Compute the constant multinomial component of the SECR log likelihood
logmultinom(capthist, grp = NULL)The numeric value of the log likelihood component.
capthist object
factor defining group membership, or a list (see Details)
For a particular dataset and grouping, the multinomial coefficient is
a constant; it does not depend on the parameters and may be ignored
when maximizing the likelihood to obtain parameter
estimates. Nevertheless, the log likelihood reported by
secr.fit includes this component unless the
detector type is `signal', `polygon', `polygonX', `transect' or
`transectX' (from 2.0.0).
If grp is NULL then all animals are assumed to belong to one
group. Otherwise, the length of grp should equal the number of rows of
capthist.
grp may also be any vector that can be coerced
to a factor. If capthist is a multi-session capthist object
then grp should be a list with one factor per session.
If capture histories are not assigned to groups the value is the logarithm of $${{n}\choose{n_1, ..., n_C}} = {{n!} \over {n_1! n_2! ... n_C!}} $$ where \(n\) is the total number of capture histories and \(n_1\) ... \(n_C\) are the frequencies with which each of the \(C\) unique capture histories were observed.
If capture histories are assigned to \(G\) groups the value is the logarithm of $${ \prod_{g=1}^{G} {{n_g!} \over {n_{g1}! n_{g2}! ... n_{gC_g}}!}} $$ where \(n_g\) is the number of capture histories of group \(g\) and \(n_{g1}\) ... \(n_{gC_g}\) are the frequencies with which each of the \(C_g\) unique capture histories were observed for group \(g\).
For multi-session data, the value is the sum of the single-session values. Both session structure and group structure therefore affect the value computed. Users will seldom need this function.
Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum likelihood methods for capture--recapture studies. Biometrics 64, 377--385.
Efford, M. G., Borchers D. L. and Byrom, A. E. (2009) Density estimation by spatially explicit capture--recapture: likelihood-based methods. In: D. L. Thompson, E. G. Cooch and M. J. Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer. Pp. 255--269.
stoatDNA
## no groups
logmultinom(stoatCH)
Run the code above in your browser using DataLab