Re: [R] cdplot error

2011-08-02 Thread Allan Engelhardt (CYBAEA)
On 03/08/11 05:52, wildernessness wrote: Fairly new at this. Trying to create a conditional density plot. cdplot(status~harvd.l,data=phy) Error in cdplot.formula(status~harvd.l,data=phy): dependent variable should be a factor What does this error mean? Status is a binary response of infestat

Re: [R] convert a splus randomforest object to R

2011-08-02 Thread Duncan Mackay
Hi Jimmy Years ago I think that Splus introduced an argument when dumping of old.style = T or something similar to dump it into a form that could be read into R. This may only be for data.frames etc not things like random forest objects Regards Duncan Duncan Mackay Department of Agronomy

Re: [R] Error while trying to install a package

2011-08-02 Thread Patrick Connolly
On Mon, 01-Aug-2011 at 02:55PM -0400, Sushil Amirisetty wrote: |> |> Hi Everyone, |> |> When i try to install a package using |> |> > install.packages("agricolae") |> --- Please select a CRAN mirror for use in this session --- |> | |> |> |> The cursor keeps blinking i dont get a popup m

Re: [R] create a list under constraints

2011-08-02 Thread Dennis Murphy
Hi: Here's one way; using the mdply() function in the plyr package: k <- c(1,2,3,4,5) i <- c(0,1,3,2,1) # Takes two scalars k and i as input, outputs a data frame ff <- function(k, i) data.frame(k = rep(k, i+1), i = seq(0, i, by = 1)) library('plyr') mdply(data.frame(k, i), ff) # returns a da

[R] AICcmodavg functions and 'mer' class models

2011-08-02 Thread RonnyG
What is teh reason some functions in the AICcmodavg package do not work with 'mer' class models? One such example would be the 'importance' function. Thanks Ronny -- View this message in context: http://r.789695.n4.nabble.com/AICcmodavg-functions-and-mer-class-models-tp3714534p3714534.html Sent

Re: [R] How to make a nomogam and Calibration plot

2011-08-02 Thread sytangping
Dear Harrell, Many thanks for your quick response! However, after try and try, I still have difficulty to solve my questions. I post my questions again. I hope someone can help me run the data and draw the nomogram and calibration plot for me. I know that is not good but indeed I have no way to go

[R] cdplot error

2011-08-02 Thread wildernessness
Fairly new at this. Trying to create a conditional density plot. >cdplot(status~harvd.l,data=phy) Error in cdplot.formula(status~harvd.l,data=phy): dependent variable should be a factor What does this error mean? Status is a binary response of infestation (0/1) and harvd.l is the log of timber

Re: [R] expand.gird with constraints?

2011-08-02 Thread Berwin A Turlach
G'day Kathie, On Tue, 2 Aug 2011 19:56:00 -0700 (PDT) Kathie wrote: > Hi, R users, > > Here is an example. > > k <- c(1,2,3,4,5) > i <- c(0,1,3,2,1) > > if k=1, then j=0 from i > if k=2, then j=0, 1 from i > if k=3, then j=0, 1, 2, 3 from i > if k=4, then j=0, 1, 2 from i > if k=5, then j=0,

[R] expand.gird with constraints?

2011-08-02 Thread Kathie
Hi, R users, Here is an example. k <- c(1,2,3,4,5) i <- c(0,1,3,2,1) if k=1, then j=0 from i if k=2, then j=0, 1 from i if k=3, then j=0, 1, 2, 3 from i if k=4, then j=0, 1, 2 from i if k=5, then j=0, 1 from i so i'd like to create a list like below. > list k j 1 1 0 2 2 0 3 2 1 4 3 0 5

[R] create a list under constraints

2011-08-02 Thread Kathie
Hi, R users, Here is an example. k <- c(1,2,3,4,5) i <- c(0,1,3,2,1) if k=1, then i=0 if k=2, then i=0, 1 if k=3, then i=0, 1, 2, 3 if k=4, then i=0, 1, 2 if k=5, then i=0, 1 so i'd like to create a list like below. > list k i 1 1 0 2 2 0 3 2 1 4 3 0 5 3 1 6 3 2 7 3 3 8 4 0 9 4 1 1

Re: [R] Extract rows from a matrix according to value in column

2011-08-02 Thread Ista Zahn
Hi Sverre, On Tue, Aug 2, 2011 at 10:22 PM, Sverre Stausland wrote: > Dear helpers, > > I'm trying to extract certain rows from a matrix according to the > values the rows have in a certain column. I've been googling for a > while without result. > > Here's a reproducible example of a matrix (and

[R] Extract rows from a matrix according to value in column

2011-08-02 Thread Sverre Stausland
Dear helpers, I'm trying to extract certain rows from a matrix according to the values the rows have in a certain column. I've been googling for a while without result. Here's a reproducible example of a matrix (and the one I was playing with initially): > myrepo<-getOption("repos") > myrepo["CR

[R] convert a splus randomforest object to R

2011-08-02 Thread Zhiming Ni
Hi, I have a randomforest object "cost.rf" that was created in splus 8.0, now I need to use this trained RF model in R. So in Splus, I dump the RF file as below data.dump("cost.rf", file="cost.rf.txt", oldStyle=T) then in R, restore the dumped file, library(foreign) data.restore("cost.rf.tx

[R] Writing multiple regression in one function

2011-08-02 Thread Darius H
Hello all, I am newbie to R and have not been able to find too much stuff on a version of VAR(p) I am working on. Would someone be able to tell me if there is a more elegant way of writing A function for the following? Many thanks in advance. Darius I am regressing returns of 8 asset classes

[R] Matplot & Polygon

2011-08-02 Thread Kitty Lee
I used matplot to plot multiple lines (over 300 lines). I'd like to draw a polygon and shade the area between upper and lower boundary. I know the plot function works pretty well with polygon(). How about matplot? I have too many lines and my upper/lower boundaries are formed by many different

Re: [R] Is a string all blanks?

2011-08-02 Thread jim holtman
If the question is that the string contains all blanks, then a regular expression will probably be best: > OneBlank <- " " > TwoBlanks <- " " > ThreeBlanks <- " " > NoBlanks <- "NoBlanks" > bvec <- c(OneBlank, TwoBlanks ,ThreeBlanks ,NoBlanks) > bvec <- c(OneBlank, TwoBlanks ,ThreeBlanks ,NoBla

Re: [R] Is a string all blanks?

2011-08-02 Thread Peter Langfelder
On Tue, Aug 2, 2011 at 5:07 PM, John Sorkin wrote: > windows 7 > R 2.12.1 > > Is there any easy way to determine if a sting contains nothing but blanks? I > need to check a series of strings of various length. > > OneBlank <- " " > TwoBlanks <- "  " > ThreeBlanks <- "   " > NoBlanks <- "NoBlanks"

Re: [R] How to find the parameter of a power function to fit simulation data to it for the tail?

2011-08-02 Thread David Winsemius
From a search at Barons site with "fitting distribution truncated power" http://finzi.psych.upenn.edu/R/library/brainwaver/html/fitting.html http://finzi.psych.upenn.edu/R/library/gamlss/doc/gamlss-manual.pdf http://finzi.psych.upenn.edu/R/library/bipartite/html/degreedistr.html http://finzi.ps

Re: [R] Is a string all blanks?

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 8:07 PM, John Sorkin wrote: windows 7 R 2.12.1 Is there any easy way to determine if a sting contains nothing but blanks? I need to check a series of strings of various length. OneBlank <- " " TwoBlanks <- " " ThreeBlanks <- " " NoBlanks <- "NoBlanks" What I want wou

[R] Is a string all blanks?

2011-08-02 Thread John Sorkin
windows 7 R 2.12.1 Is there any easy way to determine if a sting contains nothing but blanks? I need to check a series of strings of various length. OneBlank <- " " TwoBlanks <- " " ThreeBlanks <- " " NoBlanks <- "NoBlanks" What I want would be a function such as ALLBLANKS that would return

Re: [R] [Rd] example package for devel newcomers

2011-08-02 Thread Alexandre Aguiar
Em Segunda 01 Agosto 2011, você escreveu: > Is there a preferred language you would like to use in your package > development? I randomly downloaded packages until I found some that > helped me along my way, and might be able to help you pick one. If you > are just looking at building a package of

[R] xlsx error

2011-08-02 Thread Andrew Winterman
Hey All, I'm trying to use the xlsx package to read a series of excel spreadsheets into R, but my code is failing at the first step. I setwd into my the directory with the spreadsheets, and, as a test ask for the first one: read.xlsx(file = "Argentina Final.xls", sheetIndex = 1) I promptly

[R] Wrong values when projecting LatLong in UTM

2011-08-02 Thread Colin Bergeron
Hi R helpers, I tried to convert a list of LatLong coordinates (in DD format) into UTM zone 11 NAD 27. I first tried this from PBSmapping: library(PBSmapping) LatLong<-cbind(c(56.85359, 56.85478),c(-118.4109, -118.4035)) colnames(LatLong)<-c("X","Y") attr(LatLong, "projection") <- "UTM" attr(Lat

Re: [R] Help with R

2011-08-02 Thread Gavin Simpson
On Thu, 2011-07-28 at 11:58 -0400, Sarah Goslee wrote: > Hi Mark, > > On Thu, Jul 28, 2011 at 10:44 AM, wrote: > > > > 1. How can I plot the entire tree produced by rpart? > > What does plot() not do that you are expecting? Not do any labelling... ;-) text(tree) where `tree` is your fitte

Re: [R] Calculate mean ignore null

2011-08-02 Thread R. Michael Weylandt
Are you sure it doesn't? na.rm=T works for me, so I think your problem is elsewhere. Specifically, the example given below consists of 27 character strings, not numbers, so there' so surprise R doesn't want to give you a mean -- to R, it's as logical as asking for the average of "a" and "Q5" Try

[R] Calculate mean ignore null

2011-08-02 Thread Jeffrey Joh
I have the following: Tout = c(".", ".", + "-51.0", " -9.6", " -9.6", " -9.6", " -9.6", " -9.6", " -9.6", + " -9.6", " -9.5", " -9.5", " -9.6", " -9.5", " -9.6", " -9.6", + " -9.5", " -9.4", " -9.3", " -9.3", " -9.3", " -9.2", " -9.0", + " -9.0", " -8.9", " -8.9", " -8.9") How ca

Re: [R] Inverse of FAQ 7.31.

2011-08-02 Thread Rolf Turner
Thanks to Peter Dalgaard and to Baptiste Auguie (off-list) for the insights they provided. cheers, Rolf turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] How to find the parameter of a power function to fit simulation data to it for the tail?

2011-08-02 Thread Paul Menzel
Dear R folks, having simulation data in a vector n2off, I know that they should be similar to a power function f [1], f(n) = n^(-1/r), r ∈ ℕ\{0}, and I want to find the value for r best fitting the simulation data. Furthermore I know that this is only true for big n, that means n2off(n) ~ f(n) ⇔

Re: [R] 3D Bar Graphs in ggplot2?

2011-08-02 Thread Duncan Murdoch
On 11-08-02 2:39 PM, wwreith wrote: Does anyone know how to create a 3D Bargraph using ggplot2/qplot. I don't mean 3D as in x,y,z coordinates. Just a 2D bar graph with a 3D shaped bard. See attached excel file for an example. Before anyone asks I know that 3D looking bars don't add anything exce

Re: [R] 3D Bar Graphs in ggplot2?

2011-08-02 Thread Brian Diggs
On 8/2/2011 11:39 AM, wwreith wrote: Does anyone know how to create a 3D Bargraph using ggplot2/qplot. I don't mean 3D as in x,y,z coordinates. Just a 2D bar graph with a 3D shaped bard. See attached excel file for an example. It is not possible. Before anyone asks I know that 3D looking bars

Re: [R] density plot for weighted data

2011-08-02 Thread Thomas Lumley
On Wed, Aug 3, 2011 at 5:11 AM, r student wrote: > Like below? > > plot(density(oh$FINCP,weights=oh$PWGTP/sum(oh$PWGTP))) > Yes If you are doing lots of analyses with weighted data you might want to look at the survey package. It also has a density estimator, in svysmooth(), which works very mu

[R] 3D Bar Graphs in ggplot2?

2011-08-02 Thread wwreith
Does anyone know how to create a 3D Bargraph using ggplot2/qplot. I don't mean 3D as in x,y,z coordinates. Just a 2D bar graph with a 3D shaped bard. See attached excel file for an example. Before anyone asks I know that 3D looking bars don't add anything except "prettiness". http://r.789695.n4.

[R] Need to compute density as done by panel.histogram

2011-08-02 Thread Sébastien Bihorel
Hi, This might be a simple problem but I don't know how to calculate a random variable density the way panel.histogram does it before it creates the actual density rectangles. The documentation says that it uses the density function but the actual code suggests that the hist.constructor function (

Re: [R] Extract names from vector according to their values

2011-08-02 Thread Dennis Murphy
Hi: One more possibility: > names(my.vector[grep('recommended', my.vector)]) [1] "Matrix" "boot" "class" "cluster""codetools" [6] "foreign""KernSmooth" "lattice""MASS" "Matrix" [11] "mgcv" "nlme" "nnet" "rpart" "spatial" [16] "survival" >

Re: [R] Extract names from vector according to their values

2011-08-02 Thread Jean V Adams
Sverre, Try this: my.list <- split(names(my.vector), my.vector) my.list$base my.list$recommended Jean `·.,, ><(((º> `·.,, ><(((º> `·.,, ><(((º> Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA From: Sverre Sta

Re: [R] Extract names from vector according to their values

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 2:21 PM, Sverre Stausland wrote: Dear helpers, I can create a vector with the priority of the packages that came with R, like this: installed.packages()[,"Priority"]->my.vector my.vector base boot class cluster codetools "base" "re

Re: [R] Data frame to matrix - revisited

2011-08-02 Thread Dennis Murphy
Hi: Here are a couple of ways. Since your data frame does not contain a 'c' in ID2, we redefine the factor to give it all five levels rather than the observed four: > df <- read.table(textConnection(" + ID1 ID2 Value + a b 1 + b d 1 + c a 2 + c e 1 + d a 1 + e d 2"), header = TRUE) str(df) > str(

[R] Extract names from vector according to their values

2011-08-02 Thread Sverre Stausland
Dear helpers, I can create a vector with the priority of the packages that came with R, like this: > installed.packages()[,"Priority"]->my.vector > my.vector base boot class cluster codetools "base" "recommended" "recommended" "recommended" "recommended"

Re: [R] density plot for weighted data

2011-08-02 Thread r student
Like below? plot(density(oh$FINCP,weights=oh$PWGTP/sum(oh$PWGTP))) On Tue, Aug 2, 2011 at 10:06 AM, David Winsemius wrote: > > On Aug 2, 2011, at 12:51 PM, r student wrote: > >> I'm trying to create a density plot using census data, where the >> weights don't sum to 1. >> >> >>> plot(density

Re: [R] Memory limit in Aggregate()

2011-08-02 Thread peter dalgaard
On Aug 2, 2011, at 19:09 , Guillaume wrote: > Hi Peter, > > Yes I have a large number of factors in the listBy table. > > Do you mean that aggregate() creates a complete cartesian product of the > "by" columns ? (and creates combinations of values that do not exist in the > orignial "by" table,

Re: [R] Inserting column in between -- "better" way?

2011-08-02 Thread peter dalgaard
On Aug 2, 2011, at 19:17 , Bert Gunter wrote: > Thanks for this Peter: > >> >> Sarah (sic) is on the right track, just lose the commas so that you don't >> drop to a vector: >> >>> x <- data.frame(A=1:3, B=1:3, C=1:3, D=1:3, E=1:3) >>> newcol <- 4:6 >>> cbind(x[1], newcol, x[2:ncol(x)]) >> A

Re: [R] Data frame to matrix - revisited

2011-08-02 Thread Jean V Adams
Jagz, Assuming that your data frame is called df, try this ... tapply(df$Value, list(df$ID1, df$ID2), mean) Jean `·.,, ><(((º> `·.,, ><(((º> `·.,, ><(((º> Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA 715-627-

Re: [R] density plot for weighted data

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 1:11 PM, r student wrote: Like below? plot(density(oh$FINCP,weights=oh$PWGTP/sum(oh$PWGTP))) I don't understand why you are asking for approval. You are the one with the data and know where they came from. We have none of that background. -- David. On Tue, Aug 2, 20

Re: [R] Inserting column in between -- "better" way?

2011-08-02 Thread Bert Gunter
Thanks for this Peter: > > Sarah (sic) is on the right track, just lose the commas so that you don't > drop to a vector: > >> x <- data.frame(A=1:3, B=1:3, C=1:3, D=1:3, E=1:3) >> newcol <- 4:6 >> cbind(x[1], newcol, x[2:ncol(x)]) >  A newcol B C D E > 1 1      4 1 1 1 1 > 2 2      5 2 2 2 2 > 3

[R] Data frame to matrix - revisited

2011-08-02 Thread Jagz Bell
Hi, I've tried to look through all the previous related Threads/posts but can't find a solution to what's probably a simple question.   I have a data frame comprised of three columns e.g.:   ID1 ID2 Value a b 1 b d 1 c a 2 c e 1 d a 1 e d 2   I'd like to convert the data to a matrix i.e.:    a b c

Re: [R] Memory limit in Aggregate()

2011-08-02 Thread Guillaume
Hi Peter, Yes I have a large number of factors in the listBy table. Do you mean that aggregate() creates a complete cartesian product of the "by" columns ? (and creates combinations of values that do not exist in the orignial "by" table, before removing them when returning the aggregated table?)

Re: [R] density plot for weighted data

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 12:51 PM, r student wrote: I'm trying to create a density plot using census data, where the weights don't sum to 1. plot(density(oh$FINCP,weights=oh$PWGTP)) Warning message: In density.default(oh$FINCP, weights = oh$PWGTP) : sum(weights) != 1 -- will not get true dens

Re: [R] lattice: index plot

2011-08-02 Thread Peter Ehlers
Does xyplot(y ~ seq_along(y), xlab = "Index") do what you want? Peter Ehlers On 2011-08-02 09:07, Thaler, Thorn, LAUSANNE, Applied Mathematics wrote: Dear all, How can I make an index plot with lattice, that is plotting a vector simply against its particular index in the vector, i.e. someth

Re: [R] identifying weeks (dates) that certain days (dates) fall into

2011-08-02 Thread Dimitri Liakhovitski
Thanks a lot, everyone! Dimitri On Tue, Aug 2, 2011 at 12:34 PM, Dennis Murphy wrote: > Hi: > > You could try the lubridate package: > > library(lubridate) > week(weekly$week) > week(july4) > [1] 27 27 > >> week > function (x) > yday(x)%/%7 + 1 > > > which is essentially Gabor's code :) > > HTH,

[R] density plot for weighted data

2011-08-02 Thread r student
I'm trying to create a density plot using census data, where the weights don't sum to 1. >plot(density(oh$FINCP,weights=oh$PWGTP)) Warning message: In density.default(oh$FINCP, weights = oh$PWGTP) : sum(weights) != 1 -- will not get true density How would I go about doing this? Thanks!

Re: [R] Inserting column in between -- "better" way?

2011-08-02 Thread peter dalgaard
On Aug 1, 2011, at 20:50 , David L Carlson wrote: > Actually Sara's method fails if the insertion is after the first or before > the last column: > >> x <- data.frame(A=1:3, B=1:3, C=1:3, D=1:3, E=1:3) >> newcol <- 4:6 >> cbind(x[,1], newcol, x[,2:ncol(x)]) > Sarah (sic) is on the right track,

Re: [R] identifying weeks (dates) that certain days (dates) fall into

2011-08-02 Thread Dennis Murphy
Hi: You could try the lubridate package: library(lubridate) week(weekly$week) week(july4) [1] 27 27 > week function (x) yday(x)%/%7 + 1 which is essentially Gabor's code :) HTH, Dennis On Tue, Aug 2, 2011 at 7:36 AM, Dimitri Liakhovitski wrote: > Hello! > > I have dates for the beginning of

Re: [R] Loops to assign a unique ID to a column

2011-08-02 Thread Bert Gunter
Whoa! 1. First and most important, there is very likely no reason you need to do this. R can handle multiple groupings automatically in fitting and plotting without creating artificial labels of the sort you appear to want to create. Please read an "Intro to R" and/or get help to see how. 2. The

[R] lattice: index plot

2011-08-02 Thread Thaler, Thorn, LAUSANNE, Applied Mathematics
Dear all, How can I make an index plot with lattice, that is plotting a vector simply against its particular index in the vector, i.e. something similar to y <- rnorm(10) plot(y) I don't want to specify the x's manually, as this could become cumbersome when having multiple panels. I tried some

Re: [R] Help with aggregate syntax for a multi-column function please.

2011-08-02 Thread Dennis Murphy
Hi: Another way to do this is to use one of the summarization packages. The following uses the plyr package. The first step is to create a function that takes a data frame as input and outputs either a data frame or a scalar. In this case, the function returns a scalar, but if you want to carry a

Re: [R] Memory limit in Aggregate()

2011-08-02 Thread peter dalgaard
On Aug 2, 2011, at 17:10 , Guillaume wrote: > Hi Peter, > Thanks for your answer. > I made a mistake in the script I copied sorry ! > > The description of the object : listX has 3 column, listBy has 4 column, and So what is the contents of listBy? If they are all factors with 100 levels, t

Re: [R] how to get the percentile of a number in a vector

2011-08-02 Thread Jean V Adams
Does this help? x <- c(3, 8, 5, 2, 9, 33, 21) # the 43rd percentile quantile(x, 0.43) # the proportion of the distribution that is less than 7 mean(x<7) Jean `·.,, ><(((?> `·.,, ><(((?> `·.,, ><(((?> Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East

Re: [R] SSOAP & chemspider

2011-08-02 Thread Benton, Paul
Has anyone got SSOAP working on anything besides KEGG? I just tried another 3 SOAP servers. Both the WSDL and constructing the .SOAP call. Again the perl and ruby interface worked without any hitches. Paul > library(SSOAP) > massBank<-processWSDL("http://www.massbank.jp/api/services/MassBankAPI

Re: [R] how to get the percentile of a number in a vector

2011-08-02 Thread R. Michael Weylandt
Would this work for you? if you want to know where the i-th element falls percentage-wise in the distribution of a vector: sum(x <= x[i])/length(x) This could be turned into a function: pEmpirical <- function(i,x) { if (length(i) > 1) return(apply(as.matrix(i), 1, pEmpirical,x)) r = sum

Re: [R] Standard Deviation of a matrix

2011-08-02 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of chakri > Sent: Tuesday, August 02, 2011 6:31 AM > To: r-help@r-project.org > Subject: Re: [R] Standard Deviation of a matrix > > Thank you everyone for your kind input, > > I fo

Re: [R] how to get the percentile of a number in a vector

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 10:14 AM, ראובן אברמוביץ wrote: I'm familiar with the quantile() command, but what if I have a specific number that I want to know its location in a vector? I know that in known distributions, (for example the normal distribution), there is pnorm and qnorm, bu

Re: [R] My R code is not efficient

2011-08-02 Thread Jeff Newmiller
?expand.grid --- Jeff Newmiller The . . Go Live... DCN: Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rock

[R] Extract p value from coxme object

2011-08-02 Thread Catarina Miranda
Dear R experts; I am trying to extract the p values from a coxme object (package coxme). I can see the value in the model output, but I wanted to have the result with a higher number of decimal places. I have searched the mailing list and followed equivalent suggestions for nlme/lme objects, but I

[R] My R code is not efficient

2011-08-02 Thread Kathie
Dear R users, I have two n*1 integer vectors, y1 and y2, where n is very very large. I'd like to compute elbp = 4^(y1) * 5^(y2) * sum_{i=0}^{max(y1, y2)} [{ (y1-i)! * (i)! * (y2-i)! }^(-1)]; that is, I need to compute "elbp" for each (y1, y2) pair. So I made R code like below, but I don't t

Re: [R] Memory limit in Aggregate()

2011-08-02 Thread Guillaume
Hi Peter, Thanks for your answer. I made a mistake in the script I copied sorry ! The description of the object : listX has 3 column, listBy has 4 column, and they have 9000 rows : print(paste("ncol x ", length((listX print(paste("ncol By ", length((listBy print(paste("nrow ", length(

[R] how to get the percentile of a number in a vector

2011-08-02 Thread ראובן אברמוביץ
I'm familiar with the quantile() command, but what if I have a specific number that I want to know its location in a vector? I know that in known distributions, (for example the normal distribution), there is pnorm and qnorm, but how can I do it with unknown vector? thanks in adva

Re: [R] Standard Deviation of a matrix

2011-08-02 Thread chakri
Thank you everyone for your kind input, I forgot to add that I have decimal points in my matrix ! Enclosed input file (reduced to 10 X 10 matrix), scripts and output for your suggesions: Code 1: library(stats) Matrix<-read.table("test_input", head=T, sep=" ", dec=".") SD<-sd(as.numeric(Matrix))

Re: [R] identifying weeks (dates) that certain days (dates) fall into

2011-08-02 Thread Gabor Grothendieck
On Tue, Aug 2, 2011 at 10:36 AM, Dimitri Liakhovitski wrote: > Hello! > > I have dates for the beginning of each week, e.g.: > weekly<-data.frame(week=seq(as.Date("2010-04-01"), > as.Date("2011-12-26"),by="week")) > week  # each week starts on a Monday > > I also have a vector of dates I am intere

Re: [R] Display/show the evaluation result of R commands automatically

2011-08-02 Thread Anthony Ching Ho Ng
R-help and Barry Thank you for your suggestions. It works, and may I ask how I am able to do the opposite (disable the call back, so that I could control when to show and suppress the output). I would like to make a function to enable/disable the callback similar to the one as follow: enableOutpu

[R] vglm: warnings and errors

2011-08-02 Thread Sramkova, Anna (IEE)
Hello, I am using multinomial logit regression for the first time, and I am trying to understand the warnings and errors I get. My data consists of 200 to 600 samples with ~25 predictors (these are principal components). The response has three categories. I use the function "vglm" from the pa

Re: [R] Loops to assign a unique ID to a column

2011-08-02 Thread David L Carlson
How about this? > indx <- unique(cbind(Dates, Groups)) > indx DatesGroups [1,] "12/10/2010" "A" [2,] "12/10/2010" "B" [3,] "13/10/2010" "A" [4,] "13/10/2010" "B" [5,] "13/10/2010" "C" > indx <- data.frame(indx, id=1:nrow(indx)) > indx Dates Groups id 1 12/10/2010

Re: [R] Help with aggregate syntax for a multi-column function please.

2011-08-02 Thread Jean V Adams
Michael, The function aggregate() is not going to work for your situation. The function is applied to the individual columns of the subsetted data, not the subsetted data frame as a whole. The help file reads: "Then, each of the variables (columns) in x is split into subsets of cases (rows) o

Re: [R] identifying weeks (dates) that certain days (dates) fall into

2011-08-02 Thread David Winsemius
The findInterval function should surely be tried in some form or another. On Aug 2, 2011, at 10:36 AM, Dimitri Liakhovitski wrote: Hello! I have dates for the beginning of each week, e.g.: weekly<-data.frame(week=seq(as.Date("2010-04-01"), as.Date("2011-12-26"),by="week")) week # each week

Re: [R] execute r-code stored in a string variable

2011-08-02 Thread Samuel Le
Yes, you can use: eval(parse(text=c)) On the other hand I would not recommend to use c as a variable name as it is the name of a very important function in the R language to aggregate data. HTH, Samuel -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-projec

[R] merging lists within lists via time stamp

2011-08-02 Thread tomtomme
>From multiple data.frames I created two lists, one with temperature, one with gps data. With your help and lapply I managed to interpolate the timestamps of gps and temperature data. Now I want to merge/join both lists via the time-stamp, taking only times, where both lists have data. For the sin

[R] matrix indexing (igraph ?)

2011-08-02 Thread Robinson, David G
I realize that matrix indexing has been addressed in various flavors, but I'm stumped and didn't find anything in the archives. It's not clear if it is an igraph issue or a more general problem. Thanks in advance for your patience. I am using igraph to read a gml file (http://www-personal.umic

[R] identifying weeks (dates) that certain days (dates) fall into

2011-08-02 Thread Dimitri Liakhovitski
Hello! I have dates for the beginning of each week, e.g.: weekly<-data.frame(week=seq(as.Date("2010-04-01"), as.Date("2011-12-26"),by="week")) week # each week starts on a Monday I also have a vector of dates I am interested in, e.g.: july4<-as.Date(c("2010-07-04","2011-07-04")) I would like to

[R] Help with aggregate syntax for a multi-column function please.

2011-08-02 Thread Michael Karol
Dear R-experts: I am using a function called AUC whose arguments are data, time, id, and dv. data is the name of the dataframe, time is the independent variable column name, id is the subject id and dv is the dependent variable. The function computes area under the curve by trapezoidal

Re: [R] Memory limit in Aggregate()

2011-08-02 Thread peter dalgaard
On Aug 2, 2011, at 11:45 , Guillaume wrote: > Dear all, > I am trying to aggregate a table (divided in two lists here), but get a > memory error. > Here is the code I'm running : > > sessionInfo() > > print(paste("memory.limit() ", memory.limit())) > print(paste("memory.size() ",

Re: [R] execute r-code stored in a string variable

2011-08-02 Thread Ista Zahn
Hi Kim, You can use eval(parse(text = c)) Best, Ista On Tue, Aug 2, 2011 at 8:22 AM, Kim Lillesøe wrote: > Dear all > > I have a simple R question. How do I execute R-code stored in a variable? > > E.g if I have a variable which contains some R-code: > c = "reg <- lm(sales$sales~sales$price)" >

Re: [R] Functions for Sum of determinants of ranges of matrix subsets

2011-08-02 Thread Dennis Murphy
Hi: Try this: > z <- matrix(rnorm(100), nrow = 10) > sum(sapply(seq_len(nrow(z)), function(k) det(z[-k, -k]))) [1] 1421.06 where > sapply(seq_len(nrow(z)), function(k) det(z[-k, -k])) [1] 432.11613 81.65449 516.95791 54.72775 804.32097 -643.35436 [7] -411.15932 394.18780 84.13173 10

Re: [R] Identifying US holidays

2011-08-02 Thread Dimitri Liakhovitski
Thanks a lot, Michael - that's exactly what I was looking for! Dimitri On Tue, Aug 2, 2011 at 9:48 AM, R. Michael Weylandt wrote: > Now that I'm back at my computer, I'll actually suggest you do something > else entirely. > > If you look at the code of holidayNYSE() or by calling listHolidays()

Re: [R] efficient way to reduce running time

2011-08-02 Thread Dennis Murphy
Hi: Could you please provide a reproducible example? In your code, (i) n is undefined; (ii) logbp is undefined. A description of what you want to do and/or a reproducible example with an expected outcome would be useful. As the bottom of each e-mail to R-help says... PLEASE do read the posti

Re: [R] Identifying US holidays

2011-08-02 Thread R. Michael Weylandt
Now that I'm back at my computer, I'll actually suggest you do something else entirely. If you look at the code of holidayNYSE() or by calling listHolidays() of the timeDate package you'll see that there are many many functions that get every conceivable holiday directly. I'll let you pick the hol

Re: [R] Clean up a scatterplot with too much data

2011-08-02 Thread Paul Hiemstra
On 08/02/2011 01:07 PM, Dennis Murphy wrote: > In addition to the other responses (all of which I liked), a couple of > other alternatives to consider are 2D density plots (see ?kde2d in the > MASS package, for example) or geom_tile() in the ggplot2 package, > which you can think of as a 3D histog

Re: [R] Clean up a scatterplot with too much data

2011-08-02 Thread Dennis Murphy
In addition to the other responses (all of which I liked), a couple of other alternatives to consider are 2D density plots (see ?kde2d in the MASS package, for example) or geom_tile() in the ggplot2 package, which you can think of as a 3D histogram projected to 2D with color corresponding to (relat

[R] Odp: Using Function

2011-08-02 Thread Petr PIKAL
Hi > > Hi, > > I have some simple statistics to calculate for a large > number of variables. > I created a simple function to apply to variables. > I would like the variable name to be placed automatically. > I tried the following function but is not working. > > desc = function(x){ >

[R] execute r-code stored in a string variable

2011-08-02 Thread Kim Lillesøe
Dear all I have a simple R question. How do I execute R-code stored in a variable? E.g if I have a variable which contains some R-code: c = "reg <- lm(sales$sales~sales$price)" Is it possible to execute c E.g like Exec(c) I hope someone can help. Thank you Kim Lillesøe [[alternative H

[R] Problem Installing/Uninstalling Rattle

2011-08-02 Thread adarwish
Rattle won't install properly on my Windows 7 64 bit laptop. Here is what I've tried: I've followed the instructions here: http://rattle.togaware.com/rattle-install-mswindows.html I had R installed already. I downloaded the GTK+ packages, unzipped the 32 bit one into c:\gtkwin32. I put c:\gtkwin

[R] Functions for Sum of determinants of ranges of matrix subsets

2011-08-02 Thread john james
Dear R-help list, Pls I have this problem. Suppose I have a matrix of size nxn say, generated as follows   z<-matrix(rnorm(n*n,0,1),nrow=n)   I want to write a function such that for i in 1:n, I will remove the rows and columns corresponding to i (so, will be left with n-1*n-1 submatrix in each

Re: [R] Standard Deviation of a matrix

2011-08-02 Thread David Winsemius
On Aug 2, 2011, at 8:48 AM, Petr PIKAL wrote: Hi Hi! The sample below should give you what you want: M = matrix(runif(100), 10, 10) sd(as.numeric(M)) So the as.numeric command is the key. It transforms the matrix to a 1D vector. Or alternatively without using as.numeric: M = matrix(run

Re: [R] Standard Deviation of a matrix

2011-08-02 Thread Petr PIKAL
Hi > Hi! > > The sample below should give you what you want: > > M = matrix(runif(100), 10, 10) > sd(as.numeric(M)) > > So the as.numeric command is the key. It transforms the matrix to a 1D > vector. Or alternatively without using as.numeric: > > M = matrix(runif(100), 10, 10) > M > dim(M) =

Re: [R] Errors, driving me nuts

2011-08-02 Thread Paul Hiemstra
On 08/01/2011 08:47 PM, Matt Curcio wrote: > Greetings all, > I am getting this error that is driving me nuts... (not a long trip, haha) > > I have a set of files and in these files I want to calculate ttests on > rows 'compareA' and 'compareB' (these will change over time there I > want a variabl

Re: [R] Standard Deviation of a matrix

2011-08-02 Thread Paul Hiemstra
Hi! The sample below should give you what you want: M = matrix(runif(100), 10, 10) sd(as.numeric(M)) So the as.numeric command is the key. It transforms the matrix to a 1D vector. Or alternatively without using as.numeric: M = matrix(runif(100), 10, 10) M dim(M) = 100 M sd(M) Here I use the d

[R] Using Function

2011-08-02 Thread Silvano
Hi, I have some simple statistics to calculate for a large number of variables. I created a simple function to apply to variables. I would like the variable name to be placed automatically. I tried the following function but is not working. desc = function(x){ media = mean(x, n

[R] Standard Deviation of a matrix

2011-08-02 Thread chakri
Hello, My R knowledge could not take me any further, so this request ! I have a matrix of dimensions (1185 X 1185). I want to calculate standard deviation of entire matrix. sd function of {stats} calculates standard deviation for each row/column, giving 1 X 1185 matrix as result. I would like to

[R] efficient way to reduce running time

2011-08-02 Thread Kathie
Dear R users, Would you plz tell me how to avoid this "for" loop blow?? I think there might be a better way to reduce running time. -- ## y1 and y2 are n*1 vectors for (k in 1:n){

[R] Memory limit in Aggregate()

2011-08-02 Thread Guillaume
Dear all, I am trying to aggregate a table (divided in two lists here), but get a memory error. Here is the code I'm running : sessionInfo() print(paste("memory.limit() ", memory.limit())) print(paste("memory.size() ", memory.size())) print(paste("memory.size(TRUE) ", memory.size

Re: [R] Is R the right choice for simulating first passage times of random walks?

2011-08-02 Thread Paul Menzel
Dear Dennis and Steve, Am Sonntag, den 31.07.2011, 23:32 -0400 schrieb Steve Lianoglou: […] > How about trying to write the of this `f4` function below using the > rcpp/inline combo. The C/C++ you will need to write looks to be quite > trivial, let's change f4 to accept an x argument as a vecto

Re: [R] Plotting question

2011-08-02 Thread Karl Ove Hufthammer
Andrew McCulloch wrote: > I use R to draw my graphs. I have 100 points on a simple xy-plot. The > points are distinguished by a third variable which is categorical with 10 > levels. I have been plotting x against y and using gray scales to > distinguish the level of the categorical variable for ea

  1   2   >