command line arguments

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command line arguments

Postby northernbio » Mon Apr 25, 2016 11:07 am

Hi:

I was wondering if there is documentation on the presence.exe command line arguments. In particular, the meaning of maxfn=? lmt=? link=[c|s] nsig=? ndec=? zero=? nboot=?

Some of these are exposed in the .out file, and others I can guess, but it would be helpful when writing batch files to have documentation.

==>-help
usage: presence i=infile j=desmatfile l=outfile model=xxx name=model_name
maxfn=? lmt=? link=[c|s] nsig=? ndec=? zero=? nboot=? boot2=?
amoebo hess verbose debug seed=? vc help
sim_psi=.7 sim_p=.4 sim_nsites=200 sim_nintsites=100 sim_nintvisits=9
sim_nother=5 sim_removal sim_nsims=100 sim_fname=?

Rob
northernbio
 
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Joined: Thu Nov 18, 2010 11:08 am

Re: command line arguments

Postby 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)
jhines
 
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Location: Laurel, MD, USA

Re: command line arguments

Postby northernbio » Mon Apr 25, 2016 1:13 pm

Thanks Jim!

I am writing an interface for Presence that will automate some of our work (see image below). The interface creates batch files, and reads output from .out files. Some projects involve > 50 species, so it will help reduce transcription errors and let us explore various model options a little more effectively. I still like exploring models species by species at the early stages, but eventually we need to speed things up when we get to standard reporting stage.

Image
northernbio
 
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Joined: Thu Nov 18, 2010 11:08 am

Re: command line arguments

Postby jhines » Mon Apr 25, 2016 2:39 pm

Just curious... what language did you code the interface in?
jhines
 
Posts: 386
Joined: Fri May 16, 2003 9:24 am
Location: Laurel, MD, USA

Re: command line arguments

Postby northernbio » Tue Apr 26, 2016 8:24 am

Hi Jim:

VB.net. You are welcome to the code or the . exe if you are interested.

Rob
northernbio
 
Posts: 20
Joined: Thu Nov 18, 2010 11:08 am


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