Title: R-Language Based Calculus Operations for Teaching
Description: Software to support the introductory *MOSAIC Calculus*
textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>),
one of many data- and modeling-oriented educational resources developed by
Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and
numerical differentiation and integration, as well as support for
applied linear algebra (for data science), and differential equations/dynamics.
Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc.
The software is suitable for general use, but intended mainly for teaching calculus.
Author: Daniel T. Kaplan <kaplan@macalester.edu>, Randall Pruim <rpruim@calvin.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Daniel Kaplan <kaplan@macalester.edu>
Diff between mosaicCalc versions 0.5.1 dated 2020-05-07 and 0.6.0 dated 2022-09-14
mosaicCalc-0.5.1/mosaicCalc/R/connector.R |only mosaicCalc-0.5.1/mosaicCalc/R/findZeros.R |only mosaicCalc-0.5.1/mosaicCalc/R/fitModel.R |only mosaicCalc-0.5.1/mosaicCalc/R/simplify.R |only mosaicCalc-0.5.1/mosaicCalc/R/spliner.R |only mosaicCalc-0.5.1/mosaicCalc/R/symbolicInt.R |only mosaicCalc-0.5.1/mosaicCalc/man/connector.Rd |only mosaicCalc-0.5.1/mosaicCalc/man/findZeros.Rd |only mosaicCalc-0.5.1/mosaicCalc/man/spliner.Rd |only mosaicCalc-0.5.1/mosaicCalc/tests/testthat/test-symbolicInt.R |only mosaicCalc-0.6.0/mosaicCalc/DESCRIPTION | 35 mosaicCalc-0.6.0/mosaicCalc/MD5 | 237 +++- mosaicCalc-0.6.0/mosaicCalc/NAMESPACE | 81 + mosaicCalc-0.6.0/mosaicCalc/NEWS.md | 68 + mosaicCalc-0.6.0/mosaicCalc/R/Aquaman.R |only mosaicCalc-0.6.0/mosaicCalc/R/Basis_sets.R |only mosaicCalc-0.6.0/mosaicCalc/R/Body_fat.R |only mosaicCalc-0.6.0/mosaicCalc/R/Boyle.R |only mosaicCalc-0.6.0/mosaicCalc/R/CPUs.R |only mosaicCalc-0.6.0/mosaicCalc/R/Calculus.R | 248 +--- mosaicCalc-0.6.0/mosaicCalc/R/Chirps.R |only mosaicCalc-0.6.0/mosaicCalc/R/Covid_US.R |only mosaicCalc-0.6.0/mosaicCalc/R/EbolaAll.R |only mosaicCalc-0.6.0/mosaicCalc/R/Effective_oxygen.R |only mosaicCalc-0.6.0/mosaicCalc/R/Engines.R |only mosaicCalc-0.6.0/mosaicCalc/R/Fly_ball.R |only mosaicCalc-0.6.0/mosaicCalc/R/Globals.R |only mosaicCalc-0.6.0/mosaicCalc/R/HDD_Minneapolis.R |only mosaicCalc-0.6.0/mosaicCalc/R/Home_utilities.R |only mosaicCalc-0.6.0/mosaicCalc/R/Integrate.R |only mosaicCalc-0.6.0/mosaicCalc/R/Kepler.R |only mosaicCalc-0.6.0/mosaicCalc/R/M2014F.R |only mosaicCalc-0.6.0/mosaicCalc/R/Picket.R |only mosaicCalc-0.6.0/mosaicCalc/R/Planet_solar.R |only mosaicCalc-0.6.0/mosaicCalc/R/Planets.R |only mosaicCalc-0.6.0/mosaicCalc/R/Robot_stations.R |only mosaicCalc-0.6.0/mosaicCalc/R/Runners.R |only mosaicCalc-0.6.0/mosaicCalc/R/SSA_2007.R |only mosaicCalc-0.6.0/mosaicCalc/R/Shapes.R |only mosaicCalc-0.6.0/mosaicCalc/R/Tides.R |only mosaicCalc-0.6.0/mosaicCalc/R/UK_GDP.R |only mosaicCalc-0.6.0/mosaicCalc/R/US_income.R |only mosaicCalc-0.6.0/mosaicCalc/R/Vowels.R |only mosaicCalc-0.6.0/mosaicCalc/R/Zeros.R |only mosaicCalc-0.6.0/mosaicCalc/R/argM.R |only mosaicCalc-0.6.0/mosaicCalc/R/box_set.R |only mosaicCalc-0.6.0/mosaicCalc/R/constraints.R |only mosaicCalc-0.6.0/mosaicCalc/R/contour_plot.R |only mosaicCalc-0.6.0/mosaicCalc/R/create_num_antiD.R |only mosaicCalc-0.6.0/mosaicCalc/R/df2matrix.R |only mosaicCalc-0.6.0/mosaicCalc/R/domain.R |only mosaicCalc-0.6.0/mosaicCalc/R/dynamics.R |only mosaicCalc-0.6.0/mosaicCalc/R/inline.R |only mosaicCalc-0.6.0/mosaicCalc/R/inscribed_circle.R |only mosaicCalc-0.6.0/mosaicCalc/R/integrateODE.R | 60 - mosaicCalc-0.6.0/mosaicCalc/R/interactive_plot.R |only mosaicCalc-0.6.0/mosaicCalc/R/is_in_domain.R |only mosaicCalc-0.6.0/mosaicCalc/R/iterate.R |only mosaicCalc-0.6.0/mosaicCalc/R/makeODE.R |only mosaicCalc-0.6.0/mosaicCalc/R/musical-notes.R |only mosaicCalc-0.6.0/mosaicCalc/R/numD.R | 230 +--- mosaicCalc-0.6.0/mosaicCalc/R/potential_energy.R |only mosaicCalc-0.6.0/mosaicCalc/R/projection.R |only mosaicCalc-0.6.0/mosaicCalc/R/qspliner.R |only mosaicCalc-0.6.0/mosaicCalc/R/re-export.R |only mosaicCalc-0.6.0/mosaicCalc/R/simpleYacasIntegrate.R |only mosaicCalc-0.6.0/mosaicCalc/R/slice_plot.R |only mosaicCalc-0.6.0/mosaicCalc/R/symbolicD.R | 186 ++- mosaicCalc-0.6.0/mosaicCalc/R/traj_plot.R |only mosaicCalc-0.6.0/mosaicCalc/R/traj_plot_3D.R |only mosaicCalc-0.6.0/mosaicCalc/R/unbound.R |only mosaicCalc-0.6.0/mosaicCalc/R/utilities.R |only mosaicCalc-0.6.0/mosaicCalc/R/vectorfield_plot.R |only mosaicCalc-0.6.0/mosaicCalc/README.md | 2 mosaicCalc-0.6.0/mosaicCalc/build/vignette.rds |binary mosaicCalc-0.6.0/mosaicCalc/data |only mosaicCalc-0.6.0/mosaicCalc/inst/Test_shinyapps_env |only mosaicCalc-0.6.0/mosaicCalc/inst/data_raw |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/Calculus_with_R.R | 43 mosaicCalc-0.6.0/mosaicCalc/inst/doc/Calculus_with_R.Rmd | 221 +++- mosaicCalc-0.6.0/mosaicCalc/inst/doc/Calculus_with_R.html | 546 ++++++++-- mosaicCalc-0.6.0/mosaicCalc/inst/doc/Instructors.R |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/Instructors.Rmd |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/Instructors.html |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/quick-reference.R |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/quick-reference.Rmd |only mosaicCalc-0.6.0/mosaicCalc/inst/doc/quick-reference.html |only mosaicCalc-0.6.0/mosaicCalc/man/Aquaman.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Body_fat.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Boyle.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/CPUs.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Calculus.Rd | 53 mosaicCalc-0.6.0/mosaicCalc/man/Cello.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Chirps.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Covid_US.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/EbolaAll.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Effective_oxygen.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Engines.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Fly_ball.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/HDD_Minneapolis.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Home_utilities.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Integrate.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Iterate.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Kepler.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/M2014F.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/PE_fun1.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Picket.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Planet_solar.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Planets.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Robot_stations.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Runners.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/SSA_2007.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Shapes.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Tides.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/UK_GDP.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/US_income.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Vowel_ee.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/Zeros.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/argM.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/basis_sets.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/bounds.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/box_set.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/contour_plot.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/create_num_antiD.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/df2matrix.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/dynamics.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/first_three_args.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/gradient_plot.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/inequality_constraint.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/infer_RHS.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/inline.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/inscribed_circle.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/integrateODE.Rd | 25 mosaicCalc-0.6.0/mosaicCalc/man/is_in_domain.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/makeODE.Rd |only mosaicCalc-0.6.0/mosaicCalc/man/numD.Rd | 21 mosaicCalc-0.6.0/mosaicCalc/man/qspliner.Rd |only 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mosaicCalc-0.6.0/mosaicCalc/tests/testthat/test-peek_inside.R |only mosaicCalc-0.6.0/mosaicCalc/tests/testthat/test-symbolic-diff.R |only mosaicCalc-0.6.0/mosaicCalc/tests/testthat/test-symbolic-int.R |only mosaicCalc-0.6.0/mosaicCalc/tests/testthat/test-zeros.R |only mosaicCalc-0.6.0/mosaicCalc/tests/testthat/test_arguments.R |only mosaicCalc-0.6.0/mosaicCalc/vignettes/Calculus_with_R.Rmd | 221 +++- mosaicCalc-0.6.0/mosaicCalc/vignettes/Instructors.Rmd |only mosaicCalc-0.6.0/mosaicCalc/vignettes/quick-reference.Rmd |only mosaicCalc-0.6.0/mosaicCalc/vignettes/www |only 163 files changed, 1621 insertions(+), 716 deletions(-)
Title: Collection of Functions for Matrix Calculations
Description: A collection of functions to support matrix calculations
for probability, econometric and numerical analysis. There are
additional functions that are comparable to APL functions which
are useful for actuarial models such as pension mathematics.
This package is used for teaching and research purposes at the
Department of Finance and Risk Engineering, New York
University, Polytechnic Institute, Brooklyn, NY 11201.
Horn, R.A. (1990) Matrix Analysis. ISBN 978-0521386326.
Lancaster, P. (1969) Theory of Matrices. ISBN 978-0124355507.
Lay, D.C. (1995) Linear Algebra: And Its Applications. ISBN 978-0201845563.
Author: Frederick Novomestky <fnovomes@poly.edu>
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between matrixcalc versions 1.0-5 dated 2021-07-28 and 1.0-6 dated 2022-09-14
DESCRIPTION | 10 +- MD5 | 122 ++++++++++++++++----------------- man/D.matrix.Rd | 96 +++++++++++++------------- man/E.matrices.Rd | 98 +++++++++++++------------- man/H.matrices.Rd | 106 ++++++++++++++-------------- man/K.matrix.Rd | 96 +++++++++++++------------- man/L.matrix.Rd | 96 +++++++++++++------------- man/N.matrix.Rd | 82 +++++++++++----------- man/T.matrices.Rd | 98 +++++++++++++------------- man/commutation.matrix.Rd | 100 +++++++++++++-------------- man/creation.matrix.Rd | 92 ++++++++++++------------ man/direct.prod.Rd | 76 ++++++++++---------- man/direct.sum.Rd | 70 +++++++++--------- man/duplication.matrix.Rd | 100 +++++++++++++-------------- man/elimination.matrix.Rd | 98 +++++++++++++------------- man/entrywise.norm.Rd | 92 ++++++++++++------------ man/fibonacci.matrix.Rd | 78 ++++++++++----------- man/frobenius.matrix.Rd | 84 +++++++++++----------- man/frobenius.norm.Rd | 74 ++++++++++---------- man/frobenius.prod.Rd | 86 +++++++++++------------ man/hadamard.prod.Rd | 96 +++++++++++++------------- man/hankel.matrix.Rd | 76 ++++++++++---------- man/hilbert.matrix.Rd | 70 +++++++++--------- man/hilbert.schmidt.norm.Rd | 74 ++++++++++---------- man/inf.norm.Rd | 78 ++++++++++----------- man/is.diagonal.matrix.Rd | 70 +++++++++--------- man/is.idempotent.matrix.Rd | 116 +++++++++++++++---------------- man/is.indefinite.Rd | 144 +++++++++++++++++++-------------------- man/is.negative.definite.Rd | 140 ++++++++++++++++++------------------- man/is.negative.semi.definite.Rd | 142 +++++++++++++++++++------------------- man/is.non.singular.matrix.Rd | 80 ++++++++++----------- man/is.positive.definite.Rd | 140 ++++++++++++++++++------------------- man/is.positive.semi.definite.Rd | 140 ++++++++++++++++++------------------- man/is.singular.matrix.Rd | 80 ++++++++++----------- man/is.skew.symmetric.matrix.Rd | 80 ++++++++++----------- man/is.square.matrix.Rd | 54 +++++++------- man/is.symmetric.matrix.Rd | 68 +++++++++--------- man/lower.triangle.Rd | 56 +++++++-------- man/lu.decomposition.Rd | 104 ++++++++++++++-------------- man/matrix.inverse.Rd | 58 +++++++-------- man/matrix.power.Rd | 74 ++++++++++---------- man/matrix.rank.Rd | 76 ++++++++++---------- man/matrix.trace.Rd | 58 +++++++-------- man/maximum.norm.Rd | 76 ++++++++++---------- man/one.norm.Rd | 76 ++++++++++---------- man/pascal.matrix.Rd | 86 +++++++++++------------ man/s.Rd | 70 +++++++++--------- man/set.submatrix.Rd | 68 +++++++++--------- man/shift.down.Rd | 58 +++++++-------- man/shift.left.Rd | 58 +++++++-------- man/shift.right.Rd | 58 +++++++-------- man/shift.up.Rd | 58 +++++++-------- man/spectral.norm.Rd | 96 +++++++++++++------------- man/stirling.matrix.Rd | 100 +++++++++++++-------------- man/svd.inverse.Rd | 72 +++++++++---------- man/symmetric.pascal.matrix.Rd | 80 ++++++++++----------- man/toeplitz.matrix.Rd | 68 +++++++++--------- man/u.vectors.Rd | 80 ++++++++++----------- man/upper.triangle.Rd | 56 +++++++-------- man/vandermonde.matrix.Rd | 81 +++++++++++---------- man/vec.Rd | 54 +++++++------- man/vech.Rd | 62 ++++++++-------- 62 files changed, 2594 insertions(+), 2591 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and only
adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019)
<https://almob.biomedcentral.com/articles/10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre],
Guillem Rigaill [aut],
Nathalie Vialaneix [aut],
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.6.5 dated 2022-08-18 and 0.6.6 dated 2022-09-14
DESCRIPTION | 10 MD5 | 16 NEWS.md | 4 build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/hicClust.html | 379 +++---------------- inst/doc/notesCHAC.html | 493 +++----------------------- inst/doc/snpClust.html | 394 ++++---------------- tests/testthat/test_dense_sparse_comparison.R | 33 + 9 files changed, 267 insertions(+), 1067 deletions(-)
Title: Functions for Web Development
Description: Organizational framework for web development in R including functions to
serve static and dynamic content via HTTP methods, includes the html5 package to
create HTML pages, and offers other utility functions for common tasks related
to web development.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between webdeveloper versions 1.0.3 dated 2022-08-08 and 1.0.4 dated 2022-09-14
DESCRIPTION | 7 +- MD5 | 6 +- R/webdeveloper.R | 159 +++++++++++++++++++++++++++++++++++++------------------ man/serveHTTP.Rd | 4 + 4 files changed, 118 insertions(+), 58 deletions(-)
Title: Interface to the Numerai Machine Learning Tournament API
Description: Routines to interact with the Numerai Machine Learning Tournament
API <https://numer.ai>. The functionality includes the ability to automatically download the
current tournament data, submit predictions, and to get information for your
user.
Author: Omni Analytics Group [aut],
Eric Hare [cre],
Yogesh Bansal [ctb]
Maintainer: Eric Hare <eric@omnianalytics.org>
Diff between Rnumerai versions 3.0.0 dated 2022-08-25 and 3.0.1 dated 2022-09-14
DESCRIPTION | 6 +- MD5 | 13 +++- NAMESPACE | 3 + R/baseapi.R | 74 ++++++++++++++++++++++++++++ R/queries.R | 92 +++++++++++++++++++++++++++++++++++ README.md | 30 ++++++++++- man/daily_model_performances.Rd |only man/daily_submission_performances.Rd |only man/run_query.Rd |only 9 files changed, 208 insertions(+), 10 deletions(-)
Title: Data Analysis of Pesticide Application Technology
Description: In total it has 7 functions, three for calculating machine calibration, which determine application rate (L/ha), nozzle flow (L/min) and amount of product (L or kg) to be added. to the tank with each sprayer filling. Two functions for graphs of the flow distribution of the nozzles (L/min) in the application bar and, of the temporal variability of the meteorological conditions (air temperature, relative humidity of the air and wind speed). Two functions to determine the spray deposit (uL/cm2), through the methodology called spectrophotometry, with the aid of bright blue (Palladini, L.A., Raetano, C.G., Velini, E.D. (2005), <doi:10.1590/S0103-90162005000500005>) or metallic markers (Chaim, A., Castro, V.L.S.S., Correles, F.M., Galvão, J.A.H., Cabral, O.M.R., Nicolella, G. (1999), <doi:10.1590/S0100-204X1999000500003>). The package supports the analysis and representation of information, using a single free software that meets the most diverse areas of activity in application [...truncated...]
Author: Rodrigo Yudi Palhaci Marubayashi [aut, cre]
,
Gabriel Danilo Shimizu [aut, ctb]
,
Otavio Jorge Grigoli Abi Saab [aut, ctb]
Maintainer: Rodrigo Yudi Palhaci Marubayashi <marubayashi@uel.br>
Diff between AgroTech versions 1.0.1 dated 2022-01-25 and 1.0.2 dated 2022-09-14
AgroTech-1.0.1/AgroTech/man/figures |only AgroTech-1.0.2/AgroTech/DESCRIPTION | 10 +++++----- AgroTech-1.0.2/AgroTech/MD5 | 6 +++--- AgroTech-1.0.2/AgroTech/build |only AgroTech-1.0.2/AgroTech/man/AgroTech-package.Rd | 4 +--- 5 files changed, 9 insertions(+), 11 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses. The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.12 dated 2022-07-11 and 0.2.13 dated 2022-09-14
DESCRIPTION | 6 MD5 | 492 NEWS.md | 13 R/JAGS-formula.R | 17 R/JAGS-marglik.R | 34 R/model-averaging-plots.R | 9 R/model-averaging.R | 2 R/priors-density.R | 9 R/summary-tables.R | 138 build/partial.rdb |binary inst/doc/ComparisonR.html | 21 inst/doc/SpikeAndSlab.html | 17 man/BayesTools.Rd | 54 man/BayesTools_model_tables.Rd | 9 man/JAGS_diagnostics.Rd | 234 man/JAGS_evaluate_formula.Rd | 66 man/add_column.Rd | 70 man/interpret.Rd | 74 man/parameter_names.Rd | 76 man/transform_orthonormal_samples.Rd | 48 tests/testthat.R | 10 tests/testthat/_snaps/JAGS-fit/jags-fit-posterior.svg | 492 tests/testthat/_snaps/JAGS-fit/jags-model-prior-11.svg | 124 tests/testthat/_snaps/JAGS-fit/jags-model-prior-factor-1.svg |20298 ++++----- tests/testthat/_snaps/JAGS-fit/jags-model-prior-factor-2.svg | 162 tests/testthat/_snaps/JAGS-fit/jags-model-prior-factor-3.svg |20316 ++++----- tests/testthat/_snaps/JAGS-fit/jags-model-prior-vector-1.svg |20304 ++++----- 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182 tests/testthat/test-summary-tables.R | 16 247 files changed, 71589 insertions(+), 71425 deletions(-)
Title: Distributional Regression for Time to Event Data
Description: Semiparametric distributional regression methods (expectile, quantile and mode regression) for time-to-event variables with right-censoring; uses inverse probability of censoring weights or accelerated failure time models with auxiliary likelihoods. Expectile regression using inverse probability of censoring weights has been introduced in Seipp et al. (2021) "Weighted Expectile Regression for Right-Censored Data" <doi:10.1002/sim.9137>, mode regression for time-to-event variables has been introduced in Seipp et al. (2022) "Flexible Semiparametric Mode Regression for Time-to-Event Data" <doi:10.1177/09622802221122406>.
Author: Alexander Seipp [aut, cre],
Fabian Otto-Sobotka [aut]
Maintainer: Alexander Seipp <alexander.seipp@uni-oldenburg.de>
Diff between dirttee versions 1.0 dated 2022-08-18 and 1.0.1 dated 2022-09-14
DESCRIPTION | 14 +++++++------- MD5 | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-)
Title: Economics and Pricing Tools
Description: Functions to aid in micro and macro economic analysis and handling of price and
currency data. Includes extraction of relevant inflation and exchange rate data from World Bank
API, data cleaning/parsing, and standardisation. Inflation adjustment
calculations as found in Principles of Macroeconomics by Gregory Mankiw et al (2014). Current
and historical end of day exchange rates for 171 currencies from the European Central Bank
Statistical Data Warehouse (2020) <https://sdw.ecb.europa.eu/curConverter.do>.
Author: Steve Condylios [aut, cre],
Bruno Mioto [ctb],
Bryan Shalloway [ctb]
Maintainer: Steve Condylios <steve.condylios@gmail.com>
Diff between priceR versions 0.1.64 dated 2022-09-01 and 0.1.66 dated 2022-09-14
DESCRIPTION | 20 ++-- MD5 | 13 +-- NAMESPACE | 4 R/adjust_for_inflation.R | 2 R/currencies.R | 190 ++++++++++++++++++++++++++++++++++++++++++--- man/convert_currencies.Rd |only man/currency_info.Rd | 17 ++-- man/from_to_dates_rates.Rd |only man/pminmax.Rd |only 9 files changed, 210 insertions(+), 36 deletions(-)
Title: Ethnicity Annotation from Whole-Exome and Targeted Sequencing
Data
Description: Reliable and rapid ethnicity annotation from whole exome and targeted sequencing data.
Author: Alessandro Romanel [aut, cre],
Davide Dalfovo [aut]
Maintainer: Alessandro Romanel <alessandro.romanel@unitn.it>
Diff between EthSEQ versions 2.1.4 dated 2021-02-18 and 3.0.0 dated 2022-09-14
EthSEQ-2.1.4/EthSEQ/inst/extdata/Annotations_Test.txt |only EthSEQ-2.1.4/EthSEQ/inst/extdata/Reference_SS2_10000SNPs.gds |only EthSEQ-2.1.4/EthSEQ/inst/extdata/Samples_SS2_10000SNPs.vcf |only EthSEQ-2.1.4/EthSEQ/inst/extdata/VCF_Test_1.vcf |only EthSEQ-2.1.4/EthSEQ/inst/extdata/VCF_Test_2.vcf |only EthSEQ-3.0.0/EthSEQ/DESCRIPTION | 22 EthSEQ-3.0.0/EthSEQ/MD5 | 61 EthSEQ-3.0.0/EthSEQ/NAMESPACE | 5 EthSEQ-3.0.0/EthSEQ/NEWS | 7 EthSEQ-3.0.0/EthSEQ/R/RcppExports.R |only EthSEQ-3.0.0/EthSEQ/R/aseq_Run.R | 23 EthSEQ-3.0.0/EthSEQ/R/combine_Models.R | 182 -- EthSEQ-3.0.0/EthSEQ/R/create_Target_Model.R | 124 - EthSEQ-3.0.0/EthSEQ/R/ethseq_Analysis.R | 114 - EthSEQ-3.0.0/EthSEQ/R/ethseq_RM.R | 228 +- EthSEQ-3.0.0/EthSEQ/R/ethseq_Utilities.R | 4 EthSEQ-3.0.0/EthSEQ/R/get_Ethnicity.R | 12 EthSEQ-3.0.0/EthSEQ/R/get_InfoAnnot.R |only EthSEQ-3.0.0/EthSEQ/R/get_Model.R | 26 EthSEQ-3.0.0/EthSEQ/R/plot_Report.R | 2 EthSEQ-3.0.0/EthSEQ/R/process_Population_Matrix.R | 45 EthSEQ-3.0.0/EthSEQ/R/space_Operations.R | 6 EthSEQ-3.0.0/EthSEQ/build/vignette.rds |binary EthSEQ-3.0.0/EthSEQ/inst/doc/EthSEQ.R | 138 - EthSEQ-3.0.0/EthSEQ/inst/doc/EthSEQ.Rmd | 166 - EthSEQ-3.0.0/EthSEQ/inst/doc/EthSEQ.html | 895 ++++++---- EthSEQ-3.0.0/EthSEQ/inst/extdata/Annotations_Test_v3.txt |only EthSEQ-3.0.0/EthSEQ/inst/extdata/RefSample1.vcf |only EthSEQ-3.0.0/EthSEQ/inst/extdata/RefSample2.vcf |only EthSEQ-3.0.0/EthSEQ/inst/extdata/Reference.Gencode.Exome.10000SNPs.gds |only EthSEQ-3.0.0/EthSEQ/inst/extdata/Samples.HGDP.10000SNPs.gds |only EthSEQ-3.0.0/EthSEQ/inst/extdata/Samples.HGDP.10000SNPs.vcf |only EthSEQ-3.0.0/EthSEQ/inst/extdata/exonic_kits_map.tsv |only EthSEQ-3.0.0/EthSEQ/inst/extdata/samplesPop_map.tsv |only EthSEQ-3.0.0/EthSEQ/man/ethseq.Analysis.Rd | 52 EthSEQ-3.0.0/EthSEQ/man/ethseq.RM.Rd | 20 EthSEQ-3.0.0/EthSEQ/man/getModelsList.Rd |only EthSEQ-3.0.0/EthSEQ/man/getSamplesInfo.Rd |only EthSEQ-3.0.0/EthSEQ/src |only EthSEQ-3.0.0/EthSEQ/vignettes/EthSEQ.Rmd | 166 - 40 files changed, 1228 insertions(+), 1070 deletions(-)
Title: Scalable Joint Species Distribution Modeling
Description: A scalable method to estimate joint Species Distribution Models (jSDMs) for big community datasets based on a Monte Carlo approximation of the joint likelihood. The numerical approximation is based on 'PyTorch' and 'reticulate', and can be run on CPUs and GPUs alike. The method is described in Pichler & Hartig (2021) <doi:10.1111/2041-210X.13687>. The package contains various extensions, including support for different response families, ability to account for spatial autocorrelation, and deep neural networks instead of the linear predictor in jSDMs.
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.2 dated 2022-06-23 and 1.0.3 dated 2022-09-14
DESCRIPTION | 7 MD5 | 19 NEWS.md | 11 R/sjSDM_configs.R | 2 R/sjSDM_cv.R | 5 build/sjSDM.pdf |binary inst/doc/Dependencies.html | 152 +++---- inst/doc/sjSDM.html | 191 +++++----- inst/python/tests/__pycache__/test_sjSDM.cpython-37-pytest-7.1.3.pyc |only man/RMSprop.Rd | 2 tests/testthat/Rplots.pdf |binary 11 files changed, 202 insertions(+), 187 deletions(-)
Title: Interactive Conditional Visualization for Supervised and
Unsupervised Models in Shiny
Description: Constructs a shiny app function with interactive displays for conditional visualization of models,
data and density functions. An extended version of package 'condvis'.
Catherine B. Hurley, Mark O'Connell,Katarina Domijan (2021) <doi:10.1080/10618600.2021.1983439>.
Author: Catherine Hurley [aut, cre],
Mark OConnell [aut],
Katarina Domijan [aut]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between condvis2 versions 0.1.1 dated 2020-09-25 and 0.1.2 dated 2022-09-14
condvis2-0.1.1/condvis2/man/arrangeC.Rd |only condvis2-0.1.1/condvis2/man/createCVServer.Rd |only condvis2-0.1.1/condvis2/man/createCVUI.Rd |only condvis2-0.1.1/condvis2/vignettes/vignettefigs |only condvis2-0.1.2/condvis2/DESCRIPTION | 18 condvis2-0.1.2/condvis2/MD5 | 116 ++-- condvis2-0.1.2/condvis2/NAMESPACE | 4 condvis2-0.1.2/condvis2/NEWS.md | 6 condvis2-0.1.2/condvis2/R/CVpredict.R | 71 ++ condvis2-0.1.2/condvis2/R/arrangeC.R | 10 condvis2-0.1.2/condvis2/R/colours.R | 121 ++-- condvis2-0.1.2/condvis2/R/conditionplots.R | 43 - condvis2-0.1.2/condvis2/R/createServer.R | 252 +++++---- condvis2-0.1.2/condvis2/R/createUI.R | 17 condvis2-0.1.2/condvis2/R/diagnostics.R | 7 condvis2-0.1.2/condvis2/R/fitpath.R | 44 - condvis2-0.1.2/condvis2/R/helper.R | 123 +--- condvis2-0.1.2/condvis2/R/sectionplot3dprobs.R | 30 - condvis2-0.1.2/condvis2/R/sectionplots.R | 291 ++++------- condvis2-0.1.2/condvis2/R/similarityweight.R | 113 ---- condvis2-0.1.2/condvis2/README.md | 17 condvis2-0.1.2/condvis2/build/vignette.rds |binary condvis2-0.1.2/condvis2/inst/doc/Keras.R | 2 condvis2-0.1.2/condvis2/inst/doc/Keras.Rmd | 5 condvis2-0.1.2/condvis2/inst/doc/Keras.html | 408 ++++++++-------- condvis2-0.1.2/condvis2/inst/doc/introduction.R | 15 condvis2-0.1.2/condvis2/inst/doc/introduction.Rmd | 37 + condvis2-0.1.2/condvis2/inst/doc/introduction.html | 289 +++++++---- condvis2-0.1.2/condvis2/inst/doc/mclust.R | 2 condvis2-0.1.2/condvis2/inst/doc/mclust.Rmd | 2 condvis2-0.1.2/condvis2/inst/doc/mclust.html | 268 ++++++---- condvis2-0.1.2/condvis2/inst/doc/mlr.R | 2 condvis2-0.1.2/condvis2/inst/doc/mlr.Rmd | 2 condvis2-0.1.2/condvis2/inst/doc/mlr.html | 151 +++-- condvis2-0.1.2/condvis2/inst/doc/parsnip.R | 2 condvis2-0.1.2/condvis2/inst/doc/parsnip.Rmd | 2 condvis2-0.1.2/condvis2/inst/doc/parsnip.html | 146 +++-- condvis2-0.1.2/condvis2/man/CVpredict.Rd | 118 +++- condvis2-0.1.2/condvis2/man/clusPath.Rd | 12 condvis2-0.1.2/condvis2/man/fitPath.Rd | 10 condvis2-0.1.2/condvis2/man/pathInterpolate.Rd | 8 condvis2-0.1.2/condvis2/man/tours.Rd | 8 condvis2-0.1.2/condvis2/tests/testthat/Rplots.pdf |only condvis2-0.1.2/condvis2/tests/testthat/test-CVpredict.R | 119 ++-- condvis2-0.1.2/condvis2/vignettes/Boston.png |only condvis2-0.1.2/condvis2/vignettes/Keras.Rmd | 5 condvis2-0.1.2/condvis2/vignettes/Pima.png |only condvis2-0.1.2/condvis2/vignettes/dens3Right2.png |only condvis2-0.1.2/condvis2/vignettes/introduction.Rmd | 37 + condvis2-0.1.2/condvis2/vignettes/iris.png |only condvis2-0.1.2/condvis2/vignettes/left1.png |only condvis2-0.1.2/condvis2/vignettes/mclust.Rmd | 2 condvis2-0.1.2/condvis2/vignettes/mclustda1.png |only condvis2-0.1.2/condvis2/vignettes/mclustda6.png |only condvis2-0.1.2/condvis2/vignettes/mlr.Rmd | 2 condvis2-0.1.2/condvis2/vignettes/ozone.png |only condvis2-0.1.2/condvis2/vignettes/ozone1.png |only condvis2-0.1.2/condvis2/vignettes/ozone3.png |only condvis2-0.1.2/condvis2/vignettes/ozone4.png |only condvis2-0.1.2/condvis2/vignettes/ozone5.png |only condvis2-0.1.2/condvis2/vignettes/ozone6.png |only condvis2-0.1.2/condvis2/vignettes/parsnip.Rmd | 2 62 files changed, 1601 insertions(+), 1338 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.9.1 dated 2022-05-05 and 2.10.0 dated 2022-09-14
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 4 R/lookfor.R | 6 R/var_label.R | 12 - build/vignette.rds |binary inst/doc/intro_labelled.html | 187 +++++++++++++++--------------- inst/doc/look_for.html | 266 ++++++++++++++++++++++--------------------- inst/doc/missing_values.html | 13 +- man/look_for.Rd | 2 man/to_labelled.Rd | 6 11 files changed, 277 insertions(+), 247 deletions(-)
Title: Mediterranean Forest Simulation
Description: Functions to simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre] ,
Shengli Huang [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Aitor Ameztegui [ctb] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Nicolas Martin-StPaul [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 2.7.3 dated 2022-05-10 and 2.8.0 dated 2022-09-14
DESCRIPTION | 8 MD5 | 94 +++---- R/RcppExports.R | 68 ++--- R/defaultControl.R | 20 - R/fireHazard.R | 41 ++- R/fordyn.R | 22 + R/hydraulics_supplyFunctionPlot.R | 21 - R/plot.spwb.R | 19 + R/plot_internals.R | 29 +- R/shinyplot.R | 8 R/summary.forest.R | 24 - R/summary.spwb.R | 4 data/SpParamsDefinition.rda |binary data/SpParamsMED.rda |binary data/SpParamsUS.rda |binary data/exampleforestMED.rda |binary data/examplemeteo.rda |binary data/exampleobs.rda |binary inst/include/medfate_RcppExports.h | 40 +-- man/defaultControl.Rd | 18 - man/examplemeteo.Rd | 4 man/fireHazard.Rd | 32 ++ man/fordyn.Rd | 2 man/growth.Rd | 28 -- man/hydraulics_supplyfunctions.Rd | 65 +--- man/modelInput.Rd | 8 man/plot.spwb.Rd | 5 man/spwb.Rd | 38 +- man/spwb_day.Rd | 11 man/spwb_ldrCalibration.Rd | 9 man/transp_modes.Rd | 7 man/transp_stomatalregulation.Rd | 19 - src/RcppExports.cpp | 285 +++++++-------------- src/carbon.cpp | 1 src/growth.cpp | 366 ++++++++++++++------------- src/hydraulics.cpp | 207 ++++++--------- src/hydraulics.h | 55 ---- src/modelInput.cpp | 85 +++--- src/paramutils.cpp | 75 ++++- src/photosynthesis.cpp | 56 ++-- src/photosynthesis.h | 4 src/root.cpp | 5 src/spwb.cpp | 447 ++++++++++++++++++---------------- src/spwb.h | 4 src/transpiration.h | 3 src/transpiration_advanced.cpp | 386 +++++++++++++++++------------ src/transpiration_basic.cpp | 167 ++++++++++-- tests/testthat/test_post_processing.R | 17 - 48 files changed, 1502 insertions(+), 1305 deletions(-)
Title: A High-Performance Local Taxonomic Database Interface
Description: Creates a local database of many commonly used taxonomic authorities
and provides functions that can quickly query this data.
Author: Carl Boettiger [aut, cre] ,
Kari Norman [aut] ,
Jorrit Poelen [aut] ,
Scott Chamberlain [aut] ,
Noam Ross [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between taxadb versions 0.1.5 dated 2022-05-03 and 0.1.6 dated 2022-09-14
DESCRIPTION | 10 MD5 | 30 +- NEWS.md | 7 R/taxa_tbl.R | 2 R/td_create.R | 2 R/tl_import.R | 8 build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/backends.html | 17 - inst/doc/data-sources.Rmd | 2 inst/doc/data-sources.html | 6 inst/extdata/common_itis_test.tsv |only inst/extdata/dwc_itis_test.tsv |only inst/extdata/prov.json | 509 +++++++++++++++++++++++++++++++++----- man/td_create.Rd | 2 tests/testthat/test-tl_import.R | 6 vignettes/data-sources.Rmd | 2 17 files changed, 507 insertions(+), 99 deletions(-)
Title: Performing Bayesian Inference for Repeated-Measures Designs
Description: A Bayesian credible interval is interpreted with respect to posterior probability,
and this interpretation is far more intuitive than that of a frequentist confidence interval.
However, standard highest-density intervals can be wide due to between-subjects variability and tends
to hide within-subjects effects, rendering its relationship with the Bayes factor less clear
in within-subjects (repeated-measures) designs.
This urgent issue can be addressed by using within-subjects intervals in within-subjects designs,
which integrate four methods including the Loftus-Masson (1994) <doi:10.3758/BF03210951>,
the Rouder-Morey-Speckman-Province (2012) <doi:10.1016/j.jmp.2012.08.001>,
the Nathoo-Kilshaw-Masson (2018) <doi:10.1016/j.jmp.2018.07.005>,
and the Heck (2019) <doi:10.31234/osf.io/whp8t> interval estimates.
Author: Zhengxiao Wei [aut, cre] ,
Farouk S. Nathoo [aut] ,
Michael E.J. Masson [aut]
Maintainer: Zhengxiao Wei <zhengxiao@uvic.ca>
Diff between rmBayes versions 0.1.14 dated 2022-09-12 and 0.1.15 dated 2022-09-14
DESCRIPTION | 8 +-- MD5 | 64 +++++++++++++------------- R/rmHDI.R | 17 ++++-- README.md | 3 + inst/stan/HDIc.stan | 2 inst/stan/HDIcCauchy.stan | 2 inst/stan/HDIcUnif.stan | 2 inst/stan/HDId.stan | 2 inst/stan/HDIdCauchy.stan | 2 inst/stan/HDIdCauchyFixed.stan | 2 inst/stan/HDIdFixed.stan | 2 inst/stan/HDIdUnif.stan | 2 inst/stan/HDIdUnifFixed.stan | 2 inst/stan/HDIstandard.stan | 2 inst/stan/HDIstandardFixed.stan | 2 inst/stan/HDIstandardHetero.stan | 2 man/rmHDI.Rd | 17 ++++-- src/stanExports_HDIc.h | 2 src/stanExports_HDIcCauchy.h | 2 src/stanExports_HDIcUnif.h | 2 src/stanExports_HDId.h | 2 src/stanExports_HDIdCauchy.h | 2 src/stanExports_HDIdCauchyFixed.h | 2 src/stanExports_HDIdFixed.h | 2 src/stanExports_HDIdUnif.h | 2 src/stanExports_HDIdUnifFixed.h | 2 src/stanExports_HDIstandard.h | 2 src/stanExports_HDIstandardFixed.h | 2 src/stanExports_HDIstandardHetero.h | 2 tests/testthat/test-errors.R | 14 ++--- tests/testthat/test-fixed_methods.R | 8 +-- tests/testthat/test-heteroscedastic_methods.R | 12 ++-- tests/testthat/test-regular_methods.R | 14 ++--- 33 files changed, 107 insertions(+), 98 deletions(-)
Title: Pedigree-based Relatedness Coefficients
Description: Recursive algorithms for computing various relatedness
coefficients, including pairwise kinship, kappa and identity
coefficients. Both autosomal and X-linked coefficients are computed.
Founders are allowed to be inbred, which enables construction of any
given kappa coefficients, as described in Vigeland (2020)
<doi:10.1007/s00285-020-01505-x>. In addition to the standard
coefficients, 'ribd' also computes a range of lesser-known
coefficients, including generalised kinship coefficients (Karigl
(1981) <doi:10.1111/j.1469-1809.1981.tb00341.x>; Weeks and Lange
(1988) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1715269>),
two-locus coefficients (Thompson (1988) <doi:10.1093/imammb/5.4.261>)
and multi-person coefficients. This package is part of the 'ped
suite', a collection of packages for pedigree analysis in R. Several
methods of 'ribd' are featured in the online app 'QuickPed' available
at <https://magnusdv.shinyapps.io/quickped>. See Vigeland (2022)
<d [...truncated...]
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ribd versions 1.4.0 dated 2022-04-16 and 1.5.0 dated 2022-09-14
DESCRIPTION | 35 ++++---- MD5 | 61 +++++++------- NAMESPACE | 6 + NEWS.md | 23 +++++ R/ELR.R |only R/coeffTable.R | 138 ++++++++++++++++++++++++-------- R/condensedIdentity.R | 4 R/gKinship.R | 22 ++--- R/identityCoefs.R | 12 ++ R/kinship.R | 2 R/realisedIbdVariance.R |only R/twoLocusGeneralisedKinship.R | 11 +- R/twoLocusGeneralisedKinship_boundary.R | 42 ++++++--- R/twoLocusIBD.R | 128 +++++++++++++++++------------ R/twoLocusIdentity.R | 44 +++++----- R/twoLocusInbreeding.R |only R/twoLocusKinship.R | 12 -- R/twoLocusPlot.R | 54 ++++++++---- R/twoLocus_utils.R | 76 +++++++++-------- R/utils.R | 13 ++- README.md | 20 ++-- build/partial.rdb |binary inst/WORDLIST | 76 ++++++++++++++++- man/ELR.Rd |only man/coeffTable.Rd | 59 ++++++++++--- man/condensedIdentity.Rd | 4 man/gKinship.Rd | 22 ++--- man/identityCoefs.Rd | 6 - man/realisedIbdVariance.Rd |only man/twoLocusIBD.Rd | 119 ++++++++++++++++----------- man/twoLocusIdentity.Rd | 20 +++- man/twoLocusInbreeding.Rd |only man/twoLocusKinship.Rd | 12 -- man/twoLocusPlot.Rd | 12 ++ tests/spelling.R |only 35 files changed, 669 insertions(+), 364 deletions(-)
Title: Non-Local Prior Based Iterative Variable Selection Tool for
Genome-Wide Association Studies
Description: Performs variable selection with data from Genome-wide association studies (GWAS), or other high-dimensional data, combining in an iterative framework, the computational efficiency of the screen-and-select variable selection approach based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors as described in Sanyal et al. (2019) <DOI:10.1093/bioinformatics/bty472>.
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>
Diff between GWASinlps versions 1.2 dated 2018-07-19 and 2.0 dated 2022-09-14
GWASinlps-1.2/GWASinlps/ChangeLog |only GWASinlps-1.2/GWASinlps/R/nlpsLM.R |only GWASinlps-1.2/GWASinlps/man/nlpsLM.rd |only GWASinlps-2.0/GWASinlps/DESCRIPTION | 30 - GWASinlps-2.0/GWASinlps/MD5 | 25 - GWASinlps-2.0/GWASinlps/NAMESPACE | 7 GWASinlps-2.0/GWASinlps/NEWS |only GWASinlps-2.0/GWASinlps/NEWS.md |only GWASinlps-2.0/GWASinlps/R/GWASinlps.R | 507 ++++++++++++++++------- GWASinlps-2.0/GWASinlps/R/RcppExports.R |only GWASinlps-2.0/GWASinlps/R/welcome_msg.R |only GWASinlps-2.0/GWASinlps/README.md |only GWASinlps-2.0/GWASinlps/man/GWASinlps-package.Rd | 32 + GWASinlps-2.0/GWASinlps/man/GWASinlps.Rd | 149 ++++-- GWASinlps-2.0/GWASinlps/man/figures |only GWASinlps-2.0/GWASinlps/man/nlps.Rd |only GWASinlps-2.0/GWASinlps/src |only 17 files changed, 522 insertions(+), 228 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
Description: A collection of functions allowing to derive the posterior distribution of the model parameters in random-effects meta-analysis or meta-regression, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.; For more details, see also Roever C (2020) <doi:10.18637/jss.v093.i06>, or Roever C and Friede T (2022) <arXiv:2209.06004>.
Author: Christian Roever [aut, cre] ,
Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 3.0 dated 2022-02-21 and 3.1 dated 2022-09-14
bayesmeta-3.0/bayesmeta/data/BaetenEtAl2013.R |only bayesmeta-3.0/bayesmeta/data/BucherEtAl1997.R |only bayesmeta-3.0/bayesmeta/data/Cochran1954.R |only bayesmeta-3.0/bayesmeta/data/CrinsEtAl2014.R |only bayesmeta-3.0/bayesmeta/data/GoralczykEtAl2011.R |only bayesmeta-3.0/bayesmeta/data/HinksEtAl2010.R |only bayesmeta-3.0/bayesmeta/data/KarnerEtAl2014.R |only bayesmeta-3.0/bayesmeta/data/NicholasEtAl2019.R |only bayesmeta-3.0/bayesmeta/data/Peto1980.R |only bayesmeta-3.0/bayesmeta/data/RobergeEtAl2017.R |only bayesmeta-3.0/bayesmeta/data/Rubin1981.R |only bayesmeta-3.0/bayesmeta/data/SidikJonkman2007.R |only bayesmeta-3.0/bayesmeta/data/SnedecorCochran.R |only bayesmeta-3.1/bayesmeta/DESCRIPTION | 10 - bayesmeta-3.1/bayesmeta/MD5 | 69 ++++---- bayesmeta-3.1/bayesmeta/R/bayesmeta.R | 18 +- bayesmeta-3.1/bayesmeta/R/bmr.R | 65 +++++--- bayesmeta-3.1/bayesmeta/build/partial.rdb |binary bayesmeta-3.1/bayesmeta/build/vignette.rds |binary bayesmeta-3.1/bayesmeta/data/BaetenEtAl2013.rda |only bayesmeta-3.1/bayesmeta/data/BucherEtAl1997.rda |only bayesmeta-3.1/bayesmeta/data/Cochran1954.rda |only bayesmeta-3.1/bayesmeta/data/CrinsEtAl2014.rda |only bayesmeta-3.1/bayesmeta/data/GoralczykEtAl2011.rda |only bayesmeta-3.1/bayesmeta/data/HinksEtAl2010.rda |only bayesmeta-3.1/bayesmeta/data/KarnerEtAl2014.rda |only bayesmeta-3.1/bayesmeta/data/NicholasEtAl2019.rda |only bayesmeta-3.1/bayesmeta/data/Peto1980.rda |only bayesmeta-3.1/bayesmeta/data/RobergeEtAl2017.rda |only bayesmeta-3.1/bayesmeta/data/Rubin1981.rda |only bayesmeta-3.1/bayesmeta/data/SchmidliEtAl2017.rda |only bayesmeta-3.1/bayesmeta/data/SidikJonkman2007.rda |only bayesmeta-3.1/bayesmeta/data/SnedecorCochran.rda |only bayesmeta-3.1/bayesmeta/inst/doc/Roever2020-bayesmeta.pdf |binary bayesmeta-3.1/bayesmeta/inst/doc/RoeverFriede2022-UsingBayesmetaForMetaRegression.pdf |only bayesmeta-3.1/bayesmeta/inst/doc/RoeverFriede2022-UsingBayesmetaForMetaRegression.pdf.asis |only bayesmeta-3.1/bayesmeta/inst/doc/bayesmeta.html | 78 +++++----- bayesmeta-3.1/bayesmeta/man/BaetenEtAl2013.Rd | 5 bayesmeta-3.1/bayesmeta/man/BucherEtAl1997.Rd | 7 bayesmeta-3.1/bayesmeta/man/CrinsEtAl2014.Rd | 12 + bayesmeta-3.1/bayesmeta/man/NicholasEtAl2019.Rd | 4 bayesmeta-3.1/bayesmeta/man/RobergeEtAl2017.Rd | 4 bayesmeta-3.1/bayesmeta/man/SchmidliEtAl2017.Rd |only bayesmeta-3.1/bayesmeta/man/bayesmeta-package.Rd | 29 ++- bayesmeta-3.1/bayesmeta/man/bmr.Rd | 4 bayesmeta-3.1/bayesmeta/man/forestplot.bmr.Rd | 4 bayesmeta-3.1/bayesmeta/man/forestplot.escalc.Rd | 3 bayesmeta-3.1/bayesmeta/man/summary.bmr.Rd | 5 bayesmeta-3.1/bayesmeta/man/traceplot.bayesmeta.Rd | 11 + bayesmeta-3.1/bayesmeta/man/weightsplot.bayesmeta.Rd | 5 bayesmeta-3.1/bayesmeta/vignettes/RoeverFriede2022-UsingBayesmetaForMetaRegression.pdf.asis |only 51 files changed, 217 insertions(+), 116 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [ctb] ,
Jeffrey Wong [ctb [...truncated...]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 9.0.0 dated 2022-08-10 and 9.0.0.1 dated 2022-09-14
DESCRIPTION | 6 +- MD5 | 8 +-- NEWS.md | 4 + tests/testthat/test-dplyr-funcs-datetime.R | 60 +++++++---------------------- tests/testthat/test-dplyr-funcs-string.R | 5 +- 5 files changed, 30 insertions(+), 53 deletions(-)
Title: Single Cell Cluster-Based Annotation Toolkit for Cellular
Heterogeneity
Description: An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) <doi:10.1016/j.isci.2020.100882> for more details.
Author: Xin Shao
Maintainer: Xin Shao<xin_shao@zju.edu.cn>
Diff between scCATCH versions 3.1 dated 2022-05-14 and 3.2 dated 2022-09-14
scCATCH-3.1/scCATCH/man/findcelltype-scCATCH-method.Rd |only scCATCH-3.1/scCATCH/man/findmarkergene-scCATCH-method.Rd |only scCATCH-3.2/scCATCH/DESCRIPTION | 6 - scCATCH-3.2/scCATCH/MD5 | 34 ++++---- scCATCH-3.2/scCATCH/NAMESPACE | 3 scCATCH-3.2/scCATCH/R/class.R | 39 --------- scCATCH-3.2/scCATCH/R/methods.R | 37 ++++----- scCATCH-3.2/scCATCH/R/rev_gene.R | 3 scCATCH-3.2/scCATCH/README.md | 9 +- scCATCH-3.2/scCATCH/build/vignette.rds |binary scCATCH-3.2/scCATCH/data/cellmatch.rda |binary scCATCH-3.2/scCATCH/data/geneinfo.rda |binary scCATCH-3.2/scCATCH/inst/doc/tutorial.Rmd | 13 ++- scCATCH-3.2/scCATCH/inst/doc/tutorial.html | 59 ++++++--------- scCATCH-3.2/scCATCH/man/cellmatch.Rd | 2 scCATCH-3.2/scCATCH/man/findcelltype.Rd | 2 scCATCH-3.2/scCATCH/man/findmarkergene.Rd | 6 - scCATCH-3.2/scCATCH/man/geneinfo.Rd | 2 scCATCH-3.2/scCATCH/vignettes/tutorial.Rmd | 13 ++- 19 files changed, 97 insertions(+), 131 deletions(-)
Title: Clustering Time Series While Resisting Outliers
Description: Robust Clustering of Time Series (RCTS) has the functionality to cluster time series using both the classical and the robust interactive fixed effects framework.
The classical framework is developed in Ando & Bai (2017) <doi:10.1080/01621459.2016.1195743>. The implementation within this package excludes the SCAD-penalty on the estimations of beta.
This robust framework is developed in Boudt & Heyndels (2022) <doi:10.1016/j.ecosta.2022.01.002> and is made robust against different kinds of outliers.
The algorithm iteratively updates beta (the coefficients of the observable variables), group membership, and the latent factors (which can be common and/or group-specific) along
with their loadings. The number of groups and factors can be estimated if they are unknown.
Author: Ewoud Heyndels [aut, cre]
Maintainer: Ewoud Heyndels <ewoud.heyndels@vub.be>
Diff between RCTS versions 0.2.2 dated 2022-06-20 and 0.2.3 dated 2022-09-14
DESCRIPTION | 8 MD5 | 51 +- NAMESPACE | 4 R/03_IFE_algorithm_functions.R | 348 +++++++++++++------ R/07_IFE_robust_lambda.R | 11 R/functions_parallel.R | 124 ++++-- build/partial.rdb |binary man/add_metrics.Rd | 2 man/add_pic.Rd | 6 man/add_pic_parallel.Rd | 20 - man/calculate_XB_estimated.Rd | 4 man/calculate_lambda.Rd | 6 man/calculate_lambda_group.Rd | 20 - man/define_object_for_initial_clustering_macropca.Rd | 6 man/estimate_algorithm.Rd |only man/estimate_beta.Rd | 11 man/estimate_factor.Rd | 8 man/estimate_factor_group.Rd | 24 + man/initialise_beta.Rd | 12 man/initialise_clustering.Rd | 10 man/initialise_commonfactorstructure_macropca.Rd | 8 man/iterate.Rd | 8 man/make_df_pic_parallel.Rd | 4 man/parallel_algorithm.Rd | 7 man/reassign_if_empty_groups.Rd | 4 man/run_config.Rd | 7 man/update_g.Rd | 13 27 files changed, 486 insertions(+), 240 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 2.0.2 dated 2022-05-24 and 2.0.3 dated 2022-09-14
DESCRIPTION | 8 - MD5 | 42 ++++----- NAMESPACE | 2 NEWS | 3 R/openssh.R | 31 +++++++ R/ssh2.R | 7 - R/write.R | 8 - R/writessh.R | 59 +++++++++++++ build/vignette.rds |binary inst/doc/bignum.html | 143 +++++++++++++++----------------- inst/doc/crypto_hashing.html | 119 ++++++++++++-------------- inst/doc/keys.html | 159 +++++++++++++++++------------------- inst/doc/secure_rng.html | 129 +++++++++++++---------------- man/write_pem.Rd | 13 ++ src/ssl.c | 3 src/write.c | 13 ++ tests/testthat/test_keys_dsa.R | 2 tests/testthat/test_keys_ecdsa.R | 2 tests/testthat/test_keys_ecdsa384.R | 2 tests/testthat/test_keys_ecdsa521.R | 2 tests/testthat/test_keys_ed25519.R | 2 tests/testthat/test_keys_rsa.R | 2 22 files changed, 425 insertions(+), 326 deletions(-)
Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between EnrichIntersect versions 0.2 dated 2022-08-10 and 0.3 dated 2022-09-14
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/enrichment.R | 18 ++++++++++++------ R/intersectSankey.R | 17 +++++++++-------- inst/doc/EnrichIntersect.Rmd | 8 ++++---- inst/doc/EnrichIntersect.html | 5 +++-- man/enrichment.Rd | 8 +++++--- man/intersectSankey.Rd | 1 - vignettes/EnrichIntersect.Rmd | 8 ++++---- 11 files changed, 59 insertions(+), 43 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Title: Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells
Description: Tools to construct (or add to) cell-type signature matrices using flow sorted or single cell samples and deconvolve bulk gene expression data.
Useful for assessing the quality of single cell RNAseq experiments, estimating the accuracy of signature matrices, and determining cell-type spillover.
Please cite: Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells <doi:10.1371/journal.pone.0224693>.
Author: Samuel A Danziger
Maintainer: Samuel A Danziger <sam.danziger@gmail.com>
Diff between ADAPTS versions 1.0.21 dated 2021-10-05 and 1.0.22 dated 2022-09-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/MakeSigMatrix.R | 24 ++++++++++++------------ build/vignette.rds |binary 4 files changed, 18 insertions(+), 18 deletions(-)
More information about elections.dtree at CRAN
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