Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.21 dated 2018-12-10 and 1.22 dated 2019-03-08
DESCRIPTION | 14 - MD5 | 74 ++--- NAMESPACE | 3 NEWS.md | 44 +++ R/defaults.R | 7 R/engine.R | 128 +++++++-- R/hooks-html.R | 5 R/hooks-md.R | 13 R/output.R | 21 + R/package.R | 6 R/pandoc.R | 71 ++--- R/plot.R | 6 R/spin.R | 4 R/table.R | 27 + R/utils-conversion.R | 36 +- R/utils-sweave.R | 17 - R/utils.R | 44 +-- README.md | 2 build/vignette.rds |binary inst/doc/knit_expand.html | 4 inst/doc/knit_print.html | 222 ++++++++-------- inst/doc/knitr-intro.html | 26 - inst/doc/knitr-markdown.html | 2 inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-spin.R | 3 inst/examples/knitr-spin.html | 568 +++++++++++++++++++++++++++--------------- inst/misc/knitr-template.Rnw | 2 man/Sweave2knitr.Rd | 7 man/kable.Rd | 21 - man/knit2html.Rd | 4 man/knit2pandoc.Rd | 7 man/knit2pdf.Rd | 4 man/knit2wp.Rd | 4 man/opts_chunk.Rd | 7 man/pandoc.Rd | 36 +- tests/testit/test-output.R | 8 tests/testit/test-table.R | 8 tests/testit/test-utils.R | 17 - 38 files changed, 893 insertions(+), 579 deletions(-)
Title: Convert Dates to Arbitrary Week Definitions
Description: Which day a week starts depends heavily on the either the local or
professional context. This package is designed to be a lightweight solution
to easily switching between week-based date definitions.
Author: Zhian N. Kamvar [aut, cre]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between aweek versions 0.1.0 dated 2019-03-06 and 0.2.0 dated 2019-03-08
DESCRIPTION | 6 - MD5 | 31 ++++----- NAMESPACE | 2 NEWS.md | 10 ++ R/conversions.R | 70 +++++++++++++++++++- R/date2week.R | 20 +++++ R/print.aweek.R | 97 +++++++++++++++++++++++++++- R/utils.R | 14 ++++ R/week2date.R | 38 ----------- inst/doc/introduction.R | 37 ++++++++-- inst/doc/introduction.Rmd | 78 ++++++++++++++++++++-- inst/doc/introduction.html | 133 ++++++++++++++++++++++++++------------- man/aweek-class.Rd |only man/aweek-conversions.Rd |only man/date2week.Rd | 38 ++++------- tests/testthat/test-subset.R |only tests/testthat/test_conversion.R | 20 ++++- vignettes/introduction.Rmd | 78 ++++++++++++++++++++-- 18 files changed, 515 insertions(+), 157 deletions(-)
Title: Missing Item Responses Imputation for Test and Assessment Data
Description: Functions for imputing missing item responses for dichotomous and
polytomous test and assessment data. This package enables missing imputation
methods that are suitable for test and assessment data, including: listwise (LW)
deletion, treating as incorrect (IN), person mean imputation (PM), item mean
imputation (IM), two-way imputation (TW), logistic regression imputation (LR),
and EM imputation.
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Diff between TestDataImputation versions 1.0 dated 2016-08-11 and 1.1 dated 2019-03-08
DESCRIPTION | 21 +++++++++++---------- MD5 | 22 +++++++++++----------- R/ImputeTestData.r | 13 +++++++++++-- R/TwoWay.r | 14 ++++++++++++-- man/EMimpute.Rd | 1 - man/ImputeTestData.Rd | 9 +++++---- man/ItemMean.Rd | 1 - man/Listwise.Rd | 1 - man/LogsticReg.Rd | 1 - man/PersonMean.Rd | 1 - man/TreatIncorrect.Rd | 1 - man/Twoway.Rd | 5 +++-- 12 files changed, 53 insertions(+), 37 deletions(-)
More information about TestDataImputation at CRAN
Permanent link
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable().
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.59 dated 2018-05-07 and 0.60 dated 2019-03-08
DESCRIPTION | 13 ++++------ MD5 | 46 +++++++++++++++++++------------------- R/dataframe.R | 7 +++-- R/diagnose.R | 2 - R/openmx.R | 8 ++---- R/util.R | 2 - build/vignette.rds |binary inst/doc/customitem.html | 2 - inst/doc/diagnostics.html | 42 +++++++++++++++++----------------- inst/doc/flexmirt-plots.html | 6 ++-- man/ChenThissen1997.Rd | 3 +- man/SitemFit1.Rd | 3 +- man/compressDataFrame.Rd | 4 ++- src/dataframe.cpp | 2 - src/diagnose.cpp | 14 +++++------ src/eap.cpp | 2 - src/glue.cpp | 5 +--- src/m2.cpp | 2 - src/rpf.h | 16 ++++++------- tests/testthat/test-dTheta.R | 1 tests/testthat/test-fit.R | 1 tests/testthat/test-ld.R | 1 tests/testthat/test-mirt-icc.R | 1 tests/testthat/test-multinomial.R | 4 +-- 24 files changed, 96 insertions(+), 91 deletions(-)
Title: Read 'IPUMS' Extract Files
Description: An easy way to import census, survey and geographic data provided by 'IPUMS'
into R plus tools to help use the associated metadata to make analysis easier. 'IPUMS'
data describing 1.4 billion individuals drawn from over 750 censuses and surveys is
available free of charge from our website <https://ipums.org>.
Author: Greg Freedman Ellis [aut, cre],
Derek Burk [ctb],
Joe Grover [ctb],
Minnesota Population Center [cph]
Maintainer: Greg Freedman Ellis <gfellis@umn.edu>
Diff between ipumsr versions 0.3.0 dated 2018-09-27 and 0.4.0 dated 2019-03-08
DESCRIPTION | 14 MD5 | 102 +- NAMESPACE | 4 NEWS.md | 16 R/RcppExports.R | 4 R/callbacks.r | 14 R/ddi_read.r | 20 R/ipums_info.r | 442 ++++++------ R/ipumsr.r |only R/lbl_helpers.r | 8 R/list_files.r | 154 ++-- R/micro_read.r | 210 +---- R/micro_read_chunked.r | 217 +----- R/micro_read_helpers.r |only R/micro_read_yield.r |only R/shape_read.r | 4 R/utils.r | 15 R/viewer.r | 450 ++++++------ README.md | 9 build/vignette.rds |binary inst/doc/ipums-bigdata.R | 75 ++ inst/doc/ipums-bigdata.Rmd | 171 ++++ inst/doc/ipums-bigdata.html | 883 +++++++++++------------- inst/doc/ipums-cps.html | 680 ++++++------------- inst/doc/ipums-geography.R | 81 +- inst/doc/ipums-geography.Rmd | 1099 +++++++++++++++---------------- inst/doc/ipums-geography.html | 713 +++++++------------- inst/doc/ipums-nhgis.R | 21 inst/doc/ipums-nhgis.Rmd | 647 +++++++++--------- inst/doc/ipums-nhgis.html | 653 ++++++------------ inst/doc/ipums-terra.html | 530 ++++---------- inst/doc/ipums.Rmd | 562 +++++++-------- inst/doc/ipums.html | 701 ++++++------------- inst/doc/value-labels.html | 830 ++++++++--------------- man/figures |only man/ipumsr-package.Rd |only man/read_ipums_micro.Rd | 14 man/read_ipums_micro_chunked.Rd | 13 man/read_ipums_micro_yield.Rd |only man/read_ipums_sf.Rd | 1 man/read_nhgis.Rd | 1 man/read_terra_area.Rd | 1 man/read_terra_micro.Rd | 1 man/read_terra_raster.Rd | 1 src/RcppExports.cpp | 9 src/set_attributes.cpp | 12 tests/testthat/test_ipums_bind_rows.r | 8 tests/testthat/test_micro.r | 12 tests/testthat/test_micro_yield.r |only tests/testthat/test_parse_manual_code.r | 58 - tests/testthat/test_select_style.r | 286 ++++---- tests/testthat/test_set_var_attributes.r |only vignettes/ipums-bigdata.Rmd | 171 ++++ vignettes/ipums-geography.Rmd | 1099 +++++++++++++++---------------- vignettes/ipums-nhgis.Rmd | 647 +++++++++--------- vignettes/ipums.Rmd | 562 +++++++-------- 56 files changed, 5489 insertions(+), 6736 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Tao Yang [aut],
Zonglin He [aut],
Adam Elder [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2019.3-6 dated 2019-03-07 and 2019.3-8 dated 2019-03-08
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/chngpt-vignette.pdf |binary src/fastgrid_binomial_wrapper.cpp | 2 +- 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Robust Rank-Based Tests
Description: Implements two-sample tests for paired data with missing values (Fong, Huang, Lemos and McElrath 2018, Biostatics, <doi:10.1093/biostatistics/kxx039>) and modified Wilcoxon-Mann-Whitney two sample location test, also known as the Fligner-Policello test.
Author: Youyi Fong <youyifong@gmail.com>
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between robustrank versions 2018.10-1 dated 2018-09-20 and 2019.3-7 dated 2019-03-08
ChangeLog | 4 ++-- DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/unitTests/runit.mod.wmw.test.R | 1 + inst/unitTests/runit.mw.mw.2.perm.R | 1 + inst/unitTests/runit.pair.wmw.R | 1 + inst/unitTests/runit.paired.with.replicates.R | 1 + inst/unitTests/runit.partiallymatched.R | 1 + 8 files changed, 17 insertions(+), 12 deletions(-)
Title: Functions to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L Davis [aut, cre],
Paul Gilbert [aut]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.4 dated 2018-11-29 and 1.0.5 dated 2019-03-08
DESCRIPTION | 15 +++++---- LICENSE | 7 +++- MD5 | 10 +++--- NEWS.md | 13 +++++--- R/find_python_cmd.r | 6 +-- README.md | 79 ++++++++++++++++++++++++++++++++++------------------ 6 files changed, 83 insertions(+), 47 deletions(-)
Title: Community Dynamics Metrics
Description: Univariate and multivariate temporal and spatial diversity indices,
rank abundance curves, and community stability measures. The functions
implement measures that are either explicitly temporal and include the
option to calculate them over multiple replicates, or spatial and include
the option to calculate them over multiple time points. Functions fall into
five categories: static diversity indices, temporal diversity indices,
spatial diversity indices, rank abundance curves, and community stability
measures. The diversity indices are temporal and spatial analogs to
traditional diversity indices. Specifically, the package includes functions
to calculate community richness, evenness and diversity at a given point in
space and time. In addition, it contains functions to calculate species
turnover, mean rank shifts, and lags in community similarity between two
time points.
Author: Lauren Hallett [aut],
Meghan L. Avolio [aut],
Ian T. Carroll [aut],
Sydney K. Jones [aut],
A. Andrew M. MacDonald [aut],
Dan F. B. Flynn [aut],
Peter Slaughter [aut],
Julie Ripplinger [aut],
Scott L. Collins [aut],
Corinna Gries [aut],
Matthew B. Jones [aut, cre]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 2.0.0 dated 2018-06-12 and 2.0.1 dated 2019-03-08
codyn-2.0.0/codyn/R/multivariate_change.R |only codyn-2.0.0/codyn/R/multivariate_difference.R |only codyn-2.0.0/codyn/man/EQ.Rd |only codyn-2.0.0/codyn/man/Evar.Rd |only codyn-2.0.0/codyn/man/S.Rd |only codyn-2.0.0/codyn/man/add_rank_abundance.Rd |only codyn-2.0.0/codyn/man/add_ranks.Rd |only codyn-2.0.0/codyn/man/check_args.Rd |only codyn-2.0.0/codyn/man/check_multispp.Rd |only codyn-2.0.0/codyn/man/check_names.Rd |only codyn-2.0.0/codyn/man/check_numeric.Rd |only codyn-2.0.0/codyn/man/check_single.Rd |only codyn-2.0.0/codyn/man/check_single_onerep.Rd |only codyn-2.0.0/codyn/man/check_sppvar.Rd |only codyn-2.0.0/codyn/man/codyn.Rd |only codyn-2.0.0/codyn/man/curve_dissim.Rd |only codyn-2.0.0/codyn/man/cyclic_shift_onerep.Rd |only codyn-2.0.0/codyn/man/df_intersect.Rd |only codyn-2.0.0/codyn/man/fill_species.Rd |only codyn-2.0.0/codyn/man/fill_zeros.Rd |only codyn-2.0.0/codyn/man/lag_i.Rd |only codyn-2.0.0/codyn/man/lagged_distances.Rd |only codyn-2.0.0/codyn/man/lagged_slope.Rd |only codyn-2.0.0/codyn/man/rank_onerep.Rd |only codyn-2.0.0/codyn/man/shuffle_community.Rd |only codyn-2.0.0/codyn/man/split_apply_combine.Rd |only codyn-2.0.0/codyn/man/stability_onerep.Rd |only codyn-2.0.0/codyn/man/synch_onerep.Rd |only codyn-2.0.0/codyn/man/transpose_community.Rd |only codyn-2.0.0/codyn/man/turnover_allyears.Rd |only codyn-2.0.0/codyn/man/turnover_twoyears.Rd |only codyn-2.0.0/codyn/man/variance_ratio_longformdata.Rd |only codyn-2.0.0/codyn/man/variance_ratio_matrixdata.Rd |only codyn-2.0.1/codyn/DESCRIPTION | 19 codyn-2.0.1/codyn/MD5 | 115 -- codyn-2.0.1/codyn/NAMESPACE | 1 codyn-2.0.1/codyn/NEWS | 13 codyn-2.0.1/codyn/R/RAC_change.R | 69 + codyn-2.0.1/codyn/R/RAC_difference.R | 147 ++- codyn-2.0.1/codyn/R/abundance_change.R | 30 codyn-2.0.1/codyn/R/abundance_difference.R | 105 +- codyn-2.0.1/codyn/R/codyn-package.R | 5 codyn-2.0.1/codyn/R/community_diversity.R | 61 - codyn-2.0.1/codyn/R/community_stability.R | 40 codyn-2.0.1/codyn/R/community_structure.R | 64 - codyn-2.0.1/codyn/R/curve_change.R | 29 codyn-2.0.1/codyn/R/curve_difference.R | 65 - codyn-2.0.1/codyn/R/multivariate_change_and_difference.R |only codyn-2.0.1/codyn/R/rank_shift.R | 29 codyn-2.0.1/codyn/R/rate_change.R | 46 codyn-2.0.1/codyn/R/synchrony.R | 20 codyn-2.0.1/codyn/R/temporal_torus_translation.R | 24 codyn-2.0.1/codyn/R/turnover.R | 49 - codyn-2.0.1/codyn/R/utilities.R | 291 +++--- codyn-2.0.1/codyn/R/variance_ratio.R | 22 codyn-2.0.1/codyn/build/vignette.rds |binary codyn-2.0.1/codyn/inst/doc/Community_Stability_Metrics.html | 433 ++------- codyn-2.0.1/codyn/inst/doc/Temporal_Diversity_Indices.html | 462 ++-------- codyn-2.0.1/codyn/inst/doc/codyn_overview.html | 219 ---- codyn-2.0.1/codyn/man/RAC_change.Rd | 64 - codyn-2.0.1/codyn/man/RAC_difference.Rd | 94 +- codyn-2.0.1/codyn/man/abundance_change.Rd | 38 codyn-2.0.1/codyn/man/abundance_difference.Rd | 85 + codyn-2.0.1/codyn/man/codyn-package.Rd |only codyn-2.0.1/codyn/man/community_diversity.Rd | 41 codyn-2.0.1/codyn/man/community_stability.Rd | 28 codyn-2.0.1/codyn/man/community_structure.Rd | 44 codyn-2.0.1/codyn/man/curve_change.Rd | 41 codyn-2.0.1/codyn/man/curve_difference.Rd | 44 codyn-2.0.1/codyn/man/cyclic_shift.Rd | 4 codyn-2.0.1/codyn/man/multivariate_change.Rd | 81 + codyn-2.0.1/codyn/man/multivariate_difference.Rd | 84 + codyn-2.0.1/codyn/man/variance_ratio.Rd | 3 codyn-2.0.1/codyn/tests/testthat/test_multivariate_change.R | 11 codyn-2.0.1/codyn/tests/testthat/test_multivariate_difference.R | 2 codyn-2.0.1/codyn/vignettes/biblio.bib | 84 - 76 files changed, 1446 insertions(+), 1660 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis [aut, cre],
Allen Day [ctb] (Some documentation and examples ported from the getopt
package.),
Python Software Foundation [ctb] (Some documentation from the optparse
Python module.),
Paul Newell [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.0.0 dated 2018-11-30 and 2.0.1 dated 2019-03-08
DESCRIPTION | 10 +++--- MD5 | 14 ++++---- NAMESPACE | 1 NEWS.md | 7 ++++ R/argparse.R | 66 +++++++++++++---------------------------- README.md | 15 +++------ inst/doc/argparse.html | 44 ++++++++++++++------------- tests/testthat/test-argparse.R | 13 ++++++-- 8 files changed, 80 insertions(+), 90 deletions(-)
Title: Tidy Characterizations of Model Performance
Description: Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between yardstick versions 0.0.2 dated 2018-11-05 and 0.0.3 dated 2019-03-08
DESCRIPTION | 8 - MD5 | 110 ++++++++++++---------- NAMESPACE | 12 ++ NEWS.md | 34 +++++++ R/aaa.R | 10 +- R/class-detection_prevalence.R | 5 - R/class-f_meas.R | 2 R/class-j_index.R | 6 - R/class-kap.R | 2 R/class-npv.R | 5 - R/class-ppv.R | 5 - R/class-precision.R | 11 +- R/class-recall.R | 11 +- R/class-spec.R | 11 +- R/conf_mat.R | 98 ++++++++++++++++++++ R/metrics.R | 36 ++++++- R/num-ccc.R | 2 R/num-huber_loss.R |only R/num-mase.R |only R/num-pseudo_huber_loss.R |only R/num-smape.R |only R/prob-gain_capture.R | 12 ++ R/prob-gain_curve.R | 10 ++ R/prob-roc_auc.R | 13 +- R/template.R | 5 - README.md | 2 inst/doc/custom-metrics.html | 85 ++++++++++------- inst/doc/metric-types.html | 52 +++++++++- inst/doc/multiclass.html | 4 man/ccc.Rd | 18 ++- man/conf_mat.Rd | 22 ++++ man/gain_capture.Rd | 11 ++ man/gain_curve.Rd | 11 ++ man/huber_loss.Rd |only man/huber_loss_pseudo.Rd |only man/j_index.Rd | 6 - man/kap.Rd | 2 man/lift_curve.Rd | 2 man/mae.Rd | 12 +- man/mape.Rd | 14 ++ man/mase.Rd |only man/metric_set.Rd | 4 man/pr_curve.Rd | 2 man/rmse.Rd | 14 ++ man/roc_curve.Rd | 2 man/rpd.Rd | 7 + man/rpiq.Rd | 7 + man/rsq.Rd | 7 + man/rsq_trad.Rd | 7 + man/smape.Rd |only tests/testthat/helper-data.R | 35 +++++-- tests/testthat/helper-data.rds |only tests/testthat/test-class-f_meas.R | 65 +++++++++++++ tests/testthat/test-class-precision.R | 14 ++ tests/testthat/test-class-recall.R | 14 ++ tests/testthat/test-numeric.R | 155 +++++++++++++++++++++++++++++++- tests/testthat/test-prob-gain_capture.R | 29 +++++ tests/testthat/test-prob-roc.R | 18 +++ tests/testthat/test_autoplot.R | 86 +++++++++++++++++ tests/testthat/test_autoplot.rds |only tests/testthat/test_metrics.R | 11 ++ 61 files changed, 934 insertions(+), 192 deletions(-)
Title: Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Description: Provides functions for the Bayesian analysis of extreme value
models. The 'rust' package <https://cran.r-project.org/package=rust> is
used to simulate a random sample from the required posterior distribution.
The functionality of 'revdbayes' is similar to the 'evdbayes' package
<https://cran.r-project.org/package=evdbayes>, which uses Markov Chain
Monte Carlo ('MCMC') methods for posterior simulation. Also provided
are functions for making inferences about the extremal index, using
the K-gaps model of Suveges and Davison (2010) <doi:10.1214/09-AOAS292>.
Also provided are d,p,q,r functions for the Generalised Extreme Value
('GEV') and Generalised Pareto ('GP') distributions that deal
appropriately with cases where the shape parameter is very close to zero.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between revdbayes versions 1.3.2 dated 2018-02-12 and 1.3.3 dated 2019-03-08
revdbayes-1.3.2/revdbayes/R/ts_post.R |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-kgaps-vignette.R |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-kgaps-vignette.Rmd |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-kgaps-vignette.html |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-predictive-vignette.R |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-predictive-vignette.Rmd |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-predictive-vignette.html |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-using-rcpp-vignette.R |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-using-rcpp-vignette.Rmd |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-using-rcpp-vignette.html |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-vignette.R |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-vignette.Rmd |only revdbayes-1.3.2/revdbayes/inst/doc/revdbayes-vignette.html |only revdbayes-1.3.2/revdbayes/vignettes/revdbayes-kgaps-vignette.Rmd |only revdbayes-1.3.2/revdbayes/vignettes/revdbayes-predictive-vignette.Rmd |only revdbayes-1.3.2/revdbayes/vignettes/revdbayes-using-rcpp-vignette.Rmd |only revdbayes-1.3.2/revdbayes/vignettes/revdbayes-vignette.Rmd |only revdbayes-1.3.3/revdbayes/DESCRIPTION | 16 revdbayes-1.3.3/revdbayes/MD5 | 134 revdbayes-1.3.3/revdbayes/NAMESPACE | 1 revdbayes-1.3.3/revdbayes/NEWS.md | 220 revdbayes-1.3.3/revdbayes/R/bayesplot.R | 2 revdbayes-1.3.3/revdbayes/R/distributions.R | 953 +- revdbayes-1.3.3/revdbayes/R/frequentist.R | 1781 +-- revdbayes-1.3.3/revdbayes/R/informative_priors.R | 389 revdbayes-1.3.3/revdbayes/R/init.R | 1106 +- revdbayes-1.3.3/revdbayes/R/kgaps.R | 820 - revdbayes-1.3.3/revdbayes/R/likelihoods.R | 8 revdbayes-1.3.3/revdbayes/R/misc.R | 734 - revdbayes-1.3.3/revdbayes/R/predictive.R | 2180 ++-- revdbayes-1.3.3/revdbayes/R/priors.R | 1797 ++- revdbayes-1.3.3/revdbayes/R/revdbayes.R | 306 revdbayes-1.3.3/revdbayes/R/rposterior.R | 1811 ++-- revdbayes-1.3.3/revdbayes/R/rposterior_rcpp.R | 1701 +-- revdbayes-1.3.3/revdbayes/R/rprior.R | 706 - revdbayes-1.3.3/revdbayes/R/sample_diagnostics.R | 64 revdbayes-1.3.3/revdbayes/README.md | 4 revdbayes-1.3.3/revdbayes/build/vignette.rds |binary revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-a-vignette.R |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-a-vignette.Rmd |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-a-vignette.html |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-b-using-rcpp-vignette.R |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-b-using-rcpp-vignette.Rmd |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-b-using-rcpp-vignette.html |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-c-predictive-vignette.R |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-c-predictive-vignette.Rmd |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-c-predictive-vignette.html |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-d-kgaps-vignette.R |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-d-kgaps-vignette.Rmd |only revdbayes-1.3.3/revdbayes/inst/doc/revdbayes-d-kgaps-vignette.html |only revdbayes-1.3.3/revdbayes/inst/include/revdbayes.h | 18 revdbayes-1.3.3/revdbayes/inst/include/revdbayes_RcppExports.h | 4500 +++++----- revdbayes-1.3.3/revdbayes/man/binpost.Rd | 8 revdbayes-1.3.3/revdbayes/man/gev.Rd | 12 revdbayes-1.3.3/revdbayes/man/gev_beta.Rd | 3 revdbayes-1.3.3/revdbayes/man/gev_loglognorm.Rd | 3 revdbayes-1.3.3/revdbayes/man/gev_prob.Rd | 19 revdbayes-1.3.3/revdbayes/man/gev_quant.Rd | 11 revdbayes-1.3.3/revdbayes/man/gom.Rd | 2 revdbayes-1.3.3/revdbayes/man/gp.Rd | 9 revdbayes-1.3.3/revdbayes/man/gp_beta.Rd | 3 revdbayes-1.3.3/revdbayes/man/gp_mdi.Rd | 2 revdbayes-1.3.3/revdbayes/man/kgaps_mle.Rd | 2 revdbayes-1.3.3/revdbayes/man/kgaps_post.Rd | 21 revdbayes-1.3.3/revdbayes/man/kgaps_stats.Rd | 20 revdbayes-1.3.3/revdbayes/man/plot.evpost.Rd | 4 revdbayes-1.3.3/revdbayes/man/pp_check.evpost.Rd | 2 revdbayes-1.3.3/revdbayes/man/predict.evpost.Rd | 28 revdbayes-1.3.3/revdbayes/man/print.summary.evpost.Rd |only revdbayes-1.3.3/revdbayes/man/quantile_to_gev.Rd | 6 revdbayes-1.3.3/revdbayes/man/rDir.Rd | 9 revdbayes-1.3.3/revdbayes/man/revdbayes.Rd | 2 revdbayes-1.3.3/revdbayes/man/rpost.Rd | 23 revdbayes-1.3.3/revdbayes/man/rpost_rcpp.Rd | 31 revdbayes-1.3.3/revdbayes/man/rprior_prob.Rd | 29 revdbayes-1.3.3/revdbayes/man/rprior_quant.Rd | 16 revdbayes-1.3.3/revdbayes/man/set_bin_prior.Rd | 6 revdbayes-1.3.3/revdbayes/man/set_prior.Rd | 104 revdbayes-1.3.3/revdbayes/man/summary.evpost.Rd | 3 revdbayes-1.3.3/revdbayes/src/RcppExports.cpp | 444 revdbayes-1.3.3/revdbayes/vignettes/revdbayes-a-vignette.Rmd |only revdbayes-1.3.3/revdbayes/vignettes/revdbayes-b-using-rcpp-vignette.Rmd |only revdbayes-1.3.3/revdbayes/vignettes/revdbayes-c-predictive-vignette.Rmd |only revdbayes-1.3.3/revdbayes/vignettes/revdbayes-d-kgaps-vignette.Rmd |only revdbayes-1.3.3/revdbayes/vignettes/revdbayes.bib | 576 - 85 files changed, 10749 insertions(+), 9900 deletions(-)
Title: A Simple Needmining Implementation
Description: Showcasing needmining (the semi-automatic extraction of customer needs from
social media data) with Twitter data. It uses the handling of the Twitter API provided by
the package 'rtweet' and the textmining algorithms provided by the package 'tm'.
Niklas Kuehl (2016) <doi:10.1007/978-3-319-32689-4_14> wrote an introduction to the topic of needmining.
Author: Dorian Proksch <dorian.proksch@hhl.de>, Timothy P. Jurka [ctb], Yoshimasa Tsuruoka [ctb], Loren Collingwood [ctb], Amber E. Boydstun [ctb], Emiliano Grossman [ctb], Wouter van Atteveldt [ctb]
Maintainer: Dorian Proksch <dorian.proksch@hhl.de>
Diff between needmining versions 0.1.0 dated 2019-02-27 and 0.1.1 dated 2019-03-08
DESCRIPTION | 13 +-- MD5 | 10 +- NAMESPACE | 18 +++- NEWS |only R/filterTweetsMachineLearning.R | 142 ++++++++++++++++++++++++++++++++++--- R/matrix_container-classes.R |only man/filterTweetsMachineLearning.Rd | 5 + 7 files changed, 163 insertions(+), 25 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.11.1.1 dated 2019-01-26 and 1.12.0 dated 2019-03-08
DESCRIPTION | 6 - MD5 | 74 +++++++++---------- NAMESPACE | 1 NEWS | 39 ++++++++++ R/ClusterFuture-class.R | 4 - R/Future-class.R | 22 ++--- R/FutureCondition-class.R | 29 ++----- R/FutureResult-class.R | 43 ++++++++--- R/MulticoreFuture-class.R | 2 R/backtrace.R | 2 R/conditions_OP.R | 1 R/globals_OP.R | 2 R/label_OP.R | 1 R/lazy_OP.R | 1 R/makeClusterPSOCK.R | 41 ++++++++-- R/multicore.R | 2 R/options.R | 2 R/resolve.R | 9 +- R/seed_OP.R | 1 R/signalEarly.R | 6 - R/stdout_OP.R | 1 R/utils.R | 12 +++ R/zzz.plan.R | 2 inst/doc/future-1-overview.html | 80 ++++++++++----------- inst/doc/future-1-overview.md.rsp | 80 ++++++++++----------- inst/vignettes-static/future-1-overview.md.rsp.rsp | 4 - man/FutureCondition.Rd | 2 man/FutureResult.Rd | 15 ++- man/future.options.Rd | 2 man/makeClusterPSOCK.Rd | 4 - man/plan.Rd | 2 man/requestCore.Rd | 4 - man/resolve.Rd | 2 man/result.Rd | 4 - tests/FutureError.R | 6 - tests/cluster.R | 2 tests/resolve.R | 13 --- vignettes/future-1-overview.md.rsp | 80 ++++++++++----------- 38 files changed, 346 insertions(+), 257 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.7 dated 2018-07-12 and 0.8 dated 2019-03-08
RSSL-0.7/RSSL/inst/doc |only RSSL-0.8/RSSL/DESCRIPTION | 8 RSSL-0.8/RSSL/MD5 | 117 +++++------ RSSL-0.8/RSSL/R/LearningCurve.R | 4 RSSL-0.8/RSSL/inst/examples/example-S4VM.R | 4 RSSL-0.8/RSSL/inst/examples/example-TSVM.R | 31 +- RSSL-0.8/RSSL/man/CrossValidationSSL.Rd | 13 - RSSL-0.8/RSSL/man/EMLeastSquaresClassifier.Rd | 1 RSSL-0.8/RSSL/man/EMLinearDiscriminantClassifier.Rd | 1 RSSL-0.8/RSSL/man/GRFClassifier.Rd | 6 RSSL-0.8/RSSL/man/ICLeastSquaresClassifier.Rd | 8 RSSL-0.8/RSSL/man/ICLinearDiscriminantClassifier.Rd | 1 RSSL-0.8/RSSL/man/KernelICLeastSquaresClassifier.Rd | 7 RSSL-0.8/RSSL/man/KernelLeastSquaresClassifier.Rd | 1 RSSL-0.8/RSSL/man/LaplacianKernelLeastSquaresClassifier.Rd | 1 RSSL-0.8/RSSL/man/LaplacianSVM.Rd | 1 RSSL-0.8/RSSL/man/LearningCurveSSL.Rd | 18 - RSSL-0.8/RSSL/man/LeastSquaresClassifier.Rd | 4 RSSL-0.8/RSSL/man/LinearDiscriminantClassifier.Rd | 1 RSSL-0.8/RSSL/man/LinearSVM.Rd | 1 RSSL-0.8/RSSL/man/LinearTSVM.Rd | 5 RSSL-0.8/RSSL/man/LogisticLossClassifier.Rd | 5 RSSL-0.8/RSSL/man/LogisticRegression.Rd | 1 RSSL-0.8/RSSL/man/LogisticRegressionFast.Rd | 4 RSSL-0.8/RSSL/man/MCLinearDiscriminantClassifier.Rd | 1 RSSL-0.8/RSSL/man/MCNearestMeanClassifier.Rd | 1 RSSL-0.8/RSSL/man/MCPLDA.Rd | 1 RSSL-0.8/RSSL/man/MajorityClassClassifier.Rd | 1 RSSL-0.8/RSSL/man/NearestMeanClassifier.Rd | 4 RSSL-0.8/RSSL/man/QuadraticDiscriminantClassifier.Rd | 1 RSSL-0.8/RSSL/man/S4VM.Rd | 5 RSSL-0.8/RSSL/man/SSLDataFrameToMatrices.Rd | 1 RSSL-0.8/RSSL/man/SVM.Rd | 1 RSSL-0.8/RSSL/man/SelfLearning.Rd | 5 RSSL-0.8/RSSL/man/TSVM.Rd | 36 +-- RSSL-0.8/RSSL/man/USMLeastSquaresClassifier.Rd | 1 RSSL-0.8/RSSL/man/WellSVM.Rd | 1 RSSL-0.8/RSSL/man/add_missinglabels_mar.Rd | 1 RSSL-0.8/RSSL/man/df_to_matrices.Rd | 1 RSSL-0.8/RSSL/man/evaluation-measures.Rd | 17 - RSSL-0.8/RSSL/man/generate2ClassGaussian.Rd | 4 RSSL-0.8/RSSL/man/generateABA.Rd | 1 RSSL-0.8/RSSL/man/generateCrescentMoon.Rd | 1 RSSL-0.8/RSSL/man/generateFourClusters.Rd | 1 RSSL-0.8/RSSL/man/generateParallelPlanes.Rd | 1 RSSL-0.8/RSSL/man/generateSlicedCookie.Rd | 1 RSSL-0.8/RSSL/man/generateSpirals.Rd | 1 RSSL-0.8/RSSL/man/generateTwoCircles.Rd | 1 RSSL-0.8/RSSL/man/line_coefficients-methods.Rd | 1 RSSL-0.8/RSSL/man/loss-methods.Rd | 14 - RSSL-0.8/RSSL/man/missing_labels.Rd | 1 RSSL-0.8/RSSL/man/rssl-predict.Rd | 15 - RSSL-0.8/RSSL/man/split_dataset_ssl.Rd | 1 RSSL-0.8/RSSL/man/split_random.Rd | 1 RSSL-0.8/RSSL/man/stat_classifier.Rd | 4 RSSL-0.8/RSSL/man/svmlin.Rd | 6 RSSL-0.8/RSSL/man/true_labels.Rd | 1 RSSL-0.8/RSSL/tests/testthat/test-ICLeastSquaresClassifier.R | 8 RSSL-0.8/RSSL/tests/testthat/test-LeastSquaresClassifier.R | 2 59 files changed, 216 insertions(+), 170 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.200.7.0 dated 2019-01-17 and 0.9.200.7.1 dated 2019-03-08
ChangeLog | 20 +++ DESCRIPTION | 8 - MD5 | 14 +- inst/NEWS.Rd | 11 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/op_wishrnd_meat.hpp | 143 +++++++++++------------- inst/unitTests/runit.sample.R | 5 8 files changed, 115 insertions(+), 86 deletions(-)
Title: Fire-History Analysis in R
Description: Basic tools to analyze forest fire history data (e.g. FHX) in R.
Author: Steven Malevich [aut, cre],
Christopher Guiterman [ctb],
Ellis Margolis [ctb]
Maintainer: Steven Malevich <malevich@email.arizona.edu>
Diff between burnr versions 0.3.0 dated 2019-01-07 and 0.3.1 dated 2019-03-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ README.md | 8 +++++--- inst/doc/introduction.Rmd | 6 ++---- inst/doc/introduction.html | 11 ++++------- tests/testthat/test-sea.R | 1 + vignettes/introduction.Rmd | 6 ++---- 8 files changed, 34 insertions(+), 29 deletions(-)
Title: Amend, Augment and Aid Analysis of John Snow's Cholera Map
Description: Amends errors, augments data and aids analysis of John Snow's map
of the 1854 London cholera outbreak.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between cholera versions 0.5.1 dated 2018-08-15 and 0.6.0 dated 2019-03-08
cholera-0.5.1/cholera/R/addCases.R |only cholera-0.5.1/cholera/R/addNeighborhood.R |only cholera-0.5.1/cholera/R/euclideanDistance.R |only cholera-0.5.1/cholera/R/walkingDistance.R |only cholera-0.5.1/cholera/data/anchor.case.RData |only cholera-0.5.1/cholera/data/fatalities.address.RData |only cholera-0.5.1/cholera/data/regular.cases.RData |only cholera-0.5.1/cholera/data/sim.ortho.proj.RData |only cholera-0.5.1/cholera/man/addBorder.Rd |only cholera-0.5.1/cholera/man/addCases.Rd |only cholera-0.5.1/cholera/man/addNeighborhood.Rd |only cholera-0.5.1/cholera/man/euclideanDistance.Rd |only cholera-0.5.1/cholera/man/walkingDistance.Rd |only cholera-0.6.0/cholera/DESCRIPTION | 26 cholera-0.6.0/cholera/MD5 | 306 +-- cholera-0.6.0/cholera/NAMESPACE | 24 cholera-0.6.0/cholera/NEWS | 88 cholera-0.6.0/cholera/R/addCase.R |only cholera-0.6.0/cholera/R/addDelauny.R |only cholera-0.6.0/cholera/R/addEuclideanPath.R | 38 cholera-0.6.0/cholera/R/addIndexCase.R | 10 cholera-0.6.0/cholera/R/addKernelDensity.R | 89 cholera-0.6.0/cholera/R/addLandmarks.R | 114 - cholera-0.6.0/cholera/R/addMilePosts.R | 6 cholera-0.6.0/cholera/R/addNeighborhoodCases.R |only cholera-0.6.0/cholera/R/addNeighborhoodEuclidean.R |only cholera-0.6.0/cholera/R/addNeighborhoodWalking.R |only cholera-0.6.0/cholera/R/addPlaguePit.R | 10 cholera-0.6.0/cholera/R/addPump.R | 17 cholera-0.6.0/cholera/R/addSnow.R | 32 cholera-0.6.0/cholera/R/addVoronoi.R | 48 cholera-0.6.0/cholera/R/addWalkingPath.R | 314 +-- cholera-0.6.0/cholera/R/addWhitehead.R | 22 cholera-0.6.0/cholera/R/caseLocator.R | 173 + cholera-0.6.0/cholera/R/cholera.R | 8 cholera-0.6.0/cholera/R/classifierAudit.R | 41 cholera-0.6.0/cholera/R/data.R | 43 cholera-0.6.0/cholera/R/deldirVertices.R |only cholera-0.6.0/cholera/R/distanceTime.R | 36 cholera-0.6.0/cholera/R/euclidean.R | 236 +- cholera-0.6.0/cholera/R/euclideanPath.R | 779 +++++-- cholera-0.6.0/cholera/R/fixFatalities.R |only cholera-0.6.0/cholera/R/landmarkData.R |only cholera-0.6.0/cholera/R/multiCore.R | 40 cholera-0.6.0/cholera/R/nearestPump.R | 32 cholera-0.6.0/cholera/R/neighborhoodData.R | 181 + cholera-0.6.0/cholera/R/orthogonalProjection.R |only cholera-0.6.0/cholera/R/pearlString.R | 79 cholera-0.6.0/cholera/R/pearsonResiduals.R |only cholera-0.6.0/cholera/R/profile2D.R |only cholera-0.6.0/cholera/R/profile3D.R |only cholera-0.6.0/cholera/R/pumpCase.R | 5 cholera-0.6.0/cholera/R/pumpData.R | 38 cholera-0.6.0/cholera/R/pumpLocator.R | 111 - cholera-0.6.0/cholera/R/pumpTokens.R |only cholera-0.6.0/cholera/R/segmentLength.R | 23 cholera-0.6.0/cholera/R/segmentLocator.R | 124 - cholera-0.6.0/cholera/R/simulateFatalities.R | 51 cholera-0.6.0/cholera/R/snowColors.R | 15 cholera-0.6.0/cholera/R/snowMap.R | 34 cholera-0.6.0/cholera/R/snowNeighborhood.R | 9 cholera-0.6.0/cholera/R/streetHighlight.R |only cholera-0.6.0/cholera/R/streetLength.R | 21 cholera-0.6.0/cholera/R/streetNameLocator.R | 206 +- cholera-0.6.0/cholera/R/streetNumberLocator.R | 218 +- cholera-0.6.0/cholera/R/unitMeter.R | 16 cholera-0.6.0/cholera/R/unstack.R | 131 - cholera-0.6.0/cholera/R/voronoi.R | 239 -- cholera-0.6.0/cholera/R/walking.R | 598 +---- cholera-0.6.0/cholera/R/walkingAuxillaryFunctions.R | 216 +- cholera-0.6.0/cholera/R/walkingPath.R | 1011 +++++++--- cholera-0.6.0/cholera/R/withinRadius.R |only cholera-0.6.0/cholera/README.md | 268 ++ cholera-0.6.0/cholera/build/vignette.rds |binary cholera-0.6.0/cholera/data/anchor.case.rda |only cholera-0.6.0/cholera/data/fatalities.address.rda |only cholera-0.6.0/cholera/data/landmark.squares.rda |only cholera-0.6.0/cholera/data/landmarks.rda |only cholera-0.6.0/cholera/data/regular.cases.rda |only cholera-0.6.0/cholera/data/sim.ortho.proj.rda |only cholera-0.6.0/cholera/inst/doc/duplicate.missing.cases.R | 2 cholera-0.6.0/cholera/inst/doc/duplicate.missing.cases.Rmd | 19 cholera-0.6.0/cholera/inst/doc/duplicate.missing.cases.html | 384 +++ cholera-0.6.0/cholera/inst/doc/kernel.density.R | 12 cholera-0.6.0/cholera/inst/doc/kernel.density.Rmd | 22 cholera-0.6.0/cholera/inst/doc/kernel.density.html | 341 ++- cholera-0.6.0/cholera/inst/doc/pump.neighborhoods.R | 12 cholera-0.6.0/cholera/inst/doc/pump.neighborhoods.Rmd | 46 cholera-0.6.0/cholera/inst/doc/pump.neighborhoods.html | 445 +++- cholera-0.6.0/cholera/inst/doc/roads.R | 8 cholera-0.6.0/cholera/inst/doc/roads.Rmd | 34 cholera-0.6.0/cholera/inst/doc/roads.html | 422 +++- cholera-0.6.0/cholera/inst/doc/tiles.polygons.R |only cholera-0.6.0/cholera/inst/doc/tiles.polygons.Rmd |only cholera-0.6.0/cholera/inst/doc/tiles.polygons.html |only cholera-0.6.0/cholera/inst/doc/time.series.R | 2 cholera-0.6.0/cholera/inst/doc/time.series.Rmd | 10 cholera-0.6.0/cholera/inst/doc/time.series.html | 324 ++- cholera-0.6.0/cholera/inst/doc/unstacking.bars.R | 9 cholera-0.6.0/cholera/inst/doc/unstacking.bars.Rmd | 24 cholera-0.6.0/cholera/inst/doc/unstacking.bars.html | 455 +++- cholera-0.6.0/cholera/man/addCase.Rd |only cholera-0.6.0/cholera/man/addDelauny.Rd |only cholera-0.6.0/cholera/man/addEuclideanPath.Rd | 4 cholera-0.6.0/cholera/man/addFrame.Rd |only cholera-0.6.0/cholera/man/addIndexCase.Rd | 13 cholera-0.6.0/cholera/man/addKernelDensity.Rd | 19 cholera-0.6.0/cholera/man/addLandmarks.Rd | 13 cholera-0.6.0/cholera/man/addNeighborhoodCases.Rd |only cholera-0.6.0/cholera/man/addNeighborhoodEuclidean.Rd |only cholera-0.6.0/cholera/man/addNeighborhoodWalking.Rd |only cholera-0.6.0/cholera/man/addPlaguePit.Rd | 13 cholera-0.6.0/cholera/man/addPump.Rd | 4 cholera-0.6.0/cholera/man/addRoads.Rd | 8 cholera-0.6.0/cholera/man/addSnow.Rd | 17 cholera-0.6.0/cholera/man/addVoronoi.Rd | 22 cholera-0.6.0/cholera/man/addWalkingPath.Rd | 23 cholera-0.6.0/cholera/man/addWhitehead.Rd | 19 cholera-0.6.0/cholera/man/anchor.case.Rd | 2 cholera-0.6.0/cholera/man/caseLocator.Rd | 21 cholera-0.6.0/cholera/man/cholera-package.Rd | 8 cholera-0.6.0/cholera/man/deldirVertices.Rd |only cholera-0.6.0/cholera/man/distanceTime.Rd | 10 cholera-0.6.0/cholera/man/euclideanPath.Rd | 27 cholera-0.6.0/cholera/man/fatalities.address.Rd | 4 cholera-0.6.0/cholera/man/fatalities.unstacked.Rd | 2 cholera-0.6.0/cholera/man/figures/README-euclidean-1.png |only cholera-0.6.0/cholera/man/figures/README-expected-1.png |binary cholera-0.6.0/cholera/man/figures/README-expected_area_points-1.png |only cholera-0.6.0/cholera/man/figures/README-unnamed-chunk-3-1.png |binary cholera-0.6.0/cholera/man/figures/README-virtue-1.png |only cholera-0.6.0/cholera/man/figures/README-voronoi-1.png |binary cholera-0.6.0/cholera/man/figures/README-walk-1.png |binary cholera-0.6.0/cholera/man/figures/README-walk7-1.png |binary cholera-0.6.0/cholera/man/fixFatalities.Rd | 2 cholera-0.6.0/cholera/man/landmark.squares.Rd |only cholera-0.6.0/cholera/man/landmarkData.Rd |only cholera-0.6.0/cholera/man/landmarks.Rd |only cholera-0.6.0/cholera/man/nearestPump.Rd | 4 cholera-0.6.0/cholera/man/neighborhoodData.Rd | 7 cholera-0.6.0/cholera/man/neighborhoodEuclidean.Rd | 16 cholera-0.6.0/cholera/man/neighborhoodVoronoi.Rd | 10 cholera-0.6.0/cholera/man/neighborhoodWalking.Rd | 2 cholera-0.6.0/cholera/man/orthogonalProjection.Rd |only cholera-0.6.0/cholera/man/pearsonResiduals.Rd |only cholera-0.6.0/cholera/man/plot.classifier_audit.Rd | 7 cholera-0.6.0/cholera/man/plot.euclidean.Rd | 29 cholera-0.6.0/cholera/man/plot.euclidean_path.Rd | 8 cholera-0.6.0/cholera/man/plot.neighborhood_data.Rd |only cholera-0.6.0/cholera/man/plot.profile_perspective.Rd |only cholera-0.6.0/cholera/man/plot.voronoi.Rd | 6 cholera-0.6.0/cholera/man/plot.walking.Rd | 7 cholera-0.6.0/cholera/man/plot.walking_path.Rd | 14 cholera-0.6.0/cholera/man/print.euclidean.Rd | 4 cholera-0.6.0/cholera/man/print.euclidean_path.Rd | 4 cholera-0.6.0/cholera/man/print.voronoi.Rd | 4 cholera-0.6.0/cholera/man/print.walking_path.Rd | 11 cholera-0.6.0/cholera/man/profile2D.Rd |only cholera-0.6.0/cholera/man/profile3D.Rd |only cholera-0.6.0/cholera/man/pumpCase.Rd | 3 cholera-0.6.0/cholera/man/pumpData.Rd | 2 cholera-0.6.0/cholera/man/pumpLocator.Rd | 20 cholera-0.6.0/cholera/man/regular.cases.Rd | 4 cholera-0.6.0/cholera/man/segmentLength.Rd | 9 cholera-0.6.0/cholera/man/segmentLocator.Rd | 27 cholera-0.6.0/cholera/man/sim.ortho.proj.Rd | 2 cholera-0.6.0/cholera/man/simulateFatalities.Rd | 6 cholera-0.6.0/cholera/man/snowColors.Rd | 5 cholera-0.6.0/cholera/man/snowMap.Rd | 19 cholera-0.6.0/cholera/man/streetHighlight.Rd |only cholera-0.6.0/cholera/man/streetLength.Rd | 9 cholera-0.6.0/cholera/man/streetNameLocator.Rd | 26 cholera-0.6.0/cholera/man/streetNumberLocator.Rd | 26 cholera-0.6.0/cholera/man/unitMeter.Rd | 5 cholera-0.6.0/cholera/man/unstackFatalities.Rd | 4 cholera-0.6.0/cholera/man/walkingPath.Rd | 24 cholera-0.6.0/cholera/vignettes/duplicate.missing.cases.Rmd | 19 cholera-0.6.0/cholera/vignettes/kernel.density.Rmd | 22 cholera-0.6.0/cholera/vignettes/pump.neighborhoods.Rmd | 46 cholera-0.6.0/cholera/vignettes/roads.Rmd | 34 cholera-0.6.0/cholera/vignettes/tiles.polygons.Rmd |only cholera-0.6.0/cholera/vignettes/time.series.Rmd | 10 cholera-0.6.0/cholera/vignettes/unstacking.bars.Rmd | 24 183 files changed, 6034 insertions(+), 3373 deletions(-)
Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam'
with 64-bit integers. Loading this package together with the R package
spam enables the sparse matrix class spam to handle huge sparse matrices
with more than 2^31-1 non-zero elements.
Author: Reinhard Furrer [aut, cre],
Florian Gerber [aut],
Roman Flury [aut],
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Youcef Saad [prg] (SPARSEKIT
http://www-users.cs.umn.edu/~saad/software/SPARSKIT/),
Esmond G. Ng [prg] (Fortran Cholesky routines),
Barry W. Peyton [prg] (Fortran Cholesky routines),
Joseph W.H. Liu [prg] (Fortran Cholesky routines),
Alan D. George [prg] (Fortran Cholesky routines),
Lehoucq B. Rich [prg] (ARPACK),
Maschhoff Kristi [prg] (ARPACK),
Sorensen C. Danny [prg] (ARPACK),
Yang Chao [prg] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam64 versions 2.2-1 dated 2018-12-20 and 2.2-2 dated 2019-03-08
DESCRIPTION | 54 +++++++++++++++++++++++++++--------------------------- MD5 | 2 +- 2 files changed, 28 insertions(+), 28 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Author: Reinhard Furrer [aut, cre],
Florian Gerber [aut],
Roman Flury [aut],
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Youcef Saad [prg] (SPARSEKIT
http://www-users.cs.umn.edu/~saad/software/SPARSKIT/),
Esmond G. Ng [prg] (Fortran Cholesky routines),
Barry W. Peyton [prg] (Fortran Cholesky routines),
Joseph W.H. Liu [prg] (Fortran Cholesky routines),
Alan D. George [prg] (Fortran Cholesky routines),
Lehoucq B. Rich [prg] (ARPACK),
Maschhoff Kristi [prg] (ARPACK),
Sorensen C. Danny [prg] (ARPACK),
Yang Chao [prg] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 2.2-1 dated 2018-12-20 and 2.2-2 dated 2019-03-08
spam-2.2-1/spam/vignettes/spam.html |only spam-2.2-2/spam/DESCRIPTION | 54 ++-- spam-2.2-2/spam/MD5 | 153 ++++++-------- spam-2.2-2/spam/NEWS.md | 7 spam-2.2-2/spam/R/apply.R | 4 spam-2.2-2/spam/R/constructors.R | 4 spam-2.2-2/spam/R/covmat.R | 4 spam-2.2-2/spam/R/definitions.R | 4 spam-2.2-2/spam/R/deprecated.R | 4 spam-2.2-2/spam/R/diff.R | 4 spam-2.2-2/spam/R/dim.R | 4 spam-2.2-2/spam/R/dist.R | 4 spam-2.2-2/spam/R/eigen.R | 4 spam-2.2-2/spam/R/foreign.R | 4 spam-2.2-2/spam/R/helper.R | 4 spam-2.2-2/spam/R/kronecker.R | 4 spam-2.2-2/spam/R/math.R | 4 spam-2.2-2/spam/R/mle.R | 4 spam-2.2-2/spam/R/norm.R | 4 spam-2.2-2/spam/R/permutation.R | 4 spam-2.2-2/spam/R/plotting.R | 4 spam-2.2-2/spam/R/precmat.R | 4 spam-2.2-2/spam/R/profile.R | 4 spam-2.2-2/spam/R/rep_len64.R | 4 spam-2.2-2/spam/R/rmvnorm.R | 4 spam-2.2-2/spam/R/rowcolstats.R | 4 spam-2.2-2/spam/R/s3only.R | 4 spam-2.2-2/spam/R/s4coerce.R | 4 spam-2.2-2/spam/R/spam_solve.R | 4 spam-2.2-2/spam/R/spamlist.R | 4 spam-2.2-2/spam/R/subset.R | 4 spam-2.2-2/spam/R/summary.R | 4 spam-2.2-2/spam/R/tailhead.R | 4 spam-2.2-2/spam/R/tcrossprod.R | 4 spam-2.2-2/spam/R/toepliz.R | 4 spam-2.2-2/spam/R/xybind.R | 4 spam-2.2-2/spam/inst/doc/spam.pdf |binary spam-2.2-2/spam/tests/demo_article-jss-example1.R | 4 spam-2.2-2/spam/tests/demo_article-jss-example1.Rout.save | 12 - spam-2.2-2/spam/tests/demo_article-jss-example2.R | 4 spam-2.2-2/spam/tests/demo_article-jss-example2.Rout.save | 12 - spam-2.2-2/spam/tests/demo_article-jss.R | 4 spam-2.2-2/spam/tests/demo_article-jss.Rout.save | 12 - spam-2.2-2/spam/tests/demo_cholesky.R | 4 spam-2.2-2/spam/tests/demo_cholesky.Rout.save | 12 - spam-2.2-2/spam/tests/demo_jss15-BYM.R | 4 spam-2.2-2/spam/tests/demo_jss15-BYM.Rout.save | 12 - spam-2.2-2/spam/tests/demo_jss15-Leroux.R | 4 spam-2.2-2/spam/tests/demo_jss15-Leroux.Rout.save | 12 - spam-2.2-2/spam/tests/demo_spam.R | 4 spam-2.2-2/spam/tests/demo_spam.Rout.save | 12 - spam-2.2-2/spam/tests/demo_timing.R | 4 spam-2.2-2/spam/tests/demo_timing.Rout.save | 12 - spam-2.2-2/spam/tests/jss_areal_counts.R | 4 spam-2.2-2/spam/tests/jss_areal_counts.Rout.save | 12 - spam-2.2-2/spam/tests/testthat.R | 4 spam-2.2-2/spam/tests/testthat/helper.R | 4 spam-2.2-2/spam/tests/testthat/test-constructors.R | 20 + spam-2.2-2/spam/tests/testthat/test-covmat.R | 4 spam-2.2-2/spam/tests/testthat/test-crossprod.R | 4 spam-2.2-2/spam/tests/testthat/test-diff.R | 4 spam-2.2-2/spam/tests/testthat/test-dim.R | 4 spam-2.2-2/spam/tests/testthat/test-dist.R | 4 spam-2.2-2/spam/tests/testthat/test-eigen.R | 4 spam-2.2-2/spam/tests/testthat/test-helper.R | 4 spam-2.2-2/spam/tests/testthat/test-kronecker.R | 4 spam-2.2-2/spam/tests/testthat/test-math.R | 4 spam-2.2-2/spam/tests/testthat/test-mle.R | 4 spam-2.2-2/spam/tests/testthat/test-ops.R | 4 spam-2.2-2/spam/tests/testthat/test-overall.R | 4 spam-2.2-2/spam/tests/testthat/test-permutation.R | 4 spam-2.2-2/spam/tests/testthat/test-profile.R | 4 spam-2.2-2/spam/tests/testthat/test-rep_len64.R | 4 spam-2.2-2/spam/tests/testthat/test-rowcolstats.R | 4 spam-2.2-2/spam/tests/testthat/test-solve.R | 4 spam-2.2-2/spam/tests/testthat/test-spamlist.R | 4 spam-2.2-2/spam/tests/testthat/test-subset.R | 4 spam-2.2-2/spam/tests/testthat/test-xybind.R | 4 78 files changed, 301 insertions(+), 293 deletions(-)
Title: Lower Confidence Bounds for Binomial Series System
Description: Calculate lower confidence bounds for binomial series system reliability. The R 'shiny' application, launched by launch_app(), weaves together a workflow of customized simulations and delta coverage calculations to output a ranked list of lower confidence bound methods.
Author: Edward Schuberg
Maintainer: Edward Schuberg <eschu003@ucr.edu>
Diff between serieslcb versions 0.2.0 dated 2018-07-19 and 0.3.0 dated 2019-03-08
DESCRIPTION | 8 - MD5 | 8 + R/functions.R | 14 +++ inst/app.R | 231 ++++++++++++++++++++++++++++++++++++++++---------------- inst/www |only man/rmse.LCB.Rd |only 6 files changed, 189 insertions(+), 72 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.99.16 dated 2018-03-28 and 0.100.18 dated 2019-03-08
DESCRIPTION | 9 MD5 | 170 ++-- NAMESPACE | 25 R/arc3d.R |only R/ashape3d.R |only R/callbacks.R | 17 R/convertScene.R | 7 R/enum.R | 2 R/getscene.R | 2 R/grid3d.R | 6 R/material.R | 20 R/mesh3d.R | 208 +++++ R/par3d.R | 118 +-- R/pch3d.R | 72 +- R/persp3d.R | 17 R/plot3d.R | 85 ++ R/plotmath3d.R | 23 R/r3d.rgl.R | 31 R/rglwidget.R | 34 R/scene.R | 72 +- R/shapelist3d.R | 6 R/subdivision.mesh3d.R | 3 R/subscenes.R | 27 R/thigmophobe3d.R |only R/zzz.R | 5 build/vignette.rds |binary demo/mouseCallbacks.R | 13 demo/rglExamples.R | 10 demo/shapes3d.R | 2 demo/subdivision.r | 10 inst/NEWS | 61 + inst/doc/WebGL.html | 56 + inst/doc/legacyWebGL.html | 231 +++++- inst/doc/rgl.R | 4 inst/doc/rgl.Rmd | 136 ++- inst/doc/rgl.html | 665 +++++++++++------- inst/htmlwidgets/lib/rglClass/rglClass.src.js | 133 +++ man/3dobjects.Rd | 3 man/arc3d.Rd |only man/as.mesh3d.ashape3d.Rd |only man/attributes.Rd | 6 man/callbacks.Rd | 48 - man/material.Rd | 23 man/mesh3d.Rd | 39 + man/par3d.Rd | 14 man/pch3d.Rd | 22 man/persp3d.Rd | 53 - man/persp3d.deldir.Rd | 6 man/persp3d.tri.Rd |only man/plot3d.Rd | 2 man/plot3d.formula.Rd |only man/plot3d.lm.Rd |only man/plotmath3d.Rd | 2 man/postscript.Rd | 2 man/rgl-internal.Rd | 4 man/rgl.select.Rd | 6 man/rgl.user2window.Rd | 3 man/select3d.Rd | 4 man/shinyGetPar3d.Rd |only man/subscene3d.Rd | 37 - man/texts.Rd | 14 man/thigmophobe3d.Rd |only src/ABCLineSet.cpp | 45 - src/BBoxDeco.cpp | 3 src/Material.cpp | 10 src/Material.h | 3 src/SceneNode.h | 1 src/Shape.cpp | 19 src/Shape.h | 6 src/SpriteSet.cpp | 28 src/SpriteSet.h | 11 src/TextSet.cpp | 19 src/TextSet.h | 7 src/Viewpoint.cpp | 26 src/Viewpoint.h | 5 src/api.cpp | 175 ++-- src/api.h | 15 src/callbacks.cpp | 68 + src/fps.cpp | 4 src/glgui.cpp | 66 + src/glgui.h | 30 src/init.cpp | 20 src/par3d.cpp | 914 +++++++++++++------------- src/rglview.cpp | 680 ++----------------- src/rglview.h | 111 --- src/scene.cpp | 47 + src/scene.h | 3 src/subscene.cpp | 623 +++++++++++++++++ src/subscene.h | 151 ++++ src/x11gui.cpp | 10 vignettes/rgl.Rmd | 136 ++- 91 files changed, 3588 insertions(+), 2216 deletions(-)
Title: 'CARTOColors' Palettes
Description: Provides color schemes for maps and other graphics
designed by 'CARTO' as described at <https://carto.com/carto-colors/>.
It includes four types of palettes: aggregation, diverging, qualitative,
and quantitative.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between rcartocolor versions 0.0.22 dated 2018-02-08 and 1.0.0 dated 2019-03-08
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- data/cartocolors.rda |binary data/metacartocolors.rda |binary man/carto_scale.Rd | 14 ++++++-------- 5 files changed, 15 insertions(+), 17 deletions(-)
Title: R Bindings for Gtk 2.8.0 and Above
Description: Facilities in the R language for programming
graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence <michafla@gene.com> and Duncan Temple Lang <duncan@wald.ucdavis.edu>
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between RGtk2 versions 2.20.35 dated 2018-06-12 and 2.20.36 dated 2019-03-08
DESCRIPTION | 6 MD5 | 34 +- R/gdkCoerce.R | 11 inst/doc/overview2.pdf |binary src/atkClasses.c | 96 ++++-- src/atkManuals.c | 3 src/classes.c | 31 +- src/conversion.c | 2 src/gdkClasses.c | 68 +++- src/gdkManuals.c | 27 + src/gioClasses.c | 200 ++++++++++--- src/gioManuals.c | 70 ++-- src/glib.c | 6 src/gobject.c | 7 src/gtkClasses.c | 716 ++++++++++++++++++++++++++++++++++++------------- src/gtkManuals.c | 38 +- src/pangoClasses.c | 24 + src/pangoManuals.c | 20 - 18 files changed, 980 insertions(+), 379 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular,
symmetric, and diagonal matrices, both dense and sparse and with
pattern, logical and numeric entries. Numerous methods for and
operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut],
Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Timothy A. Davis [ctb] (SuiteSparse and 'cs' C libraries, notably
CHOLMOD, AMD; collaborators listed in dir(pattern =
'^[A-Z]+[.]txt$', full.names=TRUE, system.file('doc',
'SuiteSparse', package='Matrix'))),
Jens Oehlschlägel [ctb] (initial nearPD()),
Jason Riedy [ctb] (condest() and onenormest() for octave, Copyright:
Regents of the University of California),
R Core Team [ctb] (base R matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-15 dated 2018-11-01 and 1.2-16 dated 2019-03-08
DESCRIPTION | 13 ++++++--- MD5 | 60 ++++++++++++++++++++++----------------------- R/AllClass.R | 2 - R/Auxiliaries.R | 5 +++ R/Ops.R | 52 ++++++++++++++++++++++----------------- R/diagMatrix.R | 15 +++++++++++ R/sparseMatrix.R | 38 ++++++++++++++-------------- TODO | 9 ++++-- build/partial.rdb |binary build/vignette.rds |binary data/CAex.R | 7 +++-- data/KNex.R | 6 +++- data/USCounties.R | 12 ++++++--- inst/NEWS.Rd | 26 +++++++++++++++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/test-tools-1.R | 2 + man/printSpMatrix.Rd | 8 +++--- tests/Simple.R | 12 ++++++++- tests/dg_Matrix.R | 1 tests/dpo-test.R | 2 - tests/dtpMatrix.R | 1 tests/factorizing.R | 2 - tests/group-methods.R | 38 ++++++++++++++++++++++------ tests/indexing.R | 3 +- tests/indexing.Rout.save | 35 +++++++++++++------------- tests/matprod.R | 2 - tests/validObj.R | 3 +- 31 files changed, 230 insertions(+), 124 deletions(-)
Title: Fit GLM with LEP-Based Penalized Maximum Likelihood
Description: Efficient algorithms for fitting regularization paths for
linear or logistic regression models penalized by LEP.
Author: Canhong Wen, Hao Lin, Xueqin Wang
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between glmlep versions 0.1 dated 2013-06-18 and 0.2 dated 2019-03-08
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NAMESPACE | 4 ++-- R/cv.glmlep.R | 8 ++++---- R/glmlep.R | 4 ++-- man/cv.glmlep.Rd | 4 ---- man/glmlep.Rd | 6 ------ src/glmlep_init.c |only 8 files changed, 21 insertions(+), 30 deletions(-)
Title: Apply a Function to a Margin of an Array
Description: High performance variant of apply() for a fixed set of functions.
Considerable speedup is a trade-off for universality, user defined
functions cannot be used with this package. However, 21 most currently employed
functions are available for usage. They can be divided in three types:
reducing functions (like mean(), sum() etc., giving a scalar when applied to a vector),
mapping function (like normalise(), cumsum() etc., giving a vector of the same length
as the input vector) and finally, vector reducing function (like diff() which produces
result vector of a length different from the length of input vector).
Optional or mandatory additional arguments required by some functions
(e.g. norm type for norm() or normalise() functions) can be
passed as named arguments in '...'.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between arrApply versions 2.0.1 dated 2016-11-10 and 2.1 dated 2019-03-08
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NEWS | 7 +++++++ R/RcppExports.R | 7 +++++-- man/arrApply.Rd | 6 ++++-- src/RcppExports.cpp | 12 +++++++++++- src/arrApply.cpp | 15 ++++++++++----- 7 files changed, 50 insertions(+), 23 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-10 1.2-0
2016-08-04 1.0-0
Title: Running Operations for Vectors
Description: Calculates running functions (a.k.a. windowed, rolling, cumulative)
with varying window size and missing handling options. Package brings also
running streak and running which, what extends beyond range of functions
already implemented in R packages.
Author: Dawid Kałędkowski [aut, cre]
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Diff between runner versions 0.1.0 dated 2018-08-31 and 0.2.0 dated 2019-03-08
runner-0.1.0/runner/inst/doc/runner.R |only runner-0.1.0/runner/inst/doc/runner.Rmd |only runner-0.1.0/runner/inst/doc/runner.html |only runner-0.1.0/runner/man/whichmax_run.Rd |only runner-0.1.0/runner/man/whichmin_run.Rd |only runner-0.1.0/runner/src/extremes.h |only runner-0.1.0/runner/src/helps.h |only runner-0.1.0/runner/src/others.h |only runner-0.1.0/runner/src/runner.cpp |only runner-0.1.0/runner/src/streak.h |only runner-0.1.0/runner/src/sums.h |only runner-0.1.0/runner/src/which_extremes.h |only runner-0.1.0/runner/src/whiches.h |only runner-0.1.0/runner/tests/testthat/test_whichmax_run.R |only runner-0.1.0/runner/tests/testthat/test_whichmin_run.R |only runner-0.1.0/runner/vignettes/images/running_which.png |only runner-0.1.0/runner/vignettes/images/running_window.png |only runner-0.1.0/runner/vignettes/runner.Rmd |only runner-0.2.0/runner/DESCRIPTION | 8 runner-0.2.0/runner/MD5 | 99 +++-- runner-0.2.0/runner/NAMESPACE | 4 runner-0.2.0/runner/NEWS.md |only runner-0.2.0/runner/R/RcppExports.R | 179 ++++------ runner-0.2.0/runner/README.md |only runner-0.2.0/runner/build/vignette.rds |binary runner-0.2.0/runner/inst/doc/running_window_functions_in_r.R |only runner-0.2.0/runner/inst/doc/running_window_functions_in_r.Rmd |only runner-0.2.0/runner/inst/doc/running_window_functions_in_r.html |only runner-0.2.0/runner/man/lag_run.Rd |only runner-0.2.0/runner/man/length_run.Rd |only runner-0.2.0/runner/man/max_run.Rd | 28 - runner-0.2.0/runner/man/mean_run.Rd | 4 runner-0.2.0/runner/man/min_run.Rd | 4 runner-0.2.0/runner/man/streak_run.Rd | 4 runner-0.2.0/runner/man/sum_run.Rd | 4 runner-0.2.0/runner/man/unique_run.Rd | 4 runner-0.2.0/runner/man/whicht_run.Rd | 5 runner-0.2.0/runner/man/window_run.Rd | 4 runner-0.2.0/runner/src/RcppExports.cpp | 147 ++++---- runner-0.2.0/runner/src/errors.h |only runner-0.2.0/runner/src/fill_run.cpp |only runner-0.2.0/runner/src/fill_run.h |only runner-0.2.0/runner/src/lag_run.cpp |only runner-0.2.0/runner/src/lag_run.h |only runner-0.2.0/runner/src/length_run.cpp |only runner-0.2.0/runner/src/max_run.cpp |only runner-0.2.0/runner/src/max_run.h |only runner-0.2.0/runner/src/min_run.cpp |only runner-0.2.0/runner/src/min_run.h |only runner-0.2.0/runner/src/streak_run.cpp |only runner-0.2.0/runner/src/streak_run.h |only runner-0.2.0/runner/src/sum_run.cpp |only runner-0.2.0/runner/src/sum_run.h |only runner-0.2.0/runner/src/unique_run.cpp |only runner-0.2.0/runner/src/unique_run.h |only runner-0.2.0/runner/src/which_run.cpp |only runner-0.2.0/runner/src/which_run.h |only runner-0.2.0/runner/src/window_run.cpp |only runner-0.2.0/runner/src/window_run.h |only runner-0.2.0/runner/tests/testthat/length_run.R |only runner-0.2.0/runner/tests/testthat/test_fill_run.R | 17 runner-0.2.0/runner/tests/testthat/test_lag_run.R |only runner-0.2.0/runner/tests/testthat/test_max_run.R | 37 ++ runner-0.2.0/runner/tests/testthat/test_mean_run.R | 41 ++ runner-0.2.0/runner/tests/testthat/test_min_run.R | 44 ++ runner-0.2.0/runner/tests/testthat/test_streak_run.R | 11 runner-0.2.0/runner/tests/testthat/test_sum_run.R | 33 + runner-0.2.0/runner/tests/testthat/test_unique_run.R | 38 +- runner-0.2.0/runner/tests/testthat/test_whicht_run.R | 146 ++++++-- runner-0.2.0/runner/tests/testthat/test_window_run.R | 34 + runner-0.2.0/runner/vignettes/images/hexlogo.png |only runner-0.2.0/runner/vignettes/images/options_idx.png |only runner-0.2.0/runner/vignettes/images/options_na_pad.png |only runner-0.2.0/runner/vignettes/images/options_na_rm.png |only runner-0.2.0/runner/vignettes/images/options_which_first_last.png |only runner-0.2.0/runner/vignettes/images/options_window_size.png |only runner-0.2.0/runner/vignettes/images/options_window_size_varying.png |only runner-0.2.0/runner/vignettes/running_window_functions_in_r.Rmd |only 78 files changed, 610 insertions(+), 285 deletions(-)
Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: Includes tools to calculate statistical power, minimum detectable effect size (MDES), MDES difference (MDESD), and minimum required sample size for various multilevel randomized experiments with continuous outcomes. Some of the functions can assist with planning two- and three-level cluster-randomized trials (CRTs) sensitive to moderation effects, and with planning two-level CRTs sensitive to 2-2-1 and 2-1-1 mediation effects. See 'PowerUp!' Excel series at <https://www.causalevaluation.org/>.
Author: Metin Bulus [aut, cre],
Nianbo Dong [aut],
Benjamin Kelcey [aut],
Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between PowerUpR versions 1.0.2 dated 2018-12-15 and 1.0.3 dated 2019-03-08
DESCRIPTION | 10 MD5 | 22 - NEWS.md | 4 R/cra2r2.R | 10 R/error.R | 6 R/plot.R | 355 +++++++++++++++------ R/t1t2.R | 48 ++ R/utils.R | 14 README.md | 2 inst/CITATION | 8 inst/doc/three_level_cluster_randomized_trial.html | 4 man/plot.Rd | 10 12 files changed, 350 insertions(+), 143 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-22 dated 2017-12-02 and 0.1-23 dated 2019-03-08
ChangeLog | 3 + DESCRIPTION | 8 ++-- MD5 | 22 +++++------ R/f_plotstruct.r | 2 - man/00_phyclust-package.Rd | 2 - src/R_phyclust.c | 75 ++++++++++++++++++++------------------- src/R_phyclust.h | 2 - src/R_phyclust_em_step.c | 18 +++++---- src/R_phyclust_se.c | 85 ++++++++++++++++++++++----------------------- src/R_phyclust_se.h | 2 - src/R_phyclust_se_update.c | 7 ++- src/R_phyclust_update.c | 9 ++-- 12 files changed, 122 insertions(+), 113 deletions(-)
Title: Lightweight Portable Message Queue Using 'SQLite'
Description: Temporary and permanent message queues for R. Built on top of
'SQLite' databases. 'SQLite' provides locking, and makes it possible
to detect crashed consumers. Crashed jobs can be automatically marked
as "failed", or put in the queue again, potentially a limited number of times.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between liteq versions 1.0.1 dated 2017-10-20 and 1.1.0 dated 2019-03-08
DESCRIPTION | 10 +++---- MD5 | 49 ++++++++++++++++++++------------------ NAMESPACE | 2 + NEWS.md | 15 +++++++++++ R/db.R | 43 ++++++++++++++++++++++++--------- R/messages.R | 34 ++++++++++++++++++++++++-- R/package.R | 25 ++++++++++++++++--- README.md | 2 - inst/README.Rmd | 2 - inst/README.md | 2 - man/ack.Rd | 5 +++ man/consume.Rd | 10 ++++++- man/create_queue.Rd | 1 man/delete_queue.Rd | 1 man/ensure_queue.Rd | 1 man/is_empty.Rd |only man/list_failed_messages.Rd | 4 ++- man/list_messages.Rd | 5 ++- man/list_queues.Rd | 1 man/liteq.Rd | 25 +++++++++++++++++-- man/message_count.Rd |only man/publish.Rd | 5 ++- man/remove_failed_messages.Rd | 6 +++- man/requeue_failed_messages.Rd | 6 +++- man/try_consume.Rd | 6 +++- tests/testthat/test-concurrency.R |only tests/testthat/test-messages.R | 6 +++- 27 files changed, 199 insertions(+), 67 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble
clustering framework, Chiu & Talhouk (2018)
<doi:10.1186/s12859-017-1996-y>. Results from a diverse set of
algorithms are pooled together using methods such as majority voting,
K-Modes, LinkCluE, and CSPA. There are options to compare cluster
assignments across algorithms using internal and external indices,
visualizations such as heatmaps, and significance testing for the
existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 0.5.1 dated 2018-06-11 and 0.5.2 dated 2019-03-08
DESCRIPTION | 52 LICENSE | 4 MD5 | 136 +- NAMESPACE | 74 - NEWS.md | 146 +- R/PAC.R | 91 - R/RcppExports.R | 22 R/algorithms.R | 336 +++--- R/consensus_cluster.R | 650 ++++++------ R/consensus_combine.R | 111 +- R/consensus_evaluate.R | 706 ++++++------- R/consensus_funs.R | 286 ++--- R/consensus_matrix.R | 101 - R/data.R | 20 R/dice.R | 270 ++--- R/diceR-package.R | 16 R/external_validity.R | 177 +-- R/graphs.R | 451 ++++---- R/impute.R | 166 +-- R/pcn.R | 147 +- R/prepare_data.R | 109 +- R/sigclust.R | 235 ++-- R/similarity.R | 377 +++---- R/utils.R | 268 ++--- R/zzz.R | 8 README.md | 152 +- build/vignette.rds |binary inst/doc/overview.R | 201 +-- inst/doc/overview.Rmd | 535 +++++----- inst/doc/overview.html | 1679 ++++++++++++++++---------------- man/CSPA.Rd | 69 - man/LCE.Rd | 95 - man/PAC.Rd | 103 - man/compactness.Rd | 80 - man/consensus_cluster.Rd | 308 ++--- man/consensus_combine.Rd | 93 - man/consensus_evaluate.Rd | 175 +-- man/consensus_matrix.Rd | 107 +- man/dice.Rd | 240 ++-- man/diceR-package.Rd | 80 - man/external_validity.Rd | 119 +- man/graphs.Rd | 165 +-- man/hgsc.Rd | 36 man/impute_knn.Rd | 81 - man/impute_missing.Rd | 103 - man/k_modes.Rd | 91 - man/majority_voting.Rd | 85 - man/min_fnorm.Rd | 79 - man/pcn.Rd | 107 +- man/prepare_data.Rd | 97 - man/relabel_class.Rd | 59 - man/sigclust.Rd | 117 +- man/similarity.Rd | 91 - tests/testthat.R | 8 tests/testthat/test-PAC.R | 27 tests/testthat/test-consensus_cluster.R | 108 +- tests/testthat/test-consensus_combine.R | 111 +- tests/testthat/test-consensus_funs.R | 102 - tests/testthat/test-consensus_matrix.R | 66 - tests/testthat/test-dice.R | 112 +- tests/testthat/test-external_validity.R | 31 tests/testthat/test-graphs.R | 105 +- tests/testthat/test-impute.R | 52 tests/testthat/test-pcn.R | 27 tests/testthat/test-prepare_data.R | 32 tests/testthat/test-sigclust.R | 56 - tests/testthat/test-similarity.R | 95 - tests/testthat/test-utils.R | 69 - vignettes/overview.Rmd | 535 +++++----- 69 files changed, 5870 insertions(+), 5772 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca> and portions of code contributed by Dan Linden.
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.2-0 dated 2019-02-26 and 2.2-1 dated 2019-03-08
DESCRIPTION | 12 - MD5 | 56 +++--- NAMESPACE | 17 + R/Custom.functions.R | 189 ++++++++++++++++++--- R/DIC.R | 11 + R/aictab.R | 90 +++++----- R/bictab.R | 90 +++++----- R/dictab.R | 39 ++++ R/evidence.R | 6 R/summaryOD.R | 80 ++++----- R/xtable.R | 401 +++++++++++++++++++++++++++++++++++++--------- inst/NEWS | 15 + man/AICc.Rd | 4 man/AICcCustom.Rd | 3 man/AICcmodavg-package.Rd | 180 +++++++++++++++++--- man/DIC.Rd | 15 + man/aictab.Rd | 2 man/aictabCustom.Rd | 10 - man/bictab.Rd | 2 man/bictabCustom.Rd | 10 - man/dictab.Rd | 20 +- man/evidence.Rd | 10 - man/ictab.Rd |only man/importance.Rd | 2 man/modavgCustom.Rd | 7 man/modavgEffect.Rd | 20 +- man/modavgIC.Rd |only man/modavgShrink.Rd | 14 - man/summaryOD.Rd | 38 ++-- man/xtable.Rd | 54 ++++-- 30 files changed, 1018 insertions(+), 379 deletions(-)
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
<http://pj.freefaculty.org/guides>. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette 'rockchalk' offers a
fairly comprehensive overview. The vignette 'Rstyle' has advice
about coding in R. The package title 'rockchalk' refers to our
school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre],
Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.140 dated 2019-02-19 and 1.8.144 dated 2019-03-08
DESCRIPTION | 8 MD5 | 28 +- R/outreg.R | 35 +-- inst/doc/Rchaeology.pdf |binary inst/doc/Rstyle.R | 8 inst/doc/Rstyle.Rnw | 41 +--- inst/doc/Rstyle.pdf |binary inst/doc/outreg.R | 83 +++----- inst/doc/outreg.Rnw | 100 ++------- inst/doc/outreg.pdf |binary inst/doc/rockchalk.pdf |binary vignettes/Rstyle.Rnw | 41 +--- vignettes/Rstyle.lyx | 132 +++++++------ vignettes/outreg.Rnw | 100 ++------- vignettes/outreg.lyx | 481 +++++++----------------------------------------- 15 files changed, 302 insertions(+), 755 deletions(-)
Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including
constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer
functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: ORPHANED
Diff between rioja versions 0.9-15.1 dated 2018-01-04 and 0.9-15.2 dated 2019-03-08
DESCRIPTION | 7 ++++--- MD5 | 20 ++++++++++---------- data/IK.rda |binary data/Ponds.rda |binary data/RLGH.rda |binary data/SWAP.rda |binary data/aber.rda |binary src/chclust.cpp | 25 +++++++++++++------------ src/cornellin.cpp | 16 +++++++--------- src/cornellout.cpp | 16 +++++++++------- src/tilia.cpp | 8 ++++---- 11 files changed, 47 insertions(+), 45 deletions(-)
Title: A Tool for Automating Download and Preprocessing of MODIS Land
Products Data
Description: Allows automating the creation of time series of rasters derived
from MODIS Satellite Land Products data. It performs several typical
preprocessing steps such as download, mosaicking, reprojection and resize
of data acquired on a specified time period. All processing parameters
can be set using a user-friendly GUI. Users can select which layers of
the original MODIS HDF files they want to process, which additional
Quality Indicators should be extracted from aggregated MODIS Quality
Assurance layers and, in the case of Surface Reflectance products
, which Spectral Indexes should be computed from the original reflectance
bands. For each output layer, outputs are saved as single-band raster
files corresponding to each available acquisition date. Virtual files
allowing access to the entire time series as a single file are also created.
Command-line execution exploiting a previously saved processing options
file is also possible, allowing to automatically update time series
related to a MODIS product whenever a new image is available.
Author: Lorenzo Busetto [aut, cre] (<https://orcid.org/0000-0001-9634-6038>),
Luigi Ranghetti [aut] (<https://orcid.org/0000-0001-6207-5188>),
Leah Wasser [rev] (Leah Wasser reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/184),
Jeff Hanson [rev] (Jeff Hanson reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/184)
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Diff between MODIStsp versions 1.3.7 dated 2018-12-03 and 1.3.8 dated 2019-03-08
DESCRIPTION | 8 MD5 | 72 +- NEWS.md | 27 R/MODIStsp.R | 18 R/MODIStsp_process.R | 1 R/MODIStsp_process_bands.R | 23 R/get_mod_dirs.R | 6 R/get_mod_filenames.R | 3 README.md | 29 build/vignette.rds |binary inst/ExtData/MODIStsp_ProdOpts.xml | 880 +++++++++++++++++++------- inst/ExtData/Previous/MODIStsp_ProdOpts.RData |binary inst/WORDLIST | 59 + inst/doc/MODIStsp.Rmd | 10 inst/doc/MODIStsp.pdf |binary inst/testdata/test01.json | 4 inst/testdata/test01a.json | 2 inst/testdata/test02.json | 2 inst/testdata/test03.json | 2 inst/testdata/test03a.json | 2 inst/testdata/test04.json | 2 inst/testdata/test04a.json | 2 inst/testdata/test04b.json | 2 inst/testdata/test04c.json | 2 inst/testdata/test05.json | 2 inst/testdata/test05a.json | 2 inst/testdata/test06.json | 2 inst/testdata/test07.json | 2 inst/testdata/test07b.json | 2 inst/testdata/test_MOD10A2.json | 2 inst/testdata/test_MOD13A2.json | 2 inst/testdata/test_addindex.json | 2 inst/testdata/test_extract.json | 2 inst/testdata/test_mask.json |only tests/spelling.Rout.save |only tests/testthat/test_MODIStsp_01.R | 4 tests/testthat/test_MODIStsp_readxml.R | 4 vignettes/MODIStsp.Rmd | 10 38 files changed, 854 insertions(+), 338 deletions(-)
Title: Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick
Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between magicaxis versions 2.0.4 dated 2018-11-29 and 2.0.7 dated 2019-03-08
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 2 +- NEWS | 12 ++++++++++++ R/magaxis.R | 22 ++++++++++++---------- R/magcurve.R |only R/magimage.R | 12 ++++++++++++ R/magplot.R | 8 ++++---- man/magaxis.Rd | 8 +++++++- man/magcurve.Rd |only man/magicaxis-package.Rd | 4 ++-- man/magplot.Rd | 12 +++++++++++- 12 files changed, 76 insertions(+), 32 deletions(-)
Title: Visualizations of High-Dimensional Data
Description: The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) which is a PDE-optimized violin plot for either classified or non-classified multivariate data. The MD-plot is an alternative to the box-and-whisker diagram (box plot) and bean plot. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>),
Felix Pape [aut, rev],
Onno Hansen-Goos [ctr, ctb],
Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DataVisualizations versions 1.1.5 dated 2019-02-02 and 1.1.6 dated 2019-03-08
DESCRIPTION | 16 ++--- MD5 | 46 +++++++++------- NAMESPACE | 3 + R/ClassBoxPlot.R | 6 +- R/ClassMDplot.R | 107 +++++++++++++++++++++++++++++++-------- R/ClassPDEplot.R | 30 ++++++---- R/ClassPDEplotMaxLikeli.R | 8 ++ R/Classplot.R |only R/DualaxisClassplot.R |only R/Heatmap.R | 32 ++++++++--- R/MDplot.R | 98 ++++++++++++++++++++++++++++------- R/MDplot4multiplevectors.R |only R/Plot3D.R | 19 ++++-- R/Silhouetteplot.R | 82 ++++++++++++++++++++++++----- build/partial.rdb |binary inst/NEWS | 11 ++++ inst/doc/DataVisualizations.html | 17 ++---- man/ClassBoxPlot.Rd | 19 ++++++ man/ClassMDplot.Rd | 40 ++++++++++++-- man/ClassPDEplot.Rd | 25 ++++++++- man/ClassPDEplotMaxLikeli.Rd | 18 ++++++ man/Classplot.Rd |only man/Crosstable.Rd | 7 ++ man/DualaxisClassplot.Rd |only man/MDplot.Rd | 34 +++++++++--- man/MDplot4multiplevectors.Rd |only man/Silhouetteplot.Rd | 10 ++- 27 files changed, 482 insertions(+), 146 deletions(-)
More information about DataVisualizations at CRAN
Permanent link
Title: Checking and Simplifying Validation Rule Sets
Description: Rule sets with validation rules may contain redundancies or contradictions.
Functions for finding redundancies and problematic rules are provided,
given a set a rules formulated with 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut],
Jacco Daalmans [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between validatetools versions 0.4.3 dated 2018-03-27 and 0.4.6 dated 2019-03-08
DESCRIPTION | 13 +++--- MD5 | 62 ++++++++++++++--------------- NEWS | 11 +++++ R/categorical.R | 8 +-- R/detect_boundary.R | 15 ++++++- R/detect_fixed_variables.R | 2 R/feasible.R | 5 ++ R/linear.R | 11 ++++- R/simplify_conditional.R | 11 ----- R/substitute_values.R | 2 man/detect_boundary_cat.Rd | 5 +- man/detect_boundary_num.Rd | 1 man/detect_fixed_variables.Rd | 1 man/detect_infeasible_rules.Rd | 1 man/detect_redundancy.Rd | 1 man/is_contradicted_by.Rd | 1 man/is_implied_by.Rd | 1 man/is_infeasible.Rd | 1 man/make_feasible.Rd | 1 man/remove_redundancy.Rd | 1 man/simplify_fixed_variables.Rd | 1 man/simplify_rules.Rd | 1 man/substitute_values.Rd | 3 - tests/testthat/test-contradicted.R | 2 tests/testthat/test-detect_boundary.R | 15 +++++++ tests/testthat/test-detect_fixed_values.R | 9 ++++ tests/testthat/test-feasible.R | 18 ++++++++ tests/testthat/test-linear.R | 4 + tests/testthat/test-miprule.R | 4 + tests/testthat/test-redundancy.R | 7 +++ tests/testthat/test-simplify_conditional.R | 52 ++++++++++++++++++++++++ tests/testthat/test-substitute_values.R | 8 +++ 32 files changed, 219 insertions(+), 59 deletions(-)
Title: Building, Visualizing, Exporting and Replaying Petri Nets
Description: Functions for the construction of Petri Nets. Petri Nets can be replayed by firing enabled transitions.
Silent transitions will be hidden by the execution handler. Also includes functionalities for the visualization of Petri Nets and
export of Petri Nets to PNML (Petri Net Markup Language) files.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between petrinetR versions 0.2.0 dated 2018-07-03 and 0.2.1 dated 2019-03-08
petrinetR-0.2.0/petrinetR/R/parse.R |only petrinetR-0.2.0/petrinetR/R/parsel.R |only petrinetR-0.2.0/petrinetR/man/parse.Rd |only petrinetR-0.2.0/petrinetR/man/parsel.Rd |only petrinetR-0.2.1/petrinetR/DESCRIPTION | 10 +++++----- petrinetR-0.2.1/petrinetR/MD5 | 12 ++++++------ petrinetR-0.2.1/petrinetR/NAMESPACE | 4 ++-- petrinetR-0.2.1/petrinetR/R/parse_trace.R |only petrinetR-0.2.1/petrinetR/R/parsel_trace.R |only petrinetR-0.2.1/petrinetR/man/parse_trace.Rd |only petrinetR-0.2.1/petrinetR/man/parsel_trace.Rd |only 11 files changed, 13 insertions(+), 13 deletions(-)
Title: Generalized Linear Mixed Models with Robust Random Fields for
Spatiotemporal Modeling
Description: Implements Bayesian spatial and spatiotemporal models that
optionally allow for extreme spatial deviations through time. 'glmmfields'
uses a predictive process approach with random fields implemented through
a multivariate-t distribution instead of the usual multivariate normal.
Sampling is conducted with 'Stan'. References: Anderson and Ward (2019)
<doi:10.1002/ecy.2403>.
Author: Sean C. Anderson [aut, cre],
Eric J. Ward [aut],
Trustees of Columbia University [cph]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between glmmfields versions 0.1.1 dated 2018-11-09 and 0.1.2 dated 2019-03-08
glmmfields-0.1.1/glmmfields/exec |only glmmfields-0.1.1/glmmfields/inst/chunks |only glmmfields-0.1.1/glmmfields/src/RcppExports.cpp |only glmmfields-0.1.1/glmmfields/src/include |only glmmfields-0.1.1/glmmfields/tools/make_cpp.R |only glmmfields-0.1.2/glmmfields/DESCRIPTION | 20 glmmfields-0.1.2/glmmfields/MD5 | 36 - glmmfields-0.1.2/glmmfields/NAMESPACE | 1 glmmfields-0.1.2/glmmfields/NEWS.md | 4 glmmfields-0.1.2/glmmfields/R/glmmfields-package.R |only glmmfields-0.1.2/glmmfields/R/predict.R | 4 glmmfields-0.1.2/glmmfields/R/stanmodels.R | 47 - glmmfields-0.1.2/glmmfields/R/zzz.R | 1 glmmfields-0.1.2/glmmfields/build/vignette.rds |binary glmmfields-0.1.2/glmmfields/inst/doc/spatial-glms.html | 438 ++++++++++++----- glmmfields-0.1.2/glmmfields/inst/include |only glmmfields-0.1.2/glmmfields/inst/test.R |only glmmfields-0.1.2/glmmfields/man/glmmfields-package.Rd |only glmmfields-0.1.2/glmmfields/src/Makevars | 21 glmmfields-0.1.2/glmmfields/src/Makevars.win |only glmmfields-0.1.2/glmmfields/src/Modules.cpp | 29 - glmmfields-0.1.2/glmmfields/src/init.cpp |only glmmfields-0.1.2/glmmfields/src/stan_files |only glmmfields-0.1.2/glmmfields/tools/make_cc.R |only 24 files changed, 409 insertions(+), 192 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.2.2 dated 2019-02-06 and 1.2.3 dated 2019-03-08
DESCRIPTION | 8 - MD5 | 20 +-- R/carcass_persistence_figure_functions.R | 48 ++++--- R/detection_probability_functions.R | 36 +++++ R/utility_functions.R | 4 inst/doc/GenEstGUI.html | 4 inst/doc/command-line-example.Rmd | 2 inst/doc/command-line-example.html | 122 +++++++++--------- inst/doc/solar-examples.html | 28 ++-- inst/doc/wind-examples.html | 202 +++++++++++++++---------------- vignettes/command-line-example.Rmd | 2 11 files changed, 260 insertions(+), 216 deletions(-)
Title: Extremely Fast Implementation of a Naive Bayes Classifier
Description: This is an extremely fast implementation of a Naive Bayes classifier.
This package is currently the only package that supports a Bernoulli distribution,
a Multinomial distribution, and a Gaussian distribution, making it suitable for
both binary features, frequency counts, and numerical features. Another unique
feature is the support of a mix of different event models. Only numerical variables are allowed,
however, categorical variables can be transformed into dummies and used with
the Bernoulli distribution. This implementation offers a huge performance
gain compared to the 'e1071' implementation in R. The execution times were compared
on a data set of tweets and was found to be around 330 times faster. See the vignette
for more details. This performance gain is only realized using a Bernoulli
event model. Furthermore, the Multinomial event model implementation is even slightly faster,
but incomparable since it was not implemented in 'e1071'
The implementation is largely based on the paper
"A comparison of event models for Naive Bayes anti-spam e-mail filtering" written by
K.M. Schneider (2003) <doi:10.3115/1067807>.
Any issues can be submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
Author: Martin Skogholt
Maintainer: Martin Skogholt <m.skogholt@gmail.com>
Diff between fastNaiveBayes versions 1.0.0 dated 2019-02-28 and 1.0.1 dated 2019-03-08
DESCRIPTION | 29 +++++++++++++---------- MD5 | 24 ++++++++++++------- NEWS.md | 14 ++++++++++- R/fastNaiveBayes.mixed.default.R | 6 ++-- R/predict.fastNaiveBayes.bernoulli.R | 2 - R/predict.fastNaiveBayes.gaussian.R | 2 - README.md | 19 ++++++++++++--- inst/doc/fastnaivebayes.Rmd | 43 +++++++++++++++++++++-------------- inst/doc/fastnaivebayes.html | 43 +++++++++++++++++++++-------------- tests |only vignettes/fastnaivebayes.Rmd | 43 +++++++++++++++++++++-------------- 11 files changed, 141 insertions(+), 84 deletions(-)
More information about fastNaiveBayes at CRAN
Permanent link
Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al. 2019). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <a.rauschenberger@vumc.nl>
Diff between palasso versions 0.0.3 dated 2019-02-19 and 0.0.4 dated 2019-03-08
DESCRIPTION | 10 ++-- MD5 | 25 +++++----- NEWS.md | 6 ++ R/elastic_net.R |only R/function.R | 114 +++++++++++++++++++++++++++++++++++-------------- R/hidden.R | 33 +++++++++++--- R/methods.R | 6 +- README.md | 9 +++ inst/doc/vignette.R | 2 inst/doc/vignette.Rmd | 6 +- inst/doc/vignette.html | 3 - man/other.Rd | 2 tests/testthat/test.R | 50 ++++++++++++--------- vignettes/vignette.Rmd | 6 +- 14 files changed, 182 insertions(+), 90 deletions(-)
Title: Joint Analysis and Imputation of Incomplete Data
Description: Provides joint analysis and imputation of (generalized)
linear and cumulative logit regression models, (generalized) linear and
cumulative logit mixed models and parametric (Weibull) as well as Cox
proportional hazards survival models with incomplete (covariate) data in
the Bayesian framework.
The package performs some preprocessing of the data and creates a 'JAGS'
model, which will then automatically be passed to 'JAGS'
<http://mcmc-jags.sourceforge.net> with the help of
the package 'rjags'.
It also provides summary and plotting functions for the output and allows
to export imputed values.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>
Diff between JointAI versions 0.4.0 dated 2018-12-04 and 0.5.0 dated 2019-03-08
JointAI-0.4.0/JointAI/R/helpfunctions_impmodels.R |only JointAI-0.4.0/JointAI/R/helpfunctions_post.R |only JointAI-0.4.0/JointAI/R/write_model.R |only JointAI-0.4.0/JointAI/inst/Ideas.html |only JointAI-0.4.0/JointAI/inst/Ideas.md |only JointAI-0.4.0/JointAI/man/get_imp_meth.Rd |only JointAI-0.4.0/JointAI/man/list_impmodels.Rd |only JointAI-0.5.0/JointAI/DESCRIPTION | 23 JointAI-0.5.0/JointAI/MD5 | 193 +- JointAI-0.5.0/JointAI/NAMESPACE | 11 JointAI-0.5.0/JointAI/NEWS.md | 61 JointAI-0.5.0/JointAI/R/JointAI.R | 101 + JointAI-0.5.0/JointAI/R/JointAIObject.R | 47 JointAI-0.5.0/JointAI/R/add_samples.R | 96 - JointAI-0.5.0/JointAI/R/analysismodel_clm.R |only JointAI-0.5.0/JointAI/R/analysismodel_clmm.R |only JointAI-0.5.0/JointAI/R/analysismodel_glm.R | 96 - JointAI-0.5.0/JointAI/R/analysismodel_glme.R | 168 +- JointAI-0.5.0/JointAI/R/analysismodel_lm.R | 83 - JointAI-0.5.0/JointAI/R/analysismodel_lme.R | 185 -- JointAI-0.5.0/JointAI/R/analysismodel_surv.R | 123 + JointAI-0.5.0/JointAI/R/build_model.R | 102 - JointAI-0.5.0/JointAI/R/convergence_criteria.R | 98 - JointAI-0.5.0/JointAI/R/datasets.R | 22 JointAI-0.5.0/JointAI/R/divide_matrices.R | 307 ++-- JointAI-0.5.0/JointAI/R/get_MIdat.R | 143 + JointAI-0.5.0/JointAI/R/get_coef_names.R | 27 JointAI-0.5.0/JointAI/R/get_data_list.R | 493 +++--- JointAI-0.5.0/JointAI/R/get_imp_method.R | 136 + JointAI-0.5.0/JointAI/R/get_inits.R | 72 JointAI-0.5.0/JointAI/R/get_model_dimensions.R | 201 +- JointAI-0.5.0/JointAI/R/get_params.R | 145 + JointAI-0.5.0/JointAI/R/get_refs.R | 11 JointAI-0.5.0/JointAI/R/get_subset.R |only JointAI-0.5.0/JointAI/R/helpfunctions.R | 462 +----- JointAI-0.5.0/JointAI/R/helpfunctions_JAGS.R |only JointAI-0.5.0/JointAI/R/helpfunctions_JAGSmodel.R |only JointAI-0.5.0/JointAI/R/helpfunctions_formulas.R |only JointAI-0.5.0/JointAI/R/helpfunctions_prep_impmodels.R |only JointAI-0.5.0/JointAI/R/helpfunctions_summary.R |only JointAI-0.5.0/JointAI/R/impmodel_glme.R |only JointAI-0.5.0/JointAI/R/impmodels_binary.R | 46 JointAI-0.5.0/JointAI/R/impmodels_continuous.R | 314 ---- JointAI-0.5.0/JointAI/R/impmodels_multinomial.R | 43 JointAI-0.5.0/JointAI/R/impmodels_ordinal.R | 151 +- JointAI-0.5.0/JointAI/R/md_pattern.R | 69 JointAI-0.5.0/JointAI/R/model_imp.R | 643 +++++--- JointAI-0.5.0/JointAI/R/plot_imp_distr.R |only JointAI-0.5.0/JointAI/R/plots.R | 95 + JointAI-0.5.0/JointAI/R/plots_ppc.R |only JointAI-0.5.0/JointAI/R/predict.R | 32 JointAI-0.5.0/JointAI/R/print_functions.R | 362 ++-- JointAI-0.5.0/JointAI/R/rescale.R | 40 JointAI-0.5.0/JointAI/R/scaling.R | 47 JointAI-0.5.0/JointAI/R/simulate_data.R | 146 + JointAI-0.5.0/JointAI/R/summary.JointAI.R | 182 -- JointAI-0.5.0/JointAI/README.md | 86 - JointAI-0.5.0/JointAI/build/vignette.rds |binary JointAI-0.5.0/JointAI/data/longDF.RData |binary JointAI-0.5.0/JointAI/inst/doc/AfterFitting.R | 63 JointAI-0.5.0/JointAI/inst/doc/AfterFitting.Rmd | 87 - JointAI-0.5.0/JointAI/inst/doc/AfterFitting.html | 331 ++-- JointAI-0.5.0/JointAI/inst/doc/MCMCsettings.R | 26 JointAI-0.5.0/JointAI/inst/doc/MCMCsettings.Rmd | 88 - JointAI-0.5.0/JointAI/inst/doc/MCMCsettings.html | 259 ++- JointAI-0.5.0/JointAI/inst/doc/MinimalExample.Rmd | 28 JointAI-0.5.0/JointAI/inst/doc/MinimalExample.html | 78 - JointAI-0.5.0/JointAI/inst/doc/ModelSpecification.R | 158 +- JointAI-0.5.0/JointAI/inst/doc/ModelSpecification.Rmd | 430 +++-- JointAI-0.5.0/JointAI/inst/doc/ModelSpecification.html | 748 +++++----- JointAI-0.5.0/JointAI/inst/doc/SelectingParameters.R | 91 - JointAI-0.5.0/JointAI/inst/doc/SelectingParameters.Rmd | 107 - JointAI-0.5.0/JointAI/inst/doc/SelectingParameters.html | 330 ++-- JointAI-0.5.0/JointAI/inst/doc/VisualizingIncompleteData.R | 3 JointAI-0.5.0/JointAI/inst/doc/VisualizingIncompleteData.Rmd | 26 JointAI-0.5.0/JointAI/inst/doc/VisualizingIncompleteData.html | 47 JointAI-0.5.0/JointAI/man/GR_crit.Rd | 6 JointAI-0.5.0/JointAI/man/JointAI.Rd | 60 JointAI-0.5.0/JointAI/man/JointAIObject.Rd | 47 JointAI-0.5.0/JointAI/man/MC_error.Rd | 12 JointAI-0.5.0/JointAI/man/add_samples.Rd | 30 JointAI-0.5.0/JointAI/man/default_hyperpars.Rd | 89 - JointAI-0.5.0/JointAI/man/densplot.Rd | 10 JointAI-0.5.0/JointAI/man/figures/README-unnamed-chunk-4-1.png |binary JointAI-0.5.0/JointAI/man/figures/README-unnamed-chunk-5-1.png |binary JointAI-0.5.0/JointAI/man/get_MIdat.Rd | 12 JointAI-0.5.0/JointAI/man/get_models.Rd |only JointAI-0.5.0/JointAI/man/list_models.Rd |only JointAI-0.5.0/JointAI/man/longDF.Rd | 14 JointAI-0.5.0/JointAI/man/model_imp.Rd | 277 ++- JointAI-0.5.0/JointAI/man/parameters.Rd | 4 JointAI-0.5.0/JointAI/man/plot_all.Rd | 4 JointAI-0.5.0/JointAI/man/plot_imp_distr.Rd |only JointAI-0.5.0/JointAI/man/predDF.Rd | 14 JointAI-0.5.0/JointAI/man/predict.JointAI.Rd | 13 JointAI-0.5.0/JointAI/man/set_refcat.Rd | 4 JointAI-0.5.0/JointAI/man/sharedParams.Rd | 21 JointAI-0.5.0/JointAI/man/sim_data.Rd | 31 JointAI-0.5.0/JointAI/man/summary.JointAI.Rd | 38 JointAI-0.5.0/JointAI/man/traceplot.Rd | 10 JointAI-0.5.0/JointAI/tests |only JointAI-0.5.0/JointAI/vignettes/AfterFitting.Rmd | 87 - JointAI-0.5.0/JointAI/vignettes/MCMCsettings.Rmd | 88 - JointAI-0.5.0/JointAI/vignettes/MinimalExample.Rmd | 28 JointAI-0.5.0/JointAI/vignettes/ModelSpecification.Rmd | 430 +++-- JointAI-0.5.0/JointAI/vignettes/SelectingParameters.Rmd | 107 - JointAI-0.5.0/JointAI/vignettes/VisualizingIncompleteData.Rmd | 26 107 files changed, 5607 insertions(+), 4417 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Henric Winell [aut] (<https://orcid.org/0000-0001-7995-3047>),
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Mark A. van de Wiel [aut] (<https://orcid.org/0000-0003-4780-8472>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.2-2 dated 2017-11-28 and 1.3-0 dated 2019-03-08
coin-1.2-2/coin/inst/doc/coin_implementation.R |only coin-1.2-2/coin/inst/doc/coin_implementation.Rnw |only coin-1.2-2/coin/inst/doc/coin_implementation.pdf |only coin-1.2-2/coin/man/ExpectCovar-class.Rd |only coin-1.2-2/coin/man/ExpectCovarInfluence-class.Rd |only coin-1.2-2/coin/src/Classes.c |only coin-1.2-2/coin/src/Classes.h |only coin-1.2-2/coin/src/Helpers.h |only coin-1.2-2/coin/src/LinearStatistic.c |only coin-1.2-2/coin/src/LinearStatistic.h |only coin-1.2-2/coin/vignettes/coin_implementation.Rnw |only coin-1.2-2/coin/vignettes/coin_implementation.Rout.save |only coin-1.3-0/coin/DESCRIPTION | 40 coin-1.3-0/coin/MD5 | 226 ++--- coin-1.3-0/coin/NAMESPACE | 25 coin-1.3-0/coin/R/AAA.R | 7 coin-1.3-0/coin/R/Classes.R | 113 +- coin-1.3-0/coin/R/Confints.R | 562 ++++--------- coin-1.3-0/coin/R/ContingencyTests.R | 25 coin-1.3-0/coin/R/ExactDistributions.R | 270 +++--- coin-1.3-0/coin/R/IndependenceTest.R | 8 coin-1.3-0/coin/R/InitMethods.R | 156 +-- coin-1.3-0/coin/R/LocationTests.R | 48 - coin-1.3-0/coin/R/MTP.R | 535 ++++++------ coin-1.3-0/coin/R/MarginalHomogeneityTests.R | 6 coin-1.3-0/coin/R/Methods.R | 678 ++++++++-------- coin-1.3-0/coin/R/MonteCarloDistributions.R | 76 - coin-1.3-0/coin/R/Print.R | 217 +++-- coin-1.3-0/coin/R/ScaleTests.R | 72 - coin-1.3-0/coin/R/SurvivalTests.R | 10 coin-1.3-0/coin/R/SymmetryTest.R | 14 coin-1.3-0/coin/R/SymmetryTests.R | 4 coin-1.3-0/coin/R/Transformations.R | 58 + coin-1.3-0/coin/R/helpers.R | 186 +--- coin-1.3-0/coin/R/zAccess.R | 168 ++- coin-1.3-0/coin/build/partial.rdb |only coin-1.3-0/coin/build/vignette.rds |binary coin-1.3-0/coin/inst/CITATION | 80 - coin-1.3-0/coin/inst/NEWS.Rd | 136 ++- coin-1.3-0/coin/inst/doc/Implementation.R |only coin-1.3-0/coin/inst/doc/Implementation.Rnw |only coin-1.3-0/coin/inst/doc/Implementation.pdf |only coin-1.3-0/coin/inst/doc/LegoCondInf.pdf |binary coin-1.3-0/coin/inst/doc/MAXtest.R | 4 coin-1.3-0/coin/inst/doc/MAXtest.Rnw | 4 coin-1.3-0/coin/inst/doc/MAXtest.pdf |binary coin-1.3-0/coin/inst/doc/coin.R | 4 coin-1.3-0/coin/inst/doc/coin.Rnw | 4 coin-1.3-0/coin/inst/doc/coin.pdf |binary coin-1.3-0/coin/man/CWD.Rd | 12 coin-1.3-0/coin/man/ContingencyTests.Rd | 56 - coin-1.3-0/coin/man/CorrelationTests.Rd | 2 coin-1.3-0/coin/man/GTSG.Rd | 8 coin-1.3-0/coin/man/IndependenceTest-class.Rd | 17 coin-1.3-0/coin/man/IndependenceTest.Rd | 11 coin-1.3-0/coin/man/IndependenceTestStatistic-class.Rd | 3 coin-1.3-0/coin/man/LocationTests.Rd | 11 coin-1.3-0/coin/man/MarginalHomogeneityTests.Rd | 21 coin-1.3-0/coin/man/MaximallySelectedStatisticsTests.Rd | 18 coin-1.3-0/coin/man/NullDistribution-class.Rd | 54 - coin-1.3-0/coin/man/NullDistribution-methods.Rd | 21 coin-1.3-0/coin/man/NullDistribution.Rd | 71 - coin-1.3-0/coin/man/PValue-class.Rd | 32 coin-1.3-0/coin/man/PermutationDistribution-methods.Rd | 22 coin-1.3-0/coin/man/ScaleTests.Rd | 9 coin-1.3-0/coin/man/SurvivalTests.Rd | 32 coin-1.3-0/coin/man/SymmetryProblem-class.Rd | 2 coin-1.3-0/coin/man/SymmetryTest.Rd | 10 coin-1.3-0/coin/man/SymmetryTests.Rd | 24 coin-1.3-0/coin/man/Transformations.Rd | 17 coin-1.3-0/coin/man/VarCovar-class.Rd | 2 coin-1.3-0/coin/man/alpha.Rd | 3 coin-1.3-0/coin/man/alzheimer.Rd | 3 coin-1.3-0/coin/man/asat.Rd | 3 coin-1.3-0/coin/man/coin-package.Rd | 7 coin-1.3-0/coin/man/expectation-methods.Rd | 6 coin-1.3-0/coin/man/glioma.Rd | 4 coin-1.3-0/coin/man/hohnloser.Rd | 4 coin-1.3-0/coin/man/jobsatisfaction.Rd | 29 coin-1.3-0/coin/man/malformations.Rd | 43 - coin-1.3-0/coin/man/mercuryfish.Rd | 6 coin-1.3-0/coin/man/neuropathy.Rd | 9 coin-1.3-0/coin/man/ocarcinoma.Rd | 10 coin-1.3-0/coin/man/photocar.Rd | 5 coin-1.3-0/coin/man/pvalue-methods.Rd | 109 +- coin-1.3-0/coin/man/rotarod.Rd | 1 coin-1.3-0/coin/man/statistic-methods.Rd | 41 coin-1.3-0/coin/man/treepipit.Rd | 3 coin-1.3-0/coin/man/vision.Rd | 27 coin-1.3-0/coin/src/Helpers.c | 251 +---- coin-1.3-0/coin/src/coin-init.c | 12 coin-1.3-0/coin/src/coin.h | 68 - coin-1.3-0/coin/src/coin_common.h | 6 coin-1.3-0/coin/tests/Examples/coin-Ex.Rout.save | 320 +++++-- coin-1.3-0/coin/tests/bugfixes.R | 27 coin-1.3-0/coin/tests/bugfixes.Rout.save | 56 - coin-1.3-0/coin/tests/comparisons.R | 80 - coin-1.3-0/coin/tests/comparisons.Rout.save | 88 +- coin-1.3-0/coin/tests/regtest_2sample.R | 141 ++- coin-1.3-0/coin/tests/regtest_2sample.Rout.save | 317 ++++++- coin-1.3-0/coin/tests/regtest_Ksample.R | 36 coin-1.3-0/coin/tests/regtest_Ksample.Rout.save | 44 - coin-1.3-0/coin/tests/regtest_MTP.R | 24 coin-1.3-0/coin/tests/regtest_MTP.Rout.save | 66 - coin-1.3-0/coin/tests/regtest_contingency.R | 20 coin-1.3-0/coin/tests/regtest_contingency.Rout.save | 60 + coin-1.3-0/coin/tests/regtest_distribution.R | 1 coin-1.3-0/coin/tests/regtest_distribution.Rout.save | 7 coin-1.3-0/coin/tests/regtest_helpers.R | 33 coin-1.3-0/coin/tests/regtest_helpers.Rout.save | 39 coin-1.3-0/coin/tests/regtest_midpvalue.R | 50 - coin-1.3-0/coin/tests/regtest_midpvalue.Rout.save | 56 - coin-1.3-0/coin/tests/regtest_names.R |only coin-1.3-0/coin/tests/regtest_names.Rout.save |only coin-1.3-0/coin/tests/regtest_size.R |only coin-1.3-0/coin/tests/regtest_size.Rout.save |only coin-1.3-0/coin/tests/regtest_trafo.R | 12 coin-1.3-0/coin/tests/regtest_trafo.Rout.save | 224 +++++ coin-1.3-0/coin/vignettes/Implementation.Rnw |only coin-1.3-0/coin/vignettes/Implementation.Rout.save |only coin-1.3-0/coin/vignettes/LegoCondInf.Rout.save | 4 coin-1.3-0/coin/vignettes/MAXtest.Rnw | 4 coin-1.3-0/coin/vignettes/MAXtest.Rout.save | 7 coin-1.3-0/coin/vignettes/coin.Rnw | 4 coin-1.3-0/coin/vignettes/coin.Rout.save | 10 125 files changed, 3804 insertions(+), 2767 deletions(-)
Title: Aggregation Operators and Preordered Sets
Description: Tools supporting multi-criteria and group decision making,
including variable number of criteria, by means of
aggregation operators, spread measures,
fuzzy logic connectives, fusion functions,
and preordered sets. Possible applications include,
but are not limited to, quality management, scientometrics,
software engineering, etc.
Author: Marek Gagolewski [aut, cre],
Anna Cena [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between agop versions 0.1-4 dated 2014-09-14 and 0.2-2 dated 2019-03-08
agop-0.1-4/agop/R/preorders.R |only agop-0.1-4/agop/inst |only agop-0.1-4/agop/man/closure_total_fair.Rd |only agop-0.1-4/agop/man/closure_transitive.Rd |only agop-0.1-4/agop/man/de_transitive.Rd |only agop-0.1-4/agop/man/get_equivalence_classes.Rd |only agop-0.1-4/agop/man/get_incomparable_pairs.Rd |only agop-0.1-4/agop/man/get_independent_sets.Rd |only agop-0.1-4/agop/man/is_reflexive.Rd |only agop-0.1-4/agop/man/is_total.Rd |only agop-0.1-4/agop/man/is_transitive.Rd |only agop-0.1-4/agop/src/preorders.cpp |only agop-0.2-2/agop/.Rinstignore |only agop-0.2-2/agop/DESCRIPTION | 40 +- agop-0.2-2/agop/MD5 | 136 +++++-- agop-0.2-2/agop/NAMESPACE | 78 +++- agop-0.2-2/agop/NEWS | 53 ++- agop-0.2-2/agop/R/agop-package.R | 105 +----- agop-0.2-2/agop/R/agops-classical.R | 126 ++++--- agop-0.2-2/agop/R/agops-dispersion.R |only agop-0.2-2/agop/R/agops-impact.R | 176 ++++++---- agop-0.2-2/agop/R/check-comonotonicity.R |only agop-0.2-2/agop/R/distrib-dpareto2-estimators.R |only agop-0.2-2/agop/R/distrib-dpareto2.R |only agop-0.2-2/agop/R/distrib-exp-adtest.R |only agop-0.2-2/agop/R/distrib-pareto2-adtest.R |only agop-0.2-2/agop/R/distrib-pareto2-estimators.R | 105 +++--- agop-0.2-2/agop/R/distrib-pareto2-ftest.R | 94 ++--- agop-0.2-2/agop/R/distrib-pareto2.R | 35 +- agop-0.2-2/agop/R/fuzzylogic-implication.R |only agop-0.2-2/agop/R/fuzzylogic-negation.R |only agop-0.2-2/agop/R/fuzzylogic-tconorm.R |only agop-0.2-2/agop/R/fuzzylogic-tnorm.R |only agop-0.2-2/agop/R/rel-DELETE_ME.R |only agop-0.2-2/agop/R/rel-antisymmetry.R |only agop-0.2-2/agop/R/rel-assymetry.R |only agop-0.2-2/agop/R/rel-cyclicity.R |only agop-0.2-2/agop/R/rel-examples.R |only agop-0.2-2/agop/R/rel-hasse.R |only agop-0.2-2/agop/R/rel-irreflexivity.R |only agop-0.2-2/agop/R/rel-other.R |only agop-0.2-2/agop/R/rel-reflexivity.R |only agop-0.2-2/agop/R/rel-symmetry.R |only agop-0.2-2/agop/R/rel-totality.R |only agop-0.2-2/agop/R/rel-transitivity.R |only agop-0.2-2/agop/R/sysdata.rda |only agop-0.2-2/agop/R/visualization.R | 52 +-- agop-0.2-2/agop/man/DiscretizedPareto2.Rd |only agop-0.2-2/agop/man/Pareto2.Rd | 27 - agop-0.2-2/agop/man/agop-package.Rd | 93 ----- agop-0.2-2/agop/man/check_comonotonicity.Rd |only agop-0.2-2/agop/man/d2owa.Rd |only agop-0.2-2/agop/man/dpareto2_estimate_mle.Rd |only agop-0.2-2/agop/man/exp_test_ad.Rd |only agop-0.2-2/agop/man/fuzzylogic_implication.Rd |only agop-0.2-2/agop/man/fuzzylogic_negation.Rd |only agop-0.2-2/agop/man/fuzzylogic_tconorm.Rd |only agop-0.2-2/agop/man/fuzzylogic_tnorm.Rd |only agop-0.2-2/agop/man/index_g.Rd | 40 +- agop-0.2-2/agop/man/index_h.Rd | 41 +- agop-0.2-2/agop/man/index_lp.Rd | 43 +- agop-0.2-2/agop/man/index_maxprod.Rd | 31 + agop-0.2-2/agop/man/index_rp.Rd | 24 - agop-0.2-2/agop/man/index_w.Rd | 17 agop-0.2-2/agop/man/owa.Rd | 40 +- agop-0.2-2/agop/man/owmax.Rd | 49 +- agop-0.2-2/agop/man/pareto2_estimate_mle.Rd | 19 - agop-0.2-2/agop/man/pareto2_estimate_mmse.Rd | 21 - agop-0.2-2/agop/man/pareto2_test_ad.Rd |only agop-0.2-2/agop/man/pareto2_test_f.Rd | 17 agop-0.2-2/agop/man/plot_producer.Rd | 27 - agop-0.2-2/agop/man/pord_nd.Rd |only agop-0.2-2/agop/man/pord_spread.Rd |only agop-0.2-2/agop/man/pord_weakdom.Rd | 87 ++++- agop-0.2-2/agop/man/rel_antisymmetric.Rd |only agop-0.2-2/agop/man/rel_asymmetric.Rd |only agop-0.2-2/agop/man/rel_cyclic.Rd |only agop-0.2-2/agop/man/rel_graph.Rd | 43 +- agop-0.2-2/agop/man/rel_hasse.Rd |only agop-0.2-2/agop/man/rel_irreflexive.Rd |only agop-0.2-2/agop/man/rel_reflexive.Rd |only agop-0.2-2/agop/man/rel_symmetric.Rd |only agop-0.2-2/agop/man/rel_total.Rd |only agop-0.2-2/agop/man/rel_transitive.Rd |only agop-0.2-2/agop/src/adtest.cpp |only agop-0.2-2/agop/src/agop.cpp | 88 ++++- agop-0.2-2/agop/src/agop.h | 231 ++++++++++--- agop-0.2-2/agop/src/agops_classical.cpp | 112 +++--- agop-0.2-2/agop/src/agops_dispersion.cpp |only agop-0.2-2/agop/src/agops_impact.cpp | 174 +++++----- agop-0.2-2/agop/src/check_comonotonicity.cpp |only agop-0.2-2/agop/src/distrib_pareto2.cpp |only agop-0.2-2/agop/src/fuzzylogic_implication.cpp |only agop-0.2-2/agop/src/fuzzylogic_negation.cpp |only agop-0.2-2/agop/src/fuzzylogic_tconorm.cpp |only agop-0.2-2/agop/src/fuzzylogic_tnorm.cpp |only agop-0.2-2/agop/src/prepare_arg.cpp | 411 ++++++++++++++---------- agop-0.2-2/agop/src/rel_antisymmetry.cpp |only agop-0.2-2/agop/src/rel_asymmetry.cpp |only agop-0.2-2/agop/src/rel_cyclicity.cpp |only agop-0.2-2/agop/src/rel_examples.cpp |only agop-0.2-2/agop/src/rel_hasse.cpp |only agop-0.2-2/agop/src/rel_irreflexivity.cpp |only agop-0.2-2/agop/src/rel_reflexivity.cpp |only agop-0.2-2/agop/src/rel_symmetry.cpp |only agop-0.2-2/agop/src/rel_totality.cpp |only agop-0.2-2/agop/src/rel_transitivity.cpp |only 107 files changed, 1585 insertions(+), 1050 deletions(-)
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 3.0.1 dated 2018-11-05 and 4.0.0 dated 2019-03-08
cgraph-3.0.1/cgraph/R/cgraph.R |only cgraph-3.0.1/cgraph/R/library.R |only cgraph-3.0.1/cgraph/R/operators.R |only cgraph-3.0.1/cgraph/man/abs_grad.Rd |only cgraph-3.0.1/cgraph/man/acos_grad.Rd |only cgraph-3.0.1/cgraph/man/acosh_grad.Rd |only cgraph-3.0.1/cgraph/man/add_grad_x.Rd |only cgraph-3.0.1/cgraph/man/add_grad_y.Rd |only cgraph-3.0.1/cgraph/man/approx_grad.Rd |only cgraph-3.0.1/cgraph/man/as_double_grad.Rd |only cgraph-3.0.1/cgraph/man/asin_grad.Rd |only cgraph-3.0.1/cgraph/man/asinh_grad.Rd |only cgraph-3.0.1/cgraph/man/atan_grad.Rd |only cgraph-3.0.1/cgraph/man/atanh_grad.Rd |only cgraph-3.0.1/cgraph/man/cg_active.Rd |only cgraph-3.0.1/cgraph/man/cg_add_parms.Rd |only cgraph-3.0.1/cgraph/man/cg_adj_mat.Rd |only cgraph-3.0.1/cgraph/man/cg_colMeans.Rd |only cgraph-3.0.1/cgraph/man/cg_colSums.Rd |only cgraph-3.0.1/cgraph/man/cg_const.Rd |only cgraph-3.0.1/cgraph/man/cg_default_library.Rd |only cgraph-3.0.1/cgraph/man/cg_equal.Rd |only cgraph-3.0.1/cgraph/man/cg_get_parms.Rd |only cgraph-3.0.1/cgraph/man/cg_gradients.Rd |only cgraph-3.0.1/cgraph/man/cg_greater.Rd |only cgraph-3.0.1/cgraph/man/cg_greater_equal.Rd |only cgraph-3.0.1/cgraph/man/cg_initialize.Rd |only cgraph-3.0.1/cgraph/man/cg_less.Rd |only cgraph-3.0.1/cgraph/man/cg_less_equal.Rd |only cgraph-3.0.1/cgraph/man/cg_not.Rd |only cgraph-3.0.1/cgraph/man/cg_not_equal.Rd |only cgraph-3.0.1/cgraph/man/cg_opr.Rd |only cgraph-3.0.1/cgraph/man/cg_parm.Rd |only cgraph-3.0.1/cgraph/man/cg_plot.Rd |only cgraph-3.0.1/cgraph/man/cg_reshape.Rd |only cgraph-3.0.1/cgraph/man/cg_rowMeans.Rd |only cgraph-3.0.1/cgraph/man/cg_rowSums.Rd |only cgraph-3.0.1/cgraph/man/cg_run.Rd |only cgraph-3.0.1/cgraph/man/cg_set.Rd |only cgraph-3.0.1/cgraph/man/cg_val.Rd |only cgraph-3.0.1/cgraph/man/cgraph.Rd |only cgraph-3.0.1/cgraph/man/colMeans_grad.Rd |only cgraph-3.0.1/cgraph/man/colSums_grad.Rd |only cgraph-3.0.1/cgraph/man/const.Rd |only cgraph-3.0.1/cgraph/man/cos_grad.Rd |only cgraph-3.0.1/cgraph/man/cosh_grad.Rd |only cgraph-3.0.1/cgraph/man/crossprod_grad_x.Rd |only cgraph-3.0.1/cgraph/man/crossprod_grad_y.Rd |only cgraph-3.0.1/cgraph/man/div_grad_x.Rd |only cgraph-3.0.1/cgraph/man/div_grad_y.Rd |only cgraph-3.0.1/cgraph/man/equal_grad_x.Rd |only cgraph-3.0.1/cgraph/man/equal_grad_y.Rd |only cgraph-3.0.1/cgraph/man/exp_grad.Rd |only cgraph-3.0.1/cgraph/man/gradients.Rd |only cgraph-3.0.1/cgraph/man/greater_equal_grad_x.Rd |only cgraph-3.0.1/cgraph/man/greater_equal_grad_y.Rd |only cgraph-3.0.1/cgraph/man/greater_grad_x.Rd |only cgraph-3.0.1/cgraph/man/greater_grad_y.Rd |only cgraph-3.0.1/cgraph/man/input.Rd |only cgraph-3.0.1/cgraph/man/less_equal_grad_x.Rd |only cgraph-3.0.1/cgraph/man/less_equal_grad_y.Rd |only cgraph-3.0.1/cgraph/man/less_grad_x.Rd |only cgraph-3.0.1/cgraph/man/less_grad_y.Rd |only cgraph-3.0.1/cgraph/man/linear.Rd |only cgraph-3.0.1/cgraph/man/linear_grad_x.Rd |only cgraph-3.0.1/cgraph/man/linear_grad_y.Rd |only cgraph-3.0.1/cgraph/man/linear_grad_z.Rd |only cgraph-3.0.1/cgraph/man/ln_grad.Rd |only cgraph-3.0.1/cgraph/man/log10_grad.Rd |only cgraph-3.0.1/cgraph/man/log2_grad.Rd |only cgraph-3.0.1/cgraph/man/matmul_grad_x.Rd |only cgraph-3.0.1/cgraph/man/matmul_grad_y.Rd |only cgraph-3.0.1/cgraph/man/max_grad.Rd |only cgraph-3.0.1/cgraph/man/mean_grad.Rd |only cgraph-3.0.1/cgraph/man/min_grad.Rd |only cgraph-3.0.1/cgraph/man/mul_grad_x.Rd |only cgraph-3.0.1/cgraph/man/mul_grad_y.Rd |only cgraph-3.0.1/cgraph/man/neg_grad.Rd |only cgraph-3.0.1/cgraph/man/not_equal_grad_x.Rd |only cgraph-3.0.1/cgraph/man/not_equal_grad_y.Rd |only cgraph-3.0.1/cgraph/man/not_grad.Rd |only cgraph-3.0.1/cgraph/man/opr.Rd |only cgraph-3.0.1/cgraph/man/parm.Rd |only cgraph-3.0.1/cgraph/man/pmax_grad_x.Rd |only cgraph-3.0.1/cgraph/man/pmax_grad_y.Rd |only cgraph-3.0.1/cgraph/man/pmin_grad_x.Rd |only cgraph-3.0.1/cgraph/man/pmin_grad_y.Rd |only cgraph-3.0.1/cgraph/man/pos_grad.Rd |only cgraph-3.0.1/cgraph/man/pow_grad_x.Rd |only cgraph-3.0.1/cgraph/man/pow_grad_y.Rd |only cgraph-3.0.1/cgraph/man/prod_grad.Rd |only cgraph-3.0.1/cgraph/man/reshape_grad_dim.Rd |only cgraph-3.0.1/cgraph/man/reshape_grad_x.Rd |only cgraph-3.0.1/cgraph/man/rowMeans_grad.Rd |only cgraph-3.0.1/cgraph/man/rowSums_grad.Rd |only cgraph-3.0.1/cgraph/man/run.Rd |only cgraph-3.0.1/cgraph/man/set.Rd |only cgraph-3.0.1/cgraph/man/sigmoid.Rd |only cgraph-3.0.1/cgraph/man/sigmoid_grad.Rd |only cgraph-3.0.1/cgraph/man/sin_grad.Rd |only cgraph-3.0.1/cgraph/man/sinh_grad.Rd |only cgraph-3.0.1/cgraph/man/sqrt_grad.Rd |only cgraph-3.0.1/cgraph/man/sub_grad_x.Rd |only cgraph-3.0.1/cgraph/man/sub_grad_y.Rd |only cgraph-3.0.1/cgraph/man/sum_grad.Rd |only cgraph-3.0.1/cgraph/man/t_grad.Rd |only cgraph-3.0.1/cgraph/man/tan_grad.Rd |only cgraph-3.0.1/cgraph/man/tanh_grad.Rd |only cgraph-3.0.1/cgraph/man/tcrossprod_grad_x.Rd |only cgraph-3.0.1/cgraph/man/tcrossprod_grad_y.Rd |only cgraph-3.0.1/cgraph/man/val.Rd |only cgraph-3.0.1/cgraph/src/cgraph.c |only cgraph-3.0.1/cgraph/src/library.c |only cgraph-3.0.1/cgraph/tests/testthat/test.array.R |only cgraph-3.0.1/cgraph/tests/testthat/test.cgraph.R |only cgraph-3.0.1/cgraph/tests/testthat/test.math.R |only cgraph-3.0.1/cgraph/tests/testthat/test.misc.R |only cgraph-3.0.1/cgraph/tests/testthat/test.transform.R |only cgraph-3.0.1/cgraph/tests/testthat/test.trig.R |only cgraph-4.0.0/cgraph/DESCRIPTION | 9 cgraph-4.0.0/cgraph/MD5 | 258 +++++------------ cgraph-4.0.0/cgraph/NAMESPACE | 52 +-- cgraph-4.0.0/cgraph/NEWS.md | 27 + cgraph-4.0.0/cgraph/R/array.R |only cgraph-4.0.0/cgraph/R/function.R |only cgraph-4.0.0/cgraph/R/graph.R |only cgraph-4.0.0/cgraph/R/internal.R | 53 +-- cgraph-4.0.0/cgraph/R/math.R |only cgraph-4.0.0/cgraph/R/node.R |only cgraph-4.0.0/cgraph/R/session.R | 295 +------------------- cgraph-4.0.0/cgraph/R/zzz.R | 14 cgraph-4.0.0/cgraph/man/approx_gradients.Rd |only cgraph-4.0.0/cgraph/man/bsum.Rd | 10 cgraph-4.0.0/cgraph/man/cg_abs.Rd | 6 cgraph-4.0.0/cgraph/man/cg_acos.Rd | 6 cgraph-4.0.0/cgraph/man/cg_acosh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_add.Rd | 8 cgraph-4.0.0/cgraph/man/cg_as_double.Rd | 8 cgraph-4.0.0/cgraph/man/cg_as_numeric.Rd | 8 cgraph-4.0.0/cgraph/man/cg_asin.Rd | 6 cgraph-4.0.0/cgraph/man/cg_asinh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_atan.Rd | 6 cgraph-4.0.0/cgraph/man/cg_atanh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_colsums.Rd |only cgraph-4.0.0/cgraph/man/cg_constant.Rd |only cgraph-4.0.0/cgraph/man/cg_cos.Rd | 6 cgraph-4.0.0/cgraph/man/cg_cosh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_crossprod.Rd | 8 cgraph-4.0.0/cgraph/man/cg_div.Rd | 8 cgraph-4.0.0/cgraph/man/cg_exp.Rd | 6 cgraph-4.0.0/cgraph/man/cg_function.Rd |only cgraph-4.0.0/cgraph/man/cg_graph.Rd |only cgraph-4.0.0/cgraph/man/cg_graph_gradients.Rd |only cgraph-4.0.0/cgraph/man/cg_graph_run.Rd |only cgraph-4.0.0/cgraph/man/cg_input.Rd | 28 - cgraph-4.0.0/cgraph/man/cg_linear.Rd | 17 - cgraph-4.0.0/cgraph/man/cg_ln.Rd | 6 cgraph-4.0.0/cgraph/man/cg_log10.Rd | 8 cgraph-4.0.0/cgraph/man/cg_log2.Rd | 8 cgraph-4.0.0/cgraph/man/cg_matmul.Rd | 8 cgraph-4.0.0/cgraph/man/cg_max.Rd | 8 cgraph-4.0.0/cgraph/man/cg_mean.Rd | 8 cgraph-4.0.0/cgraph/man/cg_min.Rd | 8 cgraph-4.0.0/cgraph/man/cg_mul.Rd | 10 cgraph-4.0.0/cgraph/man/cg_neg.Rd | 6 cgraph-4.0.0/cgraph/man/cg_operator.Rd |only cgraph-4.0.0/cgraph/man/cg_parameter.Rd |only cgraph-4.0.0/cgraph/man/cg_pmax.Rd | 10 cgraph-4.0.0/cgraph/man/cg_pmin.Rd | 10 cgraph-4.0.0/cgraph/man/cg_pos.Rd | 6 cgraph-4.0.0/cgraph/man/cg_pow.Rd | 8 cgraph-4.0.0/cgraph/man/cg_prod.Rd | 10 cgraph-4.0.0/cgraph/man/cg_rowsums.Rd |only cgraph-4.0.0/cgraph/man/cg_session_graph.Rd |only cgraph-4.0.0/cgraph/man/cg_session_set_graph.Rd |only cgraph-4.0.0/cgraph/man/cg_sigmoid.Rd | 8 cgraph-4.0.0/cgraph/man/cg_sin.Rd | 6 cgraph-4.0.0/cgraph/man/cg_sinh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_sqrt.Rd | 6 cgraph-4.0.0/cgraph/man/cg_sub.Rd | 8 cgraph-4.0.0/cgraph/man/cg_sum.Rd | 10 cgraph-4.0.0/cgraph/man/cg_t.Rd | 6 cgraph-4.0.0/cgraph/man/cg_tan.Rd | 6 cgraph-4.0.0/cgraph/man/cg_tanh.Rd | 6 cgraph-4.0.0/cgraph/man/cg_tcrossprod.Rd | 8 cgraph-4.0.0/cgraph/src/class.c |only cgraph-4.0.0/cgraph/src/class.h |only cgraph-4.0.0/cgraph/src/function.c |only cgraph-4.0.0/cgraph/src/function.h |only cgraph-4.0.0/cgraph/src/graph.c |only cgraph-4.0.0/cgraph/src/graph.h |only cgraph-4.0.0/cgraph/src/init.c | 77 ++--- cgraph-4.0.0/cgraph/src/internal.c | 213 +++++++++++--- cgraph-4.0.0/cgraph/src/internal.h |only cgraph-4.0.0/cgraph/src/math.c |only cgraph-4.0.0/cgraph/src/math.h |only cgraph-4.0.0/cgraph/src/node.c |only cgraph-4.0.0/cgraph/src/node.h |only cgraph-4.0.0/cgraph/src/session.c |only cgraph-4.0.0/cgraph/src/session.h |only cgraph-4.0.0/cgraph/src/stack.c | 98 ++---- cgraph-4.0.0/cgraph/src/stack.h | 36 +- cgraph-4.0.0/cgraph/tests/testthat.R | 14 cgraph-4.0.0/cgraph/tests/testthat/test_array.R |only cgraph-4.0.0/cgraph/tests/testthat/test_graph.R |only cgraph-4.0.0/cgraph/tests/testthat/test_math.R |only 206 files changed, 634 insertions(+), 851 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and
evaluation, ensemble of models.
Author: Wilfried Thuiller [aut, cre],
Damien Georges [aut, cre],
Robin Engler [aut],
Frank Breiner [aut]
Maintainer: Damien Georges <damien.georges2@gmail.com>
Diff between biomod2 versions 3.3-7 dated 2016-03-01 and 3.3-7.1 dated 2019-03-08
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 +- R/Biomod.Models_RE.R | 4 ++-- R/biomod2_models-class.R | 2 +- man/BIOMOD_Modeling.Rd | 2 +- man/BIOMOD_ModelingOptions.Rd | 4 ++-- 7 files changed, 20 insertions(+), 19 deletions(-)
Title: Read, Analyze and Plot River Networks
Description: Functions for reading, analysing and plotting river networks.
For this package, river networks consist of sections and nodes with associated attributes,
e.g. to characterise their morphological, chemical and biological state.
The package provides functions to read this data from text files, to analyse the network
structure and network paths and regions consisting of sections and nodes that fulfill
prescribed criteria, and to plot the river network and associated properties.
Author: Peter Reichert
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Diff between rivernet versions 1.1 dated 2017-05-12 and 1.2 dated 2019-03-08
DESCRIPTION | 10 - MD5 | 39 ++++--- NAMESPACE | 3 R/adjacentreaches.rivernet.r | 48 ++++++++ R/analyze.rivernet.r | 187 ++++++++++++++++++++--------------- R/getregionconnections.R |only R/plot.rivernet.r | 21 ++- R/prune.rivernet.r | 66 ++++++++---- R/rivernet.read.r | 6 - R/splitreach.rivernet.r |only R/upstreamconnectivity.rivernet.r | 29 +++++ inst/NEWS | 39 +++++++ man/analyze.Rd | 13 +- man/analyze.rivernet.Rd | 12 +- man/getregionconnectiions.Rd |only man/plot.rivernet.Rd | 5 man/prune.Rd | 20 +-- man/prune.rivernet.Rd | 20 +-- man/rivernet-package.Rd | 18 ++- man/splitreach.Rd |only man/splitreach.rivernet.Rd |only man/upstreamconnectivity.Rd | 3 man/upstreamconnectivity.rivernet.Rd | 5 23 files changed, 369 insertions(+), 175 deletions(-)
Title: Spatial Implementation of Bayesian Networks and Mapping
Description: Allows spatial implementation of Bayesian networks and mapping in geographical space. It makes maps of expected value (or most likely state) given known and unknown conditions, maps of uncertainty measured as coefficient of variation or Shannon index (entropy), maps of probability associated to any states of any node of the network. Some additional features are provided as well: parallel processing options, data discretization routines and function wrappers designed for users with minimal knowledge of the R language. Outputs can be exported to any common GIS format. Development was funded by the European Union FP7 (2007-2013), under project ROBIN (<http://robinproject.info>).
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between bnspatial versions 1.0.3 dated 2017-11-17 and 1.0.4 dated 2019-03-08
DESCRIPTION | 12 +++---- MD5 | 24 +++++++------- NEWS.md | 6 +++ build/vignette.rds |binary inst/doc/bnspatial.R | 12 +++++++ inst/doc/bnspatial.Rmd | 14 +++++++- inst/doc/bnspatial.html | 80 ++++++++++++++++++++++++++++++++++-------------- man/bnspatial.Rd | 4 +- man/dataDiscretize.Rd | 1 man/linkNode.Rd | 1 man/queryNet.Rd | 1 man/setClasses.Rd | 1 vignettes/bnspatial.Rmd | 14 +++++++- 13 files changed, 121 insertions(+), 49 deletions(-)
Title: Data Set for the 'benchmarkme' Package
Description: Crowd sourced benchmarks from running the 'benchmarkme' package.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between benchmarkmeData versions 1.0.0 dated 2019-01-27 and 1.0.1 dated 2019-03-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 ++++- data/past_results.RData |binary data/past_results_v2.RData |binary 5 files changed, 11 insertions(+), 8 deletions(-)
More information about benchmarkmeData at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-03 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-10 1.2
2011-11-20 1.1
2010-04-07 1.0