Title: 'Jupyter' Display Machinery
Description: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>.
Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRdisplay versions 0.7.0 dated 2018-11-29 and 1.0 dated 2021-01-20
IRdisplay-0.7.0/IRdisplay/man/display_-less-than-image-greater-than.Rd |only IRdisplay-0.7.0/IRdisplay/man/display_-less-than-text-greater-than.Rd |only IRdisplay-1.0/IRdisplay/DESCRIPTION | 10 ++- IRdisplay-1.0/IRdisplay/MD5 | 26 +++++----- IRdisplay-1.0/IRdisplay/NAMESPACE | 2 IRdisplay-1.0/IRdisplay/R/display.r | 2 IRdisplay-1.0/IRdisplay/R/display_images.r | 20 ++++--- IRdisplay-1.0/IRdisplay/R/display_textual.r | 15 +++-- IRdisplay-1.0/IRdisplay/R/options.r | 3 - IRdisplay-1.0/IRdisplay/R/utils.r | 6 +- IRdisplay-1.0/IRdisplay/README.md | 4 - IRdisplay-1.0/IRdisplay/man/IRdisplay-options.Rd | 8 +-- IRdisplay-1.0/IRdisplay/man/display-images.Rd |only IRdisplay-1.0/IRdisplay/man/display-textual.Rd |only IRdisplay-1.0/IRdisplay/man/display.Rd | 17 ++++-- IRdisplay-1.0/IRdisplay/tests/testthat/test_display_functions_images.r | 4 - 16 files changed, 71 insertions(+), 46 deletions(-)
Title: Methods for Nonparametric Changepoint Detection
Description: Implements the multiple changepoint algorithm PELT with a nonparametric cost function based on the empirical distribution of the data. This package extends the changepoint package (see Killick, R and Eckley, I (2014) <doi:10.18637/jss.v058.i03> ).
Author: Kaylea Haynes [aut],
Rebecca Killick [aut],
Paul Fearnhead [ths, ctb],
Idris Eckley [ths],
Daniel Grose [ctb, cre]
Maintainer: Daniel Grose <changepoints@lancaster.ac.uk>
Diff between changepoint.np versions 1.0.2 dated 2020-05-15 and 1.0.3 dated 2021-01-20
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/CROPS.R | 4 ++-- R/cpt.R | 5 +++-- R/range_of_penalties.R | 16 +++++++++++----- build/partial.rdb |binary man/HeartRate.Rd | 4 +++- man/cpt.np.Rd | 5 ++++- 8 files changed, 35 insertions(+), 23 deletions(-)
More information about changepoint.np at CRAN
Permanent link
Title: Find Free Versions of Scholarly Publications via Unpaywall
Description: This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly
oaDOI, a service finding free full-texts of academic papers by linking DOIs with
open access journals and repositories. It provides unified access to various data sources
for open access full-text links including Crossref and the Directory of Open Access
Journals (DOAJ). API usage is free and no registration is required.
Author: Najko Jahn [aut, cre],
Tuija Sonkkila [rev] (Tuija Sonkkila reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-6892-9305>),
Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-3520-2046>),
Anne Hobert [ctb] (<https://orcid.org/0000-0003-2429-2995>),
Delwen Franzen [ctb]
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between roadoi versions 0.6 dated 2019-09-15 and 0.7 dated 2021-01-20
roadoi-0.6/roadoi/inst/img |only roadoi-0.7/roadoi/DESCRIPTION | 23 - roadoi-0.7/roadoi/MD5 | 34 - roadoi-0.7/roadoi/NAMESPACE | 1 roadoi-0.7/roadoi/NEWS | 13 roadoi-0.7/roadoi/R/oadoi_fetch.r | 116 ++++- roadoi-0.7/roadoi/R/roadoi-package.r | 26 - roadoi-0.7/roadoi/R/utils.r | 4 roadoi-0.7/roadoi/README.md | 298 +++++++-------- roadoi-0.7/roadoi/build/vignette.rds |binary roadoi-0.7/roadoi/inst/doc/intro.R | 78 +--- roadoi-0.7/roadoi/inst/doc/intro.Rmd | 129 ++---- roadoi-0.7/roadoi/inst/doc/intro.html | 388 +++++++++----------- roadoi-0.7/roadoi/man/figures |only roadoi-0.7/roadoi/man/oadoi_fetch.Rd | 90 +++- roadoi-0.7/roadoi/man/oadoi_fetch_.Rd | 16 roadoi-0.7/roadoi/man/roadoi-package.Rd | 26 - roadoi-0.7/roadoi/tests/testthat/test_oadoi_fetch.r | 38 + roadoi-0.7/roadoi/vignettes/intro.Rmd | 129 ++---- 19 files changed, 706 insertions(+), 703 deletions(-)
Title: Interface to the 'Orcid.org' API
Description: Client for the 'Orcid.org' API (<https://orcid.org/>).
Functions included for searching for people, searching by 'DOI',
and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rorcid versions 0.6.4 dated 2020-02-06 and 0.7.0 dated 2021-01-20
rorcid-0.6.4/rorcid/README.md |only rorcid-0.6.4/rorcid/build |only rorcid-0.6.4/rorcid/inst/doc |only rorcid-0.6.4/rorcid/inst/vign |only rorcid-0.6.4/rorcid/vignettes |only rorcid-0.7.0/rorcid/DESCRIPTION | 13 ++--- rorcid-0.7.0/rorcid/LICENSE | 2 rorcid-0.7.0/rorcid/MD5 | 27 ++++-------- rorcid-0.7.0/rorcid/NEWS.md | 13 ++++- rorcid-0.7.0/rorcid/R/auth.R | 71 ++++++++++++++++++++++---------- rorcid-0.7.0/rorcid/R/orcid.r | 24 ++++------ rorcid-0.7.0/rorcid/R/orcid_search.R | 13 ++++- rorcid-0.7.0/rorcid/R/zzz.R | 5 +- rorcid-0.7.0/rorcid/man/orcid.Rd | 24 ++++------ rorcid-0.7.0/rorcid/man/orcid_auth.Rd | 61 ++++++++++++++++++--------- rorcid-0.7.0/rorcid/man/orcid_search.Rd | 11 ++++ 16 files changed, 161 insertions(+), 103 deletions(-)
Title: Computing Individual Components of the Gini and the Theil
Indices
Description: Computes individual contributions to the overall Gini and
Theil's T and Theil's L measures and their decompositions by groups
such as race, gender, national origin, with the three functions of
iGini(), iTheiT(), and iTheilL(). For details, see Tim F. Liao (2019)
<doi:10.1177/0049124119875961>.
Author: Tim Liao
Maintainer: Tim Liao <tfliao@illinois.edu>
Diff between iIneq versions 1.0.1 dated 2020-03-20 and 1.0.2 dated 2021-01-20
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/iGini.R | 4 ++-- R/iTheilL.R | 4 ++-- R/iTheilT.R | 4 ++-- man/iGini.Rd | 2 +- man/iTheilL.Rd | 2 +- man/iTheilT.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: An Implementation of the TSIR Model
Description: An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <doi:10.1371/journal.pone.0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <doi:10.1111/1467-9876.00187>.
Author: Alexander D. Becker [aut, cre],
Sinead E. Morris [ctb],
Ottar N. Bjornstad [ctb]
Maintainer: Alexander D. Becker <adbecker@princeton.edu>
Diff between tsiR versions 0.4.2 dated 2019-07-09 and 0.4.3 dated 2021-01-20
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- R/estpars_function.R | 11 +++++++---- R/globals.R | 2 +- R/plotres_function.R | 8 ++++---- R/runtsir_function.R | 5 ++++- R/simulatetsir_function.R | 11 ++++------- R/subplots_functions.R | 10 +++++++--- README.md | 3 +++ man/estpars.Rd | 18 ++++++++++++++---- man/maxthreshold.Rd | 14 +++++++++++--- man/mcmcestpars.Rd | 22 +++++++++++++++++----- man/mcmctsir.Rd | 32 +++++++++++++++++++++++++------- man/runtsir.Rd | 31 ++++++++++++++++++++++++------- man/simulatetsir.Rd | 17 +++++++++++++---- 15 files changed, 154 insertions(+), 70 deletions(-)
Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.2.3 dated 2019-03-22 and 0.2.4 dated 2021-01-20
DESCRIPTION | 8 MD5 | 72 +- NAMESPACE | 1 R/lib_kl.R |only R/lib_mixkl.R |only R/zooroh.R | 1492 +++++++++++++++++++++++++------------------ R/zooroh_accessor.R | 584 +++++++++------- R/zooroh_model.R | 319 ++++----- R/zplot_vertical.R | 460 ++++++------- build/vignette.rds |binary inst/doc/zooroh-vignette.R | 630 +++++++++--------- inst/doc/zooroh-vignette.pdf |binary man/BBB_NMP_GP_subset.Rd | 6 man/BBB_NMP_ad_subset.Rd | 6 man/BBB_NMP_pl_subset.Rd | 6 man/BBB_PE_gt_subset.Rd | 6 man/BBB_samples.Rd | 6 man/RZooRoH.Rd | 1 man/genoex.Rd | 6 man/genosim.Rd | 6 man/probhbd.Rd | 11 man/rara_mix10r.Rd | 4 man/rohbd.Rd | 10 man/soay_mix10r.Rd | 4 man/typs.Rd | 6 man/typsfrq.Rd | 6 man/wilt_mix10r.Rd | 4 man/zoodata.Rd | 12 man/zoomodel.Rd | 49 - man/zooplot_hbdseg.Rd | 15 man/zooplot_individuals.Rd | 3 man/zooplot_partitioning.Rd | 16 man/zooplot_prophbd.Rd | 3 man/zoorun.Rd | 17 man/zoosimd.Rd |only src/RZooRoH_init.c | 12 src/zooSIM.f90 |only src/zoolayerEM.f90 |only src/zoolayerFB.f90 |only src/zoolayerViterbi.f90 |only src/zoolayerlik.f90 |only 41 files changed, 2113 insertions(+), 1668 deletions(-)
Title: Fitting Nonlinear Models with Scale Mixture of Skew-Normal
Distributions
Description: Fit univariate non-linear scale mixture of skew-normal(NL-SMSN) regression, details in Garay, Lachos and Abanto-Valle (2011) <doi:10.1016/j.jkss.2010.08.003> and Lachos, Bandyopadhyay and Garay (2011) <doi:10.1016/j.spl.2011.03.019>.
Author: Marcos Prates [aut, cre, trl],
Victor Lachos [aut],
Aldo Garay [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between nlsmsn versions 0.0-5 dated 2019-11-14 and 0.0-6 dated 2021-01-20
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 4 ++-- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Basic R Input Output
Description: Functions to handle basic input output, these functions always
read and write UTF-8 (8-bit Unicode Transformation Format) files and provide
more explicit control over line endings.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between brio versions 1.1.0 dated 2020-08-31 and 1.1.1 dated 2021-01-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/write_file.R | 4 ++-- man/write_file.Rd | 5 +++-- src/file_line_endings.c | 4 ++-- 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Luca Rossi (API design), Obaida Hanteer (mdlpa, flat_ec, flat_nw, some community eval. functions), Davide Vega (API and code design), Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from these libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 3.3.1 dated 2020-06-02 and 3.3.2 dated 2021-01-20
multinet-3.3.1/multinet/src/src/community/VertexCommunity.hpp |only multinet-3.3.1/multinet/src/src/community/VertexLayerCommunity.hpp |only multinet-3.3.1/multinet/src/src/core/olap/datastructures/CCube.hpp |only multinet-3.3.1/multinet/src/src/networks/_impl/olap |only multinet-3.3.2/multinet/DESCRIPTION | 12 multinet-3.3.2/multinet/MD5 | 268 +++++----- multinet-3.3.2/multinet/NEWS | 11 multinet-3.3.2/multinet/man/Communities.Rd | 44 + multinet-3.3.2/multinet/man/CommunityGeneration.Rd |only multinet-3.3.2/multinet/man/Generation.Rd | 4 multinet-3.3.2/multinet/src/Makevars | 4 multinet-3.3.2/multinet/src/Makevars.win | 4 multinet-3.3.2/multinet/src/eclat/eclat/src/eclat.c | 14 multinet-3.3.2/multinet/src/eclat/eclat/src/eclat.h | 1 multinet-3.3.2/multinet/src/eclat/tract/src/report.c | 4 multinet-3.3.2/multinet/src/r_functions.cpp | 163 +++++- multinet-3.3.2/multinet/src/r_functions.h | 55 +- multinet-3.3.2/multinet/src/rcpp_module_definition.cpp | 56 +- multinet-3.3.2/multinet/src/rcpp_utils.cpp | 18 multinet-3.3.2/multinet/src/rcpp_utils.h | 14 multinet-3.3.2/multinet/src/src/CMakeLists.txt |only multinet-3.3.2/multinet/src/src/algorithms/BFS.hpp | 79 ++ multinet-3.3.2/multinet/src/src/algorithms/BFS.ipp | 101 +++ multinet-3.3.2/multinet/src/src/algorithms/DFS.hpp | 78 ++ multinet-3.3.2/multinet/src/src/algorithms/DFS.ipp | 105 +++ multinet-3.3.2/multinet/src/src/algorithms/components.ipp | 3 multinet-3.3.2/multinet/src/src/algorithms/sssp.ipp | 4 multinet-3.3.2/multinet/src/src/community/Community.hpp | 4 multinet-3.3.2/multinet/src/src/community/CommunityStructure.hpp | 7 multinet-3.3.2/multinet/src/src/community/MLCPMCommunity.hpp | 24 multinet-3.3.2/multinet/src/src/community/PillarCommunity.hpp | 83 +-- multinet-3.3.2/multinet/src/src/community/_impl/abacus_utils.hpp | 20 multinet-3.3.2/multinet/src/src/community/_impl/abacus_utils.ipp | 112 +++- multinet-3.3.2/multinet/src/src/community/_impl/common.hpp | 26 multinet-3.3.2/multinet/src/src/community/_impl/cutils.cpp | 12 multinet-3.3.2/multinet/src/src/community/_impl/cutils.hpp | 44 - multinet-3.3.2/multinet/src/src/community/_impl/glouvain2_utils.cpp | 106 +-- multinet-3.3.2/multinet/src/src/community/_impl/glouvain2_utils.hpp | 12 multinet-3.3.2/multinet/src/src/community/_impl/infomap_utils.hpp | 47 - multinet-3.3.2/multinet/src/src/community/_impl/louvain_utils.cpp | 14 multinet-3.3.2/multinet/src/src/community/_impl/louvain_utils.hpp | 10 multinet-3.3.2/multinet/src/src/community/abacus.hpp | 15 multinet-3.3.2/multinet/src/src/community/abacus.ipp | 25 multinet-3.3.2/multinet/src/src/community/community_stats.hpp |only multinet-3.3.2/multinet/src/src/community/community_stats.ipp |only multinet-3.3.2/multinet/src/src/community/flat.hpp |only multinet-3.3.2/multinet/src/src/community/flat.ipp |only multinet-3.3.2/multinet/src/src/community/glouvain.hpp | 15 multinet-3.3.2/multinet/src/src/community/glouvain.ipp | 30 - multinet-3.3.2/multinet/src/src/community/glouvain2.hpp | 11 multinet-3.3.2/multinet/src/src/community/glouvain2.ipp | 15 multinet-3.3.2/multinet/src/src/community/infomap.hpp | 13 multinet-3.3.2/multinet/src/src/community/infomap.ipp | 12 multinet-3.3.2/multinet/src/src/community/label_propagation.hpp | 8 multinet-3.3.2/multinet/src/src/community/label_propagation.ipp | 8 multinet-3.3.2/multinet/src/src/community/louvain.hpp | 10 multinet-3.3.2/multinet/src/src/community/louvain.ipp | 8 multinet-3.3.2/multinet/src/src/community/ml-cpm.hpp | 12 multinet-3.3.2/multinet/src/src/community/ml-cpm.ipp | 16 multinet-3.3.2/multinet/src/src/community/mlp.hpp |only multinet-3.3.2/multinet/src/src/community/modularity.hpp | 26 multinet-3.3.2/multinet/src/src/community/omega_index.hpp |only multinet-3.3.2/multinet/src/src/config.hpp.in |only multinet-3.3.2/multinet/src/src/core/attributes/AttributeValueMap.hpp | 3 multinet-3.3.2/multinet/src/src/core/attributes/MainMemoryAttributeValueMap.hpp | 3 multinet-3.3.2/multinet/src/src/core/datastructures/containers/PtrSortedRandomSet.hpp | 1 multinet-3.3.2/multinet/src/src/core/datastructures/containers/SortedRandomSet.hpp | 47 + multinet-3.3.2/multinet/src/src/core/datastructures/observers/ObserverStore.hpp | 6 multinet-3.3.2/multinet/src/src/core/datastructures/observers/UnionObserver.hpp |only multinet-3.3.2/multinet/src/src/core/olap/datastructures/Cube.hpp | 1 multinet-3.3.2/multinet/src/src/core/olap/datastructures/NCube.hpp | 17 multinet-3.3.2/multinet/src/src/core/olap/operators/rollup.hpp |only multinet-3.3.2/multinet/src/src/core/olap/operators/slice.hpp | 89 --- multinet-3.3.2/multinet/src/src/core/olap/operators/slice.ipp |only multinet-3.3.2/multinet/src/src/core/olap/selection/All.cpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/All.hpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/EntryIterator.hpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/IndexIterator.cpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/IndexIterator.hpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Indexes.cpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Indexes.hpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Range.cpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Range.hpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Set.cpp | 2 multinet-3.3.2/multinet/src/src/core/olap/selection/Set.hpp | 2 multinet-3.3.2/multinet/src/src/core/stores/ObjectStore.hpp | 3 multinet-3.3.2/multinet/src/src/core/stores/UnionObjectStore.hpp |only multinet-3.3.2/multinet/src/src/core/utils/vector.cpp |only multinet-3.3.2/multinet/src/src/core/utils/vector.hpp |only multinet-3.3.2/multinet/src/src/core/utils/vector.ipp |only multinet-3.3.2/multinet/src/src/generation/communities.cpp |only multinet-3.3.2/multinet/src/src/generation/communities.hpp |only multinet-3.3.2/multinet/src/src/generation/sample.hpp |only multinet-3.3.2/multinet/src/src/generation/standard_graphs.cpp | 61 ++ multinet-3.3.2/multinet/src/src/generation/standard_graphs.hpp | 21 multinet-3.3.2/multinet/src/src/io/_impl/MultilayerIOFileSection.hpp | 2 multinet-3.3.2/multinet/src/src/io/_impl/read_common.cpp | 5 multinet-3.3.2/multinet/src/src/io/_impl/read_ml_common.cpp | 15 multinet-3.3.2/multinet/src/src/io/_impl/read_ml_common.hpp | 19 multinet-3.3.2/multinet/src/src/io/read_multilayer_communities.hpp |only multinet-3.3.2/multinet/src/src/io/read_multilayer_communities.ipp |only multinet-3.3.2/multinet/src/src/io/read_multilayer_network.cpp | 1 multinet-3.3.2/multinet/src/src/io/write_multilayer_communities.hpp |only multinet-3.3.2/multinet/src/src/io/write_multilayer_communities.ipp |only multinet-3.3.2/multinet/src/src/io/write_multilayer_network.cpp |only multinet-3.3.2/multinet/src/src/io/write_multilayer_network.hpp | 12 multinet-3.3.2/multinet/src/src/io/write_multilayer_network.ipp | 2 multinet-3.3.2/multinet/src/src/networks/MultiNetwork.hpp | 3 multinet-3.3.2/multinet/src/src/networks/MultilayerNetwork.hpp | 2 multinet-3.3.2/multinet/src/src/networks/Network.hpp | 7 multinet-3.3.2/multinet/src/src/networks/OrderedMultiplexNetwork.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/Graph.hpp | 4 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrMultiEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrSimpleEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrVertexStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttributedDynamicInterlayerSimpleEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/DynamicInterlayerSimpleEdgeStore.hpp | 5 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MDEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MDSimpleEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MultiEdgeStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/SimpleEdgeStore.hpp | 3 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexOverlappingLayerStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexOverlappingOrderedLayerStore.hpp | 2 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexStore.hpp | 17 multinet-3.3.2/multinet/src/src/objects/MLVertex.hpp |only multinet-3.3.2/multinet/src/src/olap |only multinet-3.3.2/multinet/src/src/operations/_impl/add_predefined_subgraphs.ipp | 5 multinet-3.3.2/multinet/src/src/operations/flatten.ipp | 24 multinet-3.3.2/multinet/src/src/operations/union.ipp | 14 multinet-3.3.2/multinet/src/src/utils/summary.ipp | 2 130 files changed, 1507 insertions(+), 716 deletions(-)
Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing the landscape of a tree space, and for
calculating the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 1.2.1 dated 2020-09-17 and 2.0.0 dated 2021-01-20
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TreeDist-2.0.0/TreeDist/man/TreeDistance.Rd | 37 TreeDist-2.0.0/TreeDist/man/VisualizeMatching.Rd | 8 TreeDist-2.0.0/TreeDist/man/figures |only TreeDist-2.0.0/TreeDist/man/median.multiPhylo.Rd | 7 TreeDist-2.0.0/TreeDist/src/RcppExports.cpp | 60 + TreeDist-2.0.0/TreeDist/src/day_1985.cpp |only TreeDist-2.0.0/TreeDist/src/ints.h | 3 TreeDist-2.0.0/TreeDist/src/nni_distance.cpp | 2 TreeDist-2.0.0/TreeDist/src/tree_distance_functions.cpp | 6 TreeDist-2.0.0/TreeDist/src/tree_distances.cpp | 170 +++- TreeDist-2.0.0/TreeDist/src/tree_distances.h | 1 TreeDist-2.0.0/TreeDist/tests/figs/deps.txt | 2 TreeDist-2.0.0/TreeDist/tests/figs/plot-r/jrf-vm-matchzeros-false.svg |only TreeDist-2.0.0/TreeDist/tests/figs/plot-r/rf-collapse-a-node.svg |only TreeDist-2.0.0/TreeDist/tests/figs/plot-r/rf-collapse-and-change.svg |only TreeDist-2.0.0/TreeDist/tests/figs/plot-r/rf-vm-single-splits-plainedges.svg |only TreeDist-2.0.0/TreeDist/tests/figs/plot-r/visualize-mci-matching.svg |only TreeDist-2.0.0/TreeDist/tests/testthat/test-ClusterTable.R |only TreeDist-2.0.0/TreeDist/tests/testthat/test-day_1985.cpp.r |only TreeDist-2.0.0/TreeDist/tests/testthat/test-plot.R | 44 - TreeDist-2.0.0/TreeDist/tests/testthat/test-tree_distance.R | 20 TreeDist-2.0.0/TreeDist/tests/testthat/test-tree_distance_utilities.R | 10 TreeDist-2.0.0/TreeDist/vignettes/CID_talk.png |only TreeDist-2.0.0/TreeDist/vignettes/Generalized-RF.Rmd | 20 TreeDist-2.0.0/TreeDist/vignettes/Robinson-Foulds.Rmd | 30 TreeDist-2.0.0/TreeDist/vignettes/Using-TreeDist.Rmd | 7 TreeDist-2.0.0/TreeDist/vignettes/information.Rmd | 107 ++ TreeDist-2.0.0/TreeDist/vignettes/treespace.Rmd |only TreeDist-2.0.0/TreeDist/vignettes/using-distances.Rmd | 7 94 files changed, 1845 insertions(+), 1071 deletions(-)
Title: Simulation of Pleiotropic, Linked and Epistatic Phenotypes
Description: The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.
Author: Samuel Fernandes [aut, cre] (<https://orcid.org/0000-0001-8269-535X>),
Alexander Lipka [aut] (<https://orcid.org/0000-0003-1571-8528>)
Maintainer: Samuel Fernandes <samuelf@illinois.edu>
Diff between simplePHENOTYPES versions 1.2.4 dated 2020-05-06 and 1.3.0 dated 2021-01-20
simplePHENOTYPES-1.2.4/simplePHENOTYPES/R/QTN_linkage.R |only simplePHENOTYPES-1.2.4/simplePHENOTYPES/R/QTN_partially_pleiotropic.R |only simplePHENOTYPES-1.2.4/simplePHENOTYPES/R/QTN_pleiotropic.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/DESCRIPTION | 14 simplePHENOTYPES-1.3.0/simplePHENOTYPES/MD5 | 67 - simplePHENOTYPES-1.3.0/simplePHENOTYPES/NAMESPACE | 2 simplePHENOTYPES-1.3.0/simplePHENOTYPES/NEWS.md | 62 + simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/base_line_multi_traits.R | 39 simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/base_line_single_trait.R | 4 simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/create_phenotypes.R | 406 +++++++--- simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/file_loader.R | 40 simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/genetic_effect.R | 23 simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/genotypes.R | 10 simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/make_pd.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/phenotypes.R | 339 +++++--- simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_from_user.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_linkage.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_partially_pleiotropic.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_pleiotropic.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/zzz.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/README.md | 171 ++-- simplePHENOTYPES-1.3.0/simplePHENOTYPES/build/partial.rdb |binary simplePHENOTYPES-1.3.0/simplePHENOTYPES/build/vignette.rds |binary simplePHENOTYPES-1.3.0/simplePHENOTYPES/inst/CITATION |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/inst/doc/simplePHENOTYPES.R | 33 simplePHENOTYPES-1.3.0/simplePHENOTYPES/inst/doc/simplePHENOTYPES.Rmd | 44 - simplePHENOTYPES-1.3.0/simplePHENOTYPES/inst/doc/simplePHENOTYPES.html | 307 +------ simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/base_line_multi_traits.Rd | 3 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/base_line_single_trait.Rd | 3 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/create_phenotypes.Rd | 67 + simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/file_loader.Rd | 5 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/genetic_effect.Rd | 3 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/genotypes.Rd | 5 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/make_pd.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/phenotypes.Rd | 4 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_from_user.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_linkage.Rd | 12 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_partially_pleiotropic.Rd | 8 simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_pleiotropic.Rd | 8 simplePHENOTYPES-1.3.0/simplePHENOTYPES/vignettes/Supplementary.pdf |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/vignettes/simplePHENOTYPES.Rmd | 44 - 41 files changed, 1087 insertions(+), 636 deletions(-)
More information about simplePHENOTYPES at CRAN
Permanent link
Title: Stratified and Personalised Models Based on Model-Based Trees
and Forests
Description: Model-based trees for subgroup analyses in clinical trials and
model-based forests for the estimation and prediction of personalised
treatment effects (personalised models). Currently partitioning of linear
models, lm(), generalised linear models, glm(), and Weibull models,
survreg(), is supported. Advanced plotting functionality is supported for
the trees and a test for parameter heterogeneity is provided for the
personalised models. For details on model-based trees for subgroup analyses
see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for
details on model-based forests for estimation of individual treatment effects
see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre],
Achim Zeileis [aut],
Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>
Diff between model4you versions 0.9-6 dated 2020-11-25 and 0.9-7 dated 2021-01-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/pmodel.R | 2 +- inst/NEWS.Rd | 7 +++++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'.
Provides 'ggplot2' themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata',
'Excel', and 'The Wall Street Journal', among others.
Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre] (<https://orcid.org/0000-0001-9953-3904>),
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb] (Code from the ggplot2 package.),
Justin Talbot [ctb] (Code from the labeling package),
Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 4.2.0 dated 2019-05-13 and 4.2.4 dated 2021-01-20
DESCRIPTION | 12 - MD5 | 242 +++++++++++++++++----------------- NAMESPACE | 6 NEWS.md | 23 +++ R/canva.R | 11 - R/colorblind.R | 2 R/economist.R | 11 - R/few.R | 4 R/fivethirtyeight.R | 12 - R/geom-rangeframe.R | 3 R/geom-tufteboxplot.R | 3 R/hc.R | 14 - R/pander.R | 4 R/scales.R | 4 R/shapes.R | 6 R/solarized.R | 6 R/stat-fivenumber.R | 8 + R/stata.R | 4 R/tableau.R | 7 R/wsj.R | 2 build/ggthemes.pdf |binary data/ggthemes_data.rda |binary inst/WORDLIST | 8 - inst/examples/ex-geom_rangeframe.R | 6 inst/examples/ex-theme_tufte.R | 1 man/bank_slopes.Rd | 3 man/calc_pal.Rd | 3 man/calc_shape_pal.Rd | 3 man/canva_palettes.Rd | 16 -- man/circlefill_shape_pal.Rd | 13 - man/cleveland_shape_pal.Rd | 13 - man/colorblind.Rd | 58 ++++---- man/economist_pal.Rd | 3 man/excel_new_pal.Rd | 7 man/excel_pal.Rd | 7 man/few_pal.Rd | 5 man/fivethirtyeight_pal.Rd | 7 man/gdocs_pal.Rd | 3 man/geom_rangeframe.Rd | 42 ++++- man/geom_tufteboxplot.Rd | 42 +++-- man/ggthemes.Rd | 1 man/ggthemes_data.Rd | 4 man/hc_pal.Rd | 11 - man/palette_pander.Rd | 5 man/ptol_pal.Rd | 3 man/range_breaks.Rd | 9 - man/scale_calc.Rd | 59 ++++---- man/scale_color_tableau.Rd | 37 +++-- man/scale_colour_gradient2_tableau.Rd | 33 +++- man/scale_colour_gradient_tableau.Rd | 49 ++++-- man/scale_economist.Rd | 59 ++++---- man/scale_excel.Rd | 63 ++++---- man/scale_excel_new.Rd | 62 ++++---- man/scale_few.Rd | 59 ++++---- man/scale_fivethirtyeight.Rd | 63 ++++---- man/scale_gdocs.Rd | 59 ++++---- man/scale_hc.Rd | 59 ++++---- man/scale_linetype_stata.Rd | 50 +++---- man/scale_pander.Rd | 61 ++++---- man/scale_ptol.Rd | 59 ++++---- man/scale_shape_calc.Rd | 50 +++---- man/scale_shape_circlefill.Rd | 58 ++++---- man/scale_shape_cleveland.Rd | 58 ++++---- man/scale_shape_stata.Rd | 47 +++--- man/scale_shape_tableau.Rd | 50 +++---- man/scale_shape_tremmel.Rd | 58 ++++---- man/scale_solarized.Rd | 59 ++++---- man/scale_stata.Rd | 56 ++++--- man/scale_wsj.Rd | 59 ++++---- man/smart_digits.Rd | 4 man/solarized_pal.Rd | 5 man/solarized_rebase.Rd | 2 man/stat_fivenumber.Rd | 29 ++-- man/stata_linetype_pal.Rd | 3 man/stata_pal.Rd | 2 man/tableau_color_pal.Rd | 21 +- man/tableau_gradient_pal.Rd | 9 - man/tableau_shape_pal.Rd | 5 man/theme_base.Rd | 12 - man/theme_calc.Rd | 2 man/theme_clean.Rd | 10 - man/theme_economist.Rd | 30 ++-- man/theme_excel.Rd | 5 man/theme_excel_new.Rd | 5 man/theme_few.Rd | 4 man/theme_fivethirtyeight.Rd | 6 man/theme_foundation.Rd | 11 - man/theme_gdocs.Rd | 2 man/theme_hc.Rd | 16 +- man/theme_igray.Rd | 12 - man/theme_map.Rd | 2 man/theme_pander.Rd | 23 ++- man/theme_par.Rd | 12 - man/theme_solarized.Rd | 4 man/theme_solid.Rd | 10 - man/theme_stata.Rd | 4 man/theme_tufte.Rd | 3 man/theme_wsj.Rd | 10 - man/tremmel_shape_pal.Rd | 13 - man/wsj_pal.Rd | 5 tests/testthat/helper-utils.R | 6 tests/testthat/helper-vdiffr.R | 14 - tests/testthat/test-banking.R | 6 tests/testthat/test-base.R | 18 +- tests/testthat/test-calc.R | 2 tests/testthat/test-canva.R | 2 tests/testthat/test-colorblind.R | 2 tests/testthat/test-economist.R | 12 - tests/testthat/test-excel.R | 8 - tests/testthat/test-few.R | 8 - tests/testthat/test-gdocs.R | 4 tests/testthat/test-hc.R | 4 tests/testthat/test-igray.R | 2 tests/testthat/test-pander.R | 2 tests/testthat/test-shapes.R | 22 +-- tests/testthat/test-show.R | 6 tests/testthat/test-solarized.R | 4 tests/testthat/test-stata.R | 4 tests/testthat/test-tableau.R | 10 - tests/testthat/test-theme_map.R | 2 tests/testthat/test-theme_solid.R | 2 tests/testthat/test-tufte.R | 2 122 files changed, 1327 insertions(+), 1020 deletions(-)
Title: R Access to the 'FMP Cloud' and 'Financial Modeling Prep' API
Description: Use R to access to the 'FMP Cloud' API <https://fmpcloud.io/> and
'Financial Modeling Prep' API <https://financialmodelingprep.com/developer/docs/>.
Data available includes stock prices, market indexes, company fundamentals,
13F holdings data, and much more. A valid API token must be set to enable
functions.
Author: Tony Trevisan [aut, cre]
Maintainer: Tony Trevisan <anthonytrevisan@gmail.com>
Diff between fmpcloudr versions 0.1.1 dated 2020-11-03 and 0.1.2 dated 2021-01-20
fmpcloudr-0.1.1/fmpcloudr/man/fmpc_symbols_sp500.Rd |only fmpcloudr-0.1.2/fmpcloudr/DESCRIPTION | 6 +- fmpcloudr-0.1.2/fmpcloudr/MD5 | 18 +++--- fmpcloudr-0.1.2/fmpcloudr/NAMESPACE | 2 fmpcloudr-0.1.2/fmpcloudr/NEWS.md | 8 ++- fmpcloudr-0.1.2/fmpcloudr/R/marketInfo.R | 17 +++--- fmpcloudr-0.1.2/fmpcloudr/README.md | 29 ++++++----- fmpcloudr-0.1.2/fmpcloudr/man/fmpc_symbols_index.Rd |only fmpcloudr-0.1.2/fmpcloudr/tests/testthat/test-financials.R | 34 ++++++------- fmpcloudr-0.1.2/fmpcloudr/tests/testthat/test-marketInfo.R | 10 +-- fmpcloudr-0.1.2/fmpcloudr/tests/testthat/test-pricing.R | 4 - 11 files changed, 70 insertions(+), 58 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds
has developed flexible code for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<http://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess,
S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview
of the field.
Author: Stephane Hess [aut],
David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>
Diff between apollo versions 0.2.2 dated 2020-12-05 and 0.2.3 dated 2021-01-20
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/apollo_estimate.R | 3 +++ R/apollo_lc.R | 5 +++-- R/apollo_lrTest.R | 2 +- R/apollo_makeCluster.R | 3 ++- inst/doc/apollofirstexample.html | 18 +++++++++--------- 7 files changed, 29 insertions(+), 24 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>),
Andreas Mayr [aut],
Nora Fenske [aut],
Janek Thomas [aut],
Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between gamboostLSS versions 2.0-1.1 dated 2020-04-02 and 2.0-5 dated 2021-01-20
ChangeLog | 4078 +++++++++++++++++++------------------- DESCRIPTION | 8 MD5 | 39 R/mboostLSS.R | 1 R/methods.R | 18 README.md | 2 build/partial.rdb |only build/vignette.rds |binary data/india.RData |binary data/india.bnd.RData |binary inst/NEWS.Rd | 45 inst/doc/gamboostLSS_Tutorial.R | 985 ++++----- inst/doc/gamboostLSS_Tutorial.pdf |binary man/as.families.Rd | 2 man/cvrisk.Rd | 4 man/families.Rd | 12 man/gamboostLSS-package.Rd | 6 man/mboostLSS.Rd | 6 man/stabsel.mboostLSS.Rd | 4 tests/bugfixes.R | 56 tests/regtest-noncyclic_fitting.R | 12 21 files changed, 2693 insertions(+), 2585 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and
the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census
geographies.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 0.11 dated 2020-12-14 and 0.11.4 dated 2021-01-20
DESCRIPTION | 8 +++--- MD5 | 19 +++++++------- NEWS.md |only R/acs.R | 27 +++++++++++++++++--- R/load_data.R | 12 ++++----- R/pums.R | 6 ++-- README.md | 62 ------------------------------------------------ data/pums_variables.rda |binary man/get_acs.Rd | 6 ++-- man/get_pums.Rd | 4 +-- man/pums_variables.Rd | 2 - 11 files changed, 52 insertions(+), 94 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load and simmr_mcmc. The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@mu.ie>
Diff between simmr versions 0.4.2 dated 2020-06-11 and 0.4.4 dated 2021-01-20
DESCRIPTION | 18 MD5 | 115 +-- NAMESPACE | 1 NEWS.md | 34 R/combine_sources.R | 191 ++--- R/compare_groups.R | 354 ++++----- R/compare_sources.R | 269 +++---- R/data.R | 16 R/plot.simmr_input.R | 451 ++++-------- R/plot.simmr_output.R | 260 +++---- R/posterior_predictive.simmr_output.R | 195 ++--- R/print.simmr_input.R | 28 R/print.simmr_output.R | 14 R/prior_viz.simmr_output.R | 178 ++-- R/simmr.R | 69 - R/simmr_elicit.R | 162 ++-- R/simmr_load.R | 200 ++--- R/simmr_mcmc.R | 619 +++++++---------- R/simmr_mcmc_tdf.R | 316 ++++---- R/summary.simmr_output.R | 132 +-- R/summary.simmr_output_tdf.R | 117 --- build/vignette.rds |binary data/geese_data.rda |binary data/simmr_data_2.rda |binary inst/doc/quick_start.R | 10 inst/doc/quick_start.Rmd | 10 inst/doc/quick_start.html | 97 +- inst/doc/simmr.R | 37 - inst/doc/simmr.Rmd | 58 + inst/doc/simmr.html | 503 +++++++------ man/combine_sources.Rd | 60 - man/compare_groups.Rd | 128 --- man/compare_sources.Rd | 56 - man/geese_data.Rd | 2 man/geese_data_day1.Rd | 2 man/plot.simmr_input.Rd | 200 +---- man/plot.simmr_output.Rd | 41 - man/posterior_predictive.Rd | 36 man/prior_viz.Rd | 41 - man/simmr.Rd | 42 - man/simmr_data_1.Rd | 3 man/simmr_data_2.Rd | 3 man/simmr_elicit.Rd | 49 - man/simmr_load.Rd | 33 man/simmr_mcmc.Rd | 331 +++------ man/simmr_mcmc_tdf.Rd | 92 +- man/square_data.Rd | 4 man/summary.simmr_output.Rd | 47 - man/summary.simmr_output_tdf.Rd | 59 - tests/testthat/test_simmr_combine_sources.R | 205 ++++- tests/testthat/test_simmr_compare_sources_and_groups.R |only tests/testthat/test_simmr_input_plots.R | 205 ++--- tests/testthat/test_simmr_load.R | 77 +- tests/testthat/test_simmr_mcmc_simple.R | 96 +- tests/testthat/test_simmr_misc_functions.R |only tests/testthat/test_simmr_plot_output.R | 49 - tests/testthat/test_simmr_print_summary.R | 101 +- tests/testthat/test_simmr_tdf_estimation.R |only vignettes/quick_start.Rmd | 10 vignettes/simmr.Rmd | 58 + 60 files changed, 3073 insertions(+), 3411 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut],
Nicolas Lambert [aut],
Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.2.0 dated 2019-10-16 and 0.3.0 dated 2021-01-20
MTA-0.2.0/MTA/R/mapmst.R |only MTA-0.2.0/MTA/man/mapmst.Rd |only MTA-0.3.0/MTA/DESCRIPTION | 10 MTA-0.3.0/MTA/MD5 | 67 - MTA-0.3.0/MTA/NAMESPACE | 15 MTA-0.3.0/MTA/NEWS |only MTA-0.3.0/MTA/R/bidev.R |only MTA-0.3.0/MTA/R/gdev.R | 61 - MTA-0.3.0/MTA/R/internals.R | 4 MTA-0.3.0/MTA/R/map_bidev.R |only MTA-0.3.0/MTA/R/map_mst.R |only MTA-0.3.0/MTA/R/mas.R | 98 -- MTA-0.3.0/MTA/R/mst.R | 90 - MTA-0.3.0/MTA/R/package.R | 16 MTA-0.3.0/MTA/R/plot_bidev.R |only MTA-0.3.0/MTA/R/plot_mst.R |only MTA-0.3.0/MTA/R/sdev.R | 45 MTA-0.3.0/MTA/R/tdev.R | 74 - MTA-0.3.0/MTA/README.md | 19 MTA-0.3.0/MTA/build/vignette.rds |binary MTA-0.3.0/MTA/inst/doc/MTA.R | 6 MTA-0.3.0/MTA/inst/doc/MTA.Rmd | 39 MTA-0.3.0/MTA/inst/doc/MTA.html | 38 MTA-0.3.0/MTA/inst/doc/MTA_Scenario.R | 742 +++++++++------- MTA-0.3.0/MTA/inst/doc/MTA_Scenario.Rmd | 1075 +++++++++++++---------- MTA-0.3.0/MTA/inst/doc/MTA_Scenario.html | 1402 ++++++++++++++++--------------- MTA-0.3.0/MTA/man/MTA.Rd | 11 MTA-0.3.0/MTA/man/bidev.Rd |only MTA-0.3.0/MTA/man/com.Rd | 10 MTA-0.3.0/MTA/man/ept.Rd | 8 MTA-0.3.0/MTA/man/gdev.Rd | 56 - MTA-0.3.0/MTA/man/map_bidev.Rd |only MTA-0.3.0/MTA/man/map_mst.Rd |only MTA-0.3.0/MTA/man/mas.Rd | 44 MTA-0.3.0/MTA/man/mst.Rd | 61 - MTA-0.3.0/MTA/man/plot_bidev.Rd |only MTA-0.3.0/MTA/man/plot_mst.Rd |only MTA-0.3.0/MTA/man/sdev.Rd | 41 MTA-0.3.0/MTA/man/tdev.Rd | 71 - MTA-0.3.0/MTA/vignettes/MTA.Rmd | 39 MTA-0.3.0/MTA/vignettes/MTA_Scenario.Rmd | 1075 +++++++++++++---------- 41 files changed, 2787 insertions(+), 2430 deletions(-)
Title: Additional Families for Generalized Linear Models
Description: Creates family objects identical to stats
family but for new links.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between extendedFamily versions 0.1.1 dated 2020-06-21 and 0.2.0 dated 2021-01-20
DESCRIPTION | 11 +- MD5 | 15 +- NEWS | 9 + R/binomialEF.R | 40 ++++++- README.md | 72 +++++++------ man/binomialEF.Rd | 14 +- man/figures |only man/heart.Rd | 6 - tests/testthat/test_binomialEF.R | 202 +++++++++++++++++++++++++++++++++++++-- 9 files changed, 303 insertions(+), 66 deletions(-)
More information about extendedFamily at CRAN
Permanent link
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph]
(<https://orcid.org/0000-0001-7776-0903>),
Matthias Studer [aut] (<https://orcid.org/0000-0002-6269-1412>),
Reto Buergin [aut],
Tim Liao [ctb],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.6.0 dated 2020-04-24 and 0.6.1 dated 2021-01-20
DESCRIPTION | 14 ++++++++------ MD5 | 26 +++++++++++++++++--------- NAMESPACE | 18 ++++++++++++++---- R/seqindic-dyn.R |only R/seqplot-tentrop.R | 5 +++-- R/seqpolyads.R |only build |only data |only inst/CITATION | 46 +++++++++++++++++++++++++++++++++------------- inst/NEWS | 17 ++++++++++++++++- inst/NEWS.Rd | 28 +++++++++++++++++++++++++++- man/plot.dynin.Rd |only man/polyads.Rd |only man/seqCompare.Rd | 2 +- man/seqemlt.Rd | 2 +- man/seqimplic.Rd | 6 +++--- man/seqindic-dyn.Rd |only man/seqpolyads.Rd |only 18 files changed, 123 insertions(+), 41 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between fsbrain versions 0.4.0 dated 2020-09-10 and 0.4.1 dated 2021-01-20
DESCRIPTION | 14 LICENSE | 2 MD5 | 60 +- NAMESPACE | 4 R/cbar.R | 8 R/coloredmesh.R | 32 + R/fsdir_abstraction_subject.R | 6 R/helpers.R | 187 +++++++- R/rglactions.R | 33 + R/vis.R | 9 R/vis_dti_tracks.R |only inst/CITATION |only inst/doc/fsbrain.html | 815 +++++++++++++----------------------- inst/doc/fsbrain_faq.R | 26 + inst/doc/fsbrain_faq.Rmd | 36 + inst/doc/fsbrain_faq.html | 443 +++++-------------- inst/doc/fsbrain_vol.html | 333 ++------------ man/coloredmesh.from.label.Rd | 5 man/deg2rad.Rd |only man/flc.Rd |only man/limit_fun_na.Rd | 7 man/limit_fun_na_inside.Rd |only man/path.colors.from.orientation.Rd |only man/path.slopes.Rd |only man/rad2deg.Rd |only man/scale.to.range.zero.one.Rd |only man/subject.label.Rd | 5 man/track.length.Rd |only man/vis.dti.trk.Rd |only man/vis.labeldata.on.subject.Rd | 5 man/vis.path.along.verts.Rd | 15 man/vis.paths.Rd |only tests/testthat.R | 4 tests/testthat/helper-functions.R | 15 tests/testthat/teardown-cran.R |only tests/testthat/test-vis_group.R | 1 tests/testthat_vz.R |only vignettes/fsbrain_faq.Rmd | 36 + 38 files changed, 916 insertions(+), 1185 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.10.0 dated 2021-01-07 and 1.10.1 dated 2021-01-20
DESCRIPTION | 8 +++---- MD5 | 16 +++++++------- NEWS.md | 9 +++++++ R/make.R | 10 +++++--- R/tools.R | 24 +-------------------- inst/NEWS.rd | 11 ++++++++- inst/doc/An_Introduction_to_fakemake.html | 34 +++++++++++++++--------------- inst/doc/Building_Packages.html | 12 +++++----- man/touch.Rd | 10 -------- 9 files changed, 62 insertions(+), 72 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.11.1 dated 2020-11-17 and 1.12.0 dated 2021-01-20
DESCRIPTION | 8 ++--- MD5 | 37 +++++++++++++------------- NEWS.md | 36 ++++++++++++++++++++++++++ R/Connection.R | 31 +++++++++++++++++++--- R/DataTypes.R | 4 +- R/Driver.R | 6 ++++ R/Options.R | 35 ++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 40 ----------------------------- inst/doc/aws_s3_backend.html | 40 ----------------------------- inst/doc/changing_backend_file_parser.html | 40 ----------------------------- inst/doc/convert_and_save_cost.html | 40 ----------------------------- inst/doc/getting_started.html | 40 ----------------------------- inst/doc/how_to_retry.html | 40 ----------------------------- man/dbConnect-AthenaDriver-method.Rd | 5 +++ man/dbGetPartition.Rd | 7 +++-- man/dbRemoveTable.Rd | 3 ++ tests/testthat/test-bigint.R |only tests/testthat/test-dplyr-sql-trans-env.R | 2 + tests/testthat/test-metadata.R | 12 +++++++- 20 files changed, 159 insertions(+), 267 deletions(-)
Title: The Reinert Method for Textual Data Clustering
Description: An R implementation of the Reinert text clustering method. For more
details about the algorithm see the included vignettes or Reinert (1990)
<doi:10.1177/075910639002600103>.
Author: Julien Barnier [aut, cre],
Florian Privé [ctb]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rainette versions 0.1.1 dated 2020-05-09 and 0.1.2 dated 2021-01-20
DESCRIPTION | 12 - MD5 | 29 +- NEWS.md | 5 R/import.R | 4 R/rainette.R | 2 R/rainette2.R | 4 README.md | 4 build/partial.rdb |only build/vignette.rds |binary inst/doc/algorithmes.html | 196 +++++++++++++++++++ inst/doc/introduction_en.html | 349 +++++++++++++++++++++++++++------- inst/doc/introduction_usage.html | 392 +++++++++++++++++++++++++++++---------- man/import_corpus_iramuteq.Rd | 2 man/rainette.Rd | 2 man/rainette2.Rd | 2 tests/testthat/test_plots.R | 14 - 16 files changed, 816 insertions(+), 201 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.9.1 dated 2020-11-17 and 1.10.0 dated 2021-01-20
DESCRIPTION | 8 ++--- MD5 | 37 +++++++++++++------------- NEWS.md | 32 ++++++++++++++++++++++- R/Connection.R | 30 ++++++++++++++++++--- R/DataTypes.R | 4 +- R/Driver.R | 6 ++++ R/Options.R | 33 +++++++++++++++++++++++ build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 40 ----------------------------- inst/doc/aws_s3_backend.html | 40 ----------------------------- inst/doc/changing_backend_file_parser.html | 40 ----------------------------- inst/doc/convert_and_save_cost.html | 40 ----------------------------- inst/doc/getting_started.html | 40 ----------------------------- inst/doc/how_to_retry.html | 40 ----------------------------- man/dbConnect-AthenaDriver-method.Rd | 5 +++ man/dbGetPartition.Rd | 7 +++-- man/dbRemoveTable.Rd | 3 ++ tests/testthat/test-bigint.R |only tests/testthat/test-dplyr-sql-trans-env.R | 2 + tests/testthat/test-metadata.R | 13 +++++++-- 20 files changed, 152 insertions(+), 268 deletions(-)
Title: Model Agnostic Explainers for Individual Predictions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Break Down Table shows contributions of every variable to a final prediction.
Break Down Plot presents variable contributions in a concise graphical way.
This package work for binary classifiers and general regression models.
Author: Przemyslaw Biecek [aut, cre],
Aleksandra Grudziaz [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between breakDown versions 0.2.0 dated 2020-04-05 and 0.2.1 dated 2021-01-20
breakDown-0.2.0/breakDown/inst/doc/break_caret.R |only breakDown-0.2.0/breakDown/inst/doc/break_caret.Rmd |only breakDown-0.2.0/breakDown/inst/doc/break_caret.html |only breakDown-0.2.0/breakDown/inst/doc/break_randomForest.R |only breakDown-0.2.0/breakDown/inst/doc/break_randomForest.Rmd |only breakDown-0.2.0/breakDown/inst/doc/break_randomForest.html |only breakDown-0.2.0/breakDown/inst/doc/break_ranger.R |only breakDown-0.2.0/breakDown/inst/doc/break_ranger.Rmd |only breakDown-0.2.0/breakDown/inst/doc/break_ranger.html |only breakDown-0.2.0/breakDown/vignettes/break_caret.Rmd |only breakDown-0.2.0/breakDown/vignettes/break_randomForest.Rmd |only breakDown-0.2.0/breakDown/vignettes/break_ranger.Rmd |only breakDown-0.2.1/breakDown/DESCRIPTION | 10 breakDown-0.2.1/breakDown/MD5 | 30 - breakDown-0.2.1/breakDown/build/vignette.rds |binary breakDown-0.2.1/breakDown/inst/doc/break_glm.html | 115 ++++++ breakDown-0.2.1/breakDown/inst/doc/break_lm.html | 115 ++++++ breakDown-0.2.1/breakDown/inst/doc/break_svm.html | 123 ++++++- breakDown-0.2.1/breakDown/inst/doc/break_xgboost.R | 38 +- breakDown-0.2.1/breakDown/inst/doc/break_xgboost.Rmd | 38 +- breakDown-0.2.1/breakDown/inst/doc/break_xgboost.html | 226 +++++++++---- breakDown-0.2.1/breakDown/vignettes/break_xgboost.Rmd | 38 +- 22 files changed, 567 insertions(+), 166 deletions(-)
Title: Contour Plots, 3D Plots, Vector Fields and Heatmaps
Description: Combined contour/heatmap plots, 3d bar/surface plots, 2d/3d triangular plots, isosurface plots and 2d/3d vector fields. By default, uses vector graphics, but it's possible to use raster graphics for regular heatmaps. Builds on the colorspace package (Zeileis, et al., 2020 <doi:10.18637/jss.v096.i01>), by supporting smooth multiband color interpolation, in sRGB, HSV and HCL color spaces.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between barsurf versions 0.6.1 dated 2020-08-28 and 0.7.0 dated 2021-01-20
barsurf-0.6.1/barsurf/man/63_color_conversion.Rd |only barsurf-0.7.0/barsurf/DESCRIPTION | 15 - barsurf-0.7.0/barsurf/MD5 | 59 +++--- barsurf-0.7.0/barsurf/NAMESPACE | 2 barsurf-0.7.0/barsurf/R/bs.r | 22 +- barsurf-0.7.0/barsurf/R/colfs.r | 14 - barsurf-0.7.0/barsurf/R/colfs2.r | 31 ++- barsurf-0.7.0/barsurf/R/colvs.r | 7 barsurf-0.7.0/barsurf/R/global.r | 62 +++--- barsurf-0.7.0/barsurf/R/litmus.r | 8 barsurf-0.7.0/barsurf/R/plot2d.r | 40 ++-- barsurf-0.7.0/barsurf/R/plot3d.r | 22 +- barsurf-0.7.0/barsurf/R/plot3v.r | 10 - barsurf-0.7.0/barsurf/R/plotf.r | 16 - barsurf-0.7.0/barsurf/R/plotvec.r | 12 - barsurf-0.7.0/barsurf/R/projection.r | 4 barsurf-0.7.0/barsurf/R/val_iso.r | 4 barsurf-0.7.0/barsurf/R/val_xy.r | 4 barsurf-0.7.0/barsurf/build/vignette.rds |binary barsurf-0.7.0/barsurf/inst/doc/barsurf.R | 81 ++++----- barsurf-0.7.0/barsurf/inst/doc/barsurf.Rnw | 39 ++-- barsurf-0.7.0/barsurf/inst/doc/barsurf.pdf |binary barsurf-0.7.0/barsurf/man/11_main_plotting_functions.Rd | 89 ++++++---- barsurf-0.7.0/barsurf/man/12_functional_versions.Rd | 8 barsurf-0.7.0/barsurf/man/22_standardized_palette_interface.Rd | 36 +--- barsurf-0.7.0/barsurf/man/32_multi-litmus_objects.Rd | 2 barsurf-0.7.0/barsurf/man/52_predefined_litmus_objects.Rd | 3 barsurf-0.7.0/barsurf/man/53_predefined_litmus-fitting_functions.Rd | 5 barsurf-0.7.0/barsurf/man/54_color_sequence_functions.Rd | 4 barsurf-0.7.0/barsurf/man/71_deprecated.Rd | 12 - barsurf-0.7.0/barsurf/vignettes/barsurf.Rnw | 39 ++-- 31 files changed, 351 insertions(+), 299 deletions(-)
Title: Evaluation of Tweedie Exponential Family Models
Description: Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi:10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
Author: Peter K. Dunn [cre, aut]
Maintainer: Peter K. Dunn <pdunn2@usc.edu.au>
Diff between tweedie versions 2.3.2 dated 2017-12-14 and 2.3.3 dated 2021-01-20
tweedie-2.3.2/tweedie/NEWS |only tweedie-2.3.3/tweedie/DESCRIPTION | 12 +++---- tweedie-2.3.3/tweedie/MD5 | 30 +++++++++--------- tweedie-2.3.3/tweedie/NEWS.md |only tweedie-2.3.3/tweedie/R/tweedie.R | 13 ++++--- tweedie-2.3.3/tweedie/build/partial.rdb |binary tweedie-2.3.3/tweedie/inst/CITATION | 7 +--- tweedie-2.3.3/tweedie/man/AICtweedie.Rd | 6 +-- tweedie-2.3.3/tweedie/man/dtweedie.Rd | 44 +++++++++++++-------------- tweedie-2.3.3/tweedie/man/dtweedie.dldphi.Rd | 24 +++++++------- tweedie-2.3.3/tweedie/man/dtweedie.saddle.Rd | 10 +++--- tweedie-2.3.3/tweedie/man/logLik.tweedie.Rd | 6 +-- tweedie-2.3.3/tweedie/man/tweedie-package.Rd | 12 +++---- tweedie-2.3.3/tweedie/man/tweedie.convert.Rd | 2 - tweedie-2.3.3/tweedie/man/tweedie.dev.Rd | 38 +++++++++++------------ tweedie-2.3.3/tweedie/man/tweedie.plot.Rd | 30 +++++++++--------- tweedie-2.3.3/tweedie/man/tweedie.profile.Rd | 10 +++--- 17 files changed, 121 insertions(+), 123 deletions(-)
Title: Basic Routing for Shiny Web Applications
Description: It is a simple router for your Shiny apps.
The router allows you to create dynamic web applications with real-time
User Interface and easily share url to pages within your Shiny apps.
Author: Filip Stachura [aut],
Dominik Krzemiński [cre, aut],
Krystian Igras [aut],
Appsilon [cph]
Maintainer: Dominik Krzemiński <dominik@appsilon.com>
Diff between shiny.router versions 0.2.1 dated 2021-01-15 and 0.2.2 dated 2021-01-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + R/pages.R | 7 +++++-- R/zzz.R | 3 +-- 5 files changed, 14 insertions(+), 11 deletions(-)
More information about mobilityIndexR at CRAN
Permanent link
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return 'coda' mcmc objects that can then be summarized
using the 'coda' package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Ross Ihaka [cph], The R Development Core Team [cph], The R Foundation [cph], Pierre L'Ecuyer [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.4-9 dated 2020-08-02 and 1.5-0 dated 2021-01-20
DESCRIPTION | 8 +- MD5 | 144 +++++++++++++++++++-------------------- R/HDPHMMnegbin.R | 8 +- R/HDPHMMpoisson.R | 9 +- R/HDPHSMMnegbin.R | 6 - R/HMMpanelFE.R | 3 R/HMMpanelRE.R | 5 - R/MCMCSVDreg.R | 2 R/MCMCbinaryChange.R | 9 +- R/MCMCdynamicEI.R | 2 R/MCMCdynamicIRT1d.R | 4 - R/MCMCfactanal.R | 2 R/MCMChierEI.R | 2 R/MCMCirt1d.R | 2 R/MCMCirtHier1d.R | 2 R/MCMCirtKd.R | 2 R/MCMCirtKdRob.R | 2 R/MCMClogit.R | 2 R/MCMCmetrop1R.R | 2 R/MCMCmixfactanal.R | 5 - R/MCMCmnl.R | 2 R/MCMCnegbin.R | 4 - R/MCMCnegbinChange.R | 6 - R/MCMCoprobit.R | 2 R/MCMCoprobitChange.R | 4 - R/MCMCordfactanal.R | 2 R/MCMCpoisson.R | 2 R/MCMCpoissonChange.R | 8 +- R/MCMCprobit.R | 3 R/MCMCprobitChange.R | 4 - R/MCMCregress.R | 2 R/MCMCregressChange.R | 15 +--- R/MCMCresidualBreakAnalysis.R | 4 - R/MCMCtobit.R | 6 - R/make.breaklist.R | 7 + R/testpanelGroupBreak.R | 2 R/testpanelSubjectBreak.R | 2 inst/CITATION | 4 - man/HDPHMMnegbin.Rd | 8 +- man/HDPHMMpoisson.Rd | 9 +- man/HDPHSMMnegbin.Rd | 6 - man/HMMpanelFE.Rd | 3 man/HMMpanelRE.Rd | 4 - man/MCMCSVDreg.Rd | 2 man/MCMCbinaryChange.Rd | 9 +- man/MCMCdynamicEI.Rd | 2 man/MCMCdynamicIRT1d.Rd | 4 - man/MCMCfactanal.Rd | 2 man/MCMChierEI.Rd | 2 man/MCMCirt1d.Rd | 2 man/MCMCirtHier1d.Rd | 2 man/MCMCirtKd.Rd | 2 man/MCMCirtKdRob.Rd | 2 man/MCMClogit.Rd | 2 man/MCMCmetrop1R.Rd | 2 man/MCMCmixfactanal.Rd | 2 man/MCMCmnl.Rd | 2 man/MCMCnegbin.Rd | 4 - man/MCMCnegbinChange.Rd | 6 - man/MCMCoprobit.Rd | 2 man/MCMCoprobitChange.Rd | 4 - man/MCMCordfactanal.Rd | 2 man/MCMCpoisson.Rd | 2 man/MCMCpoissonChange.Rd | 6 + man/MCMCprobit.Rd | 3 man/MCMCprobitChange.Rd | 4 - man/MCMCregress.Rd | 2 man/MCMCregressChange.Rd | 13 +-- man/MCMCresidualBreakAnalysis.Rd | 4 - man/MCMCtobit.Rd | 4 - man/make.breaklist.Rd | 7 + man/testpanelGroupBreak.Rd | 2 man/testpanelSubjectBreak.Rd | 2 73 files changed, 227 insertions(+), 207 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party party package, but on core R
only.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 1.0.0 dated 2021-01-11 and 1.1.0 dated 2021-01-20
fritools-1.0.0/fritools/R/is_not_false.R |only fritools-1.0.0/fritools/inst/runit_tests/runit-is_not_false.R |only fritools-1.1.0/fritools/DESCRIPTION | 10 fritools-1.1.0/fritools/MD5 | 77 +++-- fritools-1.1.0/fritools/NAMESPACE | 11 fritools-1.1.0/fritools/NEWS.md | 14 fritools-1.1.0/fritools/R/boolean.R |only fritools-1.1.0/fritools/R/call.R |only fritools-1.1.0/fritools/R/find_files.R | 1 fritools-1.1.0/fritools/R/installed.R |only fritools-1.1.0/fritools/R/is_version_sufficient.R | 3 fritools-1.1.0/fritools/R/is_windows.R | 1 fritools-1.1.0/fritools/R/load_internal_functions.R | 1 fritools-1.1.0/fritools/R/options.R |only fritools-1.1.0/fritools/R/search_files.R | 59 +++ fritools-1.1.0/fritools/R/strip_off_attributes.R |only fritools-1.1.0/fritools/R/test_helpers.R | 23 - fritools-1.1.0/fritools/R/touch.R | 5 fritools-1.1.0/fritools/inst/NEWS.rd | 15 - fritools-1.1.0/fritools/inst/doc/An_Introduction_to_fritools.html | 2 fritools-1.1.0/fritools/inst/runit_tests/runit-batch.R | 150 +++++----- fritools-1.1.0/fritools/inst/runit_tests/runit-boolean.R |only fritools-1.1.0/fritools/inst/runit_tests/runit-call.R |only fritools-1.1.0/fritools/inst/runit_tests/runit-installed.R |only fritools-1.1.0/fritools/inst/runit_tests/runit-load_internal_functions.R | 4 fritools-1.1.0/fritools/inst/runit_tests/runit-options.R |only fritools-1.1.0/fritools/inst/runit_tests/runit-search_files.R | 48 ++- fritools-1.1.0/fritools/inst/runit_tests/runit-strip_off_attributes.R |only fritools-1.1.0/fritools/inst/runit_tests/runit-test_helpers.R | 8 fritools-1.1.0/fritools/man/call_conditionally.Rd |only fritools-1.1.0/fritools/man/call_safe.Rd |only fritools-1.1.0/fritools/man/find_files.Rd | 6 fritools-1.1.0/fritools/man/get_options.Rd |only fritools-1.1.0/fritools/man/get_run_r_tests.Rd | 8 fritools-1.1.0/fritools/man/is_false.Rd |only fritools-1.1.0/fritools/man/is_force.Rd |only fritools-1.1.0/fritools/man/is_installed.Rd |only fritools-1.1.0/fritools/man/is_not_false.Rd | 25 + fritools-1.1.0/fritools/man/is_null_or_true.Rd |only fritools-1.1.0/fritools/man/is_r_package_installed.Rd |only fritools-1.1.0/fritools/man/is_running_on_fvafrcu_machines.Rd | 8 fritools-1.1.0/fritools/man/is_running_on_gitlab_com.Rd | 11 fritools-1.1.0/fritools/man/is_version_sufficient.Rd | 5 fritools-1.1.0/fritools/man/is_windows.Rd | 1 fritools-1.1.0/fritools/man/load_internal_functions.Rd | 1 fritools-1.1.0/fritools/man/search_files.Rd | 21 + fritools-1.1.0/fritools/man/set_options.Rd |only fritools-1.1.0/fritools/man/set_run_r_tests.Rd | 8 fritools-1.1.0/fritools/man/strip_off_attributes.Rd |only fritools-1.1.0/fritools/man/summary.filesearch.Rd |only fritools-1.1.0/fritools/man/touch.Rd | 1 51 files changed, 355 insertions(+), 172 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo (MCMC) and MCMC based on parallel
importance sampling type weighted estimators
(Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>).
Gaussian, Poisson, binomial, negative binomial, and Gamma
observation densities and basic stochastic volatility models
with linear-Gaussian state dynamics,
as well as general non-linear Gaussian models and discretised
diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 1.0.1-1 dated 2020-11-12 and 1.1.0 dated 2021-01-20
DESCRIPTION | 16 ++- MD5 | 159 ++++++++++++++++++----------------- NAMESPACE | 4 NEWS | 23 ++++- R/RcppExports.R | 16 +++ R/approx.R | 4 R/as.data.frame.mcmc_output.R | 18 ++++ R/as_bssm.R | 12 +- R/bootstrap_filter.R | 59 ++++++++++--- R/bssm-package.R | 2 R/ekpf_filter.R | 16 ++- R/importance_sample.R | 18 +++- R/init_mode.R | 2 R/kfilter.R | 9 +- R/loglik.R | 65 +++++++++----- R/models.R | 85 +++++++++++------- R/particle_smoother.R | 67 +++++++++++--- R/post_correction.R |only R/predict.R | 2 R/print_mcmc.R | 73 ++++++++-------- R/priors.R | 32 ++++++- R/run_mcmc.R | 175 ++++++++++++++++++++++++++++----------- R/sim_smoother.R | 2 inst/doc/bssm.R | 4 inst/doc/bssm.Rmd | 10 +- inst/doc/bssm.html | 78 ++++++++++------- inst/doc/growth_model.R | 15 +-- inst/doc/growth_model.Rmd | 23 ++--- inst/doc/growth_model.html | 59 ++++++++----- inst/doc/psi_pf.R | 22 ++-- inst/doc/psi_pf.Rmd | 22 ++-- inst/doc/psi_pf.html | 12 ++ man/ar1_lg.Rd | 7 + man/ar1_ng.Rd | 13 +- man/as.data.frame.mcmc_output.Rd | 19 ++++ man/as_bssm.Rd | 9 ++ man/asymptotic_var.Rd |only man/bootstrap_filter.Rd | 16 +-- man/bsm_ng.Rd | 21 +++- man/bssm.Rd | 2 man/ekpf_filter.Rd | 11 +- man/gaussian_approx.Rd | 5 + man/importance_sample.Rd | 18 +++- man/kfilter.Rd | 12 ++ man/logLik.Rd | 16 +-- man/logLik.ssm_nlg.Rd | 8 - man/logLik.ssm_sde.Rd | 12 +- man/particle_smoother.Rd | 19 ++-- man/post_correct.Rd |only man/print.mcmc_output.Rd | 7 - man/priors.Rd | 10 ++ man/run_mcmc.Rd | 3 man/run_mcmc.ssm_nlg.Rd | 14 +-- man/run_mcmc.ssm_sde.Rd | 16 +-- man/run_mcmc_g.Rd | 25 +++++ man/run_mcmc_ng.Rd | 60 ++++++++++--- man/sim_smoother.Rd | 2 man/ssm_mlg.Rd | 8 + man/ssm_sde.Rd | 2 man/suggest_N.Rd |only man/summary.mcmc_output.Rd | 10 ++ man/svm.Rd | 2 src/R_importance_sample.cpp | 43 +++++---- src/R_mcmc.cpp | 29 ++++-- src/R_postcorrection.cpp |only src/R_predict_past.cpp | 12 +- src/RcppExports.cpp | 108 ++++++++++++++++++++++++ src/approx_mcmc.cpp | 2 src/approx_mcmc.h | 7 - src/model_ar1_lg.cpp | 8 + src/model_ar1_ng.cpp | 8 + src/model_bsm_lg.cpp | 21 +++- src/model_bsm_ng.cpp | 26 ++++- src/model_ssm_mng.cpp | 21 +++- src/model_ssm_nlg.cpp | 17 +-- src/model_ssm_ulg.h | 2 src/model_ssm_ung.cpp | 79 +++++++++-------- src/model_svm.cpp | 7 + tests/testthat/test_mcmc.R | 45 +++++----- tests/testthat/test_models.R | 2 vignettes/bssm.Rmd | 10 +- vignettes/growth_model.Rmd | 23 ++--- vignettes/psi_pf.Rmd | 22 ++-- 83 files changed, 1331 insertions(+), 612 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb],
Damir Pulatov [ctb]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between llama versions 0.9.4 dated 2021-01-07 and 0.10 dated 2021-01-20
DESCRIPTION | 14 - MD5 | 64 +++--- NAMESPACE | 3 NEWS | 3 R/bsFolds.R | 33 ++- R/cvFolds.R | 35 ++- R/helpers.R | 19 + R/imputeCensored.R | 26 +- R/input.R | 141 +++++++++---- R/misc.R | 114 +++++++++-- R/misclassificationPenalties.R | 26 ++ R/parscores.R | 42 +++- R/regression.R | 140 ++++++++++--- R/regressionPairs.R | 236 ++++++++++++++++++----- R/successes.R | 39 ++- R/trainTest.R | 21 +- man/input.Rd | 25 ++ man/llama-package.Rd | 11 - man/regression.Rd | 14 - man/regressionPairs.Rd | 18 + tests/testthat/helper_mockLearners.R | 38 +++ tests/testthat/helper_testData.R | 50 ++++ tests/testthat/test.bsFolds.R | 71 ++++++ tests/testthat/test.cvFolds.R | 109 ++++++++++ tests/testthat/test.imputeCensored.R | 38 +++ tests/testthat/test.input.R | 151 ++++++++++---- tests/testthat/test.misc.R | 210 ++++++++++++++++++++ tests/testthat/test.misclassificationPenalties.R | 43 ++++ tests/testthat/test.parscores.R | 101 +++++++++ tests/testthat/test.regression.R | 39 +++ tests/testthat/test.regressionPairs.R | 96 +++++++++ tests/testthat/test.successes.R | 86 ++++++++ tests/testthat/test.trainTest.R | 94 +++++++++ 33 files changed, 1858 insertions(+), 292 deletions(-)
Title: Individual Tree Growth Modeling
Description: Individual tree model is an instrument to support the decision with
regard to forest management. This package provides functions that let you work
with data for this model. Also other support functions and extension related to
this model are available.
Author: Clayton Vieira Fraga Filho, Gilson Fernandes da Silva, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Diff between ITGM versions 0.41 dated 2018-11-19 and 0.42 dated 2021-01-20
DESCRIPTION | 13 - MD5 | 56 +++++-- NAMESPACE | 56 +++++-- R/addSettings.R |only R/avaliaModeloEspecial.R |only R/avaliaVolumeAvancado2.R |only R/criaModeloExclusivo2.R |only R/criaModeloGenerico2.R |only R/firstsMeasurements.R | 50 +++--- R/getAllEstatisticsFn.R |only R/getAllGraphicsFn.R |only R/getGraphicVolumeTotal.R |only R/getModelsExclusiveOfLiterature.R | 28 +-- R/getggplot2GraphicObservadoXEstimadoTotal.R |only R/maiTOmdd.R | 176 ++++++++++++------------ R/plotRB.R |only R/preparaFormula.R |only R/project.R | 74 +++++----- R/removeColsSuspicious.R |only R/runAndReport.R |only man/addSettings.Rd |only man/avaliaModeloEspecial.Rd |only man/avaliaVolumeAvancado2.Rd |only man/criaModeloExclusivo2.Rd |only man/criaModeloGenerico2.Rd |only man/firstsMeasurements.Rd | 54 +++---- man/getAllEstatisticsFn.Rd |only man/getAllGraphicsFn.Rd |only man/getGraphicVolumeTotal.Rd |only man/getModelosLiteraturaExclusivos.Rd | 35 ++-- man/getModelosLiteraturaGenericos.Rd | 28 +-- man/getModelsExclusiveOfLiterature.Rd | 35 ++-- man/getModelsGenericOfLiterature.Rd | 28 +-- man/getggplot2GraphicObservadoXEstimadoTotal.Rd |only man/maiTOmdd.Rd | 92 +++++++----- man/plotRB.Rd |only man/preparaFormula.Rd |only man/project.Rd | 69 +++++---- man/removeColsSuspicious.Rd |only man/runAndReport.Rd |only tests/testthat.R | 8 - tests/testthat/testPrimeirasMedicoes.R | 18 +- 42 files changed, 446 insertions(+), 374 deletions(-)
Title: Effect Estimates from All Models
Description: Estimates and plots effect estimates from models with all possible
combinations of a list of variables. It can be used for assessing treatment
effects in clinical trials or risk factors in bio-medical and epidemiological
research. Like Stata command 'confall' (Wang Z (2007) <doi:10.1177/1536867X0700700203> ),
'allestimates' calculates and stores all effect estimates, and plots them against p values or
Akaike information criterion (AIC) values. It currently has functions for linear
regression: all_lm(), logistic and Poisson regression: all_glm() and all_speedglm(),
and Cox proportional hazards regression: all_cox().
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>
Diff between allestimates versions 0.1.9 dated 2020-09-29 and 0.2.1 dated 2021-01-20
DESCRIPTION | 10 +++--- MD5 | 14 ++++---- NAMESPACE | 54 +++++++++++++++++----------------- NEWS.md | 9 +++-- R/all_speedglm.R | 57 ++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/allestimates-vignette.html | 38 ++++++++++++++++++------ man/all_speedglm.Rd | 2 - 8 files changed, 112 insertions(+), 72 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.5.0 dated 2020-09-01 and 0.6.0 dated 2021-01-20
mcmcsae-0.5.0/mcmcsae/man/labels.dc.Rd |only mcmcsae-0.6.0/mcmcsae/DESCRIPTION | 16 mcmcsae-0.6.0/mcmcsae/MD5 | 113 ++- mcmcsae-0.6.0/mcmcsae/NAMESPACE | 4 mcmcsae-0.6.0/mcmcsae/NEWS |only mcmcsae-0.6.0/mcmcsae/R/MCMCsim.R | 81 ++ mcmcsae-0.6.0/mcmcsae/R/MH.R | 4 mcmcsae-0.6.0/mcmcsae/R/MatrixUtils.R | 72 +- mcmcsae-0.6.0/mcmcsae/R/RcppExports.R | 8 mcmcsae-0.6.0/mcmcsae/R/TMVN_sampler.R | 35 - mcmcsae-0.6.0/mcmcsae/R/cholesky.R | 2 mcmcsae-0.6.0/mcmcsae/R/family.R | 2 mcmcsae-0.6.0/mcmcsae/R/formulas.R | 6 mcmcsae-0.6.0/mcmcsae/R/kronprod.R | 33 - mcmcsae-0.6.0/mcmcsae/R/mc_block.R | 140 +++- mcmcsae-0.6.0/mcmcsae/R/mc_gen.R | 16 mcmcsae-0.6.0/mcmcsae/R/mc_mec.R |only mcmcsae-0.6.0/mcmcsae/R/mc_reg.R | 2 mcmcsae-0.6.0/mcmcsae/R/mc_vfac.R | 2 mcmcsae-0.6.0/mcmcsae/R/model_eval.R | 2 mcmcsae-0.6.0/mcmcsae/R/modelmatrix.R | 29 - mcmcsae-0.6.0/mcmcsae/R/models.R | 2 mcmcsae-0.6.0/mcmcsae/R/parallel.R | 3 mcmcsae-0.6.0/mcmcsae/R/prediction.R | 130 ++-- mcmcsae-0.6.0/mcmcsae/R/priors.R | 51 + mcmcsae-0.6.0/mcmcsae/R/random.R | 2 mcmcsae-0.6.0/mcmcsae/R/samplers.R | 243 +++++--- mcmcsae-0.6.0/mcmcsae/R/sparse_template.R | 23 mcmcsae-0.6.0/mcmcsae/R/tabMatrix.R | 4 mcmcsae-0.6.0/mcmcsae/build/vignette.rds |binary mcmcsae-0.6.0/mcmcsae/inst/doc/area_level.Rmd | 2 mcmcsae-0.6.0/mcmcsae/inst/doc/area_level.html | 368 +++---------- mcmcsae-0.6.0/mcmcsae/inst/doc/linear_weighting.Rmd | 7 mcmcsae-0.6.0/mcmcsae/inst/doc/linear_weighting.html | 340 ++---------- mcmcsae-0.6.0/mcmcsae/inst/doc/unit_level.Rmd | 4 mcmcsae-0.6.0/mcmcsae/inst/doc/unit_level.html | 320 ++--------- mcmcsae-0.6.0/mcmcsae/man/MCMC-object-conversion.Rd | 8 mcmcsae-0.6.0/mcmcsae/man/create_TMVN_sampler.Rd | 3 mcmcsae-0.6.0/mcmcsae/man/create_sampler.Rd | 55 + mcmcsae-0.6.0/mcmcsae/man/generate_data.Rd | 7 mcmcsae-0.6.0/mcmcsae/man/labels.Rd |only mcmcsae-0.6.0/mcmcsae/man/mcmcsae-family.Rd | 2 mcmcsae-0.6.0/mcmcsae/man/mec.Rd |only mcmcsae-0.6.0/mcmcsae/man/par_names.Rd | 2 mcmcsae-0.6.0/mcmcsae/man/pr_fixed.Rd |only mcmcsae-0.6.0/mcmcsae/man/pr_gig.Rd |only mcmcsae-0.6.0/mcmcsae/man/read_draws.Rd | 5 mcmcsae-0.6.0/mcmcsae/src/RcppExports.cpp | 25 mcmcsae-0.6.0/mcmcsae/src/c_export.cpp | 2 mcmcsae-0.6.0/mcmcsae/src/chMatrix.c | 14 mcmcsae-0.6.0/mcmcsae/src/mcmcsae_init.c | 8 mcmcsae-0.6.0/mcmcsae/src/random.cpp | 31 - mcmcsae-0.6.0/mcmcsae/src/speed_ups.cpp | 55 + mcmcsae-0.6.0/mcmcsae/tests/testthat/test_Cholesky.R | 7 mcmcsae-0.6.0/mcmcsae/tests/testthat/test_Kronecker.R | 8 mcmcsae-0.6.0/mcmcsae/tests/testthat/test_linreg.R | 82 +- mcmcsae-0.6.0/mcmcsae/tests/testthat/test_negbinreg.R | 34 + mcmcsae-0.6.0/mcmcsae/tests/testthat/test_prior_sampling.R | 2 mcmcsae-0.6.0/mcmcsae/vignettes/area_level.Rmd | 2 mcmcsae-0.6.0/mcmcsae/vignettes/linear_weighting.Rmd | 7 mcmcsae-0.6.0/mcmcsae/vignettes/unit_level.Rmd | 4 61 files changed, 1170 insertions(+), 1259 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-18 0.0.6
2020-11-11 0.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-19 2.6.0
2020-08-05 2.5.0
2020-06-04 2.4.0
2020-05-13 2.3.0
2020-03-18 2.2.0
2020-02-08 2.1.0
2019-12-10 2.0.0
2019-10-10 1.6.0
2019-08-01 1.5.0
2019-06-08 1.4.0
2019-04-23 1.3.0
2019-02-15 1.2.0
2019-01-23 1.1.0
2019-01-02 1.0.0
2018-12-12 0.4.0
2018-11-23 0.3.0
2018-11-19 0.2.0
2018-10-14 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-03 0.1.2
2020-09-03 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-07 0.1.1
2020-10-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-15 1.2.1
2020-02-24 1.1.0
2020-02-11 1.0.0
2019-10-22 0.2.0
2019-07-31 0.1.2
2019-03-10 0.1.1
2018-12-03 0.0.1
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Mathilde Hagens [ctb],
Andreas Hofmann [ctb],
Jens-Daniel Mueller [ctb],
Aurélien Proye [ctb],
James Rae [ctb],
Karline Soetaert [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.2.14 dated 2020-10-30 and 3.2.15 dated 2021-01-20
seacarb-3.2.14/seacarb/R/at.R |only seacarb-3.2.14/seacarb/man/at.Rd |only seacarb-3.2.15/seacarb/ChangeLog | 5 +++++ seacarb-3.2.15/seacarb/DESCRIPTION | 10 +++++----- seacarb-3.2.15/seacarb/MD5 | 8 ++++---- seacarb-3.2.15/seacarb/R/fCO2insi.R |only seacarb-3.2.15/seacarb/man/fCO2insi.Rd |only 7 files changed, 14 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-04 1.4.8
2019-11-25 1.4.7
2019-03-21 1.4.6
2015-07-16 1.4.5
2014-02-14 1.4.4
2013-12-24 1.4.3
2013-02-06 1.4.2
2010-01-29 1.4.1
2009-01-22 1.4
2006-12-06 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-07 1.0.2
2020-03-09 1.0.1
2020-02-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-08 1.0.10
2020-02-12 1.0.9
2019-11-02 1.0.8
2019-09-03 1.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-01 1.1.24
2020-03-10 1.1.23
2020-02-12 1.1.22
2020-02-04 1.1.21
2020-01-11 1.1.20
2019-12-17 1.1.19
2019-11-04 1.1.18
2019-09-29 1.1.17
2019-09-02 1.1.16
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] (Methods for mutating vertical tabs &
updateMultiInput),
Wil Davis [ctb] (numericRangeInput function),
Spencer Matthews [ctb] (autoNumeric methods)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.5.5 dated 2021-01-13 and 0.5.6 dated 2021-01-20
DESCRIPTION | 6 MD5 | 514 - NAMESPACE | 336 NEWS.md | 7 R/actionBttn.R | 360 - R/addSpinner.R | 504 - R/bootstrap-utils.R | 200 R/chooseSliderSkin.R | 408 - R/demos.R | 136 R/dependencies.R | 656 - R/drop-menu.R | 482 - R/execute_safely.R | 112 R/input-actiongroupbuttons.R | 192 R/input-airDatepicker.R | 762 +- R/input-autonumeric.R | 1218 +-- R/input-awesomecheckbox.R | 690 - R/input-awesomeradio.R | 510 - R/input-checkboxgroupbuttons.R | 674 - R/input-circlebutton.R | 152 R/input-colorselector.R | 356 - R/input-dropdown.R | 486 - R/input-favbutton.R | 180 R/input-icon.R | 592 - R/input-knob.R | 430 - R/input-materialswitch.R | 182 R/input-multi.R | 438 - R/input-noUiSlider.R | 556 - R/input-numericRange.R | 212 R/input-pretty.R | 1472 ++-- R/input-radiogroupbuttons.R | 606 - R/input-search.R | 336 R/input-selectpicker.R | 618 - R/input-sliderText.R | 444 - R/input-spectrum.R | 340 R/input-switch.R | 636 - R/input-textaddon.R | 100 R/module-pickerGroup.R | 602 - R/module-selectizeGroup.R | 524 - R/module-utils.R | 108 R/onLoad.R | 80 R/pickerOptions.R | 236 R/progressBars.R | 366 - R/set-background.R | 422 - R/setShadow.R | 238 R/setSliderColor.R | 164 R/shinyWidgets.R | 24 R/shinyWidgetsGallery.R | 44 R/stati-card.R | 168 R/sw-dropdown.R | 484 - R/sweetalert.R | 1306 +-- R/useArgonDash.R | 336 R/useBs4Dash.R | 266 R/useShinydashboard.R | 220 R/useShinydashboardPlus.R | 402 - R/useTablerDash.R | 50 R/utils.R | 386 - R/vertical-tab.R | 670 - README.md | 478 - inst/assets/air-datepicker/datepicker-bindings.js | 480 - inst/assets/air-datepicker/datepicker.min.css | 2 inst/assets/air-datepicker/i18n/datepicker.it.js | 24 inst/assets/air-datepicker/i18n/datepicker.ja.js | 22 inst/assets/air-datepicker/i18n/datepicker.ru.js | 24 inst/assets/air-datepicker/i18n/datepicker.tr.js | 24 inst/assets/air-datepicker2/datepicker-bindings.js | 476 - inst/assets/air-datepicker2/i18n/datepicker.it.js | 24 inst/assets/air-datepicker2/i18n/datepicker.ja.js | 24 inst/assets/animate/LICENSE | 42 inst/assets/animate/animate-config.json | 242 inst/assets/animate/animate.min.css | 20 inst/assets/autonumeric/autoNumeric.min.js | 12 inst/assets/autonumeric/autonumeric-bindings.js | 168 inst/assets/awesome-bootstrap-checkbox/LICENSE | 40 inst/assets/awesome-bootstrap-checkbox/awesome-bootstrap-checkbox.min.css | 4 inst/assets/awesome-bootstrap-checkbox/awesome-bootstrap-checkbox.scss | 544 - inst/assets/awesome-bootstrap-checkbox/awesomeCheckbox-bindings.js | 188 inst/assets/awesome-bootstrap-checkbox/awesomeRadio-bindings.js | 176 inst/assets/awesome-bootstrap-checkbox/compile-css.R | 104 inst/assets/bootstrap-select/css/bootstrap-select.min.css | 10 inst/assets/bootstrap-select/js/i18n/defaults-am_ET.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-ar_AR.js | 98 inst/assets/bootstrap-select/js/i18n/defaults-bg_BG.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-cs_CZ.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-da_DK.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-de_DE.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-en_US.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-es_CL.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-es_ES.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-et_EE.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-eu.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-fa_IR.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-fi_FI.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-fr_FR.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-hr_HR.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-hu_HU.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-id_ID.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-it_IT.js | 78 inst/assets/bootstrap-select/js/i18n/defaults-ja_JP.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-kh_KM.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-ko_KR.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-lt_LT.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-lv_LV.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-nb_NO.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-nl_NL.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-pl_PL.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-pt_BR.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-pt_PT.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-ro_RO.js | 76 inst/assets/bootstrap-select/js/i18n/defaults-ru_RU.js | 76 inst/assets/bootstrap-select/js/i18n/defaults-sk_SK.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-sl_SI.js | 84 inst/assets/bootstrap-select/js/i18n/defaults-sr_SP.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-sv_SE.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-th_TH.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-tr_TR.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-ua_UA.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-vi_VN.js | 88 inst/assets/bootstrap-select/js/i18n/defaults-zh_CN.js | 74 inst/assets/bootstrap-select/js/i18n/defaults-zh_TW.js | 74 inst/assets/bootstrap-select/picker-bindings.js | 156 inst/assets/bootstrap-switch/LICENSE.txt | 42 inst/assets/bootstrap-switch/bootstrap-switch-3.3.4/bootstrap-switch.min.css | 18 inst/assets/bootstrap-switch/bootstrap-switch-3.3.4/bootstrap-switch.min.js | 20 inst/assets/bootstrap-switch/switch-bindings.js | 132 inst/assets/bounty/bounty-wrapper.js | 186 inst/assets/bttn/bttn.min.css | 24 inst/assets/buttons-group/checkboxGroupButtons-bindings.js | 320 inst/assets/buttons-group/checkboxGroupButtons.css | 94 inst/assets/buttons-group/radioGroupButtons-bindings.js | 266 inst/assets/buttons-group/radioGroupButtons.css | 200 inst/assets/circleButton/circle-button.css | 168 inst/assets/colorSelector/sw-color-selector.css | 70 inst/assets/dropdown/dropdown-click.js | 194 inst/assets/favButton/fav-button-14.js | 380 - inst/assets/favButton/fav-button-16.js | 262 inst/assets/favButton/fav-button-5.js | 208 inst/assets/favButton/fav-button-8.js | 312 inst/assets/favButton/fav-button.css | 286 inst/assets/favButton/fav-icons.css | 104 inst/assets/favButton/mo.min.js | 26 inst/assets/jquery-knob/jquery.knob.min.js | 2 inst/assets/jquery-knob/knob-bindings.js | 410 - inst/assets/material-switch/material-switch.css | 96 inst/assets/modules/styles-modules.css | 44 inst/assets/multi/multi-bindings.js | 166 inst/assets/multi/multi-shiny.css | 12 inst/assets/nouislider/nouislider-bindings.js | 264 inst/assets/numeric/numeric-icon-bindings.js | 282 inst/assets/numeric/text-icon-bindings.js | 150 inst/assets/numericRange/js/numericRange-bindings.js | 108 inst/assets/popper/popper.min.js | 10 inst/assets/search-input/search-bindings.js | 156 inst/assets/shinyWidgets-bindings.min.js | 2 inst/assets/shinyWidgets.css | 594 - inst/assets/shinyWidgets.min.css | 2 inst/assets/sliderText/sliderTextInput-bindings.js | 268 inst/assets/spectrum/spectrum-bindings.js | 150 inst/assets/spectrum/spectrum.css | 946 +- inst/assets/spectrum/spectrum.min.css | 14 inst/assets/spectrum/spectrum.min.js | 14 inst/assets/spectrum/sw-spectrum.css | 96 inst/assets/spinner/spin.css | 1464 ++-- inst/assets/stati/stati.css | 136 inst/assets/sw-dropdown/sw-dropdown.css | 112 inst/assets/sw-dropdown/sw-dropdown.js | 288 inst/assets/sweetalert2/LICENSE.txt | 44 inst/assets/sweetalert2/sweetalert-bindings.js | 198 inst/assets/tippy/dist/animations.min.css | 2 inst/assets/tippy/dist/themes.min.css | 2 inst/assets/tippy/dist/tippy-bundle.iife.min.js | 4 inst/assets/tippy/drop-menu-bindings.js | 156 inst/assets/uglify.R | 128 inst/assets/vertical-tab-panel/vertical-tab-panel-bindings.js | 92 inst/assets/vertical-tab-panel/vertical-tab-panel.css | 178 inst/assets/vertical-tab-panel/vertical-tab-panel.js | 52 inst/examples/airDatepicker/datepicker/app.R | 254 inst/examples/airDatepicker/months/app.R | 196 inst/examples/airDatepicker/timepicker/app.R | 176 inst/examples/airDatepicker/update/app.R | 206 inst/examples/airDatepicker/years/app.R | 176 inst/examples/bookmarking/test-sw.R | 96 inst/examples/bookmarking/test-switchInput.R | 44 inst/examples/bootstrapSwitch/server.R | 94 inst/examples/bootstrapSwitch/ui.R | 214 inst/examples/checkboxGroupButtons/server.R | 98 inst/examples/checkboxGroupButtons/ui.R | 292 inst/examples/colorSelector/example.R | 210 inst/examples/dropdown/ex-color-dropdown.R | 126 inst/examples/dropdown/ex-renderUI.R | 92 inst/examples/dropdown/ex-sw-dropdown.R | 78 inst/examples/examples-spin.R | 98 inst/examples/jQueryKnob/app.R | 154 inst/examples/multi/test-update.R | 130 inst/examples/nouislider/behaviour/app.R | 168 inst/examples/nouislider/color/app.R | 212 inst/examples/nouislider/format/app.R | 178 inst/examples/nouislider/more/app.R | 290 inst/examples/nouislider/update/app.R | 278 inst/examples/numericRange/app.R | 42 inst/examples/pretty/pretty_readme.R | 136 inst/examples/progressBars/app.R | 212 inst/examples/radioGroupButtons/server.R | 98 inst/examples/radioGroupButtons/ui.R | 300 inst/examples/selectPicker/server.R | 90 inst/examples/selectPicker/ui.R | 460 - inst/examples/shinyWidgets/code_dropdown.R | 124 inst/examples/shinyWidgets/code_dropdownButton.R | 116 inst/examples/shinyWidgets/code_sa.R | 116 inst/examples/shinyWidgets/global.R | 270 inst/examples/shinyWidgets/server.R | 732 +- inst/examples/shinyWidgets/ui.R | 3466 +++++----- inst/examples/update_switchInput.R | 298 man/airDatepicker.Rd | 400 - man/autonumericInput.Rd | 574 - man/formaNumericInputUpdate.Rd | 188 man/formatNumericInput.Rd | 252 man/numericInputIcon.Rd | 230 man/numericRangeInput.Rd | 130 man/stati-card.Rd | 2 man/textInputIcon.Rd | 202 man/updateAutonumericInput.Rd | 218 tests/testthat.R | 8 tests/testthat/helper.R | 42 tests/testthat/test-SweetAlert.R | 338 tests/testthat/test-airdatepicker.R | 176 tests/testthat/test-autonumeric.R | 234 tests/testthat/test-bsplus.R | 144 tests/testthat/test-checkboxGroupButtons.R | 358 - tests/testthat/test-chooseSliderSkin.R | 86 tests/testthat/test-colorSelector.R | 62 tests/testthat/test-drop-menu.R | 104 tests/testthat/test-dropdown.R | 60 tests/testthat/test-dropdownButton.R | 52 tests/testthat/test-input-icon.R | 122 tests/testthat/test-knob.R | 106 tests/testthat/test-modules.R | 158 tests/testthat/test-multi.R | 106 tests/testthat/test-noUiSlider.R | 38 tests/testthat/test-numericRange.R | 140 tests/testthat/test-panel.R | 76 tests/testthat/test-pickerOptions.R | 40 tests/testthat/test-radioGroupButtons.R | 358 - tests/testthat/test-set-background.R | 60 tests/testthat/test-setShadow.R | 30 tests/testthat/test-shinyWidgetsGallery.R | 34 tests/testthat/test-sliderText.R | 144 tests/testthat/test-spectrum.R | 48 tests/testthat/test-spinners.R | 188 tests/testthat/test-textInputAddon.R | 32 tests/testthat/test-updateAwesomeCheckbox.R | 40 tests/testthat/test-updateAwesomeCheckboxGroup.R | 40 tests/testthat/test-updateAwesomeRadio.R | 40 tests/testthat/test-updateCheckboxGroupButtons.R | 86 tests/testthat/test-updateMaterialSwitch.R | 38 tests/testthat/test-updateRadioGroupButtons.R | 86 tests/testthat/test-updateSwitchInput.R | 42 tests/testthat/test-utilityinputs.R | 100 tests/testthat/test-vertical-tab.R | 100 258 files changed, 27972 insertions(+), 27965 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb]
(<https://orcid.org/0000-0002-2951-6647>, R/blav_compare.R,
R/ctr_bayes_fit.R),
Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>,
R/ctr_bayes_fit.R, R/ctr_ppmc.R),
Huub Hoofs [ctb] (R/ctr_bayes_fit.R),
Rens van de Schoot [ctb] (R/ctr_bayes_fit.R)
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.3-13 dated 2021-01-18 and 0.3-14 dated 2021-01-20
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- inst/testdata/sysdata.rda |binary tests/lavExport |only 4 files changed, 7 insertions(+), 5 deletions(-)