Title: eXtraction of ENTity
Diff between x.ent versions 0.0.4 dated 2014-08-20 and 1.0.6 dated 2014-11-02
Description: x.ent is a system for extracting information (entities and relations between them) in text datasets. It also emphasizes results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. x.ent has been written in perl and use javascript to define user preferences through a browser. Local grammars are defined and compiled with the tool Unitex, developed by University Paris Est, and supporting multiple languages. See ?xconfig for an introduction.
Author: Nicolas Turenne
Maintainer: Tien T. Phan
x.ent-0.0.4/x.ent/inst/README |only
x.ent-1.0.6/x.ent/DESCRIPTION | 14
x.ent-1.0.6/x.ent/MD5 | 66 +--
x.ent-1.0.6/x.ent/NAMESPACE | 3
x.ent-1.0.6/x.ent/NEWS |only
x.ent-1.0.6/x.ent/R/parse.R | 215 ----------
x.ent-1.0.6/x.ent/R/stat.R | 436 ----------------------
x.ent-1.0.6/x.ent/R/xdata.R |only
x.ent-1.0.6/x.ent/R/xdata_value.R |only
x.ent-1.0.6/x.ent/R/xhist.R |only
x.ent-1.0.6/x.ent/R/xplot.R |only
x.ent-1.0.6/x.ent/R/xprop.R |only
x.ent-1.0.6/x.ent/R/xshow.R |only
x.ent-1.0.6/x.ent/R/xvenn.R |only
x.ent-1.0.6/x.ent/README |only
x.ent-1.0.6/x.ent/inst/Perl/Main.pl | 29 -
x.ent-1.0.6/x.ent/inst/Perl/Modules/Entite.pm | 83 ++--
x.ent-1.0.6/x.ent/inst/Perl/Modules/Evaluation.pm | 50 +-
x.ent-1.0.6/x.ent/inst/Perl/Modules/Parametre.pm | 1
x.ent-1.0.6/x.ent/inst/Perl/Modules/Relation.pm | 280 +++++---------
x.ent-1.0.6/x.ent/inst/Perl/Modules/Structure.pm | 318 +++++++++++++++-
x.ent-1.0.6/x.ent/inst/Perl/Modules/Utils.pm | 294 +++-----------
x.ent-1.0.6/x.ent/inst/dico/avoid.txt | 60 +--
x.ent-1.0.6/x.ent/inst/dico/blacklist_ville.txt | 8
x.ent-1.0.6/x.ent/inst/dico/dico-b_v3.txt | 13
x.ent-1.0.6/x.ent/inst/dico/dico-f_v3.txt | 20 -
x.ent-1.0.6/x.ent/inst/dico/dico-m_v3.txt | 27 +
x.ent-1.0.6/x.ent/inst/dico/dico-n_v1.txt |only
x.ent-1.0.6/x.ent/inst/dico/dico-p_v3.txt | 20 -
x.ent-1.0.6/x.ent/inst/dico/dico-r_v1.txt |only
x.ent-1.0.6/x.ent/inst/dico/dico-v_v3.txt | 6
x.ent-1.0.6/x.ent/inst/dico/replace.txt | 3
x.ent-1.0.6/x.ent/inst/www/config.html | 12
x.ent-1.0.6/x.ent/inst/www/config/ini.json | 17
x.ent-1.0.6/x.ent/man/xconfig.Rd | 8
x.ent-1.0.6/x.ent/man/xdata.Rd |only
x.ent-1.0.6/x.ent/man/xhist.Rd | 8
x.ent-1.0.6/x.ent/man/xplot.Rd | 17
x.ent-1.0.6/x.ent/man/xprop.Rd |only
x.ent-1.0.6/x.ent/man/xshow.Rd | 12
x.ent-1.0.6/x.ent/man/xvenn.Rd | 15
41 files changed, 785 insertions(+), 1250 deletions(-)
Title: Shrinkage Covariance Matrix Estimators
Diff between ShrinkCovMat versions 1.0.2 dated 2014-10-20 and 1.0.3 dated 2014-11-02
Description: The package ShrinkCovMat provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
inst/CITATION | 7 +++----
inst/NEWS | 4 ++++
man/ShrinkCovMat-package.Rd | 2 +-
man/shrinkcovmat.equal.Rd | 2 +-
man/shrinkcovmat.identity.Rd | 2 +-
man/shrinkcovmat.unequal.Rd | 2 +-
man/targetselection.Rd | 2 +-
9 files changed, 24 insertions(+), 21 deletions(-)
Title: JSON for R
Diff between rjson versions 0.2.14 dated 2014-06-10 and 0.2.15 dated 2014-11-02
Description: Converts R object into JSON objects and vice-versa
Author: Alex Couture-Beil
Maintainer: Alex Couture-Beil
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
inst/changelog.txt | 6 ++----
inst/doc/json_rpc_server.pdf |binary
src/dump.cpp | 10 +++++++---
src/parser.c | 2 +-
6 files changed, 20 insertions(+), 18 deletions(-)
Title: R wrapper of ARPACK for large scale eigenvalue/vector problems,
on both dense and sparse matrices
Diff between rARPACK versions 0.6-0 dated 2014-08-24 and 0.7-0 dated 2014-11-02
Description: rARPACK is an R wrapper of the ARPACK library
(http://www.caam.rice.edu/software/ARPACK/) to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the eigs() function which does the similar job as in Matlab,
Octave, Python SciPy and Julia. It also provides the svds() function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu
rARPACK-0.6-0/rARPACK/src/MatOp_dgCMatrix.h |only
rARPACK-0.6-0/rARPACK/src/MatOp_dgRMatrix.h |only
rARPACK-0.6-0/rARPACK/src/rarpack-win.def |only
rARPACK-0.7-0/rARPACK/AUTHORS | 8
rARPACK-0.7-0/rARPACK/DESCRIPTION | 12
rARPACK-0.7-0/rARPACK/MD5 | 77 ++--
rARPACK-0.7-0/rARPACK/NAMESPACE | 24 -
rARPACK-0.7-0/rARPACK/NEWS | 41 ++
rARPACK-0.7-0/rARPACK/R/00_eigs.R | 263 +++++++++++-----
rARPACK-0.7-0/rARPACK/R/10_eigs_real_gen.R | 5
rARPACK-0.7-0/rARPACK/R/20_eigs_real_sym.R | 3
rARPACK-0.7-0/rARPACK/R/25_eigs_function.R |only
rARPACK-0.7-0/rARPACK/R/30_svds.R | 75 +++-
rARPACK-0.7-0/rARPACK/R/40_svds_real_gen.R | 3
rARPACK-0.7-0/rARPACK/R/50_svds_real_sym.R | 3
rARPACK-0.7-0/rARPACK/README.md | 100 +++---
rARPACK-0.7-0/rARPACK/inst/AUTHORS | 8
rARPACK-0.7-0/rARPACK/man/eigs.Rd | 206 ++++++++-----
rARPACK-0.7-0/rARPACK/man/svds.Rd | 61 ++-
rARPACK-0.7-0/rARPACK/src/ARPACK.h | 4
rARPACK-0.7-0/rARPACK/src/Eigs.cpp | 85 ++---
rARPACK-0.7-0/rARPACK/src/Eigs.h | 43 +-
rARPACK-0.7-0/rARPACK/src/EigsGen.cpp | 396 +++++++++++++++++--------
rARPACK-0.7-0/rARPACK/src/EigsGen.h | 51 ++-
rARPACK-0.7-0/rARPACK/src/EigsSym.cpp | 89 ++---
rARPACK-0.7-0/rARPACK/src/EigsSym.h | 67 ++++
rARPACK-0.7-0/rARPACK/src/MatOp.h | 14
rARPACK-0.7-0/rARPACK/src/MatOp_dgeMatrix.h | 14
rARPACK-0.7-0/rARPACK/src/MatOp_dsyMatrix.h | 31 +
rARPACK-0.7-0/rARPACK/src/MatOp_function.cpp |only
rARPACK-0.7-0/rARPACK/src/MatOp_function.h |only
rARPACK-0.7-0/rARPACK/src/MatOp_matrix.cpp | 26 -
rARPACK-0.7-0/rARPACK/src/MatOp_matrix.h | 16 -
rARPACK-0.7-0/rARPACK/src/MatOp_sparseMatrix.h |only
rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.cpp | 14
rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.h | 13
rARPACK-0.7-0/rARPACK/src/MatTypes.h | 43 ++
rARPACK-0.7-0/rARPACK/src/SVDsGen.cpp | 351 ++++------------------
rARPACK-0.7-0/rARPACK/src/SVDsGen.h |only
rARPACK-0.7-0/rARPACK/src/SVDsSym.cpp | 152 ++++-----
rARPACK-0.7-0/rARPACK/src/SVDsSym.h |only
rARPACK-0.7-0/rARPACK/src/eigs_funs.cpp | 96 +++---
rARPACK-0.7-0/rARPACK/src/rARPACK-win.def |only
rARPACK-0.7-0/rARPACK/src/rands.h |only
rARPACK-0.7-0/rARPACK/src/svds_funs.cpp | 89 ++---
45 files changed, 1428 insertions(+), 1055 deletions(-)
Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for
phylogenetic Comparative hypotHeses
Diff between mvSLOUCH versions 1.1.3 dated 2014-07-31 and 1.1.4 dated 2014-11-02
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/PhyloSDEestim.R | 20 ++++++++++++++++++--
3 files changed, 23 insertions(+), 7 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Diff between mvabund versions 3.9.1 dated 2014-06-28 and 3.9.3 dated 2014-11-02
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
DESCRIPTION | 15 ++++-----
MD5 | 26 +++++++--------
NAMESPACE | 2 -
R/anova.manyglm.R | 7 +++-
R/best.r.sq.R | 37 ++++++++++++++--------
R/default.plot.manyglm.R | 13 +++----
R/default.plot.mvformula.R | 74 +++++++++++++++++++++++++++------------------
R/manyglm.R | 7 +++-
R/plot.mvformula.R | 12 ++++---
man/best.r.sq.Rd | 44 +++++++++++++++-----------
man/plot.mvabund.Rd | 7 ++--
src/Makevars.in | 11 +-----
src/Makevars.win | 4 +-
src/glm.cpp | 7 +---
14 files changed, 150 insertions(+), 116 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Diff between multgee versions 1.4 dated 2013-12-03 and 1.5.0 dated 2014-11-02
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
multgee-1.4/multgee/NEWS |only
multgee-1.5.0/multgee/DESCRIPTION | 8 ++++----
multgee-1.5.0/multgee/MD5 | 10 +++++-----
multgee-1.5.0/multgee/NAMESPACE | 1 +
multgee-1.5.0/multgee/inst/CITATION | 25 ++++++++++++-------------
multgee-1.5.0/multgee/inst/NEWS |only
multgee-1.5.0/multgee/man/multgee-package.Rd | 2 ++
7 files changed, 24 insertions(+), 22 deletions(-)
Title: Generate Functions to Get or Set Global Options
Diff between GlobalOptions versions 0.0.2 dated 2014-10-07 and 0.0.3 dated 2014-11-02
Description: Generate functions to get or set global options
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 11 ++--
MD5 | 20 ++++----
NAMESPACE | 11 ++--
NEWS | 9 +++
R/setGlobalOptions.R | 11 +++-
inst/doc/GlobalOptions.R | 24 +++++-----
inst/doc/GlobalOptions.Rnw | 37 ++++++++-------
inst/doc/GlobalOptions.pdf |binary
inst/tests/test.R | 44 ++++++++++++++++--
man/setGlobalOptions.rd | 104 ++++++++++++++++++++++----------------------
vignettes/GlobalOptions.Rnw | 37 ++++++++-------
11 files changed, 179 insertions(+), 129 deletions(-)
Title: Computing optimal cutpoints in diagnostic tests
Diff between OptimalCutpoints versions 1.1-2 dated 2014-05-13 and 1.1-3 dated 2014-11-02
More information about OptimalCutpoints at CRAN
Description: This package enables users to compute one or more optimal cutpoints for diagnostic tests or continuous markers. Various approaches for selecting optimal cutoffs have been implemented, including methods based on cost-benefit analysis and diagnostic test accuracy measures (Sensitivity/Specificity, Predictive Values and Diagnostic Likelihood Ratios). Numerical and graphical output for all methods is easily obtained.
Author: Monica Lopez-Raton, Maria Xose Rodriguez-Alvarez
Maintainer: Monica Lopez Raton
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
NEWS | 4 ++++
inst |only
man/OptimalCutpoints-package.Rd | 9 ++++++---
man/optimal.cutpoints.Rd | 4 +++-
6 files changed, 23 insertions(+), 13 deletions(-)
Permanent link
Title: Nonlinear Calibration
Diff between nCal versions 13.12-01 dated 2013-12-01 and 14.10-31 dated 2014-11-02
Description: nCal is a package that performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong
Maintainer: Youyi Fong
nCal-13.12-01/nCal/R/youtilcopy.R |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_lar1.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_mixnorm.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_norm.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_replicate_re.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_t4.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_classical_tar1.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_lar1.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_mixnorm.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_norm.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_norm_4pl.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_replicate_re.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_t4.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_t4_4pl.txt |only
nCal-13.12-01/nCal/inst/jags_script/model_gh_tar1.txt |only
nCal-13.12-01/nCal/man/plot.bcrm.Rd |only
nCal-14.10-31/nCal/ChangeLog | 16
nCal-14.10-31/nCal/DESCRIPTION | 15
nCal-14.10-31/nCal/MD5 | 87 +
nCal-14.10-31/nCal/NAMESPACE | 8
nCal-14.10-31/nCal/R/5pl.R | 21
nCal-14.10-31/nCal/R/5pl_parameterization_calculus.R | 56 -
nCal-14.10-31/nCal/R/bcrm.R | 478 +++++-----
nCal-14.10-31/nCal/R/crm.fit.R |only
nCal-14.10-31/nCal/R/drm.fit.R | 206 +---
nCal-14.10-31/nCal/R/glspl.R |only
nCal-14.10-31/nCal/R/gnls_fit.R |only
nCal-14.10-31/nCal/R/inla.R |only
nCal-14.10-31/nCal/R/mle.R |only
nCal-14.10-31/nCal/R/ncal.R | 261 +++--
nCal-14.10-31/nCal/R/ssfct.R |only
nCal-14.10-31/nCal/data/elisa.prior.rda |only
nCal-14.10-31/nCal/inst/doc/nCal-vignette.R | 2
nCal-14.10-31/nCal/inst/doc/nCal-vignette.Rnw | 34
nCal-14.10-31/nCal/inst/doc/nCal-vignette.pdf |binary
nCal-14.10-31/nCal/inst/jags_script/classical_lar1.jags |only
nCal-14.10-31/nCal/inst/jags_script/classical_mixnorm.jags |only
nCal-14.10-31/nCal/inst/jags_script/classical_norm.jags |only
nCal-14.10-31/nCal/inst/jags_script/classical_replicate_re.jags |only
nCal-14.10-31/nCal/inst/jags_script/classical_t4.jags |only
nCal-14.10-31/nCal/inst/jags_script/classical_tar1.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_lar1.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_mix2.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_mixnorm.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_norm.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_norm_4pl.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_replicate_re.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_t4.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_t4_4pl.jags |only
nCal-14.10-31/nCal/inst/jags_script/gh_tar1.jags |only
nCal-14.10-31/nCal/inst/unitTests/runit.bcrm.R | 96 +-
nCal-14.10-31/nCal/inst/unitTests/runit.ncal.R | 87 +
nCal-14.10-31/nCal/man/5PL.Rd | 14
nCal-14.10-31/nCal/man/bcrm.Rd | 73 +
nCal-14.10-31/nCal/man/crm.fit.Rd |only
nCal-14.10-31/nCal/man/drm.fit.Rd | 33
nCal-14.10-31/nCal/man/elisa.R.gh.Rd |only
nCal-14.10-31/nCal/man/gnls.fit.Rd |only
nCal-14.10-31/nCal/man/ncal.Rd | 47
nCal-14.10-31/nCal/man/plot5PL.Rd | 18
nCal-14.10-31/nCal/vignettes/figure/minimal-Example1bcrm.pdf |binary
nCal-14.10-31/nCal/vignettes/figure/minimal-Example1drm.pdf |binary
nCal-14.10-31/nCal/vignettes/figure/minimal-Example2.pdf |binary
nCal-14.10-31/nCal/vignettes/nCal-vignette.Rnw | 34
nCal-14.10-31/nCal/vignettes/nCal-vignette.bib | 14
65 files changed, 928 insertions(+), 672 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Diff between blocksdesign versions 1.1 dated 2014-10-03 and 1.2 dated 2014-11-02
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks strata are optimized hierarchically with each set of
nested blocks optimized within the levels of the preceding set. Block sizes
are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson
DESCRIPTION | 6
MD5 | 22 -
R/blocks.r | 679 +++++++++++++++++++++++---------------------
R/blocksdesign-package.r | 31 +-
R/pairwise_effics.r | 12
R/upper_bounds.r | 8
build/vignette.rds |binary
man/blocks.Rd | 72 ++--
man/blocksdesign-package.Rd | 32 +-
man/efficiencies.Rd | 12
man/upper_bounds.Rd | 8
vignettes/blocksdesign.Rmd | 40 +-
12 files changed, 478 insertions(+), 444 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.1 dated 2014-10-01 and 1.1.1 dated 2014-11-02
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
EpiModel-1.1.1/EpiModel/DESCRIPTION | 12
EpiModel-1.1.1/EpiModel/MD5 | 100 +++---
EpiModel-1.1.1/EpiModel/NAMESPACE | 8
EpiModel-1.1.1/EpiModel/NEWS | 57 ++-
EpiModel-1.1.1/EpiModel/R/EpiModel-package.r | 8
EpiModel-1.1.1/EpiModel/R/control.R | 19 -
EpiModel-1.1.1/EpiModel/R/dcm.R | 6
EpiModel-1.1.1/EpiModel/R/icm.R | 24 +
EpiModel-1.1.1/EpiModel/R/icm.mod.init.R | 24 -
EpiModel-1.1.1/EpiModel/R/init.R | 10
EpiModel-1.1.1/EpiModel/R/net.mod.init.R | 28 +
EpiModel-1.1.1/EpiModel/R/net.mod.simnet.R | 39 ++
EpiModel-1.1.1/EpiModel/R/net.mod.status.R | 55 ++-
EpiModel-1.1.1/EpiModel/R/net.mod.vital.R | 45 +-
EpiModel-1.1.1/EpiModel/R/net.utils.R | 39 --
EpiModel-1.1.1/EpiModel/R/netdx.R | 84 +++--
EpiModel-1.1.1/EpiModel/R/netest.R | 8
EpiModel-1.1.1/EpiModel/R/netsim.R | 34 +-
EpiModel-1.1.1/EpiModel/R/param.R | 27 +
EpiModel-1.1.1/EpiModel/R/plot.R | 179 +++++++---
EpiModel-1.1.1/EpiModel/R/print.r | 66 +++
EpiModel-1.1.1/EpiModel/R/test.R |only
EpiModel-1.1.1/EpiModel/R/utils.R | 265 +++++++---------
EpiModel-1.1.1/EpiModel/R/verbose.R | 34 +-
EpiModel-1.1.1/EpiModel/build/vignette.rds |binary
EpiModel-1.1.1/EpiModel/inst/doc/Intro.R | 9
EpiModel-1.1.1/EpiModel/inst/doc/Intro.Rmd |only
EpiModel-1.1.1/EpiModel/inst/doc/Intro.html |only
EpiModel-1.1.1/EpiModel/inst/shiny/dcm/app.R |only
EpiModel-1.1.1/EpiModel/inst/shiny/icm/app.R |only
EpiModel-1.1.1/EpiModel/man/EpiModel-package.Rd | 8
EpiModel-1.1.1/EpiModel/man/comp_plot.Rd | 16
EpiModel-1.1.1/EpiModel/man/control.dcm.Rd | 21 -
EpiModel-1.1.1/EpiModel/man/deleteAttr.Rd |only
EpiModel-1.1.1/EpiModel/man/get_args.Rd |only
EpiModel-1.1.1/EpiModel/man/mcat.Rd |only
EpiModel-1.1.1/EpiModel/man/netdx.Rd | 4
EpiModel-1.1.1/EpiModel/man/netsim.Rd | 13
EpiModel-1.1.1/EpiModel/man/netsim_parallel.Rd | 34 +-
EpiModel-1.1.1/EpiModel/man/param.net.Rd | 27 +
EpiModel-1.1.1/EpiModel/man/plot.netdx.Rd | 13
EpiModel-1.1.1/EpiModel/man/plot.netsim.Rd | 54 +--
EpiModel-1.1.1/EpiModel/man/ssample.Rd |only
EpiModel-1.1.1/EpiModel/man/test_icm.Rd |only
EpiModel-1.1.1/EpiModel/man/test_net.Rd |only
EpiModel-1.1.1/EpiModel/man/verbose.dcm.Rd |only
EpiModel-1.1.1/EpiModel/man/verbose.icm.Rd |only
EpiModel-1.1.1/EpiModel/tests/testthat/test-dcm-long.R |only
EpiModel-1.1.1/EpiModel/tests/testthat/test-icm-long.R |only
EpiModel-1.1.1/EpiModel/tests/testthat/test-net-long.R |only
EpiModel-1.1.1/EpiModel/tests/testthat/test-netattr.R | 32 +
EpiModel-1.1.1/EpiModel/tests/testthat/test-netdx.R |only
EpiModel-1.1.1/EpiModel/tests/testthat/test-netsim.R | 71 ++++
EpiModel-1.1.1/EpiModel/tests/testthat/test-netvary.R | 25 -
EpiModel-1.1.1/EpiModel/tests/testthat/test-newdcm.R | 60 +++
EpiModel-1.1.1/EpiModel/vignettes/Intro.Rmd |only
EpiModel-1.1/EpiModel/inst/doc/Intro.Rnw |only
EpiModel-1.1/EpiModel/inst/doc/Intro.pdf |only
EpiModel-1.1/EpiModel/inst/shiny/dcm/server.R |only
EpiModel-1.1/EpiModel/inst/shiny/dcm/ui.R |only
EpiModel-1.1/EpiModel/inst/shiny/icm/server.R |only
EpiModel-1.1/EpiModel/inst/shiny/icm/ui.R |only
EpiModel-1.1/EpiModel/tests/testthat/test-diagnostics.R |only
EpiModel-1.1/EpiModel/vignettes/Intro.Rnw |only
64 files changed, 1047 insertions(+), 511 deletions(-)
Title: Behavioral change point analysis of animal movement
Diff between bcpa versions 1.0 dated 2013-10-26 and 1.1 dated 2014-11-02
Description: The Behavioral Change Point Analysis (BCPA) is a method of
identifying hidden shifts in the underlying parameters of a time series,
developed specifically to be applied to animal movement data which is
irregularly sampled. The method is based on: E.
Gurarie, R. Andrews and K. Laidre A novel method for identifying
behavioural changes in animal movement data (2009) Ecology Letters 12:5
395-408.
Author: Eliezer Gurarie
Maintainer: Eliezer Gurarie
bcpa-1.0/bcpa/R/ChangePointSummary.r |only
bcpa-1.0/bcpa/R/GetBestBreak.r |only
bcpa-1.0/bcpa/R/GetDoubleL.r |only
bcpa-1.0/bcpa/R/GetModels.r |only
bcpa-1.0/bcpa/R/GetRho.r |only
bcpa-1.0/bcpa/R/PartitionParameters.r |only
bcpa-1.0/bcpa/R/RcppExports.r |only
bcpa-1.0/bcpa/R/WindowSweep.r |only
bcpa-1.0/bcpa/R/bcpa.R-internal.r |only
bcpa-1.1/bcpa/DESCRIPTION | 18 ++----
bcpa-1.1/bcpa/MD5 | 70 ++++++++++++++-------------
bcpa-1.1/bcpa/NAMESPACE | 3 -
bcpa-1.1/bcpa/R/ChangePointSummary.R |only
bcpa-1.1/bcpa/R/GetBestBreak.R |only
bcpa-1.1/bcpa/R/GetDoubleL.R |only
bcpa-1.1/bcpa/R/GetModels.R |only
bcpa-1.1/bcpa/R/GetRho.R |only
bcpa-1.1/bcpa/R/GetVT.r | 12 +++-
bcpa-1.1/bcpa/R/MakeTrack.R |only
bcpa-1.1/bcpa/R/PartitionParameters.R |only
bcpa-1.1/bcpa/R/PhasePlot.r | 7 +-
bcpa-1.1/bcpa/R/RcppExports.R |only
bcpa-1.1/bcpa/R/WindowSweep.R |only
bcpa-1.1/bcpa/R/bcpa.R-internal.R |only
bcpa-1.1/bcpa/R/plot.bcpa.r | 16 +++---
bcpa-1.1/bcpa/build |only
bcpa-1.1/bcpa/inst/doc/bcpa.R | 28 ++--------
bcpa-1.1/bcpa/inst/doc/bcpa.pdf |binary
bcpa-1.1/bcpa/inst/doc/bcpa.rnw | 14 ++++-
bcpa-1.1/bcpa/man/ChangePointSummary.Rd | 44 ++++++++--------
bcpa-1.1/bcpa/man/DiagPlot.Rd | 18 +++---
bcpa-1.1/bcpa/man/GetBestBreak.Rd | 36 ++++++++-----
bcpa-1.1/bcpa/man/GetDoubleL.Rd | 26 +++++-----
bcpa-1.1/bcpa/man/GetModels.Rd | 37 ++++++--------
bcpa-1.1/bcpa/man/GetRho.Rd | 22 ++++----
bcpa-1.1/bcpa/man/GetVT.Rd | 44 ++++++++++------
bcpa-1.1/bcpa/man/MakeTrack.Rd |only
bcpa-1.1/bcpa/man/PartitionParameters.Rd | 21 +++-----
bcpa-1.1/bcpa/man/PathPlot.Rd | 17 +++---
bcpa-1.1/bcpa/man/PhasePlot.Rd | 19 ++++---
bcpa-1.1/bcpa/man/WindowSweep.Rd | 39 +++++++--------
bcpa-1.1/bcpa/man/plot.bcpa.Rd | 25 +++++----
bcpa-1.1/bcpa/man/plot.track.Rd | 5 -
bcpa-1.1/bcpa/src/GetL.cpp | 11 ----
bcpa-1.1/bcpa/src/RcppExports.cpp | 8 +--
bcpa-1.1/bcpa/vignettes/bcpa-concordance.tex |only
bcpa-1.1/bcpa/vignettes/bcpa.rnw | 14 ++++-
47 files changed, 283 insertions(+), 271 deletions(-)