[R] path.diagram in SEM--display covariances without variances

[John Fox]

Dear Dustin,

> -----Original Message-----
> From: Dustin Fife [mailto:fife.dustin at gmail.com]
> Sent: November-09-11 2:12 PM
> To: John Fox
> Cc: r-help at r-project.org
> Subject: Re: [R] path.diagram in SEM--display covariances without
> variances
> 
> Thanks for the quick response...I've never edited someone else's
> package before. How do I go about doing that?

I wouldn't change the sem package, but rather create your own version of
pathDiagram(). You could examine the package sources, but, more simply, to
see the code for the function, type its name at the command prompt:

> library(sem)
Loading required package: MASS
Loading required package: matrixcalc
> pathDiagram
function (model, ...) 
{
    UseMethod("pathDiagram")
}
<bytecode: 0000000006E1CEA8>
<environment: namespace:sem>

So pathDiagram() is a generic function. What methods are available?

> methods(pathDiagram)
[1] pathDiagram.sem*

   Non-visible functions are asterisked

There is, therefore just one method, for objects of class "sem", hidden in
the sem namespace. To see it (most lines elided):

> sem:::pathDiagram.sem
function (model, file, min.rank = NULL, max.rank = NULL, same.rank = NULL, 
    variables = model$var.names, parameters = rownames(model$ram), 
    ignore.double = TRUE, edge.labels = c("names", "values", 
        "both"), size = c(8, 8), node.font = c("Helvetica", 14), 
    edge.font = c("Helvetica", 10), rank.direction = c("LR", 
        "TB"), digits = 2, standardize = FALSE, output.type = c("graphics", 
        "dot"), graphics.fmt = "pdf", dot.options = NULL, ...) 
{
. . .
    cat(file = handle, "}\n")
    if (output.type == "graphics" && !missing(file)) {
        cmd <- paste("dot -T", graphics.fmt, " -o ", graph.file, 
            " ", dot.options, " ", dot.file, sep = "")
        cat("Running ", cmd, "\n")
        result <- try(system(cmd))
    }
    invisible(NULL)
}
<bytecode: 00000000071B9568>
<environment: namespace:sem>

Just copy the functions into an editor and make whatever changes you want.

Best,
 John

> 
> On Wed, Nov 9, 2011 at 12:47 PM, John Fox <jfox at mcmaster.ca> wrote:
> > Dear Dustin,
> >
> >> -----Original Message-----
> >> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> >> project.org] On Behalf Of Dustin Fife
> >> Sent: November-09-11 10:57 AM
> >> To: r-help at r-project.org
> >> Subject: [R] path.diagram in SEM--display covariances without
> >> variances
> >>
> >> Forgive me if I'm posting to the wrong place....It's my first time
> >> posting.
> >>
> >> Here's the situation: I'm using the sem package and making path
> >> diagrams using path.diagrams. Suppose I have the following code:
> >>
> > . . .
> >
> >> The diagram is produces is hard to read because of the many
> variances
> >> that are shown. The covariance estimates are important for my
> >> diagram, but the variances are not. Is there a way to suppress the
> >> variance arrows without suppressing the covariance arrows?
> >
> > No, but (1) pathDiagram() (the name of the function in the current
> > version of the sem package) produces an editable text file, from
> which
> > you could remove the arrows that you don't want to see; and (2) you
> > could modify
> > pathDiagram() -- the code for the function is, after all, available
> to
> > you
> > -- so that it does what you want.
> >
> > I hope this helps,
> >  John
> >
> > --------------------------------
> > John Fox
> > Senator William McMaster
> >  Professor of Social Statistics
> > Department of Sociology
> > McMaster University
> > Hamilton, Ontario, Canada
> > http://socserv.mcmaster.ca/jfox
> >
> >
> >
> >>
> >> --
> >> Dustin Fife
> >> Graduate Student, Quantitative Psychology University of Oklahoma
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html and provide commented, minimal, self-contained,
> >> reproducible code.
> >
> >
> 
> 
> 
> --
> Dustin Fife
> Fife Photography
> www.fifephotography.com
> info at fifephotography.com
> fife.dustin at gmail.com
> 405.414.5599