Displaying 20 results from an estimated 100 matches similar to: "PERMANOVA+ and adonis in vegan package"
2010 Mar 16
1
memory failure in adonis function (permanova)
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,
2011 Sep 09
2
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
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
2009 May 12
1
adonis help - (non-parametric (permutational) manova)
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
2009 Nov 03
1
why is adnonis function called adonis {package vegan}
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
2008 Jun 16
1
contrasts using adonis function
Hi,
Somebody knows how to make contrasts if i'm using the function adonis?
Thanks.
2009 Aug 11
1
nested repeated measures MANOVA using adonis
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
2011 Oct 04
2
Adonis and nmds help and questions for a novice.
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
2008 Apr 10
1
adonis (vegan package) and subsetted factors
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
2012 Oct 11
2
In vegan package: running adonis (or similar) on a distance matrix
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
2010 Feb 25
1
adonis(), design
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
2012 Feb 02
0
Two-Way PERMANOVA with Repeated Measurements
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,
2010 Aug 09
0
permanova on MICE object
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
2011 Jan 12
0
adonis, amova and haplotype frequency
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
2013 Jul 10
0
permanova for multivariate repeat measures toxicology data set
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 -
2008 Apr 27
1
An ANOVA test that uses a distance matrix like hierarchical cluster analysis?
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
2009 Oct 10
7
SPSS long variable names
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
2014 Sep 13
1
vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)
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
2008 Jan 23
6
Two-way non-parametric ANOVA?
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
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2007 Nov 16
1
Nonparametric manova
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
2013 Nov 28
1
Multivariate dispersion & distances
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