Clustering with mvpart and rpartpca, graphs fill the pane normally in
Windows 7 as copied into Word 7, But with the same script and datasets,
they only occupy the upper left-hand quarter of the pane in Windows 10
on SURFACE BOOK, again, as copied into a Word 7 document.
when I test graphic pa
I've been using mvpart with graphic output (a tree displaying env. data
governing splits), augmented by rpart.pca, to explore environmental
relations of vegetation data on my old Toshiba satellite computer with R
version 2.15.0 (x32).
I've loaded R version 3.3.3 (x64) on a Surface Book.
Grap
hello Ansley,
You might want to look at the multi-respnse permutation procedure (mrpp
in R), which examines the difference among clusters, that is, how much
greater similarity the elements of cluster have to each other as
compared to the overall similarity of elements of the data. I am not
well
All, How can I save (rename as a vector?) the "where" output of plot
assignment to groups from mvpart() to use as input to mrpp of the same data?
Mike Marsh
On 9/10/2015 3:00 AM, r-sig-ecology-requ...@r-project.org wrote:
Send R-sig-ecology mailing list submissions to
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Tim, I've used mvpart to cluster, and then rpart.pca the resulting
regression clustering.
mvpart requires a corresponding environmental data set.
The pca plot has what you require, polygons like ordihull based on and
showing plots (rows in your data), and vectors to named species.
I have assumed
Reading David Warton's reply to Rajendra made me realize that my
question (below) is related to his, and that I should specify the
objectives of my investigation. I'm interested to see if there are
separate, distinguishable plant communities/associations related to
environmental variables, and
Is there a method in R for testing for independence of vegetation
samples, for example because of relative proximity of different samples?
I would like to treat the 3 radially arranged transects of Jornada Line
Point Index plots as different sample units.
Mike Marsh
Washington Native Plant Soci
I am trying to obtain biplots of NMDS results, ideally like the
rpart.pca() result with mvpart.
Can someone easily tell me why I get this error:
Error in 1L:n : argument of length 0
from this script, and graphical output (below) lacking labels for either
sites or species?
x and y matrices are s
I test differences between frequency of hits of exotic annual forbs in
plots on two sites, Q and WD.
> Q<-c(13,0,10,2,0,0,1,0,0,1,5)
> WD<-c(0,0,1,0,0,0,0,0,0,0,1)
> t.test(Q,WD)
Welch Two Sample t-test
data: Q and WD
t = 1.9807, df = 10.158, p-value = 0.07533
alternative hypothesis:
Gian,
Your question,
"how can I extract the names of the species (and even their
abundances) that are common and the species that are not common between the
different samples in my dataset?"
is a common question in ecological literature about what are called "Indicator
Species". These are specie
If you want a measure of exposure, i. e., heat, I suggest using the
"heatload" transformation suggested by McCune and Grace (2002). Their
assumption is that mid-afternoon, when the sun is in the southwest, is
usually the warmest time of day. The formula at the end of Chapter 3
follows:
heat l
To any who looked at this dumb question, I found the problem by looking
at the hclust output. Two symbols were exactly superimposed in ordicluster.
Thanks
Mike
I up-graded to R version 2.15.0. Now script that I had run successfully
in version 2.12 cannot complete an identify-ordicluster in this
I up-graded to R version 2.15.0. Now script that I had run successfully
in version 2.12 cannot complete an identify-ordicluster in this version.
My vegetation transect data is sub-setted to treat different life forms
separately. A call for all the vegetation graphs successfully, with all
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