Displaying 20 results from an estimated 3000 matches similar to: "adonis, amova and haplotype frequency"
2008 May 22
1
AMOVA results from ade4 different than in the reference publication
Hello,
I am trying to run some AMOVA analyses with the amova function in the
package ade4.
When running the example dataset provided in ade4, I noticed a
difference between the published results from the same data (Excoffier
et al. 1992) and what ade4 calculates.
Below are the data for "within sample/population" from ade4 and from the
haplotypic distance matrix in the paper:
2006 Nov 14
0
question about amova (ade4)
Hello,
I am interested in using the amova function of ade4 package of R. I
would like to know if there is any possibility to perform an amova with
a specific anova model, as a factorial anova with some factors nested,
or, if this could not be done, how could I perform an anova with my
specific model but with molecular distance data?
I would be very grateful if you could help me with this fact in
2012 Feb 11
1
AMOVA error: 'bin' must be numeric or a factor
Hi!
I am trying to analyse my data using amova
(http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova):
My input to R is a DNA sequence file, format=fasta
dna<- read.dna("XX.fasta", format="fasta") #left other options as
default
d<- dist.dna(dna, model="raw")
g<- read.table("XXX.design")
Load necessary libraries:
library(pegas)
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
2011 Jul 09
1
PERMANOVA+ and adonis in vegan package
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
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2010 Nov 24
0
AMOVA in R
Hi,
I'd like to conduct an amova in R from diploid genotpyic data. The packages
pegas and ade4 require a Euclidian distance matrix.
Is there a simple method to generate a dist object from genotypic data at
the individual level? I think the dist.genet of ade4 only generates
distances at the population level.
Thanks for any help,
Mike.
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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
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
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,
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
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
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
2008 Oct 14
1
question about amova (ade4)
Was there ever an answer to this question about how to do amova with factorial data?
t hundley
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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
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
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
2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
Hi All,
I am using canonical correspondence analysis to compare a community
composition matrix to a matrix of sample spatial relationships and
environmental variables. In order to parse out how much variance is
explained purely by space (S/E) or the environment (E/S) I am using a
conditional (partial) CCA. I want to test significance via Monte Carlo but
I can not find a way to do this with a
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 -
2010 Nov 09
0
haplotype and epistasis analysis using 3 or more SNPs?
Dear Mme/Mr.
Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers).
In addition can you please inform me how I can perform Haplotype analysis and if there is an
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,