similar to: Canberra distance

Hi, we have a split-plot experiment in which we measured the yield of crop fields. The factors we studied were: B : 3 blocks I : 2 main plots for presence of Irrigation V : 2 plots for Varieties N : 3 levels of Nitrogen Each block contains two plots (irrigated or not) . Each plot is divided into two secondary parcels for the two varieties. Each of these parcels is divided into three subplots

Bonjour, we wanted to fit a manova as descripted in Marieta /et al./ 2003, "convergent habitat segregation of /Aedes aegyptii/ and /Aedes albopictus/ (Diptera: /Culicidae/) in Southern Brazil and Florida", /J. Med. Entomol./, *40* (6), 785-794. They did their analysis with SAS software. We have the same kind of data with two insect species and city, habitat and season factors. We

Dear R-helpers, I have two data frames, op and em4: > str(op) 'data.frame': 37 obs. of 5 variables: $ m : num 0.202 0.336 0.122 0.139 0.14 ... $ lln : num 0.798 0.643 0.863 0.835 0.823 ... $ rrn : num 0.789 0.702 0.894 0.895 0.923 ... $ asym2: num 0.177 0.304 0.108 0.187 0.274 ... $ asym3: num 0.0755 0.0975 0.0818 0.0651 0.13 ... > str(rownames(op)) chr

Is it possible to make disappear the id numbers from scatter.dudi (mc analysis) ? a <- as.factor(c(1, 2, 3, 2, 1)) b <- as.factor(c(3, 2, 3, 1, 1)) x <- as.factor(c(1, 2, 2, 1, 3)) y <- as.factor(c(2, 2, 3, 1, 1)) dat <- data.frame(a=a, b=b,x=x,y=y) summary(dat) dat require(ade4) dat.acm <- dudi.acm(dat, scann = FALSE, nf = 2) scatter.dudi(dat.acm) Thank you very much !

Hi, we noticed there was a error in the "arules" package. After reading the source code, we saw that the Dice similarity index was "miscalculated" in "dissimilarity" function : an copy-paste from Jaccard Index was not corrected (2* a_b_c, ie 2*(a+b+c) in the code instead of 2*a +b + c !!!). After our mail to R-help (21/11/2006), we thought the authors could do

Dear All, I am using the scatter.dudi finction in the 'ade4' package to produce correspondence analysis (nice) plots. I do not seem to figure out how to plot the raw coordinates only -- or column coordinates only. I would appreciate any help in doing that. Here is the example I am following -- from the package. data(banque) > banque.acm <- dudi.acm(banque, scann = FALSE, nf =

Hi, I am using R 2.9.0. It seems the documentation for the calculation of Canberra distance using stats::dist is ambiguous. Does anyone have the original definition given in the Lance & Williams paper from Aust. Comput. J. 1, 15-20, 1967? When there are zeros at certain position in both vectors, they are not omitted as documented in the function (see below). Instead, Canberra distance is

Hello I have some kind of problem with R. I want to do a pca (I work on R and ade4 library) but R doesn't wan to realize my pca because of my data: I have some binary variable (presence/absence of birds, hole, vegetals...) and metric variable (cliff 's size...) and each time I have an error message because of the mix of the 2 type of variable. So, what can I do? Famille SALMON

Hello R-ers, I'm trying to do a weighted principal components analysis. I couldn't find any such option with princomp or prcomp. Does anyone know of a package or way to do this? More specifically, the observations I'm working with are averages from populations of varying sizes. I thus need to weight the observations by sample size. Ideally I could apply these weights at the cell

Dear R-users How can I get the eigenvalues out of an lda analysis? thanks a lot christoph -- Christoph Lehmann <christoph.lehmann at gmx.ch>

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

Hello, I am trying to run a PCA in R and I cannot get the PC scores for each of the values. Using pcX <- princomp(X) then loadings(pcX) I can get a listing of the eigenvectors but not the actual PC scores for each value in the dataset. I greatly appreciate any help anyone can offer Thanks Ken

Hi the list, According to what I know, the Canberra distance between X et Y is : sum[ (|x_i - y_i|) / (|x_i|+|y_i|) ] (with | | denoting the function 'absolute value') In the source code of the canberra distance in the file distance.c, we find : sum = fabs(x[i1] + x[i2]); diff = fabs(x[i1] - x[i2]); dev = diff/sum; which correspond to the formula : sum[ (|x_i - y_i|) /

> Hi > I'm Ph.D student and I need an R code to compute the chi square diistance between n profile rows in a matrix. > > could you help me please? > Thanks > > Paola > ____________________________________________________________

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

Hi all I?m trying to tests the significance of loadings from a ordination of 46 variables (caategorical, ordinal and nominal). I used dudi.mix from ade4 for the ordination. A years ago Jari Oksanen wrote this script implementing Peres-Neto et al. 2003 (Ecology) bootstraping method: netoboot <- function (x, permutations=1000, ...) { pcnull <- princomp(x, cor = TRUE, ...) res

Dear R-user, I am trying to use the function 'parLapply' from the 'snow' package which is supposed to work the same wys as 'lapply' but for a parallelized cluster of computers. The function I am trying to call in parallel is 'dudi.pca' (from the 'ade4' package) which performs principal component analyses. When I call this function on a list of

Hola compañeros de la lista. Qué tal. Tengo un análisis de componentes principales, en el que se evalúan aproximadamente 1000 variables. Usando la función dudi.pca e inertia.dudi obtengo una cantidad de información sobre la influencia de las variables sobre los dos componentes principales. Me gustaría saber si existe alguna función que sobre esta información me arrojara la lista de

Dear R-users, Is there an easy way to avoid points one upon another when ploting rows and columns of 'dudi' objects ? Maybe there is a function in ade4 or in an other package, or maybe someone has his or her own function to do this (for example to automatically modify a little the coordinates of these points to get a readable plot ?). Thanks in advance. Best regards, Jacques VESLOT

Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c("x","x2") I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=",") and now, I just need a function to transform this string into a adequate