Title: Robust Change-Point Tests
Description: Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. One can detect changes in location, scale and dependence structure of a possibly multivariate time series. Procedures are based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <arXiv:1905.06201>.
Author: Sheila Goerz [aut, cre],
Alexander Duerre [aut]
Maintainer: Sheila Goerz <sheila.goerz@tu-dortmund.de>
Diff between robcp versions 0.2.5 dated 2020-01-24 and 0.3.0 dated 2021-03-30
robcp-0.2.5/robcp/R/robcp.R |only robcp-0.2.5/robcp/R/robcp2.R |only robcp-0.2.5/robcp/man/h_cumsum.Rd |only robcp-0.2.5/robcp/man/sigma2.Rd |only robcp-0.2.5/robcp/man/teststat.Rd |only robcp-0.2.5/robcp/src/robcp.c |only robcp-0.3.0/robcp/DESCRIPTION | 15 +++++---- robcp-0.3.0/robcp/MD5 | 53 ++++++++++++++++++++++++-------- robcp-0.3.0/robcp/NAMESPACE | 17 ++++++---- robcp-0.3.0/robcp/R/CUSUM.R |only robcp-0.3.0/robcp/R/RcppExports.R |only robcp-0.3.0/robcp/R/huber_cusum.R |only robcp-0.3.0/robcp/R/lrv.R |only robcp-0.3.0/robcp/R/medianDiff.R |only robcp-0.3.0/robcp/R/modifChol.R |only robcp-0.3.0/robcp/R/pBessel.R |only robcp-0.3.0/robcp/R/pKSdist.R |only robcp-0.3.0/robcp/R/psi.R |only robcp-0.3.0/robcp/R/psi_cumsum.R |only robcp-0.3.0/robcp/man/CUSUM.Rd |only robcp-0.3.0/robcp/man/huber_cusum.Rd | 36 +++++++++++++-------- robcp-0.3.0/robcp/man/lrv.Rd |only robcp-0.3.0/robcp/man/medianDiff.Rd |only robcp-0.3.0/robcp/man/modifChol.Rd | 10 +++--- robcp-0.3.0/robcp/man/pKSdist.Rd | 36 +++++++++++---------- robcp-0.3.0/robcp/man/psi.Rd | 30 +++++++++--------- robcp-0.3.0/robcp/man/psi_cumsum.Rd |only robcp-0.3.0/robcp/man/weightedMedian.Rd |only robcp-0.3.0/robcp/man/zeros.Rd | 42 ++++++++++++------------- robcp-0.3.0/robcp/src/CUSUM.c |only robcp-0.3.0/robcp/src/RcppExports.cpp |only robcp-0.3.0/robcp/src/kthPair.cpp |only robcp-0.3.0/robcp/src/lrv.c |only robcp-0.3.0/robcp/src/modifChol.c |only robcp-0.3.0/robcp/src/pKS.c |only robcp-0.3.0/robcp/src/psi.c |only robcp-0.3.0/robcp/tests |only 37 files changed, 143 insertions(+), 96 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of univariate and multivariate spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including models similar to Bernardinelli et al. (1995) <doi:10.1002/sim.4780142112> and Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001>. Full details are given in the vignette accompanying this package. The creation and development of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grants EP/J017442/1 and EP/T004878/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth, Gary Napier and William Pettersson
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 3.1.1 dated 2021-02-04 and 3.2 dated 2021-03-30
CARBayesST-3.1.1/CARBayesST/R/binomial.CARar.R |only CARBayesST-3.1.1/CARBayesST/R/gaussian.CARar.R |only CARBayesST-3.1.1/CARBayesST/R/poisson.CARar.R |only CARBayesST-3.1.1/CARBayesST/src/registerDynamicSymbol.c |only CARBayesST-3.1.1/CARBayesST/tests |only CARBayesST-3.1.1/CARBayesST/vignettes/SMRmap.png |only CARBayesST-3.1.1/CARBayesST/vignettes/salesmap.png |only CARBayesST-3.2/CARBayesST/DESCRIPTION | 16 CARBayesST-3.2/CARBayesST/MD5 | 92 CARBayesST-3.2/CARBayesST/NAMESPACE | 8 CARBayesST-3.2/CARBayesST/R/MVST.CARar.R |only CARBayesST-3.2/CARBayesST/R/RcppExports.R | 144 CARBayesST-3.2/CARBayesST/R/ST.CARar.R | 55 CARBayesST-3.2/CARBayesST/R/W.estimate.R |only CARBayesST-3.2/CARBayesST/R/binomial.CARadaptive.R | 23 CARBayesST-3.2/CARBayesST/R/binomial.CARanova.R | 20 CARBayesST-3.2/CARBayesST/R/binomial.CARar1.R |only CARBayesST-3.2/CARBayesST/R/binomial.CARar2.R |only CARBayesST-3.2/CARBayesST/R/binomial.CARlinear.R | 18 CARBayesST-3.2/CARBayesST/R/binomial.CARlocalised.R | 10 CARBayesST-3.2/CARBayesST/R/binomial.CARsepspatial.R | 16 CARBayesST-3.2/CARBayesST/R/binomial.MVCARar1.R |only CARBayesST-3.2/CARBayesST/R/binomial.MVCARar2.R |only CARBayesST-3.2/CARBayesST/R/coef.CARBayesST.R | 2 CARBayesST-3.2/CARBayesST/R/common.functions.R | 108 CARBayesST-3.2/CARBayesST/R/gaussian.CARadaptive.R | 10 CARBayesST-3.2/CARBayesST/R/gaussian.CARar1.R |only CARBayesST-3.2/CARBayesST/R/gaussian.CARar2.R |only CARBayesST-3.2/CARBayesST/R/gaussian.MVCARar1.R |only CARBayesST-3.2/CARBayesST/R/gaussian.MVCARar2.R |only CARBayesST-3.2/CARBayesST/R/poisson.CARadaptive.R | 19 CARBayesST-3.2/CARBayesST/R/poisson.CARanova.R | 24 CARBayesST-3.2/CARBayesST/R/poisson.CARar1.R |only CARBayesST-3.2/CARBayesST/R/poisson.CARar2.R |only CARBayesST-3.2/CARBayesST/R/poisson.CARlinear.R | 16 CARBayesST-3.2/CARBayesST/R/poisson.CARlocalised.R | 10 CARBayesST-3.2/CARBayesST/R/poisson.CARsepspatial.R | 16 CARBayesST-3.2/CARBayesST/R/poisson.MVCARar1.R |only CARBayesST-3.2/CARBayesST/R/poisson.MVCARar2.R |only CARBayesST-3.2/CARBayesST/build/vignette.rds |binary CARBayesST-3.2/CARBayesST/inst/doc/CARBayesST.R | 30 CARBayesST-3.2/CARBayesST/inst/doc/CARBayesST.Rnw | 164 CARBayesST-3.2/CARBayesST/inst/doc/CARBayesST.pdf |binary CARBayesST-3.2/CARBayesST/man/CARBayesST-package.Rd | 30 CARBayesST-3.2/CARBayesST/man/MVST.CARar.Rd |only CARBayesST-3.2/CARBayesST/man/ST.CARadaptive.Rd | 4 CARBayesST-3.2/CARBayesST/man/ST.CARanova.Rd | 4 CARBayesST-3.2/CARBayesST/man/ST.CARar.Rd | 33 CARBayesST-3.2/CARBayesST/man/ST.CARlinear.Rd | 4 CARBayesST-3.2/CARBayesST/man/ST.CARlocalised.Rd | 4 CARBayesST-3.2/CARBayesST/man/ST.CARsepspatial.Rd | 4 CARBayesST-3.2/CARBayesST/man/W.estimate.Rd |only CARBayesST-3.2/CARBayesST/src/CARBayesST.cpp | 6481 ++++++++++------ CARBayesST-3.2/CARBayesST/src/RcppExports.cpp | 799 + CARBayesST-3.2/CARBayesST/vignettes/CARBayesST.Rnw | 164 CARBayesST-3.2/CARBayesST/vignettes/JSS2728.bib | 9 CARBayesST-3.2/CARBayesST/vignettes/SMRmap.pdf |only CARBayesST-3.2/CARBayesST/vignettes/salesmap.pdf |only 58 files changed, 5174 insertions(+), 3163 deletions(-)
Title: Tools for Creating Swimmers Plots using 'ggplot2'
Description: Used for creating swimmers plots with functions to customize the bars, add points, add lines, add text, and add arrows.
Author: Jessica Weiss <jessica.weiss@uhnresearch.ca>, Wei Xu<Wei.Xu@uhnresearch.ca>
Maintainer: Jessica Weiss <jessica.weiss@uhnresearch.ca>
Diff between swimplot versions 1.1 dated 2021-01-25 and 1.2.0 dated 2021-03-30
DESCRIPTION | 10 MD5 | 38 ++- NAMESPACE | 3 NEWS.md |only R/data.R | 15 + R/swimplot.R | 250 +++++++++++++++++------ README.md |only build/vignette.rds |binary data/ClinicalTrial.RData |binary inst/doc/Introduction.to.swimplot.R | 51 +++- inst/doc/Introduction.to.swimplot.Rmd | 79 +++++-- inst/doc/Introduction.to.swimplot.html | 231 ++++++++++++++++++--- inst/doc/Using.swimplot.to.display.toxicity.R |only inst/doc/Using.swimplot.to.display.toxicity.Rmd |only inst/doc/Using.swimplot.to.display.toxicity.html |only man/ClinicalTrial.Stage.Rd |only man/swimmer_arrows.Rd | 245 +++++++++++----------- man/swimmer_lines.Rd | 5 man/swimmer_plot.Rd | 175 +++++++++------- man/swimmer_points.Rd | 5 man/swimmer_points_from_lines.Rd | 181 ++++++++-------- man/swimmer_text.Rd |only vignettes/Introduction.to.swimplot.Rmd | 79 +++++-- vignettes/Using.swimplot.to.display.toxicity.Rmd |only 24 files changed, 895 insertions(+), 472 deletions(-)
Title: Power Calculations Under Genetic Model Misspecification
Description: Power and sample size calculations for genetic association studies allowing
for misspecification of the model of genetic susceptibility.
"Hum Hered. 2019;84(6):256-271.<doi:10.1159/000508558>. Epub 2020 Jul 28."
Power and/or sample size can be calculated for logistic (case/control study design)
and linear (continuous phenotype) regression models, using additive, dominant,
recessive or degree of freedom coding of the genetic covariate while assuming
a true dominant, recessive or additive genetic effect. In addition, power and
sample size calculations can be performed for gene by environment interactions.
These methods are extensions of Gauderman (2002)
<doi:10.1093/aje/155.5.478> and Gauderman (2002) <doi:10.1002/sim.973>
and are described in:
Moore CM, Jacobson S, Fingerlin TE. Power and Sample Size Calculations
for Genetic Association Studies in the Presence of Genetic Model Misspecification.
American Society of Human Genetics.
October 2018, San Diego.
Author: Camille Moore [aut, cre],
Sean Jacobson [aut]
Maintainer: Camille Moore <moorec@njhealth.org>
Diff between genpwr versions 1.0.3 dated 2021-03-22 and 1.0.4 dated 2021-03-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating
heterogeneous types of data. mixKernel aims at providing methods to combine
kernel for unsupervised exploratory analysis. Different solutions are
provided to compute a meta-kernel, in a consensus way or in a way that
best preserves the original topology of the data. mixKernel also integrates
kernel PCA to visualize similarities between samples in a non linear space
and from the multiple source point of view. Functions to assess and display
important variables are also provided in the package. Jerome Mariette and
Nathalie Villa-Vialaneix (2018) <doi:10.1093/bioinformatics/btx682>.
Author: Jerome Mariette [aut, cre],
Celine Brouard [aut],
Remi Flamary [aut],
Nathalie Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inrae.fr>
Diff between mixKernel versions 0.4 dated 2020-02-26 and 0.5 dated 2021-03-30
mixKernel-0.4/mixKernel/R/ukfs.R |only mixKernel-0.4/mixKernel/man/ukfs.Rd |only mixKernel-0.5/mixKernel/DESCRIPTION | 23 ++-- mixKernel-0.5/mixKernel/MD5 | 43 ++++--- mixKernel-0.5/mixKernel/NAMESPACE | 3 mixKernel-0.5/mixKernel/NEWS | 6 + mixKernel-0.5/mixKernel/R/center.scale.R |only mixKernel-0.5/mixKernel/R/cim.kernel.R | 2 mixKernel-0.5/mixKernel/R/combine.kernels.R | 2 mixKernel-0.5/mixKernel/R/compute.kernel.R | 2 mixKernel-0.5/mixKernel/R/kernel.pca.R | 2 mixKernel-0.5/mixKernel/R/kernel.pca.permute.R | 2 mixKernel-0.5/mixKernel/R/kernels.R | 2 mixKernel-0.5/mixKernel/R/plotVar.kernel.pca.R | 2 mixKernel-0.5/mixKernel/R/select.features.R |only mixKernel-0.5/mixKernel/R/user.guide.R | 2 mixKernel-0.5/mixKernel/R/zzz.R | 8 - mixKernel-0.5/mixKernel/inst/CITATION | 15 +- mixKernel-0.5/mixKernel/inst/doc |only mixKernel-0.5/mixKernel/inst/python/center_scale.py |only mixKernel-0.5/mixKernel/inst/python/kokfs.py |only mixKernel-0.5/mixKernel/inst/python/ukfs.py | 111 ++++++++++---------- mixKernel-0.5/mixKernel/man/center.scale.Rd |only mixKernel-0.5/mixKernel/man/cim.kernel.Rd | 4 mixKernel-0.5/mixKernel/man/combine.kernels.Rd | 4 mixKernel-0.5/mixKernel/man/kernel.pca.permute.Rd | 4 mixKernel-0.5/mixKernel/man/select.features.Rd |only 27 files changed, 128 insertions(+), 109 deletions(-)
Title: Graphical User Interface for the Package 'SPOT'
Description: A graphical user interface for the Sequential Parameter Optimization Toolbox (package 'SPOT').
It includes a quick, graphical setup for spot, interactive 3D plots, export possibilities and more.
Author: Frederik Rehbach [aut, cre],
Martin Zaefferer [aut],
Thomas Bartz-Beielstein [ctb],
Andreas Fischbach [ctb],
Lorenzo Gentile [ctb]
Maintainer: Frederik Rehbach <frederik.rehbach@th-koeln.de>
Diff between spotGUI versions 0.2.1 dated 2018-10-10 and 0.2.3 dated 2021-03-30
spotGUI-0.2.1/spotGUI/README.md |only spotGUI-0.2.3/spotGUI/DESCRIPTION | 11 spotGUI-0.2.3/spotGUI/MD5 | 62 +- spotGUI-0.2.3/spotGUI/NAMESPACE | 1 spotGUI-0.2.3/spotGUI/NEWS | 13 spotGUI-0.2.3/spotGUI/R/getServer.R | 221 +++++++++- spotGUI-0.2.3/spotGUI/R/getUi.R | 35 + spotGUI-0.2.3/spotGUI/R/readHelpFiles.R | 8 spotGUI-0.2.3/spotGUI/R/runSpotGUI.R | 1 spotGUI-0.2.3/spotGUI/R/testFunctions.R | 20 spotGUI-0.2.3/spotGUI/R/xmlDynamicUI.R | 10 spotGUI-0.2.3/spotGUI/inst/config.xml | 31 + spotGUI-0.2.3/spotGUI/inst/slurm.tmpl |only spotGUI-0.2.3/spotGUI/man/LIST_ITEMS_PER_ROW.Rd | 4 spotGUI-0.2.3/spotGUI/man/dot-onAttach.Rd |only spotGUI-0.2.3/spotGUI/man/packageDataEnv.Rd | 4 spotGUI-0.2.3/spotGUI/tests/testthat/testZShinyGui.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/3dimBranin-current |only spotGUI-0.2.3/spotGUI/tests/testthat/tests/3dimBranin.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/basicCreateDOE.R | 6 spotGUI-0.2.3/spotGUI/tests/testthat/tests/basicRunSpot.R | 3 spotGUI-0.2.3/spotGUI/tests/testthat/tests/basicSpotThenDOEThenSPOT.R | 5 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testBranin_RF_LBFGSB_UR.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testFunBranin.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testFunRastrigin.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testGenoud4DimRF-current |only spotGUI-0.2.3/spotGUI/tests/testthat/tests/testGenoud4DimRF.R | 15 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testOnlyRLog.R | 2 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testSmoofBirdFunction-current |only spotGUI-0.2.3/spotGUI/tests/testthat/tests/testSmoofBirdFunction.R | 5 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testWrongEnvironmentFunction.R | 4 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testWrongInputCreateDOE.R | 4 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testWrongInputEvaluatePoints.R | 6 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testWrongInputInBounds.R | 4 spotGUI-0.2.3/spotGUI/tests/testthat/tests/testWrongInputProposeNewPoint.R | 4 35 files changed, 392 insertions(+), 97 deletions(-)
Title: Functions to Work with 'incidence2' Objects
Description: Provides functions to work with 'incidence2' objects, including a
simplified interface for trend fitting and peak estimation. This package is
part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for
outbreak analysis (<https://www.reconverse.org/).
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between i2extras versions 0.0.2 dated 2020-10-30 and 0.1.0 dated 2021-03-30
DESCRIPTION | 24 -- MD5 | 81 ++++-- NAMESPACE | 30 ++ NEWS.md |only R/add_rolling_average.R | 72 +++--- R/bootstrap.R | 112 +++++---- R/dplyr.R | 122 ++++++---- R/estimate_peak.R | 222 ++++++++----------- R/find_peak.R | 75 +++--- R/fit_curve.R | 158 +++++++------ R/fit_model.R |only R/flag_low_counts.R |only R/growth_rate.R | 27 +- R/is_okerr.R | 16 - R/plot_fit.R | 64 ++++- R/plot_rolling_average.R | 41 ++- R/reexports.R |only R/utils.R | 50 +++- README.md | 23 - build/vignette.rds |binary inst/doc/fitting_epicurves.R | 24 -- inst/doc/fitting_epicurves.Rmd | 26 +- inst/doc/fitting_epicurves.html | 396 ++++++++++++++-------------------- inst/doc/peak_estimation.R | 8 inst/doc/peak_estimation.Rmd | 8 inst/doc/peak_estimation.html | 384 ++++++++++++++++++++++---------- man/NA_counts_.Rd |only man/add_rolling_average.Rd | 8 man/bootstrap.Rd | 21 - man/brms_model.Rd |only man/estimate_peak.Rd | 38 +-- man/find_peak.Rd | 29 +- man/fit_curve.Rd | 11 man/fit_model.Rd |only man/flag_low_counts.Rd |only man/glm_model.Rd |only man/glm_nb_model.Rd |only man/growth_rate.Rd | 14 + man/incidence.Rd |only man/is_okerr.Rd | 14 - man/lm_model.Rd |only man/plot.incidence2_fit.Rd | 10 man/plot.incidence2_rolling.Rd | 8 tests/testthat/test-bootstrap.R | 61 ++--- tests/testthat/test-flag_low_counts.R |only tests/testthat/test-rolling_average.R | 2 vignettes/fitting_epicurves.Rmd | 26 +- vignettes/peak_estimation.Rmd | 8 48 files changed, 1251 insertions(+), 962 deletions(-)
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.4.0 dated 2021-03-22 and 1.4.1 dated 2021-03-30
styler-1.4.0/styler/inst/WORDLIST |only styler-1.4.0/styler/man/ensure_correct_str_txt.Rd |only styler-1.4.0/styler/man/identify_insufficiently_parsed_strings.Rd |only styler-1.4.1/styler/DESCRIPTION | 11 styler-1.4.1/styler/MD5 | 36 +- styler-1.4.1/styler/NAMESPACE | 1 styler-1.4.1/styler/NEWS.md | 9 styler-1.4.1/styler/R/parse.R | 65 ++--- styler-1.4.1/styler/R/transform-block.R | 2 styler-1.4.1/styler/R/ui-styling.R | 43 ++- styler-1.4.1/styler/R/utils-cache.R | 6 styler-1.4.1/styler/inst/doc/customizing_styler.html | 6 styler-1.4.1/styler/inst/hooks |only styler-1.4.1/styler/man/ensure_correct_txt.Rd |only styler-1.4.1/styler/man/is_insufficiently_parsed_string.Rd |only styler-1.4.1/styler/man/style_dir.Rd | 8 styler-1.4.1/styler/man/style_file.Rd | 11 styler-1.4.1/styler/man/style_pkg.Rd | 10 styler-1.4.1/styler/man/style_text.Rd | 14 - styler-1.4.1/styler/tests/testthat/test-cache-high-level-api.R | 2 styler-1.4.1/styler/tests/testthat/test-cache-interaction-base-indention.R | 130 ++++++++++ styler-1.4.1/styler/tests/testthat/test-parsing.R | 11 22 files changed, 292 insertions(+), 73 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox
regression models using lasso or nonconvex penalties, in particular the
minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD)
penalty, with options for additional L2 penalties (the "elastic net" idea).
Utilities for carrying out cross-validation as well as post-fitting
visualization, summarization, inference, and prediction are also provided.
For more information, see Breheny and Huang (2011) <doi:10.1214/10-AOAS388>
or visit the ncvreg homepage <https://pbreheny.github.io/ncvreg/>.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>)
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.12.0 dated 2020-07-09 and 3.13.0 dated 2021-03-30
DESCRIPTION | 14 ++++--- MD5 | 55 ++++++++++++++------------- NEWS.md | 6 +++ R/auc.R | 17 +++++--- R/cv-ncvreg.R | 1 R/ncvfit.R | 83 ++++++++++++++++++++++++++++++------------ R/ncvreg.R | 1 README.md | 10 ++--- build/partial.rdb |only build/vignette.rds |binary inst/doc/getting-started.html | 18 +++++++-- inst/doc/getting-started.rmd | 4 +- inst/tinytest/ncvfit.R | 16 ++++++++ man/Prostate.Rd | 2 - man/cv-ncvreg.Rd | 20 ++++++---- man/ncvfit.Rd | 67 +++++++++++++++++++++++++-------- man/ncvreg-package.Rd | 16 +++++--- man/ncvreg.Rd | 14 ++++--- man/ncvsurv.Rd | 6 +-- man/plot-cv-ncvreg.Rd | 10 +++-- man/plot-ncvreg.Rd | 10 +++-- man/predict-ncvsurv.Rd | 13 ++++-- man/predict.Rd | 10 +++-- man/summary-cv-ncvreg.Rd | 10 +++-- src/ncvreg_init.c | 4 +- src/rawfit_gaussian.c | 42 ++++++++++++--------- tests/test.R | 2 - vignettes/getting-started.rmd | 4 +- vignettes/web/models.rmd | 2 - 29 files changed, 305 insertions(+), 152 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of linear
regression, GLM, and Cox regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge. For more
information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>,
Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang
(2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015)
<doi:10.1111/biom.12300>, or visit the package homepage
<https://pbreheny.github.io/grpreg/>.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>),
Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.3.0 dated 2020-06-10 and 3.3.1 dated 2021-03-30
grpreg-3.3.0/grpreg/NEWS |only grpreg-3.3.0/grpreg/inst/tests |only grpreg-3.3.1/grpreg/DESCRIPTION | 23 ++++--- grpreg-3.3.1/grpreg/MD5 | 67 +++++++++++----------- grpreg-3.3.1/grpreg/NEWS.md |only grpreg-3.3.1/grpreg/R/auc.R | 10 ++- grpreg-3.3.1/grpreg/README.md | 12 +-- grpreg-3.3.1/grpreg/build/partial.rdb |only grpreg-3.3.1/grpreg/build/vignette.rds |binary grpreg-3.3.1/grpreg/inst/doc/getting-started.html | 38 ++++++++++-- grpreg-3.3.1/grpreg/inst/doc/getting-started.rmd | 8 +- grpreg-3.3.1/grpreg/inst/tinytest |only grpreg-3.3.1/grpreg/man/Lung.Rd | 2 grpreg-3.3.1/grpreg/man/auc.Rd | 4 - grpreg-3.3.1/grpreg/man/cv-grpreg.Rd | 2 grpreg-3.3.1/grpreg/man/gBridge.Rd | 14 ++-- grpreg-3.3.1/grpreg/man/grpreg-package.Rd | 38 ++++++------ grpreg-3.3.1/grpreg/man/grpreg.Rd | 34 +++++------ grpreg-3.3.1/grpreg/man/grpsurv.Rd | 39 +++++------- grpreg-3.3.1/grpreg/man/predict-grpsurv.Rd | 4 - grpreg-3.3.1/grpreg/src/gdfit_gaussian.c | 1 grpreg-3.3.1/grpreg/tests/test.R | 2 grpreg-3.3.1/grpreg/vignettes/getting-started.rmd | 8 +- grpreg-3.3.1/grpreg/vignettes/web/penalties.rmd | 10 +-- 24 files changed, 175 insertions(+), 141 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] (<https://orcid.org/0000-0002-9807-4686>),
Edwin de Jonge [aut] (<https://orcid.org/0000-0002-6580-4718>),
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.0.1 dated 2020-12-08 and 1.0.2 dated 2021-03-30
DESCRIPTION | 10 ++--- MD5 | 51 ++++++++++++++----------- NAMESPACE | 1 NEWS | 19 +++++++++ R/compare.R | 7 +++ R/confrontation.R | 17 +++++--- R/expressionset.R | 33 ++++++++++++++-- R/indicator.R | 30 ++++++--------- R/sugar.R | 7 +++ R/syntax.R | 49 ++++++++++++++++++++++++ R/utils.R | 12 +++--- build/vignette.rds |binary inst/CITATION | 33 +++++++++++----- inst/doc/JSS_3483.Rnw | 2 - inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.R | 8 ++-- inst/doc/cookbook.Rmd | 26 ++++++++++--- inst/doc/cookbook.html | 76 ++++++++++++++++++++++---------------- inst/tinytest/test_gh_issue_109.R |only inst/tinytest/test_gh_issue_112.R |only inst/tinytest/test_gh_issue_128.R |only inst/tinytest/test_syntax.R | 2 - man/is_unique.Rd | 6 +++ man/occurs.Rd |only man/satisfying.Rd | 12 +++--- vignettes/JSS_3483.Rnw | 2 - vignettes/cookbook.Rmd | 26 ++++++++++--- vignettes/jss3483.pdf |binary vignettes/v97i10.pdf |only 29 files changed, 299 insertions(+), 130 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>),
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.30 dated 2021-03-04 and 0.31 dated 2021-03-30
DESCRIPTION | 17 ++++++++++------- MD5 | 14 +++++++------- R/latex.R | 17 ++++++++++++----- R/tlmgr.R | 18 ++++++++++++------ man/check_installed.Rd | 4 ++-- man/latexmk.Rd | 5 +++-- man/tlmgr.Rd | 3 ++- tests/test-cran/test-latex.R | 8 ++++++++ 8 files changed, 56 insertions(+), 30 deletions(-)
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 0.2.2 dated 2020-11-12 and 1.0.0 dated 2021-03-30
incidence2-0.2.2/incidence2/R/arg_to_values.R |only incidence2-0.2.2/incidence2/R/check_boundaries.R |only incidence2-0.2.2/incidence2/R/check_dates.R |only incidence2-0.2.2/incidence2/R/check_interval.R |only incidence2-0.2.2/incidence2/R/check_presence.R |only incidence2-0.2.2/incidence2/R/check_timespan.R |only incidence2-0.2.2/incidence2/R/check_week.R |only incidence2-0.2.2/incidence2/R/get_interval.R |only incidence2-0.2.2/incidence2/R/get_n.R |only incidence2-0.2.2/incidence2/R/get_timespan.R |only incidence2-0.2.2/incidence2/R/get_week.R |only incidence2-0.2.2/incidence2/R/group_dates.R |only incidence2-0.2.2/incidence2/R/make_breaks.R |only incidence2-0.2.2/incidence2/R/make_incidence.R |only incidence2-0.2.2/incidence2/R/scale_x_incidence.R |only incidence2-0.2.2/incidence2/R/trim_observations.R |only incidence2-0.2.2/incidence2/R/utils-pipe.R |only incidence2-0.2.2/incidence2/R/valid_interval.R |only incidence2-0.2.2/incidence2/man/pipe.Rd |only incidence2-0.2.2/incidence2/man/pool.Rd |only incidence2-0.2.2/incidence2/tests/testthat/Rplots.pdf |only incidence2-0.2.2/incidence2/tests/testthat/test-non-exported.R |only incidence2-0.2.2/incidence2/tests/testthat/test-standards.R |only incidence2-1.0.0/incidence2/DESCRIPTION | 38 incidence2-1.0.0/incidence2/MD5 | 113 - incidence2-1.0.0/incidence2/NAMESPACE | 52 incidence2-1.0.0/incidence2/NEWS.md | 14 incidence2-1.0.0/incidence2/R/accessors.R | 214 +- incidence2-1.0.0/incidence2/R/cumulate.R | 26 incidence2-1.0.0/incidence2/R/dplyr.R | 66 incidence2-1.0.0/incidence2/R/incidence.R | 646 +++--- incidence2-1.0.0/incidence2/R/keep.R |only incidence2-1.0.0/incidence2/R/make_grate.R |only incidence2-1.0.0/incidence2/R/plot.R | 403 ++-- incidence2-1.0.0/incidence2/R/print.R | 36 incidence2-1.0.0/incidence2/R/regroup.R | 59 incidence2-1.0.0/incidence2/R/summary.R | 36 incidence2-1.0.0/incidence2/R/utils.R |only incidence2-1.0.0/incidence2/R/zzz.R | 15 incidence2-1.0.0/incidence2/build/vignette.rds |binary incidence2-1.0.0/incidence2/inst/doc/Introduction.R | 47 incidence2-1.0.0/incidence2/inst/doc/Introduction.Rmd | 72 incidence2-1.0.0/incidence2/inst/doc/Introduction.html | 252 +- incidence2-1.0.0/incidence2/inst/doc/customizing_incidence_plots.R | 23 incidence2-1.0.0/incidence2/inst/doc/customizing_incidence_plots.Rmd | 37 incidence2-1.0.0/incidence2/inst/doc/customizing_incidence_plots.html | 200 -- incidence2-1.0.0/incidence2/inst/doc/handling_incidence_objects.R | 68 incidence2-1.0.0/incidence2/inst/doc/handling_incidence_objects.Rmd | 84 incidence2-1.0.0/incidence2/inst/doc/handling_incidence_objects.html | 585 ++---- incidence2-1.0.0/incidence2/man/accessors.Rd | 81 incidence2-1.0.0/incidence2/man/cumulate.Rd | 1 incidence2-1.0.0/incidence2/man/deprecated-accessors.Rd |only incidence2-1.0.0/incidence2/man/get_interval.Rd |only incidence2-1.0.0/incidence2/man/incidence.Rd | 173 - incidence2-1.0.0/incidence2/man/keep.Rd |only incidence2-1.0.0/incidence2/man/plot.incidence2.Rd | 53 incidence2-1.0.0/incidence2/man/regroup.Rd | 4 incidence2-1.0.0/incidence2/tests/testthat/_snaps/incidence.md | 959 +++++++--- incidence2-1.0.0/incidence2/tests/testthat/_snaps/period.new.md |only incidence2-1.0.0/incidence2/tests/testthat/_snaps/plots |only incidence2-1.0.0/incidence2/tests/testthat/test-accessors.R | 37 incidence2-1.0.0/incidence2/tests/testthat/test-conversions.R | 4 incidence2-1.0.0/incidence2/tests/testthat/test-cumulate.R | 38 incidence2-1.0.0/incidence2/tests/testthat/test-dplyr.R | 179 - incidence2-1.0.0/incidence2/tests/testthat/test-incidence.R | 912 +++++---- incidence2-1.0.0/incidence2/tests/testthat/test-keep.R |only incidence2-1.0.0/incidence2/tests/testthat/test-plots.R |only incidence2-1.0.0/incidence2/tests/testthat/test-regroup.R | 26 incidence2-1.0.0/incidence2/vignettes/Introduction.Rmd | 72 incidence2-1.0.0/incidence2/vignettes/customizing_incidence_plots.Rmd | 37 incidence2-1.0.0/incidence2/vignettes/handling_incidence_objects.Rmd | 84 71 files changed, 3065 insertions(+), 2681 deletions(-)
Title: Simulate Admixture of Genomes
Description: Individual-based simulations forward in time,
simulating how patterns in ancestry along the genome change after
admixture. Full description can be found in Janzen (2020)
<doi:10.1101/2020.10.19.343491>.
Author: Thijs Janzen [aut, cre],
Fernando Diaz G. [ctb],
Richèl J.C. Bilderbeek [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between GenomeAdmixR versions 2.0.2 dated 2021-02-26 and 2.1.1 dated 2021-03-30
DESCRIPTION | 8 MD5 | 26 - inst/doc/Demonstrate_isofemales.html | 333 ++++----------------- inst/doc/Empirical_data.html | 467 ++++++++---------------------- inst/doc/Joyplots.html | 277 ++---------------- inst/doc/Visualization.html | 214 -------------- inst/doc/Walkthrough.html | 533 +++++++++++------------------------ man/GenomeAdmixR-package.Rd | 2 src/Makevars | 2 src/RcppExports.cpp | 5 src/helper_functions.cpp | 33 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-fst.R | 6 tests/testthat/test-utilities.R | 1 14 files changed, 476 insertions(+), 1431 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: An R package that provides the EMU Speech
Database Management System (EMU-SDMS) with database management, data
extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between emuR versions 2.1.1 dated 2020-09-30 and 2.2.0 dated 2021-03-30
DESCRIPTION | 10 MD5 | 53 NAMESPACE | 2 NEWS.md | 18 R/cr.R | 2 R/emuR-bundleList.R | 98 + R/emuR-create_seglists.R | 180 +- R/emuR-dataDocs.R | 2 R/emuR-database.flatfiledata.R |only R/emuR-emuDBhandle.R | 2 R/emuR-emuRsegs.R | 4 R/emuR-export_TextGridCollection.R | 194 +-- R/emuR-get_trackdata.R | 5 R/emuR-plotting.R |only R/emuR-query.database.R | 1476 ++++++++--------------- R/emuR-requery.database.R | 235 ++- R/emuR-server.R | 70 - R/misc.R | 2 inst/js |only man/create_spectrogram_image_as_raster.Rd |only man/crplot.Rd | 2 man/demo.vowels.fm.Rd | 2 man/query.Rd | 29 man/requery_hier.Rd | 2 man/requery_seq.Rd | 2 man/sortmatrix.Rd | 2 man/write_bundleList.Rd | 13 tests/testthat/test_emuR-database.flatfiledata.R |only tests/testthat/test_emuR-get_trackdata.R | 582 ++++----- tests/testthat/test_emuR-query.database.R | 108 + 30 files changed, 1452 insertions(+), 1643 deletions(-)
Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.7.2 dated 2021-01-22 and 2.7.3 dated 2021-03-30
DESCRIPTION | 18 +++++++++++------- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/WDI.R | 44 ++++++++++++++++++++++++-------------------- tests/testthat/test-all.R | 6 +++--- 5 files changed, 47 insertions(+), 34 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <http://spark.apache.org>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>),
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] (<https://orcid.org/0000-0003-1469-9396>),
Wil Davis [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparklyr versions 1.6.1 dated 2021-03-23 and 1.6.2 dated 2021-03-30
DESCRIPTION | 7 ++--- MD5 | 28 ++++++++++----------- NAMESPACE | 2 + NEWS.md | 15 +++++++++++ R/connection_spark.R | 11 +++++++- R/dplyr_spark.R | 20 ++++++++++++++- R/install_spark.R | 2 - R/livy_connection.R | 2 - R/livy_install.R | 2 - R/spark_compile.R | 2 - R/tidyr_fill.R | 61 ++++++++++++++++++++++++++++++++--------------- R/utils.R | 16 ++++++++++++ README.md | 8 +++--- build/partial.rdb |binary man/spark-connections.Rd | 11 +++++++- 15 files changed, 139 insertions(+), 48 deletions(-)
Title: Transformation Models with Mixed Effects
Description: Likelihood-based estimation of mixed-effects transformation models using the Template
Model Builder (TMB, Kristensen et al., 2016, <doi:10.18637/jss.v070.i05>). The technical details
of transformation models are given in Hothorn et al. (2018, <doi:10.1111/sjos.12291>). Likelihood
contributions of exact, randomly censored (left, right, interval) and truncated observations are
supported. The random effects are assumed to be normally distributed on the scale of the
transformation function, the marginal likelihood is evaluated using the Laplace approximation,
and the gradients are calculated with automatic differentiation (AD).
Author: Balint Tamasi [aut, cre] (<https://orcid.org/0000-0002-2629-7362>),
Torsten Hothorn [ctb] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Balint Tamasi <balint.tamasi@uzh.ch>
Diff between tramME versions 0.0.4 dated 2021-02-04 and 0.1.0 dated 2021-03-30
tramME-0.0.4/tramME/R/utils.R |only tramME-0.0.4/tramME/man/dot-check_coef.Rd |only tramME-0.0.4/tramME/man/dot-check_varcov.Rd |only tramME-0.0.4/tramME/man/dot-dummy_ctm.Rd |only tramME-0.0.4/tramME/man/dot-mlt_data.Rd |only tramME-0.0.4/tramME/man/dot-paridx.Rd |only tramME-0.0.4/tramME/man/dot-re_data.Rd |only tramME-0.0.4/tramME/man/dot-renames.Rd |only tramME-0.0.4/tramME/man/dot-subbars.Rd |only tramME-0.0.4/tramME/man/dot-tramME.Rd |only tramME-0.0.4/tramME/man/refit.tramME.Rd |only tramME-0.0.4/tramME/src/tramME.cpp |only tramME-0.0.4/tramME/tests/LmME.Rout.save |only tramME-0.0.4/tramME/tests/basics.Rout.save |only tramME-0.0.4/tramME/tests/methods.Rout.save |only tramME-0.0.4/tramME/tests/predict.Rout.save |only tramME-0.0.4/tramME/tests/simulate.Rout.save |only tramME-0.0.4/tramME/tests/test_util.Rout.save |only tramME-0.1.0/tramME/DESCRIPTION | 16 tramME-0.1.0/tramME/MD5 | 198 +- tramME-0.1.0/tramME/NAMESPACE | 41 tramME-0.1.0/tramME/NEWS.md | 23 tramME-0.1.0/tramME/R/AaregME.R |only tramME-0.1.0/tramME/R/LmME.R |only tramME-0.1.0/tramME/R/SurvregME.R |only tramME-0.1.0/tramME/R/lpterms.R |only tramME-0.1.0/tramME/R/methods.R | 1065 ++++++++------ tramME-0.1.0/tramME/R/models.R | 725 +++++---- tramME-0.1.0/tramME/R/predict.R | 241 ++- tramME-0.1.0/tramME/R/simulate.R | 168 +- tramME-0.1.0/tramME/R/trafo.R | 44 tramME-0.1.0/tramME/R/tramTMB.R |only tramME-0.1.0/tramME/R/util.R |only tramME-0.1.0/tramME/build/vignette.rds |binary tramME-0.1.0/tramME/demo |only tramME-0.1.0/tramME/inst/doc/tramME.R | 1747 ++++++++++++---------- tramME-0.1.0/tramME/inst/doc/tramME.Rnw | 1749 ++++++++++++----------- tramME-0.1.0/tramME/inst/doc/tramME.pdf |binary tramME-0.1.0/tramME/man/AaregME.Rd |only tramME-0.1.0/tramME/man/BoxCoxME.Rd | 31 tramME-0.1.0/tramME/man/ColrME.Rd | 34 tramME-0.1.0/tramME/man/CoxphME.Rd | 31 tramME-0.1.0/tramME/man/LehmannME.Rd | 31 tramME-0.1.0/tramME/man/LmME.Rd | 29 tramME-0.1.0/tramME/man/PolrME.Rd | 34 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tramME-0.1.0/tramME/tests/SurvregME.R |only tramME-0.1.0/tramME/tests/basics.R | 132 - tramME-0.1.0/tramME/tests/methods.R | 301 +++ tramME-0.1.0/tramME/tests/predict.R | 149 + tramME-0.1.0/tramME/tests/simulate.R | 66 tramME-0.1.0/tramME/tests/test_util.R | 27 tramME-0.1.0/tramME/tests/tramTMB.R |only tramME-0.1.0/tramME/vignettes/tramME.Rnw | 1749 ++++++++++++----------- 139 files changed, 5338 insertions(+), 3836 deletions(-)
Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on
an additive model where non-linear trends are fit with yearly, weekly, and
daily seasonality, plus holiday effects. It works best with time series
that have strong seasonal effects and several seasons of historical data.
Prophet is robust to missing data and shifts in the trend, and typically
handles outliers well.
Author: Sean Taylor [cre, aut],
Ben Letham [aut]
Maintainer: Sean Taylor <sjtz@pm.me>
Diff between prophet versions 0.6.1 dated 2020-04-29 and 1.0 dated 2021-03-30
DESCRIPTION | 20 +- MD5 | 53 +++--- NAMESPACE | 2 R/diagnostics.R | 273 ++++++++++++++++++++++++++--------- R/plot.R | 40 ++++- R/prophet.R | 94 +++++++++--- R/utilities.R |only R/zzz.R | 5 build/vignette.rds |binary data/generated_holidays.rda |binary inst/doc/quick_start.R | 14 - inst/doc/quick_start.html | 67 +++----- inst/stan/prophet.stan | 36 ++-- man/cross_validation.Rd | 20 ++ man/flat_growth_init.Rd |only man/flat_trend.Rd |only man/linear_growth_init.Rd | 2 man/mdape.Rd |only man/performance_metrics.Rd | 12 - man/prophet.Rd | 4 man/regressor_coefficients.Rd |only man/rolling_median_by_h.Rd |only man/set_date.Rd | 9 - man/single_cutoff_forecast.Rd |only man/smape.Rd |only src/Makevars | 10 - src/Makevars.win | 11 - src/stanExports_prophet.h | 230 +++++++++++++++++++++-------- tests/testthat/test_diagnostics.R | 68 +++++++- tests/testthat/test_prophet.R | 23 ++ tests/testthat/test_stan_functions.R | 2 tests/testthat/test_utilities.R |only 32 files changed, 707 insertions(+), 288 deletions(-)
Title: Data and Tools for Analyzing the Pali Canon
Description: Provides access to the complete Pali Canon, or
Tipitaka, the canonical scripture for Theravadin Buddhists
worldwide. Based on the Chattha Sangayana Tipitaka version
4 (Vipassana Research Institute, 1990).
Author: Dan Zigmond [aut, cre]
Maintainer: Dan Zigmond <djz@shmonk.com>
Diff between tipitaka versions 0.1.1 dated 2020-11-24 and 0.1.2 dated 2021-03-30
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ man/figures/README-dendogram-1.png |binary man/figures/README-freq-by-word-1.png |binary man/figures/README-kmeans-1.png |binary man/figures/README-wordclouds-1.png |binary 7 files changed, 16 insertions(+), 11 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.5.0 dated 2018-11-14 and 0.6.0 dated 2021-03-30
packrat-0.5.0/packrat/tests/testthat/repo-empty |only packrat-0.5.0/packrat/tests/testthat/repo/src/contrib/packrat/packrat_0.4.9-15.tar.gz |only packrat-0.6.0/packrat/DESCRIPTION | 6 packrat-0.6.0/packrat/MD5 | 95 ++-- packrat-0.6.0/packrat/R/aaa-globals.R | 6 packrat-0.6.0/packrat/R/available-packages.R | 4 packrat-0.6.0/packrat/R/available-updates.R | 69 +++ packrat-0.6.0/packrat/R/bitbucket.R | 51 +- packrat-0.6.0/packrat/R/cache.R | 4 packrat-0.6.0/packrat/R/dependencies.R | 135 ++++-- packrat-0.6.0/packrat/R/descfile.R | 1 packrat-0.6.0/packrat/R/downloader.R | 7 packrat-0.6.0/packrat/R/gitlab.R |only packrat-0.6.0/packrat/R/hooks.R | 2 packrat-0.6.0/packrat/R/install.R | 17 packrat-0.6.0/packrat/R/library-support.R | 2 packrat-0.6.0/packrat/R/options.R | 5 packrat-0.6.0/packrat/R/packrat-mode.R | 2 packrat-0.6.0/packrat/R/packrat.R | 8 packrat-0.6.0/packrat/R/paths.R | 14 packrat-0.6.0/packrat/R/pkg.R | 176 +++++--- packrat-0.6.0/packrat/R/restore.R | 210 ++++++++-- packrat-0.6.0/packrat/R/snapshot.R | 20 packrat-0.6.0/packrat/R/testthat-helpers.R | 14 packrat-0.6.0/packrat/R/utils.R | 47 +- packrat-0.6.0/packrat/README.md | 20 packrat-0.6.0/packrat/inst/resources/init-rprofile.R | 2 packrat-0.6.0/packrat/inst/resources/init.R | 6 packrat-0.6.0/packrat/inst/resources/mac_r_userlib.sh | 6 packrat-0.6.0/packrat/man/gitlab_pwd.Rd |only packrat-0.6.0/packrat/man/gitlab_user.Rd |only packrat-0.6.0/packrat/man/packrat-mode.Rd | 2 packrat-0.6.0/packrat/tests/testthat/packages/packrat/DESCRIPTION | 5 packrat-0.6.0/packrat/tests/testthat/projects/falsy-bitbucket |only packrat-0.6.0/packrat/tests/testthat/projects/falsy-gitlab |only packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/PACKAGES | 14 packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/PACKAGES.gz |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/PACKAGES.rds |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/bread/bread_1.0.0.tar.gz |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/breakfast/breakfast_1.0.0.tar.gz |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/egg/egg_1.0.0.tar.gz |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/oatmeal/oatmeal_1.0.0.tar.gz |binary packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/packrat/packrat_0.6.0.tar.gz |only packrat-0.6.0/packrat/tests/testthat/repo/src/contrib/toast/toast_1.0.0.tar.gz |binary packrat-0.6.0/packrat/tests/testthat/resources/broken-chunks.Rmd |only packrat-0.6.0/packrat/tests/testthat/resources/descriptions |only packrat-0.6.0/packrat/tests/testthat/resources/loading-packages.R |only packrat-0.6.0/packrat/tests/testthat/test-bundle.R | 5 packrat-0.6.0/packrat/tests/testthat/test-cache.R | 10 packrat-0.6.0/packrat/tests/testthat/test-dependencies.R | 22 + packrat-0.6.0/packrat/tests/testthat/test-gitlab.R |only packrat-0.6.0/packrat/tests/testthat/test-packrat.R | 126 ++++-- packrat-0.6.0/packrat/tests/testthat/test-with_extlib.R | 3 53 files changed, 846 insertions(+), 270 deletions(-)
Title: NHS Data Dictionary Toolset for NHS Lookups
Description: Providing a common set of simplified web scraping tools for working with the NHS Data Dictionary <https://datadictionary.nhs.uk/data_elements_overview.html>.
The intended usage is to access the data elements section of the NHS Data Dictionary to access key lookups.
The benefits of having it in this package are that the lookups are the live lookups on the website and will not need to be maintained.
This package was commissioned by the NHS-R community to provide this consistency of lookups.
The OpenSafely lookups have now been added <https://codelists.opensafely.org/>.
Author: Gary Hutson [aut, cre],
Calum Polwart [aut]
Maintainer: Gary Hutson <g.hutson@nhs.net>
Diff between NHSDataDictionaRy versions 1.2.1 dated 2021-02-17 and 1.2.2 dated 2021-03-30
DESCRIPTION | 18 +++++-- MD5 | 19 ++++---- NAMESPACE | 2 NEWS.md |only R/nhs_data_elements.R | 5 +- R/openSafely_listR.R |only README.md | 23 ++++++---- inst/doc/introduction.R | 25 ++++++---- inst/doc/introduction.Rmd | 35 ++++++++++----- inst/doc/introduction.html | 103 +++++++++++++++++++++++---------------------- man/openSafely_listR.Rd |only vignettes/introduction.Rmd | 35 ++++++++++----- 12 files changed, 160 insertions(+), 105 deletions(-)
More information about NHSDataDictionaRy at CRAN
Permanent link
Title: General Linear Mixed Models for Gene-Level Differential
Expression
Description: Using random and fixed effects to model expression at an individual gene level can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, therefore do not capture interaction terms. This package uses negative binomial mixed effects models to fit gene expression with matched samples. This is particularly useful for investigating changes in gene expression between groups of individuals over time, as seen in: Rivellese F., Surace A.E.A., Goldmann K., Sciacca E., Giorli G., Cubuk C., John C.R., Nerviani A., Fossati-Jimack L., Thorborn G., Humby F., Bombardieri M., Lewis M.J., Pitzalis C. (2021) "Molecular Pathology Profiling of Synovial Tissue Predicts Response to Biologic Treatment in Rheumatoid Arthritis" [Manuscript in preparation].
Author: Myles Lewis [aut] (<https://orcid.org/0000-0001-9365-5345>),
Katriona Goldmann [aut, cre] (<https://orcid.org/0000-0002-9073-6323>),
Elisabetta Sciacca [aut] (<https://orcid.org/0000-0001-7525-1558>),
Cankut Cubuk [ctb] (<https://orcid.org/0000-0003-4646-0849>),
Anna Surace [ctb] (<https://orcid.org/0000-0001-9589-3005>)
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>
Diff between glmmSeq versions 0.0.1 dated 2021-03-11 and 0.1.0 dated 2021-03-30
DESCRIPTION | 10 MD5 | 38 NAMESPACE | 2 NEWS.md | 10 R/fcPlot.R | 156 +- R/glmmGene.R | 57 R/glmmQvals.R | 30 R/glmmSeq.R | 249 +-- R/maPlot.R | 2 README.md | 3 inst/WORDLIST | 9 inst/doc/glmmSeq.R | 83 - inst/doc/glmmSeq.html | 3879 +++++++++++++++++++++++++++----------------------- inst/doc/glmmSeq.rmd | 68 man/fcPlot.Rd | 22 man/glmerApply.Rd | 4 man/glmmGene.Rd | 10 man/glmmQvals.Rd | 9 man/glmmSeq.Rd | 44 vignettes/glmmSeq.rmd | 68 20 files changed, 2685 insertions(+), 2068 deletions(-)
Title: Stability Measures for Feature Selection
Description: An implementation of many measures for the
assessment of the stability of feature selection. Both simple measures
and measures which take into account the similarities between features
are available, see Bommert (2020) <doi:10.17877/DE290R-21906>.
Author: Andrea Bommert [aut, cre] (<https://orcid.org/0000-0002-1005-9351>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Andrea Bommert <bommert@statistik.tu-dortmund.de>
Diff between stabm versions 1.1.4 dated 2020-12-08 and 1.2.0 dated 2021-03-30
DESCRIPTION | 11 +- MD5 | 70 +++++++------- R/bibentries.R | 13 ++ R/plot_features.R | 8 - R/stability_functions_adjusted.R | 14 +- R/stability_functions_corrected.R | 14 +- R/stability_functions_uncorrected.R | 12 +- README.md | 17 +++ build/partial.rdb |binary inst/doc/stabm.R | 118 ++++++++++++++++++++++++ inst/doc/stabm.Rmd | 172 ++++++++++++++++++++++++++++++++++-- inst/doc/stabm.pdf |binary man/plotFeatures.Rd | 2 man/stabilityDavis.Rd | 5 + man/stabilityDice.Rd | 5 + man/stabilityHamming.Rd | 5 + man/stabilityIntersectionCount.Rd | 9 + man/stabilityIntersectionGreedy.Rd | 9 + man/stabilityIntersectionMBM.Rd | 9 + man/stabilityIntersectionMean.Rd | 9 + man/stabilityJaccard.Rd | 5 + man/stabilityKappa.Rd | 5 + man/stabilityLustgarten.Rd | 5 + man/stabilityNogueira.Rd | 5 + man/stabilityNovovicova.Rd | 5 + man/stabilityOchiai.Rd | 5 + man/stabilityPhi.Rd | 5 + man/stabilitySechidis.Rd | 5 + man/stabilitySomol.Rd | 5 + man/stabilityUnadjusted.Rd | 9 + man/stabilityWald.Rd | 5 + man/stabilityYu.Rd | 5 + man/stabilityZucknick.Rd | 5 + man/stabm-package.Rd | 2 vignettes/references.bib | 13 ++ vignettes/stabm.Rmd | 172 ++++++++++++++++++++++++++++++++++-- 36 files changed, 666 insertions(+), 92 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.13.1 dated 2021-03-18 and 0.13.2 dated 2021-03-30
DESCRIPTION | 7 +- MD5 | 82 ++++++++++++++-------------- NEWS.md | 25 ++++++++ R/bootstrap.R | 101 +++++++++++++++++------------------ R/clean.R | 2 R/cli.R | 34 ++++++----- R/dependencies.R | 42 ++++++++++++++ R/extsoft.R | 4 - R/infrastructure.R | 5 + R/init.R | 7 -- R/install.R | 2 R/lockfile.R | 5 + R/purge.R | 2 R/python-virtualenv.R | 2 R/rebuild.R | 2 R/rehash.R | 2 R/remotes.R | 5 + R/report.R |only R/repos.R | 7 +- R/restore.R | 4 - R/retrieve.R | 3 + R/settings.R | 7 ++ R/snapshot.R | 4 - R/status.R | 41 ++++++++++++-- R/tests.R | 4 + R/update.R | 4 - R/upgrade.R | 2 build/vignette.rds |binary inst/doc/docker.html | 4 - inst/doc/local-sources.Rmd | 2 inst/doc/local-sources.html | 2 inst/doc/lockfile.html | 2 inst/doc/renv.html | 6 +- inst/doc/rsconnect.Rmd | 2 inst/doc/rsconnect.html | 2 inst/resources/activate.R | 101 +++++++++++++++++------------------ man/init.Rd | 5 - man/settings.Rd | 2 tests/testthat/resources/targets.R |only tests/testthat/test-dependencies.R | 5 + tests/testthat/test-infrastructure.R | 12 ++++ vignettes/local-sources.Rmd | 2 vignettes/rsconnect.Rmd | 2 43 files changed, 344 insertions(+), 210 deletions(-)
Title: APSIM Next Generation
Description: The Agricultural Production Systems sIMulator ('APSIM') is a widely
used to simulate the agricultural systems for multiple crops. This package
is designed to create, modify and run 'apsimx' files in the 'APSIM' Next
Generation <https://www.apsim.info/>.
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Diff between rapsimng versions 0.1.0 dated 2020-10-13 and 0.2.0 dated 2021-03-30
rapsimng-0.1.0/rapsimng/inst/Models.xml |only rapsimng-0.2.0/rapsimng/DESCRIPTION | 12 rapsimng-0.2.0/rapsimng/MD5 | 56 rapsimng-0.2.0/rapsimng/NAMESPACE | 7 rapsimng-0.2.0/rapsimng/R/cultivar.R | 23 rapsimng-0.2.0/rapsimng/R/json_tree.R |only rapsimng-0.2.0/rapsimng/R/models.R | 53 rapsimng-0.2.0/rapsimng/R/modify.R | 126 rapsimng-0.2.0/rapsimng/R/program.R |only rapsimng-0.2.0/rapsimng/R/simulations.R |only rapsimng-0.2.0/rapsimng/R/utility.R | 11 rapsimng-0.2.0/rapsimng/README.md | 15 rapsimng-0.2.0/rapsimng/build/vignette.rds |binary rapsimng-0.2.0/rapsimng/inst/Models.Rds |only rapsimng-0.2.0/rapsimng/inst/Wheat.json |10311 -------------- rapsimng-0.2.0/rapsimng/inst/doc/modify.R | 1 rapsimng-0.2.0/rapsimng/inst/doc/modify.Rmd | 1 rapsimng-0.2.0/rapsimng/inst/doc/modify.html | 24 rapsimng-0.2.0/rapsimng/inst/doc/sensitivity.R |only rapsimng-0.2.0/rapsimng/inst/doc/sensitivity.Rmd |only rapsimng-0.2.0/rapsimng/inst/doc/sensitivity.html |only rapsimng-0.2.0/rapsimng/inst/wheat.apsimx | 2099 +- rapsimng-0.2.0/rapsimng/man/get_cultivar.Rd | 50 rapsimng-0.2.0/rapsimng/man/get_metfile.Rd |only rapsimng-0.2.0/rapsimng/man/get_parent.Rd |only rapsimng-0.2.0/rapsimng/man/get_simulations.Rd |only rapsimng-0.2.0/rapsimng/man/insert_models.Rd |only rapsimng-0.2.0/rapsimng/man/keep_simulations.Rd |only rapsimng-0.2.0/rapsimng/man/minimum_apsimng.Rd |only rapsimng-0.2.0/rapsimng/man/search_node.Rd | 94 rapsimng-0.2.0/rapsimng/man/set_parameter_value.Rd |only rapsimng-0.2.0/rapsimng/tests/testthat/test-cultivar.R | 5 rapsimng-0.2.0/rapsimng/tests/testthat/test-modify.R | 98 rapsimng-0.2.0/rapsimng/tests/testthat/test-search.R | 6 rapsimng-0.2.0/rapsimng/tests/testthat/test-simulations.R |only rapsimng-0.2.0/rapsimng/tests/testthat/test-tree.R |only rapsimng-0.2.0/rapsimng/vignettes/modify.Rmd | 1 rapsimng-0.2.0/rapsimng/vignettes/sensitivity.Rmd |only 38 files changed, 2475 insertions(+), 10518 deletions(-)
Title: Methods for Calculating Gradient Surface Metrics
Description: Methods for calculating gradient surface metrics for
continuous analysis of landscape features. See github.com/bioXgeo/geodiv to report
bugs or to download the working version of the package.
Author: Annie C. Smith, Phoebe Zarnetske, Kyla Dahlin, Adam Wilson, Andrew Latimer
Maintainer: Annie C. Smith <annie.smith@dnr.wa.gov>
Diff between geodiv versions 0.2.0 dated 2020-09-09 and 1.0.0 dated 2021-03-30
geodiv-0.2.0/geodiv/data/datalist |only geodiv-1.0.0/geodiv/DESCRIPTION | 16 - geodiv-1.0.0/geodiv/MD5 | 124 ++++---- geodiv-1.0.0/geodiv/NAMESPACE | 3 geodiv-1.0.0/geodiv/NEWS.md | 8 geodiv-1.0.0/geodiv/R/aacf.R | 28 - geodiv-1.0.0/geodiv/R/basics.R | 20 - geodiv-1.0.0/geodiv/R/bearingarea.R | 54 +-- geodiv-1.0.0/geodiv/R/focalmetrics.R |only geodiv-1.0.0/geodiv/R/fourier.R | 192 ++++++++---- geodiv-1.0.0/geodiv/R/localsurface.R | 16 - geodiv-1.0.0/geodiv/R/movingwindow.R | 311 +++++++-------------- geodiv-1.0.0/geodiv/R/sdq.R | 4 geodiv-1.0.0/geodiv/R/sfd.R | 4 geodiv-1.0.0/geodiv/R/surfacearea.R | 10 geodiv-1.0.0/geodiv/R/utilities.R | 24 + geodiv-1.0.0/geodiv/R/zshift.R | 4 geodiv-1.0.0/geodiv/build |only geodiv-1.0.0/geodiv/inst |only geodiv-1.0.0/geodiv/man/aacf.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/area_above.Rd | 104 +++---- geodiv-1.0.0/geodiv/man/bearing_area.Rd | 64 ++-- geodiv-1.0.0/geodiv/man/bestfitplane.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/dot-calculate_met_focal.Rd |only geodiv-1.0.0/geodiv/man/dot-maxdist.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/dot-mindist.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/find_flat.Rd | 76 ++--- geodiv-1.0.0/geodiv/man/findpeaks.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/findvalleys.Rd | 72 ++-- geodiv-1.0.0/geodiv/man/fitplane.Rd | 70 ++-- geodiv-1.0.0/geodiv/man/flatsa.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/focal_metrics.Rd |only geodiv-1.0.0/geodiv/man/height_ba.Rd | 58 +-- geodiv-1.0.0/geodiv/man/pad_edges.Rd | 62 ++-- geodiv-1.0.0/geodiv/man/plot_ba_curve.Rd | 72 ++-- geodiv-1.0.0/geodiv/man/remove_plane.Rd | 70 ++-- geodiv-1.0.0/geodiv/man/rotate.Rd |only geodiv-1.0.0/geodiv/man/sa.Rd | 56 +-- geodiv-1.0.0/geodiv/man/sbi.Rd | 52 +-- geodiv-1.0.0/geodiv/man/sci.Rd | 56 +-- geodiv-1.0.0/geodiv/man/scl.Rd | 96 +++--- geodiv-1.0.0/geodiv/man/sdc.Rd | 70 ++-- geodiv-1.0.0/geodiv/man/sdr.Rd | 62 ++-- geodiv-1.0.0/geodiv/man/simpsons.Rd | 92 +++--- geodiv-1.0.0/geodiv/man/sk.Rd | 58 +-- geodiv-1.0.0/geodiv/man/sku.Rd | 66 ++-- geodiv-1.0.0/geodiv/man/slopecalc.Rd | 70 ++-- geodiv-1.0.0/geodiv/man/smean.Rd | 52 +-- geodiv-1.0.0/geodiv/man/sph.Rd | 52 +-- geodiv-1.0.0/geodiv/man/spk.Rd | 58 +-- geodiv-1.0.0/geodiv/man/sq.Rd | 58 +-- geodiv-1.0.0/geodiv/man/srw.Rd | 80 ++--- geodiv-1.0.0/geodiv/man/ssc.Rd | 54 +-- geodiv-1.0.0/geodiv/man/ssk.Rd | 62 ++-- geodiv-1.0.0/geodiv/man/std.Rd | 78 ++--- geodiv-1.0.0/geodiv/man/stxr.Rd | 86 ++--- geodiv-1.0.0/geodiv/man/surface_area.Rd | 68 ++-- geodiv-1.0.0/geodiv/man/sv.Rd | 52 +-- geodiv-1.0.0/geodiv/man/svi.Rd | 56 +-- geodiv-1.0.0/geodiv/man/svk.Rd | 58 +-- geodiv-1.0.0/geodiv/man/texture_image.Rd | 221 +++++++------- geodiv-1.0.0/geodiv/man/window_metric.Rd | 176 ++++------- geodiv-1.0.0/geodiv/man/zshift.Rd | 100 +++--- geodiv-1.0.0/geodiv/tests/testthat/test_inputs.R | 14 geodiv-1.0.0/geodiv/vignettes |only 65 files changed, 1921 insertions(+), 1944 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', 'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 4.3.0 dated 2021-02-20 and 4.3.1 dated 2021-03-30
cobalt-4.3.0/cobalt/build/cobalt.pdf |only cobalt-4.3.1/cobalt/DESCRIPTION | 10 cobalt-4.3.1/cobalt/MD5 | 37 +- cobalt-4.3.1/cobalt/NEWS.md | 6 cobalt-4.3.1/cobalt/R/bal.plot.R | 1 cobalt-4.3.1/cobalt/R/base.bal.tab.R | 4 cobalt-4.3.1/cobalt/R/functions_for_processing.R | 132 ++++--- cobalt-4.3.1/cobalt/R/get.w.R | 18 - cobalt-4.3.1/cobalt/R/x2base.R | 73 ++-- cobalt-4.3.1/cobalt/build/partial.rdb |binary cobalt-4.3.1/cobalt/inst/doc/cobalt.html | 39 +- cobalt-4.3.1/cobalt/inst/doc/cobalt_A1_other_packages.R | 33 + cobalt-4.3.1/cobalt/inst/doc/cobalt_A1_other_packages.Rmd | 3 cobalt-4.3.1/cobalt/inst/doc/cobalt_A1_other_packages.html | 166 ++++------ cobalt-4.3.1/cobalt/inst/doc/cobalt_A2_segmented_data.html | 137 ++++---- cobalt-4.3.1/cobalt/inst/doc/cobalt_A3_longitudinal_treat.html | 21 - cobalt-4.3.1/cobalt/inst/doc/cobalt_A4_love.plot.html | 31 + cobalt-4.3.1/cobalt/man/bal.tab.sbw.Rd | 4 cobalt-4.3.1/cobalt/man/macros/macros.Rd | 9 cobalt-4.3.1/cobalt/vignettes/cobalt_A1_other_packages.Rmd | 3 20 files changed, 403 insertions(+), 324 deletions(-)
Title: Data Sharpening
Description: Functions and data sets inspired by data sharpening -
data perturbation to achieve improved performance in
nonparametric estimation, as described in Choi, E., Hall, P.
and Rousson, V. (2000).
Capabilities for enhanced local linear regression function
and derivative estimation are included, as well as an
asymptotically correct iterated data sharpening estimator
for any degree of local polynomial regression estimation.
A cross-validation-based bandwidth selector is included which,
in concert with the iterated sharpener, will often provide
superior performance, according to a median integrated squared
error criterion. Sample data sets are provided to illustrate
function usage.
Author: W. John Braun <john.braun@ubc.ca>
Maintainer: W.J. Braun <john.braun@ubc.ca>
Diff between sharpData versions 1.3 dated 2021-01-15 and 1.4 dated 2021-03-30
sharpData-1.3/sharpData/src/sharpData.f |only sharpData-1.4/sharpData/DESCRIPTION | 30 +++++++++++++++--------------- sharpData-1.4/sharpData/MD5 | 14 +++++++++----- sharpData-1.4/sharpData/NAMESPACE | 7 ++----- sharpData-1.4/sharpData/R/MonoMat.R | 4 ++-- sharpData-1.4/sharpData/man/LLsharpen.Rd | 6 ++++++ sharpData-1.4/sharpData/src/Makevars |only sharpData-1.4/sharpData/src/afun.f |only sharpData-1.4/sharpData/src/init.c |only sharpData-1.4/sharpData/src/kern.f |only sharpData-1.4/sharpData/src/monomat.h |only 11 files changed, 34 insertions(+), 27 deletions(-)
Title: Difference Benchmarking for Multivariate Small Area Estimation
Description: Implements Benchmarking Method for Multivariate Small Area Estimation under Fay Herriot Model. Multivariate Small Area Estimation (MSAE) is a development of Univariate Small Area Estimation that considering the correlation among response variables and borrowing the strength from related areas and auxiliary variables to increase the effectiveness of sample size, the multivariate model in this package is based on multivariate model 1 proposed by Roberto Benavent and Domingo Morales (2016) <doi:10.1016/j.csda.2015.07.013>. Benchmarking in Small Area Estimation is a modification of Small Area Estimation model to guarantee that the aggregate weighted mean of the county predictors equals the corresponding weighted mean of survey estimates. Difference Benchmarking is the simplest benchmarking method but widely used by multiplying empirical best linear unbiased prediction (EBLUP) estimator by the common adjustment factors (J.N.K Rao and Isabel Molina, 2015).
Author: Zaza Yuda Perwira, Azka Ubaidillah
Maintainer: Zaza Yuda Perwira <221710086@stis.ac.id>
Diff between msaeDB versions 0.1.3 dated 2021-03-03 and 0.2.0 dated 2021-03-30
DESCRIPTION | 6 +++--- MD5 | 33 ++++++++++++++++++++++----------- NAMESPACE | 4 ++++ R/datamsaeDBns.R |only R/msaeDB-Package.R | 8 ++++++-- R/msaedb.R | 4 ++-- R/msaedbns.R |only R/msaefh.R | 2 ++ R/msaefhns.R |only R/saedb.R | 2 ++ R/saedbns.R |only R/saefh.R | 2 ++ R/saefhns.R |only data/datamsaeDBns.rda |only man/datamsaeDBns.Rd |only man/msaedb.Rd | 2 ++ man/msaedbns.Rd |only man/msaefh.Rd | 2 ++ man/msaefhns.Rd |only man/saedb.Rd | 2 ++ man/saedbns.Rd |only man/saefh.Rd | 2 ++ man/saefhns.Rd |only 23 files changed, 51 insertions(+), 18 deletions(-)
Title: Data Sets from Montgomery, Peck and Vining
Description: Most of this package consists of data sets from the
textbook Introduction
to Linear Regression Analysis (3rd ed), by Montgomery, Peck
and Vining.
Some additional data sets and functions are also included.
Author: W.J. Braun and S. MacQueen
Maintainer: W.J. Braun <john.braun@ubc.ca>
Diff between MPV versions 1.56 dated 2021-01-09 and 1.57 dated 2021-03-30
MPV-1.56/MPV/data/Juliet.R |only MPV-1.56/MPV/data/Wpgtemp.R |only MPV-1.56/MPV/data/bp.R |only MPV-1.56/MPV/data/cigbutts.R |only MPV-1.56/MPV/data/earthquake.R |only MPV-1.56/MPV/data/fires.R |only MPV-1.56/MPV/data/gasdata.R |only MPV-1.56/MPV/data/lengthguesses.R |only MPV-1.56/MPV/data/lesions.R |only MPV-1.56/MPV/data/motor.R |only MPV-1.56/MPV/data/noisyimage.R |only MPV-1.56/MPV/data/oldwash.R |only MPV-1.56/MPV/data/pathoeg.R |only MPV-1.56/MPV/data/seismictimings.R |only MPV-1.56/MPV/data/stain.R |only MPV-1.56/MPV/data/tarimage.R |only MPV-1.56/MPV/data/windWin80.R |only MPV-1.57/MPV/DESCRIPTION | 6 ++-- MPV-1.57/MPV/MD5 | 49 ++++++++++++++--------------------- MPV-1.57/MPV/data/Juliet.rda |binary MPV-1.57/MPV/data/Wpgtemp.rda |only MPV-1.57/MPV/data/bp.rda |only MPV-1.57/MPV/data/cigbutts.rda |binary MPV-1.57/MPV/data/earthquake.rda |only MPV-1.57/MPV/data/fires.rda |only MPV-1.57/MPV/data/gasdata.rda |binary MPV-1.57/MPV/data/lengthguesses.rda |binary MPV-1.57/MPV/data/lesions.rda |only MPV-1.57/MPV/data/motor.rda |binary MPV-1.57/MPV/data/noisyimage.rda |binary MPV-1.57/MPV/data/oldwash.rda |binary MPV-1.57/MPV/data/pathoeg.rda |binary MPV-1.57/MPV/data/seismictimings.rda |only MPV-1.57/MPV/data/stain.rda |binary MPV-1.57/MPV/data/tarimage.rda |binary MPV-1.57/MPV/data/tree.sample.rda |only MPV-1.57/MPV/data/windWin80.rda |binary MPV-1.57/MPV/man/tree.sample.Rd |only 38 files changed, 23 insertions(+), 32 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
httr development team [ctb] (Original OAuth listener code),
Scott Holden [ctb] (Advice on AAD authentication),
Chris Stone [ctb] (Advice on AAD authentication),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureAuth versions 1.3.0 dated 2021-01-11 and 1.3.1 dated 2021-03-30
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++++------------- NEWS.md | 7 +++++++ R/AzureAuth.R | 19 ++++++++----------- R/token.R | 18 +++++++++++++----- README.md | 4 +--- build/vignette.rds |binary inst/doc/scenarios.Rmd |only inst/doc/scenarios.html |only inst/doc/token.Rmd | 6 +++--- inst/doc/token.html | 6 +++--- man/AzureR_dir.Rd | 4 ++-- man/get_azure_token.Rd | 14 +++++++++++--- tests/testthat/test11_v1_token_misc.R | 4 ++-- tests/testthat/test21_v2_token_misc.R | 6 +++--- vignettes/images |only vignettes/scenarios.Rmd |only vignettes/token.Rmd | 6 +++--- 18 files changed, 78 insertions(+), 54 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>
Diff between twang versions 1.6 dated 2020-02-27 and 2.0 dated 2021-03-30
twang-1.6/twang/src/kspval.h |only twang-1.6/twang/src/psmirnov2x.c |only twang-2.0/twang/DESCRIPTION | 24 twang-2.0/twang/LICENSE | 1348 ++++++------ twang-2.0/twang/MD5 | 212 + twang-2.0/twang/NAMESPACE | 82 twang-2.0/twang/R/MetricI.R | 14 twang-2.0/twang/R/bal.stat.R | 157 - twang-2.0/twang/R/bal.stat.fast.R |only twang-2.0/twang/R/bal.table.R | 127 - twang-2.0/twang/R/bal.table.hidden.R | 76 twang-2.0/twang/R/bal.table.mnps.R | 225 +- twang-2.0/twang/R/bal.table.ps.R | 4 twang-2.0/twang/R/boxplot.mnps.R | 190 + twang-2.0/twang/R/boxplot.ps.R | 58 twang-2.0/twang/R/calcES.R |only twang-2.0/twang/R/calcKS.R |only twang-2.0/twang/R/cb.evaluation.log.R |only twang-2.0/twang/R/cb.print.evaluation.R |only twang-2.0/twang/R/check.err.R | 70 twang-2.0/twang/R/desc.wts.R | 200 - twang-2.0/twang/R/desc.wts.fast.R |only twang-2.0/twang/R/diag.plot.R | 336 +-- twang-2.0/twang/R/diag.plot.color.R | 410 +-- twang-2.0/twang/R/displayPlots.R | 88 twang-2.0/twang/R/dx.wts.R | 316 +- twang-2.0/twang/R/esStat.R | 170 - twang-2.0/twang/R/gen.bal.data.R |only twang-2.0/twang/R/get.weights.R | 187 - twang-2.0/twang/R/get.weights.num.R | 27 twang-2.0/twang/R/get.weights.unstab.R | 51 twang-2.0/twang/R/iptw.R | 317 +- twang-2.0/twang/R/iptw.fast.R |only twang-2.0/twang/R/iptw.old.R |only twang-2.0/twang/R/ksStat.R | 202 - twang-2.0/twang/R/makePlotDat.R | 274 +- twang-2.0/twang/R/makeWeightsMNPS.R | 28 twang-2.0/twang/R/means.table.R | 183 - twang-2.0/twang/R/mnps.R | 336 +-- twang-2.0/twang/R/mnps.fast.R |only twang-2.0/twang/R/mnps.old.R |only twang-2.0/twang/R/mnps2.R | 636 ++--- twang-2.0/twang/R/pairwiseComp.R | 176 - twang-2.0/twang/R/pairwiseCompForPlot.R | 44 twang-2.0/twang/R/pairwiseComparison.R | 247 +- twang-2.0/twang/R/plot.dxwts.R | 31 twang-2.0/twang/R/plot.iptw.R | 119 - twang-2.0/twang/R/plot.mniptw.R | 138 - twang-2.0/twang/R/plot.mnps.2.R | 530 ++-- twang-2.0/twang/R/plot.mnps.R | 1151 +++++----- twang-2.0/twang/R/plot.ps.R | 62 twang-2.0/twang/R/plotTruePairs.R | 190 - twang-2.0/twang/R/pred.xgboost.R |only twang-2.0/twang/R/print.dxwts.R | 14 twang-2.0/twang/R/print.iptw.R |only twang-2.0/twang/R/print.mniptw.R |only twang-2.0/twang/R/print.mnps.R |only twang-2.0/twang/R/print.ps.R |only twang-2.0/twang/R/print.summary.iptw.R | 33 twang-2.0/twang/R/print.summary.mniptw.R | 34 twang-2.0/twang/R/print.summary.mnps.R | 111 - twang-2.0/twang/R/print.summary.ps.R | 31 twang-2.0/twang/R/ps.R | 531 ++-- twang-2.0/twang/R/ps.fast.R |only twang-2.0/twang/R/ps.old.R |only twang-2.0/twang/R/ps.summary.new.R | 291 +- twang-2.0/twang/R/ps.summary.new2.R | 318 +- twang-2.0/twang/R/sensitivity.R | 842 ++++--- twang-2.0/twang/R/stop.methods.R | 124 - twang-2.0/twang/R/summary.iptw.R | 45 twang-2.0/twang/R/summary.mniptw.R | 34 twang-2.0/twang/R/summary.mnps.R | 89 twang-2.0/twang/R/summary.ps.R | 84 twang-2.0/twang/R/surveytable.R |only twang-2.0/twang/R/twang.R |only twang-2.0/twang/R/zzz.R |only twang-2.0/twang/build/vignette.rds |binary twang-2.0/twang/inst/doc/iptw.R | 315 +- twang-2.0/twang/inst/doc/iptw.pdf |binary twang-2.0/twang/inst/doc/iptw.rnw | 736 +++--- twang-2.0/twang/inst/doc/mnps.R | 526 ++-- twang-2.0/twang/inst/doc/mnps.pdf |binary twang-2.0/twang/inst/doc/mnps.rnw | 1524 +++++++------- twang-2.0/twang/inst/doc/twang.R | 885 +++----- twang-2.0/twang/inst/doc/twang.pdf |binary twang-2.0/twang/inst/doc/twang.rnw | 3002 +++++++++++----------------- twang-2.0/twang/man/bal.stat.Rd | 107 twang-2.0/twang/man/bal.table.Rd | 131 - twang-2.0/twang/man/boxplot.mnps.Rd | 78 twang-2.0/twang/man/boxplot.ps.Rd | 53 twang-2.0/twang/man/displayPlots.Rd |only twang-2.0/twang/man/dx.wts.Rd | 114 - twang-2.0/twang/man/get.weights.Rd | 49 twang-2.0/twang/man/get.weights.num.Rd | 33 twang-2.0/twang/man/get.weights.unstab.Rd | 59 twang-2.0/twang/man/iptw.Rd | 172 + twang-2.0/twang/man/means.table.Rd | 46 twang-2.0/twang/man/mnps.Rd | 235 +- twang-2.0/twang/man/plot.dxwts.Rd |only twang-2.0/twang/man/plot.iptw.Rd |only twang-2.0/twang/man/plot.mniptw.Rd |only twang-2.0/twang/man/plot.mnps.Rd | 139 - twang-2.0/twang/man/plot.ps.Rd | 78 twang-2.0/twang/man/print.dxwts.Rd | 22 twang-2.0/twang/man/print.iptw.Rd |only twang-2.0/twang/man/print.mniptw.Rd |only twang-2.0/twang/man/print.mnps.Rd |only twang-2.0/twang/man/print.ps.Rd |only twang-2.0/twang/man/print.summary.iptw.Rd |only twang-2.0/twang/man/print.summary.mniptw.Rd |only twang-2.0/twang/man/print.summary.mnps.Rd |only twang-2.0/twang/man/print.summary.ps.Rd |only twang-2.0/twang/man/ps.Rd | 296 +- twang-2.0/twang/man/raceprofiling.Rd | 2 twang-2.0/twang/man/sensitivity.Rd | 56 twang-2.0/twang/man/stop.methods.Rd | 37 twang-2.0/twang/man/summary.iptw.Rd |only twang-2.0/twang/man/summary.mniptw.Rd |only twang-2.0/twang/man/summary.mnps.Rd | 31 twang-2.0/twang/man/summary.ps.Rd | 29 twang-2.0/twang/man/twang-package.Rd |only twang-2.0/twang/src/init.c | 35 twang-2.0/twang/src/ks.c |only twang-2.0/twang/src/ks.h |only twang-2.0/twang/vignettes/iptw.rnw | 736 +++--- twang-2.0/twang/vignettes/mnps.rnw | 1524 +++++++------- twang-2.0/twang/vignettes/twang.rnw | 3002 +++++++++++----------------- 127 files changed, 12955 insertions(+), 12714 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. This packaged is described by
Collyer & Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] (<https://orcid.org/0000-0003-0238-2201>),
Dean Adams [aut] (<https://orcid.org/0000-0001-9172-7894>)
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 0.6.2 dated 2021-01-11 and 1.0.0 dated 2021-03-30
RRPP-0.6.2/RRPP/man/print.classify.Rd |only RRPP-0.6.2/RRPP/man/summary.classify.Rd |only RRPP-1.0.0/RRPP/DESCRIPTION | 21 - RRPP-1.0.0/RRPP/MD5 | 35 + RRPP-1.0.0/RRPP/NAMESPACE | 8 RRPP-1.0.0/RRPP/NEWS.md | 10 RRPP-1.0.0/RRPP/R/RRPP.support.code.r | 239 ++++++++++--- RRPP-1.0.0/RRPP/R/RRPP.utils.r | 69 +-- RRPP-1.0.0/RRPP/R/RcppExports.R |only RRPP-1.0.0/RRPP/R/coef.lm.rrpp.r | 9 RRPP-1.0.0/RRPP/R/convert2ggplot.r |only RRPP-1.0.0/RRPP/R/lm.rrpp.r | 72 ++- RRPP-1.0.0/RRPP/R/ordinate.r | 8 RRPP-1.0.0/RRPP/R/shared.support.code.r | 13 RRPP-1.0.0/RRPP/build/vignette.rds |binary RRPP-1.0.0/RRPP/inst/doc/ANOVA.vs.MANOVA.html | 276 ++------------- RRPP-1.0.0/RRPP/inst/doc/Using.RRPP.html | 472 ++++++++------------------ RRPP-1.0.0/RRPP/man/RRPP-package.Rd | 5 RRPP-1.0.0/RRPP/man/convert2ggplot.Rd |only RRPP-1.0.0/RRPP/man/lm.rrpp.Rd | 24 - RRPP-1.0.0/RRPP/tests |only 21 files changed, 534 insertions(+), 727 deletions(-)
Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique
for determining the overall within-individual relationship among paired measures
assessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence
interval including optional bootstrapping, as well as graphing. Also includes
several example datasets. For more details, see Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash, Laura R. Marusich
Maintainer: Laura R. Marusich <laura.m.cooper20.civ@mail.mil>
Diff between rmcorr versions 0.4.1 dated 2020-08-26 and 0.4.2 dated 2021-03-30
rmcorr-0.4.1/rmcorr/inst/doc/Combined_paper_figures.R |only rmcorr-0.4.1/rmcorr/inst/doc/Combined_paper_figures.Rmd |only rmcorr-0.4.1/rmcorr/inst/doc/Combined_paper_figures.html |only rmcorr-0.4.1/rmcorr/vignettes/Combined_paper_figures.Rmd |only rmcorr-0.4.2/rmcorr/DESCRIPTION | 11 rmcorr-0.4.2/rmcorr/MD5 | 42 rmcorr-0.4.2/rmcorr/NEWS.md | 5 rmcorr-0.4.2/rmcorr/R/rmcorr-package.R | 2 rmcorr-0.4.2/rmcorr/R/rmcorr.R | 22 rmcorr-0.4.2/rmcorr/build/partial.rdb |binary rmcorr-0.4.2/rmcorr/build/vignette.rds |binary rmcorr-0.4.2/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.R |only rmcorr-0.4.2/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.Rmd |only rmcorr-0.4.2/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.html |only rmcorr-0.4.2/rmcorr/man/rmcorr-package.Rd | 2 rmcorr-0.4.2/rmcorr/man/rmcorr.Rd | 2 rmcorr-0.4.2/rmcorr/vignettes/New_rmcorr_paper_analyses_figures.Rmd |only rmcorr-0.4.2/rmcorr/vignettes/plots/AppendixC_Figure1.eps | 991 ++++------ rmcorr-0.4.2/rmcorr/vignettes/plots/AppendixC_Figure1.pdf |only rmcorr-0.4.2/rmcorr/vignettes/plots/AppendixC_Figure2.eps | 327 +-- rmcorr-0.4.2/rmcorr/vignettes/plots/AppendixC_Figure2.pdf |only rmcorr-0.4.2/rmcorr/vignettes/plots/Figure1_Rmcorr_vs_reg.pdf |binary rmcorr-0.4.2/rmcorr/vignettes/plots/Figure2_Rmcorr_vs_OLS.pdf |binary rmcorr-0.4.2/rmcorr/vignettes/plots/Figure3_Transformations.pdf |binary rmcorr-0.4.2/rmcorr/vignettes/plots/Figure4_Power_curve.pdf |only rmcorr-0.4.2/rmcorr/vignettes/plots/Figure5_Volume_Age.pdf |binary rmcorr-0.4.2/rmcorr/vignettes/plots/Figure6_Visual_Search.pdf |binary rmcorr-0.4.2/rmcorr/vignettes/plots/Figure_rmcorr_diagnostic.pdf |only 28 files changed, 706 insertions(+), 698 deletions(-)
Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest'
algorithm used to impute mixed-type data sets by chaining random
forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012)
<doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the
lightning fast random jungle package 'ranger'. Between the iterative
model fitting, we offer the option of using predictive mean matching.
This firstly avoids imputation with values not already present in the
original data (like a value 0.3334 in 0-1 coded variable). Secondly,
predictive mean matching tries to raise the variance in the resulting
conditional distributions to a realistic level. This would allow e.g.
to do multiple imputation when repeating the call to missRanger(). A
formula interface allows to control which variables should be imputed
by which.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between missRanger versions 2.1.1 dated 2021-03-20 and 2.1.3 dated 2021-03-30
DESCRIPTION | 19 MD5 | 12 NEWS.md | 6 inst/doc/censored_variables.html | 380 +++++------------- inst/doc/missRanger.html | 770 ++++++++++++++------------------------ inst/doc/multiple_imputation.html | 354 ++++------------- tests/testthat/test-missRanger.R | 36 - 7 files changed, 537 insertions(+), 1040 deletions(-)
Title: Molecular Detection Mapping and Analysis Platform
Description: Runs a Shiny web application that merges raw 'qPCR' fluorescence data with related
metadata to visualize species presence/absence detection patterns and assess data quality.
The application calculates threshold values from raw fluorescence data using a method based
on the second derivative method, Luu-The et al (2005) <doi:10.2144/05382RR05>, and utilizes
the ‘chipPCR’ package by Rödiger, Burdukiewicz, & Schierack (2015) <doi:10.1093/bioinformatics/btv205>
to calculate Cq values. The application has the ability to connect to a custom developed MySQL
database to populate the applications interface. The application allows users to interact with
visualizations such as a dynamic map, amplification curves and standard curves, that allow for
zooming and/or filtering. It also enables the generation of customized exportable reports based
on filtered mapping data.
Author: Alka Benawra <alkabenawra@rogers.com>
Maintainer: Alka Benawra <alkabenawra@rogers.com>
Diff between MDMAPR versions 0.2.0 dated 2021-03-05 and 0.2.1 dated 2021-03-30
DESCRIPTION | 9 ++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/qPCRFileTransformation.R | 4 +++- R/shinyAppServer.R | 1 + README.md | 38 +++++++++++++++++++++++++++++++++++--- 6 files changed, 49 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-08 3.0.0
2019-10-02 2.0.0
2019-07-03 1.7.5
2018-10-30 1.7
2018-06-29 1.6
2017-12-05 1.4
2017-12-01 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-16 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-09 0.4.0
2020-12-16 0.3.0
2020-09-28 0.2.0
2020-02-19 0.1.5
2020-02-05 0.1.4
2019-10-29 0.1.3
2019-08-26 0.1.2
2019-08-01 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-05 0.2.0
2020-11-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-01 0.5.3