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Using print.data.table() with character truncation
using datatable.prettyprint.char no longer errors with
NA entries, #6441.
Thanks to @r2evans
for the bug report, and @joshhwuu for the fix.
Fixed a segfault in fcase(), #6448.
Thanks @ethanbsmith for reporting with reprex,
@aitap for finding the
root cause, and @MichaelChirico for the PR.
fread() automatically detects timestamps with
sub-second accuracy again, #6440.
This was a regression due to interference with new
dec='auto' support. Thanks @kav2k for the concise report and @MichaelChirico for
the fix.
Using a namespace-qualified call on the RHS of by=,
e.g. DT[,.N,by=base::mget(v)], works again, fixing #6493.
Thanks to @mmoisse
for the report and @MichaelChirico for the fix.
Restore some join operations on x and i
(e.g. an anti-join x[!i]) where i is an
extended data.frame, but not a data.table (e.g. a tbl), #6501.
Thanks @MichaelChirico for the report and
PR.
Fixed a typo in the NEWS for the last release – that’s version 1.16.0, not 1.6.0; apologies. Thanks @r2evans for flagging, #6443.
Continued work to remove non-API C functions, #6180. Thanks Ivan Krylov for the PR and for writing a clear and concise guide about the R API: https://aitap.codeberg.page/R-api/.
data.table again properly detects OpenMP support
when built using gcc on macOS, #6409.
Thanks @barracuda156 for the report and @kevinushey for the
fix.
The translations submitted for 1.16.0 are now actually shipped with the package – our deepest apologies to the translators for the omission. We have added a CI check to ensure that the .mo binaries which get shipped with the package are always up-to-date.
droplevels(in.place=TRUE) is deprecated in favor of
calling setdroplevels(), #6014.
Given the associated risks/pain points, we strongly prefer all
in-place/by-reference behavior within data.table come from functions
set* (and :=) to make it as clear as possible
that inputs are mutable. See below and ?setdroplevels for
more.
`[.data.table` is un-exported again. This was
exported to support an experimental feature (DT()
functional form of [) that never made it to release, but we
forgot to claw back this export in the NAMESPACE; sorry about that. We
didn’t find anyone calling the method directly (which is inadvisable to
begin with).
We continue to consider user feedback to prioritize development. See #3189 for the current list of most-requested issues. In this release we add five highly-requested features:
Using dt[, names(.SD) := lapply(.SD, fx)] now works
to update all columns, #795. Of
course this also works when .SD is only a subset of the
columns:
dt[, names(.SD) := lapply(.SD, fx), .SDcols = is.numeric].
Thanks to @brodieG
for the report, 20 or so others for chiming in, and @ColeMiller1 for
PR.
fread() now supports automatic detection of
dec (as either . or ,, the latter
being common
in many places in Europe, Africa, and South America); this behavior
is now the default, i.e. dec='auto', #2431.
Thanks @mattdowle
for the original issue, 50 or more others for expressing support, and
@MichaelChirico for the fix.
fcase() supports vectors in default=
(so the default can vary by row) and default= is now lazily
evaluated, #4258.
Thanks @sindribaldur for the feature request,
@shrektan for doing
most of the implementation, and @MichaelChirico for sewing things up.
Thanks also to @DavisVaughan for some design guidance
before release to remove an extraneous feature, #6352.
[.data.table gains argument
showProgress, allowing users to toggle progress printing
for slow “group by” operations, #3060.
The progress bar reports information such as the number of groups
processed, total groups, total time elapsed and estimated time until
completion. This feature doesn’t apply to GForce-optimized
operations. Thanks to @eatonya and @zachmayer for filing FRs, and to everyone
else that up-voted/chimed in on the issue. Thanks to @joshhwuu for the
PR.
rbindlist(l, use.names=TRUE) and
rbind() now work correctly on columns with different class
attributes across the inputs for certain classes such as
Date, IDate, ITime,
POSIXct and AsIs with matched columns of
similar classes, e.g.,
rbind(data.table(d = Sys.Date()), data.table(d = as.IDate(Sys.Date()-1))).
The conversion is done automatically and the class attribute of the
final column is determined by the first class attribute encountered in
the binding list, #5309,
#4934,
#5391.
rbindlist(l, ignore.attr=TRUE) and rbind()
also gain argument ignore.attr (default FALSE)
to manually deactivate the safety net preventing binding columns with
different column classes, #3911,
#5542.
Thanks to @dcaseykc,
@fox34, @adrian-quintario,
@berg-michael,
@arunsrinivasan, @statquant, @pkress, @jrausch12, @therosko, @OfekShilon, @iMissile, @tdhock for the requests and
@ben-schwen for
the PR.
print.data.table() shows empty (NULL)
list column entries as [NULL] for emphasis. Previously they
would just print nothing (indistinguishable from an empty string). Part
of #4198.
Thanks @sritchie73
for the proposal and fix.
data.table(a=list(NULL, ""))
# a
# <list>
# 1: [NULL]
# 2:.datatable.aware = FALSE works correctly to signal
it’s not safe to call data.table methods, #5654.
Thanks @dvg-p4 for the
request and PR. See vignette("datatable-importing") for
more on this feature.
The split() method for data.tables is
more consistent with that for base methods:
f can be a formula, #5392,
mirroring the same in base::split.data.frame since R 4.1.0
(May 2021). Thanks to @XiangyunHuang for the request, and
@ben-schwen for
the PR.
sep= is recognized when splitting with
by=, just like the default and data.frame methods #5417.
Thanks @MichaelChirico for the request and
PR.
Namespace-qualifying data.table::shift(),
data.table::first(), or data.table::last()
will not deactivate GForce, #5942.
Thanks @MichaelChirico for the proposal and
fix. Namespace-qualifying other calls like stats::sum(),
base::prod(), etc., continue to work as an escape valve to
avoid GForce, e.g. to ensure S3 method dispatch.
transpose() gains list.cols= argument
(default FALSE), #5639.
Use this to return output with list columns and avoid type promotion (an
exception is factor columns which are promoted to
character for consistency between
list.cols=TRUE and list.cols=FALSE). This is
convenient for creating a row-major representation of a table. Thanks to
@MLopez-Ibanez
for the request, and @ben-schwen for the PR.
fread()’s fill argument now also
accepts an integer in addition to boolean values – an upper
bound on the number of columns in the file. fread always
guesses the number of columns based on reading a sample of rows in the
file. When fill=TRUE, fread() stops reading
and ignores subsequent rows when this estimate winds up too low,
e.g. when the sampled rows happen to exclude some rows that are even
wider, #2691,
#4130,
#3436,
#1812
and #5378.
The suggestion for fill to allow a manual estimate of the
number of columns instead comes from #2727.
Using fill=Inf reads the full file for estimating the
number of columns. Thanks to @jangorecki, @christellacaze, @Yiguan, @alexdthomas, @ibombonato, @Befrancesco, @TobiasGold for
reporting/requesting, and @ben-schwen for the PR.
Computations in j can return a matrix or array
if it is one-dimensional, e.g. a row or column vector, when
j is a list of columns during grouping, #783.
Previously a matrix could be provided in DT[, expr, by]
form, but not DT[, list(expr), by] form; this resolves that
inconsistency. It is still an error to return a “true” array, e.g. a
2x3 matrix.
measure() helper for melt() now
supports user-specified cols argument, which can be useful
to specify a subset of columns to reshape without having to use a regex,
#5063.
Thanks to @UweBlock
and @Henrik-P for
reporting, and @tdhock
for the PR.
setDT() is faster for data with many columns, thanks
@MichaelChirico for reporting and
fixing the issue, #5426.
dcast() gains value.var.in.dots,
value.var.in.LHSdots and value.var.in.RHSdots
arguments, #5824.
This allows the value.var variable(s) in
dcast() to be represented by ... in the
formula (if not otherwise mentioned). Thanks to @iago-pssjd for the report and
PR.
fread() loads .bgz files directly, #5461.
Thanks to @TMRHarrison for the request with
proposed fix, and @ben-schwen for the PR.
New setdroplevels() as a by-reference version of the
droplevels() method, which returns a copy of its input, #6014.
Thanks @MichaelChirico for the suggestion
and implementation.
dcast(fill=NULL) only computes default fill value if
necessary, which eliminates some previous warnings which were
potentially confusing (for example, when fun.aggregate=min
or max, warning was “NAs introduced by coercion to integer
range”), #5512,
#5390.
Thanks to @tdhock for
the report and fix.
patterns() helper for .SDcols now
accepts arguments ignore.case, perl,
fixed, and useBytes, which are passed to
grep(), #5387. Thanks to @iago-pssjd for the feature request, and
@tdhock for the
implementation.
print() method for data.tables:
Now handles combination multibyte characters correctly when truncating wide string entries, #5096. Thanks to @MichaelChirico for the report and @joshhwuu for the fix.
Prints the indicator --- in every value column when
truncation is needed and row.names = FALSE instead of
adding a blank column where the rownames would have been
just to include ---, #4083.
Thanks @MichaelChirico for the report and
@joshhwuu for the
fix.
Honors na.print, as seen in
print.default, allowing for string replacement of
NA values when printing. Thanks @HughParsonage for the report and
@joshhwuu for the
fix.
Gains new argument show.indices (with corresponding
option datatable.show.indices) that allows the user to
print a data.table’s indices as columns without having to
modify the data.table itself. Thanks @MichaelChirico for the report and
@joshhwuu for the
PR.
Displays integer64 columns correctly by loading
{bit64} if needed, #6224.
Thanks @renkun-ken
for the report and @MichaelChirico for the fix.
unique() returns a copy when
nrows(x) <= 1 instead of a mutable alias, #5932.
This is consistent with existing unique() behavior when the
input has no duplicates but more than one row. Thanks to @brookslogan for the
report and @dshemetov for the fix.
dcast() handles coercion of fill to
integer64 correctly, #4561.
Thanks to @emallickhossain for the bug report
and @MichaelChirico for the fix.
Optimized shift() per group produces the right
results when simultaneously subsetting, for example,
DT[i==1L, shift(x), by=group], #5962.
Thanks to @renkun-ken for the report and @ben-schwen for the
fix.
fwrite(x, row.names=TRUE) with x a
matrix writes row.names when present, not row
numbers, #5315.
Thanks to @Liripo for
the report, and @ben-schwen for the fix.
Adding a list column to an empty data.table works
consistently with other column types, #5738.
Thanks to Benjamin Schwendinger for the report and the fix.
In DT[,j,by], by retains its attributes
(e.g. class) when j is GForce optimized, #5567.
Thanks to @danwwilson for the report, and @ben-schwen for the
PR.
dt[,,by=año] (i.e., using a column name containing a
non-ASCII character in by as a plain symbol) no longer
errors with “object ‘año’ not found”, #4708. Thanks @pfv07 for the report, and
@MichaelChirico for the fix. Also
thanks to @aitap for
suggesting an improvement to the corresponding test, #6339.
Fixed some memory management issues in the C routines backing
melt(), froll(), and GForce
mean(), as identified by rchk. Thanks Tomas
Kalibera and the CRAN team for setting up the rchk system,
and @MichaelChirico for the fix.
data.table’s all.equal() method now dispatches to
each column’s own all.equal() method as appropriate, #4543.
Thanks @MichaelChirico for the report and
fix. Note that this had two noteworthy changes to data.table’s own test
suite that might affect you:
The former might be a matter of preference requiring you to specify a
different tolerance=, while the latter was clearly a
bug.
rbindlist() and shift() could lead to a
protection stack overflow when applied to a list containing many nested
lists exceeding the pointer protection stack size, #4536.
Thanks to @ProfFancyPants for reporting, and
@ben-schwen
(rbindlist) and @MichaelChirico (shift)
for the fix.
fread(x, colClasses="POSIXct") now also works for
columns containing only NA values, #6208.
Thanks to @markus-schaffer for the report, and
@ben-schwen for
the fix.
fread() is more careful about detecting that a file
is compressed in bzip2 format, #6304.
In particular, we also check the 4th byte of the file is a digit; in
rare cases, a legitimate uncompressed CSV file could match ‘BZh’ as the
first 3 bytes. We think an uncompressed CSV file matching ‘BZh[1-9]’ is
all the more rare and unlikely to be encountered in “real” examples.
Other formats (zip, gzip) are friendly enough to use non-printable
characters in their magic numbers. Thanks @grainnemcguire for the report and
@MichaelChirico for the fix.
Selecting the key column like DT[, .(key1, key2)]
will retain the key without a performance penalty, #4498.
Thanks to @user9439449 on StackOverflow for the
report and @MichaelChirico for the fix.
Passing functions programmatically with env= doesn’t
produce an opaque error,
e.g. DT[, f(b), env = list(f=sum)], #6026.
Note that it’s much better to pass functions like f="sum"
instead. Thanks to @MichaelChirico for the bug report
and fix.
transform() method for data.table sped up
substantially when creating new columns on large tables. Thanks to @OfekShilon for the
report and PR. The implemented solution was proposed by @ColeMiller1.
The documentation for the fill argument in
rbind() and rbindlist() now notes the expected
behaviour for missing list columns when
fill=TRUE, namely to use NULL (not
NA), #4198.
Thanks @sritchie73
for the proposal and fix.
data.table now depends on R 3.3.0 (2016) instead of 3.1.0 (2014).
Recent versions of R have good features that we would gradually like to
incorporate, and we see next to no usage of these very old versions of
R. We originally attempted to bump only to R 3.2.0 in this release, but
our vignette engine {knitr} requiring 3.3.0 and R CMD check
lacking an --ignore-vignettes option until 3.3.0
essentially forced our hands.
Erroneous assignment calls in [ with a trailing
comma (e.g. DT[, `:=`(a = 1, b = 2,)]) get a friendlier
error since this situation is common during refactoring and easy to miss
visually. Thanks @MichaelChirico for the fix.
Input files are now kept open during mmap() when
running under Emscripten, emscripten-core/emscripten#20459.
This avoids an error in fread() when running in
WebAssembly, #5969.
Thanks to @maek-ies
for the report and @georgestagg for the PR.
dcast() improves behavior for the situation that the
fun.aggregate value of length() is used but
not provided by the user.
This now triggers a warning, not a message, since relying on this
default often signals unexpected duplicates in the data, #5386.
The warning is classed as dt_missing_fun_aggregate_warning,
allowing for more targeted handling in user code. Thanks @MichaelChirico for
the suggestion and @Nj221102 for the fix.
The warning itself does better explaining the behavior and suggesting alternatives, #5217. Thanks @MichaelChirico for the suggestion and @Nj221102 for the fix.
Updated a test relying on operator > working for
comparing language objects to a string, which will be deprecated by R,
#5977;
no user-facing effect. Thanks to R-core for continuously improving the
language.
Improved OpenMP detection when building from source on Mac, #4348. Thanks @jameshester and @kevinushey for the request and @kevinushey for the PR, @jameslamb for the advice and @s-u of R-core for ensuring CRAN machines are configured to support the expected setup.
test.data.table() runs more robustly:
In sessions where the digits or warn
options are not their defaults (7 and 0,
respectively), #5285.
Thanks @OfekShilon
for the report and suggested fix and @MichaelChirico for the PR.
In locales where letters != sort(letters),
e.g. Latvian, #3502.
Thanks @minemR for the
report and @MichaelChirico for the fix.
Initialises the numeric rounding value to 0 using
setNumericRounding(0) to avoid failed tests if the user has
set a different value, #6082.
The user’s value is restored on exit. Thanks to @MichaelChirico for the report and
for describing the solution, and @markseeto for implementing.
To enable this, setNumericRounding() now invisibly
returns the old rounding value instead of NULL, which is
consistent with similar behavior by setwd(),
options(), etc. Thanks @MichaelChirico for the report and
@joshhwuu for the
fix.
The measure() and patterns() helpers
for [ and melt() are now exported to ensure
consistency with other non-standard evaluation (NSE) exports like
.N and :=. This change addresses #5604,
allowing package developers to import these names and avoid
R CMD check NOTEs about undefined variables.
Thanks to @MichaelChirico and @ylelkes for their
suggestions, and to @Nj221102 for the implementation.
We plan to export similar placeholders for . and
J in roughly one year (e.g. data.table 1.18.0), but
excluded them from this release to avoid back-compatibility issues.
Specifically, some packages doing import(plyr) and
import(data.table), and/or with those packages in
Depends, will error when data.table starts exporting
. (and similarly for a potential conflict with
rJava::J()). We discourage using data.table (or any
package, really) in Depends; blanket import() of package is
also generally best avoided. See
vignette("datatable-importing").
fwrite() header rows are no longer quoted
automatically when na argument is given, #2964.
Thanks @jangorecki
for the report and @joshhwuu for the fix.
Removed a warning about the now totally-obsolete option
datatable.CJ.names, as discussed in previous
releases.
Refactored some non-API calls in the package C code, #6180. There should be no user-visible change. Thanks to various R users, R core, and especially Luke Tierney for pushing to have a clearer definition of “API” for R and for offering clear documentation and suggested workarounds. Thanks @MichaelChirico and @TysonStanley for implementing changes for this release; more will follow.
C code is more unified in how failures to allocate memory
(malloc()/calloc()) are handled, #1115.
No OOM issues were reported, as these regions of code typically request
relatively small blocks of memory, but it is good to handle memory
pressure consistently. Thanks @elfring for the report and @MichaelChirico for
the clean-up effort and future-proofing linter.
The internal routine for finding sort order
(forder()) will now re-use any existing index. A similar
optimization was already present in R code, but this has now been pushed
to C and covers a wider range of use cases and collects more statistics
about its input (e.g. whether any infinite entries were found), opening
the possibility for more optimizations in other functions.
Functions setindex() (and setindexv()) will
now compute groups’ positions as well. setindex() also
collects the extra statistics alluded to above.
Finding sort order in other routines (for example subset
d2[id==1L]) does not include those extra statistics so as
not to impose a slowdown.
d2 = data.table(id=2:1, v2=1:2)
setindexv(d2, "id")
str(attr(attr(d2, "index"), "__id"))
# int [1:2] 2 1
# - attr(*, "starts")= int [1:2] 1 2
# - attr(*, "maxgrpn")= int 1
# - attr(*, "anyna")= int 0
# - attr(*, "anyinfnan")= int 0
# - attr(*, "anynotascii")= int 0
# - attr(*, "anynotutf8")= int 0
d2 = data.table(id=2:1, v2=1:2)
invisible(d2[id==1L])
str(attr(attr(d2, "index"), "__id"))
# int [1:2] 2 1This feature also enables re-use of sort index during joins, in cases where one of the calls to find sort order is made from C code.
d1 = data.table(id=1:2, v1=1:2)
d2 = data.table(id=2:1, v2=1:2)
setindexv(d2, "id")
d1[d2, on="id", verbose=TRUE]
#...
#Starting bmerge ...
#forderReuseSorting: using existing index: __id
#forderReuseSorting: opt=2, took 0.000s
#...This feature resolves #4387, #2947, #4380, and #1321. Thanks to @jangorecki, @jan-glx, and @MichaelChirico for the reports and @jangorecki for implementing.
set() now adds new columns even if no rows are
updated, #5409.
This behavior is now consistent with :=, thanks to @mb706 for the report and
@joshhwuu for the
fix.
The internal init() function in the
fread.c module has been marked as static, #6328.
This obviates name collisions, and the resulting segfaults, with other
libraries visible to the R process that might expose the same symbol
name. This was observed in Cray HPE environments where the
libsci library providing LAPACK to R already has an
init symbol. Thanks to @rtobar for the report and fix.
?melt has long documented that the returned
variable column should contain integer column indices when
measure.vars is a list, but when the list length is 1,
variable is actually a character column name, which is
inconsistent with the documentation, #5209.
To increase consistency in the next release, we plan to change
variable to integer, so users who were relying on this
behavior should change measure.vars=list("col_name")
(variable currently is a column name but will be a column
index/integer after this planned change) to
measure.vars="col_name" (variable is column
name before and after the planned change). For now, relying on this
undocumented behavior throws a new warning.
?dcast has always required
fun.aggregate to return a single value, and when
fill=NULL, dcast would indeed error if a
vector with length!=1 was returned, but an undefined result
was silently returned for non-NULL fill. Now
dcast() will additionally warn that this is undefined
behavior when fill is not NULL, #6032.
In particular, this will warn for fun.aggregate=identity,
which was observed in several revdeps. We may change this to an error in
a future release, so revdeps should fix their code as soon as possible.
Thanks to @tdhock for
the PR, and @MichaelChirico for analysis of
GitHub revdeps.
Fix a typo in a Mandarin translation of an error message that was hiding the actual error message, #6172. Thanks @trafficfan for the report and @MichaelChirico for the fix.
data.table is now translated into Brazilian Portuguese (pt_BR)
and Spanish (es)
as well as Mandarin (zh_CN). Thanks to the new translation
teams consisting initially of @rffontenelle, @leofontenelle, and @italo-07 for Portuguese;
and @rikivallalba, @rivaquiroga, and @MaraDestefanis for Spanish. The
teams are open if you’d also like to join and support maintenance of
these translations.
A more helpful error message for using := inside the
first argument (i) of [.data.table is now
available in translation, #6293.
Previously, the code to display this assumed an earlier message was
printed in English. The solution is for calling := directly
(i.e., outside the second argument j of
[.data.table) to throw an error of class
dt_invalid_let_error. Thanks to Spanish translator @rikivillalba for
spotting the issue and @MichaelChirico for the fix.
shift per group produced wrong results when
simultaneously subsetting, for example,
DT[i==1L, shift(x), by=group], #5962.
Thanks to @renkun-ken for the report and Benjamin
Schwendinger for the fix.> working for comparing
language objects to a string, which will be deprecated by R, #5977;
no user-facing effect. Thanks to R-core for continuously improving the
language.An error in fwrite() is more robust across platforms
– CRAN found the use of PRId64 does not always match the
output of xlength(), e.g. on some Mac M1 builds #5935.
Thanks CRAN for identifying the issue and @ben-schwen for the fix.
shift() of a vector in grouped queries (under
GForce) returns a vector, consistent with shift() in other
contexts, #5939.
Thanks @shrektan for
the report and @MichaelChirico for the fix.
shift and nafill will now raise error
input must not be matrix or array when matrix
or array is provided on input, rather than giving useless
result, #5287.
Thanks to @ethanbsmith for reporting.nafill() now applies fill= to the
front/back of the vector when type="locf|nocb", #3594.
Thanks to @ben519 for
the feature request. It also now returns a named object based on the
input names. Note that if you are considering joining and then using
nafill(...,type='locf|nocb') afterwards, please review
roll=/rollends= which should achieve the same
result in one step more efficiently. nafill() is for when
filling-while-joining
(i.e. roll=/rollends=/nomatch=)
cannot be applied.
mean(na.rm=TRUE) by group is now GForce optimized,
#4849.
Thanks to the h2oai/db-benchmark
project for spotting this issue. The 1 billion row example in the issue
shows 48s reduced to 14s. The optimization also applies to type
integer64 resulting in a difference to the
bit64::mean.integer64 method: data.table
returns a double result whereas bit64 rounds
the mean to the nearest integer.
fwrite() now writes UTF-8 or native csv files by
specifying the encoding= argument, #1770.
Thanks to @shrektan
for the request and the PR.
data.table() no longer fills empty vectors with
NA with warning. Instead a 0-row data.table is
returned, #3727.
Since data.table() is used internally by .(),
this brings the following examples in line with expectations in most
cases. Thanks to @shrektan for the suggestion and PR.
DT = data.table(A=1:3, B=letters[1:3])
DT[A>3, .(ITEM='A>3', A, B)] # (1)
DT[A>3][, .(ITEM='A>3', A, B)] # (2)
# the above are now equivalent as expected and return:
Empty data.table (0 rows and 3 cols): ITEM,A,B
# Previously, (2) returned :
ITEM A B
<char> <int> <char>
1: A>3 NA <NA>
Warning messages:
1: In as.data.table.list(jval, .named = NULL) :
Item 2 has 0 rows but longest item has 1; filled with NA
2: In as.data.table.list(jval, .named = NULL) :
Item 3 has 0 rows but longest item has 1; filled with NADT = data.table(A=1:3, B=letters[1:3], key="A")
DT[.(1:3, double()), B]
# new result :
character(0)
# old result :
[1] "a" "b" "c"
Warning message:
In as.data.table.list(i) :
Item 2 has 0 rows but longest item has 3; filled with NA%like% on factors with a large number of levels is
now faster, #4748.
The example in the PR shows 2.37s reduced to 0.86s on a factor length
100 million containing 1 million unique 10-character strings. Thanks to
@statquant for
reporting, and @shrektan for implementing.
keyby= now accepts
TRUE/FALSE together with by=, #4307.
The primary motivation is benchmarking where by= vs
keyby= is varied across a set of queries. Thanks to Jan
Gorecki for the request and the PR.
DT[, sum(colB), keyby="colA"]
DT[, sum(colB), by="colA", keyby=TRUE] # samefwrite() gains a new
datatable.fwrite.sep option to change the default
separator, still "," by default. Thanks to Tony Fischetti
for the PR. As is good practice in R in general, we usually resist new
global options for the reason that a user changing the option for their
own code can inadvertently change the behaviour of any package using
data.table too. However, in this case, the global option
affects file output rather than code behaviour. In fact, the very reason
the user may wish to change the default separator is that they know a
different separator is more appropriate for their data being passed to
the package using fwrite but cannot otherwise change the
fwrite call within that package.
melt() now supports NA entries when
specifying a list of measure.vars, which translate into
runs of missing values in the output. Useful for melting wide data with
some missing columns, #4027.
Thanks to @vspinu for
reporting, and @tdhock
for implementing.
melt() now supports multiple output variable columns
via the variable_table attribute of
measure.vars, #3396 #2575 #2551,
#4998.
It should be a data.table with one row that describes each
element of the measure.vars vector(s). These data/columns
are copied to the output instead of the usual variable column. This is
backwards compatible since the previous behavior (one output variable
column) is used when there is no variable_table. New
functions measure() and measurev() which use
either a separator or a regex to create a measure.vars
list/vector with variable_table attribute; useful for
melting data that has several distinct pieces of information encoded in
each column name. See new ?measure and new section in
reshape vignette. Thanks to Matthias Gomolka, Ananda Mahto, Hugh
Parsonage, Mark Fairbanks for reporting, and to Toby Dylan Hocking for
implementing. Thanks to @keatingw for testing before release,
requesting measure() accept single groups too #5065,
and Toby for implementing.
A new interface for programming on data.table has been
added, closing #2655
and many other linked issues. It is built using base R’s
substitute-like interface via a new env
argument to [.data.table. For details see the new vignette
programming on data.table, and the new
?substitute2 manual page. Thanks to numerous users for
filing requests, and Jan Gorecki for implementing.
DT = data.table(x = 1:5, y = 5:1)
# parameters
in_col_name = "x"
fun = "sum"
fun_arg1 = "na.rm"
fun_arg1val = TRUE
out_col_name = "sum_x"
# parameterized query
#DT[, .(out_col_name = fun(in_col_name, fun_arg1=fun_arg1val))]
# desired query
DT[, .(sum_x = sum(x, na.rm=TRUE))]
# new interface
DT[, .(out_col_name = fun(in_col_name, fun_arg1=fun_arg1val)),
env = list(
in_col_name = "x",
fun = "sum",
fun_arg1 = "na.rm",
fun_arg1val = TRUE,
out_col_name = "sum_x"
)]DT[, if (...) .(a=1L) else .(a=1L, b=2L), by=group]
now returns a 1-column result with warning
j may not evaluate to the same number of columns for each group,
rather than error
'names' attribute [2] must be the same length as the vector,
#4274.
Thanks to @robitalec for reporting, and Michael
Chirico for the PR.
Typo checking in i available since 1.11.4 is
extended to work in non-English sessions, #4989.
Thanks to Michael Chirico for the PR.
fifelse() now coerces logical NA to
other types and the na argument supports vectorized input,
#4277
#4286
#4287.
Thanks to @michaelchirico and @shrektan for reporting,
and @shrektan for
implementing.
.datatable.aware is now recognized in the calling
environment in addition to the namespace of the calling package, dtplyr#184.
Thanks to Hadley Wickham for the idea and PR.
New convenience function %plike% maps to
like(..., perl=TRUE), #3702.
%plike% uses Perl-compatible regular expressions (PCRE)
which extend TRE, and may be more efficient in some cases. Thanks @KyleHaynes for the
suggestion and PR.
fwrite() now accepts sep="", #4817.
The motivation is an example where the result of paste0()
needs to be written to file but paste0() takes 40 minutes
due to constructing a very large number of unique long strings in R’s
global character cache. Allowing fwrite(, sep="") avoids
the paste0 and saves 40 mins. Thanks to Jan Gorecki for the
request, and Ben Schwen for the PR.
data.table printing now supports customizable
methods for both columns and list column row items, part of #1523.
format_col is S3-generic for customizing how to print whole
columns and by default defers to the S3 format method for
the column’s class if one exists; e.g. format.sfc for
geometry columns from the sf package, #2273.
Similarly, format_list_item is S3-generic for customizing
how to print each row of list columns (which lack a format method at a
column level) and also by default defers to the S3 format
method for that item’s class if one exists. Thanks to @mllg who initially filed #3338
with the seed of the idea, @franknarf1 who earlier suggested the
idea of providing custom formatters, @fparages who submitted a patch to improve
the printing of timezones for #2842,
@RichardRedding for pointing out an
error relating to printing wide expression columns in #3011,
@JoshOBrien for
improving the output for geometry columns, and @MichaelChirico for implementing. See
?print.data.table for examples.
tstrsplit(,type.convert=) now accepts a named list
of functions to apply to each part, #5094.
Thanks to @Kamgang-B for the request and
implementing.
as.data.table(DF, keep.rownames=key='keyCol') now
works, #4468.
Thanks to Michael Chirico for the idea and the PR.
dcast() now supports complex values in
value.var, #4855.
This extends earlier support for complex values in formula.
Thanks Elio Campitelli for the request, and Michael Chirico for the
PR.
melt() was pseudo generic in that
melt(DT) would dispatch to the melt.data.table
method but melt(not-DT) would explicitly redirect to
reshape2. Now melt() is standard generic so
that methods can be developed in other packages, #4864.
Thanks to @odelmarcelle for suggesting and
implementing.
DT[i, nomatch=NULL] where i contains
row numbers now excludes NA and any outside the range
[1,nrow], #3109 #3666.
Before, NA rows were returned always for such values;
i.e. nomatch=0|NULL was ignored. Thanks Michel Lang and
Hadley Wickham for the requests, and Jan Gorecki for the PR. Using
nomatch=0 in this case when i is row numbers
generates the warning
Please use nomatch=NULL instead of nomatch=0; see news item 5 in v1.12.0 (Jan 2019).
DT = data.table(A=1:3)
DT[c(1L, NA, 3L, 5L)] # default nomatch=NA
# A
# <int>
# 1: 1
# 2: NA
# 3: 3
# 4: NA
DT[c(1L, NA, 3L, 5L), nomatch=NULL]
# A
# <int>
# 1: 1
# 2: 3DT[, head(.SD,n), by=grp] and tail are
now optimized when n>1, #5060 #523.
n==1 was already optimized. Thanks to Jan Gorecki and
Michael Young for requesting, and Benjamin Schwendinger for the
PR.
setcolorder() gains before= and
after=, #4358.
Thanks to Matthias Gomolka for the request, and both Benjamin
Schwendinger and Xianghui Dong for implementing. Also thanks to Manuel
López-Ibáñez for testing dev and mentioning needed documentation before
release.
base::droplevels() gains a fast method for
data.table, #647.
Thanks to Steve Lianoglou for requesting, Boniface Kamgang and Martin
Binder for testing, and Jan Gorecki and Benjamin Schwendinger for the
PR. fdroplevels() for use on vectors has also been
added.
shift() now also supports
type="cyclic", #4451.
Arguments that are normally pushed out by type="lag" or
type="lead" are re-introduced at this type at the
first/last positions. Thanks to @RicoDiel for requesting, and Benjamin
Schwendinger for the PR.
# Usage
shift(1:5, n=-1:1, type="cyclic")
# [[1]]
# [1] 2 3 4 5 1
#
# [[2]]
# [1] 1 2 3 4 5
#
# [[3]]
# [1] 5 1 2 3 4
# Benchmark
x = sample(1e9) # 3.7 GB
microbenchmark::microbenchmark(
shift(x, 1, type="cyclic"),
c(tail(x, 1), head(x,-1)),
times = 10L,
unit = "s"
)
# Unit: seconds
# expr min lq mean median uq max neval
# shift(x, 1, type = "cyclic") 1.57 1.67 1.71 1.68 1.70 2.03 10
# c(tail(x, 1), head(x, -1)) 6.96 7.16 7.49 7.32 7.64 8.60 10fread() now supports “0” and “1” in
na.strings, #2927.
Previously this was not permitted since “0” and “1” can be recognized as
boolean values. Note that it is still not permitted to use “0” and “1”
in na.strings in combination with
logical01 = TRUE. Thanks to @msgoussi for the request, and Benjamin
Schwendinger for the PR.
setkey() now supports type raw as value
columns (not as key columns), #5100.
Thanks Hugh Parsonage for requesting, and Benjamin Schwendinger for the
PR.
shift() is now optimized by group, #1534.
Thanks to Gerhard Nachtmann for requesting, and Benjamin Schwendinger
for the PR. Thanks to @neovom for testing dev and filing a bug
report, #5547
which was fixed before release. This helped also in improving the logic
for when to turn on optimization by group in general, making it more
robust.
N = 1e7
DT = data.table(x=sample(N), y=sample(1e6,N,TRUE))
shift_no_opt = shift # different name not optimized as a way to compare
microbenchmark(
DT[, c(NA, head(x,-1)), y],
DT[, shift_no_opt(x, 1, type="lag"), y],
DT[, shift(x, 1, type="lag"), y],
times=10L, unit="s")
# Unit: seconds
# expr min lq mean median uq max neval
# DT[, c(NA, head(x, -1)), y] 8.7620 9.0240 9.1870 9.2800 9.3700 9.4110 10
# DT[, shift_no_opt(x, 1, type = "lag"), y] 20.5500 20.9000 21.1600 21.3200 21.4400 21.5200 10
# DT[, shift(x, 1, type = "lag"), y] 0.4865 0.5238 0.5463 0.5446 0.5725 0.5982 10Example from stackoverflow
set.seed(1)
mg = data.table(expand.grid(year=2012:2016, id=1:1000),
value=rnorm(5000))
microbenchmark(v1.9.4 = mg[, c(value[-1], NA), by=id],
v1.9.6 = mg[, shift_no_opt(value, n=1, type="lead"), by=id],
v1.14.4 = mg[, shift(value, n=1, type="lead"), by=id],
unit="ms")
# Unit: milliseconds
# expr min lq mean median uq max neval
# v1.9.4 3.6600 3.8250 4.4930 4.1720 4.9490 11.700 100
# v1.9.6 18.5400 19.1800 21.5100 20.6900 23.4200 29.040 100
# v1.14.4 0.4826 0.5586 0.6586 0.6329 0.7348 1.318 100rbind() and rbindlist() now support
fill=TRUE with use.names=FALSE instead of
issuing the warning
use.names= cannot be FALSE when fill is TRUE. Setting use.names=TRUE.,
#5444.
Thanks to @sindribaldur, @dcaseykc, @fox34, @adrian-quintario and @berg-michael for
testing dev and filing a bug report which was fixed before release.
DT1
# A B
# <int> <int>
# 1: 1 5
# 2: 2 6
DT2
# foo
# <int>
# 1: 3
# 2: 4
rbind(DT1, DT2, fill=TRUE) # no change
# A B foo
# <int> <int> <int>
# 1: 1 5 NA
# 2: 2 6 NA
# 3: NA NA 3
# 4: NA NA 4
rbind(DT1, DT2, fill=TRUE, use.names=FALSE)
# was:
# A B foo
# <int> <int> <int>
# 1: 1 5 NA
# 2: 2 6 NA
# 3: NA NA 3
# 4: NA NA 4
# Warning message:
# In rbindlist(l, use.names, fill, idcol) :
# use.names= cannot be FALSE when fill is TRUE. Setting use.names=TRUE.
# now:
# A B
# <int> <int>
# 1: 1 5
# 2: 2 6
# 3: 3 NA
# 4: 4 NAfread() already made a good guess as to whether
column names are present by comparing the type of the fields in row 1 to
the type of the fields in the sample. This guess is now improved when a
column contains a string in row 1 (i.e. a potential column name) but all
blank in the sample rows, #2526.
Thanks @st-pasha for
reporting, and @ben-schwen for the PR.
fread() can now read .zip and
.tar directly, #3834.
Moreover, if a compressed file name is missing its extension,
fread() now attempts to infer the correct filetype from its
magic bytes. Thanks to Michael Chirico for the idea, and Benjamin
Schwendinger for the PR.
DT[, let(...)] is a new alias for the functional
form of :=; i.e. DT[, ':='(...)], #3795.
Thanks to Elio Campitelli for requesting, and Benjamin Schwendinger for
the PR.
DT = data.table(A=1:2)
DT[, let(B=3:4, C=letters[1:2])]
DT
# A B C
# <int> <int> <char>
# 1: 1 3 a
# 2: 2 4 bweighted.mean() is now optimized by group, #3977.
Thanks to @renkun-ken for requesting, and Benjamin
Schwendinger for the PR.
as.xts.data.table() now supports non-numeric xts
coredata matrixes, 5268.
Existing numeric only functionality is supported by a new
numeric.only parameter, which defaults to TRUE
for backward compatibility and the most common use case. To convert
non-numeric columns, set this parameter to FALSE.
Conversions of data.table columns to a matrix
now uses data.table::as.matrix, with all its performance
benefits. Thanks to @ethanbsmith for the report and
fix.
unique.data.table() gains cols to
specify a subset of columns to include in the resulting
data.table, #5243.
This saves the memory overhead of subsetting unneeded columns, and
provides a cleaner API for a common operation previously needing more
convoluted code. Thanks to @MichaelChirico for the suggestion
& implementation.
:= is now optimized by group, #1414.
Thanks to Arun Srinivasan for suggesting, and Benjamin Schwendinger for
the PR. Thanks to @clerousset, @dcaseykc, @OfekShilon, @SeanShao98, and @ben519 for testing dev and filing detailed
bug reports which were fixed before release and their tests added to the
test suite.
.I is now available in by for rowwise
operations, #1732.
Thanks to Rafael H. M. Pereira for requesting, and Benjamin Schwendinger
for the PR.
DT
# V1 V2
# <int> <int>
# 1: 3 5
# 2: 4 6
DT[, sum(.SD), by=.I]
# I V1
# <int> <int>
# 1: 1 8
# 2: 2 10New functions yearmon() and yearqtr
give a combined representation of year() and
month()/quarter(). These and also
yday, wday, mday,
week, month and year are now
optimized for memory and compute efficiency by removing the
POSIXlt dependency, #649.
Thanks to Matt Dowle for the request, and Benjamin Schwendinger for the
PR. Thanks to @berg-michael for testing dev and
filing a bug report for special case of missing values which was fixed
before release.
New function %notin% provides a convenient
alternative to !(x %in% y), #4152.
Thanks to Jan Gorecki for suggesting and Michael Czekanski for the PR.
%notin% uses half the memory because it computes the result
directly as opposed to ! which allocates a new vector to
hold the negated result. If x is long enough to occupy more
than half the remaining free memory, this can make the difference
between the operation working, or failing with an out-of-memory
error.
tables() is faster by default by excluding the size
of character strings in R’s global cache (which may be shared) and
excluding the size of list column items (which also may be shared).
mb= now accepts any function which accepts a
data.table and returns a higher and better estimate of its
size in bytes, albeit more slowly;
e.g. mb = utils::object.size.
by=.EACHI when i is keyed but
on= different columns than i’s key could
create an invalidly keyed result, #4603 #4911.
Thanks to @myoung3
and @adamaltmejd
for reporting, and @ColeMiller1 for the PR. An invalid key
is where a data.table is marked as sorted by the key
columns but the data is not sorted by those columns, leading to
incorrect results from subsequent queries.
print(DT, trunc.cols=TRUE) and the corresponding
datatable.print.trunc.cols option (new feature 3 in
v1.13.0) could incorrectly display an extra column, #4266.
Thanks to @tdhock for
the bug report and @MichaelChirico for the PR.
fread(..., nrows=0L) now works as intended and the
same as nrows=0; i.e. returning the column names and typed
empty columns determined by the large sample, #4686,
#4029.
Thanks to @hongyuanjia and @michaelpaulhirsch for reporting,
and Benjamin Schwendinger for the PR. Also thanks to @HughParsonage for
testing dev and reporting a bug which was fixed before release.
Passing .SD to frankv() with
ties.method='random' or with na.last=NA failed
with .SD is locked, #4429.
Thanks @smarches for
the report.
Filtering data.table using which=NA to return
non-matching indices will now properly work for non-optimized subsetting
as well, closes #4411.
When j returns an object whose class
"X" inherits from data.table; i.e. class
c("X", "data.table", "data.frame"), the derived class
"X" is no longer incorrectly dropped from the class of the
data.table returned, #4324.
Thanks to @HJAllen
for reporting and @shrektan for the PR.
as.data.table() failed with
.subset2(x, i, exact = exact): attempt to select less than one element in get1index
when passed an object inheriting from data.table with a
different [[ method, such as the class dfidx
from the dfidx package, #4526.
Thanks @RicoDiel for
the report, and Michael Chirico for the PR.
rbind() and rbindlist() of length-0
ordered factors failed with
Internal error: savetl_init checks failed, #4795 #4823.
Thanks to @shrektan
and @dbart79 for
reporting, and @shrektan for fixing.
data.table(NULL)[, firstCol:=1L] created
data.table(firstCol=1L) ok but did not update the internal
row.names attribute, causing
Error in '$<-.data.frame'(x, name, value) : replacement has 1 row, data has 0
when passed to packages like ggplot which use
DT as if it is a data.frame, #4597.
Thanks to Matthew Son for reporting, and Cole Miller for the
PR.
X[Y, .SD, by=] (joining and grouping in the same
query) could segfault if i) by= is supplied custom data
(i.e. not simple expressions of columns), and ii) some rows of
Y do not match to any rows in X, #4892.
Thanks to @Kodiologist for reporting, @ColeMiller1 for
investigating, and @tlapak for the PR.
Assigning a set of 2 or more all-NA values to a factor column could segfault, #4824. Thanks to @clerousset for reporting and @shrektan for fixing.
as.data.table(table(NULL)) now returns
data.table(NULL) rather than error
attempt to set an attribute on NULL, #4179.
The result differs slightly to as.data.frame(table(NULL))
(0-row, 1-column) because 0-column works better with other
data.table functions like rbindlist(). Thanks
to Michael Chirico for the report and fix.
melt with a list for measure.vars would
output variable inconsistently between
na.rm=TRUE and FALSE, #4455.
Thanks to @tdhock for
reporting and fixing.
by=...get()... could fail with
object not found, #4873 #4981.
Thanks to @sindribaldur for reporting, and @OfekShilon for
fixing.
print(x, col.names='none') now removes the column
names as intended for wide data.tables whose column names
don’t fit on a single line, #4270.
Thanks to @tdhock for
the report, and Michael Chirico for fixing.
DT[, min(colB), by=colA] when colB is
type character would miss blank strings ("")
at the beginning of a group and return the smallest non-blank instead of
blank, #4848.
Thanks to Vadim Khotilovich for reporting and for the PR fixing
it.
Assigning a wrong-length or non-list vector to a list column could segfault, #4166 #4667 #4678 #4729. Thanks to @fklirono, Kun Ren, @kevinvzandvoort and @peterlittlejohn for reporting, and to Václav Tlapák for the PR.
as.data.table() on xts objects
containing a column named x would return an
index of type plain integer rather than
POSIXct, #4897.
Thanks to Emil Sjørup for reporting, and Jan Gorecki for the
PR.
A fix to as.Date(c("", ...)) in R 4.0.3, 17909, has
been backported to data.table::as.IDate() so that it too
now returns NA for the first item when it is blank, even in
older versions of R back to 3.1.0, rather than the incorrect error
character string is not in a standard unambiguous format,
#4676.
Thanks to Arun Srinivasan for reporting, and Michael Chirico both for
the data.table PR and for submitting the patch to R that
was accepted and included in R 4.0.3.
uniqueN(DT, by=character()) is now equivalent to
uniqueN(DT) rather than internal error
'by' is either not integer or is length 0, #4594.
Thanks Marco Colombo for the report, and Michael Chirico for the PR.
Similarly for unique(), duplicated() and
anyDuplicated().
melt() on a data.table with
list columns for measure.vars would silently
ignore na.rm=TRUE, #5044.
Now the same logic as is.na() from base R is used; i.e. if
list element is scalar NA then it is considered missing and removed.
Thanks to Toby Dylan Hocking for the PRs.
fread(fill=TRUE) could segfault if the input
contained an improperly quoted character field, #4774 #5041.
Thanks to @AndeolEvain and @e-nascimento for reporting and to
Václav Tlapák for the PR.
fread(fill=TRUE, verbose=TRUE) would segfault on the
out-of-sample type bump verbose output if the input did not contain
column names, 5046.
Thanks to Václav Tlapák for the PR.
.SDcols=-V2:-V1 and .SDcols=(-1) could
error with xcolAns does not pass checks and
argument specifying columns specify non existing column(s),
#4231.
Thanks to Jan Gorecki for reporting and the PR. Thanks Toby Dylan
Hocking for tracking down an error caused by the initial fix and Michael
Chirico for fixing it.
.SDcols=<logical vector> is now documented in
?data.table and it is now an error if the logical vector’s
length is not equal to the number of columns (consistent with
data.table’s no-recycling policy; see new feature 1 in
v1.12.2 Apr 2019), #4115.
Thanks to @Henrik-P
for reporting and Jan Gorecki for the PR.
melt() now outputs scalar logical NA
instead of NULL in rows corresponding to missing list
columns, for consistency with non-list columns when using
na.rm=TRUE, #5053.
Thanks to Toby Dylan Hocking for the PR.
as.data.frame(DT), setDF(DT) and
as.list(DT) now remove the "index" attribute
which contains any indices (a.k.a. secondary keys), as they already did
for other data.table-only attributes such as the primary
key stored in the "sorted" attribute. When indices were
left intact, a subsequent subset, assign, or reorder of the
data.frame by data.frame-code in base R or
other packages would not update the indices, causing incorrect results
if then converted back to data.table, #4889.
Thanks @OfekShilon
for the report and the PR.
dplyr::arrange(DT) uses
vctrs::vec_slice which retains data.table’s
class but uses C to bypass [ method dispatch and does not
adjust data.table’s attributes containing the index row
numbers, #5042.
data.table’s long-standing .internal.selfref
mechanism to detect such operations by other packages was not being
checked by data.table when using indexes, causing
data.table filters and joins to use invalid indexes and
return incorrect results after a dplyr::arrange(DT). Thanks
to @Waldi73 for
reporting; @avimallu, @tlapak, @MichaelChirico, @jangorecki and @hadley for investigating
and suggestions; and @mattdowle for the PR. The intended way to
use data.table is
data.table::setkey(DT, col1, col2, ...) which reorders
DT by reference in parallel, sets the primary key for
automatic use by subsequent data.table queries, and permits
rowname-like usage such as DT["foo",] which returns the
now-contiguous-in-memory block of rows where the first column of
DT’s key contains "foo". Multi-column-rownames
(i.e. a primary key of more than one column) can be looked up using
DT[.("foo",20210728L), ]. Using == in
i is also optimized to use the key or indices, if you
prefer using column names explicitly and ==. An alternative
to setkey(DT) is returning a new ordered result using
DT[order(col1, col2, ...), ].
A segfault occurred when nrow/throttle < nthread,
#5077.
With the default throttle of 1024 rows (see ?setDTthreads),
at least 64 threads would be needed to trigger the segfault since there
needed to be more than 65,535 rows too. It occurred on a server with 256
logical cores where data.table uses 128 threads by default.
Thanks to Bennet Becker for reporting, debugging at C level, and fixing.
It also occurred when the throttle was increased so as to use fewer
threads; e.g. at the limit
setDTthreads(throttle=nrow(DT)).
fread(file=URL) now works rather than error
does not exist or is non-readable, #4952.
fread(URL) and fread(input=URL) worked before
and continue to work. Thanks to @pnacht for reporting and @ben-schwen for the
PR.
fwrite(DF, row.names=TRUE) where DF has
specific integer rownames (e.g. using
rownames(DF) <- c(10L,20L,30L)) would ignore the integer
rownames and write the row numbers instead, #4957.
Thanks to @dgarrimar for reporting and @ColeMiller1 for the
PR. Further, when quote='auto' (default) and the rownames
are integers (either default or specific), they are no longer
quoted.
test.data.table() would fail on test 1894 if the
variable z was defined by the user, #3705.
The test suite already ran in its own separate environment. That
environment’s parent is no longer .GlobalEnv to isolate it
further. Thanks to Michael Chirico for reporting, and Matt Dowle for the
PR.
fread(text="a,b,c") (where input data contains no
\n but text= has been used) now works instead
of error file not found: a,b,c, #4689.
Thanks to @trainormg for reporting, and @ben-schwen for the
PR.
na.omit(DT) did not remove NA in
nanotime columns, #4744.
Thanks Jean-Mathieu Vermosen for reporting, and Michael Chirico for the
PR.
DT[, min(intCol, na.rm=TRUE), by=grp] would return
Inf for any groups containing all NAs, with a type change
from integer to numeric to hold the
Inf, and with warning. Similarly max would
return -Inf. Now NA is returned for such
all-NA groups, without warning or type change. This is almost-surely
less surprising, more convenient, consistent, and efficient. There was
no user request for this, likely because our desire to be consistent
with base R in this regard was known
(base::min(x, na.rm=TRUE) returns Inf with
warning for all-NA input). Matt Dowle made this change when reworking
internals, #5105. The
old behavior seemed so bad, and since there was a warning too, it seemed
appropriate to treat it as a bug.
DT
# A B
# <char> <int>
# 1: a 1
# 2: a NA
# 3: b 2
# 4: b NA
DT[, min(B,na.rm=TRUE), by=A] # no change in behavior (no all-NA groups yet)
# A V1
# <char> <int>
# 1: a 1
# 2: b 2
DT[3, B:=NA] # make an all-NA group
DT
# A B
# <char> <int>
# 1: a 1
# 2: a NA
# 3: b NA
# 4: b NA
DT[, min(B,na.rm=TRUE), by=A] # old result
# A V1
# <char> <num> # V1's type changed to numeric (inconsistent)
# 1: a 1
# 2: b Inf # Inf surprising
# Warning message: # warning inconvenient
# In gmin(B, na.rm = TRUE) :
# No non-missing values found in at least one group. Coercing to numeric
# type and returning 'Inf' for such groups to be consistent with base
DT[, min(B,na.rm=TRUE), by=A] # new result
# A V1
# <char> <int> # V1's type remains integer (consistent)
# 1: a 1
# 2: b NA # NA because there are no non-NA, naturally
# no inconvenient warningOn the same basis, min and max methods for
empty IDate input now return NA_integer_ of
class IDate, rather than NA_double_ of class
IDate together with base R’s warning
no non-missing arguments to min; returning Inf, #2256.
The type change and warning would cause an error in grouping, see
example below. Since NA was returned before it seems clear
that still returning NA but of the correct type and with no
warning is appropriate, backwards compatible, and a bug fix. Thanks to
Frank Narf for reporting, and Matt Dowle for fixing.
DT
# d g
# <IDat> <char>
# 1: 2020-01-01 a
# 2: 2020-01-02 a
# 3: 2019-12-31 b
DT[, min(d[d>"2020-01-01"]), by=g]
# was:
# Error in `[.data.table`(DT, , min(d[d > "2020-01-01"]), by = g) :
# Column 1 of result for group 2 is type 'double' but expecting type
# 'integer'. Column types must be consistent for each group.
# In addition: Warning message:
# In min.default(integer(0), na.rm = FALSE) :
# no non-missing arguments to min; returning Inf
# now :
# g V1
# <char> <IDat>
# 1: a 2020-01-02
# 2: b <NA>DT[, min(int64Col), by=grp] (and max)
would return incorrect results for bit64::integer64
columns, #4444.
Thanks to @go-see for
reporting, and Michael Chirico for the PR.
fread(dec=',') was able to guess
sep=',' and return an incorrect result, #4483.
Thanks to Michael Chirico for reporting and fixing. It was already an
error to provide both sep=',' and dec=','
manually.
fread('A|B|C\n1|0,4|a\n2|0,5|b\n', dec=',') # no problem
# A B C
# <int> <num> <char>
# 1: 1 0.4 a
# 2: 2 0.5 b
fread('A|B,C\n1|0,4\n2|0,5\n', dec=',')
# A|B C # old result guessed sep=',' despite dec=','
# <char> <int>
# 1: 1|0 4
# 2: 2|0 5
# A B,C # now detects sep='|' correctly
# <int> <num>
# 1: 1 0.4
# 2: 2 0.5IDateTime() ignored the tz= and
format= arguments because ... was not passed
through to submethods, #2402.
Thanks to Frank Narf for reporting, and Jens Peder Meldgaard for the
PR.
IDateTime("20171002095500", format="%Y%m%d%H%M%S")
# was :
# Error in charToDate(x) :
# character string is not in a standard unambiguous format
# now :
# idate itime
# <IDat> <ITime>
# 1: 2017-10-02 09:55:00DT[i, sum(b), by=grp] (and other optimized-by-group
aggregates: mean, var, sd,
median, prod, min,
max, first, last,
head and tail) could segfault if
i contained row numbers and one or more were NA, #1994.
Thanks to Arun Srinivasan for reporting, and Benjamin Schwendinger for
the PR.
identical(fread(text="A\n0.8060667366\n")$A, 0.8060667366)
is now TRUE, #4461.
This is one of 13 numbers in the set of 100,000 between 0.80606 and
0.80607 in 0.0000000001 increments that were not already identical. In
all 13 cases R’s parser (same as read.table) and
fread straddled the true value by a very similar small
amount. fread now uses /10^n rather than
*10^-n to match R identically in all cases. Thanks to Gabe
Becker for requesting consistency, and Michael Chirico for the PR.
for (i in 0:99999) {
s = sprintf("0.80606%05d", i)
r = eval(parse(text=s))
f = fread(text=paste0("A\n",s,"\n"))$A
if (!identical(r, f))
cat(s, sprintf("%1.18f", c(r, f, r)), "\n")
}
# input eval & read.table fread before fread now
# 0.8060603509 0.806060350899999944 0.806060350900000055 0.806060350899999944
# 0.8060614740 0.806061473999999945 0.806061474000000056 0.806061473999999945
# 0.8060623757 0.806062375699999945 0.806062375700000056 0.806062375699999945
# 0.8060629084 0.806062908399999944 0.806062908400000055 0.806062908399999944
# 0.8060632774 0.806063277399999945 0.806063277400000056 0.806063277399999945
# 0.8060638101 0.806063810099999944 0.806063810100000055 0.806063810099999944
# 0.8060647118 0.806064711799999944 0.806064711800000055 0.806064711799999944
# 0.8060658349 0.806065834899999945 0.806065834900000056 0.806065834899999945
# 0.8060667366 0.806066736599999945 0.806066736600000056 0.806066736599999945
# 0.8060672693 0.806067269299999944 0.806067269300000055 0.806067269299999944
# 0.8060676383 0.806067638299999945 0.806067638300000056 0.806067638299999945
# 0.8060681710 0.806068170999999944 0.806068171000000055 0.806068170999999944
# 0.8060690727 0.806069072699999944 0.806069072700000055 0.806069072699999944
#
# remaining 99,987 of these 100,000 were already identicaldcast(empty-DT) now returns an empty
data.table rather than error
Cannot cast an empty data.table, #1215.
Thanks to Damian Betebenner for reporting, and Matt Dowle for
fixing.
DT[factor("id")] now works rather than error
i has evaluated to type integer. Expecting logical, integer or double,
#1632.
DT["id"] has worked forever by automatically converting to
DT[.("id")] for convenience, and joins have worked forever
between char/fact, fact/char and fact/fact even when levels mismatch, so
it was unfortunate that DT[factor("id")] managed to escape
the simple automatic conversion to DT[.(factor("id"))]
which is now in place. Thanks to @aushev for reporting, and Matt Dowle for the
fix.
All-NA character key columns could segfault, #5070. Thanks to @JorisChau for reporting and Benjamin Schwendinger for the fix.
In v1.13.2 a version of an old bug was reintroduced where during a grouping operation list columns could retain a pointer to the last group. This affected only attributes of list elements and only if those were updated during the grouping operation, #4963. Thanks to @fujiaxiang for reporting and @avimallu and Václav Tlapák for investigating and the PR.
shift(xInt64, fill=0) and
shift(xInt64, fill=as.integer64(0)) (but not
shift(xInt64, fill=0L)) would error with
INTEGER() can only be applied to a 'integer', not a 'double'
where xInt64 conveys bit64::integer64,
0 is type double and 0L is type
integer, #4865.
Thanks to @peterlittlejohn for reporting and
Benjamin Schwendinger for the PR.
DT[i, strCol:=classVal] did not coerce using the
as.character method for the class, resulting in either an
unexpected string value or an error such as
To assign integer64 to a target of type character, please use as.character() for clarity.
Discovered during work on the previous issue, #5189.
DT
# A
# <char>
# 1: a
# 2: b
# 3: c
DT[2, A:=as.IDate("2021-02-03")]
DT[3, A:=bit64::as.integer64("4611686018427387906")]
DT
# A
# <char>
# 1: a
# 2: 2021-02-03 # was 18661
# 3: 4611686018427387906 # was error 'please use as.character'tables() failed with
argument "..." is missing when called from within a
function taking ...;
e.g. function(...) { tables() }, #5197.
Thanks @greg-minshall for the report and
@michaelchirico for the fix.
DT[, prod(int64Col), by=grp] produced wrong results
for bit64::integer64 due to incorrect optimization, #5225.
Thanks to Benjamin Schwendinger for reporting and fixing.
fintersect(..., all=TRUE) and
fsetdiff(..., all=TRUE) could return incorrect results when
the inputs had columns named x and y, #5255.
Thanks @Fpadt for the
report, and @ben-schwen for the fix.
fwrite() could produce not-ISO-compliant timestamps
such as 2023-03-08T17:22:32.:00Z when under a whole second
by less than numerical tolerance of one microsecond, #5238.
Thanks to @avraam-inside for the report and
Václav Tlapák for the fix.
merge.data.table() silently ignored the
incomparables argument, #2587.
It is now implemented and any other ignored arguments
(e.g. misspellings) are now warned about. Thanks to @GBsuperman for the
report and @ben-schwen for the fix.
DT[, c('z','x') := {x=NULL; list(2,NULL)}] now
removes column x as expected rather than incorrectly
assigning 2 to x as well as z, #5284.
The x=NULL is superfluous while the
list(2,NULL) is the final value of {} whose
items correspond to c('z','x'). Thanks @eutwt for the report, and
@ben-schwen for
the fix.
as.data.frame(DT, row.names=) no longer silently
ignores row.names, #5319.
Thanks to @dereckdemezquita for the fix and
PR, and @ben-schwen for guidance.
data.table(...) unnamed arguments are deparsed in an
attempt to name the columns but when called from do.call()
the input data itself was deparsed taking a very long time, #5501.
Many thanks to @OfekShilon for the report and fix, and
@michaelchirico for guidance. Unnamed
arguments to data.table(...) may now be faster in other
cases not involving do.call() too; e.g. expressions
spanning a lot of lines or other function call constructions that led to
the data itself being deparsed.
DF = data.frame(a=runif(1e6), b=runif(1e6))
DT1 = data.table(DF) # 0.02s before and after
DT2 = do.call(data.table, list(DF)) # 3.07s before, 0.02s after
identical(DT1, DT2) # TRUEfread(URL) with https: and
ftps: could timeout if proxy settings were not guessed
right by curl::curl_download, #1686.
fread(URL) now uses download.file() as default
for downloading files from urls. Thanks to @cderv for the report and Benjamin
Schwendinger for the fix.
split.data.table() works for downstream methods that
don’t implement DT[i] form (i.e., requiring
DT[i, j] form, like plain data.frames), for
example sf’s [.sf, #5365.
Thanks @barryrowlingson for the report and
@michaelchirico for the fix.
New feature 29 in v1.12.4 (Oct 2019) introduced zero-copy
coercion. Our thinking is that requiring you to get the type right in
the case of 0 (type double) vs 0L (type
integer) is too inconvenient for you the user. So such coercions happen
in data.table automatically without warning. Thanks to
zero-copy coercion there is no speed penalty, even when calling
set() many times in a loop, so there’s no speed penalty to
warn you about either. However, we believe that assigning a character
value such as "2" into an integer column is more likely to
be a user mistake that you would like to be warned about. The type
difference (character vs integer) may be the only clue that you have
selected the wrong column, or typed the wrong variable to be assigned to
that column. For this reason we view character to numeric-like coercion
differently and will warn about it. If it is correct, then the warning
is intended to nudge you to wrap the RHS with
as.<type>() so that it is clear to readers of your
code that a coercion from character to that type is intended. For
example :
x = c(2L,NA,4L,5L)
nafill(x, fill=3) # no warning; requiring 3L too inconvenient
nafill(x, fill="3") # warns in case either x or "3" was a mistake
nafill(x, fill=3.14) # warns that precision has been lost
nafill(x, fill=as.integer(3.14)) # no warning; the as.<type> conveys intentCsubsetDT exported C function has been renamed to
DT_subsetDT. This requires
R_GetCCallable("data.table", "CsubsetDT") to be updated to
R_GetCCallable("data.table", "DT_subsetDT"). Additionally
there is now a dedicated header file for data.table C exports
include/datatableAPI.h, #4643,
thanks to @eddelbuettel, which makes it easier to
import data.table C functions.
In v1.12.4, fractional fread(..., stringsAsFactors=)
was added. For example if stringsAsFactors=0.2, any
character column with fewer than 20% unique strings would be cast as
factor. This is now documented in ?fread as
well, #4706.
Thanks to @markderry for the PR.
cube(DT, by="a") now gives a more helpful error that
j is missing, #4282.
v1.13.0 (July 2020) fixed a segfault/corruption/error (depending
on version of R and circumstances) in dcast() when
fun.aggregate returned NA (type
logical) in an otherwise character result, #2394.
This fix was the result of other internal rework and there was no news
item at the time. A new test to cover this case has now been added.
Thanks Vadim Khotilovich for reporting, and Michael Chirico for
investigating, pinpointing when the fix occurred and adding the
test.
DT[subset] where DT[(subset)] or
DT[subset==TRUE] was intended; i.e., subsetting by a
logical column whose name conflicts with an existing function, now gives
a friendlier error message, #5014.
Thanks @michaelchirico for the suggestion
and PR, and @ColeMiller1 for helping with the
fix.
Grouping by a list column has its error message
improved stating this is unsupported, #4308.
Thanks @sindribaldur for filing, and @michaelchirico for
the PR. Please add your vote and especially use cases to the #1597
feature request.
OpenBSD 6.9 released May 2021 uses a 16 year old version of zlib
(v1.2.3 from 2005) plus cherry-picked bug fixes (i.e. a semi-fork of
zlib) which induces Compress gzip error: -9 from
fwrite(), #5048.
Thanks to Philippe Chataignon for investigating and fixing. Matt asked
on OpenBSD’s mailing list if zlib could be upgraded to 4 year old zlib
1.2.11 but forgot his tin hat:
https://marc.info/?l=openbsd-misc&m=162455479311886&w=1.
?".", ?"..", ?".(", and
?".()" now point to ?data.table, #4385 #4407.
To help users find the documentation for these convenience features
available inside DT[...]. Recall that . is an
alias for list, and ..var tells
data.table to look for var in the calling
environment as opposed to a column of the table.
DT[, lhs:=rhs] and set(DT, , lhs, rhs)
no longer raise a warning on zero length lhs, #4086.
Thanks to Jan Gorecki for the suggestion and PR. For example,
DT[, grep("foo", names(dt)) := NULL] no longer warns if
there are no column names containing "foo".
melt()’s internal C code is now more memory
efficient, #5054.
Thanks to Toby Dylan Hocking for the PR.
?merge and ?setkey have been updated to
clarify that the row order is retained when sort=FALSE, and
why NAs are always first when sort=TRUE, #2574 #2594.
Thanks to Davor Josipovic and Markus Bonsch for the reports, and Jan
Gorecki for the PR.
For nearly two years, since v1.12.4 (Oct 2019) (note 11 below in
this NEWS file), using options(datatable.nomatch=0) has
produced the following message :
The option 'datatable.nomatch' is being used and is not set to the default NA. This option
is still honored for now but will be deprecated in future. Please see NEWS for 1.12.4 for
detailed information and motivation. To specify inner join, please specify `nomatch=NULL`
explicitly in your calls rather than changing the default using this option.The message is now upgraded to warning that the option is now ignored.
The options datatable.print.class and
datatable.print.keys are now TRUE by default.
They have been available since v1.9.8 (Nov 2016) and v1.11.0 (May 2018)
respectively.
Thanks to @ssh352, Václav Tlapák, Cole Miller, András Svraka and Toby Dylan Hocking for reporting and bisecting a significant performance regression in dev. This was fixed before release thanks to a PR by Jan Gorecki, #5463.
key(x) <- value is now fully deprecated (from
warning to error). Use setkey() to set a table’s key. We
started warning not to use this approach in 2012, with a stronger
warning starting in 2019 (1.12.2). This function will be removed in the
next release.
Argument logicalAsInt to fwrite() now
warns. Use logical01 instead. We stated the intention to
begin removing this option in 2018 (v1.11.0). It will be upgraded to an
error in the next release before being removed in the subsequent
release.
Option datatable.CJ.names no longer has any effect,
after becoming TRUE by default in v1.12.2 (2019). Setting
it now gives a warning, which will be dropped in the next
release.
In the NEWS for v1.11.0 (May 2018), section “NOTICE OF INTENDED
FUTURE POTENTIAL BREAKING CHANGES” item 2, we stated the intention to
eventually change logical01 to be TRUE by
default. After some consideration, reflection, and community input, we
have decided not to move forward with this plan, i.e.,
logical01 will remain FALSE by default in both
fread() and fwrite(). See discussion in #5856;
most importantly, we think changing the default would be a major
disruption to reading “sharded” CSVs where data with the same schema is
split into many files, some of which could be converted to
logical while others remain integer. We will
retain the option datatable.logical01 for users who wish to
use a different default – for example, if you are doing input/output on
tables with a large number of logical columns, where writing ‘0’/‘1’ to
the CSV many millions of times is preferable to writing
‘TRUE’/‘FALSE’.
Some clarity is added to ?GForce for the case when
subtle changes to j produce different results because of
differences in locale. Because data.table always
uses the “C” locale, small changes to queries which activate/deactivate
GForce might cause confusingly different results when sorting is
involved, #5331.
The inspirational example compared
DT[, .(max(a), max(b)), by=grp] and
DT[, .(max(a), max(tolower(b))), by=grp] – in the latter
case, GForce is deactivated owing to the ad-hoc column, so the
result for max(a) might differ for the two queries. An
example is added to ?GForce. As always, there are several
options to guarantee consistency, for example (1) use namespace
qualification to deactivate GForce:
DT[, .(base::max(a), base::max(b)), by=grp]; (2) turn off
all optimizations with options(datatable.optimize = 0); or
(3) set your R session to always sort in C locale with
Sys.setlocale("LC_COLLATE", "C") (or temporarily with
e.g. withr::with_locale()). Thanks @markseeto for the example and @michaelchirico for
the improved documentation.
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