Re: [R] points marking

Dear Gregory , Thnaks for your reply and help. I am explaining you my problems again, below is my script for the same . Dom -c (195,568,559) fkbp - barplot (Dom, col=black, xlab=, border = NA, space = 7, xlim=c(0,650), ylim =c(0, 87), las = 2, horiz = TRUE) axis (1, at = seq(0,600,10), las

[R] ff package when reading .csv files

Hi My aim is to read a large .csv file into R. I ran the following code and am using R version 10.1 on Windows. library(ff)

Re: [R] points marking

Hi I am not sure if you can do what you want. Segments are not points so your pch option is (I believe) ignored. You could play with lmitre and lend parameters, but it probably would not help much. You cold try to look at ?symbols but you probably need to change source code to suit your

Re: [R] Retrieving the 2 row of dist computations

Edit: I'm stupid and visualized the dist matrix incorrectly in my head. Should be Column # = x, Row # = y. n = 827-(x-2) index = y-1+(n+827)(827-n+1)/2 Everything works just fine. Thanks! Jeff08 wrote: Edit: There is something funky about the code. It definitely returns the right

Re: [R] Desolve package: How to pass thousand of parameters to C compiled code?

On 6/8/2010 2:03 PM, Ben Bolker wrote: cmmu_mileat yahoo.com writes: Hi, I have used DeSolve package for my ODE problem regarding infectious disease transmission and currently am trying to pass lots (roughly a thousand) of model parameters to the C compiled model (I have to use C

[R] Calculation of r squared from a linear regression

Hi, I'm trying to verify the calculation of coefficient of determination (r squared) for linear regression. I've done the calculation manually with a simple test case and using the definition of r squared outlined in summary(lm) help. There seems to be a discrepancy between the what R produced

Re: [R] Misplacement of Greek letter

Newlines are not supported within expressions for mathematical notation. See ?lotmath Best, Uwe Ligges On 11.06.2010 07:36, beloitstudent wrote: Hello. I am trying to get my axis label to read as follows (The symbol) Delta AUC blah blah... then below it...(some other text) The problem

Re: [R] HOW to install RSQLite database

Are you asking how to install the RSQLite package or how to create a SQLite database? The two are somewhat distinct questions. RSQLite is just a package of functions for R to be able to access data in an SQLite database. There isn't a separate SQLite program - just a library that is compiled into

Re: [R] setting the current working directory to the location of the source file

Isn't this what source(..., chdir=TRUE) is for? See help(source). /H On Fri, Jun 11, 2010 at 2:33 AM, Marcin Gomulka mrgo...@gmail.com wrote: AFAIK a script run through source() does not have any legit way to learn about it's own location. I need this to make sure that the script will find

Re: [R] Calculation of r squared from a linear regression

On 2010-06-11 2:16, Sandra Hawthorne wrote: Hi, I'm trying to verify the calculation of coefficient of determination (r squared) for linear regression. I've done the calculation manually with a simple test case and using the definition of r squared outlined in summary(lm) help. There seems

Re: [R] Calculation of r squared from a linear regression

On Fri, 2010-06-11 at 01:16 -0700, Sandra Hawthorne wrote: Hi, I'm trying to verify the calculation of coefficient of determination (r squared) for linear regression. I've done the calculation manually with a simple test case and using the definition of r squared outlined in summary(lm)

[R] Clustering algorithms don't find obvious clusters

I have a directed graph which is represented as a matrix on the form 0 4 0 1 6 0 0 0 0 1 0 5 0 0 4 0 Each row correspond to an author (A, B, C, D) and the values says how many times this author have cited the other authors. Hence the first row says that author A have cited author B four

Re: [R] Misplacement of Greek letter

Not that I want to encourage the creation of the infamous skyscraper plot (which has an extremely low information/ink ratio), but if you're having trouble with axis labelling, it's probably best to look at mtext(). You can use several mtext calls to place parts of your label on different margin

Re: [R] ff package when reading .csv files

On 2010-06-11 0:37, dhanush wrote: Hi My aim is to read a large .csv file into R. I ran the following code and am using R version 10.1 on Windows. library(ff)

Re: [R] Clustering algorithms don't find obvious clusters

Le 11/06/2010 12:45, Henrik Aldberg a écrit : I have a directed graph which is represented as a matrix on the form 0 4 0 1 6 0 0 0 0 1 0 5 0 0 4 0 Each row correspond to an author (A, B, C, D) and the values says how many times this author have cited the other authors. Hence the first

Re: [R] Cforest and Random Forest memory use

You say you're on a 64-bit box, but are you running 64-bit R? -Peter Ehlers On 2010-06-10 4:36, Matthew OKane wrote: Hi all, I'm having great trouble working with the Cforest (from the party package) and Random forest functions. Large data set seem to create very large model objects which

[R] glm-test?

Dear R-users, I would like to test, whether a sample distribution differs significantly from a population distribution. They are not normally distributed. How should I proceed? Using somehow glm-models? How? The population and the sample data are here. They can be loaded using the

Re: [R] How to adjust plot size?

I'm not sure what part of the process is giving you trouble, but if you play around with the mar part of the code, you get a lot of flexibility over the margins. Also, if you pre-set the dimensions of the window the plot is created in, you get even more control. E.g. x11(width=9, height=6,

Re: [R] glm-test?

Which test do you want to use? Once you know that, tell us and we'll tell you where to find it in R. Cheers Joris On Fri, Jun 11, 2010 at 1:50 PM, Atte Tenkanen atte...@utu.fi wrote: Dear R-users, I would like to test, whether a sample distribution differs significantly from a population

Re: [R] Cforest and Random Forest memory use

Also, you have not said: - your OS - your version of R - your version of party - your code - what Large data set means - what very large model objects means So... how is anyone suppose to help you? Max __ R-help@r-project.org mailing list

Re: [R] glm-test?

Take a look at this document: http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf All information you need is in there. Cheers Joris On Fri, Jun 11, 2010 at 2:50 PM, Atte Tenkanen atte...@utu.fi wrote: I would have tried z-test (n=67) but since the distribution is not normally

[R] R in Linux: problem with special characters

Hi, I’m working with the 64 bit version of R 2.11.0 for Linux. My session info is: R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base When I try to print words with

[R] r code to broaden the boarder of the bars of a histogram

To whom it may concern, I have a problem concerning the design of a histogram. How do I change the border widths of the bars of a histogram. The initial command is: hist (punkte,breaks=30, xlab=Punkte, ylab=Häufigkeit, main=Histogramm, col= heat.colors(30), border= red) I suspect that it

[R] Unable to load an object

R-help, I seem not to get an object saved neither with .RData extension nor output via dput. Whenever I try to import the above object in another worspace I just get nothing. geoFeatures - load(geoFeatures.RData) geoFeatures [1] geoFeatures The geoFeatures.RData workspace contains an

[R] lm without error

this is not an important question, but I wonder why lm returns an error, and whether this can be shut off. it would seem to me that returning NA's would make more sense in some cases---after all, the problem is clearly that coefficients cannot be computed. I know that I can trap the lm.fit()

Re: [R] glm-test?

I would have tried z-test (n=67) but since the distribution is not normally distributed, but positive skew, I should somehow transform the data? Values are between 0 and 1. atte Which test do you want to use? Once you know that, tell us and we'll tell you where to find it in R. Cheers

Re: [R] Unable to load an object

Read the posting guide please. You can perfectly save and load the RData file. You just didn't save what you think you saved, but why that is can only be solved when we get to see your actual code. Cheers Joris On Fri, Jun 11, 2010 at 10:28 AM, Luis Ridao Cruz lu...@hav.fo wrote: R-help, I

Re: [R] lm without error

Obvious solution : check your data before you throw it in the lm. lm() shouldn't work in that situation, and if it would, I'd no longer use R. Cheers Joris On Fri, Jun 11, 2010 at 2:49 PM, ivo welch ivo...@gmail.com wrote: this is not an important question, but I wonder why lm returns an

[R] removing a non empty directory

I'd like to remove automatically a directory that may be non empty. I tried: file.remove(NewDir, recursive=TRUE) [1] FALSE Warning message: In file.remove(NewDir, recursive = TRUE) : cannot remove file 'Prostate_Validated_mirWalk', reason 'Directory not empty' Is there another command to

Re: [R] Unable to load an object

If file 'geoFeatures.RData' contains an object with name 'geoFeatures', it is loaded if you do: load(geoFeatures.RData); However, when you do: geoFeatures - load(geoFeatures.RData); it will be loaded, but immediately overwritten because you create a new object with the same name. Note that

Re: [R] lm without error

1) please use reproducible, minimal examples when discussing behavior of R. 2) perhaps ?try could help. ivo welch wrote: this is not an important question, but I wonder why lm returns an error, and whether this can be shut off. it would seem to me that returning NA's would make more sense in

[R] Documentation of B-spline function

Goodmorning, This is a documentation related question about the B-spline function in R. In the help file it is stated that: df degrees of freedom; one can specify df rather than knots; bs() then chooses df-degree-1 knots at suitable quantiles of x (which will ignore missing values).

[R] Odp: r code to broaden the boarder of the bars of a histogram

Hi Look at the source code. graphics:::plot.histogram You can find that boxes are actually drawn by rect So if you want to use standard graphics, you probably need to modify source code and set up your version of plot.histogram. Maybe with ggplot2 package you can find some way how to do what

Re: [R] R in Linux: problem with special characters

On Fri, Jun 11, 2010 at 2:48 PM, daniel fernandes danielpas...@hotmail.com wrote: This as problem has something to do with the locale settings? If I run the locale command in the Linux server, I get: Possibly. print(dúvida) [1] dúvida sessionInfo() R version 2.10.1 (2009-12-14)

Re: [R] r code to broaden the boarder of the bars of a histogram

Use truehist() in pkg:MASS. -Peter Ehlers On 2010-06-11 7:09, Andreas Baranowski wrote: To whom it may concern, I have a problem concerning the design of a histogram. How do I change the border widths of the bars of a histogram. The initial command is: hist (punkte,breaks=30, xlab=Punkte,

Re: [R] lm without error

thanks, everybody. joris---let me disagree with you, please. there are so many possibilities of how lm.fit could fail that by the time I am done with pre-checking, I may as well write my own lm() routine. eric--let me disagree with you, too. I did know about ?try and it is useful when the

Re: [R] points marking

Those graphs look like chromosome maps, if so, you may want to look into the bioconductor project, they may have some prewritten functions to do this. If not, the lend argument (see ?par) may be something to look at. If you really want points and segments you will need to plot the points with

[R] Windows, OSX and Linux: updating a graphic device and double buffering

Hello there, I'm struggling with the base graphics system on different operating systems. I would like to get an animation effect by re-plotting with the plot function. See the attached code example: move the slider quick from one side to the other. I experience different levels of success,

Re: [R] removing a non empty directory

?unlink - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley

[R] Managing list elements

Hello, I have two lists with the same number of elements tail(LHS) [[1]] [1] antecedentes.factor_riesgo=17 antecedentes.estado=1 antecedentes.medio=4 tarjetas_flagrancia.adquiriente2= [[2]] [1] antecedentes.riesgo=1 antecedentes.estado=1 antecedentes.medio=4

[R] passing constrasts=FALSE to contrast functions -- why does this exist?

Hello, I've noticed that all contrast functions, like contr.treatment, contr.poly, etc., take a logical argument called 'contrasts'. The default is TRUE, in which case they do their normal thing of returning a n x n-1 matrix whose columns are linearly-independent of the intercept. If

[R] rules-class

Hellos I have a rules-class element which I got from the apriori function in the arules package, no I would like to stay just with a subset of the rules. Does anybody know how can I create an object which has only the subset corresponding from some indices I give him. For example if I have the

Re: [R] Managing list elements

Luis - I *think* that mapply(list,LHS,RHS,SIMPLIFY=FALSE) will give you what you want, but without a reproducible example it's hard to tell. - Phil Spector Statistical Computing Facility

[R] Transforming simulation data which is spread across many files into a barplot

I'm an R newbie, and I'm just trying to use some of it's graphing capabilities, but I'm a bit stuck - basically in massaging the already available data into a format R likes. I have a simulation environment which produces logs, which represent a number of different things. I then run a python

Re: [R] Transforming simulation data which is spread across many files into a barplot

On Fri, Jun 11, 2010 at 1:32 PM, Ian Bentley ian.bent...@gmail.com wrote: I'm an R newbie, and I'm just trying to use some of it's graphing capabilities, but I'm a bit stuck - basically in massaging the already available data into a format R likes. I have a simulation environment which

[R] How to code mixed model with nested factors in lmer

Hi, I have coding question on mixed model in R. I am using R2.11.0 in windows. I have an experiment with 2 fixed effect factors - A and B. The levels of B are within the levels of A factor. The model is very similar to a split plot design except the nesting relationship between the 2 fixed

Re: [R] Transforming simulation data which is spread across manyfiles into a barplot

Ouch! Lousy plot. Instead, plot the 50 (mean sent, mean received)pairs as a y vs x scatterplot to see the relationship. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Hadley

Re: [R] Transforming simulation data which is spread across manyfiles into a barplot

I'm not trying to see the relation between sent and received, but rather to show how these grow across the increasing complexity of the 50 data points. On 11 June 2010 15:02, Bert Gunter gunter.ber...@gene.com wrote: Ouch! Lousy plot. Instead, plot the 50 (mean sent, mean received)pairs as a

Re: [R] Transforming simulation data which is spread across many files into a barplot

Try this: base - file # replace as appropriate N - 50 filenames - paste(base, seq_len(N)*100, .log, sep = ) mat - sapply(filenames, function(fn) colMeans(read.table(fn, col.names = c(Sent, Received))) ) barplot(mat) On Fri, Jun 11, 2010 at 2:32 PM, Ian Bentley ian.bent...@gmail.com

Re: [R] Transforming simulation data which is spread acrossmanyfiles into a barplot

So two time series? Fair enough. But less is more. Plot them as separates series of points connected by lines, different colors for the two different series. Or as two trellises plots. You may also wish to overlay a smooth to help the reader see the trend(e.g via a loess or other nonparametric

[R] comparing reshape's

I thought I would share the following. System: Mac Pro 2.26GHz, OSX, 8GB of memory (not a constraint), R 2.11.0, 64bit version. Task: I have a long data set: 2.2 million long observations (factor xid, factor yid, variable zcontent), which I want to map into a sparse matrix of 948 columns and

Re: [R] glm-test?

Thanks! Atte Take a look at this document: http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf All information you need is in there. Cheers Joris On Fri, Jun 11, 2010 at 2:50 PM, Atte Tenkanen atte...@utu.fi wrote: I would have tried z-test (n=67) but since the

[R] Handling character string

Dear all, Is there any R function to say these 2 character strings temp  and temp are actually same? If I type following code R says there are indeed different : temp  == temp[1] FALSE Is there any way out? [[alternative HTML version deleted]]

Re: [R] lm without error

This will give the coefficients of each regression for which there are no missing values in the dependent variable and NAs for the rest: # test data set.seed(123) y - cbind(y1 = 1:4, y2 = c(NA, 2:4)) x - 1:4 + rnorm(4) qr.coef(qr(cbind(1, x)), y) y1 y2 0.8607244 NA x 0.6049789

Re: [R] Handling character string

Megh Dal wrote: Dear all, Is there any R function to say these 2 character strings temp and temp are actually same? If I type following code R says there are indeed different : temp == temp[1] FALSE You don't say how you're defining same, but it definitely requires more explanation,

[R] Rgui crashed on Windows XP Home

Hi there, I just installed R 2.11.1 on my PC, which runs a Windows XP Home. The installation is successful, however, when I double click on the R icon, I get the following error message: R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the

Re: [R] Clustering algorithms don't find obvious clusters

Henrik, The clustering algorithms you refer to (and almost all others) expect the matrix to be symmetric. They do not seek a graph-theoretic solution, but rather proximity in geometric or topological space. How did you convert y9oru matrix to a dissimilarity? Dave Roberts Henrik

Re: [R] Handling character string

I think the poster wants ?regex. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Erik Iverson Sent: Friday, June 11, 2010 2:06 PM To: Megh Dal Cc: r-h...@stat.math.ethz.ch

[R] Decision values from KSVM

Hi, I'm working on a project using the kernlab library. For one phase, I want the decision values from the SVM prediction, not the class label. the e1071 library has this function, but I can't find the equivalent in ksvm. In general, when an SVM is used for classification, the label of an

Re: [R] R in Linux: problem with special characters

daniel fernandes wrote: Hi, I’m working with the 64 bit version of R 2.11.0 for Linux. My session info is: R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base When I try

Re: [R] Rgui crashed on Windows XP Home

Jinsong Zhao wrote: Hi there, I just installed R 2.11.1 on my PC, which runs a Windows XP Home. The installation is successful, however, when I double click on the R icon, I get the following error message: R for Windows GUI front-end has encountered a problem and needs to close. We are

Re: [R] Documentation of B-spline function

On Fri, 11 Jun 2010, Christos Argyropoulos wrote: Goodmorning, This is a documentation related question about the B-spline function in R. In the help file it is stated that: df degrees of freedom; one can specify df rather than knots; bs() then chooses df-degree-1 knots at suitable

[R] lmer() with no intercept

Hi, I asked this before, but haven't got any response. So would like to have another try. thanks for help. Also tried twice to join the model mailing list so that I can ask question there, but still haven't got permission to join that list yet. === Hi, I am wondering how I can

Re: [R] lm without error

On Fri, Jun 11, 2010 at 5:28 PM, ivo welch ivo.we...@gmail.com wrote: thanks, everybody. joris---let me disagree with you, please.  there are so many possibilities of how lm.fit could fail that by the time I am done with pre-checking, I may as well write my own lm() routine. If we all would

Re: [R] lm without error

did it again... it has to be getOut - which(colSums(is.na(y))==dim(y)[1]) lm( y[,-getOut] ~ x ) off course. Cheers Joris On Sat, Jun 12, 2010 at 2:22 AM, Joris Meys jorism...@gmail.com wrote: On Fri, Jun 11, 2010 at 5:28 PM, ivo welch ivo.we...@gmail.com wrote: thanks, everybody.

Re: [R] lmer() with no intercept

Try a different example: set.seed(123) N - 24 k - 6 x - 1:N f - rep(rnorm(k, 0, 4), each = N/k) e - rnorm(N) y - x + f + e fac - gl(k, N/k) library(lme4) fm1 - lmer(y ~ x + (1|fac)); fm1 fm0 - lmer(y ~ x -1 + (1|fac)); fm0 plot(y, fitted(fm0)) abline(a = 0, b = 1, lty = 2, col = blue)

[R] sharing experience - installing R Spatial Views

Hi Guys, I would like to share my experience when installing the Spatial views packages for R. I could not install 32 packages which are parts of the Spatial views, and I use google-search and search to solve ALL those problems for about 2 days. I hope maybe somebody would benefit from my

[R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

Hello all, I came acrosshttp://www.r-bloggers.com/performance-benefits-of-linking-r-to-multithreaded-math-libraries/ David Smith's new post Performance benefits of linking R to multithreaded math librarieshttp://blog.revolutionanalytics.com/2010/06/performance-benefits-of-multithreaded-r.html

Re: [R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

The reason that the BLAS libraries are not installed as part of the standard distribution is that its desirable that the standard distribution be the same on all machines whereas you need a different BLAS library for each different CPU type. __

[R] R can't find gcc library that other programs can.

R is used in the Sage project. R is building on Solaris 10 with SPARC processors. Until recently, I did not give it much more thought, as it appeard to build ok. More recently someone noticed a test failure. It would appear a number of modules are not building (Matrix, class, mgcv, nnet,

Re: [R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

In the case of REvolution R, David mentioned using the Intel MKL, proprietary library which may not be distributed in the way R is distributed. Maybe REvolution has a license to redistribute the library. For the others, I suspect Gabor has the right idea, that the R-core team would rather not keep

Re: [R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

On 11 June 2010 at 23:01, Matt Shotwell wrote: | In the case of REvolution R, David mentioned using the Intel MKL, | proprietary library which may not be distributed in the way R is | distributed. Maybe REvolution has a license to redistribute the library. | For the others, I suspect Gabor has

Re: [R] Decision values from KSVM

Any suggestions? ?predict.ksvm has an argument called type: one of response, probabilities ,votes, decision indicating the type of output: predicted values, matrix of class probabilities, matrix of vote counts, or matrix of decision values. Max __

Re: [R] Overlay of barchart and xyplot

Hi, I have an example below of adding a key to the merged plot. You can not have the key on the right hand side because that viewport is used by the second ylab (ylab2 from doubleYScale). Well, if you really wanted to, you could do it with the grid package, using frameGrob or somesuch.

Re: [R] Date conversion

Thanks Joshua, I wanted to use some kind of date format in latex but ended up using exactly what you and Marc suggested.   Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA - Original Message From: Joshua Wiley