Learn R Programming

nimbleSCR (version 0.2.1)

Spatial Capture-Recapture (SCR) Methods Using 'nimble'

Description

Provides utility functions, distributions, and fitting methods for Bayesian Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) modelling using the nimble package (de Valpine et al. 2017 ). Development of the package was motivated primarily by the need for flexible and efficient analysis of large-scale SCR data (Bischof et al. 2020 ). Computational methods and techniques implemented in nimbleSCR include those discussed in Turek et al. 2021 ; among others. For a recent application of nimbleSCR, see Milleret et al. (2021) .

Copy Link

Version

Install

install.packages('nimbleSCR')

Monthly Downloads

214

Version

0.2.1

License

GPL-3

Maintainer

Daniel Turek

Last Published

November 30th, 2022

Functions in nimbleSCR (0.2.1)

dDispersal_exp

Bivariate exponential dispersal distribution for activity centers
calculateDensity

NIMBLE function to calculate the density of individuals alive in each habitat cell.
dbernppACmovement_normal

Bernoulli point process for activity center movement (normal kernel)
dbernppDetection_normal

Bernoulli point process detection model
dHabitatMask

Ones trick distribution for irregular habitat shapes
dbernppAC

Bernoulli point process for the distribution of activity centers
calcWindowSizes

Window size calculation
dbernppACmovement_exp

Bernoulli point process for activity center movement (exponential kernel)
dbernppLocalACmovement_exp

Local evaluation of a Bernoulli point process for activity center movement (exponential kernel)
dbernppLocalACmovement_normal

Local evaluation of a Bernoulli point process for activity center movement (normal kernel)
dbernppLocalDetection_normal

Local evaluation for a Bernoulli point process detection model
dnormalizer

Normalizing constant generator
dcatState2Alive2Dead

Density and random generation of a categorical distribution describing state transition with two alive and two dead states.
dbinomLocal_normal

Local evaluation of a binomial SCR detection process
dbinomLocal_normalPlateau

Local evaluation of a binomial SCR observation process
dbinom_vector

Vectorized binomial distribution
dmultiLocal_normal

Local evaluation of a multinomial SCR detection process
dcatState1Alive2Dead

Density and random generation of a categorical distribution describing state transition with one alive and two dead states.
dbinomLocal_exp

Local evaluation of a binomial SCR observation process
dcatState1Alive1Dead

Density and random generation of a categorical distribution describing state transition with one alive and one dead states.
getMidPointNodes

Generate midpoint integration nodes
getWindowIndex

Get window index
getHomeRangeArea

Computation of home range radius and area
dpoisppAC

Poisson point process for the distribution of activity centers
dpoisLocal_normal

Local evaluation of a Poisson SCR detection process
getSparseY

Sparse Matrix Preparation
getWindowCoords

Get lower and upper windows coordinates
dpoisppLocalDetection_normal

Local evaluation for a Poisson point process detection model
dpoisppDetection_normal

Poisson point process detection model
getLocalObjects

Local Objects Identification
marginalVoidProbNumIntegration

Marginal void probability
integrateIntensity_normal

Integrate the multivariate normal intensity
localTrapCalculations

Local Trap Calculations
integrateIntensity_exp

Integrate the multivariate exponential intensity
marginalVoidProbIntegrand

Integrand of the marginal void probability integral
integrateIntensityLocal_exp

Integrate the multivariate exponential intensity with local evaluation
integrateIntensityLocal_normal

Integrate the multivariate normal intensity with local evaluation
sampler_categorical_general

nimble MCMC sampler function for general categorial distributions
scaleCoordsToHabitatGrid

Scale x- and y-coordinates to grid cells coordinates.
makeConstantNimbleFunction

nimble constant function generator
stratRejectionSampler_normal

Stratified rejection sampler for multivariate normal point process
stratRejectionSampler_exp

Stratified rejection sampler for multivariate exponential point process