search for: cl1

...ike it. Though, I have one problem: I cannot find a way to update a method on an existing object. The flexibility that scripting gives (really needed for interactive data analysis) is lost if everything have to be recalculated all the time. For example I would normally work something like this: cl1 <- setRefClass("cl1", ? fields=list(x="data.frame"), ? methods=list( ? ? init=function(){"Read and process data"}, ? ? fitModel=function(){"Fit different kind of models and keep the results in x and other fields"}, ? ? plotFit1=function(){"Plot the fi...

Dear all, I need to create a for-loop in which I can compute multiple histograms My code is the following : #singlefile includes huge csv file #I want to specify the binsize #I would like to compute in the for -loop the histograms numfiles <- length(singlefile) for (i in 1 :51) { binsize <- -20 :20/2 hist(singlefile(singlefile$GVC[singlefile$new_id==i]], break=seq(),

...e snippet: setGeneric("doNothing<-", function(object, value) standardGeneric("doNothing<-")) setReplaceMethod("doNothing", signature(object = "Spatial", value = "ANY"), function(object, value) object) dosth = function(obj) { cl1 = class(obj) doNothing(obj) = TRUE cl2 = class(obj) if (!identical(cl1, cl2)) { print(paste(cl1, cl2)) stopifnot(identical(cl1, cl2)) } obj } When things go wrong, dosth and doNothing are called with a subclass of Spatial, e.g. an object of class SpatialGrid, bu...

Dear R community, I am new to R, a reforming SAS user :) I am running R 2.10.1 on a Windows XP machine. I would like to write linear functions of my coefficient parameter estimates from a glm, but am having a difficult time understanding the parameterization R uses. In the toy example below I am running a glm on binomial data, with clones and lines within clones as fixed effects, each with 6

...r Filesystem 1K-blocks Used Available Use% Mounted on /dev/drbd0 83883484 80071096 3812388 96% /cluster $ df -i /cluster Filesystem Inodes IUsed IFree IUse% Mounted on /dev/drbd0 20970871 20017778 953093 96% /cluster dd test on CL1-N1 -- FAILING: $ dd if=/dev/zero of=`hostname`.tst bs=1M count=10 dd: writing `cl1-n1.tst': No space left on device 1+0 records in 0+0 records out 1032192 bytes (1,0 MB) copied, 1,56907 s, 658 kB/s same dd test on CL1-N2 -- OK: $ dd if=/dev/zero of=`hostname`.tst bs=1M count=10...

...(26.1:6, 17.1:8):60, (((((((41.1:0, 1.1:3):0, (9.1:0, 27.1:0):1):2, (5.1:0, 10.1:0):3):1, (38.1:1, (4.1:1, (24.1:0, 18.1:0):2):0):0):16, 36.1:19):8, (32.1:0, 33.1:1):29):33, (40.1:18, ((23.1:0, 12.1:1):3, 34.1:2):16):42):1):82);" t<-read.tree(text=un) # following example from ape package cl1 <- collapsed.intervals(ci,0) cl2 <- collapsed.intervals(ci,0.0119) sk1 <- skyline(cl1) # from collapsed intervals sk1 <- skyline(ci) # from coalescent intervals sk1 <- skyline(tree.hiv) # from tree sk2 <- skyline(cl2) # from collapsed intervals sk2 <- skyline(ci, 0.0119) # fro...

My data looks like: A,B,C,D,Class 1,2,0,2,cl1 1,5,1,9,cl1 3,2,1,2,cl2 7,2,1,2,cl2 2,2,1,2,cl2 1,2,1,5,cl2 0,2,1,2,cl2 4,2,1,2,cl2 3,5,1,2,cl2 3,2,12,3,cl2 3,2,4,2,cl2 **The steps followed are: trainfile <- read.csv("TrainFile",head=TRUE) datatrain <- subset(trainfile,select=c(-Class)) classtrain <- (subset(trainfile,select=...

...] "" $major [1] "2" $minor [1] "5.1" $year [1] "2007" $month [1] "06" $day [1] "27" $`svn rev` [1] "42083" $language [1] "R" $version.string [1] "R version 2.5.1 (2007-06-27)" >library(cluster) >cl1 ## clustering labels [1] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 [30] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 [59] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 [88] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 [117] 2 2 2 2 2 2 2 2 2...

...ince there is no character ahead of the superscript (I saw examples in the archives where there was a preceeding character). Also, the construction of the string seems to not be working as I expect either. So, I think there are two problems here. Here is a sample of what doesn't quite work: Cl1 <- rbinom(1000, size = 1, prob = 0.25) pCl1 <- histogram(Cl1, main = expression(Cl[1]), xlab = "", ylab = "", scales = list(draw = FALSE), ylim = c(0:80)) plot(pCl1) # This works fine but doesn't have everything I want: leg.txt1 <- paste("Based upon:\n", &...

Dear members. I am having problems to understand the kmeans- results in R. I am applying kmeans-algorithms to my big data file, and it is producing the results of the clusters. Q1) Does anybody knows how to find out in which cluster (I have fixed numberofclusters = 5 ) which data have been used? COMMAND (kmeans.results <- kmeans(mydata,centers =5, iter.max= 1000, nstart =10000)) Q2) When I

...3.4, 453.8, 452.2, 450.7, 450.6, 451.4, 447.5, 18.34, 18.29, 17.65, 17.52, 16.96, 17.41, 18.51, 19.02, 19.43, 20.76, 20.76, 21.59, 22.28, 22.4, 22.63, 22.26, 22.71, 22.27, 21.75, 21.65), .Dim = c(20L, 4L), .Dimnames = list(NULL, c("TY1.lev", "SP1.lev", "GC1.lev", "CL1.lev")), index = structure(c(10959, 10960, 10961, 10962, 10963, 10966, 10967, 10968, 10969, 10970, 10973, 10974, 10975, 10976, 10977, 10980, 10981, 10982, 10983, 10984), class = "Date"), class = "zoo") What I want to do is to calculate simple return on each column (return=P...

...ks something like: [Drive C] "Path"="/c" "Type"="hd" "Label"="MS-DOS" "Windows"="c:\\windows" "System"="c:\\windows\system" *****end of config***** I used samba to mount a windows share at /mnt/cl1 & ln -s /c c:\\ and run the following command: wine /mnt/cl1/foo/setup.exe I'm getting an error message: Warning: the specified windows directory L"c:\\Windows" is not accessible. What does this error mean and how do I fix it? BTW, the having a sample config file on a web p...

Hi, i want a cluster-analysis with clara, but getting an error because in cldat are NA's. Error in clara(cldat[, 1:3], 4) : Each of the random samples contains objects between which no distance can be computed. cldatx <- subset(cldat,select=c(A,B,C)) cldaty <- na.omit(cldatx) Now , clara works but cldat has ~193.000 obs and cldatx without NA's ~75.000 obs. How could i match

Hi All, A question from a newbie using R 2-5-0 on windows XP. Why is it that kmeans clustering with apparently the exact same parameters behaves so differently between the two following examples : > cl1 <- kmeans(subset(pointsUXO15555, select = c(2:4)), 10) Takes about 2 seconds to deliver a result > cl1 <- clust(subset(pointsUXO15555, select = c(2:4)), k=10, method="kmeansHartigan") Dies after about 10 minutes and fills up RAM : *** running kmeansHartigan cluster algori...

Hi, I am getting intermittent error messages in the log when my mail client tries to create/open a folder named ".imhoprefs". Some accounts seem to able to do it, but I have at least one that gives the log error: Feb 7 09:29:54 acad-cl1 dovecot: imap(tkay): close() failed with index file (in-memory index): Bad file descriptor I traced through the code, and it seems to be coming from mail_index_close() (line 1527 of mail-index.c), which seems to be attempting to close a file descriptor for an index. The funny thing is that since I...

...axis should be the estimated OR (with upper and lower conf. limits), and the horizontal exis should be fixed values: (1,0.8,0.7,0.6,0.5,0.4) Here is a part of my code: ...ests=matrix(ncol=3,nrow=6) ests[,1]<-c(mean(or1),mean(or14),mean(or15),mean(or16),mean(or17),mean(or18)) ests[,2]<-c(cl1,cl14,cl15,cl16,cl17,cl18) ests[,3]<-c(cu1,cu14,cu15,cu16,cu17,cu18) x1<-c(1,0.8,0.7,0.6,0.5,0.4)... Now I have a matrix with three columns: estimate, lower limit of the confidende interval, and upper limit of the confidence interval: [,1] [,2] [,3] [1,] 1.011794 0.64007...

Hi all, I am using R trying to get a inverse matrix of (X^T)X , but I keep getting the error message like: no b argument and no default value for sprintf(gettext(fmt, domain = domain), ...) . -------------------------------------------------------------------------------------------- # my code X<-Matrix(rep(1,500),100,5) X[lower.tri(X)]<-1-10^-7 XtX<- t(X)%*% X XtXu<-lu(XtX)

While trying to train randomForest with my dataset, I am ending up with the following error Error in randomForest.default(datatrain, classtrain) : length of response must be the same as predictors My data looks like: A,B,C,D,Class 1,2,1,2,cl1 1,2,1,2,cl1 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,1,2,cl2 3,2,12,3,cl2 3,2,1,2,cl2 Actual dataset has around 4000 features and two classes. And number of instances is also around 4000. The steps followed are: trainfile <- read.csv("TrainFile",head...

...NULL) Error: Error in names(class_ids) <- nms : 'names' attribute [150] must be the same length as the vector [0] In addition: Warning message: In is.nan(class) : is.nan() applied to non-(list or vector) of type 'NULL' another example of such an error is: Code: library(RWeka) cl1 <- SimpleKMeans(iris[, -5], Weka_control(N = 3)) Error: Error in names(class_ids) <- nms : 'names' attribute [150] must be the same length as the vector [0] In addition: Warning message: In is.nan(class) : is.nan() applied to non-(list or vector) of type 'NULL' I even cop...

...snow is not working on a windows cluster with MPICH2 and Rmpi. There is an error in makeCluster: launch failed: CreateProcess(/usr/bin/env "RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS=" C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error 3 - Das System kann den angegbenen Pfad nicht finden. I looked into makeMPIcluster. It could not work, mpi.comm.spawn gets the shell command for unix to start the slaves. A simple solution is to use the windows-code from mpi.spawn.rslaves, then it looks like this. And is wor...