Re: [R] levelplot question

2009-05-05 Thread Dieter Menne
Antje niederlein-rstat at yahoo.de writes: thanks for your answer. The color-vector has the same length like the at-vector but the recycling cannot be the reason, because only values slightly above my threshold doe not appear blue. I cannot find a good explanation of which colors are

Re: [R] levelplot question

2009-05-04 Thread Dieter Menne
Antje niederlein-rstat at yahoo.de writes: I have a question concerning the behaviour of the colouring with levelplot. If I give the parameters at and col.regions like this: at - c(1,2,3,4,5,6) col.regions - c(blue,blue,blue,yellow,yellow,yellow) Which color would have the value 3.5?

Re: [R] Newbie R question PART2

2009-04-29 Thread Dieter Menne
Tena Sakai tsakai at gallo.ucsf.edu writes: I learned 3 new tricks. (Not bad for a newbie?) $ R --silent --no-save barebone.R $ R --quiet --no-save barebone.R $ R --slave barebone.R And don't forget R --vanilla which I like most because of the taste. Dieter

Re: [R] correlation coefficient

2009-04-29 Thread Dieter Menne
Bert Gunter gunter.berton at gene.com writes: Martin's reply provides an appropriate response, so nothing to add. But my questions dig deeper: Why do so many (presumably nonstatisticians, but ?) belong to this R^2 religion? Is it because: 1) This is what they are taught in their Stat 101

Re: [R] correlation coefficient

2009-04-29 Thread Dieter Menne
Dieter Menne dieter.menne at menne-biomed.de writes: q(paper) = 10* n(pvalues) + 5*n(R^2) + 3.5*n(Error Bars) Values above 300 qualify for immediate acceptance, and Journals like Lancet, New English and British Journal of XXX provide professional advice. I noted the and was misleading

Re: [R] Question of nlme package

2009-04-28 Thread Dieter Menne
Helen Chen 96258011 at nccu.edu.tw writes: I would like to run some panel regressions with R. Therefore I want to use fixed effect model. The focus of lme is on mixed models, but gls in nlme can handle fixed-only problems. I doubt, however that it is exactly what you want for your case. I

Re: [R] Setting R not to try to contact a CRAN repository

2009-04-28 Thread Dieter Menne
Richard Croy Richard.Croy at fonterra.com writes: I have a computer running R that cannot see the Internet. When I start RGui it asks me to select a CRAN mirror. This always fails, of course. RGui does not ask for a connection to the Internet by default, so some installation must have mucked

Re: [R] help on bwplot function

2009-04-28 Thread Dieter Menne
He, Yulei he at hcp.med.harvard.edu writes: I am using R function bwplot to plot box plots. I would like to change some parameters of the typical box plots. For example, I would like to try different types of whisker lines. I can use whiskerline=x in boxplot function but not in bwplot

Re: [R] Change font type PNG device with Lattice xyplot

2009-04-28 Thread Dieter Menne
RBlonk robbert.blonk at gmail.com writes: I have some problems with changing the default font (Arial) in a xyplot which is printed using the PNG-device. Although some things have been mentioned about this in the forum, I still couldn't figure it out. Can someone help me out?n Thanks in

Re: [R] Why there is no p-value from likelihood ratio test using anova in GAM model fitting?

2009-04-28 Thread Dieter Menne
willow1980 jianghua.liu at shef.ac.uk writes: However, when I run LRT to compare them, the test did not return F value and p-value for me. What's the reason? Analysis of Deviance Table Model 1: sum_surv15 ~ s(FLBS) + s(byear) + s(FLBS,

Re: [R] Dropping 'empty' panels from lattice

2009-04-28 Thread Dieter Menne
amvds at xs4all.nl writes: I have 8 cofactors possibly affecting one and only one variable. I make conditional histograms: -pdf(file=tst3.pdf,paper=special,width=36,height=36) -histogram(~Oversized|dat$c1*dat$c2*dat$c5*dat$c6*dat$c7*dat$c8*

Re: [R] Problem with R 2.9.0 vs. R2.8.1 with eith er survival package or predict function

2009-04-27 Thread Dieter Menne
Dimitri Liakhovitski ld7631 at gmail.com writes: Just wanted to alert everyone regarding a problem that I only experience with R2.9.0 and not with R2.8.1 when I run both using exactly the same script and the same data. Here is what I do with my data MyData, 2 predictors (V1 and V2) and my

Re: [R] what is this experimental design (mixed-effects model)?

2009-04-24 Thread Dieter Menne
J S-19 wrote: I am wondering what experimental design I am dealing with? I study the effect of daily air temperature on daily body temperature of the overwintering turtles (i.e. sleeping in soil). The model is a cosine wave with the air temperature as a covariate. Not sure if I

Re: [R] omit empty cells in crosstab?

2009-04-24 Thread Dieter Menne
sjaffe sjaffe at riskspan.com writes: I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table()

Re: [R] My surprising experience in trying out REvolution's R

2009-04-22 Thread Dieter Menne
Jason Liao JLIAO at hes.hmc.psu.edu writes: I care a lot about R's speed. So I decided to give REvolution's R (http://revolution-computing.com/) a try, which bills itself as an optimized R. Note that I used the free version. My machine is a Intel core 2 duo under Windows XP professional.

Re: [R] plot confidence intervals as shaded band

2009-04-22 Thread Dieter Menne
BARRES-DE-ALMEIDA U. u.b.almeida at durham.ac.uk writes: does anyone know how do I plot confidence intervals as a shaded band around a curve, rather than as errors bars? http://had.co.nz/ggplot2/geom_smooth.html Dieter __ R-help@r-project.org

Re: [R] automatic exploration of all possible loglinear models?

2009-04-21 Thread Dieter Menne
Christopher W. Ryan cryan at binghamton.edu writes: Is there a way to automate fitting and assessing loglinear models for several nominal variables . . . something akin to step or drop1 or add1 for linear or logistic regression? Not strictly for loglinear, but glm works with stepAIC. Make

Re: [R] bug when subtracting decimals?

2009-04-21 Thread Dieter Menne
Petr PIKAL petr.pikal at precheza.cz writes: Maybe that is because of Excel is so widespread now and gives expected results (it probably silently rounds all decimal numbers before calculation). Marc Schwartz already reminded me of that one, and it's a good point to explicitly mention in

Re: [R] broken example: lme() + multcomp() Tukey on repeated measures design

2009-04-21 Thread Dieter Menne
William Simpson william.a.simpson at gmail.com writes: I am trying to do Tukey HSD comparisons on a repeated measures expt. I found the following example on r-help and quoted approvingly elsewhere. It is broken. Can anyone please tell me how to get it to work? I am using R 2.4.1.

Re: [R] plotCI (plotrix) problem

2009-04-20 Thread Dieter Menne
Derek Ogle DOgle at northland.edu writes: I am attempting to create a plot with intervals stretched in the x-direction using plotCI() in the plotrix package. The same data provides an appropriate set of intervals when stretched in the y-direction but I only get a lower interval when

Re: [R] Sweave: Changing the background color, adding a border

2009-04-20 Thread Dieter Menne
Christophe Genolini cgenolin at u-paris10.fr writes: ... Thanks for your answer. I finally succeed. I used the listings package to define an environment that put code in a grey box. The command is \lstnewenvironment{Sinput}[1][]{ ... This is too nice code to be lost, but it suffers from

Re: [R] setting levels in contourplot()

2009-04-20 Thread Dieter Menne
Cable, Samuel B Samuel.Cable at hanscom.af.mil writes: Does the contourplot() routine have an argument analogous to the levels argument in the contour() routine? More generally, is there a way for the user to fix the contour levels in contourplot()? Thanks. Assuming lattice: cuts Dieter

Re: [R] R graph into MS Word: which format to use?

2009-04-20 Thread Dieter Menne
Uwe Ligges ligges at statistik.tu-dortmund.de writes: The journal I am publishing in requires MS Word files. What is my best option for getting a high quality image of a graph done in R into Word? JPEG? Postscript? Windows metafile, if you are under Windows anyway. But make sure that

Re: [R] How to force axis to have the same range

2009-04-20 Thread Dieter Menne
Sebastien Bihorel Sebastien.Bihorel at cognigencorp.com writes: I am trying to produce (standard and trellis) scatterplots which use the same range of the x and y axes. In addition, I would like the plots to be physically square. Is there one or more specific argument(s) to plot and xyplot

Re: [R] bug when subtracting decimals?

2009-04-20 Thread Dieter Menne
wolfgang.siewert wolfgang.siewert at gmail.com writes: There is a way around: round(0.7-0.3,1)==0.4 (TRUE) Obviously there is a problem with some combinations of decimal subtractions, that - we have the feeling - shouldt be solved. Oh no, not that one again! This was lecture two in my

Re: [R] plotCI (plotrix) problem

2009-04-19 Thread Dieter Menne
Derek Ogle DOgle at northland.edu writes: I am attempting to create a plot with intervals stretched in the x-direction using plotCI() in the plotrix package. The same data provides an appropriate set of intervals when stretched in the y-direction but I only get a lower interval when

Re: [R] Sweave and executive summaries

2009-04-16 Thread Dieter Menne
Karen_Byron at bd.com writes: I'm learning to use R/Sweave/LaTeK to write my stat reports. Is there a way to have an executive summary in the beginning while still having the analysis code embedded? Thanks to Ulrich Dietz from the German latex forum, I have an excellent

Re: [R] Function call error in cph/survest (package Design)

2009-04-15 Thread Dieter Menne
Dieter Menne wrote: I do not know if this a problem with me, my data or cph/survest in package design. The example below works with a standard data set, but not with my data, but I cannot locate the problem. Dieter Menne found out after hours, that in one case and explicit cast

Re: [R] Histogram and moving average

2009-04-14 Thread Dieter Menne
Vallat Morgan morgan.vallat at epfl.ch writes: I have a 'basic' issue and hope someone has a bit of code to solve it. I have two populations plotted as histograms on the same figure. Basically I want to add the moving average (based on hist) for both populations on my graph. I'm also

[R] Function call error in cph/survest (package Design)

2009-04-14 Thread Dieter Menne
Dear UseR, I do not know if this a problem with me, my data or cph/survest in package design. The example below works with a standard data set, but not with my data, but I cannot locate the problem. Note that I am using an older package of survival to avoid a problem with the newly renamed

Re: [R] Lattice xyplot with two y axis

2009-04-14 Thread Dieter Menne
taz9 alienz747 at gmail.com writes: I have some data which needs to be plotted with lattice. library(lattice) cars - c(0.1, 0.3, 0.6, 0.4, 0.9) trucks - c(0.2, 0.5, 0.4, 0.5, 0.1) drivers-c(121,145,167,200, 210) year-c(2005,2006,2007,2008,2009) type-c(local,local,foreign,foreign,foreign)

Re: [R] Problem with bargraph.CI in Sciplot package

2009-04-11 Thread Dieter Menne
Metconnection simontbate at hotmail.co.uk writes: Hi there, I wonder if anyone can help me. I'm trying to use bargraph.CI in the Sciplot package when there is a missing combination of the factor levels. Unfortunately the standard errors on the plot do not appear to be correct. ...

Re: [R] combine words and dataframe

2009-04-09 Thread Dieter Menne
Ravi S. Shankar ravis at ambaresearch.com writes: I am trying to get an output like this Hi Hello 1 a b # The easy way: good for logging of results, but commands print too, # depending how you run it df = data.frame(a=rep(a,3),b=rep(b,3)) sink(file=a.txt) cat(Hello\n)

Re: [R] reading an image and adding a legend

2009-04-09 Thread Dieter Menne
Simon Pickett simon.pickett at bto.org writes: But my code returns an error x-read.pnm(C:/Documents and Settings/simonp/My Documents/Simon BTO/RELU/GIS data/ten km areas in analysis.bmp) Error in pm.readmagicnumber(con) : Not a PNM format file Error message seems quite clear: bmp a

Re: [R] how to adjust titles on sub-plots in levelplot / contour plot?

2009-04-08 Thread Dieter Menne
Mike Williamson this.is.mvw at gmail.com writes: I have a (relatively long) function script that generates a levelplot. I don't want to include all of the code, so I have attached in file miniDataSet.csv an example for the data set miniDataSet that is called below. Thanks for providing a

Re: [R] extract values from summary

2009-04-07 Thread Dieter Menne
Felipe Carrillo mazatlanmexico at yahoo.com writes: # How can I extract the 'Forecasts' from the 'summary(predicted)' from the example below? .. # I would like to extract the three predicted values and # make a line plot with the 'Point Forecast' values only. # I tried str(predicted)

Re: [R] Confidence interval?

2009-04-07 Thread Dieter Menne
Thomas Seth Davis Thomas.Davis at nau.edu writes: I need help fitting/plotting a confidence interval to a frequency distribution In many medical journals, reviewers only want to see some error bars. In 90% of the cases, these are wrong or misleading, but it is hopeless to argue with

Re: [R] Need help in calculating studentized residuals/leve rage values of non-linear model [nls()]

2009-04-07 Thread Dieter Menne
rkevinburton at charter.net writes: Is the output of residuals() the studentized residuals or just the residuals? As the name says, studentizing is left as an easy student exercise. Destudentizing is more difficult and usually called professorizing. Dieter

Re: [R] change default output size when using Sweave

2009-04-07 Thread Dieter Menne
Mark Heckmann mark.heckmann at gmx.de writes: I am trying to create a graphic output in Sweave but I do not want it to be standard size. I want the whole graphic to be 80mm of height only, just like the viewport below. fig=TRUE, echo=TRUE= pushViewport(viewport(height = unit(80, mm)))

Re: [R] Need help in calculating studentized residuals/leve rage values of non-linear model [nls()]

2009-04-07 Thread Dieter Menne
Giam Xingli giam at nus.edu.sg writes: I need the studentized residuals. In linear models, they can be computed by using rstudent( ) function, but there seems to be no such function for nls( ) output. I darkly remember having read this message before. Homework still not done?

Re: [R] Need help in calculating studentized residuals/leve rage values of non-linear model [nls()]

2009-04-06 Thread Dieter Menne
Giam Xingli giam at nus.edu.sg writes: I hope I can get advice regarding the calculation of leverage values or studentized residual values of a non-linear regression model. It seems like rstudent() does not work on a nls object. residuals() should work for nls. Dieter

Re: [R] Problem with Dynamo-Package

2009-04-06 Thread Dieter Menne
Mohammad Sabr mohammad_sabr at yahoo.com writes: I am facing a problem when I am installing the dynamo-package and loading it. After I installed the package, I received the following warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~2\R\R-28~1.1/doc/html/packages.html',

Re: [R] R package: Where to put code to Run Once Only?

2009-04-06 Thread Dieter Menne
Uwe Ligges ligges at statistik.tu-dortmund.de writes: That fine, in principle, convention is to have code in zzz.R, see Writing R Extzensions. Finally I got it, zzz comes from Extzensions. In the fields I normally work in, zzz mean the LAST thing to do before going to sleep or to crash the

Re: [R] nlme weighted

2009-04-06 Thread Dieter Menne
Mollet, Fabian Fabian.Mollet at wur.nl writes: I'm fitting a non linear model (energy allocation model to individual growth data) using your nlme routine. For each individual I have thus a number of observations (age and size) to which I fit the nonlinear function, with random effects for the

Re: [R] Quick Question - MLE for Geometric Brownian Motion Process with Jumps

2009-04-05 Thread Dieter Menne
John-Paul Taylor johnpaul.taylor at ryerson.ca writes: I am tying to run a maxlik regression and keep getting the error, NA in the initial gradient My Code is below: gbmploglik-function(param){ mu-param[1] sigma-param[2] lamda-param[3] nu-param[4]

Re: [R] Multiple use of par()

2009-04-04 Thread Dieter Menne
Hesen Peng-2 wrote: I created a plot function which used par(mfcol=c(2,1)) so that I could have two plots together using just one command. For exampe: plot.foo - function(data){ par(mfcol=c(2,1)) hist(data) plot(data) } Later I wanted to show 4 of these foo objects in the

Re: [R] Planned contrast on repeated measures

2009-04-04 Thread Dieter Menne
Bugzilla from rmh3...@gmail.com wrote: I have an anova model that looks like this: aov(log(Y)~X+Error(Participant/X)) Is there a way to do a planned contrast on a repeated measures model... something with an error term? I get an error when I do this: contrasts(X)=cbind(-3,-1,1,3)

Re: [R] Multiple use of par()

2009-04-04 Thread Dieter Menne
Hesen Peng wrote: Thanks a lot for reminding me of this. The original code is too complicated and stems from several other objects. So I guess this simplified code may help: a - rnorm(100) class(a) - foo plot.foo - function(data){ ## opar-par() par(mfcol=c(1,2)) hist(data)

Re: [R] extract tables as data.frames from HTML source

2009-04-03 Thread Dieter Menne
Yihui Xie wrote: I wonder whether there is any convenient function (or package) to extract tables from a HTML page? e.g. from http://www.google.com/finance/historical?q=SHE:002251 Try a search on R (I prefer markmail search) http://r-project.markmail.org/search/?q=extract%20html

Re: [R] how to sort and plot data?

2009-04-03 Thread Dieter Menne
Hem wrote: user_id website time 20google0930 21yahoo0935 20facebook1000 25facebook1015 61google0940 ... My problem is how to sort the data? So that, I can get information about one

Re: [R] finding best fitting model

2009-04-03 Thread Dieter Menne
Benedikt Niesterok wrote: Is there a function in r to find the best fitting model for a set of data? I would like to know if my data are related exponentially,linearly or if there is a logarithmic correlation between my x and y values. There is no one-stop method to do this. I would

Re: [R] Fit unequal variance model in R

2009-04-03 Thread Dieter Menne
Feng Jingyu wrote: I used gls and it still does not provide me different estimates of variance for each treatment group. Did I do anything wrong? lm3-gls(GSI~treatment,data=z,weights=varIdent(form=~treatment),method=ML) try weights = varIdent(form~1|treatment) See the example in

Re: [R] Fit unequal variance model in R

2009-04-03 Thread Dieter Menne
Feng Jingyu wrote: Thanks a lot. The problem is solved. It took me a while to understand the output from the R. With little calculation, I am able to match results from R to SAS. To conserve you sanity, don't try it. They will be different. Dieter -- View this message in context:

Re: [R] Fit unequal variance model in R

2009-04-03 Thread Dieter Menne
Feng Jingyu wrote: Hi For my purpose, I need to match variance estimates for each group from R and SAS. They do match now. Consider yourself a lucky man! Dieter -- View this message in context: http://www.nabble.com/Fit-unequal-variance-model-in-R-tp22829549p22874048.html Sent from

Re: [R] Tick label orientation

2009-04-02 Thread Dieter Menne
Murray Jorgensen wrote: I had hoped that plot(c(0,24),c(0,-6),xlab=Time,ylab=Day, type=n, main=This Week,axes=FALSE) axis(2,at=0:(-6), labels = c(Sun,Mon,Tues,Wed,Thurs,Fri,Sat),hadj=TRUE) axis(1,at=seq(0,24,4)) would give me horizontal tick labels. It doesn't. What

Re: [R] paste to collapse vector to string

2009-04-02 Thread Dieter Menne
Xiao-Jun Ma-2 wrote: I'm trying to collapse a character vector to strings, but I am getting unexpected behaviors in list context: A - a B - c(b,c) xx - list(A=A, B=B) lapply(xx, paste, collaplse=.) Typing error in collapLse Dieter -- View this message in context:

Re: [R] all subsets for glm

2009-04-02 Thread Dieter Menne
Harald von Waldow wrote: For the purpose of model selection I am looking for a way to exhaustively (and efficiently) search for best subsets of predictor variables for a logistic regression model. Of all the dangerous ways of doing this and getting confusing results, gl1ce in lasso2

Re: [R] Variable Wildcard Value

2009-04-01 Thread Dieter Menne
Francis Smart fsmart at gmail.com writes: Is there a wildcard value for vector values in r? For instance: M - *wildcard (M==1) TRUE (M==peanut butter) TRUE is.na(M) FALSE If grep on a vector does not help, maybe the following comes closer? Finding all variables

Re: [R] How can I use R through command line?

2009-04-01 Thread Dieter Menne
minben minbenh at gmail.com writes: Suppose I have written a R program and saved it in test.R . How can I call the program in the command line? Assuming Windows (might work under linux) rterm --vanilla --no-save myrfile.r Dieter __

Re: [R] Generating EPS figures automatically (like Sweave)

2009-04-01 Thread Dieter Menne
eariasca eariasca at math.ucsd.edu writes: Is there a way to generate EPS figures automatically out of a chunk of code? Basically, I would like to do something like Sweave does (I just find it a little cumbersome to create a .Rnw file and then keep track of the figure numbering). I

[R] How to prevent inclusion of intercept in lme with interaction

2009-04-01 Thread Dieter Menne
? Some bracket missing? I tried a few variants. Dieter Menne # library(nlme) library(lattice) # Generated data set.seed(4711) subject = as.factor(letters[1:5]) varslope = rnorm(length(subject),0,0.02) cslope = c (0.1,0.15) grd = expand.grid(t=seq(5,15,by=5

Re: [R] How to prevent inclusion of intercept in lme with interaction

2009-04-01 Thread Dieter Menne
ONKELINX, Thierry Thierry.ONKELINX at inbo.be writes: With t*treat the model allows for a different slope AND a different intercept for each treatment. If you only want different slopes and all intercepts equal to 0, then t:treat - 1 or t + t:treat - 1 is the model you are looking for.

Re: [R] Fit unequal variance model in R

2009-04-01 Thread Dieter Menne
Feng, Jingyu wrote: I'am trying to develop some code if R, which would correspond to what I did in SAS. The data look like: TreatmentReplicategroup1 GSI .. The SAS code is: proc mixed data=data_name order=data method=ml; *scoring=10; classes group1; model

Re: [R] Help with mixed-effects model with temporal pseudoreplication!

2009-04-01 Thread Dieter Menne
Bugzilla from rmh3...@gmail.com wrote: Responses: CompletionTIme VisitedTargets Fixed-factors: Targets (4-levels): 4, 9, 14, 19 Entropy (3-levels): Low, Medium, High Random-factors: Participants: 31 total participants Replicates: 5 (this could also be viewed as a time factor I

Re: [R] Latex symbols in R (\perp and \parallel)

2009-04-01 Thread Dieter Menne
Lorenzo Isella wrote: I am sure this is a one-liner, but I cannot find the R command to generate the LaTex symbols \perp and \parallel. As often, the most helpful how-to resource is by Prof. Brian Ripley http://markmail.org/thread/kauzftprydrhqq5m if you manage to get around the many

Re: [R] To save Trellis Plots on A3 size paper (Portrait and Landscape)

2009-03-31 Thread Dieter Menne
Debabrata Midya Debabrata.Midya at commerce.nsw.gov.au writes: I like to save Trellis Plots on A3 size paper (Portrait and Landscape). Since a3 is not among the paper choices, you could give the width and height in inches (b...) explicitly. Dieter

Re: [R] To save Trellis Plots on A3 size paper (Portrait and Landscape)

2009-03-31 Thread Dieter Menne
Debabrata Midya wrote: I like to save Trellis Plots on A3 size paper (Portrait and Landscape). Since a3 is not among the paper choices, you could give the width and height in inches (b...) explicitly. Dieter -- View this message in context:

Re: [R] Convert date to integer

2009-03-31 Thread Dieter Menne
thoeb t.hoebinger at gmail.com writes: Hello, I have a dataframe containing dates, times and other parameters. The times have the format h:m, e.g. 13:00 or 5:30, R classes them as factors. Probably you have read in the data from a file with read.table; check stringsAsFactors in the docs to

Re: [R] R Language Bloggers and Web Sites Owners

2009-03-31 Thread Dieter Menne
Ajay ohri ohri2007 at gmail.com writes: Apologies in advance for non bloggers for the spam on the slightly off topic. This is an invitation to all R language bloggers to help spread the world at a forum where leading authors come together. Since the author has a notorious history of

Re: [R] naming vectors/ matrices in R

2009-03-31 Thread Dieter Menne
emj83 stp08emj at shef.ac.uk writes: I would like to create a series of vectors in a loop and name them with letters. I know the command letters gives me the 26 letters of the alphabet. For example, I have a dataframe, called A, with 6 columns. B-length(A) C-letters(1:B) [1] a b

Re: [R] Nonparametric analysis of repeated measurements dat a with sm library

2009-03-31 Thread Dieter Menne
Alphonse Monkamg amonkamg at yahoo.fr writes: Does anybody know how to get more evaluation points in performing Nonparametric analysis of repeated measurements data with sm library. Try ... paramter ngrid: ngrid the number of divisions of the above interval to be considered. Default:

Re: [R] 3d cloud plot with point size reflecting variable value

2009-03-31 Thread Dieter Menne
R User R User ruser2008 at googlemail.com writes: I'm using the cloud function to plot the iris data as per the document: http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf I'd like to change the point size to reflect a fourth variable, as done here

Re: [R] simple example for linear mixed effects model

2009-03-29 Thread Dieter Menne
Edna Bell wrote: Could someone point me to a small example of a linear mixed effects model, please? Check R_HOME/library/nlme/scripts/ch01.R But better get the book by Pinheiro/Bates (PB) Edna Bell wrote: Ideally, this example would only have a few data points so I could calculate

Re: [R] re form data for aov()?

2009-03-29 Thread Dieter Menne
Dan Kelley kelley.dan at gmail.com writes: I have data in a file named hands.dat, which is given at the end of this question. (It's from a stats textbook example on anova). I'd like to do an aov on this, which I guess would be d - read.table(~/hands.dat, header=TRUE)

Re: [R] R: Fortran-90 and R

2009-03-26 Thread Dieter Menne
mauede at alice.it writes: I do hope the chapte about Interfacing R and Fortran is sufficient. I have a heavy load of work from two projects and no previous experience in either cases (analysis packages, algorithms, and so on ...). I am a postdoc. In that case, think hard if you are not

Re: [R] Reading in files with variable parts to names

2009-03-26 Thread Dieter Menne
Steve Murray smurray444 at hotmail.com writes: I'm trying to read in a whole directory of files which have two variable parts to the file name: year and month. E.g. comp198604.asc represents April of 1986 - 'comp' is fixed in each case. Years range between 1986 to 1995 and months are

Re: [R] how to identify a symbol is defined from which package

2009-03-25 Thread Dieter Menne
hong shen hshen_1998 at yahoo.com writes: I encountered a situation that a data frame is defined by two packages. Both of them are loaded by library(). 2. If I want to reference the data frame from package A insted of B, how can I do it? Either change the loading sequence of library(). Or,

Re: [R] need help with ordering of plots

2009-03-25 Thread Dieter Menne
Cable, Samuely at hanscom.af.mil I want to do a series of contour plots, 4 in all. The data is coming from a data frame named nd.frame, which has elements xdf, ydf, zdf, and pndt. I am treating pndt as a factor, and it has four levels. I make a call to the lattice graphics routine

Re: [R] Workspace Image

2009-03-24 Thread Dieter Menne
Yikan Liu u4297812 at anu.edu.au writes: I'm wondering how to delete previously saved workspace in R. file.remove(mywork.rdata) Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Is this sample size big enough to test for statisti cal significance?

2009-03-21 Thread Dieter Menne
J S yulya258 at hotmail.com writes: Is this sample size large enough to study differences between two groups of the populations? Q1: do the body temperatures differ between the two groups of the overwintering turtles juveniles and adults? One group (adults) has 6

Re: [R] Howto Supress Extra Blank Page in gridBase

2009-03-20 Thread Dieter Menne
Gundala Viswanath gundalav at gmail.com writes: I have a simple plot using gridBase like this. The problem occurs whenever I execute this code there is always a blank page created before the actual plot. How can we disable that blank page? __ BEGIN__ library(grid) library(gridBase)

Re: [R] Simple Plot with Grid's Viewport

2009-03-19 Thread Dieter Menne
Gundala Viswanath gundalav at gmail.com writes: I have the following code that try to plot simple sinus curve into 2x2 grid in 1 page. But this code of mine create 4 plots in 1 page each. What's wrong with my approach? ... library(lattice) library(grid) test.plot - function(x,y) {

Re: [R] How to keep attributes when dropping factor levels?

2009-03-19 Thread Dieter Menne
Heinz Tuechler tuechler at gmx.at writes: to drop unused factor levels two ways are outlined in R-help. In both cases a label attribute is lost. Brian Ripley has posted this http://markmail.org/message/pl2odydwzv64v3u3 Dieter __

Re: [R] Extreme AIC or BIC values in glm(), logistic regression

2009-03-18 Thread Dieter Menne
Maggie Wang haitian at ust.hk writes: I use glm() to do logistic regression and use stepAIC() to do stepwise model selection. The common AIC value comes out is about 100, a good fit is as low as around 70. But for some model, the AIC went to extreme values like 1000. When I check the

Re: [R] Cumulative Plot with Given X-Axis

2009-03-18 Thread Dieter Menne
Gundala Viswanath gundalav at gmail.com writes: ...In which I want to plot accumulative value of dat1 with respect to x-axis. Also plot it together with dat2. #x-axis dat1 dat2 -10 0.0140149 0.0140146 -9 0.00890835 0.00891768 -8 0.00672276

[R] Draft mode for confint in multcomp

2009-03-18 Thread Dieter Menne
around this, but it would be easier if I could request some draft mode with less accurate results and set this to final in the later revisions. I tried to set type=bonferroni, but this parameter seems not to be used. Any idea? Dieter Menne __ R-help@r

Re: [R] Help_Unable to run glmer

2009-03-16 Thread Dieter Menne
David Winsemius dwinsemius at comcast.net writes: Maybe there was a run on the British bit and the bit banks are a wee short? Runs are by definition in the order of TeraBits. Bits are peanuts and freely available. D __ R-help@r-project.org mailing

Re: [R] Tukey, planned contrasts or t-test without ANOV A? What is correct?

2009-03-15 Thread Dieter Menne
J S yulya258 at hotmail.com writes: I compare mean monthly body temperature between two age classes of turtles overwintering underground. lm(body_tem ~ Month*Year*Age_Class) TukeyHSD(aov(body_tem ~ Month*Year*Age_Class, a)) The Tukey HSD as well as the planned contrasts method showed

Re: [R] Mixed model help!

2009-03-14 Thread Dieter Menne
Martín Quiroga mquiroga at ssdfe.com.ar writes: The response variable has a binomial distribution (males or females). I’ve been reading for a while and found the MASS and lmer packages that will allow me to do such a thing with my data. I found the script I should write “lmer(y~fixed+(time |

Re: [R] (RODBC) defining variable as text

2009-03-14 Thread Dieter Menne
baked Toast baked.toast at gmail.com writes: Now the problem is that when I want to import this data to R with the RODBC package (the used code is displayed on the bottom of this message) it converts this marker to a number and cuts of the starting zero's. Use parameter as.is in odbcQuery,

Re: [R] changing function argument

2009-03-13 Thread Dieter Menne
Thomas Mang thomas.mang at fiwi.at writes: I wonder if the following is possible in R: Suppose a function takes an argument, and wants to modify this argument so that the change is visible _at the call side_. It would be what is for example known as pass-by-reference-to-non-const in C++.

Re: [R] Windows binary version of DPpackage

2009-03-13 Thread Dieter Menne
Debabrata Midya Debabrata.Midya at commerce.nsw.gov.au writes: This has reference to the package “DPpackage”. The binary version is available on Mac OS, but I am using Windows XP. May I request you to assist me in the followings: How can I prepare Windows binary of DPpackage from

Re: [R] Windows binary version of DPpackage

2009-03-13 Thread Dieter Menne
Prof Brian Ripley ripley at stats.ox.ac.uk writes: The maintainer has been informed (probably many times via the automated notification system). With 1700 packages, the volunteers have no time to spend correcting packages for non-responsive maintainers (we do quite a lot for responsive

Re: [R] How to combine xtable and minipage with Sweave ?

2009-03-13 Thread Dieter Menne
Ptit_Bleu ptit_bleu at yahoo.fr writes: I'm trying to put a dynamic table and a dynamic graph side by side in a pdf document using Sweave. The data.frame used to generate the table is called rg (rg.txt): Date; Code; Data1; Data2 2009-03-10;1;1958;147 2009-03-10;2;302;144 ... The Sweave

Re: [R] How to combine xtable and minipage with Sweave ?

2009-03-13 Thread Dieter Menne
Ptit_Bleu ptit_bleu at yahoo.fr writes: Concerning the point 3, I'm a bit lost. Is it a problem of place to put the table and the graph side by side (my english is quite as low as my skills in Latex) ? I tried with \begin{minipage}{0.45\textwidth} instead of 0.7 and I put //tiny but no

Re: [R] Windows binary version of DPpackage

2009-03-13 Thread Dieter Menne
Debabrata Midya Debabrata.Midya at commerce.nsw.gov.au writes: 2. Is there any possibility to have a copy of Windows binary of DPpackage in the near future in the site http://www.cran.r-project.org/? I contacted Alejandro (now Conception/Chile), and he will upload a new version this

Re: [R] malformed plot symbols in lattice pdf

2009-03-13 Thread Dieter Menne
Mark Wilkinson wilkinsonmr at gmail.com writes: I'm using panel.polygon inside a custom panel function to generate filled polygons for an xyplot. Everything is as expected until I specify a value 1 for alpha to fill with a semi-transparent color and output to pdf. The plot symbols appear

Re: [R] Ggplot2: saving a grid with multiple plots

2009-03-12 Thread Dieter Menne
ONKELINX, Thierry Thierry.ONKELINX at inbo.be writes: I have managed to create a figure on the screen with multiple plots in it. Something like the example below. When I save that with ggsave(), only the last plot gets saved (pPath in the example) instead of the entire figure. Any suggestions

Re: [R] nlme: problem with fitting logistic function

2009-03-10 Thread Dieter Menne
Douglas Bates bates at stat.wisc.edu writes: 3) Use lmer in lme4. Your mileage may vary, I could not find a speedup   for my problems, but larger problem might give one. Did you mean nlmer in the lme4 package? If so, it may be worthwhile trying the development branch but that is not

Re: [R] nlme: problem with fitting logistic function

2009-03-10 Thread Dieter Menne
Douglas Bates bates at stat.wisc.edu writes: 3) Use lmer in lme4. Your mileage may vary, I could not find a speedup   for my problems, but larger problem might give one. Did you mean nlmer in the lme4 package? If so, it may be worthwhile trying the development branch but that is not

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