Re: [Rd] requesting a new SIG mailing list
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/02/12 17:30, Mauricio Zambrano-Bigiarini wrote: Dear R developers, Due to the increasing use R in hydrology and other close-related environmental sciences, I would like to ask if it would be possible to create a new Special Interest Group mailing list, called 'R-sig-hydro', specially devoted those topics. If possible to do so, I'd offer myself to maintain such mailing list (if needed). I think it would be more useful to use the R-sig-geo for that, as hydrology (please correct me if I am wrong - I am not an expert in hydrology) is mainly spatial. A fragmentation of the lists would need to duplicate effort by members. Cheers, Rainer Thanks in advance, Mauricio Zambrano-Bigiarini - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk86HRQACgkQoYgNqgF2egp1pwCfXrUJEBhQ8+50iwv7iYEZXa1C 7l4Anj9EmGCL3QE61VGZ/bw+/3r8n5b4 =bVRp -END PGP SIGNATURE- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] requesting a new SIG mailing list
On 14/02/12 09:36, Rainer M Krug wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/02/12 17:30, Mauricio Zambrano-Bigiarini wrote: Dear R developers, Due to the increasing use R in hydrology and other close-related environmental sciences, I would like to ask if it would be possible to create a new Special Interest Group mailing list, called 'R-sig-hydro', specially devoted those topics. If possible to do so, I'd offer myself to maintain such mailing list (if needed). I think it would be more useful to use the R-sig-geo for that, as hydrology (please correct me if I am wrong - I am not an expert in hydrology) is mainly spatial. A fragmentation of the lists would need to duplicate effort by members. I don't want to duplicate efforts, but I'm not sure about R-sig-geo as the right mailing list for hydrology and close-related environmental sciences. It is true that hydrology has much to do with spatial analysis (interpolation techniques, use of satellite images as input for hydrological models, mapping, etc), but it has also a strong link to time series analysis (trend detection, stationary and non-stationary water quantity and quality modelling, climate change modelling, and a long etc), and probably the latter topics would be considered off-topic in the R-sig-geo Another possibility could be to use the R-sig-ecology, which seems to be more related to hydrology: analytical techniques and topics that are appropriate for discussion on R-sig-ecology are quite broad. For examples of what might be appropriate for discussion on this list, please see the Environmentrics Task View (http://cran.r-project.org/web/views/Environmetrics.html) (taken from: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology) However, I did a quick search on the archives of 'R-sig-ecology' for the year 2011, and I could only found one single mail related to hydrology: https://stat.ethz.ch/pipermail/r-sig-ecology/2011-July/002274.html (in the same search I couldn't find any single reference to hydrology in the R-sig-geo during the year 2011) I think the lack of posts related to hydrological sciences in dedicated R-sig-xxx mailing lists is not due to a lack of interest (in the same period I got several questions regarding the hydroTSM and hydroGOF packages), but they may be due to the fact that r-sig-geo or r-sig-ecology are not very intuitive for hydrologists So, if you think that creating a new mailing list only for hydrology and related sciences could lead to fragmentation of the community and a duplication of efforts, we could start using the 'R-sig-ecology' mailing list. Cheers, Mauricio Zambrano-Bigiarini -- === FLOODS Action Water Resources Unit (H01) Institute for Environment and Sustainability (IES) European Commission, Joint Research Centre (JRC) TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), Italy webinfo: http://floods.jrc.ec.europa.eu/ === DISCLAIMER: The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission. === Linux user #454569 -- Ubuntu user #17469 === The greatest inspiration is often born of desperation. (Comer Cotrell) Cheers, Rainer Thanks in advance, Mauricio Zambrano-Bigiarini - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk86HRQACgkQoYgNqgF2egp1pwCfXrUJEBhQ8+50iwv7iYEZXa1C 7l4Anj9EmGCL3QE61VGZ/bw+/3r8n5b4 =bVRp -END PGP SIGNATURE- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] method using several (and different) arguments in turn
Dear R-developers community, I have the following generic:
setGeneric(
name=newsample,
def=function(x,y,z,a,b,c,...){standardGeneric(newsample)}
And I can build several methods for this generic. One useful thing is to use
newsample
with only one of the 6 arguments listed. At the moment this is what I do:
setMethod(
f=newsample,
signature=c(missing,missing,numeric,missing,missing,missing),
function(x,y,z,a,b,c,...)
{
..
..
}
)
This would be used when the single argument is z:
newsample(z=12.5)
To use newsample with another argument (say x) I should implement the same as
before,
but with signature
c(numeric,missing,missing,missing,missing,missing).
Is there another shorter and easier way to do this?
J
--
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Re: [Rd] requesting a new SIG mailing list
Have you asked the maintainers of those lists? Or the person who would have to do the work to set the list up (Martin Maechler, who is currently on vacation, or colleagues at ETHZ)? My suspicion is that there would be too little traffic to make a separate list worthwhile to administer. (You might feel so too: list administrators end up dealing with a lot of nuisance traffic.) On 14/02/2012 16:31, Mauricio Zambrano-Bigiarini wrote: On 14/02/12 09:36, Rainer M Krug wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/02/12 17:30, Mauricio Zambrano-Bigiarini wrote: Dear R developers, Due to the increasing use R in hydrology and other close-related environmental sciences, I would like to ask if it would be possible to create a new Special Interest Group mailing list, called 'R-sig-hydro', specially devoted those topics. If possible to do so, I'd offer myself to maintain such mailing list (if needed). I think it would be more useful to use the R-sig-geo for that, as hydrology (please correct me if I am wrong - I am not an expert in hydrology) is mainly spatial. A fragmentation of the lists would need to duplicate effort by members. I don't want to duplicate efforts, but I'm not sure about R-sig-geo as the right mailing list for hydrology and close-related environmental sciences. It is true that hydrology has much to do with spatial analysis (interpolation techniques, use of satellite images as input for hydrological models, mapping, etc), but it has also a strong link to time series analysis (trend detection, stationary and non-stationary water quantity and quality modelling, climate change modelling, and a long etc), and probably the latter topics would be considered off-topic in the R-sig-geo Another possibility could be to use the R-sig-ecology, which seems to be more related to hydrology: analytical techniques and topics that are appropriate for discussion on R-sig-ecology are quite broad. For examples of what might be appropriate for discussion on this list, please see the Environmentrics Task View (http://cran.r-project.org/web/views/Environmetrics.html) (taken from: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology) However, I did a quick search on the archives of 'R-sig-ecology' for the year 2011, and I could only found one single mail related to hydrology: https://stat.ethz.ch/pipermail/r-sig-ecology/2011-July/002274.html (in the same search I couldn't find any single reference to hydrology in the R-sig-geo during the year 2011) I think the lack of posts related to hydrological sciences in dedicated R-sig-xxx mailing lists is not due to a lack of interest (in the same period I got several questions regarding the hydroTSM and hydroGOF packages), but they may be due to the fact that r-sig-geo or r-sig-ecology are not very intuitive for hydrologists So, if you think that creating a new mailing list only for hydrology and related sciences could lead to fragmentation of the community and a duplication of efforts, we could start using the 'R-sig-ecology' mailing list. Cheers, Mauricio Zambrano-Bigiarini -- Brian D. Ripley, rip...@stats.ox.ac.uk 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-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] method using several (and different) arguments in turn
On 02/14/2012 08:43 AM, james.fo...@diamond.ac.uk wrote:
Dear R-developers community, I have the following generic:
setGeneric(
name=newsample,
def=function(x,y,z,a,b,c,...){standardGeneric(newsample)}
And I can build several methods for this generic. One useful thing is to use
newsample
with only one of the 6 arguments listed. At the moment this is what I do:
setMethod(
f=newsample,
signature=c(missing,missing,numeric,missing,missing,missing),
function(x,y,z,a,b,c,...)
{
..
..
}
)
This would be used when the single argument is z:
newsample(z=12.5)
To use newsample with another argument (say x) I should implement the same as
before,
but with signature
c(numeric,missing,missing,missing,missing,missing).
Is there another shorter and easier way to do this?
Hi James --
A matter of opinion, but multiple dispatch like this can be very
complicated, e.g., figuring out the 'next' method when dispatching on
two or more arguments; I'd really discourage it.
A different approach, assuming that x, y, z, ... are all numeric() but
that the sample to be drawn differs, is to define a small class
hierarchy to be used for dispatch.
setClass(TypeOfSample)
setClass(XSample, contains=TypeOfSample)
XSample - new(XSample) ## a 'singleton', used for dispatch
setClass(YSample, contains=TypeOfSample)
YSample - new(YSample)
and then
setGeneric(newsample,
function(type, x=numeric(), ...) standardGeneric(newsample),
signature=type)
setMethod(newsample, XSample, function(type, x=numeric(), ...) {
XSample
})
setMethod(newsample, YSample, function(type, x=numeric(), ...) {
YSample
})
One could implement a default method on TypeOfSample, and use
callNextMethod() after initial transformation, if that were the pattern.
To use:
newsample(XSample, x=1:100)
Martin
J
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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Re: [Rd] requesting a new SIG mailing list
On 14/02/12 17:45, Prof Brian Ripley wrote: Have you asked the maintainers of those lists? Or the person who would have to do the work to set the list up (Martin Maechler, who is currently on vacation, or colleagues at ETHZ)? No, I haven't done yet, but I'll do it, to know which list is the right one for hydrology. My suspicion is that there would be too little traffic to make a separate list worthwhile to administer. (You might feel so too: list administrators end up dealing with a lot of nuisance traffic.) Probably you are right, and it is worth to wait until the traffic in some of those lists be enough to justify a different mailing list. Thank you very much for your feedback prof. Ripley. All the best, Mauricio Zambrano-Bigiarini -- === FLOODS Action Water Resources Unit (H01) Institute for Environment and Sustainability (IES) European Commission, Joint Research Centre (JRC) TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), Italy webinfo: http://floods.jrc.ec.europa.eu/ === DISCLAIMER: The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission. === Linux user #454569 -- Ubuntu user #17469 === On 14/02/2012 16:31, Mauricio Zambrano-Bigiarini wrote: On 14/02/12 09:36, Rainer M Krug wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/02/12 17:30, Mauricio Zambrano-Bigiarini wrote: Dear R developers, Due to the increasing use R in hydrology and other close-related environmental sciences, I would like to ask if it would be possible to create a new Special Interest Group mailing list, called 'R-sig-hydro', specially devoted those topics. If possible to do so, I'd offer myself to maintain such mailing list (if needed). I think it would be more useful to use the R-sig-geo for that, as hydrology (please correct me if I am wrong - I am not an expert in hydrology) is mainly spatial. A fragmentation of the lists would need to duplicate effort by members. I don't want to duplicate efforts, but I'm not sure about R-sig-geo as the right mailing list for hydrology and close-related environmental sciences. It is true that hydrology has much to do with spatial analysis (interpolation techniques, use of satellite images as input for hydrological models, mapping, etc), but it has also a strong link to time series analysis (trend detection, stationary and non-stationary water quantity and quality modelling, climate change modelling, and a long etc), and probably the latter topics would be considered off-topic in the R-sig-geo Another possibility could be to use the R-sig-ecology, which seems to be more related to hydrology: analytical techniques and topics that are appropriate for discussion on R-sig-ecology are quite broad. For examples of what might be appropriate for discussion on this list, please see the Environmentrics Task View (http://cran.r-project.org/web/views/Environmetrics.html) (taken from: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology) However, I did a quick search on the archives of 'R-sig-ecology' for the year 2011, and I could only found one single mail related to hydrology: https://stat.ethz.ch/pipermail/r-sig-ecology/2011-July/002274.html (in the same search I couldn't find any single reference to hydrology in the R-sig-geo during the year 2011) I think the lack of posts related to hydrological sciences in dedicated R-sig-xxx mailing lists is not due to a lack of interest (in the same period I got several questions regarding the hydroTSM and hydroGOF packages), but they may be due to the fact that r-sig-geo or r-sig-ecology are not very intuitive for hydrologists So, if you think that creating a new mailing list only for hydrology and related sciences could lead to fragmentation of the community and a duplication of efforts, we could start using the 'R-sig-ecology' mailing list. Cheers, Mauricio Zambrano-Bigiarini The greatest inspiration is often born of desperation. (Comer Cotrell) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] requesting a new SIG mailing list
Hello, I'm one of the maintainers of the r-sig-ecology list, and I think it would be entirely appropriate to include hydrology within the scope of the list. There hasn't been much hydrologic discussion, as you noted, but not because we wish to exclude it. Sarah On Tue, Feb 14, 2012 at 11:31 AM, Mauricio Zambrano-Bigiarini mauricio.zambr...@jrc.ec.europa.eu wrote: Another possibility could be to use the R-sig-ecology, which seems to be more related to hydrology: analytical techniques and topics that are appropriate for discussion on R-sig-ecology are quite broad. For examples of what might be appropriate for discussion on this list, please see the Environmentrics Task View (http://cran.r-project.org/web/views/Environmetrics.html) (taken from: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology) However, I did a quick search on the archives of 'R-sig-ecology' for the year 2011, and I could only found one single mail related to hydrology: https://stat.ethz.ch/pipermail/r-sig-ecology/2011-July/002274.html (in the same search I couldn't find any single reference to hydrology in the R-sig-geo during the year 2011) -- Sarah Goslee http://www.functionaldiversity.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] method using several (and different) arguments in turn
Dear Martin,
I could not entirely follow your suggestion.
I can see how you define two classes inheriting from TypeOfSample, and how
these two
classes have two associated methods (incidentally, I'm unfamiliar with the:
function(type,x=numeric(),...)to do.
J
expression. What is type?
But then I'm lost. I wouldn't know how to carry on from here.
I don't know if I have explained the key point clear enough before. For the
person using
newsample it makes sense which name (x or y or z, etc) is used.
newsample(x=12.4) would
give something different from newsample(y=12.4); and yet another result would
be obtained if
using a combination, like newsample(x=12.4,y=12.4).
I wanted to use a simple function with default values at first, but I'm in the
middle of developing
a package using S4 formalism. I'm not sure this would be a wise thing
Sent: 14 February 2012 17:00
To: Foadi, James (Imperial Coll.,RAL,DIA)
Cc: r-devel@r-project.org
Subject: Re: [Rd] method using several (and different) arguments in turn
On 02/14/2012 08:43 AM, james.fo...@diamond.ac.uk wrote:
Dear R-developers community, I have the following generic:
setGeneric(
name=newsample,
def=function(x,y,z,a,b,c,...){standardGeneric(newsample)}
And I can build several methods for this generic. One useful thing is to use
newsample
with only one of the 6 arguments listed. At the moment this is what I do:
setMethod(
f=newsample,
signature=c(missing,missing,numeric,missing,missing,missing),
function(x,y,z,a,b,c,...)
{
..
..
}
)
This would be used when the single argument is z:
newsample(z=12.5)
To use newsample with another argument (say x) I should implement the same as
before,
but with signature
c(numeric,missing,missing,missing,missing,missing).
Is there another shorter and easier way to do this?
Hi James --
A matter of opinion, but multiple dispatch like this can be very
complicated, e.g., figuring out the 'next' method when dispatching on
two or more arguments; I'd really discourage it.
A different approach, assuming that x, y, z, ... are all numeric() but
that the sample to be drawn differs, is to define a small class
hierarchy to be used for dispatch.
setClass(TypeOfSample)
setClass(XSample, contains=TypeOfSample)
XSample - new(XSample) ## a 'singleton', used for dispatch
setClass(YSample, contains=TypeOfSample)
YSample - new(YSample)
and then
setGeneric(newsample,
function(type, x=numeric(), ...) standardGeneric(newsample),
signature=type)
setMethod(newsample, XSample, function(type, x=numeric(), ...) {
XSample
})
setMethod(newsample, YSample, function(type, x=numeric(), ...) {
YSample
})
One could implement a default method on TypeOfSample, and use
callNextMethod() after initial transformation, if that were the pattern.
To use:
newsample(XSample, x=1:100)
Martin
J
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
--
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Re: [Rd] Task views
A couple of (lengthier!) suggestions: topic-area resources or task-oriented resources Ravi From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Patrick Burns [pbu...@pburns.seanet.com] Sent: Monday, February 13, 2012 4:32 AM To: Barry Rowlingson Cc: Hans W Borchers; r-devel Subject: Re: [Rd] Task views I feel compelled to rebuff Barry's attack on the word Task Views. I think it is a fine description (I was not involved in originating it), though of course I'd be open to better suggestions. Look at all these things you can do with R is also nice but lacks a certain amount of brevity. Pat On 12/02/2012 10:43, Barry Rowlingson wrote: On Sat, Feb 11, 2012 at 5:55 PM, Patrick Burnspbu...@pburns.seanet.com wrote: Now it could be that people are not trying very hard to solve their own problems, but to be fair it is a pretty gruelling process to find the Task Views. May I suggest that there be a Task Views item on the left sidebar of the R website in the Documentation section? I'd go further, and suggest that the list of Task Views appears on the home page of www.r-project.org under the heading Look at all these things you can do with R. (Maybe to replace the 8 year old clustering graphic (or maybe someone could do something in ggplot2 that looks nice n shiny?) ) Task Views (stupid name, who's idea was that?) are an absolute GEM and shouldn't be slotted between 'What's New?' and Search on CRAN mirror sites. The CRAN Task Views page doesn't even say what Task Views are. Here's some text that might help: Task Views are short documents outlining the functionality of R in a given field or methodology. Since most of R's power comes from add-on packages downloaded from CRAN, Task Views tend to concentrate on summarising the packages that are relevant. If you ever find yourself thinking 'how do I do X in R?' then the list of Task Views should be your first stop. Barry -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] read.spss issues
Someone supplied me with a small SPSS datafile that caused a buffer overflow and then a crash when reading it in R. It seems like a pretty serious issue to me. Unfortunately I can't supply the dataset at hand and I have a hard time reproducing it with a toy example. But I found at least 2 issues that might be related. The first one is that when the spss dataset has a 'string' variable that is longer than 200 characters, it generates a bunch of warnings and then additional variables in the dataset. E.g: library(foreign) x - read.spss(http://www.stat.ucla.edu/~jeroen/spss/longstring.sav;); str(x); The second problem is that the spss dataformat allows to specify 'duplicate labels', whereas this is not allowed for factors. read.spss does not deal with this and creates a bad factor x - read.spss(http://www.stat.ucla.edu/~jeroen/spss/duplicate_labels.sav;, use.value.labels=T); levels(x$opinion); which causes issues downstream. I am not sure if this is an issue in read.spss() or as.factor(), but I guess it might be wise to try to detect duplicate levels and assign them all with one and the same integer value when converting to a factor. Thank you, Jeroen __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
