[R] xmlToDataFrame very slow

2013-07-30 Thread Stavros Macrakis
I have a modest-size XML file (52MB) in a format suited to xmlToDataFrame (package XML). I have successfully read it into R by splitting the file 10 ways then running xmlToDataFrame on each part, then rbind.fill (package plyr) on the result. This takes about 530 s total, and results in a

Re: [R] execute array of functions

2012-02-14 Thread Stavros Macrakis
That won't work because R has special rules for evaluating things in the function position. Examples: *OK* min(1:2) min(1:2) f-min; f(1:2) do.call(min,list(1:2)) do.call(min,list(1:2)) # do.call converts string-function *Not OK* (min)(1:2) # string in function position is

Re: [R] R development master class: NYC, Dec 12-13

2011-11-15 Thread Stavros Macrakis
Last time, I was told that I couldn't list my R package and associated papers as a research activity with substantial impact because it was outside my official scope of work. (Even though I wrote it so I could *do* my work.) That seems wrong. My impression is that method papers were frequent

[R] Kleinberg's burst detection algorithm

2011-10-21 Thread Stavros Macrakis
Has anyone here implemented Jon Kleinberg's burst detection algorithm (Bursty and Hierarchical Structure in Streams http://www.cs.cornell.edu/home/kleinber/bhs.pdf)? I'd rather not reimplement if there's already running code available Thanks, -s [[alternative HTML

Re: [R] Reading name-value data

2011-07-29 Thread Stavros Macrakis
? That does match up columns by name. Hadley On Thu, Jul 28, 2011 at 5:23 PM, Stavros Macrakis macra...@alum.mit.edu wrote: I have a file of data where each line is a series of name-value pairs, but where the names are not necessarily the same from line to line, e.g. a=1,b=2,d=5 b=4,c=3,e

[R] Reading name-value data

2011-07-28 Thread Stavros Macrakis
I have a file of data where each line is a series of name-value pairs, but where the names are not necessarily the same from line to line, e.g. a=1,b=2,d=5 b=4,c=3,e=3 a=5,d=1 I would like to create a data frame which lines up the data in the corresponding columns. In this case, this

[R] Composing two n-dimensional arrays into one n+1-dimensional array

2011-06-13 Thread Stavros Macrakis
If I have 2 n-dimensional arrays, how do I compose them into a n+1-dimension array? Is there a standard R function that's something like the following, but that gives clean errors, handles all the edge cases, etc. abind - function(a,b) structure( c(a,b), dim = c(dim(a), 2) ) m1 -

[R] Approximate name matching

2011-05-09 Thread Stavros Macrakis
Is there R software available for doing approximate matching of personal names? I have data about the same people produced by different organizations and the only matching key I have is the name. I know that commercial solutions exist, and I know I code code this from scratch, but I'd prefer to

Re: [R] General binary search?

2011-04-06 Thread Stavros Macrakis
On Wed, Apr 6, 2011 at 12:59, Martin Morgan mtmor...@fhcrc.org wrote: On 04/04/2011 01:50 PM, William Dunlap wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Stavros Macrakis Sent: Monday, April 04, 2011 1:15 PM To: r

[R] General binary search?

2011-04-04 Thread Stavros Macrakis
Is there a generic binary search routine in a standard library which a) works for character vectors b) runs in O(log(N)) time? I'm aware of findInterval(x,vec), but it is restricted to numeric vectors. I'm also aware of various hashing solutions (e.g. new.env(hash=TRUE) and fastmatch),

[R] Stricter read.table?

2010-12-10 Thread Stavros Macrakis
read.table gives idiosyncratic results when the input is formatted strangely, for example: read.table(textConnection(a'b\nc'd\n),header=FALSE,fill=TRUE,sep=,quote=') = c'd a'b c'd read.table(textConnection(a'b\nc'd\nf'\n'\n),header=FALSE,fill=TRUE,sep=,quote=') = f' \na b c'd f' \n

[R] Quantile with discrete types

2010-12-10 Thread Stavros Macrakis
I don't understand why 'quantile' works in this case: tt - rep(c('a','b'),c(10,3)) sapply(0:6/6,function(q) quantile(tt,probs=q,type=1)) 0% 16.7% 33.3% 50% 66.7% 83.3% 100% a a a a a b b and also

Re: [R] solving cubic/quartic equations non-iteratively

2010-01-22 Thread Stavros Macrakis
On Tue, Jan 5, 2010 at 5:25 PM, Carl Witthoft c...@witthoft.com wrote: quote: There are certainly formulas for solving polynomials numerically up to 4th degree non-iteratively, but you will almost certainly get better results using iterative methods. I must be missing something here.

Re: [R] solving cubic/quartic equations non-iteratively

2010-01-05 Thread Stavros Macrakis
There are certainly formulas for solving polynomials numerically up to 4th degree non-iteratively, but you will almost certainly get better results using iterative methods. Even the much more trivial formula for the 2nd degree (quadratic) is tricky to implement correctly and accurately, see: *

Re: [R] Problem with expand.grid

2009-12-22 Thread Stavros Macrakis
Unfortunately, expand.grid doesn't validate the class of its argument, so it is reporting an internal error rather than something more intelligible. On Tue, Dec 22, 2009 at 11:19 AM, Keith Jewell k.jew...@campden.co.ukwrote: Just confirming it isn't the bug fixed in 2.11.0dev, and giving an

[R] Method dispatch for function

2009-11-18 Thread Stavros Macrakis
How can I determine what S3 method will be called for a particular first-argument class? I was imagining something like functionDispatch('str','numeric') = utils:::str.default , but I can't find anything like this. For that matter, I was wondering if anyone had written a version of `methods`

[R] Suppressing final spaces in data.frame printouts

2009-11-11 Thread Stavros Macrakis
When printing data.frames, R aligns columns by padding with spaces. For example, print(data.frame(x=c('a','bb','ccc')),right=FALSE)   x 1 a  |-- vertical bar shows end of line 2 bb |-- vertical bar shows end of line 3 ccc|-- vertical bar shows end

Re: [R] Suppressing final spaces in data.frame printouts

2009-11-11 Thread Stavros Macrakis
M. Heiberger r...@temple.eduwrote: Stavros Macrakis wrote: I could of course write my own print function for this, but was wondering if there was a standard way of doing it. If not in R, perhaps there is some way to have ESS delete the final spaces? ESS, or more precisely emacs, can

Re: [R] Suppressing final spaces in data.frame printouts

2009-11-11 Thread Stavros Macrakis
complication which made me hope that someone had already solved the problem in R or ESS -s On Wed, Nov 11, 2009 at 8:43 PM, RICHARD M. HEIBERGER r...@temple.eduwrote: On Wed, Nov 11, 2009 at 8:12 PM, Stavros Macrakis macra...@alum.mit.edu wrote: Thanks for the suggestion

Re: [R] Book on R programming

2009-08-31 Thread Stavros Macrakis
I recommend you skim the Chambers book at Google Books or Amazon before buying it as a guide to programming in R. It is a fascinating book, but is more a discursive reflection on the history and philosophy of R than a practical guide to programming in R. It certainly explains the rationale for

Re: [R] Is there a construct for conditional comment?

2009-08-21 Thread Stavros Macrakis
On Thu, Aug 20, 2009 at 1:27 PM, David Winsemiusdwinsem...@comcast.net wrote: ... But an extremely simple modification succeeds:  if ( 0 ) {  commented with zero  } else {  commented with one  } Returns: [1] \ncommented with one\n Yes, but of course that executes neither one nor the

[R] Keeping track of memory usage

2009-08-20 Thread Stavros Macrakis
How can I determine how much memory a given piece of my code is allocating (directly or indirectly)? -- essentially, the space analogue of system.time, something like this: system.space( x - rnorm(1) ) 1 Vcells system.space( for (i in 1:1000) x - rnorm(1) )

Re: [R] Object equality for S4 objects

2009-07-30 Thread Stavros Macrakis
On Thu, Jul 30, 2009 at 12:01 PM, Martin Morganmtmor...@fhcrc.org wrote: S4 objects do not have the semantics of environments, but of lists (or of most other R objects), so it is as meaningful to ask why identical(s1, s2) returns TRUE as it is to ask why identical(list(x=1), list(x=1))

Re: [R] Object equality for S4 objects

2009-07-30 Thread Stavros Macrakis
On Thu, Jul 30, 2009 at 4:03 PM, Martin Morganmtmor...@fhcrc.org wrote: S4 objects are mutable in the sense that one can write replacement methods for them Understood, but I don't think that's the usual meaning of 'mutable'. -s __

[R] Object equality for S4 objects

2009-07-29 Thread Stavros Macrakis
To test two environments for object equality (Lisp EQ), I can use 'identity': e1 - environment(local(function()x)) e2 - environment(local(function()x)) identical(e1,e2) # compares object identity [1] FALSE identical(as.list(e1),as.list(e2))# compares values as

Re: [R] dereferencing in R

2009-07-16 Thread Stavros Macrakis
What do you mean by 'passing an array reference' and 'dereferencing' and what do you mean by an 'R script'? What language(s) are you accustomed to? If you mean 'passing an array value' to an 'R function', you just use the argument name. Since R uses call-by-value (modulo the substitute

Re: [R] Simple cat statement - output truncated

2009-07-16 Thread Stavros Macrakis
Kevin, The habitués of this mailing list get irritated when users mail in problem reports which don't include enough information to reproduce the problem, as requested in the standard footer of r-help mail (PLEASE ... provide commented, minimal, self-contained, reproducible code.) This irritation

Re: [R] quoting expressions in a list

2009-07-16 Thread Stavros Macrakis
On Thu, Jul 16, 2009 at 4:44 PM, Erik Iversoneiver...@nmdp.org wrote: I have a list of logical expressions, and I would really like it if the names of the components of the list were identical to the corresponding logical expression. So, as an example: df.example - data.frame(a = 1:10, b

Re: [R] Trig functions strange results

2009-07-14 Thread Stavros Macrakis
On Tue, Jul 14, 2009 at 1:45 PM, Nair, Murlidharan T mn...@iusb.edu wrote: I am trying to calculate coordinate transformations and in the process of debugging my code using debug I found the following Browse[1] direction[i] [1] -1.570796 Browse[1] cos(direction[i]) [1] 6.123032e-17

Re: [R] strange strsplit gsub problem 0 is this a bug or a string length limitation?

2009-07-10 Thread Stavros Macrakis
On Fri, Jul 10, 2009 at 8:58 AM, Marc Schwartz marc_schwa...@me.com wrote: Review the Note in ?as.character: as.character truncates components of language objects to 500 characters (was about 70 before 1.3.1). If this limitation is too hard to fix, shouldn't it at least give a warning or an

Re: [R] Numbering sequences of non-NAs in a vector

2009-07-07 Thread Stavros Macrakis
Here's one possibility: vv - c(10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9) (1+cumsum(diff(is.na(c(vv[1],vv)))==1)) * !is.na(vv) [1] 1 1 1 1 1 1 0 0 0 0 2 2 2 0 0 0 3 3 3 3 On Tue, Jul 7, 2009 at 5:08 PM, Krishna Tateneni taten...@gmail.com wrote: Greetings, I have a vector of the

Re: [R] Question in using e1071 svm routine

2009-07-07 Thread Stavros Macrakis
Isn't the initial value of the variable T equal to the constant TRUE? So unless he's modified the value of T, shouldn't it work? -s On 7/7/09, Max Kuhn mxk...@gmail.com wrote: Unlike Splus, R does not use T for TRUE. On Tue, Jul 7, 2009 at 6:05 PM, Michaelcomtech@gmail.com

Re: [R] Automatically placing a legend in an area with the most white space...

2009-06-28 Thread Stavros Macrakis
install.packages('plotrix') On Sun, Jun 28, 2009 at 3:51 PM, Jason Rupert jasonkrup...@yahoo.comwrote: ... Error in legend(emptyspace(rep(x_vals_1, 3), c(y1_vals, y2_vals, y3_vals)), : could not find function emptyspace I've searched via RSeek, but I have not been able to find anything

Re: [R] How to avoid ifelse statement converting factor to character

2009-06-26 Thread Stavros Macrakis
It gives me a headache, too! I think you'll have to wait for a more expert user than me to supply explanations of these behaviors and their rationales. -s On 6/26/09, Craig P. Pyrame crap...@gmail.com wrote: Stavros Macrakis wrote: On Thu, Jun 25, 2009 at 12:47 PM, Craig P

Re: [R] How do I get just the two last tokens of each string in a vector?

2009-06-26 Thread Stavros Macrakis
One way is: a - c( %L H*L L*H H%, %L H* H%, %L L*H %, %L L*H % ) sub(^.*(^| )([^ ]+ [^ ]+$),\\2,a) [1] L*H H% H* H% L*H % L*H % Just be aware that this is not terribly efficient for very large strings. -s On Fri, Jun 26, 2009 at 7:21 AM, Fredrik Karlssondargo...@gmail.com

Re: [R] How to avoid ifelse statement converting factor to character

2009-06-25 Thread Stavros Macrakis
On Wed, Jun 24, 2009 at 9:04 PM, Rolf Turnerr.tur...@auckland.ac.nz wrote:  Do not get your knickers in a twist.  R works simply and straightforwardly  in simple straightforward situations. Though I find R an incredibly useful tool, alas, it is simply not true that R works simply and

Re: [R] How to avoid ifelse statement converting factor to character

2009-06-25 Thread Stavros Macrakis
Erratum:     ifelse(TRUE,dd,dd) = 1230786000 (class numeric) should be ifelse(TRUE,tt,tt) = 1230786000 (class numeric) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] How to avoid ifelse statement converting factor to character

2009-06-25 Thread Stavros Macrakis
On Thu, Jun 25, 2009 at 12:47 PM, Craig P. Pyramecrap...@gmail.com wrote: The man page Stavros quotes states that the class attribute of the result is taken from 'test', which clearly is not the case: Actually, the behavior is documented pretty clearly: The mode of the answer will be

Re: [R] How to avoid ifelse statement converting factor to character

2009-06-24 Thread Stavros Macrakis
On Wed, Jun 24, 2009 at 12:34 PM, Mark Namtb...@gmail.com wrote: The problem is that after running the ifelse statement, data$SOCIAL_STATUS is converted from a factor to a character. Is there some way I can avoid this conversion? I'm afraid that ifelse has very bizarre semantics when the yes

Re: [R] first value...

2009-06-23 Thread Stavros Macrakis
I think what you mean is that you want to find the position of the first non-NA value in the vector. is.na returns a boolean vector of the NA values, so: xx - c(NA,NA,NA,2,3,NA,4) which(!is.na(xx))[1] [1] 4 The other proposed solution, which(diff(is.na(inc)) 0) is incorrect:

Re: [R] [Rd] Floating point precision / guard digits? (PR#13771)

2009-06-20 Thread Stavros Macrakis
(I am replacing R-devel and r-bugs with r-help as addressees.) On Sat, Jun 20, 2009 at 9:45 AM, Dr. D. P. Kreil dpkr...@gmail.com wrote: So if I request a calculation of 0.3-0.1-0.1-0.1 and I do not get 0, that is not an issue of rounding / underflow (or whatever the correct technical term

Re: [R] [Rd] Floating point precision / guard digits? (PR#13771)

2009-06-20 Thread Stavros Macrakis
On Sat, Jun 20, 2009 at 4:10 PM, Dr. D. P. Kreil dpkr...@gmail.com wrote: Ah, that's probably where I went wrong. I thought R would take the 0.1, the 0.3, the 3, convert them to extended precision binary representations, do its calculations, an the reduction to normal double precision binary

Re: [R] tapply with cbinded x

2009-06-16 Thread Stavros Macrakis
On Tue, Jun 16, 2009 at 5:16 AM, Stefan Uhmann stefan.uhm...@googlemail.com wrote: why does this not work? df - data.frame(var1 = c(3,2,1), var2 = c(6,5,4), var3 = c(9,8,7), fac = c('A', 'A', 'B')) tapply(cbind(df$var1, df$var2, df$var3), df$fac, mean) Because tapply is defined for

Re: [R] function inside ifelse

2009-06-15 Thread Stavros Macrakis
Of course functions can be used inside ifelse. They should return vectors. Be careful of the effect of recycling: ifelse(c(F,T,F,T,F,T),1:3,10:20) [1] 10 2 12 1 14 3 with functions: f- function(x) x/mean(x) ifelse(c(F,T,F,T,F,T),sqrt(1:3),f(10:20)) [1] 0.667 1.4142136 0.800

Re: [R] Referencing data frames

2009-06-15 Thread Stavros Macrakis
On Mon, Jun 15, 2009 at 12:38 PM, Payam Minoofar payam.minoo...@meissner.com wrote: ...I would like to have a function acquire an object by reference, and within the function create new objects based on the original object and then use the name of the original object as the base for the names

Re: [R] Tables without names

2009-06-12 Thread Stavros Macrakis
On Fri, Jun 12, 2009 at 6:09 AM, Duncan Murdoch murd...@stats.uwo.cawrote: On 11/06/2009 5:35 PM, Stavros Macrakis wrote: A table without names displays like a vector: unname(table(2:3)) [1] 1 1 1 and preserves the table class (as with unname in general): dput(unname(table(2

[R] Tables without names

2009-06-11 Thread Stavros Macrakis
A table without names displays like a vector: unname(table(2:3)) [1] 1 1 1 and preserves the table class (as with unname in general): dput(unname(table(2:3))) structure(c(1L, 1L), .Dim = 2L, class = table) Does that make sense? R is not consistent in its treatment of such

Re: [R] Splicing factors without losing levels

2009-06-09 Thread Stavros Macrakis
Various people have provided technical solutions to your problem. May I suggest, though, that 'splice' isn't quite the right word for this operation? Splicing two pieces of rope / movie film / audio tape / wires / etc. means connecting them at their ends, either at an extremity or in the middle,

Re: [R] Splicing factors without losing levels

2009-06-09 Thread Stavros Macrakis
On Tue, Jun 9, 2009 at 11:16 AM, Titus von der Malsburg malsb...@gmail.comwrote: On Tue, Jun 09, 2009 at 11:04:03AM -0400, Stavros Macrakis wrote: This may seem like a minor point, but I think it is worthwhile using descriptive names for functions. Makes sense. I thought I've seen

Re: [R] using regular expressions to retrieve a digit-digit-dot structure from a string

2009-06-09 Thread Stavros Macrakis
On Tue, Jun 9, 2009 at 7:44 AM, Mark Heckmann mark.heckm...@gmx.de wrote: Thanks for your help. Your answers solved the problem I posted and that is just when I noticed that I misspecified the problem ;) My problem is to separate a German texts by sentences. Unfortunately I haven't found an R

Re: [R] if else

2009-06-08 Thread Stavros Macrakis
On Mon, Jun 8, 2009 at 1:48 PM, Cecilia Carmo cecilia.ca...@ua.pt wrote: I have the following dataframe: firm-c(rep(1:3,4)) year-c(rep(2001:2003,4)) X1-rep(c(10,NA),6) X2-rep(c(5,NA,2),4) data-data.frame(firm, year,X1,X2) data So I want to obtain the same dataframe with a variable X3

Re: [R] if else

2009-06-08 Thread Stavros Macrakis
On Mon, Jun 8, 2009 at 3:36 PM, Don MacQueen m...@llnl.gov wrote: Though I do agree that the way you've written the general case with any/ is.na and sum/na.rm is cleaner and clearer because more general, I don't agree at all with what you say about nested ifelse's vs. a series of assignments:

Re: [R] Done: Fast way of finding top-n values of a long vector

2009-06-05 Thread Stavros Macrakis
On Fri, Jun 5, 2009 at 4:09 AM, Allan Engelhardt all...@cybaea.com wrote: I'm all done now. The max2 version below is what I went with in the end for my proposed change to caret::nearZeroVar (which used the sort method). Max Kuhn will make it available on CRAN soon. It speeds up that routine

[R] all.equal(0,0i)

2009-06-02 Thread Stavros Macrakis
all.equal(0,0i) [1] Modes: numeric, complex [2] target is numeric, current is complex all.equal(1,1+0i) [1] Modes: numeric, complex [2] target is numeric, current is complex Is this the intended behavior? In general, all.equal is strict about argument mode, thus TRUE/1 and 1/'1' do not

Re: [R] Error:non-numeric argument in my function

2009-06-01 Thread Stavros Macrakis
. If the message said that a list of class 'data.frame' was found (probably the leading case), then that would be much more helpful. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) Stavros

Re: [R] Error:non-numeric argument in my function

2009-05-31 Thread Stavros Macrakis
On Sun, May 31, 2009 at 6:10 PM, jim holtman jholt...@gmail.com wrote: Message is very clear: 1 * 'a' Error in 1 * a : non-numeric argument to binary operator Though the user should have been able to figure this out, perhaps the error message could be improved? After all, it is not the

[R] max.col specification

2009-05-29 Thread Stavros Macrakis
I'm not sure I understand the max.col spec or its rationale. In particular: * What is the significance and effect of assuming that the entries are probabilities, as they do not seem to be limited to the interval [0,1]? * In what contexts is it useful for max.col to consider numbers within a

Re: [R] maxtrix to permutation vector

2009-05-29 Thread Stavros Macrakis
Not sure what you mean by permutations here. I think what you mean is that given a matrix m, you want a matrix whose rows are c(i,j,m[i,j]) for all i and j. You can use the `melt` function in the `reshape` package for this. See below. Hope this helps, -s library(reshape)

Re: [R] maxtrix to permutation vector

2009-05-29 Thread Stavros Macrakis
value 1 a x 1 2 b x 2 3 a y 3 4 b y 4 as.matrix(melt(m)) x y value [1,] a x 1 [2,] b x 2 [3,] a y 3 [4,] b y 4 On Fri, May 29, 2009 at 2:53 PM, Stavros Macrakis macra...@alum.mit.eduwrote: Not sure what you mean by permutations here. I think what you mean

Re: [R] custom sort?

2009-05-28 Thread Stavros Macrakis
I agree that it is surprising that R doesn't provide a sort function with a comparison function as argument. Perhaps that is partly because calling out to a function for each comparison is relatively expensive; R prefers vector operations. That said, many useful custom sorts are easy to define by

[R] RODBC package: how to check whether connection is open

2009-05-28 Thread Stavros Macrakis
What is the recommended way of checking whether an RODBC connection is open? Since odbcValidChannel is not exported from namespace RODBC, I suppose I shouldn't be using it. This is the best I could come up with, but it seems a bit 'dirty' to be using a tryCatch for something like this:

Re: [R] custom sort?

2009-05-28 Thread Stavros Macrakis
I couldn't get your suggested method to work: `==.foo` - function(a,b) unclass(a)==unclass(b) `.foo` - function(a,b) unclass(a) unclass(b) # invert comparison is.na.foo - function(a)is.na(unclass(a)) sort(structure(sample(5),class=foo)) #- 1:5 -- not reversed What am I missing?

Re: [R] How to exclude a column by name?

2009-05-27 Thread Stavros Macrakis
On Wed, May 27, 2009 at 6:37 AM, Zeljko Vrba zv...@ifi.uio.no wrote: Given an arbitrary data frame, it is easy to exclude a column given its index: df[,-2]. How to do the same thing given the column name? A naive attempt df[,-name] did not work :) Various ways: Boolean index vector:

Re: [R] Defining functions - an interesting problem

2009-05-27 Thread Stavros Macrakis
The 'ties.method' argument to 'rank' is the *third* positional argument to 'rank', so either you need to put it in the third position or you need to use a named argument. The fact that the variable you're using to represent ties.method is called ties.method is irrelevant. That is, this:

[R] R Books listing on R-Project

2009-05-27 Thread Stavros Macrakis
I was wondering what the criteria were for including books on the Books Related to R page http://www.r-project.org/doc/bib/R-books.html. (There is no maintainer listed on this page.) In particular, I was wondering why the following two books are not listed: * Andrew Gelman, Jennifer Hill, *Data

[R] OWL (Web Ontology Language) in R?

2009-05-26 Thread Stavros Macrakis
Is anyone working on an R package for manipulating OWL (Web Ontology Language), either natively or via an external library? I don't see anything obviously relevant in CRAN, though of course OWL functionality could be built up starting with the XML package. Thanks, -s

Re: [R] XML parse error

2009-05-24 Thread Stavros Macrakis
On Sun, May 24, 2009 at 12:28 PM, kulwinder banipal kbani...@hotmail.comwrote: It is for sure little complicated then a plain XML file. The format of binary file is according to XML schema. I have been able to get C parser going to get information from binary with one caveat - I have to

Re: [R] Class for time of day?

2009-05-22 Thread Stavros Macrakis
On Thu, May 21, 2009 at 8:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: It uses hours/minutes/seconds for values 1 day and uses days and fractions of a day otherwise. Yes, my examples were documenting this idiosyncracy. For values and operations that it has not considered it

Re: [R] Class for time of day?

2009-05-22 Thread Stavros Macrakis
On Fri, May 22, 2009 at 10:03 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Regarding division you could contribute that to the chron package. I've contributed a few missing items and they were incorporated. Good to know. Maybe I'll do that Giving an error when it does not

Re: [R] Class for time of day?

2009-05-22 Thread Stavros Macrakis
On Fri, May 22, 2009 at 12:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: ...The way this might appear in code is if someone wanted to calculate the number of one hour intervals in 18 hours. One could write: t18 - times(18:00:00) t1 - times(1:00:00) as.numeric(t18) /

Re: [R] Class for time of day?

2009-05-21 Thread Stavros Macrakis
On Wed, May 20, 2009 at 12:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: There is a times class in the chron package. Perfect! Just what I was looking for. On Wed, May 20, 2009 at 12:19 PM, jim holtman jholt...@gmail.com wrote: If you want the hours from a POSIXct, here is one

Re: [R] Functions returning functions

2009-05-20 Thread Stavros Macrakis
On Wed, May 20, 2009 at 7:21 AM, Paulo Grahl pgr...@gmail.com wrote: A - function(parameters) { # calculations w/ parameters returning 'y' tmpf - function(x) { # function of 'y' } return(tmpf) } The value of the parameters are stored in an environment local to the function.

Re: [R] Too large a data set to be handled by R?

2009-05-20 Thread Stavros Macrakis
On Tue, May 19, 2009 at 11:59 PM, tsunhin wong thjw...@gmail.com wrote: In order to save time, I am planning to generate a data set of size 1500 x 2 with each data point a 9-digit decimal number, in order to save my time. I know R is limited to 2^31-1 and that my data set is not going to

[R] Class for time of day?

2009-05-20 Thread Stavros Macrakis
What is the recommended class for time of day (independent of calendar date)? And what is the recommended way to get the time of day from a POSIXct object? (Not a string representation, but a computable representation.) I have looked in the man page for DateTimeClasses, in the Time Series

Re: [R] exists function on list objects gives always a FALSE

2009-05-19 Thread Stavros Macrakis
On Tue, May 19, 2009 at 12:07 PM, Žroutík zrou...@gmail.com wrote: SmoothData - list(exists=TRUE, span=0.001) exists(SmoothData$span) FALSE As others have said, this just checks for the existence of a variable with the (strange) name SmoothData$span. In some sense, in R semantics, xxx$yyy

Re: [R] Concatenating two vectors into one

2009-05-18 Thread Stavros Macrakis
If you want to concatenate the *vectors*, you need 'c', which will also coerce the elements to a common type. If you want to concatenate the corresponding *elements* of the vectors, you need 'paste', which will coerce them to character strings. -s On 5/18/09, Henning Wildhagen

[R] Generic 'diff'

2009-05-18 Thread Stavros Macrakis
I would like to apply a function 'f' to the lagged version of a vector and the vector itself. This is easy to do explicitly: mapply( f, v[-1], v[-length(v)] ) or in the case of a pointwise vector function, simply f( v[-1], v[-length(v)] ) This is essentially the same as 'diff' but

Re: [R] Generic 'diff'

2009-05-18 Thread Stavros Macrakis
for that. For some examples see: methods(diff) On Mon, May 18, 2009 at 4:24 PM, Stavros Macrakis macra...@alum.mit.edu wrote: I would like to apply a function 'f' to the lagged version of a vector and the vector itself. This is easy to do explicitly: mapply( f, v[-1], v[-length(v

Re: [R] Generic 'diff'

2009-05-18 Thread Stavros Macrakis
not understanding your objection. -s On Mon, May 18, 2009 at 5:48 PM, Stavros Macrakis macra...@alum.mit.edu wrote: I guess I wasn't very clear. The goal is not to define diff on a different object type, but to have a different 'subtraction' operator with the same lag logic. An easy

Re: [R] newbie: closing unused connection + readline

2009-05-16 Thread Stavros Macrakis
On Sat, May 16, 2009 at 8:34 AM, Aval Sarri aval.sa...@gmail.com wrote: # Create a socket from which to read lines - one at a time (record) reader.socket -   socketConnection( host = 'localhost', 5000,                                     server = TRUE, blocking = TRUE,                          

Re: [R] newbie: closing unused connection + readline

2009-05-16 Thread Stavros Macrakis
On Sat, May 16, 2009 at 9:11 AM, Aval Sarri aval.sa...@gmail.com wrote: ...I tried something line this also: mydataframe - read.table (socket, sep=,); but does not work says no input lines. this also. mydataframe - read.table (readLine(socket), sep=,); Sorry, I didn't see this before my

Re: [R] Gamma function

2009-05-16 Thread Stavros Macrakis
What exactly is the R code you wrote for your function f? Without that, it will be hard to help you. -s On Sat, May 16, 2009 at 2:48 AM, Kon Knafelman konk2...@hotmail.com wrote: Hi Guy, I am having trouble graphing the following function √2Γ(n/2)/[√n - 1Γ((n - 1)/2 for the

Re: [R] can you tell what .Random.seed *was*?

2009-05-15 Thread Stavros Macrakis
On Thu, May 14, 2009 at 3:36 PM, G. Jay Kerns gke...@ysu.edu wrote: set.seed(something) x - rnorm(100) y - runif(500) # bunch of other stuff ... Now, I give you a copy of my script.R (with the set.seed statement removed, of course) together with the .RData file that was generated by the

Re: [R] can you tell what .Random.seed *was*?

2009-05-15 Thread Stavros Macrakis
On Fri, May 15, 2009 at 12:07 PM, Stavros Macrakis macra...@alum.mit.edu wrote: system.time(whatseed(runif(1))) Sorry, though I got lucky and my overall result is roughly correct, this is an incorrect time measure. It should be r - runif(1); system.time(whatseed(r)) because R's call

[R] Converting numbers to and from raw

2009-05-15 Thread Stavros Macrakis
How can I convert an integer or double to and from their internal representation as raws of length 4 and 8? The following works for positive integers (including those represented as floats): # Convert integer (represented as integer or double) to sequence # of raw bytes, least-significant byte

[R] Inconsistency in representation of variables

2009-05-11 Thread Stavros Macrakis
In stats::D, I was wondering why variables are represented as symbols in expressions, but as strings in lists of variables: D(quote(x^2),x) = 2*x D(quote(x^2),quote(x)) = error Variable must be a character string Strings are not allowed in the expression to denote variables:

Re: [R] Beyond double-precision?

2009-05-11 Thread Stavros Macrakis
On Sat, May 9, 2009 at 12:17 PM, Berwin A Turlach ber...@maths.uwa.edu.au wrote: log(H) = log(n) - log( 1/x_1 + 1/x_2 + ... + 1/x_n) ...But we need to calculate the logarithm of a sum from the logarithms of the individual terms. ...The way to calculate log(x+y) from lx=log(x) and ly=log(y) ...

Re: [R] integrate lgamma from 0 to Inf

2009-04-27 Thread Stavros Macrakis
On Wed, Apr 22, 2009 at 3:28 AM, Andreas Wittmann andreas_wittm...@gmx.de wrote: i try to integrate lgamma from 0 to Inf. Both gamma and log are positive and monotonically increasing for large arguments. What can you conclude about the integrability of log(gamma(x))? -s

[R] The assign(paste(...,i),...) idiom

2009-04-20 Thread Stavros Macrakis
Judging from the traffic on this mailing list, a lot of R beginners are trying to write things like assign( paste( myvar, i), ...) where they really should probably be writing myvar[i] - ... Do we have any idea where this bizarre habit comes from? -s

Re: [R] (no subject)

2009-04-18 Thread Stavros Macrakis
mylist - c( 2,1,3,5,4 ) make a vector of numbers sort(mylist) [1] 1 2 3 4 5in sorted order mylist - c( this, is, a, test) sort(mylist) [1] ais test this in sorted order order(mylist) [1] 3 2 4 1 original positions, e.g.

Re: [R] Loop question

2009-04-18 Thread Stavros Macrakis
On Fri, Apr 17, 2009 at 10:12 PM, Brendan Morse morse.bren...@gmail.com wrote: ...I would like to automatically generate a series of matrices and give them successive names. Here is what I thought at first: t1-matrix(0, nrow=250, ncol=1) for(i in 1:10){        t1[i]-rnorm(250) } What I

Re: [R] Using trace

2009-04-17 Thread Stavros Macrakis
()) + cat(sprintf(X is %i\n,x)) + print(ans) + } fact(4) fact(x - 1) X is 0 [1] 1 fact(x - 1) X is 1 [1] 1 fact(x - 1) X is 2 [1] 2 fact(x - 1) X is 3 [1] 6 fact(4) X is 4 [1] 24 2009/4/13 Stavros Macrakis macra...@alum.mit.edu: I would like to trace functions, displaying

Re: [R] Using trace

2009-04-17 Thread Stavros Macrakis
({cat(sprintf(x= %i\n,x));return}),print=T) [1] fact fact(4) Tracing fact(4) on entry x= 4 Tracing fact(x - 1) on entry x= 3 Tracing fact(x - 1) on entry x= 2 Tracing fact(x - 1) on entry x= 1 Tracing fact(x - 1) on entry x= 0 [1] 24 2009/4/17 Stavros Macrakis macra...@alum.mit.edu

Re: [R] Intersection of two sets of intervals

2009-04-15 Thread Stavros Macrakis
There is a very nice intervals package in CRAN. It is impressively efficient even for intersections of many millions of intervals. If I remember correctly, it is purely in-core, so on a 32-bit R you'll be limited to something like 100 million intervals. Is that enough for your application?

Re: [R] Automating object creation

2009-04-14 Thread Stavros Macrakis
It is certainly possible to create x2, x4, etc. using something like assign( sprintf(x%d,i), ...value... ). But are you sure you need separate *variables* x2, x4, etc.? Why not create a list of vectors addressible as x[2] etc.? You can do that with x - list() (to define the data type of x as

Re: [R] Forcing the extrapolation of loess through the origin

2009-04-14 Thread Stavros Macrakis
On Tue, Apr 14, 2009 at 1:08 PM, jimm-pa...@gmx.de wrote: I'm fitting a line to my dataset. Later I want to predict missing values that exceed the [min,max] interval of my empirical data, therefore I choose surface=direct for extrapolation.

Re: [R] Physical Units in Calculations

2009-04-13 Thread Stavros Macrakis
On Sun, Apr 12, 2009 at 11:01 PM, bill.venab...@csiro.au wrote: It is, however, an interesting problem and there are the tools there to handle it.  Basically you need to create a class for each kind of measure you want to handle (length, area, volume, weight, and so on) and then overload

Re: [R] Finding the 5th percentile

2009-04-13 Thread Stavros Macrakis
quantile( dsamp100, 0.05 ) On Mon, Apr 13, 2009 at 10:41 AM, Henry Cooper henry.1...@hotmail.co.uk wrote: dsamp100-coef(100,39.83,5739,2869.1,49.44) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] Concatenation, was Re: Physical Units in Calculations

2009-04-13 Thread Stavros Macrakis
On Mon, Apr 13, 2009 at 5:15 AM, Peter Dalgaard p.dalga...@biostat.ku.dk wrote: Stavros Macrakis wrote: ...c of two time differences is currently a numeric vector, losing its units (hours, days, etc.) completely. That's actually a generic feature/issue of c(). ... There is some potential

[R] Using trace

2009-04-12 Thread Stavros Macrakis
I would like to trace functions, displaying their arguments and return value, but I haven't been able to figure out how to do this with the 'trace' function. After some thrashing, I got as far as this: fact - function(x) if(x1) 1 else x*fact(x-1) tracefnc - function()

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