search for: nrepet

.....- attr(*, "Upper")= logi FALSE (...) > str(lmantel) List of 7 $ :List of 5 ..$ sim : num [1:99] 0.007734 0.002429 -0.021489 -0.000181 0.021703 ... ..$ obs : num 0.785 ..$ rep : int 99 ..$ pvalue: num 0.01 ..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet) ..- attr(*, "class")= chr "rtest" $ :List of 5 ..$ sim : num [1:99] 0.00749 0.02850 -0.01301 -0.01376 0.00883 ... ..$ obs : num 0.785 ..$ rep : int 99 ..$ pvalue: num 0.01 ..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet) ....

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

...ere "el" is a data frame of 75 columns and 124 rows. Therefore, the list of distances matrices, made out of it should have 75 elements each containing 124 rows and 124 columns. I, unsuccessfully, tried the following command >mantel.rtest(as.dist(q), lapply(el, function(x) dist(x)), nrepet = 9999) Do you have any clue?? Thanks in advance Eliza [[alternative HTML version deleted]]

...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 out an instruction to follow on from this result. > mantel.rtest(sample.dists, cat.dists, nrepet = 9999) Monte-Carlo test Observation: 0.4431225 Call: mantel.rtest(m1 = sample.dists, m2 = cat.dists, nrepet = 9999) Based on 9999 replicates Simulated p-value: 1e-04 Colin. -- View this message in context: http://n4.nabble.com/Mantel-results-shown-in-a-graphical-histogram-form-tp1009216p1009216....

...d like to adjust the p values for multiple comparisons using Holm correction. When I run the fourthcorner I obtain the results in yellow. What do I need to do to be able to aply the Holm correction to those p values? > library(ade4) > four1 <- fourthcorner(tabR, tabL, tabQ, modeltype = 1, nrepet = 999, tr01 = FALSE) > summary(four1) Fourth-corner Statistics Permutation method 1 ( 999 permutations) --- Var. R Var. Q Stat. Value Prob. RABINT / SPAN r -0.0478943 0.038 * RABINT / TREE r 0 1.000 RABINT / SHRU r 0...

...d I have quickly found myself in a place where "Google-ing" has no longer proven useful. Below are my scripts and error messages. Using Vegan: > vare.cca <- cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + > Condition(Env2)..., HabitatSpaceR.csv) > randtest(vare.cca, nrepet = 1000) Error in randtest.cca(vare.cca, nrepet = 1000) : Object of class dudi expected Using ade4: > vare.cca <- cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + > Condition(Env2)..., HabitatSpaceR.csv) Error in cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + Condition...

...8493 1.5749603 8 9 2 3 4 5 6 7 8 9 3.3777063 10 2.8790276 3.6806114 And then, I follow from help: > pco1 = dudi.pco(dist1, nf=2, scannf=F) > pco2 = dudi.pco(dist2, nf=2, scannf=F) > coi = coinertia(pco1, pco2, nf=2, scannf=F) > testco1 = randtest.coinertia(coi, nrepet=1000) The result is: > Error in randtest.coinertia(coi, nrepet = 1000) : Not yet available Could anyone help with this? Best, PM --Forwarded Message Attachment-- From: eva.nordstrom at yahoo.com To: r-help at r-project.org Date: Mon, 23 Aug 2010 12:50:01 -0700 Subject: [R] "easiest&...