[R] question

hello can you explain to me about package shapes in R software? especially about order procGPA? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] question about heatmap.2, controlling the visual heights of two dendrograms

Hi, I have a question for gplots function heatmap.2. In this function, is there any way to control/know the heights of two dendrograms, such as how many pixels or how many percentage of the whole image the dendrogram have? I need to know the coordinates of northwest corner of real heatmap in the

Re: [R] Control y axis

Hi, The bracket after lty=1 should be replaced with comma (,).  x-1:15  y--8:6  plot(x, y, type =o, xlab=Panelist, ylab=T value,lwd=1.5,lty=1,xlim=range(1:14),ylim=range(-8:8),las=1) A.K. - Original Message - From: stefaniewind wind.stefa...@gmail.com To: r-help@r-project.org Cc:

Re: [R] library XML in R version 2.15.1

HI, I have XML library installed in R2.15 and is working fine.  I used it only a few times, it was working.  I am using Ubuntu 12.04. A.K. - Original Message - From: Santosh santosh2...@gmail.com To: r-help r-help@r-project.org Cc: Sent: Friday, July 20, 2012 11:03 PM Subject: [R]

Re: [R] GOstats: get genes for corresponding enriched GO term

Hello, I guess this should be posted in the bioconductor mailing list to get better response.  I never used Gostats before, but I think BINGO and DAVID are very good in giving these information. I would choose BINGO plugin in cytoscape installed.  But, you may have specific reasons to use

Re: [R] Control y axis

Hi, You can try this:  x-1:15  y--8:6   plot(x, y, type =o, xlab=Panelist, ylab=T value,lwd=1.5,axes=FALSE) axis(1,at=c(0,2,4,6,8,10,12,14,16)) axis(2,at=c(-8,-6,-4,-2,0,2,4,6,8)) A.K. From: Stefanie Wind wind.stefa...@gmail.com To: arun smartpink...@yahoo.com

Re: [R] fitting Ornstein-Uhlenbeck process by MAXIMUM LIKELYHOOD

Hello, When computing Sxx, Syy and you are mistaking the square of the sum for the sum of squares. The same goes for the crossed term Sxy, it's the sum of the products, not the product of the sums Sx and Sy. Hope this helps, Rui Barradas Em 20-07-2012 23:04, cesare orsini escreveu: Dear

Re: [R] qplot/ggplot

Hello, You can try either one of these methods:: #Simple line plot dat1-read.table(text= Gene1 10 14 12 23 11 11 33 1 Gene2 4 2 1 1 3 4 1 2 Gene3 2 5 7 5 6 89 7 3 Gene4 1 9 8 3 90 8 8 5 ,sep=,header=FALSE,stringsAsFactors=FALSE) dat2-as.data.frame(t(dat1[,-1]))  

Re: [R] library XML in R version 2.15.1

Hi, So, you got the same error message for R 2.14.1 and R 2.15? Or is it only for R 2.15? It is always good to install the current version.  Try this: install.packages(XML,dependencies=TRUE) #Warning message suggests dependencies. A.K. - Original Message - From: Santosh

Re: [R] question

On Saturday, July 21, 2012, Mehrab Nodehi wrote: hello can you explain to me about package shapes in R software? especially about order procGPA? Not unless you read the posting guide and formulate a more specific question. Sarah -- Sarah Goslee http://www.stringpage.com

Re: [R] information

On 07/18/2012 09:11 PM, Karan Anand wrote: hi, i am new to using R, so if u can help me in merging my csv file having different sheets .if u can help me with the commands for it. Hi karan, I didn't see an answer for your question. If you are reading in several CSV files with the same

[R] alternative to rbind for data.table

Hi I want to add a row to a data.table in each round of a for loop. rbind seems to be a inefficient way to implement this. How would you do this? The slow solution: library(data.table) Rprof(test.out) dt - data.table() for (i in (1:1)) { # algorithm that generates a list with different

Re: [R] 'symbols' not plotting correct circle radii

On 07/20/2012 12:33 AM, Stuart Leask wrote: You're right - easily tested by just re-sizing the graphics box - sort of counter-intuitive until I remember the clue is in the name - this generates a CIRCLE, come what may... Stuart From: Sarah Goslee [mailto:sarah.gos...@gmail.com] Sent: 19 July

Re: [R] Speeding up a loop

next for loop question. I need a loop that removes a row from a matrix if it is worse in positions 1,2,3,4 than another row in the matrix. right now my matrix is 503028x26. Rule to define worse position1 is smaller, position2 is smaller, position3 is higher, and position4 is smaller Example:

[R] EM for missing data

Hi list, I am wondering if there is a way to use EM algorithm to handle missing data and get a completed data set in R? I usually do it in SPSS because EM in SPSS kind of fill in the estimated value for the missing data, and then the completed dataset can be saved and used for further

[R] combined EM dataset for missing data?

Hi list, I am wondering if there is a way to use EM algorithm to handle missing data and get a completed data set in R? I usually do it in SPSS because EM in SPSS kind of fill in the estimated value for the missing data, and then the completed dataset can be saved and used for further

Re: [R] changing cex pointwise in lattice

I'm sorry I misunderstood your original request. You're right, use subscripts for panel-specific argument values. Peter Ehlers On 2012-07-20 19:35, José M. Blanco Moreno wrote: Sorry about that, when I asked before I meant that I had tried your proposed syntax. That has a problem, and it is

Re: [R] combined EM dataset for missing data?

Search yourself! 1. Google on Impute missing data in R 2. See the ?RSiteSearch function 3. Go to Rseek.org and enter in keywords. 4. Download and install the sos package and use its search functionality. R has multiple packages and functions with multiple approaches to missing data imputation.

[R] deactivate my account from your members

please don't send email to this email address: mehdi.p...@gmail.com lots of thanks [[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

Re: [R] Speeding up a loop

Hello, Maybe it would have been better to start a new thread, if the question is different. To show that it's a continuation, the subject line could be extended with part 2 or something like that. This solution runs in 3.6 hours. to.keep - function(x){ keep - function(i, env){

Re: [R] overlay contourplot with labels over spplot with color regions?

Martin Ivanov tramni at abv.bg writes: Dear R users, I have the following problem. I plot a SpatialPixelsDataFrame object with spplot and I need to add a contourplot of another spatial variable. ... You may find that posting to R-sig-geo will help. It would also help to include a

Re: [R] alternative to rbind for data.table

You need to preallocate. [See the R Inferno] n - 1 dt - as.data.table(matrix(0, nrow = n, ncol = 5)) for(i in seq_len(n)){ dt[i, ] - ### Whatever } Note that this *might* be somewhat trickier with data.tables and their fancy indexing. It might be easier to simply assign into the matrix

Re: [R] EM for missing data

Hello Ya. I am no expert, so I am eager to read suggestions from other people in the mailing list. But just a few pointers I am (somewhat) sure of - You can try using this package: http://cran.r-project.org/web/packages/imputation/imputation.pdf And use something like kNNImpute. KNN solving is

Re: [R] FIML using lavaan returns zeroes for coefficients

On 07/20/2012 10:35 PM, Andrew Miles wrote: Hello! I am trying to reproduce (for a publication) analyses that I ran several months ago using lavaan, I'm not sure which version, probably 0.4-12. A sample model is given below: pathmod='mh30days.log.w2 ~ mh30days.log + joingroup + leavegroup +

Re: [R] Speeding up a loop

Any chance I could ask for an idiots guide for function to.keep(x). I understand how to use it but not what some of the lines are doing. Comments would be extremely helpful. -- View this message in context: http://r.789695.n4.nabble.com/Speeding-up-a-loop-tp4637201p4637316.html Sent from the R

Re: [R] Speeding up a loop

Ok, sorry, I should have included some comments. The function is divided in three parts, 1. intro, 2. decision, 3. keep rows. Part 3 is the function keep(), internal to to.keep(). Let's start with 1. 1. Setup some variables first. 1.a) The variables 'a'. If the input object 'x' is a matrix

Re: [R] combined EM dataset for missing data?

It is not clear what you actually want. Do you want to save imputed data sets for further analysis? That is pretty simple. What do you mean by combining the data sets? Are you confusing single imputation with multiple imputation? In addition to the packages you mentioned, there are many others.

[R] contour line labels in trellis contourplot

Hello, In the classical function contour labels are drawn so that each contour line is broken at the place of the label, so that the label does not overlap the line. In the trellis contoourplot the labels are placed beside or over the line, controlled by the label.style parameter, but I could

Re: [R] EM for missing data

The EM algorithm does not impute missing data, rather it estimates parameters when you have missing data (those parameters can then be used to impute the missing values, but that is separate from the EM algorithm). If you create a dataset that has missing values imputed (a single time) and then

[R] two questions re: the use of lattice

Dear friends, I have two questions regarding the use of lattice. First some code: ## begin code z - cbind(rep(c(BIC, ICL, s_v, Q_v, sig-q, s_lsk, s_lML, s_mlsk, s_mlML, s_la8, s_haar), each = 250), rep(c(5, 10, 20, 30, 50), each = 50)) z - rbind(cbind(z, 0), cbind(z, 20),

Re: [R] combined EM dataset for missing data?

Thanks Bert. So far I have not found any way that output a single data set which combines all the imputed data sets (say, 50 imputed data sets). Probably I missed something, but could you share some information about it, maybe a link? Thank you very much for helping. ya From: Bert Gunter

[R] car::Anova - Can it be used for ANCOVA with repeated-measures factors.

Dear list, I would like to run an ANCOVA using car::Anova with repeated measures factors, but I can't figure out how to do it. My (between-subjects) covariate always interacts with my within-subject factors. As far as I understand ANCOVA, covariates usually do not interact with the effects of

Re: [R] Control y axis

Hi, No problem. I was gettting -8 and 6 for the code I sent to you.  I am using R 2.15.  This code gets -8 and 8 for the y axis:  x-1:17 y- -8:8    plot(x, y, type =o, xlab=Panelist, ylab=T value,lwd=1.5,axes=FALSE) axis(1,at=c(0,2,4,6,8,10,12,14,16,18))

Re: [R] deactivate my account from your members

Hello, Probably, you didn't know about this option.  You could deactivate your membership from Rhelp by clicking on the link below i.e (https://stat.ethz.ch/mailman/listinfo/r-help). A.K. - Original Message - From: mehdi azizi mehdi.p...@gmail.com To: R-help@r-project.org Cc: Sent:

[R] Library control

All, 1. Is there a command that tells you what libraries are loaded? 2. How do you remove a library that has been loaded? 3. If you have loaded a library that masks previously loaded objects, how can you tell which object is being run? In Matlab, I would run which f to determine the location of

Re: [R] Library control

They are called packages, not libraries. On Jul 21, 2012, at 5:19 PM, darnold dwarnol...@suddenlink.net wrote: All, 1. Is there a command that tells you what libraries are loaded? Loaded is a fluid idea** in a namespace world, but search() will let you know what's on the search path

Re: [R] two questions re: the use of lattice

Answer to you first question, try this at the start of bwplot to specify ordering: bwplot(Error~factor(Method, levels = unique(Method)) On Sat, Jul 21, 2012 at 2:42 PM, Ranjan Maitra maitra.mbox.igno...@inbox.com wrote: Dear friends, I have two questions regarding the use of lattice. First

Re: [R] Control y axis

Using x/yaxp also works: plot(x, y, type =o, xlab=Panelist, ylab=T value, lwd=1.5, xaxp=c(0, 18, 9), yaxp=c(-8, 8, 8), las=1) -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352

[R] rhsape2 bug?

All, I believe I am running the latest version of rshape2 (1.2.1). But this code: library(reshape2) tmp - melt(smiths, id.vars=1:2, measure.vars=c(age,weight,height), variable.name=myvars, value.name=myvals ) names(tmp) Produces this output: names(tmp) [1] subject time

[R] memory size

Dear R community, I'm running a mlogit function with a very large data set. Since the data size is so large, I got the Error: Error: cannot allocate vector of size 5.4 Mb In addition: Warning messages: 1: In mapply(*, X, P, SIMPLIFY = FALSE) : Reached total allocation of 16340Mb: see

Re: [R] rhsape2 bug?

Hi David, Your example works as expected for me (see sessionInfo below). What version of R are you using? What other packages are loaded? R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8

Re: [R] two questions re: the use of lattice

Run this before the bwplot() command: z$Method - factor(z$Method, levels = c(BIC, ICL, s_v, Q_v, sig-q, s_lsk, s_lML, s_mlsk, s_mlML, s_la8, s_haar)) I don't have an answer for the 2nd question. Seems like it must be possible. -- David L Carlson

Re: [R] rhsape2 bug?

Ista, You are correct. search() [1] .GlobalEnvpackage:reshape package:plyr [4] package:reshape2 tools:rstudio package:stats [7] package:graphics package:grDevices package:utils [10] package:datasets package:methods Autoloads [13] package:base Thanks.

Re: [R] two questions re: the use of lattice

Take a look at useOuterStrips() in package latticeExtra. --- David -Original Message- From: David L Carlson [mailto:dcarl...@tamu.edu] Sent: Saturday, July 21, 2012 6:51 PM To: 'jim holtman'; 'Ranjan Maitra' Cc: 'r-help@r-project.org' Subject: RE: [R] two questions re: the use

[R] Excel file Import - to Matrix format

Hi, New to R. Need a bit of help. Thanks I am trying to import data from Excel file. The package I am trying to use requires data in Matrix format. Excel - R Matrix with the constraint that the very first column in Excel file should became the names for rows of the matrix. Example. Data has

Re: [R] memory size

There are many possibilities, but they all begin with reading the posting guide and following the recommendations therein so we don't have to guess what your actual configuration is. However, since your first task is to read, you might consider reading the FAQs on memory use and Windows