Re: [R] selecting rows for inclusion in lm
Why not use the subset option? Something like:
lm(diff ~ Age + Race, data=data, subset=data$Meno=="PRE")
should do the trick, and be much easier to read!
On 18/01/07, John Sorkin <[EMAIL PROTECTED]> wrote:
> I am having trouble selecting rows of a dataframe that will be included
> in a regression. I am trying to select those rows for which the variable
> Meno equals PRE. I have used the code below:
>
> difffitPre<-lm(data[,"diff"]~data[,"Age"]+data[,"Race"],data=data[data[,"Meno"]=="PRE",])
> summary(difffitPre)
>
> The output from the summary indicates that more than 76 rows are
> included in the regression:
>
> Residual standard error: 2.828 on 76 degrees of freedom
>
> where in fact only 22 rows should be included as can be seen from the
> following:
>
> print(data[length(data[,"Meno"]=="PRE","Meno"]))
> [1] 22
>
> I would appreciate any help in modifying the data= parameter of the lm
> so that I include only those subjects for which Meno=PRE.
>
> R 2.3.1
> Windows XP
>
> Thanks,
> John
>
> John Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> Baltimore VA Medical Center GRECC,
> University of Maryland School of Medicine Claude D. Pepper OAIC,
> University of Maryland Clinical Nutrition Research Unit, and
> Baltimore VA Center Stroke of Excellence
>
> University of Maryland School of Medicine
> Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
>
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> [EMAIL PROTECTED]
>
> Confidentiality Statement:
> This email message, including any attachments, is for the so...{{dropped}}
>
> __
> 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
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Re: [R] 3D Plot
> About 3D plots: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/6439.html Many other plot examples: http://addictedtor.free.fr/graphiques/allgraph.php I used rgl, it can produce interactive plots, which can be rotated, increased and decreased with the mouse. > Hi all R users, > > I want to draw a 3D plot, where the Z-axis will represent the normal > densities each with zero mean but different volatilities, Y-axis will > represent the SD [volatilities), and X-axis will represent time at which > these SD are calculated. > > Can anyone give me any clue? Your help will be highly appreciated. > > Thanks and regards, > Arun > > [[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] about rgl package.
The statement that it is for windows only in the first link in my previous post seems to me obsolete now. Unfortunately, I don't remember exactly, probably, I have used it in Linux. __ 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] selecting rows for inclusion in lm
> Why not use the subset option? Something like: > > lm(diff ~ Age + Race, data=data, subset=data$Meno=="PRE") > should do the trick, and be much easier to read! "data$" could be omitted, simply lm(diff ~ Age + Race, data=data, subset=Meno=="PRE") __ 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] curious about dimension of 'apply' output when MARGIN=1
On Wed, 17 Jan 2007, Patrick Burns wrote: > A logical reason for the phenomenon is that > matrices are stored down their columns. For > example: > > > matrix(1:15,5) > [,1] [,2] [,3] > [1,]16 11 > [2,]27 12 > [3,]38 13 > [4,]49 14 > [5,]5 10 15 > > When an 'apply' across rows is done, it will be > the values corresponding to each of the rows that > are together. > > For matrices, merely transposing the result fixes > the "problem", but it is considerably more complex > in higher dimensional arrays. [I don't think so, using aperm.] > There could be a spectrum of opinion from: > > the original programmer was lazy and didn't adequately > serve users > > to: > > the simpler the program the fewer bugs there will be. Or that the vision of the original designer was not limited to matrices. It just so happens that in this example the replacement is a single dimension the same size as the single margin used. That's atypical, and normally the result dimension has no connection to the margin. The design is to put the result dimension first, and the first item in the 'seealso' list is aperm(). To my mind the only general solutions are to put the result dimension first or last. I would have used last, but using first is slightly more efficient for the reason Pat gives. apply() is for arrays, operating over one or more margins with a function returning a 'scalar', vector or array result. Perhaps any 'lazy'-ness / limit of vision is not in handling array results as well as might be possible. > 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") -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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 to get the index of entry with max value in an array?
Thank you guys! I got it. Best, Feng - Original Message - From: "Benilton Carvalho" <[EMAIL PROTECTED]> To: "Feng Qiu" <[EMAIL PROTECTED]> Cc: Sent: Thursday, January 18, 2007 12:20 AM Subject: Re: [R] how to get the index of entry with max value in an array? > which.max() > b > > On Jan 17, 2007, at 11:20 PM, Feng Qiu wrote: > >> Hi all: >> A short question: >> For example, a=[3,4,6,2,3], obviously the 3rd entry of >> the array has the maxium value, what I want is index of the maxium >> value: 3. is there a neat expression to get this index? >> >> Thank you! >> >> Best, >> >> Feng __ 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] label option in 'barplot'?
Hello all, When using the 'barplot' function, how would one go about creating labels on the top of the bars corresponding to the actual frequency values (i.e., the height of the bar). For histograms, one can use the 'LABEL=T' parameter to this effect, but it is not available for barplot. Must one manually create such labels for a barplot (perhaps using mtext)? Thanks. Justin Gengler __ 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] curious about dimension of 'apply' output when MARGIN=1
On 18 Jan 2007, at 08:42, Prof Brian Ripley wrote:
> On Wed, 17 Jan 2007, Patrick Burns wrote:
>
>> A logical reason for the phenomenon is that
>> matrices are stored down their columns. For
>> example:
>
[snip]
> Or that the vision of the original designer was not limited to
> matrices.
> It just so happens that in this example the replacement is a single
> dimension the same size as the single margin used. That's
> atypical, and
> normally the result dimension has no connection to the margin. The
> design
> is to put the result dimension first, and the first item in the
> 'seealso'
> list is aperm().
>
> To my mind the only general solutions are to put the result dimension
> first or last. I would have used last, but using first is slightly
> more
> efficient for the reason Pat gives.
>
The case Brian Ripley mentions above is indeed atypical,
but it's encountered reasonably often, at least in the world of
high-dimensional magic hypercubes.
The most prominent examples would be sort() and the identity function.
Although the emphasis is different,
matlab's "sort" function when called with two
arguments, as in "sort(a,i)", sorts along dimension "i",
leaving the dimensions of the returned array unchanged.
R-and-octave.txt includes the following:
a <- array(1:24,2:4)
%Sort is a bit of a problem, due to the behaviour of apply():
sort(a,1) aperm(apply(a,c(2,3),sort),c(1,2,3))
sort(a,2) aperm(apply(a,c(1,3),sort),c(2,1,3))
sort(a,3) aperm(apply(a,c(1,2),sort),c(2,3,1))
It's possible to get round this by defining a little function:
asort <- function(a,i){
j <- 1:length(dim(a))
aperm(apply(a,j[-i],sort),append(j[-1],1,i-1))
}
Then R's asort(a,1) will return the same as Octave's sort(a,1).
Function asort() could easily be adapted to take a function name as a
third argument.
> apply() is for arrays, operating over one or more margins with a
> function
> returning a 'scalar', vector or array result. Perhaps any 'lazy'-
> ness /
> limit of vision is not in handling array results as well as might be
> possible.
>
>> 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")
>
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
> __
> R-help@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.
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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Re: [R] label option in 'barplot'?
Try this where you probably only want one of the last two lines: # population of 5 US states pop <- state.x77[1:5,1] bp <- barplot(pop, ylim = range(pop) * c(0, 1.1)) text(bp, pop, pop, adj = c(0.5, -0.5)) # place num above bar mtext(1, at = bp, text = pop, line = 3) # place num below label On 1/17/07, Justin Gengler <[EMAIL PROTECTED]> wrote: > Hello all, > > When using the 'barplot' function, how would one go about creating > labels on the top of the bars corresponding to the actual frequency > values (i.e., the height of the bar). For histograms, one can use > the 'LABEL=T' parameter to this effect, but it is not available for > barplot. Must one manually create such labels for a barplot (perhaps > using mtext)? > > Thanks. > > Justin Gengler > > __ > 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.
Re: [R] label option in 'barplot'?
Probably, you have to manually create, but it is easy: # for beside=F mp <- barplot(VADeaths) text(mp,y<-t(apply(VADeaths,2,cumsum)),y) # labels are values itself # or mp <- barplot(VADeaths) text(mp,t(apply(VADeaths,2,cumsum)),VADeaths) # labels are cumsum of values # for besides=T mp <- barplot(VADeaths,beside=T) text(mp,VADeaths,VADeaths) ## maybe some adjustment is required for y position, then, for example, mp <- barplot(VADeaths,beside=T) text(mp,VADeaths+3,VADeaths) HTH On 1/18/07, Justin Gengler <[EMAIL PROTECTED]> wrote: > Hello all, > > When using the 'barplot' function, how would one go about creating > labels on the top of the bars corresponding to the actual frequency > values (i.e., the height of the bar). For histograms, one can use > the 'LABEL=T' parameter to this effect, but it is not available for > barplot. Must one manually create such labels for a barplot (perhaps > using mtext)? > > Thanks. > > Justin Gengler > > __ > 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.
Re: [R] label option in 'barplot'?
Justin Gengler wrote: > Hello all, > > When using the 'barplot' function, how would one go about creating > labels on the top of the bars corresponding to the actual frequency > values (i.e., the height of the bar). For histograms, one can use > the 'LABEL=T' parameter to this effect, but it is not available for > barplot. Must one manually create such labels for a barplot (perhaps > using mtext)? Yes, I believe you would need to add those labels yourself. Use text() rather than mtext() to get something similar to what hist() does when labels=TRUE. Here is how you could put the labels either just below or just above the top of the bar: # Below X <- barplot(VADeaths, beside=TRUE, ylim=c(0,80)) text(X, VADeaths, labels=VADeaths, pos=1, offset=.5, col="red") # Above X <- barplot(VADeaths, beside=TRUE, ylim=c(0,80)) text(X, VADeaths, labels=VADeaths, pos=3, offset=.5) > Thanks. > > Justin Gengler > > __ > 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ 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] How to formulate an analytical gradient?
How to formulate an analytical gradient?
Suppose I have the following function/expression:
fr<-function(x){
x1=x[1]
x2=x[2]
x3=x[3]
x4=x[4]
x5=x[5]
z<-((gamma(x1+n)))/((gamma(x1)*factorial(n))*((1+(e/x2))^x1)*((1+(x2/e))^n))
v<-((gamma(x3+n)))/((gamma(x3)*factorial(n))*((1+(e/x4))^x3)*((1+(x4/e))^n))
sum(log( (x5*z)+ ((1-x5)*v) ))
}
These are a mix of two negative binomial distributions, where n and e are
know vectors, and I would like to calculate the maxiumum likelihood
estimates of the parameters x1,x2,x3,x4 and X5
I am relying on numerical gradients but I think if I use an analytical one
it will be more accurate especially when number of parameters is more than
4.
Thanks.
--
View this message in context:
http://www.nabble.com/How-to-formulate-an-analytical-gradient--tf3033293.html#a8428063
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] selecting rows for inclusion in lm
At 08:19 18/01/2007, David Barron wrote:
>Why not use the subset option? Something like:
>
>lm(diff ~ Age + Race, data=data, subset=data$Meno=="PRE")
>
>should do the trick, and be much easier to read!
And indeed the advice in
> library(fortunes)
> fortune("dog")
Firstly, don't call your matrix 'matrix'. Would you call your dog 'dog'?
Anyway, it might clash with the function 'matrix'.
-- Barry Rowlingson
R-help (October 2004)
>
also helps to make life clearer I find
>On 18/01/07, John Sorkin <[EMAIL PROTECTED]> wrote:
>>I am having trouble selecting rows of a dataframe that will be included
>>in a regression. I am trying to select those rows for which the variable
>>Meno equals PRE. I have used the code below:
>>
>>difffitPre<-lm(data[,"diff"]~data[,"Age"]+data[,"Race"],data=data[data[,"Meno"]=="PRE",])
>>summary(difffitPre)
>>
>>The output from the summary indicates that more than 76 rows are
>>included in the regression:
>>
>>Residual standard error: 2.828 on 76 degrees of freedom
>>
>>where in fact only 22 rows should be included as can be seen from the
>>following:
>>
>>print(data[length(data[,"Meno"]=="PRE","Meno"]))
>>[1] 22
>>
>>I would appreciate any help in modifying the data= parameter of the lm
>>so that I include only those subjects for which Meno=PRE.
>>
>>R 2.3.1
>>Windows XP
>>
>>Thanks,
>>John
>>
>>John Sorkin M.D., Ph.D.
>>Chief, Biostatistics and Informatics
>>Baltimore VA Medical Center GRECC,
>>University of Maryland School of Medicine Claude D. Pepper OAIC,
>>University of Maryland Clinical Nutrition Research Unit, and
>>Baltimore VA Center Stroke of Excellence
>>
>>University of Maryland School of Medicine
>>Division of Gerontology
>>Baltimore VA Medical Center
>>10 North Greene Street
>>GRECC (BT/18/GR)
>>Baltimore, MD 21201-1524
>>
>>(Phone) 410-605-7119
>>(Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>[EMAIL PROTECTED]
>>
>>Confidentiality Statement:
>>This email message, including any attachments, is for the so...{{dropped}}
>>
>>__
>>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
>
>
Michael Dewey
http://www.aghmed.fsnet.co.uk
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Re: [R] Fast Removing Duplicates from Every Column
Thx Jim. The Code works perfect when I run it in a plain way.
It gives a dataframe with 160 columns (like it should)
But when I run the code in a function it gives a dataframe with 161 columns
and the order of the columns has changed into an alfabethical order. Do you
know why this occurs?
Selection = function ()
{
TestUnique <- apply(Selection,2,unique)
MaxLen <- max(sapply(TestUnique,length))
TestUnique <- lapply(TestUnique,function(x)
{
c(x,rep('0',MaxLen-length(x)))
})
Selection.Unique <<- data.frame(TestUnique)
}
_
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: 18 January 2007 02:28
To: Bert Jacobs
Cc: Petr Pikal; R help list
Subject: Re: [R] Fast Removing Duplicates from Every Column
Here is one way of doing it by 'padding' all the elements to the same
length:
> x <- "Col1 Col2 Col3 Col159 Col160
+ Row1 0 0 LD 0 VD
+ Row2 HD0 0 0 MD
+ Row3 0 HDHD 0 LD
+ Row4 LDHDHD 0 0
+ LastRowHDHDLD 0 MD"
> input <- read.table(textConnection(x), header=TRUE)
> Uniq <- apply(input, 2, unique)
> # find maximum length of an element
> maxLen <- max(sapply(Uniq, length))
> # pad with '0' all element to maxLen
> Uniq <- lapply(Uniq, function(x){
+ c(x, rep('0', maxLen - length(x)))
+ })
> as.data.frame(Uniq)
Col1 Col2 Col3 Col159 Col160
100 LD 0 VD
2 HD HD0 0 MD
3 LD0 HD 0 LD
4000 0 0
On 1/17/07, Bert Jacobs <[EMAIL PROTECTED]> wrote:
Hi,
Working further on this dataframe : my_data
Col1 Col2 Col3 ... Col 159 Col 160
Row 1 0 0 LD ... 0 VD
Row 2 HD0 0 0 MD
Row 3 0 HDHD 0 LD
Row 4 LDHDHD 0 0
......
LastRowHDHDLD 0 MD
Running this line of code:
Test = apply(X=my_data, MARGIN=2, FUN=unique)
I get this list:
$Col1
[1] "0" "HD" "LD"
$Col2
[1] "0" "HD"
$Col3
[1] "LD" "0" "HD"
...
$Col159
[1] "0"
$Col160
[1] "VD" "MD" "LD" "0"
Now I was wondering how I can get this list into a data.frame:
because a simple data.frame doesn't work (error: arguments imply differing
number of rows)
Can someone help me out on this. Thx
So that I get the following result:
Col1 Col2 Col3 ... Col 159 Col 160
Row 1 0 0LD 0VD
Row 2 HD HD 00MD
Row 3 LD 0HD 0LD
Row 4 00000
-Original Message-
From: Petr Pikal [mailto:[EMAIL PROTECTED]
Sent: 05 January 2007 11:51
To: Bert Jacobs; 'R help list'
Subject: Re: [R] Fast Removing Duplicates from Every Column
Hi
I am not sure if I understand how do you want to select unique items.
with
sapply(DF, function(x) !duplicated(x))
you can get data frame with TRUE when an item in particular column is
unique and FALSE in opposite. However then you need to choose which
rows to keep or discard
e.g.
DF[rowSums(sapply(comp, function(x) !duplicated(x)))>1,]
selects all rows in which are 2 or more unique values.
HTH
Petr
On 5 Jan 2007 at 9:54, Bert Jacobs wrote:
From: "Bert Jacobs" <[EMAIL PROTECTED]>
To: "'R help list'" <
r-help@stat.math.ethz.ch>
Date sent:Fri, 5 Jan 2007 09:54:17 +0100
Subject: Re: [R] Fast Removing Duplicates from Every Column
> Hi,
>
> I'm looking for some lines of code that does the following:
> I have a dataframe with 160 Columns and a number of rows (max 30):
>
> Col1 Col2 Col3 ... Col 159 Col 160
> Row 1 0 0 LD ... 0 VD
> Row 2 HD0 0 0 MD
> Row 3 0 HDHD 0 LD
> Row 4 LDHDHD 0 0
> ... ...
> LastRow HDHDLD 0 MD
>
>
> Now I want a dataframe that looks like this. As you see all duplicates
> are removed. Can this dataframe be constructed in a fast way?
>
> Col1 Col2 Col3 ... Col 159 Col 160
> Row 1 00LD 0 VD
> Row 2 HD HD 00MD
> Row 3 LD 0HD 0LD
>
> Thx for helping me out.
> Bert
>
> __
> 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.
Petr Pikal
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
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[R] arima function
I want to modify the arima function. Can anyone can tell me what are the objects: R_ARIMA_transPars,R_ARIMA_Like, R_ARIMA_Invtrans, R_ARIMA_undoPars...? Thanks. best regards. YG - [[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] eval while keeping NA-s
Dear R-people,
I would like to construct a model frame while keeping eventual NA-s in
it. The code looks like in lm():
m <- match(c("formula", "data", "subset", "weights", "na.action",
"offset"), names(mf), 0)
mfO <- mf[c(1, m)]
mfO$drop.unused.levels <- TRUE
mfO[[1]] <- as.name("model.frame")
names(mfO)[2] <- "formula"
mfO <- eval(mfO, parent.frame())
The problem is that eval() removes all the observation which include
NA-s.
Are there ways to get the frames and keep NA-s? I see, I can play
around with the "na.action" attribute of the resulting frame, but how
can I set the na.action?
Thanks in advance,
Ott
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Re: [R] Memory leak with character arrays?
Dear Peter, >The file that I'm reading contains the upstream regions of the yeast >genome, with each upstream region labeled using a FASTA header, i.e.: > > FASTA header for gene 1 > upstream region. > . > > FASTA header for gene 2 > upstream > you may want to have a look at the read.fasta() function in the seqinr package. There is an example page 16 of this document: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-6.pdf about importing the content of a fasta file with 21,161 sequences from Arabidopsis thaliana into an object which is about 15 Mb in RAM. HTH, -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 27 56 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ 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] help with regexpr in gsub
On Thu, 2007-01-18 at 04:49 +, Prof Brian Ripley wrote:
> One thing to watch with experiments like this is that the locale will
> matter. Character operations will be faster in a single-byte locale (as
> used here) than in a variable-byte locale (and I suspect Seth and Marc
> used UTF-8), and the relative speeds may alter. Also, the PCRE regexps
> are often much faster, and 'useBytes' can be much faster with ASCII data
> in UTF-8.
>
> For example:
>
> # R-devel, x86_64 Linux
> library(GO)
> goids <- ls(GOTERM)
> gids <- paste(goids, "ISS", sep=".")
> go.ids <- rep(gids, 10)
> > length(go.ids)
> [1] 205950
>
> # In en_GB (single byte)
>
> > system.time(z <- gsub("[.].*", "", go.ids))
> user system elapsed
>1.709 0.004 1.716
> > system.time(z <- gsub("[.].*", "", go.ids, perl=TRUE))
> user system elapsed
>0.241 0.004 0.246
>
> > system.time(z <- gsub('\\..+$','', go.ids))
> user system elapsed
>2.254 0.018 2.286
> > system.time(z <- gsub('([^.]+)\\..*','\\1',go.ids))
> user system elapsed
>2.890 0.002 2.895
> > system.time(z <- sub("([GO:0-9]+)\\..*$", "\\1", go.ids))
> user system elapsed
>2.716 0.002 2.721
> > system.time(z <- sub("\\..+", "", go.ids))
> user system elapsed
>1.724 0.001 1.725
> > system.time(z <- substr(go.ids, 0, 10))
> user system elapsed
>0.084 0.000 0.084
>
> # in en_GB.utf8
>
> > system.time(z <- gsub("[.].*", "", go.ids))
> user system elapsed
>1.689 0.020 1.712
> > system.time(z <- gsub("[.].*", "", go.ids, perl=TRUE))
> user system elapsed
>0.718 0.017 0.736
> > system.time(z <- gsub("[.].*", "", go.ids, perl=TRUE, useByte=TRUE))
> user system elapsed
>0.243 0.001 0.244
>
> > system.time(z <- gsub('\\..+$','', go.ids))
> user system elapsed
>2.509 0.024 2.537
> > system.time(z <- gsub('([^.]+)\\..*','\\1',go.ids))
> user system elapsed
>3.772 0.004 3.779
> > system.time(z <- sub("([GO:0-9]+)\\..*$", "\\1", go.ids))
> user system elapsed
>4.088 0.007 4.099
> > system.time(z <- sub("\\..+", "", go.ids))
> user system elapsed
>1.920 0.004 1.927
> > system.time(z <- substr(go.ids, 0, 10))
> user system elapsed
>0.096 0.002 0.098
>
> substr still wins, but by a much smaller margin.
Just to confirm Prof. Ripley's suspicion, that I am indeed running in
en_US.UTF-8.
Thanks for taking the time to point this out.
Best regards,
Marc
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[R] How to optimize this loop ?
Dear R Users,
I request your help to optimize a loop.
Given a series of observations, I want to know how many consecutive past
observations are below the last one.
e.g :
my_series <- c(3, 4, 10,14,8,3,4,6,9)
As the last number (9) is higher than the four preceding numbers (6, 4, 3, 8),
this function should return 4.
my_series <- c(3, 4, 10,14,8,3,4,11,9)
Here, it should return 0, as 9 is immediately preceeded by a higher number.
So far, I do this awful loop :
result <- 0
for (i in 1:length(my_series-1))
{
if (my_series[length(my_series)-i]>end(my_series)[1])
{ result <- i-1 ; break }
}
I thing there's a better way...
my_series > my_series[end][1] returns :
TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE
, which seems more appealing (once the last "FALSE" is removed), but now, how to
know the size of the last consecutive series of "TRUE" ?
Can you see a better way ?
Thanks.
__
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Re: [R] eval while keeping NA-s
On Thu, 18 Jan 2007, Ott Toomet wrote:
> Dear R-people,
>
> I would like to construct a model frame while keeping eventual NA-s in
> it. The code looks like in lm():
>
> m <- match(c("formula", "data", "subset", "weights", "na.action",
>"offset"), names(mf), 0)
> mfO <- mf[c(1, m)]
> mfO$drop.unused.levels <- TRUE
> mfO[[1]] <- as.name("model.frame")
> names(mfO)[2] <- "formula"
> mfO <- eval(mfO, parent.frame())
>
> The problem is that eval() removes all the observation which include
> NA-s.
>
> Are there ways to get the frames and keep NA-s? I see, I can play
> around with the "na.action" attribute of the resulting frame, but how
> can I set the na.action?
Set na.action=na.pass on the call, or reset in your code (as that resets
drop.unused.levels).
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] How to optimize this loop ?
Hi
discard your loop do not optimise it.
rle is your friend
> my_fun<-function(x) {
+
+ len<-length(x)
+ x1<-rle(x[len]>x[1:len-1])
+ last<-length(x1$values)
+ ifelse(x1$values[last],x1$lengths[last],0)
+ }
> my_fun(my_series)
[1] 0
> my_series <- c(3, 4, 10,14,8,3,4,6,9)
> my_fun(my_series)
[1] 4
>
and vectorise, vectorise, vectorise.
HTH
Petr
On 18 Jan 2007 at 14:11, Nicolas Prune wrote:
Date sent: Thu, 18 Jan 2007 14:11:11 +0100
From: Nicolas Prune <[EMAIL PROTECTED]>
To: r-help@stat.math.ethz.ch
Subject:[R] How to optimize this loop ?
> Dear R Users,
>
> I request your help to optimize a loop.
>
> Given a series of observations, I want to know how many consecutive
> past observations are below the last one.
>
> e.g :
> my_series <- c(3, 4, 10,14,8,3,4,6,9)
>
> As the last number (9) is higher than the four preceding numbers (6,
> 4, 3, 8), this function should return 4.
>
> my_series <- c(3, 4, 10,14,8,3,4,11,9)
> Here, it should return 0, as 9 is immediately preceeded by a higher
> number.
>
> So far, I do this awful loop :
>
> result <- 0
> for (i in 1:length(my_series-1))
> {
> if (my_series[length(my_series)-i]>end(my_series)[1])
> { result <- i-1 ; break }
> }
>
> I thing there's a better way...
>
> my_series > my_series[end][1] returns :
> TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE
> , which seems more appealing (once the last "FALSE" is removed), but
> now, how to know the size of the last consecutive series of "TRUE" ?
>
> Can you see a better way ?
>
> Thanks.
>
> __
> 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.
Petr Pikal
[EMAIL PROTECTED]
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[R] building R on freebsd 6.2 (amd64)
Hi, I updated my os to freebsd 6.2 and built R-patched with no changes in configure. I pass make check and copy the R executable to /usr/local/bin/R. Then when I start R, I get /libexec/ld-elf.so.1: Shared object "libRblas.so" not found, required by "R" and have to copy/link the two shared object files (libRblas.so and libRlapack.so) to somewhere "visible" like /usr/local/lib/ as well. I didn't have to do this last step in freebsd 6.1. Is there some configure setting I can use to avoid having to move the two shared object files? h. -- -- Hiroyuki Kawakatsu Business School Dublin City University Dublin 9, Ireland Tel +353 (0)1 700 7496 __ 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 to optimize this loop ?
Nicolas Prune wrote:
> Dear R Users,
>
> I request your help to optimize a loop.
>
> Given a series of observations, I want to know how many consecutive past
> observations are below the last one.
>
> e.g :
> my_series <- c(3, 4, 10,14,8,3,4,6,9)
>
> As the last number (9) is higher than the four preceding numbers (6, 4, 3,
> 8),
> this function should return 4.
>
> my_series <- c(3, 4, 10,14,8,3,4,11,9)
> Here, it should return 0, as 9 is immediately preceeded by a higher number.
>
> So far, I do this awful loop :
>
> result <- 0
> for (i in 1:length(my_series-1))
> {
> if (my_series[length(my_series)-i]>end(my_series)[1])
> { result <- i-1 ; break }
> }
>
> I thing there's a better way...
Just in terms of finding out which values are bigger than the
preceding value and avoiding the explicit loop, you could do something
like this:
seriesA <- c(3,4,10,14,8,3,4,6,9)
seriesB <- c(3,4,10,14,8,3,4,11,9)
sign(diff(seriesA)) == 1
[1] TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE
sign(diff(seriesB)) == 1
[1] TRUE TRUE TRUE FALSE FALSE TRUE TRUE FALSE
> my_series > my_series[end][1] returns :
> TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE
> , which seems more appealing (once the last "FALSE" is removed), but now, how
> to
> know the size of the last consecutive series of "TRUE" ?
>
> Can you see a better way ?
>
> Thanks.
>
> __
> 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.
--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] How to optimize this loop ?
Petr Pikal schrieb:
> Hi
>
> discard your loop do not optimise it.
> rle is your friend
>
I do not agree. For some purposes, an efficient loop is faster. IMHO
this is one of these purposes.
I propose the following modification of the loop (to increase speed):
myfun1 <- function(series=c(3, 4, 10,14,8,3,4,6,9)) {
len<-length(series)
for (i in (len-1):1)
{
if (series[i]>series[len])
{ result <- i-1 ; break }
}
return(result)
}
The speed measurement, in comparison with the rle approach:
> system.time(for (i in 1:1) erg<-my_fun(c(3, 4, 10,14,8,3,4,6,9)))
[1] 4.48 0.00 4.48 NA NA
> system.time(for (i in 1:1) erg<-myfun1(c(3, 4, 10,14,8,3,4,6,9)))
[1] 0.33 0.00 0.33 NA NA
Regards, Martin
>
>> my_fun<-function(x) {
>>
> +
> + len<-length(x)
> + x1<-rle(x[len]>x[1:len-1])
> + last<-length(x1$values)
> + ifelse(x1$values[last],x1$lengths[last],0)
> + }
>
>> my_fun(my_series)
>>
> [1] 0
>
>> my_series <- c(3, 4, 10,14,8,3,4,6,9)
>> my_fun(my_series)
>>
> [1] 4
>
>
> and vectorise, vectorise, vectorise.
>
> HTH
> Petr
>
>
>
>
> On 18 Jan 2007 at 14:11, Nicolas Prune wrote:
>
> Date sent:Thu, 18 Jan 2007 14:11:11 +0100
> From: Nicolas Prune <[EMAIL PROTECTED]>
> To: r-help@stat.math.ethz.ch
> Subject: [R] How to optimize this loop ?
>
>
>> Dear R Users,
>>
>> I request your help to optimize a loop.
>>
>> Given a series of observations, I want to know how many consecutive
>> past observations are below the last one.
>>
>> e.g :
>> my_series <- c(3, 4, 10,14,8,3,4,6,9)
>>
>> As the last number (9) is higher than the four preceding numbers (6,
>> 4, 3, 8), this function should return 4.
>>
>> my_series <- c(3, 4, 10,14,8,3,4,11,9)
>> Here, it should return 0, as 9 is immediately preceeded by a higher
>> number.
>>
>> So far, I do this awful loop :
>>
>> result <- 0
>> for (i in 1:length(my_series-1))
>> {
>> if (my_series[length(my_series)-i]>end(my_series)[1])
>> { result <- i-1 ; break }
>> }
>>
>> I thing there's a better way...
>>
>> my_series > my_series[end][1] returns :
>> TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE
>> , which seems more appealing (once the last "FALSE" is removed), but
>> now, how to know the size of the last consecutive series of "TRUE" ?
>>
>> Can you see a better way ?
>>
>> Thanks.
>>
>> __
>> 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.
>>
>
> Petr Pikal
> [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.
>
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Re: [R] curious about dimension of 'apply' output when MARGIN=1
Thanks to all for your insightful comments. I must admit I was unaware of the application to arrays. Ben Prof Brian Ripley wrote: > Or that the vision of the original designer was not limited to > matrices. It just so happens that in this example the replacement is a > single dimension the same size as the single margin used. That's > atypical, and normally the result dimension has no connection to the > margin. The design is to put the result dimension first, and the > first item in the 'seealso' list is aperm(). > > To my mind the only general solutions are to put the result dimension > first or last. I would have used last, but using first is slightly > more efficient for the reason Pat gives. > > apply() is for arrays, operating over one or more margins with a > function returning a 'scalar', vector or array result. Perhaps any > 'lazy'-ness / limit of vision is not in handling array results as well > as might be possible. __ 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] building R on freebsd 6.2 (amd64)
Hi, Hiroyuki Kawakatsu wrote: > Hi, > > I updated my os to freebsd 6.2 and built R-patched with no changes in > configure. I pass make check and copy the R executable to > /usr/local/bin/R. Then when I start R, I get > > /libexec/ld-elf.so.1: Shared object "libRblas.so" not found, required by "R" > > and have to copy/link the two shared object files (libRblas.so and > libRlapack.so) to somewhere "visible" like /usr/local/lib/ as well. I > didn't have to do this last step in freebsd 6.1. Is there some > configure setting I can use to avoid having to move the two shared > object files? > have you tried to build R over the ports system? regards, Gordon __ 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 to optimize this loop ? (correction)
Sorry, I accidentaly lost one line of the function code (result <-0),
see below...
Regards, Martin
Martin Becker schrieb:
>
> myfun1 <- function(series=c(3, 4, 10,14,8,3,4,6,9)) {
result <- 0# NEW
> len<-length(series)
> for (i in (len-1):1)
> {
>if (series[i]>series[len])
>{ result <- i-1 ; break }
> }
> return(result)
> }
>
...
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] building R on freebsd 6.2 (amd64)
On Thu, 18 Jan 2007, Hiroyuki Kawakatsu wrote: > Hi, > > I updated my os to freebsd 6.2 and built R-patched with no changes in > configure. I pass make check and copy the R executable to > /usr/local/bin/R. Then when I start R, I get > > /libexec/ld-elf.so.1: Shared object "libRblas.so" not found, required by "R" > > and have to copy/link the two shared object files (libRblas.so and > libRlapack.so) to somewhere "visible" like /usr/local/lib/ as well. I > didn't have to do this last step in freebsd 6.1. Is there some > configure setting I can use to avoid having to move the two shared > object files? The R front end sets LD_LIBRARY_PATH to include the place it puts libR.so. It looks like that is not effective on your machine, but you will have to investigate for us why. I am pretty sure other FreeBSD users (6.2 and 7) on AMD64 reported success on R 2.4.x. How does FreeBSD 6.2 handle 64-bit systems? Most OSes would use /usr/local/lib64, and there is a configure setting LIBnn to cover that issue. Another solution for ELF systems is to include R_HOME/lib in the list of directories known to ldconfig. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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 with niave bayes
Hello I have a rather simple code and for some reason it produces an error message. If someone can tell me why and how to fix it, I would be very greatful. Thank you in advance. # create data set.seed(10) n <- 200 # number of training points n.test <- 200 # number of test points p<-2# dimension of input space z <- matrix(rnorm((n+n.test)*p),ncol=p) x <- matrix(0,nrow=n+n.test,ncol=p) for (i in 1:p) x[,i] <- z%*%rnorm(p) truecoef <- c(1,2) prob1 <- exp(x%*%truecoef)/(1+exp(x%*%truecoef)) # prob is the true probability of class 1 y <- rbinom(n+n.test,1,prob1) # separate the data into train and test sets mydata <- data.frame(y=y[1:n],x=x[1:n,]) mydata.test <- data.frame(y=y[n+(1:n.test)],x=x[n+(1:n.test),]) ## library(e1071) mydt.nb<-naiveBayes(y~ ., data=mydata) m.pr<-predict(mydt.nb, mydata[,-1], type="class") regards, Leah [[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] Problems replicating rows and associated increasing index
I have a dataset like this: IDvalue week of visit 1 4.2 0 (baseline) 1 2.5 6 1 4.1 10 1 3.0 12 . . . And so on for more than 11000 records (more than 1000 subjects). I need to add rows in order to have 52 records per patients (corresponding to the 52 weeks of the year); that is that weeks 1-2-3-4-5 will have the same content of baseline one, except for the column "week of visit". The fact is that each of the rows can have a very different timing, so the only thing I can do is creating a vector giving the number of replications needed for each row, but how can I practically replicate them increasing the index ok the week? thanks niccolò [[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 with problem - multilevel model?
I have what is probably a very simple problem but I would be very grateful to the list for any help or pointers to implement a solution in R. We have two types of measurements on the eye that we have collected in 62 patients at 5 fixed time points during a clinical visit over an office day. We want to establish if there is an association between the measurements. Obviously it would be wrong to generate a simple scatterplot of all 62*5 observations and consider something like a simple correlation coefficient. What I really need is to set up a 2-level model with measurements nested within patients and use, perhaps, one variable as a response and the other as a predictor. I would also like to add in time of day (probably as a categorical) to check this isn't affecting things. I haven't used multi-level modelling in R and wonder how I can simply go about fitting this model and looking at the significance of the estimates in R. I also have a plot in my mind - 62 little regression lines (n=5) and think that this might be informative. Any help or pointers will be gratefully received - Many Thanks. Dr. David Crabb Department of Optometry and Visual Science, City University, Northampton Square, London EC1V OHB Tel: 44 207 040 0191 [EMAIL PROTECTED] http://www.city.ac.uk/optometry/about/staff/crabb.html __ 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 to optimize this loop ? (correction)
Thanks to everyone who answered, in public or in private. I successfully rewrote my function with rle. For my sample, the total computation times (I call this function around 1000 times) are roughly the same. However, I thank you for letting me know rle, and S Poetry. Regards, Nicolas __ 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] Help with problem - multilevel model?
This should get you started tmp <- data.frame(y1=rnorm(62*5), y2=rnorm(62*5), time=rep(1:5, 62), id=factor(rep(1:62, each=5)) ) xyplot(y1 ~ y2 | id, data=tmp, group=time, pch=as.character(1:5)) tmp.aov <- aov(y1 ~ y2*factor(time) + Error(id), data=tmp) summary(tmp.aov) __ 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] Problems replicating rows and associated increasing index
Try this. It does a small sample with 15 weeks and only 10 patients, but
the algorithm is easily changed for 52.
require(zoo) # need the 'zoo' library for 'na.locf'
# create test data
visits <- data.frame(id=rep(1:10, each=10),value=runif(100),
week=sample(1:15,100,TRUE))
# removed duplicated values
visits <- visits[!duplicated(paste(visits$id, visits$week)),]
# now do the algorithm
full <- by(visits, visits$id, function(x){
# fill to 15 weeks and add a baseline (0)
x <- rbind(x, data.frame(id=x$id[1], value=runif(1), week=0))
# determine which weeks are missing
missing <- setdiff(1:15, x$week) # change to 52 for your case
# add missing weeks
x <- rbind(x, data.frame(id=x$id[1], value=NA, week=missing))
# sort by week
x <- x[order(x$week),]
# replace 'value' with previous good value
x$value <- na.locf(x$value)
x
})
# create new data frame
(full <- do.call(rbind, full))
On 1/18/07, Niccolò Bassani <[EMAIL PROTECTED]> wrote:
>
> I have a dataset like this:
>
> IDvalue week of visit
> 1 4.2 0 (baseline)
> 1 2.5 6
> 1 4.1 10
> 1 3.0 12
> .
> .
> .
>
> And so on for more than 11000 records (more than 1000 subjects). I need to
> add rows in order to have 52 records per patients (corresponding to the
> 52
> weeks of the year); that is that weeks 1-2-3-4-5 will have the same
> content
> of baseline one, except for the column "week of visit". The fact is that
> each of the rows can have a very different timing, so the only thing I can
> do is creating a vector giving the number of replications needed for each
> row, but how can I practically replicate them increasing the index ok the
> week?
> thanks
> niccolò
>
>[[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.
>
>
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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[R] How to specify arguments in lme() ?
Hi, I have a question about the function lme() in R. I have a 2*2*3 layout with some missing data (labelled as *). These 3 factors are labelled as A,B,C, the response is Score. The layout is as follows:- A B CScore 1 1 1 5 1 1 2 * 1 1 3 1 1 2 1 4 1 2 2 4 1 2 3 * 2 1 1 3 2 1 2 * 2 1 3 4 2 2 1 2 2 2 2 * 2 2 3 5 Suppose these data are stored in a data frame called "test". If all these 3 factors are fixed, then I can fit a model without the 3-way interaction as:- fit1<-lm(Score~A*B+A*C+B*C,data=test) If one of these factors, say A, is a random effect variable, then I need to fit a mixed effect model using lme(). I have read the R documention on lme(), but I am still not clear how to specify the random argument. I tried to do:- fit2<-lme(Score~A*B+A*C+B*C,data=test,random=~A, na.action=na.pass) but the system give a message as follows:- Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups So how should I specify the arguments? Thank you very much for your help! Jiajie __ 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] Help with problem - multilevel model?
Aov is not the right function for this problem. Lmer is designed for
multilevel modeling. There are a lot of resources, but start with the
following vignette
Library(lme4)
vignette("MlmRevSoft")
And then turn to Pinhiero and Bates
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Richard M. Heiberger
> Sent: Thursday, January 18, 2007 10:22 AM
> To: Crabb, David; r-help@stat.math.ethz.ch
> Subject: Re: [R] Help with problem - multilevel model?
>
> This should get you started
>
>
> tmp <- data.frame(y1=rnorm(62*5),
> y2=rnorm(62*5),
> time=rep(1:5, 62),
> id=factor(rep(1:62, each=5))
> )
>
> xyplot(y1 ~ y2 | id, data=tmp, group=time, pch=as.character(1:5))
>
> tmp.aov <- aov(y1 ~ y2*factor(time) + Error(id), data=tmp)
> summary(tmp.aov)
>
> __
> 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.
>
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[R] [R-pkgs] Version 2.0-9 of bayesm
Version 2.0-9 of bayesm is now available on CRAN changes include- 1. addition of rhierLinearMixture -- linear hierarchical models with a mixture of normals prior 2. mixDenBi is now fully vectorized and run more than 10 times faster 3. minor documentation corrections have been made 4. rnmixGibbs allows the user to specify only one component peter rossi ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] The math underlying the `betareg' package?
Folks,
The betareg package appears to be polished and works well. But I would
like to look at the exact formulas for the underlying model being
estimated, the likelihood function, etc. E.g. if one has to compute
\frac{\partial E(y)}{\partial x_i}, this requires careful calculations
through these formulas. I read "Regression analysis of variates
observed on (0,1): percentages, proportions and fractions", by
Kieschnick & MucCullogh, `Statistical Modelling" 2003, 3:193-213. They
say that the beta regression that they show is a proposal of theirs -
is this the same as what betareg does, or is this the Standard
Formulation?
What else should I be reading about beta regressions? :-)
--
Ajay Shah http://www.mayin.org/ajayshah
[EMAIL PROTECTED] http://ajayshahblog.blogspot.com
<*(:-? - wizard who doesn't know the answer.
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[R] fitCopula method in R
-- Hello, I am attempting to fit monthly stock returns to possible copula functions using the copula package in R. Below is my code (mat2 is a 2x119 matrix of the two stock returns): my.cop <- normalCopula(param=.3, dim = 2, dispstr = "un") myfit <- fitCopula(mat2,my.cop, start=.65, optim.control= list(NULL), method = "BFGS") myfit Unfortunately, I continue to receive this error: Error in optim(start, loglikCopula, method = method, copula = copula, : initial value in 'vmmin' is not finite In addition: Warning message: NaNs produced in: qnorm(p, mean, sd, lower.tail, log.p) I don't know why my start value is wrong or how to choose a correct one. Any help is greatly appreicated. Thanks. Adam __ 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 to specify arguments in lme() ?
On 1/18/07, w jj <[EMAIL PROTECTED]> wrote: > I have a question about the function lme() in R. > > I have a 2*2*3 layout with some missing data (labelled as *). These 3 > factors are labelled as A,B,C, the response is Score. The layout is as > follows:- > > A B CScore > 1 1 1 5 > 1 1 2 * > 1 1 3 1 > 1 2 1 4 > 1 2 2 4 > 1 2 3 * > 2 1 1 3 > 2 1 2 * > 2 1 3 4 > 2 2 1 2 > 2 2 2 * > 2 2 3 5 > > Suppose these data are stored in a data frame called "test". > > If all these 3 factors are fixed, then I can fit a model without the 3-way > interaction as:- > fit1<-lm(Score~A*B+A*C+B*C,data=test) > > If one of these factors, say A, is a random effect variable, then I need to > fit a mixed effect model using lme(). I have read the R documention on > lme(), but I am still not clear how to specify the random argument. I tried > to do:- You could do it but you don't really want to try to fit a model with several random effects generated by a factor with only two levels. Estimating variances, which is what is done for a random effect, is more difficult than estimating means or other linear combinations of the responses, which is what fixed effects parameters end up being expressed as. Trying to estimate a variance when observing a factor at only two levels is overly optimistic. Just for the record, the call to lmer in the lme4 package would be fit2 <- lmer(Score ~ B*C+(1|A/B)+(1|C:A), data = test) > fit2<-lme(Score~A*B+A*C+B*C,data=test,random=~A, na.action=na.pass) I don't think you want to use na.pass here. The underlying C code for fitting lme or lmer models doesn't take kindly to finding NA's in the data. > > but the system give a message as follows:- > Error in getGroups.data.frame(dataMix, groups) : > Invalid formula for groups > > So how should I specify the arguments? > > Thank you very much for your help! > > Jiajie > > > > __ > 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.
Re: [R] The math underlying the `betareg' package?
On Thu, 2007-01-18 at 20:00 +0530, Ajay Narottam Shah wrote:
> Folks,
>
> The betareg package appears to be polished and works well. But I would
> like to look at the exact formulas for the underlying model being
> estimated, the likelihood function, etc. E.g. if one has to compute
> \frac{\partial E(y)}{\partial x_i}, this requires careful calculations
> through these formulas. I read "Regression analysis of variates
> observed on (0,1): percentages, proportions and fractions", by
> Kieschnick & MucCullogh, `Statistical Modelling" 2003, 3:193-213. They
> say that the beta regression that they show is a proposal of theirs -
> is this the same as what betareg does, or is this the Standard
> Formulation?
If you want to know, the best place to look is the source code for the
package, available as a tar.gz file from all good CRAN Mirrors.
I suggest this as the Windows binary might not contain the original
source (i.e unprocessed with comments etc) - I forget now exactly how
the binaries on that platform differ.
>
> What else should I be reading about beta regressions? :-)
The reference cited in the References section of ?betareg would also be
a good start, esp to understand what the betareg package is doing and
how it compares to the other ref you cite.
HTH
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] The math underlying the `betareg' package?
>What else should I be reading about beta regressions? :-) Ajay, you could begin by reading the paper cited in betareg package: FERRARI, S.L.P., CRIBARI-NETO, F. (2004). Beta regression for modeling rates and proportions. Journal of Applied Statistics, v. 31, n. 7, p. 799-815 I'd bet that there are answers to some of your questions there. HTH, Rogerio __ 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] problem in adf command
this command is used in tseries
adf.test(x, alternative = c("stationary", "explosive"),
k = trunc((length(x)-1)^(1/3)))
this command apply adf test on data given in x .here general
equatiuon
that is, equation with constant and trend is used.if i did not include
constant or trend in the equation and run the
command then how i can run this command in tseries.
-
Never miss an email again!
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Re: [R] sleep data
Thank you, Chuck and Tom. I'd gladly improve the help page, particularly if you can provide a patch against https://svn.R-project.org/R/trunk/src/library/datasets/man/sleep.Rd where I've already added the Cushny and Peebles reference, thanks to Chuck. Regards, Martin Maechler, ETH Zurich > "ChuckB" == Charles C Berry <[EMAIL PROTECTED]> > on Wed, 17 Jan 2007 10:48:13 -0800 writes: ChuckB> Yes, you refer to ChuckB> Cushny, A. R. and Peebles, A. R. The action of ChuckB> optical isomers: II hyoscines. The Journal of ChuckB> Physiology, 1905, 32: 501.510. ChuckB> which was used by 'Student' to illustrate the paired ChuckB> t-test. ChuckB> This is indeed a crossover design. ChuckB> On Wed, 17 Jan 2007, Tom Backer Johnsen wrote: >> When reading the documentation for the "sleep" data set >> in R, the impression is clear, this is an "independent >> groups" kind of design (two groups of 10 subjects each). >> However, when browsing the original article (referred to >> in the help file), my impression is quite clear, this is >> really a "repeated measures" kind of data (one group of >> 10 subjects, two observations). What is correct? >> >> 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. >> ChuckB> Charles C. Berry (858) 534-2098 Dept of ChuckB> Family/Preventive Medicine E ChuckB> mailto:[EMAIL PROTECTED] UC San Diego ChuckB> http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego ChuckB> 92093-0901 ChuckB> __ ChuckB> R-help@stat.math.ethz.ch mailing list ChuckB> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE ChuckB> do read the posting guide ChuckB> http://www.R-project.org/posting-guide.html and ChuckB> provide commented, minimal, self-contained, ChuckB> 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.
Re: [R] building R on freebsd 6.2 (amd64)
On Thu, 18 Jan 2007, Hiroyuki Kawakatsu wrote: > On 1/18/07, Prof Brian D Ripley <[EMAIL PROTECTED]> wrote: >> >> The R front end sets LD_LIBRARY_PATH to include the place it puts libR.so. >> It looks like that is not effective on your machine, but you will have to >> investigate for us why. I am pretty sure other FreeBSD users (6.2 and 7) >> on AMD64 reported success on R 2.4.x. > > echo returns > LD_LIBRARY_PATH: Undefined variable. But I said 'The R front end sets LD_LIBRARY_PATH', so you need to check this from inside R, e.g. by Sys.getenv(). >> How does FreeBSD 6.2 handle 64-bit systems? Most OSes would use >> /usr/local/lib64, and there is a configure setting LIBnn to cover that >> issue. > > I have /usr/lib/, /usr/lib32/, /usr/local/lib/, but no /usr/local/lib64/ > >> Another solution for ELF systems is to include R_HOME/lib in the list of >> directories known to ldconfig. > > Thanks for that tip. I suppose if I symlink to R_HOME/lib/ I won't > have to redo them every time I rebuild R-patched. Just as note to > myself, the following appears to work > > ln -s /opt/acml3.6.0/gnu64/lib/libacml.so /usr/local/lib/libRblas.so > ln -s /opt/acml3.6.0/gnu64/lib/libacml_mv.so /usr/local/lib/libacml_mv.so > ln -s R_HOME/lib/libRlapack.so /usr/local/lib/libRlapack.so > > h. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] building R on freebsd 6.2 (amd64)
On 1/18/07, Prof Brian D Ripley <[EMAIL PROTECTED]> wrote: > > The R front end sets LD_LIBRARY_PATH to include the place it puts libR.so. > It looks like that is not effective on your machine, but you will have to > investigate for us why. I am pretty sure other FreeBSD users (6.2 and 7) > on AMD64 reported success on R 2.4.x. echo returns LD_LIBRARY_PATH: Undefined variable. > How does FreeBSD 6.2 handle 64-bit systems? Most OSes would use > /usr/local/lib64, and there is a configure setting LIBnn to cover that > issue. I have /usr/lib/, /usr/lib32/, /usr/local/lib/, but no /usr/local/lib64/ > Another solution for ELF systems is to include R_HOME/lib in the list of > directories known to ldconfig. Thanks for that tip. I suppose if I symlink to R_HOME/lib/ I won't have to redo them every time I rebuild R-patched. Just as note to myself, the following appears to work ln -s /opt/acml3.6.0/gnu64/lib/libacml.so /usr/local/lib/libRblas.so ln -s /opt/acml3.6.0/gnu64/lib/libacml_mv.so /usr/local/lib/libacml_mv.so ln -s R_HOME/lib/libRlapack.so /usr/local/lib/libRlapack.so h. -- -- Hiroyuki Kawakatsu Business School Dublin City University Dublin 9, Ireland Tel +353 (0)1 700 7496 __ 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] options("digits") and print.default()
Prof Brian Ripley wrote: > On Mon, 15 Jan 2007, Ulrich Keller wrote: > >> Hello everyone, >> >> I use latex() (Hmisc) for report generation and thus have been affected by >> the problem with rounding decimals described, for example, in this post: >> >> http://thread.gmane.org/gmane.comp.lang.r.general/73287/focus=73287 >> >> In short, numbers often are printed with 15 or so decimals even if there >> far less significant digits. The problem has been confirmed by Frank >> Harrell and Thomas Dupont according to this post: >> >> http://thread.gmane.org/gmane.comp.lang.r.general/73172/focus=73186 >> >> But it has still not been fixed. Rather than changing all my reports I >> decided I'd look at format.df() in Hmisc myself and try to fix the problem >> there. I found that the problem is not in Hmisc at all, but in R itself: >> >>> print(1.001) >> [1] 1.001 >>> options(digits=16) #format.df does this >>> print(1.001) >> [1] 1.001 >>> print(round(1.001, 3)) #rounding does not help >> [1] 1.001 >> >> This does not seem to be the behaviour described in the documentation, >> which says: >> >> "The same number of decimal places is used throughout a vector,[sic!] This >> means that digits specifies the minimum number of significant digits to be >> used, and that at least one entry will be encoded with that minimum >> number. However, if all the encoded elements then have trailing zeroes, >> the number of decimal places is reduced until at least one element has a >> non-zero final digit." >> >> If print.default() exhibited the behaviour desribed in the docs, >> format.df() and thus latex() would work as advertised, I think. I would >> have written a bug report instead of posting here, but the fact (?) that >> Frank and Thomas have confirmed the bug seems to indicate that the problem >> does indeed lie with Hmisc. Am I misunderstanding something here? >> >> I use R version 2.4.1 Patched (2007-01-13 r40470) on Windows. > > The bug is that Hmisc uses more digits than the representation provides: > >> .Machine$double.eps > [1] 2.22044604925031e-16 > > If it used 15 digits (as R does for as.character) all would be well. > Since R has to do the calculations you quote in binary arithmetic, they > are also subject to representation error and there is no way they can be > done to 16 significant figures. (I've traced the example, and that is > what happens.) See ?as.character for more details. > Is there an R object that contains the value of DBL_DIG for the current machine? I have checked '.Machine' and '.Platform' and neither have the value of DBL_DIG in them. Thank you Charles Dupont -- Charles Dupont Computer System Analyst School of Medicine Department of Biostatistics Vanderbilt University __ 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] options("digits") and print.default()
On Thu, 18 Jan 2007, Charles Dupont wrote: > Prof Brian Ripley wrote: >> On Mon, 15 Jan 2007, Ulrich Keller wrote: >> >>> Hello everyone, >>> >>> I use latex() (Hmisc) for report generation and thus have been affected by >>> the problem with rounding decimals described, for example, in this post: >>> >>> http://thread.gmane.org/gmane.comp.lang.r.general/73287/focus=73287 >>> >>> In short, numbers often are printed with 15 or so decimals even if there >>> far less significant digits. The problem has been confirmed by Frank >>> Harrell and Thomas Dupont according to this post: >>> >>> http://thread.gmane.org/gmane.comp.lang.r.general/73172/focus=73186 >>> >>> But it has still not been fixed. Rather than changing all my reports I >>> decided I'd look at format.df() in Hmisc myself and try to fix the problem >>> there. I found that the problem is not in Hmisc at all, but in R itself: >>> print(1.001) >>> [1] 1.001 options(digits=16) #format.df does this print(1.001) >>> [1] 1.001 print(round(1.001, 3)) #rounding does not help >>> [1] 1.001 >>> >>> This does not seem to be the behaviour described in the documentation, >>> which says: >>> >>> "The same number of decimal places is used throughout a vector,[sic!] This >>> means that digits specifies the minimum number of significant digits to be >>> used, and that at least one entry will be encoded with that minimum >>> number. However, if all the encoded elements then have trailing zeroes, >>> the number of decimal places is reduced until at least one element has a >>> non-zero final digit." >>> >>> If print.default() exhibited the behaviour desribed in the docs, >>> format.df() and thus latex() would work as advertised, I think. I would >>> have written a bug report instead of posting here, but the fact (?) that >>> Frank and Thomas have confirmed the bug seems to indicate that the problem >>> does indeed lie with Hmisc. Am I misunderstanding something here? >>> >>> I use R version 2.4.1 Patched (2007-01-13 r40470) on Windows. >> >> The bug is that Hmisc uses more digits than the representation provides: >> >>> .Machine$double.eps >> [1] 2.22044604925031e-16 >> >> If it used 15 digits (as R does for as.character) all would be well. Since >> R has to do the calculations you quote in binary arithmetic, they are also >> subject to representation error and there is no way they can be done to 16 >> significant figures. (I've traced the example, and that is what happens.) >> See ?as.character for more details. >> > > Is there an R object that contains the value of DBL_DIG for the current > machine? I have checked '.Machine' and '.Platform' and neither have the > value of DBL_DIG in them. No, but please do as I suggested and read ?as.character: it is 15 on all current platforms. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] Robust PCA?
Hi. I'm checking into robust methods for principal components analysis. There seem to be several floating around. I'm currently focusing my attention on a method of Hubert, Rousseeuw, and Vanden Branden (http://wis.kuleuven.be/stat/Papers/robpca.pdf) mainly because I'm familiar with other work by Rousseeuw and Hubert in robust methodologies. Of course, I'd like to obtain code for this method, or another good robust PCA method, if there's one out there. I haven't noticed the existence on CRAN of a package for robust PCA (the authors of the ROBPCA method do provide MATLAB code). -- TMK -- 212-460-5430home 917-656-5351cell __ 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] weighted MDS, alscal
Hello! I need to perform weighted multidimensional scaling analysis(WMDS). I did rsitesearch, googled, but I could find no info on how to perform WMDS using R. In several places they say it is possible with the ALSCAL algorithm, but I could not find the relevant function to carry it out. - Заложете на късмета си със Спортингбет! __ 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] multiple seasonal time series models
Is there an R package that can model time series with multiple seasonal cycles, e.g., 7 wkdy x 24 hr , I have tried searching the Help, but have been unable to find anything. Any help would be appreciated. thank you, Spencer [[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.
Re: [R] weighted MDS, alscal
Hello. --- Martin Ivanov <[EMAIL PROTECTED]> wrote: > I need to perform weighted multidimensional scaling > analysis(WMDS). I did rsitesearch, googled, but I > could find no info on how to perform WMDS using R. > In several places they say it is possible with the > ALSCAL algorithm, but I could not find the relevant > function to carry it out. > I dont't know whether ALSCAL is available for R. However there's ALSCAL fortran code available in http://forrest.psych.unc.edu/research/alscal.html. Regards. __ 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] Laplace correction for rpart class probability estimate
Hello everybody, I'm using rpart to fit a classification tree. I'm interested in the way rpart estimates the class membership probabilities. Does it implement the Laplace correction rule? Is there any parameter I can use to ask rpart to do that? I was not able to find this option in the manual or on the internet. thank you, regards, Roberto __ 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] selecting rows for inclusion in lm
I must express thanks to Peter Konings, Gary Collins, David Barron,
Prof. Brian Ripley, Vladimir Eremeev, and Michael Dewey (I hope I did
not leave anyone out) all of whom suggested I used the subset parameter
of lm to restrict the subjects included in my lm. R is a special
programming language and statistics package, both because of the
wonderful features of R (thank you R developers), but equally
importantly because of the community of people who willingly give of
there time and knowledge to help other users. Many thanks.
If any R developers are out there, may I suggest that the help page for
lm include more information (perhaps an example) on how one uses the
subset option. The current documentation states:
subsetan optional vector specifying a subset of observations to be used
in the fitting process.
Although I read the help page, I could not get subset to work until the
kind people mentioned above sent me examples.
Again, many thanks to one and all!
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC,
University of Maryland School of Medicine Claude D. Pepper OAIC,
University of Maryland Clinical Nutrition Research Unit, and
Baltimore VA Center Stroke of Excellence
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
[EMAIL PROTECTED]
>>> Prof Brian Ripley <[EMAIL PROTECTED]> 1/18/2007 3:38 AM >>>
On Thu, 18 Jan 2007, David Barron wrote:
> Why not use the subset option? Something like:
>
> lm(diff ~ Age + Race, data=data, subset=data$Meno=="PRE")
>
> should do the trick, and be much easier to read!
And
lm(diff ~ Age + Race, data = data, subset = (Meno=="PRE"))
would be easier still.
>
> On 18/01/07, John Sorkin <[EMAIL PROTECTED]> wrote:
>> I am having trouble selecting rows of a dataframe that will be
included
>> in a regression. I am trying to select those rows for which the
variable
>> Meno equals PRE. I have used the code below:
>>
>>
difffitPre<-lm(data[,"diff"]~data[,"Age"]+data[,"Race"],data=data[data[,"Meno"]=="PRE",])
You are missing a comma in data = data[<...>, ]
>> summary(difffitPre)
>>
>> The output from the summary indicates that more than 76 rows are
>> included in the regression:
>>
>> Residual standard error: 2.828 on 76 degrees of freedom
>>
>> where in fact only 22 rows should be included as can be seen from
the
>> following:
>>
>> print(data[length(data[,"Meno"]=="PRE","Meno"]))
>> [1] 22
>>
>> I would appreciate any help in modifying the data= parameter of the
lm
>> so that I include only those subjects for which Meno=PRE.
>>
>> R 2.3.1
>> Windows XP
>>
>> Thanks,
>> John
>>
>> John Sorkin M.D., Ph.D.
>> Chief, Biostatistics and Informatics
>> Baltimore VA Medical Center GRECC,
>> University of Maryland School of Medicine Claude D. Pepper OAIC,
>> University of Maryland Clinical Nutrition Research Unit, and
>> Baltimore VA Center Stroke of Excellence
>>
>> University of Maryland School of Medicine
>> Division of Gerontology
>> Baltimore VA Medical Center
>> 10 North Greene Street
>> GRECC (BT/18/GR)
>> Baltimore, MD 21201-1524
>>
>> (Phone) 410-605-7119
>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>> [EMAIL PROTECTED]
>>
>> Confidentiality Statement:
>> This email message, including any attachments, is for the
so...{{dropped}}
>>
>> __
>> 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 ( http://www.r/
)-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
Confidentiality Statement:
This email message, including any attachments, is for the so...{{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.
[R] Reading contingency tables
I am trying to read an ftable using read.ftable, but I get the
following error message:
> jobSatTable <-
> read.ftable("http://definetti.uark.edu/~gpetris/stat5333/jobSatisfaction.dat",skip=2)
Error in seek(file, where = 0) : no applicable method for "seek"
In addition: Warning messages:
1: no non-missing arguments to max; returning -Inf
2: no non-missing arguments to max; returning -Inf
I also tried to play with the argument col.vars, to remove blank
lines in the file, to remove the blank in "Not
satisfied". Unfortunately nothing worked.
Can anybody give me a suggestion on how to read that table?
Thanks in advance,
Giovanni
ps:
> version
_
platform sparc-sun-solaris2.8
arch sparc
os solaris2.8
system sparc, solaris2.8
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
--
Giovanni Petris <[EMAIL PROTECTED]>
Associate Professor
Department of Mathematical Sciences
University of Arkansas - Fayetteville, AR 72701
Ph: (479) 575-6324, 575-8630 (fax)
http://definetti.uark.edu/~gpetris/
__
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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] sleep data
A further note. The Cushny & Peebles article can be viewed here: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1465734 and the page with the data is here: http://www.pubmedcentral.nih.gov/pagerender.fcgi?artid=1465734&pageindex=9 A machine readable version of the data is at: https://biostat.ucsd.edu/~cberry/t-test/sleep.dat The version published in Student's Biometrika article has a typographical error, but it is evident that Student's computations were unaffected. Chuck Berry On Wed, 17 Jan 2007, Charles C. Berry wrote: > > Yes, you refer to > >Cushny, A. R. and Peebles, A. R. The action of optical isomers: II >hyoscines. The Journal of Physiology, 1905, 32: 501.510. > > which was used by 'Student' to illustrate the paired t-test. > > This is indeed a crossover design. > > On Wed, 17 Jan 2007, Tom Backer Johnsen wrote: > >> When reading the documentation for the "sleep" data set in R, the >> impression is clear, this is an "independent groups" kind of design >> (two groups of 10 subjects each). However, when browsing the original >> article (referred to in the help file), my impression is quite clear, >> this is really a "repeated measures" kind of data (one group of 10 >> subjects, two observations). What is correct? >> >> 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. >> > > Charles C. Berry(858) 534-2098 > Dept of Family/Preventive Medicine > E mailto:[EMAIL PROTECTED] UC San Diego > http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 > > > > Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 __ 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] Robust PCA?
You seem not to have received a reply. You can use cov.rob in MASS or cov.Mcd in robustbase or undoubtedly others to obtain a robust covariance matrix and then use that for PCA. -- Bert Bert Gunter Nonclinical Statistics 7-7374 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Talbot Katz Sent: Thursday, January 18, 2007 11:44 AM To: r-help@stat.math.ethz.ch Subject: [R] Robust PCA? Hi. I'm checking into robust methods for principal components analysis. There seem to be several floating around. I'm currently focusing my attention on a method of Hubert, Rousseeuw, and Vanden Branden (http://wis.kuleuven.be/stat/Papers/robpca.pdf) mainly because I'm familiar with other work by Rousseeuw and Hubert in robust methodologies. Of course, I'd like to obtain code for this method, or another good robust PCA method, if there's one out there. I haven't noticed the existence on CRAN of a package for robust PCA (the authors of the ROBPCA method do provide MATLAB code). -- TMK -- 212-460-5430home 917-656-5351cell __ 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.
Re: [R] Robust PCA?
Hi Bert. Thank you, that sounds like an excellent idea. After my initial post, I also found an implementation of ROBPCA in S-PLUS at (http://wis.kuleuven.be/stat/robust/programs.html). -- TMK -- 212-460-5430home 917-656-5351cell >From: Bert Gunter <[EMAIL PROTECTED]> >To: "'Talbot Katz'" <[EMAIL PROTECTED]>, >Subject: RE: [R] Robust PCA? >Date: Thu, 18 Jan 2007 15:28:47 -0800 > >You seem not to have received a reply. > >You can use cov.rob in MASS or cov.Mcd in robustbase or undoubtedly others >to obtain a robust covariance matrix and then use that for PCA. > >-- Bert > > >Bert Gunter >Nonclinical Statistics >7-7374 > >-Original Message- >From: [EMAIL PROTECTED] >[mailto:[EMAIL PROTECTED] On Behalf Of Talbot Katz >Sent: Thursday, January 18, 2007 11:44 AM >To: r-help@stat.math.ethz.ch >Subject: [R] Robust PCA? > >Hi. > >I'm checking into robust methods for principal components analysis. There >seem to be several floating around. I'm currently focusing my attention on >a method of Hubert, Rousseeuw, and Vanden Branden >(http://wis.kuleuven.be/stat/Papers/robpca.pdf) mainly because I'm familiar >with other work by Rousseeuw and Hubert in robust methodologies. Of >course, > >I'd like to obtain code for this method, or another good robust PCA method, >if there's one out there. I haven't noticed the existence on CRAN of a >package for robust PCA (the authors of the ROBPCA method do provide MATLAB >code). > >-- TMK -- >212-460-5430 home >917-656-5351 cell > >__ >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] integrate and quadratic forms
Hi all.
I'm trying to numerically invert the characteristic function
of a quadratic form following Imhof's (1961, Biometrika 48)
procedure.
The parameters are:
lambda=c(.6,.3,.1)
h=c(2,2,2)
sigma=c(0,0,0)
q=3
I've implemented Imhof's procedure two ways that, for me,
should give the same answer:
#more legible
integral1 = function(u) {
o=(1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) - q*u/2
rho=prod((1+lambda^2*u^2)^(h/4))*exp(
(1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )
integrand = sin(o)/(u*rho)
}
#same as above
integral2= function(u) {
((1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) - q*u/2)/
(u*(prod((1+lambda^2*u^2)^(h/4))*
exp( (1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )))
}
The following should be near 0.18. However, nor the answers are near this
value neither they agree each other!
> 1/2+(1/pi)*integrate(integral1,0,Inf)$value
[1] 1.022537
> 1/2+(1/pi)*integrate(integral2,0,Inf)$value
[1] 1.442720
What's happening? Is this a bug or OS specific? Shouldn't they give the
same answer? Why do I get results so different from 0.18? In time:
the procedure works fine for q=.2.
I'm running R 2.4.1 in a PC with Windows XP 32bits. Other ways (in R) to
find the distribution of general quadratic forms are welcome.
Thanks in advance.
Rogerio.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] integrate and quadratic forms
The do give the same answer, unfortunately the examples you sent were not
the same. Integral2 was missing a 'sin'. So I would assume there might be
something else wrong with your functions. You might want to try breaking it
down into smaller steps so you can see what you are doing. It definitely is
hard to read in both cases.
> integral1 = function(u) {
+ o=(1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) - q*u/2
+ rho=prod((1+lambda^2*u^2)^(h/4))*exp(
(1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )
+ integrand = sin(o)/(u*rho)
+ }
>
> #same as above
> integral2= function(u) {
+ sin((1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) -
q*u/2)/
+ (u*(prod((1+lambda^2*u^2)^(h/4))*
+ exp( (1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )))
+ }
>
>
> 1/2+(1/pi)*integrate(integral1,0,Inf)$value
[1] 1.022537
> 1/2+(1/pi)*integrate(integral2,0,Inf)$value
[1] 1.022537
>
>
On 1/18/07, rdporto1 <[EMAIL PROTECTED]> wrote:
>
> Hi all.
>
> I'm trying to numerically invert the characteristic function
> of a quadratic form following Imhof's (1961, Biometrika 48)
> procedure.
>
> The parameters are:
>
> lambda=c(.6,.3,.1)
> h=c(2,2,2)
> sigma=c(0,0,0)
> q=3
>
> I've implemented Imhof's procedure two ways that, for me,
> should give the same answer:
>
> #more legible
> integral1 = function(u) {
> o=(1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) - q*u/2
> rho=prod((1+lambda^2*u^2)^(h/4))*exp(
> (1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )
> integrand = sin(o)/(u*rho)
> }
>
> #same as above
> integral2= function(u) {
> ((1/2)*sum(h*atan(lambda*u)+sigma^2*lambda*u/(1+lambda^2*u^2)) - q*u/2)/
> (u*(prod((1+lambda^2*u^2)^(h/4))*
> exp( (1/2)*sum((sigma*lambda*u)^2/(1+lambda^2*u^2)) )))
> }
>
> The following should be near 0.18. However, nor the answers are near this
> value neither they agree each other!
>
> > 1/2+(1/pi)*integrate(integral1,0,Inf)$value
> [1] 1.022537
> > 1/2+(1/pi)*integrate(integral2,0,Inf)$value
> [1] 1.442720
>
> What's happening? Is this a bug or OS specific? Shouldn't they give the
> same answer? Why do I get results so different from 0.18? In time:
> the procedure works fine for q=.2.
>
> I'm running R 2.4.1 in a PC with Windows XP 32bits. Other ways (in R) to
> find the distribution of general quadratic forms are welcome.
>
> Thanks in advance.
>
> Rogerio.
>
> __
> 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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[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.
[R] Problem with loading tkrplot
I asked the maintainer and he indicated that it might be a dll problem. Has
anyone see this problem? I had installed the latest copy of tkrplot. I was
trying to use teachingDemos when I first got the error.
On 1/18/07, Luke Tierney <[EMAIL PROTECTED]> wrote:
> Looks like tcl can't find the dll or something along those lines. As
> this is windows you'll have to ask someone who uses that platform
> to help figure out why.
>
> luke
>
> On Thu, 18 Jan 2007, jim holtman wrote:
>
> > I was trying to use the teachingDemos package and was getting an error
> > trying to load tkrplot.
> >
> > I downloaded the latest copy and here is what I am getting on the
> console.
> > You were mentioned as the maintainer on the manual page. Do you know
> why
> > this error might be occuring?
> >
> >
> >
> >> utils:::menuInstallPkgs()
> > --- Please select a CRAN mirror for use in this session ---
> > trying URL '
> > http://www.stathy.com/cran/bin/windows/contrib/2.4/tkrplot_0.0-16.zip'
> > Content type 'application/zip' length 24119 bytes
> > opened URL
> > downloaded 23Kb
> >
> > package 'tkrplot' successfully unpacked and MD5 sums checked
> >
> > The downloaded packages are in
> > C:\Documents and Settings\Compaq_Administrator\Local
> > Settings\Temp\RtmpqEShrb\downloaded_packages
> > updating HTML package descriptions
> >> library(tkrplot)
> > Loading required package: tcltk
> > Loading Tcl/Tk interface ... done
> > Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
> > "tclObj") :
> > [tcl] could not find interpreter "Rplot".
> > Error in library(tkrplot) : .First.lib failed for 'tkrplot'
> >> sessionInfo()
> > R version 2.4.1 (2006-12-18)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] "tcltk" "stats" "utils"
> "datasets" "graphics" "grDevices"
> > "methods" "base"
> >>
> >
> >
> >
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[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] Problem with loading tkrplot
On 1/18/2007 8:57 PM, jim holtman wrote:
> I asked the maintainer and he indicated that it might be a dll problem. Has
> anyone see this problem? I had installed the latest copy of tkrplot. I was
> trying to use teachingDemos when I first got the error.
I just installed tkrplot in R 2.4.1 and it worked fine. I've never seen
the error you're reporting. However, I see what looks like a typo that
might affect some systems:
In the tkrplot .First.lib function, I see
> if (is.character(.Platform$r_arch) && .Platform$r_arch !=
> "")
> path <- file.path("libs", .Platform$r_arc, dlname)
> else path <- file.path("libs", dlname)
On the 3rd line, I think .Platform$r_arc should be .Platform$r_arch. On
my system I never execute that line, but if .Platform$r_arch is set on
your system, it would likely cause problems.
Duncan Murdoch
>
> On 1/18/07, Luke Tierney <[EMAIL PROTECTED]> wrote:
>
>> Looks like tcl can't find the dll or something along those lines. As
>> this is windows you'll have to ask someone who uses that platform
>> to help figure out why.
>>
>> luke
>>
>> On Thu, 18 Jan 2007, jim holtman wrote:
>>
>>> I was trying to use the teachingDemos package and was getting an error
>>> trying to load tkrplot.
>>>
>>> I downloaded the latest copy and here is what I am getting on the
>> console.
>>> You were mentioned as the maintainer on the manual page. Do you know
>> why
>>> this error might be occuring?
>>>
>>>
>>>
utils:::menuInstallPkgs()
>>> --- Please select a CRAN mirror for use in this session ---
>>> trying URL '
>>> http://www.stathy.com/cran/bin/windows/contrib/2.4/tkrplot_0.0-16.zip'
>>> Content type 'application/zip' length 24119 bytes
>>> opened URL
>>> downloaded 23Kb
>>>
>>> package 'tkrplot' successfully unpacked and MD5 sums checked
>>>
>>> The downloaded packages are in
>>> C:\Documents and Settings\Compaq_Administrator\Local
>>> Settings\Temp\RtmpqEShrb\downloaded_packages
>>> updating HTML package descriptions
library(tkrplot)
>>> Loading required package: tcltk
>>> Loading Tcl/Tk interface ... done
>>> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
>>> "tclObj") :
>>> [tcl] could not find interpreter "Rplot".
>>> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
sessionInfo()
>>> R version 2.4.1 (2006-12-18)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] "tcltk" "stats" "utils"
>> "datasets" "graphics" "grDevices"
>>> "methods" "base"
>>>
>>>
>
>
>
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[R] kate editor for R
Like kile for LaTeX, Linux/KDE's kate editor is an excellent editor for
R, with easy code submission to a running R process. Syntax
highlighting is good. I have not been able to figure out two things:
- how to automatically reformat a line or region of text using good
indentation rules (Emacs/ESS make this so easy by just hitting Tab while
the cursor is in a line, or highlighting a region and hitting Esq q)
- how to cause auto-indenting as you type braces. For me, kate puts a {
in column one
Thanks for any pointers.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] if else statement
Hello,
I'm doing some scripting and I've noticed that R doesn't seem to
have an
if (cond){
do
}ifelse (cond) {
do
} else {
do
}
type block.
Is this correct or am I missing something.
THX
Paul
--
Research Technician
Mass Spectrometry
o The
/
o Scripps
\
o Research
/
o Institute
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Re: [R] How to optimize this loop ? (correction)
G'day Martin and others,
On Thu, 18 Jan 2007 15:22:07 +0100
Martin Becker <[EMAIL PROTECTED]> wrote:
> Sorry, I accidentaly lost one line of the function code (result <-0),
> see below...
But even with that line, the code doesn't work properly. :)
Since you changed the order of the for loop (from "i in 1:(len-1)" to
"i in (len-1):1") you broke the logic of the code and the result
returned is wrong (should be something like "result <- len-i" instead
of "result <- i-1").
I agree that your function is faster than the one based on rle(),
presumably because rle() does just too many additional computations
that are not necessary to solve the problem at hand. But I still don't
like to see for() loops in R code. :) I would suggest the following
solution (which is only marginally slower than yours on these example
inputs):
myfun2 <- function(x){
len <- length(x)
which.max(c(x[len] <= rev(x[-len]), TRUE) ) - 1
}
The concatenation of TRUE at the end of the logical vector is necessary
for the case that all elements before the last are smaller than the
last one. It also has the side benefit that myfun(2) will return 0
instead of numeric(0) (or something similar). On my machine:
> system.time(for (i in 1:1) erg<-my_fun(c(3, 4, 10,14,8,3,4,6,9)))
[1] 2.860 0.016 2.950 0.000 0.000
> system.time(for (i in 1:1) erg<-myfun1(c(3, 4, 10,14,8,3,4,6,9)))
[1] 0.256 0.000 0.256 0.000 0.000
> system.time(for (i in 1:1) erg<-myfun2(c(3, 4, 10,14,8,3,4,6,9)))
[1] 0.280 0.000 0.283 0.000 0.000
Cheers,
Berwin
=== Full address =
Berwin A TurlachTel.: +65 6515 4416 (secr)
Dept of Statistics and Applied Probability+65 6515 6650 (self)
Faculty of Science FAX : +65 6872 3919
National University of Singapore
6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED]
Singapore 117546http://www.stat.nus.edu.sg/~statba
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] if else statement
On Thu, 18 Jan 2007 19:02:49 -0800,
"H. Paul Benton" <[EMAIL PROTECTED]> wrote:
> Hello,
> I'm doing some scripting and I've noticed that R doesn't seem to
> have an
> if (cond){
> do
> }ifelse (cond) {
> do
> } else {
> do
> }
> type block.
It's legal to join if else statements together:
if (cond) {
do X
} else if (cond) {
do Y
} else if (cond) {
do Z
} else do W
--
Seb
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with loading tkrplot
On my system it is not set: so it must be something else. It happens on
both of my windows systems. Guess I will have to look somewhere else to see
what might be missing.
> .Platform
$OS.type
[1] "windows"
$file.sep
[1] "/"
$dynlib.ext
[1] ".dll"
$GUI
[1] "Rgui"
$endian
[1] "little"
$pkgType
[1] "win.binary"
$path.sep
[1] ";"
$r_arch
[1] ""
>
On 1/18/07, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
> On 1/18/2007 8:57 PM, jim holtman wrote:
> > I asked the maintainer and he indicated that it might be a dll
> problem. Has
> > anyone see this problem? I had installed the latest copy of tkrplot. I
> was
> > trying to use teachingDemos when I first got the error.
>
> I just installed tkrplot in R 2.4.1 and it worked fine. I've never seen
> the error you're reporting. However, I see what looks like a typo that
> might affect some systems:
>
> In the tkrplot .First.lib function, I see
>
> > if (is.character(.Platform$r_arch) && .Platform$r_arch !=
> > "")
> > path <- file.path("libs", .Platform$r_arc, dlname)
> > else path <- file.path("libs", dlname)
>
> On the 3rd line, I think .Platform$r_arc should be .Platform$r_arch. On
> my system I never execute that line, but if .Platform$r_arch is set on
> your system, it would likely cause problems.
>
> Duncan Murdoch
>
> >
> > On 1/18/07, Luke Tierney <[EMAIL PROTECTED]> wrote:
> >
> >> Looks like tcl can't find the dll or something along those lines. As
> >> this is windows you'll have to ask someone who uses that platform
> >> to help figure out why.
> >>
> >> luke
> >>
> >> On Thu, 18 Jan 2007, jim holtman wrote:
> >>
> >>> I was trying to use the teachingDemos package and was getting an error
> >>> trying to load tkrplot.
> >>>
> >>> I downloaded the latest copy and here is what I am getting on the
> >> console.
> >>> You were mentioned as the maintainer on the manual page. Do you know
> >> why
> >>> this error might be occuring?
> >>>
> >>>
> >>>
> utils:::menuInstallPkgs()
> >>> --- Please select a CRAN mirror for use in this session ---
> >>> trying URL '
> >>> http://www.stathy.com/cran/bin/windows/contrib/2.4/tkrplot_0.0-16.zip'
> >>> Content type 'application/zip' length 24119 bytes
> >>> opened URL
> >>> downloaded 23Kb
> >>>
> >>> package 'tkrplot' successfully unpacked and MD5 sums checked
> >>>
> >>> The downloaded packages are in
> >>> C:\Documents and Settings\Compaq_Administrator\Local
> >>> Settings\Temp\RtmpqEShrb\downloaded_packages
> >>> updating HTML package descriptions
> library(tkrplot)
> >>> Loading required package: tcltk
> >>> Loading Tcl/Tk interface ... done
> >>> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class
> =
> >>> "tclObj") :
> >>> [tcl] could not find interpreter "Rplot".
> >>> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
> sessionInfo()
> >>> R version 2.4.1 (2006-12-18)
> >>> i386-pc-mingw32
> >>>
> >>> locale:
> >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> >>> States.1252;LC_MONETARY=English_United
> >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >>>
> >>> attached base packages:
> >>> [1] "tcltk" "stats" "utils"
> >> "datasets" "graphics" "grDevices"
> >>> "methods" "base"
> >>>
> >>>
> >
> >
> >
>
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[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] kate editor for R
On Thu, 2007-01-18 at 20:30 -0600, Frank E Harrell Jr wrote:
> Like kile for LaTeX, Linux/KDE's kate editor is an excellent editor for
> R, with easy code submission to a running R process. Syntax
> highlighting is good. I have not been able to figure out two things:
>
> - how to automatically reformat a line or region of text using good
> indentation rules (Emacs/ESS make this so easy by just hitting Tab while
> the cursor is in a line, or highlighting a region and hitting Esq q)
>
> - how to cause auto-indenting as you type braces. For me, kate puts a {
> in column one
>
> Thanks for any pointers.
Frank,
I'm not sure if what I found provides an optimistic outlook, however,
you might find the following helpful:
See the questions:
Can I use different indenters for different files?
How can I get KatePart to autoindent XXX code?
at http://kate-editor.org/faq. KatePart is the text editing component
in Kate.
In the two answers, there are links to articles that provide additional
insight into implementing indentation functionality in Kate.
HTH,
Marc
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[R] ability estimate with GRM of IRT
Hi my friends,
I have an issue with ability estimates when running GRM of IRT. I
have responses from 242 subjects but got 183 ability estimates.
Below is what I did to get the estimates.
1) I have a csv file "P1.csv" and I imported it into R and loaded
the "ltm" package by doing:
p1<-read.table("P1.csv",header=TRUE,sep=",")
library(ltm)
2) I created a subset that included columns 2 to 9 for the
analysis by doing:
s1<-p1[,2:9]
3) I converted the subset into data.frame format by doing:
s1df=data.frame(s1)
4) I checked the descriptive stats for the s1df by doing:
ds1df=descript(s1df)
ds1df
And it was confirmed that 242 subjects' responses were imported.
5)I ran GRM on the s1df dataset by doing:
grm<-grm(s1df, Hessian=T)
grm
6)Finally, I ran the ability estimated by doing:
aes1=factor.scores(grm)
aes1
And I got 183 factor-scores for observed response patterns.
Besides, the 183 estimates are not for the first 183 subjects of
the 242 because the response patterns of No 1 on the factor-scores
list do not match those of No 1 in the s1 dataset and the same
thing holds true for the rest of the response patterns.
Could you help me find out what the problem is?
Many thanks in advance!
Feng
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Re: [R] Problem with loading tkrplot
As it happens I used TeachingDemos/tkrplot on Windows (R 2.4.1) with a
class example yesterday.
It looks to me as if the issue is in the R installation. Remember that Tcl
support is optional when R is installed, and can be influenced by
environment variables. So my first check would be that the tcltk demos
all work.
On Thu, 18 Jan 2007, jim holtman wrote:
> I asked the maintainer and he indicated that it might be a dll problem. Has
> anyone see this problem? I had installed the latest copy of tkrplot. I was
> trying to use teachingDemos when I first got the error.
>
> On 1/18/07, Luke Tierney <[EMAIL PROTECTED]> wrote:
>
>> Looks like tcl can't find the dll or something along those lines. As
>> this is windows you'll have to ask someone who uses that platform
>> to help figure out why.
>>
>> luke
>>
>> On Thu, 18 Jan 2007, jim holtman wrote:
>>
>>> I was trying to use the teachingDemos package and was getting an error
>>> trying to load tkrplot.
>>>
>>> I downloaded the latest copy and here is what I am getting on the
>> console.
>>> You were mentioned as the maintainer on the manual page. Do you know
>> why
>>> this error might be occuring?
>>>
>>>
>>>
utils:::menuInstallPkgs()
>>> --- Please select a CRAN mirror for use in this session ---
>>> trying URL '
>>> http://www.stathy.com/cran/bin/windows/contrib/2.4/tkrplot_0.0-16.zip'
>>> Content type 'application/zip' length 24119 bytes
>>> opened URL
>>> downloaded 23Kb
>>>
>>> package 'tkrplot' successfully unpacked and MD5 sums checked
>>>
>>> The downloaded packages are in
>>> C:\Documents and Settings\Compaq_Administrator\Local
>>> Settings\Temp\RtmpqEShrb\downloaded_packages
>>> updating HTML package descriptions
library(tkrplot)
>>> Loading required package: tcltk
>>> Loading Tcl/Tk interface ... done
>>> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
>>> "tclObj") :
>>> [tcl] could not find interpreter "Rplot".
>>> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
sessionInfo()
>>> R version 2.4.1 (2006-12-18)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] "tcltk" "stats" "utils"
>> "datasets" "graphics" "grDevices"
>>> "methods" "base"
>>>
>>>
>>>
>
>
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] Vectorize rearrangement within each column
Consider a matrix like > ma = matrix(10:15, nr = 3) > ma [,1] [,2] [1,] 10 13 [2,] 11 14 [3,] 12 15 I want to rearrange each column according to row indexes (1 to 3) given in another matrix, as in > idx = matrix(c(1,3,2, 2,3,1), nr = 3) > idx [,1] [,2] [1,]12 [2,]33 [3,]21 The new matrix mb will have for each column the corresponding column of ma indexed by the corresponding column of idx, as in > mb = ma > for (j in 1:2) mb[,j] = ma[idx[,j], j] > mb [,1] [,2] [1,] 10 14 [2,] 12 15 [3,] 11 13 Can I avoid the for() loop? I'm specially interested to find out if a fast implementation using lapply() would be feasible for large input matrices (analogues of ma and idx) transformed into data frames. Roberto Osorio __ 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] Reading contingency tables
You cannot seek on a url() connection. Try downloading the file and
reading it locally.
There's a bug in the function which forgets to open its temporary file: I
will attend to that.
On Thu, 18 Jan 2007, Giovanni Petris wrote:
>
> I am trying to read an ftable using read.ftable, but I get the
> following error message:
>
>> jobSatTable <-
>> read.ftable("http://definetti.uark.edu/~gpetris/stat5333/jobSatisfaction.dat",skip=2)
> Error in seek(file, where = 0) : no applicable method for "seek"
> In addition: Warning messages:
> 1: no non-missing arguments to max; returning -Inf
> 2: no non-missing arguments to max; returning -Inf
>
>
> I also tried to play with the argument col.vars, to remove blank
> lines in the file, to remove the blank in "Not
> satisfied". Unfortunately nothing worked.
>
> Can anybody give me a suggestion on how to read that table?
>
> Thanks in advance,
> Giovanni
>
> ps:
>
>> version
> _
> platform sparc-sun-solaris2.8
> arch sparc
> os solaris2.8
> system sparc, solaris2.8
> status
> major 2
> minor 4.1
> year 2006
> month 12
> day18
> svn rev40228
> language R
> version.string R version 2.4.1 (2006-12-18)
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@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] Reading contingency tables
On Fri, 19 Jan 2007, Prof Brian Ripley wrote:
> You cannot seek on a url() connection. Try downloading the file and reading
> it locally.
You will need to edit it to fit the ftable format as well.
> There's a bug in the function which forgets to open its temporary file: I
> will attend to that.
It was a bit worse than just that: fixed in 2.4.1 patched.
>
> On Thu, 18 Jan 2007, Giovanni Petris wrote:
>
>>
>> I am trying to read an ftable using read.ftable, but I get the
>> following error message:
>>
>>> jobSatTable <-
>>> read.ftable("http://definetti.uark.edu/~gpetris/stat5333/jobSatisfaction.dat",skip=2)
>> Error in seek(file, where = 0) : no applicable method for "seek"
>> In addition: Warning messages:
>> 1: no non-missing arguments to max; returning -Inf
>> 2: no non-missing arguments to max; returning -Inf
>>
>>
>> I also tried to play with the argument col.vars, to remove blank
>> lines in the file, to remove the blank in "Not
>> satisfied". Unfortunately nothing worked.
>>
>> Can anybody give me a suggestion on how to read that table?
>>
>> Thanks in advance,
>> Giovanni
>>
>> ps:
>>
>>> version
>> _
>> platform sparc-sun-solaris2.8
>> arch sparc
>> os solaris2.8
>> system sparc, solaris2.8
>> status
>> major 2
>> minor 4.1
>> year 2006
>> month 12
>> day18
>> svn rev40228
>> language R
>> version.string R version 2.4.1 (2006-12-18)
>>
>>
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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