Re: [R] Merging yields "Error: unexpected input ..."

2011-06-16 Thread Daniel Malter
Note what are supposed to be quotation marks around "ID" in your post are "a circumflex" instead. Maybe the problem is that the quotation marks that are supposed to be around ID are not recognized by your R version. May you do not use the proper font encoding. Use straight quotation marks or apost

Re: [R] Scatter plot produces "'x' and 'y' lengths differ"

2011-06-16 Thread Daniel Malter
It likely means that your x and y are differently long. That is, affect1 and adh1scr do not contain the same number of values in that instance. That precludes them from being plotted against each other. abline and lowess would fail for the same reason. x<-c(1,2,3) y<-c(2,4) plot(y~x) complete.case

[R] [RExcel] please help me to set up RExcel via a remote server

2011-06-16 Thread Takatsugu Kobayashi
Hi RUsers, I am currently tying to use RExcel via R installed in my remote server (CentOS 5.5). Could you please help me set up a R remote server? All I know about the server is its IPAddress. Apologies for my fundamental question. Thank you so much! Taka _

[R] Rcmdr Plugin error

2011-06-16 Thread Erin Hodgess
Dear R People: (particularly those who have build Rcmdr Plugin packages): I'm building a new Plugin and keep getting the following error: Error in if (is.null(where) || where >= n) rbind(object1, object2) else if (where < : missing value where TRUE/FALSE needed Error in library(RcmdrPlugin H

Re: [R] optimization with Sparse matrices

2011-06-16 Thread Berend Hasselman
Dube, Jean-Pierre wrote: > > To whom it may concern, > > I am trying to maximize a log-likelihood function using optim. This is a > simple problem with only 18 parameters. To conserve memory, I am using > sparse matrices (SLAM) for some of the data matrices used in the > computation of the lik

Re: [R] Merging rows in a dataframe

2011-06-16 Thread Scott Chamberlain
Something like this could work for you (note that a few other packages would be faster, such as data.table), but plyr is intuitive. require(plyr) # example data set dat <- data.frame(col1 = rep(c("a","b"), each=5), col2 = rep(c("prog1","prog2","prog3","prog4","prog5"), 2), col3 = rnorm(10), co

[R] optimization with Sparse matrices

2011-06-16 Thread Dube, Jean-Pierre
To whom it may concern, I am trying to maximize a log-likelihood function using optim. This is a simple problem with only 18 parameters. To conserve memory, I am using sparse matrices (SLAM) for some of the data matrices used in the computation of the likelihood. However, optim appears to co

[R] how to customize row order from clustering in a heatmap?

2011-06-16 Thread CZ
Hi, I am working on a heatmap and clustering all the rows with the method of 'ward'. But I notice that my rows are in a weird order which is not what I want / expect. Could anyone help on this? My questions are with the figure below. Thanks in advance http://r.789695.n4.nabble.com/file/n360381

[R] Scatter plot produces "'x' and 'y' lengths differ"

2011-06-16 Thread Alspach, Steven E.
Hello, I am working on a project to create some scatter plots. I have syntax for 26 plots, and 22 of them display as they should. But here, for example, is a sample of the command syntax I am using: good <- complete.cases(affect1,adh1scr) plot (jitter(affect1,2.0),jitter(adh1scr,1.0),xli

[R] Merging rows in a dataframe

2011-06-16 Thread Will Parbury
Hi R Help list I'm looking to visualise US foreign aid 1946-2009 and I have the dataset for this. The trouble is it's a bit too complex and I need to simply it I want to merge all of the rows with the same country together and add up the individual totals to make one total figure per country

[R] I need help with the mean equation in rgarch package

2011-06-16 Thread mariam achkir
Dear R users, I hope this email finds you well, My name is Mariam and I am currently using R in my thesis project. I is about modeling investors' sentiment. My R skills are very modest and I am trying to solve a Garch in mean equation using the "rgarch" package. The main issue I am facing is with

Re: [R] matching by gender and age

2011-06-16 Thread 1Rnwb
the examples work great but it gives me this error on this file http://r.789695.n4.nabble.com/file/n3603737/il1ra_L.csv il1ra_L.csv > Age.co<-c(dat2b$Dr_Age) > Sex.co<-as.factor(dat2b$Sex) > casecont.co<-as.factor(dat2b$Self_T1D) > stat.co<-as.factor(dat2b$status) > > m <- matchControls(Sex.co~A

[R] coxph: cumulative mortality hazard over time with associated confidence intervals

2011-06-16 Thread Lise Aubry
Dear R-users, I computed a simple coxph model and plotted survival over time with associated confidence intervals for 2 covariate levels (males and females). M1 <- coxph(survobject~sex, data=surv) M1 survsex <- survfit(survobject~sex,data=surv) summary(survsex) plot(survsex, conf.int=T, col=c("b

Re: [R] Fwd: varimp_in_party_package

2011-06-16 Thread Jinrui Xu
Sorry, Patrick and other victims. My bad~~ The data file can be accessed at http://zhanglab.ccmb.med.umich.edu/TM-fold/featureSelection_rec.vectors The code is attached below. Error happens at "data.cforest.varimp <- varimp(data.cforest, conditional = TRUE)": "Error in model.matrix.default

Re: [R] Multiply list objects

2011-06-16 Thread mdvaan
I am still thinking about this problem. The solution could look something like this (it's net yet working): k<-lapply(h, function (x) x*0) # I keep the same format as h, but set all values to 0 years<-c(1997:1999) # I define the years for (t in 1:length(years)) { year = as.characte

[R] Merging yields "Error: unexpected input ..."

2011-06-16 Thread William Mabe
I am new to R and am having difficulty merging 2 data sets, both of which have the same 30 variables and about 2,000 records. I've looked high and low—Paul Johnson's help page, through some of the 5,420 (yikes!) results for “merge” on the R list archives, and google searches—and I'm ge

Re: [R] combining strings

2011-06-16 Thread Richard M. Heiberger
I made different assumptions than Josh. xf<-c("W",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA) xg<-c(NA,"k","h",NA,"g","r","j",NA,"v","d",NA,"v",NA,"z","r","r","i") xf xg unlist(apply(cbind(xf,xg), 1, function(x) x[!is.na(x)])) as.vector(unlist(apply(cbind(xf,xg), 1, function(x) x[!is.na(x)]))

Re: [R] combining strings

2011-06-16 Thread Joshua Wiley
Hi, You did not specify what assumptions you can make about xf and xg (such as will they have identical lengths and is it possible both could contain nonmissing values in the same element?), but this seems a straightforward approach in your little example: index <- is.na(xf) xf[index] <- xg[index

[R] combining strings

2011-06-16 Thread Erin Hodgess
Dear R People: Suppose I have the following two character vectors: xf [1] "W" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > xg [1] NA "k" "h" NA "g" "r" "j" NA "v" "d" NA "v" NA "z" "r" "r" "i" > I want to end up with "W" "k" "h" ... What is the best way to achieve t

Re: [R] When models and anova(model) disagree...

2011-06-16 Thread Frank Harrell
Without seeing the model I'm not clear on the cause. In general it is not very useful to compute 1 d.f. tests for parameters that represent only part of a meaningful hypothesis. Note that anova.lrm computes Wald statistics, which are subject to the Hauck-Donner effect (which may not be the cause

[R] caret for non-numeric data

2011-06-16 Thread Yang Zhang
caret has many useful preprocessing facilities for numeric predictors, such as removing near-zero-variance predictors, removing correlated predictors, removing linear combinations, centering/scaling, and Box-Cox transformations. However, these don't work for factor data, which is common in many le

Re: [R] Matching vector order by indicators in a matrix

2011-06-16 Thread Bert Gunter
Folks: This is sufficiently "tricky" that a word of explanation might be helpful to reveal the magic. > > Rates <- c(0.006280048, 0.330934659) > Index.Matrix <- matrix(c(1, 2, 1, 2), 2, 2) > >> Rates > [1] 0.006280048 0.330934659 > >> Index.Matrix >     [,1] [,2] > [1,]    1    1 > [2,]    2    2

Re: [R] Matching vector order by indicators in a matrix

2011-06-16 Thread Marc Schwartz
On Jun 16, 2011, at 4:52 PM, Jeremy Beaulieu wrote: > Hi all~ > > I have a bit of stupid question. And I promise, I have struggled through this > and it sort of pains me to post this question... > > I have the following vector which is are the estimated parameter values > output from "optim".

[R] Matching vector order by indicators in a matrix

2011-06-16 Thread Jeremy Beaulieu
Hi all~ I have a bit of stupid question. And I promise, I have struggled through this and it sort of pains me to post this question... I have the following vector which is are the estimated parameter values output from "optim". $Rates [1] 0.006280048 0.330934659 I want to match the order in

[R] Polygon question

2011-06-16 Thread Muhammad Rahiz
Hi all, I have the following script which fills the values which are less than the mean of a given timeseries. If you look closely, the colored regions are "out of line". Any suggestions how I can rectify this? Thanks Muhammad # - #rm(list=ls()) x <- abs(rnorm(100)) tt <- 1:100 m <- m

Re: [R] Placing Text on ggplot2 graphics vs. xyplot

2011-06-16 Thread baptiste auguie
Hi, As far as I know secondary y-axis and multiple pages are not possible in ggplot2 (there are workarounds for the latter in the ggplot2 list archives). For the subtitle, you could implement it with grid.text and grid viewports, library(gridExtra) library(ggplot2) grid.arrange( qplot(1,1), sub

[R] Placing Text on ggplot2 graphics vs. xyplot

2011-06-16 Thread Guy Jett
Greetings to the help mailing list. I am in the process of translating a large graphic from xyplot to ggplot2 (13 columns by about rows). I have been unsuccessful trying to understand how to place the following text strings after three days of: * Perusing Wickham's "gg2plot" book; * Searching hi

[R] Asymetrical Confidence Interval

2011-06-16 Thread Muhuri, Pradip (SAMHSA/CBHSQ)
Dear List, I wanted to calculate the asymmetrical confidence interval based on the sample statistic and standard error that available from the published report (complex survey-based). The calculation details can be seen from pages 17-18 of the document at the following link: http://www.oas.sa

Re: [R] NonParametric Anova

2011-06-16 Thread Greg Snow
You could do this using permutation tests. If everything is balanced and orthogonal then you can permute the predictors, otherwise you can follow these main steps: 1. Formulate the test of interest as a full and reduced model test and find the F statistic (or other, but I will assume F) for th

Re: [R] prediction intervals

2011-06-16 Thread Greg Snow
I don't think that this approach is appropriate here. Each iteration after the 1st the lm/predict combination will assume that the new data is exact when in fact it is an estimate with some error involved. To properly do this you need to take into account that variability. There is a time ser

Re: [R] Fwd: varimp_in_party_package

2011-06-16 Thread Patrick Connolly
On Thu, 16-Jun-2011 at 09:19AM -0400, Jinrui Xu wrote: > Thanks for your feedback. > I think the problem is not because of many levels. There is only 1 > column with two levels as class labels in my input data. > > Below is my code. The commandline "data.cforest.varimp <- > varimp(data.cforest

Re: [R] lines(..., lwd=3) inaccuracy

2011-06-16 Thread Sarah Goslee
On Thu, Jun 16, 2011 at 3:43 PM, Prof Brian Ripley wrote: > On Thu, 16 Jun 2011, Sarah Goslee wrote: > >> Hi Frank, >> >> It's not inaccuracy, exactly, and it's intentional. >> >> The default behavior is to use a round endcap on a line, and with such >> a large linewidth that endcap is arcing belo

Re: [R] lines(..., lwd=3) inaccuracy

2011-06-16 Thread Prof Brian Ripley
On Thu, 16 Jun 2011, Sarah Goslee wrote: Hi Frank, It's not inaccuracy, exactly, and it's intentional. The default behavior is to use a round endcap on a line, and with such a large linewidth that endcap is arcing below and above the starting points. This being R, there's a par for that: putt

Re: [R] animation error

2011-06-16 Thread Yihui Xie
Hi, If 100 frames can work but 730 cannot, I think this might be due to the limit of ImageMagick. If that is the case, I do not have any solutions from R's aspect, instead, you may want to try GraphicsMagick, which is similar to ImageMagick. I'm not sure if it is better than ImageMagick in terms o

Re: [R] lines(..., lwd=3) inaccuracy

2011-06-16 Thread Sarah Goslee
Hi Frank, It's not inaccuracy, exactly, and it's intentional. The default behavior is to use a round endcap on a line, and with such a large linewidth that endcap is arcing below and above the starting points. This being R, there's a par for that: putting lend=1 in your lines() statements will g

[R] lines(..., lwd=3) inaccuracy

2011-06-16 Thread Frank Harrell
Using a line width > 1 results in not only a thicker line but also some fuzz in the other direction, as shown in this example program. You will see that the thick vertical black lines extend below the gray scale horizontal lines. Does anyone know whether this is intended or is it a bug? The appl

Re: [R] Rmpi installation

2011-06-16 Thread Hugo Mildenberger
Kristian, > Another update: I ditched the pre-installed version of openmpi and > installed openmpi from source (./configure --without-openib). A very reasonable approach. Remembering my own struggles with SuSE years ago, I did not dare to propose that procedure. > Compiling and running your tes

[R] lmer: How to plot a spline from function

2011-06-16 Thread Caro
Hi, my problem sounds simple but I've been trying and looking for a solution, but just can not find out how to solve it. I have a dataset and want to do a GAM with binomial link function, random effects (for individuals as there are severeal measurements for everyone) and a time-spline. For thi

Re: [R] functions for polynomial and rational interplation?

2011-06-16 Thread dslowik
Bill, Thank you for the correction; yes, Nevilles' is an algorithm to produce the same Lagrange interpolating polynomial. And thank you for the polynomF package! Don Slowik -- View this message in context: http://r.789695.n4.nabble.com/functions-for-polynomial-and-rational-interplation-tp359533

[R] Specify ID variable in daisy{cluster}

2011-06-16 Thread adlynch
Hi All - I am using the daisy function from the cluster library to create a dissimilarity matrix. I'm going to use that matrix to run a cluster analysis. My participants are identified with the variable, hhid. However, when I try to keep hhid in the dataset that I use to create the dissimilarity

[R] prediction intervals

2011-06-16 Thread Dave Evens
Dear members, I'm fitting linear model using "lm" which has numerous auto-regressive terms as well as other explanatory variables. In order to calculate prediction intervals, i've used a for-loop as the auto-regressive parameters need to be updated each time so that a new forecast and corresp

[R] waiting at end of script

2011-06-16 Thread Meesters, Christian
Hi, I am working under Linux and have an executable R script like this: #! /usr/bin/env Rscript

Re: [R] NonParametric Anova

2011-06-16 Thread Uddin, Sharif [ATRMUS]
Non- Parametric equivalent to parametric anova is Kruskal-Wallis test - I am not sure R has any function for this - I am new to R (I think R should have it already) - SAS has this option. Sharif -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org

Re: [R] How to generate bivariate exponential distribution?

2011-06-16 Thread xuyongdeng
Petr Savicky-2, thanks you. It seems the code works very well. I use rate=1, so "common" is between 0 to 1. Thanks again. -- View this message in context: http://r.789695.n4.nabble.com/How-to-generate-bivariate-exponential-distribution-tp3596944p3602539.html Sent from the R help mailing list arch

Re: [R] Replacing values without looping

2011-06-16 Thread Joshua Wiley
Hi, If you truly have an array, this is option that should be much faster than a loop: index <- which(is.na(dat)) dat[index] <- dat[index - 1] the only catch is that when there previous value is NA, you may have to go through the process a few times to get them all. One way to automate this wou

Re: [R] Hauck-Donner

2011-06-16 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 06/16/2011 01:47 PM, Rob James wrote: > Ben, > > Thanks for this. Very helpful and clearly others have tripped over the > same problem > I would have supposed that the solution was to ask lrm (or glm) to use > LR rather than Wald, but I don't see s

[R] proportion explained by each term in a GAM

2011-06-16 Thread Samuel Turgeon
Dear list, I have read several posts on this topic. I would use the same methodology as proposed by Simon Wood in this post: http://r.789695.n4.nabble.com/variance-explained-by-each-term-in-a-GAM-td836513.html My first question is: Does anyone know a scientific source (paper, book,...) that exp

Re: [R] R in MAC add many extra <´s

2011-06-16 Thread Jonathan Daily
Do you mean prompts (the > that indicates R is waiting for input)? Your issue is not clear. Please post a copy/paste of your session, as well as your sessionInfo(). On Thu, Jun 16, 2011 at 7:16 AM, Rosario Garcia Gil wrote: > Hello > > I have a annoying problem with R (which I am running in MAC).

[R] Question about R.oo package

2011-06-16 Thread Kaisers
Dear R.oo package users, while testing some functionality of the R.oo, I found that during the first construction of a object from a class, the constructor is twice called, but only one object is finalized. In all subsequent creation processes, the constructor is (expectedly) called once. Here

[R] R in MAC add many extra <´s

2011-06-16 Thread Rosario Garcia Gil
Hello I have a annoying problem with R (which I am running in MAC). Every time I enter a function and I press enter to run it, I get many additional "<´s", it is really bothering me. I have tried to google to find out how to fix the problem but I did not succeed. Anyone with similar experience

Re: [R] Multiple (7) Y axes?

2011-06-16 Thread Philip Rhoades
Jannis, Beautiful! Thanks for the useful responses from others as well. Regards, Phil. On Thu, 16 Jun 2011 12:49:58 +0100 (BST), Jannis wrote: Try something like: par(mar=c(4,2,1,12),tcl=0.2,mgp=c(1,0,0)) plot(1:10,1:10) for (i in 1:7) { par(new=TRUE) plot(1:10,(i+(1:10)+rnorm(10,0

[R] Replacing values without looping

2011-06-16 Thread wuffmeister
I got an array similar to the one below, and want to replace all NAs with the previous value. 99 8.2 b NA 8.3 x NA 7.9 x 98 8.1 b NA 7.7 x 99 9.3 b ... i.e. the first two NAs should be replaced to 99, whereas the last one should be 98. I would like to apply a function to reach row, checking if th

[R] problem with missing package

2011-06-16 Thread Eric Elguero
Hi everybody, I just tried to run R on one of my projects but it did not want to run: R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) Loading required package: utils Error in loadNamespace(i

[R] Best package suggestion

2011-06-16 Thread Bruce Miller
Hi all, What is the best package to use to evaluate correlations between events by time (species co-occurrence). Chron? I would like to determine fi there is any solid relationship between the occurrence of critter A given critter B is present at a given time frame. Bruce

Re: [R] When models and anova(model) disagree...

2011-06-16 Thread Ben Bolker
Greg Snow imail.org> writes: > The individual tests on coefficients in logistic regression > are generally based on a Wald test statistic. > Unfortunately there is a bit of a paradox possible in this > case where the coefficient is highly > significant, but due to a flattening of the likelihoo

Re: [R] Problems with nls

2011-06-16 Thread Daniel Malter
Those are in fact the coefficients for p and q they are estimating, though their M is different. Who knows what they did with that. The data source was: Title: Diffusion models of mobile telephony in Greece Source: Telecommunications policy [0308-5961] Michalakelis yr:2008 vol:32 iss:3-4 pg:234

Re: [R] Do a corelational analysis in R

2011-06-16 Thread Daniel Malter
I am not sure what you actually want to accomplish. If you try to correlate numeric/rank data with text data, I have no clue how that could be achieved (other than with text length, or presence/absence of a comment). If you try to figure out how you prevent the cor() function to fail when it encoun

[R] Odp: alphahull: is low level plotting possible?

2011-06-16 Thread Petr PIKAL
Hi > > Dear R users, > I am using package alphahull version 0.2-0 with R-2.13.0. Here is my problem. > I have produced a 2-D plot of points and need to draw convex hulls around > some subsets of these points. So I just need to add the convex hulls to > the already existing plot. That is why I

Re: [R] Problem auto.arima() in R

2011-06-16 Thread Ben Bolker
On 06/16/2011 03:04 AM, siddharth arun wrote: > > I will break my query into 2 parts: > > 1. My main idea is to give some data as an input and if any seasonality > is there in the input, it should be captured automatically and the > corresponding frequency automatically generated. please comment

[R] alphahull: is low level plotting possible?

2011-06-16 Thread Martin Ivanov
Dear R users, I am using package alphahull version 0.2-0 with R-2.13.0. Here is my problem. I have produced a 2-D plot of points and need to draw convex hulls around some subsets of these points. So I just need to add the convex hulls to the already existing plot. That is why I cannot use the pl

Re: [R] cannot install Rcmdr on ubuntu 11.4

2011-06-16 Thread Dirk Eddelbuettel
On 16 June 2011 at 07:17, Frans Marcelissen wrote: | | Hello, | For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4 system. | I run R as root When I try to install Rcmdr, then whatever mirror I select, I get the message: Rcmd is an Ubuntu package too, so just do $ s

Re: [R] Porting "unmaintained" packages to post R 2.10.0 era

2011-06-16 Thread Prof Brian Ripley
On Thu, 16 Jun 2011, Mr Rhelp wrote: Hi all, I am trying to re-compile some "unmaintained" (it seems) packages, namely rSoNIA and dynamicnetwork from: http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/ These packages predates R 2.10.0 so they need to be recompile. Well, re-installed. A

Re: [R] Escape sequence in eval ()

2011-06-16 Thread Uwe Ligges
On 15.06.2011 15:58, Franc Lucas wrote: Hello, I am wondering how to get the quotation marks into a variable expression. I can't escape it with the backslash \ ... Example: I can access my data frame via TABLE$"2011-01-02"$columnD Now I want to do this automatically

Re: [R] Clarks 2Dt function in R

2011-06-16 Thread Ronald Bialozyt
bbolker wrote: > > biologie.uni-marburg.de> writes: > >> you answerd to Nancy Shackelford about Clarks 2Dt function. >> Since the thread ended just after your reply, >> I would like to ask, if you have an idea how to use this function in R > > I got started on your problem, but I didn't finish

Re: [R] Clarks 2Dt function in R

2011-06-16 Thread Ronald Bialozyt
bbolker wrote: > > biologie.uni-marburg.de> writes: > >> you answerd to Nancy Shackelford about Clarks 2Dt function. >> Since the thread ended just after your reply, >> I would like to ask, if you have an idea how to use this function in R > > I got started on your problem, but I didn't finish

Re: [R] Porting "unmaintained" packages to post R 2.10.0 era

2011-06-16 Thread Uwe Ligges
On 16.06.2011 14:46, Ben Rhelp wrote: Hi all, I am trying to re-compile some "unmaintained" (it seems) packages, namely rSoNIA and dynamicnetwork from: http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/ These packages predates R 2.10.0 so they need to be recompile. After split the single

Re: [R] Read file line by line

2011-06-16 Thread Prof Brian Ripley
On Thu, 16 Jun 2011, Joel wrote: Found what was wrong with my code Please follow the posting guide, and give the context asked for there. changed: inFile <- file('gwas_data_chr10.gen') to: inFile <- file('gwas_data_chr10.gen','r') Dunno why its important but it is :P You didn't open the f

Re: [R] how to update a bugs-model from inside R using R2WinBUGS

2011-06-16 Thread Frederic Holzwarth
The script command "coda" is not necessary, unless you want to read in in coda-format output. Necessary are the other commands: "history & save (odc)". "save (txt)" lets you read the on-screen output of winbugs later as a text-file. Another way is also to take the saved last values of the chains a

Re: [R] Read file line by line

2011-06-16 Thread Joel
Found what was wrong with my code changed: inFile <- file('gwas_data_chr10.gen') to: inFile <- file('gwas_data_chr10.gen','r') Dunno why its important but it is :P -- View this message in context: http://r.789695.n4.nabble.com/Read-file-line-by-line-tp3602349p3602399.html Sent from the R help m

[R] Porting "unmaintained" packages to post R 2.10.0 era

2011-06-16 Thread Ben Rhelp
Hi all, I am trying to re-compile some "unmaintained" (it seems) packages, namely rSoNIA and dynamicnetwork from: http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/ These packages predates R 2.10.0 so they need to be recompile. After split the single big file in /man in each packages into

[R] Read file line by line

2011-06-16 Thread Joel
Hi I got a file that looks like this: (i have shorten it alot the real file is over 200k rows long) chr10 rs7909677 101955 A G 0 1 0 1 0 0... chr10 rs2436025 238506 C G 1 0 0 1 0 0... chr10 rs11253562 148946 C T 0 1 0 0 1 ... chr10 rs1105116 230788 G T 0 0 1 0 0 1... chr10 rs4881551 149076 A G 0

Re: [R] texi2dvi runs but produces no output

2011-06-16 Thread Duncan Murdoch
On 11-06-16 7:50 AM, christiaan pauw wrote: Hi everybody. Was the problem below ever solved? I have the same problem on Windows 7 with R 2.13.0 and LyX 2 - everything freshly installed. My Rweave.bat and MakeSweave.R files are similar to below (I followed http://wiki.lyx.org/uploads/LaTeX/Sweave

Re: [R] texi2dvi runs but produces no output

2011-06-16 Thread christiaan pauw
Hi everybody. Was the problem below ever solved? I have the same problem on Windows 7 with R 2.13.0 and LyX 2 - everything freshly installed. My Rweave.bat and MakeSweave.R files are similar to below (I followed http://wiki.lyx.org/uploads/LaTeX/SweaveR/lyx_with_r_and_sweave_instructions.pdf ) I a

Re: [R] Multiple (7) Y axes?

2011-06-16 Thread Jannis
Try something like: par(mar=c(4,2,1,12),tcl=0.2,mgp=c(1,0,0)) plot(1:10,1:10) for (i in 1:7) { par(new=TRUE) plot(1:10,(i+(1:10)+rnorm(10,0,0.4)),yaxt='n',col=i,type='l') axis(4,line=(i-1)*1.5,col=i-1,col.ticks=i-1) } You may need to tweek around the options a bit and check that the t

Re: [R] Constrained Optimization

2011-06-16 Thread Uwe Ligges
On 16.06.2011 10:25, Animesh wrote: I am trying to optimize a simple function, but I want to optimize it for values of k between 0 and 1. I read the help file for constrOptim function but it is always giving me the error constrOptim((0.4),simulation,NULL,ui=rbind(c(0,0),c(1,1))) Your param

Re: [R] Rmpi installation

2011-06-16 Thread Unger, Kristian, Dr.
Another update: I ditched the pre-installed version of openmpi and installed openmpi from source (./configure --without-openib). Compiling and running your test programme gives me the following error: unger@zytosrv01dmi:~/R_projects/OS> ./mtest [zytosrv01dmi:6094] *** An error occurred in MPI_Sen

Re: [R] Escape sequence in eval ()

2011-06-16 Thread Jim Holtman
get(a)[[b]][[c]] with b <- "2011-01-02" Sent from my iPad On Jun 15, 2011, at 9:58, "Franc Lucas" wrote: > > Hello, > I am wondering how to get the quotation marks into a variable expression. I > can't escape it with the backslash \ ... > Example: > I can access my data frame via

Re: [R] Save the results of data analysis in R

2011-06-16 Thread Paul Hiemstra
On 06/16/2011 09:23 AM, Jim Lemon wrote: > On 06/16/2011 07:12 PM, amrita gs wrote: >> Hi everyone, >> >> I want to do data analysis using the values retrieved from a MySQL >> database. Is there a way to save the results of data analysis in R. >> > Hi amrita, > If you mean "save the output of

Re: [R] Multiple (7) Y axes?

2011-06-16 Thread Jim Lemon
On 06/16/2011 07:12 PM, Philip Rhoades wrote: People, I want to create seven plots on the one graph - each with it's own Y axis and scale - I want the plots overlaid because it is the shape of the graphs that I want to compare, not so much the values. I have found examples where people show how

Re: [R] Save the results of data analysis in R

2011-06-16 Thread Jim Lemon
On 06/16/2011 07:12 PM, amrita gs wrote: Hi everyone, I want to do data analysis using the values retrieved from a MySQL database. Is there a way to save the results of data analysis in R. Hi amrita, If you mean "save the output of an analysis", there are several ways. 1) Enter "sink() b

Re: [R] Multiple (7) Y axes?

2011-06-16 Thread ONKELINX, Thierry
Dear Philip, If the values are not important, then you don't need different Y-axes. Why not standardise the seven datasets so they have a common scale? Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur-

[R] Multiple (7) Y axes?

2011-06-16 Thread Philip Rhoades
People, I want to create seven plots on the one graph - each with it's own Y axis and scale - I want the plots overlaid because it is the shape of the graphs that I want to compare, not so much the values. I have found examples where people show how to put two Y axes on the left of the plot

[R] Save the results of data analysis in R

2011-06-16 Thread amrita gs
Hi everyone, I want to do data analysis using the values retrieved from a MySQL database. Is there a way to save the results of data analysis in R. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.

Re: [R] cannot install Rcmdr on ubuntu 11.4

2011-06-16 Thread Prof Brian Ripley
On Thu, 16 Jun 2011, Frans Marcelissen wrote: Hello, For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4 system. I run R as root When I try to install Rcmdr, then whatever mirror I select, I get the message: install.packages('Rcmdr',dependencies=TRUE) Installing pack

[R] Do a corelational analysis in R

2011-06-16 Thread amrita gs
Hi everyone, I retrieved the values of form elements such as radiobuttons, text area,textbox etc into MySQL database. I retieved the values from MySQL db to R using RODBC package. If i want to do a corelational analysis using the values in textarea and radiobutton how is it possible as textarea m

Re: [R] plot with two y axes BUT unaligned x axis

2011-06-16 Thread Jim Lemon
On 06/15/2011 09:51 PM, bjmjarrett wrote: Hi all, I have scoured the archives of this forum but nothing quite seems to fit the bill... I would like to plot a graph displaying two variables (y axes) that share date as the x axis. However, the date values for each variable are not the same - for

[R] NonParametric Anova

2011-06-16 Thread Loo Yim Ling
Dear Sir, I would like to ask whether there is any tool in R, developed for the function of non parametric Anova, where the non parametric analysis is able to compute the p-value for interaction as well (similar to Anova)? If not, would sir like to suggest any of the other statistical software

[R] cannot install Rcmdr on ubuntu 11.4

2011-06-16 Thread Frans Marcelissen
Hello, For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4 system. I run R as root When I try to install Rcmdr, then whatever mirror I select, I get the message: install.packages('Rcmdr',dependencies=TRUE) Installing package(s) into ‘/usr/local/lib/R/site-library’ (as

[R] Constrained Optimization

2011-06-16 Thread Animesh
I am trying to optimize a simple function, but I want to optimize it for values of k between 0 and 1. I read the help file for constrOptim function but it is always giving me the error > constrOptim((0.4),simulation,NULL,ui=rbind(c(0,0),c(1,1))) "Error in ui %*% theta : non-conformable arguments

Re: [R] Fwd: varimp_in_party_package

2011-06-16 Thread Torsten Hothorn
Hello everyone, I use the following command lines to get important variable from training dataset. data.controls <- cforest_unbiased(ntree=500, mtry=3) data.cforest <- cforest(V1~.,data=rawinput,controls=data.controls) data.cforest.varimp <- varimp(data.cforest, conditional = TRUE) I got er

[R] package VGAM: vglm.fit()

2011-06-16 Thread Martin Spindler
Dear all, I am estimating a bivariate probit model using the package VGAM: fit1 = vglm(cbind(y1, y2) ~ x1+x2, binom2.rho, data=dat, trace=TRUE) I would like to estimate this via the method vglm.fit (in an analogous way as lm.fit for lm or glm.fit for glm). Unfortunately my trials did no

Re: [R] plot with two y axes BUT unaligned x axis

2011-06-16 Thread Yuliya Matveyeva
Use the `xlim` parameter of the `plot` function. IFor example, if X1 and X2 are the variables that contain the values of your x-axis, do xlim1 <- range(X1,X2), than do plot(, xlim = xlim1,...) Hope this helps. 2011/6/15 bjmjarrett > Hi all, > > I have scoured the archives of this foru

Re: [R] Problem auto.arima() in R

2011-06-16 Thread siddharth arun
I will break my query into 2 parts: 1. My main idea is to give some data as an input and if any seasonality is there in the input, it should be captured automatically and the corresponding frequency automatically generated. please comment whether this is possible with auto.arima() 2. If frequenc