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

## 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