Re: [R] factor manipulation: edgelist to a matrix?

2007-12-19 Thread Veslot Jacques
do.call(rbind,lapply(split(as.character(z[,2]),z[,1]), function(x) c(x, rep(NA, max(table(z[,1]))-length(x) Jacques VESLOT CEMAGREF - UR Hydrobiologie Route de Cézanne - CS 40061 13182 AIX-EN-PROVENCE Cedex 5, France Tél + 0033 04 42 66 99 76 email [EMAIL PROTECTED] >

[R] factor manipulation: edgelist to a matrix?

2007-12-19 Thread Christopher Marcum
Hello All, I have had considerable bad luck with attempting the following with for loops. Here is the problem: # Suppose we have a data.frame with the following data, which can be considered a type of edgelist (for those with networks backgrounds): # # V1 V2 # 1 A #

Re: [R] Question about which kind of plot to use

2007-12-19 Thread Jim Lemon
Max wrote: > Hi Everyone, > > I've got a question about data representation. I have some psychometric > data with 5 scores for 15 different groups. I've been asked to show > some kind of mean plots. The data below is the mean and SD for a given > group, unfortunately my employer doesn't want me

Re: [R] assigning and saving datasets in a loop, with names changing with "i"

2007-12-19 Thread Moshe Olshansky
Won't it be simpler to do: for (i in 1:12){ data <- my.fun(my.list[i])) save(data,file = paste("data",i,".RData", sep="")) } --- Marie Pierre Sylvestre <[EMAIL PROTECTED]> wrote: > Dear R users, > > I am analysing a very large data set and I need to > perform several data > manipulations. T

Re: [R] Question about which kind of plot to use

2007-12-19 Thread Eric
Deepayan Sarkar wrote: > On 12/19/07, Dylan Beaudette <[EMAIL PROTECTED]> wrote: > >> On Wednesday 19 December 2007, Max wrote: >> >>> Hi Everyone, >>> >>> I've got a question about data representation. I have some psychometric >>> data with 5 scores for 15 different groups. I've been asked

[R] mle

2007-12-19 Thread Antonio Gasparrini
Dear all, I'm trying to estimate the parameters of a special case of a poisson model, where the specified equation has an integral and several fixed parameters. I think that the MLE command in STATS4 package could be a good choice, but it's a little complicated. I've got some problems with the off

Re: [R] Calculate remainer

2007-12-19 Thread Moshe Olshansky
> 50 %% 12 [1] 2 > 50 %/% 12 [1] 4 > ?Arithmetic --- livia <[EMAIL PROTECTED]> wrote: > > Hello everyone, > > I have got a question about a simple calculation. If > I would like to > calculate 50/12 and return the result as 4 and the > remainer 2. Is there a > function of doing this? > > Man

Re: [R] Question about which kind of plot to use

2007-12-19 Thread Deepayan Sarkar
On 12/19/07, Dylan Beaudette <[EMAIL PROTECTED]> wrote: > On Wednesday 19 December 2007, Max wrote: > > Hi Everyone, > > > > I've got a question about data representation. I have some psychometric > > data with 5 scores for 15 different groups. I've been asked to show > > some kind of mean plots. T

Re: [R] "gam()" in "gam" package

2007-12-19 Thread Kunio takezawa
R-users E-mail: r-help@r-project.org I found the answer myself. '.Fortran("baklo",' in lo.wam() and .Fortran("bakfit",in s.wam() may carry out backfitting. But I cannot create an R code which gives the same results as those of "bakfit". If someone knows the detail of "bakfit" algorithm, pleas

Re: [R] Question about which kind of plot to use

2007-12-19 Thread Dylan Beaudette
On Wednesday 19 December 2007, Max wrote: > Hi Everyone, > > I've got a question about data representation. I have some psychometric > data with 5 scores for 15 different groups. I've been asked to show > some kind of mean plots. The data below is the mean and SD for a given > group, unfortunately

[R] Question about which kind of plot to use

2007-12-19 Thread Max
Hi Everyone, I've got a question about data representation. I have some psychometric data with 5 scores for 15 different groups. I've been asked to show some kind of mean plots. The data below is the mean and SD for a given group, unfortunately my employer doesn't want me posting full datasets.

[R] clim.pact package ncdf dependency/ netcdf.h

2007-12-19 Thread Sam McClatchie
System: Linux kernel 2.6.22-14 Ubuntu 7.10 gutsy ESS 5.3.0 on Emacs 22.1.1 R version 2.6.0 Colleagues I would like to use the user contributed package "clim.pact". I'm having trouble with the dependency of "clim.pact" on "ncdf". Like others I am finding that R CMD INSTALL does not find the netcdf

Re: [R] can optimize solve paired euqations?

2007-12-19 Thread jim holtman
In your first case you seem to be missing a comma after the "^2"; also missing value for 'y'. Probably should be something like: optimize(function(x,y) ((327.727-(1-0.114^10)*y*(1-x)/x/(1-x^y))+(9517.336-327.727 *(1+(1-x)*(1+y)/x-327.727)))^2, interval=c(0,1), y=1) On Dec 19, 2007 5:12 PM, Xin

Re: [R] median of binned values

2007-12-19 Thread Moshe Olshansky
Alternatively levels(df$binname)[which(df$freq >= 0.5*cumsum(df$freq)[nrow(df)])[1]] --- Chuck Cleland <[EMAIL PROTECTED]> wrote: > Martin Tomko wrote: > > Dear list, > > I have a vector (array, table row, whatever is > best) of frequency values > > for categories (or bins), and I need to find t

[R] can optimize solve paired euqations?

2007-12-19 Thread Xin
I used the command below, but R gives me the error message--syntax error. can anyone see the mistakes I made? optimize(function(x,y) + ((327.727-(1-0.114^10)*y*(1-x)/x/(1-x^y))+(9517.336-327.727 *(1+(1-x)*(1+y)/x-327.727)))^2 + interval=c(0,1)) At the same time, I use nlm() but R gives me the

Re: [R] creating a database

2007-12-19 Thread Moshe Olshansky
If all your entries are double precision then you are using 8 bytes per entry, so 20,000*n entries are just 160,000*n bytes, i.e. less than 160*n Kb. If your n is 100 you get 16 Mb which is not that much (especially if you pre-allocate it only once). So just use the matrix and don't worry! --- dxc

Re: [R] library(rpart) or library(tree)

2007-12-19 Thread Prof Brian Ripley
You appear to have fitted a regression tree, which does not seem to be what your interpretation of 'pnV22' requires. I have little idea what you actually did, but am confident that it is not what you claim you did. Also, note fortune("dog"): Firstly, don't call your matrix 'matrix'. Would you

Re: [R] Function reference

2007-12-19 Thread Tony Plate
R does this sort of thing easily without any parse/eval acrobatics needed. E.g., you can do: > stu <- function(x) {return( 1 + (2*x*x) - (3*x) )} > (x <- 0:3) [1] 0 1 2 3 > stu(x) [1] 1 0 3 10 > metafun <- function(FUN, data) FUN(data) > metafun(stu, x) [1] 1 0 3 10 > # if you want

Re: [R] lattice: axes drawn when relation='free' or relation='sliced' but not when relation='same'

2007-12-19 Thread Deepayan Sarkar
On 12/19/07, John G. Bullock <[EMAIL PROTECTED]> wrote: > > I'm using lattice to draw a multi-panel figure: 5 rows, 4 columns. The > y-axis for > each panel is determined by > > yaxs<- list(draw=T > , labels=c(0, '.5', '1', '1.5') >

[R] lattice: axes drawn when relation='free' or relation='sliced' but not when relation='same'

2007-12-19 Thread John G. Bullock
I'm using lattice to draw a multi-panel figure: 5 rows, 4 columns. The y-axis for each panel is determined by yaxs<- list(draw=T , labels=c(0, '.5', '1', '1.5') , at=c(0, .5, 1, 1.5) , tck=c(.4, 0)

[R] Function reference

2007-12-19 Thread Talbot Katz
Hi. I'm looking for an R equivalent to something like function pointers in C/C++. I have a search procedure that evaluates the fitness of each point it reaches as it moves along, and decides where to move next based on its fitness evaluation. I want to be able to pass different fitness func

Re: [R] adding lines to a barchart

2007-12-19 Thread Deepayan Sarkar
On 12/19/07, Spilak,Jacqueline [Edm] <[EMAIL PROTECTED]> wrote: > Hi all > I can't find what I am looking for so I am asking here. I have a > dataset that looks something like this. > > Year season percent_below > 2000 Winter 6.9179870 > 2000 Spring 1.6829436 > 2000 Summer 1.8463501

[R] Biostatistician & Epidemiologist posting

2007-12-19 Thread Turpin, Jennifer
Good afternoon. I would like to post some positions on your site. Is this possible? Jen Jennifer C. Turpin Human Resources Coordinator Wayne State University Services in Support of the NIH Perinatology Research Branch 4 Brush South - Office 4723 3990 John R. - Detroit, MI 48201 31

Re: [R] question

2007-12-19 Thread John Kane
I think this is what you want. Y[Y>0] <- 1 --- "Armelini, Guillermo" <[EMAIL PROTECTED]> wrote: > Hello everyone! > > Is anybody can help me to solve this silly question > that unfortunately I haven't found the right way to > address it. > > Supose I have a matrix X[n,n] dimension > > I wo

[R] (no subject)

2007-12-19 Thread Jiaming Zuo
Dear R Users, I am working for the United Nations to construct a complete life table from an abridged table. I want to use the code of Hydman Filter by Rob J Hydman but an error sentence always appears and it simply doesn't run-- source("C:/R/Jamie/HymanFilter.R") Error in

Re: [R] unexpected behavior from gzfile and unz

2007-12-19 Thread Matthew Suderman
I figured out the problem: functions gzfile/unz/file/... create a connection to a file but do not *open* the connection unless the 'open' argument is specified. ... a little R gotcha for people who use other programming languages and expect similar concepts/behavior. > I get unexpected behavio

Re: [R] Factor Madness

2007-12-19 Thread Johannes Graumann
As Tony assumed: a data frame. Joh John Kane wrote: > What was spectrum orginally? > > > --- Johannes Graumann <[EMAIL PROTECTED]> > wrote: > >> Why is class(spectrum[["Ion"]]) after this "factor"? >> >> spectrum <- cbind(spectrum,Ion=rep("", >> nrow(spectrum)),Deviation.AMU=rep(0.0, >> nrow

[R] adding lines to a barchart

2007-12-19 Thread Spilak,Jacqueline [Edm]
Hi all I can't find what I am looking for so I am asking here. I have a dataset that looks something like this. Year season percent_below 2000 Winter 6.9179870 2000 Spring 1.6829436 2000 Summer 1.8463501 2000 Autumn 3.8184993 2001 Winter 2.8832806 2001 Sprin

[R] (no subject)

2007-12-19 Thread Jiaming Zuo
Dear R Users, I am working for the United Nations to construct a complete life table from an abridged table. I want to use the code of Hydman Filter by Rob J Hydman but an error sentence always appears and it simply doesn't run-- source("C:/R/Jamie/HymanFilter.R") Error in

[R] unexpected behavior from gzfile and unz

2007-12-19 Thread Matthew Suderman
I get unexpected behavior from "readLines()" and "scan()" depending on how the file is opened with "gzfile" or "unz". More specifically: > file <- gzfile("file.gz") > readLines(file,1) [1] "a\tb\tc" > readLines(file,1) [1] "a\tb\tc" > close(file) It seems that the stream is rewound between calls

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread Dirk Eddelbuettel
On Wed, Dec 19, 2007 at 07:51:47PM +0200, Adrian Dusa wrote: > Hi James, > > On Wednesday 19 December 2007, David James wrote: > > Hi, > > > > I'm sorry I'm also coming late to this discussion, but like Dirk, I > > fail to understand what's wrong with using dbConnect() the way > > the documentati

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread Adrian Dusa
Hi James, On Wednesday 19 December 2007, David James wrote: > Hi, > > I'm sorry I'm also coming late to this discussion, but like Dirk, I > fail to understand what's wrong with using dbConnect() the way > the documentation, (see ?MySQL) suggests. > > RMySQL was developed in a fully distributed cl

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread Adrian Dusa
On Wednesday 19 December 2007, Dirk Eddelbuettel wrote: > [...] > > Err, I am late to this but > > dbConnect(drv, user="mysqluser", password="mysqlpassword", > dbname="anydatabase", host="xxx.xxx.xxx") > > works fine for me (eg on Ubuntu with a remote MySQL on some other > box). What's the proble

[R] question

2007-12-19 Thread Armelini, Guillermo
Hello everyone! Is anybody can help me to solve this silly question that unfortunately I haven't found the right way to address it. Supose I have a matrix X[n,n] dimension I would like to calculate the product of the vectors Y=X[1,n]*X[n,1] Then I would like to run the following operatio

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread David James
Hi, I'm sorry I'm also coming late to this discussion, but like Dirk, I fail to understand what's wrong with using dbConnect() the way the documentation, (see ?MySQL) suggests. RMySQL was developed in a fully distributed client/server environment, and it uses the MySQL-provided client API. The

[R] Genetic algorithm for feature selection

2007-12-19 Thread Rolf Wester
Hi, I'm looking for a R-package that does feature selection for PLS using a genetic optimization algorithm. I couldn't find one on CRAN and I wonder whether there is a free one. I would be very appreciative for any help. Regards Rolf __ R-help@r-pro

Re: [R] Reshape Dataframe

2007-12-19 Thread John Kane
I think if you use Gabor's suggested addtion of add.missing to the original cast command you get what you want. cast(dfm, ... ~ Var3, add.missing=TRUE) --- Bert Jacobs <[EMAIL PROTECTED]> wrote: > > Thx Hadley, > It works, but I need some finetuning. > > If I use the following expression: > Ne

Re: [R] Different labels by panel in barchart

2007-12-19 Thread Deepayan Sarkar
On 12/19/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > Dear all, > > I'm analysing a survey, and creating a barchart of the different responses > for each question. The questions are grouped according to a number of > categories, so I'm using lattice to create a plot with each question in a >

Re: [R] Aggregating by a grouping

2007-12-19 Thread Henrique Dallazuanna
try this: apply(sapply(basic_map, function(x)tapply(df$Value, df$Book, sum)[x]), 2, sum) On 19/12/2007, Kondamani, Arjun (GMI - NY Corporate Bonds) <[EMAIL PROTECTED]> wrote: > Suppose I have: > > BookValue > A 10 > B 11 > C 9 > D 8 > A 12 > C 4 > D 5

Re: [R] Aggregating by a grouping

2007-12-19 Thread Richard . Cotton
> Suppose I have: > > Book Value > A 10 > B 11 > C 9 > D 8 > A 12 > C 4 > D 5 > B 7 > > I want to summarize above not by Book but by groupings of Books as in > (below) > > I have a list ... basic_map <- list(c("A",B"),c("C,D")) > Big_names <- c("A1", "A2") > Names(basi

[R] library(rpart) or library(tree)

2007-12-19 Thread Ingo Holz
Hi, I have a problem with library (rpart) (and/or library(tree)). I use a data.frame with variables "pnV22" (observation: 1, 0 or yes, no) "JTemp" (mean temperature) "SNied" (summer rain) I used function "rpart" to build a model: library(rpart) attach(data.frame) res

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread Dirk Eddelbuettel
On Wed, Dec 19, 2007 at 04:34:26PM +0200, Adrian Dusa wrote: > On Saturday 15 December 2007, Gabor Grothendieck wrote: > > Use ssh forwarding to forward local port 3307 to remote port 3306 > > specifying the remote account and password. Then if you use local port > > 3306 you can access your local

[R] Code for articles in R news?

2007-12-19 Thread Ajay Shah
I went to the article on np in R news 7/2 (October 2007). What's the general technique to get the source code associated with the article as a .R file that I can play with? -- Ajay Shah http://www.mayin.org/ajayshah [EMAIL PROTECTED]

[R] Aggregating by a grouping

2007-12-19 Thread Kondamani, Arjun (GMI - NY Corporate Bonds)
Suppose I have: BookValue A 10 B 11 C 9 D 8 A 12 C 4 D 5 B 7 I want to summarize above not by Book but by groupings of Books as in (below) I have a list ... basic_map <- list(c("A",B"),c("

Re: [R] How can I extract the AIC score from a mixed model object produced using lmer?

2007-12-19 Thread David Hewitt
David Barron-3 wrote: > > You can calculate the AIC as follows: > > (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) > aic1 <- AIC(logLik(fm1)) > > Is AIC() [extractAIC()] "valid" for models with random effects? I noticed that the help page for extractAIC() does not list models wi

Re: [R] Factor Madness

2007-12-19 Thread John Kane
What was spectrum orginally? --- Johannes Graumann <[EMAIL PROTECTED]> wrote: > Why is class(spectrum[["Ion"]]) after this "factor"? > > spectrum <- cbind(spectrum,Ion=rep("", > nrow(spectrum)),Deviation.AMU=rep(0.0, > nrow(spectrum))) > > slowly going crazy ... > > Joh > > _

Re: [R] plot cummulative sum from calendar time

2007-12-19 Thread John Kane
I am not sure I really understand what you want but will this work? tt<-c("03-Nov-1997","09-Oct-1991","27-Aug-1992","01-Jul-1994","19-Jan-1990", "12-Nov-1993","08-Oct-1993","10-Nov-1982","08-Dec-1986","23-Dec-1987","02-Aug-1995", "20-Oct-1998","29-Apr-1991","16-Mar-1994","20-May-1991","28-Dec-1987

Re: [R] bar plot colors

2007-12-19 Thread John Kane
--- Jim Lemon <[EMAIL PROTECTED]> wrote: > John Kane wrote: > > I think you're going to find that barchart with > that > > many values in a bar is going to be pretty well > > uninterpretable. > > > > Jim Lemon gives the desired barchart but it is > very > > difficult to read. > > > > Steali

Re: [R] connecting [logging] RMySQL to an external server - SOLVED

2007-12-19 Thread Adrian Dusa
On Saturday 15 December 2007, Gabor Grothendieck wrote: > Use ssh forwarding to forward local port 3307 to remote port 3306 > specifying the remote account and password. Then if you use local port > 3306 you can access your local version of MySQL and if you > use port 3307 you can access the remot

[R] Standard input and R

2007-12-19 Thread Jon Clayden
Dear all, I am trying to wrap a *nix shell script around R for a particular purpose, for which I need to get R to execute predetermined commands but retain interactivity and allow user input during their execution. A straight redirection of standard input is therefore not appropriate, and

Re: [R] Correlation when one variable has zero variance (polychoric?)

2007-12-19 Thread John Fox
Dear Jose, > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > project.org] On Behalf Of Jose Quesada > Sent: December-19-07 7:54 AM > To: [EMAIL PROTECTED] > Subject: [R] Correlation when one variable has zero variance > (polychoric?) > > Hi, > > I'm running this

Re: [R] array addition

2007-12-19 Thread N. Lapidus
Hi Robin, Before someone gives a better solution, you can try this : x1<-array(1:10,c(2,5)) x2<-array(1:9,c(3,3)) ArrayAdd<-function(array1,array2){ x<-array(0,c(max(nrow(array1),nrow(array2)),max(ncol(array1),ncol(array2 x[1:nrow(array1),1:ncol(array1)]<-x[1:nrow(array1),1:ncol(array1

Re: [R] recode based on filter

2007-12-19 Thread Donatas G.
On Wednesday 19 December 2007 14:12:16 rašėte: > sapply(levels(DATA$know1), function(x)subset(DATA, (know1==x & > know2==x)), simplify=F) Hey, thanks, that seems to work! -- Donatas Glodenis http://dg.lapas.info __ R-help@r-project.org mailing list ht

Re: [R] want to make a plot similar to ecdf

2007-12-19 Thread jim holtman
This should give you what you want: x <- scan(textConnection("0. 2.3972 4.3500 -4.1972 0.6361 1.0806 5.9056 -1.8722 2.1333 -1.1806 3.6167 0.8778 8.3389 3.8417 1. -3.7611 -11.6778 -2.0306 6.9

Re: [R] Obtaining replicates numbers of a vector

2007-12-19 Thread jim holtman
Here is another way of doing it: > x <- c('A','B','A','C','C','B') > ave(rep(1, length(x)), x, FUN=cumsum) [1] 1 1 2 1 2 2 > On Dec 19, 2007 5:36 AM, Eric Lecoutre <[EMAIL PROTECTED]> wrote: > Dear R-help, > > I am trying to have a generic way to assess the replicates in a character > vector. >

Re: [R] using rcorr.cens for Goodman Kruskal gamma

2007-12-19 Thread Frank E Harrell Jr
Colin Robertson wrote: > Dear List, > > > > I would like to calculate the Goodman-Kruskal gamma for the predicted > classes obtained from an ordinal regression model using lrm in the Design > package. I couldn't find a way to get gamma for predicted values in Design > so have found previous pos

[R] Correlation when one variable has zero variance (polychoric?)

2007-12-19 Thread Jose Quesada
Hi, I'm running this for a simulation study, so many combinations of parameter produce many predictions that I need to correlate with data. The problem I'm using rating data with 3 to 5 categories (e.g., too low, correct, too high). The underlying continuous scales should be

[R] scale estimation for Gamma distribution

2007-12-19 Thread lubaroz
Hey, I make a regression for Gamma distribution with log link, in R and in SAS. In R, the dispersion is estimated by \phi=Deviance/(#_of_observations), In SAS, there are two options: \phi=Deviance/(#_of_observations-#_of_params) or \phi=Pearson/(#_of_observations-#_of_params). I understand that

Re: [R] plot cummulative sum from calendar time

2007-12-19 Thread jim holtman
Here is an example of plotting the number of observations per month. You can change this to any period you want. # create some test data x.d <- as.Date("2000-1-1") + runif(1000, 1, 500) # create buckets of one month (or whatever period you want) x.cut <- cut(x.d, breaks=seq(as.Date('2000-1-1'), ma

[R] want to make a plot similar to ecdf

2007-12-19 Thread gallon li
I have a sample of observations: > yy [1] 0. 2.3972 4.3500 -4.1972 0.6361 [6] 1.0806 5.9056 -1.8722 2.1333 -1.1806 [11] 3.6167 0.8778 8.3389 3.8417 1. [16] -3.7611 -11.6778 -2.0306

[R] Obtaining replicates numbers of a vector

2007-12-19 Thread Eric Lecoutre
Dear R-help, I am trying to have a generic way to assess the replicates in a character vector. Say that I have the following vector: x <- c('A','B','A','C','C','B') I would like to obtain: replicates <- c(1,1,2,1,2,2) each number beeing the time we see the corresponding value in x. Any clever

Re: [R] Obtaining replicates numbers of a vector

2007-12-19 Thread Eric Lecoutre
Thank you very much! This does indeed what I am looking for and really have R-ish look and feel. I just have turned that into a little handy function 'replicates' Best wishes, Eric 2007/12/19, Henrique Dallazuanna <[EMAIL PROTECTED]>: > > Try this: > > replicate <- vector("numeric", len=lengt

Re: [R] recode based on filter

2007-12-19 Thread Henrique Dallazuanna
Perhaps you can try subset the data: sapply(levels(DATA$know1), function(x)subset(DATA, (know1==x & know2==x)), simplify=F) On 19/12/2007, Donatas G. <[EMAIL PROTECTED]> wrote: > Hi, I have a data frame DATA, which (simplified of course) looks like this: > > know1 = c("Y","N","N","Y","N","N","Y",

[R] FW: cgh package

2007-12-19 Thread Celine Carret
Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features reso

[R] recode based on filter

2007-12-19 Thread Donatas G.
Hi, I have a data frame DATA, which (simplified of course) looks like this: know1 = c("Y","N","N","Y","N","N","Y","Y","N") par1=c(1,4,5,3,3,2,3,3,5) know2 = c("Y","Y","N","Y","N","N","N","Y","Y") par2=c(3,4,4,3,5,2,4,3,2) DATA=data.frame(know1,par1,know2,par2) it represents answers in a questionn

Re: [R] median of binned values

2007-12-19 Thread Chuck Cleland
Martin Tomko wrote: > Thank you, Chuck, > would you mind commenting a bit on the code, it is not all clear... HOw > would you go to retrieve only the numeric value (not the category name)? > I am just starting with R, and the functionality of replicate and levels > is not quite clear. I tried the

[R] randomForest() for regression produces offset predictions

2007-12-19 Thread Joshua Knowles
Hi all, I have observed that when using the randomForest package to do regression, the predicted values of the dependent variable given by a trained forest are not centred and have the wrong slope when plotted against the true values. This means that the R^2 value obtained by squaring the Pea

Re: [R] Obtaining replicates numbers of a vector

2007-12-19 Thread Henrique Dallazuanna
Try this: replicate <- vector("numeric", len=length(x)) replicate[order(x)] <- unlist(sapply(rle(sort(x))$lengths, seq_len)) On 19/12/2007, Eric Lecoutre <[EMAIL PROTECTED]> wrote: > Dear R-help, > > I am trying to have a generic way to assess the replicates in a character > vector. > Say that I

Re: [R] array addition

2007-12-19 Thread Richard . Cotton
Try this: "%add%" <- function(x1, x2) { dim1 <- dim(x1) dim2 <- dim(x2) seq1 <- list();for(i in 1:length(dim1)) seq1[[i]]=seq(dim1[i]) filter1 <- paste(seq1, collapse=",") cmd1 <- paste("out[", filter1, "]", sep="") seq2 <- list();for(i in 1:length(dim2)) seq2[[i]]=seq(

[R] Help me

2007-12-19 Thread Nitish Kumar Mishra
Hello R Users, I am interested in using R to generate quantitative structure-activity relationships (QSARs) for small molecules given a set of molecular descriptors and biological data tab-delimited or excel file. In which fist value colum of each row is biological value and rest all are its d

Re: [R] Calculate remainer

2007-12-19 Thread Chuck Cleland
livia wrote: > Hello everyone, > > I have got a question about a simple calculation. If I would like to > calculate 50/12 and return the result as 4 and the remainer 2. Is there a > function of doing this? > > Many thanks. ?"%%" to see how to get the remainder. You might put the "result" and re

[R] Calculate remainer

2007-12-19 Thread livia
Hello everyone, I have got a question about a simple calculation. If I would like to calculate 50/12 and return the result as 4 and the remainer 2. Is there a function of doing this? Many thanks. -- View this message in context: http://www.nabble.com/Calculate-remainer-tp14414906p14414906.html

Re: [R] plotting magnitude

2007-12-19 Thread Jim Lemon
[EMAIL PROTECTED] wrote: > I am plotting fishing vessel positions and want these points to be > relative in size to the catch at that point. Is this possible? I am just > begining to use R and my search of the help section didnt help in this > area. Heres what Im using so far > > xyplot(data$lat

Re: [R] median of binned values

2007-12-19 Thread Martin Tomko
Thank you, Chuck, would you mind commenting a bit on the code, it is not all clear... HOw would you go to retrieve only the numeric value (not the category name)? I am just starting with R, and the functionality of replicate and levels is not quite clear. I tried the documentation, but am not any

Re: [R] plot cummulative sum from calendar time

2007-12-19 Thread Gavin Simpson
On Wed, 2007-12-19 at 14:59 +0800, gallon li wrote: > I have the following list of observations of calendar time: > > [1] 03-Nov-1997 09-Oct-1991 27-Aug-1992 01-Jul-1994 19-Jan-1990 12-Nov-1993 > [7] 08-Oct-1993 10-Nov-1982 08-Dec-1986 23-Dec-1987 02-Aug-1995 20-Oct-1998 > [13] 29-Apr-1991 16-Ma

Re: [R] R on EEE PC

2007-12-19 Thread Paul Bennett
Someone asked about R on the EEE PC. That was the second thing I installed when I received mine (the first being the full KDE desktop). I don't recall any issues with the installation. I used the standard debian package (the native linux on the EEE is Xandros, a derivation of debian). The caveat be

Re: [R] 4 questions regarding hypothesis testing, survey package, ts on samples, plotting

2007-12-19 Thread James Reilly
On 19/12/07 8:39 PM, eugen pircalabelu wrote: > 2. How can i find the median of a variable in survey package? > a<-c(1:10) > b<-sample(1:20, 10, replace=T) > b1<-sample(0:1, 10, replace=T) > c<-data.frame(a,b, b1) > library(survey) > design<-svydesign(id=~1, data=c) > svymean(~b, design) > > svyme

[R] prop.trend.test() and Cochran-Armitage Trend test

2007-12-19 Thread R R
Hi, I was just wondering if prop.trend.test() is equivalent to the Cochran-Armitage Trend test? Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read th

[R] Execute R-code from vim on Mac OS X

2007-12-19 Thread Vincent Nijs
I just posted a vim-script at http://www.vim.org/scripts/script.php?script_id=2104 that allows sending selected lines of R code in a vim-buffer to the R- gui. There are alternatives for Windows and Linux (http://www.vim.org/ scripts/script.php?script_id=1048) but i never found anything that works o

Re: [R] GLM and factor in forular

2007-12-19 Thread Knut Krueger
Mark Leeds schrieb: > That's because the first factor is being used as the "baseline". This is > explained in any intro to GLMs text. > > > Thank you Mark, I didn't found that hint. Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailm

Re: [R] Random forests

2007-12-19 Thread Gavin Simpson
On Tue, 2007-12-18 at 16:27 -0600, Naiara Pinto wrote: > Dear all, > > I would like to use a tree regression method to analyze my dataset. I > am interested in the fact that random forests creates in-bag and > out-of-bag datasets, but I also need an estimate of support for each > split. That seems

Re: [R] median of binned values

2007-12-19 Thread Chuck Cleland
Martin Tomko wrote: > Dear list, > I have a vector (array, table row, whatever is best) of frequency values > for categories (or bins), and I need to find the median category. > Trivial to do by hand, but I was wondering if there is a means to do it > in R in an elegant way. > > The obvious me

Re: [R] bar plot colors

2007-12-19 Thread Jim Lemon
John Kane wrote: > I think you're going to find that barchart with that > many values in a bar is going to be pretty well > uninterpretable. > > Jim Lemon gives the desired barchart but it is very > difficult to read. > > Stealing his code to create the same matrix I'd > suggest may be lookin

[R] array addition

2007-12-19 Thread Robin Hankin
Hi suppose I have two arrays x1,x2 of dimensions a1,b1,c1 and a2,b2,c2 respectively. I want x = x1 "+" x2 with dimensions c(max(a1,a2), max(b1,b2),max (c1,c2)) with x[a,b,c] = x1[a1,b1,c1] + x2[a2,b2,c2] ifa <=min(a1,a2) , b<=min (b1,b2), c<=min(c1,c2) and the other bits either x1 o

[R] using rcorr.cens for Goodman Kruskal gamma

2007-12-19 Thread Colin Robertson
Dear List, I would like to calculate the Goodman-Kruskal gamma for the predicted classes obtained from an ordinal regression model using lrm in the Design package. I couldn't find a way to get gamma for predicted values in Design so have found previous positings suggesting to use : Rcorr.ce

[R] Different labels by panel in barchart

2007-12-19 Thread Richard . Cotton
Dear all, I'm analysing a survey, and creating a barchart of the different responses for each question. The questions are grouped according to a number of categories, so I'm using lattice to create a plot with each question in a category on it. The problem is that the response set for differe

Re: [R] Analyzing Publications from Pubmed via XML

2007-12-19 Thread Armin Goralczyk
On Dec 18, 2007 9:39 PM, David Winsemius <[EMAIL PROTECTED]> wrote: > "Armin Goralczyk" <[EMAIL PROTECTED]> wrote in > news:[EMAIL PROTECTED]: > > > It's not the spaces, the problem is the tag (sorry that I didn't > > specify this), or maybe the string []. I am working on a Mac OS X 10.4 > > with R

[R] median of binned values

2007-12-19 Thread Martin Tomko
Dear list, I have a vector (array, table row, whatever is best) of frequency values for categories (or bins), and I need to find the median category. Trivial to do by hand, but I was wondering if there is a means to do it in R in an elegant way. The obvious medioan(vector) returns the median f

Re: [R] Factor Madness

2007-12-19 Thread Johannes Graumann
Yep, but I figured that out quite fast ;0) Thanks for giving me a hand ... you want believe a many times I skimmed the cbind help without actually seeing this ... well, it was 0:30 ... Thanks again, Joh Tony Plate wrote: > Whoops, it looks like there's a typo in ?cbind (R version 2.6.0 Patched >