Re: [R] getWinProgressBar does not return previous value
On Fri, 9 May 2008, Michael DiPersio wrote: I am trying to use winProgressBar, however I find that although setWinProgressBar updates the value on the screen, getWinProgressBar does not return this value. E.g pb - winProgressBar() setWinProgressBar(pb, 0.2) getWinProgressBar(pb) [1] 0 It does, but rounded to an integer. Look at typeof() on the value, or pb - winProgressBar(max=100) setWinProgressBar(pb, 20) getWinProgressBar(pb) It would be more flexible to allow the user to round, so I'll change it. I tried the same with tkProgressBar, and it is working as I would expect from the documentation. pb - tkProgressBar() setTkProgressBar(pb, 0.5) getTkProgressBar(pb) [1] 0.5 ... and I get the same result using txtProgressBar . Does anyone using winProgressBar find the same behaviour, or know the reason for it? A search for winProgressBar in R-help archive did not reveal anything, I believe it is a new function to v2.7.0. sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base Thanks, Michael __ R-help@r-project.org 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org 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.
Re: [R] lme nesting/interaction advice
On Fri, May 9, 2008 at 4:04 AM, Federico Calboli [EMAIL PROTECTED] wrote: Note that random can be a list: a one-sided formula of the form ~x1+...+xn, or a pdMat object with a formula (i.e. a non-NULL value for formula(object)), or a list of such formulas or pdMat objects. If you can translate that into *informative* English I'd be grateful. I have the Pinheiro and Bates book under my nose now, and I suspect it's pretty more extensive that the helpfile, but it's still nowhere close to providing a straigtforward answer to my question. Federico, I think you'll be more likely to receive the type of response you're looking for if you formulate your question more clearly. The inclusion of commented, minimal, self-contained, reproducible code (as is requested at the bottom of every email sent by r-help) is an effective way to clarify the issues. Also, when asking a question about fitting a model it's helpful to describe the specific research questions you want the model to answer. I'll offer my interpretation of your study design so you can see where questions might arise. It sounds like you have protein measures (on how many units?) at various levels of 'male' (which at first you described as presence/absence, but later as continuous - also you descibed 'male' as fixed and continuous but then entered it in the formula as though it were a random grouping factor), within the second level of 'selection' (e.g. large1), within the first level of selection (e.g. large), within a random block (what are the blocks?) within a random month. Is this right -- multiple observations within 4 levels of nesting - some of which are random and some fixed? Finally, I'll point out that there's an R list dedicated to mixed models, with a particular focus on the lmer function, which might be the right tool for your analyses ( https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models ). Kingsford Jones Cheers, Federico -- 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-help@r-project.org 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-help@r-project.org 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] problem reading .por SPSS file
Hello, I've a .por file from 1998. I've tried to read it with library(foreign) read.spss(mhp_hu.por) at this point R simply stops working and my whole system is close to unusable I've found one related thread, but even there no real solution was given https://stat.ethz.ch/pipermail/r-help/2007-February/125071.html Unfortunately, I have no SPSS, and I can't convert it to txt or any other format. I was trying to use PSPP as well, but I could not understand how to open a file in it. :( Does any of you have an idea? Thanks, Viktor __ R-help@r-project.org 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.
Re: [R] Create pairwise table from columns?
Here is a suggestion con - textConnection(AnimalA,AnimalB,Score A1,A2,1 A1,A3,2 A1,A4,3 A2,A3,4 A2,A4,5 A3,A4,6 ) tst - read.csv(con) close(con) an - with(tst, sort(unique(c(as.character(AnimalA), as.character(AnimalB) M - array(0, c(length(an), length(an)), list(an, an)) i - match(tst$AnimalA, an) j - match(tst$AnimalB, an) M[cbind(i,j)] - M[cbind(j,i)] - tst$Score M A1 A2 A3 A4 A1 0 1 2 3 A2 1 0 4 5 A3 2 4 0 6 A4 3 5 6 0 Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of knussear Sent: Saturday, 10 May 2008 10:18 AM To: r-help@r-project.org Subject: [R] Create pairwise table from columns? Hi Group I have a large data set of individual pairwise values (250,000 rows) that I need to reshape into a pairwise matrix for mantel tests of these values versus genetic distances. the data are currently in columns formatted like so AnimalA, AnimalB, Score A1, A2, S1 A1, A3, S2 A1, A4, S3 A2, A3, S4 A2, A4, S5 A3, A4, S6 ...,, I need the final matrix to be formatted as A1A2A3A4 A1 0 S1S2S3 A2 S10 S4S5 A3 S2S4 0 S6 A4 S3S4 S6 0 are there any functions/packages that will make this easier? Thanks Ken -- View this message in context: http://www.nabble.com/Create-pairwise-table-from-columns--tp17158538p171 58538.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] function in nls argument -- robust estimation
Hi Kate and Fernando, I'm late into this thread, but from reading it I get the impression that Fernando really wants to do *robust* (as opposed to least-squares) non-linear model fitting. His proposal to set residuals to zero when they are outside a given bound is a very special case of an M-estimator, namely (if I'm not mistaken) the so-called Huber skipped-mean, an M-estimator with psi-function psi - function(x, k) ifelse(abs(x) = k, x, 0) It is known that this can be far from optimal, and either using Huber-psi or a redescender such as Tukey's biweight can be considerably better. Also note that the standard inference (std.errors, P-values, ...) that you'd get from summary(nlsfit) or anova(nls1, nl2) is *invalid* here, since you are effectively using *random* weighting. The nlrob() function in package 'robustbase' implements M-estimation of nonlinear models directly. Unfortunately, how to do correct inference in this situation is a hard problem, probably even an open research question in parts. I would expect that the bootstrap should work if you only have a few outliers. I don't have time at the moment to look at the example data and the model, and show you how to use it for nlrob(); if you find a way to you it for nls() , then the same should work for nlrob(). I'm CCing this to the specialists for Robust Stats with R mailing list, R-SIG-robust. Best regards, Martin Maechler ETH Zurich KateM == Katharine Mullen [EMAIL PROTECTED] on Fri, 9 May 2008 15:50:08 +0200 (CEST) writes: KateM You can take minpack.lm_1.1-0 (source code and MS Windows build, KateM respectively) from here: KateM http://www.nat.vu.nl/~kate/minpack.lm_1.1-0.tar.gz KateM http://www.nat.vu.nl/~kate/minpack.lm_1.1-0.zip KateM The bug that occurs when nprint = 0 is fixed. Also fixed is another KateM problem suggested your example: when the argument par is a list, calling KateM summary on the output of nls.lm was not working. KateM I'll submit the new version to CRAN soon. KateM This disscusion has been fruitful - thanks for it. KateM On Fri, 9 May 2008, Katharine Mullen wrote: You indeed found a bug. I can reproduce it (which I should have tried to do on other examples in the first place!). Thanks for finding it. It will be fixed in version 1.1-0 which I will submit to CRAN soon. On Fri, 9 May 2008, elnano wrote: Find the data (data_nls.lm_moyano.txt) here: ftp://ftp.bgc-jena.mpg.de/pub/outgoing/fmoyano Katharine Mullen wrote: Thanks for the details - it sounds like a bug. You can either send me the data in an email off-list or make it available on-line somewhere, so that I and other people can download it. __ R-help@r-project.org 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. -- View this message in context: http://www.nabble.com/function-in-nls-argument-tp17108100p17146812.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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. KateM __ KateM R-help@r-project.org mailing list KateM https://stat.ethz.ch/mailman/listinfo/r-help KateM PLEASE do read the posting guide http://www.R-project.org/posting-guide.html KateM and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org 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.
Re: [R] problem reading .por SPSS file
And how are we supposed to help without knowing your version of R, the version of 'foreign', anything about your system (or you) and without access to the file? Please do consult the posting guide and supply enough information that we have a chance of helping you. On Sat, 10 May 2008, Viktor Nagy wrote: Hello, I've a .por file from 1998. I've tried to read it with library(foreign) read.spss(mhp_hu.por) at this point R simply stops working and my whole system is close to unusable I've found one related thread, but even there no real solution was given https://stat.ethz.ch/pipermail/r-help/2007-February/125071.html That is not about .por files. Unfortunately, I have no SPSS, and I can't convert it to txt or any other format. I was trying to use PSPP as well, but I could not understand how to open a file in it. :( Does any of you have an idea? Thanks, Viktor __ R-help@r-project.org 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org 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] How many random numbers needed?
Hello R-People! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Perhaps this is another stupid question of me, but I was wondering how I know the needed random (set.seed) numbers, when running randomForest (library randomForest) on a large dataset. Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008, 10.00 Uhr bis 02.00 Uhr Campus Irchel, Winterthurerstrasse 190, 8057 Zürich Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft __ R-help@r-project.org 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] Hashes as S4 Classes, or: How to separate environments
For learning purposes mainly I attempted to implement hashes/maps/dictionaries
(Python lingua) as S4 classes, see the coding below. I came across some rough S4
edges, but in the end it worked (for one dictionary).
When testing ones sees that the dictionaries D1 and D2 share their environments
[EMAIL PROTECTED] and [EMAIL PROTECTED], though I thought a new and empty
environment would be
generated each time 'new(Dict)' is called.
QUESTION: How can I separate the environments [EMAIL PROTECTED] and [EMAIL
PROTECTED] ?
Reading the articles mentioned in Tipps and Tricks didn't help me really.
Of course, I will welcome other corrections and improvements as well.
Working in R 2.7.0 under Windows.
Hans Werner
#-- Class and method definition for dictionaries ---
setClass(Dict,
representation (hash = environment),
prototype (hash = new.env(hash=T, parent = emptyenv()))
)
setMethod(show, signature(object=Dict),
definition = function(object) ls([EMAIL PROTECTED])
)
setGeneric(hclear, function(object) standardGeneric(hclear))
setMethod(hclear, signature(object=Dict),
function(object) rm(list=ls([EMAIL PROTECTED]), [EMAIL PROTECTED])
)
setGeneric(hput, function(object, key, value) standardGeneric(hput))
setMethod(hput, signature(object=Dict, key=character, value=ANY),
function(object, key, value) assign(key, value, [EMAIL PROTECTED])
)
setGeneric(hget, function(object, key, ...) standardGeneric(hget))
setMethod(hget, signature(object=Dict, key=character),
function(object, key) {
if (exists(key, [EMAIL PROTECTED], inherits = FALSE)) {
get(key, [EMAIL PROTECTED])
} else {
return(NULL)
}
}
)
# Some tests
D1 - new(Dict)
hput(D1, a, 1) # Same as: [EMAIL PROTECTED] - 1
hput(D1, b, 2)
hget(D1, a)
hget(D1, b)
show(D1)
D2 - new(Dict)
hput(D2, c, 3)
hput(D2, d, 4)
hget(D2, a) # Wrong: was defined only for D1
hget(D2, b)
show(D2)
hclear(D2) # Wrong: clears D1 too
show(D1)
#-
__
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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.
Re: [R] irregular time series and multiple, overlaid plots
Look at the zoo and quantmod packages. On Sat, May 10, 2008 at 12:51 AM, falcon [EMAIL PROTECTED] wrote: I am new to R and am trying to solve the following problem: I have a data file containing tick-by-tick, millisecond level prices for some stocks. I have another file or two containing orders and trades, again, with millisecond time-stamps. Both of these files are irregularly spaced and the time stamps are in an iso format (date time.millisecond) I would like to create a price chart, and overlay on it the times and prices at which orders were sent out and trades were received. My purpose is basically to visualize the data to help me pinpoint problems and visually describe a day's trading activity. I am not (yet) interested in any detailed statistical analysis. From what I have read, the basic time series (ts) object is not appropriate since it is only for regularly spaced time series. The few examples I have seen for the 'its' package, generate an artificial time series, rather than reading from a file, extracting out relevant columns (say a time stamp column and a price column) and converting that to the right time series object (including taking care of time stamp formats). Any idea how I can approach this problem? Thanks Falcon -- View this message in context: http://www.nabble.com/irregular-time-series-and-multiple%2C-overlaid-plots-tp17159961p17159961.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] problem reading .por SPSS file
sorry, but it turned out that only the file was bigger than my patience (next time I will be more careful about the posting guide as well) thanks for your time! Viktor 2008/5/10 Prof Brian Ripley [EMAIL PROTECTED]: And how are we supposed to help without knowing your version of R, the version of 'foreign', anything about your system (or you) and without access to the file? Please do consult the posting guide and supply enough information that we have a chance of helping you. On Sat, 10 May 2008, Viktor Nagy wrote: Hello, I've a .por file from 1998. I've tried to read it with library(foreign) read.spss(mhp_hu.por) at this point R simply stops working and my whole system is close to unusable I've found one related thread, but even there no real solution was given https://stat.ethz.ch/pipermail/r-help/2007-February/125071.html That is not about .por files. Unfortunately, I have no SPSS, and I can't convert it to txt or any other format. I was trying to use PSPP as well, but I could not understand how to open a file in it. :( Does any of you have an idea? Thanks, Viktor __ R-help@r-project.org 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org 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.
Re: [R] Create pairwise table from columns?
Fantastic! Thanks very much! Where can I read more about the double assignment statement at the bottom? Closest I could get was a double for loop, which takes a long time Bill.Venables wrote: Here is a suggestion con - textConnection(AnimalA,AnimalB,Score A1,A2,1 A1,A3,2 A1,A4,3 A2,A3,4 A2,A4,5 A3,A4,6 ) tst - read.csv(con) close(con) an - with(tst, sort(unique(c(as.character(AnimalA), as.character(AnimalB) M - array(0, c(length(an), length(an)), list(an, an)) i - match(tst$AnimalA, an) j - match(tst$AnimalB, an) M[cbind(i,j)] - M[cbind(j,i)] - tst$Score M A1 A2 A3 A4 A1 0 1 2 3 A2 1 0 4 5 A3 2 4 0 6 A4 3 5 6 0 Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of knussear Sent: Saturday, 10 May 2008 10:18 AM To: r-help@r-project.org Subject: [R] Create pairwise table from columns? Hi Group I have a large data set of individual pairwise values (250,000 rows) that I need to reshape into a pairwise matrix for mantel tests of these values versus genetic distances. the data are currently in columns formatted like so AnimalA, AnimalB, Score A1, A2, S1 A1, A3, S2 A1, A4, S3 A2, A3, S4 A2, A4, S5 A3, A4, S6 ...,, I need the final matrix to be formatted as A1A2A3A4 A1 0 S1S2S3 A2 S10 S4S5 A3 S2S4 0 S6 A4 S3S4 S6 0 are there any functions/packages that will make this easier? Thanks Ken -- View this message in context: http://www.nabble.com/Create-pairwise-table-from-columns--tp17158538p171 58538.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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. -- View this message in context: http://www.nabble.com/Create-pairwise-table-from-columns--tp17158538p17162698.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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.
Re: [R] Hashes as S4 Classes, or: How to separate environments
Hi Hans --
Hans W Borchers [EMAIL PROTECTED] writes:
For learning purposes mainly I attempted to implement hashes/maps/dictionaries
(Python lingua) as S4 classes, see the coding below. I came across some rough
S4
edges, but in the end it worked (for one dictionary).
When testing ones sees that the dictionaries D1 and D2 share their
environments
[EMAIL PROTECTED] and [EMAIL PROTECTED], though I thought a new and empty
environment would be
generated each time 'new(Dict)' is called.
QUESTION: How can I separate the environments [EMAIL PROTECTED] and [EMAIL
PROTECTED] ?
The prototype is created once, at class creation time. So all objects
derived from the prototype share the same environment (other types
like 'list' would have the illusion of being created anew, because of
copy-on-change semantics). A solution is to have an initialize method
that recreates the hash each time.
setMethod(initialize, signature=signature(.Object=Dict),
function(.Object,
hash=new.env(hash=TRUE, parent=emptyenv()),
...) {
callNextMethod(.Object, hash=hash, ...)
})
Another solution is to have a constructor that feeds Dict a new
environment
Dict - function() {
new(Dict, hash=new.env(hash=TRUE, parent=emptyenv())
}
The latter is perhaps preferable, both from an aesthetic / user point
of view ('Dict()' better than 'new(Dict)') and from the
nuances-of-S4 point of view (e.g., the default 'initialize' method is
documented, though not in so many words, as a copy constructor, taking
slots in it's first argument as defaults; 'initialize' above does not
satisfy that contract).
I know others have implemented Dict objects; it would be fun to hear
from them.
Martin
Reading the articles mentioned in Tipps and Tricks didn't help me really.
Of course, I will welcome other corrections and improvements as well.
Working in R 2.7.0 under Windows.
Hans Werner
#-- Class and method definition for dictionaries
---
setClass(Dict,
representation (hash = environment),
prototype (hash = new.env(hash=T, parent = emptyenv()))
)
setMethod(show, signature(object=Dict),
definition = function(object) ls([EMAIL PROTECTED])
)
setGeneric(hclear, function(object) standardGeneric(hclear))
setMethod(hclear, signature(object=Dict),
function(object) rm(list=ls([EMAIL PROTECTED]), [EMAIL PROTECTED])
)
setGeneric(hput, function(object, key, value) standardGeneric(hput))
setMethod(hput, signature(object=Dict, key=character, value=ANY),
function(object, key, value) assign(key, value, [EMAIL PROTECTED])
)
setGeneric(hget, function(object, key, ...) standardGeneric(hget))
setMethod(hget, signature(object=Dict, key=character),
function(object, key) {
if (exists(key, [EMAIL PROTECTED], inherits = FALSE)) {
get(key, [EMAIL PROTECTED])
} else {
return(NULL)
}
}
)
# Some tests
D1 - new(Dict)
hput(D1, a, 1) # Same as: [EMAIL PROTECTED] - 1
hput(D1, b, 2)
hget(D1, a)
hget(D1, b)
show(D1)
D2 - new(Dict)
hput(D2, c, 3)
hput(D2, d, 4)
hget(D2, a) # Wrong: was defined only for D1
hget(D2, b)
show(D2)
hclear(D2) # Wrong: clears D1 too
show(D1)
#-
__
R-help@r-project.org 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.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
__
R-help@r-project.org 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.
Re: [R] How many random numbers needed?
On Sat, 2008-05-10 at 13:21 +0200, Birgit Lemcke wrote: Hello R-People! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Perhaps this is another stupid question of me, but I was wondering how I know the needed random (set.seed) numbers, when running randomForest (library randomForest) on a large dataset. The seed is just a starting point for the RNG. You can draw as many numbers as you like once the RNG has been seeded. The ability to set the seed allows repeated runs of functions like randomForest to provide the same results for each run. This is a basic requirement of reproducible research. require(randomForest) set.seed(1) mod1 - randomForest(Species ~ ., data = iris) mod2 - randomForest(Species ~ ., data = iris) set.seed(1) mod3 - randomForest(Species ~ ., data = iris) all.equal(mod1, mod2) all.equal(mod1, mod3) You could put whatever (within reason - up to limits of an integer in R) into the set.seed function, but the point is to provide the same number in the seed if you want to make sure your results are reproducible. HTH G Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008, 10.00 Uhr bis 02.00 Uhr Campus Irchel, Winterthurerstrasse 190, 8057 Zürich Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft __ R-help@r-project.org 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org 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.
Re: [R] Create pairwise table from columns?
On Fri, May 9, 2008 at 7:17 PM, knussear [EMAIL PROTECTED] wrote: Hi Group I have a large data set of individual pairwise values (250,000 rows) that I need to reshape into a pairwise matrix for mantel tests of these values versus genetic distances. the data are currently in columns formatted like so AnimalA, AnimalB, Score A1, A2, S1 A1, A3, S2 A1, A4, S3 A2, A3, S4 A2, A4, S5 A3, A4, S6 ...,, I need the final matrix to be formatted as A1A2A3A4 A1 0 S1S2S3 A2 S10 S4S5 A3 S2S4 0 S6 A4 S3S4 S6 0 One approach would be to use the reshape package (http://had.co.nz/reshape) - dfm - melt(mydf, id = c(AnimalA, AnimalB)) cast(dfm, AnimalA ~ AnimalB) Hadley -- http://had.co.nz/ __ R-help@r-project.org 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.
Re: [R] Hashes as S4 Classes, or: How to separate environments
On May 10, 2008, at 7:30 AM, Hans W Borchers wrote:
For learning purposes mainly I attempted to implement hashes/maps/
dictionaries
(Python lingua) as S4 classes, see the coding below. I came across
some rough S4
edges, but in the end it worked (for one dictionary).
When testing ones sees that the dictionaries D1 and D2 share their
environments
[EMAIL PROTECTED] and [EMAIL PROTECTED], though I thought a new and empty environment
would be
generated each time 'new(Dict)' is called.
QUESTION: How can I separate the environments [EMAIL PROTECTED] and [EMAIL
PROTECTED] ?
The problem you are encountering is that the prototype is only
created once. Because environments are passed by reference, [EMAIL PROTECTED]
and [EMAIL PROTECTED] are the exact same environment:
D1 - new(Dict)
D1
[EMAIL PROTECTED]
environment: 0x182ac870
D2 - new(Dict)
[EMAIL PROTECTED]
environment: 0x182ac870
You have assumed that setClass will be executed for each new
dictionary, or at least that the prototype(...) part of it would run
each time. Not wanting right now to dig into the internals of
setClass, my guess is that it only creates a prototype once, and then
just reuses it each time, with something like an assignment operator.
One solution, very similar to what Martin just suggested, is below. I
believe another solution might be to have the hash be a list
containing an environment, though I haven't tried that.
The solution is to create a constructor function, the function
newDict below:
setClass(Dict,
representation (hash = environment))
)
newDict - function() {
obj - new(Dict)
[EMAIL PROTECTED] - new.env(hash=T, parent = emptyenv())
obj
}
In practice, you would probably want newDict to accept an arguments,
which may be a list or another Dict object, and then use that as a
starting point for the new hash.
Here's a sample run:
# Some tests
D1 - newHash()
D2 - newHash()
[EMAIL PROTECTED]
environment: 0x1e80c98
[EMAIL PROTECTED]# Notice the different address
environment: 0x1e868fc
hput(D1, a, 1)
hget(D1, a)
[1] 1
show(D1)
[1] a
hput(D2, c, 3)
hget(D2, a) # Does the correct thing this time
NULL
hget(D2, c)
[1] 3
show(D2)
[1] c
hclear(D2)
show(D1)# Works properly now
[1] a
#-
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
Reading the articles mentioned in Tipps and Tricks didn't help me
really.
Of course, I will welcome other corrections and improvements as well.
Working in R 2.7.0 under Windows.
Hans Werner
#-- Class and method definition for dictionaries
---
setClass(Dict,
representation (hash = environment),
prototype (hash = new.env(hash=T, parent = emptyenv()))
)
setMethod(show, signature(object=Dict),
definition = function(object) ls([EMAIL PROTECTED])
)
setGeneric(hclear, function(object) standardGeneric(hclear))
setMethod(hclear, signature(object=Dict),
function(object) rm(list=ls([EMAIL PROTECTED]), [EMAIL PROTECTED])
)
setGeneric(hput, function(object, key, value) standardGeneric
(hput))
setMethod(hput, signature(object=Dict, key=character,
value=ANY),
function(object, key, value) assign(key, value, [EMAIL PROTECTED])
)
setGeneric(hget, function(object, key, ...) standardGeneric(hget))
setMethod(hget, signature(object=Dict, key=character),
function(object, key) {
if (exists(key, [EMAIL PROTECTED], inherits = FALSE)) {
get(key, [EMAIL PROTECTED])
} else {
return(NULL)
}
}
)
# Some tests
D1 - new(Dict)
hput(D1, a, 1) # Same as: [EMAIL PROTECTED] - 1
hput(D1, b, 2)
hget(D1, a)
hget(D1, b)
show(D1)
D2 - new(Dict)
hput(D2, c, 3)
hput(D2, d, 4)
hget(D2, a) # Wrong: was defined only for D1
hget(D2, b)
show(D2)
hclear(D2) # Wrong: clears D1 too
show(D1)
#-
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Re: [R] How many random numbers needed?
Thank you Gavin. I knew about the meaning set.seed for reproducability but I did not realise that it is only the starting point. Is it possible that very small or very big random numbers cause any kind of bias? B. Am 10.05.2008 um 14:50 schrieb Gavin Simpson: On Sat, 2008-05-10 at 13:21 +0200, Birgit Lemcke wrote: Hello R-People! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Perhaps this is another stupid question of me, but I was wondering how I know the needed random (set.seed) numbers, when running randomForest (library randomForest) on a large dataset. The seed is just a starting point for the RNG. You can draw as many numbers as you like once the RNG has been seeded. The ability to set the seed allows repeated runs of functions like randomForest to provide the same results for each run. This is a basic requirement of reproducible research. require(randomForest) set.seed(1) mod1 - randomForest(Species ~ ., data = iris) mod2 - randomForest(Species ~ ., data = iris) set.seed(1) mod3 - randomForest(Species ~ ., data = iris) all.equal(mod1, mod2) all.equal(mod1, mod3) You could put whatever (within reason - up to limits of an integer in R) into the set.seed function, but the point is to provide the same number in the seed if you want to make sure your results are reproducible. HTH G Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008, 10.00 Uhr bis 02.00 Uhr Campus Irchel, Winterthurerstrasse 190, 8057 Zürich Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft __ R-help@r-project.org 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008, 10.00 Uhr bis 02.00 Uhr Campus Irchel, Winterthurerstrasse 190, 8057 Zürich Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft __ R-help@r-project.org 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.
Re: [R] function in nls argument -- robust estimation
Dear Martin, Thanks for the ideas regarding the relation of what Fernando is doing with robust regression. Indeed, it's an important point that he can't consider the standard error estimates on his parameters correct. I know from discussion off-list that he's happy with the results he has now; nevertheless the robust regression route may be an interesting alternative. I'm posting a scipt to R-SIG-robust now that compares the 3 ways (nls, nlrob and nls.lm w/residuals above a certain quantile set to zero). best, Kate On Sat, 10 May 2008, Martin Maechler wrote: Hi Kate and Fernando, I'm late into this thread, but from reading it I get the impression that Fernando really wants to do *robust* (as opposed to least-squares) non-linear model fitting. His proposal to set residuals to zero when they are outside a given bound is a very special case of an M-estimator, namely (if I'm not mistaken) the so-called Huber skipped-mean, an M-estimator with psi-function psi - function(x, k) ifelse(abs(x) = k, x, 0) It is known that this can be far from optimal, and either using Huber-psi or a redescender such as Tukey's biweight can be considerably better. Also note that the standard inference (std.errors, P-values, ...) that you'd get from summary(nlsfit) or anova(nls1, nl2) is *invalid* here, since you are effectively using *random* weighting. The nlrob() function in package 'robustbase' implements M-estimation of nonlinear models directly. Unfortunately, how to do correct inference in this situation is a hard problem, probably even an open research question in parts. I would expect that the bootstrap should work if you only have a few outliers. I don't have time at the moment to look at the example data and the model, and show you how to use it for nlrob(); if you find a way to you it for nls() , then the same should work for nlrob(). I'm CCing this to the specialists for Robust Stats with R mailing list, R-SIG-robust. Best regards, Martin Maechler ETH Zurich KateM == Katharine Mullen [EMAIL PROTECTED] on Fri, 9 May 2008 15:50:08 +0200 (CEST) writes: KateM You can take minpack.lm_1.1-0 (source code and MS Windows build, KateM respectively) from here: KateM http://www.nat.vu.nl/~kate/minpack.lm_1.1-0.tar.gz KateM http://www.nat.vu.nl/~kate/minpack.lm_1.1-0.zip KateM The bug that occurs when nprint = 0 is fixed. Also fixed is another KateM problem suggested your example: when the argument par is a list, calling KateM summary on the output of nls.lm was not working. KateM I'll submit the new version to CRAN soon. KateM This disscusion has been fruitful - thanks for it. KateM On Fri, 9 May 2008, Katharine Mullen wrote: You indeed found a bug. I can reproduce it (which I should have tried to do on other examples in the first place!). Thanks for finding it. It will be fixed in version 1.1-0 which I will submit to CRAN soon. On Fri, 9 May 2008, elnano wrote: Find the data (data_nls.lm_moyano.txt) here: ftp://ftp.bgc-jena.mpg.de/pub/outgoing/fmoyano Katharine Mullen wrote: Thanks for the details - it sounds like a bug. You can either send me the data in an email off-list or make it available on-line somewhere, so that I and other people can download it. __ R-help@r-project.org 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. -- View this message in context: http://www.nabble.com/function-in-nls-argument-tp17108100p17146812.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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. KateM __ KateM R-help@r-project.org mailing list KateM https://stat.ethz.ch/mailman/listinfo/r-help KateM PLEASE do read the posting guide http://www.R-project.org/posting-guide.html KateM and provide commented, minimal, self-contained, reproducible code. __
Re: [R] Error while making R package
Vidhu Choudhary wrote: Hi All, *I am still facing the problems in making R package on windows. * -- Making package t1 adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runavg.o windres --preprocessor=gcc-sjlj -E -xc -DRC_INVOKED -I C:/R/R-2.6.2/include -i t1_res.rc -o t1_res. o gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o runavg.o t1_res.o -L C:/R/R-2.6.2/bin-lR ... DLL made installing DLL installing R files installing data files rm: failed to get attributes of `/': No such file or directory Do you have the recent Rtools and none else? Where is the package located and how do you invoke the install command? I have no further ideas. It works for me some lines further on but I do not have all 120 or so packages installed that are required (although I do have all CRAN and BioC packages for R-2.7.x for Windows installed). Uwe Ligges make[2]: *** [c:/R/R-2.6.2/library/t1/data] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-t1] Error 2 *** Installation of t1 failed *** Removing 'c:/R/R-2.6.2/library/t1' Restoring previous 'c:/R/R-2.6.2/library/t1' *I have made registry changes also as per the link : https://stat.ethz.ch/pipermail/r-devel/2008-January/048059.html * *I can successfully make the package on Linux. * But when I try to R CMD INSTALL on windows( package made in linux) I get the same error of rm: failed to get attributes of `/': No such file or directory make[2]: *** [c:/R/R-2.6.2/library/t1/data] Error 1 I am attaching the .tar file made on windows2000 Thank you Best Regards Vidhu __ R-help@r-project.org 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] Simple regex problem
I am cleaning up some character data to convert to dates using chron. The regex that I am using work fine but there should be a better way to do this. Can anyone suggest a cleaner bit of code than the gsub, sub approach? Thanks #Test Run on dates. xx - c(May 1, 2007, May 2, 2007, May 3, 2007, May 4, 2007, May 5, 2007, May 6, 2007, May 7, 2007, May 8, 2007, May 9, 2007, May 10, 2007, May 11, 2007, May 12, 2007) yy - gsub( +, /, xx) ; yy zz - sub(,, , yy) ; zz library(chron) ttdates - chron(zz, format = c(dates = mon/d/y)) __ R-help@r-project.org 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] [R-pkgs] AER: Applied Econometrics with R
The package AER accompanying the forthcoming book Applied Econometrics with R by Christian Kleiber and me in the Springer useR! series has (finally!) been released to CRAN: http://CRAN.R-project.org/package=AER It contains some new R functionality o tobit regression convenience interface (to survival) o instrumental variables regression (two-stage least squares) o (over-) dispersion test (via auxiliary regression) but the main feature are ~100 data sets taken from popular econometrics text books and the data archives of JAE (Journal of Applied Econometrics) and JBES (Journal of Business and Economic Statistics). Extensive examples are provided with the data sets, reproducing many of the analyses in the books/papers they were taken from. In particular, all data sets from the following books with many of the associated examples are provided: o Econometrics (Baltagi, 2002) o Econometric Analysis (Greene, 2003) o Introduction to Econometrics (Stock Watson, 2007) Until the book becomes available in autumn 2008, we will add vignettes to the package reproducing the examples from our book. Best wishes, Z ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org 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] Compact Indicator Matrices
An indicator matrix is a binary matrix with orthogonal columns whose rows sum to 1. A row of this matrix could be [0 1 0 0]. My problem is to group the similar rows (profiles) so that to create a compact form of the matrix. Is there an R function that deals with this problem or do I have to write it from scratch? Thanks, Angelos Markos Dr. Applied Informatics, University of Macedonia, Greece __ R-help@r-project.org 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] help needed with rbftrain
Hello everybody, I'm new to R. I'm trying to set up a Rbf network using the rbftrain function but I get an error I can't understand. this is what I type: rbftrain(input,3,output,visual=F) where input is a matrix with 198 rows and 6 columns and output is a matrix with 198 rows and one column. Both matrices are missing values free. This is what I get from R: Error in kmeans(inp[, i], neurons) : more cluster centers than distinct data points. I don't understand this. Moreover, I can actually train a rbf network with 2 neurons but not with 3 neurons. I'm sure I have far more than 3 distinct data point both in input and in output so I don't get the meaning. Can you please help me? Thank you so much everybody. Invernomuto -- View this message in context: http://www.nabble.com/help-needed-with-rbftrain-tp17161948p17161948.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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.
Re: [R] For Social Network Analysis-Graph Analysis - How to convert 2 mode data to 1 mode data?
Solomon, if i understand two-mode networks properly (they're bipartite, right?),
then this is not hard to do with igraph. Basically, for each vertex create an
order=2 neighborhood, and then create a graph from the adjacency list,
it is something like this:
two.to.one - function(g, keep) {
neis - neighborhood(g, order=2)
neis - lapply(seq(neis), function(x) neis[[x]][ neis[[x]] != x-1]) ## drop
self-loops
neis - lapply(neis, function(x) x[ x %in% keep ]) ## keep
only these
neis - lapply(seq(neis), function(x) t(cbind(x-1, neis[[x]]))) ## create
edge lists
neis[-keep-1] - NULL ## these
are not needed
neis - matrix(unlist(neis), byrow=TRUE, nc=2) ## a
single edge list
neis - neis[ neis[,1] neis[,2], ]## count
an edge once only
mode(neis) - character
g2 - graph.edgelist(neis, dir=FALSE)
V(g2)$id - V(g2)$name ## 'id'
is used in Pajek
g2
}
It does not check that the graph is indeed two-mode, and it keeps the
vertices given in the 'keep' argument. 'keep' is made of igraph vertex ids.
You can use it like this:
g - graph.ring(10)
keep - seq(0,8,by=2) ## we keep the 'even' vertices
g2 - two.to.one(g, keep)
write.graph(two.to.one(g, keep), format=pajek, file=/tmp/a.net)
I haven't tested it much. We'll have a better function in the next igraph
version.
Gabor
On Fri, May 09, 2008 at 03:37:05PM -0400, Messing, Solomon O. wrote:
Hi,
Does anyone know of a package in R that has a function to convert
network data (e.g. an adjacency matrix or ) from 2-mode to 1-mode? I am
conducting social network analysis. I know that Pajek has this function
under Net -- Transform -- 2-mode to 1-mode -- Rows. I have searched
the documentation under packages 'sna', 'network', 'igraph', and
'dynamicgraph' but I was not able to identify a comparable function.
I would just export my data to Pajek and import it to R, but I'm going
to have to generate hundreds of these graphs, so it would take quite a
bit of time to do it this way.
Thanks,
Solomon
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--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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Re: [R] Simple regex problem
On 10-May-08 16:49:20, John Kane wrote: I am cleaning up some character data to convert to dates using chron. The regex that I am using work fine but there should be a better way to do this. Can anyone suggest a cleaner bit of code than the gsub, sub approach? Thanks #Test Run on dates. xx - c(May 1, 2007, May 2, 2007, May 3, 2007, May 4, 2007, May 5, 2007, May 6, 2007, May 7, 2007, May 8, 2007, May 9, 2007, May 10, 2007, May 11, 2007, May 12, 2007) yy - gsub( +, /, xx) ; yy zz - sub(,, , yy) ; zz You can do it in one stroke with gsub(,*[ ]+, /, xx) [1] May/1/2007 May/2/2007 May/3/2007 May/4/2007 [5] May/5/2007 May/6/2007 May/7/2007 May/8/2007 [9] May/9/2007 May/10/2007 May/11/2007 May/12/2007 library(chron) ttdates - chron(zz, format = c(dates = mon/d/y)) Best wishes, Ted E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 10-May-08 Time: 18:14:33 -- XFMail -- __ R-help@r-project.org 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.
Re: [R] Simple regex problem
Try this (no gsub required): as.chron(as.Date(xx, %b %d, %Y)) On Sat, May 10, 2008 at 12:49 PM, John Kane [EMAIL PROTECTED] wrote: I am cleaning up some character data to convert to dates using chron. The regex that I am using work fine but there should be a better way to do this. Can anyone suggest a cleaner bit of code than the gsub, sub approach? Thanks #Test Run on dates. xx - c(May 1, 2007, May 2, 2007, May 3, 2007, May 4, 2007, May 5, 2007, May 6, 2007, May 7, 2007, May 8, 2007, May 9, 2007, May 10, 2007, May 11, 2007, May 12, 2007) yy - gsub( +, /, xx) ; yy zz - sub(,, , yy) ; zz library(chron) ttdates - chron(zz, format = c(dates = mon/d/y)) __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] Error while making R package
There isn't enough information there to really know but I would at least try this: - upgrade to R 2.7 - make sure you are using the most recent version of rtools from Duncan Murdoch's site - remove the data directory in your package since its the last thing referred to prior to the errors - if that still has a problem remove any vignettes too - if you still have a problem remove all non-R code On Thu, May 1, 2008 at 4:20 PM, Vidhu Choudhary [EMAIL PROTECTED] wrote: Hi All, I am trying to make R package using R 2.6.2 And I am getting following error. When I give R CMD check t1\ -- Making package t1 adding build stamp to DESCRIPTION making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runavg.o windres --preprocessor=gcc-sjlj -E -xc -DRC_INVOKED -I c:/R/R-2.6.2/include -i t1_res.rc -o t1_res.o gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o runavg.o t1_res.o -Lc:/R/R-2.6.2/bin-lR ... DLL made installing DLL installing R files installing data files rm: failed to get attributes of `/': No such file or directory make[2]: *** [C:/Vidhu/CGH/RPackage/t1.Rcheck/t1/data] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-t1] Error 2 *** Installation of t1 failed *** Can you please suggest what could be the probable cause of the error Thank you Vidhu __ R-help@r-project.org 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] Random number generation
Colleagues, I have encountered behavior of random number generation that eludes me. I generate a random integer in a particular range using the following code: sample(1000:, size=1) This code exists within a script that starts with the command: remove(list=ls()) Each time that I run the script, it yields the same random number: 6420. I thought that the problem might result from deleting the random seed. However, list=ls() does not include .RandomSeed. To my surprise, I can't replicate the problem with a 2-line script: remove(list-ls()) sample(1000:, size=1) Also, the same problem occurs if I use runif instead of sample. Thoughts? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com [[alternative HTML version deleted]] __ R-help@r-project.org 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] BiodiversityRGUI_problem2
After some investigation I found out that constrained ordination is working fine under R version 6.5.0 and 6.5.1 but not under any of newer versions. Is it posible to repair/make something in for example newest version of R 7.0 lito enble correct using of constrained ordination under BiodiversityRGUI environment? [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] substitute in graphics - Uwe's help desk
Thank to both of you. I found an interesting document by Uwe Ligges in Rnews December 2002 (Vol 2/3) The following seems encouraging x=seq(1,180,by=1) beta=10 eta=5 plot(x,log(x),type=p,xlab=x,ylab=h(x),main=substitute(Failure rate * eta==myeta * , * beta ,list(myeta=eta,mybeta=beta)) ) but then it fails : x=seq(1,180,by=1) beta=10 eta=5 plot(x,log(x),type=p,xlab=x,ylab=h(x),main=substitute(Failure rate from W( * eta==myeta * , * beta==mybeta , ) ,list(myeta=eta,mybeta=beta)) ) Any idea ? Thank you very much 2008/5/9 Henrique Dallazuanna [EMAIL PROTECTED]: Try this: plot(x, log(x), xlab = x, ylab = h(x), main = bquote(Failure~rate~from~W(eta == .(eta), beta == .(beta))) On Fri, May 9, 2008 at 11:31 AM, Gustave Lefou [EMAIL PROTECTED] wrote: Hello, I have to do a few graphics of the same function and this function is parametrized by two arguments. What I would like is to be able to change the value of these two arguments without changing the plot command. So as to copy paste. I tried the following : x=1:100 eta=10 beta=5 plot(x,h(x),xlab=x,ylab=h(x),main=substitute( expression( paste(Failure rate from,W(eta==myeta,beta==mybeta) ) ) ,list(myeta=eta,mybeta=beta) ) ) But it doesn't work. It's written expression ( Failure rate from W(eta=10,) ... on the plot with eta as a greek letter. Thank you very much ! [[alternative HTML version deleted]] __ R-help@r-project.org 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] Error while making R package
On 10/05/2008 4:54 PM, Duncan Murdoch wrote: On 09/05/2008 11:58 AM, Vidhu Choudhary wrote: rm: failed to get attributes of `/': No such file or directory I believe that's a sign of using a bad toolset. Make sure if you have Cygwin installed, it comes *after* the Rtools on your path. It contains some incompatible tools. No, sorry, I forgot: that's caused by a Cygwin uninstall bug. See this message: http://finzi.psych.upenn.edu/R/R-devel/archive/27028.html Duncan Murdoch __ R-help@r-project.org 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.
Re: [R] BiodiversityRGUI_problem2
Branimir, You would be better off addressing these issues with the package maintainer. See the details for the package on CRAN for example to find out the email address of the maintainer. You could always use vegan the old-fashioned way and type the relevant commands at the prompt. If your species data are in 'spp' and the constraints in env, then it can be little more than require(vegan) mod - cca(spp ~ ., data = env) ## for CCA or mod2 - rda(spp ~ ., data = env) ## for RDA Then see the helpfiles to see how to fit a model with a minimal set of constraints. G On Sat, 2008-05-10 at 20:09 +0200, Branimir Hackenberger wrote: After some investigation I found out that constrained ordination is working fine under R version 6.5.0 and 6.5.1 but not under any of newer versions. Is it posible to repair/make something in for example newest version of R 7.0 lito enble correct using of constrained ordination under BiodiversityRGUI environment? [[alternative HTML version deleted]] __ R-help@r-project.org 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org 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] subset rows in two dataframes
Dear list: I have two dataframes, say dat1 and dat2. Each has several variables but 3 of each are common in both, (say v1, v2 and v3). v1 and v2 are factores while v3 is numeric. Now, I need a subset to extract the rows in which v1, v2 and v3 are the same in both dataframes. I tried: subset(dat1, dat1$v1 %in% dat2$v1 dat1$v2 %in% dat2$v2 dat1$v3 %in% dat2$v3) I dont know why, but this is not working as I was expecting. Any suggestion to improve my code? Thanks in advance Justin -- [EMAIL PROTECTED] -- __ R-help@r-project.org 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.
Re: [R] subset rows in two dataframes
This seems to work for me: set.seed(1) df1 - data.frame(v1=factor(sample(1:4,20,TRUE)), v2=factor(sample(1:3,20,TRUE)), v3=sample(1:3,20,TRUE)) df2 - data.frame(v1=factor(sample(1:2,20,TRUE)), v2=factor(sample(1:2,20,TRUE)), v3=sample(1:2,20,TRUE)) subset(df1, (df1$v1 %in% df2$v1) (df1$v2 %in% df2$v2) (df1$v3 %in% df2$v3)) v1 v2 v3 2 2 1 2 5 1 1 2 11 1 2 2 14 2 1 1 Exactly what problems are you having? A sample of your actual data would be useful. On Sat, May 10, 2008 at 6:31 PM, [EMAIL PROTECTED] wrote: Dear list: I have two dataframes, say dat1 and dat2. Each has several variables but 3 of each are common in both, (say v1, v2 and v3). v1 and v2 are factores while v3 is numeric. Now, I need a subset to extract the rows in which v1, v2 and v3 are the same in both dataframes. I tried: subset(dat1, dat1$v1 %in% dat2$v1 dat1$v2 %in% dat2$v2 dat1$v3 %in% dat2$v3) I dont know why, but this is not working as I was expecting. Any suggestion to improve my code? Thanks in advance Justin -- [EMAIL PROTECTED] -- __ R-help@r-project.org 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org 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.
Re: [R] subset rows in two dataframes
Thanks for your reply. In fact I dont get none error message, I just simply found that some rows do not match in both dataframes. I thought it was some evident problem with my code, but it seems it is not. I'll try to check and if I can, I'll post a reproducible example. Justin On Sat, 10 May 2008 18:42:51 -0400, jim holtman [EMAIL PROTECTED] said: This seems to work for me: set.seed(1) df1 - data.frame(v1=factor(sample(1:4,20,TRUE)), v2=factor(sample(1:3,20,TRUE)), v3=sample(1:3,20,TRUE)) df2 - data.frame(v1=factor(sample(1:2,20,TRUE)), v2=factor(sample(1:2,20,TRUE)), v3=sample(1:2,20,TRUE)) subset(df1, (df1$v1 %in% df2$v1) (df1$v2 %in% df2$v2) (df1$v3 %in% df2$v3)) v1 v2 v3 2 2 1 2 5 1 1 2 11 1 2 2 14 2 1 1 Exactly what problems are you having? A sample of your actual data would be useful. On Sat, May 10, 2008 at 6:31 PM, [EMAIL PROTECTED] wrote: Dear list: I have two dataframes, say dat1 and dat2. Each has several variables but 3 of each are common in both, (say v1, v2 and v3). v1 and v2 are factores while v3 is numeric. Now, I need a subset to extract the rows in which v1, v2 and v3 are the same in both dataframes. I tried: subset(dat1, dat1$v1 %in% dat2$v1 dat1$v2 %in% dat2$v2 dat1$v3 %in% dat2$v3) I dont know why, but this is not working as I was expecting. Any suggestion to improve my code? Thanks in advance Justin -- [EMAIL PROTECTED] -- __ R-help@r-project.org 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- [EMAIL PROTECTED] -- __ R-help@r-project.org 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] predict lmer
The following function is designed to work with a logit link. It can
easily be generalized to work with any link. The SEs and CIs are
evaluated accounting for all sources of random variation. The plot
may not be much help unless there is just one explanatory variate.
`ciplot` -
function(obj=glmm2, data=data.site, xcol=2, nam=litter){
cilim - function(obj, xcol){
b - fixef(obj)
vcov - summary(obj)@vcov
X - unique(model.matrix(obj))
hat - X%*%b
pval - exp(hat)/(1+exp(hat)) # NB, designed for logit link
U - chol(as.matrix(summary(obj)@vcov))
se - sqrt(apply(X%*%t(U), 1, function(x)sum(x^2)))
list(hat=hat, se=se, x=X[,xcol])
}
limfo - cilim(obj, xcol)
hat - limfo$hat
se - limfo$se
x - limfo$x
upper - hat+2*se
lower - hat-2*se
ord - order(x)
plot(x, hat, yaxt=n, type=l, xlab=nam, ylab=)
rug(x)
lines(x[ord], lower[ord])
lines(x[ord], upper[ord])
ploc - c(0.01, 0.05, 0.1, 0.2, 0.5, 0.8, 0.9)
axis(2, at=log(ploc/(1-ploc)), labels=paste(ploc), las=2)
}
## Usage
glmm2 - lmer(rcr ~ litter + (1 | Farm), family=binomial,
data=data.site)
ciplot(obj=glmm2)
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
On 8 May 2008, at 8:00 PM, [EMAIL PROTECTED] wrote:
From: May, Roel [EMAIL PROTECTED]
Date: 8 May 2008 12:23:15 AM
To: r-help@r-project.org
Subject: [R] predict lmer
Hi,
I am using lmer to analyze habitat selection in wolverines using the
following model:
(me.fit.of -
lmer(USED~1+STEP+ALT+ALT2+relM+relM:ALT+(1|ID)+(1|
ID:TRKPT2),data=vdata,
control=list(usePQL=TRUE),family=poisson,method=Laplace))
Here, the habitat selection is calaculated using a so-called discrete
choice model where each used location has a certain number of
alternatives which the animal could have chosen. These sets of
locations
are captured using the TRKPT2 random grouping. However, these sets are
also clustered over the different individuals (ID). USED is my binary
dependent variable which is 1 for used locations and zero for unused
locations. The other are my predictors.
I would like to predict the model fit at different values of the
predictors, but does anyone know whether it is possible to do this? I
have looked around at the R-sites and in help but it seems that there
doesn't exist a predict function for lmer???
I hope someone can help me with this; point me to the right
functions or
tell me to just forget it
Thanks in advance!
Cheers Roel
Roel May
Norwegian Institute for Nature Research
Tungasletta 2, NO-7089 Trondheim, Norway
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[R] Creating data.frames dynamically
I have time series data in named vectors. They are all the same length for
the same dates.
The dates are in a separate vector.
I want to create a vector of numeric data for every named series, associated
with the dates in a data.frame.
So if...
Names - c(a, b, c)
d - data.frame(dates=Dates, a=vector(mode=numeric, length=length(Dates),
b=vector(mode=numeric, length=length(Dates), c=vector(mode=numeric,
length=length(Dates))
Then I copy the processed data into d
for(i in SomeVectorOfFactors){
for(N in Names){
d[[N]][i] - FunctionCallOfSomeSort(i)
}
}
I want to create the data.frame, d, in the same style I access it.
d - data.frame(dates=Dates, [[Names]]=vectors(.))
Then it is much simpler to add new columns.
Worik ST
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