similar to: plot error bars on skyline plot

Dear all, Does anyone know how can one loop through the newick phylogenetic trees stored in a nexus file and generate an "average" skyline plot with coalescent intervals? I have managed to generate the plot with one tree, but is it possible to create that "consensus/average" plot in R? tr<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1,

Hi all: I get the following error message that I am not able to resolve. Error in if (const(t, min(1e-08, mean(t)/1e+06))) { : missing value where TRUE/FALSE needed It appears right before the last data.frame statement. Below is the program that simulates data from one way random effects model and then computes normality and bootstrap confidence interval for

My data looks like: A,B,C,D,Class 1,2,0,2,cl1 1,5,1,9,cl1 3,2,1,2,cl2 7,2,1,2,cl2 2,2,1,2,cl2 1,2,1,5,cl2 0,2,1,2,cl2 4,2,1,2,cl2 3,5,1,2,cl2 3,2,12,3,cl2 3,2,4,2,cl2 **The steps followed are: trainfile <- read.csv("TrainFile",head=TRUE) datatrain <- subset(trainfile,select=c(-Class)) classtrain <- (subset(trainfile,select=Class)) rf <- randomForest(datatrain, classtrain)

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 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0, (20.1:1, 4.1:0):0):1, ((37.1:0,

List, In order to get rid of some old, unreadable S3 code in package sp, I'm trying to rewrite things using S4 methods. Somewhere I fail, and I cannot sort out why. In order to isolate the problem, I created two functions, doNothing<- and dosth, and both should do nothing. The issue is that in most cases they do nothing, but in some cases dosth(obj) changes the class of obj and breaks with

Dear all, I need to create a for-loop in which I can compute multiple histograms My code is the following : #singlefile includes huge csv file #I want to specify the binsize #I would like to compute in the for -loop the histograms numfiles <- length(singlefile) for (i in 1 :51) { binsize <- -20 :20/2 hist(singlefile(singlefile$GVC[singlefile$new_id==i]], break=seq(),

Dear R community, I am new to R, a reforming SAS user :) I am running R 2.10.1 on a Windows XP machine. I would like to write linear functions of my coefficient parameter estimates from a glm, but am having a difficult time understanding the parameterization R uses. In the toy example below I am running a glm on binomial data, with clones and lines within clones as fixed effects, each with 6

--=====================_24736660==_ Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable SVD-Error on R 1.1.0 Windows 98 I get the following error applying svd on a positive definite matrix : > sk2 [,1] [,2] [,3] [,4] [,5] [1,] 1.0460139783 0.084356992 -2.810553e-04

Hi All, Just 10 days after 3.0.7 we''re releasing 3.0.8 with support for SQLite3. In combination with our demo application, this makes trying out Skyline CMS a breeze. We also enabled Github issues for Skyline to track bugs and issues with Skyline CMS. Besides the SQLite3 support the most notable change since 3.0.7 is the improved API documentation which you can find on

I am trying to use knn to do a nearest neighbor classification. I tried using my dataset and got an error message so I used a simple example to try and understand what I was doing wrong and got the same message. Here is what I typed into R: try [,1] [,2] [,3] [,4] r "A" "A" "T" "G" r "A" "A" "T" "G" f

While trying to train randomForest with my dataset, I am ending up with the following error Error in randomForest.default(datatrain, classtrain) : length of response must be the same as predictors My data looks like: A,B,C,D,Class 1,2,1,2,cl1 1,2,1,2,cl1 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,12,3,cl2 3,2,1,2,cl2 Actual dataset has around 4000

Hi all, I am using R trying to get a inverse matrix of (X^T)X , but I keep getting the error message like: no b argument and no default value for sprintf(gettext(fmt, domain = domain), ...) . -------------------------------------------------------------------------------------------- # my code X<-Matrix(rep(1,500),100,5) X[lower.tri(X)]<-1-10^-7 XtX<- t(X)%*% X XtXu<-lu(XtX)

the following config-file triggers a couple of odd corner-cases in 3.08-pre5 ; SERIAL 0 19200 CONSOLE 0 APPEND console=ttyS0,19200n81 root=/dev/hda1 IMPLICIT 0 #DEFAULT sk1 #DEFAULT menu.c32 DEFAULT sk1 PROMPT 0 MENU TITLE Simple Boot Menu LABEL sk1 KERNEL vmlinuz-2.6.10-sk1 APPEND console=ttyS0,19200n81 root=/dev/nfs

Mates, I'm trying to solve some log errors I getting. I have samba 3.0.7 installed on Suse 9.0. It has been happening intermittently for several months. I don't know if this is XP client related or what. Any thoughts: The errors are: Feb 9 20:00:33 skyline smbd[14408]: [2005/02/09 20:00:33, 0] lib/util_sock.c:get_peer_addr(1000) Feb 9 20:00:33 skyline smbd[14408]: getpeername

The function knn.cv in the class package doesn't have error checking to ensure that the length of the classlabel argument is equal to the number of rows in the test set. If the classlabel is short, the result is often a segfault. > library(class) > dat <- matrix(rnorm(1000), nrow=10) > cl <- c(rep(1,5), rep(2,5)) > cl2 <- c(rep(1,5), rep(2,4)) > knn.cv(dat, cl) [1] 2

Greetings R-users, I have been using the fpc package in R to cluster my data. Speficically I am using kmeansruns clustering. I would like to know how I use R to partition data into clusters. What I am doing is as follows. # Use csv file as input ##################### wholeset = read.csv("Spellman800genesImputed.csv") # exclude first col (gene names) ##########################

http://bugzilla.netfilter.org/show_bug.cgi?id=704 CZ <huangj at qualcomm.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|RESOLVED |REOPENED Resolution|FIXED | --- Comment #4 from CZ <huangj at qualcomm.com>

There was talk a few weeks ago about the possibility of a Tk-based user management tool that never happened. I'm planning on trying to do this myself. What features were to be in the one that never materialized? What features might people want in it? To begin, the program will only be able to do things that can be done straight through the existing command line tools (net, smbpasswd,

I don't know the final answer BUT if you have something simmilar to a cyber-cafe LAN (I mean, users use all the computers, and maybe some users come back to login with the same name) then you have to install a printer only once in a computer, loging as the administrator and installing drivers. Then what users will have to do is JUST add the printer without installing. I know that it's

Hello all, A few years ago, I added the inalloca feature to LLVM IR so that Clang could be C++ ABI compatible with MSVC on 32-bit x86. The feature works, but there is room for improvement. I recently took the time to write up a design using token values that will hopefully be better named and easier to work with and around. For the technical details of the proposal, I've written up the RFC