Displaying 20 results from an estimated 700 matches similar to: "memory failure in adonis function (permanova)"
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
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 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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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
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
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 -
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
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
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
2008 Jun 16
1
contrasts using adonis function
Hi,
Somebody knows how to make contrasts if i'm using the function adonis?
Thanks.
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
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
2013 Feb 08
1
vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande
---------- Forwarded message ----------
From: <r-help-owner@r-project.org>
Date: 2013/2/8
Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector
especificado es muy grande
To: caro.bello58@gmail.com
Message rejected by filter rule match
---------- Mensaje reenviado ----------
From: caro bello <caro.bello58@gmail.com>
To: r-help@r-project.org
Cc:
Date: Fri, 8 Feb 2013
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
2010 Feb 02
2
hvcluster() with distance method from vegdist(), package = vegan
hello,
i'd be happy if someone could provide help with the following problem:
i have a dist.matrix that comes from vegdist() function of the vegan
package. the used method = "horn" is not accepted as argument in
hvcluster(...,dist.method="...").
is there a way to incorporate the method "horn" in hvcluster()?
thanks in advance!
yours,
kay
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2013 Apr 11
1
Cannot find ldfortran (R on Cygwin)
Hi
I am new to Cygwin and Linux.
I installed R under Cygwin as part of the setup
I chose "All" during installation, for all packages. So I have the FULL
installlation of cygwin up and running, including gfortran.
*Under Cygwin, how do I check and configure the path to the various
libraries?*
I am trying below command and it says, cannot find "lgfortran"
But I have installed
2011 May 17
1
simprof test using jaccard distance
Dear All,
I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function:
> simprof
function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average",
method.distance = "euclidean", method.transform =
2014 Jul 04
2
[LLVMdev] MOS6502 target
I suppose that once you've got a 6502 working, adding support for a 4510
shouldn't be too difficult....
(http://c65gs.blogspot.com.au/)
On Fri, Jul 4, 2014 at 10:38 AM, Bruce Hoult <bruce at hoult.org> wrote:
> On Fri, Jul 4, 2014 at 12:02 PM, Edwin Amsler <edwinguy at gmail.com> wrote:
>
>> Well, the stack pointer be a single byte, so pushing things on there
2009 Mar 19
2
Server 2008 and Samba 3.0.25b
Hi Folks -
I'm experiencing a very strange problem with Server 2008 machines (for
all intents and purposes related to Samba, it's Vista) connecting to a
Samba Server. The Samba machine is a RHEL4.6 machine running Samba
3.0.25b. I am joined to the mixed mode AD domain via the command "net
rpc join -U administrator <domain>". I am not using winbind or
kerberos. Or