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#' @include PT.Survey.R
#' @include generic.functions.R
#' @title Class "Single.Obs.PT.Survey"
#'
#' @description An S4 class containing an instance of a population
#' and a set of transects.
#'
#' @name Single.Obs.PT.Survey-class
#' @title S4 Class "Single.Obs.LT.Survey"
#' @keywords classes
setClass(Class = "Single.Obs.PT.Survey",
contains = "PT.Survey"
)
setMethod(
f="initialize",
signature="Single.Obs.PT.Survey",
definition=function(.Object, population, point.transect, rad.truncation){
#Input pre-processing
.Object@population <- population
.Object@transect <- point.transect
.Object@radial.truncation <- rad.truncation
#Check object is valid
validObject(.Object)
# return object
return(.Object)
}
)
setValidity("Single.Obs.PT.Survey",
function(object){
return(TRUE)
}
)
# GENERIC METHODS DEFINITIONS --------------------------------------------
#' @rdname create.survey.results-methods
#' @export
setMethod(
f="create.survey.results",
signature="Single.Obs.PT.Survey",
definition=function(object, dht.tables = FALSE, ...){
population <- object@population
point.transect <- object@transect
poss.distances <- calc.poss.detect.dists.points(population, point.transect, rad.truncation = object@radial.truncation)
n.in.covered <- poss.distances$distance
dist.data <- simulate.detections(poss.distances, population@detectability)
dist.data <- rename.duplicates(dist.data)
# Get the covariate names
all.col.names <- names(object@population@population)
cov.param.names <- all.col.names[!all.col.names %in% c("object", "x", "y", "strata", "scale.param", "shape.param")]
dist.data <- dist.data[,c("object", "transect.ID", "distance", "x", "y", cov.param.names)]
# Check if we need to remove missing distances
if(!is.null(point.transect@sampler.info$ac.simple)){
# Remove distance for simple nodes
simple.nodes <- point.transect@sampler.info$ID[point.transect@sampler.info$ac.simple]
dist.data$distance <- ifelse(dist.data$transect.ID %in% simple.nodes, NA, dist.data$distance)
}
ddf.data.obj <- new(Class = "Single.Obs.DDF.Data", data = dist.data)
if(dht.tables){
region.table <- create.region.table(object, ...)
sample.table <- create.sample.table(object)
obs.table <- data.frame(object = dist.data$object, Sample.Label = dist.data$transect.ID)
obs.table <- merge(obs.table, sample.table@sample.table, by = "Sample.Label")[,c("object","Sample.Label","Region.Label")]
obs.table.obj <- new(Class = "Obs.Table", data = obs.table)
return(list(ddf.data = ddf.data.obj, obs.table = obs.table.obj, sample.table = sample.table, region.table = region.table, n.in.covered = n.in.covered))
}else{
return(list(ddf.data = ddf.data.obj, n.in.covered = n.in.covered))
}
}
)
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