Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-61 dated 2015-06-11 and 0.1-62 dated 2015-08-24
DESCRIPTION | 12 ++++----- MD5 | 34 +++++++++++++++++--------- NAMESPACE | 53 ++++++++++++++++++++++++++++++++++------- NEWS | 4 +++ R/BifixedContCont.R | 3 +- R/MixedContContIT.R | 4 +-- R/SummaryTrialLevelContCont.R |only R/TrialLevelContCont.R |only R/TwoStageSurvSurv.R |only R/UnimixedContCont.R | 20 +++++++-------- R/plot.TrialLevelContCont.R |only R/plot.TwoStageSurvSurv.R |only R/summary.TwoStageSurvSurv.R |only data/Ovarian.rda |only man/BifixedContCont.Rd | 2 - man/BimixedContCont.Rd | 2 - man/Ovarian.Rd |only man/TrialLevelContCont.Rd |only man/TwoStageSurvSurv.Rd |only man/UnifixedContCont.Rd | 2 - man/UnimixedContCont.Rd | 2 - man/plot.TrialLevelContCont.Rd |only man/plot.TwoStageSurvSurv.Rd |only man/summary.gen.Rd | 4 +++ 24 files changed, 100 insertions(+), 42 deletions(-)
Title: Incremental Decomposition Methods
Description: Principal Component Analysis and Multiple Correspondence Analysis using incremental eigenvalue decomposition methods.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.0 dated 2015-06-03 and 1.2 dated 2015-08-24
idm-1.0/idm/R/add_svd.r |only idm-1.2/idm/DESCRIPTION | 10 +- idm-1.2/idm/MD5 | 40 +++++----- idm-1.2/idm/NAMESPACE | 2 idm-1.2/idm/R/add_eig.r | 166 +++++++++++++++++++++--------------------- idm-1.2/idm/R/add_svd.R |only idm-1.2/idm/R/do_eig.r | 90 +++------------------- idm-1.2/idm/R/h_exact_mca.r | 45 ++++------- idm-1.2/idm/R/i_mca.r | 9 +- idm-1.2/idm/R/i_pca.r | 11 +- idm-1.2/idm/R/r_live_mca.r | 62 ++++++--------- idm-1.2/idm/R/update_mca.R | 41 +++------- idm-1.2/idm/R/update_pca.R | 41 +++++----- idm-1.2/idm/man/add_eig.Rd | 34 ++++---- idm-1.2/idm/man/add_svd.Rd | 67 +++++++++++----- idm-1.2/idm/man/do_eig.Rd | 5 - idm-1.2/idm/man/i_mca.Rd | 27 +++--- idm-1.2/idm/man/i_pca.Rd | 7 + idm-1.2/idm/man/idm.Rd | 10 +- idm-1.2/idm/man/plot.i_mca.Rd | 2 idm-1.2/idm/man/update_mca.Rd | 11 +- idm-1.2/idm/man/update_pca.Rd | 25 +++--- 22 files changed, 322 insertions(+), 383 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide
methods for automatically determining breaks and labels
for axes and legends.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 0.2.5 dated 2015-06-12 and 0.3.0 dated 2015-08-24
DESCRIPTION | 6 +-- MD5 | 67 +++++++++++++++++++++--------------------- NAMESPACE | 16 +++++++--- NEWS | 12 ++++++- R/bounds.r | 6 ++- R/colour-manip.r | 49 +++++++++++++++--------------- R/colour-mapping.r | 10 +++--- R/date-time.r | 2 - R/formatter.r | 6 +-- R/pal-brewer.r | 4 +- R/pal-dichromat.r | 2 - R/pal-gradient.r | 53 ++++++++++++++------------------- R/pal-grey.r | 2 - R/pal-hue.r | 2 - R/scale-continuous.r | 24 ++++++++------- R/scale-discrete.r | 14 ++++++-- R/scales.r | 4 +- R/trans-date.r | 22 ++++++------- R/trans.r | 2 - README.md | 2 - build/partial.rdb |binary man/alpha.Rd | 2 - man/brewer_pal.Rd | 4 +- man/date_trans.Rd | 4 +- man/dichromat_pal.Rd | 2 - man/div_gradient_pal.Rd | 12 +++---- man/gradient_n_pal.Rd | 4 +- man/rescale.Rd | 2 - man/seq_gradient_pal.Rd | 6 +-- man/time_trans.Rd | 4 +- man/train_continuous.Rd |only man/train_discrete.Rd |only tests/testthat/test-alpha.r | 4 +- tests/testthat/test-range.r | 25 --------------- tests/testthat/test-rescale.R |only tests/testthat/test-scale.r | 2 - 36 files changed, 190 insertions(+), 186 deletions(-)
Title: Efficient Authenticated Interaction with the O*NET API
Description: Provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API <www.onetonline.org>. The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Author: Eric Knudsen
Maintainer: Eric Knudsen <eknudsen@gc.cuny.edu>
Diff between ONETr versions 1.0.2 dated 2015-01-23 and 1.0.3 dated 2015-08-24
ONETr-1.0.2/ONETr/README.md |only ONETr-1.0.3/ONETr/DESCRIPTION | 12 +-- ONETr-1.0.3/ONETr/MD5 | 89 ++++++++++++++-------------- ONETr-1.0.3/ONETr/NAMESPACE | 2 ONETr-1.0.3/ONETr/R/abilities.R | 10 --- ONETr-1.0.3/ONETr/R/education.R | 15 ---- ONETr-1.0.3/ONETr/R/interests.R | 18 +---- ONETr-1.0.3/ONETr/R/jobTitles.R | 10 --- ONETr-1.0.3/ONETr/R/jobZone.R | 10 --- ONETr-1.0.3/ONETr/R/keySearch.R | 2 ONETr-1.0.3/ONETr/R/knowledge.R | 10 --- ONETr-1.0.3/ONETr/R/occupation.R | 12 +-- ONETr-1.0.3/ONETr/R/relatedOccupations.R | 14 ---- ONETr-1.0.3/ONETr/R/sim.index.R |only ONETr-1.0.3/ONETr/R/skills.R | 10 --- ONETr-1.0.3/ONETr/R/socSearch.R | 4 - ONETr-1.0.3/ONETr/R/tasks.R | 10 --- ONETr-1.0.3/ONETr/R/technology.R | 10 --- ONETr-1.0.3/ONETr/R/tools.R | 11 +-- ONETr-1.0.3/ONETr/R/workActivities.R | 10 --- ONETr-1.0.3/ONETr/R/workContext.R | 10 --- ONETr-1.0.3/ONETr/R/workStyles.R | 10 --- ONETr-1.0.3/ONETr/R/workValues.R | 10 --- ONETr-1.0.3/ONETr/data/jobData2.rda |only ONETr-1.0.3/ONETr/man/ONETr-package.Rd | 64 ++++++++++---------- ONETr-1.0.3/ONETr/man/abilities.Rd | 78 ++++++++++++------------ ONETr-1.0.3/ONETr/man/cacheEnv.Rd | 16 ++--- ONETr-1.0.3/ONETr/man/education.Rd | 74 +++++++++++------------ ONETr-1.0.3/ONETr/man/interests.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/jobData.Rd | 26 ++++---- ONETr-1.0.3/ONETr/man/jobData2.Rd |only ONETr-1.0.3/ONETr/man/jobTitles.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/jobZone.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/keySearch.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/knowledge.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/occupation.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/relatedOccupations.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/setCreds.Rd | 72 +++++++++++----------- ONETr-1.0.3/ONETr/man/sim.index.Rd |only ONETr-1.0.3/ONETr/man/skills.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/socSearch.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/tasks.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/technology.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/tools.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workActivities.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workContext.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workStyles.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workValues.Rd | 76 +++++++++++------------ 48 files changed, 882 insertions(+), 953 deletions(-)
Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard
errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE
computation for expectation and quantile estimators is
supported as well as multivariate estimations. The package also provides
functions for computing effective sample size and for plotting
Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes
<hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>
Diff between mcmcse versions 1.1-1 dated 2015-07-31 and 1.1-2 dated 2015-08-24
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- R/confRegion.R | 3 +-- R/multiESS.R | 10 ++++++++-- build/vignette.rds |binary inst/doc/mcmcse_vignette.pdf |binary man/confRegion.Rd | 18 ++++++++---------- man/ess.Rd | 2 +- man/mcmcse-package.Rd | 8 +++++--- man/mcse.mat.Rd | 2 +- man/mcse.multi.Rd | 8 ++++++++ man/multiESS.Rd | 2 +- vignettes/mcmcse_vignette.fdb_latexmk |only 13 files changed, 49 insertions(+), 35 deletions(-)
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (http://turfjs.org/) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.1.0 dated 2015-05-16 and 0.1.4 dated 2015-08-24
lawn-0.1.0/lawn/inst/ignore |only lawn-0.1.4/lawn/DESCRIPTION | 13 - lawn-0.1.4/lawn/MD5 | 47 ++--- lawn-0.1.4/lawn/NAMESPACE | 22 ++ lawn-0.1.4/lawn/NEWS | 18 + lawn-0.1.4/lawn/R/as_feature.R | 2 lawn-0.1.4/lawn/R/centroid.R | 2 lawn-0.1.4/lawn/R/flip.R | 2 lawn-0.1.4/lawn/R/hex_grid.R | 1 lawn-0.1.4/lawn/R/lawn-package.R | 3 lawn-0.1.4/lawn/R/print_methods.R |only lawn-0.1.4/lawn/R/random.R | 2 lawn-0.1.4/lawn/R/tbldf.R |only lawn-0.1.4/lawn/README.md | 195 +++++++-------------- lawn-0.1.4/lawn/build/vignette.rds |binary lawn-0.1.4/lawn/data/lawn_data.rda |binary lawn-0.1.4/lawn/inst/doc/lawn_vignette.Rmd | 1 lawn-0.1.4/lawn/inst/doc/lawn_vignette.html | 228 +++++++------------------ lawn-0.1.4/lawn/man/as_feature.Rd | 2 lawn-0.1.4/lawn/man/lawn_flip.Rd | 2 lawn-0.1.4/lawn/man/lawn_hex_grid.Rd | 1 lawn-0.1.4/lawn/man/lawn_random.Rd | 2 lawn-0.1.4/lawn/man/print-methods.Rd |only lawn-0.1.4/lawn/man/type_sum.Rd |only lawn-0.1.4/lawn/tests/testthat/test-centroid.R | 4 lawn-0.1.4/lawn/tests/testthat/test-onload.R | 6 lawn-0.1.4/lawn/vignettes/lawn_vignette.Rmd | 1 27 files changed, 221 insertions(+), 333 deletions(-)
Title: Independent Component Analysis
Description: Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between ica versions 1.0-0 dated 2014-09-02 and 1.0-1 dated 2015-08-24
ica-1.0-0/ica/R/acyidx.R |only ica-1.0-0/ica/man/acyidx.Rd |only ica-1.0-1/ica/ChangeLog |only ica-1.0-1/ica/DESCRIPTION | 8 - ica-1.0-1/ica/MD5 | 39 ++--- ica-1.0-1/ica/NAMESPACE | 6 ica-1.0-1/ica/R/acy.R |only ica-1.0-1/ica/R/congru.R | 31 +++- ica-1.0-1/ica/R/icafast.R | 159 ++++++++++++--------- ica-1.0-1/ica/R/icaimax.R | 140 ++++++++++-------- ica-1.0-1/ica/R/icajade.R | 119 ++++++++------- ica-1.0-1/ica/R/icaplot.R | 20 +- ica-1.0-1/ica/R/icasamp.R | 285 +++++++++++++++++++++----------------- ica-1.0-1/ica/R/sdiag.R | 2 ica-1.0-1/ica/man/acy.Rd |only ica-1.0-1/ica/man/congru.Rd | 35 +++- ica-1.0-1/ica/man/ica-internal.Rd | 2 ica-1.0-1/ica/man/ica-package.Rd | 2 ica-1.0-1/ica/man/icafast.Rd | 47 ++---- ica-1.0-1/ica/man/icaimax.Rd | 47 ++---- ica-1.0-1/ica/man/icajade.Rd | 45 ++---- ica-1.0-1/ica/man/icaplot.Rd | 13 + ica-1.0-1/ica/man/icasamp.Rd | 10 - 23 files changed, 561 insertions(+), 449 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.12 dated 2015-08-21 and 0.99.13 dated 2015-08-24
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 3 NEWS | 17 ++ R/DescTools.r | 206 ----------------------------------- R/FastDesc.R | 274 +++++++++++++++++++++++++++++------------------ man/DescTools-package.Rd | 2 man/GCD.Rd | 2 man/StrTrim.Rd | 10 - src/aux_fct.cpp | 74 +++++++----- 10 files changed, 250 insertions(+), 366 deletions(-)
Title: Variational Bayesian Mixture Models
Description: Variational algorithms and methods for fitting mixture
models. Main functions are varbayes, vbcomp, vbconstr, mppca,
mmppca and gmmkmsock.
Author: Pierrick Bruneau
Maintainer: Pierrick Bruneau <pbruneau@gmail.com>
Diff between VBmix versions 0.2.17 dated 2014-05-06 and 0.3.1 dated 2015-08-24
VBmix-0.2.17/VBmix/R/classicEM.R |only VBmix-0.2.17/VBmix/configure.win |only VBmix-0.2.17/VBmix/man/Rdct.Rd |only VBmix-0.2.17/VBmix/man/Rdct2D.Rd |only VBmix-0.2.17/VBmix/man/RinvDct2D.Rd |only VBmix-0.2.17/VBmix/man/classicEM.Rd |only VBmix-0.2.17/VBmix/man/readLabelFile.Rd |only VBmix-0.2.17/VBmix/man/readPixmapFile.Rd |only VBmix-0.2.17/VBmix/src/config.h.win |only VBmix-0.2.17/VBmix/src/readDataFile.cpp |only VBmix-0.3.1/VBmix/DESCRIPTION | 14 VBmix-0.3.1/VBmix/MD5 | 63 +- VBmix-0.3.1/VBmix/NAMESPACE | 3 VBmix-0.3.1/VBmix/R/Rutils.R | 21 VBmix-0.3.1/VBmix/R/displayScatter.R | 7 VBmix-0.3.1/VBmix/R/interfaces.R | 94 ++- VBmix-0.3.1/VBmix/README | 3 VBmix-0.3.1/VBmix/configure | 932 +++--------------------------- VBmix-0.3.1/VBmix/configure.ac | 16 VBmix-0.3.1/VBmix/data/VBmix.RData |binary VBmix-0.3.1/VBmix/inst/lowerpack.pdf |only VBmix-0.3.1/VBmix/inst/suffstats.pdf |only VBmix-0.3.1/VBmix/man/EM.Rd |only VBmix-0.3.1/VBmix/man/gdist.Rd |only VBmix-0.3.1/VBmix/man/getCouple.Rd | 3 VBmix-0.3.1/VBmix/man/getLabels.Rd | 2 VBmix-0.3.1/VBmix/man/mkmeans.Rd |only VBmix-0.3.1/VBmix/man/mvndensity.Rd | 5 VBmix-0.3.1/VBmix/man/mvnradiusdensity.Rd |only VBmix-0.3.1/VBmix/man/varbayes.Rd | 2 VBmix-0.3.1/VBmix/src/EM.c |only VBmix-0.3.1/VBmix/src/EM.h |only VBmix-0.3.1/VBmix/src/config.h |only VBmix-0.3.1/VBmix/src/config.h.in | 33 - VBmix-0.3.1/VBmix/src/getLabels.c | 9 VBmix-0.3.1/VBmix/src/mkmeans.c |only VBmix-0.3.1/VBmix/src/mkmeans.h |only VBmix-0.3.1/VBmix/src/mppca.cpp | 41 - VBmix-0.3.1/VBmix/src/mppca.h | 5 VBmix-0.3.1/VBmix/src/test.c |only VBmix-0.3.1/VBmix/src/test.h |only VBmix-0.3.1/VBmix/src/utils.c | 459 +++++++++++--- VBmix-0.3.1/VBmix/src/utils.h | 40 + VBmix-0.3.1/VBmix/src/varbayes.c | 8 44 files changed, 661 insertions(+), 1099 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.6 dated 2015-04-03 and 0.7 dated 2015-08-24
DESCRIPTION | 18 +++---- MD5 | 23 +++++---- NAMESPACE | 7 ++ NEWS | 7 ++ R/V8.R | 12 +++- build/vignette.rds |binary configure | 133 +++++++++++++++++++++++++++++------------------------ man/JS.Rd | 2 man/new_context.Rd | 2 src/Makevars.in |only src/Makevars.win | 20 ++++--- tools/v8-315.rb |only tools/version.cpp |only tools/winlibs.R | 17 +++++- 14 files changed, 146 insertions(+), 95 deletions(-)
Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using
structural equations, with emphasis on problems in causal inference.
Specify interventions and simulate from intervened data generating
distributions. Define and evaluate treatment-specific means, the average
treatment effects and coefficients from working marginal structural models.
User interface designed to facilitate the conduct of transparent and
reproducible simulation studies, and allows concise expression of complex
functional dependencies for a large number of time-varying nodes. See the
package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between simcausal versions 0.2.0 dated 2015-06-12 and 0.3.0 dated 2015-08-24
DESCRIPTION | 10 MD5 | 72 NAMESPACE | 24 NEWS | 19 R/DAG_node_R6.R |only R/distributions.R | 31 R/interface.r | 14 R/network.R |only R/node.R | 299 --- R/parserfunctions.r | 571 +++--- R/parserfunctions_R6.r |only R/simcausal-package.r | 6 R/simcausal.r | 513 +++-- R/simulation.r | 1213 ++++++------- R/targetparam.r | 800 ++++----- R/zzz.R | 29 README.md | 6 inst/doc/simcausal_vignette.R | 2 inst/doc/simcausal_vignette.Rnw | 2 inst/doc/simcausal_vignette.pdf |binary man/DAG_Class.Rd |only man/Define_sVar.Rd |only man/NetInd.to.sparseAdjMat.Rd |only man/NetIndClass.Rd |only man/Node_Class.Rd |only man/doLTCF.Rd | 2 man/eval.target.Rd | 5 man/igraph.to.sparseAdjMat.Rd |only man/network.Rd |only man/node.Rd | 13 man/plotDAG.Rd | 5 man/plotSurvEst.Rd | 14 man/set.DAG.Rd | 4 man/sim.Rd | 9 man/simfull.Rd | 5 man/simobs.Rd | 7 man/sparseAdjMat.to.NetInd.Rd |only man/sparseAdjMat.to.igraph.Rd |only tests/RUnit/example.simnets.R |only tests/RUnit/runit.simnets.R |only tests/RUnit/runittests.R | 3197 +++++++++++++++++++----------------- tests/RUnit/sim.impute.examples12.R | 2 tests/test-all.R | 4 vignettes/simcausal_vignette.Rnw | 2 44 files changed, 3528 insertions(+), 3352 deletions(-)
Title: Semiparametric Bivariate Regression Models
Description: Routine for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.5 dated 2015-07-22 and 3.6 dated 2015-08-24
ChangeLog | 4 DESCRIPTION | 9 MD5 | 84 ++--- NAMESPACE | 11 R/AT.r | 176 ++++++++-- R/LM.bpm.r | 2 R/OR.r | 49 ++ R/RR.r | 47 ++ R/S.m.r | 12 R/SemiParBIVProbit.fit.R | 24 - R/SemiParBIVProbit.fit.post.r | 28 + R/SemiParBIVProbit.r | 359 +++++++++++++++------ R/adjCov.r | 26 + R/adjCovSD.r | 27 + R/bprobgHs.r | 189 +++++------ R/bprobgHsCont.r | 49 +- R/bprobgHsCont3.r |only R/bprobgHsContUniv.r | 22 - R/bprobgHsContUniv3.r |only R/bprobgHsPO.r | 109 ++---- R/bprobgHsPO0.r | 46 +- R/bprobgHsSS.r | 120 +++---- R/conv.check.r | 4 R/copgHs.r | 2 R/copgHs2.r | 2 R/copgHsAT.r | 4 R/copgHsCont.r | 7 R/distrHs.r | 609 ++++++++++++++++++++++++------------- R/distrHsAT.r | 33 +- R/gt.bpm.R | 12 R/logLik.SemiParBIVProbit.r | 2 R/pen.r | 57 ++- R/polys.setup.r |only R/post.check.R |only R/print.SemiParBIVProbit.r | 35 +- R/print.summary.SemiParBIVProbit.r | 70 +++- R/resp.check.R | 61 +++ R/summary.SemiParBIVProbit.r | 304 ++++++++++++------ R/working.comp.r | 20 + man/SemiParBIVProbit.Rd | 10 man/bprobgHsCont3.Rd |only man/bprobgHsContUniv3.Rd |only man/hiv.Rd | 57 +++ man/polys.setup.Rd |only man/post.check.Rd |only man/prev.Rd | 3 man/resp.check.Rd | 7 47 files changed, 1804 insertions(+), 888 deletions(-)
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Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.5 dated 2015-05-03 and 1.0.6 dated 2015-08-24
DESCRIPTION | 12 ++-- MD5 | 45 ++++++++++------ NAMESPACE | 2 R/fun.r | 49 +++++++++++++---- R/mvBM.r | 38 +++++++++---- R/mvEB.r | 26 ++++++--- R/mvLLIK.r | 120 +++++++++++++++++++++++++++++++------------- R/mvOU.r | 24 ++++++-- R/mvSHIFT.r | 35 ++++++++---- R/mvSIM.r | 6 +- R/mvmorphPrecalc.r | 20 +++++-- README.md |only build |only inst |only man/mvBM.Rd | 10 ++- man/mvEB.Rd | 5 + man/mvLL.Rd | 7 +- man/mvMORPH-package.Rd | 4 - man/mvOU.Rd | 12 ++-- man/mvSHIFT.Rd | 2 src/weight-matrix-mvmorph.c | 1 tests |only vignettes |only 23 files changed, 290 insertions(+), 128 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.4 dated 2015-08-03 and 0.4.2 dated 2015-08-24
DESCRIPTION | 10 - MD5 | 53 +++--- NAMESPACE | 2 NEWS | 5 R/0_higherOrder.R |only R/1_functions4Fitting.R | 2 R/1_supplementaryPlot.R | 7 R/5_statisticalTests.R | 144 +++++++++++------- R/RcppExports.R | 8 + inst/doc/BayesianInference.pdf |binary inst/doc/CTMC.pdf |binary inst/doc/an_introduction_to_markovchain_package.R | 100 +++++++++--- inst/doc/an_introduction_to_markovchain_package.Rnw | 147 +++++++++++++++++-- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.pdf |binary man/HigherOrderMarkovChain-class.Rd |only man/fitHigherOrderMarkovChain.Rd |only man/markovchain-package.Rd | 4 man/verifyMarkovProperty.Rd | 25 +-- src/0_classesAndMethods.cpp | 1 src/1_ctmcFunctions4Fitting.cpp | 2 src/1_fitHigherOrder.cpp |only src/1_functions4Fitting.cpp | 12 + src/2_probabilistic.cpp | 7 src/3_multinomCI.cpp | 8 - src/RcppExports.cpp | 23 ++ tests/testthat/testHigerOrder.R |only tests/testthat/testInference.R | 16 -- vignettes/an_introduction_to_markovchain_package.Rnw | 147 +++++++++++++++++-- vignettes/markovchainBiblio.bib | 44 +++++ 30 files changed, 580 insertions(+), 187 deletions(-)
Title: Estimation of Meiotic Recombination Rates Using Marey Maps
Description: Local recombination rates are graphically estimated across a genome using marey maps.
Author: Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between MareyMap versions 1.3.0 dated 2015-07-08 and 1.3.1 dated 2015-08-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/mmspline3.R | 5 +++-- build/vignette.rds |binary inst/doc/vignette.pdf |binary 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-629 dated 2015-04-18 and 0.1-630 dated 2015-08-24
cheddar-0.1-629/cheddar/build |only cheddar-0.1-630/cheddar/DESCRIPTION | 10 cheddar-0.1-630/cheddar/MD5 | 20 - cheddar-0.1-630/cheddar/NAMESPACE | 7 cheddar-0.1-630/cheddar/inst/doc/CheddarQuickstart.pdf |binary cheddar-0.1-630/cheddar/inst/doc/Collections.pdf |binary cheddar-0.1-630/cheddar/inst/doc/Community.pdf |binary cheddar-0.1-630/cheddar/inst/doc/ImportExport.pdf |binary cheddar-0.1-630/cheddar/inst/doc/PlotsAndStats.pdf |binary cheddar-0.1-630/cheddar/man/cheddar.Rd | 6 cheddar-0.1-630/cheddar/src/trophic_chains.cpp | 174 ++++++++--------- cheddar-0.1-630/cheddar/tests/graph_tests.R |only 12 files changed, 112 insertions(+), 105 deletions(-)