Package index

Data preparation

Functions for reading, formatting, and preparing acoustic SCR data.

read.acre()

Combining all data for plotting and model fitting

create.mask()

Create mask object

location_density()

Calculate location density

Model fitting

Fit acoustic SCR models and compute core model quantities.

fit.acre()

Fitting a spatial capture-recapture model

esa()

Estimated effective sampling areas

Model summaries

Extract fitted values, parameter estimates, uncertainty, and model diagnostics.

summary(<acre>)

Summarise acre Model Fits

coef(<acre>)

Extract coefficients from the output of acre model

stdEr()

Title

stdEr(<acre>)

Extract standard errors of the estimated parameters from acre models

vcov(<acre>)

Extract variance covariance matrix of the estimated parameters from acre models

confint(<acre>)

Extract confidence interval for acre.tmb models

logLik(<acre>)

Extract (negative) log-likelihood for a fitted acre object

AIC(<acre>)

Calculate AIC for acre Models

predict(<acre>)

Title

Bootstrap methods

Bootstrap fitted acre models and summarize bootstrap output.

boot.acre()

Bootstrapping a fitted acre model

coef(<acreboot>)

Title

stdEr(<acreboot>)

Title

vcov(<acreboot>)

Title

confint(<acreboot>)

Title

predict(<acreboot>)

Title

Plotting

Plot acre data, masks, fitted models, and diagnostic outputs.

plot(<acre>)

Plotting acre model objects

plot(<acre_data>)

Plotting acre data

Simulation

Simulate acoustic SCR data and run simulation studies.

sim.capt()

Simulating SCR data

sim_data()

Simulate acre-formatted SCR data.

sim_study()

Runs a simulation study