[Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
Martin Maechler
m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Tue Sep 17 18:17:03 CEST 2019
>>>>> Fox, John
>>>>> on Tue, 17 Sep 2019 12:32:13 +0000 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 <jfox using mcmaster.ca> 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 <hpages using fredhutch.org> 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 <maechler using stat.math.ethz.ch>
>>>> 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
>>>>> <gabembecker using gmail.com> 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 11 21 31 41 51 61 71 81 91
>>>>>>>
>>>>>>> [2,] 2 12 22 32 42 52 62 72 82 92
>>>>>>>
>>>>>>> [3,] 3 13 23 33 43 53 63 73 83 93
>>>>>>>
>>>>>>> [4,] 4 14 24 34 44 54 64 74 84 94
>>>>>>>
>>>>>>> [5,] 5 15 25 35 45 55 65 75 85 95
>>>>>>>
>>>>>>> [6,] 6 16 26 36 46 56 66 76 86 96
>>>>>>>
>>>>>>>> *head2(mat)*
>>>>>>>
>>>>>>> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
>>>>>>>
>>>>>>> [1,] 1 11 21 31 41 51 61 71 81 91
>>>>>>>
>>>>>>> [2,] 2 12 22 32 42 52 62 72 82 92
>>>>>>>
>>>>>>> [3,] 3 13 23 33 43 53 63 73 83 93
>>>>>>>
>>>>>>> [4,] 4 14 24 34 44 54 64 74 84 94
>>>>>>>
>>>>>>> [5,] 5 15 25 35 45 55 65 75 85 95
>>>>>>>
>>>>>>> [6,] 6 16 26 36 46 56 66 76 86 96
>>>>>>>
>>>>>>>> *head2(mat, c(2, 3))*
>>>>>>>
>>>>>>> [,1] [,2] [,3]
>>>>>>>
>>>>>>> [1,] 1 11 21
>>>>>>>
>>>>>>> [2,] 2 12 22
>>>>>>>
>>>>>>>> *head2(mat, c(2, -9))*
>>>>>>>
>>>>>>> [,1]
>>>>>>>
>>>>>>> [1,] 1
>>>>>>>
>>>>>>> [2,] 2
>>>>>>>
>>>>>>>
>>>>>>> Now one thing to keep in mind here, is that I think we'd
>>>>>>> either a) have to make the non-recycling behavior
>>>>>>> permanent, or b) have head treat data.frames and matrices
>>>>>>> different with respect to the subsets they grab (which
>>>>>>> strikes me as a *Bad Plan *(tm)).
>>>>>>>
>>>>>>> So I don't think the default behavior would ever be
>>>>>>> mat[1:6, 1:6], not because of backwards compatibility,
>>>>>>> but because at least in my intuition that is just not
>>>>>>> what head on a data.frame should do by default, and I
>>>>>>> think the behaviors for the basic rectangular datatypes
>>>>>>> should "stick together". I mean, also because of
>>>>>>> backwards compatibility, but that could *in theory*
>>>>>>> change across a long enough deprecation cycle, but the
>>>>>>> conceptually right thing to do with a data.frame probably
>>>>>>> won't.
>>>>>>>
>>>>>>> All of that said, is head(mat, c(6, 6)) really that much
>>>>>>> easier to type/better than just mat[1:6, 1:6, drop=FALSE]
>>>>>>> (I know this will behave differently if any of the dims
>>>>>>> of mat are less than 6, but if so why are you heading it
>>>>>>> in the first place ;) )? I don't really have a strong
>>>>>>> feeling on the answer to that.
>>>>>>>
>>>>>>> I'm happy to put a patch for head.matrix,
>>>>>>> head.data.frame, tail.matrix and tail.data.frame, plus
>>>>>>> documentation, if people on R-core are interested in
>>>>>>> this.
>>>>>>>
>>>>>>> Note, as most here probably know, and as alluded to
>>>>>>> above, length(n) > 1 for head or tail currently give an
>>>>>>> error, so this would be an extension of the existing
>>>>>>> functionality in the mathematical extension sense, where
>>>>>>> all existing behavior would remain identical, but the
>>>>>>> support/valid parameter space would grow.
>>>>>>>
>>>>>>> Best, ~G
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jul 12, 2019 at 4:03 PM Abby Spurdle
>>>>>>> <spurdle.a using gmail.com> wrote:
>>>>>>>
>>>>>>>>> I assume there are lots of backwards-compatibility
>>>>>>>> issues as well as valid > use cases for this behavior,
>>>>>>>> so I guess defaulting to M[1:6, 1:6] is out of > the
>>>>>>>> question.
>>>>>>>>
>>>>>>>> Agree.
>>>>>>>>
>>>>>>>>> Is there any scope for adding a new argument to
>>>>>>>> head.matrix that would > allow this flexibility?
>>>>>>>>
>>>>>>>> I agree with what you're trying to achieve. However,
>>>>>>>> I'm not sure this is as simple as you're suggesting.
>>>>>>>>
>>>>>>>> What if the user wants "head" in rows but "tail" in
>>>>>>>> columns. Or "head" in rows, and both "head" and "tail"
>>>>>>>> in columns. With head and tail alone, there's a
>>>>>>>> combinatorial explosion.
>>>>>>>>
>>>>>>>> Also, when using tail on an unnamed matrix, it may be
>>>>>>>> desirable to name rows and columns.
>>>>>>>>
>>>>>>>> And all of this assumes standard matrix objects. Add in
>>>>>>>> a matrix subclasses and related objects, and things get
>>>>>>>> more complex still.
>>>>>>>>
>>>>>>>> As I suggested in a another thread, a few days ago, I'm
>>>>>>>> planning to write an R package for matrices and
>>>>>>>> matrix-like objects (possibly extending the Matrix
>>>>>>>> package), with an initial emphasis on subsetting,
>>>>>>>> printing and formatting. So, I'm interested to hear
>>>>>>>> more suggestions on this topic.
>>>>>>>>
>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>
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>>>>>>>
>>>>>
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>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages using fredhutch.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
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>>
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