Description Usage Arguments Details Value Author(s) References
A function for computing MLEs for a specified CormackJollySeber open
population capturerecapture model for processed dataframe x
with
user specified formulas in parameters
that create list of design
matrices dml
. This function can be called directly but is most easily
called from crm
that sets up needed arguments.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 
x 
processed dataframe created by process.data 
ddl 
list of dataframes for design data; created by call to

dml 
list of design matrices created by 
model_data 
a list of all the relevant data for fitting the model including imat, Phi.dm,p.dm,Phi.fixed,p.fixed, and time.intervals. It is used to save values and avoid accumulation again if the model was rererun with an additional call to cjs when using autoscale or restarting with initial values. It is stored with returned model object. 
parameters 
equivalent to 
accumulate 
if TRUE will accumulate capture histories with common value and with a common design matrix for Phi and p to speed up execution 
initial 
list of initial values for parameters if desired; if each is a named vector from previous run it will match to columns with same name 
method 
method to use for optimization; see 
hessian 
if TRUE will compute and return the hessian 
debug 
if TRUE will print out information for each iteration 
chunk_size 
specifies amount of memory to use in accumulating capture histories; amount used is 8*chunk_size/1e6 MB (default 80MB) 
refit 
nonzero entry to refit 
itnmax 
maximum number of iterations 
control 
control string for optimization functions 
scale 
vector of scale values for parameters 
use.admb 
if TRUE creates data file for admbcjs.tpl and runs admb optimizer 
crossed 
if TRUE it uses cjs.tpl or cjs_reml.tpl if reml=FALSE or TRUE respectively; if FALSE, then it uses cjsre which can use GaussHermite integration 
compile 
if TRUE forces recompilation of tpl file 
extra.args 
optional character string that is passed to admb if use.admb==TRUE 
reml 
if set to TRUE uses cjs_reml if crossed 
clean 
if TRUE, deletes the tpl and executable files for amdb if use.admb=T 
... 
any remaining arguments are passed to additional parameters
passed to 
It is easiest to call cjs
through the function crm
.
Details are explained there.
Be cautious with this function at present. It does not include many checks
to make sure values like fixed values will remain in the specified range of
the data. Normally this would not be a big problem but because
cjs.lnl
calls an external FORTRAN subroutine, if it gets a
subscript out of bounds, it will cause R to terminate. So make sure to save
your workspace frequently if you use this function in its current
implementation.
The resulting value of the function is a list with the class of
crm,cjs such that the generic functions print and coef can be used.
Elements are 1) beta: named vector of parameter estimatesm 2) lnl: 2*log
likelihood, 3) AIC: lnl + 2* number of parameters, 4) convergence: result from optim
; if 0 optim
thinks it
converged, 5) count:optim
results of number of function
evaluations, 6) reals: dataframe of data and real Phi and p estimates for
each animaloccasion excluding those that occurred before release, 7) vcv:varcov matrix of betas if hessian=TRUE was set.
Jeff Laake
Pledger, S., K. H. Pollock, et al. (2003). Open capturerecapture models with heterogeneity: I. CormackJollySeber model. Biometrics 59(4):786794.
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