Displaying 20 results from an estimated 400 matches similar to: "Help with dudi.pca"
2011 Nov 05
1
testing significance of axis loadings from multivariate dudi.mix
Hi all
I?m trying to tests the significance of loadings from a ordination of 46 variables
(caategorical, ordinal and nominal). I used dudi.mix from ade4 for the ordination. A
years ago Jari Oksanen wrote this script implementing Peres-Neto et al. 2003 (Ecology)
bootstraping method:
netoboot <- function (x, permutations=1000, ...)
{
pcnull <- princomp(x, cor = TRUE, ...)
res
2005 Oct 06
1
Compare two distance matrices
Hi all,
I am trying to compare two distance matrices with R. I would like to
create a XY plot of these matrices and do some linear regression on
it. But, I am a bit new to R, so i have a few questions (I searched in
the documentation with no success).
The first problem is loading a distance matrix into R. This matrix is
the output of a the Phylip program Protdist and lookes like this:
5
2007 Oct 16
2
Canberra distance
Hi,
I misunderstand the definition of Canberra distance in R.
On Internet and in function description pages of dist() from stats and
Dist() from amap, Canberra distance between vectors x and y, d(x,y), is :
d(x,y) = sum(abs(x-y)/(x+y))
But in use, through simple examples, we find that the formula is :
d(x,y) = (NZ + 1)/NZ * sum(abs(x-y)/(x+y))
with NZ = nb of pairs of coordinates that are
2005 Nov 11
1
Snow parLapply
Dear R-user,
I am trying to use the function 'parLapply' from the 'snow' package
which is supposed to work the same wys as 'lapply' but for a
parallelized cluster of computers. The function I am trying to call in
parallel is 'dudi.pca' (from the 'ade4' package) which performs
principal component analyses. When I call this function on a list of
2006 Oct 01
0
New package 'ade4TkGUI', a Tcl/Tk GUI for ade4
Dear R-Users,
ade4TkGUI is a new package available on CRAN. It implements a Tcl/Tk
graphical user interface (GUI) for the ade4 package.
Only the most basic functions of ade4 have a GUI in this first
version : classical one-table data analysis methods (PCA, COA,
MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA),
and two-tables analysis methods (Coinertia analysis, CCA, PCAIV).
2006 Oct 01
0
New package 'ade4TkGUI', a Tcl/Tk GUI for ade4
Dear R-Users,
ade4TkGUI is a new package available on CRAN. It implements a Tcl/Tk
graphical user interface (GUI) for the ade4 package.
Only the most basic functions of ade4 have a GUI in this first
version : classical one-table data analysis methods (PCA, COA,
MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA),
and two-tables analysis methods (Coinertia analysis, CCA, PCAIV).
2004 Jul 31
1
dudi.pca behaviour and discrimin
Hello,
I not have attached in this e-mail the zipped
list of matrices I am using because it has 1 meg
once zipped and anyway we cannot send attached
files on r-help mailling list.
First, after running the code that is written
bellow, I realized that the printout of dudi.pca
gives me for both of my matrices
$cw length that are unequal to either respective $rank or $eig lengths.
Is that
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 !
2013 Aug 27
2
Encontrar las variables más importantes en componentes principales
Hola compañeros de la lista. Qué tal.
Tengo un análisis de componentes principales, en el que se evalúan
aproximadamente 1000 variables. Usando la función dudi.pca e
inertia.dudi obtengo una cantidad de información sobre la influencia de
las variables sobre los dos componentes principales. Me gustaría saber
si existe alguna función que sobre esta información me arrojara la lista
de
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 =
2006 Jul 20
2
Correspondence analysis with R -follow up
Hi all,
thank you for your answers; i've tried both cca from vegan library, and
dudi.coa from ade4 library; one last question: my deal is mainly with
contingency tables, like the one i'm posting here
acciaieria<-c(.41,.02,.44,.04,.09)
laminatoio<-c(.34,.28,.26,.01,.11)
fonderia<-c(.48,.05,.34,.08,.05)
leghe<-c(.45,.19,.25,.03,.08)
2013 Aug 29
1
Resumen de R-help-es, Vol 54, Envío 22
Hola! No he podido consultar la doc. del paquete ade4, algo debe estar caído en CRAN ahora mismo.
Dos cosas sobre la metodología -aun desconociendo los detalles de cómo lo hace ade4:
El output de un PCA, los "pesos" de cada variable en las dimensiones de los componentes se interpretan como correlaciones, a mayor valor absoluto mayor asociación variable-componente. Ahora, como tales
2013 Oct 01
5
Análisis de componentes principales con ade4 y FactoMineR
Hola compañeros de la lista, qué tal.
Estoy haciendo un análisis de componentes principales utilizando
las funciones "dudi.pca" (paquete "ade4") y "PCA" (paquete
"FactoMineR"). Sucede que al comparar las coordenadas de cada individuo
que obtiene cada función, las que corresponden al segundo componente
principal tienen idéntica magnitud pero con
2017 Jun 24
9
Limit IMAP/IMAPS listening IPs
Hello list.
I am running dovecot v2.2.13 on debian 8.8;
I tried to add a "address =" statement for only localhost and one private IP, but then I got a complaint from system:
dovecot[20515]: Error: systemd listens on port 143, but it's not configured in Dovecot. Closing.
What is the proper way to resolve this?
TIA & Regards,
Dudi
2013 Oct 01
3
Análisis de componentes principales con ade4 y FactoMineR
Instalo ade4 correctamente y no me abren los datos como por ejemplo
data(bsetal97)
¿Qué piensan de eso?
De: r-help-es-bounces en r-project.org [mailto:r-help-es-bounces en r-project.org]
En nombre de Francesc Carmona
Enviado el: Tuesday, October 01, 2013 7:30 AM
Para: r-help-es en r-project.org
Asunto: Re: [R-es] Análisis de componentes principales con ade4 y FactoMineR
Por definición
2004 Jul 01
1
Factors.
Hello,
I'm new with R. I need some help; I have a matrix of data to wich i want to
apply the function dudi.acm to perform multiple correspondence analysis.
However to use it all variables must be factors, so how can i turn each column
of the matrix into a factor? I've tried as.factor. It works isolated for each
column, but when I form the matrix of all factors it doesnt work.
Please
2019 Sep 20
2
7.7.1908, interface bonding, and default route
Hi!
I just upgraded a machine to 7.7.1908 and the default route is not being
set on boot. This particular server has a bonded interface, and the
corresponding configuration for the master is (
/etc/sysconfig/network-scripts/ifcfg-bond0):
TYPE=Bond
BOOTPROTO=none
DEFROUTE=yes
IPV4_FAILURE_FATAL=yes
NAME=bond0
DEVICE=bond0
ONBOOT=yes
IPADDR=10.3.20.131
PREFIX=24
2014 May 28
1
vnet device not appearing
Hello
I have a virtual server with 3 existing VMs running on it without issue.
The host has 4 NICs installed; em1 for the host, em2 and em3 already in
use by other VMs.
I would like to dedicate em4 to my new VM however when I create the bridge
like I did for the others I do not get a vnet3 device show up in the list
as shown below.
I tried using the GUI and virsh to create the bridge. I ended
2012 Jul 25
2
Obtain residuals from a Principal Component Analysis
Hi everyone,
I am relatively new to R, and I need to perform the principal components
analysis of a data matrix. I know that there are a bunch of methods to do it
(dudi.pca, princomp, prcomp...) but I have not managed to find a method that
can return the residuals obtained by retaining X principal components of the
original data, as this MATLAB function can do: http://is.gd/6WeUFF
Suggestions?
2012 Nov 18
1
help interpreting dudi.pco
I am working on morphometry of hairs and want to see if selected variables
are giving significantly distinct groups.
I am new to both R and principal coordinate analysis. Scatter plot is
showing distinct groups but i dont know how to refine the analysis and
interprete it.
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