Displaying 20 results from an estimated 4000 matches similar to: "testing difference (or similarities) between two distance matrices (not independent)"
2013 Apr 06
1
list of distance matrices
Dear UseRs,
i want to apply mantel test by comparing a list of 124 distance matrices with a reference distance matrix "q". The list of distance matrices was created by the following command..
u<-lapply(el, function(x) dist(x))
where "el" is a data frame of 75 columns and 124 rows. Therefore, the list of distances matrices, made out of it should have 75 elements each
2005 Oct 06
1
Compare two distance matrices
Hi all,
I am trying to compare two distance matrices with R. I would like to
create a XY plot of these matrices and do some linear regression on
it. But, I am a bit new to R, so i have a few questions (I searched in
the documentation with no success).
The first problem is loading a distance matrix into R. This matrix is
the output of a the Phylip program Protdist and lookes like this:
5
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
2008 Jul 25
1
Write lower half of distance matrix only
Hi,
I'm very new to R. I want to know if there is any way to write only the
lower half of a distance matrix created in R to a csv file for example. I
get the 'cannot coerce class "dist" into a data.frame' message when I try.
I have used as.matrix and can write to a file this way, but as a full
matrix.
The reason I only want the lower half is that I've been doing some
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
2007 Nov 16
4
Permutation of a distance matrix
Hi there,
I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test.
Specifically, the permutation has to accomplish something like this:
Original matrix addresses:
a11 a12 a13
a21 a22 a23
a31 a32 a33
Example
2006 Oct 02
1
finding correlation between two matrices
Dear all,
I would like to compare two distance matrices to find the correlation
between those and create a XY plot.could you please kindly help me and
let me know how I can do that using R.(Mantel test?).
Your help is very much appreciated!! Many thanks!
Regards,
Sima Fakheran
...............................................................
Sima Fakheran Esfahani
PhD Student
Institute of
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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2000 Jul 26
3
Correlation matrices
Hello,
are there any good methods in R that will test if two correlation matrices (obtained in different ways) are equal? Something better than the Mantel test would be preferable.
Regards,
Patrik Waldmann
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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
2008 Mar 13
1
Convert a List of Distances to a Distance Matrix
Hello,
Is there an easy function for switching list to matrix. My list is of
genetic distances between species pairs:
A A 0
A B .5
A C .25
B C .5
and I want a distance matrix such as:
A B C
A 0 .5 .25
B .5 0 .5
C .25 .5 0
for use in a mantel test.
Thank you for the help!
cheers,
charlie
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Charles G. Willis
Department of Organismic
2004 Nov 16
5
Difference between two correlation matrices
Hi
Now a more theoretical question. I have two correlation matrices - one
of a set of variables under a particular condition, the other of the
same set of variables under a different condition. Is there a
statistical test I can use to see if these correlation matrices are
"different"?
Thanks
Mick
2011 Jun 28
1
plotting survival curves with model parameters
Hello.
I am trying to write an R function to plot the survival function (and
associated hazard and density) for a Siler competing hazards model.
This model is similar to the Gompertz-Makeham, with the addition of a
juvenile component that includes two parameters---one that describes
the initial infant mortality rate, and a negative exponential that
describes typical mortality decline over the
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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2010 Apr 04
2
"mantel.haenszel.test for trend in S-plus doesn't work i R"
Dear R'ers,
When I used S-plus i wrote a small program for a Mantel-Haenszel test
for trend (I think it worked). Unfortunately I can't get it working in
R.
It appears as if my use of 'el' is the problem but I can't sort it out.
Error in apply(array, c(, 2, 3), function(el) el * 1:s) :
argument is missing, with no default
Further down in the program I use 'el'
2009 Dec 28
2
WHO Anthro growth curve macros and R
Hi all,
I've got a project where I have to calculate weight-for-age Z-scores,
preferably using the WHO standards.
WHO have been very nice to publish macros for doing this in both
STATA,SPSS, SAS and Splus formats
(see http://www.who.int/childgrowth/software/en/), but for some reason
have chosen not to use the free R alternative to Splus.
In the Splus zipfile there are nine datafiles with a
2013 May 06
2
BIOENV
Dear all,
Does anyone knows why the results of a BIOENV (PRIMER v. 6.1.15) are
diferent of the bioenv() + mantel() in vegan? Not the spearman correlation,
indeed the pseudo-p value.
I know that the approach bioenv() + mantel() is biased. So, how the BIOENV
(PRIMER) ends with larger p values (permutated).
Acctualy how the permutation test in BIOENV (PRIMER) is conducted. The user
guide does not
2011 Jan 20
1
Problems with ecodist
Dear Dr.Goslee and anyone may intrested in matrix manipulate,
I am using your ecodist to do mantel and partial mantel test, I have
locality data and shape variation data, and the two distance matrixs are
given as belowings. When I run the analysis, it is always report that the
matrix is not square, but I didn't know what's wrong with my data. Would you
please help me on this. I am quite
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
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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