version 0.6-1

ChangeLog

@@ -1,56 +1,63 @@
-Release 0.6-0 (12/12/2016):
+Release 0.6-1:
+  * Added data.frame methods.
+  * Registered native routines.
+  * Fixed rchk errors.
+  * Fixed many -Wextra compiler warnings.
+  * Fixed bug in naomit for large matrices.
+
+Release 0.6-0:
   * Added inverse method.
   * Added C99 configure test.
   * Added internal C lib tests and benchmarks.
   * Minor C lib refactoring.
   * Fixed a few memory errors.
   * Switch to LaTeX vignettes.
 
-Release 0.5-1 (7/7/2016):
+Release 0.5-1:
   * Added scaler() to center and/or scale efficiently.
   * Better safety in internal OpenMP statements (default(none)).
   * Added tcosine(), tpcor(), tcovar().
   * Added blocked xpose and symmetrize.
 
-Release 0.5-0 (4/24/2016):
+Release 0.5-0:
   * Implemented inplace methods for correlation and covariance (correlation is
 	always doneinplance)
   * Added 'inplace' argument.
   * Implemented use='pairwise.complete.obs' methods.
   * Several small performance improvements.
 
-Release 0.4-0 (4/4/2016):
+Release 0.4-0:
   * Implemented a fast naomit for dense internals.
   * Added 'use' argument.
   * Implemented 'use' with "everything", "all.obs", and "complete.obs".
   * Added fix to coop_covar_vecvec for older compilers.
 
-Release 0.3-1 (3/22/2016):
+Release 0.3-1:
   * Added support for dgCMatrix from Matrix.
   * Lowered cost (time/mem) to rebuild the vignette.
   * Retained column names as row/col names in all co-operations.
 
-Release 0.3-0 (3/17/2016):
+Release 0.3-0:
   * Renamed package to 'coop'.
   * 'Namespaced' the internal lib.
   * Improved vignettes, package description.
   * Use https in inst/CITATION.
   * Released to CRAN.
 
-Release 0.2-2 (3/11/2016);
+Release 0.2-2;
   * Split vignette into 2.
   * Improved R help.
 
-Release 0.2-1 (3/9/2016):
+Release 0.2-1:
   * Better memory allocation checking.
   * Moved sparsity functions from wrappers.c to sparse_utils.c.
 
-Release 0.2-0 (3/6/2016):
+Release 0.2-0:
   * Added covariance and pearson correlation.
   * Renamed package from fastcosim to fastco.
   * Major re-organization of internals.
   * Better tests.
 
-Release 0.1-0 (12/9/2016):
+Release 0.1-0:
   * Added cosine() function.
   * Added dense matrix, dense vector-vector, and sparse matrix methods.

DESCRIPTION

@@ -2,7 +2,7 @@ Package: coop
 Type: Package
 Title: Co-Operation: Fast Covariance, Correlation, and Cosine
         Similarity Operations
-Version: 0.6-0
+Version: 0.6-1
 Description: Fast implementations of the co-operations: covariance,
     correlation, and cosine similarity.  The implementations are
     fast and memory-efficient and their use is resolved
@@ -23,8 +23,8 @@ Authors@R: c(person("Drew", "Schmidt", role=c("aut", "cre"),
     memory errors."))
 Maintainer: Drew Schmidt <wrathematics@gmail.com>
 RoxygenNote: 5.0.1
-Packaged: 2016-12-12 17:11:05 UTC; iao
+Packaged: 2017-11-14 16:25:44 UTC; mschmid3
 Author: Drew Schmidt [aut, cre],
   Christian Heckendorf [ctb] (Caught some memory errors.)
 Repository: CRAN
-Date/Publication: 2016-12-13 01:21:11
+Date/Publication: 2017-11-14 16:53:17 UTC

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2015-2016
+YEAR: 2015-2017
 COPYRIGHT HOLDER: Drew Schmidt

MD5

@@ -1,21 +1,21 @@
-d6e21b8f581264b7b65260a0b040057d *ChangeLog
-6dcceb2b3fe86a22663fe7636b34ce18 *DESCRIPTION
-32151991ac40f1c2a881a4fde17f3991 *LICENSE
-780f4778973ddedce8fe710e5103fefb *NAMESPACE
+f936edccefbdf61f6a903fd07c06300f *ChangeLog
+25f13e64ff688c7a598466c19bb69a24 *DESCRIPTION
+10b47d87d13685f46d05fbcdc6eb2631 *LICENSE
+dc682275ac72d8981ad89dc0c0b2b904 *NAMESPACE
 94a06c3901cce73726005c8e21c472e1 *R/00_global.r
 a4d161d59c68c8530158c9088e74c3e6 *R/coop-package.r
-b8fb90f62ebebe09c1cd6e11c0cae914 *R/cosine.r
-0d458777e8b206bd0ea9a843a0a45c75 *R/covar.r
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+c6f7663ddc53049e3fdb85e3ee2c8de8 *R/covar.r
 3f4ba4111bcb5d251f8fa9e56fc82eef *R/maxco.r
 208d30a6ea68b44106fce0300b0648a4 *R/naomit.r
-54bdc451886276146d8408807578196f *R/pcor.r
+7d0a5c2160fd99ea1057c45807d6bb5d *R/pcor.r
 9de718aac140bceb36138ee3b8bd264b *R/scaler.r
 c4bca881ce1b7667433e2df8599ca50e *R/sparse_utils.r
 a51da2a78ef6b009800a7b156f8dbb5f *R/utils.r
 c38b0b37d63c90780173e029d4a63f78 *R/weighted.r
-f892819b1297ee39728d5c37887d69dc *R/wrappers_dense.r
+3b9cb472164b3648db1846588c87c872 *R/wrappers_dense.r
 36327f12f0204abe5abfb429d3ec0217 *R/wrappers_sparse.r
-40bdb72f2309cd16ea12187abf743d39 *README.md
+fe0d9251aed24770d5571b7aa6a2a614 *README.md
 cea65614abad0d8dcc74fe1636ab2a39 *cleanup
 b5530b8555dc17eeb91776d98f5a0798 *configure
 c6dd3e936cff072a8b121aee6f53477d *configure.ac
@@ -28,63 +28,61 @@ bc34ef6d7e008b47c3e817392edf9e96 *inst/benchmarks/covar_dense.r
 e280faf5ccb89b4003e58121ad59e771 *inst/benchmarks/pairwise.r
 888bf1c07127c388735c255052205e21 *inst/benchmarks/pcor_dense.r
 7825bc7cfe3d4789cef0012624b96f57 *inst/benchmarks/scale.r
-9d7abae18251ba5894ae133050e9126a *inst/doc/algos.Rnw
-36bbc565ddf309f3c8911a663333e629 *inst/doc/algos.pdf
-9efd979cc64c48cb90e28a48282aeab6 *inst/doc/coop.Rnw
-1ea4771529586a7bd9c88f0786b6938e *inst/doc/coop.pdf
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+a5649f6515ded650af0c46fcbdb8f4ec *inst/doc/algos.pdf
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 76c872383c2b5e7e4fb63bbacd75da35 *man/coop-package.Rd
-0ceb6ce4d87ad098f28ad385f9938317 *man/cosine.Rd
-110b522a5bc973ee60ff9c475a7235e9 *man/covar.Rd
-6b355c75bdec6e6e478b31be3676959d *man/pcor.Rd
+811dc58956fe4ca598579897667cd76a *man/cosine.Rd
+3f209be4dab8303ba6cab330c2dc878a *man/covar.Rd
+b7815eaf86aa5afcc98597951ab85be2 *man/pcor.Rd
 b31dd318a55fbb3f1eac735a6ec3b0ec *man/scaler.Rd
 4af2b676cdaf23b229abc9009feab152 *man/sparsity.Rd
 8582a329b5a3b3cad8a219e6ec86e58a *man/weighted.Rd
 189087126049e969612cebc6f8a59615 *src/Makevars
-4f215a0274261b678d47b1d644e8414f *src/R_checks.c
-9bee5d616891765df180d141f33d8f47 *src/R_naomit.c
-681b9e1c50d041d9c5f3850da2aed7d3 *src/R_wrapper.c
-f4e21198cd9c5ae8a99a9bbd200f9c7b *src/coop.h
-80658d9b26f3f58959a57282ebdc39b1 *src/dense.c
-7033f694bcbac05f0e06a7bd5cf12988 *src/dense_inplace.c
-b8d24fdcb6f48bd7ae58c433ed5b8b46 *src/dense_pairwise.c
-840637f5a2c2b6c6463973cc9d754243 *src/experimental/dense_minmax.c
-52418b13ebd46ccfdd6cb19b1e5692b6 *src/experimental/dense_wt.c
-5de142fc94d4918aca5d498adf8bba3d *src/experimental/inv.c
-f84f574109f98efb7b9fd2d97ada00c0 *src/scale.c
-29688c18026f970724631ecced8bc7dc *src/sparse.c
-015cb54f5813da3894c26f1a718d0dc1 *src/utils/cdefs.h
-2da932fd1c6d77f97dfb454cea568214 *src/utils/copy.h
-e3f30615048b9a276293c76e126288fa *src/utils/fill.h
+2a8b0b3c23de8131cb7d7c1d0879c5e3 *src/R_checks.c
+cc67b192f940375393e43909a9f6cb41 *src/R_naomit.c
+a354120bc9106a10735a3511a13ac341 *src/R_wrapper.c
+7ce83959dc414718455ea86084f68346 *src/coop.h
+ea8d59e6b0629ffee9c284c5e870714a *src/coop_native.c
+0f28749663b0edcee58849e7a3e4308a *src/dense.c
+920c1de730967739ac036b05f6ca9208 *src/dense_inplace.c
+8711c32cb65e67b3053d764753a34a72 *src/dense_pairwise.c
+f97dd87091159d026f0f76d55a290ea1 *src/scale.c
+b4b097f094a903ecb012caaf2ac0d76d *src/sparse.c
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 66760a063b310236e234d5626a72a716 *src/utils/internal/all_equal.h
 ef457916daf1d742cdc3370d2ecb821c *src/utils/internal/gen.h
 921969898bdde69fd08e1fd2f8e7fdcf *src/utils/internal/printer.h
 8d9f3f5ab537f869745bdcf298774e6c *src/utils/internal/timer.h
-ee69c8f9e63ebb354e4d53d2d9952547 *src/utils/inverse.h
-ae25d2e710f74e934f6b159452946a2b *src/utils/lapack.h
-cb61e545e9373dbf80ce4c48ea923305 *src/utils/mmult.h
+96b43118c942d259fa02f4fdb33a89bf *src/utils/inverse.h
+c9133064bfe73ced829510c695ff9537 *src/utils/lapack.h
+c3ecf917aa0b344c58a73cc4dfdbcf96 *src/utils/mmult.h
 595ee45b6bc661ba6e953bad25fda856 *src/utils/naive/symmetrize.h
 0c45f260b608b08926b80341d73d5533 *src/utils/naive/xpose.h
 216b5b1f0a6d8c7b0515ba396ad5090d *src/utils/safeomp.h
-216beb3176623b967751f7d788b95153 *src/utils/scale.h
-2fb6bc06df7d851eddfb8cb7871f2d57 *src/utils/sparsity.h
-d65479d2f8838776727278ae22e01023 *src/utils/special_vals.h
-878360907fde3511241ef17d11ae3944 *src/utils/sumstats.h
-c2c91a30df022143b467c6b125673b68 *src/utils/xpose.h
+b485c2aed652f41e8c20e74ab17e12c7 *src/utils/scale.h
+a3c9e0080ac24643996d0292892bdfdf *src/utils/sparsity.h
+dd7603b6b068858dc4216bdc5b44b6a0 *src/utils/special_vals.h
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 8f266963acf0b1df0a9846ad930871b1 *tests/dense_matrix.R
 19c3610270e4fa5a370773ddf164094c *tests/dense_matrix_inplace.R
 7cfb2bc3227633874c8e604109cecfb8 *tests/dense_matrix_pairwise.R
 1e3e7830c1338674932cfdf828925218 *tests/dense_vecvec.R
-e05204bebb84ca65fc52a9bf50417367 *tests/naomit.R
-f8abc7e254dca27354eb6d631aa40950 *tests/run
+4d5c591519937d07aaf1fe9f4e5e8ad9 *tests/naomit.R
 12a6f577465682702d315f9e879499dd *tests/scale.R
 943664fb36d0c4e46916e7bb61ca78b0 *tests/sparse_matrix.R
 e8d9e924fc96fac47bf482bac1384aa3 *tests/sparse_utils.R
 b4541bf5bde1f8de7214e13f2bad9ea2 *tests/use_method.R
-9d7abae18251ba5894ae133050e9126a *vignettes/algos.Rnw
+a0959dd349daa6071095a83e82826367 *vignettes/algos.Rnw
 6fdbe0bfece0e5500fe8688d0b3d6125 *vignettes/build_pdf.sh
-9efd979cc64c48cb90e28a48282aeab6 *vignettes/coop.Rnw
+55291517729b3bad72b00c3e869659e1 *vignettes/coop.Rnw
 1f1790fff9ca358690e809d36eceaec7 *vignettes/include/00-acknowledgement.tex
 618c6b3a2cf2cce15c91434ed0d943b5 *vignettes/include/bench.png
 e1330e87376f9670b558a083d20b9a54 *vignettes/include/coop.bib
-95b6a826d34db7aba7847917bf3cf948 *vignettes/include/settings.tex
+41551bf44f2b38b2f3161cb128cf2ecf *vignettes/include/lastpage.sty
+55199fb95476c82545fc32022862a4ad *vignettes/include/settings.tex
 c361b262c34785162574e5dcd1fc559b *vignettes/include/uch_small.png

NAMESPACE

@@ -1,17 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(cosine,data.frame)
 S3method(cosine,default)
 S3method(cosine,dgCMatrix)
 S3method(cosine,matrix)
 S3method(cosine,simple_triplet_matrix)
+S3method(covar,data.frame)
 S3method(covar,default)
 S3method(covar,matrix)
+S3method(pcor,data.frame)
 S3method(pcor,default)
 S3method(pcor,matrix)
 S3method(sparsity,matrix)
 S3method(sparsity,simple_triplet_matrix)
+S3method(tcosine,data.frame)
 S3method(tcosine,matrix)
+S3method(tcovar,data.frame)
 S3method(tcovar,matrix)
+S3method(tpcor,data.frame)
 S3method(tpcor,matrix)
 export(cosine)
 export(covar)

R/cosine.r

@@ -9,7 +9,7 @@
 #' See \code{?coop-package} for implementation details.
 #' 
 #' @param x
-#' A numeric matrix or vector.
+#' A numeric dataframe/matrix or vector.
 #' @param y
 #' A vector (when \code{x} is a vector) or missing (blank) when 
 #' \code{x} is a matrix.
@@ -48,6 +48,16 @@ cosine.matrix <- function(x, y, use="everything", inverse=FALSE)
   co_matrix(x, y, CO_SIM, use, inplace=FALSE, inverse=inverse)
 }
 
+#' @export
+cosine.data.frame <- function(x, y, use="everything", inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  cosine.matrix(x_mat, y, use=use, inverse=inverse)
+}
+
 
 
 #' @export
@@ -114,7 +124,7 @@ cosine.dgCMatrix <- function(x, y, use="everything", inverse=FALSE)
 
 
 
-# tcosine
+### tcosine
 
 #' @rdname cosine
 #' @export
@@ -127,3 +137,13 @@ tcosine.matrix <- function(x, y, use="everything", inverse=FALSE)
 {
   co_matrix(x, y, CO_SIM, use, inplace=FALSE, trans=TRUE, inverse=inverse)
 }
+
+#' @export
+tcosine.data.frame <- function(x, y, use="everything", inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  tcosine.matrix(x_mat, y, use=use, inverse=inverse)
+}

R/covar.r

@@ -6,7 +6,7 @@
 #' See \code{?coop-package} for implementation details.
 #' 
 #' @param x
-#' A numeric matrix or vector.
+#' A numeric dataframe/matrix or vector.
 #' @param y
 #' A vector (when \code{x} is a vector) or missing (blank) when 
 #' \code{x} is a matrix.
@@ -48,6 +48,16 @@ covar.matrix <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
   co_matrix(x, y, CO_VAR, use, inplace, trans=FALSE, inverse=inverse)
 }
 
+#' @export
+covar.data.frame <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  covar.matrix(x_mat, y, use=use, inplace=inplace, inverse=inverse)
+}
+
 
 
 #' @export
@@ -58,7 +68,7 @@ covar.default <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
 
 
 
-# tcovar
+### tcovar
 
 #' @rdname covar
 #' @export
@@ -71,3 +81,13 @@ tcovar.matrix <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
 {
   co_matrix(x, y, CO_VAR, use, inplace, trans=TRUE, inverse=inverse)
 }
+
+#' @export
+tcovar.data.frame <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  tcovar.matrix(x_mat, y, use=use, inplace=inplace, inverse=inverse)
+}

R/pcor.r

@@ -7,7 +7,7 @@
 #' See \code{?coop} for implementation details.
 #' 
 #' @param x
-#' A numeric matrix or vector.
+#' A numeric dataframe/matrix or vector.
 #' @param y
 #' A vector (when \code{x} is a vector) or missing (blank) when 
 #' \code{x} is a matrix.
@@ -49,6 +49,16 @@ pcor.matrix <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
   co_matrix(x, y, CO_ORR, use, inplace, trans=FALSE, inverse=inverse)
 }
 
+#' @export
+pcor.data.frame <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  pcor.matrix(x_mat, y, use=use, inplace=inplace, inverse=inverse)
+}
+
 
 
 #' @export
@@ -59,7 +69,7 @@ pcor.default <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
 
 
 
-# tpcor
+### tpcor
 
 #' @rdname pcor
 #' @export
@@ -72,3 +82,13 @@ tpcor.matrix <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
 {
   co_matrix(x, y, CO_ORR, use, inplace, trans=TRUE, inverse=inverse)
 }
+
+#' @export
+tpcor.data.frame <- function(x, y, use="everything", inplace=FALSE, inverse=FALSE)
+{
+  x_mat = as.matrix(x)
+  if (!missing(y) && is.data.frame(y))
+    y = as.matrix(y)
+
+  tpcor.matrix(x_mat, y, use=use, inplace=inplace, inverse=inverse)
+}