Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files, sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.6.0 dated 2016-07-05 and 3.6.1 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 15 +++++++++------ NEWS | 8 ++++++++ R/readMat.R | 26 ++++++++++++++++++-------- R/writeMat.R | 2 +- inst/mat-files/Matrix-v6.mat |only inst/mat-files/Matrix-v7.3.mat |only inst/mat-files/Matrix-v7.mat |only man/R.matlab-package.Rd | 2 +- tests/readMat.R | 13 +++++++++++++ 10 files changed, 54 insertions(+), 20 deletions(-)
Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph
proposed by Rosenbaum is useful
for checking some properties of various
sorts of latent scale, this program generates commands
to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between latdiag versions 0.2-2 dated 2016-03-14 and 0.2-3 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ inst/CITATION | 6 +++--- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Author: Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, and David A. MacIntyre
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 1.0 dated 2016-10-12 and 1.1 dated 2016-10-19
DESCRIPTION | 8 MD5 | 30 +-- R/KOD.R | 38 +-- build/vignette.rds |binary inst/doc/KODAMA.Rmd | 4 inst/doc/KODAMA.pdf | 498 +++++++++++++++++++++++++-------------------------- man/core_cpp.Rd | 3 man/k.test.Rd | 2 man/knn.kodama.Rd | 1 man/loads.Rd | 2 man/mcplot.Rd | 6 man/pls.kodama.Rd | 1 src/RcppExports.cpp | 4 src/kd_split.cpp | 6 src/prova.cpp | 355 ++++++++++++------------------------ vignettes/KODAMA.Rmd | 4 16 files changed, 429 insertions(+), 533 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.1.6.0 dated 2016-08-29 and 0.1.7.0 dated 2016-10-19
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/RcppExports.R | 20 +++++++++++++------- R/jmcm.R | 6 +++--- man/acd_estimation.Rd | 8 ++++++-- man/hpc_estimation.Rd | 8 ++++++-- man/mcd_estimation.Rd | 8 ++++++-- src/RcppExports.cpp | 44 +++++++++++++++++++++++++------------------- src/acd.cpp | 9 +++++++-- src/acd.h | 8 ++++++++ src/external.cpp | 46 ++++++++++++++++++++++++++++++++++++++-------- src/hpc.cpp | 9 +++++++-- src/hpc.h | 8 ++++++++ src/mcd.cpp | 9 +++++++-- src/mcd.h | 8 ++++++++ 15 files changed, 159 insertions(+), 66 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between gamboostLSS versions 1.2-1 dated 2016-03-11 and 1.2-2 dated 2016-10-19
gamboostLSS-1.2-1/gamboostLSS/vignettes/cvrisk |only gamboostLSS-1.2-2/gamboostLSS/DESCRIPTION | 10 - gamboostLSS-1.2-2/gamboostLSS/MD5 | 38 ++--- gamboostLSS-1.2-2/gamboostLSS/build/vignette.rds |binary gamboostLSS-1.2-2/gamboostLSS/data/india.RData |binary gamboostLSS-1.2-2/gamboostLSS/data/india.bnd.RData |binary gamboostLSS-1.2-2/gamboostLSS/inst/CITATION | 32 ++-- gamboostLSS-1.2-2/gamboostLSS/inst/NEWS.Rd | 10 + gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.R | 71 +++------- gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.Rnw | 39 +++-- gamboostLSS-1.2-2/gamboostLSS/inst/doc/gamboostLSS_Tutorial.pdf |binary gamboostLSS-1.2-2/gamboostLSS/man/as.families.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/cvrisk.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/families.Rd | 2 gamboostLSS-1.2-2/gamboostLSS/man/gamboostLSS-package.Rd | 8 - gamboostLSS-1.2-2/gamboostLSS/man/mboostLSS.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/methods.Rd | 6 gamboostLSS-1.2-2/gamboostLSS/man/weighted_median.Rd | 7 gamboostLSS-1.2-2/gamboostLSS/vignettes/bib.bib | 8 - gamboostLSS-1.2-2/gamboostLSS/vignettes/fig-crossvalidation.pdf |only gamboostLSS-1.2-2/gamboostLSS/vignettes/gamboostLSS_Tutorial.Rnw | 39 +++-- 21 files changed, 153 insertions(+), 135 deletions(-)
Title: Logistic Regression
Description: The BayesLogit package does posterior simulation for binomial and
multinomial logistic regression using the Polya-Gamma latent variable
technique. This method is fully automatic, exact, and fast. A routine to
efficiently sample from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle <jesse.windle@gmail.com>
Diff between BayesLogit versions 0.5.1 dated 2014-07-21 and 0.6 dated 2016-10-19
DESCRIPTION | 8 +++--- MD5 | 36 ++++++++++++++--------------- NAMESPACE | 5 +++- R/LogitWrapper.R | 3 +- man/logit.combine.Rd | 3 +- src/CUBS_update.cpp | 6 ++++ src/DynExpFamMH.cpp | 6 ++++ src/FSF_nmix.cpp | 6 ++++ src/InvertY.cpp | 7 +++++ src/LogitWrapper.cpp | 6 ++++ src/Matrix.h | 27 +++++++++++++++++++++ src/MatrixFrame.cpp | 3 ++ src/MatrixFrame.h | 62 ++++++++++++++++++++++++++++++++++++++++++++++++-- src/PolyaGamma.cpp | 24 +++++++++++++++++++ src/PolyaGamma.h | 2 - src/PolyaGammaAlt.cpp | 6 ++++ src/PolyaGammaSP.cpp | 6 ++++ src/RNG.cpp | 7 +++++ src/RRNG.cpp | 7 +++++ 19 files changed, 202 insertions(+), 28 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.6 dated 2015-10-20 and 1.7 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Barnard.c | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 2.0 dated 2016-08-01 and 2.2 dated 2016-10-19
DESCRIPTION | 8 - MD5 | 14 +- R/dom_optimal_allocation.R | 226 ++++++++++++++++++------------------------ R/expvar.R | 87 ++++++++-------- inst/CITATION | 4 inst/NEWS | 4 man/expvar.Rd | 2 man/surveyplanning-package.Rd | 4 8 files changed, 169 insertions(+), 180 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Hierarchical Latent Space Network Model (HLSM)
Description: R-package to implement Hierarchical Latent Space Network Model (HLSM) for ensemble of networks as described in Sweet et. al. (2012).<DOI:10.3102/1076998612458702>.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari <asam.cmu@gmail.com>
Diff between HLSM versions 0.5 dated 2015-11-15 and 0.6 dated 2016-10-19
DESCRIPTION | 12 +++---- MD5 | 16 ++++----- NAMESPACE | 17 +++------- R/HLSM_run.R | 68 +++++++++++++++++++++++++++-------------- R/HLSM_run_fixedEF.R | 76 ++++++++++++++++++++++++++++++---------------- R/covFunction.R | 7 +--- demo/HLSM.school.advice.R | 4 -- man/plots.Rd | 23 ------------- src/HLSM.cpp | 46 +++++++++++++++------------ 9 files changed, 141 insertions(+), 128 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-01 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-20 1.2.2
2016-07-18 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-13 1.1.6
2016-05-17 1.1.5
2016-01-08 1.1.4
2015-11-15 1.1.2
2015-07-24 1.0.6
Title: A Package for Sparse VAR/VECM Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation
using penalties like ENET, SCAD and MCP.
Author: Simone Vazzoler [aut, cre],
Lorenzo Frattarolo [aut],
Monica Billio [aut]
Maintainer: Simone Vazzoler <svazzole@gmail.com>
Diff between sparsevar versions 0.0.7 dated 2016-07-06 and 0.0.9 dated 2016-10-19
sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.RData |only sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.rdb |only sparsevar-0.0.7/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_7ce18901aee92ab7c7661d60f1ba4e1b.rdx |only sparsevar-0.0.9/sparsevar/DESCRIPTION | 12 sparsevar-0.0.9/sparsevar/MD5 | 52 - sparsevar-0.0.9/sparsevar/NAMESPACE | 2 sparsevar-0.0.9/sparsevar/NEWS.md | 7 sparsevar-0.0.9/sparsevar/R/createSparseMatrix.R | 75 -- sparsevar-0.0.9/sparsevar/R/fitVAR.R | 172 +++-- sparsevar-0.0.9/sparsevar/R/fitVECM.R | 15 sparsevar-0.0.9/sparsevar/R/simulateVAR.R | 86 +- sparsevar-0.0.9/sparsevar/R/timeSlice.R | 218 ++++--- sparsevar-0.0.9/sparsevar/R/utilsVAR.R | 311 ++++++---- sparsevar-0.0.9/sparsevar/README.md | 27 sparsevar-0.0.9/sparsevar/inst/doc/using.R | 10 sparsevar-0.0.9/sparsevar/inst/doc/using.Rmd | 31 sparsevar-0.0.9/sparsevar/inst/doc/using.pdf |binary sparsevar-0.0.9/sparsevar/man/computeForecasts.Rd |only sparsevar-0.0.9/sparsevar/man/createSparseMatrix.Rd | 9 sparsevar-0.0.9/sparsevar/man/fitVAR.Rd | 12 sparsevar-0.0.9/sparsevar/man/informCrit.Rd |only sparsevar-0.0.9/sparsevar/man/simulateVAR.Rd | 6 sparsevar-0.0.9/sparsevar/man/testGranger.Rd | 2 sparsevar-0.0.9/sparsevar/vignettes/using.Rmd | 31 sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.RData |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.rdb |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-10_3875fca48dd018157a6c4a96b6a44b9a.rdx |only sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-4_3897a5d4efc534c41ac499bc2c9439b6.rdb |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-4_3897a5d4efc534c41ac499bc2c9439b6.rdx |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-5_18789e32a330a381ec44593f5f2f6b41.rdb |binary sparsevar-0.0.9/sparsevar/vignettes/using_cache/latex/unnamed-chunk-5_18789e32a330a381ec44593f5f2f6b41.rdx |binary 31 files changed, 646 insertions(+), 432 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.63 dated 2016-07-21 and 0.68 dated 2016-10-19
REBayes-0.63/REBayes/R/predict.R |only REBayes-0.68/REBayes/DESCRIPTION | 8 +- REBayes-0.68/REBayes/MD5 | 90 ++++++++++++++++-------------- REBayes-0.68/REBayes/NAMESPACE | 6 +- REBayes-0.68/REBayes/R/Bmix.R | 4 + REBayes-0.68/REBayes/R/GLmix.R | 2 REBayes-0.68/REBayes/R/KWDual.R | 2 REBayes-0.68/REBayes/R/Pmix.R | 6 +- REBayes-0.68/REBayes/R/medde.R | 44 +++++++++----- REBayes-0.68/REBayes/R/predict.Bmix.R |only REBayes-0.68/REBayes/R/predict.GLmix.R |only REBayes-0.68/REBayes/R/predict.Pmix.R |only REBayes-0.68/REBayes/build |only REBayes-0.68/REBayes/demo/00Index | 1 REBayes-0.68/REBayes/demo/Silverman.R |only REBayes-0.68/REBayes/inst/ChangeLog | 17 +++++ REBayes-0.68/REBayes/inst/Readme | 9 +-- REBayes-0.68/REBayes/inst/doc/rebayes.R |only REBayes-0.68/REBayes/inst/doc/rebayes.Rnw |only REBayes-0.68/REBayes/inst/doc/rebayes.pdf |binary REBayes-0.68/REBayes/man/Bmix.Rd | 15 +++-- REBayes-0.68/REBayes/man/Cosslett.Rd | 10 +-- REBayes-0.68/REBayes/man/GLmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/GVmix.Rd | 14 ++-- REBayes-0.68/REBayes/man/Gammamix.Rd | 14 ++-- REBayes-0.68/REBayes/man/Gompertzmix.Rd | 16 ++--- REBayes-0.68/REBayes/man/KWDual.Rd | 8 +- REBayes-0.68/REBayes/man/L1norm.Rd | 4 - REBayes-0.68/REBayes/man/Norberg.Rd | 4 - REBayes-0.68/REBayes/man/Pmix.Rd | 22 ++++--- REBayes-0.68/REBayes/man/Rxiv.Rd | 2 REBayes-0.68/REBayes/man/TLmix.Rd | 12 ++-- REBayes-0.68/REBayes/man/Tncpmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/WGLVmix.Rd | 16 ++--- REBayes-0.68/REBayes/man/WGVmix.Rd | 2 REBayes-0.68/REBayes/man/WLVmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/WTLVmix.Rd | 18 +++--- REBayes-0.68/REBayes/man/Weibullmix.Rd | 14 ++-- REBayes-0.68/REBayes/man/bball.Rd | 16 ++--- REBayes-0.68/REBayes/man/flies.Rd | 10 +-- REBayes-0.68/REBayes/man/medde.Rd | 30 ++++++---- REBayes-0.68/REBayes/man/plot.medde.Rd | 2 REBayes-0.68/REBayes/man/predict.Bmix.Rd |only REBayes-0.68/REBayes/man/predict.GLmix.Rd | 14 +++- REBayes-0.68/REBayes/man/predict.Pmix.Rd |only REBayes-0.68/REBayes/man/qmedde.Rd | 2 REBayes-0.68/REBayes/man/rmedde.Rd | 2 REBayes-0.68/REBayes/man/tacks.Rd | 12 ++-- REBayes-0.68/REBayes/man/tannenbaum.Rd | 2 REBayes-0.68/REBayes/man/traprule.Rd | 2 REBayes-0.68/REBayes/vignettes |only 51 files changed, 286 insertions(+), 220 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix. This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Diff between PopED versions 0.3.0 dated 2015-12-29 and 0.3.1 dated 2016-10-19
PopED-0.3.0/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only PopED-0.3.0/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.R |only PopED-0.3.0/PopED/inst/examples/ex.2.c.warfarin.discrete.optimization.R |only PopED-0.3.0/PopED/inst/examples/ex.2.d.warfarin.ODE.compiled.R |only PopED-0.3.0/PopED/inst/examples/ex.2.e.warfarin.ED.R |only PopED-0.3.0/PopED/inst/examples/ex.2.f.warfarin.Ds.R |only PopED-0.3.0/PopED/inst/examples/ex.8.a.tmdd_qss_one_target.R |only PopED-0.3.0/PopED/inst/examples/ex.8.b.tmdd_qss_one_target_compiled.R |only PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt |only PopED-0.3.0/PopED/tests/testthat/Rplots.pdf |only PopED-0.3.1/PopED/DESCRIPTION | 18 PopED-0.3.1/PopED/MD5 | 319 ++-- PopED-0.3.1/PopED/NAMESPACE | 5 PopED-0.3.1/PopED/NEWS | 28 PopED-0.3.1/PopED/R/PopED.R | 4 PopED-0.3.1/PopED/R/a_line_search.R | 6 PopED-0.3.1/PopED/R/blockfinal.R | 62 PopED-0.3.1/PopED/R/blockheader.R | 3 PopED-0.3.1/PopED/R/build_sfg.R | 20 PopED-0.3.1/PopED/R/calc_ofv_and_fim.R | 75 PopED-0.3.1/PopED/R/cell.R | 2 PopED-0.3.1/PopED/R/create.poped.database.R | 431 +++-- PopED-0.3.1/PopED/R/create_design.R | 16 PopED-0.3.1/PopED/R/create_design_space.R | 179 ++ PopED-0.3.1/PopED/R/downsizing_general_design.R | 6 PopED-0.3.1/PopED/R/ed_laplace_ofv.R | 181 +- PopED-0.3.1/PopED/R/ed_mftot.R | 33 PopED-0.3.1/PopED/R/evaluate.e.ofv.fim.R | 3 PopED-0.3.1/PopED/R/evaluate_design.R |only PopED-0.3.1/PopED/R/fileparts.R | 2 PopED-0.3.1/PopED/R/fprintf.R | 5 PopED-0.3.1/PopED/R/inv.R | 16 PopED-0.3.1/PopED/R/m1.R | 3 PopED-0.3.1/PopED/R/m3.R | 149 + PopED-0.3.1/PopED/R/mc_mean.R |only PopED-0.3.1/PopED/R/median_hilow_poped.R |only PopED-0.3.1/PopED/R/mf.R | 2 PopED-0.3.1/PopED/R/mf3.R | 8 PopED-0.3.1/PopED/R/mf6.R | 110 - PopED-0.3.1/PopED/R/model_prediction.R | 19 PopED-0.3.1/PopED/R/ofv_criterion.R | 10 PopED-0.3.1/PopED/R/optim_ARS.R | 8 PopED-0.3.1/PopED/R/optim_LS.R | 2 PopED-0.3.1/PopED/R/plot_efficiency_of_windows.R | 184 +- PopED-0.3.1/PopED/R/plot_model_prediction.R | 34 PopED-0.3.1/PopED/R/poped_gui.R |only PopED-0.3.1/PopED/R/poped_optim.R | 479 +++++- PopED-0.3.1/PopED/R/summary.poped_optim.R |only PopED-0.3.1/PopED/R/test_for_zeros.R | 4 PopED-0.3.1/PopED/R/tic.R | 2 PopED-0.3.1/PopED/R/toc.R | 2 PopED-0.3.1/PopED/R/update_designinlist.R | 30 PopED-0.3.1/PopED/R/v.R | 17 PopED-0.3.1/PopED/README.md | 5 PopED-0.3.1/PopED/build |only PopED-0.3.1/PopED/inst/doc |only PopED-0.3.1/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 82 - PopED-0.3.1/PopED/inst/examples/ex.1.b.PK.1.comp.oral.md.re-parameterize.R | 97 - PopED-0.3.1/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.10.PKPD.HCV.compiled.R | 11 PopED-0.3.1/PopED/inst/examples/ex.2.a.warfarin.evaluate.R | 27 PopED-0.3.1/PopED/inst/examples/ex.2.b.warfarin.optimize.R | 100 - PopED-0.3.1/PopED/inst/examples/ex.2.c.warfarin.ODE.compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.2.d.warfarin.ED.R |only PopED-0.3.1/PopED/inst/examples/ex.2.e.warfarin.Ds.R |only PopED-0.3.1/PopED/inst/examples/ex.3.a.PKPD.1.comp.oral.md.imax.D-opt.R | 59 PopED-0.3.1/PopED/inst/examples/ex.3.b.PKPD.1.comp.oral.md.imax.ED-opt.R | 58 PopED-0.3.1/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R | 58 PopED-0.3.1/PopED/inst/examples/ex.5.PD.emax.hill.R | 55 PopED-0.3.1/PopED/inst/examples/ex.6.PK.1.comp.oral.sd.R | 210 -- PopED-0.3.1/PopED/inst/examples/ex.7.PK.1.comp.maturation.R | 151 +- PopED-0.3.1/PopED/inst/examples/ex.8.tmdd_qss_one_target_compiled.R |only PopED-0.3.1/PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R | 96 - PopED-0.3.1/PopED/inst/examples/one_comp_oral_CL.c | 6 PopED-0.3.1/PopED/inst/shinyapp/server.R | 754 +++++++++- PopED-0.3.1/PopED/inst/shinyapp/ui.R | 347 +++- PopED-0.3.1/PopED/man/Doptim.Rd | 4 PopED-0.3.1/PopED/man/Dtrace.Rd | 4 PopED-0.3.1/PopED/man/LEDoptim.Rd | 2 PopED-0.3.1/PopED/man/LinMatrixH.Rd | 5 PopED-0.3.1/PopED/man/LinMatrixL.Rd | 4 PopED-0.3.1/PopED/man/LinMatrixLH.Rd | 5 PopED-0.3.1/PopED/man/LinMatrixL_occ.Rd | 5 PopED-0.3.1/PopED/man/PopED.Rd | 81 - PopED-0.3.1/PopED/man/RS_opt.Rd | 6 PopED-0.3.1/PopED/man/RS_opt_gen.Rd | 5 PopED-0.3.1/PopED/man/a_line_search.Rd | 9 PopED-0.3.1/PopED/man/bfgsb_min.Rd | 4 PopED-0.3.1/PopED/man/blockexp.Rd | 4 PopED-0.3.1/PopED/man/blockfinal.Rd | 6 PopED-0.3.1/PopED/man/blockheader.Rd | 4 PopED-0.3.1/PopED/man/blockopt.Rd | 4 PopED-0.3.1/PopED/man/calc_autofocus.Rd | 4 PopED-0.3.1/PopED/man/calc_ofv_and_fim.Rd | 9 PopED-0.3.1/PopED/man/calc_ofv_and_grad.Rd | 4 PopED-0.3.1/PopED/man/cell.Rd | 2 PopED-0.3.1/PopED/man/create.poped.database.Rd | 313 ++-- PopED-0.3.1/PopED/man/create_design_space.Rd | 31 PopED-0.3.1/PopED/man/downsizing_general_design.Rd | 4 PopED-0.3.1/PopED/man/ed_laplace_ofv.Rd | 53 PopED-0.3.1/PopED/man/ed_mftot.Rd | 6 PopED-0.3.1/PopED/man/efficiency.Rd |only PopED-0.3.1/PopED/man/evaluate.e.ofv.fim.Rd | 19 PopED-0.3.1/PopED/man/evaluate.fim.Rd | 5 PopED-0.3.1/PopED/man/evaluate_design.Rd |only PopED-0.3.1/PopED/man/fileparts.Rd | 2 PopED-0.3.1/PopED/man/get_rse.Rd | 1 PopED-0.3.1/PopED/man/gradf_eps.Rd | 5 PopED-0.3.1/PopED/man/inv.Rd | 6 PopED-0.3.1/PopED/man/log_prior_pdf.Rd | 4 PopED-0.3.1/PopED/man/mc_mean.Rd |only PopED-0.3.1/PopED/man/median_hilow_poped.Rd |only PopED-0.3.1/PopED/man/mf.Rd | 1 PopED-0.3.1/PopED/man/mf3.Rd | 1 PopED-0.3.1/PopED/man/mf5.Rd | 1 PopED-0.3.1/PopED/man/mf6.Rd | 1 PopED-0.3.1/PopED/man/mf7.Rd | 1 PopED-0.3.1/PopED/man/mf8.Rd | 1 PopED-0.3.1/PopED/man/mfea.Rd | 25 PopED-0.3.1/PopED/man/mftot.Rd | 5 PopED-0.3.1/PopED/man/mftot0.Rd | 5 PopED-0.3.1/PopED/man/mftot1.Rd | 5 PopED-0.3.1/PopED/man/mftot2.Rd | 1 PopED-0.3.1/PopED/man/mftot3.Rd | 1 PopED-0.3.1/PopED/man/mftot4.Rd | 5 PopED-0.3.1/PopED/man/mftot5.Rd | 5 PopED-0.3.1/PopED/man/mftot6.Rd | 5 PopED-0.3.1/PopED/man/mftot7.Rd | 5 PopED-0.3.1/PopED/man/model_prediction.Rd | 2 PopED-0.3.1/PopED/man/ofv_criterion.Rd | 5 PopED-0.3.1/PopED/man/ofv_fim.Rd | 7 PopED-0.3.1/PopED/man/optim_ARS.Rd | 2 PopED-0.3.1/PopED/man/optim_LS.Rd | 2 PopED-0.3.1/PopED/man/plot_efficiency_of_windows.Rd | 58 PopED-0.3.1/PopED/man/plot_model_prediction.Rd | 28 PopED-0.3.1/PopED/man/poped_gui.Rd |only PopED-0.3.1/PopED/man/poped_optim.Rd | 127 + PopED-0.3.1/PopED/man/poped_optimize.Rd | 30 PopED-0.3.1/PopED/man/test_for_zeros.Rd | 1 PopED-0.3.1/PopED/man/tic.Rd | 2 PopED-0.3.1/PopED/man/toc.Rd | 2 PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 298 +-- PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_RS.txt |only PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 112 - PopED-0.3.1/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 174 -- PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_LEDoptim.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt_gen.R | 5 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_a_line_search.R | 5 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_create_design_space.R | 15 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_ed_laplace_ofv.R | 50 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_evaluate_design.R |only PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_mfea.R | 21 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_ofv_fim.R | 2 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 75 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped_optim.R | 93 - PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_poped_optimize.R | 26 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/examples_test_for_zeros.R | 1 PopED-0.3.1/PopED/tests/testthat/examples_fcn_doc/warfarin_optimize.R | 4 PopED-0.3.1/PopED/tests/testthat/helper_options.R | 2 PopED-0.3.1/PopED/tests/testthat/test_E_family.R |only PopED-0.3.1/PopED/tests/testthat/test_create_databases.R | 2 PopED-0.3.1/PopED/tests/testthat/test_evaluate_design.R |only PopED-0.3.1/PopED/tests/testthat/test_examples.R | 52 PopED-0.3.1/PopED/tests/testthat/test_optimization.R | 70 PopED-0.3.1/PopED/vignettes |only 166 files changed, 4134 insertions(+), 2424 deletions(-)
Title: Organic Mass Spectrometry
Description: Organic/biological mass spectrometry data analysis.
Author: Nathan Dodder [cre, aut, cph],
Katharine Mullen [ctb]
Maintainer: Nathan Dodder <ndodder@mail.sdsu.edu>
Diff between OrgMassSpecR versions 0.4-4 dated 2014-05-23 and 0.4-6 dated 2016-10-19
DESCRIPTION | 20 - LICENSE | 4 MD5 | 122 +++++------ NAMESPACE | 47 ++-- R/ConvertConcentration.R | 128 ++++++------ R/ConvertPeptide.R | 156 +++++++-------- R/DeadVolume.R | 14 - R/Digest.R | 262 ++++++++++++------------- R/DrawChromatogram.R | 80 +++---- R/ExchangeableAmides.R | 18 - R/FlowTime.R | 18 - R/FragmentPeptide.R | 312 +++++++++++++++--------------- R/IsotopicDistribution.R | 170 ++++++++-------- R/IsotopicDistributionHDX.R | 228 ++++++++++----------- R/IsotopicDistributionN.R | 236 +++++++++++----------- R/ListFormula.R | 88 ++++---- R/MolecularWeight.R | 72 +++--- R/MonoisotopicMass.R | 78 +++---- R/PeptideSpectrum.R | 206 +++++++++---------- R/ReadMspDirectory.R | 100 ++++----- R/ReadMspFile.R | 58 ++--- R/RetentionIndex.R | 14 - R/SpectrumSimilarity.R | 116 +++++------ R/WriteMspFile.R | 66 +++--- build/vignette.rds |binary data/example.chromatogram.multiple.txt.gz |binary data/example.chromatogram.single.txt.gz |binary data/example.sequence.rda |binary data/example.spectrum.authentic.txt.gz |binary data/example.spectrum.labeled.txt.gz |binary data/example.spectrum.peptide.txt.gz |binary data/example.spectrum.unknown.txt.gz |binary inst/NEWS.Rd | 202 ++++++++++--------- inst/doc/OrgMassSpecR-examples.R | 167 +++++++--------- inst/doc/OrgMassSpecR-examples.Rmd | 308 ++++++++++++++--------------- man/ConvertConcentration.Rd | 94 ++++----- man/ConvertPeptide.Rd | 56 ++--- man/DeadVolume.Rd | 26 +- man/Digest.Rd | 146 +++++++------- man/DrawChromatogram.Rd | 106 +++++----- man/ExchangeableAmides.Rd | 46 ++-- man/FlowTime.Rd | 34 +-- man/FragmentPeptide.Rd | 124 +++++------ man/IsotopicDistribution.Rd | 90 ++++---- man/IsotopicDistributionHDX.Rd | 90 ++++---- man/IsotopicDistributionN.Rd | 164 +++++++-------- man/ListFormula.Rd | 64 +++--- man/MolecularWeight.Rd | 56 ++--- man/MonoisotopicMass.Rd | 122 +++++------ man/OrgMassSpecR-package.Rd | 26 +- man/PeptideSpectrum.Rd | 66 +++--- man/ReadMspDirectory.Rd | 68 +++--- man/ReadMspFile.Rd | 54 ++--- man/RetentionIndex.Rd | 32 +-- man/SpectrumSimilarity.Rd | 84 ++++---- man/WriteMspFile.Rd | 104 +++++----- man/example.chromatogram.single.Rd | 26 +- man/example.sequence.Rd | 18 - man/example.spectrum.labeled.Rd | 24 +- man/example.spectrum.peptide.Rd | 22 +- man/example.spectrum.unknown.Rd | 28 +- vignettes/OrgMassSpecR-examples.Rmd | 308 ++++++++++++++--------------- 62 files changed, 2691 insertions(+), 2677 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:10.1080/00401706.2015.1054436>. The main fitting function is oem() and the functions cv.oem() and xval.oem() are for cross validation, the latter being an accelerated cross validation function for linear models. The big.oem() function allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 1.02.1 dated 2014-01-06 and 2.0.1 dated 2016-10-19
oem-1.02.1/oem/R/coef.oemfit.R |only oem-1.02.1/oem/R/cv.oemfit.R |only oem-1.02.1/oem/R/getmin.R |only oem-1.02.1/oem/R/lambda.interp.R |only oem-1.02.1/oem/R/plot.oemfit.R |only oem-1.02.1/oem/R/predict.oemfit.R |only oem-1.02.1/oem/R/print.oemfit.R |only oem-1.02.1/oem/data |only oem-1.02.1/oem/man/calHousing.Rd |only oem-1.02.1/oem/man/example9.Rd |only oem-1.02.1/oem/man/oem-package.Rd |only oem-1.02.1/oem/man/oemfit.Rd |only oem-1.02.1/oem/man/plot.oemfit.Rd |only oem-1.02.1/oem/man/predict.oemfit.Rd |only oem-1.02.1/oem/man/print.oemfit.Rd |only oem-1.02.1/oem/src/Makevars00 |only oem-2.0.1/oem/DESCRIPTION | 36 + oem-2.0.1/oem/MD5 | 91 +++- oem-2.0.1/oem/NAMESPACE | 65 ++- oem-2.0.1/oem/R/big_oem.R |only oem-2.0.1/oem/R/cv_oem.R |only oem-2.0.1/oem/R/deprecated_functions.R |only oem-2.0.1/oem/R/methods.R |only oem-2.0.1/oem/R/oem.R | 603 ++++++++++++++++++++++++++---- oem-2.0.1/oem/R/oem_xtx.R |only oem-2.0.1/oem/R/oem_xval.R |only oem-2.0.1/oem/R/utils.R |only oem-2.0.1/oem/README.md |only oem-2.0.1/oem/build |only oem-2.0.1/oem/inst |only oem-2.0.1/oem/man/big.oem.Rd |only oem-2.0.1/oem/man/cv.oem.Rd |only oem-2.0.1/oem/man/deprecated.Rd |only oem-2.0.1/oem/man/logLik.Rd |only oem-2.0.1/oem/man/oem.Rd |only oem-2.0.1/oem/man/oem.xtx.Rd |only oem-2.0.1/oem/man/plot.Rd |only oem-2.0.1/oem/man/predict.cv.oem.Rd |only oem-2.0.1/oem/man/predict.oem.Rd |only oem-2.0.1/oem/man/predict.xval.oem.Rd |only oem-2.0.1/oem/man/print.Rd |only oem-2.0.1/oem/man/summary.Rd |only oem-2.0.1/oem/man/xval.oem.Rd |only oem-2.0.1/oem/src/DataStd.h |only oem-2.0.1/oem/src/Makevars | 9 oem-2.0.1/oem/src/Makevars.win | 14 oem-2.0.1/oem/src/Rutils.cpp |only oem-2.0.1/oem/src/Rutils.h |only oem-2.0.1/oem/src/Spectra |only oem-2.0.1/oem/src/lanczos.cpp |only oem-2.0.1/oem/src/lanczos.h |only oem-2.0.1/oem/src/oem_base.h |only oem-2.0.1/oem/src/oem_big.cpp |only oem-2.0.1/oem/src/oem_big.h |only oem-2.0.1/oem/src/oem_dense.cpp |only oem-2.0.1/oem/src/oem_dense.h |only oem-2.0.1/oem/src/oem_logistic_dense.cpp |only oem-2.0.1/oem/src/oem_logistic_dense.h |only oem-2.0.1/oem/src/oem_logistic_sparse.cpp |only oem-2.0.1/oem/src/oem_logistic_sparse.h |only oem-2.0.1/oem/src/oem_sparse.cpp |only oem-2.0.1/oem/src/oem_sparse.h |only oem-2.0.1/oem/src/oem_xtx.cpp |only oem-2.0.1/oem/src/oem_xtx.h |only oem-2.0.1/oem/src/oem_xval_dense.cpp |only oem-2.0.1/oem/src/oem_xval_dense.h |only oem-2.0.1/oem/src/utils.cpp |only oem-2.0.1/oem/src/utils.h |only oem-2.0.1/oem/vignettes |only 69 files changed, 689 insertions(+), 129 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 6.1.0 dated 2016-09-04 and 6.1.1 dated 2016-10-19
DESCRIPTION | 8 MD5 | 161 +++--- NAMESPACE | 4 NEWS | 23 R/AUC_ROC.R | 2 R/MCVfold.R | 144 +++++- R/block.pls.R | 5 R/block.plsda.R | 7 R/block.spls.R | 6 R/block.splsda.R | 6 R/check_entry.R | 14 R/circosPlot.R | 3 R/internal_graphic.perf.R | 31 - R/internal_graphicModule.R | 23 R/internal_mint.block.R | 6 R/internal_mint.block_helpers.R | 33 + R/internal_predict.DA.R | 59 +- R/internal_wrapper.mint.R | 2 R/internal_wrapper.mint.block.R | 2 R/mint.pca.R |only R/perf.R | 35 + R/perf.diablo.R | 931 ++++++++++++++++++++++++---------------- R/plot.perf.R | 65 ++ R/plot.tune.R | 21 R/plotIndiv.R | 101 +++- R/plotIndiv.mint.R | 17 R/plotIndiv.pca.R | 3 R/plotIndiv.pls.R | 5 R/plotIndiv.sgcca.R | 5 R/plotLoadings.R | 2 R/plotLoadings.mint.splsda.R | 2 R/plotLoadings.pca.R |only R/plotLoadings.spls.R | 1 R/plotVar.R | 23 R/plsda.R | 2 R/predict.mint.block.pls.R | 73 ++- R/roc_utils.R | 3 R/selectVar.R | 8 R/splsda.R | 2 R/tune.diablo.R | 209 ++++++-- R/tune.splsda.R | 26 - R/wrapper.rgcca.R | 2 R/wrapper.sgcca.R | 4 data/breast.TCGA.rda |binary data/breast.tumors.rda |binary data/linnerud.rda |binary data/liver.toxicity.rda |binary data/multidrug.rda |binary data/nutrimouse.rda |binary data/srbct.rda |binary data/stemcells.rda |binary data/vac18.rda |binary data/vac18.simulated.rda |binary data/yeast.rda |binary man/auroc.Rd | 6 man/block.pls.Rd | 4 man/block.plsda.Rd | 4 man/block.spls.Rd | 4 man/block.splsda.Rd | 8 man/cim.Rd | 2 man/circosPlot.Rd | 2 man/mint.block.pls.Rd | 4 man/mint.block.plsda.Rd | 4 man/mint.block.spls.Rd | 4 man/mint.block.splsda.Rd | 4 man/mint.pca.Rd |only man/mint.pls.Rd | 2 man/mint.plsda.Rd | 2 man/mint.spls.Rd | 2 man/mint.splsda.Rd | 2 man/perf.Rd | 38 + man/plot.perf.Rd | 23 man/plot.tune.Rd | 6 man/plotContrib.Rd | 31 - man/plotIndiv.Rd | 8 man/plotLoadings.Rd | 10 man/plotVar.Rd | 2 man/predict.Rd | 26 - man/selectVar.Rd | 14 man/tune.block.splsda.Rd | 11 man/tune.splsda.Rd | 6 man/wrapper.rgcca.Rd | 6 man/wrapper.sgcca.Rd | 8 83 files changed, 1541 insertions(+), 781 deletions(-)
Title: A Lending Club API Wrapper
Description: Functions to access Lending Club's API and assist the investor manage
their account. Lending Club is a peer-to-peer lending service where loans are
broken up into $25 notes that investors buy with the expectation of earning a
return on the interest. You can learn more about the API here:
<http://www.lendingclub.com/developers/lc-api.action>.
Author: Ryan Kuhn
Maintainer: Ryan Kuhn <kuhnrl30@gmail.com>
Diff between LendingClub versions 0.1.2 dated 2016-09-26 and 1.0.0 dated 2016-10-19
LendingClub-0.1.2/LendingClub/R/BuySecondary.R |only LendingClub-0.1.2/LendingClub/man/BuySecondary.Rd |only LendingClub-0.1.2/LendingClub/man/DetailedNotesOwned.Rd |only LendingClub-0.1.2/LendingClub/man/FolioBuy.Rd |only LendingClub-1.0.0/LendingClub/DESCRIPTION | 19 +-- LendingClub-1.0.0/LendingClub/MD5 | 82 ++++++------- LendingClub-1.0.0/LendingClub/NAMESPACE | 2 LendingClub-1.0.0/LendingClub/R/AccountSummary.R | 5 LendingClub-1.0.0/LendingClub/R/AddFunds.R | 10 - LendingClub-1.0.0/LendingClub/R/AvailableCash.R | 5 LendingClub-1.0.0/LendingClub/R/CancelTransfer.R | 4 LendingClub-1.0.0/LendingClub/R/CleanData.R | 23 ++- LendingClub-1.0.0/LendingClub/R/CreatePortfolio.R | 4 LendingClub-1.0.0/LendingClub/R/DetailedNotesOwned.R | 8 - LendingClub-1.0.0/LendingClub/R/FolioBuy.R | 25 +-- LendingClub-1.0.0/LendingClub/R/FolioSell.R | 17 +- LendingClub-1.0.0/LendingClub/R/LC_GET.R | 3 LendingClub-1.0.0/LendingClub/R/LC_POST.R | 1 LendingClub-1.0.0/LendingClub/R/ListedLoans.R | 15 +- LendingClub-1.0.0/LendingClub/R/MakeCredential.R | 13 +- LendingClub-1.0.0/LendingClub/R/MakeURL.R | 1 LendingClub-1.0.0/LendingClub/R/NotesOwned.R | 18 ++ LendingClub-1.0.0/LendingClub/R/Print.R | 2 LendingClub-1.0.0/LendingClub/R/SubmitOrder.R | 13 +- LendingClub-1.0.0/LendingClub/R/WithdrawFunds.R | 2 LendingClub-1.0.0/LendingClub/README.md | 48 +++++-- LendingClub-1.0.0/LendingClub/build/vignette.rds |binary LendingClub-1.0.0/LendingClub/man/AccountSummary.Rd | 4 LendingClub-1.0.0/LendingClub/man/AddFunds.Rd | 10 - LendingClub-1.0.0/LendingClub/man/AvailableCash.Rd | 4 LendingClub-1.0.0/LendingClub/man/CancelTransfer.Rd | 4 LendingClub-1.0.0/LendingClub/man/CleanData.Rd | 1 LendingClub-1.0.0/LendingClub/man/CreatePortfolio.Rd | 4 LendingClub-1.0.0/LendingClub/man/FolioSell.Rd | 24 ++- LendingClub-1.0.0/LendingClub/man/LC_GET.Rd | 1 LendingClub-1.0.0/LendingClub/man/LC_POST.Rd | 1 LendingClub-1.0.0/LendingClub/man/ListedLoans.Rd | 8 + LendingClub-1.0.0/LendingClub/man/MakeCredential.Rd | 15 ++ LendingClub-1.0.0/LendingClub/man/MakeURL.Rd | 1 LendingClub-1.0.0/LendingClub/man/NotesOwned.Rd | 19 ++- LendingClub-1.0.0/LendingClub/man/SubmitOrder.Rd | 12 + LendingClub-1.0.0/LendingClub/man/WithdrawFunds.Rd | 2 LendingClub-1.0.0/LendingClub/man/print.LendingClub_api.Rd | 1 LendingClub-1.0.0/LendingClub/vignettes/LendingClub.Rmd | 2 44 files changed, 263 insertions(+), 170 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.6 dated 2016-07-24 and 1.7 dated 2016-10-19
DESCRIPTION | 8 MD5 | 140 NAMESPACE | 73 NEWS | 155 R/data-SCB.R | 28 R/deprecated.R | 78 R/htmlTable.R | 2168 +- R/htmlTable_helpers.R | 1958 +- R/htmlTable_render.R | 512 R/interactiveTable.R | 474 R/txtFrmt.R | 590 README.md | 2358 +- build/vignette.rds |binary inst/doc/general.R | 342 inst/doc/general.Rmd | 634 inst/doc/general.html | 8356 ++++----- inst/doc/tables.R | 450 inst/doc/tables.Rmd | 830 inst/doc/tables.html |20466 ++++++++++++------------ inst/examples/data-SCB_example.R | 60 inst/examples/htmlTable_example.R | 106 inst/examples/interactiveTable_example.R | 38 inst/html_components/button.html | 4 inst/javascript/button.js | 48 inst/javascript/toggler.js | 80 man/SCB.Rd | 104 man/htmlTable.Rd | 772 man/interactiveTable.Rd | 152 man/outputInt.Rd | 40 man/prAddCells.Rd | 104 man/prAddSemicolon2StrEnd.Rd | 56 man/prAttr4RgroupAdd.Rd | 46 man/prConvertDfFactors.Rd | 38 man/prGetAlign.Rd | 46 man/prGetCgroupHeader.Rd | 148 man/prGetRgroupLine.Rd | 108 man/prGetRowlabelPos.Rd | 76 man/prGetScriptString.Rd | 40 man/prGetStyle.Rd | 68 man/prGetThead.Rd | 188 man/prMergeClr.Rd | 46 man/prPrepareAlign.Rd | 86 man/prPrepareCgroup.Rd | 90 man/prPrepareColors.Rd | 50 man/prPrepareCss.Rd | 68 man/prSkipRownames.Rd | 40 man/prTblNo.Rd | 64 man/pvalueFormatter.Rd | 38 man/splitLines4Table.Rd | 38 man/tblNoLast.Rd | 52 man/tblNoNext.Rd | 52 man/txtInt.Rd | 72 man/txtMergeLines.Rd | 78 man/txtPval.Rd | 98 man/txtRound.Rd | 114 tests/testInteractive.R | 54 tests/testthat.R | 6 tests/testthat/test-htmlTable.R | 690 tests/testthat/test-htmlTable_cgroup.R | 228 tests/testthat/test-htmlTable_dates.R |only tests/testthat/test-htmlTable_rgroup_tspanner.R | 462 tests/testthat/test-htmlTable_total.R | 118 tests/testthat/test-interactiveTable.R | 632 tests/testthat/test-txtFrmt.R | 292 tests/testthat/test-txtMergeLines.R | 48 tests/visual_tests/htmlTable_vtests.R | 230 tests/visual_tests/pandoc_test.Rmd | 58 tests/visual_tests/word_test.Rmd | 84 tests/visual_tests/word_test.html |only vignettes/custom.css | 324 vignettes/general.Rmd | 634 vignettes/tables.Rmd | 830 72 files changed, 23884 insertions(+), 23734 deletions(-)
Title: Extra Additive Terms for GAMLSS Models
Description: Interface for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>, Bob Rigby, Vlasios Voudouris, Daniil Kiose
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>
Diff between gamlss.add versions 4.3-4 dated 2015-07-17 and 5.0-1 dated 2016-10-19
gamlss.add-4.3-4/gamlss.add/R/gam_gamlss.R |only gamlss.add-5.0-1/gamlss.add/DESCRIPTION | 14 +- gamlss.add-5.0-1/gamlss.add/MD5 | 33 +++--- gamlss.add-5.0-1/gamlss.add/NAMESPACE | 104 ++++++++++----------- gamlss.add-5.0-1/gamlss.add/R/ba.R |only gamlss.add-5.0-1/gamlss.add/R/freeKnots-18-06-13.R | 6 - gamlss.add-5.0-1/gamlss.add/R/ga_new.R |only gamlss.add-5.0-1/gamlss.add/man/blag.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/fitFixedKnots.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/fk.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/ga.Rd | 85 +++++++++-------- gamlss.add-5.0-1/gamlss.add/man/gamlss.fk.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/gamlss.ga.Rd | 12 +- gamlss.add-5.0-1/gamlss.add/man/gamlss.nn.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/la.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/nn.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/penLags.Rd | 2 gamlss.add-5.0-1/gamlss.add/man/plotNN.Rd | 4 gamlss.add-5.0-1/gamlss.add/man/tr.Rd | 9 + 19 files changed, 150 insertions(+), 133 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.9.4 dated 2016-07-25 and 2.10.3 dated 2016-10-19
frailtypack-2.10.3/frailtypack/DESCRIPTION | 10 frailtypack-2.10.3/frailtypack/MD5 | 171 frailtypack-2.10.3/frailtypack/NAMESPACE | 3 frailtypack-2.10.3/frailtypack/NEWS | 14 frailtypack-2.10.3/frailtypack/R/additivePenal.R | 21 frailtypack-2.10.3/frailtypack/R/frailtyPenal.R | 20 frailtypack-2.10.3/frailtypack/R/longiPenal.R | 97 frailtypack-2.10.3/frailtypack/R/plot.frailtyPenal.R | 90 frailtypack-2.10.3/frailtypack/R/plot.predJoint.R | 94 frailtypack-2.10.3/frailtypack/R/prediction.R | 2181 +-- frailtypack-2.10.3/frailtypack/R/print.predJoint.R | 42 frailtypack-2.10.3/frailtypack/R/waldtest.R | 84 frailtypack-2.10.3/frailtypack/inst/doc/Package_summary.Rmd | 54 frailtypack-2.10.3/frailtypack/inst/doc/Package_summary.html | 29 frailtypack-2.10.3/frailtypack/man/frailtyPenal.Rd | 7 frailtypack-2.10.3/frailtypack/man/plot.predJoint.Rd | 6 frailtypack-2.10.3/frailtypack/man/plotFrailtyPenal.Rd | 3 frailtypack-2.10.3/frailtypack/man/prediction.Rd | 43 frailtypack-2.10.3/frailtypack/src/AparamMultive.f90 | 284 frailtypack-2.10.3/frailtypack/src/aGhermite.f90 | 518 frailtypack-2.10.3/frailtypack/src/aaOptim.f90 | 3205 ++-- frailtypack-2.10.3/frailtypack/src/aaOptimres.f90 | 1676 +- frailtypack-2.10.3/frailtypack/src/aaUseFunction.f90 | 14 frailtypack-2.10.3/frailtypack/src/aaUseFunctionG.f90 | 36 frailtypack-2.10.3/frailtypack/src/aamarq98o.f90 | 928 - frailtypack-2.10.3/frailtypack/src/additive.f90 | 4867 +++---- frailtypack-2.10.3/frailtypack/src/afuncpasres.f90 | 3 frailtypack-2.10.3/frailtypack/src/aresidusMartingale.f90 | 50 frailtypack-2.10.3/frailtypack/src/atestWald.f90 | 13 frailtypack-2.10.3/frailtypack/src/distance.f90 | 93 frailtypack-2.10.3/frailtypack/src/epoce.f90 | 16 frailtypack-2.10.3/frailtypack/src/epoce_log.f90 | 1535 +- frailtypack-2.10.3/frailtypack/src/epoce_long.f90 | 220 frailtypack-2.10.3/frailtypack/src/frailtypack.f90 | 95 frailtypack-2.10.3/frailtypack/src/funcpaG_tps.f90 | 705 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm.f90 | 907 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm_intcens.f90 | 995 - frailtypack-2.10.3/frailtypack/src/funcpaGcpm_log.f90 | 855 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines.f90 | 859 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines_intcens.f90 | 853 - frailtypack-2.10.3/frailtypack/src/funcpaGsplines_log.f90 | 873 - frailtypack-2.10.3/frailtypack/src/funcpaGweib.f90 | 661 frailtypack-2.10.3/frailtypack/src/funcpaGweib_intcens.f90 | 669 - frailtypack-2.10.3/frailtypack/src/funcpaGweib_log.f90 | 666 - frailtypack-2.10.3/frailtypack/src/funcpaMultivCpm.f90 | 689 - frailtypack-2.10.3/frailtypack/src/funcpaMultivSplines.f90 | 1150 - frailtypack-2.10.3/frailtypack/src/funcpaMultivWeib.f90 | 498 frailtypack-2.10.3/frailtypack/src/funcpaacpm.f90 | 1370 +- frailtypack-2.10.3/frailtypack/src/funcpaasplines.f90 | 1346 +- frailtypack-2.10.3/frailtypack/src/funcpaaweib.f90 | 1119 - frailtypack-2.10.3/frailtypack/src/funcpaj_tps.f90 | 881 - frailtypack-2.10.3/frailtypack/src/funcpajcpm.f90 | 545 frailtypack-2.10.3/frailtypack/src/funcpajcpm_log.f90 | 546 frailtypack-2.10.3/frailtypack/src/funcpajgeneral.f90 | 675 - frailtypack-2.10.3/frailtypack/src/funcpajsplines.f90 | 736 - frailtypack-2.10.3/frailtypack/src/funcpajsplines_fam.f90 | 745 - frailtypack-2.10.3/frailtypack/src/funcpajsplines_intcens.f90 | 661 frailtypack-2.10.3/frailtypack/src/funcpajsplines_log.f90 | 730 - frailtypack-2.10.3/frailtypack/src/funcpajweib.f90 | 459 frailtypack-2.10.3/frailtypack/src/funcpajweib_fam.f90 | 410 frailtypack-2.10.3/frailtypack/src/funcpajweib_intcens.f90 | 457 frailtypack-2.10.3/frailtypack/src/funcpajweib_log.f90 | 465 frailtypack-2.10.3/frailtypack/src/funcpancpm.f90 | 1163 - frailtypack-2.10.3/frailtypack/src/funcpansplines.f90 | 1238 - frailtypack-2.10.3/frailtypack/src/funcpanweib.f90 | 814 - frailtypack-2.10.3/frailtypack/src/funcpas_tps.f90 | 847 - frailtypack-2.10.3/frailtypack/src/funcpascpm.f90 | 660 frailtypack-2.10.3/frailtypack/src/funcpascpm_intcens.f90 | 653 frailtypack-2.10.3/frailtypack/src/funcpascpm_log.f90 | 616 frailtypack-2.10.3/frailtypack/src/funcpassplines.f90 | 621 frailtypack-2.10.3/frailtypack/src/funcpassplines_intcens.f90 | 743 - frailtypack-2.10.3/frailtypack/src/funcpassplines_log.f90 | 635 frailtypack-2.10.3/frailtypack/src/funcpasweib.f90 | 467 frailtypack-2.10.3/frailtypack/src/funcpasweib_intcens.f90 | 561 frailtypack-2.10.3/frailtypack/src/funcpasweib_log.f90 | 507 frailtypack-2.10.3/frailtypack/src/joint.f90 | 6634 +++++----- frailtypack-2.10.3/frailtypack/src/joint_longi.f90 | 51 frailtypack-2.10.3/frailtypack/src/multiveJoint.f90 | 4 frailtypack-2.10.3/frailtypack/src/nested.f90 | 5325 ++++---- frailtypack-2.10.3/frailtypack/src/prediction.f90 | 831 + frailtypack-2.10.3/frailtypack/src/prediction_biv.f90 | 65 frailtypack-2.10.3/frailtypack/src/prediction_sha_logn.f90 | 448 frailtypack-2.10.3/frailtypack/src/prediction_tri.f90 | 64 frailtypack-2.10.3/frailtypack/src/risque.f90 | 260 frailtypack-2.10.3/frailtypack/src/survival.f90 | 1070 - frailtypack-2.10.3/frailtypack/vignettes/Package_summary.Rmd | 54 frailtypack-2.9.4/frailtypack/src/prediction_log.f90 |only 87 files changed, 31540 insertions(+), 30838 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.6 dated 2016-09-05 and 4.4.7 dated 2016-10-19
DESCRIPTION | 17 - MD5 | 53 ++-- NEWS | 5 R/as.char.R | 4 R/call.dots.R | 45 ++- R/do.par.R | 20 - R/dot.R | 74 ++++- R/dotlib.R | 14 - R/earth.R | 4 R/evimp.R | 2 R/lib.R | 120 ++++++--- R/plot.earth.R | 24 - R/printcall.R | 4 R/stop.if.dots.R | 9 R/varmod.R | 2 inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/doc/index.html | 8 inst/slowtests/test.full.R | 2 inst/slowtests/test.full.Rout.save | 6 inst/slowtests/test.varmod.Rout.save | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.weights.Rout.save | 2 man/earth.Rd | 371 ------------------------------ man/earth.object.Rd |only man/format.earth.Rd | 4 man/plot.evimp.Rd | 2 man/plot.varmod.Rd | 2 28 files changed, 275 insertions(+), 523 deletions(-)
Title: Functions, Data and Code for Count Data
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe <hilbe@asu.edu>
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between COUNT versions 1.3.2 dated 2014-08-15 and 1.3.4 dated 2016-10-19
DESCRIPTION | 12 ++++++------ MD5 | 48 ++++++++++++++++++++++++------------------------ NAMESPACE | 5 +++++ data/affairs.rda |binary data/azcabgptca.rda |binary data/azdrg112.rda |binary data/azpro.rda |binary data/azprocedure.rda |binary data/badhealth.rda |binary data/fasttrakg.rda |binary data/fishing.rda |binary data/lbw.rda |binary data/lbwgrp.rda |binary data/loomis.rda |binary data/mdvis.rda |binary data/medpar.rda |binary data/nuts.rda |binary data/rwm.rda |binary data/rwm1984.rda |binary data/rwm5yr.rda |binary data/ships.rda |binary data/smoking.rda |binary data/titanic.rda |binary data/titanicgrp.rda |binary man/nuts.Rd | 25 ++++++++++++++----------- 25 files changed, 49 insertions(+), 41 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.9.0 dated 2016-06-06 and 0.9.1 dated 2016-10-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/MetFunctions.R | 11 +++++++++-- README.md | 5 +++++ man/loadMet.Rd | 1 + 5 files changed, 23 insertions(+), 10 deletions(-)