Re: [R] ddply to count frequency of combinations

Brian, I'm a bit confused about how the following line works, specifically, what is happening in freq=length(x)? Is it just taking the length of x after it has been summarized by different combinations x & y? I guess that must be the case, because that gives the same result as using freq=length(y)

Re: [R] Saved EPS does not match screen when using bquote(.(i))

Hi: As Uwe suggested... pdf('testgraph.pdf') layout( matrix( 1:2 , nrow=2 ) ) for ( i in 1:2 ) { plot( 0 , 0 , xlab=bquote(mu[.(i)]) ) } dev.off() postscript('testgraph.ps') layout( matrix( 1:2 , nrow=2 ) ) for ( i in 1:2 ) { plot( 0 , 0 , xlab=bquote(mu[.(i)]) ) } dev.off() png('testgrap

Re: [R] Hardy Weinberg

On Wed, 22 Jun 2011, Jim Silverton wrote: I am generating 1,000 replicates of 10,000 of these 2 x 3 tables but R cannot seem to save it. Its over 1 Gig. Any ideas on how I can store this large amount of data? Should I use a list or a matrix? Is English your first language? If so, you can pro

Re: [R] Hardy Weinberg

On Jun 22, 2011, at 11:57 PM, Jim Silverton wrote: I am generating 1,000 replicates of 10,000 of these 2 x 3 tables but R cannot seem to save it. What does that mean? Error messages? Its over 1 Gig. Any ideas on how I can store this large amount of data? Should I use a list or a matrix? H

Re: [R] Hardy Weinberg

I am generating 1,000 replicates of 10,000 of these 2 x 3 tables but R cannot seem to save it. Its over 1 Gig. Any ideas on how I can store this large amount of data? Should I use a list or a matrix? Jim On Wed, Jun 22, 2011 at 10:21 PM, Mike Miller wrote: > On Thu, 23 Jun 2011, David Duffy wro

Re: [R] lme convergence failure within a loop

I am not an expert in this. But try try() :) hth, Daniel Sam Nicol wrote: > > Hi R-users, > > I'm attempting to fit a number of mixed models, all with the same > structure, across a spatial grid with data points collected at various > time points within each grid cell. I'm trying to use a

[R] Saved EPS does not match screen when using bquote(.(i))

Here's a fairly minimal-case example in which the saved EPS does not match the screen. The error comes when using bquote(.(i)) instead of bquote(1), as demonstrated by the two minimally different cases below. Very strange. Any clues as to why? # begin --- # Version

Re: [R] Time-series analysis with treatment effects - statistical approach

If you have any specific features of the time series of soil moisture, you could either model that or directly estimate it and test for differences in the 4 treatments. If you do not have any such specific considerations, you might want to consider some nonparametric approaches such as function

Re: [R] numerical integration and 'non-finite function value' error

In the limit as x goes to infinity, the integrand x f(x) should go to 0 sufficiently fast in order for the integral to be finite. The error indicates that the integrand becomes infinite for large x. Check to ensure that the integrand is correctly specified. I don't understand how you can repla

Re: [R] Problem with mclapply -- losing output/data

Hi Elizabeth, I just found your thread after experiencing a similar problem (I was also using some IRanges/GenomicRanges functions). You've probably figured it out by this time - I'm actually curious to know what you found? I think I've tracked it down in my case, where a small minority of the

Re: [R] Subsetting data systematically

Tena koe Nate You can use the fact that R recycles. If yourData is a dataframe, then (as examples): yourData[c(TRUE,FALSE),] will give you every second row, starting with the first. Similarly, yourData[c(FALSE,TRUE,FALSE),] will give every third row, starting with the second; and yourData[c(

Re: [R] Hardy Weinberg

On Thu, 23 Jun 2011, David Duffy wrote: I am interested in simulating 10,000 2 x 3 tables for SNPs data with the Hardy Weinberg formulation. Is there a quick way to do this? I am assuming that the minor allelle frequency is uniform in (0.05, 0.25). rmultinom() with HWE expectations I'm als

Re: [R] BY GROUP IN GEV

I am trying to run gev (general extreme value) function in “evir” package. My data is divided by state. I am using the following codes but it is not working. I will appreciate any help.   #Split data MAS <- split(MA, MA$states)   CP  <- lapply(MAS, function(x){gev(MAS$CP1, 100, method = "BFGS", c

[R] lme convergence failure within a loop

Hi R-users, I'm attempting to fit a number of mixed models, all with the same structure, across a spatial grid with data points collected at various time points within each grid cell. I'm trying to use a 'for' loop to try the model fit on each grid cell. In some cells lme does not converge, g

[R] Subsetting data systematically

I would like to subset data from a larger dataset and generate a smaller dataset. However, I don't want to use sample() because it does it randomly. I would like to take non-random subsamples, for example, every 2nd number, or every 3rd number. Is there a procedure that does this? Thanks, Nate

[R] numerical integration and 'non-finite function value' error

Dear R users, I have a question about numerical integration in R. I am facing the 'non-finite function value' error while integrating the function xf(x) using 'integrate'. f(x) is a probability density function and assumed to follow the three parameter (min = 0) beta

Re: [R] Time-series analysis with treatment effects - statistical approach

> Date: Wed, 22 Jun 2011 17:21:52 -0700 > From: jmo...@student.canterbury.ac.nz > To: r-help@r-project.org > Subject: Re: [R] Time-series analysis with treatment effects - statistical > approach > > Hi Mike, here's a sample of my data so that you get an idea what I'm working > with. Thanks,

Re: [R] Re; Getting SNPS from PLINK to R

Resending to correct bad subject line... On Mon, 20 Jun 2011, Jim Silverton wrote: I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? All the SNPs you hav

Re: [R] several messages

On Mon, 20 Jun 2011, Jim Silverton wrote: I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? All the SNPs you have are listed in the .map file. An easy way

Re: [R] plotmath: unexpected SPECIAL

Dennis, Thanks. That makes sense, but I don't think it's clearly documented. The default assumption that I and at least some others in this discussion made is that everything in the list of plotmath features in the helpfile works the same way, since they're all in the same list. And if for some o

Re: [R] plotmath: unexpected SPECIAL

Hi: >From the plotmath help page: x %->% y x right-arrow y so this is behaving like a binary operator. There happen to be several of these in plotmath On Wed, Jun 22, 2011 at 5:49 PM, Sarah Goslee wrote: > Interesting. I don't know the explanation, but look at this: > # works > plot(1:

Re: [R] plotmath: unexpected SPECIAL

Thanks to both David and Sarah. I'm glad I asked, as I had tried some of the combos Sarah suggested and observed the same behavior, which puzzled me. David, thanks for reminding me about ~ as that is a different way to get a space into the string. I just don't use plotmath often enough t

Re: [R] plotmath: unexpected SPECIAL

On Jun 22, 2011, at 8:10 PM, Bryan Hanson wrote: Hello R Masters and the Rest of Us: The first of these works fine, the 2nd is accepted but too literal (the "%->%" is shown in the plot label and in the wrong position). The 3rd throws and error due to "unexpected SPECIAL". Would someone

Re: [R] plotmath: unexpected SPECIAL

Interesting. I don't know the explanation, but look at this: # works plot(1:10, 1:10, xlab=expression(a %->% b)) # doesn't work plot(1:10, 1:10, xlab=expression(%->%)) # works plot(1:10, 1:10, xlab=expression(paste("something" %->% "else"))) # doesn't work plot(1:10, 1:10, xlab=expression(paste("s

Re: [R] Time-series analysis with treatment effects - statistical approach

Hi Mike, here's a sample of my data so that you get an idea what I'm working with. http://r.789695.n4.nabble.com/file/n3618615/SampleDataSet.txt SampleDataSet.txt Also, I've uploaded an image showing a sample graph of daily soil moisture by treatment. The legend shows IP, IP+, PP, PP+ which are

[R] plotmath: unexpected SPECIAL

Hello R Masters and the Rest of Us: The first of these works fine, the 2nd is accepted but too literal (the "%->%" is shown in the plot label and in the wrong position). The 3rd throws and error due to "unexpected SPECIAL". Would someone recommend a way to format this? I want the two phr

Re: [R] Fantastic! So many interesting and useful!

http://bakaneko.fr/friends.page.php?igjhotmailID=28aq2 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the post

Re: [R] question about read.columns

On Wed, Jun 22, 2011 at 7:07 PM, Changbin Du wrote: > INstalling of "RSQLite" was successful. > > in R: >> packageVersion("RSQLite") > [1] '0.9.4' > > > > When I try to install "sqldf", I found the following errors: > >> install.packages("sqldf") > Installing package(s) into '/house/homedirs/c/cdu

Re: [R] question about read.columns

INstalling of "RSQLite" was successful. in R: > packageVersion("RSQLite") [1] '0.9.4' When I try to install "sqldf", I found the following errors: > install.packages("sqldf") Installing package(s) into '/house/homedirs/c/cdu/library/' (as 'lib' is unspecified) trying URL 'http://cran.cnr.Berke

Re: [R] question about read.columns

I will try this first. Thanks, Gabor! On Wed, Jun 22, 2011 at 3:15 PM, Gabor Grothendieck wrote: > On Wed, Jun 22, 2011 at 6:10 PM, Changbin Du wrote: > > My R is 2.12.0. > > > >> R.version.string > > [1] "R version 2.12.0 (2010-10-15)" > >> packageVersion("RSQLite") > > [1] '0.8.0' > >> pac

Re: [R] question about read.columns

On Wed, Jun 22, 2011 at 6:10 PM, Changbin Du wrote: > My R is 2.12.0. > >> R.version.string > [1] "R version 2.12.0 (2010-10-15)" >> packageVersion("RSQLite") > [1] '0.8.0' >> packageVersion("sqldf") > [1] '0.3.5' > > So it seems I have to update or install the 2.13.0 version in my linux > machine

Re: [R] question about read.columns

My R is 2.12.0. > R.version.string [1] "R version 2.12.0 (2010-10-15)" > packageVersion("RSQLite") [1] '0.8.0' > packageVersion("sqldf") [1] '0.3.5' So it seems I have to update or install the 2.13.0 version in my linux machine. On Wed, Jun 22, 2011 at 3:04 PM, Gabor Grothendieck wrote: >

Re: [R] question about read.columns

On Wed, Jun 22, 2011 at 6:01 PM, Changbin Du wrote: > I found the following errors: > > >> library(sqldf) > Loading required package: DBI > Loading required package: RSQLite > Loading required package: RSQLite.extfuns > Error: package 'RSQLite' 0.8-0 is loaded, but >= 0.9.1 is required by > 'RSQLi

Re: [R] question about read.columns

I found the following errors: > library(sqldf) Loading required package: DBI Loading required package: RSQLite Loading required package: RSQLite.extfuns *Error: package 'RSQLite' 0.8-0 is loaded, but >= 0.9.1 is required by 'RSQLite.extfuns'* > hh<-read.csv.sql("/house/homedirs/c/cdu/operon/gh5/

Re: [R] question about read.columns

Hi, Gabor, Thanks so much, I will try it and let you know the results. Appreciated! On Wed, Jun 22, 2011 at 2:54 PM, Gabor Grothendieck wrote: > On Wed, Jun 22, 2011 at 5:45 PM, Changbin Du wrote: > > HI, Dear R community, > > > > I have a large data set names dd.txt, the columns are: there

Re: [R] Hardy Weinberg

I am interested in simulating 10,000 2 x 3 tables for SNPs data with the Hardy Weinberg formulation. Is there a quick way to do this? I am assuming that the minor allelle frequency is uniform in (0.05, 0.25). rmultinom() with HWE expectations __ R-

Re: [R] question about read.columns

On Wed, Jun 22, 2011 at 5:45 PM, Changbin Du wrote: > HI, Dear R community, > > I have a large data set names dd.txt, the columns are: there are 2402 > variables. > > a1, b1, ..z1, a11, b11, ...z11, a111, b111, ..z111.. > > IF I dont know the relative position of the columns, but I know I need the

[R] question about read.columns

HI, Dear R community, I have a large data set names dd.txt, the columns are: there are 2402 variables. a1, b1, ..z1, a11, b11, ...z11, a111, b111, ..z111.. IF I dont know the relative position of the columns, but I know I need the following variables: var<-c(a1, c1,a11,b11,f111) Can I use read.

Re: [R] Appending to list

You lost me with the TRN and TRN_CLUSTER bits, but are you trying to make a list of lists? > Data_ <- list() > SN <- 1:12 > for(sn in SN) { + Data_[[sn]] <- list() + for(i in 1:10) { + Data.X <- rnorm(5, 0, 10) + Data_[[sn]][[i]] <- Data.X + }} > > Data_[[3]][[2]] [1] -5.687070 -2.365589 12.378359

Re: [R] Unreasonable syntax error

I second the fortune nomination, probably the 1st paragraph is sufficient for a fortune. -- 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-bounces@r-

Re: [R] Factor Analysis with orthogonal and oblique rotation

Varimax is orthogonal, promax is oblique. Varimax is generally not recommended. See: Preacher, K. J., & MacCallum, R. C. (2003). Repairing Tom Swift's electric factor analysis machine. Understanding Statistics, 2(1), 13-43. (Google the title and you'll find a PDF). The fa() function in the psy

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 4:09 PM, Brian Diggs wrote: > On 6/22/2011 1:37 PM, Alexander Shenkin wrote: >> On 6/22/2011 3:34 PM, Brian Diggs wrote: >>> On 6/22/2011 12:09 PM, Luke Miller wrote: For what it's worth, I cannot reproduce this problem under a nearly identical instance of R (R 2.12.1, Win 7

[R] Factor Analysis with orthogonal and oblique rotation

Hello I seem to find only two types of rotation for the factanal function in R, the Varimax and Promax, but is it possible to run a orthogonal and oblique rotations in R? Thanks in advance Rosario __ R-help@r-project.org mailing list https://stat.ethz.

Re: [R] mlogit model that contains both individual-specific parameters and universal parameters

On Wed, 22 Jun 2011, Quang Anh Duong wrote: Hello,? I am pretty new to mlogit, and still trying to figure out what models to use.I have a data set of N individuals, each of which faces I alternatives. The utility function of individual n, for choice i is:? u(i,n) = alpha(i) * x1(i,n) + beta

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 1:37 PM, Alexander Shenkin wrote: On 6/22/2011 3:34 PM, Brian Diggs wrote: On 6/22/2011 12:09 PM, Luke Miller wrote: For what it's worth, I cannot reproduce this problem under a nearly identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't reproduce the problem with R 2

[R] AIC() vs. mle.aic() vs. step()?

I know this a newbie question, but I've only just started using AIC for model comparison and after a bunch of different keyword searches I've failed to find a page laying out what the differences are between the AIC scores assigned by AIC() and mle.aic() using default settings. I started by usin

[R] Appending to list

So im here now b/c im incredibly frustrated. Please consider the following: #Try 1 Data_<-list() Sn<-1:12 for(sn in Sn){ for(i in 1:10){ Data.X <- rnorm(100,0,10) Data_[[paste(sn,i,sep="-")]]<-Data.X } } ##Try 2 Data_<-list() Sn<-1:12 for(sn

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 1:23 PM, William Dunlap wrote: The isdst value -1 doesn't seem right. Shouldn't it be either 0 (not daylight savings time) or 1 (yes dst)? I've only seen isdst==-1 when all the other entries were NA (that happens when the string doesn't match the format). A isdst of -1 indicates t

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 3:34 PM, Brian Diggs wrote: > On 6/22/2011 12:09 PM, Luke Miller wrote: >> For what it's worth, I cannot reproduce this problem under a nearly >> identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't >> reproduce the problem with R 2.13.0. You've got something truly weird

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 12:09 PM, Luke Miller wrote: For what it's worth, I cannot reproduce this problem under a nearly identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't reproduce the problem with R 2.13.0. You've got something truly weird going on with your particular instance of R. is

Re: [R] strange date problem - May 3, 1992 is NA

Wow. Setting my timezone to UTC -5 Bogota (where there is no daylight savings time), I get the error: > is.na(strptime("5/3/1992", format="%m/%d/%Y")) [1] TRUE But setting it to UTC -5 East Coast Time (whether or not I tell windows to adjust for DST) I get: > is.na(strptime("5/3/1992", format="

Re: [R] strange date problem - May 3, 1992 is NA

I can reproduce your problem when using a time that doesn't exist because it is between 2am and 3am on the Sunday that we switch from winter time to summer time: > z <- strptime(paste(paste(sep="/", 4, 5, 1992), "2:30"), format="%m/%d/%Y %H:%M") > z [1] "1992-04-05 02:30:00" > is.na(z) [1] TRUE >

Re: [R] strange date problem - May 3, 1992 is NA

The isdst value -1 doesn't seem right. Shouldn't it be either 0 (not daylight savings time) or 1 (yes dst)? I've only seen isdst==-1 when all the other entries were NA (that happens when the string doesn't match the format). In the parts of the US where daylight savings time is used the switchove

Re: [R] setting 'layout' locally within functions

Hi On 23/06/2011 2:58 a.m., Simon Goodman wrote: Using layout I've created a function that makes a 2 panel plot - comprising a main plot, and a sub-panel with custom legend. I would now like to use layout to create multiple panels with plots created by my function, however the values for layout

Re: [R] Package warnings

Thanks all the issue is closed. in this case I had a data element FILE.PARAMETERS = list() the .Rd files created by package.skelton() for data objects had the following for \usage. \usage{data(FILE.PARAMETERS)} I left that as is and CHECK throws a warning. "checking for code/d

[R] mlogit model that contains both individual-specific parameters and universal parameters

Hello,  I am pretty new to mlogit, and still trying to figure out what models to use.I have a data set of N individuals, each of which faces I alternatives. The utility function of individual n, for choice i is:  u(i,n) = alpha(i) * x1(i,n) + beta * x2(i,n)  where alpha(i) is the individual sp

[R] caret's Kappa for categorical resampling

Hello, When evaluating different learning methods for a categorization problem with the (really useful!) caret package, I'm getting confusing results from the Kappa computation. The data is about 20,000 rows and a few dozen columns, and the categories are quite asymmetrical, 4.1% in one category a

Re: [R] Linking 2 columns in 2 databases and applying a function

Daniel, That indeed does work... and I didn't even need to learn a new function. Thanks! -- Ryan Utz, Ph.D. Aquatic Ecologist/STREON Scientist National Ecological Observatory Network Home/Cell: (724) 272-7769 Work: (720) 746-4844 ext. 2488 [[alternative HTML version deleted]] ___

Re: [R] strange date problem - May 3, 1992 is NA

For what it's worth, I cannot reproduce this problem under a nearly identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't reproduce the problem with R 2.13.0. You've got something truly weird going on with your particular instance of R. > is.na(strptime("5/3/1992", format="%m/%d/%Y")

Re: [R] Linking 2 columns in 2 databases and applying a function

1st of all Dr Utz, thanks for your recent pubs on regional differences between the piedmont and coastal plain streams. and to add to Daniels post (giving your binary yes/no): df<-merge(x,y,all.x=T,all.y=F) df["exceed"] <- ifelse(df$Q>df$Threshold_Q , 1, 0) ## now look at df df Daniel Mal

Re: [R] Documenting variables, dataframes and files?

The memisc package also offers functionality for documenting data. Jan On 06/22/2011 04:57 PM, Robert Lundqvist wrote: Every now and then I realize that my attempts to document what all dataframes consist of are unsufficient. So far, I have been writing notes in an external file. Are there an

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 1:34 PM, Sarah Goslee wrote: > On Wed, Jun 22, 2011 at 2:28 PM, David Winsemius > wrote: >> >> On Jun 22, 2011, at 2:03 PM, Sarah Goslee wrote: >> >>> Hi, >>> >>> On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin >>> wrote: > > is.na(strptime("5/2/1992", format="%m/%d/%Y")

Re: [R] Help Needed on Merging Columns by Summation

I assume that you are working in package MatrixCalc. Let’s say you have a matrix X. You can call the columns of X this way: X[,1] for the first column X[,2] for the second column X[,3] for the third column Etc. So let’s say that you want to add the first and third column, then you would just

Re: [R] strange date problem - May 3, 1992 is NA

On Wed, Jun 22, 2011 at 2:28 PM, David Winsemius wrote: > > On Jun 22, 2011, at 2:03 PM, Sarah Goslee wrote: > >> Hi, >> >> On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin >> wrote: is.na(strptime("5/2/1992", format="%m/%d/%Y")) >>> >>> [1] FALSE is.na(strptime("5/3/1992",

Re: [R] Linking 2 columns in 2 databases and applying a function

For example, you can merge the two data frames and do a direct comparison: df<-merge(x,y,all.x=T,all.y=F) df df$Q>df$Threshold_Q HTH, Daniel Ryan Utz-2 wrote: > > Hi all, > > I have two datasets, one that represents a long-term time series and one > that represents summary data for the time

Re: [R] strange date problem - May 3, 1992 is NA

On Jun 22, 2011, at 2:03 PM, Sarah Goslee wrote: Hi, On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin wrote: is.na(strptime("5/2/1992", format="%m/%d/%Y")) [1] FALSE is.na(strptime("5/3/1992", format="%m/%d/%Y")) [1] TRUE I can't reproduce your problem on R 2.13.0 on linux: I als

Re: [R] strange date problem - May 3, 1992 is NA

On 6/22/2011 1:03 PM, Sarah Goslee wrote: > Hi, > > On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin wrote: >>> is.na(strptime("5/2/1992", format="%m/%d/%Y")) >> [1] FALSE >>> is.na(strptime("5/3/1992", format="%m/%d/%Y")) >> [1] TRUE > > I can't reproduce your problem on R 2.13.0 on linux: >

Re: [R] strange date problem - May 3, 1992 is NA

Hi, On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin wrote: >> is.na(strptime("5/2/1992", format="%m/%d/%Y")) > [1] FALSE >> is.na(strptime("5/3/1992", format="%m/%d/%Y")) > [1] TRUE I can't reproduce your problem on R 2.13.0 on linux: > strptime("5/2/1992", format="%m/%d/%Y") [1] "1992-05-0

[R] Linking 2 columns in 2 databases and applying a function

Hi all, I have two datasets, one that represents a long-term time series and one that represents summary data for the time series. It looks something like this: x<-data.frame(Year=c(2001,2001,2001,2001,2001,2001,2002,2002,2002,2002,2002,2002), Month=c(1,1,1,2,2,2),Q=c(5,5,5,6,6,6,3,3,3,4,4,5)) y<

Re: [R] binary in R

Jürg. It's not that nobody knows the answer, necessarily, it's that your inquiry is so vague we don't know what the *question* is, let alone the answer. We don't know anything about your data, your intended function and model, anything. A toy reproducible example with clear explanation would be

[R] strange date problem - May 3, 1992 is NA

> is.na(strptime("5/2/1992", format="%m/%d/%Y")) [1] FALSE > is.na(strptime("5/3/1992", format="%m/%d/%Y")) [1] TRUE Any idea what's going on with this? Running strptime against all dates from around 1946, only 5/3/1992 was converted as "NA". Even stranger, it still seems to have a value associa

[R] binary in R

Does really nobody has a coment to this question? Dear R-help members I would like to use the R package goalprog, weighted and lexicographical goal programming and optimization to optimize a location problem. In my model I need a "yes" or "no" decision - in this case, whether to select a site

[R] VAR with excluded lags

Hi, I would like to fit a Vector Auto Regression with lags that are not consecutive with the vars package (or other if there is one as good). Is it possible? For example, rather than having lags 1, 2, 3, 4, 5 have 1, 2, 5. Thanks. -- View this message in context: http://r.789695.n4.nabble.com

[R] VGAM constraints-related puzzle

Hello R users, I have a puzzle with the VGAM package, on my first excursion into generalized additive models, in that this very nice package seems to want to do either more or less than what I want. Precisely, I have a 4-component outcome, y, and am fitting multinomial logistic regression with one

Re: [R] Hardy Weinberg

H-W only gives you the expected frequency of AA, AB, and BB genotypes (i.e. a 1x3 table): minor <- runif(1, 0.05, 0.25) major <- 1-minor AA <- minor^2 AB <- 2*minor*major BB <- major^2 df <- cbind(AA, AB, BB) -Aaron On Tue, Jun 21, 2011 at 9:30 PM, Jim Silverton wrote: > Hello all, > I am

Re: [R] Documenting variables, dataframes and files?

Have a look at the AnnotatedDataFrame class in the Biobase package [1]. Here is the description from the manual: An ‘AnnotatedDataFrame’ consists of two parts. There is a collection of samples and the values of variables measured on those samples. There is also a description of each variable measu

Re: [R] Documenting variables, dataframes and files?

There is a 'comment' function. It sets an attribute which gets carried along with the dataframe when it is saved or copied: > df1 <-data.frame(NA) > df1 NA. 1 NA > comment(df1) <- "empty dataframe" > comment(df1) [1] "empty dataframe" > df2 <- df1 > comment(df2) <- c(comment(df1), "copy of d

Re: [R] Package warnings

Thanks Duncan, I'll join Dev and ask the questions over there. Steve On Wed, Jun 22, 2011 at 7:19 AM, Duncan Murdoch wrote: > On 11-06-21 11:58 PM, steven mosher wrote: > >> Thanks to all your help I've just finished my first package and I have a >> couple of questions >> >> >> >> I want to su

Re: [R] error using glmmML()

Tom, thanks for spotting a bug in glmmML; internally, glmmML sorts data by cluster. The bug is that I missed to sort the weights accordingly. Weights are produced when the response is a two-column matrix, as in your case. So, glmmML calls glm.fit with wrong weights, and the warning comes from that

Re: [R] analysing a three level reponse

The best method would probably be proportional odds regression using polyr() in 'MASS'. At least it's a starting point. At 09:19 AM 6/22/2011, Matt Ellis \(Research\) wrote: Hello, I am struggling to figure out how to analyse a dataset I have inherited (please note this was conducted some tim

[R] setting 'layout' locally within functions

Using layout I've created a function that makes a 2 panel plot - comprising a main plot, and a sub-panel with custom legend. I would now like to use layout to create multiple panels with plots created by my function, however the values for layout set in the function act globally, stopping me from

Re: [R] Setting up list of many equations for systemfit

Thanks for the suggestion, Dennis. Unfortunately, I was not able to make it work. Maybe I'm not using as.formula properly. I posted below some new things I tried. What am I doing wrong? Thanks for any feedback! Rita First attempt: > eqSystem2 <-paste(paste("form", 1:4, sep=""), as.formula(paste

[R] Documenting variables, dataframes and files?

Every now and then I realize that my attempts to document what all dataframes consist of are unsufficient. So far, I have been writing notes in an external file. Are there any better ways to do this within R? One possibility could be to set up the data as packages, but I would like to have a sol

Re: [R] How to add label to lines()

On Jun 21, 2011, at 10:31 AM, Nevil Amos wrote: I am plotting a number of lines on a standard plot. I would like to add labels at the end (rhs) of each line. is there a way to do this other than defining the individual xy coordinates and placing each label using text() Without an examp

Re: [R] Tricky (?) conversion from data.frame to matrix where not all pairs exist

On Jun 22, 2011, at 9:46 AM, Marius Hofert wrote: Hi David, thanks for the quick response. That's nice. Is there also a way without loading an additional package? I'd prefer loading less packages if possible. > xtb <- xtabs(value ~ year + block, data = df) > xtb block year a b c

Re: [R] analysing a three level reponse

You could analyze these data with a multinomial logit model, with an ordinal response. I don't have my copy handy, but I know that Agresti (Categorical Data Analysis, Wiley) covers these models. Cheers David Cross d.cr...@tcu.edu www.davidcross.us On Jun 22, 2011, at 8:19 AM, Matt Ellis (R

Re: [R] Package warnings

On 11-06-21 11:58 PM, steven mosher wrote: Thanks to all your help I've just finished my first package and I have a couple of questions I want to submit to CRAN but I have 1 warning " checking for code/documentation mismatches ... WARNING Data sets with usage in documentation object 'FI

Re: [R] Help Needed on Merging Columns by Summation

On Wed, Jun 22, 2011 at 2:35 AM, Nabila Binte Zahur wrote: > Dear Sirs/Madam, > > I am a beginner to R, and I am currently working on a data matrix which looks > like this: > >> head(oligo) > >        ko:K1 ko:K3 ko:K5 ko:K8 ko:K9 ko:K00010 ko:K00012 > AAA       370          6

Re: [R] How to add label to lines()

On 11-06-21 10:31 AM, Nevil Amos wrote: I am plotting a number of lines on a standard plot. I would like to add labels at the end (rhs) of each line. is there a way to do this other than defining the individual xy coordinates and placing each label using text() Probably, but what you describe

Re: [R] Tricky (?) conversion from data.frame to matrix where not all pairs exist

Hi David, thanks for the quick response. That's nice. Is there also a way without loading an additional package? I'd prefer loading less packages if possible. Cheers, Marius On 2011-06-22, at 15:38 , David Winsemius wrote: > > On Jun 22, 2011, at 9:19 AM, Marius Hofert wrote: > >> Hi, >>

Re: [R] Help Needed on Merging Columns by Summation

Hi: Based on the information you provided, I would suggest looking into the transform() and within() functions in base R, and perhaps the mutate() function in package plyr. HTH, Dennis On Tue, Jun 21, 2011 at 11:35 PM, Nabila Binte Zahur wrote: > Dear Sirs/Madam, > > I am a beginner to R, and I

[R] How to add label to lines()

I am plotting a number of lines on a standard plot. I would like to add labels at the end (rhs) of each line. is there a way to do this other than defining the individual xy coordinates and placing each label using text() Thanks Nevil Amos __ R-h

[R] How to plot 4 variable/distribution as tetrahedral

Dear all, I am a new user of R. I want use R to plot four momentum vectors(variable) in form of tetrahedral. The data(momentum vector) is in form of distribution(e.g. momentum of particle1 vs intensity). Thanks in advance. Best Regards Rajesh -- View this message in context: http://r.78969

[R] Help with winbugs code

Good afternoon sir, i'm a student in Indonesia who study technology management, i need to review the software i'v been develop, i was told to use bayesian SEM because i don't have large sample. i don't know much about statistics but i try to make a code via winbugs.. and a i got a problem. here i a

[R] analysing a three level reponse

Hello, I am struggling to figure out how to analyse a dataset I have inherited (please note this was conducted some time ago, so the data is as it is, and I know it isn't perfect!). A brief description of the experiment follows: Pots of grass were grown in 1l pots of standad potting medium for 1

[R] Help Needed on Merging Columns by Summation

Dear Sirs/Madam, I am a beginner to R, and I am currently working on a data matrix which looks like this: > head(oligo) ko:K1 ko:K3 ko:K5 ko:K8 ko:K9 ko:K00010 ko:K00012 AAA 370 631 365 67 164 455

Re: [R] Tricky (?) conversion from data.frame to matrix where not all pairs exist

On Jun 22, 2011, at 9:19 AM, Marius Hofert wrote: Hi, and what's the simplest way to obtain a *data.frame* with all years? The matching seems more difficult here because the years can/will show up several times... (df <- data.frame(year=c(2000, 2001, 2002, 2001, 2000, 2001),

Re: [R] Help interpreting ANCOVA results

I think you should write out your model formula and then go over it term by term to see which term adds what to your understanding of the data. If necessary, pick up a text about the interpretation of coefficients. For example, you will find that Reduction is not just the slope for the condition QF

Re: [R] Tricky (?) conversion from data.frame to matrix where not all pairs exist

Hi, and what's the simplest way to obtain a *data.frame* with all years? The matching seems more difficult here because the years can/will show up several times... (df <- data.frame(year=c(2000, 2001, 2002, 2001, 2000, 2001), block=c("a","a","a","b","c","c"), value=1:6)) (df.

[R] (no subject)

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