cbindlist

add cbind by reference, timing

R prototype of mergelist

wording

use lower overhead funs

stick to int32 for now, correct R_alloc

bmerge C refactor for codecov and one loop for speed

address revealed codecov gaps

refactor vecseq for codecov

seqexp helper, some alloccol export on C

bmerge codecov, types handled in R bmerge already

better comment seqexp

bmerge mult=error #655

multiple new C utils

swap if branches

explain new C utils

comments mostly

reduce conflicts to PR #4386

comment C code

address multiple matches during update-on-join #3747

Revert "address multiple matches during update-on-join #3747"

This reverts commit b64c0c3.

merge.dt has temporarily mult arg, for testing

minor changes to cbindlist c

dev mergelist, for single pair now

add quiet option to cc()

mergelist tests

add check for names to perhaps.dt

rm mult from merge.dt method

rework, clean, polish multer, fix righ and full joins

make full join symmetric

mergepair inner function to loop on

extra check for symmetric

mergelist manual

ensure no df-dt passed where list expected

comments and manual

handle 0 cols tables

more tests

more tests and debugging

move more logic closer to bmerge, simplify mergepair

more tests

revert not used changes

reduce not needed checks, cleanup

copy arg behavior, manual, no tests yet

cbindlist manual, export both

cleanup processing bmerge to dtmatch

test function match order for easier preview

vecseq gets short-circuit

batch test allow browser

big cleanup

remmove unneeded stuff, reduce diff

more cleanup, minor manual fixes

add proper test scripts

Merge branch 'master' into cbind-merge-list

comment out not used code for coverage

more tests, some nocopy opts

rename sql test script, should fix codecov

simplify dtmatch inner branch

more precise copy, now copy only T or F

unused arg not yet in api, wording

comments and refer issues

codecov

hasindex coverage

codecov gap

tests for join using key, cols argument

fix missing import forderv

more tests, improve missing on handling

more tests for order of inner and full join for long keys

new allow.cartesian option, #4383, #914

reduce diff, improve codecov

reduce diff, comments

need more DT, not lists, mergelist 3+ tbls

proper escape heavy check

unit tests

more tests, address overalloc failure

mergelist and cbindlist retain index

manual, examples

fix manual

minor clarify in manual

retain keys, right outer join for snowflake schema joins

duplicates in cbindlist

recycling in cbindlist

escape 0 input in copyCols

empty input handling

closing cbindlist

vectorized _on_ and _join.many_ arg

rename dtmatch to dtmerge

vectorized args: how, mult
push down input validation
add support for cross join, semi join, anti join

full join, reduce overhead for mult=error

mult default value dynamic

fix manual

add "see details" to Rd

mention shared on in arg description

amend feedback from Michael

semi and anti joins will not reorder x columns

Merge branch 'master' into cbind-merge-list

spelling, thx to @jan-glx

check all new funs used and add comments

bugfix, sort=T needed for now

Merge branch 'master' into cbind-merge-list

Update NEWS.md

Merge branch 'master' into cbind-merge-list

Merge branch 'master' into cbind-merge-list

NEWS placement

numbering

ascArg->order

Merge remote-tracking branch 'origin/cbind-merge-list' into cbind-merge-list

attempt to restore from master

Update to stopf() error style

Need isFrame for now

More quality checks: any(!x)->!all(x); use vapply_1{b,c,i}

really restore from master

try to PROTECT() before duplicate()

update error message in test

appease the rchk gods

extraneous space

missing ';'

use catf

simplify perhapsDataTableR

move sqlite.Rraw.manual into other.Rraw

simplify for loop

Merge remote-tracking branch 'origin/cbind-merge-list' into cbind-merge-list

Author: MichaelChirico

NAMESPACE

@@ -59,6 +59,7 @@ export(nafill)
 export(setnafill)
 export(.Last.updated)
 export(fcoalesce)
+export(cbindlist)
 export(substitute2)
 #export(DT)  # mtcars |> DT(i,j,by)  #4872 #5472
 

R/mergelist.R

@@ -0,0 +1,9 @@
+cbindlist = function(l, copy=TRUE) {
+  ans = .Call(Ccbindlist, l, copy)
+  if (anyDuplicated(names(ans))) { ## invalidate key and index
+    setattr(ans, "sorted", NULL)
+    setattr(ans, "index", integer())
+  }
+  setDT(ans)
+  ans
+}

inst/tests/mergelist.Rraw

@@ -0,0 +1,72 @@
+require(methods)
+
+if (exists("test.data.table", .GlobalEnv, inherits=FALSE)) {
+  if ((tt<-compiler::enableJIT(-1))>0)
+    cat("This is dev mode and JIT is enabled (level ", tt, ") so there will be a brief pause around the first test.\n", sep="")
+} else {
+  require(data.table)
+  test = data.table:::test
+}
+
+addresses = function(x) vapply(x, address, "")
+
+# cbindlist
+
+l = list(
+  d1 = data.table(x=1:3, v1=1L),
+  d2 = data.table(y=3:1, v2=2L),
+  d3 = data.table(z=2:4, v3=3L)
+)
+ans = cbindlist(l)
+expected = data.table(l$d1, l$d2, l$d3)
+test(11.01, ans, expected)
+test(11.02, intersect(addresses(ans), addresses(expected)), character())
+ans = cbindlist(l, copy=FALSE)
+expected = setDT(c(l$d1, l$d2, l$d3))
+test(11.03, ans, expected)
+test(11.04, length(intersect(addresses(ans), addresses(expected))), ncol(expected))
+test(11.05, cbindlist(list(data.table(a=1L), data.table(), data.table(d=2L), data.table(f=3L))), data.table(a=1L,d=2L,f=3L))
+rm(expected)
+## codecov
+test(12.01, cbindlist(data.frame(a=1L), data.frame(b=1L)), error="must be a list")
+test(12.02, cbindlist(TRUE, FALSE), error="must be a list")
+test(12.03, cbindlist(list(), NA), error="must be TRUE or FALSE")
+test(12.04, cbindlist(list(data.table(a=1L), 1L)), error="is not of data.table type")
+test(12.05, options = c(datatable.verbose=TRUE), cbindlist(list(data.table(a=1:2), data.table(b=1:2))), data.table(a=1:2, b=1:2), output="cbindlist.*took")
+test(12.06, cbindlist(list(data.table(), data.table(a=1:2), data.table(b=1:2))), data.table(a=1:2, b=1:2))
+test(12.07, cbindlist(list(data.table(), data.table(a=1:2), list(b=1:2))), data.table(a=1:2, b=1:2))
+test(12.08, cbindlist(list(data.table(a=integer()), list(b=integer()))), data.table(a=integer(), b=integer()))
+## duplicated names
+test(12.09, cbindlist(list(data.table(a=1L, b=2L), data.table(b=3L, d=4L))), data.table(a=1L, b=2L, b=3L, d=4L))
+ans = cbindlist(list(setindexv(data.table(a=2:1, b=1:2),"a"), data.table(a=1:2, b=2:1, key="a"), data.table(a=2:1, b=1:2)))
+test(12.10, ans, data.table(a=2:1, b=1:2, a=1:2, b=2:1, a=2:1, b=1:2))
+test(12.11, indices(ans), NULL)
+## recycling, first ensure cbind recycling that we want to match to
+test(12.12, cbind(data.table(x=integer()), data.table(a=1:2)), data.table(x=c(NA_integer_,NA), a=1:2))
+test(12.13, cbind(data.table(x=1L), data.table(a=1:2)), data.table(x=c(1L,1L), a=1:2))
+test(12.14, cbindlist(list(data.table(a=integer()), data.table(b=1:2))), error="recycling.*not yet implemented")
+test(12.15, cbindlist(list(data.table(a=1L), data.table(b=1:2))), error="recycling.*not yet implemented")
+test(12.16, cbindlist(list(data.table(a=integer()), data.table(b=1:2)), copy=FALSE), error="has to have equal nrow")
+test(12.17, cbindlist(list(data.table(a=1L), data.table(b=1:2)), copy=FALSE), error="has to have equal nrow")
+
+## retain indices
+d = data.table(x=1:2, y=2:1, z=2:1, v1=1:2) ## ensure setDT will retain key and indices when it is called on the list, bc Ccbindlist returns list
+setkeyv(d, "x"); setindexv(d, list("y", "z"))
+a = attributes(d)
+attributes(d) = a[!names(a) %in% c("class",".internal.selfref","row.names")]
+test(13.01, class(d), "list")
+setDT(d)
+test(13.02, key(d), "x")
+# test(13.03, hasindex(d, "y") && hasindex(d, "z"))
+l = list(
+  data.table(id1=1:5, id2=5:1, id3=1:5, v1=1:5),
+  data.table(id4=5:1, id5=1:5, v2=1:5),
+  data.table(id6=5:1, id7=1:5, v3=1:5),
+  data.table(id8=5:1, id9=5:1, v4=1:5)
+)
+setkeyv(l[[1L]], "id1"); setindexv(l[[1L]], list("id1", "id2", "id3", c("id1","id2","id3"))); setindexv(l[[3L]], list("id6", "id7")); setindexv(l[[4L]], "id9")
+ii = lapply(l, indices)
+ans = cbindlist(l)
+test(13.04, key(ans), "id1")
+test(13.05, indices(ans), c("id1","id2","id3","id1__id2__id3","id6","id7","id9"))
+test(13.06, ii, lapply(l, indices)) ## this tests that original indices have not been touched, shallow_duplicate in mergeIndexAttrib

man/cbindlist.Rd

@@ -0,0 +1,36 @@
+\name{cbindlist}
+\alias{cbindlist}
+\alias{cbind}
+\alias{cbind.data.table}
+\title{Column bind multiple data.tables}
+\description{
+  Column bind multiple \code{data.table}s.
+}
+\usage{
+  cbindlist(l, copy=TRUE)
+}
+\arguments{
+  \item{l}{ \code{list} of \code{data.table}s to merge. }
+  \item{copy}{ \code{logical}, decides if columns has to be copied into resulting object (default) or just referred. }
+}
+\details{
+  Column bind only stacks input elements. Works like \code{\link{data.table}}, but takes \code{list} type on input. Zero-column tables in \code{l} are omitted. Tables in \code{l} should have matching row count; recycling of length-1 rows is not yet implemented. Indices of the input tables are transferred to the resulting table, as well as the \emph{key} of the first keyed table.
+}
+\value{
+  A new \code{data.table} based on the stacked objects. Eventually when \code{copy} is \code{FALSE}, then resulting object will share columns with \code{l} tables.
+}
+\note{
+  If output object has any duplicate names, then key and indices are removed.
+}
+\seealso{
+  \code{\link{data.table}}, \code{\link{rbindlist}}
+}
+\examples{
+l = list(
+  d1 = data.table(x=1:3, v1=1L),
+  d2 = data.table(y=3:1, v2=2L),
+  d3 = data.table(z=2:4, v3=3L)
+)
+cbindlist(l)
+}
+\keyword{ data }

src/data.table.h

@@ -284,6 +284,9 @@ SEXP substitute_call_arg_namesR(SEXP expr, SEXP env);
 //negate.c
 SEXP notchin(SEXP x, SEXP table);
 
+// mergelist.c
+SEXP cbindlist(SEXP x, SEXP copyArg);
+
 // functions called from R level .Call/.External and registered in init.c
 // these now live here to pass -Wstrict-prototypes, #5477
 // all arguments must be SEXP since they are called from R level

src/init.c

@@ -149,6 +149,7 @@ R_CallMethodDef callMethods[] = {
 {"CstartsWithAny", (DL_FUNC)&startsWithAny, -1},
 {"CconvertDate", (DL_FUNC)&convertDate, -1},
 {"Cnotchin", (DL_FUNC)&notchin, -1},
+{"Ccbindlist", (DL_FUNC) &cbindlist, -1},
 {"Cwarn_matrix_column_r", (DL_FUNC)&warn_matrix_column_r, -1},
 {NULL, NULL, 0}
 };

src/mergelist.c

@@ -0,0 +1,81 @@
+#include "data.table.h"
+
+void mergeIndexAttrib(SEXP to, SEXP from) {
+  if (!isInteger(to) || LENGTH(to)!=0)
+    internal_error(__func__, "'to' must be integer() already"); // # nocov
+  if (isNull(from))
+    return;
+  SEXP t = ATTRIB(to), f = ATTRIB(from);
+  if (isNull(f))
+    return;
+  if (isNull(t))
+    SET_ATTRIB(to, shallow_duplicate(f));
+  else {
+    for (t = ATTRIB(to); CDR(t) != R_NilValue; t = CDR(t));
+    SETCDR(t, shallow_duplicate(f));
+  }
+  return;
+}
+
+SEXP cbindlist(SEXP x, SEXP copyArg) {
+  if (!isNewList(x) || isFrame(x))
+    error(_("'%s' must be a list"), "x");
+  if (!IS_TRUE_OR_FALSE(copyArg))
+    error(_("'%s' must be TRUE or FALSE"), "copy");
+  bool copy = (bool)LOGICAL(copyArg)[0];
+  const bool verbose = GetVerbose();
+  double tic = 0;
+  if (verbose)
+    tic = omp_get_wtime();
+  int nx = length(x), nans = 0, nr = -1, *nnx = (int*)R_alloc(nx, sizeof(int));
+  bool recycle = false;
+  for (int i=0; i<nx; ++i) {
+    SEXP thisx = VECTOR_ELT(x, i);
+    if (!perhapsDataTable(thisx))
+      error(_("Element %d of 'l' list is not a data.table."), i+1);
+    nnx[i] = n_columns(thisx);
+    if (!nnx[i])
+      continue;
+    int thisnr = n_rows(thisx);
+    if (nr < 0) // first (non-zero length table) iteration
+      nr = thisnr;
+    else if (nr != thisnr) {
+      if (!copy)
+        error(_("For copy=FALSE all non-empty tables in 'l' have to have the same number of rows, but l[[%d]] has %d rows which differs from the previous non-zero number of rows (%d)."), i+1, thisnr, nr);
+      recycle = true;
+    }
+    nans += nnx[i];
+  }
+  if (recycle)
+    error(_("Recycling rows is not yet implemented.")); // dont we have a routines for that already somewhere?
+  SEXP ans = PROTECT(allocVector(VECSXP, nans));
+  SEXP index = PROTECT(allocVector(INTSXP, 0));
+  SEXP key = R_NilValue;
+  setAttrib(ans, sym_index, index);
+  SEXP names = PROTECT(allocVector(STRSXP, nans));
+  for (int i=0, ians=0; i<nx; ++i) {
+    int protecti =0;
+    SEXP thisx = VECTOR_ELT(x, i);
+    SEXP thisnames = PROTECT(getAttrib(thisx, R_NamesSymbol)); protecti++;
+    for (int j=0; j<nnx[i]; ++j, ++ians) {
+      SEXP thisxcol;
+      if (copy) {
+        thisxcol = PROTECT(duplicate(VECTOR_ELT(thisx, j))); protecti++;
+      } else {
+        thisxcol = VECTOR_ELT(thisx, j);
+      }
+      SET_VECTOR_ELT(ans, ians, thisxcol);
+      SET_STRING_ELT(names, ians, STRING_ELT(thisnames, j));
+    }
+    mergeIndexAttrib(index, getAttrib(thisx, sym_index));
+    if (isNull(key)) // first key is retained
+      key = getAttrib(thisx, sym_sorted);
+    UNPROTECT(protecti);
+  }
+  setAttrib(ans, R_NamesSymbol, names);
+  setAttrib(ans, sym_sorted, key);
+  if (verbose)
+    Rprintf(_("cbindlist: took %.3fs\n"), omp_get_wtime()-tic);
+  UNPROTECT(3);
+  return ans;
+}

tests/mergelist.R

@@ -0,0 +1,2 @@
+require(data.table)
+test.data.table(script="mergelist.Rraw")