Title: Dynamical Systems Approach to Immune Response Modeling
Description: Simulation models (apps) of various within-host immune response scenarios.
The purpose of the package is to help individuals learn
about within-host infection and immune response modeling from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Cody Dailey [ctb],
Yang Ge [ctb],
Spencer Hall [ctb],
Brian McKay [ctb],
Sina Solaimanpour [ctb],
Alexis Vittengl [ctb],
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIRM versions 0.8.7 dated 2021-03-20 and 0.9.3 dated 2021-07-28
DSAIRM-0.8.7/DSAIRM/R/generate_equations.R |only DSAIRM-0.8.7/DSAIRM/R/simulate_basicvirus_ode.R |only DSAIRM-0.8.7/DSAIRM/R/simulate_basicvirus_stochastic.R |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/bacteriaexploration_documentation.Rmd |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/bacteriaexploration_documentation.html |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/references.bib |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/virusexploration_documentation.Rmd |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/virusexploration_documentation.html |only DSAIRM-0.8.7/DSAIRM/inst/docsfordevelopers |only DSAIRM-0.8.7/DSAIRM/inst/helperfunctions |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/Environmental_Transmission_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SEIRSd_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SIRSd_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SIR_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/Vector_transmission_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_ode.R |only DSAIRM-0.8.7/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_stochastic.R |only DSAIRM-0.8.7/DSAIRM/man/generate_equations.Rd |only DSAIRM-0.8.7/DSAIRM/man/simulate_basicvirus_ode.Rd |only DSAIRM-0.8.7/DSAIRM/man/simulate_basicvirus_stochastic.Rd |only DSAIRM-0.8.7/DSAIRM/tests/testthat/test-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/DESCRIPTION | 15 DSAIRM-0.9.3/DSAIRM/MD5 | 230 ++-- DSAIRM-0.9.3/DSAIRM/NAMESPACE | 5 DSAIRM-0.9.3/DSAIRM/NEWS.md | 11 DSAIRM-0.9.3/DSAIRM/R/DSAIRM.R | 31 DSAIRM-0.9.3/DSAIRM/R/generate_documentation.R | 4 DSAIRM-0.9.3/DSAIRM/R/generate_fctcall.R | 101 + DSAIRM-0.9.3/DSAIRM/R/generate_ggplot.R | 26 DSAIRM-0.9.3/DSAIRM/R/generate_shinyinput.R | 21 DSAIRM-0.9.3/DSAIRM/R/run_model.R | 106 +- DSAIRM-0.9.3/DSAIRM/R/simulate_Basic_Virus_Model_ode.R |only DSAIRM-0.9.3/DSAIRM/R/simulate_Basic_Virus_Model_stochastic.R |only DSAIRM-0.9.3/DSAIRM/R/simulate_basicbacteria_modelexploration.R | 224 ++-- DSAIRM-0.9.3/DSAIRM/R/simulate_basicbacteria_ode.R | 4 DSAIRM-0.9.3/DSAIRM/R/simulate_basicvirus_fit.R | 373 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_basicvirus_modelexploration.R | 245 ++-- DSAIRM-0.9.3/DSAIRM/R/simulate_confint_fit.R | 399 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_drugresistance_stochastic.R | 6 DSAIRM-0.9.3/DSAIRM/R/simulate_fludrug_fit.R | 405 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_modelcomparison_fit.R | 463 ++++---- DSAIRM-0.9.3/DSAIRM/R/simulate_pkpdmodel_ode.R | 12 DSAIRM-0.9.3/DSAIRM/R/simulate_usanalysis.R | 8 DSAIRM-0.9.3/DSAIRM/R/simulate_virusandtx_ode.R | 2 DSAIRM-0.9.3/DSAIRM/build/vignette.rds |binary DSAIRM-0.9.3/DSAIRM/inst/DSAIRM/app.R | 43 DSAIRM-0.9.3/DSAIRM/inst/appinformation/apptable.tsv | 32 DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_documentation.Rmd | 515 ++++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_documentation.html | 208 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_documentation.Rmd |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_documentation.html |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_documentation.Rmd | 446 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_documentation.html | 111 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_documentation.Rmd |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_documentation.html |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.Rmd | 432 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.html | 131 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_documentation.Rmd | 405 +++++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_documentation.html | 160 +-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/dsairm_references.bib |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_documentation.Rmd | 529 ++++++---- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_documentation.html | 183 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_documentation.Rmd | 304 +++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_documentation.html | 116 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitfludrug_documentation.Rmd | 358 ++++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitfludrug_documentation.html | 148 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitfludrug_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitmodelcomparison_documentation.Rmd | 425 ++++---- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitmodelcomparison_documentation.html | 130 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitmodelcomparison_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/modelvariants_documentation.Rmd | 492 ++++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/modelvariants_documentation.html | 153 ++ DSAIRM-0.9.3/DSAIRM/inst/appinformation/modelvariants_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/pkpdmodel_documentation.Rmd | 463 ++++++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/pkpdmodel_documentation.html | 146 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/pkpdmodel_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/startup_script.R |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_documentation.Rmd | 460 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_documentation.html | 157 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_documentation.Rmd | 453 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_documentation.html | 143 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_documentation.Rmd | 502 ++++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_documentation.html | 180 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/doc/DSAIRM.Rmd | 21 DSAIRM-0.9.3/DSAIRM/inst/doc/DSAIRM.html | 59 - DSAIRM-0.9.3/DSAIRM/inst/mbmodels/Basic_Bacteria_model.Rds |only DSAIRM-0.9.3/DSAIRM/inst/mbmodels/Basic_Virus_model.Rds |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_Basic_Virus_Model_ode.R |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_Basic_Virus_Model_stochastic.R |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_modelexploration.R | 224 ++-- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_ode.R | 4 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_fit.R | 373 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_modelexploration.R | 245 ++-- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_confint_fit.R | 399 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_drugresistance_stochastic.R | 6 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_fludrug_fit.R | 405 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_modelcomparison_fit.R | 463 ++++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_pkpdmodel_ode.R | 12 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_usanalysis.R | 8 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_virusandtx_ode.R | 2 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulatorfunctions.zip |binary DSAIRM-0.9.3/DSAIRM/man/DSAIRM.Rd | 67 - DSAIRM-0.9.3/DSAIRM/man/generate_fctcall.Rd | 46 DSAIRM-0.9.3/DSAIRM/man/generate_ggplot.Rd | 4 DSAIRM-0.9.3/DSAIRM/man/simulate_Basic_Virus_Model_ode.Rd |only DSAIRM-0.9.3/DSAIRM/man/simulate_Basic_Virus_Model_stochastic.Rd |only DSAIRM-0.9.3/DSAIRM/man/simulate_basicbacteria_ode.Rd | 2 DSAIRM-0.9.3/DSAIRM/man/simulate_basicvirus_fit.Rd | 234 ++-- DSAIRM-0.9.3/DSAIRM/man/simulate_confint_fit.Rd | 188 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_drugresistance_stochastic.Rd | 188 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_fludrug_fit.Rd | 194 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_modelcomparison_fit.Rd | 228 ++-- DSAIRM-0.9.3/DSAIRM/man/simulate_usanalysis.Rd | 28 DSAIRM-0.9.3/DSAIRM/man/simulate_virusandtx_ode.Rd | 200 +-- DSAIRM-0.9.3/DSAIRM/tests/testthat/Rplots.pdf |binary DSAIRM-0.9.3/DSAIRM/tests/testthat/test-basicbacteria-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-basicvirus-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-fit-apps.R | 83 + DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_documentation.R | 4 DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_ggplot.R | 61 - DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_plotly.R | 61 - DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_shinyinput.R | 21 DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_usplot.R | 124 +- DSAIRM-0.9.3/DSAIRM/tests/testthat/test-individual-apps.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-run_model.R | 156 ++ DSAIRM-0.9.3/DSAIRM/tests/testthat/test-stochastic-virus-app.R | 120 +- DSAIRM-0.9.3/DSAIRM/vignettes/DSAIRM.Rmd | 21 DSAIRM-0.9.3/DSAIRM/vignettes/mainmenu.png |binary DSAIRM-0.9.3/DSAIRM/vignettes/modelexample.png |binary 140 files changed, 8792 insertions(+), 5975 deletions(-)
Title: Safe, Multiple, Simultaneous String Substitution
Description: Designed to enable simultaneous substitution in strings in a safe fashion.
Safe means it does not rely on placeholders (which can cause errors in same length matches).
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Diff between mgsub versions 1.7.2 dated 2020-07-22 and 1.7.3 dated 2021-07-28
DESCRIPTION | 9 ++--- MD5 | 24 +++++++------- NEWS.md | 3 + inst/doc/Safe-Censoring.R | 23 ------------- inst/doc/Safe-Censoring.Rmd | 28 ---------------- inst/doc/Safe-Censoring.html | 33 +------------------ inst/doc/Safe-Substitution.R | 46 --------------------------- inst/doc/Safe-Substitution.Rmd | 67 +--------------------------------------- inst/doc/Safe-Substitution.html | 59 +---------------------------------- man/censor_worker.Rd | 10 +---- man/mgsub_censor.Rd | 10 +---- vignettes/Safe-Censoring.Rmd | 28 ---------------- vignettes/Safe-Substitution.Rmd | 67 +--------------------------------------- 13 files changed, 32 insertions(+), 375 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between rscorecard versions 0.19.1 dated 2021-07-20 and 0.20.0 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/sysdata.rda |binary tests/testthat/test-dictionary.R | 4 ++-- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
For details see Niku et al. (2019a) <doi:10.1371/journal.pone.0216129> and
Niku et al. (2019b) <doi:10.1111/2041-210X.13303>.
Author: Jenni Niku [aut, cre],
Wesley Brooks [aut],
Riki Herliansyah [aut],
Francis K.C. Hui [aut],
Sara Taskinen [aut],
David I. Warton [aut],
Bert van der Veen [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 1.3.0 dated 2021-04-30 and 1.3.1 dated 2021-07-28
gllvm-1.3.0/gllvm/build |only gllvm-1.3.0/gllvm/data/sim_bacteria.RData |only gllvm-1.3.0/gllvm/inst/doc |only gllvm-1.3.0/gllvm/man/optima.Rd |only gllvm-1.3.0/gllvm/man/sim_bacteria.Rd |only gllvm-1.3.0/gllvm/vignettes |only gllvm-1.3.1/gllvm/DESCRIPTION | 16 gllvm-1.3.1/gllvm/MD5 | 93 - gllvm-1.3.1/gllvm/NAMESPACE | 13 gllvm-1.3.1/gllvm/NEWS.md | 16 gllvm-1.3.1/gllvm/R/TMBtrait.R | 510 ++++-- gllvm-1.3.1/gllvm/R/anova.gllvm.R | 26 gllvm-1.3.1/gllvm/R/confint.gllvm.R | 106 + gllvm-1.3.1/gllvm/R/ecoCoefs.gllvm.R | 213 -- gllvm-1.3.1/gllvm/R/getLV.gllvm.R | 48 gllvm-1.3.1/gllvm/R/getPredictErr.gllvm.R | 41 gllvm-1.3.1/gllvm/R/getResidualCor.gllvm.R | 8 gllvm-1.3.1/gllvm/R/getResidualCov.gllvm.R | 152 + gllvm-1.3.1/gllvm/R/gllvm.R | 410 ++++- gllvm-1.3.1/gllvm/R/gllvm.TMB.R | 982 +++++++++--- gllvm-1.3.1/gllvm/R/gllvm.auxiliary.R | 1836 +++++++++++++++++------ gllvm-1.3.1/gllvm/R/gllvm.makeform.R |only gllvm-1.3.1/gllvm/R/logLik.gllvm.R | 8 gllvm-1.3.1/gllvm/R/ordiplot.gllvm.R | 273 ++- gllvm-1.3.1/gllvm/R/plot.gllvm.R | 5 gllvm-1.3.1/gllvm/R/predict.gllvm.R | 212 +- gllvm-1.3.1/gllvm/R/predictLVs.gllvm.R | 74 gllvm-1.3.1/gllvm/R/randomCoefplot.R | 5 gllvm-1.3.1/gllvm/R/residuals.gllvm.R | 24 gllvm-1.3.1/gllvm/R/se.gllvm.R | 266 ++- gllvm-1.3.1/gllvm/R/simulate.gllvm.R | 60 gllvm-1.3.1/gllvm/R/summary.gllvm.R | 204 ++ gllvm-1.3.1/gllvm/man/AICc.Rd | 48 gllvm-1.3.1/gllvm/man/ecoCoefs.Rd |only gllvm-1.3.1/gllvm/man/getLV.gllvm.Rd | 6 gllvm-1.3.1/gllvm/man/getPredictErr.gllvm.Rd | 2 gllvm-1.3.1/gllvm/man/getResidualCor.gllvm.Rd | 6 gllvm-1.3.1/gllvm/man/getResidualCov.gllvm.Rd | 24 gllvm-1.3.1/gllvm/man/gllvm.Rd | 99 - gllvm-1.3.1/gllvm/man/ordiplot.gllvm.Rd | 36 gllvm-1.3.1/gllvm/man/plot.gllvm.Rd | 4 gllvm-1.3.1/gllvm/man/predict.gllvm.Rd | 16 gllvm-1.3.1/gllvm/man/se.gllvm.Rd | 64 gllvm-1.3.1/gllvm/man/summary.gllvm.Rd | 33 gllvm-1.3.1/gllvm/src/gllvm.cpp | 881 ++++++++--- gllvm-1.3.1/gllvm/tests/testthat/test-fitgllvm.R | 2 46 files changed, 4983 insertions(+), 1839 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, restricted
quantile regression, and directional quantile classification. A vignette
is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and
included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code,
<https://orcid.org/0000-0002-7104-5826>),
Cinzia Viroli [ctb] (Contributions to dqc code,
<https://orcid.org/0000-0002-3278-5266>)
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Diff between Qtools versions 1.5.4 dated 2021-02-07 and 1.5.5 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 24 ++++++++++---------- NEWS | 8 ++++++ R/Qtools.R | 60 +++++++++++++++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/Qtools.html | 26 +++++++++++++++++++++ man/Qtools-package.Rd | 6 ++--- man/cmidecdf.Rd | 2 - man/midq2q.Rd | 14 +++++++++-- man/midrq.Rd | 9 +++++-- man/midrqControl.Rd | 2 - man/summary.midrq.Rd | 2 - man/vcov.midrq.Rd | 2 - 13 files changed, 114 insertions(+), 49 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.0.1 dated 2021-05-14 and 1.0.2 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 21 ++++++++-------- NEWS | 6 ++++ R/hybrids.R | 66 +++++++++++++++++++++++++++++++++++++++++++++------- R/pullGeno.R | 34 ++++++++++++++++++++------ README.md | 2 + build/vignette.rds |binary inst/CITATION | 2 - inst/doc/intro.html | 6 ++-- inst/doc/traits.pdf |binary man/setPhenoGCA.Rd | 39 ++++++++++++++++++++++++++---- src/OCS.cpp |only 12 files changed, 144 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-10 1.995
2021-07-01 1.993
2021-03-15 1.977
2021-01-14 1.971
2020-10-16 1.964
2020-07-09 1.946
2020-07-01 1.941
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Eamon B. O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 3.4 dated 2021-05-13 and 3.5 dated 2021-07-28
pomp-3.4/pomp/R/aaa.R |only pomp-3.4/pomp/data/blowflies.csv |only pomp-3.4/pomp/data/parus.csv |only pomp-3.5/pomp/DESCRIPTION | 18 +- pomp-3.5/pomp/MD5 | 37 ++-- pomp-3.5/pomp/R/bake.R | 291 +++++++++++++++++++++++++++--------- pomp-3.5/pomp/R/bsmc2.R | 6 pomp-3.5/pomp/R/concat.R | 4 pomp-3.5/pomp/R/objfun.R | 10 + pomp-3.5/pomp/build/partial.rdb |binary pomp-3.5/pomp/data/LondonYorke.rda |binary pomp-3.5/pomp/data/blowflies.csv.xz |only pomp-3.5/pomp/data/bsflu.rda |binary pomp-3.5/pomp/data/ebolaWA2014.rda |binary pomp-3.5/pomp/data/ewcitmeas.rda |binary pomp-3.5/pomp/data/ewmeas.rda |binary pomp-3.5/pomp/data/parus.csv.gz |only pomp-3.5/pomp/inst/NEWS | 46 +++++ pomp-3.5/pomp/inst/NEWS.Rd | 27 +++ pomp-3.5/pomp/inst/doc/index.html | 86 ++++------ pomp-3.5/pomp/man/bake.Rd | 124 +++++++++++++-- pomp-3.5/pomp/man/partrans.Rd | 5 22 files changed, 492 insertions(+), 162 deletions(-)
Title: Analytic Insurance Rating Techniques
Description: Methods for insurance rating. It helps actuaries to implement GLMs within all relevant steps needed to construct
a risk premium from raw data. It provides a data driven strategy for the construction of insurance tariff classes.
This strategy is based on the work by Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>. It also provides recipes
on how to easily perform one-way, or univariate, analyses on an insurance portfolio. In addition it adds functionality
to include reference categories in the levels of the coefficients in the output of a generalized linear regression analysis.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.6.6 dated 2021-05-19 and 0.6.7 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/construct_tariff_classes.R | 5 +++-- R/model_refinement.R | 24 ++++++++++++++++++++++++ R/rows_per_date.R | 6 ++++-- R/utils_refinement.R | 8 ++++++++ man/figures/normalitysim-1.png |binary man/get_data.Rd |only 10 files changed, 57 insertions(+), 15 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library
simplifies training fast and accurate neural networks
using modern best practices. It is based on research
in to deep learning best practices undertaken
at 'fast.ai', including 'out of the box' support
for vision, text, tabular, audio, time series, and
collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>
Diff between fastai versions 2.0.8 dated 2021-05-16 and 2.0.9 dated 2021-07-28
DESCRIPTION | 7 -- MD5 | 50 +++++++++------ NEWS.md | 8 ++ R/generics_mask.R | 30 --------- R/install_fastai.R | 44 ++++--------- R/package.R | 2 R/stats.R | 4 - README.md | 2 build/vignette.rds |binary inst/doc/optimizer.Rmd | 2 inst/doc/optimizer.html | 2 man/abs.fastai.torch_core.TensorMask.Rd | 11 --- man/greater-than-equals-.fastai.torch_core.TensorMask.Rd | 9 -- man/install_fastai.Rd | 4 - man/lr_find.Rd | 3 man/mask_eq.Rd | 8 -- man/max.fastai.torch_core.TensorMask.Rd | 9 -- tests/testthat/test-GAN.R |only tests/testthat/test-collab.R |only tests/testthat/test-experimental.R |only tests/testthat/test-generics-tensor.R |only tests/testthat/test-image.R |only tests/testthat/test-medical.R |only tests/testthat/test-medical_image_render.R |only tests/testthat/test-model_load.R |only tests/testthat/test-modify.R |only tests/testthat/test-nn_module.R |only tests/testthat/test-predict_medical.R |only tests/testthat/test-pretrained_in_cnn_learner.R |only tests/testthat/test-regression.R |only tests/testthat/test-tabular.R |only tests/testthat/test-text-load.R |only tests/testthat/test-text.R |only vignettes/optimizer.Rmd | 2 34 files changed, 68 insertions(+), 129 deletions(-)
Title: Deep Learning
Description: Implementation of some Deep Learning methods. Includes multilayer perceptron, different activation functions, regularisation strategies, stochastic gradient descent and dropout. Thanks go to the following references for helping to inspire and develop the package: Ian Goodfellow, Yoshua Bengio, Aaron Courville, Francis Bach (2016, ISBN:978-0262035613) Deep Learning. Terrence J. Sejnowski (2018, ISBN:978-0262038034) The Deep Learning Revolution. Grant Sanderson (3brown1blue) <https://www.youtube.com/playlist?list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi> Neural Networks YouTube playlist. Michael A. Nielsen <http://neuralnetworksanddeeplearning.com/> Neural Networks and Deep Learning.
Author: Benjamin Taylor [aut, cre]
Maintainer: Benjamin Taylor <benjamin.taylor.software@gmail.com>
Diff between deepNN versions 1.0 dated 2020-03-05 and 1.1 dated 2021-07-28
DESCRIPTION | 8 +-- MD5 | 38 +++++++++--------- R/cost_functions.R | 98 +++++++++++++++++++++++------------------------ R/miscellaneous.R | 14 ++++-- R/networks.R | 25 ----------- R/optimisation.R | 28 ++++++------- R/prediction.R | 27 +----------- R/regularisation.R | 56 +++++++++++++------------- man/L1_regularisation.Rd | 10 ---- man/L2_regularisation.Rd | 10 ---- man/NNpredict.Rd | 25 ----------- man/Qloss.Rd | 15 ------- man/deepNN-package.Rd | 4 + man/download_mnist.Rd | 6 +- man/dropoutProbs.Rd | 15 ------- man/multinomial.Rd | 13 ------ man/no_regularisation.Rd | 11 ----- man/train.Rd | 25 ----------- man/wQloss.Rd | 15 ------- man/wmultinomial.Rd | 13 ------ 20 files changed, 139 insertions(+), 317 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between protolite versions 2.1 dated 2020-01-13 and 2.1.1 dated 2021-07-28
DESCRIPTION | 9 ++++----- MD5 | 13 +++++++------ NEWS | 4 ++++ cleanup | 3 +-- configure | 48 ++++++++++++++++++++++++++---------------------- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ 8 files changed, 48 insertions(+), 36 deletions(-)
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.2-6 dated 2021-04-02 and 0.2-7 dated 2021-07-28
DESCRIPTION | 7 ++++--- MD5 | 29 ++++++++++++++++------------- NAMESPACE | 4 ++++ R/RcppExports.R | 4 ++++ R/wrap_x.R |only configure | 20 ++++++++++++++++++-- configure.ac | 6 +++++- man/st_wrap_x.Rd |only src/Makevars.ucrt |only src/Makevars.win | 23 ++++++++++------------- src/RcppExports.cpp | 19 +++++++++++++++++++ src/lwgeom.cpp | 18 ++++++++++++++++++ tests/dist.R | 1 + tests/dist.Rout.save | 8 +++++--- tests/geod.Rout.save | 18 +++++++++++------- tests/testthat.Rout.save | 12 +++++++----- tests/testthat/test_lwgeom.R | 16 ++++++++++++++++ 17 files changed, 138 insertions(+), 47 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Google Inc [cph] (CLD3 C++ library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between cld3 versions 1.4.1 dated 2021-01-11 and 1.4.2 dated 2021-07-28
DESCRIPTION | 7 +++---- MD5 | 7 ++++--- NEWS | 3 +++ src/Makevars.ucrt |only src/Makevars.win | 2 +- 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] (<https://orcid.org/0000-0003-0637-3812>),
Branislav Panic [ctb] (<https://orcid.org/0000-0001-8349-8550>),
Jernej Klemenc [ctb] (<https://orcid.org/0000-0002-6778-6728>),
Simon Oman [ctb] (<https://orcid.org/0000-0001-8213-0818>)
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.13.0 dated 2021-07-14 and 2.13.1 dated 2021-07-28
rebmix-2.13.0/rebmix/data/sensorless.drive.rda |only rebmix-2.13.0/rebmix/data/steel.plates.rda |only rebmix-2.13.0/rebmix/man/sensorless.drive.Rd |only rebmix-2.13.0/rebmix/man/steel.plates.Rd |only rebmix-2.13.1/rebmix/DESCRIPTION | 6 rebmix-2.13.1/rebmix/MD5 | 98 +++++------ rebmix-2.13.1/rebmix/R/RCLRMIX.R | 2 rebmix-2.13.1/rebmix/R/RCLSMIX.R | 4 rebmix-2.13.1/rebmix/R/REBMIX.R | 2 rebmix-2.13.1/rebmix/R/RNGMIX.R | 2 rebmix-2.13.1/rebmix/build/partial.rdb |binary rebmix-2.13.1/rebmix/build/vignette.rds |binary rebmix-2.13.1/rebmix/data/adult.rda |binary rebmix-2.13.1/rebmix/data/bearings.rda |binary rebmix-2.13.1/rebmix/data/datalist | 4 rebmix-2.13.1/rebmix/data/galaxy.rda |binary rebmix-2.13.1/rebmix/data/iris.rda |binary rebmix-2.13.1/rebmix/data/sensorlessdrive.rda |only rebmix-2.13.1/rebmix/data/steelplates.rda |only rebmix-2.13.1/rebmix/data/truck.rda |binary rebmix-2.13.1/rebmix/data/weibull.rda |binary rebmix-2.13.1/rebmix/data/weibullnormal.rda |binary rebmix-2.13.1/rebmix/data/wine.rda |binary rebmix-2.13.1/rebmix/demo/rebmix.fault.detection.R | 88 ++++----- rebmix-2.13.1/rebmix/demo/rebmix.galaxy.R | 6 rebmix-2.13.1/rebmix/demo/rebmix.mixed.continuous.discrete.R | 4 rebmix-2.13.1/rebmix/demo/rebmix.multivariate.normal.R | 2 rebmix-2.13.1/rebmix/demo/rebmix.truck.R | 6 rebmix-2.13.1/rebmix/demo/rebmix.univariate.normal.R | 2 rebmix-2.13.1/rebmix/demo/rebmix.weibullnormal.R | 6 rebmix-2.13.1/rebmix/inst/NEWS.Rd | 6 rebmix-2.13.1/rebmix/inst/doc/rebmix.R | 12 - rebmix-2.13.1/rebmix/inst/doc/rebmix.Rnw | 34 +-- rebmix-2.13.1/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.13.1/rebmix/man/RCLS.chunk.Rd | 2 rebmix-2.13.1/rebmix/man/RCLSMIX.Rd | 2 rebmix-2.13.1/rebmix/man/REBMIX.boot.Rd | 2 rebmix-2.13.1/rebmix/man/REBMIX.plot.Rd | 2 rebmix-2.13.1/rebmix/man/adult.Rd | 4 rebmix-2.13.1/rebmix/man/bearings.Rd | 4 rebmix-2.13.1/rebmix/man/demix.Rd | 2 rebmix-2.13.1/rebmix/man/galaxy.Rd | 2 rebmix-2.13.1/rebmix/man/iris.Rd | 4 rebmix-2.13.1/rebmix/man/sensorlessdrive.Rd |only rebmix-2.13.1/rebmix/man/split.Rd | 2 rebmix-2.13.1/rebmix/man/steelplates.Rd |only rebmix-2.13.1/rebmix/man/truck.Rd | 4 rebmix-2.13.1/rebmix/man/weibull.Rd | 4 rebmix-2.13.1/rebmix/man/weibullnormal.Rd | 4 rebmix-2.13.1/rebmix/man/wine.Rd | 4 rebmix-2.13.1/rebmix/src/emf.cpp | 21 +- rebmix-2.13.1/rebmix/src/rebmixf.cpp | 12 - rebmix-2.13.1/rebmix/src/rngmixf.cpp | 2 rebmix-2.13.1/rebmix/vignettes/rebmix.Rnw | 34 +-- 54 files changed, 196 insertions(+), 199 deletions(-)
More information about MedianaDesigner at CRAN
Permanent link
Title: Fair Data Adaptation with Quantile Preservation
Description: An implementation of the fair data adaptation with quantile
preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>.
The adaptation procedure uses the specified causal graph to pre-process the
given training and testing data in such a way to remove the bias caused by
the protected attribute. The procedure uses tree ensembles for quantile
regression.
Author: Drago Plecko [aut, cre]
Maintainer: Drago Plecko <drago.plecko@stat.math.ethz.ch>
Diff between fairadapt versions 0.1.0 dated 2019-11-28 and 0.2.0 dated 2021-07-28
fairadapt-0.1.0/fairadapt/R/Fair_Adaptation.R |only fairadapt-0.1.0/fairadapt/R/Input_Verification.R |only fairadapt-0.1.0/fairadapt/R/utility.R |only fairadapt-0.1.0/fairadapt/man/figures |only fairadapt-0.2.0/fairadapt/DESCRIPTION | 42 ++++-- fairadapt-0.2.0/fairadapt/MD5 | 111 ++++++++++++++++- fairadapt-0.2.0/fairadapt/NAMESPACE | 48 +++++++ fairadapt-0.2.0/fairadapt/NEWS.md |only fairadapt-0.2.0/fairadapt/R/checks.R |only fairadapt-0.2.0/fairadapt/R/data.R |only fairadapt-0.2.0/fairadapt/R/fairadapt.R |only fairadapt-0.2.0/fairadapt/R/generics.R |only fairadapt-0.2.0/fairadapt/R/graphs.R |only fairadapt-0.2.0/fairadapt/R/quants.R |only fairadapt-0.2.0/fairadapt/R/utils.R |only fairadapt-0.2.0/fairadapt/README.md | 101 ++++++++++------ fairadapt-0.2.0/fairadapt/build |only fairadapt-0.2.0/fairadapt/data |only fairadapt-0.2.0/fairadapt/inst |only fairadapt-0.2.0/fairadapt/man/adaptedData.Rd |only fairadapt-0.2.0/fairadapt/man/computeQuants.Rd |only fairadapt-0.2.0/fairadapt/man/fairTwins.Rd |only fairadapt-0.2.0/fairadapt/man/fairadapt.Rd | 142 +++++++++++++---------- fairadapt-0.2.0/fairadapt/man/gov_census.Rd |only fairadapt-0.2.0/fairadapt/man/graphModel.Rd |only fairadapt-0.2.0/fairadapt/man/linearQuants.Rd |only fairadapt-0.2.0/fairadapt/man/mcqrnnQuants.Rd |only fairadapt-0.2.0/fairadapt/man/rangerQuants.Rd |only fairadapt-0.2.0/fairadapt/man/uni_admission.Rd |only fairadapt-0.2.0/fairadapt/man/visualizeGraph.Rd |only fairadapt-0.2.0/fairadapt/tests |only fairadapt-0.2.0/fairadapt/vignettes |only 32 files changed, 325 insertions(+), 119 deletions(-)
Title: Co-Clustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The 'blockcluster' package provides a bridge between the C++
core library build on top of the 'STK++' library, and the R statistical
computing environment. This package allows to co-cluster binary
<doi:10.1016/j.csda.2007.09.007>, contingency <doi:10.1080/03610920903140197>,
continuous <doi:10.1007/s11634-013-0161-3> and categorical data-sets
<doi:10.1007/s11222-014-9472-2>. It also provides utility functions to
visualize the results. This package may be useful for various applications
in fields of Data mining, Information retrieval, Biology, computer vision
and many more. More information about the project and comprehensive tutorial
can be found on the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Josselin Demont [ctb],
Vincent Brault [ctb],
Vincent Kubicki [ctb],
Gerard Goavert [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 4.5.0 dated 2021-07-13 and 4.5.1 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 14 +++++------ inst/NEWS.Rd | 5 ++-- inst/doc/blockcluster_tutorial.pdf |binary src/coclust/src/Models/BinaryLBModelequalepsilon.cpp | 23 +++++++------------ src/coclust/src/Models/BinaryLBModelequalepsilon.h | 3 -- src/coclust/src/Models/CategoricalLBModel.cpp | 4 +-- src/coclust/src/Models/ContinuousLBModel.cpp | 13 +++++----- 8 files changed, 32 insertions(+), 38 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel+tergm@unsw.edu.au>
Diff between tergm versions 4.0.1 dated 2021-06-24 and 4.0.2 dated 2021-07-28
DESCRIPTION | 10 +-- MD5 | 63 ++++++++++++------------- R/InitErgmProposal.DynMoME.R | 11 +++- R/InitErgmTerm.netseries.R | 25 +++++---- R/control.stergm.R | 4 + R/simulate.tergm.R | 8 +-- R/stergm.R | 2 R/stergm.utils.R | 22 +++++--- R/tergm.EGMME.GD.R | 4 - R/tergm.EGMME.R | 4 - R/tergm.EGMME.SA.R | 8 +-- R/tergm.EGMME.initialfit.R | 24 ++++----- R/tergm.R | 2 R/tergm.getMCMCsample.R | 2 R/tergm.godfather.R | 2 build/partial.rdb |binary build/tergm.pdf |binary inst/CITATION | 4 - inst/NEWS.Rd | 25 +++++++++ man/control.stergm.Rd | 4 + man/stergm.Rd | 2 man/tergm.Rd | 2 src/changestats_duration.c | 9 +++ src/discordTNT.c | 13 ++--- tests/testthat/test-EGMME-initialfit.R | 14 ++--- tests/testthat/test-discord-proposals.R | 28 +++++------ tests/testthat/test-edgelist_with_lasttoggle.R |only tests/testthat/test-extract-formulae.R | 36 +++++++------- tests/testthat/test-simulate.R | 26 +++++----- tests/testthat/test-term-.SubsetStatistics.R | 18 +++---- tests/testthat/test-term-Change.R | 28 +++++------ tests/testthat/test-term-Cross.R | 50 +++++++++---------- tests/testthat/test-terms-Form-Persist-Diss.R | 48 +++++++++---------- 33 files changed, 280 insertions(+), 218 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.5 dated 2021-03-22 and 0.1.6 dated 2021-07-28
DESCRIPTION | 9 +-- MD5 | 31 +++++----- NAMESPACE | 1 NEWS.md | 11 +++ R/opq.R | 86 ++++++++++++++++++++++++++++-- R/osmdata-methods.R | 1 build/vignette.rds |binary inst/WORDLIST | 26 +++++++++ inst/doc/osm-sf-translation.html | 11 ++- inst/doc/osmdata-sc.html | 11 ++- inst/doc/osmdata.R | 50 +++-------------- inst/doc/osmdata.Rmd | 111 ++++++++++++++++----------------------- inst/doc/osmdata.html | 59 ++++++++------------ man/add_osm_features.Rd |only src/RcppExports.cpp | 5 + tests/testthat/test-osmdata.R | 1 vignettes/osmdata.Rmd | 111 ++++++++++++++++----------------------- 17 files changed, 291 insertions(+), 233 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, and to plot the curves and their underlying data, as well as functions to calibrate radiocarbon dates.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between IntCal versions 0.2.1 dated 2021-07-19 and 0.2.2 dated 2021-07-28
IntCal-0.2.1/IntCal/man/mix.curves.Rd |only IntCal-0.2.2/IntCal/DESCRIPTION | 8 IntCal-0.2.2/IntCal/MD5 | 46 ++-- IntCal-0.2.2/IntCal/NAMESPACE | 6 IntCal-0.2.2/IntCal/NEWS.md | 8 IntCal-0.2.2/IntCal/R/IntCal.R | 154 +++------------ IntCal-0.2.2/IntCal/R/calibrate.R | 243 +----------------------- IntCal-0.2.2/IntCal/R/plots.R |only IntCal-0.2.2/IntCal/build/partial.rdb |binary IntCal-0.2.2/IntCal/build/vignette.rds |binary IntCal-0.2.2/IntCal/inst/doc/calculations.R | 11 + IntCal-0.2.2/IntCal/inst/doc/calculations.Rmd | 21 ++ IntCal-0.2.2/IntCal/inst/doc/calculations.html | 240 +++++++++++++++++++++++- IntCal-0.2.2/IntCal/inst/doc/intro.R | 9 IntCal-0.2.2/IntCal/inst/doc/intro.Rmd | 23 +- IntCal-0.2.2/IntCal/inst/doc/intro.html | 244 +++++++++++++++++++++++-- IntCal-0.2.2/IntCal/inst/doc/plots.Rmd | 3 IntCal-0.2.2/IntCal/inst/doc/plots.html | 233 ++++++++++++++++++++++- IntCal-0.2.2/IntCal/man/calBP.14C.Rd |only IntCal-0.2.2/IntCal/man/calibrate.Rd | 19 + IntCal-0.2.2/IntCal/man/draw.ccurve.Rd | 2 IntCal-0.2.2/IntCal/man/draw.dates.Rd |only IntCal-0.2.2/IntCal/man/glue.ccurves.Rd |only IntCal-0.2.2/IntCal/man/mix.ccurves.Rd |only IntCal-0.2.2/IntCal/vignettes/calculations.Rmd | 21 ++ IntCal-0.2.2/IntCal/vignettes/intro.Rmd | 23 +- IntCal-0.2.2/IntCal/vignettes/plots.Rmd | 3 27 files changed, 884 insertions(+), 433 deletions(-)
Title: Fit Repeated Linear Regressions
Description: When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz//regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Author: Lijun Wang [aut, cre, cph]
Maintainer: Lijun Wang <szcfweiya@gmail.com>
Diff between fRLR versions 1.1 dated 2019-01-08 and 1.2 dated 2021-07-28
fRLR-1.1/fRLR/inst/doc/fRLR.Rnw |only fRLR-1.1/fRLR/inst/doc/fRLR.pdf |only fRLR-1.1/fRLR/man/frlr.Rd |only fRLR-1.1/fRLR/vignettes/fRLR.Rnw |only fRLR-1.2/fRLR/DESCRIPTION | 16 fRLR-1.2/fRLR/MD5 | 34 fRLR-1.2/fRLR/NAMESPACE | 9 fRLR-1.2/fRLR/R/RcppExports.R | 42 - fRLR-1.2/fRLR/R/package.R |only fRLR-1.2/fRLR/build/vignette.rds |binary fRLR-1.2/fRLR/configure | 1525 +++++++++++++++++++++++++++++++++++++- fRLR-1.2/fRLR/configure.ac | 12 fRLR-1.2/fRLR/inst/doc/fRLR.R | 48 - fRLR-1.2/fRLR/inst/doc/fRLR.Rmd |only fRLR-1.2/fRLR/inst/doc/fRLR.html |only fRLR-1.2/fRLR/man/frlr1.Rd | 40 fRLR-1.2/fRLR/man/frlr2.Rd | 52 - fRLR-1.2/fRLR/src/Makevars.in | 5 fRLR-1.2/fRLR/src/Makevars.win | 4 fRLR-1.2/fRLR/src/RcppExports.cpp | 19 fRLR-1.2/fRLR/src/frlr.cpp | 256 +----- fRLR-1.2/fRLR/vignettes/fRLR.Rmd |only 22 files changed, 1726 insertions(+), 336 deletions(-)
Title: Find Pattern in Files of All Branches of a 'git' Repository
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given 'git' repository, including all its branches. The results can also be returned in a dataframe.
Author: Stéphane Laurent [aut, cre],
Rob Burns [cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between findInGit versions 0.1.0 dated 2021-07-27 and 0.1.1 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/findInGit.R | 14 ++++++++++++-- R/grepInGit.R | 26 ++++++++++++++++++-------- man/findInGit-shiny.Rd | 5 +++++ man/findInGit.Rd | 5 +++++ 7 files changed, 54 insertions(+), 19 deletions(-)
Title: Partially Observed Integrated Functional Depth
Description: Integrated Depths for Partially Observed Functional Data (PoFD). Applications to visualization, outlier detection and classification. Software companion for Elías, Antonio, Jiménez, Raúl, Paganoni, Anna M. and Sangalli, Laura M., (2020), "Integrated Depth for Partially Observed Functional Data".
Author: Antonio Elías [aut, cre],
Raúl Jiménez [ctb],
Anna M. Paganoni [ctb],
Laura M. Sangalli [ctb]
Maintainer: Antonio Elías <antonioefz91@gmail.com>
Diff between fdaPOIFD versions 1.0.0 dated 2021-01-13 and 1.0.1 dated 2021-07-28
DESCRIPTION | 8 +++++--- MD5 | 13 +++++++++---- NEWS.md | 3 +++ R/gaussianPoFD.R | 27 ++++++++++++++++++++++++--- build |only inst |only man/gaussian_PoFD.Rd | 5 ++++- vignettes |only 8 files changed, 45 insertions(+), 11 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-7 dated 2021-05-23 and 1.7-8 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/gknn.R | 16 +++++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary man/gknn.Rd | 2 +- 9 files changed, 28 insertions(+), 20 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Unverified black box model is the path to the failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack of direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Szymon Maksymiuk [aut] (<https://orcid.org/0000-0002-3120-1601>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.2.1 dated 2021-06-01 and 2.3.0 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 1 + R/misc_loss_functions.R | 16 ++++++---------- R/model_performance.R | 10 ++++------ R/plot_list.R |only R/plot_model_performance.R | 9 +++++---- man/plot.list.Rd |only 8 files changed, 26 insertions(+), 28 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-210X.13270>,
Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>,
Fleming et al (2020) <doi:10.1101/2020.06.12.130195>,
and
Noonan et al (2021) <doi:10.1111/2041-210X.13597>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc],
Autumn-Lynn Harrison [dtc],
Ronaldo G. Morato [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.6.0 dated 2021-01-10 and 0.6.1 dated 2021-07-28
DESCRIPTION | 13 MD5 | 153 +++++------ NAMESPACE | 6 NEWS.md | 141 ++++++---- R/1.R | 12 R/QP.R | 2 R/acf.R | 2 R/animate.R |only R/circle.R |only R/cluster.R | 615 +++++++++++++++++++++++++++++----------------- R/covm.R | 10 R/ctmm.R | 30 +- R/ctpm.R |only R/export.R | 19 + R/extent.R | 43 ++- R/fit.R | 247 ++++++++++++------ R/kalman.R | 21 + R/kde.R | 1 R/krige.R | 200 ++++++++++---- R/likelihood.R | 242 +++++++++++------- R/matrix.R | 8 R/mean.R | 7 R/meta.chisq.R | 74 ++--- R/optim.R | 37 +- R/outlier.R | 16 - R/overlap.R | 4 R/parameters.R | 251 +++++++++++++----- R/plot.telemetry.R | 82 +++--- R/plot.variogram.R | 189 +++++++++----- R/projection.R | 2 R/rsf.R | 214 +++++++++++++++- R/select.R | 60 +++- R/speed.R | 18 - R/stats.R | 96 +++++-- R/str.R | 7 R/summary.ctmm.R | 20 - R/telemetry.R | 237 +++++++++++++++-- R/uere.R | 416 +++++++++++++++++++++---------- R/units.R | 217 ++++++++++------ R/variogram.R | 169 +++++++----- R/variogram.fit.R | 124 +++++---- TODO | 12 build/partial.rdb |binary build/vignette.rds |binary data/buffalo.rda |binary data/coati.rda |binary data/gazelle.rda |binary data/jaguar.rda |binary data/pelican.rda |binary data/turtle.rda |binary data/wolf.rda |binary inst/doc/akde.html | 68 +---- inst/doc/error.R | 25 + inst/doc/error.Rmd | 34 +- inst/doc/error.html | 162 ++++++------ inst/doc/periodogram.Rmd | 4 inst/doc/periodogram.html | 176 +++++-------- inst/doc/variogram.html | 220 +++++++--------- man/as.telemetry.Rd | 22 + man/cluster.Rd |only man/ctmm-FAQ.Rd | 2 man/ctmm-package.Rd | 4 man/ctmm.boot.Rd | 30 +- man/ctmm.fit.Rd | 4 man/encounter.Rd | 4 man/export.Rd | 38 +- man/meta.Rd | 7 man/outlie.Rd | 7 man/pelican.Rd | 2 man/plot.variogram.Rd | 2 man/residuals.Rd | 4 man/simulate.ctmm.Rd | 11 man/summary.UD.Rd | 3 man/summary.ctmm.Rd | 8 man/uere.Rd | 4 man/variogram.Rd | 10 man/variogram.fit.Rd | 5 man/video.Rd |only vignettes/error.Rmd | 34 +- vignettes/periodogram.Rmd | 4 80 files changed, 3186 insertions(+), 1725 deletions(-)
Title: Simulate and Estimate Close-Kin Dispersal Kernels
Description: Functions for simulating and estimating kinship-related dispersal. Based
on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A.
Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship
reveals limited intergenerational dispersal in the yellow fever mosquito".
Assumes an additive variance model of dispersal in two dimensions, compatible with
Wright's neighbourhood area. Simple and composite dispersal simulations are supplied,
as well as the functions needed to estimate parent-offspring dispersal for simulated or
empirical data, and to undertake sampling design for future field studies of dispersal.
For ease of use an integrated Shiny app is also included.
Author: Moshe-Elijah Jasper [aut, cre]
(<https://orcid.org/0000-0003-4541-3223>)
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>
Diff between kindisperse versions 0.10.1 dated 2021-07-17 and 0.10.2 dated 2021-07-28
DESCRIPTION | 6 MD5 | 27 - NAMESPACE | 3 R/app.R | 8 R/kindisperse-package.R | 1 README.md | 577 +++++++++++++------------- build/partial.rdb |binary inst/doc/using-kindisperse.R | 2 inst/doc/using-kindisperse.Rmd | 149 +++--- inst/doc/using-kindisperse.html | 441 +++++++++++-------- man/figures/README-graphical_simulation-1.png |binary man/figures/README-simgraphhist-1.png |binary man/figures/README-simgraphpin-1.png |binary vignettes/KDPackageRefs.bibtex |only vignettes/using-kindisperse.Rmd | 149 +++--- 15 files changed, 728 insertions(+), 635 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-19 1.0.0
Title: Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Also offers fuzzy text search based on various string
distance measures. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. This package is built for speed and
runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>),
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb],
Johannes Gruber [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.6.3 dated 2020-10-09 and 0.9.7 dated 2021-07-28
DESCRIPTION | 7 +++---- MD5 | 22 ++++++++++++---------- NEWS | 12 ++++++++++++ R/stringsim.R | 4 ++-- R/utils.R | 2 +- build/vignette.rds |binary inst/doc/RJournal_6_111-122-2014.pdf |binary inst/doc/stringdist_C-Cpp_api.pdf |binary inst/tinytest/test_gh_issue_78.R |only inst/tinytest/test_gh_issue_88.R |only inst/tinytest/test_stringsim.R | 2 +- src/Rstringdist.c | 17 ++++++----------- src/utils.c | 15 ++++++++++++--- 13 files changed, 49 insertions(+), 32 deletions(-)
Title: Circular, Periodic, or Framed Data Clustering: Fast, Optimal,
and Reproducible
Description: Fast, optimal, and reproducible clustering algorithms for
circular, periodic, or framed data. The algorithms introduced here
are based on a core algorithm for optimal framed clustering the authors
have developed (Debnath & Song 2021) <doi:10.1109/TCBB.2021.3077573>.
The runtime of these algorithms is O(K N log^2 N), where K is the number
of clusters and N is the number of circular data points. On a desktop
computer using a single processor core, millions of data points can be
grouped into a few clusters within seconds. One can apply the algorithms
to characterize events along circular DNA molecules, circular RNA
molecules, and circular genomes of bacteria, chloroplast, and
mitochondria. One can also cluster climate data along any given
longitude or latitude. Periodic data clustering can be formulated as
circular clustering. The algorithms offer a general high-performance
solution to circular, periodic, or framed data clustering.
Author: Tathagata Debnath [aut] (<https://orcid.org/0000-0001-6445-275X>),
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between OptCirClust versions 0.0.3 dated 2020-12-18 and 0.0.4 dated 2021-07-28
DESCRIPTION | 37 ++-- MD5 | 49 ++--- NAMESPACE | 1 NEWS.md | 11 + R/CirClust.R | 6 R/FramedClust.R | 9 - build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/REFERENCES.bib |only inst/doc/CircularGenomes.R | 5 inst/doc/CircularGenomes.Rmd | 12 - inst/doc/CircularGenomes.html | 267 +++--------------------------- inst/doc/Performance.R | 12 - inst/doc/Performance.Rmd | 20 +- inst/doc/Performance.html | 271 +++--------------------------- inst/doc/Tutorial_CirClust.Rmd | 8 inst/doc/Tutorial_CirClust.html | 328 +++++++------------------------------ inst/doc/Tutorial_FramedClust.Rmd | 8 inst/doc/Tutorial_FramedClust.html | 320 ++++++------------------------------ man/CirClust.Rd | 7 man/FramedClust.Rd | 6 src/RcppExports.cpp | 5 vignettes/CircularGenomes.Rmd | 12 - vignettes/Performance.Rmd | 20 +- vignettes/Tutorial_CirClust.Rmd | 8 vignettes/Tutorial_FramedClust.Rmd | 8 27 files changed, 345 insertions(+), 1085 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 1.0-4 dated 2021-06-03 and 1.0-5 dated 2021-07-28
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Pulling Clean Data from Covid19india.org
Description: Pull raw and pre-cleaned versions of national and state-level
COVID-19 time-series data from covid19india.org <https://www.covid19india.org>.
Easily obtain and merge case count data, testing data, and vaccine data.
Also assists in calculating the time-varying effective reproduction number
with sensible parameters for COVID-19.
Author: Max Salvatore [aut, cre],
Michael Kleinsasser [aut]
Maintainer: Max Salvatore <mmsalva@umich.edu>
Diff between covid19india versions 0.1.2 dated 2021-07-21 and 0.1.3 dated 2021-07-28
DESCRIPTION | 17 ++++++------ MD5 | 38 ++++++++++++++------------- NAMESPACE | 7 +++-- R/check_for_data_correction.R |only R/extract_latest.R | 5 ++- R/get_all_data.R | 6 ++-- R/get_cfr.R | 6 ++-- R/get_metrics_tables.R | 34 +++++++++++++------------ R/get_nat_counts.R | 21 +++++++++++++-- R/get_nat_tests.R | 4 +- R/get_r0.R | 53 +++++++++++++++++++++++++++++++-------- R/get_state_counts.R | 27 +++++++++++++++++-- R/get_state_tests.R | 5 ++- R/get_state_vax.R | 4 -- README.md | 15 ++++++++--- man/check_for_data_correction.Rd |only man/get_all_data.Rd | 4 ++ man/get_metrics_tables.Rd | 4 ++ man/get_nat_counts.Rd | 7 +++-- man/get_r0.Rd | 5 ++- man/get_state_counts.Rd | 5 ++- 21 files changed, 184 insertions(+), 83 deletions(-)
Title: Download Data from the Wittgenstein Human Capital Data Explorer
Description: Download and plot education specific demographic data from the Wittgenstein Human Capital Data Explorer <http://dataexplorer.wittgensteincentre.org/>.
Author: Guy J. Abel [aut, cre, ctb] (<https://orcid.org/0000-0002-4893-5687>),
Samir K.C. [ctb] (<https://orcid.org/0000-0002-5213-9181>),
Michaela Potancokova [ctb],
Claudia Reiter [ctb] (<https://orcid.org/0000-0002-1485-3851>),
Andrea Tamburini [ctb],
Dilek Yildiz [ctb] (<https://orcid.org/0000-0001-6192-0634>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between wcde versions 0.0.1 dated 2021-06-23 and 0.0.2 dated 2021-07-28
wcde-0.0.1/wcde/R/epop_ssp2.R |only wcde-0.0.1/wcde/data/epop_ssp2.rda |only wcde-0.0.1/wcde/man/epop_ssp2.Rd |only wcde-0.0.2/wcde/DESCRIPTION | 42 +++++---- wcde-0.0.2/wcde/MD5 | 47 +++++----- wcde-0.0.2/wcde/NAMESPACE | 1 wcde-0.0.2/wcde/NEWS.md | 8 + wcde-0.0.2/wcde/R/edu_group_sum.R | 4 wcde-0.0.2/wcde/R/find_indicators.R | 3 wcde-0.0.2/wcde/R/get_wcde.R | 10 +- wcde-0.0.2/wcde/R/past_epop.R |only wcde-0.0.2/wcde/R/wcde_pull.R | 11 -- wcde-0.0.2/wcde/R/wic_indicators.R | 2 wcde-0.0.2/wcde/R/wic_scenarios.R | 2 wcde-0.0.2/wcde/data/past_epop.rda |only wcde-0.0.2/wcde/data/wic_scenarios.rda |binary wcde-0.0.2/wcde/inst/doc/intro.R | 73 +++++++++++++--- wcde-0.0.2/wcde/inst/doc/intro.Rmd | 94 +++++++++++++++++--- wcde-0.0.2/wcde/inst/doc/intro.html | 127 +++++++++++++++++----------- wcde-0.0.2/wcde/man/edu_group_sum.Rd | 4 wcde-0.0.2/wcde/man/figures/world4_ssp2.gif |only wcde-0.0.2/wcde/man/find_indicator.Rd | 2 wcde-0.0.2/wcde/man/get_wcde.Rd | 8 - wcde-0.0.2/wcde/man/past_epop.Rd |only wcde-0.0.2/wcde/man/wcde_pull.Rd | 4 wcde-0.0.2/wcde/man/wic_indicators.Rd | 2 wcde-0.0.2/wcde/man/wic_scenarios.Rd | 2 wcde-0.0.2/wcde/vignettes/intro.Rmd | 94 +++++++++++++++++--- 28 files changed, 375 insertions(+), 165 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between covid19italy versions 0.3.0 dated 2020-07-21 and 0.3.1 dated 2021-07-28
covid19italy-0.3.0/covid19italy/man/figures/README-pressure-1.png |only covid19italy-0.3.0/covid19italy/man/figures/case_dist.png |only covid19italy-0.3.0/covid19italy/man/figures/positive_dist.png |only covid19italy-0.3.0/covid19italy/man/figures/province_pie.png |only covid19italy-0.3.0/covid19italy/man/figures/region_bar_plot.png |only covid19italy-0.3.1/covid19italy/DESCRIPTION | 14 covid19italy-0.3.1/covid19italy/MD5 | 46 - covid19italy-0.3.1/covid19italy/NEWS.md | 9 covid19italy-0.3.1/covid19italy/R/data.R | 49 - covid19italy-0.3.1/covid19italy/R/data_refresh.R | 21 covid19italy-0.3.1/covid19italy/README.md | 44 - covid19italy-0.3.1/covid19italy/build/vignette.rds |binary covid19italy-0.3.1/covid19italy/data/italy_province.rda |binary covid19italy-0.3.1/covid19italy/data/italy_region.rda |binary covid19italy-0.3.1/covid19italy/data/italy_total.rda |binary covid19italy-0.3.1/covid19italy/inst/doc/dashboard.Rmd |only covid19italy-0.3.1/covid19italy/inst/doc/dashboard.html |only covid19italy-0.3.1/covid19italy/inst/doc/intro.Rmd | 2 covid19italy-0.3.1/covid19italy/inst/doc/intro.html | 425 ++++++---- covid19italy-0.3.1/covid19italy/man/figures/Italy_province.png |binary covid19italy-0.3.1/covid19italy/man/figures/case_dist.svg |only covid19italy-0.3.1/covid19italy/man/figures/positive_dist.svg |only covid19italy-0.3.1/covid19italy/man/figures/province_pie.svg |only covid19italy-0.3.1/covid19italy/man/figures/region_bar_plot.svg |only covid19italy-0.3.1/covid19italy/man/italy_province.Rd | 18 covid19italy-0.3.1/covid19italy/man/italy_region.Rd | 16 covid19italy-0.3.1/covid19italy/man/italy_total.Rd | 14 covid19italy-0.3.1/covid19italy/tests/testthat/test_data_valid.R | 12 covid19italy-0.3.1/covid19italy/vignettes/dashboard.Rmd |only covid19italy-0.3.1/covid19italy/vignettes/intro.Rmd | 2 30 files changed, 421 insertions(+), 251 deletions(-)
Title: Missing Item Responses Imputation for Test and Assessment Data
Description: Functions for imputing missing item responses for dichotomous and
polytomous test and assessment data. This package enables missing imputation
methods that are suitable for test and assessment data, including:
listwise (LW) deletion (see De Ayala et al. 2001 <doi:10.1111/j.1745-3984.2001.tb01124.x>),
treating as incorrect (IN, see Lord, 1974 <doi: 10.1111/j.1745-3984.1974.tb00996.x>;
Mislevy & Wu, 1996 <doi: 10.1002/j.2333-8504.1996.tb01708.x>;
Pohl et al., 2014 <doi: 10.1177/0013164413504926>), person mean imputation (PM),
item mean imputation (IM), two-way (TW) and response function (RF) imputation
(see Sijtsma & van der Ark, 2003 <doi: 10.1207/s15327906mbr3804_4>),
logistic regression (LR) imputation, and expectation–maximization (EM)
imputation (see Finch, 2008 <doi: 10.1111/j.1745-3984.2008.00062.x>).
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Diff between TestDataImputation versions 1.2 dated 2020-11-16 and 2.1 dated 2021-07-28
TestDataImputation-1.2/TestDataImputation/man/LogsticReg.Rd |only TestDataImputation-2.1/TestDataImputation/DESCRIPTION | 17 TestDataImputation-2.1/TestDataImputation/MD5 | 38 +- TestDataImputation-2.1/TestDataImputation/NAMESPACE | 29 - TestDataImputation-2.1/TestDataImputation/R/EMimpute.r | 7 TestDataImputation-2.1/TestDataImputation/R/ImputeTestData.r | 81 +++- TestDataImputation-2.1/TestDataImputation/R/ItemMean.r | 2 TestDataImputation-2.1/TestDataImputation/R/Listwise.r | 2 TestDataImputation-2.1/TestDataImputation/R/LogisticReg.r | 7 TestDataImputation-2.1/TestDataImputation/R/PersonMean.r | 2 TestDataImputation-2.1/TestDataImputation/R/ResponseFun.r |only TestDataImputation-2.1/TestDataImputation/R/TreatIncorrect.r | 9 TestDataImputation-2.1/TestDataImputation/R/TwoWay.r | 5 TestDataImputation-2.1/TestDataImputation/man/EMimpute.Rd | 74 ++-- TestDataImputation-2.1/TestDataImputation/man/ImputeTestData.Rd | 171 +++++----- TestDataImputation-2.1/TestDataImputation/man/ItemMean.Rd | 58 +-- TestDataImputation-2.1/TestDataImputation/man/Listwise.Rd | 64 +-- TestDataImputation-2.1/TestDataImputation/man/LogisticReg.Rd |only TestDataImputation-2.1/TestDataImputation/man/PersonMean.Rd | 76 ++-- TestDataImputation-2.1/TestDataImputation/man/ResponseFun.Rd |only TestDataImputation-2.1/TestDataImputation/man/TreatIncorrect.Rd | 88 ++--- TestDataImputation-2.1/TestDataImputation/man/Twoway.Rd | 79 ++-- 22 files changed, 437 insertions(+), 372 deletions(-)
More information about TestDataImputation at CRAN
Permanent link
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.9.9 dated 2021-03-19 and 1.0.0 dated 2021-07-28
summarytools-0.9.9/summarytools/inst/doc/Introduction.R |only summarytools-0.9.9/summarytools/inst/doc/Introduction.Rmd |only summarytools-0.9.9/summarytools/inst/doc/Introduction.html |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.R |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.Rmd |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.html |only summarytools-0.9.9/summarytools/vignettes/Introduction.Rmd |only summarytools-0.9.9/summarytools/vignettes/Recommendations-rmarkdown.Rmd |only summarytools-0.9.9/summarytools/vignettes/define_keywords.png |only summarytools-0.9.9/summarytools/vignettes/dfSummary_in_RStudio_Viewer.png |only summarytools-0.9.9/summarytools/vignettes/dfSummary_md.png |only summarytools-1.0.0/summarytools/DESCRIPTION | 10 summarytools-1.0.0/summarytools/MD5 | 105 +- summarytools-1.0.0/summarytools/NAMESPACE | 3 summarytools-1.0.0/summarytools/NEWS.md | 61 + summarytools-1.0.0/summarytools/R/args_validation.R | 58 - summarytools-1.0.0/summarytools/R/cleartmp.R | 19 summarytools-1.0.0/summarytools/R/ctable.R | 128 +- summarytools-1.0.0/summarytools/R/define_keywords.R | 181 ++-- summarytools-1.0.0/summarytools/R/descr.R | 93 +- summarytools-1.0.0/summarytools/R/dfSummary.R | 325 ++++--- summarytools-1.0.0/summarytools/R/freq.R | 36 summarytools-1.0.0/summarytools/R/helpers.R | 40 summarytools-1.0.0/summarytools/R/label.R | 8 summarytools-1.0.0/summarytools/R/print.list.R | 2 summarytools-1.0.0/summarytools/R/print.stby.R | 34 summarytools-1.0.0/summarytools/R/print.summarytools.R | 444 ++++++---- summarytools-1.0.0/summarytools/R/st_css.R | 13 summarytools-1.0.0/summarytools/R/st_options.R | 164 +++ summarytools-1.0.0/summarytools/R/stby.R | 4 summarytools-1.0.0/summarytools/R/summarytools.R | 29 summarytools-1.0.0/summarytools/R/tabagisme.R | 2 summarytools-1.0.0/summarytools/R/use_custom_lang.R | 37 summarytools-1.0.0/summarytools/R/view.R | 19 summarytools-1.0.0/summarytools/R/zzz.R | 31 summarytools-1.0.0/summarytools/build/vignette.rds |binary summarytools-1.0.0/summarytools/inst/doc/introduction.R |only summarytools-1.0.0/summarytools/inst/doc/introduction.Rmd |only summarytools-1.0.0/summarytools/inst/doc/introduction.html |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.R |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.Rmd |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.html |only summarytools-1.0.0/summarytools/inst/includes/fig-valign.tex |only summarytools-1.0.0/summarytools/inst/includes/stylesheets/summarytools.css | 2 summarytools-1.0.0/summarytools/man/cleartmp.Rd | 7 summarytools-1.0.0/summarytools/man/ctable.Rd | 128 +- summarytools-1.0.0/summarytools/man/define_keywords.Rd | 38 summarytools-1.0.0/summarytools/man/descr.Rd | 89 +- summarytools-1.0.0/summarytools/man/dfSummary.Rd | 129 +- summarytools-1.0.0/summarytools/man/format_number.Rd |only summarytools-1.0.0/summarytools/man/freq.Rd | 29 summarytools-1.0.0/summarytools/man/print.list.Rd | 93 +- summarytools-1.0.0/summarytools/man/print.stby.Rd | 93 +- summarytools-1.0.0/summarytools/man/print.summarytools.Rd | 173 ++- summarytools-1.0.0/summarytools/man/st_css.Rd | 14 summarytools-1.0.0/summarytools/man/st_options.Rd | 85 + summarytools-1.0.0/summarytools/man/summarytools-package.Rd | 29 summarytools-1.0.0/summarytools/man/tabagisme.Rd | 2 summarytools-1.0.0/summarytools/man/view.Rd | 122 +- summarytools-1.0.0/summarytools/vignettes/assets |only summarytools-1.0.0/summarytools/vignettes/introduction.Rmd |only summarytools-1.0.0/summarytools/vignettes/rmarkdown.Rmd |only 62 files changed, 1785 insertions(+), 1094 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.2 dated 2021-04-30 and 2.0.3 dated 2021-07-28
BiDAG-2.0.2/BiDAG/data/Asiamatrix.rda |only BiDAG-2.0.2/BiDAG/data/gsimmatrix.rda |only BiDAG-2.0.2/BiDAG/man/plotdiffs.DBN.Rd |only BiDAG-2.0.3/BiDAG/DESCRIPTION | 13 - BiDAG-2.0.3/BiDAG/MD5 | 77 ++++--- BiDAG-2.0.3/BiDAG/NAMESPACE | 6 BiDAG-2.0.3/BiDAG/R/DBNdata.R | 1 BiDAG-2.0.3/BiDAG/R/DBNfns.R | 81 ++++---- BiDAG-2.0.3/BiDAG/R/RcppExports.R | 8 BiDAG-2.0.3/BiDAG/R/corescore.R | 4 BiDAG-2.0.3/BiDAG/R/extractors.R |only BiDAG-2.0.3/BiDAG/R/graphhelpfns.R | 12 - BiDAG-2.0.3/BiDAG/R/initpar.R | 17 + BiDAG-2.0.3/BiDAG/R/main.R | 8 BiDAG-2.0.3/BiDAG/R/performanceassess.R | 28 +- BiDAG-2.0.3/BiDAG/R/plotS3.R | 24 +- BiDAG-2.0.3/BiDAG/R/plotfns.R | 22 +- BiDAG-2.0.3/BiDAG/R/plotusingrgraphviz.R | 274 +++++++++++++++++----------- BiDAG-2.0.3/BiDAG/R/printmethods.R | 72 +++---- BiDAG-2.0.3/BiDAG/R/scoreagainstdag.R | 32 ++- BiDAG-2.0.3/BiDAG/R/summary.R | 4 BiDAG-2.0.3/BiDAG/data/Asiamat.rda |only BiDAG-2.0.3/BiDAG/data/gsimmat.rda |only BiDAG-2.0.3/BiDAG/man/DBNdata.Rd | 7 BiDAG-2.0.3/BiDAG/man/compact2full.Rd | 12 - BiDAG-2.0.3/BiDAG/man/compareDBNs.Rd | 10 - BiDAG-2.0.3/BiDAG/man/full2compact.Rd | 10 - BiDAG-2.0.3/BiDAG/man/getDAG.Rd |only BiDAG-2.0.3/BiDAG/man/getMCMCscore.Rd |only BiDAG-2.0.3/BiDAG/man/getSpace.Rd |only BiDAG-2.0.3/BiDAG/man/getTrace.Rd |only BiDAG-2.0.3/BiDAG/man/iterativeMCMC.Rd | 5 BiDAG-2.0.3/BiDAG/man/iterativeMCMCclass.Rd | 4 BiDAG-2.0.3/BiDAG/man/kirc.Rd | 2 BiDAG-2.0.3/BiDAG/man/kirp.Rd | 2 BiDAG-2.0.3/BiDAG/man/orderMCMC.Rd | 5 BiDAG-2.0.3/BiDAG/man/partitionMCMC.Rd | 3 BiDAG-2.0.3/BiDAG/man/plotDBN.Rd | 10 - BiDAG-2.0.3/BiDAG/man/plotdiffsDBN.Rd |only BiDAG-2.0.3/BiDAG/man/plotpcor.Rd | 6 BiDAG-2.0.3/BiDAG/man/plotpedges.Rd | 4 BiDAG-2.0.3/BiDAG/man/scoreagainstDAG.Rd | 12 + BiDAG-2.0.3/BiDAG/man/scoreparameters.Rd | 6 BiDAG-2.0.3/BiDAG/src/RcppExports.cpp | 33 +-- BiDAG-2.0.3/BiDAG/src/cppfns.cpp | 20 +- 45 files changed, 480 insertions(+), 354 deletions(-)