Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, and identify cut points. Also includes three example data
sets of administrative education records for learning how to process records
with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between eeptools versions 1.2.1 dated 2018-10-21 and 1.2.2 dated 2019-03-18
DESCRIPTION | 9 MD5 | 14 - NEWS.md | 6 build/vignette.rds |binary inst/doc/intro.html | 402 ++++++++++++++++++++-------------------- man/crosstabplot.Rd | 4 man/moves_calc.Rd | 5 tests/testthat/test-statamode.r | 274 +++++++++++++-------------- 8 files changed, 372 insertions(+), 342 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
David Granjon [aut] (jQuery Knob shiny interface & sliders appearance),
Ian Fellows [ctb] (Methods for mutating vertical tabs &
updateMultiInput),
Wil Davis [ctb] (numericRangeInput function),
SnapAppointments [cph] (bootstrap-select),
Mattia Larentis [ctb, cph] (Bootstrap Switch),
Emanuele Marchi [ctb, cph] (Bootstrap Switch),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Flatlogic [cph] (Awesome Bootstrap Checkbox),
mouse0270 [ctb, cph] (Material Design Switch),
Tristan Edwards [ctb, cph] (SweetAlert),
Fabian Lindfors [ctb, cph] (multi.js),
Anthony Terrien [ctb, cph] (jQuery Knob),
Daniel Eden [ctb, cph] (animate.css),
Ganapati V S [ctb, cph] (bttn.css),
Brian Grinstead [ctb, cph] (Spectrum),
Lokesh Rajendran [ctb, cph] (pretty-checkbox),
Leon Gersen [ctb, cph] (wnumb & noUiSlider),
Timofey Marochkin [ctb, cph] (air-datepicker),
Tobias Ahlin [ctb, cph] (CSS spin)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.4.7 dated 2019-03-12 and 0.4.8 dated 2019-03-18
shinyWidgets-0.4.7/shinyWidgets/tests/testthat/test-onLoad.R |only shinyWidgets-0.4.8/shinyWidgets/DESCRIPTION | 6 - shinyWidgets-0.4.8/shinyWidgets/MD5 | 11 +-- shinyWidgets-0.4.8/shinyWidgets/NAMESPACE | 1 shinyWidgets-0.4.8/shinyWidgets/NEWS.md | 7 ++ shinyWidgets-0.4.8/shinyWidgets/R/addSpinner.R | 35 +++++++++-- shinyWidgets-0.4.8/shinyWidgets/man/addSpinner.Rd | 4 - 7 files changed, 47 insertions(+), 17 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized
linear models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [cre, aut],
Anthony Williams [cph],
Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between parglm versions 0.1.2 dated 2019-03-14 and 0.1.3 dated 2019-03-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary src/LAPACK_wrappers.cpp | 2 +- src/LAPACK_wrappers.h | 2 +- src/parallel_glm.cpp | 13 ++++++++----- src/parallel_qr.cpp | 3 +-- 7 files changed, 20 insertions(+), 18 deletions(-)
Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium,
deemed D-statistics, for pairs of loci. Beissinger et al. (2016) <doi:10.1038/hdy.2015.81>.
Author: Paul F. Petrowski <pfpetrowski@mail.missouri.edu> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@mail.missouri.edu>
Diff between ohtadstats versions 2.0.0 dated 2018-08-30 and 2.1.0 dated 2019-03-18
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 1 + R/dfilter.R |only man/dfilter.Rd |only 5 files changed, 10 insertions(+), 7 deletions(-)
Title: R Interface for US EPA's SWMM
Description: Functions to connect the widely used Storm Water Management Model (SWMM)
of the United States Environmental Protection Agency (US EPA)
<https://www.epa.gov/water-research/storm-water-management-model-swmm> to R with
currently two main goals: (1) Run a SWMM simulation from R and (2) provide fast
access to simulation results, i.e. SWMM's binary '.out'-files. High performance is achieved
with help of Rcpp. Additionally, reading SWMM's '.inp' and '.rpt' files is supported to
glance model structures and to get direct access to simulation summaries.
Author: Dominik Leutnant [aut, cre] (<https://orcid.org/0000-0003-3293-2315>),
Anneke Doering [aut],
Malte Henrichs [ctb],
Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>)
Maintainer: Dominik Leutnant <leutnant@fh-muenster.de>
Diff between swmmr versions 0.8.1 dated 2018-04-10 and 0.9.0 dated 2019-03-18
swmmr-0.8.1/swmmr/R/plot_inp.R |only swmmr-0.9.0/swmmr/DESCRIPTION | 26 swmmr-0.9.0/swmmr/MD5 | 112 swmmr-0.9.0/swmmr/NAMESPACE | 4 swmmr-0.9.0/swmmr/NEWS.md | 34 swmmr-0.9.0/swmmr/R/assign_parameters.R | 532 ++-- swmmr-0.9.0/swmmr/R/autoplot.R |only swmmr-0.9.0/swmmr/R/convert_to_sf.R | 177 - swmmr-0.9.0/swmmr/R/estimate_version.R |only swmmr-0.9.0/swmmr/R/inp_to_files.R | 154 - swmmr-0.9.0/swmmr/R/parse_section.R | 1300 +++------- swmmr-0.9.0/swmmr/R/read_inp.R | 16 swmmr-0.9.0/swmmr/R/read_out.R | 59 swmmr-0.9.0/swmmr/R/read_out_helper.R | 294 -- swmmr-0.9.0/swmmr/R/read_rpt.R | 50 swmmr-0.9.0/swmmr/R/run_swmm.R | 53 swmmr-0.9.0/swmmr/R/summary.R |only swmmr-0.9.0/swmmr/R/swmmr.R | 5 swmmr-0.9.0/swmmr/R/utils.R |only swmmr-0.9.0/swmmr/R/write_inp.R | 2 swmmr-0.9.0/swmmr/R/zzz.R |only swmmr-0.9.0/swmmr/README.md | 101 swmmr-0.9.0/swmmr/build/vignette.rds |binary swmmr-0.9.0/swmmr/inst/doc/How_swmmr_reads_and_writes_files.html | 32 swmmr-0.9.0/swmmr/inst/doc/How_to_autocalibrate_a_SWMM_model_with_swmmr.R | 173 - swmmr-0.9.0/swmmr/inst/doc/How_to_autocalibrate_a_SWMM_model_with_swmmr.Rmd | 6 swmmr-0.9.0/swmmr/inst/doc/How_to_autocalibrate_a_SWMM_model_with_swmmr.html | 237 + swmmr-0.9.0/swmmr/inst/doc/How_to_convert_between_GIS_data_and_SWMM_with_swmmr.html | 391 +-- swmmr-0.9.0/swmmr/man/add_column_if_missing.Rd |only swmmr-0.9.0/swmmr/man/add_columns_if_missing.Rd |only swmmr-0.9.0/swmmr/man/assign_parameters.conduits.Rd | 4 swmmr-0.9.0/swmmr/man/assign_parameters.coverages.Rd | 6 swmmr-0.9.0/swmmr/man/assign_parameters.infiltration.Rd | 6 swmmr-0.9.0/swmmr/man/assign_parameters.subareas.Rd | 4 swmmr-0.9.0/swmmr/man/assign_parameters.subcatchments.Rd | 4 swmmr-0.9.0/swmmr/man/check_package_and_class.Rd |only swmmr-0.9.0/swmmr/man/convert_to_sf.Rd | 9 swmmr-0.9.0/swmmr/man/dot-get_exec_on_linux_or_mac.Rd |only swmmr-0.9.0/swmmr/man/dot-get_exec_on_windows.Rd |only swmmr-0.9.0/swmmr/man/dot-get_iIndex.Rd |only swmmr-0.9.0/swmmr/man/dot-get_iType.Rd |only swmmr-0.9.0/swmmr/man/dot-get_os.Rd |only swmmr-0.9.0/swmmr/man/dot-get_vIndex.Rd |only swmmr-0.9.0/swmmr/man/estimate_version.Rd |only swmmr-0.9.0/swmmr/man/estimate_version.inp.Rd |only swmmr-0.9.0/swmmr/man/estimate_version.rpt.Rd |only swmmr-0.9.0/swmmr/man/figures/README-example-1.png |binary swmmr-0.9.0/swmmr/man/figures/README-example-2.png |binary swmmr-0.9.0/swmmr/man/figures/README-visualization-1.png |binary swmmr-0.9.0/swmmr/man/get_column_defaults.Rd |only swmmr-0.9.0/swmmr/man/get_out_content.Rd |only swmmr-0.9.0/swmmr/man/get_out_version.Rd |only swmmr-0.9.0/swmmr/man/has_incomplete_features.Rd |only swmmr-0.9.0/swmmr/man/inp_to_files.Rd | 6 swmmr-0.9.0/swmmr/man/parse_section.flow_classification_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.groundwater_continuity.Rd |only swmmr-0.9.0/swmmr/man/parse_section.groundwater_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.highest_continuity_errors.Rd |only swmmr-0.9.0/swmmr/man/parse_section.lid_control_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.lid_performance_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.node_surcharge_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.pumping_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.storage_volume_summary.Rd |only swmmr-0.9.0/swmmr/man/parse_section.time_step_critical_elements.Rd |only swmmr-0.9.0/swmmr/man/plot.Rd |only swmmr-0.9.0/swmmr/man/read_out.Rd | 3 swmmr-0.9.0/swmmr/man/run_swmm.Rd | 13 swmmr-0.9.0/swmmr/man/section_to_tbl.Rd | 2 swmmr-0.9.0/swmmr/man/separate_into.Rd |only swmmr-0.9.0/swmmr/man/shp_to_inp.Rd | 6 swmmr-0.9.0/swmmr/man/skip_head.Rd |only swmmr-0.9.0/swmmr/man/summary.Rd |only swmmr-0.9.0/swmmr/tests/testthat/test_plot.R |only swmmr-0.9.0/swmmr/tests/testthat/test_swmm.R | 75 swmmr-0.9.0/swmmr/tests/testthat/test_utils.R |only swmmr-0.9.0/swmmr/vignettes/How_to_autocalibrate_a_SWMM_model_with_swmmr.Rmd | 6 76 files changed, 1854 insertions(+), 2048 deletions(-)
Title: Regularized Structural Equation Modeling
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional structural
equation models. Also contains a function to perform exploratory mediation (XMed).
Author: Ross Jacobucci[aut,cre],
Kevin J. Grimm [ctb],
Andreas M. Brandmaier [ctb],
Sarfaraz Serang [ctb],
Rogier A. Kievit [ctb],
Florian Scharf [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 1.2.3 dated 2019-01-02 and 1.3.3 dated 2019-03-18
DESCRIPTION | 11 MD5 | 102 - NAMESPACE | 67 - R/RAMmult.R | 56 - R/RcppExports.R | 128 +- R/coord_desc.R | 1252 +++++++++++----------- R/cv_regsem.R | 2076 ++++++++++++++++++------------------- R/efaModel.R |only R/extractMatrices.R | 906 ++++++++-------- R/fiml_calc.R | 182 +-- R/fiml_calc2.R | 204 +-- R/fit_fun.R | 140 +- R/fit_indices.R | 522 ++++----- R/grad_fun.R | 192 +-- R/grad_ram.R | 226 ++-- R/grad_ram_wMean.R | 194 +-- R/hess_ram.R | 112 +- R/hess_ramParallel.R | 138 +- R/hessian.R | 60 - R/hessian_parallel.R | 80 - R/multi_optim.R | 782 +++++++------ R/parse_parameters.R | 48 R/plot.R | 244 ++-- R/ram_calc.R | 154 +- R/regsem.R | 2459 ++++++++++++++++++++++---------------------- R/ret_hess.R | 16 R/soft.R | 132 +- R/summary.cvregsem.R | 102 - R/summary.regsem.R | 78 - R/trace.R | 8 R/xmed.R | 320 ++--- build/vignette.rds |binary inst/doc/short_intro.R | 96 - inst/doc/short_intro.Rmd | 204 +-- inst/doc/short_intro.html | 670 +++++------ man/cv_regsem.Rd | 425 +++---- man/efaModel.Rd |only man/extractMatrices.Rd | 56 - man/fit_indices.Rd | 74 - man/multi_optim.Rd | 299 ++--- man/parse_parameters.Rd | 42 man/plot.cvregsem.Rd | 94 - man/rcpp_RAMmult.Rd | 60 - man/rcpp_fit_fun.Rd | 58 - man/rcpp_grad_ram.Rd | 74 - man/rcpp_quasi_calc.Rd | 40 man/regsem.Rd | 404 +++---- man/summary.cvregsem.Rd | 32 man/summary.regsem.Rd | 32 man/xmed.Rd | 142 +- src/RcppExports.cpp | 40 src/regsem_rcpp_fit_fun.cpp | 22 vignettes/short_intro.Rmd | 204 +-- 53 files changed, 7051 insertions(+), 7008 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6.6 dated 2018-02-02 and 1.6.7 dated 2019-03-18
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++----------- NAMESPACE | 2 R/boot.R | 5 +- R/constants.R | 4 + R/hmm-dists.R | 8 +++ R/hmm.R | 6 +- R/msm.R | 74 ++++++++++++++++++++-------------- R/optim.R | 5 +- R/outputs.R | 12 +++-- R/pearson.R | 2 build/vignette.rds |binary inst/NEWS | 10 ++++ inst/doc/msm-manual.R | 8 +-- inst/doc/msm-manual.pdf |binary man/hmm-dists.Rd | 10 ++++ src/hmm.c | 12 +++++ src/hmm.h | 2 src/hmmderiv.c | 56 +++++++++++++++++++++++++ src/lik.c | 5 +- tests/testthat/test_deriv.r | 20 ++++++++- tests/testthat/test_models.r | 5 +- tests/testthat/test_models_hmmmulti.r | 7 ++- tests/testthat/test_models_misc.r | 5 ++ tests/testthat/test_utils.r | 2 vignettes/msm-manual.Rnw | 31 ++++++++++---- 26 files changed, 259 insertions(+), 90 deletions(-)
Title: Headers for the 'xtensor' Library
Description: The 'xtensor' C++ library for numerical analysis with
multi-dimensional array expressions is provided as a header-only
C++14 library. It offers an extensible expression system enabling
lazy broadcasting; an API following the idioms of the C++ standard
library; and tools to manipulate array expressions and build upon 'xtensor'.
Author: Johan Mabille, Sylvain Corlay and Wolf Vollprecht
Maintainer: Sylvain Corlay <sylvain.corlay@gmail.com>
Diff between xtensor versions 0.9.0-0 dated 2018-12-12 and 0.10.1-0 dated 2019-03-18
xtensor-0.10.1-0/xtensor/DESCRIPTION | 8 xtensor-0.10.1-0/xtensor/LICENSE | 2 xtensor-0.10.1-0/xtensor/MD5 | 221 +- xtensor-0.10.1-0/xtensor/NAMESPACE | 5 xtensor-0.10.1-0/xtensor/README.md |only xtensor-0.10.1-0/xtensor/configure |only xtensor-0.10.1-0/xtensor/configure.win |only xtensor-0.10.1-0/xtensor/inst/include/xsimd |only xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/rarray.hpp | 100 + xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/rcontainer.hpp | 44 xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/rcpp_extensions.hpp | 28 xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/roptional.hpp |only xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/rtensor.hpp | 27 xtensor-0.10.1-0/xtensor/inst/include/xtensor-r/xtensor_r_config.hpp | 2 xtensor-0.10.1-0/xtensor/inst/include/xtensor.h | 3 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xaccumulator.hpp | 13 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xadapt.hpp | 480 +++--- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xassign.hpp | 12 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xbuffer_adaptor.hpp | 149 + xtensor-0.10.1-0/xtensor/inst/include/xtensor/xbuilder.hpp | 41 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xcomplex.hpp | 1 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xcontainer.hpp | 4 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xcsv.hpp | 11 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xdynamic_view.hpp | 5 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xexception.hpp | 28 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xexpression.hpp | 76 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xexpression_holder.hpp | 4 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xfunction.hpp | 12 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xfunctor_view.hpp | 656 +++++--- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xhistogram.hpp | 2 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xindex_view.hpp | 1 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xiterable.hpp | 220 +- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xiterator.hpp | 4 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xmanipulation.hpp | 5 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xmasked_value.hpp | 2 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xmath.hpp | 176 +- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xmime.hpp | 25 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xnorm.hpp | 34 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoffset_view.hpp | 42 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoperation.hpp | 283 ++- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoptional.hpp | 10 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoptional_assembly.hpp | 3 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoptional_assembly_base.hpp | 4 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xoptional_assembly_storage.hpp | 7 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xrandom.hpp | 2 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xreducer.hpp | 122 + xtensor-0.10.1-0/xtensor/inst/include/xtensor/xscalar.hpp | 58 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xslice.hpp | 58 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xsort.hpp | 30 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xstorage.hpp | 195 +- xtensor-0.10.1-0/xtensor/inst/include/xtensor/xstrided_view_base.hpp | 32 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xstrides.hpp | 36 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xtensor.hpp | 106 + xtensor-0.10.1-0/xtensor/inst/include/xtensor/xtensor_config.hpp | 22 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xtensor_forward.hpp | 10 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xutils.hpp | 15 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xview.hpp | 61 xtensor-0.10.1-0/xtensor/inst/include/xtensor/xview_utils.hpp | 9 xtensor-0.10.1-0/xtensor/inst/include/xtl/xmeta_utils.hpp | 61 xtensor-0.10.1-0/xtensor/inst/include/xtl/xtl_config.hpp | 2 xtensor-0.10.1-0/xtensor/inst/include/xtl/xtype_traits.hpp | 12 xtensor-0.10.1-0/xtensor/inst/include/xtl/xvariant_impl.hpp | 770 +++++++--- xtensor-0.10.1-0/xtensor/man/figures |only xtensor-0.10.1-0/xtensor/src/test-arithmetic.cpp |only xtensor-0.10.1-0/xtensor/src/test-in-place.cpp |only xtensor-0.10.1-0/xtensor/src/test-reshape.cpp |only xtensor-0.10.1-0/xtensor/src/test-types.cpp |only xtensor-0.10.1-0/xtensor/tests |only xtensor-0.10.1-0/xtensor/tools |only xtensor-0.9.0-0/xtensor/R |only xtensor-0.9.0-0/xtensor/inst/include/xtensor/xconcepts.hpp |only xtensor-0.9.0-0/xtensor/inst/lib |only xtensor-0.9.0-0/xtensor/src/RcppExports.cpp |only 73 files changed, 3060 insertions(+), 1291 deletions(-)
Title: Wavelet Approaches to Studies of Synchrony in Ecology and Other
Fields
Description: Tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. Some tools will be useful for studying community synchrony. See, for instance, Sheppard et al (2016) <doi: 10.1038/NCLIMATE2991>, Sheppard et al (2017) <doi: 10.1051/epjnbp/2017000>, Sheppard et al (2019) <doi: 10.1371/journal.pcbi.1006744>.
Author: Daniel C. Reuman [aut, cre],
Thomas L. Anderson [aut],
Jonathan A. Walter [aut],
Lei Zhao [aut],
Lawrence W. Sheppard [aut]
Maintainer: Daniel C. Reuman <reuman@ku.edu>
Diff between wsyn versions 1.0.0 dated 2019-01-22 and 1.0.1 dated 2019-03-18
DESCRIPTION | 8 MD5 | 143 +++++----- R/cleandat.R | 2 R/clust_methods.R | 4 R/plotmag.R | 6 R/plotphase.R | 2 R/plotrank.R | 6 R/predsync.R | 2 R/print.summary_wsyn.R | 6 R/syncexpl.R | 2 R/wlm.R | 2 R/wlmfit.R | 2 R/wlmtest.R | 2 R/wpmf.R | 2 README.md | 2 inst/doc/wsynvignette.Rmd | 8 inst/doc/wsynvignette.pdf |binary man/cleandat.Rd | 2 man/plotmag.Rd | 2 man/plotrank.Rd | 2 man/predsync.Rd | 2 man/print.summary_wsyn.Rd | 6 man/syncexpl.Rd | 2 man/wlm.Rd | 2 man/wlmfit.Rd | 2 man/wlmtest.Rd | 2 man/wpmf.Rd | 2 tests/figs/plotmag/test-plotmag-coh.svg | 6 tests/figs/plotphase/test-plotphase-coh.svg | 12 tests/figs/plotrank/test-plotrank-coh-2.svg |only tests/figs/plotrank/test-plotrank-coh.svg | 6 tests/testthat/tests_clust_methods.R | 13 tests/testthat/tests_plotrank.R | 9 vignettes/wsynvignette.Rmd | 8 vignettes/wsynvignette_files/figure-latex/abuse_cor-1.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-1.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-2.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-3.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-4.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-5.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-6.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-7.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-8.pdf |binary vignettes/wsynvignette_files/figure-latex/coh_example_call_fast-1.pdf |binary vignettes/wsynvignette_files/figure-latex/coh_plot-1.pdf |binary vignettes/wsynvignette_files/figure-latex/detect_tsspecific_sync-1.pdf |binary vignettes/wsynvignette_files/figure-latex/detect_tsspecific_sync-2.pdf |binary vignettes/wsynvignette_files/figure-latex/display_p_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd1_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd1_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd2_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd2_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/dropdirrel_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropdirrel_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_2-1.pdf |binary vignettes/wsynvignette_files/figure-latex/pearson_synmat-1.pdf |binary vignettes/wsynvignette_files/figure-latex/plotphase_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/plotrank_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmf_example_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-2.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-3.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1_cors-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1_plotts-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_plot-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_plotphase-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_power-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_2-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_2-2.pdf |binary vignettes/wsynvignette_refs.bib | 8 73 files changed, 157 insertions(+), 128 deletions(-)
Title: Read and Write 'Matlab' Files
Description: Read and write 'Matlab' MAT files from R. The 'rmatio'
package supports reading MAT version 4, MAT version 5 and MAT
compressed version 5. The 'rmatio' package can write version 5 MAT
files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] (Author of the R interface to the C-library
matio),
Christopher Hulbert [aut] (Author of the C-library matio,
http://sourceforge.net/projects/matio/)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between rmatio versions 0.13.0 dated 2019-03-10 and 0.14.0 dated 2019-03-18
DESCRIPTION | 6 MD5 | 22 NEWS | 9 src/matio/mat.c | 35 src/matio/mat4.c | 4 src/matio/mat5.c | 3599 +++++++++++++++++++++++++++++++++++++--------- src/matio/mat5.h | 5 src/matio/matio_private.h | 7 src/matio/matvar_cell.c | 2 src/matio/matvar_struct.c | 5 src/matio/read_data.c | 1550 +++++++++++++++++-- src/rmatio.c | 59 12 files changed, 4365 insertions(+), 938 deletions(-)
Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation and joint maximum
likelihood estimation for unidimensional and multidimensional
item response models. The package functionality covers the
Rasch model, 2PL model, 3PL model, generalized partial credit model,
multi-faceted Rasch model, nominal item response model,
structured latent class model, mixture distribution IRT models,
and located latent class models. Latent regression models and
plausible value imputation are also supported. For details see
Adams, Wilson and Wang, 1997 <doi:10.1177/0146621697211001>,
Adams, Wilson and Wu, 1997 <doi:10.3102/10769986022001047>,
Formann, 1982 <doi:10.1002/bimj.4710240209>,
Formann, 1992 <doi:10.1080/01621459.1992.10475229>.
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 3.0-21 dated 2018-12-10 and 3.1-45 dated 2019-03-18
TAM-3.0-21/TAM/R/tam.parameterfix.defaults.R |only TAM-3.1-45/TAM/DESCRIPTION | 10 TAM-3.1-45/TAM/MD5 | 223 ++++++------ TAM-3.1-45/TAM/NAMESPACE | 5 TAM-3.1-45/TAM/R/IRT.RISE.R | 13 TAM-3.1-45/TAM/R/IRT.expectedCounts.tam.R | 4 TAM-3.1-45/TAM/R/IRT.irfprob.tam.R | 108 ++--- TAM-3.1-45/TAM/R/IRTLikelihood.cfa.R | 10 TAM-3.1-45/TAM/R/RcppExports.R | 2 TAM-3.1-45/TAM/R/add.lead.R | 5 TAM-3.1-45/TAM/R/anova.tam.R | 11 TAM-3.1-45/TAM/R/cfa.extract.itempars.R | 17 TAM-3.1-45/TAM/R/designMatrices.mfr.R | 4 TAM-3.1-45/TAM/R/designMatrices.mfr2.R | 4 TAM-3.1-45/TAM/R/extend.label.group.R | 10 TAM-3.1-45/TAM/R/logLik_tam.R | 12 TAM-3.1-45/TAM/R/msq.itemfit.R | 10 TAM-3.1-45/TAM/R/summary.tam.R | 9 TAM-3.1-45/TAM/R/summary.tam.np.R |only TAM-3.1-45/TAM/R/summary_tamaan_3pl_intro.R | 4 TAM-3.1-45/TAM/R/tam.fa.R | 7 TAM-3.1-45/TAM/R/tam.mml.2pl.R | 18 TAM-3.1-45/TAM/R/tam.mml.3pl.R | 14 TAM-3.1-45/TAM/R/tam.mml.R | 31 - TAM-3.1-45/TAM/R/tam.mml.mfr.R | 13 TAM-3.1-45/TAM/R/tam.np.R | 111 +++++ TAM-3.1-45/TAM/R/tam_colSums.R |only TAM-3.1-45/TAM/R/tam_dnorm_discrete.R |only TAM-3.1-45/TAM/R/tam_dtnorm.R | 9 TAM-3.1-45/TAM/R/tam_fa_reliability_nonlinearSEM.R | 30 - TAM-3.1-45/TAM/R/tam_generate_B_fixed_estimated.R |only TAM-3.1-45/TAM/R/tam_generate_xsi_fixed_estimated.R |only TAM-3.1-45/TAM/R/tam_group_lasso_norm.R |only TAM-3.1-45/TAM/R/tam_irt_parameterization.R |only TAM-3.1-45/TAM/R/tam_jml_version1_calc_xsi.R | 90 ++-- TAM-3.1-45/TAM/R/tam_jml_version2_calc_xsi.R | 42 -- TAM-3.1-45/TAM/R/tam_mml_3pl_calc_ll.R | 2 TAM-3.1-45/TAM/R/tam_mml_3pl_calc_prob.R | 7 TAM-3.1-45/TAM/R/tam_mml_3pl_calc_total_ll.R | 17 TAM-3.1-45/TAM/R/tam_mml_3pl_mstep_item_intercepts.R | 38 +- TAM-3.1-45/TAM/R/tam_mml_constraint_check.R |only TAM-3.1-45/TAM/R/tam_mml_ic.R | 8 TAM-3.1-45/TAM/R/tam_mml_mfr_proc_multiple_person_ids.R | 11 TAM-3.1-45/TAM/R/tam_mml_progress_em.R | 31 + TAM-3.1-45/TAM/R/tam_mml_progress_em0.R | 9 TAM-3.1-45/TAM/R/tam_np_2pl_calc_probs.R |only TAM-3.1-45/TAM/R/tam_np_2pl_grad_fn.R |only TAM-3.1-45/TAM/R/tam_np_2pl_hess_fn.R |only TAM-3.1-45/TAM/R/tam_np_2pl_irf_probs.R |only TAM-3.1-45/TAM/R/tam_np_2pl_optim_fn.R |only TAM-3.1-45/TAM/R/tam_np_2pl_optim_fn_grad_hess.R |only TAM-3.1-45/TAM/R/tam_np_create_spline_basis.R |only TAM-3.1-45/TAM/R/tam_np_create_spline_basis_bsplines.R |only TAM-3.1-45/TAM/R/tam_np_create_spline_basis_hermite.R |only TAM-3.1-45/TAM/R/tam_np_group_lasso_update.R |only TAM-3.1-45/TAM/R/tam_np_information_criteria.R |only TAM-3.1-45/TAM/R/tam_np_inits.R | 11 TAM-3.1-45/TAM/R/tam_np_mstep_items.R |only TAM-3.1-45/TAM/R/tam_np_mstep_trait_distribution.R |only TAM-3.1-45/TAM/R/tam_np_optim_ridge_penalty.R |only TAM-3.1-45/TAM/R/tam_orthonormalize_design_matrix.R |only TAM-3.1-45/TAM/R/tam_print_call.R | 9 TAM-3.1-45/TAM/R/tam_prior_eval_log_density_one_parameter.R | 4 TAM-3.1-45/TAM/R/tam_weighted_cross_product.R |only TAM-3.1-45/TAM/R/weighted_kurtosis.R | 4 TAM-3.1-45/TAM/R/weighted_mean.R | 6 TAM-3.1-45/TAM/R/weighted_quantile.R | 4 TAM-3.1-45/TAM/R/weighted_quantile_type_selection.R | 4 TAM-3.1-45/TAM/R/weighted_sd.R | 7 TAM-3.1-45/TAM/R/weighted_skewness.R | 6 TAM-3.1-45/TAM/R/weighted_table.R | 8 TAM-3.1-45/TAM/R/weighted_var.R | 6 TAM-3.1-45/TAM/build/partial.rdb |binary TAM-3.1-45/TAM/inst/NEWS | 28 + TAM-3.1-45/TAM/man/IRT.WrightMap.Rd | 4 TAM-3.1-45/TAM/man/IRT.drawPV.Rd | 4 TAM-3.1-45/TAM/man/IRT.expectedCounts.tam.Rd | 4 TAM-3.1-45/TAM/man/IRT.factor.scores.tam.Rd | 4 TAM-3.1-45/TAM/man/IRT.informationCurves.Rd | 4 TAM-3.1-45/TAM/man/IRT.irfprob.tam.Rd | 4 TAM-3.1-45/TAM/man/IRT.itemfit.Rd | 4 TAM-3.1-45/TAM/man/IRT.likelihood.tam.Rd | 6 TAM-3.1-45/TAM/man/IRT.linearCFA.Rd | 4 TAM-3.1-45/TAM/man/IRT.residuals.Rd | 4 TAM-3.1-45/TAM/man/IRT.threshold.Rd | 4 TAM-3.1-45/TAM/man/IRT.truescore.Rd | 4 TAM-3.1-45/TAM/man/TAM-utilities.Rd | 9 TAM-3.1-45/TAM/man/anova.tam.Rd | 15 TAM-3.1-45/TAM/man/cfa.extract.itempars.Rd | 4 TAM-3.1-45/TAM/man/data.cqc.Rd | 4 TAM-3.1-45/TAM/man/data.ctest.Rd | 4 TAM-3.1-45/TAM/man/data.examples.Rd | 4 TAM-3.1-45/TAM/man/data.fims.Aus.Jpn.Rd | 4 TAM-3.1-45/TAM/man/data.geiser.Rd | 4 TAM-3.1-45/TAM/man/data.gpcm.Rd | 4 TAM-3.1-45/TAM/man/data.janssen.Rd | 4 TAM-3.1-45/TAM/man/data.mc.Rd | 4 TAM-3.1-45/TAM/man/data.numeracy.Rd | 4 TAM-3.1-45/TAM/man/data.sim.mfr.Rd | 4 TAM-3.1-45/TAM/man/data.sim.rasch.Rd | 4 TAM-3.1-45/TAM/man/data.timssAusTwn.Rd | 4 TAM-3.1-45/TAM/man/designMatrices.Rd | 4 TAM-3.1-45/TAM/man/doparse.Rd | 4 TAM-3.1-45/TAM/man/lavaanify.IRT.Rd | 4 TAM-3.1-45/TAM/man/msq.itemfit.Rd | 4 TAM-3.1-45/TAM/man/plot.tam.Rd | 4 TAM-3.1-45/TAM/man/plotDevianceTAM.Rd | 4 TAM-3.1-45/TAM/man/predict.Rd | 4 TAM-3.1-45/TAM/man/tam.ctt.Rd | 6 TAM-3.1-45/TAM/man/tam.fa.Rd | 8 TAM-3.1-45/TAM/man/tam.fit.Rd | 10 TAM-3.1-45/TAM/man/tam.jml.Rd | 6 TAM-3.1-45/TAM/man/tam.latreg.Rd | 6 TAM-3.1-45/TAM/man/tam.mml.3pl.Rd | 6 TAM-3.1-45/TAM/man/tam.mml.Rd | 73 +++ TAM-3.1-45/TAM/man/tam.modelfit.Rd | 8 TAM-3.1-45/TAM/man/tam.np.Rd | 176 ++++++++- TAM-3.1-45/TAM/man/tam.pv.Rd | 11 TAM-3.1-45/TAM/man/tam.se.Rd | 4 TAM-3.1-45/TAM/man/tam.threshold.Rd | 4 TAM-3.1-45/TAM/man/tam.wle.Rd | 10 TAM-3.1-45/TAM/man/tamaan.Rd | 6 TAM-3.1-45/TAM/man/tamaanify.Rd | 6 TAM-3.1-45/TAM/src/RcppExports.cpp | 2 TAM-3.1-45/TAM/src/init.c | 2 125 files changed, 968 insertions(+), 576 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight and simpler than both), tools
for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.7 dated 2019-03-07 and 0.2.8 dated 2019-03-18
DESCRIPTION | 8 MD5 | 34 NAMESPACE | 3 NEWS.md | 14 R/cache-tools.R | 78 + R/cloud.R | 227 +++- R/options.R | 2 R/packages.R | 101 +- R/postProcess.R | 6 R/prepInputs.R | 5 R/robustDigest.R | 5 build/vignette.rds |binary inst/doc/Intro-to-Cache.html | 1889 ++++++++++++++++++++--------------------- man/cache-helpers.Rd |only man/cloudCache.Rd | 16 man/cloudExtras.Rd | 6 man/cloudSyncCache.Rd | 15 tests/testthat/test-cloud.R |only tests/testthat/test-packages.R | 209 ++-- 19 files changed, 1442 insertions(+), 1176 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data,
including the Royston-Parmar spline model, generalized gamma and
generalized F distributions. Any user-defined parametric
distribution can be fitted, given at least an R function defining
the probability density or hazard. There are also tools for
fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson [aut, cre],
Paul Metcalfe [ctb],
Jordan Amdahl [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 1.1 dated 2017-03-27 and 1.1.1 dated 2019-03-18
flexsurv-1.1.1/flexsurv/Changelog | 6 flexsurv-1.1.1/flexsurv/DESCRIPTION | 14 flexsurv-1.1.1/flexsurv/MD5 | 134 - flexsurv-1.1.1/flexsurv/NAMESPACE | 4 flexsurv-1.1.1/flexsurv/R/GenGamma.R | 2 flexsurv-1.1.1/flexsurv/R/Gompertz.R | 2 flexsurv-1.1.1/flexsurv/R/Llogis.R | 5 flexsurv-1.1.1/flexsurv/R/RcppExports.R | 36 flexsurv-1.1.1/flexsurv/R/WeibullPH.R | 2 flexsurv-1.1.1/flexsurv/R/custom.R | 2 flexsurv-1.1.1/flexsurv/R/deriv.R | 380 ++-- flexsurv-1.1.1/flexsurv/R/flexsurvreg.R | 659 ------- flexsurv-1.1.1/flexsurv/R/fracpoly.R | 94 - flexsurv-1.1.1/flexsurv/R/mstate.R | 15 flexsurv-1.1.1/flexsurv/R/plot.flexsurvreg.R |only flexsurv-1.1.1/flexsurv/R/summary.flexsurvreg.R |only flexsurv-1.1.1/flexsurv/R/utils.R | 1 flexsurv-1.1.1/flexsurv/build/vignette.rds |binary flexsurv-1.1.1/flexsurv/data/bc.txt.gz |only flexsurv-1.1.1/flexsurv/inst/CITATION | 40 flexsurv-1.1.1/flexsurv/inst/NEWS | 25 flexsurv-1.1.1/flexsurv/inst/doc/flexsurv-examples.pdf |binary flexsurv-1.1.1/flexsurv/inst/doc/flexsurv.pdf |binary flexsurv-1.1.1/flexsurv/man/GenF.Rd | 15 flexsurv-1.1.1/flexsurv/man/GenF.orig.Rd | 15 flexsurv-1.1.1/flexsurv/man/GenGamma.Rd | 15 flexsurv-1.1.1/flexsurv/man/GenGamma.orig.Rd | 15 flexsurv-1.1.1/flexsurv/man/Gompertz.Rd | 17 flexsurv-1.1.1/flexsurv/man/Llogis.Rd | 13 flexsurv-1.1.1/flexsurv/man/Survspline.Rd | 15 flexsurv-1.1.1/flexsurv/man/WeibullPH.Rd | 13 flexsurv-1.1.1/flexsurv/man/basis.Rd | 9 flexsurv-1.1.1/flexsurv/man/bc.Rd | 1 flexsurv-1.1.1/flexsurv/man/bos.Rd | 1 flexsurv-1.1.1/flexsurv/man/coef.flexsurvreg.Rd | 7 flexsurv-1.1.1/flexsurv/man/flexsurv-package.Rd | 18 flexsurv-1.1.1/flexsurv/man/flexsurvreg.Rd | 15 flexsurv-1.1.1/flexsurv/man/flexsurvspline.Rd | 7 flexsurv-1.1.1/flexsurv/man/hazard.Rd | 20 flexsurv-1.1.1/flexsurv/man/lines.flexsurvreg.Rd | 9 flexsurv-1.1.1/flexsurv/man/means.Rd | 46 flexsurv-1.1.1/flexsurv/man/model.frame.flexsurvreg.Rd | 8 flexsurv-1.1.1/flexsurv/man/msfit.flexsurvreg.Rd | 7 flexsurv-1.1.1/flexsurv/man/normboot.flexsurvreg.Rd | 11 flexsurv-1.1.1/flexsurv/man/pars.fmsm.Rd | 1 flexsurv-1.1.1/flexsurv/man/plot.flexsurvreg.Rd | 9 flexsurv-1.1.1/flexsurv/man/pmatrix.fs.Rd | 7 flexsurv-1.1.1/flexsurv/man/pmatrix.simfs.Rd | 7 flexsurv-1.1.1/flexsurv/man/qgeneric.Rd | 1 flexsurv-1.1.1/flexsurv/man/rmst_generic.Rd | 1 flexsurv-1.1.1/flexsurv/man/sim.fmsm.Rd | 7 flexsurv-1.1.1/flexsurv/man/summary.flexsurvreg.Rd | 34 flexsurv-1.1.1/flexsurv/man/totlos.fs.Rd | 7 flexsurv-1.1.1/flexsurv/man/totlos.simfs.Rd | 7 flexsurv-1.1.1/flexsurv/man/unroll.function.Rd | 8 flexsurv-1.1.1/flexsurv/src/RcppExports.cpp | 36 flexsurv-1.1.1/flexsurv/src/flexsurv-init.c | 84 flexsurv-1.1.1/flexsurv/src/gompertz.cpp | 8 flexsurv-1.1.1/flexsurv/tests/test_base.R | 6 flexsurv-1.1.1/flexsurv/tests/testthat/test_custom.R | 334 +-- flexsurv-1.1.1/flexsurv/tests/testthat/test_deriv.R | 184 +- flexsurv-1.1.1/flexsurv/tests/testthat/test_flexsurvreg.R | 39 flexsurv-1.1.1/flexsurv/tests/testthat/test_gengamma.R | 3 flexsurv-1.1.1/flexsurv/tests/testthat/test_gompertz.R | 6 flexsurv-1.1.1/flexsurv/tests/testthat/test_llogis.R | 5 flexsurv-1.1.1/flexsurv/tests/testthat/test_mstate.R | 241 +- flexsurv-1.1.1/flexsurv/tests/testthat/test_spline.R | 1 flexsurv-1.1.1/flexsurv/vignettes/flexsurv.Rnw | 2 flexsurv-1.1.1/flexsurv/vignettes/flexsurv.bib | 1236 +++++++------- flexsurv-1.1/flexsurv/data/bc.txt |only 70 files changed, 1766 insertions(+), 2206 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
for further details on estimation and the package structure.
For tutorials on how to use the CDM package see
George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as
Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 7.2-30 dated 2019-02-08 and 7.3-17 dated 2019-03-18
DESCRIPTION | 10 +- MD5 | 80 ++++++++-------- NAMESPACE | 7 + R/RcppExports.R | 2 R/cdm_attach_exported_function.R |only R/cdm_attach_internal_function.R |only R/cdm_calc_increment_regularization.R | 5 - R/gdina.R | 2 R/gdina_designmatrices_create_Aj.R | 9 - R/gdina_mstep_item_ml.R | 61 ++++-------- R/gdina_mstep_item_ml_algorithm.R | 6 - R/gdina_mstep_item_ml_mono_optim_function.R |only R/gdina_mstep_item_ml_update_parameter.R | 14 +- R/gdina_mstep_item_ml_update_parameter_regularization.R | 2 R/gdina_mstep_item_parameters.R | 2 R/gdina_mstep_mono_constraints_penalty.R | 6 - R/gdina_postproc_regularized_constrained_parameters.R | 2 R/gdina_proc_noninvariance_multiple_groups.R | 11 +- R/gdina_proc_regularization.R | 3 R/gdina_proc_sequential_items.R | 13 +- R/gdm.R | 19 ++- R/gdm_progress_em_algorithm.R | 6 - R/gdm_thetadesign.R | 6 - R/plot.gdm.R | 12 +- R/plot_item_mastery.R |only R/plot_item_mastery_main.R |only R/reglca.R | 2 R/reglca_calc_probs.R | 11 +- R/reglca_fit_probabilities.R | 7 - R/reglca_mstep_item_parameters.R | 5 - R/reglca_update_parameter.R | 6 - R/sequential.items.R | 6 - R/slca_est_Xlambda.R | 2 R/slca_est_Xlambda_calc_increment.R | 2 R/slca_print_progress_em_algorithm.R | 14 +- R/summary.gdina.R | 4 R/summary.gdm.R | 5 - build/partial.rdb |binary inst/NEWS | 18 +++ man/CDM-utilities.Rd | 7 + man/gdina.Rd | 2 man/plot_item_mastery.Rd |only src/RcppExports.cpp | 2 src/init.c | 2 44 files changed, 200 insertions(+), 173 deletions(-)
Title: Formal Psychological Models of Categorization and Learning
Description: Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.
Author: Andy Wills, Lenard Dome, Charlotte Edmunds, Garrett Honke, Angus Inkster, René Schlegelmilch, Stuart Spicer
Maintainer: Andy Wills <andy@willslab.co.uk>
Diff between catlearn versions 0.6.1 dated 2019-02-18 and 0.6.2 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 2 +- tests/testthat.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization
facilities of MOSEK available from the R-language. The interface supports
large-scale optimization of many kinds: Mixed-integer and continuous linear,
second-order cone, exponential cone and power cone optimization, as well as
continuous semidefinite optimization. Rmosek and the R-language are
open-source projects. MOSEK is a proprietary product, but
unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>
Diff between Rmosek versions 1.3.2 dated 2019-02-15 and 1.3.3 dated 2019-03-18
DESCRIPTION | 6 ++-- MD5 | 6 ++-- NEWS | 7 +++++ R/builder.R | 74 ++++++++++++++++++++++++++++++++++++++++++++++++------------ 4 files changed, 73 insertions(+), 20 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including those
where counts or mortality rates of the reference population are used.
Currently supported: excess hazard models, rates, mean survival times,
relative survival, and standardized incidence and mortality ratios
(SIRs/SMRs), all of which can be easily adjusted for by covariates such as
age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi')
and other computations achieved using 'data.table'.
Author: Joonas Miettinen [aut, cre],
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.4.6 dated 2019-02-14 and 0.4.7 dated 2019-03-18
DESCRIPTION | 8 MD5 | 266 - NAMESPACE | 178 NEWS.md | 289 - R/S3_definitions.R | 2946 ++++++++-------- R/aggregating.R | 1232 +++--- R/data_document.R | 352 - R/direct_adjusting.R | 314 - R/evaluation.R | 1986 +++++----- R/flexyargs.R | 332 - R/fractional_years.R | 300 - R/incidence_rates.R | 692 +-- R/incidence_rates_utils.R | 266 - R/lexpand.R | 1880 +++++----- R/lexpand2.R | 278 - R/lifetime_function.R | 564 +-- R/ltable.R | 502 +- R/mean_survival.R | 1326 +++---- R/popEpi_package.r | 60 R/pophaz.R | 140 R/prevalence.R | 282 - R/relative_poisson.R | 1220 +++--- R/relative_poisson_net_survival.R | 352 - R/sir.R | 2904 +++++++-------- R/sir_utils.R | 226 - R/splitLexisDT.R | 602 +-- R/splitMulti.R | 548 +- R/splitting_utility_functions.R | 2852 +++++++-------- R/startup_message.R | 96 R/survival_aggregated.R | 1780 ++++----- R/survival_lexis.R | 1188 +++--- R/survival_utility_functions.R | 1276 +++--- R/utility_functions.R | 2830 +++++++-------- R/weighted_table.R | 1324 +++---- README.md | 378 +- build/vignette.rds |binary inst/WORDLIST | 174 inst/doc/sir.R | 128 inst/doc/sir.Rmd | 318 - inst/doc/sir.html | 737 ++-- inst/doc/survtab_examples.R | 340 - inst/doc/survtab_examples.Rmd | 592 +-- inst/doc/survtab_examples.html | 959 ++--- man/ICSS.Rd | 76 man/Lexis_fpa.Rd | 164 man/RPL.Rd | 44 man/adjust.Rd | 48 man/aggre.Rd | 372 +- man/all_names_present.Rd | 62 man/as.Date.yrs.Rd | 84 man/as.aggre.Rd | 154 man/as.data.frame.ratetable.Rd | 66 man/as.data.table.ratetable.Rd | 68 man/cast_simple.Rd | 100 man/cut_bound.Rd | 56 man/direct_standardization.Rd | 312 - man/fac2num.Rd | 80 man/flexible_argument.Rd | 336 - man/get.yrs.Rd | 156 man/is.Date.Rd | 82 man/is_leap_year.Rd | 56 man/lexpand.Rd | 742 ++-- man/lines.sirspline.Rd | 86 man/lines.survmean.Rd | 72 man/lines.survtab.Rd | 122 man/longDF2ratetable.Rd | 60 man/lower_bound.Rd | 36 man/ltable.Rd | 290 - man/makeWeightsDT.Rd | 306 - man/meanpop_fi.Rd | 60 man/na2zero.Rd | 54 man/plot.rate.Rd | 68 man/plot.sir.Rd | 140 man/plot.sirspline.Rd | 94 man/plot.survmean.Rd | 78 man/plot.survtab.Rd | 128 man/poisson.ci.Rd | 52 man/popEpi.Rd | 68 man/pophaz.Rd | 118 man/popmort.Rd | 64 man/prepExpo.Rd | 210 - man/print.aggre.Rd | 54 man/print.rate.Rd | 48 man/print.survtab.Rd | 68 man/rate.Rd | 220 - man/rate_ratio.Rd | 142 man/relpois.Rd | 238 - man/relpois_ag.Rd | 192 - man/robust_values.Rd | 102 man/rpcurve.Rd | 144 man/setaggre.Rd | 106 man/setclass.Rd | 54 man/setcolsnull.Rd | 64 man/sibr.Rd | 80 man/sir.Rd | 396 +- man/sir_exp.Rd | 208 - man/sir_ratio.Rd | 164 man/sire.Rd | 78 man/sirspline.Rd | 286 - man/splitLexisDT.Rd | 178 man/splitMulti.Rd | 276 - man/stdpop101.Rd | 58 man/stdpop18.Rd | 62 man/summary.aggre.Rd | 66 man/summary.survtab.Rd | 192 - man/survmean.Rd | 564 +-- man/survtab.Rd | 620 +-- man/survtab_ag.Rd | 786 ++-- man/try2int.Rd | 54 tests/testthat.R | 26 tests/testthat/test_aggre.R | 454 +- tests/testthat/test_epi.R | 70 tests/testthat/test_expo.R | 98 tests/testthat/test_lexpand.R | 744 ++-- tests/testthat/test_prevtab.R | 40 tests/testthat/test_rate.R | 624 +-- tests/testthat/test_relpois_mean_curve.R | 136 tests/testthat/test_sir.R | 882 ++-- tests/testthat/test_splitLexisDT.R | 264 - tests/testthat/test_splitMulti.R | 290 - tests/testthat/test_splitting_attributes.R | 188 - tests/testthat/test_splitting_breaks.R | 160 tests/testthat/test_splitting_randomly_on_fixed_data.R | 280 - tests/testthat/test_splitting_randomly_on_random_data.R | 118 tests/testthat/test_survmean.R | 604 +-- tests/testthat/test_survtab_adjusted.R | 152 tests/testthat/test_survtab_bad_surv_ints.R | 190 - tests/testthat/test_survtab_observed.R | 284 - tests/testthat/test_survtab_relative.R | 392 +- tests/testthat/test_survtab_usage.R | 960 ++--- tests/testthat/test_utils.R | 968 ++--- tests/testthat/test_weighter.R | 278 - vignettes/sir.Rmd | 318 - vignettes/survtab_examples.Rmd | 592 +-- 134 files changed, 27397 insertions(+), 27396 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Add Multiple Colors to your Console Output
Description: Add multiple colors to text that is printed to the console.
Author: Amanda Dobbyn [aut, cre],
Hernando Cortina [aut] (<https://orcid.org/0000-0001-6790-4870>)
Maintainer: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>
Diff between multicolor versions 0.1.1 dated 2018-09-25 and 0.1.2 dated 2019-03-18
DESCRIPTION | 18 ++++++++++-------- MD5 | 34 +++++++++++++++++++++++----------- NAMESPACE | 4 ++++ NEWS.md | 6 ++++++ R/crawl.R | 4 ++-- R/logo.R |only R/multi_color.R | 25 +++++++++++++++++-------- R/newhope.R |only R/textshapes.R |only R/utils.R | 7 +++++++ R/zzz.R | 5 ++++- README.md | 32 ++++++++++++++++++++------------ build |only inst |only man/center_string.Rd |only man/multi_color.Rd | 2 +- man/multicolor_logo.Rd |only man/starwars_intro.Rd |only man/things.Rd | 2 +- man/triangle_string.Rd |only tests/testthat/test-multicolor.R | 27 +++++++++++++++------------ vignettes |only 22 files changed, 110 insertions(+), 56 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between lavaSearch2 versions 1.4.1 dated 2018-11-20 and 1.5.3 dated 2019-03-18
lavaSearch2-1.4.1/lavaSearch2/man/estfun.lvmfit.Rd |only lavaSearch2-1.5.3/lavaSearch2/DESCRIPTION | 21 lavaSearch2-1.5.3/lavaSearch2/MD5 | 117 +- lavaSearch2-1.5.3/lavaSearch2/NAMESPACE | 20 lavaSearch2-1.5.3/lavaSearch2/NEWS | 9 lavaSearch2-1.5.3/lavaSearch2/R/0onload.R | 7 lavaSearch2-1.5.3/lavaSearch2/R/RcppExports.R |only lavaSearch2-1.5.3/lavaSearch2/R/Utils-formula.R |only lavaSearch2-1.5.3/lavaSearch2/R/Utils-nlme.R | 69 + lavaSearch2-1.5.3/lavaSearch2/R/calcDistMax.R | 8 lavaSearch2-1.5.3/lavaSearch2/R/calcType1postSelection.R | 8 lavaSearch2-1.5.3/lavaSearch2/R/calibrateType1.R | 488 ++++++---- lavaSearch2-1.5.3/lavaSearch2/R/clean.R |only lavaSearch2-1.5.3/lavaSearch2/R/compare2.R | 311 ++++-- lavaSearch2-1.5.3/lavaSearch2/R/conditionalMoment.R | 9 lavaSearch2-1.5.3/lavaSearch2/R/createContrast.R | 32 lavaSearch2-1.5.3/lavaSearch2/R/effects2.R |only lavaSearch2-1.5.3/lavaSearch2/R/estimate2.R | 50 - lavaSearch2-1.5.3/lavaSearch2/R/getVarCov2.R | 17 lavaSearch2-1.5.3/lavaSearch2/R/iid2.R | 2 lavaSearch2-1.5.3/lavaSearch2/R/information2.R | 274 +++++ lavaSearch2-1.5.3/lavaSearch2/R/initVarlink.R | 110 -- lavaSearch2-1.5.3/lavaSearch2/R/lavaSearch2-package.R | 2 lavaSearch2-1.5.3/lavaSearch2/R/leverage.R | 8 lavaSearch2-1.5.3/lavaSearch2/R/methods-modelsearch2.R | 15 lavaSearch2-1.5.3/lavaSearch2/R/modelsearch2.R | 69 + lavaSearch2-1.5.3/lavaSearch2/R/multcomp.R | 125 ++ lavaSearch2-1.5.3/lavaSearch2/R/residuals2.R | 5 lavaSearch2-1.5.3/lavaSearch2/R/sCorrect.R | 198 +++- lavaSearch2-1.5.3/lavaSearch2/R/score2.R | 12 lavaSearch2-1.5.3/lavaSearch2/R/skeleton.R | 6 lavaSearch2-1.5.3/lavaSearch2/R/summary2.R | 16 lavaSearch2-1.5.3/lavaSearch2/R/vcov2.R | 8 lavaSearch2-1.5.3/lavaSearch2/inst/doc/overview.pdf |binary lavaSearch2-1.5.3/lavaSearch2/man/autoplot.modelsearch2.Rd | 5 lavaSearch2-1.5.3/lavaSearch2/man/calcType1postSelection.Rd | 4 lavaSearch2-1.5.3/lavaSearch2/man/calibrateType1.Rd | 40 lavaSearch2-1.5.3/lavaSearch2/man/clean.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/combineFormula.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/compare2.Rd | 6 lavaSearch2-1.5.3/lavaSearch2/man/convFormulaCharacter.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/createContrast.Rd | 6 lavaSearch2-1.5.3/lavaSearch2/man/dfSigmaRobust.Rd | 4 lavaSearch2-1.5.3/lavaSearch2/man/effects2.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/estfun.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/getVarCov2.Rd | 12 lavaSearch2-1.5.3/lavaSearch2/man/glht2.Rd | 2 lavaSearch2-1.5.3/lavaSearch2/man/information2-internal.Rd | 13 lavaSearch2-1.5.3/lavaSearch2/man/information2.Rd |only lavaSearch2-1.5.3/lavaSearch2/man/modelsearch2.Rd | 5 lavaSearch2-1.5.3/lavaSearch2/man/sCorrect.Rd | 26 lavaSearch2-1.5.3/lavaSearch2/man/score2.Rd | 4 lavaSearch2-1.5.3/lavaSearch2/man/selectRegressor.Rd | 2 lavaSearch2-1.5.3/lavaSearch2/man/selectResponse.Rd | 2 lavaSearch2-1.5.3/lavaSearch2/src |only lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-Utils-nlme.R | 90 + lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-cluster-lava.R | 4 lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-sCorrect-dVcov.R | 124 +- lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-sCorrect-missingValues.R | 23 lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-sCorrect-summary2.R | 29 lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test1-sCorrect-validObjects.R | 8 lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test2-calcType1postSelection.R | 10 lavaSearch2-1.5.3/lavaSearch2/tests/testthat/test3-multcomp.R | 4 lavaSearch2-1.5.3/lavaSearch2/vignettes/overview.org | 114 +- 64 files changed, 1713 insertions(+), 840 deletions(-)
More information about DistributionOptimization at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-08 0.3.5
2017-03-20 0.3.4
2016-06-13 0.1
Title: Apache Thrift Client Server
Description: Pure R implementation of Apache Thrift.
This library doesn't require any code generation.
To learn more about Thrift go to <https://thrift.apache.org>.
Author: Marek Jagielski [aut, cre, cph],
Lixin Yu [aut, cph]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between thriftr versions 1.1.4 dated 2019-03-09 and 1.1.5 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/protocol_binary.R | 19 ++++++++++++++++--- R/thrift.R | 6 ++++-- R/transport_socket.R | 6 +----- demo/ping_server.R | 2 +- demo/sleep_server.R | 2 +- 7 files changed, 33 insertions(+), 22 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>),
Nicolas Müller [aut],
Reto Bürgin [aut],
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
(<https://orcid.org/0000-0001-7776-0903>)
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.0-10 dated 2018-11-18 and 2.0-11 dated 2019-03-18
TraMineR-2.0-10/TraMineR/src/tmrformat.cpp |only TraMineR-2.0-10/TraMineR/src/tmrformat.h |only TraMineR-2.0-11/TraMineR/DESCRIPTION | 21 ++-- TraMineR-2.0-11/TraMineR/MD5 | 44 ++++------ TraMineR-2.0-11/TraMineR/NEWS | 20 ++++ TraMineR-2.0-11/TraMineR/R/TraMineR-checkcost.R | 16 +-- TraMineR-2.0-11/TraMineR/R/plot.stslist.statd.R | 7 + TraMineR-2.0-11/TraMineR/R/seqdef.R | 30 ++++-- TraMineR-2.0-11/TraMineR/R/seqdist.R | 11 +- TraMineR-2.0-11/TraMineR/R/seqformat-SPELL_to_STS.R | 8 - TraMineR-2.0-11/TraMineR/R/seqtab.R | 8 + TraMineR-2.0-11/TraMineR/R/seqxtract.R | 6 - TraMineR-2.0-11/TraMineR/build/vignette.rds |binary TraMineR-2.0-11/TraMineR/data/ex1.rda |binary TraMineR-2.0-11/TraMineR/data/ex2.rda |binary TraMineR-2.0-11/TraMineR/data/famform.rda |binary TraMineR-2.0-11/TraMineR/inst/NEWS.Rd | 25 +++++ TraMineR-2.0-11/TraMineR/inst/doc/TraMineR-state-sequence.pdf |binary TraMineR-2.0-11/TraMineR/man/TraMineR-package.Rd | 2 TraMineR-2.0-11/TraMineR/man/plot.stslist.statd.Rd | 3 TraMineR-2.0-11/TraMineR/man/seqecreate.Rd | 6 + TraMineR-2.0-11/TraMineR/src/eventseq.cpp | 27 ++++-- TraMineR-2.0-11/TraMineR/src/eventseq.h | 2 TraMineR-2.0-11/TraMineR/src/tmrsequence.cpp | 4 24 files changed, 161 insertions(+), 79 deletions(-)
Title: Tools for Statistical Content Analysis
Description: A framework for statistical analysis in content analysis. In addition to a pipeline for preprocessing text corpora and linking to the latent Dirichlet allocation from the 'lda' package, plots are offered for the descriptive analysis of text corpora and topic models. In addition, an implementation of Chang's intruder words and intruder topics is provided.
Author: Lars Koppers [aut, cre] (<https://orcid.org/0000-0002-1642-9616>),
Jonas Rieger [aut] (<https://orcid.org/0000-0002-0007-4478>),
Karin Boczek [ctb] (<https://orcid.org/0000-0003-1516-4094>),
Gerret von Nordheim [ctb] (<https://orcid.org/0000-0001-7553-3838>)
Maintainer: Lars Koppers <koppers@statistik.tu-dortmund.de>
Diff between tosca versions 0.1-3 dated 2019-01-17 and 0.1-4 dated 2019-03-18
DESCRIPTION | 12 MD5 | 156 +-- R/LDAgen.R | 4 R/LDAprep.R | 6 R/as.textmeta.corpus.R | 8 R/readTextmeta.R | 2 R/readWhatsApp.R | 16 R/tidy.textmeta.R | 2 build/vignette.rds |binary data/datalist | 4 data/economy.rda |binary data/politics.rda |binary inst/doc/Vignette.R | 555 +++++------ inst/doc/Vignette.Rmd | 2 inst/doc/Vignette.pdf |binary man/LDAgen.Rd | 150 +- man/LDAprep.Rd | 90 - man/as.corpus.textmeta.Rd | 2 man/cleanTexts.Rd | 144 +- man/clusterTopics.Rd | 114 +- man/deleteAndRenameDuplicates.Rd | 92 - man/duplist.Rd | 126 +- man/intruderTopics.Rd | 144 +- man/intruderWords.Rd | 116 +- man/makeWordlist.Rd | 76 - man/mergeLDA.Rd | 88 - man/mergeTextmeta.Rd | 94 - man/plotArea.Rd | 126 +- man/plotFreq.Rd | 206 ++-- man/plotHeat.Rd | 124 +- man/plotScot.Rd | 170 +-- man/plotTopic.Rd | 216 ++-- man/plotTopicWord.Rd | 288 ++--- man/plotWordSub.Rd | 232 ++-- man/plotWordpt.Rd | 276 ++--- man/readTextmeta.Rd | 92 - man/readWiki.Rd | 70 - man/readWikinews.Rd | 40 man/removeXML.Rd | 106 +- man/textmeta.Rd | 132 +- man/topTexts.Rd | 104 +- man/topicsInText.Rd | 110 +- man/wikinews.Rd | 52 - tests/testthat/data/WhatsApp |only tests/testthat/test_LDAgen.R | 2 tests/testthat/test_as.corpus.textmeta.R |only tests/testthat/test_as.textmeta.corpus.R |only tests/testthat/test_filterDate.R | 1 tests/testthat/test_intruderTopics.R | 2 tests/testthat/test_intruderWords.R | 2 tests/testthat/test_plotArea.R | 2 tests/testthat/test_plotFreq.R | 1 tests/testthat/test_plotHeat.R | 1 tests/testthat/test_plotScot.R | 1 tests/testthat/test_plotTopic.R | 1 tests/testthat/test_plotTopicWord.R | 1 tests/testthat/test_plotWordSub.R | 3 tests/testthat/test_plotWordpt.R | 1 tests/testthat/test_readWhatsApp.R |only tests/testthat/test_tidy.textmeta.R |only vignettes/Vignette.Rmd | 2 vignettes/Vignette_files/figure-latex/unnamed-chunk-15-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-16-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-17-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-17-2.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-18-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-18-2.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-19-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-42-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-43-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-44-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-45-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-46-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-47-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-48-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-49-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-50-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-51-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-52-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-53-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-54-1.pdf |binary 81 files changed, 2198 insertions(+), 2169 deletions(-)
Title: Network-Based Interpretation of Changes in Compositional Data
Description: Provides a set of functions to interpret changes in
compositional data based on a network representation of all pairwise ratio
comparisons: computation of all pairwise ratio, construction of a
p-value matrix of all pairwise tests of these ratios between
conditions, conversion of this matrix to a network.
Author: Emmanuel Curis [aut, cre] (<https://orcid.org/0000-0001-8382-1493>)
Maintainer: Emmanuel Curis <emmanuel.curis@parisdescartes.fr>
Diff between SARP.compo versions 0.0.8 dated 2018-11-07 and 0.1.0 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++++--------- R/arbre.R | 9 ++++++--- R/creer_graphe.R | 9 ++++++++- R/distances.R | 7 ++++++- R/equiv.R |only R/simuler_H1.R | 4 +++- data/generef.csv.gz |only man/arbres.Rd | 7 ++++++- man/creer_graphe.Rd | 12 ++++++++++-- man/equiv.Rd |only man/generef.Rd |only man/rapports.Rd | 2 -- man/test.Rd | 2 ++ 14 files changed, 58 insertions(+), 24 deletions(-)
Title: 'R x C Ecological Inference With Optional Incorporation of
Survey Information'
Description: Fits the R x C inference model described in Greiner and
Quinn (2009). Allows incorporation of survey results.
Author: D. James Greiner, Paul Baines, and Kevin M. Quinn
Maintainer: Kevin M. Quinn <kmq@umich.edu>
Diff between RxCEcolInf versions 0.1-3 dated 2013-07-24 and 0.1-4 dated 2019-03-18
RxCEcolInf-0.1-3/RxCEcolInf/dos2unix.sh |only RxCEcolInf-0.1-4/RxCEcolInf/DESCRIPTION | 16 ++++----- RxCEcolInf-0.1-4/RxCEcolInf/MD5 | 28 ++++++++--------- RxCEcolInf-0.1-4/RxCEcolInf/NAMESPACE | 27 ++++++++-------- RxCEcolInf-0.1-4/RxCEcolInf/R/Analyze.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/R/AnalyzeWithExitPoll.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/R/Tune.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/R/TuneWithExitPoll.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/R/gq_restart.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/R/rnchg.R | 2 - RxCEcolInf-0.1-4/RxCEcolInf/man/Analyze.Rd | 1 RxCEcolInf-0.1-4/RxCEcolInf/man/AnalyzeWithExitPoll.Rd | 1 RxCEcolInf-0.1-4/RxCEcolInf/src/Makevars | 1 RxCEcolInf-0.1-4/RxCEcolInf/src/RxCEcolInf_init.c |only RxCEcolInf-0.1-4/RxCEcolInf/src/jimsmatrixinterface.c | 5 +++ RxCEcolInf-0.1-4/RxCEcolInf/src/nchg.c | 4 +- 16 files changed, 50 insertions(+), 45 deletions(-)
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and
implements multivariate outlier detection and univariate normality of marginal
distributions through plots and tests, and performs multivariate Box-Cox transformation
(Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).
Author: Selcuk Korkmaz [aut, cre],
Dincer Goksuluk [aut],
Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 5.6 dated 2019-01-30 and 5.7 dated 2019-03-18
DESCRIPTION | 8 ++--- MD5 | 10 +++---- R/mvn.R | 73 +++++++++++++++++++++++++++++++----------------------- inst/doc/MVN.Rnw | 2 - inst/doc/MVN.pdf |binary vignettes/MVN.Rnw | 2 - 6 files changed, 54 insertions(+), 41 deletions(-)
Title: Management of Survey Data and Presentation of Analysis Results
Description: An infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) 'SPSS' and
'Stata' files is provided. Further, the package allows to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to 'LaTeX' and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.14.12 dated 2018-10-01 and 0.99.17.1 dated 2019-03-18
memisc-0.99.14.12/memisc/src/ord_union.c |only memisc-0.99.17.1/memisc/DESCRIPTION | 8 - memisc-0.99.17.1/memisc/MD5 | 103 ++++++------- memisc-0.99.17.1/memisc/NAMESPACE | 26 +++ memisc-0.99.17.1/memisc/R/AllClasses.R | 2 memisc-0.99.17.1/memisc/R/AllGenerics.R | 7 memisc-0.99.17.1/memisc/R/aaa.R | 5 memisc-0.99.17.1/memisc/R/annotation.R | 5 memisc-0.99.17.1/memisc/R/codebook-format-html.R | 8 - memisc-0.99.17.1/memisc/R/codebook-methods.R | 1 memisc-0.99.17.1/memisc/R/codeplan.R |only memisc-0.99.17.1/memisc/R/collect.R | 2 memisc-0.99.17.1/memisc/R/dataset-methods.R | 3 memisc-0.99.17.1/memisc/R/import-internal-spss-syntax.R | 8 - memisc-0.99.17.1/memisc/R/import-internal-spss-sysfile.R | 10 + memisc-0.99.17.1/memisc/R/importer-methods.R | 116 +++++++++++---- memisc-0.99.17.1/memisc/R/item-more-methods-datetime.R | 28 +++ memisc-0.99.17.1/memisc/R/mtable-format-html.R | 38 ++++ memisc-0.99.17.1/memisc/R/mtable-format-latex.R | 71 ++++++++- memisc-0.99.17.1/memisc/R/mtable-format-print.R | 43 +++++ memisc-0.99.17.1/memisc/R/mtable-manip.R | 5 memisc-0.99.17.1/memisc/R/mtable.R | 81 ++++++++-- memisc-0.99.17.1/memisc/R/percentages.R | 2 memisc-0.99.17.1/memisc/R/spss-portable-methods.R | 14 + memisc-0.99.17.1/memisc/R/spss-syntax-methods.R | 6 memisc-0.99.17.1/memisc/R/spss-sysfile-methods.R | 22 +- memisc-0.99.17.1/memisc/R/stata-methods.R | 2 memisc-0.99.17.1/memisc/R/syntactic-sugar.R |only memisc-0.99.17.1/memisc/R/toLatex-tools.R | 8 + memisc-0.99.17.1/memisc/R/value-label-duplicates.R |only memisc-0.99.17.1/memisc/R/value-labels.R | 13 + memisc-0.99.17.1/memisc/R/xx-getSummary.R | 1 memisc-0.99.17.1/memisc/R/yy-mtable-ext-AchimZeileis.R | 1 memisc-0.99.17.1/memisc/R/zzz.R | 3 memisc-0.99.17.1/memisc/build/vignette.rds |binary memisc-0.99.17.1/memisc/inst/ChangeLog | 57 +++++++ memisc-0.99.17.1/memisc/inst/NEWS.Rd | 32 ++-- memisc-0.99.17.1/memisc/inst/doc/anes48.html | 44 +---- memisc-0.99.17.1/memisc/inst/doc/items.html | 3 memisc-0.99.17.1/memisc/inst/doc/mtable-html.html | 7 memisc-0.99.17.1/memisc/man/Iconv.Rd | 2 memisc-0.99.17.1/memisc/man/codebook.Rd | 2 memisc-0.99.17.1/memisc/man/codeplan.Rd |only memisc-0.99.17.1/memisc/man/dataSets.Rd | 1 memisc-0.99.17.1/memisc/man/duplicated-labels.Rd |only memisc-0.99.17.1/memisc/man/importers.Rd | 2 memisc-0.99.17.1/memisc/man/items.Rd | 2 memisc-0.99.17.1/memisc/man/mtable-format-html.Rd | 13 + memisc-0.99.17.1/memisc/man/mtable-format-latex.Rd | 20 ++ memisc-0.99.17.1/memisc/man/mtable.Rd | 25 ++- memisc-0.99.17.1/memisc/man/syntactic-sugar.Rd |only memisc-0.99.17.1/memisc/src/init-memisc.c | 10 - memisc-0.99.17.1/memisc/src/memisc.h | 6 memisc-0.99.17.1/memisc/src/pspp-portableStream-for-R.c | 27 ++- memisc-0.99.17.1/memisc/src/pspp-system-for-R.c | 45 ++--- memisc-0.99.17.1/memisc/src/update_data_frame.c | 4 56 files changed, 694 insertions(+), 250 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat learning methods, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.3.6 dated 2019-03-09 and 2.4.7 dated 2019-03-18
HEMDAG-2.3.6/HEMDAG/inst/HEMDAG_2.3.6.pdf |only HEMDAG-2.4.7/HEMDAG/DESCRIPTION | 6 HEMDAG-2.4.7/HEMDAG/MD5 | 36 - HEMDAG-2.4.7/HEMDAG/NEWS.md | 17 HEMDAG-2.4.7/HEMDAG/R/GPAV.R | 182 +++--- HEMDAG-2.4.7/HEMDAG/R/TPR-DAG.R | 483 ++++++++-------- HEMDAG-2.4.7/HEMDAG/R/graph.utility.R | 8 HEMDAG-2.4.7/HEMDAG/R/heuristic.methods.R | 162 +++-- HEMDAG-2.4.7/HEMDAG/R/htd.R | 176 +++-- HEMDAG-2.4.7/HEMDAG/R/perf.meas.R | 83 +- HEMDAG-2.4.7/HEMDAG/inst/HEMDAG_2.4.7.pdf |only HEMDAG-2.4.7/HEMDAG/man/Do.GPAV.Rd | 42 - HEMDAG-2.4.7/HEMDAG/man/Do.GPAV.holdout.Rd | 49 + HEMDAG-2.4.7/HEMDAG/man/Do.HTD.Rd | 39 - HEMDAG-2.4.7/HEMDAG/man/Do.HTD.holdout.Rd | 43 - HEMDAG-2.4.7/HEMDAG/man/Do.heuristic.methods.Rd | 37 - HEMDAG-2.4.7/HEMDAG/man/Do.heuristic.methods.holdout.Rd | 32 - HEMDAG-2.4.7/HEMDAG/man/TPR-DAG-cross-validation.Rd | 106 ++- HEMDAG-2.4.7/HEMDAG/man/TPR-DAG-holdout.Rd | 91 +-- HEMDAG-2.4.7/HEMDAG/man/TPR-DAG-variants.Rd | 76 +- 20 files changed, 1000 insertions(+), 668 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny GUI) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Author: Ross Ihaka [aut],
Paul Murrell [aut] (<https://orcid.org/0000-0002-3224-8858>),
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Jason C. Fisher [aut] (<https://orcid.org/0000-0001-9032-8912>),
Reto Stauffer [aut] (<https://orcid.org/0000-0002-3798-5507>),
Claus O. Wilke [aut] (<https://orcid.org/0000-0002-7470-9261>),
Claire D. McWhite [aut] (<https://orcid.org/0000-0001-7346-3047>),
Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 1.4-0 dated 2019-01-13 and 1.4-1 dated 2019-03-18
DESCRIPTION | 13 - MD5 | 112 +++++++------- NEWS.md | 33 ++++ R/choose_palette.R | 6 R/colorspace.R | 1 R/cvd.R | 4 R/cvd_image.R | 3 R/demoplot.R | 3 R/desaturate.R | 3 R/divergingx_hcl.R | 52 ++++-- R/hcl_color_picker.R | 3 R/hcl_palettes.R | 65 ++++---- R/hclplot.R | 3 R/lighten.R | 3 R/scale_diverging.R | 4 R/scale_divergingx.R | 6 R/scale_qualitative.R | 4 R/scale_sequential.R | 4 R/simulate_cvd.R | 8 - R/specplot.R | 20 +- R/swatchplot.R | 3 build/partial.rdb |binary build/vignette.rds |binary data/USSouthPolygon.rda |binary data/max_chroma_table.rda |binary demo/viridis.R | 3 inst/CITATION | 36 ++-- inst/doc/colorspace.Rmd | 84 ++++++----- inst/doc/colorspace.html | 49 +++--- inst/doc/hcl-colors.pdf |binary man/choose_palette.Rd | 6 man/cvd.Rd | 4 man/cvd_emulator.Rd | 5 man/demoplot.Rd | 5 man/desaturate.Rd | 5 man/divergingx_hcl.Rd | 22 ++ man/hcl_color_picker.Rd | 5 man/hcl_palettes.Rd | 8 - man/hclplot.Rd | 5 man/lighten.Rd | 5 man/polarLUV.Rd | 1 man/scale_colour_continuous_diverging.Rd | 2 man/scale_colour_continuous_divergingx.Rd | 4 man/scale_colour_continuous_qualitative.Rd | 2 man/scale_colour_continuous_sequential.Rd | 2 man/scale_colour_discrete_diverging.Rd | 2 man/scale_colour_discrete_divergingx.Rd | 2 man/scale_colour_discrete_qualitative.Rd | 2 man/scale_colour_discrete_sequential.Rd | 2 man/simulate_cvd.Rd | 8 - man/specplot.Rd | 4 man/swatchplot.Rd | 5 tests/Examples/colorspace-Ex.Rout.save | 30 ++-- tests/cvd.R | 5 tests/cvd.Rout.save | 12 - vignettes/color.bib | 217 +++++++++++++++++++++++++++-- vignettes/colorspace.Rmd | 84 ++++++----- 57 files changed, 684 insertions(+), 295 deletions(-)
Title: Implementation of Unsupervised Neural Architectures
Description: Implementation of several unsupervised neural networks,
from building their architecture to their training and evaluation. Available
networks are auto-encoders including their main variants: sparse, contractive,
denoising, robust and variational, as described in Charte et al. (2018)
<doi:10.1016/j.inffus.2017.12.007>.
Author: David Charte [aut, cre] (<https://orcid.org/0000-0002-4830-9512>),
Francisco Charte [aut] (<https://orcid.org/0000-0002-3083-8942>),
Francisco Herrera [aut]
Maintainer: David Charte <fdavidcl@ugr.es>
Diff between ruta versions 1.0.2 dated 2018-05-08 and 1.1.0 dated 2019-03-18
ruta-1.0.2/ruta/R/classes.R |only ruta-1.0.2/ruta/vignettes/architectures_cache |only ruta-1.1.0/ruta/DESCRIPTION | 12 ruta-1.1.0/ruta/MD5 | 104 ++-- ruta-1.1.0/ruta/NAMESPACE | 3 ruta-1.1.0/ruta/R/00classes.R |only ruta-1.1.0/ruta/R/autoencoder.R | 71 ++- ruta-1.1.0/ruta/R/autoencoder_contractive.R | 31 - ruta-1.1.0/ruta/R/autoencoder_sparse.R | 2 ruta-1.1.0/ruta/R/autoencoder_variational.R | 2 ruta-1.1.0/ruta/R/derivative.R | 2 ruta-1.1.0/ruta/R/evaluate.R | 5 ruta-1.1.0/ruta/R/filter.R | 35 + ruta-1.1.0/ruta/R/jacobian.R |only ruta-1.1.0/ruta/R/layers.R | 127 +++++ ruta-1.1.0/ruta/R/network.R | 9 ruta-1.1.0/ruta/R/util.R | 9 ruta-1.1.0/ruta/build/vignette.rds |binary ruta-1.1.0/ruta/inst/CITATION |only ruta-1.1.0/ruta/inst/doc/architectures.html | 541 +++++++++++++---------- ruta-1.1.0/ruta/inst/doc/troubleshooting.Rmd |only ruta-1.1.0/ruta/inst/doc/troubleshooting.html |only ruta-1.1.0/ruta/man/autoencode.Rd | 3 ruta-1.1.0/ruta/man/autoencoder.Rd | 1 ruta-1.1.0/ruta/man/autoencoder_contractive.Rd | 1 ruta-1.1.0/ruta/man/autoencoder_denoising.Rd | 1 ruta-1.1.0/ruta/man/autoencoder_robust.Rd | 1 ruta-1.1.0/ruta/man/autoencoder_sparse.Rd | 1 ruta-1.1.0/ruta/man/autoencoder_variational.Rd | 1 ruta-1.1.0/ruta/man/contraction.Rd | 1 ruta-1.1.0/ruta/man/conv.Rd |only ruta-1.1.0/ruta/man/correntropy.Rd | 1 ruta-1.1.0/ruta/man/dense.Rd | 8 ruta-1.1.0/ruta/man/dropout.Rd | 8 ruta-1.1.0/ruta/man/evaluate.Rd | 12 ruta-1.1.0/ruta/man/generate.Rd | 5 ruta-1.1.0/ruta/man/input.Rd | 8 ruta-1.1.0/ruta/man/layer_keras.Rd | 12 ruta-1.1.0/ruta/man/loss_variational.Rd | 1 ruta-1.1.0/ruta/man/noise_cauchy.Rd | 1 ruta-1.1.0/ruta/man/noise_gaussian.Rd | 1 ruta-1.1.0/ruta/man/noise_ones.Rd | 1 ruta-1.1.0/ruta/man/noise_saltpepper.Rd | 1 ruta-1.1.0/ruta/man/noise_zeros.Rd | 1 ruta-1.1.0/ruta/man/output.Rd | 7 ruta-1.1.0/ruta/man/to_keras.ruta_filter.Rd |only ruta-1.1.0/ruta/man/to_keras.ruta_layer_input.Rd | 4 ruta-1.1.0/ruta/man/train.ruta_autoencoder.Rd | 4 ruta-1.1.0/ruta/man/variational_block.Rd | 8 ruta-1.1.0/ruta/vignettes/getting-started_cache |only ruta-1.1.0/ruta/vignettes/troubleshooting.Rmd |only 51 files changed, 692 insertions(+), 354 deletions(-)
Title: Latent Markov Models with and without Covariates
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT)
Maintainer: Francesco Bartolucci <bart@stat.unipg.it>
Diff between LMest versions 2.4.3 dated 2018-09-11 and 2.4.4 dated 2019-03-18
DESCRIPTION | 11 +-- MD5 | 21 +++--- NAMESPACE | 4 - R/est_lm_basic.R | 6 + R/est_lm_basic_cont.R | 148 +++++++++++++++++++++++++++++++++++++++------ R/est_lm_cov_latent.R | 1 R/est_lm_cov_latent_cont.R | 14 +++- R/lk_comp_latent_cont.R | 2 R/lk_obs_cont.R |only R/summary.LMbasiccont.R | 16 ++-- man/LMest-package.Rd | 4 - man/est_lm_basic_cont.Rd | 5 - 12 files changed, 183 insertions(+), 49 deletions(-)
Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct
social-ecological models that simulate the management of populations and
stakeholder actions. These models build off of a previously developed
management strategy evaluation (MSE) framework to simulate all aspects of
management: population dynamics, manager observation of populations, manager
decision making, and stakeholder responses to management decisions. The
newly developed generalised management strategy evaluation (GMSE)
framework uses genetic algorithms to mimic the decision-making process of
managers and stakeholders under conditions of change, uncertainty, and
conflict. Simulations can be run using gmse(), gmse_apply(), and
gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>),
Nils Bunnefeld [ctb, fnd] (<https://orcid.org/0000-0002-1349-4463>),
Jeremy Cusack [ctb] (<https://orcid.org/0000-0003-3004-1586>),
Isabel Jones [ctb] (<https://orcid.org/0000-0002-8361-1370>),
Jeroen Minderman [ctb] (<https://orcid.org/0000-0002-8451-5540>),
Erlend Nilsen [ctb] (<https://orcid.org/0000-0002-5119-8331>),
Rocio Pozo [ctb] (<https://orcid.org/0000-0002-7546-8076>),
Sarobidy Rakotonarivo [ctb] (<https://orcid.org/0000-0002-8032-1431>),
Bram Van Moorter [ctb] (<https://orcid.org/0000-0002-3196-1993>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between GMSE versions 0.4.0.7 dated 2018-08-22 and 0.4.0.11 dated 2019-03-18
DESCRIPTION | 12 MD5 | 70 ++--- R/gmse.R | 4 R/gmse_apply.R | 2 R/gmse_summary.R | 2 README.md | 18 - build/vignette.rds |binary inst/doc/SI1.pdf |binary inst/doc/SI2.pdf |binary inst/doc/SI3.pdf |binary inst/doc/SI4.pdf |binary inst/doc/SI5.pdf |binary inst/doc/SI6.pdf |binary inst/doc/SI7.pdf |binary inst/doc/ms.pdf |binary man/gmse.Rd | 4 man/gmse_apply.Rd | 2 man/gmse_table.Rd | 2 src/manager.c | 29 +- src/observation.c | 29 +- src/resource.c | 29 +- src/user.c | 29 +- tests/testthat.R | 4 tests/testthat/test-gmse_apply.R | 452 ++++++++++++++++++++++++++++----- tests/testthat/test-make_agents.R | 33 +- tests/testthat/test-make_costs.R | 88 ++++-- tests/testthat/test-make_interaction.R | 75 ++--- tests/testthat/test-make_landscape.R | 54 ++- tests/testthat/test-make_resource.R | 114 ++++++-- tests/testthat/test-make_utilities.R | 117 ++++++-- tests/testthat/test-manager.R | 238 +++++++++++------ tests/testthat/test-observation.R | 254 +++++++++++++----- tests/testthat/test-resource.R | 128 +++++---- tests/testthat/test-summary.R | 34 +- tests/testthat/test-user.R | 317 +++++++++++++++++------ tests/testthat/test-utility_layer.R | 37 ++ 36 files changed, 1602 insertions(+), 575 deletions(-)
Title: Synoptic Climate Classification and Spatial Regionalization of
Environmental Data
Description: Computes a synoptic climate classification through daily reanalysis data and
creates a climate or environmental regionalization based on the previous synoptic climate classification.
Author: Marc Lemus-Canovas, Dominic Roye
Maintainer: Marc Lemus-Canovas <mlemus@ub.edu>
Diff between synoptReg versions 0.2.1 dated 2019-01-02 and 0.2.2 dated 2019-03-18
DESCRIPTION | 8 +-- MD5 | 22 ++++---- R/pca_decision.R | 2 R/raster_clas.R | 4 - R/raster_ct2env.R | 4 - R/synoptclas.R |binary R/tidy_cuttime_nc.R | 125 +++++++++++++++++++++++++++++++++++-------------- man/pca_decision.Rd | 2 man/raster_clas.Rd | 2 man/raster_ct2env.Rd | 4 - man/synoptclas.Rd | 2 man/tidy_cuttime_nc.Rd | 19 ++----- 12 files changed, 123 insertions(+), 71 deletions(-)
Title: Packed Bar Charts with 'plotly'
Description: Packed bar charts are a variation of treemaps for visualizing skewed data. The concept was introduced by Xan Gregg at 'JMP'.
Author: Adam Spannbauer [aut, cre]
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between rPackedBar versions 0.1.0 dated 2018-01-31 and 0.2.1 dated 2019-03-18
DESCRIPTION | 10 MD5 | 24 - NAMESPACE | 10 R/gen_color_bars.R | 5 R/gen_gray_bars.R | 5 R/renderPackedBar.R |only build/vignette.rds |binary inst/doc/Visualizing_Twitter_Data_with_a_Packed_Barchart.html | 72 ++- man/gen_color_bars.Rd | 4 man/packed_bar_shiny.Rd |only man/plotly_packed_bar.Rd | 4 tests/testthat/test-gen_color_bars.R | 77 --- tests/testthat/test-gen_gray_bars.R | 230 ---------- tests/testthat/test-plotly_packed_bar.R | 1 14 files changed, 91 insertions(+), 351 deletions(-)
Title: Approximate Bayesian Computations for Phylogenetic Comparative
Methods
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2019) <10.5506/APhysPolBSupp.12.25>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between pcmabc versions 1.0.2 dated 2019-02-06 and 1.0.3 dated 2019-03-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- inst/CITATION | 15 +++++++-------- man/PCM_ABC.Rd | 4 ++-- man/draw_phylproc.Rd | 4 ++-- man/get_phylogenetic_sample.Rd | 4 ++-- man/pcmabc-package.Rd | 4 ++-- man/simulate_phenotype_on_tree.Rd | 4 ++-- man/simulate_phylproc.Rd | 4 ++-- man/simulate_sde_on_branch.Rd | 4 ++-- 10 files changed, 35 insertions(+), 36 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
and nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.0-16 dated 2018-12-11 and 3.1-37 dated 2019-03-18
miceadds-3.0-16/miceadds/R/antilogit.R |only miceadds-3.1-37/miceadds/DESCRIPTION | 10 miceadds-3.1-37/miceadds/MD5 | 232 +++++----- miceadds-3.1-37/miceadds/R/RcppExports.R | 2 miceadds-3.1-37/miceadds/R/cronbach_alpha.R |only miceadds-3.1-37/miceadds/R/datalist2mids.R | 4 miceadds-3.1-37/miceadds/R/draw.pv.ctt.R | 66 -- miceadds-3.1-37/miceadds/R/files_move.R | 16 miceadds-3.1-37/miceadds/R/grep.vec.R | 8 miceadds-3.1-37/miceadds/R/grepvec.R | 6 miceadds-3.1-37/miceadds/R/inverse_logit.R |only miceadds-3.1-37/miceadds/R/lmer_vcov2.R | 3 miceadds-3.1-37/miceadds/R/load.data.R | 54 +- miceadds-3.1-37/miceadds/R/load.files.R | 4 miceadds-3.1-37/miceadds/R/ma.wtd.aux.data.R | 6 miceadds-3.1-37/miceadds/R/ma_lme4_formula_design_matrices.R | 8 miceadds-3.1-37/miceadds/R/ma_lme4_formula_terms.R | 5 miceadds-3.1-37/miceadds/R/mi.anova.R | 22 miceadds-3.1-37/miceadds/R/mice.1chain.R | 19 miceadds-3.1-37/miceadds/R/mice.impute.2l.contextual.pmm.R | 9 miceadds-3.1-37/miceadds/R/mice.impute.2l.pls2.R | 36 - miceadds-3.1-37/miceadds/R/mice.impute.2l.pmm.R | 10 miceadds-3.1-37/miceadds/R/mice.impute.2lonly.function.R | 13 miceadds-3.1-37/miceadds/R/mice.impute.bygroup.R | 12 miceadds-3.1-37/miceadds/R/mice.impute.grouped.R | 7 miceadds-3.1-37/miceadds/R/mice.impute.ml.lmer.R | 15 miceadds-3.1-37/miceadds/R/mice.impute.plausible.values.R | 102 ++-- miceadds-3.1-37/miceadds/R/mice.impute.pls.R | 9 miceadds-3.1-37/miceadds/R/mice.impute.pmm3.R | 9 miceadds-3.1-37/miceadds/R/mice.impute.pmm4.R | 9 miceadds-3.1-37/miceadds/R/mice.impute.pmm5.R | 9 miceadds-3.1-37/miceadds/R/mice.impute.pmm6.R | 10 miceadds-3.1-37/miceadds/R/mice.impute.tricube.pmm.R | 116 +++-- miceadds-3.1-37/miceadds/R/mice.impute.tricube.pmm2.R | 91 --- miceadds-3.1-37/miceadds/R/mice.nmi.R | 23 miceadds-3.1-37/miceadds/R/mice_imputation_create_interactions.R | 4 miceadds-3.1-37/miceadds/R/mice_imputation_factor_pmm_convert_factor.R |only miceadds-3.1-37/miceadds/R/mice_imputation_factor_pmm_prepare.R |only miceadds-3.1-37/miceadds/R/mice_imputation_prepare_2l_functions.R | 4 miceadds-3.1-37/miceadds/R/mice_imputation_tricube_pmm_match.R |only miceadds-3.1-37/miceadds/R/mice_impute_2l_lmer.R | 4 miceadds-3.1-37/miceadds/R/micombine.chisquare.R | 159 +----- miceadds-3.1-37/miceadds/R/ml_mcmc.R | 30 - miceadds-3.1-37/miceadds/R/ml_mcmc_proc_data.R | 2 miceadds-3.1-37/miceadds/R/source.Rcpp.all.R | 5 miceadds-3.1-37/miceadds/R/string_to_matrix.R | 5 miceadds-3.1-37/miceadds/R/write.mice.imputation.R | 183 ++++--- miceadds-3.1-37/miceadds/R/write.pspp.R | 148 ++---- miceadds-3.1-37/miceadds/build/partial.rdb |binary miceadds-3.1-37/miceadds/inst/NEWS | 43 + miceadds-3.1-37/miceadds/man/GroupMean.Rd | 4 miceadds-3.1-37/miceadds/man/NMIwaldtest.Rd | 12 miceadds-3.1-37/miceadds/man/NestedImputationList.Rd | 4 miceadds-3.1-37/miceadds/man/Reval.Rd | 4 miceadds-3.1-37/miceadds/man/Rhat.mice.Rd | 6 miceadds-3.1-37/miceadds/man/Rsessinfo.Rd | 4 miceadds-3.1-37/miceadds/man/complete.miceadds.Rd | 4 miceadds-3.1-37/miceadds/man/crlrem.Rd | 4 miceadds-3.1-37/miceadds/man/cxxfunction.copy.Rd | 4 miceadds-3.1-37/miceadds/man/data.allison.Rd | 4 miceadds-3.1-37/miceadds/man/data.enders.Rd | 4 miceadds-3.1-37/miceadds/man/data.graham.Rd | 4 miceadds-3.1-37/miceadds/man/data.internet.Rd | 4 miceadds-3.1-37/miceadds/man/data.largescale.Rd | 4 miceadds-3.1-37/miceadds/man/data.ma.Rd | 4 miceadds-3.1-37/miceadds/man/data.smallscale.Rd | 4 miceadds-3.1-37/miceadds/man/datalist2mids.Rd | 6 miceadds-3.1-37/miceadds/man/datlist_create.Rd | 4 miceadds-3.1-37/miceadds/man/draw.pv.ctt.Rd | 6 miceadds-3.1-37/miceadds/man/filename_split.Rd | 19 miceadds-3.1-37/miceadds/man/files_move.Rd | 7 miceadds-3.1-37/miceadds/man/grep.vec.Rd | 10 miceadds-3.1-37/miceadds/man/index.dataframe.Rd | 4 miceadds-3.1-37/miceadds/man/kernelpls.fit2.Rd | 8 miceadds-3.1-37/miceadds/man/library_install.Rd | 4 miceadds-3.1-37/miceadds/man/lm.cluster.Rd | 8 miceadds-3.1-37/miceadds/man/load.Rdata.Rd | 4 miceadds-3.1-37/miceadds/man/load.data.Rd | 30 - miceadds-3.1-37/miceadds/man/ma.scale2.Rd | 6 miceadds-3.1-37/miceadds/man/ma.wtd.statNA.Rd | 4 miceadds-3.1-37/miceadds/man/mi.anova.Rd | 13 miceadds-3.1-37/miceadds/man/mice.1chain.Rd | 12 miceadds-3.1-37/miceadds/man/mice.impute.2l.contextual.pmm.Rd | 6 miceadds-3.1-37/miceadds/man/mice.impute.2l.latentgroupmean.ml.Rd | 4 miceadds-3.1-37/miceadds/man/mice.impute.eap.Rd | 8 miceadds-3.1-37/miceadds/man/mice.impute.grouped.Rd | 4 miceadds-3.1-37/miceadds/man/mice.impute.hotDeck.Rd | 4 miceadds-3.1-37/miceadds/man/mice.impute.plausible.values.Rd | 4 miceadds-3.1-37/miceadds/man/mice.impute.pls.Rd | 8 miceadds-3.1-37/miceadds/man/mice.impute.pmm3.Rd | 16 miceadds-3.1-37/miceadds/man/mice.impute.tricube.pmm.Rd | 23 miceadds-3.1-37/miceadds/man/mice.impute.weighted.pmm.Rd | 8 miceadds-3.1-37/miceadds/man/mice.nmi.Rd | 4 miceadds-3.1-37/miceadds/man/mice_impute_2l_lmer.Rd | 4 miceadds-3.1-37/miceadds/man/miceadds-defunct.Rd | 7 miceadds-3.1-37/miceadds/man/micombine.F.Rd | 4 miceadds-3.1-37/miceadds/man/micombine.chisquare.Rd | 6 miceadds-3.1-37/miceadds/man/micombine.cor.Rd | 6 miceadds-3.1-37/miceadds/man/mids2datlist.Rd | 6 miceadds-3.1-37/miceadds/man/ml_mcmc.Rd | 4 miceadds-3.1-37/miceadds/man/output.format1.Rd | 4 miceadds-3.1-37/miceadds/man/pca.covridge.Rd | 6 miceadds-3.1-37/miceadds/man/pool.mids.nmi.Rd | 10 miceadds-3.1-37/miceadds/man/pool_mi.Rd | 8 miceadds-3.1-37/miceadds/man/round2.Rd | 6 miceadds-3.1-37/miceadds/man/save.Rdata.Rd | 4 miceadds-3.1-37/miceadds/man/save.data.Rd | 4 miceadds-3.1-37/miceadds/man/scale_datlist.Rd | 4 miceadds-3.1-37/miceadds/man/scan.vector.Rd | 4 miceadds-3.1-37/miceadds/man/source.all.Rd | 4 miceadds-3.1-37/miceadds/man/stats0.Rd | 4 miceadds-3.1-37/miceadds/man/str_C.expand.grid.Rd | 4 miceadds-3.1-37/miceadds/man/subset_datlist.Rd | 4 miceadds-3.1-37/miceadds/man/sumpreserving.rounding.Rd | 4 miceadds-3.1-37/miceadds/man/systime.Rd | 4 miceadds-3.1-37/miceadds/man/tw.imputation.Rd | 4 miceadds-3.1-37/miceadds/man/with.miceadds.Rd | 8 miceadds-3.1-37/miceadds/man/write.mice.imputation.Rd | 6 miceadds-3.1-37/miceadds/man/write.pspp.Rd | 6 miceadds-3.1-37/miceadds/src/RcppExports.cpp | 2 120 files changed, 959 insertions(+), 1018 deletions(-)
Title: An R-Shiny Application for Smith's Mean Measure of Divergence
(MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>)
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 2.5.2 dated 2018-10-29 and 2.5.3 dated 2019-03-18
DESCRIPTION | 13 +++++++------ LICENSE |only MD5 | 9 ++++++--- NEWS.md |only README.md |only inst/AnthropMMDShinyApp/ui.R | 4 ++-- man/AnthropMMD-package.Rd | 6 +++--- 7 files changed, 18 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-28 0.5
Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming
to complement existing R packages. The functionality includes among others
multidimensional compensatory and noncompensatory IRT models
(Reckase, 2009, <doi:10.1007/978-0-387-89976-3>),
MCMC for hierarchical IRT models and testlet models
(Fox, 2010, <doi:10.1007/978-1-4419-0742-4>),
NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>),
Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>;
Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>),
faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011,
<doi:10.1111/j.1745-3984.2011.00143.x>),
ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>),
DETECT statistic (Stout, Habing, Douglas & Kim, 1996,
<doi:10.1177/014662169602000403>), local structural equation modeling
(LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016,
<doi:10.1080/00273171.2016.1142856>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 3.2-39 dated 2019-02-08 and 3.3-26 dated 2019-03-18
sirt-3.2-39/sirt/R/MAR_normalized.R |only sirt-3.2-39/sirt/R/btm_fit.R |only sirt-3.3-26/sirt/DESCRIPTION | 16 - sirt-3.3-26/sirt/MD5 | 91 +++++---- sirt-3.3-26/sirt/NAMESPACE | 11 - sirt-3.3-26/sirt/R/RcppExports.R | 2 sirt-3.3-26/sirt/R/Rhat_sirt.R | 39 ++-- sirt-3.3-26/sirt/R/btm.R | 51 ++--- sirt-3.3-26/sirt/R/btm_fit_combine_tables.R | 5 sirt-3.3-26/sirt/R/btm_fit_statistics.R |only sirt-3.3-26/sirt/R/btm_sim.R |only sirt-3.3-26/sirt/R/class.accuracy.rasch.R | 33 +-- sirt-3.3-26/sirt/R/data.wide2long.R | 14 - sirt-3.3-26/sirt/R/invariance_alignment_cfa_config.R | 14 + sirt-3.3-26/sirt/R/invariance_alignment_cfa_config_estimate.R | 12 - sirt-3.3-26/sirt/R/invariance_alignment_constraints.R | 7 sirt-3.3-26/sirt/R/invariance_alignment_constraints_summary_print_item_summary.R | 6 sirt-3.3-26/sirt/R/invariance_alignment_find_parameter_constraints.R | 23 +- sirt-3.3-26/sirt/R/invgamma2.R | 23 -- sirt-3.3-26/sirt/R/linking_haberman_als_residual_weights.R | 4 sirt-3.3-26/sirt/R/lsem.estimate.R | 32 +-- sirt-3.3-26/sirt/R/lsem.permutationTest.R | 5 sirt-3.3-26/sirt/R/lsem_define_lavaan_est_fun.R |only sirt-3.3-26/sirt/R/lsem_fitsem.R | 53 ++--- sirt-3.3-26/sirt/R/lsem_fitsem_raw_data_define_pseudo_weights.R |only sirt-3.3-26/sirt/R/lsem_fitsem_raw_data_lavaan_survey.R |only sirt-3.3-26/sirt/R/lsem_local_weights.R |only sirt-3.3-26/sirt/R/lsem_residualize.R | 47 +--- sirt-3.3-26/sirt/R/lsem_weighted_cov.R | 6 sirt-3.3-26/sirt/R/mad_normalized.R |only sirt-3.3-26/sirt/R/qmc.nodes.R | 3 sirt-3.3-26/sirt/R/read.fwf2.R | 17 - sirt-3.3-26/sirt/R/sirt_trim_increment.R |only sirt-3.3-26/sirt/R/summary.btm.R | 28 +- sirt-3.3-26/sirt/R/summary.invariance_alignment_constraints.R | 8 sirt-3.3-26/sirt/R/summary.lsem.R | 8 sirt-3.3-26/sirt/R/summary.lsem.permutationTest.R | 7 sirt-3.3-26/sirt/R/truescore.irt.R | 59 +----- sirt-3.3-26/sirt/R/truescore_irt_irf.R |only sirt-3.3-26/sirt/R/wle.rasch.R | 93 ++++----- sirt-3.3-26/sirt/R/write.format2.R | 15 - sirt-3.3-26/sirt/R/write.fwf2.R | 61 ++---- sirt-3.3-26/sirt/build/partial.rdb |binary sirt-3.3-26/sirt/inst/NEWS | 32 +++ sirt-3.3-26/sirt/man/R2conquest.Rd | 6 sirt-3.3-26/sirt/man/btm.Rd | 75 +++++++ sirt-3.3-26/sirt/man/class.accuracy.rasch.Rd | 6 sirt-3.3-26/sirt/man/invariance.alignment.Rd | 17 + sirt-3.3-26/sirt/man/linking.haebara.Rd | 4 sirt-3.3-26/sirt/man/lsem.estimate.Rd | 96 +++++++++- sirt-3.3-26/sirt/man/noharm.sirt.Rd | 6 sirt-3.3-26/sirt/src/RcppExports.cpp | 2 52 files changed, 603 insertions(+), 434 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.0.2 dated 2019-03-07 and 2.0.3 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/phyltree_paths.R | 5 +++++ man/drawPhylProcess.Rd | 5 +++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Amos Donald D. [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 2.3 dated 2019-02-21 and 2.3.1 dated 2019-03-18
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/dfunctions.R | 34 ++++++++++++---------------------- 3 files changed, 19 insertions(+), 29 deletions(-)
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth <nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>
with contributions by Simone Langhans and Christian Michel
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.2.1 dated 2018-09-28 and 1.2.2 dated 2019-03-18
DESCRIPTION | 8 MD5 | 32 R/lake.morphol.2016.r | 378 ++--- R/msk.macrophytes.2017.doc.R | 633 +++++--- R/msk.macrophytes.2017.prepare.data.R | 291 ++- R/msk.macrophytes.2017.read.compile.evaluate.R | 78 - R/msk.morphol.1998.r | 64 data/ecoval_data.RData |binary inst/NEWS | 18 inst/ecoval.dictionaries.default.dat | 1871 +++++++++++++++---------- inst/msk.macrophytes.2017_ListTaxa.dat | 802 +++++----- man/ecoval-package.Rd | 4 man/figures/lakemorphol2016.pdf |binary man/figures/lakemorphol2016.png |binary man/figures/lakemorphol2016French.pdf |binary man/figures/lakemorphol2016German.pdf |binary man/lake.morphol.2016.read.attrib.Rd | 20 17 files changed, 2446 insertions(+), 1753 deletions(-)
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>
Diff between distances versions 0.1.5 dated 2018-12-12 and 0.1.7 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ R/input_check.R | 2 ++ src/libann/Makefile | 2 +- src/nn_search_ann.cpp | 6 +++--- tests/testthat/test_distance_matrix.R | 5 +++++ tests/testthat/test_input_check.R | 2 ++ 8 files changed, 34 insertions(+), 15 deletions(-)
Title: Anomaly Detection with Normal Probability Functions
Description: Implements anomaly detection as binary classification for cross-sectional data. Uses maximum likelihood estimates and normal probability functions to classify observations as anomalous. The method is presented in the following lecture from the Machine Learning course by Andrew Ng: <https://www.coursera.org/learn/machine-learning/lecture/C8IJp/algorithm/>, and is also described in: Aleksandar Lazarevic, Levent Ertoz, Vipin Kumar, Aysel Ozgur, Jaideep Srivastava (2003) <doi:10.1137/1.9781611972733.3>.
Author: Dmitriy Bolotov [aut, cre]
Maintainer: Dmitriy Bolotov <dbolotov@live.com>
Diff between amelie versions 0.2.0 dated 2018-04-08 and 0.2.1 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- build/vignette.rds |binary inst/doc/amelie-introduction.html | 27 ++++++++++++++++++++++++++- man/ad.Rd | 4 ++-- man/predict.ad.Rd | 4 ++-- tests/testthat/test_ad.R | 8 ++++++++ tests/testthat/test_predict.ad.R | 3 +++ tests/testthat/test_utils.R | 2 ++ 10 files changed, 61 insertions(+), 19 deletions(-)
Title: Platform for EDGAR Filing Management and Textual Analysis
Description: In the USA, companies file different forms with the U.S.
Securities and Exchange Commission (SEC) through EDGAR (Electronic
Data Gathering, Analysis, and Retrieval system). The EDGAR
database automated system collects all the different necessary
filings and makes it publicly available. Investors, regulators,
and researchers often require these forms for various purposes.
This package helps in bulk data gathering and textual analysis of
EDGAR filings. It downloads filings from SEC server in bulk with
a single query. Additionally, it provides various useful functions:
extracts 8-K triggering events, extract "Business (Item 1)" and
"Management's Discussion and Analysis(Item 7)" sections of annual
statements, search filings for desired words, provides sentiment
measures, parse filing header information, and provides HTML
view of SEC filings.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil
<bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.9 dated 2017-06-04 and 2.0.0 dated 2019-03-18
edgar-1.0.9/edgar/R/getSentimentCount.R |only edgar-1.0.9/edgar/R/getWordHistogram.R |only edgar-1.0.9/edgar/R/getWordcloud.R |only edgar-1.0.9/edgar/R/getWordfrquency.R |only edgar-1.0.9/edgar/R/mergeCompustat.R |only edgar-1.0.9/edgar/data/negwords.txt.gz |only edgar-1.0.9/edgar/data/poswords.txt.gz |only edgar-1.0.9/edgar/man/getSentimentCount.Rd |only edgar-1.0.9/edgar/man/getWordHistogram.Rd |only edgar-1.0.9/edgar/man/getWordcloud.Rd |only edgar-1.0.9/edgar/man/getWordfrquency.Rd |only edgar-1.0.9/edgar/man/mergeCompustat.Rd |only edgar-1.0.9/edgar/man/negwords.Rd |only edgar-1.0.9/edgar/man/poswords.Rd |only edgar-2.0.0/edgar/DESCRIPTION | 38 +-- edgar-2.0.0/edgar/MD5 | 50 ++-- edgar-2.0.0/edgar/NAMESPACE | 23 + edgar-2.0.0/edgar/R/get8KItems.R |only edgar-2.0.0/edgar/R/getBusinessDescr.R |only edgar-2.0.0/edgar/R/getDailyMaster.R | 235 +++++++++++--------- edgar-2.0.0/edgar/R/getFilingHeader.R |only edgar-2.0.0/edgar/R/getFilingInfo.R | 126 ++++++++-- edgar-2.0.0/edgar/R/getFilings.R | 303 +++++++++++++++----------- edgar-2.0.0/edgar/R/getFilingsHTML.R |only edgar-2.0.0/edgar/R/getMasterIndex.R | 233 ++++++++++--------- edgar-2.0.0/edgar/R/getMgmtDisc.R |only edgar-2.0.0/edgar/R/getSentiment.R |only edgar-2.0.0/edgar/R/searchFilings.R |only edgar-2.0.0/edgar/data/LMMasterDictionary.rda |only edgar-2.0.0/edgar/man/LMMasterDictionary.Rd |only edgar-2.0.0/edgar/man/get8KItems.Rd |only edgar-2.0.0/edgar/man/getBusinDescr.Rd |only edgar-2.0.0/edgar/man/getDailyMaster.Rd | 19 - edgar-2.0.0/edgar/man/getFilingHeader.Rd |only edgar-2.0.0/edgar/man/getFilingInfo.Rd | 37 ++- edgar-2.0.0/edgar/man/getFilings.Rd | 56 ++-- edgar-2.0.0/edgar/man/getFilingsHTML.Rd |only edgar-2.0.0/edgar/man/getMasterIndex.Rd | 42 +-- edgar-2.0.0/edgar/man/getMgmtDisc.Rd |only edgar-2.0.0/edgar/man/getSentiment.Rd |only edgar-2.0.0/edgar/man/searchFilings.Rd |only 41 files changed, 693 insertions(+), 469 deletions(-)
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points. Two methods make use of dynamic
programming and pruning, with no distributional
assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods
are included. All methods return the set of estimated change-
points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Wenyu Zhang <wz258@cornell.edu>
Diff between ecp versions 3.1.0 dated 2017-12-15 and 3.1.1 dated 2019-03-18
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 3 ++- NEWS | 6 ++++++ R/energyChangePoint.R | 10 ++++++++++ R/kernelCPA.R |only build/vignette.rds |binary man/kernelCPA.rd |only src/kernelcpa.cpp |only 9 files changed, 30 insertions(+), 10 deletions(-)
Title: Balance Check for Multiple Covariates in Matched Observational
Studies
Description: Two practical tests are provided for assessing whether multiple covariates in a treatment group and a matched control group are balanced in observational studies.
Author: Hao Chen and Dylan Small
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between BalanceCheck versions 0.1 dated 2016-09-15 and 0.2 dated 2019-03-18
DESCRIPTION | 8 - MD5 | 13 +-- R/BalanceCheck.r | 183 ++++++++++++++++++++++++++++---------------- man/BalanceCheck-package.Rd | 2 man/CrossMST.Rd | 7 - man/CrossNN.Rd | 5 - man/getD.Rd | 2 man/getDk.Rd |only 8 files changed, 138 insertions(+), 82 deletions(-)