Title: Performs the Joint Graphical Lasso for Sparse Inverse Covariance
Estimation on Multiple Classes
Description: The Joint Graphical Lasso is a generalized method for
estimating Gaussian graphical models/ sparse inverse covariance
matrices/ biological networks on multiple classes of data. We
solve JGL under two penalty functions: The Fused Graphical
Lasso (FGL), which employs a fused penalty to encourage inverse
covariance matrices to be similar across classes, and the Group
Graphical Lasso (GGL), which encourages similar network
structure between classes. FGL is recommended over GGL for
most applications. Reference: Danaher P, Wang P, Witten DM. (2013)
<doi:10.1111/rssb.12033>.
Author: Patrick Danaher
Maintainer: Patrick Danaher <pdanaher@uw.edu>
Diff between JGL versions 2.3 dated 2013-04-16 and 2.3.1 dated 2018-11-30
DESCRIPTION | 16 - MD5 | 54 ++-- NAMESPACE | 12 NEWS.md |only R/JGL.r | 572 ++++++++++++++++++++++----------------------- R/admm.iters.r | 164 ++++++------ R/admm.iters.unconnected.r | 168 ++++++------- R/crit.R | 40 +-- R/dsgl.R | 58 ++-- R/flsa.general.R | 278 ++++++++++----------- R/gcrit.R | 40 +-- R/net.edges.R | 1 R/screen.fgl.R | 128 +++++----- R/screen.ggl.R | 100 +++---- R/subnetworks.R | 108 ++++---- README.md |only man/JGL-internal.Rd | 22 - man/JGL-package.Rd | 92 +++---- man/JGL.Rd | 187 +++++++------- man/crit.Rd | 100 +++---- man/example.data.Rd | 56 ++-- man/gcrit.Rd | 98 +++---- man/net.degree.Rd | 84 +++--- man/net.edges.Rd | 86 +++--- man/net.hubs.Rd | 86 +++--- man/net.neighbors.Rd | 92 +++---- man/screen.fgl.Rd | 102 ++++---- man/screen.ggl.Rd | 92 +++---- man/subnetworks.Rd | 80 +++--- 29 files changed, 1465 insertions(+), 1451 deletions(-)
More information about ggnormalviolin at CRAN
Permanent link
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb],
R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 4.0-3 dated 2018-08-19 and 4.1-0 dated 2018-11-30
effects-4.0-3/effects/inst/doc/effectsMethods.R |only effects-4.0-3/effects/inst/doc/effectsMethods.Rnw |only effects-4.0-3/effects/inst/doc/effectsMethods.pdf |only effects-4.0-3/effects/man/plot.predictoreff.Rd |only effects-4.0-3/effects/vignettes/effectsMethods.Rnw |only effects-4.0-3/effects/vignettes/effectsMethods.bib |only effects-4.1-0/effects/DESCRIPTION | 10 effects-4.1-0/effects/MD5 | 66 - effects-4.1-0/effects/NAMESPACE | 160 +- effects-4.1-0/effects/NEWS | 616 ++++----- effects-4.1-0/effects/R/Effect-methods.R | 9 effects-4.1-0/effects/R/Effect.R | 26 effects-4.1-0/effects/R/effectsHexsticker.R |only effects-4.1-0/effects/R/effectspoLCA.R | 135 +- effects-4.1-0/effects/R/plot-methods.R | 64 effects-4.1-0/effects/R/plot.effpoly.R | 149 +- effects-4.1-0/effects/R/predictorEffects.R | 334 ++--- effects-4.1-0/effects/R/utilities.R | 36 effects-4.1-0/effects/build/vignette.rds |binary effects-4.1-0/effects/inst/CITATION | 110 + effects-4.1-0/effects/inst/doc/adding-Effect-methods.R |only effects-4.1-0/effects/inst/doc/adding-Effect-methods.Rnw |only effects-4.1-0/effects/inst/doc/adding-Effect-methods.pdf |only effects-4.1-0/effects/inst/doc/effects-hex.pdf |only effects-4.1-0/effects/inst/doc/partial-residuals.R | 320 ++-- effects-4.1-0/effects/inst/doc/partial-residuals.Rnw | 648 +++++----- effects-4.1-0/effects/inst/doc/partial-residuals.pdf |binary effects-4.1-0/effects/inst/doc/predictor-effects-gallery.R |only effects-4.1-0/effects/inst/doc/predictor-effects-gallery.Rnw |only effects-4.1-0/effects/inst/doc/predictor-effects-gallery.pdf |only effects-4.1-0/effects/man/LegacyArguments.Rd | 247 +-- effects-4.1-0/effects/man/effect-methods.Rd | 4 effects-4.1-0/effects/man/effect.Rd | 55 effects-4.1-0/effects/man/effects-package.Rd | 162 +- effects-4.1-0/effects/man/effectsHexsticker.Rd |only effects-4.1-0/effects/man/plot.effect.Rd |only effects-4.1-0/effects/man/predictorEffects.Rd | 64 effects-4.1-0/effects/man/summary.effect.Rd | 493 +------ effects-4.1-0/effects/vignettes/adding-Effect-methods.Rnw |only effects-4.1-0/effects/vignettes/adding-Effect-methods.bib |only effects-4.1-0/effects/vignettes/partial-residuals.Rnw | 648 +++++----- effects-4.1-0/effects/vignettes/partial-residuals.bib | 15 effects-4.1-0/effects/vignettes/predictor-effects-gallery.Rnw |only effects-4.1-0/effects/vignettes/predictor-effects-gallery.bib |only 44 files changed, 2125 insertions(+), 2246 deletions(-)
Title: Polyhedra Database
Description: A polyhedra database scraped from various sources as R6 objects and 'rgl' visualizing capabilities.
Author: Alejandro Baranek [aut, com, cre, cph],
Leonardo Belen [aut, com, cph]
Maintainer: Alejandro Baranek <abaranek@dc.uba.ar>
Diff between Rpolyhedra versions 0.2.8 dated 2018-10-05 and 0.3.0 dated 2018-11-30
Rpolyhedra-0.2.8/Rpolyhedra/inst/doc/poly_original_help_message.R |only Rpolyhedra-0.2.8/Rpolyhedra/inst/doc/poly_original_help_message.Rmd |only Rpolyhedra-0.2.8/Rpolyhedra/inst/doc/poly_original_help_message.html |only Rpolyhedra-0.3.0/Rpolyhedra/DESCRIPTION | 11 Rpolyhedra-0.3.0/Rpolyhedra/MD5 | 329 ++-- Rpolyhedra-0.3.0/Rpolyhedra/NAMESPACE | 22 Rpolyhedra-0.3.0/Rpolyhedra/R/db-lib.R | 711 +++++--- Rpolyhedra-0.3.0/Rpolyhedra/R/ledger-lib.R | 247 ++- Rpolyhedra-0.3.0/Rpolyhedra/R/polyhedra-lib.R | 791 ++++++---- Rpolyhedra-0.3.0/Rpolyhedra/R/serialization-lib.R | 19 Rpolyhedra-0.3.0/Rpolyhedra/R/zzz.R | 75 Rpolyhedra-0.3.0/Rpolyhedra/README.md | 26 Rpolyhedra-0.3.0/Rpolyhedra/inst/doc/Rpolyhedra.Rmd | 26 Rpolyhedra-0.3.0/Rpolyhedra/inst/doc/Rpolyhedra.html | 76 Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra.RDS |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/1b53af19.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/2d13193a.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/75a525aa.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/98d9147f.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/9cfe921d.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/b844f693.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/c26dab1e.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/c2ed6fc0.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/dmccooey/cecb7eda.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/011e6aa5.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/013c8d56.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/018facb1.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/02bf6e28.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/049fcc28.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/06592c44.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/06678c92.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/0bea582b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/1151cc88.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/135d3b3b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/13811592.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/15cafb47.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/162e6ada.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/16bc8c3a.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/1834f5c8.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/1cecd28f.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/1ed7c4eb.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/1f94cbba.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/2120e77b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/249171d0.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/249e5125.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/254037c6.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/25ea7772.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/265d43e2.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/275a5b5b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/27ea68b1.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/2be179dc.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/3346351c.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/3435c65e.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/34543164.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/346c21b0.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/34fe1260.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/35a6eff7.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/35db309a.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/369ad7b5.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/3bc5094f.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/3c4269ff.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/3d52d6c8.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/41ad8983.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/4437a6ca.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/463c0548.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/4b857767.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/53052db5.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/558ff660.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/5c2b6919.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/61116952.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/64b18a31.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/65a81360.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/65e51458.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/6879c873.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/69383818.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/6a8c3470.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/6b18eb73.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/7512b922.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/75be1c96.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/7635b688.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/7740b215.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/7b4af8a0.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/7b6d0744.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/81d5378a.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/822a6cae.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/8726b2d6.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/92006619.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/92add8a6.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/9ae4c50c.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/9b01d03f.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/9bc04794.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/9d826ad9.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/9f5c91aa.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a2e04824.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a47e4645.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a4dc42bf.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a4e2664a.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a6a91780.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/a8df0712.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/aed25469.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/b0f480ed.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/b4fa93d6.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/b515817d.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/b634e818.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/b7034094.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/bb6dd324.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/bbbfe93f.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/bcabaf81.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/bd38db04.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/c05b78f2.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/c17b0137.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/c301260e.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/c677f079.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/c9954f75.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/cbcb4124.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/cbcffbb9.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/cbdc1cef.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/ce24aaa5.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/cf4e183c.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/d0af0bc9.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/d484e616.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/d685b90c.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/d94f33b9.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/d9998a7b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/dc9fa583.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/dde7ac72.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/de7688cc.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/e0c587d5.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/e18d5c68.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/e3d9b0db.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/e5fa243c.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/e9a22c75.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/edfd962d.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/eff7e53b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f3295a93.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f399e005.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f4091898.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f7071c7d.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f8a1789b.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/f95d36c6.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/fa1459bf.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/fe70d311.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/polyhedra/netlib/ff3a53a7.RDS.zip |binary Rpolyhedra-0.3.0/Rpolyhedra/inst/extdata/version | 2 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedraDatabase.class.Rd | 31 Rpolyhedra-0.3.0/Rpolyhedra/man/Polyhedron.class.Rd | 23 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronState.class.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronStateDefined.class.Rd | 71 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronStateDmccoeyScraper.class.Rd | 7 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronStateNetlibScraper.class.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronTestTask.class.Rd | 4 Rpolyhedra-0.3.0/Rpolyhedra/man/PolyhedronTestTaskScrape.class.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/checkDatabaseVersion.Rd | 7 Rpolyhedra-0.3.0/Rpolyhedra/man/checkVertices.Rd | 4 Rpolyhedra-0.3.0/Rpolyhedra/man/getAvailablePolyhedra.Rd | 4 Rpolyhedra-0.3.0/Rpolyhedra/man/getAvailableSources.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/getGitCommit.Rd | 6 Rpolyhedra-0.3.0/Rpolyhedra/man/getPercentilPolyhedraQuant.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/getPolyhedron.Rd | 12 Rpolyhedra-0.3.0/Rpolyhedra/man/isCompatiblePolyhedraRDS.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/polyhedronToXML.Rd | 3 Rpolyhedra-0.3.0/Rpolyhedra/man/scrapePolyhedra.Rd | 7 Rpolyhedra-0.3.0/Rpolyhedra/man/scrapePolyhedraSources.Rd | 8 Rpolyhedra-0.3.0/Rpolyhedra/man/switchToFullDatabase.Rd | 6 Rpolyhedra-0.3.0/Rpolyhedra/man/updatePolyhedraDatabase.Rd | 5 Rpolyhedra-0.3.0/Rpolyhedra/tests/testthat/test_rpolyhedra_lib.R | 57 Rpolyhedra-0.3.0/Rpolyhedra/vignettes/Rpolyhedra.Rmd | 26 167 files changed, 1613 insertions(+), 1021 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Bill Venables [ctb],
Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.0 dated 2018-11-18 and 2.1 dated 2018-11-30
DESCRIPTION | 9 +--- MD5 | 84 ++++++++++++++++++++-------------------- NEWS | 17 +++++--- R/mc.pwbart.R | 6 +- R/pwbart.R | 10 ++-- build/vignette.rds |binary configure | 27 ++++++------ configure.ac | 15 ++++--- data/ACTG175.rda |binary data/Alligator.RData |binary data/arq.rda |binary data/bladder.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/00Index | 6 +- demo/alligator.R | 41 ++++++++++++++----- demo/cube.lbart.R | 2 demo/sparse.wbart.R | 19 +++++++-- inst/doc/bincat.pdf |binary inst/doc/computing.pdf |binary inst/doc/cont1.pdf |binary inst/doc/cont2.pdf |binary inst/doc/hwbart.pdf |binary inst/doc/time-to-event.pdf |binary man/gbart.Rd | 4 - man/lbart.Rd | 2 man/mbart.Rd | 2 man/mc.lbart.Rd | 2 man/mc.pbart.Rd | 2 man/pbart.Rd | 2 man/pwbart.Rd | 7 +++ vignettes/figures/alligator.pdf |binary vignettes/figures/boston1.pdf |binary vignettes/figures/boston2.pdf |binary vignettes/figures/boston3.pdf |binary vignettes/figures/boston4.pdf |binary vignettes/figures/boston5.pdf |binary vignettes/figures/boston6.pdf |binary vignettes/references.bib | 24 ++++++++++- 43 files changed, 179 insertions(+), 102 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis [aut, cre],
Allen Day [ctb] (Some documentation and examples ported from the getopt
package.),
Python Software Foundation [ctb] (Some documentation from the optparse
Python module.),
Paul Newell [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 1.1.1 dated 2018-01-24 and 2.0.0 dated 2018-11-30
argparse-1.1.1/argparse/NEWS |only argparse-2.0.0/argparse/DESCRIPTION | 29 ++- argparse-2.0.0/argparse/MD5 | 25 +- argparse-2.0.0/argparse/NAMESPACE | 2 argparse-2.0.0/argparse/NEWS.md |only argparse-2.0.0/argparse/R/argparse.R | 146 +++++++++++++---- argparse-2.0.0/argparse/README.md |only argparse-2.0.0/argparse/build/vignette.rds |binary argparse-2.0.0/argparse/exec/display_file.R | 2 argparse-2.0.0/argparse/exec/example.R | 2 argparse-2.0.0/argparse/inst/COPYRIGHTS | 6 argparse-2.0.0/argparse/inst/doc/argparse.html | 46 ++--- argparse-2.0.0/argparse/tests/test_help.Rout.save | 1 argparse-2.0.0/argparse/tests/test_version.Rout.save | 1 argparse-2.0.0/argparse/tests/testthat/test-argparse.R | 87 ++++++++-- 15 files changed, 248 insertions(+), 99 deletions(-)
Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Diff between ARTP2 versions 0.9.44 dated 2018-09-11 and 0.9.45 dated 2018-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 14 ++++++++++---- configure.ac | 15 +++++++++++---- 4 files changed, 28 insertions(+), 15 deletions(-)
Title: Calculates Critical Test Statistics to Control False Discovery
Rates in Marginal Effects Plots
Description: Implements the procedures suggested in Esarey and Sumner (2017) <http://justinesarey.com/interaction-overconfidence.pdf> for controlling the false discovery rate when constructing marginal effects plots for models with interaction terms.
Author: Justin Esarey and Jane Lawrence Sumner
Maintainer: Justin Esarey <justin@justinesarey.com>
Diff between interactionTest versions 1.0.1 dated 2017-03-21 and 1.1 dated 2018-11-30
DESCRIPTION | 18 +++---- MD5 | 16 +++--- NAMESPACE | 4 - R/bootFun.R | 116 +++----------------------------------------------- R/fdrInteraction.R | 4 + R/findMultiLims.R | 104 ++------------------------------------------ man/bootFun.Rd | 76 +------------------------------- man/fdrInteraction.Rd | 2 man/findMultiLims.Rd | 78 +-------------------------------- 9 files changed, 41 insertions(+), 377 deletions(-)
More information about interactionTest at CRAN
Permanent link
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 6.500 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.1.10.0.1 dated 2018-10-30 and 0.1.11.1.1 dated 2018-11-30
ChangeLog | 8 ++ DESCRIPTION | 12 ++-- MD5 | 30 +++++----- NEWS.md | 9 +++ README.md | 4 - inst/CITATION |only inst/include/ensmallen.hpp | 4 - inst/include/ensmallen_bits/ens_version.hpp | 6 +- inst/include/ensmallen_bits/function/sfinae_utility.hpp | 6 +- inst/include/ensmallen_bits/grid_search/grid_search_impl.hpp | 22 ------- inst/include/ensmallen_bits/sgd/decay_policies/no_decay.hpp | 6 +- inst/include/ensmallen_bits/sgd/sgd.hpp | 8 +- inst/include/ensmallen_bits/sgd/sgd_impl.hpp | 12 ++-- inst/include/ensmallen_bits/sgd/update_policies/nesterov_momentum_update.hpp | 7 +- inst/include/ensmallen_bits/wn_grad |only man/RcppEnsmallen-package.Rd | 2 16 files changed, 69 insertions(+), 67 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <http://jmlr.org/papers/v18/15-481.html>). Both Cayley, footrule, Kendall, and Spearman distances are supported in the models. The rank data to be analyzed can be the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen, Valeria Vitelli, Marta Crispino, Qinghua Liu
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 0.1.1 dated 2018-10-15 and 0.2.0 dated 2018-11-30
BayesMallows-0.1.1/BayesMallows/R/compute_cp_consensus.R |only BayesMallows-0.1.1/BayesMallows/R/compute_map_consensus.R |only BayesMallows-0.1.1/BayesMallows/inst/examples/compute_cp_consensus_example.R |only BayesMallows-0.1.1/BayesMallows/inst/examples/compute_map_consensus_example.R |only BayesMallows-0.2.0/BayesMallows/DESCRIPTION | 12 BayesMallows-0.2.0/BayesMallows/MD5 | 132 - BayesMallows-0.2.0/BayesMallows/NAMESPACE | 4 BayesMallows-0.2.0/BayesMallows/NEWS.md |only BayesMallows-0.2.0/BayesMallows/R/RcppExports.R | 18 BayesMallows-0.2.0/BayesMallows/R/assess_convergence.R | 213 +- BayesMallows-0.2.0/BayesMallows/R/compute_consensus.R |only BayesMallows-0.2.0/BayesMallows/R/compute_mallows.R | 110 - BayesMallows-0.2.0/BayesMallows/R/compute_mallows_mixtures.R | 11 BayesMallows-0.2.0/BayesMallows/R/compute_posterior_intervals.R | 4 BayesMallows-0.2.0/BayesMallows/R/generate_initial_ranking.R | 16 BayesMallows-0.2.0/BayesMallows/R/generate_transitive_closure.R | 14 BayesMallows-0.2.0/BayesMallows/R/plot.BayesMallows.R | 22 BayesMallows-0.2.0/BayesMallows/R/plot_elbow.R | 2 BayesMallows-0.2.0/BayesMallows/R/plot_top_k.R | 18 BayesMallows-0.2.0/BayesMallows/R/predict_top_k.R | 46 BayesMallows-0.2.0/BayesMallows/R/print.BayesMallows.R |only BayesMallows-0.2.0/BayesMallows/R/print.BayesMallowsMixtures.R |only BayesMallows-0.2.0/BayesMallows/R/rank_conversion.R | 33 BayesMallows-0.2.0/BayesMallows/R/sample_mallows.R | 71 BayesMallows-0.2.0/BayesMallows/R/sysdata.rda |binary BayesMallows-0.2.0/BayesMallows/R/tidy_mcmc.R | 52 BayesMallows-0.2.0/BayesMallows/build/partial.rdb |binary BayesMallows-0.2.0/BayesMallows/inst/doc/BayesMallowsPackage.R | 56 BayesMallows-0.2.0/BayesMallows/inst/doc/BayesMallowsPackage.Rmd | 87 - BayesMallows-0.2.0/BayesMallows/inst/doc/BayesMallowsPackage.html | 814 ++++++---- BayesMallows-0.2.0/BayesMallows/inst/examples/compute_consensus_example.R |only BayesMallows-0.2.0/BayesMallows/inst/examples/compute_mallows_example.R | 31 BayesMallows-0.2.0/BayesMallows/inst/examples/compute_mallows_mixtures_example.R | 19 BayesMallows-0.2.0/BayesMallows/inst/examples/generate_initial_ranking_example.R | 6 BayesMallows-0.2.0/BayesMallows/inst/examples/plot.BayesMallows_example.R | 12 BayesMallows-0.2.0/BayesMallows/inst/examples/plot_top_k_example.R | 33 BayesMallows-0.2.0/BayesMallows/inst/examples/sample_mallows_example.R | 8 BayesMallows-0.2.0/BayesMallows/inst/examples/tidy_mcmc_example.R | 52 BayesMallows-0.2.0/BayesMallows/man/assess_convergence.Rd | 17 BayesMallows-0.2.0/BayesMallows/man/compute_consensus.Rd |only BayesMallows-0.2.0/BayesMallows/man/compute_cp_consensus.Rd | 12 BayesMallows-0.2.0/BayesMallows/man/compute_mallows.Rd | 71 BayesMallows-0.2.0/BayesMallows/man/compute_mallows_mixtures.Rd | 27 BayesMallows-0.2.0/BayesMallows/man/compute_map_consensus.Rd | 59 BayesMallows-0.2.0/BayesMallows/man/compute_posterior_intervals.Rd | 4 BayesMallows-0.2.0/BayesMallows/man/generate_initial_ranking.Rd | 6 BayesMallows-0.2.0/BayesMallows/man/get_rank_distance.Rd | 3 BayesMallows-0.2.0/BayesMallows/man/get_summation_distances.Rd | 2 BayesMallows-0.2.0/BayesMallows/man/plot.BayesMallows.Rd | 18 BayesMallows-0.2.0/BayesMallows/man/plot_elbow.Rd | 19 BayesMallows-0.2.0/BayesMallows/man/plot_top_k.Rd | 26 BayesMallows-0.2.0/BayesMallows/man/predict_top_k.Rd | 22 BayesMallows-0.2.0/BayesMallows/man/print.BayesMallows.Rd |only BayesMallows-0.2.0/BayesMallows/man/print.BayesMallowsMixtures.Rd |only BayesMallows-0.2.0/BayesMallows/man/rank_conversion.Rd | 2 BayesMallows-0.2.0/BayesMallows/man/rmallows.Rd | 5 BayesMallows-0.2.0/BayesMallows/man/run_mcmc.Rd | 9 BayesMallows-0.2.0/BayesMallows/man/sample_mallows.Rd | 75 BayesMallows-0.2.0/BayesMallows/man/tidy_mcmc.Rd | 52 BayesMallows-0.2.0/BayesMallows/src/RcppExports.cpp | 10 BayesMallows-0.2.0/BayesMallows/src/clustering.cpp | 4 BayesMallows-0.2.0/BayesMallows/src/clustering.h | 2 BayesMallows-0.2.0/BayesMallows/src/distfuns.cpp | 10 BayesMallows-0.2.0/BayesMallows/src/parameterupdates.cpp | 6 BayesMallows-0.2.0/BayesMallows/src/rmallows.cpp | 9 BayesMallows-0.2.0/BayesMallows/src/run_mcmc.cpp | 16 BayesMallows-0.2.0/BayesMallows/tests/testthat/test_assess_convergence.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_compute_mallows.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_distance_function.R | 6 BayesMallows-0.2.0/BayesMallows/tests/testthat/test_partition_function.R | 5 BayesMallows-0.2.0/BayesMallows/tests/testthat/test_plot.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_plot_elbow.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_plot_top_k.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_print.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_rank_conversion.R |only BayesMallows-0.2.0/BayesMallows/tests/testthat/test_sample_mallows.R |only BayesMallows-0.2.0/BayesMallows/vignettes/BayesMallowsPackage.Rmd | 87 - 77 files changed, 1459 insertions(+), 1021 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the 'stringr'
or 'stringi' packages. The foremost of these is the extraction of numbers
from strings. 'stringr' and 'stringi' make you figure out the regular
expression for yourself; 'strex' takes care of this for you. There are many
other handy functionalities in 'strex'. Contributions to this package are
encouraged: it is intended as a miscellany of string manipulation functions
that cannot be found in 'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 0.1.2 dated 2018-10-20 and 0.1.3 dated 2018-11-30
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ build/partial.rdb |binary inst/doc/alphordering-numbers.html | 4 ++-- inst/doc/argument-matching.html | 4 ++-- inst/doc/before-and-after.html | 4 ++-- inst/doc/important-miscellany.html | 4 ++-- inst/doc/numbers-in-strings.html | 4 ++-- 9 files changed, 29 insertions(+), 23 deletions(-)
Title: Locally Gaussian Distributions: Estimation and Methods
Description: An implementation of locally Gaussian distributions. It provides methods for
implementing the locally Gaussian density estimator (LGDE) by Otneim and Tjøstheim (2017)
<doi:10.1007/s11222-016-9706-6>, as well as the corresponding estimator for conditional
density functions by Otneim and Tjøstheim (2018) <doi:10.1007/s11222-017-9732-z>.
Author: Håkon Otneim [aut, cre]
Maintainer: Håkon Otneim <hakon.otneim@nhh.no>
Diff between lg versions 0.2.0 dated 2018-10-05 and 0.3.0 dated 2018-11-30
DESCRIPTION | 10 - MD5 | 26 +++-- NAMESPACE | 4 NEWS.md | 11 +- R/bandwidth_selection.R | 47 +++++++++ R/checks.R | 10 + R/contagion.R |only R/ind_tests.R |only R/lg.R | 2 R/test_conditional_independence.R | 66 ++++++++---- R/transform.R | 12 ++ README.md | 193 ++++++++++++++++++++++++++++++-------- man/bw_simple.Rd |only man/ci_test.Rd | 2 man/cont_test.Rd |only man/ind_test.Rd |only man/ind_teststat.Rd |only 17 files changed, 305 insertions(+), 78 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.2.7 dated 2018-05-18 and 0.3 dated 2018-11-30
DESCRIPTION | 8 MD5 | 16 - NEWS | 7 R/SeqFeatR_GUI.R | 82 ++++++++- R/assocpoint.R | 100 ++++++++--- build/vignette.rds |binary inst/doc/SeqFeatR_tutorial.pdf |binary inst/extdata/config.cfg | 12 - man/assocpoint.Rd | 364 +++++++++++++++++++++-------------------- 9 files changed, 365 insertions(+), 224 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) to work with microbial and antimicrobial properties by using
evidence-based methods.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, rev] (<https://orcid.org/0000-0001-5809-5995>),
Erwin E.A. Hassing [ctb],
Corinna Glasner [ths] (<https://orcid.org/0000-0003-1241-1328>),
Alex W. Friedrich [ths] (<https://orcid.org/0000-0003-4881-038X>),
Bhanu Sinha [ths] (<https://orcid.org/0000-0003-1634-0010>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 0.4.0 dated 2018-10-01 and 0.5.0 dated 2018-11-30
AMR-0.4.0/AMR/R/eucast.R |only AMR-0.4.0/AMR/R/n_rsi.R |only AMR-0.4.0/AMR/man/EUCAST.Rd |only AMR-0.4.0/AMR/man/MDRO.Rd |only AMR-0.4.0/AMR/man/n_rsi.Rd |only AMR-0.4.0/AMR/tests/testthat/test-eucast.R |only AMR-0.5.0/AMR/DESCRIPTION | 29 AMR-0.5.0/AMR/MD5 | 160 +- AMR-0.5.0/AMR/NAMESPACE | 37 AMR-0.5.0/AMR/NEWS.md | 85 + AMR-0.5.0/AMR/R/abname.R | 23 AMR-0.5.0/AMR/R/atc.R | 8 AMR-0.5.0/AMR/R/count.R | 115 + AMR-0.5.0/AMR/R/data.R | 41 AMR-0.5.0/AMR/R/eucast_rules.R |only AMR-0.5.0/AMR/R/first_isolate.R | 102 - AMR-0.5.0/AMR/R/freq.R | 514 ++++--- AMR-0.5.0/AMR/R/g.test.R | 11 AMR-0.5.0/AMR/R/get_locale.R |only AMR-0.5.0/AMR/R/ggplot_rsi.R | 13 AMR-0.5.0/AMR/R/globals.R | 8 AMR-0.5.0/AMR/R/join_microorganisms.R | 142 -- AMR-0.5.0/AMR/R/mdro.R | 309 ++-- AMR-0.5.0/AMR/R/mic.R | 7 AMR-0.5.0/AMR/R/misc.R | 36 AMR-0.5.0/AMR/R/mo.R | 438 +++--- AMR-0.5.0/AMR/R/mo_property.R | 221 ++- AMR-0.5.0/AMR/R/portion.R | 123 + AMR-0.5.0/AMR/R/read.4d.R |only AMR-0.5.0/AMR/R/resistance_predict.R | 8 AMR-0.5.0/AMR/R/rsi.R | 28 AMR-0.5.0/AMR/R/rsi_calc.R | 66 AMR-0.5.0/AMR/R/zzz.R | 4 AMR-0.5.0/AMR/README.md | 435 +++--- AMR-0.5.0/AMR/data/datalist |only AMR-0.5.0/AMR/data/microorganisms.certe.rda |binary AMR-0.5.0/AMR/data/microorganisms.old.rda |binary AMR-0.5.0/AMR/data/microorganisms.oldDT.rda |only AMR-0.5.0/AMR/data/microorganisms.prevDT.rda |only AMR-0.5.0/AMR/data/microorganisms.rda |binary AMR-0.5.0/AMR/data/microorganisms.unprevDT.rda |only AMR-0.5.0/AMR/data/microorganismsDT.rda |only AMR-0.5.0/AMR/data/septic_patients.rda |binary AMR-0.5.0/AMR/inst/doc/AMR.Rmd | 47 AMR-0.5.0/AMR/inst/doc/AMR.html | 100 + AMR-0.5.0/AMR/inst/doc/freq.html | 1552 +++++++++++++++++++--- AMR-0.5.0/AMR/inst/rstudio/addins.dcf | 12 AMR-0.5.0/AMR/man/AMR.Rd | 4 AMR-0.5.0/AMR/man/antibiotics.Rd | 2 AMR-0.5.0/AMR/man/as.atc.Rd | 1 AMR-0.5.0/AMR/man/as.mic.Rd | 2 AMR-0.5.0/AMR/man/as.mo.Rd | 25 AMR-0.5.0/AMR/man/as.rsi.Rd | 2 AMR-0.5.0/AMR/man/count.Rd | 58 AMR-0.5.0/AMR/man/eucast_rules.Rd |only AMR-0.5.0/AMR/man/figures/rsi_example2.png |binary AMR-0.5.0/AMR/man/figures/rsi_example3.png |binary AMR-0.5.0/AMR/man/figures/rsi_example4.png |binary AMR-0.5.0/AMR/man/first_isolate.Rd | 21 AMR-0.5.0/AMR/man/freq.Rd | 66 AMR-0.5.0/AMR/man/get_locale.Rd |only AMR-0.5.0/AMR/man/ggplot_rsi.Rd | 13 AMR-0.5.0/AMR/man/join.Rd | 29 AMR-0.5.0/AMR/man/key_antibiotics.Rd | 2 AMR-0.5.0/AMR/man/mdro.Rd |only AMR-0.5.0/AMR/man/microorganisms.Rd | 8 AMR-0.5.0/AMR/man/microorganisms.certe.Rd | 2 AMR-0.5.0/AMR/man/microorganisms.old.Rd | 4 AMR-0.5.0/AMR/man/microorganisms.umcg.Rd | 2 AMR-0.5.0/AMR/man/mo_property.Rd | 86 - AMR-0.5.0/AMR/man/portion.Rd | 46 AMR-0.5.0/AMR/man/read.4D.Rd |only AMR-0.5.0/AMR/man/resistance_predict.Rd | 8 AMR-0.5.0/AMR/man/rsi.Rd | 4 AMR-0.5.0/AMR/man/septic_patients.Rd | 2 AMR-0.5.0/AMR/man/supplementary_data.Rd |only AMR-0.5.0/AMR/tests/testthat/Rplots.pdf |binary AMR-0.5.0/AMR/tests/testthat/test-abname.R | 5 AMR-0.5.0/AMR/tests/testthat/test-count.R | 27 AMR-0.5.0/AMR/tests/testthat/test-data.R | 29 AMR-0.5.0/AMR/tests/testthat/test-eucast_rules.R |only AMR-0.5.0/AMR/tests/testthat/test-first_isolate.R | 9 AMR-0.5.0/AMR/tests/testthat/test-freq.R | 21 AMR-0.5.0/AMR/tests/testthat/test-get_locale.R |only AMR-0.5.0/AMR/tests/testthat/test-mdro.R | 22 AMR-0.5.0/AMR/tests/testthat/test-misc.R | 3 AMR-0.5.0/AMR/tests/testthat/test-mo.R | 52 AMR-0.5.0/AMR/tests/testthat/test-mo_property.R | 20 AMR-0.5.0/AMR/tests/testthat/test-portion.R | 36 AMR-0.5.0/AMR/tests/testthat/test-read.4d.R |only AMR-0.5.0/AMR/tests/testthat/test-rsi.R | 13 AMR-0.5.0/AMR/vignettes/AMR.Rmd | 47 92 files changed, 3772 insertions(+), 1573 deletions(-)
Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables.
Author: Maja Pohar Perme [aut, cre]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.2-2 dated 2018-10-18 and 2.2-3 dated 2018-11-30
relsurv-2.2-2/relsurv/inst/citation.txt |only relsurv-2.2-3/relsurv/DESCRIPTION | 8 ++++---- relsurv-2.2-3/relsurv/MD5 | 14 +++++++------- relsurv-2.2-3/relsurv/inst/CITATION |only relsurv-2.2-3/relsurv/inst/news.Rd | 7 +++++++ relsurv-2.2-3/relsurv/man/cmprel.Rd | 3 +++ relsurv-2.2-3/relsurv/man/nessie.Rd | 5 +++-- relsurv-2.2-3/relsurv/man/rsdiff.Rd | 5 +++-- relsurv-2.2-3/relsurv/man/rssurv.Rd | 7 +++---- 9 files changed, 30 insertions(+), 19 deletions(-)
Title: Robust Multiple Imputation with Generalized Additive Models for
Location Scale and Shape
Description: Provides new imputation methods for the 'mice' package based on generalized additive models for location, scale, and shape (GAMLSS) as described in de Jong, van Buuren and Spiess <doi:10.1080/03610918.2014.911894>.
Author: Daniel Salfran [aut, cre],
Martin Spieß [aut, ths]
Maintainer: Daniel Salfran <danielsalfran@gmail.com>
Diff between ImputeRobust versions 1.3 dated 2018-07-01 and 1.3-1 dated 2018-11-30
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 5 +++++ R/imp_gamlss_fit.R | 16 +++++++++++++--- R/mice_impute_gamlss.R | 5 ++--- man/ImpGamlssFit.Rd | 8 ++++---- man/mice.impute.gamlss.Rd | 4 ++-- 7 files changed, 37 insertions(+), 23 deletions(-)
Title: Compute, Handle, Plot and Model 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 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut],
Zhian N. Kamvar [aut, cre],
Rich FitzJohn [aut],
Jun Cai [ctb],
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between incidence versions 1.5.0 dated 2018-11-01 and 1.5.2 dated 2018-11-30
DESCRIPTION | 8 ++-- MD5 | 57 ++++++++++++++++-------------- NEWS.md | 33 +++++++++++++++++ R/check_dates.R | 2 + R/check_groups.R | 7 ++- R/check_timespan.R |only R/conversion.R | 3 + R/extract_info.R | 6 +-- R/get_info.R | 2 - R/plot.R | 17 ++++----- R/print.R | 2 - R/subset.R | 7 +++ R/zzz.R |only demo/incidence-demo.R | 47 +++++++++++++++---------- inst/WORDLIST |only inst/doc/conversions.html | 4 +- inst/doc/customize_plot.R | 2 - inst/doc/customize_plot.Rmd | 15 +++++--- inst/doc/customize_plot.html | 26 ++++++------- inst/doc/incidence_class.Rmd | 2 - inst/doc/incidence_class.html | 6 +-- inst/doc/incidence_fit_class.Rmd | 6 +-- inst/doc/incidence_fit_class.html | 71 +++++++++++++++++++------------------- inst/doc/overview.Rmd | 4 +- inst/doc/overview.html | 54 ++++++++++++++-------------- tests/testthat/test-incidence.R | 13 ++++++ tests/testthat/test-subset.R | 5 ++ vignettes/customize_plot.Rmd | 15 +++++--- vignettes/incidence_class.Rmd | 2 - vignettes/incidence_fit_class.Rmd | 6 +-- vignettes/overview.Rmd | 4 +- 31 files changed, 257 insertions(+), 169 deletions(-)
Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical
spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvconnect versions 1.0.5 dated 2018-11-17 and 1.0.7 dated 2018-11-30
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/eval.R | 57 ++++++++++++++++++++++++++++++--------------------------- 3 files changed, 37 insertions(+), 34 deletions(-)
Title: Case-Wise and Cluster-Wise Derivatives for Mixed Effects Models
Description: Compute analytic case-wise and cluster-wise derivative for
mixed effects models with respect to fixed effects parameter, random effect (co)variances,
and residual variance.
Author: Ting Wang [aut, cre],
Edgar Merkle [aut]
Maintainer: Ting Wang <twb8d@mail.missouri.edu>
Diff between merDeriv versions 0.1-5 dated 2018-09-12 and 0.1-6 dated 2018-11-30
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ R/estfun.lmerMod.R | 21 ++++++++++++++------- R/vcov.glmerMod.R |only README.md | 2 +- build |only inst |only man/bread.lmerMod.Rd | 6 +++--- man/estfun.lmerMod.Rd | 6 +++--- man/llcont.lmerMod.Rd | 6 +++--- man/vcov.glmerMod.Rd |only man/vcov.lmerMod.Rd | 6 +++--- 13 files changed, 44 insertions(+), 31 deletions(-)
Title: R Logging Package
Description: Pure R implementation of the ubiquitous log4j package. It offers hierarchic
loggers, multiple handlers per logger, level based filtering, space handling in messages
and custom formatting.
Author: Mario Frasca [aut],
Walerian Sokolowski [cre]
Maintainer: Walerian Sokolowski <r-logging@wlogsolutions.com>
Diff between logging versions 0.7-103 dated 2013-04-12 and 0.8-104 dated 2018-11-30
logging-0.7-103/logging/R/version.R |only logging-0.8-104/logging/DESCRIPTION | 38 logging-0.8-104/logging/MD5 | 43 - logging-0.8-104/logging/NAMESPACE | 45 - logging-0.8-104/logging/R/logger.R | 303 +++---- logging-0.8-104/logging/R/namedLevels.R | 61 - logging-0.8-104/logging/R/oo.R | 287 +++--- logging-0.8-104/logging/R/updateOptions.R | 55 - logging-0.8-104/logging/R/utils.R | 102 +- logging-0.8-104/logging/R/zzz.R | 29 logging-0.8-104/logging/inst/unitTest/runit.automatic-format.R |only logging-0.8-104/logging/inst/unitTest/runit.data.interaction.R | 429 +++++----- logging-0.8-104/logging/man/addHandler.Rd | 4 logging-0.8-104/logging/man/basicConfig.Rd | 6 logging-0.8-104/logging/man/getHandler.Rd | 4 logging-0.8-104/logging/man/getLogger.Rd | 4 logging-0.8-104/logging/man/handler-actions.Rd | 4 logging-0.8-104/logging/man/levels.Rd | 4 logging-0.8-104/logging/man/log.Rd | 21 logging-0.8-104/logging/man/logging-internal.Rd | 4 logging-0.8-104/logging/man/logging-package.Rd | 2 logging-0.8-104/logging/man/setLevel.Rd | 2 logging-0.8-104/logging/tests/doSvUnit.R | 45 - logging-0.8-104/logging/tests/report.xml |only 24 files changed, 798 insertions(+), 694 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.3.2 dated 2018-10-28 and 0.3.3 dated 2018-11-30
DESCRIPTION | 10 +- MD5 | 62 +++++++------ NAMESPACE | 10 ++ NEWS | 20 ++++ R/alaplace.R | 54 ++++++------ R/alm.R | 99 ++++++++++++++++++---- R/fnorm.R | 8 - R/isFunctions.R | 42 +-------- R/laplace.R | 50 +++++------ R/lmCombine.R | 36 ++++++-- R/lmDynamic.R | 11 +- R/methods.R | 111 +++++++++++++++++------- R/stepwise.R | 6 - R/svet.R | 70 +++++++-------- R/tplnorm.R |only R/xregTransformer.R |only README.md | 37 ++++---- build/partial.rdb |binary inst/doc/alm.Rmd | 123 ++++++++++++++++++++------- inst/doc/alm.html | 193 +++++++++++++++++++++++++++---------------- inst/doc/greybox.html | 16 +-- inst/doc/ro.Rmd | 15 +-- inst/doc/ro.html | 52 ++++++----- man/alaplace-distribution.Rd | 24 ++--- man/alm.Rd | 19 ++-- man/fnorm-distribution.Rd | 2 man/laplace-distribution.Rd | 22 ++-- man/lmCombine.Rd | 6 + man/s-distribution.Rd | 22 ++-- man/tplnorm-distribution.Rd |only man/xregTransformer.Rd |only vignettes/alm.Rmd | 123 ++++++++++++++++++++------- vignettes/library.bib | 48 ++++++++++ vignettes/ro.Rmd | 15 +-- 34 files changed, 836 insertions(+), 470 deletions(-)
Title: Import Various Data File Types as a Rectangular Form Using a
File Picker Dialogue Box
Description: Easy data importing for the most frequently used file formats in a 'tibble' form.
Author: JooYoung Seo [aut, cre],
Soyoung Choi [aut]
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Diff between ezpickr versions 0.1.1 dated 2018-11-28 and 0.1.2 dated 2018-11-30
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NEWS.md | 5 +++++ R/pick.R | 5 +++-- README.md | 4 ++++ inst/NEWS |only inst/doc/ezpickr_vignette.html | 4 ++-- man/ezpickr-package.Rd | 4 ++-- man/pick.Rd | 4 +++- 9 files changed, 32 insertions(+), 19 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on three testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for the goodness-of-fit testing problem with an estimated nuisance parameter. An application of this testing problem is the one of testing for heterogeneous treatment effects in a randomized control trial.
Author: Mauricio Olivares-Gonzalez [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares-Gonzalez <maurice.olivares@gmail.com>
Diff between RATest versions 0.1.3 dated 2018-10-31 and 0.1.4 dated 2018-11-30
RATest-0.1.3/RATest/inst/doc/Permutation_Tests.pdf |only RATest-0.1.4/RATest/DESCRIPTION | 15 ++++++++------- RATest-0.1.4/RATest/MD5 | 12 +++++++----- RATest-0.1.4/RATest/NAMESPACE | 2 ++ RATest-0.1.4/RATest/R/PT.Khmaladze.fit.R |only RATest-0.1.4/RATest/R/summary.PT.Khmaladze.fit.R |only RATest-0.1.4/RATest/build/vignette.rds |binary RATest-0.1.4/RATest/inst/doc/RDperm.pdf |binary RATest-0.1.4/RATest/man/PT.Khmaladze.fit.Rd |only 9 files changed, 17 insertions(+), 12 deletions(-)