Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.
Author: David van Dijk [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between Rmagic versions 1.0.0 dated 2018-07-10 and 1.3.0 dated 2018-09-21
Rmagic-1.0.0/Rmagic/inst/examples/bonemarrow_tutorial.md |only Rmagic-1.0.0/Rmagic/inst/examples/bonemarrow_tutorial_files |only Rmagic-1.0.0/Rmagic/inst/examples/emt_tutorial.md |only Rmagic-1.0.0/Rmagic/inst/examples/emt_tutorial_files |only Rmagic-1.3.0/Rmagic/DESCRIPTION | 12 Rmagic-1.3.0/Rmagic/MD5 | 46 Rmagic-1.3.0/Rmagic/R/magic.R | 572 +++++----- Rmagic-1.3.0/Rmagic/R/utils.R | 50 Rmagic-1.3.0/Rmagic/README.md | 14 Rmagic-1.3.0/Rmagic/inst/examples/BMMSC_data_R_after_magic.png |binary Rmagic-1.3.0/Rmagic/inst/examples/BMMSC_data_R_pca_colored_by_magic.png |binary Rmagic-1.3.0/Rmagic/inst/examples/BMMSC_data_R_phate_colored_by_magic.png |binary Rmagic-1.3.0/Rmagic/inst/examples/EMT_data_R_after_magic.png |binary Rmagic-1.3.0/Rmagic/inst/examples/EMT_data_R_pca_colored_by_magic.png |binary Rmagic-1.3.0/Rmagic/inst/examples/bonemarrow_tutorial.Rmd | 373 +++--- Rmagic-1.3.0/Rmagic/inst/examples/bonemarrow_tutorial.html |only Rmagic-1.3.0/Rmagic/inst/examples/emt_tutorial.Rmd | 335 ++--- Rmagic-1.3.0/Rmagic/inst/examples/emt_tutorial.html |only Rmagic-1.3.0/Rmagic/man/install.magic.Rd | 11 Rmagic-1.3.0/Rmagic/man/magic.Rd | 11 20 files changed, 726 insertions(+), 698 deletions(-)
More information about LocalControlStrategy at CRAN
Permanent link
Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross-
sectional surveys, and for calibrating tests for recent infection.
Implements and extends the method of Kassanjee et al. (2012)
<doi:10.1097/EDE.0b013e3182576c07>.
Author: Alex Welte [aut],
Eduard Grebe [cre, aut],
Avery McIntosh [aut],
Petra Bäumler [aut],
Reshma Kassanjee [ctb],
Hilmarie Brand [ctb],
Cari Van Schalkwyk [ctb],
Yuruo Li [ctb],
Simon Daniel [ctb],
Stefano Ongarello [aut],
Yusuke Asai [ctb],
Jeffrey Eaton [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>
Diff between inctools versions 1.0.11 dated 2018-01-03 and 1.0.14 dated 2018-09-21
DESCRIPTION | 17 MD5 | 52 - NAMESPACE | 1 R/calibration_frr.R | 64 + R/calibration_mdri.R | 732 ++++++++++++++-------- R/excalibdata.R | 13 R/incidence.R | 23 R/inctools.R | 25 R/power.R | 1241 ++++++++++++++++---------------------- R/precision.R | 103 ++- build/vignette.rds |binary inst/doc/EstimatingIncidence.html | 28 inst/doc/Introduction.Rmd | 55 - inst/doc/Introduction.html | 139 ++-- inst/doc/SurveyDesign.html | 40 - inst/doc/TestCalibration.R | 19 inst/doc/TestCalibration.Rmd | 50 + inst/doc/TestCalibration.html | 188 ++++- man/frrcal.Rd | 15 man/inccounts.Rd | 4 man/incpower.Rd | 21 man/incprecision.Rd | 9 man/incprops.Rd | 6 man/inctools.Rd | 2 man/mdrical.Rd | 59 + vignettes/Introduction.Rmd | 55 - vignettes/TestCalibration.Rmd | 50 + 27 files changed, 1686 insertions(+), 1325 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.8.6 dated 2018-08-30 and 0.8.7 dated 2018-09-21
finalfit-0.8.6/finalfit/NEWS |only finalfit-0.8.6/finalfit/inst/doc/finalfit_basics.R |only finalfit-0.8.6/finalfit/inst/doc/finalfit_basics.Rmd |only finalfit-0.8.6/finalfit/inst/doc/finalfit_basics.html |only finalfit-0.8.6/finalfit/vignettes/finalfit_basics.Rmd |only finalfit-0.8.7/finalfit/DESCRIPTION | 15 - finalfit-0.8.7/finalfit/MD5 | 53 ++- finalfit-0.8.7/finalfit/NAMESPACE | 2 finalfit-0.8.7/finalfit/NEWS.md |only finalfit-0.8.7/finalfit/R/ff_newdata.R | 4 finalfit-0.8.7/finalfit/R/finalfit_internal_functions.R | 1 finalfit-0.8.7/finalfit/R/missing_pattern.R | 79 +++++ finalfit-0.8.7/finalfit/README.md | 223 ---------------- finalfit-0.8.7/finalfit/build/vignette.rds |binary finalfit-0.8.7/finalfit/inst/doc/bootstrap.R |only finalfit-0.8.7/finalfit/inst/doc/bootstrap.Rmd |only finalfit-0.8.7/finalfit/inst/doc/bootstrap.html |only finalfit-0.8.7/finalfit/inst/doc/export.R |only finalfit-0.8.7/finalfit/inst/doc/export.Rmd |only finalfit-0.8.7/finalfit/inst/doc/export.html |only finalfit-0.8.7/finalfit/inst/doc/finalfit.R |only finalfit-0.8.7/finalfit/inst/doc/finalfit.Rmd |only finalfit-0.8.7/finalfit/inst/doc/finalfit.html |only finalfit-0.8.7/finalfit/inst/doc/missing.R |only finalfit-0.8.7/finalfit/inst/doc/missing.Rmd |only finalfit-0.8.7/finalfit/inst/doc/missing.html |only finalfit-0.8.7/finalfit/man/dependent_label.Rd | 1 finalfit-0.8.7/finalfit/man/ff_newdata.Rd | 3 finalfit-0.8.7/finalfit/man/figures |only finalfit-0.8.7/finalfit/man/missing_predictorMatrix.Rd |only finalfit-0.8.7/finalfit/vignettes/bootstrap.Rmd |only finalfit-0.8.7/finalfit/vignettes/export.Rmd |only finalfit-0.8.7/finalfit/vignettes/export_cache |only finalfit-0.8.7/finalfit/vignettes/finalfit.Rmd |only finalfit-0.8.7/finalfit/vignettes/missing.Rmd |only 35 files changed, 144 insertions(+), 237 deletions(-)
More information about blockingChallenge at CRAN
Permanent link
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.6-0 dated 2018-06-09 and 0.6-1 dated 2018-09-21
units-0.6-0/units/R/ud_units.R |only units-0.6-1/units/DESCRIPTION | 18 - units-0.6-1/units/MD5 | 100 ++++--- units-0.6-1/units/NAMESPACE | 20 + units-0.6-1/units/NEWS.md | 12 units-0.6-1/units/R/RcppExports.R | 4 units-0.6-1/units/R/arith.R | 12 units-0.6-1/units/R/conversion.R | 42 ++- units-0.6-1/units/R/init.R | 1 units-0.6-1/units/R/make_units.R | 80 ++++-- units-0.6-1/units/R/math.R | 15 - units-0.6-1/units/R/misc.R | 101 ++----- units-0.6-1/units/R/mixed.R |only units-0.6-1/units/R/options.R | 62 ++++ units-0.6-1/units/R/plot.R | 22 + units-0.6-1/units/R/summaries.R | 29 -- units-0.6-1/units/R/symbolic_units.R | 70 +++-- units-0.6-1/units/R/user_conversion.R | 24 + units-0.6-1/units/R/valid_udunits.R | 51 ++- units-0.6-1/units/build/vignette.rds |binary units-0.6-1/units/configure | 46 +-- units-0.6-1/units/configure.ac | 28 -- units-0.6-1/units/inst/doc/measurement_units_in_R.R | 47 +-- units-0.6-1/units/inst/doc/measurement_units_in_R.Rmd | 76 ++--- units-0.6-1/units/inst/doc/measurement_units_in_R.html | 116 +++------ units-0.6-1/units/inst/doc/units.html | 205 ++++++++-------- units-0.6-1/units/man/as_units.Rd | 22 - units-0.6-1/units/man/boxplot.units.Rd |only units-0.6-1/units/man/deparse_unit.Rd | 1 units-0.6-1/units/man/drop_units.Rd | 30 +- units-0.6-1/units/man/hist.units.Rd | 4 units-0.6-1/units/man/install_conversion_constant.Rd | 4 units-0.6-1/units/man/install_symbolic_unit.Rd | 13 - units-0.6-1/units/man/mixed_units.Rd |only units-0.6-1/units/man/plot.units.Rd | 1 units-0.6-1/units/man/tibble.Rd | 14 - units-0.6-1/units/man/ud_units.Rd | 2 units-0.6-1/units/man/units.Rd | 8 units-0.6-1/units/man/units_options.Rd | 22 + units-0.6-1/units/man/valid_udunits.Rd | 13 - units-0.6-1/units/src/RcppExports.cpp | 12 units-0.6-1/units/src/io.c | 4 units-0.6-1/units/src/udunits.cpp | 57 ++-- units-0.6-1/units/tests/plot.R | 3 units-0.6-1/units/tests/testthat/test_arith.R | 15 - units-0.6-1/units/tests/testthat/test_conversion.R | 46 +++ units-0.6-1/units/tests/testthat/test_misc.R | 22 + units-0.6-1/units/tests/testthat/test_mixed.R |only units-0.6-1/units/tests/testthat/test_summaries.R | 2 units-0.6-1/units/tests/testthat/test_symbolic_units.R | 17 + units-0.6-1/units/tests/testthat/test_udunits.R |only units-0.6-1/units/tests/testthat/test_unit_creation.R | 6 units-0.6-1/units/tests/testthat/test_user_conversion.R | 12 units-0.6-1/units/vignettes/measurement_units_in_R.Rmd | 76 ++--- 54 files changed, 911 insertions(+), 676 deletions(-)
Title: Selection of Training Populations by Genetic Algorithm
Description: Combining Predictive Analytics and Experimental Design to Optimize Results. To be utilized to select a test data calibrated training population in high dimensional prediction problems and assumes that the explanatory variables are observed for all of the individuals. Once a "good" training set is identified, the response variable can be obtained only for this set to build a model for predicting the response in the test set. The algorithms in the package can be tweaked to solve some other subset selection problems.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between STPGA versions 5.1 dated 2018-08-16 and 5.2 dated 2018-09-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/GenAlgForSubsetSelection.R | 11 +++++++++-- R/GenAlgForSubsetSelectionNoTest.R | 12 +++++++++--- man/CRITERIA.Rd | 4 ++++ man/GenAlgForSubsetSelection.Rd | 5 ++++- man/GenAlgForSubsetSelectionNoTest.Rd | 6 +++++- 7 files changed, 42 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-21 0.9
2013-02-02 0.7
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.54.3 dated 2018-08-08 and 0.56.1 dated 2018-09-21
DESCRIPTION | 14 MD5 | 108 - NAMESPACE | 2 NEWS | 24 R/aliasmodel.R | 25 R/blockingstructure.R | 10 R/calcblocksizes.R | 10 R/calcnoncentralparam.R | 9 R/calculatepower.R | 4 R/constructRunMatrix.R | 10 R/contr.simplex.R | 38 R/disallowed_combinations.R | 8 R/effectpower.R | 15 R/effectpowermc.R | 6 R/eval_design.R | 417 +++--- R/eval_design_custom_mc.R | 100 - R/eval_design_mc.R | 521 ++++---- R/eval_design_survival_mc.R | 186 +- R/extractPvalues.R | 10 R/gen_anticoef.R | 42 R/gen_binomial_anticoef.R | 6 R/gen_design.R | 993 ++++++++------- R/gen_exponential_anticoef.R | 2 R/gen_momentsmatrix.R | 66 - R/gen_poisson_anticoef.R | 2 R/genhypmatrix.R | 8 R/genparammatrix.R | 6 R/parameterpower.R | 23 R/pipeimport.R |only R/plot_correlations.R | 90 - R/plot_fds.R | 77 - R/priorlevels.R | 2 R/quad.R | 14 R/reduceRunMatrix.R | 20 R/skprGUI.R | 1816 ++++++++++++++-------------- R/skprGUIserver.R | 2092 +++++++++++++++++---------------- inst/shiny/skprGUI/server.R | 1390 ++++++++++----------- inst/shiny/skprGUI/ui.R | 488 +++---- man/calcnoncentralparam.Rd | 4 man/contr.simplex.Rd | 10 man/effectpower.Rd | 4 man/eval_design.Rd | 63 man/eval_design_custom_mc.Rd | 34 man/eval_design_mc.Rd | 83 - man/eval_design_survival_mc.Rd | 30 man/gen_design.Rd | 147 +- man/parameterpower.Rd | 4 man/pipe.Rd |only man/plot_correlations.Rd | 16 man/plot_fds.Rd | 4 src/genOptimalDesign.cpp | 219 ++- tests/testthat/Rplots.pdf |binary tests/testthat/testDeltaProcessing.R | 94 - tests/testthat/testExampleCode.R | 473 +++---- tests/testthat/testExtractPvalues.R | 16 tests/testthat/testPlottingFunctions.R | 38 56 files changed, 5085 insertions(+), 4808 deletions(-)
Title: Functions for Time Series Analysis and Forecasting
Description: Provides a set of tools for descriptive and predictive analysis of time series data. That includes functions for interactive visualization of time series objects and as well utility functions for automation time series forecasting.
Author: Rami Krispin
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between TSstudio versions 0.1.1 dated 2018-02-07 and 0.1.2 dated 2018-09-21
TSstudio-0.1.1/TSstudio/R/ts_decompose.R |only TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.R |only TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.Rmd |only TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.html |only TSstudio-0.1.1/TSstudio/vignettes/TSstudio_Intro.Rmd |only TSstudio-0.1.2/TSstudio/DESCRIPTION | 20 TSstudio-0.1.2/TSstudio/MD5 | 94 TSstudio-0.1.2/TSstudio/NAMESPACE | 47 TSstudio-0.1.2/TSstudio/NEWS.md |only TSstudio-0.1.2/TSstudio/R/correlation_functions.R | 966 +++-- TSstudio-0.1.2/TSstudio/R/data.R | 173 - TSstudio-0.1.2/TSstudio/R/forecast_tools.R | 566 +-- TSstudio-0.1.2/TSstudio/R/train_functions.R |only TSstudio-0.1.2/TSstudio/R/ts_plot.R | 683 ++-- TSstudio-0.1.2/TSstudio/R/ts_seasonal.R | 2126 +++++++++++-- TSstudio-0.1.2/TSstudio/R/util_functions.R | 839 +++-- TSstudio-0.1.2/TSstudio/README.md | 132 TSstudio-0.1.2/TSstudio/build/vignette.rds |binary TSstudio-0.1.2/TSstudio/data/Coffee_Prices.rda |only TSstudio-0.1.2/TSstudio/data/EURO_Brent.rda |binary TSstudio-0.1.2/TSstudio/data/Michigan_CS.rda |binary TSstudio-0.1.2/TSstudio/data/USUnRate.rda |binary TSstudio-0.1.2/TSstudio/data/USVSales.rda |binary TSstudio-0.1.2/TSstudio/data/US_indicators.rda |only TSstudio-0.1.2/TSstudio/data/USgas.rda |binary TSstudio-0.1.2/TSstudio/inst/doc/Plotting_Time_Series.R |only TSstudio-0.1.2/TSstudio/inst/doc/Plotting_Time_Series.Rmd |only TSstudio-0.1.2/TSstudio/inst/doc/Plotting_Time_Series.html |only TSstudio-0.1.2/TSstudio/man/Coffee_Prices.Rd |only TSstudio-0.1.2/TSstudio/man/EURO_Brent.Rd | 44 TSstudio-0.1.2/TSstudio/man/Michigan_CS.Rd | 44 TSstudio-0.1.2/TSstudio/man/USUnRate.Rd | 44 TSstudio-0.1.2/TSstudio/man/USVSales.Rd | 44 TSstudio-0.1.2/TSstudio/man/US_indicators.Rd |only TSstudio-0.1.2/TSstudio/man/USgas.Rd | 44 TSstudio-0.1.2/TSstudio/man/check_res.Rd | 60 TSstudio-0.1.2/TSstudio/man/plot_forecast.Rd |only TSstudio-0.1.2/TSstudio/man/res_hist.Rd | 68 TSstudio-0.1.2/TSstudio/man/test_forecast.Rd | 97 TSstudio-0.1.2/TSstudio/man/ts_acf.Rd | 55 TSstudio-0.1.2/TSstudio/man/ts_backtesting.Rd |only TSstudio-0.1.2/TSstudio/man/ts_decompose.Rd | 58 TSstudio-0.1.2/TSstudio/man/ts_heatmap.Rd | 53 TSstudio-0.1.2/TSstudio/man/ts_info.Rd |only TSstudio-0.1.2/TSstudio/man/ts_lags.Rd | 81 TSstudio-0.1.2/TSstudio/man/ts_ma.Rd |only TSstudio-0.1.2/TSstudio/man/ts_pacf.Rd | 57 TSstudio-0.1.2/TSstudio/man/ts_plot.Rd | 92 TSstudio-0.1.2/TSstudio/man/ts_polar.Rd | 66 TSstudio-0.1.2/TSstudio/man/ts_quantile.Rd |only TSstudio-0.1.2/TSstudio/man/ts_reshape.Rd | 52 TSstudio-0.1.2/TSstudio/man/ts_seasonal.Rd | 85 TSstudio-0.1.2/TSstudio/man/ts_split.Rd | 75 TSstudio-0.1.2/TSstudio/man/ts_sum.Rd |only TSstudio-0.1.2/TSstudio/man/ts_surface.Rd | 34 TSstudio-0.1.2/TSstudio/man/xts_to_ts.Rd | 44 TSstudio-0.1.2/TSstudio/man/zoo_to_ts.Rd | 46 TSstudio-0.1.2/TSstudio/vignettes/Plotting_Time_Series.Rmd |only TSstudio-0.1.2/TSstudio/vignettes/gif |only 59 files changed, 4569 insertions(+), 2320 deletions(-)
Title: Interface with General Bikeshare Feed Specification Files
Description: Supplies a set of functions to interface with General Bikeshare
Feed Specification .json feeds in R, allowing users to save and accumulate
tidy .rds datasets for specified cities/bikeshare programs.
Author: Kaelyn Rosenberg [aut],
Simon P. Couch [aut, cre],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.0.0 dated 2018-05-11 and 1.1.0 dated 2018-09-21
gbfs-1.0.0/gbfs/build |only gbfs-1.0.0/gbfs/inst |only gbfs-1.0.0/gbfs/vignettes |only gbfs-1.1.0/gbfs/DESCRIPTION | 18 ++++---- gbfs-1.1.0/gbfs/MD5 | 40 ++++++++---------- gbfs-1.1.0/gbfs/NAMESPACE | 1 gbfs-1.1.0/gbfs/R/gbfs_description.R | 5 +- gbfs-1.1.0/gbfs/R/get_dynamic_feeds.R | 53 ++++++++++++++++++++---- gbfs-1.1.0/gbfs/R/get_gbfs.R | 50 +++++++++++++--------- gbfs-1.1.0/gbfs/R/get_static_feeds.R | 21 ++++++--- gbfs-1.1.0/gbfs/README.md | 53 ++++++++++++++---------- gbfs-1.1.0/gbfs/man/get_free_bike_status.Rd | 5 -- gbfs-1.1.0/gbfs/man/get_gbfs.Rd | 7 --- gbfs-1.1.0/gbfs/man/get_gbfs_cities.Rd |only gbfs-1.1.0/gbfs/man/get_station_information.Rd | 6 +- gbfs-1.1.0/gbfs/man/get_station_status.Rd | 4 - gbfs-1.1.0/gbfs/man/get_system_alerts.Rd | 3 - gbfs-1.1.0/gbfs/man/get_system_calendar.Rd | 3 - gbfs-1.1.0/gbfs/man/get_system_hours.Rd | 3 - gbfs-1.1.0/gbfs/man/get_system_information.Rd | 3 - gbfs-1.1.0/gbfs/man/get_system_pricing_plans.Rd | 6 +- gbfs-1.1.0/gbfs/man/get_system_regions.Rd | 3 - 22 files changed, 176 insertions(+), 108 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <http://codecov.io> or
'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Müller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyzanowski [ctb],
Markus Wamser [ctb],
Karl Forner [ctb],
Gergely Daróczi [ctb],
Jouni Helske [ctb],
Kun Ren [ctb],
Jeroen Ooms [ctb],
Ken Williams [ctb],
Chris Campbell [ctb],
David Hugh-Jones [ctb],
Qin Wang [ctb],
Ivan Sagalaev [ctb, cph] (highlight.js library),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library)
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.1.0 dated 2018-05-18 and 3.2.0 dated 2018-09-21
covr-3.1.0/covr/inst/www/shiny.css |only covr-3.1.0/covr/man/covr-deprecated.Rd |only covr-3.2.0/covr/DESCRIPTION | 29 +- covr-3.2.0/covr/MD5 | 72 +++--- covr-3.2.0/covr/NAMESPACE | 6 covr-3.2.0/covr/NEWS.md | 63 ++++- covr-3.2.0/covr/R/compiled.R | 22 +- covr-3.2.0/covr/R/covr.R | 71 +++++- covr-3.2.0/covr/R/display_name.R | 5 covr-3.2.0/covr/R/gitlab.R |only covr-3.2.0/covr/R/icc.R | 2 covr-3.2.0/covr/R/parallel.R | 6 covr-3.2.0/covr/R/parse_data.R | 41 +++ covr-3.2.0/covr/R/report.R | 264 ++++++++++++++++++------ covr-3.2.0/covr/R/summary_functions.R | 6 covr-3.2.0/covr/R/trace_calls.R | 5 covr-3.2.0/covr/R/zzz.R | 1 covr-3.2.0/covr/README.md | 3 covr-3.2.0/covr/build/vignette.rds |binary covr-3.2.0/covr/inst/doc/how_it_works.R | 2 covr-3.2.0/covr/inst/doc/how_it_works.Rmd | 2 covr-3.2.0/covr/inst/doc/how_it_works.html | 8 covr-3.2.0/covr/inst/www/report.css |only covr-3.2.0/covr/inst/www/shared |only covr-3.2.0/covr/man/coveralls.Rd | 3 covr-3.2.0/covr/man/covr-package.Rd | 7 covr-3.2.0/covr/man/display_name.Rd |only covr-3.2.0/covr/man/environment_coverage.Rd |only covr-3.2.0/covr/man/figures |only covr-3.2.0/covr/man/file_report.Rd |only covr-3.2.0/covr/man/gitlab.Rd |only covr-3.2.0/covr/man/print.coverage.Rd | 4 covr-3.2.0/covr/man/system_check.Rd | 4 covr-3.2.0/covr/man/system_output.Rd | 4 covr-3.2.0/covr/man/trace_calls.Rd | 5 covr-3.2.0/covr/tests/testthat/test-braceless.R | 39 +++ covr-3.2.0/covr/tests/testthat/test-covr.R | 18 + covr-3.2.0/covr/tests/testthat/test-gitlab.R |only covr-3.2.0/covr/vignettes/how_it_works.Rmd | 2 39 files changed, 537 insertions(+), 157 deletions(-)
Title: Measuring Information Flow Between Time Series with Shannon and
Renyi Transfer Entropy
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Author: Simon Behrendt [aut, cre],
David Zimmermann [aut],
Thomas Dimpfl [aut],
Franziska Peter [aut]
Maintainer: Simon Behrendt <simon.behrendt@zu.de>
Diff between RTransferEntropy versions 0.2.5 dated 2018-07-25 and 0.2.7 dated 2018-09-21
RTransferEntropy-0.2.5/RTransferEntropy/R/TEclass.R |only RTransferEntropy-0.2.5/RTransferEntropy/man/coef.TEResult.Rd |only RTransferEntropy-0.2.5/RTransferEntropy/man/is.TEResult.Rd |only RTransferEntropy-0.2.5/RTransferEntropy/man/print.TEResult.Rd |only RTransferEntropy-0.2.5/RTransferEntropy/man/summary.TEResult.Rd |only RTransferEntropy-0.2.7/RTransferEntropy/DESCRIPTION | 10 RTransferEntropy-0.2.7/RTransferEntropy/MD5 | 64 RTransferEntropy-0.2.7/RTransferEntropy/NAMESPACE | 9 RTransferEntropy-0.2.7/RTransferEntropy/R/bootstrap_renyi.R | 25 RTransferEntropy-0.2.7/RTransferEntropy/R/bootstrap_shannon.R | 21 RTransferEntropy-0.2.7/RTransferEntropy/R/calc_ete.R | 8 RTransferEntropy-0.2.7/RTransferEntropy/R/calc_te.R | 10 RTransferEntropy-0.2.7/RTransferEntropy/R/calc_te_renyi.R | 8 RTransferEntropy-0.2.7/RTransferEntropy/R/calc_te_shannon.R | 4 RTransferEntropy-0.2.7/RTransferEntropy/R/code_sample.R | 1 RTransferEntropy-0.2.7/RTransferEntropy/R/combine_sample.R | 5 RTransferEntropy-0.2.7/RTransferEntropy/R/markov_boot_step.R | 11 RTransferEntropy-0.2.7/RTransferEntropy/R/shuffle_renyi.R | 13 RTransferEntropy-0.2.7/RTransferEntropy/R/shuffle_shannon.R | 1 RTransferEntropy-0.2.7/RTransferEntropy/R/te_class.R |only RTransferEntropy-0.2.7/RTransferEntropy/R/te_renyi.R | 62 RTransferEntropy-0.2.7/RTransferEntropy/R/te_shannon.R | 57 RTransferEntropy-0.2.7/RTransferEntropy/R/transfer_entropy.R | 122 - RTransferEntropy-0.2.7/RTransferEntropy/R/zzz.R | 59 RTransferEntropy-0.2.7/RTransferEntropy/README.md | 170 + RTransferEntropy-0.2.7/RTransferEntropy/inst/doc/transfer-entropy.Rmd | 14 RTransferEntropy-0.2.7/RTransferEntropy/inst/doc/transfer-entropy.html | 982 ++++++---- RTransferEntropy-0.2.7/RTransferEntropy/man/calc_ete.Rd | 12 RTransferEntropy-0.2.7/RTransferEntropy/man/calc_te.Rd | 12 RTransferEntropy-0.2.7/RTransferEntropy/man/coef.transfer_entropy.Rd |only RTransferEntropy-0.2.7/RTransferEntropy/man/is.transfer_entropy.Rd |only RTransferEntropy-0.2.7/RTransferEntropy/man/print.transfer_entropy.Rd |only RTransferEntropy-0.2.7/RTransferEntropy/man/summary.transfer_entropy.Rd |only RTransferEntropy-0.2.7/RTransferEntropy/man/transfer_entropy.Rd | 27 RTransferEntropy-0.2.7/RTransferEntropy/tests/testthat/test.calculate_transition_probabilities.R | 3 RTransferEntropy-0.2.7/RTransferEntropy/tests/testthat/test.cluster_gen.R | 2 RTransferEntropy-0.2.7/RTransferEntropy/tests/testthat/test.transfer_entropy.R | 94 RTransferEntropy-0.2.7/RTransferEntropy/vignettes/transfer-entropy.Rmd | 14 38 files changed, 1086 insertions(+), 734 deletions(-)
More information about RTransferEntropy at CRAN
Permanent link
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Peter Rousseeuw [ctb] (Qn and Sn),
Christophe Croux [ctb] (Qn and Sn),
Valentin Todorov [aut] (most robust Cov),
Andreas Ruckstuhl [aut] (nlrob, anova, glmrob),
Matias Salibian-Barrera [aut] (lmrob orig.),
Tobias Verbeke [ctb, fnd] (mc, adjbox),
Manuel Koller [aut] (mc, lmrob, psi-func.),
Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob),
Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.93-2 dated 2018-07-27 and 0.93-3 dated 2018-09-21
DESCRIPTION | 14 - MD5 | 66 ++-- build/partial.rdb |binary inst/NEWS.Rd | 10 inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf | 384 +++++++++++++++-------------- inst/doc/psi_functions.pdf | 101 +++---- src/robustbase.h | 9 tests/NAcoef.R | 4 tests/NAcoef.Rout.save | 4 tests/nlregrob-tst.R | 15 - vignettes/plot-fig-AdB2-1.pdf |binary vignettes/plot-fig-Mscale-all.pdf |binary vignettes/plot-fig-Mscale.pdf |binary vignettes/plot-fig-cpr.pdf |binary vignettes/plot-fig-efficiency-all.pdf |binary vignettes/plot-fig-efficiency.pdf |binary vignettes/plot-fig-emp-level.pdf |binary vignettes/plot-fig-example-design.pdf |binary vignettes/plot-fig-lqq-level.pdf |binary vignettes/plot-fig-max-asymptotic-bias.pdf |binary vignettes/plot-fig-meanscale.pdf |binary vignettes/plot-fig-power-1-0_2.pdf |binary vignettes/plot-fig-power-1-0_4.pdf |binary vignettes/plot-fig-power-1-0_6.pdf |binary vignettes/plot-fig-power-1-0_8.pdf |binary vignettes/plot-fig-power-1-1.pdf |binary vignettes/plot-fig-pred-points.pdf |binary vignettes/plot-fig-psi-functions.pdf |binary vignettes/plot-fig-qscale-all.pdf |binary vignettes/plot-fig-qscale.pdf |binary vignettes/plot-fig-sdAdB2-1.pdf |binary vignettes/plot-fig-sdscale-1.pdf |binary vignettes/plot-fig-sdscale-all.pdf |binary 34 files changed, 317 insertions(+), 290 deletions(-)
Title: An Installation Framework for Shiny Apps
Description: Installs shiny apps packaged as stand-alone Electron apps using Inno Setup, an open source software that builds installers for Windows programs <http://www.jrsoftware.org/ishelp/>.
Author: Jon Hill [aut, cre, cph],
W. Lee Pang [aut, cph] (DesktopDeployR project at
https://github.com/wleepang/DesktopDeployR),
Hanjo Odendaal [ctb],
William Bradley [ctb],
Brent (Tom) Bailey [ctb],
Mikolaj Rybinski [ctb],
Chase Clark [ctb],
Damien Soukhavong [ctb],
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Gábor Csárdi [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
RStudio [cph],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Mango Solutions [cph]
Maintainer: Jon Hill <jon.mark.hill@gmail.com>
Diff between RInno versions 1.0.0 dated 2018-09-21 and 1.0.1 dated 2018-09-21
DESCRIPTION | 12 +++++------- MD5 | 6 +++--- inst/doc/Introduction.html | 6 +++--- inst/doc/cont-installation.html | 4 ++-- 4 files changed, 13 insertions(+), 15 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat learning methods, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.2.4 dated 2018-08-18 and 2.2.5 dated 2018-09-21
HEMDAG-2.2.4/HEMDAG/CHANGELOG |only HEMDAG-2.2.4/HEMDAG/inst/extdata/edges.txt |only HEMDAG-2.2.4/HEMDAG/inst/extdata/gene2pheno.txt |only HEMDAG-2.2.4/HEMDAG/inst/extdata/graph.edges.txt |only HEMDAG-2.2.5/HEMDAG/DESCRIPTION | 13 HEMDAG-2.2.5/HEMDAG/MD5 | 85 +-- HEMDAG-2.2.5/HEMDAG/NAMESPACE | 5 HEMDAG-2.2.5/HEMDAG/NEWS.md |only HEMDAG-2.2.5/HEMDAG/R/GPAV.R | 62 +- HEMDAG-2.2.5/HEMDAG/R/IO.fun.R | 78 ++- HEMDAG-2.2.5/HEMDAG/R/TPR-DAG.R | 67 +- HEMDAG-2.2.5/HEMDAG/R/graph.utility.R | 124 +++- HEMDAG-2.2.5/HEMDAG/R/heuristic.methods.R | 28 - HEMDAG-2.2.5/HEMDAG/R/htd.R | 32 - HEMDAG-2.2.5/HEMDAG/R/perf.meas.R | 414 +++++++++------- HEMDAG-2.2.5/HEMDAG/R/pkg.import.R | 1 HEMDAG-2.2.5/HEMDAG/inst/doc/HEMDAG.pdf |binary HEMDAG-2.2.5/HEMDAG/inst/extdata/edges.txt.gz |only HEMDAG-2.2.5/HEMDAG/inst/extdata/gene2pheno.txt.gz |only HEMDAG-2.2.5/HEMDAG/inst/extdata/graph.edges.txt.gz |only HEMDAG-2.2.5/HEMDAG/man/AUPRC.Rd | 14 HEMDAG-2.2.5/HEMDAG/man/AUROC.Rd | 14 HEMDAG-2.2.5/HEMDAG/man/Do.GPAV.Rd | 18 HEMDAG-2.2.5/HEMDAG/man/Do.GPAV.holdout.Rd | 16 HEMDAG-2.2.5/HEMDAG/man/Do.HTD.Rd | 18 HEMDAG-2.2.5/HEMDAG/man/Do.HTD.holdout.Rd | 20 HEMDAG-2.2.5/HEMDAG/man/Do.heuristic.methods.Rd | 10 HEMDAG-2.2.5/HEMDAG/man/Do.heuristic.methods.holdout.Rd | 10 HEMDAG-2.2.5/HEMDAG/man/FMM.Rd | 15 HEMDAG-2.2.5/HEMDAG/man/GPAV.Rd | 12 HEMDAG-2.2.5/HEMDAG/man/GPAV.over.examples.Rd | 4 HEMDAG-2.2.5/HEMDAG/man/GPAV.parallel.Rd | 4 HEMDAG-2.2.5/HEMDAG/man/PXR.Rd | 51 + HEMDAG-2.2.5/HEMDAG/man/TPR-DAG-cross-validation.Rd | 24 HEMDAG-2.2.5/HEMDAG/man/TPR-DAG-holdout.Rd | 27 - HEMDAG-2.2.5/HEMDAG/man/TPR-DAG-variants.Rd | 2 HEMDAG-2.2.5/HEMDAG/man/create.stratified.fold.df.Rd |only HEMDAG-2.2.5/HEMDAG/man/do.edges.from.HPO.obo.Rd | 11 HEMDAG-2.2.5/HEMDAG/man/do.unstratified.cv.data.Rd | 6 HEMDAG-2.2.5/HEMDAG/man/find.best.f.Rd | 16 HEMDAG-2.2.5/HEMDAG/man/read.graph.Rd | 7 HEMDAG-2.2.5/HEMDAG/man/read.undirected.graph.Rd | 6 HEMDAG-2.2.5/HEMDAG/man/specific.annotation.matrix.Rd | 8 HEMDAG-2.2.5/HEMDAG/man/stratified.cross.validation.Rd | 11 HEMDAG-2.2.5/HEMDAG/man/tupla.matrix.Rd | 18 HEMDAG-2.2.5/HEMDAG/man/weighted.adjacency.matrix.Rd | 18 HEMDAG-2.2.5/HEMDAG/man/write.graph.Rd | 9 HEMDAG-2.2.5/HEMDAG/src/GPAV.cpp | 6 48 files changed, 727 insertions(+), 557 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.8 dated 2017-12-16 and 2.9 dated 2018-09-21
multiplex-2.8/multiplex/R/iinc.R |only multiplex-2.8/multiplex/R/is.mc.R |only multiplex-2.8/multiplex/man/iinc.Rd |only multiplex-2.8/multiplex/man/is.mc.Rd |only multiplex-2.9/multiplex/DESCRIPTION | 10 multiplex-2.9/multiplex/MD5 | 74 +++-- multiplex-2.9/multiplex/R/as.semigroup.R | 153 ++++++++++- multiplex-2.9/multiplex/R/cngr.R | 66 ++--- multiplex-2.9/multiplex/R/decomp.R | 230 ++++++++++-------- multiplex-2.9/multiplex/R/diagram.R | 102 ++++++- multiplex-2.9/multiplex/R/edgS.R |only multiplex-2.9/multiplex/R/fact.R |only multiplex-2.9/multiplex/R/mlvl.R |only multiplex-2.9/multiplex/R/partial.order.R | 97 ++++--- multiplex-2.9/multiplex/R/perm.R | 5 multiplex-2.9/multiplex/R/pi.rels.R | 118 +++++++-- multiplex-2.9/multiplex/R/reducs.R | 90 ++----- multiplex-2.9/multiplex/R/strings.R | 128 +++++++++- multiplex-2.9/multiplex/R/strng.R |only multiplex-2.9/multiplex/R/transf.R | 179 ++++++++++++-- multiplex-2.9/multiplex/R/zbind.R | 24 + multiplex-2.9/multiplex/data/incA.RData |only multiplex-2.9/multiplex/data/incB.RData |only multiplex-2.9/multiplex/data/incC.RData |only multiplex-2.9/multiplex/data/incD.RData |only multiplex-2.9/multiplex/inst/CHANGELOG | 32 +- multiplex-2.9/multiplex/inst/doc/TwoModeNetworks.R | 12 multiplex-2.9/multiplex/inst/doc/TwoModeNetworks.Rnw | 43 ++- multiplex-2.9/multiplex/inst/doc/TwoModeNetworks.pdf |binary multiplex-2.9/multiplex/man/as.semigroup.Rd | 20 + multiplex-2.9/multiplex/man/cngr.Rd | 10 multiplex-2.9/multiplex/man/decomp.Rd | 23 + multiplex-2.9/multiplex/man/diagram.Rd | 26 +- multiplex-2.9/multiplex/man/edgS.Rd |only multiplex-2.9/multiplex/man/fact.Rd |only multiplex-2.9/multiplex/man/incubs.Rd | 23 + multiplex-2.9/multiplex/man/mlvl.Rd |only multiplex-2.9/multiplex/man/multiplex-package.Rd | 4 multiplex-2.9/multiplex/man/partial.order.Rd | 11 multiplex-2.9/multiplex/man/pi.rels.Rd | 11 multiplex-2.9/multiplex/man/semigroup.Rd | 4 multiplex-2.9/multiplex/man/strings.Rd | 14 - multiplex-2.9/multiplex/man/strng.Rd |only multiplex-2.9/multiplex/man/transf.Rd | 11 multiplex-2.9/multiplex/man/zbind.Rd | 3 multiplex-2.9/multiplex/vignettes/TwoModeNetworks.Rnw | 43 ++- 46 files changed, 1114 insertions(+), 452 deletions(-)
Title: Detecting Anomalies in Data
Description: An implementation of CAPA (Collective And Point Anomaly) for the detection of anomalies in time series data. The package also contains Kepler lightcurve data and shows how CAPA can be applied to detect exoplanets.
Author: Alex Fisch [aut],
Daniel Grose [ctb, cre],
Idris Eckley [ths],
Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 1.0.0 dated 2018-06-30 and 1.1.0 dated 2018-09-21
DESCRIPTION | 12 +++---- MD5 | 26 +++++++++------- NAMESPACE | 2 + R/anomaly_series.R | 56 ++++++++++++++++++++++++++++++----- R/plot.anomaly_series.R | 22 ++++++++++--- README.md |only build/partial.rdb |binary data/Lightcurves.RData |binary man/anomaly_series.Rd | 11 ++++++ man/plot.anomaly_series.Rd | 3 + src/Functions.h | 32 ++++++++++++++++++++ src/check_user_interrupt.c |only src/init.c | 2 + src/meanvarwithanomaly_mean.c |only src/meanvarwithanomalysupport.c | 4 +- src/meanvarwithanomalysupport_mean.c |only 16 files changed, 137 insertions(+), 33 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Matthieu Stigler [ctb],
Eric Persson [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.5-12 dated 2018-06-28 and 0.5-13 dated 2018-09-21
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++++------------- R/SDMXData-methods.R | 10 ++++++- R/SDMXServiceProvider-methods.R | 12 +++++++- R/rsdmx.R | 4 +- README.md | 2 - inst/doc/quickstart.Rmd | 4 +- inst/doc/quickstart.html | 2 - man/rsdmx.Rd | 4 +- tests/testthat/test_CompactData.R | 2 - tests/testthat/test_CrossSectionalData.R | 2 - tests/testthat/test_DataFlows.R | 2 - tests/testthat/test_DataStructureDefinition.R | 4 -- tests/testthat/test_DataStructures.R | 4 -- tests/testthat/test_GenericData.R | 6 ---- tests/testthat/test_Main_Helpers.R | 35 +++++++++++++++++++++++++ tests/testthat/test_MessageGroup.R | 2 - tests/testthat/test_StructureSpecificData.R | 2 - vignettes/quickstart.Rmd | 4 +- 19 files changed, 87 insertions(+), 58 deletions(-)
Title: An Installation Framework for Shiny Apps
Description: Installs shiny apps packaged as stand-alone Electron apps using Inno Setup, an open source software that builds installers for Windows programs <http://www.jrsoftware.org/ishelp/>.
Author: Jon Hill [aut, cre, cph],
W. Lee Pang [aut, cph] (DesktopDeployR project at
https://github.com/wleepang/DesktopDeployR),
Hanjo Odendaal [ctb],
William Bradley [ctb],
Brent (Tom) Bailey [ctb],
Mikolaj Rybinski [ctb],
Chase Clark [ctb],
Damien Soukhavong [ctb],
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Gábor Csárdi [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
RStudio [cph],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Mango Solutions [cph]
Maintainer: Jon Hill <jon.mark.hill@gmail.com>
Diff between RInno versions 0.2.1 dated 2018-06-11 and 1.0.0 dated 2018-09-21
RInno-0.2.1/RInno/R/flexdashboard_check.R |only RInno-0.2.1/RInno/R/standardize_pkgs.R |only RInno-0.2.1/RInno/inst/app/local |only RInno-0.2.1/RInno/inst/doc/Introduction.R |only RInno-0.2.1/RInno/inst/installation/app.R |only RInno-0.2.1/RInno/man/cran_version.Rd |only RInno-0.2.1/RInno/tests/testthat/test_code_run_tasks.R |only RInno-0.2.1/RInno/tests/testthat/test_copy_installation.R |only RInno-0.2.1/RInno/tests/testthat/test_create_app.R |only RInno-0.2.1/RInno/tests/testthat/test_create_config.R |only RInno-0.2.1/RInno/tests/testthat/test_directives.R |only RInno-0.2.1/RInno/tests/testthat/test_files.R |only RInno-0.2.1/RInno/tests/testthat/test_icons.R |only RInno-0.2.1/RInno/tests/testthat/test_languages.R |only RInno-0.2.1/RInno/tests/testthat/test_setup.R |only RInno-1.0.0/RInno/DESCRIPTION | 43 +- RInno-1.0.0/RInno/MD5 | 135 ++++--- RInno-1.0.0/RInno/NAMESPACE | 19 - RInno-1.0.0/RInno/NEWS.md | 10 RInno-1.0.0/RInno/R/code_section.R | 3 RInno-1.0.0/RInno/R/compile_iss.R | 29 + RInno-1.0.0/RInno/R/copy_installation.R | 6 RInno-1.0.0/RInno/R/create_app.R | 160 +++++--- RInno-1.0.0/RInno/R/create_config.R | 58 +-- RInno-1.0.0/RInno/R/download_packages.R |only RInno-1.0.0/RInno/R/files_section.R | 14 RInno-1.0.0/RInno/R/get_Chrome.R | 2 RInno-1.0.0/RInno/R/get_R.R | 28 - RInno-1.0.0/RInno/R/get_Rtools.R | 8 RInno-1.0.0/RInno/R/get_pandoc.R | 4 RInno-1.0.0/RInno/R/install_inno.R | 16 RInno-1.0.0/RInno/R/install_nodejs.R |only RInno-1.0.0/RInno/R/nativefy_app.R |only RInno-1.0.0/RInno/R/remotes_bioc.R |only RInno-1.0.0/RInno/R/remotes_circular.R |only RInno-1.0.0/RInno/R/remotes_cran.R |only RInno-1.0.0/RInno/R/remotes_dcf.R |only RInno-1.0.0/RInno/R/remotes_decompress.R |only RInno-1.0.0/RInno/R/remotes_deps.R |only RInno-1.0.0/RInno/R/remotes_devel.R |only RInno-1.0.0/RInno/R/remotes_download.R |only RInno-1.0.0/RInno/R/remotes_git.R |only RInno-1.0.0/RInno/R/remotes_github.R |only RInno-1.0.0/RInno/R/remotes_install-github.R |only RInno-1.0.0/RInno/R/remotes_install-remote.R |only RInno-1.0.0/RInno/R/remotes_install.R |only RInno-1.0.0/RInno/R/remotes_json.R |only RInno-1.0.0/RInno/R/remotes_package-deps.R |only RInno-1.0.0/RInno/R/remotes_package.R |only RInno-1.0.0/RInno/R/remotes_parse-git.R |only RInno-1.0.0/RInno/R/remotes_submodule.R |only RInno-1.0.0/RInno/R/remotes_system.R |only RInno-1.0.0/RInno/R/remotes_utils.R |only RInno-1.0.0/RInno/R/utils.R |only RInno-1.0.0/RInno/README.md | 35 + RInno-1.0.0/RInno/build/vignette.rds |binary RInno-1.0.0/RInno/inst/app/bin |only RInno-1.0.0/RInno/inst/app/server.R | 10 RInno-1.0.0/RInno/inst/doc/Introduction.Rmd | 46 +- RInno-1.0.0/RInno/inst/doc/Introduction.html | 237 +++++-------- RInno-1.0.0/RInno/inst/doc/cont-installation.Rmd | 4 RInno-1.0.0/RInno/inst/doc/cont-installation.html | 8 RInno-1.0.0/RInno/inst/installation/ensure.R | 111 ------ RInno-1.0.0/RInno/inst/installation/get_app_from_app_url.R | 27 - RInno-1.0.0/RInno/inst/installation/launch_app.R |only RInno-1.0.0/RInno/inst/installation/package_manager.R | 65 +-- RInno-1.0.0/RInno/man/add_pkgs.Rd | 5 RInno-1.0.0/RInno/man/code_section.Rd | 2 RInno-1.0.0/RInno/man/copy_installation.Rd | 7 RInno-1.0.0/RInno/man/create_app.Rd | 58 +-- RInno-1.0.0/RInno/man/create_config.Rd | 18 RInno-1.0.0/RInno/man/directives_section.Rd | 10 RInno-1.0.0/RInno/man/download_packages.Rd |only RInno-1.0.0/RInno/man/files_section.Rd | 5 RInno-1.0.0/RInno/man/flexdashboard_check.Rd | 3 RInno-1.0.0/RInno/man/get_Pandoc.Rd | 2 RInno-1.0.0/RInno/man/get_R.Rd | 2 RInno-1.0.0/RInno/man/get_Rtools.Rd | 2 RInno-1.0.0/RInno/man/grapes-greater-than-grapes.Rd |only RInno-1.0.0/RInno/man/install_nodejs.Rd |only RInno-1.0.0/RInno/man/nativefy_app.Rd |only RInno-1.0.0/RInno/man/sanitize_R_version.Rd | 13 RInno-1.0.0/RInno/man/standardize_pkgs.Rd | 11 RInno-1.0.0/RInno/tests/testthat/test-code_run_tasks.R |only RInno-1.0.0/RInno/tests/testthat/test-copy_installation.R |only RInno-1.0.0/RInno/tests/testthat/test-create_app.R |only RInno-1.0.0/RInno/tests/testthat/test-create_config.R |only RInno-1.0.0/RInno/tests/testthat/test-directives.R |only RInno-1.0.0/RInno/tests/testthat/test-files.R |only RInno-1.0.0/RInno/tests/testthat/test-icons.R |only RInno-1.0.0/RInno/tests/testthat/test-languages.R |only RInno-1.0.0/RInno/tests/testthat/test-sanitize_R_version.R |only RInno-1.0.0/RInno/tests/testthat/test-setup.R |only RInno-1.0.0/RInno/tests/testthat/test-standardize_pkgs.R | 10 RInno-1.0.0/RInno/vignettes/Introduction.Rmd | 46 +- RInno-1.0.0/RInno/vignettes/cont-installation.Rmd | 4 96 files changed, 650 insertions(+), 626 deletions(-)
Title: Average Positive Predictive Values (AP) for Binary Outcomes and
Censored Event Times
Description: We provide tools to estimate two prediction accuracy metrics,
the average positive predictive values (AP) as well as the well-known AUC
(the area under the receiver operator characteristic curve) for risk scores.
The outcome of interest is either binary or censored event time.
Note that for censored event time, our functions' estimates, the AP and the
AUC, are time-dependent for pre-specified time interval(s). A function that
compares the APs of two risk scores/markers is also included. Optional
outputs include positive predictive values and true positive fractions at
the specified marker cut-off values, and a plot of the time-dependent AP
versus time (available for event time data).
Author: Hengrui Cai <hengruicai@gmail.com>, Yan Yuan <yyuan@ualberta.ca>, Qian
Michelle Zhou <qz70@msstate.edu>, Bingying Li<dorisli1120@gmail.com>
Maintainer: Hengrui Cai <hengruicai@gmail.com>
Diff between APtools versions 5.1 dated 2018-07-16 and 6.8.8 dated 2018-09-21
APtools-5.1/APtools/R/APtools.R |only APtools-5.1/APtools/man/APtools.Rd |only APtools-6.8.8/APtools/DESCRIPTION | 18 +- APtools-6.8.8/APtools/MD5 | 22 +- APtools-6.8.8/APtools/NAMESPACE | 2 APtools-6.8.8/APtools/R/APBinary.R | 256 +++++++++++++++++---------------- APtools-6.8.8/APtools/R/APSurv.R | 166 ++++++++++----------- APtools-6.8.8/APtools/R/CompareAP.R | 165 +++++++++++---------- APtools-6.8.8/APtools/R/sum.I.R | 38 ++-- APtools-6.8.8/APtools/man/APBinary.Rd | 4 APtools-6.8.8/APtools/man/APSurv.Rd | 212 +++++++++++++-------------- APtools-6.8.8/APtools/man/CompareAP.Rd | 220 +++++++++++++--------------- APtools-6.8.8/APtools/man/mayo.Rd | 12 - 13 files changed, 567 insertions(+), 548 deletions(-)