Re: [R] Cannot update.packages (error message)

Richardson, Patrick wrote: When trying to update (various) packages using update.packages() I get the following error message for various packages package 'fBasics' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle

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

willow1980 wrote: Hi, Dieter, I did add (test=F) in my script, but it does not matter. The following is my whole script. # modelsurs_fer13-gam(sum_surv15~s(FLBS)+SES+s(byear)+s(FLBS,byear),family=quasipoisson)

[R] combining distributions

Hi all, I am trying to generate a series of random numbers. What I want to do is create n random Poisson numbers (easily done with the rpois function) and then use those generated numbers as the number of genenerated from another distribution (in this case, a function for the bounded Pareto

Re: [R] R-2.9.0 malformed bundle DESCRIPTION file, no Contains field

Why do you post more than once? I have answered your former (almost) identical message minutes ago. Best, Uwe Ligges Richardson, Patrick wrote: When trying to update (various) packages using update.packages() I get the following error message for various packages package 'fBasics'

Re: [R] help working with date values

Gabor, These options will work just fine. Thank you Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147

[R] Odp: help working with date values

Hi r-help-boun...@r-project.org napsal dne 28.04.2009 15:04:01: My data contains a variable observation_date and it contains values as: 1985-09-02 1985-09-15 1985-07-31 1985-09-02 I need to process data annually rather than daily, therefore I'm trying to 1) either extract the

Re: [R] effects package --- add abline to plot

On Apr 28, 2009, at 12:00 AM, Prew, Paul wrote: Hello, I am not having success in a simple task. Using the effects package, I would like to add reference lines at probability values of 0.1 – 0.6 on a plot of the effects. I have concerns that you are considering these probabilities. They

[R] image3d in misc3d

Hi, I'm trying to make sense of the image3d plots in misc3d. Unfortunately I can't find any authors on the help pages of the function to e-mail directly. In the following toy example, I'm puzzled as to why (1) the positions of the image plot on the axes include negative values when I think

Re: [R] duplicate 'row.names' are not allowed

Hi r-help-boun...@r-project.org napsal dne 28.04.2009 15:09:55: Thanks, I can't use the name as a variable because I need to create a matrix which does include only numerical values! If you are 100% sure about dimensions let your numeric matrix be without row names and put names into

Re: [R] help with random forest package

That was very helpful. Using the predict.all option I got exactly what I need. Is there any way of visualizing the predictions? using MDS plot is the best way? Also, I want to run random Forest using three different schemes (e.g. training set 70% and test se 30%, cross validation with k=10, etc).

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

How would I paste factors c1...c10 to one grouping factor? Can you give an example? Thanks much! Alex 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)

Re: [R] Cannot update.packages (error message)

Hi Uwe, I was able to reinstall every package you suggested except for gregmisc (see below) package 'gregmisc' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle DESCRIPTION file, no Contains field I've again tried

Re: [R] image3d in misc3d

On 4/28/2009 10:06 AM, Colin Beale wrote: Hi, I'm trying to make sense of the image3d plots in misc3d. Unfortunately I can't find any authors on the help pages of the function to e-mail directly. In the following toy example, I'm puzzled as to why (1) the positions of the image plot on the axes

[R] latticeExtra: useOuterStrips and axis.line$lwd

Hi, I'm working on some lattice wireframe figures that have two conditioning factors, and I want the strips labelled on the top and left of the entire plot, rather than above each individual panel. useOuterStrips() does this, but it draws internal axis lines, even after I explicitly set axis.line

Re: [R] combining distributions

Rachel Taylor-2 wrote: Hi all, I am trying to generate a series of random numbers. What I want to do is create n random Poisson numbers (easily done with the rpois function) and then use those generated numbers as the number of genenerated from another distribution (in this case, a

Re: [R] question about adaboost.

Cecilia Lezama wrote: Thanks for your quickly answer. I feel embarrassed but I didn't understand it. 1 - diag(table) / sum(table)Which diagonal? Both of them? Could you explain it to me with a practical example? Whoops, this meant to be 1 - sum(diag(table)) / sum(table) i.e. 1 -

[R] Problem with Random Forest predict

I am trying to run a partialPlot with Random Forest (as I have done many times before). First I run my forest... Cell is a 6 level factor that is the dependent variable - all other variables are predictors, most of these are factors as well.

[R] problems understanding error term in aov()

Hi all, I'm having some trouble in understanding how to ste the Error() term in the aov() function when fitting a hierarchical ANOVA. I have data concerning the expression of 2 miRNAs in 3 different cell lines, with 2 different extraction methods. The data is organized as follows : Line

Re: [R] Cannot update.packages (error message)

Richardson, Patrick wrote: Hi Uwe, I was able to reinstall every package you suggested except for gregmisc (see below) package 'gregmisc' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle DESCRIPTION file, no

Re: [R] save history only option under Linux

I put savehistory() in my profile file, and it works nicely. Thank you very much, jdeisenberg. alex jdeisenberg wrote: alex lee wrote: Is there any options that I can save history only? The only save option is --save, which saves both data and history. However I want to restore the

[R] estimate abnormality

I have identified the outlier of the time series duration of conversation in minutes of the telephone traffic to an operator, through residuals analysis.I must provide an estimate of the abnormality and I thought to consider the value of the residual and multiply by the coefficient of variation

Re: [R] question about adaboost.

Thanks for your quickly answer. I feel embarrassed but I didn't understand it. 1 - diag(table) / sum(table)Which diagonal? Both of them? Could you explain it to me with a practical example? CONFUSION MATRIX Observed Class Predicted Class A

[R] plot.lm cex.caption

Hello dear R users, My objective is to change the size of this graphic : plot(lm(a~b), 4) (Cook's distance) I have found the help on the internet saying to change the size of a title on a graphic plot(lm(a ~ b), 4), I should use the graphic parameter cex.caption

Re: [R] Random Sample with Unique function

Thanks Uwe, Your strata suggestion works, thank you, but it has created a dataset of random rows but without the data, other columns involved. You see I would further like to use this random sample for a DFA (lda) analysis. Can you suggest how I would use the strata function to sample a

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

Hi, Dieter, I did add (test=F) in my script, but it does not matter. The following is my whole script. # modelsurs_fer13-gam(sum_surv15~s(FLBS)+SES+s(byear)+s(FLBS,byear),family=quasipoisson)

[R] How to read the summary

How can I from the summary function, decide which glm (fit1, fit2 or fit3) fits to data best? I don't know what to look after, so I would please explain the important output. fit1 - glm(Y~X, family=gaussian(link=identity)) fit2 - glm(Y~X, family=gaussian(link=log)) fit3 - glm(Y~X,

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

Hi, Simon, I am using mgcv:gam and the version number is mgcv_1.5-2. I also exchanged the order of two models in anova, but this also did not help. From the differences in DF(0.77246) and deviance (-0.02), these two models seem to be not significantly different. Isn't it? Thank you anyway!

Re: [R] correlation coefficient

BN == Benedikt Niesterok kleinerhaifi...@gmx.net on Tue, 28 Apr 2009 15:33:02 +0200 writes: BN Hello, BN I would like to get a correlation coefficient (R-squared) for my model. {{ arrrgh... how many people think they need an R^2 when they fit a model ?? }} BN I

Re: [R] effects package --- add abline to plot

Dear David, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: April-28-09 10:12 AM To: Prew, Paul Cc: r-help@r-project.org Subject: Re: [R] effects package --- add abline to plot On Apr 28, 2009, at

[R] tiff graphics

My Linux installation of R is x86_64-redhat-linux-gnu-library When I tried to write a tiff file the system responded that tiff was not supported with this version. Which version of R on a linux environment does support tiff graphic files ? Thank you Steve Steve Friedman Ph. D. Spatial

Re: [R] Problem with survival

It is likely a problem with survival, since 2.9 merged in a large number of changes that had occured in my source tree that had not propogated to the R tree my test suite doesn't have a test for this particular case (2 factors) and - Murphy's law

Re: [R] How to read the summary

Hi! mathallan wrote: How can I from the summary function, decide which glm (fit1, fit2 or fit3) fits to data best? I don't know what to look after, so I would please explain the important output. Start with the AIC value (Akaike Information Criterion). The model having the lowest AIC is the

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

The issue isn't really about which order you supply the models to `anova'. The problem is that there is no meaningful test to perform with these two models, because the `larger' model has actually been estimated as having a *larger* deviance than the `smaller' model, so there is never going

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

On 4/28/09, am...@xs4all.nl am...@xs4all.nl wrote: How would I paste factors c1...c10 to one grouping factor? Can you give an example? In this case interaction would be conceptually more appropriate histogram(~Oversized | with(dat, interaction(c1, c2, c5, c6, c7, c8, c9, c10)),

Re: [R] duplicate 'row.names' are not allowed

Clearly, you can specify the 'extra' row names as you had already specified the duplicate names: x1 - rnorm(10,5,1) x2 - runif(10,0,1) nam1 - paste(A,1:4,sep=.) nam2 - paste(A,6:9,sep=.) nam - c(nam1,A.4a,nam2,A.9a) mydata - data.frame(x1,x2) rownames(mydata) - nam But you should obviously pay

[R] package geoR question

How do you create a geodata object with borders information (such as in the built-in data set, ca20)? I've looked at the documentation for as.geodata but do not see instructions on how to do this. Thank you. -- Laura *** Laura Chihara Professor of

Re: [R] duplicate 'row.names' are not allowed

Apologies; my earlier reply preceded this extra info. If you are reading a large file with duplicate row names, try reading it in as is, then simply converting the numeric parts to a matrix. For example, if you had the same kind of data frame as before x1 - rnorm(11,5,1) x2 - runif(11,0,1) nam -

[R] Generalized linear models (GLM)

Hi I got a dataset loss max.loss grp 1 10 50 2 2 15 33 1 3 18 49 2 4 33 38 1 5 8 50 3 6 19 29 1 7 22 51 4 8 50 50

[R] problems with clipboard

Hi I'm a mac user. I have problems loading data from mac excel in R. I'm using these script: library(utils) data2 - read.table(file(clipboard), header =T, sep =\t) but this is the message that I have from R_ Error in open.connection(file, r) : cannot open the connection In addition:

Re: [R] correlation coefficient

Dear Colleagues: 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 courses by statisticians? 2) ... by

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

OK, here we go. I am trying to attach a data file test.data.txt) Below is the script: sample.data-read.delim(file=test.data.txt) (dim(sample.data)) (names(sample.data)) names(sample.data)-c(time,ID,Choice,V1,V2,Set,id) sample.data$V1-as.factor(sample.data$V1)

Re: [R] re fit with binomial model (lme4)

Thanks for sending that, Ben. I have incorporated a slightly modified version, with attribution, in the lme4 sources. On Tue, Apr 28, 2009 at 8:03 AM, Ben Bolker bol...@ufl.edu wrote: I think the following works, but use with caution -- I just wrote it last night. setMethod(refit,

Re: [R] problems with clipboard

Jamie, Try it as: data2 - read.table(pipe('pbpaste'), header = T) I have a read.clipboard() function defined in ~/.Rprofile: read.clipboard - function(){read.table(pipe('pbpaste'), header = T)} Also see the Clipboard section of ?pipe. Cheers, Kevin

Re: [R] Problem with survival

Glad we know where the problem lies now. Dimitri On Tue, Apr 28, 2009 at 11:55 AM, Terry Therneau thern...@mayo.edu wrote:  It is likely a problem with survival, since        2.9 merged in a large number of changes that had occured in my source tree that had not propogated to the R tree      

[R] [macosx] improving quartz Aqua Tk behaviour outside of RGui

Hello, On Mac OS X, certain Aqua/Quartz UI functionality requires an application to be launched from within an app bundle, or (alternatively) requires a Carbon application with a resource fork. Playing with the wxWidgets distribution, I discovered that it is quite easy and transparent to make

Re: [R] problems with clipboard

On Tue, 28 Apr 2009, Jamie.lannister wrote: Hi I'm a mac user. I have problems loading data from mac excel in R. I'm using these script: library(utils) data2 - read.table(file(clipboard), header =T, sep =\t) but this is the message that I have from R_ Error in open.connection(file,

Re: [R] FW: Install of R 2.9.0

Thanks, Uwe. It seems that the filesystem did not have enough inodes. Mark Lyman -Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Tuesday, April 28, 2009 5:58 AM To: Lyman, Mark Cc: r-help@r-project.org Subject: Re: [R] FW: Install of R 2.9.0 Lyman,

Re: [R] Generalized linear models (GLM)

I think you are off-track because max.loss does not sound like a proper Y variable. Because max.loss is an amount that is known, in the insurance applications I have seen it would have been modeled within an offset term. Many of the examples have used number of ships or buildings or the

Re: [R] effects package --- add abline to plot

Dear John and David, thank you for your help. I apologize for not defining the analysis as an ordinal regression, or including a structure --- could have taken some of the guesswork out for you. John --- for the ticks, I would still like to make this work for future analyses, but still not

Re: [R] Generalized linear models (GLM)

Actually both max.loss and loss are known values (in dollars). I'm very much doubt, what to choose. glm(max.loss~loss,family=gaussian(link=identity) or glm(formula = sum ~ claims * as.factor(grp), family = gaussian(link = identity)) or glm(loss~max.loss,family=gaussian(link=identity) we

[R] Producing customized tickmarks when producing a graph using curve

Hello! I am using function curve to create a line graph. I was wondering, if it's possible to turn off the default tick marks and introduce those tick marks in specific locations. For example, currently in my X axis tick marks are (automatically) at 10, 11, 12, 13 but I want them to be in 5

Re: [R] Generalized linear models (GLM)

Although both are known now, there is a time element involved in which one, max.loss was fixed at the time of underwriting and loss was unknown at that time. This *is* an insurance question is it not? Wouldn't the question be: Can one use the group variable to estimate the proportion of

Re: [R] Producing customized tickmarks when producing a graph using curve

It is possible in any of the flavors of graphics available in R. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- David On Apr 28, 2009, at 2:56 PM, Dimitri Liakhovitski wrote: Hello! I am

Re: [R] effects package --- add abline to plot

Dear Paul, -Original Message- From: Prew, Paul [mailto:paul.p...@ecolab.com] Sent: April-28-09 2:19 PM To: John Fox; David Winsemius Cc: r-help@r-project.org Subject: RE: [R] effects package --- add abline to plot Dear John and David, thank you for your help. I apologize for

Re: [R] Producing customized tickmarks when producing a graph using curve

Dimitri Liakhovitski schrieb: I was wondering, if it's possible to turn off the default tick marks and introduce those tick marks in specific locations. use search. rseek for example. use help. ?axis for example leads you to an example how to do so... (works also for curve) and please try to

[R] Understanding padding in lattice

Dear R-users, I am trying to understand what the different padding arguments in trellis.par.set are exactly controlling the space around lattice plots. I have used the following code as a basis for testing but it did not really help me to visualize how the value of each argument changes the

Re: [R] Build Windows binary

Many thanks. nobody else of the 20 authors who submitted packages sent a notice. I guess that puts me in the top 5th percentile of people unafraid of asking stupid questions. Matthew Fero On Apr 28, 2009, at 4:10 AM, Uwe Ligges wrote: Duncan Murdoch wrote: On 27/04/2009 8:35 PM,

[R] Updating to 2.9 - ' no slot call in the result'

I have updated to R version 2.9. I also have R version 2.7 running on the same box. I get the following error in R 2.9; the command goes through without any errors in R 2.7. Would appreciate any feedback. Raghu _

[R] send command to other program

Hello, does anybody know about how to send a command or a text line from R to another program? I have written a script in which several calculations are made and outputfiles (csv) are generated. Afterwards I open another program (Fortran) via shell.exec. This program asks for the names if the

[R] Newbie R question

Hi, I am a newbie with R. My environment is linux and I have a file. I call it barebone.R, which has one line: cat ('Hello World!\n') I execute this file as: R --no-save barebone.R And it does what I expect. What I get is 20+/- lines of text, one of which is 'Hello World!'. How would I

Re: [R] Producing customized tickmarks when producing a graph using curve

Dear Phil, thank you so much for refering me to the axis function. It helped me find the solution! Come on, guys, I was just asking for a pointer, not for a solution. Dimitri On Tue, Apr 28, 2009 at 3:37 PM, Phil Spector spec...@stat.berkeley.edu wrote: Dimitri -   First, suppress the xaxis

[R] colored PCA biplot

Hi- I'm trying to make my PCA (princomp) colored. In my csv excel sheet, I have the first column numbered according to the groupings I want to assign to the PCA. I've played around with trying to set this first column as the color vector, but haven't had any luck. Any suggestions? Thanks, Hillary

Re: [R] Producing customized tickmarks when producing a graph usingcurve

Come on, Dmitri, you could have found it yourself with help.search(tickmarks) or help.search(axis) ;-) Bert Gunter Nonclinical Biostatistics 467-7374 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dimitri Liakhovitski

Re: [R] Newbie R question

Tena Sakai wrote: Hi, I am a newbie with R. My environment is linux and I have a file. I call it barebone.R, which has one line: cat ('Hello World!\n') I execute this file as: R --no-save barebone.R And it does what I expect. What I get is 20+/- lines of text, one of which is

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

Hi Here's one way ... xyplot(y~x,data=a, ylab=y-axis, xlab=x-axis, ylim=c(0,5), par.settings=list(axis.line=list(lwd=1.5), strip.border=list(lwd=2), # This is the important bit grid.pars=list(fontfamily=mono)),

Re: [R] Finding rows common to two datasets

I think merge() can do what's wanted, but you do have to be careful that values match exactly. Here's an example where two data frames print the same in a row for columns 'a' and 'b', but are not exactly same. merge() returns zero rows. This problem can be fixed in this case by rounding,

Re: [R] Two 3D cones in one graph

On Thu, Apr 23, 2009 at 4:22 AM, Jaakko Nevalainen jaakko.nevalai...@uta.fi wrote: Dear R-users: The following code produces two cones in two panels. What I would like to have is to have them in one, and to meet in the origin. Does anyone have any good ideas how to do this? wireframe gets

Re: [R] generate individual panel keys/legends in lattice barchart

On Thu, Apr 23, 2009 at 1:23 AM, Rebecca Fisher rebecca_fishe...@yahoo.com.au wrote: Dear R users. I am wondering what is the simplest way is to generate individual keys for each panel in a lattice barchart? The help pages said: To use more than one legend, or to have arbitrary legends not

Re: [R] Newbie R question

On 28-Apr-09 20:42:45, Tena Sakai wrote: Hi, I am a newbie with R. My environment is linux and I have a file. I call it barebone.R, which has one line: cat ('Hello World!\n') I execute this file as: R --no-save barebone.R And it does what I expect. What I get is 20+/- lines

Re: [R] Cannot update.packages (error message)

Uwe, I deleted gregmisc from by library folder and ran update.packages() again and I still get the same error: package 'fBasics' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle DESCRIPTION file, no Contains field

Re: [R] Changing color of points in violin plot

On Mon, Apr 27, 2009 at 12:15 PM, John Poulsen jpoul...@zoo.ufl.edu wrote: Hello, I am trying to graph a violin plot like the example in panel.violin(lattice) with the singer data - see below Does anyone know how to change the color of the boxplot on the graph from blue to green?  I tried a

[R] Regression Tree Question

Dear all, I have a question about the regression tree function in R. After applying the tree() function for my data, I found out the n value in the output (the (weighted) number of cases reaching that node) is always less than my total sample size. My guess is becasue some of the cases are not

Re: [R] problem with symbol function

The my.symbols function in the TeachingDemos package works here. It was designed to work like symbols, but with user defined symbols: library(TeachingDemos) theta - seq(0, 2*pi, len=256) circ - cbind( cos(theta), sin(theta) ) x - runif(10) y - rnorm(10, 100, 20) z - runif(10, .5, 1)

Re: [R] Newbie R question PART2

Hi, Many thanks to Wacek Kusnierczyk and Ted Harding. 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 With slight differences, they all do what I wanted. Moving right along my tiny agenda...

Re: [R] Grouping multiple runs of multiple datasets in lattice's xyplot

On Mon, Apr 27, 2009 at 12:33 PM, Daniel Kornhauser d...@northwestern.edu wrote: Hi: I don't know if my explanation below is clear, so afterwards, I wrote a small a self contained annotated example that generates two plots. I execute simulations with different parameters settings that create

[R] Error in Getlim()

Hi all, Do I need to define limits as the error message seems to suggest? The error message, my code, the output and the first few lines of my data are all below. Thank you! Error in Getlim(at, allow.null = TRUE, need.all = TRUE) : variable dmodel.df does not have limits defined in fit or

Re: [R] latticeExtra: useOuterStrips and axis.line$lwd

On Tue, Apr 28, 2009 at 7:40 AM, tyler tyler.sm...@mail.mcgill.ca wrote: Hi, I'm working on some lattice wireframe figures that have two conditioning factors, and I want the strips labelled on the top and left of the entire plot, rather than above each individual panel. useOuterStrips() does

[R] help with Rtools and Rgraphviz

Hi all, I want to install the package Rgraphviz on R2.9.0 (after installing Graphviz 2.22). I have not been successful in installing from the binary on a win XP pc. After looking up previous posts on the R and bioconductor lists, I installed the Rtools29. I have checked that the paths are

Re: [R] send command to other program

Does ?system help? Ranjan On Tue, 28 Apr 2009 13:00:28 -0700 (PDT) thoeb t.hoebin...@gmail.com wrote: Hello, does anybody know about how to send a command or a text line from R to another program? I have written a script in which several calculations are made and outputfiles (csv) are

Re: [R] Understanding padding in lattice

On Tue, Apr 28, 2009 at 11:51 AM, Sebastien Bihorel sebastien.biho...@cognigencorp.com wrote: Dear R-users, I am trying to understand what the different padding arguments in trellis.par.set are exactly controlling the space around lattice plots. I have used the following code as a basis for

Re: [R] help with Rtools and Rgraphviz

On 28/04/2009 3:47 PM, ravi wrote: Hi all, I want to install the package Rgraphviz on R2.9.0 (after installing Graphviz 2.22). I have not been successful in installing from the binary on a win XP pc. After looking up previous posts on the R and bioconductor lists, I installed the Rtools29. I

Re: [R] latticeExtra: useOuterStrips and axis.line$lwd

Deepayan Sarkar deepayan.sar...@gmail.com writes: On Tue, Apr 28, 2009 at 7:40 AM, tyler tyler.sm...@mail.mcgill.ca wrote: Hi, I'm working on some lattice wireframe figures that have two conditioning factors, and I want the strips labelled on the top and left of the entire plot, rather than

Re: [R] effects package --- add abline to plot

John, Thank you for the code, it looks like just what's needed. I'll give it a try tomorrow. The desire for reference lines is to aid comparisons of different factor levels, to look at whether confidence intervals overlap. I've attached a graphic file of the particular allEffects plot,

Re: [R] Error in Getlim()

On Apr 28, 2009, at 6:19 PM, x wrote: Hi all, Do I need to define limits as the error message seems to suggest? The error message, my code, the output and the first few lines of my data are all below. Thank you! Error in Getlim(at, allow.null = TRUE, need.all = TRUE) : variable

[R] Help on apply() function

Hi all, can you please clarify me what is the wrong with following codes : set.seed(30) z = matrix(rnorm(10), 5, 2) apply(z, 1, function(x) sum(z[x,1]*1, z[x,2]*3)) However I can not get the desired result. For example, sum(z[1,1]*1, z[1,2]*3) gives -5.822442 which is actually correct. Am I

Re: [R] Help on apply() function

You are indeed missing something. x is _one row_ of z, not the index specifying that row. So what you want is: apply(z, 1, function(x)sum(x[1]*1, x[2]*3)) Thanks for including a reproducible example. Sarah On Tue, Apr 28, 2009 at 9:02 PM, megh megh700...@yahoo.com wrote: Hi all, can you

Re: [R] Help on apply() function

In the function call in 'apply', you are passed the values in the rows: set.seed(30) z = matrix(rnorm(10), 5, 2) apply(z, 1, function(x) sum(z[x,1]*1, z[x,2]*3)) [1] -0.908321 0.00 0.00 -5.822442 -5.822442 z [,1] [,2] [1,] -1.2885182 -1.5113079 [2,] -0.3476894

[R] RweaveHTML (R2HTML) Help

I have found Sweave() to be great for producing PDF documents. I have been experimenting with RweaveHTML (from the R2HTML) package and have had moderate success. My main issue has been that I simply want the R output to be shown verbatim in the HTML document but RweaveHTML tends to convert most

[R] Re moving unwanted double values in list

I have a procedure that goes sorts out some numbers based on specidifed criteria and for some reason the list contains double values in some of the rows such as: TAZs - [[84]] [1] 638 [[85]] [1] 643 [[86]] [1] 644 732 [[87]] [1] 651 801 i would like to check list TAZs for double values and

[R] Select the same rows

Hi all, I have a problem selecting some rows from a random data. I'd like to select the same rows (before 0) . For example: A [1] 0 [2] 1 [3] 2 [4] 0 [5] 1 [6] 0 [7] 1 [8] 2 [9] 3 [10] 4 I'd like to select the row where a = 2 1 4 I searched on the search of the R site

Re: [R] Select the same rows

It is unclear what you really want so here are two solutions to two different questions: A - matrix(c(0,1,2,0,1,0,1,2,3,4), ncol=1) A [,1] [1,]0 [2,]1 [3,]2 [4,]0 [5,]1 [6,]0 [7,]1 [8,]2 [9,]3 [10,]4 A[A[,1] %in% c(2,1,4) , ] [1] 1 2 1

Re: [R] Re moving unwanted double values in list

PDXRugger wrote: I have a procedure that goes sorts out some numbers based on specidifed criteria and for some reason the list contains double values in some of the rows such as: TAZs - [[84]] [1] 638 [[85]] [1] 643 [[86]] [1] 644 732 [[87]] [1] 651 801 i would like to check list TAZs for

Re: [R] The .tex version of the manual in foo.Rcheck

G'day Bendix, On Mon, 27 Apr 2009 22:52:02 +0200 BXC (Bendix Carstensen) b...@steno.dk wrote: In version 2.8.1, running Rcmd check on the package foo would leave the file foo-manual.tex in the folder foo.Rcheck. But as of 2.9.0 only foo-manual.pdf and foo-manual.log are there. Is this

[R] Batch importing data with respective naming

I'm trying to import data from 100 text files and create data frames that reflect their numbering. The slow way would be to do the following: peak1 - read.table(1--peak--hist.txt, sep=,, header=TRUE) peak2 - read.table(2--peak--hist.txt, sep=,, header=TRUE) peak3 - read.table(3--peak--hist.txt,

[R] kernlab - custom kernel

hi, I am using R's kernlab package, exactly i am doing classification using ksvm(.) and predict.ksvm(.).I want use of custom kernel. I am getting some error. # Following R code works (with promotergene dataset): library(kernlab) s - function(x, y) { sum((x*y)^1.25) } class(s) - kernel

Re: [R] Batch importing data with respective naming

On Tue, Apr 28, 2009 at 07:09:04PM -1000, Taylor Hermes wrote: I tried the following: Add this before for(): peak - list() for (i in 1:100) { peak[[i]] - read.table(paste(i,--one--hist.txt, sep=), sep=,, header=TRUE) } __

[R] question about adaboost.

Hello, I would like to know how to obtain the misclassification error when performing a boosting analisis with ADABAG package? With: prop.table(Tesis.boostcv$confusion) I obtain the confusion matrix, but not the overall missclassification error. Thanks in advance, BSc. Cecilia Lezama Facultad

Re: [R] Extract one element from yahooKeystats data

On Mon, Apr 27, 2009 at 5:42 PM, David Winsemius dwinsem...@comcast.net wrote: Using str(data) would have been more informative. data it turns out is a dataframe with a single column. which is a factor with rownames. Not the most typical of constructions, but the authors must have had their

[R] help on bwplot function

Dear all: 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 function. Could you tell me how I can do

[R] Build Windows binary

Hi everyone, I'm trying to use the online resource, http://win-builder.r- project.org/ in order to build an R package for colleagues on Windows machines (I'm on Mac OS X). I'm not getting an email response from the server (even in my junk mail box). The site explains that the email

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