Re: [R] invert 160000x160000 matrix

A variety of tricks would need to be used to invert a matrix of this size. If there are any other properties of the matrix that you know (symmetric, positive definite, etc, sparse) then they could be useful too. You could partition the matrix first, then use an in-place inverse technique for eac

[R] diffusing GIS data in maps

Hi- I am trying to find a way to diffuse GIS data on a European map. I have a dataset consisting of particular locations scattered across Europe, along with magnitude and value information. I can plot these as discrete points with something like the following: "geocode" is a dataframe with four c

Re: [R] State Space Modelling

try >help.search("state space") you will get pointer where you want to go cm.state(CreditMetrics) Computation of state space dlmLL(dlm)Log likelihood evaluation for a state space model SS(dse1) State Space Models

Re: [R] vertically oriented color key in heatmaps

colorbar() from the package matlab. nightly.py wrote: > > Hi, I have some data which I was plotting using image(). I wanted to > add a vertical color key to the plot and I found that heatmap.2 in > gplots does let me add a color key. However, I was thinking of a > vertical bar with the co

[R] Fatal Error - R in Windows XP

I would greatly appreciate if someone can tell me how to solve the issue I have been facing. After creating a large sparse matrix (6300 by 8300 matrix), I saved image of it in my work space to do further computation. Since then whenever I start R (version 2.5.1 on Windows XP, SP2), I seem to ge

[R] State Space Modelling

Hey all, I am trying to work under a State Space form, but I didn't get the help exactly. Have anyone eles used this functions? I was used to work with S-PLUS, but I have some codes I need to adpt. Thanks alot, Bernardo [[alternative HTML version deleted]]

Re: [R] invert 160000x160000 matrix

While inverting the matrix may be a problem, if you need to solve an equation A*x = b you do not need to invert A, there exist iterative methods which do need A or inv(A) - all you need to provide is a function that computes A*x for an arbitrary vector x. For such a large matrix this may be slow bu

Re: [R] binomial simulation

As I understand this, P(T+ | D-)=1-P(T+ | D+)=0.05 is the probability not to detect desease for a person at ICU who has the desease. Correct? What I asked was whether it is possible to mistakenly detect the desease for a person who does not have it? Assuming that this is impossible the formula i

Re: [R] Legend on graph

You can get the legend outside the plot region by 1. First changing the clipping region via par(xpd = TRUE) ; (or xpd=NA). see ?par 2. Specifying x and y coodinates for legend placement outside the limits of the plot region. This allows you to include a legend without adding a bunch of useless w

Re: [R] Artifacts in pdf() of image() (w/o comments)

Hi Duncan, Hi Michael, Duncan Murdoch stats.uwo.ca> writes: > On 8/13/2007 1:33 PM, Michael Kubovy wrote: > > - You saw ugly artifacts in a graph you produced. That's a bug. The > question is, what caused it? > - You rightly asked on R-help. It might have been a bug in the way > you we

Re: [R] deldir package - voronoi

Team, we figured this out, Roger at XLSOLUTIONS solved the puzzle for us..!! Okay you can easily change the color palette. see below: library(MASS) library(deldir) set.seed(1123) y <- runif(20) x <- runif(20) #run voronoi from deldir package ddd <- deldir(x,y) ttt <- tile.list(ddd) plot.deld

[R] predict kernelmatrix

HI I got a problem in the predict function of the kernlab. I want to use ksvm and predict with kernelmatrix (S4 method for signature 'kernelMatrix') #executing the following sentences library(kernlab) # identity kernel k <- function(x,y) { n<-length(x) cont<-0 for(i in 1:n){ if(

[R] Legend on graph

Hi Akki, Then you may need to increase y-axis scale by ylim=c(min,max) Cheers Nguyen On 8/12/07, akki <[EMAIL PROTECTED]> wrote: > Hi, > I have a problem when I want to put a legend on the graph. > I do: > > legend("topright", names(o), cex=0.9, col=plot_colors,lty=1:5, bty="n") > > but the legen

[R] Reading polygon shapefiles in splancs

Dear List, I'm trying to import a multiple polygon shapefile in splancs. I've found the following command but it seems to work only for single polygons: Name_of_splancs_polygon<-getPolygonCoordsSlot (getPolygonsPolygonsSlot(getSpPpolygonsSlot(name_of_sp_polygon) [[1]]) [[1]]) I've tried to

Re: [R] help with scatterplot3d

Ryan Briscoe Runquist ucdavis.edu> writes: > > > Hello, > > I am having a bit of trouble with scatterplot3d(). > > I was able to plot a 3d cloud of points using the following code: > > >my.3dplot<-scatterplot3d(my.coords, pch=19, zlim=c(0,1), scale.y=0.5, > angle=30, box=FALSE) > > where my

[R] Error message when using zero-inflated count regression model in package zicounts

I have data on number of vines per tree for ~550 trees. Over half of the trees did not have any vines and the data is fairly skewed (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to investigate whether plot location (four sites), species (I'm using only the four most common

[R] simulate data from multivariate normal with pre-specified correlation matrix

For example, the correlation matrix is 3x3 and looks like 1 0.75 0 0 0 0.751 0 0 0 0 0 0 0 0 Can I write the code like this? p<- 3 # number of variables per observation N<- 10 # number of samples # define population correlation matrix sigma sigma<-matrix(0,p,p

Re: [R] invert 160000x160000 matrix

I don't think you can define a matrix this large in R, even if you have the memory. Then, of course, inverting it there may be other programs that have limitations. Paul Jiao Yang wrote: > Can R invert a 16x16 matrix with all positive numbers? Thanks a lot! > > ___

Re: [R] Q: how to extract coefisients from one glm and implement them in to an other glm?

Part of the homework you were supposed to do before asking this question: help.search("coefficients") . . . coef(stats) Extract Model Coefficients . . . So, go read ?coef and > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html As your emai

Re: [R] invert 160000x160000 matrix

You would need 200GB to store a since image, so if you have about 1TB of physical memory on your computer, it might be possible. On 8/13/07, Jiao Yang <[EMAIL PROTECTED]> wrote: > Can R invert a 16x16 matrix with all positive numbers? Thanks a lot! > >

Re: [R] 'From' and 'to' arguments in panel.abline

Thanks Deepayan, I actually looked at the upper section but couldn't not spot these arguments. I thought they were optional arguments in '...'. I will try to open my eyes next time ;) Deepayan Sarkar a écrit : > On 8/13/07, Sébastien <[EMAIL PROTECTED]> wrote: > >> Dear R-users, >> >> The

[R] BDS test - results unclear to me

Hello, I would like to use the BDS test from the tseries package, but there is something I don't understand in the results of the test. Let's say, I want the BDS values for an embedding dimension equal to 2 : > bds.test(c, m = 2, eps = seq(0.5 * sd(c), 2 * sd(c), length = 4),trace=FALSE); Her

[R] invert 160000x160000 matrix

Can R invert a 16x16 matrix with all positive numbers? Thanks a lot! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide c

[R] R^2 for multilevel models

Hi there, In multiple regression one way to view R^2 is as (the square of) the correlation between original y's and the estimated y's. Suppose you fit a multilevel model with random intercept for each cluster. Would it be valid to compute an R^2 by using fixed effects plus the group intercept

Re: [R] 'From' and 'to' arguments in panel.abline

On 8/13/07, Sébastien <[EMAIL PROTECTED]> wrote: > Dear R-users, > > The help does not give much details on the use of the arguments 'from' > and 'to' in the panel.abline function. Not surprising, since panel.abline doesn't actually have arguments called 'from' and 'to'. > I have looked in the ar

Re: [R] GML with tweedie: AIC=NA

Dear Catarina, I prefer to leave the AIC value as NA for the tweedie GLM family because it takes extra time to compute and is only occasionally wanted. It's easy to compute the AIC yourself using the dtweedie() function of the tweedie package. Best wishes Gordon At 03:05 AM 14/08/2007, Catari

[R] vertically oriented color key in heatmaps

Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap.2 in gplots does let me add a color key. However, I was thinking of a vertical bar with the color range rather than the style that gplots provides. Is there a

[R] 'From' and 'to' arguments in panel.abline

Dear R-users, The help does not give much details on the use of the arguments 'from' and 'to' in the panel.abline function. I have looked in the archives but did not find how to implement them. My different tries failed miserably. E.g, the following code doesn't seem to work, in a sense that th

Re: [R] Extract part of vector

This should do it: > txt [1] "\nhttp://www.mysite.com/system/empty.asp?P=2&VID=default&SID=421384237289476&S=1&C=18631"; [2] "\nhttp://www.mysite.com/system/empty.asp?P=123&VID=default&SID=421384237289476&S=1&C=18643"; [3] "\nhttp://www.mysite.com/system/empty.asp?P=342&VID=default&SID=42138423

Re: [R] help with scatterplot3d

On 8/13/2007 3:03 PM, Ryan Briscoe Runquist wrote: > Hello, > > I am having a bit of trouble with scatterplot3d(). > > I was able to plot a 3d cloud of points using the following code: > >>my.3dplot<-scatterplot3d(my.coords, pch=19, zlim=c(0,1), scale.y=0.5, > angle=30, box=FALSE) > > where my.

Re: [R] xyplot() with segments() superposed?

On 8/13/07, Yuelin Li <[EMAIL PROTECTED]> wrote: > Thanks for the quick response. The general use is like the following. > Suppose I have another variable, tkmark, which for cohort "1970" is > coded 1.0 at x = c(7, 19) and 0 otherwise. For cohort "1980", tkmark > is coded 1.0 at x = c(2, 11, 12,

Re: [R] rfImpute

I seem to recall that rfImpute() can sometimes come up with NAs at some point in the iterations. Could you please send me a (small) set of data/code that reproduces the problem? Andy From: Eric Turkheimer > > I am having trouble with the rfImpute function in the > randomForest package. > Here

[R] help with scatterplot3d

Hello, I am having a bit of trouble with scatterplot3d(). I was able to plot a 3d cloud of points using the following code: >my.3dplot<-scatterplot3d(my.coords, pch=19, zlim=c(0,1), scale.y=0.5, angle=30, box=FALSE) where my.coords is a data frame that contains x, y, and z coordinates for grid

[R] Problem with fisher.g.test

I am trying to analyse a mouse dataset with 45000 genes and 24 or 48 timpoints to find cycling genes using GeneCycle. However the function fisher.g.test never runs. I am pasting the input/output summary below. I would be grateful if someone could provide any insight. I 've run GeneCycle successful

Re: [R] xyplot() with segments() superposed?

Thanks for the quick response. The general use is like the following. Suppose I have another variable, tkmark, which for cohort "1970" is coded 1.0 at x = c(7, 19) and 0 otherwise. For cohort "1980", tkmark is coded 1.0 at x = c(2, 11, 12, 19) and 0 otherwise. For each "cohort", I want to mark w

[R] rates and rate ratios for survey-weighted data

Hello, I am looking at data on child survival from a survey with a stratified two-stage design. I have been trying out the excellent survey package, with which I have done a descriptive analysis and Cox models. I need to calculate rates (with a child-year denominator) and various rate ratios plus

[R] Q: how to extract coefisients from one glm and implement them in to an other glm?

Dear R ussers, I'm still working with the categorical models, and i can not do cross validation on them because odf their nature. not cv works perfectly on other models so i wonderd if it is possible to extract the beta's from a categorical model, then use their value in a 0/1 glm. Their formu

[R] SEM for categorical data

Hi I am looking for a structural equation modeling package in R which can be used for categorical data. Is anyone aware of the existence of such a package? Would appreciate any help on this. Thank you Upasna -- - Upasna Sharma

Re: [R] Unexpected behavior in PBSmapping package

Thank you, Rowan, for the explanation and another workaround. I think my major confusion stemmed from the idea that the plotted point colors would change only as a result of changing the limits of the plot. I was and still am confused by the disparity between the plot using PBSmapping and the

[R] Extract part of vector

Dear R-users, How do I extract numbers between asp?P= and &VID from my txt vector? I have tried grep function with no luck. txt <- c(" http://www.mysite.com/system/empty.asp?P=2&VID=default&SID=421384237289476&S=1&C=18631";, " http://www.mysite.com/system/empty.asp?P=123&VID=default&SID=421384237

Re: [R] Artifacts in pdf() of image() (w/o comments)

On 8/13/2007 1:33 PM, Michael Kubovy wrote: > Hi Duncan, > > I was trying to learn to remove the artifacts by setting the > parameters of the image so that anti-aliasing wouldn't produce them > (analogous to making sure that the screens of two halftone screen > process images are in register

Re: [R] Artifacts in pdf() of image() (w/o comments)

Hi Duncan, I was trying to learn to remove the artifacts by setting the parameters of the image so that anti-aliasing wouldn't produce them (analogous to making sure that the screens of two halftone screen process images are in register before combining them so as to avoid Moiré patterns).

Re: [R] Unexpected behavior in PBSmapping package

Hi David, Thanks for the message. Essentially, the argument 'col' is treated like a vector which remains independent from (X,Y) and is simply repeated as need for the number of points. If you specify col=c("red","blue","green","yellow") as below, and there are only 2 points, only "red" and "blue" w

Re: [R] Systematically biased count data regression model

Dear all, Thank you for your helpful comments. I have acquired and read Steyerberg (2001). I may try some of the methods from that paper. This did prompt a thorough examination of the data. Sure enough, my worst outlier, where little diversity was observed and the NDVI measurment was very high

Re: [R] xyplot() with segments() superposed?

On 8/11/07, Yuelin Li <[EMAIL PROTECTED]> wrote: > In the hypothetical example below, how do I add two segments() into > the two panels, respectively? Say segments(x0=5, y0=10, x1=5, y1=20) > on the left and segments(x0=15, y0=-10, x1=15, y1=-2) on the right? > Many thanks in advance, > > Yuelin L

Re: [R] Artifacts in pdf() of image() (w/o comments)

On 8/13/2007 11:43 AM, Michael Kubovy wrote: > But is it a bug? Can a program anti-alias text and line drawings and > not bitmaps? Anti-aliasing is the removal of artifacts caused by displaying an image on a low-resolution bitmapped display. Introducing artifacts is a bug. If it wasn't a bug,

[R] feature's contribution into classification

Hi, there: The following question is more of statistics: assume i have 5 features in a classification, and I am wondering which methodology can help me identify which feature "contributes" the most to classify a specific sample? I knew some simple modeling like logistic regression probably can d

Re: [R] Artifacts in pdf() of image() (w/o comments)

But is it a bug? Can a program anti-alias text and line drawings and not bitmaps? On Aug 13, 2007, at 9:30 AM, Duncan Murdoch wrote: > On 8/13/2007 11:07 AM, Michael Kubovy wrote: >> Dear Friends, >> Thanks for your input. >> FYI: Preview doesn't show PDF aliasing in the image I produced if >

Re: [R] Convert factor to numeric vector of labels

This is one of R's rather _endearing_ little idiosyncrasies. I ran into it a while ago. http://finzi.psych.upenn.edu/R/Rhelp02a/archive/98090.html For some reason, possibly historical, the option "stringAsFactors" is set to TRUE. As Prof Ripley says FAQ 7.10 will tell you as.numeric(as.chara

Re: [R] Artifacts in pdf() of image() (w/o comments)

On 8/13/2007 11:07 AM, Michael Kubovy wrote: > Dear Friends, > > Thanks for your input. > > FYI: Preview doesn't show PDF aliasing in the image I produced if I > uncheck the "Anti-alias text and line art" box under the PDF tab in > Preferences. So I'm not yet ready to drop Preview from my too

Re: [R] Artifacts in pdf() of image() (w/o comments)

Dear Friends, Thanks for your input. FYI: Preview doesn't show PDF aliasing in the image I produced if I uncheck the "Anti-alias text and line art" box under the PDF tab in Preferences. So I'm not yet ready to drop Preview from my toolbox. MK On Aug 13, 2007, at 12:02 AM, Mark Wardle wrote:

Re: [R] Odp: Very new - beginners questions

>>> Petr PIKAL <[EMAIL PROTECTED]> 13/08/2007 14:10:40 >>> >> How do I read one row of data so as to load site2 into a variable >>called site2? > >?read.table and other read. commands. Don't forget scan(). But Petr is right, you probably do not need to read one row at a time. >> Once

Re: [R] Very new - beginners questions

Hi Richard, No specific answers for your data questions but for learning R there are any number of resources. There are links to references for books and a large number of on-line materials on the R website. Have a look at the list on the bottom left of the screen for "books" and "other" which l

[R] Problem with axes plotting

Hi, I've 2 little questions: Is possible change the size of the values of x and y axes, when I do plot?? How can I put a range of 0.0001 to 5.5000, although my max value is 4 on 'y' axe log scale (without pattern 1e-0'X')? Thanks. [[alternative HTML version deleted]]

[R] Odp: Very new - beginners questions

Hi [EMAIL PROTECTED] napsal dne 13.08.2007 14:04:50: > Dear all, > > > I have 4 sites and want to determine how different they are from each other. > For this I have decided to use R though it seems a bit daunting to learn. > I have read data in from a CSV the structure is : > >Specie

[R] statdataml question

Hi, I was wondering if Statdataml is currently the preferred way to represent statistical data in XML in R. And also if the Statdataml api provides ways to load the XML as a HTTP GET? If so can you give me an easy example of this. Thanks. Cheers, Bryan Rasmussen

Re: [R] Very new - beginners questions

Hi. You should study "An Introduction to R" manual. It is installed with R in PDF format and is accessible from the menu (Help -> Manuals (in PDF) -> ) There are several links in the R web site. Go to http://www.r-project.org/ and see links under the word "Documentation" in the left frame. There

[R] Robust estimators for ordered logistic regression

Hello, I am trying to estimate an ordered logistic regression in R, and I wish to use robust estimators. Can this be (simply) done? More specifically, can this be done using polr (in MASS) together with sandwich. I am using R 2.5.1 on Mac OS 10.4.10. If not, is there any other way? I can fit a mo

[R] Very new - beginners questions

Dear all, I have 4 sites and want to determine how different they are from each other. For this I have decided to use R though it seems a bit daunting to learn. I have read data in from a CSV the structure is : Species1 Species2 Species3 Site1 4 4 7 Site2 3 1 0 Site3 0 99 6

Re: [R] Values in horizontal versus vertical position on 'y' axe

? par# then scroll down to look at 'las' You probably want par(las=1) HTH, Mike. akki wrote: > > hi, > When I do a graph. the values on y axe are vertical position. How can I > put > the values in horizontal position? > > thanks > > [[alternative HTML version deleted]] > >

Re: [R] Values in horizontal versus vertical position on 'y' axe

On Mon, 2007-08-13 at 13:37 +0200, akki wrote: > hi, > When I do a graph. the values on y axe are vertical position. How can I put > the values in horizontal position? > > thanks If you mean "How do I rotate the tick labels?" then look at ?par and parameter 'las'. E.g. this shows the options avai

[R] Values in horizontal versus vertical position on 'y' axe

hi, When I do a graph. the values on y axe are vertical position. How can I put the values in horizontal position? thanks [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] question regarding is.factor()

See ?class -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O On 13/08/07, Jabez Wilson <[EMAIL PROTECTED]> wrote: > > Dear all, please help with what must be a straightforward question which I > can't answer. > > I add a column of my dataframe as factor of an existing

Re: [R] question regarding is.factor()

typeof() for 'types'. However, "factor" is not a type but a class, so class() is probably what you want. On Mon, 13 Aug 2007, Jabez Wilson wrote: > Dear all, please help with what must be a straightforward question which > I can't answer. But 'An Introduction to R' could. > I add a column o

[R] question regarding is.factor()

Dear all, please help with what must be a straightforward question which I can't answer. I add a column of my dataframe as factor of an existing column e.g. df[,5] <- factor(df[,2]) and can test that it is by is.factor() but if I did not know in advance what "types" the col

Re: [R] How to write to a table column by column?

Assuming that the daily.incomes are the same lengths, then your loop could be: Lst <- list() for (i in 1:count) Lst[[i]] <- list(..) Lst.col <- do.call('cbind', Lst) On 8/12/07, Yuchen Luo <[EMAIL PROTECTED]> wrote: > Dear friends. > Every loop of my program will result in a list that is very

Re: [R] How to store the parameter estimated by nls( ) to a variable?

On Sun, Aug 12, 2007 at 10:50:59AM -0700, Yuchen Luo wrote: > Dear Professor Murdoch. > Thank you so much > > Best Wishes > Yuchen Luo > > On 8/12/07, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > > > > Yuchen Luo wrote: > > > Dear Colleagues. > > > > > > I believe this should be a problem enco

Re: [R] need help to manipulate function and time interval

a) I agreed with your suggestion about the condition "else". L = Level of noise fluctuates during the various moments of the day (i.e L= L+5 between 18:00:00 and 21:59:59; L=L+10 between 22:00:00 and 05:59:59 and L = L else). b) mytab is a data table including Time column, Level column, , T

Re: [R] need help to manipulate function and time interval

KOITA Lassana - STAC/ACE wrote: > Hi, > data are extracted from MS Access with the format: ("%d/%m%Y %H%M%S"); ex: > 16/09/2006 03:38:37 1. the example you gave in your first message is still not reproducible, you gave the following: myfunc <- function(mytab, Time, Level) { vect <- rep(0, le

Re: [R] RServe

yoo wrote: > Yea, I found the shutdown function in the java interface as well.. but is > there a way I can send a shutdown command through linux shell? (something > that I can cron?) Write a minimal java program that sends the shutdown command, then run that from your shell... Barry _

Re: [R] p value statistic for lm object

Arjun Bhandari adia.ae> writes: > I conduct a univariate regression with lm function. I would like to get > the p value for the regression. Is there a method that would enable me to > extract the p value into a variable. # From lm docs (Sorry, Annette, for misusing your data) ctl <- c(4.17,5.5

Re: [R] creating unique and sorted values by combining columns

apply(tmp, 1, function(x) paste(sort(unique(x[x!=0])),collapse="_")) Jacques VESLOT INRA - Biostatistique & Processus Spatiaux Site Agroparc 84914 Avignon Cedex 9, France Tel: +33 (0) 4 32 72 21 58 Fax: +33 (0) 4 32 72 21 84 [EMAIL PROTECTED] a écrit : > > Hi List, > > I am combining column

Re: [R] need help to manipulate function and time interval

Hi, data are extracted from MS Access with the format: ("%d/%m%Y %H%M%S"); ex: 16/09/2006 03:38:37 I still have error messneger Thank you for your help. Lassana KOITA Chargé d'Etudes de Sécurité Aéroportuaire et d'Analyse Statistique / Project Engineer Airport Safety Studies & Statistical an

Re: [R] binomial simulation

Hi, The probability of false detection is: P(T+ | D-)=1-P(T+ | D+)=0.05. and I want to find the joint probability P(T+,D+)=P(T+|D+)*P(D+) Thank you for your reply, Sigalit. On 8/13/07, Moshe Olshansky <[EMAIL PROTECTED]> wrote: > > Hi Sigalit, > > Do you want to find the probability P(T+ = t AND

Re: [R] need help with pdf-plot

Thank you both! The hint with the pty="s" was very useful. I did not know it before. Ciao, Antje Ivar Herfindal schrieb: > Dear Antje > > I cannot see that you have got any replies yet, so I will make and > attempt. However, I am sure other have more formally correct solutions. > > When you c

[R] creating unique and sorted values by combining columns

Hi List, I am combining column values of a dataframe to create a new variable that is the sorted and unqiue combination of the columns (and excluding 0). The following works, but surely there is a more elegant way of doing this? t1<-NULL for(i in 1:nrow(tmp)) { if(i == 1){ sort(c(tmp[i,1],