Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++++-- NAMESPACE | 2 +- R/symscorestat.R |only inst |only man/symscorestat.Rd |only src/signtestperm.f90 |only 7 files changed, 11 insertions(+), 7 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.7.0 dated 2015-10-01 and 0.7.1 dated 2015-10-05
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Allele Imputation and Haplotype Reconstruction from Pedigree
Databases
Description: Simulation of alphanumeric alleles, imputation of genetic missing data and reconstruction of non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many different factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used either simulated datasets or loaded databases (in .ped file biallelic format). Haplotype reconstruction can be performed even with missing data because of alleHap, firstly imputes the genotypes. All this considering that each member (due to meiosis) should unequivocally have two alleles, one inherited from each parent.
Author: Nathan Medina-Rodriguez and Angelo Santana
Maintainer: Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>
Diff between alleHap versions 0.7.2 dated 2014-08-10 and 0.9.2 dated 2015-10-05
alleHap-0.7.2/alleHap/R/buildFunctions.R |only alleHap-0.7.2/alleHap/R/buildHaps.R |only alleHap-0.7.2/alleHap/R/simFams.R |only alleHap-0.7.2/alleHap/R/simFunctions.R |only alleHap-0.7.2/alleHap/man/buildHaps.Rd |only alleHap-0.7.2/alleHap/man/simFams.Rd |only alleHap-0.9.2/alleHap/DESCRIPTION | 26 ++++------ alleHap-0.9.2/alleHap/MD5 | 33 +++++++++---- alleHap-0.9.2/alleHap/NAMESPACE | 13 +++-- alleHap-0.9.2/alleHap/R/alleImputer.R |only alleHap-0.9.2/alleHap/R/alleLoader.R |only alleHap-0.9.2/alleHap/R/alleSimulator.R |only alleHap-0.9.2/alleHap/R/hapPhaser.R |only alleHap-0.9.2/alleHap/build |only alleHap-0.9.2/alleHap/inst |only alleHap-0.9.2/alleHap/man/alleHap-package.Rd | 65 ++++++++++++++++++--------- alleHap-0.9.2/alleHap/man/alleImputer.Rd |only alleHap-0.9.2/alleHap/man/alleLoader.Rd |only alleHap-0.9.2/alleHap/man/alleSimulator.Rd |only alleHap-0.9.2/alleHap/man/hapPhaser.Rd |only alleHap-0.9.2/alleHap/vignettes |only 21 files changed, 88 insertions(+), 49 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>
Diff between mev versions 1.2 dated 2015-08-24 and 1.3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 2 NEWS | 21 ++ R/RcppExports.R | 93 ++++++++-- R/rmev_wrapper.R | 263 +++++++++++++++++++++++----- man/rmev.Rd | 22 +- man/rmevspec.Rd | 2 src/RcppExports.cpp | 78 +++++++- src/ev_sampling.cpp | 472 +++++++++++++++++++++++++++++++++++----------------- 10 files changed, 736 insertions(+), 243 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-2 dated 2015-09-11 and 0.1-3 dated 2015-10-05
gimme-0.1-2/gimme/man/gimme.Rd |only gimme-0.1-3/gimme/DESCRIPTION | 20 - gimme-0.1-3/gimme/MD5 | 34 + gimme-0.1-3/gimme/NAMESPACE | 25 + gimme-0.1-3/gimme/R/aggSEM.R | 41 +- gimme-0.1-3/gimme/R/deconvolve_funcs.R |only gimme-0.1-3/gimme/R/gimme-pkg.R | 21 - gimme-0.1-3/gimme/R/gimme.R | 529 +++++++++++++++--------------- gimme-0.1-3/gimme/R/gimmeInteractive.R |only gimme-0.1-3/gimme/R/indSEM.R | 40 +- gimme-0.1-3/gimme/R/spm_funcs.R |only gimme-0.1-3/gimme/man/aggSEM.Rd | 28 - gimme-0.1-3/gimme/man/gimme-package.Rd | 14 gimme-0.1-3/gimme/man/gimmeInteractive.Rd |only gimme-0.1-3/gimme/man/gimmeSEM.Rd |only gimme-0.1-3/gimme/man/indSEM.Rd | 33 - gimme-0.1-3/gimme/man/ts1.Rd | 3 gimme-0.1-3/gimme/man/ts2.Rd | 3 gimme-0.1-3/gimme/man/ts3.Rd | 3 gimme-0.1-3/gimme/man/ts4.Rd | 3 gimme-0.1-3/gimme/man/ts5.Rd | 3 21 files changed, 435 insertions(+), 365 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.0 dated 2015-09-07 and 0.8.1 dated 2015-10-05
future-0.8.0/future/R/tweakExpression.R |only future-0.8.0/future/tests/MulticoreFutureRegistry.R |only future-0.8.1/future/DESCRIPTION | 8 future-0.8.1/future/MD5 | 43 ++-- future-0.8.1/future/NEWS | 14 + future-0.8.1/future/R/FutureRegistry.R |only future-0.8.1/future/R/MulticoreFuture.R | 48 ---- future-0.8.1/future/R/availableCores.R | 2 future-0.8.1/future/R/eager.R | 13 + future-0.8.1/future/R/globals.R |only future-0.8.1/future/R/lazy.R | 32 --- future-0.8.1/future/R/multicore.R | 14 + future-0.8.1/future/build/vignette.rds |binary future-0.8.1/future/inst/doc/future.html | 10 future-0.8.1/future/inst/doc/future.md.rsp | 10 future-0.8.1/future/inst/doc/issues.html |only future-0.8.1/future/inst/doc/issues.md.rsp |only future-0.8.1/future/man/eager.Rd | 130 ++++++------ future-0.8.1/future/man/lazy.Rd | 212 ++++++++++---------- future-0.8.1/future/man/multicore.Rd | 161 +++++++-------- future-0.8.1/future/man/plan.Rd | 190 ++++++++--------- future-0.8.1/future/tests/FutureRegistry.R |only future-0.8.1/future/tests/dotdotdot.R |only future-0.8.1/future/tests/eager.R | 15 - future-0.8.1/future/tests/multicore.R | 29 +- future-0.8.1/future/vignettes/future.md.rsp | 10 future-0.8.1/future/vignettes/issues.md.rsp |only 27 files changed, 475 insertions(+), 466 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfmta versions 1.3-2 dated 2015-04-29 and 1.3-3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 12 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 7 files changed, 63 insertions(+), 89 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-4 dated 2015-09-11 and 2.1-5 dated 2015-10-05
DESCRIPTION | 8 MD5 | 14 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 src/plateau.cpp | 4 8 files changed, 66 insertions(+), 92 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements t-tests (independent and dependent samples), ANOVA (including between-within subject designs) and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut],
Felix Schoenbrodt [ctr]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.3-2 dated 2015-07-23 and 0.4-0 dated 2015-10-05
WRS2-0.3-2/WRS2/R/tsplit.R |only WRS2-0.3-2/WRS2/man/tsplit.Rd |only WRS2-0.4-0/WRS2/DESCRIPTION | 29 +++++------ WRS2-0.4-0/WRS2/MD5 | 92 +++++++++++++++++++++++------------- WRS2-0.4-0/WRS2/NAMESPACE | 12 ++++ WRS2-0.4-0/WRS2/R/ancboot.R | 8 ++- WRS2-0.4-0/WRS2/R/ancova.R | 22 +++++++- WRS2-0.4-0/WRS2/R/bwtrim.R |only WRS2-0.4-0/WRS2/R/mest.R |only WRS2-0.4-0/WRS2/R/msmedse.R | 2 WRS2-0.4-0/WRS2/R/pairdepb.R | 3 - WRS2-0.4-0/WRS2/R/pb2gen.R | 2 WRS2-0.4-0/WRS2/R/pbad2way.R | 34 +++++++------ WRS2-0.4-0/WRS2/R/print.mcp2.R |only WRS2-0.4-0/WRS2/R/print.pb2.R |only WRS2-0.4-0/WRS2/R/print.rmanovab.R | 2 WRS2-0.4-0/WRS2/R/print.yuen.R | 3 - WRS2-0.4-0/WRS2/R/rmmcp.R | 2 WRS2-0.4-0/WRS2/R/rungen.R |only WRS2-0.4-0/WRS2/R/runhat.R |only WRS2-0.4-0/WRS2/R/runmbo.R |only WRS2-0.4-0/WRS2/R/runmean.R |only WRS2-0.4-0/WRS2/R/sppba.R | 66 ++++++++++++------------- WRS2-0.4-0/WRS2/R/sppbb.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/sppbi.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/t2way.R | 9 ++- WRS2-0.4-0/WRS2/R/trimse.R | 2 WRS2-0.4-0/WRS2/R/tsub.R | 2 WRS2-0.4-0/WRS2/R/winmean.R |only WRS2-0.4-0/WRS2/R/winse.R |only WRS2-0.4-0/WRS2/R/yuen.R | 3 - WRS2-0.4-0/WRS2/R/yuenbt.R | 7 +- WRS2-0.4-0/WRS2/R/yuend.R | 43 +++++++++------- WRS2-0.4-0/WRS2/build |only WRS2-0.4-0/WRS2/data/Pygmalion.rda |only WRS2-0.4-0/WRS2/data/chile.rda |only WRS2-0.4-0/WRS2/data/electric.rda |only WRS2-0.4-0/WRS2/data/eurosoccer.rda |only WRS2-0.4-0/WRS2/data/goggles.rda |binary WRS2-0.4-0/WRS2/data/hangover.rda |only WRS2-0.4-0/WRS2/data/swimming.rda |only WRS2-0.4-0/WRS2/inst/NEWS.Rd | 12 ++++ WRS2-0.4-0/WRS2/inst/doc |only WRS2-0.4-0/WRS2/man/Pygmalion.Rd |only WRS2-0.4-0/WRS2/man/WineTasting.Rd | 2 WRS2-0.4-0/WRS2/man/ancova.Rd | 16 +----- WRS2-0.4-0/WRS2/man/bwtrim.Rd |only WRS2-0.4-0/WRS2/man/chile.Rd |only WRS2-0.4-0/WRS2/man/electric.Rd |only WRS2-0.4-0/WRS2/man/eurosoccer.Rd |only WRS2-0.4-0/WRS2/man/goggles.Rd | 8 ++- WRS2-0.4-0/WRS2/man/hangover.Rd |only WRS2-0.4-0/WRS2/man/rmanova.Rd | 2 WRS2-0.4-0/WRS2/man/rmanovab.Rd | 2 WRS2-0.4-0/WRS2/man/runmean.Rd |only WRS2-0.4-0/WRS2/man/swimming.Rd |only WRS2-0.4-0/WRS2/man/t3way.Rd | 2 WRS2-0.4-0/WRS2/man/trimse.Rd |only WRS2-0.4-0/WRS2/man/yuen.Rd | 21 +++----- WRS2-0.4-0/WRS2/man/yuend.Rd |only WRS2-0.4-0/WRS2/vignettes |only 61 files changed, 310 insertions(+), 202 deletions(-)
Title: Simulating Phylogenetic Trees
Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>
Diff between TreeSim versions 2.1 dated 2014-09-18 and 2.2 dated 2015-10-05
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- R/LTT.plot.gen.R | 35 ++++++++++++++++++++++------------- R/collapse.singles.R |only man/LTT.plot.Rd | 13 +++++++++++++ man/LTT.plot.gen.Rd | 40 +++++++++++++++++++++------------------- man/TreeSim-package.Rd | 8 ++++---- 8 files changed, 77 insertions(+), 50 deletions(-)
Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE).
Includes routines that: (1) generate gradient and Jacobian matrices (full and banded),
(2) find roots of non-linear equations by the Newton-Raphson method,
(3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running,
(4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ODEs
by numerical differencing (using the method-of-lines approach).
Includes fortran code.
Author: Karline Soetaert [aut, cre],
yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between rootSolve versions 1.6.5.1 dated 2014-11-06 and 1.6.6 dated 2015-10-05
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 6 ++++-- R/stode.R | 5 ++++- R/stodes.R | 3 +++ build/vignette.rds |binary 6 files changed, 24 insertions(+), 15 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.5 dated 2015-07-17 and 0.1.6 dated 2015-10-05
RcppRedis-0.1.5/RcppRedis/R/RcppExports.R |only RcppRedis-0.1.5/RcppRedis/src/RcppExports.cpp |only RcppRedis-0.1.6/RcppRedis/ChangeLog | 27 +++ RcppRedis-0.1.6/RcppRedis/DESCRIPTION | 8 - RcppRedis-0.1.6/RcppRedis/MD5 | 15 - RcppRedis-0.1.6/RcppRedis/README.md | 4 RcppRedis-0.1.6/RcppRedis/inst/NEWS.Rd | 23 ++ RcppRedis-0.1.6/RcppRedis/inst/tests/runit.basicRtests.R | 7 RcppRedis-0.1.6/RcppRedis/inst/tests/runit.listTests.R |only RcppRedis-0.1.6/RcppRedis/src/Redis.cpp | 117 +++++++++++++-- 10 files changed, 174 insertions(+), 27 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.2.0 dated 2015-03-31 and 0.5.0 dated 2015-10-05
gvc-0.2.0/gvc/R/block_matrix.R |only gvc-0.2.0/gvc/R/minus_block_matrix.R |only gvc-0.2.0/gvc/man/block_matrix.Rd |only gvc-0.2.0/gvc/man/minus_block_matrix.Rd |only gvc-0.2.0/gvc/tests/testthat/test_block_matrix.R |only gvc-0.2.0/gvc/tests/testthat/test_minus_block_matrix.R |only gvc-0.5.0/gvc/DESCRIPTION | 18 +-- gvc-0.5.0/gvc/MD5 | 47 +++++--- gvc-0.5.0/gvc/NAMESPACE | 9 + gvc-0.5.0/gvc/NEWS | 32 +++++ gvc-0.5.0/gvc/R/dfddva.R |only gvc-0.5.0/gvc/R/dfdfva.R |only gvc-0.5.0/gvc/R/downstream.R |only gvc-0.5.0/gvc/R/e2r.R | 18 +++ gvc-0.5.0/gvc/R/ffddva.R |only gvc-0.5.0/gvc/R/gvc.R |only gvc-0.5.0/gvc/R/i2e.R | 19 +++ gvc-0.5.0/gvc/R/nrca.R | 36 +----- gvc-0.5.0/gvc/R/upstream.R |only gvc-0.5.0/gvc/README.md | 96 ++++++++++++++--- gvc-0.5.0/gvc/build |only gvc-0.5.0/gvc/inst |only gvc-0.5.0/gvc/man/dfddva.Rd |only gvc-0.5.0/gvc/man/dfdfva.Rd |only gvc-0.5.0/gvc/man/downstream.Rd |only gvc-0.5.0/gvc/man/e2r.Rd | 19 +++ gvc-0.5.0/gvc/man/ffddva.Rd |only gvc-0.5.0/gvc/man/gvc.Rd |only gvc-0.5.0/gvc/man/i2e.Rd | 19 +++ gvc-0.5.0/gvc/man/nrca.Rd | 8 - gvc-0.5.0/gvc/man/upstream.Rd |only gvc-0.5.0/gvc/tests/testthat/test_e2r.R |only gvc-0.5.0/gvc/tests/testthat/test_i2e.R |only gvc-0.5.0/gvc/tests/testthat/test_nrca.R |only gvc-0.5.0/gvc/vignettes |only 35 files changed, 240 insertions(+), 81 deletions(-)
Title: Risk Regression Models for Survival Analysis with Competing
Risks
Description: Risk regression models for survival analysis with and without
competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 1.1.1 dated 2014-12-10 and 1.1.7 dated 2015-10-05
riskRegression-1.1.1/riskRegression/src/matrix.h |only riskRegression-1.1.7/riskRegression/DESCRIPTION | 17 riskRegression-1.1.7/riskRegression/MD5 | 71 +-- riskRegression-1.1.7/riskRegression/NAMESPACE | 23 + riskRegression-1.1.7/riskRegression/R/CSC.R | 180 ++++++---- riskRegression-1.1.7/riskRegression/R/FGR.R | 8 riskRegression-1.1.7/riskRegression/R/coef.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/plot.CauseSpecificCox.R | 34 + riskRegression-1.1.7/riskRegression/R/plot.predictedRisk.R | 2 riskRegression-1.1.7/riskRegression/R/plot.riskRegression.R | 9 riskRegression-1.1.7/riskRegression/R/plotEffects.R | 9 riskRegression-1.1.7/riskRegression/R/predict.CauseSpecificCox.R | 2 riskRegression-1.1.7/riskRegression/R/predict.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/predict.riskRegression.R | 5 riskRegression-1.1.7/riskRegression/R/print.CauseSpecificCox.R | 12 riskRegression-1.1.7/riskRegression/R/print.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/print.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/print.subjectWeights.R | 2 riskRegression-1.1.7/riskRegression/R/print.timevarCoefList.R | 2 riskRegression-1.1.7/riskRegression/R/riskRegression-package.R | 4 riskRegression-1.1.7/riskRegression/R/riskRegression.R | 11 riskRegression-1.1.7/riskRegression/R/subjectWeights.R | 14 riskRegression-1.1.7/riskRegression/R/summary.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/summary.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/man/CSC.Rd | 78 ++-- riskRegression-1.1.7/riskRegression/man/FGR.Rd | 44 +- riskRegression-1.1.7/riskRegression/man/Melanoma.Rd | 21 - riskRegression-1.1.7/riskRegression/man/plot.riskRegression.Rd | 52 +- riskRegression-1.1.7/riskRegression/man/plotEffects.Rd | 58 +-- riskRegression-1.1.7/riskRegression/man/predict.riskRegression.Rd | 21 - riskRegression-1.1.7/riskRegression/man/riskRegression.Rd | 100 ++--- riskRegression-1.1.7/riskRegression/man/subjectWeights.Rd | 61 +-- riskRegression-1.1.7/riskRegression/src/matrix.c | 2 riskRegression-1.1.7/riskRegression/src/riskregression.h | 50 ++ riskRegression-1.1.7/riskRegression/tests/test-FGR.R | 21 + riskRegression-1.1.7/riskRegression/tests/testthat/CauseSpecificCoxRegression.R | 7 riskRegression-1.1.7/riskRegression/tests/testthat/brier.R | 4 37 files changed, 547 insertions(+), 389 deletions(-)
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Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 1.5.1 dated 2014-12-10 and 1.5.5 dated 2015-10-05
prodlim-1.5.1/prodlim/R/contrastMethods.R |only prodlim-1.5.1/prodlim/R/modelMatrix.R |only prodlim-1.5.1/prodlim/R/readFormula.R |only prodlim-1.5.5/prodlim/DESCRIPTION | 11 prodlim-1.5.5/prodlim/MD5 | 132 ++++----- prodlim-1.5.5/prodlim/NAMESPACE | 34 ++ prodlim-1.5.5/prodlim/R/EventHistory.frame.R | 3 prodlim-1.5.5/prodlim/R/Hist.R | 4 prodlim-1.5.5/prodlim/R/List2Matrix.R |only prodlim-1.5.5/prodlim/R/atRisk.R | 113 ++++---- prodlim-1.5.5/prodlim/R/backGround.R | 63 ++-- prodlim-1.5.5/prodlim/R/checkCauses.R |only prodlim-1.5.5/prodlim/R/dimColor.R | 4 prodlim-1.5.5/prodlim/R/followup.R |only prodlim-1.5.5/prodlim/R/getStates.R | 6 prodlim-1.5.5/prodlim/R/jackknife.R | 4 prodlim-1.5.5/prodlim/R/lifeTab.competing.risks.R | 275 ++++++++++---------- prodlim-1.5.5/prodlim/R/lifeTab.survival.R | 4 prodlim-1.5.5/prodlim/R/plot.Hist.R | 3 prodlim-1.5.5/prodlim/R/plot.prodlim.R | 161 ++++++++--- prodlim-1.5.5/prodlim/R/predict.prodlim.R | 77 ++--- prodlim-1.5.5/prodlim/R/print.Hist.R | 3 prodlim-1.5.5/prodlim/R/print.IntIndex.R | 3 prodlim-1.5.5/prodlim/R/print.neighborhood.R | 3 prodlim-1.5.5/prodlim/R/print.prodlim.R | 3 prodlim-1.5.5/prodlim/R/print.quantile.prodlim.R | 31 +- prodlim-1.5.5/prodlim/R/print.summary.prodlim.R | 39 +- prodlim-1.5.5/prodlim/R/prodlim-package.R |only prodlim-1.5.5/prodlim/R/prodlim.R | 90 +++--- prodlim-1.5.5/prodlim/R/prodlimIcensSurv.R | 158 +++++------ prodlim-1.5.5/prodlim/R/quantile.prodlim.R | 50 ++- prodlim-1.5.5/prodlim/R/strip.terms.R | 4 prodlim-1.5.5/prodlim/R/summary.Hist.R | 3 prodlim-1.5.5/prodlim/R/summary.prodlim.R | 154 ++++++----- prodlim-1.5.5/prodlim/man/EventHistory.frame.Rd | 71 ++--- prodlim-1.5.5/prodlim/man/Hist.Rd | 159 +++++------ prodlim-1.5.5/prodlim/man/List2Matrix.Rd |only prodlim-1.5.5/prodlim/man/PercentAxis.Rd | 13 prodlim-1.5.5/prodlim/man/SimCompRisk.Rd | 14 - prodlim-1.5.5/prodlim/man/SimSurv.Rd | 17 - prodlim-1.5.5/prodlim/man/SmartControl.Rd | 47 +-- prodlim-1.5.5/prodlim/man/atRisk.Rd | 61 +--- prodlim-1.5.5/prodlim/man/backGround.Rd | 31 +- prodlim-1.5.5/prodlim/man/confInt.Rd | 47 +-- prodlim-1.5.5/prodlim/man/crModel.Rd | 13 prodlim-1.5.5/prodlim/man/dimColor.Rd | 17 - prodlim-1.5.5/prodlim/man/getEvent.Rd | 22 - prodlim-1.5.5/prodlim/man/getStates.Rd | 7 prodlim-1.5.5/prodlim/man/jackknife.Rd | 35 +- prodlim-1.5.5/prodlim/man/leaveOneOut.Rd | 16 - prodlim-1.5.5/prodlim/man/markTime.Rd | 24 - prodlim-1.5.5/prodlim/man/meanNeighbors.Rd | 11 prodlim-1.5.5/prodlim/man/model.design.Rd | 91 ++---- prodlim-1.5.5/prodlim/man/neighborhood.Rd | 49 +-- prodlim-1.5.5/prodlim/man/parseSpecialNames.Rd | 21 - prodlim-1.5.5/prodlim/man/plot.Hist.Rd | 85 ++---- prodlim-1.5.5/prodlim/man/plot.prodlim.Rd | 275 ++++++++++---------- prodlim-1.5.5/prodlim/man/plotCompetingRiskModel.Rd | 12 prodlim-1.5.5/prodlim/man/plotIllnessDeathModel.Rd | 18 - prodlim-1.5.5/prodlim/man/predict.prodlim.Rd | 94 +++--- prodlim-1.5.5/prodlim/man/predictSurvIndividual.Rd | 14 - prodlim-1.5.5/prodlim/man/print.prodlim.Rd | 15 - prodlim-1.5.5/prodlim/man/prodlim.Rd | 266 ++++++++----------- prodlim-1.5.5/prodlim/man/quantile.prodlim.Rd | 32 +- prodlim-1.5.5/prodlim/man/row.match.Rd | 21 - prodlim-1.5.5/prodlim/man/sindex.Rd | 42 +-- prodlim-1.5.5/prodlim/man/strip.terms.Rd | 35 +- prodlim-1.5.5/prodlim/man/summary.Hist.Rd | 21 - prodlim-1.5.5/prodlim/man/summary.prodlim.Rd | 90 +++--- prodlim-1.5.5/prodlim/man/survModel.Rd | 12 prodlim-1.5.5/prodlim/tests/testthat/prodlim.R | 29 +- 71 files changed, 1708 insertions(+), 1554 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2.4.4 dated 2014-12-05 and 2.4.7 dated 2015-10-05
pec-2.4.4/pec/data/GBSG2.RData |only pec-2.4.7/pec/DESCRIPTION | 15 pec-2.4.7/pec/MD5 | 152 +++-- pec-2.4.7/pec/NAMESPACE | 63 ++ pec-2.4.7/pec/R/R2.R | 2 pec-2.4.7/pec/R/calPlot.R | 625 +++++++++++++++-------- pec-2.4.7/pec/R/cindex.R | 92 +-- pec-2.4.7/pec/R/crps.R | 2 pec-2.4.7/pec/R/ibs.R | 2 pec-2.4.7/pec/R/ipcw.R | 16 pec-2.4.7/pec/R/marginal.prodlim.R | 6 pec-2.4.7/pec/R/pec-package.R | 5 pec-2.4.7/pec/R/pec.R | 78 +- pec-2.4.7/pec/R/plot.Cindex.R | 2 pec-2.4.7/pec/R/plot.calibrationPlot.R |only pec-2.4.7/pec/R/plot.confScoreSurv.R | 2 pec-2.4.7/pec/R/plot.pec.R | 94 ++- pec-2.4.7/pec/R/plot.riskReclassification.R |only pec-2.4.7/pec/R/plotPredictEventProb.R | 2 pec-2.4.7/pec/R/plotPredictSurvProb.R | 2 pec-2.4.7/pec/R/predictEventProb.R | 32 - pec-2.4.7/pec/R/predictEventProb.coxboost.R | 8 pec-2.4.7/pec/R/predictEventProb.pseudoForest.R | 4 pec-2.4.7/pec/R/predictEventProb.selectFGR.R | 6 pec-2.4.7/pec/R/predictLifeYearsLost.R | 19 pec-2.4.7/pec/R/predictRestrictedMeanTime.R |only pec-2.4.7/pec/R/predictSurvProb.FastBw.R | 35 - pec-2.4.7/pec/R/predictSurvProb.R | 60 +- pec-2.4.7/pec/R/predictSurvProb.cforest.R | 6 pec-2.4.7/pec/R/predictSurvProb.ctree.R | 4 pec-2.4.7/pec/R/predictSurvProb.penfitS3.R | 2 pec-2.4.7/pec/R/predictSurvProb.pseudoForest.R | 4 pec-2.4.7/pec/R/print.Cindex.R | 2 pec-2.4.7/pec/R/print.ConfScoreSurv.R | 2 pec-2.4.7/pec/R/print.IPCW.R | 2 pec-2.4.7/pec/R/print.R2.R | 2 pec-2.4.7/pec/R/print.calibrationPlot.R |only pec-2.4.7/pec/R/print.crps.R | 2 pec-2.4.7/pec/R/print.method.R | 2 pec-2.4.7/pec/R/print.multiSplitTest.R | 2 pec-2.4.7/pec/R/print.pec.R | 19 pec-2.4.7/pec/R/print.reclassification.R |only pec-2.4.7/pec/R/print.splitMethod.R | 2 pec-2.4.7/pec/R/print.vandeWielTest.R | 2 pec-2.4.7/pec/R/pseudoPecMethods.R | 41 - pec-2.4.7/pec/R/reclass.R |only pec-2.4.7/pec/R/resolveSplitMethod.R | 2 pec-2.4.7/pec/R/selectCox.R | 7 pec-2.4.7/pec/R/simCost.R | 4 pec-2.4.7/pec/R/summary.Cindex.R | 2 pec-2.4.7/pec/R/summary.confScoreSurv.R | 2 pec-2.4.7/pec/R/summary.pec.R | 2 pec-2.4.7/pec/R/wallyPlot.R |only pec-2.4.7/pec/data/GBSG2.csv.gz |only pec-2.4.7/pec/man/GBSG2.Rd | 21 pec-2.4.7/pec/man/Pbc3.Rd | 35 - pec-2.4.7/pec/man/R2.Rd | 58 +- pec-2.4.7/pec/man/Special.Rd | 48 - pec-2.4.7/pec/man/calPlot.Rd | 248 +++++---- pec-2.4.7/pec/man/cindex.Rd | 395 ++++++-------- pec-2.4.7/pec/man/cost.Rd | 19 pec-2.4.7/pec/man/coxboost.Rd | 42 - pec-2.4.7/pec/man/crps.Rd | 49 - pec-2.4.7/pec/man/ipcw.Rd | 100 +-- pec-2.4.7/pec/man/pec.Rd | 635 ++++++++++-------------- pec-2.4.7/pec/man/pecCforest.Rd | 17 pec-2.4.7/pec/man/pecCtree.Rd | 4 pec-2.4.7/pec/man/pecRpart.Rd | 11 pec-2.4.7/pec/man/plot.calibrationPlot.Rd |only pec-2.4.7/pec/man/plot.pec.Rd | 118 ++-- pec-2.4.7/pec/man/plotPredictEventProb.Rd | 85 +-- pec-2.4.7/pec/man/plotPredictSurvProb.Rd | 84 +-- pec-2.4.7/pec/man/predictEventProb.Rd | 43 - pec-2.4.7/pec/man/predictLifeYearsLost.Rd | 49 - pec-2.4.7/pec/man/predictRestrictedMeanTime.Rd |only pec-2.4.7/pec/man/predictSurvProb.Rd | 103 ++- pec-2.4.7/pec/man/print.pec.Rd | 24 pec-2.4.7/pec/man/reclass.Rd |only pec-2.4.7/pec/man/resolvesplitMethod.Rd | 39 - pec-2.4.7/pec/man/selectCox.Rd | 31 - pec-2.4.7/pec/man/selectFGR.Rd | 35 - pec-2.4.7/pec/man/simCost.Rd | 7 pec-2.4.7/pec/man/wallyPlot.Rd |only pec-2.4.7/pec/src/auc.c |only 84 files changed, 1949 insertions(+), 1788 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.3.0 dated 2015-06-15 and 0.4.0 dated 2015-10-05
diagonals-0.3.0/diagonals/R/diag.R |only diagonals-0.3.0/diagonals/man/diag-set.Rd |only diagonals-0.4.0/diagonals/DESCRIPTION | 6 diagonals-0.4.0/diagonals/MD5 | 20 - diagonals-0.4.0/diagonals/NEWS | 6 diagonals-0.4.0/diagonals/R/fatdiag.R | 139 ++++++---- diagonals-0.4.0/diagonals/R/matricise.R |only diagonals-0.4.0/diagonals/README.md | 1 diagonals-0.4.0/diagonals/build/vignette.rds |binary diagonals-0.4.0/diagonals/inst/doc/fatdiag.html | 323 +++++++++++++++++------- diagonals-0.4.0/diagonals/man/fatdiag.Rd | 12 diagonals-0.4.0/diagonals/man/matricise.Rd |only diagonals-0.4.0/diagonals/tests |only 13 files changed, 357 insertions(+), 150 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-4 dated 2015-09-17 and 0.9-5 dated 2015-10-05
DESCRIPTION | 14 ++++----- MD5 | 41 ++++++++++++++-------------- NAMESPACE | 1 R/optics.R | 66 +++++++++++++++++++++++----------------------- README.md |only inst/NEWS | 8 ++++- inst/tests/test-lof.R | 11 +++++-- inst/tests/test-optics.R | 26 +++++++++++++++--- man/dbscan.Rd | 2 + man/lof.Rd | 1 man/optics.Rd | 17 +++++++++-- src/ANN.cpp | 6 ++-- src/R_kNN.cpp | 7 ++-- src/R_optics.cpp | 44 ++++++++++++++++++------------ src/R_regionQuery.cpp | 2 - src/kd_dump.cpp | 2 - src/kd_fix_rad_search.cpp | 10 +++--- src/kd_pr_search.cpp | 12 ++++---- src/kd_search.cpp | 12 ++++---- src/kd_util.cpp | 10 +++--- src/pr_queue.h | 10 +++--- src/pr_queue_k.h | 2 - 22 files changed, 177 insertions(+), 127 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.3 dated 2015-09-09 and 1.0.4 dated 2015-10-05
DESCRIPTION | 10 - MD5 | 37 +++---- NAMESPACE | 1 R/adjust_functions.R | 21 ++-- R/cate.R | 225 +++++++++++++++++++++++++++++++------------- R/factor_functions.R | 1 R/other_methods.R | 81 +++++++++------ R/simulate_functions.R | 5 build/vignette.rds |binary inst/doc/cate-vignette.R | 21 ++-- inst/doc/cate-vignette.Rnw | 43 +++++--- inst/doc/cate-vignette.pdf |binary man/adjust.latent.Rd | 8 - man/cate.Rd | 54 +++++++--- man/est.confounder.num.Rd | 15 +- man/gen.sim.data.Rd | 4 man/gender.sm.Rd | 1 man/parse.cate.formula.Rd |only man/wrapper.Rd | 32 +++--- vignettes/cate-vignette.Rnw | 43 +++++--- 20 files changed, 397 insertions(+), 205 deletions(-)