From mikko.korpela at aalto.fi  Mon Feb 15 11:31:51 2016
From: mikko.korpela at aalto.fi (Mikko Korpela)
Date: Mon, 15 Feb 2016 12:31:51 +0200
Subject: [Rd] inconsistency in treatment of USE.NAMES argument
In-Reply-To: <CAOQ5Nydc506OsZ27vg0yJHywjbRM090E5v5iAC4pyi+Oeg-rRQ@mail.gmail.com>
References: <56B8E312.1060707@fredhutch.org>
	<22201.53140.811577.447542@stat.math.ethz.ch>
	<CAOQ5Nydc506OsZ27vg0yJHywjbRM090E5v5iAC4pyi+Oeg-rRQ@mail.gmail.com>
Message-ID: <56C1A917.7030609@aalto.fi>

The two CRAN packages I'm (co)authoring, dplR and sisal, would both be
OK with the change. (Cc'ing to the Maintainer of dplR and my other email
address)

- Mikko

On 11.02.2016 17:02, Michael Lawrence wrote:
> Changing the vapply() behavior makes sense in principle. I analyzed
> the CRAN code base using the R parser and found 143 instances of
> calling vapply with USE.NAMES=FALSE. These would need to be inspected
> to understand the consequences of the change.
> 
> For reference:
> /AzureML/R/datasets.R:226
> /BBmisc/R/toRangeStr.R:33
> /DBI/R/DBDriver.R:205
> /Kmisc/R/str_rev.R:37
> /Matrix/R/diagMatrix.R:98
> /MuMIn/R/utils-models.R:110
> /OpenMx/R/MxNamespace.R:702
> /OrthoPanels/R/opm.R:167
> /XML2R/R/utils.R:16
> /assertive.base/tests/testthat/test-utils.R:14
> /bigrquery/R/utils.r:13
> /bold/R/zzz.R:29
> /checkmate/R/checkList.r:56
> /coin/R/ExactDistributions.R:80
> /coin/R/ExactDistributions.R:97
> /coin/R/ExactDistributions.R:234
> /coin/R/SymmetryTests.R:217
> /copula/R/aux-acopula.R:950
> /covr/R/data_frame.R:13
> /covr/R/display_name.R:40
> /cplm/R/lme4_lmer.R:423
> /crunch/R/batches.R:71
> /crunch/R/batches.R:102
> /crunch/R/categorical-array.R:87
> /crunch/R/hide-variables.R:78
> /crunch/R/misc.R:68
> /crunch/R/share.R:11
> /crunch/R/shoji-catalog.R:39
> /crunch/R/show.R:88
> /crunch/R/subvariables.R:76
> /crunch/R/subvariables.R:95
> /dplR/R/common.interval.R:8
> /dplR/R/fill.internal.NA.R:47
> /dplR/R/helpers.R:3
> /dplyr/R/dataframe.R:49
> /dplyr/R/glimpse.R:38
> /dplyr/R/id.r:36
> /dplyr/R/tbl-cube.r:98
> /dplyr/R/utils.r:15
> /fulltext/R/chunks.R:352
> /fulltext/R/chunks.R:356
> /ggvis/R/transform.R:56
> /httr/R/oauth-token-utils.R:23
> /igraph/R/lazyeval.R:219
> /jsonlite/R/asJSON.data.frame.R:74
> /jsonlite/R/deparse_vector.R:26
> /jsonlite/R/simplifyDataFrame.R:14
> /jsonlite/R/unescape_unicode.R:10
> /knitr/R/utils.R:207
> /knitrBootstrap/R/knit_bootstrap.R:303
> /lazyeval/R/names.R:27
> /learningr/R/buggy_count.R:67
> /lintr/R/absolute_paths_linter.R:35
> /lintr/R/absolute_paths_linter.R:71
> /loo/R/helpers.R:13
> /loo/R/helpers.R:20
> /matconv/R/convEasySyntax.R:71
> /matconv/R/convFunctionCalls.R:11
> /matconv/R/utils.R:113
> /micropan/R/biostrings.R:80
> /micropan/R/biostrings.R:106
> /mime/R/mime.R:129
> /packrat/R/bundle.R:137
> /packrat/R/hooks.R:45
> /packrat/R/lockfile.R:56
> /pixiedust/R/sprinkle_colnames.R:66
> /plyr/R/id.r:38
> /polyCub/R/polyCub.SV.R:110
> /polyCub/R/polyCub.exact.Gauss.R:99
> /polyCub/R/polyCub.iso.R:130
> /polyCub/R/polyCub.iso.R:166
> /polyCub/R/polyCub.iso.R:168
> /pryr/R/dots.r:25
> /rappdirs/R/utils.r:39
> /rbison/R/bison.R:181
> /rcrossref/R/cr_ft_text.R:191
> /rcrossref/R/get_styles.R:16
> /rebus.base/R/internal.R:29
> /rerddap/R/info.R:73
> /rerddap/R/info.R:80
> /rerddap/R/search.R:37
> /rerddap/R/search_adv.R:64
> /reutils/R/ecitmatch.R:33
> /reutils/R/parse-docsum.R:53
> /reutils/R/utils.R:44
> /reutils/R/utils.R:51
> /reutils/R/utils.R:55
> /rgbif/R/occ_search.r:230
> /rgbif/R/zzz.r:120
> /rjstat/R/rjstat.R:75
> /rlist/R/internal.R:155
> /rnoaa/R/homr.R:140
> /rnoaa/R/storm_shp.R:42
> /roxygen2/R/template.R:27
> /rplos/R/fulltext.R:29
> /rplos/R/fulltext.R:82
> /shiny/inst/tests/test-bootstrap.r:12
> /shinyjs/inst/examples/demo/helpers.R:49
> /simcausal/R/network.R:319
> /sisal/R/sisalTable.R:806
> /sisal/R/sisalTable.R:829
> /sisal/R/sisalTable.R:853
> /sisal/R/sisalTable.R:915
> /sisal/R/sisalTable.R:924
> /sisal/R/sisalTable.R:933
> /stringdist/R/seqdist.R:130
> /stringdist/R/stringdist.R:286
> /surveillance/R/calibration_null.R:25
> /surveillance/R/calibration_null.R:185
> /surveillance/R/epidata.R:356
> /surveillance/R/epidata.R:362
> /surveillance/R/hhh4.R:311
> /surveillance/R/hhh4_methods.R:403
> /surveillance/R/hhh4_oneStepAhead.R:126
> /surveillance/R/hhh4_plot.R:419
> /surveillance/R/hhh4_plot.R:691
> /surveillance/R/hhh4_plot.R:744
> /surveillance/R/pit.R:29
> /surveillance/R/pit.R:45
> /surveillance/R/spatial_tools.R:261
> /surveillance/R/spatial_tools.R:264
> /surveillance/R/twinSIR_profile.R:229
> /surveillance/R/twinSIR_simulation.R:284
> /surveillance/R/twinSIR_simulation.R:288
> /surveillance/R/twinstim.R:212
> /surveillance/R/twinstim.R:553
> /surveillance/R/twinstim_epitest.R:188
> /surveillance/R/twinstim_helper.R:139
> /surveillance/R/twinstim_siaf.R:176
> /surveydata/R/questions.R:164
> /sweidnumbr/R/luhn_algo.R:75
> /sweidnumbr/R/oin.R:104
> /sweidnumbr/R/oin.R:134
> /sweidnumbr/R/pin.R:202
> /sweidnumbr/R/pin.R:440
> /taxize/R/gni_parse.R:29
> /taxize/inst/ignore/taxonclass.R:117
> /taxize/inst/ignore/taxonclass2.R:157
> /testthat/R/utils.r:13
> /textreuse/R/TextReuseCorpus.R:137
> /textreuse/R/minhash.R:46
> /textreuse/R/similarity.R:111
> /tidyr/R/id.R:17
> 
> On Tue, Feb 9, 2016 at 3:37 AM, Martin Maechler
> <maechler at stat.math.ethz.ch> wrote:
>>>>>>> Herv? Pag?s <hpages at fredhutch.org>
>>>>>>>     on Mon, 8 Feb 2016 10:48:50 -0800 writes:
>>
>>     > Hi,
>>     > Both vapply() and sapply() support the 'USE.NAMES' argument. According
>>     > to the man page:
>>
>>     > USE.NAMES: logical; if ?TRUE? and if ?X? is character, use ?X? as
>>     >    ?names? for the result unless it had names already.
>>
>>     > But if 'X' has names already and 'USE.NAMES' is FALSE, it's not clear
>>     > what will happen to the names. Are they going to propagate to the
>>     > result or not? Unfortunately, vapply() and sapply() give a different
>>     > answer:
>>
>>     >> vapply(list(A="a", B=1:2), is.integer, logical(1), USE.NAMES=FALSE)
>>     > [1] FALSE  TRUE
>>
>>     >> sapply(list(A="a", B=1:2), is.integer, USE.NAMES=FALSE)
>>     > A     B
>>     > FALSE  TRUE
>>
>> This is very unfortunate, and I was not aware of this.
>>
>> You know that sapply()  is an order of magnitude older than vapply()
>> and you probably don't know that lapply() is also somewhat older
>> than sapply() [but that part is pre-R (but S-) history ...]
>> which explains part:
>>
>> 1) lapply() does *not* have a  USE.NAMES  argument and it
>>    always keeps names when they are there in X.
>>
>> 2) sapply() has been designed as "s"implified l"apply" where
>>    in this case "simplified" also was to mean "user-friendly" /
>>    "simple to use".
>>    For that reason,
>>    a) sapply() also keeps names when they are there (as lapply).
>>    b) If USE.NAMES=TRUE (as by default) is also constructs names
>>       in cases where lapply() does not contain, i.e., in case of
>>       character X.
>>
>> 3) IIRC, the goals for vapply() had been  "like sapply", with two advantages:
>>    a. faster
>>    b. "error-checking" in the sense of ensuring consistent
>>        results of the single function calls.
>>
>>     > Wouldn't it make sense to have vapply() and sapply() treat the
>>     > 'USE.NAMES' argument consistently?
>>
>> Yes, but from what I wrote above, I believe  vapply() would have
>> to change.
>>
>> Martin
>>
>>
>>     > The behavior of vapply() seems
>>     > to make more sense to me. Note that it's consistent with what mapply()
>>     > does:
>>
>>     >> mapply(is.integer, list(A="a", B=1:2), USE.NAMES=FALSE)
>>     > [1] FALSE  TRUE
>>
>>     > If the behavior of sapply() cannot be changed, at least the man page
>>     > could clarify what happens when 'USE.NAMES' is FALSE, which is
>>     > different for each function.
>>
>>     > Thanks,
>>     > H.
>>
>>     > --
>>     > 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
>>
>>     > E-mail: hpages at fredhutch.org
>>     > Phone:  (206) 667-5791
>>     > Fax:    (206) 667-1319
>>
>>     > ______________________________________________
>>     > R-devel at r-project.org mailing list
>>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
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>



[Rd] inconsistency in treatment of USE.NAMES argument
Mikko Korpela