Title: Standard and User-Defined RGB Color Spaces, with Conversion
Between RGB and CIE XYZ
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesRGB versions 1.4-0 dated 2021-12-06 and 1.5-0 dated 2024-01-23
DESCRIPTION | 8 MD5 | 54 +-- NAMESPACE | 13 NEWS.md | 10 R/HLG.R | 8 R/OETFs.R | 28 - R/OOTF.R | 12 R/PODT.R | 4 R/PQ.R | 2 R/RRT.R | 8 R/SSTS.R | 6 R/TransferFunction.R | 32 +- R/conversion.R | 12 R/elemTransferFunction.R | 347 +++++++++++----------- R/installation.R | 38 +- R/logging.R | 8 R/plot.R | 18 - R/tonescales.R | 2 R/utils.R | 16 - build/vignette.rds |binary inst/CGATS.R | 46 +- inst/doc/spacesRGB-guide.Rmd | 15 inst/doc/spacesRGB-guide.html | 658 +++++++++++++++++++++++++++++------------- man/RGBfromXYZ.Rd | 11 man/RGBspaces.Rd | 3 man/XYZfromRGB.Rd | 15 tests/CGATS.RR | 46 +- vignettes/spacesRGB-guide.Rmd | 15 28 files changed, 879 insertions(+), 556 deletions(-)
Title: Sample Size Calculations for Longitudinal Data
Description: Compute power and sample size for linear models of longitudinal
data. Supported models include mixed-effects models and models fit by
generalized least squares and generalized estimating equations. The package
is described in Iddi and Donohue (2022) <DOI:10.32614/RJ-2022-022>. Relevant
formulas are derived by Liu and Liang (1997) <DOI:10.2307/2533554>,
Diggle et al (2002) <ISBN:9780199676750>, and Lu, Luo, and Chen (2008)
<DOI:10.2202/1557-4679.1098>.
Author: Michael C. Donohue [aut, cre],
Steve D. Edland [ctb],
Nan Hu [ctb]
Maintainer: Michael C. Donohue <mdonohue@usc.edu>
Diff between longpower versions 1.0.24 dated 2023-01-11 and 1.0.25 dated 2024-01-23
DESCRIPTION | 12 +-- MD5 | 17 ++--- NAMESPACE | 2 R/lmmpower.R | 3 R/longpower-package.R | 43 +------------ build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 128 +++++++++++++++++----------------------- inst/doc/longpower.html | 147 ++++++++++++++++++++++++----------------------- man/longpower-package.Rd | 50 +++++---------- 10 files changed, 174 insertions(+), 228 deletions(-)
Title: Tools for Building Regression and Classification Models
Description: Collection of tools for regression and classification tasks. The package implements a consistent user interface to the most popular regression and classification algorithms, such as random forest, neural networks, C5 trees and support vector machines, and complements it with a handful of auxiliary functions, such as variable importance and a tuning function for the parameters.
Author: Andri Signorell [aut, cre],
Bernhard Compton [ctb],
Marcel Dettling [ctb],
Alexandre Hainard [ctb],
Max Kuhn [ctb],
Frederique Lisacek [ctb],
Michal Majka [ctb],
Markus Mueller [ctb],
Dan Putler [ctb],
Jean-Charles Sanchez [ctb],
Natalia Tiberti [ctb] [...truncated...]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between ModTools versions 0.9.4 dated 2021-07-26 and 0.9.6 dated 2024-01-23
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++++++--------- NAMESPACE | 35 +++++++++++++++++++++++++++++------ NEWS | 13 +++++++++++++ R/CoefTest.R | 29 +++++++++++++++++++++++++++++ R/ModTools.R | 28 ++++++++++++++++++++++------ R/zeroinfl.R |only build/partial.rdb |binary data/bioChemists.rda |only man/CoeffDiffCI.Rd |only man/LogitBoost.Rd | 2 -- man/ModTools-package.Rd | 2 +- man/PredictCI.Rd |only man/RobSummary.Rd | 2 +- man/bioChemists.Rd |only man/predict.zeroinfl.Rd |only man/zeroinfl.Rd |only man/zeroinfl.control.Rd |only 18 files changed, 118 insertions(+), 31 deletions(-)
Title: Automate Data Exploration and Treatment
Description: Automated data exploration process for analytic tasks and predictive modeling, so
that users could focus on understanding data and extracting insights. The package scans and
analyzes each variable, and visualizes them with typical graphical techniques. Common
data processing methods are also available to treat and format data.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>
Diff between DataExplorer versions 0.8.2 dated 2020-12-15 and 0.8.3 dated 2024-01-23
DESCRIPTION | 9 LICENSE | 2 MD5 | 70 +- NEWS.md | 7 R/DataExplorer-package.r | 15 R/plot.r | 80 +- R/plot_boxplot.r | 10 R/plot_missing.r | 24 R/plot_scatterplot.r | 12 README.md | 35 - build/vignette.rds |binary inst/doc/dataexplorer-intro.html | 986 ++++++++++++++++-------------- inst/rmd_template/report.rmd | 1 man/DataExplorer-package.Rd | 27 man/configure_report.Rd | 4 man/figures/README-plot-bar-1.png |binary man/figures/README-plot-bar-by-1.png |binary man/figures/README-plot-bar-prepare-1.png |binary man/figures/README-plot-bar-prepare-2.png |binary man/figures/README-plot-density-1.png |binary man/figures/README-plot-histogram-1.png |binary man/figures/README-plot-intro-1.png |binary man/figures/README-plot-missing-1.png |binary man/figures/README-plot-qq-1.png |binary man/figures/README-plot-qq-cut-1.png |binary man/figures/README-plot_boxplot-1.png |binary man/figures/README-plot_correlation-1.png |binary man/figures/README-plot_prcomp-1.png |binary man/figures/README-plot_prcomp-2.png |binary man/figures/README-plot_scatterplot-1.png |binary man/plotDataExplorer.single.Rd | 4 man/plot_boxplot.Rd | 7 man/plot_correlation.Rd | 3 man/plot_missing.Rd | 9 man/plot_scatterplot.Rd | 12 tests/testthat/test-plot-missing.r | 4 36 files changed, 738 insertions(+), 583 deletions(-)
Title: Helper Functions for Second Primary Cancer Analyses
Description: A collection of helper functions for analyzing Second Primary Cancer data,
including functions to reshape data, to calculate patient states and analyze cancer incidence.
Author: Marian Eberl [aut, cre]
Maintainer: Marian Eberl <marian.eberl@tum.de>
Diff between msSPChelpR versions 0.9.0 dated 2022-06-10 and 0.9.1 dated 2024-01-23
msSPChelpR-0.9.0/msSPChelpR/R/utils-tidy-eval.R |only msSPChelpR-0.9.0/msSPChelpR/man/tidyeval.Rd |only msSPChelpR-0.9.1/msSPChelpR/DESCRIPTION | 14 msSPChelpR-0.9.1/msSPChelpR/MD5 | 106 - msSPChelpR-0.9.1/msSPChelpR/NAMESPACE | 11 msSPChelpR-0.9.1/msSPChelpR/NEWS.md | 438 +++-- msSPChelpR-0.9.1/msSPChelpR/R/asir.R | 169 +- msSPChelpR-0.9.1/msSPChelpR/R/calc_futime.R | 29 msSPChelpR-0.9.1/msSPChelpR/R/calc_futime_tt.R | 37 msSPChelpR-0.9.1/msSPChelpR/R/calc_refrates.R | 242 +-- msSPChelpR-0.9.1/msSPChelpR/R/data.R | 1 msSPChelpR-0.9.1/msSPChelpR/R/histgroups_iarc.R |only msSPChelpR-0.9.1/msSPChelpR/R/msSPChelpR-package.R |only msSPChelpR-0.9.1/msSPChelpR/R/msSPChelpR.R | 9 msSPChelpR-0.9.1/msSPChelpR/R/pat_status.R | 9 msSPChelpR-0.9.1/msSPChelpR/R/pat_status_tt.R | 329 ++-- msSPChelpR-0.9.1/msSPChelpR/R/renumber_time_id_tt.R | 8 msSPChelpR-0.9.1/msSPChelpR/R/reshape_long_tt.R | 6 msSPChelpR-0.9.1/msSPChelpR/R/reshape_wide_tt.R | 21 msSPChelpR-0.9.1/msSPChelpR/R/sir_byfutime.R | 628 ++++---- msSPChelpR-0.9.1/msSPChelpR/R/summarize_sir_results.R | 128 - msSPChelpR-0.9.1/msSPChelpR/R/vital_status.R | 2 msSPChelpR-0.9.1/msSPChelpR/R/vital_status_tt.R | 12 msSPChelpR-0.9.1/msSPChelpR/README.md | 6 msSPChelpR-0.9.1/msSPChelpR/build/vignette.rds |binary msSPChelpR-0.9.1/msSPChelpR/data/standard_population.rda |binary msSPChelpR-0.9.1/msSPChelpR/data/us_second_cancer.rda |binary msSPChelpR-0.9.1/msSPChelpR/inst/CITATION | 2 msSPChelpR-0.9.1/msSPChelpR/inst/doc/introduction.R | 6 msSPChelpR-0.9.1/msSPChelpR/inst/doc/introduction.Rmd | 4 msSPChelpR-0.9.1/msSPChelpR/inst/doc/introduction.html | 1135 +++++++-------- msSPChelpR-0.9.1/msSPChelpR/man/asir.Rd | 2 msSPChelpR-0.9.1/msSPChelpR/man/calc_futime.Rd | 5 msSPChelpR-0.9.1/msSPChelpR/man/calc_futime_tt.Rd | 7 msSPChelpR-0.9.1/msSPChelpR/man/calc_refrates.Rd | 5 msSPChelpR-0.9.1/msSPChelpR/man/histgroup_iarc.Rd |only msSPChelpR-0.9.1/msSPChelpR/man/msSPChelpR-package.Rd |only msSPChelpR-0.9.1/msSPChelpR/man/msSPChelpR.Rd | 1 msSPChelpR-0.9.1/msSPChelpR/man/pat_status.Rd | 4 msSPChelpR-0.9.1/msSPChelpR/man/pat_status_tt.Rd | 6 msSPChelpR-0.9.1/msSPChelpR/man/pipe.Rd | 24 msSPChelpR-0.9.1/msSPChelpR/man/population_us.Rd | 50 msSPChelpR-0.9.1/msSPChelpR/man/reshape_long.Rd | 90 - msSPChelpR-0.9.1/msSPChelpR/man/reshape_long_tidyr.Rd | 86 - msSPChelpR-0.9.1/msSPChelpR/man/reshape_long_tt.Rd | 86 - msSPChelpR-0.9.1/msSPChelpR/man/reshape_wide.Rd | 96 - msSPChelpR-0.9.1/msSPChelpR/man/reshape_wide_tidyr.Rd | 90 - msSPChelpR-0.9.1/msSPChelpR/man/reshape_wide_tt.Rd | 78 - msSPChelpR-0.9.1/msSPChelpR/man/sir_byfutime.Rd | 14 msSPChelpR-0.9.1/msSPChelpR/man/sir_ratio.Rd | 120 - msSPChelpR-0.9.1/msSPChelpR/man/standard_population.Rd | 46 msSPChelpR-0.9.1/msSPChelpR/man/summarize_sir_results.Rd | 164 +- msSPChelpR-0.9.1/msSPChelpR/man/us_refrates_icd2.Rd | 60 msSPChelpR-0.9.1/msSPChelpR/man/us_second_cancer.Rd | 67 msSPChelpR-0.9.1/msSPChelpR/man/vital_status.Rd | 124 - msSPChelpR-0.9.1/msSPChelpR/man/vital_status_tt.Rd | 124 - msSPChelpR-0.9.1/msSPChelpR/vignettes/introduction.Rmd | 4 57 files changed, 2477 insertions(+), 2228 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Hannes Riebl [ctb],
Henrik Singmann [ctb]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.9.0 dated 2023-12-18 and 1.10.0 dated 2024-01-23
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++------------- NEWS.md | 12 +++++ R/emmGrid-methods.R | 6 ++ R/helpers.R | 12 +++-- R/lqm-support.R | 22 ++++----- R/ref-grid.R | 6 +- R/summary.R | 9 ++- R/transformations.R | 88 +++++++++++++++++++++++++++++-------- R/xtable-method.R | 2 inst/doc/AQuickStart.html | 4 - inst/doc/FAQs.html | 8 +-- inst/doc/basics.html | 4 - inst/doc/comparisons.html | 8 +-- inst/doc/confidence-intervals.html | 14 ++--- inst/doc/interactions.html | 18 +++---- inst/doc/messy-data.html | 4 - inst/doc/models.Rmd | 12 ++--- inst/doc/models.html | 43 +++++++++++------- inst/doc/predictions.html | 4 - inst/doc/re-engineering-clds.html | 4 - inst/doc/sophisticated.html | 4 - inst/doc/transformations.html | 4 - inst/doc/utilities.html | 4 - inst/doc/vignette-topics.html | 4 - inst/doc/xplanations.html | 4 - inst/doc/xtending.html | 8 +-- man/make.tran.Rd | 56 ++++++++++++++++------- man/update.emmGrid.Rd | 3 + tests/testthat/test-ref_grid.R | 7 ++ vignettes/models.Rmd | 12 ++--- 31 files changed, 288 insertions(+), 166 deletions(-)
Title: Retrieve Genomic and Clinical Data from CBioPortal Including
TCGA Data
Description: The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see <https://www.cbioportal.org/> for more information).
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between TCGAretriever versions 1.7 dated 2023-07-10 and 1.9.1 dated 2024-01-23
TCGAretriever-1.7/TCGAretriever/R/tcgaretriever_v_1_7.R |only TCGAretriever-1.7/TCGAretriever/man/basic_tcga_query.Rd |only TCGAretriever-1.7/TCGAretriever/man/get_ext_mutation.Rd |only TCGAretriever-1.7/TCGAretriever/man/get_profile_data.Rd |only TCGAretriever-1.7/TCGAretriever/man/show_head.Rd |only TCGAretriever-1.9.1/TCGAretriever/DESCRIPTION | 21 TCGAretriever-1.9.1/TCGAretriever/MD5 | 44 TCGAretriever-1.9.1/TCGAretriever/NAMESPACE | 9 TCGAretriever-1.9.1/TCGAretriever/R/tcgaretriever_v_1_9e.R |only TCGAretriever-1.9.1/TCGAretriever/build/vignette.rds |binary TCGAretriever-1.9.1/TCGAretriever/data |only TCGAretriever-1.9.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.R | 103 +- TCGAretriever-1.9.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.Rmd | 174 ++- TCGAretriever-1.9.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.html | 478 +++++----- TCGAretriever-1.9.1/TCGAretriever/man/TCGAretriever-package.Rd | 33 TCGAretriever-1.9.1/TCGAretriever/man/blcaOutputExamples.Rd |only TCGAretriever-1.9.1/TCGAretriever/man/cb_query.Rd |only TCGAretriever-1.9.1/TCGAretriever/man/expand_cases.Rd | 32 TCGAretriever-1.9.1/TCGAretriever/man/fetch_all_tcgadata.Rd | 45 TCGAretriever-1.9.1/TCGAretriever/man/get_cancer_studies.Rd | 24 TCGAretriever-1.9.1/TCGAretriever/man/get_cancer_types.Rd | 23 TCGAretriever-1.9.1/TCGAretriever/man/get_case_lists.Rd | 28 TCGAretriever-1.9.1/TCGAretriever/man/get_clinical_data.Rd | 32 TCGAretriever-1.9.1/TCGAretriever/man/get_gene_identifiers.Rd |only TCGAretriever-1.9.1/TCGAretriever/man/get_genetic_profiles.Rd | 23 TCGAretriever-1.9.1/TCGAretriever/man/get_molecular_data.Rd |only TCGAretriever-1.9.1/TCGAretriever/man/get_mutation_data.Rd |only TCGAretriever-1.9.1/TCGAretriever/man/make_groups.Rd | 6 TCGAretriever-1.9.1/TCGAretriever/vignettes/getting_started_with_TCGAretriever.Rmd | 174 ++- 29 files changed, 727 insertions(+), 522 deletions(-)
Title: Robust Functional Linear Regression
Description: Functions for implementing robust methods for functional linear regression. In the functional linear regression, we consider scalar-on-function linear regression and function-on-function linear regression. More details, see Beyaztas, U., and Shang, H. L. (2021) <arXiv:2111.01238> and Beyaztas, U., and Shang, H. L. (2022) <arXiv:2203.05065>.
Author: Ufuk Beyaztas [aut, cre, cph] ,
Han Lin Shang [aut]
Maintainer: Ufuk Beyaztas <ufukbeyaztas@gmail.com>
Diff between robflreg versions 1.1 dated 2023-01-10 and 1.2 dated 2024-01-23
robflreg-1.1/robflreg/inst |only robflreg-1.1/robflreg/vignettes |only robflreg-1.2/robflreg/ChangeLog | 4 ++++ robflreg-1.2/robflreg/DESCRIPTION | 8 ++++---- robflreg-1.2/robflreg/MD5 | 12 +++--------- robflreg-1.2/robflreg/man/robflreg-package.Rd | 14 ++++++++++---- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Regression using GMDH Algorithms
Description: Regression using GMDH algorithms from Prof. Alexey G. Ivakhnenko.
Group Method of Data Handling (GMDH), or polynomial neural networks, is a family of inductive algorithms
that performs gradually complicated polynomial models and selecting the best solution by an external criterion.
In other words, inductive GMDH algorithms give possibility finding automatically interrelations in data, and
selecting an optimal structure of model or network.
The package includes GMDH Combinatorial, GMDH MIA (Multilayered Iterative Algorithm), GMDH GIA (Generalized Iterative Algorithm) and GMDH Combinatorial with Active Neurons.
Author: Manuel Villacorta Tilve
Maintainer: Manuel Villacorta Tilve <mvt.oviedo@gmail.com>
Diff between GMDHreg versions 0.2.2 dated 2021-07-05 and 0.2.3 dated 2024-01-23
DESCRIPTION | 11 - MD5 | 20 +-- NEWS.md | 4 R/fun.svd_1.R | 2 R/fun.svd_2.R | 2 R/fun.svd_3.R | 2 build/vignette.rds |binary inst/doc/GMDHreg.html | 330 ++++++++++++++++++++++++++++++++++++++++++++------ man/fun.svd_1.Rd | 4 man/fun.svd_2.Rd | 4 man/fun.svd_3.Rd | 4 11 files changed, 323 insertions(+), 60 deletions(-)
Title: Hacks for 'ggplot2'
Description: A 'ggplot2' extension that does a variety of little
helpful things. The package extends 'ggplot2' facets through
customisation, by setting individual scales per panel, resizing panels
and providing nested facets. Also allows multiple colour and fill
scales per plot. Also hosts a smaller collection of stats, geoms and axis
guides.
Author: Teun van den Brand [aut, cre]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between ggh4x versions 0.2.7 dated 2023-12-22 and 0.2.8 dated 2024-01-23
DESCRIPTION | 8 +- MD5 | 52 ++++++------- NAMESPACE | 5 - NEWS.md | 8 ++ R/borrowed_ggplot2.R | 26 +++--- R/conveniences.R | 8 +- R/facet_grid2.R | 4 - R/facet_nested.R | 12 +-- R/facet_nested_wrap.R | 8 +- R/facet_wrap2.R | 131 +++++++++++++++++++++------------- R/facetted_pos_scales.R | 5 - R/geom_box.R | 7 - R/geom_rectrug.R | 4 - R/geom_text_aimed.R | 8 +- R/guide_axis_manual.R | 8 +- R/guide_axis_truncated.R | 16 ++-- R/guide_stringlegend.R | 4 - R/help_secondary.R | 27 +++---- R/scale_facet.R | 8 +- R/scale_listed.R | 24 +++--- R/scale_manual.R | 16 ++-- R/stat_theodensity.R | 24 +++--- R/strip_themed.R | 8 +- R/strip_vanilla.R | 12 +-- tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/scale_listed.md | 2 tests/testthat/test-help_secondary.R | 7 - 27 files changed, 237 insertions(+), 205 deletions(-)
Title: 'ggplot2' Extension for Seasonal and Trading Day Adjustment with
'RJDemetra'
Description: Provides 'ggplot2' functions to return the results of seasonal and trading day adjustment
made by 'RJDemetra'. 'RJDemetra' is an 'R' interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>),
the seasonal adjustment software officially recommended to the members of the European Statistical System and
the European System of Central Banks.
Author: Alain Quartier-la-Tente [aut, cre]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between ggdemetra versions 0.2.6 dated 2023-10-04 and 0.2.7 dated 2024-01-23
ggdemetra-0.2.6/ggdemetra/man/deprecated-ggdemetra.Rd |only ggdemetra-0.2.7/ggdemetra/DESCRIPTION | 11 +- ggdemetra-0.2.7/ggdemetra/MD5 | 19 ++-- ggdemetra-0.2.7/ggdemetra/NAMESPACE | 1 ggdemetra-0.2.7/ggdemetra/NEWS.md | 6 + ggdemetra-0.2.7/ggdemetra/R/autoplot.R | 55 ++++++++------ ggdemetra-0.2.7/ggdemetra/R/extract_cmp.R | 17 ---- ggdemetra-0.2.7/ggdemetra/README.md | 12 ++- ggdemetra-0.2.7/ggdemetra/inst/doc/ggdemetra.R | 4 - ggdemetra-0.2.7/ggdemetra/inst/doc/ggdemetra.html | 10 +- ggdemetra-0.2.7/ggdemetra/man/figures/README-sa-out-1.png |binary 11 files changed, 74 insertions(+), 61 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings mat [...truncated...]
Author: Niels Waller [aut, cre],
Justin Kracht [ctb],
Jeff Jones [ctb],
Casey Giordano [ctb],
Hoang V. Nguyen [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 2.3 dated 2023-03-19 and 2.4.2 dated 2024-01-23
fungible-2.3/fungible/inst/doc/fungible-manual.pdf |only fungible-2.4.2/fungible/DESCRIPTION | 26 ++-- fungible-2.4.2/fungible/MD5 | 81 ++++++++++--- fungible-2.4.2/fungible/NAMESPACE | 21 +++ fungible-2.4.2/fungible/R/CompleteRcvx.R | 2 fungible-2.4.2/fungible/R/CompleteRdev.R | 26 ++++ fungible-2.4.2/fungible/R/RGen.R |only fungible-2.4.2/fungible/R/Ravgr.R |only fungible-2.4.2/fungible/R/Rbounds.R |only fungible-2.4.2/fungible/R/SchmidLeiman.R | 2 fungible-2.4.2/fungible/R/TR.R |only fungible-2.4.2/fungible/R/TaylorRussell.R |only fungible-2.4.2/fungible/R/VolElliptope.R |only fungible-2.4.2/fungible/R/cb.R |only fungible-2.4.2/fungible/R/cfi.R |only fungible-2.4.2/fungible/R/corDensity.R |only fungible-2.4.2/fungible/R/faMain.R | 4 fungible-2.4.2/fungible/R/faSort.R | 2 fungible-2.4.2/fungible/R/get_wb_mod.R |only fungible-2.4.2/fungible/R/noisemaker.R |only fungible-2.4.2/fungible/R/obj_func.R |only fungible-2.4.2/fungible/R/rmsea.R |only fungible-2.4.2/fungible/R/semify.R |only fungible-2.4.2/fungible/R/simFA.R | 6 fungible-2.4.2/fungible/R/summary.monte.R | 34 ++--- fungible-2.4.2/fungible/R/summary.monte1.R | 2 fungible-2.4.2/fungible/R/tkl.R |only fungible-2.4.2/fungible/R/wb.R |only fungible-2.4.2/fungible/build |only fungible-2.4.2/fungible/inst/CITATION | 6 fungible-2.4.2/fungible/inst/doc/simulate-model-error.R |only fungible-2.4.2/fungible/inst/doc/simulate-model-error.Rmd |only fungible-2.4.2/fungible/inst/doc/simulate-model-error.html |only fungible-2.4.2/fungible/man/RGen.Rd |only fungible-2.4.2/fungible/man/Ravgr.Rd |only fungible-2.4.2/fungible/man/Rbounds.Rd |only fungible-2.4.2/fungible/man/SchmidLeiman.Rd | 2 fungible-2.4.2/fungible/man/TR.Rd |only fungible-2.4.2/fungible/man/TaylorRussell.Rd |only fungible-2.4.2/fungible/man/VolElliptope.Rd |only fungible-2.4.2/fungible/man/cb.Rd |only fungible-2.4.2/fungible/man/cfi.Rd |only fungible-2.4.2/fungible/man/corDensity.Rd |only fungible-2.4.2/fungible/man/faMain.Rd | 4 fungible-2.4.2/fungible/man/faSort.Rd | 2 fungible-2.4.2/fungible/man/get_wb_mod.Rd |only fungible-2.4.2/fungible/man/noisemaker.Rd |only fungible-2.4.2/fungible/man/obj_func.Rd |only fungible-2.4.2/fungible/man/rmsea.Rd |only fungible-2.4.2/fungible/man/semify.Rd |only fungible-2.4.2/fungible/man/simFA.Rd | 6 fungible-2.4.2/fungible/man/summary.monte.Rd | 33 ++--- fungible-2.4.2/fungible/man/summary.monte1.Rd | 2 fungible-2.4.2/fungible/man/tkl.Rd |only fungible-2.4.2/fungible/man/wb.Rd |only fungible-2.4.2/fungible/tests |only fungible-2.4.2/fungible/vignettes |only 57 files changed, 179 insertions(+), 82 deletions(-)
Title: Estimation of Meiotic Recombination Rates Using Marey Maps
Description: Local recombination rates are graphically estimated across a genome using Marey maps.
Author: Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between MareyMap versions 1.3.6 dated 2020-12-04 and 1.3.7 dated 2024-01-23
MareyMap-1.3.6/MareyMap/inst/about.txt |only MareyMap-1.3.7/MareyMap/DESCRIPTION | 12 ++++---- MareyMap-1.3.7/MareyMap/MD5 | 26 +++++++++---------- MareyMap-1.3.7/MareyMap/R/PlotArea.R | 2 - MareyMap-1.3.7/MareyMap/build/vignette.rds |binary MareyMap-1.3.7/MareyMap/inst/CITATION |only MareyMap-1.3.7/MareyMap/inst/doc/vignette.Rnw | 2 - MareyMap-1.3.7/MareyMap/inst/doc/vignette.pdf |binary MareyMap-1.3.7/MareyMap/man/Arabidopsis_thaliana.Rd | 2 - MareyMap-1.3.7/MareyMap/man/Interpolation-class.Rd | 2 - MareyMap-1.3.7/MareyMap/man/MareyMap-class.Rd | 2 - MareyMap-1.3.7/MareyMap/man/MareyMap-methods.Rd | 4 +- MareyMap-1.3.7/MareyMap/man/SpeciesMaps-methods.Rd | 2 - MareyMap-1.3.7/MareyMap/man/interpolation-methods.Rd | 2 - MareyMap-1.3.7/MareyMap/vignettes/vignette.Rnw | 2 - 15 files changed, 27 insertions(+), 31 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.8.0 dated 2023-07-12 and 0.9.0 dated 2024-01-23
mapSpain-0.8.0/mapSpain/R/layer_spatraster.R |only mapSpain-0.8.0/mapSpain/man/layer_spatraster.Rd |only mapSpain-0.8.0/mapSpain/tests/testthat/test-layer_spatraster.R |only mapSpain-0.9.0/mapSpain/DESCRIPTION | 11 mapSpain-0.9.0/mapSpain/MD5 | 188 +-- mapSpain-0.9.0/mapSpain/NAMESPACE | 3 mapSpain-0.9.0/mapSpain/NEWS.md | 15 mapSpain-0.9.0/mapSpain/R/addProviderEspTiles.R | 64 - mapSpain-0.9.0/mapSpain/R/data.R | 165 +- mapSpain-0.9.0/mapSpain/R/esp_cache.R | 59 mapSpain-0.9.0/mapSpain/R/esp_cache_clear.R | 10 mapSpain-0.9.0/mapSpain/R/esp_check_access.R | 2 mapSpain-0.9.0/mapSpain/R/esp_dict.R | 190 +-- mapSpain-0.9.0/mapSpain/R/esp_getTiles.R | 39 mapSpain-0.9.0/mapSpain/R/esp_get_can_box.R | 41 mapSpain-0.9.0/mapSpain/R/esp_get_capimun.R | 79 - mapSpain-0.9.0/mapSpain/R/esp_get_ccaa.R | 65 - mapSpain-0.9.0/mapSpain/R/esp_get_comarca.R | 24 mapSpain-0.9.0/mapSpain/R/esp_get_country.R | 15 mapSpain-0.9.0/mapSpain/R/esp_get_grid_BDN.R | 284 ++-- mapSpain-0.9.0/mapSpain/R/esp_get_grid_EEA.R | 306 ++--- mapSpain-0.9.0/mapSpain/R/esp_get_grid_ESDAC.R | 48 mapSpain-0.9.0/mapSpain/R/esp_get_grid_MTN.R | 33 mapSpain-0.9.0/mapSpain/R/esp_get_gridmap.R | 14 mapSpain-0.9.0/mapSpain/R/esp_get_hydrobasin.R | 6 mapSpain-0.9.0/mapSpain/R/esp_get_hypsobath.R | 7 mapSpain-0.9.0/mapSpain/R/esp_get_munic.R | 43 mapSpain-0.9.0/mapSpain/R/esp_get_nuts.R | 36 mapSpain-0.9.0/mapSpain/R/esp_get_prov.R | 22 mapSpain-0.9.0/mapSpain/R/esp_get_railway.R | 6 mapSpain-0.9.0/mapSpain/R/esp_get_rivers.R | 7 mapSpain-0.9.0/mapSpain/R/esp_get_roads.R | 25 mapSpain-0.9.0/mapSpain/R/esp_get_simplified.R | 8 mapSpain-0.9.0/mapSpain/R/esp_make_provider.R | 5 mapSpain-0.9.0/mapSpain/R/esp_move_can.R |only mapSpain-0.9.0/mapSpain/R/sysdata.rda |binary mapSpain-0.9.0/mapSpain/R/utils_download_sianedata.R | 28 mapSpain-0.9.0/mapSpain/R/utils_siane.R | 29 mapSpain-0.9.0/mapSpain/R/utils_tiles.R | 72 - mapSpain-0.9.0/mapSpain/README.md | 12 mapSpain-0.9.0/mapSpain/build/partial.rdb |binary mapSpain-0.9.0/mapSpain/build/vignette.rds |binary mapSpain-0.9.0/mapSpain/data/esp_codelist.rda |binary mapSpain-0.9.0/mapSpain/data/esp_munic.sf.rda |binary mapSpain-0.9.0/mapSpain/data/esp_nuts.sf.rda |binary mapSpain-0.9.0/mapSpain/data/esp_tiles_providers.rda |binary mapSpain-0.9.0/mapSpain/data/leaflet.providersESP.df.rda |binary mapSpain-0.9.0/mapSpain/data/pobmun19.rda |binary mapSpain-0.9.0/mapSpain/inst/WORDLIST | 34 mapSpain-0.9.0/mapSpain/inst/doc/imagery.R | 2 mapSpain-0.9.0/mapSpain/inst/doc/mapSpain.Rmd | 13 mapSpain-0.9.0/mapSpain/inst/doc/mapSpain.html | 122 -- mapSpain-0.9.0/mapSpain/inst/schemaorg.json |only mapSpain-0.9.0/mapSpain/man/addProviderEspTiles.Rd | 5 mapSpain-0.9.0/mapSpain/man/esp_check_access.Rd | 3 mapSpain-0.9.0/mapSpain/man/esp_clear_cache.Rd | 9 mapSpain-0.9.0/mapSpain/man/esp_codelist.Rd | 83 - mapSpain-0.9.0/mapSpain/man/esp_detect_cache_dir.Rd |only mapSpain-0.9.0/mapSpain/man/esp_dict.Rd | 6 mapSpain-0.9.0/mapSpain/man/esp_getTiles.Rd | 27 mapSpain-0.9.0/mapSpain/man/esp_get_can_box.Rd | 14 mapSpain-0.9.0/mapSpain/man/esp_get_capimun.Rd | 17 mapSpain-0.9.0/mapSpain/man/esp_get_ccaa.Rd | 19 mapSpain-0.9.0/mapSpain/man/esp_get_comarca.Rd | 8 mapSpain-0.9.0/mapSpain/man/esp_get_country.Rd | 9 mapSpain-0.9.0/mapSpain/man/esp_get_grid_BDN.Rd | 12 mapSpain-0.9.0/mapSpain/man/esp_get_grid_EEA.Rd | 10 mapSpain-0.9.0/mapSpain/man/esp_get_grid_ESDAC.Rd | 8 mapSpain-0.9.0/mapSpain/man/esp_get_grid_MTN.Rd | 6 mapSpain-0.9.0/mapSpain/man/esp_get_gridmap.Rd | 8 mapSpain-0.9.0/mapSpain/man/esp_get_hydrobasin.Rd | 6 mapSpain-0.9.0/mapSpain/man/esp_get_hypsobath.Rd | 7 mapSpain-0.9.0/mapSpain/man/esp_get_munic.Rd | 7 mapSpain-0.9.0/mapSpain/man/esp_get_nuts.Rd | 10 mapSpain-0.9.0/mapSpain/man/esp_get_prov.Rd | 9 mapSpain-0.9.0/mapSpain/man/esp_get_railway.Rd | 6 mapSpain-0.9.0/mapSpain/man/esp_get_rivers.Rd | 7 mapSpain-0.9.0/mapSpain/man/esp_get_roads.Rd | 9 mapSpain-0.9.0/mapSpain/man/esp_get_simplified.Rd | 8 mapSpain-0.9.0/mapSpain/man/esp_make_provider.Rd | 2 mapSpain-0.9.0/mapSpain/man/esp_move_can.Rd |only mapSpain-0.9.0/mapSpain/man/esp_munic.sf.Rd | 18 mapSpain-0.9.0/mapSpain/man/esp_nuts.sf.Rd | 52 mapSpain-0.9.0/mapSpain/man/esp_set_cache_dir.Rd | 5 mapSpain-0.9.0/mapSpain/man/figures/logo.png |binary mapSpain-0.9.0/mapSpain/man/leaflet.providersESP.df.Rd | 2 mapSpain-0.9.0/mapSpain/man/pobmun19.Rd | 18 mapSpain-0.9.0/mapSpain/tests/testthat/test-esp_cache.R | 4 mapSpain-0.9.0/mapSpain/tests/testthat/test-esp_getTiles.R | 604 +++++----- mapSpain-0.9.0/mapSpain/tests/testthat/test-esp_get_ccaa.R | 4 mapSpain-0.9.0/mapSpain/tests/testthat/test-esp_get_prov.R | 8 mapSpain-0.9.0/mapSpain/tests/testthat/test-esp_move_can.R |only mapSpain-0.9.0/mapSpain/vignettes/basic-1.png |binary mapSpain-0.9.0/mapSpain/vignettes/basic2-1.png |binary mapSpain-0.9.0/mapSpain/vignettes/basic3-1.png |binary mapSpain-0.9.0/mapSpain/vignettes/choro-1.png |binary mapSpain-0.9.0/mapSpain/vignettes/giscoR-1.png |binary mapSpain-0.9.0/mapSpain/vignettes/mapSpain.Rmd | 13 mapSpain-0.9.0/mapSpain/vignettes/thematic-1.png |binary 99 files changed, 1570 insertions(+), 1605 deletions(-)
Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner [cre, aut],
Mike Meredith [ctb]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between jagsUI versions 1.5.2 dated 2021-06-18 and 1.6.1 dated 2024-01-23
jagsUI-1.5.2/jagsUI/NEWS |only jagsUI-1.5.2/jagsUI/R/bindmcmc.R |only jagsUI-1.5.2/jagsUI/R/datacheck.R |only jagsUI-1.5.2/jagsUI/R/geninits.R |only jagsUI-1.5.2/jagsUI/R/get_plot_info.R |only jagsUI-1.5.2/jagsUI/R/getdim.R |only jagsUI-1.5.2/jagsUI/R/orderparams.R |only jagsUI-1.5.2/jagsUI/R/plot.R |only jagsUI-1.5.2/jagsUI/R/populate.R |only jagsUI-1.5.2/jagsUI/R/print.R |only jagsUI-1.5.2/jagsUI/R/processinput.R |only jagsUI-1.5.2/jagsUI/R/processoutput.R |only jagsUI-1.5.2/jagsUI/R/runmodel.R |only jagsUI-1.5.2/jagsUI/R/runparallel.R |only jagsUI-1.5.2/jagsUI/R/setfactories.R |only jagsUI-1.5.2/jagsUI/R/setmodules.R |only jagsUI-1.5.2/jagsUI/R/summary.R |only jagsUI-1.5.2/jagsUI/R/summarymatrix.R |only jagsUI-1.5.2/jagsUI/R/testrhat.R |only jagsUI-1.5.2/jagsUI/R/translateparams.R |only jagsUI-1.5.2/jagsUI/R/updatebasic.R |only jagsUI-1.5.2/jagsUI/R/utils.R |only jagsUI-1.6.1/jagsUI/DESCRIPTION | 17 +- jagsUI-1.6.1/jagsUI/MD5 | 90 +++++++----- jagsUI-1.6.1/jagsUI/NAMESPACE | 35 +--- jagsUI-1.6.1/jagsUI/NEWS.md |only jagsUI-1.6.1/jagsUI/R/S3_methods.R |only jagsUI-1.6.1/jagsUI/R/autojags.R | 236 ++++++++++++++++---------------- jagsUI-1.6.1/jagsUI/R/densityplot.R | 57 ++++--- jagsUI-1.6.1/jagsUI/R/jags.R | 117 ++++----------- jagsUI-1.6.1/jagsUI/R/jags_View.R | 2 jagsUI-1.6.1/jagsUI/R/jagsbasic.R | 86 +++-------- jagsUI-1.6.1/jagsUI/R/mcmc_tools.R | 128 +++++++++++------ jagsUI-1.6.1/jagsUI/R/plot_tools.R |only jagsUI-1.6.1/jagsUI/R/ppcheck.R | 4 jagsUI-1.6.1/jagsUI/R/process_input.R |only jagsUI-1.6.1/jagsUI/R/process_output.R |only jagsUI-1.6.1/jagsUI/R/run_rjags.R |only jagsUI-1.6.1/jagsUI/R/traceplot.R | 14 + jagsUI-1.6.1/jagsUI/R/update.R | 150 +++++++++++--------- jagsUI-1.6.1/jagsUI/R/whiskerplot.R | 12 + jagsUI-1.6.1/jagsUI/build |only jagsUI-1.6.1/jagsUI/inst |only jagsUI-1.6.1/jagsUI/man/jags_View.Rd | 2 jagsUI-1.6.1/jagsUI/tests |only jagsUI-1.6.1/jagsUI/vignettes |only 46 files changed, 476 insertions(+), 474 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Diff between crmPack versions 1.0.3 dated 2022-09-02 and 1.0.4 dated 2024-01-23
crmPack-1.0.3/crmPack/README.md |only crmPack-1.0.3/crmPack/inst/crmPack.pdf |only crmPack-1.0.4/crmPack/DESCRIPTION | 6 +- crmPack-1.0.4/crmPack/MD5 | 26 ++++---- crmPack-1.0.4/crmPack/NEWS.md | 7 +- crmPack-1.0.4/crmPack/build/vignette.rds |binary crmPack-1.0.4/crmPack/inst/doc/example.pdf |binary crmPack-1.0.4/crmPack/inst/doc/guidelines.Rmd | 6 +- crmPack-1.0.4/crmPack/inst/doc/guidelines.html | 30 ++++------ crmPack-1.0.4/crmPack/man/DualEndpointOld-class.Rd | 2 crmPack-1.0.4/crmPack/man/DualEndpointRW-class.Rd | 2 crmPack-1.0.4/crmPack/man/pinvGamma.Rd | 2 crmPack-1.0.4/crmPack/man/qinvGamma.Rd | 2 crmPack-1.0.4/crmPack/man/simulate-DualResponsesSamplesDesign-method.Rd | 6 +- crmPack-1.0.4/crmPack/vignettes/guidelines.Rmd | 6 +- 15 files changed, 46 insertions(+), 49 deletions(-)
Title: Change-Points Detections for Changes in Variance
Description: Detection of change-points for variance of heteroscedastic Gaussian variables with piecewise constant variance function. Adelfio, G. (2012), Change-point detection for variance piecewise constant models, Communications in Statistics, Simulation and Computation, 41:4, 437-448, <doi:10.1080/03610918.2011.592248>.
Author: Gianluca Sottile [cre],
Giada Adelfio [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between changepointsVar versions 0.1.0 dated 2018-01-10 and 0.1.1 dated 2024-01-23
changepointsVar-0.1.0/changepointsVar/man/jumpointsVar-internal.Rd |only changepointsVar-0.1.0/changepointsVar/man/jumpointsVar-package.Rd |only changepointsVar-0.1.1/changepointsVar/DESCRIPTION | 7 +++---- changepointsVar-0.1.1/changepointsVar/MD5 | 8 ++++---- changepointsVar-0.1.1/changepointsVar/R/jumpointsVar.R | 4 ++-- changepointsVar-0.1.1/changepointsVar/man/changepointsVar-internal.Rd |only changepointsVar-0.1.1/changepointsVar/man/changepointsVar-package.Rd |only 7 files changed, 9 insertions(+), 10 deletions(-)
More information about changepointsVar at CRAN
Permanent link
Title: Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between Rsurrogate versions 3.1 dated 2021-11-14 and 3.2 dated 2024-01-23
DESCRIPTION | 7 +++---- MD5 | 14 +++++++------- man/R.multiple.surv.Rd | 4 ++-- man/R.s.estimate.me.Rd | 4 ++-- man/calculate.var.np.Rd | 11 +++++------ man/delta.multiple.surv.Rd | 2 +- man/fieller.calculate.me.Rd | 2 +- man/me.variance.estimate.Rd | 3 +-- 8 files changed, 22 insertions(+), 25 deletions(-)
Title: Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM), Tenenhaus, Esposito Vinzi, Chatelin, Lauro (2005) <doi:10.1016/j.csda.2004.03.005>,
analysis for both metric and non-metric data, as well as REBUS analysis, Esposito Vinzi, Trinchera, Squillacciotti, and Tenenhaus (2008) <doi:10.1002/asmb.728>.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plspm versions 0.5.0 dated 2023-03-13 and 0.5.1 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 5 +++++ build/vignette.rds |binary inst/doc/plspm_introduction.Rnw | 6 ++---- inst/doc/plspm_introduction.pdf |binary man/futbol.Rd | 2 +- man/spainfoot.Rd | 2 +- vignettes/plspm_introduction.Rnw | 6 ++---- 9 files changed, 23 insertions(+), 22 deletions(-)
Title: Neighborhood Deprivation Indices
Description: Computes various metrics of socio-economic deprivation and disparity in
the United States. Some metrics are considered "spatial" because they
consider the values of neighboring (i.e., adjacent) census geographies in
their computation, while other metrics are "aspatial" because they only
consider the value within each census geography. Two types of aspatial
neighborhood deprivation indices (NDI) are available: including:
(1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x>
and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066>
and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002>
who use variables chosen by Roux and Mair (2010)
<doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple
demographic characteristics from the U.S. Census Bureau American Community
Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5
(2005-2009 onward), the package can also (1) compute the spatial Racial Iso [...truncated...]
Author: Ian D. Buller [aut, cre, cph] ,
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between ndi versions 0.1.4 dated 2023-02-01 and 0.1.5 dated 2024-01-23
DESCRIPTION | 11 +++++---- MD5 | 56 +++++++++++++++++++++++++------------------------- NEWS.md | 19 +++++++++++++--- R/anthopolos.R | 44 +++++++++++++++++++-------------------- R/atkinson.R | 44 +++++++++++++++++++-------------------- R/bell.R | 40 +++++++++++++++++------------------ R/bemanian_beyer.R | 42 ++++++++++++++++++------------------- R/bravo.R | 16 +++++++------- R/duncan.R | 42 ++++++++++++++++++------------------- R/krieger.R | 24 ++++++++++----------- R/messer.R | 24 ++++++++++----------- R/package.R | 12 +++++----- R/powell_wiley.R | 32 ++++++++++++++-------------- R/sudano.R | 44 +++++++++++++++++++-------------------- R/white.R | 40 +++++++++++++++++------------------ README.md | 20 ++++++++--------- inst/CITATION | 10 ++++---- man/anthopolos.Rd | 44 +++++++++++++++++++-------------------- man/atkinson.Rd | 44 +++++++++++++++++++-------------------- man/bell.Rd | 40 +++++++++++++++++------------------ man/bemanian_beyer.Rd | 42 ++++++++++++++++++------------------- man/bravo.Rd | 16 +++++++------- man/duncan.Rd | 42 ++++++++++++++++++------------------- man/krieger.Rd | 24 ++++++++++----------- man/messer.Rd | 24 ++++++++++----------- man/ndi-package.Rd | 12 +++++----- man/powell_wiley.Rd | 32 ++++++++++++++-------------- man/sudano.Rd | 44 +++++++++++++++++++-------------------- man/white.Rd | 40 +++++++++++++++++------------------ 29 files changed, 468 insertions(+), 456 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre] ,
Jonathan Keane [ctb],
Maelle Salmon [ctb]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 4.2.1 dated 2023-06-12 and 4.2.2 dated 2024-01-23
DESCRIPTION | 6 - MD5 | 30 +++---- NEWS.md | 4 R/httptest.R | 2 R/mock-api.R | 2 R/redact.R | 2 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/faq.html | 14 +-- inst/doc/httptest.R | 2 inst/doc/httptest.html | 202 ++++++++++++++++++++++++------------------------ inst/doc/redacting.html | 88 ++++++++++---------- inst/doc/vignettes.html | 32 +++---- man/as-redactor.Rd | 2 man/httptest.Rd | 20 ++++ man/use_mock_api.Rd | 2 16 files changed, 217 insertions(+), 192 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.29 dated 2023-09-05 and 1.1.30 dated 2024-01-23
DESCRIPTION | 8 ++-- MD5 | 74 +++++++++++++++++++------------------- NEWS.md | 14 +++++++ R/by_element_est.R | 46 +++++++++++++++++++++-- R/fix_wavs.R | 4 +- R/gaps.R | 8 ++-- R/info_sound_files.R | 2 - R/mp32wav.R | 2 - R/query_xc.R | 9 +++- R/resample_est.R | 4 +- R/selection_table.R | 31 +++++++++++---- R/simulate_songs.R | 33 ++++++++++++---- R/spectro_analysis.R | 60 +++++++++++++++++++++++++++--- README.md | 10 ++--- build/vignette.rds |binary data/comp_matrix.rda |binary data/lbh_selec_table.rda |binary data/lbh_selec_table2.rda |binary data/new_function_names.rda |binary data/selec.table.rda |binary data/sim_coor_sing.rda |binary inst/doc/Intro_to_warbleR.R | 26 ++++++------- inst/doc/Intro_to_warbleR.html | 73 +++++++++++++++++++------------------ inst/doc/warbleR_workflow_01.R | 70 +++++++++++++++++------------------ inst/doc/warbleR_workflow_01.html | 4 +- inst/doc/warbleR_workflow_02.R | 36 +++++++++--------- inst/doc/warbleR_workflow_02.html | 6 +-- inst/doc/warbleR_workflow_03.R | 68 +++++++++++++++++----------------- inst/doc/warbleR_workflow_03.html | 8 ++-- man/fix_wavs.Rd | 2 - man/gaps.Rd | 2 - man/info_sound_files.Rd | 2 - man/mp32wav.Rd | 2 - man/query_xc.Rd | 2 - man/resample_est.Rd | 2 - man/sim_songs.Rd | 3 + man/simulate_songs.Rd | 13 ++++-- man/warbleR.Rd | 2 - 38 files changed, 382 insertions(+), 244 deletions(-)
Title: Simulation-Based Landscape Construction for Dynamical Systems
Description: A toolbox for constructing potential landscapes for dynamical
systems using Monte Carlo simulation. The method is based on the
potential landscape definition by Wang et al. (2008)
<doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016
<doi:10.1063/1.4943096> for further mathematical discussions) and can
be used for a large variety of models.
Author: Jingmeng Cui [aut, cre]
Maintainer: Jingmeng Cui <jingmeng.cui@outlook.com>
Diff between simlandr versions 0.3.0 dated 2022-11-15 and 0.3.1 dated 2024-01-23
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------ NEWS.md | 4 ++ R/check_conv.R | 2 - R/kernel_api.R | 1 R/single_simulation_landscape.R | 3 + README.md | 6 +-- build/partial.rdb |binary inst/doc/simlandr.pdf |binary man/check_conv.Rd | 2 - man/make_kernel_dist.Rd | 62 +++++++++++++++++++--------------------- 11 files changed, 56 insertions(+), 52 deletions(-)
Title: Estimation and Visualization of Linear Panel Event Studies
Description: Estimates linear panel event study models. Plots coefficients following the recommendations in Freyaldenhoven et al. (2021) <doi:10.3386/w29170>. Includes sup-t bands, testing for key hypotheses, least wiggly path through the Wald region. Allows instrumental variables estimation following Freyaldenhoven et al. (2019) <doi:10.1257/aer.20180609>.
Author: Simon Freyaldenhoven [aut],
Christian Hansen [aut],
Jorge Perez Perez [aut],
Jesse Shapiro [aut],
Veli Andirin [aut],
Richard Calvo [aut],
Santiago Hermo [aut],
Nathan Schor [aut],
Emily Wang [aut, cre],
JMSLab [cph],
Ryan Kessler [cph]
Maintainer: Emily Wang <emwang@hbs.edu>
Diff between eventstudyr versions 1.1.1 dated 2023-06-07 and 1.1.2 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/SmPathHelpers.R | 4 ++-- inst/doc/documentation.R | 2 +- inst/doc/documentation.html | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Fast Spatial Regression using Moran Eigenvectors
Description: Functions for estimating spatial varying coefficient models, mixed models, and other spatial regression models for Gaussian and non-Gaussian data. Moran eigenvectors are used to an approximate spatial Gaussian processes. These processes are used for modeling the spatial processes in residuals and regression coefficients. For details see Murakami (2021) <arXiv:1703.04467>.
Author: Daisuke Murakami <dmuraka@ism.ac.jp>
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.2.2.9 dated 2023-04-28 and 0.2.3 dated 2024-01-23
DESCRIPTION | 10 MD5 | 62 NAMESPACE | 103 R/addlearn_local.R |only R/besf_vc.R | 2881 +++++++------- R/coef_marginal_vc.R | 135 R/esf.R | 450 +- R/lsem.R | 368 - R/lslm.R | 684 +-- R/meigen0.R | 115 R/meigen_f.R | 13 R/plot_n.R | 132 R/plot_s.R | 229 - R/predict0.R | 2081 ++++++---- R/predict0_vc.R | 8 R/resf.R | 330 - R/resf_qr.R | 916 ++-- R/resf_vc.R | 6032 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/vignette_spmoran_nongaussian.pdf |binary man/addlearn_local.Rd |only man/besf.Rd | 156 man/besf_vc.Rd | 31 man/esf.Rd | 132 man/meigen.Rd | 86 man/meigen0.Rd | 57 man/meigen_f.Rd | 75 man/nongauss_y.Rd | 158 man/predict0.Rd | 143 man/predict0_vc.Rd | 169 man/resf.Rd | 294 - man/resf_qr.Rd | 2 man/resf_vc.Rd | 359 - 33 files changed, 8497 insertions(+), 7714 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model as described in Zinn (2014) <doi:10.34196/IJM.00105>.
Author: Sabine Zinn [aut, cre],
Claudio Bosco [ctb],
Maurizio Teobaldell [ctb]
Maintainer: Sabine Zinn <szinn@diw.de>
Diff between MicSim versions 2.0.0 dated 2023-01-09 and 2.0.1 dated 2024-01-23
DESCRIPTION | 8 MD5 | 16 R/micSim.r | 7 build/vignette.rds |binary inst/doc/MicSim_vignette.R | 2 inst/doc/MicSim_vignette.html | 740 +++++++++++++++++++++--------------------- man/MicSim-package.Rd | 4 man/micSim.Rd | 2 man/micSimParallel.Rd | 16 9 files changed, 399 insertions(+), 396 deletions(-)
Title: Remove Vocals from a Song
Description: Attempts to remove vocals from a stereo '.wav' recording of a song.
Author: John R. Dixon
Maintainer: John R. Dixon <gbm2sas@gmail.com>
Diff between karaoke versions 1.0 dated 2016-03-03 and 2.0 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 13 ++++++++++--- man/karaoke-package.Rd | 10 +--------- man/karaoke.Rd | 4 +++- 5 files changed, 22 insertions(+), 21 deletions(-)
Title: Convert GBM Object Trees to SAS Code
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
Author: John R. Dixon
Maintainer: John R. Dixon <gbm2sas@gmail.com>
Diff between gbm2sas versions 2.1 dated 2015-11-10 and 3.0 dated 2024-01-23
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 13 ++++++++++--- man/gbm2sas-package.Rd | 9 --------- man/gbm2sas.Rd | 3 +++ 5 files changed, 22 insertions(+), 21 deletions(-)
Title: Ecological Regression using Aggregate and Individual Data
Description: Estimating individual-level covariate-outcome associations
using aggregate data ("ecological inference") or a combination of
aggregate and individual-level data ("hierarchical related regression").
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between ecoreg versions 0.2.3 dated 2020-03-24 and 0.2.4 dated 2024-01-23
DESCRIPTION | 8 MD5 | 17 R/eco.R | 1090 ++++++++++++++++++++++----------------------- README.md | 15 build/vignette.rds |binary inst/CITATION | 4 inst/NEWS | 7 inst/doc/ecoreg-guide.R |only inst/doc/ecoreg-guide.pdf |binary vignettes/ecoreg-guide.Rnw | 2 10 files changed, 584 insertions(+), 559 deletions(-)
Title: Multi-Trait and Multi-Trial Genome Wide Association Studies
Description: Fast multi-trait and multi-trail Genome Wide Association Studies
(GWAS) following the method described in Zhou and Stephens. (2014),
<doi:10.1038/nmeth.2848>. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zheng [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenQTLxT versions 1.0.1 dated 2023-04-04 and 1.0.2 dated 2024-01-23
DESCRIPTION | 10 MD5 | 24 - NEWS.md | 4 R/RcppExports.R | 16 - R/statgenQTLxT.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenQTLxT.html | 637 ++++++++++++++++++++++----------------------- man/LLQuadFormDiagCPP.Rd | 79 ++--- man/estEffsCPP.Rd | 116 ++++---- man/updateFA.Rd | 16 - src/EMFA.cpp | 8 src/estEffsCPP.cpp | 8 13 files changed, 459 insertions(+), 465 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-10 1.1.1
2022-11-18 1.1.0
2022-10-18 1.0.3
2022-08-23 1.0.2
Title: Simple Definition Of Time Intervals
Description: Simple definition of time intervals for the current, previous, and next week, month, quarter and year.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between timeperiodsR versions 0.7.1 dated 2023-04-20 and 0.7.3 dated 2024-01-23
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 6 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tpr_intro.html | 403 ++++++++++++++++++++++---------------------- man/timeperiodsR-package.Rd | 1 8 files changed, 219 insertions(+), 213 deletions(-)
Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based
spatial relative risk functions that are estimated using the 'sparr' package.
Details about the 'sparr' package methods can be found in the tutorial: Davies
et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation
can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More
information about relative risk functions using kernel density estimation can
be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Derek W. Brown [aut, cph] ,
Mitchell J. Machiela [ctb] ,
Timothy A. Myers [ctb],
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between sparrpowR versions 0.2.7 dated 2023-02-01 and 0.2.8 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/pval_correct.R | 20 ++++---------------- R/utils.R | 12 ++++++++++++ README.md | 4 ++-- man/pval_correct.Rd | 2 +- 7 files changed, 33 insertions(+), 29 deletions(-)
Title: Design Clinical Trials using Sequential Predictive Probability
Monitoring
Description: Functions are available to calibrate designs over a range of posterior and predictive thresholds, to plot the various design options, and to obtain the operating characteristics of optimal accuracy and optimal efficiency designs.
Author: Emily C. Zabor [aut, cre] ,
Brian P. Hobbs [aut],
Michael J. Kane [aut]
Maintainer: Emily C. Zabor <zabore2@ccf.org>
Diff between ppseq versions 0.2.2 dated 2023-04-17 and 0.2.3 dated 2024-01-23
ppseq-0.2.2/ppseq/tests/testthat/_snaps/plot |only ppseq-0.2.2/ppseq/tests/testthat/test-plot.R |only ppseq-0.2.3/ppseq/DESCRIPTION | 6 ppseq-0.2.3/ppseq/MD5 | 28 ppseq-0.2.3/ppseq/NEWS.md | 5 ppseq-0.2.3/ppseq/README.md | 2 ppseq-0.2.3/ppseq/build/vignette.rds |binary ppseq-0.2.3/ppseq/inst/CITATION |only ppseq-0.2.3/ppseq/inst/doc/one_sample_expansion.R | 2 ppseq-0.2.3/ppseq/inst/doc/one_sample_expansion.html | 466 +++++----- ppseq-0.2.3/ppseq/inst/doc/two_sample_randomized.R | 2 ppseq-0.2.3/ppseq/inst/doc/two_sample_randomized.html | 466 +++++----- ppseq-0.2.3/ppseq/tests/testthat/_snaps/calc_decision_rules.md | 2 ppseq-0.2.3/ppseq/tests/testthat/test-calc_decision_rules.R | 2 14 files changed, 538 insertions(+), 443 deletions(-)
Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of
information and tables optionally based on search words from
PDF (Portable Document Format) files and enables the visualization
of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Diff between PDE versions 1.4.7 dated 2023-12-11 and 1.4.8 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/PDE.R | 10 +++++----- inst/doc/PDE.html | 4 ++-- 5 files changed, 17 insertions(+), 14 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.0.6 dated 2023-09-26 and 2.1.0 dated 2024-01-23
ChangeLog | 10 ++++--- DESCRIPTION | 8 +++--- MD5 | 48 ++++++++++++++++++------------------- R/gh_mixture.R | 5 +++ R/mixture.R | 20 +++++++-------- R/pcm.R | 4 +-- R/st_mixture.R | 5 +++ R/t_mixture.R | 5 +++ R/vg_mixture.R | 5 +++ man/ghpcm.Rd | 5 +++ man/gpcm.Rd | 5 +++ man/mixture.Rd | 4 +-- man/pcm.Rd | 5 +++ man/stpcm.Rd | 6 +++- man/tpcm.Rd | 6 +++- man/vgpcm.Rd | 5 +++ src/GH_Model/GH_Mixture_Model.h | 8 ++---- src/GH_Model/GH_VVE.hpp | 38 +++++++++++++++++++++++------ src/ST_Model/ST_Mixture_Model.h | 5 ++- src/ST_Model/ST_VVE.hpp | 26 +++++++++++++++++++- src/T_Model/Covariance_Methods.hpp | 26 +++++++++++++++++++- src/T_Model/General_Methods.hpp | 5 ++- src/VG_Model/VG_Mixture_Model.h | 13 ++++++---- src/VG_Model/VG_VVE.hpp | 25 ++++++++++++++++++- src/gpcm_arma.hpp | 39 ++++++++++++++++++++++++------ 25 files changed, 244 insertions(+), 87 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between lavaSearch2 versions 2.0.1 dated 2023-04-11 and 2.0.2 dated 2024-01-23
DESCRIPTION | 10 MD5 | 324 +- NAMESPACE | 431 +-- NEWS | 166 - R/0onload.R | 52 R/IntDensTri.R | 550 ++-- R/Objective_gaussian_weight.R | 334 +- R/RcppExports.R | 30 R/Scorrect-confint2.R | 216 - R/Scorrect-model.tables.R | 256 +- R/Utils.R | 524 ++-- R/autoplot.calibrateType1.R | 314 +- R/calcType1postSelection.R | 326 +- R/calibrateType1.R | 1494 ++++++------- R/checkData.R | 194 - R/clean.R | 194 - R/coefByType.R | 672 ++--- R/coefType.R | 796 +++---- R/createContrast.R | 884 +++---- R/createGrid.R | 384 +-- R/defineCategoricalLink.R | 334 +- R/evalInParentEnv.R | 110 R/formula.R | 70 R/iidJack.R | 532 ++-- R/initVarlink.R | 262 +- R/lavaSearch2-package.R | 150 - R/link.R | 685 +++--- R/matrixPower.R | 178 - R/modelsearch2-calcDistMax.R | 838 +++---- R/modelsearch2-methods.R | 646 ++--- R/modelsearch2-print.R | 56 R/modelsearch2-summary.R | 164 - R/modelsearch2.R | 1670 +++++++------- R/nobs.R | 48 R/p.adjust2.R | 138 - R/sCorrect-coef2.R | 236 +- R/sCorrect-compare2.R | 866 +++---- R/sCorrect-dInformation2.R | 804 +++---- R/sCorrect-effects2.R | 570 ++--- R/sCorrect-estimate2.R | 592 ++--- R/sCorrect-extractData.R | 176 - R/sCorrect-getGroups2.R | 190 - R/sCorrect-getIndexOmega.R | 170 - R/sCorrect-getVarCov2.R | 166 - R/sCorrect-glht2.R | 762 +++--- R/sCorrect-hessian2.R | 610 ++--- R/sCorrect-information2.R | 358 +-- R/sCorrect-leverage2.R | 352 +-- R/sCorrect-moments2.R | 1155 +++++----- R/sCorrect-nobs2.R | 130 - R/sCorrect-residuals2.R | 402 +-- R/sCorrect-score2.R | 382 +-- R/sCorrect-skeleton.R | 1517 ++++++------- R/sCorrect-sscCoxSnell.R | 658 ++--- R/sCorrect-sscResiduals.R | 554 ++-- R/sCorrect-summary.glht2.R | 382 +-- R/sCorrect-summary2.R | 362 +-- R/sCorrect-updateMoment.R | 704 +++--- R/sCorrect-vcov2.R | 234 +- R/sCorrect.R | 100 R/sampleRepeated.R | 168 - R/summary.calibrateType1.R | 320 +- R/symmetrize.R | 98 R/transformSummaryTable.R | 136 - R/tryWithWarnings.R | 130 - R/var2dummy.R | 216 - build/vignette.rds |binary inst/doc-software/changes.sty | 1054 ++++----- inst/doc-software/overview.aux | 96 inst/doc-software/overview.loc | 2 inst/doc-software/overview.log | 1692 +++++++------- inst/doc-software/overview.org | 2102 +++++++++--------- inst/doc-software/overview.tex | 2380 ++++++++++----------- inst/doc/overview.pdf |binary inst/doc/overview.pdf.asis | 8 man/addLink.Rd | 132 - man/autoplot.intDensTri.Rd | 52 man/autoplot.modelsearch2.Rd | 124 - man/autoplot_calibrateType1.Rd | 150 - man/calcDistMax.Rd | 274 +- man/calcType1postSelection.Rd | 206 - man/calibrateType1.Rd | 294 +- man/checkData.Rd | 80 man/clean.Rd | 90 man/coef2.Rd | 102 man/coefByType.Rd | 348 +-- man/coefType.Rd | 216 - man/combination.Rd | 66 man/combineFormula.Rd | 66 man/compare2.Rd | 262 +- man/confint2.Rd | 160 - man/contrast2name.Rd | 52 man/convFormulaCharacter.Rd | 42 man/createContrast.Rd | 188 - man/createGrid.Rd | 162 - man/defineCategoricalLink.Rd | 118 - man/dfSigma.Rd | 68 man/dot-dinformation2-internal.Rd | 68 man/effects2.Rd | 166 - man/estimate2.Rd | 232 +- man/evalInParentEnv.Rd | 32 man/extractData.Rd | 110 man/findNewLink.Rd | 148 - man/gaussian_weight.Rd | 190 - man/getIndexOmega.Rd | 84 man/getNewLink.Rd | 78 man/getNewModel.Rd | 80 man/getStep.Rd | 78 man/getVarCov2.Rd | 106 man/glht2.Rd | 208 - man/hessian2-internal.Rd | 68 man/hessian2.Rd | 136 - man/iid2.Rd | 146 - man/iid2plot.Rd | 32 man/iidJack.Rd | 152 - man/information2-internal.Rd | 60 man/information2.Rd | 132 - man/initVarLink.Rd | 128 - man/intDensTri.Rd | 248 +- man/lavaSearch2.Rd | 112 man/leverage2.Rd | 124 - man/matrixPower.Rd | 102 man/modelsearch2.Rd | 306 +- man/moments2.Rd | 278 +- man/nStep.Rd | 72 man/nobs2.Rd | 74 man/residuals2.Rd | 166 - man/sCorrect.Rd | 54 man/sampleRepeated.Rd | 60 man/score2-internal.Rd | 58 man/score2.Rd | 158 - man/selectRegressor.Rd | 82 man/selectResponse.Rd | 90 man/setLink.Rd | 92 man/skeleton.Rd | 166 - man/summary.calibrateType1.Rd | 76 man/summary.glht2.Rd | 72 man/summary.modelsearch2.Rd | 44 man/summary2.Rd | 176 - man/symmetrize.Rd | 58 man/transformSummaryTable.Rd | 40 man/tryWithWarnings.Rd | 68 man/var2dummy.Rd | 96 man/vcov2-internal.Rd | 36 man/vcov2.Rd | 158 - tests/test-all.R | 12 tests/testthat/test-coefType.R | 584 ++--- tests/testthat/test-initVar.R | 130 - tests/testthat/test-matrixPower.R | 90 tests/testthat/test-previousBug.R | 276 +- tests/testthat/test1-sCorrect-effects2.R | 162 - tests/testthat/test1-sCorrect-missingValues.R | 330 +- tests/testthat/test1a-sCorrect-validObjects.R | 140 - tests/testthat/test1b-sCorrect-conditionalMoment.R | 1066 ++++----- tests/testthat/test1c-sCorrect-ssc.R | 1006 ++++---- tests/testthat/test1d-sCorrect-compare2.R | 656 ++--- tests/testthat/test1d-sCorrect-residuals2.R | 294 +- tests/testthat/test1d-sCorrect-summary2.R | 536 ++-- tests/testthat/test2-IntDensTri.R | 178 - tests/testthat/test2-calcType1postSelection.R | 164 - tests/testthat/test2-modelsearch2.R | 152 - tests/testthat/test3-multcomp.R | 438 +-- vignettes/overview.pdf.asis | 8 163 files changed, 24920 insertions(+), 24920 deletions(-)
Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper; see <doi:10.1177/0962280219842890> and discussed in a tutorial <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, ctb]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.5.1 dated 2023-05-15 and 1.5.2 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/islasso-internal.Rd | 17 +++++++++++++++++ man/islasso-package.Rd | 4 ++-- man/simulXy.Rd | 1 - 5 files changed, 27 insertions(+), 11 deletions(-)
Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, MDS maps and biplots obtained by PCA, PFA or WALS (weighted alternating least squares); See Graffelman & De Leeuw (2023) <doi: 10.1080/00031305.2023.2186952>.
Author: Jan Graffelman [aut, cre],
Jan De Leeuw [aut]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between Correlplot versions 1.0.9 dated 2024-01-21 and 1.1.0 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/CorrelplotManual.Rmd | 4 ++-- inst/doc/CorrelplotManual.html | 23 +++++++++-------------- vignettes/Correlplot.bib | 6 ------ vignettes/CorrelplotManual.Rmd | 4 ++-- 6 files changed, 22 insertions(+), 33 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better than a random observation drawn from the other group (Mann-Whitney parameter). The net benefit and win ratio statistics, i.e. the difference and ratio between the probabilities relative to the intervention and control groups, can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test [...truncated...]
Author: Brice Ozenne [aut, cre] ,
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 2.4.0 dated 2023-03-20 and 3.0.2 dated 2024-01-23
BuyseTest-2.4.0/BuyseTest/R/autoplot.sensitivity.R |only BuyseTest-2.4.0/BuyseTest/inst/doc-Wilcoxon |only BuyseTest-2.4.0/BuyseTest/inst/optim-iid |only BuyseTest-2.4.0/BuyseTest/man/S4BuysePower-show.Rd |only BuyseTest-2.4.0/BuyseTest/man/autoplot.sensitivity.Rd |only BuyseTest-2.4.0/BuyseTest/man/boot2pvalue.Rd |only BuyseTest-2.4.0/BuyseTest/man/discreteRoot.Rd |only BuyseTest-2.4.0/BuyseTest/man/dot-information.logit.Rd |only BuyseTest-2.4.0/BuyseTest/man/dot-score.logit.Rd |only BuyseTest-2.4.0/BuyseTest/man/dot-vcov.logit.Rd |only BuyseTest-2.4.0/BuyseTest/man/internal-initialization.Rd |only BuyseTest-2.4.0/BuyseTest/man/internal-print.Rd |only BuyseTest-2.4.0/BuyseTest/man/pnormexp.Rd |only BuyseTest-2.4.0/BuyseTest/man/pnormweibull.Rd |only BuyseTest-2.4.0/BuyseTest/man/predict.logit.Rd |only BuyseTest-2.4.0/BuyseTest/man/qnormexp.Rd |only BuyseTest-2.4.0/BuyseTest/man/qnormweibull.Rd |only BuyseTest-2.4.0/BuyseTest/man/simulation.Rd |only BuyseTest-2.4.0/BuyseTest/man/testArgs.Rd |only BuyseTest-2.4.0/BuyseTest/tests/testthat/test-BuyseTest-performance.R |only BuyseTest-3.0.2/BuyseTest/DESCRIPTION | 50 BuyseTest-3.0.2/BuyseTest/MD5 | 311 - BuyseTest-3.0.2/BuyseTest/NAMESPACE | 180 BuyseTest-3.0.2/BuyseTest/NEWS | 467 + BuyseTest-3.0.2/BuyseTest/R/0-onLoad.R | 22 BuyseTest-3.0.2/BuyseTest/R/1-setGeneric.R | 130 BuyseTest-3.0.2/BuyseTest/R/BuyseMultComp.R | 907 ++- BuyseTest-3.0.2/BuyseTest/R/BuyseTTEM.R | 1318 ++--- BuyseTest-3.0.2/BuyseTest/R/BuyseTest-Peron.R | 688 +- BuyseTest-3.0.2/BuyseTest/R/BuyseTest-check.R | 1120 ++-- BuyseTest-3.0.2/BuyseTest/R/BuyseTest-inference.R | 706 +- BuyseTest-3.0.2/BuyseTest/R/BuyseTest-initialization.R | 1649 +++--- BuyseTest-3.0.2/BuyseTest/R/BuyseTest-package.R | 124 BuyseTest-3.0.2/BuyseTest/R/BuyseTest-print.R | 349 - BuyseTest-3.0.2/BuyseTest/R/BuyseTest.R | 1479 +++--- BuyseTest-3.0.2/BuyseTest/R/BuyseTest.options.R | 219 BuyseTest-3.0.2/BuyseTest/R/CasinoTest.R |only BuyseTest-3.0.2/BuyseTest/R/PairScore.R | 108 BuyseTest-3.0.2/BuyseTest/R/RcppExports.R | 450 - BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower-model.tables.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower-nobs.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower-print.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower-show.R | 82 BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower-summary.R | 392 - BuyseTest-3.0.2/BuyseTest/R/S4-BuysePower.R | 153 BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-coef.R | 632 +- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-confint.R | 1840 ++++--- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-get.R | 1597 +++--- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-model.tables.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-nobs.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-plot.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-print.R |only BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-sensitivity.R | 733 +-- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-show.R | 98 BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest-summary.R | 984 +--- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest.R | 603 +- BuyseTest-3.0.2/BuyseTest/R/S4-BuyseTest.options.R | 462 - BuyseTest-3.0.2/BuyseTest/R/as.data.table.performance.R | 279 - BuyseTest-3.0.2/BuyseTest/R/auc.R | 789 +-- BuyseTest-3.0.2/BuyseTest/R/autoplot.S4BuyseTest.R |only BuyseTest-3.0.2/BuyseTest/R/brier.R | 577 +- BuyseTest-3.0.2/BuyseTest/R/constStrata.R | 177 BuyseTest-3.0.2/BuyseTest/R/discreteRoot.R | 556 +- BuyseTest-3.0.2/BuyseTest/R/iid.S3sensitivity.R |only BuyseTest-3.0.2/BuyseTest/R/iid.prodlim.R | 388 - BuyseTest-3.0.2/BuyseTest/R/normexp.R | 420 - BuyseTest-3.0.2/BuyseTest/R/performance.R | 2420 +++++----- BuyseTest-3.0.2/BuyseTest/R/performanceResample.R | 560 +- BuyseTest-3.0.2/BuyseTest/R/plot.S3sensitivity.R |only BuyseTest-3.0.2/BuyseTest/R/powerBuyseTest.R | 1405 +++-- BuyseTest-3.0.2/BuyseTest/R/predict.logit.R | 565 +- BuyseTest-3.0.2/BuyseTest/R/rbind.performanceResample.R | 226 BuyseTest-3.0.2/BuyseTest/R/simBuyseTest.R | 1354 ++--- BuyseTest-3.0.2/BuyseTest/R/simCompetingRisks.R | 283 - BuyseTest-3.0.2/BuyseTest/R/summary.performance.R | 227 BuyseTest-3.0.2/BuyseTest/R/valid.R | 961 +-- BuyseTest-3.0.2/BuyseTest/build/vignette.rds |binary BuyseTest-3.0.2/BuyseTest/inst/CITATION | 102 BuyseTest-3.0.2/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-3.0.2/BuyseTest/inst/doc/overview.pdf.asis | 8 BuyseTest-3.0.2/BuyseTest/inst/doc/wilcoxonTest.pdf.asis | 8 BuyseTest-3.0.2/BuyseTest/man/BuyseMultComp.Rd | 223 BuyseTest-3.0.2/BuyseTest/man/BuyseTTEM.Rd | 152 BuyseTest-3.0.2/BuyseTest/man/BuyseTest-package.Rd | 101 BuyseTest-3.0.2/BuyseTest/man/BuyseTest.Rd | 622 +- BuyseTest-3.0.2/BuyseTest/man/BuyseTest.options-class.Rd | 34 BuyseTest-3.0.2/BuyseTest/man/BuyseTest.options-methods.Rd | 44 BuyseTest-3.0.2/BuyseTest/man/BuyseTest.options.Rd | 65 BuyseTest-3.0.2/BuyseTest/man/CasinoTest.Rd |only BuyseTest-3.0.2/BuyseTest/man/GPC_cpp.Rd | 370 - BuyseTest-3.0.2/BuyseTest/man/S4BuysePower-class.Rd | 35 BuyseTest-3.0.2/BuyseTest/man/S4BuysePower-model.tables.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuysePower-nobs.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuysePower-print.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuysePower-summary.Rd | 118 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-class.Rd | 35 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-coef.Rd | 131 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-confint.Rd | 254 - BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-getCount.Rd | 57 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-getIid.Rd | 151 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-getPairScore.Rd | 287 - BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-getPseudovalue.Rd | 139 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-getSurvival.Rd | 117 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-model.tables.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-nobs.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-plot.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-print.Rd |only BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-sensitivity.Rd | 184 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-show.Rd | 61 BuyseTest-3.0.2/BuyseTest/man/S4BuyseTest-summary.Rd | 291 - BuyseTest-3.0.2/BuyseTest/man/as.data.table.performance.Rd | 62 BuyseTest-3.0.2/BuyseTest/man/auc.Rd | 165 BuyseTest-3.0.2/BuyseTest/man/autoplot-S4BuyseTest.Rd |only BuyseTest-3.0.2/BuyseTest/man/brier.Rd |only BuyseTest-3.0.2/BuyseTest/man/calcIntegralSurv2_cpp.Rd | 94 BuyseTest-3.0.2/BuyseTest/man/coef.BuyseTestAuc.Rd | 38 BuyseTest-3.0.2/BuyseTest/man/coef.BuyseTestBrier.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/confint.BuyseTestAuc.Rd | 38 BuyseTest-3.0.2/BuyseTest/man/confint.BuyseTestBrier.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/constStrata.Rd | 121 BuyseTest-3.0.2/BuyseTest/man/dot-calcIntegralCif_cpp.Rd | 98 BuyseTest-3.0.2/BuyseTest/man/dot-calcIntegralSurv_cpp.Rd | 84 BuyseTest-3.0.2/BuyseTest/man/dot-colCenter_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/dot-colCumSum_cpp.Rd | 35 BuyseTest-3.0.2/BuyseTest/man/dot-colMultiply_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/dot-colScale_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/dot-rowCenter_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/dot-rowCumProd_cpp.Rd | 35 BuyseTest-3.0.2/BuyseTest/man/dot-rowCumSum_cpp.Rd | 35 BuyseTest-3.0.2/BuyseTest/man/dot-rowMultiply_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/dot-rowScale_cpp.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/iid.BuyseTestAuc.Rd | 38 BuyseTest-3.0.2/BuyseTest/man/iid.BuyseTestBrier.Rd | 39 BuyseTest-3.0.2/BuyseTest/man/iid.prodlim.Rd | 96 BuyseTest-3.0.2/BuyseTest/man/performance.Rd | 207 BuyseTest-3.0.2/BuyseTest/man/performanceResample.Rd | 109 BuyseTest-3.0.2/BuyseTest/man/plot-sensitivity.Rd |only BuyseTest-3.0.2/BuyseTest/man/powerBuyseTest.Rd | 297 - BuyseTest-3.0.2/BuyseTest/man/predict.BuyseTTEM.Rd | 57 BuyseTest-3.0.2/BuyseTest/man/rbind.performance.Rd | 122 BuyseTest-3.0.2/BuyseTest/man/simBuyseTest.Rd |only BuyseTest-3.0.2/BuyseTest/man/simCompetingRisks.Rd | 210 BuyseTest-3.0.2/BuyseTest/man/summary.performance.Rd | 45 BuyseTest-3.0.2/BuyseTest/man/validFCTs.Rd | 314 - BuyseTest-3.0.2/BuyseTest/src/FCT_buyseTest.cpp | 9 BuyseTest-3.0.2/BuyseTest/src/FCT_calcOnePair.h | 4 BuyseTest-3.0.2/BuyseTest/src/FCT_calcStatistic.h | 12 BuyseTest-3.0.2/BuyseTest/src/FCT_precompute.cpp | 2 BuyseTest-3.0.2/BuyseTest/src/RcppExports.cpp | 18 BuyseTest-3.0.2/BuyseTest/src/utils-from-riskRegression.cpp | 9 BuyseTest-3.0.2/BuyseTest/tests/testthat.R | 84 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuysePower.R | 399 - BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTTEM.R | 503 +- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 467 - BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R | 239 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 1197 ++-- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 1154 ++-- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 448 - BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-engine.R | 221 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-iid.R | 1608 +++--- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-multcomp.R | 177 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 205 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 201 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 1209 ++-- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 1199 ++-- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-restricted.R | 186 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-strata.R | 859 +-- BuyseTest-3.0.2/BuyseTest/tests/testthat/test-BuyseTest-weightObs.R | 130 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-auc.R | 268 - BuyseTest-3.0.2/BuyseTest/tests/testthat/test-initSurvival.R | 438 - BuyseTest-3.0.2/BuyseTest/tests/testthat/test-initThreshold.R | 168 BuyseTest-3.0.2/BuyseTest/tests/testthat/test-otherPackages.R | 345 - BuyseTest-3.0.2/BuyseTest/vignettes/overview.pdf.asis | 8 BuyseTest-3.0.2/BuyseTest/vignettes/vignette_CR.Rmd | 146 BuyseTest-3.0.2/BuyseTest/vignettes/wilcoxonTest.pdf.asis | 8 175 files changed, 23982 insertions(+), 23219 deletions(-)
Title: A 'Bootstrap 4' Version of 'shinydashboard'
Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power
of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
<https://github.com/ColorlibHQ/AdminLTE>.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between bs4Dash versions 2.3.0 dated 2023-06-15 and 2.3.3 dated 2024-01-23
bs4Dash-2.3.0/bs4Dash/inst/bs4Dash-2.3.0 |only bs4Dash-2.3.0/bs4Dash/inst/examples/showcase/rsconnect |only bs4Dash-2.3.3/bs4Dash/DESCRIPTION | 8 bs4Dash-2.3.3/bs4Dash/MD5 | 54 - bs4Dash-2.3.3/bs4Dash/NEWS.md | 40 bs4Dash-2.3.3/bs4Dash/R/dashboardControlbar.R | 7 bs4Dash-2.3.3/bs4Dash/R/dashboardSidebar.R | 17 bs4Dash-2.3.3/bs4Dash/R/useful-items.R | 2 bs4Dash-2.3.3/bs4Dash/R/utils.R | 6 bs4Dash-2.3.3/bs4Dash/build/bs4Dash.pdf |binary bs4Dash-2.3.3/bs4Dash/build/stage23.rdb |only bs4Dash-2.3.3/bs4Dash/build/vignette.rds |binary bs4Dash-2.3.3/bs4Dash/inst/bs4Dash-2.3.3 |only bs4Dash-2.3.3/bs4Dash/inst/doc/bs4Dash.R | 4 bs4Dash-2.3.3/bs4Dash/inst/doc/bs4Dash.html | 172 +-- bs4Dash-2.3.3/bs4Dash/inst/doc/css-preloader.R | 2 bs4Dash-2.3.3/bs4Dash/inst/doc/css-preloader.html | 166 +-- bs4Dash-2.3.3/bs4Dash/inst/doc/extra-elements.R | 4 bs4Dash-2.3.3/bs4Dash/inst/doc/extra-elements.html | 451 ++++----- bs4Dash-2.3.3/bs4Dash/inst/doc/improved-boxes.R | 12 bs4Dash-2.3.3/bs4Dash/inst/doc/improved-boxes.html | 722 +++++++-------- bs4Dash-2.3.3/bs4Dash/inst/doc/more-skins.R | 4 bs4Dash-2.3.3/bs4Dash/inst/doc/more-skins.html | 347 +++---- bs4Dash-2.3.3/bs4Dash/inst/doc/step-by-step.html | 807 ++++++++--------- bs4Dash-2.3.3/bs4Dash/man/dashboardControlbar.Rd | 7 bs4Dash-2.3.3/bs4Dash/man/dashboardSidebar.Rd | 7 bs4Dash-2.3.3/bs4Dash/man/table.Rd | 3 27 files changed, 1404 insertions(+), 1438 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.21 dated 2023-07-02 and 0.0.22 dated 2024-01-23
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/UsingAnnoyInCppWrapper.pdf |binary inst/include/RcppAnnoy.h | 2 +- man/RcppAnnoy-package.Rd | 3 --- 8 files changed, 26 insertions(+), 15 deletions(-)
Title: Mast Inference and Forecasting
Description: Analyzes production and dispersal of seeds dispersed from trees and recovered in seed traps. Motivated by long-term inventory plots where seed collections are used to infer seed production by each individual plant.
Author: James S. Clark
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between mastif versions 2.0 dated 2023-01-27 and 2.1 dated 2024-01-23
DESCRIPTION | 12 MD5 | 34 NAMESPACE | 8 R/RcppExports.R | 4 R/mastifFunctions.R | 5017 ++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/CITATION | 13 inst/doc/mastifVignette.R | 172 + inst/doc/mastifVignette.Rmd | 163 + inst/doc/mastifVignette.html | 853 ++++--- man/mastVolatility.Rd | 2 man/mastif-package.Rd | 4 man/mastif.Rd | 5 src/Makevars | 11 src/Makevars.win | 11 src/RcppExports.cpp | 16 src/cppFns.cpp | 17 vignettes/mastifVignette.Rmd | 163 + 18 files changed, 4268 insertions(+), 2237 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Elena Hsieh [ctb] ,
Debashis Ghosh [ctb] ,
Lance A. Waller [ctb] ,
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between gateR versions 0.1.13 dated 2023-02-01 and 0.1.15 dated 2024-01-23
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS.md | 105 +++++++++++++++++++++++--------------------- R/lrr_plot.R | 2 R/package.R | 2 R/pval_correct.R | 120 ++++++++++++++++++++++----------------------------- R/randCyto.R | 2 R/utils.R | 12 +++++ README.md | 17 +++++-- inst/CITATION | 8 +-- man/gateR-package.Rd | 2 man/lrr_plot.Rd | 4 - man/pval_correct.Rd | 2 man/randCyto.Rd | 2 14 files changed, 165 insertions(+), 147 deletions(-)
Title: Environmental Interpolation using Spatial Kernel Density
Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel
density-based estimation methods. For a single species with presence and absence data,
the 'envi' package uses the spatial relative risk function that is estimated using the
'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
relative risk functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Lance A. Waller [ctb, ths] ,
Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between envi versions 0.1.17 dated 2023-02-01 and 0.1.19 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/div_plot.R | 2 +- R/pval_correct.R | 24 ++++++------------------ R/seq_plot.R | 2 +- R/utils.R | 12 ++++++++++++ README.md | 6 +++--- inst/CITATION | 8 ++++---- man/div_plot.Rd | 4 ++-- man/seq_plot.Rd | 4 ++-- tests/testthat/test-plot_perturb.R | 3 ++- 12 files changed, 56 insertions(+), 47 deletions(-)
Title: Quantile-Based Estimator
Description: Quantile-based estimators (Q-estimators) can be used to fit any parametric distribution, using its quantile function. Q-estimators are usually more robust than standard maximum likelihood estimators. The method is described in: Sottile G. and Frumento P. (2022). Robust estimation and regression with parametric quantile functions. <doi:10.1016/j.csda.2022.107471>.
Author: Gianluca Sottile [aut, cre],
Paolo Frumento [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between Qest versions 1.0.0 dated 2022-04-05 and 1.0.1 dated 2024-01-23
DESCRIPTION | 6 +- MD5 | 14 +++--- NAMESPACE | 1 R/Qest_S3methods.R | 2 R/auxiliary.R | 2 build/partial.rdb |binary man/Qest-internal.rd | 108 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/Qest-package.Rd | 4 - 8 files changed, 118 insertions(+), 19 deletions(-)
Title: Streamline Building Panel Data from Panel Study of Income
Dynamics ('PSID') Raw Files
Description: Streamline the management, creation, and formatting of panel data from the Panel Study of Income Dynamics ('PSID') <https://psidonline.isr.umich.edu> using this user-friendly tool. Simply define variable names and input code book details directly from the 'PSID' official website, and this toolbox will efficiently facilitate the data preparation process, transforming raw 'PSID' files into a well-organized format ready for further analysis.
Author: Shuyi Qiu [aut, cre]
Maintainer: Shuyi Qiu <shuyi.qiu@duke.edu>
Diff between psidread versions 1.0.1 dated 2024-01-21 and 1.0.2 dated 2024-01-23
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NEWS.md | 2 + R/psid_reshape.R | 6 ----- inst/doc/my-vignette.R | 40 ++++++++++++++++++------------------- inst/doc/my-vignette.Rmd | 30 ++++++++++++++------------- inst/doc/my-vignette.html | 30 +++++++++++---------------- man/psid_reshape.Rd | 6 ----- tests/testthat/test-psid_reshape.R | 12 ----------- vignettes/my-vignette.Rmd | 30 ++++++++++++++------------- 10 files changed, 79 insertions(+), 101 deletions(-)
Title: Co-Clustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The 'blockcluster' package provides a bridge between the C++
core library build on top of the 'STK++' library, and the R statistical
computing environment. This package allows to co-cluster binary
<doi:10.1016/j.csda.2007.09.007>, contingency <doi:10.1080/03610920903140197>,
continuous <doi:10.1007/s11634-013-0161-3> and categorical data-sets
<doi:10.1007/s11222-014-9472-2>. It also provides utility functions to
visualize the results. This package may be useful for various applications
in fields of Data mining, Information retrieval, Biology, computer vision
and many more. More information about the project and comprehensive tutorial
can be found on the link me [...truncated...]
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Josselin Demont [ctb],
Vincent Brault [ctb],
Vincent Kubicki [ctb],
Gerard Goavert [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 4.5.3 dated 2023-02-17 and 4.5.4 dated 2024-01-23
blockcluster-4.5.3/blockcluster/src/Makevars.win |only blockcluster-4.5.3/blockcluster/src/coclust/get_symbolic_link.sh |only blockcluster-4.5.3/blockcluster/src/coclust/get_symbolic_link.sh.old |only blockcluster-4.5.3/blockcluster/src/init_blockcluster.c |only blockcluster-4.5.4/blockcluster/DESCRIPTION | 8 +- blockcluster-4.5.4/blockcluster/MD5 | 31 ++++------ blockcluster-4.5.4/blockcluster/build/vignette.rds |binary blockcluster-4.5.4/blockcluster/cleanup | 1 blockcluster-4.5.4/blockcluster/data/binarydata.rda |binary blockcluster-4.5.4/blockcluster/data/categoricaldata.rda |binary blockcluster-4.5.4/blockcluster/data/contingencydatalist.rda |binary blockcluster-4.5.4/blockcluster/data/contingencydataunknown.rda |binary blockcluster-4.5.4/blockcluster/data/gaussiandata.rda |binary blockcluster-4.5.4/blockcluster/inst/NEWS.Rd | 6 + blockcluster-4.5.4/blockcluster/inst/doc/blockcluster_tutorial.pdf |binary blockcluster-4.5.4/blockcluster/src/Makevars | 11 ++- blockcluster-4.5.4/blockcluster/src/Rcoclustmain.h | 12 +++ blockcluster-4.5.4/blockcluster/src/coclust/makefile | 4 - blockcluster-4.5.4/blockcluster/src/init_blockcluster.cpp |only 19 files changed, 46 insertions(+), 27 deletions(-)
Title: Measuring Concreteness in Natural Language
Description: Models for detecting concreteness in natural language. This package is built in support of Yeomans (2021) <doi:10.1016/j.obhdp.2020.10.008>, which reviews linguistic models of concreteness in several domains. Here, we provide an implementation of the best-performing domain-general model (from Brysbaert et al., (2014) <doi:10.3758/s13428-013-0403-5>) as well as two pre-trained models for the feedback and plan-making domains.
Author: Mike Yeomans
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between doc2concrete versions 0.5.6 dated 2022-06-28 and 0.6.0 dated 2024-01-23
doc2concrete-0.5.6/doc2concrete/data/finanace_list.rda |only doc2concrete-0.5.6/doc2concrete/man/finance_list.Rd |only doc2concrete-0.6.0/doc2concrete/DESCRIPTION | 8 doc2concrete-0.6.0/doc2concrete/MD5 | 24 - doc2concrete-0.6.0/doc2concrete/R/concDict.R | 2 doc2concrete-0.6.0/doc2concrete/R/data.R | 13 - doc2concrete-0.6.0/doc2concrete/R/doc2concrete.R | 12 doc2concrete-0.6.0/doc2concrete/R/ngramTokens.R | 7 doc2concrete-0.6.0/doc2concrete/build/vignette.rds |binary doc2concrete-0.6.0/doc2concrete/inst/doc/doc2concrete.R | 2 doc2concrete-0.6.0/doc2concrete/inst/doc/doc2concrete.html | 162 ++++++------- doc2concrete-0.6.0/doc2concrete/man/concDict.Rd | 4 doc2concrete-0.6.0/doc2concrete/man/doc2concrete.Rd | 2 doc2concrete-0.6.0/doc2concrete/man/ngramTokens.Rd | 3 14 files changed, 115 insertions(+), 124 deletions(-)
Title: A Rainclouds Geom for 'ggplot2'
Description: The 'geom_rain()' function adds different geoms together using 'ggplot2' to create raincloud plots.
Author: Nicholas Judd [aut, cre] ,
Jordy van Langen [aut] ,
Micah Allen [ctb] ,
Rogier Kievit [aut]
Maintainer: Nicholas Judd <nickkjudd@gmail.com>
Diff between ggrain versions 0.0.3 dated 2023-03-03 and 0.0.4 dated 2024-01-23
DESCRIPTION | 10 - MD5 | 22 +- NEWS.md | 8 + R/geom_paired_raincloud.R | 2 R/geom_rain.R | 8 - README.md | 10 - build/vignette.rds |binary inst/doc/ggrain.R | 9 - inst/doc/ggrain.Rmd | 7 inst/doc/ggrain.html | 324 ++++++++++++++++++++++--------------------- man/geom_paired_raincloud.Rd | 2 vignettes/ggrain.Rmd | 7 12 files changed, 216 insertions(+), 193 deletions(-)
Title: Data Analysis Using Rough Set and Fuzzy Rough Set Theories
Description: Implementations of algorithms for data analysis based on the
rough set theory (RST) and the fuzzy rough set theory (FRST). We not only
provide implementations for the basic concepts of RST and FRST but also
popular algorithms that derive from those theories. The methods included in the
package can be divided into several categories based on their functionality:
discretization, feature selection, instance selection, rule induction and
classification based on nearest neighbors. RST was introduced by Zdzisław
Pawlak in 1982 as a sophisticated mathematical tool to model and process
imprecise or incomplete information. By using the indiscernibility relation for
objects/instances, RST does not require additional parameters to analyze the
data. FRST is an extension of RST. The FRST combines concepts of vagueness and
indiscernibility that are expressed with fuzzy sets (as proposed by Zadeh, in
1965) and RST.
Author: Andrzej Janusz [aut],
Lala Septem Riza [aut],
Dominik Ślezak [ctb],
Chris Cornelis [ctb],
Francisco Herrera [ctb],
Jose Manuel Benitez [ctb],
Christoph Bergmeir [ctb, cre],
Sebastian Stawicki [ctb]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RoughSets versions 1.3-7 dated 2019-12-15 and 1.3-8 dated 2024-01-23
RoughSets-1.3-7/RoughSets/R/FuzzyRoughSets-introduction.R |only RoughSets-1.3-7/RoughSets/R/RoughSets-introduction.R |only RoughSets-1.3-7/RoughSets/man/A.Introduction-RoughSets.Rd |only RoughSets-1.3-7/RoughSets/man/B.Introduction-FuzzyRoughSets.Rd |only RoughSets-1.3-8/RoughSets/DESCRIPTION | 10 RoughSets-1.3-8/RoughSets/MD5 | 78 +-- RoughSets-1.3-8/RoughSets/R/BasicFuzzyRoughSets.R | 18 RoughSets-1.3-8/RoughSets/R/BasicRoughSets.OtherFuncCollections.R | 2 RoughSets-1.3-8/RoughSets/R/BasicRoughSets.R | 12 RoughSets-1.3-8/RoughSets/R/FeatureSelection.R | 11 RoughSets-1.3-8/RoughSets/R/InstanceSelection.R | 4 RoughSets-1.3-8/RoughSets/R/RoughSets-package.R | 228 ++++++++- RoughSets-1.3-8/RoughSets/R/docData.R | 14 RoughSets-1.3-8/RoughSets/man/BC.IND.relation.FRST.Rd | 67 +- RoughSets-1.3-8/RoughSets/man/BC.IND.relation.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/BC.LU.approximation.FRST.Rd | 99 ++-- RoughSets-1.3-8/RoughSets/man/BC.LU.approximation.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/BC.boundary.reg.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/BC.discernibility.mat.FRST.Rd | 59 +- RoughSets-1.3-8/RoughSets/man/BC.discernibility.mat.RST.Rd | 10 RoughSets-1.3-8/RoughSets/man/BC.negative.reg.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/BC.positive.reg.FRST.Rd | 2 RoughSets-1.3-8/RoughSets/man/BC.positive.reg.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/C.FRNN.FRST.Rd | 18 RoughSets-1.3-8/RoughSets/man/C.FRNN.O.FRST.Rd | 2 RoughSets-1.3-8/RoughSets/man/D.discretization.RST.Rd | 7 RoughSets-1.3-8/RoughSets/man/D.global.discernibility.heuristic.RST.Rd | 11 RoughSets-1.3-8/RoughSets/man/D.local.discernibility.heuristic.RST.Rd | 8 RoughSets-1.3-8/RoughSets/man/FS.DAAR.heuristic.RST.Rd | 16 RoughSets-1.3-8/RoughSets/man/FS.feature.subset.computation.Rd | 7 RoughSets-1.3-8/RoughSets/man/FS.greedy.heuristic.reduct.RST.Rd | 13 RoughSets-1.3-8/RoughSets/man/FS.greedy.heuristic.superreduct.RST.Rd | 8 RoughSets-1.3-8/RoughSets/man/FS.one.reduct.computation.Rd | 3 RoughSets-1.3-8/RoughSets/man/FS.permutation.heuristic.reduct.RST.Rd | 7 RoughSets-1.3-8/RoughSets/man/FS.quickreduct.FRST.Rd | 14 RoughSets-1.3-8/RoughSets/man/FS.quickreduct.RST.Rd | 2 RoughSets-1.3-8/RoughSets/man/IS.FRIS.FRST.Rd | 4 RoughSets-1.3-8/RoughSets/man/RoughSetData.Rd | 12 RoughSets-1.3-8/RoughSets/man/RoughSets-package.Rd | 244 +++++++++- RoughSets-1.3-8/RoughSets/man/SF.asFeatureSubset.Rd | 10 RoughSets-1.3-8/RoughSets/man/SF.read.DecisionTable.Rd | 3 RoughSets-1.3-8/RoughSets/src/RcppExports.cpp | 5 42 files changed, 744 insertions(+), 274 deletions(-)
Title: Fragmentation and Connectivity Indices for Riverscapes
Description: Indices for assessing riverscape fragmentation, including the Dendritic Connectivity Index, the Population Connectivity Index, the River Fragmentation Index, the Probability of Connectivity, and the Integral Index of connectivity. For a review, see Jumani et al. (2020) <doi:10.1088/1748-9326/abcb37> and Baldan et al. (2022) <doi:10.1016/j.envsoft.2022.105470> Functions to calculate temporal indices improvement when fragmentation due to barriers is reduced are also included.
Author: Damiano Baldan [aut, cre] ,
David Cunillera-Montcusi [ctb]
,
Andrea Funk [ctb]
Maintainer: Damiano Baldan <damiano.baldan91@gmail.com>
Diff between riverconn versions 0.3.28 dated 2023-05-05 and 0.3.31 dated 2024-01-23
DESCRIPTION | 10 MD5 | 52 +-- NAMESPACE | 68 +-- R/B_ij_fun.R | 2 R/d_index_calculation.R | 7 R/index_calculation.R | 6 R/inner_d_index_calculation.R | 6 R/inner_t_index_calculation.R | 1 README.md | 9 build/vignette.rds |binary inst/doc/Tutorial.R | 55 --- inst/doc/Tutorial.Rmd | 65 --- inst/doc/Tutorial.html | 673 ++++++++++++++++----------------------- man/B_ij_fun.Rd | 152 ++++---- man/c_ij_fun.Rd | 106 +++--- man/d_index_calculation.Rd | 176 +++++----- man/index_calculation.Rd | 264 +++++++-------- man/inner_d_index_calculation.Rd | 230 ++++++------- man/inner_t_index_calculation.Rd | 186 +++++----- man/pipe.Rd | 40 +- man/set_B_directionality.Rd | 54 +-- man/set_c_directionality.Rd | 66 +-- man/set_graph_directionality.Rd | 56 +-- man/t_index_calculation.Rd | 164 ++++----- man/t_passability_sequencer.Rd | 74 ++-- man/t_weights_sequencer.Rd | 64 +-- vignettes/Tutorial.Rmd | 65 --- 27 files changed, 1180 insertions(+), 1471 deletions(-)
Title: Model Multivariate Ordinal Responses Including Response Styles
Description: In the case of multivariate ordinal responses, parameter estimates can be severely biased if personal response styles are ignored. This packages provides methods to account for personal response styles and to explain the effects of covariates on the response style, as proposed by Schauberger and Tutz 2021 <doi:10.1177/1471082X20978034>. The method is implemented both for the multivariate cumulative model and the multivariate adjacent categories model.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between MultOrdRS versions 0.1-2 dated 2021-03-29 and 0.1-3 dated 2024-01-23
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ R/MultOrdRS-package.R | 6 +++--- R/MultOrdRS.R | 4 ++-- R/plot.multordRS.R | 37 +++++++++++++++++++++++++++++-------- R/print.multordRS.R | 6 +++--- build/partial.rdb |binary man/GLES17.Rd | 4 ++-- man/MultOrdRS-package.Rd | 2 +- man/ctrl.multordRS.Rd | 2 +- man/multordRS.Rd | 2 +- man/plot.MultOrdRS.Rd | 14 ++++++++++++-- src/RcppExports.cpp | 5 +++++ 13 files changed, 77 insertions(+), 41 deletions(-)
Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects.
Multiple breakpoints for the same variable are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.0-1 dated 2023-12-19 and 2.0-2 dated 2024-01-23
DESCRIPTION | 8 MD5 | 70 +-- NAMESPACE | 154 ++++---- NEWS | 11 R/model.matrix.stepmented.r |only R/plot.segmented.R | 14 R/plot.stepmented.r | 782 ++++++++++++++++++++--------------------- R/predict.segmented.r | 105 +++-- R/seg.Ar.fit.r | 4 R/seg.def.fit.r | 4 R/seg.glm.fit.boot.r | 8 R/seg.glm.fit.r | 21 - R/seg.lm.fit.boot.r | 15 R/seg.lm.fit.r | 22 - R/seg.num.fit.r | 39 +- R/seg.r | 2 R/segConstr.glm.fit.boot.r | 7 R/segConstr.glm.fit.r | 42 +- R/segConstr.lm.fit.boot.r | 6 R/segConstr.lm.fit.r | 55 +- R/segmented.lm.R | 3 R/segmented.numeric.R | 16 R/segreg.r | 195 +++++----- R/selgmented.R | 3 R/step.lm.fit.boot.r | 2 R/step.lm.fit.r | 20 - R/step.num.fit.r | 411 ++++++++++----------- R/stepmented.lm.R | 2 R/stepmented.numeric.r | 79 +++- R/vcov.stepmented.R | 2 man/model.matrix.stepmented.Rd |only man/plot.stepmented.Rd | 2 man/seg.Rd | 19 man/segmented-package.Rd | 4 man/segmented.Rd | 7 man/stepmented.Rd | 14 man/vcov.stepmented.Rd | 136 +++---- 37 files changed, 1261 insertions(+), 1023 deletions(-)
Title: Nonlinear and Penalized Quantile Regression Coefficients
Modeling
Description: Nonlinear and Penalized parametric modeling of quantile regression coefficient functions. Sottile G, Frumento P, Chiodi M and Bottai M (2020) <doi:10.1177/1471082X19825523>.
Author: Gianluca Sottile [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between qrcmNP versions 0.2.0 dated 2021-02-21 and 0.2.1 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/qrcmNL.R | 2 +- R/qrcmPen.R | 4 ++-- inst/CITATION | 31 ++++++++++++++----------------- man/piqr.Rd | 2 +- man/qrcmNP-internal.Rd | 44 ++++++++++++++++++++++++++++++++++++++++++-- man/qrcmNP-package.Rd | 4 ++-- 8 files changed, 72 insertions(+), 35 deletions(-)
Title: Incomplete Block Designs
Description: A collection of several utility functions related to binary incomplete block designs. Contains function to generate A- and D-efficient binary incomplete block designs with given numbers of treatments, number of blocks and block size. Contains function to generate an incomplete block design with specified concurrence matrix. There are functions to generate balanced treatment incomplete block designs and incomplete block designs for test versus control treatments comparisons with specified concurrence matrix. Allows performing analysis of variance of data and computing estimated marginal means of factors from experiments using a connected incomplete block design. Tests of hypothesis of treatment contrasts in incomplete block design set up is supported.
Author: B N Mandal [aut, cre]
Maintainer: B N Mandal <mandal.stat@gmail.com>
Diff between ibd versions 1.5 dated 2019-04-24 and 1.6 dated 2024-01-23
DESCRIPTION | 10 +++--- MD5 | 69 ++++++++++++++++++++++----------------------- NAMESPACE | 2 - R/ibd.R | 20 ++++++++++--- man/A_eff.NNP.Rd | 4 +- man/A_eff.Rd | 6 +-- man/Cmatrix.Rd | 10 +++--- man/D_eff.Rd | 9 ++--- man/LIP.Rd | 6 +-- man/NLIP.Rd | 8 ++--- man/N_to_Design.Rd | 15 +++++---- man/aov.ibd.Rd | 6 +-- man/bibd.Rd | 17 ++++++----- man/btib.Rd | 8 ++--- man/btib1.Rd | 6 +-- man/btibgen.Rd | 6 +-- man/ccmat.Rd | 12 +++---- man/ccmat_LP.Rd | 12 +++---- man/check.orthogonality.Rd | 8 ++--- man/check.validity.NNP.Rd | 8 ++--- man/design_to_N.Rd | 16 ++++++---- man/do.exist.NBIB.Rd | 6 +-- man/g.Rd | 12 +++---- man/gts.Rd | 12 +++---- man/ibd.Rd | 21 +++++-------- man/ibddata.Rd | 2 - man/ibdgen.Rd | 6 +-- man/ibdtvc.Rd | 12 +++---- man/interchange.NNP.Rd | 6 +-- man/is.connected.Rd | 8 ++--- man/is.equir.Rd | 10 +++--- man/is.orthogonal.Rd | 6 +-- man/is.proper.Rd | 6 +-- man/is.vb.Rd | 6 +-- man/is.wholenumber.Rd | 10 +++--- man/randomize.Rd |only 36 files changed, 201 insertions(+), 180 deletions(-)
Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting
use in other R packages. Uses 'rappdirs' for cross-platform paths.
Provides utilities to manage cache directories, including targeting
files by path or by key; cached directories can be compressed and
uncompressed easily to save disk space.
Author: Scott Chamberlain [aut] ,
Tamas Stirling [ctb, cre]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between hoardr versions 0.5.3 dated 2023-01-26 and 0.5.4 dated 2024-01-23
hoardr-0.5.3/hoardr/tests/test-all.R |only hoardr-0.5.4/hoardr/DESCRIPTION | 7 - hoardr-0.5.4/hoardr/MD5 | 18 ++-- hoardr-0.5.4/hoardr/NEWS.md | 8 + hoardr-0.5.4/hoardr/README.md | 12 -- hoardr-0.5.4/hoardr/build/vignette.rds |binary hoardr-0.5.4/hoardr/inst/doc/hoardr_vignette.html | 26 ++---- hoardr-0.5.4/hoardr/tests/testthat.R |only hoardr-0.5.4/hoardr/tests/testthat/test-HoardClient.R | 74 ++++++++---------- hoardr-0.5.4/hoardr/tests/testthat/test-hoard.R | 33 +++----- hoardr-0.5.4/hoardr/tests/testthat/test-utils.R | 8 - 11 files changed, 88 insertions(+), 98 deletions(-)
Title: Factor-Adjusted Network Estimation and Forecasting for
High-Dimensional Time Series
Description: Implements methods for network estimation and forecasting of high-dimensional time series
exhibiting strong serial and cross-sectional correlations under a factor-adjusted vector autoregressive model.
See Barigozzi, Cho and Owens (2024+) <doi:10.1080/07350015.2023.2257270> for further descriptions of FNETS methodology and
Owens, Cho and Barigozzi (2024+) <arXiv:2301.11675> accompanying the R package.
Author: Matteo Barigozzi [aut],
Haeran Cho [cre, aut],
Dom Owens [aut]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>
Diff between fnets versions 0.1.5 dated 2023-07-17 and 0.1.6 dated 2024-01-23
DESCRIPTION | 12 ++++----- MD5 | 56 +++++++++++++++++++++++----------------------- R/common.R | 6 ++-- R/factor.R | 14 +++++------ R/factor_number.R | 5 +--- R/fnets.R | 41 +++++++++++++-------------------- R/idio.R | 36 ++++++++++------------------- R/omega.R | 8 +++--- R/sim.R | 14 +++++------ man/common.predict.Rd | 6 ++-- man/dyn.pca.Rd | 2 - man/factor.number.Rd | 4 +-- man/fnets.Rd | 32 +++++++++++--------------- man/fnets.factor.model.Rd | 10 ++++---- man/fnets.var.Rd | 21 +++++++---------- man/fnets.var.internal.Rd | 4 +-- man/hl.factor.number.Rd | 2 - man/network.fnets.Rd | 5 ---- man/par.lrpc.Rd | 8 +++--- man/plot.fnets.Rd | 9 ++----- man/plot.threshold.Rd | 6 +--- man/predict.fm.Rd | 2 - man/predict.fnets.Rd | 2 - man/print.threshold.Rd | 5 ---- man/sim.restricted.Rd | 4 +-- man/sim.unrestricted.Rd | 6 ++-- man/sim.var.Rd | 4 +-- man/threshold.Rd | 8 +----- man/tuning_plot.Rd | 5 +++- 29 files changed, 148 insertions(+), 189 deletions(-)
Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure
to analyse temporal trend in the framework of the OSPAR convention.
The analysis process run through 4 successive steps : 1) manipulate your data, 2)
select the parameters you want to analyse, 3) build your regulated
time series, 4) perform diagnosis and analysis and 5) read the results.
Statistical analysis call other package function such as Kendall tests
or cusum() function.
Author: David DEVREKER [aut, cre],
Alain LEFEBVRE [aut]
Maintainer: David DEVREKER <David.Devreker@ifremer.fr>
Diff between TTAinterfaceTrendAnalysis versions 1.5.9 dated 2023-03-24 and 1.5.10 dated 2024-01-23
TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/DESCRIPTION | 13 ++-- TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/MD5 | 29 +++------- TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/NAMESPACE | 9 --- TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/NEWS | 4 + TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/R/FULLoption.r | 8 ++ TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/R/TTAinterface.R | 2 TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/build/vignette.rds |binary TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/inst/aide/UserGuide.pdf |only TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/inst/doc/TTAVignette.pdf |binary TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/man/FULLoption.Rd | 2 TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/man/TTAinterface-package.Rd | 6 +- TTAinterfaceTrendAnalysis-1.5.10/TTAinterfaceTrendAnalysis/man/fixdata.Rd | 2 TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/R/interpTs.R |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/R/mannKen.R |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/R/seaKen.R |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/R/seasonTrend.R |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/man/interpTs.Rd |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/man/mannKen.Rd |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/man/seaKen.Rd |only TTAinterfaceTrendAnalysis-1.5.9/TTAinterfaceTrendAnalysis/man/seasonTrend.Rd |only 20 files changed, 37 insertions(+), 38 deletions(-)
More information about TTAinterfaceTrendAnalysis at CRAN
Permanent link
Title: Personalizes and Randomizes Exams Written in 'LaTeX'
Description: Randomizing exams with 'LaTeX'.
If you can compile your main document with 'LaTeX', the program should be able to compile the randomized
versions without much extra effort when creating the document.
Author: Alejandro Gonzalez Recuenco
Maintainer: Alejandro Gonzalez Recuenco <alejandrogonzalezrecuenco@gmail.com>
Diff between TexExamRandomizer versions 1.2.3 dated 2018-02-12 and 1.2.7 dated 2024-01-23
TexExamRandomizer-1.2.3/TexExamRandomizer/R/TexExamRandomizer-internal.R |only TexExamRandomizer-1.2.7/TexExamRandomizer/DESCRIPTION | 16 TexExamRandomizer-1.2.7/TexExamRandomizer/LICENSE | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/MD5 | 147 - TexExamRandomizer-1.2.7/TexExamRandomizer/NAMESPACE | 1 TexExamRandomizer-1.2.7/TexExamRandomizer/R/AnswerSheets.R | 3 TexExamRandomizer-1.2.7/TexExamRandomizer/R/DataDocumentation.R | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/R/Grading.R | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/R/PreambleAdjustment.R | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/R/RandomizingTree.R | 6 TexExamRandomizer-1.2.7/TexExamRandomizer/R/TexExamRandomizer.R | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/R/Wrappers.R | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/R/additionalFunctions.R | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/R/jsonparser.R | 206 +- TexExamRandomizer-1.2.7/TexExamRandomizer/R/latexmkCompilation.R | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/R/package-init.R | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/R/structuringdocument.R | 13 TexExamRandomizer-1.2.7/TexExamRandomizer/README.md | 120 + TexExamRandomizer-1.2.7/TexExamRandomizer/build/vignette.rds |binary TexExamRandomizer-1.2.7/TexExamRandomizer/exec/examrandomizer | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/examrandomizer.R | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/examrandomizer.engine | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/gradeexamrandomizer | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/gradeexamrandomizer.R | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/hwrandomizer.engine | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/exec/profiling_script.R |only TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/BasicUse.R | 9 TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/BasicUse.Rmd | 123 - TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/BasicUse.html | 771 +++++-- TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/ExamOptions.R | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/ExamOptions.Rmd | 165 - TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/ExamOptions.html | 970 ++++++---- TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/GradingExams.R | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/GradingExams.Rmd | 6 TexExamRandomizer-1.2.7/TexExamRandomizer/inst/doc/GradingExams.html | 776 +++++--- TexExamRandomizer-1.2.7/TexExamRandomizer/inst/extdata/ExampleTexDocuments/exam_testing_notrandomizing.tex | 2 TexExamRandomizer-1.2.7/TexExamRandomizer/man/CompileDocument.Rd | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/man/CompileLatexDir.Rd | 40 TexExamRandomizer-1.2.7/TexExamRandomizer/man/ConstructAnswerSheet.Rd | 8 TexExamRandomizer-1.2.7/TexExamRandomizer/man/CountNumberOfSections.Rd | 8 TexExamRandomizer-1.2.7/TexExamRandomizer/man/CreateRandomExams.Rd | 24 TexExamRandomizer-1.2.7/TexExamRandomizer/man/DivideFile.Rd | 16 TexExamRandomizer-1.2.7/TexExamRandomizer/man/FindExamAnswers.Rd | 11 TexExamRandomizer-1.2.7/TexExamRandomizer/man/FindMatchingRow.Rd | 1 TexExamRandomizer-1.2.7/TexExamRandomizer/man/FindStructure.Rd | 11 TexExamRandomizer-1.2.7/TexExamRandomizer/man/GenerateHomework.Rd | 10 TexExamRandomizer-1.2.7/TexExamRandomizer/man/GenerateShortAnswerSheet.Rd | 15 TexExamRandomizer-1.2.7/TexExamRandomizer/man/GetLayerSampleIndexes.Rd | 16 TexExamRandomizer-1.2.7/TexExamRandomizer/man/GradeExams.Rd | 14 TexExamRandomizer-1.2.7/TexExamRandomizer/man/IsWellSectioned.Rd | 9 TexExamRandomizer-1.2.7/TexExamRandomizer/man/ObtainExamStats.Rd | 11 TexExamRandomizer-1.2.7/TexExamRandomizer/man/ParsePreambleForOptions.Rd | 7 TexExamRandomizer-1.2.7/TexExamRandomizer/man/RandomizeDocument.Rd | 6 TexExamRandomizer-1.2.7/TexExamRandomizer/man/ReplaceFromTable.Rd | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/man/ReplacePreambleCommand.Rd | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/man/StructureDocument.Rd | 9 TexExamRandomizer-1.2.7/TexExamRandomizer/man/TexExamRandomizer-package.Rd | 3 TexExamRandomizer-1.2.7/TexExamRandomizer/man/WhichAnswerOriginal.Rd | 19 TexExamRandomizer-1.2.7/TexExamRandomizer/man/compilation_options.Rd |only TexExamRandomizer-1.2.7/TexExamRandomizer/man/compile_latex_directory.Rd |only TexExamRandomizer-1.2.7/TexExamRandomizer/man/jsonexamparser.Rd | 9 TexExamRandomizer-1.2.7/TexExamRandomizer/man/jsonhwparser.Rd | 7 TexExamRandomizer-1.2.7/TexExamRandomizer/man/testclass.Rd | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/man/testdoc.Rd | 4 TexExamRandomizer-1.2.7/TexExamRandomizer/src/DocumentParser.cpp | 148 - TexExamRandomizer-1.2.7/TexExamRandomizer/src/RcppExports.cpp | 5 TexExamRandomizer-1.2.7/TexExamRandomizer/tests |only TexExamRandomizer-1.2.7/TexExamRandomizer/vignettes/BasicUse.Rmd | 123 - TexExamRandomizer-1.2.7/TexExamRandomizer/vignettes/ExamOptions.Rmd | 165 - TexExamRandomizer-1.2.7/TexExamRandomizer/vignettes/GradingExams.Rmd | 6 70 files changed, 2661 insertions(+), 1482 deletions(-)
More information about TexExamRandomizer at CRAN
Permanent link
Title: Differential Item Functioning in Generalized Partial Credit
Models
Description: Provides a framework to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM as proposed by Schauberger and Mair (2019) <doi:10.3758/s13428-019-01224-2>. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between GPCMlasso versions 0.1-6 dated 2022-05-03 and 0.1-7 dated 2024-01-23
DESCRIPTION | 13 ++++++------- MD5 | 8 ++++---- R/ctrl_GPCMlasso.R | 3 +-- R/plot.GPCMlasso.R | 4 ++-- man/ctrl_GPCMlasso.Rd | 3 +-- 5 files changed, 14 insertions(+), 17 deletions(-)
Title: Analyzing Categorical Time Series
Description: An implementation of several functions for feature extraction in
categorical time series datasets. Specifically, some features related to
marginal distributions and serial dependence patterns can be computed. These
features can be used to feed clustering and classification algorithms for
categorical time series, among others. The package also includes some
interesting datasets containing biological sequences. Practitioners from a
broad variety of fields could benefit from the general framework provided
by 'ctsfeatures'.
Author: Angel Lopez-Oriona [aut, cre],
Jose A. Vilar [aut]
Maintainer: Angel Lopez-Oriona <oriona38@hotmail.com>
Diff between ctsfeatures versions 1.2.0 dated 2024-01-22 and 1.2.1 dated 2024-01-23
DESCRIPTION | 8 +- MD5 | 102 ++++++++++++++++---------------- R/auxiliary_chebycheff_dispersion.R | 1 R/auxiliary_cohens_kappa_function.R | 1 R/auxiliary_cramers_vi.R | 1 R/auxiliary_cramers_vi_function.R | 1 R/auxiliary_entropy.R | 1 R/auxiliary_gini_index.R | 1 R/auxiliary_gk_lambda.R | 1 R/auxiliary_gk_tau.R | 1 R/auxiliary_pearson_measure.R | 1 R/auxiliary_phi2_measure.R | 1 R/auxiliary_sakoda_measure.R | 1 R/auxiliary_spectral_envelope.R | 1 R/auxiliary_total_correlation.R | 1 R/auxiliary_total_mixed_correlation_1.R | 2 R/auxiliary_total_mixed_correlation_2.R | 2 R/auxiliary_uncertainty_coefficient.R | 1 R/binarization.R | 4 - R/calculate_features.R | 4 - R/calculate_motifs.R | 4 - R/calculate_subfeatures.R | 4 - R/check_cts.R | 11 +++ R/conditional_probabilities.R | 4 - R/joint_probabilities.R | 4 - R/marginal_probabilities.R | 4 - R/plot_ccc.R | 4 - R/plot_cohen.R | 4 - R/plot_cramer.R | 4 - R/plot_cts.R | 4 - R/plot_ifsct.R | 4 - R/plot_mcc.R | 4 - R/plot_ph.R | 4 - R/plot_reg.R | 4 - R/plot_se.R | 3 build/partial.rdb |binary man/binarization.Rd | 2 man/calculate_features.Rd | 2 man/calculate_motifs.Rd | 2 man/calculate_subfeatures.Rd | 2 man/conditional_probabilities.Rd | 2 man/joint_probabilities.Rd | 2 man/marginal_probabilities.Rd | 2 man/plot_ccc.Rd | 2 man/plot_cohen.Rd | 2 man/plot_cramer.Rd | 2 man/plot_cts.Rd | 2 man/plot_ifsct.Rd | 2 man/plot_mcc.Rd | 2 man/plot_ph.Rd | 2 man/plot_reg.Rd | 2 man/plot_se.Rd | 2 52 files changed, 113 insertions(+), 121 deletions(-)
Title: Clusters of Effects Curves in Quantile Regression Models
Description: Clustering method to cluster both effects curves, through quantile regression coefficient modeling, and curves in functional data analysis. Sottile G. and Adelfio G. (2019) <doi:10.1007/s00180-018-0817-8>.
Author: Gianluca Sottile [aut, cre],
Giada Adelfio [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between clustEff versions 0.3.0 dated 2022-06-28 and 0.3.1 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/clustEff.R | 5 ++++- inst/CITATION | 37 +++++++++++++------------------------ man/clustEff-internal.Rd | 8 ++++++++ man/clustEff-package.Rd | 4 ++-- 6 files changed, 35 insertions(+), 35 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' as described by Schauberger and Tutz (2019) <doi:10.18637/jss.v088.i09> and Schauberger and Tutz (2017) <doi:10.1177/1471082X17693086>. BTLLasso is a method to include different types of variables in paired comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between BTLLasso versions 0.1-11 dated 2020-10-07 and 0.1-12 dated 2024-01-23
DESCRIPTION | 13 ++++----- MD5 | 59 ++++++++++++++++++++++----------------------- R/BTLLasso-package.R | 6 ++-- R/BTLLasso.R | 7 ++--- R/boot.BTLLasso.R | 2 - R/cv.BTLLasso.R | 2 - R/paths.R | 2 - R/plot.BTLLasso.R | 6 ++-- R/plot.boot.BTLLasso.R | 2 - R/predict.BTLLasso.R | 2 - R/print.BTLLasso.R | 2 - R/print.boot.BTLLasso.R | 2 - R/print.cv.BTLLasso.R | 2 - R/response.BTLLasso.R | 2 - build |only man/BTLLasso-package.Rd | 2 - man/BTLLasso.Rd | 2 - man/GLES.Rd | 2 - man/GLESsmall.Rd | 2 - man/boot.BTLLasso.Rd | 2 - man/ctrl.BTLLasso.Rd | 5 +-- man/cv.BTLLasso.Rd | 2 - man/paths.Rd | 2 - man/plot.BTLLasso.Rd | 2 - man/plot.boot.BTLLasso.Rd | 2 - man/predict.BTLLasso.Rd | 2 - man/print.BTLLasso.Rd | 2 - man/print.boot.BTLLasso.Rd | 2 - man/print.cv.BTLLasso.Rd | 2 - man/response.BTLLasso.Rd | 2 - src/RcppExports.cpp | 5 +++ 31 files changed, 75 insertions(+), 72 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between PVAClone versions 0.1-6 dated 2016-03-12 and 0.1-7 dated 2024-01-23
PVAClone-0.1-6/PVAClone/data/paurelia.rda |only PVAClone-0.1-6/PVAClone/data/redstart.rda |only PVAClone-0.1-6/PVAClone/data/songsparrow.rda |only PVAClone-0.1-6/PVAClone/inst/ChangeLog |only PVAClone-0.1-7/PVAClone/DESCRIPTION | 10 +++++----- PVAClone-0.1-7/PVAClone/MD5 | 19 ++++++++++--------- PVAClone-0.1-7/PVAClone/build |only PVAClone-0.1-7/PVAClone/data/paurelia.R |only PVAClone-0.1-7/PVAClone/data/redstart.R |only PVAClone-0.1-7/PVAClone/data/songsparrow.R |only PVAClone-0.1-7/PVAClone/inst/WORDLIST |only PVAClone-0.1-7/PVAClone/man/PVAClone-package.Rd | 5 +---- PVAClone-0.1-7/PVAClone/man/generateLatent.Rd | 2 +- PVAClone-0.1-7/PVAClone/man/growthmodels.Rd | 4 ++-- PVAClone-0.1-7/PVAClone/man/pva.Rd | 2 +- 15 files changed, 20 insertions(+), 22 deletions(-)
Title: Streaming Capabilities for 'OpenAI API' Interactions
Description: Based on the 'httr2' framework, the 'OpenAI' interface supports streaming calls and model training.
For more details on the API methods implemented, see the 'OpenAI' platform documentation at <https://platform.openai.com/docs/api-reference>.
Author: Li Gen [aut, cre]
Maintainer: Li Gen <libingfei@sina.com>
Diff between openaistream versions 0.1.9 dated 2023-11-27 and 0.2.0 dated 2024-01-23
DESCRIPTION | 13 LICENSE | 4 MD5 | 69 ++++ R/api_config.R |only R/assistants.R |only R/audio.R |only R/base_api.R |only R/chat.R |only R/chatstream.R | 37 +- R/embeddings.R |only R/files.R |only R/fine_tuning.R |only R/images.R |only R/messages.R |only R/models.R |only R/moderations.R |only R/openai.R | 597 ++++++---------------------------------- R/runs.R |only R/threads.R |only inst/exdata/assfile.csv |only inst/exdata/train.jsonl | 7 man/api_config.Rd |only man/assistants.Rd |only man/audio.Rd |only man/base_api.Rd |only man/chat.Rd |only man/embeddings.Rd |only man/figures |only man/files.Rd |only man/fine_tuning.Rd |only man/images.Rd |only man/messages.Rd |only man/models.Rd |only man/moderations.Rd |only man/openai.Rd | 700 ++---------------------------------------------- man/runs.Rd |only man/threads.Rd |only tests |only 38 files changed, 232 insertions(+), 1195 deletions(-)
Title: Global Adaptive Generative Adjustment Algorithm for Generalized
Linear Models
Description: Fits linear regression, logistic and multinomial regression models, Poisson regression, Cox model via Global Adaptive Generative Adjustment Algorithm.
For more detailed information, see Bin Wang, Xiaofei Wang and Jianhua Guo (2022) <arXiv:1911.00658>.
This paper provides the theoretical properties of Gaga linear model when the load matrix is orthogonal.
Further study is going on for the nonorthogonal cases and generalized linear models.
These works are in part supported by the National Natural Foundation of China (No.12171076).
Author: Bin Wang [aut, cre],
Xiaofei Wang [ctb],
Jianhua Guo [ths]
Maintainer: Bin Wang <eatingbeen@hotmail.com>
Diff between GAGAs versions 0.6.1 dated 2023-03-29 and 0.6.2 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/RcppExports.R | 10 +++++----- R/multinomial_GAGA.R | 2 +- man/cpp_multinomial_gaga.Rd | 2 +- man/multinomial_GAGA.Rd | 2 +- src/cox_GAGA.cpp | 26 +++++++++++++------------- 8 files changed, 35 insertions(+), 31 deletions(-)
Title: Miscellaneous Helper Tools for Epidemiologists
Description: Contains tools for formatting inline code, renaming redundant
columns, aggregating age categories, adding survey weights, finding the earliest
date of an event, plotting z-curves, generating population counts and
calculating proportions with confidence intervals. This is part of the
'R4Epis' project <https://r4epis.netlify.app/>.
Author: Alexander Spina [aut] ,
Zhian N. Kamvar [aut, cre] ,
Dirk Schumacher [aut],
Kate Doyle [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between epikit versions 0.1.5 dated 2023-02-15 and 0.1.6 dated 2024-01-23
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 4 R/relabel_proportions.R | 5 build/vignette.rds |binary inst/doc/intro.R | 2 inst/doc/intro.html | 410 ++++++++++++++++++++++++++++++++++++++---------- man/dots_to_charlist.Rd | 5 man/epikit-package.Rd | 2 9 files changed, 349 insertions(+), 101 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between conos versions 1.5.0 dated 2022-10-17 and 1.5.1 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 ++ R/conos.R | 2 +- R/de_functions.R | 2 +- R/largeVis.R | 2 ++ R/plot.R | 2 +- README.md | 2 +- man/checkCountsWholeNumbers.Rd | 2 +- man/getGlobalClusterMarkers.Rd | 2 +- man/getPercentGlobalClusters.Rd | 2 +- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 1 - 14 files changed, 28 insertions(+), 27 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction
package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>;
Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains
the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness
Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636.
<doi:10.1029/2020JG005636>;
Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing
global MODIS EVI ti [...truncated...]
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Diff between phenofit versions 0.3.8 dated 2023-02-15 and 0.3.9 dated 2024-01-23
DESCRIPTION | 8 MD5 | 60 ++-- R/D.R | 320 +++++++++++------------ R/PhenoDeriv.R | 216 +++++++-------- R/PhenoTrs.R | 316 +++++++++++------------ R/check_input.R | 20 + R/curvefit.R | 216 +++++++-------- R/doubleLogistics-init_param.R | 500 ++++++++++++++++++------------------- R/optim_pheno.R | 320 +++++++++++------------ R/process_season.R | 4 R/roughFit.R | 330 ++++++++++++------------ R/season_input.R | 306 +++++++++++----------- R/season_mov.R | 8 R/tools.R | 296 ++++++++++----------- R/tools_plyr.R | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/phenofit-procedures.R | 2 inst/doc/phenofit-procedures.html | 423 +++++++++++++++---------------- inst/doc/phenofit_CA-NS6.html | 321 +++++++++++------------ man/PhenoDeriv.Rd | 92 +++--- man/PhenoGu.Rd | 146 +++++----- man/PhenoKl.Rd | 128 ++++----- man/PhenoTrs.Rd | 140 +++++----- man/brks2rfit.Rd | 56 ++-- man/curvefit0.Rd | 38 +- man/cutoff.Rd | 52 +-- man/opt_FUN.Rd | 7 man/process_season.Rd | 8 man/roughFit.Rd | 390 ++++++++++++++-------------- tests/testthat/test-PhenoExtract.R | 134 ++++----- 31 files changed, 2440 insertions(+), 2439 deletions(-)
Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Three standard color difference metrics are included.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.2-1 dated 2022-03-31 and 1.3-0 dated 2024-01-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 5 ++++- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/adaptation.html | 45 +++++++++++++++++++++++++++++---------------- inst/doc/isotherms.pdf |binary 7 files changed, 48 insertions(+), 27 deletions(-)
Title: Bagplots, Boxplots and Rainbow Plots for Functional Data
Description: Visualizing functional data and identifying functional outliers.
Author: Han Lin Shang [aut, cre, cph] ,
Rob Hyndman [aut]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between rainbow versions 3.7 dated 2022-10-09 and 3.8 dated 2024-01-23
rainbow-3.7/rainbow/R/outliers.depth.trim.R |only rainbow-3.7/rainbow/R/quantile.outliers.pond.R |only rainbow-3.7/rainbow/R/quantile.outliers.trim.R |only rainbow-3.7/rainbow/inst |only rainbow-3.7/rainbow/vignettes |only rainbow-3.8/rainbow/ChangeLog | 4 ++++ rainbow-3.8/rainbow/DESCRIPTION | 8 ++++---- rainbow-3.8/rainbow/MD5 | 21 +++++++++------------ rainbow-3.8/rainbow/NAMESPACE | 5 +++-- rainbow-3.8/rainbow/R/foutliers.R | 15 ++++++--------- rainbow-3.8/rainbow/R/outliers.depth.pond.R | 2 +- rainbow-3.8/rainbow/R/outliers_depth_trim.R |only rainbow-3.8/rainbow/R/quantile_outliers_pond.R |only rainbow-3.8/rainbow/R/quantile_outliers_trim.R |only rainbow-3.8/rainbow/man/SVDplot.Rd | 4 ++-- 15 files changed, 29 insertions(+), 30 deletions(-)
Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggridges versions 0.5.5 dated 2023-12-15 and 0.5.6 dated 2024-01-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/gallery.html | 4 ++-- inst/doc/introduction.html | 4 ++-- tests/testthat/test_scale_cyclical.R | 14 ++++++++++++-- 6 files changed, 28 insertions(+), 14 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] ,
Han Lin Shang [aut, cre, cph]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between ftsa versions 6.3 dated 2023-09-11 and 6.4 dated 2024-01-23
ftsa-6.3/ftsa/inst |only ftsa-6.3/ftsa/vignettes |only ftsa-6.4/ftsa/ChangeLog | 5 ++ ftsa-6.4/ftsa/DESCRIPTION | 8 +-- ftsa-6.4/ftsa/MD5 | 34 ++++++--------- ftsa-6.4/ftsa/NAMESPACE | 4 + ftsa-6.4/ftsa/R/One_way_Residuals.R |only ftsa-6.4/ftsa/R/One_way_median_polish.R |only ftsa-6.4/ftsa/R/forecast.ftsm.R | 17 +++++-- ftsa-6.4/ftsa/R/ftsm.R | 29 +++++++++++-- ftsa-6.4/ftsa/man/One_way_Residuals.Rd |only ftsa-6.4/ftsa/man/One_way_median_polish.Rd |only ftsa-6.4/ftsa/man/T_stationary.Rd | 10 ++-- ftsa-6.4/ftsa/man/facf.Rd | 2 ftsa-6.4/ftsa/man/farforecast.Rd | 12 ++--- ftsa-6.4/ftsa/man/fplsr.Rd | 41 +++++++++--------- ftsa-6.4/ftsa/man/ftsa-package.Rd | 64 +++++++++++++++++++++++++++-- 17 files changed, 157 insertions(+), 69 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-12 1.0.0