by jhines » Mon Apr 25, 2016 12:31 pm
Hi Rob,
Here are the meanings of the command-line arguments. Note: some may not apply to all models.
PRESENCE command-line arguments:
i=infile : name of input pao file created by PRESENCE GUI
j=desmatfile : name of design matrix file
l=outfile : name of output file
model=xxx : indicate pre-defined model (by number) to run, not used for other models
name=model_name : name of model to appear in output (user-defined)
maxfn=? : max number of iterations before aborting max likelihood search
lmt=? : max number of sites to print in output (to save paper)
link=[c|s] : change link function to (c)loglog or (s)sin
nsig=? : number of significant digits in likelihood when maximum is assumed
ndec=? : number of digits right of decimal point to print
zero=? : highest value above zero assumed to equal zero for exp func.(default=10^(-200))
nboot=? : number of bootstrap replicates for computation of var-cov matrix
nboot2=?: number of bootstrap replicates for GOF
amoeba : use simplex algorithm for starting values
hess : * no longer used *
verbose : output input info to cmd console
debug : output debugging info to cmd console
seed=? : set random number generator seed (for simulations and/or bootstraps)
vc : print var-cov matrix of real parameters in output
nose : dont waste time computing std. errs for the model
sim_psi, sim_p, sim_nsites,... : parameters for legacy simulation routine (in Run menu)