Displaying 20 results from an estimated 200 matches similar to: "Mantel results shown in a graphical (histogram) form."
2008 Apr 24
0
Name of objects in a list
Hi useRs,
I am trying to compare several distance matrices obtained from subsets
of variables from the same experiment. I put all the subsets in a list
and then calculated the distance matrices with lapply. In order to do a
mantel test between them I wrote a function the returns a list with the
output of single tests. I would like to include the name of the tests,
so I know what each element
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
2007 Apr 11
1
Function knn.dist from knnflex library
Hello,
I am feeling that this question can have a very simple answer, but I
can't find it.
I need to use the function knn.dist from knnflex library.
Whatever I try, I get the error:
Error in as.vector.dist(x, "character") : unused argument(s) ("character")
First example:
> a<-NULL
> a<-rbind(a,c(5.2,-8.1))
> a<-rbind(a,c(8.8,-16.1))
>
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
2011 Oct 12
2
p adjustment on 4thcorner results
Hi all,
This is probably a very simple question but I cannot figure out how to do
it. I run the fourthcorner method with my data and would like to adjust the
p values for multiple comparisons using Holm correction. When I run the
fourthcorner I obtain the results in yellow. What do I need to do to be able
to aply the Holm correction to those p values?
> library(ade4)
> four1 <-
2010 Jan 25
1
PCA: Showing file datalabels on biplot
The script below successfully produces a biplot of the data but the 'site
names' (rows) and the names of the 'response variables' (columns) are shown
as simple numerals (rather than the column and row names). How might I
'enforce' the use of the row/column names used in the datafile (section of
datafile shown below)?
Can anyone help, please?
Section of datafile
sample a b
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
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
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
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,
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 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