[R] write result in matrix using loop

2009-08-13 Thread Grześ
Hello, I want call my function (use my database) and write every result in matrix "wynik" but I always get an error: Error in wynik[, i] <- dodawanie(wzorzec, wzorzec1) : number of items to replace is not a multiple of replacement length I'll be very happy if sb help me dodawanie<- function

[R] email notification after error

2009-08-13 Thread caltechneurostudy
Does anybody know if it's possible to have R send an email or execute an additional line of code in case an error is generated from a running script? I am running R on a cluster and would like to have it kill the job if R generates an error, but as it is, the job just keeps running until the wallc

[R] randomForest question--problem with ntree

2009-08-13 Thread Mary Putt
Hi, I would like to use a random Forest model to get an idea about which variables from a dataset may have some prognostic significance in a smallish study. The default for the number of trees seems to be 500. I tried changing the default to ntree=2000 or ntree=200 and the results appear ident

[R] R 2.9.2 Scheduled for August 24, 2009

2009-08-13 Thread Peter Dalgaard
This is to announce that we plan to release R version 2.9.2 on Monday, August 24, 2009. Release procedures start Friday, August 14. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available dail

Re: [R] How to rename columns that start with numbers?

2009-08-13 Thread Patrick Connolly
On Thu, 13-Aug-2009 at 04:24PM -0600, Mark Na wrote: |> Hello, |> |> My dataframe has new columns that start with the number 1 or 2 (resulting |> from a reshape cast command). |> |> Instead of having these columns automatically renamed by R so start with the |> letter X, I would like to rename t

Re: [R] Solutions of equation systems

2009-08-13 Thread Moshe Olshansky
Is your system of equations linear? --- On Fri, 14/8/09, Moreno Mancosu wrote: > From: Moreno Mancosu > Subject: [R] Solutions of equation systems > To: r-help@r-project.org > Received: Friday, 14 August, 2009, 2:29 AM > Hello all! > > Maybe it's a newbie question(in fact I _am_, a newbie), bu

Re: [R] Simulating points from GLM corresponding to new x-values

2009-08-13 Thread Jacob Nabe-Nielsen
Hi Cliff, Excellent, just what I needed -- wish I had thought of that myself. Thanks a lot! Jacob On 13 Aug 2009, at 01:49, Clifford Long wrote: Hi Jacob, At the risk of embarrassing myself, I gave it a shot. I'll throw this out on the list, if for no other reason than perhaps someone w

Re: [R] problem about t test

2009-08-13 Thread Moshe Olshansky
You could do the following: y <- apply(dat,1,function(a) t.test(a[1:10],a[11:30])$p.value) This will produce an array of 2 p-values. --- On Fri, 14/8/09, Gina Liao wrote: > From: Gina Liao > Subject: [R] problem about t test > To: r-h...@stat.math.ethz.ch > Received: Friday, 14 August, 20

[R] problem about t test

2009-08-13 Thread Gina Liao
Hello, I have a data frame >str(dat)'data.frame': 2 obs. of 30 variables it contains two information-two types of cancers:stage A(A1 to A10) and stage B(B1 to B20) ##totally 30 patients-2 sets of gene expression I'd like to find the lists for top 20 differentially expressed genes using

Re: [R] Plotting sigma symbol with unicode and turning into pdf

2009-08-13 Thread Paul Murrell
Hi Jonathan R. Blaufuss wrote: Paul, You solution worked out really well when I ran my code in R. However, when I try to turn the plot into a pdf, the unicode string no longer seems to function and instead of the sigma symbol there are just two periods (See example code below). The following i

Re: [R] glm.nb versus glm estimation of theta.

2009-08-13 Thread Bill.Venables
Whoa! Just hang on a minute. theta is NOT the dispersion parameter. Under the NB model, the variance of an observation is mu+mu^2/theta, so that's how theta enters the picture. The smaller theta is the larger the variance. glm(..., family = negative.binomial(theta = ), ...) will NOT esti

Re: [R] Coding problem: How can I extract substring of function callwithin the function

2009-08-13 Thread Steve Lianoglou
Hi Joel, On Aug 13, 2009, at 6:10 PM, Pitt, Joel wrote: Your objections are quite cogent, but I believe they are misdirected. I'm not at all interested in having my students ignore the existence of NA's and that's precisely why I'm not using the Default package as someone else suggested. B

Re: [R] joining two points in rgl

2009-08-13 Thread Duncan Murdoch
Nair, Murlidharan T wrote: Hi!! I need to draw a cylinder/tube joining two points. I am trying to make something presentable, I have been able to do it using lines3d. But is it possible to increase the thickness of the lines? The size parameter does not work. Does any one have any suggestions?

Re: [R] Browser and Debug?

2009-08-13 Thread Duncan Murdoch
rkevinbur...@charter.net wrote: If I am on Windows and don't have GDB it does'nt look like it is possible. Any tips? For debugging without a debugger, you can always use the old-fashioned method of inserting print statements (Rprintf in C). But you want to do this without a debugger *and

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread Duncan Murdoch
willow1980 wrote: Dear Professor Murdoch, That is exactly the difficulty for me. I don't know how to make a prediction with lmer using "expand.grid"; at the moment, I can use “mo...@x%*%fixef(model)” to get predicted values for existing observational data, but not data by "expand.grid". Actually,

Re: [R] glm.nb versus glm estimation of theta.

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, hesicaia wrote: Hello, I have a question regarding estimation of the dispersion parameter (theta) for generalized linear models with the negative binomial error structure. As The theta is different from the dispersion. In the usual GLM notation: E[y] = mu VAR[y] =

Re: [R] Coding problem: How can I extract substring of function call within the function

2009-08-13 Thread Pitt, Joel
Hi, As I said in my original email, I'm sure that many of you will doubt the wisdom of what I'm trying to do -- and I certainly share some of your misgivings. I have misgivings too about the use of "training wheels" for bicycles, but they are clearly useful for some people, and, in this instan

Re: [R] shading between two smoothed curves

2009-08-13 Thread Debabrata Midya
Hi Gregory, > I can plot out two nice curves using the following code, but I can't figure out how to shade in the area lying between the two curves. Use polygon. > ?polygon >>> "Graves, Gregory" 14/08/2009 4:17 am >>> I have a set of 52 weekly values, one is the desired high lake stage for

Re: [R] How to rename columns that start with numbers?

2009-08-13 Thread John Kane
Something like this. Create empty vector of correct length, paste values into it and then use names(mydata) <- myvector. x <- data.frame(aa=1:10, bb=letters[1:10]) myvector <- c(rep(NA,length(x))) for (i in 1:length(names(x))) { myvector[i] <- paste("SURV_",i, sep="") } --- On Thu, 8/13

Re: [R] R: how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Don MacQueen
You can add or remove elements from a list without affecting the other elements. It is not necessary to update the list names when adding or removing elements. Since list elements can be referred to by name, you don't have to worry about numbering them, or renumbering them, nor do you have to

[R] How to rename columns that start with numbers?

2009-08-13 Thread Mark Na
Hello, My dataframe has new columns that start with the number 1 or 2 (resulting from a reshape cast command). Instead of having these columns automatically renamed by R so start with the letter X, I would like to rename these columns to start with the characters "SURV_" (e.g., SURV_1, SURV_2).

Re: [R] R code to reproduce (while studying) Bates & Watts 1988

2009-08-13 Thread Kevin Wright
library(nlme) m2 <- gnls(conc ~ t1*(1-t2*exp(-k*time)), data = df.Chloride, start = list( t1 = 35, t2 = 0.91, k = 0.22)) summary(m2) plot(m2) lag.plot(resid(m2), do.lines=FALSE) acf(resid(m2)) m3 <- update(m2, corr=corAR1(.67)) summar

Re: [R] Coding problem: How can I extract substring of function callwithin the function

2009-08-13 Thread Pitt, Joel
Your objections are quite cogent, but I believe they are misdirected. I'm not at all interested in having my students ignore the existence of NA's and that's precisely why I'm not using the Default package as someone else suggested. But the mere existence of missing values in a data set doesn't

Re: [R] using package tm to find phrases

2009-08-13 Thread Ingo Feinerer
On Thu, Aug 13, 2009 at 03:36:22PM -0400, Mark Kimpel wrote: > I am using the package "tm" for text-mining of abstracts and would like to use > it to find instances of gene names that may contain white space. For instance > "gene regulatory protein 1". The default behavior of tm is to parse this in

Re: [R] lm coefficients output confusing

2009-08-13 Thread Daniel Malter
I have answered a similar question just hours ago. Your question either indicates an unfamiliarity with R or, more generally, an unfamiliarity with regression analysis, or both. Your anova indicates that the overall model is significant. That is, your model is an improvement over the null model wi

Re: [R] Coding problem: How can I extract substring of function callwithin the function

2009-08-13 Thread Steve Lianoglou
Hi, On Aug 13, 2009, at 5:30 PM, Pitt, Joel wrote: Thanks. It's a great solution to part of my problem. It provides the functionally I want would be no harder for students to use than my approach. I'm still interested in how to make what I was trying to do work -- simply to add to my own R

Re: [R] lm coefficients output confusing

2009-08-13 Thread Ted Harding
On 13-Aug-09 20:45:31, Ross Culloch wrote: > > Hi all, > > I have an issue with the lm() function regarding the listing of > the coefficients. My data are below, showing a list of hours (HR) > relating to the time spent resting (R) by an individual animal. > Simply i want to run a lm() to run in

[R] joining two points in rgl

2009-08-13 Thread Nair, Murlidharan T
Hi!! I need to draw a cylinder/tube joining two points. I am trying to make something presentable, I have been able to do it using lines3d. But is it possible to increase the thickness of the lines? The size parameter does not work. Does any one have any suggestions? Thanks ../Murli library

Re: [R] lm coefficients output confusing

2009-08-13 Thread Charles C. Berry
On Thu, 13 Aug 2009, Ross Culloch wrote: Hi all, I have an issue with the lm() function regarding the listing of the coefficients. My data are below, showing a list of hours (HR) relating to the time spent resting (R) by an individual animal. Simply i want to run a lm() to run in an anova() to

Re: [R] Coding problem: How can I extract substring of function callwithin the function

2009-08-13 Thread Pitt, Joel
Thanks. It's a great solution to part of my problem. It provides the functionally I want would be no harder for students to use than my approach. I'm still interested in how to make what I was trying to do work -- simply to add to my own R programming proficiency. Joel __

Re: [R] Coding problem: How can I extract substring of function call within the function

2009-08-13 Thread Gabor Grothendieck
The Defaults package can be used to change the defaults of functions and reset them back. There is some question on whether all this is advisable. It will invalidate any books, documentation, examples in the help files that come with R and other resources on R that they might have otherwise used b

Re: [R] request: Help

2009-08-13 Thread Steve Lianoglou
Hi, On Aug 13, 2009, at 3:43 PM, Sarjinder Singh wrote: Dear Sir/Madam, Good Day! How can we make output file in R? In FORTRAN, we could do as follows: WRITE (42, 107) x, y 107 FORMAT ( 2x, F9.3, 2x, F4.2) What is equivalent to this in R? See: ?file ?cat ?sprintf -steve --

Re: [R] Coding problem: How can I extract substring of function call within the function

2009-08-13 Thread Erik Iverson
Are you sure you just don't want to tell them about the :: operator? It sounds easier than what you're proposing. E.g., base::mean(c(1:10, NA)) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Pitt, Joel Sent: Thursday, August 1

[R] Coding problem: How can I extract substring of function call within the function

2009-08-13 Thread Pitt, Joel
In order to ease my students into the R environment I am developing a package which installs a variety of utility functions as well as slightly modified versions of some standard R functions -- e.g. mean, hist, barplot, In my versions of these standard R functions I either add options or al

[R] tick.number in ggplot2?

2009-08-13 Thread Ben Bolker
Another dumb ggplot2 question: a facet plot with free x scale, lots of different ranges, want to specify that the x axis ticks be sparse -- only 2 or 3. I was about to say that I could figure out how to manually set the ticks for each facet if necessary, but now that I've looked around some

[R] lm coefficients output confusing

2009-08-13 Thread Ross Culloch
Hi all, I have an issue with the lm() function regarding the listing of the coefficients. My data are below, showing a list of hours (HR) relating to the time spent resting (R) by an individual animal. Simply i want to run a lm() to run in an anova() to see if there is a significant difference in

[R] R: how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread mauede
Thank you for all your suggestiona. I tried to write a self-contained example which turned oiut to confuse people's miind. I realized also the formulation of my question was unclear. Sorry for that. What I had in mind was something similar to Fortran Parameter declaration. I spent some time dea

[R] request: Help

2009-08-13 Thread Sarjinder Singh
Dear Sir/Madam,   Good Day!   How can we make output file in R?   In FORTRAN, we could do as follows:       WRITE (42, 107) x, y 107  FORMAT ( 2x, F9.3, 2x, F4.2)   What is equivalent to this in R?   With best regards,   Sarjinder                 Updated web-page on Sept 6, 2004:   www.geo

Re: [R] Browser and Debug?

2009-08-13 Thread rkevinburton
If I am on Windows and don't have GDB it does'nt look like it is possible. Any tips? Kevin roger koenker wrote: > At points of total desperation you can always consider > the time-honored, avuncular advice -- RTFM, > in this case Section 4.4 of Writing R Extensions. > > > url:www.e

[R] Finding minimum of time subset

2009-08-13 Thread Tim Clark
Dear List, I have a data frame of data taken every few seconds. I would like to subset the data to retain only the data taken on the quarter hour, and as close to the quarter hour as possible. So far I have figured out how to subset the data to the quarter hour, but not how to keep only the m

Re: [R] Adding logical vectors

2009-08-13 Thread Ted Harding
On 13-Aug-09 19:21:36, David Huffer wrote: > When adding several logical vectors I expect each vector will be > coerced to integers and these vectors will then be added. > > That doesn't always seem to be the case. > > For example: > > > ( f1 <- as.factor ( sample ( "x" , 25 , rep = T ) ) ) >

[R] using package tm to find phrases

2009-08-13 Thread Mark Kimpel
I am using the package "tm" for text-mining of abstracts and would like to use it to find instances of gene names that may contain white space. For instance "gene regulatory protein 1". The default behavior of tm is to parse this into 4 separate words, but I would like to use the class constructor

[R] Data Envelopment Analysis

2009-08-13 Thread Thiagarajah Ramilan
Hi, solict excuese if I am reposting I am not sure I properly posted the previous message In the past I have used a DEA package known as "FEAR" on R platform. I could not see that package any more. Instead a new package is there DEA. I kindly apreciate comments or recomendations. Ramilan

[R] Adding logical vectors

2009-08-13 Thread David Huffer
When adding several logical vectors I expect each vector will be coerced to integers and these vectors will then be added. That doesn't always seem to be the case. For example: > ( f1 <- as.factor ( sample ( "x" , 25 , rep = T ) ) ) [1] x x x x x x x x x x x x x x x x x x x x x x x x x Le

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Don MacQueen
Like Ben, I wonder what the reason for doing this is. First of all, the amount of memory indicated by your example is so small I can't imagine it would make any difference. If you have such a large number of values that the amount of memory is significant -- and store them somewhere that isn't

Re: [R] How to get the n (number of observations) per conditional group

2009-08-13 Thread Dax
I found a work-around by just simply getting the sum of the conditional values and dividing this by the mean. It's not elegant but it works On Aug 13, 3:11 pm, Dax wrote: > Hello all, > > I have a huge data set that I'm cleaning up a bit. I am extracted the > means per condition, but also need to

[R] glm.nb versus glm estimation of theta.

2009-08-13 Thread hesicaia
Hello, I have a question regarding estimation of the dispersion parameter (theta) for generalized linear models with the negative binomial error structure. As I understand, there are two main methods to fit glm's using the nb error structure in R: glm.nb() or glm() with the negative.binomial(the

Re: [R] Need Advice: Considering Converting a Package from S3 to S4 -- reprise

2009-08-13 Thread Terry Therneau
I read the list in digest form which sometimes makes me late to respond. Peter Dalgaard wrote: In all fairness, it should probably be noted that quite a few people swear BY S4 in addition to those who swear AT it. Lest I give the impression of only dislike -- the coxme package (major rewrite

Re: [R] psi not functioning in nlrob?

2009-08-13 Thread Keo Ormsby
I hadn't checked this, I only had used the default. The problem stems from the reassigned weighs during nls iterations, where the psi.bisquare function can return some 0 weight values, which then returns some NaN values in the resid vector that is calculated by dividing residuals/weights. Sinc

Re: [R] shading between two smoothed curves

2009-08-13 Thread Bert Gunter
?polygon Bert Gunter Genentech Nonclinical Biostatisics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Graves, Gregory Sent: Thursday, August 13, 2009 11:17 AM To: r-help@r-project.org Subject: [R] shading between two smoothed cu

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: > > Maybe I expect too much from a non compiled language. > Anyway, I wonder whether it is possible in R to set constant values > without using any memory location that would take useless space > bacause such values are not going to be changed along the program. It's > just a way

[R] Point-to-point Truncation with truncreg possible?

2009-08-13 Thread Vivek Ayer
Hi all, Can you use the truncreg() function to do point-to-point truncation, i.e., specify a different point=, for each point in your dataset. I guess in that sense this would be a nonlinear fit. Thanks, Vivek __ R-help@r-project.org mailing list https

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: > > Maybe I expect too much from a non compiled language. > Anyway, I wonder whether it is possible in R to set constant values > without using any memory location that would take useless space > bacause such values are not going to be changed along the program. It's > just a way

Re: [R] reading a string

2009-08-13 Thread Henrique Dallazuanna
Use readLines indeed. On Thu, Aug 13, 2009 at 3:21 PM, Mohsen Jafarikia wrote: > Hello All: > > I am having the following data file named "data.dat" > > Number of people > Number of pets > Age of trees > > ifn <- "data.dat" > dat <- read.table(ifn) > > colnames(dat)<-c("Variables") > > I want R

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: > > Maybe I expect too much from a non compiled language. > Anyway, I wonder whether it is possible in R to set constant values > without using any memory location that would take useless space > bacause such values are not going to be changed along the program. It's > just a way

[R] reading a string

2009-08-13 Thread Mohsen Jafarikia
Hello All: I am having the following data file named "data.dat" Number of people Number of pets Age of trees ifn <- "data.dat" dat <- read.table(ifn) colnames(dat)<-c("Variables") I want R to read all these in a string but when I ask R to read these, it gives me error because there more than

[R] shading between two smoothed curves

2009-08-13 Thread Graves, Gregory
I have a set of 52 weekly values, one is the desired high lake stage for a week, and the other is the desired low lake stage for each week. It looks like this: week High Low 1 16 14.5 2 16 14.5 3 15.95 14.45 4 15.84 14.34 5 15.73 14.23 6 15.61 14.11 7 15.5 14 8 15.38

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: > > Maybe I expect too much from a non compiled language. > Anyway, I wonder whether it is possible in R to set constant values > without using any memory location that would take useless space > bacause such values are not going to be changed along the program. It's > just a way

Re: [R] some help with plotting a beautiful structure using rgl

2009-08-13 Thread Nair, Murlidharan T
Ok, I was able to figure out one part by using rgl.spheres. I am still trying to insert text using rgl.texts. Does any one have a simple example? -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Nair, Murlidharan T Sent: Thursday,

Re: [R] Fitting a quasipoisson distribution to univariate data

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, Nigel Harding wrote: Dear all, I am analyzing counts of seabirds made from line transects at sea. I have been fitting Poisson and negative binomial distributions to the data using the goodfit function from the vcd library. I would also like to evaluate how well a quasi-pois

[R] multiple downloads of data when evaluating plot() vs. xyplot()

2009-08-13 Thread Greg Hirson
I have noticed an interesting behavior when comparing how the base plot() function deals with a data argument that downloads data from the internet vs. how xyplot() in lattice performs the same task. The goal is to plot hourly temperature data. The data is downloaded and formatted for R using

[R] Fitting a quasipoisson distribution to univariate data

2009-08-13 Thread Nigel Harding
Dear all, I am analyzing counts of seabirds made from line transects at sea. I have been fitting Poisson and negative binomial distributions to the data using the goodfit function from the vcd library. I would also like to evaluate how well a quasi-poisson distribution fits the data. However, none

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread Gabor Grothendieck
Try this: as.chron(date.time, "%Y%m%d%H%M%S") On Thu, Aug 13, 2009 at 12:59 PM, stephen sefick wrote: > These are date and times in the format MMDDhhmmss.  I would like > to take this column and make a chron object form them.  I have tried a > couple of the split family of functions but they

Re: [R] xyplot and subscripts

2009-08-13 Thread Deepayan Sarkar
On Thu, Aug 6, 2009 at 7:27 AM, Kito Palaxou wrote: > > Hi all, > > I have a data frame like this: > > DF <- data.frame(x = rnorm(10), y = rnorm(10), gr = rep(1:5, 2)) > > and I make the following xy-plot: > > library(lattice) > xyplot(y ~ x, data = DF, groups = gr, type = "b", col = 1) > > > Is it

[R] Efficiently Extracting Meta Data from TM Corpora

2009-08-13 Thread Shad Thomas
I'm using text miner (the "tm" package) to process large numbers of blog and message board postings (about 245,000). Does anyone have any advice for how to efficiently extract the meta data from a corpus of this size? TM does a great job of using MPI for many functions (e.g. tmMap) which great

Re: [R] How to get the n (number of observations) per conditional group

2009-08-13 Thread John Kane
?length --- On Thu, 8/13/09, Dax wrote: > From: Dax > Subject: [R] How to get the n (number of observations) per conditional group > To: r-help@r-project.org > Received: Thursday, August 13, 2009, 10:11 AM > Hello all, > > I have a huge data set that I'm cleaning up a bit. I am > extracted the

Re: [R] SOLVED: Lattice: How to do error bars

2009-08-13 Thread Deepayan Sarkar
On Wed, Aug 12, 2009 at 7:19 AM, wrote: > Thank you Gerrit, > > Your suggestion proved right after all: > > This does put error bars (dy) on the points. You only need to figure out > the proper y axis scaling. > >> xyplot(y~x|f,data=xy,groups=dy,panel=function(x,y,groups,subscripts,...) > {panel.x

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread John Kane
I'm not sure that I understand your problem but if you want the vector in character rather than numeric try: library(Hmisc) library(Hmisc) time.date<- Cs(19851001001500, 19851001003000, 19851001004500, 1985100101, 19851001011500, 19851001013000, 19851001014500, 1985100102, 19851001021500

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread Henrique Dallazuanna
Try this: strptime(date.time, "%Y%m%d%H%M%s") On Thu, Aug 13, 2009 at 1:59 PM, stephen sefick wrote: > These are date and times in the format MMDDhhmmss. I would like > to take this column and make a chron object form them. I have tried a > couple of the split family of functions but they

[R] some help with plotting a beautiful structure using rgl

2009-08-13 Thread Nair, Murlidharan T
Hi!! I need some help in using the correct required symbol when plotting my DNA structure using rgl. I need to plot one strand using empty circles and the other using filled circles and if possible have sequence in the center. I tried using pch and lty but have not been able to get it to do wha

[R] split number in a vector and then make a chron object out of it

2009-08-13 Thread stephen sefick
These are date and times in the format MMDDhhmmss. I would like to take this column and make a chron object form them. I have tried a couple of the split family of functions but they need character input here is the data: date.time <- c(19851001001500, 19851001003000, 19851001004500, 198510

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread Deepayan Sarkar
On Thu, Aug 13, 2009 at 6:34 AM, willow1980 wrote: > > Dear Professor Murdoch, > That is exactly the difficulty for me. I don't know how to make a prediction > with lmer using "expand.grid"; at the moment, I can use > “mo...@x%*%fixef(model)” to get predicted values for existing observational > dat

[R] Solutions of equation systems

2009-08-13 Thread Moreno Mancosu
Hello all! Maybe it's a newbie question(in fact I _am_, a newbie), but I hope you'll find the solution. I have an equation system which has k equation and n variables (kI would like to obtain a description of the solutions (which can be the equation of lines or a plane, or everything else) wit

Re: [R] FW: R graphics

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, Mcdonald, Grant wrote: From: Mcdonald, Grant Sent: 13 August 2009 13:08 To: r-help@R-project.org Subject: R graphics Dear sir, I am trying to create a barplot showing propotions, So my data is in the format of a vector containin

Re: [R] paste first row string onto every string in column

2009-08-13 Thread Gene Leynes
I'm also a newbie, but I've been getting loads of utility out of the "grep" function and it's cousin "gsub". Using asterisks are tricky because * often means "anything of any length" in a search pattern (e.g. delete *.* means delete all your files!). To find the literal * using grep you would nee

Re: [R] metafor random effects meta-analysis

2009-08-13 Thread Viechtbauer Wolfgang (STAT)
Correct, it is not possible to fix the residual variance to 1 in the R version of lme(), which is what one (typically) wants to do in meta-analyses, where the sampling variances are assumed to be (approximately) known. This is however possible in S-Plus, if you have access to that. Adding: cont

Re: [R] Browser and Debug?

2009-08-13 Thread roger koenker
At points of total desperation you can always consider the time-honored, avuncular advice -- RTFM, in this case Section 4.4 of Writing R Extensions. url:www.econ.uiuc.edu/~rogerRoger Koenker emailrkoen...@uiuc.eduDepartment of Economics vox: 217-333-4558

Re: [R] Output to screen and file at the same time

2009-08-13 Thread Greg Snow
You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. St

Re: [R] Yet another plotting hint - choosing the proper device to produce plots for Word

2009-08-13 Thread Jason Rupert
Magically, the eps version seems to fix the "not coloring in the lines" issue observed when using the WMF device - note that the issue was observed when viewing it on the screen and after printing it out. However, with eps, the color of the points when using pch 21 appears to stay within the

[R] how to extract the order of genes after clustering

2009-08-13 Thread Rnewbie
Dear all, I used hclust() to generate a dendrogram. After clustering, I wanted to take the order of the genes for further plotting purposes. Anyone has an idea how I can reoder my raw gene list as it is shown in the dendrogram? Thanks in advance. -- View this message in context: http://www.na

Re: [R] How to get the n (number of observations) per conditional group

2009-08-13 Thread Erik Iverson
We will only be able to help if you provide a reproducible example! I'm sure this is a simple one-liner, but it's hard to tell from your example what it should be. The functions table, length, tapply, and/or nrow may play a part though. -Original Message- From: r-help-boun...@r-proje

[R] FW: R graphics

2009-08-13 Thread Mcdonald, Grant
From: Mcdonald, Grant Sent: 13 August 2009 13:08 To: r-help@R-project.org Subject: R graphics Dear sir, I am trying to create a barplot showing propotions, So my data is in the format of a vector containing 0s and 1s (i.e.successful or not) with a cor

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread willow1980
Dear Professor Murdoch, That is exactly the difficulty for me. I don't know how to make a prediction with lmer using "expand.grid"; at the moment, I can use “mo...@x%*%fixef(model)” to get predicted values for existing observational data, but not data by "expand.grid". Actually, if I know this, I

[R] How to get the n (number of observations) per conditional group

2009-08-13 Thread Dax
Hello all, I have a huge data set that I'm cleaning up a bit. I am extracted the means per condition, but also need to get the n. Strangely enough I am unable to find a function that could actually pull this off. I am unable to use replications or count the rows using nrow. What I am trying to ob

[R] [R-pkgs] dcemri: A package for medical image analysis

2009-08-13 Thread Brandon . J . Whitcher
dcemri 0.10 has been released on CRAN "dcemri" is (to the best of my knowledge) the first public-domain software package for the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI or DWI). Data import and export is availble for ANALYZE or NIfTI

Re: [R] Browser and Debug?

2009-08-13 Thread rkevinburton
This may be asking more than can be reasonably expected. But, any tips on debugging the 'C' and Fortran code without trying to put together all the tools to compile from source? Kevin Erik Iverson wrote: > This article might help: > > http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-too

Re: [R] Matrix addition function

2009-08-13 Thread Vitalie S.
On Thu, 13 Aug 2009 15:11:03 +0200, Michael Knudsen wrote: On Thu, Aug 13, 2009 at 11:35 AM, Lina Rusyte wrote: Hi Lina, What function can I use for matrices addition? I couldn’t find any information about it in the manual or in the internet. (A+B suits, when the number of matrixes is s

Re: [R] prop.test() - need algorithm or reference

2009-08-13 Thread Ronggui Huang
The help page of prop.test gives you three references. Isn't it enough? For example, Newcombe R.G. (1998) Two-Sided Confidence Intervals for the Single Proportion: Comparison of Seven Methods. _Statistics in Medicine_ *17*, 857-872. Newcombe R.G. (1998) Interval Estimation for

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Philipp Pagel
On Thu, Aug 13, 2009 at 04:05:07PM +0200, mau...@alice.it wrote: > Maybe I expect too much from a non compiled language. > Anyway, I wonder whether it is possible in R to set constant values > without using any memory location that would take useless space > bacause such values are not going to be

Re: [R] Browser and Debug?

2009-08-13 Thread Erik Iverson
This article might help: http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Inchallah Yarab Sent: Thursday, August 13, 2009 9:40 AM To: r-help@r-project.org Subject: [R] Brows

[R] prop.test() - need algorithm or reference

2009-08-13 Thread gheine
Preparing a paper for a medical journal. Using the prop.test() function in R (v2.4.0) to compare two groups' response to data like the following. A sample of 100 individuals from Population I, 18 with positive readings from a certain test, vs. A sample of 148 individuals from Population

Re: [R] Validity check when setting slot

2009-08-13 Thread Vitalie S.
Hi, RG> Hi, RG> I'm wondering if the following behaviour is normal: RG> setClass('A', representation(number='numeric'), RG> validity=function(object){ RG> if( obj...@number < -1 ) return("Invalid number"); TRUE}) >> [1] "A" RG> a <- new('A') RG> a >> An

[R] Browser and Debug?

2009-08-13 Thread Inchallah Yarab
Hi, Someone can explain to me how use Browser and Debug ? thank you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-pro

Re: [R] xyplot and subscripts

2009-08-13 Thread Juliet Hannah
I'm not sure how to do this in lattice, but here is an option with ggplot2. library(ggplot2) set.seed(123) # Make sure the data has a variable that indicates # which group is red and which one is black DF <- data.frame(x = rnorm(10), y = rnorm(10), gr = rep(1:5, 2),endpoint = c(rep("Red_Group",5)

Re: [R] When using randomForest, what's the effect to "set.seed"?

2009-08-13 Thread Daniel Malter
if you set a seed manually, it makes the results reproducible. That is, if you set a specific seed, your randomForest procedure should produce the exact same result every time (all others equal). As an example: set.seed(1234) rnorm(100) rnorm(100) set.seed(4531) rnorm(100) rnorm(100) set.seed(1

[R] metafor random effects meta-analysis

2009-08-13 Thread Mark Urban
Hello, Great to see the new metafor package for meta-analysis. I would like to perform a meta-analysis in which I initially calculate the intercept of the model with a nested random-effects structure. In lme, this would be model<- lme(v3~1, random=~1|species/study, weights = varFixed(~Wt),

[R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread mauede
Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to assign a mnemnic name to

[R] Whittle estimation for ARMA models

2009-08-13 Thread tzygmund mcfarlane
Hi, Does anyone know of a package/script that will implement the Whittle (1953) estimator for the parameters of an invertible stationary ARMA time series model? The estimator is defined on, for example, pg. 378 of Brockwell & Davis (1991). I assume that the internal call .whittle in this code due

Re: [R] R graphics

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, Mcdonald, Grant wrote: Dear sir, I am trying to create a barplot for two propotions, with proportions successful on the y and age on the x. So my data is in the formate of one vector containing 0s and 1s (i.e.successful or not) with a corresponding two level vector of

Re: [R] Matrix addition function

2009-08-13 Thread Gabor Grothendieck
If A, B and C are matrices then: L <- list(A, B, C) Reduce("+", L) On Thu, Aug 13, 2009 at 5:35 AM, Lina Rusyte wrote: > Hello, > > What function can I use for matrices addition? I couldn’t find any > information about it in the manual or in the internet. > (A+B suits, when the number of matrix

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