Re: [R] [R-SIG-Mac] morley object?

2013-11-22 Thread Steven McKinney
ystem.file("data", "morley.tab", package="datasets") > filepath [1] "C:/PROGRA~1/R/R-30~1.1/library/datasets/data/morley.tab" > mm <- read.table(filepath) > head(mm) Expt Run Speed 001 1 1 850 0021 2 740 0031 3 900 004

Re: [R] Change the text size of the title in a legend of a R plot.

2011-04-28 Thread Steven McKinney
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Victor Gabillon > Sent: April-28-11 8:22 PM > To: r-help@r-project.org > Subject: [R] Change the text size of the title in a legend of a R plot. > > Hello, > > Is it possible

Re: [R] is this an ANOVA ?

2011-04-12 Thread Steven McKinney
Quantile = 2.667 95% family-wise confidence level Linear Hypotheses: Estimate lwr upr B - A == 0 5. 2.3330 7.6670 C - A == 0 10. 7.3330 12.6670 C - B == 0 5. 2.3330 7.6670 > lmacld <- cld(lmamc)

Re: [R] Fast version of Fisher's Exact Test

2011-04-11 Thread Steven McKinney
ioned what operating system you are using, how much RAM you have or what sessionInfo() reports on your machine. That information will help to figure this out. Steven McKinney From: Jim Silverton [jim.silver...@gmail.com] Sent: April 9, 2011 9:21 AM To: Steve

Re: [R] Fast version of Fisher's Exact Test

2011-04-08 Thread Steven McKinney
ng slowly for you? Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Jim Silverton [jim.silver...@gmail.com] Sent: April 8, 2011 9:43 AM To: r-help@r-project.org Subject: Re: [R] Fast version of Fisher's

Re: [R] Where is the tcltk package?

2011-04-07 Thread Steven McKinney
rce or binaries? Steven McKinney From: Rolf Turner [r.tur...@auckland.ac.nz] Sent: April 7, 2011 5:38 PM To: Steven McKinney Cc: r-help@r-project.org Subject: Re: [R] Where is the tcltk package? On 08/04/11 12:31, Steven McKinney wrote: > Searchin

Re: [R] Where is the tcltk package?

2011-04-07 Thread Steven McKinney
to the registry If you install tcltk2, is tcltk then available? Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Rolf Turner [r.tur...@auckland.ac.nz] Sent: April 7, 2011 5:15 PM To: r-help@r-project.org

Re: [R] ANCOVA for linear regressions without intercept

2011-04-04 Thread Steven McKinney
6.1 2 2752.1 1 19444 10077 < 2.2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ### Plot the reduced model regression lines > abline(a = 0, b = coef(lmr1f)[1], col = &qu

Re: [R] Linear Model with curve fitting parameter?

2011-04-04 Thread Steven McKinney
> -Original Message- > From: stephen sefick [mailto:ssef...@gmail.com] > Sent: April-04-11 2:49 PM > To: Steven McKinney > Subject: Re: [R] Linear Model with curve fitting parameter? > > Steven: > > I am really sorry for my confusion. I hope this now makes s

Re: [R] Linear Model with curve fitting parameter?

2011-04-04 Thread Steven McKinney
> -Original Message- > From: stephen sefick [mailto:ssef...@gmail.com] > Sent: April-03-11 5:35 PM > To: Steven McKinney > Cc: R help > Subject: Re: [R] Linear Model with curve fitting parameter? > > Steven: > > You are exac

Re: [R] Linear Model with curve fitting parameter?

2011-04-01 Thread Steven McKinney
> -Original Message- > From: stephen sefick [mailto:ssef...@gmail.com] > Sent: April-01-11 5:44 AM > To: Steven McKinney > Cc: R help > Subject: Re: [R] Linear Model with curve fitting parameter? > > Setting Z=Q-A would be the incorrect dimensions. I could Z=Q

Re: [R] Linear Model with curve fitting parameter?

2011-03-31 Thread Steven McKinney
> > What is the formula that I should use? Let Z = Q - A for your logged data. Fitting lm(Z ~ R + S, data = x) should yield intercept parameter estimate = estimate for log(K) R coefficient parameter estimate = estimate for r S coefficient parameter estimate = estimate for s Steven

Re: [R] xlsx problem

2011-03-29 Thread Steven McKinney
Hi Cristoph, Glad to hear it worked - replying to r-help in case others face this issue. Cheers Steven McKinney From: Martin Knapp [mkna...@aucklanduni.ac.nz] Sent: March 28, 2011 7:28 PM To: Steven McKinney Subject: Re: [R] xlsx problem Thanks that

Re: [R] Points on Map

2011-03-28 Thread Steven McKinney
Here's a start... > require("maps") > foo <- map("state", "new york") > lines(x = range(foo$x, na.rm = TRUE), y = range(foo$y, na.rm = TRUE)) You can figure out from this how to specify the coordinates that you want for dividing up th

Re: [R] rep for multiple categories

2011-03-28 Thread Steven McKinney
d2Z 49a3Z 50b3Z 51c3Z 52d3Z 53a4Z 54b4Z 55c 4Z 56d4Z 57a5Z 58b5Z 59c5Z 60d5Z Steven McKinney Fr

Re: [R] xlsx problem

2011-03-28 Thread Steven McKinney
about anything, just about anywhere. Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Martin Knapp [mkna...@aucklanduni.ac.nz] Sent: March 28, 2011 1:43 PM To: r-help Subject: [R] xlsx problem Dear list, I'

Re: [R] Dont show zero values in line graph

2011-01-06 Thread Steven McKinney
How about this? > x<-c(1:5,NA,NA,8:10) > y<-1:10 > plot(0,0,xlim=c(0,10), ylim=c(0,10),type="n",main="Dont show the bloody 0 > values!!") > lines(x~y, col="blue", lwd=2, subset = !is.na(x)) NAs let you do l

Re: [R] Schedule R to run automatically

2010-12-13 Thread Steven McKinney
n both. In Windows, you can use the "Task Scheduler" (Control Panel - Administrative Tools on Windows 7). Set up the R script you want to run daily, and invoke it with the R CMD BATCH command. In Unix, you can use the cron scheduler to do the same. Steven McKinney > > Thanks

Re: [R] Tukey Test, lme, error: less than two groups

2010-12-03 Thread Steven McKinney
lme, linfct = mcp(Provenancef = "Tukey"))) Error in `[.data.frame`(mf, nhypo[checknm]) : undefined columns selected) Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Steven McKinney [smckin...@b

Re: [R] Tukey Test, lme, error: less than two groups

2010-12-02 Thread Steven McKinney
Comments in-line below > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Lilith > Sent: December-02-10 9:39 AM > To: r-help@r-project.org > Subject: [R] Tukey Test, lme, error: less than two groups > > > Dear R-group, > > I a

Re: [R] wilcox.test; data type conversion?

2010-10-28 Thread Steven McKinney
est data: jitter(as.integer(grade)) by sex W = 6, p-value = 0.5476 alternative hypothesis: true location shift is not equal to 0 I'll let you judge elegance. As for the barplots, I think all you need to do is specify the row and column order you'd like. Try this example >

Re: [R] How to write to sqlite files

2010-10-19 Thread Steven McKinney
the database, and running data queries. Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of lord12 [trexi...@yahoo.com] Sent: October 19, 2010 11:42 AM To: r-help@r-project.org Subject: [R] How to write to sqlite

Re: [R] help

2010-10-14 Thread Steven McKinney
3 [3,]3 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 4 [4,]4 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5 [5,]5 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6 [6,]6 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 7 > HTH Steven McKinney ___

Re: [R] [Rd] Selecting multiple columns with same name

2010-10-08 Thread Steven McKinney
This is better suited for R-help than R-devel, so I'm copying to the R-help list: > -Original Message- > From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On > Behalf Of Martin Kerr > Sent: October-08-10 3:09 AM > To: r-de...@r-project.org > Subject: [Rd] Selecti

Re: [R] interactive session

2010-09-30 Thread Steven McKinney
For those that want it all... > {cat("?"); a<-readLines(n=1) + print("hey") + print(b<-paste("t",a,sep=""))} ?ada [1] "hey" [1] "tada" > b [1] "tada" > Steven McKinney > -Original Message- &g

Re: [R] bptest

2010-09-24 Thread Steven McKinney
mula = NULL, studentize = TRUE, data = list()) ... So see if you can get package lmtest. HTH Cheers Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of robm [r.malp...@ntlworld.com] Sent: September 24, 2

Re: [R] French accents on characters

2010-08-04 Thread Steven McKinney
"\\'a") > text(3, 12, "\\'a", vfont=c("serif", "plain")) > text(1, 13, "a_acute", adj=0); text(2.5, 13, "\\`a") > text(3, 13, "\\`a", vfont=c("serif", "plain"

Re: [R] multiple R sessions from one working directory using GNU screen

2010-08-03 Thread Steven McKinney
out strategies to share bits of data and information across multiple R sessions. HTH Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Olga Lyashevska [o...@herenstraat.nl] Sent: August 3, 2010 8:04 AM To: r

Re: [R] how to do a IF ELSE in a matrix format

2010-08-02 Thread Steven McKinney
0.89838970 > edu[edu[, 1] < 0.5, 2] <- 1 > head(edu) [,1] [,2] [1,] 0.26550871 [2,] 0.37212391 [3,] 0.57285340 [4,] 0.90820780 [5,] 0.20168191 [6,] 0.89838970 > Steven McKinney > -Original Message- > From: r-help-boun..

Re: [R] how to find non-ASCII characters in .Rd files?

2010-07-29 Thread Steven McKinney
Does function showNonASCII(x) in package "tools" do what you need? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre From: r-help-boun...@r-project.org [r-help-boun...@r-p

Re: [R] re-ordering bwplot

2010-07-23 Thread Steven McKinney
s = c("Mississippi", > "Quebec")) > with(CO2, table(Type, Type2)) Type2 Type Mississippi Quebec Quebec0 42 Mississippi 42 0 > quartz() ## Your plot window type here (quartz() works on a Mac) > bwplot(

Re: [R] Can RMySQL run on Windows using a remote MySQL server?

2010-07-20 Thread Steven McKinney
ODBC Data Source Administrator widget in Windows administrative tools. Install RMySQL, configure and enjoy. Good luck! Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of neatgadgets [neatgadg...@gmail.com

Re: [R] Can RMySQL run on Windows using a remote MySQL server?

2010-07-19 Thread Steven McKinney
built. What OS are you running? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of neatgadgets [nea

Re: [R] RMySQL package on 64bit R for Windows

2010-07-16 Thread Steven McKinney
I think this is a question for R-devel so I'm cross-posting there with apologies. I've just acquired a Windows 7 64-bit box and also will need RMySQL eventually. Is there any information about issues involved with compiling RMySQL for Windows 64-bit? Steven McKinney Statistician

Re: [R] inverse function of melt

2010-06-18 Thread Steven McKinney
?cast A reproducible example would get you more feedback. Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of n.via...@libero.it [n.via...@libero.it] Sent: June 18, 2010 6:39 AM To: r-help@r-project.org

Re: [R] Competing with SPSS and SAS: improving code that loops throughrows (data manipulation)

2010-03-26 Thread Steven McKinney
onvert the matrix to a dataframe after the loop completes if needed. HTH Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Dimitri Liakhovitski [ld7...@gmail.com] Sent: March 26, 2010 6:40 PM To: Bert Gunter

Re: [R] Factor variables with GAM models

2010-03-19 Thread Steven McKinney
is a smooth function of X. Hence you might want to rethink why you'd want a factor variable as a predictor variable in a GAM. This is why the gam machinery doesn't just do the factor conversion to indicator variables as is done in lm. HTH Steven McKinney _

Re: [R] Merging Matrices

2010-03-19 Thread Steven McKinney
> From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf > Of duncandonutz [dwads...@unm.edu] > Sent: March 19, 2010 1:11 PM > To: r-help@r-project.org > Subject: [R] Merging Matrices > > I have two symmetric matrices, but of different

Re: [R] Plot frame border to start at zero?

2010-01-19 Thread Steven McKinney
on), cex=0.95) > mtext("Index Hour", side=1, line=2) > mtext("Incremental Precipitation (in)", side=2, line=2.5) > mtext("Accumulated Precipitation (in)", side=4, line=2) > dev.off() > > > Thanks for all your help, > Doug

Re: [R] help writing for loop

2009-11-25 Thread Steven McKinney
i-th row element is the solution for y = a + bx + cx^2 for the i-th row of coefficients in the parameter estimates matrix mA You can spot check with e.g. > mA[1,] %*% mB[15,] [,1] [1,] 214.7864 > mA[1,] %*% mB[5,] [,1] [1,] 27.31023 > mA[1,] [1] 0.2875775 0.9568333 0.

Re: [R] Where are usages like "== 2L" documented?

2009-11-16 Thread Steven McKinney
> -Original Message- > From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com] > Sent: Monday, November 16, 2009 4:52 PM > To: Duncan Murdoch > Cc: Steven McKinney; R Help > Subject: Re: [R] Where are usages like "== 2L" documented? > > On Mon, Nov 1

Re: [R] Where are usages like "== 2L" documented?

2009-11-16 Thread Steven McKinney
?NumericConstants will bring up a help page that mentions "All other numeric constants start with a digit or period and are either a decimal or hexadecimal constant optionally followed by L." and "An numeric constant immediately followed by L is regarded as an integer number when possible

Re: [R] Adjusting Yaxis (ylim) limits on a plotMeans(DV, IV1, IV2, error.bars="se")

2009-11-05 Thread Steven McKinney
ns(DV, IV1, IV2, error.bars="se", ylim = c(27, 99)) or whatever your desired ylim values are. HTH Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561

Re: [R] cox regression extract strata as numeric

2009-10-27 Thread Steven McKinney
uot;enum=3" "enum=3" "enum=3" [51] "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=4" "enum=4" "enum=4" [61] "enum=4" "enum=4"

Re: [R] How to apply the Wilcoxon test to a hole table at once?

2009-10-23 Thread Steven McKinney
th W = 78, p-value = 2.400e-08 alternative hypothesis: true location shift is not equal to 0 Warning message: In wilcox.test.default(x = c(67L, 72L, 74L, 62L, 56L, 66L, 65L, : cannot compute exact p-value with ties > # Same as lapply loop result HTH Steven McKinney Statistician Molecular

Re: [R] Navigate to Index page of a package from R command prompt

2009-07-24 Thread Steven McKinney
ork/Resources/library/survival/html/00Index.html" > bar Help for '' is shown in browser /usr/bin/open ... Use help("", htmlhelp = FALSE) or options(htmlhelp = FALSE) to revert. > Again, what I've been trying to achieve. When a user loads a new libr

Re: [R] Navigate to Index page of a package from R command prompt

2009-07-23 Thread Steven McKinney
> -Original Message- > From: Marc Schwartz [mailto:marc_schwa...@me.com] > Sent: Thursday, July 23, 2009 2:04 PM > To: Steven McKinney > Cc: R-help@r-project.org > Subject: Re: [R] Navigate to Index page of a package from R command > prompt > > On Jul 2

Re: [R] mathematical notation in R

2009-07-23 Thread Steven McKinney
Hi Mary, Something such as > plot(1,1) > title(expression(paste("LBAuo = -", infinity))) Is this what you're after? Best Steve McKinney From: Mary A. Marion [mms...@comcast.net] Sent: July 23, 2009 4:23 PM To: Steven McK

[R] Navigate to Index page of a package from R command prompt

2009-07-23 Thread Steven McKinney
and from the R listener that can take me directly to this "00Index.html" page of help for package "foo"? something like > help("00Index", package = "utils") (but this does not work)? Any info appreciated Best Steven McKinney Statistician Molecula

Re: [R] mathematical notation in R

2009-07-22 Thread Steven McKinney
Does this approach what you're looking for? See ?is.finite for more info > LBAuo<- - > LBAuo [1] - > if (LBAuo <= -) LBAuo <- -Inf > LBAuo [1] -Inf > HTH Steven McKinney > -Original Message- > From: r-help-boun...@r-project.org [mailto:

Re: [R] Referencing data frames

2009-06-12 Thread Steven McKinney
ble() + } > > dfnames <- c("foo", "bar", "baz") > myrbind(dfnames) > objects() [1] "bar" "dfnames" "foo" "foo.bar.baz" "myrbind" > foo.bar.baz X1 X2 X3 1 1 5 9 2 2

Re: [R] Need help understanding output from aov and from anova

2009-06-03 Thread Steven McKinney
F valuePr(>F) fac1 6.7274e-30 6.7274e-30 1.3340e+32 < 2.2e-16 *** Residuals 1 5.043e-62 5.043e-62 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Warning message: In anova.lm(lm(vtot ~ fac)) :

Re: [R] Warning trying to plot -log(log(survival))

2009-05-11 Thread Steven McKinney
es.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] survival_2.35-4 > Steven McKinney > -Original Message- > From: John Sorkin [mailto:jsor...@grecc.umaryland.edu] > Sen

Re: [R] Warning trying to plot -log(log(survival))

2009-05-11 Thread Steven McKinney
Hi John, I can't reproduce your case with built-in data sets. Your data set is small. Can you show the data for the variables involved in your example? (Time30, Died, Rx, Age) Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program British Columbia C

Re: [R] Corrupt data frame construction - bug?

2009-04-29 Thread Steven McKinney
Thanks Duncan, Comments and a proposed bug fix in-line below: > -Original Message- > From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] > Sent: Wednesday, April 29, 2009 5:10 PM > To: Steven McKinney > Cc: R-help@r-project.org > Subject: Re: [R] Corrupt data frame

[R] Corrupt data frame construction - bug?

2009-04-29 Thread Steven McKinney
en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nlme_3.1-90 loaded via a namespace (and not attached): [1] grid_2.9.0 lattice_0.17-22 tools_2.9.0 > Also occurs on Windows box w

Re: [R] create objects in a loop and adding sqlQuery content to them

2009-04-20 Thread Steven McKinney
> > > > > #Here my first try [error message on the line within the loop, saying > > something like: > > # 'recursive indexing on level 2 failed'] > > sites_object_list <- vector("list",99) > > If there's a site number larger than 99 this will be problematic. Sorry, this isn't correct - R will

Re: [R] create objects in a loop and adding sqlQuery content to them

2009-04-20 Thread Steven McKinney
a simple integer but has two numbers with a space or something in it. > > I would be very, very glad if anybody sends me a clue about this, as > I'm a obviuos Newbie using > R... > > Thanks, > > Katharina > > ___

Re: [R] what is R equivalent of Fortran DOUBLE PRECISION ?

2009-03-30 Thread Steven McKinney
uble precision format. The functions as.single and single are identical to as.double and double except they set the attribute Csingle that is used in the .C and .Fortran interface, and they are intended only to be used in that context. HTH Steven McKinney, Ph.D. Statistician Molecul

Re: [R] Combining columns from two dataframes

2009-03-17 Thread Steven McKinney
-10-01 > c$a <- as.Date(c$a) > c a 1 2008-07-27 2 2008-10-01 3 2008-08-15 4 2008-08-14 5 2008-08-14 6 2008-09-20 7 2008-07-27 8 2008-10-01 > lapply(c, class) $a [1] "Date" > Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program Br

Re: [R] How do I set the Windows temporary directory in R?

2009-03-17 Thread Steven McKinney
the following rule. The environment variables TMPDIR, TMP and TEMP are checked in turn and the first found which points to a writable directory is used: if none succeeds ‘/tmp’ is used. HTH Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program British Columbia Can

Re: [R] Is it possible for R to import a SigmaPlot file?

2009-01-22 Thread Steven McKinney
Hi Jason Have you checked out Stat/Transfer? www.stattransfer.com They state they handle SYSTAT files, and SigmaPlot is a SYSTAT product. Stat/Transfer has a demo download you could use to test. I've used it to good effect (though for other than SYSTAT datasets) in the past. HTH S

Re: [R] Problem with subset() function?

2009-01-20 Thread Steven McKinney
age))) and density(mydf[mydf$ht >= 150.0 & mydf$wt <= 150.0, "age"]) so it is subset(mydf, ht >= 150.0 & wt <= 150.0, select = c(age), drop = TRUE) that is equivalent to mydf[mydf$ht >= 150.0 & mydf$wt <= 150.0, "age"] Apologies and thanks for s

[R] Problem with subset() function?

2009-01-20 Thread Steven McKinney
attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] Matrix_0.999375-16 grid_2.8.0 lattice_0.17-15lme4_0.99875-9 [5] nlme_3.1-89 > Steven McKinney Statistician Molecular Oncology

Re: [R] Compare matrices

2009-01-19 Thread Steven McKinney
Use the is.na() function to assign NA values: > is.na(A) <- !B > A [,1] [,2] [,3] [1,]3 NA NA [2,]333 [3,]33 NA > C <- matrix(c(3,3,3,NA,3,3,NA,3,NA),3,3) > all.equal(A, C) [1] TRUE Steven McKinney Statistician Molecular Oncology

Re: [R] coercing a list into matrix

2009-01-14 Thread Steven McKinney
,]65 NA > A <- list(c(3,2,3), c(1,2,3,4), c(5,6)) > matrixFromList(A) [,1] [,2] [,3] [,4] [1,]323 NA [2,]1234 [3,]56 NA NA > class(matrixFromList(A)) [1] "matrix" Best Steven McKinney Statistician Molecular

Re: [R] Memory Efficiency of Symmetric Matrix

2009-01-06 Thread Steven McKinney
See also the dist() function documentation. If you use indexing as described in ?dist it is straightforward to maintain and use a vector of the distances. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at

Re: [R] Problems installing lme4 on Ubuntu

2008-12-19 Thread Steven McKinney
This may just be version incompatibilities. A similar discussion recently transpired on r-sig-mixed-models, see e.g. https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001526.html HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer

Re: [R] How can I draw bars

2008-12-09 Thread Steven McKinney
oconductor package "VanillaICE" to add a chromosome graphic to the bottom of data plots of genomic data. You can see examples in the vignette PDFs. HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL P

Re: [R] Help with reading code

2008-12-03 Thread Steven McKinney
sage in context: http://www.nabble.com/Help-with-reading- > code-tp20823979p20823979.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PL

Re: [R] AIC function and Step function

2008-11-27 Thread Steven McKinney
), AIC(el, k = k) names(val) <- c("df", "AIC") Call <- match.call() Call$k <- NULL row.names(val) <- as.character(Call[-1]) val } else AIC(ll(object), k = k) } Steven McKinney Statistician Molecular Onc

Re: [R] AIC function and Step function

2008-11-27 Thread Steven McKinney
c(edf, -2 * loglik + k * edf) } extractAIC.survreg <- function(fit, scale, k = 2, ...) { edf <- sum(fit$df) c(edf, -2 * fit$loglik[2] + k * edf) } extractAIC.glm <- function(fit, scale = 0, k = 2, ...) { n <- length(fit$residuals) edf <- n - fit$df.residual

Re: [R] 64bit R for Mac

2008-11-24 Thread Steven McKinney
version is working well. You might also want to follow the r-sig-mac list for mac-specific information. HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncolog

Re: [R] 64bit R for Mac

2008-11-24 Thread Steven McKinney
(Apologies if this repost is a duplicate, my first submission did not appear to make it through.) -Original Message- From: Steven McKinney Sent: Mon 11/24/2008 4:28 PM To: 'Blanchette, Marco'; R-help Subject: RE: [R] 64bit R for Mac Dear Marco Check out http://r.research.att

Re: [R] how to test for the empty set

2008-11-24 Thread Steven McKinney
0 > y <- letters[1:3] > z <- letters[4:6] > x <- intersect(y,z) > class(x) [1] "character" > length(x) [1] 0 > y <- 1:3 > z <- 4:6 > x <- intersect(y,z) > class(x) [1] "integer" > length(x) [1] 0 > HTH Steven McKinne

Re: [R] lmer p-values for fixed effects missing

2008-11-18 Thread Steven McKinney
es of freedom and other model attributes more difficult to calculate compared to fixed effects models. Research and debate is ongoing as to the best way to handle model assessment, not all classical summary statistics and associated p-values map to lmer models in a straightforward fashion. Steve

Re: [R] lines.formula with subset

2008-11-13 Thread Steven McKinney
herwise, the data objects y and x that you set up should have been passed downwards in some fashion for evaluation. R-core members who know the rules better than I will have to determine how best to handle this one. HTH Steven McKinney Statistician Molecular Oncology and Brea

Re: [R] bizarre axes with xyplot, problem in data?

2008-10-30 Thread Steven McKinney
s, from the origin in the lower left, not top-down as in a table." ) Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor

Re: [R] Computational problems in R

2008-10-28 Thread Steven McKinney
ities greater than zero, so that's not an issue in this calculation (this 'B' not being the same as the 'B' in Amy's original description). Thanks again to Duncan Murdoch, and my apologies for my misinterpretation. Steven McKinney -Original Message- From: Ro

Re: [R] Computational problems in R

2008-10-24 Thread Steven McKinney
data set? Perhaps then they need to be set aside and investigated separately, etc. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West

Re: [R] combining data from different datasets

2008-10-24 Thread Steven McKinney
enough to give your labels enough room. HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z

Re: [R] help regarding levels

2008-10-03 Thread Steven McKinney
Your column of data has some character data in it, perhaps an Excel #VALUE! or a blank or some such entry not strictly numeric. When R reads in such a column, it makes that column variable into a 'factor' variable instead of a numeric variable, because the values are not all numeric. You can spec

Re: [R] print.data.frame : row.name = FALSE not having intendedeffect

2008-09-23 Thread Steven McKinney
Here's the current method for printing a data frame: > print.data.frame function (x, ..., digits = NULL, quote = FALSE, right = TRUE, row.names = TRUE) { n <- length(row.names(x)) if (length(x) == 0L) { cat("NULL data frame with", n, "rows\n") } else if (n == 0L) {

Re: [R] sort a data matrix by all the values and keep the names

2008-09-22 Thread Steven McKinney
Is something missing in the melt()? > x<-data.frame(x1=c(1,7),x2=c(4,6),x3=c(8,2)) > require("reshape") Loading required package: reshape > dfm <- melt(x, id = c()) Error in if (!missing(id.var) && !(id.var %in% varnames)) { : missing value where TRUE/FALSE needed > dfm[order(dfm$value), ] Erro

Re: [R] how to keep up with R?

2008-09-19 Thread Steven McKinney
One thing that R does very well that SAS does not is graphics - graphical portrayal of data is important, and you can keep up with R by supplementing your SAS analyses with R graphics. Steve McKinney -Original Message- From: [EMAIL PROTECTED] on behalf of Barry Rowlingson Sent: Fri 9/19

Re: [R] Different PCA results under Windows and Linux

2008-09-16 Thread Steven McKinney
Not likely that anyone can explain, as there is not enough information in your email. Including the contents of the freqtest.txt file was a good idea, as the posting guide suggests (the posting guide is that clearly labeled bit at the bottom that looks like this: PLEASE do read the posting guide

Re: [R] Using quasibinomial family in lmer

2008-09-16 Thread Steven McKinney
ept) -0.1374 0.1219 -1.127 > sessionInfo() R version 2.7.1 Patched (2008-06-25 r45988) powerpc-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.6-0 DBI_0.2-4

Re: [R] bootstrapping - number of items to replace is not a multiple of replacement length

2008-09-09 Thread Steven McKinney
Hello, Your theta() function is returning different sets of coefficients depending on the results of step(). You'll need to add code to theta() to figure out which variables were selected, and store them into the right positions of a vector of length 20 (the apparent number of covariates you desc

Re: [R] lattice command equivalent to points

2008-09-02 Thread Steven McKinney
This is close, but maybe not optimal lattice coding. I haven't yet figured out how to suppress the x axis labeling. bwplot(yield ~ 1|year, panel = function(x, y, ...){panel.bwplot(x, y, ..., pch = "|"); panel.points(x, mean(y), ..., pch=17)}, data = barley, horizontal = FALSE, xlab = "") Ste

Re: [R] Newbie: Examples on functions callling a library etc.

2008-08-28 Thread Steven McKinney
Hi Ed, Here's a simple example showing your needs: myfun <- function(n1, n2, n3) { mat1 <- matrix(rep(1), nrow = n1, ncol = 3) mat2 <- matrix(rep(2), nrow = n2, ncol = 4) mat3 <- matrix(rep(3), nrow = n3, ncol = 5) require("survival") ## make sure the package you need is loaded mypk

Re: [R] conditional with and operators

2008-08-19 Thread Steven McKinney
Did you try it with the vector '&' and operator? d<-sapply(res,function(.df){(.df$TimesVisited[.df$Tick>912 & .df$Id>0])}) (The '&&' operator is designed for use in e.g. if() clauses where you want a scalar logical answer) HTH Steve McKinney -Original Message- From: [EMAIL PROTECTED

Re: [R] Detecting duplicate values

2008-08-14 Thread Steven McKinney
> -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of [EMAIL PROTECTED] > Sent: Thursday, August 14, 2008 2:00 PM > To: r-help@r-project.org > Subject: [R] Detecting duplicate values > > This is another "how do I do it" type of question. It seems that for

Re: [R] missing TRUE/FALSE error in conditional construct

2008-08-13 Thread Steven McKinney
> -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of rcoder > Sent: Wednesday, August 13, 2008 3:17 PM > To: r-help@r-project.org > Subject: [R] missing TRUE/FALSE error in conditional construct > > > Hi everyone, > > I posted something similar to thi

Re: [R] Conditional statement used in sapply()

2008-08-13 Thread Steven McKinney
> -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Altaweel, Mark R. > Sent: Wednesday, August 13, 2008 3:03 PM > To: r-help@r-project.org > Subject: [R] Conditional statement used in sapply() > > Hi, > > I have data stored in a list that I would lik

Re: [R] ignoring zeros or converting to NA

2008-08-12 Thread Steven McKinney
The help page for is.na() is worth reading repeatedly. > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of stephen sefick > Sent: Tuesday, August 12, 2008 6:53 PM > To: Charles C. Berry > Cc: Mike Prager; [EMAIL PROTECTED] > Subject: Re: [R] ignori

Re: [R] source a script file straight from a subversion repository

2008-08-01 Thread Steven McKinney
} I can wrap this in a function where needed as Marc suggests. Thanks again for the help Best Steve McKinney > -Original Message- > From: Marc Schwartz [mailto:[EMAIL PROTECTED] > Sent: Fri 8/1/2008 5:42 PM > To: Steven McKinney > Cc: r-help@r-project.org > Subject

[R] source a script file straight from a subversion repository

2008-08-01 Thread Steven McKinney
Hi useRs I'm trying to figure out how to source an R script file straight from a subversion repository, without having to put a copy of the script into the local working directory. Has anyone done this? Something such as source(file = paste("svn://myrepo.xxx.org/opt/svn/repos/",

Re: [R] sort rows of matrix by rows of another matrix

2008-07-31 Thread Steven McKinney
I came up with the same solution as Mark Leeds. > a1roworders <- t(apply(a1, 1, order)) > a2ord <- t(sapply(seq(nrow(a1)), function(x) a2[x, a1roworders[x,]] )) > a2ord [,1] [,2] [,3] [1,] 102 101 103 [2,] 102 101 103 [3,] 103 101 102 [4,] 101 102 103 Mark's question about the o

Re: [R] 64-bit R on Mac OS X 10.4.5

2008-07-25 Thread Steven McKinney
Hello I haven't found better instructions, it's just not an easy thing to do. You might also consider joining the r-sig-mac group and reviewing threads there for additional information. Rather than try to configure, make and install with one giant command, I'd suggest breaking the task down unt

Re: [R] Calling LISP programs in R

2008-07-23 Thread Steven McKinney
Have you reviewed the old xlisp machinery that used to be in R? Check out the RXLisp library at http://www.omegahat.org/RXLisp/ and see if this will work. The PDF http://www.omegahat.org/RXLisp/examples.pdf reviews calling xlisp from R. HTH Steve McKinney -Original Message- From: [E

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