similar to: Dendrogram with the UPGMA method

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

Hola a tod en s, Soy nuevo en R-help-es, por lo que perdonadme si debería haber mandado este email a una sección en particular. Quería consultaros un error que me aparece en R al hacer una matriz de disimilitud a partir de una tabla con 6000 columnas x 11000 filas. El mensaje que da R es "cannot allocate vector of size 10Gb", y me resulta extraño ya que tengo 64 Gb de RAM disponible.

Hola Rubén, Totalmente de acuerdo con los consejos de Carlos. Ten en cuenta que aunque R disponga de varios (bastantes) GB de memoria, algunos de los objetos que va creando durante el proceso pueden consumirla por completo. Es decir, que aunque tu ordenador tenga 64GB de RAM, es posible que no queden 10 GB libres para almacenar un objeto (porque ya hay demasiados objetos grandes en la

Antes de nada, me gustaría daros las gracias por toda vuestra ayuda. He estado probando todo lo que me habéis dicho a la vez, y no hay manera, sigo teniendo el problema con el espacio. En cuanto al tamaño de la base de datos, es más grande de lo que puse, me equivoqué y puse el tamaño de una base anterior con la que estuve trabajando, la actual tiene 36866 filas x 6500 columnas. He seguido todas

Yo creo que el problema principal está en betapart.core(), que crea y mantiene simultáneamente en memoria varios objetos de alrededor de 1 Gb que luego combina en una lista... Probablemente es entre las líneas el código de betaper.core donde hay que ir eliminando objetos. Saludos, Marcelino El 22/12/2015 a las 18:26, Carlos J. Gil Bellosta escribió: > Hola, ¿qué tal? > > Yo no

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.fr

Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot the relative abundance of each OTU, against the number of significant pair-wise correlations

Dear all, To draw a lowess line on a plot was a piece of cake; to draw a loess line, however, seems not that easy. Is the loess plotting implemented at all in relation to the loess function, or do I have to look in add-on packages? Thanks, Marcin

Hello, I am relatively new to R and I am working through the code that is provided in the book Numerical Ecology with R and I have run across an error message that I can't seem to figure out. I am using the vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe,

Hi all, Can someone tell me how to justify (right or left) the labels on the branches of a dendrogram tree? I have produced a dendrogram via agnes and plotted it with pltree. The dendrogram terminal branch labels seem to be centre-justified by default and I was hoping to change this to left justification. Thanks, Duncan ***************************************** Dr. Duncan Mackay School of

Hi, Consider this simple plot: > plot(1:25,runif(25,0,1),ylab="First Y-axis label",xaxt="n") I want to add an additional axis as > axis(4,at=seq(0.2,1,.2), labels=1:5) I have no idea how to add now the title of the new axis as "Second Y-axis label". I want this text to be vertically directed from bottom to top. I can't find the function in text() to write

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

I am trying to make the lines thicker in a graph (for a ppt presentation). Here is what I currently have: plot(x,y,type="l", ylab="Number of OTUs", xlab="Number of Samples Collected", col="Black", pch=1, ylim=c(0,6000)) points(x, Sobs$Chao_1_Mean, type="l", col="Gray", pch=1) (this is one of the added lines in the graph). I believe

Dear R-help listers, Is anyone aware of a function that outputs dendrogram ultrametrics? Cheers, Lisa. PS please reply to me personally as well as to the list because the website wasn't letting me subscribe for some reason. thanks... Lisa Holman Research Officer, Vegetation Dynamics Policy & Science Division NSW Department of Environment & Conservation PO Box 1967, Hurstville 2220.

Hi, I want to add boxplots to a scatterplot: plot(x,y, xlim=c(80,120),ylim=c(80,120)) boxplot(y,add=TRUE,at=118) boxplot(x,add=TRUE,at=118,horizontal=TRUE) How can I control the width of the boxes (say, I'd like them to be of width 3 in the variables' scales). I've tried the "width" parameter but failed. Thanks in advance, Marcin

Dear list, is there a way how to add information to internal nodes (branching points) in dendrogram created via plot.agnes function (package cluster)? I wish to place colored circles on the nodes, but I don't know how to proceed... I'll be grateful for any suggestion Ond?ej -- Ond?ej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97,

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

Hi, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <-

I am trying to input an OTU table into EstimateS, however, the format of the OTU table has to be changed to fit the format EstimateS will accept. In R, I would like to change the format of the OTU table (from excel). Here is what I need to do, take Example 1 and create Example 2. The problem is that I have hundreds of OTUs, so I can't do this by hand (and I'd love to have a code that I