[datatable-help] fread: skip

Matthew Dowle mdowle at mdowle.plus.com
Sun May 12 16:14:00 CEST 2013 

Agreed too. colClasses was committed yesterday as luck would have it.

?fread now has :

    colClasses : A character vector of classes (named or unnamed), as 
read.csv. Or, type list enables setting ranges of columns by numeric 
position. colClasses in fread is intended for rare overrides, not for 
routine use. fread will only promote a column to a higher type if 
colClasses requests it. It won't downgrade a column to a lower type 
since NAs would result. You have to coerce such columns afterwards 
yourself, if you really require data loss.

The tests so far are as follows :

input = 'A,B,C\n01,foo,3.140\n002,bar,6.28000\n'

test(952, fread(input, colClasses=c(C="character")), 
data.table(A=1:2,B=c("foo","bar"),C=c("3.140","6.28000")))
test(953, fread(input, colClasses=c(C="character",A="numeric")), 
data.table(A=c(1.0,2.0),B=c("foo","bar"),C=c("3.140","6.28000")))
test(954, fread(input, colClasses=c(C="character",A="double")), 
data.table(A=c(1.0,2.0),B=c("foo","bar"),C=c("3.140","6.28000")))
test(955, fread(input, colClasses=list(character="C",double="A")), 
data.table(A=c(1.0,2.0),B=c("foo","bar"),C=c("3.140","6.28000")))
test(956, fread(input, colClasses=list(character=2:3,double="A")), 
data.table(A=c(1.0,2.0),B=c("foo","bar"),C=c("3.140","6.28000")))
test(957, fread(input, colClasses=list(character=1:3)), 
data.table(A=c("01","002"),B=c("foo","bar"),C=c("3.140","6.28000")))
test(958, fread(input, colClasses="character"), 
data.table(A=c("01","002"),B=c("foo","bar"),C=c("3.140","6.28000")))
test(959, fread(input, colClasses=c("character","double","numeric")), 
data.table(A=c("01","002"),B=c("foo","bar"),C=c(3.14,6.28)))

test(960, fread(input, colClasses=c("character","double")), 
error="colClasses is unnamed and length 2 but there are 3 columns. See")
test(961, fread(input, colClasses=1:3), error="colClasses is not type 
list or character vector")
test(962, fread(input, colClasses=list(1:3)), error="colClasses is type 
list but has no names")
test(963, fread(input, colClasses=list(character="D")), error="Column 
name 'D' in colClasses not found in data")
test(964, fread(input, colClasses=c(D="character")), error="Column name 
'D' in colClasses not found in data")
test(965, fread(input, colClasses=list(character=0)), error="Column 
number 0 (colClasses..1...1.) is out of range .1,ncol=3.")
test(966, fread(input, colClasses=list(character=2:4)), error="Column 
number 4 (colClasses..1...3.) is out of range .1,ncol=3.")

More detailed/trace info is provided when verbose=TRUE.


On embedded quotes there are known and documented problems still to 
resolve. The issue there is subtle: when reading character columns, part 
of fread's speed comes from pointing mkCharLen() directly to the field 
in memory mapped region of RAM i.e. the field isn't copied into any 
intermediate buffer at all. But for embedded quotes (either doubled or 
escaped) we do need to copy to a buffer so we can remove the doubled 
quote, or escape character (i.e. change the field) before calling 
mkCharLen().  That's not a problem per se, but just a new twist to the C 
code to implement. In order to not slow down, it need only copy that 
field to a buffer if a doubled or escaped quote was actually present in 
that particular field.

Matthew


On 12.05.2013 14:24, Gabor Grothendieck wrote:
> Sorry, I did indeed miss the portion of the reply at the very bottom.
> Yes, that seems good.
>
> What about colClasses too?   I would think that there would be cases
> where an automatic approach might not give the result wanted.  For
> example, order numbers might all be numeric but you would want to
> store them as character in case there are leading zeros.  In other
> cases similar fields might validly have leading zeros but you would
> want them regarded as numeric so there is no way to distinguish the
> two cases except by having the user indicate their intention.
>
> Also, there exist cases where
> - fields are unquoted,
> - fields are quoted and doubling the quotes are used to indicate an
> actual quote and
> - where fields are quoted but a backslash quote it used to denote an
> actual quote.
> Ideally all these situations could be handled through some 
> combination
> of automatic and specified arguments.  In the case of R's read.table
> it cannot handle the back slashed quote case but handles the others
> mentioned.
>
>
> On Sun, May 12, 2013 at 9:01 AM, Matthew Dowle
> <mdowle at mdowle.plus.com> wrote:
>>
>> Hi,
>>
>> I suspect you may not have scrolled further down in my reply where I 
>> wrote
>> more?
>>
>> Matthew
>>
>>
>>
>> On 12.05.2013 13:26, Gabor Grothendieck wrote:
>>>
>>> 1.8.8 is the most recent version on CRAN so I have now installed 
>>> 1.8.9
>>> from R-Forge now and the sample csv I was using does indeed work
>>> attempting to do the best it can with the mucked up header.   Maybe
>>> this is sufficient and a skip is not needed but the fact is that 
>>> there
>>> is no facility to skip over the bad header had I wanted to.
>>>
>>> On Sun, May 12, 2013 at 6:29 AM, Matthew Dowle
>>> <mdowle at mdowle.plus.com> wrote:
>>>>
>>>> On 12.05.2013 00:47, Gabor Grothendieck wrote:
>>>>>
>>>>>
>>>>> Not with the csv I tried.  The header is messed up (most of the 
>>>>> header
>>>>> fields are missing) and it misconstrues it as data.
>>>>
>>>>
>>>>
>>>> That was fixed a while ago in v1.8.9, from NEWS :
>>>>
>>>> "  [fread] If some column names are blank they are now given 
>>>> default
>>>> names
>>>>    rather than causing the header row to be read as a data row "
>>>>
>>>>
>>>>> The automation is great but some way to force its behavior when 
>>>>> you
>>>>> know what it should do seems essential since heuristics can't be
>>>>> expected to work in all cases.
>>>>
>>>>
>>>>
>>>> I suspect the heuristics in v1.8.9 work on all your examples so 
>>>> far, but
>>>> ok
>>>> point taken.
>>>>
>>>> fread allows control of 'autostart' already. This is a line number
>>>> (default
>>>> 30) within the regular data block used to detect the separator and 
>>>> search
>>>> upwards from to find the first data row and/or column names.
>>>>
>>>> Will add 'skip' then. It'll be like setting autostart=skip+1 but 
>>>> turning
>>>> off
>>>> the search upwards part. Line skip+1 will be used to detect the 
>>>> separator
>>>> when sep="auto" and used as column names according to
>>>> header="auto"|TRUE|FALSE as usual.  It'll be an error to specify 
>>>> both
>>>> autostart and skip in the same call.  If that sounds ok?
>>>>
>>>> Matthew
>>>>
>>>>
>>>>
>>>>>
>>>>> On Sat, May 11, 2013 at 6:35 PM, Matthew Dowle
>>>>> <mdowle at mdowle.plus.com> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Does the auto skip feature of fread cover both of those?  From 
>>>>>> ?fread :
>>>>>>
>>>>>>   " Once the separator is found on line autostart, the number of
>>>>>> columns
>>>>>> is
>>>>>> determined. Then the file is searched backwards from autostart 
>>>>>> until a
>>>>>> row
>>>>>> is found that doesn't have that number of columns, or the start 
>>>>>> of file
>>>>>> is
>>>>>> reached. Thus, the first data row is found and any human 
>>>>>> readable
>>>>>> banners
>>>>>> are automatically skipped. This feature can be particularly 
>>>>>> useful for
>>>>>> loading a set of files which may not all have consistently sized
>>>>>> banners.
>>>>>> "
>>>>>>
>>>>>> There were also some issue with header=FALSE in the first 
>>>>>> release
>>>>>> (1.8.8)
>>>>>> which have since been fixed in 1.8.9.
>>>>>>
>>>>>> Matthew
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11.05.2013 23:16, Gabor Grothendieck wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I would find it useful if fread had a skip= argument as in 
>>>>>>> read.table
>>>>>>> since I have files from time to time that have garbage at the 
>>>>>>> top.
>>>>>>> Another situation I find from time to time is that the header 
>>>>>>> is
>>>>>>> messed up but one can still read the file if one can skip over 
>>>>>>> the
>>>>>>> header and specify header = FALSE.
>>>>>>>
>>>>>>> An extra feature that would be nice but less important would be 
>>>>>>> if one
>>>>>>> could specify skip = "string" and have it skip all lines until 
>>>>>>> it
>>>>>>> found one with "string": in it and then start reading from the 
>>>>>>> matched
>>>>>>> row onward.   Normally the string would be chosen to be a 
>>>>>>> string found
>>>>>>> in the header and not likely found prior to the header. 
>>>>>>> read.xls in
>>>>>>> gdata has a similar feature  and I find it quite handy at 
>>>>>>> times.
>>>>>>>
>>>>>>> --
>>>>>>> Statistics & Software Consulting
>>>>>>> GKX Group, GKX Associates Inc.
>>>>>>> tel: 1-877-GKX-GROUP
>>>>>>> email: ggrothendieck at gmail.com
>>>>>>> _______________________________________________
>>>>>>> datatable-help mailing list
>>>>>>> datatable-help at lists.r-forge.r-project.org
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>>>
>>>
>>>
>>>
>>> --
>>> Statistics & Software Consulting
>>> GKX Group, GKX Associates Inc.
>>> tel: 1-877-GKX-GROUP
>>> email: ggrothendieck at gmail.com
>>
>>

More information about the datatable-help mailing list