Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.100.5.0 dated 2018-08-16 and 0.9.200.4.0 dated 2018-11-10
RcppArmadillo-0.9.100.5.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.R |only RcppArmadillo-0.9.100.5.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.Rnw |only RcppArmadillo-0.9.100.5.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |only RcppArmadillo-0.9.100.5.0/RcppArmadillo/vignettes/RcppArmadillo-unitTests.Rnw |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/ChangeLog | 46 RcppArmadillo-0.9.200.4.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.9.200.4.0/RcppArmadillo/MD5 | 170 +-- RcppArmadillo-0.9.200.4.0/RcppArmadillo/README.md | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/build/vignette.rds |binary RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/NEWS.Rd | 25 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo | 6 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/MapMat_meat.hpp | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 8 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_meat.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_bones.hpp | 12 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_meat.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp | 22 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 371 +++--- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_bones.hpp | 1 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_meat.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp | 3 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp | 18 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_cmath.hpp | 104 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 14 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_bones.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 30 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 226 +++- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 5 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/def_lapack.hpp | 22 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/diskio_bones.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 533 +--------- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 5 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 1 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 5 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 93 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_cond.hpp | 25 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 57 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 13 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_size.hpp | 36 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_spones.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_spsolve.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp | 129 ++ RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trig.hpp | 46 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp | 3 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 28 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_bones.hpp | 20 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_meat.hpp | 28 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_cond_bones.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_cond_meat.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_bones.hpp | 8 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_meat.hpp | 88 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_meat.hpp | 33 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_bones.hpp | 6 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp | 88 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_minus.hpp | 78 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_plus.hpp | 82 + RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_schur.hpp | 220 +--- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp | 189 +-- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 9 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_meat.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_elem_helper_bones.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_elem_helper_meat.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_bones.hpp | 2 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_meat.hpp | 114 +- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_kron_meat.hpp | 6 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_bones.hpp | 13 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_meat.hpp | 306 ++++- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_bones.hpp | 11 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_meat.hpp | 261 +++- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_schur_bones.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_schur_meat.hpp |only RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_bones.hpp | 26 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_meat.hpp | 338 +++++- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_bones.hpp | 15 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_meat.hpp | 219 +++- RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_bones.hpp | 10 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp | 47 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_repmat_meat.hpp | 6 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_meat.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_trimat_meat.hpp | 4 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 7 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_lapack.hpp | 48 RcppArmadillo-0.9.200.4.0/RcppArmadillo/inst/unitTests/runit.sparseConversion.R | 75 - 91 files changed, 3008 insertions(+), 1504 deletions(-)
Title: Run 'R CMD check' from 'R' and Capture Results
Description: Run 'R CMD check' from 'R' programmatically, and capture the
results of the individual checks.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rcmdcheck versions 1.3.1 dated 2018-11-05 and 1.3.2 dated 2018-11-10
DESCRIPTION | 6 +- MD5 | 35 +++++++++++---- R/build.R | 8 ++- inst/NEWS.md | 5 ++ tests/testthat.R | 4 - tests/testthat/REDCapR-fail-ascii.log |only tests/testthat/REDCapR-ok-ascii.log |only tests/testthat/RSQLServer-install-ascii |only tests/testthat/bad1/tests/testthat.R | 4 - tests/testthat/bikedata-ok-ascii.log |only tests/testthat/comparison-newly-failing-ascii.txt |only tests/testthat/dataonderivatives-test-ascii |only tests/testthat/fixtures/test-error-ascii.txt |only tests/testthat/libpath-1-27382.out |only tests/testthat/libpath-2-27382.out |only tests/testthat/minimal-ee-ascii.log |only tests/testthat/minimal-ewn-ascii.log |only tests/testthat/minimal-ok-ascii.log |only tests/testthat/parse-install-fail-ascii.txt |only tests/testthat/parse-test-fail-ascii.txt |only tests/testthat/test-build.R | 2 tests/testthat/test-comparison.R | 25 +++++++++- tests/testthat/test-parse.R | 51 ++++++++++++++++++---- tests/testthat/test-rcmdcheck.R | 12 +++-- 24 files changed, 111 insertions(+), 41 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.2.0 dated 2018-11-04 and 0.2.1 dated 2018-11-10
DESCRIPTION | 9 +++++---- MD5 | 8 ++++++-- build |only inst/NEWS.Rd | 8 ++++++++ inst/doc |only vignettes |only 6 files changed, 19 insertions(+), 6 deletions(-)
Title: R Package to Detect Character Encoding
Description: R port of 'universalchardet', that is the encoding detector
library of Mozilla.
Author: Heewon Jeon
Maintainer: ORPHANED
Diff between Ruchardet versions 0.0-3 dated 2014-02-07 and 0.0-3.1 dated 2018-11-10
DESCRIPTION | 13 ++++++++----- MD5 | 4 ++-- src/Makevars.win | 20 ++++++++++---------- 3 files changed, 20 insertions(+), 17 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: A set of tools for processing and modeling high-throughput and
high-content chemical screening data. The package was developed for the
the chemical screening data generated by the US EPA ToxCast program, but
can be used for diverse chemical screening efforts.
Author: Richard S Judson [cre, ths],
Dayne L Filer [aut],
Jason Brown [ctb],
Parth Kothiya [ctb],
Woodrow R Setzer [ctb],
Matthew T Martin [ctb, ths]
Maintainer: Richard S Judson <Judson.Richard@epa.gov>
Diff between tcpl versions 1.4.3 dated 2018-05-20 and 2.0.0 dated 2018-11-10
tcpl-1.4.3/tcpl/inst/doc/tcpl_Overview.R |only tcpl-1.4.3/tcpl/inst/doc/tcpl_Overview.Rnw |only tcpl-1.4.3/tcpl/inst/doc/tcpl_Overview.pdf |only tcpl-1.4.3/tcpl/inst/sql |only tcpl-1.4.3/tcpl/vignettes/tcpl_Overview.Rnw |only tcpl-2.0.0/tcpl/DESCRIPTION | 38 tcpl-2.0.0/tcpl/MD5 | 419 ++++-- tcpl-2.0.0/tcpl/NAMESPACE | 192 +-- tcpl-2.0.0/tcpl/NEWS | 252 ++-- tcpl-2.0.0/tcpl/R/Models.R | 72 - tcpl-2.0.0/tcpl/R/assay_funcs.R | 99 - tcpl-2.0.0/tcpl/R/attachFormals.R | 16 tcpl-2.0.0/tcpl/R/blineShift.R | 106 - tcpl-2.0.0/tcpl/R/buildAssayQ.R | 212 +-- tcpl-2.0.0/tcpl/R/chemQueries.R | 192 +-- tcpl-2.0.0/tcpl/R/clearSQLite.R | 34 tcpl-2.0.0/tcpl/R/config_funcs.R | 110 - tcpl-2.0.0/tcpl/R/convertNames.R | 50 tcpl-2.0.0/tcpl/R/data.R |only tcpl-2.0.0/tcpl/R/drawCircles.R | 112 - tcpl-2.0.0/tcpl/R/flareFunc.R | 136 +- tcpl-2.0.0/tcpl/R/getConfFile.R | 62 tcpl-2.0.0/tcpl/R/hill_utils.R | 106 - tcpl-2.0.0/tcpl/R/interlaceFunc.R | 148 +- tcpl-2.0.0/tcpl/R/is.odd.R | 48 tcpl-2.0.0/tcpl/R/load6DR.R | 108 - tcpl-2.0.0/tcpl/R/lu.R | 41 tcpl-2.0.0/tcpl/R/lw.R | 41 tcpl-2.0.0/tcpl/R/mc1.R | 275 ++-- tcpl-2.0.0/tcpl/R/mc2.R | 248 +-- tcpl-2.0.0/tcpl/R/mc2_mthds.R | 282 ++-- tcpl-2.0.0/tcpl/R/mc3.R | 328 ++--- tcpl-2.0.0/tcpl/R/mc3_mthds.R | 1120 +++++++++--------- tcpl-2.0.0/tcpl/R/mc4.R | 318 ++--- tcpl-2.0.0/tcpl/R/mc4_mthds.R |only tcpl-2.0.0/tcpl/R/mc5.R | 562 ++++----- tcpl-2.0.0/tcpl/R/mc5_mthds.R | 275 ++-- tcpl-2.0.0/tcpl/R/mc6.R | 231 +-- tcpl-2.0.0/tcpl/R/mc6_mthds.R | 490 +++---- tcpl-2.0.0/tcpl/R/mthd_funcs.R | 136 +- tcpl-2.0.0/tcpl/R/multProc.R | 47 tcpl-2.0.0/tcpl/R/multiplotFit.R |only tcpl-2.0.0/tcpl/R/onAttach.R | 32 tcpl-2.0.0/tcpl/R/onLoad.R | 50 tcpl-2.0.0/tcpl/R/plateHeat.R | 291 ++-- tcpl-2.0.0/tcpl/R/plotFit.R | 1026 ++++++++-------- tcpl-2.0.0/tcpl/R/prepField.R | 72 - tcpl-2.0.0/tcpl/R/query_funcs.R | 71 - tcpl-2.0.0/tcpl/R/registerMthd.R | 98 - tcpl-2.0.0/tcpl/R/rgstr_funcs.R | 155 +- tcpl-2.0.0/tcpl/R/sc1.R | 328 ++--- tcpl-2.0.0/tcpl/R/sc1_mthds.R | 498 ++++---- tcpl-2.0.0/tcpl/R/sc2.R | 230 +-- tcpl-2.0.0/tcpl/R/sc2_mthds.R | 250 ++-- tcpl-2.0.0/tcpl/R/sink.reset.R | 54 tcpl-2.0.0/tcpl/R/tcplAICProb.R | 116 - tcpl-2.0.0/tcpl/R/tcplAddModel.R | 156 +- tcpl-2.0.0/tcpl/R/tcplAppend.R | 230 ++- tcpl-2.0.0/tcpl/R/tcplCascade.R | 156 +- tcpl-2.0.0/tcpl/R/tcplCode2CASN.R | 122 - tcpl-2.0.0/tcpl/R/tcplConf.R | 119 + tcpl-2.0.0/tcpl/R/tcplConfDefault.R | 30 tcpl-2.0.0/tcpl/R/tcplConfExample.R |only tcpl-2.0.0/tcpl/R/tcplConfList.R | 32 tcpl-2.0.0/tcpl/R/tcplConfLoad.R | 54 tcpl-2.0.0/tcpl/R/tcplConfReset.R | 63 - tcpl-2.0.0/tcpl/R/tcplConfSave.R | 104 - tcpl-2.0.0/tcpl/R/tcplCytoPt.R | 349 ++--- tcpl-2.0.0/tcpl/R/tcplDelete.R | 93 - tcpl-2.0.0/tcpl/R/tcplFit.R | 1036 +++++++++------- tcpl-2.0.0/tcpl/R/tcplGetAeid.R |only tcpl-2.0.0/tcpl/R/tcplHillACXX.R | 30 tcpl-2.0.0/tcpl/R/tcplHillConc.R | 28 tcpl-2.0.0/tcpl/R/tcplHillVal.R | 28 tcpl-2.0.0/tcpl/R/tcplListFlds.R | 135 +- tcpl-2.0.0/tcpl/R/tcplLiteInit.R |only tcpl-2.0.0/tcpl/R/tcplLoadAcid.R | 50 tcpl-2.0.0/tcpl/R/tcplLoadAeid.R | 52 tcpl-2.0.0/tcpl/R/tcplLoadAid.R | 50 tcpl-2.0.0/tcpl/R/tcplLoadAsid.R | 49 tcpl-2.0.0/tcpl/R/tcplLoadChem.R | 181 +- tcpl-2.0.0/tcpl/R/tcplLoadClib.R | 172 +- tcpl-2.0.0/tcpl/R/tcplLoadData.R | 1068 ++++++++--------- tcpl-2.0.0/tcpl/R/tcplLoadUnit.R | 102 - tcpl-2.0.0/tcpl/R/tcplLvlCount.R |only tcpl-2.0.0/tcpl/R/tcplMakeAeidMultiPlts.R |only tcpl-2.0.0/tcpl/R/tcplMakeAeidPlts.R | 183 +- tcpl-2.0.0/tcpl/R/tcplMakeChidMultiPlts.R |only tcpl-2.0.0/tcpl/R/tcplMthdAssign.R | 98 - tcpl-2.0.0/tcpl/R/tcplMthdClear.R | 60 tcpl-2.0.0/tcpl/R/tcplMthdList.R | 59 tcpl-2.0.0/tcpl/R/tcplMthdLoad.R | 119 - tcpl-2.0.0/tcpl/R/tcplMultiplot.R |only tcpl-2.0.0/tcpl/R/tcplObjCnst.R | 72 - tcpl-2.0.0/tcpl/R/tcplObjGnls.R | 112 - tcpl-2.0.0/tcpl/R/tcplObjHill.R | 92 - tcpl-2.0.0/tcpl/R/tcplPlotFitc.R | 298 ++-- tcpl-2.0.0/tcpl/R/tcplPlotFits.R | 259 ++-- tcpl-2.0.0/tcpl/R/tcplPlotM4ID.R | 141 +- tcpl-2.0.0/tcpl/R/tcplPlotPlate.R | 240 +-- tcpl-2.0.0/tcpl/R/tcplPrepOtpt.R | 218 +-- tcpl-2.0.0/tcpl/R/tcplQuery.R | 148 +- tcpl-2.0.0/tcpl/R/tcplRegister.R | 94 - tcpl-2.0.0/tcpl/R/tcplRun.R | 682 +++++----- tcpl-2.0.0/tcpl/R/tcplSendQuery.R | 155 +- tcpl-2.0.0/tcpl/R/tcplSubsetChid.R | 220 +-- tcpl-2.0.0/tcpl/R/tcplUpdate.R | 117 - tcpl-2.0.0/tcpl/R/tcplVarMat.R | 547 ++++---- tcpl-2.0.0/tcpl/R/tcplWriteData.R | 376 +++--- tcpl-2.0.0/tcpl/R/tcplWriteLvl0.R | 241 +-- tcpl-2.0.0/tcpl/R/tcpldbStats.R |only tcpl-2.0.0/tcpl/build/vignette.rds |binary tcpl-2.0.0/tcpl/data |only tcpl-2.0.0/tcpl/inst/TCPL.config |only tcpl-2.0.0/tcpl/inst/csv |only tcpl-2.0.0/tcpl/inst/doc/Data_processing.R |only tcpl-2.0.0/tcpl/inst/doc/Data_processing.Rmd |only tcpl-2.0.0/tcpl/inst/doc/Data_processing.html |only tcpl-2.0.0/tcpl/inst/doc/Data_retrieval.R |only tcpl-2.0.0/tcpl/inst/doc/Data_retrieval.Rmd |only tcpl-2.0.0/tcpl/inst/doc/Data_retrieval.html |only tcpl-2.0.0/tcpl/inst/doc/Introduction_Appendices.R |only tcpl-2.0.0/tcpl/inst/doc/Introduction_Appendices.Rmd |only tcpl-2.0.0/tcpl/inst/doc/Introduction_Appendices.html |only tcpl-2.0.0/tcpl/inst/example |only tcpl-2.0.0/tcpl/man/MC2_Methods.Rd | 108 - tcpl-2.0.0/tcpl/man/MC3_Methods.Rd | 292 ++-- tcpl-2.0.0/tcpl/man/MC4_Methods.Rd |only tcpl-2.0.0/tcpl/man/MC5_Methods.Rd | 82 - tcpl-2.0.0/tcpl/man/MC6_Methods.Rd | 132 +- tcpl-2.0.0/tcpl/man/Models.Rd | 245 ++- tcpl-2.0.0/tcpl/man/SC1_Methods.Rd | 184 +- tcpl-2.0.0/tcpl/man/SC2_Methods.Rd | 104 - tcpl-2.0.0/tcpl/man/assay_funcs.Rd | 141 +- tcpl-2.0.0/tcpl/man/blineShift.Rd | 56 tcpl-2.0.0/tcpl/man/chdat.Rd |only tcpl-2.0.0/tcpl/man/config_funcs.Rd | 175 +- tcpl-2.0.0/tcpl/man/dot-buildAssayQ.Rd |only tcpl-2.0.0/tcpl/man/dot-convertNames.Rd |only tcpl-2.0.0/tcpl/man/dot-load6DR.Rd |only tcpl-2.0.0/tcpl/man/dot-plateHeat.Rd |only tcpl-2.0.0/tcpl/man/dot-prepField.Rd |only tcpl-2.0.0/tcpl/man/flareFunc.Rd | 56 tcpl-2.0.0/tcpl/man/hill_utils.Rd | 142 +- tcpl-2.0.0/tcpl/man/interlaceFunc.Rd | 62 tcpl-2.0.0/tcpl/man/is.odd.Rd | 45 tcpl-2.0.0/tcpl/man/lu.Rd | 61 tcpl-2.0.0/tcpl/man/lw.Rd | 61 tcpl-2.0.0/tcpl/man/mc1.Rd | 88 - tcpl-2.0.0/tcpl/man/mc2.Rd | 94 - tcpl-2.0.0/tcpl/man/mc3.Rd | 96 - tcpl-2.0.0/tcpl/man/mc4.Rd | 98 - tcpl-2.0.0/tcpl/man/mc5.Rd | 94 - tcpl-2.0.0/tcpl/man/mc6.Rd | 94 - tcpl-2.0.0/tcpl/man/mcdat.Rd |only tcpl-2.0.0/tcpl/man/mthd_funcs.Rd | 176 +- tcpl-2.0.0/tcpl/man/query_funcs.Rd | 104 - tcpl-2.0.0/tcpl/man/registerMthd.Rd | 58 tcpl-2.0.0/tcpl/man/rgstr_funcs.Rd | 177 +- tcpl-2.0.0/tcpl/man/sc1.Rd | 92 - tcpl-2.0.0/tcpl/man/sc2.Rd | 90 - tcpl-2.0.0/tcpl/man/scdat.Rd |only tcpl-2.0.0/tcpl/man/sink.reset.Rd | 43 tcpl-2.0.0/tcpl/man/tcplAICProb.Rd | 78 - tcpl-2.0.0/tcpl/man/tcplAddModel.Rd | 124 - tcpl-2.0.0/tcpl/man/tcplAppend.Rd | 46 tcpl-2.0.0/tcpl/man/tcplCascade.Rd | 64 - tcpl-2.0.0/tcpl/man/tcplCode2CASN.Rd | 60 tcpl-2.0.0/tcpl/man/tcplCytoPt.Rd | 230 +-- tcpl-2.0.0/tcpl/man/tcplDelete.Rd | 54 tcpl-2.0.0/tcpl/man/tcplFit.Rd | 96 - tcpl-2.0.0/tcpl/man/tcplGetAeid.Rd |only tcpl-2.0.0/tcpl/man/tcplListFlds.Rd | 56 tcpl-2.0.0/tcpl/man/tcplLoadChem.Rd | 118 - tcpl-2.0.0/tcpl/man/tcplLoadClib.Rd | 126 +- tcpl-2.0.0/tcpl/man/tcplLoadData.Rd | 165 +- tcpl-2.0.0/tcpl/man/tcplLoadUnit.Rd | 44 tcpl-2.0.0/tcpl/man/tcplLvlCount.Rd |only tcpl-2.0.0/tcpl/man/tcplMakeAeidMultiPlts.Rd |only tcpl-2.0.0/tcpl/man/tcplMakeAeidPlts.Rd | 90 - tcpl-2.0.0/tcpl/man/tcplMakeChidMultiPlts.Rd |only tcpl-2.0.0/tcpl/man/tcplMultiplot.Rd |only tcpl-2.0.0/tcpl/man/tcplPlotFitc.Rd | 50 tcpl-2.0.0/tcpl/man/tcplPlotFits.Rd | 155 +- tcpl-2.0.0/tcpl/man/tcplPlotM4ID.Rd | 96 - tcpl-2.0.0/tcpl/man/tcplPlotPlate.Rd | 114 - tcpl-2.0.0/tcpl/man/tcplPrepOtpt.Rd | 112 - tcpl-2.0.0/tcpl/man/tcplRun.Rd | 109 - tcpl-2.0.0/tcpl/man/tcplSubsetChid.Rd | 130 +- tcpl-2.0.0/tcpl/man/tcplVarMat.Rd | 235 +-- tcpl-2.0.0/tcpl/man/tcplWriteData.Rd | 76 - tcpl-2.0.0/tcpl/man/tcplWriteLvl0.Rd | 82 - tcpl-2.0.0/tcpl/man/tcpldbStats.Rd |only tcpl-2.0.0/tcpl/vignettes/Data_processing.Rmd |only tcpl-2.0.0/tcpl/vignettes/Data_retrieval.Rmd |only tcpl-2.0.0/tcpl/vignettes/Introduction_Appendices.Rmd |only 196 files changed, 12871 insertions(+), 12086 deletions(-)
Title: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation
Description: An R wrapper around the fast T-distributed Stochastic
Neighbor Embedding implementation by Van der Maaten (see <https://github.com/lvdmaaten/bhtsne/> for more information on the original implementation).
Author: Jesse Krijthe [aut, cre],
Laurens van der Maaten [cph] (Author of original C++ code)
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between Rtsne versions 0.13 dated 2017-04-14 and 0.15 dated 2018-11-10
Rtsne-0.13/Rtsne/src/init.c |only Rtsne-0.15/Rtsne/DESCRIPTION | 15 Rtsne-0.15/Rtsne/LICENSE | 73 + Rtsne-0.15/Rtsne/MD5 | 44 Rtsne-0.15/Rtsne/NAMESPACE | 3 Rtsne-0.15/Rtsne/NEWS.md |only Rtsne-0.15/Rtsne/R/RcppExports.R | 12 Rtsne-0.15/Rtsne/R/Rtsne.R | 137 ++- Rtsne-0.15/Rtsne/R/neighbors.R |only Rtsne-0.15/Rtsne/R/utils.R |only Rtsne-0.15/Rtsne/README.md | 47 - Rtsne-0.15/Rtsne/man/Rtsne.Rd | 94 +- Rtsne-0.15/Rtsne/man/normalize_input.Rd |only Rtsne-0.15/Rtsne/src/Makevars | 3 Rtsne-0.15/Rtsne/src/Makevars.win | 3 Rtsne-0.15/Rtsne/src/RcppExports.cpp | 74 + Rtsne-0.15/Rtsne/src/Rtsne.cpp | 158 +-- Rtsne-0.15/Rtsne/src/datapoint.h |only Rtsne-0.15/Rtsne/src/normalize_input.cpp |only Rtsne-0.15/Rtsne/src/sptree.cpp | 578 ++++++------ Rtsne-0.15/Rtsne/src/sptree.h | 138 +-- Rtsne-0.15/Rtsne/src/tsne.cpp | 1028 +++++++++-------------- Rtsne-0.15/Rtsne/src/tsne.h | 56 - Rtsne-0.15/Rtsne/src/vptree.h | 377 +++----- Rtsne-0.15/Rtsne/tests/testthat/test_Rtsne.R | 164 ++- Rtsne-0.15/Rtsne/tests/testthat/test_neighbors.R |only Rtsne-0.15/Rtsne/tools/example-1.png |binary 27 files changed, 1585 insertions(+), 1419 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] (R/stan_jm.R),
AstraZeneca [ctb] (R/stan_jm.R),
Trustees of Columbia University [cph],
Simon Wood [cph] (R/stan_gamm4.R),
R Core Deveopment Team [cph] (R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Paul-Christian Burkner [cph] (R/misc.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.18.1 dated 2018-10-21 and 2.18.2 dated 2018-11-10
DESCRIPTION | 8 MD5 | 62 +- NEWS.md | 6 inst/doc/aov.R | 32 - inst/doc/aov.html | 46 - inst/doc/betareg.R | 128 ++--- inst/doc/betareg.html | 59 -- inst/doc/binomial.R | 152 ++---- inst/doc/binomial.html | 78 --- inst/doc/continuous.R | 196 +++----- inst/doc/continuous.html | 101 ---- inst/doc/count.R | 76 +-- inst/doc/count.html | 32 - inst/doc/glmer.R | 84 +-- inst/doc/glmer.html | 67 -- inst/doc/jm.R | 206 ++++---- inst/doc/jm.html | 345 -------------- inst/doc/lm.R | 66 +- inst/doc/lm.html | 87 --- inst/doc/polr.R | 68 +- inst/doc/polr.html | 94 --- inst/doc/pooling.R | 474 +++++++++----------- inst/doc/pooling.html | 152 ------ inst/doc/priors.html | 6 inst/doc/rstanarm.R | 150 ++---- inst/doc/rstanarm.html | 120 ----- inst/include/csr_matrix_times_vector2.hpp | 4 inst/include/meta_header.hpp | 6 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/include/csr_matrix_times_vector2.hpp | 4 tests/testthat/include/meta_header.hpp | 6 32 files changed, 848 insertions(+), 2071 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>),
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>),
Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>),
Rune Haubo Bojesen Christensen [ctb]
(<https://orcid.org/0000-0002-4494-3399>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Bin Dai [ctb],
Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>),
Gabor Grothendieck [ctb],
Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>),
John Fox [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-18-1 dated 2018-08-17 and 1.1-19 dated 2018-11-10
lme4-1.1-18-1/lme4/inst/utils |only lme4-1.1-18-1/lme4/src/mcmcsamp.cpp |only lme4-1.1-19/lme4/DESCRIPTION | 54 ++++++----- lme4-1.1-19/lme4/MD5 | 52 +++++----- lme4-1.1-19/lme4/NAMESPACE | 25 +++-- lme4-1.1-19/lme4/R/allFit.R |only lme4-1.1-19/lme4/R/bootMer.r | 18 +-- lme4-1.1-19/lme4/R/checkConv.R | 40 +++++--- lme4-1.1-19/lme4/R/lmer.R | 103 +-------------------- lme4-1.1-19/lme4/R/lmerControl.R | 4 lme4-1.1-19/lme4/R/methods.R |only lme4-1.1-19/lme4/R/modular.R | 2 lme4-1.1-19/lme4/R/predict.R | 5 - lme4-1.1-19/lme4/R/profile.R | 26 +---- lme4-1.1-19/lme4/R/rePCA.R |only lme4-1.1-19/lme4/R/utilities.R | 64 ++++++++++--- lme4-1.1-19/lme4/R/vcconv.R | 6 + lme4-1.1-19/lme4/inst/NEWS.Rd | 52 ++++++++-- lme4-1.1-19/lme4/man/allFit.Rd |only lme4-1.1-19/lme4/man/convergence.Rd | 8 - lme4-1.1-19/lme4/man/influence.merMod.Rd |only lme4-1.1-19/lme4/man/isSingular.Rd |only lme4-1.1-19/lme4/man/lmerControl.Rd | 4 lme4-1.1-19/lme4/man/mkReTrms.Rd | 11 +- lme4-1.1-19/lme4/man/rePCA.Rd |only lme4-1.1-19/lme4/src/Makevars.win | 2 lme4-1.1-19/lme4/tests/Rplots.pdf |only lme4-1.1-19/lme4/tests/lmer-1.Rout.save | 32 ++++-- lme4-1.1-19/lme4/tests/testthat/test-formulaEval.R | 14 ++ lme4-1.1-19/lme4/tests/testthat/test-glmer.R | 14 +- lme4-1.1-19/lme4/tests/testthat/test-methods.R | 2 lme4-1.1-19/lme4/tests/testthat/test-summary.R | 17 ++- 32 files changed, 297 insertions(+), 258 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-30 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-24 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-12 0.0.2
2016-10-06 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-04 1.0.1
2017-11-27 1.0.0
Title: Interaction Analysis of Repeatedly Measured Data
Description: Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Fei Zhou, Jie Ren, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between interep versions 0.1.0 dated 2018-09-03 and 0.2.0 dated 2018-11-10
interep-0.1.0/interep/R/CorrR.R |only interep-0.1.0/interep/R/ScoreU.R |only interep-0.1.0/interep/R/dmcp.R |only interep-0.1.0/interep/R/interep.R |only interep-0.1.0/interep/R/reformat.R |only interep-0.2.0/interep/DESCRIPTION | 19 - interep-0.2.0/interep/MD5 | 38 ++- interep-0.2.0/interep/NAMESPACE | 19 - interep-0.2.0/interep/R/RcppExports.R |only interep-0.2.0/interep/R/cv.interep.R | 349 ++++++++------------------------ interep-0.2.0/interep/data/dat.rda |binary interep-0.2.0/interep/man/CorrR.Rd | 85 +++---- interep-0.2.0/interep/man/cv.interep.Rd | 125 +++++------ interep-0.2.0/interep/man/dat.Rd | 34 +-- interep-0.2.0/interep/man/dmcp.Rd | 67 +++--- interep-0.2.0/interep/man/interep.Rd | 150 ++++++------- interep-0.2.0/interep/man/reformat.Rd | 49 ++-- interep-0.2.0/interep/src |only 18 files changed, 387 insertions(+), 548 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroskedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 1.3 dated 2017-11-08 and 2.0.0 dated 2018-11-10
REndo-1.3/REndo/R/checkAssumptions.R |only REndo-1.3/REndo/R/cop_Cont1.R |only REndo-1.3/REndo/R/cop_Cont2.R |only REndo-1.3/REndo/R/cop_Discrete.R |only REndo-1.3/REndo/R/cop_bootsSE.R |only REndo-1.3/REndo/R/cop_logLik.R |only REndo-1.3/REndo/R/cop_pStar.R |only REndo-1.3/REndo/R/copulaCorrection.R |only REndo-1.3/REndo/R/copulaCorrection_class.R |only REndo-1.3/REndo/R/f_hetErrorsIV.R |only REndo-1.3/REndo/R/f_multilevelGMM.R |only REndo-1.3/REndo/R/hetErrorsIV.R |only REndo-1.3/REndo/R/hetErrorsIV_class.R |only REndo-1.3/REndo/R/higherMomentsIV.R |only REndo-1.3/REndo/R/internalIV.R |only REndo-1.3/REndo/R/latentIV.R |only REndo-1.3/REndo/R/latentIV_class.R |only REndo-1.3/REndo/R/latentIV_loglik.R |only REndo-1.3/REndo/R/methods_copulaCorrection.R |only REndo-1.3/REndo/R/methods_hetErrorsIV.R |only REndo-1.3/REndo/R/methods_latentIV.R |only REndo-1.3/REndo/R/methods_multilevelIV.R |only REndo-1.3/REndo/R/multilevelIV.R |only REndo-1.3/REndo/R/multilevelIV_class.R |only REndo-1.3/REndo/data/dataCopC1.RData |only REndo-1.3/REndo/data/dataCopC2.RData |only REndo-1.3/REndo/data/dataCopDis.RData |only REndo-1.3/REndo/data/dataHetIV.RData |only REndo-1.3/REndo/data/dataHigherMoments.RData |only REndo-1.3/REndo/data/dataLatentIV.RData |only REndo-1.3/REndo/data/dataMultilevelIV.RData |only REndo-1.3/REndo/man/boots.Rd |only REndo-1.3/REndo/man/checkAssumptions.Rd |only REndo-1.3/REndo/man/coef-copulaREndo-method.Rd |only REndo-1.3/REndo/man/coef-hetREndo-method.Rd |only REndo-1.3/REndo/man/coef-livREndo-method.Rd |only REndo-1.3/REndo/man/coef-mixedREndo-method.Rd |only REndo-1.3/REndo/man/copulaCont1.Rd |only REndo-1.3/REndo/man/copulaDiscrete.Rd |only REndo-1.3/REndo/man/copulaMethod2.Rd |only REndo-1.3/REndo/man/copulaPStar.Rd |only REndo-1.3/REndo/man/copulaRendo-class.Rd |only REndo-1.3/REndo/man/dataCopC1.Rd |only REndo-1.3/REndo/man/dataCopC2.Rd |only REndo-1.3/REndo/man/dataMultilevelIV.Rd |only REndo-1.3/REndo/man/hetREndo-class.Rd |only REndo-1.3/REndo/man/internalIV.Rd |only REndo-1.3/REndo/man/livREndo-class.Rd |only REndo-1.3/REndo/man/logL.Rd |only REndo-1.3/REndo/man/logLL.Rd |only REndo-1.3/REndo/man/mixedREndo.Rd |only REndo-1.3/REndo/man/multilevelGMM.Rd |only REndo-1.3/REndo/man/summary-copulaREndo-method.Rd |only REndo-1.3/REndo/man/summary-hetREndo-method.Rd |only REndo-1.3/REndo/man/summary-livREndo-method.Rd |only REndo-1.3/REndo/man/summary-mixedREndo-method.Rd |only REndo-2.0.0/REndo/DESCRIPTION | 52 +-- REndo-2.0.0/REndo/MD5 | 141 +++++---- REndo-2.0.0/REndo/NAMESPACE | 68 +++- REndo-2.0.0/REndo/NEWS.md |only REndo-2.0.0/REndo/R/REndo-package.R |only REndo-2.0.0/REndo/R/data.R |only REndo-2.0.0/REndo/R/f_checkinput_copulacorrection.R |only REndo-2.0.0/REndo/R/f_checkinput_helperfunctions.R |only REndo-2.0.0/REndo/R/f_checkinput_heterrorsIV.R |only REndo-2.0.0/REndo/R/f_checkinput_highermomentsiv.R |only REndo-2.0.0/REndo/R/f_checkinput_latentIV.R |only REndo-2.0.0/REndo/R/f_copulacorrection_LL.R |only REndo-2.0.0/REndo/R/f_copulacorrection_interface.R |only REndo-2.0.0/REndo/R/f_copulacorrection_linearmodel.R |only REndo-2.0.0/REndo/R/f_copulacorrection_optimizeLL.R |only REndo-2.0.0/REndo/R/f_copulacorrectionpstar_continuous.R |only REndo-2.0.0/REndo/R/f_copulacorrectionpstar_discrete.R |only REndo-2.0.0/REndo/R/f_formula_helpers.R |only REndo-2.0.0/REndo/R/f_helper_demean.R |only REndo-2.0.0/REndo/R/f_heterrorsIV.R |only REndo-2.0.0/REndo/R/f_heterrorsIV_IIV.R |only REndo-2.0.0/REndo/R/f_highermomentsIV.R |only REndo-2.0.0/REndo/R/f_highermomentsIV_IIV.R |only REndo-2.0.0/REndo/R/f_latentIV.R |only REndo-2.0.0/REndo/R/f_latentIV_LL.R |only REndo-2.0.0/REndo/R/f_multilevelIV.R |only REndo-2.0.0/REndo/R/f_new_rendoivreg.R |only REndo-2.0.0/REndo/R/f_new_rendooptimLL.R |only REndo-2.0.0/REndo/R/f_new_rendopstarlm.R |only REndo-2.0.0/REndo/R/f_s3_rendoivreg.R |only REndo-2.0.0/REndo/R/f_s3_rendooptimLL.R |only REndo-2.0.0/REndo/R/f_s3_rendopstarlm.R |only REndo-2.0.0/REndo/README.md |only REndo-2.0.0/REndo/data/dataCopCont.rda |only REndo-2.0.0/REndo/data/dataCopCont2.rda |only REndo-2.0.0/REndo/data/dataCopDis.rda |only REndo-2.0.0/REndo/data/dataCopDis2.rda |only REndo-2.0.0/REndo/data/dataCopDisCont.rda |only REndo-2.0.0/REndo/data/dataHetIV.rda |only REndo-2.0.0/REndo/data/dataHigherMoments.rda |only REndo-2.0.0/REndo/data/dataLatentIV.rda |only REndo-2.0.0/REndo/man/REndo.Rd |only REndo-2.0.0/REndo/man/confint.rendo.pstar.lm.Rd |only REndo-2.0.0/REndo/man/copulaCorrection.Rd | 220 ++++++++++----- REndo-2.0.0/REndo/man/dataCopCont.Rd |only REndo-2.0.0/REndo/man/dataCopCont2.Rd |only REndo-2.0.0/REndo/man/dataCopDis.Rd | 36 +- REndo-2.0.0/REndo/man/dataCopDis2.Rd |only REndo-2.0.0/REndo/man/dataCopDisCont.Rd |only REndo-2.0.0/REndo/man/dataHetIV.Rd | 32 +- REndo-2.0.0/REndo/man/dataHigherMoments.Rd | 39 +- REndo-2.0.0/REndo/man/dataLatentIV.Rd | 40 +- REndo-2.0.0/REndo/man/hetErrorsIV.Rd | 118 +++++--- REndo-2.0.0/REndo/man/higherMomentsIV.Rd | 183 ++++++------ REndo-2.0.0/REndo/man/latentIV.Rd | 143 +++++---- REndo-2.0.0/REndo/man/multilevelIV.Rd | 56 --- REndo-2.0.0/REndo/tests |only 113 files changed, 666 insertions(+), 462 deletions(-)
Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or scintigraphic measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.4.01 dated 2017-05-10 and 0.4.3 dated 2018-11-10
gastempt-0.4.01/gastempt/exec |only gastempt-0.4.01/gastempt/inst/chunks |only gastempt-0.4.01/gastempt/inst/shiny/rsconnect |only gastempt-0.4.01/gastempt/src/Modules.cpp |only gastempt-0.4.01/gastempt/src/include |only gastempt-0.4.01/gastempt/tools/make_cpp.R |only gastempt-0.4.3/gastempt/DESCRIPTION | 25 gastempt-0.4.3/gastempt/MD5 | 102 +- gastempt-0.4.3/gastempt/NAMESPACE | 83 - gastempt-0.4.3/gastempt/R/fitfuncs.r | 328 +++--- gastempt-0.4.3/gastempt/R/fitnlme.R | 470 +++++----- gastempt-0.4.3/gastempt/R/fitparams.R | 140 +- gastempt-0.4.3/gastempt/R/gastempt-internal.R | 254 ++--- gastempt-0.4.3/gastempt/R/runshiny.R | 22 gastempt-0.4.3/gastempt/R/simulate_gastempt.R | 366 +++---- gastempt-0.4.3/gastempt/R/stan_gastempt.R | 344 +++---- gastempt-0.4.3/gastempt/R/stan_model_names.R | 40 gastempt-0.4.3/gastempt/R/stanmodels.R | 76 - gastempt-0.4.3/gastempt/R/zzz.R | 9 gastempt-0.4.3/gastempt/README.md | 134 +- gastempt-0.4.3/gastempt/build/vignette.rds |binary gastempt-0.4.3/gastempt/inst/doc/gastempt.Rmd | 34 gastempt-0.4.3/gastempt/inst/doc/gastempt.html | 306 +++++- gastempt-0.4.3/gastempt/inst/include |only gastempt-0.4.3/gastempt/inst/shiny/global.R | 102 +- gastempt-0.4.3/gastempt/inst/shiny/server.R | 405 ++++---- gastempt-0.4.3/gastempt/inst/shiny/ui.R | 238 ++--- gastempt-0.4.3/gastempt/inst/shiny/www/gastempt.css | 202 ++-- gastempt-0.4.3/gastempt/man/coef.nlme_gastempt.Rd | 38 gastempt-0.4.3/gastempt/man/coef.stan_gastempt.Rd | 38 gastempt-0.4.3/gastempt/man/gastemptfunc.Rd | 181 +-- gastempt-0.4.3/gastempt/man/nlme_gastempt.Rd | 150 +-- gastempt-0.4.3/gastempt/man/plot.nlme_gastempt.Rd | 38 gastempt-0.4.3/gastempt/man/plot.stan_gastempt.Rd | 40 gastempt-0.4.3/gastempt/man/run_shiny.Rd | 28 gastempt-0.4.3/gastempt/man/simulate_gastempt.Rd | 136 +- gastempt-0.4.3/gastempt/man/stan_gastempt.Rd | 136 +- gastempt-0.4.3/gastempt/man/stan_model_names.Rd | 45 gastempt-0.4.3/gastempt/man/t50.Rd | 38 gastempt-0.4.3/gastempt/src/Makevars | 21 gastempt-0.4.3/gastempt/src/Makevars.win | 24 gastempt-0.4.3/gastempt/src/stan_files |only gastempt-0.4.3/gastempt/tests/test-all.R | 10 gastempt-0.4.3/gastempt/tests/testthat/test-fitfuncs.R | 312 +++--- gastempt-0.4.3/gastempt/tests/testthat/test-fitnlme.R | 219 ++-- gastempt-0.4.3/gastempt/tests/testthat/test-fitparams.R | 238 ++--- gastempt-0.4.3/gastempt/tests/testthat/test-simulate_gastempt.R | 218 ++-- gastempt-0.4.3/gastempt/tests/testthat/test-stan.R | 346 +++---- gastempt-0.4.3/gastempt/tools/make_cc.R |only gastempt-0.4.3/gastempt/vignettes/gastempt.Rmd | 34 50 files changed, 3093 insertions(+), 2877 deletions(-)
Title: Furniture for Quantitative Scientists
Description: Contains three main functions (i.e., three pieces of furniture):
table1() which produces a well-formatted table of descriptives common as Table 1
in research articles, tableC() which produces a well-formatted table of correlations,
tableF() which provides frequency counts, and washer() which
is helpful in cleaning up the data. These furniture-themed functions are designed
to simplify common tasks in quantitative analysis. Other data summary and cleaning tools
are also available.
Author: Tyson S. Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>),
Emily Brignone [aut],
Daniel J. Laxman [aut]
Maintainer: Tyson S. Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.8.0 dated 2018-09-19 and 1.8.7 dated 2018-11-10
DESCRIPTION | 19 + MD5 | 51 ++--- NAMESPACE | 19 + NEWS.md | 8 R/Table1.R | 176 ++++++++--------- R/operators.R | 3 R/table1_utils.R | 247 +++++++++++++----------- R/tableF.R | 115 ++++++----- R/tableX.R | 1 R/table_cor.R | 108 +++++----- R/to_latex2.R | 24 +- R/utils.R | 84 ++++---- R/washer.R | 16 - R/zzz.R | 19 + data/nhanes_2010.rda |binary inst/CITATION |only inst/doc/Furniture.R | 2 inst/doc/Furniture.Rmd | 12 - inst/doc/Furniture.html | 426 +++++++++++++++++++++++-------------------- inst/doc/Table1.R | 4 inst/doc/Table1.Rmd | 10 - inst/doc/Table1.html | 192 +++++++++---------- man/furniture.Rd | 15 + man/table1.Rd | 16 - tests/testthat/test_table1.R | 25 ++ vignettes/Furniture.Rmd | 12 - vignettes/Table1.Rmd | 10 - 27 files changed, 897 insertions(+), 717 deletions(-)
Title: Load Avro file into 'Apache Spark'
Description: Load Avro Files into 'Apache Spark' using 'sparklyr'. This
allows to read files from 'Apache Avro' <https://avro.apache.org/>.
Author: Aki Ariga
Maintainer: Aki Ariga <chezou@gmail.com>
Diff between sparkavro versions 0.1.0 dated 2017-11-17 and 0.2.0 dated 2018-11-10
DESCRIPTION | 11 ++--- MD5 | 11 ++--- NAMESPACE | 16 +++---- NEWS.md |only R/dependencies.R | 4 + man/spark_read_avro.Rd | 100 ++++++++++++++++++++++++------------------------ man/spark_write_avro.Rd | 45 +++++++++++---------- 7 files changed, 96 insertions(+), 91 deletions(-)
Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Diff between telegram.bot versions 1.0.0 dated 2018-02-12 and 2.0.0 dated 2018-11-10
telegram.bot-1.0.0/telegram.bot/man/delete_webhook.Rd |only telegram.bot-1.0.0/telegram.bot/man/get_updates.Rd |only telegram.bot-1.0.0/telegram.bot/man/get_webhook_info.Rd |only telegram.bot-1.0.0/telegram.bot/man/set_webhook.Rd |only telegram.bot-2.0.0/telegram.bot/DESCRIPTION | 21 telegram.bot-2.0.0/telegram.bot/MD5 | 99 telegram.bot-2.0.0/telegram.bot/NAMESPACE | 11 telegram.bot-2.0.0/telegram.bot/NEWS.md |only telegram.bot-2.0.0/telegram.bot/R/bot.R | 1405 +++++++++- telegram.bot-2.0.0/telegram.bot/R/callbackqueryhandler.R | 4 telegram.bot-2.0.0/telegram.bot/R/commandhandler.R | 6 telegram.bot-2.0.0/telegram.bot/R/dispatcher.R | 3 telegram.bot-2.0.0/telegram.bot/R/handler.R | 3 telegram.bot-2.0.0/telegram.bot/R/inlinequeryresult.R |only telegram.bot-2.0.0/telegram.bot/R/messagehandler.R | 2 telegram.bot-2.0.0/telegram.bot/R/replymarkup.R |only telegram.bot-2.0.0/telegram.bot/R/telegram.bot-package.R | 12 telegram.bot-2.0.0/telegram.bot/R/update.R | 12 telegram.bot-2.0.0/telegram.bot/R/updater.R | 44 telegram.bot-2.0.0/telegram.bot/R/utils.R | 57 telegram.bot-2.0.0/telegram.bot/README.md |only telegram.bot-2.0.0/telegram.bot/build |only telegram.bot-2.0.0/telegram.bot/inst |only telegram.bot-2.0.0/telegram.bot/man/Bot.Rd | 69 telegram.bot-2.0.0/telegram.bot/man/CommandHandler.Rd | 2 telegram.bot-2.0.0/telegram.bot/man/ForceReply.Rd |only telegram.bot-2.0.0/telegram.bot/man/Handler.Rd | 2 telegram.bot-2.0.0/telegram.bot/man/InlineKeyboardButton.Rd |only telegram.bot-2.0.0/telegram.bot/man/InlineKeyboardMarkup.Rd |only telegram.bot-2.0.0/telegram.bot/man/InlineQueryResult.Rd |only telegram.bot-2.0.0/telegram.bot/man/KeyboardButton.Rd |only telegram.bot-2.0.0/telegram.bot/man/MessageHandler.Rd | 2 telegram.bot-2.0.0/telegram.bot/man/ReplyKeyboardMarkup.Rd |only telegram.bot-2.0.0/telegram.bot/man/ReplyKeyboardRemove.Rd |only telegram.bot-2.0.0/telegram.bot/man/Updater.Rd | 15 telegram.bot-2.0.0/telegram.bot/man/answerCallbackQuery.Rd |only telegram.bot-2.0.0/telegram.bot/man/answerInlineQuery.Rd |only telegram.bot-2.0.0/telegram.bot/man/bot_token.Rd |only telegram.bot-2.0.0/telegram.bot/man/deleteMessage.Rd |only telegram.bot-2.0.0/telegram.bot/man/deleteWebhook.Rd |only telegram.bot-2.0.0/telegram.bot/man/editMessageReplyMarkup.Rd |only telegram.bot-2.0.0/telegram.bot/man/forwardMessage.Rd |only telegram.bot-2.0.0/telegram.bot/man/getFile.Rd |only telegram.bot-2.0.0/telegram.bot/man/getMe.Rd |only telegram.bot-2.0.0/telegram.bot/man/getUpdates.Rd |only telegram.bot-2.0.0/telegram.bot/man/getUserProfilePhotos.Rd |only telegram.bot-2.0.0/telegram.bot/man/getWebhookInfo.Rd |only telegram.bot-2.0.0/telegram.bot/man/leaveChat.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendAnimation.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendAudio.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendChatAction.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendDocument.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendLocation.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendMessage.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendPhoto.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendSticker.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendVideo.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendVideoNote.Rd |only telegram.bot-2.0.0/telegram.bot/man/sendVoice.Rd |only telegram.bot-2.0.0/telegram.bot/man/setWebhook.Rd |only telegram.bot-2.0.0/telegram.bot/man/set_token.Rd |only telegram.bot-2.0.0/telegram.bot/man/start_polling.Rd | 4 telegram.bot-2.0.0/telegram.bot/man/stop_polling.Rd | 2 telegram.bot-2.0.0/telegram.bot/man/telegram.bot.Rd | 10 telegram.bot-2.0.0/telegram.bot/man/user_id.Rd |only telegram.bot-2.0.0/telegram.bot/vignettes |only 66 files changed, 1557 insertions(+), 228 deletions(-)
Title: The Variable Infiltration Capacity (VIC) Model
Description: The Variable Infiltration Capacity (VIC) model is a macroscale
hydrologic model that solves full water and energy balances, originally
developed by Xu Liang at the University of Washington (UW).
The version of VIC source code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>,
see Hamman et al. (2018).
Development and maintenance of the current official version
of the VIC model at present is led by the UW Hydro (Computational Hydrology
group) in the Department of Civil and Environmental Engineering at UW. VIC is
a research model and in its various forms it has been applied to most of the
major river basins around the world, as well as globally. If you make use of
this model, please acknowledge the appropriate references listed in the help
page of this package or on the references page
<http://vic.readthedocs.io/en/master/Documentation/References/>
of the VIC official documentation website.
These should include Liang et al. (1994) plus any references relevant to the
features you are using Reference: Liang, X., D. P. Lettenmaier, E. F. Wood, and
S. J. Burges (1994), A simple hydrologically based model of land surface water
and energy fluxes for general circulation models, J. Geophys. Res., 99(D7),
14415-14428, <doi:10.1029/94JD00483>. Hamman et al. (2018) about VIC 5.0.1 also can
be considered:
Hamman, J. J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The
Variable Infiltration Capacity model version 5 (VIC-5): infrastructure improvements
for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496,
<doi:10.5194/gmd-11-3481-2018>.
Author: Ruida Zhong [aut, cre],
Xiaohong Chen [aut, ctb],
Zhaoli Wang [aut, ctb],
Chengguang Lai [aut, ctb],
Joseph J Hamman [ctb] (Contributor and maintainer of VIC source code),
Keith Cherkauer [ctb]
Maintainer: Ruida Zhong <zrd2017@163.com>
Diff between VICmodel versions 0.1.1 dated 2018-10-06 and 0.1.2 dated 2018-11-10
DESCRIPTION | 7 MD5 | 63 ++--- NAMESPACE | 4 NEWS.md | 8 R/utils.R | 139 ++++++++++++ R/vic.R | 118 +++++++++- README.md | 9 inst/COPYRIGHTS | 23 - man/NSE.Rd |only man/vic.Rd | 23 + src/make_params.cpp | 9 src/vic/drivers/shared_all/src/compute_derived_state_vars.c | 11 src/vic/drivers/shared_all/src/compute_lake_params.c | 7 src/vic/drivers/shared_all/src/generate_default_state.c | 9 src/vic/drivers/shared_all/src/initialize_options.c | 2 src/vic/vic_run/include/vic_def.h | 10 src/vic/vic_run/src/calc_atmos_energy_bal.c | 9 src/vic/vic_run/src/calc_surf_energy_bal.c | 15 - src/vic/vic_run/src/frozen_soil.c | 29 +- src/vic/vic_run/src/func_surf_energy_bal.c | 7 src/vic/vic_run/src/ice_melt.c | 11 src/vic/vic_run/src/lake_utils.c | 13 - src/vic/vic_run/src/lakes.eb.c | 37 +-- src/vic/vic_run/src/root_brent.c | 41 +-- src/vic/vic_run/src/runoff.c | 9 src/vic/vic_run/src/snow_intercept.c | 11 src/vic/vic_run/src/snow_melt.c | 7 src/vic/vic_run/src/solve_snow.c | 13 - src/vic/vic_run/src/surface_fluxes.c | 21 - src/vic/vic_run/src/vic_run.c | 25 -- src/vic/vic_run/src/write_layer.c | 2 src/vic_run_cell.cpp | 2 src/vic_version.cpp | 2 33 files changed, 440 insertions(+), 256 deletions(-)
Title: Spatio-Temporal Bayesian Modelling
Description: Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTimer versions 3.2 dated 2018-10-25 and 3.3 dated 2018-11-10
DESCRIPTION | 8 MD5 | 6 R/useful_commands.R | 2463 +++++++++++++++++++++++++--------------------------- inst/ChangeLog | 5 4 files changed, 1243 insertions(+), 1239 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.6-7 dated 2018-04-11 and 0.6-8 dated 2018-11-10
ChangeLog | 2 +- DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- README | 2 +- inst/Rprofile | 2 ++ src/internal.c | 6 ++++-- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.7.7 dated 2018-10-16 and 0.7.8 dated 2018-11-10
dplyr-0.7.7/dplyr/vignettes/viprex.R |only dplyr-0.7.7/dplyr/vignettes/viprex.html |only dplyr-0.7.8/dplyr/DESCRIPTION | 12 dplyr-0.7.8/dplyr/MD5 | 124 ++++---- dplyr-0.7.8/dplyr/NAMESPACE | 5 dplyr-0.7.8/dplyr/NEWS.md | 18 + dplyr-0.7.8/dplyr/R/RcppExports.R | 4 dplyr-0.7.8/dplyr/R/colwise.R | 6 dplyr-0.7.8/dplyr/R/compat-dbplyr.R | 4 dplyr-0.7.8/dplyr/R/dataframe.R | 13 dplyr-0.7.8/dplyr/R/distinct.R | 5 dplyr-0.7.8/dplyr/R/do.r | 11 dplyr-0.7.8/dplyr/R/funs.R | 12 dplyr-0.7.8/dplyr/R/group-by.r | 5 dplyr-0.7.8/dplyr/R/grouped-df.r | 16 - dplyr-0.7.8/dplyr/R/join-vars.R | 2 dplyr-0.7.8/dplyr/R/order-by.R | 2 dplyr-0.7.8/dplyr/R/rowwise.r | 9 dplyr-0.7.8/dplyr/R/tbl-cube.r | 2 dplyr-0.7.8/dplyr/R/tbl-df.r | 15 - dplyr-0.7.8/dplyr/R/utils-expr.R | 5 dplyr-0.7.8/dplyr/R/utils.r | 6 dplyr-0.7.8/dplyr/R/zzz.r | 10 dplyr-0.7.8/dplyr/inst/doc/compatibility.html | 71 ++--- dplyr-0.7.8/dplyr/inst/doc/programming.R | 56 +-- dplyr-0.7.8/dplyr/inst/doc/programming.Rmd | 77 +---- dplyr-0.7.8/dplyr/inst/doc/programming.html | 227 ++++++---------- dplyr-0.7.8/dplyr/inst/doc/two-table.html | 56 +-- dplyr-0.7.8/dplyr/inst/doc/window-functions.html | 48 +-- dplyr-0.7.8/dplyr/inst/include/dplyr/GroupedDataFrame.h | 2 dplyr-0.7.8/dplyr/inst/include/dplyr/HybridHandler.h | 2 dplyr-0.7.8/dplyr/inst/include/dplyr/registration.h | 2 dplyr-0.7.8/dplyr/inst/include/dplyr_RcppExports.h | 11 dplyr-0.7.8/dplyr/man/all_equal.Rd | 4 dplyr-0.7.8/dplyr/man/arrange_all.Rd | 3 dplyr-0.7.8/dplyr/man/as.table.tbl_cube.Rd | 4 dplyr-0.7.8/dplyr/man/backend_dbplyr.Rd | 5 dplyr-0.7.8/dplyr/man/bench_compare.Rd | 4 dplyr-0.7.8/dplyr/man/copy_to.Rd | 3 dplyr-0.7.8/dplyr/man/group_by_all.Rd | 3 dplyr-0.7.8/dplyr/man/join.Rd | 6 dplyr-0.7.8/dplyr/man/join.tbl_df.Rd | 10 dplyr-0.7.8/dplyr/man/recode.Rd | 3 dplyr-0.7.8/dplyr/man/sample.Rd | 3 dplyr-0.7.8/dplyr/man/scoped.Rd | 3 dplyr-0.7.8/dplyr/man/select_all.Rd | 3 dplyr-0.7.8/dplyr/man/summarise_all.Rd | 3 dplyr-0.7.8/dplyr/src/RcppExports.cpp | 35 +- dplyr-0.7.8/dplyr/src/group_by.cpp | 11 dplyr-0.7.8/dplyr/src/group_indices.cpp | 8 dplyr-0.7.8/dplyr/src/hybrid.cpp | 2 dplyr-0.7.8/dplyr/src/init.cpp | 2 dplyr-0.7.8/dplyr/tests/testthat/test-binds.R | 4 dplyr-0.7.8/dplyr/tests/testthat/test-colwise-mutate.R | 2 dplyr-0.7.8/dplyr/tests/testthat/test-colwise.R | 5 dplyr-0.7.8/dplyr/tests/testthat/test-do.R | 9 dplyr-0.7.8/dplyr/tests/testthat/test-funs.R | 2 dplyr-0.7.8/dplyr/tests/testthat/test-hybrid.R | 12 dplyr-0.7.8/dplyr/tests/testthat/test-joins.r | 16 - dplyr-0.7.8/dplyr/tests/testthat/test-mutate.r | 4 dplyr-0.7.8/dplyr/tests/testthat/test-sets.R | 10 dplyr-0.7.8/dplyr/tests/testthat/test-summarise.r | 2 dplyr-0.7.8/dplyr/tests/testthat/test-utils.R | 2 dplyr-0.7.8/dplyr/vignettes/programming.Rmd | 77 +---- 64 files changed, 515 insertions(+), 583 deletions(-)
Title: Spatial Variable Selection
Description: Perform variable selection for the spatial Poisson regression model under the adaptive elastic net penalty. Spatial count data with covariates is the input. We use a spatial Poisson regression model to link the spatial counts and covariates. For maximization of the likelihood under adaptive elastic net penalty, we implemented the penalized quasi-likelihood (PQL) and the approximate penalized loglikelihood (APL) methods. The proposed methods can automatically select important covariates, while adjusting for possible spatial correlations among the responses. More details are available in Xie et al. (2018, <arXiv:1809.06418>). The package also contains the Lyme disease dataset, which consists of the disease case data from 2006 to 2011, and demographic data and land cover data in Virginia. The Lyme disease case data were collected by the Virginia Department of Health. The demographic data (e.g., population density, median income, and average age) are from the 2010 census. Land cover data were obtained from the Multi-Resolution Land Cover Consortium for 2006.
Author: Yili Hong, Li Xu, Yimeng Xie, and Zhongnan Jin
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between SpatialVS versions 1.0 dated 2018-09-30 and 1.1 dated 2018-11-10
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/Rpackage-functions.r | 12 ++++++++++++ R/lyme.svs.eco0.dat.R | 1 + R/lyme.svs.eco1.dat.R | 1 + data/lyme.svs.eco0.RData |binary data/lyme.svs.eco1.RData |binary man/SpatialVS.Rd | 2 +- man/lyme.svs.eco0.dat.Rd | 44 ++++++++++++++++++++++++++++++++++++-------- man/lyme.svs.eco1.dat.Rd | 45 ++++++++++++++++++++++++++++++++++++--------- man/small.test.dat.Rd | 2 +- 12 files changed, 103 insertions(+), 34 deletions(-)
Title: Semi-Confirmatory Structural Equation Modeling via Penalized
Likelihood
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) with LASSO or minimax concave penalty (MCP).
Author: Po-Hsien Huang [cre, aut],
Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>
Diff between lslx versions 0.6.3 dated 2018-08-09 and 0.6.4 dated 2018-11-10
DESCRIPTION | 8 MD5 | 52 +- R/RcppExports.R | 8 R/lslx-extract-method.R | 591 ++++++++++++++++------------ R/lslx-fit-method.R | 113 ----- R/lslx-initialize-method.R | 196 ++++----- R/lslx-print-method.R | 2 R/lslx-set-coefficient-method.R | 16 R/lslx-set-heterogeneity-method.R | 39 - R/lslx-summarize-method.R | 20 R/lslx-test-method.R | 37 + R/lslx-validate-method.R | 65 +-- R/lslx.R | 35 - R/lslxData.R | 97 ++++ R/lslxFitting.R | 494 +++++++++++++++++------ R/lslxModel.R | 606 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/factor-analysis.html | 104 ++-- inst/doc/missing-data-analysis.Rmd | 2 inst/doc/multi-group-analysis.Rmd | 2 inst/doc/regression-analysis.html | 92 +++- inst/doc/structural-equation-modeling.html | 3 man/lslx.Rd | 35 - src/RcppExports.cpp | 26 - src/lslxOptimizer.cpp | 329 +++++++++------ vignettes/missing-data-analysis.Rmd | 2 vignettes/multi-group-analysis.Rmd | 2 27 files changed, 1714 insertions(+), 1262 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.3.0 dated 2018-10-09 and 1.3.1 dated 2018-11-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/align.R | 10 ++++++++-- R/derivePHMM.R | 5 +++-- R/weight.R | 3 ++- README.md | 1 - 6 files changed, 21 insertions(+), 14 deletions(-)