Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
(<https://orcid.org/0000-0002-3131-3814>),
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.4.0 dated 2019-10-09 and 0.4.2 dated 2019-11-09
DESCRIPTION | 6 +- MD5 | 78 ++++++++++++++------------- NAMESPACE | 1 R/RcppExports.R | 4 - R/add_object.R | 4 - R/generate_cornell.R | 12 ++-- R/generate_ground.R | 14 ++-- R/materials.R | 77 +++++++++++++++++++++------ R/objects.R | 129 ++++++++++++++++++++++++---------------------- R/pig.R | 36 ++++++------ R/r_obj.R | 6 +- R/render_scene.R | 24 +++++--- R/utils-pipe.R | 2 man/add_object.Rd | 4 - man/cube.Rd | 6 +- man/cylinder.Rd | 12 ++-- man/dielectric.Rd | 6 +- man/diffuse.Rd |only man/disk.Rd | 14 ++-- man/ellipsoid.Rd | 8 +- man/generate_ground.Rd | 14 ++-- man/lambertian.Rd | 75 ++------------------------ man/metal.Rd | 2 man/obj_model.Rd | 18 +++--- man/pipe.Rd | 2 man/r_obj.Rd | 6 +- man/render_scene.Rd | 11 ++- man/segment.Rd | 8 +- man/sphere.Rd | 6 +- man/triangle.Rd | 10 +-- man/xy_rect.Rd | 10 +-- man/xz_rect.Rd | 10 +-- man/yz_rect.Rd | 10 +-- src/RcppExports.cpp | 9 +-- src/buildscene.h | 28 ++++++++- src/disney.h |only src/material.h | 50 +++++++++++++++++ src/mathinline.h | 84 +++++++++++++++++++++++++++-- src/pdf.h | 32 +++++++++++ src/render_scene_rcpp.cpp | 40 +++++++------- src/vec3.h | 1 41 files changed, 526 insertions(+), 343 deletions(-)
Title: Leaflet Providers
Description: Contains third-party map tile provider information from
'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>, to be
used with the 'leaflet' R package. Additionally, 'leaflet.providers'
enables users to retrieve up-to-date provider information between package
updates.
Author: Leslie Huang [aut],
Barret Schloerke [ctb, cre] (<https://orcid.org/0000-0001-9986-114X>),
Leaflet Providers contributors [ctb, cph] (Leaflet Providers plugin),
RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between leaflet.providers versions 1.8.0 dated 2019-07-15 and 1.9.0 dated 2019-11-09
leaflet.providers-1.8.0/leaflet.providers/inst/leaflet-providers_1.8.0.js |only leaflet.providers-1.9.0/leaflet.providers/DESCRIPTION | 16 +- leaflet.providers-1.9.0/leaflet.providers/MD5 | 10 - leaflet.providers-1.9.0/leaflet.providers/NEWS.md | 7 - leaflet.providers-1.9.0/leaflet.providers/R/providers_data.R | 69 +++++----- leaflet.providers-1.9.0/leaflet.providers/README.md | 2 leaflet.providers-1.9.0/leaflet.providers/inst/leaflet-providers_1.9.0.js |only 7 files changed, 62 insertions(+), 42 deletions(-)
More information about leaflet.providers at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-09 13.4.13
2018-01-04 10.1.9
2015-07-29 5.1.6
2015-04-04 5.1.3
2014-05-07 3.2.0-3
2014-03-06 3.1.3-2
2013-08-08 2.2.8-8
2013-04-20 2.1.4-19
2013-02-11 2.1.2-10
2013-02-09 2.1.2-8
2012-12-17 2.0.12-17
2012-11-12 2.0.11-11
2012-11-04 2.0.11-4
2012-07-31 1.2.7-31
2012-01-06 1.1.1-7
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut],
National ICT Australia (NICTA) [cph],
Michael A. Maniscalco [ctb, cph],
Choon Hui Teo [ctb]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>
Diff between kernlab versions 0.9-27 dated 2018-08-10 and 0.9-28 dated 2019-11-09
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/ranking.R | 12 ++++-------- build/vignette.rds |binary data/income.rda |binary data/musk.rda |binary data/promotergene.rda |binary data/reuters.rda |binary data/spam.rda |binary data/spirals.rda |binary data/ticdata.rda |binary inst/doc/kernlab.pdf |binary man/kcca.Rd | 10 ++++++---- man/kha.Rd | 2 +- man/ranking.Rd | 2 +- src/dcauchy.c | 10 +++++++--- src/lcp.cpp | 7 +++++-- 17 files changed, 43 insertions(+), 38 deletions(-)
Title: Amino Acid Substitution Effect Analyser
Description: Given a protein multiple sequence alignment, it is daunting task to assess the effects of substitutions along sequence length. 'aaSEA' package is intended to help researchers to rapidly analyse property changes caused by single, multiple and correlated amino acid substitutions in proteins. Methods for identification of co-evolving positions from multiple sequence alignment are as described in : Pelé et al., (2017) <doi:10.4172/2379-1764.1000250>.
Author: Raja Sekhara Reddy D.M
Maintainer: Raja Sekhara Reddy D.M <raja.duvvuru@gmail.com>
Diff between aaSEA versions 1.0.0 dated 2019-08-01 and 1.1.0 dated 2019-11-09
DESCRIPTION | 8 +- MD5 | 12 +-- R/getCorSites.R | 26 +++---- inst/doc/aaSEA_Documentation.R | 2 inst/doc/aaSEA_Documentation.Rmd | 2 inst/doc/aaSEA_Documentation.html | 129 ++++++++++++++++++++++++++++---------- vignettes/aaSEA_Documentation.Rmd | 2 7 files changed, 124 insertions(+), 57 deletions(-)
Title: Computerized Adaptive Multistage Testing
Description: Assemble the panels of computerized adaptive multistage testing by the
bottom-up and the top-down approach, and simulate the administration of the assembled
panels. The full documentation and tutorials are at <https://github.com/xluo11/Rmst>.
Reference: Luo and Kim (2018) <doi:10.1111/jedm.12174>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Diff between Rmst versions 0.0.1 dated 2019-11-01 and 0.0.2 dated 2019-11-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/assembly.R | 1 + R/simulator.R | 2 +- man/assembly.Rd | 1 + man/sim.Rd | 2 +- 6 files changed, 12 insertions(+), 10 deletions(-)
Title: Multi-Resolution Kriging Based on Markov Random Fields
Description: Methods for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach but
provides a surface fitting method
that can approximate standard spatial data models.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for
this method can approximate the Matern covariance family but also
allows for a multi-resolution model and supports efficient
computation of the profile likelihood for estimating covariance
parameters. This is accomplished through compactly supported basis
functions and a Markov random field model for the basis
coefficients. These features lead to sparse matrices for the
computations and this package makes of the R spam package for sparse
linear algebra.
An extension of this version over previous ones ( < 5.4 ) is the
support for different geometries besides a rectangular domain. The
Markov random field approach combined with a basis function
representation makes the implementation of different geometries
simple where only a few specific R functions need to be added with
most of the computation and evaluation done by generic routines that
have been tuned to be efficient. One benefit of this package's
model/approach is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances
and also the case when the observations are a linear combination
(e.g. an integral) of the spatial process. Included are generic
methods for prediction, standard errors for prediction, plotting of
the estimated surface and conditional and unconditional simulation.
See the 'LatticeKrig' GitHub repository for a vignette of this package.
Development of this package was supported in part by the National
Science Foundation Grant 1417857 and the National Center for
Atmospheric Research.
Author: Douglas Nychka [aut, cre],
Dorit Hammerling [aut],
Stephan Sain [aut],
Nathan Lenssen [aut],
Colette Smirniotis [aut],
Matthew Iverson [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 7.0 dated 2018-04-30 and 8.4 dated 2019-11-09
LatticeKrig-7.0/LatticeKrig/man/figures |only LatticeKrig-8.4/LatticeKrig/DESCRIPTION | 47 ++- LatticeKrig-8.4/LatticeKrig/MD5 | 105 +++---- LatticeKrig-8.4/LatticeKrig/NAMESPACE | 1 LatticeKrig-8.4/LatticeKrig/R/LKDiag.R |only LatticeKrig-8.4/LatticeKrig/R/LKDist.R | 9 LatticeKrig-8.4/LatticeKrig/R/LKDistComponents.R | 22 - LatticeKrig-8.4/LatticeKrig/R/LKDistGrid.R | 13 LatticeKrig-8.4/LatticeKrig/R/LKDistGridComponents.R | 9 LatticeKrig-8.4/LatticeKrig/R/LKRectangleFastNormalization.R | 3 LatticeKrig-8.4/LatticeKrig/R/LKSphere-Internal.R | 4 LatticeKrig-8.4/LatticeKrig/R/LKrig.sim.conditional.R | 11 LatticeKrig-8.4/LatticeKrig/R/LKrigSetup.R | 23 + LatticeKrig-8.4/LatticeKrig/R/ModelBox.R | 10 LatticeKrig-8.4/LatticeKrig/R/ModelCylinder.R | 12 LatticeKrig-8.4/LatticeKrig/R/ModelInterval.R | 7 LatticeKrig-8.4/LatticeKrig/R/ModelLKSphere.R | 50 ++- LatticeKrig-8.4/LatticeKrig/R/ModelRectangle.R | 31 +- LatticeKrig-8.4/LatticeKrig/R/ModelRing.R | 13 LatticeKrig-8.4/LatticeKrig/R/print.LKinfo.R | 4 LatticeKrig-8.4/LatticeKrig/data |only LatticeKrig-8.4/LatticeKrig/inst/CITATION | 2 LatticeKrig-8.4/LatticeKrig/man/IcosohedronGrid.Rd | 32 +- LatticeKrig-8.4/LatticeKrig/man/KrigingExampleData.Rd |only LatticeKrig-8.4/LatticeKrig/man/LKDiag.Rd |only LatticeKrig-8.4/LatticeKrig/man/LKDist.Rd | 2 LatticeKrig-8.4/LatticeKrig/man/LKGeometry.Rd | 8 LatticeKrig-8.4/LatticeKrig/man/LKRectangle.Rd | 16 - LatticeKrig-8.4/LatticeKrig/man/LKrig.MLE.Rd | 12 LatticeKrig-8.4/LatticeKrig/man/LKrig.Rd | 48 +-- LatticeKrig-8.4/LatticeKrig/man/LKrig.basis.Rd | 12 LatticeKrig-8.4/LatticeKrig/man/LKrig.sim.Rd | 4 LatticeKrig-8.4/LatticeKrig/man/LKrigDefaultFixedFunction.Rd | 2 LatticeKrig-8.4/LatticeKrig/man/LKrigInternal.Rd | 8 LatticeKrig-8.4/LatticeKrig/man/LKrigLatticeCenters.Rd | 6 LatticeKrig-8.4/LatticeKrig/man/LKrigNormalizeBasis.Rd | 4 LatticeKrig-8.4/LatticeKrig/man/LKrigSAR.Rd | 4 LatticeKrig-8.4/LatticeKrig/man/LKrigSetup.Rd | 88 +++--- LatticeKrig-8.4/LatticeKrig/man/LKrigSetupAwght.Rd | 2 LatticeKrig-8.4/LatticeKrig/man/LKrigSetupLattice.Rd | 63 ++-- LatticeKrig-8.4/LatticeKrig/man/LatticeKrig.Rd | 38 +- LatticeKrig-8.4/LatticeKrig/man/PeriodicGeometry.Rd | 144 ++++++---- LatticeKrig-8.4/LatticeKrig/man/Radial.Basis.Rd | 2 LatticeKrig-8.4/LatticeKrig/man/VignetteExamples.Rd |only LatticeKrig-8.4/LatticeKrig/man/directionCosines.Rd | 17 - LatticeKrig-8.4/LatticeKrig/man/nonstationaryModels.Rd | 119 +++++++- LatticeKrig-8.4/LatticeKrig/man/registerdFORTRAN.Rd | 9 LatticeKrig-8.4/LatticeKrig/src/LKDiag.f90 |only LatticeKrig-8.4/LatticeKrig/src/LKdist.f | 4 LatticeKrig-8.4/LatticeKrig/src/LKdistgrid.f | 6 LatticeKrig-8.4/LatticeKrig/src/zzzinit.c | 31 +- LatticeKrig-8.4/LatticeKrig/tests/LKrig.LKSphere.test.R | 2 LatticeKrig-8.4/LatticeKrig/tests/LKrig.testFindAwght.R | 25 - LatticeKrig-8.4/LatticeKrig/tests/LKrig.testFindAwght.Rout.save | 19 - 54 files changed, 663 insertions(+), 440 deletions(-)
Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs.
Also provides functions for obtaining system specifications, such as
RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre] (<https://orcid.org/0000-0003-1787-0275>)
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between benchmarkme versions 1.0.2 dated 2019-08-19 and 1.0.3 dated 2019-11-09
benchmarkme-1.0.2/benchmarkme/R/Rnorm.R |only benchmarkme-1.0.2/benchmarkme/R/globalVariables.R |only benchmarkme-1.0.2/benchmarkme/R/zzz.r |only benchmarkme-1.0.3/benchmarkme/DESCRIPTION | 8 benchmarkme-1.0.3/benchmarkme/MD5 | 74 +++--- benchmarkme-1.0.3/benchmarkme/NEWS.md | 5 benchmarkme-1.0.3/benchmarkme/R/benchmark_io.R | 3 benchmarkme-1.0.3/benchmarkme/R/benchmark_matrix_calculations.R | 34 +-- benchmarkme-1.0.3/benchmarkme/R/benchmark_matrix_functions.R | 64 +++-- benchmarkme-1.0.3/benchmarkme/R/benchmark_parallel.R | 13 - benchmarkme-1.0.3/benchmarkme/R/benchmark_programming.R | 112 +++++----- benchmarkme-1.0.3/benchmarkme/R/benchmark_std.R | 3 benchmarkme-1.0.3/benchmarkme/R/benchmarkme-package.R | 2 benchmarkme-1.0.3/benchmarkme/R/benchmarks.R | 4 benchmarkme-1.0.3/benchmarkme/R/clean_ram_output.R | 18 - benchmarkme-1.0.3/benchmarkme/R/get_byte_compiler.R | 12 - benchmarkme-1.0.3/benchmarkme/R/get_cpu.R | 24 +- benchmarkme-1.0.3/benchmarkme/R/get_hard_disk.R | 6 benchmarkme-1.0.3/benchmarkme/R/get_linear_algebra.R | 1 benchmarkme-1.0.3/benchmarkme/R/get_ram.R | 34 ++- benchmarkme-1.0.3/benchmarkme/R/get_sys_details.R | 22 - benchmarkme-1.0.3/benchmarkme/R/global_variables.R |only benchmarkme-1.0.3/benchmarkme/R/plot_results.R | 33 +- benchmarkme-1.0.3/benchmarkme/R/rank_results.R | 2 benchmarkme-1.0.3/benchmarkme/R/rnorm.R |only benchmarkme-1.0.3/benchmarkme/R/timing_mean.R | 2 benchmarkme-1.0.3/benchmarkme/R/zzz.R |only benchmarkme-1.0.3/benchmarkme/inst/doc/a_introduction.Rmd | 2 benchmarkme-1.0.3/benchmarkme/man/benchmark_io.Rd | 3 benchmarkme-1.0.3/benchmarkme/man/bm_matrix_cal_manip.Rd | 6 benchmarkme-1.0.3/benchmarkme/man/bm_matrix_fun_fft.Rd | 6 benchmarkme-1.0.3/benchmarkme/man/bm_prog_fib.Rd | 3 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-bm_parallel.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-byte_compiler.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-plot_results.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-ram.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-ranking.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-sys_details.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-timings.R | 2 benchmarkme-1.0.3/benchmarkme/tests/testthat/test-upload_results.R | 2 benchmarkme-1.0.3/benchmarkme/vignettes/a_introduction.Rmd | 2 41 files changed, 278 insertions(+), 236 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.51 dated 2019-08-07 and 5.52 dated 2019-11-09
DESCRIPTION | 11 +++++++---- MD5 | 10 +++++----- R/rqss.R | 2 +- inst/ChangeLog | 20 ++++++++++++++++++++ inst/FAQ | 22 ++++++++++++++++++++++ man/summary.crq.Rd | 3 ++- 6 files changed, 57 insertions(+), 11 deletions(-)
Title: Easily Add Markdown Help Files to 'shiny' App Elements
Description: Creates a lightweight way to add markdown helpfiles to 'shiny' apps,
using modal dialog boxes, with no need to observe each help button separately.
Author: Chris Mason-Thom [aut, cre]
Maintainer: Chris Mason-Thom <christopher.w.thom@outlook.com>
Diff between shinyhelper versions 0.3.1 dated 2018-10-28 and 0.3.2 dated 2019-11-09
shinyhelper-0.3.1/shinyhelper/inst/example/helpfiles/Clusters.md |only shinyhelper-0.3.2/shinyhelper/DESCRIPTION | 8 ++-- shinyhelper-0.3.2/shinyhelper/MD5 | 20 +++++----- shinyhelper-0.3.2/shinyhelper/NEWS.md | 4 ++ shinyhelper-0.3.2/shinyhelper/R/helper.R | 12 +++++- shinyhelper-0.3.2/shinyhelper/R/observe_helpers.R | 8 +++- shinyhelper-0.3.2/shinyhelper/README.md | 15 ++++++- shinyhelper-0.3.2/shinyhelper/inst/assets/shinyhelper.js | 3 + shinyhelper-0.3.2/shinyhelper/inst/example/helpfiles/clusters.md |only shinyhelper-0.3.2/shinyhelper/inst/example/rsconnect/shinyapps.io/cwthom94/shinyhelper-demo.dcf | 4 +- shinyhelper-0.3.2/shinyhelper/inst/example/ui.R | 6 ++- shinyhelper-0.3.2/shinyhelper/man/helper.Rd | 10 ++++- 12 files changed, 67 insertions(+), 23 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>,
David Barrios <metal@usal.es>,
Carlos Prieto <cprietos@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 0.3.2 dated 2018-12-16 and 1.1.23 dated 2019-11-09
netCoin-0.3.2/netCoin/R/MultiGraph |only netCoin-0.3.2/netCoin/inst/doc/sanderson |only netCoin-0.3.2/netCoin/man/cbarCoin.Rd |only netCoin-1.1.23/netCoin/DESCRIPTION | 10 netCoin-1.1.23/netCoin/MD5 | 178 netCoin-1.1.23/netCoin/NAMESPACE | 9 netCoin-1.1.23/netCoin/R/barplot.R | 197 netCoin-1.1.23/netCoin/R/multigraph.R | 220 netCoin-1.1.23/netCoin/R/netcoin.R | 1171 +++- netCoin-1.1.23/netCoin/R/network.R | 333 - netCoin-1.1.23/netCoin/R/timeline.R | 19 netCoin-1.1.23/netCoin/R/utils.R | 292 - netCoin-1.1.23/netCoin/README |only netCoin-1.1.23/netCoin/build/vignette.rds |binary netCoin-1.1.23/netCoin/data/ess.RData |only netCoin-1.1.23/netCoin/data/sociologists.RData |binary netCoin-1.1.23/netCoin/inst/doc/netCoin.R | 30 netCoin-1.1.23/netCoin/inst/doc/netCoin.Rmd | 32 netCoin-1.1.23/netCoin/inst/doc/netCoin.html | 412 + netCoin-1.1.23/netCoin/inst/doc/surCoin.R |only netCoin-1.1.23/netCoin/inst/doc/surCoin.Rmd |only netCoin-1.1.23/netCoin/inst/doc/surCoin.html |only netCoin-1.1.23/netCoin/inst/extdata |only netCoin-1.1.23/netCoin/inst/www/barplot.js | 1236 +++- netCoin-1.1.23/netCoin/inst/www/ca.js |only netCoin-1.1.23/netCoin/inst/www/colorScales.js | 250 netCoin-1.1.23/netCoin/inst/www/d3.min.js | 7 netCoin-1.1.23/netCoin/inst/www/en.js | 157 netCoin-1.1.23/netCoin/inst/www/es.js | 157 netCoin-1.1.23/netCoin/inst/www/functions.js | 962 ++- netCoin-1.1.23/netCoin/inst/www/include.html |only netCoin-1.1.23/netCoin/inst/www/jspdf.min.js | 573 +- netCoin-1.1.23/netCoin/inst/www/multigraph.js | 159 netCoin-1.1.23/netCoin/inst/www/network.js | 6448 ++++++++++++++----------- netCoin-1.1.23/netCoin/inst/www/polygraph.js | 38 netCoin-1.1.23/netCoin/inst/www/reset.css | 90 netCoin-1.1.23/netCoin/inst/www/styles.css | 732 +- netCoin-1.1.23/netCoin/inst/www/template.html | 22 netCoin-1.1.23/netCoin/inst/www/timeline.js | 1058 ++-- netCoin-1.1.23/netCoin/man/allNet.Rd | 9 netCoin-1.1.23/netCoin/man/asNodes.Rd | 5 netCoin-1.1.23/netCoin/man/barCoin.Rd | 53 netCoin-1.1.23/netCoin/man/coin.Rd | 7 netCoin-1.1.23/netCoin/man/coocur.rd | 2 netCoin-1.1.23/netCoin/man/dichotomize.Rd | 19 netCoin-1.1.23/netCoin/man/distant.Rd | 2 netCoin-1.1.23/netCoin/man/edgeList.Rd | 13 netCoin-1.1.23/netCoin/man/ess.Rd |only netCoin-1.1.23/netCoin/man/fromIgraph.Rd | 11 netCoin-1.1.23/netCoin/man/glmCoin.Rd |only netCoin-1.1.23/netCoin/man/layoutCircle.Rd | 2 netCoin-1.1.23/netCoin/man/layoutGrid.Rd | 2 netCoin-1.1.23/netCoin/man/lower.Rd | 2 netCoin-1.1.23/netCoin/man/multigraphCreate.Rd | 19 netCoin-1.1.23/netCoin/man/netCoin-package.Rd | 2 netCoin-1.1.23/netCoin/man/netCoin.Rd | 33 netCoin-1.1.23/netCoin/man/netCorr.Rd | 3 netCoin-1.1.23/netCoin/man/propCoin.Rd |only netCoin-1.1.23/netCoin/man/savePajek.Rd | 5 netCoin-1.1.23/netCoin/man/shinyCoin.Rd |only netCoin-1.1.23/netCoin/man/sim.Rd | 10 netCoin-1.1.23/netCoin/man/surCoin.Rd | 8 netCoin-1.1.23/netCoin/man/timeCoin.Rd | 8 netCoin-1.1.23/netCoin/man/toIgraph.Rd | 2 netCoin-1.1.23/netCoin/vignettes/Dice.png |binary netCoin-1.1.23/netCoin/vignettes/Finches.png |binary netCoin-1.1.23/netCoin/vignettes/Padgett.png |binary netCoin-1.1.23/netCoin/vignettes/ess-a.png |only netCoin-1.1.23/netCoin/vignettes/ess-b.png |only netCoin-1.1.23/netCoin/vignettes/ess-c.png |only netCoin-1.1.23/netCoin/vignettes/ess-d.png |only netCoin-1.1.23/netCoin/vignettes/ess-e.png |only netCoin-1.1.23/netCoin/vignettes/ess-f.png |only netCoin-1.1.23/netCoin/vignettes/netCoin.Rmd | 32 netCoin-1.1.23/netCoin/vignettes/surCoin.Rmd |only 75 files changed, 8835 insertions(+), 6206 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-08 1.2.0
2018-10-22 1.1.6
2018-10-09 1.1.5
2018-05-30 1.1.4
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Noah Simon [aut],
Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 2.0-18 dated 2019-05-20 and 3.0 dated 2019-11-09
glmnet-2.0-18/glmnet/ChangeLog |only glmnet-2.0-18/glmnet/R/check_dots.R |only glmnet-2.0-18/glmnet/R/getmin.R |only glmnet-2.0-18/glmnet/inst/doc/Coxnet.rnw |only glmnet-2.0-18/glmnet/inst/doc/glmnet_beta.R |only glmnet-2.0-18/glmnet/inst/doc/glmnet_beta.Rmd |only glmnet-2.0-18/glmnet/inst/doc/glmnet_beta.pdf |only glmnet-2.0-18/glmnet/vignettes/Coxnet.rnw |only glmnet-2.0-18/glmnet/vignettes/VignetteExample.rdata |only glmnet-2.0-18/glmnet/vignettes/glmnet_beta.Rmd |only glmnet-2.0-18/glmnet/vignettes/glmnet_beta.html |only glmnet-3.0/glmnet/DESCRIPTION | 40 - glmnet-3.0/glmnet/MD5 | 176 +++-- glmnet-3.0/glmnet/NAMESPACE | 120 ++- glmnet-3.0/glmnet/NEWS.md |only glmnet-3.0/glmnet/R/Cindex.R |only glmnet-3.0/glmnet/R/assess.coxnet.R |only glmnet-3.0/glmnet/R/assess.glmnet.R |only glmnet-3.0/glmnet/R/bigGlm.R |only glmnet-3.0/glmnet/R/blend.relaxed.R |only glmnet-3.0/glmnet/R/buildPredmat.array.R |only glmnet-3.0/glmnet/R/buildPredmat.coxnetlist.R |only glmnet-3.0/glmnet/R/buildPredmat.default.R |only glmnet-3.0/glmnet/R/check.dots.R |only glmnet-3.0/glmnet/R/coef.cv.glmnet.R | 4 glmnet-3.0/glmnet/R/coef.cv.relaxed.R |only glmnet-3.0/glmnet/R/coef.glmnet.R | 6 glmnet-3.0/glmnet/R/coef.relaxed.R |only glmnet-3.0/glmnet/R/confusion.glmnet.R |only glmnet-3.0/glmnet/R/coxgrad.R |only glmnet-3.0/glmnet/R/coxnet.R | 5 glmnet-3.0/glmnet/R/coxnet.deviance.R | 114 ++- glmnet-3.0/glmnet/R/cv.coxnet.R | 71 -- glmnet-3.0/glmnet/R/cv.elnet.R | 55 - glmnet-3.0/glmnet/R/cv.fishnet.R | 52 - glmnet-3.0/glmnet/R/cv.glmnet.R | 324 +++++++--- glmnet-3.0/glmnet/R/cv.glmnet.raw.R |only glmnet-3.0/glmnet/R/cv.lognet.R | 149 +--- glmnet-3.0/glmnet/R/cv.mrelnet.R | 51 - glmnet-3.0/glmnet/R/cv.multnet.R | 81 -- glmnet-3.0/glmnet/R/cv.relaxed.raw.R |only glmnet-3.0/glmnet/R/cvcompute.R | 31 glmnet-3.0/glmnet/R/cvstats.R |only glmnet-3.0/glmnet/R/cvtype.R | 6 glmnet-3.0/glmnet/R/deviance.glmnet.R | 33 + glmnet-3.0/glmnet/R/family.glmnet.R |only glmnet-3.0/glmnet/R/getOptcv.glmnet.R |only glmnet-3.0/glmnet/R/getOptcv.relaxed.R |only glmnet-3.0/glmnet/R/glmnet-package.R |only glmnet-3.0/glmnet/R/glmnet.R | 326 ++++++++++ glmnet-3.0/glmnet/R/glmnet.control.R | 86 ++ glmnet-3.0/glmnet/R/glmnet.measures.R |only glmnet-3.0/glmnet/R/glmnet_softmax.R | 11 glmnet-3.0/glmnet/R/makeX.R |only glmnet-3.0/glmnet/R/pb.R |only glmnet-3.0/glmnet/R/plot.cv.glmnet.R | 66 +- glmnet-3.0/glmnet/R/plot.cv.relaxed.R |only glmnet-3.0/glmnet/R/plot.glmnet.R | 37 + glmnet-3.0/glmnet/R/plot.mrelnet.R | 5 glmnet-3.0/glmnet/R/plot.multnet.R | 5 glmnet-3.0/glmnet/R/plot.relaxed.R |only glmnet-3.0/glmnet/R/plotCoef.R | 4 glmnet-3.0/glmnet/R/predict.coxnet.R | 2 glmnet-3.0/glmnet/R/predict.cv.glmnet.R | 57 + glmnet-3.0/glmnet/R/predict.cv.relaxed.R |only glmnet-3.0/glmnet/R/predict.elnet.R | 2 glmnet-3.0/glmnet/R/predict.fishnet.R | 2 glmnet-3.0/glmnet/R/predict.glmnet.R | 87 ++ glmnet-3.0/glmnet/R/predict.lognet.R | 2 glmnet-3.0/glmnet/R/predict.mrelnet.R | 2 glmnet-3.0/glmnet/R/predict.multnet.R | 2 glmnet-3.0/glmnet/R/predict.relaxed.R |only glmnet-3.0/glmnet/R/print.bigGlm.R |only glmnet-3.0/glmnet/R/print.confusion.table.R |only glmnet-3.0/glmnet/R/print.cv.glmnet.R |only glmnet-3.0/glmnet/R/print.cv.relaxed.R |only glmnet-3.0/glmnet/R/print.glmnet.R | 43 + glmnet-3.0/glmnet/R/relax.glmnet.R |only glmnet-3.0/glmnet/R/response.coxnet.R | 4 glmnet-3.0/glmnet/R/rmult.R | 11 glmnet-3.0/glmnet/R/roc.glmnet.R |only glmnet-3.0/glmnet/README.md |only glmnet-3.0/glmnet/build/vignette.rds |binary glmnet-3.0/glmnet/inst/doc/Coxnet.R | 39 - glmnet-3.0/glmnet/inst/doc/Coxnet.Rmd |only glmnet-3.0/glmnet/inst/doc/Coxnet.pdf |binary glmnet-3.0/glmnet/inst/doc/glmnet.R |only glmnet-3.0/glmnet/inst/doc/glmnet.Rmd |only glmnet-3.0/glmnet/inst/doc/glmnet.pdf |only glmnet-3.0/glmnet/inst/doc/relax.R |only glmnet-3.0/glmnet/inst/doc/relax.Rmd |only glmnet-3.0/glmnet/inst/doc/relax.pdf |only glmnet-3.0/glmnet/inst/mortran/README.Rmd |only glmnet-3.0/glmnet/inst/mortran/glmnet5dpclean.m | 100 +-- glmnet-3.0/glmnet/man/Cindex.Rd |only glmnet-3.0/glmnet/man/assess.glmnet.Rd |only glmnet-3.0/glmnet/man/beta_CVX.Rd | 26 glmnet-3.0/glmnet/man/bigGlm.Rd |only glmnet-3.0/glmnet/man/coxgrad.Rd |only glmnet-3.0/glmnet/man/coxnet.deviance.Rd |only glmnet-3.0/glmnet/man/cv.glmnet.Rd | 381 ++++++----- glmnet-3.0/glmnet/man/deviance.glmnet.Rd | 67 +- glmnet-3.0/glmnet/man/glmnet-internal.Rd | 52 + glmnet-3.0/glmnet/man/glmnet-package.Rd | 105 +-- glmnet-3.0/glmnet/man/glmnet.Rd | 606 ++++++++++--------- glmnet-3.0/glmnet/man/glmnet.control.Rd | 87 +- glmnet-3.0/glmnet/man/glmnet.measures.Rd |only glmnet-3.0/glmnet/man/makeX.Rd |only glmnet-3.0/glmnet/man/na.replace.Rd |only glmnet-3.0/glmnet/man/plot.cv.glmnet.Rd | 93 +- glmnet-3.0/glmnet/man/plot.glmnet.Rd | 75 +- glmnet-3.0/glmnet/man/predict.cv.glmnet.Rd | 106 ++- glmnet-3.0/glmnet/man/predict.glmnet.Rd | 178 +++-- glmnet-3.0/glmnet/man/print.cv.glmnet.Rd |only glmnet-3.0/glmnet/man/print.glmnet.Rd | 59 + glmnet-3.0/glmnet/man/rmult.Rd |only glmnet-3.0/glmnet/src/glmnet5dpclean.f | 70 +- glmnet-3.0/glmnet/src/glmnet_init.c | 27 glmnet-3.0/glmnet/src/pb.c |only glmnet-3.0/glmnet/vignettes/Coxnet.Rmd |only glmnet-3.0/glmnet/vignettes/assets |only glmnet-3.0/glmnet/vignettes/glmnet.Rmd |only glmnet-3.0/glmnet/vignettes/relax.Rmd |only 123 files changed, 2633 insertions(+), 1510 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines" <doi:10.1214/aos/1176347963>.
(The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 5.1.1 dated 2019-04-12 and 5.1.2 dated 2019-11-09
DESCRIPTION | 8 MD5 | 90 NEWS | 14 R/earth.R | 49 R/earth.leaps.R | 68 build/partial.rdb |binary inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 inst/slowtests/test.allowedfunc.bat | 2 inst/slowtests/test.big.bat | 2 inst/slowtests/test.bpairs.Rout.save | 32 inst/slowtests/test.bpairs.bat | 2 inst/slowtests/test.cv.Rout.save |10287 +++++++++++++++--------------- inst/slowtests/test.cv.bat | 2 inst/slowtests/test.earthc.mak | 2 inst/slowtests/test.earthmain.gcc.bat | 2 inst/slowtests/test.earthmain.gcc64.bat | 10 inst/slowtests/test.earthmain.vc.bat | 2 inst/slowtests/test.expand.bpairs.bat | 2 inst/slowtests/test.full.Rout.save | 62 inst/slowtests/test.full.bat | 2 inst/slowtests/test.glm.Rout.save | 34 inst/slowtests/test.glm.bat | 2 inst/slowtests/test.incorrect.bat | 2 inst/slowtests/test.mem.R | 26 inst/slowtests/test.mem.Rout.save | 66 inst/slowtests/test.mem.bat | 2 inst/slowtests/test.mods.bat | 2 inst/slowtests/test.multresp.Rout.save | 3 inst/slowtests/test.multresp.bat | 2 inst/slowtests/test.offset.bat | 2 inst/slowtests/test.plotd.Rout.save | 20 inst/slowtests/test.plotd.bat | 2 inst/slowtests/test.pmethod.cv.Rout.save | 340 inst/slowtests/test.pmethod.cv.bat | 2 inst/slowtests/test.varmod.R | 6 inst/slowtests/test.varmod.Rout.save | 2252 +++--- inst/slowtests/test.varmod.bat | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 156 inst/slowtests/test.varmod.mgcv.bat | 2 inst/slowtests/test.weights.R | 9 inst/slowtests/test.weights.Rout.save | 124 inst/slowtests/test.weights.bat | 2 src/leaps.f | 7 src/rentries.c | 6 46 files changed, 6919 insertions(+), 6792 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the
tree in various orders. Aggregate, cumulate, print, plot, convert to and from
data.frame and more. Useful for decision trees, machine learning, finance,
conversion from and to JSON, and many other applications.
Author: Russ Hyde [ctb] (improve dependencies),
Chris Hammill [ctb] (improve getting),
Facundo Munoz [ctb] (improve list conversion),
Markus Wamser [ctb] (fixed some typos),
Pierre Formont [ctb] (additional features),
Kent Russel [ctb] (documentation),
Noam Ross [ctb] (fixes),
Duncan Garmonsway [ctb] (fixes),
Christoph Glur [aut, cre] (R interface)
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.7.8 dated 2018-09-24 and 0.7.11 dated 2019-11-09
data.tree-0.7.11/data.tree/DESCRIPTION | 28 data.tree-0.7.11/data.tree/MD5 | 60 data.tree-0.7.11/data.tree/NAMESPACE | 13 data.tree-0.7.11/data.tree/NEWS | 12 data.tree-0.7.11/data.tree/R/node_conversion_dataframe.R | 11 data.tree-0.7.11/data.tree/R/node_conversion_igraph.R | 17 data.tree-0.7.11/data.tree/R/node_conversion_list.R | 18 data.tree-0.7.11/data.tree/R/node_conversion_rpart.R |only data.tree-0.7.11/data.tree/R/node_methods_sideeffect.R | 7 data.tree-0.7.11/data.tree/R/node_methods_traversal.R | 6 data.tree-0.7.11/data.tree/R/node_plot.R | 52 data.tree-0.7.11/data.tree/R/register-s3.R |only data.tree-0.7.11/data.tree/R/zzz.R |only data.tree-0.7.11/data.tree/build/vignette.rds |binary data.tree-0.7.11/data.tree/inst/doc/applications.Rmd | 16 data.tree-0.7.11/data.tree/inst/doc/applications.html | 414 +- data.tree-0.7.11/data.tree/inst/doc/data.tree.Rmd | 13 data.tree-0.7.11/data.tree/inst/doc/data.tree.html | 1736 +++++++++- data.tree-0.7.11/data.tree/man/ToDiagrammeRGraph.Rd | 3 data.tree-0.7.11/data.tree/man/as.Node.Rd | 3 data.tree-0.7.11/data.tree/man/as.Node.data.frame.Rd | 2 data.tree-0.7.11/data.tree/man/as.Node.dendrogram.Rd | 2 data.tree-0.7.11/data.tree/man/as.Node.list.Rd | 3 data.tree-0.7.11/data.tree/man/as.Node.phylo.Rd | 3 data.tree-0.7.11/data.tree/man/as.Node.rpart.Rd |only data.tree-0.7.11/data.tree/man/as.igraph.Node.Rd | 8 data.tree-0.7.11/data.tree/man/as.list.Node.Rd | 11 data.tree-0.7.11/data.tree/man/s3_register.Rd |only data.tree-0.7.11/data.tree/tests/testthat/test-draw.R | 40 data.tree-0.7.11/data.tree/tests/testthat/test-treeConversionDataFrame.R | 10 data.tree-0.7.11/data.tree/tests/testthat/test-treeConversionList.R |only data.tree-0.7.11/data.tree/tests/testthat/test-treeConversionRpart.R |only data.tree-0.7.11/data.tree/vignettes/applications.Rmd | 16 data.tree-0.7.11/data.tree/vignettes/data.tree.Rmd | 13 data.tree-0.7.8/data.tree/tests/testthat/test-treeConversion.R |only 35 files changed, 2264 insertions(+), 253 deletions(-)
Title: Density Estimation for Grouped Data
Description: Functions for density estimation based on
grouped data, and next-generation gene expression
data.
Author: Bin Wang <bwang831@gmail.com>
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between bda versions 10.1.9 dated 2018-01-04 and 13.4.13 dated 2019-11-09
bda-10.1.9/bda/R/GLDsmooth.R |only bda-10.1.9/bda/R/MetaMeanTest.R |only bda-10.1.9/bda/R/ROC.R |only bda-10.1.9/bda/R/ccusum.R |only bda-10.1.9/bda/R/fitDagum.R |only bda-10.1.9/bda/R/lt50.R |only bda-10.1.9/bda/R/mediation.R |only bda-10.1.9/bda/R/ppower.R |only bda-10.1.9/bda/data/robot.rda |only bda-10.1.9/bda/man/FMKLGLD.Rd |only bda-10.1.9/bda/man/MetaMeanTest.Rd |only bda-10.1.9/bda/man/NGSPermTest.Rd |only bda-10.1.9/bda/man/ROC.Rd |only bda-10.1.9/bda/man/bemmix.Rd |only bda-10.1.9/bda/man/cusum.Rd |only bda-10.1.9/bda/man/lt50.logit.Rd |only bda-10.1.9/bda/man/lt50.logitfit.Rd |only bda-10.1.9/bda/man/medtest.Rd |only bda-10.1.9/bda/man/nmixCopula.Rd |only bda-10.1.9/bda/man/ppower.Rd |only bda-10.1.9/bda/man/rsdata.Rd |only bda-13.4.13/bda/DESCRIPTION | 12 bda-13.4.13/bda/MD5 | 112 ++-- bda-13.4.13/bda/NAMESPACE | 74 +-- bda-13.4.13/bda/PORTING | 105 ---- bda-13.4.13/bda/R/AIC.R |only bda-13.4.13/bda/R/Copula.R |only bda-13.4.13/bda/R/Dagum.R |only bda-13.4.13/bda/R/FSD.R |only bda-13.4.13/bda/R/GPD.R |only bda-13.4.13/bda/R/LogNormal.R |only bda-13.4.13/bda/R/NGS.R | 729 +++++++++----------------------- bda-13.4.13/bda/R/Pareto.R |only bda-13.4.13/bda/R/SMJ.R |only bda-13.4.13/bda/R/Zipf.R |only bda-13.4.13/bda/R/binning.R | 24 - bda-13.4.13/bda/R/compare.R | 98 +++- bda-13.4.13/bda/R/degtest.R |only bda-13.4.13/bda/R/fitGLD.R |only bda-13.4.13/bda/R/fitGPD.R |only bda-13.4.13/bda/R/fitPareto.R |only bda-13.4.13/bda/R/gof.R | 124 +++-- bda-13.4.13/bda/R/lpsmooth.R | 38 + bda-13.4.13/bda/R/mixLogNormal.R |only bda-13.4.13/bda/R/mixture.R | 9 bda-13.4.13/bda/R/oddsratio.R | 50 -- bda-13.4.13/bda/R/permTest.R |only bda-13.4.13/bda/R/qtest.R |only bda-13.4.13/bda/R/zzz.R | 3 bda-13.4.13/bda/data/FSD.RData |only bda-13.4.13/bda/data/LCL.RData |only bda-13.4.13/bda/data/hhi.rda |binary bda-13.4.13/bda/data/zr.RData |binary bda-13.4.13/bda/man/CopulaNMix.Rd |only bda-13.4.13/bda/man/DEGTest.Rd | 7 bda-13.4.13/bda/man/EMNGS.Rd |only bda-13.4.13/bda/man/EMmixBin.Rd |only bda-13.4.13/bda/man/FSD.Rd |only bda-13.4.13/bda/man/FSDdata.Rd |only bda-13.4.13/bda/man/GBSmooth.Rd | 2 bda-13.4.13/bda/man/GLDFMKL.Rd |only bda-13.4.13/bda/man/GLDFitting.Rd | 7 bda-13.4.13/bda/man/GPD.Rd |only bda-13.4.13/bda/man/Pareto.Rd |only bda-13.4.13/bda/man/PermTest.Rd |only bda-13.4.13/bda/man/RNALCL.Rd |only bda-13.4.13/bda/man/Zipf.Rd |only bda-13.4.13/bda/man/compare.Rd | 1 bda-13.4.13/bda/man/fitGLDsmj.Rd |only bda-13.4.13/bda/man/fitGPD.Rd |only bda-13.4.13/bda/man/fitLogNormal.Rd | 20 bda-13.4.13/bda/man/fitPareto.Rd |only bda-13.4.13/bda/man/gof.Rd | 18 bda-13.4.13/bda/man/lognormalmixture.Rd |only bda-13.4.13/bda/man/mlognormal.Rd |only bda-13.4.13/bda/man/oddsratio.Rd | 38 - bda-13.4.13/bda/man/qtest.Rd |only bda-13.4.13/bda/man/zr.Rd | 2 bda-13.4.13/bda/src/AS176.f | 457 ++++++++++---------- bda-13.4.13/bda/src/AS254.f | 310 ++++++------- bda-13.4.13/bda/src/Ckernel.c | 95 ++-- bda-13.4.13/bda/src/Fkernel.f | 45 - bda-13.4.13/bda/src/Pareto.c |only bda-13.4.13/bda/src/em.c |only bda-13.4.13/bda/src/init.c | 97 +++- bda-13.4.13/bda/src/lognormal.c |only bda-13.4.13/bda/src/permtest.c |only 87 files changed, 1167 insertions(+), 1310 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.1 dated 2019-03-25 and 1.4 dated 2019-11-09
ChangeLog | 6 DESCRIPTION | 8 - MD5 | 36 ++--- R/estVC.R | 264 ++++++++++++++++++++++++++++--------------- R/pedRecode.R | 172 ++++++++++++++-------------- R/scan.R | 80 +++---------- data/miscEx.RData |binary inst/doc/QTLRel_Tutorial.pdf |binary man/pedRecode.Rd | 6 src/QTLRelR.c | 4 src/QTLRelR.h | 56 ++++----- src/dqrcf.f | 2 src/dqrls.f | 6 src/init.c | 14 -- src/rgdat.c | 10 - src/sc10.f | 113 ++---------------- src/sc11.f | 115 +++--------------- src/sc20.f | 116 ++---------------- src/sc21.f | 116 +++--------------- 19 files changed, 440 insertions(+), 684 deletions(-)
Title: Calculate the RR for the GAM
Description: To calculate the relative risk (RR) for the generalized additive model.
Author: Zhicheng Du, Wangjian Zhang, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between gamRR versions 0.6.0 dated 2019-03-20 and 0.7.0 dated 2019-11-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/gamRR.R | 1 + R/gamRR.boot.R | 1 + man/gamRR.Rd | 2 ++ man/gamRR.boot.Rd | 2 ++ 6 files changed, 15 insertions(+), 9 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.1-6 dated 2019-11-06 and 3.1-7 dated 2019-11-09
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- R/cox.zph.R | 47 ++++++++++++++++++++++++++++++----------------- inst/NEWS.Rd | 13 ++++++++++++- inst/doc/adjcurve.pdf |binary inst/doc/approximate.pdf |binary inst/doc/compete.pdf |binary inst/doc/concordance.pdf |binary inst/doc/multi.pdf |binary inst/doc/other.pdf |binary inst/doc/population.pdf |binary inst/doc/splines.pdf |binary inst/doc/survival.pdf |binary inst/doc/tiedtimes.pdf |binary inst/doc/timedep.pdf |binary inst/doc/validate.pdf |binary man/cox.zph.Rd | 23 +++++++++++++++++++---- noweb/code.nw | 47 ++++++++++++++++++++++++++++++----------------- noweb/zph.Rnw | 47 ++++++++++++++++++++++++++++++----------------- tests/multi2.R | 6 ++++++ tests/multi2.Rout.save | 15 ++++++++++++++- 21 files changed, 165 insertions(+), 81 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-30 dated 2019-10-24 and 1.8-31 dated 2019-11-09
ChangeLog | 11 +++++++++-- DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/bam.r | 3 ++- R/gam.fit4.r | 8 ++++---- R/gamm.r | 36 ++++++++++++++++++++++-------------- R/mgcv.r | 4 ++-- man/gamm.Rd | 6 +++++- src/mat.c | 15 ++++++++++----- src/mgcv.h | 10 +++++----- 10 files changed, 71 insertions(+), 46 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a combination
of narrative, figures, videos, exercises, and quizzes to create self-paced
tutorials for learning about R and R packages.
Author: Barret Schloerke [aut, cre] (<https://orcid.org/0000-0001-9986-114X>),
JJ Allaire [aut],
Barbara Borges [aut],
RStudio, Inc. [cph],
Ajax.org B.V. [ctb, cph] (Ace library),
Zeno Rocha [ctb, cph] (clipboard.js library),
Nick Payne [ctb, cph] (Bootbox library),
Jake Archibald [ctb, cph] (idb-keyval library)
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between learnr versions 0.9.2.1 dated 2018-06-29 and 0.10.0 dated 2019-11-09
learnr-0.10.0/learnr/DESCRIPTION | 32 learnr-0.10.0/learnr/MD5 | 126 + learnr-0.10.0/learnr/NAMESPACE | 40 learnr-0.10.0/learnr/NEWS.md | 40 learnr-0.10.0/learnr/R/ace.R | 1 learnr-0.10.0/learnr/R/available_tutorials.R |only learnr-0.10.0/learnr/R/evaluators.R | 61 learnr-0.10.0/learnr/R/events.R | 95 - learnr-0.10.0/learnr/R/exercise.R | 317 ++-- learnr-0.10.0/learnr/R/feedback.R | 34 learnr-0.10.0/learnr/R/html-dependencies.R | 19 learnr-0.10.0/learnr/R/html_selector.R |only learnr-0.10.0/learnr/R/http-handlers.R | 147 - learnr-0.10.0/learnr/R/identifiers.R | 38 learnr-0.10.0/learnr/R/initialize.R | 34 learnr-0.10.0/learnr/R/install_tutorial_dependencies.R |only learnr-0.10.0/learnr/R/knitr-hooks.R | 104 - learnr-0.10.0/learnr/R/mutate_tags.R |only learnr-0.10.0/learnr/R/options.R | 18 learnr-0.10.0/learnr/R/package.R | 7 learnr-0.10.0/learnr/R/praise.R |only learnr-0.10.0/learnr/R/question_checkbox.R |only learnr-0.10.0/learnr/R/question_methods.R |only learnr-0.10.0/learnr/R/question_radio.R |only learnr-0.10.0/learnr/R/question_text.R |only learnr-0.10.0/learnr/R/quiz.R | 738 +++++++-- learnr-0.10.0/learnr/R/quiz_print.R |only learnr-0.10.0/learnr/R/run.R | 157 +- learnr-0.10.0/learnr/R/storage.R | 196 +- learnr-0.10.0/learnr/R/tutorial-format.R | 79 - learnr-0.10.0/learnr/R/utils.R | 79 + learnr-0.10.0/learnr/inst/lib/ace/ace.js | 164 -- learnr-0.10.0/learnr/inst/lib/idb-keyval |only learnr-0.10.0/learnr/inst/lib/tutorial/tutorial.css | 18 learnr-0.10.0/learnr/inst/lib/tutorial/tutorial.js | 772 +++++----- learnr-0.10.0/learnr/inst/rmarkdown/templates/tutorial/resources/rstudio-theme.css | 83 + learnr-0.10.0/learnr/inst/rmarkdown/templates/tutorial/resources/tutorial-format.css | 5 learnr-0.10.0/learnr/inst/rmarkdown/templates/tutorial/resources/tutorial-format.htm | 107 + learnr-0.10.0/learnr/inst/tutorials/ex-data-basics |only learnr-0.10.0/learnr/inst/tutorials/ex-data-filter |only learnr-0.10.0/learnr/inst/tutorials/ex-data-mutate |only learnr-0.10.0/learnr/inst/tutorials/ex-data-summarise |only learnr-0.10.0/learnr/inst/tutorials/ex-setup-r |only learnr-0.10.0/learnr/inst/tutorials/quiz_question |only learnr-0.10.0/learnr/inst/tutorials/slidy/slidy.Rmd | 4 learnr-0.10.0/learnr/man/available_tutorials.Rd |only learnr-0.10.0/learnr/man/disable_all_tags.Rd |only learnr-0.10.0/learnr/man/duplicate_env.Rd |only learnr-0.10.0/learnr/man/filesystem_storage.Rd | 4 learnr-0.10.0/learnr/man/format_quiz.Rd |only learnr-0.10.0/learnr/man/initialize_tutorial.Rd | 4 learnr-0.10.0/learnr/man/knit_print.Rd |only learnr-0.10.0/learnr/man/mark_as_correct_incorrect.Rd |only learnr-0.10.0/learnr/man/question_checkbox.Rd |only learnr-0.10.0/learnr/man/question_methods.Rd |only learnr-0.10.0/learnr/man/question_radio.Rd |only learnr-0.10.0/learnr/man/question_text.Rd |only learnr-0.10.0/learnr/man/quiz.Rd | 87 - learnr-0.10.0/learnr/man/random_praise.Rd |only learnr-0.10.0/learnr/man/run_tutorial.Rd | 22 learnr-0.10.0/learnr/man/safe.Rd |only learnr-0.10.0/learnr/man/safe_env.Rd |only learnr-0.10.0/learnr/man/tutorial.Rd | 19 learnr-0.10.0/learnr/man/tutorial_html_dependency.Rd | 2 learnr-0.10.0/learnr/man/tutorial_options.Rd | 14 learnr-0.10.0/learnr/tests/testthat/test-available-tutorials.R |only learnr-0.10.0/learnr/tests/testthat/test-duplicate_env.R |only learnr-0.10.0/learnr/tests/testthat/test-install-dependencies.R |only learnr-0.10.0/learnr/tests/testthat/test-mark_as.R |only learnr-0.10.0/learnr/tests/testthat/test-question-checkbox.R |only learnr-0.10.0/learnr/tests/testthat/test-question.R |only learnr-0.10.0/learnr/tests/testthat/test-question_messages.R |only learnr-0.10.0/learnr/tests/testthat/test-quiz.R | 57 learnr-0.10.0/learnr/tests/testthat/test-safe.R |only learnr-0.9.2.1/learnr/LICENSE |only learnr-0.9.2.1/learnr/inst/htmlwidgets |only learnr-0.9.2.1/learnr/inst/lib/localforage |only learnr-0.9.2.1/learnr/inst/tutorials/hello/hello.html |only learnr-0.9.2.1/learnr/inst/tutorials/slidy/slidy.html |only 79 files changed, 2503 insertions(+), 1221 deletions(-)
Title: Predict Gender from Names Using Historical Data
Description: Infers state-recorded gender categories from first names and dates of birth using historical
datasets. By using these datasets instead of lists of male and female names,
this package is able to more accurately infer the gender of a name, and it
is able to report the probability that a name was male or female. GUIDELINES:
This method must be used cautiously and responsibly. Please be sure to see the
guidelines and warnings about usage in the 'README' or the package documentation.
Author: Lincoln Mullen [aut, cre] (<https://orcid.org/0000-0001-5103-6917>),
Cameron Blevins [ctb],
Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between gender versions 0.5.2 dated 2018-03-07 and 0.5.3 dated 2019-11-09
DESCRIPTION | 24 ++-- MD5 | 24 ++-- NEWS | 5 R/gender-package.r | 40 +++++++ README.md | 104 +++++++++++++----- build/vignette.rds |binary inst/doc/predicting-gender.Rmd | 4 inst/doc/predicting-gender.html | 228 ++++++++++++++++++++++------------------ man/gender-package.Rd | 32 +++++ man/gender.Rd | 4 man/gender_df.Rd | 4 tests/run-all.R | 2 vignettes/predicting-gender.Rmd | 4 13 files changed, 322 insertions(+), 153 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 1.17 dated 2019-10-28 and 1.18 dated 2019-11-09
aqp-1.17/aqp/NEWS |only aqp-1.18/aqp/.Rinstignore | 6 aqp-1.18/aqp/DESCRIPTION | 18 aqp-1.18/aqp/MD5 | 147 ++++--- aqp-1.18/aqp/NAMESPACE | 19 aqp-1.18/aqp/NEWS.md |only aqp-1.18/aqp/R/Class-SoilProfileCollection.R | 15 aqp-1.18/aqp/R/SPC-find_horizons.R | 62 +-- aqp-1.18/aqp/R/SoilProfileCollection-coercion.R | 10 aqp-1.18/aqp/R/SoilProfileCollection-methods.R | 127 +++++- aqp-1.18/aqp/R/SoilProfileCollection-slice-methods.R | 22 - aqp-1.18/aqp/R/addBracket.R | 250 ++++++------ aqp-1.18/aqp/R/addVolumeFraction.R | 62 ++- aqp-1.18/aqp/R/aggregateColor.R | 73 ++- aqp-1.18/aqp/R/colorContrast.R |only aqp-1.18/aqp/R/colorContrastPlot.R |only aqp-1.18/aqp/R/colorQuantiles.R | 16 aqp-1.18/aqp/R/contrastChart.R |only aqp-1.18/aqp/R/contrastClass.R |only aqp-1.18/aqp/R/denormalize.R |only aqp-1.18/aqp/R/explainPlotSPC.R | 9 aqp-1.18/aqp/R/generalize.hz.R | 13 aqp-1.18/aqp/R/get.increase.matrix.R | 2 aqp-1.18/aqp/R/getSurfaceHorizonDepth.R | 2 aqp-1.18/aqp/R/glom.R | 77 ++- aqp-1.18/aqp/R/huePosition.R |only aqp-1.18/aqp/R/munsell2rgb.R | 18 aqp-1.18/aqp/R/plotSPC.R | 104 +++-- aqp-1.18/aqp/R/previewColors.R | 13 aqp-1.18/aqp/R/profile_compare.R | 22 - aqp-1.18/aqp/R/rebuildSPC.R | 8 aqp-1.18/aqp/R/setters.R | 10 aqp-1.18/aqp/R/sketch-utils.R |only aqp-1.18/aqp/R/slab.R | 47 +- aqp-1.18/aqp/R/soilColorSignature.R | 14 aqp-1.18/aqp/R/soilPalette.R |only aqp-1.18/aqp/R/tauW.R | 392 +++++++++---------- aqp-1.18/aqp/R/texture-low-rv-high.R | 276 ++++++------- aqp-1.18/aqp/R/union.R | 9 aqp-1.18/aqp/R/unroll.R | 2 aqp-1.18/aqp/data/jacobs2000.rda |only aqp-1.18/aqp/data/sp5.rda |binary aqp-1.18/aqp/demo/aqp.R | 282 ++++++------- aqp-1.18/aqp/inst/_pkgdown.yml |only aqp-1.18/aqp/inst/example-data |only aqp-1.18/aqp/man/SPC-plotting.Rd | 40 + aqp-1.18/aqp/man/SPC-slab-methods.Rd | 53 ++ aqp-1.18/aqp/man/SPC-slice-methods.Rd | 29 - aqp-1.18/aqp/man/SoilProfileCollection-class.Rd | 3 aqp-1.18/aqp/man/addBracket.Rd | 148 +++---- aqp-1.18/aqp/man/addVolumeFraction.Rd | 22 - aqp-1.18/aqp/man/aggregateColor.Rd | 3 aqp-1.18/aqp/man/brierScore.Rd | 52 +- aqp-1.18/aqp/man/colorContrast.Rd |only aqp-1.18/aqp/man/colorContrastPlot.Rd |only aqp-1.18/aqp/man/colorQuantiles.Rd | 3 aqp-1.18/aqp/man/confusionIndex.Rd | 70 +-- aqp-1.18/aqp/man/contrastChart.Rd |only aqp-1.18/aqp/man/contrastClass.Rd |only aqp-1.18/aqp/man/denormalize.Rd |only aqp-1.18/aqp/man/f.noise.Rd | 310 +++++++-------- aqp-1.18/aqp/man/fixOverlap.Rd |only aqp-1.18/aqp/man/generalize.hz.Rd | 29 + aqp-1.18/aqp/man/glom.Rd | 2 aqp-1.18/aqp/man/huePosition.Rd |only aqp-1.18/aqp/man/jacobs2000.Rd |only aqp-1.18/aqp/man/munsell2rgb.Rd | 25 + aqp-1.18/aqp/man/plot_distance_graph.Rd | 78 +-- aqp-1.18/aqp/man/profile_compare-methods.Rd | 372 +++++++++--------- aqp-1.18/aqp/man/resample.twotheta.Rd | 94 ++-- aqp-1.18/aqp/man/rruff.sample.Rd | 74 +-- aqp-1.18/aqp/man/shannonEntropy.Rd | 74 +-- aqp-1.18/aqp/man/soilPalette.Rd |only aqp-1.18/aqp/man/soil_minerals.Rd | 140 +++--- aqp-1.18/aqp/man/sp6.Rd | 114 ++--- aqp-1.18/aqp/man/tauW.Rd | 216 +++++----- aqp-1.18/aqp/man/texture.triangle.low.rv.high.Rd | 131 +++--- aqp-1.18/aqp/man/union.Rd | 2 aqp-1.18/aqp/tests/testthat/test-SPC-objects.R | 76 +++ aqp-1.18/aqp/tests/testthat/test-SPC-union.R | 31 + aqp-1.18/aqp/tests/testthat/test-aggregateColor.R |only aqp-1.18/aqp/tests/testthat/test-color-conversion.R | 39 + aqp-1.18/aqp/tests/testthat/test-colorContrast.R |only aqp-1.18/aqp/tests/testthat/test-denormalize.R |only aqp-1.18/aqp/tests/testthat/test-genhz.R |only aqp-1.18/aqp/tests/testthat/test-overlap.R |only aqp-1.18/aqp/tests/testthat/test-plotSPC.R |only aqp-1.18/aqp/tests/testthat/test-profile_compare.R | 16 aqp-1.18/aqp/tests/testthat/test-surface-thickness.R | 2 89 files changed, 2505 insertions(+), 1870 deletions(-)