[ADMB Users] Integrating R and ADMB to generalize TPL files

Jeff Laake jefflaake at gmail.com
Fri Nov 2 04:32:16 PDT 2012

Non-linear models can have linear components where parameters in the
non-linear base model are expressed as a linear function of covariates.
This makes model.matrix useful to generalize the tpl file. The example I
originally posted for distance sampling cannot be posed solely with
model.matrix. I wasn't saying that. However, the parameters can be
expressed as linear functions of the covariates which enables a base tpl
file to work for a much broader set of models without modification and

Here is another example where passing design matrices can be useful. The
tpl file will fit any Cormack-Jolly-Seber model to mark-recapture data to
estimate survival.  Both survival and capture probability are specified
with a design matrix on the logit scale. It could be generalized with other
link functions (eg. sin, probit)


I'm incorporating this into an R package which creates the admbcjs.dat file
from a dataframe and formulas in R.  The above admbcjs.dat example is for
the well-known dipper data with phi(.)p(t) (constant survival and
time-varying capture prob).

ADMB is a great piece of software. It will become more widely used outside
of fisheries if it is integrated with other platforms like R  Ignoring that
potential and making snide comments about R and R-users is not useful.

regards --jeff
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