Re: [R] several plots on several pages - bug in par(mfg())?
Greg Snow wrote: Oops, I read further down in your original post and see that you already knew about par(mfg=c(2,1)). To get it to advance to page 2 for the 4th plot try calling plot.new() which should move you to the next page, then doing par(mfg=c(1,1)) should cause the next graph to be at the top. Hope this helps, Thanks - I found plot.new() and it is working. But: If the first plot command fails, par(mfg=c(2,1)) does NOT move to the second one - if you try the code below, you will see. Is this a bug or am I doing something wrong? ## Set layout to three rows and only oine column par( mfcol=c(3,1), oma=c(0,0,0,0), mar=c(4, 4, 2, 2) ) ## First row par(mfg=c(1,1)) try( plot(runif(ff)) ) ## plot fails due to something. ## Second row par(mfg=c(2,1)) try( plot(runif(100)) ) ##actually is plotted in first row ## Third row par(mfg=c(3,1)) plot(runif(1000)) ## plotted in third row -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Plant Conservation Unit Department of Botany University of Cape Town Rondebosch 7701 South Africa Tel:+27 - (0)21 650 5776 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] several plots on several pages
Hi
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
I want to create a pdf withe three graphs on a page and with two pages:
-
| 1 |
-
| 2 |
-
| 3 |
-
NEW PAGE
-
| 4 |
-
| 5 |
-
| 6 |
-
Graph 1 should ALWAYS be at that spot, graph two also, even if graph one
produces an error when plotting (the area can be empty, but doesn't have
to.)
I produced the foolowing code below, but I have a few problems:
1) how can I create a new page in the pdf?
2) how can I make sure that the second graph is in position 2 when graph
one produces an error when plotting I(as in the example)? Everything
works OK (for the firsat page) when graph one is plotted.
I have the feeling, that I am thinking to complicated.
Any help welcome,
Rainer
pdf(test.pdf)
try(
{
## Set layout to three rows and only oine column
par( mfcol=c(3,1), oma=c(0,0,0,0), mar=c(4, 4, 2, 2) )
## First row
par(mfg=c(1,1))
try( plot(runif(ff)) )
## Second row
par(mfg=c(2,1))
try( plot(runif(100)) )
## Third row
par(mfg=c(3,1))
plot(runif(1000))
## THE NEXT THREE SHOULD BE ON A NEW PAGE IN THE PDF
## Set layout to three rows and only oine column
par( mfcol=c(3,1), oma=c(0,0,0,0), mar=c(4, 4, 2, 2) )
## First row
par(mfg=c(1,1))
try( plot(runif(ff)) )
## Second row
par(mfg=c(2,1))
try( plot(runif(100)) )
## Third row
par(mfg=c(3,1))
plot(runif(1000))
}
)
dev.off()
--
NEW EMAIL ADDRESS AND ADDRESS:
[EMAIL PROTECTED]
[EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Plant Conservation Unit
Department of Botany
University of Cape Town
Rondebosch 7701
South Africa
Tel:+27 - (0)21 650 5776 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 650 2440 (w)
Cell: +27 - (0)83 9479 042
Skype: RMkrug
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] several plots on several pages
Hi Thierry
ONKELINX, Thierry wrote:
Dear Rainer,
Have you considered using Sweave?
No - and I am sure it will do what I want, but I guess it might be an
overkill. These arew just draft outputs for myself for different
datasets which should be easy to compare. SO I guess that Sweave might
be an overkill (especially as I found plot.new() which jumpd to a new page).
Thanks and I will keep it in mind for the future,
Rainer
HTH,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[EMAIL PROTECTED]
www.inbo.be
Do not put your faith in what statistics say until you have carefully
considered what they do not say. ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens Rainer M. Krug
Verzonden: donderdag 16 augustus 2007 14:58
Aan: r-help
Onderwerp: [R] several plots on several pages
Hi
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
I want to create a pdf withe three graphs on a page and with
two pages:
-
| 1 |
-
| 2 |
-
| 3 |
-
NEW PAGE
-
| 4 |
-
| 5 |
-
| 6 |
-
Graph 1 should ALWAYS be at that spot, graph two also, even
if graph one produces an error when plotting (the area can be
empty, but doesn't have
to.)
I produced the foolowing code below, but I have a few problems:
1) how can I create a new page in the pdf?
2) how can I make sure that the second graph is in position 2
when graph one produces an error when plotting I(as in the
example)? Everything works OK (for the firsat page) when
graph one is plotted.
I have the feeling, that I am thinking to complicated.
Any help welcome,
Rainer
pdf(test.pdf)
try(
{
## Set layout to three rows and only oine column
par( mfcol=c(3,1), oma=c(0,0,0,0), mar=c(4, 4, 2, 2) )
## First row
par(mfg=c(1,1))
try( plot(runif(ff)) )
## Second row
par(mfg=c(2,1))
try( plot(runif(100)) )
## Third row
par(mfg=c(3,1))
plot(runif(1000))
## THE NEXT THREE SHOULD BE ON A NEW PAGE IN THE PDF
## Set layout to three rows and only oine column
par( mfcol=c(3,1), oma=c(0,0,0,0), mar=c(4, 4, 2, 2) )
## First row
par(mfg=c(1,1))
try( plot(runif(ff)) )
## Second row
par(mfg=c(2,1))
try( plot(runif(100)) )
## Third row
par(mfg=c(3,1))
plot(runif(1000))
}
)
dev.off()
--
NEW EMAIL ADDRESS AND ADDRESS:
[EMAIL PROTECTED]
[EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Plant Conservation Unit
Department of Botany
University of Cape Town
Rondebosch 7701
South Africa
Tel: +27 - (0)21 650 5776 (w)
Fax: +27 - (0)86 516 2782
Fax: +27 - (0)21 650 2440 (w)
Cell:+27 - (0)83 9479 042
Skype: RMkrug
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
NEW EMAIL ADDRESS AND ADDRESS:
[EMAIL PROTECTED]
[EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Plant Conservation Unit
Department of Botany
University of Cape Town
Rondebosch 7701
South Africa
Tel:+27 - (0)21 650 5776 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 650 2440 (w)
Cell: +27 - (0)83 9479 042
Skype: RMkrug
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generating vetor (shapefiles) from AscGrid raster in R
What about using grass 6, combined with spgrass6 and the command r.to.vect? Rainer Milton Cezar Ribeiro wrote: Hi there, I need to convert a raster (ascGrid) format to Shape files. Is there a way of to do that on R? Kind regards miltinho http://yahoo.com.br/oqueeuganhocomisso [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] make sample() faster
Hi I have a simulation which is relatively slow. I used Rprofile() and identified the calls to sample() as the culprit is sample(): summaryRprof(Documents/PostDoc/Aloe_Pillansii/R/create.out) $by.self self.time self.pct total.time total.pct sample 1.30 44.2 1.52 51.7 ifelse 0.46 15.6 2.44 83.0 . . . I am using sample() as follow: result - sample( x=d.growth.seedling$growth, size=1, prob=d.growth.seedling$p, replace ) d.growth.seedling$p and d.growth.seedling$growth have a length of 1024 and are calculated initially by using density(). My question: is there any way to make this faster, i.e. replace sample() as I use it with another faster algorithm (if necessary implemented in C)? Thanks in advance, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] make sample() faster
Thanks for the info - so the solution would (likely) be to draw several samples and use these whenever I need a new one. tHANKS, i'LL TRY IT OUT, rAINER P.S: somebody said once that the caps-lock key is the most useless key on the keyboard and he is right... Prof Brian Ripley wrote: I think the problem is not sample (which is written in C), but that you are calling it with size=1. Taking one sample with probabilities from a large discrete distribution is necessarily slow, but you can take a large sample for little more cost. On Thu, 14 Jun 2007, Rainer M. Krug wrote: Hi I have a simulation which is relatively slow. I used Rprofile() and identified the calls to sample() as the culprit is sample(): summaryRprof(Documents/PostDoc/Aloe_Pillansii/R/create.out) $by.self self.time self.pct total.time total.pct sample 1.30 44.2 1.52 51.7 ifelse 0.46 15.6 2.44 83.0 . . . I am using sample() as follow: result - sample( x=d.growth.seedling$growth, size=1, prob=d.growth.seedling$p, replace ) d.growth.seedling$p and d.growth.seedling$growth have a length of 1024 and are calculated initially by using density(). My question: is there any way to make this faster, i.e. replace sample() as I use it with another faster algorithm (if necessary implemented in C)? Thanks in advance, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Where to find nprq?
roger koenker wrote: It has been folded into my quantreg package. Thanks a lot - it is working now Rainer url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On May 28, 2007, at 4:32 AM, Rainer M. Krug wrote: Hi I am trying to install the package pheno, but it needs the package nprq by Roger Koenker et al. which I can I find this package? It does not seem to be on CRAN and googling also doesn't give me an URL - is it still somewhere available? Thanks, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell:+27 - (0)83 9479 042 Skype:RMkrug email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Where to find nprq?
Hi I am trying to install the package pheno, but it needs the package nprq by Roger Koenker et al. which I can I find this package? It does not seem to be on CRAN and googling also doesn't give me an URL - is it still somewhere available? Thanks, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question concerning pastecs package
Dear Philippe Thanks a lot for your information - it is extremely usefull Rainer Philippe Grosjean wrote: Hello, I already answered privately to your question. No, there is no translation of pastecs.pdf. The English documentation is accessible, as usual, by: ?turnpoints Regarding your specific question, 'info' is the quantity of information I associated with the turning points: I = -log2 P(t) where P is the probability to observe a turning point at time t under the null hypothesis that the time series is purely random, and thus, the distribution of turning points follows a normal distribution with: E(p) = 2/3*(n-2) var(p) = (16*n - 29)/90 with p, the number of observed turning points and n the number of observations. Ibanez (1982, in French, sorry... not my fault!) demonstrated that P(t) is: P(t) = 2*(1/n(t-1)! * (n-1)!) As you can easily imagine, from this point on, it is straightforward to construct a test to determine if the series is random (regarding the distribution of the turning points), more or less monotonic (more or less turning points than expected), See also the ref cited in the online help (Kendall 1976). References: --- Ibanez, F., 1982. Sur une nouvelle application de la théorie de l'information à la description des séries chronologiques planctoniques. J. Exp. Mar. Biol. Ecol., 4:619-632 Kendall, M.G., 1976. Time-series, 2nd ed. Charles Griffin Co, London Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Rainer M. Krug wrote: Hi I just installed the pastecs package and I am wondering: is there an english (or german) translation of the file pastecs.pdf? If not, is there an explanation somewhere of the object of type 'turnpoints' as a result of turnpoints(), especially the info field? Thanks, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question concerning pastecs package
Hi I just installed the pastecs package and I am wondering: is there an english (or german) translation of the file pastecs.pdf? If not, is there an explanation somewhere of the object of type 'turnpoints' as a result of turnpoints(), especially the info field? Thanks, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Identifying last record in individual growth data over different time intervalls
Hi
I have a plist t which contains size measurements of individual plants,
identified by the field plate. It contains, among other, a field
year indicating the year in which the individual was measured and the
height. The number of measurements range from 1 to 4 measurements in
different years.
My problem is that I would need the LAST measurement. I only came up
with the solution below which is probably way to complicated, but I
can't think of another solution.
Does anybody has an idea how to do this more effectively?
Finally I would like to have a data.frame t2 which only contains the
entries of the last measurements.
Thanks in advance,
Rainer
unlist(
sapply(
split(t, t$plate),
function(i)
{
i[i$year==max(i$year),]$id
}
)
)
15 20 33 43 44 47 64 D72S200
S201
2006001 2006003 2006005 2006007 2006008 2006009 2006014 2006015 2006016
2006017
S202S203S204S205S206S207S208S209S210
S211
2004095 2006019 2006020 2006021 2006022 2006023 2006024 2006025 2006026
2006027
S212S213S214S215S216S217S218S219S220
S222
2006028 2006029 2006030 2006031 2006032 2006033 2006034 2006035 2006036
2006037
S223S224S225S226S227S228S229S230S231
S232
2006038 2006039 2006040 2006041 2006042 2006043 2006044 2006045 2006046
2006047
t
id plate year height
2004007 200400715 2004 0.40
2005024 200502415 2005 0.43
2006001 200600115 2006 0.44
2004012 200401220 2004 0.90
2005026 200502620 2005 0.94
2006003 200600320 2006 0.98
2004025 200402533 2004 0.15
2005027 200502733 2005 0.15
2006005 200600533 2006 0.16
2004035 200403543 2004 0.26
2005038 200503843 2005 0.30
2006007 200600743 2006 0.38
2004036 200403644 2004 0.32
2005030 200503044 2005 0.39
2006008 200600844 2006 0.46
2004039 200403947 2004 0.50
2005025 200502547 2005 0.55
2006009 200600947 2006 0.63
2004055 200405564 2004 0.45
2005029 200502964 2005 0.58
2006014 200601464 2006 0.67
2006015 2006015 D72 2006 0.30
2004093 2004093 S200 2004 0.68
2005040 2005040 S200 2005 0.74
2006016 2006016 S200 2006 0.84
2004094 2004094 S201 2004 0.46
2005041 2005041 S201 2005 0.49
2006017 2006017 S201 2006 0.53
2004095 2004095 S202 2004 0.17
2004096 2004096 S203 2004 0.23
2005032 2005032 S203 2005 0.23
2006019 2006019 S203 2006 0.23
2004097 2004097 S204 2004 0.25
2005031 2005031 S204 2005 0.29
2006020 2006020 S204 2006 0.41
2004098 2004098 S205 2004 0.22
2005039 2005039 S205 2005 0.26
2006021 2006021 S205 2006 0.37
2004099 2004099 S206 2004 0.19
2005035 2005035 S206 2005 0.25
2006022 2006022 S206 2006 0.37
2004100 2004100 S207 2004 0.29
2005003 2005003 S207 2005 0.36
2006023 2006023 S207 2006 0.41
2004101 2004101 S208 2004 0.17
2005005 2005005 S208 2005 0.20
2006024 2006024 S208 2006 0.16
2004102 2004102 S209 2004 0.16
2005008 2005008 S209 2005 0.19
2006025 2006025 S209 2006 0.24
2004103 2004103 S210 2004 0.09
2005007 2005007 S210 2005 0.14
2006026 2006026 S210 2006 0.15
2004104 2004104 S211 2004 0.12
2005006 2005006 S211 2005 0.12
2006027 2006027 S211 2006 0.22
2004105 2004105 S212 2004 0.61
2005011 2005011 S212 2005 0.71
2006028 2006028 S212 2006 0.81
2004106 2004106 S213 2004 0.28
2005010 2005010 S213 2005 0.37
2006029 2006029 S213 2006 0.44
2004107 2004107 S214 2004 0.47
2005009 2005009 S214 2005 0.59
2006030 2006030 S214 2006 0.67
2004108 2004108 S215 2004 0.43
2005004 2005004 S215 2005 0.53
2006031 2006031 S215 2006 0.66
2004109 2004109 S216 2004 0.35
2005019 2005019 S216 2005 0.38
2006032 2006032 S216 2006 0.41
2004110 2004110 S217 2004 0.20
2005018 2005018 S217 2005 0.21
2006033 2006033 S217 2006 0.32
2004111 2004111 S218 2004 0.19
2005014 2005014 S218 2005 0.21
2006034 2006034 S218 2006 0.27
2004112 2004112 S219 2004 0.21
2005034 2005034 S219 2005 0.24
2006035 2006035 S219 2006 0.24
2004113 2004113 S220 2004 0.19
2005021 2005021 S220 2005 0.19
2006036 2006036 S220 2006 0.25
2004114 2004114 S222 2004 0.34
2005020 2005020 S222 2005 0.35
2006037 2006037 S222 2006 0.46
2005013 2005013 S223 2005 0.04
2006038 2006038 S223 2006 0.04
2005012 2005012 S224 2005 0.13
2006039 2006039 S224 2006 0.14
--
NEW EMAIL ADDRESS AND ADDRESS:
[EMAIL PROTECTED]
[EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Leslie Hill Institute for Plant Conservation
University of Cape Town
Rondebosch 7701
South Africa
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 650 2440 (w)
Cell
Re: [R] Identifying last record in individual growth data over different time intervalls
Hi jim holtman wrote: What is wrong with the method that you have? It looks reasonable Actually there is nothing wrong with the approach I am using - it just seemed to be quite complicated and I assumed that there is an easier approach around. The dataset is not that large that I really have to worry about efficiency. Thanks a lot , Rainer efficient. As with other languages, there are always other ways of doing it. Here is another to consider, but it is basically the same: sapply(split(t, t$plate), function(x) x$id[which.max(x$year)]) 15 20 33 43 44 47 64 D72S200 S201S202S203S204 2006001 2006003 2006005 2006007 2006008 2006009 2006014 2006015 2006016 2006017 2004095 2006019 2006020 S205S206S207S208S209S210S211S212S213 S214S215S216S217 2006021 2006022 2006023 2006024 2006025 2006026 2006027 2006028 2006029 2006030 2006031 2006032 2006033 S218S219S220S222S223S224 2006034 2006035 2006036 2006037 2006038 2006039 On 3/5/07, Rainer M. Krug [EMAIL PROTECTED] wrote: Hi I have a plist t which contains size measurements of individual plants, identified by the field plate. It contains, among other, a field year indicating the year in which the individual was measured and the height. The number of measurements range from 1 to 4 measurements in different years. My problem is that I would need the LAST measurement. I only came up with the solution below which is probably way to complicated, but I can't think of another solution. Does anybody has an idea how to do this more effectively? Finally I would like to have a data.frame t2 which only contains the entries of the last measurements. Thanks in advance, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying last record in individual growth data over different time intervalls
Hi Chris Chris Stubben wrote: Finally I would like to have a data.frame t2 which only contains the entries of the last measurements. You could also use aggregate to get the max year per plate then join that back to the original dataframe using merge on year and plate (common columns in both dataframes). Thanks for the idea to use aggregate and merge - as I like SQL, this seems to be a nice approach. Rainer x-data.frame(id=(1:8), plate=c(15,15,15,20,20,33,43,43), year=c(2004,2005,2006,2004,2005,2004,2005,2006), height=c(0.40,0.43,0.44,0.90,0.94,0.15,0.30,0.38)) merge(x, aggregate(list(year=x$year), list(plate=x$plate), max)) plate year id height 115 2006 3 0.44 220 2005 5 0.94 333 2004 6 0.15 443 2006 8 0.38 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question concerning survival analysis
Hi I have a data set consisting of pictures on which individual plants were identified and categorized into alive, dead and unknown if it was not clear. The time of these pictures ranges from 1937 to today and the intervals range between 13 and 1 year. I am trying to get an understanding of the mortality rate which I can then use in an individual based model. Therefore I thought of using survival analysis. I have ordered my data in the required format, and classified the events as interval censored (event=3) for the cases where the plant died and right censored (event=0) but I have still a problem I managed to obtain a Surv() object by calling surv - with(survival, Surv(time, time2, event, type=interval)) where survival is my dataset surv [1] [13, 16] 68+ 16+ 68+ 68+ 68+ [26, 34] 68+ [9] 68+ 16+ [54, 58] [64, 67] 68+ [34, 54] [34, 54] [58, 63] [17] [48, 58] [48, 63] [34, 54] And it looks correct (I set the year 1937 to 0) But where to from here? I understand that most of the analysis can not be done with interval censored data? As far as I understand it, I have to use interval censored as the observation intervals are not equal and in addition quite large. The data is from one site, no interference. As I said, I would like to have an estimate of the hazard function (I guess) to get information about the mortality rate of the individuals. Any help welcome, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Mailing list in Cape Town - South Africa
Hi I hope that I don't break any rules - I just want to announce that we started a mailing list for R in Cape Town. The address is: https://cbio.uct.ac.za/mailman/listinfo/sabior The basic idea of the mailing list is to bring R users in the region around Cape Town and in South Africa closer together and probably arrange informal gettogethers. We also try to provide a forum to discuss issues concerning R in Biology and distribute announcements of R courses and similar events in the Cape Town area. We definitely do not want to establish an alternative forum to the official R lists and do not want to draw subscribers away from them - it is a huge advantage that one large list provides the main forum to get help. I hope that the new mailing list will be a useful medium to spread the word and information about R in South Africa, Rainer -- [EMAIL PROTECTED] Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
Douglas Bates wrote: On 2/19/07, Nils Höller [EMAIL PROTECTED] wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? I don't think it is possible to reattach to a process started in one ssh session from another ssh session. However, you can put a session No, it is. Check out the screen command - it is backgrounding your session, you can have several running at the same time and reattach and they persist between logouts (obviously, if you switch the computer of, it is gone...) Rainer into the background with the -f flag to ssh. You haven't told us what operating system you are starting the ssh connection on and what system will run the R process. If I had an X server running on the local system and the remote system provided X clients like xterm I would do this by ssh -X -f [EMAIL PROTECTED] xterm This should spring up an autonomous xterm window on the local machine after which you can run R in it. I hope this helps. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I create an object in the Global environment from a function
[EMAIL PROTECTED] wrote: Hi all, Say I have created an object b in my function myfunc - function() b - 34 myfunc - function() b - 34 - Rainer How can I make b an object in the Global environment and not just in the environment of myfunc? Thanks, Tim __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop is going to take 26 hours - needs to be quicker!
Jenny Barnes wrote:
Dear R-help,
I have a loop, which is set to take about 26 hours to run at the rate it's
going
- this is ridiculous and I really need your help to find a more efficient way
of
loading up my array gpcc.array:
#My data is stored in a table format with all the data in one long column
#running though every longitute, for every latitude, for every year. The
#original data is sotred as gpcc.data2 where dim(gpcc.data2) = [476928,5]
where
#the 5th column is the data:
#make the array in the format I need [longitude,latitude,years]
gpcc.array - array(NA, c(144,72,46))
n=0
for(k in 1:46){
for(j in 1:72){
for(i in 1:144){
n - n+1
gpcc.array[i,j,k] - gpcc.data2[n,5]
print(j)
}
}
}
I don't know if it is faster - but adding three columns to qpcc.data,
one for longitude, one for lattitude and one for year (using rep() as
they are in sequence) and the using reshape() might be faster?
So it runs through all the longs for every lat for every year - which is the
order the data is running down the column in gpcc.data2 so n increses by 1
each
time and each data point is pulled off
It needs to be a lot quicker, I'd appreciate any ideas!
Many thanks for taking time to read this,
Jenny Barnes
~~
Jennifer Barnes
PhD student - long range drought prediction
Climate Extremes
Department of Space and Climate Physics
University College London
Holmbury St Mary, Dorking
Surrey
RH5 6NT
01483 204149
07916 139187
Web: http://climate.mssl.ucl.ac.uk
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 808 3304 (w)
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop is going to take 26 hours - needs to be quicker!
David Barron wrote:
What about
gpcc.array - array(gpcc.data2[,5], dim=c(144,72,46))
I guess this will be slightly faster then my suggestion :-) ?
On 14/12/06, Rainer M Krug [EMAIL PROTECTED] wrote:
Jenny Barnes wrote:
Dear R-help,
I have a loop, which is set to take about 26 hours to run at the
rate it's going
- this is ridiculous and I really need your help to find a more
efficient way of
loading up my array gpcc.array:
#My data is stored in a table format with all the data in one long
column
#running though every longitute, for every latitude, for every year.
The
#original data is sotred as gpcc.data2 where dim(gpcc.data2) =
[476928,5] where
#the 5th column is the data:
#make the array in the format I need [longitude,latitude,years]
gpcc.array - array(NA, c(144,72,46))
n=0
for(k in 1:46){
for(j in 1:72){
for(i in 1:144){
n - n+1
gpcc.array[i,j,k] - gpcc.data2[n,5]
print(j)
}
}
}
I don't know if it is faster - but adding three columns to qpcc.data,
one for longitude, one for lattitude and one for year (using rep() as
they are in sequence) and the using reshape() might be faster?
So it runs through all the longs for every lat for every year -
which is the
order the data is running down the column in gpcc.data2 so n
increses by 1 each
time and each data point is pulled off
It needs to be a lot quicker, I'd appreciate any ideas!
Many thanks for taking time to read this,
Jenny Barnes
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 808 3304 (w)
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] exporting a table to latex
Dieter Menne wrote: Rainer M Krug RKrug at sun.ac.za writes: I am using the latex() command from the Hmisc package to export table to latex. For formating of the values, I use the format() function. But I don't manage to get the format of the values right: I don't want scientific notation, but if I say scientific=FALSE, I get many digits after the decimal point which I can not control with digits=... and nsmall=... in the format command. Is there another way of formating the values to three decimal digits? Or another way of exporting them to LaTeX? There were a few bugs in the current versions of format.df (called by latex), and the scientific problem could have been among them. Try to download latex.s from http://biostat.mc.vanderbilt.edu/svn/R/Hmisc/branches/release_3.2-1/R/latex.s do library(Hmisc) source(latex.s) Thanks - I did it but it still doesn't work. I should have mentioned that I am using the function format() from the base package to create a data.frame which I then give to latex() to export - without formating from latex(). I am not using the format functions of the Hmisc package as I read that there are problems with them. Rainer and check if the problem disappears. If it does, write a mail to [charles.dupont at vanderbilt.edu] and ask him to make the version public as soon as possible. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] exporting a table to latex
Rau, Roland wrote: Hi, -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rainer M Krug Sent: Wednesday, December 13, 2006 8:47 AM To: r-help@stat.math.ethz.ch Subject: [R] exporting a table to latex Is there another way of formating the values to three decimal digits? Or another way of exporting them to LaTeX? I hope I did not oversee any emails concerning your question. Typically, No, you didn't. I use the xtable-package. Please let me know if the following code is not doing what you hope for. It's perfect. Doing exactly what I wanted it to do - Thanks a lot Raienr Best, Roland mydata - data.frame(Category=LETTERS[1:10], Percentage=runif(10)) library(xtable) xtable(mydata, digits=c(0,0,3)) ### LaTeX format = default you can even create an HTML table print(xtable(mydata, digits=c(0,0,5)), type=HTML) -- This mail has been sent through the MPI for Demographic Research. Should you receive a mail that is apparently from a MPI user without this text displayed, then the address has most likely been faked. If you are uncertain about the validity of this message, please check the mail header or ask your system administrator for assistance. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] exporting a table to latex
Hi I am using the latex() command from the Hmisc package to export table to latex. For formating of the values, I use the format() function. But I don't manage to get the format of the values right: I don't want scientific notation, but if I say scientific=FALSE, I get many digits after the decimal point which I can not control with digits=... and nsmall=... in the format command. Is there another way of formating the values to three decimal digits? Or another way of exporting them to LaTeX? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two ggplot and colour=x question
Hi I am using ggplot with the aesthetic=list(..., colour=x, ...) ggplot() ggline() I have four different values in x (ren, cyn, mixed, bare) and I have two questions 1) I would like to assign specific colours to the values, i.e. green, red, blue and brown. How can I do this? I did not understand map_colour_brewer. 2) I don't want the legend top be plot. How can I disable the legend to be plotted? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] two ggplot and colour=x question
Thanks a lot for your help - I'll try it out and let you know if I still have problems. Rainer hadley wickham wrote: I am using ggplot with the aesthetic=list(..., colour=x, ...) ggplot() ggline() I have four different values in x (ren, cyn, mixed, bare) and I have two questions 1) I would like to assign specific colours to the values, i.e. green, red, blue and brown. How can I do this? I did not understand map_colour_brewer. There's not really an easy way to do this at the moment. However, you can create a new variable containing the colours you want to use and then use a manual scale so they aren't converted automatically: df$colour - c(red,blue,yellow,orange)[df$myvar] p - ggplot(data=df, aes=list(x=x,y=y,colour=colour) scmanual(p, colour) 2) I don't want the legend top be plot. How can I disable the legend to be plotted? If you use a manual scale (as above) there won't be a legend, or more generally you can do: p$legend.position - none to turn of the legend (see ?ggopt for other options) Hadley -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling R functions in Delphi
Anna Belova wrote:
Hello All,
We would like to call quantile() function from the R-package STATS in a
Delphi program. If this is possible, could anyone provide us with an
example?
Hi Anna
There was a translation of the header files from C to Delphi, so that
you could used R directly without using DCom - Hans-Peter Suter
translated / made them.
I'll mail you the version which he send me off list.
Rainer
Thanks in advance.
--Anna
-
Anna Belova
Abt Associates Inc.
4800 Montgomery Ln, St 600
Bethesda, MD-20814
phone: 301-347-5304
fax: 301-652-7530
http://www.abtassociates.com/environment
-
This message may contain privileged and confidential informa...{{dropped}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 808 3304 (w)
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] specify point shape for ggplot (equivalent to pch)?
Hi is it possible to specify the shape of the point to be used in ggplot (as with pch in plot)? I couldn't find anything in the help. Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Combining factors
Hi I know this is a basic question and I know I have done it before but I can't find the answer any more. I have a data set, say: F1, F2, Value F1 and F2 are Factors. I would like to plot plot(TheCombinationOf(F1, F2), Value) I remember there was a function for TheCombinationOf() but I don't remember the name. I could create a new factor based on F1 and F2, but I would prefer the other soluytion. Any help welcome, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining factors
Peter Dalgaard wrote: Rainer M Krug [EMAIL PROTECTED] writes: Hi I know this is a basic question and I know I have done it before but I can't find the answer any more. I have a data set, say: F1, F2, Value F1 and F2 are Factors. I would like to plot plot(TheCombinationOf(F1, F2), Value) I remember there was a function for TheCombinationOf() but I don't remember the name. I could create a new factor based on F1 and F2, but I would prefer the other soluytion. Any help welcome, F1:F2 interaction(F1,F2) There are some differences so lookup the help page for the latter. Thanks a lot Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error in format.df when using dec
When using format.df with dec, the formating does not work (see code below). Any help appreciated how I could do the formating (I want to export to LaTeX), Rainer I am using the newest version of Hmisc from CRAN, R version: version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) x - data.frame(a=c(1.12345812,2.225415478547775566), b=3:4) x$m - matrix(5:8,nrow=2) dim(x) [1] 2 3 x a b m.1 m.2 1 1.123458 3 5 7 2 2.225415 4 6 8 format.df(x) a b m 1 m 2 1 1.123458 3 5 7 2 2.225415 4 6 8 attr(,col.just) [1] r r r r format.df(x, dec=2) a b m 1 m 2 1 1.120 3 5 7 2 2.230 4 6 8 attr(,col.just) [1] r r r r -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compare linear regressios for significant differences of the slopes
Dieter Menne wrote: Rainer M Krug wrote: I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Sorry for my (probably incorrect) usage of group and measure. Here a (probably better) description of my design: I ran 96 different simulations (spread of a species along a transect) over four generations, based on different parameter sets. These resulted in 96 results (groups). Now I have 8 different ways to describe the result of one simulation based on x individuals further away then distance d, where x is replaced by 1, 5, 10, 50, 100, 500, 1000 and 5000 (measures). For each group / simulation, I did linear regressions for each measure lm.measure_1 - lm(distance ~ generation) ... resulting in lm.measure_1 to lm.measure_8 Within each group (based on one simulation), I get a different slope for each measure. What I want to know is if these resulting slopes differ within one group / simulation. Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. Instead of doing this in two steps, you would better use lme in package nlme to test the hypothesis in one run. I don't understand the details of you design, but is looks like the oxboys example in Pinheiro/Bates (the book of nlme) could give you a first starter. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compare linear regressios for significant differences of the slopes
Hi I haven't received any ideas yet - I just wanted to confirm if this is a simple question? Should I follow the idea of checking if slope +- stddev slope overlap? Thanks, Rainer Rainer M Krug wrote: Hi I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. I also read in previous discussions in this list, that I can see if the slope +- stddev(slope) overlap, but this seems a long process for the huge number of comparisons. Therefore my question: is there a way to compare the slopes of lm() which are based on different datasets and what is the easiest way to do it for this large number of datasets? Thanks in advance for your help, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Compare linear regressios for significant differences of the slopes
Hi I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. I also read in previous discussions in this list, that I can see if the slope +- stddev(slope) overlap, but this seems a long process for the huge number of comparisons. Therefore my question: is there a way to compare the slopes of lm() which are based on different datasets and what is the easiest way to do it for this large number of datasets? Thanks in advance for your help, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simplification of code using stamp?
hadley wickham wrote:
I get the following, which is not what I am looking for.
test[1:10,]
expertxx seeds runvalue
1 BW x001025 1 rsqs, slope, d.slope, intercept, d.intercept
2 BW x001025 2 rsqs, slope, d.slope, intercept, d.intercept
3 BW x001025 3 rsqs, slope, d.slope, intercept, d.intercept
4 BW x001025 4 rsqs, slope, d.slope, intercept, d.intercept
5 BW x001025 5 rsqs, slope, d.slope, intercept, d.intercept
6 BW x001028 1 rsqs, slope, d.slope, intercept, d.intercept
7 BW x001028 2 rsqs, slope, d.slope, intercept, d.intercept
8 BW x001028 3 rsqs, slope, d.slope, intercept, d.intercept
9 BW x001028 4 rsqs, slope, d.slope, intercept, d.intercept
10 BW x001028 5 rsqs, slope, d.slope, intercept, d.intercept
That's because stamp doesn't produce great output at the moment (have
a look at the str(test) to see that you have a data frame containing a
list of vectors)
The following code should put it a more reasonable form:
tidy - function(x) {
bind - function(i) data.frame(x[i, -ncol(x),drop=FALSE], t(a$value[[i]]))
l - lapply(1:nrow(x), bind)
do.call(rbind.fill, l)
}
tidy(test)
Thanks Hadley - I'll look at the code.
(but unless you provide a reproducible example I can't be sure that it
works with your data)
Regards,
Hadley
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Error bars in ggplot?
Hi Is it possible to put error bars in ggplot? I couldn't find anything so far. Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installation of RGrace
Hi I try to install RGrace, but always get the following error below. Might it have to do that RGtk is not installed and where can I find it to install it? I have GTK 1.2.10 installed. My R version and platform: version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) 09:26:46 (1.32 MB/s) - `/tmp/RtmpDCW8km/downloaded_packages/RGrace_0.5-5.tar.gz' saved [164119/164119] * Installing *source* package 'RGrace' ... ** libs gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/gtk-1.2 -I/usr/include/glib-1.2 -I/usr/lib/glib/include -I/usr/local/include -fpic -c gdk_draw.c -o gdk_draw.o gdk_draw.c:3:21: error: gdk/gdk.h: No such file or directory gdk_draw.c:4:21: error: gtk/gtk.h: No such file or directory gdk_draw.c: In function ‘draw_rubber_box’: gdk_draw.c:9: error: ‘GtkWidget’ undeclared (first use in this function) gdk_draw.c:9: error: (Each undeclared identifier is reported only once gdk_draw.c:9: error: for each function it appears in.) gdk_draw.c:9: error: ‘drawing_widget’ undeclared (first use in this function) gdk_draw.c:9: error: syntax error before ‘)’ token gdk_draw.c:10: error: ‘GdkColor’ undeclared (first use in this function) gdk_draw.c:11: error: ‘GdkGC’ undeclared (first use in this function) gdk_draw.c:11: error: ‘gc1’ undeclared (first use in this function) gdk_draw.c:12: error: ‘Color’ undeclared (first use in this function) gdk_draw.c:17: error: ‘GDK_XOR’ undeclared (first use in this function) gdk_draw.c:19: error: ‘GDK_LINE_SOLID’ undeclared (first use in this function) gdk_draw.c:19: error: ‘GDK_CAP_PROJECTING’ undeclared (first use in this function) gdk_draw.c:19: error: ‘GDK_JOIN_MITER’ undeclared (first use in this function) gdk_draw.c:20: error: ‘GDK_SOLID’ undeclared (first use in this function) make: *** [gdk_draw.o] Error 1 ERROR: compilation failed for package 'RGrace' ** Removing '/usr/lib/R/library/RGrace' -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error bars in ggplot?
hadley wickham wrote: Is it possible to put error bars in ggplot? I couldn't find anything so far. Have a look at ggerrorbar. Thanks - exactly what I was looking for. By the way - ggerrorbar is not mentioned in ?ggplot. Rainer Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simplification of code using stamp?
Hi I have the following code which I would like to simplify. Id does linear regressions and returns the r-squares, and the coefficients. It runs slow, as it is doing the regressions for each - is it possible to get the values in a dataframe which looks as follow: expert | xx | seeds | r.squared | slope | intercept Thanks in advance, Rainer library(reshape) rsqs - as.data.frame( stamp( tc.long, expert * xx * seeds ~ ., function(df) try( summary( lm(distance ~ generation, data=df))$r.squared, silent=TRUE ) ) ) slope - as.data.frame( stamp( tc.long, expert * xx * seeds ~ ., function(df) try( summary( lm(distance ~ generation, data=df))$coefficients[2], silent=TRUE ) ) ) d.slope - as.data.frame( stamp( tc.long, expert * xx * seeds ~ ., function(df) try( summary( lm(distance ~ generation, data=df))$coefficients[4], silent=TRUE ) ) ) intercept - as.data.frame( stamp( tc.long, expert * xx * seeds ~ ., function(df) try( summary( lm(distance ~ generation, data=df))$coefficients[1], silent=TRUE ) ) ) d.intercept - as.data.frame( stamp( tc.long, expert * xx * seeds ~ ., function(df) try( summary( lm(distance ~ generation, data=df))$coefficients[3], silent=TRUE ) ) ) -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simplification of code using stamp?
ONKELINX, Thierry wrote:
Resending the function because of a typo in the result vector.
function(df){
fit - summary(lm(distance ~ generation, data=df))
result - c(fit$r.squared, fit$coefficients[2],
fit$coefficients[4],
fit$coefficients[1], fit$coefficients[3])
names(result) - c(rsqs, slope, d.slope, intercept,
d.intercept),
}
You are right - the problem is that it isd calculating the regressions
five time. I implemented your code, and when I print the resulting
data.frame from
test - as.data.frame(
stamp(
tc.long,
expert * xx * seeds * run ~ .,
function(df)
{
try(
{
fit - summary( lm(distance ~
generation, data=df) )
result - c(fit$r.squared,
fit$coefficients[2], fit$coefficients[4], fit$coefficients[1],
fit$coefficients[3])
names(result) - c(rsqs, slope,
d.slope, intercept, d.intercept)
},
silent=TRUE
)
}
)
)
I get the following, which is not what I am looking for.
test[1:10,]
expertxx seeds runvalue
1 BW x001025 1 rsqs, slope, d.slope, intercept, d.intercept
2 BW x001025 2 rsqs, slope, d.slope, intercept, d.intercept
3 BW x001025 3 rsqs, slope, d.slope, intercept, d.intercept
4 BW x001025 4 rsqs, slope, d.slope, intercept, d.intercept
5 BW x001025 5 rsqs, slope, d.slope, intercept, d.intercept
6 BW x001028 1 rsqs, slope, d.slope, intercept, d.intercept
7 BW x001028 2 rsqs, slope, d.slope, intercept, d.intercept
8 BW x001028 3 rsqs, slope, d.slope, intercept, d.intercept
9 BW x001028 4 rsqs, slope, d.slope, intercept, d.intercept
10 BW x001028 5 rsqs, slope, d.slope, intercept, d.intercept
Cheers,
Thierry
-
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[EMAIL PROTECTED]
www.inbo.be
Do not put your faith in what statistics say until you have carefully
considered what they do not say. ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Question concerning ggplot
Hi I am using ggplot under R 2.4 / Linux. When using ggsmooth(method=lm) is there a way to show the results of the separate linear regressions? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question concerning ggplot
hadley wickham wrote: When using ggsmooth(method=lm) is there a way to show the results of the separate linear regressions? Do you mean doing a seperate linear regression for each group in your data? If so, have a look at ?gggroup for some examples of exactly that. No. I do the following: p - ggplot(cc, . ~ expert, aesthetic=list(y=x0050, x=generation)) ggjitter(p) ggsmooth(method=lm) And I get six columns in the graph, one for each expert and ggsmooth(method=lm) draws the linear regression lines into the graphs. I would like to have the coefficients and the R-square values of the linear regressions to analyse them further and to print them in the graphs. Hadley -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question concerning ggplot
hadley wickham wrote: Do you mean doing a seperate linear regression for each group in your data? If so, have a look at ?gggroup for some examples of exactly that. No. I do the following: p - ggplot(cc, . ~ expert, aesthetic=list(y=x0050, x=generation)) ggjitter(p) ggsmooth(method=lm) And I get six columns in the graph, one for each expert and ggsmooth(method=lm) draws the linear regression lines into the graphs. I would like to have the coefficients and the R-square values of the linear regressions to analyse them further and to print them in the graphs. Ok - In that case you have to do the regressions yourself and add the lines etc. Maybe something along these lines: Thanks a lot - I thought so. I'll take a look at your suggestions below and come back to you if I don't get it to work. Rainer p - ggpoint(ggplot(mtcars, aes=list(x=wt, y=mpg), formula= . ~ cyl)) models - stamp(mtcars, . ~ . | cyl, function(df) lm(mpg ~ wt, data=df)) lapply(models, coef) sapply(models, function(x) summary(x)$r.squared) or rsqs - as.data.frame(stamp(mtcars, cyl ~ ., function(df) summary(lm(mpg ~ wt, data=df))$r.squared)) rsqs$wt - 4 rsqs$mpg - 32 ggtext(p, data=rsqs, aes=list(label=value)) But that doesn't work for some reason I don't understand yet (but I'm working on it) Hadley -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question concerning ggplot
hadley wickham wrote: rsqs - as.data.frame(stamp(mtcars, cyl ~ ., function(df) summary(lm(mpg ~ wt, data=df))$r.squared)) rsqs$wt - 4 rsqs$mpg - 32 ggtext(p, data=rsqs, aes=list(label=value)) But that doesn't work for some reason I don't understand yet (but I'm working on it) Ooops - I just had the wrong version of reshape installed. It should work with the version available on cran. Thanks again for the example - but I don't seem to be able to get it to work in my context: p - ggplot(tc, . ~ expert, aesthetic=list(y=x0050, x=generation)) ggjitter(p) ggsmooth(method=lm) rsqs - as.data.frame( stamp( tc, expert ~ ., function(df) summary(lm(x0050 ~ generation, data=df))$r.squared)) rsqs expert value 1 BW 0.9056925 2 DM 0.9280401 3 DR 0.8044774 4 JH 0.7531401 5 Mean 0.9452478 6 TG 0.8816820 ggtext(data=rsqs, aesthetics=list(label=value, x=1, y=8000)) Error in data.frame(data[, c(variables), drop = FALSE], result = data$value) : arguments imply differing number of rows: 6, 0 Can you give me a hint what I am doing wrong? Rainer Hadley -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Latex editor recommendations
I use LyX ( http://www.lyx.org/ ) and I am happy with it - it's advantage is that one does not need to know LaTeX in detail to use it. I only know it from Linux, but it is also available for Windows Rainer Stefan Grosse wrote: For LaTeX I use the winedt editor: http://www.winedt.com which is extremely powerful and there exists an add-on for the use with R (but I prefer using Tinn-R for R). Winedt is shareware, you have a trial period of 30 days. It has an affordable price and discount for academics if I remember correctly. A very good freeware is TeXnicCenter: http://www.texniccenter.org/ There are many other editors being capable of LaTeX editing like Jedit (which has a LaTeX plugin), xemacs plus auctex and so on but the two mentioned are the LaTeX specialists and in my opinion easier to use. (PS if you look for a nice reference-library for the use with LaTeX Jabref is very good http://jabref.sourceforge.net/ free and works excellent together with winedt (inserts citation into winedt by mouse-click), has a connection to citeseer and medline for receiving citations, can import endnote libraries and so on and so forth) Tom Backer Johnsen schrieb: This question is not oriented towards R, but is posted here because I have the impression that there are at least some Latex users among the contributors. The question is: What editors for Latex are to be recommended? I have located one: http://www.latexeditor.org/ What other alternatives are there? I am (for the most part) using Windows XP. Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Piping commands from Kate to R in xterm (Linux)
Hi I don't know if this quaifies as an R question, but it relates to using R. I use R under Linux and use Kate as my script editor. I would like to be able to pipe the selected block to an R instance which is in an xterm session (not the console in Kate!). Is it possible to configure Kate that it sends the selection to a pipe which can be read from R (like in vim and eclipse)? Has anybody done something like this with Kate? Thanks a lot for your help, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Update to Dillo browser question
I start the html help with help.start(browser=dillo) and all subsequent requests with ? open in dillo Rainer Dylan Beaudette wrote: hi, how exactly do you get R to open the page in dillo ... ? thanks! On Thursday 21 September 2006 23:54, Rainer M Krug wrote: Hi I asked about if there is any way of opening URLs from the help browser in the same window of the same dillo browser - here is the answer. Just to reiterate: dillo is for me the perfect browser for the help of R when you use ?... Rainer Original Message Subject: Re: [Dillo-dev] Opening new URL in same instance and -s option Date: Thu, 21 Sep 2006 21:31:57 -0400 From: Jorge Arellano Cid [EMAIL PROTECTED] To: Rainer M Krug [EMAIL PROTECTED] References: [EMAIL PROTECTED] On Thu, Sep 21, 2006 at 02:10:28PM +0200, Rainer M Krug wrote: Hi Hi. I have two questions first: I would like to be able to have only one instance of dillo open and when I try to open a new url (from outside dillo), that this url is opened in the old instance. Is this possible, and if yes, how? Not now. The idea is to implement this with dpip (dillo plugin protocol) but it has not being done yet, becuase of lack of manpower. second: I have seen emails concerning running dillo in server mode (dillo -s server). I tried it, but dillo didn't know -s. Is this feature imp[lemented, and if yes, how can I access it? Not in the official dillo. Thanks a lot for a brilliant lightning fast browser, :-) -- Cheers Jorge.- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Update to Dillo browser question
Hi I asked about if there is any way of opening URLs from the help browser in the same window of the same dillo browser - here is the answer. Just to reiterate: dillo is for me the perfect browser for the help of R when you use ?... Rainer Original Message Subject: Re: [Dillo-dev] Opening new URL in same instance and -s option Date: Thu, 21 Sep 2006 21:31:57 -0400 From: Jorge Arellano Cid [EMAIL PROTECTED] To: Rainer M Krug [EMAIL PROTECTED] References: [EMAIL PROTECTED] On Thu, Sep 21, 2006 at 02:10:28PM +0200, Rainer M Krug wrote: Hi Hi. I have two questions first: I would like to be able to have only one instance of dillo open and when I try to open a new url (from outside dillo), that this url is opened in the old instance. Is this possible, and if yes, how? Not now. The idea is to implement this with dpip (dillo plugin protocol) but it has not being done yet, becuase of lack of manpower. second: I have seen emails concerning running dillo in server mode (dillo -s server). I tried it, but dillo didn't know -s. Is this feature imp[lemented, and if yes, how can I access it? Not in the official dillo. Thanks a lot for a brilliant lightning fast browser, :-) -- Cheers Jorge.- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Beginners manual for emacs and ess
Thanks for all of your information. I will look into all of them Rainer Gavin Simpson wrote: On Wed, 2006-09-20 at 17:03 +0200, Rainer M Krug wrote: Hi I heard so much about Emacs and ESS that I decided to try it out - but I am stuck at the beginning. Is there anywhere a beginners manual for Emacs ESS to be used with R? even M-x S tells me it can't start S-Plus - obviously - but I want it to start R... Er, M-x R starts R (after you've chosen a working directory) unless I misunderstood your question? Have you tried: http://ess.r-project.org/ And the ESS manual contained there? If not, that would be my first port of call. Any help welcome (otherwise I will be stuck with Eclipse and R) Rainer G -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] transforming factor back to numbers
Hi I generate a new dataframe by doing: npl.agg - aggregate(npl$DensPlants, list(year=npl$year, sim=npl$sim), mean, na.rm=TRUE ) Now I want to plot it by using coplot(npl.agg$x ~ npl.agg$year | npl.agg$sim, type=l) but, as npl.agg$year is seen as a factor, the order of the points on the x-axis (time axis) does not follow the numerical sorting 1...100, but rather the text sorting of the factor npl.agg$year Is there any way that I can 'defactor' npl.agg$year so that I have again the numerical values for year? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transforming factor back to numbers
Thanks a lot David. Just a suggestion - it might help if this is added to the help of factor() Rainer David Barron wrote: That's an FAQ: 7.10 How do I convert factors to numeric? It may happen that when reading numeric data into R (usually, when reading in a file), they come in as factors. If f is such a factor object, you can use as.numeric(as.character(f)) to get the numbers back. More efficient, but harder to remember, is as.numeric(levels(f))[as.integer(f)] In any case, do not call as.numeric() or their likes directly for the task at hand (as as.numeric() or unclass() give the internal codes). On 21/09/06, Rainer M Krug [EMAIL PROTECTED] wrote: Hi I generate a new dataframe by doing: npl.agg - aggregate(npl$DensPlants, list(year=npl$year, sim=npl$sim), mean, na.rm=TRUE ) Now I want to plot it by using coplot(npl.agg$x ~ npl.agg$year | npl.agg$sim, type=l) but, as npl.agg$year is seen as a factor, the order of the points on the x-axis (time axis) does not follow the numerical sorting 1...100, but rather the text sorting of the factor npl.agg$year Is there any way that I can 'defactor' npl.agg$year so that I have again the numerical values for year? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Other editor with completion apart from emacs?
Hi is there any other editor for Linux, apart from emacs, which has the completion feature (i.e. I enter libTAB and it offers me among other options library) Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Other editor with completion apart from emacs?
Hi Thanks for the tip - sounds interesting. I installed JGR, but I can't get it to work. I installed it as mentioned on via install.packages() and if I try to load it, I get the following: library(JGR) Loading required package: rJava Loading required package: JavaGD Loading required package: iplots *** caught segfault *** address 0xc, cause 'memory not mapped' Traceback: 1: .External(RinitJVM, classpath, parameters, PACKAGE = rJava) 2: .jinit(cp, parameters = -Xmx512m, silent = TRUE) 3: f(libname, pkgname) 4: firstlib(which.lib.loc, package) 5: try(firstlib(which.lib.loc, package)) 6: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) 7: .getRequiredPackages2(pkgInfo) 8: library(JGR) Possible actions: 1: abort (with core dump) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: I updated the packages to the versions on http://www.rosuda.org/R , but still the same. Any ideas? Rainer ronggui wrote: JGR support completion. It can runs under Linux,though JGR is more than a editor. On 9/21/06, Rainer M Krug [EMAIL PROTECTED] wrote: Hi is there any other editor for Linux, apart from emacs, which has the completion feature (i.e. I enter libTAB and it offers me among other options library) Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linux configuration (Ubuntu)
Frank E Harrell Jr wrote: SNIP After R starts you can manage help files nicely using help.start() to use a browser. I often use dillo, the world's fastest graphical browser, by specifying options(browser='dillo') before help.start(). WOW - dillo is BRILLIANT for this purpose. Thanks for the tip! Do you have any idea on how to convince dillo to reuse the same browser window again instead of using a new one when using ? ? Frank Thanks in advance, Brian -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calculating mean together with split
Hi I have a table called npl containing results of simulations. It contains about 19000 entries and the structure looks like this: NoPlants sim run year DensPlants 16 lng_cs99_renosterbos 140.00192 . . . it has 43 different entries for sim and year goes from 1 to 100, and run from 1 to 5. I would like to calculate the mean of DensPlants for each simulation and each year seperately, i.e. calculating the mean for all combinations of sim and year over run. I can use split(npl, npl$sim) to split npl into different groups each containing the entries for one parameterset - but where to go from there? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculating mean together with split
Hi David aggregate is what I was looking for, as I wanted to have it in the tabular format to plot it. Thanks Rainer David Barron wrote: Of course, aggregate will work too, depends on how you want the output to be formatted. You could also look at summarize in the Hmisc package. On 20/09/06, David Barron [EMAIL PROTECTED] wrote: Sorry, that should have been package gdata, not gtools...they're both in the same bundle, though. On 20/09/06, Rainer M Krug [EMAIL PROTECTED] wrote: Hi I have a table called npl containing results of simulations. It contains about 19000 entries and the structure looks like this: NoPlants sim run year DensPlants 16 lng_cs99_renosterbos 140.00192 . . . it has 43 different entries for sim and year goes from 1 to 100, and run from 1 to 5. I would like to calculate the mean of DensPlants for each simulation and each year seperately, i.e. calculating the mean for all combinations of sim and year over run. I can use split(npl, npl$sim) to split npl into different groups each containing the entries for one parameterset - but where to go from there? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Beginners manual for emacs and ess
Hi I heard so much about Emacs and ESS that I decided to try it out - but I am stuck at the beginning. Is there anywhere a beginners manual for Emacs ESS to be used with R? even M-x S tells me it can't start S-Plus - obviously - but I want it to start R... Any help welcome (otherwise I will be stuck with Eclipse and R) Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] execution of source() command
Hi
Linux SuSE 10
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
I have two questions concerning the source(test.R) command.
1) Is there any command which I can put into the test.R script file
which aborts the execution of the script? At the moment I use
CodeToBeExecutedInScript
if (FALSE)
{
CodeNotToBeExecutedInScript
}
which is not elegant, but it works. I would prefer something like:
CodeToBeExecutedInScript
CommandToAbotrExecutionOfScriptFile
CodeNotToBeExecutedInScript
2) When I call source(test.R) and it is running for some time. Does
changing the file test.R while it is executed change the execution, i.e.
does the call of source() load the script file into memory and parses
and executes it from there or does it parse and execute the file on the
disk?
Thanks in advance,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] execution of source() command
Prof Brian Ripley wrote:
On Fri, 15 Sep 2006, Rainer M Krug wrote:
Hi
I have two questions concerning the source(test.R) command.
1) Is there any command which I can put into the test.R script file
which aborts the execution of the script? At the moment I use
CodeToBeExecutedInScript
if (FALSE)
{
CodeNotToBeExecutedInScript
}
which is not elegant, but it works. I would prefer something like:
CodeToBeExecutedInScript
CommandToAbotrExecutionOfScriptFile
CodeNotToBeExecutedInScript
?stop or ?q, depending on what you mean by 'aborts the execution'.
Thanks - I would have expected to find it together with the other
flowcontrol commands like if, while, ...
2) When I call source(test.R) and it is running for some time. Does
changing the file test.R while it is executed change the execution, i.e.
does the call of source() load the script file into memory and parses
and executes it from there or does it parse and execute the file on
the disk.
The help file says:
'source' causes R to accept its input from the named file or URL
(the name must be quoted) or connection. Input is read and
'parse'd by from that file until the end of the file is reached,
then the parsed expressions are evaluated sequentially in the
chosen environment.
library(fortunes); fortune(WTFM)
Again - thanks a lot for the clarification
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with putting objects in list
Well - it must be that the whole concept of lists, vectors / matrices,
objects, data frames is not that clear to me. From my background
(Delphi, Basic), I am used to that, when referencing dr[i] I get the
object which is stored in the list.
Is there any manual / technical manual / reference available which
explains all this? The normal manual (Introduction into R) didn't made
it clear to me.
Rainer
jim holtman wrote:
What is the problem with referencing it with 'dr[[i]]', the way a list
is supposed to be referenced?
On 9/6/06, Rainer M Krug [EMAIL PROTECTED] wrote:
Antonio, Fabio Di Narzo wrote:
Use 'sapply' instead of 'lapply'. Type
If I use sapply it seems to simplify / collapse to much.
?lapply
for details
Antonio, Fabio Di Narzo.
University of Bologna, Italy
2006/9/6, Rainer M Krug [EMAIL PROTECTED]:
Hi
I use the following code and it stores the results of density() in the
list dr:
dens - function(run) { density( positions$X[positions$run==run],
bw=3,
cut=-2 ) }
dr - lapply(1:5, dens)
but the results are stored in dr[[i]] and not dr[i], i.e.
plot(dr[[1]])
works, but plot([1]) doesn't.
Is there any way that I can store them in dr[i]?
Thanks a lot,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
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--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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Re: [R] problem with putting objects in list
Thanks a lot - it looks like the sort of manual I was looking for -
Could I suggest of including it into the list of manuals for R? (If it
is already there, my apologies)
Rainer
Patrick Burns wrote:
S Poetry should help you understand this. See
especially the section of chapter 1 on subscripting.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Rainer M Krug wrote:
Hi
I use the following code and it stores the results of density() in the
list dr:
dens - function(run) { density( positions$X[positions$run==run], bw=3,
cut=-2 ) }
dr - lapply(1:5, dens)
but the results are stored in dr[[i]] and not dr[i], i.e. plot(dr[[1]])
works, but plot([1]) doesn't.
Is there any way that I can store them in dr[i]?
Thanks a lot,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] problem with putting objects in list
Thanks a lot Tony
this explains a lot.
I am not aware to have read such a good explanation about this issue
before. I would suggest to add it to the FAQs.
Rainer
Tony Plate wrote:
I suspect you are not thinking about the list and the
subsetting/extraction operators in the right way.
A list contains a number of components.
To get a subset of the list, use the '[' operator. The subset can
contain zero or more components of the list, and it is a list itself.
So, if x is a list, then x[2] is a list containing a single component.
To extract a component from the list, use the '[[' operator. You can
only extract one component at a time. If you supply a vector index with
more than one element, it will index recursively.
x - list(1,2:3,letters[1:3])
x
[[1]]
[1] 1
[[2]]
[1] 2 3
[[3]]
[1] a b c
# a subset of the list
x[2:3]
[[1]]
[1] 2 3
[[2]]
[1] a b c
# a list with one component:
x[2]
[[1]]
[1] 2 3
# the second component itself
x[[2]]
[1] 2 3
# recursive indexing
x[[c(2,1)]]
[1] 2
x[[c(3,2)]]
[1] b
Rainer M Krug wrote:
Hi
I use the following code and it stores the results of density() in the
list dr:
dens - function(run) { density( positions$X[positions$run==run], bw=3,
cut=-2 ) }
dr - lapply(1:5, dens)
but the results are stored in dr[[i]] and not dr[i], i.e. plot(dr[[1]])
works, but plot([1]) doesn't.
Is there any way that I can store them in dr[i]?
Thanks a lot,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] problem with putting objects in list
Hi
I use the following code and it stores the results of density() in the
list dr:
dens - function(run) { density( positions$X[positions$run==run], bw=3,
cut=-2 ) }
dr - lapply(1:5, dens)
but the results are stored in dr[[i]] and not dr[i], i.e. plot(dr[[1]])
works, but plot([1]) doesn't.
Is there any way that I can store them in dr[i]?
Thanks a lot,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with putting objects in list
Antonio, Fabio Di Narzo wrote:
Use 'sapply' instead of 'lapply'. Type
If I use sapply it seems to simplify / collapse to much.
?lapply
for details
Antonio, Fabio Di Narzo.
University of Bologna, Italy
2006/9/6, Rainer M Krug [EMAIL PROTECTED]:
Hi
I use the following code and it stores the results of density() in the
list dr:
dens - function(run) { density( positions$X[positions$run==run], bw=3,
cut=-2 ) }
dr - lapply(1:5, dens)
but the results are stored in dr[[i]] and not dr[i], i.e. plot(dr[[1]])
works, but plot([1]) doesn't.
Is there any way that I can store them in dr[i]?
Thanks a lot,
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] density() with from, to or cut and comparrison of density()
Hi the function density() does normally integrate to one - I've checked it and it works and I also read the previous threads. But I realised that it does not integrate to one if I use from, to or cut. My scenario: I simulated densities of a plants originating from an sseed source at distance zero. Therefore the density of the plants will be highest close to zero. Is there anything I can do to have this pattern? If I use 'from' or 'cut', the resulting densities do not integrate to one which I need as I want to compare different density curves. Ny second question is concerning the bandwidth. An I correct in saying that if I want to compare different density estimates that the bandwidth should be the same for all of them? Thanks in advance for your help, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] some EPS rotated in journal preview
This is a very late rply to this topic, but I had a similar problem and
I got different results with using ps.options() then using
postscript(...) and the one with ps.options produced the results
expected. The problem were the size of the graph and the paper and the
rotation.
If you want to know details, I have to dig them out.
Rainer
Knut Krueger wrote:
Prof. Brian Ripley schrieb:
CoverLetter.pdf
The problem is a well-known one in viewers looking at whole pages,
especially PS - PDF converters. R figures are particularly
vulnerable as they have text running both horizontally and vertically
(with normal axes).
Please do follow exactly the advice on the postscript help page.
The postscript produced for a single R plot is EPS (_Encapsulated
PostScript_) compatible, and can be included into other documents,
e.g., into LaTeX, using '\includegraphics{filename}'. For use
in this way you will probably want to set 'horizontal = FALSE,
onefile = FALSE, paper = special'.
If you have done that, suggest to your publisher that they turn auto
rotation off.
There are the reproducible codes (from the help file). The first one
with the long text is rotated the second is not rotated.
Seems that they rotate the page, if the text of the y-axes is longer
than the text of the x-axes.
Are you able to see any other reason for the rotation.
I will contact the journal again, if there is no other reason especially
of the R-code.
Regards
Knut Krueger.
postscript(c:/r/test/regline2.eps,horizontal = FALSE,onefile=FALSE,
paper = special ,pointsize=20,
height=8,width=8,family = Helvetica, font = Helvetica)
data(Davis)
attach(Davis)
mod.M-lm(repwt~weight, subset=sex==M)
mod.F-lm(repwt~weight, subset=sex==F)
plot(weight, repwt, pch=c(1,2)[sex],ylab=
,xlab= )
reg.line(mod.M)
reg.line(mod.F, lty=2)
dev.off()
postscript(c:/r/test/regline3.eps,horizontal = FALSE,onefile=FALSE,
paper = special ,pointsize=20,
height=8,width=8,family = Helvetica, font = Helvetica)
data(Davis)
attach(Davis)
mod.M-lm(repwt~weight, subset=sex==M)
mod.F-lm(repwt~weight, subset=sex==F)
plot(weight, repwt, pch=c(1,2)[sex])
reg.line(mod.M)
reg.line(mod.F, lty=2)
dev.off()
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--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] RMySQL...Can't initialize driver???
Stephane Cruveiller wrote: Rainer M Krug wrote: I followed your instruction. Here is my .my.cnf: --- [client] user=steff password=XX database=justforfun --- with it, I can connect to my MYSQL server without problem and then I try to connect through R: --- library(RMySQL) Loading required package: DBI m - dbDriver(MySQL) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) --- It still produces the error. I really do not know what is going on here... Sorry - no idea. I guess you are using Linux? And all packages are up to date? Rainer Then you do: library(RMySQL) m - dbDriver(MySQL) con - dbConnect(m, group = renpatch) q - TheSQLQuery rs - dbSendQuery(con, q) TheResults - fetch(rs, n = -1) dbDisconnect(con) rm(con) and it should work - at least that is what it is doing for me. Rainer Stephane. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RMySQL...Can't initialize driver???
Stephane Cruveiller wrote: Duncan Murdoch wrote: On 6/27/2006 8:51 AM, Stephane Cruveiller wrote: Dear R users, I would like to query a MySQL database through R. I have installed the latest required packages (RMySQL and DBI) in R (v2.3.1). A MySQL server (v5.0.22) is running on my local machine but I can't initialize MYSQL driver: library(RMySQL) Loading required package: DBI MySQL(max.con = 10, fetch.default.rec = 500, force.reload = F) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) - Could somebody tell me what I have missed? I am running R 2.3.0 under Linux and connect to a MySQl 4.1 server. You have to create a file in your home directory which has the connection infos. It should look like that: [renpatch] user = UserName password = PassWord database = ... host = ... [renpatch_renosterbos] user = UserName password = PassWord database = ... host = .. and be called .my.conf Then you do: library(RMySQL) m - dbDriver(MySQL) con - dbConnect(m, group = renpatch) q - TheSQLQuery rs - dbSendQuery(con, q) TheResults - fetch(rs, n = -1) dbDisconnect(con) rm(con) and it should work - at least that is what it is doing for me. Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to use mle or similar with integrate?
Hi I have the following formula (I hope it is clear - if no, I can try to do better the next time) h(x, a, b) = integral(0 to pi/2) ( ( integral(D/sin(alpha) to Inf) ( ( f(x, a, b) ) dx ) dalpha ) and I want to do an mle with it. I know how to use mle() and I also know about integrate(). My problem is to give the parameter values a and b to the integrate function. In other words, how can I write h - function... so that I can estimate a and b? Thanks, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with integrate() - correction
Sorry should read: ip - function(x) 1240 * x^(-0.88) Rainer M Krug wrote: Hi System: Linux, SuSE 10 R 2.3.0 I try to do the following ip - function(x) 1240*dip(x, 0.88) iip - function(x) integrate(ip, x - 0.045, x + 0.045)$value f - integrate(iip, 10, 100) Error in integrate(iip, 10, 100) : evaluation of function gave a result of wrong length How can I solve this? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problem with integrate() - correction
Thanks a lot - the symbolic solution will work and I understand what is
wrong with my function
Rainer
Frede Aakmann Tøgersen wrote:
Well why not do it symbolically, e.g.
int(a*x^b,x) = \frac{a}{b+1}x^{b+1}
and integrating this again gives
\frac{a}{(b+1)(b+2)}x^{b+2},
of course for resonable values of a and b such that things are well defined.
But if you follow the link
https://stat.ethz.ch/pipermail/r-help/2005-January/064026.html
you may come to this solution:
ip - function(x) 1240 * x^(-0.88)
iip - function(x){
res - rep(NA,length(x))
for (i in seq(along=x))
res[i] - integrate(ip, x[i] - 0.045, x[i] + 0.045)$value
return(res)
}
f - integrate(iip, 10, 100)
which may not be an effective way to do it.
Med venlig hilsen
Frede Aakmann Tøgersen
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af Rainer M Krug
Sendt: 22. juni 2006 14:03
Til: [EMAIL PROTECTED]
Cc: R help list
Emne: [R] problem with integrate() - correction
Sorry
should read:
ip - function(x) 1240 * x^(-0.88)
Rainer M Krug wrote:
Hi
System:
Linux, SuSE 10
R 2.3.0
I try to do the following
ip - function(x) 1240*dip(x, 0.88)
iip - function(x) integrate(ip, x - 0.045, x + 0.045)$value f -
integrate(iip, 10, 100)
Error in integrate(iip, 10, 100) : evaluation of function gave a
result of wrong length
How can I solve this?
Thanks
Rainer
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Department of Conservation Ecology and Entomology University
of Stellenbosch Matieland 7602 South Africa
Tel: +27 - (0)72 808 2975 (w)
Fax: +27 - (0)21 808 3304
Cell:+27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
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Re: [R] hello Excel... (native/Package/BETA)
Hans-Peter wrote: Dear list members I am pleased to annonce that I have just finished a native Excel reader/writer. It's wrapped up in two packages: either xlsReadWrite (open source) or the slightly beefed-up xlsReadWritePro (shareware). Working with Excel data is now as easy as writing read.xls and write.xls. Some more details: - Infos and download: http://treetron.googlepages.com - for detailed documentation pls. download and see: help files, DESCRIPTION and README. - I set up a newsgroup for technical questions and feedback: http://groups.google.ch/group/supportR - while it could be ported to other platforms, currently it is WINDOWS only (see technical below) SNIP If I understand it right, the the flexcel library includes the components for kylix as well - therefore I would try to compile it for Linux, I would suggest to use CrossKylix to compile it. Rainer SNIP -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Question concerning mle
Thanks a lot Spencer for your tips - I'll look into all of them. Rainer Spencer Graves wrote: It's difficult to say much at this level of generality, but I have four suggestions: 1. Have you tried creating a reasonable grid of starting values using expand.grid and then plotting the resulting likelihood surface? If you have more than 2 parameters, you may want to use 'lattice' graphics. This should tell you if the functions seems unimodal, convex, etc., in the region you covered and at the resolution of your grid. 2. Have you tried method=SANN = simulated annealing? I might try one pass with SANN, then refine the solution found by SANN using BFGS. 3. After you have a solution, you can then try profile likelihod. Unfortunately, my experience with profile.mle has been mixed. I actually made local copies of mle and profile.mle and found and fixed some of the deficiencies of each. I didn't test them enough to offer the results to the R Core Team, however. 4. Have you looked at Venables and Ripley (2002) Modern Applied Statistics with S, 4th ed. (Springer)? It's a great book for many things, including the use of expand.grid and 'optim'. hope this helps. Spencer Graves Rainer M Krug wrote: Hi I hope this is the right forum - if not, point me please to a better one. I am using R 2.3.0 on Linux, SuSE 10. I have a question concerning mle (method=BFGS). I have a few models which I am fitting to existing data points. I realised, that the likelihood is quite sensitive to the start values for one parameter. I am wondering: what is the best approach to identify the right initial values? Do I have to do it recursively, and if yes, how can I automate it? Or do I have to play with the system? I am quite confident that the resulting parameters are the optimal for my problem - but can I verify it? Thanks, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Question concerning mle
Hi I hope this is the right forum - if not, point me please to a better one. I am using R 2.3.0 on Linux, SuSE 10. I have a question concerning mle (method=BFGS). I have a few models which I am fitting to existing data points. I realised, that the likelihood is quite sensitive to the start values for one parameter. I am wondering: what is the best approach to identify the right initial values? Do I have to do it recursively, and if yes, how can I automate it? Or do I have to play with the system? I am quite confident that the resulting parameters are the optimal for my problem - but can I verify it? Thanks, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to create list of objects?
Thanks everybody - it's working Rainer Dimitris Rizopoulos wrote: try something like: lapply(f, summary) sapply(f, function(x) AIC(logLik(x))) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Rainer M Krug [EMAIL PROTECTED] To: R help list r-help@stat.math.ethz.ch Sent: Tuesday, June 06, 2006 4:38 PM Subject: [R] How to create list of objects? Hi I am doing several mle and want to store them in a list (or whatever is the right construct) to be able to analyse them later. at the moment I am doing: f - list() f$IP - mle(...) f$NE - mle(...) but when I say: summary(f) I get: Length Class Mode IP 0 mle list NE 0 mle list I don't get the output I would have, i.e. the one from summary(f$IP) summary(f$IP) Maximum likelihood estimation Call: mle(minuslogl = IPNeglogPoisL, method = L-BFGS-B, fixed = list(), control = list(maxit = 1e+08, factr = 1e-20)) Coefficients: Estimate Std. Error a 1242.0185506 44.92341097 b0.8802538 0.01685811 -2 log L: 145.3509 What I want to do is something like: AICs - AIC(logLik(f)) and then have all the AICs in the vector AICs. It must be possible or is this again a namespace issue? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to create list of objects?
Hi I am doing several mle and want to store them in a list (or whatever is the right construct) to be able to analyse them later. at the moment I am doing: f - list() f$IP - mle(...) f$NE - mle(...) but when I say: summary(f) I get: Length Class Mode IP 0 mle list NE 0 mle list I don't get the output I would have, i.e. the one from summary(f$IP) summary(f$IP) Maximum likelihood estimation Call: mle(minuslogl = IPNeglogPoisL, method = L-BFGS-B, fixed = list(), control = list(maxit = 1e+08, factr = 1e-20)) Coefficients: Estimate Std. Error a 1242.0185506 44.92341097 b0.8802538 0.01685811 -2 log L: 145.3509 What I want to do is something like: AICs - AIC(logLik(f)) and then have all the AICs in the vector AICs. It must be possible or is this again a namespace issue? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem with mle
Hi Ben Thanks a lot for your help - it solved my problem and I understand a little bit more. Just one more question along this line: If I want to use another likelihood estimator, e.g. negative binominal, I guess I have to use -sum(dpois(SumSeeds,size=???, prob=???,log=TRUE)) instead of -sum(dnbinom(SumSeeds,lambda=est,log=TRUE)) But what do I use for size and prob? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Calculation of AIC BIC from mle
R 2.3.0, all packages up to date
Linux, SuSE 10.0
Hi
I want to calculate AIC or BIC from several results from mle calculation.
I found the AIC function, but it does not seem to work with objects of
class mle -
If I execute the following:
ml1 - mle(...)
AIC(ml1)
I get the following error messale:
Error in logLik(object) : no applicable method for logLik
Therefore I am using the following to calculate the AIC:
#AICmle calculate AIC from mle object
AICmle - function( m, k=2)
{
lL - logLik(m)
edf - attr(lL, df)
LL - lL[1]
- 2 * LL + k * edf
}
1) Why is AIC not working with objects of class mle - am I doing
something wrong, is it a bug or by design?
2) Just for confirmation - is my calculation of AIC correct?
Thanks
Rainer
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Re: [R] Calculation of AIC BIC from mle
Thanks a lot for your and Martin's help - I understand now why it is not
working and am using AIC(logLik(ml1)).
Thanks
Rainer
Prof Brian Ripley wrote:
You are mixing S3 and S4 classes and generics here. AIC(logLik(ml1))
will work.
This a namespace issue: stats4 contains a version of logLik, but the
default method for AIC is from stats, and so dispatches on stats::logLik
and not stats4::logLik. There is something fundamentally unsatisfactory
about converting S3 generics to S4 generics where namespaces are involved.
I have put a workaround in R-devel.
On Mon, 5 Jun 2006, Rainer M KRug wrote:
R 2.3.0, all packages up to date
Linux, SuSE 10.0
Hi
I want to calculate AIC or BIC from several results from mle calculation.
I found the AIC function, but it does not seem to work with objects of
class mle -
If I execute the following:
ml1 - mle(...)
AIC(ml1)
I get the following error messale:
Error in logLik(object) : no applicable method for logLik
Therefore I am using the following to calculate the AIC:
#AICmle calculate AIC from mle object
AICmle - function( m, k=2)
{
lL - logLik(m)
edf - attr(lL, df)
LL - lL[1]
- 2 * LL + k * edf
}
1) Why is AIC not working with objects of class mle - am I doing
something wrong, is it a bug or by design?
2) Just for confirmation - is my calculation of AIC correct?
Not quite. The correct function is
stats:::AIC.logLik
function (object, ..., k = 2)
-2 * c(object) + k * attr(object, df)
environment: namespace:stats
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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[R] Problem with mle
R 2.3.0
Linux, SuSE 10.0
Hi
I have two problems with mle - probably I am using it the wrong way so
please let me know.
I want to fit different distributions to an observed count of seeds and
in the next step use AIC or BIC to identify the best distribution.
But when I run the script below (which is part of my original script), I
get one error message for the first call of mle:
Error in solve.default(oout$hessian) : Lapack routine dgesv: system is
exactly singular
In addition: Warning messages:
1: NaNs produced in: dweibull(x, shape, scale, log)
2: NaNs produced in: dweibull(x, shape, scale, log)
3: NaNs produced in: dweibull(x, shape, scale, log)
4: NaNs produced in: dweibull(x, shape, scale, log)
What can I do to avoid this problem?
The second one is following the second call of mle:
summary(fit.NE) gives me the summary of the fit, but
profile(fit.NE) gives me the following error message:
Error in onestep(step) : profiling has found a better solution, so
original fit had not converged
In addition: Warning messages:
1: NaNs produced in: dexp(x, 1/rate, log)
2: NaNs produced in: dexp(x, 1/rate, log)
3: NaNs produced in: dexp(x, 1/rate, log)
4: NaNs produced in: dexp(x, 1/rate, log)
5: NaNs produced in: dexp(x, 1/rate, log)
6: NaNs produced in: dexp(x, 1/rate, log)
What can I do in this case - which parameters do I have to change that
it converges?
Rainer
##
library(stats4)
SumSeeds - c(762, 406, 288, 260, 153, 116, 57, 33, 40, 44, 36,
24, 35, 23, 36, 25, 35, 30)
X - c(1.74924, 3.49848, 5.24772, 6.99696, 8.74620, 17.49240, 26.23860,
34.98480, 43.73100, 52.47720, 61.22340, 69.96960, 71.71880, 73.46810,
75.21730, 76.96650, 78.71580, 80.46500 )
#Sum of log of values in vector
SumLog - function (x)
{
sum(log(x))
}
#-ln(L) with Poisson Likelihood estimator
NeglogPoisL - function (obs, est)
{
sel - est != 0
SumLogObs - SumLog(obs[sel])
-sum( obs[sel] * log(est[sel]) - est[sel]- SumLogObs )
}
#-ln(L) for Negative Exponential
NENeglogPoisL - function(a=0.2, rate=0.04)
{
NeglogPoisL( SumSeeds, a * dexp( X, rate) )
}
#-ln(L) for Weibull
WBNeglogPoisL - function(a=100, shape=0.12, scale=1e+37)
{
NeglogPoisL( SumSeeds, a * dweibull(X, shape, scale) )
}
fit.WB - mle(
WBNeglogPoisL
, start=list(a=1, shape=0.1, scale=1)
, fixed=list()
, control=list(maxit=1)
)
fit.NE - mle(
NENeglogPoisL
, start=list(a=1, rate=1)
, fixed=list()
, control=list(maxit=1)
)
##
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Re: [R] pattern instead of colors in bargraph
Uwe Ligges wrote: Rainer M KRug wrote: Hi I am using R 2.2.0 under SuSE 10. I am creating a graph by using the following script: DietF - read.csv (DietFem.csv, header = TRUE, as.is=TRUE) attach (DietF) PP - array(c(bud,flower,shoot,melon,seed.pod,detritus,other), c(16,7)) M - paste (Month) detach (DietF) png(filename=DietF.png, width=960) barplot (t(PP), ylim=c(0,1), names.arg=M, space=0.3, ylab=proportion of diet) dev.off() The problem is that I would need the bars to be filled with pattern (striped, diagonal striped, dotted, ...) instead of the colors as it is extremely difficult to see which is which. I didn't find anything in the help which showed me how to do it. Then please re-read it and look at the arguments desnity and angle. Uwe Ligges Thanks a lot (I mean it!) - it must have been to late on Saturday evening when I looked at it. Rainer __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Title for secondary y-axis (axis(4)) in barplot?
Hi I am using the following script to plot a barplot with a secondary axis in a bargplot for the line. It works, but I would like to have a title for the secondary y-axis on the right hand side of the axis - is this possible? Rainer RainFog - read.csv (Climate.csv, header = TRUE, as.is=TRUE) PP - array(c(RainFog$Rain, RainFog$Fog), c(16,2)) M - paste (RainFog$Month) png(filename=RainFog.png, width=960) barplot (t(PP), ylim=c(0,8),names.arg=M, space=0.3, ylab=precipitation in mm) lines (seq(0.8,20.3, by=1.3), RainFog$Rel.Hum./10, type=o) axis (4, at=seq(0, 8, by=2), labels=seq (0, 80, by=20)) dev.off() __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] More elegant way to do this?
Hi I am using R 2.2.0 under SuSE 10. I am creating a matrix MT to be used by barplot. DietF - read.csv (DietFem.csv, header = TRUE, as.is=TRUE) attach (DietF) PP - array(c(bud,flower,shoot,melon,seed.pod,detritus,other), c(16,7)) M - paste (Month) MT - t(PP) It works, but I have the feeling, there is a more elegant way of doing it, but I can't think of it. Thanks a lot, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Title for secondary y-axis (axis(4)) in barplot?
Uwe Ligges wrote: Rainer M KRug wrote: Hi I am using the following script to plot a barplot with a secondary axis in a bargplot for the line. It works, but I would like to have a title for the secondary y-axis on the right hand side of the axis - is this possible? Rainer RainFog - read.csv (Climate.csv, header = TRUE, as.is=TRUE) PP - array(c(RainFog$Rain, RainFog$Fog), c(16,2)) M - paste (RainFog$Month) png(filename=RainFog.png, width=960) barplot (t(PP), ylim=c(0,8),names.arg=M, space=0.3, ylab=precipitation in mm) lines (seq(0.8,20.3, by=1.3), RainFog$Rel.Hum./10, type=o) axis (4, at=seq(0, 8, by=2), labels=seq (0, 80, by=20)) dev.off() See ?mtext Thanks - exactly what I was looking for Rainer __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] pattern instead of colors in bargraph
Hi I am using R 2.2.0 under SuSE 10. I am creating a graph by using the following script: DietF - read.csv (DietFem.csv, header = TRUE, as.is=TRUE) attach (DietF) PP - array(c(bud,flower,shoot,melon,seed.pod,detritus,other), c(16,7)) M - paste (Month) detach (DietF) png(filename=DietF.png, width=960) barplot (t(PP), ylim=c(0,1), names.arg=M, space=0.3, ylab=proportion of diet) dev.off() The problem is that I would need the bars to be filled with pattern (striped, diagonal striped, dotted, ...) instead of the colors as it is extremely difficult to see which is which. I didn't find anything in the help which showed me how to do it. Is it possible, and if yes how? Thanks a lot, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Create graphs from text console
Hi I am using R 2.2.1 under Linux (SuSE 10) and would like to know if it is possible to create graphs, i.e. jpeg(filename=fn) try( coplot( mor$I_Morisita ~ mor$Year | mor$RunStr, show.given=FALSE) ) dev.off() from a text console? It gives me an error message on the jpeg() command: Error in X11(..snip..) unable to start device jpeg In addition: warning message: unable to open connection to X11 display. Are there any ways to create the plot and save it into a jpeg file from a text console? Thanks, Rainer -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Create graphs from text console
Thanks a lot for all your help and tips. As I don't need publishhable quality, I will go with the bitmap option. Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R, Eclipse and StatEt plugin under Linux
Hi I try to use the R plugin StatET 3.1-M2 (0.2.1) under eclipse 3.1.1 in Linux. Everything works fine, except of the integration of the R console into eclipse. On the StatET website (http://www.walware.de/goto/statet) it states: *** Do you know, how to start R inside Eclipse on Unix/Linux preventing the batch-modus, which parameters are useful? Let me know. *** and this is exactly the problem. I managed to convince R not to start in batch mobe by using the parameter --save, --no-save or --vanilla, but it is stuck before reaching the input prompt. The last thing it says is: [Previously saved workspace restored] and that is it - and eclipse's progress bar is stuck. I can cancel it by pressing the cancel button, but the console closes. Any ides on how to solve the problem? Thanks, Rainer -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to get the intercept from lm?
Hi I am using R 2.2.0 under SuSE 10 I want to use lm() to get the slope and intercept for several daatasets and store them in a database. So far so good - but how do I extract the slope and the intercept from the result from lm()? my code looks like this: lmNNDens - lm(log(DensNN$MeanNN) ~ log(DensNN$MeanDensity)) anovaLM - anova(lmNNDens) Results$slope[No] - ???lmNNDens??? Results$intercept[No] - ???lmNNDens??? any help welcome, Rainer -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10
Hi I have problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10. It installs fine, all dependances are OK (at least Yast does not complain) but when I try to run R, it gives the following error message: symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename and R quits. blas version: 3.0-926 Any help appreciated, Rainer -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10
Nope - If I enter rpm -qf `which gfortran` I get gcc-fortran-4.0.2_20050901-3 Rainer Peter Dalgaard wrote: Rainer M Krug [EMAIL PROTECTED] writes: Hi I have problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10. It installs fine, all dependances are OK (at least Yast does not complain) but when I try to run R, it gives the following error message: symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename and R quits. blas version: 3.0-926 Any help appreciated, Rainer I suspect you're missing turmalin:~/rpm -qf `which gfortran` gcc-fortran-4.0.2_20050901-3 -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10
I used the SuSE 10 CDs as installation sources and added afterwards OpenSuse sources and extra CDs for Suse 10 and OpenSuse. By the way, I decided to compile it from source and it worked without problems - no errors. I guess that one of the versions used in the compilation for the rpms is not compatible with a newer version. Thanks for your help, Rainer Peter Dalgaard wrote: Rainer M Krug [EMAIL PROTECTED] writes: Nope - If I enter rpm -qf `which gfortran` I get gcc-fortran-4.0.2_20050901-3 Rainer Hmm, where did the blas come in? I don't seem to have it on the SuSE 10 machine that I have access to (but it is running R-base-2.2.0-0). Peter Dalgaard wrote: Rainer M Krug [EMAIL PROTECTED] writes: Hi I have problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10. It installs fine, all dependances are OK (at least Yast does not complain) but when I try to run R, it gives the following error message: symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename and R quits. blas version: 3.0-926 Any help appreciated, Rainer I suspect you're missing turmalin:~/rpm -qf `which gfortran` gcc-fortran-4.0.2_20050901-3 -- -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Why is bubbles() creating empty png graphs?
This code below produces empty XXX.png files - if I use plot(), it works
and if I enter the commands
png(filename=fn)
bubble(positions, do.sqrt=FALSE, main=q)
dev.off()
manually, it works as well.
I am lost - any help appreciated.
The weird thing is that it worked before I made some changes... (I don't
have a copy of the working version...).
R version:
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major2
minor2.0
year 2005
month10
day 06
svn rev 35749
language R
Operating system: SuSE 10
Rainer
-
library(gstat)
library(RMySQL)
library(DAAG)
m - dbDriver(MySQL)
con - dbConnect(m, group = renpatch_renosterbos)
tbls - dbListTables(con)
runs - 1:5
years - seq(98, 0, -7)
progress_end - length(tbls) * length(runs) * length(years)
progress - 0
for (year in years)
{
fd - paste(/home/rkrug/Documents/R/plots/Y, year, sep=)
dir.create(fd, showWarnings=FALSE, recursive = TRUE)
for (run in runs)
{
for (tn in tbls)
{
fn - paste(fd, /, tn, _R, run, _Y, year, .png, sep=)
progress - progress + 1
cat(progress, 'of', progress_end, | , fn, | )
flush.console()
if (!file.exists(fn))
{
q - paste(select X,Y,RX from, tn, where (_run=, run, ) AND
(_Year=, year, ))
rs - dbSendQuery(con, q)
positions - fetch(rs, n = -1)
while (!dbHasCompleted(rs))
{
cat(.)
flush.console()
}
cat(length(positions$X), points)
png(filename=fn)
bubble(positions, do.sqrt=FALSE, main=q)
#plot(positions)
dev.off()
pause()
cat( | Done \n)
}
}
}
}
--
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:+27 - (0)83 9479 042
email:[EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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Re: [R] Why is bubbles() creating empty png graphs?
Thanks a lot for yor help - it is working now
Rainer
Roger Bivand wrote:
On Thu, 15 Dec 2005, Rainer M Krug wrote:
This code below produces empty XXX.png files - if I use plot(), it works
and if I enter the commands
png(filename=fn)
bubble(positions, do.sqrt=FALSE, main=q)
dev.off()
manually, it works as well.
This a hidden FAQ 7.22: Why do lattice/trellis graphics not work?
bubble() in package sp or gstat calls lattice function xyplot internally,
so doing print(bubble(...)) should work.
I am lost - any help appreciated.
The weird thing is that it worked before I made some changes... (I don't
have a copy of the working version...).
R version:
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major2
minor2.0
year 2005
month10
day 06
svn rev 35749
language R
Operating system: SuSE 10
Rainer
-
library(gstat)
library(RMySQL)
library(DAAG)
m - dbDriver(MySQL)
con - dbConnect(m, group = renpatch_renosterbos)
tbls - dbListTables(con)
runs - 1:5
years - seq(98, 0, -7)
progress_end - length(tbls) * length(runs) * length(years)
progress - 0
for (year in years)
{
fd - paste(/home/rkrug/Documents/R/plots/Y, year, sep=)
dir.create(fd, showWarnings=FALSE, recursive = TRUE)
for (run in runs)
{
for (tn in tbls)
{
fn - paste(fd, /, tn, _R, run, _Y, year, .png, sep=)
progress - progress + 1
cat(progress, 'of', progress_end, | , fn, | )
flush.console()
if (!file.exists(fn))
{
q - paste(select X,Y,RX from, tn, where (_run=, run, ) AND
(_Year=, year, ))
rs - dbSendQuery(con, q)
positions - fetch(rs, n = -1)
while (!dbHasCompleted(rs))
{
cat(.)
flush.console()
}
cat(length(positions$X), points)
png(filename=fn)
bubble(positions, do.sqrt=FALSE, main=q)
#plot(positions)
dev.off()
pause()
cat( | Done \n)
}
}
}
}
--
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:+27 - (0)83 9479 042
email:[EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] O-ring statistic in R?
Hi Thorsten Wiegand used in his paper Wiegand T., and K. A. Moloney 2004. Rings, circles and null-models for point pattern analysis in ecology. Oikos 104: 209-229 a statistic he called O-Ring statistic which is similar to Ripley's K, only that it uses rings instead of circles. http://www.oesa.ufz.de/towi/towi_programita.html#ring Is this statistic included in one of the packages in R? Thanks, Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell:+27 - (0)83 9479 042 email:[EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install.packages under SuSE 10 behind proxy, R 2.2.0 from source
Hi I figured it out. if I use install.packages(..., method=wget) it works but if I use the default method, it doesn't. Rainer Rainer M. Krug wrote: Hi I installed R 2.2.0 from source and want to use install.packages but it doesn't work. http_proxy is set to http://proxy.sun.ac.za:3128 but it still can't connect to the repository. The mirror is available, I can connect to it via the internet. Any help welcome, Rainer -- NEW TELEPHONE NUMBER Tel:+27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] tcltk package problems (R 2.2.0, SuSE 10)
Hi I installed R 2.2.0 from source and I have the packages for tcl and tk installed on my system, but the package tcltk says, when I try to load the library tcltk: Tcl/Tk support is not available on this system. Are there any settings / variables which I have to set so that R recognises that Tcl/Tk support is installed on the system? Rainer -- NEW TELEPHONE NUMBER Tel:+27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] install.packages under SuSE 10 behind proxy, R 2.2.0 from source
Hi I installed R 2.2.0 from source and want to use install.packages but it doesn't work. http_proxy is set to http://proxy.sun.ac.za:3128 but it still can't connect to the repository. The mirror is available, I can connect to it via the internet. Any help welcome, Rainer -- NEW TELEPHONE NUMBER Tel:+27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Show Progress in loop
Hi
I have a loop which is doing time consuming calculations and I would
like to be able to have some feedback on where it is in it's
calculations. I tried to simply show the counter variable in the loop,
but id doesn't work as all display seems to be delayed until the loop is
completed. Is there any way of displaying the progress of a loop?
Rainer
The loop:
for (i in 2:Result$NoSims)
{
ppp - runifpoint(Result$NoPlants)
K - Kest(ppp)
Result$LSim[i,] - sqrt(K$iso / pi) - K$r
CM - (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
Result$SigCM[i] - sum(CM, na.rm=TRUE)
i #Doesn't display in the loop
}
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
__
R-help@stat.math.ethz.ch mailing list
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Re: [R] Show Progress in loop
I put print(i) in the loop instead of i, but it still only prints (in
the Windows R GUI) i after it finished the calculations.
I guess it might be due to the output buffering you mentioned - but how
do I unset it?
Rainer
Peter Dalgaard wrote:
Rainer M. Krug [EMAIL PROTECTED] writes:
Hi
I have a loop which is doing time consuming calculations and I would
like to be able to have some feedback on where it is in it's
calculations. I tried to simply show the counter variable in the loop,
but id doesn't work as all display seems to be delayed until the loop is
completed. Is there any way of displaying the progress of a loop?
Rainer
The loop:
for (i in 2:Result$NoSims)
{
ppp - runifpoint(Result$NoPlants)
K - Kest(ppp)
Result$LSim[i,] - sqrt(K$iso / pi) - K$r
CM - (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
Result$SigCM[i] - sum(CM, na.rm=TRUE)
i #Doesn't display in the loop
}
Just print(i) and if on Windows, remember to unset output buffering.
--
NEW TELEPHONE NUMBER
Tel:+27 - (0)72 808 2975 (w)
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Show Progress in loop
Thanks - flush.console() did the trick.
As you might guess, I am quite new to R. I like the idea of vectorizing
the calculation, but I guess it is not possible in this case - I will
ask in a new thread.
Thanks,
Rainer
Uwe Ligges wrote:
Rainer M. Krug wrote:
Hi
I have a loop which is doing time consuming calculations and I would
like to be able to have some feedback on where it is in it's
calculations. I tried to simply show the counter variable in the loop,
but id doesn't work as all display seems to be delayed until the loop
is completed. Is there any way of displaying the progress of a loop?
Rainer
The loop:
for (i in 2:Result$NoSims)
{
ppp - runifpoint(Result$NoPlants)
K - Kest(ppp)
Result$LSim[i,] - sqrt(K$iso / pi) - K$r
CM - (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
Result$SigCM[i] - sum(CM, na.rm=TRUE)
i #Doesn't display in the loop
}
- Update your console (I guess you are on Windows?) by using
flush.console().
- You might want to measure time consumption, hence see ?Rprof.
- Save some more time by moving as much as possible out of your loop by
doing it in a vectorized way (I don't know all the functions you are
using, hence cannot make any further recommendations).
Uwe Ligges
--
NEW TELEPHONE NUMBER
Tel:+27 - (0)72 808 2975 (w)
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Vectorizing loop
Hi
I have the following loop and would like to vectorize it. Any ideas if
it is possible?
Thanks,
Rainer
Tha Loop:
for (i in 2:Result$NoSims)
{
ppp - runifpoint(Result$NoPlants)
K - Kest(ppp)
Result$LSim[i,] - sqrt(K$iso / pi) - K$r
CM - (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
Result$SigCM[i] - sum(CM, na.rm=TRUE)
print(i)
flush.console()
}
--
NEW TELEPHONE NUMBER
Tel:+27 - (0)72 808 2975 (w)
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
