[R] UpSetR

[Evan Kransdorf]

Hello,

Does anyone use UpSetR for set visualization?

I am wanting to re-order the sets in the diagram.

Thanks, Evan

[[alternative HTML version deleted]]

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Re: [R] Interquartile Range

[Michael Artz]

I already found a solution, you suggested I try to find a non hacky
solution, which was not really my priority. I should have declined
politely, which I will do now. Or, ifyou just want me to post reproducible
code because you are bored or because you like solving problems then let me
know and I will accommodate. You have been helpful and I wouldnt mind in
that case.  Also, IQR was not a help from the beginning. If it supplies one
value, then its not even a candidate to be helpful for my problem. I
already talked about the format i was looking for.  I dont think I violated
any posting guideline, I asked for help, and people pointed me in a
direction and it helped me. Thanks again, I appreciate it.
On Apr 19, 2016 10:53 PM, "Bert Gunter"  wrote:

> ???
>
> IQR returns a single number.
>
> > IQR(rnorm(10))
> [1] 1.090168
>
> To your 2nd response:
> "I could have used average, min, max, they all would have returned the
> same thing., "
>
> I can only respond: huh?? Are all your values identical?
>
> You really need to provide a small reproducible example as requested
> by the posting guide -- I certainly don't get it, and I'm done
> guessing. Maybe others will see what I am missing and say something
> useful. I clearly can't.
>
> Cheers,
> Bert
>
>
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Apr 19, 2016 at 5:29 PM, Michael Artz 
> wrote:
> > Again, IQR returns two both a .25 and a .75 value and it failed, which is
> > why I didn't use it before. Also, the first function just returns tha
> same
> > value repeating.  Since they are the same, before the second call, using
> the
> > mode function is just a way to grab one value. I could have used average,
> > min, max, they all would have returned the same thing.
> >
> > Mike
> >
> > On Tue, Apr 19, 2016 at 7:24 PM, Marc Schwartz 
> wrote:
> >>
> >> Hi,
> >>
> >> Jumping into this thread mainly on the point of the mode of the
> >> distribution, while also supporting Bert's comments below on theory.
> >>
> >> If the vector 'x' that is being passed to this function is an integer
> >> vector, then a tabulation of the integers can yield a 'mode', presuming
> of
> >> course that there is only one unique mode. You may have to decide how
> you
> >> want to handle a multi-modal discrete distribution.
> >>
> >> If the vector 'x' is continuous (e.g. contains floating point values),
> >> then a tabulation is going to be problematic for a variety of reasons.
> >>
> >> In that case, prior discussions on this point, have yielded the
> following
> >> estimation of the mode of a continuous distribution by using:
> >>
> >> Mode <- function(x) {
> >>   D <- density(x)
> >>   D$x[which.max(D$y)]
> >> }
> >>
> >> where the second line of the function gets you the value of 'x' at the
> >> maximum of the density estimate. Of course, there is still the
> possibility
> >> of a multi-modal distribution and the nuances of which kernel is used,
> etc.,
> >> etc.
> >>
> >> Food for thought.
> >>
> >> Regards,
> >>
> >> Marc Schwartz
> >>
> >>
> >> > On Apr 19, 2016, at 7:07 PM, Bert Gunter 
> wrote:
> >> >
> >> > Well, instead of your functions try:
> >> >
> >> > Mode <- function(x) {
> >> > tabx <- table(x)
> >> > tabx[which.max(tabx)]
> >> > }
> >> >
> >> > and use R's IQR function instead of yours.
> >> >
> >> > ... so I still don't get why you want to return a character string
> >> > instead of a value for the IQR;
> >> > and the mode of a sample defined as above is generally a bad estimator
> >> > of the mode of the distribution. To say more than that would take me
> >> > too far afield. Post on stats.stackexchange.com if you want to know
> >> > why (if it's even relevant).
> >> >
> >> > Cheers,
> >> > Bert
> >> > Bert Gunter
> >> >
> >> > "The trouble with having an open mind is that people keep coming along
> >> > and sticking things into it."
> >> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >> >
> >> >
> >> > On Tue, Apr 19, 2016 at 4:25 PM, Michael Artz  >
> >> > wrote:
> >> >> Hi,
> >> >>  Here is what I am doing
> >> >>
> >> >> notGroupedAll <- ddply(data
> >> >> ,~groupColumn
> >> >> ,summarise
> >> >> ,col1_mean=mean(col1)
> >> >> ,col2_mode=Mode(col2) #Function I wrote for getting
> the
> >> >> mode shown below
> >> >> ,col3_Range=myIqr(col3)
> >> >> )
> >> >>
> >> >> groupedAll <- ddply(data
> >> >> ,~groupColumn
> >> >> ,summarise
> >> >> ,col1_mean=mean(col1)
> >> >> ,col2_mode=Mode(col2) #Function I wrote for getting
> the
> >> >> mode shown below
> >> >> ,col3_Range=Mode(col3)
> >> 

Re: [R] Creating two new variables conditional on retaining values from previous rows

[Jim Lemon]

Hi pele,
There are probably more elegant ways to do this using some function,
but this might help:

psdat<-read.table(text="ID DATE ITEM
 1   1/1/2014P1
 1   1/15/2014   P2
 1   1/20/2014   P3
 1   1/22/2014   P4
 1   3/10/2015   P5
 2   1/13/2015   P1
 2   1/20/2015   P2
 2   1/28/2015   P3
 2   2/28/2015   P4
 2   3/20/2015   P5",
 header=TRUE)
psdat$DATE<-as.Date(as.character(psdat$DATE),"%m/%d/%Y")
psdat$GROUP<-1
psdat$GROUPDATE<-psdat$DATE[1]
for(case in 2:dim(psdat)[1]) {
 # start a new ID
 if(lastID != psdat$ID[case-1]) {
  lastID<-psdat$ID[case]
  psdat$GROUP[case]<-1
  psdat$GROUPDATE[case]<-psdat$DATE[case]
 } else {
  if((psdat$DATE[case] - psdat$DATE[case-1]) > 10 ||
   (psdat$DATE[case] - psdat$GROUPDATE[case-1]) > 10) {
   psdat$GROUP[case]<-psdat$GROUP[case-1]+1
   psdat$GROUPDATE[case]<-psdat$DATE[case]
  } else {
   psdat$GROUP[case]<-psdat$GROUP[case-1]
   psdat$GROUPDATE[case]<-psdat$GROUPDATE[case-1]
  }
 }
}
psdat

Jim

On Wed, Apr 20, 2016 at 8:59 AM, pele.s--- via R-help
 wrote:
> Hello,
>
> Iam looking for an R solution that can efficiently produce the output shown 
> below. I can produce this easily in SAS with retain statement and a few lines 
> of if-then-else logic, etc.. but I am not find anything similar on the Rforum 
> archives. Below is the logic I am trying to apply to produce the output table 
> below. Thanks in any help!
>
> if the ID is the first ID encountered then group=1 and groupdate=date or else 
> if not first ID and date - previous date > 10 or date - previous group date 
> >10 then group=previous group # + 1 and groupdate = date or else if not first 
> ID and date - previous date <= 10 or date - previous group date<=10 then 
> group=previous group # and groupdate = previous date.
>
> Input:
>
> ID  DATEITEM
> 1   1/1/2014P1
> 1   1/15/2014   P2
> 1   1/20/2014   P3
> 1   1/22/2014   P4
> 1   3/10/2015   P5
> 2   1/13/2015   P1
> 2   1/20/2015   P2
> 2   1/28/2015   P3
> 2   2/28/2015   P4
> 2   3/20/2015   P5
> Desired Output
>
> ID  DATEITEMGROUP   GROUPDATE
> 1   1/1/2014P1  1   1/1/2014
> 1   1/15/2014   P2  2   1/15/2014
> 1   1/20/2014   P3  2   1/15/2014
> 1   1/22/2014   P4  2   1/15/2014
> 1   3/10/2015   P5  3   3/10/2015
> 2   1/13/2015   P1  1   1/13/2015
> 2   1/20/2015   P2  1   1/13/2015
> 2   1/28/2015   P3  2   1/28/2015
> 2   2/28/2015   P4  3   2/28/2015
> 2   3/20/2015   P5  4   3/20/2015
>
> Thanks for any help!
>
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> 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
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Re: [R] Interquartile Range

[Bert Gunter]

???

IQR returns a single number.

> IQR(rnorm(10))
[1] 1.090168

To your 2nd response:
"I could have used average, min, max, they all would have returned the
same thing., "

I can only respond: huh?? Are all your values identical?

You really need to provide a small reproducible example as requested
by the posting guide -- I certainly don't get it, and I'm done
guessing. Maybe others will see what I am missing and say something
useful. I clearly can't.

Cheers,
Bert





Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 5:29 PM, Michael Artz  wrote:
> Again, IQR returns two both a .25 and a .75 value and it failed, which is
> why I didn't use it before. Also, the first function just returns tha same
> value repeating.  Since they are the same, before the second call, using the
> mode function is just a way to grab one value. I could have used average,
> min, max, they all would have returned the same thing.
>
> Mike
>
> On Tue, Apr 19, 2016 at 7:24 PM, Marc Schwartz  wrote:
>>
>> Hi,
>>
>> Jumping into this thread mainly on the point of the mode of the
>> distribution, while also supporting Bert's comments below on theory.
>>
>> If the vector 'x' that is being passed to this function is an integer
>> vector, then a tabulation of the integers can yield a 'mode', presuming of
>> course that there is only one unique mode. You may have to decide how you
>> want to handle a multi-modal discrete distribution.
>>
>> If the vector 'x' is continuous (e.g. contains floating point values),
>> then a tabulation is going to be problematic for a variety of reasons.
>>
>> In that case, prior discussions on this point, have yielded the following
>> estimation of the mode of a continuous distribution by using:
>>
>> Mode <- function(x) {
>>   D <- density(x)
>>   D$x[which.max(D$y)]
>> }
>>
>> where the second line of the function gets you the value of 'x' at the
>> maximum of the density estimate. Of course, there is still the possibility
>> of a multi-modal distribution and the nuances of which kernel is used, etc.,
>> etc.
>>
>> Food for thought.
>>
>> Regards,
>>
>> Marc Schwartz
>>
>>
>> > On Apr 19, 2016, at 7:07 PM, Bert Gunter  wrote:
>> >
>> > Well, instead of your functions try:
>> >
>> > Mode <- function(x) {
>> > tabx <- table(x)
>> > tabx[which.max(tabx)]
>> > }
>> >
>> > and use R's IQR function instead of yours.
>> >
>> > ... so I still don't get why you want to return a character string
>> > instead of a value for the IQR;
>> > and the mode of a sample defined as above is generally a bad estimator
>> > of the mode of the distribution. To say more than that would take me
>> > too far afield. Post on stats.stackexchange.com if you want to know
>> > why (if it's even relevant).
>> >
>> > Cheers,
>> > Bert
>> > Bert Gunter
>> >
>> > "The trouble with having an open mind is that people keep coming along
>> > and sticking things into it."
>> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> >
>> >
>> > On Tue, Apr 19, 2016 at 4:25 PM, Michael Artz 
>> > wrote:
>> >> Hi,
>> >>  Here is what I am doing
>> >>
>> >> notGroupedAll <- ddply(data
>> >> ,~groupColumn
>> >> ,summarise
>> >> ,col1_mean=mean(col1)
>> >> ,col2_mode=Mode(col2) #Function I wrote for getting the
>> >> mode shown below
>> >> ,col3_Range=myIqr(col3)
>> >> )
>> >>
>> >> groupedAll <- ddply(data
>> >> ,~groupColumn
>> >> ,summarise
>> >> ,col1_mean=mean(col1)
>> >> ,col2_mode=Mode(col2) #Function I wrote for getting the
>> >> mode shown below
>> >> ,col3_Range=Mode(col3)
>> >> )
>> >>
>> >> #custom Mode function
>> >> Mode <- function(x) {
>> >>  ux <- unique(x)
>> >>  ux[which.max(tabulate(match(x, ux)))]
>> >>
>> >> #the range function
>> >> myIqr <- function(x) {
>> >>  paste(round(quantile(x,0.375),0),round(quantile(x,0.625),0),sep="-")
>> >> }
>> >>
>> >>
>> >> }
>> >>
>> >>
>> >> Here is what I am doing!! :)
>> >>
>> >>
>> >>
>> >> On Tue, Apr 19, 2016 at 2:57 PM, William Dunlap 
>> >> wrote:
>> >>>
>> >>> If you show us, not just tell us about, a self-contained example
>> >>> someone might show you a non-hacky way of getting the job done.
>> >>> (I don't see an argument to plyr::ddply called 'transform'.)
>> >>>
>> >>> Bill Dunlap
>> >>> TIBCO Software
>> >>> wdunlap tibco.com
>> >>>
>> >>> On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz
>> >>> 
>> >>> wrote:
>> 
>>  Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!
>>  I
>>  ended up just using the transform argument in the ddply function.  It
>> 

[R] XLConnect Package

[Keith S Weintraub]

Folks,
I am using the XLConnect package. I can download all the named ranges except a 
couple that are defined by the Excel function “Offset”.

For example I have this named range:
   =OFFSET(APA!$A$1,0,0,APA!$K$11,3)

I am pretty sure that this won’t work but I thought I would give it a shot 
here. 

Thanks for your time,
Best,
KW

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

Re: [R] Interquartile Range

[Michael Artz]

Again, IQR returns two both a .25 and a .75 value and it failed, which is
why I didn't use it before. Also, the first function just returns tha same
value repeating.  Since they are the same, before the second call, using
the mode function is just a way to grab one value. I could have used
average, min, max, they all would have returned the same thing.

Mike

On Tue, Apr 19, 2016 at 7:24 PM, Marc Schwartz  wrote:

> Hi,
>
> Jumping into this thread mainly on the point of the mode of the
> distribution, while also supporting Bert's comments below on theory.
>
> If the vector 'x' that is being passed to this function is an integer
> vector, then a tabulation of the integers can yield a 'mode', presuming of
> course that there is only one unique mode. You may have to decide how you
> want to handle a multi-modal discrete distribution.
>
> If the vector 'x' is continuous (e.g. contains floating point values),
> then a tabulation is going to be problematic for a variety of reasons.
>
> In that case, prior discussions on this point, have yielded the following
> estimation of the mode of a continuous distribution by using:
>
> Mode <- function(x) {
>   D <- density(x)
>   D$x[which.max(D$y)]
> }
>
> where the second line of the function gets you the value of 'x' at the
> maximum of the density estimate. Of course, there is still the possibility
> of a multi-modal distribution and the nuances of which kernel is used,
> etc., etc.
>
> Food for thought.
>
> Regards,
>
> Marc Schwartz
>
>
> > On Apr 19, 2016, at 7:07 PM, Bert Gunter  wrote:
> >
> > Well, instead of your functions try:
> >
> > Mode <- function(x) {
> > tabx <- table(x)
> > tabx[which.max(tabx)]
> > }
> >
> > and use R's IQR function instead of yours.
> >
> > ... so I still don't get why you want to return a character string
> > instead of a value for the IQR;
> > and the mode of a sample defined as above is generally a bad estimator
> > of the mode of the distribution. To say more than that would take me
> > too far afield. Post on stats.stackexchange.com if you want to know
> > why (if it's even relevant).
> >
> > Cheers,
> > Bert
> > Bert Gunter
> >
> > "The trouble with having an open mind is that people keep coming along
> > and sticking things into it."
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >
> >
> > On Tue, Apr 19, 2016 at 4:25 PM, Michael Artz 
> wrote:
> >> Hi,
> >>  Here is what I am doing
> >>
> >> notGroupedAll <- ddply(data
> >> ,~groupColumn
> >> ,summarise
> >> ,col1_mean=mean(col1)
> >> ,col2_mode=Mode(col2) #Function I wrote for getting the
> >> mode shown below
> >> ,col3_Range=myIqr(col3)
> >> )
> >>
> >> groupedAll <- ddply(data
> >> ,~groupColumn
> >> ,summarise
> >> ,col1_mean=mean(col1)
> >> ,col2_mode=Mode(col2) #Function I wrote for getting the
> >> mode shown below
> >> ,col3_Range=Mode(col3)
> >> )
> >>
> >> #custom Mode function
> >> Mode <- function(x) {
> >>  ux <- unique(x)
> >>  ux[which.max(tabulate(match(x, ux)))]
> >>
> >> #the range function
> >> myIqr <- function(x) {
> >>  paste(round(quantile(x,0.375),0),round(quantile(x,0.625),0),sep="-")
> >> }
> >>
> >>
> >> }
> >>
> >>
> >> Here is what I am doing!! :)
> >>
> >>
> >>
> >> On Tue, Apr 19, 2016 at 2:57 PM, William Dunlap 
> wrote:
> >>>
> >>> If you show us, not just tell us about, a self-contained example
> >>> someone might show you a non-hacky way of getting the job done.
> >>> (I don't see an argument to plyr::ddply called 'transform'.)
> >>>
> >>> Bill Dunlap
> >>> TIBCO Software
> >>> wdunlap tibco.com
> >>>
> >>> On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz  >
> >>> wrote:
> 
>  Oh thanks for that clarification Bert!  Hope you enjoyed your
> coffee!  I
>  ended up just using the transform argument in the ddply function.  It
> worked
>  and it repeated, then I called a mode function in another call to
> ddply that
>  summarised.  Kinda hacky but oh well!
> 
>  On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter  >
>  wrote:
> >
> > ... and I'm getting another cup of coffee...
> >
> > -- Bert
> > Bert Gunter
> >
> > "The trouble with having an open mind is that people keep coming
> along
> > and sticking things into it."
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >
> >
> > On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter <
> bgunter.4...@gmail.com>
> > wrote:
> >> NO NO  -- I am wrong! The paste() expression is of course evaluated.
> >> It's just that a character string is returned of the form
> "something -
> >> something".
> >>
> >> I apologize for the confusion.

Re: [R] Interquartile Range

[Marc Schwartz]

Hi,

Jumping into this thread mainly on the point of the mode of the distribution, 
while also supporting Bert's comments below on theory.

If the vector 'x' that is being passed to this function is an integer vector, 
then a tabulation of the integers can yield a 'mode', presuming of course that 
there is only one unique mode. You may have to decide how you want to handle a 
multi-modal discrete distribution.

If the vector 'x' is continuous (e.g. contains floating point values), then a 
tabulation is going to be problematic for a variety of reasons.

In that case, prior discussions on this point, have yielded the following 
estimation of the mode of a continuous distribution by using:

Mode <- function(x) {
  D <- density(x)
  D$x[which.max(D$y)]
}

where the second line of the function gets you the value of 'x' at the maximum 
of the density estimate. Of course, there is still the possibility of a 
multi-modal distribution and the nuances of which kernel is used, etc., etc.

Food for thought.

Regards,

Marc Schwartz


> On Apr 19, 2016, at 7:07 PM, Bert Gunter  wrote:
> 
> Well, instead of your functions try:
> 
> Mode <- function(x) {
> tabx <- table(x)
> tabx[which.max(tabx)]
> }
> 
> and use R's IQR function instead of yours.
> 
> ... so I still don't get why you want to return a character string
> instead of a value for the IQR;
> and the mode of a sample defined as above is generally a bad estimator
> of the mode of the distribution. To say more than that would take me
> too far afield. Post on stats.stackexchange.com if you want to know
> why (if it's even relevant).
> 
> Cheers,
> Bert
> Bert Gunter
> 
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> 
> 
> On Tue, Apr 19, 2016 at 4:25 PM, Michael Artz  wrote:
>> Hi,
>>  Here is what I am doing
>> 
>> notGroupedAll <- ddply(data
>> ,~groupColumn
>> ,summarise
>> ,col1_mean=mean(col1)
>> ,col2_mode=Mode(col2) #Function I wrote for getting the
>> mode shown below
>> ,col3_Range=myIqr(col3)
>> )
>> 
>> groupedAll <- ddply(data
>> ,~groupColumn
>> ,summarise
>> ,col1_mean=mean(col1)
>> ,col2_mode=Mode(col2) #Function I wrote for getting the
>> mode shown below
>> ,col3_Range=Mode(col3)
>> )
>> 
>> #custom Mode function
>> Mode <- function(x) {
>>  ux <- unique(x)
>>  ux[which.max(tabulate(match(x, ux)))]
>> 
>> #the range function
>> myIqr <- function(x) {
>>  paste(round(quantile(x,0.375),0),round(quantile(x,0.625),0),sep="-")
>> }
>> 
>> 
>> }
>> 
>> 
>> Here is what I am doing!! :)
>> 
>> 
>> 
>> On Tue, Apr 19, 2016 at 2:57 PM, William Dunlap  wrote:
>>> 
>>> If you show us, not just tell us about, a self-contained example
>>> someone might show you a non-hacky way of getting the job done.
>>> (I don't see an argument to plyr::ddply called 'transform'.)
>>> 
>>> Bill Dunlap
>>> TIBCO Software
>>> wdunlap tibco.com
>>> 
>>> On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz 
>>> wrote:
 
 Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!  I
 ended up just using the transform argument in the ddply function.  It 
 worked
 and it repeated, then I called a mode function in another call to ddply 
 that
 summarised.  Kinda hacky but oh well!
 
 On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter 
 wrote:
> 
> ... and I'm getting another cup of coffee...
> 
> -- Bert
> Bert Gunter
> 
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> 
> 
> On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter 
> wrote:
>> NO NO  -- I am wrong! The paste() expression is of course evaluated.
>> It's just that a character string is returned of the form "something -
>> something".
>> 
>> I apologize for the confusion.
>> 
>> -- Bert
>> 
>> 
>> 
>> 
>> Bert Gunter
>> 
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> 
>> 
>> On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter 
>> wrote:
>>> To be precise:
>>> 
>>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> 
>>> is an expression that evaluates to a character string:
>>> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
>>> 
>>> no matter what the argument of your 

Re: [R] Creating two new variables conditional on retaining values from previous rows

[Bert Gunter]

I do not have the tenacity to decipher your logic, but I would suggest
that you go through an R tutorial or two instead of limiting yourself
to R-Help (not R forum?) archives. You probably are going about it
wrongly in R (I suspect you need indexing). In fact, I would guess
that you probably don't want to go about things this way at all in R,
but of course that would require my knowing the underlying problem you
are trying to solve, which I do not.  My point is that you need to
change your programming paradigm and learn R instead of trying to
overlay SAS paradigms. And yup, it requires time and effort to do
this.

Note that there are various "R for SAS programmers" tutorials out
there, which might be helpful, either for your specific query or more
generally.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 3:59 PM, pele.s--- via R-help
 wrote:
> Hello,
>
> Iam looking for an R solution that can efficiently produce the output shown 
> below. I can produce this easily in SAS with retain statement and a few lines 
> of if-then-else logic, etc.. but I am not find anything similar on the Rforum 
> archives. Below is the logic I am trying to apply to produce the output table 
> below. Thanks in any help!
>
> if the ID is the first ID encountered then group=1 and groupdate=date or else 
> if not first ID and date - previous date > 10 or date - previous group date 
> >10 then group=previous group # + 1 and groupdate = date or else if not first 
> ID and date - previous date <= 10 or date - previous group date<=10 then 
> group=previous group # and groupdate = previous date.
>
> Input:
>
> ID  DATEITEM
> 1   1/1/2014P1
> 1   1/15/2014   P2
> 1   1/20/2014   P3
> 1   1/22/2014   P4
> 1   3/10/2015   P5
> 2   1/13/2015   P1
> 2   1/20/2015   P2
> 2   1/28/2015   P3
> 2   2/28/2015   P4
> 2   3/20/2015   P5
> Desired Output
>
> ID  DATEITEMGROUP   GROUPDATE
> 1   1/1/2014P1  1   1/1/2014
> 1   1/15/2014   P2  2   1/15/2014
> 1   1/20/2014   P3  2   1/15/2014
> 1   1/22/2014   P4  2   1/15/2014
> 1   3/10/2015   P5  3   3/10/2015
> 2   1/13/2015   P1  1   1/13/2015
> 2   1/20/2015   P2  1   1/13/2015
> 2   1/28/2015   P3  2   1/28/2015
> 2   2/28/2015   P4  3   2/28/2015
> 2   3/20/2015   P5  4   3/20/2015
>
> Thanks for any help!
>
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[R-es] Script sin resultados

[Manuel Máquez]

Carlos:

Te agradezco mucho tu respuesta tan rápida.

Se trata de obtener las incidencias en cada uno de los 39 grupos, aquellos
que lo hacen con mayor frecuencia. Es decir del grupo 'n' cuántas veces
sucede 1, 2, ... hasta 10. Con este resumen que va ir cambiando, aplicarle
loess.

Por lo que se refiere a los valores que indico, los obtuve contando
físicamente de los datos de TAB.

Nuevamente te repito las gracias más cumplidas.

*MANOLO MÁRQUEZ P.*

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Re: [R] Interquartile Range

[Bert Gunter]

Well, instead of your functions try:

Mode <- function(x) {
 tabx <- table(x)
 tabx[which.max(tabx)]
}

and use R's IQR function instead of yours.

... so I still don't get why you want to return a character string
instead of a value for the IQR;
and the mode of a sample defined as above is generally a bad estimator
of the mode of the distribution. To say more than that would take me
too far afield. Post on stats.stackexchange.com if you want to know
why (if it's even relevant).

Cheers,
Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 4:25 PM, Michael Artz  wrote:
> Hi,
>   Here is what I am doing
>
> notGroupedAll <- ddply(data
>  ,~groupColumn
>  ,summarise
>  ,col1_mean=mean(col1)
>  ,col2_mode=Mode(col2) #Function I wrote for getting the
> mode shown below
>  ,col3_Range=myIqr(col3)
>  )
>
> groupedAll <- ddply(data
>  ,~groupColumn
>  ,summarise
>  ,col1_mean=mean(col1)
>  ,col2_mode=Mode(col2) #Function I wrote for getting the
> mode shown below
>  ,col3_Range=Mode(col3)
>  )
>
> #custom Mode function
> Mode <- function(x) {
>   ux <- unique(x)
>   ux[which.max(tabulate(match(x, ux)))]
>
> #the range function
> myIqr <- function(x) {
>   paste(round(quantile(x,0.375),0),round(quantile(x,0.625),0),sep="-")
> }
>
>
> }
>
>
> Here is what I am doing!! :)
>
>
>
> On Tue, Apr 19, 2016 at 2:57 PM, William Dunlap  wrote:
>>
>> If you show us, not just tell us about, a self-contained example
>> someone might show you a non-hacky way of getting the job done.
>> (I don't see an argument to plyr::ddply called 'transform'.)
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>> On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz 
>> wrote:
>>>
>>> Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!  I
>>> ended up just using the transform argument in the ddply function.  It worked
>>> and it repeated, then I called a mode function in another call to ddply that
>>> summarised.  Kinda hacky but oh well!
>>>
>>> On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter 
>>> wrote:

 ... and I'm getting another cup of coffee...

 -- Bert
 Bert Gunter

 "The trouble with having an open mind is that people keep coming along
 and sticking things into it."
 -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


 On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter 
 wrote:
 > NO NO  -- I am wrong! The paste() expression is of course evaluated.
 > It's just that a character string is returned of the form "something -
 > something".
 >
 > I apologize for the confusion.
 >
 > -- Bert
 >
 >
 >
 >
 > Bert Gunter
 >
 > "The trouble with having an open mind is that people keep coming along
 > and sticking things into it."
 > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
 >
 >
 > On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter 
 > wrote:
 >> To be precise:
 >>
 >> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
 >>
 >> is an expression that evaluates to a character string:
 >> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
 >>
 >> no matter what the argument of your function, x. Hence
 >>
 >> return(paste(...)) will return this exact character string and never
 >> evaluates x.
 >>
 >>
 >> Cheers,
 >> Bert
 >>
 >>
 >>
 >>
 >>
 >>
 >>
 >>
 >> Bert Gunter
 >>
 >> "The trouble with having an open mind is that people keep coming
 >> along
 >> and sticking things into it."
 >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
 >>
 >>
 >> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
 >>  wrote:
  That didn't work Jim!
 >>>
 >>> It always helps to say how the suggestion did not work.  Jim's
 >>> function had a typo in it - was that the problem?  Or did you not
 >>> change the call to ddply to use that function.  Here is something
 >>> that might "work" for you:
 >>>
 >>>  library(plyr)
 >>>
 >>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
 >>>  myIqr <- function(x) {
 >>>
 >>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
 >>>  }
 >>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
 >>> col1_IQR=stats::IQR(col1))
 >>>  #  groupColumn col1_myIqr 

[R] Creating two new variables conditional on retaining values from previous rows

[pele.s--- via R-help]

Hello,

Iam looking for an R solution that can efficiently produce the output shown 
below. I can produce this easily in SAS with retain statement and a few lines 
of if-then-else logic, etc.. but I am not find anything similar on the Rforum 
archives. Below is the logic I am trying to apply to produce the output table 
below. Thanks in any help!

if the ID is the first ID encountered then group=1 and groupdate=date or else 
if not first ID and date - previous date > 10 or date - previous group date >10 
then group=previous group # + 1 and groupdate = date or else if not first ID 
and date - previous date <= 10 or date - previous group date<=10 then 
group=previous group # and groupdate = previous date.

Input:

ID  DATEITEM
1   1/1/2014P1
1   1/15/2014   P2
1   1/20/2014   P3
1   1/22/2014   P4
1   3/10/2015   P5
2   1/13/2015   P1
2   1/20/2015   P2
2   1/28/2015   P3
2   2/28/2015   P4
2   3/20/2015   P5
Desired Output

ID  DATEITEMGROUP   GROUPDATE
1   1/1/2014P1  1   1/1/2014
1   1/15/2014   P2  2   1/15/2014
1   1/20/2014   P3  2   1/15/2014
1   1/22/2014   P4  2   1/15/2014
1   3/10/2015   P5  3   3/10/2015
2   1/13/2015   P1  1   1/13/2015
2   1/20/2015   P2  1   1/13/2015
2   1/28/2015   P3  2   1/28/2015
2   2/28/2015   P4  3   2/28/2015
2   3/20/2015   P5  4   3/20/2015

Thanks for any help!

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Re: [R] Interquartile Range

[Michael Artz]

Hi,
  Here is what I am doing

notGroupedAll <- ddply(data
 ,~groupColumn
 ,summarise
 ,col1_mean=mean(col1)
 ,col2_mode=Mode(col2) #Function I wrote for getting the
mode shown below
 ,col3_Range=myIqr(col3)
 )

groupedAll <- ddply(data
 ,~groupColumn
 ,summarise
 ,col1_mean=mean(col1)
 ,col2_mode=Mode(col2) #Function I wrote for getting the
mode shown below
 ,col3_Range=Mode(col3)
 )

#custom Mode function
Mode <- function(x) {
  ux <- unique(x)
  ux[which.max(tabulate(match(x, ux)))]

#the range function
myIqr <- function(x) {
  paste(round(quantile(x,0.375),0),round(quantile(x,0.625),0),sep="-")
}


}


Here is what I am doing!! :)



On Tue, Apr 19, 2016 at 2:57 PM, William Dunlap  wrote:

> If you show us, not just tell us about, a self-contained example
> someone might show you a non-hacky way of getting the job done.
> (I don't see an argument to plyr::ddply called 'transform'.)
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz 
> wrote:
>
>> Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!  I
>> ended up just using the transform argument in the ddply function.  It
>> worked and it repeated, then I called a mode function in another call to
>> ddply that summarised.  Kinda hacky but oh well!
>>
>> On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter 
>> wrote:
>>
>>> ... and I'm getting another cup of coffee...
>>>
>>> -- Bert
>>> Bert Gunter
>>>
>>> "The trouble with having an open mind is that people keep coming along
>>> and sticking things into it."
>>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>>
>>>
>>> On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter 
>>> wrote:
>>> > NO NO  -- I am wrong! The paste() expression is of course evaluated.
>>> > It's just that a character string is returned of the form "something -
>>> > something".
>>> >
>>> > I apologize for the confusion.
>>> >
>>> > -- Bert
>>> >
>>> >
>>> >
>>> >
>>> > Bert Gunter
>>> >
>>> > "The trouble with having an open mind is that people keep coming along
>>> > and sticking things into it."
>>> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>> >
>>> >
>>> > On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter 
>>> wrote:
>>> >> To be precise:
>>> >>
>>> >> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> >>
>>> >> is an expression that evaluates to a character string:
>>> >> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
>>> >>
>>> >> no matter what the argument of your function, x. Hence
>>> >>
>>> >> return(paste(...)) will return this exact character string and never
>>> >> evaluates x.
>>> >>
>>> >>
>>> >> Cheers,
>>> >> Bert
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> Bert Gunter
>>> >>
>>> >> "The trouble with having an open mind is that people keep coming along
>>> >> and sticking things into it."
>>> >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>> >>
>>> >>
>>> >> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
>>> >>  wrote:
>>>  That didn't work Jim!
>>> >>>
>>> >>> It always helps to say how the suggestion did not work.  Jim's
>>> >>> function had a typo in it - was that the problem?  Or did you not
>>> >>> change the call to ddply to use that function.  Here is something
>>> >>> that might "work" for you:
>>> >>>
>>> >>>  library(plyr)
>>> >>>
>>> >>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>>> >>>  myIqr <- function(x) {
>>> >>>
>>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> >>>  }
>>> >>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
>>> >>> col1_IQR=stats::IQR(col1))
>>> >>>  #  groupColumn col1_myIqr col1_IQR
>>> >>>  #1   11-10
>>> >>>  #2   22-41
>>> >>>  #3   3  12-24   12
>>> >>>  #4   4112-320  208
>>> >>>  #5   5  2048-8192 6144
>>> >>>
>>> >>> The important point is that
>>> >>>
>>>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> >>> is not a function, it is an expression.   ddplyr wants functions.
>>> >>>
>>> >>>
>>> >>> Bill Dunlap
>>> >>> TIBCO Software
>>> >>> wdunlap tibco.com
>>> >>>
>>> >>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz <
>>> michaelea...@gmail.com>
>>> >>> wrote:
>>> >>>
>>>  That didn't work Jim!
>>> 
>>>  Thanks anyway
>>> 
>>>  On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon 
>>> wrote:
>>> 
>>>  > Hi Michael,
>>>  > At a guess, try this:
>>>  >
>>>  > iqr<-function(x) {
>>>  >
>>> 
>>> 

Re: [R-es] Script sin resultados completos

[Carlos Ortega]

Hola,

Te comento varias cosas:

   - No obtengo ningún tipo de error, ni warning al ejecutar el script.
   - Los resultados que obtengo de smas[,2] y smas[,3] son diferentes a los
   que obtienes en los dos casos (el bueno y el malo).

> smas[,2]
 [1] 17 NA  5  7 NA NA NA NA NA NA 17 NA  5  7 NA NA NA NA NA NA 17 NA  5
 7 NA NA NA NA NA NA 17 NA  5  7
[35] NA NA NA NA NA
> smas[,3]
 [1] 16 19 10 14 NA  5 NA NA  4 NA 16 19 10 14 NA  5 NA NA  4 NA 16 19 10
14 NA  5 NA NA  4 NA 16 19 10 14
[35] NA  5 NA NA  4

Y bueno, si hay tanta diferencia con respecto a lo que dices que debiera de
salir, no he mirado mucho más. Pero de todas formas, para seguir el bucle,
lo mejor es ir incluyendo variables intermedias e ir mostrándolas en
consola.

Aunque una estrategia mucho mejor es saber qué quieres hacer con tu fichero
y ver si este triple bucle es la mejora forma de atacar el problema o hay
alguna alternativa más eficiente y clara.

Saludos,
Carlos Ortega
www.qualityexcellence.es


El 19 de abril de 2016, 19:38, Manuel Máquez 
escribió:

> Hola Colegas:
> Tengo el siguiente script donde no se en donde esta el error, ojalá que
> alguno de ustedes me pueda ayudar.
> Anticipo las gracias más cumplidas por anticipado.
> bas <- read.csv('TAB.csv', header = F)
> sv <- 0
> sm <- 0
> lg <- 0
> smas <- matrix (1:390)
> for (i in 1:39) {
> #   if (i == 8) {break}
>for (j in 1:10) {
>   #  sm[i] <- 0
>   sm[j] <- 0
>   for (k in 1:127) {
>  if(bas[i,k] == 0) next(j)
>  if(bas[i, k] == j)
> sm[j] <- sm[j] + 1
>  #   smas <- matrix (sm, 10, i)
>  sv[j*i] <- sm[j]
>  smas <- matrix (sv, 39, i, byrow = T)
>  lg <- lg + sm[j]  # sm es el ultimo valor de sm
>  #  sm[j + 1] <- 0
>   }  # de k
>}  # de j
> }  # de i
> # ME DA warnings PERO DA RESULTADOS INCORRECTOS
> # AL PONER smas [,2] da 17 10 8 3 7 4 3 9 6 10 debiendo ser 17 19 16 9 5
> 11 5 2 5 3
> # AL PONER smas [,3] da 10 17 10 8 3 7 4 3 9 6 debiendo ser 16 15 9 11 8 9
> 7 5 3 2
>
> sv tampoco me proporciona resultados completos; parece que al cambiar de i
> <- 1 a 2 se le perdiera la pista de en dónde se encuentra y la verdad no
> encuentro de donde toma los resultados que saca; lo que sí me parece es que
> recicla algún otro vector.
> Adjunto el archivo Tab.csv.
> Reitero las gracias por la atención que se sirvan darme.
> Atentamente,
>
> *MANOLO MÁRQUEZ P.*
>
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-- 
Saludos,
Carlos Ortega
www.qualityexcellence.es

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Re: [R] Merge sort

[Duncan Murdoch]

On 19/04/2016 3:39 PM, Gaston wrote:

Hello everyone,

I am learning R since recently, and as a small exercise I wanted to
write a recursive mergesort. I was extremely surprised to discover that
my sorting, although operational, is deeply inefficient in time. Here is
my code :


merge <- function(x,y){
   if (is.na(x[1])) return(y)
   else if (is.na(y[1])) return(x)
   else if (x[1] 0 && length(x2) > 0) {
# compare the first values
if (x1[1] < x2[1]) {
  result[i + 1] <- x1[1]
  x1 <- x1[-1]
} else {
  result[i + 1] <- x2[1]
  x2 <- x2[-1]
}
i <- i + 1
  }

  # put the smaller one into the result
  # delete it from whichever vector it came from
  # repeat until one of x1 or x2 is empty
  # copy both vectors (one is empty!) onto the end of the results
  result <- c(result, x1, x2)
  result
}

If I were going for speed, I wouldn't modify the x1 and x2 vectors, and 
I'd pre-allocate result to the appropriate length, rather than growing 
it in the while loop.  But that was a different class!


Duncan Murdoch

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[R] Merge sort

[Gaston]

Hello everyone,

I am learning R since recently, and as a small exercise I wanted to 
write a recursive mergesort. I was extremely surprised to discover that 
my sorting, although operational, is deeply inefficient in time. Here is 
my code :

> merge <- function(x,y){
>   if (is.na(x[1])) return(y)
>   else if (is.na(y[1])) return(x)
>   else if (x[1]   else return(c(y[1],merge(x,y[-1])))
> }
>
> division <- function(x){
>   if (is.na(x[3])) return(cbind(x[1],x[2]))
>   else 
> return(cbind(c(x[1],division(x[-c(1,2)])[,1]),c(x[2],division(x[-c(1,2)])[,2])))
> }
>
> mergesort <- function(x){
>   if (is.na(x[2])) return(x)
>   else{
> print(x)
> t=division(x)
> return(merge(mergesort(t[,1]),mergesort(t[,2])))
>   }
> }

I tried my best to write it "the R-way", but apparently I failed. I 
suppose some of the functions I used are quite heavy. I would be 
grateful if you could give a hint on how to change that!

I hope I made myself clear and wish you a nice day,

Cheers,

Gaston

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[R] Matrix: How create a _row-oriented_ sparse Matrix (=dgRMatrix)?

[Henrik Bengtsson]

Using the Matrix package, how can I create a row-oriented sparse
Matrix from scratch populated with some data?  By default a
column-oriented one is created and I'm aware of the note that the
package is optimized for column-oriented ones, but I'm only interested
in using it for holding my sparse row-oriented data and doing basic
subsetting by rows (even using drop=FALSE).

Here is what I get when I set up a column-oriented sparse Matrix:

> Cc <- Matrix(0, nrow=5, ncol=5, sparse=TRUE)
> Cc[1:3,1] <- 1
> Cc
5 x 5 sparse Matrix of class "dgCMatrix"

[1,] 1 . . . .
[2,] 1 . . . .
[3,] 1 . . . .
[4,] . . . . .
[5,] . . . . .
> str(Cc)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i   : int [1:3] 0 1 2
  ..@ p   : int [1:6] 0 3 3 3 3 3
  ..@ Dim : int [1:2] 5 5
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ x   : num [1:3] 1 1 1
  ..@ factors : list()

When I try to do the analogue for a row-oriented matrix, I get a
"dgTMatrix", whereas I would expect a "dgRMatrix":

> Cr <- Matrix(0, nrow=5, ncol=5, sparse=TRUE)
> Cr <- as(Cr, "dsRMatrix")
> Cr[1,1:3] <- 1
> Cr
5 x 5 sparse Matrix of class "dgTMatrix"

[1,] 1 1 1 . .
[2,] . . . . .
[3,] . . . . .
[4,] . . . . .
[5,] . . . . .
> str(Cr)
Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
  ..@ i   : int [1:3] 0 0 0
  ..@ j   : int [1:3] 0 1 2
  ..@ Dim : int [1:2] 5 5
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ x   : num [1:3] 1 1 1
  ..@ factors : list()


Trying with explicit coercion does not work:

> as(Cc, "dgRMatrix")
Error in as(Cc, "dgRMatrix") :
  no method or default for coercing "dgCMatrix" to "dgRMatrix"

> as(Cr, "dgRMatrix")
Error in as(Cr, "dgRMatrix") :
  no method or default for coercing "dgTMatrix" to "dgRMatrix"


Am I doing some wrong here?  Or is this what means that the package is
optimized for the column-oriented representation and I shouldn't
really work with row-oriented ones?  I'm really only interested in
access to efficient Cr[row,,drop=FALSE] subsetting (and a small memory
footprint).

Thanks,

Henrik

__
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] installation of dplyr

[Ben Tupper]

Hi,

OK - that can be fixed by our IT whizzes.  

Thanks,
Ben

P.S.  Thanks for dplyr!

> On Apr 19, 2016, at 4:10 PM, Hadley Wickham  wrote:
> 
> You normally see these errors when compiling on a vm that has very
> little memory.
> Hadley
> 
> On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
>> Hello,
>> 
>> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
>> 3.2.3, including dplyr package. I am unable to successfully install it.  
>> Below I show the failed installation using utils::install.packages() and 
>> then again using devtools::install_github().  Each yields an error similar 
>> to the other but not quite exactly the same - the error messages sail right 
>> over my head.
>> 
>> I can contact the package author if that would be better, but thought it 
>> best to start here.
>> 
>> Thanks!
>> Ben
>> 
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>> 
>>> sessionInfo()
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> Running under: CentOS release 6.7 (Final)
>> 
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>> [9] LC_ADDRESS=C   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> 
>> 
>> 
>> #   utils::install.packages()
>> 
>> 
>>> install.packages("dplyr", repo = "http://cran.r-project.org;)
>> Installing package into ‘/usr/lib64/R/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
>> Content type 'application/x-gzip' length 655997 bytes (640 KB)
>> ==
>> downloaded 640 KB
>> 
>> * installing *source* package ‘dplyr’ ...
>> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
>> ** libs
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
>> RcppExports.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
>> In file included from ../inst/include/dplyr.h:131,
>> from arrange.cpp:1:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
>> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
>> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
>> used uninitialized in this function
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
>> combine_variables.o
>> g++ 

Re: [R] installation of dplyr

[Hadley Wickham]

You normally see these errors when compiling on a vm that has very
little memory.
Hadley

On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
> Hello,
>
> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
> 3.2.3, including dplyr package. I am unable to successfully install it.  
> Below I show the failed installation using utils::install.packages() and then 
> again using devtools::install_github().  Each yields an error similar to the 
> other but not quite exactly the same - the error messages sail right over my 
> head.
>
> I can contact the package author if that would be better, but thought it best 
> to start here.
>
> Thanks!
> Ben
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
>> sessionInfo()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: CentOS release 6.7 (Final)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
>
>
> 
> #   utils::install.packages()
> 
>
>> install.packages("dplyr", repo = "http://cran.r-project.org;)
> Installing package into ‘/usr/lib64/R/library’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
> Content type 'application/x-gzip' length 655997 bytes (640 KB)
> ==
> downloaded 640 KB
>
> * installing *source* package ‘dplyr’ ...
> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
> ** libs
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
> RcppExports.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
> In file included from ../inst/include/dplyr.h:131,
>  from arrange.cpp:1:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
> used uninitialized in this function
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
> combine_variables.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 

Re: [R] Interquartile Range

[William Dunlap via R-help]

If you show us, not just tell us about, a self-contained example
someone might show you a non-hacky way of getting the job done.
(I don't see an argument to plyr::ddply called 'transform'.)

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Apr 19, 2016 at 12:18 PM, Michael Artz 
wrote:

> Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!  I
> ended up just using the transform argument in the ddply function.  It
> worked and it repeated, then I called a mode function in another call to
> ddply that summarised.  Kinda hacky but oh well!
>
> On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter 
> wrote:
>
>> ... and I'm getting another cup of coffee...
>>
>> -- Bert
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>
>>
>> On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter 
>> wrote:
>> > NO NO  -- I am wrong! The paste() expression is of course evaluated.
>> > It's just that a character string is returned of the form "something -
>> > something".
>> >
>> > I apologize for the confusion.
>> >
>> > -- Bert
>> >
>> >
>> >
>> >
>> > Bert Gunter
>> >
>> > "The trouble with having an open mind is that people keep coming along
>> > and sticking things into it."
>> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> >
>> >
>> > On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter 
>> wrote:
>> >> To be precise:
>> >>
>> >> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> >>
>> >> is an expression that evaluates to a character string:
>> >> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
>> >>
>> >> no matter what the argument of your function, x. Hence
>> >>
>> >> return(paste(...)) will return this exact character string and never
>> >> evaluates x.
>> >>
>> >>
>> >> Cheers,
>> >> Bert
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Bert Gunter
>> >>
>> >> "The trouble with having an open mind is that people keep coming along
>> >> and sticking things into it."
>> >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> >>
>> >>
>> >> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
>> >>  wrote:
>>  That didn't work Jim!
>> >>>
>> >>> It always helps to say how the suggestion did not work.  Jim's
>> >>> function had a typo in it - was that the problem?  Or did you not
>> >>> change the call to ddply to use that function.  Here is something
>> >>> that might "work" for you:
>> >>>
>> >>>  library(plyr)
>> >>>
>> >>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>> >>>  myIqr <- function(x) {
>> >>>
>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> >>>  }
>> >>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
>> >>> col1_IQR=stats::IQR(col1))
>> >>>  #  groupColumn col1_myIqr col1_IQR
>> >>>  #1   11-10
>> >>>  #2   22-41
>> >>>  #3   3  12-24   12
>> >>>  #4   4112-320  208
>> >>>  #5   5  2048-8192 6144
>> >>>
>> >>> The important point is that
>> >>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> >>> is not a function, it is an expression.   ddplyr wants functions.
>> >>>
>> >>>
>> >>> Bill Dunlap
>> >>> TIBCO Software
>> >>> wdunlap tibco.com
>> >>>
>> >>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz > >
>> >>> wrote:
>> >>>
>>  That didn't work Jim!
>> 
>>  Thanks anyway
>> 
>>  On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon 
>> wrote:
>> 
>>  > Hi Michael,
>>  > At a guess, try this:
>>  >
>>  > iqr<-function(x) {
>>  >
>> 
>> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>  > }
>>  >
>>  > .col3_Range=iqr(datat$tenure)
>>  >
>>  > Jim
>>  >
>>  >
>>  >
>>  > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz <
>> michaelea...@gmail.com>
>>  > wrote:
>>  > > Hi,
>>  > >   I am trying to show an interquartile range while grouping
>> values
>>  using
>>  > > the function ddply().  So my function call now is like
>>  > >
>>  > > groupedAll <- ddply(data
>>  > >  ,~groupColumn
>>  > >  ,summarise
>>  > >  ,col1_mean=mean(col1)
>>  > >  ,col2_mode=Mode(col2) #Function I wrote for
>> getting
>>  the
>>  > > mode shown below
>>  > >
>>  > >
>> ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>>  > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>>  > >  )
>>  > >
>>  > > #custom Mode function
>>  > > Mode <- function(x) {
>>  > >   ux <- unique(x)
>> 

[R] installation of dplyr

[Ben Tupper]

Hello,

I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
3.2.3, including dplyr package. I am unable to successfully install it.  Below 
I show the failed installation using utils::install.packages() and then again 
using devtools::install_github().  Each yields an error similar to the other 
but not quite exactly the same - the error messages sail right over my head.

I can contact the package author if that would be better, but thought it best 
to start here.

Thanks!
Ben

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base   
  



#   utils::install.packages()


> install.packages("dplyr", repo = "http://cran.r-project.org;)
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
Content type 'application/x-gzip' length 655997 bytes (640 KB)
==
downloaded 640 KB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
In file included from ../inst/include/dplyr.h:131,
 from arrange.cpp:1:
../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
used uninitialized in this function
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
combine_variables.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic  -c distinct.cpp -o distinct.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
-I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
-I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions 

Re: [R] Interquartile Range

[Michael Artz]

Oh thanks for that clarification Bert!  Hope you enjoyed your coffee!  I
ended up just using the transform argument in the ddply function.  It
worked and it repeated, then I called a mode function in another call to
ddply that summarised.  Kinda hacky but oh well!

On Tue, Apr 19, 2016 at 12:31 PM, Bert Gunter 
wrote:

> ... and I'm getting another cup of coffee...
>
> -- Bert
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter 
> wrote:
> > NO NO  -- I am wrong! The paste() expression is of course evaluated.
> > It's just that a character string is returned of the form "something -
> > something".
> >
> > I apologize for the confusion.
> >
> > -- Bert
> >
> >
> >
> >
> > Bert Gunter
> >
> > "The trouble with having an open mind is that people keep coming along
> > and sticking things into it."
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >
> >
> > On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter 
> wrote:
> >> To be precise:
> >>
> >> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> >>
> >> is an expression that evaluates to a character string:
> >> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
> >>
> >> no matter what the argument of your function, x. Hence
> >>
> >> return(paste(...)) will return this exact character string and never
> >> evaluates x.
> >>
> >>
> >> Cheers,
> >> Bert
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Bert Gunter
> >>
> >> "The trouble with having an open mind is that people keep coming along
> >> and sticking things into it."
> >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >>
> >>
> >> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
> >>  wrote:
>  That didn't work Jim!
> >>>
> >>> It always helps to say how the suggestion did not work.  Jim's
> >>> function had a typo in it - was that the problem?  Or did you not
> >>> change the call to ddply to use that function.  Here is something
> >>> that might "work" for you:
> >>>
> >>>  library(plyr)
> >>>
> >>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
> >>>  myIqr <- function(x) {
> >>>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> >>>  }
> >>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
> >>> col1_IQR=stats::IQR(col1))
> >>>  #  groupColumn col1_myIqr col1_IQR
> >>>  #1   11-10
> >>>  #2   22-41
> >>>  #3   3  12-24   12
> >>>  #4   4112-320  208
> >>>  #5   5  2048-8192 6144
> >>>
> >>> The important point is that
> >>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> >>> is not a function, it is an expression.   ddplyr wants functions.
> >>>
> >>>
> >>> Bill Dunlap
> >>> TIBCO Software
> >>> wdunlap tibco.com
> >>>
> >>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
> >>> wrote:
> >>>
>  That didn't work Jim!
> 
>  Thanks anyway
> 
>  On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon 
> wrote:
> 
>  > Hi Michael,
>  > At a guess, try this:
>  >
>  > iqr<-function(x) {
>  >
> 
> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>  > }
>  >
>  > .col3_Range=iqr(datat$tenure)
>  >
>  > Jim
>  >
>  >
>  >
>  > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz <
> michaelea...@gmail.com>
>  > wrote:
>  > > Hi,
>  > >   I am trying to show an interquartile range while grouping values
>  using
>  > > the function ddply().  So my function call now is like
>  > >
>  > > groupedAll <- ddply(data
>  > >  ,~groupColumn
>  > >  ,summarise
>  > >  ,col1_mean=mean(col1)
>  > >  ,col2_mode=Mode(col2) #Function I wrote for
> getting
>  the
>  > > mode shown below
>  > >
>  > >
> ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>  > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>  > >  )
>  > >
>  > > #custom Mode function
>  > > Mode <- function(x) {
>  > >   ux <- unique(x)
>  > >   ux[which.max(tabulate(match(x, ux)))]
>  > > }
>  > >
>  > > I am not sre what is going wrong on my interquartile range
> function, it
>  > > works on its own outside of ddply()
>  > >
>  > > [[alternative HTML version deleted]]
>  > >
>  > > __
>  > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>  > > https://stat.ethz.ch/mailman/listinfo/r-help
>  > > 

Re: [R] Problem with X11

[klerer]

Dear Lorenzo, Dear R list,[a] to all recipients: sorry, this email is 
html-against my own believes and because of inevitable constraints so far.[b] 
to Lorenzo: "...and I have recently update my R environment" sounds as that 
would be a gift of heaven! How did you manage to update and how exactly went 
the process of updating the whole R environment, as you put it? I turn to you 
since I have not received an understandable answer to that question yet (see 
[d] below for sessionInfo() details).[c] to all R users: I use as OS a debian 
derivative (Kubuntu) long-term service version; this spring/ early summer as I 
was told, a new LTS would be released. Has a new/ revised R version in release 
in 2016 any Achille's heel that is already known? I perceive that some of the 
(package) update issues I experience might be due to OS compatibility (see [d] 
below for sessionInfo() details).[d]> sessionInfo()R version 3.0.2 
(2013-09-25)Platform: x86_64-pc-linux-gnu (64-bit)locale: [1]
LC_CTYPE=de_DE.UTF-8  LC_NUMERIC=C  [3] 
LC_TIME=de_DE.UTF-8   LC_COLLATE=de_DE.UTF-8    [5] 
LC_MONETARY=de_DE.UTF-8   LC_MESSAGES=de_DE.UTF-8   [7] 
LC_PAPER=de_DE.UTF-8  LC_NAME=de_DE.UTF-8   [9] 
LC_ADDRESS=de_DE.UTF-8    LC_TELEPHONE=de_DE.UTF-8 [11] 
LC_MEASUREMENT=de_DE.UTF-8    LC_IDENTIFICATION=de_DE.UTF-8attached base 
packages:[1] stats graphics  grDevices utils datasets  methods   base   
  other attached packages:[1] rkward_0.6.1loaded via a namespace (and not 
attached):[1] tools_3.0.2Best regards,Markus HofstetterLorenzo Isella 
 schrieb (19.04.2016 17:23):Dear All,
I have never had this problem before. I run debian testing on my box
and I have recently update my R environment.
Now, see what happens when I try the most trivial of all plots

> plot(seq(22))
Error in (function (display = "", width, height, pointsize, gamma, bg,
:
  X11 module cannot be loaded
  In addition: Warning message:
  In (function (display = "", width, height, pointsize, gamma, bg,  :
unable to load shared object '/usr/lib/R/modules//R_X11.so':
  /usr/lib/x86_64-linux-gnu/libpng12.so.0: version `PNG12_0' not
  found (required by /usr/lib/R/modules//R_X11.so)

and this is my sessionInfo()

> sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_GB.utf8   LC_NUMERIC=C
  [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
   [5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base


Anybody understands what is going on here?
Regards

Lorenzo

__
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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.


[[alternative HTML version deleted]]

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

Re: [R] Problem with X11

[Tom Wright]

I don't have my debian box available so can't confirm. But I would try
$apt-get install libpng

On Tue, Apr 19, 2016 at 11:23 AM, Lorenzo Isella 
wrote:

> Dear All,
> I have never had this problem before. I run debian testing on my box
> and I have recently update my R environment.
> Now, see what happens when I try the most trivial of all plots
>
> plot(seq(22))
>>
> Error in (function (display = "", width, height, pointsize, gamma, bg,
> :
>  X11 module cannot be loaded
>  In addition: Warning message:
>  In (function (display = "", width, height, pointsize, gamma, bg,  :
>unable to load shared object '/usr/lib/R/modules//R_X11.so':
>  /usr/lib/x86_64-linux-gnu/libpng12.so.0: version `PNG12_0' not
>  found (required by /usr/lib/R/modules//R_X11.so)
>
> and this is my sessionInfo()
>
> sessionInfo()
>>
> R version 3.2.4 Revised (2016-03-16 r70336)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux stretch/sid
>
> locale:
> [1] LC_CTYPE=en_GB.utf8   LC_NUMERIC=C
>  [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8
>[7] LC_PAPER=en_GB.utf8   LC_NAME=C
> [9] LC_ADDRESS=C  LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
>
> Anybody understands what is going on here?
> Regards
>
> Lorenzo
>
> __
> 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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R-es] Script sin resultados completos

[Manuel Máquez]

Hola Colegas:
Tengo el siguiente script donde no se en donde esta el error, ojalá que
alguno de ustedes me pueda ayudar.
Anticipo las gracias más cumplidas por anticipado.
bas <- read.csv('TAB.csv', header = F)
sv <- 0
sm <- 0
lg <- 0
smas <- matrix (1:390)
for (i in 1:39) {
#   if (i == 8) {break}
   for (j in 1:10) {
  #  sm[i] <- 0
  sm[j] <- 0
  for (k in 1:127) {
 if(bas[i,k] == 0) next(j)
 if(bas[i, k] == j)
sm[j] <- sm[j] + 1
 #   smas <- matrix (sm, 10, i)
 sv[j*i] <- sm[j]
 smas <- matrix (sv, 39, i, byrow = T)
 lg <- lg + sm[j]  # sm es el ultimo valor de sm
 #  sm[j + 1] <- 0
  }  # de k
   }  # de j
}  # de i
# ME DA warnings PERO DA RESULTADOS INCORRECTOS
# AL PONER smas [,2] da 17 10 8 3 7 4 3 9 6 10 debiendo ser 17 19 16 9 5 11
5 2 5 3
# AL PONER smas [,3] da 10 17 10 8 3 7 4 3 9 6 debiendo ser 16 15 9 11 8 9
7 5 3 2

sv tampoco me proporciona resultados completos; parece que al cambiar de i
<- 1 a 2 se le perdiera la pista de en dónde se encuentra y la verdad no
encuentro de donde toma los resultados que saca; lo que sí me parece es que
recicla algún otro vector.
Adjunto el archivo Tab.csv.
Reitero las gracias por la atención que se sirvan darme.
Atentamente,

*MANOLO MÁRQUEZ P.*
5,3,5,7,1,1,4,2,4,10,10,2,1,11,1,2,5,9,5,14,13,9,2,4,2,3,1,2,16,4,1,5,8,2,1,2,2,1,6,5,11,13,8,2,3,3,20,17,4,11,1,3,2,7,8,8,2,5,3,1,1,5,9,3,4,9,1,1,1,3,9,4,9,9,3,8,8,4,10,1,1,3,10,2,5,9,8,3,5,9,1,5,4,1,3,2,2,13,31,5,3,4,1,2,4,4,2,9,7,7,16,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
6,1,1,3,2,2,1,6,7,2,3,1,14,10,2,11,4,2,25,3,3,2,2,1,8,1,6,2,6,2,6,4,15,4,1,3,1,4,6,9,12,6,8,7,9,5,2,3,10,2,3,6,3,1,9,2,4,1,5,3,3,1,5,3,1,12,11,3,2,6,4,11,1,16,1,2,7,10,19,19,1,2,6,2,20,1,7,3,4,5,2,7,11,16,2,21,4,9,11,2,6,3,3,9,5,3,1,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
4,1,18,5,6,3,1,13,1,7,6,7,15,3,2,7,2,2,13,2,6,1,17,4,14,1,5,1,2,2,5,8,3,8,2,2,6,4,5,2,2,2,14,5,3,1,9,4,1,17,1,4,4,1,4,5,7,3,6,6,12,9,9,2,2,13,15,6,3,1,4,8,7,2,11,5,10,14,15,5,4,16,10,1,6,3,7,7,8,2,15,6,1,3,8,4,22,1,4,1,3,12,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
4,9,9,5,1,1,1,7,10,8,17,3,1,5,7,1,6,6,11,7,14,9,2,6,4,1,10,1,3,1,5,4,1,1,13,10,7,5,3,2,1,2,6,1,3,11,2,1,1,1,3,1,8,4,3,7,11,15,4,1,10,3,2,10,1,6,3,2,2,10,16,4,3,1,1,24,5,2,2,1,5,4,3,3,2,2,8,1,6,7,4,7,1,1,2,15,3,3,3,9,3,1,5,7,2,3,13,2,1,1,2,2,12,6,6,5,1,2,16,3,1,12,3,0,0,0,0,0,0,0
2,5,1,8,11,13,10,2,4,1,3,3,20,1,1,4,8,1,5,3,11,7,5,17,5,3,2,16,4,13,1,4,4,4,15,20,11,8,4,2,3,5,1,1,1,25,3,8,2,9,5,14,3,6,11,2,20,9,2,2,21,2,3,22,3,6,5,6,9,21,2,4,2,4,1,2,2,2,5,1,1,15,2,5,4,19,6,6,5,5,10,3,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1,1,6,3,1,17,1,3,10,5,7,1,2,6,1,1,4,8,10,1,3,4,1,2,2,11,1,1,8,13,3,5,13,3,2,2,7,8,11,9,5,1,8,2,1,2,8,3,7,2,1,11,1,2,2,6,3,2,1,10,4,6,2,7,13,5,13,8,3,9,3,6,3,4,1,17,7,18,10,1,1,10,9,2,1,13,1,1,15,1,1,4,2,8,3,21,3,6,5,1,21,15,6,4,1,2,1,8,1,2,1,5,1,2,1,8,1,0,0,0,0,0,0,0,0,0,0,0,0,0
5,10,5,17,1,3,10,1,6,2,2,5,9,5,17,3,1,1,3,3,3,16,8,3,3,7,2,18,12,5,1,9,5,1,2,3,4,1,6,1,2,4,1,6,16,8,3,5,3,4,12,2,1,1,3,11,6,3,7,2,4,3,1,3,6,17,25,1,6,3,1,6,3,1,2,2,9,6,2,10,5,16,11,1,7,24,1,2,8,10,6,1,3,1,11,8,6,7,8,1,5,10,4,1,5,6,1,4,7,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
2,8,3,3,5,3,10,2,3,8,10,4,13,8,5,16,1,5,3,1,3,14,3,1,9,4,1,23,14,1,8,2,7,2,4,1,11,1,1,9,2,6,3,12,2,6,6,2,6,5,4,6,10,7,19,1,4,2,14,6,4,2,1,2,5,14,10,6,5,3,2,4,8,1,7,7,5,2,11,2,1,9,4,2,5,6,6,2,4,2,9,7,13,5,2,3,10,7,3,1,7,1,4,14,1,13,4,7,2,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
6,3,5,10,3,6,1,1,19,9,19,5,4,1,12,4,2,11,1,5,10,1,1,9,1,4,15,5,8,1,2,5,9,2,3,2,9,1,5,4,8,4,2,9,6,5,5,4,13,8,32,1,9,1,2,1,8,1,15,30,3,3,4,21,9,3,1,5,6,4,9,2,4,5,11,4,6,1,2,1,1,2,15,4,1,5,2,9,1,6,5,10,2,7,1,18,19,3,4,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
8,7,26,8,6,1,3,4,2,6,4,4,1,3,15,2,8,5,3,27,3,6,6,2,20,3,1,1,3,1,3,6,25,3,1,10,3,6,14,8,5,1,12,5,14,1,4,4,10,5,13,5,9,7,5,2,8,9,1,5,2,5,1,1,5,25,4,5,3,3,1,9,2,2,4,5,3,1,5,4,1,3,2,11,2,2,8,10,5,2,1,3,4,6,3,2,1,1,1,1,8,7,2,6,8,1,3,2,1,12,3,1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
6,2,1,10,6,5,1,7,3,13,1,3,8,13,6,11,6,6,1,6,1,6,1,5,3,8,12,11,1,5,6,14,5,1,2,13,9,13,7,11,9,1,18,1,17,6,1,2,1,3,2,15,6,1,3,3,12,1,5,7,8,5,6,9,1,5,3,23,15,7,1,3,6,2,7,5,4,2,1,3,4,12,7,4,1,2,5,6,16,15,10,7,1,2,1,7,2,1,3,3,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
11,2,4,7,2,7,23,12,1,4,4,2,16,12,10,2,4,4,1,7,6,3,3,5,7,14,8,4,3,2,1,13,4,3,12,1,14,5,11,5,5,6,1,21,1,1,10,7,12,13,1,4,3,6,3,4,12,4,1,1,3,5,13,2,2,11,1,3,2,1,6,1,10,12,2,1,2,2,1,8,5,1,3,5,4,5,22,1,9,2,4,11,4,2,1,5,1,4,1,8,2,2,4,1,4,15,5,3,5,3,3,2,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1,1,2,1,5,19,8,4,4,5,1,2,7,13,2,8,2,5,3,1,8,25,4,1,16,1,4,5,5,15,5,11,19,4,4,5,3,3,10,2,12,1,8,1,6,12,8,2,3,8,5,3,1,1,6,1,2,7,7,3,5,4,1,3,4,1,5,4,7,6,1,2,11,8,1,1,17,5,2,1,1,5,9,3,6,6,6,9,1,2,2,1,5,2,8,6,10,18,20,1,11,23,2,1,10,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Re: [R] Interquartile Range

[Bert Gunter]

... and I'm getting another cup of coffee...

-- Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 10:30 AM, Bert Gunter  wrote:
> NO NO  -- I am wrong! The paste() expression is of course evaluated.
> It's just that a character string is returned of the form "something -
> something".
>
> I apologize for the confusion.
>
> -- Bert
>
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter  wrote:
>> To be precise:
>>
>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>
>> is an expression that evaluates to a character string:
>> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
>>
>> no matter what the argument of your function, x. Hence
>>
>> return(paste(...)) will return this exact character string and never
>> evaluates x.
>>
>>
>> Cheers,
>> Bert
>>
>>
>>
>>
>>
>>
>>
>>
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>
>>
>> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
>>  wrote:
 That didn't work Jim!
>>>
>>> It always helps to say how the suggestion did not work.  Jim's
>>> function had a typo in it - was that the problem?  Or did you not
>>> change the call to ddply to use that function.  Here is something
>>> that might "work" for you:
>>>
>>>  library(plyr)
>>>
>>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>>>  myIqr <- function(x) {
>>>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>>  }
>>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
>>> col1_IQR=stats::IQR(col1))
>>>  #  groupColumn col1_myIqr col1_IQR
>>>  #1   11-10
>>>  #2   22-41
>>>  #3   3  12-24   12
>>>  #4   4112-320  208
>>>  #5   5  2048-8192 6144
>>>
>>> The important point is that
>>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> is not a function, it is an expression.   ddplyr wants functions.
>>>
>>>
>>> Bill Dunlap
>>> TIBCO Software
>>> wdunlap tibco.com
>>>
>>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
>>> wrote:
>>>
 That didn't work Jim!

 Thanks anyway

 On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:

 > Hi Michael,
 > At a guess, try this:
 >
 > iqr<-function(x) {
 >
 return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
 > }
 >
 > .col3_Range=iqr(datat$tenure)
 >
 > Jim
 >
 >
 >
 > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
 > wrote:
 > > Hi,
 > >   I am trying to show an interquartile range while grouping values
 using
 > > the function ddply().  So my function call now is like
 > >
 > > groupedAll <- ddply(data
 > >  ,~groupColumn
 > >  ,summarise
 > >  ,col1_mean=mean(col1)
 > >  ,col2_mode=Mode(col2) #Function I wrote for getting
 the
 > > mode shown below
 > >
 > >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
 > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
 > >  )
 > >
 > > #custom Mode function
 > > Mode <- function(x) {
 > >   ux <- unique(x)
 > >   ux[which.max(tabulate(match(x, ux)))]
 > > }
 > >
 > > I am not sre what is going wrong on my interquartile range function, it
 > > works on its own outside of ddply()
 > >
 > > [[alternative HTML version deleted]]
 > >
 > > __
 > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 > > https://stat.ethz.ch/mailman/listinfo/r-help
 > > PLEASE do read the posting guide
 > http://www.R-project.org/posting-guide.html
 > > and provide commented, minimal, self-contained, reproducible code.
 >

 [[alternative HTML version deleted]]

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

>>>
>>> [[alternative HTML version deleted]]
>>>
>>> 

Re: [R] Interquartile Range

[Bert Gunter]

NO NO  -- I am wrong! The paste() expression is of course evaluated.
It's just that a character string is returned of the form "something -
something".

I apologize for the confusion.

-- Bert




Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 10:25 AM, Bert Gunter  wrote:
> To be precise:
>
> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>
> is an expression that evaluates to a character string:
> "round(quantile(x,.25),0) - round(quantile(x,0.75),0)"
>
> no matter what the argument of your function, x. Hence
>
> return(paste(...)) will return this exact character string and never
> evaluates x.
>
>
> Cheers,
> Bert
>
>
>
>
>
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
>  wrote:
>>> That didn't work Jim!
>>
>> It always helps to say how the suggestion did not work.  Jim's
>> function had a typo in it - was that the problem?  Or did you not
>> change the call to ddply to use that function.  Here is something
>> that might "work" for you:
>>
>>  library(plyr)
>>
>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>>  myIqr <- function(x) {
>>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>  }
>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
>> col1_IQR=stats::IQR(col1))
>>  #  groupColumn col1_myIqr col1_IQR
>>  #1   11-10
>>  #2   22-41
>>  #3   3  12-24   12
>>  #4   4112-320  208
>>  #5   5  2048-8192 6144
>>
>> The important point is that
>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> is not a function, it is an expression.   ddplyr wants functions.
>>
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
>> wrote:
>>
>>> That didn't work Jim!
>>>
>>> Thanks anyway
>>>
>>> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>>>
>>> > Hi Michael,
>>> > At a guess, try this:
>>> >
>>> > iqr<-function(x) {
>>> >
>>> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> > }
>>> >
>>> > .col3_Range=iqr(datat$tenure)
>>> >
>>> > Jim
>>> >
>>> >
>>> >
>>> > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
>>> > wrote:
>>> > > Hi,
>>> > >   I am trying to show an interquartile range while grouping values
>>> using
>>> > > the function ddply().  So my function call now is like
>>> > >
>>> > > groupedAll <- ddply(data
>>> > >  ,~groupColumn
>>> > >  ,summarise
>>> > >  ,col1_mean=mean(col1)
>>> > >  ,col2_mode=Mode(col2) #Function I wrote for getting
>>> the
>>> > > mode shown below
>>> > >
>>> > >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>>> > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>>> > >  )
>>> > >
>>> > > #custom Mode function
>>> > > Mode <- function(x) {
>>> > >   ux <- unique(x)
>>> > >   ux[which.max(tabulate(match(x, ux)))]
>>> > > }
>>> > >
>>> > > I am not sre what is going wrong on my interquartile range function, it
>>> > > works on its own outside of ddply()
>>> > >
>>> > > [[alternative HTML version deleted]]
>>> > >
>>> > > __
>>> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> > > https://stat.ethz.ch/mailman/listinfo/r-help
>>> > > PLEASE do read the posting guide
>>> > http://www.R-project.org/posting-guide.html
>>> > > and provide commented, minimal, self-contained, reproducible code.
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> 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 

Re: [R] Interquartile Range

[Bert Gunter]

To be precise:

paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")

is an expression that evaluates to a character string:
"round(quantile(x,.25),0) - round(quantile(x,0.75),0)"

no matter what the argument of your function, x. Hence

return(paste(...)) will return this exact character string and never
evaluates x.


Cheers,
Bert








Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 8:34 AM, William Dunlap via R-help
 wrote:
>> That didn't work Jim!
>
> It always helps to say how the suggestion did not work.  Jim's
> function had a typo in it - was that the problem?  Or did you not
> change the call to ddply to use that function.  Here is something
> that might "work" for you:
>
>  library(plyr)
>
>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>  myIqr <- function(x) {
>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>  }
>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
> col1_IQR=stats::IQR(col1))
>  #  groupColumn col1_myIqr col1_IQR
>  #1   11-10
>  #2   22-41
>  #3   3  12-24   12
>  #4   4112-320  208
>  #5   5  2048-8192 6144
>
> The important point is that
> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> is not a function, it is an expression.   ddplyr wants functions.
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
> wrote:
>
>> That didn't work Jim!
>>
>> Thanks anyway
>>
>> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>>
>> > Hi Michael,
>> > At a guess, try this:
>> >
>> > iqr<-function(x) {
>> >
>> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> > }
>> >
>> > .col3_Range=iqr(datat$tenure)
>> >
>> > Jim
>> >
>> >
>> >
>> > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
>> > wrote:
>> > > Hi,
>> > >   I am trying to show an interquartile range while grouping values
>> using
>> > > the function ddply().  So my function call now is like
>> > >
>> > > groupedAll <- ddply(data
>> > >  ,~groupColumn
>> > >  ,summarise
>> > >  ,col1_mean=mean(col1)
>> > >  ,col2_mode=Mode(col2) #Function I wrote for getting
>> the
>> > > mode shown below
>> > >
>> > >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>> > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>> > >  )
>> > >
>> > > #custom Mode function
>> > > Mode <- function(x) {
>> > >   ux <- unique(x)
>> > >   ux[which.max(tabulate(match(x, ux)))]
>> > > }
>> > >
>> > > I am not sre what is going wrong on my interquartile range function, it
>> > > works on its own outside of ddply()
>> > >
>> > > [[alternative HTML version deleted]]
>> > >
>> > > __
>> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > > https://stat.ethz.ch/mailman/listinfo/r-help
>> > > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> [[alternative HTML version deleted]]
>
> __
> 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] Interquartile Range

[William Dunlap via R-help]

Can you show us a self-contained example, along with the output of
running conflicts()?

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Apr 19, 2016 at 8:57 AM, Michael Artz 
wrote:

> HI that did not work for me either.  The value I got returned from that
> function was " - "  :(. thanks for the reply
> through
>
> On Tue, Apr 19, 2016 at 10:34 AM, William Dunlap 
> wrote:
>
>> > That didn't work Jim!
>>
>> It always helps to say how the suggestion did not work.  Jim's
>> function had a typo in it - was that the problem?  Or did you not
>> change the call to ddply to use that function.  Here is something
>> that might "work" for you:
>>
>>  library(plyr)
>>
>>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>>  myIqr <- function(x) {
>>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>  }
>>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
>> col1_IQR=stats::IQR(col1))
>>  #  groupColumn col1_myIqr col1_IQR
>>  #1   11-10
>>  #2   22-41
>>  #3   3  12-24   12
>>  #4   4112-320  208
>>  #5   5  2048-8192 6144
>>
>> The important point is that
>> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> is not a function, it is an expression.   ddplyr wants functions.
>>
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
>> wrote:
>>
>>> That didn't work Jim!
>>>
>>> Thanks anyway
>>>
>>> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>>>
>>> > Hi Michael,
>>> > At a guess, try this:
>>> >
>>> > iqr<-function(x) {
>>> >
>>> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>>> > }
>>> >
>>> > .col3_Range=iqr(datat$tenure)
>>> >
>>> > Jim
>>> >
>>> >
>>> >
>>> > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz >> >
>>> > wrote:
>>> > > Hi,
>>> > >   I am trying to show an interquartile range while grouping values
>>> using
>>> > > the function ddply().  So my function call now is like
>>> > >
>>> > > groupedAll <- ddply(data
>>> > >  ,~groupColumn
>>> > >  ,summarise
>>> > >  ,col1_mean=mean(col1)
>>> > >  ,col2_mode=Mode(col2) #Function I wrote for getting
>>> the
>>> > > mode shown below
>>> > >
>>> > >
>>> ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>>> > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>>> > >  )
>>> > >
>>> > > #custom Mode function
>>> > > Mode <- function(x) {
>>> > >   ux <- unique(x)
>>> > >   ux[which.max(tabulate(match(x, ux)))]
>>> > > }
>>> > >
>>> > > I am not sre what is going wrong on my interquartile range function,
>>> it
>>> > > works on its own outside of ddply()
>>> > >
>>> > > [[alternative HTML version deleted]]
>>> > >
>>> > > __
>>> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> > > https://stat.ethz.ch/mailman/listinfo/r-help
>>> > > PLEASE do read the posting guide
>>> > http://www.R-project.org/posting-guide.html
>>> > > and provide commented, minimal, self-contained, reproducible code.
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>

[[alternative HTML version deleted]]

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

Re: [R] Interquartile Range

[Michael Artz]

HI that did not work for me either.  The value I got returned from that
function was " - "  :(. thanks for the reply
through

On Tue, Apr 19, 2016 at 10:34 AM, William Dunlap  wrote:

> > That didn't work Jim!
>
> It always helps to say how the suggestion did not work.  Jim's
> function had a typo in it - was that the problem?  Or did you not
> change the call to ddply to use that function.  Here is something
> that might "work" for you:
>
>  library(plyr)
>
>  data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
>  myIqr <- function(x) {
>  paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>  }
>  ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
> col1_IQR=stats::IQR(col1))
>  #  groupColumn col1_myIqr col1_IQR
>  #1   11-10
>  #2   22-41
>  #3   3  12-24   12
>  #4   4112-320  208
>  #5   5  2048-8192 6144
>
> The important point is that
> paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> is not a function, it is an expression.   ddplyr wants functions.
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
> wrote:
>
>> That didn't work Jim!
>>
>> Thanks anyway
>>
>> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>>
>> > Hi Michael,
>> > At a guess, try this:
>> >
>> > iqr<-function(x) {
>> >
>> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> > }
>> >
>> > .col3_Range=iqr(datat$tenure)
>> >
>> > Jim
>> >
>> >
>> >
>> > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
>> > wrote:
>> > > Hi,
>> > >   I am trying to show an interquartile range while grouping values
>> using
>> > > the function ddply().  So my function call now is like
>> > >
>> > > groupedAll <- ddply(data
>> > >  ,~groupColumn
>> > >  ,summarise
>> > >  ,col1_mean=mean(col1)
>> > >  ,col2_mode=Mode(col2) #Function I wrote for getting
>> the
>> > > mode shown below
>> > >
>> > >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>> > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>> > >  )
>> > >
>> > > #custom Mode function
>> > > Mode <- function(x) {
>> > >   ux <- unique(x)
>> > >   ux[which.max(tabulate(match(x, ux)))]
>> > > }
>> > >
>> > > I am not sre what is going wrong on my interquartile range function,
>> it
>> > > works on its own outside of ddply()
>> > >
>> > > [[alternative HTML version deleted]]
>> > >
>> > > __
>> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > > https://stat.ethz.ch/mailman/listinfo/r-help
>> > > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>

[[alternative HTML version deleted]]

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

Re: [R] Problem with X11

[Rainer Schuermann]

Probably wrong list, but anyway:
Same problem here, after a 
   apt-get dist-upgrade


On Tuesday, April 19, 2016 05:23:37 PM Lorenzo Isella wrote:
> Dear All,
> I have never had this problem before. I run debian testing on my box
> and I have recently update my R environment.
> Now, see what happens when I try the most trivial of all plots
> 
> > plot(seq(22))
> Error in (function (display = "", width, height, pointsize, gamma, bg,
> :
>   X11 module cannot be loaded
>   In addition: Warning message:
>   In (function (display = "", width, height, pointsize, gamma, bg,  :
> unable to load shared object '/usr/lib/R/modules//R_X11.so':
>   /usr/lib/x86_64-linux-gnu/libpng12.so.0: version `PNG12_0' not
>   found (required by /usr/lib/R/modules//R_X11.so)
> 
> and this is my sessionInfo()
> 
> > sessionInfo()
> R version 3.2.4 Revised (2016-03-16 r70336)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux stretch/sid
> 
> locale:
>  [1] LC_CTYPE=en_GB.utf8   LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
>[5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8
> [7] LC_PAPER=en_GB.utf8   LC_NAME=C
>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
>  [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> 
> Anybody understands what is going on here?
> Regards
> 
> Lorenzo
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Interquartile Range

[William Dunlap via R-help]

> That didn't work Jim!

It always helps to say how the suggestion did not work.  Jim's
function had a typo in it - was that the problem?  Or did you not
change the call to ddply to use that function.  Here is something
that might "work" for you:

 library(plyr)

 data <- data.frame(groupColumn=rep(1:5,1:5), col1=2^(0:14))
 myIqr <- function(x) {
 paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
 }
 ddply(data, ~groupColumn, summarise, col1_myIqr=myIqr(col1),
col1_IQR=stats::IQR(col1))
 #  groupColumn col1_myIqr col1_IQR
 #1   11-10
 #2   22-41
 #3   3  12-24   12
 #4   4112-320  208
 #5   5  2048-8192 6144

The important point is that
paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
is not a function, it is an expression.   ddplyr wants functions.


Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
wrote:

> That didn't work Jim!
>
> Thanks anyway
>
> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>
> > Hi Michael,
> > At a guess, try this:
> >
> > iqr<-function(x) {
> >
> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> > }
> >
> > .col3_Range=iqr(datat$tenure)
> >
> > Jim
> >
> >
> >
> > On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
> > wrote:
> > > Hi,
> > >   I am trying to show an interquartile range while grouping values
> using
> > > the function ddply().  So my function call now is like
> > >
> > > groupedAll <- ddply(data
> > >  ,~groupColumn
> > >  ,summarise
> > >  ,col1_mean=mean(col1)
> > >  ,col2_mode=Mode(col2) #Function I wrote for getting
> the
> > > mode shown below
> > >
> > >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
> > > as.character(round(quantile(data$tenure,c(.75, sep = "-")
> > >  )
> > >
> > > #custom Mode function
> > > Mode <- function(x) {
> > >   ux <- unique(x)
> > >   ux[which.max(tabulate(match(x, ux)))]
> > > }
> > >
> > > I am not sre what is going wrong on my interquartile range function, it
> > > works on its own outside of ddply()
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] Interquartile Range

[Michael Artz]

Hi bert,

I understand the difference between a character string and a number. I need
to return a character string, that is a requirement.  It needs to be in
that format.  Getting the range with IQR is trivial I already tried it. The
grouping function accepts only one return value,  and IQR returns two.
Thanks for the reply though sir.
On Apr 19, 2016 10:20 AM, "Bert Gunter"  wrote:

> Are you aware that there *already is* a function that does this?
>
> ?IQR
>
> (also your "function" iqr" is just a character string and would have
> to be parsed and evaluated to become a function. But this is a
> TERRIBLE way to do things in R as it completely circumvents R's
> central functional programming paradigm).
>
> Cheers,
> Bert
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz 
> wrote:
> > That didn't work Jim!
> >
> > Thanks anyway
> >
> > On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
> >
> >> Hi Michael,
> >> At a guess, try this:
> >>
> >> iqr<-function(x) {
> >>
> return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> >> }
> >>
> >> .col3_Range=iqr(datat$tenure)
> >>
> >> Jim
> >>
> >>
> >>
> >> On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
> >> wrote:
> >> > Hi,
> >> >   I am trying to show an interquartile range while grouping values
> using
> >> > the function ddply().  So my function call now is like
> >> >
> >> > groupedAll <- ddply(data
> >> >  ,~groupColumn
> >> >  ,summarise
> >> >  ,col1_mean=mean(col1)
> >> >  ,col2_mode=Mode(col2) #Function I wrote for getting
> the
> >> > mode shown below
> >> >
> >> >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
> >> > as.character(round(quantile(data$tenure,c(.75, sep = "-")
> >> >  )
> >> >
> >> > #custom Mode function
> >> > Mode <- function(x) {
> >> >   ux <- unique(x)
> >> >   ux[which.max(tabulate(match(x, ux)))]
> >> > }
> >> >
> >> > I am not sre what is going wrong on my interquartile range function,
> it
> >> > works on its own outside of ddply()
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > __
> >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> > https://stat.ethz.ch/mailman/listinfo/r-help
> >> > PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> > and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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[R] Problem with X11

[Lorenzo Isella]

Dear All,
I have never had this problem before. I run debian testing on my box
and I have recently update my R environment.
Now, see what happens when I try the most trivial of all plots


plot(seq(22))

Error in (function (display = "", width, height, pointsize, gamma, bg,
:
 X11 module cannot be loaded
 In addition: Warning message:
 In (function (display = "", width, height, pointsize, gamma, bg,  :
   unable to load shared object '/usr/lib/R/modules//R_X11.so':
 /usr/lib/x86_64-linux-gnu/libpng12.so.0: version `PNG12_0' not
 found (required by /usr/lib/R/modules//R_X11.so)

and this is my sessionInfo()


sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
[1] LC_CTYPE=en_GB.utf8   LC_NUMERIC=C
 [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
  [5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8
   [7] LC_PAPER=en_GB.utf8   LC_NAME=C
[9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base


Anybody understands what is going on here?
Regards

Lorenzo

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Re: [R] Interquartile Range

[Bert Gunter]

Are you aware that there *already is* a function that does this?

?IQR

(also your "function" iqr" is just a character string and would have
to be parsed and evaluated to become a function. But this is a
TERRIBLE way to do things in R as it completely circumvents R's
central functional programming paradigm).

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Apr 19, 2016 at 7:56 AM, Michael Artz  wrote:
> That didn't work Jim!
>
> Thanks anyway
>
> On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:
>
>> Hi Michael,
>> At a guess, try this:
>>
>> iqr<-function(x) {
>>  return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
>> }
>>
>> .col3_Range=iqr(datat$tenure)
>>
>> Jim
>>
>>
>>
>> On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
>> wrote:
>> > Hi,
>> >   I am trying to show an interquartile range while grouping values using
>> > the function ddply().  So my function call now is like
>> >
>> > groupedAll <- ddply(data
>> >  ,~groupColumn
>> >  ,summarise
>> >  ,col1_mean=mean(col1)
>> >  ,col2_mode=Mode(col2) #Function I wrote for getting the
>> > mode shown below
>> >
>> >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
>> > as.character(round(quantile(data$tenure,c(.75, sep = "-")
>> >  )
>> >
>> > #custom Mode function
>> > Mode <- function(x) {
>> >   ux <- unique(x)
>> >   ux[which.max(tabulate(match(x, ux)))]
>> > }
>> >
>> > I am not sre what is going wrong on my interquartile range function, it
>> > works on its own outside of ddply()
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Interquartile Range

[Michael Artz]

That didn't work Jim!

Thanks anyway

On Mon, Apr 18, 2016 at 9:02 PM, Jim Lemon  wrote:

> Hi Michael,
> At a guess, try this:
>
> iqr<-function(x) {
>  return(paste(round(quantile(x,0.25),0),round(quantile(x,0.75),0),sep="-")
> }
>
> .col3_Range=iqr(datat$tenure)
>
> Jim
>
>
>
> On Tue, Apr 19, 2016 at 11:15 AM, Michael Artz 
> wrote:
> > Hi,
> >   I am trying to show an interquartile range while grouping values using
> > the function ddply().  So my function call now is like
> >
> > groupedAll <- ddply(data
> >  ,~groupColumn
> >  ,summarise
> >  ,col1_mean=mean(col1)
> >  ,col2_mode=Mode(col2) #Function I wrote for getting the
> > mode shown below
> >
> >  ,col3_Range=paste(as.character(round(quantile(datat$tenure,c(.25,
> > as.character(round(quantile(data$tenure,c(.75, sep = "-")
> >  )
> >
> > #custom Mode function
> > Mode <- function(x) {
> >   ux <- unique(x)
> >   ux[which.max(tabulate(match(x, ux)))]
> > }
> >
> > I am not sre what is going wrong on my interquartile range function, it
> > works on its own outside of ddply()
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] Indicator Species analysis; trouble with multipatt

[John Kane]

Hi Ansley
It looks good to me but I did not run the analysis as I am too lazy to install 
"indicspecies".  The inclusion of the raw data is a great help.

John Kane
Kingston ON Canada

-Original Message-
From: daily.p...@gmail.com
Sent: Tue, 19 Apr 2016 08:16:54 -0400
To: jrkrid...@inbox.com
Subject: Re: [R] Indicator Species analysis; trouble with multipatt

Thanks for the replies.

I have fixed the problem.  I only need to reorganized my data.  Now my question 
is about asking questions correctly.  I hope I've got it.  Please find the 
script attached here.

R Version 3.2.2

I am looking for indicator species with Indicspecies package.  After running 
the function multipatt, I get the following error:

Error in is.factor(x) : object 'groups1' not found

**Is this reproducibility satisfactory?  I fixed the problem by reorganizing my 
csv file.  I was trying to be efficient when making my groups and that was 
causing the trouble.

Thanks.

On Tue, Apr 19, 2016 at 6:47 AM, John Kane  wrote:

Hi Ansely,
 As Jim points out we really need some sample data to go with the code.

 Have a look at ?dput which is the best way to supply sample data here or have 
a look at 
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
 
[http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example]
 and/or http://adv-r.had.co.nz/Reproducibility.html 
[http://adv-r.had.co.nz/Reproducibility.html] for some general suggestions on 
asking questions here---including discussions of using dput()

 John Kane
 Kingston ON Canada

 > -Original Message-
 > From: daily.p...@gmail.com
 > Sent: Mon, 18 Apr 2016 16:33:54 -0400
 > To: r-help@r-project.org
 > Subject: [R] Indicator Species analysis; trouble with multipatt
 >
 > Hello,
 >
 > *Error in tx  %*% comb : non-conformable arguments*
 >
 > Suggestions greatly appreciated.  I am a beginner and this is my first
 > time
 > posting.
 >
 > I would like to get the summary for indicator species analysis, using
 > package indicspecies with multipatt.  I am getting errors, I believe, do
 > to
 > my data organization.  After reorganizing and reorganizing, nothing has
 > helped.
 >
 >> data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",")
 >> ap<-data[c(1:24, 1:81)]
 >> groups<-c(rep(1:4,6))
 >> indval<- multipatt(ap, groups, control = how(nperm=999))
 > *Error in tx  %*% comb : non-conformable arguments*
 >
 >
 >
 > --
 > Ansley Silva
 >
 >
 > *"The clearest way into the Universe is through a forest wilderness."
 > John
 > Muir*
 >
 >
 > *Graduate Research Assistant*
 > __
 > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 > https://stat.ethz.ch/mailman/listinfo/r-help 
 > [https://stat.ethz.ch/mailman/listinfo/r-help]
 > PLEASE do read the posting guide
 > http://www.R-project.org/posting-guide.html 
 > [http://www.R-project.org/posting-guide.html]
 > and provide commented, minimal, self-contained, reproducible code.

 
 FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
 Check it out at http://www.inbox.com/earth [http://www.inbox.com/earth]

-- 

Ansley Silva

_
_

_"The clearest way into the Universe is through a forest wilderness." 
John Muir_

_
_

_Graduate Research Assistant_
__

_University of Georgia_
__

_D.B. Warnell School of Forestry and Natural Resources_
__

_180 East Green Street_
__

_Athens, GA 30602_


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__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Indicator Species analysis; trouble with multipatt

[Ansley Silva]

Thanks for the replies.

I have fixed the problem.  I only need to reorganized my data.  Now my
question is about asking questions correctly.  I hope I've got it.  Please
find the script attached here.

R Version 3.2.2

I am looking for indicator species with Indicspecies package.  After
running the function multipatt, I get the following error:

Error in is.factor(x) : object 'groups1' not found

**Is this reproducibility satisfactory?  I fixed the problem by
reorganizing my csv file.  I was trying to be efficient when making my
groups and that was causing the trouble.

Thanks.


On Tue, Apr 19, 2016 at 6:47 AM, John Kane  wrote:

> Hi Ansely,
> As Jim points out we really need some sample data to go with the code.
>
> Have a look at ?dput which is the best way to supply sample data here or
> have a look at
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> and/or http://adv-r.had.co.nz/Reproducibility.html for some general
> suggestions on asking questions here---including discussions of using dput()
>
> John Kane
> Kingston ON Canada
>
>
> > -Original Message-
> > From: daily.p...@gmail.com
> > Sent: Mon, 18 Apr 2016 16:33:54 -0400
> > To: r-help@r-project.org
> > Subject: [R] Indicator Species analysis; trouble with multipatt
> >
> > Hello,
> >
> > *Error in tx  %*% comb : non-conformable arguments*
> >
> > Suggestions greatly appreciated.  I am a beginner and this is my first
> > time
> > posting.
> >
> > I would like to get the summary for indicator species analysis, using
> > package indicspecies with multipatt.  I am getting errors, I believe, do
> > to
> > my data organization.  After reorganizing and reorganizing, nothing has
> > helped.
> >
> >> data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",")
> >> ap<-data[c(1:24, 1:81)]
> >> groups<-c(rep(1:4,6))
> >> indval<- multipatt(ap, groups, control = how(nperm=999))
> > *Error in tx  %*% comb : non-conformable arguments*
> >
> >
> >
> > --
> > Ansley Silva
> >
> >
> > *"The clearest way into the Universe is through a forest wilderness."
> > John
> > Muir*
> >
> >
> > *Graduate Research Assistant*
> > __
> > 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.
>
> 
> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
>
>
>


-- 
Ansley Silva


*"The clearest way into the Universe is through a forest wilderness." John
Muir*


*Graduate Research Assistant*

*University of Georgia*

*D.B. Warnell School of Forestry and Natural Resources*

*180 East Green Street*

*Athens, GA 30602*
install.packages("indicspecies")
library(indicspecies)

mydata<-
structure(list(necsur = structure(c(6L, 1L, 1L, 4L, 4L, 2L), .Label = c("0", 
"1", "11", "2", "24", "3", "4", "42", "5", "8", "9", "PA"), class = "factor"), 
necame = structure(c(11L, 2L, 5L, 5L, 17L, 9L), .Label = c("0", 
"1", "10", "11", "12", "13", "15", "2", "20", "22", "3", 
"4", "5", "6", "7", "8", "9", "PA"), class = "factor"), niccar = 
structure(c(1L, 
1L, 1L, 2L, 1L, 1L), .Label = c("0", "1", "19", "2", "3", 
"4", "5", "6", "PA"), class = "factor"), nicorb = structure(c(1L, 
18L, 19L, 17L, 1L, 27L), .Label = c("0", "1", "10", "11", 
"12", "13", "15", "16", "18", "19", "2", "20", "21", "23", 
"25", "29", "3", "30", "31", "32", "33", "36", "4", "40", 
"42", "44", "48", "5", "50", "6", "61", "7", "8", "9", "PA"
), class = "factor"), nicpus = structure(c(1L, 1L, 1L, 1L, 
1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"), 
nictor = structure(c(1L, 1L, 2L, 1L, 1L, 1L), .Label = c("0", 
"1", "10", "11", "16", "18", "2", "22", "3", "4", "5", "6", 
"7", "8", "9", "PA"), class = "factor"), oicina = structure(c(1L, 
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "15", "2", "3", 
"PA"), class = "factor"), delgib = structure(c(37L, 5L, 7L, 
11L, 11L, 43L), .Label = c("0", "1", "10", "104", "11", "12", 
"126", "13", "14", "15", "16", "18", "19", "2", "20", "21", 
"22", "23", "24", "25", "26", "27", "28", "29", "3", "30", 
"31", "32", "33", "34", "35", "37", "39", "4", "40", "43", 
"5", "50", "6", "61", "63", "65", "68", "7", "72", "8", "81", 
"82", "97", "PA"), class = "factor"), cancha = structure(c(1L, 
1L, 2L, 7L, 7L, 10L), .Label = c("0", "1", "11", "12", "16", 
"17", "2", "27", "3", "4", "5", "6", "7", "8", "9", "PA"), class = 
"factor"), 
melbis = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("0", 
"1", "11", "17", "18", "2", "3", "4", "5", "6", "8", "9", 
"PA"), class = "factor"), atelec = structure(c(1L, 1L, 1L, 
22L, 7L, 2L), 

Re: [R] heatmap2 error key

[Jim Lemon]

Hi Catalina,
The error message is pretty clear. min(diff(breaks)/100) evaluates to
a negative number. Perhaps the sort order for the values in "breaks"
has changed.

Jim


On Tue, Apr 19, 2016 at 9:35 AM, Catalina Aguilar Hurtado
 wrote:
> Hi I am trying to understand what happen with the heatmap.2 code that it
> used to work (last used in October 2015). I am able to get a heatmap but my
> colour key doesn't come up and instead I get an error in all my files the
> used to work. Does anyone has any idea of what could have changed? or how
> to fix this.
>
> Thanks.
>
> #
>
> Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :
>   wrong sign in 'by' argument
> In addition: Warning message:
> In image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 +  :
>   unsorted 'breaks' will be sorted before use
>
> ##
>
> library("RColorBrewer")
> library("gplots")
>
> library ("gtools")
>
> GO_Fil=read.table("1h-6h-up-down-v4.csv", sep=",", header=T)
>
> data =data.matrix (GO_Fil[,3:4]) # define which columns to use for the
> heatmap
>
> rownames(data) <- GO_Fil$Description
>
> summary (data)
>
> pairs.breaks <- c(seq(-6, -0.01, length.out=50), seq(-0.02,
> 0.01,length.out=150), seq(0.02, 3.9,length.out=80))
>
> hmcols<- colorRampPalette(c("blue","white", "red"))(length(pairs.breaks)-1)
>
> pdf("Heat_1hv6h-updown-key.pdf",
> width = 15,
> height = 20,
> pointsize = 5)
>
> hm<- heatmap.2(data, breaks=pairs.breaks, col=hmcols, na.color="white",
>trace="none",Colv=FALSE,
>dendrogram = "none",
>density.info="none",
>key="TRUE",
>keysize = 2,
>key.xlab = "Log2FC",
>key.title = "key",
>cexCol=3.0,
>cexRow=2,
>lwid= c(0.4,1),
>lhei = c(0.1, 4),
>margins= c(50,80),
>symm=F,symkey=F,symbreaks=T, scale="none")
>
> dev.off()
>
>> R.version
>_
> platform   x86_64-apple-darwin13.4.0
> arch   x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major  3
> minor  2.2
> year   2015
> month  08
> day14
> svn rev69053
> language   R
> version.string R version 3.2.2 (2015-08-14)
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] heatmap2 error key

[John Kane]

Data?  Please have a look at
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
 and/or http://adv-r.had.co.nz/Reproducibility.html



John Kane
Kingston ON Canada


> -Original Message-
> From: cata...@gmail.com
> Sent: Tue, 19 Apr 2016 09:35:14 +1000
> To: r-help@r-project.org
> Subject: [R] heatmap2 error key
> 
> Hi I am trying to understand what happen with the heatmap.2 code that it
> used to work (last used in October 2015). I am able to get a heatmap but
> my
> colour key doesn't come up and instead I get an error in all my files the
> used to work. Does anyone has any idea of what could have changed? or how
> to fix this.
> 
> Thanks.
> 
> #
> 
> Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :
>   wrong sign in 'by' argument
> In addition: Warning message:
> In image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 +  :
>   unsorted 'breaks' will be sorted before use
> 
> ##
> 
> library("RColorBrewer")
> library("gplots")
> 
> library ("gtools")
> 
> GO_Fil=read.table("1h-6h-up-down-v4.csv", sep=",", header=T)
> 
> data =data.matrix (GO_Fil[,3:4]) # define which columns to use for the
> heatmap
> 
> rownames(data) <- GO_Fil$Description
> 
> summary (data)
> 
> pairs.breaks <- c(seq(-6, -0.01, length.out=50), seq(-0.02,
> 0.01,length.out=150), seq(0.02, 3.9,length.out=80))
> 
> hmcols<- colorRampPalette(c("blue","white",
> "red"))(length(pairs.breaks)-1)
> 
> pdf("Heat_1hv6h-updown-key.pdf",
> width = 15,
> height = 20,
> pointsize = 5)
> 
> hm<- heatmap.2(data, breaks=pairs.breaks, col=hmcols, na.color="white",
>trace="none",Colv=FALSE,
>dendrogram = "none",
>density.info="none",
>key="TRUE",
>keysize = 2,
>key.xlab = "Log2FC",
>key.title = "key",
>cexCol=3.0,
>cexRow=2,
>lwid= c(0.4,1),
>lhei = c(0.1, 4),
>margins= c(50,80),
>symm=F,symkey=F,symbreaks=T, scale="none")
> 
> dev.off()
> 
>> R.version
>_
> platform   x86_64-apple-darwin13.4.0
> arch   x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major  3
> minor  2.2
> year   2015
> month  08
> day14
> svn rev69053
> language   R
> version.string R version 3.2.2 (2015-08-14)
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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__
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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] Indicator Species analysis; trouble with multipatt

[John Kane]

Hi Ansely,
As Jim points out we really need some sample data to go with the code.

Have a look at ?dput which is the best way to supply sample data here or have a 
look at 
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
 and/or http://adv-r.had.co.nz/Reproducibility.html for some general 
suggestions on asking questions here---including discussions of using dput()

John Kane
Kingston ON Canada


> -Original Message-
> From: daily.p...@gmail.com
> Sent: Mon, 18 Apr 2016 16:33:54 -0400
> To: r-help@r-project.org
> Subject: [R] Indicator Species analysis; trouble with multipatt
> 
> Hello,
> 
> *Error in tx  %*% comb : non-conformable arguments*
> 
> Suggestions greatly appreciated.  I am a beginner and this is my first
> time
> posting.
> 
> I would like to get the summary for indicator species analysis, using
> package indicspecies with multipatt.  I am getting errors, I believe, do
> to
> my data organization.  After reorganizing and reorganizing, nothing has
> helped.
> 
>> data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",")
>> ap<-data[c(1:24, 1:81)]
>> groups<-c(rep(1:4,6))
>> indval<- multipatt(ap, groups, control = how(nperm=999))
> *Error in tx  %*% comb : non-conformable arguments*
> 
> 
> 
> --
> Ansley Silva
> 
> 
> *"The clearest way into the Universe is through a forest wilderness."
> John
> Muir*
> 
> 
> *Graduate Research Assistant*
> __
> 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] A Neural Network question

[Charles Determan]

Hi Phil,

I don't think this is the correct list for this.  You question has nothing
to do with R specifically which is the purpose here.  I suggest you pursue
other help lists related to neural networks to try and find someone to
assist you.

Regards,
Charles

On Sat, Apr 16, 2016 at 2:08 AM, Philip Rhoades  wrote:

> People,
>
> I thought I needed to have some familiarity with NNs for some of my
> current (non-profit, brain-related) projects so I started looking at
> various programming environments including R and I got this working:
>
>   http://gekkoquant.com/2012/05/26/neural-networks-with-r-simple-example
>
> however I needed pictures to help understand what was going on and then I
> found this:
>
>
> https://jamesmccaffrey.files.wordpress.com/2012/11/backpropagationcalculations.jpg
>
> which I thought was almost intelligible so I had an idea which I thought
> would help the learning process:
>
> - Create a very simple NN implemented as a spreadsheet where each sheet
> would correspond to an iteration
>
> I started doing this on LibreOffice:
>
> - I think am already starting to get a better idea of how NNs work just
> from the stuff I have done on the spreadsheet already
>
> - I have now transferred my LibreOffice SpreadSheet (SS) to a shared
> Google Docs Calc file and can share it for editing with others
>
>
> https://docs.google.com/spreadsheets/d/1eSCgGU5qeI3_PmQhwZn4RH0NznUekVP5BP7w4MpKSUc/pub?output=pdf
>
> - I think I have the SS calculations correct so far except for the stuff
> in the dashed purple box in the diagram
>
> - I am not sure how to implement the purple box . . so I thought I would
> ask for help on this mailing list
>
> If someone can help me with the last bit of the SS, from there I think I
> can then repeat the FR and BP sheets and see how the Diffs evolve . .
>
> Is anyone interested in helping to get this last bit of the spreadsheet
> working so I can move on to doing actual work with the R packages with
> better understanding?
>
> Thanks,
>
> Phil.
> --
> Philip Rhoades
>
> PO Box 896
> Cowra  NSW  2794
> Australia
> E-mail:  p...@pricom.com.au
>
> __
> 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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and provide commented, minimal, self-contained, reproducible code.

[R] heatmap2 error key

[Catalina Aguilar Hurtado]

Hi I am trying to understand what happen with the heatmap.2 code that it
used to work (last used in October 2015). I am able to get a heatmap but my
colour key doesn't come up and instead I get an error in all my files the
used to work. Does anyone has any idea of what could have changed? or how
to fix this.

Thanks.

#

Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :
  wrong sign in 'by' argument
In addition: Warning message:
In image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 +  :
  unsorted 'breaks' will be sorted before use

##

library("RColorBrewer")
library("gplots")

library ("gtools")

GO_Fil=read.table("1h-6h-up-down-v4.csv", sep=",", header=T)

data =data.matrix (GO_Fil[,3:4]) # define which columns to use for the
heatmap

rownames(data) <- GO_Fil$Description

summary (data)

pairs.breaks <- c(seq(-6, -0.01, length.out=50), seq(-0.02,
0.01,length.out=150), seq(0.02, 3.9,length.out=80))

hmcols<- colorRampPalette(c("blue","white", "red"))(length(pairs.breaks)-1)

pdf("Heat_1hv6h-updown-key.pdf",
width = 15,
height = 20,
pointsize = 5)

hm<- heatmap.2(data, breaks=pairs.breaks, col=hmcols, na.color="white",
   trace="none",Colv=FALSE,
   dendrogram = "none",
   density.info="none",
   key="TRUE",
   keysize = 2,
   key.xlab = "Log2FC",
   key.title = "key",
   cexCol=3.0,
   cexRow=2,
   lwid= c(0.4,1),
   lhei = c(0.1, 4),
   margins= c(50,80),
   symm=F,symkey=F,symbreaks=T, scale="none")

dev.off()

> R.version
   _
platform   x86_64-apple-darwin13.4.0
arch   x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major  3
minor  2.2
year   2015
month  08
day14
svn rev69053
language   R
version.string R version 3.2.2 (2015-08-14)

[[alternative HTML version deleted]]

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[R] (Small) programming job related to network analysis

[Michael Haenlein]

Dear all,

I am looking for help in programming three functions. Those functions
should simulate (social) networks according to the process described in :

(1) A.H. Dekker - "Realistic Social Networks for Simulation using Network
Rewiring" (
http://www.mssanz.org.au/MODSIM07/papers/13_s20/RealisticSocial_s20_Dekker_.pdf
)

(2) Konstantin Klemm and Vıctor M. Eguıluz - "Growing scale-free networks
with small-world behavior" (http://ifisc.uib-csic.es/victor/Nets/sw.pdf)

(3) Petter Holme and Beom Jun Kim - "Growing Scale-Free Networks with
Tunable Clustering" (http://arxiv.org/pdf/cond-mat/0110452.pdf)

I am looking for three functions (e.g., sample_dekker, sample_klemm,
sample_holme) that generate an output similar to the functions sample_pa
and sample_smallworld in the R package igraph. The input should be the
number of nodes in the network (e.g., 1000) and any other parameters those
models require.

In case this is of relevance please get in touch with me by email to
discuss further details.

Thanks,

Michael



Michael Haenlein
Professor of Marketing
ESCP Europe

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