Title: Particle Tracking and Demography
Description: Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in evolutionary and ecological studies.
Author: Marjolein Bruijning, Marco D. Visser, Caspar A. Hallmann, Eelke Jongejans
Maintainer: Marjolein Bruijning <mbruijning@princeton.edu>
Diff between trackdem versions 0.5.1 dated 2020-01-21 and 0.5.2 dated 2020-02-27
DESCRIPTION | 10 +++--- MD5 | 18 +++++----- R/identifyFunctions.R | 2 - R/simulationFunctions.R | 77 +++++++++++++++++++++++------------------------ R/trackFunctions.R | 65 +++++++++++++++++++++++++++------------ inst/doc/tutorial.pdf |binary man/identifyParticles.Rd | 2 - man/mergeTracks.Rd | 6 +++ man/simulTrajec.Rd | 16 ++++----- man/trackParticles.Rd | 10 +++++- 10 files changed, 121 insertions(+), 85 deletions(-)
Title: Factor Adjusted Robust Multiple Testing
Description: Performs robust multiple testing for means in the presence of known and unknown latent factors (Fan et al., 2019).
It implements a series of adaptive Huber methods combined with fast data-drive tuning schemes (Ke et al., 2019) to estimate model parameters and construct test statistics that are robust against heavy-tailed and/or asymmetric error distributions.
Extensions to two-sample simultaneous mean comparison problems are also included.
As by-products, this package also contains functions that compute adaptive Huber mean and covariance matrix estimators that are of independent interest.
Author: Xiaoou Pan [aut, cre],
Yuan Ke [aut],
Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between FarmTest versions 2.0.0 dated 2020-01-13 and 2.0.1 dated 2020-02-27
FarmTest-2.0.0/FarmTest/man/FarmTest.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestFac.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestFacBoot.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwo.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwoFac.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwoFacBoot.Rd |only FarmTest-2.0.0/FarmTest/man/getRej.Rd |only FarmTest-2.0.0/FarmTest/man/huberCov.Rd |only FarmTest-2.0.0/FarmTest/man/huberMean.Rd |only FarmTest-2.0.0/FarmTest/man/rmTest.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestBoot.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestTwo.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestTwoBoot.Rd |only FarmTest-2.0.1/FarmTest/DESCRIPTION | 23 + FarmTest-2.0.1/FarmTest/MD5 | 40 +- FarmTest-2.0.1/FarmTest/NAMESPACE | 1 FarmTest-2.0.1/FarmTest/R/FarmTest-package.R |only FarmTest-2.0.1/FarmTest/R/FarmTest.R | 95 +----- FarmTest-2.0.1/FarmTest/R/RcppExports.R | 115 -------- FarmTest-2.0.1/FarmTest/R/generateNs.R |only FarmTest-2.0.1/FarmTest/README.md | 14 - FarmTest-2.0.1/FarmTest/man/FarmTest-package.Rd |only FarmTest-2.0.1/FarmTest/man/farm.cov.Rd | 2 FarmTest-2.0.1/FarmTest/man/farm.fdr.Rd | 4 FarmTest-2.0.1/FarmTest/man/farm.test.Rd | 22 + FarmTest-2.0.1/FarmTest/src/FarmTest.cpp | 299 +++++----------------- FarmTest-2.0.1/FarmTest/src/Makevars | 4 FarmTest-2.0.1/FarmTest/src/Makevars.win | 4 FarmTest-2.0.1/FarmTest/src/RcppExports.cpp | 18 + 29 files changed, 189 insertions(+), 452 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel
hydraulics. Provides functions for computing normal and critical depths,
steady-state water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.2-1 dated 2019-03-12 and 1.2-2 dated 2020-02-27
DESCRIPTION | 10 MD5 | 43 - NAMESPACE | 2 NEWS.md | 15 R/route_wave_v4.r | 1 build/vignette.rds |binary inst/doc/publication-reproduction.R | 4 inst/doc/publication-reproduction.html | 990 ++++++++++++++++----------------- inst/doc/quickstart.R | 12 inst/doc/quickstart.html | 126 ++-- inst/doc/technical-vignette.R | 2 inst/doc/technical-vignette.html | 20 man/channel_geom.Rd | 76 +- man/compute_profile.Rd | 156 ++--- man/conveyance.Rd | 56 - man/critical_depth.Rd | 78 +- man/demo_shiny.Rd | 52 - man/figures |only man/froude.Rd | 76 +- man/normal_depth.Rd | 88 +- man/rivr-package.Rd | 30 - man/route_wave.Rd | 256 ++++---- man/waterolympics.Rd | 76 +- 23 files changed, 1114 insertions(+), 1055 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre],
Adam Elder [aut],
Hyunju Son [aut],
Zonglin He [aut],
Tao Yang [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2019.11-30 dated 2019-12-02 and 2020.2-26 dated 2020-02-27
ChangeLog | 47 +++ DESCRIPTION | 8 MD5 | 40 +- NAMESPACE | 10 R/chngpt.test.R | 2 R/chngptm.R | 526 +++++++++++++++++++++++----------- R/double.hinge.R | 174 ++++++++--- R/sim.chngpt.R | 40 +- data/nutrition.rda |only inst/doc/chngpt-vignette.pdf |binary inst/unitTests/runit.chngptm.linear.R | 94 ++++-- inst/unitTests/runit.double.hinge.R | 17 - man/chngptm.Rd | 47 +-- man/convert.coef.Rd |only man/double.hinge.Rd | 70 +++- man/nutrition.Rd |only man/sim.chngpt.Rd | 29 - src/M10.cc | 10 src/M20.cc | 1 src/M20c.cc |only src/doublehinge.c | 87 +++-- src/fastgrid2.cc | 19 + src/fastgrid_helper.h | 7 23 files changed, 872 insertions(+), 356 deletions(-)
Title: Create Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 1.1.3 dated 2019-12-04 and 1.1.4 dated 2020-02-27
Ternary-1.1.3/Ternary/R/ReleaseQuestions.R |only Ternary-1.1.3/Ternary/man/cbPalette15.Rd |only Ternary-1.1.3/Ternary/man/cbPalette8.Rd |only Ternary-1.1.3/Ternary/tests/testthat/Rplots.pdf |only Ternary-1.1.4/Ternary/DESCRIPTION | 11 Ternary-1.1.4/Ternary/MD5 | 112 Ternary-1.1.4/Ternary/NAMESPACE | 2 Ternary-1.1.4/Ternary/NEWS.md | 20 Ternary-1.1.4/Ternary/R/Contours.R | 158 Ternary-1.1.4/Ternary/R/Coordinates.R | 69 Ternary-1.1.4/Ternary/R/TernaryPlot.R | 280 Ternary-1.1.4/Ternary/R/data.R | 60 Ternary-1.1.4/Ternary/R/zzz.R |only Ternary-1.1.4/Ternary/README.md | 2 Ternary-1.1.4/Ternary/build/partial.rdb |binary Ternary-1.1.4/Ternary/data/cbPalette13.rda |only Ternary-1.1.4/Ternary/data/cbPalette15.rda |binary Ternary-1.1.4/Ternary/data/cbPalette8.rda |binary Ternary-1.1.4/Ternary/inst/WORDLIST |only Ternary-1.1.4/Ternary/inst/doc/Ternary.R | 41 Ternary-1.1.4/Ternary/inst/doc/Ternary.Rmd | 17 Ternary-1.1.4/Ternary/inst/doc/Ternary.html | 29 Ternary-1.1.4/Ternary/man/AddToTernary.Rd | 42 Ternary-1.1.4/Ternary/man/ColourTernary.Rd | 35 Ternary-1.1.4/Ternary/man/CoordinatesToXY.Rd | 7 Ternary-1.1.4/Ternary/man/OutsidePlot.Rd | 27 Ternary-1.1.4/Ternary/man/ReflectedEquivalents.Rd | 10 Ternary-1.1.4/Ternary/man/Ternary-package.Rd | 6 Ternary-1.1.4/Ternary/man/TernaryContour.Rd | 15 Ternary-1.1.4/Ternary/man/TernaryCoords.Rd | 29 Ternary-1.1.4/Ternary/man/TernaryDensityContour.Rd | 22 Ternary-1.1.4/Ternary/man/TernaryPlot.Rd | 80 Ternary-1.1.4/Ternary/man/TernaryPointValues.Rd | 55 Ternary-1.1.4/Ternary/man/TernaryTiles.Rd | 9 Ternary-1.1.4/Ternary/man/TernaryXRange.Rd | 12 Ternary-1.1.4/Ternary/man/TriangleCentres.Rd | 20 Ternary-1.1.4/Ternary/man/XYToTernary.Rd | 14 Ternary-1.1.4/Ternary/man/cbPalettes.Rd |only Ternary-1.1.4/Ternary/tests/figs/contour-plotting/contours-skiwiff.svg | 5454 +++++----- Ternary-1.1.4/Ternary/tests/figs/contour-plotting/contours.svg | 16 Ternary-1.1.4/Ternary/tests/figs/contour-plotting/density-contours-2.svg | 4 Ternary-1.1.4/Ternary/tests/figs/contour-plotting/density-contours-3.svg | 4 Ternary-1.1.4/Ternary/tests/figs/contour-plotting/density-contours.svg | 4 Ternary-1.1.4/Ternary/tests/figs/contour-plotting/lo-res-density-contours.svg | 16 Ternary-1.1.4/Ternary/tests/figs/contour-plotting/rgbcolours.svg |only Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/axisstyle.svg |only Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-down-anticlockwise.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-down.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-le-anticlockwise.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-le.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-plot.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-right-anticlockwise.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-right.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-up-anticlockwise.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/blank-up.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/cartesian.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/colours-and-water.svg | 2384 ++++ Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/plot-to-ternary-x.svg | 4 Ternary-1.1.4/Ternary/tests/figs/ternary-plotting/plot-to-ternary-y.svg | 4 Ternary-1.1.4/Ternary/tests/testthat/test-Contours.R | 10 Ternary-1.1.4/Ternary/tests/testthat/test-ternary.R | 61 Ternary-1.1.4/Ternary/vignettes/Ternary.Rmd | 17 62 files changed, 6001 insertions(+), 3201 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 2.1-0 dated 2018-08-22 and 2.3-3 dated 2020-02-27
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/test_automation |only inst/java/SDMX.jar |binary man/RJSDMX-package.Rd | 1 - 5 files changed, 8 insertions(+), 8 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.14 dated 2019-11-12 and 0.0.15 dated 2020-02-27
ChangeLog | 18 ++++ DESCRIPTION | 8 +- MD5 | 18 ++-- R/annoy.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 7 + inst/doc/UsingAnnoyInCcppWrapper.pdf |binary inst/include/annoylib.h | 134 +++++++++++++++++++---------------- inst/include/mman.h | 66 ++++++++--------- man/AnnoyIndex.Rd | 2 10 files changed, 149 insertions(+), 106 deletions(-)
Title: Piecewise Constant Hazards Models for Censored and Truncated
Data
Description: Using piecewise constant hazards models is a very flexible approach
for the analysis of survival data. The time line is divided into sub-intervals;
for each interval, a different hazard is estimated using Poisson regression.
Author: Paolo Frumento
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between pch versions 1.3 dated 2016-11-06 and 1.4 dated 2020-02-27
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS.md | 6 +++--- R/pch.R | 15 ++++++++------- man/pchreg.Rd | 2 +- man/predict.pch.Rd | 2 +- man/splinex.Rd | 2 +- 8 files changed, 28 insertions(+), 27 deletions(-)
Title: Diagnostics for Nonlinear Mixed-Effect Models
Description: A model building aid for nonlinear mixed-effects
(population) model analysis using NONMEM, facilitating data set
checkout, exploration and visualization, model diagnostics, candidate
covariate identification and model comparison. The methods are described
in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999)
<doi:10.1016/s0169-2607(98)00067-4>.
Author: Andrew C. Hooker [aut, cre, cph],
Mats O. Karlsson [aut, cph],
Justin J. Wilkins [aut],
E. Niclas Jonsson [aut, trl, cph],
Ron Keizer [ctb] (functionality for bootstrap of GAM and SCM)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Diff between xpose4 versions 4.6.1 dated 2018-03-08 and 4.7.0 dated 2020-02-27
DESCRIPTION | 24 +- MD5 | 328 +++++++++++++++--------------- NEWS.md | 10 R/absval.cwres.vs.pred.by.cov.R | 38 +-- R/absval.iwres.cwres.vs.ipred.pred.R | 2 R/absval.iwres.vs.ipred.R | 6 R/basic.gof.R | 25 -- R/bootgam.R | 2 R/calc.npar.R | 10 R/change.xvardef.R | 7 R/cov.summary.R | 28 +- R/cwres.dist.qq.R | 19 - R/dv.vs.ipred.by.cov.R | 161 +++++++------- R/dv.vs.pred.by.cov.R | 78 +++---- R/ind.plots.wres.hist.R | 10 R/ind.plots.wres.qq.R | 10 R/kaplan.plot.R | 13 - R/parm.summary.R | 24 +- R/read.phi.R | 4 R/xpose.data.R | 5 README.md | 86 ++++--- inst/CITATION | 15 + man/GAM_summary_and_plot.Rd | 70 ++++-- man/absval.cwres.vs.cov.bw.Rd | 120 ++++++---- man/absval.cwres.vs.pred.Rd | 123 ++++++----- man/absval.cwres.vs.pred.by.cov.Rd | 140 +++++++----- man/absval.iwres.cwres.vs.ipred.pred.Rd | 242 ++++++++++++---------- man/absval.iwres.vs.cov.bw.Rd | 120 ++++++---- man/absval.iwres.vs.idv.Rd | 130 +++++++---- man/absval.iwres.vs.ipred.Rd | 137 +++++++----- man/absval.iwres.vs.ipred.by.cov.Rd | 131 +++++++---- man/absval.iwres.vs.pred.Rd | 130 +++++++---- man/absval.wres.vs.cov.bw.Rd | 120 ++++++---- man/absval.wres.vs.idv.Rd | 132 +++++++----- man/absval.wres.vs.pred.Rd | 130 +++++++---- man/absval.wres.vs.pred.by.cov.Rd | 132 +++++++----- man/absval_delta_vs_cov_model_comp.Rd | 178 ++++++++++------ man/add.grid.table.Rd | 26 +- man/add.model.comp.Rd | 13 - man/add_transformed_columns.Rd | 44 ++-- man/addid.Rd | 27 ++ man/addit.gof.Rd | 132 +++++++----- man/autocorr.cwres.Rd | 130 +++++++---- man/autocorr.iwres.Rd | 130 +++++++---- man/autocorr.wres.Rd | 130 +++++++---- man/basic.gof.Rd | 131 ++++++----- man/basic.model.comp.Rd | 133 +++++++----- man/boot.hist.Rd | 41 ++- man/bootscm.import.Rd | 51 +++- man/cat.dv.vs.idv.sb.Rd | 166 +++++++++------ man/cat.pc.Rd | 145 ++++++++----- man/categorical.table.Rd | 21 + man/change.xvardef.Rd | 21 + man/change_graphical_parameters.Rd | 44 ++-- man/change_misc_parameters.Rd | 67 ++++-- man/compute.cwres.Rd | 84 ++++--- man/create.mirror.Rd | 11 - man/cwres.dist.hist.Rd | 121 ++++++----- man/cwres.dist.qq.Rd | 138 ++++++------ man/cwres.vs.cov.Rd | 131 +++++++---- man/cwres.vs.idv.Rd | 120 ++++++---- man/cwres.vs.idv.bw.Rd | 120 ++++++---- man/cwres.vs.pred.Rd | 120 ++++++---- man/cwres.vs.pred.bw.Rd | 119 ++++++---- man/cwres_wres_vs_x.Rd | 142 ++++++++---- man/dOFV.vs.cov.Rd | 139 +++++++----- man/dOFV.vs.id.Rd | 157 ++++++++------ man/dOFV1.vs.dOFV2.Rd | 139 +++++++----- man/data.checkout.Rd | 182 ++++++++++------ man/data_extract_or_assign.Rd | 53 +++- man/db.names.Rd | 45 ++-- man/dv.preds.vs.idv.Rd | 130 +++++++---- man/dv.vs.idv.Rd | 121 ++++++----- man/dv.vs.ipred.Rd | 120 ++++++---- man/dv.vs.ipred.by.cov.Rd | 135 +++++++----- man/dv.vs.ipred.by.idv.Rd | 120 ++++++---- man/dv.vs.pred.Rd | 121 ++++++----- man/dv.vs.pred.by.cov.Rd | 135 +++++++----- man/dv.vs.pred.by.idv.Rd | 120 ++++++---- man/dv.vs.pred.ipred.Rd | 133 +++++++----- man/export.graph.par.Rd | 46 ++-- man/export.variable.definitions.Rd | 44 ++-- man/figures/readme_example_figure_1-1.png |binary man/find.right.table.Rd | 14 + man/gof.Rd | 148 ++++++++----- man/import.graph.par.Rd | 44 ++-- man/import.variable.definitions.Rd | 44 ++-- man/ind.plots.Rd | 162 +++++++++----- man/ind.plots.wres.hist.Rd | 156 ++++++++------ man/ind.plots.wres.qq.Rd | 160 ++++++++------ man/ipred.vs.idv.Rd | 120 ++++++---- man/iwres.dist.hist.Rd | 120 ++++++---- man/iwres.dist.qq.Rd | 120 ++++++---- man/iwres.vs.idv.Rd | 120 ++++++---- man/kaplan.plot.Rd | 188 +++++++++++------ man/make.sb.data.Rd | 44 ++-- man/npc.coverage.Rd | 27 +- man/nsim.Rd | 45 ++-- man/par_cov_hist.Rd | 120 ++++++---- man/par_cov_qq.Rd | 120 ++++++---- man/par_cov_splom.Rd | 166 +++++++++------ man/par_cov_summary.Rd | 85 ++++--- man/parm.vs.cov.Rd | 130 +++++++---- man/parm.vs.parm.Rd | 131 +++++++---- man/pred.vs.idv.Rd | 120 ++++++---- man/randtest.hist.Rd | 30 +- man/ranpar.vs.cov.Rd | 130 +++++++---- man/read.TTE.sim.data.Rd | 53 +++- man/read.nm.tables.Rd | 60 +++-- man/read.npc.vpc.results.Rd | 25 +- man/read.vpctab.Rd | 31 +- man/read_NM_output.Rd | 46 ++-- man/read_nm_table.Rd | 54 +++- man/runsum.Rd | 142 +++++++----- man/simprazExample.Rd | 44 ++-- man/tabulate.parameters.Rd | 44 ++-- man/wres.dist.hist.Rd | 120 ++++++---- man/wres.dist.qq.Rd | 121 ++++++----- man/wres.vs.cov.Rd | 10 man/wres.vs.idv.Rd | 121 ++++++----- man/wres.vs.idv.bw.Rd | 120 ++++++---- man/wres.vs.pred.Rd | 121 ++++++----- man/wres.vs.pred.bw.Rd | 120 ++++++---- man/xlabel.Rd | 45 ++-- man/xp.boot.par.est.Rd | 22 +- man/xp.boot.par.est.corr.Rd | 13 - man/xp.daic.npar.plot.Rd | 39 ++- man/xp.distr.mod.size.Rd | 10 man/xp.dofv.npar.plot.Rd | 39 ++- man/xp.dofv.plot.Rd | 9 man/xp.get.disp.Rd | 10 man/xp.inc.cond.stab.cov.Rd | 44 ++-- man/xp.inc.ind.cond.stab.cov.Rd | 48 ++-- man/xp.inc.prob.Rd | 11 - man/xp.inc.prob.comb.2.Rd | 11 - man/xp.inc.stab.cov.Rd | 44 ++-- man/xp.incl.index.cov.Rd | 47 ++-- man/xp.incl.index.cov.comp.Rd | 10 man/xp.incl.index.cov.ind.Rd | 47 ++-- man/xp.scope3.Rd | 35 ++- man/xpose.VPC.Rd | 174 +++++++++------ man/xpose.VPC.both.Rd | 159 ++++++++------ man/xpose.VPC.categorical.Rd | 178 ++++++++++------ man/xpose.ask.for.filename.Rd | 8 man/xpose.bootgam.Rd | 25 +- man/xpose.create.title.Rd | 23 +- man/xpose.data.Rd | 68 ++++-- man/xpose.gam.Rd | 37 ++- man/xpose.multiple.plot.Rd | 24 +- man/xpose.multiple.plot.default.Rd | 18 + man/xpose.panel.bw.Rd | 34 ++- man/xpose.panel.default.Rd | 203 +++++++++++++----- man/xpose.panel.histogram.Rd | 45 +++- man/xpose.panel.qq.Rd | 12 - man/xpose.panel.splom.Rd | 28 +- man/xpose.plot.bw.Rd | 48 +++- man/xpose.plot.default.Rd | 65 ++++- man/xpose.plot.histogram.Rd | 42 ++- man/xpose.plot.qq.Rd | 41 ++- man/xpose.plot.splom.Rd | 47 +++- man/xpose.print.Rd | 45 ++-- man/xpose.yscale.components.log10.Rd | 2 man/xpose4-package.Rd | 204 +++++++++++------- man/xpose4.Rd | 4 man/xsubset.Rd | 46 ++-- 165 files changed, 8082 insertions(+), 5196 deletions(-)
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.3.1 dated 2020-02-07 and 1.3.2 dated 2020-02-27
sen2r |only 1 file changed
Title: Local Variable Importance via Oscillations of Ceteris Paribus
Profiles
Description: Provides an easy to calculate variable importance measure based on
Ceteris Paribus plot and is calculated in eight variants. We obtain eight
variants measure through the possible combinations of three parameters such as
absolute_deviation, point and density.
Author: Anna Kozak [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Anna Kozak <anna1993kozak@gmail.com>
Diff between vivo versions 0.1.1 dated 2019-09-03 and 0.1.2 dated 2020-02-27
DESCRIPTION | 6 MD5 | 31 +-- NEWS.md | 5 R/calculate_variable_split.R | 9 - R/calculate_weight.R | 9 - R/local_variable_importance.R | 41 ++-- R/plot_local_importance.R | 13 - README.md | 101 +++++++---- build/vignette.rds |binary inst/doc/vignette_apartments.R | 16 - inst/doc/vignette_apartments.html | 341 +++++++++++++++++++++++++++++++------- man/calculate_variable_split.Rd | 4 man/calculate_weight.Rd | 9 - man/figures |only man/local_variable_importance.Rd | 20 +- man/plot.local_importance.Rd | 5 tests/testthat/test_measure.R | 4 17 files changed, 444 insertions(+), 170 deletions(-)
Title: Superfast Likelihood Inference for Stationary Gaussian Time
Series
Description: Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
Author: Yun Ling [aut],
Martin Lysy [aut, cre]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between SuperGauss versions 1.0.1 dated 2019-03-12 and 1.0.2 dated 2020-02-27
DESCRIPTION | 10 MD5 | 25 - R/RcppExports.R | 28 - build/vignette.rds |binary configure | 2 configure.ac | 7 inst/doc/SuperGauss-quicktut.R | 16 inst/doc/SuperGauss-quicktut.html | 416 +++++++++---------- inst/doxygen |only inst/include/GSchur.h | 684 ++++++++++++-------------------- inst/include/Toeplitz.h | 807 +++++++++++++++++--------------------- inst/include/VectorFFT.h | 179 +++----- man/SuperGauss.Rd | 1 src/RcppExports.cpp | 56 +- 14 files changed, 996 insertions(+), 1235 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: Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, Lane Burgette, Matthew Cefalu
<mcefalu@rand.org>
Maintainer: Matthew Cefalu <mcefalu@rand.org>
Diff between twang versions 1.5 dated 2017-07-01 and 1.6 dated 2020-02-27
DESCRIPTION | 19 LICENSE |only MD5 | 33 R/bal.table.R | 8 R/dx.wts.R | 8 R/get.weights.R | 6 R/get.weights.unstab.R | 6 R/pairwiseComparison.R | 2 R/plot.mniptw.R | 2 R/ps.R | 2 R/ps.summary.new2.R | 15 build/vignette.rds |binary inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.R | 118 - inst/doc/twang.pdf |binary inst/doc/twang.rnw | 3435 ++++++++++++++++++++++++------------------------- vignettes/twang.rnw | 3435 ++++++++++++++++++++++++------------------------- 18 files changed, 3548 insertions(+), 3541 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(<http://www.gnu.org/software/gsl/>) and 'Rcpp'
(<http://dirk.eddelbuettel.com/code/rcpp.html>) 'R' / 'C++' classes.
Author: Yi Wang [aut],
Ulrike Naumann [aut],
Dirk Eddelbuettel [aut],
John Wilshire [aut],
David Warton [aut, cre],
Julian Byrnes [ctb],
Ralph dos Santos Silva [ctb, cph],
Jenni Niku [ctb],
Ian Renner [ctb],
Stephen Wright [ctb]
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 4.0.1 dated 2019-01-07 and 4.1.3 dated 2020-02-27
DESCRIPTION | 8 ++--- MD5 | 28 ++++++++--------- R/anova.manyany.R | 3 + R/anova.manyglm.R | 4 +- R/default.print.anova.manyglm.R | 13 +++----- R/manyany.R | 12 ++++--- R/manyglm.R | 63 ++++++++++++++++++++++++++++++++++------ cleanup | 2 - man/Tasmania.Rd | 3 - man/anova.manyglm.Rd | 2 - man/manyglm.Rd | 17 +++------- man/residuals.manyglm.Rd | 4 -- src/Makevars | 13 +++++--- src/Rinterface.cpp | 11 +++--- src/resampTest.h | 33 +++++--------------- 15 files changed, 122 insertions(+), 94 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay and Charles Reynard.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 1.0-11 dated 2020-01-23 and 1.0-13 dated 2020-02-27
DESCRIPTION | 8 +-- MD5 | 26 +++++----- NEWS | 24 ++++++++-- R/epi.2by2.R | 108 ++++++++++++++++++++++++++++----------------- R/epi.smr.R |only R/epi.ssdetect.R | 123 ++++++++++++++++++++++++++-------------------------- man/epi.2by2.Rd | 6 +- man/epi.smr.Rd |only man/epi.ssdetect.Rd | 24 ++++------ man/epi.ssequb.Rd | 2 man/epi.ssequc.Rd | 2 man/epi.ssninfb.Rd | 38 ++++++++-------- man/epi.ssninfc.Rd | 12 ++--- man/epi.sssupb.Rd | 4 - man/epi.sssupc.Rd | 2 15 files changed, 215 insertions(+), 164 deletions(-)
Title: Sample Size Calculation for the Comparison of Means or
Proportions in Phase III Clinical Trials
Description: There are four categories of Phase III clinical trials according to different research goals, including (1) Testing for equality, (2) Superiority trial, (3) Non-inferiority trial, and (4) Equivalence trial. This package aims to help researchers to calculate sample size when comparing means or proportions in Phase III clinical trials with different research goals.
Author: Hongchao Qi, Fang Zhu
Maintainer: Hongchao Qi <hcqi.biostat@gmail.com>
Diff between SampleSize4ClinicalTrials versions 0.1.2 dated 2020-01-31 and 0.2.1 dated 2020-02-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/ssc_meancomp.R | 12 ++++++------ R/ssc_propcomp.R | 10 +++++----- man/ssc_meancomp.Rd | 6 +++--- man/ssc_propcomp.Rd | 4 ++-- 6 files changed, 24 insertions(+), 24 deletions(-)
More information about SampleSize4ClinicalTrials at CRAN
Permanent link
Title: Matrix Bending
Description: Bending non-positive-definite (symmetric) matrices to positive-definite, using weighted and unweighted methods.
Jorjani, H., et al. (2003) <doi:10.3168/jds.S0022-0302(03)73646-7>.
Schaeffer, L. R. (2010) <http://animalbiosciences.uoguelph.ca/~lrs/piksLRS/PDforce.pdf>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between mbend versions 1.2.3 dated 2019-10-31 and 1.2.4 dated 2020-02-27
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 1 NEWS.md | 5 R/bend.R | 314 +++++++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/demo.R | 26 ++-- inst/doc/demo.html | 204 +++++++++++++++++++++++++++++----- man/bend.Rd | 10 + 9 files changed, 392 insertions(+), 192 deletions(-)
Title: Integrative Analysis of Several Related Data Matrices
Description: A generalization of principal component analysis for integrative
analysis. The method finds principal components that describe single matrices
or that are common to several matrices. The solutions are sparse. Rank of
solutions is automatically selected using cross validation. The method is
described in Kallus, Johansson, Nelander and Jörnsten (2019)
<arXiv:1911.04927>.
Author: Jonatan Kallus [aut, cre]
Maintainer: Jonatan Kallus <kallus@chalmers.se>
Diff between mmpca versions 1.0.2 dated 2019-12-05 and 1.0.3 dated 2020-02-27
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/mmpca.R | 8 +++++++- man/mmpca.Rd | 2 +- 4 files changed, 16 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-29 0.1.0
Title: Tools for Accessing the Botanical Information and Ecology
Network Database
Description: Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <http://Bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
Author: Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between BIEN versions 1.2.3 dated 2018-05-09 and 1.2.4 dated 2020-02-27
BIEN-1.2.3/BIEN/vignettes/BIEN.md |only BIEN-1.2.4/BIEN/DESCRIPTION | 11 BIEN-1.2.4/BIEN/MD5 | 179 + BIEN-1.2.4/BIEN/NAMESPACE | 23 BIEN-1.2.4/BIEN/NEWS | 18 BIEN-1.2.4/BIEN/R/BIEN.R | 915 +++++++--- BIEN-1.2.4/BIEN/R/BIEN_info.R | 4 BIEN-1.2.4/BIEN/R/BIEN_sql.R | 18 BIEN-1.2.4/BIEN/R/internals.R | 63 BIEN-1.2.4/BIEN/build/vignette.rds |binary BIEN-1.2.4/BIEN/inst/doc/BIEN.html | 321 ++- BIEN-1.2.4/BIEN/inst/doc/BIEN_tutorial.R | 134 - BIEN-1.2.4/BIEN/inst/doc/BIEN_tutorial.Rmd | 120 - BIEN-1.2.4/BIEN/inst/doc/BIEN_tutorial.html | 895 +-------- BIEN-1.2.4/BIEN/man/BIEN.Rd | 37 BIEN-1.2.4/BIEN/man/BIEN_list_all.Rd | 56 BIEN-1.2.4/BIEN/man/BIEN_list_country.Rd | 89 BIEN-1.2.4/BIEN/man/BIEN_list_county.Rd | 120 - BIEN-1.2.4/BIEN/man/BIEN_list_spatialpolygons.Rd | 86 BIEN-1.2.4/BIEN/man/BIEN_list_state.Rd | 99 - BIEN-1.2.4/BIEN/man/BIEN_metadata_citation.Rd | 86 BIEN-1.2.4/BIEN/man/BIEN_metadata_database_version.Rd | 58 BIEN-1.2.4/BIEN/man/BIEN_metadata_list_political_names.Rd | 64 BIEN-1.2.4/BIEN/man/BIEN_metadata_match_data.Rd | 80 BIEN-1.2.4/BIEN/man/BIEN_occurrence_box.Rd | 147 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_country.Rd | 133 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_county.Rd | 162 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_family.Rd | 124 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_genus.Rd | 126 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_records_per_species.Rd | 68 BIEN-1.2.4/BIEN/man/BIEN_occurrence_spatialpolygons.Rd | 132 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_species.Rd | 126 - BIEN-1.2.4/BIEN/man/BIEN_occurrence_state.Rd | 148 - BIEN-1.2.4/BIEN/man/BIEN_phylogeny_complete.Rd | 72 BIEN-1.2.4/BIEN/man/BIEN_phylogeny_conservative.Rd | 57 BIEN-1.2.4/BIEN/man/BIEN_phylogeny_label_nodes.Rd |only BIEN-1.2.4/BIEN/man/BIEN_plot_country.Rd | 132 - BIEN-1.2.4/BIEN/man/BIEN_plot_dataset.Rd | 125 - BIEN-1.2.4/BIEN/man/BIEN_plot_datasource.Rd | 121 - BIEN-1.2.4/BIEN/man/BIEN_plot_list_datasource.Rd | 65 BIEN-1.2.4/BIEN/man/BIEN_plot_list_sampling_protocols.Rd | 65 BIEN-1.2.4/BIEN/man/BIEN_plot_metadata.Rd | 79 BIEN-1.2.4/BIEN/man/BIEN_plot_name.Rd | 125 - BIEN-1.2.4/BIEN/man/BIEN_plot_sampling_protocol.Rd | 121 - BIEN-1.2.4/BIEN/man/BIEN_plot_spatialpolygons.Rd |only BIEN-1.2.4/BIEN/man/BIEN_plot_state.Rd | 147 - BIEN-1.2.4/BIEN/man/BIEN_ranges_box.Rd | 122 - BIEN-1.2.4/BIEN/man/BIEN_ranges_genus.Rd | 137 - BIEN-1.2.4/BIEN/man/BIEN_ranges_intersect_species.Rd | 117 - BIEN-1.2.4/BIEN/man/BIEN_ranges_list.Rd | 77 BIEN-1.2.4/BIEN/man/BIEN_ranges_load_species.Rd | 85 BIEN-1.2.4/BIEN/man/BIEN_ranges_shapefile_to_skinny.Rd |only BIEN-1.2.4/BIEN/man/BIEN_ranges_skinny_ranges_to_richness_raster.Rd |only BIEN-1.2.4/BIEN/man/BIEN_ranges_spatialpolygons.Rd | 119 - BIEN-1.2.4/BIEN/man/BIEN_ranges_species.Rd | 137 - BIEN-1.2.4/BIEN/man/BIEN_ranges_species_bulk.Rd |only BIEN-1.2.4/BIEN/man/BIEN_stem_datasource.Rd | 120 - BIEN-1.2.4/BIEN/man/BIEN_stem_family.Rd | 122 - BIEN-1.2.4/BIEN/man/BIEN_stem_genus.Rd | 122 - BIEN-1.2.4/BIEN/man/BIEN_stem_sampling_protocol.Rd | 112 - BIEN-1.2.4/BIEN/man/BIEN_stem_species.Rd | 122 - BIEN-1.2.4/BIEN/man/BIEN_taxonomy_family.Rd | 60 BIEN-1.2.4/BIEN/man/BIEN_taxonomy_genus.Rd | 60 BIEN-1.2.4/BIEN/man/BIEN_taxonomy_species.Rd | 60 BIEN-1.2.4/BIEN/man/BIEN_trait_country.Rd |only BIEN-1.2.4/BIEN/man/BIEN_trait_family.Rd | 92 - BIEN-1.2.4/BIEN/man/BIEN_trait_genus.Rd | 70 BIEN-1.2.4/BIEN/man/BIEN_trait_list.Rd | 65 BIEN-1.2.4/BIEN/man/BIEN_trait_mean.Rd | 79 BIEN-1.2.4/BIEN/man/BIEN_trait_species.Rd | 92 - BIEN-1.2.4/BIEN/man/BIEN_trait_trait.Rd | 98 - BIEN-1.2.4/BIEN/man/BIEN_trait_traitbyfamily.Rd | 105 - BIEN-1.2.4/BIEN/man/BIEN_trait_traitbygenus.Rd | 105 - BIEN-1.2.4/BIEN/man/BIEN_trait_traitbyspecies.Rd | 105 - BIEN-1.2.4/BIEN/man/BIEN_trait_traits_per_species.Rd | 69 BIEN-1.2.4/BIEN/man/dot-BIEN_sql.Rd |only BIEN-1.2.4/BIEN/man/dot-collection_check.Rd |only BIEN-1.2.4/BIEN/man/dot-collection_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-collection_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-cultivated_check.Rd |only BIEN-1.2.4/BIEN/man/dot-cultivated_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-cultivated_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-genus_check.Rd |only BIEN-1.2.4/BIEN/man/dot-is_char.Rd |only BIEN-1.2.4/BIEN/man/dot-is_log.Rd |only BIEN-1.2.4/BIEN/man/dot-is_num.Rd |only BIEN-1.2.4/BIEN/man/dot-md_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-md_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-native_check.Rd |only BIEN-1.2.4/BIEN/man/dot-native_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-native_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-natives_check.Rd |only BIEN-1.2.4/BIEN/man/dot-natives_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-natives_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-newworld_check.Rd |only BIEN-1.2.4/BIEN/man/dot-newworld_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-newworld_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-observation_check.Rd |only BIEN-1.2.4/BIEN/man/dot-political_check.Rd |only BIEN-1.2.4/BIEN/man/dot-political_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-political_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-political_check_traits.Rd |only BIEN-1.2.4/BIEN/man/dot-source_check_traits.Rd |only BIEN-1.2.4/BIEN/man/dot-species_check.Rd |only BIEN-1.2.4/BIEN/man/dot-taxonomy_check.Rd |only BIEN-1.2.4/BIEN/man/dot-taxonomy_check_plot.Rd |only BIEN-1.2.4/BIEN/man/dot-taxonomy_check_stem.Rd |only BIEN-1.2.4/BIEN/man/dot-taxonomy_check_traits.Rd |only BIEN-1.2.4/BIEN/man/dot-vfoi_check_stem.Rd |only BIEN-1.2.4/BIEN/tests/testthat/test-BIEN.r | 65 BIEN-1.2.4/BIEN/vignettes/BIEN_tutorial.Rmd | 120 - 111 files changed, 4504 insertions(+), 3884 deletions(-)