[R] summary of linear fixed effects model is different than the HSAUR book
Running R 2.5.1 and a newly downloaded lme4 package on WinXP I'm trying to work my way through Everitt and Hothorn's Handbook of Statistical Analyses Using R, c 2006. (No, it's not homework.) Chapter 10 discusses linear mixed effects models for longitudinal data. I've called my long data frame BtheB.long Here's the model from the book, which I run. lmer1 - lmer(bdi ~ bdi.pre + months + treatment + drug + length + (1 | subject), data = BtheB.long, method = ML, na.action = na.omit) Here is the summary of the model that I see: summary(lmer1) Linear mixed-effects model fit by maximum likelihood Formula: bdi ~ bdi.pre + months + treatment + drug + length + (1 | subject) Data: BtheB.long AIC BIC logLik MLdeviance REMLdeviance 1885 1910 -935.3 1871 1866 Random effects: Groups NameVariance Std.Dev. subject (Intercept) 48.299 6.9498 Residual 25.129 5.0128 number of obs: 280, groups: subject, 97 Fixed effects: Estimate Std. Error t value (Intercept) 5.943722.24915 2.643 bdi.pre 0.638190.07759 8.225 months -0.717030.14606 -4.909 treatmentBtheB -2.373111.66368 -1.426 drugYes-2.797861.71993 -1.627 length6m 0.256391.63213 0.157 Correlation of Fixed Effects: (Intr) bdi.pr months trtmBB drugYs bdi.pre -0.678 months -0.264 0.023 tretmntBthB -0.389 0.121 0.022 drugYes -0.071 -0.237 -0.025 -0.323 length6m -0.238 -0.242 -0.043 0.002 0.158 But on page 169, summary() is shown to produce additional columns in the fixed effects section, namely degrees of freedom and the P-value (with significance stars). How can I produce that output? Am I doing something wrong? Has lme4 changed? Thanks. -- Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] THANK YOU: Updating R version
This sounds like a solution I've been looking for. With this setup now in place, when you download and install some new packages, where will they be put? Into C:\myRlib ? Thanks. --Chris Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] Raghu Naik wrote: Based on the feedback received, I did the following: a) moved my lib sub-directory from the existing installed R version to c:\myRLib b) installed the updated R version c) created .Renviron file in the home directory (C:\R-2.5.1) with the line R_LIBS=c:/myRLib d) used .libPaths() command to confirm that the new R installation was recognizing the myRLib sub-directory e) deleted my old R installation Things worked fine. Thanks you. -- Forwarded message -- From: Raghu Naik [EMAIL PROTECTED] Date: Jun 2, 2007 5:13 PM Subject: Updating R version To: r-help@stat.math.ethz.ch A quick question. I am trying to understand how I could move the installed packages in my R 2.3 version to the newly installed R 2.5 version, without having to install all the packages again. I copied the files under the old library subdirectory to the new library subdirectory. But still the newer version is not recognizing the packages that were copied over. Thanks. [[alternative HTML version deleted]] __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] installing, removing, upgrading, and downgrading packages
I'm very new to R, trying to learn it. I started with R 2.4, but I have since upgraded to 2.5.0, on WindowsXP. I understand that 2.5.1 is now available. Last night in the course of things I loaded libraries coin and survival. I received warning messages that they had been built under version 2.5.1. However, as far as I could tell, they worked OK. But this brought some questions to mind: I found the remove.packages() command. Is there a way to revert a package back to a previous version without removing it? If not, and I remove one version, how do I specify downloading a particular (earlier) version? Was that warning of any consequence? Are there times when a package will not work properly with an earlier version of R, and will this be obvious to me when I try to use it? Or in a more general sense, are there foreseeable circumstances in which an older version of a package would be necessary, rather than the newest one? Should I keep my packages in a library folder outside of the R install folder? Right now, it appears that all the packages I download get installed into a library subdirectory under my R250 directory. Advantages and disadvantages of either method? Thanks. -- Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] elementary statistics with R (rkward?)
As a fellow beginner, I also found Handbook of Statistical Analyses Using R, by Brian Everitt, to be a very useful book. There is an accompanying R package, HSAUR. Also Using R for Introductory Statistics, by John Verzani. There is an accompanying R package, UsingR. Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] Charles Annis, P.E. wrote: Face the music and buy the book: _Introductory Statistics with R_ by Peter Dalgaard. It's perfect for what you need. It's clear and concise and will teach you statistics AND R as painlessly as such a thing can be. It's inexpensive and you can get it on Amazon.com and every other major bookseller, including the nearest university bookstore. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donatas G. Sent: Wednesday, July 11, 2007 9:27 AM To: r-help@stat.math.ethz.ch Subject: [R] elementary statistics with R (rkward?) Hi, I am trying to learn some basic statistics stuff but I cannot find any elementary statistics exercises using R language. Using RKward would be even better... I need that in analysing sociological data, obtained through questionnairres - findind corelations between variables, relations between different types of data, etc. Could anyone recommend simple tutorials/exercises, available on www for me to work on? I realize it would be much simple to do this introductory stuff with spss, that everyone around me is using here in Lithuania, but I'd really like to learn to do it with R instead... __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] running Rcmdr
I am very much a novice R user, and this is my first post to the List, but given that disclaimer, perhaps you could put library(Rcmdr) as a line in your Rprofile.site file? I think this contains commands that are run every time R is opened. [At least, I noticed after I installed my Tinn-R and got it to communicate with R, that certain R packages necessary for use of Tinn-R now get run every time I open Tinn-R (and R opens with it.)] That way, typing R on the command line (might!) run Rcmdr too. --Chris Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] Manuel wrote: Yes, of course, i know it, and i have installed all packages i need, but this is not what i am searching. I want to do that only with a command line without have to type only first R and after library(Rcmdr); i only want to type something like R library(Rcmdr) but i know it´s doesn´t work and i´m looking for something like that. I hope you have already understood my question. Thank you Felipe Carrillo escribió: If you have already installed Rcmdr from the internet (Cran site) then when you open R window if you type library(Rcmdr) you should see the R commander window and use it just like you would use R command window. */Manuel [EMAIL PROTECTED]/* wrote: Thanks for your answer, but i think i dont do correctly my question. I need the command line to run Rmdr, like that: R Rcmdr or R loadRcmdr.R where loadRcmdr has library(Rcmdr). or something like that. I tried the last example, but when Rcmdr is executed, later it is closed. About RProfile.site, i dont know what i have to change. If you think its useful to me, please explain me. Thanks. Felipe Carrillo escribió: First, you need to install the Rcmdr packages and then in the R Command window or Tinn-R window type library(Rcmdr) without the quotation marks. In addition, if you want Rcmdr to start automatically everytime you start R, go to the following path C:\Program Files\R\R-2.5.0\etc\RProfile.site if you installed R in program files, otherwise follow your own path and type the same command library(Rcmdr) and the R commander window should pop up everytime you start R */Manuel /* wrote: Hi to all, i want to know how can run Rcmdr automatically , or how to load a library in the call of R greetings __ 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 and provide commented, minimal, self-contained, reproducible code. Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. __ 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 and provide commented, minimal, self-contained, reproducible code. Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://us.rd.yahoo.com/evt=48246/*http://autos.yahoo.com/green_center/;_ylc=X3oDMTE5cDF2bXZzBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW4tY2VudGVy __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
