Title: Inference and Prediction in an Illness-Death Model
Description: Newly developed methods for the estimation of several probabilities
in an illness-death model. The package can be used to obtain nonparametric and
semiparametric estimates for: transition probabilities, occupation probabilities,
cumulative incidence function and the sojourn time distributions.
Additionally, it is possible to fit proportional hazards regression models
in each transition of the Illness-Death Model. Several auxiliary
functions are also provided which can be used for marginal
estimation of the survival functions.
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between survidm versions 1.0.0 dated 2017-10-11 and 1.1.0 dated 2018-03-17
DESCRIPTION | 8 +- MD5 | 10 +-- R/CIF.R | 150 +++++++++++++++++++-------------------------- R/CIF_ini.R | 180 ++++++++++++++++++++++++++++-------------------------- build/partial.rdb |binary man/CIF.Rd | 16 ++++ 6 files changed, 182 insertions(+), 182 deletions(-)
Title: An R Wrapper of the 'Inform' C Library for Information Analysis
of Complex Systems
Description: An R wrapper of the 'Inform' v1.0.0 C library for performing
information analysis of complex systems. As for the 'Inform' library, 'rinform' is
structured around the concepts of: 1) discrete empirical probability distributions
which form the basis for all of the information-theoretic measures; 2) classic
information-theoretic measures built upon empirical distributions (e.g., Shannon entropy,
mutual information, cross entropy); and 3) advanced measures of information dynamics
for time series (e.g., transfer entropy, active information, evidence of integration).
In addition to the core components, 'rinform' also provides a collection of utilities to
manipulate time series (e.g., binning of continuous values, black-boxing of time series).
Author: Gabriele Valentini [aut, cre, cph],
Douglas G. Moore [ctb, cph]
Maintainer: Gabriele Valentini <gvalent3@asu.edu>
Diff between rinform versions 1.0.0 dated 2018-03-13 and 1.0.1 dated 2018-03-17
DESCRIPTION | 27 ++-- LICENSE | 3 MD5 | 161 ++++++++++++++--------------- NEWS.md |only R/activeinfo.R | 6 - R/binning.R | 6 - R/blackbox.R | 6 - R/blockentropy.R | 6 - R/check_parameters.R | 16 ++ R/coalesce.R | 6 - R/conditionalentropy.R | 6 - R/crossentropy.R | 6 - R/dist.R | 6 - R/effectiveinfo.R | 6 - R/encoding.R | 6 - R/entropyrate.R | 6 - R/excessentropy.R | 6 - R/infoflow.R | 6 - R/integrationevidence.R | 6 - R/mutualinfo.R | 6 - R/partitioning.R | 6 - R/predictiveinfo.R | 6 - R/relativeentropy.R | 6 - R/rinfom.R | 8 - R/separableinfo.R | 6 - R/seriestotpm.R | 6 - R/shannon.R | 6 - R/transferentropy.R | 6 - README.md | 23 ++-- inst/doc/rinform-vignette.Rmd | 7 - inst/doc/rinform-vignette.html | 19 +-- src/inform-1.0.0/Makevars | 27 ++++ src/inform-1.0.0/src/predictive_info.c | 10 + src/rinform_active_info.c | 5 src/rinform_binning.c | 5 src/rinform_black_box.c | 9 + src/rinform_block_entropy.c | 5 src/rinform_coalesce.c | 5 src/rinform_conditional_entropy.c | 5 src/rinform_cross_entropy.c | 5 src/rinform_dist.c | 5 src/rinform_effective_info.c | 5 src/rinform_encoding.c | 5 src/rinform_entropyrate.c | 5 src/rinform_excess_entropy.c | 5 src/rinform_info_flow.c | 5 src/rinform_init.c | 5 src/rinform_init.h | 6 + src/rinform_integration_evidence.c | 9 + src/rinform_mutual_info.c | 5 src/rinform_partitioning.c | 5 src/rinform_predictive_info.c | 5 src/rinform_relativeentropy.c | 5 src/rinform_separable_info.c | 5 src/rinform_series_to_tpm.c | 5 src/rinform_shannon.c | 5 src/rinform_transfer_entropy.c | 5 tests/testthat.R | 5 tests/testthat/test_active_info.R | 5 tests/testthat/test_binning.R | 5 tests/testthat/test_black_box.R | 5 tests/testthat/test_black_box_parts.R | 5 tests/testthat/test_block_entropy.R | 5 tests/testthat/test_coalesce.R | 5 tests/testthat/test_conditional_entropy.R | 5 tests/testthat/test_cross_entropy.R | 5 tests/testthat/test_dist.R | 5 tests/testthat/test_effective_info.R | 5 tests/testthat/test_encoding.R | 5 tests/testthat/test_entropy_rate.R | 5 tests/testthat/test_excess_entropy.R | 5 tests/testthat/test_info_flow.R | 5 tests/testthat/test_integration_evidence.R | 5 tests/testthat/test_mutual_info.R | 5 tests/testthat/test_partitioning.R | 5 tests/testthat/test_predictive_info.R | 10 + tests/testthat/test_relative_entropy.R | 5 tests/testthat/test_separable_info.R | 5 tests/testthat/test_series_to_tpm.R | 5 tests/testthat/test_shannon.R | 5 tests/testthat/test_transfer_entropy.R | 5 vignettes/rinform-vignette.Rmd | 7 - 82 files changed, 488 insertions(+), 206 deletions(-)
Title: Parallel Utilities for Lambda Selection along a Regularization
Path
Description: Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.
Author: Zachary Kurtz [aut, cre],
Christian Müller [aut, ctb]
Maintainer: Zachary Kurtz <zdkurtz@gmail.com>
Diff between pulsar versions 0.3.1 dated 2018-03-01 and 0.3.2 dated 2018-03-17
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 9 +++++++++ R/batchPulsarSelect.R | 2 +- build/vignette.rds |binary inst/doc/other-criteria.html | 4 ++-- inst/doc/pulsar.html | 2 +- man/batch.pulsar.Rd | 2 +- tests/testthat/test_batchtools.R | 8 +++----- 9 files changed, 28 insertions(+), 21 deletions(-)
Title: Demographic Modelling Using Projection Matrices
Description: Tools for modelling populations and demography using matrix projection models,
with deterministic and stochastic model implementations. Includes population projection,
indices of short- and long-term population size and growth, perturbation analysis,
convergence to stability or stationarity, and diagnostic and manipulation tools.
Author: Iain Stott [aut, cre],
Dave Hodgson [aut],
Stuart Townley [aut],
Stephen Ellner [ctb]
Maintainer: Iain Stott <iainmstott@gmail.com>
Diff between popdemo versions 0.2-3 dated 2016-05-18 and 1.3-0 dated 2018-03-17
popdemo-0.2-3/popdemo/R/Cohen.cumulative.R |only popdemo-0.2-3/popdemo/R/Keyfitz.delta.R |only popdemo-0.2-3/popdemo/R/convergence.time.R |only popdemo-0.2-3/popdemo/R/firststepatt.R |only popdemo-0.2-3/popdemo/R/inertia.tfa.R |only popdemo-0.2-3/popdemo/R/inertia.tfamatrix.R |only popdemo-0.2-3/popdemo/R/inertia.tfsens.R |only popdemo-0.2-3/popdemo/R/inertia.tfsensmatrix.R |only popdemo-0.2-3/popdemo/R/is.matrix_ergodic.R |only popdemo-0.2-3/popdemo/R/is.matrix_irreducible.R |only popdemo-0.2-3/popdemo/R/is.matrix_primitive.R |only popdemo-0.2-3/popdemo/R/minCS.R |only popdemo-0.2-3/popdemo/R/plot.projection.R |only popdemo-0.2-3/popdemo/R/plot.tfa.R |only popdemo-0.2-3/popdemo/R/plot.tfamatrix.R |only popdemo-0.2-3/popdemo/R/print.projection.R |only popdemo-0.2-3/popdemo/R/print.tfa.R |only popdemo-0.2-3/popdemo/R/print.tfamatrix.R |only popdemo-0.2-3/popdemo/R/projection.distance.R |only popdemo-0.2-3/popdemo/R/reactivity.R |only popdemo-0.2-3/popdemo/R/tf.R |only popdemo-0.2-3/popdemo/R/tfa.R |only popdemo-0.2-3/popdemo/R/tfamatrix.R |only popdemo-0.2-3/popdemo/R/tfsens.R |only popdemo-0.2-3/popdemo/R/tfsensmatrix.R |only popdemo-0.2-3/popdemo/data/Tort.rda |only popdemo-0.2-3/popdemo/demo |only popdemo-0.2-3/popdemo/man/Cohen.cumulative.Rd |only popdemo-0.2-3/popdemo/man/Keyfitz.delta.Rd |only popdemo-0.2-3/popdemo/man/convergence.time.Rd |only popdemo-0.2-3/popdemo/man/firststepatt.Rd |only popdemo-0.2-3/popdemo/man/inertia.tfa.Rd |only popdemo-0.2-3/popdemo/man/inertia.tfamatrix.Rd |only popdemo-0.2-3/popdemo/man/inertia.tfsens.Rd |only popdemo-0.2-3/popdemo/man/is.matrix_ergodic.Rd |only popdemo-0.2-3/popdemo/man/is.matrix_irreducible.Rd |only popdemo-0.2-3/popdemo/man/is.matrix_primitive.Rd |only popdemo-0.2-3/popdemo/man/minCS.Rd |only popdemo-0.2-3/popdemo/man/plot.projection.Rd |only popdemo-0.2-3/popdemo/man/plot.tfamatrix.Rd |only popdemo-0.2-3/popdemo/man/projection.distance.Rd |only popdemo-0.2-3/popdemo/man/reactivity.Rd |only popdemo-0.2-3/popdemo/man/tf.Rd |only popdemo-0.2-3/popdemo/man/tfa.Rd |only popdemo-0.2-3/popdemo/man/tfamatrix.Rd |only popdemo-0.2-3/popdemo/man/tfsens.Rd |only popdemo-1.3-0/popdemo/ChangeLog | 104 +++ popdemo-1.3-0/popdemo/DESCRIPTION | 36 - popdemo-1.3-0/popdemo/MD5 | 167 ++--- popdemo-1.3-0/popdemo/NAMESPACE | 110 ++- popdemo-1.3-0/popdemo/R/CohenD.R |only popdemo-1.3-0/popdemo/R/KeyfitzD.R |only popdemo-1.3-0/popdemo/R/Kreiss.R | 92 ++ popdemo-1.3-0/popdemo/R/Matlab2R.R | 40 + popdemo-1.3-0/popdemo/R/R2Matlab.R | 44 + popdemo-1.3-0/popdemo/R/S3-plot.tfa.R |only popdemo-1.3-0/popdemo/R/S3-plot.tfam.R |only popdemo-1.3-0/popdemo/R/S3-print.R |only popdemo-1.3-0/popdemo/R/S4-ProjectionClass.R |only popdemo-1.3-0/popdemo/R/blockmatrix.R | 109 ++- popdemo-1.3-0/popdemo/R/convt.R |only popdemo-1.3-0/popdemo/R/data.R |only popdemo-1.3-0/popdemo/R/dr.R | 55 + popdemo-1.3-0/popdemo/R/eig.R |only popdemo-1.3-0/popdemo/R/elas.R | 47 + popdemo-1.3-0/popdemo/R/hidden-minCS.R |only popdemo-1.3-0/popdemo/R/hidden-rmc.R |only popdemo-1.3-0/popdemo/R/hidden-tf.R |only popdemo-1.3-0/popdemo/R/inertia.R | 87 ++ popdemo-1.3-0/popdemo/R/isErgodic.R |only popdemo-1.3-0/popdemo/R/isIrreducible.R |only popdemo-1.3-0/popdemo/R/isPrimitive.R |only popdemo-1.3-0/popdemo/R/maxamp.R | 112 +++ popdemo-1.3-0/popdemo/R/maxatt.R | 109 +++ popdemo-1.3-0/popdemo/R/popdemo-deprecated.R |only popdemo-1.3-0/popdemo/R/popdemo-onAttach.R |only popdemo-1.3-0/popdemo/R/popdemo-package.R |only popdemo-1.3-0/popdemo/R/project.R | 645 ++++++++++++++++++--- popdemo-1.3-0/popdemo/R/projectionD.R |only popdemo-1.3-0/popdemo/R/reac.R |only popdemo-1.3-0/popdemo/R/sens.R | 48 + popdemo-1.3-0/popdemo/R/stoch.R |only popdemo-1.3-0/popdemo/R/tfa_inertia.R |only popdemo-1.3-0/popdemo/R/tfa_lambda.R |only popdemo-1.3-0/popdemo/R/tfam_inertia.R |only popdemo-1.3-0/popdemo/R/tfam_lambda.R |only popdemo-1.3-0/popdemo/R/tfs_inertia&tfsm_inertia.R |only popdemo-1.3-0/popdemo/R/tfs_lambda&tfsm_lambda.R |only popdemo-1.3-0/popdemo/R/truelambda.R | 86 ++ popdemo-1.3-0/popdemo/build |only popdemo-1.3-0/popdemo/data/Pbear.R |only popdemo-1.3-0/popdemo/data/Tort.R |only popdemo-1.3-0/popdemo/inst |only popdemo-1.3-0/popdemo/man/CohenD.Rd |only popdemo-1.3-0/popdemo/man/KeyfitzD.Rd |only popdemo-1.3-0/popdemo/man/Kreiss.Rd | 161 ++--- popdemo-1.3-0/popdemo/man/Matlab2R.Rd | 70 +- popdemo-1.3-0/popdemo/man/Pbear.Rd |only popdemo-1.3-0/popdemo/man/Projection-class.Rd |only popdemo-1.3-0/popdemo/man/Projection-plots.Rd |only popdemo-1.3-0/popdemo/man/R2Matlab.Rd | 76 +- popdemo-1.3-0/popdemo/man/Tort.Rd | 63 +- popdemo-1.3-0/popdemo/man/blockmatrix.Rd | 80 +- popdemo-1.3-0/popdemo/man/convt.Rd |only popdemo-1.3-0/popdemo/man/dr.Rd | 100 +-- popdemo-1.3-0/popdemo/man/eigs.Rd |only popdemo-1.3-0/popdemo/man/elas.Rd | 82 +- popdemo-1.3-0/popdemo/man/inertia.Rd | 168 ++--- popdemo-1.3-0/popdemo/man/isErgodic.Rd |only popdemo-1.3-0/popdemo/man/isIrreducible.Rd |only popdemo-1.3-0/popdemo/man/isPrimitive.Rd |only popdemo-1.3-0/popdemo/man/maxamp.Rd | 226 +++---- popdemo-1.3-0/popdemo/man/maxatt.Rd | 225 +++---- popdemo-1.3-0/popdemo/man/plot.tfa.Rd | 119 +-- popdemo-1.3-0/popdemo/man/plot.tfam.Rd |only popdemo-1.3-0/popdemo/man/popdemo-deprecated.Rd |only popdemo-1.3-0/popdemo/man/popdemo-package.Rd | 150 ++-- popdemo-1.3-0/popdemo/man/project.Rd | 383 ++++++++---- popdemo-1.3-0/popdemo/man/projectionD.Rd |only popdemo-1.3-0/popdemo/man/reac.Rd |only popdemo-1.3-0/popdemo/man/sens.Rd | 90 +- popdemo-1.3-0/popdemo/man/stoch.Rd |only popdemo-1.3-0/popdemo/man/tfa_inertia.Rd |only popdemo-1.3-0/popdemo/man/tfa_lambda.Rd |only popdemo-1.3-0/popdemo/man/tfam_inertia.Rd |only popdemo-1.3-0/popdemo/man/tfam_lambda.Rd |only popdemo-1.3-0/popdemo/man/tfs_inertia.Rd |only popdemo-1.3-0/popdemo/man/tfs_lambda.Rd |only popdemo-1.3-0/popdemo/man/truelambda.Rd | 163 ++--- popdemo-1.3-0/popdemo/vignettes |only 130 files changed, 2776 insertions(+), 1271 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Zachary Fisher [ctb],
Cara Arizmendi [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.3-2 dated 2017-12-15 and 0.3-3 dated 2018-03-17
DESCRIPTION | 8 MD5 | 58 ++-- NAMESPACE | 76 ++--- R/gimme-pkg.R | 70 ++-- R/new_aggSEM.R | 266 +++++++++--------- R/new_funcs.R | 66 ++-- R/new_gimme.R | 283 ++++++++++---------- R/new_indSEM.R | 280 +++++++++---------- R/new_setup.R | 632 ++++++++++++++++++++++----------------------- man/aggSEM.Rd | 182 ++++++------ man/count.excellent.Rd | 36 +- man/determine.subgroups.Rd | 76 ++--- man/expand.grid.unique.Rd | 48 +-- man/final.org.Rd | 60 ++-- man/fit.model.Rd | 42 +- man/get.params.Rd | 52 +-- man/gimme-package.Rd | 70 ++-- man/gimmeSEM.Rd | 336 +++++++++++------------ man/highest.mi.Rd | 74 ++--- man/indSEM.Rd | 200 +++++++------- man/indiv.search.Rd | 48 +-- man/lowest.z.Rd | 62 ++-- man/prune.paths.Rd | 92 +++--- man/recode.vars.Rd | 46 +-- man/return.mis.Rd | 38 +- man/return.zs.Rd | 38 +- man/search.paths.Rd | 100 +++---- man/simData.Rd | 30 +- man/ts.Rd | 30 +- man/w2e.Rd | 36 +- 30 files changed, 1734 insertions(+), 1701 deletions(-)
Title: Nominal Dates, Times, and Durations
Description: Provides methods for working with nominal dates, times, and
durations. Base R has sophisticated facilities for handling time, but these
can give unexpected results if, for example, timezone is not handled properly.
This package provides a more casual approach to support cases which
do not require rigorous treatment. It systematically deconstructs the
concepts origin and timezone, and de-emphasizes the display of seconds. It
also converts among nominal durations such as seconds, hours, days, and weeks.
See '?datetime' and '?duration' for examples. Adapted from 'metrumrg'
<http://r-forge.r-project.org/R/?group_id=1215>.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between datetime versions 0.1.2 dated 2017-05-03 and 0.1.3 dated 2018-03-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 5 +++++ man/as.second.Rd | 1 - man/temporal.Rd | 1 - man/toSAS.Rd | 1 - 6 files changed, 13 insertions(+), 11 deletions(-)
Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kent Russell [aut, cre] (R interface),
Gregor Aisch [aut, cph] (d3-jetpack creator,
https://github.com/gka/d3-jetpack),
Adam Pearce [aut] (core contributor to d3-jetpack),
Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 0.7.1 dated 2017-11-22 and 0.8.0 dated 2018-03-17
DESCRIPTION | 8 +++---- MD5 | 26 ++++++++++++++--------- NAMESPACE | 1 NEWS.md | 6 +++++ R/dependencies.R | 46 +++++++++++++++++++++++++++++++++++++----- inst/www/d3/v4/API.md | 4 ++- inst/www/d3/v4/dist/d3.min.js | 4 +-- inst/www/d3/v5 |only man/d3_dep_jetpack.Rd | 4 +++ man/d3_dep_v3.Rd | 9 +++++++- man/d3_dep_v4.Rd | 9 +++++++- man/d3_dep_v5.Rd |only tests/testthat/test_deps.R | 7 ++++++ 13 files changed, 100 insertions(+), 24 deletions(-)
Title: World Population Prospects 2017
Description: Provides data from the United Nation's World Population Prospects 2017.
Author: United Nations Population Division
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wpp2017 versions 1.1-2 dated 2018-02-08 and 1.2-0 dated 2018-03-17
ChangeLog | 7 +++++++ DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++------- data/datalist | 4 ++++ data/pop.R | 25 +++++++++---------------- data/popFT.R |only data/popFTproj.R |only data/popMT.R |only data/popMTproj.R |only data/popproj.R | 23 +++++++++-------------- man/PopByAge.Rd | 19 ++++++++++++++++--- man/wpp2017-package.Rd | 5 +++-- 12 files changed, 64 insertions(+), 47 deletions(-)
Title: Calculate Task Split Half Reliability Estimates
Description: A series of functions to calculate the split
half reliability of RT based tasks. The core function performs a Monte Carlo
procedure to process a user defined number of random splits in order to
provide a better reliability estimate. The current functions target the dot-
probe task, however, can be modified for other tasks.
Author: Sam Parsons [aut, cre]
Maintainer: Sam Parsons <sam.parsons@psy.ox.ac.uk>
Diff between splithalf versions 0.2.0 dated 2017-04-26 and 0.3.1 dated 2018-03-17
splithalf-0.2.0/splithalf/R/DPsplithalf.R |only splithalf-0.2.0/splithalf/R/DPsplithalfABM.R |only splithalf-0.2.0/splithalf/R/DPsplithalfall.R |only splithalf-0.2.0/splithalf/R/TSTsplithalf.R |only splithalf-0.2.0/splithalf/man/DPsplithalf.ABM.Rd |only splithalf-0.2.0/splithalf/man/DPsplithalf.Rd |only splithalf-0.2.0/splithalf/man/DPsplithalf.all.Rd |only splithalf-0.2.0/splithalf/man/TSTsplithalf.Rd |only splithalf-0.3.1/splithalf/DESCRIPTION | 10 splithalf-0.3.1/splithalf/MD5 | 37 splithalf-0.3.1/splithalf/NAMESPACE | 20 splithalf-0.3.1/splithalf/R/splithalf.R | 259 ++-- splithalf-0.3.1/splithalf/R/splithalf_ACC.R |only splithalf-0.3.1/splithalf/R/splithalf_ACC_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_ACC_diff_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_diff_diff.R |only splithalf-0.3.1/splithalf/build/vignette.rds |binary splithalf-0.3.1/splithalf/inst/CITATION |only splithalf-0.3.1/splithalf/inst/doc/DPsplithalf-vignette.R | 23 splithalf-0.3.1/splithalf/inst/doc/DPsplithalf-vignette.Rmd | 26 splithalf-0.3.1/splithalf/inst/doc/DPsplithalf-vignette.html | 684 ++++++++--- splithalf-0.3.1/splithalf/man/splithalf.Rd | 11 splithalf-0.3.1/splithalf/man/splithalf_ACC.Rd |only splithalf-0.3.1/splithalf/man/splithalf_ACC_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_ACC_diff_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_diff_diff.Rd |only splithalf-0.3.1/splithalf/vignettes/DPsplithalf-vignette.Rmd | 26 29 files changed, 806 insertions(+), 290 deletions(-)
Title: Polyhedra Database
Description: A polyhedra database scraped from various sources as R6 objects and 'rgl' visualizing capabilities.
Author: Alejandro Baranek [aut, com, cre, cph],
Leonardo Belen [aut, com, cph]
Maintainer: Alejandro Baranek <abaranek@dc.uba.ar>
Diff between Rpolyhedra versions 0.2.2 dated 2018-03-15 and 0.2.3 dated 2018-03-17
Rpolyhedra-0.2.2/Rpolyhedra/inst/extdata/polyhedra.complexity.csv |only Rpolyhedra-0.2.3/Rpolyhedra/DESCRIPTION | 6 Rpolyhedra-0.2.3/Rpolyhedra/MD5 | 25 - Rpolyhedra-0.2.3/Rpolyhedra/R/db-lib.R | 42 +-- Rpolyhedra-0.2.3/Rpolyhedra/R/ledger-lib.R | 139 +++++++--- Rpolyhedra-0.2.3/Rpolyhedra/R/polyhedra-lib.R | 16 - Rpolyhedra-0.2.3/Rpolyhedra/R/zzz.R | 2 Rpolyhedra-0.2.3/Rpolyhedra/inst/doc/Rpolyhedra.Rmd | 2 Rpolyhedra-0.2.3/Rpolyhedra/inst/doc/Rpolyhedra.html | 2 Rpolyhedra-0.2.3/Rpolyhedra/inst/extdata/polyhedra.RDS |binary Rpolyhedra-0.2.3/Rpolyhedra/inst/extdata/polyhedra.preloaded.data.csv |only Rpolyhedra-0.2.3/Rpolyhedra/man/ScraperLedger.class.Rd | 12 Rpolyhedra-0.2.3/Rpolyhedra/man/getAvailablePolyhedra.Rd | 4 Rpolyhedra-0.2.3/Rpolyhedra/man/maxWithoutNA.Rd |only Rpolyhedra-0.2.3/Rpolyhedra/vignettes/Rpolyhedra.Rmd | 2 15 files changed, 154 insertions(+), 98 deletions(-)
Title: Subspace Clustering Based on Arbitrarily Oriented Projected
Cluster Generation
Description: Functions to perform subspace clustering and classification.
Author: Gero Szepannek
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between orclus versions 0.2-5 dated 2013-02-26 and 0.2-6 dated 2018-03-17
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NAMESPACE | 14 ++++++++------ man/orclass.Rd | 14 +++++++++----- man/orclus.Rd | 14 +++++++++----- man/predict.orclass.Rd | 11 +++++++---- man/predict.orclus.Rd | 3 ++- 7 files changed, 48 insertions(+), 34 deletions(-)
Title: Optimal Design of Experiments
Description: Several function related to Experimental Design are implemented here, see
"Optimal Experimental Design with R" by Rasch D. et. al (ISBN 9781439816974).
Author: Petr Simecek <simecek@gmail.com>,
Juergen Pilz <juergen.pilz@aau.at>,
Mingui Wang <mail.mwang@gmail.com>,
Albrecht Gebhardt <albrecht.gebhardt@aau.at>.
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between OPDOE versions 1.0-9 dated 2014-01-15 and 1.0-10 dated 2018-03-17
DESCRIPTION | 17 +++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 14 ++++++++++++++ data/cattle.rda |binary data/hadamard.table.rda |binary data/heights.rda |binary data/hemp.rda |binary 7 files changed, 29 insertions(+), 14 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) Use of CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.3.3 dated 2017-08-16 and 0.4.0 dated 2018-03-17
NonCompart-0.3.3/NonCompart/tests |only NonCompart-0.4.0/NonCompart/DESCRIPTION | 10 +-- NonCompart-0.4.0/NonCompart/MD5 | 35 ++++--------- NonCompart-0.4.0/NonCompart/NAMESPACE | 3 + NonCompart-0.4.0/NonCompart/R/DetSlope.R |only NonCompart-0.4.0/NonCompart/R/sNCA.R | 5 + NonCompart-0.4.0/NonCompart/R/tblNCA.R | 4 - NonCompart-0.4.0/NonCompart/inst/NEWS.Rd | 5 + NonCompart-0.4.0/NonCompart/inst/doc/NonCompart-manual.pdf |binary NonCompart-0.4.0/NonCompart/man/BestSlope.Rd | 2 NonCompart-0.4.0/NonCompart/man/DetSlope.Rd |only NonCompart-0.4.0/NonCompart/man/NonCompart-package.Rd | 2 NonCompart-0.4.0/NonCompart/man/sNCA.Rd | 3 - NonCompart-0.4.0/NonCompart/man/tblNCA.Rd | 3 - 14 files changed, 35 insertions(+), 37 deletions(-)
Title: Modelling Dispersion in GLM
Description: Functions for estimating Gaussian dispersion regression models (Aitkin, 1987 <doi:10.2307/2347792>), overdispersed binomial logit models (Williams, 1987 <doi:10.2307/2347977>), and overdispersed Poisson log-linear models (Breslow, 1984 <doi:10.2307/2347661>), using a quasi-likelihood approach.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between dispmod versions 1.1 dated 2012-02-13 and 1.2 dated 2018-03-17
dispmod-1.1/dispmod/CHANGES |only dispmod-1.1/dispmod/COPYING |only dispmod-1.1/dispmod/INDEX |only dispmod-1.1/dispmod/Misc |only dispmod-1.1/dispmod/data/holford.txt.gz |only dispmod-1.1/dispmod/data/minitab.txt.gz |only dispmod-1.1/dispmod/data/orobanche.txt.gz |only dispmod-1.1/dispmod/data/salmonellaTA98.txt.gz |only dispmod-1.2/dispmod/DESCRIPTION | 26 +++-- dispmod-1.2/dispmod/MD5 | 25 ++--- dispmod-1.2/dispmod/NAMESPACE | 10 +- dispmod-1.2/dispmod/R/dispmod.R | 113 +++++++++++++++---------- dispmod-1.2/dispmod/data/holford.txt |only dispmod-1.2/dispmod/data/minitab.txt |only dispmod-1.2/dispmod/data/orobanche.txt |only dispmod-1.2/dispmod/data/salmonellaTA98.txt |only dispmod-1.2/dispmod/inst |only dispmod-1.2/dispmod/man/glm.binomial.disp.Rd | 43 +++++---- dispmod-1.2/dispmod/man/glm.poisson.disp.Rd | 79 ++++++++++------- dispmod-1.2/dispmod/man/lm.disp.Rd | 86 +++++++++++-------- 20 files changed, 229 insertions(+), 153 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between tree versions 1.0-38 dated 2018-03-15 and 1.0-39 dated 2018-03-17
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/grow.c | 10 +++++----- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.6.3) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb],
Jeroen Ooms [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.2-16 dated 2017-11-21 and 1.2-18 dated 2018-03-17
ChangeLog | 85 ++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++--- MD5 | 38 ++++++++--------- R/Class-CRSx.R | 13 ++++++ R/make_EPSG.R | 7 ++- R/ogr.R | 28 ++++++++++--- R/ogr_sp.R | 17 +++++--- R/ogr_write.R | 18 ++++++-- build/vignette.rds |binary configure | 18 ++++---- inst/ChangeLog | 85 ++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary man/make_EPSG.Rd | 5 +- src/Makevars.win | 27 +++++++----- src/OGR_write.cpp | 36 +++++++++++----- src/projectit.cpp | 31 ++++++++++++++ tests/test_proj.R | 4 + tests/test_proj.Rout.save | 10 +++- tools/winlibs.R | 6 +- 20 files changed, 362 insertions(+), 84 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-07 1.1.1
2017-10-31 1.1.0
2017-05-17 1.0.0
2017-01-18 0.0.1
Title: Automatic Tail Recursion Optimisation
Description: Implements meta-programming functions for automatically
translating recursive functions into looping functions or trampolines.
Author: Thomas Mailund [aut, cre]
Maintainer: Thomas Mailund <mailund@birc.au.dk>
Diff between tailr versions 0.1.0 dated 2018-02-28 and 0.1.1 dated 2018-03-17
DESCRIPTION | 10 ++- MD5 | 28 +++++---- NEWS.md | 4 + R/loop-transformation.R | 48 +++++++++++----- R/user-defined-transformations.R | 38 +++++------- README.md | 63 +++++++++++++-------- man/can_loop_transform.Rd | 6 +- man/figures/README-unnamed-chunk-10-1.png |only man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-9-1.png |binary man/loop_transform.Rd | 5 + man/user_transform.Rd | 18 +----- man/user_transform_rec.Rd | 4 + tests/testthat/test-loop-transformation.R | 58 +++++++++++++++++++ tests/testthat/test-user-defined-transformations.R | 35 +++++++++++ 16 files changed, 218 insertions(+), 99 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.8.3 dated 2018-02-16 and 0.3.8.4 dated 2018-03-17
DESCRIPTION | 8 - MD5 | 68 ++++++++------- NAMESPACE | 2 R/ARMA.R | 24 ++--- R/ARMA_optim.R |only R/Causal_matrix.R | 5 - R/Causation.R | 37 +------- R/Normalization.R | 14 ++- R/Partial_Moments.R | 83 +++++++++---------- R/Partition_Map.R | 31 +++++-- R/Regression.R | 13 +- R/SD_Efficient_Set.R | 6 - R/Stack.R | 26 ++--- R/dy_dx.R | 2 R/gvload.R | 4 inst/doc/NNSvignette_Clustering_and_Regression.R | 22 ++--- inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 32 +++---- inst/doc/NNSvignette_Clustering_and_Regression.html | 60 +++++++------ inst/doc/NNSvignette_Correlation_and_Dependence.R | 6 - inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 14 +-- inst/doc/NNSvignette_Correlation_and_Dependence.html | 16 ++- inst/doc/NNSvignette_Forecasting.R | 27 ++++-- inst/doc/NNSvignette_Forecasting.Rmd | 51 +++++++++-- inst/doc/NNSvignette_Forecasting.html | 57 +++++++++---- inst/doc/NNSvignette_Partial_Moments.R | 4 inst/doc/NNSvignette_Partial_Moments.Rmd | 14 +-- inst/doc/NNSvignette_Partial_Moments.html | 27 +++--- man/NNS.ARMA.optim.Rd |only man/NNS.reg.Rd | 5 - man/NNS.stack.Rd | 8 - man/PM.matrix.Rd | 15 +-- man/dy.dx.Rd | 2 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 32 +++---- vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 14 +-- vignettes/NNSvignette_Forecasting.Rmd | 51 +++++++++-- vignettes/NNSvignette_Partial_Moments.Rmd | 14 +-- 36 files changed, 452 insertions(+), 342 deletions(-)
Title: Distribution of Largest Root for Single and Double Wishart
Settings
Description: Functions for hypothesis testing in single and double Wishart
settings, based on Roy's largest root. This test statistic is especially
useful in multivariate analysis. The computations are based on results by
Chiani (2014) <DOI:10.1016/j.jmva.2014.04.002> and Chiani (2016)
<DOI:10.1016/j.jmva.2015.10.007>. They use the fact that the CDF is related
to the Pfaffian of a matrix that can be computed in a finite number of
iterations. This package takes advantage of the Boost and Eigen C++ libraries
to perform multi-precision linear algebra.
Author: Maxime Turgeon [aut, cre]
Maintainer: Maxime Turgeon <maxime.turgeon@mail.mcgill.ca>
Diff between rootWishart versions 0.4.0 dated 2017-04-30 and 0.4.1 dated 2018-03-17
DESCRIPTION | 7 ++++--- MD5 | 17 ++++++++++------- NEWS.md | 4 ++++ R/RcppExports.R | 4 ++-- R/functions.R | 20 ++++++++++---------- man/largestRoot.Rd | 4 ++-- src/RcppExports.cpp | 4 ++-- src/init.c | 8 ++++---- tests |only 9 files changed, 38 insertions(+), 30 deletions(-)
Title: Obtain and Visualize Regulome-Gene Expression Correlations in
Cancer
Description: Builds a 'SQLite' database file of pre-calculated transcription
factor/microRNA-gene correlations (co-expression) in cancer from the
Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and
'miRCancerdb' databases (in press). Provides custom classes and functions
to query, tidy and plot the correlation data.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Diff between cRegulome versions 0.1.0 dated 2018-02-13 and 0.1.1 dated 2018-03-17
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 9 +++++++-- README.md | 15 +++++++++++---- inst/doc/case_study.R | 9 --------- inst/doc/case_study.Rmd | 10 ---------- inst/doc/case_study.html | 11 ++--------- vignettes/case_study.Rmd | 10 ---------- 8 files changed, 33 insertions(+), 57 deletions(-)