similar to: help interpreting dudi.pco

I have a presence/absence matrix for which I create a distance matrix and then perform pco analysis on. /library(ecodist) table <- read.table("matrix.pa") dist <- dist(table, method = "euclidean", diag = FALSE, upper = FALSE) dist.pco <- pco(dist)/ When I plot the pco analysis of the distance matrix I want to be able to distinguish between certain characters, for

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

I tried to bootstrap the correlation between two variables x1 and x2. The resulting distribution has two distinct peaks, how should I interprete it? The original code is attached. Y. C. Tao ---------------- library(boot); my.correl<-function(d, i) cor(d[i,1], d[i,2]) x1<-c(-2.612,-0.7859,-0.5229,-1.246,1.647,1.647,0.1811,-0.07097,0.8711,0.4323,0.1721,2.143,

Hello, I not have attached in this e-mail the zipped list of matrices I am using because it has 1 meg once zipped and anyway we cannot send attached files on r-help mailling list. First, after running the code that is written bellow, I realized that the printout of dudi.pca gives me for both of my matrices $cw length that are unequal to either respective $rank or $eig lengths. Is that

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

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 fitting GLM?s and I can?t interprete the coefficients when I run a model with interaction terms. When I run the simpliest model there is no problem: Model1<-glm (Fishes ~ Year + I(Year^2) + Kind.Geographic + Kind.Fishers + Zone.2 + Hours + Fishers + Month, family = poisson(log)) # Fishes, Year, Hours, and Fishers are numeric, Kind.Geographic, Kind.Fishers, Zone.2 and

I want to compute the distances in a mixed variable matrix using the Gower coefficient. I understand it is possible to calculate distances in a matrix with mixed variables using the dudi.pco command. How would this work? Jorine

Dear R-Users, ade4TkGUI is a new package available on CRAN. It implements a Tcl/Tk graphical user interface (GUI) for the ade4 package. Only the most basic functions of ade4 have a GUI in this first version : classical one-table data analysis methods (PCA, COA, MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA), and two-tables analysis methods (Coinertia analysis, CCA, PCAIV).

Dear R-Users, ade4TkGUI is a new package available on CRAN. It implements a Tcl/Tk graphical user interface (GUI) for the ade4 package. Only the most basic functions of ade4 have a GUI in this first version : classical one-table data analysis methods (PCA, COA, MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA), and two-tables analysis methods (Coinertia analysis, CCA, PCAIV).

Dear all, I was looking for methods in R that allow assessing the number of significant principal coordinates. Unfortunatly I was not very successful. I expanded my search to the web and Current Contents, however, the information I found is very limited. Therefore, I tried to write code for doing a randomization. I would highly appriciate if somebody could comment on the following approach.

I'm sory for my weak english. I need to analyze this subject : x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 y 0 0 1 0 0 1 0 0 1 0 czarne 1 1 0 0 0 0 1 0 0 0 rude 0 0 1 0 0 1 1 0 0 0 braz 0 0 1 0 1 0 1 0 0 0 blond 1 0 0 0 0 1 0 0 0 1 rude 1 1 0 0 0 0 0 0 0 1 blond 0 0 1 1 0 0 0 0 1 0 czarne 1 0 0 1 0 0 1 0 0 0 blond 0 0 1 0 0 1 1 0 0 0 blond 1 0 0 0 0 1 1 0 0 0 czarne 0 0 1 0 0 1 0 0 0 1 czarne 1 0 1 0 0 0

I have been pulling my hairs out about this for a while now. Running the latest version of SuSE with all patches applied, I have my machine joined to the domain no problem. But when I go to use mount -t smbfs I get this error. Mounting share failed, smbmnt must be installed suid root for direct user mounts (1000,1000) smbmnt failed:1 Of course I hit Google and the list archives first before

Hi Jeff, We are splitting hairs because R is splitting hairs, and causing us problems. Integer and numeric are different R classes with different properties, mathematical relationships notwithstanding. For instance, the counterintuitive result: > identical(as.integer(1), as.numeric(1)) [1] FALSE Unfortunately the reply-to chain doesn't extend far enough -- here is the original

Use all.equal instead of identical if you want to gloss over integer/numeric class differences and minor floating point differences (and a host of others). Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Apr 11, 2016 at 5:25 PM, Paulson, Ariel <apa at stowers.org> wrote: > Hi Jeff, > > > We are splitting hairs because R is splitting hairs, and causing us > problems.

Hello, I haven't received a reply since I sent my last logs in, so I thought I'd ask again and update the thread.? I had trouble getting the server to work properly on dovecot 2.3.2 so I rebuilt the server back on 2.2.27.? I've got the quota enforcement itself working, but the warnings still fail to fire. ? I've attached logs with mail_debug=yes for the period from the send which

Hello, Most of the work was done with dovecot 2.2.27 but I just upgraded to 2.3.2 and didn't see any change.? Some debug logs are below, is there something specific I could search them for? Sep 17 23:19:16 ezm11-pco dovecot: auth-worker(8299): Debug: Loading modules from directory: /usr/lib/dovecot/modules/auth Sep 17 23:19:16 ezm11-pco dovecot: auth-worker(8299): Debug: Module loaded:

On 11/04/2016 8:25 PM, Paulson, Ariel wrote: > Hi Jeff, > > > We are splitting hairs because R is splitting hairs, and causing us problems. Integer and numeric are different R classes with different properties, mathematical relationships notwithstanding. For instance, the counterintuitive result: The issue here is that R has grown. The as() function is newer than the as.numeric()

Hello, I'm trying to implement quota enforcement in our mailservers, and it is all working properly except that the quota warnings are not firing when the quota levels are passed.? the server stops accepting email when the quota is reached, and you can see tyhe quota usage through the email client connected through, but as the quota passes the set levels the /usr/local/bin/quota-warning.sh

Hi, I have some difficulties in interpreting the prediction of a svm model using the package e1071. y1 is the variable I want to predict. It is of type factor and has got two levels: "< 50%" and "> 50%". z is the dataset. > model <- svm(y1 ~ ., data = z,type="C-classification", cross=10) > model Call: svm(formula = y1 ~ ., data = z, type =