similar to: adonis help - (non-parametric (permutational) manova)

h <- structure(list(V1 = c(-0.351714766, 0.188298251, 0.042951816, -0.072490327, -0.691885485, -0.816169763, -0.7066502, -0.856286332, -0.839723411, -0.427242353, -0.372911996, 0.326707494, 0.07847893, 0.687447841, 0.516105863, 0.267076547, 0.727867663, 0.432699191, 0.258610632), V2 = c(0.256636068, -0.824072121, -0.149185618, 0.153280492, 0.01649528, 0.409410528, 0.286015324, 0.366323539,

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, 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:

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, 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

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

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,

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

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

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

updn.gg <- (structure(list(date = structure(c(11808, 11869, 11961, 11992, 12084, 12173, 12265, 12418, 12600, 12631, 12753, 12996, 13057, 13149), class = "Date"), unrestored = c(1.13789418691602, 0.704948049842955, 0.276777348238899, 0.417586861554189, 0.504870337754768, 0.673201771716216, 0.560704221510771, 0.835737007551542, 1.10773858390693, 0.197070828834836, 0.942350681588179,

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

melt.updn <- structure(list(date = structure(c(11808, 11869, 11961, 11992, 12084, 12173, 12265, 12418, 12600, 12631, 12753, 12996, 13057, 13149, 11808, 11869, 11961, 11992, 12084, 12173, 12265, 12418, 12600, 12631, 12753, 12996, 13057, 13149), class = "Date"), variable = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,

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 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 R community, I have the following problem I hoped you could help me with. My data is save in thousand of files with a weird extension containing for numbers and a z. For example *.1405z. With list.files I managed to load this data into R. It looks like this (the row numbers are not in the original file): 35 :LATEST STAGE 3.60 FT AT 730 AM CST ON 0102 36

Hi all, after installing samba 2.2.5 (on Solaris8 running NIS+) it is not possible to create user entries in smbpasswd. I generated the smbpasswd file by # cat /dev/null | /samba/samba-2.2.5/source/script/mksmbpasswd.sh > /usr/local/samba/private/smbpasswd ----- then tried to create user entry "dummy" in smbpasswd by (user "dummy" exists under NIS+) # smbpasswd -a dummy

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