[R] Accessing methods and extending S4 classes of existing packages
Dear all, I am trying to understand how to access S4 methods after loading a package, using the online documentation of getMethod and friends. This is what I have been trying: library(coin) findMethods(ApproxNullDistribution) list() Warning message: In findMethods(ApproxNullDistribution) : nicht-generische Funktion an findMethods() übergeben whereas in the source of coin I can see the lines: setGeneric(ApproxNullDistribution, function(object, ...) standardGeneric(ApproxNullDistribution)) It seems that I am not getting what is going on here. Could anybody give me a hint? Greetings Johannes -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:[EMAIL PROTECTED] from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Parallel R
Juan Pablo Romero Méndez [EMAIL PROTECTED] writes: Hello, The problem I'm working now requires to operate on big matrices. I've noticed that there are some packages that allows to run some commands in parallel. I've tried snow and NetWorkSpaces, without much success (they are far more slower that the normal functions) Do you mean like this? library(Rmpi) mpi.spawn.Rslaves(nsl=2) # dual core on my laptop m - matrix(0, 1, 1000) system.time(x1 - apply(m, 2, sum), gcFirst=TRUE) user system elapsed 0.644 0.148 1.017 system.time(x2 - mpi.parApply(m, 2, sum), gcFirst=TRUE) user system elapsed 5.188 2.844 10.693 ? (This is with Rmpi, a third alternative you did not mention; 'elapsed' time seems to be relevant here.) The basic problem is that the overhead of dividing the matrix up and communicating between processes outweighs the already-efficient computation being performed. One solution is to organize your code into 'coarse' grains, so the FUN in apply does (considerably) more work. A second approach is to develop a better algorithm / use an appropriate R paradigm, e.g., system.time(x3 - colSums(m), gcFirst=TRUE) user system elapsed 0.060 0.000 0.088 (or even faster, x4 - rep(0, ncol(m)) ;) A third approach, if your calculations make heavy use of linear algebra, is to build R with a vectorized BLAS library; see the R Installation and Administration guide. A fourth possibility is to use Tierney's 'pnmath' library mentioned in this thread https://stat.ethz.ch/pipermail/r-help/2007-December/148756.html The README file needs to be consulted for the not-exactly-trivial (on my system) task of installing the package. Specific functions are parallelized, provided the length of the calculation makes it seem worth-while. system.time(exp(m), gcFirst=TRUE) user system elapsed 0.108 0.000 0.106 library(pnmath) system.time(exp(m), gcFirst=TRUE) user system elapsed 0.096 0.004 0.052 (elapsed time about 2x faster). Both BLAS and pnmath make much better use of resources, since they do not require multiple R instances. None of these approaches would make a colSums faster -- the work is just too small for the overhead. Martin My problem is very simple, it doesn't require any communication between parallel tasks; only that it divides simetricaly the task between the available cores. Also, I don't want to run the code in a cluster, just my multicore machine (4 cores). What solution would you propose, given your experience? Regards, Juan Pablo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calculating quarterly statistics for time series object
I have time series observation on daily frequencies : library(zoo) SD=1 date1 = seq(as.Date(01/01/01, format = %m/%d/%y), as.Date(12/31/02, format = %m/%d/%y), by = 1) len1 = length(date1); data1 = zoo(matrix(rnorm(len1, mean=0, sd=SD*0.5), nrow = len1), date1) plot(data1) Now I want to calculate 1. Quarterly statistics like mean, variance etc and 2. Weekly statistics, where as per my definition week starts from Wednesday and ends on Tuesday. I can define some 'for' loop for doing those. However it takes considerably amount of time. Is there any advance methods in R to do the same? Regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculating quarterly statistics for time series object
See ?aggregate.zoo, ?as.yearqtr and vignette(zoo-quickref) and
the other zoo vignettes.
library(zoo)
SD - 1
date1 - seq(as.Date(2001-01-01), as.Date(2002-12-1), by = day)
len1 - length(date1)
set.seed(1) # to make it reproducible
data1 - zoo(rnorm(len1), date1)
plot(data1)
# quarterly summary
data1q.mean - aggregate(data1, as.yearqtr, mean)
data1q.sd - aggregate(data1, as.yearqtr, sd)
plot(cbind(mean = data1q.mean, sd = data1q.sd), main = Quarterly)
# weekly summary - week ends on tuesday
# Given a date find the next Tuesday.
# Based on formula in Prices and Returns section of zoo-quickref vignette.
nexttue - function(x) 7 * ceiling(as.numeric(x - 2 + 4)/7) + as.Date(2 - 4)
data1w - cbind(
mean = aggregate(data1, nexttue, mean),
sd = aggregate(data1, nexttue, sd)
)
head(data1w)
plot(data1w, main = Weekly)
### ALTERNATIVE ###
# Create function ag like aggregate but takes vector of
# function names.
FUNs - c(mean, sd)
ag - function(z, by, FUNs) {
f - function(f) aggregate(z, by, f)
do.call(cbind, sapply(FUNs, f, simplify = FALSE))
}
data1q - ag(data1, as.yearqtr, c(mean, sd))
data1w - ag(data1, nexttue, c(mean, sd))
On Sun, Jun 29, 2008 at 3:17 AM, Megh Dal [EMAIL PROTECTED] wrote:
I have time series observation on daily frequencies :
library(zoo)
SD=1
date1 = seq(as.Date(01/01/01, format = %m/%d/%y), as.Date(12/31/02,
format = %m/%d/%y), by = 1)
len1 = length(date1); data1 = zoo(matrix(rnorm(len1, mean=0, sd=SD*0.5), nrow
= len1), date1)
plot(data1)
Now I want to calculate 1. Quarterly statistics like mean, variance etc and
2. Weekly statistics, where as per my definition week starts from Wednesday
and ends on Tuesday.
I can define some 'for' loop for doing those. However it takes considerably
amount of time. Is there any advance methods in R to do the same?
Regards,
[[alternative HTML version deleted]]
__
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[R] How to get an argument dynamically from a list?
Hi,
I'd like to get an argument (I think it's the right term) dynamically from a
list, but cannot manage to do it.
Here is the code I use:
#output given by database
BOB - c('A/A', 'C/C', '15/27')
MARY - c('A/A', NA, '13/12')
JOHN - c('A/A', 'C/A', '154/35')
CLIFF - c('A/C', 'C/C', '15/12')
PAM - c('A/C', 'C/A', '13/12')
sampleList - c(BOB, MARY, JOHN, CLIFF, PAM)
polyList - c(rs123, rs124, rs555)
#make dataframe with data
data.raw - data.frame(t(do.call(data.frame, lapply(sampleList, get
names(data.raw) - polyList
row.names(data.raw) - sampleList
I want to get, for example, data.raw$rs124 using polyList.
I tried
get(paste(data.raw$, polyList[2], sep=))
Error in get(paste(data.raw$, polyList[2], sep = )) :
variable data.raw$rs124 was not found
but it's obviously not the right way, data.raw$rs124 not being a variable per
se.
Any idea about how I could do that?
Thanks,
Stephane
__
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Re: [R] Interactive plot
Install the GTK runtime: http://www.ggobi.org/rgtk2/ On Sun, Jun 29, 2008 at 9:06 AM, Ron Michael [EMAIL PROTECTED] wrote: whenever I try to load playwith package I get following error : library(playwith) Loading required package: lattice Loading required package: grid Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'playwith' What to do? --- On Sun, 29/6/08, Liviu Andronic [EMAIL PROTECTED] wrote: From: Liviu Andronic [EMAIL PROTECTED] Subject: Re: [R] Interactive plot To: Ron Michael [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Date: Sunday, 29 June, 2008, 7:46 PM On 6/29/08, Ron Michael [EMAIL PROTECTED] wrote: Now I want to present the plot in some interactive manner. I want to put a slider in the plot where user move the slider for the 1st element of the vector vary and automatically this result will be reflected at the plot window. playwith: A GUI for interactive plots using GTK+ ? [1] [1] http://cran.at.r-project.org/web/packages/playwith/index.html Send instant messages to your online friends http://uk.messenger.yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Arial font in R
Hi, I have created a couple of plots in R and would like text in the plots to be size 12 Arial or Helvetica font. Is this possible? Thanks. Kobby __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get an argument dynamically from a list?
Is this what you want:
you have to use data.raw[[polyList[2]]] to access the data. (see ?[[)
lapply(polyList, function(x) as.character(data.raw[[x]]))
[[1]]
[1] A/A A/A A/A A/C A/C
[[2]]
[1] C/C NAC/A C/C C/A
[[3]]
[1] 15/27 13/12 154/35 15/12 13/12
On Sun, Jun 29, 2008 at 3:24 PM, Stephane Bourgeois [EMAIL PROTECTED] wrote:
Hi,
I'd like to get an argument (I think it's the right term) dynamically from a
list, but cannot manage to do it.
Here is the code I use:
#output given by database
BOB - c('A/A', 'C/C', '15/27')
MARY - c('A/A', NA, '13/12')
JOHN - c('A/A', 'C/A', '154/35')
CLIFF - c('A/C', 'C/C', '15/12')
PAM - c('A/C', 'C/A', '13/12')
sampleList - c(BOB, MARY, JOHN, CLIFF, PAM)
polyList - c(rs123, rs124, rs555)
#make dataframe with data
data.raw - data.frame(t(do.call(data.frame, lapply(sampleList, get
names(data.raw) - polyList
row.names(data.raw) - sampleList
I want to get, for example, data.raw$rs124 using polyList.
I tried
get(paste(data.raw$, polyList[2], sep=))
Error in get(paste(data.raw$, polyList[2], sep = )) :
variable data.raw$rs124 was not found
but it's obviously not the right way, data.raw$rs124 not being a variable per
se.
Any idea about how I could do that?
Thanks,
Stephane
__
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Accessing methods and extending S4 classes of existing packages
Johannes Huesing [EMAIL PROTECTED] [Sun, Jun 29, 2008 at 08:13:27AM CEST]: Dear all, I am trying to understand how to access S4 methods after loading a package, using the online documentation of getMethod and friends. I am just realizing that the lack of online documentation on S4 methods, which was lamented so long, has apparently been filled by How S4 Methods Work by John Chambers. So please hang on until I have read this piece and will be able to ask more educated questions about that matter. -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:[EMAIL PROTECTED] from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interactive plot
Hi, whenever I try to load the playwith package I am getting following warning : Â library(playwith) Loading required package: lattice Loading required package: grid Warning message: In namespaceImportFrom(self, asNamespace(ns)) : Â replacing previous import: addhandler Can anyone please tell me why I am getting that warning? --- On Sun, 29/6/08, Gabor Grothendieck [EMAIL PROTECTED] wrote: From: Gabor Grothendieck [EMAIL PROTECTED] Subject: Re: [R] Interactive plot To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Date: Sunday, 29 June, 2008, 8:18 PM Install the GTK runtime: http://www.ggobi.org/rgtk2/ On Sun, Jun 29, 2008 at 9:06 AM, Ron Michael [EMAIL PROTECTED] wrote: whenever I try to load playwith package I get following error : library(playwith) Loading required package: lattice Loading required package: grid Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'playwith' What to do? --- On Sun, 29/6/08, Liviu Andronic [EMAIL PROTECTED] wrote: From: Liviu Andronic [EMAIL PROTECTED] Subject: Re: [R] Interactive plot To: Ron Michael [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Date: Sunday, 29 June, 2008, 7:46 PM On 6/29/08, Ron Michael [EMAIL PROTECTED] wrote: Now I want to present the plot in some interactive manner. I want to put a slider in the plot where user move the slider for the 1st element of the vector vary and automatically this result will be reflected at the plot window. playwith: A GUI for interactive plots using GTK+ ? [1] [1] http://cran.at.r-project.org/web/packages/playwith/index.html Send instant messages to your online friends http://uk.messenger.yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Send instant messages to your online friends http://uk.messenger.yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interactive plot
Hi all R users. I already done through some of the examples given with playwith
packages and feel nowhere they are matching with my requirement. Can amyone
please suggest me how to create my desired interactive plot with tkrplot ?
Â
I want following. Let look at following codes :
Â
mat = cbind(c(0.59710430,0.23057380), c(0.23057380, 0.5971089))
set.seed = 1000 vary = runif(dim(mat)[1], 2000, 3000) calc = function(mat, vary)
{
result = vector(length = (length(vary)+1))
result[1] = sqrt(t(vary) %*% vary)
for (i in 1 : length(vary))
{
result[(i+1)] = sum(vary)*sum(vary*mat[,i])
}
barplot(result)
return(result)
}
Â
Now I want to put a slider in the plot where user move the slider for the 1st
element of the vector vary and automatically this result will be reflected at
the plot window. Can anyone please tell me how to do that with tkrplot or
TeachingDemos ?
Â
Â
--- On Sun, 29/6/08, Ron Michael [EMAIL PROTECTED] wrote:
From: Ron Michael [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: Gabor Grothendieck [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 11:48 PM
Hi, whenever I try to load the playwith package I am getting following warning :
Â
library(playwith)
Loading required package: lattice
Loading required package: grid
Warning message:
In namespaceImportFrom(self, asNamespace(ns)) :
 replacing previous import: addhandler
Can anyone please tell me why I am getting that warning?
--- On Sun, 29/6/08, Gabor Grothendieck [EMAIL PROTECTED] wrote:
From: Gabor Grothendieck [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 8:18 PM
Install the GTK runtime:
http://www.ggobi.org/rgtk2/
On Sun, Jun 29, 2008 at 9:06 AM, Ron Michael [EMAIL PROTECTED]
wrote:
whenever I try to load playwith package I get following error
:
library(playwith)
Loading required package: lattice
Loading required package: grid
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library
'C:/PROGRA~1/R/R-27~1.1/library/RGtk2/libs/RGtk2.dll':
LoadLibrary failure: The specified module could not be found.
Error: package/namespace load failed for 'playwith'
What to do?
--- On Sun, 29/6/08, Liviu Andronic [EMAIL PROTECTED] wrote:
From: Liviu Andronic [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: Ron Michael [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 7:46 PM
On 6/29/08, Ron Michael [EMAIL PROTECTED] wrote:
Now I want to present the plot in some interactive manner. I want to
put
a slider in the plot where user move the slider for the 1st element of the
vector vary and automatically this result will be reflected at
the
plot window.
playwith: A GUI for interactive plots using GTK+ ? [1]
[1] http://cran.at.r-project.org/web/packages/playwith/index.html
Send instant messages to your online friends http://uk.messenger.yahoo.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Send instant messages to your online friends http://uk.messenger.yahoo.com
[[alternative HTML version
deleted]]__
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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.
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[[alternative HTML version deleted]]
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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] Interactive plot
In ?playwith the third example seems pretty close to what you
want. Here it is changed to correspond to your setup.
Remove the barplot line from calc since we don't want calc to do
any plotting and then try this:
library(lattice)
playwith(barchart(seq_along(result) ~ result,
data = data.frame(result = calc(mat, c(alpha, vary[2],
parameters = list(alpha = seq(2000, 3000, by = 10)))
On Sun, Jun 29, 2008 at 1:07 PM, Ron Michael [EMAIL PROTECTED] wrote:
Hi all R users. I already done through some of the examples given with
playwith packages and feel nowhere they are matching with my requirement. Can
amyone please suggest me how to create my desired interactive plot with
tkrplot ?
I want following. Let look at following codes :
mat = cbind(c(0.59710430,0.23057380), c(0.23057380,
0.5971089)) set.seed = 1000 vary = runif(dim(mat)[1], 2000, 3000) calc =
function(mat, vary)
{
result = vector(length = (length(vary)+1))
result[1] = sqrt(t(vary) %*% vary)
for (i in 1 : length(vary))
{
result[(i+1)] = sum(vary)*sum(vary*mat[,i])
}
barplot(result)
return(result)
}
Now I want to put a slider in the plot where user move the slider for the 1st
element of the vector vary and automatically this result will be reflected
at the plot window. Can anyone please tell me how to do that with tkrplot or
TeachingDemos ?
--- On Sun, 29/6/08, Ron Michael [EMAIL PROTECTED] wrote:
From: Ron Michael [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: Gabor Grothendieck [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 11:48 PM
Hi, whenever I try to load the playwith package I am getting following
warning :
library(playwith)
Loading required package: lattice
Loading required package: grid
Warning message:
In namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: addhandler
Can anyone please tell me why I am getting that warning?
--- On Sun, 29/6/08, Gabor Grothendieck [EMAIL PROTECTED] wrote:
From: Gabor Grothendieck [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 8:18 PM
Install the GTK runtime:
http://www.ggobi.org/rgtk2/
On Sun, Jun 29, 2008 at 9:06 AM, Ron Michael [EMAIL PROTECTED]
wrote:
whenever I try to load playwith package I get following error
:
library(playwith)
Loading required package: lattice
Loading required package: grid
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library
'C:/PROGRA~1/R/R-27~1.1/library/RGtk2/libs/RGtk2.dll':
LoadLibrary failure: The specified module could not be found.
Error: package/namespace load failed for 'playwith'
What to do?
--- On Sun, 29/6/08, Liviu Andronic [EMAIL PROTECTED] wrote:
From: Liviu Andronic [EMAIL PROTECTED]
Subject: Re: [R] Interactive plot
To: Ron Michael [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Date: Sunday, 29 June, 2008, 7:46 PM
On 6/29/08, Ron Michael [EMAIL PROTECTED] wrote:
Now I want to present the plot in some interactive manner. I want to
put
a slider in the plot where user move the slider for the 1st element of the
vector vary and automatically this result will be reflected at
the
plot window.
playwith: A GUI for interactive plots using GTK+ ? [1]
[1] http://cran.at.r-project.org/web/packages/playwith/index.html
Send instant messages to your online friends http://uk.messenger.yahoo.com
[[alternative HTML version deleted]]
__
R-help@r-project.org 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.
Send instant messages to your online friends http://uk.messenger.yahoo.com
[[alternative HTML version
deleted]]__
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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.
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[[alternative HTML version deleted]]
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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] Arial font in R
Kobby Essien kobby at seas.upenn.edu writes: Hi, I have created a couple of plots in R and would like text in the plots to be size 12 Arial or Helvetica font. Is this possible? Thanks. Kobby Well, 12 point Helvetica is actually the default for PDF and PostScript files (see ?pdf and ?postscript, especially the family and pointsize arguments). Can you be more specific about what you need if the default is not working for you? Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Survival Analysis with two different events
Hello all, I am hoping to use survival analysis to examine whether parasite attack increases nest death in a species of social wasp. I therefore have data for 1. Whether the nest died in the 6 week census period (Status, where 1=died, 0=survived) 2. The day number of death/last recorded day it was observed alive. 3. Whether the nest was attacked by the parasite (0/1 as with 1.) 4. The day number of attack/ last recorded day the nest was observed without a parasite. i.e. example dataset: status death para paraday 0 42 0 42 1 32 0 42 1 25 1 13 0 42 1 25 ... I've looked over r-help, as well as in Crawley etc., but I have yet to find a solution. Can anyone point me in the right direction or literature? Many thanks, Edd Almond -- View this message in context: http://www.nabble.com/Survival-Analysis-with-two-different-events-tp18183526p18183526.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interactive plot
It is not working here. I am getting following errors [big list :( ]Â : Â library(playwith) Loading required package: grid Warning message: In namespaceImportFrom(self, asNamespace(ns)) : Â replacing previous import: addhandler library(lattice) playwith(barchart(seq_along(result) ~ result, + data = data.frame(result = calc(mat, c(alpha, vary[2], + parameters = list(alpha = seq(2000, 3000, by = 10))) Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Go back to previous plot call) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Go forward to next plot call) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Redraw the current plot (hold Shift for full reload)) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Show help page for this plot function) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Loading required package: RGtk2 Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Always show this window) : Â Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Keep this window, do not replace it (open next plot in a new window)) : Â Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Copy this plot to the clipboard (as a bitmap)) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = View and edit attached data objects) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Change the plot type and settings) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Choose Lattice theme) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Time mode: scroll along the x-axis) : Â Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Choose a panel to expand and focus (for further interaction)) : Â Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Identify data points by clicking on them) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Add your own labels to the plot) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Add an arrow to the plot) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Edit annotations (including arrows)) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Remove labels and annotations) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Select a new plot region with the mouse) : Â Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject,
Re: [R] Survival Analysis with two different events
sickboyedd sickboyedd at gmail.com writes: Hello all, I am hoping to use survival analysis to examine whether parasite attack increases nest death in a species of social wasp. I therefore have data for 1. Whether the nest died in the 6 week census period (Status, where 1=died, 0=survived) 2. The day number of death/last recorded day it was observed alive. 3. Whether the nest was attacked by the parasite (0/1 as with 1.) 4. The day number of attack/ last recorded day the nest was observed without a parasite. i.e. example dataset: status death para paraday 0 42 0 42 1 32 0 42 1 25 1 13 0 42 1 25 ... I've looked over r-help, as well as in Crawley etc., but I have yet to find a solution. Can anyone point me in the right direction or literature? You might want to send this to r-sig-ecology if you need further discussion. In the meantime, the very simplest thing (conditioning on whether the nest was attacked or not) would be library(survival) c1 = coxph(Surv(death,status)~para,data=mydata) (you should definitely read up a bit on survival analysis, Cox proportional hazards, etc.. I think there's a chapter in the book by Scheiner and Gurevitch, geared towards ecologists). Dealing with parasite attack in a more fine-grained way (i.e. assessing mortality before and after parasitism) would be a little trickier, but I wouldn't worry about it until after you've understood the first stage of the analysis. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Accessing methods and extending S4 classes of existing packages
Johannes Huesing [EMAIL PROTECTED] [Sun, Jun 29, 2008 at 08:13:27AM CEST]: Dear all, I am trying to understand how to access S4 methods after loading a package, using the online documentation of getMethod and friends. This is what I have been trying: library(coin) findMethods(ApproxNullDistribution) list() Warning message: In findMethods(ApproxNullDistribution) : nicht-generische Funktion an findMethods() übergeben whereas in the source of coin I can see the lines: setGeneric(ApproxNullDistribution, function(object, ...) standardGeneric(ApproxNullDistribution)) It seems that I am not getting what is going on here. Could anybody give me a hint? It seems like the package authors chose not to export the ApproxNullDistribution generic method from the package, as seen in the NAMESPACE file of the package. Does it mean that if I want to write personal extensions to the package, the correct approach is to take the whole package and modify it? -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:[EMAIL PROTECTED] from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interactive plot
I get those errors too but it works anyways. On Sun, Jun 29, 2008 at 2:09 PM, Ron Michael [EMAIL PROTECTED] wrote: It is not working here. I am getting following errors [big list :( ] : library(playwith) Loading required package: grid Warning message: In namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: addhandler library(lattice) playwith(barchart(seq_along(result) ~ result, + data = data.frame(result = calc(mat, c(alpha, vary[2], + parameters = list(alpha = seq(2000, 3000, by = 10))) Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Go back to previous plot call) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Go forward to next plot call) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Redraw the current plot (hold Shift for full reload)) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Show help page for this plot function) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Loading required package: RGtk2 Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Always show this window) : Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Keep this window, do not replace it (open next plot in a new window)) : Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Copy this plot to the clipboard (as a bitmap)) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = View and edit attached data objects) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Change the plot type and settings) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Choose Lattice theme) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Time mode: scroll along the x-axis) : Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Choose a panel to expand and focus (for further interaction)) : Cannot find 'tooltip-text' to set in GtkToggleToolButton, GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Identify data points by clicking on them) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Add your own labels to the plot) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Add an arrow to the plot) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Edit annotations (including arrows)) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Remove labels and annotations) : Cannot find 'tooltip-text' to set in GtkToolButton, GtkToolItem, GtkBin, GtkContainer, GtkWidget, GtkObject, GInitiallyUnowned, GObject, RGtkObject Error in `[[-.GObject`(`*tmp*`, tooltip-text, value = Select a new plot region with the mouse) : Cannot find
[R] function to export data
Hi,
Im trying to built a simple function that allows me to export
automatically some results to a text file. Ive tried the two following
approaches but none worked.
exportdata-function(x) {
+ dataexp-summary(x)
+ export(dataexp,type=ascii,file=dataexp.txt)
+ }
exportdata(glm.poisson0)
Error in eval(expr, envir, enclos) : object dataexp not found
exportdata2-function(x) {
sink(exportdata2.txt)
summary(x)
sink()
}
exportdata2(glm.poisson0) # the file is created but with no data in it.
Can anyone give me some hints on what Im missing here? I would be very
grateful for that.
Thanks.
Daniel Pires
Daniel Pires
Faculdade de Ciências da Universidade de Lisboa
Dep. Biologia Animal
Ed. C2, piso 2
Campo Grande 1749-016 Lisboa
Portugal
http://ffishgul.fc.ul.pt/ http://ffishgul.fc.ul.pt/
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and provide commented, minimal, self-contained, reproducible code.
[R] help
Dear : I am a college student, one R beginner, now i am doing one exercise with mclust package. I want to try one hierarchy cluster ananlysis on my data and my aim is to find out the clusters from the result and what are the members for each cluster? So can you give me some advices thanks in advance! chunping wang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help
mclust is not doing the hierarchicial clustering, if I understand your question correctly. Presumably you define certain distance measure, hclust and cut funtions should do the job. On the other hand, if the purpose is to extract the classification labels from mclust package, it should be straightforward based on its documentation. X 王春萍 写道: Dear : I am a college student, one R beginner, now i am doing one exercise with mclust package. I want to try one hierarchy cluster ananlysis on my data and my aim is to find out the clusters from the result and what are the members for each cluster? So can you give me some advices thanks in advance! chunping wang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: cannot install the package RMySQL
Hi, I first report the installing error to the r-sig-mac mailing list but it seems nobody ever encounter this annoying problem and I got no replies. so I am trying to forward it to this list, hope it never bothers. Anyone had the same problem, or what does the warning message mean ? Thank you in advance ! Begin forwarded message: From: Peng Jiang [EMAIL PROTECTED] Date: 2008å¹´6æ29æ¥ ä¸å11æ¶06å22ç§ To: [EMAIL PROTECTED] Subject: cannot install the package RMySQL Hi, I am writing to report the error when installed the package RMySQL. I tried installing for like 5 times and it gives the following error every time. gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now is it because all the downloading error or something else ? I am running Mac OS X 10.5.3 with R 2.7.1. thanks in advance. best regards --- Peng Jiang (æ±é¹), Ph.D. Candidate Antai College of Economics Management å®æ³°ç»æµç®¡çå¦é¢ Department of Mathematics æ°å¦ç³» Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China --- Peng Jiang æ±é¹ ,Ph.D. Candidate Antai College of Economics Management å®æ³°ç»æµç®¡çå¦é¢ Department of Mathematics æ°å¦ç³» Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help
Assuming that you have installed and loaded the mclust library, type ?Mclust in the R-prompt. An example is provided there with the popular iris dataset. It seems to be as simple as Mclust(yourdata), where yourdata contains the dataset (data columns of your dataset) on which you want to perform cluster analysis; see the documentation for options. By standard, Mclust looks for 1to 9 clusters. - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von ??? Gesendet: Sunday, June 29, 2008 11:10 PM An: [EMAIL PROTECTED]; [EMAIL PROTECTED] Betreff: [R] help Dear : I am a college student, one R beginner, now i am doing one exercise with mclust package. I want to try one hierarchy cluster ananlysis on my data and my aim is to find out the clusters from the result and what are the members for each cluster? So can you give me some advices thanks in advance! chunping wang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Parallel R
Thanks! It turned out that Rmpi was a good option for this problem after all. Nevetheless, pnmath seems very promising, although it doesn't load in my system: library(pnmath) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/jpablo/extra/R-271/lib/R/library/pnmath/libs/pnmath.so': libgomp.so.1: shared object cannot be dlopen()ed Error: package/namespace load failed for 'pnmath' I find it odd, because libgomp.so.1 is in /usr/lib, so R should find it. Juan Pablo On Sun, Jun 29, 2008 at 1:36 AM, Martin Morgan [EMAIL PROTECTED] wrote: Juan Pablo Romero Méndez [EMAIL PROTECTED] writes: Hello, The problem I'm working now requires to operate on big matrices. I've noticed that there are some packages that allows to run some commands in parallel. I've tried snow and NetWorkSpaces, without much success (they are far more slower that the normal functions) Do you mean like this? library(Rmpi) mpi.spawn.Rslaves(nsl=2) # dual core on my laptop m - matrix(0, 1, 1000) system.time(x1 - apply(m, 2, sum), gcFirst=TRUE) user system elapsed 0.644 0.148 1.017 system.time(x2 - mpi.parApply(m, 2, sum), gcFirst=TRUE) user system elapsed 5.188 2.844 10.693 ? (This is with Rmpi, a third alternative you did not mention; 'elapsed' time seems to be relevant here.) The basic problem is that the overhead of dividing the matrix up and communicating between processes outweighs the already-efficient computation being performed. One solution is to organize your code into 'coarse' grains, so the FUN in apply does (considerably) more work. A second approach is to develop a better algorithm / use an appropriate R paradigm, e.g., system.time(x3 - colSums(m), gcFirst=TRUE) user system elapsed 0.060 0.000 0.088 (or even faster, x4 - rep(0, ncol(m)) ;) A third approach, if your calculations make heavy use of linear algebra, is to build R with a vectorized BLAS library; see the R Installation and Administration guide. A fourth possibility is to use Tierney's 'pnmath' library mentioned in this thread https://stat.ethz.ch/pipermail/r-help/2007-December/148756.html The README file needs to be consulted for the not-exactly-trivial (on my system) task of installing the package. Specific functions are parallelized, provided the length of the calculation makes it seem worth-while. system.time(exp(m), gcFirst=TRUE) user system elapsed 0.108 0.000 0.106 library(pnmath) system.time(exp(m), gcFirst=TRUE) user system elapsed 0.096 0.004 0.052 (elapsed time about 2x faster). Both BLAS and pnmath make much better use of resources, since they do not require multiple R instances. None of these approaches would make a colSums faster -- the work is just too small for the overhead. Martin My problem is very simple, it doesn't require any communication between parallel tasks; only that it divides simetricaly the task between the available cores. Also, I don't want to run the code in a cluster, just my multicore machine (4 cores). What solution would you propose, given your experience? Regards, Juan Pablo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
