Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written based on an accompanying 'RESTful' API.
Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more.
This package also supports experimental access to http://www.sealifebase.org data, which contains nearly
200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.1 dated 2015-08-15 and 2.0.2 dated 2015-09-01
DESCRIPTION | 6 - MD5 | 109 ++++++++++++------------ NAMESPACE | 2 NEWS | 5 + build/vignette.rds |binary inst/doc/tutorial.R |only inst/doc/tutorial.Rmd | 128 ++++++++++++++++++++++++++++ inst/doc/tutorial.html | 133 +++++++++++++++++++++++++++++- man/common_names.Rd | 2 man/common_to_sci.Rd | 2 man/diet.Rd | 2 man/distribution.Rd | 2 man/docs.Rd | 2 man/ecology.Rd | 2 man/ecosystem.Rd | 2 man/faoareas.Rd | 2 man/fecundity.Rd | 2 man/fishbase.Rd | 2 man/fooditems.Rd | 2 man/heartbeat.Rd | 2 man/introductions.Rd | 2 man/length_freq.Rd | 2 man/length_length.Rd | 2 man/length_weight.Rd | 2 man/list_fields.Rd | 2 man/load_taxa.Rd | 2 man/maturity.Rd | 2 man/morphology.Rd | 2 man/morphometrics.Rd | 2 man/occurrence.Rd | 2 man/oxygen.Rd | 2 man/ping.Rd | 2 man/popchar.Rd | 2 man/popgrowth.Rd | 2 man/popqb.Rd | 2 man/predators.Rd | 2 man/ration.Rd | 2 man/reproduction.Rd | 2 man/rfishbase-package.Rd | 2 man/sci_to_common.Rd | 2 man/sealifebase.Rd | 2 man/spawning.Rd | 2 man/species.Rd | 2 man/species_fields.Rd | 2 man/species_list.Rd | 2 man/species_names.Rd | 2 man/speed.Rd | 2 man/stocks.Rd | 2 man/swimming.Rd | 2 man/synonyms.Rd | 2 man/validate_names.Rd | 2 tests/testthat/helper_rfishbase.R | 2 tests/testthat/test_list_fields.R | 3 tests/testthat/test_load_taxa.R | 2 tests/testthat/test_population_dynamics.R | 3 vignettes/tutorial.Rmd | 2 56 files changed, 374 insertions(+), 107 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7 dated 2015-08-01 and 1.7.1 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/rcbalance-internal.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.4 dated 2015-08-27 and 0.5 dated 2015-09-01
nhanesA-0.4/nhanesA/R/sysdata.rda |only nhanesA-0.5/nhanesA/DESCRIPTION | 10 - nhanesA-0.5/nhanesA/INDEX | 2 nhanesA-0.5/nhanesA/MD5 | 19 +- nhanesA-0.5/nhanesA/NAMESPACE | 6 nhanesA-0.5/nhanesA/R/nhanes.R | 199 +++++++++++++++++------------ nhanesA-0.5/nhanesA/man/nhanes.Rd | 21 +-- nhanesA-0.5/nhanesA/man/nhanesAttr.Rd | 13 - nhanesA-0.5/nhanesA/man/nhanesTableVars.Rd | 19 +- nhanesA-0.5/nhanesA/man/nhanesTables.Rd | 19 +- nhanesA-0.5/nhanesA/man/nhanesTranslate.Rd | 25 +-- 11 files changed, 186 insertions(+), 147 deletions(-)
Title: Multi-Group Sparse Discriminant Analysis
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of 'I.Gaynanova, J.Booth and M.Wells (2015), Simultaneous sparse estimation of canonical vectors in the p>>N setting'.
Author: Irina Gaynanova
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between MGSDA versions 1.1 dated 2014-08-28 and 1.2 dated 2015-09-01
MGSDA-1.1/MGSDA/R/constructD.R |only MGSDA-1.1/MGSDA/R/solveVcoordf2.R |only MGSDA-1.1/MGSDA/R/solveVcoordf2C.R |only MGSDA-1.2/MGSDA/DESCRIPTION | 14 +- MGSDA-1.2/MGSDA/MD5 | 22 +-- MGSDA-1.2/MGSDA/NAMESPACE | 2 MGSDA-1.2/MGSDA/R/SolveMyLasso.R |only MGSDA-1.2/MGSDA/R/SolveMyLassoF.R |only MGSDA-1.2/MGSDA/R/createY.R |only MGSDA-1.2/MGSDA/R/cv.dLDA.R | 88 ++++++++------- MGSDA-1.2/MGSDA/R/dLDA.R | 40 +++--- MGSDA-1.2/MGSDA/man/MGSDA-package.Rd | 10 - MGSDA-1.2/MGSDA/man/cv.dLDA.Rd | 4 MGSDA-1.2/MGSDA/man/dLDA.Rd | 5 MGSDA-1.2/MGSDA/src/solveVcoordf2st.c | 199 ++++++++++++++++++++-------------- 15 files changed, 216 insertions(+), 168 deletions(-)
Title: Functions for Analysis of Data with General Recognition Theory
Description: Tools associated with General
Recognition Theory (Townsend & Ashby, 1986), including Gaussian model fitting of 4x4 and more
general confusion matrices, associated plotting and model comparison tools,
and tests of marginal response invariance and report independence.
Author: Robert X.D. Hawkins <rxdh@stanford.edu>, Joe Houpt
<joseph.houpt@wright.edu>, Noah Silbert <noahpoah@gmail.com>, Leslie
Blaha <Leslie.Blaha@wpafb.af.mil>, Thomas D. Wickens
<twickens@socrates.berkeley.edu>
Maintainer: Robert X.D. Hawkins <rxdh@stanford.edu>
Diff between mdsdt versions 1.0 dated 2014-09-30 and 1.1 dated 2015-09-01
DESCRIPTION | 10 ++-- MD5 | 35 +++++++------- NAMESPACE | 35 +++++++++++--- R/grt_base.R | 128 ++++++++++++++++++++++++++++++++++------------------- README.md | 9 +-- man/GOF.Rd | 29 ++++++------ man/anova.grt.Rd |only man/fit.grt.Rd | 41 ++++++---------- man/mriTest.Rd | 36 +++++--------- man/plot.grt.Rd | 21 +++----- man/print.grt.Rd | 13 ++--- man/riTest.Rd | 33 ++++--------- man/silbert09a.Rd | 17 +++---- man/silbert09b.Rd | 17 +++---- man/silbert12.Rd | 16 +++--- man/summary.grt.Rd | 13 ++--- man/thomasA.Rd | 20 +++----- man/thomasB.Rd | 20 +++----- man/wo89xt.Rd | 21 ++++---- 19 files changed, 266 insertions(+), 248 deletions(-)
Title: Efficient Approximate Bayesian Computation Sampling Schemes
Description: Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot, Thierry Faure, Nicolas Dumoulin, Carlo Albert.
Maintainer: Nicolas Dumoulin <nicolas.dumoulin@irstea.fr>
Diff between EasyABC versions 1.4 dated 2014-12-17 and 1.5 dated 2015-09-01
CHANGELOG | 6 + DESCRIPTION | 16 +-- MD5 | 23 ++-- NAMESPACE | 5 - R/EasyABC-internal.R | 224 ++++++++++++++++++++++-------------------------- R/SABC-internal.R |only R/SABC.R |only build/vignette.rds |binary inst/doc/EasyABC.pdf |binary man/ABC_mcmc.Rd | 7 + man/ABC_sequential.Rd | 7 + man/EasyABC-internal.Rd | 3 man/EasyABC-package.Rd | 28 +++--- man/SABC.Rd |only 14 files changed, 162 insertions(+), 157 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-04 1.03
2012-09-20 1.02
2012-07-22 1.01
2012-06-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-28 1.4.7
2014-02-27 1.4.6
2014-01-23 1.4.5
2013-09-24 1.4.4
2013-08-27 1.4.3
2013-07-31 1.4.2
2013-01-11 1.4
2012-10-01 1.3.1
2012-07-20 1.3
2012-05-14 1.2
2012-04-11 1.1
2011-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-20 1.1-5
2014-12-05 1.1-4
2014-05-08 1.1-3
2014-04-28 1.1-2
2013-12-30 1.1-1
2013-12-13 1.1-0
2013-06-05 1.0-1
2013-02-19 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-04 9.5
2012-08-17 9.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-16 0.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-05 0.0.4
2014-02-16 0.0.3
2013-11-23 0.0.2
2013-11-18 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-10 0.4
2014-05-25 0.3
2013-07-21 0.2
2013-02-06 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 1.6.2
2014-01-16 1.6.1
2013-09-06 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 1.0.5
2014-08-07 1.0.3
2014-08-02 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-19 2.0.4
2013-04-26 2.0.3
2012-12-10 2.0.2
Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on
top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre],
Jeroen Ooms [ctb],
RStudio [cph],
R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between xml2 versions 0.1.1 dated 2015-06-02 and 0.1.2 dated 2015-09-01
xml2-0.1.1/xml2/src/Makevars |only xml2-0.1.2/xml2/DESCRIPTION | 8 +- xml2-0.1.2/xml2/MD5 | 17 ++-- xml2-0.1.2/xml2/R/RcppExports.R | 4 + xml2-0.1.2/xml2/configure | 85 ++++++++++++++++-------- xml2-0.1.2/xml2/src/Makevars.in |only xml2-0.1.2/xml2/src/RcppExports.cpp | 10 ++ xml2-0.1.2/xml2/src/xml2_init.cpp | 7 + xml2-0.1.2/xml2/src/xml2_url.cpp | 12 +++ xml2-0.1.2/xml2/tests/testthat/helper-version.R |only xml2-0.1.2/xml2/tools/winlibs.R | 2 11 files changed, 105 insertions(+), 40 deletions(-)
Title: Triangulation of Irregularly Spaced Data
Description: A constrained two-dimensional Delaunay triangulation package
providing both triangulation and generation of voronoi mosaics of
irregular spaced data.
Author: Fortran code by R. J. Renka.
R functions by Albrecht Gebhardt <albrecht.gebhardt@aau.at>.
With contributions from Stephen Eglen <stephen@anc.ed.ac.uk>,
Sergei Zuyev <sergei@stams.strath.ac.uk> and
Denis White <white.denis@epamail.epa.gov>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between tripack versions 1.3-6 dated 2013-09-16 and 1.3-7 dated 2015-09-01
tripack-1.3-6/tripack/ChangeLog |only tripack-1.3-7/tripack/DESCRIPTION | 16 +++++++++------- tripack-1.3-7/tripack/LICENSE | 2 +- tripack-1.3-7/tripack/MD5 | 7 +++---- tripack-1.3-7/tripack/NAMESPACE | 10 ++++++++++ 5 files changed, 23 insertions(+), 12 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey <buttrey@nps.edu>
Diff between lpSolve versions 5.6.11 dated 2015-04-06 and 5.6.12 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/lp_lib.c | 2 +- src/lusol1.h | 6 +++--- src/myblas.c | 4 ++-- src/myblas.h | 4 ++-- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Reliable Comparison of Floating Point Numbers
Description: Comparisons of floating point numbers are problematic due to errors
associated with the binary representation of decimal numbers.
Despite being aware of these problems, people still use numerical methods
that fail to account for these and other rounding errors (this pitfall is
the first to be highlighted in Circle 1 of Burns (2012)
[The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
This package provides new relational operators useful for performing
floating point number comparisons with a set tolerance.
Author: Alex M Chubaty [aut, cre],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between fpCompare versions 0.2.0 dated 2015-05-16 and 0.2.1 dated 2015-09-01
fpCompare-0.2.0/fpCompare/inst/doc/fpCompare.html |only fpCompare-0.2.1/fpCompare/DESCRIPTION | 14 +++---- fpCompare-0.2.1/fpCompare/MD5 | 16 ++++---- fpCompare-0.2.1/fpCompare/NEWS | 6 +++ fpCompare-0.2.1/fpCompare/README.md | 4 +- fpCompare-0.2.1/fpCompare/build/vignette.rds |binary fpCompare-0.2.1/fpCompare/inst/doc/fpCompare.Rmd | 12 +++--- fpCompare-0.2.1/fpCompare/inst/doc/fpCompare.pdf |only fpCompare-0.2.1/fpCompare/tests/testthat/test-numerical-comparisons.R | 18 +++++----- fpCompare-0.2.1/fpCompare/vignettes/fpCompare.Rmd | 12 +++--- 10 files changed, 44 insertions(+), 38 deletions(-)
Title: Bindings to the 'CommonMark' Reference Implementation
Description: The 'CommonMark' spec is a rationalized version of markdown syntax.
This package converts markdown text to various formats including html, latex
and 'groff' man. In addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.4 dated 2015-05-30 and 0.5 dated 2015-09-01
commonmark-0.4/commonmark/src/cmark/COPYING |only commonmark-0.4/commonmark/src/cmark/debug.h |only commonmark-0.4/commonmark/src/cmark/html_unescape.h |only commonmark-0.5/commonmark/DESCRIPTION | 14 commonmark-0.5/commonmark/MD5 | 84 commonmark-0.5/commonmark/NAMESPACE | 1 commonmark-0.5/commonmark/NEWS |only commonmark-0.5/commonmark/R/markdown.R | 12 commonmark-0.5/commonmark/man/commonmark.Rd | 8 commonmark-0.5/commonmark/src/Makevars | 9 commonmark-0.5/commonmark/src/cmark/bench.h | 16 commonmark-0.5/commonmark/src/cmark/blocks.c | 1795 commonmark-0.5/commonmark/src/cmark/buffer.c | 492 commonmark-0.5/commonmark/src/cmark/buffer.h | 102 commonmark-0.5/commonmark/src/cmark/chunk.h | 204 commonmark-0.5/commonmark/src/cmark/cmark.c | 21 commonmark-0.5/commonmark/src/cmark/cmark.h | 292 commonmark-0.5/commonmark/src/cmark/cmark_ctype.c | 59 commonmark-0.5/commonmark/src/cmark/cmark_version.h | 4 commonmark-0.5/commonmark/src/cmark/commonmark.c | 994 commonmark-0.5/commonmark/src/cmark/entities.inc |only commonmark-0.5/commonmark/src/cmark/houdini.h | 43 commonmark-0.5/commonmark/src/cmark/houdini_href_e.c | 121 commonmark-0.5/commonmark/src/cmark/houdini_html_e.c | 95 commonmark-0.5/commonmark/src/cmark/houdini_html_u.c | 247 commonmark-0.5/commonmark/src/cmark/html.c | 587 commonmark-0.5/commonmark/src/cmark/inlines.c | 1973 commonmark-0.5/commonmark/src/cmark/inlines.h | 6 commonmark-0.5/commonmark/src/cmark/iterator.c | 244 commonmark-0.5/commonmark/src/cmark/iterator.h | 10 commonmark-0.5/commonmark/src/cmark/latex.c |only commonmark-0.5/commonmark/src/cmark/main.c | 327 commonmark-0.5/commonmark/src/cmark/man.c | 486 commonmark-0.5/commonmark/src/cmark/node.c | 1591 commonmark-0.5/commonmark/src/cmark/node.h | 94 commonmark-0.5/commonmark/src/cmark/parser.h | 22 commonmark-0.5/commonmark/src/cmark/references.c | 202 commonmark-0.5/commonmark/src/cmark/references.h | 18 commonmark-0.5/commonmark/src/cmark/render.c |only commonmark-0.5/commonmark/src/cmark/render.h |only commonmark-0.5/commonmark/src/cmark/scanners.c |42924 ++++++++++++------- commonmark-0.5/commonmark/src/cmark/scanners.h | 47 commonmark-0.5/commonmark/src/cmark/utf8.c | 682 commonmark-0.5/commonmark/src/cmark/utf8.h | 12 commonmark-0.5/commonmark/src/cmark/xml.c | 274 commonmark-0.5/commonmark/src/config.h | 14 commonmark-0.5/commonmark/src/wrapper.c | 13 47 files changed, 33105 insertions(+), 21034 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, generalized accelerated failure time frailty models, and standard semiparametric frailty models within the context of proportional hazards, proportional odds and accelerated failure time.
Author: Haiming Zhou <zhouh@niu.edu> and Tim Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.0.2 dated 2014-12-19 and 1.0.3 dated 2015-09-01
DESCRIPTION | 16 MD5 | 63 +- NAMESPACE | 19 R/GetCurves.R | 31 - R/anovaDDP.R | 24 - R/frailtyGAFT.R | 899 +++++++++++++++++++++++------------------ R/indeptCoxph.R | 319 +++++++------- R/spCopulaCoxph.R | 392 ++++++++--------- R/spCopulaDDP.R | 33 - R/survregbayes.R |only R/wrappers.R | 17 man/GetCurves.Rd | 93 +--- man/anovaDDP.Rd | 591 +++++++++++++------------- man/baseline.Rd |only man/frailtyGAFT.Rd | 462 +++++++++------------ man/indeptCoxph.Rd | 514 +++++++++++------------ man/spBayesSurv-package.Rd | 65 +- man/spCopulaCoxph.Rd | 527 +++++++++++------------- man/spCopulaDDP.Rd | 29 - man/survregbayes.Rd |only src/spSurv_AFT.cpp |only src/spSurv_AH.cpp |only src/spSurv_Coxph_tools.cpp | 8 src/spSurv_DDP_tools.cpp | 4 src/spSurv_LDTFP_tools.cpp | 190 ++------ src/spSurv_LDTFP_tools.h | 6 src/spSurv_MPT_tools.cpp |only src/spSurv_MPT_tools.h |only src/spSurv_PH.cpp |only src/spSurv_PO.cpp |only src/spSurv_anovaDDP.cpp | 6 src/spSurv_common.h | 1 src/spSurv_frailtyLDTFP.cpp | 6 src/spSurv_indeptCoxph.cpp | 4 src/spSurv_nonfrailtyLDTFP.cpp | 8 src/spSurv_spCopulaCoxph.cpp | 4 src/spSurv_spCopulaDDP.cpp | 4 37 files changed, 2137 insertions(+), 2198 deletions(-)
Title: An Object-Oriented Framework for Geostatistical Modeling in S+
Description: An Object-oriented Framework for Geostatistical Modeling in S+
containing functions for variogram estimation, variogram fitting and kriging
as well as some plot functions. Written entirely in S, therefore works only
for small data sets in acceptable computing time.
Author: S original by James J. Majure <majure@iastate.edu> Iowa State University, R port + extensions by Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between sgeostat versions 1.0-25 dated 2013-03-01 and 1.0-26 dated 2015-09-01
sgeostat-1.0-25/sgeostat/ChangeLog |only sgeostat-1.0-25/sgeostat/LICENSE |only sgeostat-1.0-25/sgeostat/digi.R |only sgeostat-1.0-25/sgeostat/maas.dig |only sgeostat-1.0-25/sgeostat/makefile |only sgeostat-1.0-25/sgeostat/www-SGeoStat |only sgeostat-1.0-25/sgeostat/zn_map.eps |only sgeostat-1.0-25/sgeostat/zn_map.gif |only sgeostat-1.0-25/sgeostat/zn_map.ps |only sgeostat-1.0-26/sgeostat/DESCRIPTION | 21 ++++++------ sgeostat-1.0-26/sgeostat/MD5 | 44 +------------------------- sgeostat-1.0-26/sgeostat/README | 42 ++++++++++++++++++++++++ sgeostat-1.0-26/sgeostat/man/fit.variogram.Rd | 5 +- 13 files changed, 59 insertions(+), 53 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.0 dated 2015-02-07 and 2.2 dated 2015-09-01
SemiCompRisks-2.0/SemiCompRisks/R/BayesIDcor.R |only SemiCompRisks-2.0/SemiCompRisks/R/BayesSurvcor.R |only SemiCompRisks-2.0/SemiCompRisks/R/ehr.R |only SemiCompRisks-2.0/SemiCompRisks/data/scrCorData.rda |only SemiCompRisks-2.0/SemiCompRisks/man/BayesIDcor.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/BayesSurvcor.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/ehr.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/scrCorData.Rd |only SemiCompRisks-2.2/SemiCompRisks/DESCRIPTION | 16 SemiCompRisks-2.2/SemiCompRisks/MD5 | 120 SemiCompRisks-2.2/SemiCompRisks/NAMESPACE | 41 SemiCompRisks-2.2/SemiCompRisks/R/BayesID.R | 3513 +++++- SemiCompRisks-2.2/SemiCompRisks/R/BayesSurv.R | 1003 + SemiCompRisks-2.2/SemiCompRisks/R/FreqID.R |only SemiCompRisks-2.2/SemiCompRisks/R/FreqSurv.R |only SemiCompRisks-2.2/SemiCompRisks/R/initiate.startValues.R |only SemiCompRisks-2.2/SemiCompRisks/R/internalFunc.R | 160 SemiCompRisks-2.2/SemiCompRisks/R/methods.R | 5408 ++++------ SemiCompRisks-2.2/SemiCompRisks/R/simID.R | 138 SemiCompRisks-2.2/SemiCompRisks/R/simSurv.R | 69 SemiCompRisks-2.2/SemiCompRisks/data/scrData.rda |binary SemiCompRisks-2.2/SemiCompRisks/data/survData.rda |binary SemiCompRisks-2.2/SemiCompRisks/man/BMT.Rd | 42 SemiCompRisks-2.2/SemiCompRisks/man/BayesID.Rd | 590 - SemiCompRisks-2.2/SemiCompRisks/man/BayesSurv.Rd | 448 SemiCompRisks-2.2/SemiCompRisks/man/FreqID.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/FreqSurv.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/SemiCompRisks-package.Rd | 28 SemiCompRisks-2.2/SemiCompRisks/man/initiate.startValues.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/methods.Rd | 103 SemiCompRisks-2.2/SemiCompRisks/man/scrData.Rd | 68 SemiCompRisks-2.2/SemiCompRisks/man/simID.Rd | 137 SemiCompRisks-2.2/SemiCompRisks/man/simSurv.Rd | 65 SemiCompRisks-2.2/SemiCompRisks/man/survData.Rd | 37 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScr.c | 27 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScrSM.c | 27 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScrSM_Updates.c | 321 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScr_Updates.c | 324 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorSurv.c | 15 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorSurv_Updates.c | 11 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScr.c | 23 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScrSM.c | 25 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScrSM_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScr_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorSurv.c | 10 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorSurv_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeScr.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BpeScrSM.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BpeScrSM_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeScr_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeSurv.c | 8 SemiCompRisks-2.2/SemiCompRisks/src/BpeSurv_Updates.c | 4 SemiCompRisks-2.2/SemiCompRisks/src/BweibCorSurv.c | 9 SemiCompRisks-2.2/SemiCompRisks/src/BweibCorSurv_Updates.c | 2 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScr.c | 34 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScrSM.c | 34 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScrSM_Updates.c | 244 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScr_Updates.c | 249 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorSurv.c | 25 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorSurv_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScr.c | 29 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScrSM.c | 28 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScrSM_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScr_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BweibScr.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BweibScrSM.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BweibSurv.c | 49 SemiCompRisks-2.2/SemiCompRisks/src/Utilities.c | 132 68 files changed, 8812 insertions(+), 4929 deletions(-)
Title: Convert Text into Speech
Description: Convert text into speech (voice file in 'mp3' or 'wav' format) with APIs offered by Google Translate and ITRI TTS (Text-To-Speech service, Industrial Technology Research Institute, Taiwan. http://tts.itri.org.tw/). Two main functions are given corresponding these two APIs, tts_google() and tts_ITRI(). For tts_google(), only English is supported. For tts_ITRI(), English and Chinese (both traditional and simplified) are supported, and user can specify the speaker accent, speed and volume. Both functions require internet connection.
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between Rtts versions 0.3.1 dated 2015-06-03 and 0.3.2 dated 2015-09-01
DESCRIPTION | 8 ++-- MD5 | 11 +++-- NEWS |only R/tts_ITRI.R | 25 +++++++++++-- R/tts_ITRI_getID.R | 90 ++++++++++++++++++++++++++++--------------------- R/tts_ITRI_getStatus.R | 7 +++ R/tts_ITRI_getURL.R | 7 +++ 7 files changed, 97 insertions(+), 51 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-176 dated 2015-06-25 and 0.15-244 dated 2015-09-01
ChangeLog | 15 ++ DESCRIPTION | 8 - MD5 | 32 +++--- R/RhpcExt.R | 113 ++++++++++++++++++++++ R/RhpcOp.R | 16 --- man/Rhpc-package.Rd | 35 ++++++ src/Makevars.win | 2 src/RhpcMPI.c | 43 -------- src/RhpcMPIWorkerCall.h | 56 ++-------- src/RhpcMPIlapplyLB.h | 111 +++++---------------- src/RhpcMPIlapplyseq.h | 112 ++++++--------------- src/common/Rhpc.h | 2 src/worker/Rhpc.cmd.in | 14 +- src/worker/RhpcWorker.c | 10 - src/worker/RhpcWorker_LapplyLB.h | 107 ++++---------------- src/worker/RhpcWorker_Lapplyseq.h | 189 ++++++++++++++----------------------- src/worker/RhpcWorker_WorkerCall.h | 52 ++-------- 17 files changed, 380 insertions(+), 537 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-11 dated 2015-05-29 and 0.3-12 dated 2015-09-01
ChangeLog | 86 +++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++-- MD5 | 35 ++++++++-------- NAMESPACE | 6 ++ R/AAA.R | 8 +++ R/over.R | 64 ++++++++++++++++++++++-------- configure | 22 +++++----- configure.ac | 2 inst/ChangeLog | 86 +++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 man/misc-over.Rd |only man/pred-binary-gContains.Rd | 2 man/pred-binary-gCrosses.Rd | 2 man/pred-binary-gEquals.Rd | 2 man/pred-binary-gIntersects.Rd | 2 man/pred-binary-gRelate.Rd | 2 man/pred-binary-gTouches.Rd | 2 src/rgeos_R2geos.c | 16 +++---- src/rgeos_predicate_binary.c | 16 ++++--- 19 files changed, 294 insertions(+), 71 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it is possible to create and manipulate multivariate network
data with different formats, and there are effective ways available to treat multiple networks
with routines that combine algebraic systems like the partially ordered semigroup or the
semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. As well an algebraic approach for two-mode networks is made
through Galois derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.6 dated 2015-05-19 and 1.7 dated 2015-09-01
multiplex-1.6/multiplex/R/slc.R |only multiplex-1.6/multiplex/inst/doc/TwoMode.R |only multiplex-1.6/multiplex/inst/doc/TwoMode.Rnw |only multiplex-1.6/multiplex/inst/doc/TwoMode.pdf |only multiplex-1.6/multiplex/man/incubA.Rd |only multiplex-1.6/multiplex/man/slc.Rd |only multiplex-1.6/multiplex/vignettes/TwoMode.Rnw |only multiplex-1.7/multiplex/DESCRIPTION | 27 - multiplex-1.7/multiplex/MD5 | 117 ++--- multiplex-1.7/multiplex/R/as.signed.R |only multiplex-1.7/multiplex/R/bundle.census.R | 90 ++-- multiplex-1.7/multiplex/R/bundles.R | 82 +-- multiplex-1.7/multiplex/R/decomp.R | 8 multiplex-1.7/multiplex/R/dhc.R | 25 - multiplex-1.7/multiplex/R/diagram.R | 32 - multiplex-1.7/multiplex/R/diagram.levels.R | 18 multiplex-1.7/multiplex/R/dichot.R | 12 multiplex-1.7/multiplex/R/expos.R | 377 +++++++++--------- multiplex-1.7/multiplex/R/flt.R |only multiplex-1.7/multiplex/R/fltr.R | 66 ++- multiplex-1.7/multiplex/R/galois.R | 164 +++---- multiplex-1.7/multiplex/R/iinc.R | 2 multiplex-1.7/multiplex/R/jnt.R | 68 ++- multiplex-1.7/multiplex/R/neighb.R |only multiplex-1.7/multiplex/R/ngbs.R | 57 ++ multiplex-1.7/multiplex/R/pacnet.R | 76 +-- multiplex-1.7/multiplex/R/prev.R | 41 + multiplex-1.7/multiplex/R/rbox.R | 68 +-- multiplex-1.7/multiplex/R/read.gml.R | 104 ++-- multiplex-1.7/multiplex/R/read.srt.R | 95 ++-- multiplex-1.7/multiplex/R/rel.sys.R | 127 ++++-- multiplex-1.7/multiplex/R/rm.isol.R | 40 - multiplex-1.7/multiplex/R/semiring.R | 6 multiplex-1.7/multiplex/R/signed.R | 38 - multiplex-1.7/multiplex/R/strings.R | 201 ++++----- multiplex-1.7/multiplex/R/summaryBundles.R | 178 +++++--- multiplex-1.7/multiplex/R/write.dat.R | 4 multiplex-1.7/multiplex/R/write.gml.R | 6 multiplex-1.7/multiplex/R/write.srt.R | 29 - multiplex-1.7/multiplex/build/vignette.rds |binary multiplex-1.7/multiplex/data/incubA.RData |binary multiplex-1.7/multiplex/data/incubB.RData |binary multiplex-1.7/multiplex/data/incubC.RData |binary multiplex-1.7/multiplex/data/incubD.RData |binary multiplex-1.7/multiplex/data/incubs.RData |only multiplex-1.7/multiplex/inst/CHANGELOG | 25 + multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.R |only multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.Rnw |only multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.pdf |only multiplex-1.7/multiplex/man/as.signed.Rd |only multiplex-1.7/multiplex/man/bundles.Rd | 2 multiplex-1.7/multiplex/man/diagram.Rd | 4 multiplex-1.7/multiplex/man/diagram.levels.Rd | 2 multiplex-1.7/multiplex/man/dichot.Rd | 8 multiplex-1.7/multiplex/man/expos.Rd | 48 +- multiplex-1.7/multiplex/man/flt.Rd |only multiplex-1.7/multiplex/man/fltr.Rd | 36 - multiplex-1.7/multiplex/man/galois.Rd | 6 multiplex-1.7/multiplex/man/iinc.Rd | 2 multiplex-1.7/multiplex/man/incubs.Rd |only multiplex-1.7/multiplex/man/multiplex-package.Rd | 4 multiplex-1.7/multiplex/man/neighb.Rd |only multiplex-1.7/multiplex/man/partial.order.Rd | 4 multiplex-1.7/multiplex/man/perm.Rd | 1 multiplex-1.7/multiplex/man/rel.sys.Rd | 28 + multiplex-1.7/multiplex/man/semiring.Rd | 2 multiplex-1.7/multiplex/man/signed.Rd | 4 multiplex-1.7/multiplex/man/summaryBundles.Rd | 5 multiplex-1.7/multiplex/vignettes/TwoModeNetworks.Rnw |only 69 files changed, 1353 insertions(+), 986 deletions(-)
Title: Multidimensional Projection Techniques
Description: Multidimensional projection techniques are used to create two dimensional representations of multidimensional data sets.
Author: Francisco M. Fatore,
Samuel G. Fadel
Maintainer: Francisco M. Fatore <fmfatore@gmail.com>
Diff between mp versions 0.3 dated 2015-08-16 and 0.3.1 dated 2015-09-01
mp-0.3.1/mp/DESCRIPTION | 8 +- mp-0.3.1/mp/MD5 | 23 +++----- mp-0.3.1/mp/NAMESPACE | 24 ++++---- mp-0.3.1/mp/R/RcppExports.R | 30 +++++----- mp-0.3.1/mp/man/forceScheme.Rd | 112 ++++++++++++++++++++-------------------- mp-0.3.1/mp/man/is.symmetric.Rd | 36 ++++++------ mp-0.3.1/mp/man/lamp.Rd | 78 +++++++++++++-------------- mp-0.3.1/mp/man/lsp.Rd | 80 ++++++++++++++-------------- mp-0.3.1/mp/man/mp.Rd | 22 +++---- mp-0.3.1/mp/man/plmp.Rd | 74 +++++++++++++------------- mp-0.3.1/mp/man/tSNE.Rd | 84 +++++++++++++++--------------- mp-0.3.1/mp/src/lamp.cpp | 2 mp-0.3/mp/README.md |only 13 files changed, 287 insertions(+), 286 deletions(-)
Title: MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of bioassay data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut, cre], Philippe Ruiz [aut, cre], Sandrine Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon-Kam-king [ctb], Philippe Veber [ctb]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>
Diff between morse versions 1.0.2 dated 2014-07-03 and 2.0.0 dated 2015-09-01
morse-1.0.2/morse/R/plot.repro.fit.R |only morse-1.0.2/morse/R/print.repro.check.data.R |only morse-1.0.2/morse/R/print.repro.data.R |only morse-1.0.2/morse/R/print.repro.fit.R |only morse-1.0.2/morse/R/repro.check.data.R |only morse-1.0.2/morse/R/repro.convergence.R |only morse-1.0.2/morse/R/repro.cumulplot.R |only morse-1.0.2/morse/R/repro.data.R |only morse-1.0.2/morse/R/repro.fit.R |only morse-1.0.2/morse/R/repro.fullsurvplot.R |only morse-1.0.2/morse/R/repro.parfit.R |only morse-1.0.2/morse/R/repro.survplot.R |only morse-1.0.2/morse/R/summary.repro.data.R |only morse-1.0.2/morse/R/summary.repro.fit.R |only morse-1.0.2/morse/man/repro.check.data.Rd |only morse-1.0.2/morse/man/repro.convergence.Rd |only morse-1.0.2/morse/man/repro.cumulplot.Rd |only morse-1.0.2/morse/man/repro.data.Rd |only morse-1.0.2/morse/man/repro.fit.Rd |only morse-1.0.2/morse/man/repro.fullsurvplot.Rd |only morse-1.0.2/morse/man/repro.survplot.Rd |only morse-2.0.0/morse/DESCRIPTION | 23 morse-2.0.0/morse/MD5 | 90 +- morse-2.0.0/morse/NAMESPACE | 78 + morse-2.0.0/morse/NEWS | 44 - morse-2.0.0/morse/R/as.survData.R |only morse-2.0.0/morse/R/errorTable.R |only morse-2.0.0/morse/R/morse-internal.R | 1140 ++++----------------------- morse-2.0.0/morse/R/morse.R |only morse-2.0.0/morse/R/plot.reproData.R |only morse-2.0.0/morse/R/plot.reproFitTT.R |only morse-2.0.0/morse/R/plot.survData.R |only morse-2.0.0/morse/R/plot.survFitTT.R |only morse-2.0.0/morse/R/print.reproFitTT.R |only morse-2.0.0/morse/R/print.survFitTT.R |only morse-2.0.0/morse/R/reproData.R |only morse-2.0.0/morse/R/reproDataCheck.R |only morse-2.0.0/morse/R/reproFitTT.R |only morse-2.0.0/morse/R/summary.reproData.R |only morse-2.0.0/morse/R/summary.reproFitTT.R |only morse-2.0.0/morse/R/summary.survData.R |only morse-2.0.0/morse/R/summary.survFitTT.R |only morse-2.0.0/morse/R/survData.R |only morse-2.0.0/morse/R/survDataCheck.R |only morse-2.0.0/morse/R/survFitTT.R |only morse-2.0.0/morse/README.md |only morse-2.0.0/morse/build |only morse-2.0.0/morse/inst |only morse-2.0.0/morse/man/as.survData.Rd |only morse-2.0.0/morse/man/cadmium1.Rd | 73 - morse-2.0.0/morse/man/cadmium2.Rd | 67 - morse-2.0.0/morse/man/chlordan.Rd | 69 - morse-2.0.0/morse/man/copper.Rd | 71 - morse-2.0.0/morse/man/morse-package.Rd | 122 +- morse-2.0.0/morse/man/plot.reproData.Rd |only morse-2.0.0/morse/man/plot.reproFitTT.Rd |only morse-2.0.0/morse/man/plot.survData.Rd |only morse-2.0.0/morse/man/plot.survFitTT.Rd |only morse-2.0.0/morse/man/print.reproFitTT.Rd |only morse-2.0.0/morse/man/print.survFitTT.Rd |only morse-2.0.0/morse/man/reproData.Rd |only morse-2.0.0/morse/man/reproDataCheck.Rd |only morse-2.0.0/morse/man/reproFitTT.Rd |only morse-2.0.0/morse/man/summary.reproData.Rd |only morse-2.0.0/morse/man/summary.reproFitTT.Rd |only morse-2.0.0/morse/man/summary.survData.Rd |only morse-2.0.0/morse/man/summary.survFitTT.Rd |only morse-2.0.0/morse/man/survData.Rd |only morse-2.0.0/morse/man/survDataCheck.Rd |only morse-2.0.0/morse/man/survFitTT.Rd |only morse-2.0.0/morse/man/zinc.Rd | 70 - morse-2.0.0/morse/tests |only morse-2.0.0/morse/vignettes |only 73 files changed, 550 insertions(+), 1297 deletions(-)
Title: Functions to Fit Monotone Polynomials
Description: Functions for fitting monotone polynomials to data.
Author: Berwin A. Turlach [aut, cre],
Kevin Murray [ctb]
Maintainer: Berwin A. Turlach <Berwin.Turlach@gmail.com>
Diff between MonoPoly versions 0.2-8 dated 2013-11-03 and 0.2-10 dated 2015-09-01
DESCRIPTION | 19 +++++++++---------- MD5 | 22 ++++++++++++---------- NAMESPACE | 8 ++++++++ R/00MonPol.R | 26 ++++++++++++++------------ R/Nointercept.R |only R/ismonotone.R |only R/util.R | 8 +++++--- inst/CITATION | 2 +- inst/doc/MonoPoly-manual.pdf |binary man/monpol.Rd | 11 ++++++----- man/monpol.fit.Rd | 7 ++++--- man/w0.Rd | 7 ++++--- man/w2.Rd | 7 ++++--- 13 files changed, 67 insertions(+), 50 deletions(-)
More information about interactionTest at CRAN
Permanent link
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 joint modelling for recurrent events
with terminal event for clustered data or not.
5) Joint General frailty models in the context of a joint modelling for recurrent
events with terminal event data with two independent frailty terms.
Prediction values are available. 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 a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying covariates
effects in Cox, shared and joint models. 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-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.7.5 dated 2015-03-06 and 2.7.6.1 dated 2015-09-01
DESCRIPTION | 14 MD5 | 45 NAMESPACE | 9 NEWS | 4 R/frailtyPenal.R | 4005 +++++++++++++++++++-------------------- R/print.jointPenal.R | 709 +++--- R/waldtest.R | 13 demo/00Index | 2 demo/frailtypack_additivePenal.R | 4 demo/frailtypack_frailtyPenal.R | 4 demo/frailtypack_jointPenal.R | 52 demo/frailtypack_multivPenal.R | 6 demo/frailtypack_nestedPenal.R | 4 man/frailtyPenal.Rd | 67 man/frailtypack-package.Rd | 16 man/prediction.Rd | 496 ++-- src/AparamMultive.f90 | 56 src/Aparameters.f90 | 86 src/Makevars | 5 src/aaOptim.f90 | 493 ++-- src/aaOptimres.f90 | 2 src/funcpaMultivSplines.f90 | 1 src/funcpajgeneral.f90 |only src/joint.f90 | 974 ++++++--- 24 files changed, 3765 insertions(+), 3302 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.1 dated 2015-08-21 and 0.0.2 dated 2015-09-01
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NEWS | 15 +++++++++++++-- R/epifit.R | 49 +++++++++++++++++++++++++++++++++---------------- R/modules.R | 40 +++++++++++++++------------------------- R/print.epifit.R | 8 ++++---- man/epifit.Rd | 35 ++++++++++++++++++++++++++++------- 7 files changed, 107 insertions(+), 67 deletions(-)
Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino <toni.giorgino@gmail.com>,
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>
Diff between dtw versions 1.17-1 dated 2013-12-11 and 1.18-1 dated 2015-09-01
dtw-1.17-1/dtw/vignettes/alignMVM.pdf |only dtw-1.17-1/dtw/vignettes/mvmSP.pdf |only dtw-1.17-1/dtw/vignettes/object-diagram.pdf |only dtw-1.17-1/dtw/vignettes/plot-conventions.pdf |only dtw-1.18-1/dtw/DESCRIPTION | 15 ++++++----- dtw-1.18-1/dtw/MD5 | 34 +++++++++++++------------- dtw-1.18-1/dtw/NAMESPACE | 9 ++++++ dtw-1.18-1/dtw/R/backtrack.R | 14 +++++++--- dtw-1.18-1/dtw/R/dtw.R | 4 ++- dtw-1.18-1/dtw/R/zzz.R | 5 ++- dtw-1.18-1/dtw/build/vignette.rds |binary dtw-1.18-1/dtw/inst/ChangeLog | 7 +++++ dtw-1.18-1/dtw/inst/doc/dtw.Rnw | 8 +++--- dtw-1.18-1/dtw/inst/doc/dtw.pdf |binary dtw-1.18-1/dtw/man/dtw.Rd | 15 +++++++---- dtw-1.18-1/dtw/tests/dtw_test.R | 2 - dtw-1.18-1/dtw/tests/dtw_test.Rout.save | 12 --------- dtw-1.18-1/dtw/vignettes/dtw.Rnw | 8 +++--- dtw-1.18-1/dtw/vignettes/figures |only 19 files changed, 76 insertions(+), 57 deletions(-)
Title: Extended Empirical Likelihood
Description: Compute the extended empirical log likelihood ratio (Tsao & Wu, 2014) for the mean and parameters defined by estimating equations.
Author: Fan Wu and Yu Zhang
Maintainer: Yu Zhang <yuz@uvic.ca>
Diff between eel versions 1.0 dated 2015-08-19 and 1.1 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/eel.R | 20 ++++++-------------- R/eel_est.R | 15 ++++++--------- build/partial.rdb |binary man/eel-package.Rd | 2 -- 6 files changed, 21 insertions(+), 34 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.4.2 dated 2015-06-16 and 0.4.3 dated 2015-09-01
dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Name.h |only dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Reducer.h |only dplyr-0.4.2/dplyr/inst/include/dplyr/Result/TypedProcessor.h |only dplyr-0.4.2/dplyr/inst/include/tools/StrictListOf.h |only dplyr-0.4.3/dplyr/DESCRIPTION | 30 dplyr-0.4.3/dplyr/MD5 | 295 ++-- dplyr-0.4.3/dplyr/NAMESPACE | 6 dplyr-0.4.3/dplyr/R/RcppExports.R | 13 dplyr-0.4.3/dplyr/R/colwise.R | 13 dplyr-0.4.3/dplyr/R/compute-collect.r | 2 dplyr-0.4.3/dplyr/R/data-lahman.r | 4 dplyr-0.4.3/dplyr/R/data-nycflights13.r | 2 dplyr-0.4.3/dplyr/R/dataframe.R | 18 dplyr-0.4.3/dplyr/R/dbi-s3.r | 2 dplyr-0.4.3/dplyr/R/dplyr.r | 3 dplyr-0.4.3/dplyr/R/explain.r | 4 dplyr-0.4.3/dplyr/R/frame-data.R |only dplyr-0.4.3/dplyr/R/glimpse.R | 6 dplyr-0.4.3/dplyr/R/grouped-df.r | 4 dplyr-0.4.3/dplyr/R/join.r | 32 dplyr-0.4.3/dplyr/R/manip.r | 10 dplyr-0.4.3/dplyr/R/progress.R | 10 dplyr-0.4.3/dplyr/R/rank.R | 4 dplyr-0.4.3/dplyr/R/rbind.r | 39 dplyr-0.4.3/dplyr/R/rowwise.r | 4 dplyr-0.4.3/dplyr/R/src-local.r | 2 dplyr-0.4.3/dplyr/R/src-mysql.r | 4 dplyr-0.4.3/dplyr/R/src-postgres.r | 8 dplyr-0.4.3/dplyr/R/src-sqlite.r | 8 dplyr-0.4.3/dplyr/R/tally.R | 2 dplyr-0.4.3/dplyr/R/tbl-cube.r | 2 dplyr-0.4.3/dplyr/R/tbl-df.r | 9 dplyr-0.4.3/dplyr/R/tbl-dt.r | 2 dplyr-0.4.3/dplyr/R/tbl-sql.r | 7 dplyr-0.4.3/dplyr/R/translate-sql-base.r | 19 dplyr-0.4.3/dplyr/R/utils-format.r | 31 dplyr-0.4.3/dplyr/R/utils.r | 2 dplyr-0.4.3/dplyr/R/zzz.r | 3 dplyr-0.4.3/dplyr/README.md | 65 - dplyr-0.4.3/dplyr/build/vignette.rds |binary dplyr-0.4.3/dplyr/inst/doc/data_frames.R | 7 dplyr-0.4.3/dplyr/inst/doc/data_frames.Rmd | 67 - dplyr-0.4.3/dplyr/inst/doc/data_frames.html | 142 +- dplyr-0.4.3/dplyr/inst/doc/databases.Rmd | 2 dplyr-0.4.3/dplyr/inst/doc/databases.html | 114 - dplyr-0.4.3/dplyr/inst/doc/hybrid-evaluation.Rmd | 2 dplyr-0.4.3/dplyr/inst/doc/hybrid-evaluation.html | 6 dplyr-0.4.3/dplyr/inst/doc/introduction.Rmd | 114 - dplyr-0.4.3/dplyr/inst/doc/introduction.html | 378 +++-- dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.R | 2 dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.Rmd | 4 dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.html | 8 dplyr-0.4.3/dplyr/inst/doc/nse.html | 4 dplyr-0.4.3/dplyr/inst/doc/two-table.Rmd | 4 dplyr-0.4.3/dplyr/inst/doc/two-table.html | 236 ++- dplyr-0.4.3/dplyr/inst/doc/window-functions.html | 78 - dplyr-0.4.3/dplyr/inst/include/dplyr.h | 32 dplyr-0.4.3/dplyr/inst/include/dplyr/CharacterVectorOrderer.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/Collecter.h | 325 ++--- dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameAble.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameColumnSubsetVisitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameColumnVisitor.h | 54 dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameSubsetVisitors.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameVisitors.h | 104 - dplyr-0.4.3/dplyr/inst/include/dplyr/Gatherer.h | 211 --- dplyr-0.4.3/dplyr/inst/include/dplyr/GroupedDataFrame.h | 105 - dplyr-0.4.3/dplyr/inst/include/dplyr/JoinVisitor.h | 3 dplyr-0.4.3/dplyr/inst/include/dplyr/JoinVisitorImpl.h | 129 + dplyr-0.4.3/dplyr/inst/include/dplyr/MatrixColumnSubsetVectorVisitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/MatrixColumnVisitor.h | 128 - dplyr-0.4.3/dplyr/inst/include/dplyr/NamedListAccumulator.h | 63 dplyr-0.4.3/dplyr/inst/include/dplyr/OrderVisitorImpl.h | 163 +- dplyr-0.4.3/dplyr/inst/include/dplyr/Replicator.h | 139 -- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallElementProxy.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallProxy.h | 150 -- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallbackProcessor.h | 67 - dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Count_Distinct.h | 29 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/DelayedProcessor.h | 204 +-- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/First.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/GroupedCallProxy.h | 9 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/GroupedHybridCall.h | 40 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Lag.h | 85 - 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dplyr-0.4.3/dplyr/src/combine_variables.cpp | 28 dplyr-0.4.3/dplyr/src/distinct.cpp | 4 dplyr-0.4.3/dplyr/src/dplyr.cpp | 649 ++++------ dplyr-0.4.3/dplyr/src/filter.cpp | 111 + dplyr-0.4.3/dplyr/src/group_indices.cpp | 22 dplyr-0.4.3/dplyr/src/join.cpp | 170 +- dplyr-0.4.3/dplyr/src/select.cpp | 50 dplyr-0.4.3/dplyr/src/summarise.cpp | 68 - dplyr-0.4.3/dplyr/tests/testthat/test-arrange.r | 30 dplyr-0.4.3/dplyr/tests/testthat/test-cbind.R | 23 dplyr-0.4.3/dplyr/tests/testthat/test-data_frame.R | 6 dplyr-0.4.3/dplyr/tests/testthat/test-equality.r | 13 dplyr-0.4.3/dplyr/tests/testthat/test-filter.r | 73 + dplyr-0.4.3/dplyr/tests/testthat/test-frame-data.R |only dplyr-0.4.3/dplyr/tests/testthat/test-group-by.r | 7 dplyr-0.4.3/dplyr/tests/testthat/test-joins.r | 68 + dplyr-0.4.3/dplyr/tests/testthat/test-mutate-windowed.R | 81 - dplyr-0.4.3/dplyr/tests/testthat/test-mutate.r | 73 + dplyr-0.4.3/dplyr/tests/testthat/test-rbind.r | 120 + dplyr-0.4.3/dplyr/tests/testthat/test-slice.r | 26 dplyr-0.4.3/dplyr/tests/testthat/test-summarise.r | 143 +- dplyr-0.4.3/dplyr/tests/testthat/test-tbl-df.r | 9 dplyr-0.4.3/dplyr/tests/testthat/test-window.R | 9 dplyr-0.4.3/dplyr/vignettes/data_frames.Rmd | 67 - dplyr-0.4.3/dplyr/vignettes/databases.Rmd | 2 dplyr-0.4.3/dplyr/vignettes/hybrid-evaluation.Rmd | 2 dplyr-0.4.3/dplyr/vignettes/introduction.Rmd | 114 - dplyr-0.4.3/dplyr/vignettes/new-sql-backend.Rmd | 4 dplyr-0.4.3/dplyr/vignettes/two-table.Rmd | 4 157 files changed, 3771 insertions(+), 3150 deletions(-)
Title: Statistical Tests for Cryptographic Randomness
Description: Performs cryptographic randomness tests on a sequence of random integers or bits. Most of the included tests are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests. Additionally, it includes functions for the calculation of greatest common divisor, the Stirling numbers of the second kind, critical value of the topological binary test, and base conversions from base 2 to 10 and vice versa.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>
Diff between CryptRndTest versions 1.0.5 dated 2015-06-16 and 1.1.5 dated 2015-09-01
DESCRIPTION | 14 - MD5 | 62 +++++--- NAMESPACE | 24 ++- R/GCD.R | 38 +---- R/GCD.big.R |only R/GCD.q.R |only R/GCD.test.R | 111 ++++++++------- R/KSADCHRY.R | 32 +--- R/KSADdga.R | 40 ++--- R/Random.walk.D.R | 27 +-- R/Random.walk.G.R | 27 +-- R/Random.walk.Y.R | 17 -- R/Strlng2.R | 5 R/TBT.criticalValue.R |only R/adaptive.chi.square.R | 77 ++++------ R/birthday.spacings.R | 5 R/book.stack.R | 24 +-- R/dogumGunuAraliklari.R | 9 - R/random.walk.tests.R | 10 - R/toBaseTen.R |only R/toBaseTwo.R |only R/topological.binary.R | 23 +-- man/CryptRndTest-internal.Rd | 8 - man/CryptRndTest-package.Rd | 203 ++++++++++++++-------------- man/GCD.Rd | 18 +- man/GCD.big.Rd |only man/GCD.q.Rd |only man/GCD.test.Rd | 233 ++++++++++++++++----------------- man/Strlng2.Rd | 18 +- man/TBT.criticalValue.Rd |only man/adaptive.chi.square.Rd | 151 ++++++++++----------- man/birthday.spacings.Rd | 18 +- man/book.stack.Rd | 18 +- man/random.walk.tests.Rd | 302 +++++++++++++++++++++---------------------- man/toBaseTen.Rd |only man/toBaseTwo.Rd |only man/topological.binary.Rd | 131 +++++++++--------- 37 files changed, 805 insertions(+), 840 deletions(-)
Title: COnstrained B-Splines (Sparse Matrix Based)
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng <Pin.Ng@nau.edu> and Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cobs versions 1.3-0 dated 2015-01-06 and 1.3-1 dated 2015-09-01
ChangeLog | 5 +++++ DESCRIPTION | 16 ++++++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 17 +++++++++++------ R/concaveRegr.R | 4 ++-- R/l1Design.R | 2 +- R/looDesign.R | 6 +++--- R/qbsks.R | 2 +- R/scobs.R | 2 +- man/exHe.Rd | 5 +++-- 10 files changed, 44 insertions(+), 33 deletions(-)
Title: Construct Graphs of S4 Class Hierarchies
Description: Construct directed graphs of S4 class hierarchies and
visualize them. In general, these graphs typically are DAGs (directed
acyclic graphs), often simple trees in practice.
Author: Martin Maechler partly based on code from Robert Gentleman
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between classGraph versions 0.7-4 dated 2010-08-11 and 0.7-5 dated 2015-09-01
ChangeLog | 5 +++++ DESCRIPTION | 17 +++++++++-------- MD5 |only NAMESPACE | 27 ++++++++++++++++++++++----- R/S4classes-MM.R | 4 ++-- man/bGraph.Rd | 2 ++ man/classTree.Rd | 3 +-- man/mRagraph.Rd | 2 +- man/numOutEdges.Rd | 2 +- man/plotRag.Rd | 3 ++- tests/Matrix-ex.R | 3 ++- 11 files changed, 47 insertions(+), 21 deletions(-)
Title: Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures.
These are useful when data is heterogeneous, e.g. in
pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms
(flexible support size) and EM algorithms (fixed support size)
are provided for univariate and bivariate data.
Author: Peter Schlattmann <peter.schlattmann@mti.uni-jena.de>, Johannes
Hoehne, Maryna Verba
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>
Diff between CAMAN versions 0.72 dated 2014-10-23 and 0.73 dated 2015-09-01
DESCRIPTION | 17 +++++++---------- MD5 | 12 ++++++------ NAMESPACE | 10 +++++++++- R/CAMAN.R | 2 +- R/covariate_CAMAN.r | 1 + man/mixcov.Rd | 6 +++--- src/vemema_vem.cpp | 12 ++++++------ 7 files changed, 33 insertions(+), 27 deletions(-)
Title: David Scott's ASH Routines
Description: David Scott's ASH routines ported from S-PLUS to R.
Author: S original by David W. Scott
R port by Albrecht Gebhardt <albrecht.gebhardt@aau.at>
adopted to recent S-PLUS by Stephen Kaluzny <spk@insightful.com>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between ash versions 1.0-14 dated 2013-02-11 and 1.0-15 dated 2015-09-01
ash-1.0-14/ash/ChangeLog |only ash-1.0-15/ash/DESCRIPTION | 22 +++++++++++----------- ash-1.0-15/ash/MD5 | 3 +-- 3 files changed, 12 insertions(+), 13 deletions(-)