similar to: Mantel test least square line

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.

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

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

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'

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

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

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

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

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

Hi, I am trying to use a mantel test on two distance matrices. The code I have entered for each is: Gen_dists <- read.csv(file.choose(), stringsAsFactors = FALSE, na.strings = c(" "), fill = T,

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

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,

Dear all, Has anyone written R code for partial Mantel Tests- as described for instance in Legtendre & Legendre (1998) ? In other words, in a community ecology analysis, I would like to calculate the correlation between two dissimilarity matrices, controlling for a third distance matrix representing geographical distances between sites. Thanks! Christophe Bouget Biodiversité et gestion des

> Background: > OS: Linux Ubuntu Dapper > release: R 2.3.0 > editor: GNU Emacs 21.4.1 > front-end: ESS 5.2.3 > ----------------------------- > Colleagues > I have two spatial datasets (latitude, longitude, fish eggs) and (latitude, longitude, fish larvae) at the same 280 stations (i.e. 280 cases). I want to determine if the 2 datasets are spatially correlated. In other

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

In SAS, for a two-way (or 3-way, stratified) table, the CMH option in SAS PROC FREQ gives 3 tests that take ordinality of the factors into account, for both variables, just the column variable or neither. Is there an equivalent in R? The mantelhaen.test in stats gives something quite different (a test of conditional independence for *nominal* factors in a 3-way table). e.g. I'd like to

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 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]]

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