Ian,
The command summary(manova(..)) will perform a parametric manova. However,
for the datafile you sent, that operation will not be possible because the
number of variables relative to sample size (note, you posted a similar
issue about a month ago to Morphmet).
The alternative is to use permutation-based evaluation of group
differences. Permutation-based manova can be performed in numerous
R-packages, including geomorph and RRPP. These two packages also have the
ability to perform pairwise comparisons using the permutation regime
specified.
Example R-code for implementing both is found below (NOTE: I strongly
suggest you read the help files and their examples to better understand the
options for these functions: there are many).
Best,
Dean
##
mydat <- read.csv('PCWIDE1.txt', header = TRUE,sep = '\t')
spec <- as.factor(mydat[,1])
shape <- as.matrix(mydat[,-1])
summary(manova(shape~spec)) #won’t work. df issue related to N vs. P
library(geomorph)
gdf<-geomorph.data.frame(spec=spec,shape=shape)
procD.lm(shape~spec,data=gdf)
advanced.procD.lm(shape~spec,f2 = ~1, group = ~spec, data=gdf)
library(RRPP)
rdf<-rrpp.data.frame(spec=spec,shape=shape)
res <- lm.rrpp(shape~spec,data=rdf)
res.null<- lm.rrpp(shape~1,data=rdf)
anova(res)
PW <- pairwise(fit=res, groups = spec)
summary(PW)
On Thu, Oct 4, 2018 at 2:06 PM Ian <ijames...@gmail.com> wrote:
> I am trying to determine if three groups are statistically distinct from
> one another. As is my script produces P values for each x and y coordinate
> but i am unsure how to get a comparison between the groups as a whole. My
> script and example data are attached. Can anyone tell me how i would go
> about determine if the groups Rafalt, Rafnas, and Rafpon are statistically
> distinct? I have tried to make subsets to do a pairwise comparison but that
> has not been successful. Any input is much appreciated.
>
>
> data1<-PCWIDE1
>
> names(data1)
>
> Raf.manova1<-
> manova(cbind(x1,y1,x2,y2,x3,y3,x4,y4,x5,y5,x6,y6,x7,y7,x8,y8,x9,y9,x10,y10,x11,y11,x12,y12,x13,y13,x14,y14,x15,y15,x16,y16,x17,y17,x18,y18,x20,y20,x21,y21,x22,y22,x23,y23,x24,y24,x25,y25,x26,y26,x27,y27,x28,y28,x29,y29,x30,y30,x31,y31)~
> as.factor(Species),data=data1)
>
> SAV<-summary.aov(Raf.manova1)
>
> print(SAV)
>
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--
Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
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