[R] simple example for linear mixed effects model

Dear R Gurus: Could someone point me to a small example of a linear mixed effects model, please? Ideally, this example would only have a few data points so I could calculate by hand to compare results to R results, please. Thanks so much! Sincerely, Edna Bell

[R] classes and methods

gt; plot(x) > y <- new("foo",x=rnorm(50)) > class(y) [1] "foo" My question is: should I have a "foo" function which sets the class to "foo", please? or a sort of Validity checker, please? Thanks, Edna Bell ___

[R] function question

Dear R Gurus: I read somewhere that functions are considered vectors. Is this true, please? thanks Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org

[R] yet another package building question please

Hello again. I'm trying to use package.skeleton to build my package. However, my package will contain a Fortran subroutine. Can you use package.skeleton with that subroutine, please or do you need to add it manually? Thanks again, Sincerely, Edna

[R] several package building questions: found answer to the manuals

Hi again. I found out how to download the manuals from the website. Sorry __ R-help@r-project.org 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 comment

[R] several package building questions

code to be used with R, and eventually be used in a package, please? It used to be something like g77 -O2 -c test.f? Thanks for any help. Sincerely, Edna Bell . __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] builtin vs. closure

Dear R Gurus: I'm working slowly through "R Programming for Bioinformatics", which is really interesting! Anyway, my question now is: what determines if a function is a builtin vs. a closure, please? For instance: > typeof(sqrt) [1] "builtin" > typeof(mean) [1]

[R] primitives again

Dear R Gurus: How do I find the functions which are primitives, please? Thanks, Edna Bell __ R-help@r-project.org 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] difference between Primitive and Generic

Dear R Gurus: What is the difference between a Primitive and a Generic, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

[R] density estimate

are to Silverman's version from his page 15 Equation 2.2a, please? Thanks, Edna Bell __ R-help@r-project.org 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 provid

[R] adding S3 vs. S4 to a new package

Dear R Gurus: I'm building a package and am wondering whether to use S3 or S4 methods. Any advice, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] grep question

In grep, you can use the options "n" and "o" to get the line number and only the matching text. Is there a way to just get the line number, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mai

[R] 2^2 problem revisited

B 1 303.63 303.63 50.801 1.201e-05 *** Residuals 12 71.725.98 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > When you test on interaction, you reject (of course). Now, I thought that you could not test o

[R] 2^2 factorial design question

Dear R Gurus: How do you put together a 2^2 (or even 2^k) factorial problem, please? Since you have 2 levels for A and B, do you put in "A+" and "A-" as factors, please? Thanks, Edna Bell __ R-help@r-project.org mailing list

[R] [OT] factorial design

Dear R Gurus: I vaguely remember reading that if interaction was present in a factorial design, then the main effect results were suspect. However, I was reading a text which now uses the tests for main effects even if interaction is present. Which is correct, please? Thanks, Edna Bell

[R] goodness of fit test

Dear R Gurus; Is there an automated process for goodness of fit tests, please? I know there is prop.test for one at a time, but I was wondering about this, please. Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [R] setting history file

I am using R-2.7.2 on Windows XP. Sorry for the problems. Sincerely, Edna On Wed, Sep 10, 2008 at 11:54 AM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Wed, 10 Sep 2008, Edna Bell wrote: > >> Dear R Gurus: >> >> I would like to set the number of comm

[R] setting history file

Dear R Gurus: I would like to set the number of commands in the history file as 50 rather than 25. I would do this in the .First function. How do I set this, please? I tried history(max=50) and it prints what it has. I just want to set the size in .First. Thanks in advance, Sincerely, Edna __

[R] probably easy methods question

ts registered S3 method for t from namespace stats namespace:stats with value function (x, ...) UseMethod("t.test") > methods("t.test") [1] t.test.default* t.test.formula* Non-visible functions are asterisked > Ok. Now what, please? I'm sure it's really simp

[R] test for a single variance

Dear R Gurus: Is there a test for a single variance available in R, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

[R] creating a vignette

Dear R Gurus: How would I create a vignette, please? Why would a vignette be better than examples, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

[R] Latin squares in R

Dear R Gurus: What would be the best way to evaluate a Latin square problem, please? Does it work in Rcmdr, please? thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] try question

078 NaN 0.30283262 NaN [21] -0.11696872 -3.84122332 NaN NaN -0.12808690 Warning message: In log(rnorm(25)) : NaNs produced > I thought that putting the "silent = TRUE" would suppress the warnings, please. What should I do instead, please? T

[R] ls() and memory question

Hi again! I put in ls() to check the objects in my workspace. Is there a limit on how many objects I can have, please? Or does it depend on the memory, please? TIA, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo

Re: [R] more environment questions

environment e1 > > By the way, if you are doing a lot of manipulations of environments > you might want to look at the proto package which reframes the > whole thing in terms of object oriented programming. > > On Tue, Jul 29, 2008 at 12:12 PM, Edna Bell <[EMAIL PROTECTED]>

[R] table questions

there a way to set things up to have 0 - 0.4 0.5 - 0.9 etc. please? I know there is the cut functions, but breaks are required. If you don't have breaks, what should you do, please? Would using the breaks from the hist function work appropriately, pleas

[R] more environment questions

e1, please? Thanks, Edna Bell __ R-help@r-project.org 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] keywords

Hi R Gurus! When you build a package, you need to put in keywords in the Rd files. Where would you find the list of keywords, please? TIA, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

[R] environment question

e2) # this succeeds by inheritance exists("a", envir=e2, inherits = FALSE) exists("+", envir=e2) # this succeeds by inheritance My question is: how can "a" exist in e2 when the ls(e2) gives character(0), please? Thanks, Edna Bell ___

[R] read.table question

Dear R list: I have a data set that I would like to bring it. The fourth column shows as numeric, but I want it to be a factor. Is there a way to do this from the read.table statement, or should I just wait and use the factor function please? thanks, Edna Bell

[R] still more dumb questions

Hello. When I type in "median", I get the following: > median function (x, na.rm = FALSE) UseMethod("median") > How do I look at the code, please? Thanks again, Edna __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help P

[R] Cairo graphics

Hi again. Sorry to be a pest. What are Cairo graphics and how to find out about them, please? Thanks yet again, Edna __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-projec

[R] ggplot2 help

Hi yet again! Thank you for being patient with me. Is there a "how to" for ggplot2, please? I would like to look at it, but have no idea where to start, please. Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.

[R] factor question

[1] cat cat cat tree tree tree tree Levels: cat dog tree > How should I remove the dog from the level, please? Thanks in advance, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] an extremely simple question

Hi! What is the difference between using data(somedataset) vs. attach(somedataset), please? thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org

[R] printing in binary

Hi r Gurus: Is there a way to print numbers in binary format, please? I know that you can use sprintf for hex, but I'm not sure how to get binary. Thanks Edna __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] fortran question

Hi R Gurus: I have used the following in the past: g77 -O2 -c test.f g77 -shared -o test.dll test.f with success. Now I'm getting ld: dllcrt2.o no such file I have the latest version of Rtools28.exe Any suggestions would be much appreciated. Sincerely, Edna

[R] [OT] Linux/UNIX question

Dear R Gurus: I'm trying to find R on another Linux system. I'm using the find command, (surprise), but I only want to see the output where it exists, not all of the other stuff. Is there an option that I could select, please? Right now I have find / -name R TIA, Sincerely, Edna ___

[R] finding source for a function

Dear R Gurus: How do you get source for functions which say "UseMethod" when you type in their names, please? I've tried getAnywhere and getMethods...I thought that might produce them. Thanks in advance. Sincerely, Edna __ R-help@r-project.org mailin

[R] gcc and R CMD SHLIB question

Dear R Gurus: Is there an option for gcc and R CMD SHLIB such that it neither compiles nor links but shows you which libraries etc would be used, please? I saw something like it but forgot to write it down. Thanks in advance! Sincerely, Edna Bell

[R] R extensions

Dear R Gurus: I'm reading through the "Writing R Extensions" manual. I am seeing references to "load hooks" and SEXPR but have no ideas what these are. Could someone give me some direction as to finding out about these, p

[R] USA map with all states

Hi R Gurus! There was a function in S called "usa()" which would plot the US. I found map('usa') in R for the lower 48 states. Is there a way to include Alaska and Hawaii as well, please? Thanks, Edna Bell __ R-help@r-project.or

[R] [OT] putting URLs in Latex

Hi R Gurus! This is definitely off topic, but I thought I'd try: what is the way to put in url's into a Latex file, please? I know that you start with a \newcommand statement, with some kind of argument that will change, but I'm not sure how to set it up, please. th

Re: [R] generating .Rd files

Thanks to all. I did not install. (no wonder I couldn't find them...) On 11/26/07, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 26/11/2007 6:59 PM, Edna Bell wrote: > > Hi R Gurus! > > > > I have a package that I am putting together. > > > > I

[R] Please ignore previous .Rd question

If the function is f, you can use prompt(f) Sorry thanks, Edna __ R-help@r-project.org 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

[R] generating .Rd files

Hi R Gurus! I have a package that I am putting together. I waited until the end to do the documentation and would like to generate a set of "empty" .Rd files. Is there a quick way to do this, please? Thanks, Edna Bell PS I can't seem to access the "Writing R Extensions&q

Re: [R] structure vs. matrix

g that you don't know how to > do stats;). > > ## see > ?structure > ?matrix > > A structure is not a matrix. So, if you want to make a matrix, use > matrix(). Easy. > > HTH, > Mark. > > > Edna Bell wrote: > > > > Hi R Gurus! >

[R] structure vs. matrix

Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

[R] [OT] vista question

This is way off topic, but I'll try: On a windows vista machine, how can you run commands from the command prompt as administrator, please? tia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] correct wording and notation for R stuff in LaTex

Hi R Gurus: I'm putting together an article about some R stuff in Latex. I refer to packages and functions. I think that I use {\em} for packages and {\tt} for functions. Is that correct, please? Thank you in advance! Sincerely, Edna Bell __ R

[R] strsplit

Hello R Gurus: I would like to take a character string and split at the $ sign. I thought that strsplit would do it, but here are the results: > vv [1] "whine$ts1" > vv [1] "whine$ts1" > strsplit(vv,"$") [[1]] [1] "whine$ts1" Does anyone

[R] building a copy of R with certain packages in Linux

Dear R Gurus: I would like to have a version of R with certain packages only to be put together in Linux. Does something like that exist, please? I'm thinking it might be a sort of R CMD build but I don't know how to proceed. Thanks for any help. Sincerely,

[R] building packages on Windows

Hi again. I'm sure that this is really simple. I'm trying to build a package on a Windows Vista machine. I use Rcmd build --binary test but I get the "Please set TMPDIR to a valid temporary directory" I tried TMPDIR=c:\temp but to no avail. Please help. thanks __

[R] convert a tar.gz to a Windows zip

Dear R Gurus; Is there a simple way to convert a Linux produced tar.gz file (a package) to a Windows binary zip package, please? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the post

Re: [R] convert time series to data.frame

standing why you're losing the "time element". > > Jeff. > > On Oct 1, 2007, at 12:27 AM, Edna Bell wrote: > > > Dear R gurus > > > > I would like to take a monthly time series and convert it to a data > > frame without losing the tsp items, pleae

[R] convert time series to data.frame

Dear R gurus I would like to take a monthly time series and convert it to a data frame without losing the tsp items, pleae I've tried as.data.frame and data.frame but I get the series without the time element. Any suggestions, please? tia Edna

[R] fuzzy logic

Hi R Gurus! Is there a fuzzy logic package please? Thanks, Edna Bell __ R-help@r-project.org 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

[R] making R packages and compacting an entire R set up

raries set up very nicely. I would like to hand off this setup to someone else. Should I just copy things as they stand onto a CD please or is there a better way please? thanks in advance! Sincerely, Edna Bell __ R-help@r-project.org mailing

[R] Converting zoo dates to ts dates

Hi R Gurus I'm using get.hist.quote to obtain monthly historical data. This results in a zoo series. I would like to convert the zoo series to a time series within a function. How do I get the starting date for the ts from the zoo series, please? Thanks, Edna