[R] Solving equations involving banded matrices

Dear friends, I'm looking for a function which solves the system of equations Ax=B where A is a positive definite banded matrix. I know that the command solve can be used to arrive at a solution. But does it work as well with banded matrices? In GAUSS the command bandsolpd achieves this. So

Re: [R] Excel

On Monday 27 August 2007 22:21, David Scott wrote: On Tue, 28 Aug 2007, Robert A LaBudde wrote: If you format the column as Text, you won't have this problem. By leaving the cells as General, you leave it up to Excel to guess at the correct interpretation. Not true actually. I had

Re: [R] validate (package Design): error message subscript out of bounds

Thanks, I use Design version 2.1-1 (and as provided, R 2.5.1 on Windows XP). The redundancies in object names were for my own convience, as part of a larger command file, and the validation of this univariate model was only included to ease comparison with the main multivariate model. I have

[R] pca

Using rcmdr i performed a pca now i would like to build the orrelation matrix starting from the scores given by rcmdr... any function about? moreover, i should transform the pca components values from 0 to 256. tahnks duccio __

[R] R Help

I got the Warning message below when I tried to load Locfit. What is wrong? Regards Ola Asteman -- R version 2.4.0 (2006-10-03) Copyright (C) 2006 The R Foundation for Statistical Computing

[R] a problem with the varimax() fonction (stat package)

Hi,I am puzzled with different results in R, compared to SPSS and Senstools.Net. After running a PCA on the three software (for R, I use the PCA function programmed on the FactoMineR package), I extracted the loadings. In the three cases, the loadings are exactly identical.Then, I applied the

Re: [R] outdated R and package dependencies; was: R Help

Ola Asteman wrote: I got the Warning message below when I tried to load Locfit. What is wrong? Please read the posting guide which suggests to use a sensible subject line. Regards Ola Asteman

[R] Nested functions.

Hi All, I have two variables X, Y. The question is if the value of X is equal to one, then the values in Y have to be reversed other wise it should not perfom any action. I think this should be done using lapply function? Example Y values : 1 2 3 NA X Y (ORIGINAL) Y

[R] Limiting size of pairs plots

Dear R-users, I would like to add a legend at the bottom of pairs plots (it's my first use of this function). With the plot function, I usually add some additional space at the bottom when I define the size of the graphical device (using mar); grid functions then allows me to draw my legend as

Re: [R] Limiting size of pairs plots

From ?pairs The graphical parameter 'oma' will be set by 'pairs.default' unless supplied as an argument. so try pairs(iris[1:4], main = Anderson's Iris Data -- 3 species, pch = 21, bg = c(red, green3, blue)[unclass(iris$Species)], oma = c(8,3,5,3)) On Tue, 28 Aug

Re: [R] R Help

You don't have installed the akima pakage. install.packages(akima, dep=T) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 28/08/07, Ola Asteman [EMAIL PROTECTED] wrote: I got the Warning message below when I tried to load Locfit. What is wrong? Regards Ola

[R] Changing tcl in boxplot

How can I change the tick marks in a boxplot so that they lie on the inside of the x and y axes? In plot I have been setting tcl=0.2 but that doesn't do anything in boxplot. What am I missing? Thanks, Emily __ R-help@stat.math.ethz.ch mailing list

Re: [R] Column naming mystery

I'd be glad to help, but I don't think I understand the problem. Here's what I get: x - as.data.frame(matrix(ncol=3,seq(1,12),dimnames=list(c(),c(hh,total,total.inf x hh total total.inf 1 1 5 9 2 2 610 3 3 711 4 4 812

Re: [R] Excel

At 01:21 AM 8/28/2007, David wrote: On Tue, 28 Aug 2007, Robert A LaBudde wrote: If you format the column as Text, you won't have this problem. By leaving the cells as General, you leave it up to Excel to guess at the correct interpretation. Not true actually. I had converted the column to Text

Re: [R] FW: How to fit an linear model withou intercept

Hi Mark, I don't know wether you recived a sufficient reply or not, so here are my comments to your problem. Supressing the constant term in a regression model will probably lead to a violation of the classical assumptions for this model. From the OLS normal equations (in matrix notation) (1)

Re: [R] validate (package Design): error message subscript out of bounds

On 28 August 2007 at 08:04, Frank E Harrell Jr wrote: | Wentzel-Larsen, Tore wrote: | Thanks, | I use Design version 2.1-1 (and as provided, R 2.5.1 on Windows XP). | | Sorry I missed the latter. | | The redundancies in object names were for my own convience, as part of | a larger command

Re: [R] validate (package Design): error message subscript out of bounds

Wentzel-Larsen, Tore wrote: Thanks, I use Design version 2.1-1 (and as provided, R 2.5.1 on Windows XP). Sorry I missed the latter. The redundancies in object names were for my own convience, as part of a larger command file, and the validation of this univariate model was only included to

Re: [R] Column naming mystery

Hi, thank a lot for your answers! As other people get the correct result but I get this mysterious result with this script even after running it on a freshly started R, it must be a problem with my particular R setup. I'll try updating. Thanks for the help, now I know where I have to search.

Re: [R] Forcing coefficients in lm object

Hi, names(fit) fit$coefficients[[2]] - 100 -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 28/08/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear all, I would like to use predict.lm() with an existing lm object but with new arbitrary coefficients. I modify

Re: [R] R Help

[EMAIL PROTECTED] napsal dne 28.08.2007 13:33:13: You don't have installed the akima pakage. install.packages(akima, dep=T) And wait about two months and update your R version to 2.6.0. Or update now to 2.5.1 Regards Petr -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40

[R] Forcing coefficients in lm object

Dear all, I would like to use predict.lm() with an existing lm object but with new arbitrary coefficients. I modify 'fit$coef' (see example below) by hand but the actual model in 'fit' used for prediction does not seem to be altered (although fit$coef is!). Can anyone please help me do this

Re: [R] Interpreting the eigen value of a population matrix

On 28-Aug-07 14:12:22, Marie Anouk Simard wrote: It would seem (from the headers) that Marie sent her message within a TNEF attachment, which the R-help server has duly stripped off! I would suggest thatshe re-sends her message in

[R] Interpreting the eigen value of a population matrix

__ 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 commented, minimal, self-contained, reproducible code.

[R] quntile(table)?

Hi, I have data in the following form: index count -7 32 19382 22192 7 190 11 201 I'd like to get quantiles from the data. I thought about something like this: index - c(-7, 1, 2, 7, 11) count - c(32, 9382, 2192, 190, 201)

Re: [R] quntile(table)?

You could use: require(quantreg) rq(index ~ 1, weights=count, tau=0:5/5) url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678

Re: [R] oddity with method definition

Hi Dr Lumley, Thanks to you and Dr. Murdoch for your helpful explanations. See below. On Mon, 27 Aug 2007, Thomas Lumley wrote: On Mon, 27 Aug 2007, Faheem Mitha wrote: setClass(foo, representation(x=numeric)) bar - function(object) { return(0) } bar.foo - function(object) {

[R] Experimental Design with R

Dear R-users, I want to know if there is a package that allows to define different experimental designs (factorial, orthogonal, taguchi) and to compare them. I don't found one in the R-web site, but it is possible I missed it! Thank you in advance Sincerely, Marc

Re: [R] oddity with method definition

On Tue, 28 Aug 2007, Faheem Mitha wrote: Warning message: in the method signature for function bar no definition for class: “baz” in: matchSignature(signature, fdef, where) I'm being dense. That just means that the class baz has not been defined, presumably.

[R] logic operation on an array

I want to check whether all the components of a vector (or an array) are 0, and if they are I will skip the later computations. Of course I can create a loop to go through all the components. However is there an R function for this purpose more efficient than looping? Thanks a lot, Gang

[R] Interpreting the eigen value of a population matrix (2nd try)

Thanks for telling me that you could not get my message, I hope this work better... so my question was: I built a population matrix to which I applied the fonction eigen in order to find the main parameters about my population. I know that the first eigen value correspond to lambda or

[R] lm.ridge fit with some dummy variables (w/o intercept)

I have columns which sum to one. They are membership dummies, fractions are allowed - I made an example: x - c( 9.899898,6.9555431,-1.251,0.5200,0.480,0.000,-2.2384737, 16.791361,6.8924369,-3.286,0.78846154,0.2115385,0.000,-0.4720061,

Re: [R] Rmpi and x86

Hi Edna -- I have Rmpi 0.5-3 under R 2.5.1 with LAM 7.1.2 installed on an x86_64 SuSE 10.0. I installed (as a regular user, to my own disc space) LAM and ran through some basic checks (lamboot / lamhalt, checking that I could compile the demo programs) After downloading Rmpi_0.5.3.tar.gz, I

[R] Efficient way to parse string and construct data.frame

Hi all, I have this list of strings [1] 1 ,2 ,3 4 ,5 ,6 Is there an efficient way to convert it to data.frame: V1 V2 V3 1 1 23 2 4 56 Like I can use strsplit to get to a list of split strings.. and then use say a = strsplit(mylist, ,) data.frame(V1 = lapply(a,

Re: [R] Efficient way to parse string and construct data.frame

Hi, do.call(rbind, lapply(strsplit(mylist, ,), as.numeric)) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 28/08/07, yoo [EMAIL PROTECTED] wrote: Hi all, I have this list of strings [1] 1 ,2 ,3 4 ,5 ,6 Is there an efficient way to convert it to

Re: [R] Experimental Design with R

Please use R's search tools. RSiteSearch(experimental design, restr = funct) finds optBlock() in the AlgDesign package as the 10th hit. Whether this package will have what you want is another issue. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL

Re: [R] Efficient way to parse string and construct data.frame

Try this: s - c(1 ,2 ,3, 4 ,5 ,6) read.csv(textConnection(s), header = FALSE) V1 V2 V3 1 1 2 3 2 4 5 6 On 8/28/07, yoo [EMAIL PROTECTED] wrote: Hi all, I have this list of strings [1] 1 ,2 ,3 4 ,5 ,6 Is there an efficient way to convert it to data.frame: V1 V2 V3 1

Re: [R] Forcing coefficients in lm object

It is fit$coefficients, not fit$coef . From the help page: name: A literal character string or a name (possibly backtick quoted). For extraction, this is normally (see under Environments) partially matched to the 'names' of the object. Note the qualifier 'for

[R] attempt at making a polygon class failed

I was reading a presentation of Professor Peng's and typed the presentation code into R but I changed it to make plot.polygon a separate function instread of defining the function in SetMethod itself as he did. Is that the problem with the code below because plot(p) just gives me zero. Thanks.

[R] Factor levels

Dear R-users, I have found this not-so-recent post in the archives - http://tolstoy.newcastle.edu.au/R/devel/00a/0291.html - while I was looking for a particular way to reorder factor levels. The question addressed by the author was to know if the read.table function could be modified to

Re: [R] Rmpi and x86

Edna -- I'll keep this on the list, so that others will learn, and others will correct me when I give bad advice! relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used when making a shared object; recompile with -fPIC This likely means that your lam was not built with the

Re: [R] Experimental Design with R

A full factorial can be generated using expand.grid. Try AlgDesign, BHH2 and conf.design for various fractional and D-optimal design generators; they all work. I haven't tried the experiment package yet, though the synopsis looks interesting. The 'Design' package itself I found disappointing for

Re: [R] Excel

On a related note, there's one other amazingly stupid thing that Excel (2002 SP3) does - it exports to CSV the numbers as you see them displayed, and not as they were entered/imported in the first place. For example, 1.2345678 will be exported to CSV/tab delimited as 1.23 if that column is

[R] data formatting: from rows to columns

Hi All, I have some data I need to write as a file from R to use in a different program. My data comes as a numeric matrix of n rows and 2 colums, I need to transform each row as a two rows 1 col output, and separate the output of each row with a blanck line. Foe instance I need to go from

Re: [R] Factor levels

You can create your own class and pass that to read table. In the example below Fld2 is read in with factor levels C, A, B in that order. library(methods) setClass(my.levels) setAs(character, my.levels, function(from) factor(from, levels = c(C, A, B))) ### test ### Input - Fld1 Fld2 10 A

Re: [R] data formatting: from rows to columns

Hi Federico, Federico Calboli wrote: Hi All, I have some data I need to write as a file from R to use in a different program. My data comes as a numeric matrix of n rows and 2 colums, I need to transform each row as a two rows 1 col output, and separate the output of each row with a

[R] Interpreting the eigen value of a population matrix (2nd try)

Thanks for telling me that you could not get my message, I hope this work better... so my question was: I built a population matrix to which I applied the fonction eigen in order to find the main parameters about my population. I know that the first eigen value correspond to lambda or

[R] Variance explained by cluster analysis

Hello, As suggested in De'ath, 2002. Multivariate regression trees: A new technique for modelling species-environment relationships. Ecology, 83 (4):1105-1117 (for those interested), I am trying to compare the performance of a multivariate regression tree to a cluster analysis. A simple

Re: [R] logic operation on an array

an array is just a vector with attributes. all ( diag(2) == 0 ) [1] FALSE all ( diag(2)*0 == 0 ) [1] TRUE On Tue, 28 Aug 2007, Gang Chen wrote: I want to check whether all the components of a vector (or an array) are 0, and if they are I will skip the later computations. Of course I can

Re: [R] Rmpi and x86

On Tue, 28 Aug 2007, Martin Morgan wrote: Edna -- I'll keep this on the list, so that others will learn, and others will correct me when I give bad advice! relocation R_X86_64_32 against `lam_mpi_comm_world' can not be used when making a shared object; recompile with -fPIC This likely

Re: [R] ordered factors in data.frame

Sorry this has taken so long to get back to you, I have been out of the office a lot recently. The documentation for read.table suggests that since an as.ordered function exists, that you could just use ordered as a column class, but I don't know how well that works in practice. In general I

[R] RUnit and tracing errors

Hi, What's a good way to quickly determine the location of a failure in my RUnit test suite? For instance, if I do the following: == library(RUnit) runTestSuite( defineTestSuite(MyTests, src/r, testFuncRegexp=metrics) ) Executing test function

Re: [R] Forcing coefficients in lm object

The important element in the fit object is named coefficients not coef. Sometimes the partial matching can cause confusion when it tries to help. In your case it creates a copy of the coefficients, changes the 2nd value, then creates a new component to fit called coef with these values (not

Re: [R] quntile(table)?

See the wtd.quantile function in the Hmisc package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Seung Jun Sent: Tuesday,

[R] The l1ce function in lasso2: The bound and absolute.t parameters.

Dear all, I am quite puzzled about the bound and absolute.t arguments to the l1ce function in the lasso2 package. (The l1ce function estimates the regression parameter b in a regression model y=Xb+e subject to the constraint that |b|t for some value t). The doc says: boundnumeric,

Re: [R] Excel

On 28/08/2007, at 7:16 PM, J Dougherty wrote: snip PS, I quit using Excel for most important work after it returned a negative variance on some data I was collecting descriptive statistics on. Those of you who have not seen it should have a look at Jonathan Cryer's commentary on

[R] help with aggregate(): tables of means for terms in an mlm

I'm trying to extend some work in the car and heplots packages that requires getting a table of multivariate means for one (or later, more) terms in an mlm object. I can do this for concrete examples, using aggregate(), but can't figure out how to generalize it. I want to return a result that

Re: [R] Factor levels

Thanks Gabor, I have two questions: 1- Is there any difference between your code and the following one, with regards to Fld2 ? ### test ### Input - Fld1 Fld2 10 A 20 B 30 C 40 A DF - read.table(textConnection(Input), header = TRUE) DF$Fld2-factor(DF$Fld2,levels= c(C, A, B))) 2- do you see

Re: [R] Factor levels

Its not clear from your description what you want. Could you be a bit more specific including an example. On 8/28/07, Sébastien [EMAIL PROTECTED] wrote: Thanks Gabor, I have two questions: 1- Is there any difference between your code and the following one, with regards to Fld2 ? ### test ###

[R] data manipulation help

Dear All: I have a dataset like A=c(0,12,34,5,6,0,4,5,6,0,12,3,4,8,7,0,4,3,5,0,...),I want to add a column to this dataset, it must be in B=c(1,1,1,1,1,2,2,2,2,3,3,3,3,3,3,4,4,4,4,5,..), How can I create B based on the sequence of A. Appreciate. Zheng

Re: [R] Factor levels

Ok, I cannot send to you one of my dataset since they are confidential. But I can produce a dummy mini dataset to illustrate my question. Let's say I have a csv file with 3 columns and 20 rows which content is reproduced by the following line. mydata-data.frame(a=1:20,

Re: [R] data manipulation help

below works on you example but someone will have something more elegant. zeroindices-which(a == 0) rep(1:length(zeroindices),c(diff(zeroindices),(length(a)-zeroindices[len gth(zeroindices)]+1))) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zheng

Re: [R] data manipulation help

On Tue, 28 Aug 2007, Zheng Lu wrote: Dear All: I have a dataset like A=c(0,12,34,5,6,0,4,5,6,0,12,3,4,8,7,0,4,3,5,0,...),I want to add a column to this dataset, it must be in B=c(1,1,1,1,1,2,2,2,2,3,3,3,3,3,3,4,4,4,4,5,..), How can I create B based on the sequence of A. Appreciate.

Re: [R] Factor levels

Its the same principle. Just change the function to be suitable. This one arranges the levels according to the input: library(methods) setClass(my.factor) setAs(character, my.factor, function(from) factor(from, levels = unique(from))) Input - a b c 1 1 176 w 2 2 141 k 3 3 172 r 4 4

Re: [R] Factor levels

Sebastain Does the following work for you? seb - read.table(file='clipboard', header=T) seb$c [1] w k r s k p l u z s j j x r d j x w q f Levels: d f j k l p q r s u w x z seb$c - factor(seb$c, levels=unique(seb$c)) seb$c [1] w k r s k p l u z s j j x r d j x w q f Levels: w k r s p l u z j x

[R] Nodes edges with similarity matrix

Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes

Re: [R] Factor levels

Peter, Gabor: thanks to both of you. This 'unique' function is what I was looking for ! Peter Alspach a écrit : Sebastain Does the following work for you? seb - read.table(file='clipboard', header=T) seb$c [1] w k r s k p l u z s j j x r d j x w q f Levels: d f j k l p q r s u w x z

[R] How to find the likelihood function?

Hi, I am writing a BRugs code and I need to specify the likelihood for the gamma distribution and I am specifying it as the pdf: (pow(b1,a1)/(exp(loggam(a1)))*(exp(-b1*lambda[i]))*pow(lambda[i],(a1-1))) But it is not accepting it although I know that I could use the pdf in R to estimate the

[R] alternate methods to perform a calculation

Consider a data frame (x) with 2 variables, x1 and x2, having equal values. It looks like: x1 x2 11 22 33 Now, consider a second data frame (xk): xk1 xk2 0.50.5 1.00.5 1.50.5 2.00.5 0.51 1.01 1.51 2.01 0.51.5 1.01.5 1.51.5 2.01.5

[R] how to calculate mean into a list

Dear Listers: I have this task and suppose a0 is a list of 10 data.frames, I want to calculate like this (a0[[1]]+a0[[2]]+..+a[[10]])/10 Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] Nodes edges with similarity matrix

Paul, i have no idea what functionality you need from graph, but if the igraph package can do what you want then it can easily convert this to a graph for you, basically it is just threshold - 0.5 g - graph.adjacency(simthreshoold) or you can create a weighted graph: g - graph.adjacency(sim,

Re: [R] data formatting: from rows to columns

Here is a way using sprintf: x - read.table(textConnection( V2 V3 27 2032567 19 28 2035482 19 126 2472826 19 132 2473320 19 136 2035480 135 145 2062458 135 148 2074927 135 151 2102395 142 156 2027252 142 158 2473082 142)) # output the data cat(sprintf(%d\n%d\n\n, x$V2, x$V3),

[R] data formatting: from rows to columns

At 09:11 29/08/07 Jim Holtman wrote Here is a way using sprintf: x - read.table(textConnection( V2 V3 27 2032567 19 28 2035482 19 126 2472826 19 132 2473320 19 136 2035480 135 145 2062458 135 148 2074927 135 151 2102395 142 156 2027252 142 158 2473082 142)) # output the data

Re: [R] alternate methods to perform a calculation

I think you can use 'outer' outer(b$xk1, a$x1, function(y,z)abs(z-y)) outer(b$xk2, a$x2, function(y,z)abs(z-y)) On 8/28/07, dxc13 [EMAIL PROTECTED] wrote: Consider a data frame (x) with 2 variables, x1 and x2, having equal values. It looks like: x1 x2 11 22 33 Now,

[R] Recoding multiple columns consistently

Hi, I have a dataframe that contains pedigree information; that is individual, sire and dam identities as separate columns. It also has date of birth. These identifiers are not numeric, or not sequential. Obviously, an identifier can appear in one or two columns, depending on whether it was a

Re: [R] how to calculate mean into a list

try: colMeans(do.call('rbind', lapply(a0, mean))) On 8/28/07, Weiwei Shi [EMAIL PROTECTED] wrote: Dear Listers: I have this task and suppose a0 is a list of 10 data.frames, I want to calculate like this (a0[[1]]+a0[[2]]+..+a[[10]])/10 Thanks. -- Weiwei Shi, Ph.D Research Scientist

[R] extracting dataset with average imputed values from aregImpute()

extracting dataset with average imputed values from aregImpute() Dear all: after many trials, i am still quite lost on how to exact a dataset with average imputed values after running aregImpute() take the eg in the aregImpute(Hmisc) documentation(-- which also appeared in our R-archive

Re: [R] subscript out of bounds Error in predict.naivebayes

On 8/22/07, Polly He [EMAIL PROTECTED] wrote: I'm trying to fit a naive Bayes model and predict on a new data set using the functions naivebayes and predict (package = e1071). R version 2.5.1 on a Linux machine My data set looks like this. class is the response and k1 - k3 are the

Re: [R] Nodes edges with similarity matrix

Hi Paul, H. Paul Benton [EMAIL PROTECTED] writes: I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf .

Re: [R] Nodes edges with similarity matrix

Along with the example I gave using graphAM, you might also want to look at the help page for the distGraph class which may be more directly what you want: library(graph) class ? distGraph __ R-help@stat.math.ethz.ch mailing list

Re: [R] Nodes edges with similarity matrix

Try this: # test data mat - structure(c(1, 0.325141612, 0.002109751, 0.250153137, 0.0223676, 1, 0.342654, 0.1987485, 0.9723831, 0.9644216, 1, 0.7391222, 0.394331, 0.5460461, 0.7080224, 1), .Dim = c(4L, 4L), .Dimnames = list( c(a, b, c, d), c(a, b, c, d))) library(sna) # draw edges according