Re: [R] Plotting GEE confidence bands using "predict"

2011-10-17 Thread JASON M. HILL
Thank you Shige,I got the Zelig package to work for me. For anyone who cares, here's the code: library(Zelig)order(df$WEIGHT)z.out<- zelig(WEIGHT~DISTANCE, model = "normal.gee",id = "MOTHER", data = df,corstr = "exchangeable")summary(z.out)date.range<-0:51 # sequence of values over the range of DIS

Re: [R] Function to "lump" factors together?

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 9:45 PM, David Wolfskill wrote: Sorry about the odd terminology, but I suspect that my intent might be completely missed had I used "aggregate" or "classify" (each of which appears to have some rather special meanings in statistical analysis and modeling). I have some da

Re: [R] Latex question

2011-10-17 Thread Joshua Wiley
Hi Hannah, You are correct that this is not the right place for LaTeX questions. There are many resources online for TeX users. Here is one page that may help you: http://en.wikibooks.org/wiki/LaTeX/Floats,_Figures_and_Captions stackoverflow may be a better place to post questions, there are als

[R] Latex question

2011-10-17 Thread li li
Dear all, This may not be the right place for latex questions, but I do not know where else to ask the question. I have two subfigures. I want the first subfigure to have a caption on the side of it and the second subfigure to have a caption below it. Thank you. Hannah [[

[R] Function to "lump" factors together?

2011-10-17 Thread David Wolfskill
Sorry about the odd terminology, but I suspect that my intent might be completely missed had I used "aggregate" or "classify" (each of which appears to have some rather special meanings in statistical analysis and modeling). I have some data about software builds; one of the characteristics of eac

Re: [R] Remote environments, calling functions

2011-10-17 Thread William Dunlap
I don't think you said how you packaged this stuff up and that is the critical part of your question. Here is an example that does what I think you want to do. It uses save() and load() for the serialization and I serialize an environent full of data and functions. In one session of R make some da

Re: [R] Beginner's question about a time series object

2011-10-17 Thread Iara Faria
Thank you David. The plot() you sugested worked nicely.   You and Weyland both think ts class objects are difficult to use. I had not considered doing differently, but I have just gotten many tutorials on package zoo and how to use it in econometrics. Looks promising, will read everything now.

Re: [R] Remote environments, calling functions

2011-10-17 Thread Tyler Pirtle
On Mon, Oct 17, 2011 at 5:44 PM, Peter Langfelder < peter.langfel...@gmail.com> wrote: > On Mon, Oct 17, 2011 at 5:28 PM, Tyler Pirtle wrote: > > Hi there, > > > > I'm trying to do something like a migration of an R program. I've got a > > function and some variables > > in an interactive-session

Re: [R] Remote environments, calling functions

2011-10-17 Thread Peter Langfelder
On Mon, Oct 17, 2011 at 5:28 PM, Tyler Pirtle wrote: > Hi there, > > I'm trying to do something like a migration of an R program. I've got a > function and some variables > in an interactive-session: > > r <- .5 > ## estimatePi references r > estimatePi <- function(seed) { >    set.seed(seed) >  

[R] Remote environments, calling functions

2011-10-17 Thread Tyler Pirtle
Hi there, I'm trying to do something like a migration of an R program. I've got a function and some variables in an interactive-session: r <- .5 ## estimatePi references r estimatePi <- function(seed) { set.seed(seed) numDraws <- 1e+05 x <- runif(numDraws, min = -r, max = r) y <-

Re: [R] Importing all observations and variables from csv file into dataframe

2011-10-17 Thread Bert Gunter
Oh please! Try reading the relevant docs -- like an Intro to R (The chapter on Reading data from files) or the R Data Import/Export manual. You will find plenty of help on this list, but you owe us an honest effort to help yourself first. -- Bert On Mon, Oct 17, 2011 at 11:56 AM, Sally Ann Sims

Re: [R] Beginner's question about plotting variables in a time series object with the date on the x axis

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 5:23 PM, Iara Faria wrote: Dear R helpers, I am a beginner at R so please be gentle :) I have already read manuals and FAQs, with no help. I have a monthly time series data on public debt with 40 variables, it starts on January 1994 and ends on June 2011. I agree with W

[R] Aggregating Survey responses for weighting

2011-10-17 Thread Farley, Robert
I have about 27,000 survey responses from across about 150 Bus Routes, each with potentially 100 stops. I've recorded the total Ons and Offs for each stop on each bus run, as well as the stop pair each survey response corresponds to. I wish to create weights based on the On and Off stop for eac

Re: [R] using mean substitution

2011-10-17 Thread Michael Parent
That worked perfectly, thanks!! I'd assumed that it wasn't necessary for me to type out "...based on a MV normal distribution that I made into 1-7 integers by blah blah blah"; the distribution is normal-ish after I transform it around for the purposes I need for the simulations. I'll be sure to

Re: [R] Beginner's question about plotting variables in a time series object with the date on the x axis

2011-10-17 Thread R. Michael Weylandt
I'm not a huge fan of using R's ts class directly, much preferring to use zoo or xts (both of which are packages) to enhance. That said, I think your problem comes from identifying the data/variable name incorrectly. You've only "ts"ed dados, but you try to plot divliq.pib; try plot(dados[,"divliq

Re: [R] contouring x y scatter data

2011-10-17 Thread emorway
Thank you David, I'm moving forward again. I was not aware of that website, I was recently at http://www.r-project.org/ and clicked on the 'mailing list' link and didn't see it there...with 8k+ posts, maybe its worth adding? -- View this message in context: http://r.789695.n4.nabble.com/conto

Re: [R] using mean substitution

2011-10-17 Thread Rolf Turner
On 18/10/11 10:35, Michael Parent wrote: Hi, all, I'm running a monte carlo simulation with missing data. The data are arranged such that there are k columns and n rows over a set number of simulations (set to 10 right now so it runs fast while I set everything up). The data are integers, num

[R] special language character in a pie chart

2011-10-17 Thread milena
Dear List Members, I am working on a below piece of code: Initially have created pie charts with Enlish labels to present the data for Czech Republic, now however I need to print the label with original Czech fonts. When I copy paste from Word, certain fonts get 'simplified' distorting original s

[R] Beginner's question about plotting variables in a time series object with the date on the x axis

2011-10-17 Thread Iara Faria
Dear R helpers,   I am a beginner at R so please be gentle :) I have already read manuals and FAQs, with no help. I have a monthly time series data on public debt with 40 variables, it starts on January 1994 and ends on June 2011. I am loading the data into R using read.csv and the data looks ok

Re: [R] contouring x y scatter data

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 5:59 PM, emorway wrote: Hi Carlos, Thanks for the response. The plot you suggested was not in line with what I'm trying to produce in R. The last plot found at: http://www.advsofteng.com/gallery_contour.html is more along the lines of what I'm looking for. Notice th

Re: [R] contouring x y scatter data

2011-10-17 Thread emorway
Hi Carlos, Thanks for the response. The plot you suggested was not in line with what I'm trying to produce in R. The last plot found at: http://www.advsofteng.com/gallery_contour.html is more along the lines of what I'm looking for. Notice the scatter points (shown by "x") are not laid o

Re: [R] compressing/reducing data for plot

2011-10-17 Thread Carlos Ortega
Hello, One alternative is to create some kind of contourplot/levelplot which will enhance and show clearly the spikes and will smooth the rest of the information. That perhaps will be slow in generating the plot but not with the postscript file. Regards, Carlos Ortega www.qualityexcellence.es 20

Re: [R] Converting list of lists into dataframes

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 5:11 PM, xhan wrote: Hi, I have a list of lists that I would like to convert into a dataframe such that the name(?) of the individual lists is replicated as rows with each item in the list listed in another column. I have provided a partial from my list: (let's say th

Re: [R] contouring x y scatter data

2011-10-17 Thread Carlos Ortega
Hi, Please check if this representation helps you. library(lattice) library(latticeExtra) p1.gr <- cloud( ts181 ~ x * z, data=FD, panel.3d.cloud = panel.3dbars, scales = list(arrows = FALSE, just = "right")) p2.gr <- cloud( ts1825 ~ x * z, data=FD, panel.3d.cloud = panel.3dbars, scales = list(arr

[R] using mean substitution

2011-10-17 Thread Michael Parent
Hi, all, I'm running a monte carlo simulation with missing data. The data are arranged such that there are k columns and n rows over a set number of simulations (set to 10 right now so it runs fast while I set everything up). The data are integers, numbers 1-7 only (normal distribution). The si

Re: [R] Converting list of lists into dataframes

2011-10-17 Thread Dennis Murphy
In the absence of a reproducible example (your example is not reproducible as is), try this: names(help.me) <- as.character(2:4) library('plyr') newDF <- ldply(help.me, rbind) newDF[['.id']] <- as.numeric(newDF[['.id']]) ldply will create a new column named .id that contains the name of the list

Re: [R] Creation of mlogit models from text file

2011-10-17 Thread Bhargava Sana
Yes, there seem to be a lot of elements in the mlogit model object and I don't have some of that information now since the models have been estimated in Biogeme. I had been trying some of the steps that you suggested (after I posted my question) and as you mentioned, realized that this is danger

[R] Converting list of lists into dataframes

2011-10-17 Thread xhan
Hi, I have a list of lists that I would like to convert into a dataframe such that the name(?) of the individual lists is replicated as rows with each item in the list listed in another column. I have provided a partial from my list: (let's say the list is called "help.me") [[2]] [1] 18 27 11

[R] Analyze each factor separtely

2011-10-17 Thread kickout
Hello Trying to apply a model to each level of a factor For example, i have three levels of a variable I call 'Code'...I want to model the data under each level of code differently...I've attached a sample data set... http://r.789695.n4.nabble.com/file/n3913431/data.txt data.txt I.E for cod

Re: [R] Build 64-bit R Solaris 10 Sparc

2011-10-17 Thread Prof Brian Ripley
The instructions *are* in the manual, and they do work: I checked for R 2.14.0 beta only this morning. On Mon, 17 Oct 2011, Nynese Tinsley wrote: Hello All, Has anyone had success building 64-bit R on Solaris 10 Sparc with the Oracle Studio Compiler suite? Could anyone start give me a clue.

Re: [R] Creation of mlogit models from text file

2011-10-17 Thread R. Michael Weylandt
I'm not at all familiar with mlogit or Biogene so I can't really give a definitive answer, but it seems that this would be a very dangerous thing to try. Looking at the mlogit manual, I see that, like most model objects in R, mlogit has a variety of elements including many of those you specificall

Re: [R] calculating ratios from all combinations

2011-10-17 Thread R. Michael Weylandt
On Mon, Oct 17, 2011 at 4:31 PM, R. Michael Weylandt wrote: > I have no idea what's going on in the code you provided, particularly > why there are no ratios given your subject line or why you are looping > over an unused variable, but how about this: > > n <- colnames(d) > n <- n[-length(n)] # Th

Re: [R] Adjusted Means

2011-10-17 Thread John Fox
Dear Mattune, I guess that you're using the effect() function in the effects package. You've requested the effect for the covariate fixing the values of the factors, rather than vice-versa. Try effect("a*b*c", Anocova.Model) or, for more detail in the output, summary(effect("a*b*c", Anocova.Model)

[R] Build 64-bit R Solaris 10 Sparc

2011-10-17 Thread Nynese Tinsley
Hello All, Has anyone had success building 64-bit R on Solaris 10 Sparc with the Oracle Studio Compiler suite? Could anyone start give me a clue. I have tried to no avail. Thanks, Nynese Nynese Tinsley, BSEE, MSCIS UNIX Systems Analyst Harvard School of Public Health Center for Bio

Re: [R] Scatterplot with the 3rd dimension = color?

2011-10-17 Thread Kerry
Yes, the qplot works great, but do you know how to allow for multiple plots? I want one variable to be plotted say from blue to red and another say from yellow to green but in the same graph, each having there own separate legends. I've tried print() and arrange() but no luck. Thanks again, kb On

[R] Independent component analysis with only one "source" of data

2011-10-17 Thread Noah Silverman
Hi, Looking at the fastICA library. I want to test separating out different sounds from a recorded wav file. But, I only have a SINGLE stream of data (one channel wav.) It appears as if the fastICA won't let me separate more sounds than I have columns in my data matrix. is this correct? If

[R] Foreach (doMC)

2011-10-17 Thread Rui Esteves
Hello, I am trying to run a small example with foreach, but I am having some problems. Here is the code: *library(doMC) registerDoMC() zappa = list() frank = list() foreach (i = 1:4) %dopar% { zappa[[i]] = kmeans (iris[-5],4) frank[[i]] = warnings() }* The code runs without error. However th

Re: [R] Scatterplot with the 3rd dimension = color?

2011-10-17 Thread Kerry
Here's my loadable data in case it helps. It creates 2 separate plots which I'd like to be in the same graph with 2 separate legends. library(ggplot2) #Here's the 1st plot x<-rnorm(100) y<-rnorm(100) z<-rnorm(100) d <- data.frame(x,y,z) dg<-qplot(x,y,colour=z,data=d) dg + scale_colour_gradient(lo

[R] Adjusted Means

2011-10-17 Thread Mattune
I'm running the following ANCOVA model in R: X=a*b*d + d where d is the covariate. I want to produce adjusted means for X for all possible treatment combinations. a has 6 levels, b has 2 levels, c has 2 levels, so this is a 6x2x2 = 24 possible treatment combinations. When I run: effect("d", Anco

Re: [R] how to use 'which' inside of 'apply'?

2011-10-17 Thread William Dunlap
data.frames are quite efficient when you use a column at a time, but not when used a row at a time. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: Nathan Piekielek [mailto:npiekie...@gmail.com] > Sent: Monday, October 17, 2011 12:37 PM > To: William D

Re: [R] right justify right-axis tick values in lattice

2011-10-17 Thread Deepayan Sarkar
On Sun, Oct 16, 2011 at 7:20 PM, David Winsemius wrote: > > On Oct 16, 2011, at 1:17 AM, Richard M. Heiberger wrote: > >> How can I right justify the right-axis tick values?  They appear in the >> example below as left-justified. >> >> I have tried several different ways and all fail in different

Re: [R] how to use 'which' inside of 'apply'?

2011-10-17 Thread William Dunlap
Your original code works far faster when the input is a matrix that when it is a data.frame. Selecting a row from a data.frame is a very slow operation, selecting a row from a matrix is quick. Modifying a row or a single element in a data.frame is even worse compared to do it on a matrix. I comp

Re: [R] Importing all observations and variables from csv file into dataframe

2011-10-17 Thread R. Michael Weylandt
You aren't reading the file in at all: notice that, > summary("MooGoesTheCow",header=TRUE,as.is=TRUE) Length Class Mode 1 character character This is because you are asking for a summary of the string containing the file name, not the file itself. Rather, use X = read.csv("C

Re: [R] heritability estimation

2011-10-17 Thread Moohbear
Thanks for the info. I am working with Recombinant Inbred Lines(RILs), not pedigree, so most of what I could find does not apply to my work. I've found a couple of tutorials explaining how to use analysis of variance components with lme4, but I don't have multiple measurements per individual per ex

Re: [R] Importing all observations and variables from csv file into dataframe

2011-10-17 Thread jim holtman
I would assume that you would use 'read.csv'. I don't know where you got the syntax for "summary"; x <- read.csv(("C:\\Documents\\R_dfiles\\H_N_T.csv",as.is=TRUE) summary(x) On Mon, Oct 17, 2011 at 2:56 PM, Sally Ann Sims wrote: > Hello, > > I need some help getting started with data analysis.

Re: [R] Scatterplot with the 3rd dimension = color?

2011-10-17 Thread Kerry
Oh, I just saw your ggplot example, that works well too. However, it seems much of the options are hidden for changing the range of colors or the color types altogether. I'm currently looking through the ggplot ref manuals. Thanks, kb On Oct 2, 10:42 pm, Ben Bolker wrote: > Duncan Murdoch gmail

Re: [R] Scatterplot with the 3rd dimension = color?

2011-10-17 Thread Kerry
Thanks, I consider all of those options and tried some, but the z=color gradient seems the best option for my data. kb On Oct 2, 10:42 pm, Ben Bolker wrote: > Duncan Murdoch gmail.com> writes: > > > > > > > > > > > > > On 11-10-02 1:11 PM, Kerry wrote: > > > I have 3 columns of data and want to

Re: [R] Histogram for each ID value

2011-10-17 Thread Philipp Pagel
> where the first column is the chromosome location and the second column is > some value. What I'd like to do is have a histogram created for each chr > location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and > chr22). I am just having a hard time getting everything to work out

[R] Importing all observations and variables from csv file into dataframe

2011-10-17 Thread Sally Ann Sims
Hello, I need some help getting started with data analysis. I’m having trouble getting R to read my data file. I’ve referred to various R help documentation, the website, and FAQs, but I don’t see my situation listed. I saved an Excel file (post-2007 Excel version) of data as a “.csvâ

Re: [R] How to create a random matrix

2011-10-17 Thread adpb001
Thanks. bb=replicate(2, rnorm(20)) was very useful for me. -- View this message in context: http://r.789695.n4.nabble.com/How-to-create-a-random-matrix-tp901667p3912806.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.

Re: [R] calculating ratios from all combinations

2011-10-17 Thread 1Rnwb
so here is the code I need help to fix the line for 'st' when it reaches maximum, that's where i am getting stuck. thanks Sharad set.seed(100) d=data.frame(x=rnorm(20)+5, x1=rnorm(20)+5, x2=rnorm(20)+5, x3=rnorm(20)+5, x4=rnorm(20)+5, x5=rnorm(20)+5, x6=rnorm(20)+5, x7=rnorm(20)+5, x8=rno

Re: [R] mgp and axis title positions

2011-10-17 Thread Patrick Connolly
On Sun, 16-Oct-2011 at 03:05PM -0700, Benjamin Cheah wrote: |> Hi all, [...] |> It is particularly frustrating when you need to adjust axis title |> positions separately for x and y axes - i.e. specify mgp twice - |> once for each axis within the axis function. But this doesn't seem |> to work -

[R] cut data into sevral group and assign calculated values individually

2011-10-17 Thread Li, Yan
Hi All, I have some data from which I set four points to be breaks. Based on these points, I cut the dataset into four groups and assign a number to it: <=331.04 assign 0 >331.04 <=476.07 assign data-331.04/(476.07-331.04) >476.07<=608.66 assign 1 >608.66 <=791.5 assign 791.5- data/(791.5-608.

[R] contouring x y scatter data

2011-10-17 Thread emorway
Hello, I'm almost positive R can do the following, I just haven't hit upon the right package or search terms, however. Here's what I'm after: I've got concentration output from two different models that I want to qualitatively compare in a contour plot (or some variant of a contour plot). The p

Re: [R] how to use 'which' inside of 'apply'?

2011-10-17 Thread William Dunlap
Try vectorizing it a bit by looping over the columns. E.g., f1 <- function (df) { # loop (backwards) over all columns in df whose # names start with "D" to find the earliest one # that is bigger than column "thold". I tested with # df being a data.frame but a matrix sh

Re: [R] how to use 'which' inside of 'apply'?

2011-10-17 Thread R. Michael Weylandt
I think something like this should do it at a huge speed up, though I'd advise you check it to make sure it does exactly what you want: there's also nothing to guarantee that something beats the threshold, so that might make the whole thing fall apart (though I don't think it will) # Sample data d

Re: [R] Best practices for handling very small numbers?

2011-10-17 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Seref Arikan > Sent: Monday, October 17, 2011 9:11 AM > To: r-help@r-project.org > Subject: [R] Best practices for handling very small numbers? > > Greetings > I have been experi

[R] how to use 'which' inside of 'apply'?

2011-10-17 Thread Nathan Piekielek
Hello R-community, I am trying to populate a column (doy) in a large dataset with the first column number that exceeds the value in another column (thold) using the 'apply' function. Sample data: pt D1 D17 D33 D49 D65 D81 D97 D113 D129 D145 D161 D177 D193 D209 D225 D241

[R] over-estimation Negative Binomial models

2011-10-17 Thread D_Tomas
Hi! I have fitted a Negative Binomial model (glm.nb) and a Poisson model (glm family=poisson) to some count data. Both have the same explanatory variables & dataset When I call sum(fitted(model.poisson)) for my GLM-Poisson model, I obtain exactly the same number of counts as my data. However,

[R] Best practices for handling very small numbers?

2011-10-17 Thread Seref Arikan
Greetings I have been experimenting with sampling from posterior distributions using R. Assume that I have the following observations from a normal distribution, with an unscaled joint likelihood function: normsamples = rnorm(1000,8,3) joint_likelihood = function(observations, mean, sigma){ r

[R] Error in ade4 package with rlq

2011-10-17 Thread djleavitt
I am trying to run an rlq analysis on some pretty cool data. The error message I am getting states " Error in rlq(dudiR, dudiL, dudiQ, scannf = TRUE, nf = 2) : Non equal row weights" Problem for me is that the row weights are equal; that is if the set-up is correct. The contingency tables colum

[R] geoXY

2011-10-17 Thread leanne heisler
Hi Everyone, I am new to R Language and was wondering if someone could help me convert my latitude-longitude coordinates to cartesian coordiantes using geoXY() from SoDA package? I have been uploading my coordinates from a text file into R (they originate as a dataframe) and them converti

Re: [R] Extracting results from a function output

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 11:13 AM, Cem Girit wrote: Hello, I am having hard time obtaining a value from a function. "fit" is a survival function that produces some results, such as "median", "confidence intervals" etc. But str() function does not list these values. How can I extract these to b

Re: [R] Extracting results from a function output

2011-10-17 Thread William Dunlap
Often the summary() methods for the modelling functions contain the kinds of details you are looking for. Sometimes there are special extractor functions but often not. You have to study the help file for summary. and the vignettes for the package, and perhaps do a little experimentation to figure

Re: [R] multiple lines with the same data frame?

2011-10-17 Thread R. Michael Weylandt
There are indeed many, many ways in R to do something like you've described. If you are just a beginner, I'd recommend something simple: suppose your data is called df and the columns named are "id", "x'', and "y" respectively. with(df, plot(x[id == 1], y[id==1], ylim = range(y), type="l") # Call

Re: [R] Creation of mlogit models from text file

2011-10-17 Thread Bhargava Sana
Michael, Thanks for the quick response. I currently have a few models that have been estimated using Biogeme. I have attached a sample output file from the estimation. I am more concerned about creating a model object from scratch rather than the reading part. Let us just say if we have a list

[R] multiple lines with the same data frame?

2011-10-17 Thread Adel ESSAFI
Bonjour I have this data frame and I am newbie in R. I want to ask if it is possible to draw 10 lines in a plot such that: a line for every colomn, the x - axis is the second column and the y-axis is the third one. Thank you for any input 1 0 1094442 1 0.2 1163576.2 1 0.4 1238539.6 1

Re: [R] Extracting results from a function output

2011-10-17 Thread R. Michael Weylandt
Assuming I'm reading your post correctly -- fit is the output object and the lines following >fit are the console output, which implicitly calls print -- it looks like the median isn't stored in fit but is calculated on the fly in the print call. But this doesn't seem consistent with your claim tha

Re: [R] Creation of mlogit models from text file

2011-10-17 Thread R. Michael Weylandt
You're going to have to say more about your text file if you want meaningful help: specifically, what is in the file: data, output from other software, etc? There are probably two questions to deal with here: reading in whatever is in the text file and mapping it to the correct R object and settin

[R] Extracting results from a function output

2011-10-17 Thread Cem Girit
Hello, I am having hard time obtaining a value from a function. "fit" is a survival function that produces some results, such as "median", "confidence intervals" etc. But str() function does not list these values. How can I extract these to be able use them? For example, I need "median" value for

[R] Creation of mlogit models from text file

2011-10-17 Thread Bhargava Sana
Hello all, Has anyone tried to create an R mlogit model object from a text file? If yes, what would be the best way to do it? I already have models that have been estimated using other software and would like to use R to help me make predictions for new data. Thank you! Bhargava Sana

Re: [R] rpois > 0

2011-10-17 Thread knut-o
thanks guys!! your great -- View this message in context: http://r.789695.n4.nabble.com/rpois-0-tp3906239p3912203.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] Plotting GEE confidence bands using "predict"

2011-10-17 Thread Shige Song
Hi Jason, I would go for Zelig package to get simulated values and confidence intervals. It can handle gee model. Shige On Mon, Oct 17, 2011 at 9:38 AM, JASON M. HILL wrote: > Hello Fellow R > Users,I have > spent the last week trying to find a work around to this problem and I can't > seem to

Re: [R] Party package: varimp(..., conditional=TRUE) error: term 1 would require 9e+12 columns (fwd)

2011-10-17 Thread Torsten Hothorn
I would like to build a forest of regression trees to see how well some covariates predict a response variable and to examine the importance of the covariates. I have a small number of covariates (8) and large number of records (27368). The response and all of the covariates are continuous vari

Re: [R] Beginner's question about ptrend. What package to use in R and a general explanation of the statistics.

2011-10-17 Thread David Winsemius
On Oct 17, 2011, at 8:04 AM, Sarah Goslee wrote: Hi, On Sun, Oct 16, 2011 at 6:24 PM, Bob Briggs wrote: Hello I'm wanting to understand more about ptrend (a statistical explanation via an internet website if possible) and also to know what package in R would produce a ptrend. Appr

[R] compressing/reducing data for plot

2011-10-17 Thread Timo Schneider
Hello, I have simulation results in the form of Time V I 0.e+000 7.218354344368e-001 5.224478627497e-006 1.e-009 7.218354344368e-001 5.224477718002e-006 2.e-009 7.218354344368e-001 5.224477718

Re: [R] Histogram for each ID value

2011-10-17 Thread R. Michael Weylandt
Like others have suggested, I think ggplot2 is probably the best way to go about this, but if you'd rather use base graphics (and you never indicated how you felt about ggplot2), you could do something like this with tapply: fcts <- letters[sample(9,1500,T)] vals <- rnorm(1500) df <- data.frame(ca

Re: [R] Reading data with 'awk' - basics?

2011-10-17 Thread Brian Smith
Got it. Thanks! On Mon, Oct 17, 2011 at 9:40 AM, Prof Brian Ripley wrote: > On Mon, 17 Oct 2011, Brian Smith wrote: > > Hi, >> >> I had a large file for which I require a subset of rows. Instead of >> reading >> it all into memory, I use the awk command to get the relevant rows. >> However, >> I

[R] Plotting GEE confidence bands using "predict"

2011-10-17 Thread JASON M. HILL
Hello Fellow R Users,I have spent the last week trying to find a work around to this problem and I can't seem to solve it. I simply want to plot my GEE model result with 95% confidence bands. I am using the geepack package to run a basic GEE model involving nestling weights, to a Gaussian distri

Re: [R] Histogram for each ID value

2011-10-17 Thread Ben Bolker
Paul Hiemstra knmi.nl> writes: > > Hi, > > When using ggplot, take a look at facet_wrap and geom_histogram. > > regards, More specifically, try something along the lines of d <- data.frame(f=factor(paste("chr",rep(c(1,2,3,7,9,22),each=50),sep="")), v=runif(300)) library(ggplot2) ggplo

Re: [R] What does \Sexpr[results=rd]{} exactly mean in Rd?

2011-10-17 Thread Yihui Xie
Thanks a lot! Sorry for cross-posting, but I did it intentially because I tend to believe Barry Rowlingson (Why R-help Must Die!), and I will summarize the answers here later to StackOverflow. Another user also told me this worked for 2.13.1, but not later versions. Regards, Yihui -- Yihui Xie P

Re: [R] heritability estimation

2011-10-17 Thread Juliet Hannah
Search: "mcmcglmm heritability" to see some discussions using the mcmcglmm package. This package is discussed often on the mixed model list. You can also use the kinship package. It will take some time to get familiar with R. Work through a few of the examples for variance component models, and the

Re: [R] What does \Sexpr[results=rd]{} exactly mean in Rd?

2011-10-17 Thread Gavin Simpson
On Sun, 2011-10-16 at 19:36 -0500, Yihui Xie wrote: > Hi, > > I have spent a few hours on the R-exts manual and the documentation of > parse_Rd() (as well as the PDF document in the references), but I > still have not figured out what results=rd means. I thought I could > use an R code fragment to

Re: [R] Install the rugarch-package

2011-10-17 Thread John Kerpel
rugarch installs and works fine for me under windows 7 64-bit and R 2.13.1 64 bit. On Mon, Oct 17, 2011 at 7:49 AM, user84 wrote: > Hi, > > i am unable to install the rugarch package. > More than that i do not even find this package in my list of possible > packages. > Its possible than the name

Re: [R] Reading data with 'awk' - basics?

2011-10-17 Thread Prof Brian Ripley
On Mon, 17 Oct 2011, Brian Smith wrote: Hi, I had a large file for which I require a subset of rows. Instead of reading it all into memory, I use the awk command to get the relevant rows. However, I'm doing it pretty inefficiently as I write the subset to disk, before reading it into R. Is ther

Re: [R] Reading data with 'awk' - basics?

2011-10-17 Thread Gabor Grothendieck
On Mon, Oct 17, 2011 at 9:23 AM, Brian Smith wrote: > Hi, > > I had a large file for which I require a subset of rows. Instead of reading > it all into memory, I use the awk command to get the relevant rows. However, > I'm doing it pretty inefficiently as I write the subset to disk, before > readi

Re: [R] Install the rugarch-package

2011-10-17 Thread Prof Brian Ripley
On Mon, 17 Oct 2011, user84 wrote: Hi, i am unable to install the rugarch package. More than that i do not even find this package in my list of possible packages. Its possible than the name has changed, or the package is not longer availiable? No: see http://cran.r-project.org/web/packages/ru

[R] Reading data with 'awk' - basics?

2011-10-17 Thread Brian Smith
Hi, I had a large file for which I require a subset of rows. Instead of reading it all into memory, I use the awk command to get the relevant rows. However, I'm doing it pretty inefficiently as I write the subset to disk, before reading it into R. Is there a way that I can read it into an R object

Re: [R] SOLVED Legend symbols (line, points) in one column.

2011-10-17 Thread Kenneth Roy Cabrera Torres
Thank you very much for your answer. It works just as I want!. Kenneth El sáb, 15-10-2011 a las 20:39 +0530, Deepayan Sarkar escribió: > On Fri, Oct 14, 2011 at 10:02 AM, David Winsemius > wrote: > > Legends are built in columns. You need to find a graphics symbol to put in > > the "points" col

Re: [R] Editor for RD file?

2011-10-17 Thread S Ellison
Tinn-R also highlights .rd files and is free. Me, I use TextPad with a latex syntax file. S Ellison > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Bogaso Christofer > Sent: 16 October 2011 13:57 > To: r-help@r-project.org

[R] Install the rugarch-package

2011-10-17 Thread user84
Hi, i am unable to install the rugarch package. More than that i do not even find this package in my list of possible packages. Its possible than the name has changed, or the package is not longer availiable? Is there a similar package avaliable for garch modelling except the fGarch what i am usin

Re: [R] simultaneously maximizing two independent log likelihood functions using mle2

2011-10-17 Thread Ben Bolker
Adam Zeilinger umn.edu> writes: > I have a log likelihood function that I was able to optimize using > mle2. I have two years of the data used to fit the function and I would > like to fit both years simultaneously to test if the model parameter > estimates differ between years, using likelih

Re: [R] Trojan in setup file

2011-10-17 Thread Achim Zeileis
On Mon, 17 Oct 2011, Annette Prochnow wrote: Hello, I have the following problem: I successfully installed R (Version 2.1.3.0 for Windows) on my Notebook (Windows 7) in June. Now I used the same setup file for a PC (Windows XP) and got a message from the anti virus software (Avira), that the s

Re: [R] Histogram for each ID value

2011-10-17 Thread Paul Hiemstra
Hi, When using ggplot, take a look at facet_wrap and geom_histogram. regards, Paul On 10/17/2011 12:14 PM, Sarah Goslee wrote: > Hi, > > On Mon, Oct 17, 2011 at 8:07 AM, a217 wrote: >> I have a dataframe in the general format: >> >> chr1 0.5 >> chr1 0 >> chr1 0.75 >> chr2 0 >> chr2 0 >> chr3 1

Re: [R] position of the end of a text file

2011-10-17 Thread R. Michael Weylandt
Couldn't you also just count the number of characters with nchar()? Michael Weylandt On Oct 17, 2011, at 1:57 AM, Henri-Paul Indiogine wrote: > I think I have it and my apologies for spamming the list. I should > not work this late on Sunday :-) > > I think that it should be > > as.integer(r

[R] [Reading mat files into R]

2011-10-17 Thread Beata Kafel-Mitka
Dear R users, I work with Matlab & R simultaneously. Usually I used to read successfully mat files (cell, structure, etc.) into R, till Matlab 2011b release. For reading mat files (or maybe I should say, converting it into R variable or structure) I’m using *readMat* (from “R.matlab” package)

Re: [R] position of first and last axis tick

2011-10-17 Thread Jonas Stein
>> how can i set the position of the first and last tick to the >> borderline of a plot? >> >> The plot should look like this one made in Gnuplot [1]. >> Gnu-R adds some space between the ticks and the end of plot. > > do you mean like this? > > plot(rnorm(25),rnorm(25), xaxs ="i", yaxs="i", xlim=

[R] Trojan in setup file

2011-10-17 Thread Annette Prochnow
Hello, I have the following problem: I successfully installed R (Version 2.1.3.0 for Windows) on my Notebook (Windows 7) in June. Now I used the same setup file for a PC (Windows XP) and got a message from the anti virus software (Avira), that the setup file contains the Trojan "TR/ATRAPS.G

Re: [R] Histogram for each ID value

2011-10-17 Thread Sarah Goslee
Hi, On Mon, Oct 17, 2011 at 8:07 AM, a217 wrote: > I have a dataframe in the general format: > > chr1 0.5 > chr1 0 > chr1 0.75 > chr2 0 > chr2 0 > chr3 1 > chr3 1 > chr3 0.5 > chr7 0.75 > chr9 1 > chr9 1 > chr22 0.5 > chr22 0.5 Using dput to give us some reproducible data would be even better.

Re: [R] binomial GLM quasi separation

2011-10-17 Thread Gavin Simpson
On Sat, 2011-10-15 at 09:11 -0700, lincoln wrote: > #Uwe: > #Gavin: > > I have read carefully your thread but I am not sure to understand what you > are suggesting (my gaps in statistics!). You say that it should be due to > the /Hauck Donner/ effect and that it is not a quasi separation or > sep

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