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58 lines
1.7 KiB
R
58 lines
1.7 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/R-PRES.r
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\name{runPresence}
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\alias{runPresence}
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\title{call PRESENCE to produce model estimates (replaces "write_dm_and_run")}
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\usage{
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runPresence(a, dm, model, modname = "m1", fixed = NULL, initvals = NULL,
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outfile, miscopts = "")
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}
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\arguments{
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\item{a}{pao object}
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\item{dm}{list of design matrices (should be 6 in list)}
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\item{model}{model number (not used anymore)}
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\item{modname}{name of model (eg., "psi(.)p(.)")}
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\item{fixed}{data.frame of fixed values (e.g., fixed$params<-c("p[1]","p[3]"),fixed$value<-0)}
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\item{initvals}{vector of beta initial values}
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\item{outfile}{name for output file (use outfile='modname') for outfile named via model name}
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\item{miscopts}{options (VCoutput, quiet, chsq,...)}
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}
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\value{
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list(LL=log-likelihood, beta=beta estimates, betaVC=var-cov matrix of betas).
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}
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\description{
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\code{runPresence} calls PRESENCE to produce model estimates.
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}
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\details{
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Input is passed
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to PRESENCE via arguments (no pao or design matrix input files needed). There are
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three choices for output:
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\itemize{
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\item outfile=NULL - no output file saved, results in R variables only,
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\item outfile="modname" - output file saved with name of model and ".out" appended,
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\item outfile="xyz" - output file saved with user-specified name, (eg., "xyz.out")
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}
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The first option is best for running simulations of a model using "Snowfall"
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for multi-tasking. The 2nd option is useful when you would like to find
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the full text output of a model from Windows explorer. The 3rd option allows
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you to specify any output file name.
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}
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\examples{
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runPresence("test.pao",list(dm1,dm2,dm3,dm4,dm5,dm6),100,"psi(.)p(.)")
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}
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\seealso{
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\code{\link{occMod}}
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}
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\author{
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Darryl MacKenzie and Jim Hines
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}
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