search for: mantels

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

> 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

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'

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:

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'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

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

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

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

Dear all, Dose anyone know whether there is a good R packege or program for Mantel's randomization test? Thanks in advance. ------------------------ Takashi Mizuno zoono at sci.osaka-cu.ac.jp Plant Ecology Lab. Osaka City University ------------------------ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

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

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 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 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

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

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,

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

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,

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