Re: [R] windows vs. linux code

2009-02-26 Thread Wacek Kusnierczyk
(Ted Harding) wrote: There is one MAJOR issue you will have to watch out for, far more likely to turn up than calls like system(). This is that, if you want to have two or more plotting windows in use at the same time, while the first one is autoatically opened by the plot() command, you

[R] AsciiGridPredict returns error in unionDataJoin

2009-02-26 Thread Frauke Barthold
Dear list, I am using AsciiGridPredict from the yaImpute package to make a spatial prediction of a randomForest model. When I call AsciiGirdPredict I am getting an error message, that I do not understand: AsciiGridPredict(st.rf.fit, xlist, ylist, xtypes=NULL, rows=NULL, myPredFunc=NULL)

[R] Incorporating cumsum in for loop

2009-02-26 Thread joe1985
Hello Hello i have this DF: c CHR_NR diffdato1 x 1022 10395 1994-05-3011.0 39 0 1994 1 1 0 024 11 24 29100 11377

Re: [R] Problems with ARIMA models?

2009-02-26 Thread Wacek Kusnierczyk
that's interesting, marie. on his webpage [1], david s. stoffer provides concrete arguments for why the r arima function in the stats package should be considered to produce misleading, if not just wrong results. david (cc:ed for reference) reported the issue in october 2005, bug report #8231

Re: [R] Hi, Coding problem

2009-02-26 Thread Uwe Ligges
Ssophia wrote: Hi, there Below is my code to one Homework question. I couldn't come up with the reasonable answer. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html could you please help me to figure out what is

Re: [R] Strange behavior of savePlot

2009-02-26 Thread Uwe Ligges
Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same data. Only the color changes). I save them in bmp.

Re: [R] Place independent labels between values on x-axis

2009-02-26 Thread Uwe Ligges
T.D.Rudolph wrote: I conducted a frequency averaging procedure which left me with the data frame below (Bin is an artifact of a cut() procedure and can be either as.character or as.factor): Bin Freq 1 (-180,-160] 7.904032 2 (-160,-140] 5.547901 3 (-140,-120] 4.522542 4

Re: [R] survival::survfit,plot.survfit

2009-02-26 Thread Bernhard Reinhardt
Jeff Xu wrote: I am confused when trying the function survfit. my question is: what does the survival curve given by plot.survfit mean? is it the survival curve with different covariates at different points? or just the baseline survival curve? for example, I run the following code and get the

Re: [R] Strange behavior of savePlot

2009-02-26 Thread Christophe Genolini
Uwe Ligges a écrit : Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same data. Only the color changes). I

Re: [R] Importing zoo object (index contains NAs)

2009-02-26 Thread Achim Zeileis
On Wed, 25 Feb 2009, Rob Denniker wrote: Dear list, I have an irregular time series saved and exported as a zoo object. What is the trick to force zoo to ignore the missing dates when reading it back in? Thanks. Almost certainly there are no NAs in your index (although we can't say for

Re: [R] Using package ROCR

2009-02-26 Thread wiener30
Thank you very much for the response! The plot(1,1) helped to resolve the first problem. But I am still getting a second error message when running demo(ROCR) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' It seems it has something to do with compatibility of S4

[R] (no subject)

2009-02-26 Thread Tanja Srebotnjak
Hello, I'm trying to fit a generalized linear mixed model to estimate diabetes prevalence at US county level. To do this I'm using the glmer() function in package lme4. I can fit relatively simple models (i.e. few covariates) but when expanding the number of covariates I usually encounter the

Re: [R] Using package ROCR

2009-02-26 Thread William Doane
Responding to question 1... it seems the demo assumes you already have a plot window open. library(ROCR) plot(1,1) demo(ROCR) seems to work. For question 2, my environment produces the expected results... plot doesn't generate an error: * R 2.8.1 GUI 1.27 Tiger build 32-bit (5301) *

Re: [R] Strange behavior of savePlot

2009-02-26 Thread Uwe Ligges
Christophe Genolini wrote: Uwe Ligges a écrit : Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim / ylim, almost same

[R] R communication

2009-02-26 Thread ARDIA David
Dear all, Imagine that you have a small LAN with two computers. I would like to run R on both, and possible to run computations from one computer to the other one. TCP IP protocole would be preferable. Which package would you use for that? I would be very glad if you could also provide me with

Re: [R] Strange behavior of savePlot

2009-02-26 Thread Christophe Genolini
Uwe Ligges a écrit : Christophe Genolini wrote: Uwe Ligges a écrit : Christophe Genolini wrote: Hi all, I am using savePlot in a loop for saving several graph but I get some graph in 553x552, some other in 1920x1119. How comes ? My data are almost all the same (same label, same xlim /

Re: [R] Modifying Names from (x,y] into x

2009-02-26 Thread baptiste auguie
Hi, I got this problem once, and Prof. Ripley kindly added an example in the help page of ?cut, aaa - c(1,2,3,4,5,2,3,4,5,6,7) ## one way to extract the breakpoints labs - levels(cut(aaa, 3)) cbind(lower = as.numeric( sub(\\((.+),.*, \\1, labs) ), upper = as.numeric(

Re: [R] T-test by groups

2009-02-26 Thread Uwe Ligges
Ingrid Tohver wrote: I would like to run a t-test within a by group function. My dataset, error, is organized as the following (I have 133 Sites): Site week Dataset Region lat_map long_map mean_tsim diff20 diff40 diff80 ALFI 15 USACE UC 48.15625 -117.0938 8.87 1.34

Re: [R] (no subject)

2009-02-26 Thread ONKELINX, Thierry
Dear Tanja, R-Sig-Mixed-models is a better list for questions about lme4 and nlme. There you are much more likely to get an answer from the mixed models specialists. First of all I would recommend you to write the random effect as (1|fips) instead of (1|as.factor(diab$fips)). You will run into

Re: [R] Incorporating cumsum in for loop

2009-02-26 Thread Uwe Ligges
joe1985 wrote: Hello Hello i have this DF: c CHR_NR diffdato1 x 1022 10395 1994-05-3011.0 39 0 1994 1 1 0 024 11

Re: [R] T-test by groups

2009-02-26 Thread Peter Dalgaard
Uwe Ligges wrote: Ingrid Tohver wrote: I would like to run a t-test within a by group function. My dataset, error, is organized as the following (I have 133 Sites): Site week Dataset Region lat_map long_map mean_tsim diff20 diff40 diff80 ALFI 15 USACE UC 48.15625 -117.0938

Re: [R] biplot.princomp - changing score labels

2009-02-26 Thread Axel Strauß
Thanks for the hints! They seem to help me. Axel Héctor Villalobos schrieb: Perhaps this may help you. Regards data(iris3) ir - rbind(iris3[ , , 1], iris3[ , , 2], iris3[ , , 3]) ir.pca - princomp(ir) biplot(ir.pca) # Rehacer Biplot # Calcular Factor para re-escalar scores y

[R] survival::predict.coxph

2009-02-26 Thread Bernhard Reinhardt
Hi, I just came across another question concerning predict.coxph Terry Therneau states in A Package for Survival Analysis in S that term - predict(fit, type=terms) yields predicted values for the individual components of the linear predictor X*beta My coxmodel looks like: coef

Re: [R] Moving Average

2009-02-26 Thread Gabor Grothendieck
See rollapply in zoo or filter or embed in the core of R. On Thu, Feb 26, 2009 at 7:07 AM, mau...@alice.it wrote: I am looking for some help at removing low-frequency components from a signal, through Moving Average on a sliding window. I understand thiis is a smoothing procedure that I

[R] ggplot2: labels points with different colors or idnumbers

2009-02-26 Thread Tom Cohen
Dear list,   Using ggplot2 I could produce both boxplot and points in the same plot but instead of points I would like to label the different subjects with different colors or their idnumbers. Is there away to do it? Also how can I put three plots on the same graph with ggplot2? mfrow=c(3,1)

Re: [R] ggplot2: labels points with different colors or idnumbers

2009-02-26 Thread ONKELINX, Thierry
Dear Tom, I think you better switch to ggplot() instead of qplot(). library(ggplot2) dat - expand.grid(id = 1:10, time = 1:3, group = 1:3) dat$Freq - rnorm(nrow(dat), mean = dat$id * dat$time) ggplot(dat, aes(x = factor(time), y = Freq)) + geom_boxplot() + geom_jitter(aes(colour = factor(id)))

[R] kmeans: invalid length argument

2009-02-26 Thread Lowell Gould
Dear R Experts, I am running a cluter analysis using kmeans and have come across an error to which I am unable to find a solution. First, let me describe the problem: THE R CODE IS: -- # NRM is a 100 x 100 numerical matrix infile = 't:\\NRM\\NRM' groups = 7

Re: [R] statistical significance of accuracy increase in classification

2009-02-26 Thread Max Kuhn
Do you know about any good reference that discusses kappa for classification and maybe CI for kappa??? I don't, but googling on kappa and confusion matrix etc should get you there. Kappa works very well when the true classes are skewed. For example, if 10% of you samples are class A and 90%

Re: [R] Moving Average

2009-02-26 Thread David Winsemius
I saw Gabor's reply but have a clarification to request. You say you want to remove low frequency components but then you request smoothing functions. The term smoothing implies removal of high-frequency components of a series. If smoothing really is your goal then additional R resource

Re: [R] C-index for models fitted using start, stop in Surv?

2009-02-26 Thread Terry Therneau
One of my colleagues has written a technical report on how to do this, but I have not yet implemented it in the survival package. Terry Therneau http://mayoresearch.mayo.edu/mayo/research/biostat/techreports.cfm #80 Concordance for Survival Time Data: Fixed and

Re: [R] survival::predict.coxph

2009-02-26 Thread Terry Therneau
You are mostly correct. Because of the censoring issue, there is no good estimate of the mean survival time. The survival curve either does not go to zero, or gets very noisy near the right hand tail (large standard error); a smooth parametric estimate is what is really needed to deal with

Re: [R] plot.survfit

2009-02-26 Thread Terry Therneau
For a fitted Cox model, one can either produce the predicted survival curve for a particular hypothetical subject (survfit), or the predicted curve for a particular cohort of subjects (survexp). See chapter 10 of Therneau and Grambsch for a long discussion of the differences between these,

Re: [R] statistical significance of accuracy increase in classification

2009-02-26 Thread Stefan Evert
On 26 Feb 2009, at 14:14, Max Kuhn wrote: Do you know about any good reference that discusses kappa for classification and maybe CI for kappa??? You might also want to take a look at this survey article on kappa and its alternatives: Artstein, Ron and Poesio, Massimo (2008). Survey

Re: [R] survival::survfit,plot.survfit

2009-02-26 Thread Terry Therneau
plot(survfit(fit)) should plot the survival-function for x=0 or equivalently beta'=0. This curve is independent of any covariates. This is not correct. It plots the curve for a hypothetical subject with x= mean of each covariate. This is NOT the average survival of the data set.

[R] R: Moving Average

2009-02-26 Thread mauede
I apologize for my messy post which stems from my own confusion ... and depression as well. In fact I though I was done with a big chunk of a project and to my dismay I found out there is more to do. I am trying to adapt an algorithm, based on advanced wavelet analysis, to my respiration

[R] Singularity in a regression?

2009-02-26 Thread Bob Gotwals
R friends, In a matrix of 1s and 0s, I'm getting a singularity error. Any helpful ideas? lm(formula = activity ~ metaF + metaCl + metaBr + metaI + metaMe + paraF + paraCl + paraBr + paraI + paraMe) Residuals: Min 1Q Median 3QMax -4.573e-01 -7.884e-02

Re: [R] Moving Average

2009-02-26 Thread Ted Harding
On 26-Feb-09 13:54:51, David Winsemius wrote: I saw Gabor's reply but have a clarification to request. You say you want to remove low frequency components but then you request smoothing functions. The term smoothing implies removal of high-frequency components of a series. If you produce

Re: [R] Moving Average

2009-02-26 Thread stephen sefick
I wrote a little code using Fourier filtering if you would like to take a look at this: library(StreamMetabolism) library(mFilter) x - read.production(file.choose()) #contiguous.zoo(data.frame(x[,RM202DO.Conc], coredata(x[,RM202DO.Conc]))) #contiguous.zoo(data.frame(x[,RM61DO.Conc],

Re: [R] Singularity in a regression?

2009-02-26 Thread Ted Harding
On 26-Feb-09 12:58:49, Bob Gotwals wrote: R friends, In a matrix of 1s and 0s, I'm getting a singularity error. Any helpful ideas? From the degress of freedom in your output, it seems you are fitting 10 binary variables to a total of 23 observations. In such circumstances, it is not

Re: [R] Moving Average

2009-02-26 Thread David Winsemius
On Feb 26, 2009, at 9:54 AM, (Ted Harding) wrote: On 26-Feb-09 13:54:51, David Winsemius wrote: I saw Gabor's reply but have a clarification to request. You say you want to remove low frequency components but then you request smoothing functions. The term smoothing implies removal of

Re: [R] Singularity in a regression?

2009-02-26 Thread ONKELINX, Thierry
It looks like your data has not enough information to estimate the parameter for metaCl. Maybe because metaCL is identical to one of the other variables or a constant. HTH, Thierry ir. Thierry Onkelinx Instituut voor

[R] layout of igraph

2009-02-26 Thread kevinchang
Dear R users, I am trying to draw a network using igraph package. I intend to place the hub nodes (the ones with the relatively more connection with other nodes) in the center of the graph. Also, the graph need to be in the fashion that the higher the correlation between two nodes is , the

Re: [R] Singularity in a regression?

2009-02-26 Thread David Winsemius
I saw Ted's reply and it is certainly sensible. I would wonder whether to model ought to be recast so that the scientific question is more clear? You are obviously studying the effect of different substitutions (F, Cl, Br, I, Me) and different positions around an aromatic ring (meta,

Re: [R] layout of igraph

2009-02-26 Thread Gábor Csárdi
Shukai, the force based layout algorithms (layout.drl, layout.fruchterman.reingold, layout.graphopt, layout.kamada.kawai) are likely to do this; although they are not explicitly required to place hubs in the center, usually they do. I am not sure what is the correlation between two nodes. You

Re: [R] Using very large matrix

2009-02-26 Thread Jay Emerson
Corrado, Package bigmemory has undergone a major re-engineering and will be available soon (available now in Beta version upon request). The version currently on CRAN is probably of limited use unless you're in Linux. bigmemory may be useful to you for data management, at the very least, where

Re: [R] layout of igraph

2009-02-26 Thread kevinchang
Thanks Gabor's fast reply. In my research, every node has it's own vector of scores. So I can compute correlation between every pair of nodes. I used the width and color of the edge for this purpose. But visualizing the correlations by distance may be clearer. Best, Shukai Gábor Csárdi-2

Re: [R] layout of igraph

2009-02-26 Thread Gábor Csárdi
Shukai, layout.drl supports edge weights, so you could try that. An alternative is doing MDS, see ?cmdscale and maybe help.search(MDS). But both these methods are approximate, obviously, most often you cannot embed an n-dimensional (n2) graph into the 2-dimensional plane and keep all the

[R] which zip file is the emulator package?

2009-02-26 Thread eric lee
Hi. I'm trying to run the elliptic package on my computer (windows platform, version 2.7.2). I downloaded the elliptic package zip file from http://lib.stat.cmu.edu/R/CRAN/ and installed it, but it says that it needs the emulator package. Can you tell me where to download this? The only

Re: [R] survival::survfit,plot.survfit

2009-02-26 Thread Jeff Xu
Thanks very much, Bernhard and Terry. It clarify my confusion and really helps a lot. Regards Jeff Xu Terry Therneau wrote: plot(survfit(fit)) should plot the survival-function for x=0 or equivalently beta'=0. This curve is independent of any covariates. This is not correct. It plots

Re: [R] which zip file is the emulator package?

2009-02-26 Thread Duncan Murdoch
On 2/26/2009 11:08 AM, eric lee wrote: Hi. I'm trying to run the elliptic package on my computer (windows platform, version 2.7.2). I downloaded the elliptic package zip file from http://lib.stat.cmu.edu/R/CRAN/ and installed it, but it says that it needs the emulator package. Can you tell

Re: [R] which zip file is the emulator package?

2009-02-26 Thread eric lee
Hi, Duncan. I choose 'package' then ''install package' and tried 6 different U.S. mirrors. The message I always get is: Warning: unable to access index for repository http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.7 Warning: unable to access index for repository

Re: [R] which zip file is the emulator package?

2009-02-26 Thread David Winsemius
Reading this article, announcing the elliptic package (which was a distinct pleasure) and also looking at the R-FAQ, my guess is that you need the BACCO bundle. http://www.jstatsoft.org/v15/i07/paper -- David Winsemius On Feb 26, 2009, at 11:08 AM, eric lee wrote: Hi. I'm trying to run

Re: [R] which zip file is the emulator package?

2009-02-26 Thread eric lee
Thanks, Duncan. The BACCO package worked. On Thu, Feb 26, 2009 at 11:22 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 2/26/2009 11:08 AM, eric lee wrote: Hi.  I'm trying to run the elliptic package on my computer (windows platform, version 2.7.2).  I downloaded the elliptic package zip

Re: [R] windows vs. linux code

2009-02-26 Thread Paul Gilbert
Gabor Grothendieck wrote: Try if (.Platform$OS.type == windows) ... else ... Gabor has suggested what I think is the best way to do this check, but in my experience, if you are doing this check then you are almost certainly missing some feature of R that will let you avoid doing it.

Re: [R] R communication

2009-02-26 Thread Greg Snow
This could depend somewhat on which OS you have on the computers as to which packages will work or work best for you. A couple of packages to look at include, Rmpi, nws, and snow (no relation), and the other packages in the suggests field for snow. -- Gregory (Greg) L. Snow Ph.D. Statistical

[R] ftp fetch using RCurl?

2009-02-26 Thread CHD850
Hi everyone, I have to fetch about 300 to 500 zipped archives from a remote ftp server. Each of the archive is about 1Mb. I know I can get it done by using download.file() in R, but I am curious that is there a faster way to do this using RCurl. For example, are there some parameters that I can

[R] error message and convergence issues in fitting glmer in package lme4

2009-02-26 Thread Tanja Srebotnjak
I'm resending this message because I did not include a subject line in my first posting. Apologies for the inconvenience! Tanja Hello, I'm trying to fit a generalized linear mixed model to estimate diabetes prevalence at US county level. To do this I'm using the glmer() function in

Re: [R] Random Forest confusion matrix

2009-02-26 Thread Gabor Grothendieck
randomForest output is based on predict(iris.rf) whereas the code shown below uses predict(iris.rf, iris). See ?predict.randomForest for an explanation. On Thu, Feb 26, 2009 at 11:10 AM, Li GUO guol...@yahoo.com wrote: Dear R users, I have a question on the confusion matrix generated by

Re: [R] Hi, Coding problem

2009-02-26 Thread Greg Snow
It looks like what you did was something like: tmp - sim(100) table(tmp)/100 To get your results (it is easier for us to help if you tell us what you actually did, also setting a seed and telling us that seed helps us reproduce what you did exactly). The reason that you did not see 9 and 10

[R] use R Group SFBA March meeting reminder

2009-02-26 Thread Jim Porzak
All San Francisco Bay Area useRs, On March 11th, Spencer Graves Sundar Dorai-Raj will talk about Creating R Packages, and related issues. This is the first of our (now) regular monthly meetings, details here http://www.meetup.com/R-Users/calendar/9718957/ Last week Wednesday, we had over 60

Re: [R] which zip file is the emulator package?

2009-02-26 Thread Greg Snow
Are you behind a firewall? See the help for download.file for details on setting proxy information if this is the case. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From:

[R] Merge question

2009-02-26 Thread Vadlamani, Subrahmanyam {FLNA}
Hi: I am a new R user. I have the following question and would appreciate your input Data1 (data frame 1) p1,d1,d2 (p1 is text and d1 and d2 are numeric) xyz,10,25 Data2 (data frame 2) p1,d1,d2 xyz,11,15 Now I want to create a new data frame that looks like so below. The fields d1 and s2 are

[R] generalized linear mixed models with a beta distribution

2009-02-26 Thread Jeff Evans
Has there been any follow up to this question? I have found myself wondering the same thing: How then does SAS fit a beta distributed GLMM? It also fits the negative binomial distribution. Both of these would be useful in glmer/lmer if they aren't 'illegal' as Brian suggested. Especially as SAS

[R] glm with large datasets

2009-02-26 Thread Julio Gonzalez Diaz
Hi all, I have to run a logit regresion over a large dataset and I am not sure about the best option to do it. The dataset is about 20x2000 and R runs out of memory when creating it. After going over help archives and the mailing lists, I think there are two main options, though I am

Re: [R] windows vs. linux code

2009-02-26 Thread Prof Brian Ripley
On Thu, 26 Feb 2009, Paul Gilbert wrote: Gabor Grothendieck wrote: Try if (.Platform$OS.type == windows) ... else ... Gabor has suggested what I think is the best way to do this check, but in my experience, if you are doing this check then you are almost certainly missing some

Re: [R] two colors and putting lines on bar plots

2009-02-26 Thread Greg Snow
For the first question you can use %in% rather than ==, for example: ifelse( dataframe$vector_o_number %in% c('00','01), 'red', 'black') for the reference line, the abline function will draw a line the full width/height of a graph for a general reference, if you want separate lines for each

Re: [R] Merge question

2009-02-26 Thread milton ruser
Hi there, something like this? Data1-read.table(stdin(), head=T, sep=,) p1,d1,d2 xyz,10,25 kmz,100,250 Data2-read.table(stdin(), head=T, sep=,) p1,d1,d2 xyz,11,15 kmz,110,150 Data1 Data2 Data3-data.frame(rbind(Data1,Data2)) Data3 Data3.sum-aggregate(Data3[,c(d1,d2)], list(Data3$p1), sum)

Re: [R] Bug in predict function for naiveBayes?

2009-02-26 Thread joris meys
Dear all, I've sent a mail last week already. I've been trying to get this predict function work, but somehow I keep on getting the same error. Read the help files, searched the internet, but I don't seem to get what I'm doing wrong. Anybody who has experience with this function? It's contained

Re: [R] Merge question

2009-02-26 Thread Marc Schwartz
on 02/26/2009 11:52 AM Vadlamani, Subrahmanyam {FLNA} wrote: Hi: I am a new R user. I have the following question and would appreciate your input Data1 (data frame 1) p1,d1,d2 (p1 is text and d1 and d2 are numeric) xyz,10,25 Data2 (data frame 2) p1,d1,d2 xyz,11,15 Now I want to

[R] bottom legends in ggplot2 ?

2009-02-26 Thread Avram Aelony
Has anyone had success with producing legends to a qplot graph such that the legend is placed on the bottom, under the abcissa rather than to the right hand side ? The following doesn't move the legend: library(ggplot2) qplot(mpg, wt, data=mtcars, colour=cyl,

Re: [R] Bug in predict function for naiveBayes?

2009-02-26 Thread Liaw, Andy
You need to set Class as factor before you call naiveBayes(); i.e., mixture.train$Class - factor(mixture.train$Class) Then you can just do: pred.bayes -predict(Bayes.res, mixture.test, type=class) Andy -Original Message- From: r-help-boun...@r-project.org

Re: [R] windows vs. linux code

2009-02-26 Thread Jeffrey J. Hallman
Rolf Turner r.tur...@auckland.ac.nz writes: Despite the knowledge, wisdom, insight, skill, good looks, and other admirable characteristics of the members of the R-help list, few of us are skilled in telepathy or clairvoyance. Oh, yeah? Then how did I know you were going to say that, huh? --

[R] plot with pairwise joined points

2009-02-26 Thread William Simpson
I would like to do as follows plot(a,b) points(c,d,pch=19) Now join with a line segment point a[1], b[1] to c[1], d[1]; a[2], b[2] to c[2], d[2] ... a[n], b[n] to c[n], d[n] All corresponding points from the two data sets are joined by line segments. Thanks very much for any tips on how to do

Re: [R] error message and convergence issues in fitting glmer in package lme4

2009-02-26 Thread Douglas Bates
On Thu, Feb 26, 2009 at 10:58 AM, Tanja Srebotnjak tan...@u.washington.edu wrote: I'm resending this message because I did not include a subject line in my first posting. Also, it is generally more effective to send questions about lmer/glmer to the R-SIG-Mixed-Models list, which I am cc:ing

[R] Download daily weather data

2009-02-26 Thread Thomas Levine
I'm writing a program that will tell me whether I should wear a coat, so I'd like to be able to download daily weather forecasts and daily reports of recent past weather conditions. The NOAA has very promising tabular forecasts

Re: [R] generalized linear mixed models with a beta distribution

2009-02-26 Thread Douglas Bates
On Thu, Feb 26, 2009 at 12:04 PM, Jeff Evans evans...@msu.edu wrote: Has there been any follow up to this question? I have found myself wondering the same thing: How then does SAS fit a beta distributed GLMM? It also fits the negative binomial distribution. When SAS decides to open-source

Re: [R] plot with pairwise joined points

2009-02-26 Thread Greg Snow
Try: segments(a,b,c,d) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of William Simpson Sent: Thursday,

Re: [R] plot with pairwise joined points

2009-02-26 Thread Dimitris Rizopoulos
have a look at segments(), e.g., x - rnorm(5) y - rnorm(5) z - rnorm(5) w - rnorm(5) r1 - range(x, z) r2 - range(y, w) plot(r1, r2, type = n) points(x, y) points(z, w, pch = 19) segments(x, y, z, w) I hope it helps. Best, Dimitris William Simpson wrote: I would like to do as follows

Re: [R] plot with pairwise joined points

2009-02-26 Thread Rolf Turner
On 27/02/2009, at 9:46 AM, William Simpson wrote: I would like to do as follows plot(a,b) points(c,d,pch=19) Now join with a line segment point a[1], b[1] to c[1], d[1]; a[2], b[2] to c[2], d[2] ... a[n], b[n] to c[n], d[n] All corresponding points from the two data sets are joined by line

Re: [R] Download daily weather data

2009-02-26 Thread James Muller
Thomas, Have a look at the source code for the webpage (ctrl-u in firefox, don't know in internet explorer, etc.). That is what you'd have to parse in order to get the forecast from this page. Typically when I parse webpages such as this I use regular expressions to do so (and I would never

Re: [R] plot with pairwise joined points

2009-02-26 Thread William Simpson
Thanks very much Rolf, Dimitris, Greg! Bill On Thu, Feb 26, 2009 at 8:56 PM, Rolf Turner r.tur...@auckland.ac.nz wrote: On 27/02/2009, at 9:46 AM, William Simpson wrote: I would like to do as follows plot(a,b) points(c,d,pch=19) Now join with a line segment point a[1], b[1] to c[1],

Re: [R] generalized linear mixed models with a beta distribution

2009-02-26 Thread Jeff Evans
Thanks for responding Doug. I'm sure SAS just hasn't gotten around to releasing their code yet. lme4 does have a leg up on GLIMMIX in other areas, though. The latest SAS release (9.2) is now able to compute the Laplace approximation of the likelihood, but it will only fit an overdispersion

[R] Substituting in a variable file name in a Windows system command

2009-02-26 Thread Elaine Jones
I am running R version 2.8.1 on Windows XP OS. I generate and write a .csv file from my R script. Then the following command works to upload it to a remote server using a windows batch file that carries out the ftp (among other things). system(C:/upload_data/uploadq8.bat

[R] User manual or tutorial for GAM package

2009-02-26 Thread Neotropical bat risk assessments
Hi all, I would like to run the gam package, but can not quite seem to get the syntax correct for my data format as simple as it is. The gamlss package has a user manual but other than the help with gam package I can not find a user manual per se. I did install the gamair that has loads of

Re: [R] User manual or tutorial for GAM package

2009-02-26 Thread David Winsemius
On Feb 26, 2009, at 4:44 PM, Neotropical bat risk assessments wrote: Hi all, I would like to run the gam package, but can not quite seem to get the syntax correct for my data format as simple as it is. The gamlss package has a user manual but other than the help with gam package I can

Re: [R] Download daily weather data

2009-02-26 Thread Scillieri, John
Looks like you can sign up to get XML feed data from Weather.com http://www.weather.com/services/xmloap.html Hope it works out! -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of James Muller Sent: Thursday, February 26, 2009 3:57

[R] When download.file fails...

2009-02-26 Thread CHD850
Hi everyone, In the situation that the remote file does not exist, download.file fails, yet it still creates a file as provided for destfile argument. I tried to delete this bad file but got the message that it is still being used by other programs, which I assume is R. Does anyone know how

Re: [R] User manual or tutorial for GAM package

2009-02-26 Thread David Winsemius
On Feb 26, 2009, at 4:54 PM, David Winsemius wrote: On Feb 26, 2009, at 4:44 PM, Neotropical bat risk assessments wrote: Hi all, I would like to run the gam package, but can not quite seem to get the syntax correct for my data format as simple as it is. The gamlss package has a user

Re: [R] Download daily weather data

2009-02-26 Thread Wacek Kusnierczyk
Scillieri, John wrote: Looks like you can sign up to get XML feed data from Weather.com http://www.weather.com/services/xmloap.html ... and use the excellent R package XML by Duncan Temple Lang to parse the document and easily access the data with, e.g.., XPath rather than regular

Re: [R] Download daily weather data

2009-02-26 Thread James Muller
Yes, as a general thing go to regular expressions if you don't have an existing library available to do the same thing (or you're lazy like me:). Jame On Thu, Feb 26, 2009 at 5:16 PM, Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: Scillieri, John wrote: Looks like you can sign

Re: [R] Download daily weather data

2009-02-26 Thread Wacek Kusnierczyk
James Muller wrote: Yes, as a general thing go to regular expressions if you don't have an existing library available to do the same thing (or you're lazy like me:). many things are simply *much* easier with xpath than with regexes, and with the XML package you got it for free. vQ

Re: [R] User manual or tutorial for GAM package

2009-02-26 Thread Bert Gunter
-- or perhaps even the section on Additive Models in the latest edition of VR's MASS (still a useul book to have in one's library, IMHO, although, like me, it's getting grayer) Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -Original Message- From:

Re: [R] Download daily weather data

2009-02-26 Thread Barry Rowlingson
2009/2/26 Thomas Levine thomas.lev...@gmail.com: I'm writing a program that will tell me whether I should wear a coat, so I'd like to be able to download daily weather forecasts and daily reports of recent past weather conditions. The NOAA has very promising tabular forecasts

[R] Inefficiency of SAS Programming

2009-02-26 Thread Frank E Harrell Jr
If anyone wants to see a prime example of how inefficient it is to program in SAS, take a look at the SAS programs provided by the US Agency for Healthcare Research and Quality for risk adjusting and reporting for hospital outcomes at http://www.qualityindicators.ahrq.gov/software.htm . The

Re: [R] left truncated data survival analysis package

2009-02-26 Thread Göran Broström
On Thu, Feb 26, 2009 at 7:02 AM, phguard...@aol.com wrote: Hello, I d like to run a survival analysis with left truncated data. Could you recommend me a package to do this please ? The 'eha' package if you want parametric or discrete time models. Göran Thanks Philippe Guardiola

Re: [R] Download daily weather data

2009-02-26 Thread hadley wickham
See also http://umbrellatoday.com/ Hadley On Thu, Feb 26, 2009 at 2:47 PM, Thomas Levine thomas.lev...@gmail.com wrote: I'm writing a program that will tell me whether I should wear a coat, so I'd like to be able to download daily weather forecasts and daily reports of recent past weather

[R] User manual or tutorial for GAM package

2009-02-26 Thread Neotropical bat risk assessments
Hi all, Tnx for the number of suggestion to buy one of the books. Unfortunately being a non profit conservation project now w/o funding since all Central American projects were shut down 2 years ago due to lack of donor funding I have nothing now at all for books or even my support, to cover

[R] Something similar to data.frame, but allows variables with unique lengths?

2009-02-26 Thread Jason Rupert
I have a tightly coupled collection of variables with different lengths and types (some characters and others numerics).  I looked at the documentation for data.frame, but indicates that it expects all variables to have the same length, i.e. number of elements.    I was hoping the See Also

[R] complex data summary

2009-02-26 Thread James J. Roper
Dear All, I am interested in using R to summarize data so that I can THEN do some additional analyses using behavioral data. I study birds, mostly, and often behavioral data that includes timing. So, for example, each line may be the occurrence of some behavior, and it would include identifiers

Re: [R] Substituting in a variable file name in a Windows system command

2009-02-26 Thread Duncan Murdoch
Elaine Jones wrote: I am running R version 2.8.1 on Windows XP OS. I generate and write a .csv file from my R script. Then the following command works to upload it to a remote server using a windows batch file that carries out the ftp (among other things).

  1   2   >