Re: [R] extract worksheet names from an Excel file

2011-06-24 Thread Shi, Tao
Thanks, Gabor!  That's really helpful! ...Tao - Original Message - > From: Gabor Grothendieck > To: "Shi, Tao" > Cc: "r-help@r-project.org" > Sent: Friday, June 24, 2011 5:02 AM > Subject: Re: [R] extract worksheet names from an Excel file > > On Fri, Jun 24, 2011 at 12:41 AM, Shi,

[R] On .. glibc detected home/sguha/lib64/R/bin/exec/R: realloc(): invalid next size: 0x000000000209e210 ***

2011-06-24 Thread Saptarshi Guha
Hello, I'm trying to use rjson to parse a JSON object. The object can be found here http://pastebin.com/np0s5hgM (you'll probably need to add quotes around the content) fromJSON returns the error glibc detected home/sguha/lib64/R/bin/exec/R: realloc(): invalid next size: 0x0209e210 **

Re: [R] SQL Changing Data Type

2011-06-24 Thread Gabor Grothendieck
On Fri, Jun 24, 2011 at 4:12 PM, GL wrote: > Passing in two dates to a sql statement (sqldf). Is returning a factor. Tried > setting back to a Date via as.Date, but get an error the error: character > string is not in a standard unambiguous format. Any thoughts appreciated. > > Code/Results listed

Re: [R] What does class "call" mean? How do I make class "formula" into a "call"?

2011-06-24 Thread Bert Gunter
Well, this is kind of complicated. The first place you should go for help is not this list, but the R docs. Specfically ?call. This assumes familiarity with R's (S3) class system and language structure, however.. For this, I suggest ?UseMethod and consulting the R Language Definition Manual. Perh

[R] rle with NA values?

2011-06-24 Thread Justin Haynes
Happy Friday! Using this function: fixSeq <- function(df) { shift1 <- function(x) c(1, x[-length(x)]) df$state_shift<-df$state df.rle<-rle(df$state_shift) repeat { shifted.sf<-shift1(df.rle$values) change <- df.rle$values >= 4 & shifted.sf >= 4 & shifted.sf != df.rle$values if

[R] What does class "call" mean? How do I make class "formula" into a "call"?

2011-06-24 Thread Rita Carreira
I have a list called "tabs" that I would like to have the same structure as my list "eqSystem." The two look like they have the same format but they are different because when I look at their attributes, class(eqSystem[[1]]) is "call" but class(tabs[[1]]) is "formula". I want to have class(tabs

[R] reading data from password protected url

2011-06-24 Thread Steven R Corsi
I am trying to retrieve data from a password protected database. I have login information and the proper url. When I make a request to the url, I get back some info, but need to read the "hidden header" information that has JSESSIONID and NCES_JSESSIONID. They need to be used to set cookies bef

Re: [R] SQL Changing Data Type

2011-06-24 Thread Dennis Murphy
Hi: str() probably would have been more informative than summary(), but if the date is a factor, perhaps this will help: as.Date(as.character(Date), format = '%Y-%m-%d') Including the format argument is usually safer than letting the function try to figure it out on its own. Neglecting to includ

[R] Installation of bigmemory fails

2011-06-24 Thread Forafo San
Hello All, I tried to intall the bigmemory package from a CRAN mirror site and received the following output while installing. Any idea what's going on and how to fix it? The system details are provided below. - begin error messages --- * installing *source*

Re: [R] Subsetting data systematically

2011-06-24 Thread gibberish
Thanks! From: Peter Alspach-2 [via R] [mailto:ml-node+3618799-1094957657-247...@n4.nabble.com] Sent: Wednesday, June 22, 2011 9:27 PM To: Bendik, Nathan Subject: Re: Subsetting data systematically Tena ko

Re: [R] mgcv:gamm: predict to reflect random s() effects?

2011-06-24 Thread Szumiloski, John
Thanks Simon, that was quite enlightening, as I did somewhat misunderstand how gamm works. The bs='re' argument to s() is something I had not seen before. And the idea of pooling any random effects over the entire population does seem safer than trying to estimate variabilities etc from bare

[R] SQL Changing Data Type

2011-06-24 Thread GL
Passing in two dates to a sql statement (sqldf). Is returning a factor. Tried setting back to a Date via as.Date, but get an error the error: character string is not in a standard unambiguous format. Any thoughts appreciated. Code/Results listed below: > summary(df.possible.combos) Date

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Martin Morgan
On 06/24/2011 11:12 AM, Dennis Murphy wrote: Hi: Not much different from Peter's approach, but here's another try: v<- c(1, 2, 6, 5) w<- matrix(c(1, 4, 3, 5, 8, 10), ncol = 2, byrow = TRUE) w [,1] [,2] [1,]14 [2,]35 [3,]8 10 f<- function(x) v[which(v>= x[1]& v<=

Re: [R] Kalman Filter Estimation

2011-06-24 Thread Dennis Murphy
Hi: Here are a couple of places to start: http://www.jstatsoft.org/v39/i02/paper http://stats.stackexchange.com/questions/4296/r-code-for-time-series-forecasting-using-kalman-filter HTH, Dennis On Fri, Jun 24, 2011 at 6:24 AM, Patrick wrote: > Dear R users, > > I am a new R user and not very e

Re: [R] strange date problem - May 3, 1992 is NA

2011-06-24 Thread Brian Diggs
On 6/22/2011 2:28 PM, Alexander Shenkin wrote: On 6/22/2011 4:09 PM, Brian Diggs wrote: On 6/22/2011 1:37 PM, Alexander Shenkin wrote: On 6/22/2011 3:34 PM, Brian Diggs wrote: On 6/22/2011 12:09 PM, Luke Miller wrote: For what it's worth, I cannot reproduce this problem under a nearly identic

[R] try to generate graph for each element of my list

2011-06-24 Thread n.via...@libero.it
Dear all, I have the following problem. I have a List of time series dataframe.I'm trying to produce specific graph for each element of my list. The code is: This is my list: Lista_import<-lapply(Lista_import, function(x){ x2<-subset(x, select=c("ANNO","DICHIARANTE","PARTNER", "quota")) x2<-cast(x

Re: [R] ggplot2 month and year boxplot x axis order problem

2011-06-24 Thread stephen sefick
Try this out. The Date.Time variable was not a date class. str() is your friend. # library(ggplot2) x <- ( structure(list(ID = c(1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 17

Re: [R] ggplot2 month and year boxplot x axis order problem

2011-06-24 Thread philipharrison
Hi thanks for your patience, I understand what you mean now. I made some dummy data; x<-(structure(list(ID = c(1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L, 1734L

Re: [R] gaoshan

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 1:58 PM, wang peter wrote: aa file is: x 1 NA 2 y 1 NA 3 and r program is aa<-read.table("aa",row.names=1) bb<-cor(t(aa),method = "pearson",use="pairwise.complete.obs") bb x y x 1 1 y 1 1 i am confused why the pearson correlation coefficients between x and y is 1

Re: [R] gaoshan

2011-06-24 Thread Mike Miller
On Fri, 24 Jun 2011, wang peter wrote: aa file is: x 1 NA 2 y 1 NA 3 and r program is aa<-read.table("aa",row.names=1) bb<-cor(t(aa),method = "pearson",use="pairwise.complete.obs") bb x y x 1 1 y 1 1 i am confused why the pearson correlation coefficients between x and y is 1 You have

Re: [R] ggplot2 month and year boxplot x axis order problem

2011-06-24 Thread philipharrison
Hi, Thanks for your speedy reply! The file is pretty big (I have 18,000 datapoints), there is not enough room on the r screen for the entire output so I have just cut out a few lines from the end of the dput . I dont know if that helps? X <-(12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L,

[R] gaoshan

2011-06-24 Thread wang peter
aa file is: x 1 NA 2 y 1 NA 3 and r program is > aa<-read.table("aa",row.names=1) > bb<-cor(t(aa),method = "pearson",use="pairwise.complete.obs") > bb x y x 1 1 y 1 1 i am confused why the pearson correlation coefficients between x and y is 1 [[alternative HTML version deleted]]

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Dennis Murphy
Hi: Not much different from Peter's approach, but here's another try: v <- c(1, 2, 6, 5) w <- matrix(c(1, 4, 3, 5, 8, 10), ncol = 2, byrow = TRUE) > w [,1] [,2] [1,]14 [2,]35 [3,]8 10 f <- function(x) v[which(v >= x[1] & v <= x[2])] unlist(apply(w, 1, f)) [1] 1 2 5 I

Re: [R] ggplot2 month and year boxplot x axis order problem

2011-06-24 Thread stephen sefick
This needs to be made reproducible. In other words it would be helpful if you would use dput to share the data. dput(Good) copy the output to the email in this format x <- () with the output from dput inside the () then write the code for ggplot under this line so that we can then just modif

Re: [R] Side by side scatter plots with specified regression lines

2011-06-24 Thread Sigrid
Thank you so much for that. I now have this graphs, by using these commands *p=ggplot(data = test, aes(x = YEAR, y = TOTAL, colour = TREATMENT)) + geom_point() + geom_smooth(method = "lm", se=FALSE) + facet_wrap(~COUNTRY) > p +scale_x_continuous(limits=c(1,4))* http://r.789695.n4.nabble.com/file/

[R] ggplot2 month and year boxplot x axis order problem

2011-06-24 Thread philipharrison
Hi I am very new to R, I am attempting to produce a monthly boxplot with the following fish thermal telemetry data: ID TempDate.Time Month.Year Month Week Shortdate 1 1734 4.4140 04/05/2010 11:5605,2010 May 19 04/05/2010 2 1734 4.1002 04/05/2010 12:0605,2010 May

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Peter Ehlers
On 2011-06-24 09:52, Salih Tuna wrote: Hi guys, let's assume i havethe following 1 x = 2 6 5 1 4 y = 3 5 8 10 i want the code to report back 1, 2 and 5 from x. Basically it shopuld check whether each elements of x falls in the range of each row of x

Re: [R] help- subtitles for multiple charts

2011-06-24 Thread jalen
Thank you for your help, David. This is what I needed! -- View this message in context: http://r.789695.n4.nabble.com/help-subtitles-for-multiple-charts-tp3620453p3622926.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project

Re: [R] Odp: counting columns that fulfill specific criteria

2011-06-24 Thread pguilha
Thanks for your reply, but that is not quite what I am looking for...I do not want to add up all the values in the row, I want to get the number of columns in each row that meet the criteria and then get that as a percentage my understanding is that the rowSums function adds up the values does

Re: [R] new to R need urgent help!

2011-06-24 Thread StellathePug
I have taught myself R over the last few months and I learned quite a bit from reading the PDFs that accompany each package, articles on the R Journal (http://journal.r-project.org/) that cover similar problems to mine, and by asking specific questions about code to this list. I also search online

Re: [R] Error using betareg

2011-06-24 Thread oyvfos
Thanks, that solves/explaines the problem. It occured when running regressions on subsets where some levels even hade zero observations. Didn't check that. Oyvind -- View this message in context: http://r.789695.n4.nabble.com/Error-using-betareg-tp3621955p3622614.html Sent from the R help maili

[R] Model II regression

2011-06-24 Thread JEAN-LOUIS HEMPTINNE
Hello, I am using function lmodel2 to calculate RMA regression between life-history traits in ladybirds beetles. It works well but I am not able to plot an RMA regression line on the scatterplot of my data. I am of course unable to plot the confidence intervals. For ordinary least square regression

[R] Kalman Filter Estimation

2011-06-24 Thread Patrick
Dear R users, I am a new R user and not very experienced in Statistics. I would like to regress a time series variable y on several other time series variables x. I read that the Kalman Filter would provide me with a better fit for my estimation. However, I have no idea how to translate this simpl

[R] understand GEE output for wald test

2011-06-24 Thread elisheva corn
Hi I'm having some difficulty understanding my output (below) from GEE. the person who wrote the program included some comments about the '3-th term gives diff between hyp/ox at time..', and after created an L vector to use for a WALD test. I was wondering if someone could help me understand the

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Gabor Grothendieck
On Fri, Jun 24, 2011 at 11:16 AM, William Dunlap wrote: > Try using dput(f) instead of print(f) and > use eval(parse(text=capture.output(...))). > > I would tend to use something like >   OUTPUTS <- list() >   fr <- function(x) { >       on.exit(OUTPUTS[[length(OUTPUTS)+1]] <<- list(x=x,f=f)) >  

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Salih Tuna
Hi guys, let's assume i havethe following 1 x = 2 6 5 1 4 y = 3 5 8 10 i want the code to report back 1, 2 and 5 from x. Basically it shopuld check whether each elements of x falls in the range of each row of x. 1 and 2 falls in between 1-4 and 5 falls in

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Matt Shotwell
On Fri, 2011-06-24 at 12:09 -0400, David Winsemius wrote: > On Jun 24, 2011, at 11:27 AM, Matt Shotwell wrote: > > > Ravi, > > > > Consider using an environment (i.e. a 'reference' object) to store the > > results, avoiding string manipulation, and the potential for loss of > > precision: > > > >

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Gabor Grothendieck
On Fri, Jun 24, 2011 at 11:10 AM, Ravi Varadhan wrote: > Thank you very much, Jim.  That works! > > I did know that I could process the character strings using regex, but was > also wondering if there was a direct way to get this. > > Suppose, in the current example I would like to obtain a 3-col

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 11:27 AM, Matt Shotwell wrote: Ravi, Consider using an environment (i.e. a 'reference' object) to store the results, avoiding string manipulation, and the potential for loss of precision: fr <- function(x, env) { ## Rosenbrock Banana function x1 <- x[1] x2 <- x[2]

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Ravi Varadhan
I did think of this solution, Keith, but I am generally uncomfortable (may be "paranoid" is a better word) with the use of `<<-'. Perhaps, my fear is unjustified in this particular situation. Thanks, Ravi. --- Ravi Varadhan, Ph.D. Assistant Pr

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Keith Jewell
If you don't want the information as character, why are you printing it rather than storing it in a matrix? Why not something along the lines of this... fr <- function(x) { ## Rosenbrock Banana function on.exit(aMatrix <<- rbind(aMatrix,(cbind(x1, x2, f x1 <- x[1] x2 <- x[2]

Re: [R] text overlap in plot

2011-06-24 Thread Peter Ehlers
On 2011-06-24 08:00, David Winsemius wrote: On Jun 24, 2011, at 10:07 AM, David martin wrote: Hey, Here is a snippet that generated a boxplot and separates points so that they do not overlap. I have a problem to avoir text overlapping. Any help would be helpful. attach(InsectSprays) boxpl

Re: [R] mgcv:gamm: predict to reflect random s() effects?

2011-06-24 Thread Simon Wood
Given that you don't have huge numbers of subjects you could fit the model with `gam' rather than `gamm', using out.gamm <- gam( Y ~ Group + s(X, by=Group) + s(Subject,bs="re"), method="REML") Then your predictions will differ by subject (see e.g. ?random.effects for a bit mor

Re: [R] R-help

2011-06-24 Thread John Kane
http://www.r-project.org/ Manuals > Introduction to R This is not a homework forum. If you are in the middle of a problem, have a "very" specific "R" problem and clearly have done your work come back and ask for help --- On Fri, 6/24/11, Edward Bowora wrote: > From: Edward Bowora > Subject

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Matt Shotwell
Ravi, Consider using an environment (i.e. a 'reference' object) to store the results, avoiding string manipulation, and the potential for loss of precision: fr <- function(x, env) { ## Rosenbrock Banana function x1 <- x[1] x2 <- x[2] f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2 if(

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 11:10 AM, Ravi Varadhan wrote: Thank you very much, Jim. That works! I did know that I could process the character strings using regex, but was also wondering if there was a direct way to get this. Suppose, in the current example I would like to obtain a 3-column mat

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Greg Snow
Here is one approach (different from capture.output) that I believe accomplishes what you are trying to do: frtop <- function(){ out <- numeric(0) topenv <- environment() fr <- function(x) { ## Rosenbrock Banana function x1 <- x[1] x2 <-

Re: [R] Help with lmer

2011-06-24 Thread Hugo Mildenberger
Sophie, I'm myself quite new to linear mixed effect models, but "PresenceAbsence" sounds like a binary response variable. So wouldn't be m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename),familiy=binomial) the first thing to try? There is also a special mailing list for linear - mixe

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread William Dunlap
Try using dput(f) instead of print(f) and use eval(parse(text=capture.output(...))). I would tend to use something like OUTPUTS <- list() fr <- function(x) { on.exit(OUTPUTS[[length(OUTPUTS)+1]] <<- list(x=x,f=f)) ... compute and return f } so you don't have to use capture.o

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Dennis Murphy
Hi: That leaves open several possibilities. Could you please supply a small, reproducible example (i.e., one that someone can copy and paste into an R session) that illustrates the problem along with the solution you expect? TIA, Dennis On Fri, Jun 24, 2011 at 2:30 AM, Salih Tuna wrote: > Hi Di

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Ravi Varadhan
Thank you very much, Jim. That works! I did know that I could process the character strings using regex, but was also wondering if there was a direct way to get this. Suppose, in the current example I would like to obtain a 3-column matrix that contains the parameters and the function valu

Re: [R] Fwd: Extract element of a list based on an index value

2011-06-24 Thread John Kane
Is this doing what you want? It's going from the raw data not the list === library(reshape2) # sample data.frame xx <-structure(list(Warrior = c(3793L, 2013L, 3769L, 2747L, 2083L, 2085L, 2086L, 2556L, 2050L, 2158L, 3045L), SibID =

Re: [R] Fwd: Extract element of a list based on an index value

2011-06-24 Thread John Kane
Is this doing what you want? It's going from the raw data not the list === library(reshape2) # sample data.frame xx <-structure(list(Warrior = c(3793L, 2013L, 3769L, 2747L, 2083L, 2085L, 2086L, 2556L, 2050L, 2158L, 3045L), SibID =

Re: [R] text overlap in plot

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 10:07 AM, David martin wrote: Hey, Here is a snippet that generated a boxplot and separates points so that they do not overlap. I have a problem to avoir text overlapping. Any help would be helpful. > attach(InsectSprays) boxplot(count ~ spray, data = InsectSprays, ou

Re: [R] (no subject)

2011-06-24 Thread Dennis Murphy
Hi: In addition to Sarah's comments, perhaps this has been implemented by someone in one of the Bioconductor packages. If you are inclined towards genomics applications, the Bioconductor list is probably more useful. See http://www.bioconductor.org/help/mailing-list/ for further details. HTH, De

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread Hugo Mildenberger
One possibility involves applying a regular expression via gsub: as.numeric(gsub("^\\[1\\] ","",fvals)) On Friday 24 June 2011 14:39:31 Ravi Varadhan wrote: > Hi, > > I would like to know how to capture the console output from running an > algorithm for further analysis. I can capture thi

[R] mgcv:gamm: predict to reflect random s() effects?

2011-06-24 Thread Szumiloski, John
Dear useRs, I am using the gamm function in the mgcv package to model a smooth relationship between a covariate and my dependent variable, while allowing for quantification of the subjectwise variability in the smooths. What I would like to do is to make subjectwise predictions for plotting pu

Re: [R] change plot area in barplot2

2011-06-24 Thread David L Carlson
There are a couple of ways to do this. You can open a plotting window before using barplot2. If you are running R on Windows, help(windows) for how to change the plotting window dimensions (or help(quartz) for Mac, help(X11) for linux). The second method is to change the margins in the current plo

Re: [R] Fwd: Extract element of a list based on an index value

2011-06-24 Thread Corey Sparks
Solved it: oldest<-unlist(tapply(warmerge$birth.year, warmerge$SibID,function(x) ifelse (x==min(x, na.rm=T)|is.na(x)==T,1,0))) - Corey Sparks, PhD Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio 501 West Durango Blvd Monterey Build

Re: [R] How to capture console output in a numeric format

2011-06-24 Thread jim holtman
try this: > fr <- function(x) { ## Rosenbrock Banana function +on.exit(print(f)) +x1 <- x[1] +x2 <- x[2] +f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2 +f + } > > fvals <- capture.output(ans <- optim(c(-1.2,1), fr)) > # convert to numeric > fvals <- as.numeric(sub("^.* ", "", fval

[R] How to capture console output in a numeric format

2011-06-24 Thread Ravi Varadhan
Hi, I would like to know how to capture the console output from running an algorithm for further analysis. I can capture this using capture.output() but that yields a character vector. I would like to extract the actual numeric values. Here is an example of what I am trying to do. fr <- fun

Re: [R] text overlap in plot

2011-06-24 Thread Greg Snow
Look at the spread.labs function in the TeachingDemos package or the spread.labels function in the plotrix package. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David martin Sent: Friday, June 24, 2011 8:07 AM To: r-h...@stat.ma

Re: [R] Using ts and timeSeries

2011-06-24 Thread Dennis Murphy
Hi: In addition, the sos package is useful when you need to search for a function: # install.packages('sos') library(sos) findFn('augmented Dickey-Fuller') The results are sent to a Web page - this search identified the adf.test() in the tseries package and the ur.df() function in the urca packa

[R] text overlap in plot

2011-06-24 Thread David martin
Hey, Here is a snippet that generated a boxplot and separates points so that they do not overlap. I have a problem to avoir text overlapping. Any help would be helpful. > attach(InsectSprays) boxplot(count ~ spray, data = InsectSprays, outpch = NA) stripchart(count ~ spray, data = InsectSpray

[R] Fwd: Extract element of a list based on an index value

2011-06-24 Thread CS Sparks
Dear list, I have some data on a geneaology, here is a subset: warmerge[1:11,c(1,6,25)] Warrior SibID birth.year 11003793 2013 1926 4 2013 2024 1934 10943769 2024 1918 632 2747 2037 1928 176 2083 2039 1944 187 2085 2039 1949

Re: [R] counting columns that fulfill specific criteria

2011-06-24 Thread Nick Sabbe
Hello Paul. You could try something like perc<-apply(pwdiff, 1 function(currow){ mean(abs(currow) > t, na.rm=TRUE)*100 }) I haven't tested this, as you did not provide a sample pwdiff. You should probably check ?apply for more info. Two suggestions: probably best not to name any variable

Re: [R] Editor color

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 9:44 AM, Barth B. Riley wrote: Dear list Despite having set color settings for the console and script editing window, when I open R and open a script file the text is black against a black background (should be, according to the rconsole colors I saved, yellow against

[R] Editor color

2011-06-24 Thread Barth B. Riley
Dear list Despite having set color settings for the console and script editing window, when I open R and open a script file the text is black against a black background (should be, according to the rconsole colors I saved, yellow against black). I have tried repeatedly to reload and reapply the

[R] Odp: counting columns that fulfill specific criteria

2011-06-24 Thread Petr PIKAL
Hi > Hi, > > I have a matrix (pwdiff in the example below) with ~48 rows and 780 > columns. > For each row, I want to get the percentage of columns that have an absolute > value above a certain threshold "t". I then want to allocate that percentage > to matrix 'perc' in the corresponding r

Re: [R] Error using betareg

2011-06-24 Thread Achim Zeileis
On Fri, 24 Jun 2011, oyvfos wrote: The replication of the error did not "suceed" because I forgot to tell that X2 is a factor. Sorry about that. For instance: d[,3]=as.factor(d[,3]) This piece is just a small sample of a larger error for which I encouneter this error many times. You try to est

[R] Help with lmer

2011-06-24 Thread Sophie Higgins
Hey, I am having trouble with lmer. I am looking at the presence/absence of water shrews against habitat and other factors e.g so I used this: m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) But i keep getting this error up Error in mer_finalize(ans) : Downdated X'X is not posi

Re: [R] Error using betareg

2011-06-24 Thread oyvfos
The replication of the error did not "suceed" because I forgot to tell that X2 is a factor. Sorry about that. For instance: d[,3]=as.factor(d[,3]) This piece is just a small sample of a larger error for which I encouneter this error many times. Thanks -- View this message in context: http://r.

[R] counting columns that fulfill specific criteria

2011-06-24 Thread pguilha
Hi, I have a matrix (pwdiff in the example below) with ~48 rows and 780 columns. For each row, I want to get the percentage of columns that have an absolute value above a certain threshold "t". I then want to allocate that percentage to matrix 'perc' in the corresponding row. Below is my attem

Re: [R] else problem

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 7:47 AM, Petr PIKAL wrote: Hi Thank you for all your help! I did not know to use "" when searching for help, as ?mean, etc, had always worked for me in the past. It makes perfect sense why 'else' was causing me the trouble the way I was using it. I think it was wo

Re: [R] extract worksheet names from an Excel file

2011-06-24 Thread Gabor Grothendieck
On Fri, Jun 24, 2011 at 12:41 AM, Shi, Tao wrote: > Hi list, > > Is there a R function I can use to extract the worksheet names from an Excel > file?  If no, any other automatic ways (not using R) to do this? > > thanks! > Many or all of the Excel interfaces listed here: http://rwiki.sciviews.o

Re: [R] else problem

2011-06-24 Thread Petr PIKAL
Hi > > Thank you for all your help! I did not know to use "" when searching for > help, as ?mean, etc, had always worked for me in the past. > It makes perfect sense why 'else' was causing me the trouble the way I was > using it. I think it was working in my other code, despite the same > for

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Petr PIKAL
Hi > Hi Dimitris, > Thanks for your reply. But this is not exactly what i am after. I want to > find the probes that falls into certain regions. In your solution it will > ignore the second probe if it falls into the same region as the first one. > Is there any vector trickb uilt in R to find

Re: [R] Competing-risks nomogram

2011-06-24 Thread Frank Harrell
Replace the Design package with the rms package. Use the ordinary linear regression trick to predict the linear predictor from the competing risk regression, then use nomogram on this new model (that merely represents the fit of interest). Frank Firas Abdollah wrote: > > Hi R users, > > I'd lik

Re: [R] UnoC function in survAUC for censoring-adjusted C-index

2011-06-24 Thread Frank Harrell
Note that the original C-index is implemented in various validation options in the rms package related to the cph function (which calls coxph in survival). Frank = Eleni Rapsomaniki-2 wrote: > > Hello, > > I am having some trouble with the 'censoring-adjusted C-index' by Uno et > al, in the packa

Re: [R] Lattice xyplot to group by two parameters

2011-06-24 Thread Deepayan Sarkar
On Thu, Jun 23, 2011 at 10:15 PM, Guy Jett wrote: > My thanks to this mailing list and its members for their great help in the > past.  I have yet another question per the following code and comments: > > # I need individual graphs grouped by "PARLABEL" AND "Event", with "PARLABEL" > #   controll

Re: [R] Declustering data

2011-06-24 Thread Sarah Goslee
Hi, On Fri, Jun 24, 2011 at 6:09 AM, ogbos okike wrote: > Hello Everybody, > The way I learn some analyses tools in R is to install the package and play > with some examples. Excellent plan. > I am trying to see if declustering algorithm is implemented in R. I have > seen some examples examples

Re: [R] (no subject)

2011-06-24 Thread Sarah Goslee
Hi, On Fri, Jun 24, 2011 at 3:15 AM, Ungku Akashah wrote: > hi dear R crew. > may i request the script for volcano plot. > if able, pls include any tips about volcano plot. Sure. What do you think a volcano plot looks like, and what kind of data do you wish to use in constructing one? The R Gra

Re: [R] R-help

2011-06-24 Thread David Winsemius
This is not a homework help list. Please read the Posting Guide before further posting. On Jun 24, 2011, at 2:26 AM, Edward Bowora wrote: Hi Please assist me to code the attached pdf in R. Your help will be greatly appreciated. Edward Actuarial Science Student Variable.pdf>

Re: [R] Installing packages

2011-06-24 Thread David Winsemius
On Jun 24, 2011, at 4:29 AM, thomas.chesney wrote: Hi, I am trying to install the network package at my work computer. Which is a machine of what sort? (Most likely a Mac from subsequent error messages) I'm using R version 2.12.0 (2010-10-15) At home I can use the Package Installer, bu

Re: [R] R-help

2011-06-24 Thread Mike Marchywka
I'm surprised the pdf made it through mail list but many will not open these and I have just cleaned malware off my 'dohs system. Can you explain what you want to do in simple text? Subject: [R] R-help Hi Please assist me to code the attached pdf in R. Your help will be greatly appreciate

Re: [R] Error using betareg

2011-06-24 Thread Achim Zeileis
On Fri, 24 Jun 2011, oyvfos wrote: Dear all, I get an error using betrag on this data set :http://dl.dropbox.com/u/1866110/dump.csv. I run it like this regression f2.1=betareg(Y~X1+X2,data=dump) summary(f2.1) I get : Call: betareg(formula = Y ~ X1 + X2, data = dump) Standardized weighted res

Re: [R] Using ts and timeSeries

2011-06-24 Thread Setlhare Lekgatlhamang
Please see the tsDyn package for implementing the Augmented Dickey Fuller test. Lexi -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of UnitRoot Sent: Wednesday, June 15, 2011 9:06 AM To: r-help@r-project.org Subject: [R] Using ts and

[R] lag and diff with transformBy

2011-06-24 Thread Michael Ash
I have a question regarding the very useful doBy package, and specifically, the transformBy() function with the lag() and diff() functions.  It is often useful to lag or difference data within a panel, i.e., within a by-group.  Is the following code a safe use of transformBy? Is there an alternativ

[R] UnoC function in survAUC for censoring-adjusted C-index

2011-06-24 Thread Eleni Rapsomaniki
Hello, I am having some trouble with the 'censoring-adjusted C-index' by Uno et al, in the package survAUC. The relevant function is UnoC. The question has to do with what happens when I specify a time point t for the upper limit of the time range under consideration (we want to avoid using the

Re: [R] numerical integration and 'non-finite function value' error

2011-06-24 Thread Adan_Seb
The domain of the beta distribution as defined in R is 0 <= x <= 1 and as shown by David Winsemius it is undefined outside [0,1]. But thats sort of the question I have. To elaborate, I have a variable with 0 as its natural lower limit but can assume any positive number as an upper limit. So its do

[R] Error using betareg

2011-06-24 Thread oyvfos
Dear all, I get an error using betrag on this data set :http://dl.dropbox.com/u/1866110/dump.csv. I run it like this regression f2.1=betareg(Y~X1+X2,data=dump) summary(f2.1) I get : Call: betareg(formula = Y ~ X1 + X2, data = dump) Standardized weighted residuals 2: Error in quantile.default(x$

Re: [R] Is R a solution to my problem?

2011-06-24 Thread Mike Marchywka
> From: jdnew...@dcn.davis.ca.us > Date: Fri, 24 Jun 2011 02:13:29 -0700 > To: ikoro...@gmail.com; R-help@r-project.org > Subject: Re: [R] Is R a solution to my problem? > > Almost any tool can be bent to perform almost any task, but that combination > sounds like a particularly difficult way

[R] Installing packages

2011-06-24 Thread thomas.chesney
Hi, I am trying to install the network package at my work computer. I'm using R version 2.12.0 (2010-10-15) At home I can use the Package Installer, but at work this is blocked by our firewall. What I usually do is download the Mac binary and copy it to R.Framework/Resources/Library, but this isn

[R] Declustering data

2011-06-24 Thread ogbos okike
Hello Everybody, The way I learn some analyses tools in R is to install the package and play with some examples. I am trying to see if declustering algorithm is implemented in R. I have seen some examples examples of declustering data. However, I could not try them as I do not know which package t

Re: [R] concordance

2011-06-24 Thread Jim Lemon
On 06/24/2011 05:16 AM, Assieh Rashidi wrote: Is there any package for computing concordance coefficient of incomplete ranking? If there is not, please help me to write it. Hi Assieh, The muranks function in the crank package will impute missing ranks as the mean value of all missing ranks if

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Salih Tuna
Hi Dimitris, Thanks for your reply. But this is not exactly what i am after. I want to find the probes that falls into certain regions. In your solution it will ignore the second probe if it falls into the same region as the first one. Is there any vector trickb uilt in R to find whether probes fal

Re: [R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Dimitris Rizopoulos
One approach is the following: x <- rnorm(5) y <- matrix(rnorm(5*2), 5, 2) check <- y - x check[, 1] * check[, 2] < 0 I hope it helps. Best, Dimitris On 6/24/2011 10:57 AM, Salih Tuna wrote: Hi All, What is the fastest way of finding if any members of vector x fall in the range of the rows

Re: [R] Is R a solution to my problem?

2011-06-24 Thread Jeff Newmiller
Almost any tool can be bent to perform almost any task, but that combination sounds like a particularly difficult way to get started. There are a variety of purpose-built software development environments for serving dynamically-constructed web pages, including C++ libraries. However, discussio

[R] Fastest way of finding if any members of vector x fall in the range of the rows of matrix y

2011-06-24 Thread Salih Tuna
Hi All, What is the fastest way of finding if any members of vector x fall in the range of the rows of matrix y? I do not want to use two for loops as this will take forever. Any help will be appreciated, best, salih [[alternative HTML version deleted]] ___

Re: [R] VAR with excluded lags

2011-06-24 Thread Pfaff, Bernhard Dr.
?restrict > -Ursprüngliche Nachricht- > Von: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] Im Auftrag von gizmo > Gesendet: Mittwoch, 22. Juni 2011 18:26 > An: r-help@r-project.org > Betreff: [R] VAR with excluded lags > > Hi, > > I would like to fit a Vector Aut

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