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Hi everybody,<br>
<br>
First of all, thank you so much for creating such a great tool. <br>
My name is Jose, I am biochemist and I have using R and Rkward
sporadically. I try to use Rkward whenever I can, since I found R
too encrypted, however I acknowledge it power.<br>
I am sending an email to the developing team since I realized that
there are some plot types that my colleges and my self use all the
time and it will be good to add them to Rkward.<br>
The first one that I would like to propose is hierarchical
clustering (HC).<br>
<br>
A simple HC, basically a front end for hclust (transposing the data
(d) and generating a distance matrix (dist) will be necessary
first). <br>
> t.r = t(data)<br>
> dist.tr = dist(t.r)<br>
> hc.tr = hclust(dist.tr, method = “average”)<br>
> plot(hc.tr, hang = -1)<br>
<br>
Another approach could be to call pvclust, which it calculates
something similar. However it also gives p values.<br>
> result <- pvclust(data, method.dist="cor",
method.hclust="average", nboot=1000)<br>
> plot(result)<br>
<br>
What do you think? <br>
<br>
Anyway, I am not writting to just make a suggestion. I would like to
help as much as I can with this, even if I never have program
anything. I already started reading the information about how to
generate a plugin. <br>
As suggested in your plugin webpage, I guess that the best way will
be to start modifying a plugin that has a similar role. <br>
Ideally should be a pluggin that allows to compare as many variables
as we want (I was thinking to use the boxplot plugin, but I realized
that the boxplot plugin use many variables, but all separated).<br>
Any idea or suggestions?<br>
<br>
2) I am not sure if I should report this here, but I think that I
found a bug, when I try to use basic statistic the "submit" botton
does not turn on. The code is generated, I can copy and paste it in
the R console and when I hit enter I get the result in the Output
window.<br>
<br>
I am using:<span style="font-weight: 600;"> Version 0.5.4</span>,Using
KDE Development Platform 4.5.1 (KDE 4.5.1). In a LinuMint 10 box.<br>
<br>
OK, thats it for the moment, thanks again for all what you have
done!! I hope that with your help, I can make my little contribution
and sorry for the long email.<br>
<br>
Kind regards<br>
Jose<br>
<br>
PS:<br>
Here is an example of the generated code for the Basic statistic:<br>
<br>
local({<br>
## Prepare<br>
## Compute<br>
vars <- list (substitute (my.data[["var"]]))<br>
results <- data.frame ('Variable Name'=rep (NA, length (vars)),
check.names=FALSE)<br>
<br>
for (i in 1:length (vars)) {<br>
var <- eval (vars[[i]], envir=globalenv());<br>
results[i, 'Variable Name'] <- rk.get.description(vars[[i]],
is.substitute=TRUE)<br>
<br>
results[i, 'Mean'] <- mean(var,na.rm=TRUE)<br>
results[i, 'Variance'] <- var(var,na.rm=TRUE)<br>
<br>
#robust statistics<br>
}<br>
<br>
## Print result<br>
rk.header ("Univariate statistics", parameters=list (<br>
"Remove Missing values", TRUE))<br>
<br>
rk.results (results)<br>
})<br>
<br>
<pre class="moz-signature" cols="72">--
Jose Maria Polo, Ph.D.
Massachusetts General Hospital Center for Regenerative Medicine
Harvard Stem Cell Institute
185 Cambridge Street CPZN 4200
Boston MA 02114
617-643-5941 (tel)
617-643-3170 (fax)
<a class="moz-txt-link-abbreviated" href="mailto:polo.josemaria@mgh.harvard.edu">polo.josemaria@mgh.harvard.edu</a>
<a class="moz-txt-link-abbreviated" href="mailto:josemariapolo@gmail.com">josemariapolo@gmail.com</a> </pre>
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