search for: adonis

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 looking at diversity in different soils with either woodland or grassland habitats. I have run the scr...

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&quo...

...on 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 for this test which hopefully will work. This design is just to understand the principals of this test, my real data set is comprised of over a thousand specimens. Column 1 represents the ecomorph, column 2 respresents diet, column 3 represents family (nested i...

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, 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: http://r.789695.n4.nabble.com/PERMANOVA-and-ad...

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

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: i...

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, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 2: In vegd...

Hi, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in microbial eco...

...04 dn 1204 dn 0104 up 0104 up 0106 up 0106 up 0203 up 0203 up 0503 up 0503 up 0704 up 0704 up 0803 up 0803 up 0804 up 0804 up 0805 up 0805 up 1005 up 1005 up 1102 up 1102 up 1204 up 1204 up my site x species matrix is called a, so here is the call to adonis: adonis(a~site, data=b, strata=b[,"date"] ,Permutations=999) Is this the correct way of testing the null hypothesis that : There is no difference in community structure between treatments. Thank you very much in advance, and anything that you need to make this easier please don't...

...#PerMANOVA step1<-read.delim2("day20.txt", row.names=1) library(clusterSim) step2<-data.Normalization(step1,type="n10") step3<-asin(sqrt(step2))*57.3 step4<-t(step3) library(vegan) step5<-data.matrix(vegdist(step4,method="bray")) attach(step5) step6<-adonis(step5~Sample1+Sample2+Sample3,data=step5) [[alternative HTML version deleted]]

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

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

Hi everyone! I have data consisting of several response variables and several explanatory variables. I wish to do a permanova on this using the vegan library and the adonis() function. However, my data had several missing values in it. In order to 'fix' this I used the mice() function from the mice library to make 5 imputations for all the missing values. To do analysis on the 5 datasets with different imputed values, the mice library includes the with.mids()...

Hello, I want to perform a permanova where the first factor called Treatment has four levels. The second factor involves sampling the same research plots for four consecutive years, hence the repeated measurements. I have been able to use the adonis function from the package vegan to run this analysis. code below: TC.perMANOVA.adonis<-adonis(TC.PerMANOVA ~ Treatment*Year, data=TC.PerMANOVA.ENV, permutations=99, method="bray", strata = NULL) However, my concern is that this does not take into account that Year is a repeated measu...

Hello, I would like to use a permanova to analyze my repeated measures, multivariate data set using the package vegan (adonis function). I have several explanatory variables and many clinical biochemistry/hematological response variables (all continuous, non-normally distributed). My explanatory variables are: ID - 29 levels - individual subjects Treatment - 2 levels Sex - 2 levels Time - 11 levels - subjects were t...

...ns functions that earlier only had simple permutation. Of course, you do not need to use fancy permutation schemes, but the default is still simple permutation and this can be expressed by giving just the number of permutations on the command line. The functions using the new permutation scheme are adonis, anosim, anova.cca for CCA/RDA/dbRDA and hence also for ordistep etc., CCorA, envfit, mantel & mantel.partial, mrpp, mso, permutest.betadisper, permutest.cca, protest and simper. The change for functions is now complete, but same clean up and updating of documentation is still to be done. This...

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, I have seen a discussion in the R-help asking whether nonparametric manova has been implemented in R yet. This discussion is form March 2006 and there seemed to be no package or function implemented at the time. Has this changed? Is there a package that provides nonparametric manova as in McArdle and Anderson (2001) and Anderson (2001) now? Thanks, Daniel ------------------------- cuncta

Dear All, I'm using betadisper {vegan} and I'm interested not only in the dispersion within the group but also the distances between the groups. With betadisper I get distances to group centroids but is it possible to get distances to other groups centroids? It might be possible to do it by hand by the formula given in the description of the betadisper (below) but I'm a bit confused