similar to: help with hclust

Hello, I would like to cut a hclust tree into several groups at a specific similarity. I assume this can be achieved by specifying the "h" argument with the specified similarity, e.g.: clust<-hclust(dist,"average") cut<-cutree(clust,h=0.65) Now, I would like to draw rectangles around the branches of the dendrogram highlighting the corresponding clusters, as is done by

Does anyone here have any "feel" for the "Battery disconnected" and "Battery reattached" log entries? The rebooting came as a result of me turning off modems, router, external drives, monitor, cordless phone and finally, the computer, trying to locate a quiet but annoying "chirp". The "chirps" stopped when I tilted the UPS to look at the front

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

Please bear with me for a really stupid question... I have a Radeon HD 4550 video card and currently run the Catalyst driver, fglrx_6_9_0-8.741-1. I use the "package managed" method for installing, allowing me keep track of what's what: [rj at madeleine ~]$ su Password: [root at madeleine rj]# grep fglrx /var/log/yum* /var/log/yum.log:May 20 12:37:07 Updated:

Howdy - Someone''s probably already reported this, but anyhow, going here: http://wiki.rubyonrails.com/rails/show/RailsOnFedora results in: ==================== > Bad Gateway > The proxy server received an invalid response from an upstream server. > ==================== Yours, Tom

Dear R users, I am having problems trying to fit quasipoisson and negative binomials glm. My data set contains abundance (counts) of a species under different management regimens. First, I tried to fit a poisson glm: > summary(model.p<-glm(abund~mgmtcat,poisson)) Call: glm(formula = abund ~ mgmtcat, family = poisson) . . . (Dispersion parameter

Hi, I installed the maps and mapdata libraries on my R-1.8.0 on MacOSX 10.2.8 (jaguar on a powerbook G4), and failed to make the map function work properly: R : Copyright 2003, The R Development Core Team Version 1.8.0 (2003-10-08) [...] > library(maps) > map() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <- dist(USArrests) hc <- hclust(d1, "ave") d2 <-

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

I read an article today about keyboard interactive auth allowing bruteforcing. I'm afraid I have minimal understanding of what keyboard-interactive really does. What does it do, and should I have my clients set it to off in sshd_config? --- Scott Neugroschl | XYPRO Technology Corporation 4100 Guardian Street | Suite 100 |Simi Valley, CA 93063 | Phone 805 583-2874|Fax 805 583-0124 |

Hello, I analyse some free-sorting data so I use hierarchical clustering. I want to compare my proximity matrix with the tree representation to evalute the fitting. (stress, cophenetic correlation (pearson's correlation)...) "The cophenetic similarity of two objects a and b is defined as the similarity level at wich objects a and b become members of the same cluster during the course of

Is there a function available in R that implements Mojena's Upper Tail Rule or that draws a Mojena plot? I would also like to find a function that implements Duda and Hart's stopping rule. Finally with function cophenet how can I achieve a straightforward Cophenet correlation coefficient (i.e. one number for example 0.876) that gives the agreement between the structure of the

Guys, I''m designing an application currently that will ultimately be implemented in either Rails or php5 (most likely Rails). While I''ve coded many PHP (pre-5) applications in the past, OO support was so weak that my OO designs were never truly divorced from the limitations of the language, thus I never had to consider this problem. The question is: how does Rails (and how do

I haven't been keeping up with the internals, I'm afraid. Does OpenSSH have support for Port Knocking? I might be interested in looking into that, as a way of reacquainting myself with the current code base. --- Scott Neugroschl | XYPRO Technology Corporation 4100 Guardian Street | Suite 100 |Simi Valley, CA 93063 | Phone 805 583-2874|Fax 805 583-0124 |

Quoth Iain: >I'm not sure if the work being done to allow OpenSSH to be built without OpenSSL includes SHA-1 support. Hi Iain. I haven't heard of this effort before. Can you give a few more details? Thanks, ScottN --- Scott Neugroschl | XYPRO Technology Corporation 4100 Guardian Street | Suite 100 |Simi Valley, CA 93063 | Phone 805 583-2874|Fax 805 583-0124 |

Dear All, I wrote a function for cluster analysis to compute cophenetic correlations between dissimilarity matrices (using the VEGAN library) and cluster analyses of every possible clustering algorithm (SEE ATTACHED) http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . As it is now, it is extremely long, and for the future I was hoping to find a more efficient way of doing this sort of

I'd like to get a measure of goodness of fit for a heirarchical clustering result from hclust. Something that would indicate the extent to which the dendrogram accurately represents the original dissimilarity matrix. Is there an easy way to do this? Or, does anyone have code for computing distances between nodes given an hclust structure? So far, my searches have come up dry. -- David

Hi, I am running simulations that does multiple comparisons to control. For each simulation, I need to model 7 nls functions. I loop over 7 to do the nls using try if try fails, I break out of that loop, and go to next simulation. I get warnings on nls failures, but the simulation continues to run, except when the internal call (internal to nls) of the chol2inv fails.

first, congrats to monty and the whole crew for getting this close to 1.0. it's a monumental achievement reflecting a huge amount of hard work -- kudos! econd, i know the bitrate peeling feature has been pushed back until after 1.0 is out. but i'm wondering -- will oggs created with a 1.0 encoder be peelable with an as-yet-unreleased utility, or do "peelable oggs" have to be