Re: [R] howto import .xls and .ods

2008-05-02 Thread Prof Brian Ripley
There is a *manual* on R Data Import/Export, not just an FAQ. This is the first request I have seen for .ods (whatever that is -- please don't assume that a file type is determined by an extension, and we not infrequently get asked about CSV files with extension .xls). On Thu, 1 May 2008,

[R] fCopulae

2008-05-02 Thread hela mzoughi
My problem in a few words is as folow: I used the fCopulae packages because i have 2 series which are already transformed in the uniform domain (the space of the copulas functions) and i estimated with type archmList() from 1 to 22, but i don't know their names:for exemple the type=4 is the

Re: [R] Locale problem with umlauts in factor levels in 2.7.0 (patched) from grid or lattice

2008-05-02 Thread Prof Brian Ripley
The bug is in grid, in some layout calculations which need the string width. There was a 'FIXME' in the sources, and I've fixed this now. (svn r45579/80). Many other grid examples worked so it took me a while to track this down. On Thu, 1 May 2008, Dieter Menne wrote: With 2.7.0 patched

Re: [R] Optimal knot locations for splines

2008-05-02 Thread Dieter Menne
Mike Dugas mikedugas77 at gmail.com writes: Thanks for the help. I tried out the one promising lead, curfit.free.knot, and it doesn't work for linear or quadratic splines. The documentation says it should, but when I specify a linear spline, it returns a cubic. Could you demonstrate this

Re: [R] Error while making R package

2008-05-02 Thread Uwe Ligges
No idea, can you make the package available for us (after R CMD build)? Uwe Ligges Vidhu Choudhary wrote: Hi All, I am trying to make R package using R 2.6.2 And I am getting following error. When I give R CMD check t1\ -- Making package t1 adding build stamp to

[R] Help with apply and split...

2008-05-02 Thread Mike H. Ryu
I'm trying to drop all rows except for the ones with the most recent year. So I split the data frame by NPERMNO and keep just the last record of all groups. datg=t(sapply(split(datgic, datgic$NPERMNO, drop=TRUE), function(x){return( x[nrow(x),] )})) I get something like this... GVKEY

Re: [R] How to plot wind direction and strength field

2008-05-02 Thread Jenny Barnes
Thanks Greg, I'll give it a whirl and let you know how it goes (although it might not be till after the bank holiday weekend now sorry for delay!) Thanks for replying and spending time on this problem. All the best, Jenny On Thu, 1 May 2008, Greg Snow wrote: Does the following do what

[R] removing rows from matrix

2008-05-02 Thread Monna Nygård
Hi, I have a problem regarding matrix handeling. I am working with a serie of matrixes containing several columns. Now I would like to delete those rows of the matrixes,that in one of the columns contain values less than 50 or greater than 1000. How would this be possible, I have tried to

Re: [R] Help with apply and split...

2008-05-02 Thread Richard . Cotton
datg=t(sapply(split(datgic, datgic$NPERMNO, drop=TRUE), function(x){return( x[nrow(x),] )})) I get something like this... GVKEY NPERMNO GIC year 10001 12994 10001 55102010 2007 10002 19049 10002 40101015 2007 10009 16739 10009 40101010 1999 Has this been made

[R] to cairo or not to cairo

2008-05-02 Thread Arrrrr
I have installed R 2.7.0 in a Linux x64 computer and everything seems to be ok but, when I am trying to plot something, say plot(x=1:10), I am getting the following message: unable to load shared library '/usr/local/lib/R/modules//R_X11.so ...(and libpangocairo-1.0.so.0, as well)... If I use

Re: [R] to extract particular date/data

2008-05-02 Thread Richard . Cotton
If I have this daily rainfall data, how do call a particular day? Year,Month,Day,Amount 1900,12,22,1.3 1900,12,23,0 1900,12,24,0 1900,12,25,0 1900,12,26,0 1900,12,27,0 1900,12,28,0 1900,12,29,4.8 1900,12,30,0.3 1900,12,31,0.5 1901,1,1,0 1901,1,2,3 1901,1,3,0 1901,1,4,0.5

Re: [R] Lattice book

2008-05-02 Thread Michael Kubovy
I too have been studying the book and it is indeed outstanding. For my purposes the only topic missing is the straightforward drawing of error bars and bands, for which I've been using Hmisc::xYplot (where error bands seem to be broken for R) or gplots::barplot2. _

[R] Cant resolve Error Message

2008-05-02 Thread hoogeebear
Hi, Im having trouble creating the following graph. Here is my code: library(plotrix) library(prettyR) female_improvement -read.table(C://project/graphs/gender/breakdown/gender-improvement/female-improvement.csv, sep=,, header=TRUE)

Re: [R] Lattice book

2008-05-02 Thread Frank E Harrell Jr
Michael Kubovy wrote: I too have been studying the book and it is indeed outstanding. For my purposes the only topic missing is the straightforward drawing of error bars and bands, for which I've been using Hmisc::xYplot (where error bands seem to be broken for R) or gplots::barplot2. If

Re: [R] removing rows from matrix

2008-05-02 Thread Richard . Cotton
Hi, I have a problem regarding matrix handeling. I am working with a serie of matrixes containing several columns. Now I would like to delete those rows of the matrixes,that in one of the columns contain values less than 50 or greater than 1000. Try this: m - matrix(runif(150, 0, 1050),

[R] Error in downViewport.vpPath(vpPathDirect(name)

2008-05-02 Thread Andrewjohnclose
Hi, I am having trouble plotting a series of dendrograms using lattice and grid code as found in Paul Murrells book R Graphics. This is the error message I recieve: Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) : Viewport 'plot1.panel.1.1.off.vp' was not

Re: [R] Cant resolve Error Message

2008-05-02 Thread jim holtman
It appears that you have a problem in your data. Here is just the rbind in the call: rbind(rep(length(female_improvement$gender),2),freq(female_improvement$reason)[[1]]) Info entered is all relevant Room for improvement Room for Improvement [1,] 20

Re: [R] to extract particular date/data

2008-05-02 Thread Gabor Grothendieck
Have a look at the zoo package which has three vignettes and R News 4/1. On Fri, May 2, 2008 at 12:27 AM, Roslina Zakaria [EMAIL PROTECTED] wrote: Hi R-expert, If I have this daily rainfall data, how do call a particular day? Year,Month,Day,Amount 1900,12,22,1.3 1900,12,23,0 1900,12,24,0

[R] Errors bar in barchart

2008-05-02 Thread Ronaldo Reis Junior
Hi, I user barplot2 to make a plot bar with errors bars. In old times I needed to use a sequence of segments commands to make this. Now I try to make the same but using lattice. Is possible to use barplot2 in barchart function? If not, what is the simplest way to put errors bar in barchart? I

[R] stdFit

2008-05-02 Thread AGershon
Hi, I am using the stdFit function (fGarch package) to get estimates for a fitted location, scale, and degrees of freedom of a dataset. I have no errors with the code however the estimates are not identical to the estimates I am getting when using SAS and MatLab (both give me the same estimates).

Re: [R] Data manipulation for random intercept GLMM

2008-05-02 Thread Ben Bolker
Giovanni Petris GPetris at uark.edu writes: ## Example: Ratings of prime minister (Agresti, Table 12.1, p.494) rating - matrix(c(794, 86, 150, 570), 2, 2) dimnames(rating) - list(First = c(approve, disapprove), + Second = c(approve, disapprove)) rating

[R] xYplot error bands not working, was: Re: Lattice book

2008-05-02 Thread Michael Kubovy
On R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: C/C/en_US/C/C/C attached base packages: [1] splines grid grDevices datasets graphics stats utils methods base other attached packages: [1] Design_2.1-1 survival_2.34-1 Hmisc_3.4-3

[R] points size in plots

2008-05-02 Thread Irene Mantzouni
Dear list, I would like to produce a plot of variables where the size of the points will be indicative of their standard errors. How is that possible? Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org mailing

Re: [R] error in using by + median

2008-05-02 Thread Prof Brian Ripley
The help says A data frame is split by row into data frames subsetted by the values of one or more factors, and function 'FUN' is applied to each subset in turn. You attempting to apply median() to a data frame -- it does no work, unlike mean() On Fri, 2 May 2008, vito muggeo

[R] Accesing data frame members from within functions

2008-05-02 Thread David Schwab
I am writing a simple R program to execute a t-test repeatedly on data contained in a data frame. My data looks like this: Category Value1 Value2 1 .5 .8 1 .3

[R] error in using by + median

2008-05-02 Thread vito muggeo
dear all, Could anyone explain me the behaviour of median() within by()? (I am running R.2.7.0) thanks, vito H-cbind(rep(0:1,l=20),matrix(rnorm(20*2),20,2)) by(H[,-1],H[,1],mean) INDICES: 0 V1 V2 -0.2101069 0.2954377

[R] isotonic/ordered heterogeneity tests

2008-05-02 Thread Ben Bolker
dear R-help: one of my students is struggling to test an ordered alternative hypothesis on a set of groups (e.g., mu_a = mu_b = mu_c). There has been some literature on this topic -- a lot of this goes back to Bartholomew (1961); Gaines and Rice (see refs below) are the ones who've

Re: [R] Accesing data frame members from within functions

2008-05-02 Thread Henrique Dallazuanna
Try: foo - function(data, ...) { res - unlist(lapply(split(data, data$Category), function(.x)t.test(.x$Value1, .x$Value2)$p.value)) test - merge(data, as.data.frame(res), by.x=Category, by.y = 0) return(test) } x - data.frame(Category = rep(1:15, each = 10), Value1 = rnorm(150), Value2 =

Re: [R] A plot of factor data?

2008-05-02 Thread Sang Chul Choi
Thank you, Bert! I have a question one more. I have found out that mosaic function of vcd package is more interesting since I want to color different cells. The question is how to make x axis label to be vertical not horizontal. I tried las or some other options in par but I could not

Re: [R] need help on ICC for a questionnaire

2008-05-02 Thread Smita Pakhale
Dear All, I am trying to get ICC (Intra class correlation coefficient) for a questionnaire. The questionnaire has about 25 questions and was administered to 50 subjects on two occasions. I want to calculate the reproducibility of the questionnaire administered to the same group of subjects on two

[R] How to parse XML

2008-05-02 Thread Bos, Roger
I would like to learn how to parse a mixed text/xml document I downloaded from the sec.gov website (see example below). I would like to parse this to get the value for each xml tag and then access it within R, but I don't know much about xml so I don't even know where to start debugging the

[R] mosaic plot of vcd package does not stretch with 2-dimension?

2008-05-02 Thread Sang Chul Choi
Hi, I like mosaic function of vcd package. I have played around it. I have found out that mosaic plot data table is 2-dimension does not stretch when you enlarge a mosaic plot. It is okay when data table is 3 or more dimension. The first one is of 3-dimension table case, and the second

Re: [R] efficiency profiling?

2008-05-02 Thread Mike Prager
esmail bonakdarian [EMAIL PROTECTED] wrote: Yes, I have been reading the list, the amount of messages per day is simply amazing, I can hardly keep up. Do most of you read this on the web or get it as digest? I am getting them as individual e-mails (thank god for filters) ... :-) I used

Re: [R] Accesing data frame members from within functions

2008-05-02 Thread Jorge Ivan Velez
Hi David, Try this: # Data set set.seed(123) Category=as.factor(rep(1:15,each=10)) Value1 = rnorm(150) Value2= rnorm(150) yourdata=data.frame(Category,Value1,Value2) # Global function TTEST=function(mydata){ # Internal function tt=function(x,y) t.test(x,y)$p.value # p-values for(i in

Re: [R] How to parse XML

2008-05-02 Thread Martin Morgan
Hi Roger -- Bos, Roger [EMAIL PROTECTED] writes: I would like to learn how to parse a mixed text/xml document I downloaded from the sec.gov website (see example below). I would like I'm not sure of a more robust way to extract the XML, but from inspection I wrote ftp -

Re: [R] A plot of factor data?

2008-05-02 Thread Bert Gunter
This depends entirely one what the version in vcd allows you to do. Since I don't use it, I have no idea. Read the docs there, or perhaps someone else familiar with it can help. -- Bert -Original Message- From: Sang Chul Choi [mailto:[EMAIL PROTECTED] Sent: Friday, May 02, 2008 8:06 AM

Re: [R] mosaic plot of vcd package does not stretch with 2-dimension?

2008-05-02 Thread Achim Zeileis
On Fri, 2 May 2008, Sang Chul Choi wrote: Hi, I like mosaic function of vcd package. I have played around it. I have found out that mosaic plot data table is 2-dimension does not stretch when you enlarge a mosaic plot. It is okay when data table is 3 or more dimension. The first one is of

Re: [R] mosaic plot of vcd package does not stretch with 2-dimension?

2008-05-02 Thread Dieter Menne
Sang Chul Choi choi at biology.rutgers.edu writes: I like mosaic function of vcd package. I have played around it. I have found out that mosaic plot data table is 2-dimension does not stretch when you enlarge a mosaic plot. It is okay when data table is 3 or more dimension. The first

[R] Transform values from one column into column names of new dataframe

2008-05-02 Thread Matt
Hi, I have a question about reformatting data. It looks like it should be simple, but I've been working at it for awhile now and it's about time I ask for help. My data look like this: ITEM VALUE STEP item1 A first item2 C first item2 D second item1 A second

Re: [R] Transform values from one column into column names of new dataframe

2008-05-02 Thread hadley wickham
On Fri, May 2, 2008 at 11:05 AM, Matt [EMAIL PROTECTED] wrote: Hi, I have a question about reformatting data. It looks like it should be simple, but I've been working at it for awhile now and it's about time I ask for help. My data look like this: ITEM VALUE STEP item1 A

[R] wrong path to helpfiles

2008-05-02 Thread Michael Gerisch
hi, since lately i receive an error message when prompting ?help: help will not be available. path not found. It is not possible to get help for any command. I don`t know why but it seems that i need to tell R the right path for the helpfiles. How can i do that? thanks a lot cheers michael

Re: [R] Transform values from one column into column names of new dataframe

2008-05-02 Thread Henrique Dallazuanna
Try this also: noquote(with(x, tapply(VALUE, list(ITEM, STEP), paste))) On Fri, May 2, 2008 at 1:05 PM, Matt [EMAIL PROTECTED] wrote: Hi, I have a question about reformatting data. It looks like it should be simple, but I've been working at it for awhile now and it's about time I ask for

Re: [R] mosaic plot of vcd package does not stretch with 2-dimension?

2008-05-02 Thread Sang Chul Choi
Thank you very much! Sang Chul On May 2, 2008, at 12:06 PM, Dieter Menne wrote: Sang Chul Choi choi at biology.rutgers.edu writes: I like mosaic function of vcd package. I have played around it. I have found out that mosaic plot data table is 2-dimension does not stretch when you enlarge a

[R] A horizontal or vertical line draw on mosaic plot?

2008-05-02 Thread Sang Chul Choi
Hi, I want to have a horizontal line on a mosaic plot with vcd package. This would give me an idea where is 0.5 proportion in a cell. Using mosaicplot function of graphics package, I can draw a line using abline. But, with mosaic function of vcd package, I have tried to use abline

[R] png misbehaving with levelplot when inside a loop

2008-05-02 Thread David
I want to use spplot inside a loop to itteratively produce png files. for (i in 1:5){ png(file=paste(myPlot,i,.png,sep=),bg=white,height=500,width=500) library(lattice) trellis.par.set(sp.theme()) # sets bpy.colors() ramp data(meuse) coordinates(meuse) - ~x+y l2 =

Re: [R] Data manipulation for random intercept GLMM

2008-05-02 Thread Greg Snow
Is this what you are trying to do? tt - matrix( 5:10, ncol=2 ) df - as.data.frame.table(tt) df2 - df[ rep( 1:nrow(df), df$Freq ), ] And is that elegant enough? -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111

[R] partial residuals

2008-05-02 Thread Irene Mantzouni
Dear all, I am trying to estimate partial residuals for the multiple regression lm model: a.lm=lm(y~x1+x2) I use the function residuals(a.lm, type=partial) However, the results are much different when I use the manual method to get partial residuals for x2 (or for x1):

Re: [R] A horizontal or vertical line draw on mosaic plot?

2008-05-02 Thread Dieter Menne
Sang Chul Choi Choi at biology.rutgers.edu writes: I want to have a horizontal line on a mosaic plot with vcd package. This would give me an idea where is 0.5 proportion in a cell. Using mosaicplot function of graphics package, I can draw a line using abline. But, with mosaic function

[R] Post-hoc repeated measures ANOVA

2008-05-02 Thread Snorre . Bakke
Hello. I am looking for a multiple comparisons test to follow up a repeated mesures ANOVA i have conducted. Im not an expert in statistics or in R but i have managed to produce this: START fit5.lme-lme(logfaa~segment,random=~+1|fish) anova(fit5.lme) numDF denDF F-value

[R] my first post to the list

2008-05-02 Thread Rodrigo Briceño
Hello R-listers! My first post to the list is a very simple one for those who use the software continuosly. I am trying to understand the fixed-x resampling and random-x-resampling method proposed by Fox about Bootstrapping. The doubt that I have is on the side of the model run in one of the

[R] expand.grid using a repeated vector as a parameter

2008-05-02 Thread Simon Parker
Hello. I'm trying to do this (not necessarily 0:1) : expand.grid ( 0:1, 0:1, 0:1, 0:1, 0:1) etc..etc. but I want to have control over how many 0:1 are included. Any ideas please ? Thankyou. Simon Parker Imperial College - A Smarter Email.

[R] Loading large files in R

2008-05-02 Thread ajoyner
Hello, I'm attempting to load a ~110 MB text file with ~500,000 rows and 200 columns using read.table . R hangs and seems to give up. Can anyone tell me an efficient way to load a file of this size? Thank you! Alex -- View this message in context:

[R] WGEE

2008-05-02 Thread Maria Salomé Esteves Cabral
Hi! I am using geeglm (in geepack) and I need to use weights. There is in R a function that calculates the weights like in SAS PROC GENMOD . Any help would be sincerely appreciated. Thanks Salomé __ R-help@r-project.org mailing list

Re: [R] expand.grid using a repeated vector as a parameter

2008-05-02 Thread Prof Brian Ripley
?do.call On Fri, 2 May 2008, Simon Parker wrote: Hello. I'm trying to do this (not necessarily 0:1) : expand.grid ( 0:1, 0:1, 0:1, 0:1, 0:1) etc..etc. but I want to have control over how many 0:1 are included. Any ideas please ? Thankyou. Simon Parker Imperial College

Re: [R] Loading large files in R

2008-05-02 Thread Duncan Murdoch
On 5/2/2008 2:13 PM, ajoyner wrote: Hello, I'm attempting to load a ~110 MB text file with ~500,000 rows and 200 columns using read.table . R hangs and seems to give up. Can anyone tell me an efficient way to load a file of this size? It will help a lot if you specify the column types (using

Re: [R] Loading large files in R

2008-05-02 Thread Jorge Ivan Velez
Hi Alex, Perhaps http://www.nabble.com/How-to-read-HUGE-data-sets--td15729830.html#a15746400can helps. HTH, Jorge On Fri, May 2, 2008 at 2:13 PM, ajoyner [EMAIL PROTECTED] wrote: Hello, I'm attempting to load a ~110 MB text file with ~500,000 rows and 200 columns using read.table . R

[R] Extract lags from a formula

2008-05-02 Thread Kerpel, John
Hi folks! How do I extract lags from a formula? An example: mod.eq-formula(x~lag(x,-1)+lag(x,-2)) mod.eq x ~ lag(x, -1) + lag(x, -2) mod.eq[1] ~() mod.eq[2] x() mod.eq[3] lag(x, -1) + lag(x, -2)() I'm trying to extract the lags into a vector that would be simply [1,2]. How

Re: [R] expand.grid using a repeated vector as a parameter

2008-05-02 Thread Greg Snow
Try: tmp - rep( list( 0:1 ), 5 ) out - do.call(expand.grid, tmp) Then change the 5 to whatever you want. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL

Re: [R] Extract lags from a formula

2008-05-02 Thread hadley wickham
On Fri, May 2, 2008 at 1:35 PM, Kerpel, John [EMAIL PROTECTED] wrote: Hi folks! How do I extract lags from a formula? An example: mod.eq-formula(x~lag(x,-1)+lag(x,-2)) mod.eq x ~ lag(x, -1) + lag(x, -2) mod.eq[1] ~() mod.eq[2] x() mod.eq[3] lag(x, -1) +

[R] [R-pkgs] New package: profr 0.1 - an alternative display for profiling information

2008-05-02 Thread hadley wickham
profr 0.1 profr provides an alternative data structure and display for profiling data. It still uses Rprof() to collect the data, but outputs a data.frame which should be easier to manipulate. It also implements a novel visualisation which allows you to see the

Re: [R] re moving rows from matrix

2008-05-02 Thread Yasir Kaheil
you could do it using apply like the first two replies mentioned or you could just use the index way for example: (assuming your matrix name is ym and the values are greater than 25 and less than 50 and the column is column 3).. if you mean any column use the first two replies.

[R] Fwd: my first post to the list

2008-05-02 Thread Rodrigo Briceño
Hello R-listers! My first post to the list is a very simple one for those who use the software continuosly. I am trying to understand the fixed-x resampling and random-x-resampling method proposed by Fox about Bootstrapping. The doubt that I have is on the side of the model run in one of the

Re: [R] Loading large files in R

2008-05-02 Thread Duncan Murdoch
On 5/2/2008 2:52 PM, Alex Joyner wrote: Duncan, Thank you for your response. I actually am using colClasses, but the first column is a character column, and the rest are numeric. Is there any way to specify that all columns are numeric except for the first one? I couldn't find this in the

[R] cor.test like cor?

2008-05-02 Thread Sang Chul Choi
Hi, Is there a simple way to do correlation coefficient tests with cor.test like I would do with cor function? I have a data frame where each column is a list. y - data.frame(a=sample(30, 20), b=sample(30, 20), c=sample(30,20)) cor(y)

Re: [R] How to parse XML

2008-05-02 Thread Bos, Roger
Martin, I can't thank you enough for taking the time to help and providing the detailed examples of how to get started. Now I know exactly how to proceed. Thanks again, Roger -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Friday, May 02, 2008 12:02 PM To:

[R] plot size vs. text size

2008-05-02 Thread Chang Liu
Hello: I am using plot() in rpart, making a decision tree plot. I use plot() first, then text() followed, but I think due to the figure vs. text size, the bottom of the text always gets cut off. I can only “see” the text of the bottom of the tree if I make the font size REALLY small. I

[R] GLMM and data manipulation (2nd try)

2008-05-02 Thread Giovanni Petris
Hello, I posted a question yesterday but I got no replies, so I'll try to reformulate it in a more concise way. I have the following data, summarizing approval ratings on two different surveys for a random sample of 1600 individuals: ## Example: Ratings of prime minister (Agresti, Table

Re: [R] A horizontal or vertical line draw on mosaic plot?

2008-05-02 Thread Sang Chul Choi
Thank you, Dieter, very much for your answer. I'd rather avoid using mosaic. I think that I need to read more about vcd manual you mentioned. One quick question? Is it possible to color each cells with all different colors with mosaicplot? I have used mosaic function to do coloring each

[R] Errors using nlme's gls with autocorrelation

2008-05-02 Thread zerfetzen
Hi, I am trying out a generalized least squares method of forecasting that corrects for autocorrelation. I downloaded daily stock data from Yahoo Finance, and am trying to predict Close (n=7903). I have learned to use date functions to extract indicator variables for Monday - Friday (and Friday

[R] adjusting plot vs font size in a plot

2008-05-02 Thread Karen Liu
Hello: I am using plot() in rpart, making a decision tree plot. I use plot() first, then text() followed, but I think due to the figure vs. text size, the bottom of the text always gets cut off. I can only see the text of the bottom of the tree if I make the font size REALLY small. I

[R] .Rprofile is being executed twice

2008-05-02 Thread Dan Tenenbaum
Hi, After updating to R 2.7, my .Rprofile executes twice on startup. I confirmed this by putting in the following line: print(starting .Rprofile...) When I start R, I see: [1] starting .Rprofile... [1] starting .Rprofile... This seems like the obverse of the following FAQ:

Re: [R] cor.test like cor?

2008-05-02 Thread Henrique Dallazuanna
Try this: y - data.frame(a=sample(30, 20), b=sample(30, 20), c=sample(30,20)) x - diag(1, length(names(y)) cors - combn(names(y), 2, FUN = function(x)cor.test(y[,x[1]], y[,x[2]])$p.value) x[lower.tri(x)] - cors x[upper.tri(x)] - cors On 5/2/08, Sang Chul Choi [EMAIL PROTECTED]

Re: [R] Errors using nlme's gls with autocorrelation

2008-05-02 Thread Andrew Robinson
You're running out of RAM. Your options are 1) run code on a machine with more RAM 2) try the model on fewer observations 3) try a simpler model. Andrew On Fri, May 02, 2008 at 12:37:15PM -0700, zerfetzen wrote: Hi, I am trying out a generalized least squares method of forecasting that

Re: [R] GLMM and data manipulation (2nd try)

2008-05-02 Thread Andrew Robinson
On Fri, May 02, 2008 at 03:06:31PM -0500, Giovanni Petris wrote: Hello, I posted a question yesterday but I got no replies, so I'll try to reformulate it in a more concise way. I have the following data, summarizing approval ratings on two different surveys for a random sample of 1600

Re: [R] GLMM and data manipulation (2nd try)

2008-05-02 Thread Andrew Robinson
On Sat, May 03, 2008 at 06:43:22AM +1000, Andrew Robinson wrote: On Fri, May 02, 2008 at 03:06:31PM -0500, Giovanni Petris wrote: Hello, I posted a question yesterday but I got no replies, so I'll try to reformulate it in a more concise way. I have the following data,

Re: [R] points size in plots

2008-05-02 Thread Ruben Roa Ureta
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Irene Mantzouni Sent: Friday, May 02, 2008 7:52 AM To: [EMAIL PROTECTED] Subject: [R] points size in plots Dear list, I would like to produce a plot of variables where the size of the points will

Re: [R] GLMM and data manipulation (2nd try)

2008-05-02 Thread Giovanni Petris
Andrew, Thank you for your reply. In fact, I had a way of unrolling the table but I think yours look much nicer - much readable to me. Below is what I did, but I was afraid I would scare my students away from R! approval - factor(c(Approve, Disapprove), +levels =

Re: [R] Aggregate() questions

2008-05-02 Thread Henrique Dallazuanna
You need seet the FUN argument: X - with( FDP0D, ave( IAC, list( Key), FUN = mean)) On 5/1/08, Chip Barnaby [EMAIL PROTECTED] wrote: Henrique, thanks for the response. As a new user, I was unaware of with() and ave(), those are both very helpful. However, I don't think your method is quite

[R] data transformation

2008-05-02 Thread Christian Hof
Dear all, how can I, with R, transform a presence-absence (0/1) matrix of species occurrences into a presence-only table (3 columns) with the names of the species (1st column), the lat information of the sites (2nd column) and the lon information of the sites (3rd column), as given in the

[R] barplot with log base 2 scale or shift the x-axis

2008-05-02 Thread Summer Nitely
Hi, I have data that is on a log base 2 scale. It goes from negative factors of 2 to positive ones. I am using barplot. However, I don't want the data centered at 0 - I want the min of the yaxis to be just below the lowest value in the data. The plots are kind of deceptive switching between

Re: [R] data transformation

2008-05-02 Thread Christos Hatzis
Christian, You need to use reshape to convert to the 'long' format. Check the help page ?reshape for details. dat - read.table('clipboard', header=TRUE) dat site lat lon spec1 spec2 spec3 spec4 1 site1 10 11 1 0 1 0 2 site2 20 21 1 1 1 0 3 site3 30 31

Re: [R] data transformation

2008-05-02 Thread Kingsford Jones
Hi Christian, Here's a way using the reshape package: dfr site lat lon spec1 spec2 spec3 spec4 1 site1 10 11 1 0 1 0 2 site2 20 21 1 1 1 0 3 site3 30 31 0 1 1 1 library(reshape) dfr - melt(dfr[, -1], id=1:2, variable_name='species')

Re: [R] .Rprofile is being executed twice

2008-05-02 Thread Duncan Murdoch
On 02/05/2008 4:24 PM, Dan Tenenbaum wrote: Hi, After updating to R 2.7, my .Rprofile executes twice on startup. I confirmed this by putting in the following line: print(starting .Rprofile...) When I start R, I see: [1] starting .Rprofile... [1] starting .Rprofile... This seems like the

Re: [R] data transformation

2008-05-02 Thread Henrique Dallazuanna
Try this: newx - with(x, cbind(stack(x, select = grep(spec, names(x))), lat, lon)) newx[newx$values 0, -1] On 5/2/08, Christian Hof [EMAIL PROTECTED] wrote: Dear all, how can I, with R, transform a presence-absence (0/1) matrix of species occurrences into a presence-only table (3 columns)

Re: [R] Lattice book

2008-05-02 Thread Deepayan Sarkar
On 5/2/08, Michael Kubovy [EMAIL PROTECTED] wrote: I too have been studying the book and it is indeed outstanding. For my purposes the only topic missing is the straightforward drawing of error bars and bands, for which I've been using Hmisc::xYplot (where error bands seem to be broken for R)

Re: [R] Errors bar in barchart

2008-05-02 Thread Deepayan Sarkar
On 5/2/08, Ronaldo Reis Junior [EMAIL PROTECTED] wrote: Hi, I user barplot2 to make a plot bar with errors bars. In old times I needed to use a sequence of segments commands to make this. Now I try to make the same but using lattice. Is possible to use barplot2 in barchart function?

Re: [R] png misbehaving with levelplot when inside a loop

2008-05-02 Thread Paul Hiemstra
Hi David, Putting a print statement around your spplot command solves your problem. This behaviour is common for trellis graphics plot methods (such as spplot). This is the command including print: print(spplot(meuse, c(ffreq), sp.layout=list(l2,l3,l4,l5),col.regions=black,pch=c(1,2,3),

[R] Phil Spector's book

2008-05-02 Thread markleeds
Since we're on the topic of book reviews, I just received Phil Spector's new R book called Data Manipulation with R and it is also quite a nice book. I haven't gone through it all and I won't give a detailed review but I have gotten a lot out of the first 100 pages that I have read. Note

[R] interactive rotatable 3d scatterplot

2008-05-02 Thread Mark Kimpel
I would like to create a 3d scatterplot that is interactive in the sense that I can spin it on its axes to better visualize some PCA results I have. What are the options in R? I've looked at RGL and perhaps it will suffice but it wasn't apparent from the documentation I found. Any demo scripts

Re: [R] Summarize data for MCA (FactoMineR)

2008-05-02 Thread Nelson Castillo
On Sun, Apr 27, 2008 at 10:10 AM, David Winsemius [EMAIL PROTECTED] wrote: Nelson Castillo [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: (cut) That is, from: x weight var1 var2 1 1AB 2 1AB 3 2AB 4 1AB 5

[R] Excluding/removing row and column names on text output files

2008-05-02 Thread Stropharia
Dear R users, I've had no joy finding a solution to this online or in any of my R books. Many thanks in advance for any help you can give. I'm seeking to output a data frame (or matrix - it doesn't matter which for my purposes) to a .txt file, but omit any row or column names. The data frame

Re: [R] Excluding/removing row and column names on text output files

2008-05-02 Thread Yasir Kaheil
try: write.table(x, file=/Users/Desktop/Data.txt, row.names= FALSE, col.names= FALSE, sep=, append=TRUE) this should do it. If you don't want to append, just turn that opion off. Stropharia wrote: Dear R users, I've had no joy finding a solution to this online or in any of my R books.

Re: [R] interactive rotatable 3d scatterplot

2008-05-02 Thread Richard Rowe
Hi Mark, Try using ggobi via Rggobi. ggobi is aimed at higher dimension multivariate data but it does a very useful service in 3-D projections, do a manually controlled tour ... I've used this to tweak PCA results and find fine structure, Richard Mark Kimpel wrote: I would like to create

Re: [R] Excluding/removing row and column names on text output files

2008-05-02 Thread Bob Flagg
Steve, I think you can use: write.table(x, file = /Users/Desktop/Data.txt, sep = , append=T, row.names = F, col.names = F) I used that for the data PERSHRUB DISTX AGE RODENTSP 166 2100 501 290 914 201 375 1676 341 475 243

Re: [R] Extract lags from a formula

2008-05-02 Thread Gabor Grothendieck
If x is a zoo object note that zoo (and therefore dyn) allows the more compact form lag(x, -(1:2)) so if we write: mod.eq - x ~ lag(x, -(1:2)) then mod.eq[[3]][[3]] is the vector -(1:2) or if you like you can define Lag - function(x, k) lag(x, -k) in which case you can write it: mod.eq - x ~

[R] help with subset

2008-05-02 Thread partofy
Dear list: I have a problem using the subset function: dat- data.frame(treatment=c(A, B, A, C, C, D, A, D, C, D), response=rnorm(10)) I am interested in treatments A, B and D vec- c(A, B, D) But I can only obtain what I want with: subset(dat, treatment==A | treatment==B | treatment==D) What's

Re: [R] help with subset

2008-05-02 Thread Christos Hatzis
Try %in% subset(dat, treatment %in% vec) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, May 02, 2008 11:41 PM To: r-help@r-project.org Subject: [R] help with subset Dear list: I have a problem using the

Re: [R] help with subset

2008-05-02 Thread Jim Porzak
Justin, try subset(dat, treatment %in% vec) I guess thats what you want. On Fri, May 2, 2008 at 8:40 PM, [EMAIL PROTECTED] wrote: Dear list: I have a problem using the subset function: dat- data.frame(treatment=c(A, B, A, C, C, D, A, D, C, D), response=rnorm(10)) I am interested in

Re: [R] help with subset

2008-05-02 Thread partofy
Thank you Christos and Jim: That is precisely what I was after. On Sat, 3 May 2008 00:01:58 -0400, Christos Hatzis [EMAIL PROTECTED] said: Try %in% subset(dat, treatment %in% vec) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL

Re: [R] interactive rotatable 3d scatterplot

2008-05-02 Thread Yasir Kaheil
#Install library rgl #here is the is the function: rgl.plot3d-function(z, x, y, cols=red,axes=T,new=T) {xr-range(x) x01-(x-xr[1])/(xr[2]-xr[1]) yr-range(y) y01-(y-yr[1])/(yr[2]-yr[1]) zr-range(z) z01-(z-zr[1])/(zr[2]-zr[1]) if(new) rgl.clear() if(axes) {xlab-pretty(x)

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