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
<[email protected]> 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
<[email protected]> 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
<[email protected]> 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
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GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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