xtab<-function(x,caption='Table X.', file=stdout(), width='"100%"', cornername='', dec=rep(1,ncol(x))){
  nc<-ncol(x)
  lin<-paste('<table width=',width,'>', sep='')
  lin<-c(lin,sub('$','</td></tr>',sub('\\. |\\.$','.</b> ',
         sub('^', paste('<tr><td colspan=',nc+1,'><b>',sep=''), caption))))
  hr<-paste('<tr><td colspan=',nc+1,'><hr noshade></td></tr>', sep='')
  lin<-c(lin,hr)
  cnames<-colnames(x)
  cnames<-paste(sub('$','</b></td>',sub('^','<td align=right><b>',cnames)), collapse='\t')
  lin<-c(lin,paste('<tr>',paste('<td align=left><b>',cornername,'</b></td>',sep=''),cnames,'</tr>'))
  lin<-c(lin,hr)
  rnames<-sub('$','</b></td>',sub('^','<tr> <td align=left><b>',rownames(x)))
  xx<-sapply(1:ncol(x),function(i)sub('NA','  ',formatC(round(x[,i,drop=FALSE],dec[i]),digits=dec[i], format='f')))
  x<-relist(xx, skeleton=x)
  for(i in 1:nrow(x)){
    thisline<-paste(rnames[i],paste(sub('$','</td>',sub('^','<td align=right>',x[i,])), collapse='\t'),'</tr>', sep='')
    lin<-c(lin,thisline)
  }
  lin<-c(lin,hr)
  lin<-c(lin,'</table><br>\n')
  writeLines(lin,con=file)
}

xtab2<-function(x,caption='Table X.', file=stdout(), width='"100%"', cornername='', dec=matrix(1,ncol=ncol(x),nrow=nrow(x))){
  nc<-ncol(x)
  lin<-paste('<table width=',width,'>', sep='')
  lin<-c(lin,sub('$','</td></tr>',sub('\\. |\\.$','.</b> ',
         sub('^', paste('<tr><td colspan=',nc+1,'><b>',sep=''), caption))))
  hr<-paste('<tr><td colspan=',nc+1,'><hr noshade></td></tr>', sep='')
  lin<-c(lin,hr)
  cnames<-colnames(x)
  cnames<-paste(sub('$','</b></td>',sub('^','<td align=right><b>',cnames)), collapse='\t')
  lin<-c(lin,paste('<tr>',paste('<td align=left><b>',cornername,'</b></td>',sep=''),cnames,'</tr>'))
  lin<-c(lin,hr)
  rnames<-sub('$','</b></td>',sub('^','<tr> <td align=left><b>',rownames(x)))
  xx<-x
  for(i in 1:nrow(x)){
    for(j in 1:ncol(x)){
      x[i,j]<-sub('NA','  ',formatC(round(xx[i,j],dec[i,j]),digits=dec[i,j], format='f'))
    }
  }

  for(i in 1:nrow(x)){
    thisline<-paste(rnames[i],paste(sub('$','</td>',sub('^','<td align=right>',x[i,])), collapse='\t'),'</tr>', sep='')
    lin<-c(lin,thisline)
  }
  lin<-c(lin,hr)
  lin<-c(lin,'</table><br>\n')
  writeLines(lin,con=file)
}

dummyplot<-function(text='This plot is intentionally left blank'){
  plot(c(0,1),c(0,1),axes=FALSE, xlab='', ylab='' , type='n')
  box()
  text(.5,.5,labels=text)
}

tryCatch.W.E <- function(expr){ # function from demo(tryCatch)
    W <- NULL
    w.handler <- function(w){ # warning handler
	W <<- w
	invokeRestart("muffleWarning")
    }
    list(value = withCallingHandlers(tryCatch(expr, error = function(e) e),
				     warning = w.handler),
	 warning = W)
}

stampit<-function(fit) {
  x<-""  
  eee<-tryCatch.W.E(x<-system('svn info', intern=TRUE, ignore.stderr=TRUE))
  udir<-sub('/datadisk/stockassessment/userdirs/','',getwd())
  udir<-sub('user[[:digit:]]+/','',udir)
  udir<-sub('/res','',udir)
  txt<-paste("stockassessment.org",udir,sub("Revision: ", "r", x[grep("Revision",x)]), sep=', ')
  txt<-paste0(txt, " , git: ", attr(fit,"RemoteSha"))
  ## Function modified from Frank Harrell's Hmisc library 
  stamp <- function(string = "", print = TRUE, plot = TRUE) {
    opar <- par(yaxt = "s", xaxt = "s", xpd = NA)
    on.exit(par(opar))
    plt <- par("plt")
    usr <- par("usr")
    xcoord <- usr[2] + (usr[2] - usr[1])/(plt[2] - plt[1]) * (1 - plt[2]) - 0.6 * strwidth("m")
    ycoord <- usr[3] - diff(usr[3:4])/diff(plt[3:4]) * (plt[3]) + 0.6 * strheight("m")
    if (par("xlog")) xcoord <- 10^(xcoord)
    if (par("ylog")) ycoord <- 10^(ycoord)
    text(xcoord, ycoord, string, adj = 1)
    invisible(string)
  }

  oldpar <- par(mfrow = c(1, 1), cex = 0.5)
  on.exit(par(oldpar))
  stamp(string = txt, print = FALSE, plot = TRUE)
  invisible()
}

plotcounter<-1 
tit.list<-list()
setcap<-function(title="", caption=""){   
 tit.list[length(tit.list)+1]<<-paste("# Title",plotcounter)
 tit.list[length(tit.list)+1]<<-paste(title)
 tit.list[length(tit.list)+1]<<-paste("# Caption",plotcounter)
 tit.list[length(tit.list)+1]<<-paste(caption)
 plotcounter<<-plotcounter+1 
}

urlLoadFit <- function(address){
  fnam <- gsub("https://www.stockassessment.org","",address)
  if( file.exists( fnam )){
      suppressWarnings(load(fnam))
      return(fit)
  }
  tryCatch({
    con <- url(address)
    suppressWarnings(load(con))
    close(con)
    fit
  }, error = function(err) {
     }
  )
}

bioplot <-function(fit){
  miny <-min(fit$data$years)
  maxy <-max(fit$data$years)
  if(fit$conf$stockWeightModel==1){
    swa <- exp(fit$pl$logSW)
    matplot(fit$data$years, fit$data$stockMeanWeight, xlab="Year", ylab="Stock weights",xlim=c(miny,maxy+3))
    matplot(miny:(miny+nrow(swa)-8), swa[1:(nrow(swa)-7),], type="l", add=TRUE, lty="solid", lwd=2)
    abline(v=maxy, lty=2)
  }
  
  if(fit$conf$catchWeightModel==1){
    cwa <- exp(fit$pl$logCW)
    matplot(fit$data$years, fit$data$catchMeanWeight[,,1], xlab="Year", ylab="Catch weights",xlim=c(miny,maxy+3))
    matplot(miny:(miny+nrow(cwa)-8), cwa[1:(nrow(cwa)-7),,1], type="l", add=TRUE, lty="solid", lwd=2)
    abline(v=maxy, lty=2)
   
  }
  if(fit$conf$mortalityModel==1){
    ma <- exp(fit$pl$logNM)
    matplot(fit$data$years, fit$data$natMor, xlab="Year", ylab="Natural mortality",xlim=c(miny,maxy+3))
    matplot(miny:(miny+nrow(ma)-8), ma[1:(nrow(ma)-7),], type="l", add=TRUE, lty="solid", lwd=2)
    abline(v=maxy, lty=2)
    
  }
  if(fit$conf$matureModel==1){
    mo <- plogis(fit$pl$logitMO)
    matplot(fit$data$years, fit$data$propMat, xlab="Year", ylab="Proportion mature",xlim=c(miny,maxy+3))
    matplot(miny:(miny+nrow(mo)-9), mo[1:(nrow(mo)-8),], type="l", add=TRUE, lty="solid", lwd=2)
    abline(v=maxy, lty=2)
    
  }
 
}