Displaying 20 results from an estimated 300 matches similar to: "Using the mantel test in Ape Package"
2010 Sep 21
1
partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse
genetic distance data ( provided as a dist object calculated using
dist.genpop in package adegenet) with geographic distance partialled out
( provided as a distance object using dist function in veganthis method
is attempting to follow the method used by Geffen et al 2004 as
suggested by Legendre and . FORTIN (2010).
I
2002 Sep 05
0
ape 0.1 is released
Ape is an R package for "analyses of phylogenetics and evolution". The
first version (0.1) has been released on 27 August 2002 and is available on
CRAN.
>From the 'Description' file of version 0.1:
Ape provides functions for reading, and plotting
phylogenetic trees in parenthetic format (standard Newick
format), analyses of comparative data in a
2011 Dec 03
1
partial mantel tests in ecodist with intential NA values.
I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA.
This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error.
is it possible to perform this test in ecodist?
many thanks
2009 Dec 17
2
mantel test and NAs
Dear R users,
I am having a problem performing the mantel test (both with functions mantel
{vegan} and mantel.test {ape}) due to I believe the presence of NAs on my
distance matrices, which look like e.g.:
NA
1 2
1 2 3
NA 4 5 6
and
1
1 2
2 3 4
5 6 7 8
Would any of you have a solution for that?
Thank you for much for your help!
Marcia Rocha
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2009 Sep 01
2
Mantel test least square line
Hello, I performed a Mantel test and plotted communitiy similarities. I
would like to add a least square line. I thought about using abline taking
as slope the r-statistic of the Mantel test and calculating the y-intercept
analytically. Is this method correct? Is there any function for this
calculation? Thank you
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2017 Dec 31
1
Perform mantel test on subset of distance matrix
I'm trying to perform a mantel test that ignores specific pairs in my
distance matrices. The reasoning is that some geographic distances
below a certain threshold suffer from spatial autocorrelation, or
perhaps ecological relationships become less relevant that stochastic
processes above a certain threshold.
The problem is that I can't find a way to do it. If I replace values
in either or
2009 Sep 14
1
Mantel test
Hello! It is not really linked to R, but can somebody explain me why we
sometimes make a mantel test directly for to distance matrices and sometimes
we first make a gradient analysis and then a mantel test between the axis?
Thank you
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2007 May 08
3
Mantel-Haenszel relative risk with Greenland-Robins variance estimate
Does anyone know of an R function for computing the Greenland-Robins
variance for Mantel-Haenszel relative risks?
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
2008 Apr 19
1
Mantel-Haenszel for 2x2
Hi all,
Does anyone know if an R function for the Mantel-Haenszel chi-square for a
2x2 table exists? I’ve also seen it called the randomization Q statistic.
Note that I’m not looking for the Cochran-Mantel-Haenszel…I did see that out
there as cmh.test.
Thanks in advance,
Jeff
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2006 Feb 23
1
partial mantel test
I would like to know how to run a partial mantel test controlling for spatial
autocorrelation and correlation with other environmental variables. It seems that
with function included in vegan for partial mantel test I can only test for the
relationship between two variables controlling for the effect of a third one.
Thanks a lot
Alexandra
---
Lic. Alexandra Sapoznikow
Centro Nacional
2006 Oct 13
1
Mantel test!
Dear Sir/ Madam,
I would like to ask you about mantel test in R. In ade4 package, if I
want to use mantel.rtest, I get error massage "Object of class to "dist"
expected". As I already have two dissimilarity matrices, shall I again
compute distance measure using this function?
If not, could you please let me know which function/command I can use to
do?
Thank you very much in
2010 Jan 07
1
Mantel results shown in a graphical (histogram) form.
I am new at 'R' and not even sure whether I am contacting the appropriate
forum!! However, I have carried out several mantel tests (using 'R') on
genetic data and would like to plot the results in the form of a histogam of
the distribution - and preferably use a procedure that shows the critical
'r' value.
The tail end of my analysis is shown below. I just need help to dig
2011 May 31
0
Mantel - like analysis
Hello,
I've used mantel tests a fair bit for standard genetic/geographic/landscape
analyses. I realize it involves permutations of rows and columns in the
matrix to obtain correlation coefficients.
However, for a certain question, I am interested in populations that are
nearest neighbours to each other, and identifying factors that affect
genetic distance between them. So because of
2013 Mar 18
1
Mantel test for comparing two matrices
Hi everyone,
I have two matrices of 2000x2000 size. They consist of a measurement of
RMSD deviations of a protein structure. The basic question i want
to answer is the following: are there a significant differences between
the two matrices?
I aim to use the Mantel test. I don't really know if this is a good idea or
if there are better solutions for these mega matrices.
Thanks
[[alternative
2009 Mar 03
1
Mantel test!
Dear Gavin,
What is the interpretation of a simulated p-value of 1 in a mantel
test and how is the p-value derived? When we run two highly
negatively correlated matrices we get this result: r: -1, simulated p
value: 1
I would expect the high p-value of 1 to mean not significant. Could
you clarify?
Thank you,
Jason
Jason P. Sexton
Graduate Group in Ecology
University of California,
2009 Feb 27
1
Ordinal Mantel-Haenszel type inference
Hello,
I am searching for an R-Package that does an exentsion of the Mantel-Haenszel test for ordinal data as described in Liu and Agresti (1996) "A Mantel-Haenszel type inference for cummulative odds ratios". in Biometrics. I see packages such as Epi that perform it for binary data and derives a varaince for it using the Robbins and Breslow variance method. As well as another pacakge
2012 Jan 14
1
metafor: weights computation in Mantel-Haenszel method
Dear R users,
In metafor 1.6-0, the Mantel-Haenszel method is implemented by the rma.mh() function. I have observed that the sum of the weights computed by weights(x) doesn't add to 100% when x is an object of class rma.mh. The consequences of this fact can be clearly seen when a forest diagram is drawn with forest(x), which calls weights(x) (or more precisely, the method weights.rma.mh()
2007 Mar 06
1
Quick question on Cochran-Mantel-Haenszel test
Dear List,
I am looking for what B.S.Everitt refers to as Cochrane Method for testing
independence in combined 2x2 contingency tables. Is it the same method as
the Cochran-Mantel-Haenszel Chi-Squared Test for Count Data in R?
Thanks,
Serguei
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2012 Sep 18
1
Cochran-Mantel-Haenszel test
Hello,
I have some satellite tag time-at-depth (TAD) frequency data that I
would like some help with.
The data was transmitted via satellite as percent time spent in each of
7 depth bins (0m, 0-1m, 1-10m, 10-50m etc.), binned over 6-hour
intervals. I categorized each row of data corresponding to a date and
time into summer vs. winter, and day vs. night, and then summed and
averaged the given
2003 Sep 12
2
partial mantel
Dear all,
Has anyone written R code for partial Mantel Tests- as described for
instance in Legtendre & Legendre (1998) ?
In other words, in a community ecology analysis, I would like to calculate
the correlation between two dissimilarity matrices, controlling for a third
distance matrix representing geographical distances between sites.
Thanks!
Christophe Bouget
Biodiversité et gestion des