Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for
Phylogenetic Analysis)
Description: Assist performing tip-dating of phylogenetic trees with BEAST.
Author: Adrien Rieux, Camilo Khatchikian
Maintainer: Camilo Khatchikian <ckhatchikian@gmail.com>
Diff between TipDatingBeast versions 1.0-5 dated 2016-09-05 and 1.0-6 dated 2017-11-21
TipDatingBeast-1.0-5/TipDatingBeast/inst/example/Tutorial_TipDatingBEAST_Sept2016.pdf |only TipDatingBeast-1.0-5/TipDatingBeast/man/clusters.Flu.Rd |only TipDatingBeast-1.0-6/TipDatingBeast/DESCRIPTION | 11 ++-- TipDatingBeast-1.0-6/TipDatingBeast/MD5 | 25 +++++----- TipDatingBeast-1.0-6/TipDatingBeast/R/TaxonOut.R | 2 TipDatingBeast-1.0-6/TipDatingBeast/inst/example/Tutorial_TipDatingBEAST.pdf |only TipDatingBeast-1.0-6/TipDatingBeast/man/Flu_BEAST_18.clusters.Flu.Rd |only TipDatingBeast-1.0-6/TipDatingBeast/man/Flu_BEAST_232.clusters.Flu.Rd |only TipDatingBeast-1.0-6/TipDatingBeast/man/ListTaxa.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/PlotDRT.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/PlotLOOCV.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/RandomCluster.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/RandomDates.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/TaxaOut.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/TaxonOut.Rd | 3 - TipDatingBeast-1.0-6/TipDatingBeast/man/TipDatingBeast-package.Rd | 7 +- 16 files changed, 37 insertions(+), 29 deletions(-)
More information about TipDatingBeast at CRAN
Permanent link
Title: An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
Description: Allows to display a progress bar in the R
console for long running computations taking place in c++ code,
and support for interrupting those computations even in multithreaded
code, typically using OpenMP.
Author: Karl Forner <karl.forner@gmail.com>
Maintainer: Karl Forner <karl.forner@gmail.com>
Diff between RcppProgress versions 0.3 dated 2017-01-05 and 0.4 dated 2017-11-21
RcppProgress-0.3/RcppProgress/CHANGELOG |only RcppProgress-0.3/RcppProgress/R/tests.R |only RcppProgress-0.3/RcppProgress/R/zzz.R |only RcppProgress-0.3/RcppProgress/inst/examples/dev.R |only RcppProgress-0.3/RcppProgress/inst/include/progress_legacy.hpp |only RcppProgress-0.3/RcppProgress/src |only RcppProgress-0.4/RcppProgress/DESCRIPTION | 15 - RcppProgress-0.4/RcppProgress/MD5 | 36 ++- RcppProgress-0.4/RcppProgress/NAMESPACE | 2 RcppProgress-0.4/RcppProgress/R/wrap_examples.R |only RcppProgress-0.4/RcppProgress/README.md | 36 +++ RcppProgress-0.4/RcppProgress/inst/examples/RcppProgressArmadillo/src/example.cpp | 2 RcppProgress-0.4/RcppProgress/inst/examples/RcppProgressETA |only RcppProgress-0.4/RcppProgress/inst/examples/RcppProgressExample/src/dummy.cpp |only RcppProgress-0.4/RcppProgress/inst/examples/RcppProgressExample/src/example.cpp | 2 RcppProgress-0.4/RcppProgress/inst/include/interruptable_progress_monitor.hpp | 27 ++ RcppProgress-0.4/RcppProgress/inst/include/progress.hpp | 43 +++- RcppProgress-0.4/RcppProgress/inst/include/progress_bar.hpp | 98 +--------- RcppProgress-0.4/RcppProgress/inst/include/simple_progress_bar.hpp |only RcppProgress-0.4/RcppProgress/man/RcppProgress-package.Rd | 16 + RcppProgress-0.4/RcppProgress/tests |only 21 files changed, 145 insertions(+), 132 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.8.2 dated 2017-10-16 and 3.8.3 dated 2017-11-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 +++++++ R/Deriv.R | 10 +++++----- README.md | 8 ++++++-- man/Deriv-package.Rd | 8 ++++---- tests/testthat/test_Deriv.R | 4 +++- 7 files changed, 35 insertions(+), 22 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.1.0 dated 2017-10-11 and 2.2.0 dated 2017-11-21
DESCRIPTION | 18 +++++++++--------- MD5 | 19 ++++++++++++++----- NAMESPACE | 7 +++++++ NEWS.md | 8 ++++++++ R/application.R |only R/dataset.R | 25 +++++++++++++++++++++++++ R/shiny.R |only R/solvebio.R | 28 +++++++++++++++++----------- man/Application.all.Rd |only man/Application.create.Rd |only man/Application.delete.Rd |only man/Application.retrieve.Rd |only man/Application.update.Rd |only man/Dataset.template.Rd |only man/protectedServer.Rd |only 15 files changed, 80 insertions(+), 25 deletions(-)
Title: PCA, Transpose and Multicore Functionality for 'big.matrix'
Objects
Description: Adds wrappers to add functionality for big.matrix objects (see the bigmemory project).
This allows fast scalable principle components analysis (PCA), or singular value decomposition (SVD).
There are also functions for transposing, using multicore 'apply' functionality, data importing
and for compact display of big.matrix objects. Most functions also work for standard matrices if
RAM is sufficient.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>
Diff between bigpca versions 1.0.3 dated 2015-11-08 and 1.1 dated 2017-11-21
DESCRIPTION | 11 +- MD5 | 51 ++++++----- NAMESPACE | 23 ----- R/bigpca.R | 171 +++++++++++++++++++++++++++++----------- man/PC.correct.Rd | 30 +++---- man/big.PCA.Rd | 74 +++++++++-------- man/big.algebra.install.help.Rd | 13 +-- man/big.select.Rd | 17 ++- man/big.t.Rd | 12 +- man/bigpca-internal.Rd | 2 man/bigpca-package.Rd | 12 ++ man/bmcapply.Rd | 31 +++---- man/clear_active_bms.Rd |only man/estimate.eig.vpcs.Rd | 9 -- man/generate.test.matrix.Rd | 7 - man/get.big.matrix.Rd | 9 +- man/import.big.data.Rd | 39 ++++----- man/pca.scree.plot.Rd | 5 - man/prv.big.matrix.Rd | 13 +-- man/quick.elbow.Rd | 17 +-- man/quick.pheno.assocs.Rd | 11 +- man/select.least.assoc.Rd | 13 +-- man/subcor.select.Rd | 15 +-- man/subpc.select.Rd | 17 +-- man/svn.bigalgebra.install.Rd | 11 +- man/thin.Rd | 29 +++--- man/uniform.select.Rd | 15 +-- 27 files changed, 367 insertions(+), 290 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-17 1.1
2016-06-05 1.0.1
2016-06-02 1.0
Title: Rcpp Hidden Markov Model
Description: Collection of functions to evaluate sequences, decode hidden states and estimate parameters from a single or multiple sequences of a discrete time Hidden Markov Model. The observed values can be modeled by a multinomial distribution for categorical/labeled emissions, a mixture of Gaussians for continuous data and also a mixture of Poissons for discrete values. It includes functions for random initialization, simulation, backward or forward sequence evaluation, Viterbi or forward-backward decoding and parameter estimation using an Expectation-Maximization approach.
Author: Roberto A. Cardenas-Ovando, Julieta Noguez and Claudia Rangel-Escareno
Maintainer: Roberto A. Cardenas-Ovando <robalecarova@gmail.com>
Diff between RcppHMM versions 1.2 dated 2017-08-29 and 1.2.2 dated 2017-11-21
DESCRIPTION | 8 MD5 | 28 +-- man/Changes.Rd | 42 ++--- man/RcppHMM-package.Rd | 8 man/evaluation.Rd | 271 +++++++++++++++++++++++---------- man/forwardBackward.Rd | 242 +++++++++++++++++++++-------- man/generateObservations.Rd | 228 ++++++++++++++++++++------- man/initGHMM.Rd | 18 +- man/initHMM.Rd | 16 - man/initPHMM.Rd | 14 - man/learnEM.Rd | 361 +++++++++++++++++++++++++++++++------------- man/loglikelihood.Rd | 280 ++++++++++++++++++++++++---------- man/setNames.Rd | 6 man/setParameters.Rd | 261 ++++++++++++++++--------------- man/viterbi.Rd | 250 +++++++++++++++++++++--------- 15 files changed, 1385 insertions(+), 648 deletions(-)
Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between VennDiagram versions 1.6.17 dated 2016-04-18 and 1.6.18 dated 2017-11-21
VennDiagram-1.6.17/VennDiagram/tests/Rplots.pdf |only VennDiagram-1.6.18/VennDiagram/DESCRIPTION | 8 - VennDiagram-1.6.18/VennDiagram/MD5 | 11 +- VennDiagram-1.6.18/VennDiagram/NEWS | 6 + VennDiagram-1.6.18/VennDiagram/R/draw.quad.venn.R | 6 - VennDiagram-1.6.18/VennDiagram/R/venn.diagram.R | 100 ++++++++++----------- VennDiagram-1.6.18/VennDiagram/man/venn.diagram.Rd | 11 ++ 7 files changed, 78 insertions(+), 64 deletions(-)
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
<http://pj.freefaculty.org/guides>. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette 'rockchalk' offers a
fairly comprehensive overview. The vignette 'Rstyle' has advice
about coding in R. The package title 'rockchalk' refers to our
school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson <pauljohn@ku.edu>
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.109 dated 2017-11-16 and 1.8.110 dated 2017-11-21
DESCRIPTION | 8 - MD5 | 28 ++-- R/outreg.R | 288 +++++++++++++++++++++++++------------------ inst/ChangeLog | 7 + inst/doc/Rchaeology.pdf |binary inst/doc/Rstyle.pdf |binary inst/doc/rockchalk.R | 10 - inst/doc/rockchalk.Rnw | 10 - inst/doc/rockchalk.pdf |binary inst/examples/addLines-ex.R | 8 - man/addLines.Rd | 8 - man/outreg.Rd | 95 ++++++++------ vignettes/plots/plot-013.pdf |binary vignettes/rockchalk.Rnw | 10 - vignettes/rockchalk.lyx | 16 +- 15 files changed, 287 insertions(+), 201 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.6.3) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (0000-0003-2392-6140),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.2-15 dated 2017-10-30 and 1.2-16 dated 2017-11-21
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/ogr_write.R | 10 +++++++++- configure | 18 +++++++++--------- inst/ChangeLog | 30 ++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 +- inst/doc/OGR_shape_encoding.pdf |binary src/OGR_write.cpp | 29 +++++++++++++++++++++++++---- 9 files changed, 118 insertions(+), 29 deletions(-)
Title: Practical Numerical Math Functions
Description: Provides a large number of functions from numerical analysis and
linear algebra, numerical optimization, differential equations,
time series, plus some well-known special mathematical functions.
Uses 'MATLAB' function names where appropriate to simplify porting.
Author: Hans W. Borchers [aut, cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 2.0.7 dated 2017-06-21 and 2.1.1 dated 2017-11-21
DESCRIPTION | 26 +++++++++++++++----------- MD5 | 24 +++++++++++++----------- NAMESPACE | 2 +- NEWS | 22 +++++++++++++++++++++- NEWS.md |only R/ezplot.R | 2 +- R/findpeaks.R | 2 +- R/lsqlincon.R | 5 +++++ R/quadprog.R | 8 ++++++-- README.md |only data/brown72.rda |binary data/nile.rda |binary data/titanium.rda |binary man/findpeaks.Rd | 2 +- 14 files changed, 64 insertions(+), 29 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.1 dated 2017-07-18 and 0.3.1.1 dated 2017-11-21
ChangeLog | 4 DESCRIPTION | 6 MD5 | 23 NAMESPACE | 2 R/configr.R | 1 R/fetch.R |only README.md | 24 inst/doc/configr.R | 7 inst/doc/configr.Rmd | 11 inst/doc/configr.html | 1109 ++++++++++++++++++++++++++---------------- inst/doc/filetypes.html | 418 +++++++++------ man/fetch.config.Rd |only tests/testthat/test_m_fetch.R |only vignettes/configr.Rmd | 11 14 files changed, 1005 insertions(+), 611 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (0000-0001-5052-066X)
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.3.3 dated 2017-09-15 and 1.3.4 dated 2017-11-21
DESCRIPTION | 17 +++++++++------- MD5 | 20 +++++++++--------- NEWS.md | 5 ++++ R/mlm_plot.R | 2 - README.md | 34 +++++++++----------------------- inst/CITATION | 2 - inst/chunks/generated_quantities.stan | 1 inst/chunks/model.stan | 4 --- inst/chunks/transformed_parameters.stan | 6 ----- man/mlm_pars_plot.Rd | 2 - src/include/models.hpp | 18 +--------------- 11 files changed, 42 insertions(+), 69 deletions(-)
Title: Import, Manipulate and Explore the Results of an Antares
Simulation
Description: Import, manipulate and explore results generated by Antares, a
powerful software developed by RTE to simulate and study electric power systems
(more information about Antares here: <https://antares.rte-france.com>).
Author: Jalal-Edine ZAWAM [aut, cre],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between antaresRead versions 2.0.1 dated 2017-11-14 and 2.0.2 dated 2017-11-21
DESCRIPTION | 10 MD5 | 33 +-- NEWS | 5 build/vignette.rds |binary inst/doc/antares.html | 4 inst/doc/antaresH5.R |only inst/doc/antaresH5.Rmd | 39 +++ inst/doc/antaresH5.html | 16 + inst/vignetteData |only tests/testthat.R | 8 tests/testthat/helper_init.R | 7 tests/testthat/test-h5ReadAntares.R | 260 ++++++++++++------------- tests/testthat/test-h5_readInputs.R | 41 ++-- tests/testthat/test-h5_setSimulationPathH5.R | 6 tests/testthat/test-h5_write.R | 23 +- tests/testthat/test-readAntares.R | 276 +++++++++++++-------------- tests/testthat/test-viewAntares.R | 4 vignettes/antaresH5.Rmd | 39 +++ 18 files changed, 440 insertions(+), 331 deletions(-)
Title: Compute High Dimensional Orthant Probabilities
Description: Computationally efficient method to estimate orthant probabilities of high-dimensional Gaussian vectors. Further implements a function to compute conservative estimates of excursion sets under Gaussian random field priors.
Author: Dario Azzimonti
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between anMC versions 0.1.0 dated 2017-05-04 and 0.2.0 dated 2017-11-21
anMC-0.1.0/anMC/src/anMC_init.c |only anMC-0.2.0/anMC/DESCRIPTION | 10 ++--- anMC-0.2.0/anMC/MD5 | 49 ++++++++++++++-------------- anMC-0.2.0/anMC/NAMESPACE | 2 - anMC-0.2.0/anMC/NEWS.md | 10 +++++ anMC-0.2.0/anMC/R/ANMC0_2.R | 36 ++++++++++++-------- anMC-0.2.0/anMC/R/ConsEstv0_6.R | 2 - anMC-0.2.0/anMC/R/MC0_2.R | 37 ++++++++++++--------- anMC-0.2.0/anMC/R/ProbaMax.R | 2 - anMC-0.2.0/anMC/R/ProbaMin.R | 2 - anMC-0.2.0/anMC/R/RcppExports.R | 18 +++++++++- anMC-0.2.0/anMC/R/help.R | 9 ++--- anMC-0.2.0/anMC/R/optimizeEq.R | 4 +- anMC-0.2.0/anMC/README.md | 4 +- anMC-0.2.0/anMC/man/ANMC_Gauss.Rd | 2 - anMC-0.2.0/anMC/man/MC_Gauss.Rd | 2 - anMC-0.2.0/anMC/man/ProbaMax.Rd | 2 - anMC-0.2.0/anMC/man/ProbaMin.Rd | 2 - anMC-0.2.0/anMC/man/anMC.Rd | 9 +++-- anMC-0.2.0/anMC/man/conservativeEstimate.Rd | 2 - anMC-0.2.0/anMC/man/get_chronotime.Rd |only anMC-0.2.0/anMC/man/selectActiveDims.Rd | 2 - anMC-0.2.0/anMC/man/selectQdims.Rd | 2 - anMC-0.2.0/anMC/src/Makevars | 1 anMC-0.2.0/anMC/src/Makevars.win | 2 - anMC-0.2.0/anMC/src/RcppExports.cpp | 26 +++++++++++++- anMC-0.2.0/anMC/src/chronoTimer.cpp |only 27 files changed, 149 insertions(+), 88 deletions(-)
Title: Stream Editing
Description: Tools for stream editing: manipulating text files with insertions, replacements, deletions, substitutions, and commenting.
Author: Landon Sego [aut, cre]
Maintainer: Landon Sego <LHS@byu.net>
Diff between rsed versions 0.1.1 dated 2017-11-20 and 0.1.2 dated 2017-11-21
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/rsed-package.R | 6 +++--- README.md | 4 ++-- man/rsed-package.Rd | 6 +++--- 6 files changed, 27 insertions(+), 18 deletions(-)
Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct confidence intervals for the ranks of centers mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
Author: Diaa Al Mohamad and Erik W. van Zwet and Jelle J. Goeman
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>
Diff between ICRanks versions 1.2 dated 2017-11-16 and 1.3 dated 2017-11-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/PartitionByBlock.cpp | 26 +++++++++++++------------- 3 files changed, 19 insertions(+), 19 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Danning Chen [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.1.0 dated 2017-11-09 and 1.1.1 dated 2017-11-21
DESCRIPTION | 6 - MD5 | 42 ++++++------ R/generate_client.R | 2 R/generated_client.R | 114 ++++++++++++++++++++++------------- R/io.R | 14 +++- R/sysdata.rda |binary man/credentials_post_authenticate.Rd | 2 man/imports_post_files.Rd | 9 +- man/imports_post_syncs.Rd | 2 man/imports_put_syncs.Rd | 2 man/imports_put_syncs_archive.Rd | 1 man/match_targets_list.Rd | 1 man/notebooks_get.Rd | 10 ++- man/notebooks_patch.Rd | 24 ++++--- man/notebooks_post.Rd | 27 +++++--- man/notebooks_post_clone.Rd | 10 ++- man/notebooks_put.Rd | 24 ++++--- man/notebooks_put_archive.Rd | 10 ++- man/remote_hosts_list.Rd | 4 - man/remote_hosts_post.Rd | 4 - tests/testthat/data/full_spec.rds |binary tests/testthat/test_autogen.R | 28 +++++--- 22 files changed, 212 insertions(+), 124 deletions(-)
Title: Download and Aggregate Data from Public Hire Bicycle Systems
Description: Download and aggregate data from all public hire bicycle systems
which provide open data, currently including 'Santander' Cycles in London,
U.K., and from the U.S.A., 'citibike' in New York City NY, 'Divvy' in
Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA,
'Metro' in Los Angeles LA, and 'Indego' in Philadelphia PA.
Author: Mark Padgham [aut, cre],
Richard Ellison [aut],
Bea Hernández [rev] (Bea reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
Elaine McVey [rev] (Elaine reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
SQLite Consortium [ctb] (Authors of included SQLite code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between bikedata versions 0.0.4 dated 2017-08-17 and 0.1.0 dated 2017-11-21
DESCRIPTION | 16 MD5 | 62 NAMESPACE | 6 R/RcppExports.R | 82 R/bikedata-package.R | 4 R/database-stats.R | 40 R/date-time-functions.R | 15 R/distmat.R |only R/dl-bikedata.R | 24 R/stations.R | 13 R/store-bikedata.R | 45 R/tripmat.R | 91 R/utils.R | 43 inst/doc/bikedata.R | 2 inst/doc/bikedata.Rmd | 2 inst/doc/bikedata.html | 1281 +-- man/bike_distmat.Rd |only man/bike_match_matrices.Rd |only man/bike_tripmat.Rd | 12 man/dl_bikedata.Rd | 3 src/read-city-files.h | 334 src/read-station-files.h | 26 src/sqlite3db-add-data.h | 24 src/sqlite3db-setup.cpp | 26 src/sqlite3db-utils.h | 7 src/utils.cpp |only src/utils.h | 264 src/vendor/sqlite3/sqlite3.c |13314 +++++++++++++++++++++--------------- src/vendor/sqlite3/sqlite3.h | 491 - tests/testthat/test-db-stats.R | 2 tests/testthat/test-download-data.R | 2 tests/testthat/test-store-data.R | 12 tests/testthat/test-tripmat.R | 4 vignettes/bikedata.Rmd | 2 34 files changed, 9252 insertions(+), 6997 deletions(-)
Title: Satellite Nightlight Data Extraction
Description: The Rnightlights package extracts raster and zonal statistics
from satellite nightlight rasters downloaded from the United States
National Oceanic and Atmospheric Administration (<http://www.noaa.gov>)
free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly
nightlight raster data are supported. Satellite nightlight raster tiles are
downloaded and cropped to the country boundaries using shapefiles from the GADM
database of Global Administrative Areas (<http://gadm.org>). Zonal statistics
are then calculated at the lowest administrative boundary for the selected
country and cached locally for future retrieval. Finally, a simple data
explorer/browser is included that allows one to visualize the cached data e.g.
graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph],
Henrik Bengtsson [ctb] (data setup,
https://cran.r-project.org/package=R.cache),
Black Guru [ctb] (gdal zonal,
http://www.guru-gis.net/efficient-zonal-statistics-using-r-and-gdal/),
Jeff Chen [ctb] (masq function,
https://commercedataservice.github.io/tutorial_viirs_part1/),
Star Ying [ctb] (masq function,
https://commercedataservice.github.io/tutorial_viirs_part1/),
Chris Elvidge [ctb] (information + masq function)
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>
Diff between Rnightlights versions 0.1.2 dated 2017-09-09 and 0.1.3 dated 2017-11-21
DESCRIPTION | 8 MD5 | 42 - NEWS.md | 7 R/ctrynldata.R | 8 R/datapath.R | 1122 +++++++++++++++++------------------ R/downloadnltiles.R | 21 R/getnlfilename.R | 24 R/nightlights.R | 1134 ++++++++++++++++++------------------ R/options.R | 108 ++- R/stats.R | 8 R/utils.R | 25 README.md | 89 ++ inst/application/server.R | 23 man/getNlTifLclNameOLS.Rd | 2 man/getNlTileTifLclNamePathOLS.Rd | 2 man/getNlTileTifLclNamePathVIIRS.Rd | 2 man/getNlTileTifLclNameVIIRS.Rd | 2 man/getNlTileZipLclNamePath.Rd | 4 man/getNlTileZipLclNameVIIRS.Rd | 2 man/listCtryNlRasters.Rd | 6 man/pkgOptions.Rd | 51 + man/pkgReset.Rd | 8 22 files changed, 1439 insertions(+), 1259 deletions(-)
Title: Fast n-Gram 'Tokenization'
Description: An n-gram is a sequence of n "words" taken, in order, from a
body of text. This is a collection of utilities for creating,
displaying, summarizing, and "babbling" n-grams. The
'tokenization' and "babbling" are handled by very efficient C
code, which can even be built as its own standalone library.
The babbler is a simple Markov chain. The package also offers
a vignette with complete example 'workflows' and information about
the utilities offered in the package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [aut]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between ngram versions 3.0.3 dated 2017-03-24 and 3.0.4 dated 2017-11-21
ChangeLog | 7 ++- DESCRIPTION | 8 +-- MD5 | 54 ++++++++++++------------ README.md | 2 inst/doc/ngram-guide.Rnw | 2 inst/doc/ngram-guide.pdf |binary man/babble.Rd | 2 man/concatenate.Rd | 1 man/getseed.Rd | 1 man/getters.Rd | 7 +-- man/multiread.Rd | 1 man/ngram-class.Rd | 2 man/ngram-package.Rd | 1 man/ngram-print.Rd | 1 man/phrasetable.Rd | 3 - man/preprocess.Rd | 1 man/rcorpus.Rd | 1 man/splitter.Rd | 1 man/string.summary.Rd | 1 man/tokenize-asweka.Rd | 1 man/tokenize.Rd | 3 - man/wordcount.Rd | 2 src/constructor.c | 2 src/ngram/src/lex.c | 90 ++++++++++++++++++++++++++++++++++++----- tests/get.phrasetable.r |only vignettes/cover/cover.pdf |binary vignettes/include/lastpage.sty |only vignettes/include/preamble.tex | 2 vignettes/ngram-guide.Rnw | 2 29 files changed, 131 insertions(+), 67 deletions(-)
Title: Rcpp-Based Truncated Normal Distribution RNG and Family
Description: R-level and C++-level functionality
to generate random deviates from and calculate moments of a
Truncated Normal distribution using the algorithm of Robert (1995) <DOI:10.1007/BF00143942>.
In addition to RNG, functions for calculating moments, densities,
and entropies are provided at both levels.
Author: Jonathan Olmsted [aut, cre]
Maintainer: Jonathan Olmsted <jpolmsted@gmail.com>
Diff between RcppTN versions 0.2-1 dated 2017-07-09 and 0.2-2 dated 2017-11-21
RcppTN-0.2-1/RcppTN/ChangeLog |only RcppTN-0.2-1/RcppTN/build |only RcppTN-0.2-1/RcppTN/inst/doc |only RcppTN-0.2-1/RcppTN/vignettes |only RcppTN-0.2-2/RcppTN/DESCRIPTION | 12 +++++------- RcppTN-0.2-2/RcppTN/MD5 | 21 +++++---------------- RcppTN-0.2-2/RcppTN/NEWS | 6 ++++++ RcppTN-0.2-2/RcppTN/src/enttn1.cpp | 2 +- RcppTN-0.2-2/RcppTN/src/rtn1.cpp | 18 +++++++++--------- RcppTN-0.2-2/RcppTN/src/vtn1.cpp | 4 ++-- 10 files changed, 28 insertions(+), 35 deletions(-)
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: The ragt2ridges-package provides ridge maximum likelihood estimation of vector auto-regressive processes: the VAR(1), VAR(2) and VARX(1) model (more to be added). Prior knowledge may be incorporated in the estimation through a) specification of the edges believed to be absent in the time series chain graph, and b) a shrinkage target towards which the parameter estimate is shrunken for large penalty parameter values. Estimation functionality is accompanied by methodology for penalty parameter selection. In addition, the package offers supporting functionality for the exploitation of estimated models. Among others, i) a procedure to infer the support of the non-sparse ridge estimate (and thereby of the time series chain graph) is implemented, ii) a table of node-wise network summary statistics, iii) mutual information analysis, and iv) impulse response analysis. Cf. Miok et al. (2017) <DOI:10.1002/bimj.201500269> and submitted follow-up work for details on the implemented methods.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.3.0 dated 2017-11-10 and 0.3.1 dated 2017-11-21
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++++----- NAMESPACE | 2 -- R/evaluateVAR1fit.r | 6 +----- R/motifStatsVAR1.r |only R/pruneMotifStats.r |only inst/NEWS.Rd | 7 +++++++ man/motifStatsVAR1.Rd |only man/pruneMotifStats.Rd |only man/ragt2ridges-package.Rd | 2 +- 10 files changed, 25 insertions(+), 20 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Description: Estimate the size of a networked population based on
respondent-driven sampling data. The package is part of the "RDS Analyst"
suite of packages for the analysis of respondent-driven sampling data.
See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923> and
Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>.
Author: Mark S. Handcock [aut, cre, cph],
Krista J. Gile [aut, cph]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between sspse versions 0.5-4 dated 2017-11-19 and 0.5-5 dated 2017-11-21
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/dsizeprior.R | 6 +++--- R/summary.size.R | 6 +++--- man/dsizeprior.Rd | 6 +++--- man/summary.sspse.Rd | 6 +++--- src/cmp.c | 11 ++++++----- src/dis.c | 5 +++-- src/likelihoodcmp.c | 27 ++++++++++++++++----------- src/mcmc.c | 12 ++++++++++-- src/posteriorcmp.c | 29 +++++++++++++++++------------ src/posteriorcmpdisease.c | 23 +++++++++++++++-------- src/posteriornbinom.c | 16 ++++++++++++---- src/posteriorpln.c | 10 ++++++---- src/posteriorplndisease.c | 14 +++++++++----- src/ppspolya.c | 5 +++-- src/size.c | 8 ++++---- src/sizeall.c | 6 +++--- 18 files changed, 137 insertions(+), 95 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
K. Colyvas;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.53-2 dated 2017-10-08 and 1.54-0 dated 2017-11-21
spatstat-1.53-2/spatstat/man/methods.units.Rd |only spatstat-1.54-0/spatstat/DESCRIPTION | 15 spatstat-1.54-0/spatstat/MD5 | 192 +++++---- spatstat-1.54-0/spatstat/NAMESPACE | 57 ++ spatstat-1.54-0/spatstat/NEWS | 161 ++++++++ spatstat-1.54-0/spatstat/R/Kmeasure.R | 7 spatstat-1.54-0/spatstat/R/affine.R | 6 spatstat-1.54-0/spatstat/R/areadiff.R | 138 +++++-- spatstat-1.54-0/spatstat/R/areainter.R | 33 + spatstat-1.54-0/spatstat/R/blur.R | 8 spatstat-1.54-0/spatstat/R/boundingbox.R | 26 + spatstat-1.54-0/spatstat/R/clip.psp.R | 4 spatstat-1.54-0/spatstat/R/closepairs.R | 2 spatstat-1.54-0/spatstat/R/colourtables.R | 25 - spatstat-1.54-0/spatstat/R/colourtools.R | 24 + spatstat-1.54-0/spatstat/R/connected.R | 14 spatstat-1.54-0/spatstat/R/density.psp.R | 75 ++- spatstat-1.54-0/spatstat/R/discarea.R | 23 - spatstat-1.54-0/spatstat/R/distfun.R | 5 spatstat-1.54-0/spatstat/R/eval.im.R | 8 spatstat-1.54-0/spatstat/R/fourierbasis.R | 15 spatstat-1.54-0/spatstat/R/fv.R | 4 spatstat-1.54-0/spatstat/R/images.R | 4 spatstat-1.54-0/spatstat/R/kppm.R | 15 spatstat-1.54-0/spatstat/R/leverage.R | 82 +++- spatstat-1.54-0/spatstat/R/lindirichlet.R | 61 ++- spatstat-1.54-0/spatstat/R/linim.R | 44 +- spatstat-1.54-0/spatstat/R/linnet.R | 6 spatstat-1.54-0/spatstat/R/lpp.R | 4 spatstat-1.54-0/spatstat/R/mpl.R | 36 + spatstat-1.54-0/spatstat/R/options.R | 6 spatstat-1.54-0/spatstat/R/pairwise.family.R | 92 ++-- spatstat-1.54-0/spatstat/R/pixellate.R | 34 + spatstat-1.54-0/spatstat/R/plot.anylist.R | 6 spatstat-1.54-0/spatstat/R/plot.im.R | 15 spatstat-1.54-0/spatstat/R/pp3.R | 39 +- spatstat-1.54-0/spatstat/R/ppp.R | 2 spatstat-1.54-0/spatstat/R/ppx.R | 13 spatstat-1.54-0/spatstat/R/profilepl.R | 11 spatstat-1.54-0/spatstat/R/psp.R | 42 ++ spatstat-1.54-0/spatstat/R/psp2pix.R | 15 spatstat-1.54-0/spatstat/R/rasterfilter.R |only spatstat-1.54-0/spatstat/R/rescale.R | 6 spatstat-1.54-0/spatstat/R/scriptUtils.R | 7 spatstat-1.54-0/spatstat/R/simulate.detPPF.R | 97 +++-- spatstat-1.54-0/spatstat/R/solist.R | 23 - spatstat-1.54-0/spatstat/R/strauss.R | 63 ++- spatstat-1.54-0/spatstat/R/strausshard.R | 45 ++ spatstat-1.54-0/spatstat/R/units.R | 84 ++-- spatstat-1.54-0/spatstat/R/window.R | 11 spatstat-1.54-0/spatstat/R/wingeom.R | 17 spatstat-1.54-0/spatstat/inst/doc/Nickname.txt | 2 spatstat-1.54-0/spatstat/inst/doc/datasets.R | 135 +++---- spatstat-1.54-0/spatstat/inst/doc/datasets.Rnw | 14 spatstat-1.54-0/spatstat/inst/doc/datasets.pdf |binary spatstat-1.54-0/spatstat/inst/doc/getstart.pdf |binary spatstat-1.54-0/spatstat/inst/doc/packagesizes.txt | 1 spatstat-1.54-0/spatstat/inst/doc/replicated.pdf |binary spatstat-1.54-0/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.54-0/spatstat/inst/doc/updates.R | 4 spatstat-1.54-0/spatstat/inst/doc/updates.Rnw | 82 ++++ spatstat-1.54-0/spatstat/inst/doc/updates.pdf |binary spatstat-1.54-0/spatstat/man/Frame.Rd | 12 spatstat-1.54-0/spatstat/man/areaGain.Rd | 5 spatstat-1.54-0/spatstat/man/boundingbox.Rd | 31 + spatstat-1.54-0/spatstat/man/colourmap.Rd | 21 - spatstat-1.54-0/spatstat/man/colouroutputs.Rd |only spatstat-1.54-0/spatstat/man/colourtools.Rd | 10 spatstat-1.54-0/spatstat/man/compatible.Rd | 11 spatstat-1.54-0/spatstat/man/connected.ppp.Rd | 21 - spatstat-1.54-0/spatstat/man/density.psp.Rd | 58 ++- spatstat-1.54-0/spatstat/man/dilated.areas.Rd | 5 spatstat-1.54-0/spatstat/man/distfun.Rd | 6 spatstat-1.54-0/spatstat/man/fourierbasis.Rd | 28 - spatstat-1.54-0/spatstat/man/integral.linim.Rd | 8 spatstat-1.54-0/spatstat/man/intensity.psp.Rd |only spatstat-1.54-0/spatstat/man/lut.Rd | 18 spatstat-1.54-0/spatstat/man/methods.linnet.Rd | 5 spatstat-1.54-0/spatstat/man/methods.unitname.Rd |only spatstat-1.54-0/spatstat/man/pixellate.owin.Rd | 9 spatstat-1.54-0/spatstat/man/pixellate.ppp.Rd | 7 spatstat-1.54-0/spatstat/man/pixellate.psp.Rd | 16 spatstat-1.54-0/spatstat/man/plot.anylist.Rd | 9 spatstat-1.54-0/spatstat/man/plot.im.Rd | 12 spatstat-1.54-0/spatstat/man/plot.listof.Rd | 9 spatstat-1.54-0/spatstat/man/plot.solist.Rd | 8 spatstat-1.54-0/spatstat/man/profilepl.Rd | 34 + spatstat-1.54-0/spatstat/man/reload.or.compute.Rd | 17 spatstat-1.54-0/spatstat/man/rescale.Rd | 9 spatstat-1.54-0/spatstat/man/spatstat-internal.Rd | 44 +- spatstat-1.54-0/spatstat/man/spatstat-package.Rd | 3 spatstat-1.54-0/spatstat/man/tweak.colourmap.Rd | 8 spatstat-1.54-0/spatstat/man/unitname.Rd | 12 spatstat-1.54-0/spatstat/src/init.c | 1 spatstat-1.54-0/spatstat/src/proto.h | 404 ++++++++++----------- spatstat-1.54-0/spatstat/src/rasterfilter.c |only spatstat-1.54-0/spatstat/tests/testsLtoM.R | 7 spatstat-1.54-0/spatstat/tests/testsQtoR.R | 8 spatstat-1.54-0/spatstat/vignettes/datasets.Rnw | 14 spatstat-1.54-0/spatstat/vignettes/updates.Rnw | 82 ++++ 100 files changed, 2014 insertions(+), 898 deletions(-)
Title: Sego Miscellaneous
Description: A collection of functions for statistical computing and data manipulation in R.
Includes routines for data ingestion, operating on dataframes and matrices, conversion to and
from lists, converting factors, filename manipulation, programming utilities, parallelization, plotting,
statistical and mathematical operations, and time series.
Author: Landon Sego [aut, cre]
Maintainer: Landon Sego <LHS@byu.net>
Diff between Smisc versions 0.3.6 dated 2016-06-23 and 0.3.9 dated 2017-11-21
Smisc-0.3.6/Smisc/inst/misc |only Smisc-0.3.9/Smisc/DESCRIPTION | 16 Smisc-0.3.9/Smisc/LICENSE | 6 Smisc-0.3.9/Smisc/MD5 | 320 +-- Smisc-0.3.9/Smisc/NAMESPACE | 180 +- Smisc-0.3.9/Smisc/NEWS.md | 565 +++--- Smisc-0.3.9/Smisc/R/PowerData.R | 36 Smisc-0.3.9/Smisc/R/Smisc-package.R | 70 Smisc-0.3.9/Smisc/R/allMissing.R | 118 - Smisc-0.3.9/Smisc/R/as.numericSilent.R | 70 Smisc-0.3.9/Smisc/R/comboList.R | 236 +- Smisc-0.3.9/Smisc/R/cumMax.R | 92 - Smisc-0.3.9/Smisc/R/cumsumNA.R | 120 - Smisc-0.3.9/Smisc/R/cusum.R | 448 ++-- Smisc-0.3.9/Smisc/R/dataIn.R | 246 +- Smisc-0.3.9/Smisc/R/df2list.R | 142 - Smisc-0.3.9/Smisc/R/dfplappy.R | 218 +- Smisc-0.3.9/Smisc/R/dframeEquiv.R | 534 ++--- Smisc-0.3.9/Smisc/R/dkbinom.R | 712 +++---- Smisc-0.3.9/Smisc/R/doCallParallel.R | 180 +- Smisc-0.3.9/Smisc/R/factor2character.R | 60 Smisc-0.3.9/Smisc/R/factor2numeric.R | 52 Smisc-0.3.9/Smisc/R/findDepMat.R | 188 +- Smisc-0.3.9/Smisc/R/formatDT.R | 796 ++++---- Smisc-0.3.9/Smisc/R/generics.R | 48 Smisc-0.3.9/Smisc/R/getExtension.R | 84 Smisc-0.3.9/Smisc/R/getPath.R | 164 - Smisc-0.3.9/Smisc/R/grabLast.R | 158 - Smisc-0.3.9/Smisc/R/hardCode.R | 158 - Smisc-0.3.9/Smisc/R/helper_functions.R | 44 Smisc-0.3.9/Smisc/R/hpd.R | 550 +++--- Smisc-0.3.9/Smisc/R/integ.R | 302 +-- Smisc-0.3.9/Smisc/R/linearMap.R | 126 - Smisc-0.3.9/Smisc/R/list2df.R | 504 ++--- Smisc-0.3.9/Smisc/R/loadObject.R | 192 +- Smisc-0.3.9/Smisc/R/more.R | 124 - Smisc-0.3.9/Smisc/R/movAvg2.R | 396 ++-- Smisc-0.3.9/Smisc/R/openDevice.R | 182 +- Smisc-0.3.9/Smisc/R/padZero.R | 202 +- Smisc-0.3.9/Smisc/R/parLapplyW.R | 224 +- Smisc-0.3.9/Smisc/R/parseJob.R | 368 ++-- Smisc-0.3.9/Smisc/R/pcbinom.R | 256 +- Smisc-0.3.9/Smisc/R/pddply.R | 344 +-- Smisc-0.3.9/Smisc/R/plapply.R | 1349 +++++++-------- Smisc-0.3.9/Smisc/R/plotFun.R | 380 ++-- Smisc-0.3.9/Smisc/R/pvar.R | 256 +- Smisc-0.3.9/Smisc/R/qbind.R | 132 - Smisc-0.3.9/Smisc/R/rma.R | 20 Smisc-0.3.9/Smisc/R/select.R | 640 +++---- Smisc-0.3.9/Smisc/R/selectElements.R | 204 +- Smisc-0.3.9/Smisc/R/sepList.R | 208 +- Smisc-0.3.9/Smisc/R/smartFilter.R | 616 +++--- Smisc-0.3.9/Smisc/R/smartRbindMat.R | 402 ++-- Smisc-0.3.9/Smisc/R/smartTimeAxis.R | 328 +-- Smisc-0.3.9/Smisc/R/sourceDir.R | 124 - Smisc-0.3.9/Smisc/R/stopifnotMsg.R | 234 +- Smisc-0.3.9/Smisc/R/stripExtension.R | 210 +- Smisc-0.3.9/Smisc/R/stripPath.R | 86 Smisc-0.3.9/Smisc/R/timeData.R | 36 Smisc-0.3.9/Smisc/R/timeDiff.R | 566 +++--- Smisc-0.3.9/Smisc/R/timeDiff.eg.R | 24 Smisc-0.3.9/Smisc/R/timeIntegration.R | 386 ++-- Smisc-0.3.9/Smisc/R/timeIt.R | 150 - Smisc-0.3.9/Smisc/R/timeStamp.R | 66 Smisc-0.3.9/Smisc/R/umvueLN.R | 230 +- Smisc-0.3.9/Smisc/R/unload_Smisc.R | 32 Smisc-0.3.9/Smisc/R/vertErrorBar.R | 348 +-- Smisc-0.3.9/Smisc/README.md | 70 Smisc-0.3.9/Smisc/TODO | 8 Smisc-0.3.9/Smisc/data/timeData.rda |binary Smisc-0.3.9/Smisc/inst/CITATION | 30 Smisc-0.3.9/Smisc/inst/doc/Smisc_tutorial.html | 22 Smisc-0.3.9/Smisc/man/PowerData.Rd | 43 Smisc-0.3.9/Smisc/man/Smisc-package.Rd | 57 Smisc-0.3.9/Smisc/man/allMissing.Rd | 107 - Smisc-0.3.9/Smisc/man/as.numericSilent.Rd | 61 Smisc-0.3.9/Smisc/man/comboList.Rd | 93 - Smisc-0.3.9/Smisc/man/cumMax.Rd | 59 Smisc-0.3.9/Smisc/man/cumsumNA.Rd | 83 Smisc-0.3.9/Smisc/man/cusum.Rd | 156 - Smisc-0.3.9/Smisc/man/dataIn.Rd | 121 - Smisc-0.3.9/Smisc/man/df2list.Rd | 87 Smisc-0.3.9/Smisc/man/dfplapply.Rd | 261 +- Smisc-0.3.9/Smisc/man/dframeEquiv.Rd | 207 +- Smisc-0.3.9/Smisc/man/dkbinom.Rd | 199 +- Smisc-0.3.9/Smisc/man/doCallParallel.Rd | 113 - Smisc-0.3.9/Smisc/man/factor2character.Rd | 63 Smisc-0.3.9/Smisc/man/factor2numeric.Rd | 59 Smisc-0.3.9/Smisc/man/findDepMat.Rd | 133 - Smisc-0.3.9/Smisc/man/formatDT.Rd | 203 +- Smisc-0.3.9/Smisc/man/generics.Rd | 33 Smisc-0.3.9/Smisc/man/getExtension.Rd | 97 - Smisc-0.3.9/Smisc/man/getPath.Rd | 79 Smisc-0.3.9/Smisc/man/grabLast.Rd | 65 Smisc-0.3.9/Smisc/man/hardCode.Rd | 97 - Smisc-0.3.9/Smisc/man/hpd.Rd | 190 +- Smisc-0.3.9/Smisc/man/integ.Rd | 146 - Smisc-0.3.9/Smisc/man/linearMap.Rd | 99 - Smisc-0.3.9/Smisc/man/list2df.Rd | 167 - Smisc-0.3.9/Smisc/man/loadObject.Rd | 120 - Smisc-0.3.9/Smisc/man/more.Rd | 77 Smisc-0.3.9/Smisc/man/movAvg2.Rd | 192 +- Smisc-0.3.9/Smisc/man/openDevice.Rd | 117 - Smisc-0.3.9/Smisc/man/padZero.Rd | 103 - Smisc-0.3.9/Smisc/man/parLapplyW.Rd | 157 - Smisc-0.3.9/Smisc/man/parseJob.Rd | 131 - Smisc-0.3.9/Smisc/man/pcbinom.Rd | 139 - Smisc-0.3.9/Smisc/man/pddply.Rd | 195 +- Smisc-0.3.9/Smisc/man/plapply.Rd | 385 ++-- Smisc-0.3.9/Smisc/man/plotFun.Rd | 143 - Smisc-0.3.9/Smisc/man/pvar.Rd | 145 - Smisc-0.3.9/Smisc/man/qbind.Rd | 97 - Smisc-0.3.9/Smisc/man/rma.Rd | 31 Smisc-0.3.9/Smisc/man/select.Rd | 169 - Smisc-0.3.9/Smisc/man/selectElements.Rd | 87 Smisc-0.3.9/Smisc/man/sepList.Rd | 165 - Smisc-0.3.9/Smisc/man/smartFilter.Rd | 197 +- Smisc-0.3.9/Smisc/man/smartRbindMat.Rd | 139 - Smisc-0.3.9/Smisc/man/smartTimeAxis.Rd | 145 - Smisc-0.3.9/Smisc/man/sourceDir.Rd | 75 Smisc-0.3.9/Smisc/man/stopifnotMsg.Rd | 145 - Smisc-0.3.9/Smisc/man/stripExtension.Rd | 111 - Smisc-0.3.9/Smisc/man/stripPath.Rd | 81 Smisc-0.3.9/Smisc/man/timeData.Rd | 43 Smisc-0.3.9/Smisc/man/timeDiff.Rd | 223 +- Smisc-0.3.9/Smisc/man/timeDiff.eg.Rd | 31 Smisc-0.3.9/Smisc/man/timeIntegration.Rd | 137 - Smisc-0.3.9/Smisc/man/timeIt.Rd | 120 - Smisc-0.3.9/Smisc/man/timeStamp.Rd | 57 Smisc-0.3.9/Smisc/man/umvueLN.Rd | 111 - Smisc-0.3.9/Smisc/man/vertErrorBar.Rd | 131 - Smisc-0.3.9/Smisc/src/init.c |only Smisc-0.3.9/Smisc/tests/runtest | 6 Smisc-0.3.9/Smisc/tests/testthat.R | 28 Smisc-0.3.9/Smisc/tests/testthat/function_list.txt | 78 Smisc-0.3.9/Smisc/tests/testthat/test_allMissing.R | 50 Smisc-0.3.9/Smisc/tests/testthat/test_as.numericSilent.R | 46 Smisc-0.3.9/Smisc/tests/testthat/test_cumMax.R | 26 Smisc-0.3.9/Smisc/tests/testthat/test_cumsumNA.R | 50 Smisc-0.3.9/Smisc/tests/testthat/test_dfplapply.R | 56 Smisc-0.3.9/Smisc/tests/testthat/test_dkbinom.R | 368 ++-- Smisc-0.3.9/Smisc/tests/testthat/test_doCallParallel.R | 50 Smisc-0.3.9/Smisc/tests/testthat/test_hardCode.R | 106 - Smisc-0.3.9/Smisc/tests/testthat/test_integ.R | 74 Smisc-0.3.9/Smisc/tests/testthat/test_more.R | 70 Smisc-0.3.9/Smisc/tests/testthat/test_openDevice.R | 52 Smisc-0.3.9/Smisc/tests/testthat/test_padZero.R | 134 - Smisc-0.3.9/Smisc/tests/testthat/test_parLapplyW.R | 112 - Smisc-0.3.9/Smisc/tests/testthat/test_parseJob.R | 40 Smisc-0.3.9/Smisc/tests/testthat/test_pddply.R | 166 - Smisc-0.3.9/Smisc/tests/testthat/test_plapply.R | 114 - Smisc-0.3.9/Smisc/tests/testthat/test_plotFun.R | 52 Smisc-0.3.9/Smisc/tests/testthat/test_pvar.R | 70 Smisc-0.3.9/Smisc/tests/testthat/test_rma.R | 38 Smisc-0.3.9/Smisc/tests/testthat/test_select.R | 664 +++---- Smisc-0.3.9/Smisc/tests/testthat/test_stripExtension.R | 84 Smisc-0.3.9/Smisc/tests/testthat/test_timeIntegration.R | 62 Smisc-0.3.9/Smisc/tests/testthat/test_timeStamp.R | 62 Smisc-0.3.9/Smisc/tests/testthat/test_umvueLN.R | 46 Smisc-0.3.9/Smisc/tests/testthat/test_vertErrorBar.R | 34 160 files changed, 13498 insertions(+), 13505 deletions(-)
Title: Handling, Visualisation and Analysis of Epidemiological Contacts
Description: A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Author: VP Nagraj [aut, cre],
Thibaut Jombart [aut],
Nistara Randhawa [aut],
Bertrand Sudre [aut],
Finlay Campbell [aut],
Thomas Crellen [aut]
Maintainer: VP Nagraj <vpnagraj@virginia.edu>
Diff between epicontacts versions 1.0.1 dated 2017-05-16 and 1.1.0 dated 2017-11-21
epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot1.rds |only epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot2.rds |only epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot3.rds |only epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot4.rds |only epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot5.rds |only epicontacts-1.0.1/epicontacts/tests/testthat/rds/plot6.rds |only epicontacts-1.1.0/epicontacts/DESCRIPTION | 8 epicontacts-1.1.0/epicontacts/MD5 | 81 +-- epicontacts-1.1.0/epicontacts/NAMESPACE | 4 epicontacts-1.1.0/epicontacts/NEWS.md | 10 epicontacts-1.1.0/epicontacts/R/codeawesome.R |only epicontacts-1.1.0/epicontacts/R/colors.R | 75 ++- epicontacts-1.1.0/epicontacts/R/graph3D.R | 112 +--- epicontacts-1.1.0/epicontacts/R/internals.R |only epicontacts-1.1.0/epicontacts/R/make_epicontacts.R | 142 +++-- epicontacts-1.1.0/epicontacts/R/plot.R | 32 - epicontacts-1.1.0/epicontacts/R/thin.R | 10 epicontacts-1.1.0/epicontacts/R/vis_epicontacts.R | 208 +++++--- epicontacts-1.1.0/epicontacts/build/vignette.rds |binary epicontacts-1.1.0/epicontacts/inst/doc/epicontacts.R | 6 epicontacts-1.1.0/epicontacts/inst/doc/epicontacts.Rmd | 13 epicontacts-1.1.0/epicontacts/inst/doc/epicontacts.html | 246 +++++----- epicontacts-1.1.0/epicontacts/inst/doc/epicontacts_class.R | 4 epicontacts-1.1.0/epicontacts/inst/doc/epicontacts_class.Rmd | 21 epicontacts-1.1.0/epicontacts/inst/doc/epicontacts_class.html | 83 +-- epicontacts-1.1.0/epicontacts/man/codeawesome.Rd |only epicontacts-1.1.0/epicontacts/man/colors.Rd | 29 - epicontacts-1.1.0/epicontacts/man/graph3D.Rd | 17 epicontacts-1.1.0/epicontacts/man/plot.epicontacts.Rd | 13 epicontacts-1.1.0/epicontacts/man/vis_epicontacts.Rd | 40 + epicontacts-1.1.0/epicontacts/tests/testthat/rds/print1.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/print2.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis1.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis2.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis3.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis4.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis5.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis6.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/rds/vis7.rds |binary epicontacts-1.1.0/epicontacts/tests/testthat/test_colors.R | 14 epicontacts-1.1.0/epicontacts/tests/testthat/test_graph3D.R | 34 - epicontacts-1.1.0/epicontacts/tests/testthat/test_plot.epicontacts.R | 2 epicontacts-1.1.0/epicontacts/tests/testthat/test_print.epicontacts.R | 1 epicontacts-1.1.0/epicontacts/tests/testthat/test_vis_epicontacts.R | 38 - epicontacts-1.1.0/epicontacts/vignettes/epicontacts.Rmd | 13 epicontacts-1.1.0/epicontacts/vignettes/epicontacts_class.Rmd | 21 46 files changed, 706 insertions(+), 571 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
for further details on estimation and the package structure.
For tutorials on how to use the CDM package see
George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as
Ravand and Robitzsch (2015, <http://pareonline.net/getvn.asp?v=20&n=11>).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 5.9-27 dated 2017-10-06 and 6.0-101 dated 2017-11-21
CDM-5.9-27/CDM/R/squeeze.cdm.R |only CDM-5.9-27/CDM/man/data.fraction1.Rd |only CDM-5.9-27/CDM/man/data.fraction2.Rd |only CDM-6.0-101/CDM/DESCRIPTION | 37 CDM-6.0-101/CDM/MD5 | 792 +++++----- CDM-6.0-101/CDM/NAMESPACE | 42 CDM-6.0-101/CDM/R/CDM_fisherz.R | 5 CDM-6.0-101/CDM/R/CDM_rbind_fill.R | 21 CDM-6.0-101/CDM/R/CDM_require_namespace.R | 11 CDM-6.0-101/CDM/R/CDM_rmvnorm.R | 1 CDM-6.0-101/CDM/R/IRT.IC.R | 16 CDM-6.0-101/CDM/R/IRT.RMSD.R | 7 CDM-6.0-101/CDM/R/IRT.anova.R | 56 CDM-6.0-101/CDM/R/IRT.compareModels.R | 186 +- CDM-6.0-101/CDM/R/IRT.data.R | 18 CDM-6.0-101/CDM/R/IRT.derivedParameters.R | 58 CDM-6.0-101/CDM/R/IRT.expectedCounts.R | 83 - CDM-6.0-101/CDM/R/IRT.factor.scores.R | 93 - CDM-6.0-101/CDM/R/IRT.frequencies.R | 8 CDM-6.0-101/CDM/R/IRT.irfprob.R | 79 CDM-6.0-101/CDM/R/IRT.irfprobPlot.R | 63 CDM-6.0-101/CDM/R/IRT.itemfit.R | 68 CDM-6.0-101/CDM/R/IRT.jackknife.R | 12 CDM-6.0-101/CDM/R/IRT.jackknife.gdina.R | 235 +- CDM-6.0-101/CDM/R/IRT.likelihood.R | 77 CDM-6.0-101/CDM/R/IRT.modelfit.R | 66 CDM-6.0-101/CDM/R/IRT.parameterTable.R | 8 CDM-6.0-101/CDM/R/IRT.posterior.R | 77 CDM-6.0-101/CDM/R/IRT.predict.R | 84 - CDM-6.0-101/CDM/R/IRT.repDesign.R | 15 CDM-6.0-101/CDM/R/IRT.se.R | 10 CDM-6.0-101/CDM/R/IRT.se.din.R | 27 CDM-6.0-101/CDM/R/IRT_RMSD_calc_distributions.R | 1 CDM-6.0-101/CDM/R/IRT_RMSD_calc_rmsd.R | 12 CDM-6.0-101/CDM/R/IRT_RMSD_proc_dist_item.R | 1 CDM-6.0-101/CDM/R/IRT_frequencies_default.R | 1 CDM-6.0-101/CDM/R/IRT_se_gdina.R |only CDM-6.0-101/CDM/R/IRT_se_gdina_calc_individual_likelihood.R |only CDM-6.0-101/CDM/R/IRT_se_gdina_calc_skill_distribution.R |only CDM-6.0-101/CDM/R/RcppExports.R | 1 CDM-6.0-101/CDM/R/WaldTest.R | 8 CDM-6.0-101/CDM/R/abs_approx.R | 12 CDM-6.0-101/CDM/R/abs_approx_D1.R |only CDM-6.0-101/CDM/R/anova.din.R | 4 CDM-6.0-101/CDM/R/array3_sum.R | 1 CDM-6.0-101/CDM/R/attach_environment.R | 6 CDM-6.0-101/CDM/R/bivariate_table_statistics.R | 1 CDM-6.0-101/CDM/R/cdi.kli.R | 52 CDM-6.0-101/CDM/R/cdm.est.calc.accuracy.R | 95 - CDM-6.0-101/CDM/R/cdm_add_ridge_diagonal.R |only CDM-6.0-101/CDM/R/cdm_calc_increment.R |only CDM-6.0-101/CDM/R/cdm_calc_increment_regularization.R |only CDM-6.0-101/CDM/R/cdm_calc_information_criteria.R | 15 CDM-6.0-101/CDM/R/cdm_calc_ll_with_counts.R |only CDM-6.0-101/CDM/R/cdm_calc_posterior.R | 9 CDM-6.0-101/CDM/R/cdm_elnet_threshold.R |only CDM-6.0-101/CDM/R/cdm_fa1.R |only CDM-6.0-101/CDM/R/cdm_fit_normal.R |only CDM-6.0-101/CDM/R/cdm_gini.R |only CDM-6.0-101/CDM/R/cdm_include_fixed_parameters.R |only CDM-6.0-101/CDM/R/cdm_increment_trimming_after_mstep.R |only CDM-6.0-101/CDM/R/cdm_lasso_threshold.R |only CDM-6.0-101/CDM/R/cdm_ll_numerical_differentiation.R |only CDM-6.0-101/CDM/R/cdm_matrix1.R |only CDM-6.0-101/CDM/R/cdm_matrix2.R |only CDM-6.0-101/CDM/R/cdm_mcp_threshold.R |only CDM-6.0-101/CDM/R/cdm_parameter_regularization.R |only CDM-6.0-101/CDM/R/cdm_pem_acceleration.R | 21 CDM-6.0-101/CDM/R/cdm_pem_acceleration_assign_output_parameters.R | 11 CDM-6.0-101/CDM/R/cdm_pem_adjust_dimension.R | 1 CDM-6.0-101/CDM/R/cdm_pem_algorithm_compute_Pnew.R | 1 CDM-6.0-101/CDM/R/cdm_pem_algorithm_compute_t.R | 1 CDM-6.0-101/CDM/R/cdm_pem_collect_parameters.R | 1 CDM-6.0-101/CDM/R/cdm_pem_create_parameter_index.R | 1 CDM-6.0-101/CDM/R/cdm_pem_extract_dimension.R | 1 CDM-6.0-101/CDM/R/cdm_pem_extract_parameters.R | 1 CDM-6.0-101/CDM/R/cdm_pem_include_ll_args.R | 1 CDM-6.0-101/CDM/R/cdm_pem_inits.R | 1 CDM-6.0-101/CDM/R/cdm_pem_inits_assign_parmlist.R | 1 CDM-6.0-101/CDM/R/cdm_pem_parameter_sequence_initial_iterations.R | 1 CDM-6.0-101/CDM/R/cdm_penalty_elnet.R |only CDM-6.0-101/CDM/R/cdm_penalty_lasso.R |only CDM-6.0-101/CDM/R/cdm_penalty_mcp.R |only CDM-6.0-101/CDM/R/cdm_penalty_ridge.R |only CDM-6.0-101/CDM/R/cdm_penalty_scad.R |only CDM-6.0-101/CDM/R/cdm_penalty_scadL2.R |only CDM-6.0-101/CDM/R/cdm_penalty_tlp.R |only CDM-6.0-101/CDM/R/cdm_penalty_tlp_approximation.R |only CDM-6.0-101/CDM/R/cdm_penalty_values.R |only CDM-6.0-101/CDM/R/cdm_positivity_restriction.R |only CDM-6.0-101/CDM/R/cdm_print_summary_call.R | 1 CDM-6.0-101/CDM/R/cdm_print_summary_computation_time.R | 1 CDM-6.0-101/CDM/R/cdm_print_summary_data_frame.R | 8 CDM-6.0-101/CDM/R/cdm_print_summary_information_criteria.R | 23 CDM-6.0-101/CDM/R/cdm_print_summary_package.R | 5 CDM-6.0-101/CDM/R/cdm_ridge_threshold.R |only CDM-6.0-101/CDM/R/cdm_scadL2_threshold.R |only CDM-6.0-101/CDM/R/cdm_scad_threshold.R |only CDM-6.0-101/CDM/R/cdm_soft_threshold.R |only CDM-6.0-101/CDM/R/cdm_sort_unique.R |only CDM-6.0-101/CDM/R/cdm_squeeze.R |only CDM-6.0-101/CDM/R/cdm_sumnorm.R | 1 CDM-6.0-101/CDM/R/cdm_sumnorm_squeeze.R |only CDM-6.0-101/CDM/R/cdm_tetrachoric.R | 38 CDM-6.0-101/CDM/R/cdm_tlp_threshold.R |only CDM-6.0-101/CDM/R/cdm_trim_increment.R |only CDM-6.0-101/CDM/R/check.input.R | 1 CDM-6.0-101/CDM/R/chisq_compute.R | 1 CDM-6.0-101/CDM/R/coef.R | 33 CDM-6.0-101/CDM/R/confint.din.R | 1 CDM-6.0-101/CDM/R/csink.R |only CDM-6.0-101/CDM/R/dataframe_summary.R | 13 CDM-6.0-101/CDM/R/deltaMethod.R | 6 CDM-6.0-101/CDM/R/din.R | 1 CDM-6.0-101/CDM/R/din.deterministic.R | 72 CDM-6.0-101/CDM/R/din.deterministic_alg.R | 48 CDM-6.0-101/CDM/R/din.equivalent.class.R |only CDM-6.0-101/CDM/R/din.partable.R | 25 CDM-6.0-101/CDM/R/din.validate.qmatrix.R | 44 CDM-6.0-101/CDM/R/din_equivalent_class_latent_response.R |only CDM-6.0-101/CDM/R/dpm_calc_probs.R |only CDM-6.0-101/CDM/R/entropy.lca.R | 50 CDM-6.0-101/CDM/R/equivalent.dina.R | 93 - CDM-6.0-101/CDM/R/equivalent.skillclasses.R | 109 - CDM-6.0-101/CDM/R/expand_matrix.R | 5 CDM-6.0-101/CDM/R/gdd.R | 10 CDM-6.0-101/CDM/R/gdina.R | 340 +++- CDM-6.0-101/CDM/R/gdina.dif.R | 15 CDM-6.0-101/CDM/R/gdina.dif_aux.R | 1 CDM-6.0-101/CDM/R/gdina.wald.R | 40 CDM-6.0-101/CDM/R/gdina.wald_aux.R | 1 CDM-6.0-101/CDM/R/gdina_attr_rpf_hogdina.R | 38 CDM-6.0-101/CDM/R/gdina_attribute_patterns_reduced_skillspace.R | 21 CDM-6.0-101/CDM/R/gdina_attribute_structure_hogdina.R | 21 CDM-6.0-101/CDM/R/gdina_calc_deviance.R | 21 CDM-6.0-101/CDM/R/gdina_calc_expected_counts.R | 5 CDM-6.0-101/CDM/R/gdina_calc_ic.R | 11 CDM-6.0-101/CDM/R/gdina_calc_individual_likelihood.R | 1 CDM-6.0-101/CDM/R/gdina_calc_individual_posterior.R | 17 CDM-6.0-101/CDM/R/gdina_calc_loglikelihood.R |only CDM-6.0-101/CDM/R/gdina_calc_prob.R | 19 CDM-6.0-101/CDM/R/gdina_calc_prob_one_item.R |only CDM-6.0-101/CDM/R/gdina_create_attribute_patterns.R | 19 CDM-6.0-101/CDM/R/gdina_create_designmatrices.R | 24 CDM-6.0-101/CDM/R/gdina_create_designmatrices_monotonicity_constraints.R |only CDM-6.0-101/CDM/R/gdina_delta_convert_into_list.R |only CDM-6.0-101/CDM/R/gdina_designmatrices.R | 1 CDM-6.0-101/CDM/R/gdina_init_class_probabilities.R | 23 CDM-6.0-101/CDM/R/gdina_init_item_parameters.R | 13 CDM-6.0-101/CDM/R/gdina_itemfit.R | 3 CDM-6.0-101/CDM/R/gdina_maximum_parameter_change.R | 1 CDM-6.0-101/CDM/R/gdina_mstep_item_ml.R | 213 +- CDM-6.0-101/CDM/R/gdina_mstep_item_ml_algorithm.R |only CDM-6.0-101/CDM/R/gdina_mstep_item_ml_rrum.R | 29 CDM-6.0-101/CDM/R/gdina_mstep_item_ml_rrum2.R | 113 - CDM-6.0-101/CDM/R/gdina_mstep_item_ml_update_parameter.R |only CDM-6.0-101/CDM/R/gdina_mstep_item_ml_update_parameter_regularization.R |only CDM-6.0-101/CDM/R/gdina_mstep_item_parameters.R | 53 CDM-6.0-101/CDM/R/gdina_mstep_item_parameters_designmatrix.R | 1 CDM-6.0-101/CDM/R/gdina_mstep_item_uls.R | 48 CDM-6.0-101/CDM/R/gdina_mstep_mono_constraints_penalty.R |only CDM-6.0-101/CDM/R/gdina_partable.R | 13 CDM-6.0-101/CDM/R/gdina_post_calc_se.R | 16 CDM-6.0-101/CDM/R/gdina_post_pattern_output.R | 7 CDM-6.0-101/CDM/R/gdina_post_posterior_output.R | 19 CDM-6.0-101/CDM/R/gdina_post_skill_pattern.R | 9 CDM-6.0-101/CDM/R/gdina_postproc_regularized_constrained_parameters.R |only CDM-6.0-101/CDM/R/gdina_prob_item_designmatrix.R |only CDM-6.0-101/CDM/R/gdina_probitem.R | 50 CDM-6.0-101/CDM/R/gdina_proc_check_admissible_rules.R | 1 CDM-6.0-101/CDM/R/gdina_proc_define_model_parameters.R | 17 CDM-6.0-101/CDM/R/gdina_proc_delta_indices.R |only CDM-6.0-101/CDM/R/gdina_proc_hogdina_theta_distribution.R | 1 CDM-6.0-101/CDM/R/gdina_proc_item_response_patterns.R | 39 CDM-6.0-101/CDM/R/gdina_proc_multiple_group_objects.R | 11 CDM-6.0-101/CDM/R/gdina_proc_noninvariance_multiple_groups.R | 1 CDM-6.0-101/CDM/R/gdina_proc_prior_distribution.R |only CDM-6.0-101/CDM/R/gdina_proc_prior_distribution_extend_normal.R |only CDM-6.0-101/CDM/R/gdina_proc_regularization.R |only CDM-6.0-101/CDM/R/gdina_proc_sequential_items.R | 1 CDM-6.0-101/CDM/R/gdina_proc_spec_rrum.R | 11 CDM-6.0-101/CDM/R/gdina_proc_split_item_response_patterns.R | 35 CDM-6.0-101/CDM/R/gdina_proc_uls_inverse_matrices.R | 1 CDM-6.0-101/CDM/R/gdina_progress_em_algorithm.R | 39 CDM-6.0-101/CDM/R/gdina_progress_start_estimation.R | 1 CDM-6.0-101/CDM/R/gdina_reduced_skillspace.R | 21 CDM-6.0-101/CDM/R/gdina_reduced_skillspace_multiple_groups.R |only CDM-6.0-101/CDM/R/gdina_reduced_skillspace_single_group.R |only CDM-6.0-101/CDM/R/gdina_se_itemwise.R | 15 CDM-6.0-101/CDM/R/gdina_standardize_weights.R | 1 CDM-6.0-101/CDM/R/gdm.R | 168 +- CDM-6.0-101/CDM/R/gdm_Qmatrix.R | 1 CDM-6.0-101/CDM/R/gdm_calc_counts.R | 13 CDM-6.0-101/CDM/R/gdm_calc_deviance.R | 7 CDM-6.0-101/CDM/R/gdm_calc_distributionmoments.R | 7 CDM-6.0-101/CDM/R/gdm_calc_ic.R | 33 CDM-6.0-101/CDM/R/gdm_calc_loglikelihood.R |only CDM-6.0-101/CDM/R/gdm_calc_post.R | 1 CDM-6.0-101/CDM/R/gdm_calc_posterior.R |only CDM-6.0-101/CDM/R/gdm_calc_prob.R | 1 CDM-6.0-101/CDM/R/gdm_collect_itempars.R | 1 CDM-6.0-101/CDM/R/gdm_constraints_itempars.R | 7 CDM-6.0-101/CDM/R/gdm_constraints_itempars2.R | 5 CDM-6.0-101/CDM/R/gdm_create_delta_designmatrix.R | 31 CDM-6.0-101/CDM/R/gdm_data_prep.R | 35 CDM-6.0-101/CDM/R/gdm_est_a.R | 52 CDM-6.0-101/CDM/R/gdm_est_a_cat.R | 20 CDM-6.0-101/CDM/R/gdm_est_a_centerslopes.R |only CDM-6.0-101/CDM/R/gdm_est_a_constraints.R |only CDM-6.0-101/CDM/R/gdm_est_b.R | 57 CDM-6.0-101/CDM/R/gdm_est_b_centerintercepts.R |only CDM-6.0-101/CDM/R/gdm_est_normalskills.R | 160 -- CDM-6.0-101/CDM/R/gdm_est_skillspace.R | 26 CDM-6.0-101/CDM/R/gdm_est_skillspace_traits.R | 29 CDM-6.0-101/CDM/R/gdm_inits_b.R |only CDM-6.0-101/CDM/R/gdm_numdiff_index.R | 38 CDM-6.0-101/CDM/R/gdm_person_parameters.R | 14 CDM-6.0-101/CDM/R/gdm_prep_calc_counts.R | 5 CDM-6.0-101/CDM/R/gdm_proc_response_indicators.R | 5 CDM-6.0-101/CDM/R/gdm_progress_em_algorithm.R | 16 CDM-6.0-101/CDM/R/gdm_thetadesign.R | 1 CDM-6.0-101/CDM/R/ideal.response.pattern.R | 27 CDM-6.0-101/CDM/R/item_by_group.R | 14 CDM-6.0-101/CDM/R/itemfit.rmsea.R | 75 CDM-6.0-101/CDM/R/itemfit.sx2.R | 138 - CDM-6.0-101/CDM/R/itemfit.sx2_aux.R | 1 CDM-6.0-101/CDM/R/itemfit_rmsea_helper.R |only CDM-6.0-101/CDM/R/jkestimates.R | 28 CDM-6.0-101/CDM/R/label_significance_level.R | 1 CDM-6.0-101/CDM/R/logLik_CDM.R | 82 - CDM-6.0-101/CDM/R/log_dgnorm.R |only CDM-6.0-101/CDM/R/logpars2rrumpars.R | 1 CDM-6.0-101/CDM/R/mcdina.R | 58 CDM-6.0-101/CDM/R/mcdina.est.item.R | 87 - CDM-6.0-101/CDM/R/mcdina.postproc.R | 57 CDM-6.0-101/CDM/R/mcdina.simul.R | 1 CDM-6.0-101/CDM/R/mcdina_alg_cppcall.R | 8 CDM-6.0-101/CDM/R/mcdina_prepare.R | 99 - CDM-6.0-101/CDM/R/modelfit.cor.R | 1 CDM-6.0-101/CDM/R/modelfit.cor.din.R | 52 CDM-6.0-101/CDM/R/modelfit.cor2.R | 1 CDM-6.0-101/CDM/R/numerical_Hessian.R | 35 CDM-6.0-101/CDM/R/numerical_Hessian_partial.R |only CDM-6.0-101/CDM/R/osink.R | 22 CDM-6.0-101/CDM/R/personfit.appropriateness.R | 1 CDM-6.0-101/CDM/R/plot.din.R | 1 CDM-6.0-101/CDM/R/plot.gdina.R | 1 CDM-6.0-101/CDM/R/plot.gdm.R | 1 CDM-6.0-101/CDM/R/plot.slca.R | 1 CDM-6.0-101/CDM/R/predict.CDM.R | 1 CDM-6.0-101/CDM/R/print.din.R | 1 CDM-6.0-101/CDM/R/print.gdina.R | 1 CDM-6.0-101/CDM/R/print.gdm.R | 1 CDM-6.0-101/CDM/R/print.mcdina.R | 1 CDM-6.0-101/CDM/R/print.slca.R | 1 CDM-6.0-101/CDM/R/print.summary.din.R | 1 CDM-6.0-101/CDM/R/reduced_skillspace_beta_2_probs.R |only CDM-6.0-101/CDM/R/reglca.R |only CDM-6.0-101/CDM/R/reglca_calc_counts.R |only CDM-6.0-101/CDM/R/reglca_calc_deviance.R |only CDM-6.0-101/CDM/R/reglca_calc_ic.R |only CDM-6.0-101/CDM/R/reglca_calc_individual_likelihood.R |only CDM-6.0-101/CDM/R/reglca_calc_individual_posterior.R |only CDM-6.0-101/CDM/R/reglca_calc_probs.R |only CDM-6.0-101/CDM/R/reglca_dpm_smoothing.R |only CDM-6.0-101/CDM/R/reglca_fit_probabilities.R |only CDM-6.0-101/CDM/R/reglca_fit_probabilities_fit_function.R |only CDM-6.0-101/CDM/R/reglca_freq_ll.R |only CDM-6.0-101/CDM/R/reglca_init_parameters.R |only CDM-6.0-101/CDM/R/reglca_init_parameters_class_probs.R |only CDM-6.0-101/CDM/R/reglca_init_parameters_item_probs.R |only CDM-6.0-101/CDM/R/reglca_monitor_random_starts.R |only CDM-6.0-101/CDM/R/reglca_mstep_item_parameters.R |only CDM-6.0-101/CDM/R/reglca_normalize_probabilities.R |only CDM-6.0-101/CDM/R/reglca_proc_data.R |only CDM-6.0-101/CDM/R/reglca_progress_em_algorithm.R |only CDM-6.0-101/CDM/R/reglca_scad_threshold.R |only CDM-6.0-101/CDM/R/reglca_update_parameter.R |only CDM-6.0-101/CDM/R/replace_NA.R | 1 CDM-6.0-101/CDM/R/rmsd_chisquare.R | 7 CDM-6.0-101/CDM/R/rowMaxs.R | 24 CDM-6.0-101/CDM/R/rowProds.R | 11 CDM-6.0-101/CDM/R/rrum.param.R | 11 CDM-6.0-101/CDM/R/rrumpars2logpars.R | 1 CDM-6.0-101/CDM/R/sequential.items.R | 5 CDM-6.0-101/CDM/R/sim.din.R | 1 CDM-6.0-101/CDM/R/sim.gdina.R | 1 CDM-6.0-101/CDM/R/skill.cor.R | 1 CDM-6.0-101/CDM/R/skillspace.approximation.R | 32 CDM-6.0-101/CDM/R/skillspace.hierarchy.R | 43 CDM-6.0-101/CDM/R/slca.R | 249 +-- CDM-6.0-101/CDM/R/slca_calc_class_probabilities.R | 5 CDM-6.0-101/CDM/R/slca_calc_counts.R | 13 CDM-6.0-101/CDM/R/slca_calc_ic.R | 20 CDM-6.0-101/CDM/R/slca_calc_likelihood.R | 5 CDM-6.0-101/CDM/R/slca_calc_loglikelihood.R | 7 CDM-6.0-101/CDM/R/slca_calc_posterior.R | 1 CDM-6.0-101/CDM/R/slca_calc_prob.R | 17 CDM-6.0-101/CDM/R/slca_calc_prob0.R | 1 CDM-6.0-101/CDM/R/slca_est_Xlambda.R | 49 CDM-6.0-101/CDM/R/slca_est_Xlambda_calc_deriv.R |only CDM-6.0-101/CDM/R/slca_est_Xlambda_calc_increment.R |only CDM-6.0-101/CDM/R/slca_est_skillspace.R | 22 CDM-6.0-101/CDM/R/slca_est_xlambda_constraint.R | 1 CDM-6.0-101/CDM/R/slca_inits_Xlambda.R | 18 CDM-6.0-101/CDM/R/slca_inits_skill_distribution.R | 1 CDM-6.0-101/CDM/R/slca_print_progress_em_algorithm.R | 23 CDM-6.0-101/CDM/R/slca_print_progress_end.R | 15 CDM-6.0-101/CDM/R/slca_proc_data.R |only CDM-6.0-101/CDM/R/slca_proc_design_matrix_xlambda.R |only CDM-6.0-101/CDM/R/slca_proc_multiple_groups.R |only CDM-6.0-101/CDM/R/slca_proc_regularization.R |only CDM-6.0-101/CDM/R/slca_set_seed.R | 1 CDM-6.0-101/CDM/R/solve_add_ridge.R | 1 CDM-6.0-101/CDM/R/summary.IRT.RMSD.R | 18 CDM-6.0-101/CDM/R/summary.IRT.RMSD_print_statistics.R | 1 CDM-6.0-101/CDM/R/summary.cdi.kli.R |only CDM-6.0-101/CDM/R/summary.din.R | 1 CDM-6.0-101/CDM/R/summary.gdina.R | 164 +- CDM-6.0-101/CDM/R/summary.gdina.dif.R | 1 CDM-6.0-101/CDM/R/summary.gdina.wald.R | 1 CDM-6.0-101/CDM/R/summary.gdm.R | 90 - CDM-6.0-101/CDM/R/summary.mcdina.R | 48 CDM-6.0-101/CDM/R/summary.reglca.R |only CDM-6.0-101/CDM/R/summary.slca.R | 46 CDM-6.0-101/CDM/R/summary_sink.R | 6 CDM-6.0-101/CDM/R/univar_table_statistics.R | 7 CDM-6.0-101/CDM/R/vcov.din.R | 46 CDM-6.0-101/CDM/R/vcov.loglike.din.R | 20 CDM-6.0-101/CDM/R/zzz.R | 36 CDM-6.0-101/CDM/README.md | 6 CDM-6.0-101/CDM/data/data.Students.rda |binary CDM-6.0-101/CDM/data/data.cdm01.rda |binary CDM-6.0-101/CDM/data/data.cdm02.rda |binary CDM-6.0-101/CDM/data/data.cdm03.rda |binary CDM-6.0-101/CDM/data/data.cdm04.rda |binary CDM-6.0-101/CDM/data/data.dcm.rda |binary CDM-6.0-101/CDM/data/data.dtmr.rda |binary CDM-6.0-101/CDM/data/data.ecpe.rda |binary CDM-6.0-101/CDM/data/data.fraction1.rda |binary CDM-6.0-101/CDM/data/data.fraction2.rda |binary CDM-6.0-101/CDM/data/data.fraction3.rda |only CDM-6.0-101/CDM/data/data.fraction4.rda |only CDM-6.0-101/CDM/data/data.fraction5.rda |only CDM-6.0-101/CDM/data/data.hr.rda |binary CDM-6.0-101/CDM/data/data.jang.rda |binary CDM-6.0-101/CDM/data/data.melab.rda |binary CDM-6.0-101/CDM/data/data.mg.rda |binary CDM-6.0-101/CDM/data/data.pgdina.rda |binary CDM-6.0-101/CDM/data/data.sda6.rda |binary CDM-6.0-101/CDM/data/data.timss03.G8.su.rda |binary CDM-6.0-101/CDM/data/data.timss07.G4.lee.rda |binary CDM-6.0-101/CDM/data/data.timss11.G4.AUT.part.rda |binary CDM-6.0-101/CDM/data/data.timss11.G4.AUT.rda |binary CDM-6.0-101/CDM/data/datalist | 3 CDM-6.0-101/CDM/data/fraction.subtraction.data.rda |binary CDM-6.0-101/CDM/data/fraction.subtraction.qmatrix.rda |binary CDM-6.0-101/CDM/data/sim.dina.rda |binary CDM-6.0-101/CDM/data/sim.dino.rda |binary CDM-6.0-101/CDM/data/sim.qmatrix.rda |binary CDM-6.0-101/CDM/inst/NEWS | 44 CDM-6.0-101/CDM/man/CDM-package.Rd | 39 CDM-6.0-101/CDM/man/CDM-utilities.Rd | 89 + CDM-6.0-101/CDM/man/Data-sim.Rd | 1 CDM-6.0-101/CDM/man/IRT.IC.Rd | 9 CDM-6.0-101/CDM/man/IRT.RMSD.Rd | 3 CDM-6.0-101/CDM/man/IRT.anova.Rd | 1 CDM-6.0-101/CDM/man/IRT.compareModels.Rd | 10 CDM-6.0-101/CDM/man/IRT.data.Rd | 28 CDM-6.0-101/CDM/man/IRT.expectedCounts.Rd | 23 CDM-6.0-101/CDM/man/IRT.factor.scores.Rd | 18 CDM-6.0-101/CDM/man/IRT.frequencies.Rd | 17 CDM-6.0-101/CDM/man/IRT.irfprob.Rd | 21 CDM-6.0-101/CDM/man/IRT.irfprobPlot.Rd | 15 CDM-6.0-101/CDM/man/IRT.itemfit.Rd | 14 CDM-6.0-101/CDM/man/IRT.jackknife.Rd | 12 CDM-6.0-101/CDM/man/IRT.likelihood.Rd | 23 CDM-6.0-101/CDM/man/IRT.modelfit.Rd | 12 CDM-6.0-101/CDM/man/IRT.parameterTable.Rd | 1 CDM-6.0-101/CDM/man/IRT.repDesign.Rd | 16 CDM-6.0-101/CDM/man/WaldTest.Rd | 1 CDM-6.0-101/CDM/man/abs_approx.Rd | 11 CDM-6.0-101/CDM/man/anova.din.Rd | 10 CDM-6.0-101/CDM/man/cdi.kli.Rd | 11 CDM-6.0-101/CDM/man/cdm.est.class.accuracy.Rd | 6 CDM-6.0-101/CDM/man/coef.Rd | 17 CDM-6.0-101/CDM/man/data.Students.Rd | 5 CDM-6.0-101/CDM/man/data.cdm.Rd | 6 CDM-6.0-101/CDM/man/data.dcm.Rd | 30 CDM-6.0-101/CDM/man/data.dtmr.Rd | 6 CDM-6.0-101/CDM/man/data.ecpe.Rd | 34 CDM-6.0-101/CDM/man/data.fraction.Rd |only CDM-6.0-101/CDM/man/data.hr.Rd | 17 CDM-6.0-101/CDM/man/data.jang.Rd | 12 CDM-6.0-101/CDM/man/data.melab.Rd | 6 CDM-6.0-101/CDM/man/data.mg.Rd | 7 CDM-6.0-101/CDM/man/data.pgdina.Rd | 1 CDM-6.0-101/CDM/man/data.sda6.Rd | 6 CDM-6.0-101/CDM/man/data.timss03.G8.su.Rd | 6 CDM-6.0-101/CDM/man/data.timss07.G4.lee.Rd | 7 CDM-6.0-101/CDM/man/data.timss11.G4.AUT.Rd | 1 CDM-6.0-101/CDM/man/deltaMethod.Rd | 1 CDM-6.0-101/CDM/man/din.Rd | 8 CDM-6.0-101/CDM/man/din.deterministic.Rd | 8 CDM-6.0-101/CDM/man/din.equivalent.class.Rd | 12 CDM-6.0-101/CDM/man/din.validate.qmatrix.Rd | 7 CDM-6.0-101/CDM/man/entropy.lca.Rd | 23 CDM-6.0-101/CDM/man/equivalent.dina.Rd | 22 CDM-6.0-101/CDM/man/fraction.subtraction.data.Rd | 1 CDM-6.0-101/CDM/man/fraction.subtraction.qmatrix.Rd | 1 CDM-6.0-101/CDM/man/gdd.Rd | 11 CDM-6.0-101/CDM/man/gdina.Rd | 245 ++- CDM-6.0-101/CDM/man/gdina.dif.Rd | 11 CDM-6.0-101/CDM/man/gdina.wald.Rd | 8 CDM-6.0-101/CDM/man/gdm.Rd | 61 CDM-6.0-101/CDM/man/ideal.response.pattern.Rd | 5 CDM-6.0-101/CDM/man/item_by_group.Rd | 9 CDM-6.0-101/CDM/man/itemfit.rmsea.Rd | 1 CDM-6.0-101/CDM/man/itemfit.sx2.Rd | 23 CDM-6.0-101/CDM/man/logLik.Rd | 17 CDM-6.0-101/CDM/man/mcdina.Rd | 24 CDM-6.0-101/CDM/man/modelfit.cor.Rd | 20 CDM-6.0-101/CDM/man/numerical_Hessian.Rd | 24 CDM-6.0-101/CDM/man/osink.Rd | 1 CDM-6.0-101/CDM/man/personfit.appropriateness.Rd | 14 CDM-6.0-101/CDM/man/plot.din.Rd | 6 CDM-6.0-101/CDM/man/predict.Rd | 18 CDM-6.0-101/CDM/man/print.summary.din.Rd | 11 CDM-6.0-101/CDM/man/reglca.Rd |only CDM-6.0-101/CDM/man/sequential.items.Rd | 7 CDM-6.0-101/CDM/man/sim.din.Rd | 22 CDM-6.0-101/CDM/man/sim.gdina.Rd | 18 CDM-6.0-101/CDM/man/skill.cor.Rd | 10 CDM-6.0-101/CDM/man/skillspace.approximation.Rd | 5 CDM-6.0-101/CDM/man/skillspace.hierarchy.Rd | 1 CDM-6.0-101/CDM/man/slca.Rd | 141 + CDM-6.0-101/CDM/man/summary.din.Rd | 7 CDM-6.0-101/CDM/man/summary_sink.Rd | 1 CDM-6.0-101/CDM/man/vcov.Rd | 17 CDM-6.0-101/CDM/src/RcppExports.cpp | 1 CDM-6.0-101/CDM/src/calc_posterior.c | 83 - CDM-6.0-101/CDM/src/cdm_kli_id_c.cpp | 172 -- CDM-6.0-101/CDM/src/din.deterministic.devcrit_c.cpp | 215 +- CDM-6.0-101/CDM/src/gdd_c.cpp | 143 - CDM-6.0-101/CDM/src/init.c | 1 CDM-6.0-101/CDM/src/irt_predict_c.cpp | 116 - CDM-6.0-101/CDM/src/itemfit_sx2_calc_scoredistribution_cdm.cpp | 61 CDM-6.0-101/CDM/src/modelfit_cor2_c.cpp | 172 +- CDM-6.0-101/CDM/src/probs_multcat_items_counts_c.cpp | 180 +- CDM-6.0-101/CDM/src/slca_cfunctions.cpp | 346 ++-- 450 files changed, 5341 insertions(+), 4687 deletions(-)
Title: Management and Exploratory Analysis of Spatial Data in Landscape
Genetics
Description: Management and exploratory analysis of spatial data in landscape genetics. Easy integration of information from multiple sources with "ecogen" objects.
Author: Leandro Roser [aut, cre],
Juan Vilardi [aut],
Beatriz Saidman [aut],
Laura Ferreyra [aut]
Maintainer: Leandro Roser <learoser@gmail.com>
Diff between EcoGenetics versions 1.2.1-1 dated 2017-11-14 and 1.2.1-2 dated 2017-11-21
DESCRIPTION | 8 - MD5 | 48 +++++----- NAMESPACE | 16 --- NEWS | 8 + R/ZZZ.R | 9 +- R/auxiliar.R | 21 ++++ R/control.R | 40 ++++++++ R/eco.format.R | 117 +++++++++++++++++++------- R/ecogen.3OF6.basic.methods.R | 12 -- R/ecogen.4OF6.brackets.R | 11 -- R/ecogen.6OF6.converters.R | 187 ++++++++++++++++++++++++++++++++++-------- R/int.convert.R | 4 R/plot.methods.R | 1 R/roxygen.auxiliar.R | 3 R/show_summary.methods.R | 3 README.md | 24 ++++- inst/CITATION |only man/EcoGenetics-package.Rd | 79 +---------------- man/eco.format.Rd | 31 ++++++ man/ecogen2geneland.Rd | 25 +++++ man/ecogen2genepop.Rd | 20 ++++ man/ecogen2gstudio.Rd | 2 man/ecogen2hierfstat.Rd | 29 +++++- man/ecogen2spagedi.Rd | 32 ++++++- man/ecogenetics_devel.Rd |only man/ecogenetics_tutorial.Rd |only man/int.check.to_numeric.Rd |only 27 files changed, 506 insertions(+), 224 deletions(-)