Displaying 20 results from an estimated 2000 matches similar to: "Write lower half of distance matrix only"
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 Sep 11
2
Save object summary to file
Hi,
Am wanting to save the summary of a PCA to file.
Have tried:
> write.table(summary(PCA), file="PCAvar.txt", sep="\t")
but receive:
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors =
stringsAsFactors) :
cannot coerce class "summary.princomp" into a data.frame
What am I doing wrong?
Thanks
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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
2010 Nov 16
3
discriminant function analysis
My objective is to look at differences in two species of fish from morphometric measurements. My morphometric measurements are head length, eye diameter, snout length, and measurements from tail to each fin. I want to use discrimanant function analyis to determine if there are differences between the two species.
I am familiar with R but new to discrimannt function analysis. I want to learn
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
2007 May 25
1
testing difference (or similarities) between two distance matrices (not independent)
Hi,
i'm looking to test if two distance matrices are statistically
different from each others.
These two matrices have been computed on the same set of data (several
population samples)
1. using a particular genetic distance
2. weighting that genetic distance with an extra factor
(we can look at this as one set is computed before applying a
treatment and the second one after applying
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 Sep 07
1
Label 2 groups in PCA different colours
Hi,
I'm wanting to do a PCA on some data which is comprised of two different
groups (to see how well the groups are discriminated). Is there a way to
change the colour of the datapoints in a biplot so that I can easily see
which group is which (eg objects 1-100, red, 101-200, black).
Might be simple, but I'm new to R and can't seem to find how to do this.
Thanks.
Paul
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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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2011 Sep 18
2
R-Help
Hi, my name is Gastón. I just read a question, made by Walter Durka, about a
nonparametric discriminant analysis. It wasn´t any answer, and I was
wondering if at this moment there is one. I have the same problem as W.
Durka. I´m trying to classify and to cross-validate samples of three
tunicates species based on morphometric data and to identify the variables
that best discriminate between
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'
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
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Charles G. Willis
Department of Organismic
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
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
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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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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Sent from the R help mailing list archive at Nabble.com.
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
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
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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