similar to: R 2.3.1 on Mac OSX: apply a function to 'dist()' ?

I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA. This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error. is it possible to perform this test in ecodist? many thanks

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a

Hi, I’m looking at RegBankSelect’s partially implemented support for deciding to split a value between multiple registers and I’m wondering if it’s actually intended to solve the problem I’m trying to use it for. RegisterBankInfo.h has this example mapping table: /// E.g., /// Let say we have a 32-bit add and a <2 x 32-bit> vadd. We /// can expand the /// <2 x 32-bit> add into

Bonjour, I would like to back up several desktop computer, and notebooks who are running under Mac OS, on a linux server with ext3 filesystem. I try several times with rsync, using include lists ( --include-from=my_include_file). The include list is working except for directory and filename with special character ( like french one : ?,?,? etc ...). The pattern in the include list don't match

I wish to generate a vector of uniformly distributed data with a defined correlation to another vector The only function I have been able to find doing something similar is corgen from the library ecodist. The following code generates data with the desired correlation to the vector x but the resulting vector y is normal and not uniform distributed library(ecodist) x <- runif(10^5) y

Hi all, I'm new on the list, so I want to say hello for everybody! I'm from Hungary and writing a LLVM backend for Tile64 processor as my master's thesis. It's a big time pressure on me, so the thesis will probably describe a backend only providing an assembly printer, but the development is likely to be continued beyond the thesis. For now, I've run into a very annoying

Hi, I'm interested in incorporating some interaction terms between my explanatory variables (distance matrices in this case) when I'm using the function MRM of the package ecodist. The function is doing a multiple regression on distance matrices. I can get the function to work perfectly on my explanatory matrices by adding a (+) sign as known. However, when I try to use the (*) sign or

On 25 October 2013 11:06, Richard Sandiford <rsandifo at linux.vnet.ibm.com>wrote: > I wanted the same thing for SystemZ, which doesn't have vectors, > in order to improve the llvmpipe code. > Hi Richard, This is a nice patch. I was wondering how hard it'd be to do that, and it seems that you're catching lots of corner cases. My interest is also due to converting odd

Dear R colleagues, a friend and I are trying to develop a modest workflow for the problem of decomposing tests of higher-order terms into interpretable sets of tests of lower order terms with conditioning. For example, if the interaction between A (3 levels) and C (2 levels) is significant, it may be of interest to ask whether or not A is significant at level 1 of C and level 2 of C. The

Dear Dr.Goslee and anyone may intrested in matrix manipulate, I am using your ecodist to do mantel and partial mantel test, I have locality data and shape variation data, and the two distance matrixs are given as belowings. When I run the analysis, it is always report that the matrix is not square, but I didn't know what's wrong with my data. Would you please help me on this. I am quite

Hi there, I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test. Specifically, the permutation has to accomplish something like this: Original matrix addresses: a11 a12 a13 a21 a22 a23 a31 a32 a33 Example

Hi all, I'm searching for a little clarification on partial mantel tests (ecodist package) I've a distance matrix (x,y), and several others containing environmental/chemical variables. Based on the help file, and the package instructions I've managed to implement the tests as; var1 ~ env1 + space to partial out the effect of space and test the relationship between the

I am using the function metaMDS with jaccard distances to ordinate a set of constituent by site matrix. I can post this data if it would be helpful, but it is large to include in an email. I can also provide reproducable code if necessary. I would like to get an R^2 value for the axes of the ordination configuration that I get with metaMDS in the vegan package is there a way to do this- is it

Hi folks, I am having trouble accessing sub-functions when the main function is stored in an array. For example, the following test code works fine: fcns = c(abs, sqrt) fcns[[1]](-2) fcns[[2]](2) However, when I try to access sub-functions declared within list() in a function, this only works directly. When I try to access these within an array only the first declared sub-function is run.

I would like to put confidence intervals on a mantel corellogram they are already calculated in the pmgram object but I am unsure how I get the x value in order to plot them? package(ecodist) X<-1:100 Y<-rnorm(1:100) Z<-rnorm(1:100) XY<-dist(data.frame(X,Y)) YX<-dist(data.frame(Y,X)) my.mgram<-mgram(XY,XZ) plot(my.mgram) print(my.mgram) > print(my.mgram) $mgram

Hi, forgive me if someone has already posted about this but I have had a look and cannot find the answer, also I am very new to R and been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am

Hi!! I am trying to generate data with specific correlation using corgen method from the ecodist package. It does not seem to generate the data properly. I am listing the code below. Secondly, when I put the code given below all in one file and source it, it is unable to complete the task. But when I execute it one at a time it is able to complete it. Can someone point out any mistake that I may

Hi all, I'm hoping someone could tell me what best practices are as far as keeping programs organized in R. In most languages, I like to keep things organized by writing small functions. So, suppose I want to write a function that would require helper functions or would just be too big to write in one piece. Below are three ways to do this: ################### Style 1 (C-style)

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

I have a table like this: Date TIME Q A a 1 A b 2 A c 3 B a 4 B b 5 B c 6 C a 7 C b 8 C c 9 I want use R language to turn it to a matrix like : a b c A 1 2 3 B 4 5 6 C 7 8 9 I am new to R , anyone can help? Thanks in advance! have a table like this: Date TIME Q A a 1 A b 2 A c 3 B a