Title: Projection Pursuit Classification Forest
Description: Implements projection pursuit forest algorithm for supervised classification.
Author: Natalia da Silva, Eun-Kyung Lee, Di Cook
Maintainer: Natalia da Silva <natalia.dasilva@fcea.edu.uy>
Diff between PPforest versions 0.1.2 dated 2021-10-14 and 0.1.3 dated 2022-09-09
DESCRIPTION | 11 MD5 | 44 +-- NEWS.md | 8 R/PPforest.R | 5 R/baggtree.R | 4 R/leukemia.R | 6 R/trees_pred.R | 4 README.md | 2 build/vignette.rds |binary inst/doc/PPforest-vignette.html | 554 +++++++++++++++++++++++++++++++++++----- man/NCI60.Rd | 4 man/PPforest.Rd | 8 man/baggtree.Rd | 12 man/crab.Rd | 4 man/fishcatch.Rd | 4 man/glass.Rd | 4 man/image.Rd | 4 man/leukemia.Rd | 18 - man/lymphoma.Rd | 4 man/olive.Rd | 4 man/parkinson.Rd | 4 man/trees_pred.Rd | 2 man/wine.Rd | 4 23 files changed, 581 insertions(+), 133 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
The package does not require any installation of Microsoft products to be able to write Microsoft
files.
Author: David Gohel [aut, cre],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Stefan Moog [ctb] ,
Greg Leleu [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.4.3 dated 2022-06-12 and 0.4.4 dated 2022-09-09
DESCRIPTION | 8 - MD5 | 40 +++---- NAMESPACE | 2 NEWS.md | 21 +++ R/formatting_properties.R | 259 +++++++++++++++++++++++++++++----------------- R/knitr_utils.R | 85 ++++++++++++--- R/ooxml.R | 29 ++++- R/ooxml_block_objects.R | 28 +++- R/ooxml_run_objects.R | 50 +++++--- R/ppt_ph_with_methods.R | 4 R/utils.R | 22 +-- man/body_add.Rd | 32 ++--- man/fp_cell.Rd | 12 +- man/fp_par.Rd | 7 + man/fpar.Rd | 2 man/opts_current_table.Rd | 55 +++++---- man/ph_with.Rd | 26 ++-- man/prop_table.Rd | 8 + man/read_docx.Rd | 6 - man/run_word_field.Rd | 9 - man/set_notes.Rd | 6 - 21 files changed, 463 insertions(+), 248 deletions(-)
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.4 dated 2022-06-29 and 1.5 dated 2022-09-09
DESCRIPTION | 14 ++++++++------ MD5 | 10 +++++----- R/UFAx_workflow.R | 12 ++++++------ inst/extdata/UFAx_parameters.xlsx |binary man/UFAx_score_coefficient_corrector.Rd | 8 ++++---- man/UFAx_workflow.Rd | 3 ++- 6 files changed, 25 insertions(+), 22 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Infrastructure for working with censored or truncated normal, logistic,
and Student-t distributions, i.e., d/p/q/r functions and distributions3
objects.
Author: Jakob Messner [aut, cre] ,
Achim Zeileis [aut] ,
Reto Stauffer [aut]
Maintainer: Jakob Messner <jakob.messner@posteo.net>
Diff between crch versions 1.1-0 dated 2022-09-07 and 1.1-1 dated 2022-09-09
DESCRIPTION | 8 +++---- MD5 | 40 +++++++++++++++++++-------------------- NAMESPACE | 14 +++++++++++++ NEWS.md | 8 +++++++ R/CensoredLogistic.R | 8 +++++++ R/CensoredNormal.R | 8 +++++++ R/CensoredStudentsT.R | 8 +++++++ R/TruncatedLogistic.R | 8 +++++++ R/TruncatedNormal.R | 8 +++++++ R/TruncatedStudentsT.R | 8 +++++++ inst/doc/crch.pdf |binary man/CensoredLogistic.Rd | 6 +++++ man/CensoredNormal.Rd | 6 +++++ man/CensoredStudentsT.Rd | 6 +++++ man/TruncatedLogistic.Rd | 5 ++++ man/TruncatedNormal.Rd | 5 ++++ man/TruncatedStudentsT.Rd | 5 ++++ src/tlogis.c | 16 +++++++-------- src/tnorm.c | 16 +++++++-------- src/tt.c | 16 +++++++-------- tests/Examples/crch-Ex.Rout.save | 10 +++++++-- 21 files changed, 159 insertions(+), 50 deletions(-)
Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed
Data
Description: Semi-parametric approach for sparse canonical correlation analysis
which can handle mixed data types: continuous, binary and truncated continuous.
Bridge functions are provided to connect Kendall's tau to latent correlation
under the Gaussian copula model. The methods are described in
Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and
Yoon, Mueller and Gaynanova (2021) <doi:10.1080/10618600.2021.1882468>.
Author: Grace Yoon [aut] ,
Mingze Huang [ctb] ,
Irina Gaynanova [aut, cre]
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between mixedCCA versions 1.5.2 dated 2022-05-25 and 1.6.2 dated 2022-09-09
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- R/bridgeInv.R | 38 ++++++++++++++++++-------------------- README.md | 4 +--- man/estimateR.Rd | 4 ++-- man/examples/estimateR_ex.R | 4 ++-- 6 files changed, 36 insertions(+), 39 deletions(-)
Title: Fast Implementation of the Diffusion Decision Model
Description: Provides the probability density function (PDF), cumulative
distribution function (CDF), and the partial derivatives of the PDF of the
diffusion decision model (DDM; e.g.,
Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) with across-trial
variability in the drift rate. Because the PDF, its partial derivatives, and
the CDF of the DDM both contain an infinite sum, they need to be approximated.
'fddm' implements all published approximations
(Navarro & Fuss, 2009, <doi:10.1016/j.jmp.2009.02.003>;
Gondan, Blurton, & Kesselmeier, 2014, <doi:10.1016/j.jmp.2014.05.002>;
Blurton, Kesselmeier, & Gondan, 2017, <doi:10.1016/j.jmp.2016.11.003>;
Hartmann & Klauer, 2021, <doi:10.1016/j.jmp.2021.102550>) plus
new approximations. All approximations are implemented purely in 'C++'
providing faster speed than existing packages.
Author: Kendal B. Foster [aut],
Henrik Singmann [ctb, cre]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between fddm versions 0.5-1 dated 2022-03-15 and 0.5-2 dated 2022-09-09
fddm-0.5-1/fddm/NEWS.md |only fddm-0.5-2/fddm/DESCRIPTION | 8 fddm-0.5-2/fddm/MD5 | 26 fddm-0.5-2/fddm/NEWS |only fddm-0.5-2/fddm/R/RcppExports.R | 4 fddm-0.5-2/fddm/build/vignette.rds |binary fddm-0.5-2/fddm/inst/doc/benchmark.html | 2489 +++++++++++++++++--------------- fddm-0.5-2/fddm/inst/doc/example.html | 860 ++++++----- fddm-0.5-2/fddm/inst/doc/math.html | 419 +++-- fddm-0.5-2/fddm/inst/doc/pfddm.html | 869 ++++++----- fddm-0.5-2/fddm/inst/doc/validity.html | 1773 ++++++++++++---------- fddm-0.5-2/fddm/man/dfddm.Rd | 2 fddm-0.5-2/fddm/man/pfddm.Rd | 2 fddm-0.5-2/fddm/src/dfddm.cpp | 2 fddm-0.5-2/fddm/src/pfddm.cpp | 2 15 files changed, 3717 insertions(+), 2739 deletions(-)
Title: Access, Retrieve, and Work with CMHC Data
Description: Wrapper around the Canadian Mortgage and Housing Corporation (CMHC) web interface. It enables programmatic and reproducible access to a wide variety of housing data from CMHC.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cmhc versions 0.2.0 dated 2022-06-15 and 0.2.1 dated 2022-09-09
cmhc-0.2.0/cmhc/man/set_cache_path.Rd |only cmhc-0.2.0/cmhc/man/show_cache_path.Rd |only cmhc-0.2.1/cmhc/DESCRIPTION | 8 - cmhc-0.2.1/cmhc/MD5 | 40 ++--- cmhc-0.2.1/cmhc/NAMESPACE | 4 cmhc-0.2.1/cmhc/NEWS.md | 6 cmhc-0.2.1/cmhc/R/cmhc.R | 18 ++ cmhc-0.2.1/cmhc/R/cmhc_geography.R | 8 - cmhc-0.2.1/cmhc/R/cmhc_tables.R | 160 ++++++++++++++++++++--- cmhc-0.2.1/cmhc/R/helpers.R | 10 - cmhc-0.2.1/cmhc/R/user_settings.R | 10 - cmhc-0.2.1/cmhc/README.md | 12 + cmhc-0.2.1/cmhc/build/vignette.rds |binary cmhc-0.2.1/cmhc/inst/doc/basic_usage.R | 2 cmhc-0.2.1/cmhc/inst/doc/basic_usage.Rmd | 2 cmhc-0.2.1/cmhc/inst/doc/basic_usage.html | 75 ++++++---- cmhc-0.2.1/cmhc/man/cmhc_cma_translation_data.Rd | 1 cmhc-0.2.1/cmhc/man/cmhc_csd_translation_data.Rd | 1 cmhc-0.2.1/cmhc/man/cmhc_ct_translation_data.Rd | 1 cmhc-0.2.1/cmhc/man/get_cmhc.Rd | 7 + cmhc-0.2.1/cmhc/man/set_cmhc_cache_path.Rd |only cmhc-0.2.1/cmhc/man/show_cmhc_cache_path.Rd |only cmhc-0.2.1/cmhc/vignettes/basic_usage.Rmd | 2 23 files changed, 275 insertions(+), 92 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
,
Richard FitzJohn [ctb],
Brandon Bertelsen [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.15 dated 2022-02-15 and 0.0.16 dated 2022-09-09
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 4 R/local_db.R | 3 README.md | 48 ++-- build/vignette.rds |binary inst/doc/arkdb.Rmd | 2 inst/doc/arkdb.html | 451 ++++++++++++++++++++++++++++++++++++-------- tests/testthat/test-arkdb.R | 4 vignettes/arkdb.Rmd | 2 10 files changed, 423 insertions(+), 117 deletions(-)
Title: United Formula Annotation (UFA) for HRMS Data Processing
Description: A pipeline to annotate peaklists from the IDSL.IPA package with molecular formula using an isotopic profile matching approach. The IDSL.UFA pipeline is especially beneficial when MS/MS data is not available. The IDSL.UFA package has functions to process user-defined adduct formulas.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFA versions 1.4 dated 2022-06-13 and 1.5 dated 2022-09-09
DESCRIPTION | 10 MD5 | 94 ++-- R/UFA_enumerated_chemical_space.R | 310 ++++++++++------ R/UFA_enumerated_chemical_space_xlsxAnalyzer.R | 6 R/UFA_profile_visualizer.R | 32 - R/UFA_profile_visualizer_xlsxAnalyzer.R | 6 R/UFA_score_coefficient_corrector.R | 61 +-- R/UFA_score_function_optimization_xlsxAnalyzer.R | 5 R/UFA_workflow.R | 12 R/UFA_xlsxAnalyzer.R | 31 - R/aligned_molecular_formula_annotator.R | 342 ++++++----------- R/detect_formula_sets.R | 37 - R/element_sorter.R | 8 R/extended_SENIOR_rule_check.R | 2 R/formula_adduct_calculator.R | 13 R/global.R | 2 R/hill_molecular_formula_printer.R | 2 R/ionization_pathway_deconvoluter.R | 24 - R/isotopic_profile_calculator.R | 22 - R/isotopic_profile_molecular_formula_feeder.R | 385 ++++++++++---------- R/molecular_formula_annotator.R | 146 ++++--- R/molecular_formula_library_search.R | 8 R/molecular_formulas_source_IPDB.R | 18 R/monoisotopic_mass_calculator.R | 6 R/score_coefficient_evaluation.R | 4 R/zero_score_function.R | 43 -- build/partial.rdb |binary inst/extdata/UFA_parameters.xlsx |binary man/IUPAC_Isotopes.Rd | 2 man/UFA_enumerated_chemical_space_xlsxAnalyzer.Rd | 3 man/UFA_locate_regex.Rd | 4 man/UFA_score_function_optimization_xlsxAnalyzer.Rd | 2 man/UFA_workflow.Rd | 2 man/aligned_molecular_formula_annotator.Rd | 2 man/detect_formula_sets.Rd | 6 man/element_sorter.Rd | 6 man/formula_adduct_calculator.Rd | 2 man/formula_vector_generator.Rd | 2 man/identification_score.Rd | 2 man/ionization_pathway_deconvoluter.Rd | 4 man/isotopic_profile_calculator.Rd | 101 ++--- man/isotopic_profile_molecular_formula_feeder.Rd | 122 +++--- man/molecular_formula_annotator.Rd | 3 man/molecular_formula_library_generator.Rd | 4 man/molecular_formulas_source_IPDB.Rd | 2 man/monoisotopic_mass_calculator.Rd | 4 man/score_coefficient_evaluation.Rd | 2 man/score_coefficients_optimization.Rd | 2 48 files changed, 976 insertions(+), 930 deletions(-)
Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs isotope pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms (EIC) and total ion chromatograms (TIC).
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 2.1 dated 2022-08-08 and 2.2 dated 2022-09-09
DESCRIPTION | 8 +-- MD5 | 72 ++++++++++++++++----------------- R/IPA_CompoundsAnnotation.R | 25 +++-------- R/IPA_PeakAlignment.R | 15 ++++++ R/IPA_PeakAnalyzer.R | 4 - R/IPA_PeaklistAnnotation.R | 33 ++++++++------- R/IPA_TargetedAnalysis.R | 4 - R/IPA_xlsxAnalyzer.R | 49 ++++++++++------------ R/peak_property_table_correlation.R |only R/plot_mz_eic.R | 10 ++-- R/plot_simple_tic.R | 4 - R/spectraList_filtering.R | 2 R/xlsxAnalyzer_EIC.R | 2 build/partial.rdb |binary inst/extdata/IPA_parameters.xlsx |binary man/EIC_plotter.Rd | 7 --- man/IPA_GapFiller.Rd | 2 man/IPA_MSdeconvoluter.Rd | 4 - man/IPA_TargetedAnalysis.Rd | 6 +- man/IPA_Workflow.Rd | 2 man/XIC.Rd | 2 man/chromatography_analysis.Rd | 26 +++-------- man/der_5points_stencil.Rd | 2 man/islocalminimum.Rd | 2 man/islocaloptimum.Rd | 2 man/mzRTindexer.Rd | 4 - man/peak_alignment.Rd | 3 - man/peak_detection.Rd | 2 man/peak_property_table_correlation.Rd |only man/plot_mz_eic.Rd | 6 +- man/plot_simple_tic.Rd | 6 +- man/primary_peak_analyzer.Rd | 11 +---- man/recursive_mass_correction.Rd | 17 ++----- man/reference_peaks_detector.Rd | 6 +- man/sample_rt_corrector.Rd | 9 +--- man/segment.Rd | 3 - man/spectraList_filtering.Rd | 5 -- man/xlsxAnalyzer_EIC.Rd | 3 - 38 files changed, 168 insertions(+), 190 deletions(-)
Title: Cone Constrained Convex Problems
Description: Routines for solving convex optimization problems with cone constraints by means of interior-point methods. The implemented algorithms are partially ported from CVXOPT, a Python module for convex optimization (see <http://cvxopt.org> for more information).
Author: Bernhard Pfaff [aut, cre],
Lieven Vandenberghe [cph] ,
Martin Andersen [cph] ,
Joachim Dahl [cph]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between cccp versions 0.2-7 dated 2020-10-30 and 0.2-9 dated 2022-09-09
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/gp.R | 2 +- R/rp.R | 2 +- src/DCP.cpp | 2 +- src/DLP.cpp | 22 +++++++++++++++------- src/DNL.cpp | 2 +- src/DQP.cpp | 2 +- src/GPP.cpp | 2 +- src/RPP.cpp | 8 ++++---- 10 files changed, 40 insertions(+), 32 deletions(-)
Title: A Quantum Computer Simulator
Description: A quantum computer simulator framework with up to 24 qubits. It allows to
define general single qubit gates and general controlled single
qubit gates. For convenience, it currently provides the
most common gates (X, Y, Z, H, Z, S, T, Rx, Ry, Rz, CNOT, SWAP, Toffoli or
CCNOT, Fredkin or CSWAP). 'qsimulatR' also implements noise models.
'qsimulatR' supports plotting of circuits and is able to
export circuits to 'Qiskit' <https://qiskit.org/>, a python package
which can be used to run on IBM's hardware <https://quantum-computing.ibm.com/>.
Author: Johann Ostmeyer [aut],
Carsten Urbach [aut, cre]
Maintainer: Carsten Urbach <urbach@hiskp.uni-bonn.de>
Diff between qsimulatR versions 1.0 dated 2020-12-09 and 1.1 dated 2022-09-09
qsimulatR-1.0/qsimulatR/inst/doc/ExponentiateModN.pdf |only qsimulatR-1.0/qsimulatR/inst/doc/addbyqft.pdf |only qsimulatR-1.0/qsimulatR/inst/doc/deutsch-jozsa.pdf |only qsimulatR-1.0/qsimulatR/inst/doc/phase_estimation.pdf |only qsimulatR-1.0/qsimulatR/inst/doc/qft.pdf |only qsimulatR-1.0/qsimulatR/vignettes/ExponentiateModN.html |only qsimulatR-1.0/qsimulatR/vignettes/Shor.html |only qsimulatR-1.0/qsimulatR/vignettes/Shor.pdf |only qsimulatR-1.0/qsimulatR/vignettes/addbyqft.html |only qsimulatR-1.0/qsimulatR/vignettes/deutsch-jozsa.html |only qsimulatR-1.0/qsimulatR/vignettes/phase_estimation.html |only qsimulatR-1.0/qsimulatR/vignettes/qft.html |only qsimulatR-1.1/qsimulatR/DESCRIPTION | 18 qsimulatR-1.1/qsimulatR/MD5 | 62 +- qsimulatR-1.1/qsimulatR/NAMESPACE | 5 qsimulatR-1.1/qsimulatR/R/ccqgate.R | 7 qsimulatR-1.1/qsimulatR/R/cnotgate.R | 26 - qsimulatR-1.1/qsimulatR/R/cnqgate.R |only qsimulatR-1.1/qsimulatR/R/cqgate.R | 7 qsimulatR-1.1/qsimulatR/R/plot-qstate.R | 65 ++ qsimulatR-1.1/qsimulatR/R/qft.R | 6 qsimulatR-1.1/qsimulatR/R/sqgate.R | 85 +++ qsimulatR-1.1/qsimulatR/R/state.R | 44 ++ qsimulatR-1.1/qsimulatR/R/swapgate.R | 28 - qsimulatR-1.1/qsimulatR/build/vignette.rds |binary qsimulatR-1.1/qsimulatR/inst/doc/ExponentiateModN.html |only qsimulatR-1.1/qsimulatR/inst/doc/addbyqft.html |only qsimulatR-1.1/qsimulatR/inst/doc/deutsch-jozsa.html |only qsimulatR-1.1/qsimulatR/inst/doc/grover.R |only qsimulatR-1.1/qsimulatR/inst/doc/grover.Rmd |only qsimulatR-1.1/qsimulatR/inst/doc/grover.html |only qsimulatR-1.1/qsimulatR/inst/doc/phase_estimation.html |only qsimulatR-1.1/qsimulatR/inst/doc/qft.html |only qsimulatR-1.1/qsimulatR/inst/doc/qsimulatR.R | 47 ++ qsimulatR-1.1/qsimulatR/inst/doc/qsimulatR.Rmd | 283 +++++++++++-- qsimulatR-1.1/qsimulatR/inst/doc/qsimulatR.html | 182 ++++++-- qsimulatR-1.1/qsimulatR/man/cnqgate.Rd |only qsimulatR-1.1/qsimulatR/man/genNoise.Rd |only qsimulatR-1.1/qsimulatR/man/hist.measurement.Rd | 3 qsimulatR-1.1/qsimulatR/man/noise.Rd |only qsimulatR-1.1/qsimulatR/man/qstate.Rd | 12 qsimulatR-1.1/qsimulatR/man/times-cnqgate-qstate-method.Rd |only qsimulatR-1.1/qsimulatR/vignettes/bibliography.bib | 9 qsimulatR-1.1/qsimulatR/vignettes/grover.Rmd |only qsimulatR-1.1/qsimulatR/vignettes/qsimulatR.Rmd | 283 +++++++++++-- 45 files changed, 1001 insertions(+), 171 deletions(-)
Title: Kriging-Based Inversion for Deterministic and Noisy Computer
Experiments
Description: Criteria and algorithms for sequentially estimating level sets of a multivariate numerical function, possibly observed with noise.
Author: Clement Chevalier [aut],
Dario Azzimonti [aut, cre] ,
David Ginsbourger [aut] ,
Victor Picheny [aut] ,
Yann Richet [ctb]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between KrigInv versions 1.4.1 dated 2018-09-11 and 1.4.2 dated 2022-09-09
DESCRIPTION | 45 ++++- MD5 | 32 ++-- R/bichon_optim.R | 46 ++--- R/computeRealVolumeConstant.R | 232 ++++++++++++++--------------- R/excursion_probability.R | 36 ++-- R/jn_optim_parallel.R | 214 +++++++++++++------------- R/jn_optim_parallel2.R | 28 +-- R/ranjan_optim.R | 44 ++--- R/timse_optim_parallel.R | 108 ++++++------- R/timse_optim_parallel2.R | 30 +-- R/tsee_optim.R | 40 ++--- R/vorob_optim_parallel.R | 4 man/KrigInv-package.Rd | 130 ++++++++-------- man/predict_nobias_km.Rd | 2 man/ranjan_optim.Rd | 2 tests/testthat.R | 8 - tests/testthat/test-print_uncertainty_2d.R | 102 ++++++------ 17 files changed, 566 insertions(+), 537 deletions(-)
Title: Analysis Framework for Monte Carlo Simulation Data in Physics
Description: Toolkit to perform statistical analyses of correlation
functions generated from Lattice Monte Carlo simulations. In
particular, a class 'cf' for correlation functions and
methods to analyse those are defined. This includes (blocked)
bootstrap (based on the 'boot' package) and jackknife, but also an
automatic determination of integrated autocorrelation
times. 'hadron' also provides a very general function
bootstrap.nlsfit() to bootstrap a non-linear least squares fit.
More specific functions are provided to extract hadronic quantities
from Lattice Quantum Chromodynamics simulations, a particular Monte
Carlo simulation,(see e.g. European Twisted Mass Collaboration, P. Boucaud et
al. (2008) <doi:10.1016/j.cpc.2008.06.013>). Here, to determine
energy eigenvalues of hadronic states, specific fitting routines
and in particular the generalised eigenvalue method (see
e.g. B. Blossier et al. (2009) <doi:10.1088/1126-6708/2009/04/094>
and M. Fischer et al. (2020)
<https://inspire [...truncated...]
Author: Bartosz Kostrzewa [aut],
Johann Ostmeyer [aut],
Martin Ueding [aut],
Carsten Urbach [aut, cre],
Nikolas Schlage [ctb],
Markus Werner [ctb],
Ferenc Pittler [ctb],
Matthias Fischer [ctb],
Vittorio Lubicz [ctb]
Maintainer: Carsten Urbach <urbach@hiskp.uni-bonn.de>
Diff between hadron versions 3.1.2 dated 2020-09-10 and 3.2.0 dated 2022-09-09
hadron-3.1.2/hadron/inst/doc/Two_Amplitudes_Model.html |only hadron-3.2.0/hadron/DESCRIPTION | 12 hadron-3.2.0/hadron/MD5 | 63 hadron-3.2.0/hadron/R/bootstrap.nlsfit.R | 8 hadron-3.2.0/hadron/R/cf.R | 3 hadron-3.2.0/hadron/R/computeDisc.R | 2 hadron-3.2.0/hadron/R/cvc_readutils.R | 70 hadron-3.2.0/hadron/R/effectivemass.R | 13 hadron-3.2.0/hadron/R/hadron-package.R | 12 hadron-3.2.0/hadron/R/plotutils.R | 175 +- hadron-3.2.0/hadron/build/partial.rdb |binary hadron-3.2.0/hadron/build/vignette.rds |binary hadron-3.2.0/hadron/configure |only hadron-3.2.0/hadron/inst/doc/Two_Amplitudes_Model.pdf |only hadron-3.2.0/hadron/inst/doc/gevp.html | 805 ++++----- hadron-3.2.0/hadron/inst/doc/hankel.html | 844 +++++----- hadron-3.2.0/hadron/inst/doc/jackknife_cov_and_missing_values.html | 809 +++++---- hadron-3.2.0/hadron/inst/doc/jackknife_error_normalization.html | 657 ++++--- hadron-3.2.0/hadron/man/InternalHadronFunctions.Rd |only hadron-3.2.0/hadron/man/cf_key_meson_3pt.Rd | 29 hadron-3.2.0/hadron/man/cf_meta.Rd | 3 hadron-3.2.0/hadron/man/correlators_key_meson_3pt.Rd | 29 hadron-3.2.0/hadron/man/cyprus_make_key_vector.Rd | 3 hadron-3.2.0/hadron/man/effectivemass.cf.Rd | 11 hadron-3.2.0/hadron/man/jackknife-after-bootstrap.Rd |only hadron-3.2.0/hadron/man/parametric.nlsfit.Rd | 9 hadron-3.2.0/hadron/man/plot.bootstrapfit.Rd | 6 hadron-3.2.0/hadron/man/plot.cf.Rd | 3 hadron-3.2.0/hadron/man/plot.coshfit.Rd | 3 hadron-3.2.0/hadron/man/plot.gevp.amplitude.Rd | 3 hadron-3.2.0/hadron/man/plot.uwerr.Rd | 3 hadron-3.2.0/hadron/man/pointswithslantederror.Rd | 3 hadron-3.2.0/hadron/man/simple.nlsfit.Rd | 11 hadron-3.2.0/hadron/man/summary.bootstrapfit.Rd | 3 hadron-3.2.0/hadron/man/tex.catwitherror.Rd | 3 35 files changed, 1883 insertions(+), 1712 deletions(-)
Title: Extensive and Tidy NCAA Men's College Basketball Data
Description: An API wrapper for cbbstat and a suite of functions to pull
and clean detailed, extensive college basketball statistics from
Barttorvik<https://barttorvik.com/>.
Author: Andrew Weatherman [aut, cre]
Maintainer: Andrew Weatherman <taw38@duke.edu>
Diff between toRvik versions 1.0.2 dated 2022-04-22 and 1.1.0 dated 2022-09-09
toRvik-1.0.2/toRvik/R/coach.R |only toRvik-1.0.2/toRvik/R/game.R |only toRvik-1.0.2/toRvik/R/player.R |only toRvik-1.0.2/toRvik/R/rating.R |only toRvik-1.0.2/toRvik/R/team.R |only toRvik-1.0.2/toRvik/R/tournament.R |only toRvik-1.0.2/toRvik/man/bart_team_schedule.Rd |only toRvik-1.0.2/toRvik/man/bart_transfers.Rd |only toRvik-1.1.0/toRvik/DESCRIPTION | 22 toRvik-1.1.0/toRvik/LICENSE | 4 toRvik-1.1.0/toRvik/MD5 | 129 + toRvik-1.1.0/toRvik/NAMESPACE | 94 - toRvik-1.1.0/toRvik/NEWS.md | 113 + toRvik-1.1.0/toRvik/R/bart_archive.R |only toRvik-1.1.0/toRvik/R/bart_coach.R |only toRvik-1.1.0/toRvik/R/bart_coach_change.R |only toRvik-1.1.0/toRvik/R/bart_conf_factors.R |only toRvik-1.1.0/toRvik/R/bart_conf_stats.R |only toRvik-1.1.0/toRvik/R/bart_factors.R |only toRvik-1.1.0/toRvik/R/bart_game_box.R |only toRvik-1.1.0/toRvik/R/bart_game_factors.R |only toRvik-1.1.0/toRvik/R/bart_game_prediction.R |only toRvik-1.1.0/toRvik/R/bart_injuryimpact.R |only toRvik-1.1.0/toRvik/R/bart_player_game.R |only toRvik-1.1.0/toRvik/R/bart_player_season.R |only toRvik-1.1.0/toRvik/R/bart_player_splits.R |only toRvik-1.1.0/toRvik/R/bart_players.R |only toRvik-1.1.0/toRvik/R/bart_poy.R |only toRvik-1.1.0/toRvik/R/bart_pregame.R |only toRvik-1.1.0/toRvik/R/bart_ratings.R |only toRvik-1.1.0/toRvik/R/bart_season_schedule.R |only toRvik-1.1.0/toRvik/R/bart_team_box.R |only toRvik-1.1.0/toRvik/R/bart_team_history.R |only toRvik-1.1.0/toRvik/R/bart_team_shooting.R |only toRvik-1.1.0/toRvik/R/bart_teams.R |only toRvik-1.1.0/toRvik/R/bart_tournament_prediction.R |only toRvik-1.1.0/toRvik/R/bart_tourney_odds.R |only toRvik-1.1.0/toRvik/R/bart_tourney_results.R |only toRvik-1.1.0/toRvik/R/bart_tourney_sheets.R |only toRvik-1.1.0/toRvik/R/globals.R | 13 toRvik-1.1.0/toRvik/R/player_recruiting_rankings.R |only toRvik-1.1.0/toRvik/R/sysdata.rda |only toRvik-1.1.0/toRvik/R/transfer_portal.R |only toRvik-1.1.0/toRvik/R/utils.R |only toRvik-1.1.0/toRvik/README.md | 483 ++++-- toRvik-1.1.0/toRvik/build/vignette.rds |binary toRvik-1.1.0/toRvik/inst/WORDLIST | 139 + toRvik-1.1.0/toRvik/inst/doc/introduction.R | 144 -- toRvik-1.1.0/toRvik/inst/doc/introduction.Rmd | 276 +-- toRvik-1.1.0/toRvik/inst/doc/introduction.html | 1290 +++++++++--------- toRvik-1.1.0/toRvik/man/bart_archive.Rd | 87 - toRvik-1.1.0/toRvik/man/bart_coach.Rd | 56 toRvik-1.1.0/toRvik/man/bart_coach_change.Rd | 58 toRvik-1.1.0/toRvik/man/bart_conf_factors.Rd | 158 +- toRvik-1.1.0/toRvik/man/bart_conf_stats.Rd | 120 - toRvik-1.1.0/toRvik/man/bart_factors.Rd | 152 -- toRvik-1.1.0/toRvik/man/bart_game_box.Rd | 64 toRvik-1.1.0/toRvik/man/bart_game_factors.Rd | 72 - toRvik-1.1.0/toRvik/man/bart_game_prediction.Rd |only toRvik-1.1.0/toRvik/man/bart_injuryimpact.Rd | 74 - toRvik-1.1.0/toRvik/man/bart_player_game.Rd | 80 - toRvik-1.1.0/toRvik/man/bart_player_season.Rd | 74 - toRvik-1.1.0/toRvik/man/bart_player_splits.Rd |only toRvik-1.1.0/toRvik/man/bart_players.Rd |only toRvik-1.1.0/toRvik/man/bart_poy.Rd | 92 - toRvik-1.1.0/toRvik/man/bart_pregame.Rd | 91 - toRvik-1.1.0/toRvik/man/bart_ratings.Rd | 100 - toRvik-1.1.0/toRvik/man/bart_season_schedule.Rd | 83 - toRvik-1.1.0/toRvik/man/bart_team_box.Rd | 71 toRvik-1.1.0/toRvik/man/bart_team_history.Rd | 102 - toRvik-1.1.0/toRvik/man/bart_team_shooting.Rd | 98 - toRvik-1.1.0/toRvik/man/bart_teams.Rd |only toRvik-1.1.0/toRvik/man/bart_tournament_prediction.Rd |only toRvik-1.1.0/toRvik/man/bart_tourney_odds.Rd | 86 - toRvik-1.1.0/toRvik/man/bart_tourney_results.Rd | 72 - toRvik-1.1.0/toRvik/man/bart_tourney_sheets.Rd | 84 - toRvik-1.1.0/toRvik/man/current_season.Rd | 24 toRvik-1.1.0/toRvik/man/player_recruiting_rankings.Rd |only toRvik-1.1.0/toRvik/man/transfer_portal.Rd |only toRvik-1.1.0/toRvik/tests/spelling.R | 6 toRvik-1.1.0/toRvik/tests/testthat.R | 12 toRvik-1.1.0/toRvik/tests/testthat/test-coach.R | 14 toRvik-1.1.0/toRvik/tests/testthat/test-game.R | 18 toRvik-1.1.0/toRvik/tests/testthat/test-player.R | 64 toRvik-1.1.0/toRvik/tests/testthat/test-rating.R | 91 - toRvik-1.1.0/toRvik/tests/testthat/test-team.R | 30 toRvik-1.1.0/toRvik/tests/testthat/test-tourney.R | 48 toRvik-1.1.0/toRvik/vignettes/introduction.Rmd | 276 +-- 88 files changed, 2737 insertions(+), 2427 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-12 dated 2021-08-10 and 1.2-13 dated 2022-09-09
ChangeLog | 6 DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 5 R/bivar.smooth.const.R | 257 +++++++++++++---- R/plot.r | 424 ++++++++++++++++++++++++++++- build/partial.rdb |binary man/smooth.construct.tescv.smooth.spec.Rd | 2 man/smooth.construct.tescx.smooth.spec.Rd | 2 man/smooth.construct.tesmd1.smooth.spec.Rd | 44 ++- man/smooth.construct.tesmd2.smooth.spec.Rd | 46 ++- man/smooth.construct.tesmi1.smooth.spec.Rd | 10 man/smooth.construct.tesmi2.smooth.spec.Rd | 42 ++ 13 files changed, 751 insertions(+), 119 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.9 dated 2021-09-09 and 2.10 dated 2022-09-09
DESCRIPTION | 12 ++--- MD5 | 82 ++++++++++++++++++------------------ NAMESPACE | 1 R/CVAdists.r | 8 +-- R/CreateL.r | 2 R/Morpho-package.R | 4 - R/ProcGPA.r | 9 ++- R/bindArr.r | 14 +++--- R/classify.r | 4 - R/computeArea.r |only R/deformGrid2d.r | 10 +++- R/deformGrid3d.r | 7 ++- R/fiducials.r | 9 +++ R/groupPCA.r | 7 +-- R/lineplot.r | 7 +-- R/meshDist.r | 5 +- R/meshDistMatrix.r | 4 - R/meshDistZExport.r | 2 R/permudist.r | 4 - R/permuvec.r | 10 ++-- R/plot.normals.r | 2 R/pls2B.r | 93 +++++++++++++++++++++++++++++++++-------- R/proc.weight.r | 2 R/procAOVsym.r | 2 R/procSym.r | 30 ++++++++----- R/readallTPS.r | 22 +++++++++ R/restoreShapes.r | 26 ++++++++++- inst/NEWS.Rd | 19 ++++++++ man/Morpho-package.Rd | 4 - man/bindArr.Rd | 4 + man/computeArea.Rd |only man/deformGrid2d.Rd | 6 ++ man/deformGrid3d.Rd | 2 man/getPLSCommonShape.Rd | 2 man/groupPCA.Rd | 7 +-- man/lineplot.Rd | 12 ++++- man/permuvec.Rd | 2 man/plotNormals.Rd | 2 man/pls2B.Rd | 9 +++ man/procSym.Rd | 1 man/readallTPS.Rd | 5 +- man/restoreShapes.Rd | 21 ++++++++- tests/testthat/test-relWarps.r | 2 43 files changed, 336 insertions(+), 140 deletions(-)
Title: Sample Size Analysis for Psychological Networks and More
Description: An implementation of the sample size computation method for network
models proposed by Constantin et al. (2021) <doi:10.31234/osf.io/j5v7u>.
The implementation takes the form of a three-step recursive algorithm
designed to find an optimal sample size given a model specification and a
performance measure of interest. It starts with a Monte Carlo simulation
step for computing the performance measure and a statistic at various sample
sizes selected from an initial sample size range. It continues with a
monotone curve-fitting step for interpolating the statistic across the entire
sample size range. The final step employs stratified bootstrapping to quantify
the uncertainty around the fitted curve.
Author: Mihai Constantin [aut, cre]
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Diff between powerly versions 1.7.4 dated 2022-05-01 and 1.8.6 dated 2022-09-09
powerly-1.7.4/powerly/inst/assets/logo/logo.png |only powerly-1.7.4/powerly/inst/assets/method |only powerly-1.8.6/powerly/DESCRIPTION | 8 - powerly-1.8.6/powerly/MD5 | 30 +++--- powerly-1.8.6/powerly/NEWS.md | 106 +++++++++++++++++++----- powerly-1.8.6/powerly/R/GgmModel.R | 84 ++++++++++++++++--- powerly-1.8.6/powerly/R/logo.R | 2 powerly-1.8.6/powerly/README.md | 50 +++++++---- powerly-1.8.6/powerly/build/partial.rdb |binary powerly-1.8.6/powerly/inst/assets/logo/logo.txt | 8 - powerly-1.8.6/powerly/man/plot.Method.Rd | 21 ++-- powerly-1.8.6/powerly/man/plot.StepOne.Rd | 5 - powerly-1.8.6/powerly/man/plot.StepThree.Rd | 5 - powerly-1.8.6/powerly/man/plot.StepTwo.Rd | 5 - powerly-1.8.6/powerly/man/plot.Validation.Rd | 5 - powerly-1.8.6/powerly/man/powerly.Rd | 8 + powerly-1.8.6/powerly/tests/testthat/test-ggm.R | 8 + 17 files changed, 240 insertions(+), 105 deletions(-)
Title: Useful Functions for Cricket Analysis
Description: Helping to calculate cricket specific problems in a tidy & simple manner.
Author: Luke Lockley [aut, cre]
Maintainer: Luke Lockley <luke.lockley@btinternet.com>
Diff between howzatR versions 1.0.0 dated 2022-06-09 and 1.0.1 dated 2022-09-09
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 7 + R/bowling_basics.R | 195 +++++++++++++++++++---------------- README.md | 33 +++-- man/bowl_econ.Rd | 35 ++++-- man/howzatR-package.Rd | 38 ++++-- tests/testthat/test-bowling_basics.R | 18 ++- 8 files changed, 214 insertions(+), 134 deletions(-)
Title: Utilities for Updating R
Description: When updating major or minor R versions all packages should
be re-installed. The utilities in this package assist in getting a
user up-and-running again by installing all previously installed R
packages. The package uses 'renv' to install; immediately replenishing
your 'renv' package cache.
Author: Daniel D. Sjoberg [aut, cre, cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between updater versions 0.1.0 dated 2022-06-17 and 0.1.1 dated 2022-09-09
DESCRIPTION | 11 +- MD5 | 13 +- NEWS.md |only R/install_pkgs.R | 173 +++++++++++++++++++------------------- R/r_version.R | 2 R/utils.R | 218 ++++++++++++++++++++++++++----------------------- README.md | 12 +- man/updater-package.Rd | 9 ++ 8 files changed, 240 insertions(+), 198 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.4.7 dated 2022-08-24 and 1.4.8 dated 2022-09-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 2 +- R/dtree.R | 6 +++--- inst/app/tools/analysis/dtree_ui.R | 7 ++++++- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Manage the Life Cycle of your Package Functions
Description: Manage the life cycle of your exported functions with shared
conventions, documentation badges, and user-friendly deprecation
warnings.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut] ,
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between lifecycle versions 1.0.1 dated 2021-09-24 and 1.0.2 dated 2022-09-09
lifecycle-1.0.1/lifecycle/tests/testthat/_snaps/badge.new.md |only lifecycle-1.0.1/lifecycle/tests/testthat/_snaps/deprecated.new.md |only lifecycle-1.0.2/lifecycle/DESCRIPTION | 43 +-- lifecycle-1.0.2/lifecycle/MD5 | 126 ++++------ lifecycle-1.0.2/lifecycle/NAMESPACE | 3 lifecycle-1.0.2/lifecycle/NEWS.md | 39 ++- lifecycle-1.0.2/lifecycle/R/arg.R | 12 lifecycle-1.0.2/lifecycle/R/badge.R | 4 lifecycle-1.0.2/lifecycle/R/deprecated.R | 63 +++-- lifecycle-1.0.2/lifecycle/R/lifecycle-package.R | 6 lifecycle-1.0.2/lifecycle/R/lint.R | 12 lifecycle-1.0.2/lifecycle/R/signal.R | 14 - lifecycle-1.0.2/lifecycle/R/spec.R | 46 +-- lifecycle-1.0.2/lifecycle/R/utils.R | 4 lifecycle-1.0.2/lifecycle/R/verbosity.R | 1 lifecycle-1.0.2/lifecycle/R/warning.R | 42 --- lifecycle-1.0.2/lifecycle/README.md | 8 lifecycle-1.0.2/lifecycle/build/vignette.rds |binary lifecycle-1.0.2/lifecycle/inst/doc/communicate.R | 12 lifecycle-1.0.2/lifecycle/inst/doc/communicate.Rmd | 19 + lifecycle-1.0.2/lifecycle/inst/doc/communicate.html | 33 ++ lifecycle-1.0.2/lifecycle/inst/doc/manage.html | 14 - lifecycle-1.0.2/lifecycle/inst/doc/stages.Rmd | 2 lifecycle-1.0.2/lifecycle/inst/doc/stages.html | 26 +- lifecycle-1.0.2/lifecycle/man/badge.Rd | 6 lifecycle-1.0.2/lifecycle/man/deprecate_soft.Rd | 6 lifecycle-1.0.2/lifecycle/man/deprecated.Rd | 11 lifecycle-1.0.2/lifecycle/man/expect_deprecated.Rd | 6 lifecycle-1.0.2/lifecycle/man/figures/lifecycle-archived.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-defunct.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-deprecated.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-experimental.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-maturing.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-questioning.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-retired.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-soft-deprecated.svg | 22 + lifecycle-1.0.2/lifecycle/man/figures/lifecycle-stable.svg | 30 ++ lifecycle-1.0.2/lifecycle/man/figures/lifecycle-superseded.svg | 22 + lifecycle-1.0.2/lifecycle/man/last_lifecycle_warnings.Rd | 1 lifecycle-1.0.2/lifecycle/man/lifecycle-package.Rd | 6 lifecycle-1.0.2/lifecycle/man/signal_experimental.Rd | 2 lifecycle-1.0.2/lifecycle/man/signal_stage.Rd | 13 - lifecycle-1.0.2/lifecycle/man/verbosity.Rd | 11 lifecycle-1.0.2/lifecycle/tests/testthat/_snaps/badge.md | 5 lifecycle-1.0.2/lifecycle/tests/testthat/_snaps/deprecated.md | 53 +++- lifecycle-1.0.2/lifecycle/tests/testthat/_snaps/signal.md | 13 + lifecycle-1.0.2/lifecycle/tests/testthat/_snaps/spec.md | 59 ++-- lifecycle-1.0.2/lifecycle/tests/testthat/_snaps/warning.md | 12 lifecycle-1.0.2/lifecycle/tests/testthat/helper-lifecycle.R | 2 lifecycle-1.0.2/lifecycle/tests/testthat/test-deprecated.R | 24 + lifecycle-1.0.2/lifecycle/tests/testthat/test-lifecycle.R | 5 lifecycle-1.0.2/lifecycle/tests/testthat/test-signal.R | 9 lifecycle-1.0.2/lifecycle/tests/testthat/test-verbosity.R | 1 lifecycle-1.0.2/lifecycle/vignettes/communicate.Rmd | 19 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-archived.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-defunct.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-deprecated.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-experimental.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-maturing.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-questioning.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-retired.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-soft-deprecated.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-stable.svg | 30 ++ lifecycle-1.0.2/lifecycle/vignettes/figures/lifecycle-superseded.svg | 22 + lifecycle-1.0.2/lifecycle/vignettes/stages.Rmd | 2 65 files changed, 928 insertions(+), 323 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>
Diff between yuima versions 1.15.3 dated 2022-01-31 and 1.15.15 dated 2022-09-09
DESCRIPTION | 8 MD5 | 238 NAMESPACE | 3 NEWS | 22 R/IC.R | 9 R/RcppExports.R | 198 R/adaBayes.R | 331 - R/fitCIR.R |only R/lambdaPPR.R | 1861 +++---- R/mmfrac.R | 3 R/qgv.R | 3 R/qmle.R | 7955 +++++++++++++++---------------- R/qmleLevy.R | 2555 ++++++--- R/simCIR.R |only R/toLatex.R | 1011 ++- R/wllag.R | 2 R/yuima.R | 919 +-- R/yuima.data.R | 422 - build/partial.rdb |binary man/CPoint.Rd | 1 man/CarmaNoise.Rd | 1 man/DataPpr.Rd | 1 man/Diagnostic.Carma.Rd | 1 man/Diagnostic.Cogarch.Rd | 1 man/IC.Rd | 1 man/Integral.sde.rd | 1 man/Integrand.rd | 1 man/Intensity.PPR.Rd | 1 man/JBtest.Rd | 5 man/LawMethods.Rd | 1 man/LogSPX.Rd | 1 man/MWK151.Rd | 1 man/adaBayes.Rd | 1 man/asymptotic_term.Rd | 1 man/bns.test.Rd | 1 man/carma.info-class.Rd | 1 man/cce.Rd | 1 man/cce.factor.Rd | 1 man/cogarch.est.incr.rd | 1 man/cogarch.est.rd | 1 man/cogarch.info-class.Rd | 1 man/cogarchNoise.Rd | 1 man/fitCIR.Rd |only man/get.counting.data.Rd | 1 man/gmm.rd | 1 man/hyavar.Rd | 3 man/info.Map.Rd | 1 man/info.Ppr.Rd | 1 man/lambdaFromData.Rd | 1 man/lasso.Rd | 1 man/limiting.gamma.Rd | 1 man/llag.Rd | 1 man/llag.test.Rd | 1 man/lm.jumptest.Rd | 1 man/lseBayes.Rd | 1 man/mllag.Rd | 1 man/mmfrac.Rd | 1 man/model.parameter-class.Rd | 1 man/mpv.Rd | 1 man/noisy.sampling.Rd | 1 man/ntv.Rd | 1 man/param.Integral.rd | 1 man/param.Map.Rd | 1 man/phi.test.Rd | 1 man/poisson.random.sampling.Rd | 1 man/pz.test.Rd | 1 man/qgv.Rd | 1 man/qmle.Rd | 5 man/qmleLevy.Rd | 1 man/rconst.Rd | 1 man/rng.Rd | 3 man/setCarma.Rd | 1 man/setCharacteristic.Rd | 1 man/setCogarch.Rd | 1 man/setData.Rd | 1 man/setFunctional.Rd | 1 man/setHawkes.Rd | 1 man/setIntegral.Rd | 1 man/setLaw.Rd | 1 man/setMap.Rd | 1 man/setModel.Rd | 1 man/setPoisson.Rd | 1 man/setPpr.Rd | 1 man/setSampling.Rd | 1 man/setYuima.Rd | 1 man/simBmllag.Rd | 3 man/simCIR.Rd |only man/simFunctional.Rd | 1 man/simulate.Rd | 1 man/snr.Rd | 1 man/spectralcov.Rd | 1 man/subsampling.Rd | 1 man/toLatex.Rd | 1 man/variable.Integral.rd | 1 man/wllag.Rd | 3 man/ybook.Rd | 1 man/yuima-class.Rd | 1 man/yuima.CP.qmle-class.Rd | 1 man/yuima.Hawkes.Rd | 1 man/yuima.Integral-class.rd | 1 man/yuima.Map-class.Rd | 1 man/yuima.PPR.qmle-class.Rd | 1 man/yuima.Ppr.Rd | 1 man/yuima.ae-class.Rd | 1 man/yuima.carma-class.Rd | 1 man/yuima.carma.qmle-class.Rd | 1 man/yuima.characteristic-class.Rd | 1 man/yuima.cogarch-class.Rd | 1 man/yuima.data-class.Rd | 1 man/yuima.functional-class.Rd | 1 man/yuima.law-class.rd | 1 man/yuima.model-class.Rd | 1 man/yuima.multimodel.Rd | 1 man/yuima.poisson-class.Rd | 1 man/yuima.qmleLevy.incr-class.Rd | 1 man/yuima.sampling-class.Rd | 1 man/yuima.snr-class.Rd | 1 src/ae.cpp | 2 src/cce_functions.c | 18 src/euler.c | 4 src/pseudoLogLikCogarchIrregularGrid.cpp | 9 src/rng.c | 6 122 files changed, 8359 insertions(+), 7332 deletions(-)
More information about truncnormbayes at CRAN
Permanent link
Title: Efficient Monitoring of Global Biodiversity Portfolios
Description: Biodiversity areas, especially primary forest, serve a
multitude of functions for local economy, regional functionality of
the ecosystems as well as the global health of our planet. Recently,
adverse changes in human land use practices and climatic responses to
increased greenhouse gas emissions, put these biodiversity areas under
a variety of different threats. The present package helps to analyse a
number of biodiversity indicators based on freely available
geographical datasets. It supports computational efficient routines
that allow the analysis of potentially global biodiversity portfolios.
The primary use case of the package is to support evidence based
reporting of an organization's effort to protect biodiversity areas
under threat and to identify regions were intervention is most duly
needed.
Author: Darius A. Goergen [aut, cre],
Om Prakash Bhandari [aut]
Maintainer: Darius A. Goergen <darius2402@web.de>
Diff between mapme.biodiversity versions 0.2.0 dated 2022-08-23 and 0.2.1 dated 2022-09-09
DESCRIPTION | 7 +- MD5 | 93 ++++++++++++++++---------------- NEWS.md | 13 ++++ R/calc_active_fire_counts.R | 2 R/calc_active_fire_properties.R | 2 R/calc_indicator.R | 4 - R/calc_soilproperties.R | 8 +- R/calc_treecover_area.R | 4 - R/calc_treecover_area_and_emissions.R | 2 R/calc_treecoverloss_emissions.R | 2 R/calc_tri.R | 2 R/get_chirps.R | 2 R/get_esalandcover.R | 2 R/get_gfw_emissions.R | 4 - R/get_gfw_lossyear.R | 4 - R/get_gfw_treecover.R | 2 R/get_nasa_grace.R | 2 R/get_nasa_srtm.R | 3 - R/get_resource.R | 2 R/get_soilgrids.R | 12 ++-- R/get_worldclim.R | 4 - R/portfolio.R | 2 README.md | 12 ---- inst/WORDLIST |only inst/doc/userguide.Rmd | 8 +- inst/doc/userguide.html | 12 ++-- man/active_fire_counts.Rd | 2 man/active_fire_properties.Rd | 2 man/calc_indicators.Rd | 2 man/chirps.Rd | 2 man/dot-get_nasagrace_url.Rd | 4 - man/dot-get_single_indicator.Rd | 2 man/gfw_emissions.Rd | 2 man/gfw_lossyear.Rd | 2 man/init_portfolio.Rd | 2 man/soilgrids.Rd | 10 +-- man/soilproperties.Rd | 8 +- man/treecover_area.Rd | 4 - man/treecover_area_and_emissions.Rd | 2 man/treecoverloss_emissions.Rd | 2 man/tri.Rd | 2 man/worldclim.Rd | 2 tests/testthat/test-get_esalandcover.R | 16 +++++ tests/testthat/test-get_gfw_emissions.R | 17 +++++ tests/testthat/test-get_gfw_lossyear.R | 16 +++++ tests/testthat/test-get_gfw_treecover.R | 17 +++++ tests/testthat/test-get_nasa_srtm.R | 16 +++++ vignettes/userguide.Rmd | 8 +- 48 files changed, 217 insertions(+), 133 deletions(-)
More information about mapme.biodiversity at CRAN
Permanent link
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax. Can also form bootstrap confidence intervals by doing
bootstrapping only once and reusing the bootstrap estimates in all
subsequent computations. Supports bootstrap confidence intervals for
standardized (partially or completely) indirect effects, conditional
effects, and conditional indirect effects as described in Cheung (2009)
<doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Model fitting can be done by structural equation
modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.1.4.0 dated 2022-09-06 and 0.1.4.3 dated 2022-09-09
DESCRIPTION | 6 - MD5 | 56 +++++----- NEWS.md | 7 + README.md | 17 ++- inst/CITATION | 4 inst/doc/do_boot.html | 50 ++++---- inst/doc/manymome.html | 4 inst/doc/med_lav.html | 4 inst/doc/med_lm.html | 4 inst/doc/mod_levels.html | 4 inst/doc/mome_lm.html | 4 tests/testthat/test_boot2est_implied.R | 6 - tests/testthat/test_boot2est_implied_lv.R | 2 tests/testthat/test_cond_indirect_effects_lavaan_do_boot.R | 4 tests/testthat/test_cond_indirect_effects_lavaan_do_boot_missing.R | 4 tests/testthat/test_cond_indirect_effects_lm_do_boot.R | 4 tests/testthat/test_cond_indirect_lavaan.R | 6 - tests/testthat/test_cond_indirect_lavaan_kway.R | 4 tests/testthat/test_cond_indirect_lm.R | 8 - tests/testthat/test_cond_indirect_lm_kway.R | 4 tests/testthat/test_cond_indirect_math.R | 24 ++-- tests/testthat/test_fit2boot_out_do_boot.R | 2 tests/testthat/test_fit2boot_out_do_boot_missing.R | 2 tests/testthat/test_indirect_simple_med_latent.R | 2 tests/testthat/test_indirect_simple_med_latent_missing.R | 2 tests/testthat/test_lm2boot_out.R | 6 - tests/testthat/test_lm2list.R | 4 tests/testthat/test_lm2ptable.R | 2 tests/testthat/test_summary_lm_list.R | 4 29 files changed, 134 insertions(+), 116 deletions(-)
Title: Spatially Explicit Capture-Recapture by Inverse Prediction
Description: Estimates the density of a spatially distributed animal population
sampled with an array of passive detectors, such as traps. Models incorporating
distance-dependent detection are fitted by simulation and inverse prediction
as proposed by Efford (2004) <doi:10.1111/j.0030-1299.2004.13043.x>.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between ipsecr versions 1.2.0 dated 2022-08-29 and 1.3.0 dated 2022-09-09
ipsecr-1.2.0/ipsecr/src/CH.cpp |only ipsecr-1.2.0/ipsecr/tests/testthat/test-misc.R |only ipsecr-1.3.0/ipsecr/DESCRIPTION | 8 - ipsecr-1.3.0/ipsecr/MD5 | 55 ++++++------- ipsecr-1.3.0/ipsecr/NAMESPACE | 3 ipsecr-1.3.0/ipsecr/NEWS | 13 +++ ipsecr-1.3.0/ipsecr/R/RcppExports.R | 8 - ipsecr-1.3.0/ipsecr/R/ipsecr.fit.R | 84 +++++++++++--------- ipsecr-1.3.0/ipsecr/R/print.ipsecr.R | 1 ipsecr-1.3.0/ipsecr/R/simCH.R | 62 +++++++++----- ipsecr-1.3.0/ipsecr/R/simpop.R | 2 ipsecr-1.3.0/ipsecr/R/summary.ipsecr.R | 7 - ipsecr-1.3.0/ipsecr/R/utility.R | 27 ------ ipsecr-1.3.0/ipsecr/data/ipsecrdemo.RData |binary ipsecr-1.3.0/ipsecr/inst/doc/ipsecr-vignette.R | 17 ++-- ipsecr-1.3.0/ipsecr/inst/doc/ipsecr-vignette.Rmd | 55 +++++++------ ipsecr-1.3.0/ipsecr/inst/doc/ipsecr-vignette.pdf |binary ipsecr-1.3.0/ipsecr/inst/example/fittedmodels.RData |binary ipsecr-1.3.0/ipsecr/inst/example/ip.Fr.RData |binary ipsecr-1.3.0/ipsecr/man/ipsecr-internal.Rd | 7 - ipsecr-1.3.0/ipsecr/man/ipsecr-package.Rd | 4 ipsecr-1.3.0/ipsecr/man/makeNewdata.ipsecr.Rd | 2 ipsecr-1.3.0/ipsecr/src/RcppExports.cpp | 39 ++++----- ipsecr-1.3.0/ipsecr/src/armaCH.cpp |only ipsecr-1.3.0/ipsecr/src/pop.cpp | 4 ipsecr-1.3.0/ipsecr/tests/testthat/test-ipsecr.R | 30 +++++-- ipsecr-1.3.0/ipsecr/tests/testthat/test-nontarget.R | 77 ++++++++++++++---- ipsecr-1.3.0/ipsecr/tests/testthat/test-proxy.R | 5 - ipsecr-1.3.0/ipsecr/tests/testthat/test-simCH.R |only ipsecr-1.3.0/ipsecr/tests/testthat/test-simpop.R |only ipsecr-1.3.0/ipsecr/vignettes/ipsecr-vignette.Rmd | 55 +++++++------ 31 files changed, 332 insertions(+), 233 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 2.5 dated 2022-09-05 and 2.6 dated 2022-09-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary src/disjonctif.h | 4 ++-- 7 files changed, 11 insertions(+), 11 deletions(-)
Title: Visualising Statistical Models using Dynamic Nomograms
Description: Demonstrate the results of a statistical model object as a dynamic nomogram in an RStudio panel or web browser. The package provides two generics functions: DynNom, which display statistical model objects as a dynamic nomogram; DNbuilder, which builds required scripts to publish a dynamic nomogram on a web server such as the <https://www.shinyapps.io/>. Current version of 'DynNom' supports stats::lm, stats::glm, survival::coxph, rms::ols, rms::Glm, rms::lrm, rms::cph, mgcv::gam and gam::gam model objects.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <amir.jalali@ul.ie>
Diff between DynNom versions 5.0.1 dated 2019-06-20 and 5.0.2 dated 2022-09-09
DESCRIPTION | 9 - MD5 | 6 - man/DNbuilder.Rd | 282 +++++++++++++++++++++++++++--------------------------- man/DynNom.Rd | 284 +++++++++++++++++++++++++++---------------------------- 4 files changed, 290 insertions(+), 291 deletions(-)
Title: Reproducible Reports in Psychology
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Knitr'/'Latex' integration within *.Rnw files.
Author: Ian G Mackenzie [cre, aut],
Carolin Dudschig [aut]
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between psychReport versions 3.0.1 dated 2021-05-06 and 3.0.2 dated 2022-09-09
DESCRIPTION | 8 ++--- LICENSE | 2 - MD5 | 18 +++++------ R/ttest.R | 81 +++++++++++++++------------------------------------- R/utils.R | 15 ++++----- man/ciStrT.Rd | 21 +++---------- man/meanStrT.Rd | 20 +++--------- man/printTable.Rd | 3 - man/statStrT.Rd | 20 +++--------- man/tValueString.Rd | 20 +++--------- 10 files changed, 70 insertions(+), 138 deletions(-)
Title: Penalized Inverse-Variance Weighted Estimator for Mendelian
Randomization
Description: The penalized inverse-variance weighted (pIVW) estimator is a Mendelian randomization method for estimating the causal effect of an exposure variable on an outcome of interest based on summary-level GWAS data. The pIVW estimator accounts for weak instruments and balanced horizontal pleiotropy simultaneously. See Xu S., Wang P., Fung W.K. and Liu Z. (2022) <doi:10.1111/biom.13732>.
Author: Siqi Xu
Maintainer: Siqi Xu <sqxu@hku.hk>
Diff between mr.pivw versions 0.1.0 dated 2022-08-16 and 0.1.1 dated 2022-09-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mr.pIVW.R | 19 ++++++++++++++++++- man/pIVW.Rd | 9 +++++---- 4 files changed, 29 insertions(+), 11 deletions(-)
More information about EvidenceSynthesis at CRAN
Permanent link
Title: Area Correction Methods
Description: Post-construction fatality monitoring studies at wind facilities are based on data from searches for bird and bat carcasses in plots beneath turbines. Bird and bat carcasses can fall outside of the search plot. Bird and bat carcasses from wind turbines often fall outside of the searched area. To compensate, area correction (AC) estimations are calculated to estimate the percentage of fatalities that fall within the searched area versus those that fall outside of it. This package provides two likelihood based methods and one physics based method (Hull and Muir (2010) <doi:10.1080/14486563.2010.9725253>, Huso and Dalthorp (2014) <doi:10.1002/jwmg.663>) to estimate the carcass fall distribution. There are also functions for calculating the proportion of area searched within one unit annuli, log logistic distribution functions, and truncated distribution functions.
Author: Paul Rabie [aut],
Daniel Riser-Espinoza [aut, cre],
Trent McDonald [ctb]
Maintainer: Daniel Riser-Espinoza <despinoza@west-inc.com>
Diff between windAC versions 1.2.8 dated 2022-04-24 and 1.2.9 dated 2022-09-09
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/dllog.R | 7 ------- R/getDistanceProbability.R | 10 ---------- R/getStartValue.R | 7 ------- R/pllog.R | 9 --------- R/qllog.R | 8 -------- R/weightFun.R | 11 ----------- R/weightedDistribution.R | 9 --------- R/weightedLikelihood.R | 12 ++---------- 10 files changed, 16 insertions(+), 85 deletions(-)
Title: Tools for Manipulating Gas Exchange Data
Description: Set of tools for manipulating gas exchange data from cardiopulmonary exercise testing.
Author: Felipe Mattioni Maturana [aut, cre]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between whippr versions 0.1.0 dated 2022-03-09 and 0.1.2 dated 2022-09-09
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 9 +++++ R/averages.R | 2 + R/incremental.R | 2 + R/interpolate.R | 2 + R/kinetics.R | 2 + R/max.R | 5 ++- R/outliers.R | 2 + R/read-data.R | 65 +++++++++++++++++++++++++++++++++++-------- README.md | 38 +++++++++++-------------- man/detect_outliers.Rd | 2 + man/incremental_normalize.Rd | 2 + man/interpolate.Rd | 2 + man/perform_average.Rd | 2 + man/perform_max.Rd | 3 + man/read_data.Rd | 5 +-- man/vo2_kinetics.Rd | 2 + man/vo2_max.Rd | 2 + man/whippr-package.Rd | 2 - 21 files changed, 138 insertions(+), 60 deletions(-)
More information about TSdeeplearning at CRAN
Permanent link
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the mixed-model-equations-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.1.8 dated 2022-09-06 and 4.1.9 dated 2022-09-09
DESCRIPTION | 8 ++-- MD5 | 60 +++++++++++++++--------------- inst/doc/v1.sommer.quick.start.pdf |binary inst/doc/v2.sommer.changes.and.faqs.pdf |binary inst/doc/v3.sommer.qg.R | 6 +-- inst/doc/v3.sommer.qg.Rmd | 6 +-- inst/doc/v3.sommer.qg.pdf |binary inst/doc/v4.sommer.gxe.R | 14 +++---- inst/doc/v4.sommer.gxe.Rmd | 14 +++---- inst/doc/v4.sommer.gxe.pdf |binary inst/doc/v5.sommer.vs.lme4.pdf |binary inst/doc/v6.sommer.spatial.pdf |binary man/DT_cornhybrids.Rd | 6 +-- man/DT_cpdata.Rd | 2 - man/DT_gryphon.Rd | 2 - man/DT_halfdiallel.Rd | 2 - man/DT_polyploid.Rd | 2 - man/DT_rice.Rd | 2 - man/DT_technow.Rd | 4 +- man/DT_wheat.Rd | 2 - man/fitted_mmec.Rd | 6 +-- man/fitted_mmer.Rd | 4 +- man/spl2Dc.Rd | 2 - vignettes/v1.sommer.quick.start.html | 12 +++--- vignettes/v2.sommer.changes.and.faqs.html | 4 +- vignettes/v3.sommer.qg.Rmd | 6 +-- vignettes/v3.sommer.qg.html | 10 ++--- vignettes/v4.sommer.gxe.Rmd | 14 +++---- vignettes/v4.sommer.gxe.html | 18 ++++----- vignettes/v5.sommer.vs.lme4.html | 4 +- vignettes/v6.sommer.spatial.html | 4 +- 31 files changed, 107 insertions(+), 107 deletions(-)
Title: Datasets and Functions for Reproducing Meta-Analyses
Description: Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise.
It contains all the data and functions to reproduce the analysis.
"Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis".
Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieß (2020) <doi:10.1249/MSS.0000000000002506>.
Author: Felipe Mattioni Maturana [aut, cre, cph]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between metabolic versions 0.1.0 dated 2020-09-25 and 0.1.1 dated 2022-09-09
DESCRIPTION | 8 +-- MD5 | 21 ++++----- NEWS.md | 4 + R/data.R | 4 - R/plot.R | 12 +++-- README.md | 91 ++++++++++++++++++++++------------------ build |only inst/CITATION | 2 man/metabolic-package.Rd | 7 --- man/metabolic_gofer.Rd | 2 man/metabolic_meta.Rd | 2 man/plot_small_study_effects.Rd | 12 +++-- 12 files changed, 92 insertions(+), 73 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre]
,
Grigorios Papageorgiou [aut],
Pedro Miranda Afonso [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.2-8 dated 2022-07-05 and 0.3-0 dated 2022-09-09
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------- NEWS.md | 13 +++++++ R/basic_methods.R | 1 R/help_functions.R | 7 +++ R/jm.R | 13 ++++--- R/jm_fit.R | 5 +- R/predict_funs.R | 9 +++- man/JMbayes2.Rd | 4 +- man/jm.Rd | 17 ++++++--- src/JMbayes2_FE.h | 43 ++++++++++++++++++----- src/JMbayes2_Funs.h | 9 ++-- src/JMbayes2_RE.h | 34 +++++++++--------- src/mcmc_fit.cpp | 95 ++++++++++++++++++++++++++-------------------------- 14 files changed, 173 insertions(+), 111 deletions(-)
Title: Acquiring and Analyzing Baseball Data
Description: Provides numerous utilities for acquiring and analyzing
baseball data from online sources such as Baseball Reference <https://www.baseball-reference.com/>,
FanGraphs <https://www.fangraphs.com/>, and the MLB Stats API <https://www.mlb.com/>.
Author: Bill Petti [aut],
Saiem Gilani [aut, cre],
Ben Baumer [ctb],
Ben Dilday [ctb],
Robert Frey [ctb],
Camden Kay [ctb]
Maintainer: Saiem Gilani <saiem.gilani@gmail.com>
Diff between baseballr versions 1.2.0 dated 2022-04-25 and 1.3.0 dated 2022-09-09
DESCRIPTION | 26 - MD5 | 63 ++-- NAMESPACE | 4 NEWS.md | 8 R/fg_team_batter.R |only R/fg_team_pitcher.R |only R/mlb_player_game_stats.R | 4 R/sptrc_league_payrolls.R |only R/sptrc_team_active_payroll.R |only README.md | 118 ++++--- build/vignette.rds |binary inst/doc/baseballr.Rmd | 6 inst/doc/baseballr.html | 317 ++++++++++++++++++--- inst/doc/ncaa_scraping.html | 310 +++++++++++++++++--- inst/doc/plotting_statcast.html | 212 +++++++++++++- inst/doc/using_statcast_pitch_data.R |only inst/doc/using_statcast_pitch_data.Rmd |only inst/doc/using_statcast_pitch_data.html |only man/baseballr-package.Rd | 5 man/bref.Rd | 84 +++-- man/chadwick.Rd | 58 ++- man/fangraphs.Rd | 128 ++++---- man/fg_team_batter.Rd |only man/fg_team_pitcher.Rd |only man/metrics.Rd | 106 +++---- man/mlb.Rd | 104 +++--- man/mlb_award.Rd | 32 +- man/ncaa.Rd | 32 +- man/sptrc_league_payrolls.Rd |only man/sptrc_team_active_payroll.Rd |only man/statcast.Rd | 138 ++++----- tests/testthat/test-fg_pitcher_leaders.R | 362 +++++++++++++++++++----- tests/testthat/test-fg_team_batter.R |only tests/testthat/test-mlb_draft_latest.R | 4 tests/testthat/test-mlb_game_status_codes.R | 3 tests/testthat/test-sptrc_league_payrolls.R |only tests/testthat/test-sptrc_team_active_payroll.R |only tests/testthat/test-statcast_leaderboards.R | 24 + vignettes/baseballr.Rmd | 6 vignettes/using_statcast_pitch_data.Rmd |only 40 files changed, 1601 insertions(+), 553 deletions(-)
Title: The R WINS Package
Description: Calculate the win statistics (win ratio, net benefit and win odds) for prioritized multiple endpoints, plot the win statistics and win proportions over study time if at least one time-to-event endpoint is analyzed, and simulate datasets with dependent endpoints. The package can handle any type of outcomes (continuous, ordinal, binary, time-to-event) and allow users to perform stratified analysis and inverse probability of censoring weighting (IPCW) analysis.
Author: Ying Cui [aut, cre],
Bo Huang [aut]
Maintainer: Ying Cui <cuiyingbeicheng@gmail.com>
Diff between WINS versions 1.2 dated 2022-07-18 and 1.3 dated 2022-09-09
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/covipcw.adjusted.KL.R | 7 +++++-- R/ipcw.adjusted.KL.R | 7 +++++-- R/win.stat.R | 9 +++++++-- inst/doc/vignette.pdf |binary man/partition_t.plot.Rd | 2 +- man/stat_t.plot.Rd | 2 +- man/win.stat.Rd | 2 +- 9 files changed, 31 insertions(+), 20 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values
in univariate time series.
Offers several imputation functions
and missing data plots.
Available imputation algorithms include:
'Mean', 'LOCF', 'Interpolation',
'Moving Average', 'Seasonal Decomposition',
'Kalman Smoothing on Structural Time Series models',
'Kalman Smoothing on ARIMA models'. Published in Moritz and Bartz-Beielstein (2017)
<doi:10.32614/RJ-2017-009>.
Author: Steffen Moritz [aut, cre, cph]
,
Sebastian Gatscha [aut],
Earo Wang [ctb] ,
Ron Hause [ctb]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 3.2 dated 2021-01-16 and 3.3 dated 2022-09-09
imputeTS-3.2/imputeTS/R/ggplot_na_intervals.R |only imputeTS-3.2/imputeTS/tests/testthat/test-ggplot_na_intervals.R |only imputeTS-3.3/imputeTS/DESCRIPTION | 24 - imputeTS-3.3/imputeTS/MD5 | 128 ++--- imputeTS-3.3/imputeTS/NAMESPACE | 4 imputeTS-3.3/imputeTS/NEWS.md | 100 ++-- imputeTS-3.3/imputeTS/R/deprecated_defunct.R | 34 + imputeTS-3.3/imputeTS/R/ggplot_na_distribution.R | 10 imputeTS-3.3/imputeTS/R/ggplot_na_distribution2.R |only imputeTS-3.3/imputeTS/R/ggplot_na_gapsize.R | 26 - imputeTS-3.3/imputeTS/R/ggplot_na_imputations.R | 18 imputeTS-3.3/imputeTS/R/imputeTS-package.R | 4 imputeTS-3.3/imputeTS/R/internal_algorithm_interface.R | 8 imputeTS-3.3/imputeTS/R/na_interpolation.R | 84 ++- imputeTS-3.3/imputeTS/R/na_kalman.R | 65 +- imputeTS-3.3/imputeTS/R/na_locf.R | 92 ++- imputeTS-3.3/imputeTS/R/na_ma.R | 35 - imputeTS-3.3/imputeTS/R/na_mean.R | 47 +- imputeTS-3.3/imputeTS/R/na_random.R | 59 +- imputeTS-3.3/imputeTS/R/na_remove.R | 22 imputeTS-3.3/imputeTS/R/na_replace.R | 39 - imputeTS-3.3/imputeTS/R/na_seadec.R | 71 ++- imputeTS-3.3/imputeTS/R/na_seasplit.R | 53 +- imputeTS-3.3/imputeTS/R/statsNA.R | 4 imputeTS-3.3/imputeTS/R/tsAirgap.R | 4 imputeTS-3.3/imputeTS/R/tsAirgapComplete.R | 4 imputeTS-3.3/imputeTS/README.md | 43 + imputeTS-3.3/imputeTS/build/partial.rdb |binary imputeTS-3.3/imputeTS/build/vignette.rds |binary imputeTS-3.3/imputeTS/inst/doc/Cheat_Sheet_imputeTS.pdf |binary imputeTS-3.3/imputeTS/inst/doc/gallery_visualizations.R | 20 imputeTS-3.3/imputeTS/inst/doc/gallery_visualizations.Rmd | 30 - imputeTS-3.3/imputeTS/inst/doc/gallery_visualizations.html | 235 ++++++---- imputeTS-3.3/imputeTS/inst/doc/imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx | 12 imputeTS-3.3/imputeTS/inst/doc/imputeTS-Time-Series-Missing-Value-Imputation-in-R.pdf |binary imputeTS-3.3/imputeTS/man/ggplot_na_distribution.Rd | 10 imputeTS-3.3/imputeTS/man/ggplot_na_distribution2.Rd |only imputeTS-3.3/imputeTS/man/ggplot_na_gapsize.Rd | 14 imputeTS-3.3/imputeTS/man/ggplot_na_imputations.Rd | 6 imputeTS-3.3/imputeTS/man/ggplot_na_intervals.Rd | 153 ------ imputeTS-3.3/imputeTS/man/imputeTS-package.Rd | 16 imputeTS-3.3/imputeTS/man/na.kalman.Rd | 8 imputeTS-3.3/imputeTS/man/na_interpolation.Rd | 32 + imputeTS-3.3/imputeTS/man/na_kalman.Rd | 9 imputeTS-3.3/imputeTS/man/na_locf.Rd | 27 - imputeTS-3.3/imputeTS/man/na_ma.Rd | 1 imputeTS-3.3/imputeTS/man/na_mean.Rd | 13 imputeTS-3.3/imputeTS/man/na_remove.Rd | 1 imputeTS-3.3/imputeTS/man/na_replace.Rd | 1 imputeTS-3.3/imputeTS/man/na_seadec.Rd | 31 + imputeTS-3.3/imputeTS/man/na_seasplit.Rd | 1 imputeTS-3.3/imputeTS/man/plotNA.distributionBar.Rd | 4 imputeTS-3.3/imputeTS/man/statsNA.Rd | 2 imputeTS-3.3/imputeTS/man/tsAirgap.Rd | 4 imputeTS-3.3/imputeTS/man/tsAirgapComplete.Rd | 4 imputeTS-3.3/imputeTS/src/RcppExports.cpp | 5 imputeTS-3.3/imputeTS/tests/testthat/test-apply_base_algorithm.R | 2 imputeTS-3.3/imputeTS/tests/testthat/test-error_handling.R |only imputeTS-3.3/imputeTS/tests/testthat/test-ggplot_na_distribution2.R |only imputeTS-3.3/imputeTS/tests/testthat/test-na_interpolation.R | 10 imputeTS-3.3/imputeTS/tests/testthat/test-na_kalman.R | 9 imputeTS-3.3/imputeTS/tests/testthat/test-na_locf.R | 4 imputeTS-3.3/imputeTS/tests/testthat/test-na_ma.R | 4 imputeTS-3.3/imputeTS/tests/testthat/test-na_mean.R | 2 imputeTS-3.3/imputeTS/tests/testthat/test-na_seadec.R | 7 imputeTS-3.3/imputeTS/tests/testthat/test-na_seasplit.R | 2 imputeTS-3.3/imputeTS/vignettes/gallery_visualizations.Rmd | 30 - imputeTS-3.3/imputeTS/vignettes/imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx | 12 68 files changed, 993 insertions(+), 706 deletions(-)