Displaying 20 results from an estimated 900 matches similar to: "Significance of Principal Coordinates"
2003 May 09
1
Principal coordinates analysis
Dear all,
Does anyone know how to run Principal Coordinates Analysis (PCoA) from a
squared euclidean dissimilarity matrix with R ?
Thanks,
*************************
Arnaud DOWKIW
Department of Primary Industries
J. Bjelke-Petersen Research Station
KINGAROY, QLD 4610
Australia
T : + 61 7 41 600 700
T : + 61 7 41 600 728 (direct)
F : + 61 7 41 600 760
**************************
2024 Oct 13
1
The RV coinertia coefficient to interpret multivariate analysis plots
Dear all community,
My issue is related to the R package (made4) that permits me to calculate
the RV coefficient of co-inertia. However, it is a theoretical question.
And if I am not mistaken, the list Usenet groups sci.stat.consult is not
currently active.
Let me explain briefly:
Through different microbiota datasets, I have plotted PCoA, db-RDA and
sPLS-DA using 3 different types of
2013 Apr 11
1
Ordination Plotting: Warning: Species scores not available
Hi,
I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:
"Warning message:
In ordiplot(x, choices = choices, type = type, display = display, :
Species scores not available"
I am using a Gower's transformation in both procedures within the metaMDS or pcoa
2011 Oct 04
0
number of analogs in significance test of MAT reconstructions using randomTF from palaeoSig
I'm trying to use the randomTF function from package palaeoSig to
test the significance of a MAT reconstruction with nine analogs and a
WA-PLS reconstruction with four components. I'm probably missing
something obvious here but how do I make sure that randomTF is testing
the reconstruction based on the desired number of analogs / components?
In:
fitmap.wapls = WAPLS( lumapspc,
2007 Sep 24
1
save 3dplot to file
I think it is an easy question but i haven´t found a solution since I
am r beginner.
I did this
plot3d(PCoA, type="p", col=rainbow(1000),size=5)
text3d(PCoA, text=Nam)
How can I save it including the labels to a jpg-file?
Thanks in advance.
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
2011 Oct 03
4
distance coefficient for amatrix with ngative valus
Hi,
I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.
Thanks.
Dilshan
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2007 Oct 22
1
plot3d with more than 8 colors
Hello R user and helper!
I would like to get a 3d plot with coloured points.
I did that:
colors<-c(rep("2",7), rep("3",12), rep("4", 24), rep("5", 13), rep
("6", 8), rep("7", 51), rep("8", 1), rep("9", 15), rep("10", 53), rep
("11",3), rep("12",3), rep("13", 8),
2010 Jan 19
0
Call drop-out on second incoming call.
Hi all,
I've got 12 Polycom 430's behind a NAT that are working pretty well except for
one thing:
If one of my users is on the phone when another call comes in, there is about
a 10 second time during which the user can't hear the call they're on. Then
it returns to normal.
My research indicated that I needed to add these setting to the phone:
2009 Oct 13
2
decostand
Hi:
I do not know why the function decostand is not found in my vegan library, I have downloaded the package recently, and it seems to work well..Do you have any suggestion?
Rosa.
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2023 Dec 08
2
regarding CCA plot
Hii rstudio members
I am learning rstudio, For my manuscript I am trying to plot CCA using
species and environmental data. But I am getting error like
Error in cca.default(sptrans, envtrans) :
all row sums must be >0 in the community data matrix
*My code is like *
library(vegan)
library(ggplot2)
library(dplyr)
rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",
2005 Nov 09
2
how to convert strings back to values?
Dear All,
It's Eszter from Hungary, a total beginner with R. My problem is the
following:
I have a dataset with binary values as a comma separated textfile. The
samples are in the coloumns and the species are in the rows.
I have to transpose it for the further PCoA analysis. There is no
problem with reading the dataset.
When I transpose the dataset, the original values become
2006 May 03
2
mca id numbers
Is it possible to make disappear the id numbers from scatter.dudi (mc
analysis) ?
a <- as.factor(c(1, 2, 3, 2, 1))
b <- as.factor(c(3, 2, 3, 1, 1))
x <- as.factor(c(1, 2, 2, 1, 3))
y <- as.factor(c(2, 2, 3, 1, 1))
dat <- data.frame(a=a, b=b,x=x,y=y)
summary(dat)
dat
require(ade4)
dat.acm <- dudi.acm(dat, scann = FALSE, nf = 2)
scatter.dudi(dat.acm)
Thank you very much !
2007 Jul 27
6
polycom custom ring tones (slightly OT)
Hi all,
Has anyone made up custom ring tones for the Polycom SIP phones? We use
different rings for different lines, but the ones it comes with are all very
similar. In the interesting of sharing, here's one I made up for paging:
<PAGE_BEEP se.pat.ringer.13.name="Page Beep"
se.pat.ringer.13.inst.1.type="chord" se.pat.ringer.13.inst.1.value="12"
2004 Jan 01
1
ade4
Dear All,
I am using the scatter.dudi finction in the 'ade4' package to produce
correspondence analysis (nice) plots.
I do not seem to figure out how to plot the raw coordinates only -- or column
coordinates only. I would appreciate any help in doing that.
Here is the example I am following -- from the package.
data(banque)
> banque.acm <- dudi.acm(banque, scann = FALSE, nf =
2009 Oct 20
1
kendall.global
Hi every body:
I need some help with kendall.global. The example in the manual seems not working well, and cannot used with my data, always the same error.
data(mite)
> mite.hel <- decostand(mite, "hel")
>
> # Reproduce the results shown in Table 2 of Legendre (2005), a single group
> mite.small <- mite.hel[c(4,9,14,22,31,34,45,53,61,69),c(13:15,23)]
>
2007 Aug 24
1
Adding new points to a metaMDS ordination ("vegan" pkg)
Hi, I've been using R for a while now but I've got a problem with
metaMDS (in the vegan package) that I can't quite figure out.
I have a set of proportion data (from 0-1, rows sum to 1) that I apply
metaMDS to using the command:
nMDS.set=metaMDS(sqrt(test.set),distance="euclidean",k=3,zerodist="add",autotransform=FALSE)
I am using a squared-chord distance
2015 May 26
2
[PATCH 2/2] nv30/draw: switch varying hookup logic to know about texcoords
On 26.05.2015 02:49, Ilia Mirkin wrote:
> On Mon, May 25, 2015 at 8:37 PM, Tobias Klausmann
> <tobias.johannes.klausmann at mni.thm.de> wrote:
>>
>> On 25.05.2015 21:29, Ilia Mirkin wrote:
>>> Commit 8acaf862dfe switched things over to use TEXCOORD instead of
>>> GENERIC, but did not update the nv30 swtnl draw paths. This teaches the
>>> draw
2007 Feb 27
1
An Open source phone based on Speex
ivo and others,
i am having a very interesting exchange about the LTP with diana. I took
it offline from speex-dev as it would not interest everyone here. I will
reply to ivo separately. I have also setup a mailing list on
http://tech.groups.yahoo.com/group/ltpdiscuss/ if anybody is interested.
but the key issues that the solves is that:
1. support p2p community based telephony that can punch
2013 Jul 23
1
Heat Map for species - code from Numerical Ecology with R
Hello, I am relatively new to R and I am working through the code that is provided in the book Numerical Ecology with R and I have run across an error message that I can't seem to figure out. I am using the vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe,
2006 Nov 07
0
Scan or read.table bug in R?
Please post general R help questions to the R-help mailing list.
The likely problem here is that your file isn't in the current working
directory. To avoid this problem, I often use the file.choose()
function to obtain a full path to the file, rather than typing the name
out myself.
Duncan Murdoch
On 11/7/2006 8:48 AM, Satya Pimputkar wrote:
> Hello R-Team,
>
>
>
>