Re: [R] installation of package 'mapproj' had non-zero exit status

2011-07-12 Thread Ray Brownrigg
On Wed, 13 Jul 2011, B77S wrote: > ## Hello.. I have asked a similar question, but this is not fixed as > before. > > ## I am running the following using Ubuntu OS: > > R version 2.13.1 (2011-07-08) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x

Re: [R] exponent function help??

2011-07-12 Thread Ben Bolker
mousy0815 gmail.com> writes: > I'm trying to make a function that will output the exponent... so f2(2,2) = 4 > and f2(2,3)=8. But I don't want to just use the x^n function, I want to do > it another way, and without a recursion. I did the follow code but for some > reason it doesn't work. Help pl

[R] question on formula and terms.formula()

2011-07-12 Thread pangdu
I'm trying to create a formula object to pass on to a function that applies the function terms.formula() to it. f <- function(formula, ...) { ... mf <- match.call() term <- terms.formula(mf$formula) ... } However, my code below gives an error. form <- as.formula("y~x") f(form, ...) The error

Re: [R] Hardy Weinberg Case Control Test in gap R package

2011-07-12 Thread Jim Silverton
Hi, I am using the gap R package to do the Hardy Weinberg Case Control test for many SNP. I am not sure what the values initial1 and initial2 should be for the test. I tried values but they failed. I emailed the author but to no avail. There seems to be some documentation that is deleted at the to

Re: [R] simple save question

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 5:43 PM, Tom La Bone wrote: Thank you for the reply Dr. Winsemius. Can you take your answer a step further and, in the context of the simple, reproducible example, illustrate how it is done? I would appreciate it. Tom The easy way is: > sfit <- summary(fit) > sfit$ta

[R] exponent function help??

2011-07-12 Thread mousy0815
I'm trying to make a function that will output the exponent... so f2(2,2) = 4 and f2(2,3)=8. But I don't want to just use the x^n function, I want to do it another way, and without a recursion. I did the follow code but for some reason it doesn't work. Help please? f2 <- function(x, n) #without r

Re: [R] What's wrong with my code? (Edited version-added my data)

2011-07-12 Thread Joshua Wiley
Dear Susie, I'm glad the pieces are working. Sorry if I wasn't clear before, when I said break down into smaller pieces, I meant for testing and figuring out what's wrong. If you have everything in separate loops, they will be completed individually, so reading all the datasets will be done a

Re: [R] What's wrong with my code? (Edited version-added my data)

2011-07-12 Thread Sarah Goslee
Take a closer look at your R code. Each loop is returning only the last value, so you're doing the same thing over and over for the last value from the previous loop. Write just the code for *one* set of graphs. Look at what needs to change to do the next set. Write a function that takes those arg

Re: [R] What's wrong with my code? (Edited version-added my data)

2011-07-12 Thread Susie
Hey Josh, Thank you so much for the help! Now I have edited my codes--breaking into smaller pieces:) R does not state the error again:) However, the problem comes, please see my codes below-- You've suggested earlier that I should move the "eight" part outside the loop; I changed the "eight"

Re: [R] Rcompression on MAC - where is it?

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 8:40 PM, Eduardo M. A. M. Mendes wrote: Hello I need to run an r-file that works on Windows on MAC. Does that mean you are using a virtual box to run Windoze on Mac hardware? The first lines of the file are: library(R.matlab) library(Rcompression) Somehow I cannot

[R] Rcompression on MAC - where is it?

2011-07-12 Thread Eduardo M. A. M. Mendes
Hello I need to run an r-file that works on Windows on MAC. The first lines of the file are: library(R.matlab) library(Rcompression) Somehow I cannot find where Rcompression is. Am I missing something? Many thanks Ed __ R-help@r-project.org mail

Re: [R] simple save question

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 5:43 PM, Tom La Bone wrote: Thank you for the reply Dr. Winsemius. Can you take your answer a step further and, in the context of the simple, reproducible example, illustrate how it is done? I would appreciate it. Of course. Would be happy to take a stab at it but

[R] problem plotting points based on different values

2011-07-12 Thread Hrishi lokhande
Hello Friends, I am new to R and stuck with a problem. i have two columns drug_A and drug_B, i have plotted a scatter plot using the ggplot2 function. My problem is with the third column, it is the p-value column. I want to color and size points differently based on the p_value, the p_value ran

Re: [R] spatial logit help

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 7:26 PM, Salifu Wahab wrote: Please I am new to R. I got the following code from a friend: gmat <- cbind(gmat,p*(1-p)*wxb) for (j in seq(1:ncol(gmat))) { gmat[,j] <- fitted(lm(gmat[,j]~zmat)) } It is for spatial logit. After defining all the matrices in it such as P, wx

Re: [R] simple save question

2011-07-12 Thread Tom La Bone
Thank you for the reply Dr. Winsemius. Can you take your answer a step further and, in the context of the simple, reproducible example, illustrate how it is done? I would appreciate it. Tom -- View this message in context: http://r.789695.n4.nabble.com/simple-save-question-tp3429148p3663645.htm

[R] LOESS function Newton optimization

2011-07-12 Thread KenjiPsyD
I have a question about running an optimization function on an existing LOESS function defined in R. I have a very large dataset (1 million observations) and have run a LOESS regression. Now, I want to run a Newton-Raphson optimization to determine the point at which the slope change is the greates

[R] spatial logit help

2011-07-12 Thread Salifu Wahab
Please I am new to R. I got the following code from a friend:   gmat <- cbind(gmat,p*(1-p)*wxb) for (j in seq(1:ncol(gmat))) {   gmat[,j] <- fitted(lm(gmat[,j]~zmat)) }   It is for spatial logit.   After defining all the matrices in it such as P, wxb, gmat, and zmat, I tried to run it in R and go

Re: [R] fitdistr() Error

2011-07-12 Thread Peter Maclean
There is no missing value nor zero values.   - Original Message From: Uwe Ligges To: Peter Maclean Cc: r-help@r-project.org Sent: Tue, July 12, 2011 2:58:10 AM Subject: Re: [R] fitdistr() Error Any NA values or values outside the support region of your distribution? UWe On 11.07.2

Re: [R] Cross K Ripley's function and "spatio-temporal interaction power"

2011-07-12 Thread Rolf Turner
On 13/07/11 00:57, ruocco wrote: Dear All, I have a collections of spatial data. I have to analyze pairs of these point patterns to test their spatial interaction. I was moving towards the cross K Ripley's function. The problem, however, are the following: 1) What is the best way to get a singl

Re: [R] Question re complex survey design and cure models

2011-07-12 Thread Thomas Lumley
On Wed, Jul 13, 2011 at 6:13 AM, Sze Liu wrote: > Hello all, > I am using AddHealth data to fit a cure, aka split population model using > nltm.  I am not sure how to account for the complex survey > design - does anyone have any suggestions?  Any help would be greatly > appreciated! This will

Re: [R] Storing and managing custom R functions for re-use

2011-07-12 Thread Bert Gunter
These sorts of tasks can be automated. See: ?Startup -- Bert On Tue, Jul 12, 2011 at 2:48 PM, Steve Taylor wrote: > My solution to the clutter problem is this: at start-up time, create a list > of functions, attach the list and then delete the list.  I haven't delved > into making packages ye

Re: [R] Storing and managing custom R functions for re-use

2011-07-12 Thread Steve Taylor
My solution to the clutter problem is this: at start-up time, create a list of functions, attach the list and then delete the list. I haven't delved into making packages yet. if (any(search()=="MyFunctions")) detach(MyFunctions) MyFunctions <- list() MyFunctions$ "%like%" <- function(x,y) { s

Re: [R] foreach not recognizing functions in memory

2011-07-12 Thread Adrienne Wootten
Roger, I think I know why you are having a problem. Your foreach is using %dopar% and judging from your output you have active parallel processing. When running something in paralell, the master is the processor used by the Rgui, and the slaves are in the background. My guess is the the functio

Re: [R] foreach not recognizing functions in memory

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 5:28 PM, Bos, Roger wrote: All, I am not understanding the scoping used in foreach when it is used inside a function. I keep getting "could not find function" errors for functions that are in memory when I try to use foreach within a function call. I have a simple exa

[R] foreach not recognizing functions in memory

2011-07-12 Thread Bos, Roger
All, I am not understanding the scoping used in foreach when it is used inside a function. I keep getting "could not find function" errors for functions that are in memory when I try to use foreach within a function call. I have a simple example below. "testFun" is in memory and works when call

Re: [R] apply (or similar preferred) for multiple columns

2011-07-12 Thread Gabor Grothendieck
On Tue, Jul 12, 2011 at 5:27 AM, Dimitris.Kapetanakis wrote: > Dear all, > > I would like to use the apply or a similar function belonging to this > family, but applying for each column (or row) but let say for each q > columns. For example I would like to apply a function FUN for the first q > co

Re: [R] qplot and for loops

2011-07-12 Thread Joshua Wiley
On Tue, Jul 12, 2011 at 2:01 PM, Reith, William [USA] wrote: > Do I need to define x in any way before I do the loop? No, you should not need to define x explicitly. Just pass the data frame you want to qplot. David was absolutely right though that inside a loop, you should wrap the call to qpl

Re: [R] wgcna

2011-07-12 Thread Peter Langfelder
Hi Meeta, yes, there was a bug in the package. Please install the newest version and try again. Best, Peter On Tue, Jul 12, 2011 at 1:20 PM, mistrm wrote: > Hi Peter and Raquel > > I am following the same tutorial and seem to have the same error appear and > I am using 30 permutations (code be

Re: [R] apply (or similar preferred) for multiple columns

2011-07-12 Thread Daniel Malter
Probably not the most elegant, but a workable solution. Assume you have a matrix x of dimensions 10 x 10. Assume further you want to calculate the mean for each successive block of two columns. One way to do this is to create a matrix that indicates the column numbers from/to which to apply the fun

Re: [R] suggestions regarding reading in a messy file

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 4:37 PM, Juliet Hannah wrote: I have a file in stata format, which I have read in, and I am trying to create a text file. I have exported the data using various delimiters, but I'm unable to read it back in. I originally read in the file with: library(foreign) myData <- rea

Re: [R] qplot and for loops

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 3:21 PM, wwreith wrote: I have 4 columns and 56 rows of made up data that I want to plot as a series of bar graphs. The idea is to create one bar graph for each of the 4 columns using a for loop. I tried the following command in RStudio and when I type x in the console

Re: [R] qplot and for loops

2011-07-12 Thread Joshua Wiley
Hi, You actually did the loop correctly. The problem is that the graphs were created very quickly so you only see the last one. One way around this is to make R wait for user input. You can turn this on and off for a particular device using: par(ask = TRUE) See ?par for details on this. To c

Re: [R] simple save question

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 2:31 PM, Tom La Bone wrote: Here is a worked example. Can you point out to me where in temp rmean is stored? Thanks. It is not. You need to read the ?print.survfit page: Value x, with the invisible flag set to prevent printing. (The default for all print functions i

Re: [R] fixed effects Tobit, Honore style?

2011-07-12 Thread Daniel Malter
Not that I know of, but the paper says that they are easy to compute. If you did, you could contribute the code. Best, Daniel David Hugh-Jones-3 wrote: > > Hi all, > > Is there any code to run fixed effects Tobit models in the style of Honore > (1992) in R? > (The original Honore article is he

[R] suggestions regarding reading in a messy file

2011-07-12 Thread Juliet Hannah
I have a file in stata format, which I have read in, and I am trying to create a text file. I have exported the data using various delimiters, but I'm unable to read it back in. I originally read in the file with: library(foreign) myData <- read.dta("mydata.dta") I then exported it with write.tab

Re: [R] wgcna

2011-07-12 Thread mistrm
Hi Peter and Raquel I am following the same tutorial and seem to have the same error appear and I am using 30 permutations (code below). Is it a bug or something that I can easily fix? I'm not quite sure how to interpret the error. multiExpr = list(A1=list(data=t(ctl)),A2=list(data=t(sz))) multiC

[R] qplot and for loops

2011-07-12 Thread wwreith
I have 4 columns and 56 rows of made up data that I want to plot as a series of bar graphs. The idea is to create one bar graph for each of the 4 columns using a for loop. I tried the following command in RStudio and when I type x in the console I get just the 4th graph instead of all four graphs.

[R] Question re complex survey design and cure models

2011-07-12 Thread Sze Liu
Hello all, I am using AddHealth data to fit a cure, aka split population model using nltm. I am not sure how to account for the complex survey design - does anyone have any suggestions? Any help would be greatly appreciated! Sincerely, Sam __ R-help

Re: [R] simple save question

2011-07-12 Thread Tom La Bone
Here is a worked example. Can you point out to me where in temp rmean is stored? Thanks. Tom > library(survival) > library(ISwR) > > dat.s <- Surv(melanom$days,melanom$status==1) > fit <- survfit(dat.s~1) > plot(fit) > summary(fit) Call: survfit(formula = dat.s ~ 1) time n.risk n.event survi

Re: [R] when to use `which'?

2011-07-12 Thread Joshua Wiley
On Tue, Jul 12, 2011 at 1:17 PM, Sam Steingold wrote: > when do I need to use which()? See ?which For examples, try: example(which) >> a <- c(1,2,3,4,5,6) >> a > [1] 1 2 3 4 5 6 >> a[a==4] > [1] 4 >> a[which(a==4)] > [1] 4 >> which(a==4) > [1] 4 >> a[which(a>2)] > [1] 3 4 5 6 >> a[a>2] > [1] 3

Re: [R] when to use `which'?

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 4:17 PM, Sam Steingold wrote: when do I need to use which()? a <- c(1,2,3,4,5,6) a [1] 1 2 3 4 5 6 a[a==4] [1] 4 a[which(a==4)] [1] 4 which(a==4) [1] 4 a[which(a>2)] [1] 3 4 5 6 a[a>2] [1] 3 4 5 6 seems unnecessary... It is unnecessary when `a` is a toy ca

Re: [R] when to use `which'?

2011-07-12 Thread Bert Gunter
Well ... which(a==4)^2 ?? -- Bert On Tue, Jul 12, 2011 at 1:17 PM, Sam Steingold wrote: > when do I need to use which()? >> a <- c(1,2,3,4,5,6) >> a > [1] 1 2 3 4 5 6 >> a[a==4] > [1] 4 >> a[which(a==4)] > [1] 4 >> which(a==4) > [1] 4 >> a[which(a>2)] > [1] 3 4 5 6 >> a[a>2] > [1] 3 4 5 6 >> >

Re: [R] How to "smoothen" a geodata set in R

2011-07-12 Thread Daniel Malter
To answer your questions: Yes, yes, and probably no. You will have to pick up any introductory manual of R where questions 1 and 2 will be discussed. For 1: you index x as in x[452,682]. For 2: there are ways to write (and avoid) loops in R (e.g. for or while loops). Often avoidance is preferable

[R] when to use `which'?

2011-07-12 Thread Sam Steingold
when do I need to use which()? > a <- c(1,2,3,4,5,6) > a [1] 1 2 3 4 5 6 > a[a==4] [1] 4 > a[which(a==4)] [1] 4 > which(a==4) [1] 4 > a[which(a>2)] [1] 3 4 5 6 > a[a>2] [1] 3 4 5 6 > seems unnecessary... -- Sam Steingold (http://sds.podval.org/) on CentOS release 5.6 (Final) X 11.0.60900031 htt

Re: [R] Deviance of zeroinfl/hurdle models

2011-07-12 Thread Ben Bolker
Carson Farmer gmail.com> writes: > > Dear list, I'm wondering if anyone can help me calculate the deviance > of either a zeroinfl or hurdle model from package pscl? > Even if someone could point me to the correct formula for calculating > the deviance, I could do the rest on my own. What a

Re: [R] Generating a histogram with R

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 3:41 PM, a217 wrote: Hello, I have a sample file: chr22 100 150 125 21 0.145 + chr22 200 300 212 13 0.05+ chr22 345 365 351 12 0.09+ chr22 500 750 510 15 0.10+ chr22 500 750

Re: [R] Generating a histogram with R

2011-07-12 Thread Bert Gunter
Hello: R has an extensive Help system. Please learn to use it. ?histogram ?help Also see the online manual tutorial "An Introduction to R" -- Bert On Tue, Jul 12, 2011 at 12:41 PM, a217 wrote: > Hello, > > I have a sample file: > > chr22   100     150     125     21      0.145   + > chr22   2

[R] Generating a histogram with R

2011-07-12 Thread a217
Hello, I have a sample file: chr22 100 150 125 21 0.145 + chr22 200 300 212 13 0.05+ chr22 345 365 351 12 0.09+ chr22 500 750 510 15 0.10+ chr22 500 750 642 9 0.02+ chr22 800 90

Re: [R] grey colored lines and overwriting labels i qqplot2

2011-07-12 Thread Brian Diggs
Merging two posts (data and questions); see inline below. On 7/11/2011 7:55 PM, Sigrid wrote: Thank you, Dennis. This is my regenerated dput codes. They should be correct as I closed off R and re-ran them based on the dput output. NB, this is the test dataset used later structure(list(year

Re: [R] Explain how it gets back out?

2011-07-12 Thread Ted Harding
On 12-Jul-11 17:18:26, mousy0815 wrote: > Probability <- function(N, f, m, b, x, t) { > #N is the number of lymph nodes > #f is the fraction of Dendritic cells (in the correct node) that have > the > antigen > #m is the number of time steps > #b is the starting position (som

[R] Deviance of zeroinfl/hurdle models

2011-07-12 Thread Carson Farmer
Dear list, I'm wondering if anyone can help me calculate the deviance of either a zeroinfl or hurdle model from package pscl? Even if someone could point me to the correct formula for calculating the deviance, I could do the rest on my own. I am trying to calculate a pseudo-R-squared measure based

Re: [R] What's wrong with my code? (Edited version-added my data)

2011-07-12 Thread Joshua Wiley
Dear Susie, See inline for some suggestions, but generally, I think you would benefit from breaking this down into smaller pieces. The error you are getting indicates the problem has to do with the plotting, but that will be trickier to isolate while also dealing with reading in data, looping, et

[R] How to "smoothen" a geodata set in R

2011-07-12 Thread Tariq
Hello, I'm new to this list. Sorry if my question or parts of it already came up before. For my research in geostatistics, I am working with large sets of data in R (basically large matrices containing discrete x and y coordinates and a value for a certain parameter). These sets are obtained by kr

Re: [R] "as.numeric"

2011-07-12 Thread Jessica Lam
It works well. Thanks so much. -- View this message in context: http://r.789695.n4.nabble.com/as-numeric-tp3661739p3662671.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/l

[R] Subsetting NaN values in localG()

2011-07-12 Thread dab98
Hi, I'm currently trying to calculate local Getis-Ord Gi* statistics for a 169x315 cell matrix of temperature values, below is the code I currently have (diffc is the data vector I am removing NaN values from, and I am moving said values to diffD; -999 represents NaN values; id contains ID values

[R] Explain how it gets back out?

2011-07-12 Thread mousy0815
Probability <- function(N, f, m, b, x, t) { #N is the number of lymph nodes #f is the fraction of Dendritic cells (in the correct node) that have the antigen #m is the number of time steps #b is the starting position (somewhere in the node or somewhere in the gap b

[R] What's wrong with my code? (Edited version-added my data)

2011-07-12 Thread Susie
I've written out codes for one particular file, and now I want to generate the same kind of graphs and files for the rest of similar data files. For example, a file "8.csv" would look like such: enc_callee inout o_duration type A out 342 de B in 234 de C

Re: [R] elimination duplicate elements sampling!

2011-07-12 Thread Brian Diggs
On 7/7/2011 3:23 PM, elephann wrote: Hi everyone! I have a data frame with 1112 time series and I am going to randomly sampling r samples for z times to compose different portfolio size(r securities portfolio). As for r=2 and z=1,that's: z=1 A=seq(1:1112) x1=sample(A,z,replace =TRUE) x2=s

[R] installation of package 'mapproj' had non-zero exit status

2011-07-12 Thread B77S
## Hello.. I have asked a similar question, but this is not fixed as before. ## I am running the following using Ubuntu OS: R version 2.13.1 (2011-07-08) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) ## when I do this:

Re: [R] For applying formula in rows

2011-07-12 Thread Joshua Wiley
Hi Vikas, Here is one way: df <- read.table("summary.txt", header = TRUE) str(df) df[, "total"] <- rowSums(df[, 3:6]) df[, 3:6] <- apply(df[, 3:6], 2, function(x) x / df[, "total"] * df[, "new"] * 2) > head(df) V1V2 CaseA CaseC CaseG CaseT new total 1 10 135344109 0 024

[R] For applying formula in rows

2011-07-12 Thread Bansal, Vikas
Dear all, I have a problem and it is very difficult for me to get a code. I am reading a file(attached with this mail) using the code- df=read.table("summary.txt",fill=T,sep="",colClasses = "character",header=T) and dataframe df is like this- V1V2 CaseA CaseC CaseG CaseT new 10 13

Re: [R] Role of na.rm inside mean()

2011-07-12 Thread Joshua Wiley
Hi Harold, Many (most?) of the statistics function have a similar argument. I suspect it is sort of to warn the user---you have to be explicit about it rather than the program just silently removing or ignoring values that would not work in the function called. I can think of one example where I

Re: [R] Role of na.rm inside mean()

2011-07-12 Thread Duncan Murdoch
On 12/07/2011 12:26 PM, Doran, Harold wrote: This is just posed out of curiosity, (not as a criticism per se). But what is the functional role of the argument na.rm inside the mean() function? If there are missing values, mean() will always return an NA as in the example below. But, is there e

Re: [R] Role of na.rm inside mean()

2011-07-12 Thread Jeff Newmiller
In SQL, the default is to ignore NULL (equivalent to NA in R). However, it can be dangerous to fail to verify how much data was actually used in an aggregation, so the logic behind the default na.rm setting may be one of encouraging the user to take responsibility for missing data. -

[R] Role of na.rm inside mean()

2011-07-12 Thread Doran, Harold
This is just posed out of curiosity, (not as a criticism per se). But what is the functional role of the argument na.rm inside the mean() function? If there are missing values, mean() will always return an NA as in the example below. But, is there ever a purpose in computing a mean only to recei

Re: [R] FW: lasso regression

2011-07-12 Thread Patrick Breheny
On 07/12/2011 09:53 AM, Heiman, Thomas J. wrote: ## define x and y x= x<-crs[,9]#predictor variables y= y<-crs[1:8,] #response variable This cannot be correct. The response variable is a vector, while the predictor variables form a matrix. You have the response variable consisting

Re: [R] What's wrong with my code?

2011-07-12 Thread Sarah Goslee
Hi Susie, At a guess, there are no non-missing arguments to min or max. But no, we can't help you. You haven't provided a minimal reproducible example, and without knowing anything about your data it is impossible for the list to offer any constructive suggestions. The posting guide offers sugge

Re: [R] plot means ?

2011-07-12 Thread Peter Ehlers
On 2011-07-12 07:03, Sam Steingold wrote: [snip] the totally unnecessary semi-colons) then why are they accepted? optional syntax elements suck... They're accepted because they *can* be useful (multiple statements on one line). Is there *any* language that can *not* be abused? Peter Ehlers

[R] What's wrong with my code?

2011-07-12 Thread Susie
I've written out codes for one particular file, and now I want to generate the same kind of graphs and files for the rest of similar data files. When I plugged in these codes, R produced only one plot for the file "eight", and it states my error(see below) I have edited and checked my codes so man

Re: [R] lm: mark sample used in estimation

2011-07-12 Thread Anirban Mukherjee
Thanks Peter, Ted! Best, Anirban On Tue, Jul 12, 2011 at 4:54 AM, Ted Harding wrote: > On 11-Jul-11 07:55:44, Anirban Mukherjee wrote: >> Hi all, >> >> I wanted to mark the estimation sample: mark what rows (observations) >> are deleted by lm due to missingness. For eg, from the original >> exam

[R] Adding a correlation value (like Rsquared) to a 4 parameter logistic fit model.

2011-07-12 Thread Kevin_McEnroy
Hello, In my lab we use a four parameter logistic fit model for our ELISA data (absorbance values). We are currently testing the use of different solvents and need to find a way to add a correlation value (such as an R squared or something similar) so we can test different solvents in making this

Re: [R] time zone - any practical solution?

2011-07-12 Thread Jeff Newmiller
If you don't need POSIXt types, as Gabor says don't use them. However, there are good reasons to use them sometimes, and the most workable solution I have found is to set your default timezone in R to a non-DST timezone before you convert from character to POSIXct. This is dependent on your OS a

Re: [R] Connecting to Empress DB using RODBC

2011-07-12 Thread Marc Schwartz
On Jul 11, 2011, at 9:16 PM, Steve Parker wrote: > Hi there, > I am using the RODBC library to connect to an Empress database. > I have installed the ODBC data source with the server DNs number and port, > and named the source "Trawl". > It is the odbcDriverConnect that seems to have the problem,

Re: [R] time zone - any practical solution?

2011-07-12 Thread Gabor Grothendieck
On Tue, Jul 12, 2011 at 8:57 AM, B Laura wrote: > Dear Gabor > > http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows&s=excel > doesnt describe handling dates with daylight saving time issues. > Two references were given and its discussed in the R News article. It was also mentioned ove

Re: [R] Reorganize data fram

2011-07-12 Thread Dennis Murphy
Hi: Try the cast() function in the reshape package. Using d as the name of your data frame, library(reshape) cast(d, Date ~ Category, value = 'Temperature') Date A B C 1 2007102 16 17 18 HTH, Dennis On Tue, Jul 12, 2011 at 5:42 AM, anglor wrote: > Hi, > > I have a data frame of about

Re: [R] FW: lasso regression

2011-07-12 Thread Steve Lianoglou
Hi, (i) As David suggested, please use `dput` to provide examples of data! (ii) The nut of your problem is that you are giving lars an object that it is not expecting. It wants a *matrix* for its `x` variable, as you'll see in the help for ?lars. So, as long as this expression: R> is.numeric(x)

Re: [R] Reorganize data fram

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 8:42 AM, anglor wrote: Hi, I have a data frame of about 700 000 rows which look something like this: DateTemperature Category 2007102 16 A 2007102 17 B 2007102 18 C but need it to be: Date T

Re: [R] FW: lasso regression

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 10:12 AM, Heiman, Thomas J. wrote: Hi, Hopefully I got the formatting down.. I am trying to do a lasso regression using the lars package with the following data (the data files is in .csv format): V1 V2 V3 V4

Re: [R] Avoiding loops to detect number of coincidences

2011-07-12 Thread Sarah Goslee
Hi Trying, It would be helpful if you provided reproducible examples. It would also be polite to sign a name so that we have something by which to address you. On Tue, Jul 12, 2011 at 8:00 AM, Trying To learn again wrote: > Hi all, > > I have this information on a file ht.txt, imagine it is a da

Re: [R] FW: lasso regression

2011-07-12 Thread Gavin Simpson
On Tue, 2011-07-12 at 10:12 -0400, Heiman, Thomas J. wrote: > Hi, > > Hopefully I got the formatting down.. I am trying to do a lasso regression > using the lars package with the following data (the data files is in .csv > format): > > V1 V2 V3

Re: [R] how to find out whether a string is a factor?

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 10:12 AM, Sam Steingold wrote: I have two data frames: str(ysmd) 'data.frame': 8325 obs. of 6 variables: $ X.stock : Factor w/ 8325 levels "A","AA","AA-",..: 2702 6547 4118 7664 7587 6350 3341 5640 5107 7589 ... $ market.cap :

[R] Cross K Ripley's function and "spatio-temporal interaction power"

2011-07-12 Thread ruocco
Dear All, I have a collections of spatial data. I have to analyze pairs of these point patterns to test their spatial interaction. I was moving towards the cross K Ripley's function. The problem, however, are the following: 1) What is the best way to get a single real value that represents the

[R] Reorganize data fram

2011-07-12 Thread anglor
Hi, I have a data frame of about 700 000 rows which look something like this: DateTemperature Category 2007102 16 A 2007102 17 B 2007102 18 C but need it to be: Date TemperatureA TemperatureB TemperatureC 2007102

[R] FW: lasso regression

2011-07-12 Thread Heiman, Thomas J.
Hi, I am trying to do a lasso regression using the lars package with the following data (see attached): FastestTime WinPercentage PlacePercentage ShowPercentage BreakAverage FinishAverage Time7Average Time3Average Finish 116.90 0.14 0.14 0.29 4.43 3.29 117.56 117.77 5.00 116.23

[R] Avoiding loops to detect number of coincidences

2011-07-12 Thread Trying To learn again
Hi all, I have this information on a file ht.txt, imagine it is a data frame without labels: 1 1 1 8 1 1 6 4 1 3 1 3 3 And on other table called "pru.txt" I have sequences similar this 4 1 1 8 1 1 6 4 1 3 1 3 3 1 6 1 8 1 1 6 4 1 3 1 3 3 1 1 1 8 1 1 6 4 1 3 1 3 3 6 6 6 8 1 1 6 4 1 3 1 3 3 I want

Re: [R] Creating a zero matrix when a condition doesn´t get it

2011-07-12 Thread Trying To learn again
Many Thanks¡¡¡ I will try this night, I have read this I think could help me. I´m conscient the question was badly formulated now, I will try to explain better next time¡¡¡ On a side note: apply always accesses the function you use at least once. If the input is a dataframe without any rows but

Re: [R] MC-Simulation with foreach: Some cores finish early

2011-07-12 Thread Markus Schmidberger
If you switch directly to the multicore package you can use the mclapply() function. There, check for the parameter mc.preschedule=T / F. You can use this parameter to improve the load balancing. I do not know a parameter to tune foreach with this parameter. Best Markus Am Dienstag, den 12.07

[R] High density scatter plot with logarithmic binning

2011-07-12 Thread adhikaa1
How can perform logarithmic binning in the scatterplot? I could only take the log of the variables and plot them, but I am sure that is not the way. I have a very huge data, and would want to plot those high density scatterplots and code then with different colors for the bins/density. -- View thi

[R] how to find out whether a string is a factor?

2011-07-12 Thread Sam Steingold
I have two data frames: > str(ysmd) 'data.frame': 8325 obs. of 6 variables: $ X.stock : Factor w/ 8325 levels "A","AA","AA-",..: 2702 6547 4118 7664 7587 6350 3341 5640 5107 7589 ... $ market.cap : num -1.00 2.97e+10 3.54e+08 3.46e+08 -1.00 ... $ X52.

[R] FW: lasso regression

2011-07-12 Thread Heiman, Thomas J.
Hi, Hopefully I got the formatting down.. I am trying to do a lasso regression using the lars package with the following data (the data files is in .csv format): V1 V2 V3 V4 V5 V6 V7

Re: [R] FW: lasso regression

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 9:53 AM, Heiman, Thomas J. wrote: Hi, I am trying to do a lasso regression using the lars package with the following data (see attached): Nothing attached. (And now you have also sent an exact duplicate.) snipped failed attempt to include data inline that was sabotaged

Re: [R] plot means ?

2011-07-12 Thread Sam Steingold
> * David Winsemius [2011-07-11 18:16:25 -0400]: > > What is the point of offering this code? To illustrate what I was talking about (code is its own specification). I hoped that there was already a package doing that (and more in that direction). > It seems to be doing what you want yes. > Ar

[R] FW: lasso regression

2011-07-12 Thread Heiman, Thomas J.
Hi, I am trying to do a lasso regression using the lars package with the following data: FastestTime WinPercentage PlacePercentage ShowPercentage BreakAverage FinishAverage Time7Average Time3Average Finish 116.90 0.14 0.14 0.29 4.43 3.29 117.56 117.77 5.00 116.23 0.29 0.43 0

Re: [R] RES: applying function to multiple columns of a matrix

2011-07-12 Thread Federico Calboli
I just realised that: apply(matrix(1:dim(my.data)[2], nrow =3), 2, function(x){my.function(my.data[,x])}) is the simplest possible method. bw F On 12 Jul 2011, at 14:44, Filipe Leme Botelho wrote: > Hi Frederico. I would keep the data as it is, create two small vectors > referring to the r

[R] FW: lasso regression

2011-07-12 Thread Heiman, Thomas J.
Hi, I am trying to do a lasso regression using the lars package with the following data (see attached): FastestTime WinPercentage PlacePercentage ShowPercentage BreakAverage FinishAverage Time7Average Time3Average Finish 116.90 0.14 0.14 0.29 4.43 3.29 117.56 117.77 5.00 116.23

Re: [R] Print file updated/created date to console?

2011-07-12 Thread Scott Chamberlain
Eik, Thanks very much! Scott On Tuesday, July 12, 2011 at 8:34 AM, Eik Vettorazzi wrote: > Hi, > file.info (http://file.info)() > does that. > > Cheers > > Am 12.07.2011 15:29, schrieb Scott Chamberlain: > > Hello, > > > > Are there any built in or user defined functions for printing the d

[R] RES: applying function to multiple columns of a matrix

2011-07-12 Thread Filipe Leme Botelho
Hi Frederico. I would keep the data as it is, create two small vectors referring to the ranges and use a mapply (as a sapply but with multiple variables) for the function. Hope the example below is helpful, although as usual someone out there will have a better solution for it. > dta <- c() > f

Re: [R] Help in error removal

2011-07-12 Thread David Hugh-Jones
On 12 July 2011 12:27, Mitra, Sumona wrote: > Dear all, > > I am new to programming in R. > You sure are ;-) I deal with microarray data,which is a data frame object type. I need to > carry out a few statistical procedures on this, one of them being the > pearson corelation. I need to do this

Re: [R] Print file updated/created date to console?

2011-07-12 Thread Eik Vettorazzi
Hi, file.info() does that. Cheers Am 12.07.2011 15:29, schrieb Scott Chamberlain: > Hello, > > Are there any built in or user defined functions for printing the date > created or date updated for a given file? Ideally a function that works > across operating systems. > > > Thanks! > Scott

Re: [R] Help in error removal

2011-07-12 Thread David Winsemius
On Jul 12, 2011, at 7:27 AM, Mitra, Sumona wrote: Dear all, I am new to programming in R. You see to think there is a "++" operation in R. That is not so. I deal with microarray data,which is a data frame object type. I need to carry out a few statistical procedures on this, one of them

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