Re: [R] Looking for knitr example for beginner (NO RStudio)
All your questions are answered by the knitr book in my first reply, which introduces knitr in a systematic manner. For the web pages, I have tried my best, and nobody can make everybody happy. I do not understand why you do not understand Rnw and markdown, and I do not quite believe a person who understands R cannot understand markdown. I understand you do not have control over your lab machines, but you still have other options like your own laptop (if you do not like RStudio, feel free to remove it and use your favorite editors after you have got the idea). Regards, Yihui -- Yihui Xie Phone: 206-667-4385 Web: http://yihui.name Fred Hutchinson Cancer Research Center, Seattle On Thu, Jul 18, 2013 at 5:50 PM, C W wrote: > Hi, > @Yihui > When I am using a public computer, say university computer lab or > financial company. I do not have control what to install. > > I'm also very happy with R editor on OS X, it integrates with Mac > well. As for my Mac Air, I am keeping installation to the minimal. > > There are a lot links on your page, I don't understand what I am > reading. What is Rnw, what is markdown? As a newbie, it's above my > level. I googled Rnw, it's refers to Sweave package, now I am > tracking back to Sweave. > > As a user, I want to spend more time using the package, not installing. > > @Simon: thanks, I will definitely rename the extension. I really hope > there will be a more thorough description somewhere soon. > > Mike __ 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] construct stem and leaf plot
Dear r-users, I would like to construct tem and leaf plot using iris data. It should be easy, but I don't understand why the plot is not right. Thank you so much for your help. dat <- iris[,1] > stem(dat) The decimal point is 1 digit(s) to the left of the | 42 | 0 44 | 46 | 00 48 | 000 50 | 000 52 | 0 54 | 0 56 | 00 58 | 00 60 | 62 | 0 64 | 66 | 00 68 | 000 70 | 00 72 | 74 | 0 76 | 0 78 | 0 [[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] Paternity data analysis
Dear R-experts!
I did an experiment with Guppy where I had two dietary groups ("High" and
"Low"). I completed all my data analysis, but stacked in "paternity
analysis". I ran the attached model to analyse them, but as a novice in R,
it's very hard for me to confirm whether this gives me the correct output
or not. I would like to examine the effect of the predictor traits (VAP,
Viability, Body FAs) on paternity success (Proportion). Here, I fitted
generalized linear models (GLMs) using a logit-link function as my data has
some zeroes and ones. I also lie to use quasi-GLMs to correct for
overdispersion. Now, I need some help from you guys to estimate the
paternity success of my high group or both groups? **
With kind regards,
Moshi
--
MD. MOSHIUR RAHMAN
PhD Candidate
School of Animal Biology/Zoology (M092)
University of Western Australia
35 Stirling Hwy, Crawley, WA, 6009
Australia.
Mob.: 061-425205507
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Looking for knitr example for beginner (NO RStudio)
Hi Mike,
As long as you have access to some user folder, you can download a
non-install version of RStudio.
Go to the page http://www.rstudio.com/ide/download/desktop and select "Show
zip/tarball downloads", download, extract, and run.
Do believe Yihui that running an example using RStudio saves you a lot of
time.
Best,
Yixuan
2013/7/18 C W
> Hi,
> @Yihui
> When I am using a public computer, say university computer lab or
> financial company. I do not have control what to install.
>
> I'm also very happy with R editor on OS X, it integrates with Mac
> well. As for my Mac Air, I am keeping installation to the minimal.
>
> There are a lot links on your page, I don't understand what I am
> reading. What is Rnw, what is markdown? As a newbie, it's above my
> level. I googled Rnw, it's refers to Sweave package, now I am
> tracking back to Sweave.
>
> As a user, I want to spend more time using the package, not installing.
>
> @Simon: thanks, I will definitely rename the extension. I really hope
> there will be a more thorough description somewhere soon.
>
> Mike
>
> On Thu, Jul 18, 2013 at 4:50 PM, Simon Zehnder
> wrote:
> > Hi Mike,
> >
> > if you browse the folders, you find always the Rscript binary (the
> executable) under
> /Library/Frameworks/R.framework/Versions/.../Resources/Rscript.
> >
> > Do not forget to give your tex file the extension .Rnw! Then surround
> each Rcode with < one; results = 'asis')>>= Here your r code as you do it in the R shell
> at the end a @. Always inside the \begin{document} \end{document} tags.
> >
> >
> >
> > Best
> >
> > Simon
> >
> > On Jul 18, 2013, at 10:22 PM, C W wrote:
> >
> >> Thanks, Simon. I would never figured it out!
> >>
> >> I apologize if I sound frustrated, because I am.
> >>
> >> @package author: you have a great package, but I think a lot of the
> >> directions are hand waving. For the newbies, this leads to more
> >> confusion.
> >>
> >> @Berend: I am using OS X.
> >>
> >> Mike
> >>
> >>
> >> On Thu, Jul 18, 2013 at 4:19 PM, Berend Hasselman
> wrote:
> >>>
> >>> On 18-07-2013, at 22:09, C W wrote:
> >>>
>
> http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165
>
> In step 3: "add the executable file (step 3)".
>
> What is the executable file? Locate package knitr directory path in
> R?
>
> >>>
> >>> From the window: Executable ==> Program. So the executable is
> Rscript.exe.
> >>>
> >>>
> >>> Berend
> >>>
> >
>
> __
> 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.
>
--
Yixuan Qiu
Department of Statistics,
Purdue University
[[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] Looking for knitr example for beginner (NO RStudio)
Hi,
@Yihui
When I am using a public computer, say university computer lab or
financial company. I do not have control what to install.
I'm also very happy with R editor on OS X, it integrates with Mac
well. As for my Mac Air, I am keeping installation to the minimal.
There are a lot links on your page, I don't understand what I am
reading. What is Rnw, what is markdown? As a newbie, it's above my
level. I googled Rnw, it's refers to Sweave package, now I am
tracking back to Sweave.
As a user, I want to spend more time using the package, not installing.
@Simon: thanks, I will definitely rename the extension. I really hope
there will be a more thorough description somewhere soon.
Mike
On Thu, Jul 18, 2013 at 4:50 PM, Simon Zehnder wrote:
> Hi Mike,
>
> if you browse the folders, you find always the Rscript binary (the
> executable) under
> /Library/Frameworks/R.framework/Versions/.../Resources/Rscript.
>
> Do not forget to give your tex file the extension .Rnw! Then surround each
> Rcode with < results = 'asis')>>= Here your r code as you do it in the R shell at the
> end a @. Always inside the \begin{document} \end{document} tags.
>
>
>
> Best
>
> Simon
>
> On Jul 18, 2013, at 10:22 PM, C W wrote:
>
>> Thanks, Simon. I would never figured it out!
>>
>> I apologize if I sound frustrated, because I am.
>>
>> @package author: you have a great package, but I think a lot of the
>> directions are hand waving. For the newbies, this leads to more
>> confusion.
>>
>> @Berend: I am using OS X.
>>
>> Mike
>>
>>
>> On Thu, Jul 18, 2013 at 4:19 PM, Berend Hasselman wrote:
>>>
>>> On 18-07-2013, at 22:09, C W wrote:
>>>
http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165
In step 3: "add the executable file (step 3)".
What is the executable file? Locate package knitr directory path in R?
>>>
>>> From the window: Executable ==> Program. So the executable is Rscript.exe.
>>>
>>>
>>> Berend
>>>
>
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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] Test if 2 samples differ if they have autocorrelation
I imagine that most readers of this list will put your question in the too hard basket. That being so, here is my inexpert take on the question. The issue is to estimate the uncertainty in the estimated difference of the means. This uncertainty depends on the nature of the serial dependence of the series. Therefore in order to get anywhere you need to *model* this dependence. Different models could yield very different values for the variance of the estimated difference of the means. If the series are observed at the same times I would suggest taking the pointwise difference of the two series: D_t = X_t - Y_t, say. Fit the best arima model that you can to D_t. Then the standard error of what is incorrectly labelled "intercept" (it is actually the estimate of the series *mean*) is the appropriate estimate of the uncertainty. The ratio of the "intercept" value to its standard error is the test statistic you are looking for. If the series are *not* observed at the same times but can be assumed to be independent then model *each* series as well as you can (different models for each series) and obtain the standard error of the "intercept" for each series. Your test statistic is then the difference of the "intercept estimates divided by sqrt(se_X^2 + se_Y^2) in what I hope is an "obvious" notation. If the series are not observed at the same times and cannot be assumed to be independent then you probably haven't got sufficient information to answer the question that you wish to answer. I hope that there is some value in the forgoing. cheers, Rolf Turner On 18/07/13 21:50, Eric Jaeger wrote: Dear all I have one question that I struggle to find an answer: Let`s assume I have 2 timeseries of daily PnL data over 2 years coming from 2 different trading strategies. I want to find out if strategy A is better than strategy B. The problem is that the two series have serial correlations, hence I cannot just do a simple t-test. I tried something like this: 1.create cumulative timeseries of PnL_A = C_A and of PnL_B = C_B 2.take the difference of both: C_A – C_B = DiffPnL (to see how the difference evolves over time) 3.do a regression: DiffPnL = beta * time + error (I thought if beta is significantly different from 0 than the two time series are different) 4.estimate beta not with OLS, but with the Newey-West method (HAC estimator) -> this corrects statistical tests, standard errors for beta heteroskedasticity and autocorrelation BUT: I read something that the tests are biased when the timeseries are unit root non-stationary (which is due to the fact that I take cumulative time series) I am lost! This should be fairly simple: test if two samples differ if they have autocorrelation? Probably my approach above is completely wrong… __ 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 code for an exponential function
Hello, First of all, you need to read the posting guide. Where is a data example? And code? As for the question, at an R prompt, type ?log. Hope this helps, Rui Barradas Em 18-07-2013 20:18, Munroe, Ryan escreveu: Hi, I ran a linear regression on a data set and got an Rsq of about .27. The plot looks as though an exponential curve would be a better fit. What codes do I use to do this? Thank you, Ryan Munroe [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How code for an exponential function
Hi, I ran a linear regression on a data set and got an Rsq of about .27. The plot looks as though an exponential curve would be a better fit. What codes do I use to do this? Thank you, Ryan Munroe [[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] combine select data from 2 dataframes sharing same variables
Wow. That is exactly what I wanted (thread viewers see output below). I
think/hope this script will be more user friendly for my needs (RTF final
output) than the loop I currently have for LaTex output. Thanks very much A.K.
Iâll need to send you a Bundt cake at some point I suppose⦠BNC
> lst1
$MWtotaleesDue
zeroNOzeroYES
Mean8.428571 0.9076923
StdError2.496256 0.4117990
Median 7.00 0.000
StdDev 6.604472 3.3200295
Min 1.00 0.000
Max17.00 17.000
NinetyPct 3.593998 0.5332467
NinetyPctLower 4.834573 0.3744456
NinetyPctUpper 12.022570 1.4409390
$OTtotaleesDue
zeroNOzeroYES
Mean6.60 1.0153846
StdError2.242023 0.4442433
Median 3.00 0.000
StdDev 7.089899 3.5816036
Min 1.00 0.000
Max23.00 23.000
NinetyPct 3.100782 0.5752594
NinetyPctLower 3.499218 0.4401252
NinetyPctUpper 9.700782 1.5906440
$OTtotalBWsDue
zeroNOzeroYES
Mean559.9440 86.14523
StdError305.7341 51.57520
Median 257.55000.0
StdDev 966.8160 415.81256
Min 15.19000.0
Max3232.9700 3232.97000
NinetyPct 422.8390 66.78575
NinetyPctLower 137.1050 19.35948
NinetyPctUpper 982.7830 152.93098
$TotalBWsFD
zeroNOzeroYES
Mean693.2973 159.99169
StdError265.0846 69.86036
Median 267.58000.0
StdDev 1026.6682 563.23225
Min 15.19000.0
Max3232.9700 3232.97000
NinetyPct 356.5468 90.46357
NinetyPctLower 336.7505 69.52812
NinetyPctUpper 1049.8442 250.45526
From: arun kirshna [via R] [mailto:ml-node+s789695n4671818...@n4.nabble.com]
Sent: Thursday, July 18, 2013 12:24 AM
To: Crombie, Burnette N
Subject: Re: combine select data from 2 dataframes sharing same variables
Hi,
Not sure if this is what you wanted:
#If columns are arranged in the same order in both data.frames.
lst1<-lapply(seq_len(ncol(StatsUTAH)),function(i)
{x1<-cbind(StatsUTAH[,i],sStatsUTAH[,i]);row.names(x1)<-row.names(StatsUTAH);colnames(x1)<-c("zeroNO","zeroYES");x1})
names(lst1)<- colnames(StatsUTAH)
A.K.
--
View this message in context:
http://r.789695.n4.nabble.com/combine-select-data-from-2-dataframes-sharing-same-variables-tp4671790p4671887.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Looking for knitr example for beginner (NO RStudio)
Hi Mike,
if you browse the folders, you find always the Rscript binary (the executable)
under /Library/Frameworks/R.framework/Versions/.../Resources/Rscript.
Do not forget to give your tex file the extension .Rnw! Then surround each
Rcode with <>= Here your r code as you do it in the R shell at the
end a @. Always inside the \begin{document} \end{document} tags.
Best
Simon
On Jul 18, 2013, at 10:22 PM, C W wrote:
> Thanks, Simon. I would never figured it out!
>
> I apologize if I sound frustrated, because I am.
>
> @package author: you have a great package, but I think a lot of the
> directions are hand waving. For the newbies, this leads to more
> confusion.
>
> @Berend: I am using OS X.
>
> Mike
>
>
> On Thu, Jul 18, 2013 at 4:19 PM, Berend Hasselman wrote:
>>
>> On 18-07-2013, at 22:09, C W wrote:
>>
>>> http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165
>>>
>>> In step 3: "add the executable file (step 3)".
>>>
>>> What is the executable file? Locate package knitr directory path in R?
>>>
>>
>> From the window: Executable ==> Program. So the executable is Rscript.exe.
>>
>>
>> Berend
>>
__
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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] Looking for knitr example for beginner (NO RStudio)
I recommend RStudio not because I want to promote it in any sense, but because of the fact that it has the best support for Rnw/knitr at the moment, and it will save you a lot of headache to get started. It seems you just do not believe me, and insist on going through all the low-level configurations as a newbie. That will lead to confusion by definition. I do not know why you do not have _access_ to it; it is free and open source, so everybody has access to it unless one does not have the Internet connection. I'm not the developer of TeXworks, so I have no control over what TeXworks can support. knitr and its website are open source; please feel free to improve them if you find anything unclear: http://yihui.name/en/2013/06/fix-typo-in-documentation/ Regards, Yihui -- Yihui Xie Phone: 206-667-4385 Web: http://yihui.name Fred Hutchinson Cancer Research Center, Seattle On Thu, Jul 18, 2013 at 1:22 PM, C W wrote: > Thanks, Simon. I would never figured it out! > > I apologize if I sound frustrated, because I am. > > @package author: you have a great package, but I think a lot of the > directions are hand waving. For the newbies, this leads to more > confusion. > > @Berend: I am using OS X. > > Mike __ 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] 'save' method for S4 class
On 18.07.2013 20:23, Christofer Bogaso wrote:
Hi Simon,
Thanks for your pointer.
However could you please explain what 'function(x, file_Path)
standardGeneric("save")' means here?
It is the definition of the generic function for save()?
The underlying help files look quite
rocket science for me!
So start reading about S4 seems to be essential, if you ask for S4
methods. Otherwise we cannot help, given you do not even understand the
code to define the generic function.
Uwe Ligges
Thanks for your time.
Thanks and regards,
On Thu, Jul 18, 2013 at 4:32 PM, Simon Zehnder wrote:
Hi Christopher,
I think, that "save" is no generic function like "plot", "show", etc. So
at first you have to determine a generic.
setGeneric("save", function(x, file_Path) standardGeneric("save"))
Now your definition via setMethod.
Best
Simon
On Jul 18, 2013, at 12:09 PM, Christofer Bogaso <
bogaso.christo...@gmail.com> wrote:
Hello again,
I am trying to define the 'save' method for my S4 class as below:
setClass("MyClass", representation(
Slot1 = "data.frame"
))
setMethod("save", "MyClass", definition = function(x, file_Path) {
write.table(x@Slot1, file = file_Path, append = FALSE,
quote = TRUE,
sep = ",",
eol = "\n", na = "NA", dec
= ".", row.names = FALSE,
col.names = TRUE, qmethod
= c("escape", "double"),
fileEncoding = "")
})
However while doing this I am getting following error:
Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
in method for ‘save’ with signature ‘list="MyClass"’: formal
arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
version = "MyClass", envir = "MyClass", compress = "MyClass",
compression_level = "MyClass", eval.promises = "MyClass", precheck =
"MyClass") omitted in the method definition cannot be in the signature
Can somebody point me what will be the correct approach to define
'save' method for S4 class?
Thanks and regards,
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Re: [R] Looking for knitr example for beginner (NO RStudio)
On 18-07-2013, at 22:22, C W wrote: > Thanks, Simon. I would never figured it out! > > I apologize if I sound frustrated, because I am. > > @package author: you have a great package, but I think a lot of the > directions are hand waving. For the newbies, this leads to more > confusion. > > @Berend: I am using OS X. > Then leave out the .exe. And you could always try something! Berend __ 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] Looking for knitr example for beginner (NO RStudio)
Thanks, Simon. I would never figured it out! I apologize if I sound frustrated, because I am. @package author: you have a great package, but I think a lot of the directions are hand waving. For the newbies, this leads to more confusion. @Berend: I am using OS X. Mike On Thu, Jul 18, 2013 at 4:19 PM, Berend Hasselman wrote: > > On 18-07-2013, at 22:09, C W wrote: > >> http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165 >> >> In step 3: "add the executable file (step 3)". >> >> What is the executable file? Locate package knitr directory path in R? >> > > From the window: Executable ==> Program. So the executable is Rscript.exe. > > > Berend > __ 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] Looking for knitr example for beginner (NO RStudio)
On 18-07-2013, at 22:09, C W wrote: > http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165 > > In step 3: "add the executable file (step 3)". > > What is the executable file? Locate package knitr directory path in R? > >From the window: Executable ==> Program. So the executable is Rscript.exe. Berend __ 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] Looking for knitr example for beginner (NO RStudio)
The executable is in case of knitr always Rscript.
On a mac it is simply Rscript on windows it is Rscript.exe. This should be on
your PATH. If you are not sure, open the Mac Terminal and type Rscript
--version. If it does not say "Command not found" all is fine.
Best
Simon
On Jul 18, 2013, at 10:09 PM, C W wrote:
> http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165
>
> In step 3: "add the executable file (step 3)".
>
> What is the executable file? Locate package knitr directory path in R?
>
> Mike
>
> On Thu, Jul 18, 2013 at 3:56 PM, C W wrote:
>> Actually, I see it at the bottom. Sorry!
>>
>> On Thu, Jul 18, 2013 at 3:44 PM, C W wrote:
>>> Hi Simon,
>>> I am on OS X Lion, I have TeXworks, I don't have knitr as an option.
>>>
>>> How do I install that into TeXworks? Seems like I have to something
>>> in terminal?
>>>
>>> Mike
>>>
>>> On Thu, Jul 18, 2013 at 3:31 PM, Simon Zehnder wrote:
Hi Mike,
I found my way with this little blog: http://yihui.name/knitr/demo/editors/
The .Rnw files are created very well in a Latex editor. Everything else
can be easily googled. The command via knitr::knit2pdf works very fine if
you use the chunks. If you are trying to compile an Rtex file, this I do
not know either (I like the symbols though in for example
https://github.com/yihui/knitr-examples/blob/master/005-latex.Rtex). But
the .Rnw files are compiled pretty nice in e.g. texmaker, as described in
the blog. Use for example this source file:
https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw
Hope this helps
Best
Simon
On Jul 18, 2013, at 8:52 PM, C W wrote:
> How do you create a .Rnw file, in R or LaTex? I don't think any
> tutorial mentions it.
>
> btw, I am very new to the terms like markdown, so I don't understand
> "markdown to HTML".
>
> I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
> that you need to compile at terminal. I do not know terminal, is
> there other ways?
>
> Could you do a video on just "simple" R? I have seen 3 videos on R
> Studio including yours.
>
> Mike
>
> On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
>> I'm not sure what your question really is. You do not have to use
>> RStudio, but it will be much easier to get started with RStudio,
>> because it does a lot of automatic conversion behind the scenes (e.g.
>> tex to PDF, markdown to HTML, ...). If you want a "pure" solution
>> without any text editor support, the answer is
>>
>> library(knitr)
>> knit('your_input_file')
>>
>> For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
>> with LaTeX, you can mess with this foo.tex now (outside of R).
>>
>> Minimal examples for different document formats are at
>> http://yihui.name/knitr/demo/minimal/ (you must have read this page),
>> and more examples at https://github.com/yihui/knitr-examples
>>
>> If you are asking about the internals of knitr, "Luke, use the
>> source": https://github.com/yihui/knitr Or for a more comprehensive
>> introduction, see http://www.crcpress.com/product/isbn/9781482203530
>>
>> Regards,
>> Yihui
>> --
>> Yihui Xie
>> Phone: 206-667-4385 Web: http://yihui.name
>> Fred Hutchinson Cancer Research Center, Seattle
>>
>>
>> On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
>>> Hi everyone,
>>>
>>> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>>>
>>> Read through Yihui's page, didn't find it helpful. Stuck on terms
>>> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
>>> reference is not helping.
>>>
>>> Is there a simple step-by-step example WITHOUT RStudio?
>>>
>>> My question:
>>> What is the procedure? The documentation explains the functions, but
>>> does not say how to operate between R and LaTex.
>>>
>>> Mike
>>>
>>> __
>>> 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-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http:/
Re: [R] Looking for knitr example for beginner (NO RStudio)
http://tex.stackexchange.com/questions/85154/knitr-with-texworks/85165#85165
In step 3: "add the executable file (step 3)".
What is the executable file? Locate package knitr directory path in R?
Mike
On Thu, Jul 18, 2013 at 3:56 PM, C W wrote:
> Actually, I see it at the bottom. Sorry!
>
> On Thu, Jul 18, 2013 at 3:44 PM, C W wrote:
>> Hi Simon,
>> I am on OS X Lion, I have TeXworks, I don't have knitr as an option.
>>
>> How do I install that into TeXworks? Seems like I have to something
>> in terminal?
>>
>> Mike
>>
>> On Thu, Jul 18, 2013 at 3:31 PM, Simon Zehnder wrote:
>>> Hi Mike,
>>>
>>> I found my way with this little blog: http://yihui.name/knitr/demo/editors/
>>>
>>> The .Rnw files are created very well in a Latex editor. Everything else can
>>> be easily googled. The command via knitr::knit2pdf works very fine if you
>>> use the chunks. If you are trying to compile an Rtex file, this I do not
>>> know either (I like the symbols though in for example
>>> https://github.com/yihui/knitr-examples/blob/master/005-latex.Rtex). But
>>> the .Rnw files are compiled pretty nice in e.g. texmaker, as described in
>>> the blog. Use for example this source file:
>>> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw
>>>
>>>
>>> Hope this helps
>>>
>>>
>>> Best
>>>
>>> Simon
>>>
>>>
>>>
>>>
>>>
>>> On Jul 18, 2013, at 8:52 PM, C W wrote:
>>>
How do you create a .Rnw file, in R or LaTex? I don't think any
tutorial mentions it.
btw, I am very new to the terms like markdown, so I don't understand
"markdown to HTML".
I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
that you need to compile at terminal. I do not know terminal, is
there other ways?
Could you do a video on just "simple" R? I have seen 3 videos on R
Studio including yours.
Mike
On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
> I'm not sure what your question really is. You do not have to use
> RStudio, but it will be much easier to get started with RStudio,
> because it does a lot of automatic conversion behind the scenes (e.g.
> tex to PDF, markdown to HTML, ...). If you want a "pure" solution
> without any text editor support, the answer is
>
> library(knitr)
> knit('your_input_file')
>
> For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
> with LaTeX, you can mess with this foo.tex now (outside of R).
>
> Minimal examples for different document formats are at
> http://yihui.name/knitr/demo/minimal/ (you must have read this page),
> and more examples at https://github.com/yihui/knitr-examples
>
> If you are asking about the internals of knitr, "Luke, use the
> source": https://github.com/yihui/knitr Or for a more comprehensive
> introduction, see http://www.crcpress.com/product/isbn/9781482203530
>
> Regards,
> Yihui
> --
> Yihui Xie
> Phone: 206-667-4385 Web: http://yihui.name
> Fred Hutchinson Cancer Research Center, Seattle
>
>
> On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
>> Hi everyone,
>>
>> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>>
>> Read through Yihui's page, didn't find it helpful. Stuck on terms
>> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
>> reference is not helping.
>>
>> Is there a simple step-by-step example WITHOUT RStudio?
>>
>> My question:
>> What is the procedure? The documentation explains the functions, but
>> does not say how to operate between R and LaTex.
>>
>> Mike
>>
>> __
>> 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-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] Looking for knitr example for beginner (NO RStudio)
Actually, I see it at the bottom. Sorry!
On Thu, Jul 18, 2013 at 3:44 PM, C W wrote:
> Hi Simon,
> I am on OS X Lion, I have TeXworks, I don't have knitr as an option.
>
> How do I install that into TeXworks? Seems like I have to something
> in terminal?
>
> Mike
>
> On Thu, Jul 18, 2013 at 3:31 PM, Simon Zehnder wrote:
>> Hi Mike,
>>
>> I found my way with this little blog: http://yihui.name/knitr/demo/editors/
>>
>> The .Rnw files are created very well in a Latex editor. Everything else can
>> be easily googled. The command via knitr::knit2pdf works very fine if you
>> use the chunks. If you are trying to compile an Rtex file, this I do not
>> know either (I like the symbols though in for example
>> https://github.com/yihui/knitr-examples/blob/master/005-latex.Rtex). But the
>> .Rnw files are compiled pretty nice in e.g. texmaker, as described in the
>> blog. Use for example this source file:
>> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw
>>
>>
>> Hope this helps
>>
>>
>> Best
>>
>> Simon
>>
>>
>>
>>
>>
>> On Jul 18, 2013, at 8:52 PM, C W wrote:
>>
>>> How do you create a .Rnw file, in R or LaTex? I don't think any
>>> tutorial mentions it.
>>>
>>> btw, I am very new to the terms like markdown, so I don't understand
>>> "markdown to HTML".
>>>
>>> I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
>>> that you need to compile at terminal. I do not know terminal, is
>>> there other ways?
>>>
>>> Could you do a video on just "simple" R? I have seen 3 videos on R
>>> Studio including yours.
>>>
>>> Mike
>>>
>>> On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
I'm not sure what your question really is. You do not have to use
RStudio, but it will be much easier to get started with RStudio,
because it does a lot of automatic conversion behind the scenes (e.g.
tex to PDF, markdown to HTML, ...). If you want a "pure" solution
without any text editor support, the answer is
library(knitr)
knit('your_input_file')
For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
with LaTeX, you can mess with this foo.tex now (outside of R).
Minimal examples for different document formats are at
http://yihui.name/knitr/demo/minimal/ (you must have read this page),
and more examples at https://github.com/yihui/knitr-examples
If you are asking about the internals of knitr, "Luke, use the
source": https://github.com/yihui/knitr Or for a more comprehensive
introduction, see http://www.crcpress.com/product/isbn/9781482203530
Regards,
Yihui
--
Yihui Xie
Phone: 206-667-4385 Web: http://yihui.name
Fred Hutchinson Cancer Research Center, Seattle
On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
> Hi everyone,
>
> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>
> Read through Yihui's page, didn't find it helpful. Stuck on terms
> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
> reference is not helping.
>
> Is there a simple step-by-step example WITHOUT RStudio?
>
> My question:
> What is the procedure? The documentation explains the functions, but
> does not say how to operate between R and LaTex.
>
> Mike
>
> __
> 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-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] Looking for knitr example for beginner (NO RStudio)
Hi Simon,
I am on OS X Lion, I have TeXworks, I don't have knitr as an option.
How do I install that into TeXworks? Seems like I have to something
in terminal?
Mike
On Thu, Jul 18, 2013 at 3:31 PM, Simon Zehnder wrote:
> Hi Mike,
>
> I found my way with this little blog: http://yihui.name/knitr/demo/editors/
>
> The .Rnw files are created very well in a Latex editor. Everything else can
> be easily googled. The command via knitr::knit2pdf works very fine if you use
> the chunks. If you are trying to compile an Rtex file, this I do not know
> either (I like the symbols though in for example
> https://github.com/yihui/knitr-examples/blob/master/005-latex.Rtex). But the
> .Rnw files are compiled pretty nice in e.g. texmaker, as described in the
> blog. Use for example this source file:
> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw
>
>
> Hope this helps
>
>
> Best
>
> Simon
>
>
>
>
>
> On Jul 18, 2013, at 8:52 PM, C W wrote:
>
>> How do you create a .Rnw file, in R or LaTex? I don't think any
>> tutorial mentions it.
>>
>> btw, I am very new to the terms like markdown, so I don't understand
>> "markdown to HTML".
>>
>> I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
>> that you need to compile at terminal. I do not know terminal, is
>> there other ways?
>>
>> Could you do a video on just "simple" R? I have seen 3 videos on R
>> Studio including yours.
>>
>> Mike
>>
>> On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
>>> I'm not sure what your question really is. You do not have to use
>>> RStudio, but it will be much easier to get started with RStudio,
>>> because it does a lot of automatic conversion behind the scenes (e.g.
>>> tex to PDF, markdown to HTML, ...). If you want a "pure" solution
>>> without any text editor support, the answer is
>>>
>>> library(knitr)
>>> knit('your_input_file')
>>>
>>> For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
>>> with LaTeX, you can mess with this foo.tex now (outside of R).
>>>
>>> Minimal examples for different document formats are at
>>> http://yihui.name/knitr/demo/minimal/ (you must have read this page),
>>> and more examples at https://github.com/yihui/knitr-examples
>>>
>>> If you are asking about the internals of knitr, "Luke, use the
>>> source": https://github.com/yihui/knitr Or for a more comprehensive
>>> introduction, see http://www.crcpress.com/product/isbn/9781482203530
>>>
>>> Regards,
>>> Yihui
>>> --
>>> Yihui Xie
>>> Phone: 206-667-4385 Web: http://yihui.name
>>> Fred Hutchinson Cancer Research Center, Seattle
>>>
>>>
>>> On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
Hi everyone,
I am using package knitr, FIRST TIME. I don't have access to RStudio.
Read through Yihui's page, didn't find it helpful. Stuck on terms
Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
reference is not helping.
Is there a simple step-by-step example WITHOUT RStudio?
My question:
What is the procedure? The documentation explains the functions, but
does not say how to operate between R and LaTex.
Mike
__
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-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] Looking for knitr example for beginner (NO RStudio)
Hi Mike,
I found my way with this little blog: http://yihui.name/knitr/demo/editors/
The .Rnw files are created very well in a Latex editor. Everything else can be
easily googled. The command via knitr::knit2pdf works very fine if you use the
chunks. If you are trying to compile an Rtex file, this I do not know either (I
like the symbols though in for example
https://github.com/yihui/knitr-examples/blob/master/005-latex.Rtex). But the
.Rnw files are compiled pretty nice in e.g. texmaker, as described in the blog.
Use for example this source file:
https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw
Hope this helps
Best
Simon
On Jul 18, 2013, at 8:52 PM, C W wrote:
> How do you create a .Rnw file, in R or LaTex? I don't think any
> tutorial mentions it.
>
> btw, I am very new to the terms like markdown, so I don't understand
> "markdown to HTML".
>
> I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
> that you need to compile at terminal. I do not know terminal, is
> there other ways?
>
> Could you do a video on just "simple" R? I have seen 3 videos on R
> Studio including yours.
>
> Mike
>
> On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
>> I'm not sure what your question really is. You do not have to use
>> RStudio, but it will be much easier to get started with RStudio,
>> because it does a lot of automatic conversion behind the scenes (e.g.
>> tex to PDF, markdown to HTML, ...). If you want a "pure" solution
>> without any text editor support, the answer is
>>
>> library(knitr)
>> knit('your_input_file')
>>
>> For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
>> with LaTeX, you can mess with this foo.tex now (outside of R).
>>
>> Minimal examples for different document formats are at
>> http://yihui.name/knitr/demo/minimal/ (you must have read this page),
>> and more examples at https://github.com/yihui/knitr-examples
>>
>> If you are asking about the internals of knitr, "Luke, use the
>> source": https://github.com/yihui/knitr Or for a more comprehensive
>> introduction, see http://www.crcpress.com/product/isbn/9781482203530
>>
>> Regards,
>> Yihui
>> --
>> Yihui Xie
>> Phone: 206-667-4385 Web: http://yihui.name
>> Fred Hutchinson Cancer Research Center, Seattle
>>
>>
>> On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
>>> Hi everyone,
>>>
>>> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>>>
>>> Read through Yihui's page, didn't find it helpful. Stuck on terms
>>> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
>>> reference is not helping.
>>>
>>> Is there a simple step-by-step example WITHOUT RStudio?
>>>
>>> My question:
>>> What is the procedure? The documentation explains the functions, but
>>> does not say how to operate between R and LaTex.
>>>
>>> Mike
>>>
>>> __
>>> 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-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] 'save' method for S4 class
Hi Christofer,
R's S4 class system builds on generics, that is one class defines the raw frame
of a function and maybe an own distinct implementation and other classes, that
(usually) inherit from this class, set their special implementations of it.
Consider a generic function in R as being an abstract function, just telling
inheriting classes how to build such a function, i.e. what to put in.
Furthermore it enables the dispatches like callNextMethod, which calls the
method from the parent (be aware if you have more than one direct parent!).
Under the hood, R must know from the input arguments what function should be
called. If you put in an B class that inherits from an A class it must know,
what to do with a user-defined "save" function when the input argument is for
example an object of class "B". If you put in an "A" class object, it should
know how to proceed this object and so on. So the generic method gives a kind
of internal map for R how to call this function in which contexts.
The standardGeneric() function: We must provide a name and a definition of the
generic function. In most cases you just want to tell, what arguments the
function should expect. With the function standardGeneric("name") R creates a
generic which can then be dispatched in form of distinct methods. So if you
call "save" R sees, that it is a generic function and checks which of the
distinct functions to call, evaluating the arguments. If it finds no specific
function for the arguments at hand, it calls a default function. If, as in your
case, the function name is already taken, R sets, when you use setGeneric, the
usual "save" function as the default method, getting called when nothing else
fits ... resulting in either an error because of mismatching function arguments
or in saving in a way you do not want to. Solution is here to define inside the
setGeneric also the default function via the argument useAsDefault = function()
{}.
So generic function (setGeneric): What should be done?
Distinct function (setMethod): How should it be done?
You find a very good introduction to the S4 class system here:
http://cran.r-project.org/doc/contrib/Genolini-S4tutorialV0-5en.pdf
Deep down information can be found for example in the books: "Programming with
Data" and "Software for Data Analysis and Computing with R", both from John
Chambers.
Best
Simon
On Jul 18, 2013, at 8:23 PM, Christofer Bogaso
wrote:
> Hi Simon,
>
> Thanks for your pointer.
>
> However could you please explain what 'function(x, file_Path)
> standardGeneric("save")' means here? The underlying help files look quite
> rocket science for me!
>
> Thanks for your time.
>
> Thanks and regards,
>
>
> On Thu, Jul 18, 2013 at 4:32 PM, Simon Zehnder wrote:
> Hi Christopher,
>
> I think, that "save" is no generic function like "plot", "show", etc. So at
> first you have to determine a generic.
>
> setGeneric("save", function(x, file_Path) standardGeneric("save"))
>
> Now your definition via setMethod.
>
>
> Best
>
> Simon
>
>
>
> On Jul 18, 2013, at 12:09 PM, Christofer Bogaso
> wrote:
>
> > Hello again,
> >
> > I am trying to define the 'save' method for my S4 class as below:
> >
> > setClass("MyClass", representation(
> > Slot1 = "data.frame"
> > ))
> >
> > setMethod("save", "MyClass", definition = function(x, file_Path) {
> >
> > write.table(x@Slot1, file = file_Path, append = FALSE, quote
> > = TRUE,
> > sep = ",",
> > eol = "\n", na = "NA", dec =
> > ".", row.names = FALSE,
> > col.names = TRUE, qmethod =
> > c("escape", "double"),
> > fileEncoding = "")
> > })
> >
> > However while doing this I am getting following error:
> >
> > Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
> > in method for save with signature list="MyClass": formal
> > arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
> > version = "MyClass", envir = "MyClass", compress = "MyClass",
> > compression_level = "MyClass", eval.promises = "MyClass", precheck =
> > "MyClass") omitted in the method definition cannot be in the signature
> >
> >
> > Can somebody point me what will be the correct approach to define
> > 'save' method for S4 class?
> >
> > Thanks and regards,
> >
> > __
> > 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 co
Re: [R] Difference between arima(1, 1, 1) of y and arima(1, 0, 1) of diff(y)
Hi Mark, This is very helpful!! Much appreciated Sent from my iPad On Jul 19, 2013, at 3:51 AM, Mark Leeds wrote: > Hi George: Assuming it's still relevant, the link below will explain why. > > http://www.stat.pitt.edu/stoffer/tsa2/Rissues.htm > > > > On Thu, Jul 18, 2013 at 2:14 PM, George Milunovich > wrote: >> Dear all, >> When I run an arima(1,1,1) on an I(1) variable, y, I get different estimates >> to when I first difference the variable myself, e.g y2<-diff(y), and then >> run arima(1,0,1) on y2. Shouldn't these two approaches give the same output? >> Any help will be much appreciated. >> george >> >> __ >> 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.
[R] extracting variance and covariance
Hi,
I am not able to extract variance and covariance
As mentioned, there are 5 stocks and changed the code [
http://www.forecastingfinancialrisk.com/3.html] as follows:
> S<-cov(returns)
> S
V1 V2 V3 V4 V5
V1 0.0004951526 0.0001256519 0.0001651016 0.0003024310 0.0003516796
V2 0.0001256519 0.0008076471 0.0001251208 0.0002005305 0.0002347568
V3 0.0001651016 0.0001251208 0.001707 0.0003158028 0.0003682633
V4 0.0003024310 0.0002005305 0.0003158028 0.0011405561 0.0008442661
V5 0.0003516796 0.0002347568 0.0003682633 0.0008442661 0.0018536153
> EWMA[1,]<-c(S)[c(1,10,5)]
> a=t(as.numeric(returns$i)) %*% as.numeric(returns$i) ---*Here we need
to change dataframe to numeric, that too only columns.*
> str(a)
num [1, 1] 0
> dim(a)
[1] 1 1
> dim(lambda*S)
[1] 5 5 -*As the dimensions are not same we can not do
%*%*
> dim((1-lambda)*a)
[1] 1 1
for(i in 2:T)
{
S<- lambda*S+ (1-lambda)*t(returns$i) %*% returns$i
EWMA[i,]=c(S)[c(1,4,2)]
}
*Original code as per* http://www.forecastingfinancialrisk.com/3.html is
EWMA = *matrix*(*nrow*=T,*ncol*=3) *# create a matrix to hold the
covariance matrix for each t*
lambda = 0.94
S = *cov*(y) *# initial (t=1) covariance matrix*
EWMA[1,] = *c*(S)[*c*(1,4,2)] *# extract the variances and covariance*
*for* (i *in* 2:T){*# loop though the sample*
S = lambda * S + (1-lambda) * *t*(y[i]) %*% y[i]
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[R] Principal component / EOF analysis of data dominated by a couple frequencies
Hi R folk, I have a time series of scalar downstream velocity data measured across a tidal channel. The variables are the locations in bins across the channel, the samples are over time. The fluctuation over the tide cycle is an enormous fraction of the time variation in the data ... 96%. The spectral energy of the tide is concentrated in a couple bands that make up the major constituents of the tide. Over short periods, we could pretend there are just two frequencies, though they are really clusters of nearby frequencies that start to diverge as the record gets long. Tidal frequencies also beat which causes monthly/14-day "spring-neap" cycles with greatly accentuated or attenuated inequalities between high tide and low tide. Despite the dominance of the tide, there is variation across the channel that is of interest. A good physical interpretation of what is happening is not just that amplitude varies across the channel but that the phase on the edge of the channel gets in and out of shape. So a data description that could characterize short-medium duration anomalies in relative phase would be really useful and hints at some sort of complex analysis. These may be excited by the spring-neap cycle, and my concern with spectral PC analysis that isolates a single band would be that it might miss that. Here are the questions: 1. Is there a variant of PC (or other) analysis in R can characterize this type of variation well? 2. Should I sweat the way a simple time fluctuation dominates the series? I don't object to having a big PC1, but it doesn't fit the textbook examples very well. Are there techniques (rotation, normalization) that are designed for this situation? I seem to run into it in all sorts of applications. Thanks, Eli [[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] cut into groups of equal nr of elements...
Here's one way:
Vec <- rnorm(30)
Vec.cut <- cut(Vec, breaks=c(quantile(Vec, probs = seq(0, 1, by = 0.20))),
labels=c("0-20","20-40","40-60","60-80","80-100"), include.lowest=TRUE)
table(Vec.cut)
or determine the breaks automatically:
cut.size <- function(x, size) {
cut.prob <- size/length(x)
if (length(x)%%size != 0) warning("Equal sized groups only possible
by dropping some elements from x")
Vec.cut <- cut(x, breaks=c(quantile(x, probs = seq(0, 1, by =
size/length(x, include.lowest=TRUE)
}
CUT <- cut.size(Vec, 6)
table(CUT)
When asking for
cut.size(Vec, 7)
this will yield 4 equal-sized groups of 7, because there is no way to
perfectly split 30 observations in groups of 7 each.
HTH,
Peter
Op 18-7-2013 18:09, Marc Schwartz schreef:
Greg,
Good catch. My recollection was that the vector would be broken up into
'breaks' groups of equal size, however it is range(x) that is split into
'breaks' intervals, each of which is equal width.
Thanks,
Marc
On Jul 18, 2013, at 10:55 AM, Greg Snow <538...@gmail.com> wrote:
Marc,
Your method works fine when the data is perfectly uniform, but try it with "Vec <-
rnorm(30)" and you will see that there are more observations in the middle groups and
fewer in the tail groups. Something like quantile needs to be used to find the unequally
spaced breaks that will give equal counts within groups.
On Wed, Jul 17, 2013 at 5:04 PM, Marc Schwartz wrote:
On Jul 17, 2013, at 4:43 PM, Witold E Wolski wrote:
I would like to "cut" a vector into groups of equal nr of elements.
looking for a function on the lines of cut but where I can specify
the size of the groups instead of the nr of groups.
In addition to the other options, if the 'breaks' argument to cut() is a single
number, rather than a vector of cut points, it defines the number of intervals
to break the 'x' vector into, which of course you can derive from length(x) /
size.
Thus:
set.seed(1)
Vec <- sample(30)
Vec
[1] 8 11 17 25 6 23 27 16 14 2 5 4 13 7 18 30 29 24 20 9 10 21
[23] 26 1 22 15 28 12 3 19
# Split into 5 groups of 6 each
split(Vec, cut(Vec, 5))
$`(0.971,6.78]`
[1] 6 2 5 4 1 3
$`(6.78,12.6]`
[1] 8 11 7 9 10 12
$`(12.6,18.4]`
[1] 17 16 14 13 18 15
$`(18.4,24.2]`
[1] 23 24 20 21 22 19
$`(24.2,30]`
[1] 25 27 30 29 26 28
Regards,
Marc Schwartz
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--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com
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Re: [R] Looking for knitr example for beginner (NO RStudio)
How do you create a .Rnw file, in R or LaTex? I don't think any
tutorial mentions it.
btw, I am very new to the terms like markdown, so I don't understand
"markdown to HTML".
I am reading here http://biostat.mc.vanderbilt.edu/wiki/Main/KnitrHowto
that you need to compile at terminal. I do not know terminal, is
there other ways?
Could you do a video on just "simple" R? I have seen 3 videos on R
Studio including yours.
Mike
On Thu, Jul 18, 2013 at 2:43 PM, Yihui Xie wrote:
> I'm not sure what your question really is. You do not have to use
> RStudio, but it will be much easier to get started with RStudio,
> because it does a lot of automatic conversion behind the scenes (e.g.
> tex to PDF, markdown to HTML, ...). If you want a "pure" solution
> without any text editor support, the answer is
>
> library(knitr)
> knit('your_input_file')
>
> For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
> with LaTeX, you can mess with this foo.tex now (outside of R).
>
> Minimal examples for different document formats are at
> http://yihui.name/knitr/demo/minimal/ (you must have read this page),
> and more examples at https://github.com/yihui/knitr-examples
>
> If you are asking about the internals of knitr, "Luke, use the
> source": https://github.com/yihui/knitr Or for a more comprehensive
> introduction, see http://www.crcpress.com/product/isbn/9781482203530
>
> Regards,
> Yihui
> --
> Yihui Xie
> Phone: 206-667-4385 Web: http://yihui.name
> Fred Hutchinson Cancer Research Center, Seattle
>
>
> On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
>> Hi everyone,
>>
>> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>>
>> Read through Yihui's page, didn't find it helpful. Stuck on terms
>> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
>> reference is not helping.
>>
>> Is there a simple step-by-step example WITHOUT RStudio?
>>
>> My question:
>> What is the procedure? The documentation explains the functions, but
>> does not say how to operate between R and LaTex.
>>
>> Mike
>>
>> __
>> 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] Difference between arima(1, 1, 1) of y and arima(1, 0, 1) of diff(y)
Hi George: Assuming it's still relevant, the link below will explain why. http://www.stat.pitt.edu/stoffer/tsa2/Rissues.htm On Thu, Jul 18, 2013 at 2:14 PM, George Milunovich < george.milunov...@mq.edu.au> wrote: > Dear all, > When I run an arima(1,1,1) on an I(1) variable, y, I get different > estimates to when I first difference the variable myself, e.g y2<-diff(y), > and then run arima(1,0,1) on y2. Shouldn't these two approaches give the > same output? > Any help will be much appreciated. > george > > __ > 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.
[R] Difference between arima(1, 1, 1) for y and arima(1, 0, 1) for diff(y)
Dear all, When I run an arima(1,1,1) on an I(1) variable, e.g. y, I get different estimates to when I first difference the variable myself, e.g y2<-diff(y), and then run arima(1,0,1) on y2. Shouldn't these two approaches give the same output? Any help will be much appreciated. george -- View this message in context: http://r.789695.n4.nabble.com/Difference-between-arima-1-1-1-for-y-and-arima-1-0-1-for-diff-y-tp4671873.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] Looking for knitr example for beginner (NO RStudio)
I'm not sure what your question really is. You do not have to use
RStudio, but it will be much easier to get started with RStudio,
because it does a lot of automatic conversion behind the scenes (e.g.
tex to PDF, markdown to HTML, ...). If you want a "pure" solution
without any text editor support, the answer is
library(knitr)
knit('your_input_file')
For example, knit('foo.Rnw') gives you foo.tex; if you are familiar
with LaTeX, you can mess with this foo.tex now (outside of R).
Minimal examples for different document formats are at
http://yihui.name/knitr/demo/minimal/ (you must have read this page),
and more examples at https://github.com/yihui/knitr-examples
If you are asking about the internals of knitr, "Luke, use the
source": https://github.com/yihui/knitr Or for a more comprehensive
introduction, see http://www.crcpress.com/product/isbn/9781482203530
Regards,
Yihui
--
Yihui Xie
Phone: 206-667-4385 Web: http://yihui.name
Fred Hutchinson Cancer Research Center, Seattle
On Thu, Jul 18, 2013 at 11:13 AM, C W wrote:
> Hi everyone,
>
> I am using package knitr, FIRST TIME. I don't have access to RStudio.
>
> Read through Yihui's page, didn't find it helpful. Stuck on terms
> Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the
> reference is not helping.
>
> Is there a simple step-by-step example WITHOUT RStudio?
>
> My question:
> What is the procedure? The documentation explains the functions, but
> does not say how to operate between R and LaTex.
>
> Mike
>
> __
> 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] 'save' method for S4 class
Hi Simon,
Thanks for your pointer.
However could you please explain what 'function(x, file_Path)
standardGeneric("save")' means here? The underlying help files look quite
rocket science for me!
Thanks for your time.
Thanks and regards,
On Thu, Jul 18, 2013 at 4:32 PM, Simon Zehnder wrote:
> Hi Christopher,
>
> I think, that "save" is no generic function like "plot", "show", etc. So
> at first you have to determine a generic.
>
> setGeneric("save", function(x, file_Path) standardGeneric("save"))
>
> Now your definition via setMethod.
>
>
> Best
>
> Simon
>
>
>
> On Jul 18, 2013, at 12:09 PM, Christofer Bogaso <
> bogaso.christo...@gmail.com> wrote:
>
> > Hello again,
> >
> > I am trying to define the 'save' method for my S4 class as below:
> >
> > setClass("MyClass", representation(
> > Slot1 = "data.frame"
> > ))
> >
> > setMethod("save", "MyClass", definition = function(x, file_Path) {
> >
> > write.table(x@Slot1, file = file_Path, append = FALSE,
> quote = TRUE,
> > sep = ",",
> > eol = "\n", na = "NA", dec
> = ".", row.names = FALSE,
> > col.names = TRUE, qmethod
> = c("escape", "double"),
> > fileEncoding = "")
> > })
> >
> > However while doing this I am getting following error:
> >
> > Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
> > in method for save with signature list="MyClass": formal
> > arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
> > version = "MyClass", envir = "MyClass", compress = "MyClass",
> > compression_level = "MyClass", eval.promises = "MyClass", precheck =
> > "MyClass") omitted in the method definition cannot be in the signature
> >
> >
> > Can somebody point me what will be the correct approach to define
> > 'save' method for S4 class?
> >
> > Thanks and regards,
> >
> > __
> > 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] restrected arima models
Thanks Sent from my iPhone On 19/07/2013, at 1:43 AM, "Prof Brian Ripley [via R]" wrote: > On 18/07/2013 16:14, george wrote: > > Dear all, > > Does anyone know if it is possible to estimate restricted arima models > > using > > the arima command in R? For instance lets say I want arima(6,0,0) but where > > the first three ar parameters are restricted to zero, ie. ar(1)=ar(2)=ar(3) > > = 0, and only the last three are actually estimated. > > Yes. > > > Any help will be much appreciated. > > Have you read the help page? Someone helped you by writing it (and > indeed, by providing the facility, which few ARIMA-fitting programs have). > > fixed: optional numeric vector of the same length as the total >number of parameters. If supplied, only âNAâ entries in >âfixedâ will be varied. âtransform.pars = TRUEâ will be >overridden (with a warning) if any AR parameters are fixed. > > E.g. > > x <- rnorm(100) > arima(x, order=c(6,0,0), fixed = c(0,0,0,NA,NA,NA,NA)) > > Coefficients: >ar1 ar2 ar3 ar4 ar5 ar6 intercept > 000 0.0423 0.0977 0.1299-0.1462 > s.e.000 0.1065 0.1075 0.1059 0.1323 > > > > george > > > > -- > Brian D. Ripley, [hidden email] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UKFax: +44 1865 272595 > > __ > [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. > > > If you reply to this email, your message will be added to the discussion > below: > http://r.789695.n4.nabble.com/restrected-arima-models-tp4671847p4671862.html > To unsubscribe from restrected arima models, click here. > NAML -- View this message in context: http://r.789695.n4.nabble.com/restrected-arima-models-tp4671847p4671867.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Difference between arima(1, 1, 1) of y and arima(1, 0, 1) of diff(y)
Dear all, When I run an arima(1,1,1) on an I(1) variable, y, I get different estimates to when I first difference the variable myself, e.g y2<-diff(y), and then run arima(1,0,1) on y2. Shouldn't these two approaches give the same output? Any help will be much appreciated. george __ 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] Looking for knitr example for beginner (NO RStudio)
Hi everyone, I am using package knitr, FIRST TIME. I don't have access to RStudio. Read through Yihui's page, didn't find it helpful. Stuck on terms Rnw, GFM (GitHub Flavored Markdown). Never used Sweave, so the reference is not helping. Is there a simple step-by-step example WITHOUT RStudio? My question: What is the procedure? The documentation explains the functions, but does not say how to operate between R and LaTex. Mike __ 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] Changing settings
On Jul 18, 2013, at 9:02 AM, Jason wrote: > How do I change my email settings? I would like to limit the emails that I > receive to only those of interest. > You can use various search engines. I like the MarkMail option. It allows me to search in various r-related groups. If you wnat to run it daily with a particular set of filters, that should be possible to automate. http://markmail.org/search/?q=list%3Aorg.r-project -- David Winsemius Alameda, CA, USA __ 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] restrected arima models
On 18/07/2013 16:14, george wrote: Dear all, Does anyone know if it is possible to estimate restricted arima models using the arima command in R? For instance lets say I want arima(6,0,0) but where the first three ar parameters are restricted to zero, ie. ar(1)=ar(2)=ar(3) = 0, and only the last three are actually estimated. Yes. Any help will be much appreciated. Have you read the help page? Someone helped you by writing it (and indeed, by providing the facility, which few ARIMA-fitting programs have). fixed: optional numeric vector of the same length as the total number of parameters. If supplied, only ‘NA’ entries in ‘fixed’ will be varied. ‘transform.pars = TRUE’ will be overridden (with a warning) if any AR parameters are fixed. E.g. x <- rnorm(100) arima(x, order=c(6,0,0), fixed = c(0,0,0,NA,NA,NA,NA)) Coefficients: ar1 ar2 ar3 ar4 ar5 ar6 intercept 000 0.0423 0.0977 0.1299-0.1462 s.e.000 0.1065 0.1075 0.1059 0.1323 george -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-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] restrected arima models
Hello,
Take a look at parameter 'fixed' of function arima. From the help page
for arima():
"fixed
optional numeric vector of the same length as the total number of
parameters. If supplied, only NA entries in fixed will be varied."
Example use ('fixed' has length 7 because we must count the intercept term):
x <- ts(cumsum(rnorm(100)))
fit <- arima(x, order = c(6,0,0), fixed = c(0, 0, 0, NA, NA, NA, NA),
transform.pars = FALSE)
fit
Hope this helps,
Rui Barradas
Em 18-07-2013 16:14, george escreveu:
Dear all,
Does anyone know if it is possible to estimate restricted arima models using
the arima command in R? For instance lets say I want arima(6,0,0) but where
the first three ar parameters are restricted to zero, ie. ar(1)=ar(2)=ar(3)
= 0, and only the last three are actually estimated.
Any help will be much appreciated.
george
--
View this message in context:
http://r.789695.n4.nabble.com/restrected-arima-models-tp4671847.html
Sent from the R help mailing list archive at Nabble.com.
__
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Changing settings
Go to Settings | Filters in Gmail and set filters to delete the r-help messages you don't want or move them to a folder for review. R-help messages are not tagged so you cannot restrict them before they are sent. - David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jason Sent: Thursday, July 18, 2013 11:03 AM To: R-help@r-project.org Subject: [R] Changing settings How do I change my email settings? I would like to limit the emails that I receive to only those of interest. __ 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] panel setting
I am guessing that you are trying to use the densityplot function from the lattice package (if you had followed the posting guidelines and told us which package you were using, then we would not need to guess). If that is the case then you are trying to mix base graphics (mfrow) and grid graphics (densityplot) and the 2 do not play nicely together (without extra effort). One option would be to use only base graphics and plot the pairs of densities yourself using plot, lines, density, and maybe other functions. Probably a little bit better is to use only lattice tools, see the help page ?print.trellis and specifically the split and more arguments for how to put multiple trellis plots onto a single page. You could mix the 2 using the gridBase package, but that is probably way more work than needed for this. You could also investigate the ggplot2 package which may make this easier using grid graphics. On Thu, Jul 18, 2013 at 1:04 AM, meng wrote: > Hi all: > My data: > f1 f2 f3 f4 y > 1 -4.45 3 6.44 3.721 > 2 25.66 121 39.03 3.55 0 > 3 -9.75 12 11.77 3.40 1 > 4 -12.09 17 13.75 3.33 0 > 5 -3.53 4 6.47 3.24 0 > 6 13.18 69 26.55 3.201 > ... ... > I want to plot f1 for y=0 and 1; f2 for y=0 and 1...and the same as f3,f4. > And I want to get 4 plots at once(2*2) > > My code: > par(mfrow=c(2,2)) > densityplot(~f1,data=dat,group=y,auto.key=T) > densityplot(~f2,data=dat,group=y,auto.key=T) > densityplot(~f3,data=dat,group=y,auto.key=T) > densityplot(~f4,data=dat,group=y,auto.key=T) > > The result is not what I want,since it produce 1 plot a time,but not 4 > plots together(2*2). > Maybe something wrong with par(mfrow=c(2,2))? > Any suggestion? Many thanks! > > Best. > [[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. > -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Changing settings
How do I change my email settings? I would like to limit the emails that I receive to only those of interest. __ 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] cut into groups of equal nr of elements...
Greg, Good catch. My recollection was that the vector would be broken up into 'breaks' groups of equal size, however it is range(x) that is split into 'breaks' intervals, each of which is equal width. Thanks, Marc On Jul 18, 2013, at 10:55 AM, Greg Snow <538...@gmail.com> wrote: > Marc, > > Your method works fine when the data is perfectly uniform, but try it with > "Vec <- rnorm(30)" and you will see that there are more observations in the > middle groups and fewer in the tail groups. Something like quantile needs to > be used to find the unequally spaced breaks that will give equal counts > within groups. > > > On Wed, Jul 17, 2013 at 5:04 PM, Marc Schwartz wrote: > On Jul 17, 2013, at 4:43 PM, Witold E Wolski wrote: > > > I would like to "cut" a vector into groups of equal nr of elements. > > looking for a function on the lines of cut but where I can specify > > the size of the groups instead of the nr of groups. > > > > In addition to the other options, if the 'breaks' argument to cut() is a > single number, rather than a vector of cut points, it defines the number of > intervals to break the 'x' vector into, which of course you can derive from > length(x) / size. > > Thus: > > set.seed(1) > Vec <- sample(30) > > > Vec > [1] 8 11 17 25 6 23 27 16 14 2 5 4 13 7 18 30 29 24 20 9 10 21 > [23] 26 1 22 15 28 12 3 19 > > > # Split into 5 groups of 6 each > > > split(Vec, cut(Vec, 5)) > $`(0.971,6.78]` > [1] 6 2 5 4 1 3 > > $`(6.78,12.6]` > [1] 8 11 7 9 10 12 > > $`(12.6,18.4]` > [1] 17 16 14 13 18 15 > > $`(18.4,24.2]` > [1] 23 24 20 21 22 19 > > $`(24.2,30]` > [1] 25 27 30 29 26 28 > > > Regards, > > Marc Schwartz > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > > -- > Gregory (Greg) L. Snow Ph.D. > 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Orders of levels affecting wilcox.test() output
The p-value and inference is the same, the only difference that I see is
the value of the W statistic. The definition of the W statistic (as
discussed in the Note section on the help page) is based on the sum of the
ranks in the **First** group, so if you change which group is first then
you should expect the W statistic to change. As long as the inference does
not change, why worry about it?
On Thu, Jul 18, 2013 at 3:18 AM, Alastair Potts wrote:
> Good day all,
>
> My first posting to this list. It looked like the best place to post this
> question.
>
> When running the wilcox.test(), I noticed that the output values change if
> you change the ordering of the levels (example below which includes a
> t.test for comparison). I think this has something to do with the change in
> ranking order, but this doesn't make much sense as I would expect the
> ranking in this case to remain constant as there are no ties. So my
> questions are: a) is this correct (i.e. not a bug)?, and b) if it is, then
> which values should I report?
>
>
> x <- cbind(data.frame((c(rep("A",50),rep("B",50,runif(100))
> colnames(x) <- c("a","b")
> wilcox.test(b~a,data=x)
> t.test(b~a,data=x)
> x$a <- relevel(x$a,ref="B")
> wilcox.test(b~a,data=x)
> t.test(b~a,data=x)
>
> Thank you in advance for your time,
> Regards,
> Alastair
>
> [[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.
>
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] cut into groups of equal nr of elements...
my fault. qcut() is a python function in pandas ;-) what i meant is cut2() in hmisc. sorry for messing up. On Jul 18, 2013 11:51 AM, "Greg Snow" <538...@gmail.com> wrote: > Wensui, > > ?qcut on my machine gives an error and ??qcut does not find anything in > the installed packages. Which package is qcut in? > > > On Wed, Jul 17, 2013 at 4:43 PM, Wensui Liu wrote: > >> ?qcut >> On Jul 17, 2013 5:45 PM, "Witold E Wolski" wrote: >> >> > I would like to "cut" a vector into groups of equal nr of elements. >> > looking for a function on the lines of cut but where I can specify >> > the size of the groups instead of the nr of groups. >> > >> > >> > >> > >> > -- >> > Witold Eryk Wolski >> > >> > __ >> > 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. >> > > > > -- > Gregory (Greg) L. Snow Ph.D. > 538...@gmail.com > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Orders of levels affecting wilcox.test() output
The short answer is whichever version you want since they are
the same. Look at the t-test results, they are also different.
In one t is positive and in the other it is negative. That is
just a result of whether the smaller mean is subtracted from
the larger mean or vice versa. The same is happening with
Wilcoxon (see
http://en.wikipedia.org/wiki/Mann-Whitney-Wilcoxon_test ) for
the specific equations.
-
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Alastair
Potts
Sent: Thursday, July 18, 2013 4:18 AM
To: r-help@r-project.org
Subject: [R] Orders of levels affecting wilcox.test() output
Good day all,
My first posting to this list. It looked like the best place
to post this
question.
When running the wilcox.test(), I noticed that the output
values change if
you change the ordering of the levels (example below which
includes a
t.test for comparison). I think this has something to do with
the change in
ranking order, but this doesn't make much sense as I would
expect the
ranking in this case to remain constant as there are no ties.
So my
questions are: a) is this correct (i.e. not a bug)?, and b) if
it is, then
which values should I report?
x <-
cbind(data.frame((c(rep("A",50),rep("B",50,runif(100))
colnames(x) <- c("a","b")
wilcox.test(b~a,data=x)
t.test(b~a,data=x)
x$a <- relevel(x$a,ref="B")
wilcox.test(b~a,data=x)
t.test(b~a,data=x)
Thank you in advance for your time,
Regards,
Alastair
[[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.
__
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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] cut into groups of equal nr of elements...
Marc, Your method works fine when the data is perfectly uniform, but try it with "Vec <- rnorm(30)" and you will see that there are more observations in the middle groups and fewer in the tail groups. Something like quantile needs to be used to find the unequally spaced breaks that will give equal counts within groups. On Wed, Jul 17, 2013 at 5:04 PM, Marc Schwartz wrote: > On Jul 17, 2013, at 4:43 PM, Witold E Wolski wrote: > > > I would like to "cut" a vector into groups of equal nr of elements. > > looking for a function on the lines of cut but where I can specify > > the size of the groups instead of the nr of groups. > > > > In addition to the other options, if the 'breaks' argument to cut() is a > single number, rather than a vector of cut points, it defines the number of > intervals to break the 'x' vector into, which of course you can derive from > length(x) / size. > > Thus: > > set.seed(1) > Vec <- sample(30) > > > Vec > [1] 8 11 17 25 6 23 27 16 14 2 5 4 13 7 18 30 29 24 20 9 10 21 > [23] 26 1 22 15 28 12 3 19 > > > # Split into 5 groups of 6 each > > > split(Vec, cut(Vec, 5)) > $`(0.971,6.78]` > [1] 6 2 5 4 1 3 > > $`(6.78,12.6]` > [1] 8 11 7 9 10 12 > > $`(12.6,18.4]` > [1] 17 16 14 13 18 15 > > $`(18.4,24.2]` > [1] 23 24 20 21 22 19 > > $`(24.2,30]` > [1] 25 27 30 29 26 28 > > > Regards, > > Marc Schwartz > > __ > 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. > -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cut into groups of equal nr of elements...
Wensui, ?qcut on my machine gives an error and ??qcut does not find anything in the installed packages. Which package is qcut in? On Wed, Jul 17, 2013 at 4:43 PM, Wensui Liu wrote: > ?qcut > On Jul 17, 2013 5:45 PM, "Witold E Wolski" wrote: > > > I would like to "cut" a vector into groups of equal nr of elements. > > looking for a function on the lines of cut but where I can specify > > the size of the groups instead of the nr of groups. > > > > > > > > > > -- > > Witold Eryk Wolski > > > > __ > > 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. > -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] restrected arima models
Dear all, Does anyone know if it is possible to estimate restricted arima models using the arima command in R? For instance lets say I want arima(6,0,0) but where the first three ar parameters are restricted to zero, ie. ar(1)=ar(2)=ar(3) = 0, and only the last three are actually estimated. Any help will be much appreciated. george -- View this message in context: http://r.789695.n4.nabble.com/restrected-arima-models-tp4671847.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] Moran's I
Dear list,
Im an undergraduate research assistant trying to create a single function
that can calculate Morans I using the ape package. The example that I
will use comes from online data about ozone levels. Here are the commands
that I have been using:
> library(ape)
> ozone<-read.table("http://www.ats.ucla.edu/stat/r/faq/ozone.csv";,
sep=",", header=T)
> head(ozone, n=10)
Station Av8top Lat Lon county
1 60 7.225806 34.13583 -117.9236 1
2 69 5.899194 34.17611 -118.3153 1
3 72 4.052885 33.82361 -118.1875 1
4 74 7.181452 34.19944 -118.5347 1
5 75 6.076613 34.06694 -117.7514 2
6 84 3.157258 33.92917 -118.2097 2
7 85 5.201613 34.01500 -118.0597 2
8 87 4.717742 34.06722 -118.2264 2
9 88 6.532258 34.08333 -118.1069 2
10 89 7.540323 34.38750 -118.5347 2
>attach(ozone)
> Moran<- function(x)
+ {
+ distmatrix<- as.matrix(dist(cbind(Lon, Lat)))
+ invdistmatrix<- 1/distmatrix
+ diag(invdistmatrix)<-0
+ Moran.I(Av8top, invdistmatrix)
+ print(Moran.I)
+ }
> Moran.I(ozone)
I either receive an error saying that the matrix is not weighted, or I
receive a significant amount of output that does not include a calculation
for Morans I. Do you have any suggestions on how to correctly create a
single function that calculates Morans I?
My ultimate goal is to run this function as a loop. I want to create a loop
that produces Morans I values for subsets of a very large database.
Specifically, I have points (block centroids) with population
characteristics. These points are nested within approximately 35,000 zip
codes. I want to create Morans I across blocks for each of the ~35,000 and
have the output stored in a new file that contains the zip code number and
Morans I values. In the example of the ozone data I show above, I would
create a loop that produces Morans I values for county 1 and county 2 and
then have the output stored in a new file with two records (one for each
county) and values for each county and the corresponding Morans I values.
Do you have any advice on creating this loop? Any help would be greatly
appreciated!
[[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] binary distance measure of the "dist" function in the "stats" package
If you read ?dist, it says that: binary: (aka asymmetric binary): The vectors are regarded as binary bits, so non-zero elements are ‘on’ and zero elements are ‘off’. The distance is the proportion of bits in which only one is on amongst those in which at least one is on. The short answer is that this is the Jaccard Distance measure. If we label the cells of a 2x2 presence absence matrix as a, b, c, d: Present Absent Present ab Absent cd Then the Jaccard Similarity index is a/(a+b+c) And the Jaccard Distance index is (1 - a/(a+b+c)) or (b+c)/(a+b+c) - David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of ?? Sent: Thursday, July 18, 2013 9:56 AM To: r-help@r-project.org Subject: [R] binary distance measure of the "dist" function in the "stats" package Dear all: I want to ask question about "binary" distance measure. As far as I know, there are many binary distance measures,eg, binary Jarcad distance, binary euclidean distance, and binary Bray-Curtis distance,etc. It is even more confusing because many have more than one name. So , I wan to know what the definite name of the binary distance measure of the "dist" function in the "stats" package is and further want to know the equation of the binary distance. Thank you very much! With my best regards. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] binary distance measure of the "dist" function in the "stats" package
Dear all: I want to ask question about "binary" distance measure. As far as I know, there are many binary distance measures,eg, binary Jarcad distance, binary euclidean distance, and binary Bray-Curtis distance,etc. It is even more confusing because many have more than one name. So , I wan to know what the definite name of the binary distance measure of the "dist" function in the "stats" package is and further want to know the equation of the binary distance. Thank you very much! With my best regards. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bland Altman summary stats for all column combinations
Hello,
I have the following data.frame
structure(list(Study = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 17L, 18L, 19L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 1L, 2L, 3L, 4L,
5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L,
19L), .Label = c("WCBP12236", "WCBP12241", "WCBP12242", "WCBP12243",
"WCBP12245", "WCBP13001", "WCBP13002", "WCBP13003", "WCBP13004",
"WCBP13005", "WCBP13006", "WCBP13007", "WCBP13008", "WCBP13009",
"WCBP13010", "WCBP13011", "WCBP13012", "WCBP13013", "WCBP13014"
), class = "factor"), G1 = c(68, 68.6, 66.6, 73.1, 51.6, 50.1,
64.1, 73, 63.7, 43.2, 62.3, 59.2, 67.5, 68.2, 54.6, 67.9, 56.5,
54.2, 67.3, 68, 68.4, 67.9, 73.3, 51.7, 50.3, 63.9, 73.9, 64,
42.9, 62.5, 59.3, 66.7, 68.4, 54, 68.2, 56.8, 54.5, 67, 53.2,
41.4, 53, 52.3, 41, 37.4, 56.9, 65.3, 36.2, 35.3, 36.1, 32.5,
56.5, 47.7, 39.4, 59.6, 38.1, 24.2, 30.2, 68.5, 68.9, 70.7, 74.9,
53.4, 51.6, 65.9, 75.7, 64.7, 42.8, 61.4, 60.8, 69.5, 68.7, 55.9,
70.7, 59.5, 51.1, 69.5), G2 = c(79.8, 72.2, 73.5, 74.4, 50.4,
54.8, 63.1, 70.4, 63.6, 45.1, 65.3, 49.4, 65.3, 76.2, 51, 63.9,
58.7, 57.8, 67, 79.6, 72.1, 73.9, 74.7, 50.5, 55.1, 62.8, 70.5,
63.3, 44.6, 65.5, 48.9, 64.9, 76.3, 50.6, 64.8, 58.6, 58.3, 67.4,
51.2, 37.7, 49.1, 53.7, 44.6, 37.3, 54.9, 64.1, 33.8, 31.9, 34.2,
30.3, 56.2, 44.6, 38.2, 63.2, 35.8, 26.5, 27.6, 80.6, 71.6, 75.4,
77.1, 52.4, 56.3, 66, 72.3, 64.5, 38.2, 64.3, 49.2, 66.9, 77.1,
52.4, 67.5, 59.6, 55.6, 69.9), S1 = c(75.1, 65.9, 72.7, 68.8,
49, 57.5, 66.5, 74.1, 60.9, 51.8, 58, 64.3, 71.1, 71.4, 58.9,
62.2, 58, 57.7, 58.6, 75.2, 66, 73.2, 69.7, 48.9, 57.7, 66.5,
74.7, 60.8, 51.4, 58.9, 65.5, 70.5, 71.4, 58.9, 65.1, 60.8, 57.7,
58.4, 54.3, 40.2, 52.6, 60.5, 42.6, 34.1, 55, 64.7, 36.3, 32.5,
39, 38.8, 58.1, 48, 40.5, 61, 40, 26.4, 28.8, 76.4, 66.5, 73.9,
72, 50.7, 59.2, 69.9, 76.3, 62.4, 50, 58.5, 66.6, 73.7, 72.3,
62.6, 69.6, 62.7, 57.9, 61.1), S2 = c(76.6, 71.6, 71.2, 72.7,
51.6, 56.7, 65.9, 73.5, 63.6, 55.2, 62.6, 62.2, 69.1, 71.1, 56.8,
61, 61.7, 60, 55.7, 76.9, 71.6, 72.3, 73.2, 51.7, 56.8, 64.5,
74.9, 63.6, 51.3, 63, 62.8, 68.7, 71.3, 56.8, 64.2, 62.8, 60.4,
55.8, 53.6, 42.5, 50, 54.4, 42.2, 36.4, 57.7, 64.1, 35.1, 30.8,
39.1, 37.4, 58.7, 47.8, 42, 58.8, 39.4, 24.2, 28.2, 78.2, 73.3,
72.3, 75.6, 53.4, 57.8, 68.3, 76.6, 63.7, 51.7, 63.4, 63.3, 71.5,
72.3, 60.2, 67.1, 65.5, 58.2, 59.1), Method = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Simple_2_ROI",
"Single_ROI", "WIG_drawn_bg", "WIG_Method"), class = "factor")), .Names =
c("Study",
"G1", "G2", "S1", "S2", "Method"), row.names = c(NA, -76L), class =
"data.frame")
This shows the measurement results of 2 operators using 4 slightly different
analysis methods. The operators analyse each data file WCBPX twice -
(G1,G2,S1,S2) and there are 4 methods (Single_ROI,Simple_2_ROI etc)
What I would like to do is get the summary statistics from a Bland Altman
(Mean vs Difference) plot for all 16 combinations.
For example for G1 and G2, I can do the following
ddply(df,.(Method),summarise,mean=mean(G1-G2, na.rm = TRUE),
sd=sd(G1-G2, na.rm = TRUE))
Eventually I want a data.frame with the format
Var1 Var2 Mean Sd Method
G1 G2 -.67 5.2 Simple_2_ROI
G1 G2 1.12 2.3 Single_ROI
G1 G2 -1.08 4.8 WIG_drawn_bg
G1 G2 -1.17 4.9 WIG_Method
G1 G1 0 0 Simple_2_ROI
Is there a simple way to achieve this structure?
>From that things get more tricky. What I would like to do is to create a
heatmap using ggplot2 (geom_tile) to provide a visual summary of the data
similar to the correlation heatmap I have produced from the same data set
Instead of filling each tile based on R^2 I would like to fill based on
standard deviation. Also I would like to add geom_text to each tile
highlighting the bias (mean difference) and the standard deviation.
Any pointers how I can achieve this. I am completely stuck.
Here is my code for the correlation heatmap
plots <- dlply(df, .(Method), function (x1) {
ggplot(subset(melt(cor(x1[sapply(x1,is.numeric)]))[lower.tri(c),],Var1
!= Var2),
aes(x=Var1,y=Var2,fill=value)) + geom_tile(aes(fill =
value),colour = "white") +
geom_text(aes(label = sprintf("%1.2f",value)), vjust = 1) +
theme_bw() +
scale_fill_gradient2(name="R^2",midpoint=0.7,low = "white", high =
"red") + xlab(NULL)+ylab(NULL) +
theme(axis.text.x=element_blank(),axis.text.y=element_blank(),
axis.ticks=element_blank(),panel.border=element_blank()) +
ggtitle(x1$Me
Re: [R] combine select data from 2 dataframes sharing same variables
Hi, Peter. Thanks for the suggestion. I will investigate ?merge. BNC From: Peter Alspach-2 [via R] [mailto:ml-node+s789695n4671809...@n4.nabble.com] Sent: Wednesday, July 17, 2013 8:08 PM To: Crombie, Burnette N Subject: Re: combine select data from 2 dataframes sharing same variables Tena koe Without reading your request in detail, I will suggest you look at ?merge. It is often the answer when 'combine' is in the question. Peter Alspach -- View this message in context: http://r.789695.n4.nabble.com/combine-select-data-from-2-dataframes-sharing-same-variables-tp4671790p4671837.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] panel setting
Hi all: My data: f1 f2 f3 f4 y 1 -4.45 3 6.44 3.721 2 25.66 121 39.03 3.55 0 3 -9.75 12 11.77 3.40 1 4 -12.09 17 13.75 3.33 0 5 -3.53 4 6.47 3.24 0 6 13.18 69 26.55 3.201 ... ... I want to plot f1 for y=0 and 1; f2 for y=0 and 1...and the same as f3,f4. And I want to get 4 plots at once(2*2) My code: par(mfrow=c(2,2)) densityplot(~f1,data=dat,group=y,auto.key=T) densityplot(~f2,data=dat,group=y,auto.key=T) densityplot(~f3,data=dat,group=y,auto.key=T) densityplot(~f4,data=dat,group=y,auto.key=T) The result is not what I want,since it produce 1 plot a time,but not 4 plots together(2*2). Maybe something wrong with par(mfrow=c(2,2))? Any suggestion? Many thanks! Best. [[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] R-squared and GLM
Haha, true true! ;) It was to be used as a measure on how good the models I use are, but I found out that the AIC would be much easier to implement, and as I understand, a better measure of how good the model fit. Thanks, Chris -- View this message in context: http://r.789695.n4.nabble.com/R-squared-and-GLM-tp4671754p4671820.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] Orders of levels affecting wilcox.test() output
Good day all,
My first posting to this list. It looked like the best place to post this
question.
When running the wilcox.test(), I noticed that the output values change if
you change the ordering of the levels (example below which includes a
t.test for comparison). I think this has something to do with the change in
ranking order, but this doesn't make much sense as I would expect the
ranking in this case to remain constant as there are no ties. So my
questions are: a) is this correct (i.e. not a bug)?, and b) if it is, then
which values should I report?
x <- cbind(data.frame((c(rep("A",50),rep("B",50,runif(100))
colnames(x) <- c("a","b")
wilcox.test(b~a,data=x)
t.test(b~a,data=x)
x$a <- relevel(x$a,ref="B")
wilcox.test(b~a,data=x)
t.test(b~a,data=x)
Thank you in advance for your time,
Regards,
Alastair
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[R] Test if 2 samples differ if they have autocorrelation
> Dear all
>
> I have one question that I struggle to find an answer:
>
> Let`s assume I have 2 timeseries of daily PnL data over 2 years coming from 2
> different trading strategies. I want to find out if strategy A is better than
> strategy B. The problem is that the two series have serial correlations,
> hence I cannot just do a simple t-test.
>
> I tried something like this:
>
> 1.create cumulative timeseries of PnL_A = C_A and of PnL_B = C_B
>
> 2.take the difference of both: C_A â C_B = DiffPnL (to see how the
> difference evolves over time)
>
> 3.do a regression: DiffPnL = beta * time + error (I thought if beta is
> significantly different from 0 than the two time series are different)
>
> 4.estimate beta not with OLS, but with the Newey-West method (HAC estimator)
> -> this corrects statistical tests, standard errors for beta
> heteroskedasticity and autocorrelation
>
> BUT: I read something that the tests are biased when the timeseries are unit
> root non-stationary (which is due to the fact that I take cumulative time
> series)
>
>
>
> I am lost! This should be fairly simple: test if two samples differ if they
> have autocorrelation? Probably my approach above is completely wrongâ¦
>
>
>
> Thanks for your help
>
> Best regards
>
> Eric
>
>
>
> The information in this e-mail is intended only for th...{{dropped:23}}
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Re: [R] Bland Altman summary stats for all column combinations
HI,
#dat1: data
Combn1<-combn(colnames(dat1)[2:5],2)
#For the first part, may be this helps:
library(plyr)
res<-lapply(split(Combn1,col(Combn1)),function(x)
{x1<-cbind(Var1=colnames(dat1[,x])[1],Var2=colnames(dat1[,x])[2],dat1[,x],Method=dat1[,6]);colnames(x1)[3:4]<-
c("V1","V2"); ddply(x1,.(Method,Var1,Var2),summarize,
mean1=mean(V1-V2,na.rm=TRUE),sd1=sd(V1-V2,na.rm=TRUE))})
res[[1]]
# Method Var1 Var2 mean1 sd1
#1 Simple_2_ROI G1 G2 -0.6684211 5.223882
#2 Single_ROI G1 G2 1.1263158 2.313929
#3 WIG_drawn_bg G1 G2 -1.0894737 4.876576
#4 WIG_Method G1 G2 -1.1684211 4.894447
Also,
G1 G1 0 0 Simple_2_ROI
#part is not clear bcz ur ddply() code didn't do that.
A.K.
Hello,
I have the following data.frame
structure(list(Study = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 1L,
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L,
16L, 17L, 18L, 19L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 1L, 2L, 3L, 4L,
5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L,
19L), .Label = c("WCBP12236", "WCBP12241", "WCBP12242", "WCBP12243",
"WCBP12245", "WCBP13001", "WCBP13002", "WCBP13003", "WCBP13004",
"WCBP13005", "WCBP13006", "WCBP13007", "WCBP13008", "WCBP13009",
"WCBP13010", "WCBP13011", "WCBP13012", "WCBP13013", "WCBP13014"
), class = "factor"), G1 = c(68, 68.6, 66.6, 73.1, 51.6, 50.1,
64.1, 73, 63.7, 43.2, 62.3, 59.2, 67.5, 68.2, 54.6, 67.9, 56.5,
54.2, 67.3, 68, 68.4, 67.9, 73.3, 51.7, 50.3, 63.9, 73.9, 64,
42.9, 62.5, 59.3, 66.7, 68.4, 54, 68.2, 56.8, 54.5, 67, 53.2,
41.4, 53, 52.3, 41, 37.4, 56.9, 65.3, 36.2, 35.3, 36.1, 32.5,
56.5, 47.7, 39.4, 59.6, 38.1, 24.2, 30.2, 68.5, 68.9, 70.7, 74.9,
53.4, 51.6, 65.9, 75.7, 64.7, 42.8, 61.4, 60.8, 69.5, 68.7, 55.9,
70.7, 59.5, 51.1, 69.5), G2 = c(79.8, 72.2, 73.5, 74.4, 50.4,
54.8, 63.1, 70.4, 63.6, 45.1, 65.3, 49.4, 65.3, 76.2, 51, 63.9,
58.7, 57.8, 67, 79.6, 72.1, 73.9, 74.7, 50.5, 55.1, 62.8, 70.5,
63.3, 44.6, 65.5, 48.9, 64.9, 76.3, 50.6, 64.8, 58.6, 58.3, 67.4,
51.2, 37.7, 49.1, 53.7, 44.6, 37.3, 54.9, 64.1, 33.8, 31.9, 34.2,
30.3, 56.2, 44.6, 38.2, 63.2, 35.8, 26.5, 27.6, 80.6, 71.6, 75.4,
77.1, 52.4, 56.3, 66, 72.3, 64.5, 38.2, 64.3, 49.2, 66.9, 77.1,
52.4, 67.5, 59.6, 55.6, 69.9), S1 = c(75.1, 65.9, 72.7, 68.8,
49, 57.5, 66.5, 74.1, 60.9, 51.8, 58, 64.3, 71.1, 71.4, 58.9,
62.2, 58, 57.7, 58.6, 75.2, 66, 73.2, 69.7, 48.9, 57.7, 66.5,
74.7, 60.8, 51.4, 58.9, 65.5, 70.5, 71.4, 58.9, 65.1, 60.8, 57.7,
58.4, 54.3, 40.2, 52.6, 60.5, 42.6, 34.1, 55, 64.7, 36.3, 32.5,
39, 38.8, 58.1, 48, 40.5, 61, 40, 26.4, 28.8, 76.4, 66.5, 73.9,
72, 50.7, 59.2, 69.9, 76.3, 62.4, 50, 58.5, 66.6, 73.7, 72.3,
62.6, 69.6, 62.7, 57.9, 61.1), S2 = c(76.6, 71.6, 71.2, 72.7,
51.6, 56.7, 65.9, 73.5, 63.6, 55.2, 62.6, 62.2, 69.1, 71.1, 56.8,
61, 61.7, 60, 55.7, 76.9, 71.6, 72.3, 73.2, 51.7, 56.8, 64.5,
74.9, 63.6, 51.3, 63, 62.8, 68.7, 71.3, 56.8, 64.2, 62.8, 60.4,
55.8, 53.6, 42.5, 50, 54.4, 42.2, 36.4, 57.7, 64.1, 35.1, 30.8,
39.1, 37.4, 58.7, 47.8, 42, 58.8, 39.4, 24.2, 28.2, 78.2, 73.3,
72.3, 75.6, 53.4, 57.8, 68.3, 76.6, 63.7, 51.7, 63.4, 63.3, 71.5,
72.3, 60.2, 67.1, 65.5, 58.2, 59.1), Method = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Simple_2_ROI",
"Single_ROI", "WIG_drawn_bg", "WIG_Method"), class = "factor")), .Names =
c("Study",
"G1", "G2", "S1", "S2", "Method"), row.names = c(NA, -76L), class =
"data.frame")
This shows the measurement results of 2 operators using 4
slightly different analysis methods. The operators analyse each data
file WCBPX twice - (G1,G2,S1,S2) and there are 4 methods
(Single_ROI,Simple_2_ROI etc)
What I would like to do is get the summary statistics from a Bland Altman (Mean
vs Difference) plot for all 16 combinations.
For example for G1 and G2, I can do the following
ddply(df,.(Method),summarise,mean=mean(G1-G2, na.rm = TRUE),
sd=sd(G1-G2, na.rm = TRUE))
Eventually I want a data.frame with the format
Var1 Var2 Mean Sd Method
G1 G2 -.67 5.2 Simple_2_ROI
G1 G2 1.12 2.3 Single_ROI
G1 G2 -1.08 4.8 WIG_drawn_bg
G1 G2 -1.17 4.9 WIG_Method
G1 G1 0 0 Simple_2_ROI
Is there a simple way to achieve this structure?
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Re: [R] Merge with transposed matrix.
Hi, m1<- matrix(NA,5,5) m1[upper.tri(m1)]<-c(2,3,8,4,9,14,5,10,15,20) One way would be: m1[lower.tri(m1)]<-t(m1)[lower.tri(t(m1))] m1 # [,1] [,2] [,3] [,4] [,5] #[1,] NA 2 3 4 5 #[2,] 2 NA 8 9 10 #[3,] 3 8 NA 14 15 #[4,] 4 9 14 NA 20 #[5,] 5 10 15 20 NA A.K. Hello ! I would like to have some simple sintax in order to fill my matrix with its transposed. That is, as an example I have a correlation matrix like this, and the transposed one: > matrix [,1] [,2] [,3] [,4] [,5] [1,] NA 2 3 4 5 [2,] NA NA 8 9 10 [3,] NA NA NA 14 15 [4,] NA NA NA NA 20 [5,] NA NA NA NA NA > transposed.matrix<-t(matrix) [,1] [,2] [,3] [,4] [,5] [1,] NA NA NA NA NA [2,] 2 NA NA NA NA [3,] 3 8 NA NA NA [4,] 4 9 14 NA NA [5,] 5 10 15 20 NA And I would like to have [,1] [,2] [,3] [,4] [,5] [1,] NA 2 3 4 5 [2,] 2 NA 8 9 10 [3,] 3 8 NA 14 15 [4,] 4 9 14 NA 20 [5,] 5 10 15 20 NA Thank you very much for your help !! __ 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] stopping functions with long execution times
On 18/07/2013 10:37, ONKELINX, Thierry wrote: Dear all, I am running the same model on several datasets, each dataset is a different species. The problem is that for some datasets the model is not converging. Currently I have an INLA model running for 35 days and still no results. The process still uses near 100% of the CPU and less than 1 GB RAM on virtual Ubuntu box with 8 GB RAM on a blade server. I can kill the process manual and make the script skip this model. However it would be more elegant if it was possible to automate this. E.g. let the model run but kill it automatically once it runs for more than 7 days. Once killed the model should throw an error so we can catch that in the error-handling. Any suggestions on how to do this? Learn how to use the R documentation. ??limit gave me some useful hits, including to how I would do this. However, as ?setTimeLimit points out, if this is running in C code, it cannot be interrupted from the R interpreter. In that case, use separate processes and your OS facilities (man ulimit, for example). Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 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 And 'Asking on R-help is no substitute for doing your own homework' * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-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] 'save' method for S4 class
On 07/18/2013 03:47 AM, Simon Zehnder wrote:
Hi Christopher,
I think, that "save" is no generic function like "plot", "show", etc. So at
first you have to determine a generic.
setGeneric("save", function(x, file_Path) standardGeneric("save"))
The implementation offered by Christofer shows write.table, and the end result
is a text file rather than a binary file expected from base::save. This makes it
seem inappropriate to use 'save' in this context.
Instead, it seems that what Cristofer wants to implement is functionality to
support write.table. ?write.table says
'write.table' prints its required argument 'x' (after converting
it to a data frame if it is not one nor a matrix)
So implementing an S3 method
as.data.frame.MyClass <-
function(x, row.names=NULL, optional=FALSE, ...)
{
x@x
}
is all that is needed, gaining lots of flexibility by re-using the code of
write.table.
myClass = new("MyClass", x=data.frame(x=1:3, y=3:1))
write.table(myClass, stdout())
In the case of a 'save' method producing binary output (but this is what save
does already...), I think it's better practice to promote the non-generic 'save'
to an S4 generic using it's existing arguments; in this case it makes sense to
restrict dispatch to '...', so
setGeneric("save", signature="...")
The resulting generic is
> getGeneric("save")
standardGeneric for "save" defined from package ".GlobalEnv"
function (..., list = character(), file = stop("'file' must be specified"),
ascii = FALSE, version = NULL, envir = parent.frame(), compress = !ascii,
compression_level, eval.promises = TRUE, precheck = TRUE)
standardGeneric("save")
Methods may be defined for arguments: ...
Use showMethods("save") for currently available ones.
This means that a method might be defined as
setMethod("save", "MyClass", function(..., list = character(),
file = stop("'file' must be specified"), ascii = FALSE, version = NULL,
envir = parent.frame(), compress = !ascii, compression_level,
eval.promises = TRUE, precheck = TRUE)
{
## check non-sensical or unsupported user input for 'MyClass'
if (!is.null(version))
stop("non-NULL 'version' not supported for 'MyClass'")
## ...
## implement save on MyClass
})
It might be that Christofer wants to implement a 'write.table-like' (text
output) or a 'save-like' (binary output) function that really does not conform
to the behavior of write.table (e.g., producing output that could not be input
by read.table) or save. Then I think the better approach is to implement
writeMyClass (for text output) or saveMyClass (for binary output).
Martin
Now your definition via setMethod.
Best
Simon
On Jul 18, 2013, at 12:09 PM, Christofer Bogaso
wrote:
Hello again,
I am trying to define the 'save' method for my S4 class as below:
setClass("MyClass", representation(
Slot1 = "data.frame"
))
setMethod("save", "MyClass", definition = function(x, file_Path) {
write.table(x@Slot1, file = file_Path, append = FALSE, quote =
TRUE,
sep = ",",
eol = "\n", na = "NA", dec =
".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape",
"double"),
fileEncoding = "")
})
However while doing this I am getting following error:
Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
in method for ‘save’ with signature ‘list="MyClass"’: formal
arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
version = "MyClass", envir = "MyClass", compress = "MyClass",
compression_level = "MyClass", eval.promises = "MyClass", precheck =
"MyClass") omitted in the method definition cannot be in the signature
Can somebody point me what will be the correct approach to define
'save' method for S4 class?
Thanks and regards,
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Re: [R] stopping functions with long execution times
Hi Henrik,
That is exactly what I was looking for.
Thanks a lot.
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
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: henrik.bengts...@gmail.com [mailto:henrik.bengts...@gmail.com] Namens
Henrik Bengtsson
Verzonden: donderdag 18 juli 2013 12:43
Aan: ONKELINX, Thierry
CC: r-help@r-project.org
Onderwerp: Re: [R] stopping functions with long execution times
See evalWithTimeout() of R.utils, e.g.
tryCatch({
evalWithTimeout({
slowFunction();
}, timeout=7*24*3600);
}, TimeoutException=function(ex) {
cat("Timeout. Skipping.\n");
})
help("evalWithTimeout") have more information and cross links.
/Henrik
On Thu, Jul 18, 2013 at 11:37 AM, ONKELINX, Thierry
wrote:
> Dear all,
>
> I am running the same model on several datasets, each dataset is a different
> species. The problem is that for some datasets the model is not converging.
> Currently I have an INLA model running for 35 days and still no results. The
> process still uses near 100% of the CPU and less than 1 GB RAM on virtual
> Ubuntu box with 8 GB RAM on a blade server.
>
> I can kill the process manual and make the script skip this model. However it
> would be more elegant if it was possible to automate this. E.g. let the model
> run but kill it automatically once it runs for more than 7 days. Once killed
> the model should throw an error so we can catch that in the error-handling.
>
> Any suggestions on how to do this?
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality
> Assurance Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> 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
>
>
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * *
> * 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.
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
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.
__
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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] 'save' method for S4 class
Hi Christopher,
I think, that "save" is no generic function like "plot", "show", etc. So at
first you have to determine a generic.
setGeneric("save", function(x, file_Path) standardGeneric("save"))
Now your definition via setMethod.
Best
Simon
On Jul 18, 2013, at 12:09 PM, Christofer Bogaso
wrote:
> Hello again,
>
> I am trying to define the 'save' method for my S4 class as below:
>
> setClass("MyClass", representation(
> Slot1 = "data.frame"
> ))
>
> setMethod("save", "MyClass", definition = function(x, file_Path) {
>
> write.table(x@Slot1, file = file_Path, append = FALSE, quote =
> TRUE,
> sep = ",",
> eol = "\n", na = "NA", dec =
> ".", row.names = FALSE,
> col.names = TRUE, qmethod =
> c("escape", "double"),
> fileEncoding = "")
> })
>
> However while doing this I am getting following error:
>
> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
> in method for ‘save’ with signature ‘list="MyClass"’: formal
> arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
> version = "MyClass", envir = "MyClass", compress = "MyClass",
> compression_level = "MyClass", eval.promises = "MyClass", precheck =
> "MyClass") omitted in the method definition cannot be in the signature
>
>
> Can somebody point me what will be the correct approach to define
> 'save' method for S4 class?
>
> Thanks and regards,
>
> __
> 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] stopping functions with long execution times
See evalWithTimeout() of R.utils, e.g.
tryCatch({
evalWithTimeout({
slowFunction();
}, timeout=7*24*3600);
}, TimeoutException=function(ex) {
cat("Timeout. Skipping.\n");
})
help("evalWithTimeout") have more information and cross links.
/Henrik
On Thu, Jul 18, 2013 at 11:37 AM, ONKELINX, Thierry
wrote:
> Dear all,
>
> I am running the same model on several datasets, each dataset is a different
> species. The problem is that for some datasets the model is not converging.
> Currently I have an INLA model running for 35 days and still no results. The
> process still uses near 100% of the CPU and less than 1 GB RAM on virtual
> Ubuntu box with 8 GB RAM on a blade server.
>
> I can kill the process manual and make the script skip this model. However it
> would be more elegant if it was possible to automate this. E.g. let the model
> run but kill it automatically once it runs for more than 7 days. Once killed
> the model should throw an error so we can catch that in the error-handling.
>
> Any suggestions on how to do this?
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> 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
>
>
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
> 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.
__
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] 'save' method for S4 class
Hello again,
I am trying to define the 'save' method for my S4 class as below:
setClass("MyClass", representation(
Slot1 = "data.frame"
))
setMethod("save", "MyClass", definition = function(x, file_Path) {
write.table(x@Slot1, file = file_Path, append = FALSE, quote =
TRUE,
sep = ",",
eol = "\n", na = "NA", dec =
".", row.names = FALSE,
col.names = TRUE, qmethod =
c("escape", "double"),
fileEncoding = "")
})
However while doing this I am getting following error:
Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
in method for ‘save’ with signature ‘list="MyClass"’: formal
arguments (list = "MyClass", file = "MyClass", ascii = "MyClass",
version = "MyClass", envir = "MyClass", compress = "MyClass",
compression_level = "MyClass", eval.promises = "MyClass", precheck =
"MyClass") omitted in the method definition cannot be in the signature
Can somebody point me what will be the correct approach to define
'save' method for S4 class?
Thanks and regards,
__
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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] truncation and approximation
Maybe you can use "round" and "trunc" functions For example if you have a vector like this: x<- c(3.000 3.125 3.250 3.375 3.500 3.625 3.750 3.875 4.000) and you want to round the numbers to 2 decimals you can use: round(x,2) [1] 3.00 3.12 3.25 3.38 3.50 3.62 3.75 3.88 4.00 if you want a numeric vector containing the integers formed by truncating the values in x trunc(x) [1] 3 3 3 3 3 3 3 3 4 I'hope it'is useful to you A.C. Def. Quota Rui Barradas : Hello, As for truncation, you can write a one line function: dec_trunc <- function(x, digits = 0) trunc(x * 10^digits)/10^digits As for approximation, maybe you're looking for ?signif. Hope this helps, Rui Barradas Em 17-07-2013 18:41, Francesco Miranda escreveu: What is the function to do the truncation to a certain decimal digit of a number. And the function approximation? Thanks. Francesco M [[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. ** IL MERITO DEGLI STUDENTI VIENE RICONOSCIUTO Il 5 per mille all'Universita' degli Studi di Napoli "Parthenope" incrementa le borse di studio agli studenti - codice fiscale 80018240632 http://www.uniparthenope.it/index.php/5xmille http://www.uniparthenope.it/index.php/it/avvisi-sito-di-ateneo/2943-la-parthenope-premia-il-tuo-voto-di-diploma-ed-il-tuo-imegno-con-i-proventi-del-5-per-mille Questa informativa e' inserita in automatico dal sistema al fine esclusivo della realizzazione dei fini istituzionali dell'ente. __ 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] EWMA error
Please reply to the list. You will have more chance to get an answer.
Pascal
2013/7/18 G Girija
> Hi,
>
> Many thanks for your hint. Yes I made a mistake there.
>
> Also could you *please* help me in rectifying the following also?
>
> I am not able to extract variance and covariance
>
> As mentioned, there are 5 stocks and changed the code [
> http://www.forecastingfinancialrisk.com/3.html] as follows:
>
> > S<-cov(returns)
>
> > S
>
> V1 V2 V3 V4 V5
>
> V1 0.0004951526 0.0001256519 0.0001651016 0.0003024310 0.0003516796
>
> V2 0.0001256519 0.0008076471 0.0001251208 0.0002005305 0.0002347568
>
> V3 0.0001651016 0.0001251208 0.001707 0.0003158028 0.0003682633
>
> V4 0.0003024310 0.0002005305 0.0003158028 0.0011405561 0.0008442661
>
> V5 0.0003516796 0.0002347568 0.0003682633 0.0008442661 0.0018536153
>
>
>
> > EWMA[1,]<-c(S)[c(1,10,5)]
>
> > a=t(as.numeric(returns$i)) %*% as.numeric(returns$i) ---*Here we need
>
>
> to change dataframe to numeric, that too only columns.*
>
> > str(a)
>
> num [1, 1] 0
>
> > dim(a)
>
> [1] 1 1
>
> > dim(lambda*S)
>
> [1] 5 5 -*As the dimensions are not same we can not do
> %*%*
>
> > dim((1-lambda)*a)
>
> [1] 1 1
>
> for(i in 2:T)
>
> {
>
> S<- lambda*S+ (1-lambda)*t(returns$i) %*% returns$i
>
> EWMA[i,]=c(S)[c(1,4,2)]
>
> }
>
>
>
> *Original code as per* http://www.forecastingfinancialrisk.com/3.html is
>
> EWMA = *matrix*(*nrow*=T,*ncol*=3) *# create a matrix to hold the
> covariance matrix for each t*
>
> lambda = 0.94
>
> S = *cov*(y) *# initial (t=1) covariance matrix*
>
> EWMA[1,] = *c*(S)[*c*(1,4,2)] *# extract the variances and covariance*
>
> *for* (i *in* 2:T){*# loop though the sample*
>
> S = lambda * S + (1-lambda) * *t*(y[i]) %*% y[i]
>
> EWMA[i,] = *c*(S)[*c*(1,4,2)] *# convert matrix to vector *
>
> }
>
>
>
> On Thu, Jul 18, 2013 at 5:54 AM, Pascal Oettli wrote:
>
>> Hello,
>>
>> 1) In the provided example, you have 2 stock returns and
>>
>> > EWMA = matrix(nrow=T, ncol=3)
>>
>> See the number of columns (2+1)
>> Please modify the number of columns according to the number of stock
>> returns.
>>
>> 2) As you have 5 stock returns, the following cannot work
>>
>> > EWMA[1,] = c(S)[c(1,4,2)]
>>
>> You have to modify this part too.
>>
>>
>> 3) Do the same modification within the loop.
>>
>> Regards,
>> Pascal
>>
>>
>>
>> 2013/7/18 G Girija
>>
>>> hi,
>>>
>>> Could anyone help me in solving the following error:
>>> I have 5 stocks returns data (returns)
>>>
>>> EWMA = matrix(nrow=T,ncol=5) # create a matrix to hold
>>> the
>>> covariance matrix for each t
>>>
>>> lambda = 0.94
>>> S<-cov(returns) # initial (t=1)
>>> covariance matrix
>>> EWMA[1,] = c(S)[c(1,4,2)] ---ERROR# extract the
>>> variances and covariancefor (i in 2:T)
>>>
>>>
>>>{# loop though the sample
>>> S<- lambda*S+(1-lambda)*t(returns[i])%*%returns[i]
>>> EWMA[i,] = c(S)[c(1,4,2)] # convert matrix to vector
>>>}
>>>
>>> *ERROR as follows:*
>>>
>>> *> EWMA[1,]<-c(S)[c(1,4,2)]*
>>> *Error in EWMA[1, ] <- c(S)[c(1, 4, 2)] : *
>>> * number of items to replace is not a multiple of replacement length*
>>>
>>> [[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.
[R] stopping functions with long execution times
Dear all, I am running the same model on several datasets, each dataset is a different species. The problem is that for some datasets the model is not converging. Currently I have an INLA model running for 35 days and still no results. The process still uses near 100% of the CPU and less than 1 GB RAM on virtual Ubuntu box with 8 GB RAM on a blade server. I can kill the process manual and make the script skip this model. However it would be more elegant if it was possible to automate this. E.g. let the model run but kill it automatically once it runs for more than 7 days. Once killed the model should throw an error so we can catch that in the error-handling. Any suggestions on how to do this? Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 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 * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * 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.
[R] Finding All paths in a graph
Hi, Do you know any function/package in R which returns all possible paths in a graph. 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.
