similar to: question about amova (ade4)

Hello, I am trying to run some AMOVA analyses with the amova function in the package ade4. When running the example dataset provided in ade4, I noticed a difference between the published results from the same data (Excoffier et al. 1992) and what ade4 calculates. Below are the data for "within sample/population" from ade4 and from the haplotypic distance matrix in the paper:

Hello, I am interested in using the amova function of ade4 package of R. I would like to know if there is any possibility to perform an amova with a specific anova model, as a factorial anova with some factors nested, or, if this could not be done, how could I perform an anova with my specific model but with molecular distance data? I would be very grateful if you could help me with this fact in

Hi! I am trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

Hello, I'm new to the installation R on Linux and I've followed the instructions on the R Installation and Administration Manual and on the FAQs. I also have changed the path at the .bash_profile file but when I try to type R at the shell prompt, it says: Fatal error: R home directory is not defined I've tried many things but all the time it says the same. Any help would be

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

Dear All, I'd like to perform adonis (from the vegan package) rather than amova (in ade4) on some haplotype data, as I have crossed factors. Is there a simple way to tweak the source to allow weights (haplotype frequencies) in a similar way to amova? Best Simon

Hi, I'd like to conduct an amova in R from diploid genotpyic data. The packages pegas and ade4 require a Euclidian distance matrix. Is there a simple method to generate a dist object from genotypic data at the individual level? I think the dist.genet of ade4 only generates distances at the population level. Thanks for any help, Mike. [[alternative HTML version deleted]]

Hi, I'm trying to install de RSPerl module and i have some problems trying to test it. I've tried to contact with the author but the e-mail address seems not to exist. Hope that anyone in this list could explain me a little about this problem. I have a bash shell and what i do is the following: #PERLLIB=/usr/lib/R/library/RSPerl/share/blib/arch:/usr/lib/R/library/RSPerl/share/blib/lib #

The ade4 package (v. 1.2-1) has been updated on CRAN. New features include: - functions based on Rao's axiomatization of diversity measures : Rao's diversity coefficient and dissimilarity coefficient (divc and disc) - functions based on Excoffier et al. analysis of molecular variance with tests of the difference among the factors (amova). - functions introducing double principal

The ade4 package (v. 1.2-1) has been updated on CRAN. New features include: - functions based on Rao's axiomatization of diversity measures : Rao's diversity coefficient and dissimilarity coefficient (divc and disc) - functions based on Excoffier et al. analysis of molecular variance with tests of the difference among the factors (amova). - functions introducing double principal

Un saludo R-inómanos: Les escribo porque tengo una duda que no he podido resolver por mis medios y actuales conocimientos. He querido instalar el paquete "ade4" en R (OP linux-ubuntu) pero no he podido por un error que según entiendo está relacionado con una librería. Me permito mostrarles el texto que me aparece luego de tratar de instalarlo desde los repositorios: >

Dear List, I tried to conduct cca using csv data but failed. The message said that data.frame is required. Please kindly share how to convert a csv-imported file to a data.frame. Thank you. Elaine code rm(list=ls()) spec <-read.csv("c:/migration/M_R_20100718_winterM_spec_vegan.csv",header=T, row.names=1) dim(spec) spec[1,] envi

Dear List, I used spec and envi for cca in ade4. (both are data.frame) However, there is a message telling that error in if (nf > rank) nf <- rank R missing value in TRUE/FALSE Please kindly help how to modify the code below. Thank you. Elaine code rm(list=ls()) spec <-read.csv("c:/migration/M_R_20100718_winterM_spec_vegan.csv",header=T, row.names=1) dim(spec) spec[1,]

Hello I'm using the package ade4 to obtain classification from a .txt file. I use the following commands: cronquist <- read.table("cronquist.txt", h = T, row.names = 8) cronquist <- as.taxo(cronquist[7:1]) cro.phy <- taxo2phylog(cronquist) in which cronquist.txt is a file with a classification of 218 genus of tree species from french Guiana. We I try to use the

Un saludo a todos. Estoy haciendo un ACC y utilizo el paquete Ade4. Cuando quiero realizar un plot del resultado utilizo plot(). el resultado son 6 gráficos: loadings, correlation, inertia axes, scores and predictions, eigenvalues y species. Lo que quería saber es cómo representar en una sola ventana (los 6 gráficos a parecen en la misma) el gráfico correspondiente a Species. Gracias por vuestra

I have used the fourthcorner function as suggest by dray and legendre (model 2 and 4 then combine). I plot the combined value with plot(four.comb, type="G"). What do the colors mean? I have both grey and black bars. many thanks, Stephen -- Stephen Sefick ************************************************** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama

Dear R-Help i have a newbie question, how edit size fonts and colors in the plots (scatter.acm or dudi.acm function) of multiple correspondence analysis in the ADE4 Package? thanks? Rafael Gutierrez Estad??stico Unidad de Tecnolog??a Cerro Matoso S.A. Tel. 4-7723350 Fax. 4-7723236 ************************************************************************************************* Este correo

Hi all: How can I calculate the cumulative variance (or variance for each component) in correspondence analysis? If were possible in ADE4 package Thank you -- Antonio Punzón Merino O__---- Instituto Español de Oceanografía c/ /'_ --- Centro Oceanográfico de Santander (*) \(*) -- Promontorio de San Martín S/N ~~~~~~~~~~ 39004-Santander; Spain PO BOX: 240 Tlf: +34 942 29 10 60 Fax: +34

Dear all, I am interested in solving a MIP problem with binary outcomes and continuous variables, which ARE NOT RESTRICTED TO BE NEGATIVE. In particular, Max {z1,z2,z3,b1} z1 + z2 + z3 (s.t.) # 7 z1 + 0 z2 + 0 z3 + b1 <= 5 # 0 z1 + 8 z2 + 0 z3 - b1 <= 5 # 0 z1 + 0 z2 + 6 z3 + b1 <= 7 # z1, z2, z3 BINARY {0,1} # -5<= b1 <=5 (i.e. b1 <= 5; -b1 <= 5 ) Using

How do I change the postion of the legend in s.value {ade4} from the defaul , bootom left? thanks Nevil Amos