similar to: Average skyline plot from newick trees stored

Hi, I have generated a skyline plot of a tree in newick format using "ape". How can I plot the error bars for this graph? I only have the the tree data. un<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (((((15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0,

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,

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

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

--=====================_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

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>

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

Andrew, Jerry and the rest of the team: Hello again! It has been quite some time since I was here and waded the waters to set up bind8 and samba 2.07 on my trust mdk 7.2 box. (by the way, it is still working like a champ) over 400 days uptime before the last extended power outage. Well, obviously a lot has changed since the 2.07 days and I am now working on a SuSE 8.2 box with samba 2.2.7a

Not sure if this got through the 1st time, so I am trying a repost. I appologize if you get this twice, but I need help! -- David C. Rankin, J.D., P.E. Rankin * Bertin, PLLC 510 Ochiltree Street Nacogdoches, Texas 75961 (936) 715-9333 (936) 715-9339 fax www.rankin-bertin.com -- ----- Original Message ----- From: "David Rankin" <drankin@cox-internet.com> To: "samba"

Mates, On my Suse 9.0 pro installation, I updated Samba from 2.2.8a to 3.0.7. The upgrade went flawlessly, Samba is happily sharing all the files it was before. However, I can no longer print via cups. I have a HP LJ4 attached to the Linux box that worked great before the upgrade. I have 2 XP clients. Now from the Windows side, I get the printer status showing 'access denied, unable to

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear R-helpers, I would like to export hierarchical clusters e.g. fit <- hclust(d, method="ward") in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package.

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

Commit-ID: f97573c5c1a47595c5a059b84b74f54cb2cd8d6d Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=f97573c5c1a47595c5a059b84b74f54cb2cd8d6d Author: Stephen Kitt <steve at sk2.org> AuthorDate: Mon, 6 Jun 2016 22:45:27 +0800 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Fri, 25 Jan 2019 02:57:21 +0000 [klibc] jobs: Handle string-based job

Commit-ID: 8115b5d06f75ea543d01355384cf5556aa388481 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=8115b5d06f75ea543d01355384cf5556aa388481 Author: Stephen Kitt <steve at sk2.org> AuthorDate: Mon, 6 Jun 2016 22:45:27 +0800 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Sat, 28 Mar 2020 21:42:54 +0000 [klibc] dash: jobs: Handle string-based

This isn't necessarily a samba problem, but its happening on my domain with a Samba PDC. I have 2 computers running XP Pro that I can only connect to intermittently. All 3 of these machines are joined to the domain and can access domain resources when logged in as a domain user through the Samba PDC. SHIPPING1 always seems to work. SHOP1 and SHOP2 are the ones that allow intermittent

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Dear all, I'm using R 2.8.1 under Windows Vista on a dual core 2,4 GhZ with 4 GB of RAM. I'm trying to reproduce a result out of "Analysis of Financial Time Series" by Ruey Tsay. In R I'm using the fGarch library. After fitting a ar(3)-garch(1,1)-model > model<-garchFit(~arma(3,0)+garch(1,1), analyse) I'm saving the results via > result<-model

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how