From j|ox @end|ng |rom mcm@@ter@c@  Tue Sep 17 14:29:17 2019
From: j|ox @end|ng |rom mcm@@ter@c@ (Fox, John)
Date: Tue, 17 Sep 2019 12:29:17 +0000
Subject: [Rd] 
 head.matrix can return 1000s of columns -- limit to n or add
 new argument?
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Message-ID: <674779E0-B1F6-4DC2-9F1C-D5D48B044B66@mcmaster.ca>

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 at 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.
> 
> 
> 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 at 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 at 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 at 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]]
>>>>>> 
>>>>>> ______________________________________________
>>>>>> R-devel at r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sOZlR-nzy_f_Sje6VGA6IXYQM01BO39OQ2zqA8mtaGI&s=VyNGYbk1jJJqirYBwnhKX60dCp31ArtS62RmXKn86O4&e=
>>>>>> 
>>>>> 
>>> 
>>>>  [[alternative HTML version deleted]]
>>> 
>>>> ______________________________________________
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>>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
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>> 
> 
> -- 
> Herv? Pag?s
> 
> 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
> 
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[Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
Fox, John