Re: [R] Asymetrical Confidence Interval

On Thu, 16-Jun-2011 at 04:43PM -0400, Muhuri, Pradip (SAMHSA/CBHSQ) wrote: | | Dear List, | | I wanted to calculate the asymmetrical confidence interval based on | the sample statistic and standard error that available from the | published report (complex survey-based). | The calculation

Re: [R] Bartlett's Test of Sphericity

Sorry for the confusion, thank you for the correction and explanation. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |

[R] Using MCMC sampling to estimate p values with a mixed model

Hi everyone, Apologies if this is a silly question but I am a student and this is my first time using R so I am still trying to educate myself on commands, models e.t.c I have a mixed model with four dichotomous fixed factors and subject as a random factor (as each person completed four

[R] help with quantification of high density region

Hello, I am entirely new to this list, and not very experienced with R yet (but very excited about it!!). I am struggling with a dataset of x and y coordinate points I am plotting as a density map as follows: trial - read.csv(file=F12.csv, sep=,, skip=32, head=TRUE) trial.sub - subset(trial,

Re: [R] prediction intervals

Thank you for your email. The problem is that i'm not quite sure how to specify the model using arima(). Here's an example of my problem: I would like to fit an ARMA model, but I'm not sure exactly how to fit it.   Here's an example of the problem.   This is my time variable, hourly

[R] [rgl] Dynamically change the color of 3d objects

Hi, I'm new here. This question concerns the package rgl. Is it possible to change the colour of a set of points drawn with plot3d /without/ removing them from the scene? The idea is to create a presentation of a clustering algorithm, step by step, representing the currently assigned cluster

Re: [R] Required libraries

On 06/18/2011 08:47 PM, Trying To learn again wrote: Hi all, I´m trying to recuperate old files I wrotte and I´m trying to execute on R version 2.13.0 (2011-04-13), the thing is I execute my old file and nothing happens...I suposse I need to install some library but there no appears no message,

[R] Multivariate HPD credible volume -- is it computable in R?

Hi all, I'm new to the list and am hoping to get some advice. I have a set of multivariate data and would like to find the densest part of the data cloud containing 95% of the data, like a 95% HPD credible volume. Is there any R code available to compute that? Thank you very much! Your help and

[R] please help! what are the different using log-link function and log transformation?

I'm new R-programming user, I need to use gam function. y-gam(a~s(b),family=gaussian(link=log),data) y-gam(loga~s(b), family =gaussian (link=identity),data) why these two command results are different? I guess these two command results are same, but actally these two command results are

Re: [R] Asymetrical Confidence Interval

Hi Muhuri, What do you suspect the underlying distribution is of your statistic? Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |

Re: [R] Applying function to all elements of a formula

Thanks for the tips. I'll give them a try! On Sat, Jun 18, 2011 at 12:07 PM, Dennis Murphy djmu...@gmail.com wrote: Much better..nice! Dennis On Sat, Jun 18, 2011 at 1:53 AM, Dimitris Rizopoulos d.rizopou...@erasmusmc.nl wrote: maybe another way is by reconstructing the formula using

[R] how to get the miminum value in the list???

hi, R users here i have one problem, if i wanna get the minimum value in the normal data, i can do this, ## which(data1==min(data1)). but if i want get the minimum value of a list which has two variables ##list1[[j]][[i]]##, i tried the codes like this, but it did not work. ##

Re: [R] [rgl] Dynamically change the color of 3d objects

On 11-06-18 3:47 PM, Fernando (Est - UnB) wrote: Hi, I'm new here. This question concerns the package rgl. Is it possible to change the colour of a set of points drawn with plot3d /without/ removing them from the scene? No, you can't modify objects other than by removing and recreating

Re: [R] please help! what are the different using log-link function and log transformation?

The problem is not that you are new to R. This is a conceptual issue. Let y be the response variable and let {x_i} be a set of predictors. Your first model (identity response and log-link) is saying that y=f(x_1)f(x_2)...f(x_n) + e, e~Normal(0,sigma) i.e. this is an additive observation-error

Re: [R] Required libraries

On 11-06-19 3:19 AM, Jim Lemon wrote: On 06/18/2011 08:47 PM, Trying To learn again wrote: Hi all, I´m trying to recuperate old files I wrotte and I´m trying to execute on R version 2.13.0 (2011-04-13), the thing is I execute my old file and nothing happens...I suposse I need to install some

Re: [R] please help! what are the different using log-link function and log transformation?

The two commands you give below are certain to lead to very different results, because they are fitting very different models. The first is a gaussian model for the response with a log link, and constant variance. The second is a gaussian model for a log-transformed response and identity

Re: [R] please help! what are the different using log-link function and log transformation?

Funny, I was going to quote your paper with Dichmont in Fisheries Research regarding this, then I forgot to do it, but you yourself came out and posted the explanation. This forum is great! Rubén -Original Message- From: r-help-boun...@r-project.org on behalf of

[R] apply kmeans into every level of the tree..

hi, r users I'm a new r user. i want to apply kmeans into every level of the tree which i built. the codes for clusterring only one level of the tree. # d - dist(data1, method = euclidean) h1 - hclust(d, method=ward) c1 - cutree(h1, 100) # 100 groups which i want to cluster cdg -

Re: [R] Using MCMC sampling to estimate p values with a mixed model

Woodcock, Helena H.E.Woodcock at liverpool.ac.uk writes: Apologies if this is a silly question but I am a student and this is my first time using R so I am still trying to educate myself on commands, models e.t.c I have a mixed model with four dichotomous fixed factors and subject as a

Re: [R] automatically generate the output name of my for loops

true, it did work using unlist() funciton, it can be found the minimum value. and for further step, if i want identify the minimum value with the list, which means the minimum value i have found is belonged to which list[[j]][[i]]. i used the codes like this ##which(list1==min(list1))## but

Re: [R] how to get the miminum value in the list

Hi, that depends on whether you want to get the minimum within each list element or the global minimum across all list elements. The first is achieved by using lapply(). The second can be achieved by unlisting the list (which assumes that all list elements are numeric) and looking for its minimum.

[R] save and load in R

I have a list of txt files that I want to convert into .rdata R data object. filenames 1. ./file1.txt 2. ./file2.txt 3. ./file3.txt 4. ./file4.txt 5. ./file5.txt 6. ./file6.txt 7. ./file7.txt 8. ./file8.txt 9. ./file9.txt 10. ./file10.txt I saved these files as for ( i in 1:10) { dataFile =

Re: [R] save and load in R

On 11-06-19 10:26 AM, Mary Kindall wrote: I have a list of txt files that I want to convert into .rdata R data object. filenames 1. ./file1.txt 2. ./file2.txt 3. ./file3.txt 4. ./file4.txt 5. ./file5.txt 6. ./file6.txt 7. ./file7.txt 8. ./file8.txt 9. ./file9.txt 10. ./file10.txt I saved these

Re: [R] save and load in R

Thanks Jeff and Duncan Assign worked for me. I did not check the other methods suggested by you. I am repreducing my code below: ## filenames = list.files(path = ., pattern = '.txt$', all.files = FALSE, full.names = TRUE, ignore.case = FALSE) #all input files numFiles =

Re: [R] Using MCMC sampling to estimate p values with a mixed model

If your alternative hypothesis is unequal variances (2-sided), both F 1 and F 1 are of interest, and rejection of the equal variance null can occur on either side. The usual ANOVA F test is 1-sided, with an alternative the numerator variance exceeds the denominator one, so this is perhaps

Re: [R] how to get the miminum value in the list

but in my case, the list is a two-variable list, list[[j]][[i]] when i use lapply(list, min) it appears Error in FUN(X[[1L]], ...) : invalid 'type' (list) of argument thanks -- View this message in context:

[R] Accessor functions in lattice graphics

I know about the current.row, current.column, and panel.number functions that are useful within panel functions written for lattice. Are there easy ways to obtain the names of the conditioning variables (those appearing after |) and their values for the current panel? Thanks Frank - Frank

Re: [R] how to get the miminum value in the list

Hi: It's just an extra step: y - list(list(c(1,5),c(2,3,4)), list(c(1, 3, 4), c(5, 7))) lapply(seq_len(length(y)), function(i) lapply(y[[i]], min)) [[1]] [[1]][[1]] [1] 1 [[1]][[2]] [1] 2 [[2]] [[2]][[1]] [1] 1 [[2]][[2]] [1] 5 unlist(lapply(seq_len(length(y)), function(i) lapply(y[[i]],

[R] Colors in a dendrogram

Hello, i'm trying to draw a dendrogram to show the clustering hierarchy. i'm working on 2 classes but each class contains more than 3000 instances. i'm using the hclust function to do that! but i can't read anything from this figure. i would like to color each class with its own color so at

Re: [R] Multivariate HPD credible volume -- is it computable in R?

Date: Sun, 19 Jun 2011 19:06:20 +1200 From: agw1...@gmail.com To: r-help@r-project.org Subject: [R] Multivariate HPD credible volume -- is it computable in R? Hi all, I'm new to the list and am hoping to get some advice. I have a set of multivariate data and would like to find the

[R] hello about proxy configuration

dear everyone system:windows XP R2.13.0 I download the windows binary from website and successfully install it ,because I use a proxy server ,when I follow the instrction as follows: I set a system property R_HOME=C:\Program Files\R\R-2.13.0 R_HOME\bin\i386\Rgui.exe

[R] extract data from a column

Hi all, I have a column that has the following format: chr1:564588..564589,+ and I want to extract only the coordinates; I have tried writing a regular expression but I couldn't figure out how I should write it. Does anyone know? Thank you, Best, Nanami [[alternative HTML version

[R] Transfer my package in CRAN

Hello, I found a problem to transfer my package on the site ftp://cran.rproject.org/incoming/ . Access is not allowed. Please,could you give me the settings for connecting to your server to transfer my package using the FileZilla. Best Regards Fadia [[alternative HTML version

[R] For loop by factor.

I have a data.frame as follows: a 3 a 2 a 1 b 3 b 2 c 2 c 3 c 1 c 1 Each factor (a, b, c) should be monotonically decreasing, notice that factor 'c' is not. I could use some help to figure out how to form a logical structure (mostly just syntax), that will check each 'next value' for

[R] Skyline plots from several trees in newick format

Dear all, I am trying to create a consensus skyline plot using the ape package(newbie). I have a nexus file that looks like the one from above containing many trees. (my_file.trees) #NEXUS begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)] tree true_tree_1 =

[R] roundoff error in recursion

Dear R users, I run into the following problem and hope someone can help me out. Thank you in advance for your time. I have a function defined recursively as follows: recFun = function(k,x){ #i is less than 10. x can be any real number. I need the value of recFun(k=1,2,3,4, x=0.12). if(k==1)

Re: [R] For loop by factor.

This works, but I'm still hunting for a more elegant final step: test - data.frame(A=c(a, a, a, b, b, c, c, c, c), B=c(3,2,1,3,2,2,3,1,1)) test2 - lapply(split(test$B, test$A), sort, dec=TRUE) test3 - data.frame(A=rep(names(test2), times=lapply(test2, length)), B=unlist(test2)) It will

Re: [R] hello about proxy configuration

Quoting 王海生 edwin_ue...@163.com: dear everyone system:windows XP R2.13.0 I download the windows binary from website and successfully install it ,because I use a proxy server ,when I follow the instrction as follows: I set a system property R_HOME=C:\Program Files\R\R-2.13.0

Re: [R] hello about proxy configuration

On 19/06/2011 7:29 PM, p_conno...@slingshot.co.nz wrote: Quoting 王海生edwin_ue...@163.com: dear everyone system:windows XP R2.13.0 I download the windows binary from website and successfully install it ,because I use a proxy server ,when I follow the instrction as follows: I set a system

Re: [R] (no subject)

Hello, Does anyone has software to simulate SNP data? Specifically I would like any package that produces 2 x 3 SNP data. -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] extract data from a column

If I understand what you want (which I may very well not) you could use something like this: If this is an example of your type of data: 564589,+ substr(x, 1, 6) as.numeric(x) Please try to post something more thorough if you would like a better answer. Sam -- View this message in context:

Re: [R] extract data from a column

So if I am given some data that look like this: head(CTSS) V1 V2 V3V4 V5 V6 V7 1 chr1 564563 564598 chr1:564588..564589,+ 1336 2 chr1 564620 564649 chr1:564644..564645,+ 94 3 chr1 565369 565404 chr1:565371..565372,+ 217 4 chr1 565463

Re: [R] extract data from a column

I figured it out: x-sub(^.*:([[:digit:]]+)..([[:digit:]]+).*, \\1 \\2, CTSS$V4) -- View this message in context: http://r.789695.n4.nabble.com/extract-data-from-a-column-tp3609890p3610147.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] For loop by factor.

try this: test - data.frame(A=c(a, a, a, b, b, c, c, c, c), B=c(3,2,1,3,2,2,3,1,1)) test A B 1 a 3 2 a 2 3 a 1 4 b 3 5 b 2 6 c 2 7 c 3 8 c 1 9 c 1 # determine which group is not decreasing tapply(test$B, test$A, function(x) any(diff(x) 0)) a b c FALSE FALSE TRUE On

Re: [R] For loop by factor.

If I understand you correctly, you are trying to find the cumulative maximum from the end within each level of the factor. If this is what you are trying to do, then here is one way you might like to do it. First, define the function: cumMax - function(x) Reduce(max, x, right = TRUE,

[R] analysis with the data from mysql database

Hi everyone, I have certain values retrieved from mysql database.How can i do certain analysis like histogram, correlational analysis tc using this data,I tried it. But when i tried to plot a histogram it actually showed error the data is not numeric evenif it was stored as integer data type

Re: [R] Skyline plots from several trees in newick format

Does read.nexus work for you? Bhoom On Sun, Jun 19, 2011 at 5:04 PM, Andra Tolbus andralia.tol...@gmail.comwrote: Dear all, I am trying to create a consensus skyline plot using the ape package(newbie). I have a nexus file that looks like the one from above containing many trees.

Re: [R] (no subject)

Hi Jim, Just want to make sure that I understand correctly.What do you mean by SNP = Single Nucleotide Polymorphism? Bhoom On Sun, Jun 19, 2011 at 5:57 PM, Jim Silverton jim.silver...@gmail.comwrote: Hello, Does anyone has software to simulate SNP data? Specifically I would like any package

Re: [R] Trouble with Optimization in Alabama Package

Hello Erik and Ravi, I am curious if Erick or Ravi have a solution to Erick's question. I have a similar problem. I wish to use auglag to solve a nonlinear optimization problem. The cost function, grad function, and constraints are all function of some parameters that are dependent upon the

[R] (no subject)

HELLO, anybody... could you help me to check the below coding for volcano. what is the mistake? what the plot could not display? #volcano_plot.r # #Author:Amsha Nahid, Jairus Bowne, Gerard Murray #Purpose:Produces a volcano plot # #Input:Data matrix as specified

[R] Error of Cross Validation

Dear R users: Recently, I tried to write a program to calculate cross-validated predicted value. My sources are as follows. However, the R reported an error. Could you please check the sources? Thanks. set.seed(100) x-rnorm(100) y-sample(rep(0:1,50),replace=T) dat-data.frame(x,y) library(rms)

[R] Model Formulae Evaluation

Hello All, I have searched but haven't been able to find an answer to this question. I'm writing a function that needs to be able evaluate the right-hand side of a general non-linear formula for different parameter values, similar to what nls() does. I looked through the nls() code but it isn't

Re: [R] Skyline plots from several trees in newick format

No, unfortunately not. It works perfectly fine with other kinds of files. Everything, but these ones...The program that generates them does not have any helpful specifications regarding this format ..*.trees On Mon, Jun 20, 2011 at 5:55 AM, Bhoom [via R]