And skip="string" is also now added and gdata credited (nice idea!)
input = "some,bad,data\n\nsome,cols\n1,2\n3,4\n\n\nreal
data:\nA,B,C\n1,3,5\n2,4,6\n"
cat(input)
some,bad,data
some,cols
1,2
3,4
real data:
A,B,C
1,3,5
2,4,6
fread(input, skip="B,C")
A B C
1: 1 3 5
2: 2 4 6
fread(input) # autostart handles this case already (since the "real
data:" line doesn't contain 2 * sep)
A B C
1: 1 3 5
2: 2 4 6
fread(input, skip="some,cols") # using skip="string" to get the
middle table
some cols
1: 1 2
2: 3 4
Warning message:
In fread(input, skip = "some,cols") :
Stopped reading at empty line, 2 lines after the 'skip' string was
found, but text exists afterwards (discarded): real data:
Further example :
input = "some,bad,data\n\nsome,cols\n1,2\n3,4\n\nreal data:\nA B\n1
3\n2 4\n"
cat(input)
some,bad,data
some,cols
1,2
3,4
real data:
A B
1 3
2 4
fread(input) # with space as separator autostart can't distinguish
the "real data:" line. header wouldn't help here.
real data:
1: A B
2: 1 3
3: 2 4
fread(input, skip="B") # skip="string" needed (skip=n onerous).
Nice!
A B
1: 1 3
2: 2 4
Matthew
On 12.05.2013 18:33, Matthew Dowle wrote:
Since I'm in the fread code at the moment I added 'skip' (rev 864).
4 tests added :
input = "some,bad,data\nA,B,C\n1,3,5\n2,4,6\n"
fread(input)
some bad data
1: A B C
2: 1 3 5
3: 2 4 6
fread(input, skip=1)
A B C
1: 1 3 5
2: 2 4 6
fread(input, skip=2)
V1 V2 V3
1: 1 3 5
2: 2 4 6
fread(input, skip=2, header=TRUE)
1 3 5
1: 2 4 6
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.
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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--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
_______________________________________________
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