Using options(max.print = 1000000) to read in data

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Using options(max.print = 1000000) to read in data

Spencer Brackett
Hello,

  I am trying to reload some data into R in order to check to see if it is
formatted as a matrix. I used the command options(max.print = 10000000) to
account for the 20,000 some rows omitted previously when just using the
basic version of this function. After entering this command, the dataset
mostly loaded into R, but 14717 rows were still omitted.

  Can I simply increase the number indicted after 'max.print =' to read in
the remaining rows, or should I use 'bigfile.sample <-' or
'bigfile.colclass <-' instead? Do I even need to read in all of the rows to
test for a matrix?

Best,

Spencer

        [[alternative HTML version deleted]]

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Re: Using options(max.print = 1000000) to read in data

Kevin E. Thorpe

> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <[hidden email]> wrote:
>
> Hello,
>
>  I am trying to reload some data into R in order to check to see if it is
> formatted as a matrix. I used the command options(max.print = 10000000) to
> account for the 20,000 some rows omitted previously when just using the
> basic version of this function. After entering this command, the dataset
> mostly loaded into R, but 14717 rows were still omitted.
>
>  Can I simply increase the number indicted after 'max.print =' to read in
> the remaining rows, or should I use 'bigfile.sample <-' or
> 'bigfile.colclass <-' instead? Do I even need to read in all of the rows to
> test for a matrix?
>
> Best,
>
> Spencer
>

I don’t think this option affects how much data is read in, just how much is printed to the screen. Use the function str() on your imported object to see how many rows, among other things, were brought in.


> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.


--
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016

______________________________________________
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Re: Using options(max.print = 1000000) to read in data

Spencer Brackett
Thank you,

Here is a summary of the resulting output....

>nrow(GBM.txt)
[1] 20530
> ncol(GBM.txt)
[1] 173

This corresponds with the info found in my global environment for the
object indicated. Now, how do I go about determining if the dataset is a
matrix?


On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]>
wrote:

>
> > On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
> [hidden email]> wrote:
> >
> > Hello,
> >
> >  I am trying to reload some data into R in order to check to see if it is
> > formatted as a matrix. I used the command options(max.print = 10000000)
> to
> > account for the 20,000 some rows omitted previously when just using the
> > basic version of this function. After entering this command, the dataset
> > mostly loaded into R, but 14717 rows were still omitted.
> >
> >  Can I simply increase the number indicted after 'max.print =' to read in
> > the remaining rows, or should I use 'bigfile.sample <-' or
> > 'bigfile.colclass <-' instead? Do I even need to read in all of the rows
> to
> > test for a matrix?
> >
> > Best,
> >
> > Spencer
> >
>
> I don’t think this option affects how much data is read in, just how much
> is printed to the screen. Use the function str() on your imported object to
> see how many rows, among other things, were brought in.
>
>
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] 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.
>
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
>
>

        [[alternative HTML version deleted]]

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Re: Using options(max.print = 1000000) to read in data

Rui Barradas
Hello,

Inline.

Às 15:26 de 08/07/19, Spencer Brackett escreveu:

> Thank you,
>
> Here is a summary of the resulting output....
>
>> nrow(GBM.txt)
> [1] 20530
>> ncol(GBM.txt)
> [1] 173
>
> This corresponds with the info found in my global environment for the
> object indicated. Now, how do I go about determining if the dataset is a
> matrix?

Try any of

str(GBM.txt)
class(GBM.txt)

Also, like Kevin said, max.print only affects how much is printed, not
the read functions. Why change max.print at all? The default value
(1000) is large enough, I have never needed to see more than this at a
time. In fact, to have an idea of the data I would rather further limit
the number of matrix lines printed with

head(object)
tail(object)



Hope this helps,

Rui Barradas

>
>
> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]>
> wrote:
>
>>
>>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
>> [hidden email]> wrote:
>>>
>>> Hello,
>>>
>>>   I am trying to reload some data into R in order to check to see if it is
>>> formatted as a matrix. I used the command options(max.print = 10000000)
>> to
>>> account for the 20,000 some rows omitted previously when just using the
>>> basic version of this function. After entering this command, the dataset
>>> mostly loaded into R, but 14717 rows were still omitted.
>>>
>>>   Can I simply increase the number indicted after 'max.print =' to read in
>>> the remaining rows, or should I use 'bigfile.sample <-' or
>>> 'bigfile.colclass <-' instead? Do I even need to read in all of the rows
>> to
>>> test for a matrix?
>>>
>>> Best,
>>>
>>> Spencer
>>>
>>
>> I don’t think this option affects how much data is read in, just how much
>> is printed to the screen. Use the function str() on your imported object to
>> see how many rows, among other things, were brought in.
>>
>>
>>>        [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] 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.
>>
>>
>> --
>> Kevin E. Thorpe
>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>> Li Ka Shing Knowledge Institute of St. Michael's
>> Assistant Professor, Dalla Lana School of Public Health
>> University of Toronto
>> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
>>
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Using options(max.print = 1000000) to read in data

Bert Gunter-2
In reply to this post by Spencer Brackett
Why did you not do as Kevin suggested??

Or, more simply, ?is.matrix
which could be found in ?matrix.

*Please* consult R's docs before posting such queries.


Bert Gunter

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


On Mon, Jul 8, 2019 at 7:27 AM Spencer Brackett <
[hidden email]> wrote:

> Thank you,
>
> Here is a summary of the resulting output....
>
> >nrow(GBM.txt)
> [1] 20530
> > ncol(GBM.txt)
> [1] 173
>
> This corresponds with the info found in my global environment for the
> object indicated. Now, how do I go about determining if the dataset is a
> matrix?
>
>
> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]>
> wrote:
>
> >
> > > On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
> > [hidden email]> wrote:
> > >
> > > Hello,
> > >
> > >  I am trying to reload some data into R in order to check to see if it
> is
> > > formatted as a matrix. I used the command options(max.print = 10000000)
> > to
> > > account for the 20,000 some rows omitted previously when just using the
> > > basic version of this function. After entering this command, the
> dataset
> > > mostly loaded into R, but 14717 rows were still omitted.
> > >
> > >  Can I simply increase the number indicted after 'max.print =' to read
> in
> > > the remaining rows, or should I use 'bigfile.sample <-' or
> > > 'bigfile.colclass <-' instead? Do I even need to read in all of the
> rows
> > to
> > > test for a matrix?
> > >
> > > Best,
> > >
> > > Spencer
> > >
> >
> > I don’t think this option affects how much data is read in, just how much
> > is printed to the screen. Use the function str() on your imported object
> to
> > see how many rows, among other things, were brought in.
> >
> >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > [hidden email] 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.
> >
> >
> > --
> > Kevin E. Thorpe
> > Head of Biostatistics,  Applied Health Research Centre (AHRC)
> > Li Ka Shing Knowledge Institute of St. Michael's
> > Assistant Professor, Dalla Lana School of Public Health
> > University of Toronto
> > email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
> >
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
[hidden email] 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: Using options(max.print = 1000000) to read in data

Spencer Brackett
In reply to this post by Rui Barradas
Using str(GBM.txt) produced the same output as last time, which lists the
number of objects acting on a particular number of variables for the said
dataset and a few rows read from the original file.

The result of class(GBM.txt) generates the following..

> class(GBM.txt)
[1] "data.frame"

Is this to say that the object is set as a 'data frame', opposed to a
'matrix' ?

I will try running ?is.matrix now



On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas <[hidden email]> wrote:

> Hello,
>
> Inline.
>
> Às 15:26 de 08/07/19, Spencer Brackett escreveu:
> > Thank you,
> >
> > Here is a summary of the resulting output....
> >
> >> nrow(GBM.txt)
> > [1] 20530
> >> ncol(GBM.txt)
> > [1] 173
> >
> > This corresponds with the info found in my global environment for the
> > object indicated. Now, how do I go about determining if the dataset is a
> > matrix?
>
> Try any of
>
> str(GBM.txt)
> class(GBM.txt)
>
> Also, like Kevin said, max.print only affects how much is printed, not
> the read functions. Why change max.print at all? The default value
> (1000) is large enough, I have never needed to see more than this at a
> time. In fact, to have an idea of the data I would rather further limit
> the number of matrix lines printed with
>
> head(object)
> tail(object)
>
>
>
> Hope this helps,
>
> Rui Barradas
> >
> >
> > On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]>
> > wrote:
> >
> >>
> >>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
> >> [hidden email]> wrote:
> >>>
> >>> Hello,
> >>>
> >>>   I am trying to reload some data into R in order to check to see if
> it is
> >>> formatted as a matrix. I used the command options(max.print = 10000000)
> >> to
> >>> account for the 20,000 some rows omitted previously when just using the
> >>> basic version of this function. After entering this command, the
> dataset
> >>> mostly loaded into R, but 14717 rows were still omitted.
> >>>
> >>>   Can I simply increase the number indicted after 'max.print =' to
> read in
> >>> the remaining rows, or should I use 'bigfile.sample <-' or
> >>> 'bigfile.colclass <-' instead? Do I even need to read in all of the
> rows
> >> to
> >>> test for a matrix?
> >>>
> >>> Best,
> >>>
> >>> Spencer
> >>>
> >>
> >> I don’t think this option affects how much data is read in, just how
> much
> >> is printed to the screen. Use the function str() on your imported
> object to
> >> see how many rows, among other things, were brought in.
> >>
> >>
> >>>        [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> [hidden email] 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.
> >>
> >>
> >> --
> >> Kevin E. Thorpe
> >> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> >> Li Ka Shing Knowledge Institute of St. Michael's
> >> Assistant Professor, Dalla Lana School of Public Health
> >> University of Toronto
> >> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
> >>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] 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]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Using options(max.print = 1000000) to read in data

Rui Barradas
Hello,

Look at the output of these two commands:

1) str(<matrix object>)

str(matrix(0, nrow = 20530, ncol =173))
num [1:20530, 1:173] 0 0 0 0 0 0 0 0 0 0 ...


The important part is

num [1:20530, 1:173]


This says it's a numeric vector with dimensions 20530 and 173, it's a matrix

2) str(<data.frame object>)

str(as.data.frame(matrix(0, nrow = 20530, ncol =173)))
'data.frame': 20530 obs. of  173 variables:
  $ V1  : num  0 0 0 0 0 0 0 0 0 0 ...
  $ V2  : num  0 0 0 0 0 0 0 0 0 0 ...
  $ V3  : num  0 0 0 0 0 0 0 0 0 0 ...
  [...]


Now it's expressly written

'data.frame': 20530 obs. of  173 variables:


There are 173 variables eac h with the same number of observations, 20530.


When you read in data files with any form of read.table (read.csv is the
same function with different arguments default values set), you will
always get a data.frame.


Hope this helps,

Rui Barradas


Às 15:43 de 08/07/19, Spencer Brackett escreveu:

> Using str(GBM.txt) produced the same output as last time, which lists
> the number of objects acting on a particular number of variables for the
> said dataset and a few rows read from the original file.
>
> The result of class(GBM.txt) generates the following..
>
>  > class(GBM.txt)
> [1] "data.frame"
>
> Is this to say that the object is set as a 'data frame', opposed to a
> 'matrix' ?
>
> I will try running ?is.matrix now
>
>
>
> On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello,
>
>     Inline.
>
>     Às 15:26 de 08/07/19, Spencer Brackett escreveu:
>      > Thank you,
>      >
>      > Here is a summary of the resulting output....
>      >
>      >> nrow(GBM.txt)
>      > [1] 20530
>      >> ncol(GBM.txt)
>      > [1] 173
>      >
>      > This corresponds with the info found in my global environment for the
>      > object indicated. Now, how do I go about determining if the
>     dataset is a
>      > matrix?
>
>     Try any of
>
>     str(GBM.txt)
>     class(GBM.txt)
>
>     Also, like Kevin said, max.print only affects how much is printed, not
>     the read functions. Why change max.print at all? The default value
>     (1000) is large enough, I have never needed to see more than this at a
>     time. In fact, to have an idea of the data I would rather further limit
>     the number of matrix lines printed with
>
>     head(object)
>     tail(object)
>
>
>
>     Hope this helps,
>
>     Rui Barradas
>      >
>      >
>      > On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe
>     <[hidden email] <mailto:[hidden email]>>
>      > wrote:
>      >
>      >>
>      >>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
>      >> [hidden email]
>     <mailto:[hidden email]>> wrote:
>      >>>
>      >>> Hello,
>      >>>
>      >>>   I am trying to reload some data into R in order to check to
>     see if it is
>      >>> formatted as a matrix. I used the command options(max.print =
>     10000000)
>      >> to
>      >>> account for the 20,000 some rows omitted previously when just
>     using the
>      >>> basic version of this function. After entering this command,
>     the dataset
>      >>> mostly loaded into R, but 14717 rows were still omitted.
>      >>>
>      >>>   Can I simply increase the number indicted after 'max.print ='
>     to read in
>      >>> the remaining rows, or should I use 'bigfile.sample <-' or
>      >>> 'bigfile.colclass <-' instead? Do I even need to read in all of
>     the rows
>      >> to
>      >>> test for a matrix?
>      >>>
>      >>> Best,
>      >>>
>      >>> Spencer
>      >>>
>      >>
>      >> I don’t think this option affects how much data is read in, just
>     how much
>      >> is printed to the screen. Use the function str() on your
>     imported object to
>      >> see how many rows, among other things, were brought in.
>      >>
>      >>
>      >>>        [[alternative HTML version deleted]]
>      >>>
>      >>> ______________________________________________
>      >>> [hidden email] <mailto:[hidden email]> 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.
>      >>
>      >>
>      >> --
>      >> Kevin E. Thorpe
>      >> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>      >> Li Ka Shing Knowledge Institute of St. Michael's
>      >> Assistant Professor, Dalla Lana School of Public Health
>      >> University of Toronto
>      >> email: [hidden email]
>     <mailto:[hidden email]>  Tel: 416.864.5776  Fax: 416.864.3016
>      >>
>      >>
>      >
>      >       [[alternative HTML version deleted]]
>      >
>      > ______________________________________________
>      > [hidden email] <mailto:[hidden email]> 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.
>      >
>

______________________________________________
[hidden email] 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
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Re: Using options(max.print = 1000000) to read in data

S Ellison-2
In reply to this post by Spencer Brackett
> This corresponds with the info found in my global environment for the
> object indicated. Now, how do I go about determining if the dataset is a
> matrix?

Consider ?is.matrix ?

S Ellison



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Re: Using options(max.print = 1000000) to read in data

Richard O'Keefe-2
In reply to this post by Spencer Brackett
The obvious question is "what do you mean, FORMATTED AS a matrix?"
Once you have read an object into R, you have no information about how it
was formatted.
Another question is "what do you mean, MATRIX"?
Do you mean the kind of R object specifically recognised by is.matrix,
or do you mean "rectangular arrangement of numbers", which would include
data frames as well?
Another obvious question is "how, EXACTLY, are you reading it?"
Why don't you *know* what you read it as?
If you use read.table or any of the other functions listed by ?read.table
you will always get a data frame, which is a rectangular arrangement that
*acts like* a matrix in many ways, but without actually being one.
If you want to read *part* of a file using one of those functions,
skip=M says to ignore the first M lines, and
nrows=N says to read the next N lines,
but the only way one of these functions would read less than all of the
input would be if memory ran out or the input was malformed.



On Tue, 9 Jul 2019 at 02:07, Spencer Brackett <
[hidden email]> wrote:

> Hello,
>
>   I am trying to reload some data into R in order to check to see if it is
> formatted as a matrix. I used the command options(max.print = 10000000) to
> account for the 20,000 some rows omitted previously when just using the
> basic version of this function. After entering this command, the dataset
> mostly loaded into R, but 14717 rows were still omitted.
>
>   Can I simply increase the number indicted after 'max.print =' to read in
> the remaining rows, or should I use 'bigfile.sample <-' or
> 'bigfile.colclass <-' instead? Do I even need to read in all of the rows to
> test for a matrix?
>
> Best,
>
> Spencer
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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: Using options(max.print = 1000000) to read in data

Michael Friendly
In reply to this post by Spencer Brackett
Why do you need it to be a matrix? A data.frame is like a matrix, but
allows columns of mixed types.

as.matrix() will coerce your data frame to a matrix if you really need this.

On 7/08/19 4:43 p.m., Spencer Brackett wrote:

> Using str(GBM.txt) produced the same output as last time, which lists the
> number of objects acting on a particular number of variables for the said
> dataset and a few rows read from the original file.
>
> The result of class(GBM.txt) generates the following..
>
>> class(GBM.txt)
> [1] "data.frame"
>
> Is this to say that the object is set as a 'data frame', opposed to a
> 'matrix' ?
>
> I will try running ?is.matrix now
>
>
>
> On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas <[hidden email]> wrote:
>
>> Hello,
>>
>> Inline.
>>
>> Às 15:26 de 08/07/19, Spencer Brackett escreveu:
>>> Thank you,
>>>
>>> Here is a summary of the resulting output....
>>>
>>>> nrow(GBM.txt)
>>> [1] 20530
>>>> ncol(GBM.txt)
>>> [1] 173
>>>
>>> This corresponds with the info found in my global environment for the
>>> object indicated. Now, how do I go about determining if the dataset is a
>>> matrix?
>>
>> Try any of
>>
>> str(GBM.txt)
>> class(GBM.txt)
>>
>> Also, like Kevin said, max.print only affects how much is printed, not
>> the read functions. Why change max.print at all? The default value
>> (1000) is large enough, I have never needed to see more than this at a
>> time. In fact, to have an idea of the data I would rather further limit
>> the number of matrix lines printed with
>>
>> head(object)
>> tail(object)
>>
>>
>>
>> Hope this helps,
>>
>> Rui Barradas
>>>
>>>
>>> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]>
>>> wrote:
>>>
>>>>
>>>>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
>>>> [hidden email]> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>>    I am trying to reload some data into R in order to check to see if
>> it is
>>>>> formatted as a matrix. I used the command options(max.print = 10000000)
>>>> to
>>>>> account for the 20,000 some rows omitted previously when just using the
>>>>> basic version of this function. After entering this command, the
>> dataset
>>>>> mostly loaded into R, but 14717 rows were still omitted.
>>>>>
>>>>>    Can I simply increase the number indicted after 'max.print =' to
>> read in
>>>>> the remaining rows, or should I use 'bigfile.sample <-' or
>>>>> 'bigfile.colclass <-' instead? Do I even need to read in all of the
>> rows
>>>> to
>>>>> test for a matrix?
>>>>>
>>>>> Best,
>>>>>
>>>>> Spencer
>>>>>
>>>>
>>>> I don’t think this option affects how much data is read in, just how
>> much
>>>> is printed to the screen. Use the function str() on your imported
>> object to
>>>> see how many rows, among other things, were brought in.
>>>>
>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> [hidden email] 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.
>>>>
>>>>
>>>> --
>>>> Kevin E. Thorpe
>>>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>>>> Li Ka Shing Knowledge Institute of St. Michael's
>>>> Assistant Professor, Dalla Lana School of Public Health
>>>> University of Toronto
>>>> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
>>>>
>>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] 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: Using options(max.print = 1000000) to read in data

Spencer Brackett
So even though a number of rows were omitted  during the ‘print in’ or
visualization of the dataset into my console, the data frame is now set as
a matrix? I believe so, per Mr. Barradas’s last email. Sorry for the
confusion, I was expecting the whole dataset to load into my console and
was concerned that perhaps if I had to set the data in the data frame as a
matrix (if not already), then I would not achieve this result.

Thanks,

Spencer

On Tue, Jul 9, 2019 at 6:21 AM Michael Friendly <[hidden email]> wrote:

> Why do you need it to be a matrix? A data.frame is like a matrix, but
> allows columns of mixed types.
>
> as.matrix() will coerce your data frame to a matrix if you really need
> this.
>
> On 7/08/19 4:43 p.m., Spencer Brackett wrote:
> > Using str(GBM.txt) produced the same output as last time, which lists the
> > number of objects acting on a particular number of variables for the said
> > dataset and a few rows read from the original file.
> >
> > The result of class(GBM.txt) generates the following..
> >
> >> class(GBM.txt)
> > [1] "data.frame"
> >
> > Is this to say that the object is set as a 'data frame', opposed to a
> > 'matrix' ?
> >
> > I will try running ?is.matrix now
> >
> >
> >
> > On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas <[hidden email]>
> wrote:
> >
> >> Hello,
> >>
> >> Inline.
> >>
> >> Às 15:26 de 08/07/19, Spencer Brackett escreveu:
> >>> Thank you,
> >>>
> >>> Here is a summary of the resulting output....
> >>>
> >>>> nrow(GBM.txt)
> >>> [1] 20530
> >>>> ncol(GBM.txt)
> >>> [1] 173
> >>>
> >>> This corresponds with the info found in my global environment for the
> >>> object indicated. Now, how do I go about determining if the dataset is
> a
> >>> matrix?
> >>
> >> Try any of
> >>
> >> str(GBM.txt)
> >> class(GBM.txt)
> >>
> >> Also, like Kevin said, max.print only affects how much is printed, not
> >> the read functions. Why change max.print at all? The default value
> >> (1000) is large enough, I have never needed to see more than this at a
> >> time. In fact, to have an idea of the data I would rather further limit
> >> the number of matrix lines printed with
> >>
> >> head(object)
> >> tail(object)
> >>
> >>
> >>
> >> Hope this helps,
> >>
> >> Rui Barradas
> >>>
> >>>
> >>> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <[hidden email]
> >
> >>> wrote:
> >>>
> >>>>
> >>>>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
> >>>> [hidden email]> wrote:
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>>    I am trying to reload some data into R in order to check to see if
> >> it is
> >>>>> formatted as a matrix. I used the command options(max.print =
> 10000000)
> >>>> to
> >>>>> account for the 20,000 some rows omitted previously when just using
> the
> >>>>> basic version of this function. After entering this command, the
> >> dataset
> >>>>> mostly loaded into R, but 14717 rows were still omitted.
> >>>>>
> >>>>>    Can I simply increase the number indicted after 'max.print =' to
> >> read in
> >>>>> the remaining rows, or should I use 'bigfile.sample <-' or
> >>>>> 'bigfile.colclass <-' instead? Do I even need to read in all of the
> >> rows
> >>>> to
> >>>>> test for a matrix?
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Spencer
> >>>>>
> >>>>
> >>>> I don’t think this option affects how much data is read in, just how
> >> much
> >>>> is printed to the screen. Use the function str() on your imported
> >> object to
> >>>> see how many rows, among other things, were brought in.
> >>>>
> >>>>
> >>>>>         [[alternative HTML version deleted]]
> >>>>>
> >>>>> ______________________________________________
> >>>>> [hidden email] 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.
> >>>>
> >>>>
> >>>> --
> >>>> Kevin E. Thorpe
> >>>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> >>>> Li Ka Shing Knowledge Institute of St. Michael's
> >>>> Assistant Professor, Dalla Lana School of Public Health
> >>>> University of Toronto
> >>>> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
> >>>>
> >>>>
> >>>
> >>>        [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> [hidden email] 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]]
> >
>
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: Using options(max.print = 1000000) to read in data

Patrick (Malone Quantitative)
Spencer, what prints into your console is not the point. As others have
said, the best way to find it if an R object is the type matrix is
is.matrix() . That will return TRUE or FALSE.

        [[alternative HTML version deleted]]

______________________________________________
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Re: Using options(max.print = 1000000) to read in data

Michael Friendly
In reply to this post by Spencer Brackett
You continue to labor under false conceptions, starting with your
subject line indicating that you should be able to *see* your huge data
set in the R console.
Take a pause, have a coffee or tea and re-read the helpful advice
various people have tried to offer before continuing this thread.

-Michael

On 7/09/19 2:44 p.m., Spencer Brackett wrote:

> So even though a number of rows were omitted  during the ‘print in’ or
> visualization of the dataset into my console, the data frame is now
> set as a matrix? I believe so, per Mr. Barradas’s last email. Sorry
> for the confusion, I was expecting the whole dataset to load into my
> console and was concerned that perhaps if I had to set the data in the
> data frame as a matrix (if not already), then I would not achieve this
> result.
>
> Thanks,
>
> Spencer
>
> On Tue, Jul 9, 2019 at 6:21 AM Michael Friendly <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Why do you need it to be a matrix? A data.frame is like a matrix, but
>     allows columns of mixed types.
>
>     as.matrix() will coerce your data frame to a matrix if you really
>     need this.
>
>     On 7/08/19 4:43 p.m., Spencer Brackett wrote:
>     > Using str(GBM.txt) produced the same output as last time, which
>     lists the
>     > number of objects acting on a particular number of variables for
>     the said
>     > dataset and a few rows read from the original file.
>     >
>     > The result of class(GBM.txt) generates the following..
>     >
>     >> class(GBM.txt)
>     > [1] "data.frame"
>     >
>     > Is this to say that the object is set as a 'data frame', opposed
>     to a
>     > 'matrix' ?
>     >
>     > I will try running ?is.matrix now
>     >
>     >
>     >
>     > On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas
>     <[hidden email] <mailto:[hidden email]>> wrote:
>     >
>     >> Hello,
>     >>
>     >> Inline.
>     >>
>     >> Às 15:26 de 08/07/19, Spencer Brackett escreveu:
>     >>> Thank you,
>     >>>
>     >>> Here is a summary of the resulting output....
>     >>>
>     >>>> nrow(GBM.txt)
>     >>> [1] 20530
>     >>>> ncol(GBM.txt)
>     >>> [1] 173
>     >>>
>     >>> This corresponds with the info found in my global environment
>     for the
>     >>> object indicated. Now, how do I go about determining if the
>     dataset is a
>     >>> matrix?
>     >>
>     >> Try any of
>     >>
>     >> str(GBM.txt)
>     >> class(GBM.txt)
>     >>
>     >> Also, like Kevin said, max.print only affects how much is
>     printed, not
>     >> the read functions. Why change max.print at all? The default value
>     >> (1000) is large enough, I have never needed to see more than
>     this at a
>     >> time. In fact, to have an idea of the data I would rather
>     further limit
>     >> the number of matrix lines printed with
>     >>
>     >> head(object)
>     >> tail(object)
>     >>
>     >>
>     >>
>     >> Hope this helps,
>     >>
>     >> Rui Barradas
>     >>>
>     >>>
>     >>> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe
>     <[hidden email] <mailto:[hidden email]>>
>     >>> wrote:
>     >>>
>     >>>>
>     >>>>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
>     >>>> [hidden email]
>     <mailto:[hidden email]>> wrote:
>     >>>>>
>     >>>>> Hello,
>     >>>>>
>     >>>>>    I am trying to reload some data into R in order to check
>     to see if
>     >> it is
>     >>>>> formatted as a matrix. I used the command options(max.print
>     = 10000000)
>     >>>> to
>     >>>>> account for the 20,000 some rows omitted previously when
>     just using the
>     >>>>> basic version of this function. After entering this command, the
>     >> dataset
>     >>>>> mostly loaded into R, but 14717 rows were still omitted.
>     >>>>>
>     >>>>>    Can I simply increase the number indicted after
>     'max.print =' to
>     >> read in
>     >>>>> the remaining rows, or should I use 'bigfile.sample <-' or
>     >>>>> 'bigfile.colclass <-' instead? Do I even need to read in all
>     of the
>     >> rows
>     >>>> to
>     >>>>> test for a matrix?
>     >>>>>
>     >>>>> Best,
>     >>>>>
>     >>>>> Spencer
>     >>>>>
>     >>>>
>     >>>> I don’t think this option affects how much data is read in,
>     just how
>     >> much
>     >>>> is printed to the screen. Use the function str() on your imported
>     >> object to
>     >>>> see how many rows, among other things, were brought in.
>     >>>>
>     >>>>
>     >>>>>         [[alternative HTML version deleted]]
>     >>>>>
>     >>>>> ______________________________________________
>     >>>>> [hidden email] <mailto:[hidden email]> 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.
>     >>>>
>     >>>>
>     >>>> --
>     >>>> Kevin E. Thorpe
>     >>>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>     >>>> Li Ka Shing Knowledge Institute of St. Michael's
>     >>>> Assistant Professor, Dalla Lana School of Public Health
>     >>>> University of Toronto
>     >>>> email: [hidden email]
>     <mailto:[hidden email]> Tel: 416.864.5776  Fax: 416.864.3016
>     >>>>
>     >>>>
>     >>>
>     >>>        [[alternative HTML version deleted]]
>     >>>
>     >>> ______________________________________________
>     >>> [hidden email] <mailto:[hidden email]> 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]]
>     >
>

--
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section
York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca   Twitter: @datavisFriendly
Toronto, ONT  M3J 1P3 CANADA


        [[alternative HTML version deleted]]

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Re: Using options(max.print = 1000000) to read in data

Spencer Brackett
 My apologies! I made this much to complicated and allowed myself to become
confused with the straightforward advice given. I tried running the lines
Mr. Barradas suggested after receiving the output for as.matrix() and I
understand now. Thank you all again for your patience.

Best,

Spencer

On Tue, Jul 9, 2019 at 9:48 AM Michael Friendly <[hidden email]> wrote:

> You continue to labor under false conceptions, starting with your subject
> line indicating that you should be able to *see* your huge data set in
> the R console.
> Take a pause, have a coffee or tea and re-read the helpful advice various
> people have tried to offer before continuing this thread.
>
> -Michael
>
> On 7/09/19 2:44 p.m., Spencer Brackett wrote:
>
> So even though a number of rows were omitted  during the ‘print in’ or
> visualization of the dataset into my console, the data frame is now set as
> a matrix? I believe so, per Mr. Barradas’s last email. Sorry for the
> confusion, I was expecting the whole dataset to load into my console and
> was concerned that perhaps if I had to set the data in the data frame as a
> matrix (if not already), then I would not achieve this result.
>
> Thanks,
>
> Spencer
>
> On Tue, Jul 9, 2019 at 6:21 AM Michael Friendly <[hidden email]> wrote:
>
>> Why do you need it to be a matrix? A data.frame is like a matrix, but
>> allows columns of mixed types.
>>
>> as.matrix() will coerce your data frame to a matrix if you really need
>> this.
>>
>> On 7/08/19 4:43 p.m., Spencer Brackett wrote:
>> > Using str(GBM.txt) produced the same output as last time, which lists
>> the
>> > number of objects acting on a particular number of variables for the
>> said
>> > dataset and a few rows read from the original file.
>> >
>> > The result of class(GBM.txt) generates the following..
>> >
>> >> class(GBM.txt)
>> > [1] "data.frame"
>> >
>> > Is this to say that the object is set as a 'data frame', opposed to a
>> > 'matrix' ?
>> >
>> > I will try running ?is.matrix now
>> >
>> >
>> >
>> > On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas <[hidden email]>
>> wrote:
>> >
>> >> Hello,
>> >>
>> >> Inline.
>> >>
>> >> Às 15:26 de 08/07/19, Spencer Brackett escreveu:
>> >>> Thank you,
>> >>>
>> >>> Here is a summary of the resulting output....
>> >>>
>> >>>> nrow(GBM.txt)
>> >>> [1] 20530
>> >>>> ncol(GBM.txt)
>> >>> [1] 173
>> >>>
>> >>> This corresponds with the info found in my global environment for the
>> >>> object indicated. Now, how do I go about determining if the dataset
>> is a
>> >>> matrix?
>> >>
>> >> Try any of
>> >>
>> >> str(GBM.txt)
>> >> class(GBM.txt)
>> >>
>> >> Also, like Kevin said, max.print only affects how much is printed, not
>> >> the read functions. Why change max.print at all? The default value
>> >> (1000) is large enough, I have never needed to see more than this at a
>> >> time. In fact, to have an idea of the data I would rather further limit
>> >> the number of matrix lines printed with
>> >>
>> >> head(object)
>> >> tail(object)
>> >>
>> >>
>> >>
>> >> Hope this helps,
>> >>
>> >> Rui Barradas
>> >>>
>> >>>
>> >>> On Mon, Jul 8, 2019 at 10:16 AM Kevin Thorpe <
>> [hidden email]>
>> >>> wrote:
>> >>>
>> >>>>
>> >>>>> On Jul 8, 2019, at 10:06 AM, Spencer Brackett <
>> >>>> [hidden email]> wrote:
>> >>>>>
>> >>>>> Hello,
>> >>>>>
>> >>>>>    I am trying to reload some data into R in order to check to see
>> if
>> >> it is
>> >>>>> formatted as a matrix. I used the command options(max.print =
>> 10000000)
>> >>>> to
>> >>>>> account for the 20,000 some rows omitted previously when just using
>> the
>> >>>>> basic version of this function. After entering this command, the
>> >> dataset
>> >>>>> mostly loaded into R, but 14717 rows were still omitted.
>> >>>>>
>> >>>>>    Can I simply increase the number indicted after 'max.print =' to
>> >> read in
>> >>>>> the remaining rows, or should I use 'bigfile.sample <-' or
>> >>>>> 'bigfile.colclass <-' instead? Do I even need to read in all of the
>> >> rows
>> >>>> to
>> >>>>> test for a matrix?
>> >>>>>
>> >>>>> Best,
>> >>>>>
>> >>>>> Spencer
>> >>>>>
>> >>>>
>> >>>> I don’t think this option affects how much data is read in, just how
>> >> much
>> >>>> is printed to the screen. Use the function str() on your imported
>> >> object to
>> >>>> see how many rows, among other things, were brought in.
>> >>>>
>> >>>>
>> >>>>>         [[alternative HTML version deleted]]
>> >>>>>
>> >>>>> ______________________________________________
>> >>>>> [hidden email] 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.
>> >>>>
>> >>>>
>> >>>> --
>> >>>> Kevin E. Thorpe
>> >>>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>> >>>> Li Ka Shing Knowledge Institute of St. Michael's
>> >>>> Assistant Professor, Dalla Lana School of Public Health
>> >>>> University of Toronto
>> >>>> email: [hidden email]  Tel: 416.864.5776  Fax:
>> 416.864.3016
>> >>>>
>> >>>>
>> >>>
>> >>>        [[alternative HTML version deleted]]
>> >>>
>> >>> ______________________________________________
>> >>> [hidden email] 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]]
>> >
>>
>>
> --
> Michael Friendly     Email: friendly AT yorku DOT ca
> Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section
> York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
> 4700 Keele Street    Web:   http://www.datavis.ca   Twitter: @datavisFriendly
> Toronto, ONT  M3J 1P3 CANADA
>
>

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