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

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Documentation for package ‘nimbleSCR’ version 0.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calcLocalTrapDists	Local Trap Calculations
calcLocalTrapExposure	Local Trap Calculations
calculateDensity	NIMBLE function to calculate the density of individuals alive in each habitat cell.
calcWindowSizes	Window size calculation
dbernppAC	Bernoulli point process for the distribution of activity centers
dbernppACmovement_exp	Bernoulli point process for activity center movement (exponential kernel)
dbernppACmovement_normal	Bernoulli point process for activity center movement (normal kernel)
dbernppDetection_normal	Bernoulli point process detection model
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
dbinomLocal_exp	Local evaluation of a binomial SCR observation process
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
dcatState1Alive1Dead	Density and random generation of a categorical distribution describing state transition with one alive and one dead states.
dcatState1Alive2Dead	Density and random generation of a categorical distribution describing state transition with one alive and two dead states.
dcatState2Alive2Dead	Density and random generation of a categorical distribution describing state transition with two alive and two dead states.
dDispersal_exp	Bivariate exponential dispersal distribution for activity centers
dHabitatMask	Ones trick distribution for irregular habitat shapes
dmultiLocal_normal	Local evaluation of a multinomial SCR detection process
dnormalizer	Normalizing constant generator
dpoisLocal_normal	Local evaluation of a Poisson SCR detection process
dpoisppAC	Poisson point process for the distribution of activity centers
dpoisppDetection_normal	Poisson point process detection model
dpoisppLocalDetection_normal	Local evaluation for a Poisson point process detection model
findLocalTraps	Local Trap Calculations
getHomeRangeArea	Computation of home range radius and area
getLocalObjects	Local Objects Identification
getLocalTrapIndices	Local Trap Calculations
getMidPointNodes	Generate midpoint integration nodes
getNumLocalTraps	Local Trap Calculations
getSparseY	Sparse Matrix Preparation
getWindowCoords	Get lower and upper windows coordinates
getWindowIndex	Get window index
integrateIntensityLocal_normal	Integrate the multivariate normal intensity with local evaluation
integrateIntensity_exp	Integrate the multivariate exponential intensity
integrateIntensity_normal	Integrate the multivariate normal intensity
localTrapCalculations	Local Trap Calculations
makeGrid	Local Trap Calculations
marginalVoidProbIntegrand	Integrand of the marginal void probability integral
marginalVoidProbNumIntegration	Marginal void probability
rbernppAC	Bernoulli point process for the distribution of activity centers
rbernppACmovement_exp	Bernoulli point process for activity center movement (exponential kernel)
rbernppACmovement_normal	Bernoulli point process for activity center movement (normal kernel)
rbernppDetection_normal	Bernoulli point process detection model
rbernppLocalACmovement_exp	Local evaluation of a Bernoulli point process for activity center movement (exponential kernel)
rbernppLocalACmovement_normal	Local evaluation of a Bernoulli point process for activity center movement (normal kernel)
rbernppLocalDetection_normal	Local evaluation for a Bernoulli point process detection model
rbinomLocal_exp	Local evaluation of a binomial SCR observation process
rbinomLocal_normal	Local evaluation of a binomial SCR detection process
rbinomLocal_normalPlateau	Local evaluation of a binomial SCR observation process
rbinom_vector	Vectorized binomial distribution
rcatState1Alive1Dead	Density and random generation of a categorical distribution describing state transition with one alive and one dead states.
rcatState1Alive2Dead	Density and random generation of a categorical distribution describing state transition with one alive and two dead states.
rcatState2Alive2Dead	Density and random generation of a categorical distribution describing state transition with two alive and two dead states.
rDispersal_exp	Bivariate exponential dispersal distribution for activity centers
rHabitatMask	Ones trick distribution for irregular habitat shapes
rmultiLocal_normal	Local evaluation of a multinomial SCR detection process
rnormalizer	Normalizing constant generator
rpoisLocal_normal	Local evaluation of a Poisson SCR detection process
rpoisppAC	Poisson point process for the distribution of activity centers
rpoisppDetection_normal	Poisson point process detection model
rpoisppLocalDetection_normal	Local evaluation for a Poisson point process detection model
sampler_categorical_general	'nimble' MCMC sampler function for general categorial distributions
scaleCoordsToHabitatGrid	Scale x- and y-coordinates to grid cells coordinates.
stratRejectionSampler_exp	Stratified rejection sampler for multivariate exponential point process
stratRejectionSampler_normal	Stratified rejection sampler for multivariate normal point process