[RkWard-devel] RKWard 0.4.5pre1, 0.4.5 release process

Sat Jan 13 12:50:53 UTC 2007

2007/1/12, Thomas Friedrichsmeier <thomas.friedrichsmeier at ruhr-uni-bochum.de
>:
>
> On Friday 12 January 2007 09:54, I. Soumpasis wrote:
> > 2) Indentation: The next line after an opening brace ('{') should always
> be
> >
> > > indented by one Tab (until the closing '}'). This makes reading the
> code
> > > structure much easier. Also, maybe you could replace the spaces that
> are
> > > used
> > > to indent the panel.cor()-block right now with tabs, as well.
> >
> > You 're right. Done.
>
> Sorry, I wasn't precise: The indentation I was worried about is the
> indentation of the generated code, not the indentation as visible in the
> .php
> file. I.e. inside the preprocess () function, you'd unindent everything by
> two tabs, inside the printout (), and cleanup () functions by one tab.
> Then,
> the generated code should look "clean". (See the new section on that in
> the
> plugin documentation:
>
> http://rkward.sourceforge.net/documents/devel/plugins/phptemplate.html#policyformatting
> )

My bad. I took off one tab from the first 2 tabs.

> 3) It would probably be useful to have the "method", and "use" options to
> >
> > > cor
> > > and cor.test as well. You can copy the relevant sections from the
> > > correlation
> > > matrix plugin. One way to make this work, would be to extend the
> > > panel.cor function with those two paramenters, then modify the call to
> > > pairs to:
> > >
> > > pairs(x, lower.panel=panel.smooth, upper.panel=function (x, y)
> > > panel.cor(x, y, use, method))
> >
> > I have done it with a different method, don't know if it is ok. I
> applied
> > use, method to the cor and cor.test functions. Tested the method and
> works.
> > Is this ok or should I try the method proposed?

I did that at the function panel.cor like this
panel.cor <- function(x, y, digits=<? getRK ("digits"); ?>, cex.cor, use="<?
getRK ("use"); ?>", method="<? getRK ("method"); ?>")

and then main function is

pairs(x, lower.panel=panel.smooth, upper.panel=panel.cor)

I think there is one advantage to the method I proposed: I would make the
> panel.cor () function truly reusable as is. All parameters would be set at
> only one single point: The function call itself. The user would not have
> to
> modify the function body itself to re-run e.g. with method "spearman"
> instead
> of "pearson". I think in this case this method would not introduce too
> much
> additional complexity, and be useful at the same time, so I think it's
> better.
>
> > 4) The "digits" and "prefix" parameters to panel.cor are effectively
> > unused,
> >
> > > currently. I don't really understand, what the prefix parameter is
> for,
> > > but
> > > maybe you could also add a GUI option for the digits parameter (that,
> or
> > > remove it to keep the code simple).
> >
> > I gave an option to the user to select precision (1,2,or 3 digits -
> Sould
> > we do something else here?). Removed prefix.
>
> It's probably nicer to use a <spinbox type="integer" min="0" max="5"
> initial="2"> instead of a <radio> for this task. After all, it's a
> numerical
> selection.

Done.

> 5) You wrap up everything in a function rk.temp.cor.graph (). I'm not
> >
> > > entirely
> > > sure, whether I like or dislike this (so far we did not use this).
> > > Anybody have an opinion already?
> >
> >   There is not a function that can do this to my knowledge so I made
> this
> > one using the example. This is the way I have implemented it in R and
> just
> > pasted here. One good thing is that you have to delete only this one
> > function stored in R (and your data). One other that someone could pass
> > scripts or functions already written in a very easy way. I don't know.
> > Should I change that?
>
> The alternative would be to rename "panel.cor" to "rk.temp.panel.cor",
> then
> change
>         rk.temp.cor.graph (rk.temp.x)
> to:
>         pairs (x, lower.panel=panel.smooth, upper.panel=rk.temp.panel.cor)
> (or considering 3) to):
>         pairs (x, lower.panel=panel.smooth, upper.panel=function (x, y)
> rk.temp.panel.cor (x, y, digits=<? getRK ("digits"); ?>, use="<? getRK
> ("use"); ?>", method="<? getRK ("method"); ?>"))
>
> However, since I'm not quite sure myself, just leave everything inside the
> rk.temp.cor.graph () function for now, until I've made up my mind.
>
> > 7) The idea of scaling the text the r is printed in according to the
> value
> >
> > > of
> > > r is definitely interesting, but I think it should be possible to turn
> it
> > > off.
> >
> > Done.
>
> Since this is a yes/no question, a <checkbox> would be better suited than
> a
> <radio>. Considering 3), you might want to add scale as a parameter to
> panel.cor, too. Also, for this type of selection, you might want to set
> the
> option value to "TRUE" or "FALSE", instead of "yes" or "no". Then you can
> simplify a statement like:
>
>         if("<? getRK ("scale"); ?>"=="yes") [...]
> to
>         if(<? getRK ("scale"); ?>) [...]

Done and used TRUE/FALSE.

I have to look at the documentation. This was a first try to see what can I
do.

> 1. I added a note with what the asterisks mean.
>
> Very useful, indeed.
>
> > 2. I  believe that the plugin should be placed under the same menu with
> > correlation matrix, I mean something like this.
> >
> > Analysis -- Correlation -- Correlation matrix
> >
> >                                   -- Correlation graph
>
> Not sure, yet. Anybody else have an opinion?
>
> Regards
> Thomas

Added also info like this

Method: pearson
Exclusion: pairwise.complete.obs
Precision: 3 digits
Scale text: TRUE

on the graph.

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