Displaying 20 results from an estimated 400 matches similar to: "restricted permutations in permtest()?"
2013 Oct 29
0
Mean error
Hi,
Try either:
res1 <- apply(mydata[,1:2],2,mean)
?res2 <- colMeans(mydata[,1:2])
?identical(res1,res2)
#[1] TRUE
# Also if you need to find means for each group ("Ungrazed vs. "Grazed")
by(mydata[,-3],mydata[,3],colMeans)
#or if column names are "V1", "V2", "V3"
aggregate(.~V3,mydata,mean)
#or
library(plyr)
2014 Sep 13
1
vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)
Dear vegan team,
Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not
2008 Aug 07
2
panel.arrows problem in custom panel function
Dear List,
I am writing a custom panel function and xyplot method to plot the
results of a procrustes analysis from the vegan package.
I am having trouble getting the call to panel.arrows to work as I wish
when conditioning. The attached file contains the function definitions
for the xyplot method and the custom panel and prepanel functions I am
using. This example, using data and functions from
2009 Dec 01
0
GLM Repeated measures test of assumptions: e.g. test for sphericity e.g. Bartletts and Levenes homogenous variances
Hello and thanks in advance
I am running a glm in R the code is as follows with residual diagnostic code
below
model4<-glm(Biomass~(Treatment+Time+Site)^2, data=bobB,
family=quasi(link="log", variance="mu"))
par(mfrow=c(2,2))
plot(model2)
to test the effect of grazing exclusion of feral horses for a Phd with
following factors:
Treatment - 3 levels which are grazed
2009 Dec 01
0
Amendment to previous post a minute ago, please amend before posting if possible
Sorry, I just posted the email below but realised I did not give a name or
details, would it be possible to adjust before posting and send what is
below, sorry again, first time user...
From: Joanne Lenehan [mailto:jlenehan@une.edu.au]
Sent: Tuesday, 1 December 2009 3:51 PM
To: 'r-help@r-project.org'
Subject: GLM Repeated measures test of assumptions: e.g. test for sphericity
e.g.
2013 Apr 24
1
RDA permutest envfit
Dear all,
I did a RDA and when I looked to the signification of the test with permutest, the output was non-significant. But when I used the envfit function, some of the vectors are significant. All the test's conditions are respected. What it means? Is it an error in the script?
Commands and output:
> permutest(rda.ind, perm=999, first=TRUE)
Permutation test for rda
Call:
2012 May 09
2
plot betadisper, change of pch
Hello!
After performing an analysis with betadisper, package vegan I would like
to plot the results - so far, so good. But I would also like to "tune" a
little bit the plotting characters, as '+' and 'x' are a little to
similar...
My (boiled down) code:
[See session info at the bottom of the mail, vegan is vegan_2.0-3]
mod <- betadisper(mydata, mygroups,
2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
Hi All,
I am using canonical correspondence analysis to compare a community
composition matrix to a matrix of sample spatial relationships and
environmental variables. In order to parse out how much variance is
explained purely by space (S/E) or the environment (E/S) I am using a
conditional (partial) CCA. I want to test significance via Monte Carlo but
I can not find a way to do this with a
2013 Nov 28
1
Multivariate dispersion & distances
Dear All,
I'm using betadisper {vegan} and I'm interested not only in the dispersion
within the group but also the distances between the groups. With betadisper
I get distances to group centroids but is it possible to get distances to
other groups centroids?
It might be possible to do it by hand by the formula given in the
description of the betadisper (below) but I'm a bit confused
2013 Mar 05
0
permutest
I'm working with capscale and permutest for the first time, and having
trouble getting statistical analyses for more than one constraining
variable. I've read the documentation, but setting first=FALSE or using
by="axis" doesn't seem to be helping. capscale seems to be fine, I receive
output for more than one constrained axis. What am I doing wrong?
2008 Apr 27
1
An ANOVA test that uses a distance matrix like hierarchical cluster analysis?
Hi All,
I have a question which does not pertain directly to the use of R but comes
from my use of R!
I have data which can be described as 3-dimensional e.g. (x,y,z), with no
negative component. The suggested way to analyze this data is via
multivariate techniques or by calculating what amounts to a levene's test on
the data and then an ANOVA on the three components if the first test is
2010 Jul 20
1
Exporting NMDS distance matris to csv
If you submit these lines, you end up with variable "vare.dis". I want
to export vare.dis to csv. Stuck I am.
library(vegan,logical.return = TRUE) #return=true verifies package is
available
library(MASS,logical.return=TRUE) #return=true verifies package is
available
data(varespec) #varespec is an example data file in the vegan package
vare.dis <- vegdist(varespec)
2013 Oct 27
2
Heteroscedasticity and mgcv.
I have a two part question one about statistical theory and the other
about implementations in R. Thank you for all help in advance.
(1) Am I correct in understanding that Heteroscedasticity is a problem for
Generalized Additive Models as it is for standard linear models? I am
asking particularly about the GAMs as implemented in the mgcv package.
Based upon my online search it seems that some
2010 Mar 23
2
Problem installing package
Dear r-help users,
I have just downloaded the package vegan and I have problems accessing
the data to go through the examples in the tutorial. I can see the data
when I type "data()" but I am told that the data doesn't exist when I
type the name of one of the variables e.g.:
> varespec
Error: object 'varespec' not found
I suspect this could be a way I have my
2008 Sep 26
1
cca constraining variables table
I performed canonical correspondence analysis (cca) with the example data of
vegan, but I'm not able to obtain a table like scores() for the constraining
variables. I can see them in the summary() mode, but it would be great to
have in a separate table. Any suggestion?, thanx Gianandrea
require(vegan)
data(varespec)
data(varechem)
vare.cca<-cca(varespec,varechem)
scores(vare.cca)
2010 Apr 27
1
cca standard error species
Dear all,
I realised a correspondence analysis with function cca() of vegan library.
Just like in Okansen (2010) in the example of R help:
library(vegan)
data(varespec)
data(varechem)
vare.cca<-cca(varespec~ Al + P + K, varechem)
With plot.cca() function I represented the species matrix in the next way:
plot(vare.cca,display="species")
Being similar to:
plot((c(-2,2)),(c(-2,2)),
2012 May 23
1
procrustes (vegan) plot of residual differences
Hello
This is a simple question but I couldn't google an answer.
In the procrustes function of the vegan package, one uses
plot(procrustes_object, kind=2) to obtain a plot of the residual
differences. For instance:
data(varespec)
vare.dist <- vegdist(wisconsin(varespec))
library(MASS)
mds.null <- isoMDS(vare.dist, tol=1e-7)
mds.alt <- isoMDS(vare.dist,
2013 Oct 25
0
moving points labels in ordinations
I'm trying to place labels so as to avoid covering points (and other labels) in an ordination plot. I've been trying to use orditkplot() for this purpose, but get an error message, even when I try to replicate the example:
>require("vegan")
>data(varespec)
> ord <- cca(varespec)
> orditkplot(ord, mar = c(4,4,1,1)+.1, font=3)
Error in
2013 Jul 12
2
vegan capscale 'subscript out of bounds' error
Hi list,
I am using the capscale function in vegan_2.0-7 to do a constrained
principal coordinates analysis, and I kept getting the following error
message:
Error in Y.r[, oo, drop = FALSE] : subscript out of bounds
I googled but I couldn't find an answer. Could anyone tell me why this
error msg and what to do?
Here is the command I used:
2011 May 23
1
help on permutation/randomization test
Hi,
I have two groups of data of different size:
group A: x1, x2, ...., x_n;
group B: y1, y2, ...., y_m; (m is not equal to n)
The two groups are independent but observations within each group are
not independent,
i.e., x1, x2, ..., x_n are not independent; but x's are independent from y's
I wonder if randomization test is still applicable to this case. Does
R have any function