[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

[R] rational or float?

Hi All, I am using the function fractions() and cognates from MASS. I would like to be able to tell if some calculations I am doing on some rationals are transformed into floats and then retransformed into rationals. For instance I suspect that as.fractions(1/8) + as.fractions(1/4) does

[R] EM unsupervised clustering

Hi All, I have a n x m matrix. The n rows are individuals, the m columns are variables. The matrix is in itself a collection of 1s (if a variable is observed for an individual), and 0s (is there is no observation). Something like: [,1] [,2] [,3] [,4] [,5] [,6] [1,]1011

Re: [R] EM unsupervised clustering

Dimitris Rizopoulos wrote: you could also have a look at function lca() from package `e1071' that performs a latent class analysis, e.g., fit1 - lca(data, 2) I tried but I got: lca(data, 2) Error in matrix(0, 2^nvar, nvar) : matrix: invalid 'nrow' value (too large or NA) In addition:

[R] fisher information matrix

Hi All, a colleague wants to calculate the Fisher information matrix for a model he wrote (not in R). He can easily get the neg-log-likelihood and the best fit parameters at the minimum. He can also get negLLs for other parameter values too. Given these data, is there a way in R to calculate

[R] fractional calculations

Hi All, is there a function in R that allows me to work with fractions without transforming them to floats (or whatever) in between? Something that would calculate something like: (1/2 + 1/8) * 1/2 = 5/16 without ever transforming to 0.5 and 0.125? Best, Federico -- Federico C. F. Calboli

Re: [R] fractional calculations

Henrique Dallazuanna wrote: require(MASS) ?as.fractions as.fractions(1/2+1/8) I thought that as.fractions did transform the fractions *first* into floats and *then* found the rational approssimation (a passage I'd rather avoid): fractionspackage:MASSR

[R] working with fractions

Hi All, I am writing a fucntion where I would like to use fractions for all the (numerous) passages. Is there a way of creating an environment *within a fucntion* so that all the numbers/calculations are fractions? Best, Fede -- Federico C. F. Calboli Department of Epidemiology and Public

Re: [R] working with fractions

Muhammad Subianto wrote: library(MASS) as.fractions(c(0, 0.15, 0.827, .06, 0.266)) [1] 0 3/20 62/75 1/15 4/15 Seems to make things a bit too slow, even though I get a good increase in precision. Fede -- Federico C. F. Calboli Department of Epidemiology and Public

[R] non permanent change of vector values

Hi All, I have the following problem: I have a vector x = rep(0,15) x[1:2] = 1 x [1] 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 I need to be able to call that vector 'x' so that if condition 'A' is true, only the first value is kept 'as is' and all the others are put to 0 if(A == T) function(x) with x

[R] ESS function highlighting

Hi, is there a way of telling Emacs + ESS to show words that are already a function in R (such as 'length') is a different colour/font? Best, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel

[R] plotting symbol

Hi All, can I have a plot where the symbol for the dots is smaller than pch =20 but bigger than pch = '.'? Best, Fede -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44

Re: [R] memory management uestion [Broadcast]

Liaw, Andy wrote: I don't see why making copies of the columns you need inside the loop is better memory management. If the data are in a matrix, accessing elements is quite fast. If you're worrying about speed of that, do what Charles suggest: work with the transpose so that you are

Re: [R] memory management uestion [Broadcast]

Charles C. Berry wrote: This is a bit different than your original post (where it appeared that you were manipulating one row of a matrix at a time), but the issue is the same. As suggested in my earlier email this looks like a caching issue, and this is not peculiar to R. Viz.

[R] memory management uestion

Hi All, I would like to ask the following. I have an array of data in an objetct, let's say X. I need to use a for loop on the elements of one or more columns of X and I am having a debate with a colleague about the best memory management. I believe that if I do: col1 = X[,1] col2 = X[,2]

Re: [R] memory management uestion

Charles C. Berry wrote: Whoa! You are accessing one ROW at a time. Either way this will tangle up your cache if you have many rows and columns in your orignal data. You might do better to do Y - t( X ) ### use '-' ! for (i in whatever ){ do something using Y[ , i ] } My

Re: [R] spss file import

Ndoye Souleymane wrote: Hi, Let me suggest you to save your spss file in txt and use the read.table function to load your file in R. That is what I use to do. The problem here is that the files are old data that were made with an ancient version of spss and cannot be changed to txt (or

[R] spss file import

Hi All, does anyone ever import old SPSS files in a sl3 format? read.spss('file.sl3') does not seem to work... it's not recognised as a supported SPSS format at all. Best, Fede -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk

[R] memory management

Hi All, just a quick (?) question while I wait my code runs... I'm comparing the identity of the lines of a dataframe, doing all possible pairwise comparisons. In doing so I use identical(), but that's by the way. I'm doing a (not so) quick and dirty check, and subsetting the data as

[R] pairs matchning

Hi All, I have two numerical matrices of 2 columns and many rows. The two coulumns of matrix (1) form a number of 'pairs' of numbers, e.g: [,1] [,2] [1,]10 [2,]34 [3,]34 [4,]58 [5,]10 [6,]10 [7,]67 Matrix (2) contains the *unique*

[R] putting stuff into bins...

Hi All, I have a vector of data, a vector of bin breakpoints and I want to put my data in the bins and then extract fanciful informations like the mean value of each bin. I know I can write my own function, but I would have thought that R should have somewhere a function that took as

[R] from character to numeric over multiple columns

Hi All, I have a data frame of three columns, all of which names. The names in the three cols overlap up to a point, so I might have *Harry* in all three columns, *Tom* in cols 1 and 3 and *Bob* in col 3 only. harry paulbob anita harry tom frank jackharry tom peteben

Re: [R] from character to numeric over multiple columns

Prof Brian Ripley wrote: Are the columns factors or character? I'll try to write code that copes with both: nm - unique(c(as.character(col1), as.character(col2), as.character(col3))) DF[] - lapply(DF, function(x) match(x, nm)) Cheers, it worked. Federico -- Federico C. F. Calboli

[R] rearranging data frame rows

Hi All, I have two data frames. The first contains data about a number of individuals, coded in the first column with a name, in an order I find convenient. The second contains different data about the same indivduals, in a different order. Both data frame have the individual names in the

[R] MLE maximum number of parameters

Hi All, I would like to know, is there a *ballpark* figure for how many parameters the minimisation routines can cope with? I'm asking because I was asked if I knew. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus

[R] diagonal matrix: rows rearrangement

Hi All, I have a non-square matrix of 0s/1s. The rows are individuals, and the colums factors. The code is 1 if a factor is present, 0 if not. I would like to rearrange the order of the rows to find if there are any diagonal blocks. Is there a fucntion that would do that already in R? Cheers,

[R] smoothing plot(x, type ='l')

Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College,

Re: [R] smoothing plot(x, type ='l')

Dimitris Rizopoulos wrote: probably you want to use the `lend' argument of ?par(); I hope it helps. Does not seem to work in my case. F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594

Re: [R] smoothing plot(x, type ='l')

Prof Brian Ripley wrote: It I understand you aright, that is done by par(lend) but the default is round. So maybe your graphics device (unstated) on your OS (unstated) does not support this. graphics device = X11 (xserver-xorg) OS = Debian GNU/Linux, Kernel 2.4.27-2-686-smp We need

[R] writing 100 files

Hi All, I need to write as text files 1000 ish variation of the same data frame, once I permute a row. I would like to use the function write.table() to write the files, and use a loop to do it: for (i in 1:1000){ bb8[2,] = sample(bb8[2,]) write.table(bb8, quote = F, sep = '\t', row.names =

[R] data manipulation docs

, so I get back close to square one annoyingly often. Cheers, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t

[R] forcing apply() to return data frame

Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep =) Unfortuantely apply puts it's results into a matrix object

[R] speeding up a recursive function

Hi All, is there any general advice about speeding up recursive functions (not mentioning 'don't use them')? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20

[R] as.matrix and one row

need as.matrix to behave in a consisten fashions, so I get as.matrix(x, whatever) [,1] [,2] x12 and as.matrix(rbind(x,y), whatever) [,1] [,2] x12 y34 I tried byrow =T, does not make a thing. Regards, Federico Calboli -- Federico C. F. Calboli Department

Re: [R] listing nodes in paths

Hi All, I found a solution for my question: I have the following adjacency matrix for a directed graph: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,]00000000 [2,]00000000 [3,]10000000 [4,]

[R] listing nodes in paths

All in all I have 3 paths (not all of the same length) between (8) and (1). Is there already a function in R (whatever the library) that will list the nodes touched in all those three paths (i.e. 8 - 6 - 1; 8 - 7 - 4 - 3 - 1; 8 - 7 - 5 - 3 - 1)? Regards, Federico Calboli -- Federico C. F

[R] finding warning point in function

Hi everyone, I would like to find out when and where exactly I get the following warning in a piece of code I've written: Error in [-(`*tmp*`, iseq, value = numeric(0)) : nothing to replace with The code is a for () loop performing a somewhat trivial calculation, modulated by a number

[R] 'less' for R?

Hi All, is there an equivalent of the Unix command 'less' (or 'more'), so I can look at what's inside a data.frame or a matrix without having it printed out on console? I am using R on Debian Linux and Mac OS 10.4.5 Cheers, F -- Federico C. F. Calboli Department of Epidemiology and Public

[R] subsetting a list of matrices

that is has a subset each matrix in the list subsetting so I get the 2nd and 3rd row of each (and all columns). How could I do that (apart from looping)? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place

Re: [R] logical condition in vector operation

On Thu, 2006-02-09 at 09:22 +0100, Christoph Buser wrote: Dear Frederico From your example it is not clear to me what you like to obtain: Please have a look on the slightly changed example here (I changed two values to show a potentially undesired side effect of your coding. test -

[R] logical condition in vector operation

HI All, I have a data frame such as: test x y p d [1,] 1 0 10 21 0 [2,] 2 3 11 12 0 [3,] 3 4 12 23 0 [4,] 3 5 13 24 0 and I want to perfor some operations on the first two coulums, conditional on the uneqaulity values on the 3rd and 4th columns. For instance: j = 3 test[test[,1] ==

[R] natural selection coefficient S

, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com

[R] replacing a factor value in a data frame

Hi All, I have the following problem, that's driving me mad. I have a dataframe of factors, from a genetic scan of SNPs. I DO have NAs in the dataframe, which would look like: V4 V5 V6 V7 V8 V9 V10 1 TT GG TT AC AG AG TT 2 AT CC TT AA AA AA TT 3 AT CC TT AC AA NA TT 4 TT

[R] partial rank correlation coefficient

Hi All, a colleague asked me if R has a function producing a Partial Rank Correlation Coefficient, sensu Blower and Dowlatabadi 1994 [1]. I personally would not have a clue, and I could not find something like that on the search page... although I would not be surprised if it's there under a

[R] indexing a vector starting from 0

. Would this be at all possible? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com

Re: [R] vectorising ifelse()

] . That's exactly my situation, and is exactly what I want to do. After taking out the typo (and bug) drow[i]0 the code seems to work fast enough... I'll tinker a bit with it, but it could be good enough as it is. Cheers, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology

[R] vectorising ifelse()

Hi All, is there any chance of vectorising the two ifelse() statements in the following code: for(i in gp){ new[i,1] = ifelse(srow[i]0, new[srow[i],zippo[i]], sample(1:100, 1, prob =Y1, rep = T)) new[i,2] = ifelse(drow[i]0, new[drow[i]0,zappo[i]], sample(1:100, 1, prob =Y1, rep = T)) }

[R] loop over large dataset

In my absentmindedness I'd forgotten to CC this to the list... and BTW, using gc() in the loop increases the runtime... My suggestion is that you try to vectorize the computation as much as you can. From what you've shown, `new' and `ped' need to have the same number of rows, right?

Re: [R] loop over large dataset

On 4 Jul 2005, at 12:41, Uwe Ligges wrote: Federico Calboli wrote: In my absentmindedness I'd forgotten to CC this to the list... and BTW, using gc() in the loop increases the runtime... If the data size increases, you cannot expect linear run time behaviour, e.g. because gc

Re: [R] loop over large dataset

On 4 Jul 2005, at 15:15, Peter Dalgaard wrote: Your original code got lost in the threading, but that order of magnitude suggests that you have N^2/2 behaviour somewhere. The typical culprit is code like x - numeric(0) for (i in 1:N){ newx - x - c(x, newx) } in which the

[R] loop over large dataset

Hi All, I'd like to ask for a few clarifications. I am doing some calculations over some biggish datasets. One has ~ 23000 rows, and 6 columns, the other has ~62 rows and 6 columns. I am using these datasets to perform a simulation of of haplotype coalescence over a pedigree (the datestes

[R] R demos

a gross figure of the number of functions in R considering the base install and all the libraries available? Apart from graphics and lattice, are there any more packages producing eye catching graphics (possibly with a survival analysis/epidemiological bend)? Cheers, Federico Calboli -- Federico C

[R] vectorisation suggestion

= made up of a number of repetitions of all the elements of vector1 vector3 = a vector of NAs that is meant to get the result of the counting My problem is that vector1 is about 6 terms, and vector2 is 62... can anyone suggest a faster code than the one I wrote? Cheers, Federico

Re: [R] vectorisation suggestion

On 20 Jun 2005, at 21:24, Erin Hodgess wrote: Hello, Federico! I'm a bit confused about your question, please: What sorts of things are in Vector1, please? numbers (as in numeric) that code individuals Why are you counting NAs in Vector3, please? I am counting how many times the code

Re: [R] R unable to run on Mac OS 10.4 Tiger

On Tue, 2005-05-24 at 18:05 +0200, Guillaume Chapron wrote: Hello, I'm running a PB G4 with Mac OS 10.4.1. I have downloaded the latest version R-2.1.0a.dmg. It appears that R does not work. It launches itself, but the window never gets ready, there is written Loading R... and a small

[R] parsing speed

above or should I actually write the statements of F1 to make the parsing faster? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193

Re: [R] [R-pkgs] Biodem 0.1/orphaning of MAlmig

of any difference in the tarball built by R 2.0.1 and 2.1.0). Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t

[R] Rd.sty problems.

for Debian from the latest .deb files for Sarge on x86 arch. Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t

Re: [R] How to create a vector with one, two, three, ...?

On Fri, 2005-04-15 at 14:30 -0400, Frank Duan wrote: Hi R people, I met a naive prolem. Could anyone give me a hint how to create such a vector with entries: one, two, three, ...? rvect - c(one, two, three) rvect [1] one two three Is it what you want? F -- Federico C. F. Calboli

[R] logistic regression weights problem

... what exacly is glm doing with the weight vector? In any case, how would I go about weighting my individuals in a logistic regression? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2

Re: [R] logistic regression weights problem

: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) ## Why such inconsistency? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place

[R] R as programming language: references?

or other reference apart from the green book and the VR S-programming? Cheers, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t

Re: [R] R as programming language: references?

On Tue, 2005-04-12 at 17:45 +0800, Feng Chen wrote: Maybe you can try this: http://cran.r-project.org/doc/manuals/fullrefman.pdf I was thinking of something that would not limit itself to defining all possible functions and that I do not have already on my HD... F -- Federico C. F. Calboli

Re: [R] R: function code

On Mon, 2005-04-11 at 12:52 +0200, Clark Allan wrote: HI sorry to be a nuisance to all!!! how can i see the code of a particular function? e.g. nnet just as an example for some function just type the function name and you get the code: ls function (name, pos = -1, envir =

RE: [R] Help with three-way anova

On Wed, 2005-04-06 at 09:11 +0100, michael watson (IAH-C) wrote: OK, so I tried using lm() instead of aov() and they give similar results: My.aov - aov(IL.4 ~ Infected + Vaccinated + Lesions, data) My.lm - lm(IL.4 ~ Infected + Vaccinated + Lesions, data) Incidentally, if you want

Re: [R] how to estimate Type I, Type III SS

On Wed, 2005-04-06 at 21:40 +0900, Kum-Hoe Hwang wrote: Howdy, R gurus I 'd like to know hwo to calculate or estimate SS of Type I and Type III in ANOVA or other anaysis in R. Thanks, If memory seves me well, try Anova in the car package F -- Federico C. F. Calboli Department of

[R] cat bailing out in a for loop

of what's in xxx$p.value, even if HWE.exact failed to calculte it. Dump anything in there! Is there any way of forcing the loop to carry on? Cheers, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2

Re: [R] Help with three-way anova

On Tue, 2005-04-05 at 15:51 +0100, michael watson (IAH-C) wrote: So, what I want to know is: 1) Given my unbalanced experimental design, is it valid to use aov? I'd say no. Use lm() instead, save your analysis in an object and then possibly use drop1() to check the analysis 2) Have I used

Re: [R] emacs + R?

On Mon, 2005-04-04 at 10:11 +0200, Giorgio Corani wrote: Dear All, As far I as I have understood reading both your past posting and the documentation, in order to have the command-line completion facility, I have to run R within emacs. However, as I try to start R within emacs as

Re: [R] Error in colMeans ... what's wrong with my data?

On Fri, 2005-04-01 at 20:27 +0200, Hartmut Weinrebe wrote: Having searched and searched I still haven't found what's the problem with my data (I've attached the relevant file). Every time I tried to use the CANCOR-Function I got error messages. So I turned to check my two sets of variables

Re: [R] Multi-plot figures with different numbers of plots in different rows

On Sat, 2005-03-26 at 17:44 +, Hess, Stephane wrote: Dear all, I have 5 plots that I would like to include in a single figure, spread over two rows. If I use mfrow=c(2,3), and produce my plots one after the other, I will end up with three plots in the first row, and 2 in the second

Re: [R] nested random effects

On Wed, 2005-03-23 at 11:58 -0500, Shaw, Philip (NIH/NIMH) wrote: Hi I am struggling with nested random effects and hope someone can help. I have individuals (ID) who are nested within families (FAM). I want to model an outcome variable, and take account of the intercorrelation of

RE: [R] nested random effects

On Wed, 2005-03-23 at 10:04 -0800, Berton Gunter wrote: An interaction random effect/fixed effect is noted as random ~1|random/fixed in your case random =~1|ID/FAM (but I don't uderstand why indiviuals withing families are fixed and and families are random, but there you go).

[R] removing message: [Previously saved workspace restored]

, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com

RE: [R] removing message: [Previously saved workspace restored]

On Tue, 2005-03-08 at 15:57 -0500, Wiener, Matthew wrote: Remove the (now empty, because you deleted all objects) file .RData from the directory. Hope this helps, Thanks, it did fix the problem. Cheers, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public

Re: [R] The hidden costs of GPL software?

obtained this way? I don't. So I'd argue that the lack of a GUI is a good thing, because it forces the users to think a bit more about what they want to do, and gives more control on what is going on. Best, Federico Calboli -- Federico C. F. Calboli Dipartimento di Biologia Evoluzionistica

[R] phylogenetic trees calculation

that will calculate the a phylogenetic tree from such data? I installed ape, but, despite reading the docs, I cannot find a function that would calculate a tree from data like mine (my sight may be getting worse though). Any suggestion is welcome. Regards, Federico Calboli -- Federico C. F

[R] how to upload [forwarded]

[ This was posted to the R-packages list (which I moderate), but definitely doesn't belong there. Martin Maechler ] --- start of forwarded message --- From: Federico Calboli [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: how to upload Date: 15 Jul 2004 18:30:26 +0100 Dear All, I

[R] plotting a table together with graphs

a nice table will come later). I know it is possible to print tables through LaTeX and the Design/Hmisc libraries, although I would not have a clue about printing it together with graphs, but I'd like something quicker if at all possible. Regards, Federico Calboli

Re: [R] Sum of Squares in a lme model

On Sat, 2004-05-22 at 03:58, Deepayan Sarkar wrote: Exactly what do you wish to square and sum ? If it's the 'errors' (which in this context is ambiguous), extract them (see ?residuals.lme), square them and sum them. But what are you planning to do with this after you get it ? Make a oh

Re: [R] Sum of Squares in a lme model

not ranting too much. Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 209 4286 f.calboli at ucl.ac.uk fcalboli at alma.unibo.it

[R] Sum of Squares in a lme model

to fit a second (and wrong in a way) model for something so trivial. I know that the issue has been dealt with before, but I could not find a clear cut answer searching through the archives. Regards Federico Calboli -- = Federico C. F. Calboli Dipartimento di

[R] RE: 1-way anova, nested model

From what I gather you have 2 treatments 6 samples nested in treatment 12 replicates in sample. I do not know what your dependent veriable is, but I would: code the two treatments as T1 and T2 code the 6 samples as a, b, c, d, e, f so the first three samples belonging to T1 are not confused

[R] Re: Debian R

I have R 1.9.0 on sid, apt-getting stuff from cran... I too noticed that cran has R 1.8.1 for Debian, but as I got R 1.9.0 I just ignored the differences in labelling. BTW, it is R that tells me it is R 1.9.0 when I fire it up. And has the stats library that I did not remember in R 1.8.*

Re: [R] Mixed-effects model for nested design data

, according to your coding of the data, this stem is not always necessary. HTH Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 209 4286 f.calboli at ucl.ac.uk fcalboli

[R] anova(my.lme.model, type=marginal) in Pinheiro and Bates

)? Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 209 4286 f.calboli at ucl.ac.uk __ [EMAIL PROTECTED] mailing list

[R] italian keyboard and ~ symbol

the desired symbol (any combination of keys seems to fail...) Can anyone advice how to produce the ~ symbol, short of a copy/paste from MS Word? Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel

RE: [R] italian keyboard and ~ symbol

On Tue, 2004-03-30 at 11:48, Henrik Bengtsson wrote: Press-Alt + Num1 + Num2 + Num6 + Release-Alt where Num1, Num2 Num6 are 1, 2 6 on the *numeric keyboard* (not the ones above the letter keys) will produce ASCII character 126 (~, tilde) on my WinXP Pro in both Rterm and Rgui for R v1.8.1.

Re: [R] italian keyboard and ~ symbol

On Tue, 2004-03-30 at 12:38, Erich Neuwirth wrote: Before using the sequence Press-Alt + Num1 + Num2 + Num6 + Release-Alt one has to make sure that the numeric keyboard is in NumLock mode, not in cursor mode. If it is in cursor mode, this trick will not work (at least it does not on my

[R] colour scheme in: plot(survfit.model)

is that the colour used for line1 at temperature 18C is not the same for line1 at temperature 28C, which I find extremely confusing. How can I specify to keep the same colour for the same line across the plot? regards, Federico Calboli -- = Federico C. F. Calboli

Re: [R] R-business case

am doing is more of an advantage, IMHO, rather than a shortcoming... from a usability standpoint I never felt I had any problem I could not deal with after some thinking, or asking the list. Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento

Re: [R] Multidimensional scaling and distance matrices

that doing things with R is going to be a better (= more sensible) option. Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 208 f.calboli at ucl.ac.uk

[R] Multidimensional scaling and distance matrices

can ONLY be performed on a distance matrix, and I can therefore reasonably expect that some form of transformation to a distance matrix has been performed by Statistica prior to the MDS. It would at least be a first step to understand what exactly Statistica did with the data. Regards, Federico

[R] plot(my.procrustes.model) from library {vegan}

on the standard plot function, but I was quite unsucessful. Can anyone give advice? I am happy to give a toy example if needed. Regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39

Re: [R] plot(my.procrustes.model) from library {vegan}

. The following should do what you asked for: plot(mod.pro$X, asp=1, pch=1) points(mod.pro$Yrot, pch=2) segments(mod.pro$X[,1], mod.pro$X[,2], mod.pro$Yrot[,1], mod.pro$Yrot[,2]) The above solves my problem. Thanks for your help. Best regards, Federico Calboli

[R] left eigenvector

Dear All, how do I compute the left eigenvector of a matrix? I gather that eigen computes the right eigenvectors... Regards, Federico Calboli -- = Federico C. F. Calboli PLEASE NOTE NEW ADDRESS Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel

[R] logical comparison of two matrices

could be happy just comparing the two diagonals. regards, Federico Calboli -- = Federico C. F. Calboli PLEASE NOTE NEW ADDRESS Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 208 f.calboli at ucl.ac.uk

Re: [R] matrix exponential: M^0

in other problems? Again, many thanks to all for the invaluable help. Regards, Federico Calboli -- = Federico C. F. Calboli PLEASE NOTE NEW ADDRESS Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 208

[R] matrix exponential: M^0

11 [2,]111 [3,]111 I would have expected the identity matrix here. I find the same result with every other square matrix I used. BTW, I am using R 1.8.1 on Linux Mandrake 9.1 Cheers, Federico Calboli -- = Federico C. F. Calboli

[R] malecot migration matrix

, Federico Calboli -- = Federico C. F. Calboli PLEASE NOTE NEW ADDRESS Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 208 f.calboli at ucl.ac.uk __ [EMAIL PROTECTED

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