Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>),
Adrian Chong [aut] (<https://orcid.org/0000-0002-9486-4728>)
Maintainer: Hongyuan Jia <hongyuanjia@cqust.edu.cn>
Diff between eplusr versions 0.15.0 dated 2021-11-17 and 0.15.1 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 16 +++++++++++++++- R/install.R | 2 +- R/param.R | 2 ++ R/run.R | 2 +- R/units.R | 24 +++++++++++++----------- tests/testthat/helper-eplus.R | 2 +- tests/testthat/test-param.R | 11 ++++++++--- 9 files changed, 52 insertions(+), 29 deletions(-)
Title: Vis-NIR Spectral Analysis Wrapper
Description: Originally designed application in the context of
resource-limited plant research and breeding programs, 'waves'
provides an open-source solution to spectral data processing and model
development by bringing useful packages together into a streamlined
pipeline. This package is wrapper for functions related to the
analysis of point visible and near-infrared reflectance measurements.
It includes visualization, filtering, aggregation, preprocessing,
cross-validation set formation, model training, and prediction
functions to enable open-source association of spectral and reference
data. This package is documented in a peer-reviewed manuscript in the
Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized
cross-validation schemes are described in detail in Jarquín et al.
(2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from
Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Author: Jenna Hershberger [aut, cre] (<https://orcid.org/0000-0002-3147-6867>),
Michael Gore [ths],
NSF BREAD IOS-1543958 [fnd]
Maintainer: Jenna Hershberger <jmh579@cornell.edu>
Diff between waves versions 0.1.1 dated 2021-04-21 and 0.2.0 dated 2022-01-20
waves-0.1.1/waves/R/AggregateSpectra.R |only waves-0.1.1/waves/R/DoPreprocessing.R |only waves-0.1.1/waves/R/FilterSpectra.R |only waves-0.1.1/waves/R/FormatCV.R |only waves-0.1.1/waves/R/PlotSpectra.R |only waves-0.1.1/waves/R/PredictFromSavedModel.R |only waves-0.1.1/waves/R/SaveModel.R |only waves-0.1.1/waves/R/TestModelPerformance.R |only waves-0.1.1/waves/R/TrainSpectralModel.R |only waves-0.1.1/waves/man/AggregateSpectra.Rd |only waves-0.1.1/waves/man/DoPreprocessing.Rd |only waves-0.1.1/waves/man/FilterSpectra.Rd |only waves-0.1.1/waves/man/FormatCV.Rd |only waves-0.1.1/waves/man/PlotSpectra.Rd |only waves-0.1.1/waves/man/PredictFromSavedModel.Rd |only waves-0.1.1/waves/man/SaveModel.Rd |only waves-0.1.1/waves/man/TestModelPerformance.Rd |only waves-0.1.1/waves/man/TrainSpectralModel.Rd |only waves-0.2.0/waves/DESCRIPTION | 61 +++++++++++++------------ waves-0.2.0/waves/MD5 | 50 ++++++++++---------- waves-0.2.0/waves/NAMESPACE | 25 +++++++++- waves-0.2.0/waves/NEWS.md | 30 +++++++++++- waves-0.2.0/waves/R/aggregate_spectra.R |only waves-0.2.0/waves/R/data.R | 15 ++---- waves-0.2.0/waves/R/filter_spectra.R |only waves-0.2.0/waves/R/format_cv.R |only waves-0.2.0/waves/R/plot_spectra.R |only waves-0.2.0/waves/R/predict_spectra.R |only waves-0.2.0/waves/R/pretreat_spectra.R |only waves-0.2.0/waves/R/rename.R |only waves-0.2.0/waves/R/save_model.R |only waves-0.2.0/waves/R/test_spectra.R |only waves-0.2.0/waves/R/train_spectra.R |only waves-0.2.0/waves/README.md | 47 +++++++++---------- waves-0.2.0/waves/man/aggregate_spectra.Rd |only waves-0.2.0/waves/man/filter_spectra.Rd |only waves-0.2.0/waves/man/format_cv.Rd |only waves-0.2.0/waves/man/ikeogu.2017.Rd | 14 ++--- waves-0.2.0/waves/man/plot_spectra.Rd |only waves-0.2.0/waves/man/predict_spectra.Rd |only waves-0.2.0/waves/man/pretreat_spectra.Rd |only waves-0.2.0/waves/man/rename.Rd |only waves-0.2.0/waves/man/save_model.Rd |only waves-0.2.0/waves/man/test_spectra.Rd |only waves-0.2.0/waves/man/train_spectra.Rd |only 45 files changed, 150 insertions(+), 92 deletions(-)
Title: NBER Working Papers
Description: Catalogue of NBER working papers published between June 1973 and December 2021.
Author: Benjamin Davies [aut, cre] (<https://orcid.org/0000-0002-1749-4567>)
Maintainer: Benjamin Davies <dev@bldavies.com>
Diff between nberwp versions 1.0.0 dated 2021-07-21 and 1.1.0 dated 2022-01-20
DESCRIPTION | 10 +++++----- MD5 | 34 ++++++++++++++++++---------------- NEWS.md |only R/authors.R | 39 +++++++++++++++++++++++++++++++++++---- R/paper_authors.R | 4 ++-- R/paper_programs.R | 4 ++-- R/papers.R | 8 ++++---- R/programs.R | 6 +++--- build |only data/authors.rda |binary data/paper_authors.rda |binary data/paper_programs.rda |binary data/papers.rda |binary data/programs.rda |binary man/authors.Rd | 40 ++++++++++++++++++++++++++++++++++++---- man/paper_authors.Rd | 4 ++-- man/paper_programs.Rd | 4 ++-- man/papers.Rd | 8 ++++---- man/programs.Rd | 6 +++--- 19 files changed, 116 insertions(+), 51 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>),
Joseph Larmarange [aut] (<https://orcid.org/0000-0001-7097-700X>),
Jessica Lavery [aut] (<https://orcid.org/0000-0002-2746-5647>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Xing Bai [ctb],
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Margie Hannum [ctb] (<https://orcid.org/0000-0002-2953-0449>),
Stephanie Lobaugh [ctb],
Shannon Pileggi [ctb] (<https://orcid.org/0000-0002-7732-4164>),
Amy Tin [ctb] (<https://orcid.org/0000-0002-8005-0694>),
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
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gtsummary-1.5.1/gtsummary/man/figures/tbl_svysummary_ex2.png |binary gtsummary-1.5.1/gtsummary/man/figures/tbl_uv_ex1.png |binary gtsummary-1.5.1/gtsummary/man/figures/tbl_uv_ex2.png |binary gtsummary-1.5.1/gtsummary/man/figures/tbl_uv_global_ex2.png |binary gtsummary-1.5.1/gtsummary/man/figures/tidy_standardize_ex1.png |binary gtsummary-1.5.1/gtsummary/man/figures/tidy_standardize_ex2.png |binary gtsummary-1.5.1/gtsummary/man/gtsummary-package.Rd | 4 gtsummary-1.5.1/gtsummary/man/inline_text.Rd | 1 gtsummary-1.5.1/gtsummary/man/inline_text.tbl_cross.Rd | 2 gtsummary-1.5.1/gtsummary/man/inline_text.tbl_regression.Rd | 2 gtsummary-1.5.1/gtsummary/man/inline_text.tbl_summary.Rd | 2 gtsummary-1.5.1/gtsummary/man/inline_text.tbl_survfit.Rd | 2 gtsummary-1.5.1/gtsummary/man/inline_text.tbl_uvregression.Rd | 2 gtsummary-1.5.1/gtsummary/man/modify.Rd | 40 gtsummary-1.5.1/gtsummary/man/modify_cols_merge.Rd | 1 gtsummary-1.5.1/gtsummary/man/modify_column_alignment.Rd |only gtsummary-1.5.1/gtsummary/man/modify_column_hide.Rd | 5 gtsummary-1.5.1/gtsummary/man/modify_fmt_fun.Rd | 3 gtsummary-1.5.1/gtsummary/man/modify_table_body.Rd | 3 gtsummary-1.5.1/gtsummary/man/modify_table_header.Rd | 3 gtsummary-1.5.1/gtsummary/man/modify_table_styling.Rd | 19 gtsummary-1.5.1/gtsummary/man/plot.Rd | 2 gtsummary-1.5.1/gtsummary/man/print_gtsummary.Rd | 1 gtsummary-1.5.1/gtsummary/man/proportion_summary.Rd | 1 gtsummary-1.5.1/gtsummary/man/ratio_summary.Rd | 1 gtsummary-1.5.1/gtsummary/man/remove_row_type.Rd | 3 gtsummary-1.5.1/gtsummary/man/select_helpers.Rd | 3 gtsummary-1.5.1/gtsummary/man/separate_p_footnotes.Rd | 2 gtsummary-1.5.1/gtsummary/man/set_gtsummary_theme.Rd | 2 gtsummary-1.5.1/gtsummary/man/style_percent.Rd | 2 gtsummary-1.5.1/gtsummary/man/style_pvalue.Rd | 2 gtsummary-1.5.1/gtsummary/man/syntax.Rd | 115 gtsummary-1.5.1/gtsummary/man/tbl_continuous.Rd | 3 gtsummary-1.5.1/gtsummary/man/tbl_cross.Rd | 13 gtsummary-1.5.1/gtsummary/man/tbl_custom_summary.Rd | 22 gtsummary-1.5.1/gtsummary/man/tbl_merge.Rd | 3 gtsummary-1.5.1/gtsummary/man/tbl_regression.Rd | 14 gtsummary-1.5.1/gtsummary/man/tbl_regression_methods.Rd | 1 gtsummary-1.5.1/gtsummary/man/tbl_split.Rd | 12 gtsummary-1.5.1/gtsummary/man/tbl_strata.Rd | 76 gtsummary-1.5.1/gtsummary/man/tbl_summary.Rd | 13 gtsummary-1.5.1/gtsummary/man/tbl_survfit.Rd | 4 gtsummary-1.5.1/gtsummary/man/tbl_survfit_errors.Rd | 1 gtsummary-1.5.1/gtsummary/man/tbl_svysummary.Rd | 8 gtsummary-1.5.1/gtsummary/man/tbl_uvregression.Rd | 17 gtsummary-1.5.1/gtsummary/man/tests.Rd | 86 gtsummary-1.5.1/gtsummary/man/theme_gtsummary.Rd | 11 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_ci.R | 13 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_difference.R | 38 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_overall.R | 31 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_p.tbl_continuous.R |only gtsummary-1.5.1/gtsummary/tests/testthat/test-add_p.tbl_cross.R | 43 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_p.tbl_summary.R | 16 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_stat.R | 30 gtsummary-1.5.1/gtsummary/tests/testthat/test-add_stat_label.R | 21 gtsummary-1.5.1/gtsummary/tests/testthat/test-as_kable.R | 13 gtsummary-1.5.1/gtsummary/tests/testthat/test-as_kable_extra.R | 31 gtsummary-1.5.1/gtsummary/tests/testthat/test-as_tibble.R | 30 gtsummary-1.5.1/gtsummary/tests/testthat/test-custom_tidiers.R | 19 gtsummary-1.5.1/gtsummary/tests/testthat/test-inline_text.R | 10 gtsummary-1.5.1/gtsummary/tests/testthat/test-modify_column_alignment.R |only gtsummary-1.5.1/gtsummary/tests/testthat/test-modify_footnote.R | 10 gtsummary-1.5.1/gtsummary/tests/testthat/test-modify_header.R | 27 gtsummary-1.5.1/gtsummary/tests/testthat/test-modify_spanning_header.R | 16 gtsummary-1.5.1/gtsummary/tests/testthat/test-separate_p_footnotes.R | 3 gtsummary-1.5.1/gtsummary/tests/testthat/test-set_gtsummary_theme.R | 21 gtsummary-1.5.1/gtsummary/tests/testthat/test-style_percent.R | 6 gtsummary-1.5.1/gtsummary/tests/testthat/test-style_pvalue.R | 6 gtsummary-1.5.1/gtsummary/tests/testthat/test-style_ratio.R | 9 gtsummary-1.5.1/gtsummary/tests/testthat/test-style_sigfig.R | 6 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_continuous.R | 23 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_cross.R | 16 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_custom_summary.R | 53 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_merge.R | 88 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_regression.R | 3 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_strata.R | 50 gtsummary-1.5.1/gtsummary/tests/testthat/test-tbl_uvregression.R | 6 gtsummary-1.5.1/gtsummary/vignettes/gallery.Rmd | 23 gtsummary-1.5.1/gtsummary/vignettes/global_options.Rmd | 2 gtsummary-1.5.1/gtsummary/vignettes/gtsummary_definition.Rmd | 2 gtsummary-1.5.1/gtsummary/vignettes/inline_text.Rmd | 12 gtsummary-1.5.1/gtsummary/vignettes/tbl_regression.Rmd | 16 gtsummary-1.5.1/gtsummary/vignettes/tbl_summary.Rmd | 16 301 files changed, 5561 insertions(+), 3547 deletions(-)
Title: Melting Temperature of Nucleic Acid Sequences
Description: This tool is extended from methods in Bio.SeqUtils.MeltingTemp of python. The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <doi:10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <doi:10.1093/clinchem/47.11.1956>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).
Author: Junhui Li
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between TmCalculator versions 1.0.1 dated 2020-07-31 and 1.0.2 dated 2022-01-20
TmCalculator-1.0.1/TmCalculator/man/TmCalculator-package.Rd |only TmCalculator-1.0.2/TmCalculator/DESCRIPTION | 10 TmCalculator-1.0.2/TmCalculator/MD5 | 47 - TmCalculator-1.0.2/TmCalculator/NAMESPACE | 15 TmCalculator-1.0.2/TmCalculator/R/GC.R | 189 ++++--- TmCalculator-1.0.2/TmCalculator/R/Tm_GC.R | 154 +++++- TmCalculator-1.0.2/TmCalculator/R/Tm_NN.R | 272 +++++++++- TmCalculator-1.0.2/TmCalculator/R/Tm_Wallace.R | 50 + TmCalculator-1.0.2/TmCalculator/R/c2s.R | 23 TmCalculator-1.0.2/TmCalculator/R/check_filter.R | 34 + TmCalculator-1.0.2/TmCalculator/R/chem_correction.R | 83 ++- TmCalculator-1.0.2/TmCalculator/R/complement.R | 25 TmCalculator-1.0.2/TmCalculator/R/print.TmCalculator.R |only TmCalculator-1.0.2/TmCalculator/R/s2c.R | 34 + TmCalculator-1.0.2/TmCalculator/R/salt_correction.R | 189 +++++-- TmCalculator-1.0.2/TmCalculator/man/GC.Rd | 63 +- TmCalculator-1.0.2/TmCalculator/man/Tm_GC.Rd | 198 ++++--- TmCalculator-1.0.2/TmCalculator/man/Tm_NN.Rd | 303 ++++++------ TmCalculator-1.0.2/TmCalculator/man/Tm_Wallace.Rd | 67 +- TmCalculator-1.0.2/TmCalculator/man/c2s.Rd | 57 +- TmCalculator-1.0.2/TmCalculator/man/check_filter.Rd | 71 +- TmCalculator-1.0.2/TmCalculator/man/chem_correction.Rd | 104 ++-- TmCalculator-1.0.2/TmCalculator/man/complement.Rd | 58 +- TmCalculator-1.0.2/TmCalculator/man/print.TmCalculator.Rd |only TmCalculator-1.0.2/TmCalculator/man/s2c.Rd | 57 +- TmCalculator-1.0.2/TmCalculator/man/salt_correction.Rd | 168 +++--- 26 files changed, 1458 insertions(+), 813 deletions(-)
Title: Create Flexible Forest Plot
Description: Create forest plot based on the layout of the data. Confidence interval in multiple columns by groups can be done easily. Editing plot, inserting/adding text, applying theme to the plot and much more.
Author: Alimu Dayimu [aut, cre] (<https://orcid.org/0000-0001-9998-7463>)
Maintainer: Alimu Dayimu <ad938@cam.ac.uk>
Diff between forestploter versions 0.0.1 dated 2022-01-11 and 0.1.1 dated 2022-01-20
forestploter-0.0.1/forestploter/man/vert_line.Rd |only forestploter-0.1.1/forestploter/DESCRIPTION | 6 forestploter-0.1.1/forestploter/MD5 | 41 +-- forestploter-0.1.1/forestploter/NEWS.md | 15 + forestploter-0.1.1/forestploter/R/add_text.r | 27 +- forestploter-0.1.1/forestploter/R/add_underline.R | 20 + forestploter-0.1.1/forestploter/R/edit_plot.R | 43 +-- forestploter-0.1.1/forestploter/R/forest.R | 59 ++++- forestploter-0.1.1/forestploter/R/helper.R | 7 forestploter-0.1.1/forestploter/R/insert_text.R | 109 ++++++---- forestploter-0.1.1/forestploter/R/legend_grob.R | 5 forestploter-0.1.1/forestploter/R/make-arrow.R | 2 forestploter-0.1.1/forestploter/R/make-xaixs.R | 4 forestploter-0.1.1/forestploter/R/makeci.R | 19 + forestploter-0.1.1/forestploter/R/theme.R | 19 + forestploter-0.1.1/forestploter/inst/doc/forestploter-intro.html | 4 forestploter-0.1.1/forestploter/man/forest.Rd | 5 forestploter-0.1.1/forestploter/man/forest_theme.Rd | 10 forestploter-0.1.1/forestploter/man/insert_text.Rd | 1 forestploter-0.1.1/forestploter/man/legend_grob.Rd | 4 forestploter-0.1.1/forestploter/man/make_arrow.Rd | 1 forestploter-0.1.1/forestploter/man/makeci.Rd | 4 22 files changed, 265 insertions(+), 140 deletions(-)
Title: Estimation of the Rasch Model for Multistage Tests
Description: Provides conditional maximum likelihood (CML) item parameter estimation of sequential as well as cumulative deterministic multistage designs (Zwitser & Maris, 2015, <doi:10.1007/s11336-013-9369-6>) as well as probabilistic sequential and cumulative multistage designs (Steinfeld & Robitzsch, 2021, <doi:10.31234/osf.io/ew27f>). Supports CML item parameter estimation of conventional linear designs and additional functions for the likelihood ratio test (Andersen, 1973, <doi:10.1007/BF02291180>) as well as functions for the simulation of several kinds of multistage designs.
Author: Jan Steinfeld [cre, aut] (<https://orcid.org/0000-0001-9853-8260>),
Alexander Robitzsch [aut] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Jan Steinfeld <jan.d.steinfeld@gmail.com>
Diff between tmt versions 0.2.1-0 dated 2019-07-05 and 0.3.0-20 dated 2022-01-20
DESCRIPTION | 17 MD5 | 97 +- NAMESPACE | 1 NEWS.md | 16 R/RcppExports.R | 8 R/data_processing_mst.R | 38 - R/data_processing_nmst.R | 1 R/helper_functions.R | 1255 +++++++++++++++++++++++++++++++--- R/lrtest.mst.R | 8 R/lrtest.nmst.R | 4 R/raschmodel.mst.R | 156 ++-- R/raschmodel.nmst.R | 16 R/sim.rm.R | 22 R/tmt.r | 11 R/tmt_gmc.R | 4 R/tmt_lrtest.R | 2 R/tmt_mstdesign.R | 110 ++ R/tmt_msttemplate.R |only R/tmt_rm.R | 17 R/tmt_sim.R | 362 ++++++--- README.md | 153 ++-- build/vignette.rds |binary inst/CITATION | 3 inst/NEWS | 12 inst/doc/introduction_to_tmt.R | 41 - inst/doc/introduction_to_tmt.Rmd | 71 - inst/doc/introduction_to_tmt.html | 645 +++++++++-------- man/tmt-package.Rd | 24 man/tmt_gmc.Rd | 21 man/tmt_lrtest.Rd | 2 man/tmt_mstdesign.Rd | 31 man/tmt_msttemplate.Rd |only man/tmt_rm.Rd | 71 - man/tmt_sim.Rd | 61 - src/RcppExports.cpp | 33 src/esf_mst_sum_vector.cpp | 517 +++++++------- src/esf_mst_sum_vector_s1.h | 15 src/esf_mst_sum_vector_s2.h | 66 + tests/testthat/test-helperfunctions.R | 804 +++++++++++++++++++-- tests/testthat/test-lrtest.R | 33 tests/testthat/test-print.R | 18 tests/testthat/test-raschmodel.R | 46 - tests/testthat/test-sim.R | 32 tests/testthat/test-summary.R | 23 tests/testthat/test-tmt_gmc.R | 5 tests/testthat/test-tmt_mstdesign.R | 314 +++++++- tests/testthat/test-tmt_msttemplate.R |only tests/testthat/test-tmt_rm.R | 216 +++++ tests/testthat/test-tmt_sim.R | 380 +++++++--- vignettes/introduction_to_tmt.Rmd | 71 - vignettes/references.bib | 28 51 files changed, 4284 insertions(+), 1597 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.1.1 dated 2021-12-03 and 3.1.2 dated 2022-01-20
testthat-3.1.1/testthat/R/utils-io.R |only testthat-3.1.2/testthat/DESCRIPTION | 11 testthat-3.1.2/testthat/MD5 | 116 +++--- testthat-3.1.2/testthat/NAMESPACE | 3 testthat-3.1.2/testthat/NEWS.md | 47 ++ testthat-3.1.2/testthat/R/capture-output.R | 9 testthat-3.1.2/testthat/R/evaluate-promise.R | 10 testthat-3.1.2/testthat/R/expect-condition.R | 14 testthat-3.1.2/testthat/R/expect-known.R | 12 testthat-3.1.2/testthat/R/local.R | 15 testthat-3.1.2/testthat/R/reporter-check.R | 10 testthat-3.1.2/testthat/R/reporter-junit.R | 4 testthat-3.1.2/testthat/R/reporter-progress.R | 24 + testthat-3.1.2/testthat/R/reporter.R | 4 testthat-3.1.2/testthat/R/skip.R | 3 testthat-3.1.2/testthat/R/snapshot-cleanup.R | 31 + testthat-3.1.2/testthat/R/snapshot-file-snaps.R | 16 testthat-3.1.2/testthat/R/snapshot-file.R | 52 ++- testthat-3.1.2/testthat/R/snapshot-manage.R | 27 + testthat-3.1.2/testthat/R/snapshot-reporter.R | 65 ++- testthat-3.1.2/testthat/R/snapshot-serialize.R | 6 testthat-3.1.2/testthat/R/snapshot.R | 105 +++++- testthat-3.1.2/testthat/R/source.R | 2 testthat-3.1.2/testthat/R/test-files.R | 2 testthat-3.1.2/testthat/R/testthat-package.R | 1 testthat-3.1.2/testthat/R/utils.R | 7 testthat-3.1.2/testthat/README.md | 2 testthat-3.1.2/testthat/inst/doc/custom-expectation.html | 2 testthat-3.1.2/testthat/inst/doc/skipping.html | 2 testthat-3.1.2/testthat/inst/doc/snapshotting.html | 167 ++++------ testthat-3.1.2/testthat/inst/doc/test-fixtures.html | 6 testthat-3.1.2/testthat/inst/doc/third-edition.html | 4 testthat-3.1.2/testthat/man/expect_error.Rd | 2 testthat-3.1.2/testthat/man/expect_snapshot.Rd | 10 testthat-3.1.2/testthat/man/expect_snapshot_file.Rd | 18 - testthat-3.1.2/testthat/man/local_snapshotter.Rd | 7 testthat-3.1.2/testthat/man/local_test_context.Rd | 8 testthat-3.1.2/testthat/man/skip.Rd | 2 testthat-3.1.2/testthat/man/snapshot_accept.Rd | 6 testthat-3.1.2/testthat/tests/testthat/_snaps/reporter-check.md | 6 testthat-3.1.2/testthat/tests/testthat/_snaps/reporter-junit.md | 6 testthat-3.1.2/testthat/tests/testthat/_snaps/snapshot-file.md | 12 testthat-3.1.2/testthat/tests/testthat/_snaps/snapshot-file/a.txt |only testthat-3.1.2/testthat/tests/testthat/_snaps/snapshot-file/secret.txt |only testthat-3.1.2/testthat/tests/testthat/_snaps/snapshot-manage.md | 32 + testthat-3.1.2/testthat/tests/testthat/_snaps/snapshot.md | 80 ++++ testthat-3.1.2/testthat/tests/testthat/setup.R | 4 testthat-3.1.2/testthat/tests/testthat/test-colour.R | 3 testthat-3.1.2/testthat/tests/testthat/test-deprec-condition.R | 8 testthat-3.1.2/testthat/tests/testthat/test-expect-known.R | 22 - testthat-3.1.2/testthat/tests/testthat/test-expect-known.txt |only testthat-3.1.2/testthat/tests/testthat/test-local.R | 9 testthat-3.1.2/testthat/tests/testthat/test-reporter.R | 9 testthat-3.1.2/testthat/tests/testthat/test-snapshot-cleanup.R | 14 testthat-3.1.2/testthat/tests/testthat/test-snapshot-file-snaps.R | 2 testthat-3.1.2/testthat/tests/testthat/test-snapshot-file.R | 36 +- testthat-3.1.2/testthat/tests/testthat/test-snapshot-manage.R | 27 + testthat-3.1.2/testthat/tests/testthat/test-snapshot-reporter.R | 60 +++ testthat-3.1.2/testthat/tests/testthat/test-snapshot-serialize.R | 9 testthat-3.1.2/testthat/tests/testthat/test-snapshot.R | 39 ++ testthat-3.1.2/testthat/tests/testthat/test-teardown/test-teardown.R | 2 61 files changed, 867 insertions(+), 345 deletions(-)
Title: Speedy Word Embedding Association Test and Extras Using R
Description: Conduct various tests for evaluating implicit biases in word embeddings: Word Embedding Association Test (Caliskan et al., 2017), <doi:10.1126/science.aal4230>, Relative Norm Distance (Garg et al., 2018), <doi:10.1073/pnas.1720347115>, Mean Average Cosine Similarity (Mazini et al., 2019) <arXiv:1904.04047>, SemAxis (An et al., 2018) <arXiv:1806.05521>, Relative Negative Sentiment Bias (Sweeney & Najafian, 2019) <doi:10.18653/v1/P19-1162>, and Embedding Coherence Test (Dev & Phillips, 2019) <arXiv:1901.07656>.
Author: Chung-hong Chan [aut, cre] (<https://orcid.org/0000-0002-6232-7530>)
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between sweater versions 0.1.2 dated 2021-11-24 and 0.1.4 dated 2022-01-20
DESCRIPTION | 10 +- MD5 | 48 +++++----- NAMESPACE | 7 + R/ect.R |only R/mac.R | 2 R/misc.R | 22 ++-- R/nas.R | 2 R/query.R | 17 ++- R/rnd.R | 2 R/rnsb.R | 2 R/s3.R |only R/semaxis.R | 2 R/sweater.R | 2 README.md | 175 +++++++++++++++++++++++++++++++------ man/calculate_es.Rd | 2 man/ect.Rd |only man/ect_es.Rd |only man/figures/README-ectplot-1.png |only man/plot_bias.Rd | 9 + man/plot_ect.Rd |only man/query.Rd | 16 ++- tests/testthat/_snaps/s3.md |only tests/testthat/test-calculate_es.R | 7 + tests/testthat/test-es.R | 1 tests/testthat/test-na.R | 20 +++- tests/testthat/test-no_es.R | 29 ++++++ tests/testthat/test-plot.R | 21 +++- tests/testthat/test-query.R | 3 tests/testthat/test-s3.R |only 29 files changed, 307 insertions(+), 92 deletions(-)
Title: Random Forests, Linear Trees, and Gradient Boosting for
Inference and Interpretability
Description: Provides fast implementations of Honest Random Forests,
Gradient Boosting, and Linear Random Forests, with an emphasis on inference
and interpretability. Additionally contains methods for variable
importance, out-of-bag prediction, regression monotonicity, and
several methods for missing data imputation. Soren R. Kunzel,
Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon (2019) <arXiv:1906.06463>.
Author: Sören Künzel [aut],
Theo Saarinen [aut, cre],
Simon Walter [aut],
Edward Liu [aut],
Allen Tang [aut],
Jasjeet Sekhon [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
Diff between Rforestry versions 0.9.0.57 dated 2021-09-02 and 0.9.0.72 dated 2022-01-20
DESCRIPTION | 12 MD5 | 77 +-- NAMESPACE | 1 R/R_preprocessing.R | 59 ++ R/RcppExports.R | 16 R/adaptive_forestry.R | 3 R/forestry.R | 609 ++++++++++++++++++++++++++-- README.md | 35 + man/adaptiveForestry-forestry.Rd | 17 man/correctedPredict-forestry.Rd |only man/forestry.Rd | 32 + man/multilayer-forestry.Rd | 32 + man/scale_center.Rd |only man/training_data_checker-forestry.Rd | 14 man/unscale_uncenter.Rd |only src/RcppExports.cpp | 36 - src/forestry.cpp | 152 +++++- src/forestry.h | 9 src/multilayerForestry.cpp | 1 src/rcpp_cppBuildInterface.cpp | 28 + src/utils.cpp | 38 + src/utils.h | 6 tests/testthat/setup.R | 2 tests/testthat/test-ExactPredict.R | 12 tests/testthat/test-OOBpredictions.R | 10 tests/testthat/test-coefs.R | 6 tests/testthat/test-compute_rf_lp.R | 2 tests/testthat/test-conformalIntervals.R | 3 tests/testthat/test-correctedPredict.R |only tests/testthat/test-deepsplitting.R | 2 tests/testthat/test-differentAggregations.R | 2 tests/testthat/test-exactOOBpredict.R |only tests/testthat/test-forestry.R | 4 tests/testthat/test-forestry_weightmatrix.R | 3 tests/testthat/test-groupSampling.R |only tests/testthat/test-impute_features.R | 4 tests/testthat/test-max-depth.R | 2 tests/testthat/test-minSplitGain.R | 5 tests/testthat/test-observationWeights.R | 2 tests/testthat/test-predictInfo.R | 7 tests/testthat/test-saveRF.R | 2 tests/testthat/test-scale.R |only tests/testthat/test-terminalNodes.R | 5 43 files changed, 1090 insertions(+), 160 deletions(-)
Title: Evaluation Metrics for Implicit-Feedback Recommender Systems
Description: Calculates evaluation metrics for implicit-feedback recommender systems
that are based on low-rank matrix factorization models, given the fitted model
matrices and data, thus allowing to compare models from a variety of libraries.
Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k),
AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k),
Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from
which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the
receiver-operating characteristic curve), and PR-AUC (area under the
precision-recall curve).
These are calculated on a per-user basis according to the ranking of items induced
by the model, using efficient multi-threaded routines. Also provides functions
for creating train-test splits for model fitting and evaluation.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between recometrics versions 0.1.5-2 dated 2021-10-14 and 0.1.6 dated 2022-01-20
DESCRIPTION | 6 ++-- LICENSE | 2 - MD5 | 16 +++++------ build/vignette.rds |binary configure | 75 ++++++++++++++++++++++++++++++++++++++++++++++------- configure.ac | 24 ++++++++++++++++ src/Makevars.in | 2 - src/Makevars.win | 2 - src/recometrics.h | 60 ++++++++++++++++++++++++------------------ 9 files changed, 138 insertions(+), 49 deletions(-)
Title: QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Description: Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.
Author: Peter Bourke [aut, cre],
Christine Hackett [ctb],
Chris Maliepaard [ctb],
Geert van Geest [ctb],
Roeland Voorrips [ctb],
Johan Willemsen [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polyqtlR versions 0.0.7 dated 2021-12-09 and 0.0.8 dated 2022-01-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/polyqtlR_functions.R | 4 ++-- inst/doc/polyqtlR_vignette.html | 4 ++-- man/convert_mappoly_to_phased.maplist.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin,
2020 <doi:10.1101/2020.10.07.329383>) can be used for
a variety of multivariate problems when count data are at play, including
principal component analysis for count data, discriminant analysis, model-based clustering and
network inference. Implements variational algorithms to fit such models accompanied with a set of
functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Mahendra Mariadassou [aut] (<https://orcid.org/0000-0003-2986-354X>),
Stéphane Robin [ctb],
François Gindraud [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 0.11.4 dated 2021-03-16 and 0.11.5 dated 2022-01-20
PLNmodels-0.11.4/PLNmodels/src/optimize.cpp |only PLNmodels-0.11.4/PLNmodels/src/optimize_ve.cpp |only PLNmodels-0.11.5/PLNmodels/DESCRIPTION | 8 PLNmodels-0.11.5/PLNmodels/MD5 | 95 - PLNmodels-0.11.5/PLNmodels/NEWS.md | 11 PLNmodels-0.11.5/PLNmodels/R/PLNLDAfit-class.R | 2 PLNmodels-0.11.5/PLNmodels/R/PLNPCAfit-class.R | 79 - PLNmodels-0.11.5/PLNmodels/R/PLNfamily-class.R | 2 PLNmodels-0.11.5/PLNmodels/R/PLNfit-class.R | 8 PLNmodels-0.11.5/PLNmodels/R/PLNmixturefamily-class.R | 21 PLNmodels-0.11.5/PLNmodels/R/PLNmixturefit-S3methods.R | 2 PLNmodels-0.11.5/PLNmodels/R/PLNmixturefit-class.R | 5 PLNmodels-0.11.5/PLNmodels/R/RcppExports.R | 28 PLNmodels-0.11.5/PLNmodels/R/import_utils.R | 2 PLNmodels-0.11.5/PLNmodels/R/utils.R | 2 PLNmodels-0.11.5/PLNmodels/build/partial.rdb |binary PLNmodels-0.11.5/PLNmodels/build/vignette.rds |binary PLNmodels-0.11.5/PLNmodels/inst/doc/Import_data.html | 4 PLNmodels-0.11.5/PLNmodels/inst/doc/PLN.html | 78 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNLDA.html | 784 +++++----- PLNmodels-0.11.5/PLNmodels/inst/doc/PLNPCA.R | 19 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNPCA.Rmd | 36 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNPCA.html | 269 +-- PLNmodels-0.11.5/PLNmodels/inst/doc/PLNmixture.R | 12 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNmixture.Rmd | 15 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNmixture.html | 248 +-- PLNmodels-0.11.5/PLNmodels/inst/doc/PLNnetwork.R | 14 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNnetwork.Rmd | 18 PLNmodels-0.11.5/PLNmodels/inst/doc/PLNnetwork.html | 246 +-- PLNmodels-0.11.5/PLNmodels/inst/doc/Trichoptera.html | 8 PLNmodels-0.11.5/PLNmodels/man/PLNPCAfit.Rd | 68 PLNmodels-0.11.5/PLNmodels/man/PLNfamily.Rd | 2 PLNmodels-0.11.5/PLNmodels/man/compute_offset.Rd | 2 PLNmodels-0.11.5/PLNmodels/man/plot.PLNmixturefit.Rd | 2 PLNmodels-0.11.5/PLNmodels/src/Makevars | 14 PLNmodels-0.11.5/PLNmodels/src/Makevars.win | 5 PLNmodels-0.11.5/PLNmodels/src/RcppExports.cpp | 98 - PLNmodels-0.11.5/PLNmodels/src/optim_diag_cov.cpp |only PLNmodels-0.11.5/PLNmodels/src/optim_full_cov.cpp |only PLNmodels-0.11.5/PLNmodels/src/optim_genet_cov.cpp |only PLNmodels-0.11.5/PLNmodels/src/optim_rank_cov.cpp |only PLNmodels-0.11.5/PLNmodels/src/optim_sparse_cov.cpp |only PLNmodels-0.11.5/PLNmodels/src/optim_spherical.cpp |only PLNmodels-0.11.5/PLNmodels/src/utils.h |only PLNmodels-0.11.5/PLNmodels/tests/testthat/Rplots.pdf |binary PLNmodels-0.11.5/PLNmodels/tests/testthat/test-pln.R | 10 PLNmodels-0.11.5/PLNmodels/tests/testthat/test-plnlda.R | 1 PLNmodels-0.11.5/PLNmodels/tests/testthat/test-plnmixture.R | 26 PLNmodels-0.11.5/PLNmodels/tests/testthat/test-plnnetworkfamily.R | 3 PLNmodels-0.11.5/PLNmodels/tests/testthat/test-plnpcafit.R | 16 PLNmodels-0.11.5/PLNmodels/vignettes/PLNPCA.Rmd | 36 PLNmodels-0.11.5/PLNmodels/vignettes/PLNmixture.Rmd | 15 PLNmodels-0.11.5/PLNmodels/vignettes/PLNnetwork.Rmd | 18 53 files changed, 1271 insertions(+), 1061 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] (<https://orcid.org/0000-0002-2195-5469>),
Kosuke Imai [aut] (<https://orcid.org/0000-0002-2748-1022>),
Gary King [aut] (<https://orcid.org/0000-0002-5327-7631>),
Elizabeth Stuart [aut] (<https://orcid.org/0000-0002-9042-8611>),
Alex Whitworth [ctb],
Noah Greifer [ctb, cre, aut] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.3.2 dated 2021-11-23 and 4.3.3 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/match.data.R | 13 +++++++++---- build/partial.rdb |binary inst/doc/MatchIt.html | 8 ++++---- inst/doc/assessing-balance.html | 6 +++--- inst/doc/estimating-effects.Rmd | 14 +------------- inst/doc/estimating-effects.html | 16 ++++++++-------- inst/doc/matching-methods.html | 4 ++-- inst/doc/sampling-weights.html | 4 ++-- man/summary.matchit.Rd | 2 +- vignettes/estimating-effects.Rmd | 14 +------------- 13 files changed, 50 insertions(+), 65 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (www.jamovi.org)
aims to make statistical analyses easy and intuitive. 'jamovi' produces
syntax that can directly be used in R (in connection with the R-package 'jmv').
Having import / export routines for the data files 'jamovi' produces ('.omv')
permits an easy transfer of analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre]
(<https://orcid.org/0000-0003-2576-5432>)
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.2.3 dated 2022-01-19 and 0.2.4 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/read_omv.R | 5 +++-- R/write_omv.R | 8 ++++---- README.md | 4 ++-- inst/doc/jmvReadWrite.html | 8 ++++---- man/write_omv.Rd | 2 +- 8 files changed, 31 insertions(+), 23 deletions(-)
Title: Efficient Implementation of Binary Segmentation
Description: Standard template library
containers are used to implement an efficient binary segmentation
algorithm, which is log-linear on average and quadratic in the
worst case.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between binsegRcpp versions 2020.9.3 dated 2020-09-14 and 2021.11.3 dated 2022-01-20
DESCRIPTION | 14 - MD5 | 50 +++- NAMESPACE | 25 +- NEWS | 61 ++++- R/RcppExports.R | 14 - R/binseg_normal.R | 317 +++++++++++++++++----------- R/binseg_normal_cv.R |only R/complexity.R |only R/random_set_vec.R |only build |only inst |only man/binsegRcpp-package.Rd | 68 +++--- man/binseg_normal.Rd | 208 ++++++++++++------ man/binseg_normal_cv.Rd |only man/case.colors.Rd |only man/case.sizes.Rd |only man/coef.binseg_normal.Rd | 44 +-- man/coef.binseg_normal_cv.Rd |only man/get_complexity.Rd |only man/get_complexity_empirical.Rd |only man/get_complexity_extreme.Rd |only man/plot.binseg_normal.Rd | 38 +-- man/plot.binseg_normal_cv.Rd |only man/plot.complexity.Rd |only man/print.binseg_normal.Rd |only man/print.binseg_normal_cv.Rd |only man/random_set_vec.Rd |only src/RcppExports.cpp | 15 - src/binseg_normal.cpp | 423 +++++++++++++++++++++++++++++--------- src/binseg_normal.h | 12 - src/interface.cpp | 35 ++- tests/testthat.R | 2 tests/testthat/test-CRAN-binseg.R | 204 ++++++++++++------ vignettes |only 34 files changed, 1036 insertions(+), 494 deletions(-)
Title: Bayesian Grouped Weighted Quantile Sum Regression
Description: Fits Bayesian grouped weighted quantile sum (BGWQS) regressions for one or more chemical groups with binary outcomes. Wheeler DC et al. (2019) <doi:10.1016/j.sste.2019.100286>.
Author: David Wheeler, Matthew Carli
Maintainer: Matthew Carli <carlimm@mymail.vcu.edu>
Diff between BayesGWQS versions 0.0.2 dated 2020-06-23 and 0.1.1 dated 2022-01-20
BayesGWQS-0.0.2/BayesGWQS/R/model_gen.R |only BayesGWQS-0.1.1/BayesGWQS/DESCRIPTION | 18 BayesGWQS-0.1.1/BayesGWQS/MD5 | 21 BayesGWQS-0.1.1/BayesGWQS/NAMESPACE | 1 BayesGWQS-0.1.1/BayesGWQS/NEWS.md |only BayesGWQS-0.1.1/BayesGWQS/R/bgwqs.fit.R | 304 +++++++++----- BayesGWQS-0.1.1/BayesGWQS/R/model_gen_fns.R |only BayesGWQS-0.1.1/BayesGWQS/R/quantile.fn.R | 1 BayesGWQS-0.1.1/BayesGWQS/R/squeeze2.R |only BayesGWQS-0.1.1/BayesGWQS/R/weight.plot.R |only BayesGWQS-0.1.1/BayesGWQS/R/zscore.fn.R |only BayesGWQS-0.1.1/BayesGWQS/man/bgwqs.fit.Rd | 23 - BayesGWQS-0.1.1/BayesGWQS/man/simdata.Rd | 6 BayesGWQS-0.1.1/BayesGWQS/man/weight.plot.Rd |only BayesGWQS-0.1.1/BayesGWQS/tests/testthat/test-bgwqs.fit.R | 26 - 15 files changed, 260 insertions(+), 140 deletions(-)
Title: Bindings for Additive TidyModels
Description: Fit Generalized Additive Models (GAM) using 'mgcv' with 'parsnip'/'tidymodels'
via 'additive' <doi:10.5281/zenodo.5884867>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'mgcv' are described in Wood (2017)
<doi:10.1201/9781315370279>.
Author: Hamada S. Badr [aut, cre] (<https://orcid.org/0000-0002-9808-2344>)
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between additive versions 0.0.3 dated 2021-09-30 and 0.0.4 dated 2022-01-20
DESCRIPTION | 12 ++++---- MD5 | 30 ++++++++++---------- NAMESPACE | 1 NEWS.md | 15 ++++++++-- R/additive.R | 2 - R/additive_init.R | 2 - R/additive_make.R | 8 ++++- README.md | 68 ++++++++++++++++++++++++----------------------- inst/CITATION | 6 ++-- inst/WORDLIST | 1 inst/doc/BugReports.html | 5 ++- inst/doc/GetStarted.R | 3 +- inst/doc/GetStarted.Rmd | 5 ++- inst/doc/GetStarted.html | 10 ++++-- man/additive.Rd | 2 - vignettes/GetStarted.Rmd | 5 ++- 16 files changed, 101 insertions(+), 74 deletions(-)
Title: R Markdown Templates to Preregister Scientific Studies
Description: Provides a collection of templates to author preregistration documents for scientific studies in PDF format.
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>),
Lisa Spitzer [aut],
Jeffrey R. Stevens [ctb] (<https://orcid.org/0000-0003-2375-1360>),
Masataka Ogawa [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between prereg versions 0.5.0 dated 2020-12-02 and 0.6.0 dated 2022-01-20
prereg-0.5.0/prereg/R/aspredicted_prereg.R |only prereg-0.5.0/prereg/R/brandt_prereg.R |only prereg-0.5.0/prereg/R/cos_prereg.R |only prereg-0.5.0/prereg/R/psyquant_prereg.R |only prereg-0.5.0/prereg/R/rr_prereg.R |only prereg-0.5.0/prereg/R/vantveer_prereg.R |only prereg-0.5.0/prereg/inst/rmarkdown/templates/psyquant_prereg |only prereg-0.5.0/prereg/inst/rmarkdown/templates/rr_prereg/skeleton/skeleton.pdf |only prereg-0.5.0/prereg/inst/rmd/apa6.csl |only prereg-0.5.0/prereg/man/aspredicted_prereg.Rd |only prereg-0.5.0/prereg/man/brandt_prereg.Rd |only prereg-0.5.0/prereg/man/cos_prereg.Rd |only prereg-0.5.0/prereg/man/psyquant_prereg.Rd |only prereg-0.5.0/prereg/man/rr_prereg.Rd |only prereg-0.5.0/prereg/man/vantveer_prereg.Rd |only prereg-0.5.0/prereg/tools/images/unnamed-chunk-1-1.png |only prereg-0.6.0/prereg/DESCRIPTION | 17 prereg-0.6.0/prereg/MD5 | 56 +- prereg-0.6.0/prereg/NAMESPACE | 3 prereg-0.6.0/prereg/R/prereg.R | 44 +- prereg-0.6.0/prereg/R/prereg_pdf.R |only prereg-0.6.0/prereg/R/utils.R | 4 prereg-0.6.0/prereg/README.md | 111 +++-- prereg-0.6.0/prereg/build |only prereg-0.6.0/prereg/inst/NEWS.md | 14 prereg-0.6.0/prereg/inst/rmarkdown/templates/aspredicted_prereg/skeleton/skeleton.Rmd | 39 + prereg-0.6.0/prereg/inst/rmarkdown/templates/brandt_prereg/skeleton/skeleton.Rmd | 4 prereg-0.6.0/prereg/inst/rmarkdown/templates/cos_prereg/skeleton/skeleton.Rmd | 2 prereg-0.6.0/prereg/inst/rmarkdown/templates/cruewell_prereg |only prereg-0.6.0/prereg/inst/rmarkdown/templates/fmri_prereg |only prereg-0.6.0/prereg/inst/rmarkdown/templates/prp_quant_prereg |only prereg-0.6.0/prereg/inst/rmarkdown/templates/rr_prereg/skeleton/skeleton.Rmd | 2 prereg-0.6.0/prereg/inst/rmarkdown/templates/vantveer_prereg/skeleton/skeleton.Rmd | 2 prereg-0.6.0/prereg/inst/rmd/apa7.csl |only prereg-0.6.0/prereg/inst/rmd/prereg_form.tex | 199 +++++++--- prereg-0.6.0/prereg/man/prereg.Rd | 47 +- prereg-0.6.0/prereg/man/prereg_pdf.Rd |only prereg-0.6.0/prereg/tests/testthat/test_skeletons.R | 84 ++++ prereg-0.6.0/prereg/tools/images/pkg-deps-1.png |only 39 files changed, 431 insertions(+), 197 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>),
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] (<https://orcid.org/0000-0003-3699-2729>),
Timothy Waterhouse [ctb] (<https://orcid.org/0000-0002-0954-9660>),
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 0.11.1 dated 2021-05-10 and 1.0.0 dated 2022-01-20
DESCRIPTION | 14 - MD5 | 142 ++++++------- NAMESPACE | 5 R/Aaaa.R | 13 - R/class_build.R | 74 ++++-- R/class_matlist.R | 2 R/class_mrgmod.R | 50 +++- R/compile.R | 3 R/data_set.R | 80 ++++--- R/events.R | 190 +++++++++++------ R/funset.R | 6 R/handle_spec_block.R | 30 ++ R/matlist.R | 213 ++++++++++++++++--- R/matrix.R | 17 - R/model_include.R | 19 + R/modlib.R | 20 + R/modspec.R | 233 +++++++++++++++++++-- R/mread.R | 436 +++++++++++++++++++++------------------- R/mrgindata.R | 57 ++--- R/mrgsim_q.R | 35 +-- R/mrgsolve.R | 71 +++--- R/nm-mode.R |only R/nmxml.R | 9 R/package.R | 41 +-- R/realize_addl.R | 67 ++++-- R/utils.R | 50 +++- inst/WORDLIST | 2 inst/base/modelheader.h | 10 inst/include/RcppInclude.h | 4 inst/include/mrgsolve.h | 6 inst/models/1005.cpp | 36 +-- inst/models/MODLIST | 1 inst/models/nm-like.cpp |only inst/models/pk2iv.cpp | 3 man/BLOCK_PARSE.Rd | 18 + man/aboutsolver.Rd | 2 man/as_data_set.Rd | 28 +- man/code.Rd | 10 man/collapse_matrices.Rd |only man/collapse_matrix.Rd |only man/data_set.Rd | 8 man/ev.Rd | 8 man/ev_assign.Rd | 10 man/ev_seq.Rd | 74 ++++-- man/expand_observations.Rd | 6 man/house.Rd | 7 man/is.mrgmod.Rd | 8 man/lctran.Rd | 20 + man/matlist.Rd | 7 man/matrix_converters.Rd | 2 man/matrix_helpers.Rd | 2 man/modlib.Rd | 3 man/mread.Rd | 5 man/mrgsim_q.Rd | 8 man/mrgsolve_package.Rd | 13 - man/nmext.Rd | 2 man/outvars.Rd | 3 man/qsim.Rd | 5 man/read_nmext.Rd | 6 man/realize_addl.Rd | 59 +++-- man/simargs.Rd | 6 man/soloc.Rd | 8 man/zero_re.Rd | 2 src/RcppExports.cpp | 5 src/devtran.cpp | 2 src/housemodel-mread-header.h | 3 src/housemodel-mread-source.cpp | 1 src/mrgsolve.cpp | 58 +++-- tests/testthat/test-carry_out.R | 9 tests/testthat/test-ev.R | 33 +++ tests/testthat/test-matlist.R | 83 ++++++- tests/testthat/test-matrix.R | 23 +- tests/testthat/test-modspec.R | 141 ++++++++++++ tests/testthat/test-utils.R | 26 ++ 74 files changed, 1822 insertions(+), 831 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Colour schemes ready for each type of data (qualitative,
diverging or sequential), with colours that are distinct for all
people, including colour-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018) <doi:
10.5194/gmd-11-2541-2018> colour schemes for use with 'graphics' or
'ggplot2'. It provides tools to simulate colour-blindness and to test
how well the colours of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>,
Université Bordeaux Montaigne),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>, Université
Bordeaux Montaigne),
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>,
Université de Montréal)
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.7.0 dated 2021-09-02 and 1.8.0 dated 2022-01-20
khroma-1.7.0/khroma/man/figures/README-usage-1.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind-1.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind-2.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind-3.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind-4.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind-5.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind1-1.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind2-3.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind2-4.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind3-1.png |only khroma-1.7.0/khroma/man/figures/README-usage-colourblind3-2.png |only khroma-1.8.0/khroma/DESCRIPTION | 30 khroma-1.8.0/khroma/MD5 | 116 - khroma-1.8.0/khroma/NAMESPACE | 148 + khroma-1.8.0/khroma/NEWS.md | 50 khroma-1.8.0/khroma/R/colour.R | 24 khroma-1.8.0/khroma/R/ggplot2.R | 91 - khroma-1.8.0/khroma/R/khroma-package.R | 6 khroma-1.8.0/khroma/R/plot.R | 42 khroma-1.8.0/khroma/R/scale_colour_crameri.R | 817 +++++++++- khroma-1.8.0/khroma/R/scale_colour_okabeito.R | 24 khroma-1.8.0/khroma/R/scale_colour_science.R | 98 + khroma-1.8.0/khroma/R/scale_colour_tol.R | 416 ++++- khroma-1.8.0/khroma/R/sysdata.rda |binary khroma-1.8.0/khroma/README.md | 206 +- khroma-1.8.0/khroma/build/partial.rdb |binary khroma-1.8.0/khroma/inst/CITATION | 13 khroma-1.8.0/khroma/inst/doc/crameri.R | 6 khroma-1.8.0/khroma/inst/doc/crameri.Rmd | 7 khroma-1.8.0/khroma/inst/doc/crameri.html | 404 +++- khroma-1.8.0/khroma/inst/doc/tol.R | 20 khroma-1.8.0/khroma/inst/doc/tol.Rmd | 23 khroma-1.8.0/khroma/inst/doc/tol.html | 381 +++- khroma-1.8.0/khroma/inst/examples/ex-pick.R |only khroma-1.8.0/khroma/inst/examples/ex-plot.R | 5 khroma-1.8.0/khroma/inst/examples/ex-tol-discrete.R | 12 khroma-1.8.0/khroma/man/colour.Rd | 15 khroma-1.8.0/khroma/man/figures/README-usage-colourblind2-1.png |binary khroma-1.8.0/khroma/man/figures/README-usage-colourblind2-2.png |binary khroma-1.8.0/khroma/man/figures/README-usage-map-1.png |only khroma-1.8.0/khroma/man/figures/README-usage-tiles-1.png |only khroma-1.8.0/khroma/man/info.Rd | 3 khroma-1.8.0/khroma/man/khroma-package.Rd | 12 khroma-1.8.0/khroma/man/plot.Rd | 28 khroma-1.8.0/khroma/man/scale_crameri_cyclic.Rd | 4 khroma-1.8.0/khroma/man/scale_crameri_diverging.Rd | 274 +++ khroma-1.8.0/khroma/man/scale_crameri_mutlisequential.Rd | 5 khroma-1.8.0/khroma/man/scale_crameri_sequential.Rd | 490 +++++ khroma-1.8.0/khroma/man/scale_land.Rd | 21 khroma-1.8.0/khroma/man/scale_okabeito_discrete.Rd | 6 khroma-1.8.0/khroma/man/scale_picker.Rd |only khroma-1.8.0/khroma/man/scale_soil.Rd | 18 khroma-1.8.0/khroma/man/scale_stratigraphy.Rd | 20 khroma-1.8.0/khroma/man/scale_tol_discrete.Rd | 141 + khroma-1.8.0/khroma/man/scale_tol_diverging.Rd | 177 ++ khroma-1.8.0/khroma/man/scale_tol_sequential.Rd | 14 khroma-1.8.0/khroma/tests/testthat/_snaps/colour.md | 110 - khroma-1.8.0/khroma/tests/testthat/_snaps/plot/tiles-bright.svg |only khroma-1.8.0/khroma/tests/testthat/test-colour.R | 31 khroma-1.8.0/khroma/tests/testthat/test-ggplot2-okabeito.R | 3 khroma-1.8.0/khroma/tests/testthat/test-ggplot2-tol.R | 3 khroma-1.8.0/khroma/tests/testthat/test-ggraph-crameri.R |only khroma-1.8.0/khroma/tests/testthat/test-ggraph-okabeito.R |only khroma-1.8.0/khroma/tests/testthat/test-ggraph-science.R |only khroma-1.8.0/khroma/tests/testthat/test-ggraph-tol.R |only khroma-1.8.0/khroma/tests/testthat/test-plot.R | 12 khroma-1.8.0/khroma/vignettes/bibliography.bib | 8 khroma-1.8.0/khroma/vignettes/crameri.Rmd | 7 khroma-1.8.0/khroma/vignettes/tol.Rmd | 23 69 files changed, 3639 insertions(+), 725 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multivariate clustering (MVC), cluster validation, visualization of regionalization results, and
exporting region map and mean timeseries into NetCDF-4 file.
The technical details are described in Badr et al. (2015) <doi:10.1007/s12145-015-0221-7>.
Author: Hamada S. Badr [aut, cre] (<https://orcid.org/0000-0002-9808-2344>),
Benjamin F. Zaitchik [aut] (<https://orcid.org/0000-0002-0698-0658>),
Amin K. Dezfuli [aut] (<https://orcid.org/0000-0003-3274-8542>)
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 2.2.0 dated 2021-05-31 and 2.2.1 dated 2022-01-20
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 7 README.md | 4 build/partial.rdb |binary inst/WORDLIST | 6 inst/doc/BugReports.html | 5 src/HiClimR.f90 | 427 +++++++++++++++++++++++------------------------ 8 files changed, 240 insertions(+), 231 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided. For tutorials, please check Ma and de la Torre (2020) <DOI:10.18637/jss.v093.i14>, Ma and de la Torre (2019) <DOI:10.1111/emip.12262>, Ma (2019) <DOI:10.1007/978-3-030-05584-4_29> and de la Torre and Akbay (2019).
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 2.8.7 dated 2021-05-31 and 2.8.8 dated 2022-01-20
DESCRIPTION | 16 ++--- MD5 | 22 +++--- NAMESPACE | 4 - NEWS.md | 3 R/GDINA.R | 1 R/GMSCDM.R | 51 ++++++++------- R/Mstep.R | 166 ++++++++++++++++++++++++++-------------------------- README.md | 18 +++-- build/vignette.rds |binary inst/doc/GDINA.html | 5 - man/sim10MCDINA2.Rd | 52 ++++++++-------- src/RcppExports.cpp | 5 + 12 files changed, 176 insertions(+), 167 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-16 0.2.1
Title: Various Useful Web Tools (Including Full CRAN Dataset Search and
Fetch)
Description: A set of useful web tools to improve your productivity. Including:
searching DuckDuckGo; finding and loading datasets across all CRAN packages
(not just those you've installed); sharing a file to a paste-bin; getting a
fast GUID.
Author: LS Malenica
Maintainer: LS Malenica <lsmalenica@gmail.com>
Diff between webtools versions 0.7.8 dated 2022-01-12 and 0.7.9 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/ddg.R | 27 ++++++++++++++------------- R/dsearch.R | 39 +++++++++++++++++++-------------------- man/ddg.Rd | 10 +++++++--- man/dfetch.Rd | 6 ++++-- man/dinfo.Rd | 10 ++++------ man/dsearch.Rd | 8 +++----- 8 files changed, 61 insertions(+), 59 deletions(-)
Title: Prediction Intervals with Random Forests and Boosted Forests
Description: Implements various prediction interval methods with random forests and boosted forests.
The package has two main functions: pibf() produces prediction intervals with boosted forests
(PIBF) as described in Alakus et al. (2021) <arXiv:2106.08217> and rfpi() builds 15 distinct
variations of prediction intervals with random forests (RFPI) proposed by Roy and Larocque (2020)
<doi:10.1177/0962280219829885>.
Author: Cansu Alakus [aut, cre],
Denis Larocque [aut],
Aurelie Labbe [aut],
Hemant Ishwaran [ctb] (Author of included randomForestSRC codes),
Udaya B. Kogalur [ctb] (Author of included randomForestSRC codes)
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Diff between RFpredInterval versions 1.0.4 dated 2021-09-14 and 1.0.5 dated 2022-01-20
RFpredInterval-1.0.4/RFpredInterval/R/plot.pi.piall.R |only RFpredInterval-1.0.4/RFpredInterval/man/plot.pi.piall.Rd |only RFpredInterval-1.0.5/RFpredInterval/DESCRIPTION | 8 - RFpredInterval-1.0.5/RFpredInterval/MD5 | 36 ++--- RFpredInterval-1.0.5/RFpredInterval/NAMESPACE | 8 - RFpredInterval-1.0.5/RFpredInterval/NEWS.md | 6 RFpredInterval-1.0.5/RFpredInterval/R/RFpredInterval-package.R | 43 ++++-- RFpredInterval-1.0.5/RFpredInterval/R/piall.R | 15 +- RFpredInterval-1.0.5/RFpredInterval/R/pibf.R | 40 +++++- RFpredInterval-1.0.5/RFpredInterval/R/plot.rfpredinterval.R |only RFpredInterval-1.0.5/RFpredInterval/R/print.rfpredinterval.R |only RFpredInterval-1.0.5/RFpredInterval/R/rfpi.R | 65 ++++++++-- RFpredInterval-1.0.5/RFpredInterval/R/zzz.R | 6 RFpredInterval-1.0.5/RFpredInterval/configure | 18 +- RFpredInterval-1.0.5/RFpredInterval/configure.ac | 2 RFpredInterval-1.0.5/RFpredInterval/man/RFpredInterval-package.Rd | 43 ++++-- RFpredInterval-1.0.5/RFpredInterval/man/piall.Rd | 3 RFpredInterval-1.0.5/RFpredInterval/man/pibf.Rd | 16 ++ RFpredInterval-1.0.5/RFpredInterval/man/plot.rfpredinterval.Rd |only RFpredInterval-1.0.5/RFpredInterval/man/print.rfpredinterval.Rd |only RFpredInterval-1.0.5/RFpredInterval/man/rfpi.Rd | 22 ++- RFpredInterval-1.0.5/RFpredInterval/tests/testthat/test.R | 12 - 22 files changed, 239 insertions(+), 104 deletions(-)
More information about RFpredInterval at CRAN
Permanent link
More information about contingencytables at CRAN
Permanent link
Title: Bindings for Bayesian TidyModels
Description: Fit Bayesian models using 'brms'/'Stan' with 'parsnip'/'tidymodels'
via 'bayesian' <doi:10.5281/zenodo.5884879>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'brms' and 'Stan' are described in Bürkner (2017)
<doi:10.18637/jss.v080.i01>, Bürkner (2018) <doi:10.32614/RJ-2018-017>,
and Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Hamada S. Badr [aut, cre] (<https://orcid.org/0000-0002-9808-2344>),
Paul-Christian Bürkner [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between bayesian versions 0.0.7 dated 2021-09-29 and 0.0.8 dated 2022-01-20
DESCRIPTION | 10 ++++---- MD5 | 28 +++++++++++----------- NAMESPACE | 2 + NEWS.md | 27 ++++++++++++++++----- R/bayesian.R | 4 ++- R/bayesian_init.R | 4 +-- R/bayesian_make.R | 51 ++++++++++++++++++++++++++++++++++++++--- README.md | 58 +++++++++++++++++++++++++---------------------- inst/CITATION | 2 - inst/WORDLIST | 1 inst/doc/BugReports.html | 5 ++-- inst/doc/GetStarted.R | 3 +- inst/doc/GetStarted.Rmd | 5 ++-- inst/doc/GetStarted.html | 28 ++++++++++++---------- vignettes/GetStarted.Rmd | 5 ++-- 15 files changed, 152 insertions(+), 81 deletions(-)
Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>.
OTP is an open source platform for multi-modal and multi-agency
journey planning written in 'Java'. The package allows you to manage a local version or
connect to remote OTP server to find walking, cycling, driving, or transit routes.
This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] (<https://orcid.org/0000-0002-9488-9183>),
Marcus Young [aut] (<https://orcid.org/0000-0003-4627-1116>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [ctb] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>
Diff between opentripplanner versions 0.3.1 dated 2020-11-09 and 0.4.0 dated 2022-01-20
DESCRIPTION | 13 - MD5 | 114 +++++--- NAMESPACE | 6 NEWS.md | 19 + R/future_tests.R |only R/otp-connect.R | 245 ++++++++++++------- R/otp-download.R | 9 R/otp-geocode.R | 7 R/otp-isochrone-batch.R | 21 + R/otp-legacy-code.R | 20 + R/otp-plan.R | 212 +++++++++------- R/otp-setup.R | 406 ++++++++++++++++++++++++-------- R/otp-surface.R |only R/otp-traveltime.R |only R/utility-functions.R | 23 + README.md | 13 - build/vignette.rds |binary inst/doc/Analyst.R |only inst/doc/Analyst.Rmd |only inst/doc/Analyst.html |only inst/doc/OTPv2.R |only inst/doc/OTPv2.Rmd |only inst/doc/OTPv2.html |only inst/doc/advanced_features.R | 2 inst/doc/advanced_features.Rmd | 34 ++ inst/doc/advanced_features.html | 68 ++++- inst/doc/known_issues.Rmd | 46 +++ inst/doc/known_issues.html | 68 +++++ inst/doc/opentripplanner.Rmd | 1 inst/doc/opentripplanner.html | 39 ++- inst/doc/prerequisites.Rmd | 6 inst/doc/prerequisites.html | 36 ++ man/json_example_drive.Rd | 34 +- man/json_example_long_drive.Rd | 34 +- man/json_example_transit.Rd | 34 +- man/otp_build_graph.Rd | 65 ++--- man/otp_check_java.Rd | 6 man/otp_check_version.Rd |only man/otp_connect.Rd | 40 +-- man/otp_dl_demo.Rd | 1 man/otp_dl_jar.Rd | 5 man/otp_geocode.Rd | 1 man/otp_isochrone.Rd | 3 man/otp_make_config.Rd | 1 man/otp_make_surface.Rd |only man/otp_plan.Rd | 1 man/otp_pointset.Rd |only man/otp_routing_options.Rd | 1 man/otp_setup.Rd | 21 + man/otp_stop.Rd | 1 man/otp_surface.Rd |only man/otp_surface_isochrone.Rd |only man/otp_traveltime.Rd |only man/otp_validate_config.Rd | 1 man/otp_validate_routing_options.Rd | 1 man/otp_write_config.Rd | 1 tests/testthat/test_01_internal_funcs.R | 6 tests/testthat/test_02_without_OTP.R | 51 +++- tests/testthat/test_03_with_OTP.R | 226 +++++++++++++---- vignettes/Analyst.Rmd |only vignettes/OTPv2.Rmd |only vignettes/advanced_features.Rmd | 34 ++ vignettes/images/analyst.jpg |only vignettes/images/raster.jpg |only vignettes/images/ttimes.jpg |only vignettes/known_issues.Rmd | 46 +++ vignettes/opentripplanner.Rmd | 1 vignettes/prerequisites.Rmd | 6 68 files changed, 1501 insertions(+), 528 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling
techniques or better understand data generating processes. The user
specifies a set of relationships between covariates, and generates
data based on these specifications. The final data sets can represent
data from randomized control trials, repeated measure (longitudinal)
designs, and cluster randomized trials. Missingness can be generated
using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] (<https://orcid.org/0000-0002-0292-8780>),
Jacob Wujciak-Jens [aut] (<https://orcid.org/0000-0002-7281-3989>)
Maintainer: Keith Goldfeld <keith.goldfeld@nyulangone.org>
Diff between simstudy versions 0.3.0 dated 2021-11-04 and 0.4.0 dated 2022-01-20
simstudy-0.3.0/simstudy/NEWS.md |only simstudy-0.3.0/simstudy/README.md |only simstudy-0.4.0/simstudy/DESCRIPTION | 10 simstudy-0.4.0/simstudy/MD5 | 70 +- simstudy-0.4.0/simstudy/NAMESPACE | 2 simstudy-0.4.0/simstudy/R/RcppExports.R | 4 simstudy-0.4.0/simstudy/R/conditions.R | 27 simstudy-0.4.0/simstudy/R/define_data.R | 162 ++++ simstudy-0.4.0/simstudy/R/generate_data.R | 117 ++- simstudy-0.4.0/simstudy/R/generate_dist.R | 7 simstudy-0.4.0/simstudy/R/simstudy-package.R | 1 simstudy-0.4.0/simstudy/R/zzz.R | 2 simstudy-0.4.0/simstudy/inst/doc/double_dot_extension.html | 2 simstudy-0.4.0/simstudy/inst/doc/longitudinal.html | 2 simstudy-0.4.0/simstudy/inst/doc/ordinal.R | 150 +++- simstudy-0.4.0/simstudy/inst/doc/ordinal.Rmd | 195 ++++- simstudy-0.4.0/simstudy/inst/doc/ordinal.html | 163 ++-- simstudy-0.4.0/simstudy/inst/doc/simstudy.R | 25 simstudy-0.4.0/simstudy/inst/doc/simstudy.Rmd | 38 - simstudy-0.4.0/simstudy/inst/doc/simstudy.html | 94 +- simstudy-0.4.0/simstudy/inst/doc/spline.html | 2 simstudy-0.4.0/simstudy/inst/doc/survival.R | 28 simstudy-0.4.0/simstudy/inst/doc/survival.Rmd | 56 + simstudy-0.4.0/simstudy/inst/doc/survival.html | 411 +++++++++++- simstudy-0.4.0/simstudy/inst/doc/treat_and_exposure.html | 62 - simstudy-0.4.0/simstudy/man/defRepeat.Rd |only simstudy-0.4.0/simstudy/man/defRepeatAdd.Rd |only simstudy-0.4.0/simstudy/man/distributions.Rd | 1 simstudy-0.4.0/simstudy/man/genOrdCat.Rd | 53 + simstudy-0.4.0/simstudy/man/simstudy-package.Rd | 2 simstudy-0.4.0/simstudy/src/RcppExports.cpp | 12 simstudy-0.4.0/simstudy/src/srcRcpp.cpp | 24 simstudy-0.4.0/simstudy/tests/testthat/test-add_data.R | 25 simstudy-0.4.0/simstudy/tests/testthat/test-define_data.R | 23 simstudy-0.4.0/simstudy/tests/testthat/test-generate_data.R | 120 +++ simstudy-0.4.0/simstudy/vignettes/ordinal.Rmd | 195 ++++- simstudy-0.4.0/simstudy/vignettes/simstudy.Rmd | 38 - simstudy-0.4.0/simstudy/vignettes/survival.Rmd | 56 + 38 files changed, 1825 insertions(+), 354 deletions(-)
Title: Tools to Generate Daily-Precipitation Time Series
Description: The method 'generate()' is extended for spatial multi-site
stochastic generation of daily precipitation. It generates precipitation
occurrence in several sites using logit regression (Generalized Linear
Models) and the approach by D.S. Wilks (1998) <doi:10.1016/S0022-1694(98)00186-3> .
Author: Emanuele Cordano
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between RGENERATEPREC versions 1.2.8 dated 2021-01-19 and 1.2.9 dated 2022-01-20
RGENERATEPREC-1.2.8/RGENERATEPREC/inst/README |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/doc/bibliography.bib |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v7.R |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v7.Rmd |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v7.html |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/gsod |only RGENERATEPREC-1.2.8/RGENERATEPREC/inst/precipitation_generator |only RGENERATEPREC-1.2.8/RGENERATEPREC/vignettes/precipitation_stochastic_generation_v7.Rmd |only RGENERATEPREC-1.2.9/RGENERATEPREC/DESCRIPTION | 14 +- RGENERATEPREC-1.2.9/RGENERATEPREC/MD5 | 36 ++--- RGENERATEPREC-1.2.9/RGENERATEPREC/R/dw.spell.R | 2 RGENERATEPREC-1.2.9/RGENERATEPREC/R/generate.PrecipitationOccurenceModel.R | 10 - RGENERATEPREC-1.2.9/RGENERATEPREC/R/predict.PrecipitationOccurenceModel.R | 4 RGENERATEPREC-1.2.9/RGENERATEPREC/README.md | 19 +-- RGENERATEPREC-1.2.9/RGENERATEPREC/build/partial.rdb |binary RGENERATEPREC-1.2.9/RGENERATEPREC/build/vignette.rds |binary RGENERATEPREC-1.2.9/RGENERATEPREC/inst/CITATION | 14 +- RGENERATEPREC-1.2.9/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v8.R |only RGENERATEPREC-1.2.9/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v8.Rmd |only RGENERATEPREC-1.2.9/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v8.html |only RGENERATEPREC-1.2.9/RGENERATEPREC/inst/doc_copy |only RGENERATEPREC-1.2.9/RGENERATEPREC/man/dw.spell.Rd | 2 RGENERATEPREC-1.2.9/RGENERATEPREC/vignettes/bibliography.bib | 62 +++++----- RGENERATEPREC-1.2.9/RGENERATEPREC/vignettes/precipitation_stochastic_generation_v8.Rmd |only 24 files changed, 82 insertions(+), 81 deletions(-)
Title: Safely Manage API Keys and Load Data from a REDCap or Other
Source
Description: The handling of an API key (misnomer for password) for protected
data can be difficult. This package provides secure convenience functions for
entering / handling API keys and pulling data directly into memory. By default
it will load from REDCap instances, but other sources are injectable via
inversion of control.
Author: Shawn Garbett [aut, cre],
Hui Wu [aut],
Cole Beck [aut]
Maintainer: Shawn Garbett <Shawn.Garbett@vumc.org>
Diff between rccola versions 1.0 dated 2022-01-15 and 1.0.2 dated 2022-01-20
rccola-1.0.2/rccola/DESCRIPTION | 8 ++++---- rccola-1.0.2/rccola/MD5 | 3 +-- rccola-1.0/rccola/tests |only 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Quantile Least Mahalanobis Distance Estimator for Tukey g-&-h
Mixture
Description: Functions for simulation, estimation, and model selection of finite mixtures of Tukey's g-and-h
distributions.
Author: Tingting Zhan [aut, cre, cph],
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between QuantileGH versions 0.1.0 dated 2021-12-17 and 0.1.1 dated 2022-01-20
DESCRIPTION | 26 - MD5 | 91 +++--- NAMESPACE | 23 + NEWS.md |only R/0Int_base_stats.R | 221 ++++++---------- R/0S4GenericDoc.R | 4 R/0setS4_QuantileGH.R | 64 ++-- R/CvM_test.R |only R/Hoaglin_GH.R | 11 R/KL_dist.R |only R/LikRatio.R | 46 ++- R/QLMDe.R | 511 +++++++++++++++++++------------------- R/QLMDp.R | 77 ++--- R/QuantileGH_info.R | 2 R/StepK_fmx.R | 45 +-- R/Step_fmx.R | 153 ++++++----- R/TukeyGH.R | 52 +-- R/clust_fmx.R | 71 +++-- R/fmx.R | 269 +++++++++++--------- R/ks_test.R |only R/mlogis.R | 50 ++- R/plot.fmx.R | 175 +++++++++---- R/reAssign.R | 12 R/vuniroot2.R | 150 ++++++++--- build/partial.rdb |binary man/CvM_test.Rd |only man/Hoaglin_GH.Rd | 11 man/K.fmx.Rd |only man/KL_dist.Rd |only man/LikRatio.Rd | 13 man/QLMDe.Rd | 89 +++--- man/QLMDp.Rd | 51 +-- man/S3_fmx_QLMDe.Rd | 39 ++ man/StepK_fmx.Rd | 21 - man/Step_fmx.Rd | 18 - man/TukeyGH.Rd | 28 +- man/allequal.Rd |only man/clust_fmx.Rd | 10 man/crossprod_inv.Rd | 9 man/drop1_fmx.Rd |only man/fmx-class.Rd | 17 - man/fmx.Rd | 65 ++-- man/fmx_QLMDe-class.Rd | 18 - man/fmx_constraint.Rd | 37 +- man/ks_test.Rd |only man/mahalanobis_int.Rd |only man/mlogis.Rd | 8 man/plot_fmx.Rd | 95 ++++--- man/quantile_vcov.Rd | 11 man/reAssign.Rd | 7 man/show_S4.Rd | 2 man/sub-fmx-ANY-ANY-ANY-method.Rd |only man/vuniroot2.Rd |only 53 files changed, 1467 insertions(+), 1135 deletions(-)
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>),
Chester Ismay [aut] (<https://orcid.org/0000-0003-2820-2547>),
Andrew Bray [ctb] (<https://orcid.org/0000-0002-4037-7414>),
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] (<https://orcid.org/0000-0002-1617-4019>),
Will Hopper [ctb] (<https://orcid.org/0000-0002-7848-1946>),
Marium Tapal [ctb] (<https://orcid.org/0000-0001-5093-6462>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.5.2 dated 2021-07-21 and 0.5.3 dated 2022-01-20
DESCRIPTION | 11 MD5 | 19 - NEWS.md | 9 R/datasets.R | 34 ++ build/vignette.rds |binary data/alaska_flights.rda |only inst/CITATION |only inst/doc/moderndive.html | 512 +++++++++++++++++++++++---------------------- man/alaska_flights.Rd |only man/orig_pennies_sample.Rd | 2 man/pennies.Rd | 2 vignettes/paper.html | 20 - 12 files changed, 334 insertions(+), 275 deletions(-)
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with 'mlr3',
e.g. grid search, random search, generalized simulated annealing and
iterated racing. Various termination criteria can be set and
combined. The class 'AutoTuner' provides a convenient way to perform
nested resampling in combination with 'mlr3'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Daniel Schalk [aut] (<https://orcid.org/0000-0003-0950-1947>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.9.0 dated 2021-09-14 and 0.10.0 dated 2022-01-20
DESCRIPTION | 14 - MD5 | 77 +++++----- NEWS.md | 14 + R/ArchiveTuning.R | 68 +++++---- R/AutoTuner.R | 2 R/ObjectiveTuning.R | 74 ++++++---- R/Tuner.R | 12 - R/TunerFromOptimizer.R | 8 - R/TunerGridSearch.R | 56 ++++++- R/TuningInstanceMulticrit.R | 43 +++-- R/TuningInstanceSingleCrit.R | 57 ++++--- R/auto_tuner.R | 21 +- R/helper.R | 12 + R/tune.R | 41 ++--- R/tune_nested.R | 24 +-- README.md | 187 ++++++++++++++++++-------- build/partial.rdb |binary man/ArchiveTuning.Rd | 46 +++++- man/AutoTuner.Rd | 16 +- man/ObjectiveTuning.Rd | 52 ++++--- man/TuningInstanceMultiCrit.Rd | 56 ++++--- man/TuningInstanceSingleCrit.Rd | 53 ++++--- man/auto_tuner.Rd | 27 ++- man/mlr3tuning-package.Rd | 6 man/mlr_tuners_cmaes.Rd | 1 man/mlr_tuners_design_points.Rd | 1 man/mlr_tuners_gensa.Rd | 1 man/mlr_tuners_grid_search.Rd | 59 +++----- man/mlr_tuners_irace.Rd | 1 man/mlr_tuners_nloptr.Rd | 1 man/mlr_tuners_random_search.Rd | 1 man/tune.Rd | 43 +++-- man/tune_nested.Rd | 12 - tests/testthat/test_AutoTuner.R | 2 tests/testthat/test_ObjectiveTuning.R | 88 +++++++----- tests/testthat/test_Tuner.R | 8 - tests/testthat/test_TunerGridSearch.R | 62 ++++++++ tests/testthat/test_TuningInstanceMultiCrit.R | 21 ++ tests/testthat/test_error_handling.R | 13 - tests/testthat/test_hotstart.R |only 40 files changed, 811 insertions(+), 469 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class
'AutoFSelector' provides a convenient way to perform nested resampling
in combination with 'mlr3'.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.6.0 dated 2021-09-13 and 0.6.1 dated 2022-01-20
mlr3fselect-0.6.0/mlr3fselect/inst/extdata |only mlr3fselect-0.6.1/mlr3fselect/DESCRIPTION | 8 mlr3fselect-0.6.1/mlr3fselect/MD5 | 50 ++-- mlr3fselect-0.6.1/mlr3fselect/NEWS.md | 11 - mlr3fselect-0.6.1/mlr3fselect/R/ArchiveFSelect.R | 14 - mlr3fselect-0.6.1/mlr3fselect/R/AutoFSelector.R | 2 mlr3fselect-0.6.1/mlr3fselect/R/FSelectInstanceMultiCrit.R | 5 mlr3fselect-0.6.1/mlr3fselect/R/FSelectInstanceSingleCrit.R | 5 mlr3fselect-0.6.1/mlr3fselect/R/FSelector.R | 4 mlr3fselect-0.6.1/mlr3fselect/R/FSelectorExhaustiveSearch.R | 4 mlr3fselect-0.6.1/mlr3fselect/R/FSelectorGeneticSearch.R | 20 - mlr3fselect-0.6.1/mlr3fselect/R/FSelectorRFE.R | 19 - mlr3fselect-0.6.1/mlr3fselect/R/FSelectorRandomSearch.R | 6 mlr3fselect-0.6.1/mlr3fselect/R/FSelectorSequential.R | 7 mlr3fselect-0.6.1/mlr3fselect/R/FSelectorShadowVariableSearch.R | 19 - mlr3fselect-0.6.1/mlr3fselect/R/fselect.R | 20 + mlr3fselect-0.6.1/mlr3fselect/README.md | 110 +++++----- mlr3fselect-0.6.1/mlr3fselect/build/partial.rdb |binary mlr3fselect-0.6.1/mlr3fselect/inst/WORDLIST |only mlr3fselect-0.6.1/mlr3fselect/man/ArchiveFSelect.Rd | 3 mlr3fselect-0.6.1/mlr3fselect/man/AutoFSelector.Rd | 1 mlr3fselect-0.6.1/mlr3fselect/man/FSelector.Rd | 2 mlr3fselect-0.6.1/mlr3fselect/man/FSelectorShadowVariableSearch.Rd | 1 mlr3fselect-0.6.1/mlr3fselect/man/fselect.Rd | 15 - mlr3fselect-0.6.1/mlr3fselect/man/mlr3fselect-package.Rd | 6 mlr3fselect-0.6.1/mlr3fselect/tests/testthat/test_ArchiveFSelect.R | 10 mlr3fselect-0.6.1/mlr3fselect/tests/testthat/test_fselect.R | 13 + 27 files changed, 188 insertions(+), 167 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.5.9 dated 2021-11-03 and 2.6.0 dated 2022-01-20
RRphylo-2.5.9/RRphylo/man/swap.phylo.Rd |only RRphylo-2.6.0/RRphylo/DESCRIPTION | 10 RRphylo-2.6.0/RRphylo/MD5 | 81 +++---- RRphylo-2.6.0/RRphylo/NAMESPACE | 2 RRphylo-2.6.0/RRphylo/R/PGLS_fossil.R | 21 - RRphylo-2.6.0/RRphylo/R/RRphylo-deprecated.R |only RRphylo-2.6.0/RRphylo/R/RRphylo-package.R | 13 - RRphylo-2.6.0/RRphylo/R/RRphylo.R | 4 RRphylo-2.6.0/RRphylo/R/conv.map.R | 25 +- RRphylo-2.6.0/RRphylo/R/cutPhylo.R | 4 RRphylo-2.6.0/RRphylo/R/distNodes.R | 4 RRphylo-2.6.0/RRphylo/R/fix.poly.R | 12 - RRphylo-2.6.0/RRphylo/R/getGenus.R |only RRphylo-2.6.0/RRphylo/R/getMommy.R | 8 RRphylo-2.6.0/RRphylo/R/getSis.R | 9 RRphylo-2.6.0/RRphylo/R/makeFossil.R | 7 RRphylo-2.6.0/RRphylo/R/phyloclust.R | 18 - RRphylo-2.6.0/RRphylo/R/plotRates.R | 1 RRphylo-2.6.0/RRphylo/R/random.evolvability.test.R | 10 RRphylo-2.6.0/RRphylo/R/rate.map.R | 4 RRphylo-2.6.0/RRphylo/R/rescaleRR.R | 2 RRphylo-2.6.0/RRphylo/R/scaleTree.R | 2 RRphylo-2.6.0/RRphylo/R/search.conv.R | 1 RRphylo-2.6.0/RRphylo/R/setBM.R | 8 RRphylo-2.6.0/RRphylo/R/sizedsubtree.R | 15 - RRphylo-2.6.0/RRphylo/R/swap.phylo.R | 196 ++++++------------ RRphylo-2.6.0/RRphylo/R/swapONE.R | 3 RRphylo-2.6.0/RRphylo/R/tree.merger.R | 37 --- RRphylo-2.6.0/RRphylo/build/vignette.rds |binary RRphylo-2.6.0/RRphylo/inst/CITATION | 25 ++ RRphylo-2.6.0/RRphylo/inst/doc/Tree-Manipulation.html | 12 - RRphylo-2.6.0/RRphylo/inst/doc/search.conv.html | 25 +- RRphylo-2.6.0/RRphylo/inst/doc/swapONE.html | 2 RRphylo-2.6.0/RRphylo/man/RRphylo-deprecated.Rd |only RRphylo-2.6.0/RRphylo/man/RRphylo-package.Rd | 16 - RRphylo-2.6.0/RRphylo/man/RRphylo.Rd | 4 RRphylo-2.6.0/RRphylo/man/conv.map.Rd | 25 +- RRphylo-2.6.0/RRphylo/man/cutPhylo.Rd | 3 RRphylo-2.6.0/RRphylo/man/fix.poly.Rd | 3 RRphylo-2.6.0/RRphylo/man/getGenus.Rd |only RRphylo-2.6.0/RRphylo/man/random.evolvability.test.Rd | 2 RRphylo-2.6.0/RRphylo/man/rate.map.Rd | 4 RRphylo-2.6.0/RRphylo/man/scaleTree.Rd | 2 RRphylo-2.6.0/RRphylo/man/swapONE.Rd | 3 44 files changed, 254 insertions(+), 369 deletions(-)
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.1.0 dated 2021-11-16 and 0.1.1 dated 2022-01-20
DESCRIPTION | 14 ++-- MD5 | 14 ++-- NEWS.md | 7 +- R/DataBackendRaster.R | 10 +- inst/WORDLIST | 108 ++++++++------------------------ inst/doc/mlr3spatial.html | 67 ++++++++----------- man/mlr3spatial-package.Rd | 4 - tests/testthat/test-DataBackendRaster.R | 3 8 files changed, 86 insertions(+), 141 deletions(-)
Title: Tools for Clinical Research
Description: Every research team have their own script for data management, statistics and
most importantly hemodynamic indices. The purpose is to standardize scripts
utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe,
and add both periods of interest (trigger-periods), and delete artifacts with deleter-files.
Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and
Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.
Author: Markus Harboe Olsen [cre, aut],
Christian Riberholt [aut],
Ronan Berg [aut],
Kirsten Moeller [aut]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Diff between clintools versions 0.9.1 dated 2022-01-19 and 0.9.2 dated 2022-01-20
clintools-0.9.1/clintools/R/pupillometer.R |only clintools-0.9.2/clintools/DESCRIPTION | 6 +++--- clintools-0.9.2/clintools/MD5 | 12 ++++++------ clintools-0.9.2/clintools/NEWS.md | 5 +++++ clintools-0.9.2/clintools/R/PLR3000.R |only clintools-0.9.2/clintools/R/clinmon.R | 4 ++-- clintools-0.9.2/clintools/man/PLR3000.Rd | 2 +- clintools-0.9.2/clintools/man/clinmon.Rd | 4 ++-- 8 files changed, 19 insertions(+), 14 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and
text styles as well.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 3.1.0 dated 2021-10-27 and 3.1.1 dated 2022-01-20
DESCRIPTION | 8 +++++--- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/ansi-hyperlink.R | 13 +++++++++++-- R/ansi-palette.R | 8 ++++---- R/progress-server.R | 2 +- README.md | 2 +- man/cli_progress_builtin_handlers.Rd | 2 +- man/style_hyperlink.Rd | 4 +++- tests/testthat/_snaps/containers.md | 3 +++ tests/testthat/_snaps/themes.md | 8 ++++---- tests/testthat/helper.R | 8 ++++++++ tests/testthat/test-ansi.R | 9 ++++++--- tests/testthat/test-cat-helpers.R | 2 +- tests/testthat/test-progress-client.R | 1 + tests/testthat/test-status-bar.R | 1 - tests/testthat/test-themes.R | 1 + 17 files changed, 71 insertions(+), 38 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>;
- rankograms and ranking by SUCRA;
- contribution matrix as described in Papakonstantinou et al. (2018) <DOI:10.12688/f1000research.14770.3> and Davies et al. (2021) <arXiv:2107.02886>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Annabel Davies [aut] (<https://orcid.org/0000-0003-2320-7701>),
Theodoros Papakonstantinou [aut]
(<https://orcid.org/0000-0002-6630-6817>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 2.0-1 dated 2021-10-27 and 2.1-0 dated 2022-01-20
DESCRIPTION | 12 +-- MD5 | 97 +++++++++++++------------ NAMESPACE | 2 NEWS.md | 74 ++++++++++++++++++- R/Baker2009.R | 2 R/Linde2016.R | 12 ++- R/contribution.matrix.R | 86 +++++++++++++++++----- R/discomb.R | 102 ++++++++++++-------------- R/forest.netcomb.R | 2 R/forest.netcomparison.R | 2 R/forest.netcomplex.R | 2 R/forest.netmeta.R | 4 - R/funnel.netmeta.R | 175 +++++++++++++++++++++++++++++++++++---------- R/hatmatrix.R | 2 R/invmat.R |only R/meta-chk.R | 21 +++-- R/meta-set.R | 19 ++++ R/metabias.netmeta.R |only R/multiarm.R | 18 ++++ R/netcomb.R | 20 ++++- R/netconnection.R | 15 +++ R/netcontrib.R | 28 ++++++- R/netleague.R | 27 +++--- R/netmeta-internal.R | 10 -- R/netmeta-package.R | 6 + R/netmeta.R | 71 +++++++++++++----- R/netmetabin.R | 9 ++ R/netsplit.R | 50 ++++++++++++ R/nma.ruecker.R | 5 - R/pairwise.R | 50 +++++++++--- R/plot.netrank.R | 2 R/prepare.R | 7 + R/print.netmeta.R | 5 - R/print.summary.netmeta.R | 2 R/rankogram.R | 178 ++++++---------------------------------------- R/ranksampling.R |only R/setref.R | 10 ++ data/Linde2016.rda |binary man/Baker2009.Rd | 2 man/Linde2016.Rd | 12 ++- man/discomb.Rd | 4 + man/funnel.netmeta.Rd | 78 +++++++++++++------- man/invmat.Rd |only man/metabias.netmeta.Rd |only man/netcomb.Rd | 4 + man/netcontrib.Rd | 14 +++ man/netleague.Rd | 27 +++--- man/netmeta-package.Rd | 6 + man/netmeta.Rd | 4 + man/netmetabin.Rd | 4 + man/netsplit.Rd | 12 +++ man/rankogram.Rd | 9 +- 52 files changed, 844 insertions(+), 459 deletions(-)
Title: Algorithms for Class Distribution Estimation
Description: Quantification is a prominent machine learning task that has received an
increasing amount of attention in the last years. The objective is to predict the
class distribution of a data sample. This package is a collection of machine learning
algorithms for class distribution estimation. This package include algorithms from
different paradigms of quantification. These methods are described in the paper:
A. Maletzke, W. Hassan, D. dos Reis, and G. Batista. The importance of the test set
size in quantification assessment. In Proceedings of the Twenty-Ninth International
Joint Conference on Artificial Intelligence, IJCAI20, pages 2640–2646, 2020.
<doi:10.24963/ijcai.2020/366>.
Author: Andre Maletzke [aut, cre],
Everton Cherman [ctb],
Denis dos Reis [ctb],
Gustavo Batista [ths]
Maintainer: Andre Maletzke <andregustavom@gmail.com>
Diff between mlquantify versions 0.1.5 dated 2021-04-13 and 0.2.0 dated 2022-01-20
DESCRIPTION | 8 ++-- MD5 | 18 +++++---- NAMESPACE | 1 R/EMQ_method.r | 75 ++++++++++------------------------------- R/MS2_method.r | 13 ++++--- R/MS_method.r | 12 +++--- R/PWK_method.r |only R/getTPRandFPRbyThreshold.r | 4 +- man/EMQ.Rd | 10 ++--- man/PWK.Rd |only man/getTPRandFPRbyThreshold.Rd | 2 - 11 files changed, 56 insertions(+), 87 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>
Diff between mexhaz versions 2.1 dated 2021-12-13 and 2.2 dated 2022-01-20
DESCRIPTION | 8 +- MD5 | 40 +++++++----- NAMESPACE | 24 ++++--- NEWS | 8 ++ R/adjsurv.R |only R/lines.predMexhaz.R | 2 R/lines.resMexhaz.R |only R/marginSurvhaz.R | 2 R/mexhazEgh.R | 4 - R/plot.predMexhaz.R | 2 R/plot.resMexhaz.R |only R/points.predMexhaz.R | 2 R/predict.mexhaz.R | 82 ++++++++++++++++---------- R/riskfunc.R |only man/adjsurv.Rd |only man/lines.predMexhaz.Rd | 5 - man/lines.resMexhaz.Rd |only man/mexhaz-package.Rd | 4 - man/mexhaz.Rd | 25 ++++---- man/plot.predMexhaz.Rd | 4 - man/plot.resMexhaz.Rd |only man/points.predMexhaz.Rd | 5 - man/predict.mexhaz.Rd | 146 +++++++++++++++++++++++++++-------------------- man/riskfunc.Rd |only man/update.mexhaz.Rd | 35 +++++------ 25 files changed, 233 insertions(+), 165 deletions(-)
Title: Publication Quality Descriptive Statistics Tables
Description: Provides functions to create descriptive statistics tables for continuous and categorical variables.
By default, summary statistics such as mean, standard deviation, quantiles, minimum and maximum for continuous
variables and relative and absolute frequencies for categorical variables are calculated. 'DescrTab2' features a sophisticated algorithm to
choose appropriate test statistics for your data and provides p-values. On top of this, confidence intervals for group
differences of appropriated summary measures are automatically produces for two-group comparison.
Tables generated by 'DescrTab2' can be integrated in a variety of document formats, including .html, .tex and .docx documents.
'DescrTab2' also allows printing tables to console and saving table objects for later use.
Author: Jan Meis [aut, cre] (<https://orcid.org/0000-0001-5407-7220>),
Lukas Baumann [aut] (<https://orcid.org/0000-0001-7931-7470>),
Maximilian Pilz [aut] (<https://orcid.org/0000-0002-9685-1613>),
Lukas Sauer [aut] (<https://orcid.org/0000-0002-1340-9994>),
Lorenz Uhlmann [ctb],
Csilla van Lunteren [ctb],
Kevin Kunzmann [ctb],
Hao Zhu [ctb] (<https://orcid.org/0000-0002-3386-6076>)
Maintainer: Jan Meis <meis@imbi.uni-heidelberg.de>
Diff between DescrTab2 versions 2.1.7 dated 2021-12-02 and 2.1.9 dated 2022-01-20
DESCRIPTION | 8 MD5 | 28 - NEWS.md | 8 R/descr.R | 10 R/misc.R | 12 R/summaryStats.R | 554 +++++++++++++++--------------- inst/doc/a_usage_guide.html | 4 inst/doc/b_test_choice_tree_pdf.pdf |binary inst/doc/c_other_software_comparison.html | 4 inst/doc/e_maintenance_guide.html | 4 tests/console/friedman.test.txt | 2 tests/rmds/tex_doc.aux | 94 ++--- tests/rmds/tex_doc.pdf |binary tests/rmds/word_doc.docx |binary tests/testthat/test_tests.R | 26 - 15 files changed, 387 insertions(+), 367 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.1.9 dated 2021-12-02 and 1.1.10 dated 2022-01-20
DESCRIPTION | 6 MD5 | 32 ++-- NEWS.md | 9 + R/ColorspacePrivates.R | 12 + R/extractOutfileMean.R | 2 R/getColors.R | 31 ++++ R/monitor_climate.R | 6 R/plot_warming_stripes.R | 248 ++++++++++++++++++++++++++++++++--- R/quicklook.R | 111 ++++++++++++---- R/render_plot.R | 3 R/render_plot_side_by_side.R | 3 R/warming_stripes_plot.R | 12 + build/partial.rdb |binary inst/extdata/quicklook_config.yml | 262 ++++++++++++++++++++++---------------- man/monitor_climate.Rd | 8 + man/quicklook.Rd | 15 ++ man/warming_stripes_plot.Rd | 9 + 17 files changed, 582 insertions(+), 187 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.2.2 dated 2021-12-02 and 1.2.3 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/box_mergetime.R | 12 +++++++++++- R/mon.anomaly.R | 15 ++++++++++++++- R/selpoint.multi.R | 11 ++++++----- build/partial.rdb |binary man/selpoint.multi.Rd | 2 +- tests/testthat/test_box_mergetime.R | 8 +++++--- 9 files changed, 53 insertions(+), 22 deletions(-)
Title: Clinical Trial Registry History
Description: Retrieves historical versions of clinical trial registry
entries.
Author: Benjamin Gregory Carlisle [aut, cre]
(<https://orcid.org/0000-0001-8975-0649>)
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Diff between cthist versions 0.1.2 dated 2021-12-15 and 0.1.3 dated 2022-01-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/drks_de_version.R | 4 +++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.3.1 dated 2021-12-02 and 3.4.0 dated 2022-01-20
DESCRIPTION | 6 - MD5 | 22 ++- NEWS.md | 10 + build/partial.rdb |binary inst/WORDLIST | 3 inst/toolbox/ColorspacePrivates.R | 12 ++ inst/toolbox/global.R | 2 inst/toolbox/server.R | 191 ++++++++++++++++++++++++++------ inst/toolbox/ui.R | 30 ++--- inst/toolbox/www/images/pal_albedo.png |only inst/toolbox/www/images/pal_albedo2.png |only inst/toolbox/www/images/pal_batlow.png |only inst/toolbox/www/images/pal_hawaii.png |only inst/toolbox/www/images/pal_mako.png |only inst/toolbox/www/images/pal_rocket.png |only 15 files changed, 217 insertions(+), 59 deletions(-)
Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions <https://github.com/stemangiola/tidygate>.
The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid (who is also author of this package). The code of 'gatepoints' was nto integrated in 'tidygate'.
The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots;
(ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre],
Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidygate versions 0.4.8 dated 2022-01-03 and 0.4.9 dated 2022-01-20
DESCRIPTION | 8 MD5 | 6 R/functions_OLD.R | 870 ++++++++++++++++++++++++++--------------------------- build/tidygate.pdf |binary 4 files changed, 442 insertions(+), 442 deletions(-)
Title: R Source Code Similarity Evaluation by Variable/Function Names
Description: Evaluates R source codes by variable and/or functions names. Similar source codes should deliver similarity coefficients near one. Since neither the frequency nor the order of the used names is considered, a manual inspection of the R source code is required to check for similarity. Possible use cases include detection of code clones for improving
software quality and of plagiarism amongst students' assignments.
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between rscc versions 0.2.0 dated 2021-11-01 and 0.2.1 dated 2022-01-20
DESCRIPTION | 12 +++--- MD5 | 40 +++++++++++---------- R/as_igraph.R | 2 - R/browse.R | 21 +++++++---- R/documents.R | 2 - R/matrix2dataframe.R | 2 - R/sim_coeff.R |only R/similarities.R | 28 ++++++++------ R/similarity_coeff.R | 28 +------------- R/sourcecode.R | 12 ++++-- R/tfidf.R | 7 +++ README.md | 1 build/vignette.rds |binary inst/doc/rscc.R | 40 +++++++++++++++------ inst/doc/rscc.Rmd | 68 ++++++++++++++++++++++++------------ inst/doc/rscc.html | 96 ++++++++++++++++++++++++++++++++------------------- man/as_igraph.Rd | 2 - man/sim_coeff.Rd |only man/similarities.Rd | 5 ++ man/sourcecode.Rd | 6 +-- man/tfidf.Rd | 5 ++ vignettes/rscc.Rmd | 68 ++++++++++++++++++++++++------------ 22 files changed, 275 insertions(+), 170 deletions(-)
Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Lai J.,Zou Y., Zhang J.,Peres-Neto P.(2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution,<DOI:10.1111/2041-210X.13800>.
Author: Jiangshan Lai,Pedro Peres-Neto,Kim Nimon
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>
Diff between rdacca.hp versions 1.0-5 dated 2022-01-12 and 1.0-6 dated 2022-01-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/permu.hp.r | 2 +- inst/CITATION | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.1-3 dated 2021-11-13 and 1.1-4 dated 2022-01-20
DESCRIPTION | 6 - MD5 | 20 ++--- NEWS.md | 15 +++ R/memoiR.R | 4 - README.md | 1 inst/rmarkdown/templates/beamer_presentation/skeleton/skeleton.Rmd | 17 ++-- inst/rmarkdown/templates/memoir/skeleton/index.Rmd | 18 ++-- inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 16 ++-- inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 18 ++-- man/add_font.Rd | 38 +++++----- man/add_hyphen.Rd | 38 +++++----- 11 files changed, 104 insertions(+), 87 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions to edit 'ggplot' object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends).
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.0.4 dated 2021-09-17 and 0.0.5 dated 2022-01-20
DESCRIPTION | 8 ++--- MD5 | 13 +++++---- NAMESPACE | 5 +++ NEWS.md | 4 ++ R/theme.R |only build/vignette.rds |binary inst/doc/ggfun.html | 63 +++++++++++++++++++++++------------------------ man/theme_nothing.Rd |only man/theme_transparent.Rd |only 9 files changed, 52 insertions(+), 41 deletions(-)
Title: Continuous Time Meta-Analysis ('CoTiMA')
Description: The 'CoTiMA' package performs meta-analyses of correlation matrices of repeatedly measured variables taken from
studies that used different time intervals. Different time intervals between measurement occasions impose problems for
meta-analyses because the effects (e.g. cross-lagged effects) cannot be simply aggregated, for example, by means of common
fixed or random effects analysis. However, continuous time math, which is applied in 'CoTiMA', can be used to extrapolate or
intrapolate the results from all studies to any desired time lag. By this, effects obtained in studies that used different
time intervals can be meta-analyzed. 'CoTiMA' fits models to empirical data using the structural equation model (SEM) package
'ctsem', the effects specified in a SEM are related to parameters that are not directly included in the model (i.e.,
continuous time parameters; together, they represent the continuous time structural equation model, CTSEM). Statistical
model comparisons and significance tests are then performed on the continuous time parameter estimates. 'CoTiMA' also allows
analysis of publication bias (Egger's test, PET-PEESE estimates, zcurve analysis etc.) and analysis of statistical power
(post hoc power, required sample sizes). See Dormann, C., Guthier, C., & Cortina, J. M. (2019) <doi:10.1177/1094428119847277>.
and Guthier, C., Dormann, C., & Voelkle, M. C. (2020) <doi:10.1037/bul0000304>.
Author: Christian Dormann [aut, cph],
Markus Homberg [aut, com, cre],
Christina Guthier [ctb],
Manuel Voelkle [ctb]
Maintainer: Markus Homberg <cotima@uni-mainz.de>
Diff between CoTiMA versions 0.5.2 dated 2021-12-09 and 0.5.4 dated 2022-01-20
DESCRIPTION | 8 MD5 | 26 - R/ctmaBiG.R | 46 +- R/ctmaFit.R | 51 ++ R/ctmaInit.R | 15 R/ctmaPRaw.R | 314 ++++++++++------ R/ctmaPlot.R | 794 +++++++++++++++++++++-------------------- R/ctmaPrep.R | 12 inst/doc/CoTiMA_User_Guide.pdf |binary man/ctmaBiG.Rd | 5 man/ctmaFit.Rd | 3 man/ctmaInit.Rd | 5 man/ctmaPRaw.Rd | 5 man/ctmaPlot.Rd | 3 14 files changed, 749 insertions(+), 538 deletions(-)
Title: Simplified Statistics for PA 606
Description: Simplifies functions assess normality for bivariate and multivariate statistical techniques. Includes functions designed to replicate plots and tables that would result from similar calls in 'SPSS', including hst(), box(), qq(), tab(), cormat(), and residplot(). Also includes simplified formulae, such as mode(), scatter(), p.corr(), ow.anova(), and rm.anova().
Author: Burrel Vann Jr [aut, cre] (<https://orcid.org/0000-0003-3066-5815>)
Maintainer: Burrel Vann Jr <bvannjr@sdsu.edu>
Diff between vannstats versions 1.2.1.8 dated 2022-01-08 and 1.2.1.19 dated 2022-01-20
DESCRIPTION | 17 ++++++++++------- MD5 | 6 ++++-- NAMESPACE | 1 + R/rev.code.R |only man/revcode.Rd |only 5 files changed, 15 insertions(+), 9 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, and ANOVA. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.6.4 dated 2021-11-25 and 0.6.5 dated 2022-01-20
sasLM-0.6.4/sasLM/inst/doc/Report-Different-Simplest2111251803.pdf |only sasLM-0.6.4/sasLM/inst/doc/Report-NOT-OKs2111251804.pdf |only sasLM-0.6.4/sasLM/inst/doc/Validation-Report-ANOVA-2111251805.pdf |only sasLM-0.6.4/sasLM/inst/doc/Validation-Report-GLM-2111251808.pdf |only sasLM-0.6.5/sasLM/DESCRIPTION | 6 +- sasLM-0.6.5/sasLM/MD5 | 18 +++--- sasLM-0.6.5/sasLM/NAMESPACE | 2 sasLM-0.6.5/sasLM/R/UNIV.R |only sasLM-0.6.5/sasLM/inst/NEWS.Rd | 30 ++++++---- sasLM-0.6.5/sasLM/inst/doc/Report-Different-Simplest2201201617.pdf |only sasLM-0.6.5/sasLM/inst/doc/Report-NOT-OKs2201201618.pdf |only sasLM-0.6.5/sasLM/inst/doc/Validation-Report-ANOVA-2201201619.pdf |only sasLM-0.6.5/sasLM/inst/doc/Validation-Report-GLM-2201201622.pdf |only sasLM-0.6.5/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.6.5/sasLM/man/UNIV.Rd |only 15 files changed, 32 insertions(+), 24 deletions(-)
Title: Calculating Optimal and D-Augmented Designs
Description: Calculates D-, Ds-, A- and I-optimal designs for non-linear models, via an implementation of the cocktail algorithm (Yu, 2011, <doi:10.1007/s11222-010-9183-2>). Compares designs via their efficiency, and D-augments any design with a controlled efficiency. An efficient rounding function has been provided to transform approximate designs to exact designs.
Author: Carlos de la Calle-Arroyo [aut, cre]
(<https://orcid.org/0000-0002-5099-888X>),
Jesús López-Fidalgo [aut] (<https://orcid.org/0000-0001-7502-8188>),
Licesio J. Rodríguez-Aragón [aut]
(<https://orcid.org/0000-0003-4970-3877>)
Maintainer: Carlos de la Calle-Arroyo <carlos.calle.arroyo@gmail.com>
Diff between optedr versions 1.0.0 dated 2021-12-01 and 1.0.1 dated 2022-01-20
DESCRIPTION | 8 MD5 | 17 NEWS.md |only README.md | 15 inst/shiny-examples/AddPoints/app.R | 1 inst/shiny-examples/AddPoints/dopt.R | 1256 ++++---- inst/shiny-examples/D-Optimality/app.R | 1463 +++++----- inst/shiny-examples/D-Optimality/dopt.R | 2952 ++++++++++----------- inst/shiny-examples/D-Optimality/presentacion.Rmd | 62 inst/shiny-examples/D-Optimality/presentacion.html | 65 10 files changed, 2904 insertions(+), 2935 deletions(-)
Title: Flexible and Reproducible Label Designs
Description: An open-source R package to deploys flexible and reproducible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>),
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between huito versions 0.1.1 dated 2021-12-14 and 0.1.2 dated 2022-01-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/include_shape.R | 2 +- R/label_print.R | 2 ++ R/shape_hexagon.R | 4 ++-- inst/doc/labels.html | 2 +- man/include_shape.Rd | 2 +- man/shape_hexagon.Rd | 2 +- vignettes/huito.zip |binary 10 files changed, 26 insertions(+), 19 deletions(-)
More information about TreeDimensionTest at CRAN
Permanent link
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (2009-2010), Terry Leitch (since 2016)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.14 dated 2021-10-06 and 0.4.15 dated 2022-01-20
ChangeLog | 60 ++++++++++++++++++++++++++++++++ DESCRIPTION | 13 +++---- MD5 | 36 +++++++++---------- NAMESPACE | 5 +- R/RcppExports.R | 8 +++- R/calendars.R | 75 ++++++++++++++++++++++++++++++++++++++--- R/zzz.R | 4 +- README.md | 5 ++ data/tsQuotes.RData |binary data/vcube.RData |binary inst/NEWS.Rd | 17 +++++++++ man/BondUtilities.Rd | 7 +-- man/Calendars.Rd | 28 ++++++++++----- man/getQuantLibCapabilities.Rd | 2 - man/getQuantLibVersion.Rd | 2 - src/RcppExports.cpp | 14 +++++++ src/bonds.cpp | 53 +++++++++++++++++++++++----- src/calendars.cpp | 23 ++++++++++++ src/utils.cpp | 30 +++++++++++----- 19 files changed, 310 insertions(+), 72 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate
generation, and method-of-moments parameter-estimation functions for the
Delaporte distribution with parameterization based on Vose (2008)
<isbn:9780470512845>. The Delaporte is a discrete probability distribution
which can be considered the convolution of a negative binomial distribution
with a Poisson distribution. Alternatively, it can be considered a counting
distribution with both Poisson and negative binomial components. It has been
studied in actuarial science as a frequency distribution which has more
variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 8.0.1 dated 2021-01-10 and 8.0.2 dated 2022-01-20
Delaporte-8.0.1/Delaporte/tests/test-all.R |only Delaporte-8.0.1/Delaporte/tests/testthat |only Delaporte-8.0.2/Delaporte/DESCRIPTION | 11 +++++------ Delaporte-8.0.2/Delaporte/MD5 | 28 ++++++++++++++-------------- Delaporte-8.0.2/Delaporte/README.md | 11 +++++++---- Delaporte-8.0.2/Delaporte/build/partial.rdb |binary Delaporte-8.0.2/Delaporte/inst/CITATION | 6 ++++-- Delaporte-8.0.2/Delaporte/inst/NEWS.Rd | 15 +++++++++++++++ Delaporte-8.0.2/Delaporte/inst/tinytest |only Delaporte-8.0.2/Delaporte/man/Delaporte.Rd | 4 ++-- Delaporte-8.0.2/Delaporte/tests/tinytest.R |only 11 files changed, 47 insertions(+), 28 deletions(-)