Re: [R] the problem about sample size

2012-02-29 Thread Petr PIKAL
Hi > > Hi, there, > > I run into the same sample size error in JM. Have you found the solution for > the error? What error? Petr > > Many thanks, > Helena > > -- > View this message in context: http://r.789695.n4.nabble.com/the-problem- > about-sample-size-tp1592855p4434009.html > Sent from

Re: [R] To define a function which includes two functions as arguments such as "plot" and "text"

2012-02-29 Thread Yashwanth M.R
Thank you for the suggestions you have included in the mail. Since this is my first job and this is the first time I am coordinating with a mailing list so I was not aware of these formalities. My objective of writing this function is to produce a personalized report using "R2HTML". We interna

[R] User defined link function with extra parameters

2012-02-29 Thread Bernardo Powaga
Hello R users, I would like to fit a generalized linear model for the binomial family with some non standard link functions. For instance, this is the Aranda-Ordaz link: η = ln( ( (1 - π)^-α - 1 )/α) I know how to define a new link function to use with glm(), but I my problem is that I have

[R] ordered lable in ROCR

2012-02-29 Thread genomenet
Hi There, I don't understand how to order the label in ROCR package in order to get the correct result. I am wondering whether you can help me. library(ROCR) data(ROCR.simple) pred <- prediction(ROCR.simple$predictions,ROCR.simple$labels) svm.auc <- performance(pred, 'tpr', 'fpr') plot(svm.auc)

[R] ordered lable in ROCR

2012-02-29 Thread genomenet
Hi There, I don't understand how to order the label in ROCR package in order to get the correct result. I am wondering whether you can help me. library(ROCR) data(ROCR.simple) pred <- prediction(ROCR.simple$predictions,ROCR.simple$labels) svm.auc <- performance(pred, 'tpr', 'fpr') plot(svm.auc)

[R] GLM with regularization

2012-02-29 Thread Dmitriy Lyubimov
Hello, Thank you for probably not so new question, but i am new to R. Does any of packages have something like glm+regularization? So far i see probably something close to that as a ridge regression in MASS but I think i need something like GLM, in particular binomial regularized versions of poly

Re: [R] the problem about sample size

2012-02-29 Thread hchui
Hi, there, I run into the same sample size error in JM. Have you found the solution for the error? Many thanks, Helena -- View this message in context: http://r.789695.n4.nabble.com/the-problem-about-sample-size-tp1592855p4434009.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] identifying a column name correctly to use in a formula

2012-02-29 Thread Rui Barradas
Hello, > > I have a large matrix (SNPs) that I want to cycle over with logistic > regression with interaction terms. I have made a loop but I am struggling > to identify to the formula the name of the column in a way which is > meaningful to the formula. It errors becasue it is not evaluated propo

Re: [R] Using a FOR LOOP to name objects

2012-02-29 Thread michaelyb
Michael - thank you so much! Just what I needed! -- View this message in context: http://r.789695.n4.nabble.com/Using-a-FOR-LOOP-to-name-objects-tp4430454p4433903.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org ma

Re: [R] How to extract numerical values from time series forecast

2012-02-29 Thread R. Michael Weylandt
Perhaps you need the forecast() function? Michael On Wed, Feb 29, 2012 at 12:01 PM, ForzaBruta wrote: > hi all. i'm busy with some time series data, starting from an earlier period > until the current day. > > i have created a time series forecast taking into account the entire data > from the e

Re: [R] How are the coefficients for the ur.ers, type DF-GLS calculated?

2012-02-29 Thread R. Michael Weylandt
Simply type ur.ers on a line by itself to see how the calculation is implemented. Michael On Wed, Feb 29, 2012 at 11:20 AM, ackbar03 wrote: > I need some real help on this, really stuck > > how are the coefficients for > ur.ers(y, type = c("DF-GLS", "P-test"), model = c("constant", "trend"), >  

Re: [R] identifying a column name correctly to use in a formula

2012-02-29 Thread R. Michael Weylandt
Your method of constructing a formula is funny: is there a term called "interaction" or do you mean an interaction in the statistical sense? Once you do that, I'd think the easiest way to proceed is to use as.formula() to construct your formula programmatically and then to pass that to glm(). Somet

Re: [R] Plotting a registered sign

2012-02-29 Thread Marc Schwartz
On Feb 29, 2012, at 7:41 PM, Dennis Fisher wrote: > R 2.14.0 > OS X > > Colleagues > > Probably a simple question but it alludes me at the moment. I want to embed > a registered sign in the text in a legend. The text would look like: > SOMETEXT® > with ® superscripted. > > Thanks in

[R] Re : Create a function "automatically" from lm formula and coefficients?

2012-02-29 Thread Pascal Oettli
Hi Keith, Do you mean as "predict.lm" can do? Regards, Pascal De : Keith Weintraub À : r-help@r-project.org Envoyé le : Jeudi 1 mars 2012 11h41 Objet : [R] Create a function "automatically" from lm formula and coefficients? I hope the subject says it all. I

[R] Simulate values from VAR

2012-02-29 Thread Keith Weintraub
Folks, What is the best way to simulate values from a fitted "VAR {vars}" model. Also I have tried to use SVAR for a cointegration fit of y~x (just two univariate time-series) but I can't figure out how to set up the "A" matrix so that x_t can be used as a contemporaneous predictor of y_t. Th

Re: [R] Create a function "automatically" from lm formula and coefficients?

2012-02-29 Thread Frank Harrell
require(rms) f <- ols(y ~ rcs(age,4)*sex + blood.pressure + rcs(height,5)) latex(f) # typeset algebraic form of model Function(f) # create an R function that computes Y hat Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r

[R] Create a function "automatically" from lm formula and coefficients?

2012-02-29 Thread Keith Weintraub
I hope the subject says it all. I want to be able to use an lm object and the associated coefficients to create function that can produce "expected" "y" values given inputs. Thanks, KW -- [[alternative HTML version deleted]] __ R-help@r-pr

[R] Plotting a registered sign

2012-02-29 Thread Dennis Fisher
R 2.14.0 OS X Colleagues Probably a simple question but it alludes me at the moment. I want to embed a registered sign in the text in a legend. The text would look like: SOMETEXT® with ® superscripted. Thanks in advance. Dennis Dennis Fisher MD P < (The "P Less Than" Company) Pho

Re: [R] Binning continuous data

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 5:01 PM, Faryabi, Robert (NIH/NCI) [F] wrote: Hi there, Here is the scenario: I have a measurement of some sort for two variables, I would like to figure out a rough pattern between them. Let say if the values of the first variable are low, middle, high, and extremely

Re: [R] Cannot use negative argument in function

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 7:05 PM, lidaky wrote: the "*" character in front of the Temp variable is there because i just wanted to bold the variable in the threade that you can see where it is used. I just restart my computer and R. Now the function is working great. No clue what was happenin

Re: [R] Contour plot- repost message

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 7:08 PM, Leong Keat Chan wrote: Hi, I would like to make a contour plot using R with the following information (data at the end): x-axis= arranged according to day (from 1 to 365, labels= use I am really getting tired of seeing this message. This must be the fourth du

[R] identifying a column name correctly to use in a formula

2012-02-29 Thread Philip Robinson
Hi, I have a large matrix (SNPs) that I want to cycle over with logistic regression with interaction terms. I have made a loop but I am struggling to identify to the formula the name of the column in a way which is meaningful to the formula. It errors becasue it is not evaluated proporly. (below

Re: [R] linear regression by column

2012-02-29 Thread Peter Ehlers
On 2012-02-29 15:45, David Winsemius wrote: On Feb 29, 2012, at 6:39 PM, David Winsemius wrote: On Feb 29, 2012, at 1:53 PM, Filoche wrote: Hi everyone. I have a DF with the first column being my independant variable and all other columns the dependent variables. Something like: x

Re: [R] TM reader with text

2012-02-29 Thread Mickael R problem
my computer run under windows vista 64 sp2. The question about encoding, I don't understand it, sorry ? -- View this message in context: http://r.789695.n4.nabble.com/TM-reader-with-text-tp4433394p4433526.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Cannot use negative argument in function

2012-02-29 Thread lidaky
the "*" character in front of the Temp variable is there because i just wanted to bold the variable in the threade that you can see where it is used. I just restart my computer and R. Now the function is working great. No clue what was happening, but now everything works. Sorry for the false notic

Re: [R] Contour plot- repost message

2012-02-29 Thread Leong Keat Chan
Hi, I would like to make a contour plot using R with the following information (data at the end): x-axis= arranged according to day (from 1 to 365, labels= use months; up to 365 days in one year), y-axis= depth (labels from 0 at the top to 7 at the bottom; this is a water depth profile), and z-a

Re: [R] R can't load a large dataset

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 7:00 PM, Francesco Sarracino wrote: Dear R listers, I have a silly problem. I am trying to load a dta (Stata) file in R. The dta is about 650 MB and contains the integrated World Values Survey/ European Value Study data-set. My problem is that I don't manage to load the fil

Re: [R] The joys of Nabble: Re: Cannot use negative argument in function

2012-02-29 Thread Duncan Murdoch
On 12-02-29 6:28 PM, Sarah Goslee wrote: This is yet another problem with the Nabble interface to the list. On Wed, Feb 29, 2012 at 6:21 PM, Richard M. Heiberger wrote: This line TT<- *Temp*+273.15 makes it unexecutable. that is not the error you mentioned. On nabble, that variable is in

Re: [R] TM reader with text

2012-02-29 Thread Richard M. Heiberger
Most, maybe all, of the example words you posted include ligatures, With "financier" for example, the leading "fi" is rendered in PDF and in most typesetting situations as a ligature with the a single complex character representing the "fi' combination. fi fl I pasted the "fi" and "fl" ligature

Re: [R] ggplot2 dot chart-start at zero

2012-02-29 Thread Robert Baer
Not sure I'm interpreting what you want to do correctly, but how about: p2 <- pa + scale_x_continuous(limits=c(0,80)) p2 -Original Message- From: John Kane Sent: Wednesday, February 29, 2012 2:32 PM To: r-help@r-project.org Subject: [R] ggplot2 dot chart-start at zero I am trying to

Re: [R] Contour plot

2012-02-29 Thread Leong Keat Chan
Hi, I would like to make a contour plot using R with the following information (data at the end): x-axis= arranged according to day (from 1 to 365, labels= use months; up to 365 days in one year), y-axis= depth (labels from 0 at the top to 7 at the bottom; this is a water depth profile), and z-a

[R] R can't load a large dataset

2012-02-29 Thread Francesco Sarracino
Dear R listers, I have a silly problem. I am trying to load a dta (Stata) file in R. The dta is about 650 MB and contains the integrated World Values Survey/ European Value Study data-set. My problem is that I don't manage to load the file. After almost 1 hour I issued the following command: data

Re: [R] puzzling results from logistic regression

2012-02-29 Thread Peter Ehlers
Michael (OP), Not that it's necessary, but you might also find confint(aa) to be instructive. Peter Ehlers On 2012-02-29 07:20, R. Michael Weylandt wrote: Formally, look at Pr(>|z|). Informally, look at the null and residual deviances from print(aa). Michael On Wed, Feb 29, 2012 at 10:14 AM

Re: [R] TM reader with text

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 6:00 PM, Mickael R problem wrote: Hello everybody, I work, I try, with TM but I have a problem with some special words in french. I think this is due to the manner to transform PDF to text, but I'm not perfectly sure. Let's see to the example : findFreqTerms(tdm1,30)

Re: [R] linear regression by column

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 6:39 PM, David Winsemius wrote: On Feb 29, 2012, at 1:53 PM, Filoche wrote: Hi everyone. I have a DF with the first column being my independant variable and all other columns the dependent variables. Something like: x y1 y2 y3 ... ... ...

Re: [R] Cannot use negative argument in function

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 2:14 PM, lidaky wrote: index.refraction <- function(Temp,Press, RH, CO2) { #define constant lambda <- 531 #nm Co <- 299792458 #m/s ww <- c(295.235,2.6422,-0.03238,0.004028) kk <- c( 238.0185 ,5792105 ,57.362 ,167917) aa <- c( 1.58123 * 10^(-6) , -2.9331 * 10^(-8)

Re: [R] linear regression by column

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 1:53 PM, Filoche wrote: Hi everyone. I have a DF with the first column being my independant variable and all other columns the dependent variables. Something like: x y1 y2 y3 ... ... ... ... ... ... ... ... What I'm trying to do

Re: [R] regular expression

2012-02-29 Thread Justin Haynes
gsub('.+; (.+);.+','\\1',x) or if you just want the value out: gsub('.+; Surv\\(months\\): ([0-9]+);.+','\\1',x) You can also look at strsplit: > strsplit(x,';') [[1]] [1] "99-625: Cell type: S"" Surv(months): 21" " STATUS(0=alive, 1=dead): 1" > lapply(strsplit(x,';'),'[',2) [

Re: [R] regular expression

2012-02-29 Thread Gabor Grothendieck
On Wed, Feb 29, 2012 at 2:24 PM, Fred G wrote: > Computer Friends, > > with the following example lines: > > [107] "98-610: Cell type: S; Surv(months): 6; STATUS(0=alive, 1=dead): 1" > > [108] "99-625: Cell type: S; Surv(months): 21; STATUS(0=alive, 1=dead): 1" > > i want to be able to isolate the

Re: [R] regular expression

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 2:24 PM, Fred G wrote: Computer Friends, with the following example lines: Modified to be correct R code. Please emulate my example in the future. inp <-c( "98-610: Cell type: S; Surv(months): 6; STATUS(0=alive, 1=dead): 1", "99-625: Cell type: S; Surv(months): 21; ST

[R] The joys of Nabble: Re: Cannot use negative argument in function

2012-02-29 Thread Sarah Goslee
This is yet another problem with the Nabble interface to the list. On Wed, Feb 29, 2012 at 6:21 PM, Richard M. Heiberger wrote: > This line > >  TT <- *Temp*+273.15 > makes it unexecutable.  that is not the error you mentioned. On nabble, that variable is in bold. When it's reformatted for the p

Re: [R] Contour plot

2012-02-29 Thread Leong Keat Chan
Hi, I would like to make a contour plot using R with the following information (data at the end): x-axis= arranged according to day (from 1 to 365, labels= use months; up to 365 days in one year), y-axis= depth (labels from 0 at the top to 7 at the bottom; this is a water depth profile), and z-a

Re: [R] Cannot use negative argument in function

2012-02-29 Thread Richard M. Heiberger
This line TT <- *Temp*+273.15 makes it unexecutable. that is not the error you mentioned. should that be TT <- "Temp"+273.15 or TT <- Temp+273.15 or something else? On Wed, Feb 29, 2012 at 2:14 PM, lidaky wrote: > here is the code: > > index.refraction <- function(Temp,Press, RH, CO2) > {

[R] TM reader with text

2012-02-29 Thread Mickael R problem
Hello everybody, I work, I try, with TM but I have a problem with some special words in french. I think this is due to the manner to transform PDF to text, but I'm not perfectly sure. Let's see to the example : findFreqTerms(tdm1,30) [33] """n" "nancement" "nancier"

[R] NaN in nlminb

2012-02-29 Thread Alexandr
Good day everybody! Please help me with NaN result in nlminb function. I use the following: The function that present weighted maximum likelihood: garchLLH<- function(parm) { mu = parm[1]; omega = parm[2]; alpha = parm[3]; beta = parm[4] z = (x-mu); Mean = mean(z^2) # Use Filter Representation: e

Re: [R] Contour plot

2012-02-29 Thread lkchan
Hi, I would like to make a contour plot with the data below, x-axis= Day (increasing order, day number is out of 365 days of a year), y-axis= Depth (varies), and z=pH. I tried to use filled.contour function, but not sure the proper way to ordinate my z results into a matrix with different x and y l

[R] regular expression

2012-02-29 Thread Fred G
Computer Friends, with the following example lines: [107] "98-610: Cell type: S; Surv(months): 6; STATUS(0=alive, 1=dead): 1" [108] "99-625: Cell type: S; Surv(months): 21; STATUS(0=alive, 1=dead): 1" i want to be able to isolate the number of months of survival for each row. is there a regula

Re: [R] function for filtering and deleting vector entries

2012-02-29 Thread Rui Barradas
Hello, babyluck wrote > > Dear helpers > > I have two data sets saved as vectors (temperature and velocity). Now I > need to "take out" a span of temperature and its corresponding velocity in > the other vector. How can I achieve that? > > I tried to write a function,which takes a vector entr

[R] linear regression by column

2012-02-29 Thread Filoche
Hi everyone. I have a DF with the first column being my independant variable and all other columns the dependent variables. Something like: x y1 y2 y3 ... ... ... ... ... ... ... ... What I'm trying to do is to perform a linear model for each of my "y". I

Re: [R] Cannot use negative argument in function

2012-02-29 Thread lidaky
here is the code: index.refraction <- function(Temp,Press, RH, CO2) { #define constant lambda <- 531 #nm Co <- 299792458 #m/s ww <- c(295.235,2.6422,-0.03238,0.004028) kk <- c( 238.0185 ,5792105 ,57.362 ,167917) aa <- c( 1.58123 * 10^(-6) , -2.9331 * 10^(-8) , 1.1043 * 10^(-10))

[R] Binning continuous data

2012-02-29 Thread Faryabi, Robert (NIH/NCI) [F]
Hi there, Here is the scenario: I have a measurement of some sort for two variables, I would like to figure out a rough pattern between them. Let say if the values of the first variable are low, middle, high, and extremely high, then what would be the corresponding pattern of the second variab

Re: [R] Quantile scores as dependent variables.. an R and general method question

2012-02-29 Thread Doran, Harold
Typically this list doesn't support general statistical questions and unfortunately I don't have a better recommendation. It may be more helpful for you to work with a statistician than seek help here. My point is simply that quantile regression is not for modeling outcomes that are quantiles.

Re: [R] Quantile scores as dependent variables.. an R and general method question

2012-02-29 Thread ilai
On Wed, Feb 29, 2012 at 1:23 PM, Doran, Harold wrote: > > The OP is looking for a way to deal with outcomes scores that are quantiles, > not a method that models different quantiles of the conditional distribution > where an outcome is a continuous variable. So, I don't think QR methods is > wh

Re: [R] function for filtering and deleting vector entries

2012-02-29 Thread andrija djurovic
Hi. Maybe this will help you: set.seed(1) temp <- 1:100 v <- rnorm(100) temp[temp<16 | temp>38] v[temp<16 | temp>38] Andrija On Wed, Feb 29, 2012 at 7:09 PM, babyluck wrote: > Dear helpers > > I have two data sets saved as vectors (temperature and velocity). Now I need > to "take out" a span

Re: [R] Trying to eliminate a for loop

2012-02-29 Thread Steven Wolf
Yes! That works. Thank you so much! -Steve -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Petr Savicky Sent: Wednesday, February 29, 2012 4:41 PM To: r-help@r-project.org Subject: Re: [R] Trying to eliminate a for loop On Wed,

Re: [R] memory management

2012-02-29 Thread Sam Steingold
> * [2012-02-29 13:55:25 -0600]: > On Wed, 29 Feb 2012, Sam Steingold wrote: >> compacting garbage collector is our best friend! > > Which R does not use because of the problems it would create for > external C/Fortran code on which R heavily relies. Well, you know better, of course. However, I

Re: [R] Cleaning up messy Excel data

2012-02-29 Thread Rolf Turner
On 01/03/12 04:43, John Kane wrote: (mydata<- as.factor(c("1","2","3", ">2", "5", ">2"))) str(mydata) newdata<- as.character(mydata) newdata[newdata==">2"]<- 0 newdata<- as.numeric(newdata) str(newdata) We really need to keep Excel (and other spreadsheets) out of peoples hands. Amen, bro'!!!

Re: [R] Trying to eliminate a for loop

2012-02-29 Thread Petr Savicky
On Wed, Feb 29, 2012 at 03:52:15PM -0500, Steven Wolf wrote: > I keep trying to eliminate for loops when I arrive at them, but this one is > stumping me. What is the nifty way to do this? > > My object data.cca is the output of the cancor function (for some two > datasets X and Y) (data.cca is a

Re: [R] Frequencies from x/y data into a 2d table (for 3d histogram or heatmap)

2012-02-29 Thread Marcio Pupin Mello
Hi David, thanks a lot! Actually, I was looking for the graph since I still have obtained the table... but It can help... Best, Marcio www.dsr.inpe.br/~mello On 2/29/12 5:34 PM, David L Carlson wrote: Something like this? x<- round(runif(100, 0, 40), 0) y<- round(runif(100, 0, 40), 0)

Re: [R] how to print km square in the form of km2

2012-02-29 Thread Rolf Turner
On 01/03/12 10:27, Elaine Kuo wrote: Hello Rolf, Thank you for the response. I tried your command but it did not work. plot(1:10,ylab="y",xlab=expression(plain(km)^2)) Please kindly advise any other method to make "2" in km2 become a uppercase number. Thanks again. The expression ``upperc

Re: [R] how to print km square in the form of km2

2012-02-29 Thread Sarah Goslee
Try plot(1:10,ylab="y",xlab=expression(km^2)) and if that fails, you'll need to tell us what you mean by "did not work." Sarah On Wed, Feb 29, 2012 at 4:27 PM, Elaine Kuo wrote: > Hello Rolf, > > Thank you for the response. > > I tried your command but it did not work. >  plot(1:10,ylab="y",xlab

Re: [R] how to print km square in the form of km2

2012-02-29 Thread Elaine Kuo
Hello Rolf, Thank you for the response. I tried your command but it did not work. plot(1:10,ylab="y",xlab=**expression(plain(km)^2)) Please kindly advise any other method to make "2" in km2 become a uppercase number. Thanks again. Elaine On Tue, Feb 21, 2012 at 8:24 AM, Rolf Turner wrote:

[R] Trying to eliminate a for loop

2012-02-29 Thread Steven Wolf
I keep trying to eliminate for loops when I arrive at them, but this one is stumping me. What is the nifty way to do this? My object data.cca is the output of the cancor function (for some two datasets X and Y) (data.cca is a numeric vector) data.cca <- cancor(X,Y) Xcen=0*X for(i in 1:dim(X)[1]

Re: [R] Frequencies from x/y data into a 2d table (for 3d histogram or heatmap)

2012-02-29 Thread David L Carlson
Something like this? x <- round(runif(100, 0, 40), 0) y <- round(runif(100, 0, 40), 0) xgroup <- cut(x, seq(0, 40, 10), include.lowest=TRUE) ygroup <- cut(y, seq(0, 40, 10), include.lowest=TRUE) xy <- table(xgroup, ygroup) image(xy) You'll still have to work with the plot commands to label it pro

[R] ggplot2 dot chart-start at zero

2012-02-29 Thread John Kane
I am trying to create a simple dot-plot in ggplot2 with a solid line from the y-axis to the dot, something I first saw in Cleveland's 1984 book What I would like is to have the graph start at zero on the x-axis but leave some space on the right side of the plot area. I assumed that I should be

Re: [R] puzzling results from logistic regression

2012-02-29 Thread Ben Bolker
Michael gmail.com> writes: > > Hi all, > > As you can see from below, the result is strange... > > I would imagined that the bb result should be much higher and close to 1, > any way to improve the fit? > > Any other classification methods? > > Thank you! > > data=data.frame(y=rep(c(0, 1),

Re: [R] Quantile scores as dependent variables.. an R and general method question

2012-02-29 Thread Doran, Harold
Rob The OP is looking for a way to deal with outcomes scores that are quantiles, not a method that models different quantiles of the conditional distribution where an outcome is a continuous variable. So, I don't think QR methods is what is needed. From

Re: [R] How can I avoid the warning messages when calling DAAG package?

2012-02-29 Thread Uwe Ligges
On 29.02.2012 15:19, Jason Love wrote: Dear R users, I'm a newbie for R and want to ask some basic questions. So, after I open the R software, I typed library(DAAG). Then, I get massive warning messages as shown below. Why does it happen? Also, here are few specific questions regarding each

Re: [R] memory management

2012-02-29 Thread luke-tierney
On Wed, 29 Feb 2012, Sam Steingold wrote: * Milan Bouchet-Valat [2012-02-29 18:18:50 +0100]: I think you're simply hitting a (terrible) OS limitation. Linux is very often not able to reclaim the memory R has used because it's fragmented. The OS can only get the pages back if nothing is above

Re: [R] orthogonal distance regression package?

2012-02-29 Thread Adam Waytz
Thanks all. This is tremendously helpful. Best, Adam On Feb 29, 2012, at 12:58 PM, David Reiner wrote: > My understanding is that TLS, EIV, and orthogonal regression are closely > related but separate concepts. > If you read the 'Talk' at the Wikipedia page referenced below, you will see >

[R] Question about tables in bigtabulate

2012-02-29 Thread steven mosher
I have a large file backed big. matrix, with millions of rows and 20 columns. The columns contain data that I simply need to tabulate. There are a few dozen unique values. and I just want a frequency count Test code with a small "big" matrix. library(bigmemory) library(bigtabulate) test <- bi

Re: [R] orthogonal distance regression package?

2012-02-29 Thread David Reiner
My understanding is that TLS, EIV, and orthogonal regression are closely related but separate concepts. If you read the 'Talk' at the Wikipedia page referenced below, you will see that many people have terminology problems as well. My take is that TLS is a special case of EIV and orthogonal line

Re: [R] Frequencies from x/y data into a 2d table (for 3d histogram or heatmap)

2012-02-29 Thread Marcio Pupin Mello
Hi Ralf, have you solved your problem?! If so, could you share? I have the same problem... Best, Marcio On 3/25/10 6:03 PM, Ralf B wrote: Hi all, I have simple x/y data from screen recording in a sequence: number,x,y 1,10,30 1,20, 1,43,110 1,74,18 1,88,112 and would like

Re: [R] Volcano Plot

2012-02-29 Thread Martin Morgan
On 02/28/2012 08:13 AM, aishsk wrote: Hi I am using the ggplot2 package for the volcano plot and I am using the following code for the same: g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold)) + + geom_point(alpha=0.4, size=1.75) + + opts(legend.position = "none") +

Re: [R] orthogonal distance regression package?

2012-02-29 Thread Mark Leeds
Hi: I can't find it anywhere on the internet but I have a book that shows that, as long as the SVD of the X matrix can be obtained, then the coefficient solution to TLS ( least angle regression ) is only a function of the eigenvectors. Therefore, principal components can be used to obtain the coef

Re: [R] Quantile scores as dependent variables.. an R and general method question

2012-02-29 Thread ilai
On Tue, Feb 28, 2012 at 3:54 PM, Rob James wrote: > I have a dataset that does not include native scores, but only serial > quantile rankings for a set of units. > > Clearly these observations are dependent (in that you can't alter one > observation without also altering others). > > Are there met

Re: [R] Computing line= for mtext

2012-02-29 Thread Richard M. Heiberger
Frank, This can be done directly with a variant of the panel.axis function. See function panel.axis.right in the HH package. This was provided for me by David Winsemius in response to my query on this list in October 2011 https://stat.ethz.ch/pipermail/r-help/2011-October/292806.html The email t

Re: [R] Coding help

2012-02-29 Thread Petr Savicky
On Wed, Feb 29, 2012 at 11:58:04AM -0500, Ayyappa Chaturvedula wrote: > Dear Group, > > I have the following dataset: >ID REPI DV CONC SS > 11 156.84 116 0 > 1 2 146.56 116 0 >13 115.13 116 0 >14 207.81 116 0 > 15 129.53 116 0 > 16 151.48

[R] function for filtering and deleting vector entries

2012-02-29 Thread babyluck
Dear helpers I have two data sets saved as vectors (temperature and velocity). Now I need to "take out" a span of temperature and its corresponding velocity in the other vector. How can I achieve that? I tried to write a function,which takes a vector entry and then decides wether to delete the t

Re: [R] orthogonal distance regression package?

2012-02-29 Thread Adam Waytz
In the age of google, I have found that concepts such as these are more complex than what Wikipedia provides. Going far beyond a cursory search, it appeared to me there are subtle differences between these terms. I was hoping this knowledgeable community could provide insight on an R package to

Re: [R] orthogonal distance regression package?

2012-02-29 Thread Bert Gunter
On Wed, Feb 29, 2012 at 7:53 AM, Adam Waytz wrote: > > Hello, > > I am extremely new to R and have found some leads to this question in the > archives, but I am still a bit uncertain. > I am looking for an R package to carry out orthogonal distance regression.  I > found some answers regarding D

Re: [R] equivalent from gladder and ladder from stata

2012-02-29 Thread Richard M. Heiberger
>From your description, I believe the ladder function in the HH package is what you are looking for. ## install.packages("HH") ## if necessary library(HH) data(tv) ladder(life.exp ~ ppl.per.phys, data=tv, scales=list(relation="free")) Rich On Wed, Feb 29, 2012 at 6:21 AM, agent dunham wrote:

Re: [R] How to simulate demographic (specifically, sub-group) data?

2012-02-29 Thread Chris Campbell
Hi Alok See ?createCovariates in MSToolkit. Best wishes Chris Chris Campbell MANGO SOLUTIONS Data Analysis that Delivers +44 1249 705450 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Bhupatkar, Alok Sent: 29 February 2012 16:

Re: [R] memory management

2012-02-29 Thread Sam Steingold
> * Milan Bouchet-Valat [2012-02-29 18:18:50 +0100]: > > I think you're simply hitting a (terrible) OS limitation. Linux is > very often not able to reclaim the memory R has used because it's > fragmented. The OS can only get the pages back if nothing is above > them, and most of the time there i

Re: [R] R newbie: Installation of package reshape exit status not 0

2012-02-29 Thread David Winsemius
On Feb 29, 2012, at 12:34 PM, ibid...@gmx.at wrote: Hello, sorry i'm an R newbie and wan't to install ggplot2 on my ubuntu system. during installation i got the error warning: Warnmeldung: In install.packages("reshape") : Installation des Pakets 'reshape' hatte Exit-Status ungleich 0 Please,

Re: [R] R newbie: Installation of package reshape exit status not 0

2012-02-29 Thread Uwe Ligges
On 29.02.2012 18:34, ibid...@gmx.at wrote: Hello, sorry i'm an R newbie and wan't to install ggplot2 on my ubuntu system. during installation i got the error warning: Warnmeldung: In install.packages("reshape") : Installation des Pakets 'reshape' hatte Exit-Status ungleich 0 Please, give m

Re: [R] To define a function which includes two functions as arguments such as "plot" and "text"

2012-02-29 Thread Uwe Ligges
On 28.02.2012 07:04, Yashwanth M.R wrote: Hi Mr. Uwe Ligges, Yashwanth M.R, this is the R-help mailing list, not my personal mail account (and "Mr." is inappropriate in any case). I really thankful for the reply. I even tried the same, means writing the new function

Re: [R] Help please

2012-02-29 Thread Uwe Ligges
On 29.02.2012 17:36, Raúl Fernández Naranjo wrote: Hi everyone, I was using rattle. I used a database with 4 individuals and 50 variables. Reading the database was OK and that was made by rattle but when y was trying to draw the tree, rattle shows the image attached. And have

Re: [R] Converting a function from Splus to R

2012-02-29 Thread William Dunlap
1.0d+0 is Fortran (not C) for a double precision value, 1.0 * 10^0. 1.0e+0 is Fortran for a single precision value, 1.0 * 10^0 and C for a double precision value. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-h

[R] R newbie: Installation of package reshape exit status not 0

2012-02-29 Thread ibidrin
Hello, sorry i'm an R newbie and wan't to install ggplot2 on my ubuntu system. during installation i got the error warning: Warnmeldung: In install.packages("reshape") : Installation des Pakets 'reshape' hatte Exit-Status ungleich 0 Please, give me a idea, how can i fix this error/warning -

[R] How to extract numerical values from time series forecast

2012-02-29 Thread ForzaBruta
hi all. i'm busy with some time series data, starting from an earlier period until the current day. i have created a time series forecast taking into account the entire data from the earlier date up until 2007, using the "forecast" package for R. i am comparing this forecasted data to the actual/

[R] How to simulate demographic (specifically, sub-group) data?

2012-02-29 Thread Bhupatkar, Alok
I am a relatively new R user and have recently built a multivariate dataset without the demographic information. Is there any package or code to simulate subgroup dataset (race, sex, age) using R? Any help would be appreciated. Thanks, Alok [[alternative HTML version deleted]] __

[R] orthogonal distance regression package?

2012-02-29 Thread Adam Waytz
Hello, I am extremely new to R and have found some leads to this question in the archives, but I am still a bit uncertain. I am looking for an R package to carry out orthogonal distance regression. I found some answers regarding Deming regression and Total Least Squares regression, but I was u

[R] Help please

2012-02-29 Thread Raúl Fernández Naranjo
Hi everyone, I was using rattle. I used a database with 4 individuals and 50 variables. Reading the database was OK and that was made by rattle but when y was trying to draw the tree, rattle shows the image attached. Please help me. Raúl Fernández

Re: [R] Error: could not find function "hier.part"

2012-02-29 Thread Amay
Thank you Michael. I also wrote to the author of this program, Palph, he suggested the same thing. It worked!! It is a very useful tool. In case for someone who is interested, I found the package here: http://cran.r-project.org/web/packages/hier.part/ -- View this message in context: http://r

Re: [R] Installing package QRMlib

2012-02-29 Thread DT54321
That worked! Thanks a lot Jeremy. -- View this message in context: http://r.789695.n4.nabble.com/Installing-package-QRMlib-tp4425269p4431895.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://st

Re: [R] How to replace the values in a column

2012-02-29 Thread Rui Barradas
Hello, Try the following. (In Andrija's code I've changed 'df' to 'DF', 'df' is a R function name) DF <- read.table( ... etc ... tc <- textConnection(" Column1(Gen)Column2(Name) A_1 Wynda A_2 A_2 B_1

[R] use of subset in lme function

2012-02-29 Thread amace
Dear all, I have an issue concerning the lme function and I couldn't find the solution elsewhere. I have a data frame with id, Ages, Parameter1 and Parameter2. The Ages can belong to one of two categories "early" or "late". Then for example an id can have several values of Parameter1 at differ

[R] How are the coefficients for the ur.ers, type DF-GLS calculated?

2012-02-29 Thread ackbar03
I need some real help on this, really stuck how are the coefficients for ur.ers(y, type = c("DF-GLS", "P-test"), model = c("constant", "trend"), lag.max = 0) The max lag is set at zero, so the regression should simply be Diff(zt) = a*z(t-1) where a is the value i'm trying to find and z(t

Re: [R] memory management

2012-02-29 Thread Milan Bouchet-Valat
Le mercredi 29 février 2012 à 11:42 -0500, Sam Steingold a écrit : > > * William Dunlap [2012-02-28 23:06:54 +]: > > > > You need to walk through the objects, checking for environments on > > each component or attribute of an object. > > so why doesn't object.size do that? > > > > f <- fun

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