Nothing
# Check map for NAs, NaNs, etc
checkMap<-function(map, filter.map){
if(!grepl('proj=utm|proj=longlat',proj4string(map))) stop("Projection needs to be in utm or longlat")
if(grepl('+proj=utm.*',proj4string(map)))
if(!grepl('+units=m',proj4string(map)))
message('Assuming UTM +units=m')
if(any(is.na(getValues(map)))) stop('NAs in habitat map. Replace with 0s')
if(any(is.nan(getValues(map)))) stop('NaNs in habitat map')
if(!is.null(filter.map)){
if(proj4string(filter.map) != proj4string(map))
stop('map and filter.map must have the same projection')
if(any(is.nan(getValues(filter.map))))
stop('NaNs in filter.map')
if(any(is.na(getValues(map))))
stop('NAs in filter.map. Replace with 0s')
if(extent(filter.map)!=extent(map))
stop('map and filter.map must have the same extent')
if(any(res(filter.map)!=res(map)))
stop('map and filter.map must have the same resolution')
}
return(map)
}
# Check parameter list for missing values, update names, etc
checkParameters<-function(pList,argList){
if(is.null(pList$maxDistQ))
pList$maxDistQ <- rep(1, length(pList$MFratio))
if(is.null(pList$wghts))
pList$wghts <- T
if(is.null(pList$filter.cutoff)){
if(!is.null(argList$filter.map)){
if(all(getValues(argList$filter.map)<=1)){
pList$filter.cutoff <- 0.95
}
}
}
if('trunk' %in% names(pList))
stop("Truncation parameter has been reworked using probabilities instead of SDs.
Use 'maxDistQ' instead of 'trunk'")
oldnames <- c('howfar', 'howmuch', 'trunk', 'HRcenter.cutoff')
newnames <- c('moveDist', 'moveDistQ', 'maxDistQ', 'habitat.cutoff')
if(any(oldnames %in% names(pList))){
old<-match(oldnames, names(pList))
names(pList)[old] <- newnames[!is.na(old)]
warning(paste('The following parameter names are deprecated:',
oldnames[!is.na(old)],
'\n Replace with: ', newnames[!is.na(old)]))
}
return(pList)
}
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