Probability of detection of the species in each location

Computes the probability of detection of the species in each location for the xsdm model, given environmental data and model parameters.

Usage

log_prob_detect(
  env_dat,
  mu,
  sigltil,
  sigrtil,
  o_mat,
  ctil,
  pd,
  return_prob = FALSE,
  num_threads = RcppParallel::defaultNumThreads()
)

Arguments

env_dat

The environmental data array, dimensions n_loc x n_time x p (number of locations x time-series length x number of environmental variables). Must be a 3-dimensional array with no missing values.

mu

Vector of optimal environmental values. Length p=dim(env_dat)[3]. Unconstrained real numbers.

sigltil

Vector specifying width of the growth-environment function. Length p=dim(env_dat)[3]. Positive real numbers, Inf entries also allowed.

sigrtil

Vector specifying width of the growth-environment function. Length p=dim(env_dat)[3]. Positive real numbers, Inf entries also allowed.

o_mat

An orthogonal matrix, dimensions p by p.

ctil

Scalar. Relates to the center of the detection-link function.

pd

Maximum probability of detection of the species. Parameter between 0 and 1.

return_prob

Logical (default FALSE). Flag to return probabilities of detection instead their logs.

num_threads

Number of threads for parallel computation. Defaults to RcppParallel::defaultNumThreads().

Value

A vector of length equal to the number of locations, containing the probabilities of detection (or their logs) of the species in each location.

Details

This is a thin R wrapper around the C++ implementation log_prob_detect_cpp; the optimizer hot path is pure C++. A pure-R reference implementation, log_prob_detect_r, is kept internal to the package and is used only by the parity tests in tests/testthat/test-log_prob_detect_r_vs_cpp.R.

Examples

mu <- c(-1, 5.046939)
sigltil <- c(1.036834, 1.556083)
sigrtil <- c(1.538972, 1.458738)
ctil <- -2
pd <- 0.9
o_mat <- matrix(c(-0.4443546, 0.8958510, -0.8958510, -0.4443546), ncol = 2)