search for: dudi

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 <- pcnull$loadings out <- matri...

...0 ... $ -R-: int 3 16 5 2 1 16 15 2 4 15 ... > str(rownames(em3)) chr [1:37] "abov-belw" "ampl-rstr" "angl-rndd" "ascn-dscn" "asym- symm" "end-bgnn" ... Thus the 37 rownames in both are the same. Now I do a pca of op: > (op.dudi <- dudi.pca(op, scale = F, scan = F)) Duality diagramm class: pca dudi $call: dudi.pca(df = op, scale = F, scannf = F) $nf: 2 axis-components saved $rank: 5 eigen values: 0.09233 0.03109 0.01322 0.002024 0.0001017 vector length mode content 1 $cw 5 numeric column weights 2 $lw...

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 dataframes with the regular lapply function it works correctly. If use the 'parLapply' there is an error message. Example: > library("snow") >...

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(d...

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 cuáles son las variables que más influyen sobre el resultado. Re...

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 normal, if not how can I solve it, or get around it? (discrimin() seems to have an issue about that) Secondly, it does not matter which matrices I am treating first, but once...

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 signos contrarios: Función dudi.pca:...

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) &...

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) pct<-cbind(acciaieria,laminato...

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

> Hi > I'm Ph.D student and I need an R code to compute the chi square diistance between n profile rows in a matrix. > > could you help me please? > Thanks > > Paola > ____________________________________________________________

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. [[alternative HTML version deleted]]

...excellence.es El 27 de agosto de 2013 23:14, Argel Gastélum Arellánez < argel.gastelum@gmail.com> escribió: > 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 cuáles son las > variables que más influyen sobre el res...

Hi all, I'm trying to do model reduction for logistic regression. I have 13 predictor (4 continuous variables and 9 binary variables). Using subject matter knowledge, I selected 4 important variables. Regarding the rest 9 variables, I tried to perform data reduction by principal component analysis (PCA). However, 8 of 9 variables were binary and only one continuous. I transformed the data by

...n 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

...de agosto de 2013 23:14, Argel Gastélum Arellánez < argel.gastelum@gmail.com<mailto:argel.gastelum@gmail.com>> escribió: 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 cuáles son las variables que más influyen sobre el resultado. Revisan...

...de dispersión. No creo que se pueda hacer directamente en la función. Saludos Francesc El 01/10/13 17:53, Argel Gastélum Arellánez ha escrit: > Hola Francesc, muchas gracias por tu respuesta. > > Entonces, si quisiera que las gráficas de los resultados de ambas > funciones dudi.pca y PCA fuesen similares, ¿sólo tendría que > multiplicar por -1 todos los valores de las coordenadas > correspondientes al segundo componente de los individuos, por ejemplo, > de la función dudi.pca?... ¿de igual forma para las coordenadas de la > gráfica de correlaciones de las...

...-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). http://pbil.univ-lyon1.fr/JTHome/ade4TkGUI.jpg One of the benefits of using ade4TkGUI is the centralized graphical display of the dudi objects created by ade4. A dudi is a list with many components http://pbil.univ-lyon1.fr/ade4html/dudi.html The GUI presents a window in which the user can click on dudi components to get predefined graphical displays : http://pbil.univ-lyon1.fr/JTHome/coa1dudi.jpg Another benefit is for complex...

...-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). http://pbil.univ-lyon1.fr/JTHome/ade4TkGUI.jpg One of the benefits of using ade4TkGUI is the centralized graphical display of the dudi objects created by ade4. A dudi is a list with many components http://pbil.univ-lyon1.fr/ade4html/dudi.html The GUI presents a window in which the user can click on dudi components to get predefined graphical displays : http://pbil.univ-lyon1.fr/JTHome/coa1dudi.jpg Another benefit is for complex...

...positive variables) : d(x,y) = 1/NZ * sum(abs(x-y)/(x+y)) Can someone help me to understand the differences in the choice of the formula and why there's a difference between calculus and explaination for dist() ? Thank you for your help. Best regards, Fred PS : Be careful with function dudi.pca() from ade4 ; in values, "norm" doesn't give you what is written in the help page : "norm" returns the vector of standard deviations of initial variables when you choose "normed" PCA and the vector of standard deviations of normed variables, ie 1, when you...