[R] Correlated Columns in data frame

2008-05-16 Thread Nataraj
Dear all, Sorry to post my query once again in the list, since I did not get attention from anyone in my previous mail to this list. Now I make it simple here that please give me a code for find out the columns of a dataframe whose correlation coefficient is below a pre-determined threshold. (For

[R] fast multipole methods(FMM)/fast Gauss transfrorm(FGT)/improved fast gauss transform (IGFT)

2008-05-16 Thread Mark.Palmer
I'm just curious, but wondering if there has been any work in making these algorithms available in R. They are aimed at accelerating matrix-vector products using approximation ideas, and might be useful in applications such as kernel machines, Gaussian processes/kriging. Thanks Mark Palmer

Re: [R] merging data frames

2008-05-16 Thread Yasir Kaheil
> DF1<- data.frame(Name=as.factor(c("A","B","C")), Age= c(21,45,30)) > DF2<- data.frame(Name=as.factor(c("A","B","X")), Age= c(50,20,10)) > DF3<- data.frame(Name=as.factor(c("B","Y","K")), Age= c(40,21,30)) > > merge(merge(DF1,DF2, by.x= "Name", by.y="Name", > all=TRUE),DF3,by.x="Name",by.y="Name

Re: [R] How to paste graph from R in Latex?

2008-05-16 Thread Vincent Goulet
Le ven. 16 mai à 21:24, Roslina Zakaria a écrit : Dear R-expert, Is it possible to save graph from R into Latex document? I can see save as metafile , PNG, pdf etc, but I'm not sure which one to use. Thank you so much for your help. If you use latex, you should go for Encapsulated PostScri

[R] How to paste graph from R in Latex?

2008-05-16 Thread Roslina Zakaria
Dear R-expert, Is it possible to save graph from R into Latex document? I can see save as metafile , PNG, pdf etc, but I'm not sure which one to use. Thank  you so much for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/

Re: [R] Dimensions of svd V matrix

2008-05-16 Thread Gad Abraham
Kenn Konstabel wrote: I'm not an expert at all, but isn't it that you really want svd(x)$u to be different (instead of V)? that would be easy to do: x <- matrix(rnorm(15), 3, 5) s1 <- svd(x) s2 <- svd(x, nv=ncol(x)) x1 <- s1$u %*% diag(s1$d) %*% t(s1$v) x2 <- cbind(s2$u,1,1) %*% diag(c(s1$d,

[R] merging data frames

2008-05-16 Thread Srinivas Iyyer
Dear group, I have 3 different data frames. I want to merge all 3 data frames for which there is intersection. Say DF 1 and DF2 has 100 common elements in Column 1. DF3 does not have many intersection either with DF1 or with DF2. For names in column 1 not present in DF3 I want to introduce NA

Re: [R] xyplot: subscripts, groups and subset

2008-05-16 Thread Deepayan Sarkar
On 5/16/08, Jim Price <[EMAIL PROTECTED]> wrote: > > I have stumbled across something in the Lattice package that is vexing me. > Consider the code below: > __ > > library(lattice) > > > myData <- expand.grid(sub = factor(1:16), time = 1:

Re: [R] interactive rotatable 3d scatterplot

2008-05-16 Thread francois Guilhaumon
The problem is arising because graphical effects are certainly turn-on on the computer. I deactivated the graphical effects and was able to rotate the 3D surface plot. Turning effects on bring me back in the original state of a non rotating scene. It seems that it is more an openGL issue. Perhaps

Re: [R] interactive rotatable 3d scatterplot

2008-05-16 Thread Ben Bolker
francois Guilhaumon gmail.com> writes: > > I am facing the same problem than Mark Kimpel with the rgl package : > > Running various 3D rendering I'm always faced with a static 3d plot, > which does not > rotate when I click and mouse over it. > > I'm running Ubuntu linux 7.10 with a 32bit pro

[R] interactive rotatable 3d scatterplot

2008-05-16 Thread francois Guilhaumon
I am facing the same problem than Mark Kimpel with the rgl package : Running various 3D rendering I'm always faced with a static 3d plot, which does not rotate when I click and mouse over it. I'm running Ubuntu linux 7.10 with a 32bit processor, thus the problem is not arising from 64bit issues.

Re: [R] autocorrelation in nlme; Error: cannot allocate vector of size

2008-05-16 Thread J S
Dear R community, Here are details of my model, which gives me trouble modeling autocorrelation. lm11<-lme(Soil.temp ~ Veg*M+Veg*year, data=a, random = list(Site=pdDiag(~Veg), Plot=pdDiag(~Veg)) dataset: a-data frame of daily m

[R] sample function

2008-05-16 Thread carol white
Hi, I use sample function in a for loop to get a new random indexing but I don't know why, I get the same indexes in different iterations of for. I have a script that uses for loop calling crossval function (the same definition as crossval in bootstrap package) defined in another script. Both s

Re: [R] autocorrelation in nlme; Error: cannot allocate vector of size

2008-05-16 Thread ONKELINX, Thierry
Dear Julia, You'll need to give more details on your model and the structure of your dataset. The problem will probably be in the specification of the random effects. But without the detail we can't check that. Thierry ---

[R] autocorrelation in nlme; Error: cannot allocate vector of size

2008-05-16 Thread J S
Dear R community, I used a linear mixed model (named lm11) to model daily soil temperature depending upon vegetation cover and air temperature. I have almost 17,000 observations for six years. I can not account for autocorrelation in my model, since I receive the error message after applying

[R] wavCWT plot

2008-05-16 Thread stephen sefick
is there a way to plot the modulus graph with a different color scheme. The contrast is very bad (for my eyes). -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals,

[R] Identify groups

2008-05-16 Thread mike Ad.
Dear group, I have hundreds of independent data sets, each data sets contains >100 values. In some data sets, all the values can be classified into several groups with clear difference between groups; while in some other data sets, all the values are randomly distributed. I would like to find a

[R] gam negative.binomial

2008-05-16 Thread Markus Loecher
Dear list members, while I appreciate the possibility to deal with overdispersion for count data either by specifying the family argument to be quasipoisson() or negative.binomial(), it estimates just one overdispersion parameter for the entire data set. In my applications I often would like the es

[R] xyplot: subscripts, groups and subset

2008-05-16 Thread Jim Price
I have stumbled across something in the Lattice package that is vexing me. Consider the code below: __ library(lattice) myData <- expand.grid(sub = factor(1:16), time = 1:10) myData$observed <- rnorm(nrow(myData)) myData$fitted <- with(my

Re: [R] Integer / floating point question

2008-05-16 Thread Berwin A Turlach
G'day Brian, On Fri, 16 May 2008 19:28:59 +0100 (BST) Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > 'numeric' is a class but not a type -- so I think the FAQ is wrongly > worded but the concept is well defined Though there may be multiple definitions. :-) Reading a bit in "R Language Definit

[R] wmtsa (wavCWT)

2008-05-16 Thread stephen sefick
I can send data along, but it is too large for the list: I am using wmtsa and the function wavCWT I would like to use the range.scale to only evaluate a subset of frequencies. deltat of the time series that I am trying to analyze is 1 d = wavCWT(RM202.ts, range.scale = c(96, 2688)) and I get the

Re: [R] R package building

2008-05-16 Thread Gabor Grothendieck
On Fri, May 16, 2008 at 2:20 PM, Doran, Harold <[EMAIL PROTECTED]> wrote: > Wow, this is going open a can :) OK, my comments below in no way > discount the enormous efforts of R core, but it is my experience. > > Using Windows, the biggest obstacles are collecting all programs needed > to build the

Re: [R] Box.test degrees of freedom

2008-05-16 Thread Prof Brian Ripley
Bear in mind that Box.test knows nothing about p or q: it says Compute the Box-Pierce or Ljung-Box test statistic for examining the null hypothesis of independence in a given time series. I think you are referring to its application to the residuals of an ARMA(p, q) fit, and that is n

Re: [R] Integer / floating point question

2008-05-16 Thread Prof Brian Ripley
'numeric' is a class but not a type -- so I think the FAQ is wrongly worded but the concept is well defined (despite the presence of is.numeric!) But it does not say that all such numbers can be represented exactly, and only some can. On Sat, 17 May 2008, Berwin A Turlach wrote: G'day Erik,

Re: [R] R package building

2008-05-16 Thread Doran, Harold
Wow, this is going open a can :) OK, my comments below in no way discount the enormous efforts of R core, but it is my experience. Using Windows, the biggest obstacles are collecting all programs needed to build the package and then structuring your OS path exactly (exactly) as D. Murdoch says it

Re: [R] R package building

2008-05-16 Thread Duncan Murdoch
On 5/16/2008 2:08 PM, Angelos Markos wrote: In a few days I'll give a talk on R package development and my personal experience, at the 3rd Free / Libre / Open Source Software (FLOSS) Conference which will take place on May 27th & 28th 2008, in the National Technical University of Athens, in Greec

[R] 64-bit R and cache memory

2008-05-16 Thread Joram Posma
Dear all, I have a few questions regarding the 64 bit version of R and the cache memory R uses. --- Computer & software info: OS: kUbuntu Feasty Fawn 7.04 (64-bit) Processor: AMD Opteron 64-bit R: version 2.7.0 (64-bit) Cache memory: currently 16 GB (was 2 GB)

[R] R package building

2008-05-16 Thread Angelos Markos
In a few days I'll give a talk on R package development and my personal experience, at the 3rd Free / Libre / Open Source Software (FLOSS) Conference which will take place on May 27th & 28th 2008, in the National Technical University of Athens, in Greece. I would appreciate if you could share your

[R] autocorrelation error: cannot allocate vector of size 220979 Kb

2008-05-16 Thread J S
Dear R community, I used a linear mixed model (named lm11) to model daily soil temperature depending upon vegetation cover and air temperature. I have almost 17,000 observations for six years. I can not account for autocorrelation in my model, since I receive the error message after applying

Re: [R] Integer / floating point question

2008-05-16 Thread Duncan Murdoch
On 5/16/2008 11:45 AM, Erik Iverson wrote: Marc - Marc Schwartz wrote: on 05/16/2008 09:56 AM Erik Iverson wrote: Dear R-help - I have thought about this question for a bit, and come up with no satisfactory answer. Say I have the numeric vector t1, given as t1 <- c(1.0, 1.5, 2.0, 2.5, 3.0

Re: [R] glm model syntax

2008-05-16 Thread Doran, Harold
Dear Berwin: Indeed, it seems I was incorrect. Using your data, it seems that only in the case that the variables are numeric would my earlier statements be true, as you note. For example, if we did lm(y ~ as.numeric(N)+as.numeric(M), dat) lm(y ~ as.numeric(N)*as.numeric(M), dat) lm(y ~ as.numeri

Re: [R] Integer / floating point question

2008-05-16 Thread Gabor Grothendieck
2, 2.0, 2e0 are all double while 2L is an integer. On Fri, May 16, 2008 at 10:56 AM, Erik Iverson <[EMAIL PROTECTED]> wrote: > Dear R-help - > > I have thought about this question for a bit, and come up with no > satisfactory answer. > > Say I have the numeric vector t1, given as > > t1 <- c(1.0,

Re: [R] Integer / floating point question

2008-05-16 Thread Berwin A Turlach
G'day Erik, On Fri, 16 May 2008 10:45:43 -0500 Erik Iverson <[EMAIL PROTECTED]> wrote: [...] > The help page for '%%' addresses this a bit, but then caveats it with > 'up to rounding error', which is really my question. Is there ever > 'rounding error' with 2.0 %% 1 as opposed to 2 %% 1? I am

Re: [R] Box.test degrees of freedom

2008-05-16 Thread markleeds
Spencer Graves has discussed this recently ( in the last couple of months ) in a thread and I think his FinTS package has a variant of the Box.test function that does what you need. On Fri, May 16, 2008 at 11:45 AM, Nuno Prista wrote: Dear colleagues, I am new to R and statistics so ple

Re: [R] aggregate(), with multiple functions in FUN?

2008-05-16 Thread jim holtman
Will something like this work for you: > d <- read.table(textConnection("ZIP DATA + 94111 12135.545 + 93105 321354.65654 + 94111 545.555 + 94706 558858.66"), header=TRUE) > closeAllConnections() > aggregate(d$DATA, list(Zip = d$ZIP), FUN=median, na.rm=T) Zip x 1

Re: [R] glm model syntax

2008-05-16 Thread Berwin A Turlach
G'day Harold, On Fri, 16 May 2008 11:43:32 -0400 "Doran, Harold" <[EMAIL PROTECTED]> wrote: > N+M gives only the main effects, N:M gives only the interaction, and > G*M gives the main effects and the interaction. I guess this begs the question what you mean with "N:M gives only the interaction"

Re: [R] heatmap on pre-established hclust output?

2008-05-16 Thread James W. MacDonald
You just have to pass in the *dendrogram* to heatmap() or heatmap.2(). So if you have an hclust object for the rows and columns (called, say rhclust and chclust): heatmap(datamatrix, Rowv = as.dendrogram(rhclust), Colv = as.dendrogram(chclust), otherargs) Best, Jim Johannes Graumann wro

Re: [R] heatmap on pre-established hclust output?

2008-05-16 Thread Jeremiah Rounds
> To: [EMAIL PROTECTED]> From: [EMAIL PROTECTED]> Date: Fri, 16 May 2008 > 17:55:26 +0200> Subject: [R] heatmap on pre-established hclust output?> > > Hi,> > Can someone please guide me towards how to produce "heatmap" output > from the> output of "hclust" run prior to the actual "heatmap" call

[R] How to get subset of rows and columns that are most strongly correlated ?

2008-05-16 Thread Ng Stanley
Hi, I have a relatively large matrix 20k rows and 1000 columns. Instead of trying all possible combinations, is there a way to identify subset of rows and columns that are most strongly correlated ? Thanks Stanley [[alternative HTML version deleted]]

Re: [R] Dimensions of svd V matrix

2008-05-16 Thread Kenn Konstabel
I'm not an expert at all, but isn't it that you really want svd(x)$u to be different (instead of V)? that would be easy to do: x <- matrix(rnorm(15), 3, 5) s1 <- svd(x) s2 <- svd(x, nv=ncol(x)) x1 <- s1$u %*% diag(s1$d) %*% t(s1$v) x2 <- cbind(s2$u,1,1) %*% diag(c(s1$d,0,0)) %*% t(s2$v) all.eq

Re: [R] How to swap and rearrange rows?

2008-05-16 Thread Dieter Menne
Roslina Zakaria yahoo.com> writes: > How to swap and rearrange the row so that I will have > Jan-Dec in order? > > est31 > p0 est.alpha est.beta est.rate > Jan 0.8802867 0.7321440 7.241757 0.1380880 > Mar 0.8598566 0.7096567 7.376367 0.1355681 > May 0.6204301 0.8657272 6.036106 0.1

[R] heatmap on pre-established hclust output?

2008-05-16 Thread Johannes Graumann
Hi, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks,

[R] logistic transformation using nlminb

2008-05-16 Thread John Pitchard
Dear all, I want to find the optimal values of a vector, x (with 6 elements) say, satisfying the following conditions: 1. for all x>=0 2. sum(x)=1 3. x[5]<=0.5 and x[6]<=0.5 For the minimisation I'm using nlminb and to satisfy the first 2 conditions the logistic transformation is used with box c

Re: [R] Integer / floating point question

2008-05-16 Thread Erik Iverson
Marc - Marc Schwartz wrote: on 05/16/2008 09:56 AM Erik Iverson wrote: Dear R-help - I have thought about this question for a bit, and come up with no satisfactory answer. Say I have the numeric vector t1, given as t1 <- c(1.0, 1.5, 2.0, 2.5, 3.0) I simply want to reliably extract the uni

Re: [R] Making slope coefficients ``relative to 0''.

2008-05-16 Thread Bert Gunter
Either lm(y~ a-1 + a:x) or lm (y~ a + (a-1):x) or lm(y~ a+ a:(x-1)) -- Bert Gunter Genentech -Original Message- From: bgunter Sent: Friday, May 16, 2008 8:39 AM To: Rolf Turner Subject: RE: [R] Making slope coefficients ``relative to 0''. lm(y ~ a + a:(x-1)) -Original Message

[R] Box.test degrees of freedom

2008-05-16 Thread Nuno Prista
Dear colleagues, I am new to R and statistics so please keep that in mind. I have doubts on the df calculation of Ljung-Box test (Box.test). The function seems to use always the df=lag=m and not df=m-p-q like suggested in Ljung and Box (1978) paper (that is referenced). Do you agree wi

Re: [R] glm model syntax

2008-05-16 Thread Doran, Harold
N+M gives only the main effects, N:M gives only the interaction, and G*M gives the main effects and the interaction. > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Birgit Lemcke > Sent: Friday, May 16, 2008 11:27 AM > To: R Hilfe > Subject: [R] g

Re: [R] Font settings in xfig

2008-05-16 Thread Greg Snow
If the main goal is to include graphs created by R in LaTeX documents and have them look nice, and using xfig was just one way of attempting this, then here are a couple other options that may or may not work better. Use the postscript graphics device and use psfrag in LaTeX to replace text in

Re: [R] reading and analyzing a text file

2008-05-16 Thread DAVID ARTETA GARCIA
here I show the first text lines and some of the data. There are actually 6272 rows in the dataframe. Actually the skip parameter works fine as some people already suggested. ATF 1.0 20 5 "Type=Mapix Results 2" "DateTime=2008/05/15 11:05:38" "ConfigFile=" "GalFile=Y:\experimental\090

[R] glm model syntax

2008-05-16 Thread Birgit Lemcke
Hello R users! What is the difference between glm(A~N+M) glm(A~N:M) glm(A~N*M) Thanks in advance. Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwi

Re: [R] Integer / floating point question

2008-05-16 Thread Marc Schwartz
on 05/16/2008 09:56 AM Erik Iverson wrote: Dear R-help - I have thought about this question for a bit, and come up with no satisfactory answer. Say I have the numeric vector t1, given as t1 <- c(1.0, 1.5, 2.0, 2.5, 3.0) I simply want to reliably extract the unique integers from t1, i.e., th

Re: [R] reading and analyzing a text file

2008-05-16 Thread Prof Brian Ripley
1) read.table has a 'skip' argument which may suffice. 2) R has the concept of 'connections' to read sequentially through a file. See the 'R Data Import/Export' manual. If that is not enough hints, showing us an example usually intrigues people enough to offer working code. On Fri, 16 May 2

[R] Integer / floating point question

2008-05-16 Thread Erik Iverson
Dear R-help - I have thought about this question for a bit, and come up with no satisfactory answer. Say I have the numeric vector t1, given as t1 <- c(1.0, 1.5, 2.0, 2.5, 3.0) I simply want to reliably extract the unique integers from t1, i.e., the vector c(1, 2, 3). This is of course sup

Re: [R] re ading and analyzing a text file

2008-05-16 Thread Ted Harding
On 16-May-08 14:35:18, Yasir Kaheil wrote: > > use the parameter 'skip' in read.table > > dat<-read.table("filename",skip=number of rows you want to skip) > > thanks > y Or, ironically, you can use scan(...,skip=number of rows to skip)! See ?scan. Best wishes, Ted. > DAVID ARTETA GARCIA wrote

Re: [R] reading and analyzing a text file

2008-05-16 Thread Doran, Harold
This may be possible using the skip argument in read.table. It's hard to know w/o a bit more info on the structure of the text file. > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of DAVID ARTETA GARCIA > Sent: Friday, May 16, 2008 10:31 AM > To: r-

Re: [R] reading and analyzing a text file

2008-05-16 Thread Erin Hodgess
Hi David! if you use read.table, there is an argument called skip. You can set that to skip=20, say. HTH, Erin On Fri, May 16, 2008 at 9:30 AM, DAVID ARTETA GARCIA <[EMAIL PROTECTED]> wrote: > Dear list, > > I have a text file from a scanner that includes 20 lines of text (scanner > settings)

Re: [R] Lattice box percentile plot

2008-05-16 Thread Yasir Kaheil
it's a good question.. my guess is using "panel.bpplot" prevents filling in the shape "the coffins"- since the box is now two mirrored graphs. i hope i'm wrong. trellis.par.get() br = trellis.par.get("box.rectangle") br$col = "black" br$fill = "lightblue" #this is the parameter that fills in

Re: [R] re ading and analyzing a text file

2008-05-16 Thread Yasir Kaheil
use the parameter 'skip' in read.table dat<-read.table("filename",skip=number of rows you want to skip) thanks y DAVID ARTETA GARCIA wrote: > > Dear list, > > I have a text file from a scanner that includes 20 lines of text > (scanner settings) before it actually starts showing the readin

[R] reading and analyzing a text file

2008-05-16 Thread DAVID ARTETA GARCIA
Dear list, I have a text file from a scanner that includes 20 lines of text (scanner settings) before it actually starts showing the readings in a tabular format (headings are ID, intensity, background and few others). I am a biologist with some experience using R and my question is if it

[R] aggregate(), with multiple functions in FUN?

2008-05-16 Thread Mike !
I've got a data frame having numerical data by zip code: ZIP DATA 94111 12135.545 93105 321354.65654 94111 545.555 94706 558858.66 ... ... I'm using this function to group records by ZIP and calculate the median of DATA: aggregate(d$DATA, list(Zip = d$ZIP), F

Re: [R] ANOVA between linear models.

2008-05-16 Thread Rune Haubo
Hi Richard You are trying to compare two models, that are not nested. This means that all usual asymptotics of the test statistics break down, hence the (second) test you are attempting is not meaningful. Usually one decides on the form of the response on other grounds such as residual analysis or

Re: [R] How to extract estimates, Std. Error, t Value and Pr(>|t|) from summary

2008-05-16 Thread Yasir Kaheil
> dat<-array(runif(30),c(15,2)); > dat<-data.frame(x=dat[,1],y=dat[,2]); > linm<-lm(y~x,data=dat); > linm.s<-summary(linm); > attributes(linm.s) #to see all attributes of the summary $names [1] "call" "terms" "residuals" "coefficients" [5] "aliased" "sigma" "d

Re: [R] (1-alpha)th percentile

2008-05-16 Thread Ben Bolker
hanen yahoo.fr> writes: > > > hello; > firstly, my gratitude to all who help me to find a function that allows me > to add confidence interval to my graph. > in order to calculate the (1-alpha)th percentile of for exemple an > F(df1,df2) distribution i do like this: > v<-df(alpha,df1,df2) > p

Re: [R] How to extract estimates, Std. Error, t Value and Pr(>|t|) from summary

2008-05-16 Thread John Kane
Here is a response some time ago from John Fox which should help. # Extracting values from various objects. # From "John Fox" <[EMAIL PROTECTED]> # Using an anova mod <- lm(mpg ~ ., data=mtcars) av <- anova(mod) names(av) #[1] "Df" "Sum

[R] Lattice box percentile plot

2008-05-16 Thread Mr Derik
Dear Nabble. I am trying to draw a box percentile plot with trellis using the panel in Hmisc. I really want to colour the plots in. I can alter several of features of the plot by changing the trellis par settings but I just can’t fill the shape in. Here is some example code which alters line c

Re: [R] Getting JRI/rJava to work

2008-05-16 Thread Prof Brian Ripley
Some off-line discussion showed that the problem was a different iconv.dll ahead of R's in the path. This is a risk for embedded applications of R, and worth checking for if this error comes up for you. (We have also seen it reported just once when the issue was Windows' locale settings.) On

[R] How to extract estimates, Std. Error, t Value and Pr(>|t|) from summary

2008-05-16 Thread Daphne Renault
__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] problem with X11 when talking via PHP web interface

2008-05-16 Thread Paul Hammer
hi members, At the moment i try to create a web-based GUI for R. I am at the beginning of this project but i have already now a strange problem. I would like to create an image which should also be saved. i realize this with following code line in my PHP file: $output= intval(shell_exec("R --n

Re: [R] Font settings in xfig

2008-05-16 Thread Kevin E. Thorpe
Scionforbai wrote: >> Is there a reason you are going through this route to get figures >> into LaTeX instead of using postscript (or PDF for pdflatex)? > > To have LaTeX-formatted text printed onto your pdf figures, to include > in LaTeX documents. > > R cannot output 'special' text in xfig. You

[R] How to determine sensible values for 'fnscale' and 'parscale' in optim

2008-05-16 Thread Karl Ove Hufthammer
the MLEs of a bivariate normal distribution using optim. Here's code for this example: --- library(MASS) # needed mvrnorm library(mvtnorm) # needed for dmvnorm set.sed(20080516) n=1000 mu1=3 mu2=5 sig1=7 sig2=20 rho=.5 sigmat=matrix(c(sig1^2,sig1*sig2

[R] (1-alpha)th percentile

2008-05-16 Thread hanen
hello; firstly, my gratitude to all who help me to find a function that allows me to add confidence interval to my graph. in order to calculate the (1-alpha)th percentile of for exemple an F(df1,df2) distribution i do like this: v<-df(alpha,df1,df2) percentile<-qf(v,df1,df2,alpha) if it is true

Re: [R] Inconsistent linear model calculations

2008-05-16 Thread Gavin Simpson
On Thu, 2008-05-15 at 14:50 +0100, e-letter wrote: > 2008/5/15 Douglas Bates <[EMAIL PROTECTED]>: > > Did you happen to notice the part at the bottom of every message about > > "provide commented, minimal, self-contained, reproducible code"? > > > Sorry, don't understand what that statement means i

Re: [R] Font settings in xfig

2008-05-16 Thread Scionforbai
> Is there a reason you are going through this route to get figures > into LaTeX instead of using postscript (or PDF for pdflatex)? To have LaTeX-formatted text printed onto your pdf figures, to include in LaTeX documents. R cannot output 'special' text in xfig. You need to post-process the .fig

Re: [R] Fedora 9?

2008-05-16 Thread Marc Schwartz
on 05/16/2008 07:22 AM Peter Dalgaard wrote: Peter Dalgaard wrote: Jonathan Baron wrote: Not to be impatient, but something seems odd. The CRAN repository has nothing for Fedora 9. The RPM of R that comes with Fedora 9 is version 2.6.2. Someone connected with the Fedora project must have

Re: [R] creating a 2d plan graphic and projecting points in it

2008-05-16 Thread Khaled OUANES
Hey Jim, In fact the 123 values range from: (minus) -1,50156 to 0,61068 and I need to enter them as graduation for the X axis (axis 1) and the other 7 values (0,45833 0,609 0,6123 0,63 0,72 1 1) I need them to form a graduation for axis 2. then I have points with coordinates (x,y) that

Re: [R] Fedora 9?

2008-05-16 Thread Peter Dalgaard
Peter Dalgaard wrote: > Jonathan Baron wrote: > >> Not to be impatient, but something seems odd. >> >> The CRAN repository has nothing for Fedora 9. >> >> The RPM of R that comes with Fedora 9 is version 2.6.2. Someone >> connected with the Fedora project must have built that. >> >> R 2.7 is no

Re: [R] Getting JRI/rJava to work

2008-05-16 Thread john seers (IFR)
Hello >Trying to run R in a non-existent locale (or at least in a charset iconv() does not understand). >However, your example (with suitably modified paths) does work for me in apparently the same locale, so > I cannot debug it for you. Thank you for trying. I do not understand the non-ex

[R] Problem in Removing Correlated Columns

2008-05-16 Thread Nataraj
Dear all, For removing correlated columns in a data frame,df. I found a code written in R in the page http://cheminfo.informatics.indiana.edu/~rguha/code/R/ of Mr.Rajarshi Guha. The code is # r2test <- function(df, cutoff=0.8) { if (cutoff > 1 || cutoff <= 0) { stop(" 0 <= c

Re: [R] parameters for a function in list format

2008-05-16 Thread Yohan Chalabi
"PDJW" == "Prof. Dr. Joachim Werner" <[EMAIL PROTECTED]> on Fri, 16 May 2008 12:55:32 +0200 PDJW> Hi, PDJW> can anybody help me concerning ther following problem: PDJW> We do simulations with fARMA and use the function armaSim, PDJW> which PDJW> requires the input paramet

Re: [R] How to swap and rearrange rows?

2008-05-16 Thread Gabor Grothendieck
This can be shortened slightly using the builtin month.abb in place of m: ind <- match(substr(rownames(est), 1, 3), month.abb) On Fri, May 16, 2008 at 5:38 AM, Abhijit Dasgupta <[EMAIL PROTECTED]> wrote: > Another possibility: > # Generate the months in sequential order: > m <- months(seq(as.Dat

[R] creating a 2d plan graphic and projecting points in it

2008-05-16 Thread Khaled OUANES
Hello; I want to create a 2 D plan with (123 values) for axis1 and 7 values for axis 2. I then want to make a projection of points with their coordonates in that plan! is that possible and how to proceed? Thanks [[alternative HTML version deleted]] ___

[R] Dimensions of svd V matrix

2008-05-16 Thread Gad Abraham
Hi, I'm trying to do PCA on a n by p wide matrix (n < p), and I'd like to get more principal components than there are rows. However, svd() only returns a V matrix of with n columns (instead of p) unless the argument nv=p is set (prcomp calls svd without setting it). Moreover, the eigenvalues

Re: [R] Fedora 9?

2008-05-16 Thread Peter Dalgaard
Jonathan Baron wrote: > Not to be impatient, but something seems odd. > > The CRAN repository has nothing for Fedora 9. > > The RPM of R that comes with Fedora 9 is version 2.6.2. Someone > connected with the Fedora project must have built that. > > R 2.7 is not in the "updates" for Fedora 9, so n

Re: [R] Font settings in xfig

2008-05-16 Thread Kevin E. Thorpe
Is there a reason you are going through this route to get figures into LaTeX instead of using postscript (or PDF for pdflatex)? Robert wrote: > If I edit the fig file with Xfig, I have to change the value of > "special flag" to "special" and the font to a LaTeX font instead of a > postscript font.

[R] parameters for a function in list format

2008-05-16 Thread Prof. Dr. Joachim Werner
Hi, can anybody help me concerning ther following problem: We do simulations with fARMA and use the function armaSim, which requires the input parameters in list format; this works perfect, however we would like to write the input for several different parameter lists (models) in a loop. I

[R] Fedora 9?

2008-05-16 Thread Jonathan Baron
Not to be impatient, but something seems odd. The CRAN repository has nothing for Fedora 9. The RPM of R that comes with Fedora 9 is version 2.6.2. Someone connected with the Fedora project must have built that. R 2.7 is not in the "updates" for Fedora 9, so nobody connected with Fedora has don

Re: [R] Getting JRI/rJava to work

2008-05-16 Thread Prof Brian Ripley
On Fri, 16 May 2008, john seers (IFR) wrote: Hello All I am trying to get the JRI examples from rJava to work on Windows XP and failing. (And as a more general and connected question is there any review/summary of front-end software for R?) I have installed rJava from the Windows binary suppl

Re: [R] Inconsistent linear model calculations

2008-05-16 Thread Petr PIKAL
Hi Maybe you shall reconsider your decision to avoid manuals especially R-intro.pdf, where you can learn basic operations and data structures. [EMAIL PROTECTED] napsal dne 16.05.2008 09:52:22: > For the record, v6 represented the averages for columns v3-v5 because > I could not quickly find th

[R] Getting JRI/rJava to work

2008-05-16 Thread john seers (IFR)
Hello All I am trying to get the JRI examples from rJava to work on Windows XP and failing. (And as a more general and connected question is there any review/summary of front-end software for R?) I have installed rJava from the Windows binary supplied. I compile and run the example supplied (rte

Re: [R] How to swap and rearrange rows?

2008-05-16 Thread Abhijit Dasgupta
Another possibility: # Generate the months in sequential order: m <- months(seq(as.Date('2000/1/1'), by='month',length=12),abbreviate=T) # Concatenate the data est=rbind(est31,est30,est28) # generate the right order ind <- match(substr(rownames(est),1,3),m) # reorder the rows est <- est[ind,] BTW,

Re: [R] How to swap and rearrange rows?

2008-05-16 Thread Richard . Cotton
> How to swap and rearrange the row so that I will have > Jan-Dec in order? > > est31 > p0 est.alpha est.beta est.rate > Jan 0.8802867 0.7321440 7.241757 0.1380880 > Mar 0.8598566 0.7096567 7.376367 0.1355681 > May 0.6204301 0.8657272 6.036106 0.1656697 > July 0.5032258 0.9928488 4.

[R] How to swap and rearrange rows?

2008-05-16 Thread Roslina Zakaria
Dear R-expert, How to swap and rearrange the row so that I will have Jan-Dec in order? > est31     p0 est.alpha est.beta  est.rate Jan  0.8802867 0.7321440 7.241757 0.1380880 Mar  0.8598566 0.7096567 7.376367 0.1355681 May  0.6204301 0.8657272 6.036106 0.1656697 July 0.5032258 0.9928488 4.0

[R] gamma parameters fitted

2008-05-16 Thread KOITA Lassana - STAC/ACE
Hi R-users, I'm fitting gamma parameters (shape and rate ) by two methods (by direct and and fitdistr of MASS library). I have realized the following code which gives me two results. However, I find that those two outcomes are significantly different. Is there any explanation to this case? Many

Re: [R] Inconsistent linear model calculations

2008-05-16 Thread e-letter
For the record, v6 represented the averages for columns v3-v5 because I could not quickly find the r instruction to calculate the average. Similiarly v7 represents square power of v2. At the time it was quicker than trawling through five or so user manuals for the formula syntax.