Re: [R] Text showing when R is launched

[George Loftus]

Hi,

Thankyou for your response

<https://1drv.ms/i/s!AkfoLX--ikbqkweYckSQiXYKXJuR>
[https://9c11xq.db.files.1drv.com/y4m7xqt5yVu7b5IG1jFuopunwB7Oa9Eij0WeZ7p1lSSmBECcSIB3XjcKjXIUhdMrJwaJdjZnBRhMeAxY0_Kko06Nq1fm5IhqaHlT6aFeI3R7gicXCteRPkzqNwmCdVxZu5DhNq66IrpwDyQ1lr8E5OFdm_xL86pMgNSLAx5HRRKLPOmFdUFWdv1ID-D1PC6LvNvAB-rT87JiQonSHRJIHouLg?width=200=150=center]
[https://res-h3.public.cdn.office.net/assets/mail/file-icon/png/cloud_blue_16x16.png]Screenshot
 2023-10-11 at 19.19.48.png
?

However this is all that exists in Users/Admin

There were a couple of R files in there which I have since deleted but I am 
still getting the same issue

Thankyou,
George


From: Rui Barradas 
Sent: 10 October 2023 12:06
To: George Loftus ; r-help@r-project.org 

Subject: Re: [R] Text showing when R is launched

�s 23:56 de 09/10/2023, George Loftus escreveu:
> Good Evening,
>
> I was wondering if you were able to help, I am running R on MacOS, it is the 
> 2020 model mac so have install the Intel arm of R which I believe is correct
>
> However when I launch R or resume the R window after going on a different 
> programme the following text is running
>
> I have also copied and pasted for ease
>
> 1   HIToolbox   0x7ff82142e0c2 
> _ZN15MenuBarInstance22RemoveAutoShowObserverEv + 30
> 2   HIToolbox   0x7ff82146a638 
> _ZL17BroadcastInternaljPvh + 167
> 3   SkyLight0x7ff81c70f23d 
> _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ + 1030
> 4   SkyLight0x7ff81ca2205a 
> _ZN21CGSDatagramReadStream26dispatchMainQueueDatagramsEv + 202
> 5   SkyLight0x7ff81ca21f81 
> ___ZN21CGSDatagramReadStream15mainQueueWakeupEv_block_invoke + 18
> 6   libdispatch.dylib   0x7ff8178867fb 
> _dispatch_call_block_and_release + 12
> 7   libdispatch.dylib   0x7ff817887a44 
> _dispatch_client_callout + 8
> 8   libdispatch.dylib   0x7ff8178947b9 
> _dispatch_main_queue_drain + 952
> 9   libdispatch.dylib   0x7ff8178943f3 
> _dispatch_main_queue_callback_4CF + 31
> 10  CoreFoundation  0x7ff817b215f0 
> __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
> 11  CoreFoundation  0x7ff817ae1b70 __CFRunLoopRun + 
> 2454
> 12  CoreFoundation  0x7ff817ae0b60 
> CFRunLoopRunSpecific + 560
> 13  HIToolbox   0x7ff82142e766 
> RunCurrentEventLoopInMode + 292
> 14  HIToolbox   0x7ff82142e576 
> ReceiveNextEventCommon + 679
> 15  HIToolbox   0x7ff82142e2b3 
> _BlockUntilNextEventMatchingListInModeWithFilter + 70
> 16  AppKit  0x7ff81ac31293 _DPSNextEvent + 909
> 17  AppKit  0x7ff81ac30114 
> -[NSApplication(NSEvent) 
> _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219
> 18  R   0x000103d60c76 -[RController 
> doProcessEvents:] + 166
> 19  R   0x000103d5b295 -[RController 
> handleReadConsole:] + 149
> 20  R   0x000103d6466f Re_ReadConsole + 
> 175
> 21  libR.dylib  0x000104442154 R_ReplDLLdo1 + 148
> 22  R   0x000103d71c47 
> run_REngineRmainloop + 263
> 23  R   0x000103d66d5f -[REngine runREPL] 
> + 143
> 24  R   0x000103d56718 main + 792
> 25  dyld0x7ff8176d4310 start + 2432
> 1   HIToolbox   0x7ff8214a1726 
> _ZN15MenuBarInstance22EnsureAutoShowObserverEv + 102
> 2   HIToolbox   0x7ff82146a638 
> _ZL17BroadcastInternaljPvh + 167
> 3   SkyLight0x7ff81c70f23d 
> _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ + 1030
> 4   SkyLight0x7ff81ca2205a 
> _ZN21CGSDatagramReadStream26dispatchMainQueueDatagramsEv + 202
> 5   SkyLight0x7ff81ca21f81 
> ___ZN21CGSDatagramReadStream15mainQueueWakeupEv_block_invoke + 18
> 6   libdispatch.dylib   0x7ff8178867fb 
> _dispatch_call_block_and_release + 12
> 7   libdispatch.dylib   0x7ff817887a44 
> _dispatch_client_callout + 8
> 8   libdispatch.dylib   0x7ff8178947b9 
> _dispatch_main_queue_drain + 952
> 9   libdispatch.dylib   0x7ff8178943f3 
> _dispatch_main_queue_callback_4CF

[R] Shaded area

[George Brida]

Dear R users,

I have an xlsx file (attached to this mail) that shows the values of a
"der" series observed on a daily basis from January 1, 2017 to January 25,
2017. This series is strictly positive during two periods: from January 8,
2017 to January 11, 2017 and from January 16, 2017 to January 20, 2017. I
would like to plot the series with two shaded areas corresponding to the
positivity of the series. Specifically, I would like to draw 4 vertical
lines intersecting the x-axis in the 4 dates mentioned above and shade the
two areas of positivity. Thanks for your help.
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[R] Logistic regression for large data

[George Brida]

Dear R users,

I have a database  called Base.csv   (attached to this email) which
contains 13 columns and 8257 rows and whose the first 8 columns are dummy
variables which take 1 or 0. The problem is when I wrote the following
instructions to do a logistic regression , R runs for hours and hours
without giving an output:

Base=read.csv("C:\\Users\\HP\\Desktop\\New\\Base.csv",header=FALSE,sep=";")
fit_1=glm(Base[,2]~Base[,1]+Base[,10]+Base[,11]+Base[,12]+Base[,13],family=binomial(link="logit"))

Apparently, there is not enough memory to have the requested output. Is
there any other function for logistic regression that handle large data and
return output in reasonable time.

Many thanks

Kind regards

George
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Re: [R] Mapping of groups of countries

[george brida]

Thanks a lot Jim. I really appreciate your help. Happy new year 2022.
George

On Wed, Dec 29, 2021 at 10:10 PM Jim Lemon  wrote:

> Hi George,
> This example is obviously a mess, but it shows the basic elements. The
> labels may be placed manually using something like boxed.labels
> (plotrix) with lines connecting the labels to the smaller countries.
> If you want the labels within the countries you will have to use a big
> graphics device.
>
> library(maps)
> map("world")
> countries=c("China","Bangladesh","Egypt","Indonesia","South
> Korea","Nigeria",
>  "Brazil","Pakistan","Philippines","Vietnam","South Africa",
>  "India","Mexico","Turkey")
> countrycol<-c(rep("red",6),rep("blue",4),"green",rep("orange",3))
> for(i in 1:length(countries)) {
>  mapinf<-map(region=countries[i],col=countrycol[i],add=TRUE)
>  xpos<-sum(mapinf$range[1:2])/2
>  ypos<-sum(mapinf$range[3:4])/2
>  text(xpos,ypos,countries[i])
> }
>
>
> Jim
>
> On Thu, Dec 30, 2021 at 7:34 AM george brida 
> wrote:
> >
> > Dear R users,
> >
> > I would like to map with R the following countries (with their names on
> the
> > map) as follows: the first group in red composed by China, Bangladesh,
> > Eypt, Indonesia, South Korea, Nigeria. The second group in blue composed
> by
> > Brazil, Pakistan, Philippines, Vietnam.
> >
> > The third group in green solely composed by South Africa.
> >
> > Finally, the fourth group in orange composed by India, Mexico and Turkey.
> >
> > I'd also like a legend that assigns the different colors to the various
> > group.
> > I tried several times with library maps but it seems that I failed to
> find
> > the real setting of xlim and ylim. Can you please help me, I will be very
> > grateful.
> >
> > Best regards
> > George
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

[R] Mapping of groups of countries

[george brida]

Dear R users,

I would like to map with R the following countries (with their names on the
map) as follows: the first group in red composed by China, Bangladesh,
Eypt, Indonesia, South Korea, Nigeria. The second group in blue composed by
Brazil, Pakistan, Philippines, Vietnam.

The third group in green solely composed by South Africa.

Finally, the fourth group in orange composed by India, Mexico and Turkey.

I'd also like a legend that assigns the different colors to the various
group.
I tried several times with library maps but it seems that I failed to find
the real setting of xlim and ylim. Can you please help me, I will be very
grateful.

Best regards
George

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Cars2

[George Bellas]

Thanks Ivan, I was a fool.

That�s the one I am looking for.

Best,
George



From: Ivan Krylov 
Sent: Thursday, August 19, 2021 5:32:43 PM
To: George Bellas 
Cc: r-help@r-project.org 
Subject: Re: [R] Cars2

On Thu, 19 Aug 2021 00:12:51 +
George Bellas  wrote:

> I'm still looking for it, it had car prices and car models in it. I
> couldn't find it through the r search link.

Could it be the third search result for a query of 'cars2'?

https://search.r-project.org/?P=cars2==10=r-manuals=r-help=cran-views=cran-info=cran-help=cran-news=cran-readme=cran-vignettes=and=query=cran-help=.%7E%7E

->

https://search.r-project.org/CRAN/refmans/fBasics/html/data-examples.html

>> cars2 contains the price, country, reliability, mileage, type,
>> weight, engine displacement and net horsepower of various car
>> models.

--
Best regards,
Ivan

[[alternative HTML version deleted]]

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[R] Cars2

[George Bellas]

Hi R Core team,

I was looking at this link for data sets,

https://stat.ethz.ch/R-manual/R-devel/library/datasets/html/00Index.html

and wanted to use cars2. I found cars2 earlier this week, but now when I look 
at the list, it's not there!

Can you tell me what happened to cars2? I have tried calling it on my version 
of R4.0.5 (backdated so Shiny works), but I can't find it anymore.

Thanks,
George


[[alternative HTML version deleted]]

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Re: [R] Mapping of countries

[george brida]

Thanks a lot Jim..

Thank you Ani and Rasmus.

Best

On Wed, Apr 1, 2020 at 2:54 AM ani jaya  wrote:

> Maybe simply add:
>
>
> points(station$Lon, station$Lat, col="red", pch=16, label="Your Country")
> text(station$Lon, station$Lat,"Your Country",
>  col="black", pos=3, cex=1)
>
> station$Lon and Lat in your coordinate position.
>
> Regards,
> Ani
>
>
> On Tue, Mar 31, 2020 at 10:58 PM george brida 
> wrote:
> >
> > Dear Jim,
> >
> > Is it possible to add also a title to this map?
> >
> > Many thanks
> >
> >
> >
> > On Tue, Mar 31, 2020 at 2:29 PM george brida 
> wrote:
> >
> > > Dear Jim,
> > >
> > > Thank you very much. I obtained now the required map. I would like to
> know
> > > how to add the names of the countries.
> > >
> > > Best
> > > George
> > >
> > > On Tue, Mar 31, 2020 at 10:10 AM Jim Lemon 
> wrote:
> > >
> > >> Hi George,
> > >> Try this:
> > >>
> > >> library(maps)
> > >> map("world",xlim=c(34.353,60.369),ylim=c(16.7,32.193),
> > >>  regions="Saudi Arabia",col="yellow",fill=TRUE)
> > >> map("world",regions="Bahrain",col="yellow",fill=TRUE,add=TRUE)
> > >> map("world",regions="Kuwait",col="lightblue",fill=TRUE,add=TRUE)
> > >> map("world",regions="Qatar",col="yellow",fill=TRUE,add=TRUE)
> > >> map("world",regions="United Arab
> > >> Emirates",col="lightblue",fill=TRUE,add=TRUE)
> > >> map("world",regions="Oman",col="lightgreen",fill=TRUE,add=TRUE)
> > >>
> > >> Jim
> > >>
> > >> On Tue, Mar 31, 2020 at 12:39 PM george brida  >
> > >> wrote:
> > >> >
> > >> > Dear R users,
> > >> >
> > >> > i would like to plot the maps of the Gulf Cooperation Council (GCC)
> > >> > countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
> > >> > constraints: i/ KSA , Qatar and Bahrain have the same face color ,
> ii/
> > >> > Kuweit and UAE with the same face color and iii/Oman  with another
> face
> > >> > color. Is there any code in R doing this task.
> > >> >
> > >> > Many thanks.
> > >> >
> > >> > [[alternative HTML version deleted]]
> > >> >
> > >> > __
> > >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > >> > https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/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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Re: [R] Mapping of countries

[george brida]

Dear Jim,

Is it possible to add also a title to this map?

Many thanks



On Tue, Mar 31, 2020 at 2:29 PM george brida  wrote:

> Dear Jim,
>
> Thank you very much. I obtained now the required map. I would like to know
> how to add the names of the countries.
>
> Best
> George
>
> On Tue, Mar 31, 2020 at 10:10 AM Jim Lemon  wrote:
>
>> Hi George,
>> Try this:
>>
>> library(maps)
>> map("world",xlim=c(34.353,60.369),ylim=c(16.7,32.193),
>>  regions="Saudi Arabia",col="yellow",fill=TRUE)
>> map("world",regions="Bahrain",col="yellow",fill=TRUE,add=TRUE)
>> map("world",regions="Kuwait",col="lightblue",fill=TRUE,add=TRUE)
>> map("world",regions="Qatar",col="yellow",fill=TRUE,add=TRUE)
>> map("world",regions="United Arab
>> Emirates",col="lightblue",fill=TRUE,add=TRUE)
>> map("world",regions="Oman",col="lightgreen",fill=TRUE,add=TRUE)
>>
>> Jim
>>
>> On Tue, Mar 31, 2020 at 12:39 PM george brida 
>> wrote:
>> >
>> > Dear R users,
>> >
>> > i would like to plot the maps of the Gulf Cooperation Council (GCC)
>> > countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
>> > constraints: i/ KSA , Qatar and Bahrain have the same face color , ii/
>> > Kuweit and UAE with the same face color and iii/Oman  with another face
>> > color. Is there any code in R doing this task.
>> >
>> > Many thanks.
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/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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Re: [R] Mapping of countries

[george brida]

Dear Gunter,

It is noted. Thanks

Best

On Tue, Mar 31, 2020 at 6:04 AM Bert Gunter  wrote:

> Probably better posted to the r-sig-geo list, where you are more
> likely to find the relevant expertise.
>
> Perhaps see also https://cran.r-project.org/web/views/Spatial.html,
> depending on what you plan to do with your maps.
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Mon, Mar 30, 2020 at 8:03 PM Erin Hodgess 
> wrote:
> >
> > Hello George!
> >
> > Do you mean to have a map of the world with these countries filled in, or
> > to have just those countries on the map, please?
> >
> > Thanks,
> > Erin
> >
> > Erin Hodgess, PhD
> > mailto: erinm.hodg...@gmail.com
> >
> >
> > On Mon, Mar 30, 2020 at 7:38 PM george brida 
> wrote:
> >
> > > Dear R users,
> > >
> > > i would like to plot the maps of the Gulf Cooperation Council (GCC)
> > > countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
> > > constraints: i/ KSA , Qatar and Bahrain have the same face color , ii/
> > > Kuweit and UAE with the same face color and iii/Oman  with another face
> > > color. Is there any code in R doing this task.
> > >
> > > Many thanks.
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/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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Re: [R] Mapping of countries

[george brida]

Dear Jim,

Thank you very much. I obtained now the required map. I would like to know
how to add the names of the countries.

Best
George

On Tue, Mar 31, 2020 at 10:10 AM Jim Lemon  wrote:

> Hi George,
> Try this:
>
> library(maps)
> map("world",xlim=c(34.353,60.369),ylim=c(16.7,32.193),
>  regions="Saudi Arabia",col="yellow",fill=TRUE)
> map("world",regions="Bahrain",col="yellow",fill=TRUE,add=TRUE)
> map("world",regions="Kuwait",col="lightblue",fill=TRUE,add=TRUE)
> map("world",regions="Qatar",col="yellow",fill=TRUE,add=TRUE)
> map("world",regions="United Arab
> Emirates",col="lightblue",fill=TRUE,add=TRUE)
> map("world",regions="Oman",col="lightgreen",fill=TRUE,add=TRUE)
>
> Jim
>
> On Tue, Mar 31, 2020 at 12:39 PM george brida 
> wrote:
> >
> > Dear R users,
> >
> > i would like to plot the maps of the Gulf Cooperation Council (GCC)
> > countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
> > constraints: i/ KSA , Qatar and Bahrain have the same face color , ii/
> > Kuweit and UAE with the same face color and iii/Oman  with another face
> > color. Is there any code in R doing this task.
> >
> > Many thanks.
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/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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Re: [R] Mapping of countries

[george brida]

Hi Erin,

Thanks for the reply. I would like to have just those countries on the map.

Best

George

On Tue, Mar 31, 2020 at 5:02 AM Erin Hodgess 
wrote:

> Hello George!
>
> Do you mean to have a map of the world with these countries filled in, or
> to have just those countries on the map, please?
>
> Thanks,
> Erin
>
> Erin Hodgess, PhD
> mailto: erinm.hodg...@gmail.com
>
>
> On Mon, Mar 30, 2020 at 7:38 PM george brida 
> wrote:
>
>> Dear R users,
>>
>> i would like to plot the maps of the Gulf Cooperation Council (GCC)
>> countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
>> constraints: i/ KSA , Qatar and Bahrain have the same face color , ii/
>> Kuweit and UAE with the same face color and iii/Oman  with another face
>> color. Is there any code in R doing this task.
>>
>> Many thanks.
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/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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[R] Mapping of countries

[george brida]

Dear R users,

i would like to plot the maps of the Gulf Cooperation Council (GCC)
countries (KSA, Qatar, Bahrain, Kuwait, UAE and Oman) with these
constraints: i/ KSA , Qatar and Bahrain have the same face color , ii/
Kuweit and UAE with the same face color and iii/Oman  with another face
color. Is there any code in R doing this task.

Many thanks.

[[alternative HTML version deleted]]

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[R] power analysis for Friedman's test

[George Karavasilis]

Hello,
I am running a non parametric repeated measures experiment with 
Friedman’s test:


    Friedman rank sum test

data:  glikozi and week and subject
Friedman chi-squared = 18.538, df = 3, p-value = 0.0003405

How could I run a power analysis for this test in R?
Thank you!

--
George Karavasilis
Department of Business Administration & 
Serres, Greece


---
Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus.
https://www.avast.com/antivirus

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Re: [R] Problem with r project in ubuntu xenial

[George Balas]

For anyone who sees this conversation.

There is a bug in installation of igraph in R language in Ubuntu. There is
a solution in stackoverflow. We have to use the devtools. Write this code:
install.packages("devtools")
library(devtools)
install_github("igraph/rigraph")

If there are errors installing devtools just install any package that
comments.

On Nov 5, 2017 00:07, "George Balas" <gbala...@gmail.com> wrote:

> -Well it seems that it is getting "el_GR.UTF-8" but still I am not able
> to read files written in greek, there are only "" instead of letters.
> -Also, I forgot to mention that I do load igraph library when I try 
> "graph_from_adjacency_matrix".
> When I check igraph in packages dialog I can not see functions with
> underscores between words, only dots.
>
> 2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:
>
>>
>> > On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
>> >
>> >
>> >> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
>> >>
>> >> I have a problem with R in Ubuntu 16.04. I do not know if it is mine
>> pc or
>> >> general problem but I was not able to find solution on Internet.
>> >> First of all I can not change locale to greek by getting this message:
>> >> "In Sys.setlocale("LC_CTYPE", "Greek") :
>> >> OS reports request to set locale to "Greek" cannot be honored"
>> >
>> > The Greek locale is likely not called "Greek" outside of Windows. More
>> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
>> Mac). These things are not standardized across platforms.
>> >
>>
>> Also
>>
>> From help(locales): Attempts to change the character set by
>> Sys.setlocale("LC_CTYPE") that implies a different character set during a
>> session may not work and are likely to lead to some confusion because it
>> may not affect the native encoding.
>>
>>
>> >> Second and more serious is that I can not use some functions like
>> >> graph_from_adjacency_matrix or print_all I get these messeges:
>> >> "could not find function "graph_from_adjacency_matrix""
>> >> "could not find function "print_all"".
>> >
>> > Missing library(igraph)?
>> >
>> > -pd
>> >
>> >> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
>> rstudio
>> >> or ubuntu terminal.
>> >> On my pc I also run win 10 with the same installs and I do not have the
>> >> above problems, but I work on ubuntu and can not change Os all the
>> time.
>> >> Please help me.
>> >>
>> >> Thank you for your time,
>> >> George
>> >> gbala...@gmail.com
>> >>
>> >>  [[alternative HTML version deleted]]
>> >>
>> >> __
>> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >
>> > --
>> > Peter Dalgaard, Professor,
>> > Center for Statistics, Copenhagen Business School
>> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> > Phone: (+45)38153501
>> > Office: A 4.23
>> > Email: pd@cbs.dk  Priv: pda...@gmail.com
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> David Winsemius
>> Alameda, CA, USA
>>
>> 'Any technology distinguishable from magic is insufficiently advanced.'
>>  -Gehm's Corollary to Clarke's Third Law
>>
>>
>>
>>
>>
>>
>

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[George Balas]

-Well it seems that it is getting "el_GR.UTF-8" but still I am not able to
read files written in greek, there are only "" instead of letters.
-Also, I forgot to mention that I do load igraph library when I try
"graph_from_adjacency_matrix".
When I check igraph in packages dialog I can not see functions with
underscores between words, only dots.

2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:

>
> > On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
> >
> >
> >> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
> >>
> >> I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc
> or
> >> general problem but I was not able to find solution on Internet.
> >> First of all I can not change locale to greek by getting this message:
> >> "In Sys.setlocale("LC_CTYPE", "Greek") :
> >> OS reports request to set locale to "Greek" cannot be honored"
> >
> > The Greek locale is likely not called "Greek" outside of Windows. More
> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
> Mac). These things are not standardized across platforms.
> >
>
> Also
>
> From help(locales): Attempts to change the character set by
> Sys.setlocale("LC_CTYPE") that implies a different character set during a
> session may not work and are likely to lead to some confusion because it
> may not affect the native encoding.
>
>
> >> Second and more serious is that I can not use some functions like
> >> graph_from_adjacency_matrix or print_all I get these messeges:
> >> "could not find function "graph_from_adjacency_matrix""
> >> "could not find function "print_all"".
> >
> > Missing library(igraph)?
> >
> > -pd
> >
> >> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
> rstudio
> >> or ubuntu terminal.
> >> On my pc I also run win 10 with the same installs and I do not have the
> >> above problems, but I work on ubuntu and can not change Os all the time.
> >> Please help me.
> >>
> >> Thank you for your time,
> >> George
> >> gbala...@gmail.com
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > --
> > Peter Dalgaard, Professor,
> > Center for Statistics, Copenhagen Business School
> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> > Phone: (+45)38153501
> > Office: A 4.23
> > Email: pd@cbs.dk  Priv: pda...@gmail.com
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Problem with r project in ubuntu xenial

[George Balas]

I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc or
general problem but I was not able to find solution on Internet.
First of all I can not change locale to greek by getting this message:
"In Sys.setlocale("LC_CTYPE", "Greek") :
  OS reports request to set locale to "Greek" cannot be honored"
Second and more serious is that I can not use some functions like
graph_from_adjacency_matrix or print_all I get these messeges:
"could not find function "graph_from_adjacency_matrix""
"could not find function "print_all"".
I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on rstudio
or ubuntu terminal.
On my pc I also run win 10 with the same installs and I do not have the
above problems, but I work on ubuntu and can not change Os all the time.
Please help me.

Thank you for your time,
George
gbala...@gmail.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] Wireframe plot inside a function

[George Trojan - NOAA Federal]

But it works ;-). According to print.trellis help, 'plot' is an alias
for 'print'.

IMO, this is an abuse of overloading: same method name does totally
different things.

On 21 April 2017 at 21:58, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> No... it is
>
> print(plot(cop1, main = "cop1 function"))
>
> --
> Sent from my phone. Please excuse my brevity.
>
> On April 21, 2017 1:56:00 PM PDT, George Trojan - NOAA Federal 
> <george.tro...@noaa.gov> wrote:
>>I see. So, if I don't care about the plot object itself,  the proper
>>incantation is
>>
>>plot(plot(cop1, main = "cop1 function"))
>>
>>Thanks again.
>>
>>On 21 April 2017 at 20:32, Jeff Newmiller <jdnew...@dcn.davis.ca.us>
>>wrote:
>>> Your original function created the cop1 plot object but did nothing
>>with it. It then created the cop2 plot and returned it from the
>>function. Since you had invoked the cplot function from the interactive
>>console, R printed that returned object automatically, which displayed
>>the plot.
>>>
>>> FYI: when you want to start presenting multiple plots and/or tables
>>together you will find that something like knitr and RMarkdown are very
>>helpful.
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On April 21, 2017 11:59:28 AM PDT, George Trojan - NOAA Federal
>><george.tro...@noaa.gov> wrote:
>>>>Thanks. After changing the function to
>>>>
>>>>cplot <- function(cop1, cop2) {
>>>>  x11()
>>>>  o <- plot(cop1, main = "cop1 function")
>>>>  print(o)
>>>>  x11()
>>>>  o <- plot(cop2, main = "cop2 function")
>>>>  print(o)
>>>>}
>>>>
>>>>I see both plots. But, since "cop2 function" was plotted before, does
>>>>it mean it is plotted twice now? Looks as a strange design.
>>>>
>>>>I did check the "Plain text mode" in Chrome, you should see only the
>>>>text part.
>>>>
>>>>George
>>>>
>>>>On 21 April 2017 at 16:27, Jeff Newmiller <jdnew...@dcn.davis.ca.us>
>>>>wrote:
>>>>> FAQ 7.22
>>>>> And don't send HTML email... you are the one making it difficult
>>for
>>>>us to read your question.
>>>>>
>>>>> --
>>>>> Sent from my phone. Please excuse my brevity.
>>>>>
>>>>> On April 21, 2017 8:27:20 AM PDT, George Trojan - NOAA Federal
>>>><george.tro...@noaa.gov> wrote:
>>>>>>Consider the following example:
>>>>>>
>>>>>>library("kdecopula")
>>>>>>library("mvtnorm")
>>>>>>
>>>>>>pobs <- function(x) rank(x) / (length(x) + 1)
>>>>>>
>>>>>>n <- 1000
>>>>>>
>>>>>>sigma1 <- diag(x = 1, 2, 2)
>>>>>>x1 <- rmvnorm(n, sigma = sigma1)
>>>>>>xx1 <- apply(x1, 2, pobs)
>>>>>>cop1 <- kdecop(xx1)
>>>>>>
>>>>>>eps <- 0.8
>>>>>>sigma2 <- matrix(c(1, eps, eps, 1), ncol = 2)
>>>>>>x2 <- rmvnorm(n, sigma = sigma2)
>>>>>>xx2 <- apply(x2, 2, pobs)
>>>>>>cop2 <- kdecop(xx2)
>>>>>>
>>>>>>x11()
>>>>>>plot(cop1, main = "cop1 main")
>>>>>>x11()
>>>>>>plot(cop2, main = "cop2 main")
>>>>>>
>>>>>>cplot <- function(cop1, cop2) {
>>>>>>  x11()
>>>>>>  plot(cop1, main = "cop1 function")
>>>>>>  x11()
>>>>>>  plot(cop2, main = "cop2 function")
>>>>>>}
>>>>>>
>>>>>>cplot(cop1, cop2)
>>>>>>
>>>>>>cat("Press  to quit")
>>>>>>readLines(file("stdin"), n
>>>>>>
>>>>>>=
>>>>>>
>>>>>>1)
>>>>>>quit()
>>>>>>
>>>>>>When I run it with Rscript all four x11 windows pop up, however the
>>>>one
>>>>>>that should display "cop1 function" is blank, the wireframe is not
>>>>>>plotted.
>>>>>>This is R 3.3.1, on Fedora 20.
>>>>>>I see similar behaviour on Fedora 24, R 3.3.3 when I run the code
>>>>from
>>>>>>RStudio (the most recent one).
>>>>>>
>>>>>>George
>>>>>>
>>>>>>   [[alternative HTML version deleted]]
>>>>>>
>>>>>>__
>>>>>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>PLEASE do read the posting guide
>>>>>>http://www.R-project.org/posting-guide.html
>>>>>>and provide commented, minimal, self-contained, reproducible code.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Wireframe plot inside a function

[George Trojan - NOAA Federal]

I see. So, if I don't care about the plot object itself,  the proper
incantation is

plot(plot(cop1, main = "cop1 function"))

Thanks again.

On 21 April 2017 at 20:32, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> Your original function created the cop1 plot object but did nothing with it. 
> It then created the cop2 plot and returned it from the function. Since you 
> had invoked the cplot function from the interactive console, R printed that 
> returned object automatically, which displayed the plot.
>
> FYI: when you want to start presenting multiple plots and/or tables together 
> you will find that something like knitr and RMarkdown are very helpful.
> --
> Sent from my phone. Please excuse my brevity.
>
> On April 21, 2017 11:59:28 AM PDT, George Trojan - NOAA Federal 
> <george.tro...@noaa.gov> wrote:
>>Thanks. After changing the function to
>>
>>cplot <- function(cop1, cop2) {
>>  x11()
>>  o <- plot(cop1, main = "cop1 function")
>>  print(o)
>>  x11()
>>  o <- plot(cop2, main = "cop2 function")
>>  print(o)
>>}
>>
>>I see both plots. But, since "cop2 function" was plotted before, does
>>it mean it is plotted twice now? Looks as a strange design.
>>
>>I did check the "Plain text mode" in Chrome, you should see only the
>>text part.
>>
>>George
>>
>>On 21 April 2017 at 16:27, Jeff Newmiller <jdnew...@dcn.davis.ca.us>
>>wrote:
>>> FAQ 7.22
>>> And don't send HTML email... you are the one making it difficult for
>>us to read your question.
>>>
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On April 21, 2017 8:27:20 AM PDT, George Trojan - NOAA Federal
>><george.tro...@noaa.gov> wrote:
>>>>Consider the following example:
>>>>
>>>>library("kdecopula")
>>>>library("mvtnorm")
>>>>
>>>>pobs <- function(x) rank(x) / (length(x) + 1)
>>>>
>>>>n <- 1000
>>>>
>>>>sigma1 <- diag(x = 1, 2, 2)
>>>>x1 <- rmvnorm(n, sigma = sigma1)
>>>>xx1 <- apply(x1, 2, pobs)
>>>>cop1 <- kdecop(xx1)
>>>>
>>>>eps <- 0.8
>>>>sigma2 <- matrix(c(1, eps, eps, 1), ncol = 2)
>>>>x2 <- rmvnorm(n, sigma = sigma2)
>>>>xx2 <- apply(x2, 2, pobs)
>>>>cop2 <- kdecop(xx2)
>>>>
>>>>x11()
>>>>plot(cop1, main = "cop1 main")
>>>>x11()
>>>>plot(cop2, main = "cop2 main")
>>>>
>>>>cplot <- function(cop1, cop2) {
>>>>  x11()
>>>>  plot(cop1, main = "cop1 function")
>>>>  x11()
>>>>  plot(cop2, main = "cop2 function")
>>>>}
>>>>
>>>>cplot(cop1, cop2)
>>>>
>>>>cat("Press  to quit")
>>>>readLines(file("stdin"), n
>>>>
>>>>=
>>>>
>>>>1)
>>>>quit()
>>>>
>>>>When I run it with Rscript all four x11 windows pop up, however the
>>one
>>>>that should display "cop1 function" is blank, the wireframe is not
>>>>plotted.
>>>>This is R 3.3.1, on Fedora 20.
>>>>I see similar behaviour on Fedora 24, R 3.3.3 when I run the code
>>from
>>>>RStudio (the most recent one).
>>>>
>>>>George
>>>>
>>>>   [[alternative HTML version deleted]]
>>>>
>>>>__
>>>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>>PLEASE do read the posting guide
>>>>http://www.R-project.org/posting-guide.html
>>>>and provide commented, minimal, self-contained, reproducible code.

__
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Re: [R] Wireframe plot inside a function

[George Trojan - NOAA Federal]

Thanks. After changing the function to

cplot <- function(cop1, cop2) {
  x11()
  o <- plot(cop1, main = "cop1 function")
  print(o)
  x11()
  o <- plot(cop2, main = "cop2 function")
  print(o)
}

I see both plots. But, since "cop2 function" was plotted before, does
it mean it is plotted twice now? Looks as a strange design.

I did check the "Plain text mode" in Chrome, you should see only the text part.

George

On 21 April 2017 at 16:27, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> FAQ 7.22
> And don't send HTML email... you are the one making it difficult for us to 
> read your question.
>
> --
> Sent from my phone. Please excuse my brevity.
>
> On April 21, 2017 8:27:20 AM PDT, George Trojan - NOAA Federal 
> <george.tro...@noaa.gov> wrote:
>>Consider the following example:
>>
>>library("kdecopula")
>>library("mvtnorm")
>>
>>pobs <- function(x) rank(x) / (length(x) + 1)
>>
>>n <- 1000
>>
>>sigma1 <- diag(x = 1, 2, 2)
>>x1 <- rmvnorm(n, sigma = sigma1)
>>xx1 <- apply(x1, 2, pobs)
>>cop1 <- kdecop(xx1)
>>
>>eps <- 0.8
>>sigma2 <- matrix(c(1, eps, eps, 1), ncol = 2)
>>x2 <- rmvnorm(n, sigma = sigma2)
>>xx2 <- apply(x2, 2, pobs)
>>cop2 <- kdecop(xx2)
>>
>>x11()
>>plot(cop1, main = "cop1 main")
>>x11()
>>plot(cop2, main = "cop2 main")
>>
>>cplot <- function(cop1, cop2) {
>>  x11()
>>  plot(cop1, main = "cop1 function")
>>  x11()
>>  plot(cop2, main = "cop2 function")
>>}
>>
>>cplot(cop1, cop2)
>>
>>cat("Press  to quit")
>>readLines(file("stdin"), n
>>
>>=
>>
>>1)
>>quit()
>>
>>When I run it with Rscript all four x11 windows pop up, however the one
>>that should display "cop1 function" is blank, the wireframe is not
>>plotted.
>>This is R 3.3.1, on Fedora 20.
>>I see similar behaviour on Fedora 24, R 3.3.3 when I run the code from
>>RStudio (the most recent one).
>>
>>George
>>
>>   [[alternative HTML version deleted]]
>>
>>__
>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Interesting quirk with fractions and rounding

[George Trojan - NOAA Federal]

The subject is messy. I vaguely remember learning this stuff on my
first numerical analysis course over 40 years ago. The classic
reference material (much newer, only 25 years old) is:
What Every Computer Scientist Should Know About Floating-Point
Arithmetic, David Goldberg, ACM Computing Surveys, Vol 23, No 1, 1991.
Available here:  http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.6768


George

I suggest you read some basic books on numerical analysis and/or talk
> with a numerical analyst. You are (like most of us) an amateur at this
> sort of thing trying to reinvent wheels. If you are concerned with
> details, talk with experts. Don't assume what you don't know. This
> list is *not* a reliable source of such expertise, although there
> *are* individuals in the R universe with considerable knowledge who
> may or may not choose to respond.
> Cheers,
> Bert
> Bert Gunter
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )



On Fri, Apr 21, 2017 at 5:19 AM, Paul Johnson https://stat.ethz.ch/mailman/listinfo/r-help>> wrote:
>* We all agree it is a problem with digital computing, not unique to R. I
*>* don't think that is the right place to stop.
*>>* What to do? The round example arose in a real funded project where 2 R
*>* programs differed in results and cause was  that one person got 57 and
*>* another got 58. The explanation was found, but its less clear how to
*>* prevent similar in future. Guidelines, anyone?
*>>* So far, these are my guidelines.
*>>* 1. Insert L on numbers to signal that you really mean INTEGER. In R,
*>* forgetting the L in a single number will usually promote whole calculation
*>* to floats.
*>* 2. S3 variables are called 'numeric' if they are integer or double storage.
*>* So avoid "is.numeric" and prefer "is.double".
*>* 3. == is a total fail on floats
*>* 4. Run print with digits=20 so we can see the less rounded number. Perhaps
*>* start sessions with "options(digits=20)"
*>* 5. all.equal does what it promises, but one must be cautious.
*>>* Are there math habits we should follow?
*>>* For example, Is it generally true in R that (100*x)/y is more accurate than
*>* 100*(x/y), if x > y?   (If that is generally true, couldn't the R
*>* interpreter do it for the user?)
*>>* I've seen this problem before. In later editions of the game theory program
*>* Gambit, extraordinary effort was taken to keep values symbolically as
*>* integers as long as possible. Avoid division until the last steps. Same in
*>* Swarm simulations. Gary Polhill wrote an essay about the Ghost in the
*>* Machine along those lines, showing accidents from trusting floats.
*>>* I wonder now if all uses of > or < with numeric variables are suspect.
*>>* Oh well. If everybody posts their advice, I will write a summary.
*>>* Paul Johnson
*>* University of Kansas
*>>* On Apr 21, 2017 12:02 AM, "PIKAL Petr" https://stat.ethz.ch/mailman/listinfo/r-help>> wrote:
*>>>* Hi
*>>>>* The problem is that people using Excel or probably other such
spreadsheets
*>>* do not encounter this behaviour as Excel silently rounds all your
*>>* calculations and makes approximate comparison without telling it does so.
*>>* Therefore most people usually do not have any knowledge of floating point
*>>* numbers representation.
*>>>>*  Cheers
*>>* Petr
*>>>>* -Original Message-
*>>* From: R-help [mailto:r-help-bounces at r-project.org
<https://stat.ethz.ch/mailman/listinfo/r-help>] On Behalf Of Paul
*>>* Johnson
*>>* Sent: Thursday, April 20, 2017 11:56 PM
*>>* To: R-help https://stat.ethz.ch/mailman/listinfo/r-help>>
*>>* Subject: [R] Interesting quirk with fractions and rounding
*>>>>* Hello, R friends
*>>>>* My student unearthed this quirk that might interest you.
*>>>>* I wondered if this might be a bug in the R interpreter. If not a bug, it
*>>* certainly stands as a good example of the dangers of floating point numbers
*>>* in computing.
*>>>>* What do you think?
*>>>>* > 100*(23/40)
*>>* [1] 57.5
*>>* > (100*23)/40
*>>* [1] 57.5
*>>* > round(100*(23/40))
*>>* [1] 57
*>>* > round((100*23)/40)
*>>* [1] 58
*>>>>* The result in the 2 rounds should be the same, I think.  Clearly some
*>>* digital number devil is at work. I *guess* that when you put in whole
*>>* numbers and group them like this (100*23), the interpreter does integer
*>>* math, but if you group (23/40), you force a fractional divisi

[R] Wireframe plot inside a function

[George Trojan - NOAA Federal]

Consider the following example:

library("kdecopula")
library("mvtnorm")

pobs <- function(x) rank(x) / (length(x) + 1)

n <- 1000

sigma1 <- diag(x = 1, 2, 2)
x1 <- rmvnorm(n, sigma = sigma1)
xx1 <- apply(x1, 2, pobs)
cop1 <- kdecop(xx1)

eps <- 0.8
sigma2 <- matrix(c(1, eps, eps, 1), ncol = 2)
x2 <- rmvnorm(n, sigma = sigma2)
xx2 <- apply(x2, 2, pobs)
cop2 <- kdecop(xx2)

x11()
plot(cop1, main = "cop1 main")
x11()
plot(cop2, main = "cop2 main")

cplot <- function(cop1, cop2) {
  x11()
  plot(cop1, main = "cop1 function")
  x11()
  plot(cop2, main = "cop2 function")
}

cplot(cop1, cop2)

cat("Press  to quit")
readLines(file("stdin"), n
​ ​
=
​ ​
1)
quit()

When I run it with Rscript all four x11 windows pop up, however the one
that should display "cop1 function" is blank, the wireframe is not plotted.
This is R 3.3.1, on Fedora 20.
I see similar behaviour on Fedora 24, R 3.3.3 when I run the code from
RStudio (the most recent one).

George

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[R] Question about logspline

[George Trojan - NOAA Federal]

I have a dataset with values of limited precision. I am trying to plot its
density using package logspline. The logspline() call with default
parameters causes oscillations in the density plot. My solution was to
fuzzify the input values, using function:

 > fuzz <- function(x, prec) x + runif(length(x), -prec / 2, prec /2)

Is there a better idea, perhaps setting mind?

Example:

> x <- seq(-1, 1, by = 0.01)
> ds <- rnorm(1000, sd = 0.2)
> hist(ds, breaks = 40, freq = FALSE)
> s <- logspline(ds)
> lines(x, dlogspline(x, s), col = "red")
> ds2 <- as.numeric(sapply(ds, function(x) sprintf("%.1f", x)))
> s2 <- logspline(ds2)
> lines(x, dlogspline(x, s2), col = "blue")
> ds3 <- fuzz(ds2, 0.1)
> s3 <- logspline(ds3)
> lines(x, dlogspline(x, s3), col = "green")
>

George

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Re: [R] Help with saving user defined functions

[George Trojan - NOAA Federal]

I want to split my computation into parts. The first script processes the
data, the second does the graphics. I want to save  results of
time-consuming calculations. My example tried to simulate this by terminate
the session without saving it, so the environment was lost on purpose. What
confuses me that ecdf can be saved and restored, but not my own derived
function.
Of course I can save parameters and redefine the function in the second
script.

Reading Chapter 8 of Advanced R, hopefully the book will clear my mind.

On Mon, Feb 13, 2017 at 12:05 AM, Bert Gunter <bgunter.4...@gmail.com>
wrote:

> It worked fine for me:
>
> > t <- rnorm(100)
> > cdf <- ecdf(t)
> >
> > trans <- function(x) qnorm(cdf(x) * 0.99)
> > saveRDS(trans, "/tmp/foo")
> > trans(1.2)
> [1] 1.042457
> > trans1 <- readRDS("/tmp/foo")
> > trans1(0)
> [1] 0.1117773
>
>
> Of course, if I remove cdf() from the global environment, it will fail:
>
> > rm(cdf)
> > trans1(0)
> Error in qnorm(cdf(x) * 0.99) : could not find function "cdf"
>
> So it looks like you're clearing you global workspace in between
> saving and loading?
>
> You may need to read up on function closures/lexical scoping : A
> user-defined function in R includes not only code but also a pointer
> to the environment in which it was defined, in your case, the global
> environment from which you apparently removed cdf(). Note that
> functions are not evauated until called, so free variables in the
> functions that do not or will not exist in the function's lexical
> scope when called will not trigger any errors until the function *is*
> called.
>
> Same comments for your second version -- if tmp is removed the
> function will fail.
>
>
>
> Cheers,
> Bert
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Sun, Feb 12, 2017 at 2:11 PM, George Trojan - NOAA Federal
> <george.tro...@noaa.gov> wrote:
> > I can't figure out how to save functions to RDS file. Here is an example
> > what I am trying to achieve:
> >
> >> t <- rnorm(100)
> >> cdf <- ecdf(t)
> >> cdf(0)
> > [1] 0.59
> >> saveRDS(cdf, "/tmp/foo")
> >>
> > Save workspace image? [y/n/c]: n
> > [gtrojan@asok petproject]$ R
> >> cdf <- readRDS("/tmp/foo")
> >> cdf
> > Empirical CDF
> > Call: ecdf(t)
> > x[1:100] = -2.8881, -2.2054, -2.0026,  ..., 2.0367, 2.0414
> >
> > This works. However when instead of saving cdf() I try to save function
> >
> >> trans <- function(x) qnorm(cdf(x) * 0.99)
> >
> > after restoring object from file I get an error:
> >
> >> trans <- readRDS("/tmp/foo")
> >> trans(0)
> > Error in qnorm(cdf(x) * 0.99) : could not find function "cdf"
> >
> > I tried to define and call cdf within the definition of trans, without
> > success:
> >
> >> tmp <- rnorm(100)
> >> trans <- function(x) { cdf <- ecdf(tmp); cdf(0); qnorm(cdf(x)) * 0.99 }
> >> saveRDS(trans, "/tmp/foo")
> > Save workspace image? [y/n/c]: n
> >
> >> trans <- readRDS("/tmp/foo")
> >> trans
> > function(x) { cdf <- ecdf(tmp); cdf(0); qnorm(cdf(x)) * 0.99 }
> >> trans(0)
> > Error in sort(x) : object 'tmp' not found
> >
> > So, here the call cdf(0) did not force evaluation of my random sample.
> What
> > am I missing?
> >
> > George
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

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[R] Help with saving user defined functions

[George Trojan - NOAA Federal]

I can't figure out how to save functions to RDS file. Here is an example
what I am trying to achieve:

> t <- rnorm(100)
> cdf <- ecdf(t)
> cdf(0)
[1] 0.59
> saveRDS(cdf, "/tmp/foo")
>
Save workspace image? [y/n/c]: n
[gtrojan@asok petproject]$ R
> cdf <- readRDS("/tmp/foo")
> cdf
Empirical CDF
Call: ecdf(t)
x[1:100] = -2.8881, -2.2054, -2.0026,  ..., 2.0367, 2.0414

This works. However when instead of saving cdf() I try to save function

> trans <- function(x) qnorm(cdf(x) * 0.99)

after restoring object from file I get an error:

> trans <- readRDS("/tmp/foo")
> trans(0)
Error in qnorm(cdf(x) * 0.99) : could not find function "cdf"

I tried to define and call cdf within the definition of trans, without
success:

> tmp <- rnorm(100)
> trans <- function(x) { cdf <- ecdf(tmp); cdf(0); qnorm(cdf(x)) * 0.99 }
> saveRDS(trans, "/tmp/foo")
Save workspace image? [y/n/c]: n

> trans <- readRDS("/tmp/foo")
> trans
function(x) { cdf <- ecdf(tmp); cdf(0); qnorm(cdf(x)) * 0.99 }
> trans(0)
Error in sort(x) : object 'tmp' not found

So, here the call cdf(0) did not force evaluation of my random sample. What
am I missing?

George

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[R] diff doesnot work

[george brida]

Dear R users,

I have a txt file entitled coc composed by one column of numeric values
without header and having 50 rows. This file is under the following path:

C:\\Users\\intel\\Documents\\TR

I have written the following lines:

xcx=read.table("C:\\Users\\intel\\Documents\\TR\\coc.txt",header=F)
xc=log(xcx)

I have obtained the series xc but when I wrote
x=diff(xc)

I obtained the following message:

data frame with 0 columns and 50 rows

I don't know where is the problem. Can you help me please

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[R] R2Cube integration errors

[George Trojan - NOAA Federal]

Why this happens?

> library("R2Cuba")
> f <- function(x) 0
> cuhre(ndim=1, ncomp=1, f)
Iteration 1:  11 integrand evaluations so far
[1] 0 +- 0  chisq 0 (0 df)
Iteration 2:  33 integrand evaluations so far
[1] 0 +- 0  chisq 0 (1 df)
integral: 0 (+-0)
nregions: 2; number of evaluations:  33; probability:  0
> vegas(ndim=1, ncomp=1, f)
Iteration 1:  1000 integrand evaluations so far
[1] 0 +- 7.02518e-18chisq 0 (0 df)
. . .
Iteration 13:  52000 integrand evaluations so far
[1] 0 +- 2.65413e-18chisq 0 (12 df)
integral: 0 (+-2.7e-18)
number of evaluations:  52000; probability:  0
failed with message  ‘Dimension out of range’
> suave(ndim=1, ncomp=1, f)
. . .
[1] 0 +- 7.02462e-17chisq 0 (411 df)
integral: 0 (+-7e-17)
nregions: 50; number of evaluations:  5; probability:  0
failed with message  ‘Dimension out of range’

Is this a bug?

George

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[R] rgl does not plot

[George Trojan - NOAA Federal]

I have installed package rgl without any problems. I can load the library,
issue commands from console without any errors showing up, however I can't
get anything plotted. Example session:

> library(rgl)
> plot3d(rnorm(100), rnorm(100), rnorm(100))
> rgl.quit()
> library(rgl)
> .check3d()
glX
 1
> plot3d(rnorm(100), rnorm(100), rnorm(100))
> > open3d()
glX
 2
> plot3d(rnorm(100), rnorm(100), rnorm(100))
> rgl.quit()

.check3d() and open3d() open a small window ~8x8 cm, copying desktop
background under it, which stays there when the window is moved. plot3d()
does not do anything. rgl.quit() closes the windows, as expected.

I am running Fedora 24 Scientific, NVIDIA video card with NVIDIA
proprietory driver that supports GLX. Any idea where to look for a solution?

George

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[R] gamlss question

[George Trojan - NOAA Federal]

What is the recommended way of accessing distribution parameters (mu,
sigma, ...) from the model fit? The indention is to use those values in
d/p/q/r calls. I came out with a wrapper

gamlss_fit <- function(x, family) {
fit <- gamlssML(x, family = family)
mu <- fitted(fit, "mu")[1]
sigma <- fitted(fit, "sigma")[1]
nu <- ifelse("nu" %in% fit$parameters, fitted(fit, "nu")[1], NA)
tau <- ifelse("tau" %in% fit$parameters, fitted(fit, "tau")[1], NA)
list(mu = mu, sigma = sigma, nu = nu, tau = tau)
}

Alternatively, I could write functions to emulate logspline calls to
density estimation.

I suspect I must be missing something obvious. I am relatively new to R.

George

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Re: [R] Matrix multiplications

[george brida]

Thank you very much Peter.

On Sat, May 21, 2016 at 9:18 PM, peter dalgaard <pda...@gmail.com> wrote:

>
> > On 21 May 2016, at 21:00 , george brida <george.br...@gmail.com> wrote:
> >
> > Dear R users:
> >
> > I have written the following lines :
> >
> >> x=c(10,11,12,13,14,17,15,16,10,11,41,25,26,14,12,14,15,20,14,22)
> >> x=matrix(x,ncol=2)
> >> a=matrix(1,nrow(x),1)
> >> X=cbind(a,x)
> >> y=c(12.00, 11.00, 13.00, 12.50, 14.00, 18.50, 15.00, 12.50, 13.75,
> 15.00)
> >
> >> b=solve(t(X)%*% X)%*% t(X)%*% y
> >
> > when I wrote the following line
> >> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))*solve(t(X)%*% X)
> > I have obtained an error message, I don't know why namely (t(y-X %*%
> > b)%*%(y-X %*% b)/(length(y)-ncol(X))) is a scalar:
> >> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))
> > [,1]
> > [1,] 3.620354
> >
> >
> > Can you please help me.
>
> Mistake is that (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X))) is NOT a
> scalar, but a 1 x 1 matrix.
>
> This works:
>
> as.vector((t(y-X %*% b)%*%(y-X %*% b))/(length(y)-ncol(X)))*solve(t(X)%*%
> X)
>
> as does recognizing the first term as a sum of squares:
>
> sum((y-X %*% b)^2)/(length(y)-ncol(X))*solve(t(X)%*% X)
>
> (And, for the Illuminati, a Kronecker product works too:
>
> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X))) %x% solve(t(X)%*% X)
>
> This could be useful for multivariate y.)
>
> >
> > Thank you
> >
> > George
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
>
>
>
>
>
>
>
>
>

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Re: [R] Matrix multiplications

[george brida]

Roy,

Yes, t(y-X %*% b) is the transpose of y-X %*% b. In principle the product
of  t(y-X %*% b) *(y-X %*% b) is a scalar, I don't know why I have an error
message after the following line:

(t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))*solve(t(X)%*% X)

Thanks


On Sat, May 21, 2016 at 9:10 PM, Roy Mendelssohn - NOAA Federal <
roy.mendelss...@noaa.gov> wrote:

> >  str(t(y-X %*% b))
>  num [1, 1:10] 0.595 -1.7538 -0.0498 -1.651 -0.6328 ...
> > str((y-X %*% b))
>  num [1:10, 1] 0.595 -1.7538 -0.0498 -1.651 -0.6328 …
>
> -Roy
>
>
> > On May 21, 2016, at 12:00 PM, george brida <george.br...@gmail.com>
> wrote:
> >
> > Dear R users:
> >
> > I have written the following lines :
> >
> >> x=c(10,11,12,13,14,17,15,16,10,11,41,25,26,14,12,14,15,20,14,22)
> >> x=matrix(x,ncol=2)
> >> a=matrix(1,nrow(x),1)
> >> X=cbind(a,x)
> >> y=c(12.00, 11.00, 13.00, 12.50, 14.00, 18.50, 15.00, 12.50, 13.75,
> 15.00)
> >
> >> b=solve(t(X)%*% X)%*% t(X)%*% y
> >
> > when I wrote the following line
> >> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))*solve(t(X)%*% X)
> > I have obtained an error message, I don't know why namely (t(y-X %*%
> > b)%*%(y-X %*% b)/(length(y)-ncol(X))) is a scalar:
> >> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))
> > [,1]
> > [1,] 3.620354
> >
> >
> > Can you please help me.
> >
> > Thank you
> >
> > George
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new address and phone***
> 110 Shaffer Road
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
>

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[R] Matrix multiplications

[george brida]

Dear R users:

I have written the following lines :

>x=c(10,11,12,13,14,17,15,16,10,11,41,25,26,14,12,14,15,20,14,22)
> x=matrix(x,ncol=2)
> a=matrix(1,nrow(x),1)
> X=cbind(a,x)
>y=c(12.00, 11.00, 13.00, 12.50, 14.00, 18.50, 15.00, 12.50, 13.75, 15.00)

>b=solve(t(X)%*% X)%*% t(X)%*% y

when I wrote the following line
>(t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))*solve(t(X)%*% X)
I have obtained an error message, I don't know why namely (t(y-X %*%
b)%*%(y-X %*% b)/(length(y)-ncol(X))) is a scalar:
> (t(y-X %*% b)%*%(y-X %*% b)/(length(y)-ncol(X)))
 [,1]
[1,] 3.620354


Can you please help me.

Thank you

George

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[R] R cannot allocate a vector of size 5.4mb

[Jijo Sunny George]

Hi,

I am trying to do mixed integer programming using R & Java. My input is a list 
of flight legs which is proportional to the number of times the loop is 
executed. The input is fed from java to R.
I cannot avoid the for loops as it is part of the logic. I am running into a 
"cannot allocate a vector of size 5.4mb" error.
The system memory available 16Gb and nearly 11Gb of it is used. I checked on 
the memory.limit() in R and it is showing as 16Gb.

Can someone guide me with this.

package used to connect r and java  - Rserve
I checked with Rserve developers to reduce the execution time of my loop but 
after doing that i ran into the above mentioned error

Thanks & Regards
Jijo Sunny


DISCLAIMER: "The information in this e-mail and any atta...{{dropped:12}}

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[R] [R-pkgs] New package 'netdiffuseR: Network Analysis for Diffusion of Innovations'

[George Vega Yon]

Dear useRs,

We are happy to announce that the R package 'netdiffuseR: Network
Analysis for Diffusion of Innovations' is now on CRAN
(https://cran.r-project.org/web/packages/netdiffuseR/). From the
package's description:

"Empirical statistical analysis, visualization and simulation of
network models of the diffusion of innovations. The package implements
algorithms for calculating network diffusion statistics such as
transmission rate, hazard rates, exposure models, network threshold
levels, infectiousness (contagion), and susceptibility. The package is
inspired by work published in Valente, et al., (2015)
; Valente (1995)
, Myers (2000) , Iyengar and
others (2011) , Burt (1987)
; among others."

Some other relevant features:
 - Allows working with relative large graphs via sparse matrices
(easily handles tenths of thousands vertices), and
 - Includes three classical network diffusion of innovations datasets:
Brazilian Farmers, Korean Family Planning and Medical Innovation

The package should be available to be installed via R's
install.packages function in the following hours as CRAN builds
binaries for Windows/OSX and mirrors have them available to be
installed.

For those of you who are interested on taking a deep look on this new
tool, we will be offering a workshop at the 2016 SUNBELT Conference
(http://insna.org/sunbelt2016/) , so we encourage you to sign in!

Best,

George G. Vega Yon
+1 (626) 381 8171
http://www.its.caltech.edu/~gvegayon/

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[R] SEM specify RAM model

[George Parish]

Dear all,
I am trying to create multiple SEM models in a loop - so that if I change the 
data they can easily be re-created rather than re-creating each RAM model line 
by line - therein lies my problem.
I have a dataframe set out as follows1 Duration - RC1  
cov1 -0.2563002  MMSE - RC1  cov2 -0.0309003   
 RC1 - Aggression  npi1  0.2310004RC1 - Apathy
  npi2  0.1043005 RC1 - Disinhibition  npi3  0.279800 ...
the specifyModel() and specifyEquations() methods need you to manually input 
each line individually. Can I simply supply the SEM method with a matrix like 
the one I have above?
Thanks,George 
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[R] New to R

[George Katsuras]

I successfully downloaded and loaded the stockPortfolio and quadprog packages, 
but when I entered the following command I got an error:


returns - getReturns(names(stocks), freq=week)
Error in file(file, rt) : cannot open the connection
In addition: Warning message:
In file(file, rt) : cannot open: HTTP status was '404 Not Found'




When I tried discovering the source of this error, it appears that the file has 
been temporarily moved to a new URL address.


I’m currently running Windows 8.1.


Is there a fix for this?




Sent from Windows Mail
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[R] Problem with plm package

[george brida]

Dear friends,
I have a csv data entitled GFS in the following path:
c:\TEG
This data is attached with this mail.
When I wrote the following lines:

y=read.csv(c:\\TEG\\GFS.csv, header=FALSE, sep=;)
  purtest(y, pmax = 4, exo = intercept, test = hadri)

I obtained the following message:

Error in Math.factor(x) : cumsum not meaningful for factors
In addition: There were 50 or more warnings (use warnings() to see the
first 50)

where's the problem? can you please help me
Thank you in advance
George
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Re: [R] Problem with plm package

[george brida]

Hi Arun
you can't open the file?


On Wed, Jan 29, 2014 at 9:23 PM, arun smartpink...@yahoo.com wrote:

 Hi,
 Your attachment didn't came through.
 A.K.





 On Wednesday, January 29, 2014 12:03 PM, george brida 
 george.br...@gmail.com wrote:
 Dear friends,
 I have a csv data entitled GFS in the following path:
 c:\TEG
 This data is attached with this mail.
 When I wrote the following lines:

 y=read.csv(c:\\TEG\\GFS.csv, header=FALSE, sep=;)
   purtest(y, pmax = 4, exo = intercept, test = hadri)

 I obtained the following message:

 Error in Math.factor(x) : cumsum not meaningful for factors
 In addition: There were 50 or more warnings (use warnings() to see the
 first 50)

 where's the problem? can you please help me
 Thank you in advance
 George

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Re: [R] Problem with plm package

[george brida]

Ah ok. the problem is somewhat great, I can't rewrite it in txt file.


On Wed, Jan 29, 2014 at 10:48 PM, george brida george.br...@gmail.comwrote:

 Ah ok. the problem is somewhat great, I can't rewrite it in txt file.


 On Wed, Jan 29, 2014 at 9:52 PM, arun smartpink...@yahoo.com wrote:

 HI George,

 Some of the attachments get stripped off by the mailing list.  Check this
 link:
   http://www.r-project.org/mail.html


 May be .txt files will be okay.
 Arun




 On Wednesday, January 29, 2014 3:43 PM, george brida 
 george.br...@gmail.com wrote:
 Hi Arun
 you can't open the file?


 On Wed, Jan 29, 2014 at 9:23 PM, arun smartpink...@yahoo.com wrote:

  Hi,
  Your attachment didn't came through.
  A.K.
 
 
 
 
 
  On Wednesday, January 29, 2014 12:03 PM, george brida 
  george.br...@gmail.com wrote:
  Dear friends,
  I have a csv data entitled GFS in the following path:
  c:\TEG
  This data is attached with this mail.
  When I wrote the following lines:
 
  y=read.csv(c:\\TEG\\GFS.csv, header=FALSE, sep=;)
purtest(y, pmax = 4, exo = intercept, test = hadri)
 
  I obtained the following message:
 
  Error in Math.factor(x) : cumsum not meaningful for factors
  In addition: There were 50 or more warnings (use warnings() to see the
  first 50)
 
  where's the problem? can you please help me
  Thank you in advance
  George
 
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[R] How can I cluster a set of formulae?

[Professor George F.Hart]

I am working on a problem in which I have derived a set of D  formulae
relating a different dependent variable to a grouping of independent variables.


D1 = intercept + ax1 + bx2 + bx3 + bx4
D2 = intercept + ex2 + fx7 + gx8
D3= intercept + hx1 + ix3 + jx7

etc to ... D8.

I have 3 categorical variables P, Q and A  [which are actually hierarchical
with A within Q with P, each containing a different number of classes]  – I
want to look at each of the categorical variables as a separate issue
clustering each of the D formulae into classes, so I can say something about
how the D's vary / interact across classes.

Intuitively this seems to be a discriminant function problem because the
classes are already known.  However, a PCA or FA might be necessary – and
then do a DFA on the clusters.  Either way I am not sure how to set it up or
even if I can interpret it to make sense.

Alternatively, I might be climbing up/down the wrong tree [pun intended]. 
Other methods might be better.

Help!

George F. Hart

I'm sending this to a number of statistics groups so apologize if you get
this note more than once.

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[R] unable to carry through object in a nested function

[Chen, George]

Hi There,
I am having trouble carrying through an object listed in the outer function 
into the inner function of a nested pair.
This is my code:

FindGreaterThanProportion- function (y, SSThreshold) {
DenomCells-length(y)
NumerCells-subset(y,ySSThreshold)
PropCells-length(NumerCells)/DenomCells
return (PropCells)
}


GetPropPlot- function (PrePropData, direction, SSThreshold, cell, stim) {
# Split up the dataframe with ddply and apply the function
print(direction)
print (SSThreshold)

if (direction==) {
PropData-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY), 
summarise,
PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
}

PlotSubset - subset(PropData, PropData$STIM==stim  PropData$CELL == cell)
PropPlot-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
geom_line() +
geom_point() +
facet_grid(SIGNAL~SUBJECT)
return(FinalPropPlot)
}

When I run the code, I get this error:
[1] 
[1] 2
Error in subset.default(y, y  SSThreshold) :
  object 'SSThreshold' not found

It seems as if SSThreshold is not being passed into FindGreaterThanProportion.

Any help would be appreciated to determine what I am doing incorrectly.
Thanks in advance.

George Chen



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Re: [R] unable to carry through object in a nested function

[Chen, George]

Hi,
This is a resend of a previous message reproduced below but with sample data to 
run.
Thanks.
George Chen



Hi There,
I am having trouble carrying through an object listed in the outer function 
into the inner function of a nested pair.

sample data below -
library(plyr)

SUBJECT-c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
STIM-c(No,No,No,No,No,No,No,No,No,No,No,No,No,No,No,No,No,No,No,No)
CELL-c(CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4,CD4)
SIGNAL-c(ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC,ABC)
DAY-c(7,7,7,7,7,7,7,7,7,7,1,1,1,1,1,1,1,1,1,1)
SIMSCORE-c(2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5,2,3,4,5)
PrePropData-data.frame(SUBJECT, STIM, CELL, SIGNAL, DAY, SIMSCORE)



This is my code:

FindGreaterThanProportion- function (y, SSThreshold) {
DenomCells-length(y)
NumerCells-subset(y,ySSThreshold)
PropCells-length(NumerCells)/DenomCells
return (PropCells)
}


GetPropPlot- function (PrePropData, direction, SSThreshold, cell, stim) {
# Split up the dataframe with ddply and apply the function
print(direction)
print (SSThreshold)

if (direction==) {
PropData-ddply(PrePropData,.(SUBJECT, STIM, CELL, SIGNAL, DAY), 
summarise,
PROP=FindGreaterThanProportion(SIMSCORE, SSThreshold))
}

PlotSubset - subset(PropData, PropData$STIM==stim  PropData$CELL == cell)
PropPlot-ggplot(data=PlotSubset, aes(x=DAY, y=PROP)) +
geom_line() +
geom_point() +
facet_grid(SIGNAL~SUBJECT)
return(FinalPropPlot)
}

GetPropPlot(PrePropData, direction=, SSThreshold=3, CD4, No)

When I run the code, I get this error:
[1] 
[1] 3
Error in subset.default(y, y  SSThreshold) :
  object 'SSThreshold' not found

It seems as if SSThreshold is not being passed into FindGreaterThanProportion.

Any help would be appreciated to determine what I am doing incorrectly.
Thanks in advance.

George Chen



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[R] How do I perform conditional annotation of lattice panel plots?

[Chen, George]

My apologies for asking this question that may have been asked before. I am 
trying to plot activity dependent on time conditioned by the subject. Code for 
sample data below.

So I have something like this

xyplot(Activity~Time|Subject).
This works fine, but now I want to show where on these activity curves Event A 
occurs. This is to explore the relationship between A and activity.

I tried this:

xyplot(EventA+Activity~Time|Subject)

but then the numerical ordering gets out of order.
Ideally Event A could be denoted by a vertical line cutting through the curve 
at the day Event A occurred, but some other way to denote it would be great!

Here is my sample data as R code:

Subject-c(1,1,1,1,1,1,2,2,2,2,2,2,3,3,3,3,3,3,4,4,4,4,4,4)
Day-c(1,2,3,4,5,6,1,2,3,4,5,6,1,2,3,4,5,6,1,2,3,4,5,6)
Activity-c(2,3,4,3,7,4,5,8,2,8,4,6,2,5,3,8,9,5,6,3,4,5,6,7)
EventA-c(Yes,NA,Yes,NA,NA,NA,Yes,NA,NA,NA,NA,NA,
  Yes,NA,NA,NA,NA,NA,NA,NA,Yes,NA,NA,NA)
Data-data.frame(cbind(Subject,Day,Activity,EventA))

  Subject Day Activity EventA
11   12Yes
21   23   NA
31   34Yes
41   43   NA
51   57   NA
61   64   NA
72   15Yes
82   28   NA
92   32   NA
10   2   48   NA
11   2   54   NA
12   2   66   NA
13   3   12Yes
14   3   25   NA
15   3   33   NA
16   3   48   NA
17   3   59   NA
18   3   65   NA
19   4   16   NA
20   4   23   NA
21   4   34Yes
22   4   45   NA
23   4   56   NA
24   4   67   NA
Any ideas on how to do this would be appreciated!

Thanks very much in advance!


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[R] restrected arima models

[george]

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 



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Re: [R] restrected arima models

[george]

Thanks

Sent from my iPhone

On 19/07/2013, at 1:43 AM, Prof Brian Ripley [via R] 
ml-node+s789695n4671862...@n4.nabble.com 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 ‘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,  [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 
 
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[R] Difference between arima(1, 1, 1) of y and arima(1, 0, 1) of diff(y)

[George Milunovich]

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

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[R] Difference between arima(1, 1, 1) for y and arima(1, 0, 1) for diff(y)

[george]

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



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Re: [R] Difference between arima(1, 1, 1) of y and arima(1, 0, 1) of diff(y)

[George Milunovich]

Hi Mark,
This is very helpful!!
Much appreciated

Sent from my iPad

On Jul 19, 2013, at 3:51 AM, Mark Leeds marklee...@gmail.com 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 
 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
 
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[R] fonts not rendering during plot

[George Dietz]

Hi,

I am having a problem where sometimes fonts for text in plots don't get 
rendered-the text just shows up as boxes. If I call R from a certain directory 
the problem goes away, otherwise the fonts don't render (but plots get made). 
In both cases, my PANGO_RC and FONTCONFIG_FILE do not change…

Thank you,
-George
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Re: [R] fonts not rendering during plot

[George Dietz]

I apologize for not going in to too much detail-I didn't want to confuse people 
with the gory details of what I'm trying to do (trying to make a portable R 
installation bundled in to a mac app, among other things).  I am on a mac, 
Mountain Lion. Anyhow, I figured out the problem was with the paths pango looks 
uses to search for font configuration files. I solved it by writing a script 
that sets these paths at run-time.

George

On Apr 24, 2013, at 7:45 PM, David Winsemius dwinsem...@comcast.net wrote:

 
 On Apr 24, 2013, at 7:29 AM, George Dietz wrote:
 
 Hi,
 
 I am having a problem where sometimes fonts for text in plots don't get 
 rendered-the text just shows up as boxes. If I call R from a certain 
 directory the problem goes away, otherwise the fonts don't render (but plots 
 get made). In both cases, my PANGO_RC and FONTCONFIG_FILE do not change…
 
 Offering the OS details is more courteous than omitting them. (And there are 
 several other courtesies expected of you listed in the Fine Posting Guide.) 
 If this happens to be on a Mac, it may mean your screen fonts are corrupt. 
 You can see their names with: names(quartzFonts()).  Using Fontbook.app will 
 sometimes reveal that there are two copies of one of the screen graphics 
 fonts and that one of them displays as blanks. These should be deleted with 
 Fontbook.app.
 
 -- 
 
 David Winsemius
 Alameda, CA, USA
 

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[R] Nomogram after Cox Random Effect (frailty) model

[george boul]

Dear R-users,
I am a novice R-user with some experience in using the RMS package for taking 
nomograms after various survival models.
This time, I am trying to plot a nomogram after a Random Effects Cox, 
implemented by the coxme package. My questions are:
1. Is it possible to take a nomogram directly after the coxme survival function?
2. If not is there a way to take the linear predictor results and plug them 
into the RMS cox model and get the nomogram I want?
Any instructions/suggestions would be highly appreciable? 
Thank you in advance
George

Dr. George Bouliotis
Research Fellow in BiostatisticsMRC-MHTMR (Midland Hub for Trials Methodology 
Research) University of BirminghamPublic Health BuildingBirmingham B115 
2TTUnited Kingdom
  
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Re: [R] How to drop unused factors in faceted R ggplot boxplot?

[Gorczynski, George]

Hi and thanks. This unfortunately doesn't work because:
ggplot2 does not currently support free scales with a non-cartesian coord or 
coord_flip.

-Original Message-
From: arun [mailto:smartpink...@yahoo.com] 
Sent: January-24-13 1:49 PM
To: Gorczynski, George
Cc: R help
Subject: Re: [R] How to drop unused factors in faceted R ggplot boxplot?

HI,
You can get the plot in the same window, but the width seems to be a problem.
stest- read.table(text=
    site year conc
    south 2001 5.3
    south 2001 4.67
    south 2001 4.98
    south 2002 5.76
    south 2002 5.93
    north 2001 4.64
    north 2001 6.32
    north 2003 11.5
    north 2003 6.3
    north 2004 9.6
    north 2004 56.11
    north 2004 63.55
    north 2004 61.35
    north 2005 67.11
    north 2006 39.17
    north 2006 43.51
    north 2006 76.21
    north 2006 158.89
    north 2006 122.27
,sep=,header=T,stringsAsFactors=T)
stest1-stest
 stest1- within(stest1,{year- factor(year)}) ggplot(stest1, aes(x=year, 
y=conc)) + geom_boxplot(horizontal=TRUE)+
 facet_wrap(~ site, ncol = 1, scales=free_x) + 
coord_flip()+scale_y_log10()+
  theme_bw() + opts(strip.text.x = theme_text()) A.K.





- Original Message -
From: Niec ggorczyn...@golder.com
To: r-help@r-project.org
Cc: 
Sent: Thursday, January 24, 2013 1:13 PM
Subject: Re: [R] How to drop unused factors in faceted R ggplot boxplot?

Thank you, Jeff. I think I should have been more clear.  I don't want to
modify my data. I need to create a series of box plots for different sites
(north and south in my example but there are many more) but I don't want
empty rows in my plot - for years when data was not collected. I tried to
make separate plots and join them with grid.arrange and it plots the layout
I want but I can't get the boxes in all plots have uniform look (width), see
the screenshot:
http://r.789695.n4.nabble.com/file/n4656535/2013-01-24_0949.png 

And thank you for pointing out the shortcomings of my posted data sample.
I'll be better prepared next time.



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[R] Fwd: Simulation of spatial Log-Gaussian Cox process in Spatstat

[George Limitsios]

Hello,

I have fitted a Log-Gaussian Cox Process on my data but when I try to
use simulate.kppm of the spatstat package I get this error:

Error in rLGCP(model = model, mu = mu, param = param, ..., win = win) :
  The spatial domain of the pixel image ‘mu’ does not cover the
simulation window ‘win’


I've used covariates as im, changed the npixel value of the spatstat
options to match the dimensions of the covariates images, but the
problem keeps showing up.

Maybe it has something to do with the irregular owin used as window of
the ppp object?



I'd appreciate any help!
Regards,
George

--
===
George Limitsios
MSc. Geography and Applied Geoinformatics
Dep. of Geography
University of the Aegean

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[R] parApply computing

[George]

I'm using /parApply/() function in snow package for parallel computing
(boostrapping repeating calculation), as the follows:

MyBoostrapping - function( i ){
 .
}
cl - makeCluster( ncluster, type = SOCK) 
i.circle - as.matrix( 1:128, , 1)
parApply( cl, i.circle, 1, FUN = MyBoostrapping)

It works.
However, I want to set more than one arguments to function MyBoostrapping,
e.g., MyBoostrapping - function( i , A, B)
Would you please help me on it?

Thank you very much.



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[R] Write to MS SQL Database

[George]

I want to update a column of a database table (in MS SQL) using sqlUpdate( )
or sqlSave( ) function in RODBC package. E.g. SQLchannel is the database
connection; SQLtable is the destination table in the database, including at
least two columns, ID and Value; Xdata is a data frame in R environment,
including two columns: ID and Value. What I wanna do is to update the Value
in SQLtable using Xdata, with ID as the primary key. Which is the fast way
to do it? Thank you very much.



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[R] How do I exactly align the right hand side of mtext relative to a plot device? Beyond adj.

[George Shirreff]

Hi,

I have a problem with aligning text which I'm adding to a plot using
mtext. I would like to specify the position of the right hand end of the
text string, relative to the device (in the left-right direction).

I've been looking at the use of the argument adj. But this can't be used
to specify the rightmost point of the text. Neither does it specify exactly
the centre of the text, so I'm not sure exactly how it works.

I could hack it and change adj accordingly but this is part of a function
which I need to generalise. So it needs to be the same regardless of the
length of the added text, or the values on the x-axis.

Here's a simple example with two versions (the first three lines of each
version are identical). I would like the right end of the added text to be
the same distance from the legend in both versions.

### v1
dev.new()
plot(c(0,1),c(0,1),ylim=c(0,2))
legend(topright,c(data1,data2),col=c(1,2),lty=1,bty=n)
mtext(text,side=3,line=-2,adj=0.8)

### v2
dev.new()
plot(c(0,1),c(0,1),ylim=c(0,2))
legend(topright,c(data1,data2),col=c(1,2),lty=1,bty=n)
mtext(really long text,side=3,line=-2,adj=0.8)


Thank you for your help,
George

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[R] cp2tform equivalent

[George Macaulay Shaw]

I'm a new R user and am looking for an R equivalent to the Matlab 'cp2tform' 
function (see: http://www.mathworks.com/help/toolbox/images/ref/cp2tform.html). 

cp2tform accepts pairs of 2D control points and produces a least-squares 
optimized spatial transformation from one set of points to the other. 
Specifically, I'm looking to produce the coefficients of a 3rd order polynomial 
transformation. 

I'm familiar with the mathematics involved, but am very new to R. If this 
functionality isn't implemented in R directly, a brief outline of the R 
functions that I'd use to implement it myself would be helpful. 

Thanks!
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[R] no non-missing arguments to max; returning -Inf

[George Kumar]

Hi,

I just wanted to object of class xts, zoo and I got the error
no non-missing arguments to max; returning -Inf
After all the values were printed. Tried searching on this forum, but no
luck.
Anyone has any idea ?

Thanks.
George

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Re: [R] Bruno's Panel LSDVC

[George Matysiak]

I'm repeating the post. Has anyone written a routine for this R? Thanks.

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Re: [R] Bruno's Panel LSDVC

[George Matysiak]

*Is there an implementation of this in R? Thanks.
*

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[R] question about linear regression and leverage

[George Markomanolis]

Dear all,

I am new to this field and I have a question about a linear regression.
I have a dataset of around to 31000 points and I want to apply a linear
regression. The R-squared is 0.9 however when I check the diagnostic
plots I can see that there are around to 250 points with big leverage
value. As I know the points with big leverage influence a lot the fit.
If I remove these points in order to check their influence, the
R-squared of the rest points is 0.71. So I removed less than 1% of my
data and the fit is not so good. Could you please give me any advice
about this? Is it right to let these 250 points in my dataset or not?
Could I do something else? The data are measured through an experiment
so even these 250 points are real values.

Thanks a lot,
George

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Re: [R] question about linear regression and leverage

[George Markomanolis]

Dear David,

Thanks for your answer. Yes now that you mentioned these points are in
the beginning of a variable range. From the plot of the residuals seems
to have non constant variance which is solved by a transformation. I
checked also for interactions by using the symbol : between two
variables and the change on the result was not so important. I am
working on computer science field but I wanted to do an analysis from
scratch because some previous results that I have seen are not good for
such cases. Moreover the data are not the same of course.

Thanks,
George

On 06/21/2011 01:08 PM, David Winsemius wrote:

 On Jun 21, 2011, at 3:49 AM, George Markomanolis wrote:

 Dear all,

 I am new to this field and I have a question about a linear regression.
 I have a dataset of around to 31000 points and I want to apply a linear
 regression. The R-squared is 0.9 however when I check the diagnostic
 plots I can see that there are around to 250 points with big leverage
 value. As I know the points with big leverage influence a lot the fit.
 If I remove these points in order to check their influence, the
 R-squared of the rest points is 0.71. So I removed less than 1% of my
 data and the fit is not so good. Could you please give me any advice
 about this? Is it right to let these 250 points in my dataset or not?
 Could I do something else? The data are measured through an experiment
 so even these 250 points are real values.

 You could be looking at the descriptive statistics on the points.
 Perhaps they are at one end of a variable range, or you perhaps have
 some other feature that is scientifically interesting. So far you have
 only been examining one set of simple linear hypotheses and have not
 (presumably) been looking at any non-linear possibilities or the
 potential that interactions are affecting the outcome. The prior 
 science of your (so far undescribed) domain should be carefully
 considered, but in your message we see no evidence of such.


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Re: [R] rcspline.plot query

[Chalikias George]

The actual dataframe that I have imported on R is

   Death   adp
1  0 58.00
2  1 18.70
3  0 21.75
4  1 25.35
5  0 20.55
6  1 28.05
7  0 50.15
8  1 31.25
9  1 32.75
10 1 28.95
11 1 15.10
12 0 45.05
13 1 19.95
14 0 32.95
15 0 22.60
16 0 10.75
17 0 41.80
18 0 27.05
19 1 26.25
20 0 34.40
21 1 24.65
22 1 42.30
23 0 19.80
24 0 47.20
25 1 25.90
26 1 30.70
27 1 28.60
28 1 25.80
29 0 27.05
30 0 14.40
31 0 28.40
32 0 48.45
33 0 17.85
34 1 30.85
35 1 24.75
36 0 16.20
37 0 34.10
38 0 12.00
39 0 24.40
40 0 69.50
41 1 36.45
42 0 41.55
43 1 17.80
44 0 40.10
45 1 21.35
46 1 22.90
47 0 63.80
48 1 45.80
49 0 70.65
50 0 54.00
51 0 26.90
52 0 50.75
53 0 28.20
54 1 23.25
55 1 18.10
56 0 29.20
57 1 52.80
58 0 46.60
59 1 32.55
60 0 74.50

The R command that I actually use is  rcspline.plot (adp, Death,
model=logistic, nk=3, knots=NULL)

and the rcspline.eval (adp, nk=3, inclx=FALSE, knots.only=FALSE,
type=ordinary)

For both the commands I receive the same message :  fewer than 6 non
missing observations. 

George

 



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Re: [R] mtext text size (cex) doesn't match plot

[George Locke]

thanks for reading the manual for me :X

2011/5/12 Prof Brian Ripley rip...@stats.ox.ac.uk:
 On Wed, 11 May 2011, George Locke wrote:

 Hi,

 I am using mtext instead of the ylab argument in some plots because i
 want to move it away from the numbers in the axis.  However, the text
 in the X axis,

 for example:
   par(mar=c(5, 5.5, 4, 2));
   plot(data, main=plot name, xlab= 'X axis', ylab=,
        font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
   mtext('Y axis', side=2, cex=1.5, line=4, font=2);

 This works fine, but if I then set

   par(mfrow=c(3,2));

 the text produced by mtext becomes much larger than the text X axis
 produced by plot, despite their having identical cex specifications.
 In this case, the words Y axis become much larger than plot name.
 Note that without par(mfrow) the size of X axis and Y axis match
 iff their cex(.lab) arguments match.

 How can I make mtext produce text that exactly matches the xlab?  In
 my limited experience fiddling around with this problem, the size of
 the mtext does not depend on par(mfrow), whereas the size of the xlab
 does, so if there were a formula that relates the actual size of text,

 Please do read the help!  ?mtext says

     cex: character expansion factor.  ‘NULL’ and ‘NA’ are equivalent
          to ‘1.0’.  This is an absolute measure, not scaled by
          ‘par(cex)’ or by setting ‘par(mfrow)’ or ‘par(mfcol)’.

 so no 'limited experience fiddling around with this problem' was needed.
  And see ?par:

     ‘cex’ A numerical value giving the amount by which plotting text
          and symbols should be magnified relative to the default.
          This starts as ‘1’ when a device is opened, and is reset when
          the layout is changed, e.g. by setting ‘mfrow’.

     ‘mfcol, mfrow’ A vector of the form ‘c(nr, nc)’.  Subsequent
          figures will be drawn in an ‘nr’-by-‘nc’ array on the device
          by _columns_ (‘mfcol’), or _rows_ (‘mfrow’), respectively.

          In a layout with exactly two rows and columns the base value
          of ‘cex’ is reduced by a factor of 0.83: if there are three
          or more of either rows or columns, the reduction factor is
          0.66.

 cex argument, and par(mfrow), then I could use that to attenuate the
 cex argument of mtext.  Any solution will do, so long as it maintains
 the relative sizes of the plot and the three text fields (main, x axis
 label, y axis label).

 library(fortunes); fortune(14) applies -- see the posting guide.

 --
 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, UK                Fax:  +44 1865 272595

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[R] mtext text size (cex) doesn't match plot

[George Locke]

Hi,

I am using mtext instead of the ylab argument in some plots because i
want to move it away from the numbers in the axis.  However, the text
in the X axis,

for example:
par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

This works fine, but if I then set

par(mfrow=c(3,2));

the text produced by mtext becomes much larger than the text X axis
produced by plot, despite their having identical cex specifications.
In this case, the words Y axis become much larger than plot name.
Note that without par(mfrow) the size of X axis and Y axis match
iff their cex(.lab) arguments match.

How can I make mtext produce text that exactly matches the xlab?  In
my limited experience fiddling around with this problem, the size of
the mtext does not depend on par(mfrow), whereas the size of the xlab
does, so if there were a formula that relates the actual size of text,
cex argument, and par(mfrow), then I could use that to attenuate the
cex argument of mtext.  Any solution will do, so long as it maintains
the relative sizes of the plot and the three text fields (main, x axis
label, y axis label).


example code to demonstrate the problem is below.

Thanks!

data = c(1:10);
par(mfrow=c(3,2));

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

par(mar=c(5, 5.5, 4, 2));
plot(data, main=plot name, xlab= 'X axis', ylab=,
 font=2, cex.lab=1.5, font.lab=2, cex.main=1.8);
mtext('Y axis', side=2, cex=1.5, line=4, font=2);

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[R] text file problem-Help needed

[George Pantop]

Hello!
I have just uninstalled the R 2.4.1 that i was using and installed the latest 
version (R 2.12.1).
In order to read a text file, i was copying the text file to C/Program 
Files/R/R 2.4.1, and the previous version was able to read it from there.

I did the same think for the new version (copy text file to C/Program Files/R/R 
2.12.1) and i tried to open it:

data - read.table('intersand.txt')

but the result was:

Error in file(file, rt) : cannot open the connection
In addition: Warning message:
In file(file, rt) :
  cannot open file 'intersand.txt': No such file or directory

Can someone tell me what the problem is? Must i copy the text file somewhere 
else?

Thank you in advance,
George Pantopoulos



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[R] text file problem-Solved!

[George Pantop]

Oh! (hits head) It was the working directory!!!
Problem solved from Change Dir...

Many thanks to Samuel and Duncan!
George



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Re: [R] Read a similarity matrix from excel

[George Kakarontzas]

Dear Petr,

It worked fine.
Thanks for helping.

George

-Original Message-
From: Petr PIKAL [mailto:petr.pi...@precheza.cz] 
Sent: Wednesday, February 02, 2011 1:18 PM
To: George Kakarontzas
Cc: r-help@r-project.org
Subject: Odp: [R] Read a similarity matrix from excel

Hi

r-help-boun...@r-project.org napsal dne 01.02.2011 10:20:48:

 Good morning,
 
 I have an excel spreadsheet with similarities among objects. The 
 format
of
 the file is the following:
 
 1st row: empty cell,object-1-name,object-name-2,...,object-N
 2nd row: object-name-1,0,s1,2,s1,3,...,s1,N
 3rd row: object-name-2,s2,1,0,s2,3,...,s2,N
 
 The table is symmetrical and contains the similarities among the 
 objects (sx,k stands for similarity among x and k). The first row 
 contains the name of the objects (strings of characters) in the same 
 order that these same names are contained in the first column. The cell
1,1 is empty.
 
 How can I read this in R so that after reading it I can perform a 
 hierarchical clustering. The table is 78x78 so it is relatively easy 
 to manually change something if it makes it easier to read.

Select your table in Excel
Press Ctrl-C
In R do
test-read.delim(clipboard)

you shall get something like that

 test
  X a  b c
1 a 1 23 3
2 b 4  5 6
3 c 7  8 9


you has to get rid of first column

 mat-as.matrix(test[,-1])

and if you want you can put row.names tou your matrix

 row.names(mat)-colnames(mat)
 mat
  a  b c
a 1 23 3
b 4  5 6
c 7  8 9
 row.names(mat)-test$X
 mat
  a  b c
a 1 23 3
b 4  5 6
c 7  8 9


Regards
Petr




 
 I found many articles about reading a data table with variables and 
 then constructing the distance matrix from within R, but I have the
similarity
 matrix instead. 
 
 Thank you for your help
 
 George
 
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[R] Read a similarity matrix from excel

[George Kakarontzas]

Good morning,

I have an excel spreadsheet with similarities among objects. The format of
the file is the following:

1st row: empty cell,object-1-name,object-name-2,...,object-N
2nd row: object-name-1,0,s1,2,s1,3,...,s1,N
3rd row: object-name-2,s2,1,0,s2,3,...,s2,N

The table is symmetrical and contains the similarities among the objects
(sx,k stands for similarity among x and k). The first row contains the
name of the objects (strings of characters) in the same order that these
same names are contained in the first column. The cell 1,1 is empty.

How can I read this in R so that after reading it I can perform a
hierarchical clustering. The table is 78x78 so it is relatively easy to
manually change something if it makes it easier to read.

I found many articles about reading a data table with variables and then
constructing the distance matrix from within R, but I have the similarity
matrix instead. 

Thank you for your help

George

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Re: [R] Johnson Distribution Fit

[Abey George]

I am trying to only fit this distribution to the data to see how well it
fits it. Getting the parameters is secondary. Did correct the square
brackets in the exponential equation but still get the same result. There is
only 1 variable to data2 and that is points. I am trying to fit this
distribution to points data scored by teams.

The result for any(data2  0.5 | data2  0.5+50) is TRUE.

Thanks
Abey


On Mon, Oct 4, 2010 at 11:33 AM, David Winsemius dwinsem...@comcast.netwrote:


 On Oct 3, 2010, at 3:47 PM, Abey George wrote:

  Hi,
 I am trying to fit a Johnson SB distribution using fitdist function in
 fitdistrplus Library. I have defined the Johnson SB distribution from (
 http://www.ntrand.com/johnson-sb-distribution/) . But it gives me the
 follwing errors. Any help would be appreciated


 Are you really trying to estimate the bounding values as well as the gamma
 and delta parameters. Those would seem to be more likely determined by the
 nature of the problem, e.g., policy limits on the insured sums if this were
 a financial problem.



 #xi = xi


  #lambda =l
 #delta =d
 #gamma = g

 djohn = function(x,xi,l,d,g)
 (d/(l*sqrt(2*pi)*((x-xi)/l)*(1-((x-xi)/l*exp[-0.5*(g +
 d*log(((x-xi)/l)/(1-((x-xi)/l^2]


 You used exp[ ] where you probably wanted exp().



 pjohn = function(x,xi,l,d,g)   pnorm(g + d*log(((x-xi)/l)/(1-((x-xi)/l

 qjohn = function(p,xi,l,d,g)   xi + (l*exp((qnorm(p) - g)/d))/(1 +
 exp((qnorm(p) - g)/d))

 f1c - fitdist(data2,john,start=list(xi = 0.5 ,l = 50, d = 1, g = 1))


 You have not given us the data2 variables, so we have no way of checking
 whether any of them appear outside the range [epsilon, lambda+epsilon].
 Using your data2 vector, what are the results of :

 any(data2  0.5 | data2  0.5+50)   #?




 Error in fitdist(data2, john, start = list(xi = 0.5, l = 50, d = 1,  :
  the function mle failed to estimate the parameters,
   with the error code 100
 In addition: Warning message:
 In log(((x)/l)/(1 - ((x)/l))) : NaNs produced


 Cheers
 AG



 David Winsemius, MD
 West Hartford, CT




-- 
Abey George

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[R] Johnson Distribution Fit

[Abey George]

Hi,
  I am trying to fit a Johnson SB distribution using fitdist function in
fitdistrplus Library. I have defined the Johnson SB distribution from (
http://www.ntrand.com/johnson-sb-distribution/) . But it gives me the
follwing errors. Any help would be appreciated

#xi = xi
#lambda =l
#delta =d
#gamma = g

djohn = function(x,xi,l,d,g)
(d/(l*sqrt(2*pi)*((x-xi)/l)*(1-((x-xi)/l*exp[-0.5*(g +
d*log(((x-xi)/l)/(1-((x-xi)/l^2]

pjohn = function(x,xi,l,d,g)   pnorm(g + d*log(((x-xi)/l)/(1-((x-xi)/l

qjohn = function(p,xi,l,d,g)   xi + (l*exp((qnorm(p) - g)/d))/(1 +
exp((qnorm(p) - g)/d))

f1c - fitdist(data2,john,start=list(xi = 0.5 ,l = 50, d = 1, g = 1))

Error in fitdist(data2, john, start = list(xi = 0.5, l = 50, d = 1,  :
  the function mle failed to estimate the parameters,
with the error code 100
In addition: Warning message:
In log(((x)/l)/(1 - ((x)/l))) : NaNs produced


Cheers
AG

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[R] Converting a line by line program into an array to perform summary stats

[George Coyle]

I am trying to turn several lines of information into a variable.  I used
the filx function to input my file then the readlines to qualify what I
want.  Essentially I have data in a file every 10 minutes through a day for
several years down a column:

date time value
9/28/10   02:00  13
9/28/10   02:10  15
9/28/10   02:20  12
9/28/10   02:30  11
etc.

I then use if statements to segment the day into various portions (2:00 to
2:30 for example) and find the average or maximum value for the time.  Next
I compare this value to another time of the day to see if the price was
reached/broken.  For example the 2:00 to 2:30 low from above is 11 at 2:30.
I would then check the 8:00 to 13:00 time period to see if the 2:00 to 2:30
low occured from 8:00 to 13:00.  If it did occur I would call this day a
qualifier and check the time 2:30 price occured in the 8:00 to 13:00 period
until the price at 13:00.  So another example if 2:30 was 11, 8:00 was 13,
8:45 was 11, and 13:00 was 20 I would say this day qualified and the price
from the am was first acheived at 8:45 in the 8:00 to 13:00 period and the
change from that price to the 13:00 period was 20-11=+9.

This example was all background to my problem.  Using the filx/readlines
methods I wind up with output for the days which qualify, but when I try to
create an array variable using the total of each line for a given column
(aka summarizing every day that my given criteria were met), something about
having used the line by line method doesn't allow me to create an array
variable.  It only gives me the last value.  The variables I declared to
fidn the qualifying days are specific to each day vs across all days that
qualified.  Is it possible to convert this line by line data into an array
wih some R code I don't know?

I considered converting the data example above into a matrix, but then I run
into tricky problems of shortened days and days missing data (the code I
used for the readlines method enables me to specify the new days without
this problem...I don't have to fill in blanks it just changes days when it
hits a new day).  Given how specific this problem is I can't find much on
the R help logs.

Perhaps outputting the line by line output to a file, then reinputting it
using a read.csv method would enable me to achieve my desired result but
then I have the laborious task of dumping into excel, converting file types,
saving as csv, reuploading to R, writing a separate program, etc.

Is there an easy fix to my problem?

Thanks

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[R] If statements for multiple arrays

[George Coyle]

Hello,

I wrote this code which works fine on a single observation:

x-100
y-200
z-125
aa-150
if(xz  yz) {aa-z}
result: 25

I am trying to apply this logic where x,y,z,and aa are arrays but with very
little success.  I have tried using loops and whiles but I always get errors
of various types.  I have consulted a few manuals but with limited success.
My hopeful outcome would be:

data:
X   Y  Z  AA
1 100  200125 150
2 125   110105140
3 110150   130200
4 90200 7565

Here row 1 would return 25, row 2 would return nothing since ZX, row 3
would be 50, row 4 would be nothing since XZ.

In this case I am trying to return something where I could call the output a
variable Z which would become an array based on the logic above where the
members would be: (25, 50)

I tried using this where the variables are arrays:
if(xz  yz) {aa-z}
But I get NULL

 I tried using this where the variables are arrays:
if(xz  yz) {aa-z} else NA
But I get NA

When I tried using a loop:
for(i in 1:length(x)) if(xz  yz) {aa-z} else NA
I got NULL

An attempt at a while statement crashed.

The time series resource (
http://cran.r-project.org/doc/contrib/Ricci-refcard-ts.pdf) is way too
involved.  Most online sources I am finding are not good for if contingent
array manipulation.  Annoyingly, just saying aa-z will work across the
entire array but for some reason my ifs fail.  I know the R help group only
wants serious emails so hopefully this will indicate I gave it a
reasonable shot.

Please help

Thanks

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[R] Latex fonts in R graphics

[KARAVASILIS GEORGE]

Hello, R users.
I am trying to embed Computer modern fonts to an R plot and I get the 
following error.


CM - Type1Font(CM,
+  c(paste(cm-lgc/fonts/afm/public/cm-lgc/,
+ c(fcmr8a.afm, fcmb8a.afm, fcmri8a.afm, fcmbi8a.afm), sep=),
+ ./cmsyase.afm))
 pdf(cm.pdf, width=3, height=3, family=CM)
 plot(1:length(y), y, xlab=ss, ylab=expression(x[2]))  ## for any 
vector y

 dev.off()
null device
  1
 embedFonts(cm.pdf, outfile=cmembed.pdf, 
fontpaths=c(cm-lgc/fonts/type1/public/cm-lgc, .))
Error in embedFonts(cm.pdf, outfile = cmembed.pdf, fontpaths = 
c(cm-lgc/fonts/type1/public/cm-lgc,  :
  status -1 in running command 'gswin32c.exe -dNOPAUSE -dBATCH -q 
-dAutoRotatePages=/None -sDEVICE=pdfwrite 
-sOutputFile=C:\DOCUME~1\user\LOCALS~1\Temp\RtmpccEtgV\Rembed28163716 
-sFONTPATH=cm-lgc/fonts/type1/public/cm-lgc;.  cm.pdf'

In addition: Warning message:
In system(cmd) : gswin32c.exe not found


Operating system: Windows XP, SP2.
cm-lgc has been unzipped in the working directory  C:/Program 
Files/R/R-2.10.1 and the AFM, PFB files are also in same directory.

Any help?

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[R] Does anybody know how to control the appearance of the end of the line in lattice?

[George Chen]

Hi All,

I am plotting vertical lines using xyplot in lattice and type=h.
It works well, but the problem is that the tops of the lines are convex and the 
bottoms are concave.
Is there a way to flatten the tops and bottoms?

Here's my code:

Source-matrix(1:30,10,3)
colnames(Source)-c(x,y1,y2)
Source-data.frame(Source)

xyplot(y2+y1~x,
data=Source,
distribute.type=TRUE,
type=c(h,h),
col=c(black,white),
lwd=20)
graphics.off()

Thanks.

George Chen

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[R] Nested if help

[George Coyle]

Hello,

I am trying to find a direct way to write a nested if of sorts to find data
for a specific time range for a specific day (across a range of days) and
have exhausted my abilities with the manuals I have at hand.  I have a good
deal of data of this approximate form:

day   time   price
1  1am5
1   2am7
1  3am 9
1  4am 12
 2  1am5
2   2am7
2  3am 9
2  4am 12
etc

I am reading from a file I loaded and using a while statement.  I then am
trying the direct approach of writing the if:

if(time=2am time =4am) { #specifying desired time range--since a while
loop format I don't think date is necessary and if it is I don't know how to
say this?
time1-time #sets first time in desired interval to base time
px1-px #sets first price in desired interval to base price
if(pxpx1){ #nested if stmt to see if subsequent times are higher than base,
thus replacing base with new max (I am seeking max in the time period in
this instance)
px2-px #px2 would be the new higher maximum
time2-time #time associated with px2
px3-px+1 #price immediately following max
time3-time+1 #time immed. follows max
out-(cur_date,px2,time2,px3,time3) #output the high price/time and the
immediately following price/time
cat(out,\n)}

This code however, does nothing.  Any help would be apreciated.  The manuals
seem to only take one so far.

Thanks,

George

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[R] Matrix to Vector

[George Coyle]

Hi All,

I am trying to turn a Matrix into a vector for analysis purposes.  I need to
select only certain columns from the entire matrix for the vector (intraday
time intervals).  Also I need to transpose the Matrix (so times are in rows)
stack each successive new column on top of each other (latest at the top
creating one long vector vs a matrix) then reassign the date to the left of
each time (right now date is only shown once by row and will be in columns
when transposed).  Any thoughts?

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Re: [R] Is it possible to rearrange the facets in ggplot while keeping everything else the same?

[George Chen]

Hi Dennis, 

It is similar to what I was trying to achieve. Is there a way to show the 
grouped time courses as separate facets. 
So in lattice, the time courses would be conditioned on Ab status and subject 
name at the same time. 

Thanks. 

George 





From: Dennis Murphy djmu...@gmail.com 
To: George Chen glc...@stanford.edu 
Cc: r-help@r-project.org 
Sent: Saturday, May 8, 2010 9:38:07 PM 
Subject: Re: [R] Is it possible to rearrange the facets in ggplot while keeping 
everything else the same? 

Hi: 

I'm not sure this is what you're looking for, but it sounds to me that you want 
to group subjects with the same Ab value together. If that's the case, then try 
this; your test data is called df ... 

df$Subject - factor(df$Subject) 
p2 - ggplot(df, aes(x = Day, y = Value, colour = Subject)) 
p2 + geom_point() + geom_line(aes(group = Subject)) + facet_grid(Variable ~ Ab) 

HTH, 
Dennis 


On Sat, May 8, 2010 at 6:56 PM, George Chen  glc...@stanford.edu  wrote: 


Hello, 

First, ggplot2 is great! 
Second, sorry for the basic nature of my question. 

I have data in the form of a melt table like this: 
Subject Day Ab Variable Value 
1 1 Yes A 3 
1 3 Yes A 5 
1 5 Yes A 7 
2 1 No A 2 
2 3 No A 4 
2 5 No A 6 
3 1 Yes A 1 
3 3 Yes A 3 
3 5 Yes A 5 
4 1 No A 4 
4 3 No A 6 
4 5 No A 8 
1 1 Yes B 3 
1 3 Yes B 5 
1 5 Yes B 7 
2 1 No B 2 
2 3 No B 4 
2 5 No B 6 
3 1 Yes B 1 
3 3 Yes B 3 
3 5 Yes B 5 
4 1 No B 4 
4 3 No B 6 
4 5 No B 8 
1 1 Yes C 3 
1 3 Yes C 5 
1 5 Yes C 7 
2 1 No C 2 
2 3 No C 4 
2 5 No C 6 
3 1 Yes C 1 
3 3 Yes C 3 
3 5 Yes C 5 
4 1 No C 4 
4 3 No C 6 
4 5 No C 8 

The table goes on like this for another 11 subjects. 

I can plot a 3 row (A,B,C) x 4 column (Sub 1,2,3,4) grid of time courses with 
the y labels for the facets being 1,2,3,4 and the x labels for the facets being 
A,B,C. 

qplot(Day,Value,data=data above) + facet_grid(Variable~Subject, 
scales=free_y) 

But, how do I rearrange the columns so that all the Yeses to Ab are together 
and the Nos to Ab are together while keeping the same labeling? 


Thanks in advance. 

George Chen 

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[R] Is it possible to rearrange the facets in ggplot while keeping everything else the same?

[George Chen]

Hello,

First, ggplot2 is great!
Second, sorry for the basic nature of my question.

I have data in the form of a melt table like this:
Subject Day Ab  VariableValue
1   1   Yes A   3
1   3   Yes A   5
1   5   Yes A   7
2   1   No  A   2
2   3   No  A   4
2   5   No  A   6
3   1   Yes A   1
3   3   Yes A   3
3   5   Yes A   5
4   1   No  A   4
4   3   No  A   6
4   5   No  A   8
1   1   Yes B   3
1   3   Yes B   5
1   5   Yes B   7
2   1   No  B   2
2   3   No  B   4
2   5   No  B   6
3   1   Yes B   1
3   3   Yes B   3
3   5   Yes B   5
4   1   No  B   4
4   3   No  B   6
4   5   No  B   8
1   1   Yes C   3
1   3   Yes C   5
1   5   Yes C   7
2   1   No  C   2
2   3   No  C   4
2   5   No  C   6
3   1   Yes C   1
3   3   Yes C   3
3   5   Yes C   5
4   1   No  C   4
4   3   No  C   6
4   5   No  C   8

The table goes on like this for another 11 subjects.

I can plot a 3 row (A,B,C) x 4 column (Sub 1,2,3,4) grid of time courses with 
the y labels for the facets being 1,2,3,4 and the x labels for the facets being 
A,B,C. 

qplot(Day,Value,data=data above) + facet_grid(Variable~Subject, 
scales=free_y)

But, how do I rearrange the columns so that all the Yeses to Ab are together 
and the Nos to Ab are together while keeping the same labeling?


Thanks in advance.

George Chen

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[R] How do I plot geoms in parallel in ggplot

[George Chen]

Hello,

I am new to ggplot.  Please forgive my ignorance!

I have patient data such that each individual is a row and then the attributes 
are in columns.  So for example:

SubjTimeHeightWeightWBCPlt
11944150
121056200
131165250
141273200
21427300
22548450
23666300
24885200
31664455
32885344
33996544
3410103213

I would like to show the data as a time course for height , weight, WBC, and 
plt for each patient but in parallel and ultimately as a matrix of time courses 
for all the subjects with each patient a row and the time course graph for 
height weight WBC plt as individual columns.

So something like this
Subj 1   Height time course(TC)   Weight TCWBC TCPlt TC
Subj 2   Height time course(TC)   Weight TCWBC TCPlt TC
Subj 3   Height time course(TC)   Weight TCWBC TCPlt TC

Ultimately I would like to be able to sort and reorder the order of the subject 
rows (so each row would become like a facet).
Could somebody give me a hint as to how or where to start looking to figure 
this out?  I suspect it involves a layer for each time course, but how does one 
move the time course for say weight over so that it does not overly that for 
height?

Thanks in advance!

George

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Re: [R] R-help Digest, Vol 87, Issue 6

[George Chen]

Hello,

I am new to ggplot.  Please forgive my ignorance!

I have patient data such that each individual is a row and then the attributes 
are in columns.  So for example:

SubjTimeHeight  Weight  WBC Plt
1   1   9   4   4   150
1   2   10  5   6   200
1   3   11  6   5   250
1   4   12  7   3   200
2   1   4   2   7   300
2   2   5   4   8   450
2   3   6   6   6   300
2   4   8   8   5   200
3   1   6   6   4   455
3   2   8   8   5   344
3   3   9   9   6   544
3   4   10  10  3   213

I would like to show the data as a time course for height , weight, WBC, and 
plt for each patient but in parallel and ultimately as a matrix of time courses 
for all the subjects with each patient a row and the time course graph for 
height weight WBC plt as individual columns.

So something like this
Subj 1   Height time course(TC)   Weight TCWBC TCPlt TC
Subj 2   Height time course(TC)   Weight TCWBC TCPlt TC
Subj 3   Height time course(TC)   Weight TCWBC TCPlt TC

Could somebody give me a hint as to how or where to start looking to figure 
this out?  I suspect it involves a layer for each time course, but how does one 
move the time course for say weight over so that it does not overly that for 
height?

Thanks in advance!

George

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[R] How to change a venn command into a named object that can be plotted like a lattice object

[George Chen]

Hello,

I am plotting data as a venn diagram but would like to be able to control how 
it is plotted like a lattice object.
Right now, it plots right away.  I would like to name it and then plot at will.
I thought to convert the whole thing to a PostScript file then get it back into 
R via grImport, but surely (please!) there must be a less roundabout way to do 
this.

Any help is appreciated.

Here is my code:

# Wrapper function to draw Venn diagram
Venn2 - function(set1, set2, names, title,...){
  stopifnot( length(names) == 2)
  # Form universe as union of both sets
  universe - sort( unique( c(set1, set2) ) )
  Counts - matrix(0, nrow=length(universe), ncol=2)
  colnames(Counts) - names
  for (i in 1:length(universe))  {
Counts[i,1] - universe[i] %in% set1
Counts[i,2] - universe[i] %in% set2
  }
  vennDiagram( vennCounts(Counts),main=title,... )
}

# How I draw the Venn diagram
Venn2(cPostArrayHitsNames,cPreArrayHitsNames,names=c(Post,Pre),title=PatientID)

Unfortunately something like this doesn't work:
VennPlot-Venn2(cPostArrayHitsNames,cPreArrayHitsNames,names=c(Post,Pre),title=PatientID)

Apologies for the imprecise terminology.

Thanks.

GLC

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Re: [R] mysterious extra spaces appearing in expression paste

[George Locke]

Hey,

So I found workaround for what I'm now pretty sure is a bug.

the reason I'm sure it's a bug is that i found that I found that
linebreaks are handled in a wonky but regular way.  There's a rule,
and it's a bad rule, ie a bug.

The wonky rule is as follows: text(x,y,expression(paste(thing1
\n,thing2))) results in printing thing1 at the requested x/y with
the linebreak failing to cause a carriage return.  That is, thing2
appears directly below the 1 in thing1.

**Bug report:
\n in paste doesn't make a carriage return, just a new line.

perhaps there's something like endl that I'm supposed to put in there
and I just don't know.  I'll bring this to the attention of
r-b...@r-project.org .



The workaround for my particular problem was to not use line breaks,
but instead break the legend up into four parts instead of 2, using
the fact that legend puts each legend=c() element on a new line.

leg - c(expression(paste(data1 \n(,rho,=1))),
expression(paste(data2 \n(,rho,=0.0
legend(bottomright,legend=leg,col=c(1,2),lwd=3, y.intersp = 2.0,adj=c(0,1.5))

becomes

leg - c(data1,expression(paste((,rho,=1))), data2,
expression(paste((,rho,=0.0
legend(bottomright,legend=leg,col=c(1,1,2,1),   lty=(1,0,1,0),
 lwd=3)

note the lty to block the extra lines.

Regards,
George

On Tue, Feb 2, 2010 at 2:17 PM, anna lippelann...@hotmail.com wrote:

 try putting sep= in your paste method

 -
 Anna Lippel
 --
 View this message in context: 
 http://n4.nabble.com/mysterious-extra-spaces-appearing-in-expression-paste-tp1460261p1460264.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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[R] mysterious extra spaces appearing in expression paste

[George Locke]

Hi,

i'm trying to put a legend on some figures and they're coming out a
bit wonky.  here's an example:

a - c(1:10)
par(mfrow=c(2,1))
plot(a,type=s,lwd=3)
leg - c(expression(paste(data1 (,rho,=1))),
expression(paste(data2 (,rho,=0.0
legend(bottomright,legend=leg,col=c(1,2),lwd=3)
plot(a,type=s,lwd=3)
leg - c(expression(paste(data1 \n(,rho,=1))),
expression(paste(data2 \n(,rho,=0.0
legend(bottomright,legend=leg,col=c(1,2),lwd=3, y.intersp = 2.0,adj=c(0,1.5))

the problem is that lots of extra space appears between the open
parenthesis and the rho.

what can be done?  (i'm running  version 2.10.1 (2009-12-14) on fedora 12)

Thanks!

George Locke

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[R] How do I juxtapose two lattice graphs with common X axes such that the X axes line up?

[George Chen]

Hello,

I would like to juxtapose two lattice graphs with common X axes such that the X 
axes line up.  I am using plot right now but the edges are not neat and it 
would be nice if I could just draw 1 X axis and not both of them.

Here is my code:


upper-bwplot(SignalUsed~as.factor(AllNormalHitsNamesCount),data=NmlOverviewArray2,
xlab=,
ylab=Intensity of Individual Antibody Responses,
main=Intensity, Frequency, Distribution,  Quantity of Normal Antibody 
Responses,
box.ratio=1,
panel = function (AllNormalHitsNamesCount,...) {
panel.bwplot(...)
}
)

lower-barchart(as.vector(table(NmlOverviewArray2$AllNormalHitsNamesCount))

~as.factor(as.numeric(names(table(NmlOverviewArray2$AllNormalHitsNamesCount,
data=NmlOverviewArray2,
ylab=Number of Individual Antibody Responses,
xlab=Occurrence of Individual Antibody Responses (Out 
of 45 Normals),
box.ratio=1)

plot (upper, newpage=TRUE, more=TRUE, position = c(0,.15,1,1))
plot (lower, newpage=FALSE, more=TRUE, position = c(0,0,1,.3))


George

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[R] How to change the default Date format for write.csv function?

[George . Zou]

Hi,

I have a data.frame containing a Date column.  When using write.csv() 
function to generate a CSV file, I always get the Date column formatted as 
-MM-DD.   I would like to have it formatted as MM/DD/, but 
could not find an  easy way to do it.Here is the test code:

d - data.frame(ticker=c(IBM, IBM), date = as.Date(c(2009-12-03, 
2009-12-04)), price=c(120.00, 123.00))
write.csv(d, file=C:/temp/test.csv, row.names=FALSE)

The test.csv generated looks like this:

ticker,date,price
IBM,2009-12-03,120
IBM,2009-12-04,123

I would like to have the date fields in the CSV formatted as MM/DD/. 
 Is there any easy way to do this?

Thanks in advance.

George Zou

The information contained in this e-mail, and any attachment, is confidential 
and is intended solely for the use of the intended recipient. Access, copying 
or re-use of the e-mail or any attachment, or any information contained 
therein, by any other person is not authorized. If you are not the intended 
recipient please return the e-mail to the sender and delete it from your 
computer. Although we attempt to sweep e-mail and attachments for viruses, we 
do not guarantee that either are virus-free and accept no liability for any 
damage sustained as a result of viruses. 

Please refer to http://disclaimer.bnymellon.com/eu.htm for certain disclosures 
relating to European legal entities.
[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to change the default Date format for write.csv function?

[George . Zou]

Hi,

This problem might be a little harder than it appears. 

I receive a few emails all suggesting that convert the Date field to 
character by calling format(date, %m/%d/%Y) in one way or another. Well, 
this is not the solution I'm looking for and it doesn't work for me.   All 
the date fields are generated with quotes around them, which will be 
treated by other software as string instead of date.   Please note, the 
write.csv() function doesn't put quotes around date.   All I need is to 
change the format behavior of Date without adding any quotes.  So the 
output of CSV I'm looking for should be:

ticker,date,price
IBM,12/03/2009,120
IBM,12/04/2009,123

Not this:

ticker,date,price
IBM,12/03/2009,120
IBM,12/04/2009,123

Thanks for trying though.

George



From:
george@bnymellon.com
To:
r-help@r-project.org
Date:
12/28/2009 10:20 AM
Subject:
[R] How to change the default Date format for write.csv function?
Sent by:
r-help-boun...@r-project.org



Hi,

I have a data.frame containing a Date column.  When using write.csv() 
function to generate a CSV file, I always get the Date column formatted as 

-MM-DD.   I would like to have it formatted as MM/DD/, but 
could not find an  easy way to do it.Here is the test code:

d - data.frame(ticker=c(IBM, IBM), date = as.Date(c(2009-12-03, 
2009-12-04)), price=c(120.00, 123.00))
write.csv(d, file=C:/temp/test.csv, row.names=FALSE)

The test.csv generated looks like this:

ticker,date,price
IBM,2009-12-03,120
IBM,2009-12-04,123

I would like to have the date fields in the CSV formatted as MM/DD/. 

 Is there any easy way to do this?

Thanks in advance.

George Zou

The information contained in this e-mail, and any attachment, is 
confidential and is intended solely for the use of the intended recipient. 
Access, copying or re-use of the e-mail or any attachment, or any 
information contained therein, by any other person is not authorized. If 
you are not the intended recipient please return the e-mail to the sender 
and delete it from your computer. Although we attempt to sweep e-mail and 
attachments for viruses, we do not guarantee that either are virus-free 
and accept no liability for any damage sustained as a result of viruses. 

Please refer to http://disclaimer.bnymellon.com/eu.htm for certain 
disclosures relating to European legal entities.
 [[alternative HTML version deleted]]

__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




The information contained in this e-mail, and any attachment, is confidential 
and is intended solely for the use of the intended recipient. Access, copying 
or re-use of the e-mail or any attachment, or any information contained 
therein, by any other person is not authorized. If you are not the intended 
recipient please return the e-mail to the sender and delete it from your 
computer. Although we attempt to sweep e-mail and attachments for viruses, we 
do not guarantee that either are virus-free and accept no liability for any 
damage sustained as a result of viruses. 

Please refer to http://disclaimer.bnymellon.com/eu.htm for certain disclosures 
relating to European legal entities.
[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to change the default Date format for write.csv function?

[George . Zou]

Nice try, but that will turn off quote for all fields.  I want quotes for 
text fields, and no quotes for date and numeric fields.   Please see the 
desired CSV output in my previous email. 

George



From:
Henrique Dallazuanna www...@gmail.com
To:
george@bnymellon.com
Cc:
r-help@r-project.org
Date:
12/28/2009 12:44 PM
Subject:
Re: [R] How to change the default Date format for write.csv function?
Sent by:
r-help-boun...@r-project.org



Use the quote argument:

write.csv(d, file=C:/temp/test.csv, row.names=FALSE, quote = FALSE)

On Mon, Dec 28, 2009 at 2:17 PM,  george@bnymellon.com wrote:
 Hi,

 This problem might be a little harder than it appears.

 I receive a few emails all suggesting that convert the Date field to
 character by calling format(date, %m/%d/%Y) in one way or another. 
Well,
 this is not the solution I'm looking for and it doesn't work for me.   
All
 the date fields are generated with quotes around them, which will be
 treated by other software as string instead of date.   Please note, the
 write.csv() function doesn't put quotes around date.   All I need is to
 change the format behavior of Date without adding any quotes.  So the
 output of CSV I'm looking for should be:

 ticker,date,price
 IBM,12/03/2009,120
 IBM,12/04/2009,123

 Not this:

 ticker,date,price
 IBM,12/03/2009,120
 IBM,12/04/2009,123

 Thanks for trying though.

 George



 From:
 george@bnymellon.com
 To:
 r-help@r-project.org
 Date:
 12/28/2009 10:20 AM
 Subject:
 [R] How to change the default Date format for write.csv function?
 Sent by:
 r-help-boun...@r-project.org



 Hi,

 I have a data.frame containing a Date column.  When using write.csv()
 function to generate a CSV file, I always get the Date column formatted 
as

 -MM-DD.   I would like to have it formatted as MM/DD/, but
 could not find an  easy way to do it.Here is the test code:

 d - data.frame(ticker=c(IBM, IBM), date = as.Date(c(2009-12-03,
 2009-12-04)), price=c(120.00, 123.00))
 write.csv(d, file=C:/temp/test.csv, row.names=FALSE)

 The test.csv generated looks like this:

 ticker,date,price
 IBM,2009-12-03,120
 IBM,2009-12-04,123

 I would like to have the date fields in the CSV formatted as 
MM/DD/.

  Is there any easy way to do this?

 Thanks in advance.

 George Zou

 The information contained in this e-mail, and any attachment, is
 confidential and is intended solely for the use of the intended 
recipient.
 Access, copying or re-use of the e-mail or any attachment, or any
 information contained therein, by any other person is not authorized. If
 you are not the intended recipient please return the e-mail to the 
sender
 and delete it from your computer. Although we attempt to sweep e-mail 
and
 attachments for viruses, we do not guarantee that either are virus-free
 and accept no liability for any damage sustained as a result of viruses.

 Please refer to http://disclaimer.bnymellon.com/eu.htm for certain
 disclosures relating to European legal entities.
 [[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.




 The information contained in this e-mail, and any attachment, is 
confidential and is intended solely for the use of the intended recipient. 
Access, copying or re-use of the e-mail or any attachment, or any 
information contained therein, by any other person is not authorized. If 
you are not the intended recipient please return the e-mail to the sender 
and delete it from your computer. Although we attempt to sweep e-mail and 
attachments for viruses, we do not guarantee that either are virus-free 
and accept no liability for any damage sustained as a result of viruses.

 Please refer to http://disclaimer.bnymellon.com/eu.htm for certain 
disclosures relating to European legal entities.
[[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.




-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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therein, by any other person is not authorized. If you

Re: [R] how to output profile plots for groups using lattice package

[George Kalema]

A million thanks Peter, subsetting fixed it.
George

On Mon, Oct 12, 2009 at 11:51 PM, Peter Ehlers ehl...@ucalgary.ca wrote:

 Hi George,

 Your problem is not with xyplot, but with the NA occurrences in
 your data. Try adding

  subset = {!is.na(MSE)},

 to your xyplot call, or (better), subset the data before
 calling xyplot.

  -Peter Ehlers


 George Kalema wrote:

 Hi Peter (and anyone else willing to help me out),
 Many thanks for your help. Having used your code plus a few other
 modifications, I only get the points plotted but without the two lines. I
 just cannot figure out what the problem is.

 My code is as follows:

 library(lattice)
 datos2 - subset(datos, samplesize != 10  parm != Theta0)
 unq - sort(unique(datos2$samplesize))
 datos2$fsamplesize - factor(datos2$samplesize, labels = paste(Sample
 size =, unq))
 datos2$parm - factor(datos2$parm, levels = c(Intercept, time,
 trt, time*trt))
 tp1.sim - xyplot(MSE ~ ntimes | fsamplesize + parm, group = group, data
 = datos2,
type = b, lty = 1:2, pch = 1:2,
scales = list(x = list(at = c(2, 4, 8, 16)), alternating = 1),
as.table = TRUE, key = list(text = list(c(GNA, PNA)), points =
 list(pch = 1:2))
 )
 plot(tp1.sim)

 I have attached my real dataset (called datos) as well.

 Kind appreciations to your efforts.

 George


 On Wed, Oct 7, 2009 at 9:20 AM, Peter Ehlers ehl...@ucalgary.ca wrote:

  see below

 George Kalema wrote:

  Dear R users,
 I am trying to have an xyplot of a data set which has the following
 variables:
 case (n=10,20,30)
 parameter (parm=a,b)
 group (grp=g1,g2)
 y (y values)
 x (x=2,4,8)

 My plot should be parameter by case such that I have 2 rows (each row=
 each
 parameter) and 3 columns (each column=each case). My R-code is as
 follows
 but I am not able to get what I want to:

 tp1.sim - xyplot(y~ x | case + parm , group=group, data = data, lty =
 1:4
 ,
 pch = 1:4)
 print(tp1.sim)

 How can I have two lines (for g1 and g2) in each plot (each box)?

  include the type=b argument

  How do I label the x-axis with only values 2, 4, 8?
 include the scales= argument or make x a factor

  How do I label each column with the corresponding case number?
 make 'case' a factor

 The following should do what you want:

 xyplot(y ~ x | factor(case) + parm, group=group, data=data,
   type='b', lty=1:2, pch=1:2,
   scales=list(x=list(at=c(2,4,8)))
 )

 I don't understand why you want 4 line types/point chars.

  -Peter Ehlers


  My hypothetical data set is as follows:

 parm x case y group
 a 2 10 0.03 g1
 b 2 10 0.02 g1
 a 4 10 0.03 g1
 b 4 10 0.02 g1
 a 8 10 0.03 g1
 b 8 10 0.02 g1
 a 2 20 0.03 g1
 b 2 20 0.02 g1
 a 4 20 0.03 g1
 b 4 20 0.02 g1
 a 8 20 0.03 g1
 b 8 20 0.02 g1
 a 2 30 0.03 g1
 b 2 30 0.02 g1
 a 4 30 0.03 g1
 b 4 30 0.02 g1
 a 8 30 0.03 g1
 b 8 30 0.02 g1
 a 2 10 0.13 g2
 b 2 10 0.12 g2
 a 4 10 0.13 g2
 b 4 10 0.12 g2
 a 8 10 0.13 g2
 b 8 10 0.12 g2
 a 2 20 0.13 g2
 b 2 20 0.12 g2
 a 4 20 0.13 g2
 b 4 20 0.12 g2
 a 8 20 0.13 g2
 b 8 20 0.12 g2
 a 2 30 0.13 g2
 b 2 30 0.12 g2
 a 4 30 0.13 g2
 b 4 30 0.12 g2
 a 8 30 0.13 g2
 b 8 30 0.12 g2

 Many thanks in advance for your response.

 George

   [[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.








-- 

George Williams KALEMA,

Schapenstraat 37/282,
3000 Leuven,
Belgium.

Cell: +32 495 33 13 02


[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] how to output profile plots for groups using lattice package

[George Kalema]

Hi Peter (and anyone else willing to help me out),
Many thanks for your help. Having used your code plus a few other
modifications, I only get the points plotted but without the two lines. I
just cannot figure out what the problem is.

My code is as follows:

library(lattice)
datos2 - subset(datos, samplesize != 10  parm != Theta0)
unq - sort(unique(datos2$samplesize))
datos2$fsamplesize - factor(datos2$samplesize, labels = paste(Sample
size =, unq))
datos2$parm - factor(datos2$parm, levels = c(Intercept, time,
trt, time*trt))
tp1.sim - xyplot(MSE ~ ntimes | fsamplesize + parm, group = group, data
= datos2,
type = b, lty = 1:2, pch = 1:2,
scales = list(x = list(at = c(2, 4, 8, 16)), alternating = 1),
as.table = TRUE, key = list(text = list(c(GNA, PNA)), points =
list(pch = 1:2))
)
plot(tp1.sim)

I have attached my real dataset (called datos) as well.

Kind appreciations to your efforts.

George


On Wed, Oct 7, 2009 at 9:20 AM, Peter Ehlers ehl...@ucalgary.ca wrote:

 see below

 George Kalema wrote:

 Dear R users,
 I am trying to have an xyplot of a data set which has the following
 variables:
 case (n=10,20,30)
 parameter (parm=a,b)
 group (grp=g1,g2)
 y (y values)
 x (x=2,4,8)

 My plot should be parameter by case such that I have 2 rows (each row=
 each
 parameter) and 3 columns (each column=each case). My R-code is as follows
 but I am not able to get what I want to:

 tp1.sim - xyplot(y~ x | case + parm , group=group, data = data, lty = 1:4
 ,
 pch = 1:4)
 print(tp1.sim)

 How can I have two lines (for g1 and g2) in each plot (each box)?

 include the type=b argument

  How do I label the x-axis with only values 2, 4, 8?

 include the scales= argument or make x a factor

  How do I label each column with the corresponding case number?

 make 'case' a factor

 The following should do what you want:

 xyplot(y ~ x | factor(case) + parm, group=group, data=data,
type='b', lty=1:2, pch=1:2,
scales=list(x=list(at=c(2,4,8)))
 )

 I don't understand why you want 4 line types/point chars.

  -Peter Ehlers


 My hypothetical data set is as follows:

 parm x case y group
 a 2 10 0.03 g1
 b 2 10 0.02 g1
 a 4 10 0.03 g1
 b 4 10 0.02 g1
 a 8 10 0.03 g1
 b 8 10 0.02 g1
 a 2 20 0.03 g1
 b 2 20 0.02 g1
 a 4 20 0.03 g1
 b 4 20 0.02 g1
 a 8 20 0.03 g1
 b 8 20 0.02 g1
 a 2 30 0.03 g1
 b 2 30 0.02 g1
 a 4 30 0.03 g1
 b 4 30 0.02 g1
 a 8 30 0.03 g1
 b 8 30 0.02 g1
 a 2 10 0.13 g2
 b 2 10 0.12 g2
 a 4 10 0.13 g2
 b 4 10 0.12 g2
 a 8 10 0.13 g2
 b 8 10 0.12 g2
 a 2 20 0.13 g2
 b 2 20 0.12 g2
 a 4 20 0.13 g2
 b 4 20 0.12 g2
 a 8 20 0.13 g2
 b 8 20 0.12 g2
 a 2 30 0.13 g2
 b 2 30 0.12 g2
 a 4 30 0.13 g2
 b 4 30 0.12 g2
 a 8 30 0.13 g2
 b 8 30 0.12 g2

 Many thanks in advance for your response.

 George

[[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.





-- 

George Williams KALEMA,

Schapenstraat 37/282,
3000 Leuven,
Belgium.

Cell: +32 495 33 13 02

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] how to output profile plots for groups using lattice package

[George Kalema]

Dear R users,
I am trying to have an xyplot of a data set which has the following
variables:
case (n=10,20,30)
parameter (parm=a,b)
group (grp=g1,g2)
y (y values)
x (x=2,4,8)

My plot should be parameter by case such that I have 2 rows (each row= each
parameter) and 3 columns (each column=each case). My R-code is as follows
but I am not able to get what I want to:

tp1.sim - xyplot(y~ x | case + parm , group=group, data = data, lty = 1:4 ,
pch = 1:4)
print(tp1.sim)

How can I have two lines (for g1 and g2) in each plot (each box)?
How do I label the x-axis with only values 2, 4, 8?
How do I label each column with the corresponding case number?

My hypothetical data set is as follows:

parm x case y group
a 2 10 0.03 g1
b 2 10 0.02 g1
a 4 10 0.03 g1
b 4 10 0.02 g1
a 8 10 0.03 g1
b 8 10 0.02 g1
a 2 20 0.03 g1
b 2 20 0.02 g1
a 4 20 0.03 g1
b 4 20 0.02 g1
a 8 20 0.03 g1
b 8 20 0.02 g1
a 2 30 0.03 g1
b 2 30 0.02 g1
a 4 30 0.03 g1
b 4 30 0.02 g1
a 8 30 0.03 g1
b 8 30 0.02 g1
a 2 10 0.13 g2
b 2 10 0.12 g2
a 4 10 0.13 g2
b 4 10 0.12 g2
a 8 10 0.13 g2
b 8 10 0.12 g2
a 2 20 0.13 g2
b 2 20 0.12 g2
a 4 20 0.13 g2
b 4 20 0.12 g2
a 8 20 0.13 g2
b 8 20 0.12 g2
a 2 30 0.13 g2
b 2 30 0.12 g2
a 4 30 0.13 g2
b 4 30 0.12 g2
a 8 30 0.13 g2
b 8 30 0.12 g2

Many thanks in advance for your response.

George

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[R] How can I use event.chart (Hmisc) to work with a single row of data?

[George Chen]

Hi Everyone,

I would like to use event.chart to make an event chart based on a single row of 
data.  It works fine for 2 or more rows, but when I set subset.r to 1 row or 
use a one row data.frame as the data, I get a dimensional error.

Does anyone know a work around or a solution?

Thanks,

George Chen

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[R] Tex fonts in R plots

[KARAVASILIS GEORGE]

Hello, R users.
I would like to display the font of Math Mode of MikTex 2.3, WinEdt 5.4 
in R plots, e.g. in xlab, ylab or legend.

How can I do that?
Thank you in advance.

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[R] mapply

[KARAVASILIS GEORGE]

Hello, R users.
I would like to count the number of triples (r_i, s_j, t_k) with r_i, 
s_j, t_k distinct and abs((r_i-t_k)-u)=0 and abs((s_j-t_k)-v)=0, where 
r_i, s_j, t_k are the elements of three vectors a,b,c with different 
lengths and u,v=1:n. I have solved this problem writing a subroutine in 
Fortran an calling .Fortran(). I would like to find another way to use  
functions like mapply. I tried this one:


 xx - mapply( function(u,v)   {
 kk - outer(a, c, function(s,t) abs((s-t)-u)==0)
 ll - outer(b, c, function(s,t) abs((s-t)-v)==0)
 sum( outer( which(kk==TRUE, TRUE)[,2], which(ll==TRUE, TRUE)[,2], 
function(s,t) s==t)  )  },

 rep(1:n, each=n), rep(1:n, times=n))

 xx - matrix(xx, nrow=n, ncol=n, byrow=TRUE)

It works but it is rather slow. Taking into account that my vectors have 
lengths 3000, and n is from 50 to 200, can I do something to improve the 
running  time of the above code?


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[R] avoid a loop

[KARAVASILIS GEORGE]

Hello, R users.
I have the following code:

a=1:10
b=-3:15
n=5
x - rep(0,n)
for (i in 1:n) x[i] - sum( outer(a,b, function(s,t)  abs(a-b-i)==0) )

Can someone tell me if I could avoid the for command?

Thank you in advance.

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[R] Drawing schematics

[George Chen]

Hi,

I would like to represent the treatment course of a subject with an arrow 
representing passage through time and various ticks, arrows, or bars 
representing treatments done to the patient along the arrow.  I would like to 
generate this sort of schematic for each patient in a database taking 
information from the database such as time of treatment and type of treatment.

Does anybody know how I can do this?  Is there a premade R package for this 
sort of thing or should I try to make a new graphics function?  If a new 
graphics function, where could I start?

Thanks in advance.

George

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[R] making an Affybatch object for expresso

[George Chen]

Hi All,

I have microarray data that does not come in a CEL file.  Currently it is in 
the form of columns = individual samples and rows = individual probes.  There 
are about 79 columns and it is in a tab delimited text file.  Is there a way to 
convert this file into an AffyBatch so that I can run expresso with it?

Thanks,

George

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[R] problem with normalize.quantiles

[George Chen]

Hi All,

I am using normalize.quantiles (package preprocessCore) to process a 8300 row x 
96 col matrix, all numerical data.

When I limit the input matrix to 8300 x 67, the function works fine and my data 
is normalized.  But when I increase the input matrix size to 8300 x 68, the 
function processes but instead of giving normalized data, it gives me all the 
same number.  With 96 columns (the whole matrix), much the same happens.

Has anyone had any experience with this and what to do about it.  I would 
really like to not have to prune my dataset.

Examples:

Limited input matrix (col = 67)
  [,1] [,2] [,3] [,4] [,5]
 [1,]   NA 5977.433 .572 6826.831 4142.117
 [2,] 3012.837 6617.005 6036.862 7796.186 5453.295
 [3,]   NA 5977.433 7192.046 7582.068 6042.775
 [4,] 1780.039 1732.662 6373.366 7825.302 6775.492
 [5,]   NA 3308.601 2297.677 7294.935 1482.699
 [6,]   NA 3569.632 3509.979 3566.683   NA
 [7,]   NA 4492.529 6399.490 4925.750 1921.428
 [8,]   NA 2416.358 3958.061 4592.030 2829.436
 [9,] 7889.050 7928.198 7929.257 7930.121 7927.907
[10,] 7542.413 7893.827 7889.407 7896.078 7894.852

78 col input matrix
[,1] [,2] [,3] [,4] [,5]
 [1,]   NA 7883.356 7883.356 7883.356 7883.356
 [2,] 7883.356 7883.356 7883.356 7883.356 7883.356
 [3,]   NA 7883.356 7883.356 7883.356 7883.356
 [4,] 7883.356 7883.356 7883.356 7883.356 7883.356
 [5,]   NA 7883.356 7883.356 7883.356 7883.356
 [6,]   NA 7883.356 7883.356 7883.356   NA
 [7,]   NA 7883.356 7883.356 7883.356 7883.356
 [8,]   NA 7883.356 7883.356 7883.356 7883.356
 [9,] 7883.356 7883.356 7883.356 7883.356 7883.356
[10,] 7883.356 7883.356 7883.356 7883.356 7883.356

whole input matrix (96 col)
 [,1] [,2] [,3] [,4] [,5]
 [1,]   NA 7747.377 7747.377 7747.377 7747.377
 [2,] 7747.377 7747.377 7747.377 7747.377 7747.377
 [3,]   NA 7747.377 7747.377 7747.377 7747.377
 [4,] 7747.377 7747.377 7747.377 7747.377 7747.377
 [5,]   NA 7747.377 7747.377 7747.377 7747.377
 [6,]   NA 7747.377 7747.377 7747.377   NA
 [7,]   NA 7747.377 7747.377 7747.377 7747.377
 [8,]   NA 7747.377 7747.377 7747.377 7747.377
 [9,] 7747.377 7747.377 7747.377 7747.377 7747.377
[10,] 7747.377 7747.377 7747.377 7747.377 7747.377

Thanks in advance,

George

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[R] Two different scales for the same axis in the same plot.

[George Chen]

Hello,

Could anyone tell me how to plot data on two different scales in the same axis 
in the same plot?
Here is my quandary:
The range of my X axis runs from 0 to 10, but the majority of my meaningful data
lies between 7 and 10.  The data from 0 to 7 is essentially noise.
Is there a way for me to present my data such that the range from 0 to 7 takes
up a smaller amount of space on the graph compared to the range from 7 to 10
so that I can see more of the details in 7 to 10?

Thanks in advance,

George Chen

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[R] Question about plotting data points in box plots

[George Chen]

Hello,

I am plotting my data as side by side box plots.
Could somebody tell me how I can plot the points from which the box plots are 
derived inside the box plots? 
I imagine some use of the plot(x,y) function with x = the data and y = location 
of box plot, but how do I distribute the points about the vertical rather than 
have them show up all on one vertical axis?

Thanks in advance,

George Chen

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