licenses/>.
#############################################################
#' Calculates the mean of the transition matrix
#'
#' \code{OQQ} calculates the mean of the transition array which is a K by K by T.
#' Each row is the state at time t-1 and the columns are time t. The Gui plot shows the
#' transition probability over time for each t-1 to t transition.
#'
#' @param nhmmobj an object created from the NHMM function
#' @param outfile a directory to put the .png plot
#' @return QQmean the transition probabilities for each time step. [K by K by T]
#' @return output: a plot where each row is the state at time t-1 and the columns are time t.
#' The GUI plot shows the transition probability over time for each t-1 to
#' t transition. If the columns are the same then the Markov property is probably weak.
#' @examples #OQQ(my.nhmm)
OQQ=function(nhmmobj, outfile=NULL)
{
T=nhmmobj$T
J=nhmmobj$J
K=nhmmobj$K
B=nhmmobj$B
A=nhmmobj$A
iters=nhmmobj$iters
burnin=nhmmobj$burnin
outboo=nhmmobj$outboo
outdir=nhmmobj$outdir
L=B+K
if(K==1){stop("K=1, there is no hidden state sequence")}
meanQQ=nhmmobj$meanQQ
if(!is.null(outfile)){ png(paste(outfile,"QQ.png",sep=""), width=K*150, height=K*150)}
par(mfrow=c(K,K), mar=c(4,4,1,1))
for(j in 1:K)
{ for(i in 1:K)
{ plot(meanQQ[j,i,],ylim=c(0,1), ylab="Probability", xlab="T")
}
}
if(!is.null(outfile)){ dev.off()}
par(mfrow=c(1,1), mar=c(4,4,4,4))
meanQQ
}
```

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