Re: [R] file.access returning -1 for a file on remote Windows drive.
Thanks Jeff. And for future readers head here:
https://github.com/eddelbuettel/digest/issues/49
and here:
https://github.com/eddelbuettel/digest/issues/13
Sam
On Fri, Feb 28, 2020 at 3:40 PM Jeff Newmiller wrote:
>
> Read the closed issues in his digest Github repo first... this discussion has
> already occurred there.
>
> On February 28, 2020 3:35:09 PM PST, Sam Albers
> wrote:
> >Great question Will. If it were my code I would definitely do this.
> >However the problem is manifesting itself for my work with Dirk's
> >great digest package here:
> >
> >https://github.com/eddelbuettel/digest/blob/947b77e82b97024a874a808a4644be21fc329275/R/digest.R#L170-L173
> >
> >So because file.access is saying the permissions aren't right, I get
> >an error message from digest and can't create a hash. Knowing full
> >well that this is some weird Windows thing but also knowing I am stuck
> >in that environment, I wanted to figure where I was seeing a
> >difference between those two functions before I went asked Dirk if
> >he'd be interested in a change to that particular bit of code.
> >
> >
> >On Fri, Feb 28, 2020 at 3:28 PM William Dunlap
> >wrote:
> >>
> >> If file.access() says the file is unreadable but file() says it can
> >be opened, why don't you
> >> just open the file and read it? You can use tryCatch to deal with
> >problems opening or
> >> reading the file.
> >>
> >> Bill Dunlap
> >> TIBCO Software
> >> wdunlap tibco.com
> >>
> >>
> >> On Fri, Feb 28, 2020 at 2:54 PM Sam Albers
> > wrote:
> >>>
> >>> Thanks Jeff. I am probably not explaining myself very well but my
> >>> question under what circumstances would
> >>>
> >>> summary(file(remote_file, "rb"))$`can read`
> >>>
> >>> be different from:
> >>>
> >>> file.access(remote_file, 4)
> >>>
> >>> If my permissions were different across remote and local should that
> >>> not be reflected in both of these functions?
> >>>
> >>> On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller
> > wrote:
> >>> >
> >>> > Dunno. They agree for me. Maybe look closer at all permissions via
> >Windows File Manager?
> >>> >
> >>> > On February 28, 2020 2:06:34 PM PST, Sam Albers
> > wrote:
> >>> > >Some additional follow-up:
> >>> > >
> >>> > >> summary(file(remote_file, "rb"))$`can read`
> >>> > >[1] "yes"
> >>> > >
> >>> > >> summary(file(local_file, "rb"))$`can read`
> >>> > >[1] "yes"
> >>> > >
> >>> > >compared to:
> >>> > >
> >>> > >> file.access(local_file, 4)
> >>> > >local.R
> >>> > > 0
> >>> > >
> >>> > >> file.access(remote_file, 4)
> >>> > >remote.R
> >>> > >-1
> >>> > >
> >>> > >Can anyone think why file.access and file would be contradicting
> >each
> >>> > >other?
> >>> > >
> >>> > >Sam
> >>> > >
> >>> > >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
> >>> > > wrote:
> >>> > >>
> >>> > >> Hi there,
> >>> > >>
> >>> > >> Looking for some help in diagnosing or developing a work around
> >to a
> >>> > >> problem I am having on a Windows machine. I am running R 3.6.2.
> >>> > >>
> >>> > >> I have two identical files, one stored locally and the other
> >stored
> >>> > >on
> >>> > >> a network drive.
> >>> > >>
> >>> > >> For access:
> >>> > >>
> >>> > >> > file.access(local_file, 4)
> >>> > >> local.R
> >>> > >> 0
> >>> > >>
> >>> > >> > file.access(remote_file, 4)
> >>> > >> remote.R
> >>> > >> -1
> >>> > >>
> >>> > >> Also for file.info
> >>> > >>
> >>> > >> > file.info(local_file)$mode:
> >>> > >> [1] "666"
> >>> > >>
> >>> > >> > file.info(remote_file)$mode:
> >>> > >> [1] "666"
> >>> > >>
> >>> > >> Ok so I am access issues. Maybe they are ephemeral and I can
> >change
> >>> > >> the permissions:
> >>> > >>
> >>> > >> > Sys.chmod('remote.R', mode = '666')
> >>> > >> > file.access(remote_file, 4)
> >>> > >> remote.R
> >>> > >> -1
> >>> > >>
> >>> > >> Nope. I am thoroughly stumped and maybe can't make it any
> >further
> >>> > >> because of Windows.
> >>> > >>
> >>> > >> Downstream I am trying to use digest::digest to create a hash
> >but
> >>> > >> digest thinks we don't have permission because file.access is
> >>> > >failing.
> >>> > >> Any thoughts on how I can get file.access to return 0 for the
> >>> > >remote.R
> >>> > >> file? Any ideas?
> >>> > >>
> >>> > >> Thanks in advance,
> >>> > >>
> >>> > >> Sam
> >>> > >
> >>> > >__
> >>> > >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.
> >>>
> >>> __
> >>> 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
>
Re: [R] file.access returning -1 for a file on remote Windows drive.
Read the closed issues in his digest Github repo first... this discussion has
already occurred there.
On February 28, 2020 3:35:09 PM PST, Sam Albers
wrote:
>Great question Will. If it were my code I would definitely do this.
>However the problem is manifesting itself for my work with Dirk's
>great digest package here:
>
>https://github.com/eddelbuettel/digest/blob/947b77e82b97024a874a808a4644be21fc329275/R/digest.R#L170-L173
>
>So because file.access is saying the permissions aren't right, I get
>an error message from digest and can't create a hash. Knowing full
>well that this is some weird Windows thing but also knowing I am stuck
>in that environment, I wanted to figure where I was seeing a
>difference between those two functions before I went asked Dirk if
>he'd be interested in a change to that particular bit of code.
>
>
>On Fri, Feb 28, 2020 at 3:28 PM William Dunlap
>wrote:
>>
>> If file.access() says the file is unreadable but file() says it can
>be opened, why don't you
>> just open the file and read it? You can use tryCatch to deal with
>problems opening or
>> reading the file.
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>>
>> On Fri, Feb 28, 2020 at 2:54 PM Sam Albers
> wrote:
>>>
>>> Thanks Jeff. I am probably not explaining myself very well but my
>>> question under what circumstances would
>>>
>>> summary(file(remote_file, "rb"))$`can read`
>>>
>>> be different from:
>>>
>>> file.access(remote_file, 4)
>>>
>>> If my permissions were different across remote and local should that
>>> not be reflected in both of these functions?
>>>
>>> On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller
> wrote:
>>> >
>>> > Dunno. They agree for me. Maybe look closer at all permissions via
>Windows File Manager?
>>> >
>>> > On February 28, 2020 2:06:34 PM PST, Sam Albers
> wrote:
>>> > >Some additional follow-up:
>>> > >
>>> > >> summary(file(remote_file, "rb"))$`can read`
>>> > >[1] "yes"
>>> > >
>>> > >> summary(file(local_file, "rb"))$`can read`
>>> > >[1] "yes"
>>> > >
>>> > >compared to:
>>> > >
>>> > >> file.access(local_file, 4)
>>> > >local.R
>>> > > 0
>>> > >
>>> > >> file.access(remote_file, 4)
>>> > >remote.R
>>> > >-1
>>> > >
>>> > >Can anyone think why file.access and file would be contradicting
>each
>>> > >other?
>>> > >
>>> > >Sam
>>> > >
>>> > >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
>>> > > wrote:
>>> > >>
>>> > >> Hi there,
>>> > >>
>>> > >> Looking for some help in diagnosing or developing a work around
>to a
>>> > >> problem I am having on a Windows machine. I am running R 3.6.2.
>>> > >>
>>> > >> I have two identical files, one stored locally and the other
>stored
>>> > >on
>>> > >> a network drive.
>>> > >>
>>> > >> For access:
>>> > >>
>>> > >> > file.access(local_file, 4)
>>> > >> local.R
>>> > >> 0
>>> > >>
>>> > >> > file.access(remote_file, 4)
>>> > >> remote.R
>>> > >> -1
>>> > >>
>>> > >> Also for file.info
>>> > >>
>>> > >> > file.info(local_file)$mode:
>>> > >> [1] "666"
>>> > >>
>>> > >> > file.info(remote_file)$mode:
>>> > >> [1] "666"
>>> > >>
>>> > >> Ok so I am access issues. Maybe they are ephemeral and I can
>change
>>> > >> the permissions:
>>> > >>
>>> > >> > Sys.chmod('remote.R', mode = '666')
>>> > >> > file.access(remote_file, 4)
>>> > >> remote.R
>>> > >> -1
>>> > >>
>>> > >> Nope. I am thoroughly stumped and maybe can't make it any
>further
>>> > >> because of Windows.
>>> > >>
>>> > >> Downstream I am trying to use digest::digest to create a hash
>but
>>> > >> digest thinks we don't have permission because file.access is
>>> > >failing.
>>> > >> Any thoughts on how I can get file.access to return 0 for the
>>> > >remote.R
>>> > >> file? Any ideas?
>>> > >>
>>> > >> Thanks in advance,
>>> > >>
>>> > >> Sam
>>> > >
>>> > >__
>>> > >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.
>>>
>>> __
>>> 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.
__
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] file.access returning -1 for a file on remote Windows drive.
Great question Will. If it were my code I would definitely do this.
However the problem is manifesting itself for my work with Dirk's
great digest package here:
https://github.com/eddelbuettel/digest/blob/947b77e82b97024a874a808a4644be21fc329275/R/digest.R#L170-L173
So because file.access is saying the permissions aren't right, I get
an error message from digest and can't create a hash. Knowing full
well that this is some weird Windows thing but also knowing I am stuck
in that environment, I wanted to figure where I was seeing a
difference between those two functions before I went asked Dirk if
he'd be interested in a change to that particular bit of code.
On Fri, Feb 28, 2020 at 3:28 PM William Dunlap wrote:
>
> If file.access() says the file is unreadable but file() says it can be
> opened, why don't you
> just open the file and read it? You can use tryCatch to deal with problems
> opening or
> reading the file.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Fri, Feb 28, 2020 at 2:54 PM Sam Albers wrote:
>>
>> Thanks Jeff. I am probably not explaining myself very well but my
>> question under what circumstances would
>>
>> summary(file(remote_file, "rb"))$`can read`
>>
>> be different from:
>>
>> file.access(remote_file, 4)
>>
>> If my permissions were different across remote and local should that
>> not be reflected in both of these functions?
>>
>> On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller
>> wrote:
>> >
>> > Dunno. They agree for me. Maybe look closer at all permissions via Windows
>> > File Manager?
>> >
>> > On February 28, 2020 2:06:34 PM PST, Sam Albers
>> > wrote:
>> > >Some additional follow-up:
>> > >
>> > >> summary(file(remote_file, "rb"))$`can read`
>> > >[1] "yes"
>> > >
>> > >> summary(file(local_file, "rb"))$`can read`
>> > >[1] "yes"
>> > >
>> > >compared to:
>> > >
>> > >> file.access(local_file, 4)
>> > >local.R
>> > > 0
>> > >
>> > >> file.access(remote_file, 4)
>> > >remote.R
>> > >-1
>> > >
>> > >Can anyone think why file.access and file would be contradicting each
>> > >other?
>> > >
>> > >Sam
>> > >
>> > >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
>> > > wrote:
>> > >>
>> > >> Hi there,
>> > >>
>> > >> Looking for some help in diagnosing or developing a work around to a
>> > >> problem I am having on a Windows machine. I am running R 3.6.2.
>> > >>
>> > >> I have two identical files, one stored locally and the other stored
>> > >on
>> > >> a network drive.
>> > >>
>> > >> For access:
>> > >>
>> > >> > file.access(local_file, 4)
>> > >> local.R
>> > >> 0
>> > >>
>> > >> > file.access(remote_file, 4)
>> > >> remote.R
>> > >> -1
>> > >>
>> > >> Also for file.info
>> > >>
>> > >> > file.info(local_file)$mode:
>> > >> [1] "666"
>> > >>
>> > >> > file.info(remote_file)$mode:
>> > >> [1] "666"
>> > >>
>> > >> Ok so I am access issues. Maybe they are ephemeral and I can change
>> > >> the permissions:
>> > >>
>> > >> > Sys.chmod('remote.R', mode = '666')
>> > >> > file.access(remote_file, 4)
>> > >> remote.R
>> > >> -1
>> > >>
>> > >> Nope. I am thoroughly stumped and maybe can't make it any further
>> > >> because of Windows.
>> > >>
>> > >> Downstream I am trying to use digest::digest to create a hash but
>> > >> digest thinks we don't have permission because file.access is
>> > >failing.
>> > >> Any thoughts on how I can get file.access to return 0 for the
>> > >remote.R
>> > >> file? Any ideas?
>> > >>
>> > >> Thanks in advance,
>> > >>
>> > >> Sam
>> > >
>> > >__
>> > >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.
>>
>> __
>> 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.
Re: [R] file.access returning -1 for a file on remote Windows drive.
If file.access() says the file is unreadable but file() says it can be
opened, why don't you
just open the file and read it? You can use tryCatch to deal with problems
opening or
reading the file.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Feb 28, 2020 at 2:54 PM Sam Albers
wrote:
> Thanks Jeff. I am probably not explaining myself very well but my
> question under what circumstances would
>
> summary(file(remote_file, "rb"))$`can read`
>
> be different from:
>
> file.access(remote_file, 4)
>
> If my permissions were different across remote and local should that
> not be reflected in both of these functions?
>
> On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller
> wrote:
> >
> > Dunno. They agree for me. Maybe look closer at all permissions via
> Windows File Manager?
> >
> > On February 28, 2020 2:06:34 PM PST, Sam Albers <
> tonightstheni...@gmail.com> wrote:
> > >Some additional follow-up:
> > >
> > >> summary(file(remote_file, "rb"))$`can read`
> > >[1] "yes"
> > >
> > >> summary(file(local_file, "rb"))$`can read`
> > >[1] "yes"
> > >
> > >compared to:
> > >
> > >> file.access(local_file, 4)
> > >local.R
> > > 0
> > >
> > >> file.access(remote_file, 4)
> > >remote.R
> > >-1
> > >
> > >Can anyone think why file.access and file would be contradicting each
> > >other?
> > >
> > >Sam
> > >
> > >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
> > > wrote:
> > >>
> > >> Hi there,
> > >>
> > >> Looking for some help in diagnosing or developing a work around to a
> > >> problem I am having on a Windows machine. I am running R 3.6.2.
> > >>
> > >> I have two identical files, one stored locally and the other stored
> > >on
> > >> a network drive.
> > >>
> > >> For access:
> > >>
> > >> > file.access(local_file, 4)
> > >> local.R
> > >> 0
> > >>
> > >> > file.access(remote_file, 4)
> > >> remote.R
> > >> -1
> > >>
> > >> Also for file.info
> > >>
> > >> > file.info(local_file)$mode:
> > >> [1] "666"
> > >>
> > >> > file.info(remote_file)$mode:
> > >> [1] "666"
> > >>
> > >> Ok so I am access issues. Maybe they are ephemeral and I can change
> > >> the permissions:
> > >>
> > >> > Sys.chmod('remote.R', mode = '666')
> > >> > file.access(remote_file, 4)
> > >> remote.R
> > >> -1
> > >>
> > >> Nope. I am thoroughly stumped and maybe can't make it any further
> > >> because of Windows.
> > >>
> > >> Downstream I am trying to use digest::digest to create a hash but
> > >> digest thinks we don't have permission because file.access is
> > >failing.
> > >> Any thoughts on how I can get file.access to return 0 for the
> > >remote.R
> > >> file? Any ideas?
> > >>
> > >> Thanks in advance,
> > >>
> > >> Sam
> > >
> > >__
> > >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.
>
> __
> 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.
Re: [R] file.access returning -1 for a file on remote Windows drive.
I don't know.
Windows uses Access Control Lists, while POSIX (e.g. Linux) uses
user/group/other classification. These two world views do not have a simple 1:1
correspondence, so you might see some difference between your file security
configuration in the file properties.
Then again there are some hints online that the problem is not new... there is
a package called R.utils that may help.
On February 28, 2020 2:53:49 PM PST, Sam Albers
wrote:
>Thanks Jeff. I am probably not explaining myself very well but my
>question under what circumstances would
>
>summary(file(remote_file, "rb"))$`can read`
>
>be different from:
>
>file.access(remote_file, 4)
>
>If my permissions were different across remote and local should that
>not be reflected in both of these functions?
>
>On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller
> wrote:
>>
>> Dunno. They agree for me. Maybe look closer at all permissions via
>Windows File Manager?
>>
>> On February 28, 2020 2:06:34 PM PST, Sam Albers
> wrote:
>> >Some additional follow-up:
>> >
>> >> summary(file(remote_file, "rb"))$`can read`
>> >[1] "yes"
>> >
>> >> summary(file(local_file, "rb"))$`can read`
>> >[1] "yes"
>> >
>> >compared to:
>> >
>> >> file.access(local_file, 4)
>> >local.R
>> > 0
>> >
>> >> file.access(remote_file, 4)
>> >remote.R
>> >-1
>> >
>> >Can anyone think why file.access and file would be contradicting
>each
>> >other?
>> >
>> >Sam
>> >
>> >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
>> > wrote:
>> >>
>> >> Hi there,
>> >>
>> >> Looking for some help in diagnosing or developing a work around to
>a
>> >> problem I am having on a Windows machine. I am running R 3.6.2.
>> >>
>> >> I have two identical files, one stored locally and the other
>stored
>> >on
>> >> a network drive.
>> >>
>> >> For access:
>> >>
>> >> > file.access(local_file, 4)
>> >> local.R
>> >> 0
>> >>
>> >> > file.access(remote_file, 4)
>> >> remote.R
>> >> -1
>> >>
>> >> Also for file.info
>> >>
>> >> > file.info(local_file)$mode:
>> >> [1] "666"
>> >>
>> >> > file.info(remote_file)$mode:
>> >> [1] "666"
>> >>
>> >> Ok so I am access issues. Maybe they are ephemeral and I can
>change
>> >> the permissions:
>> >>
>> >> > Sys.chmod('remote.R', mode = '666')
>> >> > file.access(remote_file, 4)
>> >> remote.R
>> >> -1
>> >>
>> >> Nope. I am thoroughly stumped and maybe can't make it any further
>> >> because of Windows.
>> >>
>> >> Downstream I am trying to use digest::digest to create a hash but
>> >> digest thinks we don't have permission because file.access is
>> >failing.
>> >> Any thoughts on how I can get file.access to return 0 for the
>> >remote.R
>> >> file? Any ideas?
>> >>
>> >> Thanks in advance,
>> >>
>> >> Sam
>> >
>> >__
>> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> >https://stat.ethz.ch/mailman/listinfo/r-help
>> >PLEASE do read the posting guide
>> >http://www.R-project.org/posting-guide.html
>> >and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> Sent from my phone. Please excuse my brevity.
--
Sent from my phone. Please excuse my brevity.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] file.access returning -1 for a file on remote Windows drive.
Hi Sam,
Just a guess, but your "*.R" files should be text, not binary. Windows
doesn't distinguish between the two locally if I remember correctly,
but may have to when accessing things outside the Windowsphere.
Jim
On Sat, Feb 29, 2020 at 9:07 AM Sam Albers wrote:
>
> Some additional follow-up:
>
> > summary(file(remote_file, "rb"))$`can read`
> [1] "yes"
>
> > summary(file(local_file, "rb"))$`can read`
> [1] "yes"
>
> compared to:
>
> > file.access(local_file, 4)
> local.R
> 0
>
> > file.access(remote_file, 4)
> remote.R
> -1
>
> Can anyone think why file.access and file would be contradicting each other?
>
> Sam
>
> On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
> wrote:
> >
> > Hi there,
> >
> > Looking for some help in diagnosing or developing a work around to a
> > problem I am having on a Windows machine. I am running R 3.6.2.
> >
> > I have two identical files, one stored locally and the other stored on
> > a network drive.
> >
> > For access:
> >
> > > file.access(local_file, 4)
> > local.R
> > 0
> >
> > > file.access(remote_file, 4)
> > remote.R
> > -1
> >
> > Also for file.info
> >
> > > file.info(local_file)$mode:
> > [1] "666"
> >
> > > file.info(remote_file)$mode:
> > [1] "666"
> >
> > Ok so I am access issues. Maybe they are ephemeral and I can change
> > the permissions:
> >
> > > Sys.chmod('remote.R', mode = '666')
> > > file.access(remote_file, 4)
> > remote.R
> > -1
> >
> > Nope. I am thoroughly stumped and maybe can't make it any further
> > because of Windows.
> >
> > Downstream I am trying to use digest::digest to create a hash but
> > digest thinks we don't have permission because file.access is failing.
> > Any thoughts on how I can get file.access to return 0 for the remote.R
> > file? Any ideas?
> >
> > Thanks in advance,
> >
> > Sam
>
> __
> 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] qq plot issue with ab line
Hi Ana,
I should clarify what I wrote in the previous email. You are expecting
an approximately square plot with a line running at about an angle of
45 degrees from lower left to upper right. However, the range of x and
y values that you are plotting are not approximately equal. This means
that lines with a slope of 1 will not run from corner to corner or
even parallel such a line. I hope that explains it better.
Jim
On Sat, Feb 29, 2020 at 9:54 AM Jim Lemon wrote:
>
> Hi Ana,
> I'll do my best. In the attached image, I have placed two green disks
> at (0,0) and (1,1). These points are on a line with intercept 0 and
> slope 1 as are all the other points on that line. When you ask for an
> abline with two unnamed arguments, the first is the intercept and the
> second is the slope. The abline function them draws a line with these
> values across the plot. So it has done what you asked. If you specify
> xlim=c(0,1) in the initial plot, you will get what you expect, but you
> will leave all x values greater than 1.04 off the plot.
>
> Jim
>
> On Sat, Feb 29, 2020 at 8:41 AM Ana Marija
> wrote:
> >
> > Hi Jim,
> >
> > I have in my code:
> > abline(0,1,col='red')
> >
> > can you please tell me how to change my code to have it indeed running
> > from 0 to 1?
> >
> > Thanks
> > Ana
> >
> > On Fri, Feb 28, 2020 at 3:34 PM Jim Lemon wrote:
> > >
> > > Hi Ana,
> > > Look carefully at that red line. It goes through (0,0) and scoots off
> > > the plot at (2.5,2.5). As you have specified that intercept and slope
> > > in your code, poor abline is doing the best it can. Do not punish it
> > > for doing what you request.
> > >
> > > Jim
> > >
> > > On Sat, Feb 29, 2020 at 6:10 AM Ana Marija
> > > wrote:
> > > >
> > > > Hello,
> > > >
> > > > I made the plot in attach with this function:
> > > >
> > > > qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
> > > > {
> > > > nn = length(p)
> > > > xx = -log10((1:nn)/(nn+1))
> > > > plot( xx, -sort(log10(p)),
> > > > main = MAIN, sub= SUB, cex.sub=1.3,
> > > > xlab=expression(Expected~~-log[10](italic(p))),
> > > > ylab=expression(Observed~~-log[10](italic(p))),
> > > > cex.lab=1.0,mgp=c(2,1,0))
> > > > abline(0,1,col='red')
> > > > if(BH) ## BH = include Benjamini Hochberg FDR
> > > > {
> > > >
> > > > abline(-log10(0.05),1, col='black',lty=1)
> > > > text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
> > > > abline(-log10(0.10),1, col='black',lty=1)
> > > > text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
> > > > abline(-log10(0.25),1, col='black',lty=1)
> > > > text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
> > > > #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
> > > >#col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
> > > > if (BF)
> > > > {
> > > > abline(h=-log10(0.05/nn), col='black') ## bonferroni
> > > > }
> > > > }
> > > > }
> > > >
> > > >
> > > > biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
> > > > qqunif(biob272$V2)
> > > >
> > > >
> > > > > head(biob272)
> > > > V1 V2
> > > > 1 rs2089177 0.581204
> > > > 2 rs4360974 0.418456
> > > > 3 rs6502526 0.416670
> > > > 4 rs8069906 0.568030
> > > > 5 rs9895995 0.266746
> > > > 6 rs9905280 0.510032
> > > >
> > > > But the red, abline doesn't look like it is 1:1 line.
> > > >
> > > > Can you please advise?
> > > >
> > > > Thanks
> > > > Ana
> > > > __
> > > > 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.
Re: [R] qq plot issue with ab line
Hi Ana,
I'll do my best. In the attached image, I have placed two green disks
at (0,0) and (1,1). These points are on a line with intercept 0 and
slope 1 as are all the other points on that line. When you ask for an
abline with two unnamed arguments, the first is the intercept and the
second is the slope. The abline function them draws a line with these
values across the plot. So it has done what you asked. If you specify
xlim=c(0,1) in the initial plot, you will get what you expect, but you
will leave all x values greater than 1.04 off the plot.
Jim
On Sat, Feb 29, 2020 at 8:41 AM Ana Marija wrote:
>
> Hi Jim,
>
> I have in my code:
> abline(0,1,col='red')
>
> can you please tell me how to change my code to have it indeed running
> from 0 to 1?
>
> Thanks
> Ana
>
> On Fri, Feb 28, 2020 at 3:34 PM Jim Lemon wrote:
> >
> > Hi Ana,
> > Look carefully at that red line. It goes through (0,0) and scoots off
> > the plot at (2.5,2.5). As you have specified that intercept and slope
> > in your code, poor abline is doing the best it can. Do not punish it
> > for doing what you request.
> >
> > Jim
> >
> > On Sat, Feb 29, 2020 at 6:10 AM Ana Marija
> > wrote:
> > >
> > > Hello,
> > >
> > > I made the plot in attach with this function:
> > >
> > > qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
> > > {
> > > nn = length(p)
> > > xx = -log10((1:nn)/(nn+1))
> > > plot( xx, -sort(log10(p)),
> > > main = MAIN, sub= SUB, cex.sub=1.3,
> > > xlab=expression(Expected~~-log[10](italic(p))),
> > > ylab=expression(Observed~~-log[10](italic(p))),
> > > cex.lab=1.0,mgp=c(2,1,0))
> > > abline(0,1,col='red')
> > > if(BH) ## BH = include Benjamini Hochberg FDR
> > > {
> > >
> > > abline(-log10(0.05),1, col='black',lty=1)
> > > text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
> > > abline(-log10(0.10),1, col='black',lty=1)
> > > text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
> > > abline(-log10(0.25),1, col='black',lty=1)
> > > text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
> > > #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
> > >#col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
> > > if (BF)
> > > {
> > > abline(h=-log10(0.05/nn), col='black') ## bonferroni
> > > }
> > > }
> > > }
> > >
> > >
> > > biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
> > > qqunif(biob272$V2)
> > >
> > >
> > > > head(biob272)
> > > V1 V2
> > > 1 rs2089177 0.581204
> > > 2 rs4360974 0.418456
> > > 3 rs6502526 0.416670
> > > 4 rs8069906 0.568030
> > > 5 rs9895995 0.266746
> > > 6 rs9905280 0.510032
> > >
> > > But the red, abline doesn't look like it is 1:1 line.
> > >
> > > Can you please advise?
> > >
> > > Thanks
> > > Ana
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] file.access returning -1 for a file on remote Windows drive.
Thanks Jeff. I am probably not explaining myself very well but my
question under what circumstances would
summary(file(remote_file, "rb"))$`can read`
be different from:
file.access(remote_file, 4)
If my permissions were different across remote and local should that
not be reflected in both of these functions?
On Fri, Feb 28, 2020 at 2:37 PM Jeff Newmiller wrote:
>
> Dunno. They agree for me. Maybe look closer at all permissions via Windows
> File Manager?
>
> On February 28, 2020 2:06:34 PM PST, Sam Albers
> wrote:
> >Some additional follow-up:
> >
> >> summary(file(remote_file, "rb"))$`can read`
> >[1] "yes"
> >
> >> summary(file(local_file, "rb"))$`can read`
> >[1] "yes"
> >
> >compared to:
> >
> >> file.access(local_file, 4)
> >local.R
> > 0
> >
> >> file.access(remote_file, 4)
> >remote.R
> >-1
> >
> >Can anyone think why file.access and file would be contradicting each
> >other?
> >
> >Sam
> >
> >On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
> > wrote:
> >>
> >> Hi there,
> >>
> >> Looking for some help in diagnosing or developing a work around to a
> >> problem I am having on a Windows machine. I am running R 3.6.2.
> >>
> >> I have two identical files, one stored locally and the other stored
> >on
> >> a network drive.
> >>
> >> For access:
> >>
> >> > file.access(local_file, 4)
> >> local.R
> >> 0
> >>
> >> > file.access(remote_file, 4)
> >> remote.R
> >> -1
> >>
> >> Also for file.info
> >>
> >> > file.info(local_file)$mode:
> >> [1] "666"
> >>
> >> > file.info(remote_file)$mode:
> >> [1] "666"
> >>
> >> Ok so I am access issues. Maybe they are ephemeral and I can change
> >> the permissions:
> >>
> >> > Sys.chmod('remote.R', mode = '666')
> >> > file.access(remote_file, 4)
> >> remote.R
> >> -1
> >>
> >> Nope. I am thoroughly stumped and maybe can't make it any further
> >> because of Windows.
> >>
> >> Downstream I am trying to use digest::digest to create a hash but
> >> digest thinks we don't have permission because file.access is
> >failing.
> >> Any thoughts on how I can get file.access to return 0 for the
> >remote.R
> >> file? Any ideas?
> >>
> >> Thanks in advance,
> >>
> >> Sam
> >
> >__
> >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.
__
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] file.access returning -1 for a file on remote Windows drive.
Dunno. They agree for me. Maybe look closer at all permissions via Windows File
Manager?
On February 28, 2020 2:06:34 PM PST, Sam Albers
wrote:
>Some additional follow-up:
>
>> summary(file(remote_file, "rb"))$`can read`
>[1] "yes"
>
>> summary(file(local_file, "rb"))$`can read`
>[1] "yes"
>
>compared to:
>
>> file.access(local_file, 4)
>local.R
> 0
>
>> file.access(remote_file, 4)
>remote.R
>-1
>
>Can anyone think why file.access and file would be contradicting each
>other?
>
>Sam
>
>On Fri, Feb 28, 2020 at 10:47 AM Sam Albers
> wrote:
>>
>> Hi there,
>>
>> Looking for some help in diagnosing or developing a work around to a
>> problem I am having on a Windows machine. I am running R 3.6.2.
>>
>> I have two identical files, one stored locally and the other stored
>on
>> a network drive.
>>
>> For access:
>>
>> > file.access(local_file, 4)
>> local.R
>> 0
>>
>> > file.access(remote_file, 4)
>> remote.R
>> -1
>>
>> Also for file.info
>>
>> > file.info(local_file)$mode:
>> [1] "666"
>>
>> > file.info(remote_file)$mode:
>> [1] "666"
>>
>> Ok so I am access issues. Maybe they are ephemeral and I can change
>> the permissions:
>>
>> > Sys.chmod('remote.R', mode = '666')
>> > file.access(remote_file, 4)
>> remote.R
>> -1
>>
>> Nope. I am thoroughly stumped and maybe can't make it any further
>> because of Windows.
>>
>> Downstream I am trying to use digest::digest to create a hash but
>> digest thinks we don't have permission because file.access is
>failing.
>> Any thoughts on how I can get file.access to return 0 for the
>remote.R
>> file? Any ideas?
>>
>> Thanks in advance,
>>
>> Sam
>
>__
>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.
__
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] [FORGED] Re: Help to solve modeling problem with gamm
On 29/02/20 8:11 am, Abby Spurdle wrote: There was clearly a non-linear growth pattern such that an additive mixed effects model was proposed to model the behavior of biomass as a function of time and treatments. The presence of non-linearity (in x) does not necessarily mean that you can't use a "linear model". In general, linear models work well for biological growth curves with small to medium sized data. Technically, this is off topic, however, the notion of what is linear and what is not linear, is a recurring theme on this mailing list. When plotting the residuals a clear cone-shaped pattern was observed Based on classical statistics, the obvious approach is to transform your data. This is easy to do, however, some expertise is required to back-transform parameters/estimates and interpret them. Although it is indeed off topic I would like to emphasise a point that a lot of people don't seem to get. A linear model is *linear in the parameters* not in the predictors. For example y = beta_0 + beta_1 * x + beta_2 * x^2 + E is a linear model. It is linear in (beta_0,beta_1,beta_2). It is not of course "linear in x". cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ 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] file.access returning -1 for a file on remote Windows drive.
Some additional follow-up:
> summary(file(remote_file, "rb"))$`can read`
[1] "yes"
> summary(file(local_file, "rb"))$`can read`
[1] "yes"
compared to:
> file.access(local_file, 4)
local.R
0
> file.access(remote_file, 4)
remote.R
-1
Can anyone think why file.access and file would be contradicting each other?
Sam
On Fri, Feb 28, 2020 at 10:47 AM Sam Albers wrote:
>
> Hi there,
>
> Looking for some help in diagnosing or developing a work around to a
> problem I am having on a Windows machine. I am running R 3.6.2.
>
> I have two identical files, one stored locally and the other stored on
> a network drive.
>
> For access:
>
> > file.access(local_file, 4)
> local.R
> 0
>
> > file.access(remote_file, 4)
> remote.R
> -1
>
> Also for file.info
>
> > file.info(local_file)$mode:
> [1] "666"
>
> > file.info(remote_file)$mode:
> [1] "666"
>
> Ok so I am access issues. Maybe they are ephemeral and I can change
> the permissions:
>
> > Sys.chmod('remote.R', mode = '666')
> > file.access(remote_file, 4)
> remote.R
> -1
>
> Nope. I am thoroughly stumped and maybe can't make it any further
> because of Windows.
>
> Downstream I am trying to use digest::digest to create a hash but
> digest thinks we don't have permission because file.access is failing.
> Any thoughts on how I can get file.access to return 0 for the remote.R
> file? Any ideas?
>
> Thanks in advance,
>
> Sam
__
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] qq plot issue with ab line
Hi Jim,
I have in my code:
abline(0,1,col='red')
can you please tell me how to change my code to have it indeed running
from 0 to 1?
Thanks
Ana
On Fri, Feb 28, 2020 at 3:34 PM Jim Lemon wrote:
>
> Hi Ana,
> Look carefully at that red line. It goes through (0,0) and scoots off
> the plot at (2.5,2.5). As you have specified that intercept and slope
> in your code, poor abline is doing the best it can. Do not punish it
> for doing what you request.
>
> Jim
>
> On Sat, Feb 29, 2020 at 6:10 AM Ana Marija
> wrote:
> >
> > Hello,
> >
> > I made the plot in attach with this function:
> >
> > qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
> > {
> > nn = length(p)
> > xx = -log10((1:nn)/(nn+1))
> > plot( xx, -sort(log10(p)),
> > main = MAIN, sub= SUB, cex.sub=1.3,
> > xlab=expression(Expected~~-log[10](italic(p))),
> > ylab=expression(Observed~~-log[10](italic(p))),
> > cex.lab=1.0,mgp=c(2,1,0))
> > abline(0,1,col='red')
> > if(BH) ## BH = include Benjamini Hochberg FDR
> > {
> >
> > abline(-log10(0.05),1, col='black',lty=1)
> > text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
> > abline(-log10(0.10),1, col='black',lty=1)
> > text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
> > abline(-log10(0.25),1, col='black',lty=1)
> > text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
> > #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
> >#col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
> > if (BF)
> > {
> > abline(h=-log10(0.05/nn), col='black') ## bonferroni
> > }
> > }
> > }
> >
> >
> > biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
> > qqunif(biob272$V2)
> >
> >
> > > head(biob272)
> > V1 V2
> > 1 rs2089177 0.581204
> > 2 rs4360974 0.418456
> > 3 rs6502526 0.416670
> > 4 rs8069906 0.568030
> > 5 rs9895995 0.266746
> > 6 rs9905280 0.510032
> >
> > But the red, abline doesn't look like it is 1:1 line.
> >
> > Can you please advise?
> >
> > Thanks
> > Ana
> > __
> > 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.
Re: [R] qq plot issue with ab line
Hi Ana,
Look carefully at that red line. It goes through (0,0) and scoots off
the plot at (2.5,2.5). As you have specified that intercept and slope
in your code, poor abline is doing the best it can. Do not punish it
for doing what you request.
Jim
On Sat, Feb 29, 2020 at 6:10 AM Ana Marija wrote:
>
> Hello,
>
> I made the plot in attach with this function:
>
> qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
> {
> nn = length(p)
> xx = -log10((1:nn)/(nn+1))
> plot( xx, -sort(log10(p)),
> main = MAIN, sub= SUB, cex.sub=1.3,
> xlab=expression(Expected~~-log[10](italic(p))),
> ylab=expression(Observed~~-log[10](italic(p))),
> cex.lab=1.0,mgp=c(2,1,0))
> abline(0,1,col='red')
> if(BH) ## BH = include Benjamini Hochberg FDR
> {
>
> abline(-log10(0.05),1, col='black',lty=1)
> text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
> abline(-log10(0.10),1, col='black',lty=1)
> text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
> abline(-log10(0.25),1, col='black',lty=1)
> text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
> #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
>#col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
> if (BF)
> {
> abline(h=-log10(0.05/nn), col='black') ## bonferroni
> }
> }
> }
>
>
> biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
> qqunif(biob272$V2)
>
>
> > head(biob272)
> V1 V2
> 1 rs2089177 0.581204
> 2 rs4360974 0.418456
> 3 rs6502526 0.416670
> 4 rs8069906 0.568030
> 5 rs9895995 0.266746
> 6 rs9905280 0.510032
>
> But the red, abline doesn't look like it is 1:1 line.
>
> Can you please advise?
>
> Thanks
> Ana
> __
> 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] Help with ggplot plot
Hello Rui, this is it, thank you very much, sorry if my request was confusing.
WHP
From: Rui Barradas
Sent: Friday, February 28, 2020 2:15 PM
To: Bill Poling ; r-help (r-help@r-project.org)
Subject: Re: [R] Help with ggplot plot
[External Email]
Hello,
Now I'm not understanding, you want the values in the bars? The numbers?
ggplot(tmp, aes(x = Region, y = ProductLineID, fill = ProductLineFlag)) +
geom_col() +
geom_text(aes(label = ProductLineID),
position = position_stack(vjust = 0.5), size = 3) +
facet_grid(~InOutFlagAlpha)
Hope this helps,
Rui Barradas
Às 17:38 de 28/02/20, Bill Poling escreveu:
> Hi Rui, thank you this is helpful, however, I would like the values in the or
> above the bars.
>
> I have tried 'dodge' but not working correctly.
>
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Getting
> worse again
> geom_bar(stat ="identity") +
> geom_col(position = 'dodge') +
> facet_grid("InOutFlagAlpha")
>
> Thoughts?
>
> WHP
>
> From: Rui Barradas
> Sent: Friday, February 28, 2020 11:06 AM
> To: Bill Poling ; r-help
> (mailto:r-help@r-project.org)
> Subject: Re: [R] Help with ggplot plot
>
> [External Email]
> Hello,
>
> If you want faceting, a square grid can do it.
>
>
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
> geom_bar(stat = "identity") +
> facet_grid(InOutFlagAlpha ~ ProductLineFlag)
>
>
> Hope this helps,
>
> Rui Barradas
>
> Às 16:50 de 28/02/20, Bill Poling escreveu:
>> #RStudio Version 1.2.5019
>> sessionInfo()
>> # R version 3.6.2 (2019-12-12)
>> #Platform: x86_64-w64-mingw32/x64 (64-bit)
>> #Running under: Windows 10 x64 (build 17134)
>>
>> Hello, I am sure I am missing something simple.
>>
>> Here is my data, its aggregated and if need be I can unaggregate I guess:
>>
>> dput(tmp)
>> structure(list(InOutFlagAlpha = c("NO ", "YES", "NO ", "YES",
>> "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ",
>> "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES"), ProductLineFlag =
>> structure(c(1L,
>> 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
>> 1L, 2L, 2L), .Label = c("ACH", "CARD"), class = "factor"), Region =
>> structure(c(1L,
>> 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
>> 5L, 5L, 5L), .Label = c("Frontier", "Midwest", "Northeast", "Pacific",
>> "South"), class = "factor"), ProductLineID = c(7163L, 34212L,
>> 35891L, 54177L, 8873L, 34008L, 52017L, 67881L, 7408L, 29430L,
>> 64108L, 70532L, 5984L, 21720L, 49030L, 60211L, 7330L, 34876L,
>> 46387L, 75893L)), row.names = c(NA, -20L), class = "data.frame")
>>
>> |InOutFlagAlpha |ProductLineFlag | Region| ProductLineID|
>> |:--|:---|-:|-:|
>> |NO |ACH | Frontier| 7163|
>> |YES |ACH | Frontier| 34212|
>> |NO |CARD | Frontier| 35891|
>> |YES |CARD | Frontier| 54177|
>> |NO |ACH | Midwest| 8873|
>> |YES |ACH | Midwest| 34008|
>> |NO |CARD | Midwest| 52017|
>> |YES |CARD | Midwest| 67881|
>> |NO |ACH | Northeast| 7408|
>> |YES |ACH | Northeast| 29430|
>> |NO |CARD | Northeast| 64108|
>> |YES |CARD | Northeast| 70532|
>> |NO |ACH | Pacific| 5984|
>> |YES |ACH | Pacific| 21720|
>> |NO |CARD | Pacific| 49030|
>> |YES |CARD | Pacific| 60211|
>> |NO |ACH | South| 7330|
>> |YES |ACH | South| 34876|
>> |NO |CARD | South| 46387|
>> |YES |CARD | South| 75893|
>>
>> I am trying to get the value from ProductLineID into the bars
>>
>> I have slowly stepped through to the point of having everything but the
>> values.
>>
>> Appreciate any advice, thank you.
>>
>> WHP
>>
>> #1
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
>> geom_bar(stat = "identity")
>> #2
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
>> geom_bar(stat = "identity") +
>> facet_grid("InOutFlagAlpha")
>> #3
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
>> geom_bar(stat ="identity") +
>> facet_grid("InOutFlagAlpha")
>> #4
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
>> geom_bar(stat ="identity",position = 'dodge') +
>> facet_grid("InOutFlagAlpha")
>> #5
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) +
>> geom_bar(stat ="identity",position = 'dodge') +
>> facet_grid("InOutFlagAlpha")
>> #6
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Best so
>> far
>> geom_bar(stat ="identity") +
>> geom_col() +
>> facet_grid("InOutFlagAlpha")
>> #7
>> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Not
>> working
>> geom_bar(stat ="identity") +
>> geom_col(position = 'dodge') +
>> facet_grid("InOutFlagAlpha")
>>
>> WHP
>>
>>
>> Confidentiality Notice\ \ This email and the attachments...{{dropped:11}}
>>
>> __
>> mailto: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
Re: [R] Help with ggplot plot
Hello,
Now I'm not understanding, you want the values in the bars? The numbers?
ggplot(tmp, aes(x = Region, y = ProductLineID, fill = ProductLineFlag)) +
geom_col() +
geom_text(aes(label = ProductLineID),
position = position_stack(vjust = 0.5), size = 3) +
facet_grid(~InOutFlagAlpha)
Hope this helps,
Rui Barradas
Às 17:38 de 28/02/20, Bill Poling escreveu:
Hi Rui, thank you this is helpful, however, I would like the values in the or
above the bars.
I have tried 'dodge' but not working correctly.
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Getting
worse again
geom_bar(stat ="identity") +
geom_col(position = 'dodge') +
facet_grid("InOutFlagAlpha")
Thoughts?
WHP
From: Rui Barradas
Sent: Friday, February 28, 2020 11:06 AM
To: Bill Poling ; r-help (r-help@r-project.org)
Subject: Re: [R] Help with ggplot plot
[External Email]
Hello,
If you want faceting, a square grid can do it.
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid(InOutFlagAlpha ~ ProductLineFlag)
Hope this helps,
Rui Barradas
Às 16:50 de 28/02/20, Bill Poling escreveu:
#RStudio Version 1.2.5019
sessionInfo()
# R version 3.6.2 (2019-12-12)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 17134)
Hello, I am sure I am missing something simple.
Here is my data, its aggregated and if need be I can unaggregate I guess:
dput(tmp)
structure(list(InOutFlagAlpha = c("NO ", "YES", "NO ", "YES",
"NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ",
"YES", "NO ", "YES", "NO ", "YES", "NO ", "YES"), ProductLineFlag =
structure(c(1L,
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("ACH", "CARD"), class = "factor"), Region =
structure(c(1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L), .Label = c("Frontier", "Midwest", "Northeast", "Pacific",
"South"), class = "factor"), ProductLineID = c(7163L, 34212L,
35891L, 54177L, 8873L, 34008L, 52017L, 67881L, 7408L, 29430L,
64108L, 70532L, 5984L, 21720L, 49030L, 60211L, 7330L, 34876L,
46387L, 75893L)), row.names = c(NA, -20L), class = "data.frame")
|InOutFlagAlpha |ProductLineFlag | Region| ProductLineID|
|:--|:---|-:|-:|
|NO |ACH | Frontier| 7163|
|YES |ACH | Frontier| 34212|
|NO |CARD | Frontier| 35891|
|YES |CARD | Frontier| 54177|
|NO |ACH | Midwest| 8873|
|YES |ACH | Midwest| 34008|
|NO |CARD | Midwest| 52017|
|YES |CARD | Midwest| 67881|
|NO |ACH | Northeast| 7408|
|YES |ACH | Northeast| 29430|
|NO |CARD | Northeast| 64108|
|YES |CARD | Northeast| 70532|
|NO |ACH | Pacific| 5984|
|YES |ACH | Pacific| 21720|
|NO |CARD | Pacific| 49030|
|YES |CARD | Pacific| 60211|
|NO |ACH | South| 7330|
|YES |ACH | South| 34876|
|NO |CARD | South| 46387|
|YES |CARD | South| 75893|
I am trying to get the value from ProductLineID into the bars
I have slowly stepped through to the point of having everything but the values.
Appreciate any advice, thank you.
WHP
#1
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity")
#2
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid("InOutFlagAlpha")
#3
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity") +
facet_grid("InOutFlagAlpha")
#4
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#5
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#6
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Best so far
geom_bar(stat ="identity") +
geom_col() +
facet_grid("InOutFlagAlpha")
#7
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Not working
geom_bar(stat ="identity") +
geom_col(position = 'dodge') +
facet_grid("InOutFlagAlpha")
WHP
Confidentiality Notice\ \ This email and the attachments...{{dropped:11}}
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Re: [R] Help to solve modeling problem with gamm
> There was clearly a non-linear growth pattern such that an additive mixed > effects model was proposed to model the behavior of biomass as a function of > time and treatments. The presence of non-linearity (in x) does not necessarily mean that you can't use a "linear model". In general, linear models work well for biological growth curves with small to medium sized data. Technically, this is off topic, however, the notion of what is linear and what is not linear, is a recurring theme on this mailing list. > When plotting the residuals a clear cone-shaped pattern was observed Based on classical statistics, the obvious approach is to transform your data. This is easy to do, however, some expertise is required to back-transform parameters/estimates and interpret them. While you're welcome to seek advice on mailing lists, I'd recommend you consult a biostatistician. __ 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] qq plot issue with ab line
Hello,
I made the plot in attach with this function:
qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
{
nn = length(p)
xx = -log10((1:nn)/(nn+1))
plot( xx, -sort(log10(p)),
main = MAIN, sub= SUB, cex.sub=1.3,
xlab=expression(Expected~~-log[10](italic(p))),
ylab=expression(Observed~~-log[10](italic(p))),
cex.lab=1.0,mgp=c(2,1,0))
abline(0,1,col='red')
if(BH) ## BH = include Benjamini Hochberg FDR
{
abline(-log10(0.05),1, col='black',lty=1)
text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
abline(-log10(0.10),1, col='black',lty=1)
text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
abline(-log10(0.25),1, col='black',lty=1)
text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
#legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
#col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
if (BF)
{
abline(h=-log10(0.05/nn), col='black') ## bonferroni
}
}
}
biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
qqunif(biob272$V2)
> head(biob272)
V1 V2
1 rs2089177 0.581204
2 rs4360974 0.418456
3 rs6502526 0.416670
4 rs8069906 0.568030
5 rs9895995 0.266746
6 rs9905280 0.510032
But the red, abline doesn't look like it is 1:1 line.
Can you please advise?
Thanks
Ana
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[R] file.access returning -1 for a file on remote Windows drive.
Hi there,
Looking for some help in diagnosing or developing a work around to a
problem I am having on a Windows machine. I am running R 3.6.2.
I have two identical files, one stored locally and the other stored on
a network drive.
For access:
> file.access(local_file, 4)
local.R
0
> file.access(remote_file, 4)
remote.R
-1
Also for file.info
> file.info(local_file)$mode:
[1] "666"
> file.info(remote_file)$mode:
[1] "666"
Ok so I am access issues. Maybe they are ephemeral and I can change
the permissions:
> Sys.chmod('remote.R', mode = '666')
> file.access(remote_file, 4)
remote.R
-1
Nope. I am thoroughly stumped and maybe can't make it any further
because of Windows.
Downstream I am trying to use digest::digest to create a hash but
digest thinks we don't have permission because file.access is failing.
Any thoughts on how I can get file.access to return 0 for the remote.R
file? Any ideas?
Thanks in advance,
Sam
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Re: [R] dir and pattern = ".r"
Ups... Thank you both. Indeed I must repeat lessons on regular expression... obviously forgotten... Le 28/02/2020 à 18:32, Jeremie Juste a écrit : Hello, you need dir(pattern="\\.r$",ignore.case=TRUE) remember that the pattern is a regular expression. so ".r" is [any single character]r. So basically it will give you any file that contains r (but not that starts with r) so you got what you expected with dir(pattern=".txt") just by chance. as or would have been printed as well HTH, Jeremie I have this directory contain listed at the page bottom Can somebody tell me why with dir(pattern = ".txt") dir(pattern = ".dbf") etc. I get exactly what I want (a vector with the file names correctly suffixed), but with dir(pattern = ".r") I get this: dir(pattern=".r") [1] "Article Predation" "BD Carto" [3] "broma1.txt" "broma3.txt" [5] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [7] "BufferRenard.dbf" "BufferRenard.prj" [9] "BufferRenard.shp" "BufferRenard.shx" [11] "clpboard" "DatesDiurnes.txt" [13] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [15] "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [17] "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [19] "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [21] "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [23] "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [25] "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [27] "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [29] "DatesNocturnesRegis_plus.xlsx" "Figures" [31] "ParcBuf300n.dbf" "ParcBuf300n.prj" [33] "ParcBuf300n.shp" "ParcBuf300n.shx" [35] "ParcBuf350n.dbf" "ParcBuf350n.prj" [37] "ParcBuf350n.shp" "ParcBuf350n.shx" [39] "Script_190517_preparation.r" "Script_190518_scores_AT.r" [41] "Script_190519_1430_cinetiques_IKA.r" "Script_190519_1622_transects_camp.r" [43] "Script_190530_1700_preparation2.r" "Script_190530_1903_cinetiques_IKA2.r" [45] "Script_190531_0922_scores_AT2.r" "Script_190531_1729_prey_resource.r" [47] "Script_190601_1509_graphIKAd.r" "Script_190601_1509_graphIKAd_old.r" [49] "Script_190601_1509_graphIKAn.r" "Script_190601_1509_graphIKAn_old.r" [51] "Script_190601_1955_spatial.r" "Script_190708_0930_distance.r" [53] "Script_190709_0930_impact renard.r" "Script_200117_cinetiques_article.r" [55] "Script_200119_source_stats_explore_diurne.r" "Script_200119_stats.r" [57] "Script_200122_spatial_distribution.r" "Script_200124_distance.r" [59] "Script_200124_distance_source_d.r" "Script_200124_distance_source_n.r" [61] "Script_200201_impacts_on_prey.R" "ScriptCompteLignes.r" [63] "Scripts_avant_200112.zip" "shinyPred" [65] "StudyArea.dbf" "StudyArea.prj" [67] "StudyArea.shp" "StudyArea.shx" [69] "SurfaceZoneEtude.dbf" "SurfaceZoneEtude.prj" [71] "SurfaceZoneEtude.shp" "SurfaceZoneEtude.shx" [73] "transects_camp.Rdata" How can I get all the files, only these files, suffixed with ".r" ? Thanks in advance, dir() [1] "Analyse_190523_baseline_190523_1506.docx" "Analyse_190523_baseline_190531_2110.docx" [3] "Analyse_190523_baseline_190531_2110.Rmd" "Analyse_190531_baseline.docx" [5] "Analyse_190531_baseline.Rmd" "Analyse_190531_baseline_cache" [7] "Analyse_190531_baseline_files" "Analyse_190603_spatial.docx" [9] "Analyse_190603_spatial.Rmd" "Analyse_190603_spatial_cache" [11] "Analyse_190603_spatial_files" "Article Predation" [13] "BD Carto" "Biblio" [15] "broma1.txt" "broma3.txt" [17] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [19] "BufferRenard.dbf" "BufferRenard.prj" [21] "BufferRenard.shp" "BufferRenard.shx" [23] "clpboard" "DatesDiurnes.txt" [25] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [27] "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [29] "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [31] "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [33] "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [35] "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [37] "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [39] "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [41] "DatesNocturnesRegis_plus.xlsx" "Figures" [43] "IKAZ_old.zip" "IKAZ1999.txt" [45] "IKAZ2000.txt" "IKAZ2007.txt" [47] "IKAZ2008.txt" "IKAZ2009.txt" [49] "IKAZ2010.txt" "IKAZ2011.txt" [51] "IKAZ2012.txt" "IKAZ2013.txt" [53] "IKAZ2014.txt" "IKAZ2015.txt" [55] "IKAZ2016.txt" "IKAZ2017.txt" [57] "IKAZ2018.txt" "ParcBuf300n.dbf" [59] "ParcBuf300n.prj" "ParcBuf300n.shp" [61] "ParcBuf300n.shx" "ParcBuf350n.dbf" [63] "ParcBuf350n.prj" "ParcBuf350n.shp" [65] "ParcBuf350n.shx" "Photos ZELAC" [67] "plot.ds.R" "plot.dsmodel.R" [69] "RData" "Script_190517_preparation.r" [71] "Script_190518_scores_AT.r" "Script_190519_1430_cinetiques_IKA.r" [73] "Script_190519_1622_transects_camp.r" "Script_190530_1700_preparation2.r" [75] "Script_190530_1903_cinetiques_IKA2.r" "Script_190531_0922_scores_AT2.r" [77] "Script_190531_1729_prey_resource.r"
Re: [R] dir and pattern = ".r"
You _need_ to learn how regular expressions work. There are many dozens of ways to learn this topic... web tutorials, YouTube videos, reading the ?regex help page in R. Start at the beginning, and look for special characters like ".", "$", and "\." (which has to be "\\." in R). It shouldn't take long to pick up enough skill to solve this yourself, and you will be a more complete data analyst for it. On February 28, 2020 9:23:02 AM PST, Patrick Giraudoux wrote: >I have this directory contain listed at the page bottom > >Can somebody tell me why with > >dir(pattern = ".txt") > >dir(pattern = ".dbf") > >etc. > >I get exactly what I want (a vector with the file names correctly >suffixed), but with > >dir(pattern = ".r") > >I get this: > >> dir(pattern=".r") [1] "Article Predation" "BD Carto" [3] "broma1.txt" > >"broma3.txt" [5] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [7] >"BufferRenard.dbf" "BufferRenard.prj" [9] "BufferRenard.shp" >"BufferRenard.shx" [11] "clpboard" "DatesDiurnes.txt" [13] >"DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [15] >"DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [17] >"DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [19] >"DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [21] >"DatesNocturnes.txt" "DatesNocturnes_plus.txt" [23] >"DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [25] >"DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [27] >"DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [29] >"DatesNocturnesRegis_plus.xlsx" "Figures" [31] "ParcBuf300n.dbf" >"ParcBuf300n.prj" [33] "ParcBuf300n.shp" "ParcBuf300n.shx" [35] >"ParcBuf350n.dbf" "ParcBuf350n.prj" [37] "ParcBuf350n.shp" >"ParcBuf350n.shx" [39] "Script_190517_preparation.r" >"Script_190518_scores_AT.r" [41] "Script_190519_1430_cinetiques_IKA.r" >"Script_190519_1622_transects_camp.r" [43] >"Script_190530_1700_preparation2.r" >"Script_190530_1903_cinetiques_IKA2.r" [45] >"Script_190531_0922_scores_AT2.r" "Script_190531_1729_prey_resource.r" >[47] "Script_190601_1509_graphIKAd.r" >"Script_190601_1509_graphIKAd_old.r" [49] >"Script_190601_1509_graphIKAn.r" "Script_190601_1509_graphIKAn_old.r" >[51] "Script_190601_1955_spatial.r" "Script_190708_0930_distance.r" >[53] >"Script_190709_0930_impact renard.r" >"Script_200117_cinetiques_article.r" [55] >"Script_200119_source_stats_explore_diurne.r" "Script_200119_stats.r" >[57] "Script_200122_spatial_distribution.r" "Script_200124_distance.r" >[59] "Script_200124_distance_source_d.r" >"Script_200124_distance_source_n.r" [61] >"Script_200201_impacts_on_prey.R" "ScriptCompteLignes.r" [63] >"Scripts_avant_200112.zip" "shinyPred" [65] "StudyArea.dbf" >"StudyArea.prj" [67] "StudyArea.shp" "StudyArea.shx" [69] >"SurfaceZoneEtude.dbf" "SurfaceZoneEtude.prj" [71] >"SurfaceZoneEtude.shp" "SurfaceZoneEtude.shx" [73] >"transects_camp.Rdata" > > >How can I get all the files, only these files, suffixed with ".r" ? > >Thanks in advance, > > > > >> dir() [1] "Analyse_190523_baseline_190523_1506.docx" >"Analyse_190523_baseline_190531_2110.docx" [3] >"Analyse_190523_baseline_190531_2110.Rmd" >"Analyse_190531_baseline.docx" >[5] "Analyse_190531_baseline.Rmd" "Analyse_190531_baseline_cache" [7] >"Analyse_190531_baseline_files" "Analyse_190603_spatial.docx" [9] >"Analyse_190603_spatial.Rmd" "Analyse_190603_spatial_cache" [11] >"Analyse_190603_spatial_files" "Article Predation" [13] "BD Carto" >"Biblio" [15] "broma1.txt" "broma3.txt" [17] >"BromaBusesMilanMicha.xlsx" >"Bromadiolone" [19] "BufferRenard.dbf" "BufferRenard.prj" [21] >"BufferRenard.shp" "BufferRenard.shx" [23] "clpboard" >"DatesDiurnes.txt" >[25] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [27] >"DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [29] >"DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [31] >"DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [33] >"DatesNocturnes.txt" "DatesNocturnes_plus.txt" [35] >"DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [37] >"DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [39] >"DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [41] >"DatesNocturnesRegis_plus.xlsx" "Figures" [43] "IKAZ_old.zip" >"IKAZ1999.txt" [45] "IKAZ2000.txt" "IKAZ2007.txt" [47] "IKAZ2008.txt" >"IKAZ2009.txt" [49] "IKAZ2010.txt" "IKAZ2011.txt" [51] "IKAZ2012.txt" >"IKAZ2013.txt" [53] "IKAZ2014.txt" "IKAZ2015.txt" [55] "IKAZ2016.txt" >"IKAZ2017.txt" [57] "IKAZ2018.txt" "ParcBuf300n.dbf" [59] >"ParcBuf300n.prj" "ParcBuf300n.shp" [61] "ParcBuf300n.shx" >"ParcBuf350n.dbf" [63] "ParcBuf350n.prj" "ParcBuf350n.shp" [65] >"ParcBuf350n.shx" "Photos ZELAC" [67] "plot.ds.R" "plot.dsmodel.R" [69] > >"RData" "Script_190517_preparation.r" [71] "Script_190518_scores_AT.r" >"Script_190519_1430_cinetiques_IKA.r" [73] >"Script_190519_1622_transects_camp.r" >"Script_190530_1700_preparation2.r" [75]
Re: [R] Help with ggplot plot
Hi Rui, thank you this is helpful, however, I would like the values in the or
above the bars.
I have tried 'dodge' but not working correctly.
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Getting
worse again
geom_bar(stat ="identity") +
geom_col(position = 'dodge') +
facet_grid("InOutFlagAlpha")
Thoughts?
WHP
From: Rui Barradas
Sent: Friday, February 28, 2020 11:06 AM
To: Bill Poling ; r-help (r-help@r-project.org)
Subject: Re: [R] Help with ggplot plot
[External Email]
Hello,
If you want faceting, a square grid can do it.
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid(InOutFlagAlpha ~ ProductLineFlag)
Hope this helps,
Rui Barradas
Às 16:50 de 28/02/20, Bill Poling escreveu:
> #RStudio Version 1.2.5019
> sessionInfo()
> # R version 3.6.2 (2019-12-12)
> #Platform: x86_64-w64-mingw32/x64 (64-bit)
> #Running under: Windows 10 x64 (build 17134)
>
> Hello, I am sure I am missing something simple.
>
> Here is my data, its aggregated and if need be I can unaggregate I guess:
>
> dput(tmp)
> structure(list(InOutFlagAlpha = c("NO ", "YES", "NO ", "YES",
> "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ",
> "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES"), ProductLineFlag =
> structure(c(1L,
> 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
> 1L, 2L, 2L), .Label = c("ACH", "CARD"), class = "factor"), Region =
> structure(c(1L,
> 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
> 5L, 5L, 5L), .Label = c("Frontier", "Midwest", "Northeast", "Pacific",
> "South"), class = "factor"), ProductLineID = c(7163L, 34212L,
> 35891L, 54177L, 8873L, 34008L, 52017L, 67881L, 7408L, 29430L,
> 64108L, 70532L, 5984L, 21720L, 49030L, 60211L, 7330L, 34876L,
> 46387L, 75893L)), row.names = c(NA, -20L), class = "data.frame")
>
> |InOutFlagAlpha |ProductLineFlag | Region| ProductLineID|
> |:--|:---|-:|-:|
> |NO |ACH | Frontier| 7163|
> |YES |ACH | Frontier| 34212|
> |NO |CARD | Frontier| 35891|
> |YES |CARD | Frontier| 54177|
> |NO |ACH | Midwest| 8873|
> |YES |ACH | Midwest| 34008|
> |NO |CARD | Midwest| 52017|
> |YES |CARD | Midwest| 67881|
> |NO |ACH | Northeast| 7408|
> |YES |ACH | Northeast| 29430|
> |NO |CARD | Northeast| 64108|
> |YES |CARD | Northeast| 70532|
> |NO |ACH | Pacific| 5984|
> |YES |ACH | Pacific| 21720|
> |NO |CARD | Pacific| 49030|
> |YES |CARD | Pacific| 60211|
> |NO |ACH | South| 7330|
> |YES |ACH | South| 34876|
> |NO |CARD | South| 46387|
> |YES |CARD | South| 75893|
>
> I am trying to get the value from ProductLineID into the bars
>
> I have slowly stepped through to the point of having everything but the
> values.
>
> Appreciate any advice, thank you.
>
> WHP
>
> #1
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
> geom_bar(stat = "identity")
> #2
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
> geom_bar(stat = "identity") +
> facet_grid("InOutFlagAlpha")
> #3
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
> geom_bar(stat ="identity") +
> facet_grid("InOutFlagAlpha")
> #4
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
> geom_bar(stat ="identity",position = 'dodge') +
> facet_grid("InOutFlagAlpha")
> #5
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) +
> geom_bar(stat ="identity",position = 'dodge') +
> facet_grid("InOutFlagAlpha")
> #6
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Best so
> far
> geom_bar(stat ="identity") +
> geom_col() +
> facet_grid("InOutFlagAlpha")
> #7
> ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Not
> working
> geom_bar(stat ="identity") +
> geom_col(position = 'dodge') +
> facet_grid("InOutFlagAlpha")
>
> WHP
>
>
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and provide commented, minimal,
Re: [R] dir and pattern = ".r"
Hello, you need > dir(pattern="\\.r$",ignore.case=TRUE) remember that the pattern is a regular expression. so ".r" is [any single character]r. So basically it will give you any file that contains r (but not that starts with r) so you got what you expected with > dir(pattern=".txt") just by chance. as or would have been printed as well HTH, Jeremie > I have this directory contain listed at the page bottom > > Can somebody tell me why with > > dir(pattern = ".txt") > > dir(pattern = ".dbf") > > etc. > > I get exactly what I want (a vector with the file names correctly > suffixed), but with > > dir(pattern = ".r") > > I get this: > >> dir(pattern=".r") [1] "Article Predation" "BD Carto" [3] "broma1.txt" > "broma3.txt" [5] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [7] > "BufferRenard.dbf" "BufferRenard.prj" [9] "BufferRenard.shp" > "BufferRenard.shx" [11] "clpboard" "DatesDiurnes.txt" [13] > "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [15] > "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [17] > "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [19] > "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [21] > "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [23] > "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [25] > "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [27] > "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [29] > "DatesNocturnesRegis_plus.xlsx" "Figures" [31] "ParcBuf300n.dbf" > "ParcBuf300n.prj" [33] "ParcBuf300n.shp" "ParcBuf300n.shx" [35] > "ParcBuf350n.dbf" "ParcBuf350n.prj" [37] "ParcBuf350n.shp" > "ParcBuf350n.shx" [39] "Script_190517_preparation.r" > "Script_190518_scores_AT.r" [41] "Script_190519_1430_cinetiques_IKA.r" > "Script_190519_1622_transects_camp.r" [43] > "Script_190530_1700_preparation2.r" > "Script_190530_1903_cinetiques_IKA2.r" [45] > "Script_190531_0922_scores_AT2.r" "Script_190531_1729_prey_resource.r" > [47] "Script_190601_1509_graphIKAd.r" > "Script_190601_1509_graphIKAd_old.r" [49] > "Script_190601_1509_graphIKAn.r" "Script_190601_1509_graphIKAn_old.r" > [51] "Script_190601_1955_spatial.r" "Script_190708_0930_distance.r" [53] > "Script_190709_0930_impact renard.r" > "Script_200117_cinetiques_article.r" [55] > "Script_200119_source_stats_explore_diurne.r" "Script_200119_stats.r" > [57] "Script_200122_spatial_distribution.r" "Script_200124_distance.r" > [59] "Script_200124_distance_source_d.r" > "Script_200124_distance_source_n.r" [61] > "Script_200201_impacts_on_prey.R" "ScriptCompteLignes.r" [63] > "Scripts_avant_200112.zip" "shinyPred" [65] "StudyArea.dbf" > "StudyArea.prj" [67] "StudyArea.shp" "StudyArea.shx" [69] > "SurfaceZoneEtude.dbf" "SurfaceZoneEtude.prj" [71] > "SurfaceZoneEtude.shp" "SurfaceZoneEtude.shx" [73] "transects_camp.Rdata" > > How can I get all the files, only these files, suffixed with ".r" ? > > Thanks in advance, > > > >> dir() [1] "Analyse_190523_baseline_190523_1506.docx" > "Analyse_190523_baseline_190531_2110.docx" [3] > "Analyse_190523_baseline_190531_2110.Rmd" "Analyse_190531_baseline.docx" > [5] "Analyse_190531_baseline.Rmd" "Analyse_190531_baseline_cache" [7] > "Analyse_190531_baseline_files" "Analyse_190603_spatial.docx" [9] > "Analyse_190603_spatial.Rmd" "Analyse_190603_spatial_cache" [11] > "Analyse_190603_spatial_files" "Article Predation" [13] "BD Carto" > "Biblio" [15] "broma1.txt" "broma3.txt" [17] "BromaBusesMilanMicha.xlsx" > "Bromadiolone" [19] "BufferRenard.dbf" "BufferRenard.prj" [21] > "BufferRenard.shp" "BufferRenard.shx" [23] "clpboard" "DatesDiurnes.txt" > [25] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [27] > "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [29] > "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [31] > "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [33] > "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [35] > "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [37] > "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [39] > "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [41] > "DatesNocturnesRegis_plus.xlsx" "Figures" [43] "IKAZ_old.zip" > "IKAZ1999.txt" [45] "IKAZ2000.txt" "IKAZ2007.txt" [47] "IKAZ2008.txt" > "IKAZ2009.txt" [49] "IKAZ2010.txt" "IKAZ2011.txt" [51] "IKAZ2012.txt" > "IKAZ2013.txt" [53] "IKAZ2014.txt" "IKAZ2015.txt" [55] "IKAZ2016.txt" > "IKAZ2017.txt" [57] "IKAZ2018.txt" "ParcBuf300n.dbf" [59] > "ParcBuf300n.prj" "ParcBuf300n.shp" [61] "ParcBuf300n.shx" > "ParcBuf350n.dbf" [63] "ParcBuf350n.prj" "ParcBuf350n.shp" [65] > "ParcBuf350n.shx" "Photos ZELAC" [67] "plot.ds.R" "plot.dsmodel.R" [69] > "RData" "Script_190517_preparation.r" [71] "Script_190518_scores_AT.r" > "Script_190519_1430_cinetiques_IKA.r" [73] > "Script_190519_1622_transects_camp.r" > "Script_190530_1700_preparation2.r" [75] > "Script_190530_1903_cinetiques_IKA2.r"
[R] dir and pattern = ".r"
I have this directory contain listed at the page bottom Can somebody tell me why with dir(pattern = ".txt") dir(pattern = ".dbf") etc. I get exactly what I want (a vector with the file names correctly suffixed), but with dir(pattern = ".r") I get this: > dir(pattern=".r") [1] "Article Predation" "BD Carto" [3] "broma1.txt" "broma3.txt" [5] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [7] "BufferRenard.dbf" "BufferRenard.prj" [9] "BufferRenard.shp" "BufferRenard.shx" [11] "clpboard" "DatesDiurnes.txt" [13] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [15] "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [17] "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [19] "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [21] "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [23] "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [25] "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [27] "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [29] "DatesNocturnesRegis_plus.xlsx" "Figures" [31] "ParcBuf300n.dbf" "ParcBuf300n.prj" [33] "ParcBuf300n.shp" "ParcBuf300n.shx" [35] "ParcBuf350n.dbf" "ParcBuf350n.prj" [37] "ParcBuf350n.shp" "ParcBuf350n.shx" [39] "Script_190517_preparation.r" "Script_190518_scores_AT.r" [41] "Script_190519_1430_cinetiques_IKA.r" "Script_190519_1622_transects_camp.r" [43] "Script_190530_1700_preparation2.r" "Script_190530_1903_cinetiques_IKA2.r" [45] "Script_190531_0922_scores_AT2.r" "Script_190531_1729_prey_resource.r" [47] "Script_190601_1509_graphIKAd.r" "Script_190601_1509_graphIKAd_old.r" [49] "Script_190601_1509_graphIKAn.r" "Script_190601_1509_graphIKAn_old.r" [51] "Script_190601_1955_spatial.r" "Script_190708_0930_distance.r" [53] "Script_190709_0930_impact renard.r" "Script_200117_cinetiques_article.r" [55] "Script_200119_source_stats_explore_diurne.r" "Script_200119_stats.r" [57] "Script_200122_spatial_distribution.r" "Script_200124_distance.r" [59] "Script_200124_distance_source_d.r" "Script_200124_distance_source_n.r" [61] "Script_200201_impacts_on_prey.R" "ScriptCompteLignes.r" [63] "Scripts_avant_200112.zip" "shinyPred" [65] "StudyArea.dbf" "StudyArea.prj" [67] "StudyArea.shp" "StudyArea.shx" [69] "SurfaceZoneEtude.dbf" "SurfaceZoneEtude.prj" [71] "SurfaceZoneEtude.shp" "SurfaceZoneEtude.shx" [73] "transects_camp.Rdata" How can I get all the files, only these files, suffixed with ".r" ? Thanks in advance, > dir() [1] "Analyse_190523_baseline_190523_1506.docx" "Analyse_190523_baseline_190531_2110.docx" [3] "Analyse_190523_baseline_190531_2110.Rmd" "Analyse_190531_baseline.docx" [5] "Analyse_190531_baseline.Rmd" "Analyse_190531_baseline_cache" [7] "Analyse_190531_baseline_files" "Analyse_190603_spatial.docx" [9] "Analyse_190603_spatial.Rmd" "Analyse_190603_spatial_cache" [11] "Analyse_190603_spatial_files" "Article Predation" [13] "BD Carto" "Biblio" [15] "broma1.txt" "broma3.txt" [17] "BromaBusesMilanMicha.xlsx" "Bromadiolone" [19] "BufferRenard.dbf" "BufferRenard.prj" [21] "BufferRenard.shp" "BufferRenard.shx" [23] "clpboard" "DatesDiurnes.txt" [25] "DatesDiurnes_plus.txt" "DatesDiurnes_plus.xlsx" [27] "DatesDiurnesFREDON" "DatesDiurnesFREDON_plus.txt" [29] "DatesDiurnesFREDON_plus.xlsx" "DatesDiurnesRegis.txt" [31] "DatesDiurnesRegis_plus.txt" "DatesDiurnesRegis_plus.xlsx" [33] "DatesNocturnes.txt" "DatesNocturnes_plus.txt" [35] "DatesNocturnes_plus.xlsx" "DatesNocturnesFREDON" [37] "DatesNocturnesFREDON_plus.txt" "DatesNocturnesFREDON_plus.xlsx" [39] "DatesNocturnesRegis.txt" "DatesNocturnesRegis_plus.txt" [41] "DatesNocturnesRegis_plus.xlsx" "Figures" [43] "IKAZ_old.zip" "IKAZ1999.txt" [45] "IKAZ2000.txt" "IKAZ2007.txt" [47] "IKAZ2008.txt" "IKAZ2009.txt" [49] "IKAZ2010.txt" "IKAZ2011.txt" [51] "IKAZ2012.txt" "IKAZ2013.txt" [53] "IKAZ2014.txt" "IKAZ2015.txt" [55] "IKAZ2016.txt" "IKAZ2017.txt" [57] "IKAZ2018.txt" "ParcBuf300n.dbf" [59] "ParcBuf300n.prj" "ParcBuf300n.shp" [61] "ParcBuf300n.shx" "ParcBuf350n.dbf" [63] "ParcBuf350n.prj" "ParcBuf350n.shp" [65] "ParcBuf350n.shx" "Photos ZELAC" [67] "plot.ds.R" "plot.dsmodel.R" [69] "RData" "Script_190517_preparation.r" [71] "Script_190518_scores_AT.r" "Script_190519_1430_cinetiques_IKA.r" [73] "Script_190519_1622_transects_camp.r" "Script_190530_1700_preparation2.r" [75] "Script_190530_1903_cinetiques_IKA2.r" "Script_190531_0922_scores_AT2.r" [77] "Script_190531_1729_prey_resource.r" "Script_190601_1509_graphIKAd.r" [79] "Script_190601_1509_graphIKAd_old.r" "Script_190601_1509_graphIKAn.r" [81] "Script_190601_1509_graphIKAn_old.r" "Script_190601_1955_spatial.r" [83] "Script_190708_0930_distance.r" "Script_190709_0930_impact renard.r" [85] "Script_200117_cinetiques_article.r" "Script_200119_source_stats_explore_diurne.r" [87] "Script_200119_stats.r" "Script_200122_spatial_distribution.r" [89] "Script_200124_distance.r"
Re: [R] Help with ggplot plot
Hello,
If you want faceting, a square grid can do it.
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid(InOutFlagAlpha ~ ProductLineFlag)
Hope this helps,
Rui Barradas
Às 16:50 de 28/02/20, Bill Poling escreveu:
#RStudio Version 1.2.5019
sessionInfo()
# R version 3.6.2 (2019-12-12)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 17134)
Hello, I am sure I am missing something simple.
Here is my data, its aggregated and if need be I can unaggregate I guess:
dput(tmp)
structure(list(InOutFlagAlpha = c("NO ", "YES", "NO ", "YES",
"NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ",
"YES", "NO ", "YES", "NO ", "YES", "NO ", "YES"), ProductLineFlag =
structure(c(1L,
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("ACH", "CARD"), class = "factor"), Region =
structure(c(1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L), .Label = c("Frontier", "Midwest", "Northeast", "Pacific",
"South"), class = "factor"), ProductLineID = c(7163L, 34212L,
35891L, 54177L, 8873L, 34008L, 52017L, 67881L, 7408L, 29430L,
64108L, 70532L, 5984L, 21720L, 49030L, 60211L, 7330L, 34876L,
46387L, 75893L)), row.names = c(NA, -20L), class = "data.frame")
|InOutFlagAlpha |ProductLineFlag |Region| ProductLineID|
|:--|:---|-:|-:|
|NO |ACH | Frontier| 7163|
|YES|ACH | Frontier| 34212|
|NO |CARD| Frontier| 35891|
|YES|CARD| Frontier| 54177|
|NO |ACH | Midwest| 8873|
|YES|ACH | Midwest| 34008|
|NO |CARD| Midwest| 52017|
|YES|CARD| Midwest| 67881|
|NO |ACH | Northeast| 7408|
|YES|ACH | Northeast| 29430|
|NO |CARD| Northeast| 64108|
|YES|CARD| Northeast| 70532|
|NO |ACH | Pacific| 5984|
|YES|ACH | Pacific| 21720|
|NO |CARD| Pacific| 49030|
|YES|CARD| Pacific| 60211|
|NO |ACH | South| 7330|
|YES|ACH | South| 34876|
|NO |CARD| South| 46387|
|YES|CARD| South| 75893|
I am trying to get the value from ProductLineID into the bars
I have slowly stepped through to the point of having everything but the values.
Appreciate any advice, thank you.
WHP
#1
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity")
#2
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid("InOutFlagAlpha")
#3
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity") +
facet_grid("InOutFlagAlpha")
#4
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#5
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#6
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Best so
far
geom_bar(stat ="identity") +
geom_col() +
facet_grid("InOutFlagAlpha")
#7
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Not
working
geom_bar(stat ="identity") +
geom_col(position = 'dodge') +
facet_grid("InOutFlagAlpha")
WHP
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[R] Help with ggplot plot
#RStudio Version 1.2.5019
sessionInfo()
# R version 3.6.2 (2019-12-12)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 17134)
Hello, I am sure I am missing something simple.
Here is my data, its aggregated and if need be I can unaggregate I guess:
dput(tmp)
structure(list(InOutFlagAlpha = c("NO ", "YES", "NO ", "YES",
"NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ", "YES", "NO ",
"YES", "NO ", "YES", "NO ", "YES", "NO ", "YES"), ProductLineFlag =
structure(c(1L,
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("ACH", "CARD"), class = "factor"), Region =
structure(c(1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L), .Label = c("Frontier", "Midwest", "Northeast", "Pacific",
"South"), class = "factor"), ProductLineID = c(7163L, 34212L,
35891L, 54177L, 8873L, 34008L, 52017L, 67881L, 7408L, 29430L,
64108L, 70532L, 5984L, 21720L, 49030L, 60211L, 7330L, 34876L,
46387L, 75893L)), row.names = c(NA, -20L), class = "data.frame")
|InOutFlagAlpha |ProductLineFlag |Region| ProductLineID|
|:--|:---|-:|-:|
|NO |ACH | Frontier| 7163|
|YES|ACH | Frontier| 34212|
|NO |CARD| Frontier| 35891|
|YES|CARD| Frontier| 54177|
|NO |ACH | Midwest| 8873|
|YES|ACH | Midwest| 34008|
|NO |CARD| Midwest| 52017|
|YES|CARD| Midwest| 67881|
|NO |ACH | Northeast| 7408|
|YES|ACH | Northeast| 29430|
|NO |CARD| Northeast| 64108|
|YES|CARD| Northeast| 70532|
|NO |ACH | Pacific| 5984|
|YES|ACH | Pacific| 21720|
|NO |CARD| Pacific| 49030|
|YES|CARD| Pacific| 60211|
|NO |ACH | South| 7330|
|YES|ACH | South| 34876|
|NO |CARD| South| 46387|
|YES|CARD| South| 75893|
I am trying to get the value from ProductLineID into the bars
I have slowly stepped through to the point of having everything but the values.
Appreciate any advice, thank you.
WHP
#1
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity")
#2
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat = "identity") +
facet_grid("InOutFlagAlpha")
#3
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity") +
facet_grid("InOutFlagAlpha")
#4
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=Region)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#5
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) +
geom_bar(stat ="identity",position = 'dodge') +
facet_grid("InOutFlagAlpha")
#6
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Best so
far
geom_bar(stat ="identity") +
geom_col() +
facet_grid("InOutFlagAlpha")
#7
ggplot(tmp, aes(x=Region, y=ProductLineID, fill=ProductLineFlag)) + #Not
working
geom_bar(stat ="identity") +
geom_col(position = 'dodge') +
facet_grid("InOutFlagAlpha")
WHP
Confidentiality Notice\ \ This email and the attachments...{{dropped:11}}
__
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] Help to solve modeling problem with gamm
Wrong list. Post here: https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models in **plain text** not html. 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, Feb 28, 2020 at 12:25 AM José Antonio García Pérez < garc...@hotmail.com> wrote: > I conducted an experiment where earthworms were subjected to two > treatments, with and without herbicide in the soil. Biomass measurements > were taken every 12 days for 398 days and the biomass growth curves as a > function of time were plotted. > > There was clearly a non-linear growth pattern such that an additive mixed > effects model was proposed to model the behavior of biomass as a function > of time and treatments. > > When plotting the residuals a clear cone-shaped pattern was observed, > therefore a series of additive models were proposed sequentially to deal > with violations of the assumption of homogeneity. Below we can see the > models with the following names: M.1; M.2; M.3; M.4 > > > > lmc <- lmeControl (niterEM = 5000, msMaxIter = 1000) > > f1 <- formula (Biomass ~ Treat + s (Time, by = Treat)) > > > > M.1 <-gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = > lmc, data = Acorticis) > > > > #This first model uses the experimental box factor (i.e. fcajita) as the > random element of the model. This random effects model assumes homogeneity > between the experimental boxes and within them over time > > > > M.2 <-gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = > lmc, data = Acorticis, weights = varIdent (form = ~ 1 | fcajita)) > > > > #This second model assumes heterogeneity between boxes, but homogeneity > within each box over time > > > > M.3 <- gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = > lmc, data = Acorticis, weights = varExp (form = ~ Time10)) > > > > #The third model assumes homogeneity between boxes but heterogeneity > within each box over time > > > > Finally, we decided to model the heterogeneity using the 'varComb' > function in order to combine the variances where the model allows > heterogeneity between the experimental boxes and heterogeneity within the > experimental boxes over time: > > > > M.4 <- gamm (f1, random = list (fcajita = ~ 1), data = Acorticis, method = > "REML", control = lmc, weights = varComb (varIdent (form = ~ 1 | fcajita), > varPower (form = ~ Time10))) > > > > The first three models executed perfectly and the following values of > the AIC indicator were obtained: > > > AIC (M.1 $ lme, M.2 $ lme, M.3 $ lme) > > > > df AIC > > > > M.1 8379.6464 > > > > M.215309.5736 > > > > M.3 9310.4828 > > > > Unfortunately, the execution of the M.4 model failed and the following > error message was obtained: > > > > Error in environment (attr (ret $ lme $ modelStruct $ varStruct, > "formula")) <-. GlobalEnv: > > attempt to set an attribute on NULL > > > > A final model I tried was M5: > > M.5 <- gamm(f1, random = list(fcajita =~ 1), data = Acorticis, method = > "REML", control = lmc, weights = varComb(varIdent(form = ~1|fcajita), > varExp(form =~ Time10|fcajita))) > > and this time I got the following error message: > > Error in lme.formula(y ~ X - 1, random = rand, data = strip.offset(mf), : > > nlminb problem, convergence error code = 1 > > message = function evaluation limit reached without convergence (9) > > Además: Warning message: > > In logLik.reStruct(object, conLin) : > > Singular precision matrix in level -1, block 1 > > > > My question is: Could someone help me fix these problems to run the M.4 > and M.5 models? > > > [[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.
Re: [R] offset in glm
You need weights=Holders to make the 2nd form equivalent to the first (with a
bunch of somewhat annoying and largely irrelevant warnings). This is because
300 claims from 1000 holders is more informative than 3 out of 10 even though
the rate is the same.
-pd
> On 27 Feb 2020, at 19:15 , John Smith wrote:
>
> It is simple to use the provided function glm as fit1 below. However,
> without the offset argument, I tried fit2 below. The reason I used fit2 is
> that (for X as predictors, b the coefficients)
> fit2: log(Claims/Holders) = Xb
> means
> fit1: log(Claims)=Xb + log(Holders)
>
> Obviously the results from fit2 are different from fit1.
>
> Thanks!
> ##
> library("MASS")
> ## main-effects fit as Poisson GLM with offset
> fit1 <- glm(Claims ~ District + Group + Age + offset(log(Holders)),
> data = Insurance, family = poisson)
> coef(fit1)
>> coef(fit1)
> (Intercept) District2 District3 District4 Group.L
> -1.8105078329 0.0258681909 0.0385239271 0.2342053280 0.4297075387
> Group.Q Group.C Age.L Age.Q Age.C
> 0.0046324351 -0.0292943222 -0.3944318082 -0.0003549709 -0.0167367565
>
> fit2 <- glm(Claims/Holders ~ District + Group + Age,
> data = Insurance, family = poisson)
>> coef(fit2)
> (Intercept) District2 District3 District4 Group.L Group.Q
> -1.86340418 0.17552458 0.11081521 0.15131076 0.43701544 -0.01530721
> Group.C Age.L Age.Q Age.C
> -0.06033747 -0.31976743 -0.01833841 -0.01694737
>
> [[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.
[R] Help to solve modeling problem with gamm
I conducted an experiment where earthworms were subjected to two treatments, with and without herbicide in the soil. Biomass measurements were taken every 12 days for 398 days and the biomass growth curves as a function of time were plotted. There was clearly a non-linear growth pattern such that an additive mixed effects model was proposed to model the behavior of biomass as a function of time and treatments. When plotting the residuals a clear cone-shaped pattern was observed, therefore a series of additive models were proposed sequentially to deal with violations of the assumption of homogeneity. Below we can see the models with the following names: M.1; M.2; M.3; M.4 lmc <- lmeControl (niterEM = 5000, msMaxIter = 1000) f1 <- formula (Biomass ~ Treat + s (Time, by = Treat)) M.1 <-gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = lmc, data = Acorticis) #This first model uses the experimental box factor (i.e. fcajita) as the random element of the model. This random effects model assumes homogeneity between the experimental boxes and within them over time M.2 <-gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = lmc, data = Acorticis, weights = varIdent (form = ~ 1 | fcajita)) #This second model assumes heterogeneity between boxes, but homogeneity within each box over time M.3 <- gamm (f1, random = list (fcajita = ~ 1), method = "REML", control = lmc, data = Acorticis, weights = varExp (form = ~ Time10)) #The third model assumes homogeneity between boxes but heterogeneity within each box over time Finally, we decided to model the heterogeneity using the 'varComb' function in order to combine the variances where the model allows heterogeneity between the experimental boxes and heterogeneity within the experimental boxes over time: M.4 <- gamm (f1, random = list (fcajita = ~ 1), data = Acorticis, method = "REML", control = lmc, weights = varComb (varIdent (form = ~ 1 | fcajita), varPower (form = ~ Time10))) The first three models executed perfectly and the following values of the AIC indicator were obtained: > AIC (M.1 $ lme, M.2 $ lme, M.3 $ lme) df AIC M.1 8379.6464 M.215309.5736 M.3 9310.4828 Unfortunately, the execution of the M.4 model failed and the following error message was obtained: Error in environment (attr (ret $ lme $ modelStruct $ varStruct, "formula")) <-. GlobalEnv: attempt to set an attribute on NULL A final model I tried was M5: M.5 <- gamm(f1, random = list(fcajita =~ 1), data = Acorticis, method = "REML", control = lmc, weights = varComb(varIdent(form = ~1|fcajita), varExp(form =~ Time10|fcajita))) and this time I got the following error message: Error in lme.formula(y ~ X - 1, random = rand, data = strip.offset(mf), : nlminb problem, convergence error code = 1 message = function evaluation limit reached without convergence (9) Además: Warning message: In logLik.reStruct(object, conLin) : Singular precision matrix in level -1, block 1 My question is: Could someone help me fix these problems to run the M.4 and M.5 models? [[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.
