Re: [R] Help on Multiple Structural break unit root test
Dear Eric This test is unfortunately AFAIK not implemented in R. You can nevertheless use the similar Zivot and Andrews test in package urca. library(urca) ?ur.za Best Matthieu Le 06. 06. 10 12:00, r-help-requ...@r-project.org a écrit : Message: 24 Date: Sat, 5 Jun 2010 15:45:29 +0100 From: ERIC AIDOO To:r-help@r-project.org Subject: [R] Help on Multiple Structural break unit root test Message-ID: Content-Type: text/plain Help. Please am search for R package that will enable me to perform Lumsdain and Papell unit root test with multiple structural break or minimum LM unit root test with multiple structural break thank you __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart but with boxes
On Sun, Jun 6, 2010 at 11:53 PM, Daisy Englert Duursma wrote: > Hello r-help. > > I have been working on making a graph and have several solutions but > they are tedious at best. > > Here is an example dataset: > > catg<-(c(1,2,3,2,4,3,2,1,4,3,1)) > min<-(c(1,2,3,3,4,5,6,6,3,2,1)) > max <-(c(10,6,8,6,7,3,10,9,10,8,9)) > cbind(min,max,catg) > > What I want to create is a basically a bar chart, but I define the > min (min) and max (max) for the bars. > These bars are separated into three categories (catg). Within each > category the bars are allowed to overlap. I set the bars to have a > transparent color so that I can see agreement of the items within a > category based on the darkness of color. > > One method I came up with, is to use ggplot2 and geom_tile but then I > have to give x,y coordinates for every corner of every box. > Considering the size of my real datasets, and not this little example > dataset, this seems annoying. > > I could even just graph lines with the defined min and max. With that > I could make the lines thick and achieve the effect I am looking for. > > Hopefully I have missed an obvious method to graph this. One option to look at is segplot() in the latticeExtra package. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Computing day-over-day log return for a matrix containing multiple time series
Actually the 'apply' is not necessary.
The original poster has stocks as rows
rather than the customary columns, so
the following should suffice:
retmat <- diff(log(t(pricemat)))
Questions that are specifically financial
should be sent to r-sig-finance (you need
to subscribe before posting).
On 07/06/2010 07:12, sayan dasgupta wrote:
Hope this helps
a<- matrix(runif(150),nrow=3,ncol=50)
p2r<- function(x) 100 * diff(log(x))
t(apply(a,1,function(x){p2r(c(x))}))
On Mon, Jun 7, 2010 at 8:41 AM, Anyi Zhu wrote:
Hi all,
Thanks a lot for anyone's help in advance.
I am trying to find a way to compute the day-to-day return (log return)
from
a n x r matrix containing, n different stocks and price quotes over r days.
The time series of prices are already split by using unstack function.
For the result, I would like to see a n x (r-1) matrix, where by each entry
is the day-over-day return of each stock.
I tried to look into the zoo package, however it seems to give only the
plots but not the actual data.
take a look at
vignette("zoo-quickref",package="zoo")
It gives an exact solution to your problem
Would apply function work in this case?
Thanks a lot!
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--
Patrick Burns
pbu...@pburns.seanet.com
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')
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[R] average two sets of columns
Hi R experts.
how can I average two sets of columns?
dd <- data.frame(b = c("chr2", "chr1", "chrY", "chr13", "chrX"),
w=11:15, x = 1:5, y = c(8, 3, 9, 9,7),
z = c(1, 1, 1, 2, 8))
expected result for mean(w,x) and mean(y,z) is
1 chr2 6 4.5
2 chr1 7 2
3 chrY 8 5
4 chr13 9 5.5
5 chrX 10 7.5
Yu
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[R] Subsetting subsets of data.frames
Hey Everyone, I have been stumped by this all day. Basically, I have a data.frame of multiple columns. Of concern are "id" & "date" For some reason, oftentimes there are duplicates of data with the same date. I would like to remove the duplicates per different id (removing duplicate dates for the entire data.frame would leave nothing since different id's all have the same dates) subset(x,!duplicated(x$date_)) works for just one ID, but i am having trouble figuring out how to apply this to each subset of IDs (and retaining the original data.frame structure) -- View this message in context: http://r.789695.n4.nabble.com/Subsetting-subsets-of-data-frames-tp2245556p2245556.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ols function in rms package
Hello,
I have a couple of questions about the ols function in Frank Harrell's rms
package.
Is there any way to specify variables by their column number in the data
frame rather than by the variable name?
For example,
library(rms)
x1 <- rnorm(100, 0, 1)
x2 <- rnorm(100, 0, 1)
x3 <- rnorm(100, 0, 1)
y <- x2 + x3 + rnorm(100, 0, 5)
d <- data.frame(x1, x2, x3, y)
rm(x1, x2, x3, y)
lm(y ~ d[,2] + d[,3], data = d) # This works
ols(y ~ d[,2] + d[,3], data = d) # Gives error
Error in if (!length(fname) || !any(fname == zname)) { :
missing value where TRUE/FALSE needed
However, this works:
ols(y ~ x2 + d[,3], data = d)
The reason I want to do this is to program variable selection for
bootstrap model validation.
A related question: does ols allow "y ~ ." notation?
lm(y ~ ., data = d[, 2:4]) # This works
ols(y ~ ., data = d[, 2:4]) # Gives error
Error in terms.formula(formula) : '.' in formula and no 'data' argument
Thanks for any help you can give.
Regards,
Mark
--
Mark Seeto
Statistician
National Acoustic Laboratories
Re: [R] paste together a string object later to be utilized in a function
I'm sorry for not clearer describing my motive with this--
So this is what I'm trying to do- Take a survival object and utilize
it in ggplot.
ggkm<-function(time,event,stratum) {
m2s<-Surv(time,as.numeric(event))
fit <- survfit(m2s ~ stratum)
f$time<-fit$time
f$surv<-fit$surv
f$strata<-c(rep(names(fit$strata[1]),fit$strata[1]),rep(names(fit$strata[2]),fit$strata[2]))
f$upper<-fit$upper
f$lower<-fit$lower
r<-ggplot
(f,aes(x=time,y=surv,fill=strata,group=strata))+geom_line()+geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.3)
return(r)
}
My problem is that I can have more than two strata, and I would like
the function to automatically detect the number of strata. Hence a
quick hack as to how I can create f$strata when I dont know the number
of strata would be appreciated.
The
paste("rep(names(fit$strata[",1:length(fit$strata),"]),fit$strata[",1:length(fit$strata),"])",sep="")
is as close as I get. However this results in multiple strings and I
havent discovered yet how I can pass this so f$strata is created. This
could easily be done in stata appending to a macro, but as I am a
recent convertee I dont know how to do this in R. (yet...?)
Regards,
//M
On Mon, Jun 7, 2010 at 2:50 AM, Joris Meys wrote:
> Wild guess, but it looks like you are looking at :
>
>> ts <- list(a=1:5)
>> names(ts$a) <- letters[1:5]
>> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>>
>> sapply(v,function(x){eval(parse(,text=x))})
> $`rep(names(ts$a[1]),ts$a[1])`
> [1] "a"
>
> $`rep(names(ts$a[2]),ts$a[2])`
> [1] "b" "b"
>
> $`rep(names(ts$a[3]),ts$a[3])`
> [1] "c" "c" "c"
>
> $`rep(names(ts$a[4]),ts$a[4])`
> [1] "d" "d" "d" "d"
>
> $`rep(names(ts$a[5]),ts$a[5])`
> [1] "e" "e" "e" "e" "e"
>
>> assign("test",eval(parse(text=v[3])))
>> test
> [1] "c" "c" "c"
>>
>
> Cheers
> Joris
>
> On Sun, Jun 6, 2010 at 9:51 PM, moleps wrote:
>> Dear r-listers,
>>
>> I need to pass a string to a function. However the length of the string is
>> dependent on the length of a vector.
>>
>>
>> b<-length(h)
>> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>>
>>
>> Is it possible somehow to pass this as an argument to a function later on ?
>>
>>
>>
>> Regards,
>>
>> //M
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
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Re: [R] average two sets of columns
Hi:
Using the plyr package,
summarise(dd, b = b, wx = (w + x)/2, yz = (y + z)/2)
b wx yz
1 chr2 6 4.5
2 chr1 7 2.0
3 chrY 8 5.0
4 chr13 9 5.5
5 chrX 10 7.5
HTH,
Dennis
On Sun, Jun 6, 2010 at 9:53 PM, Yuan Jian wrote:
> Hi R experts.
>
> how can I average two sets of columns?
>
> dd <- data.frame(b = c("chr2", "chr1", "chrY", "chr13", "chrX"),
> w=11:15, x = 1:5, y = c(8, 3, 9, 9,7),
>z = c(1, 1, 1, 2, 8))
> expected result for mean(w,x) and mean(y,z) is
> 1 chr2 6 4.5
> 2 chr1 7 2
> 3 chrY 8 5
> 4 chr13 9 5.5
> 5 chrX 10 7.5
>
> Yu
>
>
>
>
>
>[[alternative HTML version deleted]]
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Computing day-over-day log return for a matrix containing multiple time series
You can use diff.zoo like this:
library(zoo)
z <- zoo(matrix(1:24, 6))
z
diff(log(z))
# also try
diff(z, arith = FALSE) - 1
See ?diff.zoo
and read the three zoo vignettes (pdf documents):
vignette(package = "zoo") # lists them
vignette("zoo")
etc.
On Sun, Jun 6, 2010 at 11:11 PM, Anyi Zhu wrote:
> Hi all,
>
>
>
> Thanks a lot for anyone's help in advance.
>
>
>
> I am trying to find a way to compute the day-to-day return (log return) from
> a n x r matrix containing, n different stocks and price quotes over r days.
> The time series of prices are already split by using unstack function.
>
>
>
> For the result, I would like to see a n x (r-1) matrix, where by each entry
> is the day-over-day return of each stock.
>
>
>
> I tried to look into the zoo package, however it seems to give only the
> plots but not the actual data.
>
>
>
> Would apply function work in this case?
>
>
>
> Thanks a lot!
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
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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] Loading an image/picture (png/jpeg/...) to screen...
Joris Meys gmail.com> writes: > > There might be a way doing that in R, but if you really need to take > measures of a picture in some standardized way, I suggest you take a > look at ImageJ. More than R that seems the right tool for the job. > Some people have been experimenting with connecting ImageJ and R, but > even without connection a simple text file can get the data where it > has to be. [...] OK, maybe that helps; I just tried around... ...first want to try a pure R-way. But this might be a fallback. Thanks. Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Loading an image/picture (png/jpeg/...) to screen...
The package EBImage provides general purpose functionality for the
reading, writing, analysis and displaying of images.
> library(EBImage)
> x = readImage('lena.gif')
> display(x)
ImageJ is OK to carry out some image processing operations. But if you
need to perform quantitative image analysis or model/analyse images with
statistical models, then R + EBImage is a simple and powerful alternative.
Images are just matrices.
Kind regards,
Greg
---
Gregoire Pau
EMBL Research Officer
http://www.embl.de/~gpau/
Oliver wrote:
baptiste auguie googlemail.com> writes:
Hi,
Try this,
library(png)
example(readPNG)
[...]
If "rasterImage" would be available, I think this would be the right hint.
But it isn't.
So I can load the pic, but not display it. :(
Ciao,
Oliver
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Re: [R] Subsetting subsets of data.frames
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Uwe Ligges On 07.06.2010 09:01, Jeff08 wrote: Hey Everyone, I have been stumped by this all day. Basically, I have a data.frame of multiple columns. Of concern are "id"& "date" For some reason, oftentimes there are duplicates of data with the same date. I would like to remove the duplicates per different id (removing duplicate dates for the entire data.frame would leave nothing since different id's all have the same dates) subset(x,!duplicated(x$date_)) works for just one ID, but i am having trouble figuring out how to apply this to each subset of IDs (and retaining the original data.frame structure) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste together a string object later to be utilized in a function
It helps if you provide sample data, so we can try some things out
ourselves. Right now, I can't run your function without guessing how
your data might look like.
Yet, try something like this :
> ts <- list(a=1:5)
> names(ts$a) <- letters[1:5]
> n <- length(names(ts$a))
> tmp <- sapply(1:n,function(i){rep(names(ts$a[i]),ts$a[i])})
> strata <- unlist(tmp)
> strata
[1] "a" "b" "b" "c" "c" "c" "d" "d" "d" "d" "e" "e" "e" "e" "e"
Cheers
Joris
On Mon, Jun 7, 2010 at 10:26 AM, moleps islon wrote:
> I'm sorry for not clearer describing my motive with this--
>
> So this is what I'm trying to do- Take a survival object and utilize
> it in ggplot.
>
> ggkm<-function(time,event,stratum) {
>
>
> m2s<-Surv(time,as.numeric(event))
>
> fit <- survfit(m2s ~ stratum)
>
> f$time<-fit$time
>
> f$surv<-fit$surv
>
>
> f$strata<-c(rep(names(fit$strata[1]),fit$strata[1]),rep(names(fit$strata[2]),fit$strata[2]))
>
> f$upper<-fit$upper
> f$lower<-fit$lower
>
> r<-ggplot
> (f,aes(x=time,y=surv,fill=strata,group=strata))+geom_line()+geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.3)
> return(r)
> }
>
>
> My problem is that I can have more than two strata, and I would like
> the function to automatically detect the number of strata. Hence a
> quick hack as to how I can create f$strata when I dont know the number
> of strata would be appreciated.
>
>
> The
> paste("rep(names(fit$strata[",1:length(fit$strata),"]),fit$strata[",1:length(fit$strata),"])",sep="")
> is as close as I get. However this results in multiple strings and I
> havent discovered yet how I can pass this so f$strata is created. This
> could easily be done in stata appending to a macro, but as I am a
> recent convertee I dont know how to do this in R. (yet...?)
>
>
> Regards,
>
> //M
>
> On Mon, Jun 7, 2010 at 2:50 AM, Joris Meys wrote:
>> Wild guess, but it looks like you are looking at :
>>
>>> ts <- list(a=1:5)
>>> names(ts$a) <- letters[1:5]
>>> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>>>
>>> sapply(v,function(x){eval(parse(,text=x))})
>> $`rep(names(ts$a[1]),ts$a[1])`
>> [1] "a"
>>
>> $`rep(names(ts$a[2]),ts$a[2])`
>> [1] "b" "b"
>>
>> $`rep(names(ts$a[3]),ts$a[3])`
>> [1] "c" "c" "c"
>>
>> $`rep(names(ts$a[4]),ts$a[4])`
>> [1] "d" "d" "d" "d"
>>
>> $`rep(names(ts$a[5]),ts$a[5])`
>> [1] "e" "e" "e" "e" "e"
>>
>>> assign("test",eval(parse(text=v[3])))
>>> test
>> [1] "c" "c" "c"
>>>
>>
>> Cheers
>> Joris
>>
>> On Sun, Jun 6, 2010 at 9:51 PM, moleps wrote:
>>> Dear r-listers,
>>>
>>> I need to pass a string to a function. However the length of the string is
>>> dependent on the length of a vector.
>>>
>>>
>>> b<-length(h)
>>> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>>>
>>>
>>> Is it possible somehow to pass this as an argument to a function later on ?
>>>
>>>
>>>
>>> Regards,
>>>
>>> //M
>>>
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>> --
>> Ghent University
>> Faculty of Bioscience Engineering
>> Department of Applied mathematics, biometrics and process control
>>
>> tel : +32 9 264 59 87
>> joris.m...@ugent.be
>> ---
>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>
>
--
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
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Re: [R] Robust Asymptotic Statistics (RobASt)
Dear Alex, after installation of ROptRegTS there should be a folder "scripts" in the package directory of ROptRegTS which includes some further examples. If you are assuming normal errors you should switch to package RobRex which is "optimized" for normal errors. There you will also find a folder "scripts" in the package directory. In general, multivariate regression should work. But, I have to admit that we didn't try many multivariate examples so far. Beside that, the user interface is still rudimentary at the moment and some ideas which will clearly reduce computation time (as in the case of package RobLox) are unfortunately not yet implemented. So, if you are willing to accept these drawbacks I will be glad to give you a hand to get our estimators to work for your data. Best, Matthias On 06.06.2010 06:47, Alex Weslowski wrote: Hi all, Other than: http://www.stamats.de/F2006.r Are there other good simple examples out there of using the ROptRegTS package (part of the RobASt project)? I'm hoping to plug it in for multivariate regression. Or is this not a good idea? Just trying to find out how it compares to rlm, lts, glm, etc. Hopefully this makes sense, I'm new to the world of statistics and R. Thanks! St0x __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Matthias Kohl www.stamats.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] prettyR
On 06/07/2010 02:49 AM, Iasonas Lamprianou wrote: Hi all, does anyone have any practical examples of how this command can be used in prettyR? add.value.labels(x,value.labels) I mean, can we have the SPSS style of using numbers and/or labels if we want to? Thank you for your time Hi Jason, The value labels used in prettyR are mainly to help those users who are importing SPSS .sav files and want to see the value labels displayed in the output of some functions. Thus if you import an SPSS dataset with add.value.labels=TRUE, functions like "brkdn" will display those labels. The add.value.labels function just lets the user add value labels to variables that don't have any. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] prewhiten
HI all., I have some univariate time series that need to be prewhitened. HOw this can be performed in R. I am thinking of to fit an ARIMA model and substract this from the original series. Is this the correct way THanks in advance nuncio -- Nuncio.M Research Scientist National Center for Antarctic and Ocean research Head land Sada Vasco da Gamma Goa-403804 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] prettyR
Thank you, I'll have a go and if I have more questions I'll probably come back to you... Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Mon, 7/6/10, Jim Lemon wrote: > From: Jim Lemon > Subject: Re: [R] prettyR > To: "Iasonas Lamprianou" > Cc: r-help@r-project.org > Date: Monday, 7 June, 2010, 12:01 > On 06/07/2010 02:49 AM, Iasonas > Lamprianou wrote: > > Hi all, > > does anyone have any practical examples of how this > command can be used in prettyR? > > add.value.labels(x,value.labels) > > > > I mean, can we have the SPSS style of using numbers > and/or labels if we want to? > > > > Thank you for your time > > > Hi Jason, > The value labels used in prettyR are mainly to help those > users who are importing SPSS .sav files and want to see the > value labels displayed in the output of some functions. Thus > if you import an SPSS dataset with add.value.labels=TRUE, > functions like "brkdn" will display those labels. > > The add.value.labels function just lets the user add value > labels to variables that don't have any. > > Jim > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] prettyR
Thank you, I'll have a go and if I have more questions I'll probably come back to you... Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Mon, 7/6/10, Joris Meys wrote: > From: Joris Meys > Subject: Re: [R] prettyR > To: "Iasonas Lamprianou" > Cc: r-help@r-project.org > Date: Monday, 7 June, 2010, 2:05 > Very simple as explained in the help > files: > > > X <- 1:5 > > X > [1] 1 2 3 4 5 > > > add.value.labels(X,letters[1:5]) > [1] 1 2 3 4 5 > attr(,"value.labels") > a b c d e > 1 2 3 4 5 > > X > [1] 1 2 3 4 5 > > X didn't change. > > > X <- add.value.labels(X,letters[1:5]) > > X > [1] 1 2 3 4 5 > attr(,"value.labels") > a b c d e > 1 2 3 4 5 > > > X changed. Mind you, those value labels are only read by > functions > that use it. functions like names(), colnames(), rownames() > and the > likes won't use those labels. > > If you really want to use a kind of labels that works in > almost every > situation, just use factors. > > Cheers > Joris > > > On Sun, Jun 6, 2010 at 6:49 PM, Iasonas Lamprianou > wrote: > > Hi all, > > does anyone have any practical examples of how this > command can be used in prettyR? > > add.value.labels(x,value.labels) > > > > I mean, can we have the SPSS style of using numbers > and/or labels if we want to? > > > > Thank you for your time > > > > Jason > > > > > > Dr. Iasonas Lamprianou > > > > > > Assistant Professor (Educational Research and > Evaluation) > > Department of Education Sciences > > European University-Cyprus > > P.O. Box 22006 > > 1516 Nicosia > > Cyprus > > Tel.: +357-22-713178 > > Fax: +357-22-590539 > > > > > > Honorary Research Fellow > > Department of Education > > The University of Manchester > > Oxford Road, Manchester M13 9PL, UK > > Tel. 0044 161 275 3485 > > iasonas.lampria...@manchester.ac.uk > > > > > > > > > > __ > > R-help@r-project.org > mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, > reproducible code. > > > > > > -- > Ghent University > Faculty of Bioscience Engineering > Department of Applied mathematics, biometrics and process > control > > tel : +32 9 264 59 87 > joris.m...@ugent.be > --- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart but with boxes
On 06/07/2010 04:53 PM, Daisy Englert Duursma wrote: Hello r-help. I have been working on making a graph and have several solutions but they are tedious at best. Here is an example dataset: catg<-(c(1,2,3,2,4,3,2,1,4,3,1)) min<-(c(1,2,3,3,4,5,6,6,3,2,1)) max<-(c(10,6,8,6,7,3,10,9,10,8,9)) cbind(min,max,catg) What I want to create is a basically a bar chart, but I define the min (min) and max (max) for the bars. These bars are separated into three categories (catg). Within each category the bars are allowed to overlap. I set the bars to have a transparent color so that I can see agreement of the items within a category based on the darkness of color. One method I came up with, is to use ggplot2 and geom_tile but then I have to give x,y coordinates for every corner of every box. Considering the size of my real datasets, and not this little example dataset, this seems annoying. I could even just graph lines with the defined min and max. With that I could make the lines thick and achieve the effect I am looking for. Hi Daisy, How about this? offset<-c(-0.1,-0.1,-0.1,0,-0.1,0,0.1,0,0,0.1,0.1) plot(0,xlim=c(0.5,4.5),ylim=c(0,10),type="n") segments(catg+offset,min,catg+offset,max,lwd=5,col=3) You can program a function to calculate the offsets if you want to do lots of these. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] prewhiten
On Mon, 7 Jun 2010, nuncio m wrote: HI all., I have some univariate time series that need to be prewhitened. HOw this can be performed in R. That depends on what exactly you want to do for prewhtening. For example, if you want to prewhiten using an AR(1) model, you could apply ar() and then extract the residuals: ar(x, order.max = 1, aic = FALSE, method = ..., demean = ...)$resid and set the remaining arguments based on your preferences/needs. This can also be used for multivariate series. I am thinking of to fit an ARIMA model and substract this from the original series. Then you could use the residuals from arima()... Best, Z Is this the correct way THanks in advance nuncio -- Nuncio.M Research Scientist National Center for Antarctic and Ocean research Head land Sada Vasco da Gamma Goa-403804 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart but with boxes
Dear Daisy, This is easy woth ggplot2. Use geom_crossbar() and set the middle bar at the minimum of maximum. library(ggplot2) dataset <- data.frame(catg = (c(1,2,3,2,4,3,2,1,4,3,1)), min = (c(1,2,3,3,4,5,6,6,3,2,1)), max = (c(10,6,8,6,7,3,10,9,10,8,9))) ggplot(dataset, aes(x = catg, y = min, ymin = min, ymax = max)) + geom_crossbar(fill = "red", alpha = 0.2, fatten = 1) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie & Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics & Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey > -Oorspronkelijk bericht- > Van: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] Namens Jim Lemon > Verzonden: maandag 7 juni 2010 13:27 > Aan: Daisy Englert Duursma > CC: r-help@r-project.org > Onderwerp: Re: [R] barchart but with boxes > > On 06/07/2010 04:53 PM, Daisy Englert Duursma wrote: > > Hello r-help. > > > > I have been working on making a graph and have several > solutions but > > they are tedious at best. > > > > Here is an example dataset: > > > > catg<-(c(1,2,3,2,4,3,2,1,4,3,1)) > > min<-(c(1,2,3,3,4,5,6,6,3,2,1)) > > max<-(c(10,6,8,6,7,3,10,9,10,8,9)) > > cbind(min,max,catg) > > > > What I want to create is a basically a bar chart, but I define the > > min (min) and max (max) for the bars. > > These bars are separated into three categories (catg). Within each > > category the bars are allowed to overlap. I set the bars to have a > > transparent color so that I can see agreement of the items > within a > > category based on the darkness of color. > > > > One method I came up with, is to use ggplot2 and geom_tile > but then I > > have to give x,y coordinates for every corner of every box. > > Considering the size of my real datasets, and not this > little example > > dataset, this seems annoying. > > > > I could even just graph lines with the defined min and max. > With that > > I could make the lines thick and achieve the effect I am > looking for. > > > Hi Daisy, > How about this? > > offset<-c(-0.1,-0.1,-0.1,0,-0.1,0,0.1,0,0,0.1,0.1) > plot(0,xlim=c(0.5,4.5),ylim=c(0,10),type="n") > segments(catg+offset,min,catg+offset,max,lwd=5,col=3) > > You can program a function to calculate the offsets if you > want to do lots of these. > > Jim > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Greek letters and formatted text
The ?plotmath page and the example " ## How to combine "math" and numeric
variables :" should be helpful...?
>>> Thomas Bschorr 05/06/2010 10:36:42 >>>
Hi,
I desperately try to do s.th. like
m=1.23455
sig=0.84321
plot(1,1)
text(0.8,1,sprintf("=%1.2f±%1.2f",m,sig))
where actually the greek letter should appear for Sigma.
I have tried all sorts of combinations with expression and paste etc. but could
not work it out. Maybe someone has an idea and can help me.
Thanks a lot+
Thomas
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This email and any attachments are confidential. Any use...{{dropped:8}}
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Re: [R] Computing day-over-day log return for a matrix containing multiple time series
I did not realise making a zoo object is that convenient. Thanks a lot
Gabor.
-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com]
Sent: June-07-10 5:20 AM
To: anyi@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] Computing day-over-day log return for a matrix containing
multiple time series
You can use diff.zoo like this:
library(zoo)
z <- zoo(matrix(1:24, 6))
z
diff(log(z))
# also try
diff(z, arith = FALSE) - 1
See ?diff.zoo
and read the three zoo vignettes (pdf documents):
vignette(package = "zoo") # lists them
vignette("zoo")
etc.
On Sun, Jun 6, 2010 at 11:11 PM, Anyi Zhu wrote:
> Hi all,
>
>
>
> Thanks a lot for anyone's help in advance.
>
>
>
> I am trying to find a way to compute the day-to-day return (log return)
from
> a n x r matrix containing, n different stocks and price quotes over r
days.
> The time series of prices are already split by using unstack function.
>
>
>
> For the result, I would like to see a n x (r-1) matrix, where by each
entry
> is the day-over-day return of each stock.
>
>
>
> I tried to look into the zoo package, however it seems to give only the
> plots but not the actual data.
>
>
>
> Would apply function work in this case?
>
>
>
> Thanks a lot!
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Polar coordinate
Greetings to you all. I have two datasets - Time and magnitude. For a particular location, the magnitude of the parameter varies with time. I wish to obtain a polar coordinate distribution of time (0-24h) and magnitudes so as to visualize how magnitude varies with different times of the day (e.g., morning, midnight hours). I have searched for "polar coordinates in R" but could not get helpful hints. I would be most grateful if anyone could advise me on where to start. Thank you. Ogbos [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R2HTML problem
Err, sorry, forget my previous message. It has nothing to do with
Tinn-R or Eclipse. If you save that code in a file and you use the
source command in the console, you get the same output. Tinn-R and
Eclipse both source the code to R instead of sending it line by line.
To get what you want, you need to use the HTML() function on all
output you want to get correctly into the frame:
HTMLStart(getwd(),HTMLframe=FALSE, Title="My report",autobrowse=FALSE)
HTML(as.title("This is my first title"))
x <- 1
y<- 2
HTML(x+y)
HTMLStop()
This works from Tinn-R, Eclipse and by sourcing the file at the command line.
Cheers
Joris
On Mon, Jun 7, 2010 at 2:00 PM, Joris Meys wrote:
> It must be something with your version of R, I tried it both in
> Eclipse and in Tinn-R, and I get exactly what should come out (see
> attached file). Try updating R and R2HTML first, the problem might be
> there somewhere.
>
> Cheers
> Joris
>
> On Mon, Jun 7, 2010 at 1:31 PM, Iago Conde wrote:
>> I installed the whole eclipse and StatET thing... I try the R2HTML example
>>
>> library(R2HTML)
>>
>> HTMLStart(getwd(),HTMLframe=FALSE, Title="My report",autobrowse=FALSE)
>> as.title("This is my first title")
>> x <- 1
>> y<- 2
>> x+y
>> HTMLStop()
>>
>>
>> and still doesnt work, when I open the index html file... the title is "My
>> report" and the HTMLStop() message of
>> "Generated on: Mon Jun 07 13:36:24 2010 - R2HTML" also appears on the web
>> browser... but nothing else.
>> On Mon, Jun 7, 2010 at 3:09 AM, Joris Meys wrote:
>>>
>>> Take a look at eclipse :
>>> http://www.splusbook.com/R_Eclipse_StatET.pdf
>>>
>>> And yes, your program should work. The editor doesn't do anything else
>>> but sending your code to R. It is R that decides what to do with it.
>>>
>>> Cheers
>>> Joris
>>>
>>> On Sun, Jun 6, 2010 at 7:25 PM, RGtk2User wrote:
>>> >
>>> > Which editor could I use on Windows? The program that already works with
>>> > TinnR... will work with this new editor? Thanks!
>>> >
>>> > On Sat, Jun 5, 2010 at 11:40 PM, Joris FA Meys [via R] <
>>> >
>>> > ml-node+2244582-437396255-277...@n4.nabble.com
>>> >> wrote:
>>> >
>>> >> Tinn-R is using the R2HTML package itself for communication with R.
>>> >> You could ask JC Faria who wrote Tinn-R what exactly is going on
>>> >> there. You might get more help here :
>>> >> http://sourceforge.net/projects/tinn-r/support
>>> >>
>>> >> Personally, I'd just use a different editor in this case. I love
>>> >> Tinn-R, but it's no use programming in an editor that interacts with
>>> >> your code.
>>> >>
>>> >> Cheers
>>> >> Joris
>>> >>
>>> >> On Sat, Jun 5, 2010 at 4:57 PM, RGtk2User <[hidden
>>> >> email]>
>>> >> wrote:
>>> >>
>>> >> >
>>> >> > Im developing an application with R and Gtk+. It's just a simple GUI
>>> >> which
>>> >> > helps new users to interactuate with R. Thing is, when you do a
>>> >> statistical
>>> >> > analysis, I also want to provide a HTML report, but HTMLStart doesnt
>>> >> > work
>>> >>
>>> >> > propperly when executing from TinnR. It does create the file but not
>>> >> empty,
>>> >> > I've tried some examples from different websites, and it's always the
>>> >> same..
>>> >> > it works if I execute it from the R prompt, but doesnt when it comes
>>> >> > to
>>> >> > execute it from TinnR. So, any ideas? Im trying to divide the
>>> >> > internal
>>> >> code
>>> >> > of the HTMLStart function to find out where it crashes, but I couldnt
>>> >> find
>>> >> > it yet. Thanks in advance
>>> >> >
>>> >> > __
>>> >> > [hidden email]
>>> >> > 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.
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Ghent University
>>> >> Faculty of Bioscience Engineering
>>> >> Department of Applied mathematics, biometrics and process control
>>> >>
>>> >> tel : +32 9 264 59 87
>>> >> [hidden email]
>>> >> ---
>>> >> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>> >>
>>> >> __
>>> >> [hidden email]
>>> >> mailing list
>>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>>> >> PLEASE do read the posting guide
>>> >> http://www.R-project.org/posting-guide.html
>>> >> and provide commented, minimal, self-contained, reproducible code.
>>> >>
>>> >>
>>> >> --
>>> >> View message @
>>> >> http://r.789695.n4.nabble.com/R2HTML-problem-tp2244294p2244582.html
>>> >> To unsubscribe from R2HTML problem, click here< (link removed) ==>.
>>> >>
>>> >>
>>> >>
>>> >
>>> > --
>>> > View this message in context:
>>> > http://r.7
Re: [R] Wrong symbol rendering in plots (Ubuntu)
Hello Ben, Does the workaround pointed out later in the thread you're responding to (from the last paragraph of a very long 'Note' section of ?pdf) help? Well, I did not try to edit my fonts.conf but I feel this is not a PDF issue. I have no problem to have greek letters correctly rendered in Ubuntu 10.04 (with LaTeX, or OpenOffice Math for instance with a PDF export). This only appears in R plots. Note that other symbols do not render well too. I put a PDF output of demo(plotmath) here: http://yvonnick.noel.free.fr/wrongsymbolsinubuntu.pdf Thank you. Yvonnick > sessionInfo() R version 2.11.0 (2010-04-22) i486-pc-linux-gnu locale: [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C [3] LC_TIME=fr_FR.utf8LC_COLLATE=fr_FR.utf8 [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8 [7] LC_PAPER=fr_FR.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fit data with y = x^-1
Dear list, I am getting weired with fitting data with a 1/x-polynomial. Suggest I have the following data: x <- c(1,2,3,4,5,6,7) y <- c(100,20,4,2,1,.3,.1) I may fit this with a linear model fit1 = lm(y ~ I(x)) Getting plot out of this model I applied library(polynom) pol1 = polynomial(fit1$coefficients) f1 = as.function(pol1) plot(x,y) lines(x, f1(x), col = 2) Clearly, this model appears insufficient. Therefore I intended to aplly fit2 = lm(y ~ I(1/x)) pol2 = polynomial(fit2$coefficients) f2 = as.function(pol2) lines(x, f2(x), col = 3) as this would be much more pleasant. However, the second model does not work at all. Does anyone know about how to correctly fit an x^-1-polynomial to my data cloud? Many thanks in advance, behelfsadresse [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] raw data form .CEL file
Hi I am new in using R. I am facing problem getting the raw data like the mean value, standard deviation value form the .CEL file. Please help me, how can I get these raw information from a .CEL file into an exel file? Thanks -- View this message in context: http://r.789695.n4.nabble.com/raw-data-form-CEL-file-tp2245796p2245796.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Computing day-over-day log return for a matrix containing multiple time series
Thanks a lot Sayan, I'll give it a try and let you know how it goes.
From: sayan dasgupta [mailto:kitt...@gmail.com]
Sent: June-07-10 2:13 AM
To: anyi@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] Computing day-over-day log return for a matrix containing
multiple time series
Hope this helps
a <- matrix(runif(150),nrow=3,ncol=50)
p2r <- function(x) 100 * diff(log(x))
t(apply(a,1,function(x){p2r(c(x))}))
On Mon, Jun 7, 2010 at 8:41 AM, Anyi Zhu wrote:
Hi all,
Thanks a lot for anyone's help in advance.
I am trying to find a way to compute the day-to-day return (log return) from
a n x r matrix containing, n different stocks and price quotes over r days.
The time series of prices are already split by using unstack function.
For the result, I would like to see a n x (r-1) matrix, where by each entry
is the day-over-day return of each stock.
I tried to look into the zoo package, however it seems to give only the
plots but not the actual data.
take a look at
vignette("zoo-quickref",package="zoo")
It gives an exact solution to your problem
Would apply function work in this case?
Thanks a lot!
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Subsetting subsets of data.frames
Hi some example would be helpful. r-help-boun...@r-project.org napsal dne 07.06.2010 09:01:27: > > Hey Everyone, > > I have been stumped by this all day. > > Basically, I have a data.frame of multiple columns. Of concern are "id" & > "date" > > For some reason, oftentimes there are duplicates of data with the same date. > > I would like to remove the duplicates per different id (removing duplicate > dates for the entire data.frame would leave nothing since different id's all > have the same dates) > > subset(x,!duplicated(x$date_)) works for just one ID, but i am having However if above works on one id so use split sapply/lapply approach. Split your data according to id and use sapply or lapply wit above function for splitted object. I believe this is what ddply does so maybe it can be used too. Regards Petr > trouble figuring out how to apply this to each subset of IDs (and retaining > the original data.frame structure) > -- > View this message in context: http://r.789695.n4.nabble.com/Subsetting- > subsets-of-data-frames-tp2245556p2245556.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting subsets of data.frames
subset(x, !duplicated(paste(x$id, x$date)) On Mon, Jun 7, 2010 at 3:01 AM, Jeff08 wrote: > > Hey Everyone, > > I have been stumped by this all day. > > Basically, I have a data.frame of multiple columns. Of concern are "id" & > "date" > > For some reason, oftentimes there are duplicates of data with the same date. > > I would like to remove the duplicates per different id (removing duplicate > dates for the entire data.frame would leave nothing since different id's all > have the same dates) > > subset(x,!duplicated(x$date_)) works for just one ID, but i am having > trouble figuring out how to apply this to each subset of IDs (and retaining > the original data.frame structure) > -- > View this message in context: > http://r.789695.n4.nabble.com/Subsetting-subsets-of-data-frames-tp2245556p2245556.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: fit data with y = x^-1
Hi r-help-boun...@r-project.org napsal dne 07.06.2010 14:28:58: > Dear list, > > I am getting weired with fitting data with a 1/x-polynomial. Suggest I have > the following data: > > x <- c(1,2,3,4,5,6,7) > y <- c(100,20,4,2,1,.3,.1) > > I may fit this with a linear model > > fit1 = lm(y ~ I(x)) fit1 = lm(y ~ x) is enough > > Getting plot out of this model I applied > library(polynom) > pol1 = polynomial(fit1$coefficients) > f1 = as.function(pol1) > > plot(x,y) > lines(x, f1(x), col = 2) why not plot(x,y) lines(x, fitted(fit)) > > Clearly, this model appears insufficient. Therefore I intended to aplly > fit2 = lm(y ~ I(1/x)) > pol2 = polynomial(fit2$coefficients) > f2 = as.function(pol2) > lines(x, f2(x), col = 3) The same applies here fit3 = lm(y ~ I(1/x^3)) lines(x, fitted(fit3)) seems to give quite reasonable output. Regards Petr > > as this would be much more pleasant. However, the second model does not work > at all. > > > Does anyone know about how to correctly fit an x^-1-polynomial to my data > cloud? > > > Many thanks in advance, > > > behelfsadresse > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] raw data form .CEL file
All questions about manipulations of sequence data (guess that's the CEL file you're talking about...) can better be asked on the specific mailing list of BioConductor : http://www.bioconductor.org/docs/mailList.html And please, don't swear in church any more. We don't put things in Excel files. This is about R, not about Micro$oft. Cheers Joris On Mon, Jun 7, 2010 at 1:20 PM, aabid wrote: > > Hi > I am new in using R. I am facing problem getting the raw data like the mean > value, standard deviation value form the .CEL file. > Please help me, how can I get these raw information from a .CEL file into an > exel file? > > Thanks > -- > View this message in context: > http://r.789695.n4.nabble.com/raw-data-form-CEL-file-tp2245796p2245796.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Onequestion
Xiongqing Zhang yahoo.com> writes: > > > Dear Mr. or Ms., > > I used the R-software to run the zero-inflatoin negative binomial model, but I could not get the results. > And the error message is "solve.default(as.matrix(fit$gaussian)) ". In the model, I introduced 3 dummy > variables. I do not know the reasons fully. > We can't possibly help if you don't tell us specifically what you did. Please read the posting guide! Tell us what packages you are using, show us your data (or make up a small data set that shows the same problem), and show us what commands you tried. "Reproducible example" is the key. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] open files from ftp site
Hello, I'm running R 2.10.1 on Windows XP. I'd like to read some files from a ftp site, but I don't how to do it. I've tried the functions url, download.file but each time I have a message "cannot open URL 'ftp://ftp.cea.fr'" .. and I don't kwow why .. Thanks for the help Benoit -- Benoit Wastine Laboratoire des Sciences du Climat et de l’Environnement (LSCE/IPSL) CEA-CNRS-UVSQ CE Saclay Orme des merisiers Bât 703 - Pte 13A 91191 Gif sur Yvette Cedex France Tel : 33 (0)1 69 08 21 97 Fax : 33 (0)1 69 08 77 16 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ols function in rms package
On 06/06/2010 10:49 PM, Mark Seeto wrote:
Hello,
I have a couple of questions about the ols function in Frank Harrell's rms
package.
Is there any way to specify variables by their column number in the data
frame rather than by the variable name?
For example,
library(rms)
x1<- rnorm(100, 0, 1)
x2<- rnorm(100, 0, 1)
x3<- rnorm(100, 0, 1)
y<- x2 + x3 + rnorm(100, 0, 5)
d<- data.frame(x1, x2, x3, y)
rm(x1, x2, x3, y)
lm(y ~ d[,2] + d[,3], data = d) # This works
ols(y ~ d[,2] + d[,3], data = d) # Gives error
Error in if (!length(fname) || !any(fname == zname)) { :
missing value where TRUE/FALSE needed
However, this works:
ols(y ~ x2 + d[,3], data = d)
The reason I want to do this is to program variable selection for
bootstrap model validation.
A related question: does ols allow "y ~ ." notation?
lm(y ~ ., data = d[, 2:4]) # This works
ols(y ~ ., data = d[, 2:4]) # Gives error
Error in terms.formula(formula) : '.' in formula and no 'data' argument
Thanks for any help you can give.
Regards,
Mark
Hi Mark,
It appears that you answered the questions yourself. rms wants real
variables or transformations of them. It makes certain assumptions
about names of terms. The y ~ . should work though; sometime I'll have
a look at that.
But these are the small questions compared to what you really want. Why
do you need variable selection, i.e., what is wrong with having
insignificant variables in a model? If you indeed need variable
selection see if backwards stepdown works for you. It is built-in to
rms bootstrap validation and calibration functions.
Frank
--
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
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[R] Patch for legend.position={left,top,bottom} in ggplot2
Hi Hadley and everyone,
here's a patch for ggplot2 that fixes the behavior of
opts(legend.position={left,top,bottom}). If you try the following code
in an unmodified ggplot2
options(warn = -1)
suppressPackageStartupMessages(library("ggplot2"))
data <- data.frame(
x = c(1, 2, 3, 4, 5, 6),
y = c(2, 3, 4, 3, 4, 5),
colour = c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE))
ggplot(data, aes(x = x, y = y, colour = colour)) +
geom_line() + opts(title = "title", legend.position = "right")
ggplot(data, aes(x = x, y = y, colour = colour)) +
geom_line() + opts(title = "title", legend.position = "left")
ggplot(data, aes(x = x, y = y, colour = colour)) +
geom_line() + opts(title = "title", legend.position = "top")
ggplot(data, aes(x = x, y = y, colour = colour)) +
geom_line() + opts(title = "title", legend.position = "bottom")
you'll see that plots 2 to 4 are broken.
I think I located the bug in surround_viewports() where the graphical
elements are placed into the grid. If we increment all rows and columns
of the graphical elements for positions "left", "top", and "bottom" by
1, those graphs look sane again. I assume that a new first row and
column were added at some point in the development, but only the
parameters for the default position "right" were adjusted. Here's the patch:
--- ggplot2-orig2 2010-06-07 13:14:35.0 +0200
+++ ggplot2 2010-06-07 15:22:33.0 +0200
@@ -7003,27 +7003,27 @@
)
} else if (position == "left") {
viewports <- vpList(
- vp("panels", 2, 3),
- vp("legend_box", 2, 1),
- vp("ylabel", 2, 2),
- vp("xlabel", 3, 3),
- vp("title", 1, 3)
+ vp("panels", 3, 4),
+ vp("legend_box", 3, 2),
+ vp("ylabel", 3, 3),
+ vp("xlabel", 4, 4),
+ vp("title", 2, 4)
)
} else if (position == "top") {
viewports <- vpList(
- vp("panels", 3, 2),
- vp("legend_box", 2, 2),
- vp("ylabel", 3, 1),
- vp("xlabel", 4, 2),
- vp("title", 1, 2)
+ vp("panels", 4, 3),
+ vp("legend_box", 3, 3),
+ vp("ylabel", 4, 2),
+ vp("xlabel", 5, 3),
+ vp("title", 2, 3)
)
} else if (position == "bottom") {
viewports <- vpList(
- vp("panels", 2, 2),
- vp("legend_box", 4, 2),
- vp("ylabel", 2, 1),
- vp("xlabel", 3, 2),
- vp("title", 1, 2)
+ vp("panels", 3, 3),
+ vp("legend_box", 5, 3),
+ vp("ylabel", 3, 2),
+ vp("xlabel", 4, 3),
+ vp("title", 2, 3)
)
} else {
viewports <- vpList(
Best,
--Karsten
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Re: [R] Test
Greetings Moderators! I moderated the message below just now (one of two identical test messages). I rejected it, with a covering note to the author (John Munroe , who does not appear to be subscribed to the list) that I was doing so because approving it would serve no useful purpose, and pointing out that it had been held because the message headers matched a filter rule, probably because it was (a) from gmail.com and (b) sent via nabble. I then also ticked the box for it to be forwarded to r-help-owner, expecting that my covering note would accompany it. Since that did not happen, I'm now adding an explanation! I would suspect that John Munro has been trying to get through to R-help, and failing, as the most likely explanation for sending test messages. I feel this sort of thing is adding weight to the case for trying to alleviate the severity with which mailman treats messages from this kind of origin. What do others think? Ted. On 07-Jun-10 13:26:49, John Munroe wrote: > > Test > -- > View this message in context: > http://r.789695.n4.nabble.com/Test-tp2245933p2245933.html > Sent from the R help mailing list archive at Nabble.com. > E-Mail: (Ted Harding) Fax-to-email: +44 (0)870 094 0861 Date: 07-Jun-10 Time: 14:59:49 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Test
Apologoes for sending a message to R-help that should have gone to the moderators' mailing-list. I had overlooked that the "From:" in the MIME-attached messsage was different from the "From:" in the covering message, and I replied to the wrong address. Ted. On 07-Jun-10 14:00:02, Ted Harding wrote: > Greetings Moderators! > [...] E-Mail: (Ted Harding) Fax-to-email: +44 (0)870 094 0861 Date: 07-Jun-10 Time: 15:12:26 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting predicted values for time series.
Dear R People: I found the following code on the Internet: > x <- co2 > m <- HoltWinters(x, alpha=.1, beta=0, gamma=0) > p <- predict(m, n.ahead=240, prediction.interval=T) > plot(m, predicted.values=p) > and it works fine. My question: is there an equivalent for ARIMA objects, please? When I tried, I got the following: > x.arima <- arima(x,order=c(1,0,0)) > p1 <- predict(x.arima,n.ahead=6,prediction.interval=T) > plot(x.arima,predicted.values=p1) Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' is a list, but does not have components 'x' and 'y' > plot(x,predicted.values=p1) Warning messages: 1: In plot.window(xlim, ylim, log, ...) : "predicted.values" is not a graphical parameter 2: In title(main = main, xlab = xlab, ylab = ylab, ...) : "predicted.values" is not a graphical parameter 3: In axis(1, ...) : "predicted.values" is not a graphical parameter 4: In axis(2, ...) : "predicted.values" is not a graphical parameter 5: In box(...) : "predicted.values" is not a graphical parameter > Thanks in advance for any help! Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] graphical representation of a correlation between 3 variables (~30 datapoints)
Dear Ms and Mr R, I am seeking a visually appealing presentation of 3 variables (~30 datapoints) that are correlated and that should to into the same direction. The objective is to show that they do go in the same direction and what differences there might be while also giving an idea of the values of the variables. I had done this with simple bargraphs for 6 datapoints in the past, but for 30 this is too much. Anyone a good idea how to get this job nicely done? Thanking you and best regards, Georg. ## Georg Ehret Johns Hopkins Baltimore [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphical representation of a correlation between 3 variables (~30 datapoints)
reproducible example needed. Georg Ehret wrote: Dear Ms and Mr R, I am seeking a visually appealing presentation of 3 variables (~30 datapoints) that are correlated and that should to into the same direction. The objective is to show that they do go in the same direction and what differences there might be while also giving an idea of the values of the variables. I had done this with simple bargraphs for 6 datapoints in the past, but for 30 this is too much. Anyone a good idea how to get this job nicely done? Thanking you and best regards, Georg. ## Georg Ehret Johns Hopkins Baltimore [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generalized DCC GARCH ML estimation
Dear Anonymous
I suggest you to have a look on the code in package ccgarch, which might
help you in seeing how this have been done. A useful information would
be to know what kind of optimization algorithm the authors use.
best
Matthieu
Le 07. 06. 10 12:00, r-help-requ...@r-project.org a écrit :
> Message: 24
> Date: Sun, 6 Jun 2010 10:17:50 -0700 (PDT)
> From: drinky_1
> To:r-help@r-project.org
> Subject: [R] Generalized DCC GARCH ML estimation
> Message-ID:<1275844670290-2245135.p...@n4.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi everyone,
>
> I want to do a maximum likelihood estimation for the Generalized Dynamic
> Conditional Correlation (GDCC) Model of Hafner and Franses (2009), but I
> don't know how exactly. I hope you can help me. This is what I have so far.
>
> Well first of all Hafner models the conditional covariance matrix H_t as
> follows:
> H=D*R*D, where D is a diagonal matrix with the square root of the estimated
> univariate GARCH variances, R is a correlation matrix:
> R_t=diag(Q_t)^(-1/2)*Q_t*diag(Q_t)^(-1/2) and
> Q_t=S(1-mean(a)2-mean(b)2)+ aa' * (eps_(t-1)*eps')+ bb'*Q_(t-1)
>
> a and b are parameter vectors and S is the sample correlation matrix of the
> eps.
>
> There is a two-step estimation method, but I only need the second step.
>
> So first of all I want to calculate the correlations
>
> gdcc=function (dvar,alpha,beta)
> {
>
> T=dim(dvar)[1]
> N=dim(dvar)[2]
>
> uncR=cor(dvar)
> R=list()
>
> Q=list()
> Q[[1]]=uncR
> R[[1]]=diag(diag(uncR)^(-1/2))%*%uncR%*%diag(diag(uncR)^(-1/2))
>
>
> for (i in 2:T)
> {
>
> Q[[i]]=uncR*(1-mean(alpha)2-mean(beta)2)+tcrossprod(alpha)*tcrossprod(dvar[i-1,])+tcrossprod(beta)*Q[[i-1]]
>
>
> R[[i]]=diag(diag(Q[[i]])^(-1/2))%*%Q[[i]]%*%diag(diag(Q[[i]])^(-1/2))
>
> GDCC[i,]=as.vector(R[[i]])
> }
>
> GDCC
> }
>
> and the log-likelihood function is as follows:
>
> loglik.gdcc2=function (alpha,beta,dvar)
> {
> T<- dim(dvar)[1]
> N<- dim(dvar)[2]
> GDCC=gdcc(dvar,alpha,beta)
> lf<- numeric(N)
> for (i in 1:T) {
> R<- matrix(GDCC[i,], N, N)
> invR<- solve(R)
> lf[i]<- 0.5 * (log(det(R)) + sum(dvar[i, ] * crossprod(invR,
> dvar[i, ])))
> }
> -sum(lf)
>
> }
>
> I want to use the nlm method. How can I estimate the parameter vectors a and
> b? I really would appreciate it if anyone could help me.
>
> Thank you very much.
> Best regards, drinky_1
>
[[alternative HTML version deleted]]
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Re: [R] graphical representation of a correlation between 3 variables (~30 datapoints)
Hi Georg, Take a look at ?pairs as well as [1] and [2]. HTH, Jorge [1] http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=159 [2] http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=149 On Mon, Jun 7, 2010 at 11:16 AM, Georg Ehret <> wrote: > Dear Ms and Mr R, > I am seeking a visually appealing presentation of 3 variables (~30 > datapoints) that are correlated and that should to into the same direction. > The objective is to show that they do go in the same direction and what > differences there might be while also giving an idea of the values of the > variables. I had done this with simple bargraphs for 6 datapoints in the > past, but for 30 this is too much. Anyone a good idea how to get this job > nicely done? > > Thanking you and best regards, Georg. > ## > Georg Ehret > Johns Hopkins Baltimore > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Polar coordinate
On Mon, 7 Jun 2010, ogbos okike wrote:
Greetings to you all.
I have two datasets - Time and magnitude. For a particular location, the
magnitude of the parameter varies with time. I wish to obtain a polar
coordinate distribution of time (0-24h) and magnitudes so as to visualize
how magnitude varies with different times of the day (e.g., morning,
midnight hours).
I have searched for "polar coordinates in R" but could not get helpful
hints. I would be most grateful if anyone could advise me on where to start.
Do a better search.
RSiteSearch("polar")
Google 'polar coordinate CRAN'
Google 'polar coordinate rforge'
And if these are not useful, you need to say why none of the functions for
manipulating or plotting polar coordinates served your purpose.
Chuck
Thank you.
Ogbos
[[alternative HTML version deleted]]
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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[R] plotting predicted values for time series. Solution
Dear R People: A very fine solution exists in the "forecast" package, by using plot.forecast. Thanks though! Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Howto modify a drawn graph with igraph
See ?plot.igraph, example: plot(g, layout=mlayout, vertex.label.color = "red", vertex.color = "green", vertex.frame.color = "blue", edge.color = "orange", edge.width = 1 + (1:18)/2 ) Uwe Ligges On 06.06.2010 17:58, Etienne Cuvelier wrote: Hello, I am using the igraph package, and I wonder how to add or modify informations on a drawn graph. Example: library(igraph) M <- matrix( nc=12, nr=12 , 0) M[ 1,]=c(0,1,0,0,1,1,0,0,0,0,0,0) M[ 2,]=c(1,0,1,1,1,0,0,0,0,0,0,0) M[ 3,]=c(0,1,0,0,0,1,1,0,0,0,0,0) M[ 4,]=c(0,1,0,0,0,1,0,0,0,0,0,0) M[ 5,]=c(1,1,0,0,0,0,0,0,0,0,0,0) M[ 6,]=c(1,0,1,1,0,0,0,0,0,0,0,0) M[ 7,]=c(0,0,1,0,0,0,0,1,1,0,0,1) M[ 8,]=c(0,0,0,0,0,0,1,0,1,0,0,1) M[ 9,]=c(0,0,0,0,0,0,1,1,0,0,1,1) M[10,]=c(0,0,0,0,0,0,0,0,0,0,1,0) M[11,]=c(0,0,0,0,0,0,1,0,1,0,0,0) M[12,]=c(0,0,0,0,0,0,0,1,1,0,0,0) g <- graph.adjacency( M,mode="undirected" ) mlayout= layout.kamada.kawai(g) plot(g,layout=mlayout) #And now howto add a weight associated on edges on the "picture"? #Or howto change the color of an edge, or a vertice? Thanks for help. Etienne __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Computing day-over-day log return for a matrix containingmultiple time series
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of sayan dasgupta
> Sent: Sunday, June 06, 2010 11:13 PM
> To: anyi@gmail.com
> Cc: r-help@r-project.org
> Subject: Re: [R] Computing day-over-day log return for a
> matrix containingmultiple time series
>
> Hope this helps
>
> a <- matrix(runif(150),nrow=3,ncol=50)
> p2r <- function(x) 100 * diff(log(x))
> t(apply(a,1,function(x){p2r(c(x))}))
The following expressions compute the same
thing as that t(apply(...)) does:
100 * (log(a[,-1]) - log(a[,-ncol(a)]))
or
100 * log(a[,-1]/a[,-ncol(a)])
The [,-1] (all but the first column) and
[,-ncol(a)] (all but the last column) is
a way to work with lagged data.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
>
>
>
>
> On Mon, Jun 7, 2010 at 8:41 AM, Anyi Zhu wrote:
>
> > Hi all,
> >
> >
> >
> > Thanks a lot for anyone's help in advance.
> >
> >
> >
> > I am trying to find a way to compute the day-to-day return
> (log return)
> > from
> > a n x r matrix containing, n different stocks and price
> quotes over r days.
> > The time series of prices are already split by using
> unstack function.
> >
>
> >
> >
> > For the result, I would like to see a n x (r-1) matrix,
> where by each entry
> > is the day-over-day return of each stock.
> >
> >
> >
> > I tried to look into the zoo package, however it seems to
> give only the
> >
> plots but not the actual data.
> >
> take a look at
> vignette("zoo-quickref",package="zoo")
> It gives an exact solution to your problem
>
>
>
> >
> >
> >
> > Would apply function work in this case?
> >
> >
> >
> > Thanks a lot!
> >
> >
> >[[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
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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] Multiply Two Dataframes
Hi, I have the following two dataframes (Df1 and Df2): Df1 has a layout like ID Location Var1 Var2 Var3 . Var20 A Loc2 1 11. 1 A Loc1 0 10. 1 B Loc1 0 00. 0 A Loc3 1 01. 0 C Loc3 1 01. 0 B Loc2 0 00. 1 D . .. Df2 has a layout like ID Var1 Var2 Var3 .. Var20 A 0.2 0.30.2 0.15 B 0.1 0.1 0.1 .0.1 C00 0 . 0.50 D . . And I like to have the following result ID Location Var1 Var2 Var3 .Var20 A Loc2 0.2 0.3 0.2 . 0.15 A Loc1 00.3 0 . 0.15 B Loc1 00 0 . 0 A Loc3 0.2 00.2 . 0 C Loc3 0 00 . 0 B Loc2 0 00 . 0.1 D . .. Is this easy doable in R? I've tried to figure it out with mapply but without result. Thanks for helping me out. Bert [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiply Two Dataframes
Dear Bert, The easiest thing would be to merge both datasets and then multiply the corresponding columns. both <- merge(df1, df2) both[, 3:22] * both[, 23:42] HTH, Thierry -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org namens Bert Jacobs Verzonden: ma 7-6-2010 20:29 Aan: r-help@r-project.org Onderwerp: [R] Multiply Two Dataframes Hi, I have the following two dataframes (Df1 and Df2): Df1 has a layout like ID Location Var1 Var2 Var3 . Var20 A Loc2 1 11. 1 A Loc1 0 10. 1 B Loc1 0 00. 0 A Loc3 1 01. 0 C Loc3 1 01. 0 B Loc2 0 00. 1 D . .. Df2 has a layout like ID Var1 Var2 Var3 .. Var20 A 0.2 0.30.2 0.15 B 0.1 0.1 0.1 .0.1 C00 0 . 0.50 D . . And I like to have the following result ID Location Var1 Var2 Var3 .Var20 A Loc2 0.2 0.3 0.2 . 0.15 A Loc1 00.3 0 . 0.15 B Loc1 00 0 . 0 A Loc3 0.2 00.2 . 0 C Loc3 0 00 . 0 B Loc2 0 00 . 0.1 D . .. Is this easy doable in R? I've tried to figure it out with mapply but without result. Thanks for helping me out. Bert [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] exepath error in seqaln
Hi everyone,
I am using bio3d package for some sequence analysis because of its nice
integrated MUSCLE execution. However, I have been encountering some errors
while I was running seqaln function, which calls for installed MUSCLE program.
In my case, I stored the MUSCLE program on the desktop with pathway of
"./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from
terminal. However, when I'm calling the exepath in R, it keeps giving me error
messages. Below are some errors I have encountered. Your help will be much
appreciated.
> aa<-read.fasta("./R/test.fa", rm.dup=F)
> aln<-seqaln(aa, exepath="/Users/Fan/Desktop/muscle/src/muscle",
> file="aa_muscle.fa", protein=T)
/Users/Fan/Desktop/muscle/src/musclemuscle -in
/var/folders/v9/v95dzKP2E9SAkmd7m4T8dE+++TQ/-Tmp-//RtmpKUJVlZ/file618fb492 -out
aa_muscle.fa -stable -seqtype protein/bin/sh:
/Users/Fan/Desktop/muscle/src/musclemuscle: No such file or directory
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
cannot open file 'aa_muscle.fa': No such file or directory
I have also noticed that the example file from bio3d/seqaln does not have
quotation marks for the exepath. But it returned a different error message.
> aln<-seqaln(aa, exepath=/Users/Fan/Desktop/muscle/src/muscle,
> file="aa_muscle.fa", protein=T)
Error: unexpected '/' in "aln<-seqaln(aa, exepath=/"
or > aln<-seqaln(aa, exepath=Users/Fan/Desktop/muscle/src/muscle,
file="aa_muscle.fa", protein=T)
Error in paste(exepath, "muscle -in ", toaln, " -out ", file, " ", extra.args,
:
object 'Users' not found
Thank you for your help ahead of time!
Best wishes.
Fan
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste together a string object later to be utilized in a function
Does the collapse argument to the paste function do what you want? Possibly
nested inside another paste.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> project.org] On Behalf Of moleps
> Sent: Sunday, June 06, 2010 1:51 PM
> To: r-help@r-project.org
> Subject: [R] paste together a string object later to be utilized in a
> function
>
> Dear r-listers,
>
> I need to pass a string to a function. However the length of the string
> is dependent on the length of a vector.
>
>
> b<-length(h)
> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>
>
> Is it possible somehow to pass this as an argument to a function later
> on ?
>
>
>
> Regards,
>
> //M
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
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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] Help with seting up comparison
Hi, I tried on this, but couldn't figure it out: Suppose I have a dataframe as follows: dat <- data.frame(Day=rep(rep(c(1,2), each=4),2), Animal = rep(c(1,2), each=8), Count=c(rnorm(8, 100), rnorm(8,90))) 2 animals are being examined on 2 different days. Count is the result. Now I need to point out whether or not there is a difference between the days. I did this by an ANOVA test, while first converting the animal and day to a factor variable: dat$Animal <- as.factor(dat$Animal) dat$Day <- as.factor(dat$Day) mod <- lm(Count ~Animal * Day,dat) anova(mod) Now I have to check for difference within the animal, to see if there is a difference in count for each day. (In my real data, I have 35 animals, with 4 days, and 4 results). I thought about a Tukey HSD test, but this compares every day of every animal with every other day of every other animal. (TukeyHSD(aov(mod))) Any idea about which function (or model for lm) to use to only compare days within every animal? Best regards Bart -- View this message in context: http://r.789695.n4.nabble.com/Help-with-seting-up-comparison-tp2246106p2246106.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] as.integer
Hi, Is there a way to recursively change the variables imported with read.table(..) - and then attached with attach(..) - from as.factor to as.integer? I have about 9 variables that are now recognized as factors but I need to do statistics on them so I need to change them in as.integer. It works, but I wonder if there is a way to to this for all the variables in one go. Thanks a lot for your help Ale -- View this message in context: http://r.789695.n4.nabble.com/as-integer-tp2245987p2245987.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Source of chickwts data
I'm not sure if this is the right mailing list. My apologies if I'm sending the question to the wrong mailing list. (The r-packages list moderator suggested using the R-help list.) My question is about the "chickwts" data in the datasets package. According to help(chickwts), the source of the data is Anonymous (1948) Biometrika, 35, 214. But this reference seems irrelevant. (See http://www.jstor.org/stable/i315414.) The help document also gives "McNeil, D. R. (1977) Interactive Data Analysis. New York: Wiley" as a reference, but unfortunately my local library does not keep the book. Could someone please help me find the correct source of the data? Many thanks. Chirok __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] classification algorithms with distance matrix
Dear all, I have a problem when using some classification functions (Kmeans, PAM, FANNY...) with a distance matrix, and i would to understand how it proceeds for the positioning of centroids after one execution step. In fact, in the classical formulation of the algorithm, after each step, to re-position the center, it calculates the distance between any elements of the old cluster and its center, or in my case I used a distance matrix , so I do not understand how the algorithm can recalculates the distance between the newly generated center and other elements of the cluster knowing that the new center does not appear in the distance matrix and there is no way to calculate the distance between him and the elements of a cluster. ? Thank you for your help. Sid., LORIA France. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to parse out string separated by special character
hi, everyone: i have a data frame with one single character column as followings: DS_xxx_yyy_24hr_zzz_1 DS_xxx_yyy_24hr_zzz_2 DS_xxx_yyy_24hr_zzz_3 DS_xxx_yyy_24hr_zzz_4 DS_xxx_yyy_24hr_zzz_1 DS_xxx_yyy_24hr_zzz_2 DS_xxx_yyy_24hr_zzz_3 DS_xxx_yyy_24hr_zzz_4 DS_xxx_yyy_24hr_zzz_1 i need to parse out the time part like the followings: name time DS_xxx_yyy_24hr_zzz_1 24hr DS_xxx_yyy_24hr_zzz_2 24hr DS_xxx_yyy_24hr_zzz_3 24hr DS_xxx_yyy_24hr_zzz_4 24hr DS_xxx_yyy_24hr_zzz_1 24hr DS_xxx_yyy_24hr_zzz_2 24hr DS_xxx_yyy_24hr_zzz_3 24hr DS_xxx_yyy_24hr_zzz_4 24hr DS_xxx_yyy_24hr_zzz_1 24hr what function should I look at? i have tried: strsplit(data, '_') and get a giant list which is not what i need. thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/how-to-parse-out-string-separated-by-special-character-tp2246301p2246301.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] mgcv
Hello Sir, I am using mgcv package for my data. My model is y~x1+f(x2),I want to find out the function f(x2) . Following is the code. sm1=gam(y~x1+s(x2),family=binomial, f) summary(sm1) plot(sm1,residuals=TRUE, xlab="AGE",pch=20) In this plot I am getting S(x2,1.93) on y axixs How should I get the function for x2 from this plot.or Is there anyother procedure in R to get this function or value for that particular function.for example f(x2)= log(x2) so from that plot how can I get this kind of formula for x2 variable? How can I find variance covariance matrix for that model and confidence interval for that model ? I tried delta method but I am not getting result. Hope you understand my question? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Loading an image/picture (png/jpeg/...) to screen...
Once you have your image displayed in a plot, look at the updateusr function in the TeachingDemos package for a way to modify the coordinate system to what you want so that using locator() gives the results that you want. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of oliver > Sent: Sunday, June 06, 2010 5:46 AM > To: r-h...@stat.math.ethz.ch > Subject: [R] Loading an image/picture (png/jpeg/...) to screen... > > Hello, > > > how can I load an external picture/image file to screen? > > I want to use locator() then to get coordinates of that picture... > ...in other words I want to use R to do some measurements on a picture. > > Therefore I need to load the image into R display, > and that displaying needs to work together with locator(). > > > How to do it best? > > At the moment I need to be able to read in *.png files, > but if *.jpeg or other formats also will be supporttzed, this would be > fine. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Very OT: World Cup Statistics
Hello, Sorry for the very Off TOpic post, but I need some data on past football (soccer) world cups. I'd like to find (or calculate) the time to the first goal of each match (where a goal was scored). I''ve looked at the uefa website and can't find what I want, maybe someone here can help ? Thanks Paul. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Transforming list to data frame with corresponding columns
Hi all,
Consider the following.
a<-list(c("MHsub","MHsub","SFD","Duplex"))
b<-list(c("MHsub","MHsub","SFD"))
c<-list(c("MHpark","SFD","SFD"))
d<-list(c("MultiFam","MultiFam","MultiFam","Duplex"))
all<-list(a,b,c,d)
names(all)<-c("5","6","7","8")
all2<-list()
for(i in 1:length(all)){
all2[[i]]<-table(unlist(all[i]))
}
names(all2)<-names(all)
What i want to do is to put each of the elements of the list into a data
frame where the element represents a row and each vector is accounted for,
for all types within the entire list. So where there isnt a particular
vector a 0 is noted so that the final product looks like this:
SFD Mhsub Duplex MultiFam
5 1 11 0
6 1 10 0
7 1 10 0
8 0 01 1
Thanks for the insights.
--
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] how to parse out string separated by special character
Try this:
gsub(".*_(.*)_.*_.*", "\\1", s)
On Mon, Jun 7, 2010 at 2:21 PM, xin wei wrote:
>
> hi, everyone:
> i have a data frame with one single character column as followings:
> DS_xxx_yyy_24hr_zzz_1
> DS_xxx_yyy_24hr_zzz_2
> DS_xxx_yyy_24hr_zzz_3
> DS_xxx_yyy_24hr_zzz_4
> DS_xxx_yyy_24hr_zzz_1
> DS_xxx_yyy_24hr_zzz_2
> DS_xxx_yyy_24hr_zzz_3
> DS_xxx_yyy_24hr_zzz_4
> DS_xxx_yyy_24hr_zzz_1
>
> i need to parse out the time part like the followings:
> name time
> DS_xxx_yyy_24hr_zzz_1 24hr
> DS_xxx_yyy_24hr_zzz_2 24hr
> DS_xxx_yyy_24hr_zzz_3 24hr
> DS_xxx_yyy_24hr_zzz_4 24hr
> DS_xxx_yyy_24hr_zzz_1 24hr
> DS_xxx_yyy_24hr_zzz_2 24hr
> DS_xxx_yyy_24hr_zzz_3 24hr
> DS_xxx_yyy_24hr_zzz_4 24hr
> DS_xxx_yyy_24hr_zzz_1 24hr
>
> what function should I look at?
> i have tried: strsplit(data, '_') and get a giant list which is not what i
> need.
>
> thanks in advance
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/how-to-parse-out-string-separated-by-special-character-tp2246301p2246301.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Color scale graphic
Do you just want a rectangle with different vertical color bands? Then look at the image function. Do you want a small rectangle that goes the length of the x-axis with these color bands, but gives room for another plot above that? Then look at the subplot function (TeachingDemos package) along with the image function. If neither of those help, give us a better description and/or example of what you want your plot to look like. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Diogo_Silva > Sent: Saturday, June 05, 2010 6:03 PM > To: r-help@r-project.org > Subject: [R] Color scale graphic > > > Hello > > Recently, I've been dealing with a seemingly simple problem. I have a > table > with two columns filled with values from a test I made (say, amount of > precipitation and Months measured). Now, instead of plotting a typical > linear graphic with precipitation on the y-axis and the months in the > x-axys, I would like to "convert" the values of precipitation in a > color > gradient, resulting in a vertical gradient throughout the x-axis. In > this > way, months with higher precipitation would appear reddish while lower > precipitation would appear blueish, for example. Despite being a simple > problem (basically converting the y-values in a color gradient), I have > failed to find a way of doing this. > > If someone knows how to solve this, either using R or other program, > please > lend me a hand. > > Thanks for your attention > Diogo > -- > View this message in context: http://r.789695.n4.nabble.com/Color- > scale-graphic-tp2244657p2244657.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] as.integer
1) Give us a reproducible example. 2) You probably don't want to use attach. 3) Yes there is a way, but without an example, it's hard to say what will work. Assume a data.frame called df, maybe something like the following, which is untested... df[is.factor(df)] <- lapply(df[is.factor(df)], function(x) as.numeric(as.character(x))) aledanda wrote: Hi, Is there a way to recursively change the variables imported with read.table(..) - and then attached with attach(..) - from as.factor to as.integer? I have about 9 variables that are now recognized as factors but I need to do statistics on them so I need to change them in as.integer. It works, but I wonder if there is a way to to this for all the variables in one go. Thanks a lot for your help Ale __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with seting up comparison
Are you interested in only those 35 animals (not every going to look at any other animals other than those 35, but you want to predict what will happen for those 35)? Or are the 35 animals a sample of a larger population of animals? If the later (seems the most likely case) then you probably want to use a mixed effects model (nlme or lme4 packages) with animal as a random effect, then just look at the fixed effect of day. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Bart Joosen > Sent: Monday, June 07, 2010 9:14 AM > To: r-help@r-project.org > Subject: [R] Help with seting up comparison > > > Hi, > > I tried on this, but couldn't figure it out: > Suppose I have a dataframe as follows: > dat <- data.frame(Day=rep(rep(c(1,2), each=4),2), Animal = rep(c(1,2), > each=8), Count=c(rnorm(8, 100), rnorm(8,90))) > > 2 animals are being examined on 2 different days. Count is the result. > > Now I need to point out whether or not there is a difference between > the > days. > I did this by an ANOVA test, while first converting the animal and day > to a > factor variable: > dat$Animal <- as.factor(dat$Animal) > dat$Day <- as.factor(dat$Day) > mod <- lm(Count ~Animal * Day,dat) > anova(mod) > > Now I have to check for difference within the animal, to see if there > is a > difference in count for each day. (In my real data, I have 35 animals, > with > 4 days, and 4 results). > I thought about a Tukey HSD test, but this compares every day of every > animal with every other day of every other animal. (TukeyHSD(aov(mod))) > > Any idea about which function (or model for lm) to use to only compare > days > within every animal? > > Best regards > > Bart > > > -- > View this message in context: http://r.789695.n4.nabble.com/Help-with- > seting-up-comparison-tp2246106p2246106.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] classification algorithms with distance matrix
On Mon, Jun 7, 2010 at 9:05 AM, sidahmed BENABDERRAHMANE wrote: > Dear all, > > I have a problem when using some classification functions (Kmeans, PAM, > FANNY...) with a distance matrix, and i would to understand how it proceeds > for the positioning of centroids after one execution step. > > In fact, in the classical formulation of the algorithm, after each step, to > re-position the center, it calculates the distance between any elements of > the old cluster and its center, or in my case I used a distance matrix , so > I do not understand how the algorithm can recalculates the distance between > the newly generated center and other elements of the cluster knowing that > the new center does not appear in the distance matrix and there is no way to > calculate the distance between him and the elements of a cluster. ? > In my understading PAM stands for Partitioning Around Medoids. The medoid of a cluster is the object with the smallest mean distance to all other objects in the cluster. In each iteration, all objects are assigned to their nearest medoid, and the medoids are updated if necessary. The distance matrix is never recalculated. Someone please correct me if I'm wrong. Peter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] as.integer
Usually when read.table converts numbers to factors it means that there is a problem in the data file, an extra character somewhere. It is best to fix the problem in the source data (or a copy of the source data) so that the data imports properly rather than try to fix it post hoc. If that is not an option, then you can specify the colClasses argument to read.table to make sure that it reads the data into the type of variable that you want. If you really need the post read.table solution, then lapply will run the same function (as.integer) on each column of a data frame (element of a list). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of aledanda > Sent: Monday, June 07, 2010 8:05 AM > To: r-help@r-project.org > Subject: [R] as.integer > > > Hi, > > Is there a way to recursively change the variables imported with > read.table(..) - and then attached with attach(..) - from as.factor to > as.integer? > I have about 9 variables that are now recognized as factors but I need > to do > statistics on them so I need to change them in as.integer. It works, > but I > wonder if there is a way to to this for all the variables in one go. > > Thanks a lot for your help > > Ale > -- > View this message in context: http://r.789695.n4.nabble.com/as-integer- > tp2245987p2245987.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to parse out string separated by special character
Look at the strapply function in the gsubfn package. It may do what you want. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of xin wei > Sent: Monday, June 07, 2010 11:21 AM > To: r-help@r-project.org > Subject: [R] how to parse out string separated by special character > > > hi, everyone: > i have a data frame with one single character column as followings: > DS_xxx_yyy_24hr_zzz_1 > DS_xxx_yyy_24hr_zzz_2 > DS_xxx_yyy_24hr_zzz_3 > DS_xxx_yyy_24hr_zzz_4 > DS_xxx_yyy_24hr_zzz_1 > DS_xxx_yyy_24hr_zzz_2 > DS_xxx_yyy_24hr_zzz_3 > DS_xxx_yyy_24hr_zzz_4 > DS_xxx_yyy_24hr_zzz_1 > > i need to parse out the time part like the followings: > name time > DS_xxx_yyy_24hr_zzz_1 24hr > DS_xxx_yyy_24hr_zzz_2 24hr > DS_xxx_yyy_24hr_zzz_3 24hr > DS_xxx_yyy_24hr_zzz_4 24hr > DS_xxx_yyy_24hr_zzz_1 24hr > DS_xxx_yyy_24hr_zzz_2 24hr > DS_xxx_yyy_24hr_zzz_3 24hr > DS_xxx_yyy_24hr_zzz_4 24hr > DS_xxx_yyy_24hr_zzz_1 24hr > > what function should I look at? > i have tried: strsplit(data, '_') and get a giant list which is not > what i > need. > > thanks in advance > > -- > View this message in context: http://r.789695.n4.nabble.com/how-to- > parse-out-string-separated-by-special-character-tp2246301p2246301.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source of chickwts data
> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Chirok Han > Sent: Monday, June 07, 2010 9:51 AM > To: r-help > Subject: [R] Source of chickwts data > > I'm not sure if this is the right mailing list. My apologies if I'm > sending the question to the wrong mailing list. > (The r-packages list moderator suggested using the R-help list.) > > My question is about the "chickwts" data in the datasets package. > According to help(chickwts), the source of the data is > > Anonymous (1948) Biometrika, 35, 214. > > But this reference seems irrelevant. > (See http://www.jstor.org/stable/i315414.) > > The help document also gives "McNeil, D. R. (1977) Interactive Data > Analysis. New York: Wiley" as a reference, but unfortunately my local > library does not keep the book. Could someone please help me find the > correct source of the data? McNeil's book, page 30, attributes it to "Anonymous query, Biometrics, 1948, page 214" Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > > Many thanks. > > Chirok > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mgcv
predict(sm1,type="terms",terms="s(x2)") see ?predict.gam Cheers Joris On Mon, Jun 7, 2010 at 7:25 PM, Dipa Hari wrote: > > > Hello Sir, > I am using mgcv package for my data. > My model is y~x1+f(x2),I want to find out the function f(x2) . > Following is the code. > > sm1=gam(y~x1+s(x2),family=binomial, f) > summary(sm1) > plot(sm1,residuals=TRUE, xlab="AGE",pch=20) > > In this plot I am getting S(x2,1.93) on y axixs > How should I get the function for x2 from this plot.or Is there anyother > procedure in R to get this function or value for that particular > function.for example f(x2)= log(x2) so from that plot how can I get this kind > of formula for x2 variable? > How can I find variance covariance matrix for that model and confidence > interval for that model ? I tried delta method but I am not getting result. > Hope you understand my question? > Thanks > > > > > > [[alternative HTML version deleted]] > > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Transforming list to data frame with corresponding columns
Try this:
`colnames<-`(do.call(rbind, lapply(all2, '[', nm <-
unique(unlist(sapply(all2, names), nm)
On Mon, Jun 7, 2010 at 4:20 PM, LCOG1 wrote:
>
> Hi all,
> Consider the following.
>
>
> a<-list(c("MHsub","MHsub","SFD","Duplex"))
> b<-list(c("MHsub","MHsub","SFD"))
> c<-list(c("MHpark","SFD","SFD"))
> d<-list(c("MultiFam","MultiFam","MultiFam","Duplex"))
>
> all<-list(a,b,c,d)
> names(all)<-c("5","6","7","8")
> all2<-list()
> for(i in 1:length(all)){
> all2[[i]]<-table(unlist(all[i]))
> }
> names(all2)<-names(all)
>
> What i want to do is to put each of the elements of the list into a data
> frame where the element represents a row and each vector is accounted for,
> for all types within the entire list. So where there isnt a particular
> vector a 0 is noted so that the final product looks like this:
>
>
>SFD Mhsub Duplex MultiFam
> 5 1 11 0
> 6 1 10 0
> 7 1 10 0
> 8 0 01 1
>
> Thanks for the insights.
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Transforming-list-to-data-frame-with-corresponding-columns-tp2246423p2246423.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste together a string object later to be utilized in a function
Sorry for bothering all of you. In the end it turned out to be much simpler
than I thought. Takes a while to get used to the vectorizing idea.
require(survival)
require(ggplot2)
ggkm<-function(time,event,stratum) {
stratum<-as.factor(stratum)
m2s<-Surv(time,as.numeric(event))
fit <- survfit(m2s ~ stratum)
w<-fit$time
k<-fit$surv
o<-length(levels(stratum))
strata<-c(rep(names(fit$strata[1:o]),fit$strata[1:o]))
upper<-fit$upper
lower<-fit$lower
f<-data.frame(w,k,strata,upper,lower)
r<-ggplot
(f,aes(x=w,y=k,fill=strata,group=strata))+geom_line(aes(color=strata))+geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.3)+xlim(0,fit$maxtime)+ylim(0,1)
r<-r+scale_fill_brewer(f$strata,palette="Set1")+scale_color_brewer(f$strata,palette="Set1")
return(r)
}
data(lung)
with(lung,ggkm(time,status,sex))
with(lung,ggkm(time,status,pat.karno))
//M
On 7. juni 2010, at 22.31, Greg Snow wrote:
> Does the collapse argument to the paste function do what you want? Possibly
> nested inside another paste.
>
> --
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> greg.s...@imail.org
> 801.408.8111
>
>
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
>> project.org] On Behalf Of moleps
>> Sent: Sunday, June 06, 2010 1:51 PM
>> To: r-help@r-project.org
>> Subject: [R] paste together a string object later to be utilized in a
>> function
>>
>> Dear r-listers,
>>
>> I need to pass a string to a function. However the length of the string
>> is dependent on the length of a vector.
>>
>>
>> b<-length(h)
>> v<-paste("rep(names(ts$a[",1:b,"]),ts$a[",1:b,"])",sep="")
>>
>>
>> Is it possible somehow to pass this as an argument to a function later
>> on ?
>>
>>
>>
>> Regards,
>>
>> //M
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Very OT: World Cup Statistics
Paul The FIFA database doesn't have times that goals are scored either. The best I have found is at http://www.worldcup-history.com/, but you have to check individual match reports for the times that goals are scored. albyn On Mon, Jun 07, 2010 at 09:50:34PM +0100, Paul wrote: > Hello, > > Sorry for the very Off TOpic post, but I need some data on past football > (soccer) world cups. I'd like to find (or calculate) the time to the first > goal of each match (where a goal was scored). > > I''ve looked at the uefa website and can't find what I want, maybe someone > here can help ? > > Thanks > > Paul. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Borders on a polygon
Hi, I am trying to do some shading in R and am using the polygon() setting. I want the border on the top and bottom of the polygon, but not on the left and right. Is there a way to do this in R? Thanks in advance! beloitstudent -- View this message in context: http://r.789695.n4.nabble.com/Borders-on-a-polygon-tp2246646p2246646.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Very OT: World Cup Statistics
these websites seem to have the data. though I have not checked for completeness. the rsssf in particular is seems to be concerned with collecting and archiving these kinds of football data: http://www.rsssf.com/tablesw/worldcup.html http://wapedia.mobi/en/1930_FIFA_World_Cup_Group_1 hope that helps, daniel -- View this message in context: http://r.789695.n4.nabble.com/Very-OT-World-Cup-Statistics-tp2246551p2246730.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source of chickwts data
Many thanks. That's the right one. It would be better corrected in the next version of R. Thanks again. Chirok On Tue, Jun 8, 2010 at 6:01 AM, William Dunlap wrote: >> -Original Message- >> From: r-help-boun...@r-project.org >> [mailto:r-help-boun...@r-project.org] On Behalf Of Chirok Han >> Sent: Monday, June 07, 2010 9:51 AM >> To: r-help >> Subject: [R] Source of chickwts data >> >> I'm not sure if this is the right mailing list. My apologies if I'm >> sending the question to the wrong mailing list. >> (The r-packages list moderator suggested using the R-help list.) >> >> My question is about the "chickwts" data in the datasets package. >> According to help(chickwts), the source of the data is >> >> Anonymous (1948) Biometrika, 35, 214. >> >> But this reference seems irrelevant. >> (See http://www.jstor.org/stable/i315414.) >> >> The help document also gives "McNeil, D. R. (1977) Interactive Data >> Analysis. New York: Wiley" as a reference, but unfortunately my local >> library does not keep the book. Could someone please help me find the >> correct source of the data? > > McNeil's book, page 30, attributes it to > "Anonymous query, Biometrics, 1948, page 214" > > Bill Dunlap > Spotfire, TIBCO Software > wdunlap tibco.com > >> >> Many thanks. >> >> Chirok >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Transforming list to data frame with corresponding columns
Henrique,
The last message gave me exactly what i needed. Im still not sure whats
going on, i will need to reference the do.call function some more. Thanks for
your help.
Josh Roll
Lane Council of Governments
Transportation Planner
Office: 541-682-2454
Cell: 406-671-5069
jr...@lcog.org
www.lcog.org
From: Henrique Dallazuanna [via R]
[mailto:ml-node+2246612-389423334-103...@n4.nabble.com]
Sent: Monday, June 07, 2010 2:31 PM
To: ROLL Josh F
Subject: Re: Transforming list to data frame with corresponding columns
Try this:
`colnames<-`(do.call(rbind, lapply(all2, '[', nm <-
unique(unlist(sapply(all2, names), nm)
On Mon, Jun 7, 2010 at 4:20 PM, LCOG1 <[hidden
email]> wrote:
>
> Hi all,
> Consider the following.
>
>
> a<-list(c("MHsub","MHsub","SFD","Duplex"))
> b<-list(c("MHsub","MHsub","SFD"))
> c<-list(c("MHpark","SFD","SFD"))
> d<-list(c("MultiFam","MultiFam","MultiFam","Duplex"))
>
> all<-list(a,b,c,d)
> names(all)<-c("5","6","7","8")
> all2<-list()
> for(i in 1:length(all)){
> all2[[i]]<-table(unlist(all[i]))
> }
> names(all2)<-names(all)
>
> What i want to do is to put each of the elements of the list into a data
> frame where the element represents a row and each vector is accounted for,
> for all types within the entire list. So where there isnt a particular
> vector a 0 is noted so that the final product looks like this:
>
>
>SFD Mhsub Duplex MultiFam
> 5 1 11 0
> 6 1 10 0
> 7 1 10 0
> 8 0 01 1
>
> Thanks for the insights.
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Transforming-list-to-data-frame-with-corresponding-columns-tp2246423p2246423.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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[R] Desolve package: How to pass thousand of parameters to C compiled code?
Hi, I have used DeSolve package for my ODE problem regarding infectious disease transmission and currently am trying to pass lots (roughly a thousand) of model parameters to the C compiled model (I have to use C compiled code instead of R code purely because of the speed). I can't go define it one by one as it gonna take ages to finish and also quite difficult to revise. I have read the instructions in "Writing Code in Compiled Languages", which is very well written, but still have no clue on how to proceed. Please can anyone suggest the best way to go about this, and also the places where I can find examples of DeSolve C compiled code. Thank you very much in advance. Nar Pun CMMU/MUTH -- This message was sent on behalf of cmmu_m...@yahoo.com at openSubscriber.com http://www.opensubscriber.com/messages/r-help@r-project.org/topic.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Borders on a polygon
On Mon, Jun 7, 2010 at 6:55 PM, beloitstudent wrote: > [...] I am trying to do some shading in R and am using the polygon() setting. > I want the border on the top and bottom of the polygon, but not on the left > and right. [...] One way would be to add the borders after as lines. For example: plot.new() polygon(c(0,1,1,0), c(0,0,1,1), col = "yellow", border = NA) lines(c(0,1), c(0,0)) lines(c(0,1), c(1,1)) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart but with boxes
Thanks to all,
I did eventually come up with a solution which involved sub-setting
the data first into categories, making an empty plot, and then
plotting rectangles. I really like the ggplot2 and I will use that
next time.
My ugly script is below
Thanks,
Daisy
plot(1, xlim=c(5,45),ylim=c(0,10),xlab="Year",ylab="+/- 1 \u03c3 Mean
Patch Size (ha)",axes=F,type="n")
title(main = list("Patch Size Agreement", cex=1.4))
axis(2)
box()
mtext(c(2010,2030,2050,2070),side=1,line = 1, at=c(10,20,30,40))
position<-seq(10, 40, length.out=4 )
xlef<-position-2.5
xrig <-position+2.5
for(i in 1:nrow(sub00)){
min_y<-sub00$minsd_ha[i]
max_y<-sub00$maxsd_ha[i]
xleft<-xlef[1]
xrigh<-xrig[1]
rect(xleft, min_y, xrigh, max_y,border = NA,col=rgb(0,
0, 0, alpha=0.03))
}
for(i in 1:nrow(sub01)){
min_y<-sub01$minsd_ha[i]
max_y<-sub01$maxsd_ha[i]
xleft<-xlef[2]
xrigh<-xrig[2]
rect(xleft, min_y, xrigh, max_y,border = NA,col=rgb(0,
0, 0, alpha=0.03))
}
for(i in 1:nrow(sub02)){
min_y<-sub02$minsd_ha[i]
max_y<-sub02$maxsd_ha[i]
xleft<-xlef[3]
xrigh<-xrig[3]
rect(xleft, min_y, xrigh, max_y,border = NA,col=rgb(0,
0, 0, alpha=0.03))
}
for(i in 1:nrow(sub03)){
min_y<-sub03$minsd_ha[i]
max_y<-sub03$maxsd_ha[i]
xleft<-xlef[4]
xrigh<-xrig[4]
rect(xleft, min_y, xrigh, max_y,border = NA,col=rgb(0,
1, 0, alpha=0.03))
}
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[R] color of histgram in Psych package (pairs.panels)
Hello, I searched the archives but found no answers. How to modify the hisgram color of function pairs.panels of Psych package ? I tried col() but it was the line color modified. Thanks. Elaine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ignoring missing elements in data.frame()
Hi Joris,
Thanks very much. I think the %in% ls() was the key. I just needed to know
how to select elements that existed in ls().
Scott
On Sat, Jun 5, 2010 at 4:22 PM, Joris Meys wrote:
> Hi,
>
> One possible way to get around it is using following idea :
> X1 <- rnorm(10)
> X2 <- rnorm(10)
>
> Names <- c("X1","X2","X3")
> Names <- Names[Names %in% ls()]
>
> n <- length(Names)
> p <- 10 #length of each object
> output <- matrix(NA,ncol=n,nrow=p)
>
> for(i in 1:n){
>output[,i] <- get(Names[i])
> }
> output <- as.data.frame(output)
> names(output) <- Names
>
> You can also use an eval-parse construct like this :
> ## Alternative
> Names <- c("X1","X2","X3")
> Names <- Names[Names %in% ls()]
> Names <- paste(Names,collapse=",")
> expr = paste("output <- data.frame(",Names,")",sep="")
> eval(parse(text=expr))
>
> Both are not really the most optimal solution, but do work. It would
> be better if you made a list or matrix beforehand and then save the
> results of the calculations in that list or matrix whenever the
> calculation turns out to give a result.
>
> Cheers
> Joris
>
> On Sat, Jun 5, 2010 at 1:23 AM, Scott Chamberlain
> wrote:
> > Hello, I am trying to make a data frame from many elements after
> > running a function which creates many elements, some of which may not
> > end up being real elements due to errors or missing data. For example,
> > I have the following three elements p1s, p2s, and p3s. p9s did not
> > generate the same data as there was an error in the function for some
> > reason. I currently have to delete p9s from the data.frame() command
> > to get the data.frame to work. How can I make a data frame by somehow
> > ignoring elements (e.g., p9s) that do not exist, without having to
> > delete each missing element from data.frame()? The below is an example
> > of the code.
> >
> >> p1s
> > statistic parameter p.value
> > [1,] 3.606518 153 0.0004195377
> >> p2s
> > statistic parameter p.value
> > [1,] -3.412436 8 0.009190015
> >> p3s
> > statistic parameter p.value
> > [1,] 1.543685 599 0.1231928
> >
> >> t(data.frame(t(p1s),t(p2s),t(p3s),t(p9s)))
> > Error in t(p9s) : object 'p9s' not found
> >
> >
> > Thanks, Scott Chamberlain
> > Rice University
> > Houston, TX
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
>
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and provide commented, minimal, self-contained, reproducible code.
[R] Matrix to "database" -- best practices/efficiency?
I have a matrix of, say, M and N dimensions:
my_matrix=matrix(c(1:60),nrow=6,ncol=10)
I have two "id" vectors corresponding to the rows and columns, e.g.:
id_m=seq(10,60,by=10)
id_n=seq(100,1000,by=100)
I would like to create a "proper" database (let's say a data.frame for
this example -- i'm going to be loading these into an SQLite database,
but we'll leave that complication out of this discussion for now) of m
x n rows, and 3 columns, where the 3 columns relate to the values from
m, n, and my_matrix respectively, e.g. a single row follows the form:
c(id_m[a],id_n[b],my_matrix[a,b])
I can, of course, for-loop this thing with an if-then, e.g.:
***
for (a in 1:length(id_m))
{
for (b in 1:length(id_n))
{
if ((a==1) && (b==1))
{
my_database=c(id_m[a],id_n[b],my_matrix[a,b])
} else
{
my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
}
}
}
***
But my gut is telling me this is an incredibly inefficient way of
doing this -- is there a faster approach to doing this same process?
Thanks!
--j
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[R] R statistical program 2.10.0
Hi, I just need to know where the R was developed, for a journal article citation. Thanks Ronjon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Filtering out a data.frame
Sample Data.Frame format Name is Returns.nodup X id ticker date_ adjClose totret RankStk 427225 427225 00174410AHS 2001-11-1321.661001235 "id" uniquely defines a row What I am trying to do is filter out id's that have less than 1500 data points (by date) First, I used total<-by(Returns.nodup, Returns.nodup$id,nrow) which subsetted by ID and calculated the number of data points for each ID Now I am trying to figure out a way to use this to filter out the original data.frame (Returns.nodup) I have tried using the following, but it is VERY slow: z<-unlist(lapply(1:length(y), function(i) which(a$id==y[i]) )) Returns.filtered<-Returns.nodup[z,] Is there a faster way to do this? -- View this message in context: http://r.789695.n4.nabble.com/Filtering-out-a-data-frame-tp2246814p2246814.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] About lm.ridge in the MASS package
Hi, I had a questions about doing ridge regression in R. Why is it that when I try this on datasets with more predictors than samples (p>n) using lambda=0, it still finds coefficients for all predictors? I thought when lambda=0, it should be like ordinary regression and therefore not find coefficients for all due to singularity? I would greatly appreciate your help. Thank you, --James K. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adding in Missing Data
Sample Data.Frame format Name is Returns.names X id ticker date_ adjClose totret RankStk 427225 427225 00174410AHS 2001-11-1321.661001235 "id" uniquely defines a row What I am trying to do is add missing data for each ID. Important Information: Date is not continuous, the data points are for trading days, so weekends/certain holidays are off x<-unique(Returns.names$date_) gives me the list of all the possible trading days. For days that are missing, I would like to add a row for that date & the same totret as the previous day. I cant think of an easy way to do this -- View this message in context: http://r.789695.n4.nabble.com/Adding-in-Missing-Data-tp2246825p2246825.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R statistical program 2.10.0
Datta, Ronjon wrote: Hi, I just need to know where the R was developed, for a journal article citation. There's a function for that! citation() __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filtering out a data.frame
Jeff08 wrote: Sample Data.Frame format Name is Returns.nodup X id ticker date_ adjClose totret RankStk 427225 427225 00174410AHS 2001-11-1321.661001235 "id" uniquely defines a row What I am trying to do is filter out id's that have less than 1500 data points (by date) First, I used total<-by(Returns.nodup, Returns.nodup$id,nrow) which subsetted by ID and calculated the number of data points for each ID Now I am trying to figure out a way to use this to filter out the original data.frame (Returns.nodup) I have tried using the following, but it is VERY slow: z<-unlist(lapply(1:length(y), function(i) which(a$id==y[i]) )) Returns.filtered<-Returns.nodup[z,] Is there a faster way to do this? Most likely, yes. But without a reproducible example, it's difficult to think about the problem. Can you please give us one? If not, you can probably cobble something together using ?table and ?%in% I'm guessing. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R statistical program 2.10.0
Hi Ronjon,
>From citation():
> citation()
To cite R in publications use:
R Development Core Team (2010). R: A language and environment for
statistical computing.
R Foundation for Statistical Computing, Vienna, Austria. ISBN
3-900051-07-0, URL
http://www.R-project.org.
A BibTeX entry for LaTeX users is
@Manual{,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Development Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2010},
note = {{ISBN} 3-900051-07-0},
url = {http://www.R-project.org},
}
We have invested a lot of time and effort in creating R, please cite it when
using it for
data analysis. See also citation("pkgname") for citing R packages.
HTH,
Jorge
On Tue, Jun 8, 2010 at 12:03 AM, Datta, Ronjon <> wrote:
> Hi,
> I just need to know where the R was developed, for a journal article
> citation.
>
> Thanks
> Ronjon
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[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] Matrix to "database" -- best practices/efficiency?
Try this:
> mm <- matrix(1:6, 3, dimnames = list(LETTERS[1:3], letters[1:2]))
> mm
a b
A 1 4
B 2 5
C 3 6
> library(reshape)
> melt(mm)
X1 X2 value
1 A a 1
2 B a 2
3 C a 3
4 A b 4
5 B b 5
6 C b 6
On Mon, Jun 7, 2010 at 10:33 PM, Jonathan Greenberg
wrote:
> I have a matrix of, say, M and N dimensions:
>
> my_matrix=matrix(c(1:60),nrow=6,ncol=10)
>
> I have two "id" vectors corresponding to the rows and columns, e.g.:
>
> id_m=seq(10,60,by=10)
> id_n=seq(100,1000,by=100)
>
> I would like to create a "proper" database (let's say a data.frame for
> this example -- i'm going to be loading these into an SQLite database,
> but we'll leave that complication out of this discussion for now) of m
> x n rows, and 3 columns, where the 3 columns relate to the values from
> m, n, and my_matrix respectively, e.g. a single row follows the form:
>
> c(id_m[a],id_n[b],my_matrix[a,b])
>
> I can, of course, for-loop this thing with an if-then, e.g.:
>
> ***
>
> for (a in 1:length(id_m))
> {
> for (b in 1:length(id_n))
> {
> if ((a==1) && (b==1))
> {
> my_database=c(id_m[a],id_n[b],my_matrix[a,b])
> } else
> {
>
> my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
> }
> }
> }
>
> ***
>
> But my gut is telling me this is an incredibly inefficient way of
> doing this -- is there a faster approach to doing this same process?
> Thanks!
>
> --j
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding in Missing Data
Jeff08 wrote: Sample Data.Frame format Name is Returns.names X id ticker date_ adjClose totret RankStk 427225 427225 00174410AHS 2001-11-1321.661001235 "id" uniquely defines a row What I am trying to do is add missing data for each ID. Important Information: Date is not continuous, the data points are for trading days, so weekends/certain holidays are off x<-unique(Returns.names$date_) gives me the list of all the possible trading days. For days that are missing, I would like to add a row for that date & the same totret as the previous day. I cant think of an easy way to do this See this thread... http://www.opensubscriber.com/message/r-h...@stat.math.ethz.ch/6986471.html specifically the last post by Gabor. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix to "database" -- best practices/efficiency?
Hi Jonathan,
Following Gabor Grothendieck's advice, try also:
mm <- matrix(1:6, 3, dimnames = list(LETTERS[1:3], letters[1:2]))
as.data.frame.table(mm)
HTH,
Jorge
On Mon, Jun 7, 2010 at 10:33 PM, Jonathan Greenberg <> wrote:
> I have a matrix of, say, M and N dimensions:
>
> my_matrix=matrix(c(1:60),nrow=6,ncol=10)
>
> I have two "id" vectors corresponding to the rows and columns, e.g.:
>
> id_m=seq(10,60,by=10)
> id_n=seq(100,1000,by=100)
>
> I would like to create a "proper" database (let's say a data.frame for
> this example -- i'm going to be loading these into an SQLite database,
> but we'll leave that complication out of this discussion for now) of m
> x n rows, and 3 columns, where the 3 columns relate to the values from
> m, n, and my_matrix respectively, e.g. a single row follows the form:
>
> c(id_m[a],id_n[b],my_matrix[a,b])
>
> I can, of course, for-loop this thing with an if-then, e.g.:
>
> ***
>
> for (a in 1:length(id_m))
> {
>for (b in 1:length(id_n))
>{
>if ((a==1) && (b==1))
>{
>my_database=c(id_m[a],id_n[b],my_matrix[a,b])
>} else
>{
>
> my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
>}
>}
> }
>
> ***
>
> But my gut is telling me this is an incredibly inefficient way of
> doing this -- is there a faster approach to doing this same process?
> Thanks!
>
> --j
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix to "database" -- best practices/efficiency?
I think what you are groping for is something like this
my_matrix <- matrix(1:60, nrow = 6)
id_a <- seq(10,60,by=10)
id_b <- seq(100,1000,by=100)
my_database <- cbind(
expand.grid(id_a = id_a, id_b = id_b),
mat = as.vector(my_matrix)
)
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Jonathan Greenberg
Sent: Tuesday, 8 June 2010 12:34 PM
To: r-help
Subject: [R] Matrix to "database" -- best practices/efficiency?
I have a matrix of, say, M and N dimensions:
my_matrix=matrix(c(1:60),nrow=6,ncol=10)
I have two "id" vectors corresponding to the rows and columns, e.g.:
id_m=seq(10,60,by=10)
id_n=seq(100,1000,by=100)
I would like to create a "proper" database (let's say a data.frame for
this example -- i'm going to be loading these into an SQLite database,
but we'll leave that complication out of this discussion for now) of m
x n rows, and 3 columns, where the 3 columns relate to the values from
m, n, and my_matrix respectively, e.g. a single row follows the form:
c(id_m[a],id_n[b],my_matrix[a,b])
I can, of course, for-loop this thing with an if-then, e.g.:
***
for (a in 1:length(id_m))
{
for (b in 1:length(id_n))
{
if ((a==1) && (b==1))
{
my_database=c(id_m[a],id_n[b],my_matrix[a,b])
} else
{
my_database=rbind(my_database,c(id_m[a],id_n[b],my_matrix[a,b]))
}
}
}
***
But my gut is telling me this is an incredibly inefficient way of
doing this -- is there a faster approach to doing this same process?
Thanks!
--j
__
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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-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with seting up comparison
Greg, the animals are a sample of a larger population, as you guessed. I used lmer to estimate the effects: > lmer(Count~Animal | Day, dat) Linear mixed model fit by REML Formula: Count ~ Animal | Day Data: dat AIC BIC logLik deviance REMLdev 1554 1574 -772 15421544 Random effects: Groups NameVariance Std.Dev. Corr Day (Intercept) 1.7707e-02 0.1330678 Animal 4.0287e-05 0.0063472 1.000 Residual 2.0917e+00 1.4462790 Number of obs: 430, groups: Day, 4 Fixed effects: Estimate Std. Error t value (Intercept) 4.2423 0.1257 33.76 But how does this help me to state that there is no effect within an animal? anova doesn't seems to work (gives an empty table) I'm sorry, but I have no experience with lme models, only lm. Thanks for your time Bart > From: greg.s...@imail.org > To: bartjoo...@hotmail.com; r-help@r-project.org > Date: Mon, 7 Jun 2010 14:54:47 -0600 > Subject: RE: [R] Help with seting up comparison > > Are you interested in only those 35 animals (not every going to look at any > other animals other than those 35, but you want to predict what will happen > for those 35)? Or are the 35 animals a sample of a larger population of > animals? > > If the later (seems the most likely case) then you probably want to use a > mixed effects model (nlme or lme4 packages) with animal as a random effect, > then just look at the fixed effect of day. > > Hope this helps, > > -- > Gregory (Greg) L. Snow Ph.D. > Statistical Data Center > Intermountain Healthcare > greg.s...@imail.org > 801.408.8111 > > > > -Original Message- > > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > > project.org] On Behalf Of Bart Joosen > > Sent: Monday, June 07, 2010 9:14 AM > > To: r-help@r-project.org > > Subject: [R] Help with seting up comparison > > > > > > Hi, > > > > I tried on this, but couldn't figure it out: > > Suppose I have a dataframe as follows: > > dat <- data.frame(Day=rep(rep(c(1,2), each=4),2), Animal = rep(c(1,2), > > each=8), Count=c(rnorm(8, 100), rnorm(8,90))) > > > > 2 animals are being examined on 2 different days. Count is the result. > > > > Now I need to point out whether or not there is a difference between > > the > > days. > > I did this by an ANOVA test, while first converting the animal and day > > to a > > factor variable: > > dat$Animal <- as.factor(dat$Animal) > > dat$Day <- as.factor(dat$Day) > > mod <- lm(Count ~Animal * Day,dat) > > anova(mod) > > > > Now I have to check for difference within the animal, to see if there > > is a > > difference in count for each day. (In my real data, I have 35 animals, > > with > > 4 days, and 4 results). > > I thought about a Tukey HSD test, but this compares every day of every > > animal with every other day of every other animal. (TukeyHSD(aov(mod))) > > > > Any idea about which function (or model for lm) to use to only compare > > days > > within every animal? > > > > Best regards > > > > Bart > > > > > > -- > > View this message in context: http://r.789695.n4.nabble.com/Help-with- > > seting-up-comparison-tp2246106p2246106.html > > Sent from the R help mailing list archive at Nabble.com. > > > > __ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > > guide.html > > and provide commented, minimal, self-contained, reproducible code. _ Hotmail: betrouwbare e-mail met krachtige spambescherming. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
