Re: [R] Issues with R3.5.2

[Janh Anni]

Thanks!

On Mon, Dec 24, 2018 at 8:38 PM prof.amitmittal 
wrote:

> you can just use libpath to specify which packages to use instead of
> deleting libraries
>
> also use sessionInfo () at the beginning to see what is loaded
>
>
>
> Sent from my Samsung device
>
>
>  Original message 
> From: Jeff Newmiller 
> Date: 25/12/2018 4:39 am (GMT+05:30)
> To: Janh Anni 
> Cc: r-help@r-project.org
> Subject: Re: [R] Issues with R3.5.2
>
> Yes, that would be the personal library.
>
> There is one question in the installer that asks if you would like to
> create a personal library... I have always said yes, but I could imagine
> that saying no could lead to problems.
>
> On December 24, 2018 2:43:24 PM PST, Janh Anni  wrote:
> >I am sorry I forgot to mention - I just looked in the
> >Documents\R\win-Library directory and only found folders for previous R
> >versions, specifically R3.0, 3.1 and 3.4.  So I must have deleted the
> >R3.5
> >folder as you initially advised or it was removed during the
> >un-installation.  Unless I am misunderstanding what you mean by the
> >R3.5
> >personal package library?  Thanks again
> >
> >On Mon, Dec 24, 2018 at 4:28 PM Jeff Newmiller
> >
> >wrote:
> >
> >>
> >>
> >> On December 24, 2018 11:14:40 AM PST, Janh Anni 
> >> wrote:
> >> >Hello Jeff, Martin,
> >> >
> >> >I deleted 3.5.2 as suggested and tried 3.5.1 but still had the same
> >> >problems.  I still couldn't use read.table to load a data file and
> >> >still
> >> >had an error message when I tried to install a package. Usually
> >after
> >> >installing a new version of R, I would go to the R icon on the
> >desktop,
> >> >right click on it, click on Properties and then specify the folder
> >that
> >> >contains my data files in the "Start in" box, so that R
> >automatically
> >> >has
> >> >access to my data files.  Could that possibly be causing problems
> >with
> >> >these newer versions of R?
> >>
> >> No.
> >>
> >> > Also, there’s never a prompt during the
> >> >installation to Run as Administrator, so that could not possibly be
> >the
> >> >cause
> >>
> >> Yes, you have to go out of your way to Run As Administrator (RAA).
> >> However, regardless of how you initially encountered a problem, once
> >you
> >> did that there could be any number of files contaminated with
> >permissions
> >> issues.
> >>
> >> Specifically, I said to delete your 3.5 personal package library, but
> >your
> >> description is not specific so I suspect you may not have done that.
> >> However, any file modified by you intentionally or not while using
> >RAA
> >> could be causing your problems now, so now it is up to you to find
> >those
> >> files somehow.
> >>
> >> >
> >> > I also just tried Version 3.4.4, and had no problems whatsoever
> >either
> >> >with using read.table to load data files or downloading packages.
> >So
> >> >there
> >> >must be some changes from version 3.5 onward that created the
> >issues.
> >> >Hopefully this will be looked at more closely by the team with  a
> >view
> >> >to
> >> >resolving the issues
> >>
> >> I doubt the "team" will spend much time looking at this based on your
> >> descriptions so far. They need something reproducible, and the fact
> >that
> >> you already used RAA to "fix" the problem makes anything you did
> >prior to
> >> that almost impossible to reproduce.
> >>
> >> fortunes:::fortune(337)
> >>
> >> >
> >> >Thanks,
> >> >
> >> >Janh
> >> >
> >> >On Sun, Dec 23, 2018 at 1:31 AM Jeff Newmiller
> >> >
> >> >wrote:
> >> >
> >> >> You could delete your 3.5 personal package library (using the File
> >> >> Explorer with Run as Admin if necessary) and re-install your
> >packages
> >> >> without running as Admin. If that does not work try uninstalling R
> >> >and
> >> >> re-installing 3.5.1.
> >> >>
> >> >> On December 22, 2018 8:16:11 PM PST, Janh Anni
> >
> >> >wrote:
> >> >> >This issue only came up after I installed R3.5.2. Never had any
> >&g

Re: [R] Issues with R3.5.2

[Janh Anni]

Oddly enough, I must have done a dozen installations and re-installations
since this issue arose but don't recall ever being asked if I wished to
create a personal library.  I do recall being offered the option to install
R to a different folder other than the usual Program Files folder, or to
choose custom installation rather than the usual defaults, or to create a
desk shortcut or quick launch shortcut and so on.  But this whole RAA issue
is sobering - the fact that clicking Run as Administrator at some point or
the other, either intentionally or inadvertently can suddenly render R
inoperable ...

On Mon, Dec 24, 2018 at 6:09 PM Jeff Newmiller 
wrote:

> Yes, that would be the personal library.
>
> There is one question in the installer that asks if you would like to
> create a personal library... I have always said yes, but I could imagine
> that saying no could lead to problems.
>
> On December 24, 2018 2:43:24 PM PST, Janh Anni  wrote:
> >I am sorry I forgot to mention - I just looked in the
> >Documents\R\win-Library directory and only found folders for previous R
> >versions, specifically R3.0, 3.1 and 3.4.  So I must have deleted the
> >R3.5
> >folder as you initially advised or it was removed during the
> >un-installation.  Unless I am misunderstanding what you mean by the
> >R3.5
> >personal package library?  Thanks again
> >
> >On Mon, Dec 24, 2018 at 4:28 PM Jeff Newmiller
> >
> >wrote:
> >
> >>
> >>
> >> On December 24, 2018 11:14:40 AM PST, Janh Anni 
> >> wrote:
> >> >Hello Jeff, Martin,
> >> >
> >> >I deleted 3.5.2 as suggested and tried 3.5.1 but still had the same
> >> >problems.  I still couldn't use read.table to load a data file and
> >> >still
> >> >had an error message when I tried to install a package. Usually
> >after
> >> >installing a new version of R, I would go to the R icon on the
> >desktop,
> >> >right click on it, click on Properties and then specify the folder
> >that
> >> >contains my data files in the "Start in" box, so that R
> >automatically
> >> >has
> >> >access to my data files.  Could that possibly be causing problems
> >with
> >> >these newer versions of R?
> >>
> >> No.
> >>
> >> > Also, there’s never a prompt during the
> >> >installation to Run as Administrator, so that could not possibly be
> >the
> >> >cause
> >>
> >> Yes, you have to go out of your way to Run As Administrator (RAA).
> >> However, regardless of how you initially encountered a problem, once
> >you
> >> did that there could be any number of files contaminated with
> >permissions
> >> issues.
> >>
> >> Specifically, I said to delete your 3.5 personal package library, but
> >your
> >> description is not specific so I suspect you may not have done that.
> >> However, any file modified by you intentionally or not while using
> >RAA
> >> could be causing your problems now, so now it is up to you to find
> >those
> >> files somehow.
> >>
> >> >
> >> > I also just tried Version 3.4.4, and had no problems whatsoever
> >either
> >> >with using read.table to load data files or downloading packages.
> >So
> >> >there
> >> >must be some changes from version 3.5 onward that created the
> >issues.
> >> >Hopefully this will be looked at more closely by the team with  a
> >view
> >> >to
> >> >resolving the issues
> >>
> >> I doubt the "team" will spend much time looking at this based on your
> >> descriptions so far. They need something reproducible, and the fact
> >that
> >> you already used RAA to "fix" the problem makes anything you did
> >prior to
> >> that almost impossible to reproduce.
> >>
> >> fortunes:::fortune(337)
> >>
> >> >
> >> >Thanks,
> >> >
> >> >Janh
> >> >
> >> >On Sun, Dec 23, 2018 at 1:31 AM Jeff Newmiller
> >> >
> >> >wrote:
> >> >
> >> >> You could delete your 3.5 personal package library (using the File
> >> >> Explorer with Run as Admin if necessary) and re-install your
> >packages
> >> >> without running as Admin. If that does not work try uninstalling R
> >> >and
> >> >> re-installing 3.5.1.
> >> >>
> >> >&

Re: [R] Issues with R3.5.2

[Janh Anni]

I am sorry I forgot to mention - I just looked in the
Documents\R\win-Library directory and only found folders for previous R
versions, specifically R3.0, 3.1 and 3.4.  So I must have deleted the R3.5
folder as you initially advised or it was removed during the
un-installation.  Unless I am misunderstanding what you mean by the R3.5
personal package library?  Thanks again

On Mon, Dec 24, 2018 at 4:28 PM Jeff Newmiller 
wrote:

>
>
> On December 24, 2018 11:14:40 AM PST, Janh Anni 
> wrote:
> >Hello Jeff, Martin,
> >
> >I deleted 3.5.2 as suggested and tried 3.5.1 but still had the same
> >problems.  I still couldn't use read.table to load a data file and
> >still
> >had an error message when I tried to install a package. Usually after
> >installing a new version of R, I would go to the R icon on the desktop,
> >right click on it, click on Properties and then specify the folder that
> >contains my data files in the "Start in" box, so that R automatically
> >has
> >access to my data files.  Could that possibly be causing problems with
> >these newer versions of R?
>
> No.
>
> > Also, there’s never a prompt during the
> >installation to Run as Administrator, so that could not possibly be the
> >cause
>
> Yes, you have to go out of your way to Run As Administrator (RAA).
> However, regardless of how you initially encountered a problem, once you
> did that there could be any number of files contaminated with permissions
> issues.
>
> Specifically, I said to delete your 3.5 personal package library, but your
> description is not specific so I suspect you may not have done that.
> However, any file modified by you intentionally or not while using RAA
> could be causing your problems now, so now it is up to you to find those
> files somehow.
>
> >
> > I also just tried Version 3.4.4, and had no problems whatsoever either
> >with using read.table to load data files or downloading packages.  So
> >there
> >must be some changes from version 3.5 onward that created the issues.
> >Hopefully this will be looked at more closely by the team with  a view
> >to
> >resolving the issues
>
> I doubt the "team" will spend much time looking at this based on your
> descriptions so far. They need something reproducible, and the fact that
> you already used RAA to "fix" the problem makes anything you did prior to
> that almost impossible to reproduce.
>
> fortunes:::fortune(337)
>
> >
> >Thanks,
> >
> >Janh
> >
> >On Sun, Dec 23, 2018 at 1:31 AM Jeff Newmiller
> >
> >wrote:
> >
> >> You could delete your 3.5 personal package library (using the File
> >> Explorer with Run as Admin if necessary) and re-install your packages
> >> without running as Admin. If that does not work try uninstalling R
> >and
> >> re-installing 3.5.1.
> >>
> >> On December 22, 2018 8:16:11 PM PST, Janh Anni 
> >wrote:
> >> >This issue only came up after I installed R3.5.2. Never had any
> >> >problems
> >> >with previous installations.  So it is likely a bug in the current
> >> >version.  Any suggestions what to do now?
> >> >
> >> >On Sat, Dec 22, 2018 at 11:06 PM Jeff Newmiller
> >> >
> >> >wrote:
> >> >
> >> >> That normally only occurs if you have at some time used elevated
> >> >> permissions, beyond which point you fall into a downward spiral of
> >> >more
> >> >> permissions trouble. You are apparently already in trouble,
> >whether
> >> >it was
> >> >> of your own making or due to a bug in the installer.
> >> >>
> >> >> Also, never update the system R package library... always use a
> >> >personal
> >> >> library.
> >> >>
> >> >> On December 22, 2018 6:01:44 PM PST, Janh Anni
> >
> >> >wrote:
> >> >> >Hi Jeff,
> >> >> >
> >> >> >No, during the installation, there was not an option to Run as
> >> >> >Administration.  But *after *installation, I found that if I
> >> >selected
> >> >> >Run
> >> >> >as Administrator, then I could install packages using
> >> >install.packages
> >> >> >as
> >> >> >usual without problems.
> >> >> >
> >> >> >Thanks
> >> >> >Janh
> >> >> >
> >> >> >On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller
> >> 

Re: [R] Issues with R3.5.2

[Janh Anni]

Hello Jeff, Martin,

I deleted 3.5.2 as suggested and tried 3.5.1 but still had the same
problems.  I still couldn't use read.table to load a data file and still
had an error message when I tried to install a package. Usually after
installing a new version of R, I would go to the R icon on the desktop,
right click on it, click on Properties and then specify the folder that
contains my data files in the "Start in" box, so that R automatically has
access to my data files.  Could that possibly be causing problems with
these newer versions of R? Also, there’s never a prompt during the
installation to Run as Administrator, so that could not possibly be the
cause

 I also just tried Version 3.4.4, and had no problems whatsoever either
with using read.table to load data files or downloading packages.  So there
must be some changes from version 3.5 onward that created the issues.
Hopefully this will be looked at more closely by the team with  a view to
resolving the issues

Thanks,

Janh

On Sun, Dec 23, 2018 at 1:31 AM Jeff Newmiller 
wrote:

> You could delete your 3.5 personal package library (using the File
> Explorer with Run as Admin if necessary) and re-install your packages
> without running as Admin. If that does not work try uninstalling R and
> re-installing 3.5.1.
>
> On December 22, 2018 8:16:11 PM PST, Janh Anni  wrote:
> >This issue only came up after I installed R3.5.2. Never had any
> >problems
> >with previous installations.  So it is likely a bug in the current
> >version.  Any suggestions what to do now?
> >
> >On Sat, Dec 22, 2018 at 11:06 PM Jeff Newmiller
> >
> >wrote:
> >
> >> That normally only occurs if you have at some time used elevated
> >> permissions, beyond which point you fall into a downward spiral of
> >more
> >> permissions trouble. You are apparently already in trouble, whether
> >it was
> >> of your own making or due to a bug in the installer.
> >>
> >> Also, never update the system R package library... always use a
> >personal
> >> library.
> >>
> >> On December 22, 2018 6:01:44 PM PST, Janh Anni 
> >wrote:
> >> >Hi Jeff,
> >> >
> >> >No, during the installation, there was not an option to Run as
> >> >Administration.  But *after *installation, I found that if I
> >selected
> >> >Run
> >> >as Administrator, then I could install packages using
> >install.packages
> >> >as
> >> >usual without problems.
> >> >
> >> >Thanks
> >> >Janh
> >> >
> >> >On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller
> >> >
> >> >wrote:
> >> >
> >> >> Did you by any chance use Run As Administrator to install R? If so
> >> >then
> >> >> you need to uninstall it and delete all files created by it (e.g.
> >> >> Documents/R/win-lib/3.5/) and re-install using UAC as prompted.
> >> >>
> >> >> On December 22, 2018 5:10:27 PM PST, Janh Anni
> >
> >> >wrote:
> >> >> >Dear R Experts,
> >> >> >
> >> >> >I use Windows 10 and just installed the new R version, R3.5.2 but
> >> >when
> >> >> >I
> >> >> >tried to load a data file using read.table, I got an error
> >message
> >> >like
> >> >> >this:
> >> >> >
> >> >> >*Error in file(file, "rt") : cannot open the connection*
> >> >> >*In addition: Warning message:*
> >> >> >*In file(file, "rt") :*
> >> >> >*  cannot open file 'StreamPCB.dat': No such file or directory*
> >> >> >
> >> >> >Also, I couldn't install packages using install.packages as
> >usual,
> >> >> >unless I
> >> >> >run R as Administrator
> >> >> >
> >> >> >I wonder if anyone else had the same issues and any suggestions
> >how
> >> >to
> >> >> >fix?
> >> >> >
> >> >> >Thanks a lot
> >> >> >Janh
> >> >> >
> >> >> >   [[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.
> >> >>
> >> >> --
> >> >> Sent from my phone. Please excuse my brevity.
> >> >>
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] Issues with R3.5.2

[Janh Anni]

This issue only came up after I installed R3.5.2. Never had any problems
with previous installations.  So it is likely a bug in the current
version.  Any suggestions what to do now?

On Sat, Dec 22, 2018 at 11:06 PM Jeff Newmiller 
wrote:

> That normally only occurs if you have at some time used elevated
> permissions, beyond which point you fall into a downward spiral of more
> permissions trouble. You are apparently already in trouble, whether it was
> of your own making or due to a bug in the installer.
>
> Also, never update the system R package library... always use a personal
> library.
>
> On December 22, 2018 6:01:44 PM PST, Janh Anni  wrote:
> >Hi Jeff,
> >
> >No, during the installation, there was not an option to Run as
> >Administration.  But *after *installation, I found that if I selected
> >Run
> >as Administrator, then I could install packages using install.packages
> >as
> >usual without problems.
> >
> >Thanks
> >Janh
> >
> >On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller
> >
> >wrote:
> >
> >> Did you by any chance use Run As Administrator to install R? If so
> >then
> >> you need to uninstall it and delete all files created by it (e.g.
> >> Documents/R/win-lib/3.5/) and re-install using UAC as prompted.
> >>
> >> On December 22, 2018 5:10:27 PM PST, Janh Anni 
> >wrote:
> >> >Dear R Experts,
> >> >
> >> >I use Windows 10 and just installed the new R version, R3.5.2 but
> >when
> >> >I
> >> >tried to load a data file using read.table, I got an error message
> >like
> >> >this:
> >> >
> >> >*Error in file(file, "rt") : cannot open the connection*
> >> >*In addition: Warning message:*
> >> >*In file(file, "rt") :*
> >> >*  cannot open file 'StreamPCB.dat': No such file or directory*
> >> >
> >> >Also, I couldn't install packages using install.packages as usual,
> >> >unless I
> >> >run R as Administrator
> >> >
> >> >I wonder if anyone else had the same issues and any suggestions how
> >to
> >> >fix?
> >> >
> >> >Thanks a lot
> >> >Janh
> >> >
> >> >   [[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.
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>

[[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.

Re: [R] Issues with R3.5.2

[Janh Anni]

Hi Jeff,

No, during the installation, there was not an option to Run as
Administration.  But *after *installation, I found that if I selected Run
as Administrator, then I could install packages using install.packages as
usual without problems.

Thanks
Janh

On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller 
wrote:

> Did you by any chance use Run As Administrator to install R? If so then
> you need to uninstall it and delete all files created by it (e.g.
> Documents/R/win-lib/3.5/) and re-install using UAC as prompted.
>
> On December 22, 2018 5:10:27 PM PST, Janh Anni  wrote:
> >Dear R Experts,
> >
> >I use Windows 10 and just installed the new R version, R3.5.2 but when
> >I
> >tried to load a data file using read.table, I got an error message like
> >this:
> >
> >*Error in file(file, "rt") : cannot open the connection*
> >*In addition: Warning message:*
> >*In file(file, "rt") :*
> >*  cannot open file 'StreamPCB.dat': No such file or directory*
> >
> >Also, I couldn't install packages using install.packages as usual,
> >unless I
> >run R as Administrator
> >
> >I wonder if anyone else had the same issues and any suggestions how to
> >fix?
> >
> >Thanks a lot
> >Janh
> >
> >   [[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.
>
> --
> Sent from my phone. Please excuse my brevity.
>

[[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.

[R] Issues with R3.5.2

[Janh Anni]

Dear R Experts,

I use Windows 10 and just installed the new R version, R3.5.2 but when I
tried to load a data file using read.table, I got an error message like
this:

*Error in file(file, "rt") : cannot open the connection*
*In addition: Warning message:*
*In file(file, "rt") :*
*  cannot open file 'StreamPCB.dat': No such file or directory*

Also, I couldn't install packages using install.packages as usual, unless I
run R as Administrator

I wonder if anyone else had the same issues and any suggestions how to fix?

Thanks a lot
Janh

[[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.

[R] Monte Carlo Simulations for Human Health & Ecological Risk Assessment

[Janh Anni]

Dear R Experts!

I would really love to perform probabilistic risk assessment for human
health and ecological using Monte Carlo. I am knowledgeable in the risk
assessment part but have no idea how to incorporate Monte Carlo simulation
using R.  Is there anyone out there in the wide wide world of R who has
actually used Monte Carlo for this type of risk assessment and kind enough
to show me the way?

Many thanks in anticipation!

Janh

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] Bootstrapping One- and Two-Sample Hypothesis Tests of Proportion

[Janh Anni]

Hi Marc,

I see what you are saying.  I will  try re-running the* boot.two.per*
function using 1's  and 0's for the data and specifying mean as the
parameter and see what happens.  I will report back.  Thanks so much for
your kind assistance!

Janh

On Thu, Nov 29, 2018 at 7:07 PM Marc Schwartz  wrote:

> Hi,
>
> I don't see Duncan's reply in the archive, but consider:
>
> > 1 / 4
> [1] 0.25
>
> > mean(c(1, 0, 0, 0))
> [1] 0.25
>
>
> > 3 / 9
> [1] 0.333
>
> > mean(c(1, 1, 1, 0, 0, 0, 0, 0, 0))
> [1] 0.333
>
>
> Regards,
>
> Marc Schwartz
>
> On Nov 29, 2018, at 6:57 PM, Janh Anni  wrote:
>
> Hi Bert,
>
> You mean, just compute the test specifying the mean as the parameter but
> using 1's and 0's for the data?  Also I don't get how a proportion is a
> mean of 0/1 responses.  Could you please elaborate?  Thanks!
>
> Janh
>
> On Thu, Nov 29, 2018 at 6:45 PM Bert Gunter 
> wrote:
>
> ... but as Duncan pointed out already, I believe, a proportion **is** a
> mean -- of 0/1 responses.
>
>
> 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 Thu, Nov 29, 2018 at 3:30 PM Janh Anni  wrote:
>
> Hi Rui,
>
> Thanks a lot for responding and I apologize for my late response.  I tried
> using the *boot.two.per* function in the wBoot package which stated that
> it
> could bootstrap 2-sample tests for both means and proportions but it
> turned
> out that it only works for the mean.
>
> Thanks again,
> Janh
>
> On Wed, Nov 28, 2018 at 12:38 PM Rui Barradas 
> wrote:
>
> Hello,
>
> What have you tried?
> Reproducible example please.
>
> http://adv-r.had.co.nz/Reproducibility.html
>
>
>
> https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
>
> https://www.r-bloggers.com/minimal-reproducible-examples/
>
>
> Rui Barradas
>
> Às 22:33 de 27/11/2018, Janh Anni escreveu:
>
> Hello R Experts!
>
> Does anyone know of a relatively straightforward way to bootstrap
> hypothesis tests for proportion in R?
>
> Thanks in advance!
>
> Janh
>
>
>

[[alternative HTML version deleted]]

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Re: [R] Bootstrapping One- and Two-Sample Hypothesis Tests of Proportion

[Janh Anni]

Hi Bert,

You mean, just compute the test specifying the mean as the parameter but
using 1's and 0's for the data?  Also I don't get how a proportion is a
mean of 0/1 responses.  Could you please elaborate?  Thanks!

Janh

On Thu, Nov 29, 2018 at 6:45 PM Bert Gunter  wrote:

> ... but as Duncan pointed out already, I believe, a proportion **is** a
> mean -- of 0/1 responses.
>
>
> 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 Thu, Nov 29, 2018 at 3:30 PM Janh Anni  wrote:
>
>> Hi Rui,
>>
>> Thanks a lot for responding and I apologize for my late response.  I tried
>> using the *boot.two.per* function in the wBoot package which stated that
>> it
>> could bootstrap 2-sample tests for both means and proportions but it
>> turned
>> out that it only works for the mean.
>>
>> Thanks again,
>> Janh
>>
>> On Wed, Nov 28, 2018 at 12:38 PM Rui Barradas 
>> wrote:
>>
>> > Hello,
>> >
>> > What have you tried?
>> > Reproducible example please.
>> >
>> > http://adv-r.had.co.nz/Reproducibility.html
>> >
>> >
>> https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
>> > https://www.r-bloggers.com/minimal-reproducible-examples/
>> >
>> >
>> > Rui Barradas
>> >
>> > Às 22:33 de 27/11/2018, Janh Anni escreveu:
>> > > Hello R Experts!
>> > >
>> > > Does anyone know of a relatively straightforward way to bootstrap
>> > > hypothesis tests for proportion in R?
>> > >
>> > > Thanks in advance!
>> > >
>> > > Janh
>> > >
>> > >   [[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.
>>
>

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Re: [R] Bootstrapping One- and Two-Sample Hypothesis Tests of Proportion

[Janh Anni]

Hi Rui,

Thanks a lot for responding and I apologize for my late response.  I tried
using the *boot.two.per* function in the wBoot package which stated that it
could bootstrap 2-sample tests for both means and proportions but it turned
out that it only works for the mean.

Thanks again,
Janh

On Wed, Nov 28, 2018 at 12:38 PM Rui Barradas  wrote:

> Hello,
>
> What have you tried?
> Reproducible example please.
>
> http://adv-r.had.co.nz/Reproducibility.html
>
> https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> https://www.r-bloggers.com/minimal-reproducible-examples/
>
>
> Rui Barradas
>
> Às 22:33 de 27/11/2018, Janh Anni escreveu:
> > Hello R Experts!
> >
> > Does anyone know of a relatively straightforward way to bootstrap
> > hypothesis tests for proportion in R?
> >
> > Thanks in advance!
> >
> > Janh
> >
> >   [[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] Bootstrapping One- and Two-Sample Hypothesis Tests of Proportion

[Janh Anni]

Hello R Experts!

Does anyone know of a relatively straightforward way to bootstrap
hypothesis tests for proportion in R?

Thanks in advance!

Janh

[[alternative HTML version deleted]]

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Re: [R] wBoot Package

[Janh Anni]

Hello David, Peter,

Thank you so much for taking the trouble to look into this.  The user guide
for the *boot.two.per* function contains this statement:

*Obtains an independent-samples confidence interval and (optionally)
performs an independent samples*
*hypothesis test for the difference between two population means, medians,
proportions,*
*or some user-defined function, using the percentile bootstrap method*.

That was why I assumed it could handle the bootstrapped two-sample test for
proportions as well.  I actually tried to contact the author before
bringing the issue to R-Help, but found that unfortunately he passed away
in 2016.  Assuming there's no resolution to this problem, would you know of
any other package or function that can bootstrap one- and two-sample
proportion tests?

Thanks again!

Janh


On Sun, Nov 25, 2018 at 7:06 PM David Winsemius 
wrote:

> Look at the function's help page:
>
> No help there. The "parameter" argument is not defined in any
> substantive manner, and no examples other than `parameter=mean` appear
> in the help page.
>
> (Now) Look at the code. The parameter argument is expected to be a
> function. There is no function named `proportion` in base R that I know
> of and:
>
>  > wBoot::proportion
> Error: 'proportion' is not an exported object from 'namespace:wBoot'
>  > wBoot:::proportion
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>object 'proportion' not found
>
>
> The code in the function you are asking about does begin with:
>
> {
>
>   proportion <- mean
>
> However, that named entity, `proportion`,  is never referenced in  code
> that follows, so it appears that the package author started down one
> path and then abandoned that line of code and did something else. I
> suspect that the code was written so that `mean` was inteended to
> deliver a test of equal proportions using the normal approximation to a
> binomial test. There is a waring in the help page that would apply to
> situations where the proportion is far from 0.5.  You are advised that
> not all packages are written with scrupulous quality control and peer
> review.
>
> You should have read the posting guide. It would have told you that you
> should have addressed your concerns to the package author first, and
> also posted in plain text.
>
> --
>
> David
>
> On 11/25/18 12:59 PM, Janh Anni wrote:
> > Hello R Experts!
> >
> > I wonder if anyone is familiar with the wBoot package written by Neil
> > Weiss. I was trying to use the *boot.two.per* function in that package to
> > compute a bootstrapped two-sample hypothesis test for proportion.  Here"s
> > the *boot.two.per* script:
> >
> > boot.two.per(x, y, parameter, stacked = TRUE, variable = NULL,
> >
> > null.hyp = NULL, alternative = c("two.sided", "less", "greater"),
> >
> > conf.level = 0.95, type = NULL, R = )
> >
> > The problem is that if I specify *mean* or *median *as the parameter for
> > the test, the script runs fine, but if I specify *proportion*, I get an
> > error message that *proportion* not found
> >
> > Is there another way to specify proportion as the test parameter?
> >
> > Thanks a lot!
> >
> > Janh
> >
> >   [[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.
>
> __
> 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] wBoot Package

[Janh Anni]

Hello R Experts!

I wonder if anyone is familiar with the wBoot package written by Neil
Weiss. I was trying to use the *boot.two.per* function in that package to
compute a bootstrapped two-sample hypothesis test for proportion.  Here"s
the *boot.two.per* script:

boot.two.per(x, y, parameter, stacked = TRUE, variable = NULL,

null.hyp = NULL, alternative = c("two.sided", "less", "greater"),

conf.level = 0.95, type = NULL, R = )

The problem is that if I specify *mean* or *median *as the parameter for
the test, the script runs fine, but if I specify *proportion*, I get an
error message that *proportion* not found

Is there another way to specify proportion as the test parameter?

Thanks a lot!

Janh

[[alternative HTML version deleted]]

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Re: [R] Bootstrapped Regression

[Janh Anni]

Hello Rui,

It was perfect!  Thank you so much for your kindness.  It is greatly
appreciated.

All the best,
Janh

On Sun, Oct 15, 2017 at 3:25 AM, Rui Barradas <ruipbarra...@sapo.pt> wrote:

> Hello,
>
> Much clearer now, thanks.
> It's a matter of changing the function boot calls to return the predicted
> values at the point of interess, education = 50, income = 75.
>
> I have changed the way the function uses the indices a bit, the result is
> the same, it's just the way I usually do it.
>
> pred.duncan.function <- function(data, indices) {
> mod <- lm(prestige ~ education + income, data = data[indices, ])
> new <- data.frame(education = 50, income = 75)
> predict(mod, newdata = new)
> }
>
> set.seed(94)# make the results reproducible
>
> Predicted <- boot(Duncan, pred.duncan.function , 1000)
> head(Predicted)
> Predicted$t0
> boot.ci(Predicted, index = 1, conf = 0.95, type=c("basic", "norm",
> "perc", "bca"))
>
>
> Hope this helps,
>
> Rui Barradas
>
> Em 15-10-2017 02:22, Janh Anni escreveu:
>
>> Hello Rui,
>>
>> Thanks for your helpful suggestions.  Just for illustration, let's use the
>> well known Duncan dataset of prestige vs education + income that is
>> contained in the "car" package.  Suppose I wish to use boot function to
>> bootstrap a linear regression of prestige ~ education + income and use the
>> following script:
>>
>> duncan.function <- function(data, indices) {data = data[indices,]
>>
>> mod <- lm(prestige ~ education + income, data=data,)
>>
>> coefficients(mod)}
>>
>> Results <- boot(Duncan, duncan.function , 1000)
>> Results
>>
>> So the 1000 bootstrapped coefficients are contained in Results and I can
>> use the boot.ci function in the same boot package to obtain the
>> confidence
>> intervals for the, say, education coefficient with something like:
>>
>> boot.ci(Results, index=2, conf = 0.95, type=c("basic", "norm", "perc",
>> "bca"))
>>
>> Then, suppose I am interested in getting a confidence interval for the
>> predicted  prestige at, say, education = 50 and income = 75.  The question
>> is how do I get boot to compute 1000 values of the predicted prestige at
>> education = 50 and income = 75, so that I can subsequently (hopefully)
>> have
>> boot.ci compute the confidence intervals as it did for the bootstrapped
>> coefficients? As for prediction intervals, it wouldn't seem conceptually
>> feasible in this context?  Thanks again for all your help.
>>
>> Janh
>>
>> On Sat, Oct 14, 2017 at 11:12 AM, Bert Gunter <bgunter.4...@gmail.com>
>> wrote:
>>
>> R-help is not a free coding service. We expect users to make the effort to
>>> learn R and *may* provide help when they get stuck. Pay a local R
>>> programmer if you do not wish to make such an effort.
>>>
>>> Cheers,
>>> Bert
>>>
>>>
>>> On Oct 14, 2017 7:58 AM, "Janh Anni" <annij...@gmail.com> wrote:
>>>
>>> Greetings!
>>>
>>> We are trying to obtain confidence and prediction intervals for a
>>> predicted
>>> Y value from bootstrapped linear regression using the boot function. Does
>>> anyone know how to code it?  Greatly appreciated.
>>>
>>> Janh
>>>
>>>  [[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.
>>>
>>>
>>>
>>>
>> [[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.
>>
>>

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Re: [R] Bootstrapped Regression

[Janh Anni]

Hello Rui,

Thanks for your helpful suggestions.  Just for illustration, let's use the
well known Duncan dataset of prestige vs education + income that is
contained in the "car" package.  Suppose I wish to use boot function to
bootstrap a linear regression of prestige ~ education + income and use the
following script:

duncan.function <- function(data, indices) {data = data[indices,]

mod <- lm(prestige ~ education + income, data=data,)

coefficients(mod)}

Results <- boot(Duncan, duncan.function , 1000)
Results

So the 1000 bootstrapped coefficients are contained in Results and I can
use the boot.ci function in the same boot package to obtain the confidence
intervals for the, say, education coefficient with something like:

boot.ci(Results, index=2, conf = 0.95, type=c("basic", "norm", "perc",
"bca"))

Then, suppose I am interested in getting a confidence interval for the
predicted  prestige at, say, education = 50 and income = 75.  The question
is how do I get boot to compute 1000 values of the predicted prestige at
education = 50 and income = 75, so that I can subsequently (hopefully) have
boot.ci compute the confidence intervals as it did for the bootstrapped
coefficients? As for prediction intervals, it wouldn't seem conceptually
feasible in this context?  Thanks again for all your help.

Janh

On Sat, Oct 14, 2017 at 11:12 AM, Bert Gunter <bgunter.4...@gmail.com>
wrote:

> R-help is not a free coding service. We expect users to make the effort to
> learn R and *may* provide help when they get stuck. Pay a local R
> programmer if you do not wish to make such an effort.
>
> Cheers,
> Bert
>
>
> On Oct 14, 2017 7:58 AM, "Janh Anni" <annij...@gmail.com> wrote:
>
> Greetings!
>
> We are trying to obtain confidence and prediction intervals for a predicted
> Y value from bootstrapped linear regression using the boot function. Does
> anyone know how to code it?  Greatly appreciated.
>
> Janh
>
> [[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.
>
>
>

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[R] Bootstrapped Regression

[Janh Anni]

Greetings!

We are trying to obtain confidence and prediction intervals for a predicted
Y value from bootstrapped linear regression using the boot function. Does
anyone know how to code it?  Greatly appreciated.

Janh

[[alternative HTML version deleted]]

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Re: [R] Infinite Series

[Janh Anni]

Hello Jeff,

Thanks a lot.  I tried it and see that it prints out the entire 100 partial
sums, so I can take the last value as the partial sum for the first 100
terms. Would there be any way cumsum can print only the nth partial sum,
i.e. the last value in the array, instead of printing the entire array?
Thanks again.

Joseph

On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us
wrote:

 Please reply-all so the mailing list stays in the loop.

 cumsum(1/(1:100)^2)

 gives you the partial sums up through i=100.
 ---
 Jeff NewmillerThe .   .  Go Live...
 DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live
 Go...
   Live:   OO#.. Dead: OO#..  Playing
 Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
 /Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
 ---
 Sent from my phone. Please excuse my brevity.

 On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote:
 Hello Jeff,
 
 Thank you so much for the suggestion,  I searched cumsum as suggested
 but
 not sure it is what I had in mind.  For instance if I had the infinite
 series:[image: Inline image 1]
 
 and want to compute the sum of the, say, first 100 terms, how could I
 use
 cusum to do that?
 
 Thanks again,
 
 Janh
 
 
 On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller
 jdnew...@dcn.davis.ca.us
 wrote:
 
  ?cumsum
 

 ---
  Jeff NewmillerThe .   .  Go
 Live...
  DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live
  Go...
Live:   OO#.. Dead: OO#..
 Playing
  Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
  /Software/Embedded Controllers)   .OO#.   .OO#.
 rocks...1k
 

 ---
  Sent from my phone. Please excuse my brevity.
 
  On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com
 wrote:
  Dear All,
  
  Does anyone know of any R functions that compute partial sums of
  series?
  
  Thanks in advance!
  
  Janh
  
 [[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] Infinite Series

[Janh Anni]

Thanks Bert!

On Fri, Jul 24, 2015 at 7:57 PM, Bert Gunter bgunter.4...@gmail.com wrote:

 Janh:

 It sounds like you really need to go through an R tutorial or two
 before posting further, as this is a pretty basic query. Or am I wrong
 about this?

 An answer: Just use indexing

 cumsum(1/seq_len(100)^2)[seq(10, to = 100,by = 10)] ## keeps every 10th

  [1] 1.549768 1.596163 1.612150 1.620244 1.625133 1.628406 1.630750
 1.632512 1.633884
 [10] 1.634984


 But beware FAQ 7.31 for long series.

 Cheers,
 Bert


 Bert Gunter

 Data is not information. Information is not knowledge. And knowledge
 is certainly not wisdom.
-- Clifford Stoll


 On Fri, Jul 24, 2015 at 4:37 PM, Janh Anni annij...@gmail.com wrote:
  Hello Jeff,
 
  Thanks a lot.  I tried it and see that it prints out the entire 100
 partial
  sums, so I can take the last value as the partial sum for the first 100
  terms. Would there be any way cumsum can print only the nth partial sum,
  i.e. the last value in the array, instead of printing the entire array?
  Thanks again.
 
  Joseph
 
  On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller 
 jdnew...@dcn.davis.ca.us
  wrote:
 
  Please reply-all so the mailing list stays in the loop.
 
  cumsum(1/(1:100)^2)
 
  gives you the partial sums up through i=100.
 
 ---
  Jeff NewmillerThe .   .  Go
 Live...
  DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live
  Go...
Live:   OO#.. Dead: OO#..  Playing
  Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
  /Software/Embedded Controllers)   .OO#.   .OO#.
 rocks...1k
 
 ---
  Sent from my phone. Please excuse my brevity.
 
  On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote:
  Hello Jeff,
  
  Thank you so much for the suggestion,  I searched cumsum as suggested
  but
  not sure it is what I had in mind.  For instance if I had the infinite
  series:[image: Inline image 1]
  
  and want to compute the sum of the, say, first 100 terms, how could I
  use
  cusum to do that?
  
  Thanks again,
  
  Janh
  
  
  On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller
  jdnew...@dcn.davis.ca.us
  wrote:
  
   ?cumsum
  
 
 
 ---
   Jeff NewmillerThe .   .  Go
  Live...
   DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.
 Live
   Go...
 Live:   OO#.. Dead: OO#..
  Playing
   Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
   /Software/Embedded Controllers)   .OO#.   .OO#.
  rocks...1k
  
 
 
 ---
   Sent from my phone. Please excuse my brevity.
  
   On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com
  wrote:
   Dear All,
   
   Does anyone know of any R functions that compute partial sums of
   series?
   
   Thanks in advance!
   
   Janh
   
  [[alternative HTML version deleted]]
   
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Re: [R] Infinite Series

[Janh Anni]

Wow! So many (simpler) ways to skin a cat.  Thanks!

On Fri, Jul 24, 2015 at 8:07 PM, David Winsemius dwinsem...@comcast.net
wrote:


 On Jul 24, 2015, at 4:37 PM, Janh Anni wrote:

  Hello Jeff,
 
  Thanks a lot.  I tried it and see that it prints out the entire 100
 partial
  sums, so I can take the last value as the partial sum for the first 100
  terms. Would there be any way cumsum can print only the nth partial sum,
  i.e. the last value in the array, instead of printing the entire array?
  Thanks again.

 Wouldn't that just mean using sum instead of cumsum?

 Can even check the error from the analytical limit.

  sum(1/(1:100)^2) - pi^2/6
 [1] -0.009950167


 
  Joseph
 
  On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller 
 jdnew...@dcn.davis.ca.us
  wrote:
 
  Please reply-all so the mailing list stays in the loop.
 
  cumsum(1/(1:100)^2)
 
  gives you the partial sums up through i=100.
 
 ---
  Jeff NewmillerThe .   .  Go
 Live...
  DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live
  Go...
   Live:   OO#.. Dead: OO#..  Playing
  Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
  /Software/Embedded Controllers)   .OO#.   .OO#.
 rocks...1k
 
 ---
  Sent from my phone. Please excuse my brevity.
 
  On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote:
  Hello Jeff,
 
  Thank you so much for the suggestion,  I searched cumsum as suggested
  but
  not sure it is what I had in mind.  For instance if I had the infinite
  series:[image: Inline image 1]
 
  and want to compute the sum of the, say, first 100 terms, how could I
  use
  cusum to do that?
 
  Thanks again,
 
  Janh
 
 
  On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller
  jdnew...@dcn.davis.ca.us
  wrote:
 
  ?cumsum
 
 
 
 ---
  Jeff NewmillerThe .   .  Go
  Live...
  DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live
  Go...
   Live:   OO#.. Dead: OO#..
  Playing
  Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
  /Software/Embedded Controllers)   .OO#.   .OO#.
  rocks...1k
 
 
 
 ---
  Sent from my phone. Please excuse my brevity.
 
  On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com
  wrote:
  Dear All,
 
  Does anyone know of any R functions that compute partial sums of
  series?
 
  Thanks in advance!
 
  Janh
 
   [[alternative HTML version deleted]]
 
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  http://www.R-project.org/posting-guide.html
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 David Winsemius
 Alameda, CA, USA



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[R] Infinite Series

[Janh Anni]

Dear All,

Does anyone know of any R functions that compute partial sums of series?

Thanks in advance!

Janh

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Re: [R] Trying to install NADA in R 3.0.0

[Janh Anni]

Try contacting Dr Dennis Helsel, the developer at dhel...@practicalstats.com


On Fri, Jun 7, 2013 at 1:47 PM, David Doyle kydaviddo...@gmail.com wrote:

 Hello folks,

 I’m trying to install the NADA package in R 3.0.0


 It has been archived so I tried to downloading it and installing it
 locally.  I get

  utils:::menuInstallLocal()

 package ‘NADA’ successfully unpacked and MD5 sums checked


 But then when I load it I get

  library(NADA)

 Error in library(NADA) : ‘NADA’ is not a valid installed package

 

 Any sugestions

 [[alternative HTML version deleted]]


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Re: [R] wilcox_test function in coin package

[Janh Anni]

Hello Henric,

Thank you so much for the detailed responses and helpful information.  Much
appreciated.

Regards

Janh


On Mon, Jun 3, 2013 at 6:15 AM, Henric Winell nilsson.hen...@gmail.comwrote:

 Janh,

 Janh Anni skrev 2013-06-01 19:47:

  Hello All,
 Thanks a lot for the helpful suggestions.  I wonder how ties are handled
 for the rank sum test by wilcox_test and wilcox.exact?  For instance,


 Ties handling was mainly a problem back in the day when recursion formulas
 were used for the computation of exact p-values.  (When no ties are
 present, the form of the exact null distribution of the Wilcoxon rank-sum
 statistic depends only on the total number of observations in the two
 groups.)


  other software such as Minitab correct for ties by adjusting the
 variance of the test statistic, and actually provide the p values before
 and after adjustment for ties.


 Adjusting the variance only matters when approximating the exact
 distribution with its asymptotic Gaussian distribution.  And only when at
 least one tie is shared between the two groups.  And yes, the standardized
 statistic in 'coin' accounts for ties.  If ties are present, why would you
 want to know the unadjusted p-value?


  IIf neither wilcox_test nor wilcox.exact
 expressly corrects for ties in the Wilcoxon rank sum test, then perhaps
 one should just use the conventional wilcox.test which is the simplest

  of them all?  Thanks again

 If this was true, the 'wilcox.exact' function would be completely
 pointless since 'wilcox.test' just falls back on the asymptotic
 approximation when ties are present.

 Software like 'StatXact', 'exactRankTests', and 'coin' use algorithms that
 compute the exact p-value for any ties configuration.  Take a look at
 Torsten Hothorn's On Exact Rank Tests in R article from the very first
 issue of R News 
 http://www.r-project.org/doc/**Rnews/Rnews_2001-1.pdfhttp://www.r-project.org/doc/Rnews/Rnews_2001-1.pdf
 .


 Henric



  Janh


 On Sat, Jun 1, 2013 at 8:41 AM, Henric Winell nilsson.hen...@gmail.com
 mailto:nilsson.henric@gmail.**com nilsson.hen...@gmail.com wrote:

 Janh,

 Janh Anni skrev 2013-06-01 04:27:

 Hello peter,


 Thanks for the comment.  wilcox.exact is simpler as you pointed
 out but the
 fact that it is no longer being developed is somewhat concerning.


 Admittedly, 'coin' is being actively developed and has a lot more
 bells and whistles.  But for something as simple as this, that
 wouldn't bother me at all.  In any case, the 'exactRankTests'
 package still gets bug fixes and the algorithm used in the Wilcoxon
 case is exactly the same for both packages.

 However, if you want to stay with 'coin' you can just wrap up Greg's
 proposal in a function:

 wilcox_test.default - function(x, y, ...) {
  data -
  data.frame(values = c(x, y),
 group = rep(c(x, y), c(length(x), length(y
  wilcox_test(values ~ group, data = data, ...)
 }

 Assuming that both 'coin' and 'exactRankTests are loaded, we can now
 check that it works:

   set.seed(123)
   x - rpois(10, 3)
   y - rpois(11, 3.1)
  
   wilcox_test(x, y, alternative = less, distribution = exact)

  Exact Wilcoxon-Mann-Whitney Test

 data:  values by group (x, y)
 Z = -0.0715, p-value = 0.4844
 alternative hypothesis: true mu is less than 0

   wilcox.exact(x, y, alternative = less)

  Exact Wilcoxon rank sum test

 data:  x and y
 W = 54, p-value = 0.4844
 alternative hypothesis: true mu is less than 0


 HTH,
 Henric




 Regards
 Janh


 On Fri, May 31, 2013 at 6:50 PM, Peter Ehlers
 ehl...@ucalgary.ca mailto:ehl...@ucalgary.ca wrote:

 On 2013-05-30 20:20, Janh Anni wrote:

 Hello Greg,

 Thank you so much for your kind assistance.  It looks
 like there's no way
 around using the formula format.  I longed in vain for a
 simpler script
 more like the wilcox.test format.  Thanks again.

 Janh


 I don't see why the formula syntax would be a problem, but
 to avoid it
 you could use exactRankTests::wilcox.exact() which, I
 believe, was
 written by the same author. It uses the same syntax as
 wilcox.test().
 Note, though, that the package is no longer
 being developed.

 Peter Ehlers




 On Thu, May 30, 2013 at 6:21 PM, Greg Snow
 538...@gmail.com mailto:538...@gmail.com wrote:

Ok, it looks like the function mainly works through
 the formula syntax.

 It still would have been nice to have a
 reproducible example of what
 your

Re: [R] wilcox_test function in coin package

[Janh Anni]

Hello peter,

Thanks for the comment.  wilcox.exact is simpler as you pointed out but the
fact that it is no longer being developed is somewhat concerning.

Regards
Janh


On Fri, May 31, 2013 at 6:50 PM, Peter Ehlers ehl...@ucalgary.ca wrote:

 On 2013-05-30 20:20, Janh Anni wrote:

 Hello Greg,

 Thank you so much for your kind assistance.  It looks like there's no way
 around using the formula format.  I longed in vain for a simpler script
 more like the wilcox.test format.  Thanks again.

 Janh


 I don't see why the formula syntax would be a problem, but to avoid it
 you could use exactRankTests::wilcox.exact() which, I believe, was
 written by the same author. It uses the same syntax as wilcox.test().
 Note, though, that the package is no longer
 being developed.

 Peter Ehlers




 On Thu, May 30, 2013 at 6:21 PM, Greg Snow 538...@gmail.com wrote:

  Ok, it looks like the function mainly works through the formula syntax.
   It still would have been nice to have a reproducible example of what
 your
 data may look like, but I can show an example with simulated x and y:

  x - rpois(10, 3)
 y - rpois(11, 3.1)
 mydf - data.frame( vals = c(x,y),

 +   group=rep( c('x','y'), c( length(x), length(y) ) ) )

 wilcox_test( vals ~ group, data=mydf )


  Asymptotic Wilcoxon-Mann-Whitney Test

 data:  vals by group (x, y)
 Z = -1.3718, p-value = 0.1701
 alternative hypothesis: true mu is not equal to 0

 Does that help?  (maybe I am the heedlessness theorist after all)



 On Thu, May 30, 2013 at 4:14 PM, Janh Anni annij...@gmail.com wrote:

  I thought (hoped) wilcox_test(x,y) would do it but it doesn't and the
 package maintainer says the data have to be rearranged but does not
 specify
 how.  Thanks

 Janh



 On Thu, May 30, 2013 at 6:05 PM, Greg Snow 538...@gmail.com wrote:

  What have you tried so far?  Have you read the help page? have you run
 the examples on that page?

 I would expect that it is something as simple as

 library(coin)
 wilcox_test(x,y)

 or

 wilcox_test( y ~ group )

 But you should trust the help page more than the expectations of
 someone
 who has not read it recently (see fortune(14)).

 If that does not answer your question then give us more detail on what
 you tried, what you expected the results to be, what the results
 actually
 were, and how they differed.  Without that information we have to
 resort to
 mind reading and the current implementation of the esp package is still
 very pre-alpha, it suggests that the answer to your question is:

  esp()

 [1] selflessly vigilantly pigeon theorist heedlessness

 Which is either much to profound for the likes of me to understand or
 is
 complete gibberish (which is only slightly less helpful than an overly
 general question without a reproducible example).


 On Thu, May 30, 2013 at 2:07 PM, Janh Anni annij...@gmail.com wrote:

  Dear All,

 I have two simple data samples (no groups or factors, etc.) and would
 just
 like to compute the two-sample Wilcoxon Rank Sum test using the
 wilcox_test
 function contained in the coin package, which is reportedly better
 than
 the
 regular wilcox.test function because it performs some adjustment for
 ties.
 Would anyone know how to craft a script to perform this task?  Much
 appreciated.

 Janh

  [[alternative HTML version deleted]]

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




 --
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com





 --
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com


 [[alternative HTML version deleted]]

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





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[R] Fwd: Your message to R-help awaits moderator approval

[Janh Anni]

Hello,

I don't understand why my mails are being held up.  What could be the
problem?

Thanks

Janh
-- Forwarded message --
From: r-help-boun...@r-project.org
Date: Sat, Jun 1, 2013 at 1:48 PM
Subject: Your message to R-help awaits moderator approval
To: annij...@gmail.com


Your mail to 'R-help' with the subject

Re: [R] wilcox_test function in coin package

Is being held until the list moderator can review it for approval.

The reason it is being held:

The message headers matched a filter rule

Either the message will get posted to the list, or you will receive
notification of the moderator's decision.  If you would like to cancel
this posting, please visit the following URL:


https://stat.ethz.ch/mailman/confirm/r-help/067afe28f7ead30dfea844b8a34449526cd665d8

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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] Fwd: Your message to R-help awaits moderator approval

[Janh Anni]

Okay.  Thanks!

Janh


On Sat, Jun 1, 2013 at 3:11 PM, Ted Harding ted.hard...@wlandres.netwrote:

 [See at end]

 On 01-Jun-2013 17:52:01 Janh Anni wrote:
  Hello,
 
  I don't understand why my mails are being held up.  What could be the
  problem?
 
  Thanks
  Janh
  -- Forwarded message --
  From: r-help-boun...@r-project.org
  Date: Sat, Jun 1, 2013 at 1:48 PM
  Subject: Your message to R-help awaits moderator approval
  To: annij...@gmail.com
 
 
  Your mail to 'R-help' with the subject
 
  Re: [R] wilcox_test function in coin package
 
  Is being held until the list moderator can review it for approval.
 
  The reason it is being held:
 
  The message headers matched a filter rule
 
  Either the message will get posted to the list, or you will receive
  notification of the moderator's decision.  If you would like to cancel
  this posting, please visit the following URL:
 
 
 https://stat.ethz.ch/mailman/confirm/r-help/067afe28f7ead30dfea844b8a34449526c
  d665d8

 This can happen to anyone, depending on the current sensitivity
 of the mail-server's spam-detection filter to potential
 triggers in the message.

 It is particularly likely to arise with mails posted from a gmail
 account, as your was. This is because gmail is a major source of
 spam emails, and the spam filter is alert to these.

 I have had a look at your message (which was duly approved), and
 I see that it is in reply to a message which itself is in a thread
 that includes several messages sent via gmail. From the headers
 of your message:

 In-Reply-To: 51a9291c.70...@ucalgary.ca
 References:
 cafcodddp64mfyvttb6b_o6kgotkyr41mcb2spcc4c6anqyw...@mail.gmail.com
 cafeqcdy6+nhk2hgcwqalymyxx1a0trqjthybxx-fub9oyff...@mail.gmail.com
  CAFCoDdBcm4B1tVW7BarkHXAgpqMpTCimmjhrLc3N7=yvsse...@mail.gmail.com
  CAFEqCdz_=YBeeDYLfpDYyTAwjr6a4n2OKTbQaBsb9UC=g9s...@mail.gmail.com
  CAFCoDdC1asW6JGK5huY_kLgCQQCduw8s=yjhhdp0pta_9ya...@mail.gmail.com
  51a9291c.70...@ucalgary.ca

 so that's a total of 6 references to gmail (including your own message)
 which is probably why the spam filter felt a bit twitchy!

 Don't worry about it. As I say, it can happen to anyone (though more
 often to some than to others). If it is a proper message to R-help,
 one of the moderators will approve it (though quite possible not
 immediately).

 Hoping this helps,
 Ted (one of the moderators)

 -
 E-Mail: (Ted Harding) ted.hard...@wlandres.net
 Date: 01-Jun-2013  Time: 20:11:00
 This message was sent by XFMail
 -


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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] wilcox_test function in coin package

[Janh Anni]

Hello All,

Thanks a lot for the helpful suggestions.  I wonder how ties are handled
for the rank sum test by wilcox_test and wilcox.exact?  For instance, other
software such as Minitab correct for ties by adjusting the variance of the
test statistic, and actually provide the p values before and after
adjustment for ties.  IIf neither wilcox_test nor wilcox.exact expressly
corrects for ties in the Wilcoxon rank sum test, then perhaps one should
just use the conventional wilcox.test which is the simplest of them all?
Thanks again

Janh


On Sat, Jun 1, 2013 at 8:41 AM, Henric Winell nilsson.hen...@gmail.comwrote:

 Janh,

 Janh Anni skrev 2013-06-01 04:27:

 Hello peter,


 Thanks for the comment.  wilcox.exact is simpler as you pointed out but
 the
 fact that it is no longer being developed is somewhat concerning.


 Admittedly, 'coin' is being actively developed and has a lot more bells
 and whistles.  But for something as simple as this, that wouldn't bother me
 at all.  In any case, the 'exactRankTests' package still gets bug fixes and
 the algorithm used in the Wilcoxon case is exactly the same for both
 packages.

 However, if you want to stay with 'coin' you can just wrap up Greg's
 proposal in a function:

 wilcox_test.default - function(x, y, ...) {
 data -
 data.frame(values = c(x, y),
group = rep(c(x, y), c(length(x), length(y
 wilcox_test(values ~ group, data = data, ...)
 }

 Assuming that both 'coin' and 'exactRankTests are loaded, we can now check
 that it works:

  set.seed(123)
  x - rpois(10, 3)
  y - rpois(11, 3.1)
 
  wilcox_test(x, y, alternative = less, distribution = exact)

 Exact Wilcoxon-Mann-Whitney Test

 data:  values by group (x, y)
 Z = -0.0715, p-value = 0.4844
 alternative hypothesis: true mu is less than 0

  wilcox.exact(x, y, alternative = less)

 Exact Wilcoxon rank sum test

 data:  x and y
 W = 54, p-value = 0.4844
 alternative hypothesis: true mu is less than 0


 HTH,
 Henric




 Regards
 Janh


 On Fri, May 31, 2013 at 6:50 PM, Peter Ehlers ehl...@ucalgary.ca wrote:

  On 2013-05-30 20:20, Janh Anni wrote:

  Hello Greg,

 Thank you so much for your kind assistance.  It looks like there's no
 way
 around using the formula format.  I longed in vain for a simpler script
 more like the wilcox.test format.  Thanks again.

 Janh


 I don't see why the formula syntax would be a problem, but to avoid it
 you could use exactRankTests::wilcox.exact() which, I believe, was
 written by the same author. It uses the same syntax as wilcox.test().
 Note, though, that the package is no longer
 being developed.

 Peter Ehlers




 On Thu, May 30, 2013 at 6:21 PM, Greg Snow 538...@gmail.com wrote:

   Ok, it looks like the function mainly works through the formula
 syntax.

It still would have been nice to have a reproducible example of what
 your
 data may look like, but I can show an example with simulated x and y:

   x - rpois(10, 3)

 y - rpois(11, 3.1)
 mydf - data.frame( vals = c(x,y),

  +   group=rep( c('x','y'), c( length(x), length(y) ) ) )

  wilcox_test( vals ~ group, data=mydf )


   Asymptotic Wilcoxon-Mann-Whitney Test

 data:  vals by group (x, y)
 Z = -1.3718, p-value = 0.1701
 alternative hypothesis: true mu is not equal to 0

 Does that help?  (maybe I am the heedlessness theorist after all)



 On Thu, May 30, 2013 at 4:14 PM, Janh Anni annij...@gmail.com wrote:

   I thought (hoped) wilcox_test(x,y) would do it but it doesn't and the

 package maintainer says the data have to be rearranged but does not
 specify
 how.  Thanks

 Janh



 On Thu, May 30, 2013 at 6:05 PM, Greg Snow 538...@gmail.com wrote:

   What have you tried so far?  Have you read the help page? have you
 run

 the examples on that page?

 I would expect that it is something as simple as

 library(coin)
 wilcox_test(x,y)

 or

 wilcox_test( y ~ group )

 But you should trust the help page more than the expectations of
 someone
 who has not read it recently (see fortune(14)).

 If that does not answer your question then give us more detail on
 what
 you tried, what you expected the results to be, what the results
 actually
 were, and how they differed.  Without that information we have to
 resort to
 mind reading and the current implementation of the esp package is
 still
 very pre-alpha, it suggests that the answer to your question is:

   esp()


  [1] selflessly vigilantly pigeon theorist heedlessness

 Which is either much to profound for the likes of me to understand or
 is
 complete gibberish (which is only slightly less helpful than an
 overly
 general question without a reproducible example).


 On Thu, May 30, 2013 at 2:07 PM, Janh Anni annij...@gmail.com
 wrote:

   Dear All,


 I have two simple data samples (no groups or factors, etc.) and
 would
 just
 like to compute the two-sample Wilcoxon Rank Sum test using the
 wilcox_test
 function contained in the coin package, which is reportedly better
 than
 the
 regular

[R] wilcox_test function in coin package

[Janh Anni]

Dear All,

I have two simple data samples (no groups or factors, etc.) and would just
like to compute the two-sample Wilcoxon Rank Sum test using the wilcox_test
function contained in the coin package, which is reportedly better than the
regular wilcox.test function because it performs some adjustment for ties.
Would anyone know how to craft a script to perform this task?  Much
appreciated.

Janh

[[alternative HTML version deleted]]

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

Re: [R] wilcox_test function in coin package

[Janh Anni]

I thought (hoped) wilcox_test(x,y) would do it but it doesn't and the
package maintainer says the data have to be rearranged but does not specify
how.  Thanks

Janh



On Thu, May 30, 2013 at 6:05 PM, Greg Snow 538...@gmail.com wrote:

 What have you tried so far?  Have you read the help page? have you run the
 examples on that page?

 I would expect that it is something as simple as

 library(coin)
 wilcox_test(x,y)

 or

 wilcox_test( y ~ group )

 But you should trust the help page more than the expectations of someone
 who has not read it recently (see fortune(14)).

 If that does not answer your question then give us more detail on what you
 tried, what you expected the results to be, what the results actually were,
 and how they differed.  Without that information we have to resort to mind
 reading and the current implementation of the esp package is still very
 pre-alpha, it suggests that the answer to your question is:

  esp()
 [1] selflessly vigilantly pigeon theorist heedlessness

 Which is either much to profound for the likes of me to understand or is
 complete gibberish (which is only slightly less helpful than an overly
 general question without a reproducible example).


 On Thu, May 30, 2013 at 2:07 PM, Janh Anni annij...@gmail.com wrote:

 Dear All,

 I have two simple data samples (no groups or factors, etc.) and would just
 like to compute the two-sample Wilcoxon Rank Sum test using the
 wilcox_test
 function contained in the coin package, which is reportedly better than
 the
 regular wilcox.test function because it performs some adjustment for ties.
 Would anyone know how to craft a script to perform this task?  Much
 appreciated.

 Janh

 [[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.




 --
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com


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Re: [R] wilcox_test function in coin package

[Janh Anni]

Hello Greg,

Thank you so much for your kind assistance.  It looks like there's no way
around using the formula format.  I longed in vain for a simpler script
more like the wilcox.test format.  Thanks again.

Janh


On Thu, May 30, 2013 at 6:21 PM, Greg Snow 538...@gmail.com wrote:

 Ok, it looks like the function mainly works through the formula syntax.
  It still would have been nice to have a reproducible example of what your
 data may look like, but I can show an example with simulated x and y:

  x - rpois(10, 3)
  y - rpois(11, 3.1)
  mydf - data.frame( vals = c(x,y),
 +   group=rep( c('x','y'), c( length(x), length(y) ) ) )
  wilcox_test( vals ~ group, data=mydf )

 Asymptotic Wilcoxon-Mann-Whitney Test

 data:  vals by group (x, y)
 Z = -1.3718, p-value = 0.1701
 alternative hypothesis: true mu is not equal to 0

 Does that help?  (maybe I am the heedlessness theorist after all)



 On Thu, May 30, 2013 at 4:14 PM, Janh Anni annij...@gmail.com wrote:

 I thought (hoped) wilcox_test(x,y) would do it but it doesn't and the
 package maintainer says the data have to be rearranged but does not specify
 how.  Thanks

 Janh



 On Thu, May 30, 2013 at 6:05 PM, Greg Snow 538...@gmail.com wrote:

 What have you tried so far?  Have you read the help page? have you run
 the examples on that page?

 I would expect that it is something as simple as

 library(coin)
 wilcox_test(x,y)

 or

 wilcox_test( y ~ group )

 But you should trust the help page more than the expectations of someone
 who has not read it recently (see fortune(14)).

 If that does not answer your question then give us more detail on what
 you tried, what you expected the results to be, what the results actually
 were, and how they differed.  Without that information we have to resort to
 mind reading and the current implementation of the esp package is still
 very pre-alpha, it suggests that the answer to your question is:

  esp()
 [1] selflessly vigilantly pigeon theorist heedlessness

 Which is either much to profound for the likes of me to understand or is
 complete gibberish (which is only slightly less helpful than an overly
 general question without a reproducible example).


 On Thu, May 30, 2013 at 2:07 PM, Janh Anni annij...@gmail.com wrote:

 Dear All,

 I have two simple data samples (no groups or factors, etc.) and would
 just
 like to compute the two-sample Wilcoxon Rank Sum test using the
 wilcox_test
 function contained in the coin package, which is reportedly better than
 the
 regular wilcox.test function because it performs some adjustment for
 ties.
 Would anyone know how to craft a script to perform this task?  Much
 appreciated.

 Janh

 [[alternative HTML version deleted]]

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




 --
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com





 --
 Gregory (Greg) L. Snow Ph.D.
 538...@gmail.com


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Re: [R] Bootstrapped 1-sided confidence intervals

[Janh Anni]

Great!  Thanks to all for your assistance.

Regards

Janh


On Tue, May 7, 2013 at 11:37 PM, Pascal Oettli kri...@ymail.com wrote:

 Hello,

 You already asked that question on May 7, 2013. And David Winsemius
 already responded to you:
 https://stat.ethz.ch/**pipermail/r-help/2013-May/**353044.htmlhttps://stat.ethz.ch/pipermail/r-help/2013-May/353044.html

 Regards,
 Pascal



 On 05/08/2013 12:21 PM, Janh Anni wrote:

 Hello All,

 Does anyone know if there’s a function for computing 1-sided confidence
 intervals for bootstrapped statistics (mean, median, percentiles,
 etc.)?  Thanks
 in advance

 Janh

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

[R] Bootstrapped 1-sided confidence intervals

[Janh Anni]

Hello All,

Does anyone know if there’s a function for computing 1-sided confidence
intervals for bootstrapped statistics (mean, median, percentiles,
etc.)?  Thanks
in advance

Janh

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[R] Bootstrapped Non-Parametric 1-sided Confidence Intervals

[Janh Anni]

Hello All,

Is there a way for computing 1-sided confidence intervals for bootstrapped
statistics (mean, median, percentiles, etc.)?  It appears the
boot.cifunction in the boot package only computes 2-sided intervals.
Your assistance is greatly appreciated.

Regards
Janh

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[R] Q-Q Plot for comparing two unequal data sets

[Janh Anni]

Hello All,

Would anyone be able to help me understand how R computes a
quantile-quantile plot for comparing two data samples with unequal sample
sizes?  Normally, the procedure should be to rearrange the larger data
sample into n equally-spaced parts using interpolation, where n is the
sample size of the smaller sample, and then plot the matching data pairs.  I
tried using different plotting position formulas for the interpolation but
cannot reproduce what R is plotting.  Thanks in advance.

Regards
Janh

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

Re: [R] Q-Q Plot for comparing two unequal data sets

[Janh Anni]

Hello Michael,

Thanks for that information.

Regards

Janh


On Tue, Apr 16, 2013 at 9:13 PM, Michael Weylandt 
michael.weyla...@gmail.com wrote:



 On Apr 16, 2013, at 20:12, Janh Anni annij...@gmail.com wrote:

 Hello All,

 Would anyone be able to help me understand how R computes a
 quantile-quantile plot for comparing two data samples with unequal sample
 sizes?  Normally, the procedure should be to rearrange the larger data
 sample into n equally-spaced parts using interpolation, where n is the
 sample size of the smaller sample, and then plot the matching data pairs.
  I
 tried using different plotting position formulas for the interpolation but
 cannot reproduce what R is plotting.  Thanks in advance.


 If you type qqplot at the prompt you'll be given the code and can review
 it for yourself. It's also available online for your viewing pleasure.

 http://svn.r-project.org/R/trunk/src/library/stats/R/qqplot.R

 It seems the key is the approx (linear interpolation) function, but you
 can work out the details.

 Michael



 Regards
 Janh

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

Re: [R] boxplot

[Janh Anni]

Hello John,

Thank you so much for your kind assistance and the detailed descriptions.
I will play with the scripts and see which one is the easiest that serves
the purpose..

Best regards,
Janh


On Sun, Mar 24, 2013 at 7:50 AM, John Kane jrkrid...@inbox.com wrote:

 **
 Unless you have a really large number of wells I'd just use the brute
 force approach of reading in each data set with a simple read.table or
 read.csv  like

 well1  -  read.csv(well1.csv) type of statement and repeat for each well.

 Here is a simple example that may give you an idea of how to do the
 boxplots . I have done them two ways, one using base graphics and the other
 using ggplot2.  You will probably have to install the ggplot2 package --
 just issue the command install.packages(ggplot2)

 The base approach is initially a lot simpler but in the longer term, if
 you expect to do a lot of graphing work in R, the grid packages like
 ggplot2 or lattice seem to offer a lot more control for less actual typing,
 especially if you need publication/report quality graphics.

 ##===start code=
 set.seed(345)  #reproducable sample
   # create three sample data sets,
   well_1  -  data.frame(arsenic = rnorm(12))
   well_2  -  data.frame (arsenic = rnorm(10))
   well_3  -  data.frame (arsenic = rnorm(15))

   wells  -  rbind(well_1, well_2, well_3)  # create single data.frame

   #create an id value for each well
   well_id  - c(rep(1,nrow(well_1)), rep(2, nrow(well_2)), rep(3,
 nrow(well_3)))

   #add the well identifier
   wells  -  cbind(wells , well_id)
   str(wells) # check to see what we have

   boxplot(arsenic ~ well_id, data = wells) # plot vertical boxplot
   boxplot(arsenic ~ well_id, data = wells,
 horizontal = TRUE,col=c(red,green,blue)) #horizontal box
 plot

   # vertical boxplot using ggplot2
   library(ggplot2)

   p  -  ggplot(wells, aes(as.factor(well_id), arsenic)) + geom_boxplot()
   p

   # horizontal boxplot
   p1   -  p + coord_flip()
   p1

   p2  -  ggplot(wells, aes(as.factor(well_id), arsenic, fill =
 as.factor(well_id) )) +
 geom_boxplot() + coord_flip() +
  scale_fill_discrete(guide=FALSE)


 ##===end code==



 John Kane
 Kingston ON Canada


 -Original Message-
 *From:* annij...@gmail.com
 *Sent:* Sat, 23 Mar 2013 10:22:02 -0400
 *To:* jrkrid...@inbox.com
 *Subject:* Re: [R] boxplot

 Hello John,

 I apologize for the delayed response.  Yes I am referring to the same type
 of data in the data sets.  For example, the arsenic concentrations in
 individual groundwater monitoring wells at a groundwater contaminated site,
 where one well may have 12 concentration measurements, another well has 10,
 etc.

 Thanks
 Janh


 On Fri, Mar 22, 2013 at 5:31 PM, John Kane jrkrid...@inbox.com wrote:

 Hi Janh,

 When you say that you have multiple data sets of unequal sample sizes
 are you speaking of the same kind of data  For example are you speaking of
 data from a set of experiments where the variables measured are all the
 same and where when you graph them you expect the same x and y scales?

 Or are you talking about essentilly independent data sets that it makes
 sense to graph in a grid ?


 John Kane
 Kingston ON Canada


  -Original Message-
  From: annij...@gmail.com
  Sent: Fri, 22 Mar 2013 10:46:21 -0400
  To: dcarl...@tamu.edu
  Subject: Re: [R] boxplot
 
  Hello All,
 
  On the subject of boxplots, I have multiple data sets of unequal sample
  sizes and was wondering what would be the most efficient way to read in
  the
  data and plot side-by-side boxplots, with options for controlling the
  orientation of the plots (i.e. vertical or horizontal) and the spacing?
  Your
  assistance is greatly appreciated, but please try to be explicit as I am
  no
  R expert.  Thanks
 
  Janh
 
 
 
  On Thu, Mar 21, 2013 at 9:19 AM, David L Carlson dcarl...@tamu.edu
  wrote:
 
  Your variable loc_type combines information from two variables (loc and
  type). Since you are subsetting on loc, why not just plot by type?
 
  boxplot(var1~type, data[data$loc==nice,])
 
  --
  David L Carlson
  Associate Professor of Anthropology
  Texas AM University
  College Station, TX 77843-4352
 
  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
  project.org] On Behalf Of Jim Lemon
  Sent: Thursday, March 21, 2013 4:05 AM
  To: carol white
  Cc: r-h...@stat.math.ethz.ch
  Subject: Re: [R] boxplot
 
  On 03/21/2013 07:40 PM, carol white wrote:
  Hi,
  It must be an easy question but how to boxplot a subset of data:
 
  data = read.table(my_data.txt, header = T)
  boxplot(data$var1[data$loc == nice]~data$loc_type[data$loc ==
  nice])
  #in this case, i want to display only the boxplot loc == nice
  #doesn't display the boxplot of only loc == nice. It also displays
  loc == mice
 
  Hi Carol,
  It's them old factors sneakin' up on you. 

Re: [R] boxplot

[Janh Anni]

Hello John,

I apologize for the delayed response.  Yes I am referring to the same type
of data in the data sets.  For example, the arsenic concentrations in
individual groundwater monitoring wells at a groundwater contaminated site,
where one well may have 12 concentration measurements, another well has 10,
etc.

Thanks
Janh


On Fri, Mar 22, 2013 at 5:31 PM, John Kane jrkrid...@inbox.com wrote:

 Hi Janh,

 When you say that you have multiple data sets of unequal sample sizes
 are you speaking of the same kind of data  For example are you speaking of
 data from a set of experiments where the variables measured are all the
 same and where when you graph them you expect the same x and y scales?

 Or are you talking about essentilly independent data sets that it makes
 sense to graph in a grid ?


 John Kane
 Kingston ON Canada


  -Original Message-
  From: annij...@gmail.com
  Sent: Fri, 22 Mar 2013 10:46:21 -0400
  To: dcarl...@tamu.edu
  Subject: Re: [R] boxplot
 
  Hello All,
 
  On the subject of boxplots, I have multiple data sets of unequal sample
  sizes and was wondering what would be the most efficient way to read in
  the
  data and plot side-by-side boxplots, with options for controlling the
  orientation of the plots (i.e. vertical or horizontal) and the spacing?
  Your
  assistance is greatly appreciated, but please try to be explicit as I am
  no
  R expert.  Thanks
 
  Janh
 
 
 
  On Thu, Mar 21, 2013 at 9:19 AM, David L Carlson dcarl...@tamu.edu
  wrote:
 
  Your variable loc_type combines information from two variables (loc and
  type). Since you are subsetting on loc, why not just plot by type?
 
  boxplot(var1~type, data[data$loc==nice,])
 
  --
  David L Carlson
  Associate Professor of Anthropology
  Texas AM University
  College Station, TX 77843-4352
 
  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
  project.org] On Behalf Of Jim Lemon
  Sent: Thursday, March 21, 2013 4:05 AM
  To: carol white
  Cc: r-h...@stat.math.ethz.ch
  Subject: Re: [R] boxplot
 
  On 03/21/2013 07:40 PM, carol white wrote:
  Hi,
  It must be an easy question but how to boxplot a subset of data:
 
  data = read.table(my_data.txt, header = T)
  boxplot(data$var1[data$loc == nice]~data$loc_type[data$loc ==
  nice])
  #in this case, i want to display only the boxplot loc == nice
  #doesn't display the boxplot of only loc == nice. It also displays
  loc == mice
 
  Hi Carol,
  It's them old factors sneakin' up on you. Try this:
 
  boxplot(data$var1[data$loc == nice]~
as.character(data$loc_type[data$loc == nice]))
 
  Jim
 
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide http://www.R-project.org/posting-
  guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
  __
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 FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
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Re: [R] boxplot

[Janh Anni]

Hello All,

On the subject of boxplots, I have multiple data sets of unequal sample
sizes and was wondering what would be the most efficient way to read in the
data and plot side-by-side boxplots, with options for controlling the
orientation of the plots (i.e. vertical or horizontal) and the spacing?   Your
assistance is greatly appreciated, but please try to be explicit as I am no
R expert.  Thanks

Janh



On Thu, Mar 21, 2013 at 9:19 AM, David L Carlson dcarl...@tamu.edu wrote:

 Your variable loc_type combines information from two variables (loc and
 type). Since you are subsetting on loc, why not just plot by type?

 boxplot(var1~type, data[data$loc==nice,])

 --
 David L Carlson
 Associate Professor of Anthropology
 Texas AM University
 College Station, TX 77843-4352

  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
  project.org] On Behalf Of Jim Lemon
  Sent: Thursday, March 21, 2013 4:05 AM
  To: carol white
  Cc: r-h...@stat.math.ethz.ch
  Subject: Re: [R] boxplot
 
  On 03/21/2013 07:40 PM, carol white wrote:
   Hi,
   It must be an easy question but how to boxplot a subset of data:
  
   data = read.table(my_data.txt, header = T)
   boxplot(data$var1[data$loc == nice]~data$loc_type[data$loc ==
  nice])
   #in this case, i want to display only the boxplot loc == nice
   #doesn't display the boxplot of only loc == nice. It also displays
  loc == mice
  
  Hi Carol,
  It's them old factors sneakin' up on you. Try this:
 
  boxplot(data$var1[data$loc == nice]~
as.character(data$loc_type[data$loc == nice]))
 
  Jim
 
  __
  R-help@r-project.org mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide http://www.R-project.org/posting-
  guide.html
  and provide commented, minimal, self-contained, reproducible code.

 __
 R-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
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Re: [R] NADA

[Janh Anni]

Hello Don, Jeff,

Thanks a lot for the comments and suggestions.

Best

Janh


On Thu, Mar 21, 2013 at 10:57 AM, MacQueen, Don macque...@llnl.gov wrote:

 According to ?ros, one of the arguments is:

 reverseT: A name of a function to use for reversing the transformation
   after performing the ROS fit. Defaults to 'exp'.

 And in the Details section:

  By default, 'ros' performs a log transformation prior to, and
  after operations over the data.


 Given those statements, perhaps the expectation should be a plot in
 original units?
 Keep in mind that a main purpose is summary statistics in the original
 units.
 After running the first example in ?ros, including the plot, try these:

   unclass(myros)
   abline(h=myros$modeled,col='blue')


 -Don


 --
 Don MacQueen

 Lawrence Livermore National Laboratory
 7000 East Ave., L-627
 Livermore, CA 94550
 925-423-1062





 On 3/20/13 5:48 PM, Janh Anni annij...@gmail.com wrote:

 Dear Users
 Regarding the NADA package, would anyone be able to help me understand
 what
 values are actually plotted on the Y axis of the plot obtained by using
 the
 *ros* function on the data and plotting the result with the plot()
 function? The Y axis is labeled Values. According to the NADA user
 manual, ros performs a log transformation of the data by default, but the
 user can specify no transformation, or some other transformation besides
 log, if desired. However the values plotted on the Y axis appear to be the
 raw data values, regardless of which transformation or no transformation
 was used. If the log transformation is used for instance, I would have
 expected the logs of the original data instead of the raw data to be
 plotted on the Y axis.
 
 Thanks for your help.
 Janh
 
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[R] NADA

[Janh Anni]

Dear Users
Regarding the NADA package, would anyone be able to help me understand what
values are actually plotted on the Y axis of the plot obtained by using the
*ros* function on the data and plotting the result with the plot()
function? The Y axis is labeled Values. According to the NADA user
manual, ros performs a log transformation of the data by default, but the
user can specify no transformation, or some other transformation besides
log, if desired. However the values plotted on the Y axis appear to be the
raw data values, regardless of which transformation or no transformation
was used. If the log transformation is used for instance, I would have
expected the logs of the original data instead of the raw data to be
plotted on the Y axis.

Thanks for your help.
Janh

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