similar to: BIOENV

Dear vegan team, Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not

Hi All, I am trying to perform CCA and RDA several times to compare their performances. To do that I put this two functions of vegan package inside a for loop. Unfortunatly when I am trying to perform the anova(by=axis) to test the individual axes the function don't recognize the species data.frame. The same problem occurs whem I try to run forward selection. The same problem occur when I try

Hi everyone, I?m a student and relatively new to R so apologies in advance if this question seems stupid or obvious to you. I have collected a dataset with about 60 species of diatoms (count data from 19 different sample sites) and environmental variables for each site (salinity, pH, etc.). It?s all in the same dataset but distinct in R through the functions below diat <- diatom [, 1:60]

Dear R users, I am having a problem performing the mantel test (both with functions mantel {vegan} and mantel.test {ape}) due to I believe the presence of NAs on my distance matrices, which look like e.g.: NA 1 2 1 2 3 NA 4 5 6 and 1 1 2 2 3 4 5 6 7 8 Would any of you have a solution for that? Thank you for much for your help! Marcia Rocha -- View this message in

To all moderators i guess, my question was probably not clear this is not a homework, i am trying to understand R by doing some exercise in my book. I will however participate a course in R in august and thought it could be good to have some knowledge before. I hoped for help from you since i have no instructor to ask, that would have been my first choice. thanks anyway Lotta

> Background: > OS: Linux Ubuntu Dapper > release: R 2.3.0 > editor: GNU Emacs 21.4.1 > front-end: ESS 5.2.3 > ----------------------------- > Colleagues > I have two spatial datasets (latitude, longitude, fish eggs) and (latitude, longitude, fish larvae) at the same 280 stations (i.e. 280 cases). I want to determine if the 2 datasets are spatially correlated. In other

Dear R-help, We are conducting a distance-based redundancy analysis using capscale and then testing for statistical significance for six terms in the model for the constrained ordination using anova.cca in the vegan package. The significance test is sequential, i.e., testing for significance of a term only after accounting for all preceding terms. Could someone please provide us with either the

I would like to know how to run a partial mantel test controlling for spatial autocorrelation and correlation with other environmental variables. It seems that with function included in vegan for partial mantel test I can only test for the relationship between two variables controlling for the effect of a third one. Thanks a lot Alexandra --- Lic. Alexandra Sapoznikow Centro Nacional

Hi, I was wondering if someone can tell me what is the difference between "strata" argument (function "adonis" in "vegan" package) and using random effects in PERMANOVA+ add-on package to PRIMER6 when doing permutational MANOVA-s? Is the way permutations are done the same? Thank you very much in advance, Vesna -- View this message in context:

Hola amigos: Quisiera saber si alguna opción en R del software primer para análisis de datos multivariantes en ecología Gracias Javier [[alternative HTML version deleted]]

Hi, i'm looking to test if two distance matrices are statistically different from each others. These two matrices have been computed on the same set of data (several population samples) 1. using a particular genetic distance 2. weighting that genetic distance with an extra factor (we can look at this as one set is computed before applying a treatment and the second one after applying

Dear Gavin, What is the interpretation of a simulated p-value of 1 in a mantel test and how is the p-value derived? When we run two highly negatively correlated matrices we get this result: r: -1, simulated p value: 1 I would expect the high p-value of 1 to mean not significant. Could you clarify? Thank you, Jason Jason P. Sexton Graduate Group in Ecology University of California,

1. Emma is performing an experiment that requires individual handling of some animals. The sizes of the animals are lognormally distributed: The natural logarithms of their sizes has a normal distribution with mean 3 and standard deviation 0.4. The time (in minutes) it takes to handle each animal is given by 10 + s · 1.5 + eε for animals with s ≤ 20 20 + s · 0.8 + eε for animals with s > 20

Hello! I'm a PhD student working with coral reef fish diversity in Mexico. I want to do species accumulation curves but I have differential sampling effort for each "sample". Do you know or have developed an R script that consider the differential effort of each sample? PRIMER and other programs use each pack of species as a replica without the possibility of telling the program that

Dear all, Is there a package in R that has implemented the MANN (Multiresponse Artificial Neural Network) presented in (Olden, 2006 - Ecological Applications)? Best Wishes, -- Prof. Gilson Correia de Carvalho, M.Sc. ---------------------------------------------------- Pesquisador Associado Laboratório de Ecologia Bentônica - LEB Instituto de Biologia - UFBA Universidade Federal da Bahia - UFBA

Dear, Some analysis (linear regression) can only be done from a vectorized dataset whereas others require a matrix (Mantel tests). I use the two analyses and thus need to format my data in matrix and vector. I spent some time trying to solve the problem and I just gave up. Did anyone knows how to transform a matrix into a vector and back-transform a vector into a matrix? Thanks by

Dear all, Dose anyone know whether there is a good R packege or program for Mantel's randomization test? Thanks in advance. ------------------------ Takashi Mizuno zoono at sci.osaka-cu.ac.jp Plant Ecology Lab. Osaka City University ------------------------ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

Hii rstudio members I am learning rstudio, For my manuscript I am trying to plot CCA using species and environmental data. But I am getting error like Error in cca.default(sptrans, envtrans) : all row sums must be >0 in the community data matrix *My code is like * library(vegan) library(ggplot2) library(dplyr) rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",

I've written a function that regularly throws the "cannot allocate vector of size X Kb" error, since it contains a loop that creates large numbers of big distance matrices. I'd be very grateful for any simple advice on how to reduce the memory demands of my function. Besides increasing memory.size to the maximum available, I've tried reducing my "dist" objects to 3