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 1.0.0 dated 2023-10-03 and 1.0.1 dated 2023-10-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/currencies.R | 7 ++++++- 3 files changed, 11 insertions(+), 6 deletions(-)
Title: US Maps Including Alaska and Hawaii
Description: Obtain United States map data frames of varying region types (e.g. county,
state). The map data frames include Alaska and Hawaii conveniently placed to the
bottom left, as they appear in most maps of the US. Convenience functions for plotting
choropleths and working with FIPS codes are also provided.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <dilorenzo@hey.com>
Diff between usmap versions 0.6.2 dated 2023-06-13 and 0.6.3 dated 2023-10-21
DESCRIPTION | 12 +++---- MD5 | 26 ++++++++-------- NEWS.md | 5 +++ R/fips.R | 4 +- R/join-data.R | 6 +-- R/plot-map.R | 37 ++++++++++++---------- R/transform.R | 20 +++--------- R/usmap.R | 8 ---- inst/doc/advanced-mapping.html | 4 +- inst/doc/introduction.html | 4 +- inst/doc/mapping.html | 4 +- man/plot_usmap.Rd | 2 - man/usmap.Rd | 3 - tests/testthat/test-plot.R | 66 ++++++++++++++++++++--------------------- 14 files changed, 97 insertions(+), 104 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.1-6 dated 2023-09-09 and 3.2-1 dated 2023-10-21
DESCRIPTION | 53 ++++---- MD5 | 40 +++--- NAMESPACE | 6 NEWS | 34 +++++ R/clusterinfo.R | 241 ++++++++++++++++++---------------------- R/pkgRandomFields.R | 51 +------- R/rLGCP.R | 133 +++++++++++----------- R/random.R | 10 - R/randomcircembed.R |only R/randomfields.R |only R/randomtess.R | 21 ++- inst/doc/packagesizes.txt | 3 man/as.owin.rmhmodel.Rd | 13 -- man/macros/defns.Rd | 5 man/rLGCP.Rd | 111 +++++++++++++----- man/rMosaicField.Rd | 19 ++- man/rMosaicSet.Rd | 14 +- man/rclusterBKBC.Rd | 8 - man/rpoislinetess.Rd | 1 man/rpoispp3.Rd | 1 man/runifpoint3.Rd | 1 man/spatstat.random-internal.Rd | 12 + 22 files changed, 432 insertions(+), 345 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Several Examined and Concealed States-Dependent Speciation and
Extinction
Description: Simultaneously infers state-dependent diversification across
two or more states of a single or multiple traits while accounting for the
role of a possible concealed trait. See Herrera-Alsina et al. (2019)
<doi:10.1093/sysbio/syy057>.
Author: Leonel Herrera Alsina [aut] ,
Paul van Els [aut] ,
Thijs Janzen [ctb] ,
Hanno Hildenbrandt [ctb] ,
Pedro Santos Neves [ctb] ,
Rampal S. Etienne [cre, aut]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between secsse versions 2.6.0 dated 2023-07-06 and 3.0.2 dated 2023-10-21
secsse-2.6.0/secsse/R/cla_secsse_eval.R |only secsse-2.6.0/secsse/R/cla_secsse_loglik.R |only secsse-2.6.0/secsse/R/cla_secsse_ml.R |only secsse-2.6.0/secsse/R/cla_secsse_ml_func_def_pars.R |only secsse-2.6.0/secsse/R/data.R |only secsse-2.6.0/secsse/R/event_times.R |only secsse-2.6.0/secsse/R/plot_state_exact.R |only secsse-2.6.0/secsse/R/plot_state_exact_cla.R |only secsse-2.6.0/secsse/R/print_init_ll.R |only secsse-2.6.0/secsse/R/secsse_loglik_eval.R |only secsse-2.6.0/secsse/data/example_phy_GeoSSE.RData |only secsse-2.6.0/secsse/data/phylo_Vign.RData |only secsse-2.6.0/secsse/data/traitinfo.RData |only secsse-2.6.0/secsse/inst/doc/Using_secsse.R |only secsse-2.6.0/secsse/inst/doc/Using_secsse.Rmd |only secsse-2.6.0/secsse/inst/doc/Using_secsse.html |only secsse-2.6.0/secsse/inst/doc/setting_up_secsse.R |only secsse-2.6.0/secsse/inst/doc/setting_up_secsse.Rmd |only secsse-2.6.0/secsse/inst/doc/setting_up_secsse.html |only secsse-2.6.0/secsse/man/cla_secsse_eval.Rd |only secsse-2.6.0/secsse/man/create_default_lambda_list.Rd |only secsse-2.6.0/secsse/man/create_default_q_list.Rd |only secsse-2.6.0/secsse/man/create_lambda_matrices.Rd |only secsse-2.6.0/secsse/man/create_mus.Rd |only secsse-2.6.0/secsse/man/create_transition_matrix.Rd |only secsse-2.6.0/secsse/man/phylo_Vign.Rd |only secsse-2.6.0/secsse/man/plot_state_exact_cla.Rd |only secsse-2.6.0/secsse/man/traitinfo.Rd |only secsse-2.6.0/secsse/src/cla_loglik.cpp |only secsse-2.6.0/secsse/src/cla_loglik_threaded.cpp |only secsse-2.6.0/secsse/src/cla_secsse_store.cpp |only secsse-2.6.0/secsse/src/rhs.h |only secsse-2.6.0/secsse/src/secsse_loglik_store.cpp |only secsse-2.6.0/secsse/src/threaded_ll.h |only secsse-2.6.0/secsse/src/util.cpp |only secsse-2.6.0/secsse/src/util.h |only secsse-2.6.0/secsse/vignettes/Using_secsse.Rmd |only secsse-2.6.0/secsse/vignettes/setting_up_secsse.Rmd |only secsse-3.0.2/secsse/DESCRIPTION | 15 secsse-3.0.2/secsse/LICENSE.note | 14 secsse-3.0.2/secsse/MD5 | 181 - secsse-3.0.2/secsse/NAMESPACE | 13 secsse-3.0.2/secsse/NEWS.md |only secsse-3.0.2/secsse/R/RcppExports.R | 33 secsse-3.0.2/secsse/R/default_params_doc.R |only secsse-3.0.2/secsse/R/seccse_plot.R |only secsse-3.0.2/secsse/R/secsse_data.R |only secsse-3.0.2/secsse/R/secsse_loglik.R | 577 ++---- secsse-3.0.2/secsse/R/secsse_ml.R | 797 +++----- secsse-3.0.2/secsse/R/secsse_ml_func_def_pars.R | 404 +--- secsse-3.0.2/secsse/R/secsse_prep.R | 317 +-- secsse-3.0.2/secsse/R/secsse_sim.R | 135 - secsse-3.0.2/secsse/R/secsse_utils.R | 931 ++++++++-- secsse-3.0.2/secsse/build/partial.rdb |binary secsse-3.0.2/secsse/build/vignette.rds |binary secsse-3.0.2/secsse/data/example_phy_GeoSSE.rda |only secsse-3.0.2/secsse/data/phylo_vignette.rda |only secsse-3.0.2/secsse/data/traits.rda |only secsse-3.0.2/secsse/inst/CITATION |only secsse-3.0.2/secsse/inst/COPYRIGHTS | 15 secsse-3.0.2/secsse/inst/doc/complete_tree.R |only secsse-3.0.2/secsse/inst/doc/complete_tree.Rmd |only secsse-3.0.2/secsse/inst/doc/complete_tree.html |only secsse-3.0.2/secsse/inst/doc/plotting_states.R | 36 secsse-3.0.2/secsse/inst/doc/plotting_states.Rmd | 36 secsse-3.0.2/secsse/inst/doc/plotting_states.html | 174 - secsse-3.0.2/secsse/inst/doc/sim_with_secsse.R |only secsse-3.0.2/secsse/inst/doc/sim_with_secsse.Rmd |only secsse-3.0.2/secsse/inst/doc/sim_with_secsse.html |only secsse-3.0.2/secsse/inst/doc/starting_secsse.R |only secsse-3.0.2/secsse/inst/doc/starting_secsse.Rmd |only secsse-3.0.2/secsse/inst/doc/starting_secsse.html |only secsse-3.0.2/secsse/man/cla_id_paramPos.Rd | 16 secsse-3.0.2/secsse/man/cla_secsse_loglik.Rd | 69 secsse-3.0.2/secsse/man/cla_secsse_ml.Rd | 73 secsse-3.0.2/secsse/man/cla_secsse_ml_func_def_pars.Rd | 92 secsse-3.0.2/secsse/man/create_default_lambda_transition_matrix.Rd |only secsse-3.0.2/secsse/man/create_default_shift_matrix.Rd |only secsse-3.0.2/secsse/man/create_lambda_list.Rd |only secsse-3.0.2/secsse/man/create_mu_vector.Rd |only secsse-3.0.2/secsse/man/create_q_matrix.Rd |only secsse-3.0.2/secsse/man/default_params_doc.Rd |only secsse-3.0.2/secsse/man/event_times.Rd | 2 secsse-3.0.2/secsse/man/example_phy_GeoSSE.Rd | 5 secsse-3.0.2/secsse/man/expand_q_matrix.Rd | 23 secsse-3.0.2/secsse/man/extract_par_vals.Rd | 23 secsse-3.0.2/secsse/man/figures |only secsse-3.0.2/secsse/man/fill_in.Rd | 16 secsse-3.0.2/secsse/man/id_paramPos.Rd | 16 secsse-3.0.2/secsse/man/phylo_vignette.Rd |only secsse-3.0.2/secsse/man/plot_state_exact.Rd | 108 - secsse-3.0.2/secsse/man/prepare_full_lambdas.Rd | 11 secsse-3.0.2/secsse/man/q_doubletrans.Rd | 25 secsse-3.0.2/secsse/man/secsse-package.Rd | 1 secsse-3.0.2/secsse/man/secsse_loglik.Rd | 63 secsse-3.0.2/secsse/man/secsse_loglik_eval.Rd | 99 - secsse-3.0.2/secsse/man/secsse_ml.Rd | 75 secsse-3.0.2/secsse/man/secsse_ml_func_def_pars.Rd | 83 secsse-3.0.2/secsse/man/secsse_sim.Rd | 54 secsse-3.0.2/secsse/man/sortingtraits.Rd | 19 secsse-3.0.2/secsse/man/traits.Rd |only secsse-3.0.2/secsse/src/RcppExports.cpp | 160 - secsse-3.0.2/secsse/src/config.h | 15 secsse-3.0.2/secsse/src/odeint.h | 127 - secsse-3.0.2/secsse/src/secsse_eval.cpp |only secsse-3.0.2/secsse/src/secsse_loglik.cpp | 472 +---- secsse-3.0.2/secsse/src/secsse_loglik.h |only secsse-3.0.2/secsse/src/secsse_rhs.h |only secsse-3.0.2/secsse/src/secsse_sim.cpp | 135 + secsse-3.0.2/secsse/src/secsse_sim.h | 353 +-- secsse-3.0.2/secsse/tests/testthat/test_cla_secsse_ml.R | 46 secsse-3.0.2/secsse/tests/testthat/test_cla_secsse_ml_func_def_pars.R |only secsse-3.0.2/secsse/tests/testthat/test_geosse.R | 78 secsse-3.0.2/secsse/tests/testthat/test_hisse.R | 5 secsse-3.0.2/secsse/tests/testthat/test_integration_methods.R |only secsse-3.0.2/secsse/tests/testthat/test_lambda_setup.R | 148 - secsse-3.0.2/secsse/tests/testthat/test_ml_func_def_pars.R | 22 secsse-3.0.2/secsse/tests/testthat/test_ml_par.R | 4 secsse-3.0.2/secsse/tests/testthat/test_plotting.R | 29 secsse-3.0.2/secsse/tests/testthat/test_secsse_cla_ct.R | 110 - secsse-3.0.2/secsse/tests/testthat/test_secsse_ct.R | 42 secsse-3.0.2/secsse/tests/testthat/test_secsse_sim.R | 204 +- secsse-3.0.2/secsse/tests/testthat/test_secsse_vs_cla_secsse.R |only secsse-3.0.2/secsse/vignettes/complete_tree.Rmd |only secsse-3.0.2/secsse/vignettes/plotting_states.Rmd | 36 secsse-3.0.2/secsse/vignettes/sim_with_secsse.Rmd |only secsse-3.0.2/secsse/vignettes/starting_secsse.Rmd |only secsse-3.0.2/secsse/vignettes/timing_data.RData |only 128 files changed, 3365 insertions(+), 3172 deletions(-)
Title: Simultaneous Multi-Bias Adjustment
Description: Quantify the causal effect of a binary exposure on a binary
outcome with adjustment for multiple biases. The functions can
simultaneously adjust for any combination of uncontrolled confounding,
exposure misclassification, and selection bias. The underlying method
generalizes the concept of combining inverse probability of selection
weighting with predictive value weighting. Simultaneous multi-bias
analysis can be used to enhance the validity and transparency of
real-world evidence obtained from observational, longitudinal studies.
Based on the work from Paul Brendel, Aracelis Torres, Onyebuchi Arah
(2023) <doi:10.1093/ije/dyad001>.
Author: Paul Brendel [aut, cre, cph]
Maintainer: Paul Brendel <pcbrendel@gmail.com>
Diff between multibias versions 1.2.0 dated 2023-10-16 and 1.2.1 dated 2023-10-21
multibias-1.2.0/multibias/inst/DAGs |only multibias-1.2.1/multibias/DESCRIPTION | 9 - multibias-1.2.1/multibias/MD5 | 14 +- multibias-1.2.1/multibias/NEWS.md | 76 ++++++----- multibias-1.2.1/multibias/README.md | 218 ---------------------------------- multibias-1.2.1/multibias/build |only multibias-1.2.1/multibias/inst/doc |only multibias-1.2.1/multibias/vignettes |only 8 files changed, 57 insertions(+), 260 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.11 dated 2023-04-03 and 0.3.12 dated 2023-10-21
DESCRIPTION | 8 MD5 | 76 - NEWS.md | 19 R/autoplot-calibration-spct.R | 27 R/autoplot-cps-spct.r | 27 R/autoplot-filter-spct.r | 143 ++- R/autoplot-generic-spct.R | 11 R/autoplot-raw-spct.r | 30 R/autoplot-response-spct.r | 63 + R/autoplot-source-spct.r | 59 + R/autoplot-waveband.R | 2 R/autotitle.R | 31 R/axis-utils-wlength.R | 2 R/decoration.R | 44 - R/si-prefixes.R | 4 R/stat-wb-irrad.R | 6 R/stat-wb-mean.R | 6 R/stat-wb-relative.R | 20 R/stat-wb-sirrad.R | 7 R/stat-wb-total.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.html | 4 inst/doc/userguide1-grammar.R | 4 inst/doc/userguide1-grammar.html | 1220 ++++++++++++++--------------- inst/doc/userguide2-autoplot-methods.R | 18 inst/doc/userguide2-autoplot-methods.html | 202 ++-- inst/doc/userguide3-data-manip.R | 26 inst/doc/userguide3-data-manip.html | 164 +-- man/T_plot.Rd | 174 ++-- man/autoplot.generic_spct.Rd | 2 man/autoplot.waveband.Rd | 2 man/decoration.Rd | 2 man/exponent2prefix.Rd | 4 man/generic_plot.Rd | 2 man/scale_x_energy_eV_continuous.Rd | 150 +-- man/scale_x_frequency_continuous.Rd | 114 +- man/scale_x_wavenumber_continuous.Rd | 114 +- man/sec_axis_w_number.Rd | 2 39 files changed, 1499 insertions(+), 1297 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical
model of island biota assembly through speciation, immigration and
extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Author: Rampal S. Etienne [aut, cre] ,
Luis Valente [aut] ,
Albert B. Phillimore [aut] ,
Bart Haegeman [aut] ,
Joshua W. Lambert [aut] ,
Pedro Santos Neves [aut] ,
Shu Xie [aut] ,
Richel J.C. Bilderbeek [aut] ,
Hanno Hildenbrandt [aut] ,
Torsten Hauffe [ctb] [...truncated...]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 4.4.0 dated 2023-04-02 and 4.4.1 dated 2023-10-21
DESCRIPTION | 11 MD5 | 147 +- NEWS.md | 9 R/DAISIE_ML1.R | 2 R/DAISIE_ML_CS.R | 2 R/DAISIE_SR_loglik_CS.R | 16 R/DAISIE_loglik_CS.R | 2 R/DAISIE_loglik_CS_shift.R |only R/DAISIE_loglik_integrate.R | 22 R/DAISIE_utils.R | 2 R/create_pars.R | 8 R/default_params_doc.R | 14 build/partial.rdb |binary build/vignette.rds |binary inst/doc/demo_CSvsIW.R | 10 inst/doc/demo_CSvsIW.html | 934 +++++++++---------- inst/doc/demo_optimize.html | 54 - inst/doc/demo_sim.html | 120 +- man/DAISIE-package.Rd | 1 man/DAISIE_ML.Rd | 2 man/DAISIE_count_species.Rd | 2 man/create_CS_version.Rd | 8 man/default_params_doc.Rd | 14 man/integral_peak.Rd | 13 man/sample_relaxed_rate.Rd | 3 tests/testthat/test-DAISIE_ExpEIN.R | 22 tests/testthat/test-DAISIE_ML1.R | 10 tests/testthat/test-DAISIE_ML2.R | 4 tests/testthat/test-DAISIE_ML4.R | 4 tests/testthat/test-DAISIE_ML_CS.R | 10 tests/testthat/test-DAISIE_ONEcolonist.R | 126 +- tests/testthat/test-DAISIE_SR_loglik.R | 31 tests/testthat/test-DAISIE_convert_to_classic_plot.R | 2 tests/testthat/test-DAISIE_dataprep.R | 18 tests/testthat/test-DAISIE_extract_stt_median.R | 2 tests/testthat/test-DAISIE_format_CS.R | 88 - tests/testthat/test-DAISIE_format_CS_sampled_stt.R | 40 tests/testthat/test-DAISIE_format_CS_trait.R | 2 tests/testthat/test-DAISIE_format_GW.R | 10 tests/testthat/test-DAISIE_format_IW.R | 38 tests/testthat/test-DAISIE_format_IW_full_stt.R | 70 - tests/testthat/test-DAISIE_format_IW_sampled_stt.R | 26 tests/testthat/test-DAISIE_loglik_CS.R | 22 tests/testthat/test-DAISIE_loglik_CS_M1.R | 20 tests/testthat/test-DAISIE_loglik_integrate.R | 6 tests/testthat/test-DAISIE_sim_core_cr.R | 30 tests/testthat/test-DAISIE_sim_core_cr_shift.R | 6 tests/testthat/test-DAISIE_sim_core_time_dep.R | 22 tests/testthat/test-DAISIE_sim_core_trait_dep.R | 8 tests/testthat/test-DAISIE_sim_cr.R | 72 - tests/testthat/test-DAISIE_sim_relaxed_rate.R | 190 +-- tests/testthat/test-DAISIE_sim_time_dep.R | 28 tests/testthat/test-DAISIE_sim_trait_dep.R | 16 tests/testthat/test-DAISIE_sumstats_rates.R | 2 tests/testthat/test-DAISIE_utils.R | 122 +- tests/testthat/test-are_max_rates_gt_rates.R | 16 tests/testthat/test-are_rates.R | 68 - tests/testthat/test-are_trait_pars.R | 2 tests/testthat/test-create_area_pars.R | 6 tests/testthat/test-create_trait_pars.R | 4 tests/testthat/test-get_ana_rate.R | 2 tests/testthat/test-get_clado_rate.R | 8 tests/testthat/test-get_ext_rate.R | 4 tests/testthat/test-get_immig_rate.R | 6 tests/testthat/test-integration_DAISIE.R | 256 +++-- tests/testthat/test-is_island_ontogeny_input.R | 8 tests/testthat/test-is_sea_level_input.R | 8 tests/testthat/test-is_simulation_outputs.R | 10 tests/testthat/test-island_area.R | 10 tests/testthat/test-odeint.R | 22 tests/testthat/test-printing.R | 28 tests/testthat/test-rosenbrock_abm1_steppers.R | 4 tests/testthat/test-time_dep_vs_cr.R | 4 tests/testthat/test-update_max_rates.R | 12 tests/testthat/test-update_rates.R | 12 75 files changed, 1542 insertions(+), 1391 deletions(-)
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Author: Matthijs S. Berends [aut, cre]
,
Christian F. Luz [aut, ctb] ,
Dennis Souverein [aut, ctb] ,
Erwin E. A. Hassing [aut, ctb],
Casper J. Albers [ths] ,
Peter Dutey-Magni [ctb] ,
Judith M. Fonville [ctb],
Alex W. Friedrich [ths] ,
Corinna Glasner [ths] [...truncated...]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 2.1.0 dated 2023-07-16 and 2.1.1 dated 2023-10-21
DESCRIPTION | 8 MD5 | 60 +++--- NAMESPACE | 64 ------ NEWS.md | 14 + R/aa_amr-package.R | 6 R/aa_globals.R | 7 R/data.R | 8 R/first_isolate.R | 97 +++++++-- R/get_episode.R | 10 - R/mdro.R | 8 R/mic.R | 414 +++--------------------------------------- R/plot.R | 2 R/proportion.R | 6 R/sysdata.rda |binary R/translate.R | 11 - build/partial.rdb |binary build/vignette.rds |binary data/antibiotics.rda |binary data/antivirals.rda |binary data/clinical_breakpoints.rda |binary inst/doc/welcome_to_AMR.html | 139 +++++++++----- inst/tinytest |only man/AMR.Rd | 6 man/antibiotics.Rd | 8 man/as.mic.Rd | 3 man/as.mo.Rd | 2 man/microorganisms.Rd | 4 man/mo_property.Rd | 2 man/plot.Rd | 2 man/proportion.Rd | 6 man/translate.Rd | 9 tests/tinytest.R | 2 32 files changed, 295 insertions(+), 603 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023) <doi:10.1093/jrsssc/qlad058>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.4.3 dated 2023-08-27 and 1.4.4 dated 2023-10-21
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/sharp-package.R | 2 +- README.md | 28 ++++++++++++++++++---------- build/partial.rdb |binary inst/REFERENCES.bib | 49 +++++++++++++++++++++++++++---------------------- inst/WORDLIST | 6 +++++- inst/doc/overview.pdf |binary man/sharp-package.Rd | 2 +- 10 files changed, 70 insertions(+), 49 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] ,
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] ,
Pedro Despouy [aut],
Salim Brueggemann [ctb] ,
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.10.2 dated 2023-06-03 and 4.10.3 dated 2023-10-21
DESCRIPTION | 12 MD5 | 57 ++- NEWS.md | 14 R/ggplotly.R | 17 - R/group2NA.R | 2 R/highlight.R | 2 R/layers2traces.R | 18 - R/plotly_build.R | 6 R/utils.R | 16 - inst/examples/shiny/event_data/tests/shinytest/mytest-expected/001.json | 144 +++++----- inst/examples/shiny/event_data/tests/shinytest/mytest-expected/002.json | 144 +++++----- inst/examples/shiny/event_data/tests/shinytest/mytest-expected/003.json | 144 +++++----- inst/examples/shiny/event_data/tests/shinytest/mytest-expected/004.json | 144 +++++----- man/group2NA.Rd | 2 man/highlight.Rd | 2 man/reexports.Rd | 2 tests/testthat/_snaps/ggplot-area/area-traces-order.svg | 2 tests/testthat/_snaps/ggplot-labels/factor-labels.svg | 2 tests/testthat/_snaps/ggplot-legend/legend-varying-aes-guide.svg |only tests/testthat/_snaps/plotly-subplot/plotly-subplot-plot-list.svg | 2 tests/testthat/test-animate-highlight.R | 1 tests/testthat/test-ggplot-date.R | 5 tests/testthat/test-ggplot-hex.R | 3 tests/testthat/test-ggplot-hline.R | 5 tests/testthat/test-ggplot-legend.R | 14 tests/testthat/test-ggplot-lines.R | 2 tests/testthat/test-ggplot-point.R | 10 tests/testthat/test-ggplot-sf.R | 1 tests/testthat/test-ggplot-vline.R | 5 tests/testthat/test-plotly-sf.R | 2 30 files changed, 415 insertions(+), 365 deletions(-)
Title: Command Argument Parsing
Description: A base dependency solution with basic argument parsing for use with
'Rscript'.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between scribe versions 0.2.0 dated 2023-05-22 and 0.3.0 dated 2023-10-21
DESCRIPTION | 10 - MD5 | 40 ++--- NAMESPACE | 1 NEWS.md | 41 ++++- R/arg.R | 41 +++-- R/class-args.R | 2 R/class-command-args.R | 2 R/command-args.R | 2 R/convert.R | 34 ++++ README.md | 10 - build/vignette.rds |binary inst/doc/scribe.R | 2 inst/doc/scribe.html | 240 +++++++++++++++---------------- man/new_arg.Rd | 2 man/scribe-package.Rd | 2 man/scribeArg-class.Rd | 2 man/scribeCommandArgs-class.Rd | 2 man/value_convert.Rd | 19 ++ tests/testthat/test-class-args.R | 42 +++++ tests/testthat/test-class-command-args.R | 20 +- tests/testthat/test-convert.R | 64 ++++++++ 21 files changed, 393 insertions(+), 185 deletions(-)
Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre],
Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between geohashTools versions 0.3.2 dated 2022-11-21 and 0.3.3 dated 2023-10-21
DESCRIPTION | 12 MD5 | 38 +- NEWS.md | 4 R/gh_decode.R | 9 R/gh_encode.R | 9 R/gis_tools.R | 39 +- R/onLoad.R | 2 R/utils.R | 4 README.md | 95 ++---- build/vignette.rds |binary inst/doc/geohashTools.R | 34 +- inst/doc/geohashTools.Rmd | 34 +- inst/doc/geohashTools.html | 552 +++++++++++++++++++++++++++------------- tests/testthat.R | 4 tests/testthat/test-decode.R | 258 ++++++++++++------ tests/testthat/test-encode.R | 125 +++++---- tests/testthat/test-gis-tools.R | 217 +++++++++------ tests/testthat/test-neighbors.R | 122 +++++--- tests/testthat/test-utils.R | 8 vignettes/geohashTools.Rmd | 34 +- 20 files changed, 992 insertions(+), 608 deletions(-)
Title: Adapted Boxplot to Missing Observations
Description: Boxplots adapted to the happenstance of missing observations where drop-out probabilities can be given by the practitioner or modelled using auxiliary covariates. The paper of "Zhang, Z., Chen, Z., Troendle, J. F. and Zhang, J.(2012) <doi:10.1111/j.1541-0420.2011.01712.x>", proposes estimators of marginal quantiles based on the Inverse Probability Weighting method.
Author: Ana Maria Bianco [aut], Graciela Boente [aut], Ana Perez-Gonzalez [aut]
Maintainer: Ana Perez-Gonzalez <anapg@uvigo.es>
Diff between IPWboxplot versions 0.1.1 dated 2022-04-22 and 0.1.2 dated 2023-10-21
DESCRIPTION | 6 MD5 | 8 build/vignette.rds |binary inst/doc/my-vignette.R | 14 - inst/doc/my-vignette.html | 462 +++++++++++++++++----------------------------- 5 files changed, 192 insertions(+), 298 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.2 dated 2023-09-03 and 2.2.3 dated 2023-10-21
DESCRIPTION | 10 - MD5 | 14 - R/RcppExports.R | 422 ++++++++++++++++++++++++++-------------------------- R/mix.R | 105 +++++++++++- inst/btz794.pdf |binary man/mvr.Rd | 31 ++- src/RcppExports.cpp | 5 src/mrr20220709.cpp | 13 - 8 files changed, 355 insertions(+), 245 deletions(-)
Title: Multiform Seq2Seq Model for Time-Feature Analysis
Description: Seq2seq time-feature analysis based on variational model, with a wide range of distributions available for the latent variable.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between proteus versions 1.1.3 dated 2023-09-17 and 1.1.4 dated 2023-10-21
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 3 +++ NEWS.md | 5 +++++ R/main1.R | 39 ++++++++++++++++++++++++++++++++++++++- R/main2.R | 14 +++++++------- man/proteus.Rd | 2 +- man/proteus_random_search.Rd | 4 ++-- 8 files changed, 67 insertions(+), 22 deletions(-)
Title: Logistic Regression with Misclassification in Dependent
Variables
Description: Error in a binary dependent variable, also known as misclassification, has not drawn much attention in psychology. Ignoring misclassification in logistic regression can result in misleading parameter estimates and statistical inference. This package conducts logistic regression analysis with misspecification in outcome variables.
Author: Haiyan Liu and Zhiyong Zhang
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>
Diff between logistic4p versions 1.5 dated 2017-05-31 and 1.6 dated 2023-10-21
DESCRIPTION | 14 +++++--------- MD5 | 20 ++++++++++---------- R/logistic4p.R | 10 +++++----- build/partial.rdb |binary man/logistic.Rd | 4 ++-- man/logistic4p-package.Rd | 1 - man/logistic4p.Rd | 4 ++-- man/logistic4p.e.Rd | 4 ++-- man/logistic4p.fn.Rd | 4 ++-- man/logistic4p.fp.Rd | 4 ++-- man/logistic4p.fp.fn.Rd | 4 ++-- 11 files changed, 32 insertions(+), 37 deletions(-)
Title: Interaction Statistics
Description: Fast, model-agnostic implementation of different H-statistics
introduced by Jerome H. Friedman and Bogdan E. Popescu (2008)
<doi:10.1214/07-AOAS148>. These statistics quantify interaction
strength per feature, feature pair, and feature triple. The package
supports multi-output predictions and can account for case weights.
In addition, several variants of the original statistics are provided.
The shape of the interactions can be explored through partial
dependence plots or individual conditional expectation plots. 'DALEX'
explainers, meta learners ('mlr3', 'tidymodels', 'caret') and most
other models work out-of-the-box.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between hstats versions 0.3.0 dated 2023-09-29 and 1.0.0 dated 2023-10-21
hstats-0.3.0/hstats/R/grid.R |only hstats-0.3.0/hstats/R/utils.R |only hstats-0.3.0/hstats/man/figures/hstats3.svg |only hstats-0.3.0/hstats/man/figures/pdp3.svg |only hstats-0.3.0/hstats/man/plot.perm_importance.Rd |only hstats-0.3.0/hstats/man/print.perm_importance.Rd |only hstats-0.3.0/hstats/man/print.summary_hstats.Rd |only hstats-0.3.0/hstats/tests/testthat/test_utils.R |only hstats-1.0.0/hstats/DESCRIPTION | 6 hstats-1.0.0/hstats/MD5 | 129 - hstats-1.0.0/hstats/NAMESPACE | 10 hstats-1.0.0/hstats/NEWS.md | 29 hstats-1.0.0/hstats/R/H2.R | 28 hstats-1.0.0/hstats/R/H2_overall.R | 49 hstats-1.0.0/hstats/R/H2_pairwise.R | 45 hstats-1.0.0/hstats/R/H2_threeway.R | 44 hstats-1.0.0/hstats/R/average_loss.R | 95 - hstats-1.0.0/hstats/R/hstats.R | 274 ++- hstats-1.0.0/hstats/R/ice.R | 82 - hstats-1.0.0/hstats/R/losses.R | 7 hstats-1.0.0/hstats/R/onLoad.R |only hstats-1.0.0/hstats/R/partial_dep.R | 167 +- hstats-1.0.0/hstats/R/pd_importance.R | 57 hstats-1.0.0/hstats/R/pd_raw.R | 76 + hstats-1.0.0/hstats/R/perm_importance.R | 195 +- hstats-1.0.0/hstats/R/utils_calculate.R |only hstats-1.0.0/hstats/R/utils_grid.R |only hstats-1.0.0/hstats/R/utils_input.R |only hstats-1.0.0/hstats/R/utils_plot.R |only hstats-1.0.0/hstats/R/utils_statistics.R |only hstats-1.0.0/hstats/README.md | 229 ++- hstats-1.0.0/hstats/man/average_loss.Rd | 62 hstats-1.0.0/hstats/man/dim.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/dimnames-set-.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/dimnames.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/figures/dalex_hstats.svg | 208 +- hstats-1.0.0/hstats/man/figures/dalex_ice.svg | 328 ++-- hstats-1.0.0/hstats/man/figures/hstats.svg | 248 +-- hstats-1.0.0/hstats/man/figures/hstats_pairwise.svg | 112 - hstats-1.0.0/hstats/man/figures/ice.svg | 316 ++-- hstats-1.0.0/hstats/man/figures/importance.svg | 95 - hstats-1.0.0/hstats/man/figures/importance_perm.svg | 131 - hstats-1.0.0/hstats/man/figures/lightgbm.svg |only hstats-1.0.0/hstats/man/figures/multivariate.svg | 267 +-- hstats-1.0.0/hstats/man/figures/multivariate_ice.svg | 999 +++++--------- hstats-1.0.0/hstats/man/figures/pdp_2d.png |binary hstats-1.0.0/hstats/man/figures/pdp_ocean_age.svg | 135 - hstats-1.0.0/hstats/man/figures/xgboost.svg |only hstats-1.0.0/hstats/man/h2.Rd | 17 hstats-1.0.0/hstats/man/h2_overall.Rd | 35 hstats-1.0.0/hstats/man/h2_pairwise.Rd | 40 hstats-1.0.0/hstats/man/h2_threeway.Rd | 43 hstats-1.0.0/hstats/man/hstats.Rd | 108 - hstats-1.0.0/hstats/man/ice.Rd | 16 hstats-1.0.0/hstats/man/multivariate_grid.Rd | 7 hstats-1.0.0/hstats/man/partial_dep.Rd | 29 hstats-1.0.0/hstats/man/pd_importance.Rd | 44 hstats-1.0.0/hstats/man/perm_importance.Rd | 80 - hstats-1.0.0/hstats/man/plot.hstats.Rd | 32 hstats-1.0.0/hstats/man/plot.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/plot.ice.Rd | 25 hstats-1.0.0/hstats/man/plot.partial_dep.Rd | 30 hstats-1.0.0/hstats/man/print.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/print.hstats_summary.Rd |only hstats-1.0.0/hstats/man/print.ice.Rd | 2 hstats-1.0.0/hstats/man/print.partial_dep.Rd | 2 hstats-1.0.0/hstats/man/sub-.hstats_matrix.Rd |only hstats-1.0.0/hstats/man/summary.hstats.Rd | 15 hstats-1.0.0/hstats/man/univariate_grid.Rd | 7 hstats-1.0.0/hstats/tests/testthat/test_average_loss.R | 128 + hstats-1.0.0/hstats/tests/testthat/test_calculate.R |only hstats-1.0.0/hstats/tests/testthat/test_grid.R | 41 hstats-1.0.0/hstats/tests/testthat/test_hstats.R | 227 +-- hstats-1.0.0/hstats/tests/testthat/test_ice.R | 54 hstats-1.0.0/hstats/tests/testthat/test_partial_dep.R | 276 +++ hstats-1.0.0/hstats/tests/testthat/test_pd_importance.R | 19 hstats-1.0.0/hstats/tests/testthat/test_perm_importance.R | 241 ++- hstats-1.0.0/hstats/tests/testthat/test_statistics.R |only 78 files changed, 3387 insertions(+), 2554 deletions(-)
Title: 1d Goodness of Fit Tests
Description: Routines that allow the user to run a large number of goodness-of-fit tests.
It allows for data to be continuous or discrete. It includes routines to estimate
the power of the tests and display them as a power graph.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between Rgof versions 1.1.0 dated 2023-04-19 and 1.2.1 dated 2023-10-21
DESCRIPTION | 6 MD5 | 70 ++--- NAMESPACE | 1 NEWS.md | 12 R/RcppExports.R | 33 +- R/gof_power_cont.R | 41 ++- R/gof_power_disc.R | 43 ++- R/gof_test_cont.R | 52 +++- R/gof_test_disc.R | 51 +++ build/vignette.rds |binary inst/doc/Rgof.R | 37 ++ inst/doc/Rgof.Rmd | 63 ++++ inst/doc/Rgof.html | 648 ++++++++++++++++++++++++++------------------------ man/binner_cont.Rd | 5 man/binner_disc.Rd | 4 man/chi_test_cont.Rd | 5 man/chi_test_disc.Rd | 5 man/gof_power_cont.Rd | 5 man/gof_power_disc.Rd | 5 man/gof_test_cont.Rd | 6 man/gof_test_disc.Rd | 6 man/power_cont.Rd | 5 man/power_disc.Rd | 5 src/RcppExports.cpp | 54 ++-- src/TS_cont.cpp | 1 src/binner_cont.cpp | 8 src/binner_cont.h | 3 src/binner_disc.cpp | 7 src/binner_disc.h | 3 src/chi_test_cont.cpp | 6 src/chi_test_cont.h | 3 src/chi_test_disc.cpp | 6 src/chi_test_disc.h | 3 src/power_cont.cpp | 8 src/power_disc.cpp | 10 vignettes/Rgof.Rmd | 63 ++++ 36 files changed, 811 insertions(+), 472 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-21 0.4.6
2023-07-19 0.4.5
2023-03-06 0.4.4
2023-02-27 0.4.3
2023-02-22 0.4.2
2023-01-09 0.4.1
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.1.3 dated 2023-09-23 and 1.1.4 dated 2023-10-21
DESCRIPTION | 10 MD5 | 54 ++- R/GeoCV.R | 27 + R/GeoCompositeLik2.R | 52 ++- R/GeoCorrFct.r | 60 +--- R/GeoCovariogram.r | 5 R/GeoCovmatrix.r | 65 +--- R/GeoFit.r | 19 + R/GeoFit2.R | 12 R/GeoKrig.r | 633 ++++++++++++++++++++++------------------------ R/GeoKrigloc.R | 8 R/GeoLik.r | 38 +- data/datalist | 1 data/spanish_wind.rda |only man/CorrParam.Rd | 2 man/GeoAniso.Rd | 4 man/GeoCV.Rd | 14 - man/GeoCorrFct_Cop.Rd | 6 man/GeoCovariogram.Rd | 2 man/GeoCovmatrix.Rd | 46 --- man/GeoFit.Rd | 33 +- man/GeoFit2.Rd | 3 man/GeoKrig.Rd | 174 +++++++----- man/GeoKrigloc.Rd | 37 +- man/GeoNA.Rd | 4 man/GeoVarestbootstrap.Rd | 3 man/GeoWls.Rd | 4 man/spanish_wind.Rd |only src/TB.c | 44 +++ 29 files changed, 699 insertions(+), 661 deletions(-)
Title: Shiny/R Wrapper for 'clipboard.js'
Description: Leverages the functionality of 'clipboard.js', a JavaScript library
for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com>
for more information), and provides a reactive copy-to-clipboard UI button
component, called 'rclipButton', and a a reactive copy-to-clipboard UI link
component, called 'rclipLink', for 'shiny' R applications.
Author: Sebastien Bihorel
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between rclipboard versions 0.1.6 dated 2022-08-07 and 0.2.0 dated 2023-10-21
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NAMESPACE | 3 +- NEWS | 11 ++++++- R/rclipButton.R | 67 ++++++++++++++++++++++++++++++++++++++++------ R/rclipboardSetup.R | 3 -- README.md | 57 +++++++++++++++++---------------------- inst/lib/clipboard.min.js | 4 +- man/rclipButton.Rd | 14 ++++++--- 9 files changed, 121 insertions(+), 62 deletions(-)
Title: Group Factor Analysis
Description: Factor analysis implementation for multiple data sources, i.e., for groups of variables. The whole data analysis pipeline is provided, including functions and recommendations for data normalization and model definition, as well as missing value prediction and model visualization. The model group factor analysis (GFA) is inferred with Gibbs sampling, and it has been presented originally by Virtanen et al. (2012), and extended in Klami et al. (2015) <DOI:10.1109/TNNLS.2014.2376974> and Bunte et al. (2016) <DOI:10.1093/bioinformatics/btw207>; for details, see the citation info.
Author: Eemeli Leppaeaho [aut, cre],
Seppo Virtanen [aut],
Muhammad Ammad-ud-din [ctb],
Suleiman A Khan [ctb],
Tommi Suvitaival [ctb],
Inka Saarinen [ctb],
Samuel Kaski [ctb]
Maintainer: Eemeli Leppaeaho <eemeli.leppaaho@gmail.com>
Diff between GFA versions 1.0.4 dated 2023-10-07 and 1.0.5 dated 2023-10-21
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 6 +++--- NEWS | 4 ++++ 4 files changed, 12 insertions(+), 8 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.7 dated 2023-07-19 and 0.0.8 dated 2023-10-21
ChangeLog | 26 ++++++++++++++++++ DESCRIPTION | 9 +++--- MD5 | 26 +++++++++--------- README.md | 7 ++++ build/partial.rdb |binary demo/allUScalendars.R | 2 - inst/NEWS.Rd | 8 +++++ src/Makevars | 7 +++- src/Makevars.win | 5 ++- src/calendars.cpp | 2 - src/ql/patterns/observable.cpp | 28 +++++++++---------- src/ql/patterns/observable.hpp | 41 ++++++++-------------------- src/ql/time/calendar.cpp | 50 ++++++++++++----------------------- src/ql/time/calendars/southkorea.cpp | 1 14 files changed, 114 insertions(+), 98 deletions(-)
Title: Automated Uncertainty Analysis
Description: Methods and tools for model selection and multi-model inference (Burnham and Anderson (2002) <doi:10.1007/b97636>, among others).
'SUR' (for parameter estimation), 'logit'/'probit' (for binary classification), and 'VARMA' (for time-series forecasting) are implemented.
Evaluations are both in-sample and out-of-sample.
It is designed to be efficient in terms of CPU usage and memory consumption.
Author: Ramin Mojab [aut, cre],
Stephen Becker [cph] by Ciyou Zhu . L-BFGS-B Version 3.0 is an
algorithmic update from 2011, with coding changes by J. L. Morales)
Maintainer: Ramin Mojab <rmojab63@gmail.com>
Diff between ldt versions 0.3.2.1 dated 2023-08-07 and 0.4.2 dated 2023-10-21
ldt-0.3.2.1/ldt/R/generic.R |only ldt-0.3.2.1/ldt/build/vignette.rds |only ldt-0.3.2.1/ldt/inst/doc |only ldt-0.3.2.1/ldt/man/Search_s.Rd |only ldt-0.3.2.1/ldt/man/coefs.plot.Rd |only ldt-0.3.2.1/ldt/man/combineSearch.Rd |only ldt-0.3.2.1/ldt/man/get.items.modelcheck.Rd |only ldt-0.3.2.1/ldt/man/get.items.search.Rd |only ldt-0.3.2.1/ldt/man/get.options.metric.Rd |only ldt-0.3.2.1/ldt/man/get.options.search.Rd |only ldt-0.3.2.1/ldt/man/h.get.estim.Rd |only ldt-0.3.2.1/ldt/man/latex.matrix.Rd |only ldt-0.3.2.1/ldt/man/latex.variable.vector.Rd |only ldt-0.3.2.1/ldt/man/print.ldtsearch.Rd |only ldt-0.3.2.1/ldt/man/search.bin.stepwise.Rd |only ldt-0.3.2.1/ldt/man/search.sur.stepwise.Rd |only ldt-0.3.2.1/ldt/man/search.varma.stepwise.Rd |only ldt-0.3.2.1/ldt/man/summary.ldtsearch.Rd |only ldt-0.3.2.1/ldt/man/to.data.frame.Rd |only ldt-0.3.2.1/ldt/tests/testthat/test-generic.R |only ldt-0.3.2.1/ldt/vignettes |only ldt-0.4.2/ldt/DESCRIPTION | 10 ldt-0.4.2/ldt/MD5 | 197 +- ldt-0.4.2/ldt/NAMESPACE | 59 ldt-0.4.2/ldt/NEWS.md | 75 - ldt-0.4.2/ldt/R/RcppExports.R | 44 ldt-0.4.2/ldt/R/bin.R | 499 ++++--- ldt-0.4.2/ldt/R/data.R |only ldt-0.4.2/ldt/R/g.plots.R |only ldt-0.4.2/ldt/R/g.prints.R |only ldt-0.4.2/ldt/R/g.regression.R |only ldt-0.4.2/ldt/R/g.summary.R |only ldt-0.4.2/ldt/R/helpers.R | 566 -------- ldt-0.4.2/ldt/R/options.R | 500 ------- ldt-0.4.2/ldt/R/r-func.R |only ldt-0.4.2/ldt/R/search.R |only ldt-0.4.2/ldt/R/statistics.R | 48 ldt-0.4.2/ldt/R/steps.R |only ldt-0.4.2/ldt/R/sur.R | 473 +++--- ldt-0.4.2/ldt/R/varma.R | 767 ++++------- ldt-0.4.2/ldt/build/partial.rdb |only ldt-0.4.2/ldt/inst/REFERENCES.bib |only ldt-0.4.2/ldt/man/AIC.ldt.estim.Rd |only ldt-0.4.2/ldt/man/BIC.ldt.estim.Rd |only ldt-0.4.2/ldt/man/adjust_indices_after_remove.Rd |only ldt-0.4.2/ldt/man/boxCoxTransform.Rd |only ldt-0.4.2/ldt/man/coef.ldt.estim.Rd |only ldt-0.4.2/ldt/man/coefs.table.Rd | 7 ldt-0.4.2/ldt/man/combine.search.Rd |only ldt-0.4.2/ldt/man/endogenous.Rd |only ldt-0.4.2/ldt/man/eqList2Matrix.Rd |only ldt-0.4.2/ldt/man/estim.bin.Rd | 82 - ldt-0.4.2/ldt/man/estim.binary.model.string.Rd |only ldt-0.4.2/ldt/man/estim.sur.Rd | 130 + ldt-0.4.2/ldt/man/estim.varma.Rd | 85 - ldt-0.4.2/ldt/man/estim.varma.model.string.Rd |only ldt-0.4.2/ldt/man/exogenous.Rd |only ldt-0.4.2/ldt/man/fan.plot.Rd | 62 ldt-0.4.2/ldt/man/fitted.ldt.estim.Rd |only ldt-0.4.2/ldt/man/get.combinations.Rd |only ldt-0.4.2/ldt/man/get.data.Rd |only ldt-0.4.2/ldt/man/get.data.append.newX.Rd |only ldt-0.4.2/ldt/man/get.data.check.discrete.Rd |only ldt-0.4.2/ldt/man/get.data.check.intercept.Rd |only ldt-0.4.2/ldt/man/get.data.keep.complete.Rd |only ldt-0.4.2/ldt/man/get.indexation.Rd |only ldt-0.4.2/ldt/man/get.search.items.Rd |only ldt-0.4.2/ldt/man/get.search.metrics.Rd |only ldt-0.4.2/ldt/man/get.search.modelchecks.Rd |only ldt-0.4.2/ldt/man/get.search.options.Rd |only ldt-0.4.2/ldt/man/logLik.ldt.estim.Rd |only ldt-0.4.2/ldt/man/plot.ldt.estim.Rd |only ldt-0.4.2/ldt/man/plot.ldt.varma.prediction.Rd |only ldt-0.4.2/ldt/man/predict.ldt.estim.Rd |only ldt-0.4.2/ldt/man/predict.ldt.estim.varma.Rd |only ldt-0.4.2/ldt/man/print.ldt.estim.Rd |only ldt-0.4.2/ldt/man/print.ldt.estim.projection.Rd |only ldt-0.4.2/ldt/man/print.ldt.list.Rd |only ldt-0.4.2/ldt/man/print.ldt.search.Rd |only ldt-0.4.2/ldt/man/print.ldt.varma.prediction.Rd |only ldt-0.4.2/ldt/man/residuals.ldt.estim.Rd |only ldt-0.4.2/ldt/man/s.gld.from.moments.Rd | 5 ldt-0.4.2/ldt/man/s.metric.from.weight.Rd | 10 ldt-0.4.2/ldt/man/s.pca.Rd | 10 ldt-0.4.2/ldt/man/s.roc.Rd | 9 ldt-0.4.2/ldt/man/s.weight.from.metric.Rd | 13 ldt-0.4.2/ldt/man/search.bin.Rd | 118 - ldt-0.4.2/ldt/man/search.rfunc.Rd |only ldt-0.4.2/ldt/man/search.steps.Rd |only ldt-0.4.2/ldt/man/search.sur.Rd | 159 -- ldt-0.4.2/ldt/man/search.varma.Rd | 148 -- ldt-0.4.2/ldt/man/sim.bin.Rd | 36 ldt-0.4.2/ldt/man/sim.sur.Rd | 29 ldt-0.4.2/ldt/man/sim.varma.Rd | 8 ldt-0.4.2/ldt/man/summary.ldt.search.Rd |only ldt-0.4.2/ldt/man/summary.ldt.search.item.Rd |only ldt-0.4.2/ldt/src/RcppExports.cpp | 183 +- ldt-0.4.2/ldt/src/array.cpp | 36 ldt-0.4.2/ldt/src/array.h | 28 ldt-0.4.2/ldt/src/discrete_choice.h | 74 - ldt-0.4.2/ldt/src/discrete_choice_modelset.cpp | 351 ++--- ldt-0.4.2/ldt/src/matrix.cpp | 61 ldt-0.4.2/ldt/src/matrix.h | 40 ldt-0.4.2/ldt/src/modelset.cpp | 56 ldt-0.4.2/ldt/src/r_dc.cpp | 413 ++---- ldt-0.4.2/ldt/src/r_func.cpp |only ldt-0.4.2/ldt/src/r_ldt.cpp | 1560 +++++++---------------- ldt-0.4.2/ldt/src/r_ldt.h | 176 +- ldt-0.4.2/ldt/src/r_statistics.cpp | 44 ldt-0.4.2/ldt/src/r_sur.cpp | 403 +---- ldt-0.4.2/ldt/src/r_varma.cpp | 486 ++----- ldt-0.4.2/ldt/src/scoring.cpp | 61 ldt-0.4.2/ldt/src/scoring.h | 24 ldt-0.4.2/ldt/src/searcher.cpp | 285 ++-- ldt-0.4.2/ldt/src/searcher_reg.cpp |only ldt-0.4.2/ldt/src/searchers.h | 354 +++-- ldt-0.4.2/ldt/src/summary.cpp | 144 -- ldt-0.4.2/ldt/src/sur.cpp | 8 ldt-0.4.2/ldt/src/sur.h | 80 - ldt-0.4.2/ldt/src/sur_modelset.cpp | 297 +--- ldt-0.4.2/ldt/src/sur_simulation.cpp | 30 ldt-0.4.2/ldt/src/varma.h | 83 - ldt-0.4.2/ldt/src/varma_extended.cpp | 12 ldt-0.4.2/ldt/src/varma_modelset.cpp | 428 ++---- ldt-0.4.2/ldt/src/varma_simulation.cpp | 200 -- ldt-0.4.2/ldt/src/vmatrix.cpp |only ldt-0.4.2/ldt/tests/testthat/test-bin.R | 679 +++------- ldt-0.4.2/ldt/tests/testthat/test-data.R |only ldt-0.4.2/ldt/tests/testthat/test-statistics.R | 8 ldt-0.4.2/ldt/tests/testthat/test-sur.R | 723 +++++----- ldt-0.4.2/ldt/tests/testthat/test-varma.R | 876 ++++++------ 131 files changed, 4921 insertions(+), 7431 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-07 0.2.1
2023-04-28 0.2.0
2022-09-06 0.1.4
2020-02-19 0.1.3
2019-12-17 0.1.2
2019-12-09 0.1.1
2019-12-06 0.1.0
Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto-grading check-fields and check-boxes for 'rmarkdown'
or 'quarto' HTML. It can be used in class, when teacher share materials
and tasks, so students can solve some problems and check their work. In
contrast to the 'learnr' package, the 'checkdown' package works serverlessly
without 'shiny'.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between checkdown versions 0.0.10 dated 2023-09-24 and 0.0.11 dated 2023-10-21
DESCRIPTION | 6 - MD5 | 13 +- NAMESPACE | 4 NEWS | 5 R/check_question.R | 22 +++ R/insert_score.R |only R/zzz.R |only inst/doc/start_checkdown.html | 238 ++++++++++++++++++++++-------------------- man/insert_score.Rd |only 9 files changed, 163 insertions(+), 125 deletions(-)
Title: Boundary Overlap Statistics
Description: Analysis workflow for finding geographic boundaries of ecological or landscape traits and comparing the placement of geographic boundaries of two traits. If data are trait values, trait data are transformed to boundary intensities based on approximate first derivatives across latitude and longitude. The package includes functions to create custom null models based on the input data. The boundary statistics are described in: Fortin, Drapeau, and Jacquez (1996) <doi:10.2307/3545584>.
Author: Amy Luo [aut, cre, cph] ,
Elizabeth Derryberry [ths]
Maintainer: Amy Luo <aluo@vols.utk.edu>
Diff between BoundaryStats versions 2.0.1 dated 2023-06-28 and 2.1.1 dated 2023-10-21
DESCRIPTION | 6 +- MD5 | 34 ++++++------- NEWS.md | 17 ++++++ R/boundary_null_distrib.R | 7 +- R/define_boundary.R | 3 - R/gauss_random_field_sim.R | 7 +- R/globals.R | 2 R/mod_random_clust_sim.R | 50 +++++++++++-------- R/overlap_null_distrib.R | 17 ++++-- README.md | 3 - inst/doc/BoundaryStats.R | 8 +-- inst/doc/BoundaryStats.Rmd | 14 ++--- inst/doc/BoundaryStats.html | 108 +++++++++++++++++++++---------------------- man/boundary_null_distrib.Rd | 4 + man/define_boundary.Rd | 2 man/mod_random_clust_sim.Rd | 6 +- man/overlap_null_distrib.Rd | 10 +++ vignettes/BoundaryStats.Rmd | 14 ++--- 18 files changed, 181 insertions(+), 131 deletions(-)
Title: Color Mappings and 'C++' Header Files for Color Conversion
Description: Provides 'C++' header files to deal with color conversion
from some color spaces to hexadecimal with 'Rcpp', and exports some
color mapping functions for usage in R. Also exports functions to
convert colors from the 'HSLuv' color space for usage in R. 'HSLuv' is
a human-friendly alternative to HSL.
Author: Stephane Laurent [cre, aut],
Scott Spencer [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between RcppColors versions 0.5.0 dated 2023-09-22 and 0.6.0 dated 2023-10-21
DESCRIPTION | 6 ++--- MD5 | 23 ++++++++++---------- NAMESPACE | 1 NEWS.md | 5 ++++ R/RcppExports.R | 8 +++++++ R/hsluv.R | 52 ++++++++++++++++++++++++++++++++++++++++++++-- README.md | 4 +++ inst/include/RcppColors.h | 1 man/hsi.Rd |only man/hsl.Rd | 2 - man/hsluv.Rd | 2 - src/RcppColors.cpp | 11 +++++++++ src/RcppExports.cpp | 29 +++++++++++++++++++++++++ 13 files changed, 126 insertions(+), 18 deletions(-)