Displaying 20 results from an estimated 120 matches similar to: "mantel tests"
2011 Jun 17
0
observation limits on correlog and mantel?
Hello,
I am working with two datasets with ~5,200 observations. Apparently,
neither the correlog function (ncf package) nor the mantel function (ecodist
package) can handle these datasets. Does anyone have any experience about
the maximum number of observations these functions can handle? I am
considering partitioning them into smaller subsets.
This would not be an ideal
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 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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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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2003 Aug 07
0
Extended Mantel-Haenszel Tests
Has anyone written R code for extended Mantel-Haenszel Tests- as
described in Section 8.4.5 (eq. 8.18) of Agresti's book "Categorical
Data Analysis"?
In other words, I would like to use column scores to test for a
location shift for different groups as defined by the row variable in
a
set of rxs tables. In addition, I would like to use row and column
scores to test for a linear
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()
2017 Dec 22
0
Introducing samplesizeCMH: Power and Sample Size Calculation for the Cochran-Mantel-Haenszel Test
Dear R users,
I am happy to announce the new package `samplesizeCMH` is now available on CRAN <https://cran.r-project.org/package=samplesizeCMH>.
The `samplesizeCMH` package will compute power and sample size for the Cochran-Mantel-Haenszel test for stratified 2x2 tables. There are also several helper functions for working with 2x2 tables, such as converting a proportion into an odds
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
2003 May 26
0
as.matrix() problem in mantel.test()?
Dear all,
I get an unexpected error when using the mantel.test function in
library(ape). Is there something wrong with my matrices?
> dmatr<- read.table("obt.Loiselle.kinship.intens02.DIST.matrix.txt",head=F)
> kmatr<-
read.table("obt.Loiselle.kinship.intens02.KINSHIP.matrix.txt",head=F)
>
> mantel.test(as.matrix(kmatr), as.matrix(dmatr), nperm = 500, graph
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
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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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 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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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 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
2010 Oct 07
1
Computing a Mantel-Haenszel chi-square using a continuous variable as the matching criterion
Dear list
I would like to compute a Mantel-Haenszel chi-square in which the matching variable is a continuous variable. The MH chi-square is used to assess the relationship between two categorical variables at each level or strata defined by a third variable. Specifically I would like to know if there is a straightforward way to divide the matching variable into levels, in which each level has a
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
2012 Jun 28
2
Size of subsample in ecodist mantel()
What is the size of the boostrapped subsample in ecodist mantel()
thanks
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2017 Dec 22
0
Introducing samplesizeCMH: Power and Sample Size Calculation for the Cochran-Mantel-Haenszel Test
Dear R users,
I am happy to announce the new package `samplesizeCMH` is now available on CRAN <https://cran.r-project.org/package=samplesizeCMH>.
The `samplesizeCMH` package will compute power and sample size for the Cochran-Mantel-Haenszel test for stratified 2x2 tables. There are also several helper functions for working with 2x2 tables, such as converting a proportion into an odds