Title: Extending R's dendrogram functionality
Diff between dendextend versions 0.14.2 dated 2014-03-15 and 0.16.1 dated 2014-07-26
Description: Functions and methods for extending dendrogram objects in R.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
Gregory [ctb],
R core team [ctb] (Other than the Infastructure, some code came from
their examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Yoav Benjamini [ths]
Maintainer: Tal Galili
dendextend-0.14.2/dendextend/R/as.dendrogram.randomForest.r |only
dendextend-0.14.2/dendextend/R/attr_access.r |only
dendextend-0.14.2/dendextend/R/bk_method.r |only
dendextend-0.14.2/dendextend/R/color_branches.r |only
dendextend-0.14.2/dendextend/R/cor_bakers_gamma.r |only
dendextend-0.14.2/dendextend/R/cor_cophenetic.r |only
dendextend-0.14.2/dendextend/R/cut_lower_fun.r |only
dendextend-0.14.2/dendextend/R/cutree.dendrogram.r |only
dendextend-0.14.2/dendextend/R/dendextend-package.r |only
dendextend-0.14.2/dendextend/R/dendextend.r |only
dendextend-0.14.2/dendextend/R/entanglement.r |only
dendextend-0.14.2/dendextend/R/imports_stats.r |only
dendextend-0.14.2/dendextend/R/labels.r |only
dendextend-0.14.2/dendextend/R/labels_colors.r |only
dendextend-0.14.2/dendextend/R/nleaves.r |only
dendextend-0.14.2/dendextend/R/rotate.r |only
dendextend-0.14.2/dendextend/R/sample.dendrogram.r |only
dendextend-0.14.2/dendextend/R/tanglegram.r |only
dendextend-0.14.2/dendextend/R/trim.r |only
dendextend-0.14.2/dendextend/R/unbranch.r |only
dendextend-0.14.2/dendextend/R/untangle.r |only
dendextend-0.14.2/dendextend/R/zzz.r |only
dendextend-0.14.2/dendextend/demo/dendextend.r |only
dendextend-0.14.2/dendextend/inst/doc |only
dendextend-0.14.2/dendextend/inst/tests/test-attr_access.r |only
dendextend-0.14.2/dendextend/inst/tests/test-bk_method.r |only
dendextend-0.14.2/dendextend/inst/tests/test-cor_bakers_gamma.r |only
dendextend-0.14.2/dendextend/inst/tests/test-cut_lower_fun.r |only
dendextend-0.14.2/dendextend/inst/tests/test-cutree.dendrogram.r |only
dendextend-0.14.2/dendextend/inst/tests/test-entanglement.r |only
dendextend-0.14.2/dendextend/inst/tests/test-labels-assign.r |only
dendextend-0.14.2/dendextend/inst/tests/test-labels_colors.r |only
dendextend-0.14.2/dendextend/inst/tests/test-nleaves.r |only
dendextend-0.14.2/dendextend/inst/tests/test-rotate.r |only
dendextend-0.14.2/dendextend/inst/tests/test-trim.r |only
dendextend-0.14.2/dendextend/inst/tests/test-unbranch.r |only
dendextend-0.14.2/dendextend/inst/tests/test-untangle.r |only
dendextend-0.14.2/dendextend/tests/test-all.r |only
dendextend-0.16.1/dendextend/ChangeLog |only
dendextend-0.16.1/dendextend/DESCRIPTION | 44 -
dendextend-0.16.1/dendextend/MD5 | 262 +++---
dendextend-0.16.1/dendextend/NAMESPACE | 36
dendextend-0.16.1/dendextend/NEWS | 401 +++++-----
dendextend-0.16.1/dendextend/R/as.dendrogram.randomForest.R |only
dendextend-0.16.1/dendextend/R/attr_access.R |only
dendextend-0.16.1/dendextend/R/bk_method.R |only
dendextend-0.16.1/dendextend/R/branches_attr_by.R |only
dendextend-0.16.1/dendextend/R/color_branches.R |only
dendextend-0.16.1/dendextend/R/colored_bars.R |only
dendextend-0.16.1/dendextend/R/cor_bakers_gamma.R |only
dendextend-0.16.1/dendextend/R/cor_cophenetic.R |only
dendextend-0.16.1/dendextend/R/cut_lower_fun.R |only
dendextend-0.16.1/dendextend/R/cutree.dendrogram.R |only
dendextend-0.16.1/dendextend/R/d3dendrogram.R |only
dendextend-0.16.1/dendextend/R/dendextend-package.R |only
dendextend-0.16.1/dendextend/R/dendextend.R |only
dendextend-0.16.1/dendextend/R/dendlist.R |only
dendextend-0.16.1/dendextend/R/entanglement.R |only
dendextend-0.16.1/dendextend/R/imports_stats.R |only
dendextend-0.16.1/dendextend/R/labels.R |only
dendextend-0.16.1/dendextend/R/labels_colors.R |only
dendextend-0.16.1/dendextend/R/magrittr.R |only
dendextend-0.16.1/dendextend/R/nleaves.R |only
dendextend-0.16.1/dendextend/R/noded_with_condition.R |only
dendextend-0.16.1/dendextend/R/pvclust.R |only
dendextend-0.16.1/dendextend/R/rect.dendrogram.R |only
dendextend-0.16.1/dendextend/R/rotate.R |only
dendextend-0.16.1/dendextend/R/sample.dendrogram.R |only
dendextend-0.16.1/dendextend/R/set.dendrogram.R |only
dendextend-0.16.1/dendextend/R/tanglegram.R |only
dendextend-0.16.1/dendextend/R/trim.R |only
dendextend-0.16.1/dendextend/R/unbranch.R |only
dendextend-0.16.1/dendextend/R/untangle.R |only
dendextend-0.16.1/dendextend/R/zzz.R |only
dendextend-0.16.1/dendextend/README.md | 56 -
dendextend-0.16.1/dendextend/TODO |only
dendextend-0.16.1/dendextend/demo/dendextend.R |only
dendextend-0.16.1/dendextend/inst/tests/test-attr_access.R |only
dendextend-0.16.1/dendextend/inst/tests/test-bk_method.R |only
dendextend-0.16.1/dendextend/inst/tests/test-cor_bakers_gamma.R |only
dendextend-0.16.1/dendextend/inst/tests/test-cor_cophenetic.R |only
dendextend-0.16.1/dendextend/inst/tests/test-cut_lower_fun.R |only
dendextend-0.16.1/dendextend/inst/tests/test-cutree.dendrogram.R |only
dendextend-0.16.1/dendextend/inst/tests/test-dendlist.R |only
dendextend-0.16.1/dendextend/inst/tests/test-entanglement.R |only
dendextend-0.16.1/dendextend/inst/tests/test-labels-assign.R |only
dendextend-0.16.1/dendextend/inst/tests/test-labels_colors.R |only
dendextend-0.16.1/dendextend/inst/tests/test-nleaves.R |only
dendextend-0.16.1/dendextend/inst/tests/test-rotate.R |only
dendextend-0.16.1/dendextend/inst/tests/test-set.dendrogram.R |only
dendextend-0.16.1/dendextend/inst/tests/test-trim.R |only
dendextend-0.16.1/dendextend/inst/tests/test-unbranch.R |only
dendextend-0.16.1/dendextend/inst/tests/test-untangle.R |only
dendextend-0.16.1/dendextend/man/Bk.Rd | 69 -
dendextend-0.16.1/dendextend/man/Bk_permutations.Rd | 69 -
dendextend-0.16.1/dendextend/man/Bk_plot.Rd | 150 +--
dendextend-0.16.1/dendextend/man/DendSer.dendrogram.Rd |only
dendextend-0.16.1/dendextend/man/FM_index.Rd | 81 --
dendextend-0.16.1/dendextend/man/FM_index_R.Rd | 68 -
dendextend-0.16.1/dendextend/man/FM_index_permutation.Rd | 38
dendextend-0.16.1/dendextend/man/FM_index_profdpm.Rd | 91 +-
dendextend-0.16.1/dendextend/man/all_couple_rotations_at_k.Rd | 31
dendextend-0.16.1/dendextend/man/as.dendlist.Rd |only
dendextend-0.16.1/dendextend/man/as_hclust_fixed.Rd | 18
dendextend-0.16.1/dendextend/man/assign_dendextend_options.Rd | 1
dendextend-0.16.1/dendextend/man/assign_values_to_branches_edgePar.Rd | 33
dendextend-0.16.1/dendextend/man/assign_values_to_leaves_nodePar.Rd | 29
dendextend-0.16.1/dendextend/man/bakers_gamma_for_2_k_matrix.Rd | 16
dendextend-0.16.1/dendextend/man/branches_attr_by_clusters.Rd |only
dendextend-0.16.1/dendextend/man/branches_attr_by_labels.Rd |only
dendextend-0.16.1/dendextend/man/click_rotate.Rd |only
dendextend-0.16.1/dendextend/man/color_branches.Rd | 95 +-
dendextend-0.16.1/dendextend/man/color_labels.Rd | 59 -
dendextend-0.16.1/dendextend/man/colored_bars.Rd |only
dendextend-0.16.1/dendextend/man/cor_bakers_gamma.Rd | 90 --
dendextend-0.16.1/dendextend/man/cor_cophenetic.Rd | 79 +
dendextend-0.16.1/dendextend/man/count_terminal_nodes.Rd | 26
dendextend-0.16.1/dendextend/man/cut_lower_fun.Rd | 50 -
dendextend-0.16.1/dendextend/man/cutree-methods.Rd | 132 +--
dendextend-0.16.1/dendextend/man/cutree_1h.dendrogram.Rd | 35
dendextend-0.16.1/dendextend/man/cutree_1k.dendrogram.Rd | 65 -
dendextend-0.16.1/dendextend/man/dendextend-package.Rd | 4
dendextend-0.16.1/dendextend/man/dendextend_options.Rd | 16
dendextend-0.16.1/dendextend/man/dendlist.Rd |only
dendextend-0.16.1/dendextend/man/duplicate_leaf.Rd | 34
dendextend-0.16.1/dendextend/man/entanglement.Rd | 102 +-
dendextend-0.16.1/dendextend/man/fac2num.Rd | 24
dendextend-0.16.1/dendextend/man/fix_members_attr.dendrogram.Rd | 12
dendextend-0.16.1/dendextend/man/flatten.dendrogram.Rd | 19
dendextend-0.16.1/dendextend/man/flip_leaves.Rd | 21
dendextend-0.16.1/dendextend/man/get_branches_attr.Rd | 16
dendextend-0.16.1/dendextend/man/get_branches_heights.Rd | 24
dendextend-0.16.1/dendextend/man/get_childrens_heights.Rd | 5
dendextend-0.16.1/dendextend/man/get_leaves_attr.Rd | 23
dendextend-0.16.1/dendextend/man/get_nodes_attr.Rd | 35
dendextend-0.16.1/dendextend/man/hang.dendrogram.Rd | 32
dendextend-0.16.1/dendextend/man/heights_per_k.dendrogram.Rd | 32
dendextend-0.16.1/dendextend/man/identify.dendrogram.Rd |only
dendextend-0.16.1/dendextend/man/intersect_trees.Rd | 14
dendextend-0.16.1/dendextend/man/is.dendlist.Rd |only
dendextend-0.16.1/dendextend/man/is.dendrogram.Rd | 3
dendextend-0.16.1/dendextend/man/is.hclust.Rd | 3
dendextend-0.16.1/dendextend/man/is.natural.number.Rd | 17
dendextend-0.16.1/dendextend/man/is.phylo.Rd | 3
dendextend-0.16.1/dendextend/man/is_null_list.Rd |only
dendextend-0.16.1/dendextend/man/labels-assign.Rd | 50 -
dendextend-0.16.1/dendextend/man/labels_colors.Rd | 31
dendextend-0.16.1/dendextend/man/leaf_Colors.Rd | 11
dendextend-0.16.1/dendextend/man/lowest_common_branch.Rd | 20
dendextend-0.16.1/dendextend/man/match_order_by_labels.Rd | 27
dendextend-0.16.1/dendextend/man/match_order_dendrogram_by_old_order.Rd | 55 -
dendextend-0.16.1/dendextend/man/na_locf.Rd |only
dendextend-0.16.1/dendextend/man/nleaves.Rd | 35
dendextend-0.16.1/dendextend/man/nnodes.Rd | 16
dendextend-0.16.1/dendextend/man/noded_with_condition.Rd |only
dendextend-0.16.1/dendextend/man/order.dendrogram-assign.Rd | 13
dendextend-0.16.1/dendextend/man/order.hclust.Rd |only
dendextend-0.16.1/dendextend/man/pipe.Rd |only
dendextend-0.16.1/dendextend/man/plot.dendlist.Rd |only
dendextend-0.16.1/dendextend/man/plot_horiz.dendrogram.Rd | 88 --
dendextend-0.16.1/dendextend/man/prune.Rd | 15
dendextend-0.16.1/dendextend/man/prune_leaf.Rd | 8
dendextend-0.16.1/dendextend/man/raise.dendrogram.Rd | 8
dendextend-0.16.1/dendextend/man/rank_branches.Rd | 31
dendextend-0.16.1/dendextend/man/rank_order.dendrogram.Rd | 13
dendextend-0.16.1/dendextend/man/rect.dendrogram.Rd |only
dendextend-0.16.1/dendextend/man/remove_branches_edgePar.Rd | 13
dendextend-0.16.1/dendextend/man/remove_leaves_nodePar.Rd | 13
dendextend-0.16.1/dendextend/man/rllply.Rd | 27
dendextend-0.16.1/dendextend/man/rotate.Rd | 106 +-
dendextend-0.16.1/dendextend/man/rotate_DendSer.Rd |only
dendextend-0.16.1/dendextend/man/sample.dendrogram.Rd | 78 -
dendextend-0.16.1/dendextend/man/set.Rd |only
dendextend-0.16.1/dendextend/man/shuffle.Rd | 35
dendextend-0.16.1/dendextend/man/sort_2_clusters_vectors.Rd | 31
dendextend-0.16.1/dendextend/man/sort_dist_mat.Rd | 11
dendextend-0.16.1/dendextend/man/sort_levels_values.Rd | 51 -
dendextend-0.16.1/dendextend/man/tanglegram.Rd | 196 ++--
dendextend-0.16.1/dendextend/man/unbranch.Rd | 14
dendextend-0.16.1/dendextend/man/unclass_dend.Rd | 5
dendextend-0.16.1/dendextend/man/untangle.Rd |only
dendextend-0.16.1/dendextend/man/untangle_DendSer.Rd |only
dendextend-0.16.1/dendextend/man/untangle_random_search.Rd | 83 --
dendextend-0.16.1/dendextend/man/untangle_step_rotate_1side.Rd | 74 -
dendextend-0.16.1/dendextend/man/untangle_step_rotate_2side.Rd | 61 -
dendextend-0.16.1/dendextend/man/which_leaf.Rd |only
dendextend-0.16.1/dendextend/tests/test-all.R |only
187 files changed, 1868 insertions(+), 1914 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Diff between arules versions 1.1-3 dated 2014-06-17 and 1.1-4 dated 2014-07-26
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
build/vignette.rds |binary
data/Adult.rda |binary
data/AdultUCI.rda |binary
data/Epub.rda |binary
data/Groceries.rda |binary
data/Income.rda |binary
data/IncomeESL.rda |binary
inst/NEWS | 20 +++++++++++++-------
inst/doc/arules.pdf |binary
man/combine.Rd | 7 +++++--
src/bitmat.c | 6 ++++--
src/istree.c | 8 ++++----
src/rapriori.c | 15 ++++++++++-----
src/reclat.c | 11 +++++++----
16 files changed, 62 insertions(+), 43 deletions(-)
Title: Class and Methods for Structural Time Series Models
Diff between stsm.class versions 1.2 dated 2014-05-29 and 1.3 dated 2014-07-26
Description: This package defines an S4 class for structural time series models
and provides some basic methods to work with it.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
stsm.class-1.2/stsm.class/inst/CHANGES |only
stsm.class-1.3/stsm.class/DESCRIPTION | 8 +-
stsm.class-1.3/stsm.class/MD5 | 18 ++---
stsm.class-1.3/stsm.class/NAMESPACE | 1
stsm.class-1.3/stsm.class/R/frequency-domain.R | 15 ++--
stsm.class-1.3/stsm.class/R/stsm-class.R | 38 +++++++++++-
stsm.class-1.3/stsm.class/R/stsm-methods.R | 68 +++++++++++++++++++++-
stsm.class-1.3/stsm.class/inst/NEWS |only
stsm.class-1.3/stsm.class/man/stsm-class.Rd | 4 +
stsm.class-1.3/stsm.class/man/stsm-methods-set.Rd | 44 +++++++++++++-
stsm.class-1.3/stsm.class/man/stsm-model.Rd | 4 -
11 files changed, 171 insertions(+), 29 deletions(-)
Title: Case Influence in Structural Equation Models
Diff between influence.SEM versions 1.3 dated 2014-05-26 and 1.4 dated 2014-07-26
Description: influence.SEM provides a set of tools for evaluating several measures of case influence for Structural Equation Models following the approach of Pek and MacCallum (2011).
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore
influence.SEM-1.3/influence.SEM/man/influence.SEM-package.Rd |only
influence.SEM-1.4/influence.SEM/DESCRIPTION | 8 +--
influence.SEM-1.4/influence.SEM/MD5 | 5 --
influence.SEM-1.4/influence.SEM/R/parinfluence.R | 23 ++++-------
4 files changed, 15 insertions(+), 21 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.10.0 dated 2014-06-14 and 0.10.1 dated 2014-07-26
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: RStudio, Inc.
Maintainer: Winston Chang
shiny-0.10.0/shiny/man/runGist.Rd |only
shiny-0.10.0/shiny/man/runGitHub.Rd |only
shiny-0.10.1/shiny/DESCRIPTION | 6
shiny-0.10.1/shiny/MD5 | 83 +--
shiny-0.10.1/shiny/NAMESPACE | 2
shiny-0.10.1/shiny/NEWS | 31 +
shiny-0.10.1/shiny/R/app.R | 55 +-
shiny-0.10.1/shiny/R/bootstrap.R | 249 ++++++----
shiny-0.10.1/shiny/R/graph.R | 2
shiny-0.10.1/shiny/R/imageutils.R | 2
shiny-0.10.1/shiny/R/middleware-shiny.R | 2
shiny-0.10.1/shiny/R/middleware.R | 10
shiny-0.10.1/shiny/R/react.R | 4
shiny-0.10.1/shiny/R/reactive-domains.R | 1
shiny-0.10.1/shiny/R/run-url.R | 179 ++-----
shiny-0.10.1/shiny/R/server.R | 15
shiny-0.10.1/shiny/R/shiny.R | 15
shiny-0.10.1/shiny/R/shinyui.R | 3
shiny-0.10.1/shiny/R/shinywrappers.R | 51 +-
shiny-0.10.1/shiny/R/showcase.R | 9
shiny-0.10.1/shiny/R/tar.R | 2
shiny-0.10.1/shiny/R/update-input.R | 78 +--
shiny-0.10.1/shiny/R/utils.R | 81 ++-
shiny-0.10.1/shiny/inst/staticdocs/index.r | 5
shiny-0.10.1/shiny/inst/tests/test-bootstrap.r | 102 ++++
shiny-0.10.1/shiny/inst/tests/test-staticdocs.R | 2
shiny-0.10.1/shiny/inst/www/shared/json2-min.js |only
shiny-0.10.1/shiny/inst/www/shared/selectize/js/selectize.min.js | 2
shiny-0.10.1/shiny/inst/www/shared/shiny-showcase.js | 5
shiny-0.10.1/shiny/inst/www/shared/shiny.js | 78 ---
shiny-0.10.1/shiny/man/conditionalPanel.Rd | 7
shiny-0.10.1/shiny/man/domains.Rd | 2
shiny-0.10.1/shiny/man/htmlOutput.Rd | 7
shiny-0.10.1/shiny/man/imageOutput.Rd | 5
shiny-0.10.1/shiny/man/knitr_methods.Rd | 4
shiny-0.10.1/shiny/man/navbarPage.Rd | 5
shiny-0.10.1/shiny/man/plotOutput.Rd | 34 -
shiny-0.10.1/shiny/man/renderPlot.Rd | 18
shiny-0.10.1/shiny/man/runUrl.Rd | 56 +-
shiny-0.10.1/shiny/man/tag.Rd | 2
shiny-0.10.1/shiny/man/textOutput.Rd | 7
shiny-0.10.1/shiny/man/updateCheckboxGroupInput.Rd | 10
shiny-0.10.1/shiny/man/updateRadioButtons.Rd | 11
shiny-0.10.1/shiny/man/updateSelectInput.Rd | 19
44 files changed, 768 insertions(+), 493 deletions(-)
Title: Response Probability Functions
Diff between rpf versions 0.35 dated 2014-06-30 and 0.36 dated 2014-07-26
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]
Maintainer: Joshua Pritikin
DESCRIPTION | 10 -
MD5 | 65 +++++----
NAMESPACE | 5
R/classes.R | 31 ++++
R/diagnose.R | 14 +-
R/drm.R | 3
R/grm.R | 5
R/nrm.R | 9 -
R/openmx.R |only
R/sample.R | 24 ++-
R/util.R | 157 +++++++++++++----------
inst/doc/diagnostics.R | 2
inst/doc/diagnostics.Rmd | 2
inst/doc/diagnostics.html | 48 +++----
inst/tests/test-fit.R | 6
inst/tests/test-ld.R | 2
inst/tests/test-multinomial.R | 7 +
inst/tests/test-null.R |only
inst/tests/test-sumscore.R | 4
man/EAPscores.Rd | 4
man/as.IFAgroup.Rd |only
man/omitMostMissing.Rd |only
man/rpf.dLL.Rd | 1
man/rpf.logprob.Rd | 1
man/rpf.nrm.Rd | 6
man/rpf.prob.Rd | 1
man/sumScoreEAP.Rd | 13 -
man/sumScoreEAPTest.Rd |only
src/ba81quad.cpp | 262 ++++++--------------------------------
src/ba81quad.h | 283 +++++++++++++++++++++++++++++++++++-------
src/eap.cpp | 12 -
src/glue.cpp | 63 +++++----
src/libifa-rpf.cpp | 138 ++++++++++++++------
src/m2.cpp | 16 +-
src/rpf.h | 22 +--
vignettes/diagnostics.Rmd | 2
36 files changed, 686 insertions(+), 532 deletions(-)
Title: A set of tools for working with list objects
Diff between rlist versions 0.2.3 dated 2014-07-18 and 0.2.4 dated 2014-07-26
Description: A set of tools for working with lists as dataset,
including filtering, mapping, grouping, sorting, updating, and
many other functions. It recommends functional programming
in list operations.
Author: Kun Ren
Maintainer: Kun Ren
DESCRIPTION | 18 +++---
MD5 | 22 ++++----
NAMESPACE | 1
NEWS | 5 +
R/list.cases.R | 2
R/list.common.R |only
README.md | 121 ++++++++++++++++++++++++++++++--------------
inst/doc/Grouping.R | 6 ++
inst/doc/Grouping.html | 22 ++++++++
inst/doc/Introduction.html | 7 +-
man/list.cases.Rd | 2
man/list.common.Rd |only
tests/testthat/test-basic.R | 11 ++++
13 files changed, 156 insertions(+), 61 deletions(-)
Title: Specialized, high-performance pipeline operators
Diff between pipeR versions 0.3-1 dated 2014-06-28 and 0.3-2 dated 2014-07-26
Description: Provides specialized, high-performance operators
for chaining commands with three forward-piping
operations: first-argument piping, free piping,
and lambda piping, making command chaining clear,
fast, readable and flexible.
Author: Kun Ren
Maintainer: Kun Ren
DESCRIPTION | 10 ++---
MD5 | 19 ++++++---
NEWS | 7 +++
R/functions.R | 20 +++++-----
R/pipeR.R | 9 ++--
README.md | 82 +++++++++----------------------------------
build |only
inst |only
man/first-argument-piping.Rd | 9 ++--
9 files changed, 64 insertions(+), 92 deletions(-)
Title: Analysis of evolutionary rates in an OU framework
Diff between OUwie versions 1.42 dated 2014-04-01 and 1.43 dated 2014-07-26
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 8 ++++----
MD5 | 18 ++++++++++++------
NAMESPACE | 8 +++++---
R/OUwie.R | 5 ++---
R/OUwie.boot.R |only
R/OUwie.fixed.R | 1 -
R/OUwie.joint.R |only
R/OUwie.slice.R |only
R/varcov.ou.R | 2 +-
R/weight.mat.R | 4 ++--
man/OUwie.boot.Rd |only
man/OUwie.joint.Rd |only
man/OUwie.slice.Rd |only
13 files changed, 26 insertions(+), 20 deletions(-)
Title: Interface to Lp_solve v. 5.5 to solve linear/integer programs
Diff between lpSolve versions 5.6.9 dated 2014-06-20 and 5.6.10 dated 2014-07-26
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/lp.R | 4 ++--
src/lp_rlp.h | 4 +++-
4 files changed, 12 insertions(+), 10 deletions(-)
Title: Information-Theoretic Measures
Diff between infotheo versions 1.1.1 dated 2012-12-10 and 1.2.0 dated 2014-07-26
Description: This package implements various measures of information theory based on several entropy estimators.
Author: Patrick E. Meyer
Maintainer: Patrick E. Meyer
infotheo-1.1.1/infotheo/LICENSE |only
infotheo-1.2.0/infotheo/CHANGES | 7 ++++++-
infotheo-1.2.0/infotheo/DESCRIPTION | 20 +++++++++-----------
infotheo-1.2.0/infotheo/MD5 | 17 ++++++++---------
infotheo-1.2.0/infotheo/R/discretize.R | 6 +++---
infotheo-1.2.0/infotheo/R/entropy.R | 12 ++++--------
infotheo-1.2.0/infotheo/man/discretize.Rd | 4 ++--
infotheo-1.2.0/infotheo/src/discretize.cpp | 2 +-
infotheo-1.2.0/infotheo/src/entropy.cpp | 24 ++++++++++++------------
infotheo-1.2.0/infotheo/src/infotheo.h | 10 +++++-----
10 files changed, 50 insertions(+), 52 deletions(-)
Title: DiscML: An R package for estimating evolutionary rates of
discrete characters using maximum likelihood
Diff between DiscML versions 1.0 dated 2014-05-02 and 1.0.1 dated 2014-07-26
Description: DiscML performs rate estimation using maximum likelihood with the
options to correct for unobservable data, to implement a Gamma-distribution
for rate variation, and to estimate the prior root probabilities from the
empirical data.
Author: Tane Kim, Weilong Hao
Maintainer: Weilong Hao
DESCRIPTION | 14
MD5 | 11
NAMESPACE | 1
R/DiscML.R | 2835 ++++++++++++++++++++++++++++++--------------------
R/DiscMLprint.R | 226 +++
R/read.tree2.R |only
man/DiscML-package.Rd | 95 -
7 files changed, 1976 insertions(+), 1206 deletions(-)
Title: Splitting methods for convex clustering
Diff between cvxclustr versions 1.0.0 dated 2013-04-30 and 1.1.0 dated 2014-07-26
Description: Alternating Minimization Algorithm (AMA) and Alternating Direction
Method of Multipliers (ADMM) splitting methods for convex clustering.
Author: Eric C. Chi, Kenneth Lange
Maintainer: Eric C. Chi
cvxclustr-1.0.0/cvxclustr/R/kernel_weights.r |only
cvxclustr-1.0.0/cvxclustr/R/knn_weights.r |only
cvxclustr-1.0.0/cvxclustr/R/prox.r |only
cvxclustr-1.0.0/cvxclustr/README.md |only
cvxclustr-1.0.0/cvxclustr/man/prox.Rd |only
cvxclustr-1.0.0/cvxclustr/src/variable_splitting.f90 |only
cvxclustr-1.1.0/cvxclustr/DESCRIPTION | 24 -
cvxclustr-1.1.0/cvxclustr/MD5 | 51 +-
cvxclustr-1.1.0/cvxclustr/NAMESPACE | 10
cvxclustr-1.1.0/cvxclustr/NEWS |only
cvxclustr-1.1.0/cvxclustr/R/cvxclust.r | 77 ++--
cvxclustr-1.1.0/cvxclustr/R/cvxclust_admm.r | 121 +++++-
cvxclustr-1.1.0/cvxclustr/R/cvxclust_ama.r | 103 +++--
cvxclustr-1.1.0/cvxclustr/R/cvxclust_path_admm.r | 127 +++----
cvxclustr-1.1.0/cvxclustr/R/cvxclust_path_ama.r | 129 +++----
cvxclustr-1.1.0/cvxclustr/R/cvxclustr-package.r | 32 +
cvxclustr-1.1.0/cvxclustr/R/util.r | 229 +++++++++++--
cvxclustr-1.1.0/cvxclustr/R/weights.r |only
cvxclustr-1.1.0/cvxclustr/man/AMA_step_size.Rd |only
cvxclustr-1.1.0/cvxclustr/man/compactify_edges.Rd |only
cvxclustr-1.1.0/cvxclustr/man/create_adjacency.Rd |only
cvxclustr-1.1.0/cvxclustr/man/create_clustering_problem.Rd |only
cvxclustr-1.1.0/cvxclustr/man/cvxclust.Rd | 129 +++----
cvxclustr-1.1.0/cvxclustr/man/cvxclust_admm.Rd | 109 ++++--
cvxclustr-1.1.0/cvxclustr/man/cvxclust_ama.Rd | 99 +++--
cvxclustr-1.1.0/cvxclustr/man/cvxclust_path_admm.Rd | 120 +++---
cvxclustr-1.1.0/cvxclustr/man/cvxclust_path_ama.Rd | 123 +++---
cvxclustr-1.1.0/cvxclustr/man/cvxclustr.Rd | 76 ++--
cvxclustr-1.1.0/cvxclustr/man/find_clusters.Rd |only
cvxclustr-1.1.0/cvxclustr/man/kernel_weights.Rd | 23 -
cvxclustr-1.1.0/cvxclustr/man/knn_weights.Rd | 22 -
cvxclustr-1.1.0/cvxclustr/man/mammals.Rd | 11
cvxclustr-1.1.0/cvxclustr/man/weights_graph.Rd |only
cvxclustr-1.1.0/cvxclustr/src/cvxclustr.c |only
34 files changed, 984 insertions(+), 631 deletions(-)