mark_recapture_object: helper function for mark recapture object

In SaskiaSchirmer/CONSURE: Estimating Spatially Continuous Survival, Migratory Connectivity and Recovery Probability

helper function for mark recapture object

Description

This function defines the properties of the mark recapture object using the constructor.

Usage

mark_recapture_object(
  window = NULL,
  xrange = c(0, 0),
  yrange = c(0, 0),
  survival = NULL,
  recovery = NULL,
  marked_individuals,
  migratory_connectivity = NULL,
  observation_time,
  real_recoveries = NULL,
  origin_names = NULL,
  robust = TRUE,
  crs = "EPSG:4326"
)

Arguments

window	object of class "owin":observation window in two-dimensional plane
xrange	vector in the form of c(xmin,xmax). To define line or rectangle xrange and yrange can be used instead of window.
yrange	vector in the form of c(ymin,ymax). To define line or rectangle xrange and yrange can be used instead of window.
survival	function: survival function defined over the whole destination area, independent of the origin
recovery	constant function: recovery probability, must be constant over whole destination area
marked_individuals	integer: number of marked individuals in this origin
migratory_connectivity	either a list of functions containing one migratory connectivity function for every origin or a function with parameter b, allowing to partialize the function for every origin with purrr::partial
observation_time	length of observation window in years
real_recoveries	real-world recovery data, defaults to NULL
origin_names	character vector with origin names, defaults to NULL
robust	logical if TRUE robust linear model is calculated to estimate survival and migratory connectivity
crs	coordinate system. Defaults to "EPSG:4326" (longitude/latitude).

Value

object of class "mark_recapture_object": contains a list of the destination, origins, observation time, number of origins and spatial dimension

Examples

{
mro <- mark_recapture_object(xrange = c(0,1),
    survival = function(w) {0.5*w+.4},
    recovery = function(w) {0.01},
    marked_individuals = rep(100000,5) ,
    migratory_connectivity = function(b,w,B=B) {
        truncnorm::dtruncnorm(w,0,1, mean = seq(0.1,0.9,length.out = B)[b],
        sd = 0.3)
        },
    observation_time = 10)
}

SaskiaSchirmer/CONSURE documentation built on Sept. 3, 2023, 8:52 a.m.