Title: Generalized Regression on Orthogonal Components
Description: Robust multiple or multivariate linear regression, nonparametric regression on orthogonal components, classical or robust partial least squares models.
Author: Pierre Lafaye De Micheaux [aut, cre],
Martin Bilodeau [aut],
Jiahui Wang [cph] (covRob and related functions from orphaned package
robust),
Ruben Zamar [cph] (covRob and related functions from orphaned package
robust),
Alfio Marazzi [cph] (covRob and related functions from orphaned package
robust),
Victor Yohai [cph] (covRob and related functions from orphaned package
robust),
Matias Salibian-Barrera [cph] (covRob and related functions from
orphaned package robust),
Ricardo Maronna [cph] (covRob and related functions from orphaned
package robust),
Eric Zivot [cph] (covRob and related functions from orphaned package
robust),
David Rocke [cph] (covRob and related functions from orphaned package
robust),
Doug Martin [cph] (covRob and related functions from orphaned package
robust),
Martin Maechler [cph] (covRob and related functions from orphaned
package robust),
Kjell Konis [cph] (covRob and related functions from orphaned package
robust)
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
Diff between groc versions 1.0.6 dated 2018-05-10 and 1.0.7 dated 2020-02-06
DESCRIPTION | 63 +++++++++++++++++++++++++++++++++++++++++++------ INDEX | 1 MD5 | 14 +++++++--- NAMESPACE | 9 +++---- R/covRob.control.q |only R/covRob.q |only R/dependencemeasures.R | 2 - inst/HISTORY | 11 +++++++- man/covRob-robust.Rd |only man/covRob.control.Rd |only 10 files changed, 82 insertions(+), 18 deletions(-)
Title: Simplifies Plotting Data Inside Databases
Description: Leverages 'dplyr' to process the calculations of a plot inside a database.
This package provides helper functions that abstract the work at three levels:
outputs a 'ggplot', outputs the calculations, outputs the formula
needed to calculate bins.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between dbplot versions 0.3.2 dated 2019-07-02 and 0.3.3 dated 2020-02-06
dbplot-0.3.2/dbplot/tools |only dbplot-0.3.3/dbplot/DESCRIPTION | 16 dbplot-0.3.3/dbplot/MD5 | 88 ++--- dbplot-0.3.3/dbplot/NAMESPACE | 4 dbplot-0.3.3/dbplot/NEWS.md | 14 dbplot-0.3.3/dbplot/R/boxplot.R | 108 ++++-- dbplot-0.3.3/dbplot/R/dbbin.R | 27 - dbplot-0.3.3/dbplot/R/dbplot.R | 6 dbplot-0.3.3/dbplot/R/discrete.R | 14 dbplot-0.3.3/dbplot/R/histogram.R | 4 dbplot-0.3.3/dbplot/R/raster.R | 15 dbplot-0.3.3/dbplot/R/utils-pipe.R |only dbplot-0.3.3/dbplot/README.md | 166 +++++----- dbplot-0.3.3/dbplot/man/db_bin.Rd | 23 - dbplot-0.3.3/dbplot/man/db_compute_bins.Rd | 3 dbplot-0.3.3/dbplot/man/db_compute_boxplot.Rd | 12 dbplot-0.3.3/dbplot/man/db_compute_count.Rd | 2 dbplot-0.3.3/dbplot/man/db_compute_raster.Rd | 8 dbplot-0.3.3/dbplot/man/dbplot_histogram.Rd | 1 dbplot-0.3.3/dbplot/man/dbplot_raster.Rd | 4 dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-10-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-11-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-12-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-13-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-14-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-16-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-19-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-4-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-5-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-6-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-7-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-8-1.png |only dbplot-0.3.3/dbplot/man/figures/README-unnamed-chunk-9-1.png |only dbplot-0.3.3/dbplot/man/figures/logo.png |binary dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-10-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-11-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-12-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-13-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-14-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-15-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-17-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-20-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-5-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-6-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-7-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-8-1.png |only dbplot-0.3.3/dbplot/man/figures/unnamed-chunk-9-1.png |only dbplot-0.3.3/dbplot/man/pipe.Rd |only dbplot-0.3.3/dbplot/tests/testthat/test-boxplots.R | 16 dbplot-0.3.3/dbplot/tests/testthat/test-dbbin.R | 12 dbplot-0.3.3/dbplot/tests/testthat/test-raster.R | 8 51 files changed, 309 insertions(+), 242 deletions(-)
Title: A 'Shiny' App for Exploration of Text Collections
Description: Facilitates dynamic exploration of text collections through an
intuitive graphical user interface and the power of regular expressions.
The package contains 1) a helper function to convert a data frame to a
'corporaexplorerobject', 2) a 'Shiny' app for fast and flexible exploration
of a 'corporaexplorerobject', and 3) a 'Shiny' app for simple
retrieval/extraction of documents from a 'corporaexplorerobject' in a
reading-friendly format. The package also includes demo apps with which
one can explore Jane Austen's novels and the State of the Union Addresses
(data fra the 'janeaustenr' and 'sotu' packages respectively).
Author: Kristian Lundby Gjerde [aut, cre]
Maintainer: Kristian Lundby Gjerde <kristian.gjerde@gmail.com>
Diff between corporaexplorer versions 0.8.0 dated 2019-12-02 and 0.8.1 dated 2020-02-06
DESCRIPTION | 20 - MD5 | 101 +++--- NEWS.md | 14 R/demo_janeausten.R | 6 R/explore.R | 4 R/generic_methods.R |only R/prepare_data.R | 76 +++-- README.md | 14 data/test_data.rda |binary inst/explorer/app.R | 35 +- inst/explorer/config/config.R | 15 + inst/explorer/config/config_tests.R | 24 + inst/explorer/config/sidebar_input_values_from_function_call.R | 16 + inst/explorer/extra |only inst/explorer/global/corpus_plot_functions/convenience_functions_corpus_vis.R |only inst/explorer/global/corpus_plot_functions/create_coordinates_1_data_365.R | 22 - inst/explorer/global/corpus_plot_functions/create_coordinates_1_data_dok.R | 13 inst/explorer/global/corpus_plot_functions/create_coordinates_several_terms.R | 3 inst/explorer/global/corpus_plot_functions/create_distance_coordinates_day.R | 21 - inst/explorer/global/corpus_plot_functions/create_factors_for_labelling.R | 2 inst/explorer/global/corpus_plot_functions/plotting_corpus_data_dok.R | 4 inst/explorer/global/function_filter_corpus.R | 5 inst/explorer/global/function_plot_size.R | 10 inst/explorer/global/function_visualise_corpus.R | 147 ++++++---- inst/explorer/global/functions_info.R | 43 +- inst/explorer/global/functions_main_search_engine.R | 38 +- inst/explorer/js_css/box_width.js | 12 inst/explorer/js_css/explorer_css.css | 60 ++++ inst/explorer/server/1_startup_actions.R | 6 inst/explorer/server/2_event_search_button/UI_element_control.R | 24 + inst/explorer/server/2_event_search_button/check_search_arguments.R | 4 inst/explorer/server/2_event_search_button/corpus_map_rendering.R | 86 +++-- inst/explorer/server/2_event_search_button/subsetting.R | 68 ++++ inst/explorer/server/2_event_search_button/update_session_variables.R | 25 + inst/explorer/server/3_event_corpus_map_click.R | 5 inst/explorer/server/3_event_corpus_map_click/UI_element_control_data_365.R | 31 -- inst/explorer/server/3_event_corpus_map_click/UI_element_control_data_dok.R | 46 --- inst/explorer/server/3_event_corpus_map_click/js_auto_scroll.R | 1 inst/explorer/server/4_event_day_map_click.R | 5 inst/explorer/server/4_event_day_map_click/UI_element_control_data.R | 53 --- inst/explorer/server/7_event_plot_size_button.R |only inst/explorer/server/corpus_info_tab.R | 43 ++ inst/explorer/server/functions_checking_input.R | 4 inst/explorer/server/functions_ui_management.R | 91 ++++++ inst/explorer/server/session_variables.R | 7 inst/explorer/ui/render_ui_sidebar_checkbox_filtering.R |only inst/explorer/ui/render_ui_sidebar_date_filtering.R | 4 inst/explorer/ui/ui_corpus_box.R | 7 inst/explorer/ui/ui_sidebar.R | 46 ++- man/explore.Rd | 2 man/include_columns_for_ui_checkboxes.Rd |only man/prepare_data.Rd | 16 + man/print.corporaexplorerobject.Rd | 2 53 files changed, 844 insertions(+), 437 deletions(-)
More information about corporaexplorer at CRAN
Permanent link
Title: Fits the Bayesian Piecewise Linear Log-Hazard Model
Description: Contains posterior samplers for the Bayesian piecewise linear log-hazard and piecewise exponential hazard models, including Cox models. Posterior mean restricted survival times are also computed for non-Cox an Cox models with only treatment indicators. The ApproxMean() function can be used to estimate restricted posterior mean survival times given a vector of patient covariates in the Cox model. Functions included to return the posterior mean hazard and survival functions for the piecewise exponential and piecewise linear log-hazard models. Chapple, AG, Peak, T, Hemal, A (2020). Under Revision.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between BayesReversePLLH versions 1.2 dated 2020-02-01 and 1.3 dated 2020-02-06
DESCRIPTION | 6 ++-- MD5 | 4 +-- src/BayesReversePLLH.cpp | 58 ++++++++++++++++++++++++----------------------- 3 files changed, 35 insertions(+), 33 deletions(-)
More information about BayesReversePLLH at CRAN
Permanent link
Title: Messages, Warnings, Strings with Ascii Animals
Description: Allows printing of character strings as messages/warnings/etc.
with ASCII animals, including cats, cows, frogs, chickens, ghosts,
and more.
Author: Scott Chamberlain [aut, cre],
Amanda Dobbyn [aut],
Tyler Rinker [ctb],
Thomas Leeper [ctb],
Noam Ross [ctb],
Rich FitzJohn [ctb],
Carson Sievert [ctb],
Kiyoko Gotanda [ctb],
Andy Teucher [ctb],
Karl Broman [ctb],
Franz-Sebastian Krah [ctb],
Lucy D'Agostino McGowan [ctb],
Guangchuang Yu [ctb],
Philipp Boersch-Supan [ctb],
Andreas Brandmaier [ctb],
Marion Louveaux [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between cowsay versions 0.7.0 dated 2018-09-18 and 0.8.0 dated 2020-02-06
DESCRIPTION | 18 LICENSE | 2 MD5 | 45 - NEWS.md | 20 R/animals.r | 155 ++-- R/cowsay-package.r | 51 - R/endless_horse.R | 19 R/say.r | 153 ++-- R/utils.R | 1 R/zzz.R | 1 README.md | 1471 ++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/cowsay_tutorial.R | 56 - inst/doc/cowsay_tutorial.Rmd | 19 inst/doc/cowsay_tutorial.html | 343 ++++++--- man/animals.Rd | 2 man/cowsay.Rd | 36 - man/endless_horse.Rd | 32 man/img |only man/say.Rd | 110 +-- tests/testthat/test-say.R | 42 - vignettes/cowsay_tutorial.Rmd | 19 22 files changed, 1320 insertions(+), 1275 deletions(-)
Title: Pin, Discover and Share Resources
Description: Pin remote resources into a local cache to work offline,
improve speed and avoid recomputing; discover and share resources
in local folders, 'GitHub', 'Kaggle' or 'RStudio Connect'. Resources can
be anything from 'CSV', 'JSON', or image files to arbitrary R objects.
Author: Javier Luraschi [aut, cre],
RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between pins versions 0.3.1 dated 2020-01-10 and 0.3.2 dated 2020-02-06
DESCRIPTION | 6 ++--- MD5 | 30 ++++++++++++++--------------- NEWS.md | 10 +++++++++ R/board_github.R | 6 ++--- R/board_rsconnect.R | 21 +++++++++++++------- R/board_rsconnect_bundle.R | 12 ++++++++++- R/board_test.R | 22 +++++++++++++++++++++ R/pin.R | 35 ++++++++++++---------------------- README.md | 2 - inst/doc/boards-rsconnect.Rmd | 9 ++++++++ inst/doc/boards-rsconnect.html | 10 +++++++++ man/pin_info.Rd | 6 +++-- tests/testthat/test-board-packages.R | 2 - tests/testthat/test-board-rsconnect.R | 20 +++++++++++++++++++ tests/testthat/test-pin-info.R | 30 +++++++++++++++++++++++++++++ vignettes/boards-rsconnect.Rmd | 9 ++++++++ 16 files changed, 175 insertions(+), 55 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.2.6 dated 2019-11-26 and 0.2.7 dated 2020-02-06
DESCRIPTION | 12 ++++---- MD5 | 54 +++++++++++++++++++------------------- NEWS | 12 +++++++- R/DHARMa.R | 2 - R/createData.R | 2 - R/helper.R | 2 - R/plotResiduals.R | 8 ++++- R/simulateResiduals.R | 6 ---- R/tests.R | 19 +++++++------ R/zzz.R | 15 +++++++++- inst/doc/DHARMa.html | 32 +++++++++++----------- inst/examples/plotsHelp.R | 3 ++ man/createDHARMa.Rd | 2 - man/hist.DHARMa.Rd | 3 ++ man/plot.DHARMa.Rd | 3 ++ man/plotQQunif.Rd | 3 ++ man/plotResiduals.Rd | 7 ++++ man/testDispersion.Rd | 2 - man/testGeneric.Rd | 2 - man/testOutliers.Rd | 2 - man/testOverdispersion.Rd | 2 - man/testResiduals.Rd | 2 - man/testSimulatedResiduals.Rd | 2 - man/testSpatialAutocorrelation.Rd | 2 - man/testUniformity.Rd | 2 - man/testZeroInflation.Rd | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/testPlots.R | 14 +++++++-- 28 files changed, 134 insertions(+), 83 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for
simultaneous variable clustering and regression. This version also
(re)implements in C++ an R script proposed by Howard Bondell that fits
the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see
Sharma et al (2013) <DOI:10.1080/15533174.2012.707849>).
Author: Loic Yengo [aut, cre],
Mickaël Canouil [aut] (<https://orcid.org/0000-0002-3396-4549>)
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.4 dated 2016-03-22 and 1.2.0 dated 2020-02-06
clere-1.1.4/clere/R/Clere.R |only clere-1.1.4/clere/R/sClere-Class.R |only clere-1.1.4/clere/data/algoComp.RData |only clere-1.1.4/clere/data/numExpRealData.RData |only clere-1.1.4/clere/data/numExpSimData.RData |only clere-1.1.4/clere/inst/doc/ExampleProstate.R |only clere-1.1.4/clere/inst/doc/Methods.R |only clere-1.1.4/clere/inst/doc/RealDataExample.R |only clere-1.1.4/clere/inst/doc/SEM_vs_MCEM_simulations.R |only clere-1.1.4/clere/inst/doc/SimulatedDataExample.R |only clere-1.1.4/clere/man/clusters-methods.Rd |only clere-1.1.4/clere/man/predict-methods.Rd |only clere-1.1.4/clere/man/summary-methods.Rd |only clere-1.2.0/clere/DESCRIPTION | 48 +- clere-1.2.0/clere/MD5 | 71 +-- clere-1.2.0/clere/NAMESPACE | 40 -- clere-1.2.0/clere/NEWS.md |only clere-1.2.0/clere/R/Clere-class.R |only clere-1.2.0/clere/R/Pacs-class.R |only clere-1.2.0/clere/R/algoComp.R |only clere-1.2.0/clere/R/clere-package.R |only clere-1.2.0/clere/R/fitClere.R | 365 ++++++++++++------- clere-1.2.0/clere/R/fitPacs.R | 135 ++++--- clere-1.2.0/clere/R/numExpRealData.R |only clere-1.2.0/clere/R/numExpSimData.R |only clere-1.2.0/clere/R/sClere-class.R |only clere-1.2.0/clere/README.md |only clere-1.2.0/clere/build/vignette.rds |binary clere-1.2.0/clere/data/algoComp.rda |only clere-1.2.0/clere/data/numExpRealData.rda |only clere-1.2.0/clere/data/numExpSimData.rda |only clere-1.2.0/clere/inst/CITATION |only clere-1.2.0/clere/inst/doc/clere.R | 275 +++++++------- clere-1.2.0/clere/inst/doc/clere.Rnw | 261 +++++++------ clere-1.2.0/clere/inst/doc/clere.pdf |binary clere-1.2.0/clere/man/Clere-class.Rd | 148 +++---- clere-1.2.0/clere/man/Pacs-class.Rd | 55 +- clere-1.2.0/clere/man/algoComp.Rd | 54 +- clere-1.2.0/clere/man/clere-package.Rd | 73 +-- clere-1.2.0/clere/man/clusters.Rd |only clere-1.2.0/clere/man/figures |only clere-1.2.0/clere/man/fitClere.Rd | 150 +++++-- clere-1.2.0/clere/man/fitPacs.Rd | 94 ++-- clere-1.2.0/clere/man/numExpRealData.Rd | 65 +-- clere-1.2.0/clere/man/numExpSimData.Rd | 65 +-- clere-1.2.0/clere/man/plot-methods.Rd | 53 +- clere-1.2.0/clere/man/predict.Rd |only clere-1.2.0/clere/man/summary.Rd |only clere-1.2.0/clere/src/Makevars | 8 clere-1.2.0/clere/src/Makevars.win | 8 clere-1.2.0/clere/src/packagename_init.c |only clere-1.2.0/clere/vignettes/clere.Rnw | 261 +++++++------ 52 files changed, 1197 insertions(+), 1032 deletions(-)
Title: Virtual Machines in 'Azure'
Description: Functionality for working with virtual machines (VMs) in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/services/virtual-machines/>. Includes facilities to deploy, startup, shutdown, and cleanly delete VMs and VM clusters. Deployment configurations can be highly customised, and can make use of existing resources as well as creating new ones. A selection of predefined configurations is provided to allow easy deployment of commonly used Linux and Windows images, including Data Science Virtual Machines. With a running VM, execute scripts and install optional extensions. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureVM versions 2.1.0 dated 2019-11-03 and 2.1.1 dated 2020-02-06
DESCRIPTION | 10 MD5 | 70 +++--- NAMESPACE | 2 NEWS.md | 5 R/add_methods.R | 4 R/vm_config.R | 8 R/vmss_config.R | 12 - README.md | 4 inst/doc/intro.html | 4 inst/doc/intro.rmd | 4 man/autoscaler_config.Rd | 80 +++---- man/az_vm_resource.Rd | 84 +++---- man/az_vm_template.Rd | 180 +++++++--------- man/az_vmss_resource.Rd | 124 +++++------ man/az_vmss_template.Rd | 204 ++++++++---------- man/build_template.Rd | 104 ++++----- man/create_vm.Rd | 336 +++++++++++++++--------------- man/defunct.Rd | 40 +-- man/delete_vm.Rd | 114 +++++----- man/get_vm.Rd | 134 ++++++------ man/ip_config.Rd | 66 ++--- man/is_vm.Rd | 82 +++---- man/lb_config.Rd | 112 +++++----- man/lb_rules.Rd | 152 ++++++------- man/list_vm_sizes.Rd | 94 ++++---- man/nic_config.Rd | 70 +++--- man/nsg_config.Rd | 110 ++++----- man/nsg_rules.Rd | 104 ++++----- man/reexports.Rd | 34 +-- man/scaleset_options.Rd | 72 +++--- man/vm_config.Rd | 457 ++++++++++++++++++++--------------------- man/vm_resource_config.Rd | 82 +++---- man/vmss_config.Rd | 431 +++++++++++++++++++------------------- man/vnet_config.Rd | 78 +++--- tests/testthat/test13_custom.R | 9 vignettes/intro.rmd | 4 36 files changed, 1731 insertions(+), 1749 deletions(-)
Title: IRT Item-Person Map with 'ConQuest' Integration
Description: A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The 'WrightMap' package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. 'TAM', 'mirt', 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.), 'WrightMap' features special integration with 'ConQuest' to facilitate reading and plotting its output directly.The 'wrightMap' function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The 'CQmodel' function reads output files created using 'ConQuest' software and creates a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The 'wrightMap' function can take a 'CQmodel' object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Author: David Torres Irribarra & Rebecca Freund
Maintainer: David Torres Irribarra <david@torresirribarra.me>
Diff between WrightMap versions 1.2.1 dated 2016-03-23 and 1.2.2 dated 2020-02-06
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS | 6 ++++++ R/CQmodel.R | 3 ++- R/itemClassic.R | 4 +++- R/itemData.CQmodel.R | 9 ++++++--- R/itemModern.R | 23 ++++++++++++++++++++--- R/personDens.R | 4 ++-- README.md | 4 ++-- man/item.side.Rd | 5 ++++- 11 files changed, 62 insertions(+), 28 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical measures,
which otherwise could only be calculated with additional effort
(like Cramer's V, Phi, or effect size statistics like Eta or Omega squared),
or for which currently no functions available. Second, another focus
lies on weighted variants of common statistical measures and tests
like weighted standard error, mean, t-test, correlation, and more.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.17.8 dated 2020-01-21 and 0.17.9 dated 2020-02-06
DESCRIPTION | 6 - MD5 | 62 +++++----- NEWS.md | 7 + R/anova_stats.R | 18 ++- R/bootstrap.R | 19 +-- R/gof.R | 2 R/grpmean.R | 10 - R/samplesize_mixed.R | 2 R/se_ybar.R | 8 - R/svy_scale_weights.R | 18 +-- R/svyglmnb.R | 30 ++--- R/svyglmzip.R | 42 +++---- R/wtd_sd.R | 23 ++- build/partial.rdb |binary inst/doc/anova-statistics.html | 181 ++++++++++++++++-------------- inst/doc/bayesian-statistics.R | 10 - inst/doc/bayesian-statistics.Rmd | 10 - inst/doc/bayesian-statistics.html | 210 ++++++++++++++++++----------------- inst/doc/mixedmodels-statistics.R | 4 inst/doc/mixedmodels-statistics.Rmd | 4 inst/doc/mixedmodels-statistics.html | 166 ++++++++++++++------------- man/bootstrap.Rd | 19 +-- man/chisq_gof.Rd | 3 man/means_by_group.Rd | 10 - man/samplesize_mixed.Rd | 2 man/scale_weights.Rd | 18 +-- man/se_ybar.Rd | 8 - man/svyglm.nb.Rd | 30 ++--- man/svyglm.zip.Rd | 42 +++---- man/weighted_sd.Rd | 23 ++- vignettes/bayesian-statistics.Rmd | 10 - vignettes/mixedmodels-statistics.Rmd | 4 32 files changed, 531 insertions(+), 470 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.27 dated 2020-01-16 and 1.28 dated 2020-02-06
DESCRIPTION | 6 ++-- MD5 | 38 +++++++++++++++---------------- R/block.R | 1 R/hooks-extra.R | 26 +++++++++------------ R/output.R | 24 ++++++++++++------- R/plot.R | 32 ++++++++++++++++---------- R/utils.R | 5 ++++ inst/doc/datatables.html | 6 ++-- inst/doc/docco-classic.html | 13 ++++------ inst/doc/docco-linear.html | 16 +++++-------- inst/doc/knit_expand.html | 52 +++++++++++++++++++------------------------ inst/doc/knit_print.html | 42 +++++++++++++++++----------------- inst/doc/knitr-html.html | 6 ++-- inst/doc/knitr-intro.html | 14 +++++------ inst/doc/knitr-markdown.html | 21 ++++++++--------- inst/doc/knitr-refcard.pdf |binary man/chunk_hook.Rd | 5 +--- man/include_graphics.Rd | 22 ++++++++++-------- tests/testit/test-hooks-md.R | 2 - tests/testit/test-plot.R | 2 - 20 files changed, 172 insertions(+), 161 deletions(-)
Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between GeneNet versions 1.2.13 dated 2015-08-02 and 1.2.14 dated 2020-02-06
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 5 +++++ data/ecoli.rda |binary man/GeneNet.package.Rd | 3 --- man/arth800.Rd | 2 +- man/ggm.estimate.pcor.Rd | 1 - man/network.make.graph.Rd | 1 - 8 files changed, 18 insertions(+), 18 deletions(-)
Title: Sampling Surface Simulation for Areal Sampling Methods
Description: Sampling surface simulation is useful in the comparison of different areal sampling methods
in forestry, ecology and natural resources. The sampSurf package allows the simulation
of numerous sampling methods for standing trees and downed woody debris in a spatial context.
It also provides an S4 class and method structure that facilitates the addition of new sampling
methods.
Author: Jeffrey H. Gove
Maintainer: Jeffrey H. Gove <jgove@fs.fed.us>
Diff between sampSurf versions 0.7-4 dated 2017-09-27 and 0.7-5 dated 2020-02-06
DESCRIPTION | 20 +- MD5 | 302 ++++++++++++++++----------------- R/InclusionZoneClass.R | 4 R/MonteCarloConstructors.R | 2 R/StemContainerClass.R | 10 - R/TractClass.R | 4 R/TractConstructors.R | 2 R/izContainer.R | 6 R/sampleLogs.R | 2 R/sampleTrees.R | 2 R/setAsStem.R | 18 + R/summarySampSurf.R | 3 R/taperInterpolate.R | 2 build/vignette.rds |binary inst/doc/ArealSamplingClass.pdf |binary inst/doc/GettingStarted.pdf |binary inst/doc/InclusionZoneClass.pdf |binary inst/doc/InclusionZoneGridClass.pdf |binary inst/doc/Overview.pdf |binary inst/doc/StemClass.pdf |binary inst/doc/TractClass.pdf |binary inst/doc/sampSurfClass.pdf |binary man/Tract-methods.Rd | 2 man/Tract.Rd | 4 man/angleGauge-methods.Rd | 2 man/angleGauge.Rd | 4 man/antitheticContainer-methods.Rd | 2 man/antitheticContainer.Rd | 4 man/antitheticICHSIZ-methods.Rd | 2 man/antitheticICHSIZ.Rd | 4 man/antitheticSampling-methods.Rd | 2 man/antitheticSampling.Rd | 4 man/area-methods.Rd | 2 man/area.Rd | 4 man/bboxCheck.Rd | 4 man/bboxSum.Rd | 4 man/bboxToPoly.Rd | 4 man/boltDimensions.Rd | 4 man/bufferedTract-methods.Rd | 2 man/bufferedTract.Rd | 4 man/chainSawIZ-methods.Rd | 2 man/chainSawIZ.Rd | 4 man/checkStemDimensions.Rd | 4 man/circularPlot-methods.Rd | 2 man/circularPlot.Rd | 4 man/circularPlotIZ-methods.Rd | 2 man/circularPlotIZ.Rd | 4 man/clipStemsToTract-methods.Rd | 2 man/clipStemsToTract.Rd | 4 man/controlVariate-methods.Rd | 2 man/controlVariate.Rd | 4 man/criticalHeightIZ-methods.Rd | 2 man/criticalHeightIZ.Rd | 4 man/crudeMonteCarlo-methods.Rd | 2 man/crudeMonteCarlo.Rd | 4 man/distanceLimited-methods.Rd | 2 man/distanceLimited.Rd | 4 man/distanceLimitedIZ-methods.Rd | 2 man/distanceLimitedIZ.Rd | 4 man/distanceLimitedMCIZ-methods.Rd | 2 man/distanceLimitedMCIZ.Rd | 4 man/distanceLimitedPDSIZ-methods.Rd | 2 man/distanceLimitedPDSIZ.Rd | 4 man/downLog.Rd | 4 man/downLogIZs.Rd | 4 man/downLogs-methods.Rd | 2 man/downLogs.Rd | 4 man/fullChainSawIZ-methods.Rd | 2 man/fullChainSawIZ.Rd | 4 man/getID-methods.Rd | 2 man/getID.Rd | 4 man/getProxy.Rd | 4 man/gridCellEnhance.Rd | 4 man/heapIZ-methods.Rd | 2 man/heapIZ.Rd | 4 man/hist-methods.Rd | 2 man/hist.Rd | 4 man/horizontalLineIZ-methods.Rd | 2 man/horizontalLineIZ.Rd | 4 man/horizontalPointCMCIZ-methods.Rd | 2 man/horizontalPointCMCIZ.Rd | 4 man/horizontalPointCVIZ-methods.Rd | 2 man/horizontalPointCVIZ.Rd | 4 man/horizontalPointISIZ-methods.Rd | 2 man/horizontalPointISIZ.Rd | 4 man/horizontalPointIZ-methods.Rd | 2 man/horizontalPointIZ.Rd | 4 man/hybridDLPDSIZ-methods.Rd | 2 man/hybridDLPDSIZ.Rd | 4 man/importanceCHSIZ-methods.Rd | 2 man/importanceCHSIZ.Rd | 4 man/importanceSampling-methods.Rd | 2 man/importanceSampling.Rd | 4 man/izContainer.Rd | 4 man/izGrid-methods.Rd | 2 man/izGrid.Rd | 4 man/izGridConstruct.Rd | 4 man/izGridMirage-methods.Rd | 2 man/izGridMirage.Rd | 4 man/lineSegment.Rd | 4 man/mcsContainer-methods.Rd | 2 man/mcsContainer.Rd | 4 man/mirageTract-methods.Rd | 2 man/mirageTract.Rd | 4 man/monte-methods.Rd | 2 man/monte.Rd | 4 man/monteBSSample-methods.Rd | 2 man/monteBSSample.Rd | 4 man/monteNTSample-methods.Rd | 2 man/monteNTSample.Rd | 4 man/montePop-methods.Rd | 2 man/montePop.Rd | 4 man/omnibusDLPDSIZ-methods.Rd | 2 man/omnibusDLPDSIZ.Rd | 4 man/omnibusPDSIZ-methods.Rd | 2 man/omnibusPDSIZ.Rd | 4 man/pairedAICHSIZ-methods.Rd | 2 man/pairedAICHSIZ.Rd | 4 man/perimeter-methods.Rd | 2 man/perimeter.Rd | 4 man/perpendicularDistance-methods.Rd | 2 man/perpendicularDistance.Rd | 4 man/perpendicularDistanceIZ-methods.Rd | 2 man/perpendicularDistanceIZ.Rd | 4 man/plot-methods.Rd | 7 man/plot.Rd | 4 man/plot3D-methods.Rd | 2 man/plot3D.Rd | 6 man/pointRelascope-methods.Rd | 2 man/pointRelascope.Rd | 4 man/pointRelascopeIZ-methods.Rd | 2 man/pointRelascopeIZ.Rd | 4 man/sampSurf-methods.Rd | 2 man/sampSurf-package.Rd | 6 man/sampSurf.Rd | 4 man/sampleLogs.Rd | 4 man/sampleTrees.Rd | 4 man/sausageIZ-methods.Rd | 2 man/sausageIZ.Rd | 4 man/segmentVolume-methods.Rd | 2 man/segmentVolume.Rd | 4 man/spCircle.Rd | 4 man/standUpIZ-methods.Rd | 2 man/standUpIZ.Rd | 4 man/standingTree-methods.Rd | 2 man/standingTree.Rd | 4 man/standingTreeIZs-methods.Rd | 2 man/standingTreeIZs.Rd | 4 man/standingTrees-methods.Rd | 2 man/standingTrees.Rd | 4 man/taperInterpolate-methods.Rd | 2 man/taperInterpolate.Rd | 4 152 files changed, 405 insertions(+), 387 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.0 dated 2019-12-09 and 0.2.1 dated 2020-02-06
DESCRIPTION | 6 +- MD5 | 10 ++-- NAMESPACE | 1 NEWS.md | 20 +++++++-- R/ropenblas.R | 118 ++++++++++++++++++++++++++++++++++++++++------------------ README.md | 15 ++++--- 6 files changed, 117 insertions(+), 53 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <http://www.nserc-crsng.gc.ca>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <http://www.sshrc-crsh.gc.ca>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <http://www.sharcnet.ca>).
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-9 dated 2018-10-25 and 0.60-10 dated 2020-02-06
CHANGELOG | 39 +++++++++---- DESCRIPTION | 8 +- MD5 | 66 +++++++++++------------ R/np.copula.R | 2 R/np.plot.R | 4 - R/np.quantile.R | 2 R/np.sigtest.R | 2 R/zzz.R | 2 build/vignette.rds |binary data/cps71.rda |binary inst/doc/entropy_np.R | 12 ++-- inst/doc/entropy_np.Rnw | 3 - inst/doc/entropy_np.pdf |binary inst/doc/np.pdf |binary inst/doc/np_faq.Rnw | 120 ++++++++++++++++++++++++------------------- inst/doc/np_faq.pdf |binary man/data-oecd.Rd | 2 man/data-wage1.Rd | 4 - man/np-package.Rd | 13 ++-- man/np.condensity.bw.Rd | 4 - man/np.condistribution.bw.Rd | 4 - man/np.density.bw.Rd | 4 - man/np.deptest.Rd | 2 man/np.distribution.bw.Rd | 4 - man/np.regressioniv.Rd | 2 man/np.regressionivderiv.Rd | 2 man/np.sdeptest.Rd | 2 man/np.sigtest.Rd | 6 +- man/np.smoothcoef.bw.Rd | 4 - man/np.symtest.Rd | 2 man/np.unitest.Rd | 4 - man/se.Rd | 1 vignettes/entropy_np.Rnw | 3 - vignettes/np_faq.Rnw | 120 ++++++++++++++++++++++++------------------- 34 files changed, 242 insertions(+), 201 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.
Author: Stéphane Dray, David Bauman, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.3-7 dated 2019-06-04 and 0.3-8 dated 2020-02-06
DESCRIPTION | 8 MD5 | 53 +- NAMESPACE | 8 R/ScotchWhiskey.R |only R/TBI.R | 2 R/constr.hclust-class.R |only R/constr.hclust.R |only R/mem.select.R | 4 R/moranNP.randtest.R | 10 R/msr.4thcorner.R | 18 R/msr.varipart.R | 5 R/plot.TBI.R | 2 R/plot.constr.hclust.R |only R/stimodels.R | 10 build/vignette.rds |binary data/ScotchWhiskey.rda |only inst/doc/tutorial.R | 274 ++++++++--- inst/doc/tutorial.Rmd | 383 ++++++++++++---- inst/doc/tutorial.html | 1019 +++++++++++++++++++++++++++++--------------- man/ScotchWhiskey.Rd |only man/TBI.Rd | 2 man/constr.hclust-class.Rd |only man/constr.hclust.Rd |only man/mem.select.Rd | 4 man/plot.TBI.Rd | 2 man/plot.constr.hclust.Rd |only src/constr.hclust.c |only src/constr.hclust.h |only src/init.c | 2 vignettes/adespatial.bib | 92 +++ vignettes/adespatial.png |binary vignettes/listw_explore.png |binary vignettes/tutorial.Rmd | 383 ++++++++++++---- 33 files changed, 1646 insertions(+), 635 deletions(-)
Title: IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 1.5.2 dated 2019-07-15 and 1.5.3 dated 2020-02-06
DESCRIPTION | 12 ++-- MD5 | 26 ++++----- NAMESPACE | 2 R/imagine-internal.R | 24 -------- R/imagine-main.R | 26 ++++++--- README.md | 4 - build/vignette.rds |binary inst/doc/vignette.R | 8 +- inst/doc/vignette.html | 23 ++++---- man/basic2DFilter.Rd | 126 ++++++++++++++++++++++----------------------- man/contextualMF.Rd | 92 ++++++++++++++++----------------- man/convolutions.Rd | 135 +++++++++++++++++++++++++------------------------ man/image-package.Rd | 38 ++++++------- man/wbImage.Rd | 28 +++++----- 14 files changed, 269 insertions(+), 275 deletions(-)
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 1.0.3 dated 2020-01-14 and 1.0.4 dated 2020-02-06
dexter-1.0.3/dexter/inst/doc/dexter.R |only dexter-1.0.3/dexter/inst/doc/dexter.Rmd |only dexter-1.0.3/dexter/inst/doc/dexter.html |only dexter-1.0.3/dexter/inst/doc/profile-plots.R |only dexter-1.0.3/dexter/inst/doc/profile-plots.Rmd |only dexter-1.0.3/dexter/inst/doc/profile-plots.html |only dexter-1.0.3/dexter/vignettes/dexter.Rmd |only dexter-1.0.3/dexter/vignettes/profile-plots.Rmd |only dexter-1.0.4/dexter/DESCRIPTION | 12 - dexter-1.0.4/dexter/MD5 | 72 +++++----- dexter-1.0.4/dexter/NAMESPACE | 1 dexter-1.0.4/dexter/NEWS | 4 dexter-1.0.4/dexter/R/RcppExports.R | 4 dexter-1.0.4/dexter/R/anon_calibration.R | 31 ++++ dexter-1.0.4/dexter/R/database.R | 5 dexter-1.0.4/dexter/R/enorm.R | 8 - dexter-1.0.4/dexter/R/misc.R | 2 dexter-1.0.4/dexter/R/tia.R | 23 ++- dexter-1.0.4/dexter/build/vignette.rds |binary dexter-1.0.4/dexter/inst/doc/DIF_vignette.html | 4 dexter-1.0.4/dexter/inst/doc/Dexter.R |only dexter-1.0.4/dexter/inst/doc/Dexter.Rmd |only dexter-1.0.4/dexter/inst/doc/Dexter.html |only dexter-1.0.4/dexter/inst/doc/Equating.html | 8 - dexter-1.0.4/dexter/inst/doc/Plausible_Values.html | 14 - dexter-1.0.4/dexter/inst/doc/Profile-plots.R |only dexter-1.0.4/dexter/inst/doc/Profile-plots.Rmd |only dexter-1.0.4/dexter/inst/doc/Profile-plots.html |only dexter-1.0.4/dexter/inst/doc/Test_Individual_differences.html | 14 - dexter-1.0.4/dexter/man/fit_enorm.Rd | 2 dexter-1.0.4/dexter/man/plot.prms.Rd | 6 dexter-1.0.4/dexter/man/tia_tables.Rd | 5 dexter-1.0.4/dexter/src/RcppExports.cpp | 22 --- dexter-1.0.4/dexter/src/elsym.cpp | 29 ++-- dexter-1.0.4/dexter/src/pascal.cpp | 9 - dexter-1.0.4/dexter/tests/testthat/test_ability.R | 4 dexter-1.0.4/dexter/tests/testthat/test_data_selection.R | 11 - dexter-1.0.4/dexter/tests/testthat/test_database.R | 2 dexter-1.0.4/dexter/tests/testthat/test_enorm.R | 1 dexter-1.0.4/dexter/tests/testthat/test_oplike.r | 1 dexter-1.0.4/dexter/tests/testthat/test_plausible_values.R | 1 dexter-1.0.4/dexter/tests/testthat/test_profiles.R | 2 dexter-1.0.4/dexter/vignettes/Dexter.Rmd |only dexter-1.0.4/dexter/vignettes/Profile-plots.Rmd |only dexter-1.0.4/dexter/vignettes/dexter.bib | 7 45 files changed, 166 insertions(+), 138 deletions(-)
Title: High-Dimensional Repeated Measures
Description: Methods for testing main and interaction effects in possibly
high-dimensional parametric or nonparametric repeated measures in factorial designs for univariate or multivariate data.
The observations of the subjects are assumed to be multivariate normal if using the parametric test.
The nonparametric version tests with regard to nonparametric relative effects (based on pseudo-ranks).
It is possible to use up to 2 whole- and 3 subplot factors.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Harrar W. Solomon [aut],
Arne C. Bathke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between HRM versions 1.0.2 dated 2018-10-17 and 1.2.1 dated 2020-02-06
DESCRIPTION | 16 - MD5 | 162 +++++++++-------- NAMESPACE | 6 R/GUI.R | 314 +++++++++++++++++----------------- R/MVHRM.R |only R/Repeated.R | 139 +++++++++------ R/S3methods.R | 41 +++- R/conf_int.R | 3 R/f1.R | 319 +++++++++++++++++++++++++---------- R/f1_sub0.R | 10 - R/f2.R | 107 +++++++++++ R/f2_old.R | 290 +++++++++++++++---------------- R/f3_sub1.R | 93 +++++++++- R/f3_sub2.R | 84 ++++++++- R/f3_sub3.R | 174 +++++++++++++------ R/f4_sub2.R | 91 +++++++++ R/f4_sub3.R | 87 +++++++++ R/f4_sub4.R | 175 +++++++++++++------ R/f5_sub5.R | 178 +++++++++++++------ R/plot.R | 28 +-- R/plot2.R | 52 ++--- R/utility.R | 8 README.md | 11 - man/DualEmpirical.Rd | 32 +-- man/DualEmpirical2.Rd | 32 +-- man/EEG.Rd | 52 ++--- man/GUI_error.Rd | 32 +-- man/HRM-deprecated.Rd | 57 +++--- man/I.Rd | 28 +-- man/J.Rd | 28 +-- man/P.Rd | 28 +-- man/confint.HRM.Rd | 70 +++---- man/dot-E1.Rd | 36 +-- man/dot-E2.Rd | 36 +-- man/dot-E3.Rd | 32 +-- man/dot-E4.Rd | 32 +-- man/dot-hrm.sigcode.Rd | 28 +-- man/gui.results.Rd | 42 ++-- man/hrm.0w.2s.Rd | 80 +++++--- man/hrm.0w.3s.Rd | 79 +++++--- man/hrm.0w.4s.Rd | 80 +++++--- man/hrm.0w.5s.Rd | 81 +++++--- man/hrm.1f.Rd | 77 ++++---- man/hrm.1w.0f.Rd | 76 ++++---- man/hrm.1w.1f.Rd | 80 +++++--- man/hrm.1w.2f.Rd | 83 +++++---- man/hrm.1w.3f.Rd | 103 ++++++----- man/hrm.2w.1f.Rd | 85 +++++---- man/hrm.2w.2f.Rd | 84 +++++---- man/hrm.A.unweighted.Rd | 52 ++--- man/hrm.A.weighted.Rd | 52 ++--- man/hrm.AB.Rd | 52 ++--- man/hrm.A_B.Rd | 52 ++--- man/hrm.B.Rd | 52 ++--- man/hrm.GUI.Rd | 30 +-- man/hrm.mv.1w.1f.Rd |only man/hrm.mv.internal.Rd |only man/hrm.plot.Rd | 115 ++++++------ man/hrm.test.1.none.Rd | 56 +++--- man/hrm.test.1.one.Rd | 65 ++++--- man/hrm.test.2.between.Rd | 81 +++++--- man/hrm.test.2.between.within.Rd | 86 +++++---- man/hrm.test.2.one.Rd | 80 ++++---- man/hrm.test.2.two.Rd | 68 ++++--- man/hrm.test.2.within.Rd | 81 +++++--- man/hrm.test.3.between.Rd | 86 +++++---- man/hrm.test.3.three.Rd | 73 ++++---- man/hrm.test.4.four.Rd | 78 ++++---- man/hrm.test.5.five.Rd | 83 +++++---- man/hrm.test.dataframe-deprecated.Rd | 70 +++---- man/hrm.test.matrices.Rd | 40 ++-- man/hrm.test.matrix-deprecated.Rd | 40 ++-- man/hrm_GUI.Rd | 30 +-- man/hrm_test.Rd | 173 ++++++++++-------- man/hrm_test_internal.Rd | 80 ++++---- man/plot.HRM.Rd | 87 ++++----- tests/testthat/test_0w_1s.R | 6 tests/testthat/test_0w_3s.R | 12 - tests/testthat/test_0w_4s.R | 10 - tests/testthat/test_0w_5s.R | 12 - tests/testthat/test_1w_2s.R | 6 tests/testthat/test_2w_1s.R | 6 tests/testthat/test_2w_2s.R | 6 tests/testthat/test_mv_1w_1s.R |only 84 files changed, 3436 insertions(+), 2245 deletions(-)
Title: Automatically Search Errors or Warnings
Description: Provides environment hooks that obtain errors and warnings which
occur during the execution of code to automatically search for solutions.
Author: James Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between errorist versions 0.0.2 dated 2019-01-07 and 0.0.3 dated 2020-02-06
DESCRIPTION | 20 +++++--- MD5 | 22 ++++----- NEWS.md | 9 +++ R/errorist-package.R | 9 +++ README.md | 12 ++--- build/vignette.rds |binary inst/doc/working-with-errorist.R | 6 +- inst/doc/working-with-errorist.html | 82 +++++++++++++++++++++++++----------- man/errorist-package.Rd | 10 +--- man/errorist_init.Rd | 8 +-- man/shims.Rd | 10 ++-- tests/testthat/test-handlers.R | 8 --- 12 files changed, 121 insertions(+), 75 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. See Kosmidis et al (2019) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.6.0 dated 2019-11-08 and 0.6.1 dated 2020-02-06
DESCRIPTION | 8 ++-- MD5 | 72 ++++++++++++++++++------------------ NEWS.md | 14 +++++-- R/bracl.R | 7 ++- R/brglmControl.R | 2 - R/brglmFit.R | 6 +-- R/brmultinom.R | 14 +++---- R/check_infinite_estimates.R | 2 - R/detect_separation.R | 10 ++--- R/mis-link.R | 2 - R/separator.R | 2 - R/utils.R | 2 - README.md | 2 - build/vignette.rds |binary inst/doc/adjacent.R | 22 +++++------ inst/doc/adjacent.html | 38 ++++++++----------- inst/doc/iteration.R | 2 - inst/doc/iteration.Rmd | 2 - inst/doc/iteration.html | 19 ++++----- inst/doc/multinomial.R | 16 ++++---- inst/doc/multinomial.html | 40 +++++++++----------- inst/doc/separation.R | 12 +++--- inst/doc/separation.html | 30 ++++++--------- inst/empirical_br_tests.R | 16 +++++--- man/bracl.Rd | 16 ++++++-- man/brglm2.Rd | 1 man/brglmControl.Rd | 30 +++++++++++---- man/brglmFit.Rd | 47 ++++++++++++++++------- man/brmultinom.Rd | 15 ++++++- man/check_infinite_estimates.glm.Rd | 2 - man/detect_separation.Rd | 47 +++++++++++++++-------- man/detect_separation_control.Rd | 12 ++++-- man/predict.brmultinom.Rd | 7 +-- man/residuals.brmultinom.Rd | 6 +-- man/summary.brglmFit.Rd | 13 ++++-- man/vcov.brglmFit.Rd | 7 +-- vignettes/iteration.Rmd | 2 - 37 files changed, 306 insertions(+), 239 deletions(-)
Title: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass
Spectrometry Data
Description: Functions for processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by
Mass Spectrometry experiments (HDX-MS). 'HaDeX' introduces a new standardized and reproducible workflow
for the analysis of the HDX-MS data, including novel uncertainty intervals. Additionally, it covers
data exploration, quality control and generation of publication-quality figures. All functionalities
are also available in the in-built 'Shiny' app.
Author: Weronika Puchala [cre, aut] (<https://orcid.org/0000-0003-2163-1429>),
Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>),
Dominik Rafacz [ctb]
Maintainer: Weronika Puchala <puchala.weronika@gmail.com>
Diff between HaDeX versions 1.0 dated 2019-08-30 and 1.1 dated 2020-02-06
DESCRIPTION | 10 MD5 | 87 +++-- R/HaDeX-package.R | 2 R/calculate_kinetics.R | 13 R/calculate_state_deuteration.R | 21 - R/plot_coverage.R | 3 R/plot_kinetics.R | 4 R/quality_control.R | 56 --- R/read_hdx.R | 15 README.md | 3 inst/HaDeX/data-work.R | 40 ++ inst/HaDeX/data/two_proteins.csv |only inst/HaDeX/docs |only inst/HaDeX/readmes/about.md | 2 inst/HaDeX/report_template.Rmd | 84 +++++ inst/HaDeX/server.R | 548 +++++++++++++++++++++++++++------- inst/HaDeX/ui.R | 257 ++++++++++----- inst/HaDeX/www/HaDeX_theme.css | 18 + inst/WORDLIST | 2 inst/doc/overview.R | 29 + inst/doc/overview.Rmd | 46 ++ inst/doc/overview.html | 175 +++++++--- man/calculate_kinetics.Rd | 7 man/calculate_state_deuteration.Rd | 7 man/quality_control.Rd | 10 man/read_hdx.Rd | 5 tests/testthat/test_quality_control.R | 8 vignettes/HDX.bib | 82 +++++ vignettes/comparison.csv | 48 +- vignettes/overview.Rmd | 46 ++ 30 files changed, 1198 insertions(+), 430 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation
of repeatabilities in measurements and matrices, and general evolutionary
quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Andrade Machado, Guilherme
Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.2-6 dated 2019-04-08 and 0.2-7 dated 2020-02-06
evolqg-0.2-6/evolqg/R/CalcEigenSd.R |only evolqg-0.2-6/evolqg/man/CalcEigenSd.Rd |only evolqg-0.2-7/evolqg/DESCRIPTION | 15 +-- evolqg-0.2-7/evolqg/MD5 | 62 +++++++-------- evolqg-0.2-7/evolqg/NAMESPACE | 4 evolqg-0.2-7/evolqg/R/CalcAVG.R | 2 evolqg-0.2-7/evolqg/R/CalcEigenVar.R |only evolqg-0.2-7/evolqg/R/CalcR2CvCorrected.R | 2 evolqg-0.2-7/evolqg/R/CreateHypotMatrix.R | 14 +++ evolqg-0.2-7/evolqg/R/KrzSubspace.R | 2 evolqg-0.2-7/evolqg/R/MINT.R | 2 evolqg-0.2-7/evolqg/R/MatrixStatistics.R | 4 evolqg-0.2-7/evolqg/R/MonteCarloStat.R | 30 +++++-- evolqg-0.2-7/evolqg/R/MultivDriftTest.R | 4 evolqg-0.2-7/evolqg/R/PrintMatrix.R | 3 evolqg-0.2-7/evolqg/R/RSProjection.R | 2 evolqg-0.2-7/evolqg/R/RandomSkewers.R | 2 evolqg-0.2-7/evolqg/R/Rarefaction.R | 20 ++-- evolqg-0.2-7/evolqg/R/RelativeEigenanalysis.R |only evolqg-0.2-7/evolqg/R/RevertMatrix.R | 4 evolqg-0.2-7/evolqg/man/CalcEigenVar.Rd |only evolqg-0.2-7/evolqg/man/CalcR2CvCorrected.Rd | 2 evolqg-0.2-7/evolqg/man/KrzSubspace.Rd | 2 evolqg-0.2-7/evolqg/man/MINT.Rd | 2 evolqg-0.2-7/evolqg/man/MonteCarloRep.Rd | 13 ++- evolqg-0.2-7/evolqg/man/MonteCarloStat.Rd | 16 ++- evolqg-0.2-7/evolqg/man/MultivDriftTest.Rd | 4 evolqg-0.2-7/evolqg/man/Partition2HypotMatrix.Rd |only evolqg-0.2-7/evolqg/man/PlotRarefaction.Rd | 17 +--- evolqg-0.2-7/evolqg/man/PrintMatrix.Rd | 3 evolqg-0.2-7/evolqg/man/RSProjection.Rd | 2 evolqg-0.2-7/evolqg/man/Rarefaction.Rd | 3 evolqg-0.2-7/evolqg/man/RelativeEigenanalysis.Rd |only evolqg-0.2-7/evolqg/tests/testthat/iris.stats | 2 evolqg-0.2-7/evolqg/tests/testthat/test.CalcEigenVar.r |only evolqg-0.2-7/evolqg/tests/testthat/test.TestModularity.r | 8 + 36 files changed, 153 insertions(+), 93 deletions(-)
Title: An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
Description: Allows to display a progress bar in the R
console for long running computations taking place in c++ code,
and support for interrupting those computations even in multithreaded
code, typically using OpenMP.
Author: Karl Forner <karl.forner@gmail.com>
Maintainer: Karl Forner <karl.forner@gmail.com>
Diff between RcppProgress versions 0.4.1 dated 2018-05-11 and 0.4.2 dated 2020-02-06
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- inst/include/progress.hpp | 4 +--- 3 files changed, 9 insertions(+), 10 deletions(-)
Title: Econometric Tools for Performance and Risk Analysis
Description: Collection of econometric functions for performance and risk
analysis. In addition to standard risk and performance metrics, this
package aims to aid practitioners and researchers in utilizing the latest
research in analysis of non-normal return streams. In general, it is most
tested on return (rather than price) data on a regular scale, but most
functions will work with irregular return data as well, and increasing
numbers of functions will work with P&L or price data where possible.
Author: Brian G. Peterson [cre, aut, cph],
Peter Carl [aut, cph],
Kris Boudt [ctb, cph],
Ross Bennett [ctb],
Joshua Ulrich [ctb],
Eric Zivot [ctb],
Dries Cornilly [ctb],
Eric Hung [ctb],
Matthieu Lestel [ctb],
Kyle Balkissoon [ctb],
Diethelm Wuertz [ctb],
Anthony Alexander Christidis [ctb],
R. Douglas Martin [ctb],
Zeheng 'Zenith' Zhou [ctb],
Justin M. Shea [ctb]
Maintainer: Brian G. Peterson <brian@braverock.com>
Diff between PerformanceAnalytics versions 1.5.3 dated 2019-06-23 and 2.0.4 dated 2020-02-06
PerformanceAnalytics-1.5.3/PerformanceAnalytics/tests/testthat |only PerformanceAnalytics-1.5.3/PerformanceAnalytics/tests/testthat.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/DESCRIPTION | 29 PerformanceAnalytics-2.0.4/PerformanceAnalytics/MD5 | 482 +- PerformanceAnalytics-2.0.4/PerformanceAnalytics/NAMESPACE | 7 PerformanceAnalytics-2.0.4/PerformanceAnalytics/NEWS | 31 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/ActivePremium.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/AdjustedSharpeRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/AppraisalRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/BernadoLedoitratio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/BurkeRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CAPM.alpha.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CAPM.beta.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CAPM.epsilon.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CAPM.jensenAlpha.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CAPM.utils.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CalmarRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/CoMoments.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/DRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/DownsideDeviation.R | 13 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/DownsideFrequency.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/DrawdownPeak.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Drawdowns.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/ES.R | 63 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/FamaBeta.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Frequency.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/HerfindahlIndex.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/HurstIndex.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/InformationRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Kappa.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/KellyRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/M2Sortino.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MSquared.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MSquaredExcess.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MarketTiming.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MartinRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MeanAbsoluteDeviation.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MinTRL.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/MultivariateMoments.R | 4 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/NetSelectivity.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Omega.R | 41 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/OmegaExcessReturn.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/OmegaSharpeRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/PainIndex.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/PainRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/PortfolioRisk.R | 4 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/ProbSharpeRatio.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/ProspectRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/RPESE.control.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/RachevRatio.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.Geltner.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.annualized.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.calculate.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.clean.R | 9 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.cumulative.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.excess.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.locScaleRob.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.portfolio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.read.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Return.relative.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/Selectivity.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SemiDeviation.R | 100 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SharpeRatio.R | 45 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SharpeRatio.annualized.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SkewnessKurtosisRatio.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SmoothingIndex.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SortinoRatio.R | 70 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/SpecificRisk.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/StdDev.R | 65 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/StdDev.annualized.R 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PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RelativePerformance.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RiskReturnScatter.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RollingCorrelation.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RollingMean.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RollingPerformance.R | 6 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RollingQuantileRegression.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.RollingRegression.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.Scatter.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.SnailTrail.R | 2 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.StackedBar.R | 12 PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.TimeSeries.R | 263 - PerformanceAnalytics-2.0.4/PerformanceAnalytics/R/chart.TimeSeries.base.R | 337 - 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More information about PerformanceAnalytics at CRAN
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Title: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry
Data
Description: Dirichlet process mixture of multivariate normal, skew normal or skew t-distributions
modeling oriented towards flow-cytometry data preprocessing applications. Method is
detailed in: Hejblum, Alkhassimn, Gottardo, Caron & Thiebaut (2019) <doi: 10.1214/18-AOAS1209>.
Author: Boris P Hejblum [aut, cre],
Chariff Alkhassim [aut],
Francois Caron [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between NPflow versions 0.13.1 dated 2017-08-02 and 0.13.3 dated 2020-02-06
DESCRIPTION | 24 + LICENSE | 170 ------------- MD5 | 262 ++++++++++----------- NAMESPACE | 1 NEWS.md | 5 R/DPMGibbsN.R | 22 - R/DPMGibbsN_SeqPrior.R | 30 +- R/DPMGibbsN_parallel.R | 22 - R/DPMGibbsSkewN.R | 25 +- R/DPMGibbsSkewN_parallel.R | 37 +- R/DPMGibbsSkewT.R | 67 +++-- R/DPMGibbsSkewT_SeqPrior.R | 29 +- R/DPMGibbsSkewT_SeqPrior_parallel.R | 27 +- R/DPMGibbsSkewT_parallel.R | 23 - R/DPMpost.R | 32 +- R/Flimited.R | 11 R/MAP_sNiW_mmEM.R | 10 R/MLE_sNiW.R | 2 R/MLE_sNiW_mmEM.R | 8 R/NPflow-package.R | 14 - R/RcppExports.R | 159 ++++++------ R/SliceSampler_SkewN.R | 2 R/SliceSampler_SkewN_parallel.R | 2 R/burn.DPMM.R | 2 R/cluster_est_Fmeasure.R | 2 R/cluster_est_Mbinder_norm.R | 4 R/cluster_est_binder.R | 4 R/cluster_est_pear.R | 2 R/cytoScatter.R | 4 R/evalClustLoss.R | 6 R/mmsNiWlogpdf.R | 352 ++++++++++++++-------------- R/mvnpdf.R | 2 R/mvsnpdf.R | 2 R/mvstpdf.R | 2 R/plot_DPM.R | 6 R/plot_DPMsn.R | 10 R/plot_DPMst.R | 383 +++++++++++++++---------------- R/postProcess.DPMMclust.R | 4 R/priormix.R | 8 R/rCRP.R | 2 R/rNNiW.R | 2 R/sample_alpha.R | 2 R/similarityMat.R | 6 R/sliceSampler_N.R | 2 R/sliceSampler_N_SeqPrior.R | 2 R/sliceSampler_N_parallel.R | 4 R/sliceSampler_skewT.R | 4 R/sliceSampler_skewT_SeqPrior.R | 4 R/sliceSampler_skewT_SeqPrior_parallel.R | 4 R/sliceSampler_skewT_parallel.R | 4 R/summary.DPMMclust.R | 18 - R/update_SS.R | 12 R/update_SSsn.R | 16 - R/update_SSst.R | 148 +++++------ README.md | 44 ++- inst/CITATION | 23 - man/DPMGibbsN.Rd | 39 ++- man/DPMGibbsN_SeqPrior.Rd | 49 ++- man/DPMGibbsN_parallel.Rd | 42 ++- man/DPMGibbsSkewN.Rd | 66 +++-- man/DPMGibbsSkewN_parallel.Rd | 60 ++-- man/DPMGibbsSkewT.Rd | 90 +++++-- man/DPMGibbsSkewT_SeqPrior.Rd | 50 ++-- man/DPMGibbsSkewT_SeqPrior_parallel.Rd | 52 ++-- man/DPMGibbsSkewT_parallel.Rd | 50 ++-- man/DPMpost.Rd | 47 ++- man/Flimited.Rd | 11 man/FmeasureC_no0.Rd | 2 man/Fmeasure_costC.Rd | 8 man/MAP_sNiW_mmEM.Rd | 49 +++ man/MLE_NiW_mmEM.Rd | 13 - man/MLE_sNiW.Rd | 2 man/MLE_sNiW_mmEM.Rd | 16 + man/NPflow-package.Rd | 14 - man/NuMatParC.Rd | 4 man/burn.DPMMclust.Rd | 2 man/cluster_est_Fmeasure.Rd | 2 man/cluster_est_Mbinder_norm.Rd | 7 man/cluster_est_binder.Rd | 4 man/cluster_est_pear.Rd | 2 man/cytoScatter.Rd | 17 - man/evalClustLoss.Rd | 4 man/methods.summaryDPMMclust.Rd | 19 - man/mmNiWpdfC.Rd | 9 man/mmsNiWlogpdf.Rd | 2 man/mmsNiWpdfC.Rd | 9 man/mmvnpdfC.Rd | 2 man/mmvsnpdfC.Rd | 2 man/mmvstpdfC.Rd | 2 man/mmvtpdfC.Rd | 2 man/mvnlikC.Rd | 2 man/mvnpdf.Rd | 2 man/mvnpdfC.Rd | 7 man/mvsnlikC.Rd | 2 man/mvsnpdf.Rd | 2 man/mvstlikC.Rd | 2 man/mvstpdf.Rd | 2 man/plot_ConvDPM.Rd | 10 man/plot_DPM.Rd | 20 + man/plot_DPMsn.Rd | 16 - man/plot_DPMst.Rd | 17 + man/postProcess.DPMMclust.Rd | 13 - man/priormix.Rd | 10 man/rCRP.Rd | 2 man/rNNiW.Rd | 2 man/sampleClassC.Rd | 2 man/sample_alpha.Rd | 6 man/similarityMat.Rd | 6 man/similarityMat_nocostC.Rd | 2 man/summary.DPMMclust.Rd | 23 + src/FmeasureC.cpp | 24 - src/Makevars | 14 + src/Makevars.win | 14 + src/NuMatParC.cpp | 4 src/RcppExports.cpp | 236 +++++++++---------- src/TraceEpsC.cpp | 4 src/lgamma_mvC.cpp | 2 src/lgamma_mvC.h | 2 src/mmNiWpdfC.cpp | 23 - src/mmsNiWpdfC.cpp | 27 +- src/mmvnpdfC.cpp | 9 src/mmvsnpdfC.cpp | 11 src/mmvstpdfC.cpp | 16 - src/mmvtpdfC.cpp | 15 - src/mvnlikC.cpp | 14 - src/mvnpdfC.cpp | 13 - src/mvsnlikC.cpp | 16 - src/mvstlikC.cpp | 18 - src/sampleClassC.cpp | 6 src/similarityMatC.cpp | 2 src/similarityMat_nocostC.cpp | 2 src/vclust2mcoclustC.cpp | 2 132 files changed, 1811 insertions(+), 1634 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided.
Author: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Diff between Matching versions 4.9-6 dated 2019-05-07 and 4.9-7 dated 2020-02-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Matching.R | 12 ++++++------ tests/AbadieImbens.Rout.save | 6 +++--- tests/DehejiaWahba.Rout.save | 6 +++--- tests/GenMatch.Rout.save | 6 +++--- tests/Matchby.R | 6 +++--- tests/Matchby.Rout.save | 22 +++++++++++----------- 8 files changed, 40 insertions(+), 40 deletions(-)
Title: Holonomic Gradient Method and Gradient Descent
Description: The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization
constants of unnormalized probability distributions by utilizing holonomic
systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method
to find maximal likelihood estimates by utilizing the HGM.
Author: Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta Nishiyama
Maintainer: Nobuki Takayama <takayama@math.kobe-u.ac.jp>
Diff between hgm versions 1.17 dated 2017-04-01 and 1.18 dated 2020-02-06
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/hgm.c2wishart.R | 6 +++--- R/hgm.cwishart.R | 6 +++--- R/hgm.so3nc.R | 10 ++++++---- R/ko_orthant.R | 4 ++-- man/hgm-package.Rd | 4 ++-- man/hgm.so3nc.Rd | 13 ++++++++----- src/jack-n.c | 6 +++--- src/mh-r.c | 8 ++++---- src/so3_nc.c | 36 ++++++++++++++++++++++++++++-------- 11 files changed, 73 insertions(+), 48 deletions(-)
Title: A Deep Learning for Statistical Classification and Regression
Analysis
Description: Statistical classification and regression have been popular among various fields and stayed in the limelight of scientists of those fields. Examples of the fields include clinical trials where the statistical classification of patients is indispensable to predict the clinical courses of diseases. Considering the negative impact of diseases on performing daily tasks, correctly classifying patients based on the clinical information is vital in that we need to identify patients of the high-risk group to develop a severe state and arrange medical treatment for them at an opportune moment. Deep learning - a part of artificial intelligence - has gained much attention, and research on it burgeons during past decades: see, e.g, Kazemi and Mirroshandel (2018) <DOI:10.1016/j.artmed.2017.12.001>. It is a veritable technique which was originally designed for the classification, and hence, the Buddle package can provide sublime solutions to various challenging classification and regression problems encountered in the clinical trials. The Buddle package is based on the back-propagation algorithm - together with various powerful techniques such as batch normalization and dropout - which performs a multi-layer feed-forward neural network: see Krizhevsky et. al (2017) <DOI:10.1145/3065386>, Schmidhuber (2015) <DOI:10.1016/j.neunet.2014.09.003> and LeCun et al. (1998) <DOI:10.1109/5.726791> for more details. This package contains two main functions: TrainBuddle() and FetchBuddle(). TrainBuddle() builds a feed-forward neural network model and trains the model. FetchBuddle() recalls the trained model which is the output of TrainBuddle(), classifies or regresses given data, and make a final prediction for the data.
Author: Jiwoong Kim <jwboys26 at gmail.com>
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Diff between Buddle versions 1.0 dated 2018-12-21 and 2.0 dated 2020-02-06
Buddle-1.0/Buddle/R/Main.R |only Buddle-1.0/Buddle/man/Buddle_Main.Rd |only Buddle-1.0/Buddle/man/Buddle_Predict.Rd |only Buddle-1.0/Buddle/src/FuncLib.cpp |only Buddle-2.0/Buddle/DESCRIPTION | 22 +++---- Buddle-2.0/Buddle/MD5 | 56 ++++++++++++++++--- Buddle-2.0/Buddle/NAMESPACE | 19 ++++-- Buddle-2.0/Buddle/R/BuddleMain.R |only Buddle-2.0/Buddle/R/Img_data.R |only Buddle-2.0/Buddle/R/RcppExports.R | 17 ++--- Buddle-2.0/Buddle/data |only Buddle-2.0/Buddle/man/CheckNonNumeric.Rd |only Buddle-2.0/Buddle/man/FetchBuddle.Rd |only Buddle-2.0/Buddle/man/GetPrecision.Rd |only Buddle-2.0/Buddle/man/MakeConfusionMatrix.Rd |only Buddle-2.0/Buddle/man/OneHot2Label.Rd |only Buddle-2.0/Buddle/man/Split2TrainTest.Rd |only Buddle-2.0/Buddle/man/TrainBuddle.Rd |only Buddle-2.0/Buddle/man/mnist_data.Rd |only Buddle-2.0/Buddle/src/ActName.h |only Buddle-2.0/Buddle/src/AdaGrad.h |only Buddle-2.0/Buddle/src/Affine.h |only Buddle-2.0/Buddle/src/ArcSinH.h |only Buddle-2.0/Buddle/src/ArcTan.h |only Buddle-2.0/Buddle/src/Batchnorm.h |only Buddle-2.0/Buddle/src/BentIdentity.h |only Buddle-2.0/Buddle/src/Buddle.h |only Buddle-2.0/Buddle/src/Common.h |only Buddle-2.0/Buddle/src/Dropout.h |only Buddle-2.0/Buddle/src/ElliotSig.h |only Buddle-2.0/Buddle/src/FInv.h |only Buddle-2.0/Buddle/src/Gaussian.h |only Buddle-2.0/Buddle/src/Identity.h |only Buddle-2.0/Buddle/src/L2loss.h |only Buddle-2.0/Buddle/src/Layer.h |only Buddle-2.0/Buddle/src/LeakyRelu.h |only Buddle-2.0/Buddle/src/Link.h |only Buddle-2.0/Buddle/src/Momentum.h |only Buddle-2.0/Buddle/src/Optimization.h |only Buddle-2.0/Buddle/src/RcppExports.cpp | 79 ++++++++++----------------- Buddle-2.0/Buddle/src/Relu.h |only Buddle-2.0/Buddle/src/SGD.h |only Buddle-2.0/Buddle/src/Sigmoid.h |only Buddle-2.0/Buddle/src/SinH.h |only Buddle-2.0/Buddle/src/Sinc.h |only Buddle-2.0/Buddle/src/Sinusoid.h |only Buddle-2.0/Buddle/src/SoftPlus.h |only Buddle-2.0/Buddle/src/SoftmaxLoss.h |only Buddle-2.0/Buddle/src/TanH.h |only Buddle-2.0/Buddle/src/cppMain.cpp |only Buddle-2.0/Buddle/src/gBuddle.h |only Buddle-2.0/Buddle/src/gLayer.h |only 52 files changed, 110 insertions(+), 83 deletions(-)
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a
user-defined criterion.
Handles inapplicable data using the algorithm of
Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.
Implements Profile Parsimony (Faith and Trueman, 2001)
<doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969)
<doi:10.2307/2412182>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 0.3.2 dated 2019-06-03 and 0.4.0 dated 2020-02-06
TreeSearch-0.3.2/TreeSearch/R/Combinatorics.R |only TreeSearch-0.3.2/TreeSearch/R/Information.R |only TreeSearch-0.3.2/TreeSearch/R/Partitions.R |only TreeSearch-0.3.2/TreeSearch/R/RcppExports.R |only TreeSearch-0.3.2/TreeSearch/R/Support.R |only TreeSearch-0.3.2/TreeSearch/R/ape_interface.R |only TreeSearch-0.3.2/TreeSearch/R/helper_functions.R |only TreeSearch-0.3.2/TreeSearch/R/parse_files.R |only TreeSearch-0.3.2/TreeSearch/R/phylo.R |only TreeSearch-0.3.2/TreeSearch/R/pp_data_manipulation.R |only TreeSearch-0.3.2/TreeSearch/R/tree_display.R |only TreeSearch-0.3.2/TreeSearch/R/tree_distance.R |only TreeSearch-0.3.2/TreeSearch/R/tree_generation.R |only TreeSearch-0.3.2/TreeSearch/R/tree_numbering.R |only TreeSearch-0.3.2/TreeSearch/data/Lobo.RData |only TreeSearch-0.3.2/TreeSearch/data/brewer.R |only TreeSearch-0.3.2/TreeSearch/data/doubleFactorials.rda |only TreeSearch-0.3.2/TreeSearch/data/logDoubleFactorials.rda |only TreeSearch-0.3.2/TreeSearch/inst/doc/load-data.R |only 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TreeSearch-0.3.2/TreeSearch/man/NeworderPruningwise.Rd |only TreeSearch-0.3.2/TreeSearch/man/NonDuplicateRoot.Rd |only TreeSearch-0.3.2/TreeSearch/man/NyeTreeSimilarity.Rd |only TreeSearch-0.3.2/TreeSearch/man/OrderEdgesNumberNodes.Rd |only TreeSearch-0.3.2/TreeSearch/man/PhyToString.Rd |only TreeSearch-0.3.2/TreeSearch/man/RandomTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/ReadCharacters.Rd |only TreeSearch-0.3.2/TreeSearch/man/ReadTntTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/Renumber.Rd |only TreeSearch-0.3.2/TreeSearch/man/RenumberTips.Rd |only TreeSearch-0.3.2/TreeSearch/man/RenumberTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/RightmostCharacter.Rd |only TreeSearch-0.3.2/TreeSearch/man/RootTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/SampleOne.Rd |only TreeSearch-0.3.2/TreeSearch/man/SingleTaxonTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/SortTree.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitEntropy.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitFrequency.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitInformation.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitMatchProbability.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitMutualInformation.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitsCompatible.Rd |only TreeSearch-0.3.2/TreeSearch/man/SplitsRepeated.Rd |only TreeSearch-0.3.2/TreeSearch/man/StringToPhyDat.Rd |only TreeSearch-0.3.2/TreeSearch/man/Subtree.Rd |only TreeSearch-0.3.2/TreeSearch/man/SupportColour.Rd |only TreeSearch-0.3.2/TreeSearch/man/Tree2Splits.Rd |only TreeSearch-0.3.2/TreeSearch/man/TreesMatchingSplit.Rd |only TreeSearch-0.3.2/TreeSearch/man/UniqueSplits.Rd |only TreeSearch-0.3.2/TreeSearch/man/UnloadTreeSearch.Rd |only TreeSearch-0.3.2/TreeSearch/man/UnrootedTreesMatchingSplit.Rd |only TreeSearch-0.3.2/TreeSearch/man/VisualizeMatching.Rd |only TreeSearch-0.3.2/TreeSearch/man/brewer.Rd |only TreeSearch-0.3.2/TreeSearch/man/doubleFactorials.Rd |only TreeSearch-0.3.2/TreeSearch/man/logDoubleFactorials.Rd |only TreeSearch-0.3.2/TreeSearch/src/RcppExports.cpp |only TreeSearch-0.3.2/TreeSearch/src/ape_reorder.h |only TreeSearch-0.3.2/TreeSearch/src/phangorn_bip.cpp |only TreeSearch-0.3.2/TreeSearch/src/renumber_tree.h |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-Partitions.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-Support.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-ape-interface.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-ape-tree.nex |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-combinatorics.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-information.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-mpl-counts.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-mpl-search.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-parse-nexus.nexus |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-parsers.R |only TreeSearch-0.3.2/TreeSearch/tests/testthat/test-pp-search.R |only 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223 ++++-- TreeSearch-0.4.0/TreeSearch/R/SPR.R | 55 + TreeSearch-0.4.0/TreeSearch/R/Sectorial.R | 36 - TreeSearch-0.4.0/TreeSearch/R/SuccessiveApproximations.R | 28 TreeSearch-0.4.0/TreeSearch/R/TBR.R | 46 - TreeSearch-0.4.0/TreeSearch/R/TreeSearch.R | 59 + TreeSearch-0.4.0/TreeSearch/R/data.R | 57 - TreeSearch-0.4.0/TreeSearch/R/data_manipulation.R |only TreeSearch-0.4.0/TreeSearch/R/mpl_morphy_objects.R | 28 TreeSearch-0.4.0/TreeSearch/R/mpl_morphyex.R | 26 TreeSearch-0.4.0/TreeSearch/R/mpl_prepare_data.R | 86 -- TreeSearch-0.4.0/TreeSearch/R/pp_ProfileScore.R | 20 TreeSearch-0.4.0/TreeSearch/R/pp_info_extra_step.r | 63 - TreeSearch-0.4.0/TreeSearch/R/tree_rearrangement.R | 147 ---- TreeSearch-0.4.0/TreeSearch/R/zzz.R | 5 TreeSearch-0.4.0/TreeSearch/build/partial.rdb |binary TreeSearch-0.4.0/TreeSearch/build/vignette.rds |binary TreeSearch-0.4.0/TreeSearch/inst/CITATION | 15 TreeSearch-0.4.0/TreeSearch/inst/REFERENCES.bib | 96 -- TreeSearch-0.4.0/TreeSearch/inst/WORDLIST |only 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TreeSearch-0.4.0/TreeSearch/man/ICPerStep.Rd | 2 TreeSearch-0.4.0/TreeSearch/man/IWScore.Rd | 25 TreeSearch-0.4.0/TreeSearch/man/JackLabels.Rd |only TreeSearch-0.4.0/TreeSearch/man/LogisticPoints.Rd | 3 TreeSearch-0.4.0/TreeSearch/man/MinimumLength.Rd |only TreeSearch-0.4.0/TreeSearch/man/MorphyBootstrap.Rd | 30 TreeSearch-0.4.0/TreeSearch/man/MorphyErrorCheck.Rd | 31 TreeSearch-0.4.0/TreeSearch/man/MorphyTreeLength.Rd | 36 - TreeSearch-0.4.0/TreeSearch/man/MorphyWeights.Rd | 34 + TreeSearch-0.4.0/TreeSearch/man/NNI.Rd | 15 TreeSearch-0.4.0/TreeSearch/man/PhyDat2Morphy.Rd | 36 + TreeSearch-0.4.0/TreeSearch/man/PrepareDataProfile.Rd | 27 TreeSearch-0.4.0/TreeSearch/man/ProfileScore.Rd | 34 - TreeSearch-0.4.0/TreeSearch/man/RandomMorphyTree.Rd | 15 TreeSearch-0.4.0/TreeSearch/man/RandomTreeScore.Rd | 3 TreeSearch-0.4.0/TreeSearch/man/Ratchet.Rd | 127 ++- TreeSearch-0.4.0/TreeSearch/man/RearrangeEdges.Rd | 19 TreeSearch-0.4.0/TreeSearch/man/SPR.Rd | 23 TreeSearch-0.4.0/TreeSearch/man/SetMorphyWeights.Rd | 36 + TreeSearch-0.4.0/TreeSearch/man/SingleCharMorphy.Rd | 32 TreeSearch-0.4.0/TreeSearch/man/StopUnlessBifurcating.Rd | 4 TreeSearch-0.4.0/TreeSearch/man/SuccessiveApproximations.Rd | 6 TreeSearch-0.4.0/TreeSearch/man/SuccessiveWeights.Rd | 5 TreeSearch-0.4.0/TreeSearch/man/TBR.Rd | 20 TreeSearch-0.4.0/TreeSearch/man/TBRWarning.Rd | 5 TreeSearch-0.4.0/TreeSearch/man/TipsAreNames.Rd | 4 TreeSearch-0.4.0/TreeSearch/man/TreeSearch.Rd | 47 - TreeSearch-0.4.0/TreeSearch/man/UnloadMorphy.Rd | 40 + TreeSearch-0.4.0/TreeSearch/man/WithOneExtraStep.Rd | 2 TreeSearch-0.4.0/TreeSearch/man/congreveLamsdellMatrices.Rd | 3 TreeSearch-0.4.0/TreeSearch/man/mpl_apply_tipdata.Rd | 30 TreeSearch-0.4.0/TreeSearch/man/mpl_attach_rawdata.Rd | 34 - TreeSearch-0.4.0/TreeSearch/man/mpl_attach_symbols.Rd | 30 TreeSearch-0.4.0/TreeSearch/man/mpl_delete_Morphy.Rd | 30 TreeSearch-0.4.0/TreeSearch/man/mpl_delete_rawdata.Rd | 30 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TreeSearch-0.4.0/TreeSearch/man/mpl_update_tip.Rd | 29 TreeSearch-0.4.0/TreeSearch/man/summary.morphyPtr.Rd | 30 TreeSearch-0.4.0/TreeSearch/src/TreeSearch-init.c | 19 TreeSearch-0.4.0/TreeSearch/tests/testthat.R | 4 TreeSearch-0.4.0/TreeSearch/tests/testthat/test-Fitch.R |only TreeSearch-0.4.0/TreeSearch/tests/testthat/test-Jackknife.R |only TreeSearch-0.4.0/TreeSearch/tests/testthat/test-TreeSearch.R |only TreeSearch-0.4.0/TreeSearch/tests/testthat/test-data-manipulation.R | 26 TreeSearch-0.4.0/TreeSearch/tests/testthat/test-pp-ICS.R | 2 TreeSearch-0.4.0/TreeSearch/tests/testthat/test-pp-fitch.R | 5 TreeSearch-0.4.0/TreeSearch/tests/testthat/test-pp-random-tree.R | 92 +- TreeSearch-0.4.0/TreeSearch/tests/testthat/test-zzz-tree-rearrange.R |only TreeSearch-0.4.0/TreeSearch/vignettes/getting-started.Rmd | 2 TreeSearch-0.4.0/TreeSearch/vignettes/inapplicable.Rmd | 94 +- TreeSearch-0.4.0/TreeSearch/vignettes/profile-scores.Rmd |only TreeSearch-0.4.0/TreeSearch/vignettes/profile.Rmd | 38 - 226 files changed, 2321 insertions(+), 1642 deletions(-)
Title: Produce Forest Plots to Visualize Covariate Effects
Description: Produce forest plots to visualize covariate effects using either
the command line or an interactive 'Shiny' application.
Author: Samer Mouksassi [aut, cre] (<https://orcid.org/0000-0002-7152-6654>),
Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between coveffectsplot versions 0.0.4 dated 2019-10-09 and 0.0.5 dated 2020-02-06
coveffectsplot-0.0.4/coveffectsplot/inst/shiny/text/img |only coveffectsplot-0.0.5/coveffectsplot/DESCRIPTION | 15 coveffectsplot-0.0.5/coveffectsplot/MD5 | 61 coveffectsplot-0.0.5/coveffectsplot/NAMESPACE | 2 coveffectsplot-0.0.5/coveffectsplot/NEWS.md | 11 coveffectsplot-0.0.5/coveffectsplot/R/data.R | 13 coveffectsplot-0.0.5/coveffectsplot/R/forest_plot.R | 293 + coveffectsplot-0.0.5/coveffectsplot/R/run_interactiveforestplot.R | 16 coveffectsplot-0.0.5/coveffectsplot/README.md | 39 coveffectsplot-0.0.5/coveffectsplot/build/vignette.rds |binary coveffectsplot-0.0.5/coveffectsplot/data/prezista.rda |binary coveffectsplot-0.0.5/coveffectsplot/inst/doc/Exposure_Response_Example.R |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/Exposure_Response_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/Exposure_Response_Example.html |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PKPD_Example.R |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PKPD_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PKPD_Example.html |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PK_Example.R |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PK_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/PK_Example.html |only coveffectsplot-0.0.5/coveffectsplot/inst/doc/introduction_to_coveffectsplot.R | 174 coveffectsplot-0.0.5/coveffectsplot/inst/doc/introduction_to_coveffectsplot.Rmd | 107 coveffectsplot-0.0.5/coveffectsplot/inst/doc/introduction_to_coveffectsplot.html | 2519 +--------- coveffectsplot-0.0.5/coveffectsplot/inst/shiny/global.r | 5 coveffectsplot-0.0.5/coveffectsplot/inst/shiny/img/prezista.png |binary coveffectsplot-0.0.5/coveffectsplot/inst/shiny/img/snapshotforest.png |binary coveffectsplot-0.0.5/coveffectsplot/inst/shiny/img/snapshottable.png |only coveffectsplot-0.0.5/coveffectsplot/inst/shiny/rsconnect |only coveffectsplot-0.0.5/coveffectsplot/inst/shiny/server.R | 70 coveffectsplot-0.0.5/coveffectsplot/inst/shiny/text/howto.md | 19 coveffectsplot-0.0.5/coveffectsplot/inst/shiny/ui.R | 174 coveffectsplot-0.0.5/coveffectsplot/man/forest_plot.Rd | 572 +- coveffectsplot-0.0.5/coveffectsplot/man/get_sample_data.Rd | 26 coveffectsplot-0.0.5/coveffectsplot/man/prezista.Rd | 47 coveffectsplot-0.0.5/coveffectsplot/man/run_interactiveforestplot.Rd | 33 coveffectsplot-0.0.5/coveffectsplot/vignettes/Exposure_Response_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/vignettes/PKPD_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/vignettes/PK_Example.Rmd |only coveffectsplot-0.0.5/coveffectsplot/vignettes/introduction_to_coveffectsplot.Rmd | 107 39 files changed, 1480 insertions(+), 2823 deletions(-)
More information about coveffectsplot at CRAN
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Title: Checking and Simplifying Validation Rule Sets
Description: Rule sets with validation rules may contain redundancies or contradictions.
Functions for finding redundancies and problematic rules are provided,
given a set a rules formulated with 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut],
Jacco Daalmans [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between validatetools versions 0.4.7 dated 2019-12-19 and 0.5.0 dated 2020-02-06
DESCRIPTION | 6 +-- MD5 | 24 +++++++-------- NEWS | 4 ++ R/categorical.R | 6 +-- R/dnf.R | 7 ++-- R/expr_manip.R | 11 +++++-- R/linear.R | 2 - R/simplify_conditional.R | 3 + R/soft-rule.R | 11 ++++--- tests/testthat/test-dnf.R | 45 +++++++++++++++++++++++++++++ tests/testthat/test-simplify_conditional.R | 26 +++++++++++++++- tests/testthat/test-soft-rule.R | 2 + tests/testthat/test-substitute_values.R | 4 +- 13 files changed, 118 insertions(+), 33 deletions(-)
Title: Time Series Exploration, Modelling and Forecasting
Description: Includes: (i) tests and visualisations that can help the modeller explore time series components and perform decomposition; (ii) modelling shortcuts, such as functions to construct lagmatrices and seasonal dummy variables of various forms; (iii) an implementation of the Theta method; (iv) tools to facilitate the design of the forecasting process, such as ABC-XYZ analyses; and (v) "quality of life" functions, such as treating time series for trailing and leading values.
Author: Nikolaos Kourentzes [aut, cre],
Ivan Svetunkov [ctb],
Oliver Schaer [ctb]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between tsutils versions 0.9.0 dated 2019-01-11 and 0.9.2 dated 2020-02-06
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++++-------- NAMESPACE | 2 + NEWS.md | 8 ++++++ R/Sthief.R |only R/abc.R | 2 - R/lambdaseq.R | 4 +-- R/plotSthief.R |only R/theta.R | 4 +-- R/tsutils-package.R | 7 +++++ R/xyz.R | 2 - README.md | 69 +++++++++++++++++++++++++++++++++++++++++++++++----- man/Sthief.Rd |only man/lambdaseq.Rd | 2 - man/plotSthief.Rd |only man/tsutils.Rd | 9 ++++++ 16 files changed, 115 insertions(+), 28 deletions(-)
Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.6.1 dated 2020-01-22 and 1.6.2 dated 2020-02-06
DESCRIPTION | 8 MD5 | 43 + NEWS | 9 R/formants.R | 206 ++++++++- R/invertSpectrogram.R | 2 R/postprocessing.R | 1 R/presets.R | 1 R/soundgen.R | 88 ++-- R/source.R | 87 ++- R/utilities_segment.R | 5 data/permittedValues.rda |binary inst/doc/acoustic_analysis.html | 84 +-- inst/doc/sound_generation.R | 13 inst/doc/sound_generation.Rmd | 18 inst/doc/sound_generation.html | 876 ++++++++++++++++++++-------------------- man/generateHarmonics.Rd | 12 man/getSpectralEnvelope.Rd | 5 man/getVocalFry.Rd | 2 man/invertSpectrogram.Rd | 2 man/lockToFormants.Rd |only man/playme.Rd | 2 man/soundgen.Rd | 13 vignettes/sound_generation.Rmd | 18 23 files changed, 923 insertions(+), 572 deletions(-)
Title: Query Search Interfaces
Description: Provides a search interface to look up terms
on 'Google', 'Bing', 'DuckDuckGo', 'Startpage', 'Twitter', 'StackOverflow',
'RStudio Community', 'GitHub', and 'BitBucket'. Upon searching, a browser
window will open with the aforementioned search results.
Author: James Balamuta [aut, cre] (<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between searcher versions 0.0.4 dated 2019-07-05 and 0.0.5 dated 2020-02-06
searcher-0.0.4/searcher/tests/testthat/test-searcher.R |only searcher-0.0.5/searcher/DESCRIPTION | 12 searcher-0.0.5/searcher/MD5 | 36 + searcher-0.0.5/searcher/NAMESPACE | 1 searcher-0.0.5/searcher/NEWS.md | 42 ++ searcher-0.0.5/searcher/R/index-sites.R |only searcher-0.0.5/searcher/R/search-functions.R | 197 +++------- searcher-0.0.5/searcher/R/searcher-package.R | 36 + searcher-0.0.5/searcher/R/utilities.R | 84 +++- searcher-0.0.5/searcher/README.md | 46 ++ searcher-0.0.5/searcher/build/vignette.rds |binary searcher-0.0.5/searcher/inst/doc/search-patterns.R | 2 searcher-0.0.5/searcher/inst/doc/search-patterns.Rmd | 3 searcher-0.0.5/searcher/inst/doc/search-patterns.html | 84 ++-- searcher-0.0.5/searcher/man/search_site.Rd | 84 ++-- searcher-0.0.5/searcher/man/searcher-package.Rd | 21 - searcher-0.0.5/searcher/man/searcher.Rd | 10 searcher-0.0.5/searcher/tests/testthat/test-index-sites.R |only searcher-0.0.5/searcher/tests/testthat/test-search-functions.R |only searcher-0.0.5/searcher/tests/testthat/test-searcher-package.R |only searcher-0.0.5/searcher/tests/testthat/test-utilities.R |only searcher-0.0.5/searcher/vignettes/search-patterns.Rmd | 3 22 files changed, 421 insertions(+), 240 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <http://vcg.isti.cnr.it>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.18 dated 2018-09-28 and 0.19 dated 2020-02-06
Rvcg-0.18/Rvcg/src/typedefImport.h |only Rvcg-0.18/Rvcg/src/typedefTopo.h |only Rvcg-0.19/Rvcg/DESCRIPTION | 8 Rvcg-0.19/Rvcg/MD5 | 458 - Rvcg-0.19/Rvcg/NAMESPACE | 1 Rvcg-0.19/Rvcg/R/Rvcg-package.R | 4 Rvcg-0.19/Rvcg/R/vcgBorder.r | 1 Rvcg-0.19/Rvcg/R/vcgClean.r | 43 Rvcg-0.19/Rvcg/R/vcgClost.r | 1 Rvcg-0.19/Rvcg/R/vcgCreateKD.r | 13 Rvcg-0.19/Rvcg/R/vcgCurve.r | 2 Rvcg-0.19/Rvcg/R/vcgImport.r | 10 Rvcg-0.19/Rvcg/R/vcgIsolated.r | 40 Rvcg-0.19/Rvcg/R/vcgMeshres.r | 1 Rvcg-0.19/Rvcg/R/vcgMetro.r | 15 Rvcg-0.19/Rvcg/R/vcgPlyRead.r | 2 Rvcg-0.19/Rvcg/R/vcgPlyWrite.r | 27 Rvcg-0.19/Rvcg/R/vcgQEdecim.r | 1 Rvcg-0.19/Rvcg/R/vcgSmooth.r | 1 Rvcg-0.19/Rvcg/R/vcgVolume.r |only Rvcg-0.19/Rvcg/man/Rvcg-package.Rd | 4 Rvcg-0.19/Rvcg/man/vcgBorder.Rd | 2 Rvcg-0.19/Rvcg/man/vcgClean.Rd | 2 Rvcg-0.19/Rvcg/man/vcgClost.Rd | 6 Rvcg-0.19/Rvcg/man/vcgCurve.Rd | 2 Rvcg-0.19/Rvcg/man/vcgImport.Rd | 2 Rvcg-0.19/Rvcg/man/vcgIsolated.Rd | 2 Rvcg-0.19/Rvcg/man/vcgMeshres.Rd | 3 Rvcg-0.19/Rvcg/man/vcgObjWrite.Rd | 1 Rvcg-0.19/Rvcg/man/vcgOffWrite.Rd | 1 Rvcg-0.19/Rvcg/man/vcgPlyRead.Rd | 2 Rvcg-0.19/Rvcg/man/vcgPlyWrite.Rd | 2 Rvcg-0.19/Rvcg/man/vcgQEdecim.Rd | 2 Rvcg-0.19/Rvcg/man/vcgSmooth.Rd | 2 Rvcg-0.19/Rvcg/man/vcgStlWrite.Rd | 1 Rvcg-0.19/Rvcg/man/vcgVolume.Rd |only Rvcg-0.19/Rvcg/man/vcgWrlWrite.Rd | 1 Rvcg-0.19/Rvcg/src/Makevars | 2 Rvcg-0.19/Rvcg/src/ROneRing.cpp | 26 Rvcg-0.19/Rvcg/src/RQEdecim.cpp | 2 Rvcg-0.19/Rvcg/src/RallRead.cpp | 47 Rvcg-0.19/Rvcg/src/Rballpivot.cpp | 100 Rvcg-0.19/Rvcg/src/Rclean.cpp | 85 Rvcg-0.19/Rvcg/src/Rcurvature.cpp | 40 Rvcg-0.19/Rvcg/src/Rexport.cpp | 32 Rvcg-0.19/Rvcg/src/RgetEdge.cpp | 18 Rvcg-0.19/Rvcg/src/Rintersect.cpp | 2 Rvcg-0.19/Rvcg/src/Risolated.cpp | 66 Rvcg-0.19/Rvcg/src/Rkmeans.cpp | 10 Rvcg-0.19/Rvcg/src/Rmeshres.cpp | 4 Rvcg-0.19/Rvcg/src/Rmeshvol.cpp |only Rvcg-0.19/Rvcg/src/Rsample.cpp | 4 Rvcg-0.19/Rvcg/src/Rsubdivision.cpp | 35 Rvcg-0.19/Rvcg/src/RvcgIO.h | 12 Rvcg-0.19/Rvcg/src/init.c | 2 Rvcg-0.19/Rvcg/src/typedef.h | 13 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/attribute_seam.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/clean.h | 3645 ++++---- Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/clustering.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/convex_hull.h | 16 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/crease_cut.h | 77 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/advancing_front.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/ball_pivoting.h | 14 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/platonic.h | 96 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/plymc/plymc.h | 101 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/resampler.h | 15 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/tetramesh_support.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/create/zonohedron.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/curve_on_manifold.h | 1829 +--- Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/cut_tree.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/dual_meshing.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/edge_collapse.h | 211 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/geodesic.h | 12 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/harmonic.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/harmonic.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/hole.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/implicit_smooth.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/implicit_smooth.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/inertia.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/intersection.h | 22 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/isotropic_remeshing.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization.h | 125 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_collapse_quadric.h | 579 - Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_collapse_quadric_tex.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/mesh_assert.h | 64 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/mesh_to_matrix.h | 18 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/nring.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/outline_support.h | 40 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/distortion.h | 211 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/poisson_solver.h | 113 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/poisson_solver.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/tangent_field_operators.h | 532 - Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/uv_utils.h | 62 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/voronoi_atlas.h | 11 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/point_outlier.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/point_sampling.h | 132 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/point_sampling.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/pointcloud_normal.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_polychord_collapse.h | 10 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_support.h | 19 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/polygonal_algorithms.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/quadrangulator.h | 29 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/refine.h | 344 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/refine_loop.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/smooth.h | 2260 ++--- Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/stat.h | 222 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/symmetry.h | 5 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/tetra |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/tetra_implicit_smooth.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/color.h | 1505 +-- Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature.h | 13 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature_fitting.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/fitmaps.h | 12 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/fitmaps.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/flag.h | 787 + Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/halfedge_indexed.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/normal.h | 20 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/quality.h | 226 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/selection.h | 188 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/texture.h | 46 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/update/topology.h | 188 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_processing.h | 14 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_remesher.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_volume_sampling.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/all_types.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/allocate.h | 599 + Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/append.h | 79 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/base.h | 939 +- Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/complex.h | 20 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/exception.h | 15 Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/foreach.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/complex/used_types.h | 13 Rvcg-0.19/Rvcg/src/vcglib/vcg/container/derivation_chain.h | 27 Rvcg-0.19/Rvcg/src/vcglib/vcg/container/simple_temporary_data.h | 13 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/base.h | 14 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/camera.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/eigen.h | 8 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/eigen.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/math/gen_normal.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/histogram.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/matrix33.h | 37 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/matrix44.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/math/polar_decomposition.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/math/quadric.h | 168 Rvcg-0.19/Rvcg/src/vcglib/vcg/math/quadric.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/math/quaternion.h | 109 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/edge/component.h | 418 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/edge/pos.h | 12 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/edge/topology.h | 25 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/base.h | 23 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/component.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/component_ocf.h | 12 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/component_polygon.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/pos.h | 62 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/face/topology.h | 361 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/tetrahedron/base.h | 231 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/tetrahedron/component.h | 587 - Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/tetrahedron/pos.h | 776 - Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/tetrahedron/tetrahedron.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/tetrahedron/topology.h |only Rvcg-0.19/Rvcg/src/vcglib/vcg/simplex/vertex/component.h | 15 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/box2.h | 18 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/box3.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/colorspace.h | 8 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/deprecated_point2.h | 246 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/deprecated_point3.h | 5 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/deprecated_point4.h | 10 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/distance3.h | 14 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/fitting3.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/aabb_binary_tree/closest.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/aabb_binary_tree/kclosest.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/aabb_binary_tree/ray.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/grid_static_obj.h | 22 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/grid_static_ptr.h | 2 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/kdtree/kdtree_face.h | 76 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/octree.h | 1 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/octree_template.h | 8 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/perfect_spatial_hashing.h | 10 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/index/spatial_hashing.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/intersection2.h | 3 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/outline2_packer.h | 4 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/point_matching.h | 92 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/point_matching.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/vcg/space/polygon3.h | 174 Rvcg-0.19/Rvcg/src/vcglib/vcg/space/rasterized_outline2_packer.h | 796 + Rvcg-0.19/Rvcg/src/vcglib/vcg/space/tetra3.h | 684 - Rvcg-0.19/Rvcg/src/vcglib/vcg/space/texcoord2.h | 128 Rvcg-0.19/Rvcg/src/vcglib/wrap/callback.h | 73 Rvcg-0.19/Rvcg/src/vcglib/wrap/dae/colladaformat.h | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/dae/util_dae.h | 1 Rvcg-0.19/Rvcg/src/vcglib/wrap/gl/gl_field.h | 112 Rvcg-0.19/Rvcg/src/vcglib/wrap/gl/gl_mesh_attributes_info.h | 16 Rvcg-0.19/Rvcg/src/vcglib/wrap/gl/gl_mesh_attributes_multi_viewer_bo_manager.h | 4297 +++++----- Rvcg-0.19/Rvcg/src/vcglib/wrap/gl/pick.h | 64 Rvcg-0.19/Rvcg/src/vcglib/wrap/gl/tetramesh.h | 793 - Rvcg-0.19/Rvcg/src/vcglib/wrap/gui/rubberband.cpp | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/gui/trackball.cpp | 5 Rvcg-0.19/Rvcg/src/vcglib/wrap/gui/trackmode.cpp | 5 Rvcg-0.19/Rvcg/src/vcglib/wrap/gui/view.h | 3 Rvcg-0.19/Rvcg/src/vcglib/wrap/igl/arap_parametrization.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/igl/lscm_parametrization.h | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/igl/miq_parametrization.h | 27 Rvcg-0.19/Rvcg/src/vcglib/wrap/igl/sample |only Rvcg-0.19/Rvcg/src/vcglib/wrap/igl/smooth_field.h | 37 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_edgemesh/export_svg.h | 8 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/export_ply.h | 945 -- Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/export_tet.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/export_vtk.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/import.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/import_msh.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/import_ply.h | 1235 +- Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/io_mask.h |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_tetramesh/io_ply.h | 4 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_3ds.h | 4 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_dxf.h | 26 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_field.h | 32 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_gts.h | 27 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_obj.h | 162 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_off.h | 55 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_ply.h | 306 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_stl.h | 23 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/export_vrml.h | 15 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_ctm.h | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_fbx.h | 915 -- Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_field.h | 138 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_nvm.h | 11 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_obj.h | 2053 ++-- Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_out.h | 9 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_ply.h | 2251 ++--- Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_ptx.h | 42 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_stl.h | 113 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/import_stl.h.rej |only Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/io_material.h | 186 Rvcg-0.19/Rvcg/src/vcglib/wrap/io_trimesh/io_ply.h | 93 Rvcg-0.19/Rvcg/src/vcglib/wrap/nanoply/include/nanoply.hpp | 956 +- Rvcg-0.19/Rvcg/src/vcglib/wrap/nanoply/include/nanoplyWrapper.hpp | 2404 +++-- Rvcg-0.19/Rvcg/src/vcglib/wrap/nanoply/nanoply_vcg/main.cpp | 8 Rvcg-0.19/Rvcg/src/vcglib/wrap/openfbx |only Rvcg-0.19/Rvcg/src/vcglib/wrap/ply/plylib.cpp | 3 Rvcg-0.19/Rvcg/src/vcglib/wrap/ply/plylib.h | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/qt/Outline2ToQImage.cpp | 2 Rvcg-0.19/Rvcg/src/vcglib/wrap/qt/outline2_rasterizer.cpp | 224 Rvcg-0.19/Rvcg/src/vcglib/wrap/qt/outline2_rasterizer.h | 3 Rvcg-0.19/Rvcg/src/vcglib/wrap/qt/shot_qt.h | 123 Rvcg-0.19/Rvcg/src/vcglib/wrap/system/qgetopt.cpp | 9 Rvcg-0.19/Rvcg/src/vcglib/wrap/system/qgetopt.h | 2 247 files changed, 22145 insertions(+), 17591 deletions(-)
Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>.
OTP is an open source platform for multi-modal and multi-agency
journey planning written in 'Java'. The package allows you to manage a local version or
connect to remote OTP server.
This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] (<https://orcid.org/0000-0002-9488-9183>),
Marcus Young [aut] (<https://orcid.org/0000-0003-4627-1116>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [ctb] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>
Diff between opentripplanner versions 0.2.0.7 dated 2020-02-04 and 0.2.0.8 dated 2020-02-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/advanced_features.html | 4 ++-- inst/doc/known_issues.html | 4 ++-- inst/doc/opentripplanner.html | 4 ++-- inst/doc/prerequisites.html | 4 ++-- tests/testthat/test_02_without_OTP.R | 12 ++++++------ 8 files changed, 28 insertions(+), 24 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: Multiblock Sparse Multivariable Analysis
Description: Several functions can be used to analyze multiblock multivariable data. If the input is a single matrix, then principal components analysis (PCA) is implemented. If the input is a list of matrices, then multiblock PCA is implemented. If the input is two matrices, for exploratory and objective variables, then partial least squares (PLS) analysis is implemented. If the input is two lists of matrices, for exploratory and objective variables, then multiblock PLS analysis is implemented. Additionally, if an extra outcome variable is specified, then a supervised version of the methods above is implemented. For each method, sparse modeling is also incorporated. Functions for selecting the number of components and regularized parameters are also provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between msma versions 2.0 dated 2019-09-01 and 2.1 dated 2020-02-06
DESCRIPTION | 10 MD5 | 33 +-- NAMESPACE | 66 +++--- R/src.r | 536 ++++++++++++++++++++++++++++++++++++++++----------- build |only inst/doc |only man/cvmsma.Rd | 163 ++++++++------- man/msma-internal.Rd | 102 ++++++--- man/msma-package.Rd | 38 +-- man/msma.Rd | 291 ++++++++++++++------------- man/ncompsearch.Rd | 209 +++++++++++-------- man/optparasearch.Rd |only man/plot.msma.Rd |only man/predict.msma.Rd | 88 ++++---- man/regparasearch.Rd | 200 ++++++++++--------- man/simdata.Rd | 63 ++--- man/strsimdata.Rd | 92 ++++---- man/summary.msma.Rd | 68 +++--- vignettes |only 19 files changed, 1204 insertions(+), 755 deletions(-)
Title: Spy on Your R Session
Description: Conveniently log everything you type into the R console. Logs are
are stored as tidy data frames which can then be analyzed using 'tidyverse'
style tools.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>),
Lucy D'Agostino McGowan [aut] (<https://orcid.org/0000-0001-7297-9359>),
Jeff Leek [ldr] (<https://orcid.org/0000-0002-2873-2671>)
Maintainer: Sean Kross <sean@seankross.com>
Diff between matahari versions 0.1.2 dated 2019-12-10 and 0.1.3 dated 2020-02-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/dance.R | 6 +++++- build/vignette.rds |binary inst/doc/matahari.html | 15 ++++++--------- man/dance_start.Rd | 9 +++++++-- 7 files changed, 33 insertions(+), 22 deletions(-)
More information about googleCloudRunner at CRAN
Permanent link
Title: A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Description: S3 classes and methods to create and work
with year-quarter, year-month and year-isoweek vectors. Basic
arithmetic operations (such as adding and subtracting) are supported,
as well as formatting and converting to and from standard R date
types.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between dint versions 2.1.2 dated 2020-01-07 and 2.1.3 dated 2020-02-06
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 7 R/arithmetic.R | 1 build/vignette.rds |binary inst/doc/dint.R | 2 inst/doc/dint.Rmd | 2 inst/doc/dint.html | 14 man/date_xx_arithmetic.Rd | 2 man/scale_date_xx.Rd | 7 tests/testthat/manual_tests/ggplot_scales.html | 367 +++++++++++++++++++++---- vignettes/dint.Rmd | 2 12 files changed, 350 insertions(+), 82 deletions(-)
More information about Bayesiangammareg at CRAN
Permanent link
Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files. Once
VCF data is read into R a parser function extracts matrices of data. This
information can then be used for quality control or other purposes. Additional
functions provide visualization of genomic data. Once processing is complete
data may be written to a VCF file (*.vcf.gz). It also may be converted into
other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>),
Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>),
Eric C. Anderson [ctb],
David J. Winter [ctb],
Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.9.0 dated 2020-01-10 and 1.10.0 dated 2020-02-06
DESCRIPTION | 6 - MD5 | 36 ++++----- R/chromR_functions.R | 2 R/io_vcfR.R | 2 R/proc_chromR.R | 4 - R/ranking.R | 2 R/summary_tables.R | 2 R/vcfR_conversion.R | 2 R/vcfR_to_tidy_functions.R | 153 +++++++++++++++++++++++++---------------- R/windowing.R | 2 inst/doc/converting_data.R | 26 +++--- inst/doc/converting_data.html | 14 +-- inst/doc/intro_to_vcfR.R | 20 ++--- inst/doc/intro_to_vcfR.html | 26 +++--- inst/doc/vcf_data.R | 16 ++-- inst/doc/vcf_data.html | 94 +++++++++++-------------- inst/doc/workflow.html | 12 +-- man/proc_chromR.Rd | 2 tests/testthat/test_vcfRtidy.R | 3 19 files changed, 223 insertions(+), 201 deletions(-)
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Author: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>),
Joshua N. Pritikin [ctb],
Michael C. Neale [ctb],
Hermine Maes [ctb]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 3.0.5 dated 2019-12-06 and 3.0.6 dated 2020-02-06
umx-3.0.5/umx/man/umx_nice_data.Rd |only umx-3.0.5/umx/man/umx_pb_note.Rd |only umx-3.0.6/umx/DESCRIPTION | 27 - umx-3.0.6/umx/MD5 | 407 ++++++++-------- umx-3.0.6/umx/NAMESPACE | 9 umx-3.0.6/umx/NEWS.md | 17 umx-3.0.6/umx/R/build_run_modify.R | 161 +++--- umx-3.0.6/umx/R/fit_and_reporting.R | 30 - umx-3.0.6/umx/R/lavanify2ram.R | 104 +++- umx-3.0.6/umx/R/misc_and_utility.R | 176 +++--- umx-3.0.6/umx/R/tmx.R | 3 umx-3.0.6/umx/R/umxDoC.R |only umx-3.0.6/umx/R/umxIPnew.R | 2 umx-3.0.6/umx/R/umxPower.R | 10 umx-3.0.6/umx/R/umx_build_polychoricMatrix3.R | 27 - umx-3.0.6/umx/R/umx_build_umxACEcov_fixed.R | 10 umx-3.0.6/umx/R/umx_build_umxACEv.R | 4 umx-3.0.6/umx/R/umx_build_umxGxEbiv.R | 8 umx-3.0.6/umx/R/umx_build_umxSexLim.R | 7 umx-3.0.6/umx/R/umx_build_umxSimplex.R | 7 umx-3.0.6/umx/R/umx_nice_data.R | 22 umx-3.0.6/umx/R/xmu.R | 32 - umx-3.0.6/umx/R/xmu_make_top_twin_models.R | 67 +- umx-3.0.6/umx/inst/WORDLIST | 8 umx-3.0.6/umx/man/FishersMethod.Rd | 19 umx-3.0.6/umx/man/SE_from_p.Rd | 9 umx-3.0.6/umx/man/figures/DoC.pdf |only umx-3.0.6/umx/man/figures/DoC.png |only umx-3.0.6/umx/man/figures/umx_help_figures.graffle |binary umx-3.0.6/umx/man/install.OpenMx.Rd | 14 umx-3.0.6/umx/man/loadings.MxModel.Rd | 9 umx-3.0.6/umx/man/oddsratio.Rd | 9 umx-3.0.6/umx/man/power.ACE.test.Rd | 15 umx-3.0.6/umx/man/qm.Rd | 14 umx-3.0.6/umx/man/reliability.Rd | 9 umx-3.0.6/umx/man/tmx_is.identified.Rd | 13 umx-3.0.6/umx/man/tmx_show.Rd | 15 umx-3.0.6/umx/man/umx.Rd | 65 +- umx-3.0.6/umx/man/umxACE.Rd | 31 - umx-3.0.6/umx/man/umxACE_cov_fixed.Rd | 9 umx-3.0.6/umx/man/umxACEcov.Rd | 10 umx-3.0.6/umx/man/umxACEv.Rd | 10 umx-3.0.6/umx/man/umxAPA.Rd | 10 umx-3.0.6/umx/man/umxBrownie.Rd | 14 umx-3.0.6/umx/man/umxCP.Rd | 10 umx-3.0.6/umx/man/umxConfint.Rd | 2 umx-3.0.6/umx/man/umxCov2cor.Rd | 9 umx-3.0.6/umx/man/umxDiagnose.Rd | 3 umx-3.0.6/umx/man/umxDoC.Rd |only umx-3.0.6/umx/man/umxEquate.Rd | 4 umx-3.0.6/umx/man/umxFactor.Rd | 30 - umx-3.0.6/umx/man/umxFactorScores.Rd | 12 umx-3.0.6/umx/man/umxGetParameters.Rd | 12 umx-3.0.6/umx/man/umxGxE.Rd | 22 umx-3.0.6/umx/man/umxGxE_window.Rd | 4 umx-3.0.6/umx/man/umxGxEbiv.Rd | 8 umx-3.0.6/umx/man/umxHetCor.Rd | 13 umx-3.0.6/umx/man/umxIP.Rd | 6 umx-3.0.6/umx/man/umxJiggle.Rd | 5 umx-3.0.6/umx/man/umxLabel.Rd | 5 umx-3.0.6/umx/man/umxLav2RAM.Rd | 18 umx-3.0.6/umx/man/umxModel.Rd | 12 umx-3.0.6/umx/man/umxModify.Rd | 4 umx-3.0.6/umx/man/umxParameters.Rd | 14 umx-3.0.6/umx/man/umxPlotCP.Rd | 4 umx-3.0.6/umx/man/umxPlotDoC.Rd |only umx-3.0.6/umx/man/umxPower.Rd | 3 umx-3.0.6/umx/man/umxRAM.Rd | 6 umx-3.0.6/umx/man/umxRAM2Lav.Rd |only umx-3.0.6/umx/man/umxReduce.Rd | 15 umx-3.0.6/umx/man/umxReduceACE.Rd | 4 umx-3.0.6/umx/man/umxReduceGxE.Rd | 8 umx-3.0.6/umx/man/umxRotate.MxModelCP.Rd | 8 umx-3.0.6/umx/man/umxSexLim.Rd | 9 umx-3.0.6/umx/man/umxSimplex.Rd | 9 umx-3.0.6/umx/man/umxSummarizeTwinData.Rd | 3 umx-3.0.6/umx/man/umxSummaryACE.Rd | 3 umx-3.0.6/umx/man/umxSummaryACEcov.Rd | 3 umx-3.0.6/umx/man/umxSummaryACEv.Rd | 3 umx-3.0.6/umx/man/umxSummaryCP.Rd | 3 umx-3.0.6/umx/man/umxSummaryDoC.Rd |only umx-3.0.6/umx/man/umxSummaryGxE.Rd | 3 umx-3.0.6/umx/man/umxSummaryGxEbiv.Rd | 3 umx-3.0.6/umx/man/umxSummaryIP.Rd | 3 umx-3.0.6/umx/man/umxSummarySexLim.Rd | 3 umx-3.0.6/umx/man/umxSummarySimplex.Rd | 3 umx-3.0.6/umx/man/umxSuperModel.Rd | 4 umx-3.0.6/umx/man/umxThresholdMatrix.Rd | 4 umx-3.0.6/umx/man/umxValues.Rd | 5 umx-3.0.6/umx/man/umxVersion.Rd | 12 umx-3.0.6/umx/man/umxWeightedAIC.Rd | 19 umx-3.0.6/umx/man/umx_APA_pval.Rd | 69 ++ umx-3.0.6/umx/man/umx_aggregate.Rd | 11 umx-3.0.6/umx/man/umx_apply.Rd | 9 umx-3.0.6/umx/man/umx_array_shift.Rd | 12 umx-3.0.6/umx/man/umx_as_numeric.Rd | 4 umx-3.0.6/umx/man/umx_cont_2_quantiles.Rd | 30 - umx-3.0.6/umx/man/umx_cor.Rd | 17 umx-3.0.6/umx/man/umx_explode.Rd | 3 umx-3.0.6/umx/man/umx_explode_twin_names.Rd | 3 umx-3.0.6/umx/man/umx_find_object.Rd | 14 umx-3.0.6/umx/man/umx_fun_mean_sd.Rd | 69 ++ umx-3.0.6/umx/man/umx_get_bracket_addresses.Rd | 62 ++ umx-3.0.6/umx/man/umx_get_checkpoint.Rd | 3 umx-3.0.6/umx/man/umx_get_options.Rd | 3 umx-3.0.6/umx/man/umx_grep.Rd | 3 umx-3.0.6/umx/man/umx_is_cov.Rd | 3 umx-3.0.6/umx/man/umx_long2wide.Rd | 10 umx-3.0.6/umx/man/umx_lower2full.Rd | 4 umx-3.0.6/umx/man/umx_make.Rd | 70 ++ umx-3.0.6/umx/man/umx_make_MR_data.Rd | 4 umx-3.0.6/umx/man/umx_make_TwinData.Rd | 6 umx-3.0.6/umx/man/umx_make_fake_data.Rd | 4 umx-3.0.6/umx/man/umx_make_raw_from_cov.Rd | 4 umx-3.0.6/umx/man/umx_make_twin_data_nice.Rd |only umx-3.0.6/umx/man/umx_means.Rd | 9 umx-3.0.6/umx/man/umx_msg.Rd | 10 umx-3.0.6/umx/man/umx_names.Rd | 16 umx-3.0.6/umx/man/umx_object_as_str.Rd | 3 umx-3.0.6/umx/man/umx_open_CRAN_page.Rd | 12 umx-3.0.6/umx/man/umx_pad.Rd | 11 umx-3.0.6/umx/man/umx_paste_names.Rd | 2 umx-3.0.6/umx/man/umx_polychoric.Rd | 6 umx-3.0.6/umx/man/umx_polypairwise.Rd | 6 umx-3.0.6/umx/man/umx_polytriowise.Rd | 6 umx-3.0.6/umx/man/umx_print.Rd | 24 umx-3.0.6/umx/man/umx_r_test.Rd | 9 umx-3.0.6/umx/man/umx_read_lower.Rd | 4 umx-3.0.6/umx/man/umx_rename.Rd | 4 umx-3.0.6/umx/man/umx_reorder.Rd | 4 umx-3.0.6/umx/man/umx_residualize.Rd | 2 umx-3.0.6/umx/man/umx_rot.Rd | 3 umx-3.0.6/umx/man/umx_round.Rd | 9 umx-3.0.6/umx/man/umx_scale.Rd | 9 umx-3.0.6/umx/man/umx_scale_wide_twin_data.Rd | 2 umx-3.0.6/umx/man/umx_score_scale.Rd | 54 +- umx-3.0.6/umx/man/umx_select_valid.Rd | 4 umx-3.0.6/umx/man/umx_set_auto_plot.Rd | 3 umx-3.0.6/umx/man/umx_set_auto_run.Rd | 3 umx-3.0.6/umx/man/umx_set_checkpoint.Rd | 3 umx-3.0.6/umx/man/umx_set_condensed_slots.Rd | 3 umx-3.0.6/umx/man/umx_set_cores.Rd | 3 umx-3.0.6/umx/man/umx_set_data_variance_check.Rd | 3 umx-3.0.6/umx/man/umx_set_mvn_optimization_options.Rd | 3 umx-3.0.6/umx/man/umx_set_optimizer.Rd | 3 umx-3.0.6/umx/man/umx_set_plot_file_suffix.Rd | 3 umx-3.0.6/umx/man/umx_set_plot_format.Rd | 3 umx-3.0.6/umx/man/umx_set_separator.Rd | 3 umx-3.0.6/umx/man/umx_set_silent.Rd | 3 umx-3.0.6/umx/man/umx_set_table_format.Rd | 3 umx-3.0.6/umx/man/umx_stack.Rd | 4 umx-3.0.6/umx/man/umx_standardize.Rd | 10 umx-3.0.6/umx/man/umx_string_to_algebra.Rd | 62 ++ umx-3.0.6/umx/man/umx_time.Rd | 11 umx-3.0.6/umx/man/umx_trim.Rd | 2 umx-3.0.6/umx/man/umx_var.Rd | 9 umx-3.0.6/umx/man/umx_wide2long.Rd | 7 umx-3.0.6/umx/man/umx_write_to_clipboard.Rd | 8 umx-3.0.6/umx/man/xmuHasSquareBrackets.Rd | 10 umx-3.0.6/umx/man/xmuLabel_MATRIX_Model.Rd | 10 umx-3.0.6/umx/man/xmuLabel_Matrix.Rd | 10 umx-3.0.6/umx/man/xmuLabel_RAM_Model.Rd | 10 umx-3.0.6/umx/man/xmuMI.Rd | 10 umx-3.0.6/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 10 umx-3.0.6/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 10 umx-3.0.6/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 10 umx-3.0.6/umx/man/xmuMaxLevels.Rd | 10 umx-3.0.6/umx/man/xmuMinLevels.Rd | 10 umx-3.0.6/umx/man/xmuPropagateLabels.Rd | 10 umx-3.0.6/umx/man/xmuRAM2Ordinal.Rd | 62 ++ umx-3.0.6/umx/man/xmu_CI_merge.Rd | 10 umx-3.0.6/umx/man/xmu_CI_stash.Rd | 10 umx-3.0.6/umx/man/xmu_DF_to_mxData_TypeCov.Rd | 10 umx-3.0.6/umx/man/xmu_PadAndPruneForDefVars.Rd | 10 umx-3.0.6/umx/man/xmu_assemble_twin_supermodel.Rd | 10 umx-3.0.6/umx/man/xmu_cell_is_on.Rd | 70 ++ umx-3.0.6/umx/man/xmu_check_levels_identical.Rd | 10 umx-3.0.6/umx/man/xmu_check_needs_means.Rd | 10 umx-3.0.6/umx/man/xmu_check_variance.Rd | 10 umx-3.0.6/umx/man/xmu_clean_label.Rd | 10 umx-3.0.6/umx/man/xmu_data_swap_a_block.Rd | 4 umx-3.0.6/umx/man/xmu_describe_data_WLS.Rd | 10 umx-3.0.6/umx/man/xmu_dot_make_paths.Rd | 10 umx-3.0.6/umx/man/xmu_dot_make_residuals.Rd | 10 umx-3.0.6/umx/man/xmu_dot_maker.Rd | 10 umx-3.0.6/umx/man/xmu_dot_move_ranks.Rd | 10 umx-3.0.6/umx/man/xmu_dot_rank_str.Rd | 10 umx-3.0.6/umx/man/xmu_get_CI.Rd | 10 umx-3.0.6/umx/man/xmu_lavaan_process_group.Rd | 10 umx-3.0.6/umx/man/xmu_make_bin_cont_pair_data.Rd | 10 umx-3.0.6/umx/man/xmu_make_mxData.Rd | 10 umx-3.0.6/umx/man/xmu_make_top_twin.Rd | 10 umx-3.0.6/umx/man/xmu_match.arg.Rd | 73 ++ umx-3.0.6/umx/man/xmu_name_from_lavaan_str.Rd | 10 umx-3.0.6/umx/man/xmu_safe_run_summary.Rd | 18 umx-3.0.6/umx/man/xmu_set_sep_from_suffix.Rd | 10 umx-3.0.6/umx/man/xmu_show_fit_or_comparison.Rd | 10 umx-3.0.6/umx/man/xmu_simplex_corner.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_ACE.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_ACEcov.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_ACEv.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_CP.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_IP.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_RAM.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_SexLim.Rd | 10 umx-3.0.6/umx/man/xmu_standardize_Simplex.Rd | 10 umx-3.0.6/umx/man/xmu_start_value_list.Rd | 10 umx-3.0.6/umx/man/xmu_starts.Rd | 10 umx-3.0.6/umx/man/xmu_twin_check.Rd | 10 umx-3.0.6/umx/tests/testthat/test_lavaan.r |only 210 files changed, 2035 insertions(+), 1176 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-143 dated 2019-12-10 and 3.1-144 dated 2020-02-06
DESCRIPTION | 8 ++-- MD5 | 86 ++++++++++++++++++++++++------------------------- data/Alfalfa.rda |binary data/Assay.rda |binary data/BodyWeight.rda |binary data/Cefamandole.rda |binary data/Dialyzer.rda |binary data/Earthquake.rda |binary data/Fatigue.rda |binary data/Gasoline.rda |binary data/Glucose.rda |binary data/Glucose2.rda |binary data/Gun.rda |binary data/IGF.rda |binary data/Machines.rda |binary data/MathAchSchool.rda |binary data/MathAchieve.rda |binary data/Meat.rda |binary data/Milk.rda |binary data/Muscle.rda |binary data/Nitrendipene.rda |binary data/Oats.rda |binary data/Orthodont.rda |binary data/Ovary.rda |binary data/Oxboys.rda |binary data/Oxide.rda |binary data/PBG.rda |binary data/Phenobarb.rda |binary data/Pixel.rda |binary data/Quinidine.rda |binary data/Rail.rda |binary data/RatPupWeight.rda |binary data/Relaxin.rda |binary data/Remifentanil.rda |binary data/Soybean.rda |binary data/Spruce.rda |binary data/Tetracycline1.rda |binary data/Tetracycline2.rda |binary data/Wafer.rda |binary data/Wheat.rda |binary data/Wheat2.rda |binary data/bdf.rda |binary data/ergoStool.rda |binary man/gnls.Rd | 4 +- 44 files changed, 49 insertions(+), 49 deletions(-)
Title: Complete Environment for Bayesian Inference
Description: Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
Author: Byron Hall [aut],
Martina Hall [aut],
Statisticat, LLC [aut],
Eric Brown [ctb],
Richard Hermanson [ctb],
Emmanuel Charpentier [ctb],
Daniel Heck [ctb],
Stephane Laurent [ctb],
Quentin F. Gronau [ctb],
Henrik Singmann [cre]
Maintainer: Henrik Singmann <singmann+LaplacesDemon@gmail.com>
Diff between LaplacesDemon versions 16.1.1 dated 2018-06-30 and 16.1.4 dated 2020-02-06
LaplacesDemon-16.1.1/LaplacesDemon/data/demonchoice.txt.gz |only LaplacesDemon-16.1.1/LaplacesDemon/data/demonfx.txt.gz |only LaplacesDemon-16.1.1/LaplacesDemon/data/demonsessions.txt.gz |only LaplacesDemon-16.1.1/LaplacesDemon/data/demonsnacks.txt.gz |only LaplacesDemon-16.1.1/LaplacesDemon/data/demontexas.txt.gz |only LaplacesDemon-16.1.4/LaplacesDemon/CHANGELOG | 4 LaplacesDemon-16.1.4/LaplacesDemon/DESCRIPTION | 6 LaplacesDemon-16.1.4/LaplacesDemon/MD5 | 30 LaplacesDemon-16.1.4/LaplacesDemon/R/distributions.R | 5284 +++++----- LaplacesDemon-16.1.4/LaplacesDemon/build/partial.rdb |binary LaplacesDemon-16.1.4/LaplacesDemon/build/vignette.rds |binary LaplacesDemon-16.1.4/LaplacesDemon/data/demonchoice.txt |only LaplacesDemon-16.1.4/LaplacesDemon/data/demonfx.txt |only LaplacesDemon-16.1.4/LaplacesDemon/data/demonsessions.txt |only LaplacesDemon-16.1.4/LaplacesDemon/data/demonsnacks.txt |only LaplacesDemon-16.1.4/LaplacesDemon/data/demontexas.txt |only LaplacesDemon-16.1.4/LaplacesDemon/inst/doc/BayesianInference.pdf |binary LaplacesDemon-16.1.4/LaplacesDemon/inst/doc/Examples.pdf |binary LaplacesDemon-16.1.4/LaplacesDemon/inst/doc/LaplacesDemonTutorial.pdf |binary LaplacesDemon-16.1.4/LaplacesDemon/man/BigData.Rd | 465 LaplacesDemon-16.1.4/LaplacesDemon/man/dist.Zellner.Rd | 289 21 files changed, 3045 insertions(+), 3033 deletions(-)
Title: Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
Description: Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Author: Etienne Becht [cre, aut],
Samuel Granjeaud [ctb]
Maintainer: Etienne Becht <etienne.becht@protonmail.com>
Diff between hypergate versions 0.8.1 dated 2019-04-17 and 0.8.3 dated 2020-02-06
DESCRIPTION | 10 ++++----- MD5 | 16 +++++++------- R/hypergate.R | 7 +++--- build/vignette.rds |binary data/Samusik_01_subset.RData |binary inst/doc/Hypergate.R | 46 +++++++++++++++++++++---------------------- inst/doc/Hypergate.html | 20 +++++++++++------- man/Samusik_01_subset.Rd | 4 +-- man/plot_gating_strategy.Rd | 6 +++-- 9 files changed, 58 insertions(+), 51 deletions(-)
Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between errorlocate versions 0.2.0 dated 2019-07-01 and 0.3.0 dated 2020-02-06
DESCRIPTION | 17 ++++++------ MD5 | 45 ++++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 6 ++++ R/categorical.R | 16 +++++++++--- R/conditional.R | 3 ++ R/dnf.R | 17 +++++++++--- R/errorlocalizer.R | 10 ++++++- R/errorlocate-package.r | 2 - R/expr_manip.R | 11 ++++++-- R/linear.R | 8 ++++-- R/local_variable.R |only R/replace-errors.R | 4 +-- R/soft-rule.R | 8 +++--- R/utils.R | 15 +++++++---- man/errorlocate-package.Rd | 4 +-- man/is_categorical.Rd | 2 - tests/testthat/test-categorical.R | 5 +++ tests/testthat/test-conditional.R | 8 ++++++ tests/testthat/test-dnf.R |only tests/testthat/test-linear.R | 4 +++ tests/testthat/test-localize-errors.R | 7 +++++ tests/testthat/test-replace-errors.R | 14 ++++++++++ tests/testthat/test-soft-rule.R | 3 ++ tests/testthat/test.mps |only 25 files changed, 151 insertions(+), 59 deletions(-)
Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
import the data results of a software pipeline that predicts synergistic drug
combinations in cancer cell lines, developed by the DrugLogics research group
in NTNU. It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions or Matthews correlation coefficient score) or synergy prediction based on a given set
of observed synergies and find the average activity difference per network
node between all group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be assessed.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between emba versions 0.1.1 dated 2019-10-21 and 0.1.2 dated 2020-02-06
DESCRIPTION | 14 - MD5 | 88 +++---- NAMESPACE | 6 NEWS.md | 9 R/diff.R | 125 +++++++++- R/input.R | 62 ++++ README.md | 15 - man/biomarker_mcc_analysis.Rd | 17 - man/biomarker_synergy_analysis.Rd | 14 - man/biomarker_tp_analysis.Rd | 14 - man/calculate_mcc.Rd | 11 man/calculate_models_mcc.Rd | 18 - man/calculate_models_synergies_fn.Rd | 11 man/calculate_models_synergies_fp.Rd | 11 man/calculate_models_synergies_tn.Rd | 11 man/calculate_models_synergies_tp.Rd | 11 man/emba.Rd | 1 man/filter_network.Rd |only man/get_avg_activity_diff_based_on_mcc_clustering.Rd | 32 +- man/get_avg_activity_diff_based_on_specific_synergy_prediction.Rd | 29 +- man/get_avg_activity_diff_based_on_synergy_set_cmp.Rd | 29 +- man/get_avg_activity_diff_based_on_tp_predictions.Rd | 30 +- man/get_avg_activity_diff_mat_based_on_mcc_clustering.Rd | 29 +- man/get_avg_activity_diff_mat_based_on_specific_synergy_prediction.Rd | 29 +- man/get_avg_activity_diff_mat_based_on_tp_predictions.Rd | 28 +- man/get_avg_link_operator_diff_based_on_specific_synergy_prediction.Rd |only man/get_avg_link_operator_diff_based_on_synergy_set_cmp.Rd |only man/get_avg_link_operator_diff_mat_based_on_mcc_clustering.Rd | 29 +- man/get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction.Rd | 32 +- man/get_avg_link_operator_diff_mat_based_on_tp_predictions.Rd | 28 +- man/get_biomarkers.Rd | 3 man/get_biomarkers_per_type.Rd | 3 man/get_link_operators_from_models_dir.Rd | 6 man/get_neighbors.Rd |only man/get_synergy_biomarkers_from_dir.Rd | 8 man/make_barplot_on_models_stats.Rd | 11 man/make_barplot_on_synergy_subset_stats.Rd | 8 man/plot_avg_link_operator_diff_graph.Rd | 9 man/plot_avg_link_operator_diff_graphs.Rd | 9 man/plot_avg_state_diff_graph.Rd | 9 man/plot_avg_state_diff_graph_vis.Rd | 9 man/plot_avg_state_diff_graphs.Rd | 9 man/plot_mcc_classes_hist.Rd | 8 man/print_biomarkers_per_predicted_synergy.Rd | 7 man/update_biomarker_files.Rd | 9 man/validate_observed_synergies_data.Rd | 3 tests/testthat/test-analysis.R | 2 47 files changed, 591 insertions(+), 255 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-18 0.10.0
2013-10-11 0.9.0
Title: The Parameter Converter of the Pharmacokinetic Models
Description: Pharmacokinetics is the study of drug absorption, distribution,
metabolism, and excretion. The pharmacokinetics model explains that how the
drug concentration change as the drug moves through the different compartments
of the body. For pharmacokinetic modeling and analysis, it is essential
to understand the basic pharmacokinetic parameters. All parameters are
considered, but only some of parameters are used in the model. Therefore,
we need to convert the estimated parameters to the other parameters after
fitting the specific pharmacokinetic model. This package is developed to help
this converting work. For more detailed explanation of pharmacokinetic
parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001";
"Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>;
"Mould and Upton" (2012) <DOI: 10.1038/psp.2012.4>;
"Mould and Upton" (2013) <DOI: 10.1038/psp.2013.14>.
Author: Eun-Kyung Lee, Hye-sun Cho
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PKconverter versions 1.3 dated 2018-12-03 and 1.5 dated 2020-02-06
DESCRIPTION | 12 +-- MD5 | 68 ++++++++--------- NAMESPACE | 2 R/OneComp_Coefficient_Exponent.R | 6 - R/OneComp_Volume_Clearance.R | 8 +- R/OneComp_Volume_Clearance_HalfLife.R | 6 - R/OneComp_Volume_Exponent.R | 6 - R/OneComp_Volume_RateConstant.R | 6 - R/PKconverterApp.R | 2 R/ThreeComp_Coefficient_Exponent.R | 6 - R/ThreeComp_Volume_Clearance.R | 6 - R/ThreeComp_Volume_Clearance_HalfLife.R | 6 - R/ThreeComp_Volume_Exponent.R | 6 - R/ThreeComp_Volume_RateConstant.R | 6 - R/TwoComp_Coefficient_Exponent.R | 6 - R/TwoComp_Volume_Clearance.R | 6 - R/TwoComp_Volume_Clearance_HalfLife.R | 6 - R/TwoComp_Volume_Exponent.R | 8 +- R/TwoComp_Volume_RateConstant.R | 6 - man/OneComp_Coefficient_Exponent.Rd | 64 ++++++++-------- man/OneComp_Volume_Clearance.Rd | 71 +++++++++--------- man/OneComp_Volume_Clearance_HalfLife.Rd | 66 ++++++++--------- man/OneComp_Volume_Exponent.Rd | 66 ++++++++--------- man/OneComp_Volume_RateConstant.Rd | 66 ++++++++--------- man/PKconverterApp.Rd | 44 +++++------ man/ThreeComp_Coefficient_Exponent.Rd | 112 ++++++++++++++--------------- man/ThreeComp_Volume_Clearance.Rd | 106 +++++++++++++-------------- man/ThreeComp_Volume_Clearance_HalfLife.Rd | 106 +++++++++++++-------------- man/ThreeComp_Volume_Exponent.Rd | 112 ++++++++++++++--------------- man/ThreeComp_Volume_RateConstant.Rd | 108 +++++++++++++-------------- man/TwoComp_Coefficient_Exponent.Rd | 84 ++++++++++----------- man/TwoComp_Volume_Clearance.Rd | 86 +++++++++++----------- man/TwoComp_Volume_Clearance_HalfLife.Rd | 86 +++++++++++----------- man/TwoComp_Volume_Exponent.Rd | 87 +++++++++++----------- man/TwoComp_Volume_RateConstant.Rd | 86 +++++++++++----------- 35 files changed, 765 insertions(+), 763 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-2 dated 2019-03-07 and 0.4-3 dated 2020-02-06
DESCRIPTION | 13 +++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 8 +++++++- R/mkMatUtil.R | 4 +--- R/spRecover.R | 5 +++-- man/PM10.poly.Rd | 3 ++- man/mkSpCov.Rd | 1 - man/spGLM.Rd | 3 ++- man/spLM.Rd | 4 +++- man/spSVC.Rd | 2 +- 10 files changed, 35 insertions(+), 26 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.2.2 dated 2019-12-16 and 0.2.3 dated 2020-02-06
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 - NEWS.md | 8 ++++++++ R/Shazam.R | 1 - inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary 10 files changed, 22 insertions(+), 16 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>. For the extreme value random fields see Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and Schlather (2002) <doi.org/10.1023/A:1020977924878>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.3.7 dated 2019-12-12 and 3.3.8 dated 2020-02-06
DESCRIPTION | 11 +++++------ MD5 | 14 ++++++++------ data/ca20.rda |only man/RMmodelsTrend.Rd | 7 +++---- man/ca20.Rd |only src/Makevars.in | 4 +++- src/operator.cc | 6 ++---- src/rf_interfaces.cc | 2 ++ src/userinterfaces.cc | 4 ++-- 9 files changed, 25 insertions(+), 23 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.2 dated 2020-01-12 and 2.3 dated 2020-02-06
DESCRIPTION | 8 - MD5 | 58 ++++---- NAMESPACE | 8 + R/estimBM.R | 244 +++++++++++++++++++++++++----------- R/estimMAXLIK.R | 3 R/getESS.R | 4 R/loglik.R | 54 ++++--- R/modelparams.R | 2 R/modelparamssummary.R | 1 R/modelparamstransform.R | 6 R/phylgls.R | 21 ++- R/simulVasicekprocphyl.R | 2 R/wrappers.R | 6 man/BrownianMotionModel.Rd | 56 ++++++-- man/SummarizeBM.Rd | 56 ++++++-- man/SummarizeMVSLOUCH.Rd | 53 ++++++- man/SummarizeOUCH.Rd | 53 ++++++- man/drawPhylProcess.Rd | 2 man/estimate.evolutionary.model.Rd | 62 +++++++-- man/fitch.mvsl.Rd | 10 - man/mvSLOUCH-internal.Rd | 207 ++++++++++++++++++++++++++++++ man/mvSLOUCH-package.Rd | 43 +++++- man/mvslouchModel.Rd | 70 ++++++++-- man/ouchModel.Rd | 76 ++++++++--- man/parametric.bootstrap.Rd | 64 ++++++++- man/phyltree_paths.Rd | 2 man/simulBMProcPhylTree.Rd | 60 +++++++- man/simulMVSLOUCHProcPhylTree.Rd | 56 ++++++-- man/simulOUCHProcPhylTree.Rd | 56 ++++++-- man/simulate_clustered_phylogeny.Rd | 4 30 files changed, 1067 insertions(+), 280 deletions(-)
Title: Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
Description: Datasets and Functionality from
'Jan Beran' (1994). Statistics for Long-Memory Processes; Chapman & Hall.
Estimation of Hurst (and more) parameters for fractional Gaussian noise,
'fARIMA' and 'FEXP' models.
Author: S scripts originally by Jan Beran <jan.beran@uni-konstanz.de>;
Datasets via Brandon Whitcher <brandon@stat.washington.edu>.
Toplevel R functions and much more by Martin Maechler.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between longmemo versions 1.1-1 dated 2018-09-14 and 1.1-2 dated 2020-02-06
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- R/WhittleEst.R | 3 +- build/vignette.rds |binary inst/doc/BspecFGN.pdf |binary tests/FEXP-ex.R | 10 ++++++--- tests/FEXP-ex.Rout.save | 51 ++++++++++++++++++++++++----------------------- tests/ceta-ex.R | 14 +++++++++++- tests/ceta-ex.Rout.save | 52 +++++++++++++++++++++++++++++------------------- tests/spec-ex.R | 5 ++++ 10 files changed, 98 insertions(+), 63 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme-value and other copula families, as well as their rotations,
mixtures and asymmetrizations. Nested Archimedean copulas, related
tools and special functions. Methods for density, distribution, random
number generation, bivariate dependence measures, Rosenblatt transform,
Kendall distribution function, perspective and contour plots. Fitting of
copula models with potentially partly fixed parameters, including
standard errors. Serial independence tests, copula specification tests
(independence, exchangeability, radial symmetry, extreme-value
dependence, goodness-of-fit) and model selection based on
cross-validation. Empirical copula, smoothed versions, and
non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] (<https://orcid.org/0000-0001-8009-4665>),
Ivan Kojadinovic [aut] (<https://orcid.org/0000-0002-2903-1543>),
Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>),
Johanna G. Nešlehová [ctb] (evTestK(),
<https://orcid.org/0000-0001-9634-4796>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 0.999-19.1 dated 2019-04-22 and 0.999-20 dated 2020-02-06
copula-0.999-19.1/copula/inst/doc/AC_Liouville.R |only copula-0.999-19.1/copula/inst/doc/AR_Clayton.R |only copula-0.999-19.1/copula/inst/doc/GIG.R |only copula-0.999-19.1/copula/inst/doc/HAXC.R |only copula-0.999-19.1/copula/inst/doc/NALC.R |only copula-0.999-19.1/copula/inst/doc/copula_GARCH.R |only copula-0.999-19.1/copula/inst/doc/dNAC.R |only copula-0.999-19.1/copula/inst/doc/empiricial_copulas.R |only copula-0.999-19.1/copula/inst/doc/logL_visualization.R |only copula-0.999-19.1/copula/inst/doc/qrng.R |only copula-0.999-19.1/copula/inst/doc/wild_animals.R |only copula-0.999-19.1/copula/inst/docs/mathnb/archmCPdf.out |only copula-0.999-19.1/copula/inst/docs/mathnb/archmDer.out |only copula-0.999-19.1/copula/inst/docs/mathnb/check2Ivan.Rout |only copula-0.999-19.1/copula/inst/docs/mathnb/exprPrep.Rout |only copula-0.999-19.1/copula/inst/docs/mathnb/getDerExpr.out |only copula-0.999-20/copula/DESCRIPTION | 18 copula-0.999-20/copula/MD5 | 119 +--- copula-0.999-20/copula/NAMESPACE | 2 copula-0.999-20/copula/R/cCopula.R | 66 ++ copula-0.999-20/copula/R/empCopula.R | 2 copula-0.999-20/copula/R/evCopula.R | 11 copula-0.999-20/copula/R/evTests.R | 60 +- copula-0.999-20/copula/R/gofCopula.R | 71 ++ copula-0.999-20/copula/R/mixCopula.R | 5 copula-0.999-20/copula/R/tCopula.R | 2 copula-0.999-20/copula/TODO | 37 - copula-0.999-20/copula/build/partial.rdb |binary copula-0.999-20/copula/build/vignette.rds |binary copula-0.999-20/copula/inst/NEWS.Rd | 24 copula-0.999-20/copula/inst/Rsource/utils.R | 2 copula-0.999-20/copula/inst/doc/AC_Liouville.html | 17 copula-0.999-20/copula/inst/doc/AR_Clayton.html | 17 copula-0.999-20/copula/inst/doc/Frank-Rmpfr.pdf |binary copula-0.999-20/copula/inst/doc/GIG.html | 29 - copula-0.999-20/copula/inst/doc/HAXC.html | 23 copula-0.999-20/copula/inst/doc/NALC.html | 33 - copula-0.999-20/copula/inst/doc/copula_GARCH.html | 21 copula-0.999-20/copula/inst/doc/dNAC.html | 19 copula-0.999-20/copula/inst/doc/empiricial_copulas.html | 17 copula-0.999-20/copula/inst/doc/logL_visualization.html | 112 +--- copula-0.999-20/copula/inst/doc/nacopula-pkg.pdf |binary copula-0.999-20/copula/inst/doc/qrng.html | 21 copula-0.999-20/copula/inst/doc/rhoAMH-dilog.pdf |binary copula-0.999-20/copula/inst/doc/wild_animals.html | 93 +-- copula-0.999-20/copula/man/K.Rd | 2 copula-0.999-20/copula/man/empCopula.Rd | 7 copula-0.999-20/copula/man/evCopula.Rd | 22 copula-0.999-20/copula/man/evTestA.Rd | 17 copula-0.999-20/copula/man/fgmCopula-class.Rd | 15 copula-0.999-20/copula/man/fgmCopula.Rd | 1 copula-0.999-20/copula/man/fitLambda.Rd | 10 copula-0.999-20/copula/man/fitMvdc.Rd | 2 copula-0.999-20/copula/man/ggraph-tools.Rd | 7 copula-0.999-20/copula/man/gofTstat.Rd | 18 copula-0.999-20/copula/man/mvdc-class.Rd | 8 copula-0.999-20/copula/man/pairsRosenblatt.Rd | 4 copula-0.999-20/copula/src/copula.h | 4 copula-0.999-20/copula/src/empcop.c | 2 copula-0.999-20/copula/src/empcop.h | 4 copula-0.999-20/copula/src/evtest.c | 389 +++++++------- copula-0.999-20/copula/src/gof.c | 77 ++ copula-0.999-20/copula/src/init.c | 20 copula-0.999-20/copula/src/nacopula.h | 2 copula-0.999-20/copula/tests/Stirling-etc.R | 1 copula-0.999-20/copula/tests/mixCop-tst.R | 2 copula-0.999-20/copula/tests/pdf.R |only copula-0.999-20/copula/tests/tail-pcopula.R | 34 + copula-0.999-20/copula/tests/tail-pcopula.Rout.save | 53 + 69 files changed, 928 insertions(+), 594 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>),
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.17-3 dated 2019-05-11 and 0.17-4 dated 2020-02-06
DESCRIPTION | 8 - MD5 | 16 +- R/mat.R | 2 build/vignette.rds |binary inst/doc/analogue_methods.pdf |binary man/RMSEP.Rd | 2 man/bootstrap.Rd | 2 man/timetrack.Rd | 2 tests/Examples/analogue-Ex.Rout.save | 236 ++++++++++++++++++----------------- 9 files changed, 144 insertions(+), 124 deletions(-)
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette "AER" for a package overview.)
Author: Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>),
Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between AER versions 1.2-8 dated 2019-11-08 and 1.2-9 dated 2020-02-06
DESCRIPTION | 8 - MD5 | 240 +++++++++++++++++------------------ NEWS | 14 +- build/vignette.rds |binary data/Affairs.rda |binary data/ArgentinaCPI.rda |binary data/BankWages.rda |binary data/BenderlyZwick.rda |binary data/BondYield.rda |binary data/CASchools.rda |binary data/CPS1985.rda |binary data/CPS1988.rda |binary data/CPSSW04.rda |binary data/CPSSW3.rda |binary data/CPSSW8.rda |binary data/CPSSW9204.rda |binary data/CPSSW9298.rda |binary data/CPSSWEducation.rda |binary data/CartelStability.rda |binary data/ChinaIncome.rda |binary data/CigarettesB.rda |binary data/CigarettesSW.rda |binary data/CollegeDistance.rda |binary data/ConsumerGood.rda |binary data/CreditCard.rda |binary data/DJFranses.rda |binary data/DJIA8012.rda |binary data/DoctorVisits.rda |binary data/DutchAdvert.rda |binary data/DutchSales.rda |binary data/Electricity1955.rda |binary data/Electricity1970.rda |binary data/EquationCitations.rda |binary data/Equipment.rda |binary data/EuroEnergy.rda |binary data/Fatalities.rda |binary data/Fertility.rda |binary data/Fertility2.rda |binary data/FrozenJuice.rda |binary data/GSOEP9402.rda |binary data/GSS7402.rda |binary data/GermanUnemployment.rda |binary data/GoldSilver.rda |binary data/GrowthDJ.rda |binary data/GrowthSW.rda |binary data/Grunfeld.rda |binary data/Guns.rda |binary data/HMDA.rda |binary data/HealthInsurance.rda |binary data/HousePrices.rda |binary data/Journals.rda |binary data/KleinI.rda |binary data/Longley.rda |binary data/MASchools.rda |binary data/MSCISwitzerland.rda |binary data/ManufactCosts.rda |binary data/MarkDollar.rda |binary data/MarkPound.rda |binary data/Medicaid1986.rda |binary data/Mortgage.rda |binary data/MotorCycles.rda |binary data/MotorCycles2.rda |binary data/Municipalities.rda |binary data/MurderRates.rda |binary data/NMES1988.rda |binary data/NYSESW.rda |binary data/NaturalGas.rda |binary data/OECDGas.rda |binary data/OECDGrowth.rda |binary data/OlympicTV.rda |binary data/OrangeCounty.rda |binary data/PSID1976.rda |binary data/PSID1982.rda |binary data/PSID7682.rda |binary data/Parade2005.rda |binary data/PepperPrice.rda |binary data/PhDPublications.rda |binary data/ProgramEffectiveness.rda |binary data/RecreationDemand.rda |binary data/ResumeNames.rda |binary data/SIC33.rda |binary data/STAR.rda |binary data/ShipAccidents.rda |binary data/SmokeBan.rda |binary data/SportsCards.rda |binary data/StrikeDuration.rda |binary data/SwissLabor.rda |binary data/TeachingRatings.rda |binary data/TechChange.rda |binary data/TradeCredit.rda |binary data/TravelMode.rda |binary data/UKInflation.rda |binary data/UKNonDurables.rda |binary data/USAirlines.rda |binary data/USConsump1950.rda |binary data/USConsump1979.rda |binary data/USConsump1993.rda |binary data/USCrudes.rda |binary data/USGasB.rda |binary data/USGasG.rda |binary data/USInvest.rda |binary data/USMacroB.rda |binary data/USMacroG.rda |binary data/USMacroSW.rda |binary data/USMacroSWM.rda |binary data/USMacroSWQ.rda |binary data/USMoney.rda |binary data/USProdIndex.rda |binary data/USSeatBelts.rda |binary data/USStocksSW.rda |binary data/WeakInstrument.rda |binary inst/doc/AER.pdf |binary inst/doc/Sweave-journals.pdf |binary man/CameronTrivedi1998.Rd | 2 man/GoldSilver.Rd | 5 man/Greene2003.Rd | 2 man/WinkelmannBoes2009.Rd | 2 tests/Ch-Microeconometrics.R | 48 +++---- tests/Ch-Microeconometrics.Rout.save | 78 +++-------- tests/Ch-TimeSeries.R | 38 ++--- tests/Ch-TimeSeries.Rout.save | 75 +++------- 121 files changed, 238 insertions(+), 274 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 0.6.0 dated 2020-01-28 and 0.6.4 dated 2020-02-06
DESCRIPTION | 6 MD5 | 76 - NEWS.md | 14 R/orcid.r | 178 +- R/orcid_external_identifiers.R | 2 R/orcid_search.R | 17 R/works.R | 1 man/orcid.Rd | 25 man/orcid_external_identifiers.Rd | 4 man/orcid_search.Rd | 12 man/works.Rd | 2 tests/fixtures/as_orcid.yml | 23 tests/fixtures/as_orcid_accepts_self_or_or_cid_class.yml | 23 tests/fixtures/as_orcid_invalid_orcid_id.yml | 13 tests/fixtures/extract_bibtex.yml | 13 tests/fixtures/identifiers.yml | 358 +++-- tests/fixtures/identifiers_output_from_or_cid.yml | 167 +- tests/fixtures/identifiers_output_from_orcid.yml | 399 +++--- tests/fixtures/identifiers_output_from_orcid_doi.yml | 375 ++--- tests/fixtures/orcid.yml | 424 +++--- tests/fixtures/orcid_citations_with_bibtex.yml | 41 tests/fixtures/orcid_doi.yml | 41 tests/fixtures/orcid_doi_many_dois.yml | 26 tests/fixtures/orcid_doi_pagination.yml | 54 tests/fixtures/orcid_error.yml | 28 tests/fixtures/orcid_id.yml | 23 tests/fixtures/orcid_id_address_data.yml | 23 tests/fixtures/orcid_id_bad_orcid.yml | 13 tests/fixtures/orcid_id_keywords_data.yml | 23 tests/fixtures/orcid_pagination.yml | 54 tests/fixtures/orcid_qf_param.yml | 81 - tests/fixtures/orcid_search.yml | 957 ++++++++------- tests/fixtures/orcid_search_fail.yml | 13 tests/fixtures/orcid_search_keywords_param.yml | 49 tests/fixtures/orcid_search_no_results.yml | 14 tests/fixtures/works.yml | 205 +-- tests/fixtures/works_error.yml | 13 tests/testthat/test-orcid.R | 3 tests/testthat/test-orcid_search.R | 2 39 files changed, 2032 insertions(+), 1763 deletions(-)
Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre],
Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>
Diff between rDEA versions 1.2-5 dated 2016-11-25 and 1.2-6 dated 2020-02-06
DESCRIPTION | 7 ++++--- MD5 | 19 ++++++++++--------- NAMESPACE | 2 +- R/dea.env.robust.R | 15 ++++++--------- inst/CHANGELOG | 4 ++++ inst/tests/testthat/test-dea.env.robust.r | 3 +++ man/dea.Rd | 5 ++++- man/dea_env_robust.Rd | 5 ++++- man/dea_robust.Rd | 5 ++++- man/rts_test.Rd | 5 ++++- src/rDEA_init.c |only 11 files changed, 44 insertions(+), 26 deletions(-)
Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn 2019). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.
Author: Jong Hee Park [aut,cre], Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between NetworkChange versions 0.5 dated 2019-05-08 and 0.6 dated 2020-02-06
DESCRIPTION | 15 ++++----- MD5 | 42 ++++++++++++------------- NAMESPACE | 3 - R/BreakDiagnostic.R | 2 - R/NetworkChange-package.r | 1 R/NetworkChange.r | 8 +--- R/NetworkStatic.R | 10 +++--- R/WaicCompare.R | 8 +++- R/drawpostanalysis.R | 2 - R/plotContour.R | 4 +- R/plotU.R | 73 ++++++++++++++++++++++++++++----------------- R/plotV.R | 38 ++++++++++++----------- man/BreakDiagnostic.Rd | 2 - man/BreakPointLoss.Rd | 8 ++-- man/NetworkChange.Rd | 10 ++---- man/NetworkChangeRobust.Rd | 2 - man/NetworkStatic.Rd | 12 +++---- man/WaicCompare.Rd | 2 - man/drawPostAnalysis.Rd | 2 - man/plotContour.Rd | 4 +- man/plotU.Rd | 24 +++++++++----- man/plotV.Rd | 4 +- 22 files changed, 154 insertions(+), 122 deletions(-)
Title: Sparse Generalized Linear Model with L0 Approximation for
Feature Selection
Description: An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
Author: Wenchuan Guo, Shujie Ma, Zhenqiu Liu
Maintainer: Wenchuan Guo <wguo007@ucr.edu>
Diff between l0ara versions 0.1.5 dated 2017-07-23 and 0.1.6 dated 2020-02-06
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 3 +++ R/cv.l0ara.R | 4 ++-- R/l0ara.R | 4 ++-- 5 files changed, 16 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-11 0.1.3
2017-08-09 0.1.2
2016-05-13 0.1.1
2016-03-28 0.1.0