Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers. The package is enhanced when the 'gt' package is installed.
Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.2.3 dated 2019-11-12 and 1.2.4 dated 2019-12-16
gtsummary-1.2.3/gtsummary/man/as_tibble_methods.Rd |only gtsummary-1.2.3/gtsummary/man/assign_var_label.Rd |only gtsummary-1.2.4/gtsummary/DESCRIPTION | 8 gtsummary-1.2.4/gtsummary/MD5 | 293 gtsummary-1.2.4/gtsummary/NAMESPACE | 2 gtsummary-1.2.4/gtsummary/NEWS.md | 10 gtsummary-1.2.4/gtsummary/R/add_global_p.R | 40 gtsummary-1.2.4/gtsummary/R/add_n.R | 20 gtsummary-1.2.4/gtsummary/R/add_nevent.R | 8 gtsummary-1.2.4/gtsummary/R/add_overall.R | 4 gtsummary-1.2.4/gtsummary/R/add_p.R | 39 gtsummary-1.2.4/gtsummary/R/add_q.R | 14 gtsummary-1.2.4/gtsummary/R/add_stat_label.R | 7 gtsummary-1.2.4/gtsummary/R/as_gt.R | 8 gtsummary-1.2.4/gtsummary/R/as_kable.R | 10 gtsummary-1.2.4/gtsummary/R/as_tibble.R | 14 gtsummary-1.2.4/gtsummary/R/bold_italicise_labels_levels.R | 18 gtsummary-1.2.4/gtsummary/R/data.R | 6 gtsummary-1.2.4/gtsummary/R/inline_text.R | 22 gtsummary-1.2.4/gtsummary/R/tbl_merge.R | 66 gtsummary-1.2.4/gtsummary/R/tbl_regression.R | 115 gtsummary-1.2.4/gtsummary/R/tbl_stack.R | 8 gtsummary-1.2.4/gtsummary/R/tbl_summary.R | 34 gtsummary-1.2.4/gtsummary/R/tbl_survival.R | 17 gtsummary-1.2.4/gtsummary/R/tbl_uvregression.R | 74 gtsummary-1.2.4/gtsummary/R/tidyselect_to_list.R | 33 gtsummary-1.2.4/gtsummary/R/utils-add_p.R | 184 gtsummary-1.2.4/gtsummary/R/utils-table_headers.R | 3 gtsummary-1.2.4/gtsummary/R/utils-tbl_regression.R | 136 gtsummary-1.2.4/gtsummary/R/utils-tbl_summary.R | 153 gtsummary-1.2.4/gtsummary/README.md | 6 gtsummary-1.2.4/gtsummary/build/gtsummary.pdf |15560 +++++----- gtsummary-1.2.4/gtsummary/data/trial.rda |binary gtsummary-1.2.4/gtsummary/inst/WORDLIST | 3 gtsummary-1.2.4/gtsummary/inst/doc/gallery.R | 26 gtsummary-1.2.4/gtsummary/inst/doc/gallery.Rmd | 4 gtsummary-1.2.4/gtsummary/inst/doc/gallery.html | 2647 + gtsummary-1.2.4/gtsummary/inst/doc/global_options.R | 36 gtsummary-1.2.4/gtsummary/inst/doc/global_options.Rmd | 24 gtsummary-1.2.4/gtsummary/inst/doc/global_options.html | 485 gtsummary-1.2.4/gtsummary/inst/doc/tbl_regression.R | 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gtsummary-1.2.4/gtsummary/tests/testthat/test-inline_text.R | 22 gtsummary-1.2.4/gtsummary/tests/testthat/test-tbl_merge.R | 4 gtsummary-1.2.4/gtsummary/tests/testthat/test-tbl_regression.R | 21 gtsummary-1.2.4/gtsummary/tests/testthat/test-tbl_stack.R | 8 gtsummary-1.2.4/gtsummary/tests/testthat/test-tbl_summary.R | 50 gtsummary-1.2.4/gtsummary/tests/testthat/test-tbl_uvregression.R | 30 gtsummary-1.2.4/gtsummary/vignettes/gallery.Rmd | 4 gtsummary-1.2.4/gtsummary/vignettes/global_options.Rmd | 24 gtsummary-1.2.4/gtsummary/vignettes/tbl_regression.Rmd | 7 gtsummary-1.2.4/gtsummary/vignettes/tbl_summary.Rmd | 29 150 files changed, 16461 insertions(+), 12722 deletions(-)
Title: Covariate Adaptive Clustering
Description: Implements the predictive k-means method for clustering observations, using a mixture of experts model to allow covariates to influence cluster centers. Motivated by air pollution epidemiology settings, where cluster membership needs to be predicted across space. Includes functions for predicting cluster membership using spatial splines and principal component analysis (PCA) scores using either multinomial logistic regression or support vector machines (SVMs). For method details see Keller et al. (2017) <doi:10.1214/16-AOAS992>.
Author: Joshua Keller
Maintainer: Joshua Keller <joshua.keller@colostate.edu>
Diff between predkmeans versions 0.1.0 dated 2017-11-09 and 0.1.1 dated 2019-12-16
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++------------- NEWS.md |only R/RcppExports.R | 6 +++--- R/functions_cv.R | 8 ++++---- R/functions_predict.R | 4 ++-- R/functions_predkmeans.R | 10 +++++----- README.md |only man/createPCAmodelmatrix.Rd | 10 ++++++++-- man/createTPRSmodelmatrix.Rd | 11 +++++++++-- man/mlogit.Rd | 17 ++++++++++++++--- man/predictML.predkmeans.Rd | 38 +++++++++++++++++++++++++++++--------- man/predkmeans.Rd | 22 ++++++++++++++++++---- man/predkmeansCVest.Rd | 33 +++++++++++++++++++++++++-------- man/relevel.predkmeans.Rd | 4 +++- src/RcppExports.cpp | 12 ++++++------ 16 files changed, 146 insertions(+), 67 deletions(-)
Title: New Plots Based on 'ggplot2' and Functions to Create Regular
Shapes
Description: An extension to 'ggplot2' with miscellaneous functions. It contains
two groups of functions: Functions in the first group draw 'ggplot2' - based plots: gg_shading_bar() draws barplot
with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles
and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio
changes. annotation_transparent_text() draws labels with transparent texts. annotation_shading_polygon() draws irregular
polygons with shading colors. Functions in the second group generate coordinates for regular shapes and make linear transformations.
Author: Jiang Wu [aut, cre] (from Capital Normal University)
Maintainer: Jiang Wu <textidea@sina.com>
Diff between plothelper versions 0.1.5 dated 2019-11-16 and 0.1.6 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++++++------------- NAMESPACE | 4 ++++ R/chEck_rAw_df.R | 9 +++++---- R/geom_multi_raster.R | 20 +++++++++----------- R/geom_shading_bar.R | 22 ++++++++++++---------- R/image_crop_click.R |only R/image_keep_color.R | 4 +++- R/image_modify_hsv.R | 4 ++-- R/image_modify_local.R |only R/image_modify_local2.R |only R/image_modify_rgb.R | 4 ++-- R/raster_alpha.R |only man/geom_multi_raster.Rd | 18 ++++++++---------- man/geom_shading_bar.Rd | 22 ++++++++++++---------- man/image_crop_click.Rd |only man/image_keep_color.Rd | 4 +++- man/image_modify_hsv.Rd | 4 ++-- man/image_modify_local.Rd |only man/image_modify_local2.Rd |only man/image_modify_rgb.Rd | 4 ++-- man/raster_alpha.Rd |only 22 files changed, 89 insertions(+), 72 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre],
Lavinia Baumstark [aut],
Stephen Wirth [aut],
Anastasis Giannousakis [aut],
Renato Rodrigues [aut],
Benjamin Leon Bodirsky [aut],
Ulrich Kreidenweis [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 1.61.0 dated 2019-05-29 and 1.64.4 dated 2019-12-16
DESCRIPTION | 16 MD5 | 80 +- NAMESPACE | 6 R/calcOutput.R | 61 + R/downloadTau.R | 10 R/fullEXAMPLE.R | 60 - R/getISOlist.R | 4 R/initializeConfig.R | 79 +- R/readSource.R | 55 - R/retrieveData.R | 17 R/setConfig.R | 17 R/toolAggregate.R | 37 - R/toolConditionalReplace.R |only R/toolConvertMapping.R | 2 R/toolFillYears.R |only R/toolGetMapping.R | 2 R/toolISOhistorical.R | 50 - R/toolSubtypeSelect.R | 58 - README.md | 2 inst/doc/madrat.R | 30 inst/doc/madrat.html | 20 inst/extdata/ISOhistorical.csv | 72 - inst/extdata/country2iso.csv | 1308 ++++++++++++++++++------------------ man/calcOutput.Rd | 18 man/fullEXAMPLE.Rd | 10 man/getCalculations.Rd | 7 man/getSources.Rd | 7 man/madapply.Rd | 10 man/plotDiagnostics.Rd | 3 man/prepFunctionName.Rd | 3 man/retrieveData.Rd | 10 man/setConfig.Rd | 34 man/toolAggregate.Rd | 20 man/toolConditionalReplace.Rd |only man/toolConvertMapping.Rd | 3 man/toolCountry2isocode.Rd | 3 man/toolCountryFill.Rd | 10 man/toolFillWithRegionAvg.Rd | 12 man/toolFillYears.Rd |only man/toolGetMapping.Rd | 9 man/toolISOhistorical.Rd | 8 man/toolMappingFile.Rd | 9 tests/testthat/test-toolAggregate.R | 35 43 files changed, 1197 insertions(+), 1000 deletions(-)
Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles
of species distribution model (SDM) predictions.
Functionality is offered through R functions or a GUI (R Shiny app).
This tool can assist users in identifying spatial uncertainties and
making informed conservation and management decisions. The package is
further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between eSDM versions 0.3.1 dated 2019-10-17 and 0.3.2 dated 2019-12-16
DESCRIPTION | 11 +-- MD5 | 44 ++++++------ NAMESPACE | 2 NEWS.md | 6 + build/vignette.rds |binary inst/CITATION | 4 - inst/doc/example-analysis.R | 73 +++++++++++--------- inst/doc/example-analysis.Rmd | 43 +++++++----- inst/doc/example-analysis.html | 48 +++++++------ inst/eSDM_vignette_helper.R | 17 +++- man/eSDM-package.Rd | 52 +++++++------- man/eSDM_GUI.Rd | 30 ++++---- man/ensemble_create.Rd | 145 ++++++++++++++++++++--------------------- man/ensemble_rescale.Rd | 124 +++++++++++++++++------------------ man/evaluation_metrics.Rd | 90 ++++++++++++------------- man/gshhg.l.L16.Rd | 34 ++++----- man/model_abundance.Rd | 84 +++++++++++------------ man/overlay_sdm.Rd | 106 ++++++++++++++--------------- man/preds.Rd | 76 ++++++++++----------- man/pts2poly_centroids.Rd | 118 ++++++++++++++++----------------- man/pts2poly_vertices.Rd | 92 +++++++++++++------------- man/validation.data.Rd | 40 +++++------ vignettes/example-analysis.Rmd | 43 +++++++----- 23 files changed, 666 insertions(+), 616 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>
Diff between divo versions 1.0.0 dated 2017-10-17 and 1.0.1 dated 2019-12-16
DESCRIPTION | 10 MD5 | 50 - R/divo.R | 1508 +++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/divo-Manual.Rnw | 8 inst/doc/divo-Manual.pdf |binary inst/doc/divo-Vignette.R | 4 inst/doc/divo-Vignette.Rnw | 12 inst/doc/divo-Vignette.pdf |binary man/cvg.Rd | 2 man/divo.Rd | 2 man/dp.Rd | 2 man/dp.ht.Rd | 2 man/ens.Rd | 2 man/ens.ht.Rd | 2 man/i.in.Rd | 2 man/i.inp.Rd | 2 man/ji.Rd | 2 man/li.Rd | 2 man/mh.Rd | 2 man/pg.Rd | 2 man/pg.ht.Rd | 2 man/rd.Rd | 2 man/srd.Rd | 2 vignettes/divo-Manual.Rnw | 8 vignettes/divo-Vignette.Rnw | 12 26 files changed, 1074 insertions(+), 568 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut, cre]
(<https://orcid.org/0000-0002-0315-8888>),
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] (<https://orcid.org/0000-0001-7242-1873>),
Deepak Yadav [aut],
Ignacio Cordón [aut] (<https://orcid.org/0000-0002-3152-0231>),
Vandit Jain [ctb],
Toni Giorgino [ctb] (<https://orcid.org/0000-0001-6449-0596>)
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.8.0 dated 2019-09-14 and 0.8.1 dated 2019-12-16
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Title: A User-Oriented Statistical Toolkit for Analytical Variance
Estimation
Description: Provides a toolkit for analytical variance estimation in survey sampling. Apart from the implementation of standard variance estimators, its main feature is to help the sampling expert produce easy-to-use variance estimation "wrappers", where systematic operations (linearization, domain estimation) are handled in a consistent and transparent way.
Author: Martin Chevalier [aut, cre, cph]
Maintainer: Martin Chevalier <martin.chevalier@insee.fr>
Diff between gustave versions 0.4.0 dated 2018-08-31 and 0.4.1 dated 2019-12-16
DESCRIPTION | 10 MD5 | 48 NAMESPACE | 24 NEWS.md | 140 +- R/data.R | 266 ++-- R/define_statistic_wrapper.R | 604 +++++----- R/define_variance_wrapper.R | 798 ++++++------- R/qvar.R | 1342 +++++++++++------------ R/standard_statistic_wrapper.R | 242 ++-- R/utils.R | 734 ++++++------ R/variance_function.R | 942 ++++++++-------- README.md | 336 ++--- man/define_statistic_wrapper.Rd | 9 man/define_variance_wrapper.Rd | 14 man/qvar.Rd | 30 man/res_cal.Rd | 7 man/varDT.Rd | 13 tests/testthat.R | 8 tests/testthat/test_data.R | 30 tests/testthat/test_define_statistic_wrapper.R | 268 ++-- tests/testthat/test_define_variance_wrapper.R | 570 ++++----- tests/testthat/test_qvar.R | 1306 +++++++++++----------- tests/testthat/test_standard_statistic_wrapper.R | 38 tests/testthat/test_utils.R | 360 +++--- tests/testthat/test_variance_function.R | 190 +-- 25 files changed, 4182 insertions(+), 4147 deletions(-)
Title: Mixture Models with Component-Wise Factor Analyzers
Description: We provide functions to fit finite mixtures of multivariate normal or t-distributions to
data with various factor analytic structures adopted for the covariance/scale matrices. The
factor analytic structures available include mixtures of factor analyzers and mixtures of common
factor analyzers. The latter approach is so termed because the matrix of factor loadings is
common to components before the component-specific rotation of the component factors to
make them white noise. Note that the component-factor loadings are not common after
this rotation. Maximum likelihood estimators of model parameters are obtained via the
Expectation-Maximization algorithm. See descriptions of the algorithms used in
McLachlan GJ, Peel D (2000) <doi:10.1002/0471721182.ch8>
McLachlan GJ, Peel D (2000) <ISBN:1-55860-707-2>
McLachlan GJ, Peel D, Bean RW (2003) <doi:10.1016/S0167-9473(02)00183-4>
McLachlan GJ, Bean RW, Ben-Tovim Jones L (2007) <doi:10.1016/j.csda.2006.09.015>
Baek J, McLachlan GJ, Flack LK (2010) <doi:10.1109/TPAMI.2009.149>
Baek J, McLachlan GJ (2011) <doi:10.1093/bioinformatics/btr112>
McLachlan GJ, Baek J, Rathnayake SI (2011) <doi:10.1002/9781119995678.ch9>.
Author: Suren Rathnayake, Geoff McLachlan, David Peel, Jangsun Baek
Maintainer: Suren Rathnayake <surenr@gmail.com>
Diff between EMMIXmfa versions 2.0.7 dated 2018-10-19 and 2.0.11 dated 2019-12-16
DESCRIPTION | 10 +++++----- MD5 | 44 ++++++++++++++++++++++---------------------- R/check_para.R | 5 +++-- R/est_mcfa.R | 10 +++++----- R/est_mctfa.R | 15 ++++++++------- R/est_mfa.R | 13 +++++++------ R/est_mtfa.R | 15 ++++++++------- R/factor_scores.R | 16 ++++++++-------- R/logL_mcfa.R | 4 ++-- R/logL_tau_mctfa.R | 4 ++-- R/logL_tau_mfa.R | 12 ++++++------ R/logL_tau_mtfa.R | 12 ++++++------ R/mstep_mcfa.R | 2 +- R/mstep_mctfa.R | 2 +- R/mstep_mfa.R | 6 +++--- R/mstep_mtfa.R | 6 +++--- R/predict.R | 12 ++++++------ R/print.R | 8 ++++---- R/rmix.R | 12 ++++++------ R/tau_mcfa.R | 4 ++-- R/tau_mctfa.R | 4 ++-- R/tau_mfa.R | 12 ++++++------ R/tau_mtfa.R | 12 ++++++------ 23 files changed, 122 insertions(+), 118 deletions(-)
Title: Testing 'DBI' 'Backends'
Description: A helper that tests 'DBI' back ends for conformity
to the interface.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between DBItest versions 1.5-2 dated 2018-01-25 and 1.7.0 dated 2019-12-16
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Title: Loglinear Models for Capture-Recapture Experiments
Description: Estimation of abundance and other demographic parameters for closed
populations, open populations and the robust design in capture-recapture
experiments using loglinear models.
Author: Louis-Paul Rivest [aut, cre],
Sophie Baillargeon [aut]
Maintainer: Louis-Paul Rivest <Louis-Paul.Rivest@mat.ulaval.ca>
Diff between Rcapture versions 1.4-2 dated 2014-08-28 and 1.4-3 dated 2019-12-16
DESCRIPTION | 25 ++-- MD5 | 94 +++++++-------- NAMESPACE | 4 NEWS | 23 +++ R/closedp.Mtb.R | 24 +-- R/closedp.R | 50 ++++---- R/closedp.bc.R | 30 ++-- R/closedp.h.r | 4 R/closedp.mX.R | 4 R/closedpCI.R | 84 ++++++------- R/closedpMS.R | 125 ++++++++++---------- R/descriptive.R | 34 ++--- R/histpos.R | 4 R/internal.DRY.R | 290 ++++++++++++++++++++++++------------------------ R/internal.histfreq.R | 4 R/internal.matrices.R | 6 R/internal.valid.R | 92 +++++++-------- R/openp.R | 72 +++++------ R/periodhist.R | 2 R/profileCI.R | 40 +++--- R/robustd.0.R | 42 +++--- R/robustd.t.r | 46 +++---- R/uifit.R | 16 +- data/duck.rda |binary data/hare.rda |binary man/BBS2001.Rd | 3 man/HIV.Rd | 3 man/Rcapture.package.Rd | 6 man/bunting.Rd | 7 - man/cbird.Rd | 3 man/closedp.Mtb.Rd | 4 man/closedp.Rd | 9 - man/closedp.bc.Rd | 4 man/closedp.custom.Rd | 4 man/closedpCI.Rd | 13 +- man/closedpMS.Rd | 8 - man/descriptive.Rd | 14 -- man/duck.Rd | 5 man/hare.Rd | 3 man/ill.Rd | 4 man/lesbian.Rd | 4 man/mvole.Rd | 5 man/openp.Rd | 4 man/periodhist.Rd | 2 man/profileCI.Rd | 4 man/rbvole.Rd | 3 man/robustd.Rd | 2 man/uifit.Rd | 2 48 files changed, 617 insertions(+), 614 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.9-7 dated 2019-09-28 and 4.9-8 dated 2019-12-16
meta-4.9-7/meta/R/paulemandel.R |only meta-4.9-8/meta/DESCRIPTION | 14 meta-4.9-8/meta/MD5 | 139 - meta-4.9-8/meta/NAMESPACE | 1 meta-4.9-8/meta/NEWS | 89 + meta-4.9-8/meta/R/baujat.R | 4 meta-4.9-8/meta/R/cathet.R | 98 - meta-4.9-8/meta/R/catmeth.R | 70 meta-4.9-8/meta/R/forest.R | 2295 ++++++++++++++++++++---------- meta-4.9-8/meta/R/formatPT.R | 134 + meta-4.9-8/meta/R/funnel.R | 76 meta-4.9-8/meta/R/hetcalc.R | 229 +- meta-4.9-8/meta/R/meta-internal.R | 40 meta-4.9-8/meta/R/meta-package.R | 85 - meta-4.9-8/meta/R/metabias.R | 69 meta-4.9-8/meta/R/metabias.rm5.R | 2 meta-4.9-8/meta/R/metabin.R | 208 +- meta-4.9-8/meta/R/metabind.R | 11 meta-4.9-8/meta/R/metacont.R | 249 ++- meta-4.9-8/meta/R/metacor.R | 244 ++- meta-4.9-8/meta/R/metacr.R | 78 - meta-4.9-8/meta/R/metacum.R | 194 +- meta-4.9-8/meta/R/metagen.R | 251 +-- meta-4.9-8/meta/R/metainc.R | 118 + meta-4.9-8/meta/R/metainf.R | 183 +- meta-4.9-8/meta/R/metamean.R | 234 ++- meta-4.9-8/meta/R/metaprop.R | 126 + meta-4.9-8/meta/R/metarate.R | 132 + meta-4.9-8/meta/R/metareg.R | 50 meta-4.9-8/meta/R/print.meta.R | 155 +- meta-4.9-8/meta/R/read.rm5.R | 8 meta-4.9-8/meta/R/settings.meta.R | 103 + meta-4.9-8/meta/R/subgroup.R | 112 - meta-4.9-8/meta/R/summary.meta.R | 224 ++ meta-4.9-8/meta/R/summary.rm5.R | 2 meta-4.9-8/meta/R/trimfill.R | 38 meta-4.9-8/meta/R/update.meta.R | 107 - meta-4.9-8/meta/inst/CITATION | 19 meta-4.9-8/meta/man/as.data.frame.meta.Rd | 3 meta-4.9-8/meta/man/baujat.Rd | 31 meta-4.9-8/meta/man/bubble.Rd | 29 meta-4.9-8/meta/man/forest.Rd | 361 +++- meta-4.9-8/meta/man/funnel.Rd | 109 + meta-4.9-8/meta/man/labbe.Rd | 90 - meta-4.9-8/meta/man/meta-package.Rd | 83 - meta-4.9-8/meta/man/metabias.Rd | 21 meta-4.9-8/meta/man/metabias.rm5.Rd | 15 meta-4.9-8/meta/man/metabin.Rd | 164 +- meta-4.9-8/meta/man/metacont.Rd | 279 ++- meta-4.9-8/meta/man/metacor.Rd | 264 ++- meta-4.9-8/meta/man/metacr.Rd | 49 meta-4.9-8/meta/man/metacum.Rd | 17 meta-4.9-8/meta/man/metagen.Rd | 177 +- meta-4.9-8/meta/man/metainc.Rd | 139 + meta-4.9-8/meta/man/metainf.Rd | 9 meta-4.9-8/meta/man/metamean.Rd | 256 ++- meta-4.9-8/meta/man/metaprop.Rd | 125 + meta-4.9-8/meta/man/metarate.Rd | 127 + meta-4.9-8/meta/man/metareg.Rd | 58 meta-4.9-8/meta/man/nnt.Rd | 15 meta-4.9-8/meta/man/or2smd.Rd | 12 meta-4.9-8/meta/man/print.meta.Rd | 53 meta-4.9-8/meta/man/radial.Rd | 37 meta-4.9-8/meta/man/read.rm5.Rd | 11 meta-4.9-8/meta/man/settings.meta.Rd | 13 meta-4.9-8/meta/man/smd2or.Rd | 13 meta-4.9-8/meta/man/summary.meta.Rd | 121 + meta-4.9-8/meta/man/summary.rm5.Rd | 2 meta-4.9-8/meta/man/trimfill.Rd | 80 - meta-4.9-8/meta/man/update.meta.Rd | 124 + meta-4.9-8/meta/man/weights.meta.Rd | 8 71 files changed, 6227 insertions(+), 2859 deletions(-)
Title: Small-Sample Adjustments for Wald Tests Using Sandwich
Estimators
Description: Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between saws versions 0.9-6.1 dated 2014-01-22 and 0.9-6.2 dated 2019-12-16
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 3 +++ NEWS | 6 ++++++ R/geeUOmega.R | 8 +++++++- man/saws-package.Rd | 4 ++-- 6 files changed, 28 insertions(+), 13 deletions(-)
Title: Meta-Feature Extractor
Description: Extracts meta-features from datasets to support the design of
recommendation systems based on Meta-Learning. The meta-features, also called
characterization measures, are able to characterize the complexity of datasets
and to provide estimates of algorithm performance. The package contains not
only the standard characterization measures, but also more recent
characterization measures. By making available a large set of meta-feature
extraction functions, tasks like comprehensive data characterization, deep
data exploration and large number of Meta-Learning based data analysis can be
performed. These concepts are described in the paper: Adriano Rivolli, Luis
Garcia, Carlos Soares, Joaquin Vanschoren, and Andre de Carvalho. Towards
Reproducible Empirical Research in Meta-Learning.
Author: Adriano Rivolli [aut, cre],
Luis P. F. Garcia [aut],
Andre C. P. L. F. de Carvalho [ths]
Maintainer: Adriano Rivolli <rivolli@utfpr.edu.br>
Diff between mfe versions 0.1.3 dated 2019-08-26 and 0.1.4 dated 2019-12-16
DESCRIPTION | 13 MD5 | 42 - NAMESPACE | 12 NEWS.md | 9 R/complexity.R |only R/concept.R |only R/itemset.R |only R/metafeatures.R | 20 build/vignette.rds |binary inst/doc/mfe-vignette.html | 1177 +++++++++++++++++++++---------------- man/clustering.Rd | 9 man/complexity.Rd |only man/concept.Rd |only man/general.Rd | 7 man/infotheo.Rd | 7 man/itemset.Rd |only man/landmarking.Rd | 5 man/ls.complexity.Rd |only man/ls.concept.Rd |only man/ls.itemset.Rd |only man/metafeatures.Rd | 15 man/model.based.Rd | 5 man/relative.Rd | 5 man/statistical.Rd | 5 tests/testthat/test_complexity.R |only tests/testthat/test_concept.R |only tests/testthat/test_itemset.R |only tests/testthat/test_metafeatures.R | 12 28 files changed, 788 insertions(+), 555 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autocomplete addresses or reverse geocode POIs using the 'Geocoder' API;
(2) routing directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) real-time traffic flow and incident information from the 'Traffic' API;
(4) weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre]
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.2.0 dated 2019-11-13 and 0.2.1 dated 2019-12-16
hereR-0.2.0/hereR/R/matrix.R |only hereR-0.2.0/hereR/R/reverse.R |only hereR-0.2.1/hereR/DESCRIPTION | 8 hereR-0.2.1/hereR/MD5 | 82 ++-- hereR-0.2.1/hereR/NEWS.md | 11 hereR-0.2.1/hereR/R/autocomplete.R | 6 hereR-0.2.1/hereR/R/checks.R | 15 hereR-0.2.1/hereR/R/geocode.R | 19 - hereR-0.2.1/hereR/R/isoline.R | 13 hereR-0.2.1/hereR/R/reverse_geocode.R |only hereR-0.2.1/hereR/R/route.R | 11 hereR-0.2.1/hereR/R/route_matrix.R |only hereR-0.2.1/hereR/R/sysdata.rda |binary hereR-0.2.1/hereR/R/traffic.R | 55 ++- hereR-0.2.1/hereR/R/utils.R | 9 hereR-0.2.1/hereR/R/weather.R | 50 ++ hereR-0.2.1/hereR/README.md | 4 hereR-0.2.1/hereR/inst/doc/geocoder.R | 11 hereR-0.2.1/hereR/inst/doc/geocoder.Rmd | 13 hereR-0.2.1/hereR/inst/doc/geocoder.html | 56 ++- hereR-0.2.1/hereR/inst/doc/routing.R | 15 hereR-0.2.1/hereR/inst/doc/routing.Rmd | 15 hereR-0.2.1/hereR/inst/doc/routing.html | 80 ++-- hereR-0.2.1/hereR/inst/doc/traffic.Rmd | 6 hereR-0.2.1/hereR/inst/doc/traffic.html | 14 hereR-0.2.1/hereR/inst/doc/weather.R | 58 ++- hereR-0.2.1/hereR/inst/doc/weather.Rmd | 58 ++- hereR-0.2.1/hereR/inst/doc/weather.html | 236 +++++++------- hereR-0.2.1/hereR/man/reverse_geocode.Rd | 2 hereR-0.2.1/hereR/man/route_matrix.Rd | 2 hereR-0.2.1/hereR/man/traffic.Rd | 29 + hereR-0.2.1/hereR/man/weather.Rd | 4 hereR-0.2.1/hereR/tests/testthat/test-authentication.R |only hereR-0.2.1/hereR/tests/testthat/test-get_content.R |only hereR-0.2.1/hereR/tests/testthat/test-isoline.R | 56 +-- hereR-0.2.1/hereR/tests/testthat/test-reverse_geocode.R | 6 hereR-0.2.1/hereR/tests/testthat/test-route.R | 48 +- hereR-0.2.1/hereR/tests/testthat/test-route_matrix.R | 50 +- hereR-0.2.1/hereR/tests/testthat/test-traffic_flow.R | 55 ++- hereR-0.2.1/hereR/tests/testthat/test-traffic_incidents.R | 48 +- hereR-0.2.1/hereR/tests/testthat/test-weather_alerts.R | 46 +- hereR-0.2.1/hereR/vignettes/geocoder.Rmd | 13 hereR-0.2.1/hereR/vignettes/routing.Rmd | 15 hereR-0.2.1/hereR/vignettes/traffic.Rmd | 6 hereR-0.2.1/hereR/vignettes/weather.Rmd | 58 ++- 45 files changed, 810 insertions(+), 473 deletions(-)
Title: Regression with a Large Number of Potential Explanatory
Variables
Description: Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
Author: H. H. Hoeltgebaum
Maintainer: H. H. Hoeltgebaum <hh3015@ic.ac.uk>
Diff between HCmodelSets versions 1.0.2 dated 2018-12-17 and 1.1 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 15 +++++++++------ R/Exploratory.Phase.R | 6 +++--- data |only man/DGP.Rd | 6 +++++- man/Exploratory.Phase.Rd | 2 ++ man/LymphomaData.Rd |only man/ModelSelection.Phase.Rd | 2 ++ man/Reduction.Phase.Rd | 4 +++- 9 files changed, 28 insertions(+), 15 deletions(-)
Title: Convenience Functions, Moving Window Statistics, and Graphics
Description: Contains functions that do something convenient (e.g. create BMI categories), functions for calculating moving-window statistics efficiently, and functions for generating various figures (e.g. histograms with fitted probability mass/density function).
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between dvmisc versions 1.1.3 dated 2019-03-05 and 1.1.4 dated 2019-12-16
DESCRIPTION | 10 MD5 | 34 ++- NAMESPACE | 9 R/clean_glm.R |only R/cleancut.R |only R/create_qgroups.R |only R/create_qgroups_svy.R |only R/cut_decreasing.R |only R/dvmisc.R | 9 R/iterate.R | 32 +-- R/quant_groups.R | 3 R/reverse_cut.R |only R/sumsim.R | 4 build/vignette.rds |binary inst/doc/dvmisc.html | 485 ++++++++++++++++++++++++++++++++++------------ man/clean_glm.Rd |only man/cleancut.Rd |only man/create_qgroups.Rd |only man/create_qgroups_svy.Rd |only man/cut_decreasing.Rd |only man/dvmisc.Rd | 4 man/iterate.Rd | 17 + man/quant_groups.Rd | 3 man/reverse_cut.Rd |only 24 files changed, 442 insertions(+), 168 deletions(-)
Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.6.1 dated 2019-06-21 and 2.0.1 dated 2019-12-16
BEDMatrix-1.6.1/BEDMatrix/src/BEDMatrix.cpp |only BEDMatrix-1.6.1/BEDMatrix/src/Makevars |only BEDMatrix-1.6.1/BEDMatrix/src/Makevars.win |only BEDMatrix-2.0.1/BEDMatrix/DESCRIPTION | 11 +++++------ BEDMatrix-2.0.1/BEDMatrix/MD5 | 22 +++++++++++++--------- BEDMatrix-2.0.1/BEDMatrix/NAMESPACE | 3 +-- BEDMatrix-2.0.1/BEDMatrix/NEWS.md | 18 ++++++++++++++++++ BEDMatrix-2.0.1/BEDMatrix/R/BEDMatrix.R | 6 +++--- BEDMatrix-2.0.1/BEDMatrix/inst/include |only BEDMatrix-2.0.1/BEDMatrix/man/BEDMatrix-class.Rd | 9 +++------ BEDMatrix-2.0.1/BEDMatrix/src/BEDMatrix.c |only BEDMatrix-2.0.1/BEDMatrix/src/BEDMatrix.h |only BEDMatrix-2.0.1/BEDMatrix/src/bed.c |only BEDMatrix-2.0.1/BEDMatrix/src/bed.h |only BEDMatrix-2.0.1/BEDMatrix/src/init.c | 15 +++++---------- BEDMatrix-2.0.1/BEDMatrix/src/mapping.c |only BEDMatrix-2.0.1/BEDMatrix/src/mapping.h |only 17 files changed, 48 insertions(+), 36 deletions(-)
Title: Expectation-Maximization Binary Clustering
Description: Unsupervised, multivariate, binary clustering for meaningful annotation of data, taking into account the uncertainty in the data. A specific constructor for trajectory analysis in movement ecology yields behavioural annotation of trajectories based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator, ("Expectation-Maximization Binary Clustering for Behavioural Annotation").
Author: Joan Garriga, John R.B. Palmer, Aitana Oltra, Frederic Bartumeus
Maintainer: Joan Garriga <jgarriga@ceab.csic.es>
Diff between EMbC versions 2.0.2 dated 2019-09-04 and 2.0.3 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 26 ++++++++++++++++---------- R/functions.R | 2 +- inst/doc/EMbC_qckref.pdf |binary 5 files changed, 25 insertions(+), 19 deletions(-)
Title: Psychometric Networks for Intensive Longitudinal Data
Description: In the past decade, mental processes have been conceptualized as complex networks of interacting psychiatric symptoms. These networks that can be visualized by means of conditional independence graphs. For estimating the underlying directed graph from intensive longitudinal data, vector autoregression (VAR) is the most commonly used tool. This package wraps several methods in the VAR family that can be used to estimate conditional independence graphs (networks) from multivariate time-series data. The package can fit the simple VAR and VARX model Lutkepohl, H. (2005) <doi:10.1007/978-3-540-27752-1> that are currently available from the R package 'vars', and its sparse alternative by Basu S. and Michailidis, G.(2015) <doi:10.1214/15-AOS1315> and sparse VECM implemented in the R package 'sparsevar'. The sparse graphical VAR with covariance estimation by Wild, B., Eichler, M., Friederich, H. C., Hartmann, M., Zipfel, S., & Herzog, W. (2010) <doi:10.1186/1471-2288-10-28> from the R package 'graphicalVAR' and the dynamic factor model by Doz, Gianone & Reichlin (2011) <doi:10.1016/j.jeconom.2011.02.012> from the R package 'dynfactoR' are also available. Sparse estimation of high dimensional VAR, VARMA and VARX models using hierarchical lag structures Nicholson, W. B., Bien, J., Matteson, D. S. (2017) <arXiv:1412.5250v3> implemented in the R package 'bigtime' and mixed VAR for symptom time series with marginal distributions in the exponential family Haslbeck, J., Waldorp, L. J. (2015) <arXiv:1510.06871> from the package 'mgm' can also be used with this package. For the inference of symptom networks from multivariate time series of multiple individuals the 'psychNET' package adopts the multi-level VAR by Epskamp, S., Waldorp, L. J., Mottus, R., & Borsboom, D. (2017) <arXiv:1609.04156v6> implemented in the R package 'mlVAR' and for the high-dimensional setting the sparse time series chain graphical (group graphical VAR) model by Abegaz, F., Wit, E. (2013) <doi:10.1093/biostatistics/kxt005> available from the R package 'sparseTSCGM'.
Author: Spyros Balafas [aut, cre],
Ernst Wit [aut],
Marco Grzegorczyk [aut],
Sanne Booij [ctb],
Hanneke Wardenaar-Wigman [ctb]
Maintainer: Spyros Balafas <s.balafas@rug.nl>
Diff between psychNET versions 0.0.1 dated 2019-07-03 and 0.0.2 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++++- data |only man/MIR.Rd |only man/MOOVD.Rd |only 5 files changed, 9 insertions(+), 5 deletions(-)
Title: Genetic Algorithm for Wind Farm Layout Optimization
Description: The genetic algorithm is designed to optimize wind farms of any shape. It requires a predefined amount of turbines, a unified rotor radius and an average wind speed value for each incoming wind direction. A terrain effect model can be included that downloads an 'SRTM' elevation model and loads a Corine Land Cover raster to approximate surface roughness.
Author: Sebastian Gatscha [aut, cre]
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Diff between windfarmGA versions 2.2.2 dated 2019-08-27 and 2.2.3 dated 2019-12-16
DESCRIPTION | 7 +++---- MD5 | 29 +++++++++++++++-------------- NEWS.md | 3 +++ R/barometric_height.R | 2 +- R/make_clc_legend.R |only R/visibility.R | 7 ++----- tests/testthat/test_ga.R | 30 +++++++++++------------------- tests/testthat/test_ga_func.R | 12 ++++++------ tests/testthat/test_ga_skipcran.R | 2 +- tests/testthat/test_parallel.R | 1 + tests/testthat/test_plots.R | 6 ++++-- tests/testthat/test_terrain.R | 8 ++++---- tests/testthat/test_user_input.R | 1 + tests/testthat/test_visibility.R | 4 +++- tests/testthat/test_wake.R | 8 ++++---- tests/testthat/test_windfarmga.R | 2 ++ 16 files changed, 61 insertions(+), 61 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson, Adam Smith, Ken Kellner
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 0.13-0 dated 2019-11-12 and 0.13-1 dated 2019-12-16
DESCRIPTION | 8 +- MD5 | 36 +++++----- NEWS | 5 + R/boot.R | 129 +++++++++++-------------------------- R/occuMS.R | 2 R/occuMulti.R | 2 R/ranef.R | 2 R/unmarkedFit.R | 15 ++++ R/unmarkedFrame.R | 142 ++++++++++------------------------------- R/utils.R | 13 ++- inst/doc/cap-recap.pdf |binary inst/doc/colext.pdf |binary inst/doc/distsamp.pdf |binary inst/doc/spp-dist.pdf |binary inst/doc/unmarked.pdf |binary inst/unitTests/runit.parboot.R | 34 +++++++++ man/SSE.Rd | 6 + man/parboot.Rd | 2 man/unmarkedFit-class.Rd | 5 + 19 files changed, 175 insertions(+), 226 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Description: Bayesian geostatistical modeling of Gaussian processes using a
reparameterized and marginalized posterior sampling (RAMPS) algorithm
designed to lower autocorrelation in MCMC samples. Package performance is
tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between ramps versions 0.6-15 dated 2018-03-26 and 0.6.16 dated 2019-12-16
DESCRIPTION | 13 - MD5 | 12 - R/control.R | 6 R/utils.R | 650 ++++++++++++++++++++++++++++---------------------------- data/NURE.rda |binary data/simJSS.rda |binary man/plot.Rd | 2 7 files changed, 343 insertions(+), 340 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports
Cox-PH, proportional odds, and accelerated failure time models. Allows for
semi and fully parametric models (parametric only for accelerated failure
time models) and Bayesian parametric models. Includes functions for easy visual
diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 2.0.11 dated 2019-11-10 and 2.0.13 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 +++++++ R/user_utilities.R | 21 ++++++++++++++++----- inst/doc/icenReg.pdf |binary 5 files changed, 31 insertions(+), 13 deletions(-)
Title: Easy Microarray Data Analysis
Description: We propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.
Author: Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
Maintainer: Pierre Gestraud <pierre.gestraud@curie.fr>
Diff between EMA versions 1.4.5 dated 2016-09-07 and 1.4.6 dated 2019-12-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/anadiff.R | 4 ++-- R/explore.R | 10 +++++----- R/norm.R | 2 +- R/pca.R | 10 +++++----- man/plotSample.Rd | 3 ++- man/plotVariable.Rd | 2 ++ man/runPCA.Rd | 3 ++- 9 files changed, 30 insertions(+), 26 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.7.0 dated 2019-11-07 and 2.7.1 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/shiny.R | 1 + R/solvebio.R | 2 +- man/createEnv.Rd | 2 +- 6 files changed, 17 insertions(+), 11 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) "DART: a software to analyse root system architecture and development from captured images", Plant and Soil, <DOI:10.1007/s11104-009-0005-2>), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) "Root System Markup Language: toward a unified root architecture description language", Plant Physiology, <DOI:10.1104/pp.114.253625>). More information can be found in Delory et al (2016) "archiDART: an R package for the automated computation of plant root architectural traits", Plant and Soil, <DOI:10.1007/s11104-015-2673-4>.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 3.2 dated 2018-04-03 and 3.3 dated 2019-12-16
DESCRIPTION | 13 MD5 | 45 - NAMESPACE | 8 R/archidraw.R | 4 R/archigrow.R | 19 R/architect.R | 1384 +++++++++++++++++------------------ R/bottleneckdist.R | 2 R/dartToTable.R | 6 R/fitter.R | 17 R/latdist.R | 4 R/root.R |only R/rsmlToDART.R | 1076 +++++++++++++++++++++++---- R/rsmlToTable.R | 45 - R/trajectory.R | 25 inst/CITATION | 24 inst/doc/RSML_PlantPhysiology.pdf |binary inst/doc/archiDART_F1000Research.pdf |only inst/doc/archiDART_PlantSoil.pdf |binary man/archidraw.Rd | 2 man/archigrow.Rd | 2 man/architect.Rd | 14 man/latdist.Rd | 2 man/root.Rd |only man/rsmlToTable.Rd | 2 man/trajectory.Rd | 2 25 files changed, 1799 insertions(+), 897 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>,
chapter 6.
Author: Mark van der Loo [cre, aut] (<https://orcid.org/0000-0002-9807-4686>),
Edwin de Jonge [aut] (<https://orcid.org/0000-0002-6580-4718>),
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.9.2 dated 2019-08-28 and 0.9.3 dated 2019-12-16
DESCRIPTION | 15 +- MD5 | 150 ++++++++++++------------ NAMESPACE | 2 NEWS | 7 + R/confrontation.R | 14 +- R/parse.R | 3 R/retailers.R | 2 R/syntax.R | 80 ++++++++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/JSS_3483.Rnw |only inst/doc/JSS_3483.pdf |only inst/doc/indicators.R | 20 +-- inst/doc/indicators.html | 15 +- inst/doc/introduction.R | 62 ++++----- inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 104 ++++++++-------- inst/doc/rule_files.R | 4 inst/doc/rule_files.html | 11 - inst/tinytest/test_confrontation.R | 11 + inst/tinytest/test_syntax.R | 45 ++++++- man/aggregate-validation-method.Rd | 27 ++-- man/all-validation-method.Rd | 23 ++- man/any-validation-method.Rd | 23 ++- man/as.data.frame-cellComparison-method.Rd | 20 +-- man/as.data.frame-confrontation-method.Rd | 19 +-- man/as.data.frame-expressionset-method.Rd | 24 ++- man/as.data.frame-validatorComparison-method.Rd | 20 +-- man/as.data.frame.Rd | 20 +-- man/barplot-cellComparison-method.Rd | 27 ++-- man/barplot-validation-method.Rd | 37 +++-- man/barplot-validatorComparison-method.Rd | 27 ++-- man/cells.Rd | 16 +- man/check_that.Rd | 23 ++- man/compare.Rd | 45 +++---- man/confront.Rd | 67 +++++----- man/confrontation-class.Rd | 15 +- man/created.Rd | 21 +-- man/description.Rd | 21 +-- man/errors.Rd | 17 +- man/event.Rd | 50 ++++---- man/exists_any.Rd |only man/export_yaml.Rd | 1 man/expr.Rd | 1 man/indication-class.Rd | 6 man/is_complete.Rd | 6 man/is_unique.Rd | 8 + man/keyset.Rd | 17 +- man/label.Rd | 21 +-- man/lbj_cells-class.Rd | 3 man/lbj_rules-class.Rd | 3 man/length.Rd | 16 +- man/match_cells.Rd | 16 +- man/meta.Rd | 21 +-- man/names.Rd | 20 +-- man/origin.Rd | 21 +-- man/plot-cellComparison-method.Rd | 20 +-- man/plot-validation-method.Rd | 23 ++- man/plot-validator-method.Rd | 38 ++++-- man/plot-validatorComparison-method.Rd | 20 +-- man/plus-indicator-indicator-method.Rd | 1 man/plus-validator-validator-method.Rd | 6 man/retailers.Rd | 2 man/run_validation_file.Rd | 3 man/select.Rd | 16 +- man/sort-validation-method.Rd | 27 ++-- man/sub-subset-expressionset-method.Rd | 1 man/subset-expressionset-method.Rd | 1 man/validate-summary.Rd | 53 ++++---- man/validate.Rd | 1 man/validate_extend.Rd | 34 ++--- man/validation-class.Rd | 22 ++- man/validator.Rd | 5 man/values.Rd | 40 +++--- man/variables.Rd | 46 ++++--- man/voptions.Rd | 43 ++++-- vignettes/JSS_3483.Rnw |only vignettes/introduction.Rmd | 4 vignettes/jss3483.pdf |only 79 files changed, 976 insertions(+), 681 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions.
Author: Manos Papadakis, Michail Tsagris, Stefanos Fafalios and Marios Dimitriadis.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.0.4 dated 2019-08-05 and 0.0.5 dated 2019-12-16
Rfast2-0.0.4/Rfast2/R/colborel.mle.R |only Rfast2-0.0.4/Rfast2/R/collogitnorm.mle.R |only Rfast2-0.0.4/Rfast2/R/collognorm.mle.R |only Rfast2-0.0.4/Rfast2/R/colspml.mle.R |only Rfast2-0.0.5/Rfast2/DESCRIPTION | 10 + Rfast2-0.0.5/Rfast2/MD5 | 100 ++++++++++++----- Rfast2-0.0.5/Rfast2/NAMESPACE | 11 + Rfast2-0.0.5/Rfast2/NEWS.md | 28 ++++ Rfast2-0.0.5/Rfast2/R/benchmark.R | 1 Rfast2-0.0.5/Rfast2/R/boot.james.R |only Rfast2-0.0.5/Rfast2/R/boot.student2.R |only Rfast2-0.0.5/Rfast2/R/circ.cors1.R | 2 Rfast2-0.0.5/Rfast2/R/circaov.R |only Rfast2-0.0.5/Rfast2/R/colGroup.R | 2 Rfast2-0.0.5/Rfast2/R/column_wise_mle.R |only Rfast2-0.0.5/Rfast2/R/cor_test.R |only Rfast2-0.0.5/Rfast2/R/depth.mahala.R |only Rfast2-0.0.5/Rfast2/R/fipois.reg.R |only Rfast2-0.0.5/Rfast2/R/gamma_regression.R |only Rfast2-0.0.5/Rfast2/R/gee.reg.R | 26 +--- Rfast2-0.0.5/Rfast2/R/halfcauchy.mle.R | 81 +++++++++----- Rfast2-0.0.5/Rfast2/R/jack.mean.R |only Rfast2-0.0.5/Rfast2/R/lm.parboot.R |only Rfast2-0.0.5/Rfast2/R/mmpc.R | 76 ++++++------- Rfast2-0.0.5/Rfast2/R/multivm.mle.R |only Rfast2-0.0.5/Rfast2/R/naive.bayes.classifiers.R |only Rfast2-0.0.5/Rfast2/R/overdispreg.test.R |only Rfast2-0.0.5/Rfast2/R/perm.ttest2.R |only Rfast2-0.0.5/Rfast2/R/propols.reg.R |only Rfast2-0.0.5/Rfast2/R/riag.R |only Rfast2-0.0.5/Rfast2/R/score.zipregs.R |only Rfast2-0.0.5/Rfast2/R/sp.logiregs.R | 4 Rfast2-0.0.5/Rfast2/README.md |only Rfast2-0.0.5/Rfast2/man/Rfast2-package.Rd | 26 +--- Rfast2-0.0.5/Rfast2/man/boot.james.Rd |only Rfast2-0.0.5/Rfast2/man/boot.student2.Rd |only Rfast2-0.0.5/Rfast2/man/cauchy0.mle.Rd |only Rfast2-0.0.5/Rfast2/man/cluster.lm.Rd | 2 Rfast2-0.0.5/Rfast2/man/coljack.means.Rd |only Rfast2-0.0.5/Rfast2/man/collognorm.mle.Rd | 27 ++++ Rfast2-0.0.5/Rfast2/man/cor_test.Rd |only Rfast2-0.0.5/Rfast2/man/depth.mahala.Rd |only Rfast2-0.0.5/Rfast2/man/fipois.reg.Rd |only Rfast2-0.0.5/Rfast2/man/gammareg.Rd |only Rfast2-0.0.5/Rfast2/man/gammaregs.Rd |only Rfast2-0.0.5/Rfast2/man/gee.reg.Rd | 6 - Rfast2-0.0.5/Rfast2/man/gumbel.reg.Rd | 2 Rfast2-0.0.5/Rfast2/man/halfcauchy.mle.Rd | 5 Rfast2-0.0.5/Rfast2/man/hcf.circaov.Rd |only Rfast2-0.0.5/Rfast2/man/jack.mean.Rd |only Rfast2-0.0.5/Rfast2/man/lm.drop1.Rd | 2 Rfast2-0.0.5/Rfast2/man/lm.parboot.Rd |only Rfast2-0.0.5/Rfast2/man/mmpc2.Rd | 2 Rfast2-0.0.5/Rfast2/man/multinom.reg.Rd | 2 Rfast2-0.0.5/Rfast2/man/multivm.mle.Rd |only Rfast2-0.0.5/Rfast2/man/negbin.reg.Rd | 2 Rfast2-0.0.5/Rfast2/man/overdispreg.test.Rd |only Rfast2-0.0.5/Rfast2/man/perm.ttest2.Rd |only Rfast2-0.0.5/Rfast2/man/propols.reg.Rd |only Rfast2-0.0.5/Rfast2/man/riag.Rd |only Rfast2-0.0.5/Rfast2/man/score.zipregs.Rd |only Rfast2-0.0.5/Rfast2/man/vm.nb.Rd |only Rfast2-0.0.5/Rfast2/man/vmnb.pred.Rd |only Rfast2-0.0.5/Rfast2/man/wald.poisrat.Rd | 6 - Rfast2-0.0.5/Rfast2/man/weibull.nb.Rd |only Rfast2-0.0.5/Rfast2/man/weibullnb.pred.Rd |only Rfast2-0.0.5/Rfast2/man/zigamma.mle.Rd | 2 Rfast2-0.0.5/Rfast2/man/ztp.reg.Rd | 2 Rfast2-0.0.5/Rfast2/src/fbed_reg.cpp | 138 +++++++++++++++++------- Rfast2-0.0.5/Rfast2/src/gamma_reg.cpp |only Rfast2-0.0.5/Rfast2/src/gamma_regs.cpp |only Rfast2-0.0.5/Rfast2/src/init.c | 4 Rfast2-0.0.5/Rfast2/src/mmp_c.cpp | 2 Rfast2-0.0.5/Rfast2/src/mmp_c.h | 1 74 files changed, 374 insertions(+), 198 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6.7 dated 2019-03-18 and 1.6.8 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/boot.R | 6 ++++-- R/msm.R | 13 ++++++++++--- build/vignette.rds |binary inst/NEWS | 10 ++++++++++ inst/doc/msm-manual.pdf |binary man/hmm-dists.Rd | 4 +++- man/prevalence.msm.Rd | 5 +++++ src/lik.c | 18 +++++++++++------- src/pijt.c | 4 +++- tests/testthat/test_models.r | 18 ++++++++++++++++++ tests/testthat/test_models_hmmmulti.r | 1 - 13 files changed, 80 insertions(+), 31 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut],
Manuel Oviedo de la Fuente [aut, cre],
Pedro Galeano [ctb],
Alicia Nieto [ctb],
Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Diff between fda.usc versions 2.0.0 dated 2019-11-14 and 2.0.1 dated 2019-12-16
DESCRIPTION | 16 - MD5 | 365 +++++++++++++++--------------- NAMESPACE | 32 +- NEWS | 23 + R/Descriptive.R | 57 +++- R/Outliers.fdata.R | 2 R/S.np.R | 16 - R/accuracy.R | 13 - R/classif.DD.aux.r | 6 R/classif.DD.r | 41 ++- R/classif.ML.R | 26 +- R/classif.depth.R | 20 - R/classif.gkam.R | 37 +-- R/classif.gkam_aux.R | 2 R/classif.glm.R | 7 R/classif.gsam.R | 7 R/classif.univariate.R | 8 R/corSigma.R | 6 R/create.fdata.basis.R | 22 - R/depth.fdata.r | 20 - R/depth.mdata.R | 6 R/depth.mfdata.r | 41 +-- R/dfv.test.R | 2 R/fanova.RPm.R | 25 +- R/fanova.RPm.boot.R | 17 - R/fanova.hetero.R | 4 R/fanova.onefactor.R | 8 R/fda.usc-package.R | 5 R/fda.usc.internal.R | 3 R/fdata.R | 19 + R/fdata.methods.R | 2 R/fdata2model.R |only R/fdata2pc.R | 2 R/flm.Ftest.R | 2 R/flm.test.R | 2 R/fregre.basis.R | 9 R/fregre.basis.cv.R | 6 R/fregre.basis.cv.old.R | 2 R/fregre.gkam.r | 10 R/fregre.glm.R | 32 +- R/fregre.gls.r | 4 R/fregre.gsam.R | 4 R/fregre.gsam.vs.R | 4 R/fregre.igls.r | 10 R/fregre.lm.r | 85 ++----- R/fregre.np.r | 2 R/fregre.pc.R | 8 R/fregre.plm.R | 28 +- R/kernels.R | 4 R/kmeans.assig.groups.R | 51 ++-- R/kmeans.center.ini.R | 43 ++- R/kmeans.centers.update.R | 67 +++-- R/kmeans.fd.R | 211 ++++++++++++----- R/kmeans.fd.dist.R |only R/ldata.R | 534 +++++++++++++++++++++++++++++++++++++++------ R/metric.dist.R | 49 ++-- R/omit.fdata.R | 4 R/optim.basis.R | 2 R/optim.np.r | 2 R/plot.depth.R | 2 R/plot.fdata.R | 6 R/predict.classif.DD.R | 6 R/predict.classif.R | 281 ++++++++++++++--------- R/predict.fregre.gls.r | 3 R/rwild.R | 6 R/subset.lfdata.R | 153 ++++++------ R/summary.anova.R | 2 R/summary.classif.R | 18 - R/summary.fregre.fd.r | 2 R/zzz.r | 186 +-------------- README.md |only inst/figures |only man/CV.S.Rd | 167 ++++++-------- man/Descriptive.Rd | 352 ++++++++++++++--------------- man/FDR.Rd | 110 ++++----- man/GCCV.S.Rd | 210 +++++++++-------- man/GCV.S.Rd | 160 +++++++------ man/Kernel.Rd | 114 ++++----- man/Kernel.asymmetric.Rd | 112 ++++----- man/Kernel.integrate.Rd | 128 +++++----- man/LMDC.select.Rd | 368 ++++++++++++++++--------------- man/MCO.Rd | 112 ++++----- man/Outliers.fdata.Rd | 183 ++++++++------- man/P.penalty.Rd | 100 ++++---- man/PCvM.statistic.Rd | 154 ++++++------ man/S.basis.Rd | 129 +++++----- man/S.np.Rd | 184 +++++++-------- man/Var.y.Rd | 102 ++++---- man/accuracy.Rd | 137 +++++------ man/aemet.Rd | 118 ++++----- man/classif.DD.Rd | 457 +++++++++++++++++++------------------- man/classif.ML.Rd | 318 ++++++++++++++------------ man/classif.depth.Rd | 150 ++++++------ man/classif.gkam.Rd | 230 ++++++++++--------- man/classif.glm.Rd | 242 ++++++++++---------- man/classif.gsam.Rd | 236 ++++++++++--------- man/classif.kfold.Rd | 263 +++++++++++----------- man/classif.np.Rd | 222 ++++++++++-------- man/cond.F.Rd | 202 ++++++++--------- man/cond.mode.Rd | 142 +++++------ man/cond.quantile.Rd | 173 +++++++------- man/create.fdata.basis.Rd | 211 +++++++++-------- man/dcor.xy.Rd | 237 +++++++++---------- man/depth.fdata.Rd | 484 ++++++++++++++++++++++------------------ man/depth.mdata.Rd | 281 +++++++++++------------ man/depth.mfdata.Rd | 380 +++++++++++++++++--------------- man/dev.S.Rd | 218 +++++++++--------- man/dfv.test.Rd | 244 ++++++++++---------- man/dis.cos.cor.Rd | 90 +++---- man/fanova.RPm.Rd | 326 ++++++++++++++------------- man/fanova.hetero.Rd | 178 +++++++-------- man/fanova.onefactor.Rd | 135 +++++------ man/fda.usc-package.Rd | 311 +++++++++++++------------- man/fda.usc.internal.Rd | 256 ++++++++++----------- man/fdata.Rd | 173 +++++++------- man/fdata.bootstrap.Rd | 236 ++++++++++--------- man/fdata.cen.Rd | 80 +++--- man/fdata.deriv.Rd | 144 ++++++------ man/fdata.methods.Rd | 188 +++++++-------- man/fdata2fd.Rd | 124 +++++----- man/fdata2pc.Rd | 157 ++++++------- man/fdata2pls.Rd | 173 +++++++------- man/flm.Ftest.Rd | 172 +++++++------- man/flm.test.Rd | 497 +++++++++++++++++++++-------------------- man/fregre.basis.Rd | 286 ++++++++++++------------ man/fregre.basis.cv.Rd | 268 +++++++++++----------- man/fregre.basis.fr.Rd | 321 +++++++++++++-------------- man/fregre.bootstrap.Rd | 226 +++++++++---------- man/fregre.gkam.Rd | 269 +++++++++++----------- man/fregre.glm.Rd | 256 +++++++++++---------- man/fregre.gls.Rd | 258 +++++++++++---------- man/fregre.gsam.Rd | 300 ++++++++++++------------- man/fregre.gsam.vs.Rd | 282 ++++++++++++----------- man/fregre.igls.Rd | 235 ++++++++++--------- man/fregre.lm.Rd | 274 +++++++++++------------ man/fregre.np.Rd | 244 ++++++++++---------- man/fregre.np.cv.Rd | 279 ++++++++++++----------- man/fregre.pc.Rd | 271 +++++++++++----------- man/fregre.pc.cv.Rd | 270 +++++++++++----------- man/fregre.plm.Rd | 323 +++++++++++++-------------- man/fregre.pls.Rd | 217 +++++++++--------- man/fregre.pls.cv.Rd | 225 +++++++++--------- man/h.default.Rd | 118 +++++---- man/influence.fregre.fd.Rd | 136 +++++------ man/influence_quan.Rd | 178 +++++++-------- man/inprod.fdata.Rd | 116 ++++----- man/int.simpson.Rd | 102 ++++---- man/kmeans.fd.Rd | 222 ++++++++++-------- man/ldata.Rd | 138 ++++++----- man/metric.DTW.Rd | 171 +++++++------- man/metric.dist.Rd | 101 ++++---- man/metric.hausdorff.Rd | 108 ++++----- man/metric.kl.Rd | 179 +++++++-------- man/metric.ldata.Rd | 122 +++++----- man/metric.lp.Rd | 198 ++++++++-------- man/na.omit.fdata.Rd | 80 +++--- man/norm.fdata.Rd | 128 +++++----- man/ops.fda.usc.Rd | 91 ++++--- man/optim.basis.Rd | 278 ++++++++++++----------- man/optim.np.Rd | 279 ++++++++++++----------- man/phoneme.Rd | 106 ++++---- man/plot.fdata.Rd | 246 ++++++++++---------- man/poblenou.Rd | 100 ++++---- man/predict.classif.DD.Rd | 159 ++++++------- man/predict.classif.Rd | 147 ++++++------ man/predict.fregre.fd.Rd | 271 +++++++++++----------- man/predict.fregre.fr.Rd | 140 +++++------ man/predict.fregre.gls.Rd | 204 +++++++++-------- man/predict.fregre.lm.Rd | 313 +++++++++++++------------- man/r.ou.Rd | 84 +++---- man/rcombfdata.Rd | 129 +++++----- man/rdir.pc.Rd | 274 +++++++++++------------ man/rp.flm.statistic.Rd | 206 ++++++++--------- man/rp.flm.test.Rd | 476 ++++++++++++++++++++-------------------- man/rproc2fdata.Rd | 181 +++++++-------- man/rwild.Rd | 114 ++++----- man/semimetric.NPFDA.Rd | 302 +++++++++++++------------ man/semimetric.basis.Rd | 143 ++++++------ man/subset.fdata.Rd | 56 ++-- man/summary.classif.Rd | 128 +++++----- man/summary.fdata.comp.Rd | 123 +++++----- man/summary.fregre.fd.Rd | 169 +++++++------- man/summary.fregre.gkam.Rd | 125 +++++----- man/tecator.Rd | 80 +++--- man/weights4class.Rd | 41 +-- 185 files changed, 13252 insertions(+), 12184 deletions(-)
Title: End-Member Modelling of Grain-Size Data
Description: End-member modelling analysis of grain-size data is an approach
to unmix a data set's underlying distributions and their contribution to
the data set. EMMAgeo provides deterministic and robust protocols for
that purpose.
Author: Michael Dietze, Elisabeth Dietze
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>
Diff between EMMAgeo versions 0.9.6 dated 2019-05-17 and 0.9.7 dated 2019-12-16
EMMAgeo-0.9.6/EMMAgeo/R/EMMAgeo-internal.R |only EMMAgeo-0.9.7/EMMAgeo/DESCRIPTION | 14 - EMMAgeo-0.9.7/EMMAgeo/MD5 | 45 +++--- EMMAgeo-0.9.7/EMMAgeo/NEWS | 6 EMMAgeo-0.9.7/EMMAgeo/R/EMMA.R | 28 ++- EMMAgeo-0.9.7/EMMAgeo/R/EMMAgeo-package.R | 2 EMMAgeo-0.9.7/EMMAgeo/R/get.l.R | 4 EMMAgeo-0.9.7/EMMAgeo/R/get.limits.R | 4 EMMAgeo-0.9.7/EMMAgeo/R/get.q.R | 4 EMMAgeo-0.9.7/EMMAgeo/R/model.EM.R | 6 EMMAgeo-0.9.7/EMMAgeo/R/robust.EM.R | 31 ++-- EMMAgeo-0.9.7/EMMAgeo/R/robust.loadings.R | 164 +++++++++++++---------- EMMAgeo-0.9.7/EMMAgeo/R/test.robustness.R | 40 ++++- EMMAgeo-0.9.7/EMMAgeo/R/zzz.R | 2 EMMAgeo-0.9.7/EMMAgeo/inst/shiny/EMMA/ui.R | 2 EMMAgeo-0.9.7/EMMAgeo/man/EMMA.Rd | 19 ++ EMMAgeo-0.9.7/EMMAgeo/man/EMMAgeo-package.Rd | 2 EMMAgeo-0.9.7/EMMAgeo/man/get.q.Rd | 12 + EMMAgeo-0.9.7/EMMAgeo/man/interpolate.classes.Rd | 9 - EMMAgeo-0.9.7/EMMAgeo/man/model.EM.Rd | 2 EMMAgeo-0.9.7/EMMAgeo/man/robust.EM.Rd | 43 +++--- EMMAgeo-0.9.7/EMMAgeo/man/robust.loadings.Rd | 17 +- EMMAgeo-0.9.7/EMMAgeo/man/test.parameters.Rd | 13 + EMMAgeo-0.9.7/EMMAgeo/man/test.robustness.Rd | 16 +- 24 files changed, 312 insertions(+), 173 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>),
Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>),
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e9>s Bov<e9> [ctb],
Ma<eb>lle Salmon [ctb],
Dirk Schumacher [ctb],
Stefan Steiner [ctb],
Mikko Virtanen [ctb],
Wei Wei [ctb],
Valentin Wimmer [ctb],
R Core Team [ctb] (A few code segments are modified versions of code
from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.17.2 dated 2019-11-12 and 1.17.3 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- R/algo_call.R | 4 ++-- R/algo_hhh.R | 16 ++++++++-------- R/bodaDelay.R | 2 +- R/disProg.R | 2 +- R/epidataCS_methods.R | 25 ++++++++++++++----------- R/plot.survRes.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary demo/v77i11.R | 2 ++ inst/NEWS.Rd | 14 ++++++++++++++ inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.pdf |binary inst/doc/twinstim.pdf |binary vignettes/surveillance-hmm.pdf |binary 20 files changed, 66 insertions(+), 47 deletions(-)
Title: Data Mining Classification and Regression Methods
Description: Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.3 new metrics (e.g., macro precision, explained variance), new least squares support vector machine model and improved mparheuristic function; 1.4.2 new NMAE metric, "xgboost" and "cv.glmnet" models (16 classification and 18 regression models); 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models/algorithms, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vector Machines, Random Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression metrics (improved mmetric function); 1.2 - new input importance methods (improved Importance function); 1.0 - first version.
Author: Paulo Cortez [aut, cre]
Maintainer: Paulo Cortez <pcortez@dsi.uminho.pt>
Diff between rminer versions 1.4.2 dated 2016-09-02 and 1.4.3 dated 2019-12-16
DESCRIPTION | 12 - MD5 | 24 +-- NAMESPACE | 2 R/metrics.R | 306 ++++++++++++++++++++++++++++++++----------------- R/model.R | 170 +++++++++++++++++++++------ R/preprocess.R | 9 - man/fit.Rd | 57 ++++++++- man/mgraph.Rd | 2 man/mining.Rd | 10 + man/mmetric.Rd | 135 +++++++++++++++------ man/mparheuristic.Rd | 174 ++++++++++++++++++++++++--- man/predict-methods.Rd | 2 man/savemining.Rd | 10 + 13 files changed, 678 insertions(+), 235 deletions(-)
Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut],
Enrico Crema [aut, cre],
Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>
Diff between rcarbon versions 1.2.0 dated 2018-10-01 and 1.3.0 dated 2019-12-16
rcarbon-1.2.0/rcarbon/man/SPpermTest.Rd |only rcarbon-1.2.0/rcarbon/man/plot.spdGG.Rd |only rcarbon-1.2.0/rcarbon/man/spd2gg.Rd |only rcarbon-1.3.0/rcarbon/DESCRIPTION | 15 rcarbon-1.3.0/rcarbon/MD5 | 99 - rcarbon-1.3.0/rcarbon/NAMESPACE | 18 rcarbon-1.3.0/rcarbon/NEWS.md | 42 rcarbon-1.3.0/rcarbon/R/aggregation.R | 489 +++++++ rcarbon-1.3.0/rcarbon/R/calibration.R | 371 +++-- rcarbon-1.3.0/rcarbon/R/data.R | 44 rcarbon-1.3.0/rcarbon/R/package-rcarbon.R | 4 rcarbon-1.3.0/rcarbon/R/plots.R | 1438 ++++++++++++++------- rcarbon-1.3.0/rcarbon/R/rcarbon-deprecated.R |only rcarbon-1.3.0/rcarbon/R/tests.R | 680 +++++++-- rcarbon-1.3.0/rcarbon/R/utilities.R | 483 +++++-- rcarbon-1.3.0/rcarbon/README.md | 53 rcarbon-1.3.0/rcarbon/build/vignette.rds |binary rcarbon-1.3.0/rcarbon/data/euroevol.rda |binary rcarbon-1.3.0/rcarbon/data/ewdates.rda |only rcarbon-1.3.0/rcarbon/data/ewowin.rda |only rcarbon-1.3.0/rcarbon/inst/doc/rcarbon.Rmd | 235 ++- rcarbon-1.3.0/rcarbon/inst/doc/rcarbon.html | 317 +++- rcarbon-1.3.0/rcarbon/man/BCADtoBP.Rd | 4 rcarbon-1.3.0/rcarbon/man/BPtoBCAD.Rd | 2 rcarbon-1.3.0/rcarbon/man/SPpermTest-deprecated.Rd |only rcarbon-1.3.0/rcarbon/man/as.CalDates.Rd |only rcarbon-1.3.0/rcarbon/man/as.UncalGrid.Rd |only rcarbon-1.3.0/rcarbon/man/binPrep.Rd | 4 rcarbon-1.3.0/rcarbon/man/binsense.Rd | 2 rcarbon-1.3.0/rcarbon/man/calibrate.Rd | 25 rcarbon-1.3.0/rcarbon/man/ckde.Rd |only rcarbon-1.3.0/rcarbon/man/euroevol.Rd | 2 rcarbon-1.3.0/rcarbon/man/ewdates.Rd |only rcarbon-1.3.0/rcarbon/man/ewowin.Rd |only rcarbon-1.3.0/rcarbon/man/gaussW.Rd |only rcarbon-1.3.0/rcarbon/man/mixCurves.Rd | 25 rcarbon-1.3.0/rcarbon/man/modelTest.Rd | 43 rcarbon-1.3.0/rcarbon/man/p2pTest.Rd | 2 rcarbon-1.3.0/rcarbon/man/permTest.Rd | 11 rcarbon-1.3.0/rcarbon/man/plot.CalDates.Rd | 18 rcarbon-1.3.0/rcarbon/man/plot.CalSPD.Rd | 4 rcarbon-1.3.0/rcarbon/man/plot.SpdModelTest.Rd | 15 rcarbon-1.3.0/rcarbon/man/plot.SpdPermTest.Rd | 10 rcarbon-1.3.0/rcarbon/man/plot.compositeKDE.Rd |only rcarbon-1.3.0/rcarbon/man/plot.spatialTest.Rd | 2 rcarbon-1.3.0/rcarbon/man/plot.spdRC.Rd |only rcarbon-1.3.0/rcarbon/man/plot.stKde.Rd |only rcarbon-1.3.0/rcarbon/man/rcarbon-deprecated.Rd |only rcarbon-1.3.0/rcarbon/man/rcarbon.Rd | 4 rcarbon-1.3.0/rcarbon/man/sampleDates.Rd |only rcarbon-1.3.0/rcarbon/man/smoothGauss.Rd | 5 rcarbon-1.3.0/rcarbon/man/spd.Rd | 4 rcarbon-1.3.0/rcarbon/man/spd2rc.Rd |only rcarbon-1.3.0/rcarbon/man/spkde.Rd |only rcarbon-1.3.0/rcarbon/man/sptest.Rd |only rcarbon-1.3.0/rcarbon/man/stkde.Rd |only rcarbon-1.3.0/rcarbon/man/subset.CalDates.Rd |only rcarbon-1.3.0/rcarbon/man/summary.SpdModelTest.Rd | 6 rcarbon-1.3.0/rcarbon/man/summary.SpdPermTest.Rd | 6 rcarbon-1.3.0/rcarbon/man/thinDates.Rd |only rcarbon-1.3.0/rcarbon/man/uncalibrate.Rd | 2 rcarbon-1.3.0/rcarbon/man/which.CalDates.Rd |only rcarbon-1.3.0/rcarbon/vignettes/rcarbon.Rmd | 235 ++- 63 files changed, 3481 insertions(+), 1238 deletions(-)
Title: Pretty Print R Code in the Terminal
Description: Replace the standard print method for functions with one that
performs syntax highlighting, using ANSI colors, if the terminal
supports them.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between prettycode versions 1.0.2 dated 2018-09-11 and 1.1.0 dated 2019-12-16
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++++----------- NAMESPACE | 2 +- NEWS.md | 16 +++++++++++++--- R/brackets.R |only R/highlight.R | 7 +++++++ R/print.R | 27 ++++++++++++++++----------- R/rstudio-detect.R |only R/style.R | 36 +++++++++++++++++++++++++++++++++--- R/sysdata.rda |only R/utils.R | 2 ++ inst/README.markdown | 2 +- man/color_brackets.Rd |only man/default_style.Rd | 4 +++- tests/testthat/test-brackets.R |only tests/testthat/test-highlight.R | 7 +++++++ tests/testthat/test-style.R | 2 +- tools |only 18 files changed, 106 insertions(+), 37 deletions(-)
Title: Discretization and Grouping for Logistic Regression
Description: A Stochastic-Expectation-Maximization (SEM) algorithm (Celeux et al. (1995) <https://hal.inria.fr/inria-00074164>) associated with a Gibbs sampler which purpose is to learn a constrained representation for logistic regression that is called quantization (Ehrhardt et al. (2019) <arXiv:1903.08920>). Continuous features are discretized and categorical features' values are grouped to produce a better logistic regression model. Pairwise interactions between quantized features are dynamically added to the model through a Metropolis-Hastings algorithm (Hastings, W. K. (1970) <doi:10.1093/biomet/57.1.97>).
Author: Adrien Ehrhardt [aut, cre],
Vincent Vandewalle [aut],
Christophe Biernacki [ctb],
Philippe Heinrich [ctb]
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@centraliens-lille.org>
Diff between glmdisc versions 0.2 dated 2019-09-16 and 0.3 dated 2019-12-16
DESCRIPTION | 14 MD5 | 69 NAMESPACE | 30 R/RcppExports.R | 30 R/allClasses.R | 26 R/cut.dataset.R | 104 R/discretize.link.R | 166 - R/generic_cutpoints.R | 23 R/generic_discretize.R | 28 R/glmdisc.R | 62 R/method_cutpoints.R | 98 R/method_discretize.R | 46 R/method_plot.R | 154 - R/method_predict.R | 139 - R/methods_disc.R | 74 R/normalizedGini.R | 54 R/semDiscretization.R | 1414 +++++------ README.md |only build/vignette.rds |binary inst/doc/glmdisc.R | 386 +-- inst/doc/glmdisc.Rmd | 1024 ++++---- inst/doc/glmdisc.html | 3916 ++++++++++++++++----------------- man/contr.ltfr.Rd | 2 man/cutpoints-method.Rd | 7 man/discretize.Rd | 15 man/glmdisc-class.Rd | 1 man/glmdisc.Rd | 15 man/plot.Rd | 2 man/predict.Rd | 6 tests/testthat.R | 8 tests/testthat/test-cut-dataset.R | 88 tests/testthat/test-discretize-link.R | 54 tests/testthat/test-method_cutpoints.R | 30 tests/testthat/test-method_predict.R | 34 tests/testthat/test-normalizedgini.R | 14 vignettes/glmdisc.Rmd | 1024 ++++---- 36 files changed, 4575 insertions(+), 4582 deletions(-)
Title: An Implementation of Parametric and Nonparametric Event Study
Description: An implementation of a most commonly used event study methodology,
including both parametric and nonparametric tests. It contains variety
aspects of the rate of return estimation (the core calculation is done in
C++), as well as three classical for event study market models: mean
adjusted returns, market adjusted returns and single-index market models.
There are 6 parametric and 6 nonparametric tests provided, which examine
cross-sectional daily abnormal return (see the documentation of the
functions for more information). Parametric tests include tests proposed by
Brown and Warner (1980) <DOI:10.1016/0304-405X(80)90002-1>, Brown and Warner
(1985) <DOI:10.1016/0304-405X(85)90042-X>, Boehmer et al. (1991)
<DOI:10.1016/0304-405X(91)90032-F>, Patell (1976) <DOI:10.2307/2490543>, and
Lamb (1995) <DOI:10.2307/253695>. Nonparametric tests covered in estudy2 are
tests described in Corrado and Zivney (1992) <DOI:10.2307/2331331>,
McConnell and Muscarella (1985) <DOI:10.1016/0304-405X(85)90006-6>,
Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Cowan (1992)
<DOI:10.1007/BF00939016>, Corrado (1989) <DOI:10.1016/0304-405X(89)90064-0>,
Campbell and Wasley (1993) <DOI:10.1016/0304-405X(93)90025-7>, Savickas (2003)
<DOI:10.1111/1475-6803.00052>, Kolari and Pynnonen (2010)
<DOI:10.1093/rfs/hhq072>. Furthermore, tests for the cumulative
abnormal returns proposed by Brown and Warner (1985)
<DOI:10.1016/0304-405X(85)90042-X> and Lamb (1995) <DOI:10.2307/253695>
are included.
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Diff between estudy2 versions 0.9.0 dated 2019-04-25 and 0.9.1 dated 2019-12-16
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/apply_market_model.R | 3 ++- README.md | 2 ++ build/vignette.rds |binary inst/doc/estudy2-intro.html | 13 ++++++++----- man/returns.Rd | 3 ++- 8 files changed, 32 insertions(+), 20 deletions(-)
Title: Names Your 'R Markdown' Chunks
Description: It names the 'R Markdown' chunks of files based on the filename.
Author: Steph Locke [aut, cre],
Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>),
Ellis Valentiner [ctb],
Martin Hadley [ctb] (<https://orcid.org/0000-0002-3039-6849>),
Locke Data [fnd] (https://itsalocke.com),
Han Oostdijk [ctb] (<https://orcid.org/0000-0001-6710-4566>)
Maintainer: Steph Locke <steph@itsalocke.com>
Diff between namer versions 0.1.4 dated 2019-03-26 and 0.1.5 dated 2019-12-16
DESCRIPTION | 24 ++++++---- MD5 | 22 +++++----- NEWS.md | 6 ++ R/unname_all_chunks.R | 32 ++++++++++++-- build/vignette.rds |binary inst/doc/namer.R | 2 inst/doc/namer.Rmd | 17 +++++++ inst/doc/namer.html | 24 ++++++++-- inst/examples/example4.Rmd | 4 + man/unname_all_chunks.Rd | 20 +++++++-- tests/testthat/test-unname_all_chunks.R | 70 +++++++++++++++++++++++++++++++- vignettes/namer.Rmd | 17 +++++++ 12 files changed, 201 insertions(+), 37 deletions(-)
Title: Hierarchical Model of Species Communities
Description: Hierarchical Modelling of Species Communities (HMSC) is
a model-based approach for analyzing community ecological data.
This package implements it in the Bayesian framework with Gibbs
Markov chain Monte Carlo (MCMC) sampling.
Author: Gleb Tikhonov [aut],
Otso Ovaskainen [aut, cre] (<https://orcid.org/0000-0001-9750-4421>),
Jari Oksanen [aut],
Melinda de Jonge [aut],
Oystein Opedal [aut],
Tad Dallas [aut]
Maintainer: Otso Ovaskainen <otso.ovaskainen@helsinki.fi>
Diff between Hmsc versions 3.0-2 dated 2019-10-13 and 3.0-4 dated 2019-12-16
DESCRIPTION | 10 - MD5 | 92 +++++++-------- NAMESPACE | 4 R/Hmsc.R | 26 ++-- R/alignPosterior.R | 15 +- R/biPlot.R | 10 - R/computeInitialParameters.R | 6 R/computePredictedValues.R | 4 R/computeVariancePartitioning.R | 8 - R/computeWAIC.R | 2 R/constructGradient.R | 10 - R/evaluateModelFit.R | 5 R/plotBeta.R | 57 +++++---- R/plotGamma.R | 2 R/plotGradient.R | 8 - R/predict.R | 6 R/sampleMcmc.R | 9 - R/samplePrior.R | 2 R/setPriors.HmscRandomLevel.R | 2 R/updateBetaLambda.R | 10 - R/updateEta.R | 14 +- R/updateInvSigma.R | 4 R/updateZ.R | 2 R/updatewRRR.R | 6 README.md | 6 inst/NEWS.md |only inst/README.md |only inst/doc/vignette_3_multivariate_high.pdf |binary man/Hmsc.Rd | 32 ++++- man/HmscRandomLevel.Rd | 13 +- man/biPlot.Rd | 12 + man/computePredictedValues.Rd | 19 ++- man/computeVariancePartitioning.Rd | 9 + man/constructGradient.Rd | 3 man/constructKnots.Rd | 3 man/convertToCodaObject.Rd | 25 +++- man/getPostEstimate.Rd | 12 + man/plotBeta.Rd | 31 +++-- man/plotGamma.Rd | 24 ++- man/plotGradient.Rd | 20 ++- man/poolMcmcChains.Rd | 3 man/predict.Hmsc.Rd | 22 ++- man/predictLatentFactor.Rd | 11 + man/sampleMcmc.Rd | 24 ++- man/setPriors.Hmsc.Rd | 21 ++- man/setPriors.HmscRandomLevel.Rd | 16 ++ tests/Examples/Hmsc-Ex.Rout.save | 135 +++------------------- vignettes/vignette_3_multivariate_high.Rmd | 176 ++++++++++++++++++++--------- 48 files changed, 557 insertions(+), 374 deletions(-)
Title: Factor Modeling for Radiomics Data
Description: Functions that support stable prediction and classification with radiomics data through factor-analytic modeling. For details, see Peeters et al. (2019) <arXiv:1903.11696>.
Author: Carel F.W. Peeters [cre, aut], Caroline Ubelhor [ctb], Kevin Kunzmann [ctb]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between FMradio versions 1.1 dated 2019-05-03 and 1.1.1 dated 2019-12-16
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/FMradio.R | 14 +++++++------- README.md | 3 +++ man/FMradio-package.Rd | 3 ++- man/radioHeat.Rd | 2 +- 6 files changed, 23 insertions(+), 18 deletions(-)
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>),
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb],
Dave Foster [ctb],
Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 1.0.1 dated 2019-05-14 and 1.0.2 dated 2019-12-16
repr-1.0.1/repr/man/repr_vega-open-paren-4-slash-lite2-close-paren-.-times.Rd |only repr-1.0.2/repr/DESCRIPTION | 8 +- repr-1.0.2/repr/MD5 | 20 +++--- repr-1.0.2/repr/NAMESPACE | 6 ++ repr-1.0.2/repr/R/generics.r | 29 +++++++++ repr-1.0.2/repr/R/repr_matrix_df.r | 10 +-- repr-1.0.2/repr/R/repr_vega.r | 4 - repr-1.0.2/repr/R/utils.r | 6 +- repr-1.0.2/repr/man/repr-generics.Rd | 18 ++++++ repr-1.0.2/repr/man/repr_vega-times.Rd |only repr-1.0.2/repr/tests/testthat/test_escaping.r | 4 - repr-1.0.2/repr/tests/testthat/test_repr_array_df.r | 30 ++++++++++ 12 files changed, 110 insertions(+), 25 deletions(-)
More information about dBlockmodeling at CRAN
Permanent link
Title: Correlated Trait Locus Mapping
Description: Identification and network inference of genetic loci associated
with correlation changes in quantitative traits (called correlated trait loci, CTLs).
Arends et al. (2016) <doi:10.21105/joss.00087>.
Author: Danny Arends <Danny.Arends@gmail.com>, Yang Li, Gudrun A Brockmann,
Ritsert C Jansen, Robert W Williams, and Pjotr Prins
Maintainer: Danny Arends <Danny.Arends@gmail.com>
Diff between ctl versions 1.0.0-2 dated 2018-08-03 and 1.0.0-4 dated 2019-12-16
DESCRIPTION | 19 ++++++++++------- MD5 | 29 +++++++++++++------------- NAMESPACE | 3 +- R/ctl.effects.R |only R/ctl.image.R | 30 +++++++++++++-------------- R/ctl.lineplot.R | 2 - R/ctl.network.R | 2 - R/ctl.plot.R | 2 - R/ctl.scan.R | 8 +++---- R/ctl.statistics.R | 4 +-- inst/doc/manual.pdf |binary man/ctl-internal.Rd | 4 +++ man/ctl.image.Rd | 6 ++--- man/qtl.image.Rd | 6 +++-- src/correlation.c | 55 ++++++++++++++++++++++++++++---------------------- tests/test_ctl_long.R | 6 ++--- 16 files changed, 97 insertions(+), 79 deletions(-)
Title: Spatially Balanced Sampling
Description: Selection of spatially balanced samples. In particular, the implemented sampling designs allow to select probability samples well spread over the population of interest, in any dimension and using any distance function (e.g. Euclidean distance, Manhattan distance). For more details, Benedetti R and Piersimoni F (2017) <doi:10.1002/bimj.201600194> and Benedetti R and Piersimoni F (2017) <arXiv:1710.09116>. The implementation has been done in C++ through the use of 'Rcpp' and 'RcppArmadillo'.
Author: Francesco Pantalone [aut, cre],
Roberto Benedetti [aut],
Federica Piersimoni [aut]
Maintainer: Francesco Pantalone <pantalone.fra@gmail.com>
Diff between Spbsampling versions 1.3.0 dated 2019-08-04 and 1.3.1 dated 2019-12-16
DESCRIPTION | 6 +++--- MD5 | 29 +++++++++++++++-------------- NEWS.md | 9 ++++++++- R/RcppExports.R | 48 ++++++++++++++++++++++++------------------------ inst/CITATION |only man/hpwd.Rd | 8 ++++---- man/pwd.Rd | 8 ++++---- man/stprod.Rd | 8 ++++---- man/stsum.Rd | 6 +++--- man/swd.Rd | 8 ++++---- src/RcppExports.cpp | 40 ++++++++++++++++++++-------------------- src/hpwd.cpp | 14 +++++++------- src/pwd.cpp | 16 ++++++++-------- src/stprod.cpp | 16 ++++++++-------- src/stsum.cpp | 18 +++++++++--------- src/swd.cpp | 16 ++++++++-------- 16 files changed, 129 insertions(+), 121 deletions(-)
Title: Mixture Models with Heterogeneous and (Partially) Missing Data
Description: Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with
heterogeneous data sets and partially missing data management.
It includes models for real, categorical, counting, functional and ranking data.
This package contains the minimal R interface of the C++ 'MixtComp' library.
Author: Vincent Kubicki [aut],
Christophe Biernacki [aut],
Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb],
Matthieu Marbac-Lourdelle [ctb],
Étienne Goffinet [ctb],
Patrick Wieschollek [ctb] (for CppOptimizationLibrary),
Tobias Wood [ctb] (for CppOptimizationLibrary)
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between RMixtCompIO versions 4.0.1 dated 2019-09-02 and 4.0.2 dated 2019-12-16
RMixtCompIO-4.0.1/RMixtCompIO/inst/doc |only RMixtCompIO-4.0.2/RMixtCompIO/DESCRIPTION | 14 +-- RMixtCompIO-4.0.2/RMixtCompIO/MD5 | 39 ++++---- RMixtCompIO-4.0.2/RMixtCompIO/NAMESPACE | 1 RMixtCompIO-4.0.2/RMixtCompIO/NEWS | 5 + RMixtCompIO-4.0.2/RMixtCompIO/R/RMixtCompIO-package.R | 2 RMixtCompIO-4.0.2/RMixtCompIO/R/TEST_paramModel.R | 6 - RMixtCompIO-4.0.2/RMixtCompIO/R/rmcMultiRun.R | 45 ++++------ RMixtCompIO-4.0.2/RMixtCompIO/man/rmcMultiRun.Rd | 11 ++ RMixtCompIO-4.0.2/RMixtCompIO/src/lib/Composer/MixtureComposer.cpp | 3 RMixtCompIO-4.0.2/RMixtCompIO/src/lib/Composer/MixtureComposer.h | 2 RMixtCompIO-4.0.2/RMixtCompIO/src/lib/Manager/createAllMixtures.h | 3 RMixtCompIO-4.0.2/RMixtCompIO/src/lib/Mixture/Rank/RankMixture.h | 2 RMixtCompIO-4.0.2/RMixtCompIO/src/optim/BUILD | 2 RMixtCompIO-4.0.2/RMixtCompIO/src/optim/include/cppoptlib/solver/lbfgsbsolver.h | 13 ++ RMixtCompIO-4.0.2/RMixtCompIO/src/optim/include/cppoptlib/solver/neldermeadsolver.h | 6 - RMixtCompIO-4.0.2/RMixtCompIO/src/optim/src/examples/nonnegls2.cpp |only RMixtCompIO-4.0.2/RMixtCompIO/src/optim/src/examples/rosenbrock.cpp | 4 RMixtCompIO-4.0.2/RMixtCompIO/src/optim/src/examples/rosenbrock_float.cpp | 4 RMixtCompIO-4.0.2/RMixtCompIO/tests/testthat/test.run.R | 6 - RMixtCompIO-4.0.2/RMixtCompIO/tests/testthat/test.simpleRun.R | 2 21 files changed, 96 insertions(+), 74 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.3.0 dated 2019-11-14 and 0.3.1 dated 2019-12-16
DESCRIPTION | 13 ++++--- MD5 | 78 ++++++++++++++++++++++----------------------- NEWS.md | 12 ++++++ R/anova_test.R | 8 ++-- R/binom_test.R | 6 +-- R/chisq_test.R | 2 - R/cochran_qtest.R | 2 - R/cohens_d.R | 2 - R/doo.R | 9 ++++- R/dunn_test.R | 16 +++++++-- R/friedman_test.R | 18 +++++----- R/get_pvalue_position.R | 2 - R/kruskal_test.R | 9 ++++- R/mcnemar_test.R | 2 - R/multinom_test.R | 2 - R/outliers.R | 2 + R/p_value.R | 2 - R/prop_test.R | 2 - R/shapiro_test.R | 4 +- R/sign_test.R | 3 + R/t_test.R | 3 - R/wilcox_test.R | 2 - README.md | 12 ++++++ inst/WORDLIST | 12 ++++++ man/anova_test.Rd | 8 ++-- man/binom_test.Rd | 6 +-- man/chisq_test.Rd | 2 - man/cochran_qtest.Rd | 2 - man/cohens_d.Rd | 2 - man/dunn_test.Rd | 5 ++ man/friedman_test.Rd | 12 ++++-- man/get_pvalue_position.Rd | 2 - man/mcnemar_test.Rd | 2 - man/multinom_test.Rd | 2 - man/p_value.Rd | 2 - man/prop_test.Rd | 2 - man/shapiro_test.Rd | 4 +- man/sign_test.Rd | 3 + man/t_test.Rd | 2 - man/wilcox_test.Rd | 2 - 40 files changed, 175 insertions(+), 106 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between rmdformats versions 0.3.5 dated 2019-02-19 and 0.3.6 dated 2019-12-16
DESCRIPTION | 11 MD5 | 58 - NAMESPACE | 3 NEWS | 14 R/create.doc.R | 2 R/html_clean.R | 3 R/html_docco.R | 5 R/material.R | 3 R/pilltabs.R | 1 R/readthedown.R | 3 build/vignette.rds |binary inst/doc/introduction.html | 393 ++++++++----- inst/rmarkdown/templates/html_clean/skeleton/skeleton.Rmd | 2 inst/rmarkdown/templates/html_docco/skeleton/skeleton.Rmd | 2 inst/rmarkdown/templates/material/skeleton/skeleton.Rmd | 2 inst/rmarkdown/templates/readthedown/skeleton/skeleton.Rmd | 2 inst/templates/html_clean/html_clean.html | 2 inst/templates/material/material.css | 4 inst/templates/material/material.html | 3 inst/templates/material/material.js | 47 + inst/templates/navigation-1.1/codefolding.js | 4 inst/templates/navigation-1.1/tabsets.js | 50 + inst/templates/readthedown/readthedown.css | 13 inst/templates/readthedown/readthedown.html | 2 inst/templates/readthedown/readthedown.js | 11 man/create.doc.Rd | 2 man/html_clean.Rd | 7 man/html_docco.Rd | 6 man/material.Rd | 5 man/readthedown.Rd | 6 30 files changed, 457 insertions(+), 209 deletions(-)
Title: Solver for Partially Observable Markov Decision Processes
(POMDP)
Description: Provides an interface to pomdp-solve, a solver for Partially Observable Markov Decision Processes (POMDP). The package enables the user to simply define all components of a POMDP model and solve the problem using several methods. The package also contains functions to analyze and visualize the POMDP solutions (e.g., the optimal policy).
Author: Hossein Kamalzadeh [aut, cph, cre],
Michael Hahsler [aut, cph],
Anthony R. Cassandra [ctb, cph]
Maintainer: Hossein Kamalzadeh <hkamalzadeh@smu.edu>
Diff between pomdp versions 0.9.1-1 dated 2019-05-14 and 0.9.2 dated 2019-12-16
pomdp-0.9.1-1/pomdp/R/POMDP_model.R |only pomdp-0.9.1-1/pomdp/R/igraph_fix.R |only pomdp-0.9.1-1/pomdp/R/model.R |only pomdp-0.9.1-1/pomdp/R/solution.R |only pomdp-0.9.1-1/pomdp/R/solver_output.R |only pomdp-0.9.1-1/pomdp/R/transitions.R |only pomdp-0.9.1-1/pomdp/man/transitions.Rd |only pomdp-0.9.2/pomdp/DESCRIPTION | 10 pomdp-0.9.2/pomdp/MD5 | 59 ++-- pomdp-0.9.2/pomdp/NAMESPACE | 8 pomdp-0.9.2/pomdp/NEWS.md | 16 + pomdp-0.9.2/pomdp/R/POMDP.R |only pomdp-0.9.2/pomdp/R/plot.POMDP.R | 148 +++++++----- pomdp-0.9.2/pomdp/R/solve_POMDP.R | 259 +++++++++++---------- pomdp-0.9.2/pomdp/R/write_POMDP.R | 53 ++-- pomdp-0.9.2/pomdp/README.md | 4 pomdp-0.9.2/pomdp/data/TigerProblem.rda |binary pomdp-0.9.2/pomdp/inst/doc/POMDP.R | 102 ++------ pomdp-0.9.2/pomdp/inst/doc/POMDP.Rmd | 378 +++++++++++++++----------------- pomdp-0.9.2/pomdp/inst/doc/POMDP.pdf |binary pomdp-0.9.2/pomdp/man/POMDP.Rd | 142 ++++++------ pomdp-0.9.2/pomdp/man/TigerProblem.Rd | 8 pomdp-0.9.2/pomdp/man/plot.POMDP.Rd | 47 ++- pomdp-0.9.2/pomdp/man/policy_graph.Rd | 11 pomdp-0.9.2/pomdp/man/reward.Rd |only pomdp-0.9.2/pomdp/man/solve_POMDP.Rd | 16 + pomdp-0.9.2/pomdp/src/command-line.c | 20 + pomdp-0.9.2/pomdp/src/lp-solve/lpkit.c | 13 - pomdp-0.9.2/pomdp/src/lp-solve/solve.c | 3 pomdp-0.9.2/pomdp/src/mdp/mdp.c | 4 pomdp-0.9.2/pomdp/src/mdp/mdp.h | 5 pomdp-0.9.2/pomdp/src/mdp/parser.c | 5 pomdp-0.9.2/pomdp/src/stats.c | 5 pomdp-0.9.2/pomdp/vignettes/POMDP.Rmd | 378 +++++++++++++++----------------- pomdp-0.9.2/pomdp/vignettes/POMDP_files |only 35 files changed, 880 insertions(+), 814 deletions(-)
Title: Degrees of Freedom Adjustment for Robust Standard Errors
Description: Computes small-sample degrees of freedom adjustment for
heteroskedasticity robust standard errors, and for clustered standard errors
in linear regression. See Imbens and Kolesár (2016)
<doi:10.1162/REST_a_00552> for a discussion of these adjustments.
Author: Michal Kolesár [aut, cre] (<https://orcid.org/0000-0002-2482-7796>)
Maintainer: Michal Kolesár <kolesarmi@googlemail.com>
Diff between dfadjust versions 1.0.0 dated 2019-08-23 and 1.0.1 dated 2019-12-16
dfadjust-1.0.0/dfadjust/R/BM_StandardErrors.R |only dfadjust-1.0.1/dfadjust/DESCRIPTION | 10 ++-- dfadjust-1.0.1/dfadjust/MD5 | 16 +++---- dfadjust-1.0.1/dfadjust/NEWS.md | 6 ++ dfadjust-1.0.1/dfadjust/R/ols.R |only dfadjust-1.0.1/dfadjust/build/vignette.rds |binary dfadjust-1.0.1/dfadjust/inst/doc/dfadjust.R | 16 +++---- dfadjust-1.0.1/dfadjust/inst/doc/dfadjust.pdf |binary dfadjust-1.0.1/dfadjust/man/dfadjustSE.Rd | 14 ++++-- dfadjust-1.0.1/dfadjust/tests/testthat/test-hc2-check.R | 33 ++++++++++------ 10 files changed, 59 insertions(+), 36 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided. As of release 1.69.0-1, the following Boost libraries are
included: 'algorithm' 'align' 'any' 'atomic' 'bimap' 'bind'
'circular_buffer' 'compute' 'concept' 'config' 'container' 'date_time'
'detail' 'dynamic_bitset' 'exception' 'filesystem' 'flyweight' 'foreach'
'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer'
'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'math' 'move' 'mpl'
'multiprcecision' 'numeric' 'pending' 'phoenix' 'preprocessor'
'propery_tree' 'random' 'range' 'scope_exit' 'smart_ptr' 'sort' 'spirit'
'tuple' 'type_traits' 'typeof' 'unordered' 'utility' 'uuid'.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.69.0-1 dated 2019-01-07 and 1.72.0-1 dated 2019-12-16
BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/covariance.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/density.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/error_of.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/error_of_mean.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/extended_p_square.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/extended_p_square_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/kurtosis.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/max.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/median.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/min.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/p_square_cumul_dist.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/p_square_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/parameters |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/peaks_over_threshold.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/pot_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/pot_tail_mean.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/skewness.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/sum_kahan.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/tail.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/tail_mean.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/tail_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/tail_variate.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/tail_variate_means.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/times2_iterator.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/variates |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_covariance.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_density.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_extended_p_square.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_kurtosis.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_mean.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_median.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_moment.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_p_square_cumul_dist.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_p_square_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_peaks_over_threshold.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_skewness.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_sum.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_sum_kahan.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_tail_mean.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_tail_quantile.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_tail_variate_means.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/weighted_variance.hpp |only BH-1.69.0-1/BH/inst/include/boost/accumulators/statistics/with_error.hpp |only BH-1.69.0-1/BH/inst/include/boost/align/detail/address.hpp |only BH-1.69.0-1/BH/inst/include/boost/align/detail/addressof.hpp |only BH-1.69.0-1/BH/inst/include/boost/archive/add_facet.hpp |only BH-1.69.0-1/BH/inst/include/boost/archive/shared_ptr_helper.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/datagram_socket_service.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/deadline_timer_service.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/addressof.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/function.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/impl/task_io_service.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/impl/task_io_service.ipp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/impl/win_iocp_io_service.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/impl/win_iocp_io_service.ipp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/impl/winrt_ssocket_service_base.ipp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/shared_ptr.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/task_io_service.hpp |only BH-1.69.0-1/BH/inst/include/boost/asio/detail/task_io_service_operation.hpp |only 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BH-1.69.0-1/BH/inst/include/boost/atomic/detail/cas128strong.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/cas32strong.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/cas32weak.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/cas64strong.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/casts.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-alpha.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-armv6plus.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-atomic.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-cas.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-ppc.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-sparcv9.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/gcc-x86.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/linux-arm.hpp |only BH-1.69.0-1/BH/inst/include/boost/atomic/detail/type-classification.hpp |only 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BH-1.72.0-1/BH/inst/include/boost/asio/impl/post.hpp | 90 BH-1.72.0-1/BH/inst/include/boost/asio/impl/read.hpp | 662 BH-1.72.0-1/BH/inst/include/boost/asio/impl/read_at.hpp | 211 BH-1.72.0-1/BH/inst/include/boost/asio/impl/read_until.hpp | 2258 +- BH-1.72.0-1/BH/inst/include/boost/asio/impl/redirect_error.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/impl/serial_port_base.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/impl/serial_port_base.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/impl/system_context.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/impl/system_context.ipp | 11 BH-1.72.0-1/BH/inst/include/boost/asio/impl/system_executor.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/impl/thread_pool.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/impl/thread_pool.ipp | 21 BH-1.72.0-1/BH/inst/include/boost/asio/impl/use_awaitable.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/impl/use_future.hpp | 52 BH-1.72.0-1/BH/inst/include/boost/asio/impl/write.hpp | 613 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BH-1.72.0-1/BH/inst/include/boost/asio/ip/basic_resolver_entry.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/basic_resolver_iterator.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/basic_resolver_query.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/basic_resolver_results.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/detail/endpoint.hpp | 40 BH-1.72.0-1/BH/inst/include/boost/asio/ip/detail/impl/endpoint.ipp | 20 BH-1.72.0-1/BH/inst/include/boost/asio/ip/detail/socket_option.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/host_name.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/icmp.hpp | 14 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address.ipp | 41 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address_v4.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address_v4.ipp | 22 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address_v6.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/address_v6.ipp | 52 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/basic_endpoint.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/host_name.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/network_v4.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/network_v4.ipp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/network_v6.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/impl/network_v6.ipp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/multicast.hpp | 16 BH-1.72.0-1/BH/inst/include/boost/asio/ip/network_v4.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/network_v6.hpp |only BH-1.72.0-1/BH/inst/include/boost/asio/ip/resolver_base.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/resolver_query_base.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/ip/tcp.hpp | 18 BH-1.72.0-1/BH/inst/include/boost/asio/ip/udp.hpp | 14 BH-1.72.0-1/BH/inst/include/boost/asio/ip/unicast.hpp | 6 BH-1.72.0-1/BH/inst/include/boost/asio/ip/v6_only.hpp | 6 BH-1.72.0-1/BH/inst/include/boost/asio/is_executor.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/is_read_buffered.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/is_write_buffered.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/local/basic_endpoint.hpp | 12 BH-1.72.0-1/BH/inst/include/boost/asio/local/connect_pair.hpp | 33 BH-1.72.0-1/BH/inst/include/boost/asio/local/datagram_protocol.hpp | 8 BH-1.72.0-1/BH/inst/include/boost/asio/local/detail/endpoint.hpp | 8 BH-1.72.0-1/BH/inst/include/boost/asio/local/detail/impl/endpoint.ipp | 9 BH-1.72.0-1/BH/inst/include/boost/asio/local/stream_protocol.hpp | 8 BH-1.72.0-1/BH/inst/include/boost/asio/packaged_task.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/placeholders.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/asio/posix/basic_descriptor.hpp | 261 BH-1.72.0-1/BH/inst/include/boost/asio/posix/basic_stream_descriptor.hpp | 250 BH-1.72.0-1/BH/inst/include/boost/asio/posix/descriptor.hpp | 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BH-1.72.0-1/BH/inst/include/boost/uuid/detail/config.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/md5.hpp | 49 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_arc4random.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_bcrypt.ipp | 12 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_detect_platform.hpp | 10 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_getentropy.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_getrandom.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_include_platform.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_posix.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/random_provider_wincrypt.ipp | 12 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/sha1.hpp | 4 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/uuid_generic.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/detail/uuid_x86.ipp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/entropy_error.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/name_generator.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/name_generator_md5.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/name_generator_sha1.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/nil_generator.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/random_generator.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/string_generator.hpp | 5 BH-1.72.0-1/BH/inst/include/boost/uuid/uuid.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/uuid_generators.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/uuid_hash.hpp | 6 BH-1.72.0-1/BH/inst/include/boost/uuid/uuid_io.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/uuid/uuid_serialize.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/apply_visitor_binary.hpp | 59 BH-1.72.0-1/BH/inst/include/boost/variant/detail/apply_visitor_delayed.hpp | 11 BH-1.72.0-1/BH/inst/include/boost/variant/detail/apply_visitor_unary.hpp | 85 BH-1.72.0-1/BH/inst/include/boost/variant/detail/config.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/element_index.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/forced_return.hpp | 28 BH-1.72.0-1/BH/inst/include/boost/variant/detail/has_result_type.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/hash_variant.hpp | 3 BH-1.72.0-1/BH/inst/include/boost/variant/detail/make_variant_list.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/move.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/detail/std_hash.hpp |only BH-1.72.0-1/BH/inst/include/boost/variant/detail/visitation_impl.hpp | 19 BH-1.72.0-1/BH/inst/include/boost/variant/get.hpp | 4 BH-1.72.0-1/BH/inst/include/boost/variant/recursive_variant.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/recursive_wrapper_fwd.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/static_visitor.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/variant.hpp | 190 BH-1.72.0-1/BH/inst/include/boost/variant/variant_fwd.hpp | 2 BH-1.72.0-1/BH/inst/include/boost/variant/visitor_ptr.hpp | 29 BH-1.72.0-1/BH/inst/include/boost/version.hpp | 4 BH-1.72.0-1/BH/inst/include/boost/winapi/handles.hpp | 4 2440 files changed, 71544 insertions(+), 57421 deletions(-)
Title: Ridge-Type Penalized Estimation of a Potpourri of Models
Description: The name of the package is derived from the French, 'pour' ridge, and provides functionality for ridge-type estimation of a potpourri of models. Currently, this estimation concerns that of various Gaussian graphical models from different study designs. Among others it considers the regular Gaussian graphical model and a mixture of such models. The porridge-package implements the estimation of the former either from i) data with replicated observations by penalized loglikelihood maximization using the regular ridge penalty on the parameters (van Wieringen, Chen, 2019) or ii) from non-replicated data by means of the generalized ridge estimator that allows for both the inclusion of quantitative and qualitative prior information on the precision matrix via element-wise penalization and shrinkage (van Wieringen, 2019, <doi.org/10.1080/10618600.2019.1604374>). Additionally, the porridge-package facilitates the ridge penalized estimation of a mixture of Gaussian graphical models (Aflakparast et al., 2018, <doi.org/10.1002/bimj.201700102>).
Author: Wessel N. van Wieringen [aut, cre],
Mehran Aflakparast [ctb] (part of the R-code of the mixture
functionality)
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between porridge versions 0.0.3 dated 2019-12-05 and 0.0.4 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS.Rd | 6 ++++++ src/porridge.cpp | 25 +++++++++++++++++++++---- 4 files changed, 34 insertions(+), 11 deletions(-)
Title: Calculate the Standardized Difference for Numeric, Binary and
Category Variables
Description: Contains three main functions including
stddiff.numeric(), stddiff.binary() and stddiff.category().
These are used to calculate the standardized difference between two groups.
It is especially used to evaluate the balance between two groups
before and after propensity score matching.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between stddiff versions 2.0 dated 2017-04-12 and 3.0 dated 2019-12-16
DESCRIPTION | 7 +++---- MD5 | 6 +++--- R/stddiff.R | 10 +++------- man/stddiff.Rd | 7 +++++-- 4 files changed, 14 insertions(+), 16 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.2.1 dated 2019-07-19 and 0.2.2 dated 2019-12-16
DESCRIPTION | 10 ++-- MD5 | 88 ++++++++++++++++++------------------ NEWS.md | 8 +++ R/Baseline.R | 8 +-- R/MutationProfiling.R | 16 +++--- build/vignette.rds |binary inst/doc/Baseline-Vignette.R | 26 +++++----- inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.R | 22 ++++----- inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.R | 16 +++--- inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.R | 8 +-- inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.R | 12 ++-- inst/doc/Targeting-Vignette.pdf |binary man/calcBaseline.Rd | 16 ++++-- man/calcExpectedMutations.Rd | 10 ++-- man/calcObservedMutations.Rd | 12 +++- man/calculateMutability.Rd | 2 man/collapseClones.Rd | 20 +++++--- man/consensusSequence.Rd | 16 ++++-- man/createBaseline.Rd | 18 +++++-- man/createMutabilityMatrix.Rd | 14 ++++- man/createMutationDefinition.Rd | 3 - man/createRegionDefinition.Rd | 8 ++- man/createSubstitutionMatrix.Rd | 13 +++-- man/createTargetingModel.Rd | 19 +++++-- man/distToNearest.Rd | 30 +++++++++--- man/expectedMutations.Rd | 12 +++- man/findThreshold.Rd | 16 ++++-- man/observedMutations.Rd | 15 ++++-- man/plotBaselineDensity.Rd | 21 ++++++-- man/plotBaselineSummary.Rd | 17 +++++- man/plotDensityThreshold.Rd | 15 ++++-- man/plotGmmThreshold.Rd | 15 ++++-- man/plotMutability.Rd | 11 +++- man/plotTune.Rd | 16 ++++-- man/shazam.Rd | 1 man/shmulateSeq.Rd | 9 ++- man/shmulateTree.Rd | 13 ++++- man/slideWindowDb.Rd | 9 ++- man/slideWindowTune.Rd | 12 +++- man/slideWindowTunePlot.Rd | 22 ++++++--- man/summarizeBaseline.Rd | 3 - 45 files changed, 396 insertions(+), 206 deletions(-)
Title: Graphical User Interface for Data Science in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
collection of utilities functions for the data scientist. A
Gnome (RGtk2) based graphical interface is included with
the aim to provide a simple and intuitive introduction to R
for data science, allowing a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. A key aspect of the GUI
is that all R commands are logged and commented through the log tab.
This can be saved as a standalone R script file and as
an aid for the user to
learn R or to copy-and-paste directly into R itself.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (print.summary.nnet),
Jose Magana [ctb] (ggpairs plots),
Surendra Tipparaju [ctb] (initial RevoScaleR/XDF),
Durga Prasad Chappidi [ctb] (initial RevoScaleR/XDF),
Dinesh Manyam Venkata [ctb] (initial RevoScaleR/XDF),
Mrinal Chakraborty [ctb] (initial RevoScaleR/XDF),
Fang Zhou [ctb] (initial xgboost),
Cameron Chisholm [ctb] (risk plot on risk chart)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 5.2.0 dated 2018-08-17 and 5.3.0 dated 2019-12-16
rattle-5.2.0/rattle/R/rxkmeans.R |only rattle-5.3.0/rattle/DESCRIPTION | 19 +++---- rattle-5.3.0/rattle/MD5 | 41 +++++++--------- rattle-5.3.0/rattle/R/data.R | 63 ++++-------------------- rattle-5.3.0/rattle/R/evaluate.R | 62 +++--------------------- rattle-5.3.0/rattle/R/executeModelRF.R | 6 +- rattle-5.3.0/rattle/R/export.R | 71 +++++++--------------------- rattle-5.3.0/rattle/R/kmeans.R | 33 +++++++++---- rattle-5.3.0/rattle/R/projects.R | 4 - rattle-5.3.0/rattle/R/random_forest.R | 12 +++- rattle-5.3.0/rattle/R/rattle.R | 36 ++++++++------ rattle-5.3.0/rattle/R/rpart.R | 2 rattle-5.3.0/rattle/R/xgb.R | 15 ++++- rattle-5.3.0/rattle/R/zzz.R | 4 - rattle-5.3.0/rattle/build/vignette.rds |binary rattle-5.3.0/rattle/data/locationsAUS.RData |binary rattle-5.3.0/rattle/data/weather.RData |binary rattle-5.3.0/rattle/data/weatherAUS.RData |binary rattle-5.3.0/rattle/inst/NEWS | 52 ++++++++++++++++++++ rattle-5.3.0/rattle/inst/doc/rattle.pdf |binary rattle-5.3.0/rattle/inst/etc/rattle.ui | 2 rattle-5.3.0/rattle/inst/etc/tooltips.xml | 2 22 files changed, 196 insertions(+), 228 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb],
Ryan Moore [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 4.1.6 dated 2019-07-10 and 4.2.6 dated 2019-12-16
DESCRIPTION | 18 - MD5 | 93 +++-- NAMESPACE | 4 NEWS.md | 55 +++ R/0-params.R | 1 R/1-propr.R | 2 R/2-proprCall.R | 80 +++-- R/4-propd.R | 12 R/5-propdCall.R | 59 +-- R/6-propdViz.R | 20 + R/7-aldex2propr.R | 2 R/8-get.R | 115 +++++++ R/9-global.R | 12 R/9-posthoc.R |only R/9-pra.R | 12 README.md | 123 +++++-- build/vignette.rds |binary inst/CITATION | 95 +++-- inst/doc/a_introduction.R | 13 inst/doc/a_introduction.Rmd | 36 -- inst/doc/a_introduction.html | 477 ++++++++++++++++++----------- inst/doc/b_visualization.R | 41 +- inst/doc/b_visualization.Rmd | 63 +-- inst/doc/b_visualization.html | 453 ++++++++++++++++++---------- inst/doc/d_advanced.R | 38 -- inst/doc/d_advanced.Rmd | 68 +--- inst/doc/d_advanced.html | 559 ++++++++++++++++++++--------------- inst/doc/e_differential.R | 34 -- inst/doc/e_differential.Rmd | 85 +---- inst/doc/e_differential.html | 543 ++++++++++++++++++++------------- inst/doc/f_moderation.R | 18 - inst/doc/f_moderation.Rmd | 21 - inst/doc/f_moderation.html | 409 ++++++++++++++++--------- inst/doc/g_questions.R | 5 inst/doc/g_questions.Rmd | 18 - inst/doc/g_questions.html | 377 ++++++++++++++--------- man/all.Rd | 2 man/getColours.Rd |only man/getNormTheta.Rd |only man/posthoc.Rd |only man/propr.Rd | 4 man/updateCutoffs.Rd | 4 tests/testthat/test-ANOVA.R |only tests/testthat/test-getNormTheta.R |only tests/testthat/test-propr-parallel.R |only vignettes/a_introduction.Rmd | 36 -- vignettes/b_visualization.Rmd | 63 +-- vignettes/d_advanced.Rmd | 68 +--- vignettes/e_differential.Rmd | 85 +---- vignettes/f_moderation.Rmd | 21 - vignettes/g_questions.Rmd | 18 - 51 files changed, 2498 insertions(+), 1764 deletions(-)
Title: Streamline Physical Activity Research
Description: A collection of utilities that are useful for a broad range of
tasks that are common in physical activity research, including the
following: creation of Bland-Altman plots, formatted descriptive
statistics, metabolic calculations (e.g. basal metabolic rate predictions)
and conversions, demographic calculations (age and age-for-body-mass-index
percentile), bout analysis of moderate-to-vigorous intensity physical
activity, and analysis of bout detection algorithm performance.
Author: Paul R. Hibbing [aut, cre],
Centers for Disease Control and Prevention [ctb]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between PAutilities versions 0.3.0 dated 2019-10-29 and 0.3.1 dated 2019-12-16
DESCRIPTION | 9 +++++---- MD5 | 11 ++++++++--- NEWS.md | 6 ++++++ README.md | 4 ++++ build |only inst/doc |only vignettes |only 7 files changed, 23 insertions(+), 7 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.13.0 dated 2019-11-08 and 0.14.0 dated 2019-12-16
ggeffects-0.13.0/ggeffects/R/ggemmeans_MixMod.R |only ggeffects-0.13.0/ggeffects/R/ggemmeans_glmmTMB.R |only ggeffects-0.13.0/ggeffects/R/ggemmeans_predict_models.R |only ggeffects-0.13.0/ggeffects/R/predict_standard_errors_from_vcov.R |only ggeffects-0.13.0/ggeffects/tests/testthat/test-args.R |only ggeffects-0.14.0/ggeffects/DESCRIPTION | 32 ggeffects-0.14.0/ggeffects/MD5 | 182 - ggeffects-0.14.0/ggeffects/NAMESPACE | 24 ggeffects-0.14.0/ggeffects/NEWS.md | 24 ggeffects-0.14.0/ggeffects/R/emmeans_prediction_data.R |only ggeffects-0.14.0/ggeffects/R/get_predictions_MixMod.R | 81 ggeffects-0.14.0/ggeffects/R/get_predictions_bamlss.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_bayesx.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_clm.R | 20 ggeffects-0.14.0/ggeffects/R/get_predictions_clmm.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_coxph.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_gam2.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_gamlss.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_geeglm.R | 49 ggeffects-0.14.0/ggeffects/R/get_predictions_generic2.R | 21 ggeffects-0.14.0/ggeffects/R/get_predictions_glm.R | 4 ggeffects-0.14.0/ggeffects/R/get_predictions_glmRob.R | 4 ggeffects-0.14.0/ggeffects/R/get_predictions_glmmTMB.R | 101 - ggeffects-0.14.0/ggeffects/R/get_predictions_lm.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_lme.R | 13 ggeffects-0.14.0/ggeffects/R/get_predictions_logistf.R | 20 ggeffects-0.14.0/ggeffects/R/get_predictions_merMod.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_multinom.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_polr.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_stan.R | 12 ggeffects-0.14.0/ggeffects/R/get_predictions_survival.R | 7 ggeffects-0.14.0/ggeffects/R/get_predictions_svyglmnb.R | 4 ggeffects-0.14.0/ggeffects/R/get_predictions_wbm.R | 4 ggeffects-0.14.0/ggeffects/R/get_predictions_zeroinfl.R | 88 ggeffects-0.14.0/ggeffects/R/getter.R | 14 ggeffects-0.14.0/ggeffects/R/ggeffect.R | 129 - ggeffects-0.14.0/ggeffects/R/ggemmeans.R | 141 - ggeffects-0.14.0/ggeffects/R/ggemmeans_zi_predictions.R | 59 ggeffects-0.14.0/ggeffects/R/ggpredict.R | 222 -- ggeffects-0.14.0/ggeffects/R/new_data.R | 10 ggeffects-0.14.0/ggeffects/R/plot.R | 91 ggeffects-0.14.0/ggeffects/R/post_processing_labels.R | 27 ggeffects-0.14.0/ggeffects/R/post_processing_predictions.R | 72 ggeffects-0.14.0/ggeffects/R/predict_zero_inflation.R | 277 +- ggeffects-0.14.0/ggeffects/R/predictions.R | 184 - ggeffects-0.14.0/ggeffects/R/print.R | 108 - ggeffects-0.14.0/ggeffects/R/select_helpers.R | 3 ggeffects-0.14.0/ggeffects/R/simulate_predictions.R | 67 ggeffects-0.14.0/ggeffects/R/standard_error_predictions.R |only ggeffects-0.14.0/ggeffects/R/utils.R | 108 - ggeffects-0.14.0/ggeffects/R/utils_check_transformations.R |only ggeffects-0.14.0/ggeffects/R/utils_colors.R | 5 ggeffects-0.14.0/ggeffects/R/utils_get_cleaned_terms.R | 5 ggeffects-0.14.0/ggeffects/R/utils_get_data_grid.R | 308 +-- ggeffects-0.14.0/ggeffects/R/utils_get_representative_values.R | 149 - ggeffects-0.14.0/ggeffects/R/utils_handle_labels.R | 38 ggeffects-0.14.0/ggeffects/R/utils_is_empty.R |only ggeffects-0.14.0/ggeffects/R/utils_model_function.R | 3 ggeffects-0.14.0/ggeffects/R/utils_set_attr.R | 19 ggeffects-0.14.0/ggeffects/R/utils_typical_value.R |only ggeffects-0.14.0/ggeffects/R/vcov.R | 61 ggeffects-0.14.0/ggeffects/README.md | 143 - ggeffects-0.14.0/ggeffects/build/partial.rdb |binary ggeffects-0.14.0/ggeffects/build/vignette.rds |binary ggeffects-0.14.0/ggeffects/inst/doc/ggeffects.R | 11 ggeffects-0.14.0/ggeffects/inst/doc/ggeffects.Rmd | 34 ggeffects-0.14.0/ggeffects/inst/doc/ggeffects.html | 567 +++--- ggeffects-0.14.0/ggeffects/inst/doc/introduction_effectsatvalues.html | 222 +- ggeffects-0.14.0/ggeffects/inst/doc/introduction_plotcustomize.html | 9 ggeffects-0.14.0/ggeffects/inst/doc/introduction_plotmethod.html | 11 ggeffects-0.14.0/ggeffects/inst/doc/introduction_randomeffects.html | 244 +- ggeffects-0.14.0/ggeffects/inst/doc/practical_logisticmixedmodel.R | 24 ggeffects-0.14.0/ggeffects/inst/doc/practical_logisticmixedmodel.html | 69 ggeffects-0.14.0/ggeffects/inst/doc/technical_differencepredictemmeans.Rmd | 2 ggeffects-0.14.0/ggeffects/inst/doc/technical_differencepredictemmeans.html | 199 +- ggeffects-0.14.0/ggeffects/inst/doc/technical_stata.R | 10 ggeffects-0.14.0/ggeffects/inst/doc/technical_stata.html | 7 ggeffects-0.14.0/ggeffects/man/efc.Rd | 68 ggeffects-0.14.0/ggeffects/man/get_title.Rd | 154 - ggeffects-0.14.0/ggeffects/man/ggpredict.Rd | 924 ++++------ ggeffects-0.14.0/ggeffects/man/new_data.Rd | 98 - ggeffects-0.14.0/ggeffects/man/plot.Rd | 339 +-- ggeffects-0.14.0/ggeffects/man/pretty_range.Rd | 102 - ggeffects-0.14.0/ggeffects/man/reexports.Rd | 30 ggeffects-0.14.0/ggeffects/man/values_at.Rd | 82 ggeffects-0.14.0/ggeffects/man/vcov.Rd | 133 - ggeffects-0.14.0/ggeffects/tests/testthat/test-MixMod.R | 6 ggeffects-0.14.0/ggeffects/tests/testthat/test-brms-trial.R | 2 ggeffects-0.14.0/ggeffects/tests/testthat/test-geeglm.R | 7 ggeffects-0.14.0/ggeffects/tests/testthat/test-linear-models.R | 30 ggeffects-0.14.0/ggeffects/tests/testthat/test-logistf.R | 3 ggeffects-0.14.0/ggeffects/tests/testthat/test-polr.R | 14 ggeffects-0.14.0/ggeffects/tests/testthat/test-poly-zeroinf.R | 7 ggeffects-0.14.0/ggeffects/tests/testthat/test-tobit.R | 4 ggeffects-0.14.0/ggeffects/tests/testthat/test-zeroinfl.R | 18 ggeffects-0.14.0/ggeffects/vignettes/ggeffects.Rmd | 34 ggeffects-0.14.0/ggeffects/vignettes/technical_differencepredictemmeans.Rmd | 2 97 files changed, 3350 insertions(+), 3169 deletions(-)
Title: Bootstrap Resampling for Mixed Effects and Plain Models
Description: Performs bootstrap resampling for most models that update() works for. There
are two primary functions: bootstrap_model() performs block resampling if random effects
are present, and case resampling if not; bootstrap_ci() converts output from
bootstrap model runs into confidence intervals and p-values. By default,
bootstrap_model() calls bootstrap_ci().
Package motivated by Humphrey and Swingley (2018) <arXiv:1805.08670>.
Author: Colman Humphrey [aut, cre]
Maintainer: Colman Humphrey <humphrc@tcd.ie>
Diff between glmmboot versions 0.4.0 dated 2019-09-02 and 0.5.0 dated 2019-12-16
DESCRIPTION | 8 - MD5 | 56 ++++----- NEWS.md | 8 + R/bootstrap_ci.R | 120 ++++++-------------- R/bootstrap_methods.R | 143 ++++++++---------------- R/bootstrap_model.R | 190 +++++++++++++++----------------- README.md | 76 ++++++------ build/vignette.rds |binary inst/doc/quick_use.R | 46 ++++--- inst/doc/quick_use.Rmd | 37 ++++-- inst/doc/quick_use.html | 102 ++++++++--------- man/bootstrap_ci.Rd | 57 +++++---- man/bootstrap_individual_ci.Rd | 11 + man/bootstrap_model.Rd | 152 +++++++++++++++---------- man/bootstrap_runner.Rd | 43 +++++-- man/ci_variable.Rd | 14 +- man/combine_resampled_lists.Rd | 23 +-- man/find_bars.Rd | 5 man/gen_resampling_index.Rd | 8 - man/gen_samp_lev.Rd | 13 +- man/gen_sample.Rd | 23 ++- man/gen_vector_match.Rd | 14 +- man/get_rand.Rd | 12 -- man/list_of_matrices.Rd | 9 - man/not_error_check.Rd | 16 +- tests/testthat/test-bootstrap_ci.R | 9 + tests/testthat/test-bootstrap_methods.R | 9 + tests/testthat/test-bootstrap_model.R | 105 +++++++++++------ vignettes/quick_use.Rmd | 37 ++++-- 29 files changed, 697 insertions(+), 649 deletions(-)
Title: Dynamic Generation and Quality Checks of Formula Objects
Description: Many statistical models and analyses in R are implemented through formula objects. The formulaic package creates a unified approach for programmatically and dynamically generating formula objects. Users may specify the outcome and inputs of a model directly, search for variables to include based upon naming patterns, incorporate interactions, and identify variables to exclude. A wide range of quality checks are implemented to identify issues such as misspecified variables, duplication, a lack of contrast in the inputs, and a large number of levels in categorical data. Variables that do not meet these quality checks can be automatically excluded from the model. These issues are documented and reported in a manner that provides greater accountability and useful information to guide an investigation of the data.
Author: David Shilane [aut],
Caffrey Lee [ctb],
Zichen Huang [ctb],
Anderson Nelson [ctb, cre]
Maintainer: Anderson Nelson <an2908@columbia.edu>
Diff between formulaic versions 0.0.4 dated 2019-10-08 and 0.0.5 dated 2019-12-16
DESCRIPTION | 8 MD5 | 30 NAMESPACE | 2 NEWS.md | 9 R/create.formula.R | 48 README.md | 26 data/snack.dat.rda |binary inst/doc/Introduction-to-formulaic.R | 66 - inst/doc/Introduction-to-formulaic.Rmd | 6 inst/doc/Introduction-to-formulaic.html | 1888 ++++++++++++++++---------------- man/add.backtick.Rd | 30 man/create.formula.Rd | 124 +- man/reduce.existing.formula.Rd | 84 - man/snack.dat.Rd | 88 - tests |only vignettes/Introduction-to-formulaic.Rmd | 6 16 files changed, 1230 insertions(+), 1185 deletions(-)
Title: Echogram Visualisation and Analysis
Description: Easily import multi-frequency acoustic data stored in 'HAC' files (see <http://biblio.uqar.ca/archives/30005500.pdf> for more information on the format), and produce echogram visualisations with predefined or customized color palettes. It is also possible to merge consecutive echograms; mask or delete unwanted echogram areas; model and subtract background noise; and more important, develop, test and interpret different combinations of frequencies in order to perform acoustic filtering of the echogram's data.
Author: Héctor Villalobos [aut, cre]
Maintainer: Héctor Villalobos <hvillalo@ipn.mx>
Diff between echogram versions 0.1.1 dated 2017-08-03 and 0.1.2 dated 2019-12-16
echogram-0.1.1/echogram/data/datalist |only echogram-0.1.2/echogram/DESCRIPTION | 8 +- echogram-0.1.2/echogram/MD5 | 33 +++++------ echogram-0.1.2/echogram/NAMESPACE | 2 echogram-0.1.2/echogram/NEWS | 8 ++ echogram-0.1.2/echogram/NEWS.md | 9 +++ echogram-0.1.2/echogram/R/add.echogram.R | 2 echogram-0.1.2/echogram/R/bottom.hac.R | 2 echogram-0.1.2/echogram/R/echogram.R | 24 ++++---- echogram-0.1.2/echogram/R/join.echogram.R | 81 ++++++++++++++-------------- echogram-0.1.2/echogram/R/mask.echogram.R | 2 echogram-0.1.2/echogram/R/match.echogram.R | 2 echogram-0.1.2/echogram/R/noise.echogram.R | 2 echogram-0.1.2/echogram/R/position.hac.R | 40 ++++++------- echogram-0.1.2/echogram/R/read.echogram.R | 17 ++++- echogram-0.1.2/echogram/R/sample.echogram.R | 2 echogram-0.1.2/echogram/R/trim.echogram.R | 2 echogram-0.1.2/echogram/data/echo.noise.rda |binary 18 files changed, 131 insertions(+), 105 deletions(-)
Title: Deep Gaussian Mixture Models
Description: Deep Gaussian mixture models as proposed by Viroli and McLachlan (2019)
<doi:10.1007/s11222-017-9793-z> provide a generalization of classical Gaussian mixtures
to multiple layers. Each layer contains a set of latent variables that follow
a mixture of Gaussian distributions. To avoid overparameterized solutions, dimension
reduction is applied at each layer by way of factor models.
Author: Cinzia Viroli, Geoffrey J. McLachlan
Maintainer: Suren Rathnayake <surenr@gmail.com>
Diff between deepgmm versions 0.1.56 dated 2019-02-22 and 0.1.59 dated 2019-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/deep.sem.alg.1.R | 2 +- R/deepgmm.R | 8 ++++---- 4 files changed, 12 insertions(+), 12 deletions(-)