similar to: In vegan package: running adonis (or similar) on a distance matrix

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

Greetings, The website fivethirtyeight has a great plot. http://www.nytimes.com/interactive/2012/10/15/us/politics/swing-history.html Can this be done with R or GGobi or GGPlot? thanks, Tom

Hello all, I used google and looked at the documentation to find out why the ADONIS function is called adonis (in the vegan package). I am writing a document and would like to include a abbreviation list (similar to "ANOSIM = Analysis of Similarities"). regards, Steve

Hi, Somebody knows how to make contrasts if i'm using the function adonis? Thanks.

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:

I am trying to apply a permuation-based MANOVA (Anderson 2001) to a set of morphological data from three ecomorphs of fish reared under two different conditions and measured at two points during ontogeny. I will supply a distance matrix based on Procrustes distances calculated outside of vegan. I have not found an example of a design such as this for adonis. However, I have designed my factors

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'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: > CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but

Dear all, I am trying to get a PERMANOVA with quite large data set. I am reading a lot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs,

I am trying to apply this technique (M.J Anderson 2001) to a dataset of aquatic insect abundances. There is a sample in the unrestored and restored segement of a stream for every time period. I would like to compare the centroids of the distance matrices for the treatments up (unrestored) and dn (restored) to see if there is a difference in insect communities between the treatments. I will not

hello list, i'd appreciate help regarding formula expression in adonis(), package vegan. i'm interested in the effect of an impact on species composition and if this effect is the same for different sites. i have an impact survey with plot pairs, one plot with impact the other with similar ecolgical conditions but without impact, which is the control (factor1: impact). two different

Hello guys I am new to this list and for R too. I am wondering if there is a patch for the SPSS reading code on the foreign package, in order to be able to read long variable names. Right now read.spss() just trunc the names to 8 characters. Or if someone could help me on other way: I have to process everyday a lot of SPSS Syntax Files and Dat files that come from one system that can only export

Hi, I'm trying to build a mixed-effects model in which I'd like to include either a distance matrix or a phylogenetic tree as a random effect. The troubles I've had are that: 1. Function lmer() in package lme4 only accepts a data frame column as a random factor and not a distance matrix. 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and ultrametric phylogenetic

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

I'm working with capscale and permutest for the first time, and having trouble getting statistical analyses for more than one constraining variable. I've read the documentation, but setting first=FALSE or using by="axis" doesn't seem to be helping. capscale seems to be fine, I receive output for more than one constrained axis. What am I doing wrong?

Hi, I was recently misfortunate enough to have to use regular expressions to sort out some data in R. I'm working on a data file which contains taxonomical data of bacteria in hierarchical order. A sample of this file can be generated using: tax.data <- read.table(header=F, con <- textConnection(' G9SS7BA01D15EC Bacteria(100) Cyanobacteria(84) unclassified G9SS7BA01C9UIR

Hi All, I have a question which does not pertain directly to the use of R but comes from my use of R! I have data which can be described as 3-dimensional e.g. (x,y,z), with no negative component. The suggested way to analyze this data is via multivariate techniques or by calculating what amounts to a levene's test on the data and then an ANOVA on the three components if the first test is

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

We need a two-way non-parametric ANOVA in order to analysis properly some ecological data, do you know any reference in R? or how to do it? Thank you very much All the best diana -- View this message in context: http://www.nabble.com/Two-way-non-parametric-ANOVA--tp15039308p15039308.html Sent from the R help mailing list archive at Nabble.com.

Hi R helpers, I was wondering if anybody knows if is possible to generate bootstrap values for a cluster analysis in R. What I am trying to do is obtain some confidence on the clusters formed by resampling the data set. A similar type of analysis is used in molecular taxonomy and the confidence values of each cluster are placed in the nodes of the dendogram. Any ideas on how to do this