autoini {secr} | R Documentation

## Initial Parameter Values for SECR

### Description

Find plausible initial parameter values for `secr.fit`. A simplified model is fitted by a fast ad hoc method.

### Usage

    autoini(capthist, mask, detectfn = 0, thin = 0.2)

### Arguments

`capthist` | `capthist` object
`mask` | `mask` object compatible with the detector layout in `capthist`
`detectfn` | shape of detection function 0 = half-normal
`thin` | proportion of points to retain in mask

### Details

Plausible starting values are needed to avoid numerical problems when fitting SECR models. Actual models to be fitted will usually have more than the three basic parameters output by `autoini`; other initial values can usually be set to zero for `secr.fit`. If the algorithm encounters problems obtaining a value for g0, the default value of 0.1 is returned.

Only the half-normal detection function is available in `autoini` (cf other options in e.g. `sim.capthist`).

`autoini` implements a modified version of the algorithm proposed by Efford et al. (2004). In outline, the algorithm is

1. Find value of sigma that predicts the observed mean recapture distance d-bar (see dbar)
2. Find value of g0 that, with sigma, predicts the observed mean number of captures per individual (by algorithm of Efford et al. (2009, Appendix 2))
3. Compute the effective sampling area from g0, sigma, using thinned mask (see `esa`)
4. Compute D = n/esa(g0, sigma), where n is the number of individuals detected

Here 'find' means solve numerically for zero difference between the observed and predicted values, using `uniroot`.

Computation of d-bar fails if there no recaptures, and all returned values are NA.

A proportion 1–`thin` of the points in the mask may be discarded at random to speed execution.

### Value

A list of parameter values :

`D` | Density (animals per hectare)
`g0` | Magnitude (intercept) of detection function
`sigma` | Spatial scale of detection function (m)

### Note

`autoini` may in future include an option to use `RPSV` instead of `dbar`.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### References

Efford, M. G., Dawson, D. K. and Robbins C. S. (2004) DENSITY: software for analysing capture–recapture data from passive detector arrays. Animal Biodiversity and Conservation 27, 217–228.

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.

### See Also

`capthist`, `mask`, `secr.fit`, `dbar`

### Examples

    demotraps <- make.grid()
    demomask <- make.mask(demotraps)
    demoCH <- sim.capthist (demotraps, popn = list(D = 5, buffer = 100))
    autoini (demoCH, demomask)

[Package secr version 1.3.0 Index]