search for: upgma

Hi, I am clustering objects using the agnes() function and the UPGMA clustering method (function = "average"). Everything works well, but apparently something is wrong with the dendrogram. For example: x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(clust...

R-help folks: Thanks in the past for your help. I have another question that I hope has a simple answer. I have searched the R home pages and the R-help archives with no hits. How can I cluster data in R using UPGMA? I am not subscribed to the list (can't keep up with all the traffic!), so I would appreciate it if you could email directly to me (or to the list and to me). Thanks, Tom Isenbarger -- isen at plantpath.wisc.edu thomas a isenbarger (608) 265-0850

Hi all, Has anyone got a function to perform clustering by Flexible UPGMA (Un-weighted Pair Group Using Arithmetic Averaging) . It does not seem to exist in any R package. Regards, Ton -- Laboratoire d'Hydro?cologie Quantitative 3 bis, Quai Chauveau - CP 220 69336 LYON cedex 09 t?l. : +33 (0)4.72.20.89 20 fax : +33 (0)4.78.47.78.75 mail : ton.snelder at cemagref...

...e code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe, spe.chwo) spe is the dataframe spe.chwo came from: spe.norm <- decostand(spe, "normalize") spe.ch <- vegdist(spe.norm, "euc") spe.ch.UPGMA <- hclust(spe.ch, method = "average") spe.chwo <- reorder.hclust(spe.ch.UPGMA, spe.ch) and the error is Error in vegemite(spe, spe.chwo) : Cowardly refusing to use longer than 1 char symbols: Use scale The data in the dataframe is biomass data recorded to 4 digits. Here is a...

...o que he usado es:library(betapart)data_base # Base de datos de 6000 columnas x 11000 filasdistance <- beta.pair (data_base, index.family="sorensen") # Calculo de la matriz de disimilitud beta_similarity <- distance$beta.sim # Selecciono el tipo de medida que quiero library(cluster)UPGMA<- agnes (beta_similarity ) # Análisis UPGMA Soluciones que he intentado: Ante los problemas que he tenido, he intentado hacer la matriz de disimilitud en python. El problema es que no hay una función optimizada para la medida de disimilitud que quiero estimar (índice de simpson), y he tenido qu...

...# Base de >> datos de 6000 columnas x 11000 filasdistance <- beta.pair (data_base, >> index.family="sorensen") # Calculo de la matriz de disimilitud >> beta_similarity <- distance$beta.sim # Selecciono el tipo de medida que >> quiero >> library(cluster)UPGMA<- agnes (beta_similarity ) # Análisis UPGMA >> >> Soluciones que he intentado: Ante los problemas que he tenido, he >> intentado hacer la matriz de disimilitud en python. El problema es que no >> hay una función optimizada para la medida de disimilitud que quiero estimar...

...on los paquetes de R para gestión de Big Data como ff o bigmemory. ¿Sabéis si las matrices que se guardan como bigmemory pueden manipularse con las mismas funciones que el resto?En concreto quiero saber si voy a poder calcular la matriz de distancias con beta.pair, y hacer un análisis cluster tipo UPGMA sobre esa matriz (la función agnes () o hclust()). Saludos, Rubén > From: dirienzo.julio en gmail.com > Date: Tue, 22 Dec 2015 17:31:03 -0300 > To: marcelino.delacruz en upm.es > CC: r-help-es en r-project.org > Subject: Re: [R-es] Cannot allocate vector of size > > Si las ma...

...0 columnas x 11000 filasdistance <- beta.pair (data_base, >>>> index.family="sorensen") # Calculo de la matriz de disimilitud >>>> beta_similarity <- distance$beta.sim # Selecciono el tipo de medida que >>>> quiero >>>> library(cluster)UPGMA<- agnes (beta_similarity ) # Análisis UPGMA >>>> >>>> Soluciones que he intentado: Ante los problemas que he tenido, he >>>> intentado hacer la matriz de disimilitud en python. El problema es que no >>>> hay una función optimizada para la medida de...

Hello, My name is Sivan and I am a master degree student in statistics,my problem is as follows: I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it. The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree. does anyone

Hello, I am attempting to assign significance levels to a UPGMA cluster analysis as part my doctoral research. The pvclust function works well but doesn't include the similarity index I need (morisita's) as an option for computing a distance matrix. Morisita's is available in vegdist in the VEGAN library but I am having a hard time getting the veg...

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo because the tree...

Hello, My name is Rodrigo, I am using R program and I have a trouble. I am trying to do a dendrogram with genetics information. Let me explain... The Similarity Matrix was already did, and with this matrix I want to construct a dendrogram. So, the distance is done. I need to transform this matrix (that I have) in a dendrogram, I woud be very grateful if someone could help me. PS: I am sending