Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-1 dated 2019-10-05 and 0.3-2 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/tbm.R | 4 +++- inst/NEWS.Rd | 8 ++++++++ inst/doc/tbm_supplement.pdf |binary tests/bodyfat.R | 6 +++--- tests/bodyfat.Rout.save | 12 ++++++------ 7 files changed, 30 insertions(+), 20 deletions(-)
Title: 'Lua' filters for R Markdown
Description: A collection of 'Lua' filters that extend the functionality
of R Markdown templates (e.g., count words or post-process 'pandoc-citeproc'-
citations).
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between rmdfiltr versions 0.1.1 dated 2019-12-09 and 0.1.2 dated 2019-12-11
rmdfiltr-0.1.1/rmdfiltr/man/verify_pandoc_version.Rd |only rmdfiltr-0.1.2/rmdfiltr/DESCRIPTION | 6 - rmdfiltr-0.1.2/rmdfiltr/MD5 | 27 ++-- rmdfiltr-0.1.2/rmdfiltr/NAMESPACE | 1 rmdfiltr-0.1.2/rmdfiltr/R/add_lua_filter.R | 8 + rmdfiltr-0.1.2/rmdfiltr/R/utils.R | 58 +++++----- rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.R | 16 +- rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.Rmd | 7 + rmdfiltr-0.1.2/rmdfiltr/inst/doc/replace_ampersands.html | 21 +-- rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.R | 16 +- rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.Rmd | 7 + rmdfiltr-0.1.2/rmdfiltr/inst/doc/wordcount.html | 23 +-- rmdfiltr-0.1.2/rmdfiltr/tests/testthat/test_convenience_functions.R | 2 rmdfiltr-0.1.2/rmdfiltr/vignettes/replace_ampersands.Rmd | 7 + rmdfiltr-0.1.2/rmdfiltr/vignettes/wordcount.Rmd | 7 + 15 files changed, 118 insertions(+), 88 deletions(-)
Title: Request <https://openblender.io> API Services
Description: Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.
Author: Open Blender Inc. [cph],
Daniel V. Pinacho [aut, cre]
Maintainer: Daniel V. Pinacho <danielvpinacho@gmail.com>
Diff between openblender versions 0.3.3 dated 2019-12-06 and 0.3.4 dated 2019-12-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/get_observations.R | 16 ++++++++++++++++ R/utils.R | 10 ++-------- 4 files changed, 24 insertions(+), 14 deletions(-)
Title: Semi-Supervised Model for Geographical Document Classification
Description: Semi-supervised model for geographical document classification (Watanabe 2018) <doi:10.1080/21670811.2017.1293487>.
This package currently contains seed dictionaries in English, German, French, Spanish, Russian, Hebrew, Arabic Japanese and Chinese (Simplified and Traditional).
Author: Kohei Watanabe [aut, cre, cph],
Stefan Müller [aut],
Dani Madrid-Morales [aut],
Katerina Tertytchnaya [aut],
Ke Cheng [aut],
Chung-hong Chan [aut],
Claude Grasland [aut],
Giuseppe Carteny [aut],
Elad Segev [aut],
Dai Yamao [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between newsmap versions 0.6.9 dated 2019-07-29 and 0.7.0 dated 2019-12-11
DESCRIPTION | 23 +++++++++++---------- MD5 | 20 ++++++++++-------- NEWS.md | 4 +++ R/data.R | 16 ++++++++++++++ README.md | 19 ++++++++--------- data/data_dictionary_newsmap_ar.RData |only data/data_dictionary_newsmap_he.RData |only man/data_dictionary_newsmap_ar.Rd |only man/data_dictionary_newsmap_he.Rd |only man/predict.textmodel_newsmap.Rd | 10 +++++++-- man/textmodel_newsmap.Rd | 3 -- tests/testthat/test-data.R | 31 +++++++++++++++++++--------- tests/testthat/test-textmodel_newsmap.R | 35 +++++++++++++++++++++++++++++++- 13 files changed, 118 insertions(+), 43 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.7.1 dated 2019-07-14 and 0.7.2 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- data/divorce_margarine.rda |binary inst/script/make-divorce_margarine.R | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Calculates Power, Sample Size, or Detectable Effect for
Longitudinal Analyses
Description: Computes power, or sample size or the detectable difference for a repeated measures model with attrition. It requires the variance covariance matrix of the observations but can compute this matrix for several common random effects models. See Diggle, P, Liang, KY and Zeger, SL (1994, ISBN:9780198522843).
Author: David A. Schoenfeld
Maintainer: David A. Schoenfeld <Dschoenfeld@mgh.harvard.edu>
Diff between LPower versions 0.1.0 dated 2018-05-11 and 0.1.1 dated 2019-12-11
DESCRIPTION | 6 +++--- MD5 | 5 +++-- R/powslopes_new1.R | 8 ++++---- R/powslopes_new2.R |only 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao Alexandra
J. White (2019) A quantile-based g-computation approach to addressing
the effects of exposure mixtures; <arXiv:1902.04200> [stat.ME].
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 1.2.0 dated 2019-11-12 and 1.3.0 dated 2019-12-11
DESCRIPTION | 8 - MD5 | 44 +++--- NAMESPACE | 4 NEWS.md | 12 + R/base.R | 291 +++++++++++++++++++++++++++++------------- R/base_surv.R | 97 ++++++++------ R/data.R | 3 inst/doc/qgcomp-vignette.R | 47 ++++-- inst/doc/qgcomp-vignette.Rmd | 126 +++++++++++------- inst/doc/qgcomp-vignette.html | 197 +++++++++++++++++----------- man/coxmsm.fit.Rd | 4 man/metals.Rd | 3 man/msm.fit.Rd | 2 man/msm.predict.Rd | 2 man/plot.qgcompfit.Rd | 18 ++ man/predict.qgcompfit.Rd | 3 man/qgcomp.Rd | 20 ++ man/qgcomp.cox.boot.Rd | 26 ++- man/qgcomp.cox.noboot.Rd | 14 +- man/se_comb.Rd | 30 ++-- tests/test_asis.R |only tests/test_boot_vs_noboot.R | 9 - tests/test_cox_msmtest.R |only vignettes/qgcomp-vignette.Rmd | 126 +++++++++++------- 24 files changed, 724 insertions(+), 362 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@gmail.com>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.2.3 dated 2019-01-08 and 1.2.4 dated 2019-12-11
DESCRIPTION | 12 +- MD5 | 84 ++++++++++---------- NEWS | 6 + R/SEA.R | 16 +++ R/kdffreq.R | 17 ++-- R/paleofire-package.R | 6 + R/pfCircular.R | 2 R/pfCompositeLF.R | 23 +++-- R/pfDotMap.r | 2 R/pfGridding.R | 174 +++++++++++++++++++++++-------------------- R/pfSimpleGrid.r | 2 R/pfSiteSel.R | 4 R/pfTransform.R | 95 ++++++++++++----------- R/potveg.R | 1 R/pretreatment.R | 6 - R/zzz.R | 1 build/vignette.rds |binary inst/doc/paleofire-paper.pdf |binary man/SEA.Rd | 17 +++- man/checkGCDversion.Rd | 2 man/kdffreq.Rd | 18 +++- man/paleofire-package.Rd | 10 +- man/pfAddData.Rd | 14 ++- man/pfCircular.Rd | 3 man/pfComposite.Rd | 9 +- man/pfCompositeLF.Rd | 13 ++- man/pfDiagnostic.Rd | 21 +++-- man/pfDotMap.Rd | 20 +++- man/pfGridding.Rd | 19 +++- man/pfKruskal.Rd | 3 man/pfSimpleGrid.Rd | 33 +++++--- man/pfTransform.Rd | 22 ++++- man/plot.CHAR.Rd | 16 +++ man/plot.kdffreq.Rd | 14 ++- man/plot.pfCircular.Rd | 12 ++ man/plot.pfComposite.Rd | 12 ++ man/plot.pfCompositeLF.Rd | 16 +++ man/plot.pfGridding.Rd | 21 ++++- man/plot.pfKruskal.Rd | 3 man/plot.pfSiteSel.Rd | 16 +++ man/plot.potveg.Rd | 11 ++ man/potveg.Rd | 2 man/pretreatment.Rd | 10 +- 43 files changed, 513 insertions(+), 275 deletions(-)
Title: Nima Hejazi's R Toolbox
Description: Miscellaneous R functions developed as collateral damage over the
course of work in statistical and scientific computing for research. These
include, for example, utilities that supplement existing idiosyncrasies of
the R language, extend existing plotting functionality and aesthetics, help
prepare data objects for imputation, and extend access to command line tools
and systems-level information.
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>)
Maintainer: Nima Hejazi <nh@nimahejazi.org>
Diff between nima versions 0.5.0 dated 2018-05-21 and 0.6.1 dated 2019-12-11
nima-0.5.0/nima/R/compare.R |only nima-0.5.0/nima/R/factornum.R |only nima-0.5.0/nima/R/mse.R |only nima-0.5.0/nima/R/qrDecomp.R |only nima-0.5.0/nima/R/utilities.R |only nima-0.5.0/nima/man/compFun.Rd |only nima-0.5.0/nima/man/factornum.Rd |only nima-0.5.0/nima/man/lmPlots_gg.Rd |only nima-0.5.0/nima/man/qqPlot_gg.Rd |only nima-0.5.0/nima/man/qrD.Rd |only nima-0.5.0/nima/tests/testthat/test-compare.R |only nima-0.5.0/nima/tests/testthat/test-factornum.R |only nima-0.5.0/nima/tests/testthat/test-ggPlots.R |only nima-0.5.0/nima/tests/testthat/test-qrDecomp.R |only nima-0.6.1/nima/DESCRIPTION | 29 +- nima-0.6.1/nima/LICENSE | 2 nima-0.6.1/nima/MD5 | 79 +++--- nima-0.6.1/nima/NAMESPACE | 21 + nima-0.6.1/nima/NEWS.md | 65 ++++- nima-0.6.1/nima/R/absmax.R | 1 nima-0.6.1/nima/R/attribute_names.R | 3 nima-0.6.1/nima/R/commas.R | 1 nima-0.6.1/nima/R/discrete_by_quantile.R | 10 nima-0.6.1/nima/R/factor_to_numeric.R |only nima-0.6.1/nima/R/missing_ind.R | 1 nima-0.6.1/nima/R/plots.R | 156 +++++++------ nima-0.6.1/nima/R/risk.R |only nima-0.6.1/nima/R/simulation_tools.R |only nima-0.6.1/nima/R/theme_jetblack.R | 8 nima-0.6.1/nima/R/theme_nima.R | 1 nima-0.6.1/nima/R/uniqlen.R | 1 nima-0.6.1/nima/R/utils.R |only nima-0.6.1/nima/man/attrnames.Rd | 2 nima-0.6.1/nima/man/clear.Rd | 7 nima-0.6.1/nima/man/discrete_by_quantile.Rd | 6 nima-0.6.1/nima/man/exit.Rd | 2 nima-0.6.1/nima/man/factor_to_num.Rd |only nima-0.6.1/nima/man/hweb.Rd | 6 nima-0.6.1/nima/man/lm_plot.Rd |only nima-0.6.1/nima/man/mse.Rd | 6 nima-0.6.1/nima/man/nll.Rd |only nima-0.6.1/nima/man/openfile.Rd | 7 nima-0.6.1/nima/man/qq_plot.Rd |only nima-0.6.1/nima/man/sim_plot.Rd |only nima-0.6.1/nima/man/summarize_sim.Rd |only nima-0.6.1/nima/man/theme_jetblack.Rd | 1 nima-0.6.1/nima/man/theme_nima.Rd | 1 nima-0.6.1/nima/tests/testthat/test-absmax.R | 1 nima-0.6.1/nima/tests/testthat/test-commas.R | 1 nima-0.6.1/nima/tests/testthat/test-discrete_by_quantile.R | 1 nima-0.6.1/nima/tests/testthat/test-factor_to_num.R |only nima-0.6.1/nima/tests/testthat/test-missing_ind.R | 18 - nima-0.6.1/nima/tests/testthat/test-uniqlen.R | 1 53 files changed, 261 insertions(+), 177 deletions(-)
Title: Global Charcoal Database
Description: Contains the Global Charcoal database data. Data include charcoal
series (age, depth, charcoal quantity, associated units and methods) and
information on sedimentary sites (localisation, depositional environment, biome,
etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between GCD versions 4.0.4 dated 2018-11-28 and 4.0.5 dated 2019-12-11
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++++------- NEWS | 33 +++++++++++++++++++++- R/GCD-package.R | 70 +++++++++++++++++++++++++++++++++++++++++++++++- data/datalist | 3 ++ data/date.rda |only data/date_type.rda |only data/mat_dated.rda |only data/paleofiredata.rda |binary data/paleofiresites.rda |binary data/pub.rda |binary data/pub_key.rda |binary data/release.rda |binary man/GCD-package.Rd | 10 +++--- man/date.Rd |only man/date_type.Rd |only man/mat_dated.Rd |only 17 files changed, 130 insertions(+), 22 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.4.4 dated 2019-08-20 and 1.4.5 dated 2019-12-11
DESCRIPTION | 12 ++- MD5 | 39 ++++++----- R/GetBingMap.R | 2 R/GetMap.R | 9 +- R/GetMap.bbox.R | 7 +- R/GetMapTiles.R | 145 ++++++++++++++++++++++++++++++------------- R/LatLon2XY.centered.R | 26 +++---- R/PlotOnMapTiles.R | 36 ++++++++-- R/PlotOnStaticMap.R | 10 +-- R/genStaticMap.R | 18 ++++- R/getGeoCode.R | 153 ++++++++++++++++++++++++++-------------------- R/plotOSM.R |only man/GetBingMap.Rd | 2 man/GetMap.Rd | 12 ++- man/GetMap.bbox.Rd | 11 ++- man/GetMapTiles.Rd | 109 ++++++++++++++++++++++---------- man/PlotOnMapTiles.Rd | 10 +-- man/genStaticMap.Rd | 13 ++- man/geosphere_mercator.Rd |only man/getGeoCode.Rd | 8 +- man/osmtile_bbox.Rd |only man/plotOSM.Rd |only man/plotOSMtile.Rd |only 23 files changed, 399 insertions(+), 223 deletions(-)
Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called databionic swarm (DBS) is introduced. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>. A comparison to 26 common clustering algorithms on 15 datasets is presented on the website.
Author: Michael Thrun [aut, cre, cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DatabionicSwarm versions 1.1.1 dated 2019-01-27 and 1.1.2 dated 2019-12-11
DatabionicSwarm-1.1.1/DatabionicSwarm/R/MultipleSwarms.R |only DatabionicSwarm-1.1.2/DatabionicSwarm/DESCRIPTION | 10 DatabionicSwarm-1.1.2/DatabionicSwarm/MD5 | 33 DatabionicSwarm-1.1.2/DatabionicSwarm/NAMESPACE | 2 DatabionicSwarm-1.1.2/DatabionicSwarm/R/DBSclustering.R | 23 DatabionicSwarm-1.1.2/DatabionicSwarm/R/Delaunay4Points.R | 2 DatabionicSwarm-1.1.2/DatabionicSwarm/R/RobustNorm_BackTrafo.R |only DatabionicSwarm-1.1.2/DatabionicSwarm/R/RobustNormalization.R | 57 DatabionicSwarm-1.1.2/DatabionicSwarm/build/partial.rdb |binary DatabionicSwarm-1.1.2/DatabionicSwarm/build/vignette.rds |binary DatabionicSwarm-1.1.2/DatabionicSwarm/inst/NEWS | 11 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.R | 42 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.Rmd | 131 DatabionicSwarm-1.1.2/DatabionicSwarm/inst/doc/DatabionicSwarm.html | 1798 +++++++++- DatabionicSwarm-1.1.2/DatabionicSwarm/man/Hepta.Rd | 6 DatabionicSwarm-1.1.2/DatabionicSwarm/man/RobustNorm_BackTrafo.Rd |only DatabionicSwarm-1.1.2/DatabionicSwarm/man/RobustNormalization.Rd | 29 DatabionicSwarm-1.1.2/DatabionicSwarm/man/setGridSize.Rd | 5 DatabionicSwarm-1.1.2/DatabionicSwarm/vignettes/DatabionicSwarm.Rmd | 131 19 files changed, 1946 insertions(+), 334 deletions(-)
More information about DatabionicSwarm at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-10 0.1.4
2018-10-07 0.1.3
2018-06-12 0.1.2
2018-06-10 0.1.1
Title: Estimate Univariate Gaussian or Student's t Mixture
Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR) and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.2.0 dated 2019-08-27 and 3.2.1 dated 2019-12-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/intro-to-uGMAR.html | 4 ++-- tests/testthat/test_standardErrors.R | 28 ++++++++++++++-------------- 5 files changed, 27 insertions(+), 23 deletions(-)
Title: Standard and User-Defined RGB Color Spaces, with Conversion
Between RGB and CIE XYZ
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesRGB versions 1.2-2 dated 2019-01-30 and 1.3-0 dated 2019-12-11
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NEWS.md | 4 ++ build/vignette.rds |binary inst/doc/spacesRGB-guide.R |only inst/doc/spacesRGB-guide.html | 62 ++++++++++++++++++++++++++++++------------ tests/CGATS.RR |only tests/test-ACES.R | 7 +++- tests/test-conversions.R | 4 +- 9 files changed, 68 insertions(+), 31 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 1.3 dated 2019-11-07 and 1.4 dated 2019-12-11
landscapemetrics-1.3/landscapemetrics/src/cclabel_4.c |only landscapemetrics-1.3/landscapemetrics/src/cclabel_8.c |only landscapemetrics-1.4/landscapemetrics/DESCRIPTION | 15 landscapemetrics-1.4/landscapemetrics/MD5 | 1043 +- landscapemetrics-1.4/landscapemetrics/NAMESPACE | 1888 ++-- landscapemetrics-1.4/landscapemetrics/NEWS.md | 278 landscapemetrics-1.4/landscapemetrics/R/RcppExports.R | 206 landscapemetrics-1.4/landscapemetrics/R/calculate_correlation.R | 364 landscapemetrics-1.4/landscapemetrics/R/calculate_lsm.R | 932 +- landscapemetrics-1.4/landscapemetrics/R/check_landscape.R | 325 landscapemetrics-1.4/landscapemetrics/R/construct_buffer.R | 374 landscapemetrics-1.4/landscapemetrics/R/data.R | 250 landscapemetrics-1.4/landscapemetrics/R/data_info.R | 84 landscapemetrics-1.4/landscapemetrics/R/extract_lsm.R | 869 +- landscapemetrics-1.4/landscapemetrics/R/get_adjacencies.R | 533 - landscapemetrics-1.4/landscapemetrics/R/get_boundaries.R | 524 - landscapemetrics-1.4/landscapemetrics/R/get_circumscribingcircle.R | 402 - landscapemetrics-1.4/landscapemetrics/R/get_nearestneighbour.R | 452 - landscapemetrics-1.4/landscapemetrics/R/get_patches.R | 672 - landscapemetrics-1.4/landscapemetrics/R/get_unique_values.R | 501 - landscapemetrics-1.4/landscapemetrics/R/landscapemetrics-package.R | 110 landscapemetrics-1.4/landscapemetrics/R/list_lsm.R | 410 - landscapemetrics-1.4/landscapemetrics/R/lsm_c_ai.R | 351 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_cv.R | 303 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_mn.R | 305 landscapemetrics-1.4/landscapemetrics/R/lsm_c_area_sd.R | 303 landscapemetrics-1.4/landscapemetrics/R/lsm_c_ca.R | 301 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_cv.R | 341 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_mn.R | 335 landscapemetrics-1.4/landscapemetrics/R/lsm_c_cai_sd.R | 339 landscapemetrics-1.4/landscapemetrics/R/lsm_c_circle_cv.R | 323 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landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-cv.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-mn.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-dcore-sd.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-division.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ed.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-cv.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-mn.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-enn-sd.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ent.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-cv.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-mn.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-frac-sd.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-cv.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-mn.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-gyrate-sd.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-iji.R | 68 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-joinent.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-lpi.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-lsi.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-mesh.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-msidi.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-msiei.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-mutinf.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ndca.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-np.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pafrac.R | 66 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-cv.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-mn.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-para-sd.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pd.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pladj.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-pr.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-prd.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-rpr.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-cv.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-mn.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shape-sd.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shdi.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-shei.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-sidi.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-siei.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-split.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-ta.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-tca.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-l-te.R | 66 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-area.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-cai.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-circle.R | 54 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-contig.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-core.R | 68 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-enn.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-frac.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-gyrate.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-nca.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-para.R | 50 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-perim.R | 54 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-lsm-p-shape.R | 48 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-matrix-to-raster.R | 96 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-options-landscapemetrics.R | 25 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-pad-raster.R | 92 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-raster-to-points.R | 84 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-rcpp-get-coocurrence-matrix.R | 204 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-rcpp-get-entropy.R | 46 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-sample-lsm.R | 428 - landscapemetrics-1.4/landscapemetrics/tests/testthat/test-scale-sample.R | 200 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-scale-window.R | 172 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-cores.R | 106 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-correlation.R | 117 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-lsm.R | 96 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-show-patches.R | 74 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-spatialize-lsm.R | 152 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-unique-values.R | 26 landscapemetrics-1.4/landscapemetrics/tests/testthat/test-unpad-raster.R |only landscapemetrics-1.4/landscapemetrics/tests/testthat/test-window-lsm.R | 84 landscapemetrics-1.4/landscapemetrics/tests/testthat/test_fragstats.R | 3884 +++++----- landscapemetrics-1.4/landscapemetrics/vignettes/getstarted.Rmd | 364 526 files changed, 52835 insertions(+), 50810 deletions(-)
More information about landscapemetrics at CRAN
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Title: Miscellaneous Utilities and Functions
Description: Miscellaneous tools and functions,
including: generate descriptive statistics tables,
format output, visualize relations among variables or check
distributions, and generic functions for residual and
model diagnostics.
Author: Joshua F. Wiley [aut, cre] (<https://orcid.org/0000-0002-0271-6702>)
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between JWileymisc versions 1.0.0 dated 2019-11-22 and 1.0.1 dated 2019-12-11
DESCRIPTION | 15 ++--- MD5 | 29 +++++----- NAMESPACE | 2 NEWS.md | 9 +++ R/diagnostics.R | 103 +++++++++++++++++++++++++++++++------ R/models.R | 25 +++++--- R/plotting.R | 97 ++++++++++++++++++++++++++-------- inst/doc/diagnostics-vignette.html | 8 +- inst/doc/model-test-vignette.html | 4 - man/dot-quantilePercentiles.Rd | 6 +- man/modelDiagnostics.Rd | 14 ++++- man/modelPerformance.Rd | 25 +++++--- man/plot.modelDiagnostics.lm.Rd | 9 +-- man/plot.residualDiagnostics.Rd |only man/residualDiagnostics.Rd | 18 ++++++ tests/testthat/test-scoring.R | 8 +- 16 files changed, 276 insertions(+), 96 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Noah Simon [aut],
Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 3.0-1 dated 2019-11-15 and 3.0-2 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 12 ++++++++++++ R/assess.glmnet.R | 42 +++++++++++++++++++++++++++--------------- R/confusion.glmnet.R | 4 +++- R/cv.mrelnet.R | 2 +- R/cv.multnet.R | 2 +- R/lambda.interp.R | 6 ++++-- R/pb.R | 2 +- R/predict.multnet.R | 3 ++- inst/doc/Coxnet.pdf |binary inst/doc/glmnet.pdf |binary inst/doc/relax.pdf |binary man/assess.glmnet.Rd | 42 +++++++++++++++++++++++++++--------------- src/glmnet_init.c | 4 ++-- src/pb.c | 3 ++- 16 files changed, 101 insertions(+), 59 deletions(-)
Title: Generalized Farlie-Gumbel-Morgenstern Copula
Description: Compute bivariate dependence measures and perform bivariate competing risks analysis under the generalized Farlie-Gumbel-Morgenstern (FGM) copula. See Shih and Emura (2018) <doi:10.1007/s00180-018-0804-0> and Shih and Emura (2019) <doi:10.1007/s00362-016-0865-5> for details.
Author: Jia-Han Shih
Maintainer: Jia-Han Shih <tommy355097@gmail.com>
Diff between GFGM.copula versions 1.0.3 dated 2018-04-02 and 1.0.4 dated 2019-12-11
DESCRIPTION | 12 +- MD5 | 34 +++---- NAMESPACE | 2 R/CvM.GFGM.BurrIII.R | 2 R/Depmeasure.GFGM.R | 4 R/GFGM.BurrIII.R | 4 R/MLE.GFGM.BurrIII.R | 4 R/MLE.GFGM.spline.R | 19 +--- R/Sdist.GFGM.BurrIII.R | 4 R/Sdist.GFGM.spline.R | 4 build/partial.rdb |binary man/CvM.GFGM.BurrIII.Rd | 187 ++++++++++++++++++++++-------------------- man/Dependence.GFGM.Rd | 70 +++++++-------- man/GFGM.BurrIII.Rd | 90 ++++++++++---------- man/MLE.GFGM.BurrIII.Rd | 202 ++++++++++++++++++++++++---------------------- man/MLE.GFGM.spline.Rd | 162 +++++++++++++++++------------------- man/Sdist.GFGM.BurrIII.Rd | 98 +++++++++++----------- man/Sdist.GFGM.spline.Rd | 100 +++++++++++----------- 18 files changed, 503 insertions(+), 495 deletions(-)
Title: Exact Distributions for Rank and Permutation Tests
Description: Computes exact conditional p-values and quantiles using an
implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between exactRankTests versions 0.8-30 dated 2019-04-28 and 0.8-31 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- data/ASAT.rda |binary data/bloodp.rda |binary data/ears.rda |binary data/glioma.rda |binary data/globulin.rda |binary data/lungcancer.rda |binary data/neuropathy.rda |binary data/ocarcinoma.rda |binary data/rotarod.rda |binary data/sal.rda |binary inst/NEWS | 6 +++++- tests/exactRankTests-Ex.R | 2 +- tests/exactRankTests-Ex.Rout.save | 12 ++++++------ 15 files changed, 30 insertions(+), 26 deletions(-)
More information about exactRankTests at CRAN
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Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.0.1 dated 2019-11-22 and 1.0.2 dated 2019-12-11
DESCRIPTION | 6 +-- MD5 | 34 +++++++++--------- NEWS | 6 +++ R/anon_plausible_values.R | 8 ++-- R/plausible_scores.R | 3 + R/plausible_values.R | 17 +++++---- R/resp_data.R | 12 +++--- inst/doc/DIF_vignette.html | 4 +- inst/doc/Equating.html | 10 ++--- inst/doc/Plausible_Values.R | 4 +- inst/doc/Plausible_Values.Rmd | 4 +- inst/doc/Plausible_Values.html | 18 ++++----- inst/doc/Test_Individual_differences.html | 12 +++--- inst/doc/dexter.html | 56 +++++++++++++++--------------- inst/doc/profile-plots.html | 4 +- tests/testthat/test_data_selection.R | 20 ++++++++++ tests/testthat/test_plausible_scores.R | 4 +- vignettes/Plausible_Values.Rmd | 4 +- 18 files changed, 130 insertions(+), 96 deletions(-)
Title: Motif Analyses of Bipartite Networks
Description: Counts occurrences of motifs in bipartite networks, as well as the number of
times each node or link appears in each unique position within motifs. Has support for both
binary and weighted motifs: can calculate the mean weight of motifs and the standard deviation
of their mean weights. Intended for use in ecology, but its methods are general and can be
applied to any bipartite network.
Author: Benno Simmons [aut, cre],
Michelle Sweering [aut],
Maybritt Schillinger [aut],
Riccardo Di Clemente [aut]
Maintainer: Benno Simmons <benno.simmons@gmail.com>
Diff between bmotif versions 1.0.0 dated 2018-01-29 and 2.0.0 dated 2019-12-11
bmotif-1.0.0/bmotif/R/normalise_positions.R |only bmotif-1.0.0/bmotif/R/positions.R |only bmotif-1.0.0/bmotif/man/positions.Rd |only bmotif-1.0.0/bmotif/tests/testthat/test_positions.R |only bmotif-2.0.0/bmotif/DESCRIPTION | 33 + bmotif-2.0.0/bmotif/LICENSE | 4 bmotif-2.0.0/bmotif/MD5 | 61 ++- bmotif-2.0.0/bmotif/NAMESPACE | 5 bmotif-2.0.0/bmotif/NEWS | 30 + bmotif-2.0.0/bmotif/R/RcppExports.R |only bmotif-2.0.0/bmotif/R/large_tensor.r |only bmotif-2.0.0/bmotif/R/link_positions.r |only bmotif-2.0.0/bmotif/R/mcount.R | 191 +++++++--- bmotif-2.0.0/bmotif/R/mean_weight.R |only bmotif-2.0.0/bmotif/R/motif_info.R |only bmotif-2.0.0/bmotif/R/motif_sd.R |only bmotif-2.0.0/bmotif/R/name_edge.R |only bmotif-2.0.0/bmotif/R/node_positions.R |only bmotif-2.0.0/bmotif/R/normalise_link_positions.R |only bmotif-2.0.0/bmotif/R/normalise_node_positions.R |only bmotif-2.0.0/bmotif/R/pop_sd.r |only bmotif-2.0.0/bmotif/R/sysdata.rda |binary bmotif-2.0.0/bmotif/R/testing_functions.R |only bmotif-2.0.0/bmotif/R/weighted_node_positions_output_row_names.R |only bmotif-2.0.0/bmotif/README.md | 170 ++++++++ bmotif-2.0.0/bmotif/build |only bmotif-2.0.0/bmotif/inst |only bmotif-2.0.0/bmotif/man/figures |only bmotif-2.0.0/bmotif/man/link_positions.Rd |only bmotif-2.0.0/bmotif/man/mcount.Rd | 81 +++- bmotif-2.0.0/bmotif/man/node_positions.Rd |only bmotif-2.0.0/bmotif/src |only bmotif-2.0.0/bmotif/tests/testthat/test_check_motif.R |only bmotif-2.0.0/bmotif/tests/testthat/test_link_positions.R |only bmotif-2.0.0/bmotif/tests/testthat/test_link_positions_weights.R |only bmotif-2.0.0/bmotif/tests/testthat/test_mcount.R | 80 +++- bmotif-2.0.0/bmotif/tests/testthat/test_mean_weight.R |only bmotif-2.0.0/bmotif/tests/testthat/test_motif_info.R |only bmotif-2.0.0/bmotif/tests/testthat/test_node_positions.R |only bmotif-2.0.0/bmotif/tests/testthat/test_normalise_node_positions.R |only bmotif-2.0.0/bmotif/tests/testthat/test_sd.R |only bmotif-2.0.0/bmotif/tests/testthat/test_weighted_node_pos_v2.R |only bmotif-2.0.0/bmotif/vignettes |only 43 files changed, 532 insertions(+), 123 deletions(-)
Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications.
Credentials are stored in an encrypted 'SQLite' database. Source code of main application
is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre],
Victor Perrier [aut]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between shinymanager versions 1.0 dated 2019-06-19 and 1.0.100 dated 2019-12-11
DESCRIPTION | 11 - MD5 | 56 ++++--- NAMESPACE | 2 NEWS.md |only R/language.R | 2 R/module-admin.R | 20 ++ R/module-auth.R | 92 ------------ R/module-pwd.R | 51 ------- R/secure-app.R | 119 ++++++---------- README.md | 21 ++ build |only inst/assets/styles-auth.css | 2 inst/assets/timeout.js | 2 inst/doc |only inst/sticker |only man/check_credentials.Rd | 126 ++++++++--------- man/create_db.Rd | 118 ++++++++-------- man/db-crypted.Rd | 184 ++++++++++++------------- man/fab_button.Rd | 150 ++++++++++---------- man/figures/add_user.png |only man/figures/password_table.png |only man/figures/popup.png |only man/figures/shinymanager-login.png |binary man/figures/shinymanager-pwd.png |binary man/figures/user_table.png |only man/generate_pwd.Rd | 42 ++--- man/module-authentication.Rd | 268 ++++++++++++++++++------------------- man/module-password.Rd | 185 +++++++++++++------------ man/secure-app.Rd | 187 +++++++++++++------------ tests/testthat/test-language.R |only tests/testthat/test-modules-ui.R | 13 + vignettes |only 32 files changed, 786 insertions(+), 865 deletions(-)
Title: Bivariate Pareto Models
Description: Perform competing risks analysis under bivariate Pareto models. See Shih et al. (2019) <doi:10.1080/03610926.2018.1425450> for details.
Author: Jia-Han Shih, Wei Lee
Maintainer: Jia-Han Shih <tommy355097@gmail.com>
Diff between Bivariate.Pareto versions 1.0.2 dated 2018-04-02 and 1.0.3 dated 2019-12-11
DESCRIPTION | 14 - MD5 | 30 ++-- NAMESPACE | 3 R/Frank.Pareto.R | 2 R/Kendall.SNBP.R | 4 R/MLE.Frank.Pareto.R | 4 R/MLE.Frank.Pareto.com.R | 15 +- R/MLE.SN.Pareto.R | 19 -- R/SN.Pareto.R | 2 build/partial.rdb |binary man/Frank.Pareto.Rd | 70 ++++----- man/Kendall.SNBP.Rd | 70 ++++----- man/MLE.Frank.Pareto.Rd | 301 +++++++++++++++++++++-------------------- man/MLE.Frank.Pareto.com.Rd | 293 +++++++++++++++++++++------------------- man/MLE.SN.Pareto.Rd | 317 ++++++++++++++++++++++---------------------- man/SN.Pareto.Rd | 76 +++++----- 16 files changed, 619 insertions(+), 601 deletions(-)
More information about Bivariate.Pareto at CRAN
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Title: Taxicab Correspondence Analysis
Description: Computation and visualization of Taxicab Correspondence Analysis, Choulakian (2006) <doi:10.1007/s11336-004-1231-4>. Classical correspondence analysis (CA) is a statistical method to analyse 2-dimensional tables of positive numbers and is typically applied to contingency tables (Benzecri, J.-P. (1973). L'Analyse des Donnees. Volume II. L'Analyse des Correspondances. Paris, France: Dunod). Classical CA is based on the Euclidean distance. Taxicab CA is like classical CA but is based on the Taxicab or Manhattan distance. For some tables, Taxicab CA gives more informative results than classical CA.
Author: Jacques Allard and Vartan Choulakian
Maintainer: Jacques Allard <jacques.allard@gmail.com>
Diff between TaxicabCA versions 0.1.0 dated 2018-07-18 and 0.1.1 dated 2019-12-11
DESCRIPTION | 8 - MD5 | 45 ++++---- NAMESPACE | 2 R/CombineCollinearRowsCols.R | 2 R/data.R | 2 R/saveTCA.r | 1 R/tca.R | 80 +++++++++++---- man/CombineCollinearRowsCols.Rd | 80 +++++++-------- man/ComputeLambda.Rd | 52 +++++----- man/CreateAllBinaries.Rd | 52 +++++----- man/JitterPosition.Rd | 60 +++++------ man/ListToObjects.Rd | 50 ++++----- man/RemoveRowsColumns0sAndDuplicates.Rd | 66 ++++++------ man/SearchCrissCross.Rd | 56 +++++----- man/SearchExhaustive.Rd | 52 +++++----- man/SearchGeneticAlgoritm.Rd | 52 +++++----- man/milazzese.Rd | 48 ++++----- man/plot.tca.Rd | 101 ++++++++++--------- man/print.tca.Rd | 42 ++++---- man/rodent.Rd | 48 ++++----- man/saveTCA.Rd | 77 +++++++------- man/summary.tca.Rd | 48 ++++----- man/tca.Rd | 150 +++++++++++++++-------------- tests/testthat/test.rodent.transposed.ex.r |only 24 files changed, 616 insertions(+), 558 deletions(-)
Title: Moran Eigenvector-Based Spatial Regression Models
Description: Functions for estimating Moran's eigenvector-based
spatial regression models.
For details see Murakami (2019) <arXiv:1703.04467>.
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.1.7.1 dated 2019-07-24 and 0.1.7.2 dated 2019-12-11
DESCRIPTION | 8 MD5 | 18 R/besf.R | 390 ++++++++-------- R/besf_vc.R | 1228 ++++++++++++++++++++++++++--------------------------- R/lsem.R | 7 R/lslm.R | 6 R/resf.R | 444 +++++++++---------- R/resf_qr.R | 432 +++++++++--------- R/resf_vc.R | 4 build/vignette.rds |binary 10 files changed, 1267 insertions(+), 1270 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre],
Branislav Panic [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.10.3 dated 2018-09-27 and 2.11.0 dated 2019-12-11
DESCRIPTION | 14 MD5 | 115 ++-- NAMESPACE | 25 R/AllClasses.R | 180 ++++++- R/AllGenerics.R | 22 R/RCLRMIX.R | 2 R/RCLSMIX.R | 13 R/REBMIX.R | 367 ++++++++------ R/RNGMIX.R | 2 R/defaults.R | 15 R/dfmix.R | 12 R/dfmix.x.R | 12 R/dfmix.xy.R | 24 R/pfmix.R | 12 R/pfmix.x.R | 30 - R/pfmix.xy.R | 24 R/plot.RCLSMIX.R | 28 - R/split.R | 69 +- R/zaccessors.R | 208 ++++++++ build/vignette.rds |binary data/adult.rda |binary data/galaxy.rda |binary data/iris.rda |binary data/truck.rda |binary data/weibull.rda |binary data/weibullnormal.rda |binary data/wine.rda |binary inst/NEWS.Rd | 11 inst/doc/rebmix.R | 207 +++++++- inst/doc/rebmix.Rnw | 235 ++++++++- inst/doc/rebmix.pdf |binary man/BFSMIX.Rd | 4 man/EM.Control-class.Rd |only man/RCLRMIX.Rd | 4 man/RCLS.chunk-class.Rd | 5 man/RCLSMIX.Rd | 4 man/REBMIX-class.Rd | 22 man/REBMIX.Rd | 51 +- man/REBMIX.boot.Rd | 4 man/RNGMIX-class.Rd | 6 man/RNGMIX.Rd | 10 man/RNGMIX.Theta-class.Rd | 8 man/adult.Rd | 2 man/galaxy.Rd | 14 man/rebmix-internal.Rd | 35 + src/Rrebmix.cpp | 365 ++++++++++---- src/Rrebmvnorm.cpp | 75 ++ src/base.cpp | 290 +++++------ src/base.h | 71 ++ src/emf.cpp |only src/emf.h |only src/init.c | 25 src/rebmix.cpp | 6 src/rebmixf.cpp | 1151 ++++++++++++++++++++++++++++++++++++++++++++-- src/rebmixf.h | 58 -- src/rebmvnormf.cpp | 247 +++++---- src/rebmvnormf.h | 3 src/rngmixf.cpp | 7 vignettes/rebmix.Rnw | 235 ++++++++- vignettes/rebmix.bib | 26 - 60 files changed, 3473 insertions(+), 882 deletions(-)
Title: Joint Maximum Likelihood Estimation for High-Dimensional Item
Factor Analysis
Description: Provides constrained joint maximum likelihood estimation
algorithms for item factor analysis (IFA) based on multidimensional item response theory
models. So far, we provide functions for exploratory and confirmatory IFA based on the
multidimensional two parameter logistic (M2PL) model for binary response data. Comparing
with traditional estimation methods for IFA, the methods implemented in this package scale
better to data with large numbers of respondents, items, and latent factors. The computation
is facilitated by multiprocessing 'OpenMP' API. For more information, please refer to:
1. Chen, Y., Li, X., & Zhang, S. (2018). Joint Maximum Likelihood Estimation for
High-Dimensional Exploratory Item Factor Analysis. Psychometrika, 1-23.
<doi:10.1007/s11336-018-9646-5>;
2. Chen, Y., Li, X., & Zhang, S. (2019). Structured Latent Factor Analysis for Large-scale Data:
Identifiability, Estimability, and Their Implications. Journal of the American Statistical
Association, <doi: 10.1080/01621459.2019.1635485>.
Author: Siliang Zhang [aut, cre],
Yunxiao Chen [aut],
Xiaoou Li [aut]
Maintainer: Siliang Zhang <zhangsiliang123@gmail.com>
Diff between mirtjml versions 1.2 dated 2018-12-21 and 1.3.0 dated 2019-12-11
DESCRIPTION | 15 +++-- MD5 | 40 ++++++++------- NAMESPACE | 3 + NEWS.md | 15 +++++ R/RcppExports.R | 40 +++++++++++++-- R/mirtjml_conf.R | 15 +++-- R/mirtjml_expr.R | 81 ++++++++++++++++++++++++++++-- R/utilities.R | 20 +++++++ R/zzz.R |only README.md | 6 +- man/getMIRTthreads.Rd |only man/mirtjml_conf.Rd | 16 +++--- man/mirtjml_expr.Rd | 11 ++-- man/setMIRTthreads.Rd |only src/Makevars | 6 +- src/Makevars.win | 5 + src/RcppExports.cpp | 131 ++++++++++++++++++++++++++++++++++++++++++++++---- src/cjmle_conf.cpp | 84 ++++++++++++++++++++------------ src/cjmle_expr.cpp | 87 ++++++++++++++++++++------------- src/depend_funcs.cpp | 63 +++++++++++++++--------- src/depend_funcs.h | 4 + src/mirtjml_omp.h | 29 ++++------- src/openmp-utils.cpp |only 23 files changed, 497 insertions(+), 174 deletions(-)
Title: Body Mass Estimation Equations for Vertebrates
Description: Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., stylopodial circumference) and body mass in living taxa (Campione and Evans, 2012).
Author: Nicolas E. Campione
Maintainer: Nicolas E. Campione <ncampion@une.edu.au>
Diff between MASSTIMATE versions 1.3 dated 2016-01-13 and 1.4 dated 2019-12-11
DESCRIPTION | 12 ++-- MD5 | 20 ++++--- R/DME.R |only README.md | 2 data/dinos.csv.gz |binary data/dinosbip.csv.gz |binary man/DME.Rd |only man/MASSTIMATE-package.Rd | 72 ++++++++++++++-------------- man/QE.Rd | 110 +++++++++++++++++++++---------------------- man/bipeds.Rd | 90 +++++++++++++++++------------------ man/cQE.Rd | 116 +++++++++++++++++++++++----------------------- man/quadrupeds.Rd | 90 +++++++++++++++++------------------ 12 files changed, 258 insertions(+), 254 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>),
Grant McDermott [ctb],
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb],
Daniel Lüdecke [ctb]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.8-3 dated 2019-03-27 and 2.8-4 dated 2019-12-11
DESCRIPTION | 30 ++++-- MD5 | 78 +++++++++--------- NAMESPACE | 3 R/felm.R | 190 +++++++++++++++++++++++++++++++++++++------- R/generics.R | 85 +++++++++++++++++++ R/nlexpect.R | 4 R/utils.R | 21 +--- build/autoconf/install-sh | 36 +++++--- build/vignette.rds |binary cleanup | 2 inst/NEWS.Rd | 12 ++ inst/doc/biascorrection.pdf |binary inst/doc/identification.R | 74 ++++++++--------- inst/doc/identification.pdf |binary inst/doc/index.html | 32 +++---- inst/doc/lfehow.R | 26 +++--- inst/doc/lfehow.pdf |binary inst/doc/speed.R | 18 ++-- inst/doc/speed.pdf |binary man/bccorr.Rd | 12 ++ man/btrap.Rd | 14 ++- man/cgsolve.Rd | 3 man/demeanlist.Rd | 19 +++- man/felm.Rd | 119 ++++++++++++++++++++++----- man/fevcov.Rd | 10 +- man/getfe.Rd | 14 ++- man/is.estimable.Rd | 10 +- man/kaczmarz.Rd | 9 +- man/nlexpect.Rd | 22 +++-- man/summary.felm.Rd | 8 + man/varvars.Rd | 3 man/waldtest.Rd | 11 ++ src/demean.c | 56 +++++++++--- src/factor.c | 4 src/lfe.c | 6 + src/lfe.h | 6 - src/utils.c | 11 ++ tests/comparelm.R | 30 ++++++ tests/comparelm.Rout.save | 69 +++++++++------ tests/testthat |only tests/testthat.R |only 41 files changed, 754 insertions(+), 293 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-37 dated 2019-08-29 and 3.1-39 dated 2019-12-11
HH-3.1-37/HH/R/hh.R |only HH-3.1-37/HH/R/hh.file.R |only HH-3.1-37/HH/man/hh.Rd |only HH-3.1-39/HH/DESCRIPTION | 8 +- HH-3.1-39/HH/MD5 | 73 ++++++++++++-------------- HH-3.1-39/HH/NAMESPACE | 11 ++-- HH-3.1-39/HH/NEWS | 79 +++++++++++++++++++++++++++++ HH-3.1-39/HH/R/HHscriptnames.R | 5 + HH-3.1-39/HH/R/X.residuals.R | 2 HH-3.1-39/HH/R/aov.sufficient.R | 5 - HH-3.1-39/HH/R/likert.R | 5 + HH-3.1-39/HH/R/mmcplot.R | 13 ++-- HH-3.1-39/HH/R/position.R | 14 +---- HH-3.1-39/HH/R/residual.plots.lattice.R | 2 HH-3.1-39/HH/R/vif.R | 5 + HH-3.1-39/HH/build/partial.rdb |binary HH-3.1-39/HH/man/CIplot.Rd | 8 +- HH-3.1-39/HH/man/Discrete4.color.Rd | 17 ++---- HH-3.1-39/HH/man/HH-defunct.Rd | 10 +++ HH-3.1-39/HH/man/HH.package.Rd | 14 ++--- HH-3.1-39/HH/man/NormalAndT.Rd | 17 ++++-- HH-3.1-39/HH/man/NormalAndTplot.Rd | 3 - HH-3.1-39/HH/man/ae.dotplot7.Rd | 4 - HH-3.1-39/HH/man/ae.dotplot7a.Rd | 2 HH-3.1-39/HH/man/bivariateNormal.Rd | 6 +- HH-3.1-39/HH/man/col.hh.Rd | 2 HH-3.1-39/HH/man/col3x2.Rd | 36 ++++++++----- HH-3.1-39/HH/man/export.eps.Rd | 14 ++--- HH-3.1-39/HH/man/likert.Rd | 7 +- HH-3.1-39/HH/man/mmcPruneIsomeans.Rd | 3 - HH-3.1-39/HH/man/mmcisomeans.Rd | 8 +- HH-3.1-39/HH/man/mmcplot.Rd | 6 +- HH-3.1-39/HH/man/normalApproxBinomial.Rd | 9 ++- HH-3.1-39/HH/man/position.Rd | 33 +----------- HH-3.1-39/HH/man/pyramidLikert.Rd | 2 HH-3.1-39/HH/man/rbind.trellis.Rd | 3 - HH-3.1-39/HH/man/residual.plots.lattice.Rd | 11 ++-- HH-3.1-39/HH/man/useOuterScales.Rd | 3 - HH-3.1-39/HH/man/vif.Rd | 13 ---- 39 files changed, 268 insertions(+), 185 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-210X.13270>,
and
Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc],
Autumn-Lynn Harrison [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.7 dated 2019-10-07 and 0.5.8 dated 2019-12-11
DESCRIPTION | 23 ++-- MD5 | 121 +++++++++++----------- NAMESPACE | 3 NEWS.md | 19 +++ R/1.R | 49 ++++++++ R/anonymize.R | 4 R/color.R | 6 - R/covm.R | 7 - R/ctmm.R | 5 R/cv.R | 75 ++++++++----- R/encounter.R |only R/export.R | 2 R/extent.R | 34 +++++- R/gaussian.R |only R/generic.R | 88 ++++++---------- R/kalman.R | 7 - R/kde.R | 46 +++----- R/krige.R | 6 - R/likelihood.R | 84 ++++++++------- R/matrix.R | 4 R/mean.R | 30 ++++- R/median.R | 2 R/numDeriv.R | 23 ++-- R/optim.R | 8 - R/outlier.R | 12 +- R/overlap.R | 80 +------------- R/parameters.R | 83 ++++++++++++--- R/periodogram.R | 2 R/plot.variogram.R | 9 + R/projection.R | 23 +++- R/select.R | 251 ++++++++++++++++++++++++++++------------------ R/summary.ctmm.R | 2 R/telemetry.R | 61 ++++++----- R/temp_unzip.R | 10 - R/uere.R | 20 +-- R/units.R | 51 +++++++-- R/variogram.R | 4 R/variogram.fit.R | 2 TODO | 45 +++++--- inst/doc/akde.html | 18 +-- inst/doc/error.R | 5 inst/doc/error.Rmd | 5 inst/doc/error.html | 53 +++++---- inst/doc/periodogram.R | 6 - inst/doc/periodogram.Rmd | 6 - inst/doc/periodogram.html | 66 ++++++------ inst/doc/variogram.html | 38 +++--- man/akde.Rd | 2 man/ctmm-package.Rd | 12 +- man/ctmm.fit.Rd | 9 + man/encounter.Rd |only man/export.Rd | 12 +- man/extent.Rd | 6 + man/mean.variogram.Rd | 2 man/occurrence.Rd | 2 man/outlie.Rd | 6 - man/plot.variogram.Rd | 2 man/simulate.ctmm.Rd | 2 man/speed.Rd | 8 - man/unit.Rd | 8 + man/variogram.Rd | 2 vignettes/error.Rmd | 5 vignettes/periodogram.Rmd | 6 - 63 files changed, 931 insertions(+), 651 deletions(-)
Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>
Diff between BLPestimatoR versions 0.3.0 dated 2019-10-18 and 0.3.2 dated 2019-12-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/estimateBLP.R | 6 +++--- R/wrappers.R | 4 ++-- inst/doc/blp_intro.html | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University
generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API.
The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies.
By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers.
The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793>
and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>.
The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre]
(<https://orcid.org/0000-0002-7221-6981>),
Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>
Diff between qrandom versions 1.2 dated 2019-08-20 and 1.2.1 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/qUUID.R | 5 +++++ R/qrandom.R | 16 +++++++++++++++- R/qrandommaxint.R | 6 +++++- build/partial.rdb |binary tests/testthat/test-qUUID.R | 5 +++++ tests/testthat/test-qrandom.R | 6 +++++- tests/testthat/test-qrandommaxint.R | 4 ++++ tests/testthat/test-qrandomnorm.R | 4 ++++ tests/testthat/test-qrandomunif.R | 4 ++++ 11 files changed, 61 insertions(+), 17 deletions(-)
Title: Download Data from the European Social Survey on the Fly
Description: Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
Author: Jorge Cimentada [aut, cre],
Thomas Leeper [rev] (Thomas reviewed the package for rOpensci,see
https://github.com/ropensci/onboarding/issues/201),
Nujcharee Haswell [rev] (Nujcharee reviewed the package for rOpensci,
see https://github.com/ropensci/onboarding/issues/201),
Jorge Lopez [ctb],
François Briatte [ctb]
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>
Diff between essurvey versions 1.0.4 dated 2019-11-04 and 1.0.5 dated 2019-12-11
DESCRIPTION | 10 MD5 | 44 - NEWS.md | 16 R/download_format.R | 8 R/show_any_rounds.R | 14 R/show_funs.R | 12 inst/doc/intro_ess.R | 34 - inst/doc/intro_ess.html | 7 man/import_country.Rd | 9 man/import_rounds.Rd | 8 man/import_sddf_country.Rd | 9 man/show_countries.Rd | 3 man/show_country_rounds.Rd | 4 man/show_rounds.Rd | 3 man/show_rounds_country.Rd | 3 man/show_theme_rounds.Rd | 3 man/show_themes.Rd | 2 tests/testthat/test-1-show_.R | 437 +++++++------- tests/testthat/test-2-country.R | 946 ++++++++++++++++---------------- tests/testthat/test-3-rounds.R | 274 ++++----- tests/testthat/test-4-recode_missings.R | 277 ++++----- tests/testthat/test-6-country_lookup.R | 1 tests/testthat/test-7-set_email.R | 2 23 files changed, 1114 insertions(+), 1012 deletions(-)
Title: Data Preparation, Estimation and Prediction in Multi-State
Models
Description: Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco, with contributions by
Ronald Geskus
Maintainer: Hein Putter <H.Putter@lumc.nl>
Diff between mstate versions 0.2.11 dated 2018-04-09 and 0.2.12 dated 2019-12-11
ChangeLog | 3 ++ DESCRIPTION | 10 ++++---- MD5 | 14 +++++------ R/cuminc.R | 62 ++++++++++++++++++++------------------------------ build/vignette.rds |binary inst/doc/Tutorial.pdf |binary man/cuminc.Rd | 2 - man/msprep.Rd | 2 - 8 files changed, 43 insertions(+), 50 deletions(-)
Title: Infinite Mixtures of Infinite Factor Analysers and Related
Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2019) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre],
Cinzia Viroli [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between IMIFA versions 2.1.0 dated 2019-02-04 and 2.1.1 dated 2019-12-11
DESCRIPTION | 14 MD5 | 120 ++-- NAMESPACE | 7 R/Diagnostics.R | 110 ++-- R/FullConditionals.R | 230 +++++--- R/Gibbs_FA.R | 8 R/Gibbs_IFA.R | 1 R/Gibbs_IMFA.R | 79 +-- R/Gibbs_IMIFA.R | 254 ++++++--- R/Gibbs_MFA.R | 34 - R/Gibbs_MIFA.R | 98 ++- R/Gibbs_OMFA.R | 42 - R/Gibbs_OMIFA.R | 100 ++- R/IMIFA.R | 10 R/MainFunction.R | 65 +- R/PlottingFunctions.R | 116 ++-- R/SimulateData.R | 43 - R/data.R | 16 README.md | 4 build/vignette.rds |binary inst/CITATION | 24 inst/NEWS.md | 26 inst/doc/IMIFA.R | 75 +- inst/doc/IMIFA.Rmd | 60 +- inst/doc/IMIFA.html | 110 ++-- man/G_moments.Rd | 119 ++-- man/G_priorDensity.Rd | 114 ++-- man/IMIFA-package.Rd | 124 ++-- man/IMIFA_news.Rd | 34 - man/Ledermann.Rd | 48 - man/MGP_check.Rd | 142 ++--- man/PGMM_dfree.Rd | 102 +-- man/Procrustes.Rd | 136 ++--- man/USPSdigits.Rd | 88 +-- man/Zsimilarity.Rd | 124 ++-- man/bnpControl.Rd | 210 ++++---- man/coffee.Rd | 38 - man/get_IMIFA_results.Rd | 288 +++++------ man/gumbel_max.Rd | 122 ++-- man/heat_legend.Rd | 84 +-- man/is.cols.Rd | 50 - man/is.posi_def.Rd | 82 +-- man/mat2cols.Rd | 148 ++--- man/mcmc_IMIFA.Rd | 313 ++++++------ man/mgpControl.Rd | 187 +++---- man/mixfaControl.Rd | 243 ++++----- man/olive.Rd | 41 - man/pareto_scale.Rd | 60 +- man/plot.Results_IMIFA.Rd | 270 +++++----- man/plot_cols.Rd | 138 ++--- man/post_conf_mat.Rd | 86 +-- man/psi_hyper.Rd | 160 +++--- man/rDirichlet.Rd | 72 +- man/scores_MAP.Rd | 107 ++-- man/shift_GA.Rd | 72 +- man/show_IMIFA_digit.Rd | 125 ++-- man/show_digit.Rd | 78 +- man/sim_IMIFA.Rd | 208 ++++--- man/storeControl.Rd | 124 ++-- vignettes/IMIFA.Rmd | 60 +- vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary 61 files changed, 3215 insertions(+), 2828 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<https://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Alexandros Kokkalis [ctb],
Ibrahim Umar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 3.3-0 dated 2019-12-03 and 3.3-1 dated 2019-12-11
DESCRIPTION | 18 ++++++++++-------- MD5 | 39 ++++++++++++++++++++------------------- NEWS | 12 ++++++++++++ R/access.vocab.R |only R/catage.long.R | 4 ++-- R/catage.taf.R | 4 ++-- R/catage.xtab.R | 4 ++-- R/draft.data.R | 2 +- R/ds.file.R | 2 +- R/ds.package.R | 2 +- R/icesTAF-package.R | 2 +- R/parse.repo.R | 17 +++++++++-------- R/process.bib.R | 13 +++++++++++-- R/process.inner.R | 4 +--- R/summary.taf.R | 4 ++-- man/catage.long.Rd | 4 ++-- man/catage.taf.Rd | 4 ++-- man/catage.xtab.Rd | 4 ++-- man/icesTAF-package.Rd | 2 +- man/process.bib.Rd | 5 +++-- man/summary.taf.Rd | 4 ++-- 21 files changed, 87 insertions(+), 63 deletions(-)
Title: Interface to API 'vk.com'
Description: Load data from vk.com api about your communiti users and views,
ads performance, post on user wall and etc. For more detail see
<https://vk.com/dev/first_guide>.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rvkstat versions 2.6.2 dated 2019-07-28 and 2.6.3 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/vkGetAdStatistics.R | 4 ++++ build/partial.rdb |binary man/vkGetAdStatistics.Rd | 1 + 6 files changed, 22 insertions(+), 9 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages. These
include e.g. measures like r-squared, intraclass correlation coefficient
(Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>),
root mean squared error or functions to check models for overdispersion,
singularity or zero-inflation and more. Functions apply to a large variety of
regression models, including generalized linear models, mixed effects models
and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.4.0 dated 2019-10-21 and 0.4.2 dated 2019-12-11
DESCRIPTION | 14 MD5 | 263 ++++++++-------- NAMESPACE | 45 ++ NEWS.md | 26 + R/binned_residuals.R | 36 +- R/check_autocorrelation.R | 5 R/check_collinearity.R | 140 +++----- R/check_convergence.R | 4 R/check_distribution.R | 3 R/check_heteroscedasticity.R | 1 R/check_homogeneity.R | 9 R/check_model.R | 22 - R/check_model_diagnostics.R | 63 ++- R/check_normality.R | 8 R/check_outliers.R | 85 +++-- R/check_overdispersion.R | 44 +- R/check_singularity.R | 36 +- R/check_zeroinflation.R | 9 R/compare_performance.R | 65 +++ R/cronbachs_alpha.R | 41 ++ R/helpers.R | 86 ++++- R/icc.R | 21 - R/item_difficulty.R | 2 R/item_intercor.R | 2 R/item_reliability.R | 1 R/item_split_half.R | 1 R/logLik.R | 20 - R/looic.R | 5 R/model_performance.R | 30 + R/model_performance.bayesian.R | 14 R/model_performance.lavaan.R | 12 R/model_performance.lm.R | 14 R/model_performance.mixed.R | 25 - R/performance_accuracy.R | 8 R/performance_aicc.R | 11 R/performance_hosmer.R | 3 R/performance_logloss.R | 14 R/performance_mse.R | 20 - R/performance_pcp.R | 15 R/performance_rmse.R | 40 +- R/performance_roc.R | 6 R/performance_rse.R | 1 R/performance_score.R | 28 + R/plot-methods.R | 27 + R/print-methods.R | 111 +++++- R/r2.R | 374 +++++++++++++---------- R/r2_bayes.R | 90 ++--- R/r2_coxsnell.R | 81 ++-- R/r2_kl.R | 6 R/r2_loo.R | 14 R/r2_mcfadden.R | 56 ++- R/r2_mckelvey.R | 15 R/r2_nagelkerke.R | 84 ++--- R/r2_nakagawa.R | 1 R/r2_tjur.R | 1 R/r2_xu.R | 1 R/r2_zeroinflated.R | 6 R/skewness_kurtosis.R | 2 README.md | 66 +++- build/partial.rdb |binary man/binned_residuals.Rd | 125 +++---- man/check_autocorrelation.Rd | 73 ++-- man/check_collinearity.Rd | 122 +++---- man/check_convergence.Rd | 97 ++--- man/check_distribution.Rd | 87 ++--- man/check_heteroscedasticity.Rd | 57 +-- man/check_homogeneity.Rd | 73 ++-- man/check_model.Rd | 115 +++---- man/check_normality.Rd | 84 ++--- man/check_outliers.Rd | 373 +++++++++++----------- man/check_overdispersion.Rd | 135 ++++---- man/check_singularity.Rd | 149 ++++----- man/check_zeroinflation.Rd | 75 ++-- man/classify_distribution.Rd | 26 - man/cronbachs_alpha.Rd | 67 ++-- man/figures/unnamed-chunk-13-1.png |only man/figures/unnamed-chunk-22-1.png |only man/icc.Rd | 249 +++++++-------- man/item_difficulty.Rd | 70 ++-- man/item_intercor.Rd | 96 ++--- man/item_reliability.Rd | 87 ++--- man/item_split_half.Rd | 75 ++-- man/looic.Rd | 49 +-- man/model_performance.Rd | 157 +++++---- man/model_performance.lavaan.Rd | 121 +++---- man/model_performance.lm.Rd | 97 ++--- man/model_performance.merMod.Rd | 71 ++-- man/model_performance.stanreg.Rd | 115 +++---- man/performance_accuracy.Rd | 98 ++---- man/performance_aicc.Rd | 65 +-- man/performance_hosmer.Rd | 67 ++-- man/performance_logloss.Rd | 71 ++-- man/performance_mse.Rd | 69 ++-- man/performance_pcp.Rd | 121 +++---- man/performance_rmse.Rd | 93 ++--- man/performance_roc.Rd | 105 +++--- man/performance_rse.Rd | 53 +-- man/performance_score.Rd | 133 ++++---- man/r2.Rd | 87 ++--- man/r2_bayes.Rd | 123 +++---- man/r2_coxsnell.Rd | 75 ++-- man/r2_kullback.Rd | 55 +-- man/r2_loo.Rd | 57 +-- man/r2_mcfadden.Rd | 65 +-- man/r2_mckelvey.Rd | 83 ++--- man/r2_nagelkerke.Rd | 51 +-- man/r2_nakagawa.Rd | 83 ++--- man/r2_tjur.Rd | 57 +-- man/r2_xu.Rd | 59 +-- man/r2_zeroinflated.Rd | 75 ++-- tests/testthat/test-backticks.R |only tests/testthat/test-check_convergence.R | 2 tests/testthat/test-check_overdispersion.R | 2 tests/testthat/test-check_singularity.R | 2 tests/testthat/test-check_zeroinflation.R | 2 tests/testthat/test-compare_performance.R | 2 tests/testthat/test-coxph.R | 6 tests/testthat/test-cronbachs_alpha.R | 2 tests/testthat/test-icc.R | 2 tests/testthat/test-item_difficulty.R | 11 tests/testthat/test-item_intercor.R | 2 tests/testthat/test-item_reliability.R | 11 tests/testthat/test-item_splithalf.R | 5 tests/testthat/test-model_performance-various.R | 2 tests/testthat/test-model_performance.bayesian.R | 5 tests/testthat/test-model_performance.lm.R | 2 tests/testthat/test-model_performance.merMod.R | 2 tests/testthat/test-r2_coxsnell.R | 2 tests/testthat/test-r2_kullback.R | 2 tests/testthat/test-r2_mcfadden.R | 5 tests/testthat/test-r2_nagelkerke.R | 3 tests/testthat/test-r2_nakagawa.R | 5 tests/testthat/test-r2_tjur.R | 4 tests/testthat/test-r2_zeroinflated.R | 2 134 files changed, 3715 insertions(+), 3191 deletions(-)
Title: Penalized Composite Link Model for Efficient Estimation of
Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data)
assuming that counts are Poisson distributed and that the underlying sequence
on a fine grid to be estimated is smooth. The method is based on the composite
link model and estimation is achieved by maximizing a penalized likelihood.
Smooth detailed sequences of counts and rates are so estimated from the binned
counts. Ungrouping binned data can be desirable for many reasons: Bins can be
too coarse to allow for accurate analysis; comparisons can be hindered when
different grouping approaches are used in different histograms; and the last
interval is often wide and open-ended and, thus, covers a lot of information
in the tail area. Age-at-death distributions grouped in age classes and
abridged life tables are examples of binned data. Because of modest assumptions,
the approach is suitable for many demographic and epidemiological applications.
For a detailed description of the method and applications see
Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>),
Silvia Rizzi [aut],
Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>),
Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between ungroup versions 1.1.1 dated 2018-10-15 and 1.1.5 dated 2019-12-11
DESCRIPTION | 10 LICENSE |only MD5 | 135 +++++----- NAMESPACE | 109 ++++---- NEWS | 27 +- R/RcppExports.R | 22 - R/pclm_1D.R | 527 ++++++++++++++++++++++------------------- R/pclm_2D.R | 416 ++++++++++++++++---------------- R/pclm_CI.R | 293 +++++++++++----------- R/pclm_control.R | 163 ++++++------ R/pclm_fit.R | 424 +++++++++++++++++--------------- R/pclm_graphics.R | 345 +++++++++++++------------- R/pclm_optim.R | 173 +++++++------ R/ungroup-data.R | 78 +++--- R/ungroup-package.r | 44 +-- R/utils.R | 289 +++++++++++----------- README.md | 116 ++++----- THANKS | 38 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 68 ++--- inst/REFERENCES.bib | 193 +++++++-------- inst/doc/Intro.R | 118 ++++----- inst/doc/Intro.Rmd | 292 +++++++++++----------- inst/doc/Intro.pdf |binary man/AIC.pclm.Rd | 160 ++++++------ man/AIC.pclm2D.Rd | 160 ++++++------ man/BIC.pclm.Rd | 154 +++++------ man/BIC.pclm2D.Rd | 160 ++++++------ man/build_B_spline_basis.Rd | 72 ++--- man/build_C_matrix.Rd | 64 ++-- man/build_P_matrix.Rd | 46 +-- man/compute_standard_errors.Rd | 38 +- man/control.pclm.Rd | 102 +++---- man/control.pclm2D.Rd | 102 +++---- man/create.artificial.bin.Rd | 43 +-- man/delete.artificial.bin.Rd | 30 +- man/frac.Rd | 30 +- man/map.bins.Rd | 45 +-- man/ofun.Rd | 40 +-- man/optimize_par.Rd | 52 ++-- man/pclm.Rd | 268 ++++++++++---------- man/pclm.confidence.Rd | 65 ++--- man/pclm.confidence.dx.Rd | 30 +- man/pclm.confidence.mx.Rd | 30 +- man/pclm.fit.Rd | 109 ++++---- man/pclm.input.check.Rd | 30 +- man/pclm2D.Rd | 238 +++++++++--------- man/plot.pclm.Rd | 104 ++++---- man/plot.pclm2D.Rd | 107 ++++---- man/print.pclm.Rd | 34 +- man/print.pclm2D.Rd | 34 +- man/print.summary.pclm.Rd | 34 +- man/print.summary.pclm2D.Rd | 34 +- man/print.ungroup.data.Rd | 34 +- man/residuals.pclm.Rd | 56 ++-- man/residuals.pclm2D.Rd | 74 ++--- man/seqlast.Rd | 46 +-- man/suggest.valid.out.step.Rd | 38 +- man/summary.pclm.Rd | 34 +- man/summary.pclm2D.Rd | 42 +-- man/ungroup.Rd | 100 +++---- man/ungroup.data.Rd | 62 ++-- man/validate.nlast.Rd | 49 +-- tests/testthat.R | 8 tests/testthat/test_pclm.R | 198 +++++++-------- tests/testthat/test_pclm2D.R | 124 ++++----- vignettes/Intro.Rmd | 292 +++++++++++----------- vignettes/REFERENCES.bib | 192 +++++++------- 69 files changed, 3922 insertions(+), 3722 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.2.8 dated 2019-12-04 and 0.2.8.1 dated 2019-12-11
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/germancredit.R | 2 +- R/perf.R | 9 ++++++--- R/report.R | 4 ++-- R/woebin.R | 10 +++++++--- inst/doc/demo.html | 7 +++---- man/report.Rd | 4 ++-- man/woebin_adj.Rd | 5 ++++- 10 files changed, 44 insertions(+), 29 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.5 dated 2019-09-19 and 5.5.6 dated 2019-12-11
DESCRIPTION | 8 MD5 | 18 - R/UTILS-as-methods.R | 4 inst/NEWS.Rd | 4 inst/doc/dtwclust.pdf |binary inst/doc/parallelization-considerations.html | 3 inst/doc/timing-experiments.html | 5 tests/testthat/integration/families.R | 16 - tests/testthat/integration/proxy.R | 280 +++++++++++++-------------- tests/testthat/unit/methods.R | 4 10 files changed, 170 insertions(+), 172 deletions(-)
Title: Build Dirichlet Process Objects for Bayesian Modelling
Description: Perform nonparametric Bayesian analysis using Dirichlet
processes without the need to program the inference algorithms.
Utilise included pre-built models or specify custom
models and allow the 'dirichletprocess' package to handle the
Markov chain Monte Carlo sampling.
Our Dirichlet process objects can act as building blocks for a variety
of statistical models including and not limited to: density estimation,
clustering and prior distributions in hierarchical models.
See Teh, Y. W. (2011)
<https://www.stats.ox.ac.uk/~teh/research/npbayes/Teh2010a.pdf>,
among many other sources.
Author: Gordon J. Ross [aut],
Dean Markwick [aut, cre],
Kees Mulder [ctb] (<https://orcid.org/0000-0002-5387-3812>)
Maintainer: Dean Markwick <dean.markwick@talk21.com>
Diff between dirichletprocess versions 0.3.0 dated 2019-05-03 and 0.3.1 dated 2019-12-11
DESCRIPTION | 6 ++-- MD5 | 29 ++++++++++++----------- NEWS.md | 10 +++++++- R/dirichlet_process_mvnormal.R | 9 ++++--- R/initialise.R | 17 +++++++------ R/mvnormal_normal_wishart.R | 26 ++++++++++++++------- R/mvnormal_semi_conjugate.R | 2 - R/stick_breaking.R | 26 +++++++++++++-------- R/utilities.R | 2 - inst/doc/dirichletprocess.Rnw | 19 ++++++++------- inst/doc/dirichletprocess.pdf |binary man/DirichletProcessMvnormal.Rd | 5 +++- man/Initialise.Rd | 5 +++- tests/testthat/Rplots.pdf |only tests/testthat/test_mvnormal_normal_wishart.R | 32 ++++++++++++++++++++++++++ vignettes/dirichletprocess.Rnw | 19 ++++++++------- 16 files changed, 138 insertions(+), 69 deletions(-)
More information about dirichletprocess at CRAN
Permanent link
Title: Create Details HTML Tag for Markdown and Package Documentation
Description: Create a details HTML tag around R objects to place
in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between details versions 0.1.2 dated 2019-11-07 and 0.1.3 dated 2019-12-11
DESCRIPTION | 6 +- MD5 | 34 +++++++------- NAMESPACE | 2 NEWS.md | 5 +- R/build.R | 4 - R/details.R | 11 +++- R/read.R | 4 - R/use.R | 29 ++---------- README.md | 30 ++++++------- inst/doc/custom.html | 2 inst/doc/sessioninfo.html | 18 +++---- inst/doc/tests_and_coverage.html | 2 man/details.Rd | 6 ++ man/use_details.Rd | 2 tests/README.md | 90 ++++++++++++++++++++++----------------- tests/testthat/helpers.R | 4 - tests/testthat/test-basic.R | 7 +++ tests/testthat/test-use.R | 32 +++++++++++-- 18 files changed, 163 insertions(+), 125 deletions(-)
Title: Automatic Fixed Rank Kriging
Description: Automatic fixed rank kriging for (irregularly located)
spatial data using a class of basis functions with multi-resolution features
and ordered in terms of their resolutions. The model parameters are estimated
by maximum likelihood (ML) and the number of basis functions is determined
by Akaike's information criterion (AIC). For spatial data with either one
realization or independent replicates, the ML estimates and AIC are efficiently
computed using their closed-form expressions when no missing value occurs. Details
regarding the basis function construction, parameter estimation, and AIC calculation
can be found in Tzeng and Huang (2018) <doi:10.1080/00401706.2017.1345701>. For
data with missing values, the ML estimates are obtained using the expectation-
maximization algorithm. Apart from the number of basis functions, there are
no other tuning parameters, making the method fully automatic. Users can also
include a stationary structure in the spatial covariance, which utilizes
'LatticeKrig' package.
Author: ShengLi Tzeng [aut, cre], Hsin-Cheng Huang [aut], Wen-Ting Wang [ctb], Douglas Nychka [ctb], Colin Gillespie [ctb]
Maintainer: ShengLi Tzeng <slt.cmu@gmail.com>
Diff between autoFRK versions 1.1.0 dated 2019-03-29 and 1.2.0 dated 2019-12-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + R/autoFRK.R | 40 ++++++++++++++++------------------------ 4 files changed, 25 insertions(+), 32 deletions(-)
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2019) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre],
Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between MoEClust versions 1.2.3 dated 2019-07-29 and 1.2.4 dated 2019-12-11
DESCRIPTION | 12 - MD5 | 82 +++++----- NAMESPACE | 2 R/Functions.R | 193 +++++++++++++++++-------- R/MoEClust.R | 17 +- R/Plotting_Functions.R | 20 +- R/data.R | 3 README.md | 4 inst/CITATION | 28 +-- inst/NEWS.md | 21 ++ inst/doc/MoEClust.R | 92 ++++++------ inst/doc/MoEClust.Rmd | 45 +++-- inst/doc/MoEClust.html | 108 ++++++++------ man/CO2data.Rd | 54 +++---- man/MoEClust-package.Rd | 211 +++++++++++++-------------- man/MoE_Uncertainty.Rd | 116 +++++++-------- man/MoE_clust.Rd | 345 ++++++++++++++++++++++----------------------- man/MoE_compare.Rd | 249 ++++++++++++++++----------------- man/MoE_control.Rd | 316 +++++++++++++++++++++-------------------- man/MoE_crit.Rd | 158 ++++++++++---------- man/MoE_cstep.Rd | 136 +++++++++--------- man/MoE_dens.Rd | 126 ++++++++-------- man/MoE_estep.Rd | 144 +++++++++---------- man/MoE_gpairs.Rd | 362 ++++++++++++++++++++++++------------------------ man/MoE_mahala.Rd | 68 ++++----- man/MoE_news.Rd | 34 ++-- man/MoE_plotCrit.Rd | 77 +++++----- man/MoE_plotGate.Rd | 114 +++++++-------- man/MoE_plotLogLik.Rd | 88 +++++------ man/MoE_stepwise.Rd | 191 ++++++++++++------------- man/ais.Rd | 80 +++++----- man/aitken.Rd | 92 ++++++------ man/as.Mclust.Rd | 157 ++++++++++---------- man/drop_constants.Rd | 106 +++++++------- man/drop_levels.Rd | 98 ++++++------ man/expert_covar.Rd | 88 +++++------ man/force_posiDiag.Rd | 62 ++++---- man/noise_vol.Rd | 96 ++++++------ man/plot.MoEClust.Rd | 143 +++++++++--------- man/predict.MoEClust.Rd | 186 ++++++++++++------------ man/quant_clust.Rd | 50 +++--- vignettes/MoEClust.Rmd | 45 +++-- 42 files changed, 2365 insertions(+), 2254 deletions(-)
Title: Dealing GPL570 RAW.tar file
Description: Dealing GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array) RAW.tar file using the robust multi-array average expression measure and returning expression profile.
Author: Nan Zhang [cre],
YaKun Zhang [aut]
Maintainer: Nan Zhang <15776658849@163.com>
Diff between DealGPL570 versions 0.0.1 dated 2019-11-12 and 0.2.0 dated 2019-12-11
DESCRIPTION | 8 MD5 | 15 - NAMESPACE | 2 NEWS.md |only R/functions.R | 2 README.md | 5 inst/doc/DealGPL570-introduction.R | 10 - inst/doc/DealGPL570-introduction.html | 308 ++++++++++++++++++++++++++++------ man/DealGPL570.Rd | 62 +++--- 9 files changed, 308 insertions(+), 104 deletions(-)