similar to: Kmeans performance difference

Hi All, I just installed Cairo on R 2.5.1 on windows XP. My hope was to get to see the transparency output e.g. http://had.co.nz/ggplot2/stat_smooth.html ggplot2 - stat_smooth , which I finally managed to do. However, I find the Cairo device, which I access either through CairoWin() or Cairo(type="win"), is pretty shaky in a number of respects : - whatever portion of the Cairo

Hi All, I'm looking for ways to compute aggregate statistics (with the aggregate function) but with an option for sorting and selecting a subset of the data frame. For example, I have would like to turn this : aggregate(myDataframe$TargetValue,list(SomeFactor = myDataframe$SomeFactor),mean) into something like aggregate(myDataframe$TargetValue,list(SomeFactor =

Hello everyone, I am working with one big matrix: w=matrix(0,18000,18000) on a Linux computer with 16Go of RAM. I can actually create the matrix, and even access elements: w[10,10] 0 but if I try to change one element, it fails: w[10,10]=1 Erreur : impossible d'allouer un vecteur de taille 2531250 Ko (Failed to allocate a vector of size...) What can I do? And, maybe even more important,

Hi, I'm trying to introduce a (spatial) exponential correlation structure (with range=200 and nugget.effet of 0.3) in a lme model of this form: lme(ARBUS~YEAR, random=~1|IDSOUS). The structure of the data is "IDSOUS" "XMIN" "YMAX" "YEAR" "ARBUS" with 2 years of data and 5600 points for each year. I do:

Dear all, I am trying to aggregate a table (divided in two lists here), but get a memory error. Here is the code I'm running : sessionInfo() print(paste("memory.limit() ", memory.limit())) print(paste("memory.size() ", memory.size())) print(paste("memory.size(TRUE) ", memory.size(TRUE))) print(paste("size listX ", object.size(listX)))

hi, how can i do cluster analysis on spatial data? (longitude & latitude) Because i used the function clust of the clustTool package and it did'nt work at all: cl <- clust(dv,3,method="hclustAverage",distMethod="euclidean") thanks a lot Karine HEERAH Master 2 , océanographie et environnements marins Université Pierre et Marie Curie (Paris 6)

Dear R users, I try to use a very large file (~3 Gib) with the filehash package. The length of the dataset is around 4,000,000 obs. I get this message from R while trying to "load" the dataset (named "cc084.csv"): > dumpDF(read.csv("cc084.csv", header=T), dbName="db01") Erreur : impossible d'allouer un vecteur de taille 15.6 Mo (French) Error:

Hi all, I am running an -MNP- multinomial probit model package using R. It gives me the following objection instead of giving me the results: Erreur : impossible d'allouer un vecteur de taille 137.9 Mo (in english: cannot allocate a 137.9 Mb vector memory).  I have already increased the memory size upto 2047Mb. This problem has been discussed in 2008 (archives) but no profitable answers were

CRAN (and crantastic) updates this week New packages ------------ * DCGL (1.0) Bao-Hong Liu http://crantastic.org/packages/DCGL Functions for basic differential coexpression analyses: gene filtering, link filtering, DCG (Differentially-Coexpressed Gene) identification and DCL (Differentially-Coexpressed Links) identification.Two algorithms,named DCP and DCe, are provided for

Hi there, I run the following code in R and got the warning like that, how can I change the memory.size? Or anything else? Thanks a lot! Faye temp<-apply(Idd4.perms$permstats[-stratum1,], + 2,sort) Error: cannot allocate vector of size 47.5 Mb In addition: Warning messages: 1: In apply(Idd4.perms$permstats[-stratum1, ], 2, sort) : Reached total allocation of 1023Mb: see help(memory.size)

Dear List, today I turn to you with a next problem. I'm trying to compare species richness between various datasets (locations) using species accumulation curves (Chapter 4, page 54 in Tree diversity analysis<http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp>by Kindt & Coe). To accomplish this I'm using package BiodiversityR. My data is comprised of

Hi Being able to do object oriented programming in R is really good. I now started using the Reference Classes and really like 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

List, In order to get rid of some old, unreadable S3 code in package sp, I'm trying to rewrite things using S4 methods. Somewhere I fail, and I cannot sort out why. In order to isolate the problem, I created two functions, doNothing<- and dosth, and both should do nothing. The issue is that in most cases they do nothing, but in some cases dosth(obj) changes the class of obj and breaks with

Hi Guys, I would like to share my experience when installing the Spatial views packages for R. I could not install 32 packages which are parts of the Spatial views, and I use google-search and search to solve ALL those problems for about 2 days. I hope maybe somebody would benefit from my experience. I admitted that I do not have excellent programming skills at all. So, perhaps some of

Hello, I have a data-set containing 22 variables, after appropriate transformations etc I ran a kmeans cluster analysis for 4 clusters , I ran it 20 times to find a result with the lowest within sum of squares. My question is how best do I go about finding out what the characteristics are of each cluster? Is one cluster dominated by a particular set of variables or by a particular

Hi, I have generated a skyline plot of a tree in newick format using "ape". How can I plot the error bars for this graph? I only have the the tree data. un<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (((((15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0,

Hello, I'm very new to wine. I'm trying to use wine to run an Educational program for a grade school. The name of the educational program is "Compass Learning". [ I believe I installed the package 07252005. i.e. from July 25th of this year. ] I used winecfg to try and configure things, but it gave me an error about not being complete. I couldn't use the drop down menu

Hello, Samba list. When configuring the gMSA on Samba DC (the domain was provisioned using Samba DC, and this DC is the only one in the forest) and trying to use the created service account on Windows, I get an error: "Error 1069: The service did not start due to a logon failure." If the domain is provisioned from Windows AD DS, and Samba is the second controller in the domain

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=Class)) rf <- randomForest(datatrain, classtrain)

I have been searching all day & most of last night, but can't find any benchmarking or recommendations regarding R system requirements for very large (2-5GB) data sets to help guide our hardware configuration. If anybody has experience with this they're willing to share or could anybody point me in a direction that might be productive to research, it would be much appreciated.