object does not
contain a diagonal so your comment suggests that you did not convert the matrix
to a dist object.
David C
From: Nick Jeffery [mailto:nick.w.jeffe...@gmail.com]
Sent: Wednesday, May 6, 2015 9:34 AM
To: David L Carlson
Subject: Re: [R] Mantel test
Hi,
Thanks for the help. I get
partment of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Nick Jeffery
Sent: Monday, May 4, 2015 10:49 AM
To: r-help@r-project.org
Subject: [R] Mantel test
Dear R users,
I'm havin
Dear R users,
I'm having trouble getting my data into R in the correct format to run a
Mantel test.
I'm testing genome size differences by genetic distances of the 28S gene
for ~30 species. I'm able to get my genome size data (as a single column of
data) into matrix and dist formats in R but the
Hi,
A Mantel test doesn't test significant differences between matrices.
It tests for significant correlations between dissimilarities. If your
hypothesis is best expressed in terms of distances, then using the
Mantel test is appropriate.
As for size, 2000 by 2000 is not unmanageable, even if tho
Hi everyone,
I have two matrices of 2000x2000 size. They consist of a measurement of
RMSD deviations of a protein structure. The basic question i want
to answer is the following: are there a significant differences between
the two matrices?
I aim to use the Mantel test. I don't really know if this
You will most likely need to drop the samples that are causing the NA
values from both of your datasets. The function won't work with NA values.
Sarah
On Thu, Dec 17, 2009 at 12:33 PM, marciarocha wrote:
>
> Dear R users,
>
> I am having a problem performing the mantel test (both with functions
Could you please supply with a reproducible self sufficient script ?
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics
Dear R users,
I am having a problem performing the mantel test (both with functions mantel
{vegan} and mantel.test {ape}) due to I believe the presence of NAs on my
distance matrices, which look like e.g.:
NA
12
12 3
NA 4 5 6
and
1
1 2
2 3 4
5 6 7 8
Would any of you
On Mon, 2009-09-14 at 23:46 -0700, swertie wrote:
> oh yes of course. It is quite simple. I have two presence/absence matrices
> (one for plants, one for butterflies) and I would like to test if the
> butterfly community similarities is correlated with the plant community
> similarities. The think
oh yes of course. It is quite simple. I have two presence/absence matrices
(one for plants, one for butterflies) and I would like to test if the
butterfly community similarities is correlated with the plant community
similarities. The think is also that I don't really see the purpose of doing
a PC
Hi swertie ,
Could you please add more details ?
What field are you at, some links maybe ?
Thanks,
Tal
On Mon, Sep 14, 2009 at 8:30 PM, swertie wrote:
>
> Hello! It is not really linked to R, but can somebody explain me why we
> sometimes make a mantel test directly for to distance matrices
Hello! It is not really linked to R, but can somebody explain me why we
sometimes make a mantel test directly for to distance matrices and sometimes
we first make a gradient analysis and then a mantel test between the axis?
Thank you
--
View this message in context:
http://www.nabble.com/Mantel-
Thank you it is what I was looking for.
--
View this message in context:
http://www.nabble.com/Mantel-test-least-square-line-tp25235402p25401329.html
Sent from the R help mailing list archive at Nabble.com.
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https:
swertie voila.fr> writes:
>
> Hello, I performed a Mantel test and plotted communitiy similarities. I
> would like to add a least square line. I thought about using abline taking
> as slope the r-statistic of the Mantel test and calculating the y-intercept
> analytically. Is this method correct?
Hello, I performed a Mantel test and plotted communitiy similarities. I
would like to add a least square line. I thought about using abline taking
as slope the r-statistic of the Mantel test and calculating the y-intercept
analytically. Is this method correct? Is there any function for this
calcu
I'm not Gavin, but since you posted this to the R-help list I assume you
are open to other respondents.
Since you are asking Gavin, I assume you are using mantel() from the
vegan package (it's a good idea to specify, as there are other possibilities).
The help for that function explains the permu
Dear Gavin,
What is the interpretation of a simulated p-value of 1 in a mantel
test and how is the p-value derived? When we run two highly
negatively correlated matrices we get this result: r: -1, simulated p
value: 1
I would expect the high p-value of 1 to mean not significant. Could
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