Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre],
Mark Fredrickson [aut],
Ben Hansen [aut],
Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.3-1 dated 2022-08-10 and 0.3-2 dated 2023-02-03
DESCRIPTION | 8 ++--- MD5 | 13 ++++---- NEWS.md | 8 +++++ R/Design.R | 5 ++- R/plot.balancetest.R | 23 ++++++++------- inst/CITATION | 64 ++++++++++++++++++++----------------------- man/scale.DesignOptions.Rd |only tests/testthat/test.Design.R | 30 -------------------- 8 files changed, 65 insertions(+), 86 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 11. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.2.6 dated 2023-01-23 and 0.2.7 dated 2023-02-03
UKFE-0.2.6/UKFE/man/BivarSim.Rd |only UKFE-0.2.7/UKFE/DESCRIPTION | 6 - UKFE-0.2.7/UKFE/MD5 | 11 +-- UKFE-0.2.7/UKFE/R/All.R | 133 +------------------------------------- UKFE-0.2.7/UKFE/R/ThamesPQ.R | 2 UKFE-0.2.7/UKFE/data/ThamesPQ.rda |binary UKFE-0.2.7/UKFE/man/ThamesPQ.Rd | 2 7 files changed, 14 insertions(+), 140 deletions(-)
Title: Pedigree/Family-Based Genetic Association Tests Analysis and
Power
Description: This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Author: Thomas Hoffmann <tjhoffm@gmail.com>, with contributions from Christoph Lange <clange@hsph.harvard.edu>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between pbatR versions 2.2-13 dated 2018-04-19 and 2.2-15 dated 2023-02-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/pbat.R | 3 ++- R/pbatGUI.R | 12 ++++++++---- src/data.cpp | 3 ++- src/pbatR_init.c | 6 ++++-- 6 files changed, 26 insertions(+), 18 deletions(-)
Title: An Implementation of Ordinal Pattern Analysis
Description: Quantifies hypothesis to data fit for repeated measures
and longitudinal data, as described by Thorngate (1987)
<doi:10.1016/S0166-4115(08)60083-7> and Grice et al., (2015)
<doi:10.1177/2158244015604192>. Hypothesis and data are encoded as
pairwise relative orderings which are then compared to determine the
percentage of orderings in the data that are matched by the hypothesis.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>
Diff between opa versions 0.6 dated 2023-01-06 and 0.7.1 dated 2023-02-03
opa-0.6/opa/R/calculate_cvalues.R |only opa-0.7.1/opa/DESCRIPTION | 8 - opa-0.7.1/opa/MD5 | 27 +++--- opa-0.7.1/opa/R/RcppExports.R | 20 ++-- opa-0.7.1/opa/R/calculate_pccs.R | 31 ------- opa-0.7.1/opa/R/condition_comparison.R | 14 +-- opa-0.7.1/opa/R/fitopa.R | 44 +--------- opa-0.7.1/opa/R/utility.R | 14 --- opa-0.7.1/opa/README.md | 10 +- opa-0.7.1/opa/man/compare_conditions.Rd | 9 -- opa-0.7.1/opa/man/opa.Rd | 17 ---- opa-0.7.1/opa/src/RcppExports.cpp | 63 +++++++++------ opa-0.7.1/opa/src/cpp11.cpp | 20 ++-- opa-0.7.1/opa/src/cpp_functions.cpp | 119 +++++++++++++++++------------ opa-0.7.1/opa/tests/testthat/test-fitopa.R | 18 ---- 15 files changed, 181 insertions(+), 233 deletions(-)
Title: Alluvial Plots in 'ggplot2'
Description: Alluvial plots use variable-width ribbons and stacked bar plots to
represent multi-dimensional or repeated-measures data with categorical or
ordinal variables; see Riehmann, Hanfler, and Froehlich (2005)
<doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010)
<doi:10.1371/journal.pone.0008694>.
Alluvial plots are statistical graphics in the sense of Wilkinson (2006)
<doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and
parallel sets plots but are uniquely determined from the data and a small
set of parameters. This package extends Wickham's (2010)
<doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate
alluvial plots from tidy data.
Author: Jason Cory Brunson [aut, cre],
Quentin D. Read [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ggalluvial versions 0.12.3 dated 2020-12-05 and 0.12.4 dated 2023-02-03
ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_alluvium.jpg |only ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_empty_area.jpg |only ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_stratum.jpg |only ggalluvial-0.12.4/ggalluvial/DESCRIPTION | 12 ggalluvial-0.12.4/ggalluvial/MD5 | 149 + ggalluvial-0.12.4/ggalluvial/NAMESPACE | 17 ggalluvial-0.12.4/ggalluvial/NEWS.md | 33 ggalluvial-0.12.4/ggalluvial/R/alluvial-data.r | 60 ggalluvial-0.12.4/ggalluvial/R/geom-alluvium.r | 193 +- ggalluvial-0.12.4/ggalluvial/R/geom-flow.r | 112 - ggalluvial-0.12.4/ggalluvial/R/geom-lode.r | 4 ggalluvial-0.12.4/ggalluvial/R/geom-stratum.r | 2 ggalluvial-0.12.4/ggalluvial/R/ggalluvial-package.r | 5 ggalluvial-0.12.4/ggalluvial/R/lode-guidance-functions.r | 7 ggalluvial-0.12.4/ggalluvial/R/self-adjoin.r | 5 ggalluvial-0.12.4/ggalluvial/R/stat-alluvium.r | 13 ggalluvial-0.12.4/ggalluvial/R/stat-flow.r | 27 ggalluvial-0.12.4/ggalluvial/R/stat-stratum.r | 8 ggalluvial-0.12.4/ggalluvial/R/stat-utils.r | 11 ggalluvial-0.12.4/ggalluvial/R/utils.r | 2 ggalluvial-0.12.4/ggalluvial/README.md | 41 ggalluvial-0.12.4/ggalluvial/build/partial.rdb |only ggalluvial-0.12.4/ggalluvial/build/vignette.rds |binary ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.R | 20 ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.html | 834 ++++++-- ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.rmd | 66 ggalluvial-0.12.4/ggalluvial/inst/doc/labels.html | 542 ++++- ggalluvial-0.12.4/ggalluvial/inst/doc/labels.rmd | 16 ggalluvial-0.12.4/ggalluvial/inst/doc/order-rectangles.html | 864 +++++++-- ggalluvial-0.12.4/ggalluvial/inst/doc/order-rectangles.rmd | 20 ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.R | 455 +--- ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.Rmd | 580 ++---- ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.html | 934 +++++----- ggalluvial-0.12.4/ggalluvial/inst/examples/ex-geom-alluvium.r | 2 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-geom-flow.r | 2 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-shiny-long-data |only ggalluvial-0.12.4/ggalluvial/inst/examples/ex-shiny-wide-data |only ggalluvial-0.12.4/ggalluvial/inst/examples/ex-stat-alluvium.r | 17 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-stat-flow.r | 4 ggalluvial-0.12.4/ggalluvial/man/alluvial-data.Rd | 4 ggalluvial-0.12.4/ggalluvial/man/figures/README-unnamed-chunk-6-1.png |binary ggalluvial-0.12.4/ggalluvial/man/figures/README-unnamed-chunk-7-1.png |binary ggalluvial-0.12.4/ggalluvial/man/geom_alluvium.Rd | 41 ggalluvial-0.12.4/ggalluvial/man/geom_flow.Rd | 54 ggalluvial-0.12.4/ggalluvial/man/geom_lode.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/geom_stratum.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/ggalluvial-ggproto.Rd | 6 ggalluvial-0.12.4/ggalluvial/man/ggalluvial-package.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/lode-guidance-functions.Rd | 5 ggalluvial-0.12.4/ggalluvial/man/stat_alluvium.Rd | 37 ggalluvial-0.12.4/ggalluvial/man/stat_flow.Rd | 24 ggalluvial-0.12.4/ggalluvial/man/stat_stratum.Rd | 14 ggalluvial-0.12.4/ggalluvial/tests/testthat/_snaps |only ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-alluvium.r | 38 ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-flow.r | 18 ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-lode.r | 4 ggalluvial-0.12.4/ggalluvial/vignettes/ggalluvial.rmd | 66 ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_alluvium.png |only ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_empty_area.png |only ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_stratum.png |only ggalluvial-0.12.4/ggalluvial/vignettes/labels.rmd | 16 ggalluvial-0.12.4/ggalluvial/vignettes/order-rectangles.rmd | 20 ggalluvial-0.12.4/ggalluvial/vignettes/shiny.Rmd | 580 ++---- 63 files changed, 3493 insertions(+), 2533 deletions(-)
Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org>
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2D, 3D, 4D, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this.
Author: Jean-Romain Roussel [cph, ctb] ,
C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Pavlo Mozharovskyi [cph, aut],
David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.4.6.1 dated 2022-07-04 and 0.4.7 dated 2023-02-03
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 1 + NEWS | 40 ++++++++++++++++++++++++++++++++++++++++ R/convhulln.R | 10 +++++----- R/delaunayn.R | 43 +++++++++++++++++++++++++++++++++++++++---- R/qhull-options.R | 6 ++++-- R/surf.tri.R | 16 ++++++++-------- R/tetramesh.R | 8 ++++---- build/vignette.rds |binary inst/doc/qhull-eg.pdf |binary man/convhulln.Rd | 8 ++++---- man/delaunayn.Rd | 13 ++++++++----- man/surf.tri.Rd | 16 ++++++++-------- man/tetramesh.Rd | 4 ++-- src/Rgeometry.c | 2 +- src/global_r.c | 8 ++++---- src/rboxlib_r.c | 2 +- 18 files changed, 151 insertions(+), 70 deletions(-)
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-5 dated 2022-02-12 and 1.0-7 dated 2023-02-03
DESCRIPTION | 9 - MD5 | 38 ++--- src/RExportGen.cpp | 4 src/cgFbat.cpp | 344 ++++++++++++++++++++++++++--------------------------- src/datamatrix.cpp | 16 +- src/datamatrix.h | 10 - src/defines.h | 2 src/fbatdist.cpp | 18 +- src/fbatge.cpp | 24 +-- src/fbati_init.c | 28 ++-- src/fbatmeev.cpp | 16 +- src/fbatmeev.h | 2 src/joint.cpp | 12 - src/joint.h | 2 src/nuclify.cpp | 24 +-- src/nuclify.h | 8 - src/rmatrix.cpp | 10 - src/rmatrix.h | 2 src/rvector.cpp | 8 - src/rvector.h | 2 20 files changed, 296 insertions(+), 283 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-011-0040-5>. Subnational probabilistic projections are also supported.
Author: Hana Sevcikova , Leontine Alkema , Peiran Liu , Adrian Raftery , Bailey Fosdick , Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 7.2-2 dated 2022-12-12 and 7.3-0 dated 2023-02-03
ChangeLog | 11 ++ DESCRIPTION | 12 +- MD5 | 32 +++---- NAMESPACE | 3 R/get_outputs.R | 6 - R/plot_functions.R | 191 ++++++++++++++++++++++++++++++++++------------ R/predict_tfr.R | 19 +++- R/tfr_median_set_new.R | 54 +++++++------ R/wpp_data.R | 6 - build/partial.rdb |binary data/iso3166.rda |binary inst/CITATION | 11 -- man/tfr.map.Rd | 37 ++++++-- man/tfr.median.set.Rd | 17 ++-- man/tfr.median.set.all.Rd | 6 - tests/run_tests.R | 25 +++--- tests/test_functions.R | 148 ++++++++++++++++++++++++----------- 17 files changed, 391 insertions(+), 187 deletions(-)
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] ,
Chao Cheng [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between SASmarkdown versions 0.8.0 dated 2022-09-20 and 0.8.1 dated 2023-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sas_collectcode.r | 4 +++- man/find_sas.Rd | 2 +- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark
shapes, including Procrustes analysis, graphical displays, principal
components analysis, permutation and bootstrap tests, thin-plate
spline transformation grids and comparing covariance matrices.
See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis,
with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>
Diff between shapes versions 1.2.6 dated 2021-03-31 and 1.2.7 dated 2023-02-03
DESCRIPTION | 8 MD5 | 78 +- NEWS.md | 158 ++-- R/shapes.R | 1576 ++++++++++++++++++++++++++------------------- README.md |only data/apes.rda |binary data/brains.rda |binary data/cortical.rda |binary data/digit3.dat.rda |binary data/dna.dat.rda |binary data/gels.rda |binary data/gorf.dat.rda |binary data/gorm.dat.rda |binary data/humanmove.rda |binary data/macaques.rda |binary data/macf.dat.rda |binary data/macm.dat.rda |binary data/mice.rda |binary data/nsa.rda |binary data/panf.dat.rda |binary data/panm.dat.rda |binary data/pongof.dat.rda |binary data/pongom.dat.rda |binary data/protein.rda |binary data/qcet2.dat.rda |binary data/qlet2.dat.rda |binary data/qset2.dat.rda |binary data/rats.rda |binary data/sand.rda |binary data/schizophrenia.dat.rda |binary data/schizophrenia.rda |binary data/shells.rda |binary data/sooty.dat.rda |binary data/sooty.rda |binary data/steroids.rda |binary man/backfit.Rd |only man/pns.Rd | 11 man/pns4pc.Rd | 2 man/pnss3d.Rd | 22 man/shapes-internal.Rd | 4 man/shapes.cva.Rd | 3 41 files changed, 1102 insertions(+), 760 deletions(-)
Title: Sieve Analysis Methods for Proportional Hazards Models
Description: Implements semiparametric estimation and testing procedures for a continuous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an event of interest in a randomized treatment efficacy trial with a time-to-event endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 69(2):328 337 <doi:10.1111/biom.12016>, and in Juraska M and Gilbert PB (2016), Mark-specific hazard ratio model with missing multivariate marks. Lifetime Data Analysis 22(4): 606-25 <doi:10.1007/s10985-015-9353-9>. The former considers continuous multivariate marks fully observed in all subjects who experience the event of interest, whereas the latter extends the previous work to allow multivariate marks that are subject to missingness-at-random. For models with missing marks, two estimators are implemented based on (i) inverse probability weighting (IPW) of complete case [...truncated...]
Author: Michal Juraska [aut, cre],
Stephanie Wu [ctb],
Li Li [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between sievePH versions 1.0.3 dated 2022-08-16 and 1.0.4 dated 2023-02-03
sievePH-1.0.3/sievePH/inst |only sievePH-1.0.4/sievePH/DESCRIPTION | 14 ++++++++------ sievePH-1.0.4/sievePH/MD5 | 9 +++++---- sievePH-1.0.4/sievePH/NAMESPACE | 4 ++++ sievePH-1.0.4/sievePH/NEWS |binary sievePH-1.0.4/sievePH/R/ggplot_sieve.R |only sievePH-1.0.4/sievePH/man/ggplot_sieve.Rd |only 7 files changed, 17 insertions(+), 10 deletions(-)
Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments
that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut] ,
Benjamin D. Schalet [ctb],
Aaron J. Kaat [ctb],
David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between PROsetta versions 0.3.5 dated 2022-01-03 and 0.4.1 dated 2023-02-03
PROsetta-0.3.5/PROsetta/R/configPROsetta.R |only PROsetta-0.3.5/PROsetta/inst/shiny/app.R |only PROsetta-0.3.5/PROsetta/tests/testthat/test_runCalibration.R |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib2_5978dfb0cb71fc7d2170190dbc80afb9.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib2_5978dfb0cb71fc7d2170190dbc80afb9.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib2_5978dfb0cb71fc7d2170190dbc80afb9.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib3_58617b1d49e6f8461c01a261f8c07792.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib3_58617b1d49e6f8461c01a261f8c07792.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib3_58617b1d49e6f8461c01a261f8c07792.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib_5e32f2239b373e5c67535661a4395c43.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib_5e32f2239b373e5c67535661a4395c43.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib_5e32f2239b373e5c67535661a4395c43.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_14fe047edcd4dcfd89a1260df022f538.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_14fe047edcd4dcfd89a1260df022f538.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_14fe047edcd4dcfd89a1260df022f538.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_e335e8e5ea03ce53f98b4db348798445.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_e335e8e5ea03ce53f98b4db348798445.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_e335e8e5ea03ce53f98b4db348798445.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/fixedpar_a5ab7cefe7159359d56615973597e427.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/fixedpar_a5ab7cefe7159359d56615973597e427.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/fixedpar_a5ab7cefe7159359d56615973597e427.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_51efbc7d57a066d469dd3c90968ddc38.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_51efbc7d57a066d469dd3c90968ddc38.rdb |only 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Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust
results, without the need of repetitive coding or extensive R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.1.4 dated 2022-09-08 and 5.2.0 dated 2023-02-03
lares-5.1.4/lares/man/fb_post.Rd |only lares-5.1.4/lares/man/fb_posts.Rd |only lares-5.2.0/lares/DESCRIPTION | 8 lares-5.2.0/lares/MD5 | 254 ++++--- lares-5.2.0/lares/NAMESPACE | 4 lares-5.2.0/lares/R/audio.R | 5 lares-5.2.0/lares/R/cache.R | 2 lares-5.2.0/lares/R/checks.R | 8 lares-5.2.0/lares/R/clusters.R | 28 lares-5.2.0/lares/R/colour_palettes.R | 1 lares-5.2.0/lares/R/correlations.R | 84 +- lares-5.2.0/lares/R/cran.R | 37 - lares-5.2.0/lares/R/crosstab.R | 2 lares-5.2.0/lares/R/currency.R | 2 lares-5.2.0/lares/R/dim_reduction.R | 3 lares-5.2.0/lares/R/distribution.R | 21 lares-5.2.0/lares/R/dropbox.R | 4 lares-5.2.0/lares/R/facebook.R | 769 +++++++++--------------- lares-5.2.0/lares/R/forecasting.R | 5 lares-5.2.0/lares/R/frequencies.R | 11 lares-5.2.0/lares/R/google_sheets.R | 6 lares-5.2.0/lares/R/google_trends.R | 8 lares-5.2.0/lares/R/hubspot.R | 4 lares-5.2.0/lares/R/lares.R | 2 lares-5.2.0/lares/R/lasso.R | 2 lares-5.2.0/lares/R/linkedin.R | 3 lares-5.2.0/lares/R/logo.R |only lares-5.2.0/lares/R/mails.R | 3 lares-5.2.0/lares/R/model_functions.R | 31 lares-5.2.0/lares/R/model_metrics.R | 9 lares-5.2.0/lares/R/model_plots.R | 84 +- lares-5.2.0/lares/R/model_predict.R | 10 lares-5.2.0/lares/R/model_preprocessing.R | 28 lares-5.2.0/lares/R/object_detection.R | 2 lares-5.2.0/lares/R/onehotencoding.R | 18 lares-5.2.0/lares/R/other_functions.R | 893 ---------------------------- lares-5.2.0/lares/R/other_plots.R | 3 lares-5.2.0/lares/R/outliers.R | 2 lares-5.2.0/lares/R/scrabble.R | 17 lares-5.2.0/lares/R/shapley.R | 1 lares-5.2.0/lares/R/statusbar.R | 15 lares-5.2.0/lares/R/stocks.R | 85 +- lares-5.2.0/lares/R/text_mining.R | 24 lares-5.2.0/lares/R/theme_lares.R | 9 lares-5.2.0/lares/R/tictoc.R | 5 lares-5.2.0/lares/R/wordle.R | 25 lares-5.2.0/lares/R/wrangling.R |only lares-5.2.0/lares/R/x2y.R | 25 lares-5.2.0/lares/README.md | 2 lares-5.2.0/lares/build/vignette.rds |binary lares-5.2.0/lares/inst/doc/h2o_automl.html | 541 ++++++++-------- lares-5.2.0/lares/man/autoline.Rd | 15 lares-5.2.0/lares/man/balance_data.Rd | 11 lares-5.2.0/lares/man/bind_files.Rd | 15 lares-5.2.0/lares/man/bring_api.Rd | 18 lares-5.2.0/lares/man/categ_reducer.Rd | 11 lares-5.2.0/lares/man/clean_text.Rd | 9 lares-5.2.0/lares/man/cran_logs.Rd | 3 lares-5.2.0/lares/man/date_cuts.Rd | 11 lares-5.2.0/lares/man/date_feats.Rd | 9 lares-5.2.0/lares/man/db_download.Rd | 15 lares-5.2.0/lares/man/db_upload.Rd | 15 lares-5.2.0/lares/man/dist2d.Rd | 2 lares-5.2.0/lares/man/export_plot.Rd | 15 lares-5.2.0/lares/man/export_results.Rd | 15 lares-5.2.0/lares/man/fb_accounts.Rd | 21 lares-5.2.0/lares/man/fb_ads.Rd | 33 - lares-5.2.0/lares/man/fb_creatives.Rd | 22 lares-5.2.0/lares/man/fb_insights.Rd | 36 - lares-5.2.0/lares/man/fb_process.Rd | 30 lares-5.2.0/lares/man/fb_report_check.Rd |only lares-5.2.0/lares/man/fb_rf.Rd | 14 lares-5.2.0/lares/man/fb_token.Rd | 19 lares-5.2.0/lares/man/file_name.Rd | 52 + lares-5.2.0/lares/man/filesGD.Rd | 6 lares-5.2.0/lares/man/files_functions.Rd | 37 + lares-5.2.0/lares/man/filterdata.Rd | 29 lares-5.2.0/lares/man/font_exists.Rd | 37 + lares-5.2.0/lares/man/formatColoured.Rd | 37 + lares-5.2.0/lares/man/format_string.Rd | 93 ++ lares-5.2.0/lares/man/get_credentials.Rd | 15 lares-5.2.0/lares/man/get_mp3.Rd | 2 lares-5.2.0/lares/man/glued.Rd | 37 + lares-5.2.0/lares/man/grepm.Rd | 43 + lares-5.2.0/lares/man/h2o_predict_API.Rd | 31 lares-5.2.0/lares/man/h2o_predict_MOJO.Rd | 31 lares-5.2.0/lares/man/h2o_predict_binary.Rd | 31 lares-5.2.0/lares/man/h2o_predict_model.Rd | 31 lares-5.2.0/lares/man/h2o_selectmodel.Rd | 15 lares-5.2.0/lares/man/haveInternet.Rd | 15 lares-5.2.0/lares/man/holidays.Rd | 9 lares-5.2.0/lares/man/image_metadata.Rd | 15 lares-5.2.0/lares/man/importxlsx.Rd | 15 lares-5.2.0/lares/man/impute.Rd | 9 lares-5.2.0/lares/man/ip_data.Rd | 15 lares-5.2.0/lares/man/json2vector.Rd | 15 lares-5.2.0/lares/man/lares_logo.Rd | 2 lares-5.2.0/lares/man/left_right.Rd | 11 lares-5.2.0/lares/man/li_auth.Rd | 3 lares-5.2.0/lares/man/li_profile.Rd | 3 lares-5.2.0/lares/man/list_cats.Rd | 37 + lares-5.2.0/lares/man/listfiles.Rd | 15 lares-5.2.0/lares/man/mail_send.Rd | 15 lares-5.2.0/lares/man/model_preprocess.Rd | 5 lares-5.2.0/lares/man/move_files.Rd | 37 + lares-5.2.0/lares/man/msplit.Rd | 15 lares-5.2.0/lares/man/myip.Rd | 15 lares-5.2.0/lares/man/normalize.Rd | 11 lares-5.2.0/lares/man/num_abbr.Rd | 28 lares-5.2.0/lares/man/ohe_commas.Rd | 9 lares-5.2.0/lares/man/ohse.Rd | 9 lares-5.2.0/lares/man/quants.Rd | 27 lares-5.2.0/lares/man/queryGA.Rd | 3 lares-5.2.0/lares/man/quiet.Rd | 15 lares-5.2.0/lares/man/read.file.Rd | 15 lares-5.2.0/lares/man/replaceall.Rd | 11 lares-5.2.0/lares/man/replacefactor.Rd | 28 lares-5.2.0/lares/man/scale_x_comma.Rd | 4 lares-5.2.0/lares/man/slackSend.Rd | 3 lares-5.2.0/lares/man/statusbar.Rd | 17 lares-5.2.0/lares/man/textFeats.Rd | 9 lares-5.2.0/lares/man/textTokenizer.Rd | 9 lares-5.2.0/lares/man/tic.Rd | 28 lares-5.2.0/lares/man/trim_mp3.Rd | 5 lares-5.2.0/lares/man/try_require.Rd | 15 lares-5.2.0/lares/man/updateLares.Rd | 15 lares-5.2.0/lares/man/vector2text.Rd | 11 lares-5.2.0/lares/man/warnifnot.Rd | 37 + lares-5.2.0/lares/man/what_size.Rd |only lares-5.2.0/lares/man/year_month.Rd | 11 lares-5.2.0/lares/man/zerovar.Rd | 56 - 131 files changed, 2096 insertions(+), 2502 deletions(-)
Title: Modeling and Forecasting Visitor Counts Using Social Media
Description: Performs modeling and forecasting of park visitor counts
using social media data and (partial) on-site visitor counts.
Specifically, the model is built based on an automatic decomposition
of the trend and seasonal components of the social media-based park visitor counts,
from which short-term forecasts of the visitor counts and percent changes
in the visitor counts can be made. A reference for generating social media-based
visitor counts can be found at
Wood, Guerry, Silver, and Lacayo (2013) <doi:10.1038/srep02976>.
Author: Russell Goebel [aut],
Robert Bowen [aut, cre],
Beth Ann Brackett [ctb],
Kimihiro Noguchi [aut],
Dylan Way [aut]
Maintainer: Robert Bowen <robertbowen.bham@gmail.com>
Diff between VisitorCounts versions 1.0.1 dated 2022-04-21 and 1.0.2 dated 2023-02-03
VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.R |only VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.Rmd |only VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.pdf |only VisitorCounts-1.0.1/VisitorCounts/vignettes/VisitorCounts_Analysis.Rmd |only VisitorCounts-1.0.2/VisitorCounts/DESCRIPTION | 12 VisitorCounts-1.0.2/VisitorCounts/MD5 | 67 - VisitorCounts-1.0.2/VisitorCounts/NAMESPACE | 2 VisitorCounts-1.0.2/VisitorCounts/NEWS.md | 9 VisitorCounts-1.0.2/VisitorCounts/R/classes.R | 33 VisitorCounts-1.0.2/VisitorCounts/R/data.R | 26 VisitorCounts-1.0.2/VisitorCounts/R/function_visitation_model.R | 447 ++++++++-- VisitorCounts-1.0.2/VisitorCounts/R/helpers_visitation_model.R | 65 + VisitorCounts-1.0.2/VisitorCounts/R/methods_plot.R | 2 VisitorCounts-1.0.2/VisitorCounts/R/methods_predict.R | 51 - VisitorCounts-1.0.2/VisitorCounts/R/methods_print.R | 12 VisitorCounts-1.0.2/VisitorCounts/R/methods_summary.R | 24 VisitorCounts-1.0.2/VisitorCounts/build/vignette.rds |binary VisitorCounts-1.0.2/VisitorCounts/data/forest_visitation.rda |only VisitorCounts-1.0.2/VisitorCounts/inst/doc/VisitorCounts.Rmd | 2 VisitorCounts-1.0.2/VisitorCounts/inst/doc/VisitorCounts.html | 329 ++++++- VisitorCounts-1.0.2/VisitorCounts/man/check_arguments.Rd | 5 VisitorCounts-1.0.2/VisitorCounts/man/decompose_proxy.Rd | 8 VisitorCounts-1.0.2/VisitorCounts/man/estimate_parameters.Rd | 9 VisitorCounts-1.0.2/VisitorCounts/man/fit_model.Rd | 5 VisitorCounts-1.0.2/VisitorCounts/man/forest_visitation.Rd |only VisitorCounts-1.0.2/VisitorCounts/man/imputation.Rd |only VisitorCounts-1.0.2/VisitorCounts/man/new_visitation_forecast.Rd | 7 VisitorCounts-1.0.2/VisitorCounts/man/new_visitation_model.Rd | 10 VisitorCounts-1.0.2/VisitorCounts/man/predict.decomposition.Rd | 2 VisitorCounts-1.0.2/VisitorCounts/man/predict.visitation_model.Rd | 3 VisitorCounts-1.0.2/VisitorCounts/man/print.visitation_forecast.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/print.visitation_model.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/summary.decomposition.Rd | 2 VisitorCounts-1.0.2/VisitorCounts/man/summary.visitation_model.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/visitation_model.Rd | 31 VisitorCounts-1.0.2/VisitorCounts/man/yearsToMonths.Rd |only VisitorCounts-1.0.2/VisitorCounts/tests/testthat/test_predict.R | 6 VisitorCounts-1.0.2/VisitorCounts/vignettes/VisitorCounts.Rmd | 2 VisitorCounts-1.0.2/VisitorCounts/vignettes/VisitorCounts_Analysis.pdf |only 39 files changed, 946 insertions(+), 228 deletions(-)
Title: Quick Table Generation & Exploratory Analyses on ADaM-Ish
Datasets
Description: Provides users a quick exploratory dive into common
visualizations without writing a single line of code given the users
data follows the Analysis Data Model (ADaM) standards put forth by the
Clinical Data Interchange Standards Consortium (CDISC)
<https://www.cdisc.org>. Prominent modules/ features of the
application are the Table Generator, Population Explorer, and the
Individual Explorer. The Table Generator allows users to drag and drop
variables and desired statistics (frequencies, means, ANOVA, t-test,
and other summary statistics) into bins that automagically create
stunning tables with validated information. The Population Explorer
offers various plots to visualize general trends in the population
from various vantage points. Plot modules currently include scatter
plot, spaghetti plot, box plot, histogram, means plot, and bar plot.
Each plot type allows the user to plot uploaded variables against one
another, and dissect the population by filtering out certain subjects.
La [...truncated...]
Author: Aaron Clark [aut, cre] ,
Jeff Thompson [aut],
Teresa Wilson [aut],
Nate Mockler [ccp, led],
Maya Gans [aut],
Robert Krajcik [ctb],
Marly Gotti [ctb],
Biogen Inc [cph]
Maintainer: Aaron Clark <clark.aaronchris@gmail.com>
Diff between tidyCDISC versions 0.1.0 dated 2022-08-30 and 0.2.0 dated 2023-02-03
tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_dark2lite.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_dark2lite_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_lite2dark_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_lite2dark_aura_cropped.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_solid_blue.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_solid_blue_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/gather_rules.Rd |only tidyCDISC-0.2.0/tidyCDISC/DESCRIPTION | 57 +- tidyCDISC-0.2.0/tidyCDISC/MD5 | 77 +- tidyCDISC-0.2.0/tidyCDISC/NAMESPACE | 2 tidyCDISC-0.2.0/tidyCDISC/NEWS.md | 55 +- tidyCDISC-0.2.0/tidyCDISC/R/data-phuse_TDF_ADaM.R | 5 tidyCDISC-0.2.0/tidyCDISC/R/golem_utils_ui.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_dataComplyRules_fct_helpers.R | 2 tidyCDISC-0.2.0/tidyCDISC/R/mod_dataUpload.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExpPatEvents.R | 4 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_fct_buildEvents.R | 8 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_srv.R | 8 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_ui.R | 1 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp.R | 48 + tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_line.R | 6 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_scatter.R | 2 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_ui.R | 1 tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen.R | 267 +++++++--- tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_fct_methods.R | 116 ++-- tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_ui.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_utils.R | 175 +++++- tidyCDISC-0.2.0/tidyCDISC/R/utils_helpers.R | 6 tidyCDISC-0.2.0/tidyCDISC/README.md | 91 +-- tidyCDISC-0.2.0/tidyCDISC/build/vignette.rds |binary tidyCDISC-0.2.0/tidyCDISC/data/example_dat1.rda |binary tidyCDISC-0.2.0/tidyCDISC/data/example_dat2.rda |binary tidyCDISC-0.2.0/tidyCDISC/inst/WORDLIST | 6 tidyCDISC-0.2.0/tidyCDISC/inst/app/www/recipe.js | 242 +++------ tidyCDISC-0.2.0/tidyCDISC/inst/app/www/script.js | 80 +- tidyCDISC-0.2.0/tidyCDISC/inst/app/www/styles.css | 17 tidyCDISC-0.2.0/tidyCDISC/inst/doc/getting_started.html | 16 tidyCDISC-0.2.0/tidyCDISC/man/app_methods.Rd | 28 - tidyCDISC-0.2.0/tidyCDISC/man/data_to_filter.Rd | 12 tidyCDISC-0.2.0/tidyCDISC/man/data_to_use_str.Rd | 20 tidyCDISC-0.2.0/tidyCDISC/man/prep_adae.Rd | 12 tidyCDISC-0.2.0/tidyCDISC/man/prep_bds.Rd | 10 tidyCDISC-0.2.0/tidyCDISC/man/std_footnote.Rd |only tidyCDISC-0.2.0/tidyCDISC/man/tg_gt.Rd |only 44 files changed, 858 insertions(+), 537 deletions(-)
Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre],
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>
Diff between logrx versions 0.2.0 dated 2023-01-18 and 0.2.1 dated 2023-02-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/get.R | 18 ++++++++++++++++-- tests/testthat/test-get.R | 20 ++++++++++++++++++++ 6 files changed, 49 insertions(+), 10 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb],
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.5.0 dated 2022-12-05 and 0.5.1 dated 2023-02-03
DESCRIPTION | 18 MD5 | 61 +- NEWS.md | 17 R/compute-npc.r | 51 +- R/geom-grob.R | 4 R/geom-label-linked.r | 4 R/geom-margin-point.r | 8 R/geom-plot.R | 2 R/geom-point-linked.r | 8 R/geom-table.R | 2 R/geom-text-linked.r | 10 R/stat-dens1d-filter.r | 169 +++++-- R/stat-dens1d-labels.r | 279 +++++++++--- R/stat-dens2d-filter.r | 214 ++++++--- R/stat-dens2d-labels.r | 372 +++++++++++++--- README.md | 4 inst/doc/grammar-extensions.R | 77 ++- inst/doc/grammar-extensions.Rmd | 305 +++++++++---- inst/doc/grammar-extensions.html | 861 ++++++++++++++++++++++----------------- inst/doc/nudge-examples.R | 20 inst/doc/nudge-examples.Rmd | 26 + inst/doc/nudge-examples.html | 288 ++++++------- man/compute_npcx.Rd | 44 + man/ggpp-package.Rd | 2 man/keep_these2logical.Rd |only man/stat_dens1d_filter.Rd | 89 +++- man/stat_dens1d_labels.Rd | 115 ++++- man/stat_dens2d_filter.Rd | 96 +++- man/stat_dens2d_labels.Rd | 90 +++- man/stat_panel_counts.Rd | 506 +++++++++++----------- vignettes/grammar-extensions.Rmd | 305 +++++++++---- vignettes/nudge-examples.Rmd | 26 + 32 files changed, 2751 insertions(+), 1322 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative
divide in social science research. It uses a Boolean minimization
algorithm, resulting in a minimal causal configuration associated
with a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] ,
Ciprian Paduraru [ctb] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
lp_solve [cph] ,
Vasil Dinkov [ctb, cph] ,
Dmitry Baranovskiy [ctb, cph] ,
Emmanuel Quentin [ctb, cph] ,
Jimmy Breck-McKye [ctb, cph] ,
[...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.17 dated 2022-10-03 and 3.18 dated 2023-02-03
DESCRIPTION | 8 MD5 | 220 +++++++++++++------------- R/XYplot.R | 2 R/Xplot.R | 2 R/allExpressions.R | 2 R/calibrate.R | 2 R/causalChain.R | 2 R/combint.R | 2 R/complexity.R | 2 R/createMatrix.R | 2 R/dimnames.R | 2 R/findRows.R | 2 R/findSubsets.R | 2 R/findSupersets.R | 2 R/findTh.R | 2 R/findmin.R | 2 R/fuzzyand.R | 2 R/fuzzyor.R | 2 R/generate.R | 2 R/getRow.R | 2 R/getSolution.R | 2 R/makeChart.R | 2 R/minimize.R | 2 R/modelFit.R | 2 R/onAttach.R | 2 R/onUnload.R | 2 R/panel.R | 2 R/pof.R | 2 R/pofind.R | 2 R/print.R | 2 R/removeRedundants.R | 2 R/replaceCategories.R | 8 R/retention.R | 2 R/rowDominance.R | 2 R/runGUI.R | 2 R/solveChart.R | 2 R/sortMatrix.R | 2 R/sortVector.R | 2 R/string.R | 2 R/superSubset.R | 2 R/truthTable.R | 9 - R/verifyQCA.R | 41 ++-- R/writeSolution.R | 2 build/partial.rdb |binary data/HarKem.RData |binary data/d.HK.RData |binary data/d.partybans.RData |binary inst/CITATION | 9 - inst/ChangeLog | 6 inst/gui/server.R | 7 inst/gui/www/js/maincode.js | 4 inst/gui/www/js/utils.js | 2 inst/staticdocs/CV.html | 4 inst/staticdocs/LegacyDatasets.html | 4 inst/staticdocs/Lipset.html | 4 inst/staticdocs/QCA_package.html | 8 inst/staticdocs/RS.html | 4 inst/staticdocs/SOPexpressions.html | 4 inst/staticdocs/XYplot.html | 4 inst/staticdocs/Xplot.html | 4 inst/staticdocs/calibrate.html | 4 inst/staticdocs/causalChain.html | 4 inst/staticdocs/chartFunctions.html | 4 inst/staticdocs/export.html | 4 inst/staticdocs/factorize.html | 4 inst/staticdocs/findRows.html | 4 inst/staticdocs/findTh.html | 4 inst/staticdocs/fuzzyops.html | 4 inst/staticdocs/generate.html | 4 inst/staticdocs/implicantMatrixFunctions.html | 4 inst/staticdocs/index.html | 4 inst/staticdocs/intersection.html | 4 inst/staticdocs/minimize.html | 4 inst/staticdocs/modelFit.html | 4 inst/staticdocs/negate.html | 4 inst/staticdocs/pof.html | 4 inst/staticdocs/retention.html | 4 inst/staticdocs/runGUI.html | 4 inst/staticdocs/subsetsAndSupersets.html | 4 inst/staticdocs/truthTable.html | 4 man/QCA_package.Rd | 4 src/CCubes.c | 2 src/QCA.c | 2 src/consistency.c | 2 src/consistent_solution.c | 2 src/find_consistent_models.c | 2 src/find_min.c | 2 src/find_models.c | 2 src/generate_matrix.c | 2 src/lp_MPS.c | 20 +- src/lp_lib.c | 12 - src/lp_matrix.c | 3 src/lp_mipbb.c | 2 src/lp_params.c | 6 src/lp_presolve.c | 26 +-- src/lp_report.c | 1 src/lp_report.h | 1 src/lp_rlp.c | 6 src/lp_rlp.h | 9 - src/lp_types.h | 1 src/lp_utils.c | 1 src/lusol.c | 2 src/registerDynamicSymbol.c | 2 src/row_dominance.c | 2 src/sort_cols.c | 2 src/sort_matrix.c | 2 src/super_rows.c | 2 src/truthTable.c | 2 src/utils.c | 2 src/yacc_read.c | 32 +-- src/yacc_read.h | 4 111 files changed, 337 insertions(+), 329 deletions(-)
Title: Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain
Cost Conditions
Description: Functions for cost-sensitive multi-criteria ensemble selection (CSMES) (as described in De bock et al. (2020) <doi:10.1016/j.ejor.2020.01.052>) for cost-sensitive learning under unknown cost conditions.
Author: Koen W. De Bock, Kristof Coussement and Stefan Lessmann
Maintainer: Koen W. De Bock <kdebock@audencia.com>
Diff between CSMES versions 1.0.0 dated 2020-02-22 and 1.0.1 dated 2023-02-03
DESCRIPTION | 8 +++---- MD5 | 19 +++++++++-------- NAMESPACE | 48 ++++++++++++++++++++++----------------------- R/brierCurve.R | 3 +- R/globals.R |only R/plotBrierCurve.R | 2 - man/BFP.Rd | 5 ++-- man/CSMES.ensNomCurve.Rd | 5 ++-- man/CSMES.ensSel.Rd | 8 ++----- man/CSMES.predict.Rd | 5 ++-- man/CSMES.predictPareto.Rd | 6 ++--- 11 files changed, 56 insertions(+), 53 deletions(-)
Title: Add Logging to Functions
Description: Decorate functions to make them return enhanced output. The enhanced output consists in an object of type
'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function
was run, what were its inputs, what were the errors (if the function failed to run) and other useful information.
Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.
Author: Bruno Rodrigues [aut, cre, cph]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between chronicler versions 0.2.0 dated 2022-05-17 and 0.2.1 dated 2023-02-03
DESCRIPTION | 10 MD5 | 78 +- NAMESPACE | 82 +- NEWS.md | 21 R/chronicle.R | 1202 +++++++++++++++---------------- R/data.R | 12 R/zzz.R | 2 README.md | 940 ++++++++++++------------ build/vignette.rds |binary inst/doc/advanced-topics.R | 438 +++++------ inst/doc/advanced-topics.Rmd | 850 ++++++++++----------- inst/doc/advanced-topics.html | 1196 +++++++++++++++++++----------- inst/doc/maybe-monad.R | 68 - inst/doc/maybe-monad.Rmd | 154 +-- inst/doc/maybe-monad.html | 645 +++++++++++----- inst/doc/real-world-example.R | 131 +-- inst/doc/real-world-example.Rmd | 227 ++--- inst/doc/real-world-example.html | 792 +++++++++++++------- man/as_chronicle.Rd | 44 - man/bind_record.Rd | 52 - man/check_diff.Rd | 60 - man/check_g.Rd | 58 - man/flatten_record.Rd | 48 - man/fmap_record.Rd | 48 - man/grapes-greater-than-equals-grapes.Rd | 48 - man/is_chronicle.Rd | 34 man/make_log_df.Rd | 86 +- man/pick.Rd | 48 - man/print.chronicle.Rd | 64 - man/purely.Rd | 56 - man/read_log.Rd | 44 - man/record.Rd | 74 - man/record_many.Rd | 82 +- tests/testthat.R | 8 tests/testthat/test-run_time.R | 32 tests/testthat/test-test_chronicler.R | 218 ++--- tests/testthat/test-test_purely.R | 168 ++-- vignettes/advanced-topics.Rmd | 850 ++++++++++----------- vignettes/maybe-monad.Rmd | 154 +-- vignettes/real-world-example.Rmd | 227 ++--- 40 files changed, 5059 insertions(+), 4292 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-5 dated 2023-01-23 and 0.0-6 dated 2023-02-03
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/lme4_functions.R | 2 +- src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/include/stan/math/prim/fun/acosh.hpp | 2 +- src/include/stan/math/prim/fun/asinh.hpp | 2 +- src/include/stan/math/prim/fun/pow.hpp | 2 +- src/stan_files/continuous.hpp | 4 ++-- src/stan_sampler_includes.hpp | 10 ++++++++++ tests/testthat/test-01-continuous.R | 1 + 11 files changed, 33 insertions(+), 22 deletions(-)
Title: Read 'Excel' Binary (.xlsb) Workbooks
Description: Import data from 'Excel' binary (.xlsb) workbooks into R.
Author: Michael Allen [aut, cre]
Maintainer: Michael Allen <michael@velofrog.com>
Diff between readxlsb versions 0.1.4 dated 2020-09-29 and 0.1.5 dated 2023-02-03
DESCRIPTION | 10 - MD5 | 18 +- build/vignette.rds |binary inst/doc/read-xlsb-workbook.html | 261 +++++++++++++++++++++++---------------- src/BinaryReader.h | 1 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 src/RecordNames.h | 1 src/StreamReader.h | 1 10 files changed, 180 insertions(+), 121 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between Luminescence versions 0.9.20 dated 2022-07-16 and 0.9.21 dated 2023-02-03
DESCRIPTION | 28 +- MD5 | 309 +++++++++++++++--------------- NEWS.md | 104 +++------- R/Risoe.BINfileData-class.R | 2 R/analyse_SAR.CWOSL.R | 1 R/analyse_portableOSL.R | 107 +++++++--- R/apply_CosmicRayRemoval.R | 6 R/calc_OSLLxTxRatio.R | 2 R/combine_De_Dr.R | 14 - R/convert_PSL2CSV.R | 75 ++++++- R/convert_Wavelength2Energy.R | 2 R/fit_LMCurve.R | 101 ++++----- R/github.R | 4 R/internals_RLum.R | 2 R/plot_RadialPlot.R | 43 +--- R/read_BIN2R.R | 25 +- R/read_PSL2R.R | 6 R/write_RLum2CSV.R | 16 - README.md | 83 +++----- inst/CITATION | 3 man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/GitHub-API.Rd | 4 man/PSL2Risoe.BINfileData.Rd | 2 man/RLum-class.Rd | 6 man/RLum.Analysis-class.Rd | 18 - man/RLum.Data.Curve-class.Rd | 18 - man/RLum.Data.Image-class.Rd | 12 - man/RLum.Data.Spectrum-class.Rd | 14 - man/RLum.Results-class.Rd | 14 - man/Risoe.BINfileData-class.Rd | 10 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 2 man/analyse_Al2O3C_ITC.Rd | 2 man/analyse_Al2O3C_Measurement.Rd | 2 man/analyse_FadingMeasurement.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 3 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 2 man/analyse_pIRIRSequence.Rd | 2 man/analyse_portableOSL.Rd | 44 ++-- man/apply_CosmicRayRemoval.Rd | 8 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CobbleDoseRate.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Kars2008.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxDecomposed.Rd | 2 man/calc_OSLLxTxRatio.Rd | 4 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/calc_gSGC_feldspar.Rd | 2 man/combine_De_Dr.Rd | 2 man/convert_Activity2Concentration.Rd | 2 man/convert_BIN2CSV.Rd | 2 man/convert_Concentration2DoseRate.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 20 + man/convert_RLum2Risoe.BINfileData.Rd | 2 man/convert_SG2MG.Rd | 2 man/convert_Wavelength2Energy.Rd | 4 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/extract_ROI.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_EmissionSpectra.Rd | 2 man/fit_LMCurve.Rd | 4 man/fit_OSLLifeTimes.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/fit_ThermalQuenching.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 8 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/names_RLum.Rd | 6 man/plot_AbanicoPlot.Rd | 2 man/plot_DRCSummary.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_NRt.Rd | 2 man/plot_OSLAgeSummary.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_ROI.Rd | 2 man/plot_RadialPlot.Rd | 4 man/plot_Risoe.BINfileData.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 4 man/read_Daybreak2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_RF2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_TIFF2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/scale_GammaDose.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 6 man/structure_RLum.Rd | 6 man/template_DRAC.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/write_R2BIN.Rd | 2 man/write_R2TIFF.Rd | 2 man/write_RLum2CSV.Rd | 6 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_analyse_portableOSL.R | 19 + tests/testthat/test_combine_De_Dr.R | 4 tests/testthat/test_convert_PSL2CSV.R | 13 + tests/testthat/test_fit_CWCurve.R | 19 + tests/testthat/test_fit_LMCurve.R | 19 + tests/testthat/test_plot_RadialPlot.R |only tests/testthat/test_read_BIN2R.R | 19 + 156 files changed, 817 insertions(+), 646 deletions(-)
Title: Melt Curve Fitting and Melt Shift Analysis
Description: Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment.
McCracken (2022) <doi:10.1101/2022.12.30.522131>.
Author: Neil McCracken [aut],
Hao Liu [ctb],
Amber Mosley [cre]
Maintainer: Amber Mosley <almosley@iu.edu>
Diff between InflectSSP versions 1.4.5 dated 2022-10-03 and 1.5 dated 2023-02-03
InflectSSP-1.4.5/InflectSSP/R/ReportPANTHER.R |only InflectSSP-1.4.5/InflectSSP/man/ReportPANTHER.Rd |only InflectSSP-1.5/InflectSSP/DESCRIPTION | 10 InflectSSP-1.5/InflectSSP/MD5 | 26 -- InflectSSP-1.5/InflectSSP/NAMESPACE | 8 InflectSSP-1.5/InflectSSP/R/InflectSSP.R | 17 - InflectSSP-1.5/InflectSSP/R/MeltCalc.R | 8 InflectSSP-1.5/InflectSSP/R/ReportDataMelts.R | 2 InflectSSP-1.5/InflectSSP/R/ReportSTRING.R | 60 +++- InflectSSP-1.5/InflectSSP/inst/doc/InflectSSPVignette.Rmd | 19 - InflectSSP-1.5/InflectSSP/inst/doc/InflectSSPVignette.html | 169 +++++-------- InflectSSP-1.5/InflectSSP/man/InflectSSP.Rd | 14 - InflectSSP-1.5/InflectSSP/man/ReportDataMelts.Rd | 2 InflectSSP-1.5/InflectSSP/man/ReportSTRING.Rd | 6 InflectSSP-1.5/InflectSSP/vignettes/InflectSSPVignette.Rmd | 19 - 15 files changed, 169 insertions(+), 191 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension scores. 29 TTO and 11 VAS EQ-5D-3L
value [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.13.0 dated 2022-11-11 and 0.14.0 dated 2023-02-03
DESCRIPTION | 12 MD5 | 82 + NAMESPACE | 5 NEWS.md | 187 ++-- R/data.R | 6 R/eq5d.R | 2 R/eq5dcf.R | 49 - R/eq5dlfs.R | 6 R/eq5dlss.R | 5 R/eq5dy.R | 19 R/eqhpg.R |only R/eqhsdi.R |only R/eqpchc.R | 42 R/eqps.R |only R/eqshannon.R |only R/helpers.R | 8 R/imports.R | 1 R/sysdata.rda |binary README.md | 236 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/eq5d.R | 116 ++ inst/doc/eq5d.Rmd | 143 ++- inst/doc/eq5d.html | 930 ++++++++++----------- inst/extdata/eq5d3l_example.csv |only inst/extdata/eq5d3l_five_digit_example.csv |only inst/extdata/eq5d5l_example.csv |only inst/shiny/server.R | 157 +++ inst/shiny/ui.R | 11 man/VT.Rd | 6 man/Y.Rd | 4 man/eq5d-package.Rd | 2 man/eq5dcf.Rd | 14 man/figures/README-hpg-1.png |only man/figures/README-hsdi-1.png |only man/hpg.Rd |only man/hsdi.Rd |only man/lfs.Rd | 7 man/lss.Rd | 6 man/pchc.Rd | 19 man/ps.Rd |only man/shannon.Rd |only tests/testdata/hpg_3l_uk_tto_no_problems_false.csv |only tests/testthat/test-eq5d5l.R | 30 tests/testthat/test-eq5dy.R | 14 tests/testthat/test-eqhpg.R |only tests/testthat/test-eqhsdi.R |only tests/testthat/test-eqpchc.R | 7 tests/testthat/test-eqps.R |only tests/testthat/test-eqshannon.R |only vignettes/eq5d.Rmd | 143 ++- 51 files changed, 1565 insertions(+), 704 deletions(-)
Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in King, Tomz, and Wittenberg (2000) <doi:10.2307/2669316>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] ,
Steven Worthington [aut] ,
Stefano Iacus [aut] ,
Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between clarify versions 0.1.0 dated 2023-01-25 and 0.1.1 dated 2023-02-03
DESCRIPTION | 8 MD5 | 38 ++-- NEWS.md | 8 R/checks.R | 35 +++ R/clarify_predict.R | 5 R/sim_adrf.R | 4 R/sim_ame.R | 4 R/sim_setx.R | 4 R/summary.clarify_est.R | 21 -- README.md | 283 ++++++++++++++++--------------- build/vignette.rds |binary inst/doc/Zelig.Rmd | 2 inst/doc/clarify.R | 6 inst/doc/clarify.Rmd | 24 +- inst/doc/clarify.html | 185 ++++++++++++-------- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/summary.clarify_est.Rd | 7 vignettes/Zelig.Rmd | 2 vignettes/clarify.Rmd | 24 +- 21 files changed, 378 insertions(+), 282 deletions(-)
Title: Distribution of the 'BayesX' C++ Sources
Description: 'BayesX' performs Bayesian inference in structured additive regression (STAR) models.
The R package BayesXsrc provides the 'BayesX' command line tool for easy installation.
A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre] ,
Daniel Adler [aut],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesXsrc versions 3.0-3 dated 2022-11-03 and 3.0-4 dated 2023-02-03
DESCRIPTION | 16 ++--- MD5 | 46 ++++++++--------- inst/CITATION | 78 ++++++++++++++++------------- src/Makefile | 7 ++ src/Makefile.inner.win | 7 ++ src/Makefile.win | 5 + src/bayesxsrc/andrea/baseline.cpp | 4 - src/bayesxsrc/bib/Random.cpp | 12 ++-- src/bayesxsrc/bib/adminparse.h | 2 src/bayesxsrc/bib/bayesreg.cpp | 5 + src/bayesxsrc/bib/model.h | 2 src/bayesxsrc/bib/realvar.cpp | 2 src/bayesxsrc/bib/sparsemat.h | 2 src/bayesxsrc/bib/tarray.h | 2 src/bayesxsrc/bib/tpremat.cpp | 9 ++- src/bayesxsrc/bib/tsearcht.h | 2 src/bayesxsrc/bib/vectorn.h | 2 src/bayesxsrc/mcmc/mcmc_const.cpp | 10 +-- src/bayesxsrc/structadd/design_kriging.cpp | 2 src/dev-Makefile | 7 ++ src/dev-Makefile.inner.win | 7 ++ src/dev-Makefile.win | 5 + src/rel-Makefile | 7 ++ src/rel-Makefile.win | 7 ++ 24 files changed, 155 insertions(+), 93 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 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent 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 Sta [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut],
Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.2.1 dated 2022-11-04 and 1.2.2 dated 2023-02-03
BayesMallows-1.2.1/BayesMallows/man/plot_alpha_posterior.Rd |only BayesMallows-1.2.1/BayesMallows/man/plot_rho_posterior.Rd |only BayesMallows-1.2.2/BayesMallows/DESCRIPTION | 8 BayesMallows-1.2.2/BayesMallows/MD5 | 115 +-- BayesMallows-1.2.2/BayesMallows/NAMESPACE | 1 BayesMallows-1.2.2/BayesMallows/NEWS.md | 8 BayesMallows-1.2.2/BayesMallows/R/RcppExports.R | 42 - BayesMallows-1.2.2/BayesMallows/R/all_topological_sorts.R | 1 BayesMallows-1.2.2/BayesMallows/R/get_mallows_loglik.R | 2 BayesMallows-1.2.2/BayesMallows/R/plot.SMCMallows.R |only BayesMallows-1.2.2/BayesMallows/R/smc_mallows_deprecated.R | 39 - BayesMallows-1.2.2/BayesMallows/R/smc_post_processing_functions.R | 97 -- BayesMallows-1.2.2/BayesMallows/build/partial.rdb |binary BayesMallows-1.2.2/BayesMallows/build/vignette.rds |binary BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.R | 33 BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.Rmd | 68 - BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.html | 343 ++++------ BayesMallows-1.2.2/BayesMallows/inst/examples/metropolis_hastings_alpha_example.R | 16 BayesMallows-1.2.2/BayesMallows/inst/examples/plot.SMCMallows_example.R |only BayesMallows-1.2.2/BayesMallows/man/calculate_backward_probability.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/calculate_forward_probability.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/compute_posterior_intervals_alpha.Rd | 3 BayesMallows-1.2.2/BayesMallows/man/compute_posterior_intervals_rho.Rd | 3 BayesMallows-1.2.2/BayesMallows/man/compute_rho_consensus.Rd | 5 BayesMallows-1.2.2/BayesMallows/man/correction_kernel_pseudo.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/get_exponent_sum.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/get_sample_probabilities.Rd | 8 BayesMallows-1.2.2/BayesMallows/man/leap_and_shift_probs.Rd | 12 BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_alpha.Rd | 40 - BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_aug_ranking.Rd | 8 BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_rho.Rd | 13 BayesMallows-1.2.2/BayesMallows/man/plot.SMCMallows.Rd |only BayesMallows-1.2.2/BayesMallows/man/smc_mallows_new_item_rank.Rd | 28 BayesMallows-1.2.2/BayesMallows/man/smc_mallows_new_users.Rd | 28 BayesMallows-1.2.2/BayesMallows/src/Makevars | 2 BayesMallows-1.2.2/BayesMallows/src/Makevars.win | 2 BayesMallows-1.2.2/BayesMallows/src/RcppExports.cpp | 62 - BayesMallows-1.2.2/BayesMallows/src/parameterupdates.cpp | 2 BayesMallows-1.2.2/BayesMallows/src/smc.h | 8 BayesMallows-1.2.2/BayesMallows/src/smc_calculate_probability.cpp | 14 BayesMallows-1.2.2/BayesMallows/src/smc_correction_kernel_pseudo.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_get_exponent_sum.cpp | 2 BayesMallows-1.2.2/BayesMallows/src/smc_get_sample_probabilities.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_leap_and_shift_probs.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_item_rank.cpp | 61 - BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users.cpp | 40 - BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users.h | 9 BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users_funs.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_alpha.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_aug_ranking.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_rho.cpp | 4 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-assess_convergence.R | 1 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-bulletproofing.R | 32 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-compute_mallows.R | 2 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-get_mallows_loglik.R | 4 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_individual_functions.R | 29 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_mallows_new_item_rank.R | 29 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_mallows_partial_rankings.R | 22 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_pseudolikelihood.R | 10 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_updated_new_item_rank.R | 8 BayesMallows-1.2.2/BayesMallows/vignettes/SMC-Mallows.Rmd | 68 - 61 files changed, 595 insertions(+), 781 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>),
'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>),
'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.15 dated 2021-01-11 and 0.9.16 dated 2023-02-03
DESCRIPTION | 8 MD5 | 30 NEWS.md | 9 R/Export.R | 2 R/Registry.R | 4 R/Worker.R | 4 R/addExperiments.R | 30 R/clusterFunctionsSlurm.R | 14 R/waitForFiles.R | 2 build/vignette.rds |binary inst/CITATION | 8 inst/doc/batchtools.html | 1774 +++++++++++++++++++---------------- man/addExperiments.Rd | 5 man/makeExperimentRegistry.Rd | 4 man/makeRegistry.Rd | 4 tests/testthat/test_addExperiments.R | 1 16 files changed, 1090 insertions(+), 809 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut],
Duncan Murdoch [ctb]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan3d versions 1.1-2 dated 2018-10-25 and 1.2-0 dated 2023-02-03
DESCRIPTION | 14 ++++++++------ MD5 | 30 +++++++++++++++--------------- R/ordirgl.R | 26 +++++++++++++------------- R/orditree3d.R | 12 ++++++------ R/orglpoints.R | 2 +- R/orglsegments.R | 2 +- R/orglspantree.R | 4 ++-- R/orglspider.R | 4 ++-- R/orgltext.R | 2 +- R/rgl.isomap.R | 2 +- R/rgl.renyiaccum.R | 24 ++++++++++++------------ build/partial.rdb |binary inst/NEWS.md | 7 +++++++ man/ordirgl.Rd | 14 +++++++------- man/orditree3d.Rd | 2 +- man/vegan3d-package.Rd | 2 +- 16 files changed, 78 insertions(+), 69 deletions(-)
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', and 'kernelshap'
are added for convenience. By separating visualization and
computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.4.1 dated 2023-01-11 and 0.5.0 dated 2023-02-03
DESCRIPTION | 28 +-- MD5 | 62 ++++---- NAMESPACE | 6 NEWS.md | 28 +++ R/bee.R | 10 - R/collapse_shap.R | 67 ++++++-- R/shapviz-package.R | 2 R/shapviz.R | 98 ++++++++++--- R/shapviz_methods.R | 41 ++++- R/sv_dependence.R | 112 ++++++++++---- R/sv_force.R | 4 R/sv_importance.R | 144 ++++++++----------- R/sv_interaction.R |only R/sv_waterfall.R | 6 README.md | 35 ++++ inst/doc/shapviz.R | 11 + inst/doc/shapviz.Rmd | 32 +++- inst/doc/shapviz.html | 269 +++++++++++++++++++----------------- man/collapse_shap.Rd | 26 +-- man/extractors.Rd | 112 ++++++++------ man/figures/README-dep2.png |only man/figures/README-interactions.png |only man/potential_interactions.Rd | 17 +- man/shapviz-package.Rd | 2 man/shapviz.Rd | 25 ++- man/sv_dependence.Rd | 40 +++-- man/sv_force.Rd | 2 man/sv_importance.Rd | 14 - man/sv_interaction.Rd |only man/sv_waterfall.Rd | 2 tests/testthat/test-collapse_shap.R | 45 ++++++ tests/testthat/test-interface.R | 44 +++++ tests/testthat/test-plots.R | 56 ++++++- vignettes/shapviz.Rmd | 32 +++- 34 files changed, 899 insertions(+), 473 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2022)
<doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple
measurements per individual, time-varying and time-invariant effects, and a
wide range of discrete and continuous distributions. Estimation of these
dynamic multivariate panel models is carried out via 'Stan'.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.0.1 dated 2022-12-23 and 1.1.1 dated 2023-02-03
dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-11-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-4-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-5-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-6-1.png |only dynamite-1.0.1/dynamite/man/random.Rd |only dynamite-1.0.1/dynamite/tests/testthat/Rplots.pdf |only dynamite-1.1.1/dynamite/DESCRIPTION | 12 dynamite-1.1.1/dynamite/MD5 | 177 dynamite-1.1.1/dynamite/NAMESPACE | 7 dynamite-1.1.1/dynamite/NEWS.md | 163 dynamite-1.1.1/dynamite/R/as_data_frame.R | 37 dynamite-1.1.1/dynamite/R/as_data_table.R | 102 dynamite-1.1.1/dynamite/R/as_draws.R | 21 dynamite-1.1.1/dynamite/R/ci.R | 4 dynamite-1.1.1/dynamite/R/coef.R | 49 dynamite-1.1.1/dynamite/R/default_priors.R | 46 dynamite-1.1.1/dynamite/R/deterministic.R | 81 dynamite-1.1.1/dynamite/R/dynamite-package.R | 50 dynamite-1.1.1/dynamite/R/dynamite.R | 330 - dynamite-1.1.1/dynamite/R/dynamiteformula.R | 1166 +++-- dynamite-1.1.1/dynamite/R/exported_gets.R | 401 +- dynamite-1.1.1/dynamite/R/fitted.R | 162 dynamite-1.1.1/dynamite/R/lags.R | 25 dynamite-1.1.1/dynamite/R/latent_factor.R | 183 dynamite-1.1.1/dynamite/R/lfo.R | 621 +-- dynamite-1.1.1/dynamite/R/loo.R | 159 dynamite-1.1.1/dynamite/R/mcmc_diagnostics.R | 67 dynamite-1.1.1/dynamite/R/model_matrix.R | 75 dynamite-1.1.1/dynamite/R/plot.R | 901 ++-- dynamite-1.1.1/dynamite/R/predict.R | 1343 +++--- dynamite-1.1.1/dynamite/R/predict_helpers.R | 1995 +++++----- dynamite-1.1.1/dynamite/R/prepare_stan_input.R | 157 dynamite-1.1.1/dynamite/R/print.R | 9 dynamite-1.1.1/dynamite/R/random.R | 98 dynamite-1.1.1/dynamite/R/specials.R | 42 dynamite-1.1.1/dynamite/R/stanblocks.R | 182 dynamite-1.1.1/dynamite/R/stanblocks_families.R | 796 ++- dynamite-1.1.1/dynamite/R/summary.R | 12 dynamite-1.1.1/dynamite/R/sysdata.rda |binary dynamite-1.1.1/dynamite/R/update.R | 2 dynamite-1.1.1/dynamite/R/utilities.R | 687 +-- dynamite-1.1.1/dynamite/README.md | 92 dynamite-1.1.1/dynamite/data/categorical_example_fit.rda |binary dynamite-1.1.1/dynamite/data/gaussian_example_fit.rda |binary dynamite-1.1.1/dynamite/data/latent_factor_example_fit.rda |binary dynamite-1.1.1/dynamite/data/multichannel_example_fit.rda |binary dynamite-1.1.1/dynamite/inst/doc/dynamite.R | 42 dynamite-1.1.1/dynamite/inst/doc/dynamite.Rmd | 1122 ++--- dynamite-1.1.1/dynamite/inst/doc/dynamite.html | 453 +- dynamite-1.1.1/dynamite/man/as.data.frame.dynamitefit.Rd | 35 dynamite-1.1.1/dynamite/man/as.data.table.dynamitefit.Rd | 22 dynamite-1.1.1/dynamite/man/as_draws-dynamitefit.Rd | 29 dynamite-1.1.1/dynamite/man/categorical_example_fit.Rd | 11 dynamite-1.1.1/dynamite/man/coef.dynamitefit.Rd | 26 dynamite-1.1.1/dynamite/man/confint.dynamitefit.Rd | 2 dynamite-1.1.1/dynamite/man/dynamite.Rd | 66 dynamite-1.1.1/dynamite/man/dynamiteformula.Rd | 28 dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-10-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-7-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-8-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-9-1.png |binary dynamite-1.1.1/dynamite/man/figures/logo.png |only dynamite-1.1.1/dynamite/man/fitted.dynamitefit.Rd | 16 dynamite-1.1.1/dynamite/man/gaussian_example_fit.Rd | 20 dynamite-1.1.1/dynamite/man/get_code.Rd | 17 dynamite-1.1.1/dynamite/man/get_data.Rd | 12 dynamite-1.1.1/dynamite/man/get_parameter_names.Rd |only dynamite-1.1.1/dynamite/man/get_parameter_types.Rd |only dynamite-1.1.1/dynamite/man/get_priors.Rd | 12 dynamite-1.1.1/dynamite/man/lags.Rd | 2 dynamite-1.1.1/dynamite/man/latent_factor_example_fit.Rd | 2 dynamite-1.1.1/dynamite/man/lfactor.Rd | 12 dynamite-1.1.1/dynamite/man/lfo.Rd | 5 dynamite-1.1.1/dynamite/man/loo.dynamitefit.Rd | 5 dynamite-1.1.1/dynamite/man/mcmc_diagnostics.Rd | 4 dynamite-1.1.1/dynamite/man/multichannel_example_fit.Rd | 16 dynamite-1.1.1/dynamite/man/plot.dynamitefit.Rd | 42 dynamite-1.1.1/dynamite/man/plot_betas.Rd | 12 dynamite-1.1.1/dynamite/man/plot_deltas.Rd | 5 dynamite-1.1.1/dynamite/man/plot_nus.Rd | 14 dynamite-1.1.1/dynamite/man/predict.dynamitefit.Rd | 41 dynamite-1.1.1/dynamite/man/random_spec.Rd |only dynamite-1.1.1/dynamite/tests/testthat/test-edgecases.R | 193 dynamite-1.1.1/dynamite/tests/testthat/test-errors.R | 320 + dynamite-1.1.1/dynamite/tests/testthat/test-grunfeld.R | 17 dynamite-1.1.1/dynamite/tests/testthat/test-internals.R | 114 dynamite-1.1.1/dynamite/tests/testthat/test-output.R | 33 dynamite-1.1.1/dynamite/tests/testthat/test-predict.R | 891 ++-- dynamite-1.1.1/dynamite/tests/testthat/test-priors.R | 5 dynamite-1.1.1/dynamite/tests/testthat/test-recovery.R | 188 dynamite-1.1.1/dynamite/tests/testthat/test-scaling.R | 53 dynamite-1.1.1/dynamite/tests/testthat/test-warnings.R | 368 - dynamite-1.1.1/dynamite/tests/testthat/testmodel.stan |only dynamite-1.1.1/dynamite/vignettes/dynamite.Rmd | 1122 ++--- dynamite-1.1.1/dynamite/vignettes/dynamite.bib | 23 95 files changed, 8636 insertions(+), 7018 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 1.0.1 dated 2022-11-04 and 2.0.0 dated 2023-02-03
dsfa-1.0.1/dsfa/R/OwenT.R |only dsfa-1.0.1/dsfa/R/chainrule.R |only dsfa-1.0.1/dsfa/R/check_arguments.R |only dsfa-1.0.1/dsfa/R/comperr.R |only dsfa-1.0.1/dsfa/R/comperr_mv.R |only dsfa-1.0.1/dsfa/R/comperr_mv_mgcv.R |only dsfa-1.0.1/dsfa/R/cop.R |only dsfa-1.0.1/dsfa/R/cop_mgcv.R |only dsfa-1.0.1/dsfa/R/dsfa.R |only dsfa-1.0.1/dsfa/R/erf.R |only dsfa-1.0.1/dsfa/R/normexp.R |only dsfa-1.0.1/dsfa/R/normexp_mgcv.R |only dsfa-1.0.1/dsfa/R/normhnorm.R |only dsfa-1.0.1/dsfa/R/normhnorm_mgcv.R |only dsfa-1.0.1/dsfa/R/reparametrize.R |only dsfa-1.0.1/dsfa/R/rsp.R |only dsfa-1.0.1/dsfa/R/utility_functions.R |only dsfa-1.0.1/dsfa/R/zeta.R |only dsfa-1.0.1/dsfa/README.md |only dsfa-1.0.1/dsfa/man/OwenT.Rd |only dsfa-1.0.1/dsfa/man/check_arguments.Rd |only dsfa-1.0.1/dsfa/man/comperr_mv.Rd |only dsfa-1.0.1/dsfa/man/dcomperr.Rd |only dsfa-1.0.1/dsfa/man/dcomperr_mv.Rd |only dsfa-1.0.1/dsfa/man/erf.Rd |only dsfa-1.0.1/dsfa/man/normexp.Rd |only dsfa-1.0.1/dsfa/man/normhnorm.Rd |only dsfa-1.0.1/dsfa/man/pos_eigen.Rd |only dsfa-1.0.1/dsfa/man/reparametrize.Rd |only dsfa-1.0.1/dsfa/man/rsp.Rd |only dsfa-1.0.1/dsfa/man/zeta.Rd |only dsfa-2.0.0/dsfa/DESCRIPTION | 19 +++-- dsfa-2.0.0/dsfa/MD5 | 112 ++++++++++++++++++------------- dsfa-2.0.0/dsfa/NAMESPACE | 55 +++++++-------- dsfa-2.0.0/dsfa/NEWS.md | 16 +++- dsfa-2.0.0/dsfa/R/RcppExports.R |only dsfa-2.0.0/dsfa/R/cdf2quantile.R |only dsfa-2.0.0/dsfa/R/dcomper.R |only dsfa-2.0.0/dsfa/R/dcomper_mv.R |only dsfa-2.0.0/dsfa/R/dcop.R |only dsfa-2.0.0/dsfa/R/delta_bounds.R |only dsfa-2.0.0/dsfa/R/dnormexp.R |only dsfa-2.0.0/dsfa/R/dnormhnorm.R |only dsfa-2.0.0/dsfa/R/dsfa-package.R |only dsfa-2.0.0/dsfa/R/efficiency.R | 115 ++++++++++++++++---------------- dsfa-2.0.0/dsfa/R/elasticity.R | 81 +++++++++------------- dsfa-2.0.0/dsfa/R/manuf.R |only dsfa-2.0.0/dsfa/R/mgcv_comper.R |only dsfa-2.0.0/dsfa/R/mgcv_comper_mv.R |only dsfa-2.0.0/dsfa/R/mgcv_cop.R |only dsfa-2.0.0/dsfa/R/mom2par.R |only dsfa-2.0.0/dsfa/R/par2mom.R |only dsfa-2.0.0/dsfa/build/partial.rdb |binary dsfa-2.0.0/dsfa/data |only dsfa-2.0.0/dsfa/inst/REFERENCES.bib | 8 ++ dsfa-2.0.0/dsfa/man/cdf2quantile.Rd |only dsfa-2.0.0/dsfa/man/chainrule.Rd | 56 ++++++++------- dsfa-2.0.0/dsfa/man/comper.Rd |only dsfa-2.0.0/dsfa/man/comper_mv.Rd |only dsfa-2.0.0/dsfa/man/cop.Rd | 89 ++++++++++++++++-------- dsfa-2.0.0/dsfa/man/dcomper.Rd |only dsfa-2.0.0/dsfa/man/dcomper_mv.Rd |only dsfa-2.0.0/dsfa/man/dcop.Rd | 60 +++++++++------- dsfa-2.0.0/dsfa/man/delta_bounds.Rd |only dsfa-2.0.0/dsfa/man/derivs_transform.Rd |only dsfa-2.0.0/dsfa/man/differencerule.Rd |only dsfa-2.0.0/dsfa/man/dnormexp.Rd | 86 +++++++++++------------ dsfa-2.0.0/dsfa/man/dnormhnorm.Rd | 73 +++++++++----------- dsfa-2.0.0/dsfa/man/dsfa.Rd | 115 +++++++++++++++++++++++--------- dsfa-2.0.0/dsfa/man/efficiency.Rd | 14 +-- dsfa-2.0.0/dsfa/man/elasticity.Rd | 8 -- dsfa-2.0.0/dsfa/man/ind2joint.Rd |only dsfa-2.0.0/dsfa/man/list2derivs.Rd |only dsfa-2.0.0/dsfa/man/manuf.Rd |only dsfa-2.0.0/dsfa/man/mom2par.Rd |only dsfa-2.0.0/dsfa/man/par2mom.Rd |only dsfa-2.0.0/dsfa/man/productrule.Rd |only dsfa-2.0.0/dsfa/man/quotientrule.Rd |only dsfa-2.0.0/dsfa/man/sumrule.Rd |only dsfa-2.0.0/dsfa/man/transform.Rd |only dsfa-2.0.0/dsfa/man/trind.Rd |only dsfa-2.0.0/dsfa/man/trind_generator.Rd |only dsfa-2.0.0/dsfa/src |only 83 files changed, 509 insertions(+), 398 deletions(-)
Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the
'bbotk' package. 'miesmuschel' offers both ready-to-use optimization
algorithms, as well as their fundamental building blocks that can be used to
manually construct specialized optimization loops. The Mixed Integer Evolution
Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be
implemented, as well as the multi-objective optimization algorithms NSGA-II
by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre],
Lennart Schneider [ctb] ,
Susanne Dandl [ctb] ,
Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between miesmuschel versions 0.0.2 dated 2022-11-16 and 0.0.3 dated 2023-02-03
DESCRIPTION | 12 MD5 | 33 + NAMESPACE | 3 NEWS.md | 6 R/OptimizerMies.R | 2 R/TerminatorGenerationPerfReached.R |only R/TerminatorGenerationStagnation.R |only R/bibentries.R | 8 R/mies_methods.R | 306 +++++++++++++++++- R/utils_mo.R | 32 + R/zzz.R | 2 inst/tinytest/test_TerminatorGenerationPerfReached.R |only inst/tinytest/test_TerminatorGenerationStagnation.R |only inst/tinytest/test_mies_aggregate_single_generation.R |only inst/tinytest/test_mies_generation_apply.R |only man/OptimizerMies.Rd | 2 man/domhv.Rd |only man/mies_aggregate_generations.Rd | 8 man/mies_aggregate_single_generation.Rd |only man/mies_generation_apply.Rd |only man/mies_get_generation_results.Rd | 6 man/mlr_terminators_genperfreached.Rd |only man/mlr_terminators_genstag.Rd |only 23 files changed, 391 insertions(+), 29 deletions(-)
Title: Simulates Dice Rolls and Coin Flips
Description: Utils for basic statistical experiments, that can be used for teaching
introductory statistics. Each experiment generates a tibble.
Dice rolls and coin flips are simulated using sample().
The properties of the dice can be changed, like the number of sides.
A coin flip is simulated using a two sided dice.
Experiments can be combined with the pipe-operator.
Author: Roland Krasser [aut, cre],
Giovanni Marco Dall'Olio [aut]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between tidydice versions 0.1.1 dated 2021-04-19 and 1.0.0 dated 2023-02-03
tidydice-0.1.1/tidydice/R/plot_dice.R |only tidydice-0.1.1/tidydice/R/tidydice.R |only tidydice-1.0.0/tidydice/DESCRIPTION | 21 tidydice-1.0.0/tidydice/MD5 | 52 tidydice-1.0.0/tidydice/NAMESPACE | 8 tidydice-1.0.0/tidydice/NEWS.md | 11 tidydice-1.0.0/tidydice/R/binom.R | 16 tidydice-1.0.0/tidydice/R/coin-plot.R |only tidydice-1.0.0/tidydice/R/coin.R |only tidydice-1.0.0/tidydice/R/dice-formula.R |only tidydice-1.0.0/tidydice/R/dice-plot.R |only tidydice-1.0.0/tidydice/R/dice.R |only tidydice-1.0.0/tidydice/README.md | 123 + tidydice-1.0.0/tidydice/build/vignette.rds |binary tidydice-1.0.0/tidydice/inst/doc/tidydice.R | 43 tidydice-1.0.0/tidydice/inst/doc/tidydice.Rmd | 68 tidydice-1.0.0/tidydice/inst/doc/tidydice.html | 699 +++++++--- tidydice-1.0.0/tidydice/man/circle_points.Rd | 2 tidydice-1.0.0/tidydice/man/figures/tidydice-binom-dice-60.png |only tidydice-1.0.0/tidydice/man/figures/tidydice-roll-dice-60.png |only tidydice-1.0.0/tidydice/man/flip_coin.Rd | 2 tidydice-1.0.0/tidydice/man/force_coin.Rd | 2 tidydice-1.0.0/tidydice/man/force_dice.Rd | 2 tidydice-1.0.0/tidydice/man/parse_dice_formula.Rd |only tidydice-1.0.0/tidydice/man/parse_dice_formula_part.Rd |only tidydice-1.0.0/tidydice/man/plot_binom.Rd | 4 tidydice-1.0.0/tidydice/man/plot_coin.Rd |only tidydice-1.0.0/tidydice/man/plot_dice.Rd | 4 tidydice-1.0.0/tidydice/man/plot_single_coin.Rd |only tidydice-1.0.0/tidydice/man/plot_single_dice.Rd | 4 tidydice-1.0.0/tidydice/man/roll_dice.Rd | 2 tidydice-1.0.0/tidydice/man/roll_dice_formula.Rd |only tidydice-1.0.0/tidydice/man/top_n_dice.Rd |only tidydice-1.0.0/tidydice/tests/testthat/test_dice_formula.R |only tidydice-1.0.0/tidydice/vignettes/tidydice.Rmd | 68 35 files changed, 876 insertions(+), 255 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.2.0 dated 2022-10-13 and 3.3.0 dated 2023-02-03
DESCRIPTION | 6 ++-- MD5 | 47 ++++++++++++++++----------------- NAMESPACE | 1 R/opal.table.R | 51 ++++++++++++++++++++++++++++++++++++ inst/doc/datashield-admin.html | 4 +- inst/doc/opal-files.html | 4 +- inst/doc/opal-projects.html | 4 +- inst/doc/opal-rsession.html | 4 +- man/opal.resource_view_create.Rd | 3 +- man/opal.resource_view_reconnect.Rd | 3 +- man/opal.table_create.Rd | 3 +- man/opal.table_delete.Rd | 3 +- man/opal.table_dictionary_get.Rd | 3 +- man/opal.table_dictionary_update.Rd | 3 +- man/opal.table_exists.Rd | 3 +- man/opal.table_export.Rd | 3 +- man/opal.table_get.Rd | 3 +- man/opal.table_import.Rd | 3 +- man/opal.table_perm.Rd | 3 +- man/opal.table_perm_add.Rd | 3 +- man/opal.table_perm_delete.Rd | 3 +- man/opal.table_save.Rd | 3 +- man/opal.table_truncate.Rd | 3 +- man/opal.table_view_create.Rd | 3 +- man/opal.table_view_update.Rd |only 25 files changed, 119 insertions(+), 50 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 1.9.19 dated 2022-11-06 and 2.0.1 dated 2023-02-03
DESCRIPTION | 15 ++-- MD5 | 22 +++--- NAMESPACE | 6 - NEWS.md | 14 +++ R/HFDutils.R | 11 +-- R/HMDutils.R | 174 +++++++++++++++++++++++++++++++++++++------------ R/readHFD.R | 2 R/readHMD.R | 123 ++++++++++++++++++++++------------ inst/CITATION | 7 + man/getHFDitemavail.Rd | 2 man/getHMDitemavail.Rd | 10 -- man/readHMDweb.Rd | 8 -- 12 files changed, 263 insertions(+), 131 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.3-1 dated 2022-11-19 and 1.4-0 dated 2023-02-03
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NAMESPACE | 8 +++-- R/all_style.R |only R/line_length_style.R | 2 - R/nomagic_style.R | 77 ++++++++++++++++++++++++++++++++++++-------------- inst/NEWS.Rd | 19 ++++++++++++ man/all_style.Rd |only man/nomagic_style.Rd | 2 + tests/style-tests.R | 54 +++++++++++++++++++++++++++++++++-- 10 files changed, 147 insertions(+), 39 deletions(-)
Title: Automatically Position Non-Overlapping Text Labels with
'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid
overlapping text labels. Labels repel away from each other and away from the
data points.
Author: Kamil Slowikowski [aut, cre] ,
Alicia Schep [ctb] ,
Sean Hughes [ctb] ,
Trung Kien Dang [ctb] ,
Saulius Lukauskas [ctb],
Jean-Olivier Irisson [ctb] ,
Zhian N Kamvar [ctb] ,
Thompson Ryan [ctb] ,
Dervieux Christophe [ctb] ,
Yutani Hiroaki [ctb],
Pierr [...truncated...]
Maintainer: Kamil Slowikowski <kslowikowski@gmail.com>
Diff between ggrepel versions 0.9.2 dated 2022-11-06 and 0.9.3 dated 2023-02-03
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 12 ++++++++++++ R/geom-label-repel.R | 8 ++++---- R/geom-text-repel.R | 10 +++++----- R/utilities.R | 8 ++++++++ inst/doc/ggrepel.html | 6 +++--- tests/testthat/test-just-with-angle.R | 19 +++++++++++-------- 8 files changed, 56 insertions(+), 32 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.3.4 dated 2023-01-06 and 0.3.5 dated 2023-02-03
GE-0.3.4/GE/R/gemIntertemporalStochastic_Bank_3Periods.R |only GE-0.3.4/GE/R/gemIntertemporal_Stochastic_2_2.R |only GE-0.3.4/GE/man/gemIntertemporalStochastic_Bank_3Periods.Rd |only GE-0.3.4/GE/man/gemIntertemporal_Stochastic_2_2.Rd |only GE-0.3.5/GE/DESCRIPTION | 8 GE-0.3.5/GE/MD5 | 48 +++-- GE-0.3.5/GE/NAMESPACE | 6 GE-0.3.5/GE/R/demCreditPolicy.R | 81 +++++++++- GE-0.3.5/GE/R/gemDualLinearProgramming.R | 40 +--- GE-0.3.5/GE/R/gemInputOutputTable_8_8.R | 2 GE-0.3.5/GE/R/gemIntertemporalStochastic_Bank_ThreePeriods.R |only GE-0.3.5/GE/R/gemIntertemporalStochastic_ThreePeriods_2_2.R |only GE-0.3.5/GE/R/gemIntertemporalStochastic_TwoPeriods.R |only GE-0.3.5/GE/R/gemIntertemporal_2_2.R | 3 GE-0.3.5/GE/R/gemMoney_3_2.R | 2 GE-0.3.5/GE/R/gemResearchDevelopmentIntensity.R |only GE-0.3.5/GE/R/gem_3_4.R | 30 +++ GE-0.3.5/GE/R/output.R | 9 + GE-0.3.5/GE/R/policyMarketClearingPrice.R | 7 GE-0.3.5/GE/man/demCreditPolicy.Rd | 81 +++++++++- GE-0.3.5/GE/man/gemDualLinearProgramming.Rd | 40 +--- GE-0.3.5/GE/man/gemInputOutputTable_8_8.Rd | 2 GE-0.3.5/GE/man/gemIntertemporalStochastic_Bank_ThreePeriods.Rd |only GE-0.3.5/GE/man/gemIntertemporalStochastic_ThreePeriods_2_2.Rd |only GE-0.3.5/GE/man/gemIntertemporalStochastic_TwoPeriods.Rd |only GE-0.3.5/GE/man/gemIntertemporal_2_2.Rd | 3 GE-0.3.5/GE/man/gemMoney_3_2.Rd | 2 GE-0.3.5/GE/man/gemResearchDevelopmentIntensity.Rd |only GE-0.3.5/GE/man/gem_3_4.Rd | 30 +++ GE-0.3.5/GE/man/output.Rd | 9 + GE-0.3.5/GE/man/policyMarketClearingPrice.Rd | 5 31 files changed, 299 insertions(+), 109 deletions(-)