Displaying 20 results from an estimated 300 matches similar to: "hierarchical partitioning"
2011 Jun 05
1
tag \href not recognised in rd doc
Hi,
I have a trouble trying to use \href in a rd doc. See example below:
\references{
\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702787/}{Vaniscotte
A., Pleydell D., Raoul F., Quere J.P., Coeurdassier M., Delattre P., Li
T., Qian W., Takahashi K., Weidmann J.C., Qiu J., Giraudoux P. 2009
Modelling and spatial discrimination of small mammal assemblages: an
example from western
2012 Sep 12
7
multinomial MCMCglmm
Dear all,
I would like to add mixed effects in a multinomial model and I am trying
to use MCMCglmm for that.
The main problem I face: my data set consits of a trapping data set,
where the observation at eah trap (1 or 0 for each species) have been
aggregated per traplines. Therefore we have a proportion of
presence/absence for each species per trapline.
ex:
ID_line mesh habitat Apsy Mygl
2009 Jun 17
1
Predict Fanny Membership
Hello List,
My question is an elementary one. I have run a fuzzy kmeans cluster using
FANNY to group freshwater fish assemblages. I then went in the field to
validate that classification and have retrieved new assemblage data for a
new suite of streams. Therefore I would like to use Predict to determine how
well the original clustering fits the new data. However I have not figured
out a
2018 Mar 04
2
Random effect in GAM (mgcv)
Dear R users,
I am using the *mgcv package* to model the ratio of hectares of damaged
culture by wild boar in french departments according to some
environmental covariates. I used a _Beta distribution_ for the response.
For each department, we estimated the damaged in 3 different culture
types (??Culture??). Our statistical individual are therefore the
department crossed by the culture
2007 Aug 06
1
lda and maximum likelihood
Dear all,
I am trying to compare several methods for classify data into groups.
In that purpose I 'd like to developp model comparison and selection
using AIC.
In the lda function of the MASS library, the maximum likelihood of the
function is not given in the output and the script is not available.
Do anyone know how to extract or compute the maximum likelihood used in
the lda function?
2008 Apr 18
2
Correspondence and detrended correspondence analysis
Hi,
I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package.
2007 Dec 03
2
Why is the program too slow?
Hi,everyone.
I use the following program calculates Fisher's alpha from counts of individuals and species. The program is wrote by Prof. Kyle Harm.
However, when I run the program, it can work very quickly sometimes, but it can not work very well sometimes. It depends on the counts of individuals and species.
For example,
> calc.alpha(1000,70)
[1] 17.14375
> calc.alpha(10000,70)
[1]
2018 Mar 04
0
Random effect in GAM (mgcv)
Statistics questions are largely off topic on this list, although they do
sometimes intersect R programming issues, which are on topic. However, I
believe a statistics list like stats.stackexchange.com might be more
suitable for your query.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka
2006 Mar 16
2
hierarchical partitioning
Hello,
I would like to know what it means, when the hier.part's output has a data
frame of a negative independent contribution for variables (?IJ) and how
this can be caused.
Thank you very much.
Yours sincerely
M. Heuner
2009 Oct 28
1
hierarchical partitioning in generalized linear mixed models
dear colleagues,
I want to use hierarchical partitioning methods to evaluate variance
contributions of differente predictors within a generalized linear
mixed model framework. I don't know if this is possible, because I can
not found anything about this issue. My error is poisson and I, at
least, a random factor in the designed analysis.
I acknowledge any idea about how deal with
2018 Apr 18
0
nMDS with R: missing values
I'm not sure how you are incorporating time period into your data structure. Typically we are looking at plots or assemblages as the rows and taxa as the columns. Time period adds a third dimension that could be added as blocks of rows. For example, depending on the resolution of your data, one approach would be to have up to 8 rows for each locality: Loc1.1000, Loc1.2000, . . . Loc1.8000. If
2005 Mar 09
1
multiple comparisons for lme using multcomp
Dear R-help list,
I would like to perform multiple comparisons for lme. Can you report to me
if my way to is correct or not? Please, note that I am not nor a
statistician nor a mathematician, so, some understandings are sometimes
quite hard for me. According to the previous helps on the topic in R-help
list May 2003 (please, see Torsten Hothorn advices) and books such as
Venables &
2014 Jun 15
0
Problem with converting a list of grids to a list of polygons
Hi.
For a spatial analysis (its visualization) I need to produce a map of
conditions and traits.
When I used SpatialPixelsDataFrame (sp package) my grid cells were regular
and between each row was a small gap, which is not only messy but incorrect.
So I generated the coords of each grid from the centroids in order to
elongate the cells manually (or does anybody know another way to solve
this?).
2012 Sep 12
0
R-help Digest, Vol 115, Issue 12
Hello Amelie,
I don't have an answer to your question, but I just wanted to point out
this page I noticed recently (
http://hlplab.wordpress.com/2009/05/07/multinomial-random-effects-models-in-r/),
which might be helpful.
I'm also interested in figuring out how to do a multinomial glmm, so if you
find out anything I'd be happy to hear more about it! Based on what I've
found so
2011 Jul 27
0
Inversions in hierarchical clustering were they shouldn't be
Hi,
I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix:
library("gplots")
library("RColorBrewer")
test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77,
0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51),
ncol=4, byrow=TRUE)
2003 Aug 13
0
re: two dimentional hierarchical clustering algorithm
Dear Dr. Liaw Andy:
I have a few more questions about your heatmap function. actually heatmap is
what I am looking for.
heatmap(x, Rowv, Colv, distfun = dist, hclustfun = hclust, add.expr,
scale=c("row", "column", "none"), na.rm = TRUE, ...)
my data is a XNEW,
> dim(XNEW)
[1] 554 335
554 genes, 335 samples.
now I want to use 1-CORR as a distance
2010 Jul 22
0
snow: hierarchical parallelization
I'm parallelizing some computation on hierarchical data, and would
find it natural to do something like this (where a call to parLapply
is embedded in outer call to parLapply):
cl <- makeCluster(rep.int('localhost', 5),
type='SOCK')
clusterExport(cl, 'cl')
parLapply(cl, 1:5, function(i) parLapply(cl, 1:5, function(j) i * j))
Snow
2009 Nov 03
1
hierarchical clustering with Jaccard index
hi,
I want to do hierarchical clustering with Jaccord index. I tried to do with vegan package for finding index and hierarchical clustering with hclust function. While doing clustering it is showing an error message as "invalid distance method". I would be grateful if anyone tells how to rectify the error.
Thanks in advance,
kind regards,
Ms.Karunambigai M
PhD Scholar
Dept. of
2011 May 17
0
hierarchical gamma model in lme4
Addendum: I tried a gamma fit in glmmPQL and got the same errors.
*Ben Caldwell*
PhD Candidate
University of California, Berkeley
On Tue, May 17, 2011 at 3:51 PM, Benjamin Caldwell
<btcaldwell@berkeley.edu>wrote:
> Hello
> After seeing this (
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2011q1/005213.html) email
> I thought I would check the issue with a gamma family
2002 Jun 06
0
(E)SFQ HRR (=Hierarchical Round Robin)
> From: Martin Devera <devik@cdi.cz>
> Subject: [LARTC] (E)SFQ suggestion
> Hi,
> just simple note. Maybe it is already in progress :)
>
> There are attempts to replace hashing routine in SFQ to
> consider IPs or ports.
> What about to use HRR - roundrobin around bunch of IP
> adresses and then smaller WRR for ports per IP ?
> It would solve both