Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept
that was created by CS-UCR
<http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] (<https://orcid.org/0000-0002-5301-8672>),
Michael Yeh [res, ccp, ctb] (<https://orcid.org/0000-0002-9807-2963>),
Diego Silva [res, ccp, ctb] (<https://orcid.org/0000-0002-5184-9413>),
Yan Zhu [res, ccp, ctb] (<https://orcid.org/0000-0002-5952-2108>),
Hoang Dau [res, ccp, ctb] (<https://orcid.org/0000-0003-2439-5185>),
Michele Linardi [res, ccp, ctb]
(<https://orcid.org/0000-0002-3249-2068>)
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between tsmp versions 0.4.8 dated 2020-02-28 and 0.4.11 dated 2020-03-14
DESCRIPTION | 16 +-- MD5 | 40 ++++++--- NEWS | 10 ++ README.md | 8 + build/vignette.rds |binary inst/API-v0.3.1 |only inst/API-v0.3.2 |only inst/API-v0.3.4 |only inst/API-v0.3.5 |only inst/API-v0.4.0 |only inst/API-v0.4.10 |only inst/API-v0.4.11 |only inst/API-v0.4.8 |only inst/API-v0.4.9 |only inst/doc/press.Rmd | 156 +++++++++++++++++++------------------- inst/doc/press.html | 4 man/figures/dependency_plot-1.png |only man/motifs_discords_small.Rd | 4 man/mp_fluss_data.Rd | 6 - man/mp_gait_data.Rd | 4 man/mp_meat_data.Rd | 6 - man/mp_test_data.Rd | 6 - man/mp_toy_data.Rd | 6 - src/mpx.cpp | 36 ++++---- src/windowfunc.cpp | 2 vignettes/press.Rmd | 156 +++++++++++++++++++------------------- 26 files changed, 248 insertions(+), 212 deletions(-)
Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>),
Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>),
Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>),
Mental Health Research UK [fnd],
Wellcome Trust [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between suddengains versions 0.4.2 dated 2020-03-10 and 0.4.3 dated 2020-03-14
DESCRIPTION | 8 - MD5 | 18 +-- NEWS.md | 5 + R/check_interval.R | 4 R/create_bysg.R | 15 +-- R/extract_values.R | 20 +--- R/plot_sg.R | 16 +-- inst/doc/suddengains-tutorial.Rmd | 15 +-- inst/doc/suddengains-tutorial.html | 182 +++++++++++++++---------------------- vignettes/suddengains-tutorial.Rmd | 15 +-- 10 files changed, 135 insertions(+), 163 deletions(-)
Title: Tools for Analyzing Shapes and Patterns
Description: This is (1) An evolving and growing collection of tools for the quantification, assessment, and comparison of shape and pattern. The spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking. The spectra of results are returned in graphic and tabular formats. Additional utility tools for handling data are provided and this package will be added to as more tools are created, cleaned-up, and documented. (2) Provision of tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps. Current limitation is for binary (classes 1, 2) maps that are 64x64 cells in extent. (3) Counting the number of each first-order pattern element and converting that information into both frequency and probability vectors. See Remmel (2018) <doi:10.3390/su10103413> and Remmel and Fortin (2013) <doi:10.1007/s10980-013-9905-x>. NOTE: This is a consolidation of existing packages ('PatternClass', 'ShapePattern') to begin warehousing all shape and pattern code in a common package. Note that all future developments will appear in this package and that 'PatternClass' will eventually be archived.
Author: Tarmo K. Remmel [aut, cre] (<https://orcid.org/0000-0001-6251-876X>),
Marie-Josee Fortin [ctb],
Ferenc Csillag [ctb],
Sandor Kabos [ctb]
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between ShapePattern versions 1.0.1 dated 2016-10-26 and 2.0.2 dated 2020-03-14
DESCRIPTION | 29 ++++++++++++++++++----------- MD5 | 40 ++++++++++++++++++++++++++++++++++------ NAMESPACE | 11 ++++++++--- R/CARsimu.R |only R/KLPQ.R |only R/build.lut.R |only R/buildsurfs.R |only R/doubleplotter.R |only R/findcol.R |only R/findrow.R |only R/imaks.R |only R/patternbits.R |only R/singlemap.R |only R/singleplotter.R |only R/surfplot.R |only R/wi.R |only R/wtest.run.R |only build/partial.rdb |binary data/data.rda |binary man/CARsimu.Rd |only man/KLPQ.Rd |only man/ShapePattern-package.Rd | 29 +++++++++++++++++++++++++++-- man/build.lut.Rd |only man/buildsurfs.Rd |only man/data.Rd | 14 +++++++++----- man/doubleplotter.Rd |only man/findcol.Rd |only man/findrow.Rd |only man/imaks.Rd |only man/patternbits.Rd |only man/singlemap.Rd |only man/singleplotter.Rd |only man/surfplot.Rd |only man/wi.Rd |only man/wtest.run.Rd |only 35 files changed, 96 insertions(+), 27 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:10.1145/1089014.1089020>.
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb],
Steven L. Lee [ctb],
Keith E. Grant [ctb],
Aaron Collier [ctb],
Lawrence E. Banks [ctb],
Steve Smith [ctb],
Cosmin Petra [ctb],
Slaven Peles [ctb],
John Loffeld [ctb],
Dan Shumaker [ctb],
Ulrike Yang [ctb],
James Almgren-Bell [ctb],
Shelby L. Lockhart [ctb],
Hilari C. Tiedeman [ctb],
Ting Yan [ctb],
Jean M. Sexton [ctb],
Chris White [ctb],
Lawrence Livermore National Security [cph],
Southern Methodist University [cph],
INRAE [cph]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 5.0.0-4 dated 2020-01-08 and 5.0.0-7 dated 2020-03-14
DESCRIPTION | 10 +-- MD5 | 20 +++--- NEWS | 22 +++++++ R/RcppExports.R | 68 +++++++++++++++------- build/partial.rdb |binary inst/include/r2sundials.h | 22 +++++-- inst/unitTests/runit.r2cvodes.R | 18 ++--- man/r2cvodes.Rd | 122 +++++++++++++++++++++++++++------------- man/r2sundials-package.Rd | 12 ++- src/r2sundials.cpp | 85 +++++++++++++++++++-------- src/sunlinsol_rmumps.cpp | 1 11 files changed, 261 insertions(+), 119 deletions(-)
Title: Generalised Additive Extreme Value Models
Description: Methods for fitting various extreme value distributions with parameters of generalised additive model (GAM) form are provided. For details of distributions see Coles, S.G. (2001) <doi:10.1007/978-1-4471-3675-0>, GAMs see Wood, S.N. (2017) <doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. & Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>.
Author: Ben Youngman <b.youngman@exeter.ac.uk> [aut, cre]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between evgam versions 0.1.0 dated 2020-03-08 and 0.1.1 dated 2020-03-14
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NEWS |only R/data.R | 2 +- R/generic.R | 9 +++++---- R/nohelp.R | 2 +- R/setup_and_fit.R | 4 ++-- man/COprcp.Rd | 8 +++++--- man/FCtmax.Rd | 6 ++++-- man/colplot.Rd | 5 +---- src/aldC.cpp | 2 +- src/gradHess.cpp | 3 --- src/ppC.cpp | 2 -- 13 files changed, 37 insertions(+), 39 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989) <DOI:10.2307/1912557>.
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is partially based on
work supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle [aut, cre],
Dongjun You [aut],
Lennart Schneider [ctb],
Seongho Bae [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.5-2 dated 2018-09-25 and 0.5-3 dated 2020-03-14
nonnest2-0.5-2/nonnest2/README |only nonnest2-0.5-3/nonnest2/DESCRIPTION | 14 ++++++------ nonnest2-0.5-3/nonnest2/MD5 | 22 +++++++++---------- nonnest2-0.5-3/nonnest2/NEWS | 14 ++++++++++++ nonnest2-0.5-3/nonnest2/R/icci.R | 2 - nonnest2-0.5-3/nonnest2/R/llcont.R | 25 --------------------- nonnest2-0.5-3/nonnest2/R/vuongtest.R | 30 +++++++++++++++++++------- nonnest2-0.5-3/nonnest2/README.md |only nonnest2-0.5-3/nonnest2/build/vignette.rds |binary nonnest2-0.5-3/nonnest2/inst/doc/nonnest2.R | 20 ++++++++--------- nonnest2-0.5-3/nonnest2/inst/doc/nonnest2.pdf |binary nonnest2-0.5-3/nonnest2/man/icci.Rd | 2 - nonnest2-0.5-3/nonnest2/man/vuongtest.Rd | 15 ++++++++++--- 13 files changed, 80 insertions(+), 64 deletions(-)
Title: Artificial Neural Networks for Anomaly Detection
Description: Training of neural networks for classification and regression tasks
using mini-batch gradient descent. Special features include a function for
training autoencoders, which can be used to detect anomalies, and some
related plotting functions. Multiple activation functions are supported,
including tanh, relu, step and ramp. For the use of the step and ramp
activation functions in detecting anomalies using autoencoders, see
Hawkins et al. (2002) <doi:10.1007/3-540-46145-0_17>. Furthermore,
several loss functions are supported, including robust ones such as Huber
and pseudo-Huber loss, as well as L1 and L2 regularization. The possible
options for optimization algorithms are RMSprop, Adam and SGD with momentum.
The package contains a vectorized C++ implementation that facilitates
fast training through mini-batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>
Diff between ANN2 versions 2.3.2 dated 2019-04-13 and 2.3.3 dated 2020-03-14
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 7 ++++--- R/plotting.R | 4 ++-- README.md | 2 ++ 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Analysing Equity Portfolios
Description: Classes for analysing and implementing equity portfolios.
Author: Jeff Enos <jeff@kanecap.com> and David Kane <dave@kanecap.com>,
with contributions from Daniel Gerlanc <dgerlanc@gmail.com> and
Kyle Campbell <Kyle.W.Campbell@williams.edu>
Maintainer: Daniel Gerlanc <dgerlanc@enplusadvisors.com>
Diff between portfolio versions 0.4-7 dated 2015-01-29 and 0.5-0 dated 2020-03-14
ChangeLog | 15 ++++++ DESCRIPTION | 15 +++--- MD5 | 43 +++++++++-------- NAMESPACE | 13 ++++- R/map.market.R | 6 +- R/matchedPortfolioCollection.R | 2 R/matchit.R | 4 - R/portfolio.R | 26 +++++----- R/portfolioBasic.R | 62 ++++++++++++++----------- R/tradelist.R | 73 ++++++++++++++++-------------- build/vignette.rds |binary data/assay.RData |binary data/dow.jan.2005.RData |binary data/global.2004.RData |binary inst/doc/matching_portfolio.pdf |binary inst/doc/portfolio.pdf |binary inst/doc/tradelist.pdf |binary tests/map.market.test.R | 10 +++- tests/map.market.test.gt363.RData |only tests/portfolioBasic.exposure.test.R | 14 +++-- tests/portfolioBasic.exposure.test.RData |binary tests/tradelist.calcCandidates.test.R | 2 tests/tradelist.calcCandidates.test.RData |binary 23 files changed, 167 insertions(+), 118 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Project Nayuki [ctb] (Original author of underlying C++ code for
get_circumscribingcircle and lsm_p_circle),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 1.4.2 dated 2020-01-20 and 1.4.3 dated 2020-03-14
landscapemetrics-1.4.2/landscapemetrics/src/get_class_index_map.cpp |only landscapemetrics-1.4.2/landscapemetrics/src/get_class_index_map.h |only landscapemetrics-1.4.2/landscapemetrics/src/get_entropy.cpp |only landscapemetrics-1.4.3/landscapemetrics/DESCRIPTION | 11 landscapemetrics-1.4.3/landscapemetrics/MD5 | 92 landscapemetrics-1.4.3/landscapemetrics/NAMESPACE | 1885 ++++------ landscapemetrics-1.4.3/landscapemetrics/NEWS.md | 319 - landscapemetrics-1.4.3/landscapemetrics/R/RcppExports.R | 206 - landscapemetrics-1.4.3/landscapemetrics/R/get_circumscribingcircle.R | 425 +- landscapemetrics-1.4.3/landscapemetrics/R/get_patches.R | 673 +-- landscapemetrics-1.4.3/landscapemetrics/R/lsm_c_circle_cv.R | 331 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_c_circle_mn.R | 325 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_c_circle_sd.R | 325 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_l_circle_cv.R | 322 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_l_circle_mn.R | 318 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_l_circle_sd.R | 324 - landscapemetrics-1.4.3/landscapemetrics/R/lsm_p_circle.R | 437 +- landscapemetrics-1.4.3/landscapemetrics/R/sample_lsm.R | 1127 +++-- landscapemetrics-1.4.3/landscapemetrics/R/spatialize_lsm.R | 645 +-- landscapemetrics-1.4.3/landscapemetrics/R/window_lsm.R | 1004 ++--- landscapemetrics-1.4.3/landscapemetrics/build/vignette.rds |binary landscapemetrics-1.4.3/landscapemetrics/data/podlasie_ccilc.rda |binary landscapemetrics-1.4.3/landscapemetrics/inst/doc/getstarted.R | 190 - landscapemetrics-1.4.3/landscapemetrics/inst/doc/getstarted.html | 1194 +++--- landscapemetrics-1.4.3/landscapemetrics/man/get_circumscribingcircle.Rd | 39 landscapemetrics-1.4.3/landscapemetrics/man/landscapemetrics.Rd | 1 landscapemetrics-1.4.3/landscapemetrics/man/lsm_c_circle_cv.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_c_circle_mn.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_c_circle_sd.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_l_circle_cv.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_l_circle_mn.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_l_circle_sd.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/lsm_p_circle.Rd | 2 landscapemetrics-1.4.3/landscapemetrics/man/sample_lsm.Rd | 332 - landscapemetrics-1.4.3/landscapemetrics/man/spatialize_lsm.Rd | 19 landscapemetrics-1.4.3/landscapemetrics/man/window_lsm.Rd | 11 landscapemetrics-1.4.3/landscapemetrics/src/RcppExports.cpp | 51 landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_circle.cpp | 184 landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_circle.h |only landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_class_index_map.cpp |only landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_class_index_map.h |only landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_coocurrence_matrix.cpp | 2 landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_coocurrence_matrix_diag.cpp | 2 landscapemetrics-1.4.3/landscapemetrics/src/rcpp_get_entropy.cpp |only landscapemetrics-1.4.3/landscapemetrics/src/rcpp_smallest_circle.cpp |only landscapemetrics-1.4.3/landscapemetrics/src/rcpp_smallest_circle.h |only landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-get-circumscribungcircle.R | 127 landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-get-patches.R | 58 landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-lsm-p-circle.R | 55 landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-rcpp_get_circle.R |only landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-spatialize-lsm.R | 152 landscapemetrics-1.4.3/landscapemetrics/tests/testthat/test-window-lsm.R | 90 52 files changed, 5568 insertions(+), 5722 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.14.1 dated 2020-01-28 and 0.14.2 dated 2020-03-14
DESCRIPTION | 18 MD5 | 84 +- NAMESPACE | 3 NEWS.md | 13 R/emmeans_prediction_data.R | 2 R/get_predictions_glmmTMB.R | 7 R/get_predictions_mixor.R | 114 +- R/get_predictions_vglm.R | 4 R/ggemmeans.R | 20 R/ggpredict.R | 28 R/plot.R | 82 +- R/simulate_predictions.R | 2 R/utils.R | 21 R/utils_check_transformations.R | 38 R/utils_get_data_grid.R | 44 - R/utils_handle_labels.R | 2 R/utils_is_empty.R | 42 - R/utils_set_attr.R | 2 R/utils_typical_value.R | 192 ++-- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggeffects.html | 8 inst/doc/introduction_effectsatvalues.html | 26 inst/doc/introduction_plotcustomize.R | 2 inst/doc/introduction_plotcustomize.Rmd | 2 inst/doc/introduction_plotcustomize.html | 30 inst/doc/introduction_plotmethod.html | 40 - inst/doc/introduction_randomeffects.Rmd | 2 inst/doc/introduction_randomeffects.html | 72 - inst/doc/practical_logisticmixedmodel.html | 18 inst/doc/practical_robustestimation.html | 10 inst/doc/technical_differencepredictemmeans.html | 6 inst/doc/technical_stata.html | 6 man/figures/unnamed-chunk-4-1.png |binary man/figures/unnamed-chunk-5-1.png |binary man/figures/unnamed-chunk-6-1.png |binary man/ggpredict.Rd | 912 +++++++++++------------ tests/testthat/test-Gam2.R | 4 tests/testthat/test-brms-trial.R | 7 tests/testthat/test-zeroinfl.R | 4 vignettes/introduction_plotcustomize.Rmd | 2 vignettes/introduction_randomeffects.Rmd | 2 43 files changed, 1004 insertions(+), 871 deletions(-)
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre] (<https://orcid.org/0000-0002-3591-4203>)
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 0.7.7 dated 2020-03-04 and 0.8.8 dated 2020-03-14
tidyfst-0.7.7/tidyfst/man/mutate_when.Rd |only tidyfst-0.8.8/tidyfst/DESCRIPTION | 20 - tidyfst-0.8.8/tidyfst/MD5 | 108 ++++---- tidyfst-0.8.8/tidyfst/NAMESPACE | 32 ++ tidyfst-0.8.8/tidyfst/R/all_at_if.R | 5 tidyfst-0.8.8/tidyfst/R/arrange_dt.R | 15 - tidyfst-0.8.8/tidyfst/R/complete.R | 64 ++++ tidyfst-0.8.8/tidyfst/R/count_dt.R | 3 tidyfst-0.8.8/tidyfst/R/cummean.R |only tidyfst-0.8.8/tidyfst/R/distinct_dt.R | 27 +- tidyfst-0.8.8/tidyfst/R/dt.R | 20 + tidyfst-0.8.8/tidyfst/R/fst.R | 1 tidyfst-0.8.8/tidyfst/R/group_by.R |only tidyfst-0.8.8/tidyfst/R/group_dt.R | 30 ++ tidyfst-0.8.8/tidyfst/R/longer_dt.R | 150 ++++++----- tidyfst-0.8.8/tidyfst/R/missing.R | 25 + tidyfst-0.8.8/tidyfst/R/mutate_dt.R | 44 +-- tidyfst-0.8.8/tidyfst/R/mutate_when.R | 62 ++-- tidyfst-0.8.8/tidyfst/R/nest_dt.R | 202 ++++++++++----- tidyfst-0.8.8/tidyfst/R/nth.R |only tidyfst-0.8.8/tidyfst/R/relocate_dt.R |only tidyfst-0.8.8/tidyfst/R/sample.R | 22 + tidyfst-0.8.8/tidyfst/R/select_dt.R | 53 +++- tidyfst-0.8.8/tidyfst/R/separate.R | 4 tidyfst-0.8.8/tidyfst/R/set_dt.R |only tidyfst-0.8.8/tidyfst/R/slice_dt.R | 23 + tidyfst-0.8.8/tidyfst/R/summarise_dt.R | 43 +-- tidyfst-0.8.8/tidyfst/R/sys_time_print.R |only tidyfst-0.8.8/tidyfst/R/topn_dt.R | 68 ++--- tidyfst-0.8.8/tidyfst/R/uncount.R |only tidyfst-0.8.8/tidyfst/R/wider_dt.R | 68 +++-- tidyfst-0.8.8/tidyfst/build/vignette.rds |binary tidyfst-0.8.8/tidyfst/inst/doc/chinese_tutorial.R |only tidyfst-0.8.8/tidyfst/inst/doc/chinese_tutorial.Rmd |only tidyfst-0.8.8/tidyfst/inst/doc/chinese_tutorial.html |only tidyfst-0.8.8/tidyfst/inst/doc/example2_join.Rmd | 2 tidyfst-0.8.8/tidyfst/inst/doc/example2_join.html | 10 tidyfst-0.8.8/tidyfst/inst/doc/example3_reshape.R | 19 - tidyfst-0.8.8/tidyfst/inst/doc/example3_reshape.Rmd | 23 - tidyfst-0.8.8/tidyfst/inst/doc/example3_reshape.html | 251 ++++++++----------- tidyfst-0.8.8/tidyfst/inst/doc/example4_nest.R | 4 tidyfst-0.8.8/tidyfst/inst/doc/example4_nest.Rmd | 4 tidyfst-0.8.8/tidyfst/inst/doc/example4_nest.html | 4 tidyfst-0.8.8/tidyfst/man/all_at_if.Rd | 2 tidyfst-0.8.8/tidyfst/man/cummean.Rd |only tidyfst-0.8.8/tidyfst/man/group_by.Rd |only tidyfst-0.8.8/tidyfst/man/group_dt.Rd | 19 + tidyfst-0.8.8/tidyfst/man/longer_dt.Rd | 75 ++--- tidyfst-0.8.8/tidyfst/man/missing.Rd | 12 tidyfst-0.8.8/tidyfst/man/mutate_vars.Rd |only tidyfst-0.8.8/tidyfst/man/nest.Rd | 99 +++++-- tidyfst-0.8.8/tidyfst/man/nth.Rd |only tidyfst-0.8.8/tidyfst/man/reexports.Rd | 8 tidyfst-0.8.8/tidyfst/man/relocate_dt.Rd |only tidyfst-0.8.8/tidyfst/man/sample.Rd | 20 + tidyfst-0.8.8/tidyfst/man/select.Rd | 24 + tidyfst-0.8.8/tidyfst/man/set.Rd |only tidyfst-0.8.8/tidyfst/man/sys_time_print.Rd |only tidyfst-0.8.8/tidyfst/man/topn.Rd | 25 + tidyfst-0.8.8/tidyfst/man/uncount_dt.Rd |only tidyfst-0.8.8/tidyfst/man/wider_dt.Rd | 44 ++- tidyfst-0.8.8/tidyfst/vignettes/chinese_tutorial.Rmd |only tidyfst-0.8.8/tidyfst/vignettes/example2_join.Rmd | 2 tidyfst-0.8.8/tidyfst/vignettes/example3_reshape.Rmd | 23 - tidyfst-0.8.8/tidyfst/vignettes/example4_nest.Rmd | 4 65 files changed, 1121 insertions(+), 642 deletions(-)
Title: Import Origin(R) Project Files
Description: Read the data from Origin(R) project files ('*.opj')
<https://www.originlab.com/doc/User-Guide/Origin-File-Types>.
No write support is planned.
Author: Miquel Garriga [aut, cph],
Stefan Gerlach [aut, cph],
Ion Vasilief [aut, cph],
Alex Kargovsky [aut, cph],
Knut Franke [ctb, cph],
Alexander Semke [ctb, cph],
Tilman Benkert [ctb, cph],
Kasper Peeters [ctb, cph],
Russell Standish [ctb, cph],
Ivan Krylov [cre, cph]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>
Diff between Ropj versions 0.2-2 dated 2019-03-14 and 0.3 dated 2020-03-14
DESCRIPTION | 11 ++-- MD5 | 32 +++++++------ NAMESPACE | 5 +- NEWS | 9 +++ R/RcppExports.R | 4 - R/read.opj.R |only README.md | 20 ++------ build/partial.rdb |binary inst/tree.opj |only man/Ropj-package.Rd | 10 ---- man/read.opj.Rd | 67 ++++++++++++++++++++-------- src/RcppExports.cpp | 9 ++- src/config.h | 5 +- src/liborigin/OriginAnyParser.cpp | 6 +- src/liborigin/OriginFile.cpp | 13 +++-- src/liborigin/OriginObj.h | 29 +++++------- src/liborigin/README | 11 ---- src/read_opj.cpp | 90 ++++++++++++++++++++++++-------------- 18 files changed, 180 insertions(+), 141 deletions(-)
Title: Easily Obtain Spatial Data and Make Better Maps
Description: One of the remaining pain points in making beautiful maps via
packages like 'rayshader' is both obtaining and processing spatial data
to build from. 'spacey' aims to make it easier to obtain and use this data
for locations within the United States, providing utilities to download
'USGS' and 'ESRI' geospatial data and quickly turn it into maps.
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between spacey versions 0.1.0 dated 2020-02-28 and 0.1.1 dated 2020-03-14
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS.md | 5 ++ R/automap.R | 1 R/get_heightmap.R | 84 +++++++++++++++++++++++------------ R/get_image_overlay.R | 1 inst/doc/introduction-to-spacey.html | 8 +-- man/get_heightmap.Rd | 6 ++ tests/testthat/test-automap.R | 14 ----- 9 files changed, 80 insertions(+), 61 deletions(-)
Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and
Debian-derived Linux systems with a powerful system to resolve package
dependencies. This package offers access directly from R. This can
only work on a system with a suitable 'libapt-pkg-dev' installation
so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAPT versions 0.0.5 dated 2018-09-29 and 0.0.6 dated 2020-03-14
ChangeLog | 17 DESCRIPTION | 8 MD5 | 29 - build/vignette.rds |binary cleanup | 4 configure | 23 - inst/NEWS.Rd | 17 inst/doc/binnmuAfterR340.R | 40 - inst/doc/binnmuAfterR340.html | 938 +++++++++++++++++++++--------------------- inst/scripts/configure.bash |only src/Makevars.in | 2 src/buildDepends.cpp | 17 src/getPackages.cpp | 21 src/hasPackage.cpp | 23 - src/reverseDepends.cpp | 29 - tests/simpleTests.R | 13 16 files changed, 620 insertions(+), 561 deletions(-)
More information about languageserversetup at CRAN
Permanent link
Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'RxODE' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Yuan Xiong [aut],
Rik Schoemaker [aut] (<https://orcid.org/0000-0002-7538-3005>),
Justin Wilkins [aut] (<https://orcid.org/0000-0002-7099-9396>),
Richard Hooijmaijers [aut],
Teun Post [aut],
Robert Leary [ctb],
Wenping Wang [aut, cre],
Hadley Wickham [ctb],
Dirk Eddelbuettel [cph],
Johannes Pfeifer [ctb],
Robert B. Schnabel [ctb],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb],
David Ardia [cph],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Daniel C. Dillon [ctb],
Katharine Mullen [cph],
Ben Goodrich [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between nlmixr versions 1.1.1-5 dated 2020-01-27 and 1.1.1-6 dated 2020-03-14
nlmixr-1.1.1-5/nlmixr/tests/testthat/test-drake.R |only nlmixr-1.1.1-6/nlmixr/DESCRIPTION | 24 - nlmixr-1.1.1-6/nlmixr/MD5 | 42 +- nlmixr-1.1.1-6/nlmixr/NAMESPACE | 4 nlmixr-1.1.1-6/nlmixr/R/000.R | 17 - nlmixr-1.1.1-6/nlmixr/R/bounds.R | 66 ++- nlmixr-1.1.1-6/nlmixr/R/broom.R | 14 nlmixr-1.1.1-6/nlmixr/R/foceiFit.R | 67 ++- nlmixr-1.1.1-6/nlmixr/R/gnlmm.R | 5 nlmixr-1.1.1-6/nlmixr/R/huxtable.R | 6 nlmixr-1.1.1-6/nlmixr/R/nlme_fit.R | 26 - nlmixr-1.1.1-6/nlmixr/R/nlmixr.R | 30 - nlmixr-1.1.1-6/nlmixr/R/npde.R | 2 nlmixr-1.1.1-6/nlmixr/R/saem_fit.R | 42 +- nlmixr-1.1.1-6/nlmixr/R/saem_fit_aux.R | 4 nlmixr-1.1.1-6/nlmixr/R/simulate.R | 24 - nlmixr-1.1.1-6/nlmixr/R/ui.R | 211 +++++++----- nlmixr-1.1.1-6/nlmixr/R/utils.R | 3 nlmixr-1.1.1-6/nlmixr/R/vpc.R | 2 nlmixr-1.1.1-6/nlmixr/R/vpc.ui.R | 4 nlmixr-1.1.1-6/nlmixr/tests/testthat/test-281.R |only nlmixr-1.1.1-6/nlmixr/tests/testthat/test-bounds.R | 352 +++++++++++++++++---- nlmixr-1.1.1-6/nlmixr/tests/testthat/test-piping.R | 40 ++ 23 files changed, 650 insertions(+), 335 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.0.5 dated 2020-02-17 and 1.0.6 dated 2020-03-14
DESCRIPTION | 10 - MD5 | 58 +++--- NAMESPACE | 2 NEWS.md | 11 + R/jsPropensityGadget.R | 24 +- R/kaplan.R | 4 R/roc.R | 415 ++++++++++++++++++++++++++++++++++++++++++ R/timeroc.R | 444 ++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/jsmodule.html | 8 man/GEEModuleLinear.Rd | 12 + man/GEEModuleLogistic.Rd | 12 + man/coxModule.Rd | 16 + man/ggpairsModule.Rd | 11 - man/ggpairsModule2.Rd | 11 - man/kaplanModule.Rd | 17 + man/logistic.display2.Rd | 10 - man/logisticModule.Rd | 15 + man/logisticModule2.Rd | 15 + man/reclassificationJS.Rd | 11 - man/regress.display2.Rd | 10 - man/regressModule.Rd | 15 + man/regressModule2.Rd | 15 + man/rocModule.Rd | 74 +++++++ man/survIDINRI_helper.Rd | 12 + man/tb1module.Rd | 14 + man/tb1module2.Rd | 14 + man/tb1simple.Rd | 13 + man/tb1simple2.Rd | 14 + man/timeROChelper.Rd | 11 - man/timerocModule.Rd | 71 +++++++ 30 files changed, 1264 insertions(+), 105 deletions(-)
Title: Preprocess Data and Get Better Insights from Machine Learning
Models
Description: The main focus is on preprocessing and data visualization of machine learning models performances.
Some functions allow to fill in gaps in time series using linear interpolation on panel data, some functions
permit to draw lift effect and lift curve in order to benchmark machine learning models or you can even find
the optimal number of clusters in agglomerative clustering algorithm.
Author: Simon Corde [aut, cre]
Maintainer: Simon Corde <simon.corde@hotmail.fr>
Diff between helda versions 1.0.0 dated 2020-02-29 and 1.0.1 dated 2020-03-14
helda-1.0.0/helda/tests/testthat/plot_lift_curve_test.Rda |only helda-1.0.0/helda/tests/testthat/plot_lift_effect_test.Rda |only helda-1.0.0/helda/tests/testthat/test-lift_curve.R |only helda-1.0.0/helda/tests/testthat/test-lift_effect.R |only helda-1.0.1/helda/DESCRIPTION | 10 ++-- helda-1.0.1/helda/MD5 | 28 +++++-------- helda-1.0.1/helda/NEWS.md | 4 + helda-1.0.1/helda/R/create_formula.R | 2 helda-1.0.1/helda/data/titanic_testing.RData |binary helda-1.0.1/helda/data/titanic_training.RData |binary helda-1.0.1/helda/data/titanic_validation.RData |binary helda-1.0.1/helda/data/world_countries_pop.RData |binary helda-1.0.1/helda/man/create_formula.Rd | 2 helda-1.0.1/helda/man/titanic_testing.Rd | 6 +- helda-1.0.1/helda/man/titanic_training.Rd | 6 +- helda-1.0.1/helda/man/titanic_validation.Rd | 6 +- helda-1.0.1/helda/man/world_countries_pop.Rd | 6 +- 17 files changed, 39 insertions(+), 31 deletions(-)
Title: Model-Free Functional Chi-Squared and Exact Tests
Description: Statistical hypothesis testing methods for
inferring model-free functional dependency using asymptotic
chi-squared or exact distributions. Functional test
statistics are asymmetric and functionally optimal, unique
from other related statistics. Tests in this package reveal
evidence for causality based on the
causality-by-functionality principle. They include
asymptotic functional chi-squared tests
(Zhang & Song 2013) <arXiv:1311.2707> and an exact
functional test (Zhong & Song 2019)
<doi:10.1109/TCBB.2018.2809743>. The normalized functional
chi-squared test was used by Best Performer 'NMSUSongLab'
in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges (Hill et al 2016) <doi:10.1038/nmeth.3773>. A
function index (Zhong & Song 2019)
<doi:10.1186/s12920-019-0565-9> (Kumar et al 2018)
<doi:10.1109/BIBM.2018.8621502> derived from the
functional test statistic offers a new effect size measure
for the strength of functional dependency, a better
alternative to conditional entropy in many aspects. For
continuous data, these tests offer an advantage over
regression analysis when a parametric functional form
cannot be assumed; for categorical data, they provide a
novel means to assess directional dependency not possible
with symmetrical Pearson's chi-squared or Fisher's exact
tests.
Author: Yang Zhang [aut],
Hua Zhong [aut] (<https://orcid.org/0000-0003-1962-2603>),
Hien Nguyen [aut] (<https://orcid.org/0000-0002-7237-4752>),
Ruby Sharma [aut],
Sajal Kumar [aut] (<https://orcid.org/0000-0003-0930-1582>),
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.4.9.1 dated 2019-09-24 and 2.4.9.2 dated 2020-03-14
FunChisq-2.4.9.1/FunChisq/man/cp.chisq.test.Rd |only FunChisq-2.4.9.2/FunChisq/DESCRIPTION | 27 +- FunChisq-2.4.9.2/FunChisq/MD5 | 44 ++-- FunChisq-2.4.9.2/FunChisq/NEWS | 20 ++ FunChisq-2.4.9.2/FunChisq/R/CPChisq.R | 4 FunChisq-2.4.9.2/FunChisq/README.md | 20 +- FunChisq-2.4.9.2/FunChisq/build/partial.rdb |only FunChisq-2.4.9.2/FunChisq/build/vignette.rds |binary FunChisq-2.4.9.2/FunChisq/inst/CITATION | 54 +---- FunChisq-2.4.9.2/FunChisq/inst/REFERENCES.bib |only FunChisq-2.4.9.2/FunChisq/inst/doc/exact.fun.test.R | 4 FunChisq-2.4.9.2/FunChisq/inst/doc/exact.fun.test.html | 13 - FunChisq-2.4.9.2/FunChisq/inst/doc/fun.chisq.test.html | 11 - FunChisq-2.4.9.2/FunChisq/inst/doc/patterns.R | 18 - FunChisq-2.4.9.2/FunChisq/inst/doc/patterns.html | 27 +- FunChisq-2.4.9.2/FunChisq/man/EFT.Rd | 5 FunChisq-2.4.9.2/FunChisq/man/FunChisq-deprecated.Rd |only FunChisq-2.4.9.2/FunChisq/man/FunChisq-package.Rd | 55 ++++- FunChisq-2.4.9.2/FunChisq/man/cp.fun.chisq.test.Rd | 14 + FunChisq-2.4.9.2/FunChisq/man/fun.chisq.test.Rd | 44 +++- FunChisq-2.4.9.2/FunChisq/man/noise_model.Rd | 6 FunChisq-2.4.9.2/FunChisq/man/simulate_tables.Rd | 16 + FunChisq-2.4.9.2/FunChisq/src/EFT_DQP.cpp | 6 FunChisq-2.4.9.2/FunChisq/src/trimTable.cpp | 32 +-- FunChisq-2.4.9.2/FunChisq/tests/testthat/test_CPChisq.R | 152 ++++++++-------- 25 files changed, 313 insertions(+), 259 deletions(-)
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson [aut, cre],
Gerhard Krennrich [aut]
Maintainer: John Lawson <lawsonjsl7net@gmail.com>
Diff between daewr versions 1.2-2 dated 2020-03-11 and 1.2-3 dated 2020-03-14
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 1 + R/OptPB.R | 2 +- R/PBDes.R |only man/OptPB.Rd | 2 +- man/PBDes.Rd |only 7 files changed, 14 insertions(+), 11 deletions(-)
Title: Optimal, Fast, and Reproducible Univariate Clustering
Description: Fast, optimal, and reproducible weighted univariate
clustering by dynamic programming. Four types of problem including
univariate k-means, k-median, k-segments, and multi-channel
weighted k-means are solved with guaranteed optimality and
reproducibility. The core algorithm minimizes the sum of (weighted)
within-cluster distances using respective metrics. Its advantage
over heuristic clustering in efficiency and accuracy is pronounced
at a large number of clusters k. Weighted k-means can also process
time series to perform peak calling. Multi-channel weighted k-means
groups multiple univariate signals into k clusters. An auxiliary
function generates histograms that are adaptive to patterns in data.
This package provides a powerful set of tools for univariate data
analysis with guaranteed optimality, efficiency, and reproducibility.
Author: Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>),
Hua Zhong [aut] (<https://orcid.org/0000-0003-1962-2603>),
Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 4.3.0 dated 2019-09-07 and 4.3.2 dated 2020-03-14
DESCRIPTION | 16 ++++++++------ MD5 | 43 ++++++++++++++++++++++----------------- NEWS.md | 30 +++++++++++++++++++++++++++ README.md | 20 ++++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 3 -- inst/doc/Ckmeans.1d.dp.R | 18 ++++++++++++---- inst/doc/Ckmeans.1d.dp.Rmd | 18 ++++++++++++++-- inst/doc/Ckmeans.1d.dp.html | 47 +++++++++++++++++++++++++++---------------- inst/doc/Weights.html | 19 +++++++++-------- inst/doc/ahist.R | 14 ++++++------ inst/doc/ahist.html | 35 ++++++++++++++++---------------- man/Ckmeans.1d.dp-package.Rd | 2 - src/Ckmeans.1d.dp.cpp | 12 +++++++++- src/EWL2.h |only src/EWL2_dynamic_prog.cpp |only src/EWL2_fill_SMAWK.cpp |only src/EWL2_fill_log_linear.cpp |only src/EWL2_fill_quadratic.cpp |only src/EWL2_within_cluster.h |only src/fill_SMAWK.cpp | 3 -- src/precision.h |only src/within_cluster.h | 3 -- tests/testthat/test_MC_WUC.R | 17 ++++++++++----- vignettes/Ckmeans.1d.dp.Rmd | 18 ++++++++++++++-- 26 files changed, 217 insertions(+), 101 deletions(-)
More information about rangeModelMetadata at CRAN
Permanent link
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Li F, et al (2019) <doi:10.1158/2159-8290.CD-19-0780> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [ctb],
Hua Zhou [ctb],
Nicole Doudican [ctb],
John Carucci [ctb],
Adriana Heguy [ctb],
Boris Reizis [ctb],
Aristotelis Tsirigos [aut, ctb]
(<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.3.1 dated 2020-02-26 and 1.3.3 dated 2020-03-14
DESCRIPTION | 6 ++-- MD5 | 26 ++++++++++---------- R/F011.make.gene.model.R | 5 +++ R/F016.clust.cond.info.R | 60 +++++++++++++++++++++++++++++++++++++++++++---- R/F018.run.umap.R | 8 +----- R/F022.run.imput.R | 2 - R/F033.cell.type.pred.R | 57 +++++++++++++++++++++++++++++++++++++++++--- R/globalVariables.R | 7 +++++ R/run.anchor.R | 4 ++- R/run.mnn.R | 5 ++- man/cell.type.pred.Rd | 2 - man/clust.cond.info.Rd | 7 +++-- man/make.gene.model.Rd | 3 ++ man/run.umap.Rd | 8 +----- 14 files changed, 155 insertions(+), 45 deletions(-)
Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for simulating large
systems with Gillespie's Stochastic Simulation Algorithm ('SSA').
This package is the spiritual successor to the 'GillespieSSA' package
originally written by Mario Pineda-Krch. Benefits of this package
include major speed improvements (>100x), easier to understand documentation,
and many unit tests that try to ensure the package works as intended.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between GillespieSSA2 versions 0.2.5 dated 2019-08-22 and 0.2.6.1 dated 2020-03-14
DESCRIPTION | 14 ++-- MD5 | 64 ++++++++++---------- NEWS.md | 17 +++++ R/ssa_plot.R | 13 +++- R/ssa_simulation.R | 65 +++++++++++--------- README.md | 49 ++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/an_introduction.R | 12 +-- inst/doc/an_introduction.html | 29 ++++----- inst/doc/converting_from_GillespieSSA.R | 10 +-- inst/doc/converting_from_GillespieSSA.html | 29 ++++----- inst/doc/decaying_dimer.R | 12 +-- inst/doc/decaying_dimer.html | 23 +++---- inst/doc/epi_chain.R | 14 ++-- inst/doc/epi_chain.html | 23 +++---- inst/doc/linear_chain.R | 12 +-- inst/doc/linear_chain.html | 23 +++---- inst/doc/logistic_growth.R | 12 +-- inst/doc/logistic_growth.html | 23 +++---- inst/doc/lotka_predator_prey.R | 12 +-- inst/doc/lotka_predator_prey.html | 23 +++---- inst/doc/radioactive_decay.R | 12 +-- inst/doc/radioactive_decay.html | 23 +++---- inst/doc/rm_predator_prey.R | 12 +-- inst/doc/rm_predator_prey.html | 23 +++---- inst/doc/sir.R | 12 +-- inst/doc/sir.html | 23 +++---- man/autoplot.ssa.Rd | 12 +++ man/compile_reactions.Rd | 20 ++++-- man/reaction.Rd | 8 +- man/ssa.Rd | 90 ++++++++++++++++------------- src/ssa_simulation.cpp | 8 ++ 33 files changed, 399 insertions(+), 323 deletions(-)
Title: L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
Description: Extensive functions for L-moments (LMs) and probability-weighted moments
(PWMs), parameter estimation for distributions, LM computation for distributions, and
L-moment ratio diagrams. Maximum likelihood and maximum product of spacings estimation
are also available. LMs for right-tail and left-tail censoring by known or unknown
threshold and by indicator variable are available. Asymmetric (asy) trimmed LMs
(TL-moments, TLMs) are supported. LMs of residual (resid) and reversed (rev) resid life
are implemented along with 13 quantile function operators for reliability and survival
analyses. Exact analytical bootstrap estimates of order statistics, LMs, and variances-
covariances of LMs are provided. The Harri-Coble Tau34-squared Normality Test is available.
Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail
censoring (RC) encompasses: Asy Exponential (Exp) Power [L], Asy Triangular [L],
Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L],
Gen Extreme Value [L], Gen Lambda [L,TL], Gen Logistic [L), Gen Normal [L],
Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L],
Kumaraswamy [L], Laplace [L], Linear Mean Resid. Quantile Function [L], Normal [L],
3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice/Rician [L],
Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].
Multivariate sample L-comoments (LCMs) are implemented to measure asymmetric associations.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between lmomco versions 2.3.2 dated 2018-09-20 and 2.3.6 dated 2020-03-14
DESCRIPTION | 9 +- MD5 | 172 ++++++++++++++++++++++----------------------- NAMESPACE | 2 NEWS | 40 +++++++++- R/add.lmomco.axis.R | 23 ++++-- R/add.log.axis.R | 8 +- R/f2f.R | 11 ++ R/f2flo.R | 9 +- man/add.lmomco.axis.Rd | 4 - man/add.log.axis.Rd | 9 +- man/are.par.valid.Rd | 2 man/are.paraep4.valid.Rd | 2 man/are.parcau.valid.Rd | 2 man/are.paremu.valid.Rd | 2 man/are.parexp.valid.Rd | 2 man/are.pargam.valid.Rd | 2 man/are.pargep.valid.Rd | 2 man/are.pargev.valid.Rd | 2 man/are.pargld.valid.Rd | 2 man/are.parglo.valid.Rd | 2 man/are.pargno.valid.Rd | 2 man/are.pargov.valid.Rd | 2 man/are.pargpa.valid.Rd | 2 man/are.pargum.valid.Rd | 2 man/are.parkap.valid.Rd | 2 man/are.parkmu.valid.Rd | 2 man/are.parkur.valid.Rd | 2 man/are.parlap.valid.Rd | 2 man/are.parlmrq.valid.Rd | 2 man/are.parln3.valid.Rd | 2 man/are.parnor.valid.Rd | 2 man/are.parpe3.valid.Rd | 2 man/are.parray.valid.Rd | 2 man/are.parrevgum.valid.Rd | 2 man/are.parrice.valid.Rd | 2 man/are.parsla.valid.Rd | 2 man/are.parst3.valid.Rd | 2 man/are.partexp.valid.Rd | 2 man/are.partri.valid.Rd | 2 man/are.parwak.valid.Rd | 2 man/are.parwei.valid.Rd | 2 man/cdfgno.Rd | 2 man/clearforkporosity.Rd | 9 -- man/disfitqua.Rd | 2 man/f2f.Rd | 7 + man/f2flo.Rd | 7 + man/is.aep4.Rd | 2 man/is.cau.Rd | 2 man/is.emu.Rd | 2 man/is.exp.Rd | 2 man/is.gam.Rd | 2 man/is.gep.Rd | 2 man/is.gev.Rd | 2 man/is.gld.Rd | 2 man/is.glo.Rd | 2 man/is.gno.Rd | 2 man/is.gov.Rd | 2 man/is.gpa.Rd | 2 man/is.gum.Rd | 2 man/is.kap.Rd | 2 man/is.kmu.Rd | 2 man/is.kur.Rd | 2 man/is.lap.Rd | 2 man/is.lmrq.Rd | 2 man/is.ln3.Rd | 2 man/is.nor.Rd | 2 man/is.pe3.Rd | 2 man/is.ray.Rd | 2 man/is.revgum.Rd | 2 man/is.rice.Rd | 2 man/is.sla.Rd | 2 man/is.st3.Rd | 2 man/is.texp.Rd | 2 man/is.tri.Rd | 2 man/is.wak.Rd | 2 man/is.wei.Rd | 2 man/tlmrcau.Rd | 2 man/tlmrexp.Rd | 2 man/tlmrgev.Rd | 2 man/tlmrglo.Rd | 2 man/tlmrgno.Rd | 2 man/tlmrgpa.Rd | 2 man/tlmrgum.Rd | 2 man/tlmrln3.Rd | 2 man/tlmrnor.Rd | 2 man/tlmrpe3.Rd | 2 man/tlmrray.Rd | 2 87 files changed, 258 insertions(+), 200 deletions(-)
More information about HighestMedianRules at CRAN
Permanent link
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.4.1 dated 2020-03-06 and 1.4.2 dated 2020-03-14
DESCRIPTION | 10 +-- MD5 | 38 ++++++------- NAMESPACE | 1 R/GenEst.R | 2 R/app_download_functions.R | 29 ---------- R/app_output_utilities.R | 8 -- R/carcass_persistence_figure_functions.R | 2 R/detection_probability_figure_functions.R | 1 R/mortality_figure_functions.R | 7 +- R/searcher_efficiency_figure_functions.R | 22 ++----- R/splits_figure_functions.R | 14 +++- R/splits_functions.R | 11 +++ R/sysdata.rda |binary README.md | 2 inst/doc/GenEstGUI.html | 4 - inst/doc/command-line-example.html | 84 ++++++++++++++--------------- inst/doc/solar-examples.html | 4 - inst/doc/wind-examples.html | 6 +- man/app_download_functions.Rd | 5 - man/plot.splitFull.Rd | 6 +- 20 files changed, 111 insertions(+), 145 deletions(-)
Title: Non-Homogeneous Markov Switching Autoregressive Models
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations. Penalization methods are implemented for Markov Switching Vector Autoregressive Models of order 1 only. Most functions of the package handle missing values.
Author: Valerie Monbet
Maintainer: Valerie Monbet <valerie.monbet@gmail.com>
Diff between NHMSAR versions 1.15 dated 2019-11-22 and 1.16 dated 2020-03-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/simule.nh.MSAR.R | 21 ++++----------------- 3 files changed, 10 insertions(+), 23 deletions(-)
Title: Convert Between 'R' Objects and Javascript Object Notation
(JSON)
Description: Conversions between 'R' objects and Javascript Object Notation (JSON) using
the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
Author: David Cooley [aut, cre],
Chris Muir [ctb]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between jsonify versions 1.0.0 dated 2019-11-03 and 1.1.1 dated 2020-03-14
DESCRIPTION | 14 MD5 | 83 +-- NAMESPACE | 7 NEWS.md | 8 R/RcppExports.R | 12 R/from_json.R | 58 ++ R/pretty.R | 3 R/scratch.R |only R/scratch2.R |only R/to_json.R | 66 ++ README.md | 2 inst/doc/jsonify.R | 28 - inst/doc/jsonify.html | 4 inst/include/jsonify/from_json/api.hpp | 27 + inst/include/jsonify/from_json/from_json.hpp | 35 - inst/include/jsonify/from_json/from_json_utils.hpp | 70 +- inst/include/jsonify/from_json/simplify/simplify.hpp | 144 +++--- inst/include/jsonify/jsonify.hpp | 2 inst/include/jsonify/to_json/api.hpp | 453 ++++++++++++++++++- inst/include/jsonify/to_json/dates/dates.hpp | 101 ++-- inst/include/jsonify/to_json/utils.hpp | 21 inst/include/jsonify/to_json/writers/complex.hpp | 76 ++- inst/include/jsonify/to_json/writers/ndjson.hpp |only inst/include/jsonify/to_json/writers/scalars.hpp | 2 inst/include/jsonify/to_json/writers/simple.hpp | 428 +++++++++++++++-- man/from_ndjson.Rd |only man/to_json.Rd | 18 man/to_ndjson.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 46 + src/from_json.cpp | 6 src/pretty.cpp | 9 src/read_json.cpp | 42 + src/tests.cpp | 2 src/to_json.cpp | 25 - src/validate.cpp | 5 tests/testthat/test-as_json.R | 2 tests/testthat/test-from_json.R | 34 + tests/testthat/test-from_json_simplify.R | 14 tests/testthat/test-from_ndjson.R |only tests/testthat/test-to_json_dataframe.R | 25 - tests/testthat/test-to_json_dates.R | 10 tests/testthat/test-to_json_prettify.R | 4 tests/testthat/test-to_json_vectors.R | 4 tests/testthat/test-to_ndjson.R |only 46 files changed, 1516 insertions(+), 378 deletions(-)
Title: Versatile Curation of Table Metadata
Description: The 'yamlet' package implements a file-based
mechanism for documenting datasets. It reads and writes
YAML-formatted metadata and applies it as data
item attributes. Data and metadata are stored independently
but can be coordinated by using similar file paths with
different extensions. The 'yamlet' dialect is valid 'YAML',
but some conventions are chosen to improve readability.
Defaults and conventions can be over-ridden by the user.
See ?yamlet and ?decorate.data.frame.
See ?read_yamlet ?write_yamlet, and ?io_csv.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.4.2 dated 2020-02-29 and 0.4.6 dated 2020-03-14
DESCRIPTION | 8 +++---- MD5 | 42 ++++++++++++++++++++++---------------- NAMESPACE | 10 +++++++++ R/append_units.R | 14 +++++++++--- R/sub_units.R |only R/xtable.R |only R/yamlet.R | 24 +++++++++++++++++++++ inst/doc/yamlet-introduction.html | 4 +-- man/alias.data.frame.Rd | 2 - man/append_units.Rd | 3 +- man/append_units.data.frame.Rd | 2 - man/append_units.default.Rd | 7 ++++-- man/decorate.Rd | 2 - man/decorate.character.Rd | 2 - man/decorate.data.frame.Rd | 2 - man/decorate.list.Rd | 2 - man/decorations.Rd | 3 +- man/decorations.data.frame.Rd | 2 - man/footnote.Rd |only man/footnote.decorated.Rd |only man/print.decorated.Rd |only man/redecorate.Rd |only man/reexports.Rd | 6 +++-- man/sub_units.Rd |only man/xtable.decorated.Rd |only tests/testthat/test-yamlet.R | 16 +++++++++----- 26 files changed, 107 insertions(+), 44 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8: Google's open source JavaScript and WebAssembly
engine. This package can be compiled either with V8 version 6 and up, a NodeJS
shared library, or the legacy 3.14/3.15 branch of V8.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between V8 versions 3.0.1 dated 2020-01-22 and 3.0.2 dated 2020-03-14
DESCRIPTION | 6 ++--- MD5 | 17 ++++++++------- NEWS | 4 +++ build/partial.rdb |binary inst/doc/npm.html | 38 +++++++++++++---------------------- inst/doc/v8_intro.html | 40 ++++++++++++++----------------------- src/bindings.cpp | 2 - src/legacy/V8.cpp | 2 - tests/testthat/test-encoding.R |only tests/testthat/test_arraybuffers.R | 6 ++++- 10 files changed, 54 insertions(+), 61 deletions(-)
Title: Summarize Data for Publication
Description: A set of tools for preparing and summarizing data for publication purposes. Includes functions for tabulating models, means to produce human-readable summary statistics from raw data, macros for calculating duration of time, and simplistic hypothesis testing tools.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>
Diff between utile.tools versions 0.2.3 dated 2019-12-01 and 0.2.4 dated 2020-03-14
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 3 +++ R/calc.R | 14 ++++++++++---- README.md | 2 +- man/calc_duration.Rd | 5 +++-- 6 files changed, 27 insertions(+), 17 deletions(-)
Title: Enhanced Database Interactivity
Description: Facilitates interaction with ODBC data sources, by remembering and hiding communication settings and supporting parameterised multi-statement SQL with embedded R.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.7.0 dated 2019-11-07 and 0.7.1 dated 2020-03-14
DESCRIPTION | 10 +- MD5 | 12 +- R/SQRL.R | 202 ++++++++++++++++++++++++++++++++--------------- man/SQRL-package.Rd | 14 --- man/sqrlParams.Rd | 11 +- man/sqrlScript.Rd | 2 man/sqrlSource.Rd | 221 ++++++++++++++++++++++++++++------------------------ 7 files changed, 281 insertions(+), 191 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.19 dated 2020-02-03 and 0.10.20 dated 2020-03-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/extension.R | 22 ++++++++++++++++++++++ 4 files changed, 32 insertions(+), 6 deletions(-)
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bs0316@my.unthsc.edu>
Diff between mixIndependR versions 0.2.0 dated 2020-02-11 and 0.2.1 dated 2020-03-14
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 50 ++++++++++++++++++++++++++------------------------ NEWS.md | 9 +++++++++ R/AlleleShare_Table.R | 10 ++++++++-- R/ComposPare_X.R | 4 ++-- R/Dist_SimuChisq.R | 2 +- R/Prop_Pvalue.R |only man/ComposPare_X.Rd | 3 +-- man/Dist_SimuChisq.Rd | 2 +- man/Prop_Pvalue.Rd |only 11 files changed, 62 insertions(+), 44 deletions(-)
Title: Discriminant Adaptive Nearest Neighbor Classification
Description: Discriminant Adaptive Nearest Neighbor Classification is a
variation of k nearest neighbors where the neighborhood is elongated
along class boundaries. This package implements dann and sub_dann from
Hastie (1995) <https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between dann versions 0.1.0 dated 2019-12-10 and 0.2.0 dated 2020-03-14
DESCRIPTION | 20 +++++++++------- MD5 | 47 ++++++++++++++++++++++----------------- NAMESPACE | 2 + R/RcppExports.R |only R/dann-package.R |only R/dann.R | 27 ++++++++++++---------- R/graph_eigenvalues.R | 5 +++- R/internal_helpers.R | 5 ++++ R/sub_dann.R | 18 ++++++++++---- README.md | 24 +++++++------------ inst/doc/dann.R | 3 +- inst/doc/dann.Rmd | 3 +- inst/doc/dann.html | 26 +++++++++------------ inst/doc/sub_dann.R | 16 ++++++++----- inst/doc/sub_dann.Rmd | 16 ++++++++----- inst/doc/sub_dann.html | 33 ++++++++++++++------------- man/dann.Rd | 6 ++++ man/figures/README-Circle-1.png |binary man/figures/README-Cluster-1.png |binary man/graph_eigenvalues.Rd | 5 +++- man/sub_dann.Rd | 18 ++++++++++---- src |only vignettes/dann.Rmd | 3 +- vignettes/sub_dann.Rmd | 16 ++++++++----- 24 files changed, 173 insertions(+), 120 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 1.0-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-14 1.2.1
2019-04-15 1.2.0
2018-04-24 1.1.0
2018-01-22 1.0.1
2018-01-16 1.0.0