Title: Uncertainty Analysis for Species Distribution Models
Description: This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between usdm versions 1.1-18 dated 2017-06-25 and 2.1-6 dated 2023-07-06
usdm-1.1-18/usdm/inst/external/predictors.grd |only usdm-1.1-18/usdm/inst/external/predictors.gri |only usdm-1.1-18/usdm/inst/external/spain.grd |only usdm-1.1-18/usdm/inst/external/spain.gri |only usdm-2.1-6/usdm/DESCRIPTION | 19 usdm-2.1-6/usdm/MD5 | 48 - usdm-2.1-6/usdm/NAMESPACE | 8 usdm-2.1-6/usdm/R/AAAClasses.R | 57 - usdm-2.1-6/usdm/R/Variogram.R | 161 ++- usdm-2.1-6/usdm/R/exclude.R | 131 ++ usdm-2.1-6/usdm/R/lisa.R | 1136 ++++++++++++++++---------- usdm-2.1-6/usdm/R/plot.R | 443 ++++++---- usdm-2.1-6/usdm/R/speciesLisa.R | 168 ++- usdm-2.1-6/usdm/R/vif.R | 787 +++++++++++++++--- usdm-2.1-6/usdm/README |only usdm-2.1-6/usdm/README.md |only usdm-2.1-6/usdm/inst/external/predictors.tif |only usdm-2.1-6/usdm/inst/external/spain.tif |only usdm-2.1-6/usdm/man/RasterVariogram-class.Rd | 5 usdm-2.1-6/usdm/man/VIF-class.Rd | 80 - usdm-2.1-6/usdm/man/Variogram.Rd | 12 usdm-2.1-6/usdm/man/exclude.Rd | 10 usdm-2.1-6/usdm/man/lisa.Rd | 13 usdm-2.1-6/usdm/man/plot.RasterVariogram.Rd | 133 +-- usdm-2.1-6/usdm/man/plot.speciesLisa.Rd | 168 +-- usdm-2.1-6/usdm/man/speciesLISA-class.Rd | 82 - usdm-2.1-6/usdm/man/speciesLisa.Rd | 21 usdm-2.1-6/usdm/man/usdm-package.Rd | 4 usdm-2.1-6/usdm/man/vif.Rd | 44 - 29 files changed, 2403 insertions(+), 1127 deletions(-)
Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context [Dias et al. (2022) <doi:10.1007/s00122-022-04041-y>]. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] ,
Kaio Dias [aut, cph] ,
Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>
Diff between ProbBreed versions 1.0.1 dated 2023-06-26 and 1.0.2 dated 2023-07-06
DESCRIPTION | 6 - MD5 | 10 +- NAMESPACE | 1 R/prob_sup.R | 214 +++++++++++++++++++++++++++++------------------------------ R/recod.R |only README.md | 13 +++ man/recod.Rd |only 7 files changed, 130 insertions(+), 114 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.5.1 dated 2023-05-17 and 0.6.0 dated 2023-07-06
DESCRIPTION | 10 MD5 | 74 NAMESPACE | 14 NEWS.md | 28 R/as_bootstrap_design.R | 76 R/as_data_frame_with_weights.R | 30 R/as_jackknife_design.R |only R/calibrate_to_estimate.R | 36 R/calibrate_to_sample.R | 36 R/database-helpers.R |only R/generalized_bootstrap.R | 217 ++ R/quadratic_forms.R | 199 -- R/quadratic_forms_of_survey_design_objects.R | 19 R/redistribute_weights.R | 65 R/svrep-package.R | 8 R/variance-estimators.R |only README.md | 73 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/bootstrap-replicates.html | 589 +++---- inst/doc/nonresponse-adjustments.Rmd | 2 inst/doc/nonresponse-adjustments.html | 460 ++--- inst/doc/sample-based-calibration.html | 802 ++++----- inst/doc/two-phase-sampling.html | 841 +++++----- man/as_bootstrap_design.Rd | 33 man/as_data_frame_with_weights.Rd | 7 man/as_gen_boot_design.Rd | 114 - man/as_random_group_jackknife_design.Rd |only man/get_design_quad_form.Rd | 98 - man/getvars.Rd |only man/make_ppswor_approx_matrix.Rd | 3 man/make_quad_form_matrix.Rd | 121 - man/make_srswor_matrix.Rd | 2 man/make_twophase_quad_form.Rd | 2 man/variance-estimators.Rd |only tests/testthat/test-as_bootstrap_design.R | 15 tests/testthat/test-database-backed-designs.R |only tests/testthat/test-quadratic-forms.R | 63 tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 12 tests/testthat/test-random-group-jackknife.R |only vignettes/nonresponse-adjustments.Rmd | 2 42 files changed, 2107 insertions(+), 1948 deletions(-)
Title: 'optimx' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the R Optimization Infrastructure ('ROI') package
with the 'optimx' package.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.optimx versions 1.0-0 dated 2020-08-29 and 1.0-1 dated 2023-07-06
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- man/Example_01.Rd | 1 + 3 files changed, 12 insertions(+), 10 deletions(-)
More information about ROI.plugin.optimx at CRAN
Permanent link
Title: 'ECOS' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the Embedded Conic Solver ('ECOS') for solving conic optimization problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.ecos versions 1.0-0 dated 2020-08-30 and 1.0-2 dated 2023-07-06
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- R/plugin.R | 4 ---- man/Example_01.Rd | 1 + man/Example_02.Rd | 1 + man/Example_03.Rd | 1 + 6 files changed, 17 insertions(+), 17 deletions(-)
More information about ROI.plugin.ecos at CRAN
Permanent link
Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Functions for
analysis of resulting respirometry data are also provided. This package
provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 1.3.0 dated 2021-03-05 and 1.4.0 dated 2023-07-06
DESCRIPTION | 11 +++++------ MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS | 22 ++++++++++++++-------- R/Q10.R | 21 ++++++--------------- R/adj_by_temp.R |only R/calc_E.R | 4 ++-- R/calc_MO2.R | 7 ++++++- man/Q10.Rd | 21 ++++++--------------- man/adj_by_temp.Rd |only man/calc_E.Rd | 4 ++-- man/calc_MO2.Rd | 7 ++++++- 12 files changed, 59 insertions(+), 59 deletions(-)
Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] ,
Cameron Smith [aut] ,
George Sugihara [aut, ccp] ,
Ethan Deyle [aut] ,
Erik Saberski [ctb] ,
Hao Ye [ctb] ,
The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>
Diff between rEDM versions 1.14.0 dated 2023-01-09 and 1.14.3 dated 2023-07-06
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++-------- NEWS.md | 3 +- R/apps/Embedding.R |only build/vignette.rds |binary src/Makevars | 10 ++++++-- src/Makevars.win | 4 +-- src/cppEDM/src/CCM.cc | 7 ------ src/cppEDM/src/Parameter.cc | 7 ------ src/cppEDM/src/Simplex.cc | 2 - vignettes/rEDM-tutorial.html | 50 ++++++++++++++++++++++++------------------- 11 files changed, 56 insertions(+), 54 deletions(-)
Title: Depth Measures in Multivariate, Regression and Functional
Settings
Description: Tools to compute depth measures and implementations of related
tasks such as outlier detection, data exploration and
classification of multivariate, regression and functional data.
Author: Pieter Segaert [aut],
Mia Hubert [aut],
Peter Rousseeuw [aut],
Jakob Raymaekers [aut, cre],
Kaveh Vakili [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between mrfDepth versions 1.0.13 dated 2020-08-26 and 1.0.14 dated 2023-07-06
DESCRIPTION | 12 ++++---- MD5 | 26 +++++++++--------- NAMESPACE | 2 - src/AdjOutlyingness.cpp | 1 src/HalfSpaceDepth2D.f | 2 - src/LinAlg.f | 69 +++++++++++++++++++++++++++++++----------------- src/Makevars | 4 +- src/Makevars.win | 2 - src/Outlyingness.cpp | 1 src/auxyl.cpp | 1 src/dirOutl.h | 7 ---- src/hdepthND.cpp | 1 src/mc.cpp | 1 src/medcouple.cpp | 1 14 files changed, 76 insertions(+), 54 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.2.2 dated 2023-06-07 and 4.2.4 dated 2023-07-06
ChangeLog | 4 DESCRIPTION | 8 MD5 | 14 R/aaa.R | 6 R/equalProj.R | 2 inst/doc/browseMovebank.html | 751 ++++++++------------- inst/doc/move.html | 1414 +++++++++++++++-------------------------- tests/testthat/test.corridor.R | 2 8 files changed, 842 insertions(+), 1359 deletions(-)
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Hugues Pecout [ctb],
Ronan Ysebaert [ctb],
Ian Fellows [cph] ,
Jim Lemon [cph] ,
Florian Zenoni [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 0.6.1 dated 2022-12-12 and 0.7.0 dated 2023-07-06
DESCRIPTION | 8 MD5 | 190 ++++----- NAMESPACE | 3 NEWS.md | 24 + R/mf_annotation.R | 365 ++++++++--------- R/mf_arrow.R | 16 R/mf_background.R | 8 R/mf_base.R | 17 R/mf_choro.R | 22 - R/mf_credits.R | 6 R/mf_doc_utils.R | 32 - R/mf_export.R | 97 ++-- R/mf_get_breaks.R | 52 +- R/mf_get_links.R | 2 R/mf_get_pal.R | 10 R/mf_get_ratio.R | 50 +- R/mf_grad.R | 23 - R/mf_graticule.R |only R/mf_init.R | 24 - R/mf_inset.R | 10 R/mf_label.R | 38 + R/mf_labels_utils.R | 8 R/mf_layout.R | 5 R/mf_leg_c.R | 6 R/mf_leg_gl.R | 6 R/mf_leg_p.R | 8 R/mf_leg_p_utils.R | 5 R/mf_leg_pl.R | 5 R/mf_leg_s.R | 2 R/mf_leg_s_utils.R | 2 R/mf_leg_t.R | 8 R/mf_legend.R | 7 R/mf_map.R | 164 +++++-- R/mf_map_utils.R | 63 ++- R/mf_pkg_utils.R | 188 ++++++++- R/mf_prop.R | 6 R/mf_prop_choro.R | 22 - R/mf_prop_typo.R | 7 R/mf_raster.R | 49 +- R/mf_scale.R | 17 R/mf_symb.R | 12 R/mf_symb_choro.R | 24 - R/mf_theme.R | 278 ++++--------- R/mf_title.R | 21 - R/mf_typo.R | 7 R/mf_worldmap.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/mapsf.R | 43 -- inst/doc/mapsf.Rmd | 47 -- inst/doc/mapsf.html | 704 ++++++++++++++++++---------------- inst/tinytest/test_annotation.R | 6 inst/tinytest/test_arrow.R | 7 inst/tinytest/test_background.R | 6 inst/tinytest/test_breaks.R | 8 inst/tinytest/test_credits.R | 2 inst/tinytest/test_doc.R | 2 inst/tinytest/test_export.R | 18 inst/tinytest/test_get_links.R | 20 inst/tinytest/test_get_ratio.R | 13 inst/tinytest/test_graticule.R |only inst/tinytest/test_init.R | 8 inst/tinytest/test_inset.R | 5 inst/tinytest/test_label.R | 3 inst/tinytest/test_layout.R | 1 inst/tinytest/test_legend.R | 49 +- inst/tinytest/test_map.R | 8 inst/tinytest/test_map_g.R | 13 inst/tinytest/test_map_p.R | 1 inst/tinytest/test_map_pc.R | 10 inst/tinytest/test_map_pt.R | 7 inst/tinytest/test_map_s.R | 3 inst/tinytest/test_map_t.R | 2 inst/tinytest/test_pal.R | 7 inst/tinytest/test_pkg_utils.R |only inst/tinytest/test_raster.R | 4 inst/tinytest/test_scale.R | 7 inst/tinytest/test_theme.R | 1 man/mf_background.Rd | 2 man/mf_base.Rd | 13 man/mf_choro.Rd | 10 man/mf_export.Rd | 2 man/mf_get_pal.Rd | 10 man/mf_get_ratio.Rd | 2 man/mf_grad.Rd | 10 man/mf_graticule.Rd |only man/mf_init.Rd | 3 man/mf_inset_on.Rd | 3 man/mf_label.Rd | 11 man/mf_map.Rd | 73 ++- man/mf_prop_choro.Rd | 12 man/mf_prop_typo.Rd | 2 man/mf_raster.Rd | 5 man/mf_scale.Rd | 2 man/mf_symb_choro.Rd | 12 man/mf_theme.Rd | 52 +- vignettes/data-raw/createthumbnails.R | 494 +++++++++++------------ vignettes/mapsf.Rmd | 47 -- 98 files changed, 2064 insertions(+), 1631 deletions(-)
Title: Cleaning Geometries from Spatial Objects
Description: Provides a set of utility tools to inspect spatial objects, facilitate
handling and reporting of topology errors and geometry validity issue with sp objects.
Finally, it provides a geometry cleaner that will fix all geometry problems,
and eliminate (at least reduce) the likelihood of having issues when doing
spatial data processing.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between cleangeo versions 0.2-4 dated 2021-04-17 and 0.3 dated 2023-07-06
DESCRIPTION | 16 - MD5 | 49 ++--- NAMESPACE | 5 R/cleangeo.R | 2 R/clgeo_Clean.R | 70 +++++-- R/clgeo_CleanByPolygonation.R | 40 ++-- R/clgeo_CollectionReport.R | 5 R/clgeo_GeometryReport.R | 46 +---- R/clgeo_IsValid.R | 21 +- R/clgeo_SummaryReport.R | 12 - R/clgeo_SuspiciousFeatures.R | 12 - R/profile.R |only README.md | 16 + build/vignette.rds |binary inst/doc/quickstart.R | 14 - inst/doc/quickstart.Rmd | 22 -- inst/doc/quickstart.html | 354 ++++++++++++---------------------------- man/clgeo_Clean.Rd | 16 + man/clgeo_CollectionReport.Rd | 5 man/clgeo_GeometryReport.Rd | 9 - man/clgeo_IsValid.Rd | 5 man/clgeo_SummaryReport.Rd | 10 - man/clgeo_SuspiciousFeatures.Rd | 12 - tests/testthat/test_Clean.R | 136 +++++---------- tests/testthat/test_IsValid.R | 26 -- vignettes/quickstart.Rmd | 22 -- 26 files changed, 371 insertions(+), 554 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps.
Author: Ari Lamstein [aut, cre],
Brian Johnson [ctb],
Trulia, Inc. [cph]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>
Diff between choroplethr versions 3.7.1 dated 2022-10-05 and 3.7.2 dated 2023-07-06
DESCRIPTION | 12 +++++++----- MD5 | 43 ++++++++++++++++++++++++++++++++++++++++--- R/startup_messages.R | 2 +- R/usa.R | 2 +- build |only inst |only vignettes |only 7 files changed, 49 insertions(+), 10 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.3.4 dated 2023-06-26 and 1.3.4.1 dated 2023-07-06
CHANGELOG | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/bart_package_plots.R | 18 ++++++++++++------ R/bart_package_variable_selection.R | 4 +++- inst/doc/bartMachine.pdf |binary 6 files changed, 27 insertions(+), 15 deletions(-)
Title: Isotonic Subgroup Selection
Description: Methodology for subgroup selection in the context of isotonic regression including methods for sub-Gaussian errors, classification, homoscedastic Gaussian errors and quantile regression. See the documentation of ISS(). Details can be found in the paper by Müller, Reeve, Cannings and Samworth (2023) <arXiv:2305.04852v2>.
Author: Manuel M. Mueller [aut, cre],
Henry W. J. Reeve [aut],
Timothy I. Cannings [aut],
Richard J. Samworth [aut]
Maintainer: Manuel M. Mueller <mm2559@cam.ac.uk>
Diff between ISS versions 0.1.3 dated 2023-05-20 and 1.0.0 dated 2023-07-06
DESCRIPTION | 8 +-- MD5 | 30 +++++++----- NAMESPACE | 3 + R/ISS.R | 105 +++++++++++++++++++++++++++++--------------- R/dag_test_FS.R | 29 ++++++------ R/dag_test_ISS.R | 2 R/dag_test_MG.R | 2 R/get_p_Gaussian.R |only R/get_p_classification.R | 2 R/get_p_value.R |only build/partial.rdb |binary inst/CITATION | 2 inst/REFERENCES.bib | 7 ++ man/ISS.Rd | 37 +++++++++------ man/dag_test_FS.Rd | 14 +++-- man/get_p_Gaussian.Rd |only man/get_p_classification.Rd | 2 man/get_p_value.Rd |only 18 files changed, 152 insertions(+), 91 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.7.1 dated 2022-04-06 and 0.7.2 dated 2023-07-06
geoBayes-0.7.1/geoBayes/R/expectationsse.R |only geoBayes-0.7.2/geoBayes/DESCRIPTION | 10 geoBayes-0.7.2/geoBayes/MD5 | 51 +-- geoBayes-0.7.2/geoBayes/NEWS | 4 geoBayes-0.7.2/geoBayes/R/bf.R | 3 geoBayes-0.7.2/geoBayes/R/bfse.R | 5 geoBayes-0.7.2/geoBayes/R/geobayes-package.R | 14 geoBayes-0.7.2/geoBayes/R/mcsp2.R | 2 geoBayes-0.7.2/geoBayes/R/sploglik.R | 4 geoBayes-0.7.2/geoBayes/R/util.R | 1 geoBayes-0.7.2/geoBayes/man/geoBayes.Rd | 14 geoBayes-0.7.2/geoBayes/man/mkpredgrid2d.Rd | 3 geoBayes-0.7.2/geoBayes/src/Makevars | 2 geoBayes-0.7.2/geoBayes/src/bfse.f90 | 394 ++++++++++++++++++++++++- geoBayes-0.7.2/geoBayes/src/bfsp2.f90 | 100 ++++-- geoBayes-0.7.2/geoBayes/src/bmargin.f90 | 25 + geoBayes-0.7.2/geoBayes/src/cor_fcns.f90 | 16 - geoBayes-0.7.2/geoBayes/src/covfun.f90 | 12 geoBayes-0.7.2/geoBayes/src/flogsumexp.f90 | 16 - geoBayes-0.7.2/geoBayes/src/interfaces.f90 | 50 +-- geoBayes-0.7.2/geoBayes/src/linkdz.f90 | 12 geoBayes-0.7.2/geoBayes/src/linkfcn.f90 | 34 +- geoBayes-0.7.2/geoBayes/src/modelfcns.f90 | 68 ++-- geoBayes-0.7.2/geoBayes/src/modelfcns_link.f90 | 244 +++++++-------- geoBayes-0.7.2/geoBayes/src/modelfcns_pdfy.f90 | 90 ++--- geoBayes-0.7.2/geoBayes/src/pdfy.f90 | 20 - geoBayes-0.7.2/geoBayes/src/pdfydlnk.f90 | 10 27 files changed, 817 insertions(+), 387 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between testthat versions 3.1.9 dated 2023-06-15 and 3.1.10 dated 2023-07-06
DESCRIPTION | 12 +++--- MD5 | 41 +++++++++++--------- NEWS.md | 13 +++++- R/expect-no-condition.R | 6 +-- R/local.R | 2 - R/reporter-list.R | 11 ++++- R/test-env.R | 14 +++---- R/test-state.R | 2 - man/is_testing.Rd | 14 +++---- man/set_state_inspector.Rd | 2 - tests/testthat/_snaps/expect-no-condition.md | 49 ++++++++++++++++++++---- tests/testthat/test-browser.R |only tests/testthat/test-expect-known.R | 4 +- tests/testthat/test-expect-no-condition.R | 15 +++++++ tests/testthat/test-parallel-crash.R | 2 - tests/testthat/test-parallel-outside.R | 6 +-- tests/testthat/test-parallel-setup.R | 6 +-- tests/testthat/test-parallel-startup.R | 6 +-- tests/testthat/test-parallel-teardown.R | 6 +-- tests/testthat/test-parallel.R | 54 +++++++++++++++++++-------- tests/testthat/test-parallel/fail |only 21 files changed, 179 insertions(+), 86 deletions(-)
Title: Identify Distributions that Match Reported Sample Parameters
(SPRITE)
Description: The SPRITE algorithm creates possible distributions of discrete responses
based on reported sample parameters, such as mean, standard deviation and range
(Heathers et al., 2018, <doi:10.7287/peerj.preprints.26968v1>). This package implements it,
drawing heavily on the code for Nick Brown's 'rSPRITE' Shiny app <https://shiny.ieis.tue.nl/sprite/>.
In addition, it supports the modeling of distributions based on multi-item (Likert-type)
scales and the use of restrictions on the frequency of particular responses.
Author: Lukas Wallrich [aut, cre] ,
Aurelien Allard [ctb]
Maintainer: Lukas Wallrich <lukas.wallrich@gmail.com>
Diff between rsprite2 versions 0.2.0 dated 2022-09-27 and 0.2.1 dated 2023-07-06
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 5 ++++- R/core-functions.R | 40 +++++++++++++--------------------------- R/plot-functions.R | 11 +++++++---- R/rsprite2-package.R | 1 - README.md | 3 +-- build/partial.rdb |binary man/GRIMMER_test.Rd | 4 ++-- man/figures/logo.png |binary 10 files changed, 41 insertions(+), 51 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library <https://github.com/libxls/libxls> and '.xlsx' via
the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net/>.
Works on Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Posit, PBC [cph, fnd] ,
Marcin Kalicinski [ctb, cph] ,
Komarov Valery [ctb, cph] ,
Christophe Leitienne [ctb, cph] ,
Bob Colbert [ctb, cph] ,
David Hoerl [ctb, cph] ,
Evan Miller [ctb, cph]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between readxl versions 1.4.2 dated 2023-02-09 and 1.4.3 dated 2023-07-06
DESCRIPTION | 8 MD5 | 44 ++-- NEWS.md | 4 README.md | 22 +- build/vignette.rds |binary inst/doc/cell-and-column-types.Rmd | 20 ++ inst/doc/cell-and-column-types.html | 340 ++++++++++++++++++------------------ inst/doc/sheet-geometry.Rmd | 6 inst/doc/sheet-geometry.html | 212 +++++++++++----------- man/figures/logo.png |binary tests/testthat/_snaps/col-names.md |only tests/testthat/_snaps/col-types.md | 74 +++++++ tests/testthat/_snaps/dates.md |only tests/testthat/_snaps/problems.md |only tests/testthat/_snaps/read-excel.md |only tests/testthat/_snaps/sheets.md |only tests/testthat/setup.R |only tests/testthat/test-col-names.R | 15 - tests/testthat/test-col-types.R | 54 ++--- tests/testthat/test-dates.R | 28 +- tests/testthat/test-problems.R | 30 +-- tests/testthat/test-read-excel.R | 98 +++++----- tests/testthat/test-sheets.R | 49 ++--- tests/testthat/test-trim-ws.R | 6 vignettes/cell-and-column-types.Rmd | 20 ++ vignettes/sheet-geometry.Rmd | 6 26 files changed, 573 insertions(+), 463 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and
transparency in data processing. It provides functionality such as
automatic meta data creation and management, rudimentary quality
management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this
package to deliver everything what is needed to achieve full
reproducibility and transparency, but we believe that it supports
efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre],
Lavinia Baumstark [aut],
Stephen Wirth [aut],
Anastasis Giannousakis [aut],
Renato Rodrigues [aut],
Benjamin Leon Bodirsky [aut],
Ulrich Kreidenweis [aut],
David Klein [aut],
Pascal Fuehrlich [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 3.3.4 dated 2023-07-06 and 3.3.5 dated 2023-07-06
DESCRIPTION | 8 MD5 | 20 R/getCalculations.R | 47 README.md | 6 inst/doc/madrat-caching.R | 42 inst/doc/madrat-caching.Rmd | 42 inst/doc/madrat-caching.html | 2000 +------------------------------------- inst/doc/madrat.html | 10 man/getCalculations.Rd | 7 tests/testthat/test-metadataGFZ.R | 1 vignettes/madrat-caching.Rmd | 42 11 files changed, 192 insertions(+), 2033 deletions(-)
Title: Modern Graphs for Design of Experiments with 'ggplot2'
Description: Generate commonly used plots in the field of design of experiments using 'ggplot2'.
'ggDoE' currently supports the following plots: alias matrix, box cox transformation, boxplots, lambda plot,
regression diagnostic plots, half normal plots, main and interaction effect plots for factorial designs,
contour plots for response surface methodology, Pareto plot, and two dimensional projections of a latin hypercube design.
Author: Jose Toledo Luna [aut, cre]
Maintainer: Jose Toledo Luna <toledo60@protonmail.com>
Diff between ggDoE versions 0.7.8 dated 2022-08-23 and 0.7.9 dated 2023-07-06
ggDoE-0.7.8/ggDoE/R/adapted_epitaxial.R |only ggDoE-0.7.8/ggDoE/R/diagnostic_plots.R |only ggDoE-0.7.8/ggDoE/R/original_epitaxial.R |only ggDoE-0.7.8/ggDoE/R/twoD_projections.R |only ggDoE-0.7.8/ggDoE/build |only ggDoE-0.7.8/ggDoE/inst |only ggDoE-0.7.8/ggDoE/man/diagnostic_plots.Rd |only ggDoE-0.7.8/ggDoE/man/twoD_projections.Rd |only ggDoE-0.7.8/ggDoE/vignettes |only ggDoE-0.7.9/ggDoE/DESCRIPTION | 19 +- ggDoE-0.7.9/ggDoE/MD5 | 70 +++++---- ggDoE-0.7.9/ggDoE/NAMESPACE | 17 -- ggDoE-0.7.9/ggDoE/NEWS.md | 31 ++++ ggDoE-0.7.9/ggDoE/R/alias_matrix.R | 18 +- ggDoE-0.7.9/ggDoE/R/boxcox_transform.R | 66 +++++---- ggDoE-0.7.9/ggDoE/R/data-adapted_epitaxial.R |only ggDoE-0.7.9/ggDoE/R/data-girder.R |only ggDoE-0.7.9/ggDoE/R/data-original_epitaxial.R |only ggDoE-0.7.9/ggDoE/R/data-pulp_experiment.R |only ggDoE-0.7.9/ggDoE/R/gg_boxplots.R | 30 +--- ggDoE-0.7.9/ggDoE/R/gg_lm.R |only ggDoE-0.7.9/ggDoE/R/gg_rsm.R | 55 ++++--- ggDoE-0.7.9/ggDoE/R/globals.R | 2 ggDoE-0.7.9/ggDoE/R/half_normal.R | 29 +--- ggDoE-0.7.9/ggDoE/R/interaction_effects.R | 76 +++++----- ggDoE-0.7.9/ggDoE/R/lambda_plot.R | 27 +-- ggDoE-0.7.9/ggDoE/R/main_effects.R | 126 +++++++++-------- ggDoE-0.7.9/ggDoE/R/pair_plots.R |only ggDoE-0.7.9/ggDoE/R/pareto_plot.R | 56 ++++--- ggDoE-0.7.9/ggDoE/README.md | 187 ++++++++++++++------------ ggDoE-0.7.9/ggDoE/data/girder_experiment.rda |only ggDoE-0.7.9/ggDoE/data/pulp_experiment.rda |only ggDoE-0.7.9/ggDoE/man/adapted_epitaxial.Rd | 9 - ggDoE-0.7.9/ggDoE/man/figures/contour1.png |binary ggDoE-0.7.9/ggDoE/man/figures/contour2.png |binary ggDoE-0.7.9/ggDoE/man/figures/logo.png |only ggDoE-0.7.9/ggDoE/man/gg_boxplots.Rd | 12 - ggDoE-0.7.9/ggDoE/man/gg_lm.Rd |only ggDoE-0.7.9/ggDoE/man/gg_rsm.Rd | 15 +- ggDoE-0.7.9/ggDoE/man/girder_experiment.Rd |only ggDoE-0.7.9/ggDoE/man/half_normal.Rd | 1 ggDoE-0.7.9/ggDoE/man/main_effects.Rd | 2 ggDoE-0.7.9/ggDoE/man/original_epitaxial.Rd | 31 +++- ggDoE-0.7.9/ggDoE/man/pair_plots.Rd |only ggDoE-0.7.9/ggDoE/man/pareto_plot.Rd | 4 ggDoE-0.7.9/ggDoE/man/pulp_experiment.Rd |only 46 files changed, 502 insertions(+), 381 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 2.1.3 dated 2022-03-17 and 2.1.4 dated 2023-07-06
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- R/inline.R | 2 +- README.md | 13 +++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/include/RcppThread/ThreadPool.hpp | 5 ++++- src/detectCores.cpp | 5 ++++- 8 files changed, 27 insertions(+), 21 deletions(-)
Title: Evaluate Arbitrary Negative Binomial Convolutions
Description: Three distinct methods are implemented for evaluating the sums of arbitrary negative binomial distributions. These methods are: Furman's exact probability mass function (Furman (2007) <doi:10.1016/j.spl.2006.06.007>), saddlepoint approximation, and a method of moments approximation. Functions are provided to calculate the density function, the distribution function and the quantile function of the convolutions in question given said evaluation methods. Functions for generating random deviates from negative binomial convolutions and for directly calculating the mean, variance, skewness, and excess kurtosis of said convolutions are also provided.
Author: Gregory Bedwell [aut, cre, cph]
Maintainer: Gregory Bedwell <gregoryjbedwell@gmail.com>
Diff between nbconv versions 1.0.0 dated 2023-04-27 and 1.0.1 dated 2023-07-06
DESCRIPTION | 6 ++--- MD5 | 36 +++++++++++++++---------------- NEWS.md | 11 +++++++++ R/dnbconv.R | 31 ++++++++++++++++++++++----- R/nb_sum_exact.R | 3 ++ R/nb_sum_moments.R | 2 + R/nb_sum_saddlepoint.R | 15 +++++++------ R/nbconv_params.R | 25 +++++++++++++++++++--- R/pnbconv.R | 24 ++++++++++++++++++--- R/qnbconv.R | 24 ++++++++++++++++++--- R/rnbconv.R | 52 ++++++++++++++++++++++++++++++++++++++++------ man/dnbconv.Rd | 2 - man/nb_sum_exact.Rd | 2 - man/nb_sum_moments.Rd | 2 - man/nb_sum_saddlepoint.Rd | 5 +++- man/nbconv_params.Rd | 2 - man/pnbconv.Rd | 2 - man/qnbconv.Rd | 2 - man/rnbconv.Rd | 6 +++-- 19 files changed, 195 insertions(+), 57 deletions(-)
Title: ADaM in R Asset Library
Description: A toolbox for programming Clinical Data Interchange Standards Consortium
(CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a
mandatory part of any New Drug or Biologics License Application submitted to the
United States Food and Drug Administration (FDA). Analysis derivations are
implemented in accordance with the "Analysis Data Model Implementation Guide"
(CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Ben Straub [aut, cre],
Stefan Bundfuss [aut],
Thomas Neitmann [aut],
Samia Kabi [aut],
Gordon Miller [aut],
Teckla Akinyi [aut],
Andrew Smith [aut],
Konstantina Koukourikou [aut],
Ross Farrugia [aut],
Eric Simms [aut],
Annie Yang [aut],
Robin Koeger [...truncated...]
Maintainer: Ben Straub <ben.x.straub@gsk.com>
Diff between admiral versions 0.11.0 dated 2023-06-08 and 0.11.1 dated 2023-07-06
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 5 +++ R/derive_param_tte.R | 9 ------ README.md | 22 ++++++++-------- build/vignette.rds |binary inst/doc/bds_tte.html | 68 +++++++++++++++++++++++++------------------------- 7 files changed, 60 insertions(+), 62 deletions(-)
Title: 'osqp' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'OSQP'. More information about
'OSQP' can be found at <https://osqp.org>.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.osqp versions 1.0-0 dated 2020-09-14 and 1.0-1 dated 2023-07-06
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/Example_01.Rd | 1 + 3 files changed, 9 insertions(+), 8 deletions(-)
More information about ROI.plugin.osqp at CRAN
Permanent link
Title: 'nloptr' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the R Optimization Infrastructure ('ROI') package
with the 'NLopt' solver for solving nonlinear optimization problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.nloptr versions 1.0-0 dated 2020-08-29 and 1.0-1 dated 2023-07-06
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- man/Example_01.Rd | 1 + 3 files changed, 12 insertions(+), 10 deletions(-)
More information about ROI.plugin.nloptr at CRAN
Permanent link
Title: Policy Learning
Description: Framework for evaluating user-specified finite stage policies and learning realistic policies via doubly robust loss functions. Policy learning methods include doubly robust restricted Q-learning, sequential policy tree learning and outcome weighted learning. See Nordland and Holst (2022) <arXiv:2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.2 dated 2023-02-07 and 1.3 dated 2023-07-06
polle-1.2/polle/inst/sim |only polle-1.3/polle/DESCRIPTION | 10 polle-1.3/polle/MD5 | 77 +-- polle-1.3/polle/NAMESPACE | 8 polle-1.3/polle/NEWS.md | 5 polle-1.3/polle/R/Q_function.R | 71 ++- polle-1.3/polle/R/blip.R |only polle-1.3/polle/R/drql.R | 181 +++++++- polle-1.3/polle/R/g_function.R | 61 +- polle-1.3/polle/R/g_models.R | 218 ++++++++-- polle-1.3/polle/R/history_functions.R | 25 - polle-1.3/polle/R/owl.R | 6 polle-1.3/polle/R/policy_data.R | 2 polle-1.3/polle/R/policy_data_functions.R | 36 + polle-1.3/polle/R/policy_def.R | 26 + polle-1.3/polle/R/policy_eval.R | 67 ++- polle-1.3/polle/R/policy_eval_functions.R | 4 polle-1.3/polle/R/policy_learn.R | 8 polle-1.3/polle/R/policy_object_functions.R | 4 polle-1.3/polle/R/ptl.R | 14 polle-1.3/polle/R/q_models.R | 196 +++++++-- polle-1.3/polle/R/rql.R | 114 +++++ polle-1.3/polle/R/value_functions.R | 25 + polle-1.3/polle/man/control_blip.Rd |only polle-1.3/polle/man/g_model.Rd | 33 + polle-1.3/polle/man/get_id.Rd | 2 polle-1.3/polle/man/get_id_stage.Rd | 2 polle-1.3/polle/man/get_policy_functions.Rd | 21 polle-1.3/polle/man/plot.policy_data.Rd | 2 polle-1.3/polle/man/policy_eval.Rd | 11 polle-1.3/polle/man/policy_learn.Rd | 6 polle-1.3/polle/man/q_model.Rd | 30 + polle-1.3/polle/man/subset_id.Rd | 4 polle-1.3/polle/tests/testthat/test-g_models.R | 71 ++- polle-1.3/polle/tests/testthat/test-g_xgboost.R |only polle-1.3/polle/tests/testthat/test-policy_eval.R | 67 +++ polle-1.3/polle/tests/testthat/test-policy_g_functions.R |only polle-1.3/polle/tests/testthat/test-policy_learn_blip.R |only polle-1.3/polle/tests/testthat/test-policy_learn_drql.R | 85 +++ polle-1.3/polle/tests/testthat/test-policy_learn_ql.R | 325 +++++++++++++++ polle-1.3/polle/tests/testthat/test-q_models.R | 33 - polle-1.3/polle/tests/testthat/test-q_sl.R |only polle-1.3/polle/tests/testthat/test-q_xgboost.R |only polle-1.3/polle/tests/testthat/test-supp_warnings.R |only 44 files changed, 1562 insertions(+), 288 deletions(-)
Title: 'NEOS' Plug-in for the 'R' Optimization Interface
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with a connection to the 'neos' server. 'ROI' optimization
problems can be directly be sent to the 'neos' server
and solution obtained in the typical 'ROI' style.
Author: Ronald Hochreiter [aut],
Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.neos versions 1.0-0 dated 2020-08-29 and 1.0-1 dated 2023-07-06
ROI.plugin.neos-1.0-0/ROI.plugin.neos/man/control.Rd |only ROI.plugin.neos-1.0-1/ROI.plugin.neos/DESCRIPTION | 14 - ROI.plugin.neos-1.0-1/ROI.plugin.neos/MD5 | 22 - ROI.plugin.neos-1.0-1/ROI.plugin.neos/NAMESPACE | 18 + ROI.plugin.neos-1.0-1/ROI.plugin.neos/R/neos_client.R | 10 ROI.plugin.neos-1.0-1/ROI.plugin.neos/R/plugin.R | 111 +++++----- ROI.plugin.neos-1.0-1/ROI.plugin.neos/R/status_codes.R | 28 +- ROI.plugin.neos-1.0-1/ROI.plugin.neos/R/zzz.R | 25 +- ROI.plugin.neos-1.0-1/ROI.plugin.neos/build/vignette.rds |binary ROI.plugin.neos-1.0-1/ROI.plugin.neos/inst/doc/ROI.plugin.neos_Introduction.pdf |binary ROI.plugin.neos-1.0-1/ROI.plugin.neos/man/Example_01.Rd | 6 ROI.plugin.neos-1.0-1/ROI.plugin.neos/man/neos_control.Rd |only ROI.plugin.neos-1.0-1/ROI.plugin.neos/tests/test_ROI_plugin_neos.R | 2 13 files changed, 130 insertions(+), 106 deletions(-)
More information about ROI.plugin.neos at CRAN
Permanent link
Title: 'HiGHS' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'HiGHS'. More information about
'HiGHS' can be found at <https://highs.dev>.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.highs versions 1.0-2 dated 2022-10-29 and 1.0-3 dated 2023-07-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/zzz.R | 19 +++++++++++++------ man/Example_01.Rd | 1 + 4 files changed, 20 insertions(+), 12 deletions(-)
More information about ROI.plugin.highs at CRAN
Permanent link
Title: Optimal Treatment Regimes in Survival Contexts with
Kaplan-Meier-Like Estimators
Description: Provide methods for estimating optimal treatment regimes in survival contexts
with Kaplan-Meier-like estimators when no unmeasured confounding assumption is
satisfied (Jiang, R., Lu, W., Song, R., and Davidian, M. (2017) <doi:10.1111/rssb.12201>)
and when no unmeasured confounding assumption fails to hold and a binary instrument
is available (Xia, J., Zhan, Z., Zhang, J. (2022) <arXiv:2210.05538>).
Author: Junwen Xia [aut, cre],
Zishu Zhan [aut],
Jingxiao Zhang [aut]
Maintainer: Junwen Xia <xiajunwen@ruc.edu.cn>
Diff between otrKM versions 0.2.0 dated 2023-06-23 and 0.2.1 dated 2023-07-06
DESCRIPTION | 6 ++--- MD5 | 48 +++++++++++++++++++++---------------------- R/AIWKME.R | 3 +- R/DRKMEIV.R | 4 +-- R/Genetic.optim.AIWKME.r | 3 +- R/Genetic.optim.DRKMEIV.r | 4 +-- R/Genetic.optim.IWKME.r | 3 +- R/Genetic.optim.IWKMEIV.R | 2 - R/IWKME.R | 3 +- R/IWKMEIV.R | 2 - R/utilities.R | 15 ++++++------- man/AIWKME.Rd | 3 +- man/DRKMEIV.Rd | 4 +-- man/Fprep.AIWKME.Rd | 2 - man/Fprep.DRKMEIV.Rd | 4 +-- man/Fps.AIWKME.Rd | 2 - man/Fps.DRKMEIV.Rd | 2 - man/Fps.IWKME.Rd | 2 - man/Fps.IWKMEIV.Rd | 2 - man/Genetic.optim.AIWKME.Rd | 3 +- man/Genetic.optim.DRKMEIV.Rd | 4 +-- man/Genetic.optim.IWKME.Rd | 3 +- man/Genetic.optim.IWKMEIV.Rd | 2 - man/IWKME.Rd | 3 +- man/IWKMEIV.Rd | 2 - 25 files changed, 69 insertions(+), 62 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.3.1 dated 2023-05-12 and 1.4.0 dated 2023-07-06
DESCRIPTION | 15 MD5 | 45 NAMESPACE | 3 NEWS.md | 10 R/app.R | 9 R/dependencies.R |only R/init.R | 20 R/react.R |only R/tools.R | 2 inst/WORDLIST | 3 inst/templates/node/babel.config.json | 3 inst/templates/node/dot.eslintrc.json | 8 inst/templates/node/package-lock.json | 1976 ++++++++++++++++++++++++++++++---- inst/templates/node/package.json | 3 inst/templates/node/webpack.config.js | 7 man/dependencies.Rd |only man/react_component.Rd |only tests/e2e |only 18 files changed, 1873 insertions(+), 231 deletions(-)
Title: Efficient Algorithm for High-Dimensional Frailty Model
Description: The penalized and non-penalized Minorize-Maximization (MM) method for frailty models to fit the clustered data, multi-event data and recurrent data. Least absolute shrinkage and selection operator (LASSO), minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalized functions are implemented. All the methods are computationally efficient. These general methods are proposed based on the following papers,
Huang, Xu and Zhou (2022) <doi:10.3390/math10040538>,
Huang, Xu and Zhou (2023) <doi:10.1177/09622802221133554>.
Author: Xifen Huang [aut],
Yunpeng Zhou [aut, cre],
Jinfeng Xu [ctb]
Maintainer: Yunpeng Zhou <u3514104@connect.hku.hk>
Diff between frailtyMMpen versions 1.0.0 dated 2023-03-24 and 1.1.1 dated 2023-07-06
DESCRIPTION | 6 - MD5 | 70 +++++++++++++-------- NEWS.md | 10 ++- R/backtrackerror.R | 9 +- R/frailtyMM.R | 167 +++++++++++++++++++++++++++++++++++++-------------- R/frailtyMMcal.R | 82 +++++++++++++++++++++++-- R/frailtyMMpen.R | 169 +++++++++++++++++++++++++++++++++------------------- R/plot.R | 19 ++++- R/predict.R | 2 R/print.R | 8 +- R/simdata.R | 13 ++++ R/summary.R | 2 README.md | 7 +- data/hdCLdata.RData |only man/cluster.Rd | 34 +++++----- man/coef.fpen.Rd | 48 +++++++------- man/event.Rd | 34 +++++----- man/figures |only man/frailtyMM.Rd | 94 ++++++++++++++++++++++++---- man/frailtyMMpen.Rd | 40 ++++++++---- man/hdCLdata.Rd |only man/plot.fmm.Rd | 84 ++++++++++++------------- man/predict.fmm.Rd | 100 +++++++++++++++--------------- man/predict.fpen.Rd | 104 ++++++++++++++++---------------- man/print.fmm.Rd | 44 ++++++------- man/print.fpen.Rd | 46 +++++++------- man/simdataCL.Rd | 42 ++++++------ man/simdataME.Rd | 42 ++++++------ man/simdataRE.Rd | 42 ++++++------ 29 files changed, 822 insertions(+), 496 deletions(-)
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities related
to two-component admixture models, where the two components can belong to any
distribution (note that in the case of multinomial mixtures, the two components
must belong to the same family). Estimation methods depend on the assumptions
made on the unknown component density (see Bordes and Vandekerkhove (2010) <doi:10.3103/S1066530710010023>;
Patra and Sen (2016) <doi:10.1111/rssb.12148>); Milhaud, Pommeret, Salhi and Vandekerkhove
(2022) <doi:10.1016/j.jspi.2021.05.010>). In practice, one can estimate both the
mixture weight and the unknown component density in a wide variety of frameworks.
On top of that, hypothesis tests can be performed in one and two-sample contexts
to test the unknown component density (see Milhaud, Pommeret, Salhi, Vandekerkhove (2023)).
Finally, clustering of unknown mixture components is also feasible in a K-samples setting.
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.1-0 dated 2023-03-23 and 2.1-1 dated 2023-07-06
admix-2.1-0/admix/R/IBM_test_H0.R |only admix-2.1-0/admix/R/decontamin_cdf_unknownComp.R |only admix-2.1-0/admix/R/plot.decontamined_dens.R |only admix-2.1-0/admix/R/plot_decontamin_cdf.R |only admix-2.1-0/admix/man/IBM_test_H0.Rd |only admix-2.1-0/admix/man/decontamin_cdf_unknownComp.Rd |only admix-2.1-0/admix/man/plot.decontaminated_dens.Rd |only admix-2.1-0/admix/man/plot_decontamin_cdf.Rd |only admix-2.1-1/admix/DESCRIPTION | 8 admix-2.1-1/admix/MD5 | 104 ++--- admix-2.1-1/admix/NAMESPACE | 7 admix-2.1-1/admix/R/IBM_2samples_test.R |only admix-2.1-1/admix/R/IBM_empirical_contrast.R | 2 admix-2.1-1/admix/R/IBM_estimProp.R | 5 admix-2.1-1/admix/R/IBM_estimVarCov_gaussVect.R | 2 admix-2.1-1/admix/R/IBM_gap.R | 2 admix-2.1-1/admix/R/IBM_greenLight_criterion.R | 2 admix-2.1-1/admix/R/IBM_hessian_contrast.R | 2 admix-2.1-1/admix/R/IBM_k_samples_test.R | 238 ++++++------ admix-2.1-1/admix/R/IBM_tabul_stochasticInteg.R | 2 admix-2.1-1/admix/R/IBM_theoretical_contrast.R | 2 admix-2.1-1/admix/R/IBM_theoretical_gap.R | 2 admix-2.1-1/admix/R/admix_clustering.R | 117 ++++- admix-2.1-1/admix/R/admix_estim.R | 2 admix-2.1-1/admix/R/admix_test.R | 12 admix-2.1-1/admix/R/decontaminated_cdf.R |only admix-2.1-1/admix/R/decontaminated_density.R | 2 admix-2.1-1/admix/R/orthoBasis_test_H0.R | 2 admix-2.1-1/admix/R/plot.decontaminated_density.R |only admix-2.1-1/admix/R/print.admix_cluster.R | 21 - admix-2.1-1/admix/R/two_samples_test.R | 4 admix-2.1-1/admix/inst/doc/admixture-clustering.Rmd | 2 admix-2.1-1/admix/inst/doc/admixture-clustering.html | 105 +++-- admix-2.1-1/admix/inst/doc/admixture-weight-estimation.html | 18 admix-2.1-1/admix/inst/doc/test-hypothesis.R | 3 admix-2.1-1/admix/inst/doc/test-hypothesis.Rmd | 5 admix-2.1-1/admix/inst/doc/test-hypothesis.html | 34 + admix-2.1-1/admix/man/IBM_2samples_test.Rd |only admix-2.1-1/admix/man/IBM_empirical_contrast.Rd | 2 admix-2.1-1/admix/man/IBM_estimProp.Rd | 2 admix-2.1-1/admix/man/IBM_estimVarCov_gaussVect.Rd | 2 admix-2.1-1/admix/man/IBM_gap.Rd | 2 admix-2.1-1/admix/man/IBM_greenLight_criterion.Rd | 2 admix-2.1-1/admix/man/IBM_hessian_contrast.Rd | 2 admix-2.1-1/admix/man/IBM_k_samples_test.Rd | 10 admix-2.1-1/admix/man/IBM_tabul_stochasticInteg.Rd | 2 admix-2.1-1/admix/man/IBM_theoretical_contrast.Rd | 2 admix-2.1-1/admix/man/IBM_theoretical_gap.Rd | 2 admix-2.1-1/admix/man/PatraSen_est_mix_model.Rd | 2 admix-2.1-1/admix/man/admix-package.Rd | 2 admix-2.1-1/admix/man/admix_clustering.Rd | 16 admix-2.1-1/admix/man/admix_estim.Rd | 2 admix-2.1-1/admix/man/admix_test.Rd | 2 admix-2.1-1/admix/man/decontaminated_cdf.Rd |only admix-2.1-1/admix/man/orthoBasis_test_H0.Rd | 2 admix-2.1-1/admix/man/plot.decontaminated_density.Rd |only admix-2.1-1/admix/man/print.admix_cluster.Rd | 4 admix-2.1-1/admix/vignettes/admixture-clustering.Rmd | 2 admix-2.1-1/admix/vignettes/references.bib | 19 admix-2.1-1/admix/vignettes/test-hypothesis.Rmd | 5 60 files changed, 474 insertions(+), 315 deletions(-)
Title: Sequential Probability Ratio Tests Toolbox
Description: It is a toolbox for Sequential Probability Ratio Tests (SPRT), Wald (1945) <doi:10.2134/agronj1947.00021962003900070011x>.
SPRTs are applied to the data during the sampling process, ideally after each observation.
At any stage, the test will return a decision to either continue sampling or terminate and accept one of the specified hypotheses.
The seq_ttest() function performs one-sample, two-sample, and paired t-tests for testing one- and two-sided hypotheses (Schnuerch & Erdfelder (2019) <doi:10.1037/met0000234>).
The seq_anova() function allows to perform a sequential one-way fixed effects ANOVA (Steinhilber et al. (2023) <doi:10.31234/osf.io/m64ne>).
Learn more about the package by using vignettes "browseVignettes(package = "sprtt")" or go to the website <https://meikesteinhilber.github.io/sprtt/>.
Author: Meike Steinhilber [aut, cre] ,
Martin Schnuerch [aut, ths] ,
Anna-Lena Schubert [aut, ths]
Maintainer: Meike Steinhilber <Meike.Steinhilber@aol.com>
Diff between sprtt versions 0.1.0 dated 2021-08-06 and 0.2.0 dated 2023-07-06
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Title: Rarefaction Methods
Description: Includes functions for the calculation of spatially and non-spatially explicit rarefaction curves using different indices of taxonomic, functional and phylogenetic diversity. The user can also rarefy any biodiversity metric as provided by a self-written function (or an already existent one) that gives as output a vector with the values of a certain index of biodiversity calculated per plot (Ricotta, C., Acosta, A., Bacaro, G., Carboni, M., Chiarucci, A., Rocchini, D., Pavoine, S. (2019) <doi:10.1016/j.ecolind.2019.105606>; Bacaro, G., Altobelli, A., Cameletti, M., Ciccarelli, D., Martellos, S., Palmer, M. W., … Chiarucci, A. (2016) <doi:10.1016/j.ecolind.2016.04.026>; Bacaro, G., Rocchini, D., Ghisla, A., Marcantonio, M., Neteler, M., & Chiarucci, A. (2012) <doi:10.1016/j.ecocom.2012.05.007>).
Author: Elisa Thouverai [aut, cre],
Sandrine Pavoine [aut],
Enrico Tordoni [aut],
Duccio Rocchini [aut],
Carlo Ricotta [aut],
Alessandro Chiarucci [aut],
Giovanni Bacaro [aut]
Maintainer: Elisa Thouverai <elisa.th95@gmail.com>
Diff between Rarefy versions 1.1 dated 2021-03-11 and 1.1.1 dated 2023-07-06
DESCRIPTION | 10 MD5 | 22 R/rare_alpha.R | 4 R/rare_beta.R | 276 +++++----- R/rare_phylo.R | 228 ++++---- R/ser_phylo.R | 256 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Rarefy_basics.R | 1 inst/doc/Rarefy_basics.Rmd | 1 inst/doc/Rarefy_basics.html | 1120 +++++++++++++++++++++++++++++++++++--------- vignettes/Rarefy_basics.Rmd | 1 12 files changed, 1316 insertions(+), 603 deletions(-)
Title: Joint Models of Survival and Multivariate Longitudinal Data
Description: Fit joint models of survival and multivariate longitudinal data. The longitudinal
data is specified by generalised linear mixed models. The joint models are fit via maximum
likelihood using an approximate expectation maximisation algorithm.
Bernhardt (2015) <doi:10.1016/j.csda.2014.11.011>.
Author: James Murray [aut, cre]
Maintainer: James Murray <j.murray7@ncl.ac.uk>
Diff between gmvjoint versions 0.2.1 dated 2023-03-24 and 0.3.0 dated 2023-07-06
gmvjoint-0.2.1/gmvjoint/R/CreateDataMatrices.R |only gmvjoint-0.2.1/gmvjoint/R/bootAUC.R |only gmvjoint-0.2.1/gmvjoint/R/shape_update.R |only gmvjoint-0.2.1/gmvjoint/man/bootAUC.Rd |only gmvjoint-0.2.1/gmvjoint/man/bootAUCdiff.Rd |only gmvjoint-0.2.1/gmvjoint/src/vech2mat.cpp |only gmvjoint-0.3.0/gmvjoint/DESCRIPTION | 10 gmvjoint-0.3.0/gmvjoint/MD5 | 95 +- gmvjoint-0.3.0/gmvjoint/NAMESPACE | 19 gmvjoint-0.3.0/gmvjoint/NEWS.md | 7 gmvjoint-0.3.0/gmvjoint/R/EMUpdate.R | 211 ++--- gmvjoint-0.3.0/gmvjoint/R/ROC.R | 6 gmvjoint-0.3.0/gmvjoint/R/RcppExports.R | 92 +- gmvjoint-0.3.0/gmvjoint/R/boot.R |only gmvjoint-0.3.0/gmvjoint/R/condb.R | 110 ++ gmvjoint-0.3.0/gmvjoint/R/dynPred-draws.R | 68 - gmvjoint-0.3.0/gmvjoint/R/dynPred-prepare.R | 37 gmvjoint-0.3.0/gmvjoint/R/dynPred.R | 30 gmvjoint-0.3.0/gmvjoint/R/fit2xtab.R |only gmvjoint-0.3.0/gmvjoint/R/fitted.R | 126 +-- gmvjoint-0.3.0/gmvjoint/R/inits.R | 55 - gmvjoint-0.3.0/gmvjoint/R/joint.R | 342 +++++--- gmvjoint-0.3.0/gmvjoint/R/joint.object.R | 62 + gmvjoint-0.3.0/gmvjoint/R/loglik.R | 67 - gmvjoint-0.3.0/gmvjoint/R/makeDataMatrices.R |only gmvjoint-0.3.0/gmvjoint/R/misc.R | 49 + gmvjoint-0.3.0/gmvjoint/R/rfixef.R | 5 gmvjoint-0.3.0/gmvjoint/R/simData.R | 203 +++-- gmvjoint-0.3.0/gmvjoint/R/summary.joint.R | 106 +- gmvjoint-0.3.0/gmvjoint/R/survmod.R | 34 gmvjoint-0.3.0/gmvjoint/R/vcov.R | 183 ++-- gmvjoint-0.3.0/gmvjoint/README.md | 29 gmvjoint-0.3.0/gmvjoint/build/partial.rdb |binary gmvjoint-0.3.0/gmvjoint/man/ROC.Rd | 5 gmvjoint-0.3.0/gmvjoint/man/boot.joint.Rd |only gmvjoint-0.3.0/gmvjoint/man/cond.ranefs.Rd | 14 gmvjoint-0.3.0/gmvjoint/man/dynPred.Rd | 16 gmvjoint-0.3.0/gmvjoint/man/fitted.joint.Rd | 4 gmvjoint-0.3.0/gmvjoint/man/joint.Rd | 95 +- gmvjoint-0.3.0/gmvjoint/man/joint.object.Rd | 60 + gmvjoint-0.3.0/gmvjoint/man/plot.cond.b.joint.Rd |only gmvjoint-0.3.0/gmvjoint/man/residuals.joint.Rd | 3 gmvjoint-0.3.0/gmvjoint/man/rgenpois.Rd | 3 gmvjoint-0.3.0/gmvjoint/man/simData.Rd | 117 ++ gmvjoint-0.3.0/gmvjoint/man/summary.joint.Rd | 21 gmvjoint-0.3.0/gmvjoint/man/xtable.joint.Rd |only gmvjoint-0.3.0/gmvjoint/src/BETAUPDATES.h |only gmvjoint-0.3.0/gmvjoint/src/COMPDATASCORE.h |only gmvjoint-0.3.0/gmvjoint/src/GP1_PMF_SCALAR.cpp | 2 gmvjoint-0.3.0/gmvjoint/src/LOGLIK.h |only gmvjoint-0.3.0/gmvjoint/src/Makevars | 12 gmvjoint-0.3.0/gmvjoint/src/Makevars.win | 12 gmvjoint-0.3.0/gmvjoint/src/RcppExports.cpp | 387 ++++----- gmvjoint-0.3.0/gmvjoint/src/dynpreds.cpp | 91 -- gmvjoint-0.3.0/gmvjoint/src/funs.cpp | 928 ++++++++--------------- gmvjoint-0.3.0/gmvjoint/src/init.c | 74 - 56 files changed, 2039 insertions(+), 1751 deletions(-)
Title: Generalized Coupled Tensor Factorization
Description: Multiple matrices/tensors can be specified and decomposed simultaneously by Probabilistic Latent Tensor Factorisation (PLTF). See the reference section of GitHub README.md <https://github.com/rikenbit/gcTensor>, for details of the method.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between gcTensor versions 0.99.0 dated 2021-09-13 and 1.0.0 dated 2023-07-06
gcTensor-0.99.0/gcTensor/README.md |only gcTensor-1.0.0/gcTensor/DESCRIPTION | 9 gcTensor-1.0.0/gcTensor/LICENSE |only gcTensor-1.0.0/gcTensor/MD5 | 20 - gcTensor-1.0.0/gcTensor/R/GCTF.R | 121 ++++++---- gcTensor-1.0.0/gcTensor/build/partial.rdb |binary gcTensor-1.0.0/gcTensor/inst/NEWS | 4 gcTensor-1.0.0/gcTensor/man/GCTF.Rd | 9 gcTensor-1.0.0/gcTensor/tests/testthat.R | 2 gcTensor-1.0.0/gcTensor/tests/testthat/test_FixZ.R | 5 gcTensor-1.0.0/gcTensor/tests/testthat/test_InputObjectType.R | 5 gcTensor-1.0.0/gcTensor/tests/testthat/test_OutputObjectType.R | 18 + 12 files changed, 129 insertions(+), 64 deletions(-)
Title: Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre] ,
Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between fastDummies versions 1.7.1 dated 2023-07-05 and 1.7.3 dated 2023-07-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/utils.R | 9 ++++----- inst/doc/making-dummy-rows.html | 4 ++-- inst/doc/making-dummy-variables.html | 4 ++-- 6 files changed, 21 insertions(+), 18 deletions(-)
Title: Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion
Polls in Catalonia
Description: Easy and convenient access to the datasets of the
"Centre d'Estudis d'Opinio", the Catalan institution for polling and public
opinion. The package uses the data stored in the servers of the CEO and returns
it in a tidy format.
Author: Xavier Fernandez-i-Marin [aut, cre]
Maintainer: Xavier Fernandez-i-Marin <xavier.fim@gmail.com>
Diff between CEOdata versions 1.3.1 dated 2023-05-17 and 1.3.1.1 dated 2023-07-06
DESCRIPTION | 6 MD5 | 10 R/CEOdata.R | 2 inst/doc/cheatsheet.pdf |binary inst/doc/using_CEOdata.html | 138 +++++----- inst/doc/working_with_survey_data_using_the_CEOdata_package.html | 42 +-- 6 files changed, 99 insertions(+), 99 deletions(-)
Title: Accelerated Functional Failure Time Model with
Error-Contaminated Survival Times
Description: We aim to deal with data with measurement error in the response and misclassification censoring status under an AFT model. This package primarily contains three functions, which are used to generate artificial data, correction for error-prone data and estimate the functional covariates for an AFT model.
Author: Hsiao-Ting Huang <nikkihuang309700034@gmail.com> [cre,aut]
Li-Pang Chen <lchen723@nccu.edu.tw> [aut]
Maintainer: Hsiao-Ting Huang <nikkihuang309700034@gmail.com>
Diff between AFFECT versions 0.1.1 dated 2023-06-04 and 0.1.2 dated 2023-07-06
DESCRIPTION | 6 +- MD5 | 14 ++-- R/boosting.R | 111 +++++++++++++++++++++------------------ R/data_generation.R | 4 - R/measurement_error_correction.R | 8 +- man/Boosting.Rd | 14 +++- man/ME_correction.Rd | 7 +- man/data_gen.Rd | 4 - 8 files changed, 94 insertions(+), 74 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut] ,
Barret Schloerke [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
RStudio [cph],
jQuery Foundation [cph] [...truncated...]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.7.4 dated 2022-12-15 and 1.7.4.1 dated 2023-07-06
shiny-1.7.4.1/shiny/DESCRIPTION | 10 +- shiny-1.7.4.1/shiny/MD5 | 31 +++----- shiny-1.7.4.1/shiny/NEWS.md | 13 ++- shiny-1.7.4.1/shiny/R/globals.R | 6 - shiny-1.7.4.1/shiny/R/staticimports.R | 38 +--------- shiny-1.7.4.1/shiny/R/utils.R | 2 shiny-1.7.4.1/shiny/README.md | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny-autoreload.js | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny-showcase.css | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny-showcase.js | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny-testmode.js | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny.js | 4 - shiny-1.7.4.1/shiny/inst/www/shared/shiny.min.css | 2 shiny-1.7.4.1/shiny/inst/www/shared/shiny.min.js | 4 - shiny-1.7.4.1/shiny/inst/www/shared/shiny.min.js.map | 2 shiny-1.7.4.1/shiny/man/memoryCache.Rd | 2 shiny-1.7.4/shiny/tests/testthat/_snaps/test-shinyAppTemplate.new.md |only 17 files changed, 49 insertions(+), 75 deletions(-)
Title: Helper Functions for Structural Equation Modeling
Description: An assortment of helper functions for doing structural equation
modeling, mainly by 'lavaan' for now. Most of them are time-saving functions
for common tasks in doing structural equation modeling and reading the
output. This package is not for functions that implement advanced statistical
procedures. It is a light-weight package for simple functions that do simple
tasks conveniently, with as few dependencies as possible.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semhelpinghands versions 0.1.6 dated 2023-01-06 and 0.1.8 dated 2023-07-06
DESCRIPTION | 12 ++++++------ MD5 | 32 +++++++++++++++++++++++--------- NAMESPACE | 20 ++++++++++++++++++++ NEWS.md | 24 ++++++++++++++++++++++++ R/annotate_model.R |only R/plot_models_fm.R |only R/show_ifi.R |only R/show_more_options.R | 5 +++-- R/show_options.R |only R/to_vectors.R |only README.md | 5 +++-- build/vignette.rds |binary inst/doc/semhelpinghands.html | 2 +- man/annotate_matrices.Rd |only man/figures |only man/plot_models_fm.Rd |only man/semhelpinghands-package.Rd | 2 ++ man/show_ifi.Rd |only man/show_more_options.Rd | 5 +++-- man/show_options.Rd |only man/vector_from_lavaan.Rd |only tests/testthat/test-annotate_model.R |only tests/testthat/test-plot_models_fm.R |only tests/testthat/test-to_vectors.R |only 24 files changed, 85 insertions(+), 22 deletions(-)
More information about semhelpinghands at CRAN
Permanent link
Title: Creation, Reading and Validation of 'mzqc' Files
Description: Reads, writes and validates 'mzQC' files. The 'mzQC' format is a
standardized file format for the exchange, transmission, and archiving of
quality metrics derived from biological mass spectrometry data, as defined
by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative)
Quality Control working group.
See <https://hupo-psi.github.io/mzQC/> for details.
Author: Chris Bielow [aut, cre] ,
David Jimenez-Morales [rev, ctb]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between rmzqc versions 0.4.2 dated 2023-04-23 and 0.5.0 dated 2023-07-06
rmzqc-0.4.2/rmzqc/man/getDefaultCVVersion.Rd |only rmzqc-0.4.2/rmzqc/vignettes/test.mzQC |only rmzqc-0.5.0/rmzqc/DESCRIPTION | 8 - rmzqc-0.5.0/rmzqc/MD5 | 57 +++---- rmzqc-0.5.0/rmzqc/NAMESPACE | 4 rmzqc-0.5.0/rmzqc/NEWS.md | 4 rmzqc-0.5.0/rmzqc/R/conversion.R | 38 ++-- rmzqc-0.5.0/rmzqc/R/mzQC.R | 6 rmzqc-0.5.0/rmzqc/R/obo.R | 128 +++++++++++++--- rmzqc-0.5.0/rmzqc/R/templates.R | 10 - rmzqc-0.5.0/rmzqc/README.md | 5 rmzqc-0.5.0/rmzqc/build/vignette.rds |binary rmzqc-0.5.0/rmzqc/inst/doc/basic_guide.R | 72 ++++----- rmzqc-0.5.0/rmzqc/inst/doc/basic_guide.Rmd | 6 rmzqc-0.5.0/rmzqc/inst/doc/basic_guide.html | 13 - rmzqc-0.5.0/rmzqc/inst/doc/using_a_custom_cv.R |only rmzqc-0.5.0/rmzqc/inst/doc/using_a_custom_cv.Rmd |only rmzqc-0.5.0/rmzqc/inst/doc/using_a_custom_cv.html |only rmzqc-0.5.0/rmzqc/inst/doc/validation_guide.html | 4 rmzqc-0.5.0/rmzqc/man/CV_.Rd | 34 ++++ rmzqc-0.5.0/rmzqc/man/MzQCcontrolledVocabulary-class.Rd | 4 rmzqc-0.5.0/rmzqc/man/MzQCqualityMetric-class.Rd | 2 rmzqc-0.5.0/rmzqc/man/getCVDictionary.Rd | 23 ++ rmzqc-0.5.0/rmzqc/man/getCVInfo.Rd |only rmzqc-0.5.0/rmzqc/man/getCVSingleton.Rd | 4 rmzqc-0.5.0/rmzqc/man/getCVTemplate.Rd | 4 rmzqc-0.5.0/rmzqc/man/getDefaultCV.Rd | 7 rmzqc-0.5.0/rmzqc/man/getLocal_CV_Version.Rd |only rmzqc-0.5.0/rmzqc/man/getQualityMetricTemplate.Rd | 4 rmzqc-0.5.0/rmzqc/man/parseOBO.Rd | 2 rmzqc-0.5.0/rmzqc/tests/testthat/test_obo.R | 19 +- rmzqc-0.5.0/rmzqc/tests/testthat/test_templates.R |only rmzqc-0.5.0/rmzqc/vignettes/basic_guide.Rmd | 6 rmzqc-0.5.0/rmzqc/vignettes/using_a_custom_cv.Rmd |only 34 files changed, 310 insertions(+), 154 deletions(-)
Title: Multi-Way Component Analysis
Description: For single tensor data, any matrix factorization method can be specified the matricised tensor in each dimension by Multi-way Component Analysis (MWCA). An originally extended MWCA is also implemented to specify and decompose multiple matrices and tensors simultaneously (CoupledMWCA). See the reference section of GitHub README.md <https://github.com/rikenbit/mwTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between mwTensor versions 1.0.1 dated 2023-01-13 and 1.1.0 dated 2023-07-06
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++--------------- R/AllClasses.R | 2 + R/CoupledMWCA.R | 22 +++++++++------ R/CoupledMWCA_Check.R | 2 + R/CoupledMWCA_Initialization.R | 25 +++++++++++++++-- R/MWCA.R | 16 ++++++----- R/MWCA_Check.R | 2 + R/MWCA_Initialization.R | 32 ++++++++++++---------- R/defaultCoupledMWCAParams.R | 1 R/defaultMWCAParams.R | 1 R/mwTensor-internal.R | 4 +- build/partial.rdb |binary inst/NEWS | 4 ++ man/CoupledMWCAParams-class.Rd | 1 man/MWCAParams-class.Rd | 1 tests/testthat.R | 19 ------------- tests/testthat/test_Complex_common.R | 1 tests/testthat/test_Complex_eachData.R | 1 tests/testthat/test_Complex_specific.R | 1 tests/testthat/test_CoupledMWCA_common.R | 1 tests/testthat/test_CoupledMWCA_specific.R | 1 22 files changed, 108 insertions(+), 77 deletions(-)
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to a mixture
of dichotomous and polytomous data, calibrate online item parameters
(i.e., pretest and operational items), estimate examinees' abilities,
and examine the IRT model-data fit on item-level in different ways
as well as provide useful functions related to IRT analyses such as
IRT model-data fit evaluation and differential item functioning analysis.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function was written by modifying the bisection() function
(Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve
scoring in the est_score() function was written by modifying the [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 0.1.1 dated 2023-05-08 and 0.2.0 dated 2023-07-06
DESCRIPTION | 16 + MD5 | 50 +++--- NAMESPACE | 6 NEWS.md | 47 +++++ R/cac_lee.R |only R/cac_rud.R |only R/catsib.R | 18 +- R/est_score.R | 219 ++++++++++++++++---------- R/grdif.R | 81 +++++---- R/info.R | 425 ++++++++++++++++++++++++++++++++++++---------------- R/inv_tcc.R | 22 +- R/irtQ-package.R | 20 +- R/irtfit.R | 2 R/irtmodel.R | 4 R/ll_score.R | 184 ++++++++-------------- R/llike_score.R |only R/lwrc.R | 254 ++++++++++++++++--------------- R/rdif.R | 100 +++++++----- R/simdat.R | 9 - R/traceline.R | 191 +++++++++++++++-------- man/cac_lee.Rd |only man/cac_rud.Rd |only man/catsib.Rd | 16 + man/est_score.Rd | 43 +++-- man/grdif.Rd | 23 +- man/info.Rd | 3 man/irtQ-package.Rd | 20 +- man/llike_score.Rd |only man/rdif.Rd | 22 +- 29 files changed, 1075 insertions(+), 700 deletions(-)
Title: Selection and Ranking of Omics Biomarkers Combinations Made Easy
Description: Provides functions and a workflow to easily and powerfully calculating specificity, sensitivity and ROC curves of biomarkers combinations. Allows to rank and select multi-markers signatures as well as to find the best performing sub-signatures, now also from single-cell RNA-seq datasets. The method used was first published as a Shiny app and described in Mazzara et al. (2017) <doi:10.1038/srep45477> and further described in Bombaci & Rossi (2019) <doi:10.1007/978-1-4939-9164-8_16>, and widely expanded as a package as presented in the bioRxiv pre print Ferrari et al. <doi:10.1101/2022.01.17.476603>.
Author: Ivan Ferrari [aut] ,
Riccardo L. Rossi [aut, cre] ,
Saveria Mazzara [aut] ,
Mauro Bombaci [ccp, ctb, dtc]
Maintainer: Riccardo L. Rossi <ric.rossi@gmail.com>
Diff between combiroc versions 0.2.3 dated 2021-08-17 and 0.3.4 dated 2023-07-06
combiroc-0.2.3/combiroc/R/classify.R |only combiroc-0.2.3/combiroc/R/combiroc.R |only combiroc-0.2.3/combiroc/R/examples/classify_example.R |only combiroc-0.2.3/combiroc/R/examples/load_unclassified_data_example.R |only combiroc-0.2.3/combiroc/R/examples/se_sp_example.R |only combiroc-0.2.3/combiroc/R/load_unclassified_data.R |only combiroc-0.2.3/combiroc/R/se_sp.R |only combiroc-0.2.3/combiroc/inst/doc/combiroc_standard.R |only combiroc-0.2.3/combiroc/inst/doc/combiroc_standard.Rmd |only combiroc-0.2.3/combiroc/inst/doc/combiroc_standard.html |only combiroc-0.2.3/combiroc/man/classify.Rd |only combiroc-0.2.3/combiroc/man/combiroc.Rd |only combiroc-0.2.3/combiroc/man/load_unclassified_data.Rd |only combiroc-0.2.3/combiroc/man/se_sp.Rd |only combiroc-0.2.3/combiroc/tests/testthat/test-load_unclassified_data.R |only combiroc-0.2.3/combiroc/tests/testthat/test-se_sp.R |only combiroc-0.2.3/combiroc/vignettes/combiroc_standard.Rmd |only combiroc-0.3.4/combiroc/DESCRIPTION | 21 - combiroc-0.3.4/combiroc/LICENSE | 4 combiroc-0.3.4/combiroc/MD5 | 155 +++++----- combiroc-0.3.4/combiroc/NAMESPACE | 5 combiroc-0.3.4/combiroc/NEWS.md |only combiroc-0.3.4/combiroc/R/combi.R | 14 combiroc-0.3.4/combiroc/R/combi_score.R |only combiroc-0.3.4/combiroc/R/combiroc_long.R | 3 combiroc-0.3.4/combiroc/R/combs_with.R | 48 +-- combiroc-0.3.4/combiroc/R/demo_data.R | 9 combiroc-0.3.4/combiroc/R/demo_unclassified_data.R | 9 combiroc-0.3.4/combiroc/R/examples/combi_example.R | 9 combiroc-0.3.4/combiroc/R/examples/combi_score_example.R |only combiroc-0.3.4/combiroc/R/examples/combiroc_long_example.R | 4 combiroc-0.3.4/combiroc/R/examples/combs_with_example.R | 4 combiroc-0.3.4/combiroc/R/examples/demo_data_example.R |only combiroc-0.3.4/combiroc/R/examples/demo_unclassified_data_example.R |only combiroc-0.3.4/combiroc/R/examples/load_data_example.R | 15 combiroc-0.3.4/combiroc/R/examples/markers_distribution_example.R | 2 combiroc-0.3.4/combiroc/R/examples/ranked_combs_example.R | 10 combiroc-0.3.4/combiroc/R/examples/roc_reports_example.R | 4 combiroc-0.3.4/combiroc/R/examples/seurat_to_combiroc_example.R |only combiroc-0.3.4/combiroc/R/examples/show_markers_example.R | 4 combiroc-0.3.4/combiroc/R/examples/single_markers_statistics_example.R | 2 combiroc-0.3.4/combiroc/R/load_data.R | 73 ++-- combiroc-0.3.4/combiroc/R/markers_distribution.R | 48 +-- combiroc-0.3.4/combiroc/R/ranked_combs.R | 130 ++------ combiroc-0.3.4/combiroc/R/roc_reports.R | 31 +- combiroc-0.3.4/combiroc/R/seurat_to_combiroc.R |only combiroc-0.3.4/combiroc/R/show_markers.R | 44 +- combiroc-0.3.4/combiroc/R/single_markers_statistics.R | 104 +++--- combiroc-0.3.4/combiroc/README.md | 60 ++- combiroc-0.3.4/combiroc/build/vignette.rds |binary combiroc-0.3.4/combiroc/inst/doc/combiroc_vignette_1.R |only combiroc-0.3.4/combiroc/inst/doc/combiroc_vignette_1.Rmd |only combiroc-0.3.4/combiroc/inst/doc/combiroc_vignette_1.html |only combiroc-0.3.4/combiroc/inst/doc/combiroc_vignette_2.R |only 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combiroc-0.3.4/combiroc/vignettes/roc_curve_vign1.png |only combiroc-0.3.4/combiroc/vignettes/roc_curve_zoom.png |only 105 files changed, 872 insertions(+), 796 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph]
,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.3.0 dated 2023-05-22 and 4.3.20 dated 2023-07-06
spaMM-4.3.0/spaMM/tests/plot1.pdf |only spaMM-4.3.0/spaMM/tests/plot2.pdf |only spaMM-4.3.0/spaMM/tests/testthat/Rplots.pdf |only spaMM-4.3.20/spaMM/DESCRIPTION | 8 spaMM-4.3.20/spaMM/MD5 | 136 ++--- spaMM-4.3.20/spaMM/NAMESPACE | 2 spaMM-4.3.20/spaMM/R/HLFactorList.R | 73 +- spaMM-4.3.20/spaMM/R/HLfit_Internals.R | 132 ++-- spaMM-4.3.20/spaMM/R/HLframes.R | 27 - spaMM-4.3.20/spaMM/R/LR.R | 269 +++++++--- spaMM-4.3.20/spaMM/R/LevM_internals.R | 10 spaMM-4.3.20/spaMM/R/MakeCovEst.R | 4 spaMM-4.3.20/spaMM/R/Matern_family.R | 1 spaMM-4.3.20/spaMM/R/calc_LRT.R | 30 - spaMM-4.3.20/spaMM/R/calc_logdisp_cov.R | 4 spaMM-4.3.20/spaMM/R/constructors_IMRFs.R | 1 spaMM-4.3.20/spaMM/R/corrHLfit-internals.R | 22 spaMM-4.3.20/spaMM/R/corrMM.LRT.R | 23 spaMM-4.3.20/spaMM/R/correlationFns.R | 12 spaMM-4.3.20/spaMM/R/cov_new_fix.R | 7 spaMM-4.3.20/spaMM/R/extractors.R | 31 - spaMM-4.3.20/spaMM/R/fitme.R | 5 spaMM-4.3.20/spaMM/R/fitmecorrHLfit_body_internals.R | 48 + spaMM-4.3.20/spaMM/R/geo_info.R | 20 spaMM-4.3.20/spaMM/R/llm.fit.R | 4 spaMM-4.3.20/spaMM/R/multiFRK.R | 4 spaMM-4.3.20/spaMM/R/newPLS.R | 28 - spaMM-4.3.20/spaMM/R/numInfo.R | 15 spaMM-4.3.20/spaMM/R/postfit_internals.R | 14 spaMM-4.3.20/spaMM/R/predict.R | 28 - spaMM-4.3.20/spaMM/R/predict_mv.R | 6 spaMM-4.3.20/spaMM/R/preprocess.R | 6 spaMM-4.3.20/spaMM/R/preprocess_internals.R | 10 spaMM-4.3.20/spaMM/R/sXaug_EigenDense_QRP_Chol_scaled.R | 4 spaMM-4.3.20/spaMM/R/sXaug_Matrix_CHM_Hess.R | 21 spaMM-4.3.20/spaMM/R/sXaug_Matrix_QRP_CHM.R | 6 spaMM-4.3.20/spaMM/R/sXaug_sparsePrecisions.R | 43 - spaMM-4.3.20/spaMM/R/simulate.HL.R | 72 +- spaMM-4.3.20/spaMM/R/spaMM.data.R | 7 spaMM-4.3.20/spaMM/R/spaMM_boot.R | 102 ++- spaMM-4.3.20/spaMM/R/summary.HL.R | 52 + spaMM-4.3.20/spaMM/R/terms.R | 4 spaMM-4.3.20/spaMM/R/update.HL.R | 73 -- spaMM-4.3.20/spaMM/R/utils.R | 57 +- spaMM-4.3.20/spaMM/build/partial.rdb |binary spaMM-4.3.20/spaMM/inst/NEWS.Rd | 23 spaMM-4.3.20/spaMM/man/IMRF.Rd | 2 spaMM-4.3.20/spaMM/man/R2.Rd | 2 spaMM-4.3.20/spaMM/man/anova.HLfit.Rd | 80 +- spaMM-4.3.20/spaMM/man/betabin.Rd | 2 spaMM-4.3.20/spaMM/man/diallel.Rd | 2 spaMM-4.3.20/spaMM/man/div_info.Rd | 23 spaMM-4.3.20/spaMM/man/lev2bool.Rd |only spaMM-4.3.20/spaMM/man/mapMM.Rd | 23 spaMM-4.3.20/spaMM/man/register_cF.Rd | 2 spaMM-4.3.20/spaMM/man/seaMask.Rd | 3 spaMM-4.3.20/spaMM/man/simulate.Rd | 40 + spaMM-4.3.20/spaMM/man/spaMM.Rd | 34 - spaMM-4.3.20/spaMM/man/spaMM_boot.Rd | 61 ++ spaMM-4.3.20/spaMM/tests/test-all.R | 6 spaMM-4.3.20/spaMM/tests/testthat/extralong/test-composite-extra.R | 13 spaMM-4.3.20/spaMM/tests/testthat/extralong/test-mv-extra.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-ANOVA-&-lmerTest.R | 22 spaMM-4.3.20/spaMM/tests/testthat/test-CAR.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-DHARMa.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-LLM.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-LRT-boot.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-augZXy.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-cloglog.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-ranCoefs.R | 2 spaMM-4.3.20/spaMM/tests/testthat/test-rank.R | 5 71 files changed, 1075 insertions(+), 705 deletions(-)
Title: Non-Crossing Additive Regression Quantiles and Non-Parametric
Growth Charts
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms, including varying coefficients, via B-splines with L1-norm difference penalties.
Random intercepts and variable selection are allowed via the lasso penalties.
The smoothing parameters are estimated as part of the model fitting, see Muggeo and others (2021) <doi:10.1177/1471082X20929802>. Monotonicity and concavity
constraints on the fitted curves are allowed, see Muggeo and others (2013) <doi:10.1007/s10651-012-0232-1>,
and also <doi:10.13140/RG.2.2.12924.85122> or <doi:10.13140/RG.2.2.29306.21445> some code examples.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 1.6-2 dated 2023-05-25 and 1.7-0 dated 2023-07-06
DESCRIPTION | 12 MD5 | 43 - NAMESPACE | 4 NEWS | 17 R/gcrq.r | 174 +++++-- R/gcrq.rq.cv.R | 10 R/ncross.rq.fitXB.r | 68 ++- R/ncross.rq.fitXBsparse.r |only R/plot.gcrq.R | 5 R/predict.gcrq.R | 26 - R/summary.gcrq.R | 1 R/vcov.gcrq.r | 7 build/vignette.rds |binary inst/doc/quantregGrowth.R | 18 inst/doc/quantregGrowth.Rmd | 42 + inst/doc/quantregGrowth.html | 939 +++++++++++++----------------------------- man/gcrq.Rd | 22 man/logLik.gcrq.Rd | 3 man/ncross.rq.fitXB.Rd | 18 man/plot.gcrq.Rd | 7 man/ps.Rd | 9 man/quantregGrowth-package.Rd | 6 vignettes/quantregGrowth.Rmd | 42 + 23 files changed, 644 insertions(+), 829 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net>, Jon Bishop and Jonah McArthur
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.2.8 dated 2022-11-16 and 2.2.9 dated 2023-07-06
mrds-2.2.8/mrds/R/plot.layout.R |only mrds-2.2.8/mrds/man/plot.layout.Rd |only mrds-2.2.9/mrds/DESCRIPTION | 13 +-- mrds-2.2.9/mrds/MD5 | 89 +++++++++++++------------ mrds-2.2.9/mrds/NAMESPACE | 2 mrds-2.2.9/mrds/NEWS | 14 +++ mrds-2.2.9/mrds/R/check.mono.R | 4 - mrds-2.2.9/mrds/R/create.bins.R | 19 +++-- mrds-2.2.9/mrds/R/ddf.R | 23 ++++-- mrds-2.2.9/mrds/R/ddf.ds.R | 99 ++++++++++++++++++++++++---- mrds-2.2.9/mrds/R/ddf.io.R | 11 ++- mrds-2.2.9/mrds/R/ddf.io.fi.R | 12 ++- mrds-2.2.9/mrds/R/ddf.rem.R | 14 ++- mrds-2.2.9/mrds/R/ddf.rem.fi.R | 8 +- mrds-2.2.9/mrds/R/ddf.trial.R | 13 ++- mrds-2.2.9/mrds/R/ddf.trial.fi.R | 11 ++- mrds-2.2.9/mrds/R/detfct.fit.R | 11 +++ mrds-2.2.9/mrds/R/detfct.fit.opt.R | 2 mrds-2.2.9/mrds/R/dht.R | 102 +++++++++++++++-------------- mrds-2.2.9/mrds/R/mcds_tools.R |only mrds-2.2.9/mrds/R/nlminb_wrapper.R | 1 mrds-2.2.9/mrds/R/plot.io.R | 2 mrds-2.2.9/mrds/R/plot.io.fi.R | 2 mrds-2.2.9/mrds/R/plot.rem.R | 2 mrds-2.2.9/mrds/R/plot.rem.fi.R | 2 mrds-2.2.9/mrds/R/plot.trial.R | 2 mrds-2.2.9/mrds/R/plot.trial.fi.R | 2 mrds-2.2.9/mrds/R/plot_layout.R |only mrds-2.2.9/mrds/R/predict.ds.R | 5 + mrds-2.2.9/mrds/R/print.summary.ds.R | 1 mrds-2.2.9/mrds/R/solvecov.R | 2 mrds-2.2.9/mrds/R/summary.ds.R | 3 mrds-2.2.9/mrds/R/zzz.R | 9 ++ mrds-2.2.9/mrds/README.md | 3 mrds-2.2.9/mrds/build/partial.rdb |binary mrds-2.2.9/mrds/build/vignette.rds |only mrds-2.2.9/mrds/inst/doc |only mrds-2.2.9/mrds/man/create.command.file.Rd |only mrds-2.2.9/mrds/man/ddf.Rd | 15 +++- mrds-2.2.9/mrds/man/ddf.ds.Rd | 20 ++++- mrds-2.2.9/mrds/man/ddf.io.Rd | 12 +++ mrds-2.2.9/mrds/man/ddf.io.fi.Rd | 20 ++++- mrds-2.2.9/mrds/man/ddf.rem.Rd | 12 +++ mrds-2.2.9/mrds/man/ddf.rem.fi.Rd | 20 ++++- mrds-2.2.9/mrds/man/ddf.trial.Rd | 12 +++ mrds-2.2.9/mrds/man/ddf.trial.fi.Rd | 20 ++++- mrds-2.2.9/mrds/man/mcds_dot_exe.Rd |only mrds-2.2.9/mrds/man/plot_layout.Rd |only mrds-2.2.9/mrds/vignettes |only 49 files changed, 432 insertions(+), 182 deletions(-)
Title: Parse XML
Description: Work with XML files using a simple, consistent interface.
Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre],
Jim Hester [aut],
Jeroen Ooms [aut],
RStudio [cph, fnd],
R Foundation [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between xml2 versions 1.3.4 dated 2023-04-27 and 1.3.5 dated 2023-07-06
DESCRIPTION | 6 MD5 | 42 ++--- NEWS.md | 6 R/classes.R | 25 ++- R/xml_modify.R | 9 - README.md | 2 build/xml2.pdf |binary inst/doc/modification.R | 9 - inst/doc/modification.Rmd | 17 +- inst/doc/modification.html | 329 ++++++++++++++++++++++----------------------- src/connection.cpp | 5 src/connection.h | 2 src/init.c | 5 src/xml2_doc.cpp | 2 src/xml2_namespace.cpp | 3 src/xml2_output.cpp | 4 src/xml2_schema.cpp | 5 src/xml2_url.cpp | 2 src/xml2_utils.h | 3 src/xml2_xpath.cpp | 5 tests/testthat/test-url.R | 10 - vignettes/modification.Rmd | 17 +- 22 files changed, 279 insertions(+), 229 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and download
machine learning data, tasks and experiments. The 'OpenML' objects can
be automatically converted to 'mlr3' objects. For a more
sophisticated interface which also allows uploading to 'OpenML', see
the 'OpenML' package.
Author: Michel Lang [aut] ,
Sebastian Fischer [cre, aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3oml versions 0.7.2 dated 2023-06-12 and 0.8.0 dated 2023-07-06
mlr3oml-0.7.2/mlr3oml/R/benchmark_grid_oml.R |only mlr3oml-0.7.2/mlr3oml/man/benchmark_grid_oml.Rd |only mlr3oml-0.7.2/mlr3oml/man/oml_sugar.Rd |only mlr3oml-0.7.2/mlr3oml/tests/testthat/test_benchmark_grid_oml.R |only mlr3oml-0.7.2/mlr3oml/tests/testthat/test_list_oml_data_sets.R |only mlr3oml-0.7.2/mlr3oml/tests/testthat/test_list_oml_task.R |only mlr3oml-0.8.0/mlr3oml/DESCRIPTION | 7 mlr3oml-0.8.0/mlr3oml/MD5 | 101 +- mlr3oml-0.8.0/mlr3oml/NAMESPACE | 2 mlr3oml-0.8.0/mlr3oml/NEWS.md | 16 mlr3oml-0.8.0/mlr3oml/R/OMLCollection.R | 185 ---- mlr3oml-0.8.0/mlr3oml/R/OMLData.R | 58 - mlr3oml-0.8.0/mlr3oml/R/OMLFlow.R | 27 mlr3oml-0.8.0/mlr3oml/R/OMLObject.R | 17 mlr3oml-0.8.0/mlr3oml/R/OMLResamplingConnector.R | 5 mlr3oml-0.8.0/mlr3oml/R/OMLRun.R | 44 - mlr3oml-0.8.0/mlr3oml/R/OMLTask.R | 38 mlr3oml-0.8.0/mlr3oml/R/OMLTaskConnector.R | 6 mlr3oml-0.8.0/mlr3oml/R/cache.R | 5 mlr3oml-0.8.0/mlr3oml/R/helper.R | 16 mlr3oml-0.8.0/mlr3oml/R/list_oml_data.R | 29 mlr3oml-0.8.0/mlr3oml/R/list_oml_runs.R | 2 mlr3oml-0.8.0/mlr3oml/R/list_oml_setups.R | 3 mlr3oml-0.8.0/mlr3oml/R/list_oml_tasks.R | 2 mlr3oml-0.8.0/mlr3oml/R/sugar.R | 76 + mlr3oml-0.8.0/mlr3oml/R/utils.R | 6 mlr3oml-0.8.0/mlr3oml/R/zzz.R | 7 mlr3oml-0.8.0/mlr3oml/README.md | 413 ++-------- mlr3oml-0.8.0/mlr3oml/build/partial.rdb |binary mlr3oml-0.8.0/mlr3oml/inst/testthat/helper_expectation.R | 21 mlr3oml-0.8.0/mlr3oml/man/list_oml.Rd | 33 mlr3oml-0.8.0/mlr3oml/man/mlr3oml-package.Rd | 7 mlr3oml-0.8.0/mlr3oml/man/ocl.Rd |only mlr3oml-0.8.0/mlr3oml/man/odt.Rd |only mlr3oml-0.8.0/mlr3oml/man/oflw.Rd |only mlr3oml-0.8.0/mlr3oml/man/oml_collection.Rd | 72 - mlr3oml-0.8.0/mlr3oml/man/oml_data.Rd | 63 - mlr3oml-0.8.0/mlr3oml/man/oml_flow.Rd | 37 mlr3oml-0.8.0/mlr3oml/man/oml_object.Rd | 11 mlr3oml-0.8.0/mlr3oml/man/oml_run.Rd | 40 mlr3oml-0.8.0/mlr3oml/man/oml_task.Rd | 40 mlr3oml-0.8.0/mlr3oml/man/orn.Rd |only mlr3oml-0.8.0/mlr3oml/man/otsk.Rd |only mlr3oml-0.8.0/mlr3oml/src/init.c | 3 mlr3oml-0.8.0/mlr3oml/src/parse_arff_levels.cpp | 7 mlr3oml-0.8.0/mlr3oml/src/remove_comments.cpp | 7 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLCollection.R | 48 - mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLData.R | 32 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLFlow.R | 33 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLObject.R |only mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLRun.R | 46 - mlr3oml-0.8.0/mlr3oml/tests/testthat/test_OMLTask.R | 34 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_cache.R | 123 +- mlr3oml-0.8.0/mlr3oml/tests/testthat/test_helpers.R |only mlr3oml-0.8.0/mlr3oml/tests/testthat/test_list_oml_data.R |only mlr3oml-0.8.0/mlr3oml/tests/testthat/test_list_oml_tasks.R |only mlr3oml-0.8.0/mlr3oml/tests/testthat/test_manual.R | 6 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_read_arff.R | 2 mlr3oml-0.8.0/mlr3oml/tests/testthat/test_s3_converter.R | 1 59 files changed, 695 insertions(+), 1036 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.10 dated 2022-12-15 and 1.6.11 dated 2023-07-06
DESCRIPTION | 8 - MD5 | 34 +++---- NEWS.md | 4 R/08-geoknife-function.R | 3 R/cancel-geojob.R | 3 build/vignette.rds |binary inst/CITATION | 32 +++---- inst/doc/custom_data_sources.R | 68 +++++++-------- inst/doc/custom_data_sources.Rmd | 164 +++++++++++++++++++------------------- inst/doc/custom_data_sources.html | 64 ++++++-------- inst/doc/geoknife.html | 2 inst/doc/plot_geotiff.R | 68 +++++++-------- inst/doc/plot_geotiff.Rmd | 3 inst/doc/plot_geotiff.html | 5 - man/cancel-methods.Rd | 3 man/geoknife-methods.Rd | 3 vignettes/custom_data_sources.Rmd | 164 +++++++++++++++++++------------------- vignettes/plot_geotiff.Rmd | 3 18 files changed, 314 insertions(+), 317 deletions(-)
Title: Nonparametric Estimation of Toeplitz Covariance Matrices
Description: A nonparametric method to estimate Toeplitz covariance matrices from a sample of n independently and identically distributed p-dimensional vectors with mean zero. The data is preprocessed with the discrete cosine matrix and a variance stabilization transformation to obtain an approximate Gaussian regression setting for the log-spectral density function. Estimates of the spectral density function and the inverse of the covariance matrix are provided as well. Functions for simulating data and a protein data example are included. For details see (Klockmann, Krivobokova; 2023), <arXiv:2303.10018>.
Author: Karolina Klockmann [aut, cre],
Tatyana Krivobokova [aut]
Maintainer: Karolina Klockmann <karolina.klockmann@gmx.de>
Diff between vstdct versions 0.1 dated 2023-06-22 and 0.2 dated 2023-07-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-vst_dct_fcts.R | 20 -------------------- 3 files changed, 5 insertions(+), 25 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.10 dated 2023-01-22 and 1.0.11 dated 2023-07-06
ChangeLog | 114 +++++++++++++++++++++++++++++ DESCRIPTION | 9 +- MD5 | 72 +++++++++--------- R/Attributes.R | 10 +- R/RcppLdpath.R | 10 ++ README.md | 22 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 53 +++++-------- inst/NEWS.Rd | 35 ++++++++ inst/bib/Rcpp.bib | 18 ++-- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/config.h | 8 +- inst/include/Rcpp/sugar/functions/sapply.h | 13 ++- inst/tinytest/test_stats.R | 6 + inst/tinytest/test_sugar.R | 24 +++--- inst/tinytest/test_xptr.R | 11 ++ src/attributes.cpp | 9 +- vignettes/pdf/Rcpp-FAQ.pdf |binary vignettes/pdf/Rcpp-attributes.pdf |binary vignettes/pdf/Rcpp-extending.pdf |binary vignettes/pdf/Rcpp-introduction.pdf |binary vignettes/pdf/Rcpp-jss-2011.pdf |binary vignettes/pdf/Rcpp-libraries.pdf |binary vignettes/pdf/Rcpp-modules.pdf |binary vignettes/pdf/Rcpp-package.pdf |binary vignettes/pdf/Rcpp-quickref.pdf |binary vignettes/pdf/Rcpp-sugar.pdf |binary 37 files changed, 292 insertions(+), 122 deletions(-)
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and visualize linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
The methods and the package are explained in detail in Adämmer (2019) <doi:10.32614/RJ-2019-052>.
Author: Philipp Adaemmer [aut, cre] ,
James P. LeSage [ctb],
Mehmet Balcilar [ctb],
Jon Danielsson [ctb]
Maintainer: Philipp Adaemmer <philipp.adaemmer@uni-greifswald.de>
Diff between lpirfs versions 0.2.2 dated 2022-11-12 and 0.2.3 dated 2023-07-06
DESCRIPTION | 12 MD5 | 32 NEWS.md | 6 R/lp_lin_iv.R | 44 R/lp_lin_panel.R | 36 R/lp_nl_panel.R | 54 - R/plot_lin.R | 4 R/plot_nl.R | 8 README.md | 36 build/partial.rdb |binary build/vignette.rds |binary inst/doc/lpirfs_vignette.html | 1810 ++++++++++++++++++++-------------------- man/lp_lin_panel.Rd | 5 man/lp_nl_panel.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test-lp_lin_iv.R | 20 17 files changed, 1069 insertions(+), 1006 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-18 1.0.0
2021-09-27 0.1.3
2021-05-04 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 1.0.4
2020-08-04 1.0.3
2020-05-22 1.0.2
2020-02-05 1.0.1
2019-05-25 1.0.0
2018-12-06 0.7.2
2018-06-20 0.7.1
2017-12-14 0.7.0
2017-10-22 0.6.0