Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre],
Hugh Chipman [aut],
Robert McCulloch [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-7 dated 2018-12-18 and 0.9-11 dated 2019-04-20
dbarts-0.9-11/dbarts/DESCRIPTION | 8 dbarts-0.9-11/dbarts/MD5 | 236 + dbarts-0.9-11/dbarts/R/A_class.R | 47 dbarts-0.9-11/dbarts/R/bart.R | 53 dbarts-0.9-11/dbarts/R/data.R | 1 dbarts-0.9-11/dbarts/R/dbarts.R | 223 + dbarts-0.9-11/dbarts/R/model.R | 51 dbarts-0.9-11/dbarts/R/multipleAssignment.R | 11 dbarts-0.9-11/dbarts/R/partialDependence.R | 450 ++- dbarts-0.9-11/dbarts/R/plotTree.R | 177 - dbarts-0.9-11/dbarts/R/utility.R | 21 dbarts-0.9-11/dbarts/R/xbart.R | 30 dbarts-0.9-11/dbarts/cleanup | 4 dbarts-0.9-11/dbarts/configure | 1220 +++------- dbarts-0.9-11/dbarts/configure.ac | 39 dbarts-0.9-11/dbarts/configure.win | 10 dbarts-0.9-11/dbarts/inst/NEWS.Rd | 54 dbarts-0.9-11/dbarts/inst/common/pdData.R |only dbarts-0.9-11/dbarts/inst/include/dbarts/R_C_interface.hpp | 29 dbarts-0.9-11/dbarts/inst/include/dbarts/bartFit.hpp | 85 dbarts-0.9-11/dbarts/inst/include/dbarts/control.hpp | 21 dbarts-0.9-11/dbarts/inst/include/dbarts/data.hpp | 4 dbarts-0.9-11/dbarts/inst/include/dbarts/model.hpp | 87 dbarts-0.9-11/dbarts/inst/include/dbarts/random.hpp |only dbarts-0.9-11/dbarts/inst/include/dbarts/results.hpp | 19 dbarts-0.9-11/dbarts/inst/include/dbarts/scratch.hpp | 11 dbarts-0.9-11/dbarts/inst/include/dbarts/state.hpp | 17 dbarts-0.9-11/dbarts/inst/include/dbarts/types.hpp.in |only dbarts-0.9-11/dbarts/inst/include/dbarts/types.hpp.win |only dbarts-0.9-11/dbarts/man/bart.Rd | 80 dbarts-0.9-11/dbarts/man/pdbart.Rd | 49 dbarts-0.9-11/dbarts/man/xbart.Rd | 15 dbarts-0.9-11/dbarts/src/Makevars.in | 16 dbarts-0.9-11/dbarts/src/Makevars.win | 12 dbarts-0.9-11/dbarts/src/R_C_interface.cpp | 37 dbarts-0.9-11/dbarts/src/R_interface.cpp | 35 dbarts-0.9-11/dbarts/src/R_interface_common.cpp | 400 ++- dbarts-0.9-11/dbarts/src/R_interface_crossvalidate.cpp | 66 dbarts-0.9-11/dbarts/src/R_interface_crossvalidate.hpp | 3 dbarts-0.9-11/dbarts/src/R_interface_sampler.cpp | 438 ++- dbarts-0.9-11/dbarts/src/R_interface_sampler.hpp | 12 dbarts-0.9-11/dbarts/src/config.hpp.in | 6 dbarts-0.9-11/dbarts/src/config.hpp.win | 5 dbarts-0.9-11/dbarts/src/crossvalidate.cpp | 137 - dbarts-0.9-11/dbarts/src/crossvalidate.hpp | 2 dbarts-0.9-11/dbarts/src/dbarts/Makefile | 15 dbarts-0.9-11/dbarts/src/dbarts/bartFit.cpp | 1122 +++++---- dbarts-0.9-11/dbarts/src/dbarts/binaryIO.cpp | 368 +-- dbarts-0.9-11/dbarts/src/dbarts/binaryIO.hpp | 20 dbarts-0.9-11/dbarts/src/dbarts/birthDeathRule.cpp | 15 dbarts-0.9-11/dbarts/src/dbarts/changeRule.cpp | 39 dbarts-0.9-11/dbarts/src/dbarts/config.hpp.in | 1 dbarts-0.9-11/dbarts/src/dbarts/config.hpp.win | 4 dbarts-0.9-11/dbarts/src/dbarts/functions.cpp | 9 dbarts-0.9-11/dbarts/src/dbarts/node.cpp | 533 ++-- dbarts-0.9-11/dbarts/src/dbarts/node.hpp | 56 dbarts-0.9-11/dbarts/src/dbarts/parameterPrior.cpp | 112 dbarts-0.9-11/dbarts/src/dbarts/state.cpp | 304 -- dbarts-0.9-11/dbarts/src/dbarts/swapRule.cpp | 21 dbarts-0.9-11/dbarts/src/dbarts/tree.cpp | 200 + dbarts-0.9-11/dbarts/src/dbarts/tree.hpp | 39 dbarts-0.9-11/dbarts/src/dbarts/treePrior.cpp | 21 dbarts-0.9-11/dbarts/src/external/Makefile | 47 dbarts-0.9-11/dbarts/src/external/config.h.win | 4 dbarts-0.9-11/dbarts/src/external/io.c | 9 dbarts-0.9-11/dbarts/src/external/linearAlgebra.c | 265 -- dbarts-0.9-11/dbarts/src/external/randomBase.c | 107 dbarts-0.9-11/dbarts/src/guessNumCores.cpp | 6 dbarts-0.9-11/dbarts/src/include/external/R.h | 2 dbarts-0.9-11/dbarts/src/include/external/Rinternals.h | 2 dbarts-0.9-11/dbarts/src/include/external/linearAlgebra.h | 54 dbarts-0.9-11/dbarts/src/include/external/random.h | 10 dbarts-0.9-11/dbarts/src/include/external/stats.h | 21 dbarts-0.9-11/dbarts/src/include/misc |only dbarts-0.9-11/dbarts/src/include/rc/util.h | 10 dbarts-0.9-11/dbarts/src/makeModelMatrixFromDataFrame.c | 21 dbarts-0.9-11/dbarts/src/misc |only dbarts-0.9-11/dbarts/src/rc/Makefile | 3 dbarts-0.9-11/dbarts/src/rc/bounds.c | 22 dbarts-0.9-11/dbarts/src/rc/util.c | 51 dbarts-0.9-11/dbarts/tests/testthat.R | 1 dbarts-0.9-11/dbarts/tests/testthat/test-02-dbartsModelArgs.R | 16 dbarts-0.9-11/dbarts/tests/testthat/test-03-dbartsControl.R | 7 dbarts-0.9-11/dbarts/tests/testthat/test-04-continuousResponse.R | 19 dbarts-0.9-11/dbarts/tests/testthat/test-05-binaryResponse.R | 87 dbarts-0.9-11/dbarts/tests/testthat/test-06-dbartsSampler.R | 110 dbarts-0.9-11/dbarts/tests/testthat/test-07-multithreaded.R | 1 dbarts-0.9-11/dbarts/tests/testthat/test-08-xbart.R | 43 dbarts-0.9-11/dbarts/tests/testthat/test-09-predict.R | 7 dbarts-0.9-11/dbarts/tests/testthat/test-14-rbart.R | 1 dbarts-0.9-11/dbarts/tests/testthat/test-15-simd.R |only dbarts-0.9-11/dbarts/tests/testthat/test-16-pdbart.R |only dbarts-0.9-11/dbarts/tools/m4/ax_compiler_ext.m4 |only dbarts-0.9-11/dbarts/tools/m4/ax_compiler_vendor.m4 |only dbarts-0.9-11/dbarts/tools/m4/ax_ext.m4 | 391 +-- dbarts-0.9-11/dbarts/tools/m4/ax_func_posix_memalign.m4 | 4 dbarts-0.9-11/dbarts/tools/m4/ax_gcc_x86_avx_xgetbv.m4 | 8 dbarts-0.9-11/dbarts/tools/m4/ax_gcc_x86_cpuid.m4 | 26 dbarts-0.9-11/dbarts/tools/m4/ax_log1p_in_namespace_std.m4 |only dbarts-0.9-7/dbarts/README.md |only dbarts-0.9-7/dbarts/inst/include/dbarts/types.hpp |only dbarts-0.9-7/dbarts/src/external/adaptiveRadixTree.c |only dbarts-0.9-7/dbarts/src/external/binaryIO.c |only dbarts-0.9-7/dbarts/src/external/blockingThreadManager.c |only dbarts-0.9-7/dbarts/src/external/hierarchicalThreadManager.c |only dbarts-0.9-7/dbarts/src/external/moments.c |only dbarts-0.9-7/dbarts/src/external/pthread.c |only dbarts-0.9-7/dbarts/src/external/string.c |only dbarts-0.9-7/dbarts/src/external/thread.c |only dbarts-0.9-7/dbarts/src/include/external/adaptiveRadixTree.h |only dbarts-0.9-7/dbarts/src/include/external/alloca.h |only dbarts-0.9-7/dbarts/src/include/external/binaryIO.h |only dbarts-0.9-7/dbarts/src/include/external/stats_mt.h |only dbarts-0.9-7/dbarts/src/include/external/stddef.h |only dbarts-0.9-7/dbarts/src/include/external/string.h |only dbarts-0.9-7/dbarts/src/include/external/thread.h |only 116 files changed, 4772 insertions(+), 3683 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Contains functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs (TSD) via simulations.
Author: Detlew Labes [aut, cre],
Benjamin Lang [aut, ctb],
Helmut Schütz [aut, ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.5-1 dated 2018-04-03 and 0.5.2 dated 2019-04-20
DESCRIPTION | 10 +-- MD5 | 42 +++++++------- NEWS | 11 +++ R/adaptive_ci_limits.R | 38 +++++++------ R/final_2stage_in.R | 23 +++++-- R/interim_2stage_in.R | 74 +++++++++++++++---------- R/power_2stage_GS.R | 5 + R/power_2stage_in.R | 6 +- R/power_2stage_parallel.R | 13 +++- R/print_evaltsd.R | 26 ++++---- R/sampsiz3.R | 3 - build/partial.rdb |binary man/final.tsd.in.Rd | 73 +++++++++++++------------ man/interim.tsd.in.Rd | 134 +++++++++++++++++++++++++--------------------- man/power.tsd.GS.Rd | 22 +++---- man/power.tsd.KM.Rd | 18 +++--- man/power.tsd.Rd | 24 ++++---- man/power.tsd.fC.Rd | 44 +++++++-------- man/power.tsd.in.Rd | 86 +++++++++++++++++------------ man/power.tsd.p.Rd | 55 +++++++++--------- man/power.tsd.ssr.Rd | 10 +-- man/sampleN2.TOST.Rd | 6 +- 22 files changed, 401 insertions(+), 322 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-19 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-23 0.8.0
2016-02-21 0.7.0
2015-11-11 0.6.17
2015-05-23 0.6.5.1
2015-01-07 0.6
2014-10-07 0.5.51
2014-09-08 0.5.1
2014-01-08 0.4
2013-03-16 0.3.5
2013-01-26 0.3
2012-10-27 0.2
2012-09-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-03 0.9.4
2014-08-26 0.9.3
2014-08-22 0.9.2.1
2014-08-20 0.9.2
2014-07-21 0.9.0
2014-07-21 0.9.1
Title: Nearest Neighbor Based Multiple Imputation for Survival Data
with Missing Covariates
Description: Imputation for both missing covariates and censored observations (optional) for survival data with missing covariates by the nearest neighbor based multiple imputation algorithm as described in Hsu et al. (2006) <doi:10.1002/sim.2452>, and Hsu and Yu (2018) <doi: 10.1177/0962280218772592>. Note that the current version can only impute for a situation with one missing covariate.
Author: Di Ran, Chiu-Hsieh Hsu, Mandi Yu
Maintainer: Chiu-Hsieh Hsu <pablo1639@gmail.com>
Diff between NNMIS versions 1.0.0 dated 2017-10-18 and 1.0.1 dated 2019-04-20
DESCRIPTION | 15 +-- MD5 | 28 +++--- R/NNIMS.R | 47 +++++------ R/NNMI.R | 19 ++-- R/class.nnmi.R | 37 ++------ R/kmpool.R | 17 ++-- R/plotKM.R | 30 ------- R/pool.R | 224 ++++++++++++++++++++++++++---------------------------- R/print.nnmi.R | 77 ++++++------------ man/NNMIS.Rd | 43 ++++------ man/coxph.pool.Rd | 18 +--- man/km.pool.Rd | 2 man/nnmi.Rd | 28 +----- man/plotKM.Rd | 30 ------- man/print.nnmi.Rd | 19 ---- 15 files changed, 246 insertions(+), 388 deletions(-)
Title: Learn and Experiment with Music Theory
Description: An aid for learning and using music theory. You can build chords, scales, and chord progressions using 12-note equal temperament tuning (12-ET) or user-defined tuning. Includes functions to visualize notes on a piano using ASCII plots in the console and to plot waveforms using base graphics. It allows simple playback of notes and chords using the 'audio' package.
Author: Efstathios D. Gennatas [aut, cre]
Maintainer: Efstathios D. Gennatas <gennatas@gmail.com>
Diff between music versions 0.1.0 dated 2019-02-20 and 0.1.1 dated 2019-04-20
DESCRIPTION | 12 +++++------ MD5 | 12 +++++------ R/build.R | 6 ----- R/music_fn.R | 55 +++++++++++++++++++++++++++-------------------------- man/buildChord.Rd | 5 ---- man/buildScale.Rd | 5 ---- tests/musicTests.R | 6 ++--- 7 files changed, 47 insertions(+), 54 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research (NIBR) [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.1.1 dated 2019-03-26 and 1.2.0 dated 2019-04-20
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 8 ++++ R/high_level_UI.R | 4 +- inst/doc/hdf5r.html | 2 - tests/testthat/test-high_level_UI.R | 72 +++++++++++++++++++++++++++--------- 6 files changed, 74 insertions(+), 28 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations.
It makes it possible to easily perform routine tasks when
exploring correlation matrices such as ignoring the diagonal,
focusing on the correlations of certain variables against others,
or rearranging and visualising the matrix in terms of the
strength of the correlations.
Author: Simon Jackson [aut, cre],
Jorge Cimentada [ctb],
Edgar Ruiz [aut]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between corrr versions 0.3.1 dated 2019-03-06 and 0.3.2 dated 2019-04-20
corrr-0.3.1/corrr/inst/doc/corrr-databases.R |only corrr-0.3.1/corrr/inst/doc/corrr-databases.Rmd |only corrr-0.3.1/corrr/inst/doc/corrr-databases.html |only corrr-0.3.1/corrr/vignettes/corrr-databases.Rmd |only corrr-0.3.2/corrr/DESCRIPTION | 8 - corrr-0.3.2/corrr/MD5 | 30 ++-- corrr-0.3.2/corrr/NAMESPACE | 5 corrr-0.3.2/corrr/NEWS.md | 14 ++ corrr-0.3.2/corrr/R/correlate.R | 165 ++++++++++++------------ corrr-0.3.2/corrr/R/corrr-package.R |only corrr-0.3.2/corrr/R/zzz.R | 4 corrr-0.3.2/corrr/build/vignette.rds |binary corrr-0.3.2/corrr/inst/doc/using-corrr.R | 10 + corrr-0.3.2/corrr/inst/doc/using-corrr.Rmd | 10 + corrr-0.3.2/corrr/inst/doc/using-corrr.html | 27 ++- corrr-0.3.2/corrr/man/correlate.Rd | 5 corrr-0.3.2/corrr/man/corrr-package.Rd |only corrr-0.3.2/corrr/tests/testthat/test-tbl_sql.R | 38 +++-- corrr-0.3.2/corrr/vignettes/using-corrr.Rmd | 10 + 19 files changed, 193 insertions(+), 133 deletions(-)
Title: Fluid Data Transformations
Description: Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases.
The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 .
This package introduces the idea of control table specification of data transforms (later also adapted from 'cdata' by 'tidyr').
Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 1.0.8 dated 2019-03-30 and 1.0.9 dated 2019-04-20
cdata-1.0.8/cdata/R/draw_framec.R |only cdata-1.0.9/cdata/DESCRIPTION | 12 cdata-1.0.9/cdata/MD5 | 46 - cdata-1.0.9/cdata/NAMESPACE | 5 cdata-1.0.9/cdata/NEWS.md | 7 cdata-1.0.9/cdata/R/DefOps.R | 5 cdata-1.0.9/cdata/R/GeneralTransform.R | 6 cdata-1.0.9/cdata/R/RowsColsQ.R | 8 cdata-1.0.9/cdata/R/RowsColumns.R | 3 cdata-1.0.9/cdata/R/opspec.R | 130 +++ cdata-1.0.9/cdata/R/relops.R | 4 cdata-1.0.9/cdata/README.md | 97 +- cdata-1.0.9/cdata/inst/doc/blocksrecs.html | 426 +++--------- cdata-1.0.9/cdata/inst/doc/cdata.html | 344 +--------- cdata-1.0.9/cdata/inst/doc/control_table_keys.html | 368 ++-------- cdata-1.0.9/cdata/inst/doc/design.html | 376 ++--------- cdata-1.0.9/cdata/inst/doc/general_transform.html | 470 +++---------- cdata-1.0.9/cdata/inst/doc/operators.html | 476 +++----------- cdata-1.0.9/cdata/inst/unit_tests/iris.RDS |only cdata-1.0.9/cdata/inst/unit_tests/test_inv.R |only cdata-1.0.9/cdata/man/blocks_to_rowrecs_q.Rd | 2 cdata-1.0.9/cdata/man/convert_records.Rd | 52 + cdata-1.0.9/cdata/man/layout_by.Rd |only cdata-1.0.9/cdata/man/layout_by.blocks_to_rowrecs_spec.Rd |only cdata-1.0.9/cdata/man/layout_by.rowrecs_to_blocks_spec.Rd |only cdata-1.0.9/cdata/man/pivot_to_rowrecs.Rd | 5 cdata-1.0.9/cdata/man/unpivot_to_blocks.Rd | 6 27 files changed, 895 insertions(+), 1953 deletions(-)
Title: Coordinate System Transformations for Map Data
Description: Transform coordinates via 'PROJ' using the library directly, by
wrapping the 'proj4' package. The 'reproj' function handles the need for
radian units for either source or target and allows removing an explicit
source definition in methods that extend the generic. The 'PROJ' library is available
at <https://proj4.org/>.
Author: Michael D. Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>)
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between reproj versions 0.2.0 dated 2018-12-30 and 0.3.0 dated 2019-04-20
reproj-0.2.0/reproj/R/reproj.r |only reproj-0.3.0/reproj/DESCRIPTION | 10 +- reproj-0.3.0/reproj/MD5 | 18 ++--- reproj-0.3.0/reproj/NEWS.md | 4 + reproj-0.3.0/reproj/R/proj.R | 6 + reproj-0.3.0/reproj/R/reproj.R |only reproj-0.3.0/reproj/README.md | 79 ++++++++++++++++++++--- reproj-0.3.0/reproj/inst |only reproj-0.3.0/reproj/man/reproj-package.Rd | 10 +- reproj-0.3.0/reproj/man/reproj.Rd | 16 ++-- reproj-0.3.0/reproj/tests/testthat/test-reproj.R | 4 + 11 files changed, 110 insertions(+), 37 deletions(-)