Displaying 20 results from an estimated 1000 matches similar to: "observation limits on correlog and mantel?"
2012 Aug 11
1
Ylim problem - plot.correlog, ncf package
Hi,
I'm doing cross-correlation correlograms with the ncf package. I have four
study sites ; four correlograms.
I'd like to get the same y scale for the four of them... only, using
"ylim=c(-1,1)" does not change the y scale never and I don't know why. I
tried with plot() too.
Is there another option to change the ylim in plots ?
Example with only one correlog (all work
2011 Dec 03
1
partial mantel tests in ecodist with intential NA values.
I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA.
This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error.
is it possible to perform this test in ecodist?
many thanks
2003 Oct 29
0
P-values in ncf package
Group,
I'm currently trying to find out how the function correlog in the ncf
package may be useful to me for calculating cross-correlograms. The
function's output includes P-values for all distance classes, but it seems
that only positive values can become significant. Is this true and correct?
If so, why?
Thanks in advance.
Ren? Eschen.
_______________________________________
Ren?
2012 Jun 28
2
Size of subsample in ecodist mantel()
What is the size of the boostrapped subsample in ecodist mantel()
thanks
[[alternative HTML version deleted]]
2009 May 08
2
partial mantel tests "Ecodist"
Hi all,
I'm searching for a little clarification on partial mantel tests
(ecodist package)
I've a distance matrix (x,y), and several others containing
environmental/chemical variables.
Based on the help file, and the package instructions I've managed to
implement the tests as;
var1 ~ env1 + space
to partial out the effect of space and test the relationship between
the
2011 Jan 20
1
Problems with ecodist
Dear Dr.Goslee and anyone may intrested in matrix manipulate,
I am using your ecodist to do mantel and partial mantel test, I have
locality data and shape variation data, and the two distance matrixs are
given as belowings. When I run the analysis, it is always report that the
matrix is not square, but I didn't know what's wrong with my data. Would you
please help me on this. I am quite
2003 Sep 12
2
partial mantel
Dear all,
Has anyone written R code for partial Mantel Tests- as described for
instance in Legtendre & Legendre (1998) ?
In other words, in a community ecology analysis, I would like to calculate
the correlation between two dissimilarity matrices, controlling for a third
distance matrix representing geographical distances between sites.
Thanks!
Christophe Bouget
Biodiversité et gestion des
2011 Aug 11
1
matrix correlations with different packages
Dear all,
I'm calculating matrix correlations with permutation tests and I got this
funny result. All correlation coefficients are the same with mantel.test
{ncf} and pcol {simba} but the two functions yield dramatically different
p-values (using the same number of permutations). Could anyone please
enlighten me what is causing the difference and which result I can trust?
(My matrices
2009 Mar 03
1
Mantel test!
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
you clarify?
Thank you,
Jason
Jason P. Sexton
Graduate Group in Ecology
University of California,
2011 Oct 16
2
How to plot CI's (llim ulim) on ecodist mgram
I would like to put confidence intervals on a mantel corellogram
they are already calculated in the pmgram object but I am unsure how I
get the x value in order to plot them?
package(ecodist)
X<-1:100
Y<-rnorm(1:100)
Z<-rnorm(1:100)
XY<-dist(data.frame(X,Y))
YX<-dist(data.frame(Y,X))
my.mgram<-mgram(XY,XZ)
plot(my.mgram)
print(my.mgram)
> print(my.mgram)
$mgram
2011 May 31
0
Mantel - like analysis
Hello,
I've used mantel tests a fair bit for standard genetic/geographic/landscape
analyses. I realize it involves permutations of rows and columns in the
matrix to obtain correlation coefficients.
However, for a certain question, I am interested in populations that are
nearest neighbours to each other, and identifying factors that affect
genetic distance between them. So because of
2007 Nov 16
4
Permutation of a distance matrix
Hi there,
I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test.
Specifically, the permutation has to accomplish something like this:
Original matrix addresses:
a11 a12 a13
a21 a22 a23
a31 a32 a33
Example
2009 Dec 17
2
mantel test and NAs
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
1 2
1 2 3
NA 4 5 6
and
1
1 2
2 3 4
5 6 7 8
Would any of you have a solution for that?
Thank you for much for your help!
Marcia Rocha
--
View this message in
2010 Jan 07
1
Mantel results shown in a graphical (histogram) form.
I am new at 'R' and not even sure whether I am contacting the appropriate
forum!! However, I have carried out several mantel tests (using 'R') on
genetic data and would like to plot the results in the form of a histogam of
the distribution - and preferably use a procedure that shows the critical
'r' value.
The tail end of my analysis is shown below. I just need help to dig
2009 Sep 01
2
Mantel test least square line
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
calculation? Thank you
--
View this message in context:
2017 Dec 31
1
Perform mantel test on subset of distance matrix
I'm trying to perform a mantel test that ignores specific pairs in my
distance matrices. The reasoning is that some geographic distances
below a certain threshold suffer from spatial autocorrelation, or
perhaps ecological relationships become less relevant that stochastic
processes above a certain threshold.
The problem is that I can't find a way to do it. If I replace values
in either or
2009 Sep 14
1
Mantel test
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-test-tp25439984p25439984.html
Sent from the R help mailing list archive at Nabble.com.
2012 Sep 18
1
Cochran-Mantel-Haenszel test
Hello,
I have some satellite tag time-at-depth (TAD) frequency data that I
would like some help with.
The data was transmitted via satellite as percent time spent in each of
7 depth bins (0m, 0-1m, 1-10m, 10-50m etc.), binned over 6-hour
intervals. I categorized each row of data corresponding to a date and
time into summer vs. winter, and day vs. night, and then summed and
averaged the given
2008 Apr 19
1
Mantel-Haenszel for 2x2
Hi all,
Does anyone know if an R function for the Mantel-Haenszel chi-square for a
2x2 table exists? I’ve also seen it called the randomization Q statistic.
Note that I’m not looking for the Cochran-Mantel-Haenszel…I did see that out
there as cmh.test.
Thanks in advance,
Jeff
Internal Virus Database is out-of-date.
Checked by AVG Free Edition.
11:27 AM
[[alternative HTML version
2006 Feb 23
1
partial mantel test
I would like to know how to run a partial mantel test controlling for spatial
autocorrelation and correlation with other environmental variables. It seems that
with function included in vegan for partial mantel test I can only test for the
relationship between two variables controlling for the effect of a third one.
Thanks a lot
Alexandra
---
Lic. Alexandra Sapoznikow
Centro Nacional