R/utils.R

In unmarked: Models for Data from Unmarked Animals

genFixedNLL <- function(nll, whichFixed, fixedValues)
{
    function(params) {
        params[whichFixed] <- fixedValues
        do.call(nll, list(params))
        }
}

# nll the original negative log likelihood function
# MLE the full vector of MLE values
profileCI <- function(nll, whichPar, MLE, interval, level)
{
    stopifnot(length(whichPar) == 1)
    MLEnll <- nll(MLE)
    nPar <- length(MLE)
	chsq <- qchisq(level, 1)/2
    f <- function(value) {
        fixedNLL <- genFixedNLL(nll, whichPar, value)
            mleRestricted <- optim(MLE, fixedNLL)$value
        mleRestricted - MLEnll - chsq
        }
    lower <- tryCatch(uniroot(f, c(interval[1],MLE[whichPar]))$root,
        error = function(e) {
            warning("Lower endpoint of profile confidence interval is on the boundary.",
        call. = FALSE)
        -Inf
        })
    upper <- tryCatch(upper <- uniroot(f, c(MLE[whichPar], interval[2]))$root,
        error = function(e) {
            warning("Upper endpoint of profile confidence interval is on the boundary.",
        call. = FALSE)
        Inf
        })

    return(c(lower,upper))
}

## link functions and their gradients
logistic <- function(x) {
  1/(1 + exp(-x))
}


logistic.grad <- function(x) {
  exp(-x)/(exp(-x)+1)^2
}


# This function causes check failures on CRAN because CRAN thinks it's
# a method for the log function. I don't think it's actually used in the package?
#log.grad <- function(x) { # duh! (but for clarity)
#  1/x
#}


explink <- function(x) exp(x)

exp1 <- function(x) exp(x) + 1


identLink <- function(x) x


identLinkGrad <- function(x) 1

#Complimentary log log link
cloglog <- function(x){
  1-exp(-exp(x))
}

cloglog.grad <- function(x){
  exp(-exp(x))
}

## use logarithms to vectorize row-wise products
## this speeds things up a LOT (vs. apply(x,1,prod))
rowProds <- function(x, na.rm = FALSE)
{
  exp(rowSums(log(x), na.rm = na.rm))
}

## compute estimated asymptotic variances of parameter estimates
## using the observed information matrix

#sd.est <- function(fm) {
#    sqrt(diag(solve(fm$hessian)))
#}

## delta method for variance of proportion given variance of its logistic-
## transformed counterpart
##' @nord
#sd.prop <- function(est,sd.est) {
#    exp(-est)/(1 + exp(-est))^2 * sd.est
#}

### track linked list of parameters using a data frame
### add row to linked list
addParm <- function(list.df, parm.name, parm.length) {
    if(parm.length > 0) {
        if(nrow(list.df) == 0) {
            last.ind <- 0
        } else {
            last.ind <- list.df$end[nrow(list.df)]
        }
        parm.df <- data.frame(parameter = parm.name, start = last.ind + 1,
                              end = last.ind + parm.length,
                              stringsAsFactors = FALSE)
        list.df <- rbind(list.df, parm.df)
    }
    return(list.df)
}


parmNames <- function(list.df) {
    npar <- list.df$end[nrow(list.df)]
    names <- character(npar)
    for(i in 1:npar) {
        which.par <- which(i >= list.df$start & i <= list.df$end)
        names[i] <- list.df$parameter[which.par]
    }
    return(names)
}


# This function converts an appropriatedly formated comma-separated
# values file (.csv) to a format usable by \emph{unmarked}'s fitting
# functions (see \emph{Details}).
csvToUMF <-
function(filename, long=FALSE, type, species = NULL, ...)
{
  dfin <- read.csv(filename, stringsAsFactors=TRUE)

  if(long == TRUE) return(formatLong(dfin, species, type = type, ...))
  else return(formatWide(dfin, type = type, ...))
}

# utility function to create a variable that follows the dates as 1,2,3,...
# site id is first column
# julian date is second column

dateToObs <- function(dfin)
{
    sitecol <- dfin[[1]]
    datecol <- dfin[[2]]

    # order by site, then obs date
    dfin <- dfin[order(sitecol,datecol),]
    sitecol <- dfin[[1]]
    datecol <- dfin[[2]]

    dTab <- table(datecol,sitecol)
    sites <- unique(sitecol)
    nSite <- length(sites)
    nStop <- colSums(dTab)
    nStop <- nStop[nStop > 0]  # get rid of stops for sites with no stops

    obsNum <- numeric(length(sitecol))
    # for each site i, replace stops with 1:nStop[i]
    for(i in 1:nSite){
        stops <- which(sitecol == sites[i])
        obsNum[stops] <- 1:nStop[i]
    }

    dfout <- cbind(dfin,obsNum)
    dfout
}

# take long data set and return data list
# column names must be
# site names, first
# date, one column
# response, one column
# obs vars, one per column
formatLong <- function(dfin, species = NULL, type, ...) {
  if (type %in% c("umarkedFrameMPois", "unmarkedFrameGMM"))
    stop("Multinomial data sets are not supported.")
  if(missing(type)) stop("type must be supplied")

  ## copy dates to last column so that they are also a covdata var
  nc <- ncol(dfin)
  dfin[[nc+1]] <- dfin[[2]]
  names(dfin)[nc+1] <- "JulianDate"

  if(!is.null(species)) {
    dfin$y <- ifelse(dfin$species == species, dfin$y, 0)
    dfin$y[is.na(dfin$y)] <- 0
    dfin$species = NULL
  }
# TODO: dbl check that multiple cells per site*time are handled correctly.
#  # sum up counts within time/site
#  expr <- substitute(recast(dfin[,1:3], sv + dv ~ ..., id.var = 1:2,
#                            fun.aggregate = sum),
#                     list(sv = as.name(names(dfin)[1]),
#                          dv = as.name(names(dfin)[2])))
#  dfin2 <- eval(expr)
#  dfin1 <- dfin[!duplicated(dfin[,1:2]),]
#
#  dfin <- merge(dfin1,dfin2, by = 1:2)
#  dfin[,3] <- dfin[,length(dfin)]
#  dfin <- dfin[,-length(dfin)]
    names(dfin)[3] <- "y"
    dfin <- dateToObs(dfin)

    #Create wide version of y with matching matrix of indices
    scol <- names(dfin)[1]
    df_sub <- dfin[c(scol, "y", "obsNum")]
    df_sub$yind <- 1:nrow(df_sub)
    ywide <- reshape(df_sub, idvar=scol, timevar="obsNum", direction="wide")

    y <- unname(as.matrix(ywide[grep("^y\\.", names(ywide))]))
    yind <- as.vector(t(as.matrix(ywide[grep("yind", names(ywide))])))

    #Reorder input data frame by y-index (=no factor issues)
    #Also drop site/time/y/numObs cols
    obsvars.df <- dfin[yind, -c(1:3, ncol(dfin)), drop=FALSE]
    rownames(obsvars.df) <- NULL

    ## check for siteCovs
    obsNum <- ncol(y)
    M <- nrow(y)
    site.inds <- matrix(1:(M*obsNum), M, obsNum, byrow = TRUE)
    siteCovs <- sapply(obsvars.df, function(x) {
      obsmat <- matrix(x, M, obsNum, byrow = TRUE)
      l.u <- apply(obsmat, 1, function(y) {
        row.u <- unique(y)
        length(row.u[!is.na(row.u)])
      })
      # if there are 0 or 1 unique vals per row, we have a sitecov
      if (all(l.u <= 1)) {
        u <- apply(obsmat, 1, function(y) {
          row.u <- unique(y)
          ## only remove NAs if there are some non-NAs.
          if(!all(is.na(row.u)))
            row.u <- row.u[!is.na(row.u)]
          row.u
        })
        u
      }
    })
    siteCovs <- as.data.frame(siteCovs[!sapply(siteCovs, is.null)],
                              stringsAsFactors=TRUE)
    if(nrow(siteCovs) == 0) siteCovs <- NULL

    ## remove sitecovs from obsvars
    obsvars.df <- obsvars.df[, !(names(obsvars.df) %in% names(siteCovs)), drop = FALSE]

    if (type %in% c("unmarkedFrameDS", "unmarkedFrameGDS"))
      # obsCovs cannot be used with distsamp
      do.call(type, list(y = y, siteCovs = siteCovs, ...))
    else
      do.call(type, list(y = y, siteCovs = siteCovs, obsCovs = obsvars.df, ...))
}

# column names must be
# site (optional, but if present, labeled "site")
# response: y.1, y.2, ..., y.J
# site vars: namefoo, namebar, ...
# obs v: namefoo.1, namefoo.2, ..., namefoo.J, namebar.1, .., namebar.J,..

formatWide <- function(dfin, sep = ".", obsToY, type, ...) {
  if (type %in% c("umarkedFrameMPois", "unmarkedFrameGMM", "double", "removal"))
    stop("Multinomial data sets are not supported.")

        # escape separater if it is regexp special
    reg.specials <- c('.', '\\', ':', '|', '(', ')', '[', '{', '^', '$',
                      '*', '+', '?')
    if(sep %in% reg.specials) {
        sep.reg <- paste("\\",sep,sep="")
    } else {
        sep.reg <- sep
    }

    dfnm <- colnames(dfin)

    y <- grep(paste("^y",sep.reg,"[[:digit:]]", sep=""),dfnm)
    J <- length(y)
    y <- as.matrix(dfin[,y])
    M <- nrow(y)

    if(identical(tolower(colnames(dfin))[1],"site")) {
        dfin <- dfin[,-1]
        dfnm <- dfnm[-1]
    }

    ncols <- length(dfnm)
    obsCovsPresent <- FALSE
    siteCovsPresent <- FALSE
    i <- J + 1
    while(i <= ncols) {     # loop through columns
        if(!identical(grep(paste(sep.reg,"[[:digit:]]+$",sep=""),
                           dfnm[i]),integer(0))) { # check if is obsdata
            newvar.name <- sub(paste(sep.reg,"[[:digit:]]+$",sep=""),'',
                               dfnm[i])
            newvar <- dfin[,grep(paste(newvar.name,sep.reg,
                                       "[[:digit:]]+$",sep=""),dfnm)]
            if(obsCovsPresent) {
                if(ncol(newvar) != R) {
                    stop("Not all observation-level covariates have the same number of columns.")
                } else {
                    obsCovs[newvar.name] <- as.vector(t(newvar))
                }
            } else {
                obsCovsPresent <- TRUE
                R <- ncol(newvar)
                obsCovs <- data.frame(newvar = as.vector(t(newvar)))
            }
            colnames(obsCovs)[length(obsCovs)] <- newvar.name
            i <- i + R
        }
        else {
            if(siteCovsPresent){
                siteCovs <- cbind(siteCovs,dfin[,i])
            } else {
                siteCovsPresent <- TRUE
                siteCovs <- data.frame(newvar = dfin[,i])
            }
            colnames(siteCovs)[length(siteCovs)] <- dfnm[i]
            i <- i + 1
        }
    }

    if(!obsCovsPresent) obsCovs <- NULL
    if(!siteCovsPresent) siteCovs <- NULL

    ## if don't know obsToY yet, use RxJ matrix of ones or diag if R == J
    if(missing(obsToY)) {
        if(identical(R,J)) {
            obsToY <- diag(J)
        } else {
            obsToY <- matrix(0, R, J)
        }
    }

    do.call(type, list(y = y, siteCovs = siteCovs, obsCovs = obsCovs, ...))
}


# This convenience function converts multi-year data in long format to
# unmarkedMultFrame Object.  See Details for more information.

formatMult <- function(df.in)
{
    years <- sort(unique(df.in[[1]]))
    nY <- length(years)
    df.obs <- list()
    nsamp <- numeric()
    maxsamp <- max(table(df.in[[1]], df.in[[2]])) # the maximum samples/yr
    for(t in 1:nY){
        df.t <- df.in[df.in[[1]] == years[t],] # subset for current year
        df.t <- df.t[,-1] # remove year column
        df.t <- dateToObs(df.t)
        nsamp <- max(df.t$obsNum)
        if(nsamp < maxsamp) {
            newrows <- df.t[1:(maxsamp - nsamp), ] # just a placeholder
            newrows[,"obsNum"] <- ((nsamp + 1) : maxsamp)
            newrows[,3 : (ncol(df.t) - 1)] <- NA
            df.t <- rbind(df.t, newrows)
        }
        df.obs <- rbind(df.obs,cbind(year = years[t],df.t))
    }

    names(df.obs)[4] <- "y"
    scol <- names(df.obs)[2]
    df_sub <- df.obs[c("year", scol, "y", "obsNum")]
    df_sub$yind <- 1:nrow(df_sub)

    ywide <- reshape(df_sub, idvar=c(scol,"year"), timevar="obsNum",
                     direction="wide")
    ywide <- reshape(ywide, idvar=scol, timevar="year", direction="wide")
    #Reshape goofs up the order
    ywide <- ywide[order(ywide[,1]),]

    y <- unname(as.matrix(ywide[grep("^y\\.", names(ywide))]))
    yind <- as.vector(t(as.matrix(ywide[grep("yind", names(ywide))])))

    #Reorder input data frame by y-index (=no factor issues)
    #Also drop site/time/y/numObs cols
    obsvars.df <- df.obs[yind, -c(1:2, 4, ncol(df.obs)), drop=FALSE]
    rownames(obsvars.df) <- NULL

    ## check for siteCovs
    obsNum <- ncol(y)
    M <- nrow(y)
    site.inds <- matrix(1:(M*obsNum), M, obsNum, byrow = TRUE)
    siteCovs <- sapply(obsvars.df, function(x) {
        obsmat <- matrix(x, M, obsNum, byrow = TRUE)
        l.u <- apply(obsmat, 1, function(y) {
            row.u <- unique(y)
            length(row.u[!is.na(row.u)])
        })
        ## if there are 0 or 1 unique vals per row, we have a sitecov
        if(all(l.u %in% 0:1)) {
            u <- apply(obsmat, 1, function(y) {
                row.u <- unique(y)
                ## only remove NAs if there are some non-NAs.
                if(!all(is.na(row.u)))
                    row.u <- row.u[!is.na(row.u)]
                row.u
            })
            u
        }
    })
    siteCovs <- as.data.frame(siteCovs[!sapply(siteCovs, is.null)],
                              stringsAsFactors=TRUE)
    if(nrow(siteCovs) == 0) siteCovs <- NULL

    ## only check non-sitecovs
    obsvars.df2 <- as.data.frame(obsvars.df[, !(names(obsvars.df) %in%
                                                names(siteCovs))])
    names(obsvars.df2) <- names(obsvars.df)[!(names(obsvars.df) %in%
                                              names(siteCovs))]

    yearlySiteCovs <- sapply(obsvars.df2, function(x) {
        obsmat <- matrix(x, M*nY, obsNum/nY, byrow = TRUE)
        l.u <- apply(obsmat, 1, function(y) {
            row.u <- unique(y)
            length(row.u[!is.na(row.u)])
        })
        ## if there are 0 or 1 unique vals per row, we have a sitecov
        if(all(l.u %in% 0:1)) {
            u <- apply(obsmat, 1, function(y) {
                row.u <- unique(y)
                ## only remove NAs if there are some non-NAs.
                if(!all(is.na(row.u)))
                    row.u <- row.u[!is.na(row.u)]
                row.u
            })
            u
        }
    })
    yearlySiteCovs <- as.data.frame(yearlySiteCovs[!sapply(yearlySiteCovs,is.null)],
                                    stringsAsFactors=TRUE)
    if(nrow(yearlySiteCovs) == 0) yearlySiteCovs <- NULL

    # Extract siteCovs and yearlySiteCovs from obsvars
    finalobsvars.df <- as.data.frame(obsvars.df[, !(names(obsvars.df) %in%
                                                      c(names(siteCovs),
                                                        names(yearlySiteCovs)))])
    names(finalobsvars.df) <- names(obsvars.df)[!(names(obsvars.df) %in%
                                                    c(names(siteCovs),
                                                      names(yearlySiteCovs)))]

    umf <- unmarkedMultFrame(y = y, siteCovs = siteCovs,
                             obsCovs = finalobsvars.df, yearlySiteCovs =
                             yearlySiteCovs,
                             numPrimary = nY)
    return(umf)
}

# function to take data of form
# site  | species | count
# to
# site | spp1 | spp2 | ...

#Not used anywhere
#sppLongToWide <- function(df.in)
#{
#    df.m <- melt(df.in, id = c("site", "spp"))
#    df.out <- dcast(df.m, site ~ spp, add.missing=T, fill = 0)
#    df.out <- df.out[order(df.out$site),]
#    df.out
#}

# get estimated psi from rn fit

getPsi <-
function(lam)
{
  1-exp(-lam)
}

# get estimatd p from rn fit (only for a null type model so far)

getP.bar <-
function(lam, r)
{
    K = 30
    psi <- getPsi(lam)
    pN.k <- dpois(0:K,lam)
    pY.k <- 1 - (1 - r)^(0:30)
    sum(pY.k * pN.k)
}






meanstate <- function(x) {
    K <- length(x) - 1
    sum(x*(0:K))
}

truncateToBinary <- function(y) {
    if(max(y, na.rm = TRUE) > 1) {
        y <- ifelse(y > 0, 1, 0)
        warning("Some observations were > 1.  These were truncated to 1.")
    }
    return(y)
}


getSS <- function(phi) {
    ev.length <- nrow(phi)
    ev <- tryCatch(eigen(t(phi))$vectors[,1],
                   error = function(x) rep(NA, ev.length))
    ev/sum(ev)
}

imputeMissing <- function(umf, whichCovs = seq(length=ncol(obsCovs(umf))))
{
    ## impute observation covariates
    if(!is.null(umf@obsCovs)) {
        obsCovs <- umf@obsCovs
        J <- obsNum(umf)
        M <- nrow(obsCovs)/J
        obs <- as.matrix(obsCovs[,whichCovs])
        whichrows <- apply(obs, 1, function(x) any(!is.na(x)))
        if(sum(whichrows) == 0) return(obsCovs)
        whichels <- matrix(whichrows, M, J, byrow = TRUE)
        for(i in seq(length=length(whichCovs))) {
            obs.i <- obs[,i]
            obs.i.mat <- matrix(obs.i, M, J, byrow = TRUE) # get ith obsvar
            obs.i.missing <- is.na(obs.i.mat) & !whichels
            obs.i.imputed <- obs.i.mat
            for(j in 1:M) {
                for(k in 1:J) {
                    if(obs.i.missing[j,k])
                        if(all(is.na(obs.i.mat[j,]))) {
                            obs.i.imputed[j,k] <- mean(obs.i.mat[,k],
                                                       na.rm = T)
                        } else {
                           obs.i.imputed[j,k] <- mean(c(mean(obs.i.mat[j,],
                                                             na.rm = T),
                                                        mean(obs.i.mat[,k],
                                                             na.rm = T)))
                        }
                }
            }
            obsCovs[,whichCovs[i]] <- as.numeric(t(obs.i.imputed))
        }
        umf@obsCovs <- obsCovs
    }
    # TODO: impute site covariates
    return(umf)
}




lambda2psi <- function(lambda)
{
if(any(lambda < 0))
    stop("lambda must be >= 0")
as.numeric(1 - exp(-lambda))
}


# Convert individual-level distance data to the
# transect-level format required by distsamp()

formatDistData <- function (distData, distCol, transectNameCol, dist.breaks, occasionCol,effortMatrix)
{
  if (!is.numeric(distData[, distCol]))
    stop("The distances must be numeric")
  transects <- distData[, transectNameCol]
  if (!is.factor(transects)) {
    transects <- as.factor(transects)
    warning("The transects were converted to a factor")
  }

  if (missing(occasionCol)) {
    T <- 1
    occasions <- factor(rep(1, nrow(distData)))
  }
  else {
    occasions <- distData[, occasionCol]
    if (!is.factor(occasions)) {
      occasions <- as.factor(occasions)
      warning("The occasions were converted to a factor")
    }
    T <- nlevels(occasions)
  }
  M <- nlevels(transects)
  J <- length(dist.breaks) - 1
  if (missing(effortMatrix)) {
    effortMatrix <- matrix(nrow=M,ncol=T,1)
  }

  if (!is.numeric(effortMatrix)){
    stop("effortMatrix is not numeric")
    effortMatrix <- matrix(nrow=M,ncol=T,1)
  }


  dist.classes <- levels(cut(distData[, distCol], dist.breaks,
                             include.lowest = TRUE))
  ya <- array(NA, c(M, J, T), dimnames = list(levels(transects),
                                              dist.classes, paste("rep", 1:T, sep = "")))
  transect.levels <- levels(transects)
  occasion.levels <- levels(occasions)
  for (i in 1:M) {
    for (t in 1:T) {
      sub <- distData[transects == transect.levels[i] &
                        occasions == occasion.levels[t], , drop = FALSE]
      ya[i, , t] <- table(cut(sub[, distCol], dist.breaks,
                              include.lowest = TRUE))
    }
  }
  y <- matrix(ya, nrow = M, ncol = J * T)
  # takes into account the effortMatrix to allow for the insertion of NAs instead of 0s for surveys which were not completed
  ee <- array(NA, c(M,length(occasion.levels)*(length(dist.breaks)-1)))
  for(i in 1:length(occasion.levels)){
    ee[,((ncol(ee)/length(occasion.levels)*(i-1)+1):(ncol(ee)/length(occasion.levels)*i))] <- matrix(effortMatrix[,i], ncol=J, nrow=M)
  }
  ee[ee==0] <- NA
  y <- y * ee
  dn <- dimnames(ya)
  rownames(y) <- dn[[1]]
  if (T == 1)
    colnames(y) <- dn[[2]]
  else colnames(y) <- paste(rep(dn[[2]], times = T), rep(1:T, each = J), sep = "")
  return(y)
}


## Sight distance to perpendicular distance

sight2perpdist <- function(sightdist, sightangle)
{
    if(any(0 > sightangle | sightangle > 180))
        stop("sightangle must be degrees in [0, 180]")
    sightdist * sin(sightangle * pi / 180)
}

#Sum of squared errors method
setGeneric("SSE", function(fit, ...) standardGeneric("SSE"))

setMethod("SSE", "unmarkedFit", function(fit, ...){
    sse <- sum(residuals(fit)^2, na.rm=TRUE)
    return(c(SSE=sse))
})

setMethod("SSE", "unmarkedFitOccuMulti", function(fit, ...){
    r <- do.call(rbind, residuals(fit))
    return(c(SSE = sum(r^2, na.rm=T)))
})

# For pcountOpen. Calculate time intervals acknowledging gaps due to NAs
# The first column indicates is time since first primary period + 1
formatDelta <- function(d, yna)
{
    M <- nrow(yna)
    T <- ncol(yna)
    d <- d - min(d, na.rm=TRUE) + 1
    dout <- matrix(NA, M, T)
    dout[,1] <- d[,1]
    dout[,2:T] <- t(apply(d, 1, diff))
    for(i in 1:M) {
        if(any(yna[i,]) & !all(yna[i,])) { # 2nd test for simulate
            last <- max(which(!yna[i,]))
            y.in <- yna[i, 1:last]
            d.in <- d[i, 1:last]
            if(any(y.in)) {
                for(j in last:2) { # first will always be time since 1
                    nextReal <- which(!yna[i, 1:(j-1)])
                    if(length(nextReal) > 0)
                        dout[i, j] <- d[i, j] - d[i, max(nextReal)]
                    else
                        dout[i, j] <- d[i, j] - 1
                    }
                }
            }
        }
    return(dout)
}















# Generate zero-inflated Poisson

rzip <- function(n, lambda, psi) {
    x <- rpois(n, lambda)
    x[runif(n) < psi] <- 0
    x
}

#Converts names to indices for occuMulti() and methods
name_to_ind <- function(x,name_list){

  if(is.null(x)) return(x)

  if(is.numeric(x)){
    if(any(x>length(name_list))){
      stop("Supplied species index is invalid")
    }
    return(x)
  }

  absent_adjust <- ifelse(grepl('^-',x),-1,1)
  clean <- sub('-','',x)
  if(!all(clean %in% name_list)){
    stop("Supplied species name not found")
  }
  out <- match(clean,name_list)


  out * absent_adjust
}

#Inverts Hessian. Returns blank matrix with a warning on a failure.
invertHessian <- function(optimOut, nparam, SE){

  blankMat <- matrix(NA, nparam, nparam)
  if(!SE) return(blankMat)

  tryCatch(solve(optimOut$hessian),
    error=function(e){
      warning("Hessian is singular. Try providing starting values or using fewer covariates.", call.=FALSE)
      return(blankMat)
  })
}

#Get u and a from distance sampling data
getUA <- function(umf){

  M <- numSites(umf)
  if(inherits(umf, "unmarkedFrameGDR")){
    J <- ncol(umf@yDistance) / umf@numPrimary
  } else{
    J <- ncol(getY(umf)) / umf@numPrimary
  }
  db <- umf@dist.breaks
  w <- diff(db)

  u <- a <- matrix(NA, M, J)
    switch(umf@survey,
    line = {
        for(i in 1:M) {
            a[i,] <- umf@tlength[i] * w
            u[i,] <- a[i,] / sum(a[i,])
            }
        },
    point = {
        for(i in 1:M) {
            a[i, 1] <- pi*db[2]^2
            for(j in 2:J)
                a[i, j] <- pi*db[j+1]^2 - sum(a[i, 1:(j-1)])
            u[i,] <- a[i,] / sum(a[i,])
            }
        })
  list(a=a, u=u)

}

pHalfnorm <- function(sigma, survey, db, w, a){
  J <- length(w)
  cp <- rep(NA, J)
  switch(survey,
    line = {
      f.0 <- 2 * dnorm(0, 0, sd=sigma)
      int <- 2 * (pnorm(db[-1], 0, sd=sigma) - pnorm(db[-(J+1)], 0, sd=sigma))
      cp[1:J] <- int / f.0 / w
    },
    point = {
      for(j in 1:J) {
        cp[j] <- integrate(grhn, db[j], db[j+1],
                           sigma=sigma, rel.tol=1e-4)$value *
                           2 * pi / a[j]
      }
    }
  )
  cp
}

pExp <- function(rate, survey, db, w, a){
  J <- length(w)
  cp <- rep(NA, J)
  switch(survey,
    line = {
      for(j in 1:J) {
        cp[j] <- integrate(gxexp, db[j], db[j+1],
                           rate=rate, rel.tol=1e-4)$value / w[j]
      }
    },
    point = {
      for(j in 1:J) {
        cp[j] <- integrate(grexp, db[j], db[j+1],
                            rate=rate, rel.tol=1e-4)$value *
                            2 * pi * a[j]
      }
    }
  )
  cp
}

pHazard <- function(shape, scale, survey, db, w, a){
  J <- length(w)
  cp <- rep(NA, J)
  switch(survey,
    line = {
      for(j in 1:J) {
        cp[j] <- integrate(gxhaz, db[j], db[j+1],
                           shape=shape, scale=scale,
                           rel.tol=1e-4)$value / w[j]
      }
    },
    point = {
      for(j in 1:J) {
        cp[j] <- integrate(grhaz, db[j], db[j+1],
                           shape = shape, scale=scale,
                           rel.tol=1e-4)$value * 2 * pi / a[j]
      }
    })
    cp
}

getDistCP <- function(keyfun, param1, param2, survey, db, w, a, u){
  switch(keyfun,
    halfnorm = {
      cp <- pHalfnorm(param1, survey, db, w, a)
    },
    exp = {
      cp <- pExp(param1, survey, db, w, a)
    },
    hazard = {
      cp <- pHazard(param1, param2, survey, db, w, a)
    },
    uniform = {
      cp <- rep(1, length(u))
    })
    cp * u
}


#Modified rmultinom for handling NAs
rmultinom2 <- function(n, size, prob){
  if(is.na(size)|any(is.na(prob))){
    return(matrix(NA, length(prob), length(n)))
  }
  stats::rmultinom(n=n, size=size, prob=prob)

}

#Functions to convert character columns to factors
df_to_factor <- function(df, name="Input"){
  if(is.null(df)) return(NULL)
  stopifnot(inherits(df, "data.frame"))
  char_cols <- sapply(df, is.character)
  if(any(char_cols)){
    warning(paste(name, "contains characters. Converting them to factors."), call.=FALSE)
  }
  to_change <- df[,char_cols, drop=FALSE]
  df[,char_cols] <- lapply(to_change, as.factor)
  df
}

umf_to_factor <- function(umf){
  stopifnot(inherits(umf, "unmarkedFrame"))
  umf@siteCovs <- df_to_factor(siteCovs(umf), "siteCovs")
  umf@obsCovs <- df_to_factor(obsCovs(umf), "obsCovs")
  if(methods::.hasSlot(umf, "yearlySiteCovs")){
    umf@yearlySiteCovs <- df_to_factor(yearlySiteCovs(umf), "yearlySiteCovs")
  }
  umf
}

dzip <- function(x, lambda, psi) {
  stopifnot(length(lambda)==length(x) | length(lambda)==1)
  stopifnot(length(psi)==1)
  stopifnot(all(x>=0))
  if(length(lambda)==1) lambda <- rep(lambda, length(x))
  den <- rep(NA, length(x))
  zer <- x==0
  gr0 <- x > 0
  den[zer] <- psi + (1-psi)*exp(-lambda[zer])
  den[gr0] <- (1-psi)*dpois(x[gr0], lambda[gr0])
  den
}

# Expected value of log lambda when there is a random intercept
E_loglam <- function(log_lam, object, name){

  if(!methods::.hasSlot(object, "TMB") || is.null(object@TMB)){
    return(log_lam)
  }
  sig <- sigma(object)
  if(! name %in% sig$Model) return(log_lam)

  sig <- sig[sig$Model==name,]
  can_calculate <- (nrow(sig) == 1) & (sig$Name[1] == "(Intercept)")
  if(! can_calculate){
    stop("No support for models with > 1 random effect", call.=FALSE)
  }
  v <- sig$sigma^2
  ll <- log_lam + v/2
  ll
}