Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.6 dated 2015-08-11 and 0.4.0 dated 2015-09-04
vardpoor-0.3.6/vardpoor/R/linrmi.R |only vardpoor-0.3.6/vardpoor/man/linrmi.Rd |only vardpoor-0.4.0/vardpoor/DESCRIPTION | 8 +- vardpoor-0.4.0/vardpoor/MD5 | 44 ++++++++-------- vardpoor-0.4.0/vardpoor/NAMESPACE | 2 vardpoor-0.4.0/vardpoor/R/linrmir.R |only vardpoor-0.4.0/vardpoor/R/vardchangespoor.R | 2 vardpoor-0.4.0/vardpoor/R/vardcrospoor.R | 16 ++--- vardpoor-0.4.0/vardpoor/R/vardomh.R | 14 +++-- vardpoor-0.4.0/vardpoor/R/varpoord.R | 39 +++++++------- vardpoor-0.4.0/vardpoor/inst/CITATION | 4 - vardpoor-0.4.0/vardpoor/inst/NEWS | 6 ++ vardpoor-0.4.0/vardpoor/man/linarpr.Rd | 2 vardpoor-0.4.0/vardpoor/man/lingini.Rd | 3 - vardpoor-0.4.0/vardpoor/man/lingini2.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linpoormed.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linqsr.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linrmir.Rd |only vardpoor-0.4.0/vardpoor/man/linrmpg.Rd | 3 - vardpoor-0.4.0/vardpoor/man/vardchangespoor.Rd | 2 vardpoor-0.4.0/vardpoor/man/vardcrospoor.Rd | 4 - vardpoor-0.4.0/vardpoor/man/vardomh.Rd | 40 ++++++++++++-- vardpoor-0.4.0/vardpoor/man/vardpoor-package.Rd | 4 - vardpoor-0.4.0/vardpoor/man/variance_est.Rd | 10 +++ vardpoor-0.4.0/vardpoor/man/varpoord.Rd | 66 ++++++++++++++++++------ 25 files changed, 179 insertions(+), 99 deletions(-)
Title: Model Selection for Index of Asymmetry Distribution
Description: Calculate AIC's and AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of two normal distributions) which fit the distribution of indices of asymmetry (IAS), and plot their density, to help determine IAS distribution is unimodal or bimodal.
Author: Satoshi Takahashi
Maintainer: Satoshi Takahashi <takahasi@lisboa.ics.nara-wu.ac.jp>
Diff between IASD versions 1.0.7 dated 2013-08-07 and 1.1 dated 2015-09-04
DESCRIPTION | 12 +- MD5 | 10 - NAMESPACE | 6 + R/IASD.R | 304 ++++++++++++++++++++++++++++------------------------ man/IASD-package.Rd | 5 man/IASD.Rd | 75 +++++++++--- 6 files changed, 241 insertions(+), 171 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.2.1 dated 2014-11-13 and 1.3.1 dated 2015-09-04
entropart-1.2.1/entropart/R/bcDiversity.R |only entropart-1.2.1/entropart/R/bcDqz.R |only entropart-1.2.1/entropart/R/bcHqz.R |only entropart-1.2.1/entropart/R/bcHqzBeta.R |only entropart-1.2.1/entropart/R/bcPhyloBetaEntropy.R |only entropart-1.2.1/entropart/R/bcPhyloDiversity.R |only entropart-1.2.1/entropart/R/bcPhyloEntropy.R |only entropart-1.2.1/entropart/R/bcRao.R |only entropart-1.2.1/entropart/R/bcShannon.R |only entropart-1.2.1/entropart/R/bcShannonBeta.R |only entropart-1.2.1/entropart/R/bcSimpson.R |only entropart-1.2.1/entropart/R/bcSimpsonBeta.R |only entropart-1.2.1/entropart/R/bcTsallis.R |only entropart-1.2.1/entropart/R/bcTsallisBeta.R |only entropart-1.2.1/entropart/R/is.MCdiversity.R |only entropart-1.2.1/entropart/R/is.MCentropy.R |only entropart-1.2.1/entropart/R/is.MetaCommunity.R |only entropart-1.2.1/entropart/R/is.PPtree.R |only entropart-1.2.1/entropart/R/is.PhyloDiversity.R |only entropart-1.2.1/entropart/R/is.PhyloEntropy.R |only entropart-1.2.1/entropart/R/is.PhyloValue.R |only entropart-1.2.1/entropart/R/is.SimTest.R |only entropart-1.2.1/entropart/R/plot.DivEst.R |only entropart-1.2.1/entropart/R/plot.DivPart.R |only entropart-1.2.1/entropart/R/plot.DivProfile.R |only entropart-1.2.1/entropart/R/plot.MCdiversity.R |only entropart-1.2.1/entropart/R/plot.MCentropy.R |only entropart-1.2.1/entropart/R/plot.MetaCommunity.R |only entropart-1.2.1/entropart/R/plot.PPtree.R |only entropart-1.2.1/entropart/R/plot.PhyloValue.R |only entropart-1.2.1/entropart/R/plot.SimTest.R |only entropart-1.2.1/entropart/R/summary.DivEst.R |only entropart-1.2.1/entropart/R/summary.DivPart.R |only entropart-1.2.1/entropart/R/summary.DivProfile.R |only entropart-1.2.1/entropart/R/summary.MCdiversity.R |only entropart-1.2.1/entropart/R/summary.MCentropy.R |only entropart-1.2.1/entropart/R/summary.MetaCommunity.R |only entropart-1.2.1/entropart/R/summary.PhyloDiversity.R |only entropart-1.2.1/entropart/R/summary.PhyloEntropy.R |only entropart-1.2.1/entropart/R/summary.PhyloValue.R |only entropart-1.2.1/entropart/R/summary.SimTest.R |only entropart-1.2.1/entropart/vignettes/entropart-MCPlot.pdf |only entropart-1.2.1/entropart/vignettes/entropart-lnq.pdf |only entropart-1.3.1/entropart/DESCRIPTION | 11 entropart-1.3.1/entropart/MD5 | 207 +++++------ entropart-1.3.1/entropart/NAMESPACE | 104 +++++ entropart-1.3.1/entropart/NEWS | 18 + entropart-1.3.1/entropart/R/AbdFreqCount.R |only entropart-1.3.1/entropart/R/AllenH.R | 4 entropart-1.3.1/entropart/R/CEnvelope.R |only entropart-1.3.1/entropart/R/ChaoPD.R | 2 entropart-1.3.1/entropart/R/CheckentropartArguments.R | 269 +++++++++++---- entropart-1.3.1/entropart/R/CommunityProfile.R | 106 +++++ entropart-1.3.1/entropart/R/DivEst.R | 75 ++++ entropart-1.3.1/entropart/R/DivPart.R | 45 ++ entropart-1.3.1/entropart/R/DivProfile.R | 70 +++ entropart-1.3.1/entropart/R/Diversity.R | 69 +++ entropart-1.3.1/entropart/R/Dqz.R | 72 +++- entropart-1.3.1/entropart/R/EntropyCI.R | 10 entropart-1.3.1/entropart/R/Hqz.R | 162 ++++++++- entropart-1.3.1/entropart/R/HqzBeta.R | 98 +++++ entropart-1.3.1/entropart/R/Hurlbert.R |only entropart-1.3.1/entropart/R/HurlbertD.R |only entropart-1.3.1/entropart/R/MCdiversity.R |only entropart-1.3.1/entropart/R/MCentropy.R |only entropart-1.3.1/entropart/R/MetaCommunity.R | 40 ++ entropart-1.3.1/entropart/R/Optimal.Similarity.R |only entropart-1.3.1/entropart/R/Originality.Species.R | 9 entropart-1.3.1/entropart/R/PPtree.R |only entropart-1.3.1/entropart/R/PhyloApply.R | 6 entropart-1.3.1/entropart/R/PhyloBetaEntropy.R | 103 +++++ entropart-1.3.1/entropart/R/PhyloDiversity.R | 114 ++++++ entropart-1.3.1/entropart/R/PhyloEntropy.R | 106 +++++ entropart-1.3.1/entropart/R/PhyloValue.R |only entropart-1.3.1/entropart/R/Preprocess.Tree.R | 2 entropart-1.3.1/entropart/R/Rao.R | 72 +++- entropart-1.3.1/entropart/R/Richness.R | 172 +++++++++ entropart-1.3.1/entropart/R/Shannon.R | 172 +++++++++ entropart-1.3.1/entropart/R/ShannonBeta.R | 112 ++++++ entropart-1.3.1/entropart/R/SimTest.R | 35 + entropart-1.3.1/entropart/R/Simpson.R | 72 +++- entropart-1.3.1/entropart/R/SimpsonBeta.R | 85 ++++ entropart-1.3.1/entropart/R/SpeciesDistribution.R |only entropart-1.3.1/entropart/R/Tsallis.R | 175 +++++++++ entropart-1.3.1/entropart/R/TsallisBeta.R | 117 ++++++ entropart-1.3.1/entropart/R/expq.R | 17 entropart-1.3.1/entropart/R/lnq.R | 17 entropart-1.3.1/entropart/R/rCommunity.R |only entropart-1.3.1/entropart/build/vignette.rds |binary entropart-1.3.1/entropart/inst/CITATION | 10 entropart-1.3.1/entropart/inst/doc/entropart.R | 152 ++++++-- entropart-1.3.1/entropart/inst/doc/entropart.Rnw | 177 +++++++-- entropart-1.3.1/entropart/inst/doc/entropart.pdf |binary entropart-1.3.1/entropart/man/AbdFreqCount.Rd |only entropart-1.3.1/entropart/man/AllenH.Rd | 7 entropart-1.3.1/entropart/man/AlphaDiversity.Rd | 4 entropart-1.3.1/entropart/man/AlphaEntropy.Rd | 4 entropart-1.3.1/entropart/man/BetaDiversity.Rd | 4 entropart-1.3.1/entropart/man/BetaEntropy.Rd | 4 entropart-1.3.1/entropart/man/ChaoPD.Rd | 3 entropart-1.3.1/entropart/man/CommunityProfile.Rd | 84 ++++ entropart-1.3.1/entropart/man/DivEst.Rd | 8 entropart-1.3.1/entropart/man/DivPart.Rd | 8 entropart-1.3.1/entropart/man/DivProfile.Rd | 6 entropart-1.3.1/entropart/man/Diversity.Rd | 39 +- entropart-1.3.1/entropart/man/Dqz.Rd | 24 + entropart-1.3.1/entropart/man/EntropyCI.Rd | 16 entropart-1.3.1/entropart/man/GammaDiversity.Rd | 4 entropart-1.3.1/entropart/man/GammaEntropy.Rd | 4 entropart-1.3.1/entropart/man/Hqz.Rd | 27 + entropart-1.3.1/entropart/man/HqzBeta.Rd | 34 + entropart-1.3.1/entropart/man/Hurlbert.Rd |only entropart-1.3.1/entropart/man/Optimal.Similarity.Rd |only entropart-1.3.1/entropart/man/Paracou618.Functional.Rd | 2 entropart-1.3.1/entropart/man/Paracou618.dist.Rd | 2 entropart-1.3.1/entropart/man/PhyloApply.Rd | 2 entropart-1.3.1/entropart/man/PhyloBetaEntropy.Rd | 44 +- entropart-1.3.1/entropart/man/PhyloDiversity.Rd | 26 + entropart-1.3.1/entropart/man/PhyloEntropy.Rd | 28 + entropart-1.3.1/entropart/man/Rao.Rd | 37 +- entropart-1.3.1/entropart/man/Richness.Rd | 76 +++- entropart-1.3.1/entropart/man/Shannon.Rd | 47 +- entropart-1.3.1/entropart/man/ShannonBeta.Rd | 32 + entropart-1.3.1/entropart/man/Simpson.Rd | 32 + entropart-1.3.1/entropart/man/SimpsonBeta.Rd | 34 + entropart-1.3.1/entropart/man/SpeciesDistribution.Rd |only entropart-1.3.1/entropart/man/Tsallis.Rd | 50 ++ entropart-1.3.1/entropart/man/TsallisBeta.Rd | 23 + entropart-1.3.1/entropart/man/entropart-package.Rd | 11 entropart-1.3.1/entropart/man/expq.Rd | 9 entropart-1.3.1/entropart/man/lnq.Rd | 9 entropart-1.3.1/entropart/man/rCommunity.Rd |only entropart-1.3.1/entropart/vignettes/entropart.Rnw | 177 +++++++-- entropart-1.3.1/entropart/vignettes/entropart.bib | 101 ++++- 134 files changed, 3544 insertions(+), 565 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 1.2 dated 2015-07-27 and 2.0 dated 2015-09-04
DESCRIPTION | 24 ++++++++++++++++------ MD5 | 22 +++++++++++++------- R/conduct.comb.R |only R/get.boundary.R | 45 +++++++++++------------------------------- R/get.oc.R | 8 +++---- R/get.oc.comb.R |only R/select.mtd.R | 3 +- R/select.mtd.comb.R |only man/BOIN-package.Rd | 52 ++++++++++++++++++++++++++++++++++++------------- man/conduct.comb.Rd |only man/get.boundary.Rd | 18 ++++++---------- man/get.oc.Rd | 19 +++++++---------- man/get.oc.comb.Rd |only man/select.mtd.Rd | 24 +++++++++++----------- man/select.mtd.comb.Rd |only 15 files changed, 116 insertions(+), 99 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant <bjgrant@umich.edu>
Diff between bio3d versions 2.2-2 dated 2015-03-03 and 2.2-3 dated 2015-09-04
DESCRIPTION | 8 +++--- MD5 | 52 +++++++++++++++++++++--------------------- NAMESPACE | 4 +++ R/as.pdb.prmtop.R | 6 ++-- R/atom.select.prmtop.R | 2 - R/binding.site.R | 35 ++++++++++++++-------------- R/cnapath.R | 10 ++++---- R/filter.dccm.R | 2 - R/hmmer.R | 4 +-- R/orient.pdb.R | 25 +++++++++++--------- R/pdbaln.R | 12 ++++++++- R/plot.fluct.R | 5 ++-- R/plotb3.R | 4 +-- R/read.pdb.R | 6 ++-- R/seqaln.R | 10 +++++++- R/trim.pdbs.R | 1 R/trim.xyz.R | 3 -- build/vignette.rds |binary inst/doc/bio3d_vignettes.html | 11 ++++++++ man/hmmer.Rd | 4 +-- man/pfam.Rd | 2 - man/plot.hmmer.Rd | 2 - man/read.ncdf.Rd | 2 - man/uniprot.Rd | 2 - man/write.ncdf.Rd | 2 - tests/testthat/test-dssp.R | 4 +++ tests/testthat/test-fitting.R | 10 +++++++- 27 files changed, 138 insertions(+), 90 deletions(-)
Title: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Description: The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker
Maintainer: Katharine M. Mullen <mullenkate@gmail.com>
Diff between minpack.lm versions 1.1-8 dated 2013-08-31 and 1.1-9 dated 2015-09-04
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 5 ++++- NEWS | 2 ++ man/nls.lm.Rd | 2 +- 5 files changed, 17 insertions(+), 11 deletions(-)
Title: Tools for Aquatic Sciences
Description: Datasets, constants, conversion factors, utilities for MArine, Riverine,
Estuarine, LAcustrine and Coastal science.
The package contains among others: (1) chemical and
physical constants and datasets, e.g. atomic weights, gas
constants, the earths bathymetry; (2) conversion factors
(e.g. gram to mol to liter, barometric units,
temperature, salinity); (3) physical functions, e.g. to
estimate concentrations of conservative substances, gas
transfer and diffusion coefficients, the Coriolis force
and gravity; (4) thermophysical properties of the
seawater, as from the UNESCO polynomial or from the more
recent derivation based on a Gibbs function.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>,
Filip Meysman <filip.meysman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between marelac versions 2.1.4 dated 2014-11-04 and 2.1.5 dated 2015-09-04
DESCRIPTION | 11 - MD5 | 31 ++-- NAMESPACE | 3 R/diffcoeff.R | 44 ++++-- R/earth_surf.R | 12 - R/sw_dens.R | 4 R/xcbind.R |only build/vignette.rds |binary data/AtomicWeight.rda |binary data/Bathymetry.rda |binary data/Constants.rda |binary data/Oceans.rda |binary data/sw_sfac.rda |binary man/AtomicWeight.Rd | 8 - man/convert_p.Rd | 2 man/diffcoeff.Rd | 315 ++++++++++++++++++++++++++------------------------ man/molvol.Rd | 185 ++++++++++++++--------------- 17 files changed, 327 insertions(+), 288 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd9 versions 1.2 dated 2015-04-21 and 1.2.1 dated 2015-09-04
icd9-1.2.1/icd9/DESCRIPTION | 10 - icd9-1.2.1/icd9/MD5 | 97 ++++++++------- icd9-1.2.1/icd9/NAMESPACE | 11 + icd9-1.2.1/icd9/R/RcppExports.R | 32 ++--- icd9-1.2.1/icd9/R/benchmark.R | 27 ++-- icd9-1.2.1/icd9/R/convert.R | 1 icd9-1.2.1/icd9/R/datadocs.R | 2 icd9-1.2.1/icd9/R/ranges.R | 28 ++++ icd9-1.2.1/icd9/R/score.R | 2 icd9-1.2.1/icd9/R/util.R | 9 - icd9-1.2.1/icd9/R/zzz.R | 6 icd9-1.2.1/icd9/README.md | 14 +- icd9-1.2.1/icd9/build/vignette.rds |binary icd9-1.2.1/icd9/data/icd9Chapters.rda |binary icd9-1.2.1/icd9/data/mappingNames.rda |binary icd9-1.2.1/icd9/inst/doc/introduction.R | 1 icd9-1.2.1/icd9/inst/doc/introduction.Rmd | 5 icd9-1.2.1/icd9/inst/doc/introduction.html | 8 - icd9-1.2.1/icd9/inst/include/icd9_RcppExports.h | 102 ++++++++-------- icd9-1.2.1/icd9/man/convert.Rd | 25 ---- icd9-1.2.1/icd9/man/expandRangeWorker.Rd |only icd9-1.2.1/icd9/man/icd9AddLeadingZeroes.Rd | 8 - icd9-1.2.1/icd9/man/icd9ChaptersToMap.Rd | 5 icd9-1.2.1/icd9/man/icd9DropLeadingZeroes.Rd | 5 icd9-1.2.1/icd9/man/icd9ExpandMinor.Rd | 2 icd9-1.2.1/icd9/man/icd9Hierarchy.Rd | 2 icd9-1.2.1/icd9/man/icd9LongToWide.Rd | 5 icd9-1.2.1/icd9/man/icd9WideToLong.Rd | 5 icd9-1.2.1/icd9/man/logicalToBinary.Rd | 5 icd9-1.2.1/icd9/man/randomShortIcd9.Rd |only icd9-1.2.1/icd9/man/strMultiMatch.Rd | 5 icd9-1.2.1/icd9/man/zip_single.Rd |only icd9-1.2.1/icd9/src/RcppExports.cpp | 148 ++++++++++++------------ icd9-1.2.1/icd9/src/comorbid.cpp | 4 icd9-1.2.1/icd9/src/convert.cpp | 133 +++++++++++---------- icd9-1.2.1/icd9/src/convert.h | 4 icd9-1.2.1/icd9/src/longToWide.cpp | 6 icd9-1.2.1/icd9/src/manip.cpp | 20 +-- icd9-1.2.1/icd9/src/manip.h | 4 icd9-1.2.1/icd9/src/ranges.cpp | 22 +-- icd9-1.2.1/icd9/src/util.cpp | 3 icd9-1.2.1/icd9/tests/testthat/helper-base.R | 2 icd9-1.2.1/icd9/tests/testthat/test-comorbid.R | 8 + icd9-1.2.1/icd9/tests/testthat/test-condense.R | 2 icd9-1.2.1/icd9/tests/testthat/test-convert.R | 10 - icd9-1.2.1/icd9/tests/testthat/test-score.R | 2 icd9-1.2.1/icd9/tools/docker-ubsan-clang.sh |only icd9-1.2.1/icd9/tools/r-devel-ubsan-clang |only icd9-1.2.1/icd9/tools/rocker-devel.sh |only icd9-1.2.1/icd9/tools/rocker-san.sh |only icd9-1.2.1/icd9/tools/rocker-ubsan-clang.sh |only icd9-1.2.1/icd9/tools/rocker-vanilla.sh |only icd9-1.2.1/icd9/vignettes/introduction.Rmd | 5 icd9-1.2/icd9/R/RcppExportsShim.R |only 54 files changed, 409 insertions(+), 386 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.5 dated 2015-05-29 and 1.1.6 dated 2015-09-04
ExomeDepth-1.1.5/ExomeDepth/vignettes/.install_extras |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.R |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.pdf |only ExomeDepth-1.1.6/ExomeDepth/DESCRIPTION | 8 +- ExomeDepth-1.1.6/ExomeDepth/MD5 | 27 +++++----- ExomeDepth-1.1.6/ExomeDepth/NAMESPACE | 3 + ExomeDepth-1.1.6/ExomeDepth/R/class_definition.R | 2 ExomeDepth-1.1.6/ExomeDepth/R/plot_CNVs_method.R | 2 ExomeDepth-1.1.6/ExomeDepth/build/vignette.rds |binary ExomeDepth-1.1.6/ExomeDepth/data/Conrad.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/ExomeCount.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/exons.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/exons.hg19.X.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/genes.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.R |only ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary ExomeDepth-1.1.6/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw |only 18 files changed, 23 insertions(+), 19 deletions(-)
Title: Differential Exon Usage Test for RNA-Seq Data via Empirical
Bayes Shrinkage of the Dispersion Parameter
Description: Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.
Author: Sean Ruddy
Maintainer: Sean Ruddy <s.ruddy@yahoo.com>
Diff between DoubleExpSeq versions 1.0 dated 2014-05-14 and 1.1 dated 2015-09-04
DESCRIPTION | 15 ++++---- MD5 | 14 ++++---- NAMESPACE | 5 ++ R/DBGLM1.R | 6 ++- R/DoubleExpSeq-internal.R | 77 ++++++++++++++++++++++++++++++++++++++++++++-- R/EstimateDEBDisp.R | 21 +++++++++--- data/exon.RData |binary man/EstimateDEBDisp.Rd | 8 +++- 8 files changed, 119 insertions(+), 27 deletions(-)
Title: Multi-Resolution Estimation of the Hazard Rate
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times. Can accommodate covariates under the proportional and non-proportional hazards setting, and is ideal for analysis of survival data with long-term follow-up.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar <yolanda.hagar@colorado.edu>
Diff between MRH versions 2.0 dated 2015-01-13 and 2.1 dated 2015-09-04
MRH-2.0/MRH/man/Prune.Rd |only MRH-2.0/MRH/man/find.Rmp.Rd |only MRH-2.1/MRH/DESCRIPTION | 8 ++++---- MRH-2.1/MRH/MD5 | 24 +++++++++++------------- MRH-2.1/MRH/NAMESPACE | 10 +++++++++- MRH-2.1/MRH/R/S3functions_BA.r | 9 +++++---- MRH-2.1/MRH/inst/doc/MRH.pdf |binary MRH-2.1/MRH/man/AnalyzeMultiple.Rd | 6 ++++++ MRH-2.1/MRH/man/CalcFunction.Rd | 6 +++--- MRH-2.1/MRH/man/DIC.Rd | 10 ++++++---- MRH-2.1/MRH/man/MRH-package.Rd | 4 ++-- MRH-2.1/MRH/man/MRH.Rd | 2 +- MRH-2.1/MRH/man/estimateMRH.Rd | 18 +++++++++++++++--- MRH-2.1/MRH/man/summary.MRH.Rd | 2 ++ 14 files changed, 64 insertions(+), 35 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train supervised and self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 2.0.18 dated 2015-03-25 and 2.0.19 dated 2015-09-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 7 +++++++ NEWS | 6 ++++++ R/plot.kohonen.R | 4 ++-- 5 files changed, 22 insertions(+), 9 deletions(-)
Title: Predict Gender from Names Using Historical Data
Description: Encodes gender based on names and dates of birth using historical
datasets. By using these datasets instead of lists of male and female names,
this package is able to more accurately guess the gender of a name, and it
is able to report the probability that a name was male or female.
Author: Lincoln Mullen [aut, cre],
Cameron Blevins [ctb],
Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between gender versions 0.5.0 dated 2015-08-22 and 0.5.1 dated 2015-09-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 +++++ R/install-genderdata-package.R | 8 +++++--- README.md | 12 ++++++++++-- 5 files changed, 28 insertions(+), 13 deletions(-)
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
Diff between FRESA.CAD versions 2.0.2 dated 2015-02-22 and 2.1.3 dated 2015-09-04
FRESA.CAD-2.0.2/FRESA.CAD/R/NeRIBasedFRESA.Model.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/ReclassificationFRESA.Model.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/backVarElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/backVarNeRIElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapValidation.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapValidationNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapVarElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapVarNeRIElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/crossValidationFeatureSelection.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/crossValidationNeRIFeatureSelection.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/getKNNpredictionFromFormula.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/getVarNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/getVarReclassification.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/medianPredict.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/plot.bootstrapValidation.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/plot.bootstrapValidationNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/residualtForNeRIs.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/summaryReport.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/uniRankVar.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/update.uniRankVar.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/updateModel.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/updateNeRImodel.R |only FRESA.CAD-2.0.2/FRESA.CAD/man/NeRIBasedFRESA.Model.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/ReclassificationFRESA.Model.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/backVarElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/backVarNeRIElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapValidation.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapValidationNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapVarElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapVarNeRIElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/crossValidationFeatureSelection.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/crossValidationNeRIFeatureSelection.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/getVarNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/getVarReclassification.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/plot.bootstrapValidation.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/plot.bootstrapValidationNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/residualForNeRIs.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/updateModel.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/updateNeRImodel.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/DESCRIPTION | 11 FRESA.CAD-2.1.3/FRESA.CAD/MD5 | 132 +- FRESA.CAD-2.1.3/FRESA.CAD/NAMESPACE | 14 FRESA.CAD-2.1.3/FRESA.CAD/NEWS | 72 - FRESA.CAD-2.1.3/FRESA.CAD/R/FRESA.Model.R | 119 + FRESA.CAD-2.1.3/FRESA.CAD/R/ForwardSelection.Model.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/ForwardSelection.Model.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/backVarElimination.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/backVarElimination.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapValidation.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapValidation.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapVarElimination.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapVarElimination.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/crossValidationFeatureSelection.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/crossValidationFeatureSelection.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getKNNpredictionFromFormula.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getVar.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getVar.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/medianPredict.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/modelFitting.R | 14 FRESA.CAD-2.1.3/FRESA.CAD/R/plot.bootstrapValidation.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/plot.bootstrapValidation.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/plotModels.ROC.R | 10 FRESA.CAD-2.1.3/FRESA.CAD/R/reportEquivalentVariables.R | 45 FRESA.CAD-2.1.3/FRESA.CAD/R/residualtForFRESA.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/summary.bootstrapValidation.R | 4 FRESA.CAD-2.1.3/FRESA.CAD/R/summaryReport.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/timeSerieAnalysis.R | 86 + FRESA.CAD-2.1.3/FRESA.CAD/R/uniRankVar.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/univariateRankVariables.R | 4 FRESA.CAD-2.1.3/FRESA.CAD/R/update.uniRankVar.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/updateModel.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/updateModel.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/man/FRESA.CAD-package.Rd | 24 FRESA.CAD-2.1.3/FRESA.CAD/man/FRESA.Model.Rd | 10 FRESA.CAD-2.1.3/FRESA.CAD/man/ForwardModel.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/ForwardModel.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/backVarElimination.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/backVarElimination.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapValidation.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapValidation.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapVarElimination.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapVarElimination.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/crossValidationFeatureSelection.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/crossValidationFeatureSelection.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/getVar.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/getVar.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/heatMaps.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/improvedResiduals.Rd | 6 FRESA.CAD-2.1.3/FRESA.CAD/man/medianPredict.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/plot.bootstrapValidation.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/plot.bootstrapValidation.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/plotModels.ROC.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/predictForFresa.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/reportEquivalentVariables.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/residualForFRESA.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/summary.bootstrapValidation.Rd | 16 FRESA.CAD-2.1.3/FRESA.CAD/man/summaryReport.Rd | 10 FRESA.CAD-2.1.3/FRESA.CAD/man/uniRankVar.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/univariateRankVariables.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/updateModel.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/updateModel.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/src/FRESAcommons.cpp | 658 ++++++---- FRESA.CAD-2.1.3/FRESA.CAD/src/FRESAcommons.h | 40 FRESA.CAD-2.1.3/FRESA.CAD/src/binaryFeatureSelectionCpp.cpp | 262 ++- FRESA.CAD-2.1.3/FRESA.CAD/src/regresionFeatureSelectionCpp.cpp | 220 ++- 106 files changed, 1120 insertions(+), 659 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R
interface. It contains several machine learning model learning techniques in
classification and regression, for example classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with ExplainPrediction package.
The package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for example to discretize
numeric attributes.
Its additional feature is OrdEval algorithm and its visualization used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 0.9.46 dated 2015-06-03 and 1.47.1 dated 2015-09-04
ChangeLog | 2 DESCRIPTION | 32 MD5 | 54 - NAMESPACE | 15 R/Rinterface.R | 1888 ++++++++++++++++++++++++----------------------- R/util.R | 50 - man/CORElearn-package.Rd | 40 man/CoreModel.Rd | 20 man/discretize.Rd | 60 + man/helpCore.Rd | 10 man/modelEval.Rd | 8 man/predict.CoreModel.Rd | 1 man/rfClustering.Rd | 2 man/saveRF.Rd | 4 src/Rfront.cpp | 86 +- src/Rfront.h | 5 src/binarize.cpp | 47 + src/binarizeReg.cpp | 240 +++++ src/dataStore.h | 2 src/estimator.h | 1 src/estimatorReg.cpp | 3 src/estimatorReg.h | 3 src/expr.cpp | 7 src/frontend.cpp | 2 src/options.cpp | 18 src/options.h | 2 src/treenodeReg.cpp | 2 src/trutilReg.cpp | 112 -- 28 files changed, 1530 insertions(+), 1186 deletions(-)
Title: Chemometrics with R - Multivariate Data Analysis in the Natural
Sciences and Life Sciences
Description: Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
Author: Ron Wehren9
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ChemometricsWithR versions 0.1.8 dated 2014-08-04 and 0.1.9 dated 2015-09-04
ChemometricsWithR-0.1.8/ChemometricsWithR/R/classvec2classmat.R |only ChemometricsWithR-0.1.8/ChemometricsWithR/man/classvec2classmat.Rd |only ChemometricsWithR-0.1.9/ChemometricsWithR/DESCRIPTION | 14 +++---- ChemometricsWithR-0.1.9/ChemometricsWithR/MD5 | 6 +-- ChemometricsWithR-0.1.9/ChemometricsWithR/NAMESPACE | 18 +++++++++- 5 files changed, 26 insertions(+), 12 deletions(-)
More information about ChemometricsWithR at CRAN
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