R/addSightings.R

In secr: Spatially Explicit Capture-Recapture

###############################################################################
## package 'secr'
## addSightings.R
## 2017-03-27 tweaked to allow NULL
###############################################################################

addSightings <- function (capthist, unmarked = NULL, nonID = NULL, uncertain = NULL, verify = TRUE, ...) {
    if (ms(capthist)) {
        if (is.character(unmarked)) {
            ##pre-read and split text file as list
            unmarked <- read.table(unmarked, ...)
            session <- unmarked[,1]
            unmarked <- split(unmarked[,-1], session)
        }
        if (is.character(nonID)) {
            ##pre-read and split text file as list
            nonID <- read.table(nonID, ...)
            session <- nonID[,1]
            nonID <- split(nonID[,-1], session)
        }
        if (is.character(uncertain)) {
            ##pre-read and split text file as list
            uncertain<- read.table(uncertain, ...)
            session <- uncertain[,1]
            uncertain <- split(uncertain[,-1], session)
        }
        if (!is.null(unmarked)) {
            if (!inherits(unmarked, 'list'))
                stop ("unmarked should be a list for multi-session capthist")
            if (length(unmarked) != length(capthist))
                stop("number of sessions differs between unmarked and capthist")
        }
        if (!is.null(nonID)){
            if (!inherits(unmarked, 'list'))
                stop ("nonID should be a list for multi-session capthist")
            if (length(nonID) != length(capthist))
                stop("number of sessions differs between nonID and capthist")
        }
        if (!is.null(uncertain)){
            if (!inherits(uncertain, 'list'))
                stop ("uncertain should be a list for multi-session capthist")
            if (length(uncertain) != length(capthist))
                stop("number of sessions differs between uncertain and capthist")
        }
        for (i in 1:length(capthist)) {
            # capthist[[i]] <- addSightings(capthist[[i]], unmarked[[i]], nonID[[i]], uncertain[[i]],
            #     verify = FALSE)
            capthist[[i]] <- addSightings(capthist[[i]], unmarked[[i]], nonID[[i]], uncertain[[i]],
                verify = FALSE, ...)
        }
        if (verify) verify(capthist)
        capthist
    }
    else {
        if (is.null(markocc(traps(capthist))))
            stop("traps(capthist) lacks markocc attribute; provide this first")
        S <- ncol(capthist)
        K <- ndetector(traps(capthist))
      
        if (is.character(unmarked))
            ## discard session column as unused
            unmarked <- read.table(unmarked, ...)[1:K,2:(S+1)]
        if (is.character(nonID))
            ## discard session column as unused
            nonID <- read.table(nonID, ...)[1:K,2:(S+1)]
        if (is.character(uncertain))
            ## discard session column as unused
            uncertain <- read.table(uncertain, ...)[1:K,2:(S+1)]
        Tu(capthist) <- if (is.null(unmarked)) NULL else as.matrix(unmarked)
        Tm(capthist) <- if (is.null(nonID)) NULL else as.matrix(nonID)
        Tn(capthist) <- if (is.null(uncertain)) NULL else as.matrix(uncertain)
        if (verify) verify(capthist)
        capthist
    }
}