similar to: Error on distance matrix

Hello, I would like to retrieve data stored in MySQL database, so I installed RMySQL package. I can successfully connect with the my database using the following code > dvr<-dbDriver("MySQL") > con2<-dbConnect(dvr,group="exbardiv") > mysqlDescribeConnection(con2) <MySQLConnection:(972,0)> User: mmorag Host: localhost Dbname: exbardiv

I am currently using the function daisy in package cluster to create a dissimilarity matrix because my multivariate dataset contain missing data and variables of various types including factors, symmetric and asymmetric binary and quantitative. This is a step prior to using pco within ecodist. There is a warning which comes twice ">NAs introduced by coercion" I've used

Hi, I have the following function that I want to apply to a list of 14 matrices (1536 x 170) of binary data: DRes <- function(x, nr = 10000, metric = "mixed", ...) { require(analogue) require(ade4) m <- c() for (i in 1:nr) { set.seed(i) x1 <- x[, sample(dimnames(x)[[2]], length(x[1,])/2)] x2 <- x[, !dimnames(x)[[2]] %in% dimnames(x1)[[2]]] d1 <-

Hi all, I''ve been having trouble for a long time with backgroundrb processes that suddenly vanish without a trace. What happens is that at some point I discover that all the backgroundrb processes are suddenly gone. Nothing special is seen in any of the log files. This has happened intermittently for a long time, and I was hoping that upgrading to 1.0.4 would somehow help me out, but

Hello all, I have some trouble in reconstructing a valid expression within a function, here is my question. I am building a function : SUB<-function(DF,subset=TRUE) { #where DF is a data frame, with Var1, Var2, Fact1, Fact2, Fact3 #and subset would be an expression, eg. Fact3 == 1 #in a first time I want to build a subset from DF #I managed to, with an expression like eg. DF$Fact3, # but I

Hi I have the following barchart to which I want to add error bars. library(lattice) barchart(Change~fTreat,groups=Process,change, auto.key=list(points=FALSE,rectangles=TRUE), panel=function(x, y,...){ panel.barchart(x,y,origin = 0,...); panel.abline(h=0,col="black",...); } ) I have tried

Hi R Helpers, I'm still new to R and i experience many difficulties..I'm using vegan package (R version 2.11) trying to calculate checkerboard units for each species pair of a matrix. I've prepared the function: pair.checker=function (dataset) {designdist (dataset, method="c("(A-J)x(B-J)", terms ="binary", abcd=FALSE)} to use with function oecosimu as

Dear All I am attempting some power analyses, based on simulated data. My experimental set up is thus: Bleach: main effect, three levels (control, med, high), Fixed. Temp: main effect, two levels (cold, hot), Fixed. Main effect interactions, six levels (fixed) For each main-effect combination I have three replicates. Within each replicate I can take varying numbers of measurements (response

I making an xyplot and the y label is too long and needs to be in two rows, but when I brake it there is a huge gap between the last text string and the expression, and I can't get rid of it. Any ideas? Data: structure(list(Temp = c(8L, 8L, 8L, 8L, 8L, 8L, 12L, 12L, 12L, 12L, 12L, 12L), CO2 = c(380L, 380L, 380L, 750L, 750L, 750L, 380L, 380L, 380L, 750L, 750L, 750L), Treat = structure(c(3L,

Classification: NOT PROTECTIVELY MARKED Solaris 9 Samba 3.4.5 I know this isn't the sort of query that gets much response but I'd be really grateful of any advice people can offer. I'm getting really fed up with Samba as I've never been able to make it work properly. Either I'm missing something basic (probably) or it just doesn't behave in the way I think it should!

I would like to randomly shuffle a distance object, such as the one created by ade4{dist.binary} below. My first attempt, using sample(jc.dist) creates a shuffled vector, losing the lower triangular structure of the distance object. How can I Ishuffle the lower triangular part of a distance matrix without losing the structure? Thanks. --Dale x1 <- c(rep(0,4),1) x2 <- c(rep(0,2),rep(1,3))

Hi All, Another quick question - I noticed that COZIGAM has been removed from CRAN, and that you are referred to the archive for previous versions (last updated 23 July 2012). Is this package still ok to use? Or is there an alternative which might also fit zero-inflated GAMs? Thanks, Raeanne The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by

I posted this last week but haven't heard anything. I'm not sure if this is because nobody knows the answer (can't believe that!) or I'm missing something obvious in the documentation and people are thinking "Read The Fine Manual". Whatever the reason, if anyone has any insights into this problem I'd be very grateful for their comments. We're using Samba 3.0.23b

> 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 > ____________________________________________________________

Dear Sir/ Madam, I would like to ask you about mantel test in R. In ade4 package, if I want to use mantel.rtest, I get error massage "Object of class to "dist" expected". As I already have two dissimilarity matrices, shall I again compute distance measure using this function? If not, could you please let me know which function/command I can use to do? Thank you very much in

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

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

I was curious to read the following in the "Guidelines for Rd files" at http://developer.r-project.org/Rds.html: "For consistency, aim to use British (rather than American) spelling. (NB: British spelling often uses -ize as in `capitalize'. The view of spell -b of British spelling is a flawed American one. There are English/Scottish differences

Hi there, My question is about the 'theta' parameter in specification of a NB GAMM. I have fit a GAM with an optimum structure of: SB.gam4<-gam(count~offset(vol_offset)+ s(Depth_m, by=StnF, bs="cs")+StageF*RegionF, family=negbin(1, link=log), data=Zoop_2011[Zoop_2011$SpeciesF=='SB',]) However, this GAM shows heterogeneity in the

Estimados usuarios: Estoy intentando reproducir el ejemplo 6.4 de Thomas Lumley. Complex Survey. Editorial Wiley. 2010 (ver la página en google: