Title: Utilities for Convenient Extraction of Medical Image Metadata
Description: A collection of utilities for navigating medical image data. The DICOM and NIfTI formats
are supported. Functions provide simple interfaces to the data and metadata contained in these formats.
A particular emphasis on metadata allows simple conversion of image metadata to familiar R data structures
such as lists and data frames. Where possible, generic functions can silently process either DICOM or
NIfTI data. Additionally, image data can be extracted and viewed.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@ucdenver.edu>
Diff between radtools versions 1.0.3 dated 2019-01-16 and 1.0.4 dated 2019-03-13
DESCRIPTION | 9 MD5 | 26 + NEWS.md | 6 build/vignette.rds |binary inst/doc/oro_compare.R |only inst/doc/oro_compare.Rmd |only inst/doc/oro_compare.html |only inst/doc/radtools_usage.html | 40 +- tests/testthat/setup-dicomdata.R | 439 +++++++++++++++++++++++++------ tests/testthat/setup-niftidata.R | 243 +++++++++++++---- tests/testthat/test_image_import_dicom.R | 90 +++--- tests/testthat/test_image_import_nifti.R | 10 tests/testthat/test_metadata_dicom.R | 232 +++++++--------- tests/testthat/test_metadata_nifti.R | 25 - tests/testthat/test_view.R | 33 +- vignettes/oro_compare.Rmd |only 16 files changed, 792 insertions(+), 361 deletions(-)
Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdlocrand versions 0.3 dated 2018-03-15 and 0.4 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/rdlocrand_fun.R | 26 +++++++++++++------------- R/rdlocrand_package.R | 5 +++-- R/rdrandinf.R | 20 ++++++++++---------- R/rdrbounds.R | 4 ++-- R/rdsensitivity.R | 4 ++-- R/rdwinselect.R | 14 ++++++++------ 8 files changed, 49 insertions(+), 46 deletions(-)
Title: Mode Estimation
Description: Provides estimators of the mode of univariate
data or univariate distributions.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between modeest versions 2.3.2 dated 2018-10-30 and 2.3.3 dated 2019-03-13
DESCRIPTION | 16 ++-- MD5 | 58 ++++++++--------- NAMESPACE | 4 - NEWS.md | 12 ++- R/asselin.R | 6 - R/deal.ties.R | 3 R/distrMode.R | 12 +-- R/grenander.R | 14 ++-- R/hrm.R | 6 - R/hsm.R | 8 +- R/lientz.R | 6 - R/mlv.R | 167 +++++++++++++++++++++++++++++++-------------------- R/naive.R | 2 R/parzen.R | 93 +++++----------------------- R/reexports_statip.R | 13 --- R/tsybakov.R | 10 +-- R/venter.R | 57 ++++++++++------- R/vieu.R | 35 ++++------ README.md | 9 +- man/asselin.Rd | 2 man/grenander.Rd | 2 man/hrm.Rd | 2 man/hsm.Rd | 2 man/lientz.Rd | 2 man/mlv.Rd | 57 ++++++++--------- man/naive.Rd | 2 man/parzen.Rd | 15 +--- man/tsybakov.Rd | 8 +- man/venter.Rd | 33 +++++++--- man/vieu.Rd | 2 30 files changed, 328 insertions(+), 330 deletions(-)
Title: Path Algorithm for the General Fused Lasso Signal Approximator
Description: Implements a path algorithm for the Fused Lasso Signal Approximator.
For more details see the help files or the article by Hoefling (2009) <arXiv:0910.0526>.
Author: Holger Hoefling
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between flsa versions 1.05 dated 2013-03-23 and 1.5.1 dated 2019-03-13
flsa-1.05/flsa/inst |only flsa-1.05/flsa/src/init.cc |only flsa-1.5.1/flsa/DESCRIPTION | 15 ++++++------ flsa-1.5.1/flsa/MD5 | 36 ++++++++++++++-------------- flsa-1.5.1/flsa/NAMESPACE | 2 - flsa-1.5.1/flsa/R/FLSAGeneralInclude.R | 2 - flsa-1.5.1/flsa/man/flsa.Rd | 6 +++- flsa-1.5.1/flsa/src/FLSA.cc | 6 ++-- flsa-1.5.1/flsa/src/FLSAGeneral.cc | 6 ++-- flsa-1.5.1/flsa/src/FLSAGeneralMain.cc | 1 flsa-1.5.1/flsa/src/Groups.cc | 12 ++++++--- flsa-1.5.1/flsa/src/Groups.h | 9 ++++--- flsa-1.5.1/flsa/src/PenaltyGraph.cc | 4 +-- flsa-1.5.1/flsa/src/PenaltyGraph.h | 3 +- flsa-1.5.1/flsa/src/flsaBackwards.cc | 41 ++++++++++++++++++--------------- flsa-1.5.1/flsa/src/flsaBackwards.h | 10 ++++---- flsa-1.5.1/flsa/src/flsa_init.cc |only flsa-1.5.1/flsa/tests/test_package.R | 4 ++- flsa-1.5.1/flsa/tests/testthat |only 19 files changed, 87 insertions(+), 70 deletions(-)
Title: Visualizing Panel Data
Description: Visualizes panel data. It has two main functionalities: (1) it visualizes the treatment and missing-value statuses of each observation in a panel/time-series-cross-sectional (TSCS) dataset; and (2) it plots the outcome variable (either continuous or discrete) in a time-series fashion.
Author: Licheng Liu, Yiqing Xu
Maintainer: Yiqing Xu <yiqingxu@ucsd.edu>
Diff between panelView versions 1.0.5 dated 2018-08-20 and 1.1.2 dated 2019-03-13
DESCRIPTION | 14 LICENSE |only MD5 | 15 NAMESPACE | 7 R/panelView.R | 1488 +++++++++++++++++++++++------------------------ README.md | 8 data/panelView.RData |binary man/panelView-package.Rd | 2 man/panelView.Rd | 58 + 9 files changed, 814 insertions(+), 778 deletions(-)
Title: Oblique Random Forests for Right-Censored Time-to-Event Data
Description: Oblique random survival forests incorporate linear combinations of input variables into random survival forests (Ishwaran, 2008 <DOI:10.1214/08-AOAS169>). Regularized Cox proportional hazard models (Simon, 2016 <DOI:10.18637/jss.v039.i05>) are used to identify optimal linear combinations of input variables.
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <bcjaeger@uab.edu>
Diff between obliqueRSF versions 0.1.0 dated 2018-11-02 and 0.1.1 dated 2019-03-13
DESCRIPTION | 8 - MD5 | 24 +-- R/RcppExports.R | 214 +++++++++++++-------------- R/oblique_survival_forest_fit.R | 121 ++++++++------- R/oblique_survival_forest_predict.R | 7 README.md | 276 ++++++++++++++++-------------------- man/ORSF.Rd | 10 + man/figures/pdplot1-1.png |binary man/figures/vdplot1-1.png |binary man/figures/vdplot2-1.png |binary man/figures/vdplot3-1.png |binary src/ORSF.cpp | 178 ++++++++++++----------- src/RcppExports.cpp | 28 ++- 13 files changed, 436 insertions(+), 430 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>),
Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.18 dated 2018-07-06 and 1.19.2 dated 2019-03-13
DESCRIPTION | 12 ++-- MD5 | 18 +++--- NEWS | 39 ++++++++++++++ R/binPeaks-functions.R | 18 +++--- R/calibrateIntensity-methods.R | 2 R/determineWarpingFunctions-functions.R | 18 +++++- inst/doc/MALDIquant-intro.pdf |binary man/determineWarpingFunctions-functions.Rd | 7 ++ tests/testthat/test_binPeaks-functions.R | 9 +++ tests/testthat/test_determineWarpingFunctions-functions.R | 5 + 10 files changed, 98 insertions(+), 30 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo. The approximation
uses Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors and for
the comparison of predictive errors between models. The package also
provides methods for using stacking and other model weighting techniques
to average Bayesian predictive distributions.
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Yuling Yao [aut],
Paul-Christian Bürkner [ctb],
Ben Goodrich [ctb],
Juho Piironen [ctb],
Mans Magnusson [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 2.0.0 dated 2018-04-11 and 2.1.0 dated 2019-03-13
loo-2.0.0/loo/R/compare_models.R |only loo-2.1.0/loo/DESCRIPTION | 28 loo-2.1.0/loo/MD5 | 157 +- loo-2.1.0/loo/NAMESPACE | 12 loo-2.1.0/loo/NEWS.md | 24 loo-2.1.0/loo/R/E_loo.R | 10 loo-2.1.0/loo/R/compare.R |only loo-2.1.0/loo/R/datasets.R | 2 loo-2.1.0/loo/R/diagnostics.R | 6 loo-2.1.0/loo/R/effective_sample_sizes.R | 131 +- loo-2.1.0/loo/R/helpers.R | 22 loo-2.1.0/loo/R/kfold-generic.R |only loo-2.1.0/loo/R/kfold-helpers.R | 78 - loo-2.1.0/loo/R/loo-glossary.R |only loo-2.1.0/loo/R/loo-package.R | 5 loo-2.1.0/loo/R/loo.R | 38 loo-2.1.0/loo/R/loo_compare.R |only loo-2.1.0/loo/R/loo_model_weights.R | 2 loo-2.1.0/loo/R/print.R | 19 loo-2.1.0/loo/R/psis.R | 213 ++- loo-2.1.0/loo/R/psis_approximate_posterior.R |only loo-2.1.0/loo/R/waic.R | 6 loo-2.1.0/loo/R/zzz.R | 10 loo-2.1.0/loo/build/vignette.rds |binary loo-2.1.0/loo/inst/doc/loo2-example.R | 4 loo-2.1.0/loo/inst/doc/loo2-example.Rmd | 2 loo-2.1.0/loo/inst/doc/loo2-example.html | 418 +++++-- loo-2.1.0/loo/inst/doc/loo2-lfo.R |only loo-2.1.0/loo/inst/doc/loo2-lfo.Rmd |only loo-2.1.0/loo/inst/doc/loo2-lfo.html |only loo-2.1.0/loo/inst/doc/loo2-non-factorizable.R |only loo-2.1.0/loo/inst/doc/loo2-non-factorizable.Rmd |only loo-2.1.0/loo/inst/doc/loo2-non-factorizable.html |only loo-2.1.0/loo/inst/doc/loo2-weights.R | 4 loo-2.1.0/loo/inst/doc/loo2-weights.Rmd | 2 loo-2.1.0/loo/inst/doc/loo2-weights.html | 580 ++++++---- loo-2.1.0/loo/inst/doc/loo2-with-rstan.R | 2 loo-2.1.0/loo/inst/doc/loo2-with-rstan.Rmd | 2 loo-2.1.0/loo/inst/doc/loo2-with-rstan.html | 382 +++++- loo-2.1.0/loo/man/E_loo.Rd | 10 loo-2.1.0/loo/man/compare.Rd | 46 loo-2.1.0/loo/man/extract_log_lik.Rd | 3 loo-2.1.0/loo/man/figures/stanlogo.png |binary loo-2.1.0/loo/man/find_model_names.Rd |only loo-2.1.0/loo/man/kfold-generic.Rd |only loo-2.1.0/loo/man/kfold-helpers.Rd | 63 - loo-2.1.0/loo/man/loo-datasets.Rd | 2 loo-2.1.0/loo/man/loo-glossary.Rd |only loo-2.1.0/loo/man/loo-package.Rd | 10 loo-2.1.0/loo/man/loo.Rd | 39 loo-2.1.0/loo/man/loo_compare.Rd |only loo-2.1.0/loo/man/loo_model_weights.Rd | 20 loo-2.1.0/loo/man/nlist.Rd | 6 loo-2.1.0/loo/man/old-extractors.Rd | 5 loo-2.1.0/loo/man/pareto-k-diagnostic.Rd | 12 loo-2.1.0/loo/man/print_dims.Rd | 3 loo-2.1.0/loo/man/psis.Rd | 23 loo-2.1.0/loo/man/psis_approximate_posterior.Rd |only loo-2.1.0/loo/man/psislw.Rd | 6 loo-2.1.0/loo/man/relative_eff.Rd | 4 loo-2.1.0/loo/man/waic.Rd | 3 loo-2.1.0/loo/tests/testthat.R | 2 loo-2.1.0/loo/tests/testthat/E_loo_default_mean.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_default_quantile_10_50_90.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_default_quantile_50.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_default_var.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_matrix_mean.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_matrix_quantile_10_90.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_matrix_quantile_50.rds |binary loo-2.1.0/loo/tests/testthat/E_loo_matrix_var.rds |binary loo-2.1.0/loo/tests/testthat/compare_three_models.rds |binary loo-2.1.0/loo/tests/testthat/compare_two_models.rds |binary loo-2.1.0/loo/tests/testthat/loo.rds |binary loo-2.1.0/loo/tests/testthat/loo_compare_three_models.rds |only loo-2.1.0/loo/tests/testthat/loo_compare_two_models.rds |only loo-2.1.0/loo/tests/testthat/mcse_loo.rds |binary loo-2.1.0/loo/tests/testthat/psis.rds |only loo-2.1.0/loo/tests/testthat/test_E_loo.R | 10 loo-2.1.0/loo/tests/testthat/test_compare.R | 92 + loo-2.1.0/loo/tests/testthat/test_data_psis_approximate_posterior.rda |only loo-2.1.0/loo/tests/testthat/test_kfold_helpers.R | 64 - loo-2.1.0/loo/tests/testthat/test_loo_and_waic.R | 17 loo-2.1.0/loo/tests/testthat/test_print_plot.R | 4 loo-2.1.0/loo/tests/testthat/test_psis.R | 64 - loo-2.1.0/loo/tests/testthat/test_psis_approximate_posterior.R |only loo-2.1.0/loo/tests/testthat/test_relative_eff.R |only loo-2.1.0/loo/vignettes/children/SETTINGS-knitr.txt | 2 loo-2.1.0/loo/vignettes/loo2-example.Rmd | 2 loo-2.1.0/loo/vignettes/loo2-lfo.Rmd |only loo-2.1.0/loo/vignettes/loo2-non-factorizable.Rmd |only loo-2.1.0/loo/vignettes/loo2-weights.Rmd | 2 loo-2.1.0/loo/vignettes/loo2-with-rstan.Rmd | 2 92 files changed, 1812 insertions(+), 863 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of
raw data sets into analysis ready data sets is done in a reproducible
manner and decoupled from the usual R CMD build process so that
data sets can be processed into R objects in the data package and
the data package can then be shared, built, and installed by others
without the need to repeat computationally costly data processing.
The package maintains data provenance by turning the data processing
scripts into package vignettes, as well as enforcing documentation
and version checking of included data objects. Data packages can be
version controlled in github, and used to share data for manuscripts,
collaboration and general reproducibility.
Author: Greg Finak [aut, cre, cph],
Paul Obrecht [ctb],
Ellis Hughes [ctb],
Kara Woo [rev] (Kara reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>),
William Landau [rev] (William reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>)
Maintainer: Greg Finak <gfinak@fredhutch.org>
Diff between DataPackageR versions 0.15.5 dated 2019-03-11 and 0.15.6 dated 2019-03-13
DESCRIPTION | 8 - MD5 | 18 +-- R/dataversion.r | 6 - inst/doc/YAML_CONFIG.html | 18 +-- inst/doc/usingDataPackageR.R | 18 ++- inst/doc/usingDataPackageR.Rmd | 18 ++- inst/doc/usingDataPackageR.html | 219 +++++++++++++++++++++------------------- man/assert_data_version.Rd | 4 tests/testthat/test-document.R | 7 - vignettes/usingDataPackageR.Rmd | 18 ++- 10 files changed, 182 insertions(+), 152 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre at the
University of Leeds has developed flexible
estimation code for choice models in R.
Users are able to write their own likelihood
functions or use a mix of already available
ones. Mixing, in the form of random coefficients
and components is allowed for all models. Both
classical and Bayesian estimation are available.
Multi-threading processing is supported.
For more information on discrete choice models
see Train, K. (2009) <isbn:978-0-521-74738-7>.
Author: Stephane Hess [aut],
David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>
Diff between apollo versions 0.0.1 dated 2019-01-16 and 0.0.6 dated 2019-03-13
apollo-0.0.1/apollo/R/apollo_modeloutput.R |only apollo-0.0.1/apollo/R/apollo_validateHBcontrol.R |only apollo-0.0.1/apollo/R/apollo_validatecontrol.R |only apollo-0.0.1/apollo/R/apollo_validatedata.R |only apollo-0.0.1/apollo/inst/doc/apolloExamples.R |only apollo-0.0.1/apollo/inst/doc/apolloExamples.Rmd |only apollo-0.0.1/apollo/inst/doc/apolloExamples.html |only apollo-0.0.1/apollo/man/apollo_modeloutput.Rd |only apollo-0.0.1/apollo/man/apollo_validateHBcontrol.Rd |only apollo-0.0.1/apollo/man/apollo_validatecontrol.Rd |only apollo-0.0.1/apollo/man/apollo_validatedata.Rd |only apollo-0.0.1/apollo/man/database.Rd |only apollo-0.0.1/apollo/tests/testthat/testMNL.R |only apollo-0.0.1/apollo/vignettes/apolloExamples.Rmd |only apollo-0.0.6/apollo/DESCRIPTION | 29 apollo-0.0.6/apollo/MD5 | 198 ++ apollo-0.0.6/apollo/NAMESPACE | 54 apollo-0.0.6/apollo/R/RcppExports.R |only apollo-0.0.6/apollo/R/apollo_attach.R |only apollo-0.0.6/apollo/R/apollo_avgInterDraws.R | 94 - apollo-0.0.6/apollo/R/apollo_avgIntraDraws.R | 64 apollo-0.0.6/apollo/R/apollo_choiceAnalysis.R |only apollo-0.0.6/apollo/R/apollo_cnl.R |only apollo-0.0.6/apollo/R/apollo_combineModels.R |only apollo-0.0.6/apollo/R/apollo_combineResults.R |only apollo-0.0.6/apollo/R/apollo_conditionals.R |only apollo-0.0.6/apollo/R/apollo_deltaMethod.R |only apollo-0.0.6/apollo/R/apollo_detach.R |only apollo-0.0.6/apollo/R/apollo_dft.R |only apollo-0.0.6/apollo/R/apollo_drugChoiceData.R |only apollo-0.0.6/apollo/R/apollo_el.R |only apollo-0.0.6/apollo/R/apollo_estimate.R | 678 +++------- apollo-0.0.6/apollo/R/apollo_firstRow.R |only apollo-0.0.6/apollo/R/apollo_fitsTest.R |only apollo-0.0.6/apollo/R/apollo_initialise.R |only apollo-0.0.6/apollo/R/apollo_lc.R |only apollo-0.0.6/apollo/R/apollo_lcConditionals.R |only apollo-0.0.6/apollo/R/apollo_lcUnconditionals.r |only apollo-0.0.6/apollo/R/apollo_llCalc.R |only apollo-0.0.6/apollo/R/apollo_loadModel.R |only apollo-0.0.6/apollo/R/apollo_lrTest.R |only apollo-0.0.6/apollo/R/apollo_makeCluster.R | 86 - apollo-0.0.6/apollo/R/apollo_makeDraws.R | 325 ++-- apollo-0.0.6/apollo/R/apollo_makeLogLike.R | 124 - apollo-0.0.6/apollo/R/apollo_mdcev.R |only apollo-0.0.6/apollo/R/apollo_mdcevInside.R |only apollo-0.0.6/apollo/R/apollo_mdcevOutside.R |only apollo-0.0.6/apollo/R/apollo_mdcnev.R |only apollo-0.0.6/apollo/R/apollo_mlhs.R | 20 apollo-0.0.6/apollo/R/apollo_mnl.R | 316 +--- apollo-0.0.6/apollo/R/apollo_modeChoiceData.R | 4 apollo-0.0.6/apollo/R/apollo_modelOutput.R |only apollo-0.0.6/apollo/R/apollo_nl.R |only apollo-0.0.6/apollo/R/apollo_normalDensity.R |only apollo-0.0.6/apollo/R/apollo_ol.R |only apollo-0.0.6/apollo/R/apollo_outOfSample.R |only apollo-0.0.6/apollo/R/apollo_panelProd.R | 83 - apollo-0.0.6/apollo/R/apollo_prediction.R |only apollo-0.0.6/apollo/R/apollo_prepareProb.R | 65 apollo-0.0.6/apollo/R/apollo_readBeta.R |only apollo-0.0.6/apollo/R/apollo_saveOutput.R |only apollo-0.0.6/apollo/R/apollo_searchStart.R |only apollo-0.0.6/apollo/R/apollo_sharesTest.R |only apollo-0.0.6/apollo/R/apollo_speedTest.R |only apollo-0.0.6/apollo/R/apollo_splitDataDraws.R | 63 apollo-0.0.6/apollo/R/apollo_swissRouteChoiceData.R |only apollo-0.0.6/apollo/R/apollo_timeUseData.R |only apollo-0.0.6/apollo/R/apollo_unconditionals.R |only apollo-0.0.6/apollo/R/apollo_validateControl.R |only apollo-0.0.6/apollo/R/apollo_validateData.R |only apollo-0.0.6/apollo/R/apollo_validateHBControl.R |only apollo-0.0.6/apollo/R/apollo_validateInputs.R |only apollo-0.0.6/apollo/R/apollo_weighting.R |only apollo-0.0.6/apollo/R/apollo_writeF12.R |only apollo-0.0.6/apollo/R/apollo_writeTheta.R |only apollo-0.0.6/apollo/build/vignette.rds |binary apollo-0.0.6/apollo/data/apollo_drugChoiceData.RData |only apollo-0.0.6/apollo/data/apollo_modeChoiceData.RData |binary apollo-0.0.6/apollo/data/apollo_swissRouteChoiceData.RData |only apollo-0.0.6/apollo/data/apollo_timeUseData.RData |only apollo-0.0.6/apollo/inst/doc/apollofirstexample.R |only apollo-0.0.6/apollo/inst/doc/apollofirstexample.Rmd |only apollo-0.0.6/apollo/inst/doc/apollofirstexample.html |only apollo-0.0.6/apollo/man/apollo_attach.Rd |only apollo-0.0.6/apollo/man/apollo_avgInterDraws.Rd | 51 apollo-0.0.6/apollo/man/apollo_avgIntraDraws.Rd | 34 apollo-0.0.6/apollo/man/apollo_choiceAnalysis.Rd |only apollo-0.0.6/apollo/man/apollo_cnl.Rd |only apollo-0.0.6/apollo/man/apollo_combineModels.Rd |only apollo-0.0.6/apollo/man/apollo_combineResults.Rd |only apollo-0.0.6/apollo/man/apollo_conditionals.Rd |only apollo-0.0.6/apollo/man/apollo_deltaMethod.Rd |only apollo-0.0.6/apollo/man/apollo_detach.Rd |only apollo-0.0.6/apollo/man/apollo_dft.Rd |only apollo-0.0.6/apollo/man/apollo_drugChoiceData.Rd |only apollo-0.0.6/apollo/man/apollo_el.Rd |only apollo-0.0.6/apollo/man/apollo_estimate.Rd | 154 -- apollo-0.0.6/apollo/man/apollo_firstRow.Rd |only apollo-0.0.6/apollo/man/apollo_fitsTest.Rd |only apollo-0.0.6/apollo/man/apollo_initialise.Rd |only apollo-0.0.6/apollo/man/apollo_lc.Rd |only apollo-0.0.6/apollo/man/apollo_lcConditionals.Rd |only apollo-0.0.6/apollo/man/apollo_lcUnconditionals.Rd |only apollo-0.0.6/apollo/man/apollo_llCalc.Rd |only apollo-0.0.6/apollo/man/apollo_loadModel.Rd |only apollo-0.0.6/apollo/man/apollo_lrTest.Rd |only apollo-0.0.6/apollo/man/apollo_makeCluster.Rd | 27 apollo-0.0.6/apollo/man/apollo_makeDraws.Rd | 32 apollo-0.0.6/apollo/man/apollo_makeLogLike.Rd | 38 apollo-0.0.6/apollo/man/apollo_mdcev.Rd |only apollo-0.0.6/apollo/man/apollo_mdcevInside.Rd |only apollo-0.0.6/apollo/man/apollo_mdcevOutside.Rd |only apollo-0.0.6/apollo/man/apollo_mdcnev.Rd |only apollo-0.0.6/apollo/man/apollo_mnl.Rd | 111 - apollo-0.0.6/apollo/man/apollo_modeChoiceData.Rd |only apollo-0.0.6/apollo/man/apollo_modelOutput.Rd |only apollo-0.0.6/apollo/man/apollo_nl.Rd |only apollo-0.0.6/apollo/man/apollo_normalDensity.Rd |only apollo-0.0.6/apollo/man/apollo_ol.Rd |only apollo-0.0.6/apollo/man/apollo_outOfSample.Rd |only apollo-0.0.6/apollo/man/apollo_panelProd.Rd | 11 apollo-0.0.6/apollo/man/apollo_prediction.Rd |only apollo-0.0.6/apollo/man/apollo_prepareProb.Rd | 12 apollo-0.0.6/apollo/man/apollo_readBeta.Rd |only apollo-0.0.6/apollo/man/apollo_saveOutput.Rd |only apollo-0.0.6/apollo/man/apollo_searchStart.Rd |only apollo-0.0.6/apollo/man/apollo_sharesTest.Rd |only apollo-0.0.6/apollo/man/apollo_speedTest.Rd |only apollo-0.0.6/apollo/man/apollo_splitDataDraws.Rd | 14 apollo-0.0.6/apollo/man/apollo_swissRouteChoiceData.Rd |only apollo-0.0.6/apollo/man/apollo_timeUseData.Rd |only apollo-0.0.6/apollo/man/apollo_unconditionals.Rd |only apollo-0.0.6/apollo/man/apollo_validateControl.Rd |only apollo-0.0.6/apollo/man/apollo_validateData.Rd |only apollo-0.0.6/apollo/man/apollo_validateHBControl.Rd |only apollo-0.0.6/apollo/man/apollo_validateInputs.Rd |only apollo-0.0.6/apollo/man/apollo_weighting.Rd |only apollo-0.0.6/apollo/man/apollo_writeF12.Rd |only apollo-0.0.6/apollo/man/apollo_writeTheta.Rd |only apollo-0.0.6/apollo/src |only apollo-0.0.6/apollo/tests/testthat/MMNL_corr.csv |only apollo-0.0.6/apollo/tests/testthat/MMNL_covar.csv |only apollo-0.0.6/apollo/tests/testthat/MMNL_estimates.csv |only apollo-0.0.6/apollo/tests/testthat/MMNL_iterations.csv |only apollo-0.0.6/apollo/tests/testthat/MMNL_model.rds |only apollo-0.0.6/apollo/tests/testthat/MMNL_output.txt |only apollo-0.0.6/apollo/tests/testthat/MMNL_robcorr.csv |only apollo-0.0.6/apollo/tests/testthat/MMNL_robcovar.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_choiceAnalysis.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_corr.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_covar.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_estimates.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_iterations.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_model.rds |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_output.txt |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_robcorr.csv |only apollo-0.0.6/apollo/tests/testthat/MNL2Cores_robcovar.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_choiceAnalysis.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_corr.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_covar.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_estimates.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_iterations.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_model.rds |only apollo-0.0.6/apollo/tests/testthat/MNL_output.txt |only apollo-0.0.6/apollo/tests/testthat/MNL_robcorr.csv |only apollo-0.0.6/apollo/tests/testthat/MNL_robcovar.csv |only apollo-0.0.6/apollo/tests/testthat/test-mmnl.R |only apollo-0.0.6/apollo/tests/testthat/test-mnl.R |only apollo-0.0.6/apollo/tests/testthat/test-multicore.R |only apollo-0.0.6/apollo/vignettes/apollofirstexample.Rmd |only 170 files changed, 1159 insertions(+), 1528 deletions(-)
Title: Classification, Regression, Clustering with K Nearest Neighbors
Description: Classification, regression, and clustering with k nearest neighbors
algorithm. Implements several distance and similarity measures, covering
continuous and logical features. Outputs ranked neighbors. Most features of
this package are directly based on the PMML specification for KNN.
Author: Dmitriy Bolotov [aut, cre],
Zementis Inc [cph]
Maintainer: Dmitriy Bolotov <dmitriy.bolotov@softwareag.com>
Diff between neighbr versions 1.0 dated 2017-02-23 and 1.0.1 dated 2019-03-13
DESCRIPTION | 8 MD5 | 9 NEWS.md |only build/vignette.rds |binary inst/doc/neighbr-help.html | 614 +++++++++++++++++++++++---------------------- tests/testthat/test_knn.R | 1 6 files changed, 325 insertions(+), 307 deletions(-)
Title: Read Data Files from ActiGraph Monitors
Description: Standardize the process of bringing various modes of output files
into R. For more information, see:
<https://actigraph.desk.com/customer/en/portal/articles/2515800-what-do-the-different-mode-numbers-mean-in-a-csv-or-dat-file->.
Additionally, processes are provided to read and minimally pre-
process raw data from primary accelerometer and inertial measurement unit files,
as well as binary .gt3x files. ActiGraph monitors are used to estimate physical
activity outcomes via body-worn sensors that measure (e.g.) acceleration or
rotational velocity.
Author: Paul R. Hibbing [aut, cre],
Vincent T. van Hees [ctb],
Samuel R. LaMunion [ctb],
Daniel Judge [ctb],
Judge Maygarden [ctb],
ActiGraph LLC [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between AGread versions 0.2.0 dated 2019-02-17 and 0.2.2 dated 2019-03-13
DESCRIPTION | 24 + LICENSE | 709 -------------------------------------------------- MD5 | 12 NEWS.md | 32 ++ R/get_record_header.R | 2 README.md | 10 man/get_headers.Rd | 4 7 files changed, 63 insertions(+), 730 deletions(-)
Title: Install, Update, Load Packages from CRAN, 'GitHub', and
'Bioconductor' in One Step
Description: Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor'
packages in a single function call. By accepting bare unquoted names for packages,
it's easy to add or remove packages from the list.
Author: Desi Quintans [aut, cre]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between librarian versions 1.6.0 dated 2019-02-21 and 1.7.0 dated 2019-03-13
librarian-1.6.0/librarian/R/package_tools.R |only librarian-1.6.0/librarian/R/private_funs.R |only librarian-1.6.0/librarian/man/is_dots_empty.Rd |only librarian-1.6.0/librarian/man/suppress_lib_message.Rd |only librarian-1.6.0/librarian/man/wrap_long.Rd |only librarian-1.7.0/librarian/DESCRIPTION | 8 - librarian-1.7.0/librarian/MD5 | 57 +++++++------ librarian-1.7.0/librarian/NAMESPACE | 2 librarian-1.7.0/librarian/NEWS.md | 22 +++++ librarian-1.7.0/librarian/R/check_pkg_status.R |only librarian-1.7.0/librarian/R/console_output.R |only librarian-1.7.0/librarian/R/exported_functions.R |only librarian-1.7.0/librarian/R/internal_functions.R |only librarian-1.7.0/librarian/R/process_dots.R |only librarian-1.7.0/librarian/README.md | 16 ++- librarian-1.7.0/librarian/build/vignette.rds |binary librarian-1.7.0/librarian/inst/doc/intro-to-librarian.html | 4 librarian-1.7.0/librarian/man/browse_cran.Rd | 33 +++++-- librarian-1.7.0/librarian/man/check_attached.Rd | 26 +++-- librarian-1.7.0/librarian/man/check_installed.Rd | 24 +++-- librarian-1.7.0/librarian/man/check_pkg_status.Rd |only librarian-1.7.0/librarian/man/collapse_vec.Rd | 2 librarian-1.7.0/librarian/man/dots1_is_pkglist.Rd |only librarian-1.7.0/librarian/man/dots_is_empty.Rd |only librarian-1.7.0/librarian/man/dots_length.Rd |only librarian-1.7.0/librarian/man/fuzzy_needle.Rd | 2 librarian-1.7.0/librarian/man/is_valid_url.Rd | 2 librarian-1.7.0/librarian/man/lib_paths.Rd | 6 - librarian-1.7.0/librarian/man/lib_startup.Rd | 12 +- librarian-1.7.0/librarian/man/list_dependencies.Rd |only librarian-1.7.0/librarian/man/make_dirs.Rd | 2 librarian-1.7.0/librarian/man/nse_dots.Rd | 23 +++-- librarian-1.7.0/librarian/man/reshelf.Rd | 4 librarian-1.7.0/librarian/man/sentence.Rd |only librarian-1.7.0/librarian/man/shelf.Rd | 2 librarian-1.7.0/librarian/man/shhh.Rd |only librarian-1.7.0/librarian/man/tell_user.Rd |only librarian-1.7.0/librarian/man/unshelf.Rd | 7 + librarian-1.7.0/librarian/man/wrap_text.Rd |only 39 files changed, 162 insertions(+), 92 deletions(-)
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between gaselect versions 1.0.6 dated 2019-03-04 and 1.0.7 dated 2019-03-13
gaselect-1.0.6/gaselect/tools |only gaselect-1.0.7/gaselect/DESCRIPTION | 13 gaselect-1.0.7/gaselect/MD5 | 66 +- gaselect-1.0.7/gaselect/NAMESPACE | 4 gaselect-1.0.7/gaselect/R/evaluate.R | 4 gaselect-1.0.7/gaselect/R/genAlg.R | 6 gaselect-1.0.7/gaselect/README.md |only gaselect-1.0.7/gaselect/configure | 238 ---------- gaselect-1.0.7/gaselect/configure.ac | 19 gaselect-1.0.7/gaselect/man/GenAlg-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlg-constructor.Rd | 4 gaselect-1.0.7/gaselect/man/GenAlgControl-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlgControl-constructor.Rd | 12 gaselect-1.0.7/gaselect/man/GenAlgEvaluator-class.Rd | 6 gaselect-1.0.7/gaselect/man/GenAlgFitEvaluator-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlgFitEvaluator-constructor.Rd | 13 gaselect-1.0.7/gaselect/man/GenAlgLMEvaluator-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlgLMEvaluator-constructor.Rd | 13 gaselect-1.0.7/gaselect/man/GenAlgPLSEvaluator-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlgPLSEvaluator-constructor.Rd | 9 gaselect-1.0.7/gaselect/man/GenAlgUserEvaluator-class.Rd | 5 gaselect-1.0.7/gaselect/man/GenAlgUserEvaluator-constructor.Rd | 9 gaselect-1.0.7/gaselect/man/evaluate-methods.Rd | 19 gaselect-1.0.7/gaselect/man/fitness.Rd | 4 gaselect-1.0.7/gaselect/man/fitnessEvolution.Rd | 4 gaselect-1.0.7/gaselect/man/formatSegmentation-methods.Rd | 8 gaselect-1.0.7/gaselect/man/getEvalFun-methods.Rd | 8 gaselect-1.0.7/gaselect/man/subsets.Rd | 4 gaselect-1.0.7/gaselect/man/toCControlList-methods.Rd | 10 gaselect-1.0.7/gaselect/man/trueFitnessVal-methods.Rd | 8 gaselect-1.0.7/gaselect/man/validData-methods.Rd | 8 gaselect-1.0.7/gaselect/src/GenAlg.cpp | 74 +-- gaselect-1.0.7/gaselect/src/Makevars.in | 7 gaselect-1.0.7/gaselect/src/autoconfig.h.in | 104 +++- gaselect-1.0.7/gaselect/src/autoconfig.win.h | 4 35 files changed, 299 insertions(+), 409 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-13 1.0.3
Title: Inferring Causal Network from Mixed Observational Data Using a
Directed Acyclic Graph
Description: Learning a mixed directed acyclic graph based on both continuous and categorical data.
Author: Wujuan Zhong, Li Dong
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>
Diff between mDAG versions 1.1 dated 2019-03-01 and 1.2 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Greedy_Search.cpp | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: 'ggplot2' Faceting Utilities for Geographical Data
Description: Provides geofaceting functionality for 'ggplot2'. Geofaceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Author: Ryan Hafen [aut, cre],
Barret Schloerke [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between geofacet versions 0.1.9 dated 2018-03-29 and 0.1.10 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 1 + R/grid_docs.R | 2 +- build/vignette.rds |binary man/grid_design.Rd | 3 ++- man/grids.Rd | 2 +- tests/testthat/test-auto.R | 3 +++ tests/testthat/test-break.R | 2 ++ tests/testthat/test-examples.R | 2 ++ 10 files changed, 25 insertions(+), 16 deletions(-)
Title: Simulation and Analysis of Adaptive Bayesian Clinical Trials
Description: Simulation and analysis of Bayesian adaptive clinical trial, incorporates historical
data and allows early stopping for futility or early success.
Author: Thevaa Chandereng [aut, cre, cph]
(<https://orcid.org/0000-0003-4078-9176>),
Donald Musgrove [aut, cph],
Tarek Haddad [aut, cph],
Graeme Hickey [aut, cph],
Timothy Hanson [aut, cph],
Theodore Lystig [aut, cph]
Maintainer: Thevaa Chandereng <chandereng@wisc.edu>
Diff between bayesCT versions 0.99.0 dated 2019-01-30 and 0.99.1 dated 2019-03-13
DESCRIPTION | 11 +++---- MD5 | 38 ++++++++++++------------ NAMESPACE | 1 R/simulate.R | 1 README.md | 3 + build/vignette.rds |binary inst/doc/bayesCT.R | 5 +-- inst/doc/bayesCT.Rmd | 3 + inst/doc/bayesCT.html | 56 +++++++----------------------------- inst/doc/binomial.R | 1 inst/doc/binomial.Rmd | 1 inst/doc/normal.R | 1 inst/doc/normal.Rmd | 1 tests/testthat/test_binomialBACT.R | 1 tests/testthat/test_enrollment.R | 1 tests/testthat/test_normalBACT.R | 1 tests/testthat/test_randomization.R | 1 vignettes/bayesCT.Rmd | 3 + vignettes/binomial.Rmd | 1 vignettes/normal.Rmd | 1 20 files changed, 55 insertions(+), 76 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the
embedded 'libxls' C library <https://github.com/libxls/libxls> and
'.xlsx' via the embedded 'RapidXML' C++ library
<http://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux
without external dependencies.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd] (Copyright holder of all R code and all C/C++ code
without explicit copyright attribution),
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Komarov Valery [ctb, cph] (Author of included libxls code),
Christophe Leitienne [ctb, cph] (Author of included libxls code),
Bob Colbert [ctb, cph] (Author of included libxls code),
David Hoerl [ctb, cph] (Author of included libxls code),
Evan Miller [ctb, cph] (Author of included libxls code)
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between readxl versions 1.3.0 dated 2019-02-15 and 1.3.1 dated 2019-03-13
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ README.md | 2 +- inst/doc/cell-and-column-types.html | 12 ++++++------ inst/doc/sheet-geometry.html | 14 +++++++------- man/readxl-package.Rd | 4 ++-- tests/testthat/test-col-names.R | 24 ++++++++++++++++++++---- 8 files changed, 52 insertions(+), 32 deletions(-)
Title: Linear Algorithm for Simulating Quantiles in Multiscale
Change-Point Segmentation Problem
Description: It is a linear algorithm to simulate quantiles of multiscale statistics
under hull hypothesis for multiscale change-point segmentation.
The reference is in preparation.
Author: Chengcheng Huang [aut,cre], Housen Li[aut]
Maintainer: Chengcheng Huang <huangchengcheng12@nudt.edu.cn>
Diff between linearQ versions 1.0 dated 2018-03-01 and 2.0 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/auxFun.cpp | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between
samples is based on a modified kriging method that
accepts a genetic distance matrix and generates a map of
probability of lineage presence. This package also offers
tools to generate a map of potential contact zones
between groups with user-defined thresholds in the tree
to account for old and recent divergence. Additionally,
it has functions for IDW interpolation using genetic data
and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>
Diff between phylin versions 1.1.1 dated 2015-11-03 and 2.0 dated 2019-03-13
phylin-1.1.1/phylin/R/plot.gv_WITHMULTI.R |only phylin-1.1.1/phylin/R/real.dist.R |only phylin-1.1.1/phylin/man/real.dist.Rd |only phylin-2.0/phylin/DESCRIPTION | 14 -- phylin-2.0/phylin/MD5 | 67 ++++++---- phylin-2.0/phylin/NAMESPACE | 8 - phylin-2.0/phylin/R/gen.variogram.R | 33 +++-- phylin-2.0/phylin/R/gen.variogram.multi.R | 24 --- phylin-2.0/phylin/R/gen.variogram.single.R | 21 --- phylin-2.0/phylin/R/geo.dist.R |only phylin-2.0/phylin/R/grid.image.R | 27 ++-- phylin-2.0/phylin/R/gv.model.R | 123 +++++++++----------- phylin-2.0/phylin/R/idw.R | 12 - phylin-2.0/phylin/R/krig.R | 114 ++++++++++++------ phylin-2.0/phylin/R/mtest.gv.R | 8 - phylin-2.0/phylin/R/plot.gv.R | 88 ++++++++++---- phylin-2.0/phylin/R/predict.gv.R | 63 +++++----- phylin-2.0/phylin/R/print.gv.R |only phylin-2.0/phylin/build/vignette.rds |binary phylin-2.0/phylin/data/simulations.rda |only phylin-2.0/phylin/inst/CITATION |only phylin-2.0/phylin/inst/doc/phylin_tutorial.R | 55 +++++--- phylin-2.0/phylin/inst/doc/phylin_tutorial.Snw | 28 +++- phylin-2.0/phylin/inst/doc/phylin_tutorial.pdf |binary phylin-2.0/phylin/inst/doc/resistance_tutorial.R |only phylin-2.0/phylin/inst/doc/resistance_tutorial.Snw |only phylin-2.0/phylin/inst/doc/resistance_tutorial.pdf |only phylin-2.0/phylin/man/gen.variogram.Rd | 12 - phylin-2.0/phylin/man/geo.dist.Rd |only phylin-2.0/phylin/man/gv.model.Rd | 83 ++++++++----- phylin-2.0/phylin/man/idw.Rd | 16 ++ phylin-2.0/phylin/man/intgen.idw.Rd | 25 +++- phylin-2.0/phylin/man/krig.Rd | 86 ++++++++++--- phylin-2.0/phylin/man/multispecies.Rd | 2 phylin-2.0/phylin/man/phylin-package.Rd | 45 ++++--- phylin-2.0/phylin/man/plot.gv.Rd | 43 ++++++ phylin-2.0/phylin/man/print.gv.Rd |only phylin-2.0/phylin/man/simul.env.Rd |only phylin-2.0/phylin/man/simul.gen.dist.Rd |only phylin-2.0/phylin/man/simul.sample.Rd |only phylin-2.0/phylin/vignettes/phylin_tutorial.Snw | 28 +++- phylin-2.0/phylin/vignettes/references2.bib |only phylin-2.0/phylin/vignettes/resistance_tutorial.Snw |only 43 files changed, 634 insertions(+), 391 deletions(-)
Title: Functions for Forest Biometrics
Description: Functions for different purposes related to Forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Author: Lauri Mehtatalo
Maintainer: Lauri Mehtatalo <lauri.mehtatalo@uef.fi>
Diff between lmfor versions 1.2 dated 2017-01-05 and 1.3 dated 2019-03-13
DESCRIPTION | 14 ++++--- MD5 | 30 +++++++++++---- NAMESPACE | 5 +- R/HTest.R |only R/lmfor.R | 101 +++++++++++++++++++++++++++++++++++++-------------- data/afterthin.RData |only data/alsTree.RData |only data/foto.RData |binary data/ips.RData |only data/patti.RData |only data/plants.RData |only data/plants2.RData |only data/spati.RData |binary data/spati2.RData |binary data/stumplift.RData |binary man/HTest.Rd |only man/afterthin.Rd |only man/alsTree.Rd |only man/ips.Rd |only man/lmfor-package.Rd | 16 ++++---- man/patti.Rd |only man/plants.Rd |only man/plants2.Rd |only 23 files changed, 115 insertions(+), 51 deletions(-)
Title: Ecological Inference and Higher-Dimension Data Management
Description: Provides methods for analyzing R by C ecological contingency
tables using the extreme case analysis, ecological regression,
and Multinomial-Dirichlet ecological inference models. Also
provides tools for manipulating higher-dimension data objects.
Author: Olivia Lau <olivia.lau@post.harvard.edu>, Ryan T. Moore
<rtm@american.edu>, Michael Kellermann <mrkellermann@gmail.com>
Maintainer: Michael Kellermann <mrkellermann@gmail.com>
Diff between eiPack versions 0.1-8 dated 2018-12-07 and 0.1-9 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/rbycei.c | 6 +++++- src/rbycei2.c | 12 ++++++++---- src/rbyceicov2.c | 6 +++--- src/rbyceicov4.c | 10 +++++++--- 6 files changed, 32 insertions(+), 20 deletions(-)
Title: Critical Line Algorithm in Pure R
Description: Implements 'Markovitz' Critical Line Algorithm ('CLA') for classical
mean-variance portfolio optimization, see Markovitz (1952) <doi:10.2307/2975974>.
Care has been taken for correctness in light of previous buggy implementations.
Author: Yanhao Shi <syhelena@163.com>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between CLA versions 0.90-1 dated 2018-02-06 and 0.95-0 dated 2019-03-13
DESCRIPTION | 14 ++-- MD5 | 28 +++++--- R/CLA.R | 77 +++++++++++----------- TODO | 22 ++++-- build/partial.rdb |binary data/datalist | 1 data/muS.10ex.rda |only inst |only man/CLA.Rd | 14 ++-- man/findMu.Rd | 2 man/findSig.Rd | 2 man/muS.10ex.Rd |only man/muSigmaGarch.Rd | 5 - tests/SP500-ex.R | 173 ++++++++++++++++++++++++++++++++++++++------------- tests/findSigMu-ex.R |only tests/wtsn0.rds |binary 16 files changed, 228 insertions(+), 110 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photos, tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station including GIS export) and can visualise species activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 1.0 dated 2018-10-27 and 1.1 dated 2019-03-13
DESCRIPTION | 14 MD5 | 51 +- NEWS | 20 + R/activityOverlap.R | 10 R/appendSpeciesNames.R | 26 - R/checkSpeciesIdentification.R | 3 R/detectionHistory.R | 224 ++++++------ R/getSpeciesImages.R | 3 R/recordTableIndividual.R | 18 - R/spatialDetectionHistory.R | 4 R/variousOtherHelperFunctions.R | 170 +++++---- R/variousPlottingHelperFunctions.R | 451 ++++++++++++-------------- build/vignette.rds |binary inst/CITATION |only inst/doc/DataExploration.Rmd | 2 inst/doc/DataExploration.html | 47 ++ inst/doc/DataExtraction.R | 3 inst/doc/DataExtraction.Rmd | 7 inst/doc/DataExtraction.html | 167 +++++---- inst/doc/ImageOrganisation.Rmd | 4 inst/doc/ImageOrganisation.html | 85 +++- inst/doc/SpeciesIndividualIdentification.html | 116 +++--- man/activityOverlap.Rd | 4 man/detectionHistory.Rd | 9 vignettes/DataExploration.Rmd | 2 vignettes/DataExtraction.Rmd | 7 vignettes/ImageOrganisation.Rmd | 4 27 files changed, 790 insertions(+), 661 deletions(-)
Title: Convex Hull
Description: Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
Author: C. B. Barber [cph] (author of the Qhull library),
The Geometry Center [cph],
Stéphane Laurent [cph, aut, cre]
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Diff between cxhull versions 0.1.1 dated 2018-08-02 and 0.2.0 dated 2019-03-13
cxhull-0.1.1/cxhull/build |only cxhull-0.1.1/cxhull/inst |only cxhull-0.1.1/cxhull/vignettes |only cxhull-0.2.0/cxhull/DESCRIPTION | 12 +++++------- cxhull-0.2.0/cxhull/MD5 | 22 ++++------------------ cxhull-0.2.0/cxhull/NEWS.md | 5 +++++ cxhull-0.2.0/cxhull/src/convexhull.c | 17 ++++++++++++----- cxhull-0.2.0/cxhull/src/convexhull.h | 1 + 8 files changed, 27 insertions(+), 30 deletions(-)
More information about cloudSimplifieR at CRAN
Permanent link
Title: Safe, Multiple, Simultaneous String Substitution
Description: Designed to enable simultaneous substitution in strings in a safe fashion.
Safe means it does not rely on placeholders (which can cause errors in same length matches).
Author: Mark Ewing
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Diff between mgsub versions 1.7.0 dated 2019-01-13 and 1.7.1 dated 2019-03-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 +++++- inst/doc/Safe-Censoring.html | 10 +++++----- inst/doc/Safe-Substitution.html | 12 ++++++------ tests/testthat/test_mgsub_censor.R | 1 + 6 files changed, 25 insertions(+), 20 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, Ball-Berry stomatal conductance models,
leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, humidity unit conversions.
See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 1.3-2 dated 2017-11-28 and 1.4-4 dated 2019-03-13
DESCRIPTION | 8 MD5 | 56 +++-- NAMESPACE | 2 R/LeafEnergyBalance.R | 2 R/fitBB.R | 16 - R/fitaci.R | 48 ++++ R/fitaci_methods.R | 55 ++--- R/fitacis.R | 143 +++++--------- R/fitacis_methods.R |only R/photosyn.R | 25 +- R/tuzet.R | 2 R/utils.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_fitaci.Rmd | 2 inst/doc/Introduction_to_fitaci.html | 350 +++++++++++++++++++++++++++++------ inst/doc/fitaci-FAQ.html | 338 ++++++++++++++++++++++++++++----- inst/doc/new_T_responses.R |only inst/doc/new_T_responses.Rmd |only inst/doc/new_T_responses.html |only man/AciC4.Rd | 6 man/Photosyn.Rd | 28 +- man/PhotosynTuzet.Rd | 4 man/fitBB.Rd | 6 man/fitaci.Rd | 70 ++++--- man/fitacis.Rd | 71 +++++-- tests/testthat/testbb.R | 26 ++ tests/testthat/testfitaci.R | 63 +++++- tests/testthat/testmisc.R |only tests/testthat/testphotosyn.R | 11 - vignettes/Introduction_to_fitaci.Rmd | 2 vignettes/new_T_responses.Rmd |only 32 files changed, 967 insertions(+), 372 deletions(-)
Title: Component Models for Multi-Way Data
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints. Fit models include N-way Canonical Polyadic Decomposition, Individual Differences Scaling, Multiway Covariates Regression, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between multiway versions 1.0-5 dated 2018-06-10 and 1.0-6 dated 2019-03-13
ChangeLog | 23 +++++++++++ DESCRIPTION | 10 ++--- MD5 | 41 ++++++++++++-------- NAMESPACE | 5 ++ R/cpd.R |only R/cpd_nway.R |only R/cpd_nwayna.R |only R/fitted.cpd.R |only R/print.cpd.R |only R/reorder.cpd.R |only R/rescale.cpd.R |only R/resign.cpd.R |only R/tucker.R | 21 ++++++---- build/partial.rdb |binary man/cpd.Rd |only man/fitted.Rd | 19 +++++++-- man/multiway-internal.Rd | 2 + man/multiway-package.Rd | 13 +++++- man/parafac.Rd | 4 ++ man/parafac2.Rd | 6 +-- man/print.Rd | 17 ++++++-- man/reorder.Rd | 19 ++++++--- man/rescale.Rd | 19 ++++++--- man/resign.Rd | 21 +++++++--- man/sca.Rd | 10 ++--- man/tucker.Rd | 94 +++++++++++++++++++++++++++++++++++++++++------ 26 files changed, 244 insertions(+), 80 deletions(-)
Title: Functions for the Lognormal Distribution
Description: The lognormal distribution
(Limpert et al. (2001) <doi:10.1641/0006-3568(2001)051[0341:lndats]2.0.co;2>)
can characterize uncertainty that is bounded by zero.
This package provides estimation of distribution parameters, computation of
moments and other basic statistics, and an approximation of the distribution
of the sum of several correlated lognormally distributed variables
(Lo 2013 <doi:10.12988/ams.2013.39511>).
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between lognorm versions 0.1.4 dated 2018-11-23 and 0.1.5 dated 2019-03-13
DESCRIPTION | 8 +- MD5 | 42 +++++++++------ NAMESPACE | 6 ++ NEWS.md | 16 ++++- R/autocorr.R | 2 R/coefLognorm.R |only R/imports.R | 8 ++ R/lognormalSum.R | 12 +++- inst/doc/aggregateCorrelated.R | 65 +----------------------- inst/doc/aggregateCorrelated.Rmd | 8 +- inst/doc/aggregateCorrelated.html | 86 -------------------------------- inst/doc/lognorm.html | 24 ++++++++ inst/doc/lognormalSum.html | 26 ++++++++- inst/docu |only inst/genData/lognorm-package.Rd | 12 +++- man/estimateSumLognormalSample.Rd | 9 ++- man/getParmsLognormForLowerAndUpper.Rd |only man/getParmsLognormForMeanAndUpper.Rd |only man/getParmsLognormForMedianAndUpper.Rd |only man/getParmsLognormForModeAndUpper.Rd |only man/lognorm-package.Rd | 12 +++- man/seCor.Rd | 2 tests/testthat/test_CoefLnorm.R |only vignettes/aggregateCorrelated.Rmd | 8 +- 24 files changed, 156 insertions(+), 190 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity from multidimensional matrices. Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several basic statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.2 dated 2018-09-20 and 1.2.3 dated 2019-03-13
dispRity-1.2.3/dispRity/DESCRIPTION | 15 +- dispRity-1.2.3/dispRity/MD5 | 102 +++++++++---------- dispRity-1.2.3/dispRity/NAMESPACE | 5 dispRity-1.2.3/dispRity/NEWS.md | 35 +++++- dispRity-1.2.3/dispRity/R/Claddis.ordination.R |only dispRity-1.2.3/dispRity/R/adonis.dispRity.R | 17 ++- dispRity-1.2.3/dispRity/R/adonis.dispRity_fun.R | 22 ---- dispRity-1.2.3/dispRity/R/boot.matrix.R | 29 +++-- dispRity-1.2.3/dispRity/R/char.diff.R | 2 dispRity-1.2.3/dispRity/R/check.morpho.R | 8 - dispRity-1.2.3/dispRity/R/chrono.subsets.R | 46 ++++++-- dispRity-1.2.3/dispRity/R/clean.data.R | 2 dispRity-1.2.3/dispRity/R/custom.subsets.R | 35 ++++-- dispRity-1.2.3/dispRity/R/dispRity-package.R | 45 ++++++++ dispRity-1.2.3/dispRity/R/dispRity.R | 28 ++++- dispRity-1.2.3/dispRity/R/dispRity.metric.R | 13 -- dispRity-1.2.3/dispRity/R/dispRity.utilities.R | 59 +++++++--- dispRity-1.2.3/dispRity/R/dispRity.wrapper.R | 16 ++ dispRity-1.2.3/dispRity/R/dispRity_fun.R | 4 dispRity-1.2.3/dispRity/R/dtt.dispRity.R | 2 dispRity-1.2.3/dispRity/R/geomorph.ordination.R | 33 ++++-- dispRity-1.2.3/dispRity/R/get.bin.ages.R | 4 dispRity-1.2.3/dispRity/R/make.metric.R | 12 +- dispRity-1.2.3/dispRity/R/model.test.R | 2 dispRity-1.2.3/dispRity/R/model.test.sim.R | 6 - dispRity-1.2.3/dispRity/R/morpho.utilities.R | 12 +- dispRity-1.2.3/dispRity/R/null.test.R | 21 ++- dispRity-1.2.3/dispRity/R/null.test_fun.R | 79 ++++++++++---- dispRity-1.2.3/dispRity/R/pair.plot.R | 11 +- dispRity-1.2.3/dispRity/R/plot.dispRity.R | 73 +++++++++---- dispRity-1.2.3/dispRity/R/plot.dispRity_fun.R | 23 ++-- dispRity-1.2.3/dispRity/R/print.dispRity.R | 2 dispRity-1.2.3/dispRity/R/sanitizing.R | 95 +++++------------ dispRity-1.2.3/dispRity/R/sim.morpho.R | 8 - dispRity-1.2.3/dispRity/R/space.maker.R | 6 - dispRity-1.2.3/dispRity/R/summary.dispRity.R | 8 - dispRity-1.2.3/dispRity/R/summary.dispRity_fun.R | 7 - dispRity-1.2.3/dispRity/R/test.dispRity.R | 59 +++++++--- dispRity-1.2.3/dispRity/R/zzz.R | 2 dispRity-1.2.3/dispRity/data/BeckLee_disparity.rda |binary dispRity-1.2.3/dispRity/data/disparity.rda |binary dispRity-1.2.3/dispRity/inst/CITATION | 5 dispRity-1.2.3/dispRity/inst/References.bib | 13 ++ dispRity-1.2.3/dispRity/man/BeckLee_disparity.Rd | 20 +++ dispRity-1.2.3/dispRity/man/Claddis.ordination.Rd |only dispRity-1.2.3/dispRity/man/dispRity.metric.Rd | 6 - dispRity-1.2.3/dispRity/man/dispRity.per.group.Rd | 7 + dispRity-1.2.3/dispRity/man/dispRity.through.time.Rd | 6 - dispRity-1.2.3/dispRity/man/disparity.Rd | 21 +++ dispRity-1.2.3/dispRity/man/geomorph.ordination.Rd | 7 - dispRity-1.2.3/dispRity/man/plot.dispRity.Rd | 8 + dispRity-1.2.3/dispRity/src/char.diff.c | 4 dispRity-1.2/dispRity/R/make.dispRity.models.R |only dispRity-1.2/dispRity/README.md |only 54 files changed, 675 insertions(+), 370 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Tao Yang [aut],
Zonglin He [aut],
Adam Elder [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2019.3-8 dated 2019-03-08 and 2019.3-12 dated 2019-03-13
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/chngpt-vignette.pdf |binary src/fastgrid_binomial.cpp | 1 + 5 files changed, 11 insertions(+), 7 deletions(-)
Title: Tools to Read, Analyze and Visualize Metadynamics HILLS Files
from 'Plumed'
Description: Metadynamics is a state of the art biomolecular simulation technique.
'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
it possible to perform metadynamics using various simulation codes. The results of
metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
to calculate a free energy surface from hills. Minima can be located and plotted on
the free energy surface. Transition states can be analyzed by Nudged Elastic Band
method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy
surfaces, minima and transition paths can be plotted to produce publication quality
images.
Author: Vojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)
Maintainer: Vojtech Spiwok <spiwokv@vscht.cz>
Diff between metadynminer versions 0.1.3 dated 2018-11-05 and 0.1.4 dated 2019-03-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/readingandfes.R | 44 ++++++++++++++++++-------------------------- README.md | 12 ++++++------ 4 files changed, 31 insertions(+), 39 deletions(-)
Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.3.2 dated 2019-01-10 and 1.4.0 dated 2019-03-13
DESCRIPTION | 8 MD5 | 115 ++++---- NAMESPACE | 8 NEWS | 23 + R/SSM.R | 39 +- R/amplitude.R |only R/analyze.R | 152 ++++++---- R/formants.R | 16 - R/loudness.R | 142 ++++++++- R/modulationSpectrum.R |only R/presets.R | 57 +--- R/rolloff.R | 3 R/segment.R | 2 R/smoothContours.R | 2 R/soundgen.R | 427 ++++++++++++++---------------- R/source.R | 119 +++----- R/spectrogram.R | 43 +-- R/utilities_analyze.R | 2 R/utilities_loudness.R | 16 - R/utilities_math.R | 151 ++++++++++ R/utilities_soundgen.R | 25 + data/defaults.rda |binary data/permittedValues.rda |binary data/presets.rda |binary inst/doc/acoustic_analysis.R | 48 +++ inst/doc/acoustic_analysis.Rmd | 131 +++++++-- inst/doc/acoustic_analysis.html | 267 ++++++++++++------ inst/doc/sound_generation.R | 53 +++ inst/doc/sound_generation.Rmd | 88 ++++-- inst/doc/sound_generation.html | 186 ++++++++----- inst/shiny/soundgen_main/server.R | 416 ++++++++++++++--------------- inst/shiny/soundgen_main/ui.R | 4 inst/shiny/soundgen_main/www/n0h2ayvu.wav |only man/addFormants.Rd | 10 man/analyze.Rd | 43 ++- man/analyzeFolder.Rd | 7 man/beat.Rd | 5 man/defaults.Rd | 2 man/fart.Rd | 22 - man/gaussianSmooth2D.Rd |only man/generateHarmonics.Rd | 16 - man/generateNoise.Rd | 15 - man/getCheckerboardKernel.Rd | 12 man/getLoudness.Rd | 35 +- man/getLoudnessFolder.Rd |only man/getLoudnessPerFrame.Rd | 2 man/getNovelty.Rd | 6 man/getRMS.Rd |only man/getRMSFolder.Rd |only man/getRough.Rd |only man/getSpectralEnvelope.Rd | 6 man/logMatrix.Rd |only man/modulationSpectrum.Rd |only man/modulationSpectrumFolder.Rd |only man/normalizeFolder.Rd |only man/pDistr.Rd |only man/reformatAnchors.Rd | 2 man/reportTime.Rd | 23 + man/scaleNoiseAnchors.Rd | 2 man/scaleSPL.Rd | 13 man/soundgen.Rd | 53 +-- man/spectrogram.Rd | 2 man/ssm.Rd | 2 vignettes/acoustic_analysis.Rmd | 131 +++++++-- vignettes/sound_generation.Rmd | 88 ++++-- 65 files changed, 1936 insertions(+), 1104 deletions(-)
Title: Tools for Acquiring and Analyzing Political Data
Description: Provides useful functions for obtaining commonly-used data
in political analysis and political science, including from sources
such as the Comparative Agendas Project <https://www.comparativeagendas.net>,
which provides data on politics and policy from 20+ countries, the
MIT Election and Data Science Lab <https://www.electionlab.mit.edu>,
and FiveThirtyEight <https://www.FiveThirtyEight.com>.
Author: G. Elliott Morris [aut, cre],
Comparative Agendas Project [cph],
MIT Election and Data Science Lab [cph],
FiveThirtyEight.com [cph]
Maintainer: G. Elliott Morris <elliott@thecrosstab.com>
Diff between politicaldata versions 0.1.1 dated 2019-02-22 and 0.1.2 dated 2019-03-13
DESCRIPTION | 18 ++--- MD5 | 20 ++--- NAMESPACE | 3 NEWS.md | 6 + R/cap_get_mip.R | 2 R/get_house_nominate.R | 3 R/get_senate_nominate.R | 3 README.md | 166 +++++++++++++++++++++++++++++++---------------- data/house_results.RData |binary data/pres_results.RData |binary man/house_results.Rd | 2 11 files changed, 142 insertions(+), 81 deletions(-)
Title: Bayesian Additive Regression Trees Using Particle Gibbs Sampler
and Gibbs/Metropolis-Hastings Sampler
Description: The Particle Gibbs sampler and Gibbs/Metropolis-Hastings sampler were implemented
to fit Bayesian additive regression tree model. Construction of the model (training) and prediction
for a new data set (testing) can be separated. Our reference papers are:
Lakshminarayanan B, Roy D, Teh Y W. Particle Gibbs for Bayesian additive regression trees[C],
Artificial Intelligence and Statistics. 2015: 553-561,
<http://proceedings.mlr.press/v38/lakshminarayanan15.pdf>
and Chipman, H., George, E., and McCulloch R. (2010) Bayesian Additive Regression Trees. The Annals of Applied Statistics, 4,1, 266-298, <doi:10.1214/09-aoas285>.
Author: Pingyu Wang [aut, cre],
Dai Feng [aut],
Yang Bai [aut],
Qiuyue Shi [aut],
Zhicheng Zhao [aut],
Fei Su [aut],
Hugh Chipman [aut],
Robert McCulloch [aut]
Maintainer: Pingyu Wang <applewangpingyu@gmail.com>
Diff between pgbart versions 0.6.15 dated 2018-11-13 and 0.6.16 dated 2019-03-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Param.cpp | 3 +-- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: Viewing Binary Files
Description: Functions to view files in raw binary form like in a hex editor. Additional functions to specify and read arbitrary binary formats.
Author: Paul Murrell [aut, cre],
Chao Bian [ctb]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between hexView versions 0.3-3 dated 2014-12-17 and 0.3-4 dated 2019-03-13
DESCRIPTION | 14 +++++++----- MD5 | 20 +++++++++-------- NAMESPACE | 1 R/eviews.R | 45 ++++++++++++++++++++++++++++++++++++--- R/memBlock.R | 60 +++++++++++++++++++++++++++++++++++++++++++++-------- R/viewFormat.R | 2 - README.md |only inst/NEWS.Rd |only man/atomicBlock.Rd | 2 + man/markedBlock.Rd | 19 +++++++++++++--- man/readEViews.Rd | 4 ++- man/vectorBlock.Rd | 4 ++- 12 files changed, 138 insertions(+), 33 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [aut], Sergii Babkin <babkin.sergii@gmail.com> [aut], Jonathan Stewart <jonathan.stewart@rice.edu> [aut], Duy Vu <duy.vu@unimelb.edu.au> [aut], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 4.0-0 dated 2019-01-07 and 4.1-0 dated 2019-03-13
hergm-4.0-0/hergm/man/bali.rd |only hergm-4.0-0/hergm/man/bunt.rd |only hergm-4.0-0/hergm/man/example.rd |only hergm-4.0-0/hergm/man/kapferer.rd |only hergm-4.1-0/hergm/DESCRIPTION | 8 ++++---- hergm-4.1-0/hergm/MD5 | 18 +++++++++--------- hergm-4.1-0/hergm/R/hergm.R | 7 +++---- hergm-4.1-0/hergm/R/hergm.gof.R | 2 +- hergm-4.1-0/hergm/R/hergm.simulate.R | 2 +- hergm-4.1-0/hergm/man/bali.Rd |only hergm-4.1-0/hergm/man/bunt.Rd |only hergm-4.1-0/hergm/man/example.Rd |only hergm-4.1-0/hergm/man/hergm.Rd | 15 +++++++++++---- hergm-4.1-0/hergm/man/kapferer.Rd |only 14 files changed, 29 insertions(+), 23 deletions(-)
Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex
programming (DCP). It allows the user to formulate convex optimization problems
in a natural way following mathematical convention and DCP rules. The system
analyzes the problem, verifies its convexity, converts it into a canonical form,
and hands it off to an appropriate solver to obtain the solution.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 0.99-3 dated 2019-02-20 and 0.99-4 dated 2019-03-13
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- NEWS.md | 10 ++++++++ inst/doc/cvxr_intro.html | 4 +-- tests/manual/test-constant_atoms.R | 2 - tests/manual/test-examples.R | 6 ++--- tests/manual/test-vignette.R | 8 +++--- tests/testthat/test-g01-non_optimal.R | 2 - tests/testthat/test-g03-test_ls.R | 39 ++++++++++++++++++---------------- 9 files changed, 54 insertions(+), 41 deletions(-)
Title: Multiply Robust Methods for Missing Data Problems
Description: Multiply robust estimation for population mean (Han and Wang 2013) <doi:10.1093/biomet/ass087>, regression analysis (Han 2014) <doi:10.1080/01621459.2014.880058> (Han 2016) <doi:10.1111/sjos.12177> and quantile regression (Han et al. 2019) <doi:10.1111/rssb.12309>.
Author: Shixiao Zhang and Peisong Han
Maintainer: Shixiao Zhang <praetere@gmail.com>
Diff between MultiRobust versions 1.0.0 dated 2019-03-05 and 1.0.1 dated 2019-03-13
DESCRIPTION | 6 +- MD5 | 25 ++++---- R/MI.glm.r | 16 ++--- R/MR.mean.r | 101 ++++++++++++++++++---------------- R/MR.quantile.r | 124 ++++++++++++++++++++++-------------------- R/MR.quantreg.r | 152 +++++++++++++++++++++++++++------------------------- R/MR.reg.r | 150 ++++++++++++++++++++++++++------------------------- R/def.quantreg.r | 3 - R/ext.names.r |only man/MR.mean.Rd | 44 ++++++++------- man/MR.quantile.Rd | 50 +++++++++-------- man/MR.quantreg.Rd | 68 +++++++++++------------ man/MR.reg.Rd | 63 +++++++++++---------- man/def.quantreg.Rd | 4 - 14 files changed, 423 insertions(+), 383 deletions(-)