Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service
(WFS) for vector data, Catalogue Service (CSW) for ISO/OGC metadata and associated standards such as the common web-service specification (OWS) and
OGC Filter Encoding. The long-term purpose is to add support for additional OGC service standards such as Web Coverage Service (WCS) and
Web Processing Service (WPS).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ows4R versions 0.1-1 dated 2019-05-26 and 0.1-2 dated 2019-06-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/WFSCapabilities.R | 19 +++++++++++++++---- R/WFSClient.R | 12 +++++++++++- R/ows4R.R | 4 ++-- man/WFSCapabilities.Rd | 5 +++-- man/WFSClient.Rd | 6 +++++- man/ows4R.Rd | 4 ++-- 8 files changed, 49 insertions(+), 23 deletions(-)
Title: Analyze ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to implement analyses of plot species distributions,
topography, demography, and biomass. It also includes a torus
translation test to determine habitat associations of tree species as
described by Zuleta et al. (2018) <doi:10.1007/s11104-018-3878-0>. To
learn more about ForestGEO visit <http://www.forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
Gabriel Arellano [aut, rev],
Richard Condit [aut],
Matteo Detto [aut],
Kyle Harms [aut],
Suzanne Lao [aut, rev],
KangMin Ngo [rev],
Haley Overstreet [rev],
Sabrina Russo [aut, rev],
Daniel Zuleta [aut, rev],
CTFS-ForestGEO [cph]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.analyze versions 1.1.10 dated 2019-05-20 and 1.1.11 dated 2019-06-18
DESCRIPTION | 17 MD5 | 154 +- NAMESPACE | 156 +- NEWS.md | 44 R/abund_index.R | 62 R/abundanceperquad2.R | 178 +- R/add_cluster.R | 64 R/as-data-frame.R | 2 R/as_tibble.R | 240 +-- R/check_crucial_names.R | 56 R/demography_ctfs.R | 1308 ++++++++++---------- R/fgeo.analyze-package.R | 4 R/fgeo_topography.R | 572 ++++---- R/gather_mat.R | 128 - R/insensitive.R | 116 - R/summary.R | 108 - R/tt_test.R | 882 ++++++------- README.md | 1139 ++++++++--------- inst/WORDLIST | 95 - man/abundance.Rd | 304 ++-- man/abundance_byyr.Rd | 210 +-- man/fgeo.analyze-package.Rd | 96 - man/fgeo_habitat.Rd | 142 +- man/fgeo_topography.Rd | 136 +- man/pipe.Rd | 24 man/recruitment_ctfs.Rd | 310 ++-- man/reexports.Rd | 62 man/summary.tt_df.Rd | 98 - man/tt_test.Rd | 244 +-- tests/spelling.R | 14 tests/testthat.R | 8 tests/testthat/data-byyr_toy_vft.csv | 18 tests/testthat/ref-composed-abundance-byyr | 48 tests/testthat/ref-composed-basal-area-byyr | 96 - tests/testthat/ref-explain_tt_lst | 30 tests/testthat/ref-explain_tt_test | 586 ++++---- tests/testthat/ref-fgeo_topography_bci_head | 18 tests/testthat/ref-fgeo_topography_bci_tail | 18 tests/testthat/ref-fgeo_topography_luq_head | 18 tests/testthat/ref-fgeo_topography_luq_tail | 18 tests/testthat/ref-growth_ctfs_bci_stem | 42 tests/testthat/ref-growth_ctfs_bci_tree | 42 tests/testthat/ref-growth_ctfs_luq_stem | 42 tests/testthat/ref-growth_ctfs_luq_tree | 42 tests/testthat/ref-growth_ctfs_luq_tree_split1 | 108 - tests/testthat/ref-growth_ctfs_luq_tree_split2 | 146 +- tests/testthat/ref-luq_3sp | 32 tests/testthat/ref-luq_top3_premon | 20 tests/testthat/ref-mortality_ctfs_bci_stem | 54 tests/testthat/ref-mortality_ctfs_bci_tree | 54 tests/testthat/ref-mortality_ctfs_luq_stem | 54 tests/testthat/ref-mortality_ctfs_luq_tree | 54 tests/testthat/ref-mortality_ctfs_luq_tree_split1 | 136 +- tests/testthat/ref-mortality_ctfs_luq_tree_split2 | 168 +- tests/testthat/ref-one_sp_n50_pasoh | 54 tests/testthat/ref-recruitment_ctfs_bci_stem | 48 tests/testthat/ref-recruitment_ctfs_bci_tree | 48 tests/testthat/ref-recruitment_ctfs_luq_stem | 48 tests/testthat/ref-recruitment_ctfs_luq_tree | 48 tests/testthat/ref-recruitment_ctfs_luq_tree_split1 | 120 - tests/testthat/ref-recruitment_ctfs_luq_tree_split2 | 152 +- tests/testthat/ref-torusonesp.all.R | 236 +-- tests/testthat/test-abundance.R | 400 +++--- tests/testthat/test-abundanceperquad2.R | 62 tests/testthat/test-add_cluster.R | 52 tests/testthat/test-as_tibble.R | 294 ++-- tests/testthat/test-byyr.R | 630 ++++----- tests/testthat/test-check_crucial_names.R | 16 tests/testthat/test-data-tian_tong_elev.csv | 1094 ++++++++-------- tests/testthat/test-demography_ctfs.R | 990 +++++++-------- tests/testthat/test-fgeo_habitat.R | 169 +- tests/testthat/test-fgeo_topography.R | 356 ++--- tests/testthat/test-fill.dimension.R | 24 tests/testthat/test-gather_mat.R | 72 - tests/testthat/test-insensitive.R | 56 tests/testthat/test-refactoring.R | 64 tests/testthat/test-summary.R | 152 +- tests/testthat/test-tt_test.R | 446 +++--- 78 files changed, 7210 insertions(+), 7238 deletions(-)
Title: Cholesky Decomposition of the Wishart Distribution
Description: Sampling from the Cholesky factorization of a Wishart random
variable, sampling from the inverse Wishart distribution, sampling from
the Cholesky factorization of an inverse Wishart random variable, sampling
from the pseudo Wishart distribution, sampling from the generalized
inverse Wishart distribution, computing densities for the Wishart
and inverse Wishart distributions, and computing the multivariate gamma
and digamma functions.
Author: Geoffrey Thompson [aut, cre] (<https://orcid.org/0000-0003-2436-8822>),
R Core Team [ctb]
Maintainer: Geoffrey Thompson <gzthompson@gmail.com>
Diff between CholWishart versions 1.0.0 dated 2019-01-25 and 1.0.1 dated 2019-06-18
DESCRIPTION | 14 - MD5 | 12 - NEWS.md | 4 README.md | 129 ++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/wishart.html | 448 ++++++++++++-------------------------------------- 7 files changed, 202 insertions(+), 405 deletions(-)
Title: Simulate Joint Distribution
Description: Simulate multivariate correlated data given nonparametric marginal distributions and their covariance structure characterized by a correlation matrix. The simulator engages the problem from a purely computational perspective. It assumes no statistical models such as copulas or parametric distributions, and can approximate the target correlations regardless of theoretical feasibility. The algorithm integrates and advances the Iman-Conover approach (1982) <doi:10.1080/03610918208812265> and the Ruscio-Kaczetow iteration (2008) <doi:10.1080/00273170802285693>. Package functions are carefully implemented in C++ for pushing computing speed, suitable for large input in a manycore environment. Precision of the approximation and computing speed both outperform various CRAN packages to date by a substantial margin. Benchmarks are detailed in function examples. Additionally, a simple heuristic algorithm initially designed to optimize the simulated joint distribution demonstrated not only strong error reduction capability, but also the potential of achieving the same level of precision of approximation without the enhanced Iman-Conover-Ruscio-Kaczetow as a primer, especially when the functional relationships between marginal distributions are highly nonlinear.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between SimJoint versions 0.1.1 dated 2019-06-13 and 0.2.1 dated 2019-06-18
SimJoint-0.1.1/SimJoint/inst/doc/SimJoint.pdf |only SimJoint-0.1.1/SimJoint/inst/doc/SimJoint.pdf.asis |only SimJoint-0.1.1/SimJoint/vignettes/SimJoint.pdf.asis |only SimJoint-0.2.1/SimJoint/DESCRIPTION | 10 SimJoint-0.2.1/SimJoint/MD5 | 36 SimJoint-0.2.1/SimJoint/R/RcppExports.R | 4 SimJoint-0.2.1/SimJoint/build/vignette.rds |binary SimJoint-0.2.1/SimJoint/inst/doc/SimulatedJointDistribution.pdf |only SimJoint-0.2.1/SimJoint/inst/doc/SimulatedJointDistribution.pdf.asis |only SimJoint-0.2.1/SimJoint/man/SJpearson.Rd | 91 - SimJoint-0.2.1/SimJoint/man/SJpearsonPMF.Rd | 2 SimJoint-0.2.1/SimJoint/man/SJspearman.Rd | 1 SimJoint-0.2.1/SimJoint/man/SJspearmanPMF.Rd | 1 SimJoint-0.2.1/SimJoint/man/decor.Rd | 1 SimJoint-0.2.1/SimJoint/man/postSimOpt.Rd |only SimJoint-0.2.1/SimJoint/man/xSJpearson.Rd | 1 SimJoint-0.2.1/SimJoint/man/xSJpearsonPMF.Rd | 1 SimJoint-0.2.1/SimJoint/src/RcppExports.cpp | 17 SimJoint-0.2.1/SimJoint/src/jointSimulation.cpp | 567 +++++++++- SimJoint-0.2.1/SimJoint/tests/funtionExamples/SJpearson_eg.r | 177 +-- SimJoint-0.2.1/SimJoint/tests/funtionExamples/postSimOpt_eg.r |only SimJoint-0.2.1/SimJoint/tests/research |only SimJoint-0.2.1/SimJoint/tests/rewriteRdFiles |only SimJoint-0.2.1/SimJoint/vignettes/SimulatedJointDistribution.pdf.asis |only 24 files changed, 769 insertions(+), 140 deletions(-)
Title: Summarizes Provenance Related to Inputs and Outputs of a Script
or Console Commands
Description: Reads the provenance collected by the 'rdt' or
'rdtLite' packages, or other tools providing compatible PROV JSON output
created by the execution of a script, and provides a human-readable
summary identifying the input and output files, the script used
(if any), errors and warnings produced, and the environment in
which it was executed. It can also optionally package all the
files into a zip file. The exact format of the JSON created by
'rdt' and 'rdtLite' is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>.
More information about 'rdtLite' and associated tools is available
at <https://github.com/End-to-end-provenance/> and Barbara Lerner,
Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Barbara Lerner [cre],
Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provSummarizeR versions 1.0 dated 2019-01-25 and 1.1 dated 2019-06-18
provSummarizeR-1.0/provSummarizeR/inst/testdata/Console.R |only provSummarizeR-1.0/provSummarizeR/inst/testscript |only provSummarizeR-1.0/provSummarizeR/tests/testthat/test_provSummzarize.R |only provSummarizeR-1.1/provSummarizeR/DESCRIPTION | 10 provSummarizeR-1.1/provSummarizeR/MD5 | 33 +- provSummarizeR-1.1/provSummarizeR/NEWS.md |only provSummarizeR-1.1/provSummarizeR/R/provSummarizeR.R | 10 provSummarizeR-1.1/provSummarizeR/README.md | 34 +- provSummarizeR-1.1/provSummarizeR/inst/testdata/console.json | 120 ++++------ provSummarizeR-1.1/provSummarizeR/inst/testdata/files.json |only provSummarizeR-1.1/provSummarizeR/inst/testdata/prov.json | 108 ++------- provSummarizeR-1.1/provSummarizeR/inst/testscripts |only provSummarizeR-1.1/provSummarizeR/inst/testsummaries |only provSummarizeR-1.1/provSummarizeR/man/summarize.Rd | 4 provSummarizeR-1.1/provSummarizeR/tests/testthat/test_provSummarize.R |only 15 files changed, 142 insertions(+), 177 deletions(-)
More information about provSummarizeR at CRAN
Permanent link
Title: Logic Regression
Description: Routines for fitting Logic Regression models. Logic Regression is described
in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte
Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005)
<DOI:10.1002/gepi.20042>.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between LogicReg versions 1.5.10 dated 2018-06-14 and 1.5.12 dated 2019-06-18
DESCRIPTION | 13 ++++++++----- MD5 | 8 ++++---- R/LogicReg.R | 1 + man/logreg.Rd | 4 ++-- src/slogic.f | 50 +++++++++++++++++++++++++++++++++++++++++--------- 5 files changed, 56 insertions(+), 20 deletions(-)
Title: Plot ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to plot ForestGEO data. To learn more about ForestGEO visit
<http://www.forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.plot versions 1.1.8 dated 2019-05-31 and 1.1.9 dated 2019-06-18
DESCRIPTION | 10 MD5 | 112 - NAMESPACE | 86 - NEWS.md | 4 R/autoplot-sp_elev.R | 410 +++---- R/autoplot.fgeo_habitat.R | 54 R/autoplot_by_species.R | 320 ++--- R/caption_tag_xy.R | 136 +- R/collapse_censusid.R | 64 - R/fgeo.plot-package.R | 4 R/headers.R | 130 +- R/imports-reexports.R | 74 - R/layers.R | 256 ++-- R/plot_dbh_bubles_by_quadrat.R | 374 +++--- R/plot_sp_elev-implementation.R | 574 +++++----- R/plot_tag_status_by_subquadrat.R | 1068 +++++++++---------- R/sp_elev.R | 236 ++-- R/suffix_match.R | 134 +- R/themes.R | 214 +-- README.md | 134 +- inst/WORDLIST | 86 - man/autoplot.fgeo_habitat.Rd | 78 - man/autoplot.sp_elev.Rd | 318 ++--- man/autoplot_by_species.Rd | 52 man/autoplot_by_species.sp_elev.Rd | 262 ++-- man/elev.Rd | 98 - man/fgeo.plot-package.Rd | 66 - man/header_dbh_bubbles.Rd | 46 man/header_tag_status.Rd | 40 man/headers.Rd | 24 man/pipe.Rd | 24 man/plot_dbh_bubbles_by_quadrat.Rd | 222 +-- man/plot_tag_status_by_subquadrat.Rd | 326 ++--- man/reexports.Rd | 38 man/sp.Rd | 96 - man/sp_elev.Rd | 124 +- man/suffix_match.Rd | 96 - man/theme_dbh_bubbles.Rd | 146 +- man/theme_default.Rd | 62 - man/theme_tag_status.Rd | 158 +- man/themes.Rd | 40 tests/spelling.R | 12 tests/testthat.R | 8 tests/testthat/ref-plot_tag_status_by_subquadrat.csv | 28 tests/testthat/test-autoplot-fgeo_habitat.R | 28 tests/testthat/test-autoplot-sp_elev.R | 106 - tests/testthat/test-autoplot_by_species.R | 58 - tests/testthat/test-caption_tag_xy.R | 54 tests/testthat/test-collapse_censusid.R | 40 tests/testthat/test-headers.R | 30 tests/testthat/test-plot-fgeo_habitat.R | 28 tests/testthat/test-plot_dbh_bubles_by_quadrat.R | 110 - tests/testthat/test-plot_sp_elev-implementation.R | 200 +-- tests/testthat/test-plot_tag_status_by_subquadrat.R | 660 +++++------ tests/testthat/test-sp_elev.R | 50 tests/testthat/test-suffix_match.R | 166 +- tests/testthat/test-themes.R | 18 57 files changed, 4198 insertions(+), 4194 deletions(-)
Title: Drug Interaction Modeling Based on Loewe Additivity Following
Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based
on the Loewe additivity model, following Harbron's approach (Statistics in
Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling
of the drug interaction index and supports "2-stage" estimation in addition
to "1-stage" estimation, including bootstrap-based confidence intervals.
The method requires data on the monotherapy responses and the package
accommodates both checkerboard and ray designs. Functions are available for
graphical exploration of model goodness-of-fit and diagnostics, as well as
for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between drugCombo versions 1.0.3 dated 2018-11-13 and 1.1.0 dated 2019-06-18
DESCRIPTION | 10 - MD5 | 28 ++--- NAMESPACE | 2 R/plot.tauSurface.R | 4 R/tauSurface.R | 54 +++++++--- build/vignette.rds |binary inst/NEWS | 4 inst/doc/userGuide.html | 200 ++++++++++++++++++++++----------------- man/fitModel.Rd | 4 man/getBootTaus.Rd | 4 man/getTauSurface.Rd | 4 man/plot.HarbronFit.Rd | 3 man/tauPlot2d.Rd | 9 - man/tauPlot3d.Rd | 5 tests/testthat/test-tauSurface.R | 20 +++ 15 files changed, 214 insertions(+), 137 deletions(-)
Title: Compare Output and Run Time
Description: Quickly run experiments to compare the run time and output of
code blocks. The function mbc() can make fast comparisons of code,
and will calculate statistics comparing the resulting outputs.
It can be used to compare model fits to the same data or
see which function runs faster.
The function ffexp() runs a function using all possible combinations
of selected inputs. This is useful for comparing the effect of
different parameter values. It can also run in parallel and
automatically save intermediate results, which is very useful
for long computations.
Author: Collin Erickson [aut, cre]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between comparer versions 0.1.1 dated 2018-01-08 and 0.2.0 dated 2019-06-18
comparer-0.1.1/comparer/R/mbc.R |only comparer-0.2.0/comparer/DESCRIPTION | 26 comparer-0.2.0/comparer/MD5 | 29 comparer-0.2.0/comparer/NAMESPACE | 1 comparer-0.2.0/comparer/NEWS.md | 6 comparer-0.2.0/comparer/R/ffexp.R |only comparer-0.2.0/comparer/R/mbc_clean.R |only comparer-0.2.0/comparer/README.md | 229 +++++-- comparer-0.2.0/comparer/build/vignette.rds |binary comparer-0.2.0/comparer/inst/doc/comparer.Rmd | 4 comparer-0.2.0/comparer/inst/doc/comparer.html | 649 +++++++++++++------- comparer-0.2.0/comparer/man/ffexp.Rd |only comparer-0.2.0/comparer/man/mbc.Rd | 30 comparer-0.2.0/comparer/man/plot.mbc.Rd | 7 comparer-0.2.0/comparer/man/print.mbc.Rd | 7 comparer-0.2.0/comparer/tests/testthat/test_ffexp.R |only comparer-0.2.0/comparer/tests/testthat/test_mbc.R | 28 comparer-0.2.0/comparer/vignettes/comparer.Rmd | 4 18 files changed, 710 insertions(+), 310 deletions(-)
Title: Calculate Task Split Half Reliability Estimates
Description: Estimate the internal consistency of your tasks with a permutation based split-half reliability approach.
Unofficial release name: "Fight Milk - re-brand".
Author: Sam Parsons [aut, cre]
Maintainer: Sam Parsons <sam.parsons@psy.ox.ac.uk>
Diff between splithalf versions 0.3.1 dated 2018-03-17 and 0.5.2 dated 2019-06-18
splithalf-0.3.1/splithalf/R/data.R |only splithalf-0.3.1/splithalf/R/splithalf_ACC.R |only splithalf-0.3.1/splithalf/R/splithalf_ACC_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_ACC_diff_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_diff.R |only splithalf-0.3.1/splithalf/R/splithalf_diff_diff.R |only splithalf-0.3.1/splithalf/build |only splithalf-0.3.1/splithalf/data |only splithalf-0.3.1/splithalf/inst/doc |only splithalf-0.3.1/splithalf/man/DPdata.Rd |only splithalf-0.3.1/splithalf/man/DPdata_missing.Rd |only splithalf-0.3.1/splithalf/man/TSTdata.Rd |only splithalf-0.3.1/splithalf/man/TSTdata_missing.Rd |only splithalf-0.3.1/splithalf/man/splithalf_ACC.Rd |only splithalf-0.3.1/splithalf/man/splithalf_ACC_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_ACC_diff_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_diff.Rd |only splithalf-0.3.1/splithalf/man/splithalf_diff_diff.Rd |only splithalf-0.3.1/splithalf/vignettes |only splithalf-0.5.2/splithalf/DESCRIPTION | 23 splithalf-0.5.2/splithalf/MD5 | 41 splithalf-0.5.2/splithalf/NAMESPACE | 12 splithalf-0.5.2/splithalf/NEWS.md | 49 - splithalf-0.5.2/splithalf/R/RcppExports.R |only splithalf-0.5.2/splithalf/R/splithalf.R | 662 ++++++++++----- splithalf-0.5.2/splithalf/R/zzz.R |only splithalf-0.5.2/splithalf/README.md | 12 splithalf-0.5.2/splithalf/man/splithalf.Rd | 52 - splithalf-0.5.2/splithalf/src |only 29 files changed, 554 insertions(+), 297 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Originally described in Kamvar, Tabima, and Grünwald (2014)
<doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and
Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>),
Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>),
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
(<https://orcid.org/0000-0002-7324-7448>),
Erik Sotka [ctb],
Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>),
Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>),
Frédéric D. Chevalier [ctb] (<https://orcid.org/0000-0003-2611-8106>),
Niklaus J. Grünwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.8.2 dated 2019-03-11 and 2.8.3 dated 2019-06-18
poppr-2.8.2/poppr/NEWS |only poppr-2.8.3/poppr/DESCRIPTION | 24 +- poppr-2.8.3/poppr/MD5 | 56 +++--- poppr-2.8.3/poppr/NAMESPACE | 2 poppr-2.8.3/poppr/R/Index_calculations.r | 5 poppr-2.8.3/poppr/R/aaaMLGclass.R | 5 poppr-2.8.3/poppr/R/aaaMLGmethods.R | 36 +++- poppr-2.8.3/poppr/R/file_handling.r | 8 poppr-2.8.3/poppr/R/internal.r | 223 ------------------------- poppr-2.8.3/poppr/R/internal_methods.R | 20 +- poppr-2.8.3/poppr/R/methods.r | 195 ++++++++++++++------- poppr-2.8.3/poppr/R/mlg.r | 35 +-- poppr-2.8.3/poppr/R/msn_handlers.R | 17 + poppr-2.8.3/poppr/R/poppr.R | 8 poppr-2.8.3/poppr/R/sample_schemes.r | 6 poppr-2.8.3/poppr/README.md | 39 ++-- poppr-2.8.3/poppr/build/vignette.rds |binary poppr-2.8.3/poppr/inst/doc/algo.pdf |binary poppr-2.8.3/poppr/inst/doc/mlg.html | 57 +++--- poppr-2.8.3/poppr/inst/doc/poppr_manual.html | 39 ++-- poppr-2.8.3/poppr/man/MLG-accessors.Rd | 8 poppr-2.8.3/poppr/man/MLG-class.Rd | 2 poppr-2.8.3/poppr/man/figures/logo.png |only poppr-2.8.3/poppr/man/getfile.Rd | 3 poppr-2.8.3/poppr/man/poppr-package.Rd | 8 poppr-2.8.3/poppr/man/poppr.all.Rd | 5 poppr-2.8.3/poppr/tests/testthat/test-filter.R | 40 +++- poppr-2.8.3/poppr/tests/testthat/test-import.R | 23 ++ poppr-2.8.3/poppr/tests/testthat/test-msn.R | 2 poppr-2.8.3/poppr/tests/testthat/test-plots.R | 6 30 files changed, 420 insertions(+), 452 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include a) Tsagris M.T., Preston S. and Wood A.T.A. (2011) A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis. b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534. c) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57. d) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>. e) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554> f) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>. g) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010> Furher, we include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Compositional versions 3.4 dated 2019-03-12 and 3.5 dated 2019-06-18
Compositional-3.4/Compositional/man/pcr.tune.Rd |only Compositional-3.5/Compositional/DESCRIPTION | 10 - Compositional-3.5/Compositional/MD5 | 103 +++++------ Compositional-3.5/Compositional/NAMESPACE | 2 Compositional-3.5/Compositional/R/a.mle.R | 2 Compositional-3.5/Compositional/R/alfa.knn.R | 2 Compositional-3.5/Compositional/R/alfaknn.tune.R | 31 +-- Compositional-3.5/Compositional/R/alfapcr.tune.R | 42 +--- Compositional-3.5/Compositional/R/alfarda.tune.R | 19 -- Compositional-3.5/Compositional/R/alfareg.tune.R | 67 +++---- Compositional-3.5/Compositional/R/alfaridge.tune.R | 61 +----- Compositional-3.5/Compositional/R/beta.reg.R |only Compositional-3.5/Compositional/R/comp.knn.R | 8 Compositional-3.5/Compositional/R/compknn.tune.R | 27 +- Compositional-3.5/Compositional/R/compppr.tune.R |only Compositional-3.5/Compositional/R/diri.est.R | 14 - Compositional-3.5/Compositional/R/diri.reg.R | 4 Compositional-3.5/Compositional/R/diri.reg2.R | 1 Compositional-3.5/Compositional/R/glmpcr.tune.R | 46 ++-- Compositional-3.5/Compositional/R/js.compreg.R | 11 - Compositional-3.5/Compositional/R/klalfapcr.tune.R | 35 +-- Compositional-3.5/Compositional/R/makefolds.R |only Compositional-3.5/Compositional/R/mkde.R | 4 Compositional-3.5/Compositional/R/multinompcr.tune.R | 55 ++--- Compositional-3.5/Compositional/R/ols.compreg.R | 11 - Compositional-3.5/Compositional/R/pcr.tune.R | 53 ++--- Compositional-3.5/Compositional/R/rcompnorm.R | 2 Compositional-3.5/Compositional/R/rda.tune.R | 62 ++---- Compositional-3.5/Compositional/R/ridge.tune.R | 57 ++---- Compositional-3.5/Compositional/R/zadr.R | 6 Compositional-3.5/Compositional/R/zeroreplace.R |only Compositional-3.5/Compositional/man/Compositional-package.Rd | 10 - Compositional-3.5/Compositional/man/a.est.Rd | 1 Compositional-3.5/Compositional/man/alfa.Rd | 1 Compositional-3.5/Compositional/man/alfa.pcr.Rd | 1 Compositional-3.5/Compositional/man/alfa.profile.Rd | 3 Compositional-3.5/Compositional/man/alfa.reg.Rd | 1 Compositional-3.5/Compositional/man/alfa.ridge.Rd | 3 Compositional-3.5/Compositional/man/alfa.tune.Rd | 5 Compositional-3.5/Compositional/man/alfadist.Rd | 11 - Compositional-3.5/Compositional/man/alfainv.Rd | 11 - Compositional-3.5/Compositional/man/alfapcr.tune.Rd | 16 - Compositional-3.5/Compositional/man/alfarda.tune.Rd | 30 +-- Compositional-3.5/Compositional/man/alfareg.tune.Rd | 17 - Compositional-3.5/Compositional/man/alfaridge.tune.Rd | 22 +- Compositional-3.5/Compositional/man/alpha.mle.Rd | 1 Compositional-3.5/Compositional/man/beta.reg.Rd |only Compositional-3.5/Compositional/man/comp.ppr.Rd | 2 Compositional-3.5/Compositional/man/compknn.tune.Rd | 39 ++-- Compositional-3.5/Compositional/man/compppr.tune.Rd |only Compositional-3.5/Compositional/man/frechet.Rd | 1 Compositional-3.5/Compositional/man/glmpcr.tune.Rd | 28 +- Compositional-3.5/Compositional/man/klalfapcr.tune.Rd | 16 - Compositional-3.5/Compositional/man/makefolds.Rd |only Compositional-3.5/Compositional/man/rda.tune.Rd | 33 ++- Compositional-3.5/Compositional/man/ridge.tune.Rd | 20 +- Compositional-3.5/Compositional/man/zeroreplace.Rd |only 57 files changed, 474 insertions(+), 533 deletions(-)
Title: Prevalence to Incidence Calculations for Point-Prevalence
Studies in a Nosocomial Setting
Description: Functions to simulate point prevalence studies (PPSs) of healthcare-associated infections (HAIs) and to convert prevalence to incidence in steady state setups.
Companion package to the preprint Willrich et al., From prevalence to incidence - a new approach in the hospital setting;
<doi:10.1101/554725> , where methods are explained in detail.
Author: Niklas Willrich [aut, cre]
Maintainer: Niklas Willrich <WillrichN@rki.de>
Diff between prevtoinc versions 0.11.0 dated 2019-03-10 and 0.12.0 dated 2019-06-18
DESCRIPTION | 10 +- MD5 | 34 ++++---- NAMESPACE | 3 NEWS.md |only R/CIfunctions.R |only R/calculateIfunctions.R | 4 R/estimationfunctions.R | 6 - R/simulationsfunctions.R | 152 ++++++++++++++++++++++++++++++++++--- README.md |only inst/doc/prevtoinc_vignette.R | 8 + inst/doc/prevtoinc_vignette.Rmd | 14 +++ inst/doc/prevtoinc_vignette.html | 114 +++++++++++++++++---------- man/CI_np_bs.Rd |only man/calculate_CI_I_pp.Rd |only man/create_patient_history_add.Rd |only man/monotone_smoother.Rd | 5 - man/simulate_incidence_stats.Rd | 5 - tests/testthat/refdata/Idf4.Rds |binary tests/testthat/refdata/datapps.Rds |binary tests/testthat/testsestimation.R | 32 +++++-- vignettes/prevtoinc_vignette.Rmd | 14 +++ 21 files changed, 304 insertions(+), 97 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
(<https://orcid.org/0000-0002-2568-6489>),
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 1.7.0 dated 2018-11-06 and 1.8.0 dated 2019-06-18
DESCRIPTION | 15 LICENSE |only MD5 | 247 ++++---- NAMESPACE | 179 +++--- NEWS | 96 +-- R/LawTable.R | 212 +++---- R/LifeTable.R | 934 +++++++++++++++++-------------- R/MortalityLaw_S3.R | 322 +++++----- R/MortalityLaw_check.R | 92 +-- R/MortalityLaw_main.R | 676 +++++++++++------------ R/MortalityLaw_models.R | 1027 +++++++++++++++++------------------ R/MortalityLaws-data.R | 44 - R/MortalityLaws-package.R | 43 - R/availableHMD.R | 111 ++- R/availableLF.R | 114 ++- R/availableLaws.R | 324 +++++------ R/convertFx.R | 158 ++--- R/graphics.R | 168 ++--- R/readAHMD.R |only R/readCHMD.R |only R/readHMD.R | 635 +++++++++++---------- R/readJMD.R |only R/utils.R | 83 +- R/zzz.R | 16 README.md | 93 +-- THANKS | 28 build/vignette.rds |binary inst/doc/Installation.R | 24 inst/doc/Installation.Rmd | 122 ++-- inst/doc/Installation.pdf |binary inst/doc/Intro.R | 236 ++++---- inst/doc/Intro.Rmd | 486 ++++++++-------- inst/doc/Intro.pdf |binary man/AIC.MortalityLaw.Rd | 30 - man/AUSregions.Rd |only man/CANregions.Rd |only man/HMDcountries.Rd | 24 man/HMDindices.Rd |only man/HP.Rd | 42 - man/HP2.Rd | 42 - man/HP3.Rd | 42 - man/HP4.Rd | 42 - man/JPNregions.Rd |only man/LawTable.Rd | 234 +++---- man/LifeTable.Rd | 229 ++++--- man/LifeTable.check.Rd | 30 - man/LifeTable.core.Rd | 85 +- man/MortalityLaw.Rd | 320 +++++----- man/MortalityLaws.Rd | 74 +- man/ReadAHMD.Rd |only man/ReadCHMD.Rd |only man/ReadHMD.Rd | 219 ++++--- man/ReadHMD.core.Rd | 99 +-- man/ReadJMD.Rd |only man/addDetails.Rd | 52 - man/ageMsg.Rd |only man/ahmd.Rd | 58 - man/availableHMD.Rd | 69 +- man/availableLF.Rd | 52 - man/availableLaws.Rd | 208 +++---- man/beard.Rd | 42 - man/beard_makeham.Rd | 42 - man/bring_parameters.Rd | 40 - man/carriere1.Rd | 42 - man/carriere2.Rd | 42 - man/check.MortalityLaw.Rd | 30 - man/check_input_ReadAHMD.Rd |only man/check_input_ReadCHMD.Rd |only man/check_input_ReadHMD.Rd | 30 - man/check_input_ReadJMD.Rd |only man/choose_optim.Rd | 30 - man/coale.demeny.ax.Rd | 62 +- man/compute.ax.Rd | 46 - man/convertFx.Rd | 120 ++-- man/data_format.Rd |only man/deviance.MortalityLaw.Rd | 30 - man/df.residual.MortalityLaw.Rd | 30 - man/dx_lx.Rd | 34 - man/find.my.case.Rd | 57 - man/ggompertz.Rd | 42 - man/gompertz.Rd | 42 - man/gompertz0.Rd | 42 - man/head_tail.Rd | 54 - man/invgompertz.Rd | 44 - man/invweibull.Rd | 48 - man/kannisto.Rd | 42 - man/kannisto_makeham.Rd | 42 - man/kostaki.Rd | 42 - man/logLik.MortalityLaw.Rd | 30 - man/makeham.Rd | 42 - man/makeham0.Rd | 42 - man/martinelle.Rd | 42 - man/mx_qx.Rd | 44 - man/objective_fun.Rd | 76 +- man/opperman.Rd | 42 - man/perks.Rd | 42 - man/plot.MortalityLaw.Rd | 52 - man/predict.MortalityLaw.Rd | 70 +- man/print.LifeTable.Rd | 34 - man/print.MortalityLaw.Rd | 34 - man/print.ReadAHMD.Rd |only man/print.ReadCHMD.Rd |only man/print.ReadHMD.Rd | 34 - man/print.ReadJMD.Rd |only man/print.availableHMD.Rd | 34 - man/print.availableLF.Rd | 34 - man/print.availableLaws.Rd | 34 - man/print.summary.MortalityLaw.Rd | 34 - man/quadratic.Rd | 42 - man/rogersplanck.Rd | 42 - man/saveMsg.Rd |only man/saveOutput.Rd |only man/scale_x.Rd | 30 - man/siler.Rd | 42 - man/strehler_mildvan.Rd | 42 - man/substrRight.Rd |only man/summary.MortalityLaw.Rd | 40 - man/thiele.Rd | 42 - man/uxAbove100.Rd | 48 - man/vandermaen.Rd | 42 - man/vandermaen2.Rd | 42 - man/weibull.Rd | 50 - man/wittstein.Rd | 42 - tests/testthat.R | 14 tests/testthat/test_LawTable.R | 60 +- tests/testthat/test_LifeTable.R | 207 +++---- tests/testthat/test_MortalityLaws.R | 259 ++++---- tests/testthat/test_MortalityLaws2.R | 460 +++++++-------- tests/testthat/test_ReadAHMD.R |only tests/testthat/test_ReadCHMD.R |only tests/testthat/test_ReadHMD.R | 135 ++-- tests/testthat/test_ReadJMD.R |only tests/testthat/test_availableX.R | 59 +- tests/testthat/test_convertFx.R | 106 +-- vignettes/Installation.Rmd | 122 ++-- vignettes/Intro.Rmd | 486 ++++++++-------- vignettes/Mlaw_Refrences.bib | 420 +++++++------- 137 files changed, 6723 insertions(+), 6340 deletions(-)
Title: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data
Description: Identifying labeled compounds in a 13C-tracer experiment in non-targeted fashion is a cumbersome process. This package facilitates such type of analyses
by providing high level quality control plots, deconvoluting and evaluating spectra and performing a multitude of tests in an automatic fashion.
The main idea is to use changing intensity ratios of ion pairs from peak list generated with 'xcms' as candidates and evaluate those against
base peak chromatograms and spectra information within the raw measurement data automatically.
The functionality is described in Hoffmann et al. (2018) <doi:10.1021/acs.analchem.8b00356>.
Author: Jan Lisec [aut, cre],
Friederike Hoffmann [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between HiResTEC versions 0.58 dated 2019-06-13 and 0.59 dated 2019-06-18
HiResTEC-0.58/HiResTEC/R/dat-data.R |only HiResTEC-0.58/HiResTEC/R/xg-data.R |only HiResTEC-0.58/HiResTEC/data/dat.RData |only HiResTEC-0.58/HiResTEC/data/datalist |only HiResTEC-0.58/HiResTEC/data/xg.RData |only HiResTEC-0.58/HiResTEC/man/dat.Rd |only HiResTEC-0.58/HiResTEC/man/xg.Rd |only HiResTEC-0.59/HiResTEC/DESCRIPTION | 9 +-- HiResTEC-0.59/HiResTEC/MD5 | 27 +++------- HiResTEC-0.59/HiResTEC/R/DeconvoluteSpectrum.R | 7 +- HiResTEC-0.59/HiResTEC/R/EvaluateCandidateListAgainstRawData.R | 15 +---- HiResTEC-0.59/HiResTEC/R/EvaluatePairsFromXCMSSet.R | 11 +--- HiResTEC-0.59/HiResTEC/R/getMultipleBPC.R | 1 HiResTEC-0.59/HiResTEC/R/xcms_cand-data.R | 2 HiResTEC-0.59/HiResTEC/man/DeconvoluteSpectrum.Rd | 7 +- HiResTEC-0.59/HiResTEC/man/EvaluateCandidateListAgainstRawData.Rd | 15 +---- HiResTEC-0.59/HiResTEC/man/EvaluatePairsFromXCMSSet.Rd | 10 --- HiResTEC-0.59/HiResTEC/man/xcms_cand.Rd | 2 18 files changed, 35 insertions(+), 71 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Yixuan Qiu [ctb],
R Core Team [cph] (Cairo code from X11 device),
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.1.8 dated 2019-04-02 and 0.1.9 dated 2019-06-18
DESCRIPTION | 6 +-- MD5 | 33 ++++++++++-------- NEWS | 5 ++ R/RcppExports.R | 77 +++++-------------------------------------- R/cpp-proxies.R |only R/fontconfig.R | 12 ++++++ R/helpers-locale.R |only R/load.R | 2 + R/m_str_extents.R | 4 ++ R/raster.R | 3 + man/glyphs_match.Rd | 2 - man/raster_write.Rd | 3 + man/str_extents.Rd | 2 - man/str_metrics.Rd | 2 - man/sys_fonts.Rd | 2 - src/RcppExports.cpp | 40 +++++++++++----------- src/font_metrics.cpp | 54 +----------------------------- src/sys_fonts.cpp | 15 -------- tests/testthat/test-locale.R |only 19 files changed, 86 insertions(+), 176 deletions(-)
Title: Read, Manipulate, Explore Chess PGN Files and R API to UCI Chess
Engines
Description: Provides functions for reading *.PGN files with more than one game, including large files without copying it into RAM (using 'ff' package or 'RSQLite' package). Handle chess data and chess aggregated data, count figure moves statistics, create player profile, plot winning chances, browse openings. Set of functions of R API to communicate with UCI-protocol based chess engines.
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>
Diff between bigchess versions 1.3.2 dated 2019-05-15 and 1.5.2 dated 2019-06-18
DESCRIPTION | 17 +- MD5 | 43 ++++- NAMESPACE | 21 ++ R/eco.R |only R/lan2san.R |only R/misc.R | 410 ++++++++++++++++++++++++++++++++++++++++++++++++++ R/san2lan.R |only R/uci_cmd.R |only R/uci_debug.R |only R/uci_engine.R |only R/uci_go.R |only R/uci_isready.R |only R/uci_parse.R |only R/uci_ponderhit.R |only R/uci_position.R |only R/uci_quit.R |only R/uci_read.R |only R/uci_register.R |only R/uci_setoption.R |only R/uci_stop.R |only R/uci_uci.R |only R/uci_ucinewgame.R |only data/eco.RData |only man/eco.Rd |only man/lan2san.Rd |only man/san2lan.Rd |only man/uci_cmd.Rd |only man/uci_debug.Rd |only man/uci_engine.Rd |only man/uci_go.Rd |only man/uci_isready.Rd |only man/uci_parse.Rd |only man/uci_ponderhit.Rd |only man/uci_position.Rd |only man/uci_quit.Rd |only man/uci_read.Rd |only man/uci_register.Rd |only man/uci_setoption.Rd |only man/uci_stop.Rd |only man/uci_uci.Rd |only man/uci_ucinewgame.Rd |only 41 files changed, 480 insertions(+), 11 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.6-60 dated 2018-09-28 and 0.6-99 dated 2019-06-18
DESCRIPTION | 12 +- MD5 | 187 ++++++++++++++++++------------------ NAMESPACE | 58 ++++++++--- R/anc.ML.R | 3 R/ancThresh.R | 3 R/bd.R | 12 +- R/brownie.lite.R | 75 ++++++++++---- R/brownieREML.R | 7 - R/cophylo.R | 64 ++++++++---- R/densityMap.R | 25 ++++ R/dotTree.R | 53 +++++++--- R/estDiversity.R | 31 ++++- R/evol.rate.mcmc.R | 153 +++++++++++++++++++++++++++-- R/evolvcv.lite.R | 171 +++++++++++++++++++-------------- R/fancyTree.R | 144 ++++++++++++++------------- R/fastAnc.R | 8 - R/fitDiversityModel.R | 65 ++++++++++-- R/fitpolyMk.R |only R/ltt.R | 67 +++++++++++- R/ltt95.R | 64 +++++++++--- R/make.simmap.R | 6 - R/mcmcMk.R | 182 +++++++++++++++++++++++++++++++++-- R/multiRF.R | 4 R/optim.phylo.ls.R | 4 R/pgls.Ives.R | 5 R/phylo.impute.R |only R/phylo.to.map.R | 71 ++++++++++--- R/plotTree.wBars.R | 46 ++++++-- R/ratebystate.R | 4 R/ratebytree.R | 3 R/rerootingMethod.R | 2 R/sim.history.R | 5 R/utilities.R | 228 ++++++++++++++++++++++++++++++++++++-------- man/add.species.to.genus.Rd | 6 - man/anc.ML.Rd | 2 man/applyBranchLengths.Rd | 2 man/bd.Rd | 4 man/bind.tip.Rd | 2 man/bmPlot.Rd | 10 + man/branching.diffusion.Rd | 4 man/brownie.lite.Rd | 4 man/brownieREML.Rd | 6 - man/collapse.to.star.Rd | 2 man/compare.chronograms.Rd | 2 man/contMap.Rd | 8 - man/countSimmap.Rd | 6 - man/di2multi.simmap.Rd | 29 ++++- man/dotTree.Rd | 2 man/evol.rate.mcmc.Rd | 15 ++ man/evol.vcv.Rd | 8 - man/evolvcv.lite.Rd | 2 man/exhaustiveMP.Rd | 4 man/fancyTree.Rd | 30 +++++ man/fastAnc.Rd | 4 man/fastMRCA.Rd | 8 - man/findMRCA.Rd | 8 - man/fit.bd.Rd | 22 +++- man/fitDiversityModel.Rd | 10 + man/fitMk.Rd | 27 +++-- man/force.ultrametric.Rd | 4 man/gammatest.Rd | 12 -- man/genSeq.Rd | 8 - man/geo.legend.Rd | 10 + man/get.treepos.Rd | 13 +- man/getDescendants.Rd | 4 man/getExtant.Rd | 4 man/getSisters.Rd | 4 man/ladderize.simmap.Rd | 6 - man/lambda.transform.Rd | 5 man/likMlambda.Rd | 12 +- man/ls.tree.Rd | 5 man/ltt.Rd | 9 + man/ltt95.Rd | 6 - man/make.era.map.Rd | 6 - man/make.simmap.Rd | 24 ++-- man/map.overlap.Rd | 4 man/map.to.singleton.Rd | 16 ++- man/markChanges.Rd | 2 man/matchNodes.Rd | 15 +- man/mergeMappedStates.Rd | 8 - man/midpoint.root.Rd | 6 - man/minRotate.Rd | 6 - man/minSplit.Rd | 4 man/modified.Grafen.Rd | 5 man/mrp.supertree.Rd | 14 +- man/multi.mantel.Rd | 4 man/multiC.Rd | 4 man/optim.phylo.ls.Rd | 4 man/phyl.pca.Rd | 2 man/phyl.vcv.Rd | 5 man/phylANOVA.Rd | 2 man/phylo.impute.Rd |only man/phylo.to.map.Rd | 8 - man/phylo.toBackbone.Rd | 2 man/ratebytree.Rd | 8 + man/setMap.Rd | 14 +- 96 files changed, 1609 insertions(+), 645 deletions(-)
Title: Measuring Multivariate Dependence Using Distance Multivariance
Description: Distance multivariance is a measure of dependence which can be used to detect
and quantify dependence. The necessary functions are implemented in this packages,
and examples are given. For the theoretic background we refer to the papers:
B. Böttcher, Dependence and Dependence Structures: Estimation and Visualization Using Distance Multivariance. <arXiv:1712.06532>.
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Detecting independence of random vectors: generalized distance covariance and Gaussian covariance. VMSTA, 2018, Vol. 5, No. 3, 353-383. <arXiv:1711.07778>.
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Distance multivariance: New dependence measures for random vectors. <arXiv:1711.07775>.
G. Berschneider, B. Böttcher, On complex Gaussian random fields, Gaussian quadratic forms and sample distance multivariance. <arXiv:1808.07280>.
Author: Björn Böttcher [aut, cre],
Martin Keller-Ressel [ctb]
Maintainer: Björn Böttcher <bjoern.boettcher@tu-dresden.de>
Diff between multivariance versions 2.1.0 dated 2019-03-19 and 2.2.0 dated 2019-06-18
DESCRIPTION | 10 MD5 | 43 + NAMESPACE | 1 R/RcppExports.R | 19 R/multivariance-functions.R | 841 +++++++++++++++++++++++++++++++----- inst/NEWS | 21 man/cdm.mu.bcd.Rd | 3 man/cdms.mu.bcd.Rd | 2 man/circle.coordinates.Rd |only man/clean.graph.Rd | 30 + man/dependence.structure.Rd | 34 + man/dependence.structure.full.Rd |only man/doubleCenterSymMat.Rd | 4 man/find.cluster.Rd | 15 man/layout_on_circles.Rd |only man/lower.order.Rd |only man/match.rows.Rd |only man/match_rows.Rd |only man/multicorrelation.Rd | 2 man/multivariance.pvalue.Rd | 2 man/pearson.pvalue.Rd | 6 man/pearson.qf.Rd | 4 src/RcppExports.cpp | 13 src/multivariance.cpp | 37 + tests/testthat/Rplots.pdf |only tests/testthat/testmultivariances.R | 110 ++++ 26 files changed, 1043 insertions(+), 154 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.3 dated 2018-11-14 and 0.3.4 dated 2019-06-18
anytime-0.3.3/anytime/inst/doc/anytime-introduction.R |only anytime-0.3.3/anytime/inst/doc/anytime-introduction.Rmd |only anytime-0.3.3/anytime/tests/allFormats.R |only anytime-0.3.3/anytime/tests/assertions.R |only anytime-0.3.3/anytime/tests/bulkTest.R |only anytime-0.3.3/anytime/tests/gh_issue_12.R |only anytime-0.3.3/anytime/tests/gh_issue_33.R |only anytime-0.3.3/anytime/tests/gh_issue_5.R |only anytime-0.3.3/anytime/tests/gh_issue_56.R |only anytime-0.3.3/anytime/tests/gh_issues_36_51.R |only anytime-0.3.3/anytime/tests/r_anytime.R |only anytime-0.3.3/anytime/tests/simpleTests.R |only anytime-0.3.3/anytime/tests/utilities.R |only anytime-0.3.3/anytime/tests/validate.R |only anytime-0.3.3/anytime/vignettes/anytime-introduction.Rmd |only anytime-0.3.3/anytime/vignettes/anytime.bib |only anytime-0.3.4/anytime/ChangeLog | 151 +++++++++++++++ anytime-0.3.4/anytime/DESCRIPTION | 11 - anytime-0.3.4/anytime/MD5 | 73 +++---- anytime-0.3.4/anytime/NAMESPACE | 1 anytime-0.3.4/anytime/R/RcppExports.R | 8 anytime-0.3.4/anytime/R/anytime.R | 14 + anytime-0.3.4/anytime/R/assertions.R | 2 anytime-0.3.4/anytime/R/formats.R | 20 + anytime-0.3.4/anytime/README.md | 11 + anytime-0.3.4/anytime/build/partial.rdb |binary anytime-0.3.4/anytime/build/vignette.rds |binary anytime-0.3.4/anytime/cleanup | 4 anytime-0.3.4/anytime/inst/NEWS.Rd | 13 + anytime-0.3.4/anytime/inst/doc/anytime-introduction.Rnw |only anytime-0.3.4/anytime/inst/doc/anytime-introduction.pdf |binary anytime-0.3.4/anytime/inst/tinytest |only anytime-0.3.4/anytime/man/anytime.Rd | 12 + anytime-0.3.4/anytime/man/assertDate.Rd | 2 anytime-0.3.4/anytime/man/getFormats.Rd | 6 anytime-0.3.4/anytime/man/iso8601.Rd | 5 anytime-0.3.4/anytime/src/Makevars |only anytime-0.3.4/anytime/src/Makevars.win |only anytime-0.3.4/anytime/src/RcppExports.cpp | 11 + anytime-0.3.4/anytime/src/anytime.cpp | 39 +++ anytime-0.3.4/anytime/tests/tinytest.R |only anytime-0.3.4/anytime/vignettes/anytime-intro.pdf |only anytime-0.3.4/anytime/vignettes/anytime-introduction.Rnw |only 43 files changed, 325 insertions(+), 58 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty).
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>
Diff between mexhaz versions 1.5 dated 2018-04-15 and 1.6 dated 2019-06-18
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 3 ++- NEWS | 18 ++++++++++++++++++ R/lines.predMexhaz.R |only R/mexhaz.R | 7 +------ R/points.predMexhaz.R | 12 ++++++------ R/summary.mexhaz.R | 2 +- R/update.mexhaz.R | 7 ++++++- man/lines.predMexhaz.Rd |only man/mexhaz-package.Rd | 4 ++-- man/points.predMexhaz.Rd | 7 ++++--- 12 files changed, 55 insertions(+), 33 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 0.9.1 dated 2019-06-10 and 0.9.2 dated 2019-06-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/FileSurveyInput.R | 13 ++++++++++--- R/jsSurveyGadget.R | 12 +++++++++--- inst/doc/jsmodule.html | 4 ++-- 6 files changed, 34 insertions(+), 17 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data (including massive, with millions of observations, data) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>, P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2019). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing (to appear). <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 3.7 dated 2019-04-19 and 3.8 dated 2019-06-18
Directional-3.7/Directional/man/ESAGdensity.Rd |only Directional-3.8/Directional/DESCRIPTION | 13 ++- Directional-3.8/Directional/MD5 | 57 +++++++++-------- Directional-3.8/Directional/NAMESPACE | 13 ++- Directional-3.8/Directional/R/ESAGmle.R | 3 Directional-3.8/Directional/R/conc.test.R | 4 - Directional-3.8/Directional/R/dirda.cv.R | 1 Directional-3.8/Directional/R/dirknn.R | 12 +-- Directional-3.8/Directional/R/dirknn.tune.R | 27 +++----- Directional-3.8/Directional/R/iag.density.R |only Directional-3.8/Directional/R/iag.reg.R | 4 - Directional-3.8/Directional/R/kent.mle.R | 31 ++++++--- Directional-3.8/Directional/R/knnreg.tune.R | 55 +++++++--------- Directional-3.8/Directional/R/kuiper.R | 2 Directional-3.8/Directional/R/makefolds.R | 3 Directional-3.8/Directional/R/mediandir_2.R | 3 Directional-3.8/Directional/R/purka.density.R |only Directional-3.8/Directional/R/read.big.data.R |only Directional-3.8/Directional/R/rwrapcauchy.R |only Directional-3.8/Directional/R/spml.density.R |only Directional-3.8/Directional/R/tang.conc.R | 4 - Directional-3.8/Directional/R/vec.R | 6 + Directional-3.8/Directional/R/vmf.R | 7 +- Directional-3.8/Directional/R/vmf.reg.R | 3 Directional-3.8/Directional/R/watson.R | 2 Directional-3.8/Directional/R/wrapcauchy.density.R |only Directional-3.8/Directional/man/Directional-package.Rd | 8 +- Directional-3.8/Directional/man/dirknn.tune.Rd | 22 ++++-- Directional-3.8/Directional/man/kent.density.Rd | 31 ++++----- Directional-3.8/Directional/man/knnreg.tune.Rd | 21 +++--- Directional-3.8/Directional/man/read.big.data.Rd |only Directional-3.8/Directional/man/rvonmises.Rd | 24 +++++-- Directional-3.8/Directional/man/vm.density.Rd | 21 ++++-- Directional-3.8/Directional/man/vmf.density.Rd |only 34 files changed, 215 insertions(+), 162 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'FCI' (fast causal inference),
'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.2.2 dated 2018-05-18 and 0.2.4 dated 2019-06-18
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/getParents.R | 3 ++- R/getParentsStable.R | 3 ++- R/getRanking.R | 3 ++- R/runGIES.R | 6 ++++-- demo/simulation.R | 37 +++++++++++++++---------------------- man/getParents.Rd | 23 +++++++++++------------ man/getParentsStable.Rd | 18 +++++++++--------- man/getRanking.Rd | 24 ++++++++++++------------ man/simulateInterventions.Rd | 6 +++--- 11 files changed, 75 insertions(+), 78 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Polynomials in R
Description: Implements univariate polynomial operations in R, including
polynomial arithmetic, finding zeros, plotting, and some operations on
lists of polynomials.
Author: Bill Venables, with contribution by Kurt Hornik and Georgi Boshnakov
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between PolynomF versions 2.0-0 dated 2019-04-24 and 2.0-2 dated 2019-06-18
DESCRIPTION | 10 - MD5 | 49 +++-- NAMESPACE | 8 R/Orthogonal_polynomials.R | 98 +++------- R/PolynomF.R | 207 ++++++++++++++++------- build/vignette.rds |binary inst/doc/polynomials.R | 209 ++++++++++++++--------- inst/doc/polynomials.Rmd | 396 +++++++++++++++++++++++++++++--------------- inst/doc/polynomials.pdf |binary man/change_origin.Rd | 3 man/coef.polynom.Rd | 2 man/defunct.Rd |only man/deriv.polynom.Rd | 2 man/plot.polynom.Rd | 15 + man/poly_calc.Rd | 9 - man/poly_orth_general.Rd | 11 - man/polynom.Rd | 35 +-- man/zap.Rd | 5 vignettes/polynomials.Rmd | 396 +++++++++++++++++++++++++++++--------------- vignettes/polynomials_files |only 20 files changed, 918 insertions(+), 537 deletions(-)
Title: Adaptive Empirical Pattern Transformation
Description: Designed for optimal use in performing fast,
accurate walking strides segmentation from high-density
data collected from a wearable accelerometer worn
during continuous walking activity.
Author: Marta Karas [aut, cre] (<https://orcid.org/0000-0001-5889-3970>),
Jacek Urbanek [aut] (<https://orcid.org/0000-0002-1890-8899>),
Ciprian Crainiceanu [aut],
John Muschelli [ctb] (<https://orcid.org/0000-0001-6469-1750>),
Adi Gherman [ctb]
Maintainer: Marta Karas <marta.karass@gmail.com>
Diff between adept versions 1.0.1 dated 2019-05-24 and 1.1.2 dated 2019-06-18
DESCRIPTION | 8 +-- MD5 | 34 ++++++++-------- NAMESPACE | 3 - NEWS.md | 5 ++ R/similarityMatrix.R | 29 +++++++------ R/windowSmooth.R | 16 ------- inst/doc/adept-intro.Rmd | 2 inst/doc/adept-intro.html | 65 ++++++++++++++++--------------- inst/doc/adept-strides-segmentation.Rmd | 2 inst/doc/adept-strides-segmentation.html | 47 +++++++++++----------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-5-2.png |binary man/figures/README-unnamed-chunk-5-3.png |binary man/figures/README-unnamed-chunk-8-1.png |binary tests/testthat/test-segmentPattern.R | 63 +++++------------------------- vignettes/adept-intro.Rmd | 2 vignettes/adept-strides-segmentation.Rmd | 2 18 files changed, 119 insertions(+), 159 deletions(-)
Title: Tools for Making and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games.
This package is an alternative to the earlier sudoku-solver package,
'sudoku'. The present package uses a slightly different algorithm, has a
simpler coding and presents a few more sugar tools, such as plot and print
methods. Solved sudoku games are of some interest in Experimental Design
as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between sudokuAlt versions 0.1-11 dated 2017-05-13 and 0.2-0 dated 2019-06-18
DESCRIPTION | 16 MD5 | 50 +- NAMESPACE | 47 +- R/sudokuAlt.R | 1023 ++++++++++++++++++++++++++---------------------- build |only inst |only man/as.sudoku.Rd | 66 +-- man/as.sudoku.matrix.Rd | 50 +- man/as.sudoku.sudoku.Rd | 44 +- man/daysAgo.Rd | 58 +- man/designGame.Rd |only man/emptyGame.Rd | 59 +- man/fetchAUGame.Rd | 68 +-- man/fetchUKGame.Rd | 74 +-- man/makeGame.Rd | 68 +-- man/originalGame.Rd | 60 +- man/plot.sudoku.Rd | 74 +-- man/print.sudoku.Rd | 50 +- man/reexports.Rd | 32 - man/regulariseGame.Rd |only man/seedGame.Rd | 60 +- man/solve.sudoku.Rd | 70 +-- man/solveGame.Rd | 72 +-- vignettes |only 24 files changed, 1091 insertions(+), 950 deletions(-)
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph],
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.2.0 dated 2019-03-07 and 1.3.0 dated 2019-06-18
DESCRIPTION | 8 +++--- MD5 | 32 ++++++++++++------------ NAMESPACE | 1 NEWS | 15 +++++++++++ R/future.apply-package.R | 1 R/future_lapply.R | 56 ++++++++++++++++++++++++------------------- R/future_mapply.R | 49 ++++++++++++++++++++----------------- R/globals.R | 8 +++--- R/rng.R | 8 +++--- R/utils.R | 37 +++++++++++++++++++++++----- build/vignette.rds |binary man/future.apply.Rd | 1 man/future_apply.Rd | 5 +++ man/future_lapply.Rd | 12 +++++++-- man/future_mapply.Rd | 16 ++++++++---- tests/incl/start,load-only.R | 1 tests/utils.R | 11 ++++++-- 17 files changed, 170 insertions(+), 91 deletions(-)
Title: Web Application Framework for 'PhUSE' Scripts
Description: Make it easy to review, download and execute scripts stored in Github
'phuse-scripts' repository <https://github.com/phuse-org/phuse-scripts>. Some examples
included show the web application framework using the script metadata. The 'PhUSE'
is Pharmaceutical Users Software Exchange <http://www.phuse.eu>.
Author: Hanming Tu [aut, cre]
Maintainer: Hanming Tu <hanming.tu@gmail.com>
Diff between phuse versions 0.1.7 dated 2019-01-02 and 0.1.8 dated 2019-06-18
DESCRIPTION | 8 MD5 | 70 +-- NAMESPACE | 91 ++-- NEWS.md | 106 ++--- R/clone_github.R |only R/crt_workdir.R | 107 ++--- R/merge_lists.R | 112 ++--- R/search_api.R |only R/search_github.R | 10 R/start_app.R |only R/start_phuse.R | 140 +++---- inst/examples/02_display/DESCRIPTION | 14 inst/examples/02_display/app.R | 691 ++++++++++++++++++----------------- man/build_inputs.Rd | 58 +- man/build_script_df.Rd | 108 ++--- man/chk_workdir.Rd | 58 +- man/clone_github.Rd |only man/create_dir.Rd | 60 +-- man/crt_workdir.Rd | 66 +-- man/cvt_class2df.Rd | 50 +- man/cvt_list2df.Rd | 62 +-- man/download_fns.Rd | 68 +-- man/download_script.Rd | 68 +-- man/download_script_files.Rd | 66 +-- man/echo_msg.Rd | 90 ++-- man/extract_fns.Rd | 56 +- man/get_inputs.Rd | 64 +-- man/get_yml_inputs.Rd | 54 +- man/init_cfg.Rd | 58 +- man/is_empty.Rd | 50 +- man/merge_lists.Rd | 72 +-- man/read_yml.Rd | 54 +- man/resolve.Rd | 46 +- man/run_example.Rd | 72 +-- man/search_api.Rd |only man/search_github.Rd | 106 ++--- man/start_app.Rd |only man/start_phuse.Rd | 78 +-- man/url.exists.Rd | 54 +- 39 files changed, 1471 insertions(+), 1396 deletions(-)
Title: Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Shuchismita Sarkar [ctb],
Michael Hutt [ctb, cph],
Stephen Moshier [ctb, cph],
Rouben Rostamian [ctb, cph],
Carl Edward Rasmussen [ctb, cph],
Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between MatTransMix versions 0.1.1 dated 2019-04-06 and 0.1.2 dated 2019-06-18
MatTransMix-0.1.1/MatTransMix/demo/EMalgorithm.R |only MatTransMix-0.1.2/MatTransMix/DESCRIPTION | 8 MatTransMix-0.1.2/MatTransMix/MD5 | 29 - MatTransMix-0.1.2/MatTransMix/NEWS | 4 MatTransMix-0.1.2/MatTransMix/R/libMatTransFull.R | 8 MatTransMix-0.1.2/MatTransMix/demo/00Index | 3 MatTransMix-0.1.2/MatTransMix/demo/EMalgorithm1.R |only MatTransMix-0.1.2/MatTransMix/demo/EMalgorithm2.R |only MatTransMix-0.1.2/MatTransMix/man/MatTrans.EM.Rd | 9 MatTransMix-0.1.2/MatTransMix/src/MatTransMix.h | 62 +-- MatTransMix-0.1.2/MatTransMix/src/crosen1.c | 16 MatTransMix-0.1.2/MatTransMix/src/crosen2.c | 16 MatTransMix-0.1.2/MatTransMix/src/libFull.c | 414 +++++++++++++--------- MatTransMix-0.1.2/MatTransMix/src/libPsi.c | 24 - MatTransMix-0.1.2/MatTransMix/src/libSigma_1.c | 28 - MatTransMix-0.1.2/MatTransMix/src/libSigma_2.c | 28 - MatTransMix-0.1.2/MatTransMix/src/runFull.c | 8 17 files changed, 390 insertions(+), 267 deletions(-)