Title: Tests for Normality
Diff between nortest versions 1.0-2 dated 2012-05-30 and 1.0-3 dated 2015-02-26
Description: Five omnibus tests for testing the composite hypothesis of
normality.
Author: Juergen Gross [aut],
Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges
ChangeLog |only
DESCRIPTION | 21 ++++++++++++---------
MD5 | 7 ++++---
R/ad.test.R | 12 ++++++++----
man/cvm.test.Rd | 4 ++--
5 files changed, 26 insertions(+), 18 deletions(-)
Title: Generalized Turnbull's Estimator
Diff between gte versions 1.2-1 dated 2014-01-06 and 1.2-2 dated 2015-02-26
Description: Generalized Turnbull's estimator proposed by Dehghan and Duchesne
(2011).
Author: Mohammad Hossein Dehghan, Thierry Duchesne and Sophie Baillargeon
Maintainer: Thierry Duchesne
DESCRIPTION | 10 +-
MD5 | 16 +--
NAMESPACE | 3
NEWS | 5 +
R/gte-package.R | 4
R/gte.R | 54 ++++++-----
man/gte-package.Rd | 33 +++----
man/gte.Rd | 240 +++++++++++++++++++++--------------------------------
man/simul.Rd | 20 ++--
9 files changed, 175 insertions(+), 210 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Diff between amen versions 0.999 dated 2014-03-01 and 1.0 dated 2015-02-26
Description: Analysis of network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor
models (Hoff(2009)). Four different link functions accommodate different
relational data structures, including binary/network data (bin), normal
relational data (nrm), ordinal relational data (ord) and data from
fixed-rank nomination schemes (frn). Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this
software was supported in part by NICHD grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff
DESCRIPTION | 44 ++++++------
MD5 | 164 ++++++++++++++++++++++++++++--------------------
NAMESPACE | 33 +++++++++
R/Xbeta.R | 24 +++++++
R/ame.R | 81 +++++++++++++++++++++++
R/ame_rep.R |only
R/amen-package.R |only
R/design_array.R | 19 +++++
R/gofstats.R | 18 +++++
R/mhalf.R | 19 +++++
R/plot.ame.R | 48 ++++++++++++++
R/rUV_fc.R | 63 ++++++++++++++++++
R/rUV_rep_fc.R |only
R/rZ_bin_fc.R | 42 ++++++++++++
R/rZ_cbin_fc.R | 70 ++++++++++++++++++++
R/rZ_frn_fc.R | 80 +++++++++++++++++++++++
R/rZ_nrm_fc.R | 27 +++++++
R/rZ_ord_fc.R | 50 ++++++++++++++
R/rZ_rrl.R | 67 +++++++++++++++++++
R/raSab_bin_fc.R | 43 ++++++++++++
R/raSab_cbin_fc.R | 53 +++++++++++++++
R/raSab_frn_fc.R | 46 +++++++++++++
R/rbeta_ab_fc.R | 106 +++++++++++++++++++++++++++++++
R/rbeta_ab_rep_fc.R |only
R/rmvnorm.R | 23 ++++++
R/rrho_mh.R | 34 +++++++++
R/rrho_mh_rep.R |only
R/rs2_fc.R | 21 ++++++
R/rs2_rep.R |only
R/rwish.R | 25 +++++++
R/simY_bin.R | 26 +++++++
R/simY_frn.R | 46 +++++++++++++
R/simY_nrm.R | 26 +++++++
R/simY_ord.R | 33 +++++++++
R/simY_rrl.R | 40 +++++++++++
R/simZ.R | 24 +++++++
R/summary.ame.R | 32 +++++++++
R/zscores.R | 19 +++++
data/YX_bin_long.rda |only
data/addhealthc3.RData |only
data/addhealthc9.RData |only
data/coldwar.RData |only
data/comtrade.RData |only
data/conflict90s.RData |only
data/datalist |only
data/dutchcollege.RData |only
data/lazegalaw.RData |only
data/sampsonmonks.RData |only
man/Xbeta.Rd | 26 +++++--
man/YX_bin.Rd | 30 +++-----
man/YX_bin_long.Rd |only
man/YX_cbin.Rd | 32 ++++-----
man/YX_frn.Rd | 29 +++-----
man/YX_nrm.Rd | 29 +++-----
man/YX_ord.Rd | 28 +++-----
man/YX_rrl.Rd | 29 +++-----
man/addhealthc3.Rd |only
man/addhealthc9.Rd |only
man/ame.Rd | 142 +++++++++++++++++++++--------------------
man/ame_rep.Rd |only
man/amen-package.Rd | 45 ++++++-------
man/coldwar.Rd |only
man/comtrade.Rd |only
man/conflict90s.Rd |only
man/design_array.Rd | 36 +++++-----
man/dutchcollege.Rd |only
man/gofstats.Rd | 28 +++-----
man/lazegalaw.Rd |only
man/mhalf.Rd | 22 ++----
man/plot.ame.Rd | 27 +++----
man/rUV_fc.Rd | 52 ++++++---------
man/rUV_rep_fc.Rd |only
man/rZ_bin_fc.Rd | 43 +++++-------
man/rZ_cbin_fc.Rd | 80 +++++++++--------------
man/rZ_frn_fc.Rd | 80 +++++++++--------------
man/rZ_nrm_fc.Rd | 42 ++++--------
man/rZ_ord_fc.Rd | 42 ++++--------
man/rZ_rrl_fc.Rd | 52 ++++++---------
man/raSab_bin_fc.Rd | 62 +++++++-----------
man/raSab_cbin_fc.Rd | 70 ++++++++------------
man/raSab_frn_fc.Rd | 73 ++++++++-------------
man/rbeta_ab_fc.Rd | 77 ++++++++++------------
man/rbeta_ab_rep_fc.Rd |only
man/rmvnorm.Rd | 28 ++++----
man/rrho_mh.Rd | 40 +++++------
man/rrho_mh_rep.Rd |only
man/rs2_fc.Rd | 26 +++----
man/rs2_rep_fc.Rd |only
man/rwish.Rd | 33 +++++----
man/sampsonmonks.Rd |only
man/simY_bin.Rd | 27 +++----
man/simY_frn.Rd | 63 ++++++++----------
man/simY_nrm.Rd | 33 ++++-----
man/simY_ord.Rd | 34 ++++-----
man/simY_rrl.Rd | 41 +++++-------
man/simZ.Rd | 32 ++++-----
man/summary.ame.Rd | 45 ++++++-------
man/zscores.Rd | 27 +++----
98 files changed, 2087 insertions(+), 964 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.600.4.0 dated 2015-01-25 and 0.4.650.1.1 dated 2015-02-26
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 13
DESCRIPTION | 8
MD5 | 83
README.md | 6
inst/NEWS.Rd | 16
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/armadillo | 12
inst/include/armadillo_bits/Col_bones.hpp | 4
inst/include/armadillo_bits/Col_meat.hpp | 81
inst/include/armadillo_bits/Mat_bones.hpp | 20
inst/include/armadillo_bits/Mat_meat.hpp | 201 ++
inst/include/armadillo_bits/Row_bones.hpp | 4
inst/include/armadillo_bits/Row_meat.hpp | 81
inst/include/armadillo_bits/SpMat_bones.hpp | 57
inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 2
inst/include/armadillo_bits/SpMat_meat.hpp | 1308 +++++++--------
inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 4
inst/include/armadillo_bits/SpSubview_meat.hpp | 107 -
inst/include/armadillo_bits/arma_rng.hpp | 33
inst/include/armadillo_bits/arma_rng_cxx11.hpp | 30
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/arrayops_meat.hpp | 145 -
inst/include/armadillo_bits/compiler_setup.hpp | 17
inst/include/armadillo_bits/config.hpp | 14
inst/include/armadillo_bits/diskio_meat.hpp | 30
inst/include/armadillo_bits/eglue_core_bones.hpp | 6
inst/include/armadillo_bits/eglue_core_meat.hpp | 8
inst/include/armadillo_bits/eop_core_bones.hpp | 6
inst/include/armadillo_bits/eop_core_meat.hpp | 8
inst/include/armadillo_bits/fn_accu.hpp | 8
inst/include/armadillo_bits/fn_conv_to.hpp | 224 +-
inst/include/armadillo_bits/fn_misc.hpp | 47
inst/include/armadillo_bits/fn_randg.hpp |only
inst/include/armadillo_bits/op_pinv_meat.hpp | 14
inst/include/armadillo_bits/running_stat_vec_meat.hpp | 4
inst/include/armadillo_bits/sp_auxlib_bones.hpp | 2
inst/include/armadillo_bits/sp_auxlib_meat.hpp | 17
inst/include/armadillo_bits/subview_bones.hpp | 7
inst/include/armadillo_bits/subview_cube_bones.hpp | 6
inst/include/armadillo_bits/subview_cube_meat.hpp | 25
inst/include/armadillo_bits/subview_meat.hpp | 26
inst/include/armadillo_bits/unwrap.hpp | 24
43 files changed, 1641 insertions(+), 1073 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Diff between PDQutils versions 0.1.0 dated 2015-02-12 and 0.1.1 dated 2015-02-26
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav
PDQutils-0.1.0/PDQutils/R/appx.r |only
PDQutils-0.1.1/PDQutils/DESCRIPTION | 15 +-
PDQutils-0.1.1/PDQutils/MD5 | 37 +++---
PDQutils-0.1.1/PDQutils/NAMESPACE | 2
PDQutils-0.1.1/PDQutils/R/PDQutils.r | 10 +
PDQutils-0.1.1/PDQutils/R/cornish_fisher.r |only
PDQutils-0.1.1/PDQutils/R/edgeworth.r |only
PDQutils-0.1.1/PDQutils/R/gram_charlier.r |only
PDQutils-0.1.1/PDQutils/README.md | 151 ++++++++++++++++++++++---
PDQutils-0.1.1/PDQutils/inst/CITATION | 5
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.R | 73 +++++++++++-
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.pdf |binary
PDQutils-0.1.1/PDQutils/man/AS269.Rd | 2
PDQutils-0.1.1/PDQutils/man/NEWS.Rd | 7 +
PDQutils-0.1.1/PDQutils/man/PDQutils.Rd | 4
PDQutils-0.1.1/PDQutils/man/dapx_edgeworth.Rd |only
PDQutils-0.1.1/PDQutils/man/dapx_gca.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/qapx_cf.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/rapx_cf.Rd | 7 -
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.bib | 32 +++++
22 files changed, 540 insertions(+), 67 deletions(-)
Title: Association Analysis of CNV Data and Imputed SNPs
Diff between CNVassoc versions 2.0.1 dated 2013-09-19 and 2.1 dated 2015-02-26
Description: The CNVassoc package carries out analysis of common
Copy Number Variants (CNVs) and imputed Single Nucleotide
Polymorphisms (SNPs) in population-based studies.
It includes tools for estimating association under a series
of study designs (case-control, cohort, etc), using several
dependent variables (class status, censored data, counts)
as response, adjusting for covariates and considering
various inheritance models. Moreover, it is possible to
perform epistasis studies with pairs of CNVs or imputed SNPs.
It has been optimized in order to make feasible the analyses
of Genome Wide Association studies (GWAs) with hundreds of
thousands of genetic variants (CNVs / imputed SNPs). Also,
it incorporates functions for inferring copy number (CNV
genotype calling). Various classes and methods for generic
functions (print, summary, plot, anova, ...) have been
created to facilitate the analysis.
Author: Juan R González, Isaac Subirana
Maintainer: Isaac Subirana
DESCRIPTION | 38 ++++++++++++++++++++++----------------
MD5 | 31 ++++++++++++++++++++++---------
NAMESPACE | 10 +++++++++-
R/fastCNVassoc.R | 12 +++++++++---
R/fastCNVinter.R |only
R/getProbs.cghCall.R | 22 ++++++++++++----------
R/plapply.R | 2 +-
build |only
inst/doc/changelog.txt | 5 +++++
man/fastCNVassoc.Rd | 4 +++-
man/fastCNVinter.Rd |only
man/simCNVdataWeibull.Rd | 2 +-
src/CNVassoc.h | 10 ++++++++++
src/NRinterlogistic.c |only
src/NRinterlogisticcov.c |only
src/NRinterweibull.c |only
src/NRinterweibullcov.c |only
src/loglikinterlogistic.c |only
src/loglikinterlogisticcov.c |only
src/loglikinterweibull.c |only
src/loglikinterweibullcov.c |only
src/outerC.c |only
src/simcensrespC.c |only
23 files changed, 94 insertions(+), 42 deletions(-)
Title: Rcmdr Receiver Operator Characteristic Plug-In PACKAGE
Diff between RcmdrPlugin.ROC versions 1.0-17 dated 2014-12-20 and 1.0-18 dated 2015-02-26
More information about RcmdrPlugin.ROC at CRAN
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre],
Mihaela Hedesiu [ctb],
Andrei Achimas [ctb],
Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 6 +++---
inst/CHANGES | 2 ++
4 files changed, 13 insertions(+), 11 deletions(-)
Permanent link
Title: An R Interface to the Oniguruma Regular Expression Library
Diff between ore versions 1.0.6 dated 2015-01-01 and 1.1.0 dated 2015-02-26
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
ore-1.0.6/ore/src/main.c |only
ore-1.0.6/ore/src/main.h |only
ore-1.0.6/ore/src/onig/enc/big5.c |only
ore-1.0.6/ore/src/onig/enc/cp1251.c |only
ore-1.0.6/ore/src/onig/enc/cp932.c |only
ore-1.0.6/ore/src/onig/enc/euc_jp.c |only
ore-1.0.6/ore/src/onig/enc/euc_kr.c |only
ore-1.0.6/ore/src/onig/enc/euc_tw.c |only
ore-1.0.6/ore/src/onig/enc/gb18030.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_10.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_11.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_13.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_14.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_15.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_16.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_2.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_3.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_4.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_5.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_6.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_7.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_8.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_9.c |only
ore-1.0.6/ore/src/onig/enc/jis |only
ore-1.0.6/ore/src/onig/enc/koi8.c |only
ore-1.0.6/ore/src/onig/enc/koi8_r.c |only
ore-1.0.6/ore/src/onig/enc/sjis.c |only
ore-1.0.6/ore/src/onig/enc/utf16_be.c |only
ore-1.0.6/ore/src/onig/enc/utf16_le.c |only
ore-1.0.6/ore/src/onig/enc/utf32_be.c |only
ore-1.0.6/ore/src/onig/enc/utf32_le.c |only
ore-1.1.0/ore/DESCRIPTION | 9 +-
ore-1.1.0/ore/MD5 | 81 +++++++-----------
ore-1.1.0/ore/NAMESPACE | 5 -
ore-1.1.0/ore/NEWS | 25 +++++
ore-1.1.0/ore/R/dict.R |only
ore-1.1.0/ore/R/es.R |only
ore-1.1.0/ore/R/match.R | 92 ++++++++++++--------
ore-1.1.0/ore/R/ore.R | 23 +++--
ore-1.1.0/ore/R/workspace.R |only
ore-1.1.0/ore/README.md | 66 +++++++++++++-
ore-1.1.0/ore/man/es.Rd |only
ore-1.1.0/ore/man/matches.Rd | 6 +
ore-1.1.0/ore/man/ore.Rd | 23 +++--
ore-1.1.0/ore/man/ore.dict.Rd |only
ore-1.1.0/ore/man/ore.ismatch.Rd | 3
ore-1.1.0/ore/man/ore.lastmatch.Rd | 3
ore-1.1.0/ore/man/ore.search.Rd | 26 ++++-
ore-1.1.0/ore/man/ore.split.Rd | 3
ore-1.1.0/ore/man/ore.subst.Rd | 12 ++
ore-1.1.0/ore/src/Makevars | 4
ore-1.1.0/ore/src/compile.c |only
ore-1.1.0/ore/src/compile.h |only
ore-1.1.0/ore/src/match.c |only
ore-1.1.0/ore/src/match.h |only
ore-1.1.0/ore/src/onig/oniguruma.h | 125 +++++++++++++++-------------
ore-1.1.0/ore/src/print.c |only
ore-1.1.0/ore/src/print.h |only
ore-1.1.0/ore/src/split.c |only
ore-1.1.0/ore/src/split.h |only
ore-1.1.0/ore/src/subst.c |only
ore-1.1.0/ore/src/subst.h |only
ore-1.1.0/ore/src/zzz.c |only
ore-1.1.0/ore/src/zzz.h |only
ore-1.1.0/ore/tests/testthat/test-20-dict.R |only
ore-1.1.0/ore/tests/testthat/test-25-es.R |only
66 files changed, 324 insertions(+), 182 deletions(-)
Title: Tools for Nonlinear Regression Analysis
Diff between nlstools versions 1.0-0 dated 2014-06-25 and 1.0-1 dated 2015-02-26
Description: Several tools for assessing the quality of fit of a
gaussian nonlinear model are provided.
Author: Florent Baty
Maintainer: Florent Baty
ChangeLog | 7 ++++++-
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++++-----
NAMESPACE | 4 ++++
R/confint2.R |only
data/L.minor.rda |only
inst/CITATION | 8 ++++----
inst/NEWS | 10 +++++++++-
man/L.minor.Rd |only
man/confint2.Rd |only
10 files changed, 37 insertions(+), 16 deletions(-)
Title: Graphical Tests for Hardy-Weinberg Equilibrium
Diff between HardyWeinberg versions 1.5.4 dated 2014-08-11 and 1.5.5 dated 2015-02-26
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman
Maintainer: Jan Graffelman
HardyWeinberg-1.5.4/HardyWeinberg/R/combineC.R |only
HardyWeinberg-1.5.5/HardyWeinberg/DESCRIPTION | 25 +
HardyWeinberg-1.5.5/HardyWeinberg/MD5 | 62 +++-
HardyWeinberg-1.5.5/HardyWeinberg/NAMESPACE | 2
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineChisquare.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineExact.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/HWAlltests.R | 12
HardyWeinberg-1.5.5/HardyWeinberg/R/HWChisq.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/HWMissing.R | 137 +++++-----
HardyWeinberg-1.5.5/HardyWeinberg/R/HWPerm.R | 4
HardyWeinberg-1.5.5/HardyWeinberg/R/HWTernaryPlot.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/MakeFactor.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/mipvalue.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/missingentirerow.R |only
HardyWeinberg-1.5.5/HardyWeinberg/build |only
HardyWeinberg-1.5.5/HardyWeinberg/inst |only
HardyWeinberg-1.5.5/HardyWeinberg/man/HWAlltests.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWChisq.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWIlrPlot.Rd | 4
HardyWeinberg-1.5.5/HardyWeinberg/man/HWMissing.Rd | 32 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPerm.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPower.Rd | 9
HardyWeinberg-1.5.5/HardyWeinberg/man/HWQqplot.Rd | 2
HardyWeinberg-1.5.5/HardyWeinberg/man/HWTernaryPlot.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HardyWeinberg-package.Rd | 28 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/MakeFactor.Rd |only
HardyWeinberg-1.5.5/HardyWeinberg/man/Markers.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/vignettes |only
28 files changed, 233 insertions(+), 129 deletions(-)
Title: Tools to Deal with Fuzzy Numbers
Diff between FuzzyNumbers versions 0.3-5 dated 2014-10-01 and 0.4-1 dated 2015-02-26
Description: S4 classes and methods
to deal with fuzzy numbers. With them you can compute any arithmetic
operations (e.g. by using the Zadeh extension principle),
perform approximation of arbitrary FNs by trapezoidal and piecewise
linear FNs, prepare plots of FNs for publications, calculate
possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre],
Jan Caha [ctb]
Maintainer: Marek Gagolewski
DESCRIPTION | 19 +-
MD5 | 117 +++++++-----
NAMESPACE | 13 +
NEWS | 16 +
R/methods-Arithmetic.R | 6
R/methods-compare.R |only
R/methods-min_max.R |only
R/methods-special_functions.R |only
build/vignette.rds |binary
inst/CITATION | 6
inst/doc/FuzzyNumbersTutorial.R | 72 +++++++
inst/doc/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
inst/doc/FuzzyNumbersTutorial.pdf |binary
man/Arithmetic-methods.Rd | 31 +++
man/DiscontinuousFuzzyNumber-class.Rd | 3
man/DiscontinuousFuzzyNumber.Rd | 3
man/Extract-methods.Rd | 3
man/FuzzyNumber-class.Rd | 3
man/FuzzyNumber.Rd | 3
man/FuzzyNumbers-package.Rd | 3
man/PiecewiseLinearFuzzyNumber-class.Rd | 28 ++-
man/PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/PowerFuzzyNumber-class.Rd | 3
man/PowerFuzzyNumber.Rd | 3
man/TrapezoidalFuzzyNumber-class.Rd | 3
man/TrapezoidalFuzzyNumber.Rd | 3
man/TriangularFuzzyNumber.Rd | 3
man/alphaInterval-methods.Rd | 28 ++-
man/alphacut-methods.Rd | 3
man/ambiguity-methods.Rd | 3
man/approxInvert.Rd | 3
man/arctan2.Rd |only
man/as.FuzzyNumber.Rd | 3
man/as.PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/as.PowerFuzzyNumber.Rd | 28 ++-
man/as.TrapezoidalFuzzyNumber.Rd | 28 ++-
man/as.character-methods.Rd | 28 ++-
man/convertAlpha.Rd | 3
man/convertSide.Rd | 3
man/core-methods.Rd | 3
man/distance-methods.Rd | 3
man/evaluate-methods.Rd | 3
man/expectedInterval-methods.Rd | 28 ++-
man/expectedValue-methods.Rd | 3
man/fapply-methods.Rd | 31 +++
man/integrateAlpha-methods.Rd | 3
man/integrate_discont_val.Rd | 3
man/maximum.Rd |only
man/minimum.Rd |only
man/necessityExceedance.Rd |only
man/necessityStrictExceedance.Rd |only
man/necessityStrictUndervaluation.Rd |only
man/necessityUndervaluation.Rd |only
man/piecewiseLinearApproximation-methods.Rd | 3
man/plot-methods.Rd | 28 ++-
man/possibilityExceedance.Rd |only
man/possibilityStrictExceedance.Rd |only
man/possibilityStrictUndervaluation.Rd |only
man/possibilityUndervaluation.Rd |only
man/pow-PiecewiseLinearFuzzyNumber-numeric-method.Rd |only
man/show-methods.Rd | 3
man/supp-methods.Rd | 3
man/trapezoidalApproximation-methods.Rd | 3
man/value-methods.Rd | 3
man/weightedExpectedValue-methods.Rd | 3
man/width-methods.Rd | 3
vignettes/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
67 files changed, 866 insertions(+), 137 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Diff between forecast versions 5.8 dated 2015-01-06 and 5.9 dated 2015-02-26
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 8 +++
DESCRIPTION | 10 ++--
MD5 | 22 ++++-----
NAMESPACE | 3 -
R/arfima.R | 6 +-
R/arima.R | 135 ++++++++++++++++++++++++++++----------------------------
R/errors.R | 3 +
R/fpp.R | 31 ++++++++++--
R/getResponse.R | 4 -
R/newarima2.R | 21 ++++----
R/tbats.R | 4 -
man/accuracy.Rd | 24 ++++++++-
12 files changed, 162 insertions(+), 109 deletions(-)
Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Diff between exact2x2 versions 1.4.0 dated 2014-08-25 and 1.4.1 dated 2015-02-26
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals. Provides power and sample size calculations. Also gives melded confidence intervals for the binomial case.
Author: Michael P. Fay
Maintainer: Michael P. Fay
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/ss2x2.R | 29 +++++++++++++++++++++++++----
build/vignette.rds |binary
inst/doc/exact2x2.pdf |binary
inst/doc/exactMcNemar.R | 6 +++---
inst/doc/exactMcNemar.Rnw | 21 ++++++++++++++++-----
inst/doc/exactMcNemar.pdf |binary
man/exact2x2-package.Rd | 4 ++--
vignettes/exactMcNemar.Rnw | 21 ++++++++++++++++-----
11 files changed, 82 insertions(+), 33 deletions(-)
Title: ODBC Database Access
Diff between RODBC versions 1.3-10 dated 2013-11-25 and 1.3-11 dated 2015-02-26
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley
ChangeLog | 11 +++++
DESCRIPTION | 14 +++----
MD5 | 22 +++++------
R/RODBC.R | 4 +-
R/sql.R | 1
build/vignette.rds |binary
cleanup | 2 -
inst/doc/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
inst/doc/RODBC.pdf |binary
man/sqlColumns.Rd | 4 +-
man/sqlTypeInfo.Rd | 2 -
vignettes/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
12 files changed, 135 insertions(+), 121 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.6.6 dated 2014-09-11 and 1.7.1 dated 2015-02-26
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
lcmm-1.6.6/lcmm/R/VarCov.lcmm..R |only
lcmm-1.6.6/lcmm/R/link.confint.lcmm.R |only
lcmm-1.6.6/lcmm/R/link.confint.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.baselinerisk.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.predict.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.survival.Jointlcmm.R |only
lcmm-1.6.6/lcmm/man/link.confint.Rd |only
lcmm-1.6.6/lcmm/man/multlcmm.rd |only
lcmm-1.6.6/lcmm/man/plot.baselinerisk.Rd |only
lcmm-1.6.6/lcmm/man/plot.linkfunction.Rd |only
lcmm-1.6.6/lcmm/man/plot.postprob.Rd |only
lcmm-1.6.6/lcmm/man/plot.survival.Rd |only
lcmm-1.6.6/lcmm/src/predictDyn.f90 |only
lcmm-1.7.1/lcmm/DESCRIPTION | 17
lcmm-1.7.1/lcmm/MD5 | 187
lcmm-1.7.1/lcmm/NAMESPACE | 42
lcmm-1.7.1/lcmm/NEWS | 42
lcmm-1.7.1/lcmm/R/Contlcmm.R | 25
lcmm-1.7.1/lcmm/R/Jointlcmm.R | 2976 ++++++------
lcmm-1.7.1/lcmm/R/Ordlcmm.R | 18
lcmm-1.7.1/lcmm/R/VarCov.Jointlcmm.R | 53
lcmm-1.7.1/lcmm/R/VarCov.lcmm.R |only
lcmm-1.7.1/lcmm/R/VarCovRE.Jointlcmm.R | 314 -
lcmm-1.7.1/lcmm/R/VarCovRE.hlme.R | 39
lcmm-1.7.1/lcmm/R/VarCovRE.lcmm.R | 36
lcmm-1.7.1/lcmm/R/VarCovRE.multlcmm.R | 32
lcmm-1.7.1/lcmm/R/VarExpl.Jointlcmm.R | 251 -
lcmm-1.7.1/lcmm/R/VarExpl.hlme.R | 235
lcmm-1.7.1/lcmm/R/VarExpl.lcmm.R | 246 -
lcmm-1.7.1/lcmm/R/VarExpl.multlcmm.R | 261 -
lcmm-1.7.1/lcmm/R/WaldMult.R | 46
lcmm-1.7.1/lcmm/R/cuminc.R |only
lcmm-1.7.1/lcmm/R/dynpred.R | 1936 +++++--
lcmm-1.7.1/lcmm/R/epoce.R | 893 +--
lcmm-1.7.1/lcmm/R/estimates.Jointlcmm.R | 66
lcmm-1.7.1/lcmm/R/fitY.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.lcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.multlcmm.R |only
lcmm-1.7.1/lcmm/R/hlme.R | 21
lcmm-1.7.1/lcmm/R/lcmm.R | 42
lcmm-1.7.1/lcmm/R/multlcmm.R | 100
lcmm-1.7.1/lcmm/R/plot.Diffepoce.R | 71
lcmm-1.7.1/lcmm/R/plot.R |only
lcmm-1.7.1/lcmm/R/plot.cuminc.R |only
lcmm-1.7.1/lcmm/R/plot.dynpred.R | 632 +-
lcmm-1.7.1/lcmm/R/plot.epoce.R | 22
lcmm-1.7.1/lcmm/R/plot.predictL.R |only
lcmm-1.7.1/lcmm/R/plot.predictY.R |only
lcmm-1.7.1/lcmm/R/plot.predictlink.R |only
lcmm-1.7.1/lcmm/R/plotbaselinerisk.R |only
lcmm-1.7.1/lcmm/R/plotfit.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunction.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunctionmult.R |only
lcmm-1.7.1/lcmm/R/plotpostprob.R |only
lcmm-1.7.1/lcmm/R/plotresid.R |only
lcmm-1.7.1/lcmm/R/plotsurvival.R |only
lcmm-1.7.1/lcmm/R/postprob.Jointlcmm.R | 45
lcmm-1.7.1/lcmm/R/predictL.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictL.lcmm.R | 236
lcmm-1.7.1/lcmm/R/predictL.multlcmm.R | 173
lcmm-1.7.1/lcmm/R/predictY.Jointlcmm.R | 1238 +++--
lcmm-1.7.1/lcmm/R/predictY.hlme.R | 189
lcmm-1.7.1/lcmm/R/predictY.lcmm.R | 85
lcmm-1.7.1/lcmm/R/predictY.multlcmm.R | 59
lcmm-1.7.1/lcmm/R/predictlink.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.lcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.multlcmm.R |only
lcmm-1.7.1/lcmm/R/print.Diffepoce.R | 2
lcmm-1.7.1/lcmm/R/print.Jointlcmm.R | 187
lcmm-1.7.1/lcmm/R/risq_spl.R |only
lcmm-1.7.1/lcmm/R/risqcum_spl.R |only
lcmm-1.7.1/lcmm/R/summary.Jointlcmm.R | 565 +-
lcmm-1.7.1/lcmm/R/summarytable.R |only
lcmm-1.7.1/lcmm/man/Diffepoce.Rd | 6
lcmm-1.7.1/lcmm/man/ForInternalUse.Rd | 11
lcmm-1.7.1/lcmm/man/Jointlcmm.Rd | 119
lcmm-1.7.1/lcmm/man/VarExpl.Rd | 3
lcmm-1.7.1/lcmm/man/cuminc.Rd |only
lcmm-1.7.1/lcmm/man/data_hlme.Rd | 2
lcmm-1.7.1/lcmm/man/dynpred.Rd | 32
lcmm-1.7.1/lcmm/man/epoce.Rd | 6
lcmm-1.7.1/lcmm/man/fitY.Rd |only
lcmm-1.7.1/lcmm/man/hlme.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm-package.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm.Rd | 40
lcmm-1.7.1/lcmm/man/multlcmm.Rd |only
lcmm-1.7.1/lcmm/man/plot.cuminc.Rd |only
lcmm-1.7.1/lcmm/man/plot.dynpred.Rd | 19
lcmm-1.7.1/lcmm/man/plot.lcmm.Rd | 162
lcmm-1.7.1/lcmm/man/plot.pred.accuracy.Rd | 3
lcmm-1.7.1/lcmm/man/plot.predict.Rd | 81
lcmm-1.7.1/lcmm/man/postprob.Rd | 4
lcmm-1.7.1/lcmm/man/predictL.Rd | 41
lcmm-1.7.1/lcmm/man/predictY.Rd | 43
lcmm-1.7.1/lcmm/man/predictlink.Rd |only
lcmm-1.7.1/lcmm/man/print.lcmm.Rd | 2
lcmm-1.7.1/lcmm/man/summary.lcmm.Rd | 3
lcmm-1.7.1/lcmm/man/summarytable.Rd |only
lcmm-1.7.1/lcmm/src/AOptim.f90 | 26
lcmm-1.7.1/lcmm/src/Jointhet.f90 | 5841 +++++++++++++-----------
lcmm-1.7.1/lcmm/src/Makevars | 14
lcmm-1.7.1/lcmm/src/calculusTransfo.f90 | 6
lcmm-1.7.1/lcmm/src/cvpl.f90 | 3208 +++++++------
lcmm-1.7.1/lcmm/src/hetmixCont.f90 | 54
lcmm-1.7.1/lcmm/src/hetmixContMult.f90 | 71
lcmm-1.7.1/lcmm/src/hetmixOrd.f90 | 20
lcmm-1.7.1/lcmm/src/hetmixlin.f90 | 25
lcmm-1.7.1/lcmm/src/postprob2.f90 |only
lcmm-1.7.1/lcmm/src/predictCont.f90 | 7
lcmm-1.7.1/lcmm/src/predictMult.f90 | 4
123 files changed, 12217 insertions(+), 9042 deletions(-)
Title: Convert R Graphics to Flash Animations
Diff between R2SWF versions 0.8-2 dated 2014-12-19 and 0.9 dated 2015-02-26
Description: Using the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 12 +-
MD5 | 8 -
NEWS | 44 +++++---
R/svg2swf.R | 299 ++++++++++++++++++++++++++++----------------------------
src/image2swf.c | 2
5 files changed, 189 insertions(+), 176 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.5-1 dated 2014-10-24 and 0.5-2 dated 2015-02-26
Description: The following methods for cubature (numerical integration)
over polygonal domains are currently implemented:
the two-dimensional midpoint rule as a simple wrapper around
as.im.function() from package spatstat (Baddeley and Turner, 2005),
the product Gauss cubature by Sommariva and Vianello (2007),
an adaptive cubature for isotropic functions via line integrate()
along the boundary (Meyer and Held, 2014),
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains
(based on formulae from the Abramowitz and Stegun (1972) handbook).
For cubature over simple hypercubes, the packages "cubature" and
"R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
DESCRIPTION | 19 +++++----
MD5 | 64 ++++++++++++++++----------------
NAMESPACE | 8 +++-
R/coerce-gpc-methods.R | 22 ++++++++---
R/coerce-sp-methods.R | 63 ++++++++++++++++++++++----------
R/polyCub.exact.Gauss.R | 88 +++++++++++++++++++++++++++------------------
R/polyCub.iso.R | 41 +++++++++++++-------
R/polyCub.midpoint.R | 21 +++++-----
R/tools.R | 5 +-
R/xylist.R | 12 ++----
inst/CITATION | 10 -----
inst/NEWS.Rd | 24 ++++++++++++
man/checkintrfr.Rd | 3 +
man/circleCub.Gauss.Rd | 3 +
man/coerce-gpc-methods.Rd | 15 +++++--
man/coerce-sp-methods.Rd | 38 +++++++++++++++----
man/dotprod.Rd | 3 +
man/gpclibPermit.Rd | 3 +
man/isClosed.Rd | 3 +
man/isScalar.Rd | 3 +
man/makegrid.Rd | 3 +
man/plot_polyregion.Rd | 3 +
man/plotpolyf.Rd | 3 +
man/polyCub-package.Rd | 3 +
man/polyCub.Rd | 3 +
man/polyCub.SV.Rd | 3 +
man/polyCub.exact.Gauss.Rd | 9 ++--
man/polyCub.iso.Rd | 3 +
man/polyCub.midpoint.Rd | 10 ++++-
man/polygauss.Rd | 3 +
man/vecnorm.Rd | 3 +
man/xylist.Rd | 11 +++--
tests/test-all.R | 3 -
33 files changed, 324 insertions(+), 184 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Diff between multicool versions 0.1-2 dated 2013-07-10 and 0.1-5 dated 2015-02-26
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran
DESCRIPTION | 21 +-
MD5 | 25 ++
NAMESPACE | 20 +-
R/RcppExports.R |only
R/Stirling2.R |only
R/allPerm.R | 28 +--
R/genComp.R |only
R/initMC.r | 91 +++++-----
R/multinom.R | 11 -
R/nextPerm.R | 28 +--
README.md |only
man/Bell.Rd |only
man/Stirling2.Rd |only
man/genComp.Rd |only
src/RcppExports.cpp |only
src/compositions.cpp |only
src/multicool.cpp | 430 ++++++++++++++++++++++++++++-----------------------
src/multinomial.h | 2
18 files changed, 354 insertions(+), 302 deletions(-)