similar to: nested repeated measures MANOVA using adonis

I am trying to apply this technique (M.J Anderson 2001) to a dataset of aquatic insect abundances. There is a sample in the unrestored and restored segement of a stream for every time period. I would like to compare the centroids of the distance matrices for the treatments up (unrestored) and dn (restored) to see if there is a difference in insect communities between the treatments. I will not

Hi, I was wondering if someone can tell me what is the difference between "strata" argument (function "adonis" in "vegan" package) and using random effects in PERMANOVA+ add-on package to PRIMER6 when doing permutational MANOVA-s? Is the way permutations are done the same? Thank you very much in advance, Vesna -- View this message in context:

Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: > CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but

Hi, forgive me if someone has already posted about this but I have had a look and cannot find the answer, also I am very new to R and been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am

Hello all, I used google and looked at the documentation to find out why the ADONIS function is called adonis (in the vegan package). I am writing a document and would like to include a abbreviation list (similar to "ANOSIM = Analysis of Similarities"). regards, Steve

hello list, i'd appreciate help regarding formula expression in adonis(), package vegan. i'm interested in the effect of an impact on species composition and if this effect is the same for different sites. i have an impact survey with plot pairs, one plot with impact the other with similar ecolgical conditions but without impact, which is the control (factor1: impact). two different

Dear all, I am trying to get a PERMANOVA with quite large data set. I am reading a lot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs,

Hi, Somebody knows how to make contrasts if i'm using the function adonis? Thanks.

Hi, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

Hi, I have seen a discussion in the R-help asking whether nonparametric manova has been implemented in R yet. This discussion is form March 2006 and there seemed to be no package or function implemented at the time. Has this changed? Is there a package that provides nonparametric manova as in McArdle and Anderson (2001) and Anderson (2001) now? Thanks, Daniel ------------------------- cuncta

Dear friends, I would like to get all possible arrangements of n objects listed 1:n on a circle. Now this is easy to do in R. Keep the last spot fixed at n and fill in the rest using permuations(n-1, n-1) from the gtools package. However, what if clockwise or counterclockwise arrangements are the same? I know that half of the above (n - 1)! arrangements are redundant. Is there an easy way to

Hi, I'm having difficulty with getting a table to show with multiple rows and columns. Below is the commands that I've typed in and errors that I am getting. Thank you. Laura Table trying to enter: Diet: Binger-yes: Binger-No: Total: None 24 134 158 Healthy 9 52 61 Unhealthy 23 72 95 Dangerous 12 15 27 >

Otras variantes con y sin paquetes adicionales... > sapply(split(datIn$Gain, as.factor(datIn$Diet)), mean) d1 d2 d3 280 278 312 > by(datIn$Gain, datIn$Diet, mean) datIn$Diet: d1 [1] 280 -------------------------------------------------------------- datIn$Diet: d2 [1] 278 -------------------------------------------------------------- datIn$Diet: d3 [1] 312 > > library(dplyr) >

Me gusta la respuesta uqe has dado, pero si por ejemplo, alguno de los datos tiene datos faltantes, entonces devuelve NA. He probado con: sapply(split(datos$uno, as.factor(datos$dos)), mean(na.rm=TRUE)) pero da fallo. ¿Cómo se podría hacer para que devolviera además la media obviando los NA y que contara el numero de NA por categoria? > Date: Wed, 28 Oct 2015 00:13:45 +0100 > From: cof

Dear All, I'd like to perform adonis (from the vegan package) rather than amova (in ade4) on some haplotype data, as I have crossed factors. Is there a simple way to tweak the source to allow weights (haplotype frequencies) in a similar way to amova? Best Simon

If one is equal to the reverse of another, keep only one of the pair. B. > On Mar 29, 2018, at 9:48 PM, Ranjan Maitra <maitra at email.com> wrote: > > Dear friends, > > I would like to get all possible arrangements of n objects listed 1:n on a circle. > > Now this is easy to do in R. Keep the last spot fixed at n and fill in the rest using permuations(n-1, n-1)

Hello I ran the code below but it said: no object "'panel.xyplot.intermediate.hh'" Please kindly advise how to modify the code. thank you. (It works with panel.bwplot.intermediate.hh) Elaine code library(HH) # data input dataN <-read.csv("H:/R_data/Mig_bird_586.csv",header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) diet.code <-

Hello I want to draw a xyplot. Its dots will have three colors: red for meat, green for vegetable, and blue for both. I used the code below but could not make the dot in the same group show the same color. Please kindly advise how to modify it. Thank you. code library (lattice) diet.code <- c("Herbivore", "Omnivore", "Carnivore") Diet.colors <-

according to the documentation of the cast function in the reshape function, I would expect this bit of code from the examples to calculate marginal means over only the 'diet' variable. #Chick weight example names(ChickWeight) <- tolower(names(ChickWeight)) chick_m <- melt(ChickWeight, id=2:4, na.rm=TRUE) cast(chick_m, diet + chick ~ time, mean, margins="diet") But,