Tom,
 
Thanks for the reply to my question about books on R. WOW have I ever gotten a lot of recommendations.
 
I notice that you ended with talking about a workshop in the Great Smokey Mountains NP. My wife did her masters degree there, look at American Chestnut to do tree-ring analysis. She was working under Dr. Dave Stahle at the University of Arkansas. I helped her with field work at times and one time we almost got arrested by a park ranger when he saw us coming out of the woods carrying a chainsaw. That was fun.
 
Bob Keeland

hu, 11/18/10, Tom_Philippi@nps.gov <Tom_Philippi@nps.gov> wrote:


From: Tom_Philippi@nps.gov <Tom_Philippi@nps.gov>
Subject: Re: [R-sig-eco] New to R
To: "Bob Keeland" <keelandb@yahoo.com>
Cc: Tom_Philippi@nps.gov, tephilippi@gmail.com
Date: Thursday, November 18, 2010, 11:08 AM




Bob--

Bob Muenchen has a free 80 page pdf "R for SAS and SPSS Users":
http://RforSASandSPSSusers.com
and a larger book by the same name.

As for books, I would start with the Kuhnert & Venables book Mauricio Zapata sent a link to. You might be able to use only that as a general book, and spend your money on a couple of books on specific topics you need (e.g., Spector's little data manipulation book or Sarkar's lattice graphics book in the Springer UseR! series).

Maindonald's Data Analysis and Graphics Using R is quite good for an introductory book, but perhaps a couple of years out of date.  There's also a smaller version available as a free pdf from the page of contributed documentation:
http://cran.r-project.org/other-docs.html


I dislike Crawley's R book: I suppose one would learn by working through it, but it is thick, with only a cryptic 1 level table of contents, and not that useful of an index, and material on a given topic is spread throughout the book.  

I started out liking Everitt & Hothorn's  Statistical Analysis Using R, but after trying to teach from it, I'm annoyed at some of the later chapters (such as longitudinal analysis) being somewhat misguided as well as incomplete.  Horton & Kleinman's Using R for Data Management, Statistical Analysis, and Graphics looks pretty useful to me, but I haven't tried using it for teaching.

I find the Adler R in a Nutshell book surprisingly useful as a reference to find tools and functions in R that I didn't know about, even though I use the built in help system (?function or help(function)) for most of the syntax documentation.


Bob Muenchen has a free 80 page pdf "R for SAS and SPSS Users":
http://RforSASandSPSSusers.com
and a larger book by the same name.  [If that link doesn't work, I have a copy stashed at:
http://science.nature.nps.gov/im/monitor/stats/R/documentation/RforSASSPSSusers.pdf ]


Faraway's Extending the Linear Model ... book is quite good if you need mixed models, generalized linear models, and such.  I don't have his introductory Linear Models with R book, but folks seem to like it.  Faraway's Practical Regression and ANOVA is available as a free pdf from the contributed documentation page..

If you need generalized linear mixed models, wait for Doug Bates' book to come out in a couple of months; he posted draft pdfs at: 
http://lme4.r-forge.r-project.org/
Also, he has a vignette "lmer for SAS PROC MIXED Users": http://cran.r-project.org/web/packages/SASmixed/vignettes/Usinglmer.pdf

If you need any vegetation stuff, I recommend Dave Roberts' web page for vegetation ecology:
http://ecology.msu.montana.edu/labdsv/R/labs/
along with Jari Oksanen's vegan tutorial (vegan is the package for vegetation analyses, everything from various clustering and twinspan to various ordination forms to adonis, which partitions dissimilarity in an ANOVA-like manner based on the Marti Anderson papers.
http://cc.oulu.fi/~jarioksa/softhelp/vegan.html

Once you get your feet wet and have an idea of what specific R topics you need books on, the CRAN site has a list of books on R:
http://www.r-project.org/doc/bib/R-books.html
If you can't find the books you want on amazon or another source for 20% discount, the CRAN page has info on publisher's 20% discounts for almost every book.


Finally, I'm slowly populating a set of web pages on R for natural resources at:
http://science.nature.nps.gov/im/monitor/stats/R/index.cfm

Paul Geissler of USGS will be offering another free intermediate level webinar on R, probably starting in January, possibly not starting until the second week of February, after he and I lead our workshop at Great Smoky Mountains NP.  
http://www.fort.usgs.gov/brdscience/learnRE.htm

Tom

-------------------------------------------
Tom Philippi, Ph.D.
Quantitative Ecologist
Inventory and Monitoring Program
National Park Service
1201 Oakridge Drive, Suite 150
Ft. Collins, CO   80525-5589
Tom_philippi@NPS.gov    (970) 225-3586
Fax (970) 225 3597
http://science.nature.nps.gov/im/monitor
-------------------------------------------


-----r-sig-ecology-bounces@r-project.org wrote: -----


To: r-sig-ecology@r-project.org

Sent by: r-sig-ecology-bounces@r-project.org
Date: 11/17/2010 10:57AM
Subject: [R-sig-eco] New to R

OK all, I'm a research forest ecologist who worked for the US Fish & Wildlife Service and the US Geological Survey for 16 years after studying under Dr. Sharitz at the Savannah River Ecology Laboratory. Most of my work has been in bottomland hardwood forest and cypress/tupelo swamps of the Southeastern United States. My data analysis tool was SAS, and I do some programming in Visual Basic.  I now work with a very small company that has little in the way of data analysis or graphics capabilites. I therefore downloaded R and am trying to figure it out. 
 
Other than the "Introduction to R" manual and other things on the R website can you recommend a good book on R. My analysis needs are not that complex. I currently need to do an ANOVA on two tree populations to see if they are significantly different with respect to size (one area was polluted and the other is a control). I also need to do some point-quarter analysis for two separate forest populations, one in NE Texas and the other in S Mississipp).
 
Any help or suggestions would be appreciated.
 
Bob Keeland
Research Forest Ecologist
Forest Dynamics, Inc.
Louisiana


     
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