Re: [R] merge matrix row data

Hello arun Thanks for the answers. I understand the answer to question 2. However, about question 1, sorry I did not clarify the question. 1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID 2, and GID 3, is there any modification in need for the code ? The original

Re: [R] merge matrix row data

Hello Arun Thank for comments. You are right. GID is the first column in the matrix this time. In the second row of the first column, it used to be GID 1 in the first e-mail. But you are also right. You answered it already, and this time In the second row of the first column is 1. Below is

Re: [R] merge matrix row data

Hi Elaine, I am not sure how your original matrix keeps on changing from the original post.  Here, your statement about rownames are 1, 2, 4 (the answer I already provided in the last post) and the matrix you showed looks different.  It seems like GID is the first column in the matrix.  I

[R] EMMIX

Is the R package EMMIX available ? I tried installing it and it keeps saying the package is not available for R verseion 3.0.1 teotjunk [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] EMMIX

Hello, According to the list of available packages, there is no EMMIX package. You probably should use a web search engine to find where you can download a EMMIX version for R. Regards, Pascal 2013/8/1 Tjun Kiat Teo teotj...@gmail.com Is the R package EMMIX available ? I tried installing it

[R] R Help.

Hello R Project, I am having a little trouble with interpreting my GLM results and I wonder if you may be able to help. I am doing a generalised linear model in R studio by outcome variable is binary either effected or not effected. I have my final model structure which has been validated and

[R] Issue when using a coxph + summary function in R while using a pspline-transformed covariate

Hello   I have an issue with obtaining a confidence interval from a coxph object in R while using a spline-transformed covariate. This is a time to event analysis using coxph() from the survival package. In the model below, COVA is a continuous covariate. COVA is time-dependent hence the

Re: [R] List of lists

Hi, The solution that works now is closeAllConnections() But even if I replace the 'list' with the 'array' I get a similar error. Exception is Error in UseMethod(\close\): no applicable method for 'close' applied to an object of class \c('double', 'numeric')\\n #Write each

Re: [R] Highlight selected bar in barplot

On 08/01/2013 12:57 AM, Jurgens de Bruin wrote: Hi All, I am new at R so any help would be appreciate. Below my current R-code/script: initial.dir-getwd() setwd('/Users/jurgens/VirtualEnv/venv/Projects/QTLS/Resaved_Results') dataset- read.table(LWxANNA_FinalReport_resaved_spwc.csv,

Re: [R] merge matrix row data

Hello arun I modified your code a little bit but failed to retrieve the row.names. The response is NULL. Please kindly help and thanks. Elaine Code load(h:/b_W_line/R_workspace/dataset_Residence_2748.RData) dim(dataR) str(dataR) dataR.m- as.matrix(dataR, header=TRUE) dataR.m[,1]

Re: [R] heatmap scale parameter question

I do not want to use the b word, but can anyone who also subscribes to the r-developer list forward my observation regarding heatmap? I am pretty confident that the behaviour of heatmap in R 3.0.1 is not that one intended. On 31 July 2013 14:03, Witold E Wolski wewol...@gmail.com wrote: Would

[R] readBin into a data frame

Hello. readBin is designed to read a batch of data with the same spec, e.g. read 1 floats into a vector. In practise I read into data frame, not vector. For each data frame, I need to read a integer and a float. for (i in 1:1000) { dataframe$int[i] - readBin(con, integer(),

[R] Resampling

Thank you! I have used the replicate function. In fact, I had just found the solution when I received your answers. Best regards, Rita _ Rita Gamito Centro de Oceanografia Faculdade de Ciências, Universidade de Lisboa Campo Grande, 1749-016 Lisboa, Portugal

[R] Use of Bonferroni correction on a set of paired vectors?

Dear all, We are trying to validate a new measurement method by comparing it to a reference method, but we don't manage to find out how to do it... Here are the data we have : *** Sample# ; Ref_1 ; Ref_2 ; Ref_3 ; Ref_4 ; Ref_5 ; Ref_6 ; Ref_7 ; Ref_8 ; Ref_9 ; Ref_10 ; New_1 ; New_2 ; New_3

Re: [R] Creating DAGS with plate notation in R

Here is a way to do it with qgraph. Requires lots of manual placement though. I have been asked before to write a package to do these kind of graphics automatically from R given some model. Might do it eventually :) library(qgraph) # Placement of nodes: Layout - matrix(c( 1,1, 2,1, 3,1,

[R] GARCH Optimization Problems

Hi all, Since am new to the forums I'd like to say hello to everyone. My questions revolves around optimizing a simple GARCH process. Lets assume we have a function names garchlik and takes as inputs (parameters, data, p,q); where p and q are the ARCH and GARCH effects. Have tried the simple

Re: [R] qgraph: how to create legend (scale) for edge thickness?

Hi Maria, Thanks! I just happened to read this but normally don't read r-help. It is best to send specific questions on not well known packages to the maintainer directly. The example on my website is hardcoded in the package. I should really also add the option to make a legend like you want

Re: [R] readBin into a data frame

On 13-08-01 4:36 AM, Zhang Weiwu wrote: Hello. readBin is designed to read a batch of data with the same spec, e.g. read 1 floats into a vector. In practise I read into data frame, not vector. For each data frame, I need to read a integer and a float. for (i in 1:1000) {

Re: [R] merge matrix row data

mat1-structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,

Re: [R] Use of Bonferroni correction on a set of paired vectors?

This has nothing to do with R per se. You need to consult a local statistician and stop fooling with Internet forums. Cheers. Bert On Thu, Aug 1, 2013 at 3:10 AM, Stéph BELLEGO ion...@hotmail.com wrote: Dear all, We are trying to validate a new measurement method by comparing it to a

Re: [R] ggplot2: color histograms by quintile

There is a problem with your example data set. Series has only one value so there is no faceting. Also you refer to trim.index$Rate . Where is it coming from or is trim.index just another name for thing John Kane Kingston ON Canada -Original Message- From: david_txert...@yahoo.fr

[R] Error Help: duplicate?

Hi, I'm working through practice data in R and I am held up on this step. I am not sure why there is an error that claims there is a duplicate subscript for columns? Does anyone know what this means and how I can fix it?

[R] Error Help: duplicate?

Hi, I'm working through practice data in R and I am helped up on this step. I am not sure why there is an error that claims there is a duplicate subscript for columns? Does anyone know what this means and how I can fix it?

Re: [R] merge matrix row data

HI Elaine, From the error, it looks like there are cases where none of the elements in one of the element matches to the GID column of dataNP.m. It's only a guess as you didn't provide  information about the Islands. I was able to recreate the error you got. dataNP.m-structure(c(1L, 2L, 3L, 4L,

Re: [R] R Help.

Hi Darren, Take a look at the effects package. The documentation is good and these articles will help you get oriented: http://www.jstatsoft.org/v08/i15 http://www.jstatsoft.org/v32/i01 Best, Ista On Thu, Aug 1, 2013 at 1:56 AM, Darren Andrew Whitehead darrenwhitehe...@hotmail.com wrote: Hello

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

This problem does not seem to be widely popular, but at least affects two users (both on Linux, maybe a hint here?). To me, it looks like a bug (is it a R bug, or a OS-related bug, I don't know). Should I forward it to R-devel, or some other place where R gurus may have a chance to look at it?

Re: [R] Issue when using a coxph + summary function in R while using a pspline-transformed covariate

On Aug 1, 2013, at 1:02 AM, Dumortier, Thomas wrote: Hello I have an issue with obtaining a confidence interval from a coxph object in R while using a spline-transformed covariate. This is a time to event analysis using coxph() from the survival package. In the model below, COVA is a

[R] algorithm for clustering categorical data

Hi All, Does anyone know what algorithm for clustering categorical variables? R packages? Which is the best? If a data has both numeric and categorical data, what is the best clustering algorithm to use and R package? I tried numeric transformation of all categorical fields and doing

Re: [R] Highlight selected bar in barplot

You may be interested in the iplots package. It has methods where you can create multiple plots and select a point or points in one plot and they will be highlighted on the other plots. On Wed, Jul 31, 2013 at 8:57 AM, Jurgens de Bruin debrui...@gmail.comwrote: Hi All, I am new at R so any

Re: [R] Error Help: duplicate?

Your example is not reproducible, so we can only guess what is happening. Please read the footer of this (or any other R-help) email and follow those instructions. You may also find the discussion at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example helpful.

Re: [R] algorithm for clustering categorical data

Read up on Gower's Distance measures (available in the ecodist package) which can combine numeric and categorical data. You didn't give us any information about how you numerically transformed the categorical variables, but the usual approach is to create indicator variables that code

Re: [R] algorithm for clustering categorical data

Great! Thanks! Yeah, I just use the usual way: as.numeric(..) for numeric transformation...seemed a standardization is needed. Thank you. -Original Message- From: David Carlson [mailto:dcarl...@tamu.edu] Sent: Thursday, August 01, 2013 12:08 PM To: Li, Yan; r-help@r-project.org

Re: [R] algorithm for clustering categorical data

On Aug 1, 2013, at 9:00 AM, Li, Yan wrote: Hi All, Does anyone know what algorithm for clustering categorical variables? R packages? Many. http://cran.r-project.org/web/views/Cluster.html Which is the best? For what purpose? If a data has both numeric and categorical data, what is

Re: [R] algorithm for clustering categorical data

Thanks for the reply From the link you provided, only two packages mentioned categorical field: depmix and depmixS4. I'll look at them. -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Thursday, August 01, 2013 12:15 PM To: Li, Yan Cc:

Re: [R] Conversion of matrix in r to integer

Hi, It is better to keep it as a data.frame as matrix cannot hold different classes together, so it automatically converts the other columns into character as the first column gene is character. dat1- read.table(RP_matrix_RF_ZPTvsPGR.txt,sep=,header=TRUE,stringsAsFactors=FALSE) dat1[,-1]-

Re: [R] Error Help: duplicate?

On Aug 1, 2013, at 18:09 , Jeff Newmiller wrote: Your example is not reproducible, so we can only guess what is happening. Please read the footer of this (or any other R-help) email and follow those instructions. You may also find the discussion at

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

I see the problem on both Linux and Windows, R-3.0.1. vapply(as.numeric(9994:9995), function(x)format(x, scientific=FALSE, digits=3), ) [1] 9994 9995 vapply(as.numeric(4:5), function(x)format(x, scientific=FALSE, digits=4), ) [1] 4 5

[R] Replicate an SAS/SQL request

I am very confuse, I send with a wrong subject. All my Apologizes - De : Guibert TCHINDE Date d'envoi : jeudi 1 août 2013 18:51 À : r-help@r-project.org Cc : R help Objet : RE : [R] Conversion of matrix in r to integer Dear List, I am trying to

[R] Forest plot with sub-group analyses

Greetings. I am conducting a meta analyses that has Beta and SE values. I am wondering how to place the command to split the analyses. Could you assist me to develop the command within the syntax? I would also like to add the N and Year values in the plot. I would like my plot to look like the

[R] use Vectorized function as range of for statement

I guess this has been discussed before, but I don't know the name of this problem, thus had to ask again. Consider this scenario: fun - function(x) { print(x)} for (i in Vectorize(fun, x)(1:3)) print(OK) [1] 1 [1] 2 [1] 3 [1] OK [1] OK [1] OK The optimal behaviour is: fun - function(x)

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

Nicely spotted, Bill! You went much farther than I could have. We can basically summarize the problem with the following simple example: format(9994, digits = 3) [1] 9994 format(9995, digits = 3) [1] 9995 I'm still not sure why this is happening, though: The 'digits' parameter is used to

Re: [R] Conversion of matrix in r to integer

Assuming you have created a data.frame from the text file you sent that is called RP: str(RP) # 'data.frame': 28597 obs. of 8 variables: # $ gene : chr XLOC_01 XLOC_02 XLOC_03 XLOC_04 ... # $ ZPT.1: num 3516 342 2000 143 0 ... # $ ZPT.0: num 626 82 361 30 0 0 0 0 0 1 ... #

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

You could report it as a bug at https://bugs.r-project.org/bugzilla3/ Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: Mathieu Basille [mailto:basille@ase-research.org] Sent: Thursday, August 01, 2013 10:31 AM To: R help Cc: William Dunlap

[R] Bayesian Variance Components Estimation

Hi all, Does anyone know whether there is an R function available to find the Bayesian variance components estimators for random effects or mixed models? Thank you very much. Hanna [[alternative HTML version deleted]] __

Re: [R] Conversion of matrix in r to integer

Thanks David. It is more compact than my code. dat1- read.table(RP_matrix_RF_ZPTvsPGR.txt,sep=,header=TRUE,stringsAsFactors=FALSE) dat2- dat1 #Speed comparison: system.time(dat1[,-1]- lapply(lapply(dat1[,-1],round),as.integer))   # user  system elapsed   #0.012   0.000   0.011  

Re: [R] use Vectorized function as range of for statement

I think this is on topic here, but a reproducible example is highly desirable if not required for clarity. The Vectorize function is essentially a wrapped up for loop, so you are really executing two successive for loops. Note that the Vectorize function is not itself vectorised, so there is

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

Hi Mathieu, I don't have a full explanation, but here is some additional observations: options(digits = 4) ## Simplified example df2 - data.frame(x = rnorm(21), y = rnorm(21), id = 0:100010) apply(df2, 1, function(dfi) format(dfi[id], scientific = FALSE)) [1] 0 1 2 3

Re: [R] Bayesian Variance Components Estimation

I suggest you post this on the r-sig-mixed-models list, instead, as there are likely to be follow-up questions and that is where there is the most interest in this sort of thing. Cheers, Bert On Thu, Aug 1, 2013 at 10:56 AM, li li hannah@gmail.com wrote: Hi all, Does anyone know whether

Re: [R] Bayesian Variance Components Estimation

... and please search before posting. Googling bayesian mixed models in R brought up package blme among others. -- Bert On Thu, Aug 1, 2013 at 11:10 AM, Bert Gunter bgun...@gene.com wrote: I suggest you post this on the r-sig-mixed-models list, instead, as there are likely to be follow-up

Re: [R] 'format' behaviour in a 'apply' call depending on 'options(digits = K)'

Ista, you were right with the integer vs. double issue: I just found this out while filing a bug to the R Bugzilla. You can find the bug report here: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15411 Please let me know if it does not seem to cover all your comments, I'll add more

[R] Tracing the top border of a histogram

I want to represent a histogram by the line along its top border, *without* kernel smoothing (to show several histograms in the same plot). This works, but is there simpler recommended way? x - rnorm(1000) tmp - hist(x, border=white) for (i in 1:(length(tmp$breaks)-1)){

Re: [R] Tracing the top border of a histogram

lines( tmp$breaks, c(tmp$counts,tail(tmp$counts,1)), type='s', col='#00ff0077', lwd=5 ) On Thu, Aug 1, 2013 at 1:30 PM, Levi Waldron lwaldron.resea...@gmail.comwrote: I want to represent a histogram by the line along its top border, *without* kernel smoothing (to show several histograms in

[R] rms plot.Predict when type=p

Hi all, I'm trying to change the pch, color, lty, and lwd in a type=p plot produced by plot.Predict in the rms package. What I'm shooting for is a separate plotting symbol symbol color for each level of a factor (and also to manage the line width for the CIs). Here's what I hope is a working

Re: [R] Tracing the top border of a histogram

Very nice - thank you, I didn't know about type='s'. On Thu, Aug 1, 2013 at 3:43 PM, Greg Snow 538...@gmail.com wrote: lines( tmp$breaks, c(tmp$counts,tail(tmp$counts,1)), type='s', col='#00ff0077', lwd=5 ) On Thu, Aug 1, 2013 at 1:30 PM, Levi Waldron lwaldron.resea...@gmail.comwrote:

[R] R-Help

Greetings. I am conducting a meta analyses that has Beta and SE values. I am wondering how to place the command to split the analyses. Could you assist me to develop the command within the syntax? I would also like to add the N and Year values in the plot. I would like my plot to look like the

Re: [R] GARCH Optimization Problems

Hi Tony, Did you try the `auglag' algorithm in alabma package? Ravi [[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

[R] R runs on Windows Server 2012?

Hi- Can someone confirm whether R runs on the Windows Server 2012 OS, and if so whether there are any significant differences from running on e.g. Windows 7 that I ought to be aware of? The R for Windows FAQ (URL below) seems to indicate that running on Windows Server 2012 is possible, but

[R] Kolmogorov-Smirnov Test

Dear r-users,   I am using KS test to test the goodness of fit for my data and the got the following output.  However, I don't understand about the warning messages.  What does it mean by horizontals is not a graphical parameter   Thank you so much for any help given and it is very much

Re: [R] GO TO function in R

Does R has a GO TO function? For example, I want to run this script at a given interval and save the results.   #Step one a - Sys.time() b - paste(Figure_, a, sep = ) shape - as.numeric(a)/1 scale - as.numeric(a)/100 #I want to save the file using b object (above) as a file name

Re: [R] GO TO function in R

There is no 'GO TO'. Try wrapping your code in a while(TRUE){...} loop. while(TRUE) { ... do something ... Sys.sleep(time) } Or you could have it read from a named pipe which some other process feeds. while(length(readLines(n=1, someNamedPipe))==1) { ... do

Re: [R] GO TO function in R

On Aug 1, 2013, at 6:58 PM, Peter Maclean wrote: Does R has a GO TO function? For example, I want to run this script at a given interval and save the results. Generally communication is more effective if you make your goals clear in a natural language (English in the case of this mailing

Re: [R] merge matrix row data

Hi Elaine, I didn't find any errors by running the code. Regarding the first question, the former is of class numeric, and latter is character library(foreign) dataNP_1 -read.dbf(Anseriformes_13.dbf, as.is = FALSE) ##all the other vectors res-t(sapply(c(

[R] (no subject)

I have a comma delimited file with 62 fields of which some are comments. There are about 1.5 million records/lines. Sme of the fields which has comments and which i do not need have 40 characters. Of the 62 fields, I will need at most 12 fields. What's best way to read in the fields I need. If I

Re: [R] use Vectorized function as range of for statement

On Thu, 1 Aug 2013, Jeff Newmiller wrote: The Vectorize function is essentially a wrapped up for loop, so you are really executing two successive for loops. Note that the Vectorize function is not itself vectorised, so there is no particular advantage to using it in this way. You might as

[R] Editing code in a function?

Hi folks, I've not before had to edit code right in a function, but I think I need to. I am using lmer() and want to use a model that uses zero weights. I found this thread from 2009: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2009q1/001995.html but I'm unsure of how I would actually go

[R] install-packages

hello, i am new and I want to know how to install a packare on R thank you said filahi [[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] install-packages

Try typing this into google search bar: [R] install packages The majority of the results on the first page will help you out. On Thu, Aug 1, 2013 at 8:43 PM, Said Filahi sa.fil...@gmail.com wrote: hello, i am new and I want to know how to install a packare on R thank you said filahi

Re: [R] Editing code in a function?

1. ?:: 2. ?getAnywhere 3. Please consult the R language definition manual -- or even An Introduction to R -- to learn about R programming. It **is** a programming language, you know! Cheers, Bert On Thu, Aug 1, 2013 at 8:54 PM, Mike Rennie mikerenni...@gmail.com wrote: Hi folks, I've not

[R] X11 and printing/copying graphics from mac

Hello all, I frequently use R, but recently have switched to a mac. When creating a new graphic, I have used X11() for a new graphics window and have always (when I used my PC) have been able to copy or print from this graphic window. With my mac, it does not allow me to copy or print. Having