similar to: S4 method defined but not used

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function

Buenas tardes, Estamos intentando hacer un estudio sobre diversidad en gatos callejeros ('stray cats') de la base de datos 'nancycats' (librería 'adegenet') de R. Sin embargo, no entendemos muy bien los datos. ¿Alguien puede explicarnos a qué corresponde la variable respuesta? Entendemos que las filas son los 237 gatos (observaciones), y las columnas se corresponden con

Estimado Gemma Ruiz Olalla De curioso miré una búsqueda en internet, y se la comparto, de esta observe la página 8 http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf Estoy de acuerdo con Jorge y Carlos, pero por las dudas, es solo una codificación, yo sin mirar más no interpretaría que el heterocigota tiene un "peso" de 0.5, porque si hay sobredominancia, dominancia, etc

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

Dear list, here is a problem I met when trying to use a method for an S4 object, without loading the package in which the method was defined. I do not know if this is a bug, or a mistake of mine. Normally, I think the package in which the appropriate method is defined is loaded automatically when calling the method. The problem is that if the package is indeed loaded automatically, the

Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj'

Hello, Here is a late answer, but an answer nonetheless to the question I asked almost one year ago on this list: > On Wed, 29 Mar 2006, Thibaut Jombart wrote: >> Hello list, <http://tolstoy.newcastle.edu.au/R/help/06/03/24318.html#24322qlink1> />> / />> does anyone know if Monmonier algorithm is available in R? I've checked / />> several spatial

Hi, I am trying to calculate Moran's I test for the residuals for a regression equation, but I have trouble converting my coordinates into nb format. I have used the dnearneigh() funtion now with an arbitrarily high upper distance to make it include all plots. However, when I do the lm.morantest() I get a Moran's I value which is the same as the expected value and a P-value of 1. I

Hi, I am a new student to R and I was hoping someone could help me with the error message I keep getting when I try to use the nb2listw() function. I have 45 sites and I want to get an autocorrelation value for sites within 1000m of each other. coords<-cbind(EAST,NORTH) coords<-as.matrix(coords) nb1000<-dnearneigh(coords,0,1000,longlat=TRUE) then when I try to run the

I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row

Hi, I have collected data on trees from 5 forest plots located within the same landscape. Data within the plots are spatially autocorrelated (calculated using Moran's I). I would like to do a ANCOVA type of analysis combining these five plots, but the assumption that there is no autocorrelation in the residuals is obviously violated. Does anyone have any ideas how to incorporate these spatial

Dear all, (Mac OS X 10.4.11, R 2.6.0) I have a quantitative dataset with a lot of Na?s in it. So many, that it is not possible to delete all rows with NA?s and also not possible, to delete all variables with NA?s. Is there a function for a principal component analysis, that can deal with so many NA?s. Thanks in advance Birgit Birgit Lemcke Institut f?r Systematische Botanik

Hi everyone, I have a matrix that contains 1000 replicates of a sample of a list of values. I want to group each row (row=replicate) into my defined bin ranges and then calculate the mean and stdev for each of the bin ranges (so I will have 1000 rows but ncol=number of bin ranges). I don't know how to group rows in a matrix matrix according to another vector (which is what I think I need to

Dear R user, I am using Sweave to write my reports with R code. Unlucly my code take a lot of time to run, and I don't want to run it multiple time, if possible, as I am still developping the tools. It seems that a sweave run does not save the enviroment at the end of the process, is there a way to avoid to lunch multiple time the same commands? maybe it could be possible to store chunck of

Hi the list, I am defining a new class MyClass. Shortly, I will submit a package with it. Before, I would like to know if there is a kind of "non official list" of what method a new S4 object have. More precisely, personnaly, I use 'print', 'summary' and 'plot' a lot. So for my new class, I define these 3 methods. Is there some other method that a R user can

Hi Everyone, I am doing a project based on "Spatially Lagged Predictor Variable Models", I would like to know which package in R would execute this model. Also, I am new to this field of spatial statistics. Any suggestions for a good book on spatial regression analysis would be appreciated. Thanks Again. Cheers Arun -- View this message in context:

Dear R community, I'm working with PCA and CCA methods, and I have a theoretical question. Why is it necesary to have more temporal values than variables when the CCA O PCA are going to be used? Could you advise to me some any paper about it? Thanks in advance, [[alternative HTML version deleted]]

Dear R addicts, Back in 2006, I posted the proposition for a tweak of the Sweave driver so that PNG figures can be produced instead of eps/pdf : https://stat.ethz.ch/pipermail/r-help/2006-March/102122.html The amount of code modified is tiny (it was designed to induce minimal changes to the official code), but so far the driver seems to have been useful to a number of users. From 2006 on,

Dear R addicts, Back in 2006, I posted the proposition for a tweak of the Sweave driver so that PNG figures can be produced instead of eps/pdf : https://stat.ethz.ch/pipermail/r-help/2006-March/102122.html The amount of code modified is tiny (it was designed to induce minimal changes to the official code), but so far the driver seems to have been useful to a number of users. From 2006 on,

Dear all, I'm using the package adehabitat in R to import several .asc files (=matrix), and also create a kasc object (=dataframe) with all of them. The main idea is to use this kasc object to map the predicted values of climate-matching model for an overall area. However, I don't know how to proceed: Do I have to project the model (already stored in R) onto the kasc object directly, or