Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
Dear Herve,
The brief() generic function in the car package does something very similar to
that for data frames (and has methods for other classes of objects as well).
Best,
John
-
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: http::/socserv.mcmaster.ca/jfox
> On Sep 17, 2019, at 2:52 AM, Pages, Herve wrote:
>
> Hi,
>
> Alternatively, how about a new glance() generic that would do something
> like this:
>
>> library(DelayedArray)
>> glance <- DelayedArray:::show_compact_array
>
>> M <- matrix(rnorm(1e6), nrow = 1000L, ncol = 2000L)
>> glance(M)
> <1000 x 2000> matrix object of type "double":
>[,1][,2][,3] ...[,1999][,2000]
>[1,] -0.8854896 1.8010288 1.3051341 . -0.4473593 0.4684985
>[2,] -0.8563415 -0.7102768 -0.9309155 . -1.8743504 0.4300557
>[3,] 1.0558159 -0.5956583 1.2689806 . 2.7292249 0.2608300
>[4,] 0.7547356 0.1465714 0.1798959 . -0.1778017 1.3417423
>[5,] 0.8037360 -2.7081809 0.9766657 . -0.9902788 0.1741957
> ... . . . . . .
> [996,] 0.67220752 0.07804320 -0.38743454 . 0.4438639 -0.8130713
> [997,] -0.67349962 -1.15292067 -0.54505567 . 0.4630923 -1.6287694
> [998,] 0.03374595 -1.68061325 -0.88458368 . -0.2890962 0.2552267
> [999,] 0.47861492 1.25530912 0.19436708 . -0.5193121 -1.1695501
> [1000,] 1.52819218 2.23253275 -1.22051720 . -1.0342430 -0.1703396
>
>> A <- array(rnorm(1e6), c(50, 20, 10, 100))
>> glance(A)
> <50 x 20 x 10 x 100> array object of type "double":
> ,,1,1
> [,1] [,2] [,3] ... [,19] [,20]
> [1,] 0.78319619 0.82258390 0.09122269 . 1.7288189 0.7968574
> [2,] 2.80687459 0.63709640 0.80844430 . -0.3963161 -1.2768284
> ... . . . . . .
> [49,] -1.0696320 -0.1698111 2.0082890 . 0.4488292 0.5215745
> [50,] -0.7012526 -2.0818229 0.7750518 . 0.3189076 0.1437394
>
> ...
>
> ,,10,100
> [,1] [,2] [,3] ... [,19] [,20]
> [1,] 0.5360649 0.5491561 -0.4098350 . 0.7647435 0.5640699
> [2,] 0.7924093 -0.7395815 -1.3792913 . 0.1980287 -0.2897026
> ... . . . . . .
> [49,] 0.6266209 0.3778512 1.4995778 . -0.3820651 -1.4241691
> [50,] 1.9218715 3.5475949 0.5963763 . 0.4005210 0.4385623
>
> H.
>
>
> On 9/16/19 00:54, Michael Chirico wrote:
>> Awesome. Gabe, since you already have a workshopped version, would you like
>> to proceed? Feel free to ping me to review the patch once it's posted.
>>
>> On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler
>> wrote:
>>
Michael Chirico
on Sun, 15 Sep 2019 20:52:34 +0800 writes:
>>>
Finally read in detail your response Gabe. Looks great,
and I agree it's quite intuitive, as well as agree against
non-recycling.
>>>
Once the length(n) == length(dim(x)) behavior is enabled,
I don't think there's any need/desire to have head() do
x[1:6,1:6] anymore. head(x, c(6, 6)) is quite clear for
those familiar with head(x, 6), it would seem to me.
>>>
Mike C
>>>
>>> Thank you, Gabe, and Michael.
>>> I did like Gabe's proposal already back in July but was
>>> busy and/or vacationing then ...
>>>
>>> If you submit this with a patch (that includes changes to both
>>> *.R and *.Rd , including some example) as "wishlist" item to R's
>>> bugzilla, I'm willing/happy to check and commit this to R-devel.
>>>
>>> Martin
>>>
>>>
On Sat, Jul 13, 2019 at 8:35 AM Gabriel Becker
wrote:
>>>
> Hi Michael and Abby,
>
> So one thing that could happen that would be backwards
> compatible (with the exception of something that was an
> error no longer being an error) is head and tail could
> take vectors of length (dim(x)) rather than integers of
> length for n, with the default being n=6 being equivalent
> to n = c(6, dim(x)[2], <...>, dim(x)[k]), at least for
> the deprecation cycle, if not permanently. It not
> recycling would be unexpected based on the behavior of
> many R functions but would preserve the current behavior
> while granting more fine-grained control to users that
> feel they need it.
>
> A rapidly thrown-together prototype of such a method for
> the head of a matrix case is as follows:
>
> head2 = function(x, n = 6L, ...) { indvecs =
> lapply(seq_along(dim(x)), function(i) { if(length(n) >=
> i) { ni = n[i] } else { ni = dim(x)[i] } if(ni < 0L) ni =
> max(nrow(x) + ni, 0L) else ni = min(ni, dim(x)[i])
> seq_len(ni) }) lstargs = c(list(x),indvecs, drop = FALSE)
> do.call("[", lstargs) }
>
>
>> mat = matrix(1:100, 10, 10)
>
>> *head(mat)*
>
> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
>
> [1,] 1 1
Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
Dear Herve,
Sorry, I should have said "matrices" rather than "data frames" -- brief() has
methods for both.
Best,
John
-
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: http::/socserv.mcmaster.ca/jfox
> On Sep 17, 2019, at 8:29 AM, Fox, John wrote:
>
> Dear Herve,
>
> The brief() generic function in the car package does something very similar
> to that for data frames (and has methods for other classes of objects as
> well).
>
> Best,
> John
>
> -
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> Web: http::/socserv.mcmaster.ca/jfox
>
>> On Sep 17, 2019, at 2:52 AM, Pages, Herve wrote:
>>
>> Hi,
>>
>> Alternatively, how about a new glance() generic that would do something
>> like this:
>>
>>> library(DelayedArray)
>>> glance <- DelayedArray:::show_compact_array
>>
>>> M <- matrix(rnorm(1e6), nrow = 1000L, ncol = 2000L)
>>> glance(M)
>> <1000 x 2000> matrix object of type "double":
>> [,1][,2][,3] ...[,1999][,2000]
>> [1,] -0.8854896 1.8010288 1.3051341 . -0.4473593 0.4684985
>> [2,] -0.8563415 -0.7102768 -0.9309155 . -1.8743504 0.4300557
>> [3,] 1.0558159 -0.5956583 1.2689806 . 2.7292249 0.2608300
>> [4,] 0.7547356 0.1465714 0.1798959 . -0.1778017 1.3417423
>> [5,] 0.8037360 -2.7081809 0.9766657 . -0.9902788 0.1741957
>>... . . . . . .
>> [996,] 0.67220752 0.07804320 -0.38743454 . 0.4438639 -0.8130713
>> [997,] -0.67349962 -1.15292067 -0.54505567 . 0.4630923 -1.6287694
>> [998,] 0.03374595 -1.68061325 -0.88458368 . -0.2890962 0.2552267
>> [999,] 0.47861492 1.25530912 0.19436708 . -0.5193121 -1.1695501
>> [1000,] 1.52819218 2.23253275 -1.22051720 . -1.0342430 -0.1703396
>>
>>> A <- array(rnorm(1e6), c(50, 20, 10, 100))
>>> glance(A)
>> <50 x 20 x 10 x 100> array object of type "double":
>> ,,1,1
>>[,1] [,2] [,3] ... [,19] [,20]
>> [1,] 0.78319619 0.82258390 0.09122269 . 1.7288189 0.7968574
>> [2,] 2.80687459 0.63709640 0.80844430 . -0.3963161 -1.2768284
>> ... . . . . . .
>> [49,] -1.0696320 -0.1698111 2.0082890 . 0.4488292 0.5215745
>> [50,] -0.7012526 -2.0818229 0.7750518 . 0.3189076 0.1437394
>>
>> ...
>>
>> ,,10,100
>>[,1] [,2] [,3] ... [,19] [,20]
>> [1,] 0.5360649 0.5491561 -0.4098350 . 0.7647435 0.5640699
>> [2,] 0.7924093 -0.7395815 -1.3792913 . 0.1980287 -0.2897026
>> ... . . . . . .
>> [49,] 0.6266209 0.3778512 1.4995778 . -0.3820651 -1.4241691
>> [50,] 1.9218715 3.5475949 0.5963763 . 0.4005210 0.4385623
>>
>> H.
>>
>>
>> On 9/16/19 00:54, Michael Chirico wrote:
>>> Awesome. Gabe, since you already have a workshopped version, would you like
>>> to proceed? Feel free to ping me to review the patch once it's posted.
>>>
>>> On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler
>>> wrote:
>>>
> Michael Chirico
>on Sun, 15 Sep 2019 20:52:34 +0800 writes:
> Finally read in detail your response Gabe. Looks great,
> and I agree it's quite intuitive, as well as agree against
> non-recycling.
> Once the length(n) == length(dim(x)) behavior is enabled,
> I don't think there's any need/desire to have head() do
> x[1:6,1:6] anymore. head(x, c(6, 6)) is quite clear for
> those familiar with head(x, 6), it would seem to me.
> Mike C
Thank you, Gabe, and Michael.
I did like Gabe's proposal already back in July but was
busy and/or vacationing then ...
If you submit this with a patch (that includes changes to both
*.R and *.Rd , including some example) as "wishlist" item to R's
bugzilla, I'm willing/happy to check and commit this to R-devel.
Martin
> On Sat, Jul 13, 2019 at 8:35 AM Gabriel Becker
> wrote:
>> Hi Michael and Abby,
>>
>> So one thing that could happen that would be backwards
>> compatible (with the exception of something that was an
>> error no longer being an error) is head and tail could
>> take vectors of length (dim(x)) rather than integers of
>> length for n, with the default being n=6 being equivalent
>> to n = c(6, dim(x)[2], <...>, dim(x)[k]), at least for
>> the deprecation cycle, if not permanently. It not
>> recycling would be unexpected based on the behavior of
>> many R functions but would preserve the current behavior
>> while granting more fine-grained control to users that
>> feel they need it.
>>
>> A rapidly thrown-together prototype of such a method for
>> the head of a matrix case is as follows:
>>
>> head2 = function(x, n = 6L, ...) { indvecs =
Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
> Fox, John
> on Tue, 17 Sep 2019 12:32:13 + writes:
> Dear Herve,
> Sorry, I should have said "matrices" rather than "data frames" -- brief()
has methods for both.
> Best,
> John
> -
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> Web: http::/socserv.mcmaster.ca/jfox
>> On Sep 17, 2019, at 8:29 AM, Fox, John wrote:
>>
>> Dear Herve,
>>
>> The brief() generic function in the car package does something very
similar to that for data frames (and has methods for other classes of objects
as well).
>>
>> Best,
>> John
>>
>> -
>> John Fox, Professor Emeritus
>> McMaster University
>> Hamilton, Ontario, Canada
>> Web: http::/socserv.mcmaster.ca/jfox
>>
>>> On Sep 17, 2019, at 2:52 AM, Pages, Herve wrote:
>>>
>>> Hi,
>>>
>>> Alternatively, how about a new glance() generic that would do something
>>> like this:
>>>
library(DelayedArray)
glance <- DelayedArray:::show_compact_array
>>>
M <- matrix(rnorm(1e6), nrow = 1000L, ncol = 2000L)
glance(M)
>>> <1000 x 2000> matrix object of type "double":
>>> [,1][,2][,3] ...[,1999][,2000]
>>> [1,] -0.8854896 1.8010288 1.3051341 . -0.4473593 0.4684985
>>> [2,] -0.8563415 -0.7102768 -0.9309155 . -1.8743504 0.4300557
>>> [3,] 1.0558159 -0.5956583 1.2689806 . 2.7292249 0.2608300
>>> [4,] 0.7547356 0.1465714 0.1798959 . -0.1778017 1.3417423
>>> [5,] 0.8037360 -2.7081809 0.9766657 . -0.9902788 0.1741957
>>> ... . . . . . .
>>> [996,] 0.67220752 0.07804320 -0.38743454 . 0.4438639 -0.8130713
>>> [997,] -0.67349962 -1.15292067 -0.54505567 . 0.4630923 -1.6287694
>>> [998,] 0.03374595 -1.68061325 -0.88458368 . -0.2890962 0.2552267
>>> [999,] 0.47861492 1.25530912 0.19436708 . -0.5193121 -1.1695501
>>> [1000,] 1.52819218 2.23253275 -1.22051720 . -1.0342430 -0.1703396
>>>
A <- array(rnorm(1e6), c(50, 20, 10, 100))
glance(A)
>>> <50 x 20 x 10 x 100> array object of type "double":
>>> ,,1,1
>>> [,1] [,2] [,3] ... [,19] [,20]
>>> [1,] 0.78319619 0.82258390 0.09122269 . 1.7288189 0.7968574
>>> [2,] 2.80687459 0.63709640 0.80844430 . -0.3963161 -1.2768284
>>> ... . . . . . .
>>> [49,] -1.0696320 -0.1698111 2.0082890 . 0.4488292 0.5215745
>>> [50,] -0.7012526 -2.0818229 0.7750518 . 0.3189076 0.1437394
>>>
>>> ...
>>>
>>> ,,10,100
>>> [,1] [,2] [,3] ... [,19] [,20]
>>> [1,] 0.5360649 0.5491561 -0.4098350 . 0.7647435 0.5640699
>>> [2,] 0.7924093 -0.7395815 -1.3792913 . 0.1980287 -0.2897026
>>> ... . . . . . .
>>> [49,] 0.6266209 0.3778512 1.4995778 . -0.3820651 -1.4241691
>>> [50,] 1.9218715 3.5475949 0.5963763 . 0.4005210 0.4385623
>>>
>>> H.
Thank you, Hervé and John.
Both glance() and brief() are nice, and I think a version of one of
them could also make a nice addition to the 'utils' package.
However, there's a principal difference between them and the
proposed generalized head {or tail} :
The latter really does *return* a sub matrix/array of chosen
dimensions with modified dimnames and that *object* then is
printed if not assigned.
OTOH, glance() and brief() rather are versions of print()
and I think have a dedicated "display-only" purpose {yes, I see they do
return something; glance() returning a character object, brief()
returning the principal argument invisibly, the same as any
"correct" print() method..}
>From the above, I think it may make sense to entertain both a
generalization of head() and one such a glance() / brief()
/.. function which for a matrix shows all 4 corners of the
matrix of data frame.
There's another important criterion here: __Simplicity__ in the
code that's added (and will have to be maintained as part of R
"forever" into the future)...
AFAICS, the DelayedArray stuff is beatifully modular, but
possibly also much entangled in the dependent packages and classes we
cannot require for 'utils'.
The current source for head() and tail() and all their methods
in utils is just 83 lines of code {file utils/R/head.R minus
the initial mostly copyright comments}.
I am very reluctant to consider blowing that up by factors...
Martin
>>> On 9/16/19 00:54, Michael Chirico wrote:
Awesome. Gabe, since you already have a workshopped version, would you
like
to proceed? Feel free to ping me to review the patch once it's posted.
On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler
wrot
