Description Usage Arguments Details Value Author(s) References
A function for computing MLEs for a specified JollySeber 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 
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 js 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 
initial values for parameters if desired; if 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 
... 
any remaining arguments are passed to additional parameters
passed to 
It is easiest to call js
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
js.lnl
calls an external FORTRAN subroutine via
cjs.lnl
, if it gets a subscirpt 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,js such that the generic functions print and coef can be used.
beta 
named vector of parameter estimates 
lnl 
2*log likelihood 
AIC 
lnl + 2* number of parameters 
convergence 
result from 
count 

reals 
dataframe of data and real Phi and p estimates for each animaloccasion excluding those that occurred before release 
vcv 
varcov matrix of betas if hessian=TRUE was set 
Jeff Laake
Schwarz, C. J., and A. N. Arnason. 1996. A general methodology for the analysis of capturerecapture experiments in open populations. Biometrics 52:860873.
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