[R] SAMM package for mixed models
First, a disclaimer. I am not affiliatied with the SAMM package. I am only a user of the package, but I have been contacted (off list) by people requesting information about SAMM and so I am posting this information here. SAMM is software for fitting mixed models. Versions are available for both S-Plus and R. More information and downloads of the software (and manual) are available here: http://www.dpi.qld.gov.au/fieldcrops/14715.html This URL appears not to be indexed by Google, which is part of the reason I am posting this. Here are some personal, random notes about the package: SAMM is commercial software and requires a (non-free) license. You can test the software for free for 30 days. SAMM is short for Spatial Analysis Mixed Models. SAMM estimates variance components under a general linear mixed model by REML. In particular, the Average Information REML algorithm is used along with a sparse-matrix representation of matrices. For some types of problems, I have seen SAMM converge 100 to 1000 times faster than PROC MIXED or lme, which makes analysis of large datasets / complex models possible (sometimes in nearly real-time). 'Amazing' is a word that comes to mind. (Side note: I have heard rumors that SAS has hired a developer to look at the Average Information REML technique...) SAMM can fit two-dimensional spatial structures (such as AR1xAR1) and can plot two-dimensional variograms. The 'engine' for the mixed-models in SAMM is the same one used by Genstat and ASREML. Like all mixed-models software, SAMM has quirks such as convergence issues, degrees of freedom, model-specification, etc. The user community is small, so resources like email lists are limited. Some types of linear models can be fit using either lme/lme4 or SAMM. There are some big differences between SAMM and lme, however (cost, graphics, support, community, types of tests of fixed effects, etc.). Using both SAMM and lme to fit a model can be an experience that is tedious/painful but ultimately rewarding in a deeper understanding of the modelling process. SAMM has its origins in ASREML, which comes from a plant-breeding background. Although SAMM can be a general-purpose package, the focus is on evaluation of field experiments. For that purpose, it is an excellent tool. Kevin Wright __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Firefox keyword searches for R & S-Plus
Nice idea. A couple of comments. 1. I personally always install R in c:/R/ instead of c:/Program Files/ There are frequently comments on R-help that it is better to avoid paths with spaces. Still, you should be able to use /Progra~1/ instead of /Program Files/ 2. The search engine plugin that you have created generates a URL like this: .../SearchObject.html?q=nlme What is needed is a URL like .../SearchObject.html?%s where the %s is the string from the text box. I speculate it might be possible to change the SearchObject.html file to grab the "q=nlme" and strip off the "q=" but I have no idea if this is possible. I'm not comfortable with HTML/Java/Javascript to get this working properly. 3. My comment about editing the SearchObject.html file to change the "false" to "true" doesn't seem to cause the search to match the results obtained using the traditional way of opening the search page and typing in the text. I'm not sure why. Would love it if someone figured this out. Seems like all of this would be fairly easy for a good web programmer. Kevin > Hello Kevin, > > That's a good idea to use the functionnality of firefox to search for > help in R. > I wonder if that is possible to perform the search in the searchplugins > (like google), I tried to but there is always the characters %20= that > messed up with the one I was actually looking at. > Maybe something I don't see well, I created the following file in my > C:/Program Files/Mozilla Firefox/searchplugins directory (just copying > the google one) > > _ > # Mozilla/R plug-in by [EMAIL PROTECTED] > > name="R" >description="R search engine" >method="GET" > > action="file:///C:/Program%20Files/R/rw2000/doc/html/search/SearchObject.html" >> > > > > browserResultType="result" > charset = "UTF-8" > resultListStart="" > resultListEnd="" > resultItemStart="" > resultItemEnd="" >> > > ___ > > > Any idea ? > Sorry for my english. > > Romain. > > [EMAIL PROTECTED] a écrit : > >>If you've 'rediscovered the web' with Firefox (http://getfirefox.com), >> you >>might find this tip handy. Suppose you want to search the (local) R >>documentation for information about the lme function. Wouldn't it be >> nice >>to just type into the browser address bar: >> r lme >>and have the search performed? Here's how (on Windows): >> >>Click on this link: >>file:///C:/Progra~1/rw2000/doc/html/search/SearchObject.html?%s >> >>Bookmark the page and name the bookmark something like: R 2.0.0 doc >> search >> >>Edit the properties of the bookmark (by right-clicking on the bookmark) >>and in the keywords field enter: r >> >>Click OK. >> >> >>That's all there is to it except for a couple of notes: >> >>1. The first time the local search is performed (during a browser >>session), the java search applet has to be loaded. This takes several >>seconds. >> >>2. If you use a different operating system, a different version of R, or >>install R in a different location, change the bookmark path to the >>"SearchObject" file as appropriate. >> >>3. By default this only searches Help page titles. You may prefer a more >>comprehensive search that includes Keywords and Object names. Edit the >>SearchObject.html file and change 'false' to 'true' in the following >> line: >> line = line + document.SearchEngine.search >> (searchstring,true,true,true); >> >> >> >>Here are my R and S-Plus bookmarks. I'll just give the link, my bookmark >>name, and my bookmark keyword. >> >>http://www.google.com/u/newcastlemaths?q=%s >>R mail archive search >>rh >> >>http://www.google.com/search?q=site:www.biostat.wustl.edu+[S]+%s >>S-news archive search >>sn >> >>file:///C:/Progra~1/rw2000/doc/html/search/SearchObject.html?%s >>R 2.0.0 doc search >>r >> >> >>Happy searching! >> >>Kevin Wright >> >>__ >>[EMAIL PROTECTED] mailing list >>https://stat.ethz.ch/mailman/listinfo/r-help >>PLEASE do read the posting guide! >> http://www.R-project.org/posting-guide.html >> >> >> >> > > -- > Romain François > 25, avenue Guy Moquet > 94 400 Vitry sur seine > FRANCE > ___ > ___ > > [EMAIL PROTECTED] > 01 46 80 65 60 > 06 18 39 14 69 > > > __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Firefox keyword searches for R & S-Plus
If you've 'rediscovered the web' with Firefox (http://getfirefox.com), you might find this tip handy. Suppose you want to search the (local) R documentation for information about the lme function. Wouldn't it be nice to just type into the browser address bar: r lme and have the search performed? Here's how (on Windows): Click on this link: file:///C:/Progra~1/rw2000/doc/html/search/SearchObject.html?%s Bookmark the page and name the bookmark something like: R 2.0.0 doc search Edit the properties of the bookmark (by right-clicking on the bookmark) and in the keywords field enter: r Click OK. That's all there is to it except for a couple of notes: 1. The first time the local search is performed (during a browser session), the java search applet has to be loaded. This takes several seconds. 2. If you use a different operating system, a different version of R, or install R in a different location, change the bookmark path to the "SearchObject" file as appropriate. 3. By default this only searches Help page titles. You may prefer a more comprehensive search that includes Keywords and Object names. Edit the SearchObject.html file and change 'false' to 'true' in the following line: line = line + document.SearchEngine.search (searchstring,true,true,true); Here are my R and S-Plus bookmarks. I'll just give the link, my bookmark name, and my bookmark keyword. http://www.google.com/u/newcastlemaths?q=%s R mail archive search rh http://www.google.com/search?q=site:www.biostat.wustl.edu+[S]+%s S-news archive search sn file:///C:/Progra~1/rw2000/doc/html/search/SearchObject.html?%s R 2.0.0 doc search r Happy searching! Kevin Wright __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Suggested color schemes for points, not regions?
I have seen a couple of posts about color schemes like those at the ColorBrewer site. Most recently: http://geography.uoregon.edu/datagraphics/color_scales.htm These color schemes can work very well for regions (bars, polygons, images, etc.) but are not very suitable for points and/or lines. Is anyone aware of research/suggestions for a color scheme to use for scatter plots? I've looked at great length and have found little on this topic. My current scheme of choice is a set of fairly saturated colors along the lines of: navy brown/orange black purple red medium green This is similar to the 'paired' color scheme, but using only the saturated colors and substituting black for yellow. Depending on circumstances, I sometimes use a different glyph for each color. The hard part about all this is to make sure that each color/glyph combination has the same 'attention-getting' power. Any discussion or comments are welcome. Kevin Wright __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to use alpha transparency channel for colors?
Brian Ripley wrote:
> As so often happens, the `something wrong' is not reading the help file.
> As the NEWS file _also_ says
>
> o A 'version' argument has been added to pdf() device. If this is
> set to "1.4", the device will support transparent colours.
>
> pdf("alpha.pdf", version="1.4") should work for you: it does for me.
Thanks. I did actually spend quite a bit of time searching around before
posting to R-help (always do as a matter of courtesy) but was unlucky in
that I grep'ed for 'alpha' and not 'transparent'. Obvious mistake in
retrospect.
Kevin Wright
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[R] How to use alpha transparency channel for colors?
The release notes for R 2.0.0 states:
It is now possible to specify colours with a full alpha
transparency channel via the new 'alpha' argument to the
rgb() and hsv() functions, or as a string of the form "#RRGGBBAA".
NOTE: most devices draw nothing if a colour is not opaque,
but PDF and Quartz devices will render semitransparent colours.
A new argument 'alpha' to the function col2rgb()
provides the ability to return the alpha component of
colours (as well as the red, green, and blue components).
I'm using R 2.0.0 on Windows 2000 and wanted to try this feature. The
following simple test works fine:
pdf("c:/alpha.pdf")
plot(rnorm(1:100),rnorm(1:100),col="#55ff",pch=16)
dev.off()
But as soon as I change alpha value from "ff" to "fe", the points are no
longer visible for me. I've tried viewing the pdf with Acrobat Reader
5.1.0 and gsview4.5.
Do I need a more recent pdf viewer? Is this feature not working on
Windows? Am I doing something wrong? Any tips would be appreciated.
Thanks,
Kevin Wright
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