Title: Tools for analyzing political behaviour data
Diff between SciencesPo versions 0.03.21 dated 2014-03-20 and 0.05.21 dated 2014-05-27
Description: SciencesPo is a facility package for the political science crowd. It provides well-founded functions for analyzing random and nonrandom data. Future updates will focus on innovative techniques published in relevant journals in the field of political science.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino
SciencesPo-0.03.21/SciencesPo/R/get.poly.R |only
SciencesPo-0.03.21/SciencesPo/data/bhodrick93.RData |only
SciencesPo-0.03.21/SciencesPo/data/cgreene76.RData |only
SciencesPo-0.03.21/SciencesPo/data/galton.RData |only
SciencesPo-0.03.21/SciencesPo/data/ge2010.RData |only
SciencesPo-0.03.21/SciencesPo/data/griliches76.RData |only
SciencesPo-0.03.21/SciencesPo/data/ltaylor96.RData |only
SciencesPo-0.03.21/SciencesPo/data/mishkin92.RData |only
SciencesPo-0.03.21/SciencesPo/data/montreal.RData |only
SciencesPo-0.03.21/SciencesPo/data/nerlove63.RData |only
SciencesPo-0.03.21/SciencesPo/data/sheston91.RData |only
SciencesPo-0.03.21/SciencesPo/data/swatson93.RData |only
SciencesPo-0.03.21/SciencesPo/data/us2012.RData |only
SciencesPo-0.03.21/SciencesPo/man/get.poly.Rd |only
SciencesPo-0.05.21/SciencesPo/DESCRIPTION | 14 +-
SciencesPo-0.05.21/SciencesPo/MD5 | 88 ++++++++--------
SciencesPo-0.05.21/SciencesPo/NAMESPACE | 5
SciencesPo-0.05.21/SciencesPo/R/SciencesPo-internal.R |only
SciencesPo-0.05.21/SciencesPo/R/detail.R | 10 +
SciencesPo-0.05.21/SciencesPo/R/fptp2av.R | 14 +-
SciencesPo-0.05.21/SciencesPo/R/rescale.R | 33 ++++--
SciencesPo-0.05.21/SciencesPo/data/bhodrick93.rda |only
SciencesPo-0.05.21/SciencesPo/data/cgreene76.rda |only
SciencesPo-0.05.21/SciencesPo/data/galton.rda |only
SciencesPo-0.05.21/SciencesPo/data/ge2010.rda |only
SciencesPo-0.05.21/SciencesPo/data/griliches76.rda |only
SciencesPo-0.05.21/SciencesPo/data/ltaylor96.rda |only
SciencesPo-0.05.21/SciencesPo/data/mishkin92.rda |only
SciencesPo-0.05.21/SciencesPo/data/montreal.rda |only
SciencesPo-0.05.21/SciencesPo/data/nerlove63.rda |only
SciencesPo-0.05.21/SciencesPo/data/on2011.rda |only
SciencesPo-0.05.21/SciencesPo/data/sheston91.rda |only
SciencesPo-0.05.21/SciencesPo/data/swatson93.rda |only
SciencesPo-0.05.21/SciencesPo/data/us2012.rda |only
SciencesPo-0.05.21/SciencesPo/inst/NEWS.Rd | 18 +--
SciencesPo-0.05.21/SciencesPo/inst/doc/fptp2av.pdf |only
SciencesPo-0.05.21/SciencesPo/man/SciencesPo-package.Rd | 30 -----
SciencesPo-0.05.21/SciencesPo/man/accent.Rd | 4
SciencesPo-0.05.21/SciencesPo/man/anonymize.Rd | 4
SciencesPo-0.05.21/SciencesPo/man/beta.coef.Rd | 3
SciencesPo-0.05.21/SciencesPo/man/detail.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/dummy.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/fptp2av.Rd | 8 -
SciencesPo-0.05.21/SciencesPo/man/get.ci.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/get.ipc.Rd | 4
SciencesPo-0.05.21/SciencesPo/man/get.years.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/lsq.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/on2011.Rd |only
SciencesPo-0.05.21/SciencesPo/man/outliers.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/outtags.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/psum.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/rescale.Rd | 12 +-
SciencesPo-0.05.21/SciencesPo/man/rprob.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/shift.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/skewness.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/soundexBR.Rd | 2
SciencesPo-0.05.21/SciencesPo/man/soundexES.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/soundexFR.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/tolatex.Rd | 1
SciencesPo-0.05.21/SciencesPo/man/top.foot.Rd | 2
60 files changed, 130 insertions(+), 142 deletions(-)
Title: A Parallel Simulation Framework
Diff between harvestr versions 0.5.2 dated 2013-09-13 and 0.6.0 dated 2014-05-27
Description: Functions for easy simulation and reproducability.
Author: Andrew Redd
Maintainer: Andrew Redd
DESCRIPTION | 10 ++---
MD5 | 43 ++++++++++++-----------
NAMESPACE | 3 +
NEWS | 5 ++
R/gather.R | 28 ++++++++-------
R/utils.R | 18 +++++++++-
R/withseed.R | 18 +++++-----
build |only
inst/doc/harvestr.R |only
inst/doc/harvestr.pdf |binary
man/bale.Rd | 11 +++---
man/farm.Rd | 43 ++++++++++-------------
man/gather.Rd | 25 ++++++-------
man/harvest.Rd | 31 +++++++----------
man/harvestr.Rd | 90 ++++++++++++++++++++++++--------------------------
man/is_seeded.Rd |only
man/noattr.Rd | 9 ++---
man/plant.Rd | 36 ++++++++++----------
man/plow.Rd | 15 ++++----
man/reap.Rd | 40 +++++++++++-----------
man/seed_funs.Rd | 59 ++++++++++++++++----------------
man/sprout.Rd | 28 +++++++--------
man/total_time.Rd | 7 ++-
man/use_method.Rd | 13 +++----
24 files changed, 280 insertions(+), 252 deletions(-)
Title: Back-Projected Kernel Density Estimation
Diff between bpkde versions 1.0-2 dated 2012-12-21 and 1.0-4 dated 2014-05-27
Description: Nonparametric multivariate kernel density \
estimation using a back-projected kernel.
Author: Kjell Konis
Maintainer: Kjell Konis
bpkde-1.0-2/bpkde/R/mvbw.q |only
bpkde-1.0-2/bpkde/man/bp.support.Rd |only
bpkde-1.0-2/bpkde/man/methods.mvkde.Rd |only
bpkde-1.0-2/bpkde/man/mvbw.Rd |only
bpkde-1.0-2/bpkde/man/plot.discretize.kernel.Rd |only
bpkde-1.0-2/bpkde/man/plot.mvkde.Rd |only
bpkde-1.0-2/bpkde/man/plot.mvlinbin.Rd |only
bpkde-1.0-4/bpkde/DESCRIPTION | 22 ++++--
bpkde-1.0-4/bpkde/MD5 | 73 ++++++++++++-----------
bpkde-1.0-4/bpkde/NAMESPACE | 29 ++++++++-
bpkde-1.0-4/bpkde/R/KernSmooth.q |only
bpkde-1.0-4/bpkde/R/M0.q | 2
bpkde-1.0-4/bpkde/R/M1.q | 4 -
bpkde-1.0-4/bpkde/R/bp.support.q | 11 +--
bpkde-1.0-4/bpkde/R/bpkde.q | 14 ++--
bpkde-1.0-4/bpkde/R/contour.discretize.kernel.q |only
bpkde-1.0-4/bpkde/R/contour.mvkde.q |only
bpkde-1.0-4/bpkde/R/discretize.kernel.q | 15 ++--
bpkde-1.0-4/bpkde/R/image.discretize.kernel.q |only
bpkde-1.0-4/bpkde/R/image.mvkde.q |only
bpkde-1.0-4/bpkde/R/image.mvlinbin.q |only
bpkde-1.0-4/bpkde/R/mvlinbin.q | 33 +++-------
bpkde-1.0-4/bpkde/R/plot.discretize.kernel.q | 34 +++-------
bpkde-1.0-4/bpkde/R/plot.mvkde.q | 37 +++--------
bpkde-1.0-4/bpkde/R/plot.mvlinbin.q | 38 +++--------
bpkde-1.0-4/bpkde/data/Bimodal1.RData |binary
bpkde-1.0-4/bpkde/data/Bimodal2.RData |binary
bpkde-1.0-4/bpkde/data/Bimodal3.RData |binary
bpkde-1.0-4/bpkde/data/Bimodal4.RData |binary
bpkde-1.0-4/bpkde/data/Correlated.Normal.RData |binary
bpkde-1.0-4/bpkde/data/Kurtotic.RData |binary
bpkde-1.0-4/bpkde/data/Quadrimodal.RData |binary
bpkde-1.0-4/bpkde/data/Skewed.RData |binary
bpkde-1.0-4/bpkde/data/Trimodal1.RData |binary
bpkde-1.0-4/bpkde/data/Trimodal2.RData |binary
bpkde-1.0-4/bpkde/data/Trimodal3.RData |binary
bpkde-1.0-4/bpkde/data/Uncorrelated.Normal.RData |binary
bpkde-1.0-4/bpkde/man/bpkde.Rd | 4 -
bpkde-1.0-4/bpkde/man/discretize.kernel.Rd | 2
bpkde-1.0-4/bpkde/man/mvlinbin.Rd | 5 -
bpkde-1.0-4/bpkde/src |only
bpkde-1.0-4/bpkde/tests |only
42 files changed, 157 insertions(+), 166 deletions(-)
Title: Fitting heavy tailed distributions: the poweRlaw package
Diff between poweRlaw versions 0.20.2 dated 2013-12-19 and 0.20.3 dated 2014-05-27
Description: This package implements both the discrete and continuous maximum
likelihood estimators for fitting the power-law distribution to data.
Additionally, a goodness-of-fit based approach is used to estimate the
lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.20.2/poweRlaw/R/all_classes_ctn.R |only
poweRlaw-0.20.2/poweRlaw/R/all_classes_discrete.R |only
poweRlaw-0.20.2/poweRlaw/R/discrete_helper_functions.R |only
poweRlaw-0.20.2/poweRlaw/R/dist_cdf-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/dist_data_cdf-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/dist_ll-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/dist_pdf-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/dist_rand-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/initialize-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/lines-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/mle-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/plot-methods.R |only
poweRlaw-0.20.2/poweRlaw/R/points-methods.R |only
poweRlaw-0.20.2/poweRlaw/man/plotting-methods-distribution.Rd |only
poweRlaw-0.20.3/poweRlaw/DESCRIPTION | 39 -
poweRlaw-0.20.3/poweRlaw/MD5 | 129 ++---
poweRlaw-0.20.3/poweRlaw/NAMESPACE | 38 -
poweRlaw-0.20.3/poweRlaw/NEWS | 13
poweRlaw-0.20.3/poweRlaw/R/AllGenerics.R | 10
poweRlaw-0.20.3/poweRlaw/R/aaa_all_classes.R | 7
poweRlaw-0.20.3/poweRlaw/R/bootstrap.R | 11
poweRlaw-0.20.3/poweRlaw/R/bootstrap_p.R | 11
poweRlaw-0.20.3/poweRlaw/R/compare_distributions.R | 66 +-
poweRlaw-0.20.3/poweRlaw/R/ctn_helper_functions.R | 58 --
poweRlaw-0.20.3/poweRlaw/R/data_help_files.R | 2
poweRlaw-0.20.3/poweRlaw/R/def_conexp.R |only
poweRlaw-0.20.3/poweRlaw/R/def_conlorm.R |only
poweRlaw-0.20.3/poweRlaw/R/def_conpl.R |only
poweRlaw-0.20.3/poweRlaw/R/def_disexp.R |only
poweRlaw-0.20.3/poweRlaw/R/def_dislnorm.R |only
poweRlaw-0.20.3/poweRlaw/R/def_displ.R |only
poweRlaw-0.20.3/poweRlaw/R/def_dispois.R |only
poweRlaw-0.20.3/poweRlaw/R/def_template.R |only
poweRlaw-0.20.3/poweRlaw/R/dist_data_cdf_methods.R |only
poweRlaw-0.20.3/poweRlaw/R/estimate_xmin.R | 88 ++-
poweRlaw-0.20.3/poweRlaw/R/lines_methods.R |only
poweRlaw-0.20.3/poweRlaw/R/pldis.R | 116 ++--
poweRlaw-0.20.3/poweRlaw/R/plot_methods.R |only
poweRlaw-0.20.3/poweRlaw/R/points_methods.R |only
poweRlaw-0.20.3/poweRlaw/R/show_methods.R |only
poweRlaw-0.20.3/poweRlaw/build/vignette.rds |binary
poweRlaw-0.20.3/poweRlaw/data/bootstrap_moby.RData |binary
poweRlaw-0.20.3/poweRlaw/data/bootstrap_p_moby.RData |binary
poweRlaw-0.20.3/poweRlaw/demo/moby.R | 11
poweRlaw-0.20.3/poweRlaw/inst/doc/compare_distributions.R |only
poweRlaw-0.20.3/poweRlaw/inst/doc/compare_distributions.Rnw |only
poweRlaw-0.20.3/poweRlaw/inst/doc/compare_distributions.pdf |only
poweRlaw-0.20.3/poweRlaw/inst/doc/examples.R | 195 ++-----
poweRlaw-0.20.3/poweRlaw/inst/doc/examples.Rnw | 62 +-
poweRlaw-0.20.3/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.20.3/poweRlaw/inst/doc/poweRlaw.R | 245 +++-------
poweRlaw-0.20.3/poweRlaw/inst/doc/poweRlaw.Rnw | 67 +-
poweRlaw-0.20.3/poweRlaw/inst/doc/poweRlaw.pdf |binary
poweRlaw-0.20.3/poweRlaw/man/bootstrap_moby.Rd | 43 -
poweRlaw-0.20.3/poweRlaw/man/compare_distributions.Rd | 96 +--
poweRlaw-0.20.3/poweRlaw/man/displ.Rd | 86 +--
poweRlaw-0.20.3/poweRlaw/man/dist_cdf-methods.Rd | 64 +-
poweRlaw-0.20.3/poweRlaw/man/dist_data_cdf-methods.Rd | 31 -
poweRlaw-0.20.3/poweRlaw/man/dist_ll-methods.Rd | 36 +
poweRlaw-0.20.3/poweRlaw/man/dist_pdf-methods.Rd | 44 +
poweRlaw-0.20.3/poweRlaw/man/dist_rand-methods.Rd | 39 +
poweRlaw-0.20.3/poweRlaw/man/dplcon.Rd | 41 -
poweRlaw-0.20.3/poweRlaw/man/dpldis.Rd | 96 ++-
poweRlaw-0.20.3/poweRlaw/man/estimate_pars.Rd | 22
poweRlaw-0.20.3/poweRlaw/man/estimate_xmin.Rd | 110 ++--
poweRlaw-0.20.3/poweRlaw/man/moby.Rd | 14
poweRlaw-0.20.3/poweRlaw/man/native_american.Rd | 19
poweRlaw-0.20.3/poweRlaw/man/plot-distribution-ANY-method.Rd |only
poweRlaw-0.20.3/poweRlaw/man/plot.bs_xmin.Rd |only
poweRlaw-0.20.3/poweRlaw/man/population.Rd | 15
poweRlaw-0.20.3/poweRlaw/man/poweRlaw-package.Rd | 32 -
poweRlaw-0.20.3/poweRlaw/man/show-distribution-method.Rd |only
poweRlaw-0.20.3/poweRlaw/man/swiss_prot.Rd | 22
poweRlaw-0.20.3/poweRlaw/tests |only
poweRlaw-0.20.3/poweRlaw/vignettes/compare_distributions.Rnw |only
poweRlaw-0.20.3/poweRlaw/vignettes/examples.Rnw | 62 +-
poweRlaw-0.20.3/poweRlaw/vignettes/poweRlaw.Rnw | 67 +-
poweRlaw-0.20.3/poweRlaw/vignettes/poweRlaw.bib | 19
78 files changed, 1052 insertions(+), 1074 deletions(-)
Title: Evaluation of the proportional hazards assumption with a
standardized score process
Diff between PHeval versions 0.5 dated 2014-04-28 and 0.5.1 dated 2014-05-27
Description: This package provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
Author: Cecile Chauvel
Maintainer: Cecile Chauvel
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
man/PHeval-package.Rd | 14 +++++++-------
man/R2.Rd | 21 +++++++++++----------
man/plotscore.Rd | 4 ++--
man/standscore.Rd | 9 +++++----
6 files changed, 34 insertions(+), 32 deletions(-)
Title: methods for multigroup data analysis
Diff between multigroup versions 0.3 dated 2014-05-09 and 0.4 dated 2014-05-27
Description: This package includes several methods to study multigroup data,
where the same set of variables are measured on different groups of
individuals.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez
Questions and comments go to Aida Eslami
Maintainer: Aida Eslami
DESCRIPTION | 13 +----
MD5 | 52 ++++++++++----------
R/mgPLS.R | 113 ++-------------------------------------------
man/BGC.Rd | 60 +++++++++++------------
man/DCCSWA.Rd | 56 ++++++++++------------
man/DGPA.Rd | 57 +++++++++++-----------
man/DSTATIS.Rd | 57 +++++++++++-----------
man/FCPCA.Rd | 48 +++++++++----------
man/TBWvariance.Rd | 37 +++++++-------
man/Trace.Rd | 4 -
man/deflation.Rd | 6 +-
man/iteraite_fun_Iter.Rd | 6 +-
man/loadingsplot.Rd | 7 +-
man/mbmgPCA.Rd | 70 +++++++++++++--------------
man/mgPCA.Rd | 70 +++++++++++++--------------
man/mgPLS.Rd | 72 +++++++++++++---------------
man/normM.Rd | 6 +-
man/normv.Rd | 6 +-
man/plot.mg.Rd | 9 +--
man/prepare_data.Rd | 11 +---
man/project.Rd | 4 -
man/scoreplot.Rd | 6 +-
man/select_initial_Iter.Rd | 9 +--
man/similarity_function.Rd | 4 -
man/similarity_noncum.Rd | 6 +-
man/summarize.Rd | 22 ++++----
man/transfer_Group.Rd | 10 +--
27 files changed, 350 insertions(+), 471 deletions(-)
Title: Linked Micromap Plots
Diff between micromap versions 1.8 dated 2014-03-20 and 1.9 dated 2014-05-27
Description: This group of functions simplifies the creation of linked micromap
plots.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [cre]
Maintainer: Tom Kincaid
DESCRIPTION | 8 ++++----
MD5 | 23 ++++++++++++-----------
data/OrEcoLevel3.rda |binary
data/USstates.rda |binary
data/WSA3.rda |binary
data/edPov.rda |binary
data/lungMort.rda |binary
data/statesFlatfile.rda |binary
data/vegCov.rda |binary
inst/CITATION | 4 ++--
inst/NEWS.Rd | 16 ++++++++++++++++
inst/doc/CHANGES.pdf |binary
inst/doc/index.html |only
13 files changed, 34 insertions(+), 17 deletions(-)
Title: Regression analysis of fractional responses
Diff between frm versions 1.0 dated 2014-01-13 and 1.2 dated 2014-05-27
Description: This package estimates one- and two-part fractional regression models, tests the models' specification and calculates partial effects
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
DESCRIPTION | 8 -
MD5 | 16 +--
R/frm.R | 263 ++++++++++++++++++++++++++++++++++++++++-------------
man/frm-package.Rd | 4
man/frm.Rd | 45 +++++++--
man/frm.ggoff.Rd | 15 +--
man/frm.pe.Rd | 4
man/frm.ptest.Rd | 2
man/frm.reset.Rd | 17 ++-
9 files changed, 275 insertions(+), 99 deletions(-)
Title: Companion Animal Population Management
Diff between capm versions 0.4 dated 2014-03-25 and 0.5 dated 2014-05-27
Description: Provides functions for quantitative companion animal population
management.
Author: Oswaldo Santos [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos
tmp/cranberry39d43991aef7/capm-0.5/capm/DESCRIPTION | 8
tmp/cranberry39d43991aef7/capm-0.5/capm/MD5 | 98 ++--
tmp/cranberry39d43991aef7/capm-0.5/capm/NAMESPACE | 2
tmp/cranberry39d43991aef7/capm-0.5/capm/NEWS | 43 +
tmp/cranberry39d43991aef7/capm-0.5/capm/R/Calculate2StageSampleSize.R | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/R/CalculateGlobalSens.R | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/R/CalculateLocalSens.R | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/R/CalculatePopChange.R | 7
tmp/cranberry39d43991aef7/capm-0.5/capm/R/CalculateSimpleSampleSize.R |only
tmp/cranberry39d43991aef7/capm-0.5/capm/R/CalculateStratifiedSampleSize.R |only
tmp/cranberry39d43991aef7/capm-0.5/capm/R/DesignSurvey.R | 96 ++-
tmp/cranberry39d43991aef7/capm-0.5/capm/R/MapkmlPSU.R | 9
tmp/cranberry39d43991aef7/capm-0.5/capm/R/PlotGlobalSens.R | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/R/PlotLocalSens.R | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/R/PlotModels.R | 26 -
tmp/cranberry39d43991aef7/capm-0.5/capm/R/SampleSystematic.R | 90 ++-
tmp/cranberry39d43991aef7/capm-0.5/capm/R/SetRanges.R | 13
tmp/cranberry39d43991aef7/capm-0.5/capm/R/SolveIASA.R | 18
tmp/cranberry39d43991aef7/capm-0.5/capm/R/SolveSI.R | 4
tmp/cranberry39d43991aef7/capm-0.5/capm/R/SummarySurvey.R | 49 +-
tmp/cranberry39d43991aef7/capm-0.5/capm/R/capm-package.R | 4
tmp/cranberry39d43991aef7/capm-0.5/capm/README.md | 6
tmp/cranberry39d43991aef7/capm-0.5/capm/data/pilot.rda |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/data/psu.ssu.rda |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/data/survey.data.rda |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/CITATION | 17
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/extdata/santos.dbf |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/extdata/santos.shp |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/extdata/santos.shx |binary
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/CalculateSampleSize/server.R | 96 +++
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/CalculateSampleSize/ui.R | 106 +++-
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/SelectSamplingUnits/server.R | 177 ++++++-
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/SelectSamplingUnits/ui.R | 112 +++-
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/SurveyAnalysis/server.R | 208 +++++---
tmp/cranberry39d43991aef7/capm-0.5/capm/inst/shinyApps/SurveyAnalysis/ui.R | 243 ++++++----
tmp/cranberry39d43991aef7/capm-0.5/capm/man/Calculate2StageSampleSize.Rd | 8
tmp/cranberry39d43991aef7/capm-0.5/capm/man/CalculateGlobalSens.Rd | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/man/CalculateLocalSens.Rd | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/man/CalculatePopChange.Rd | 7
tmp/cranberry39d43991aef7/capm-0.5/capm/man/CalculateSimpleSampleSize.Rd |only
tmp/cranberry39d43991aef7/capm-0.5/capm/man/CalculateStratifiedSampleSize.Rd |only
tmp/cranberry39d43991aef7/capm-0.5/capm/man/DesignSurvey.Rd | 102 ++--
tmp/cranberry39d43991aef7/capm-0.5/capm/man/PlotGlobalSens.Rd | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/man/PlotLocalSens.Rd | 14
tmp/cranberry39d43991aef7/capm-0.5/capm/man/PlotModels.Rd | 26 -
tmp/cranberry39d43991aef7/capm-0.5/capm/man/SampleSystematic.Rd | 67 +-
tmp/cranberry39d43991aef7/capm-0.5/capm/man/SetRanges.Rd | 10
tmp/cranberry39d43991aef7/capm-0.5/capm/man/SolveIASA.Rd | 18
tmp/cranberry39d43991aef7/capm-0.5/capm/man/SolveSI.Rd | 4
tmp/cranberry39d43991aef7/capm-0.5/capm/man/SummarySurvey.Rd | 39 -
tmp/cranberry39d43991aef7/capm-0.5/capm/man/capm-package.Rd | 2
ui.R | 153 +++---
52 files changed, 1298 insertions(+), 696 deletions(-)
Title: Tools for general maximum likelihood estimation
Diff between bbmle versions 1.0.16 dated 2014-03-02 and 1.0.17 dated 2014-05-27
Description: Methods and functions for fitting maximum likelihood models in R.
This package modifies and extends the mle classes in the stats4 package.
Author: Ben Bolker
Maintainer: Ben Bolker
DESCRIPTION | 8 +++----
MD5 | 38 ++++++++++++++++++------------------
R/mle.R | 5 ++++
R/predict.R | 1
R/slice.R | 26 ++++++++++++++++--------
build/vignette.rds |binary
inst/NEWS.Rd | 9 ++++++++
inst/doc/mle2.pdf |binary
inst/doc/quasi.R | 19 ++++++++++--------
inst/doc/quasi.Rnw | 24 +++++++++++-----------
inst/doc/quasi.pdf |binary
man/predict-methods.Rd | 2 +
tests/glmcomp.R | 16 +++++++++------
tests/glmcomp.Rout.save | 38 +++++++++++++-----------------------
tests/grtest1.R | 1
tests/grtest1.Rout.save | 13 ++++++------
tests/methods.R | 1
tests/methods.Rout.save | 47 ++++++++++++++++++++++-----------------------
tests/startvals2.Rout.save | 17 ++++++++++------
vignettes/quasi.Rnw | 24 +++++++++++-----------
20 files changed, 160 insertions(+), 129 deletions(-)
Title: Shape constrained additive models
Diff between scam versions 1.1-6 dated 2013-10-02 and 1.1-7 dated 2014-05-27
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of
mgcv(gam) package are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya
Maintainer: Natalya Pya
ChangeLog | 10 ++
DESCRIPTION | 12 +--
MD5 | 66 ++++++++---------
R/plot.scam.R | 109 +++++++++++++----------------
R/scam.r | 67 ++++++++---------
man/Predict.matrix.mpi.smooth.Rd | 6 +
man/bfgs_gcv.ubre.Rd | 6 +
man/derivative.scam.Rd | 7 +
man/gcv.ubre_grad.Rd | 8 +-
man/marginal.matrices.tesmi1.ps.Rd | 7 +
man/marginal.matrices.tesmi2.ps.Rd | 6 +
man/plot.scam.Rd | 8 +-
man/predict.scam.Rd | 6 +
man/print.scam.Rd | 2
man/scam-package.Rd | 20 +++--
man/scam.Rd | 14 ++-
man/scam.check.Rd | 2
man/scam.fit.Rd | 11 ++
man/shape.constrained.smooth.terms.Rd | 6 +
man/smooth.construct.cv.smooth.spec.rd | 4 -
man/smooth.construct.cx.smooth.spec.Rd | 4 -
man/smooth.construct.mdcv.smooth.spec.Rd | 2
man/smooth.construct.mdcx.smooth.spec.Rd | 4 -
man/smooth.construct.micv.smooth.spec.Rd | 4 -
man/smooth.construct.micx.smooth.spec.Rd | 5 +
man/smooth.construct.mpd.smooth.spec.Rd | 4 -
man/smooth.construct.mpi.smooth.spec.Rd | 4 -
man/smooth.construct.tedmd.smooth.spec.Rd | 4 -
man/smooth.construct.tedmi.smooth.spec.Rd | 4 -
man/smooth.construct.tesmd1.smooth.spec.Rd | 4 -
man/smooth.construct.tesmd2.smooth.spec.Rd | 4 -
man/smooth.construct.tesmi1.smooth.spec.Rd | 4 -
man/smooth.construct.tesmi2.smooth.spec.Rd | 4 -
man/summary.scam.Rd | 4 -
34 files changed, 249 insertions(+), 183 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 3.5-1 dated 2014-05-14 and 3.6-0 dated 2014-05-27
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
meta-3.5-1/meta/R/is.installed.metafor.R |only
meta-3.5-1/meta/man/forest.meta.Rd |only
meta-3.5-1/meta/man/funnel.meta.Rd |only
meta-3.5-1/meta/man/labbe.metabin.Rd |only
meta-3.5-1/meta/man/metabias.meta.Rd |only
meta-3.5-1/meta/man/trimfill.meta.Rd |only
meta-3.6-0/meta/DESCRIPTION | 17 -
meta-3.6-0/meta/MD5 | 43 +-
meta-3.6-0/meta/NAMESPACE | 6
meta-3.6-0/meta/NEWS | 36 ++
meta-3.6-0/meta/R/baujat.R |only
meta-3.6-0/meta/R/baujat.meta.R |only
meta-3.6-0/meta/R/bubble.R |only
meta-3.6-0/meta/R/bubble.metareg.R |only
meta-3.6-0/meta/R/is.installed.package.R |only
meta-3.6-0/meta/R/metagen.R | 3
meta-3.6-0/meta/R/metareg.R | 13
meta-3.6-0/meta/R/print.meta.R | 24 -
meta-3.6-0/meta/R/update.meta.R | 13
meta-3.6-0/meta/man/amlodipine.Rd | 2
meta-3.6-0/meta/man/baujat.Rd |only
meta-3.6-0/meta/man/bubble.Rd |only
meta-3.6-0/meta/man/cisapride.Rd | 3
meta-3.6-0/meta/man/forest.Rd | 472 ++++++++++++++++++++++++++++++-
meta-3.6-0/meta/man/funnel.Rd | 132 +++++++-
meta-3.6-0/meta/man/labbe.Rd | 115 +++++++
meta-3.6-0/meta/man/metabias.Rd | 202 ++++++++++++-
meta-3.6-0/meta/man/metareg.Rd | 33 +-
meta-3.6-0/meta/man/trimfill.Rd | 155 +++++++++-
29 files changed, 1163 insertions(+), 106 deletions(-)
Title: Generalized Partially Linear Tree-based Regression Model
Diff between GPLTR versions 0.85 dated 2014-04-23 and 0.95 dated 2014-05-27
Description: Package for generalized partially linear tree-based regression model, combining a
generalized linear model with an additional tree part on the same scale.
Author: Cyprien Mbogning
Maintainer: Cyprien Mbogning
DESCRIPTION | 8 ++--
MD5 | 20 +++++-----
R/bagging.pltr.R | 88 +++++++++++++++++++++++++++++++++++-----------
R/best.tree.CV.R | 76 +++++++++++++++++++++------------------
R/predict_bagg.pltr.R | 25 +++++++++----
R/tree2indicators.R | 37 ++++++++-----------
inst/doc/GPLTR-manual.pdf |binary
man/GPLTR-package.Rd | 4 +-
man/bagging.pltr.Rd | 20 ++++++----
man/best.tree.CV.Rd | 4 +-
man/predict_bagg.pltr.Rd | 21 ++++++++--
11 files changed, 188 insertions(+), 115 deletions(-)
Title: Construction and evaluation of metamodels
Diff between DiceEval versions 1.2 dated 2013-06-10 and 1.3 dated 2014-05-27
Description: Estimation, validation and prediction of metamodels
(linear models, additive models, MARS,PolyMARS and Kriging)
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert
DiceEval-1.2/DiceEval/DiceEval-Ex.R |only
DiceEval-1.3/DiceEval/DESCRIPTION | 8
DiceEval-1.3/DiceEval/MD5 | 19 -
DiceEval-1.3/DiceEval/R/stepEvolution.R | 266 +++++++++++------------
DiceEval-1.3/DiceEval/man/DiceEval-package.Rd | 184 ++++++++-------
DiceEval-1.3/DiceEval/man/crossValidation.Rd | 138 ++++++-----
DiceEval-1.3/DiceEval/man/modelComparison.Rd | 81 +++----
DiceEval-1.3/DiceEval/man/modelFit.Rd | 168 +++++++-------
DiceEval-1.3/DiceEval/man/modelPredict.Rd | 106 ++++-----
DiceEval-1.3/DiceEval/man/stepEvolution.Rd | 2
DiceEval-1.3/DiceEval/man/testCrossValidation.Rd | 85 +++----
11 files changed, 535 insertions(+), 522 deletions(-)
Title: Population (and individual) optimal Experimental Design
Diff between PopED versions 0.1.0 dated 2014-04-28 and 0.1.1 dated 2014-05-27
Description: PopED computes optimal experimental designs for both
population studies and individual studies based on nonlinear mixed-effect models.
Often this is based on a computation of the Fisher Information Matrix (FIM).
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker
PopED-0.1.0/PopED/R/blockfinal_2.R |only
PopED-0.1.0/PopED/R/blockheader_2.R |only
PopED-0.1.0/PopED/R/blockopt_2.R |only
PopED-0.1.0/PopED/R/blockother_2.R |only
PopED-0.1.0/PopED/man/blockfinal_2.Rd |only
PopED-0.1.0/PopED/man/blockheader_2.Rd |only
PopED-0.1.0/PopED/man/blockopt_2.Rd |only
PopED-0.1.0/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal_2.R |only
PopED-0.1.0/PopED/tests/testthat/examples_fcn_doc/examples_blockheader_2.R |only
PopED-0.1.0/PopED/tests/testthat/examples_fcn_doc/examples_blockopt_2.R |only
PopED-0.1.0/PopED/tests/testthat/test_pargen.R |only
PopED-0.1.1/PopED/DESCRIPTION | 36
PopED-0.1.1/PopED/MD5 | 249 ++--
PopED-0.1.1/PopED/NAMESPACE | 1
PopED-0.1.1/PopED/NEWS | 24
PopED-0.1.1/PopED/R/Doptim.R | 52
PopED-0.1.1/PopED/R/LEDoptim.R |only
PopED-0.1.1/PopED/R/RS_opt.R | 13
PopED-0.1.1/PopED/R/RS_opt_gen.R |only
PopED-0.1.1/PopED/R/a_line_search.R | 4
PopED-0.1.1/PopED/R/blockfinal.R |only
PopED-0.1.1/PopED/R/blockheader.R |only
PopED-0.1.1/PopED/R/blockopt.R |only
PopED-0.1.1/PopED/R/blockother.R | 188 ++-
PopED-0.1.1/PopED/R/calc_ofv_and_fim.R |only
PopED-0.1.1/PopED/R/d2fimdalpha2.R | 84 -
PopED-0.1.1/PopED/R/ed_laplace_ofv.R |only
PopED-0.1.1/PopED/R/ed_mftot.R | 3
PopED-0.1.1/PopED/R/evaluate.e.ofv.fim.R | 24
PopED-0.1.1/PopED/R/get_cv.R | 40
PopED-0.1.1/PopED/R/getfulld.R | 2
PopED-0.1.1/PopED/R/gradff.R | 100 -
PopED-0.1.1/PopED/R/hesskalpha2.R | 82 -
PopED-0.1.1/PopED/R/line_search_uc.R | 29
PopED-0.1.1/PopED/R/log_prior_pdf.R | 49
PopED-0.1.1/PopED/R/mf3.R | 88 -
PopED-0.1.1/PopED/R/mfea.R | 34
PopED-0.1.1/PopED/R/mftot1.R | 32
PopED-0.1.1/PopED/R/ofv_fim.R | 2
PopED-0.1.1/PopED/R/pargen.R | 154 +-
PopED-0.1.1/PopED/R/poped_optimize.R | 69 -
PopED-0.1.1/PopED/README.md | 2
PopED-0.1.1/PopED/inst/CITATION | 11
PopED-0.1.1/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 12
PopED-0.1.1/PopED/inst/shinyapp/ui.R | 11
PopED-0.1.1/PopED/man/Doptim.Rd | 172 +-
PopED-0.1.1/PopED/man/Dtrace.Rd | 63 -
PopED-0.1.1/PopED/man/LEDoptim.Rd |only
PopED-0.1.1/PopED/man/LinMatrixH.Rd | 55
PopED-0.1.1/PopED/man/LinMatrixL.Rd | 35
PopED-0.1.1/PopED/man/LinMatrixLH.Rd | 59
PopED-0.1.1/PopED/man/LinMatrixL_occ.Rd | 54
PopED-0.1.1/PopED/man/PopED-internal.Rd | 2
PopED-0.1.1/PopED/man/PopED-package.Rd | 89 -
PopED-0.1.1/PopED/man/RS_opt.Rd | 208 +--
PopED-0.1.1/PopED/man/RS_opt_gen.Rd |only
PopED-0.1.1/PopED/man/a_line_search.Rd | 67 -
PopED-0.1.1/PopED/man/bfgsb_min.Rd | 39
PopED-0.1.1/PopED/man/blockexp.Rd | 31
PopED-0.1.1/PopED/man/blockfinal.Rd |only
PopED-0.1.1/PopED/man/blockheader.Rd |only
PopED-0.1.1/PopED/man/blockopt.Rd |only
PopED-0.1.1/PopED/man/calc_autofocus.Rd | 87 -
PopED-0.1.1/PopED/man/calc_ofv_and_fim.Rd |only
PopED-0.1.1/PopED/man/calc_ofv_and_grad.Rd | 81 -
PopED-0.1.1/PopED/man/cell.Rd | 18
PopED-0.1.1/PopED/man/convert_variables.Rd | 15
PopED-0.1.1/PopED/man/create.poped.database.Rd | 595 +++-------
PopED-0.1.1/PopED/man/diag_matlab.Rd | 30
PopED-0.1.1/PopED/man/downsizing_general_design.Rd | 26
PopED-0.1.1/PopED/man/ed_laplace_ofv.Rd |only
PopED-0.1.1/PopED/man/ed_mftot.Rd | 98 -
PopED-0.1.1/PopED/man/evaluate.e.ofv.fim.Rd | 258 ++--
PopED-0.1.1/PopED/man/evaluate.fim.Rd | 148 +-
PopED-0.1.1/PopED/man/feps.add.Rd | 62 -
PopED-0.1.1/PopED/man/feps.add.prop.Rd | 62 -
PopED-0.1.1/PopED/man/feps.prop.Rd | 62 -
PopED-0.1.1/PopED/man/feval.Rd | 22
PopED-0.1.1/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 65 -
PopED-0.1.1/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 65 -
PopED-0.1.1/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 65 -
PopED-0.1.1/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 65 -
PopED-0.1.1/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 63 -
PopED-0.1.1/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 63 -
PopED-0.1.1/PopED/man/fileparts.Rd | 24
PopED-0.1.1/PopED/man/getTruncatedNormal.Rd | 11
PopED-0.1.1/PopED/man/get_all_params.Rd | 25
PopED-0.1.1/PopED/man/get_rse.Rd | 96 -
PopED-0.1.1/PopED/man/getfulld.Rd | 14
PopED-0.1.1/PopED/man/gradf_eps.Rd | 57
PopED-0.1.1/PopED/man/isempty.Rd | 19
PopED-0.1.1/PopED/man/isfield.Rd | 21
PopED-0.1.1/PopED/man/log_prior_pdf.Rd |only
PopED-0.1.1/PopED/man/mf.Rd | 55
PopED-0.1.1/PopED/man/mf3.Rd | 58
PopED-0.1.1/PopED/man/mf5.Rd | 72 -
PopED-0.1.1/PopED/man/mf6.Rd | 66 -
PopED-0.1.1/PopED/man/mf7.Rd | 57
PopED-0.1.1/PopED/man/mf8.Rd | 70 -
PopED-0.1.1/PopED/man/mfea.Rd | 115 -
PopED-0.1.1/PopED/man/mftot.Rd | 65 -
PopED-0.1.1/PopED/man/mftot0.Rd | 67 -
PopED-0.1.1/PopED/man/mftot1.Rd | 70 -
PopED-0.1.1/PopED/man/mftot2.Rd | 61 -
PopED-0.1.1/PopED/man/mftot3.Rd | 61 -
PopED-0.1.1/PopED/man/mftot4.Rd | 84 -
PopED-0.1.1/PopED/man/mftot5.Rd | 78 -
PopED-0.1.1/PopED/man/mftot6.Rd | 68 -
PopED-0.1.1/PopED/man/mftot7.Rd | 83 -
PopED-0.1.1/PopED/man/model_prediction.Rd | 45
PopED-0.1.1/PopED/man/ofv_criterion.Rd | 59
PopED-0.1.1/PopED/man/ofv_fim.Rd | 78 -
PopED-0.1.1/PopED/man/ones.Rd | 21
PopED-0.1.1/PopED/man/pargen.Rd | 78 -
PopED-0.1.1/PopED/man/plot_efficiency_of_windows.Rd | 22
PopED-0.1.1/PopED/man/plot_model_prediction.Rd | 80 -
PopED-0.1.1/PopED/man/poped.choose.Rd | 12
PopED-0.1.1/PopED/man/poped_optimize.Rd | 310 ++---
PopED-0.1.1/PopED/man/rand.Rd | 22
PopED-0.1.1/PopED/man/randn.Rd | 22
PopED-0.1.1/PopED/man/randperm.Rd | 16
PopED-0.1.1/PopED/man/size.Rd | 22
PopED-0.1.1/PopED/man/test_for_max.Rd | 13
PopED-0.1.1/PopED/man/test_for_min.Rd | 13
PopED-0.1.1/PopED/man/test_for_zeros.Rd | 15
PopED-0.1.1/PopED/man/test_mat_size.Rd | 7
PopED-0.1.1/PopED/man/tic.Rd | 20
PopED-0.1.1/PopED/man/toc.Rd | 20
PopED-0.1.1/PopED/man/zeros.Rd | 21
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_LEDoptim.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt_gen.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_blockheader.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_blockopt.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_fim.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_ed_laplace_ofv.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_evaluate.e.ofv.fim.R | 24
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_evaluate.fim.R | 1
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_log_prior_pdf.R |only
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_pargen.R | 38
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/examples_poped_optimize.R | 42
PopED-0.1.1/PopED/tests/testthat/examples_fcn_doc/warfarin_ed.R | 14
PopED-0.1.1/PopED/tests/testthat/test_distributions.R |only
143 files changed, 3263 insertions(+), 3368 deletions(-)
Title: Inference in Meta Analysis and Meta Regression
Diff between metagen versions 0.2 dated 2014-03-21 and 1.0 dated 2014-05-27
Description: Provides methods for making inference in the random effects meta
regression model such as point estimates and confidence intervals for the
heterogeneity parameter and the regression coefficients vector. Inference
methods are based on different approaches to statistical inference.
Methods from three different schools are included: methods based on the
method of moments approach, methods based on likelihood, and methods based
on generalised inference. The package also includes tools to run extensive
simulation studies in parallel on high performance clusters in a modular
way. This allows extensive testing of custom inferential methods with all
implemented state-of-the-art methods in a standardised way. Tools for
evaluating the performance of both point and interval estimates are
provided. Also, a large collection of different pre-defined plotting
functions is implemented in a ready-to-use fashion.
Author: Thomas W. D. Möbius
Maintainer: Thomas W. D. Möbius
DESCRIPTION | 27 +++--
MD5 | 124 +++++++++++++-------------
NAMESPACE | 8 -
R/example-bcg.R | 41 ++++----
R/methods-for-batch-distribution.R | 11 +-
R/methods-for-data-generation.R | 95 ++++++++++----------
R/methods-for-experiments.R | 18 +--
R/methods-for-inference.R | 175 ++++++++++++++++++-------------------
R/plot-functions.R | 39 ++++----
R/plot-interval-estimates.R | 113 +++++++++--------------
R/plot-pivotal-distributions.R | 80 ++++++----------
R/plot-point-estimates.R | 57 ++++--------
man/bcgVaccineData.Rd | 13 +-
man/boxBias.Rd | 2
man/boxByConfidence.Rd | 2
man/boxByMethod.Rd | 2
man/boxByType.Rd | 2
man/boxMSE.Rd | 2
man/boxSD.Rd | 2
man/cbbPalette.Rd | 2
man/cbgPalette.Rd | 2
man/collectAllExperiments.Rd | 9 -
man/collectExperiments.Rd | 10 +-
man/designB.Rd | 4
man/designD.Rd | 2
man/dvec.Rd | 3
man/experimentD.Rd | 4
man/experimentY.Rd | 4
man/formulaL.Rd | 12 +-
man/formulaR.Rd | 16 +--
man/hConfidence.Rd | 8 -
man/hEstimates.Rd | 21 +---
man/intervalEstimates.Rd | 10 +-
man/joinPivotalCoefficients.Rd | 4
man/joinPivotalHeterogeneity.Rd | 4
man/lenBoxByMethod.Rd | 2
man/lenBoxByType.Rd | 2
man/lenDenByMethod.Rd | 2
man/lenDenByType.Rd | 2
man/makeConfInt.Rd | 14 +-
man/makeConfInts.Rd | 12 +-
man/metagen.Rd | 16 +--
man/metagenGeneralised.Rd | 6 -
man/metareg.Rd | 10 +-
man/performance.Rd | 13 +-
man/pfunc.Rd | 2
man/pivotalStream.Rd | 7 -
man/qfunc.Rd | 6 -
man/rB.Rd | 36 ++++---
man/rBinomGauss.Rd | 32 +++---
man/rD.Rd | 6 -
man/rY.Rd | 10 +-
man/render.Rd | 17 ++-
man/renderSVG.Rd | 17 ++-
man/sctBias.Rd | 4
man/sctMSE.Rd | 4
man/sctSD.Rd | 4
man/sctVersusC.Rd | 2
man/sctVersusH.Rd | 4
man/sdmByMethod.Rd | 2
man/sdmByType.Rd | 2
man/sdsByMethod.Rd | 2
man/sdsByType.Rd | 2
63 files changed, 563 insertions(+), 603 deletions(-)
Title: Generalized multistate simulation model
Diff between gems versions 0.9.4 dated 2014-01-30 and 0.9.5 dated 2014-05-27
Description: This package allows to simulating and analyzing multistate models with general hazard functions. It provides functionality for the preparation of hazard functions and parameters, simulation from a general multistate model and predicting future events. The multistate model is not required to be a Markov model and may take the history of previous events into account. In the basic version, it allows to simulate from transition-specific hazard function, whose parameters are multivariable normally distributed.
Author: Luisa Salazar Vizcaya, Nello Blaser, Thomas Gsponer
Maintainer: Luisa Salazar Vizcaya
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 8 +++++---
R/gems.r | 5 +++--
data |only
man/tavi.Rd |only
6 files changed, 15 insertions(+), 8 deletions(-)
Title: Network meta-analysis with R
Diff between netmeta versions 0.4-3 dated 2014-04-14 and 0.4-4 dated 2014-05-27
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NEWS | 14 ++++++++++++++
R/netmeta.R | 14 ++++++++------
R/nma.ruecker.R | 45 ++++++++++++++++++++++++++-------------------
R/prepare.R | 8 ++++----
R/print.netmeta.R | 20 +++-----------------
data/Senn2013.txt.gz |binary
8 files changed, 66 insertions(+), 57 deletions(-)
Title: Bayesian multinomial mixture
Diff between bmmix versions 0.1-1 dated 2014-05-16 and 0.1-2 dated 2014-05-27
Description: Bayesian multinomial mixture model
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 10 ++++++++++
DESCRIPTION | 11 +++++------
MD5 | 12 +++++++-----
NAMESPACE | 12 ++++++++++--
R/bmmix.R | 2 ++
R/processing.R |only
man/bmmix.Rd | 22 ++++++++++++++++------
man/process.Rd |only
8 files changed, 50 insertions(+), 19 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 3.1-1 dated 2014-03-07 and 3.1-2 dated 2014-05-27
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Ben Bolker [aut],
Julien Claude [aut],
Hoa Sien Cuong [aut],
Richard Desper [aut],
Benoit Durand [aut],
Julien Dutheil [aut],
Olivier Gascuel [aut],
Christoph Heibl [aut],
Daniel Lawson [aut],
Vincent Lefort [aut],
Pierre Legendre [aut],
Jim Lemon [aut],
Johan Nylander [aut],
Rainer Opgen-Rhein [aut],
Andrei-Alin Popescu [aut],
Klaus Schliep [aut],
Korbinian Strimmer [aut],
Damien de Vienne [aut]
Maintainer: Emmanuel Paradis
COPYING |only
DESCRIPTION | 10 +-
MD5 | 43 +++++----
NEWS | 46 ++++++++++
R/CDF.birth.death.R | 4
R/DNA.R | 6 -
R/SlowinskiGuyer.R | 1
R/ace.R | 44 +++++++---
R/all.equal.phylo.R | 12 +-
R/chronos.R | 11 +-
R/cophyloplot.R | 28 +++---
R/dist.topo.R | 4
R/plot.phylo.R | 194 ++++++++++++++++++++++++++-------------------
R/read.GenBank.R | 6 -
R/read.nexus.R | 42 ++++-----
build/vignette.rds |binary
data/hivtree.newick.rda |binary
data/landplants.newick.rda |binary
data/opsin.newick.rda |binary
inst/doc/MoranI.pdf |binary
man/ace.Rd | 39 ++++++++-
man/plot.phylo.Rd | 17 ++-
src/bionjs.c | 21 +++-
23 files changed, 338 insertions(+), 190 deletions(-)
Title: Flexible regression models for survival data.
Diff between timereg versions 1.8.4 dated 2014-02-18 and 1.8.5 dated 2014-05-27
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen and Jeremy
Silver
Maintainer: Thomas Scheike
DESCRIPTION | 12 +-
MD5 | 46 ++++----
NAMESPACE | 1
R/Gprop-odds-subdist.r | 6 -
R/comprisk.r | 7 -
R/cox-aalen.r | 6 -
R/mgresid.r | 21 +--
R/new.cox-aalen.r | 17 +--
R/new.timecox.r | 10 +
R/predict-timereg.r | 10 +
R/prop-odds-subdist.r | 219 +++++++++++++++++++++++++++++++---------
R/prop-odds.r | 5
R/read-design.r | 2
R/restricted.residual.mean.r |only
man/cum.residuals.Rd | 7 -
man/predict.timereg.Rd | 5
man/prop.odds.subdist.Rd | 27 ++--
man/restricted.residual.mean.Rd |only
src/Gprop-odds-subdist.c | 6 +
src/cox-aalen.c | 158 ++++++++++++++--------------
src/dynadd.c | 2
src/matrix.c | 24 ++--
src/mgresid.c | 28 ++++-
src/prop-odds-subdist2.c | 96 +++++++++++------
src/prop-odds.c | 7 -
25 files changed, 456 insertions(+), 266 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models.
Diff between KFAS versions 1.0.3 dated 2014-03-26 and 1.0.4 dated 2014-05-27
Description: Package KFAS provides functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization when distributions of some or all
elements of initial state vector are unknown.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-1.0.3/KFAS/src/simgaussiandebug.f95 |only
KFAS-1.0.3/KFAS/tests/testthat/glmfits.R |only
KFAS-1.0.4/KFAS/ChangeLog | 30 ++
KFAS-1.0.4/KFAS/DESCRIPTION | 8
KFAS-1.0.4/KFAS/MD5 | 93 +++---
KFAS-1.0.4/KFAS/NAMESPACE | 1
KFAS-1.0.4/KFAS/R/KFAS-package.R | 2
KFAS-1.0.4/KFAS/R/KFS.R | 37 +-
KFAS-1.0.4/KFAS/R/SSMarima.R | 4
KFAS-1.0.4/KFAS/R/SSMcustom.R | 3
KFAS-1.0.4/KFAS/R/SSMcycle.R | 38 +-
KFAS-1.0.4/KFAS/R/SSMregression.R | 4
KFAS-1.0.4/KFAS/R/SSMseasonal.R | 278 ++++++++++---------
KFAS-1.0.4/KFAS/R/SSMtrend.R | 9
KFAS-1.0.4/KFAS/R/approxSSM.R | 37 +-
KFAS-1.0.4/KFAS/R/coef.KFS.R | 10
KFAS-1.0.4/KFAS/R/extract.SSModel.R | 21 +
KFAS-1.0.4/KFAS/R/hatvalues.KFS.R | 2
KFAS-1.0.4/KFAS/R/importanceSSM.R | 4
KFAS-1.0.4/KFAS/R/interval.R | 7
KFAS-1.0.4/KFAS/R/logLik.SSModel.R | 258 +++++++++---------
KFAS-1.0.4/KFAS/R/predict.SSModel.R | 80 ++++-
KFAS-1.0.4/KFAS/R/residuals.KFS.R | 14 -
KFAS-1.0.4/KFAS/R/subset.SSModel.R | 5
KFAS-1.0.4/KFAS/README.md |only
KFAS-1.0.4/KFAS/TODO |only
KFAS-1.0.4/KFAS/man/Extract.SSModel.Rd | 26 +
KFAS-1.0.4/KFAS/man/KFS.Rd | 24 +
KFAS-1.0.4/KFAS/man/SSModel.Rd | 6
KFAS-1.0.4/KFAS/man/approxSSM.Rd | 19 -
KFAS-1.0.4/KFAS/man/importanceSSM.Rd | 4
KFAS-1.0.4/KFAS/man/logLik.SSModel.Rd | 11
KFAS-1.0.4/KFAS/man/predict.SSModel.Rd | 40 ++
KFAS-1.0.4/KFAS/src/approx.f95 | 48 +--
KFAS-1.0.4/KFAS/src/declarations.h | 5
KFAS-1.0.4/KFAS/src/deviance.f95 |only
KFAS-1.0.4/KFAS/src/glogliku.f95 | 22 -
KFAS-1.0.4/KFAS/src/gsmoothall.f95 | 363 +++++++++++++++-----------
KFAS-1.0.4/KFAS/src/init.c | 41 +-
KFAS-1.0.4/KFAS/src/isample.f95 | 4
KFAS-1.0.4/KFAS/src/isamplefilter.f95 | 3
KFAS-1.0.4/KFAS/src/kfilter.f95 | 103 ++++---
KFAS-1.0.4/KFAS/src/kfstheta.f95 | 142 +++-------
KFAS-1.0.4/KFAS/src/ldl.f95 | 2
KFAS-1.0.4/KFAS/src/ngloglik.f95 | 147 +++++-----
KFAS-1.0.4/KFAS/src/simgaussian.f95 | 2
KFAS-1.0.4/KFAS/src/smoothsim.f95 | 17 -
KFAS-1.0.4/KFAS/tests/test-all.R | 2
KFAS-1.0.4/KFAS/tests/testthat/testBasics.R |only
KFAS-1.0.4/KFAS/tests/testthat/testGLM.R |only
KFAS-1.0.4/KFAS/tests/testthat/testSSMarima.R |only
KFAS-1.0.4/KFAS/tests/testthat/testStruct.R |only
52 files changed, 1089 insertions(+), 887 deletions(-)
Title: Tools for Harnessing MLBAM Gameday data and Visualizing PITCHf/x
Diff between pitchRx versions 1.3 dated 2014-04-04 and 1.4 dated 2014-05-27
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert
DESCRIPTION | 12 ++++++------
MD5 | 44 ++++++++++++++++++++++++--------------------
NAMESPACE | 4 +++-
NEWS | 16 ++++++++++++++++
R/interactiveFX.R | 6 +++---
R/scrape.R | 41 +++++++++++++++++++++++++++++++++++------
R/update.R |only
data/fields.rda |binary
inst/tests |only
man/animateFX.Rd | 1 +
man/export.Rd | 1 +
man/fields.Rd | 1 +
man/getSnapshots.Rd | 1 +
man/gids.Rd | 1 +
man/interactiveFX.Rd | 7 ++++---
man/makeUrls.Rd | 1 +
man/pitchRx.Rd | 1 +
man/pitches.Rd | 1 +
man/players.Rd | 1 +
man/scrape.Rd | 1 +
man/scrapeFX.Rd | 1 +
man/strikeFX.Rd | 1 +
man/update_db.Rd |only
man/urlsToDataFrame.Rd | 1 +
24 files changed, 104 insertions(+), 39 deletions(-)
Title: Rcpp integration for GNU GSL vectors and matrices
Diff between RcppGSL versions 0.2.0 dated 2012-07-23 and 0.2.1 dated 2014-05-27
Description: Rcpp integration for GNU GSL vectors and matrices
The GNU Scientific Library (GSL) is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The RcppGSL package provides an easy-to-use interface between GSL data
structures and R using concepts from Rcpp which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses Rcpp to connect to another third-party library. The autoconf
script, inline plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
RcppGSL-0.2.0/RcppGSL/configure.in |only
RcppGSL-0.2.0/RcppGSL/inst/examples/RcppGSLExample/configure.in |only
RcppGSL-0.2.0/RcppGSL/vignettes/Makefile |only
RcppGSL-0.2.0/RcppGSL/vignettes/RcppGSL |only
RcppGSL-0.2.0/RcppGSL/vignettes/RcppGSL.bib |only
RcppGSL-0.2.0/RcppGSL/vignettes/unitTests |only
RcppGSL-0.2.1/RcppGSL/ChangeLog | 103
RcppGSL-0.2.1/RcppGSL/DESCRIPTION | 53
RcppGSL-0.2.1/RcppGSL/MD5 | 65
RcppGSL-0.2.1/RcppGSL/NAMESPACE | 6
RcppGSL-0.2.1/RcppGSL/R/inline.R | 5
RcppGSL-0.2.1/RcppGSL/README.md |only
RcppGSL-0.2.1/RcppGSL/build |only
RcppGSL-0.2.1/RcppGSL/cleanup | 2
RcppGSL-0.2.1/RcppGSL/configure | 3061 +++++-----
RcppGSL-0.2.1/RcppGSL/configure.ac |only
RcppGSL-0.2.1/RcppGSL/inst/NEWS.Rd | 28
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-intro.R |only
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-intro.Rnw | 819 ++
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-intro.pdf |binary
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-unitTests.R |only
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-unitTests.Rnw | 37
RcppGSL-0.2.1/RcppGSL/inst/doc/RcppGSL-unitTests.pdf |binary
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/DESCRIPTION | 11
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/NAMESPACE | 2
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/configure | 236
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/configure.ac |only
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/src/Makevars.in | 3
RcppGSL-0.2.1/RcppGSL/inst/examples/RcppGSLExample/src/Makevars.win | 3
RcppGSL-0.2.1/RcppGSL/inst/examples/bSpline |only
RcppGSL-0.2.1/RcppGSL/inst/unitTests/cpp |only
RcppGSL-0.2.1/RcppGSL/inst/unitTests/runit.client.package.R | 43
RcppGSL-0.2.1/RcppGSL/inst/unitTests/runit.gsl.R | 563 -
RcppGSL-0.2.1/RcppGSL/man/LdFlags.Rd |only
RcppGSL-0.2.1/RcppGSL/src/Makevars.in | 2
RcppGSL-0.2.1/RcppGSL/src/Makevars.win | 2
RcppGSL-0.2.1/RcppGSL/src/fastLm.cpp | 15
RcppGSL-0.2.1/RcppGSL/vignettes/RcppGSL-intro.Rnw | 819 ++
RcppGSL-0.2.1/RcppGSL/vignettes/RcppGSL-unitTests.Rnw | 37
RcppGSL-0.2.1/RcppGSL/vignettes/buildVignette.R |only
40 files changed, 3712 insertions(+), 2203 deletions(-)