Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-5 dated 2016-02-13 and 0.0-6 dated 2016-05-29
qrmtools-0.0-5/qrmtools/R/zzz.R |only qrmtools-0.0-6/qrmtools/DESCRIPTION | 12 - qrmtools-0.0-6/qrmtools/MD5 | 41 ++- qrmtools-0.0-6/qrmtools/NAMESPACE | 29 +- qrmtools-0.0-6/qrmtools/R/ARMA_GARCH.R |only qrmtools-0.0-6/qrmtools/R/GPD.R | 4 qrmtools-0.0-6/qrmtools/R/catch.R |only qrmtools-0.0-6/qrmtools/R/composite.R |only qrmtools-0.0-6/qrmtools/R/get_data.R |only qrmtools-0.0-6/qrmtools/R/graphics.R |only qrmtools-0.0-6/qrmtools/R/returns.R |only qrmtools-0.0-6/qrmtools/R/risk_measures.R | 14 - qrmtools-0.0-6/qrmtools/build |only qrmtools-0.0-6/qrmtools/demo |only qrmtools-0.0-6/qrmtools/inst |only qrmtools-0.0-6/qrmtools/man/ARMA_GARCH.Rd |only qrmtools-0.0-6/qrmtools/man/Black_Scholes.Rd | 2 qrmtools-0.0-6/qrmtools/man/VaR_bounds.Rd | 4 qrmtools-0.0-6/qrmtools/man/catch.Rd |only qrmtools-0.0-6/qrmtools/man/density_plot_matrix.Rd |only qrmtools-0.0-6/qrmtools/man/get_data.Rd |only qrmtools-0.0-6/qrmtools/man/plot_NA.Rd |only qrmtools-0.0-6/qrmtools/man/plot_matrix.Rd |only qrmtools-0.0-6/qrmtools/man/returns.Rd |only qrmtools-0.0-6/qrmtools/man/risk_measures.Rd | 2 qrmtools-0.0-6/qrmtools/vignettes/ARMA_GARCH_VaR.Rmd | 224 ++++++++++--------- qrmtools-0.0-6/qrmtools/vignettes/VaR_bounds.Rmd | 26 +- 27 files changed, 213 insertions(+), 145 deletions(-)
Title: Practical Numerical Math Functions
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 1.8.8 dated 2015-11-27 and 1.9.3 dated 2016-05-29
DESCRIPTION | 14 +++---- MD5 | 46 +++++++++++++----------- NAMESPACE | 2 + NEWS | 39 ++++++++++++++++++++ R/arclength.R | 3 + R/bvp.R | 43 +++++++--------------- R/fractalcurve.R |only R/lsqlincon.R |only R/ode23.R | 2 - R/ode23s.R | 2 - R/polyApprox.R | 12 +++--- R/polyfit.R | 98 +++++++++++++++++++++++++++++++++++++--------------- R/quadprog.R |only R/romberg.R | 3 - R/trapz.R | 30 +++++++++++++++ data/brown72.rda |binary data/nile.rda |binary data/titanium.rda |binary man/arclength.Rd | 25 +++++++++++++ man/bvp.Rd | 19 +--------- man/fractalcurve.Rd |only man/lsqlin.Rd | 8 +--- man/lsqlincon.Rd |only man/polyApprox.Rd | 23 +++++++----- man/polyfit.Rd | 50 ++++++++++++++++++++------ man/quadprog.Rd |only man/trapz.Rd | 24 +++++++++++- 27 files changed, 308 insertions(+), 135 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.2 dated 2016-04-22 and 2.3 dated 2016-05-29
DESCRIPTION | 8 - MD5 | 24 ++-- R/BOIN.R | 12 ++ R/get.oc.comb.R | 255 +++++++++++++++++++++++++-------------------- R/get.oc.comb.phase12.R | 56 ++++++++- man/get.boundary.Rd | 3 man/get.oc.Rd | 3 man/get.oc.comb.Rd | 5 man/get.oc.comb.phase12.Rd | 4 man/next.comb.Rd | 9 - man/next.subtrial.Rd | 10 - man/select.mtd.Rd | 3 man/select.mtd.comb.Rd | 8 - 13 files changed, 236 insertions(+), 164 deletions(-)
Title: Discrete and Global Optimization Routines
Description:
The R package 'adagio' will provide methods and algorithms for
discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between adagio versions 0.6.3 dated 2015-12-06 and 0.6.5 dated 2016-05-29
adagio-0.6.3/adagio/R/lsqlincon.R |only adagio-0.6.3/adagio/man/lsqlincon.Rd |only adagio-0.6.5/adagio/DESCRIPTION | 14 +++++++------- adagio-0.6.5/adagio/MD5 | 12 +++++------- adagio-0.6.5/adagio/NAMESPACE | 2 -- adagio-0.6.5/adagio/NEWS | 9 +++++---- adagio-0.6.5/adagio/R/testfunctions.R | 2 +- adagio-0.6.5/adagio/man/adagio-package.Rd | 4 ++-- 8 files changed, 20 insertions(+), 23 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.1.6 dated 2016-05-11 and 0.1.9 dated 2016-05-29
NNS-0.1.6/NNS/R/Dependence_Regression.R |only NNS-0.1.6/NNS/R/Normalization_Causation.R |only NNS-0.1.6/NNS/man/VN.dep.reg.Rd |only NNS-0.1.6/NNS/man/VN.norm.caus.Rd |only NNS-0.1.9/NNS/DESCRIPTION | 6 NNS-0.1.9/NNS/MD5 | 38 -- NNS-0.1.9/NNS/NAMESPACE | 3 NNS-0.1.9/NNS/R/ARMA.R | 18 NNS-0.1.9/NNS/R/ARMA_Regression.R | 4 NNS-0.1.9/NNS/R/Causation.R | 15 NNS-0.1.9/NNS/R/Classifier.R |only NNS-0.1.9/NNS/R/Correlation.R | 66 +-- NNS-0.1.9/NNS/R/Dependence.R | 106 +++-- NNS-0.1.9/NNS/R/Normalization.R | 7 NNS-0.1.9/NNS/R/Partial_Moments.R | 4 NNS-0.1.9/NNS/R/Partition_Map.R | 20 - NNS-0.1.9/NNS/R/Regression.R | 552 ++++++++++++++++++++++++++---- NNS-0.1.9/NNS/man/VN.class.Rd |only NNS-0.1.9/NNS/man/VN.cor.Rd | 5 NNS-0.1.9/NNS/man/VN.dep.Rd | 6 NNS-0.1.9/NNS/man/VN.norm.Rd | 4 NNS-0.1.9/NNS/man/VN.reg.Rd | 20 - NNS-0.1.9/NNS/man/partition.map.Rd | 2 23 files changed, 657 insertions(+), 219 deletions(-)
Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.14.3 dated 2016-02-07 and 2.16.0 dated 2016-05-29
ChangeLog | 53 DESCRIPTION | 11 MD5 | 67 - NAMESPACE | 124 +- NEWS | 35 R/rbamtools.r | 2119 +++++++++++++++++++++------------------ R/sampleBamFiles.r |only R/segmentize.r |only build/vignette.rds |binary inst/doc/rbamtools.R | 115 +- inst/doc/rbamtools.Rnw | 517 +++++---- inst/doc/rbamtools.pdf |binary man/bamCountAll.Rd | 30 man/bamRange-class.Rd | 66 - man/bamReader-class.Rd | 6 man/bamSave.Rd |only man/bamSort.Rd | 20 man/bamWriter-class.Rd | 13 man/exonAlignDepth-class.Rd |only man/exonLoessModel-class.Rd |only man/extractBamRegions.Rd | 4 man/extractGeneRegions.Rd |only man/gapList-class.Rd | 11 man/gapSiteList-class.Rd | 49 man/geneAlignDepth-class.Rd |only man/getQualDf.Rd | 15 man/getRefData.Rd | 18 man/groupRatio.Rd |only man/multseq.Rd |only man/rangeToFastq.Rd | 2 man/refSeqDict-class.Rd | 10 man/sampleBamFiles-class.Rd |only man/saveAldData.Rd |only man/segmentize.Rd |only src/extptr.h | 46 src/rbamtools.cpp | 106 + src/rbamtools.h | 3 tests/test-all.R | 2 tests/test_bam_align.r | 4 tests/test_vector_segmentation.r |only vignettes/rbamtools.Rnw | 196 +++ 41 files changed, 2278 insertions(+), 1364 deletions(-)
Title: Qualitative Interaction Trees
Description: Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial.
Author: Elise Dusseldorp [aut, cre, cph],
Lisa Doove [aut],
Jeanne van de Put [aut],
Cor Ninaber [ctb] (supported with the plot function),
Iven Van Mechelen [aut, cph]
Maintainer: Elise Dusseldorp <elise.dusseldorp@fsw.leidenuniv.nl>
Diff between quint versions 1.0 dated 2013-11-08 and 1.2.0 dated 2016-05-29
quint-1.0/quint/R/Bootstrap.R |only quint-1.0/quint/R/as.party.quint.R |only quint-1.0/quint/R/cmd.R |only quint-1.0/quint/R/computeC.R |only quint-1.0/quint/R/computeD.R |only quint-1.0/quint/R/cpmat.R |only quint-1.0/quint/R/csigmap.R |only quint-1.0/quint/R/ctc.R |only quint-1.0/quint/R/ctmat.R |only quint-1.0/quint/R/makedmat.R |only quint-1.0/quint/R/makedmats.R |only quint-1.0/quint/R/node_quint.R |only quint-1.0/quint/R/sdd.R |only quint-1.0/quint/R/terminal_quint.R |only quint-1.0/quint/R/to.party.R |only quint-1.0/quint/R/wav.R |only quint-1.2.0/quint/DESCRIPTION | 25 - quint-1.2.0/quint/MD5 | 72 +-- quint-1.2.0/quint/NAMESPACE | 55 ++ quint-1.2.0/quint/NEWS |only quint-1.2.0/quint/R/Bootindex.R |only quint-1.2.0/quint/R/bcrp.R |only quint-1.2.0/quint/R/bonode.R | 31 - quint-1.2.0/quint/R/bootstrap.R |only quint-1.2.0/quint/R/bos.R | 219 +++++++-- quint-1.2.0/quint/R/bovar.R | 39 - quint-1.2.0/quint/R/computeCtest.R | 113 ++--- quint-1.2.0/quint/R/determineSplits.R |only quint-1.2.0/quint/R/dmats.R |only quint-1.2.0/quint/R/leafnum.R | 22 - quint-1.2.0/quint/R/makeGchmat.R | 34 + quint-1.2.0/quint/R/nodeinfo.R |only quint-1.2.0/quint/R/plot.quint.R | 50 ++ quint-1.2.0/quint/R/plotsupport.R |only quint-1.2.0/quint/R/predict.quint.R |only quint-1.2.0/quint/R/predval.R |only quint-1.2.0/quint/R/prune.quint.R | 92 +++- quint-1.2.0/quint/R/quint-package.R |only quint-1.2.0/quint/R/quint.R | 702 +++++++++++++++++++------------- quint-1.2.0/quint/R/quint.control.R | 66 ++- quint-1.2.0/quint/R/quint.validate.R |only quint-1.2.0/quint/R/summary.quint.R | 80 ++- quint-1.2.0/quint/data/bcrp.rda |binary quint-1.2.0/quint/man/bcrp.Rd | 90 ++-- quint-1.2.0/quint/man/plot.quint.Rd | 56 +- quint-1.2.0/quint/man/predict.quint.Rd |only quint-1.2.0/quint/man/prune.quint.Rd | 73 +-- quint-1.2.0/quint/man/quint-package.Rd | 80 ++- quint-1.2.0/quint/man/quint.Rd | 128 +++-- quint-1.2.0/quint/man/quint.control.Rd | 91 ++-- quint-1.2.0/quint/man/quint.validate.Rd |only quint-1.2.0/quint/man/summary.quint.Rd | 42 - 52 files changed, 1365 insertions(+), 795 deletions(-)
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.5.1 dated 2016-05-05 and 0.5.2 dated 2016-05-29
DESCRIPTION | 8 - MD5 | 42 ++++---- NAMESPACE | 5 R/matrix.graph.R | 8 - R/metrics.graph.R | 163 +++++++++++++++----------------- R/range_expansion.R | 33 +++--- R/range_raster.R | 43 ++++++-- R/rland.graph.R | 2 R/spom.R | 3 data/rg_exp.rda |binary inst/CITATION | 2 inst/doc/MetaLandSim.pdf |binary inst/doc/range_expansion.Rnw | 213 +++++++++++++++++++++--------------------- inst/doc/range_expansion.pdf |binary man/MetaLandSim-package.Rd | 4 man/metrics.graph.Rd | 182 +++++++++++++++++++---------------- man/min_distance.Rd | 2 man/range_expansion.Rd | 6 - man/range_raster.Rd | 10 + man/rg_exp.Rd | 1 man/rland.graph.Rd | 3 vignettes/range_expansion.Rnw | 213 +++++++++++++++++++++--------------------- 22 files changed, 495 insertions(+), 448 deletions(-)
Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition,
i.e., a set of Dempster-Shafer mass functions representing the membership of objects
to clusters. The mass functions quantify the cluster-membership uncertainty of the objects.
The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM),
Constrained Evidential c-Means (CECM), EVCLUS and EK-NNclus.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evclust versions 1.0.1 dated 2016-05-28 and 1.0.2 dated 2016-05-29
DESCRIPTION | 6 - MD5 | 8 - inst/doc/Introduction.R | 71 ++++++++++++ inst/doc/Introduction.Rmd | 162 ++++++++++++++++++++++++++-- inst/doc/Introduction.html | 259 +++++++++++++++++++++++++++++++++++++++++---- 5 files changed, 468 insertions(+), 38 deletions(-)