similar to: mantel tests

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

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

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 -- View this message in context:

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 Thanks in advance, Jeff Internal Virus Database is out-of-date. Checked by AVG Free Edition. 11:27 AM [[alternative HTML version

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

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()

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

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

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

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

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

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 [[alternative HTML version deleted]]

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,

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 -- View this message in context: http://www.nabble.com/Mantel-test-tp25439984p25439984.html Sent from the R help mailing list archive at Nabble.com.

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 -- View this message in

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

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

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

What is the size of the boostrapped subsample in ecodist mantel() thanks [[alternative HTML version deleted]]

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