Add maxOrder argument to unmarkedFrameOccuMulti

[kenkellner]

With large numbers of species you can easily run out of memory just building the unmarkedFrame with occuMulti, even if you plan to later limit your analysis to just two-way interactions. You should be able to limit the order of interactions when building the frame to avoid this.

[kenkellner]

Modified function:

unmarkedFrameOccuMulti <- function(y, siteCovs = NULL, obsCovs = NULL,
                                   maxOrder, mapInfo = NULL)
{
  ylist <- y
  y <- ylist[[1]]
  J <- ncol(y)
  if(is.null(names(ylist)))
    names(ylist) <- paste('sp',1:length(ylist),sep='')

  obsCovs <- covsToDF(obsCovs, "obsCovs", J, nrow(y))

  #f design matrix guide
  S <- length(ylist)
  z <- expand.grid(rep(list(1:0),S))[,S:1]
  colnames(z) <- names(ylist)

  if(missing(maxOrder)) maxOrder <- S
  if(maxOrder == 1){
    fDesign <- as.matrix(z)
  } else {
    fDesign <- model.matrix(as.formula(paste0("~.^",maxOrder,"-1")),z)
  }

  attr(fDesign,'assign') <- NULL
  zinds <- apply(z,1,function(x) paste(x,collapse=''))
  rownames(fDesign) <- paste('psi[',zinds,']',sep='')
  colnames(fDesign) <- paste('f',1:ncol(fDesign),'[',
                             colnames(fDesign),']',sep='')

  umfmo <- new("unmarkedFrameOccuMulti", y=y, ylist = ylist, fDesign=fDesign,
               obsCovs = obsCovs, siteCovs = siteCovs, obsToY = diag(J))
  return(umfmo)
}