ascr: ascr: A package to fit acoustic spatial capture-recapture...

In b-steve/ascr: Acoustic spatial capture-recapture

ascr: A package to fit acoustic spatial capture-recapture models

Description

Functions to fit acoustic spatial capture-recapture models.

Details

Spatial capture-recapture (SCR) models estimate animal density from records of when and were individuals were detected. The first SCR methods for acoustic data were developed by Efford, Dawson, and Borchers (2009).

The ascr package fits SCR models to estimate animal density from acoustic surveys. In particular, these models can incorporate additional data like received signal strengths, times of arrival, estimated distances, and estimated bearings, which are informative about animals' locations. Other more general software packages exist for SCR (e.g., the comprehensive secr R package), but they cannot handle all data types listed above.

Models that can be fitted in ascr include those described by Efford, Dawson, and Borchers (2009), Borchers et al (2015), and Stevenson et al (2015). The package also implements some unpublished methods that are described in Stevenson (2016), a PhD thesis.

Data structure

The easiest way to prepare your data for model fitting is via the functions create.capt and create.mask. Also see the vignette on data structure, which can be viewed by running vignette("data-structure").

Model fitting

Model fitting is carried out by the fit.ascr function.

Output and plots

Useful information like parameter estimates, standard errors, confidence intervals, and variance-covariance matrices can be extracted from a fitted model object using the standard R functions, like coef, stdEr, summary, confint, and vcov (see coef.ascr, stdEr.ascr, summary.ascr, confint.ascr, and vcov.ascr).

Plots of the estimated detection function and of the detection probability surface can be obtained using show.detfn and show.detsurf, respectively. For inhomogeneous density models, show.Dsurf plots the estimated density surface. The locations function plots estimated locations of individuals or calls.

Simulation

The sim.capt function can simulate SCR data, either from user-specified parameters or estimated parameter values extracted from a fitted model object.

References

Borchers, D. L., Stevenson, B. C., Kidney, D., Thomas, L., and Marques, T. A. (2015). A unifying model for capture-recapture and distance sampling surveys of wildlife populations. Journal of the American Statistical Association, 110: 195–204.

Efford, M. G., Dawson, D. K., and Borchers, D. L. (2009). Population density estimated from locations of individuals on a passive detector array. Ecology, 90: 2676–2682.

Stevenson, B. C., Borchers, D. L., Altwegg, R., Swift, R. J., Gillespie, D. M., and Measey, G. J. (2015). A general framework for animal density estimation from acoustic detections across a fixed microphone array. Methods in Ecology and Evolution, 6: 38–48.

Stevenson, B. C. (2016) Methods in Spatially Explicit Capture-Recapture. PhD thesis, University of St Andrews.

b-steve/ascr documentation built on Aug. 15, 2022, 2:38 p.m.