similar to: mantel test and NAs

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 R users, I am just starting with R and am currently needing a lot of help! Sorry if I disturb you and thank you for your answers!!! Here goes my question: How do I make R reconize my date columns as dates? When I "summary" my table, the levels of my date column are completely out of order. Thank you again for this tip, Marcia -- View this message in context:

Dear R users, I have been having a problem since I installed the new versions of TinnR and R on my computer (1.19.4.7 and 2.6.0 respectively). I used to open R by the command "start preferred RGUI", on the "R" tab of TinnR's menu. But now, since I updated both softwares (which was necessary for some compatibility issue with Windows Vista), the path for my preferred RGui (

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

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:

Dear R users, I am having a problem with the main title of a plot. I have written a function returning a plot and I would like that the main title of this plot shows actually the name of the dataset I have used. So, for instance: if my dataset is called Chl, I would like that my plot to be entitled : "Raw periodogram of Chl". I know the function "paste". I suppose I would be

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 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

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! 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.

Hello R users, I have been using R for a while on xp and have just updated my system to vista. Have encountered some problems... First and main problem is that i cannot make R recognize my own written functions by coping them into the Rprofile.site on the etc folder. For some reason, this very useful tool seems not to be working anymore. Could someone help?? Any other suggestion to make R start

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

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

Dear all, I am trying to plot and save the plots. I have written a small function for that in which I use the jpeg and dev.off() commands. Strangely, when these commands are inside the function, they are not working anymore. For instance: dataframe<- data.frame (x=c(1:20),y=seq(0,9.5, length=20)) for (i in seq(0,15, length=4)){ setwd ("C:/R") jpeg(filename =

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

Hello R users, I have been looking through Help files and Nabble list for the answers for these simple questions, but it seems to be fruitless. 1- in a data frame with two columns, x and y, how do I get the corresponding value of x to, let's say, the minimum value of the y column (min (data$y)) ? 2- how do I solve a simple equation? Considering the equation y= exp(-x)^12, I would like to find

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