| derivedDsurface {secr} | R Documentation |
Derived Absolute Density
Description
A relative density model (one fitted by maximising the conditional likelihood) has a zero intercept for density on the default log scale (the intercept is 1.0 for the identity link).
The constant k that relates absolute density to relative density D^\prime = k^{-1} D is
obtained as described in Efford (2025).
These functions infer the value of k and use this to construct the predicted density surface
(predictDsurface is the equivalent function for full-likelihood models).
The derived method for ‘secr’ objects performs the same calculation as derivedDcoef
and also back-transforms the intercept and computes a delta-method estimate of its variance and confidence limits.
However that variance estimate is unreliable.
derivedDfit constructs an secr fitted model object resembling that from an unconditional model fit.
Usage
## S3 method for class 'secr'
derivedDcoef(object, se = FALSE, ...)
## S3 method for class 'secrlist'
derivedDcoef(object, se = FALSE, ...)
derivedDsurface(object, mask = NULL, sessnum = NULL, groups = NULL)
derivedDfit(object, vcv = TRUE)
Arguments
object |
fitted secr relative density model |
se |
logical; if TRUE the variance of beta0 is estimated by the delta method |
mask |
new mask for which to compute densities |
sessnum |
integer session number |
groups |
character vector of covariate names to define groups (optional) |
vcv |
logical; if TRUE output includes the extended variance-covariance matrix |
... |
other arguments (not used) |
Details
The theory is provided by Efford in prep.
derivedDcoef(object, se = TRUE) is equivalent to derived(object, Dweight = TRUE),
although derivedDcoef returns estimates on the link scale.
Value
For derivedDcoef –
A dataframe mimicking coef(object) with an initial row for the derived density intercept \beta_0.
For an identity link, subsequent density coefficients are scaled by the derived \beta_0.
For derivedDsurface –
Dsurface object with class c("Dsurface", "mask", "data.frame"). Multi-session if object is multi-session and sessnum = NULL.
If groups are defined the result is a list of Dsurfaces.
References
Efford, M. G. In prep. SECR models for relative density.