A function for computing MLEs for a specified Jolly-Seber open population
capture-recapture 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.
js(
x,
ddl,
dml,
model_data = NULL,
parameters,
accumulate = TRUE,
initial = NULL,
method = "BFGS",
hessian = FALSE,
debug = FALSE,
chunk_size = 1e+07,
refit,
itnmax = NULL,
control = NULL,
scale,
...
)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.
named vector of parameter estimates
-2*log likelihood
lnl + 2* number of parameters
result from optimx; if 0 optimx thinks it
converged
optimx results of number of function
evaluations
dataframe of data and real Phi and p estimates for each animal-occasion excluding those that occurred before release
var-cov matrix of betas if hessian=TRUE was set
processed dataframe created by process.data
list of dataframes for design data; created by call to
make.design.data
list of design matrices created by create.dm from
formula and design 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 re-rerun with an additional call to js when using autoscale or re-starting with initial values. It is stored with returned model object.
equivalent to model.parameters in crm
if TRUE will accumulate capture histories with common value and with a common design matrix for Phi and p to speed up execution
initial values for parameters if desired; if named vector from previous run it will match to columns with same name
method to use for optimization; see optimx
if TRUE will compute and return the hessian
if TRUE will print out information for each iteration
specifies amount of memory to use in accumulating capture histories; amount used is 8*chunk_size/1e6 MB (default 80MB)
non-zero entry to refit
maximum number of iterations
control string for optimization functions
vector of scale values for parameters
any remaining arguments are passed to additional parameters
passed to optimx or js.lnl
Jeff Laake
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.
Schwarz, C. J., and A. N. Arnason. 1996. A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52:860-873.