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 |