Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
The authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.0 dated 2021-12-06 and 0.3.27 dated 2022-12-02
salso-0.3.0/salso/R/rustlib.R |only salso-0.3.0/salso/src/rustlib |only salso-0.3.0/salso/tools/cargo.R |only salso-0.3.0/salso/tools/staticlib.R |only salso-0.3.27/salso/DESCRIPTION | 25 +++--- salso-0.3.27/salso/INSTALL | 46 ++++++++---- salso-0.3.27/salso/LICENSE | 4 - salso-0.3.27/salso/LICENSE.note |only salso-0.3.27/salso/MD5 | 87 ++++++++++++----------- salso-0.3.27/salso/NEWS | 7 + salso-0.3.27/salso/R/bell.R | 4 + salso-0.3.27/salso/R/dlso.R | 4 + salso-0.3.27/salso/R/enumerate.partitions.R | 4 + salso-0.3.27/salso/R/kall.R |only salso-0.3.27/salso/R/partition.loss.R | 15 ++- salso-0.3.27/salso/R/plot.salso.summary.R | 4 + salso-0.3.27/salso/R/psm.R | 8 ++ salso-0.3.27/salso/R/salso.R | 16 ++-- salso-0.3.27/salso/R/summary.salso.estimate.R | 4 + salso-0.3.27/salso/R/useDynLib.R |only salso-0.3.27/salso/build |only salso-0.3.27/salso/configure |only salso-0.3.27/salso/configure.win |only salso-0.3.27/salso/inst |only salso-0.3.27/salso/man/bell.Rd | 6 + salso-0.3.27/salso/man/dlso.Rd | 8 +- salso-0.3.27/salso/man/enumerate.partitions.Rd | 6 + salso-0.3.27/salso/man/iris.clusterings.Rd | 2 salso-0.3.27/salso/man/partition.loss.Rd | 15 ++- salso-0.3.27/salso/man/plot.salso.summary.Rd | 6 + salso-0.3.27/salso/man/psm.Rd | 12 ++- salso-0.3.27/salso/man/salso.Rd | 23 ++---- salso-0.3.27/salso/man/summary.salso.estimate.Rd | 12 ++- salso-0.3.27/salso/src/Makevars | 17 ---- salso-0.3.27/salso/src/Makevars.win | 18 ---- salso-0.3.27/salso/src/README.md |only salso-0.3.27/salso/src/rust |only salso-0.3.27/salso/src/shim.c | 4 - salso-0.3.27/salso/tools/cargo_run.R |only 39 files changed, 216 insertions(+), 141 deletions(-)
Title: Molecular Acquisition, Cleaning, and Evaluation in R 'MACER'
Description: To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. 'MACER' accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The 'MACER' package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.
Author: Robert G Young [aut, cre, cph]
,
Rekkab Gill [aut],
Daniel Gillis [aut],
Robert H Hanner [aut, cph]
Maintainer: Robert G Young <rgyoung6@gmail.com>
Diff between MACER versions 0.2.0 dated 2022-10-04 and 0.2.1 dated 2022-12-02
DESCRIPTION | 6 MD5 | 8 - R/barcode_clean.R | 368 +++++++++++++++++++++++++++------------------------ README.md | 8 - man/barcode_clean.Rd | 5 5 files changed, 215 insertions(+), 180 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.7.5 dated 2022-10-18 and 2.7.6 dated 2022-12-02
soilDB-2.7.5/soilDB/R/simplfyFragmentData.R |only soilDB-2.7.6/soilDB/DESCRIPTION | 10 soilDB-2.7.6/soilDB/MD5 | 143 ++++++------ soilDB-2.7.6/soilDB/NAMESPACE | 6 soilDB-2.7.6/soilDB/NEWS.md | 27 ++ soilDB-2.7.6/soilDB/R/AAAA.R | 21 + soilDB-2.7.6/soilDB/R/ISSR800.R | 13 + soilDB-2.7.6/soilDB/R/OSDquery.R | 13 - soilDB-2.7.6/soilDB/R/SDA_query.R | 6 soilDB-2.7.6/soilDB/R/SSURGO_spatial_query.R | 5 soilDB-2.7.6/soilDB/R/SoilDataViewer.R | 13 - soilDB-2.7.6/soilDB/R/fetchEDIT_tools.R | 5 soilDB-2.7.6/soilDB/R/fetchKSSL.R | 6 soilDB-2.7.6/soilDB/R/fetchLDM.R | 9 soilDB-2.7.6/soilDB/R/fetchNASIS.R | 2 soilDB-2.7.6/soilDB/R/fetchNASISLabData.R | 4 soilDB-2.7.6/soilDB/R/fetchNASISWebReport.R | 6 soilDB-2.7.6/soilDB/R/fetchNASIS_components.R | 12 - soilDB-2.7.6/soilDB/R/fetchNASIS_pedons.R | 42 +-- soilDB-2.7.6/soilDB/R/fetchNASIS_report.R | 8 soilDB-2.7.6/soilDB/R/fetchOSD.R | 39 +-- soilDB-2.7.6/soilDB/R/fetchPedonPC.R | 4 soilDB-2.7.6/soilDB/R/fetchRaCA.R | 8 soilDB-2.7.6/soilDB/R/fetchSCAN.R | 9 soilDB-2.7.6/soilDB/R/fetchSDA_spatial.R | 5 soilDB-2.7.6/soilDB/R/fetchSRI.R |only soilDB-2.7.6/soilDB/R/fetchSoilGrids.R | 9 soilDB-2.7.6/soilDB/R/fetchVegdata.R | 2 soilDB-2.7.6/soilDB/R/get_OSD.R | 10 soilDB-2.7.6/soilDB/R/get_SDA_interpretation.R | 18 - soilDB-2.7.6/soilDB/R/get_SDA_property.R | 5 soilDB-2.7.6/soilDB/R/get_component_data_from_NASIS_db.R | 20 - soilDB-2.7.6/soilDB/R/get_component_from_SDA.R | 10 soilDB-2.7.6/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 39 +-- soilDB-2.7.6/soilDB/R/get_site_data_from_NASIS_db.R | 8 soilDB-2.7.6/soilDB/R/get_site_data_from_pedon_db.R | 8 soilDB-2.7.6/soilDB/R/get_veg_data_from_NASIS_db.R | 36 --- soilDB-2.7.6/soilDB/R/get_vegplot_data_from_NASIS_db.R | 12 - soilDB-2.7.6/soilDB/R/mukey-WCS.R | 14 - soilDB-2.7.6/soilDB/R/seriesExtent.R | 23 - soilDB-2.7.6/soilDB/R/siblings.R | 10 soilDB-2.7.6/soilDB/R/simplifyFragmentData.R |only soilDB-2.7.6/soilDB/R/soilDB-package.R | 2 soilDB-2.7.6/soilDB/R/taxaExtent.R | 13 - soilDB-2.7.6/soilDB/R/uncode.R | 8 soilDB-2.7.6/soilDB/R/utils.R | 2 soilDB-2.7.6/soilDB/R/waterDayYear.R | 3 soilDB-2.7.6/soilDB/inst/CITATION | 4 soilDB-2.7.6/soilDB/man/OSDquery.Rd | 10 soilDB-2.7.6/soilDB/man/SDA_query.Rd | 7 soilDB-2.7.6/soilDB/man/SoilWeb_spatial_query.Rd | 6 soilDB-2.7.6/soilDB/man/dot-get_SRI_gdb_names.Rd |only soilDB-2.7.6/soilDB/man/fetchKSSL.Rd | 7 soilDB-2.7.6/soilDB/man/fetchLDM.Rd | 8 soilDB-2.7.6/soilDB/man/fetchNASIS.Rd | 2 soilDB-2.7.6/soilDB/man/fetchOSD.Rd | 39 +-- soilDB-2.7.6/soilDB/man/fetchRaCA.Rd | 8 soilDB-2.7.6/soilDB/man/fetchSCAN.Rd | 9 soilDB-2.7.6/soilDB/man/fetchSDA_spatial.Rd | 5 soilDB-2.7.6/soilDB/man/fetchSRI.Rd |only soilDB-2.7.6/soilDB/man/fetchSoilGrids.Rd | 9 soilDB-2.7.6/soilDB/man/get_EDIT_ecoclass_by_geoUnit.Rd | 5 soilDB-2.7.6/soilDB/man/get_NASIS_metadata.Rd | 2 soilDB-2.7.6/soilDB/man/get_OSD.Rd | 11 soilDB-2.7.6/soilDB/man/get_SDA_interpretation.Rd | 18 - soilDB-2.7.6/soilDB/man/get_SDA_property.Rd | 6 soilDB-2.7.6/soilDB/man/get_SRI.Rd |only soilDB-2.7.6/soilDB/man/get_SRI_layers.Rd |only soilDB-2.7.6/soilDB/man/get_soilDB_env.Rd |only soilDB-2.7.6/soilDB/man/get_veg_data_from_NASIS_db.Rd | 4 soilDB-2.7.6/soilDB/man/seriesExtent.Rd | 23 - soilDB-2.7.6/soilDB/man/siblings.Rd | 8 soilDB-2.7.6/soilDB/man/simplifyFragmentData.Rd | 38 +-- soilDB-2.7.6/soilDB/man/soilDB-package.Rd | 1 soilDB-2.7.6/soilDB/man/taxaExtent.Rd | 11 soilDB-2.7.6/soilDB/man/waterDayYear.Rd | 5 soilDB-2.7.6/soilDB/tests/testthat/test-fetchSRI.R |only 77 files changed, 405 insertions(+), 509 deletions(-)
Title: Unified Framework for Numerical Optimizer
Description: Provides a unified framework for numerical optimizer in R,
particularly for their inputs and outputs.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Ötting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 0.1.1 dated 2022-09-02 and 0.2.0 dated 2022-12-02
optimizeR-0.1.1/optimizeR/R/functions.R |only optimizeR-0.1.1/optimizeR/man/figures |only optimizeR-0.1.1/optimizeR/man/set_optimizer_nlm.Rd |only optimizeR-0.1.1/optimizeR/man/set_optimizer_optim.Rd |only optimizeR-0.1.1/optimizeR/man/try_silent_timed.Rd |only optimizeR-0.1.1/optimizeR/tests/testthat/test-functions.R |only optimizeR-0.2.0/optimizeR/DESCRIPTION | 15 optimizeR-0.2.0/optimizeR/MD5 | 54 +-- optimizeR-0.2.0/optimizeR/NAMESPACE | 12 optimizeR-0.2.0/optimizeR/NEWS.md | 12 optimizeR-0.2.0/optimizeR/R/optimizer.R | 236 ++++++++------ optimizeR-0.2.0/optimizeR/R/package.R | 5 optimizeR-0.2.0/optimizeR/R/utils.R | 57 --- optimizeR-0.2.0/optimizeR/README.md | 64 ++- optimizeR-0.2.0/optimizeR/man/apply_optimizer.Rd |only optimizeR-0.2.0/optimizeR/man/do.call_timed.Rd | 2 optimizeR-0.2.0/optimizeR/man/f_ackley.Rd | 6 optimizeR-0.2.0/optimizeR/man/is_number.Rd | 2 optimizeR-0.2.0/optimizeR/man/new_optimizer.Rd | 61 +-- optimizeR-0.2.0/optimizeR/man/optimizeR.Rd | 33 - optimizeR-0.2.0/optimizeR/man/optimizer_nlm.Rd |only optimizeR-0.2.0/optimizeR/man/optimizer_optim.Rd |only optimizeR-0.2.0/optimizeR/man/set_optimizer.Rd | 64 ++- optimizeR-0.2.0/optimizeR/man/timed.Rd | 4 optimizeR-0.2.0/optimizeR/man/try_silent.Rd | 2 optimizeR-0.2.0/optimizeR/man/validate_optimizer.Rd | 30 - optimizeR-0.2.0/optimizeR/tests/testthat/_snaps |only optimizeR-0.2.0/optimizeR/tests/testthat/test-optimizer.R | 98 +++++ optimizeR-0.2.0/optimizeR/tests/testthat/test-package.R |only optimizeR-0.2.0/optimizeR/tests/testthat/test-utils.R | 10 30 files changed, 427 insertions(+), 340 deletions(-)
Title: QTL Mapping for Multi Parent Populations
Description: For Multi Parent Populations (MPP) Identity By Descend (IBD)
probabilities are computed using Hidden Markov Models. These probabilities
are then used in a mixed model approach for QTL Mapping as described in
Li et al. (<doi:10.1007/s00122-021-03919-7>).
Author: Wenhao Li [aut] ,
Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenMPP versions 1.0.1.1 dated 2022-08-24 and 1.0.2 dated 2022-12-02
DESCRIPTION | 10 - MD5 | 19 +- NEWS.md | 35 ++- R/calcIBDMPP.R | 4 R/createQTLMPP.R | 3 R/effectPlot.R | 186 ++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/QTLMapping_in_MultiParentPopulations.html | 143 ++++++++-------- inst/tinytest/test_createQTLmpp.R | 2 11 files changed, 207 insertions(+), 195 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Implements the Robust Scoring Equations estimator to fit linear
mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between robustlmm versions 3.0-4 dated 2022-09-17 and 3.1-1 dated 2022-12-02
robustlmm-3.0-4/robustlmm/inst/xtraR |only robustlmm-3.0-4/robustlmm/src/DasScale.cpp |only robustlmm-3.0-4/robustlmm/src/DasScale.h |only robustlmm-3.0-4/robustlmm/src/FitEffects.cpp |only robustlmm-3.0-4/robustlmm/src/FitEffects.h |only robustlmm-3.0-4/robustlmm/src/Fitter.cpp |only robustlmm-3.0-4/robustlmm/src/Fitter.h |only robustlmm-3.0-4/robustlmm/src/fastGHQuad.cpp |only robustlmm-3.0-4/robustlmm/src/fastGHQuad.h |only robustlmm-3.0-4/robustlmm/src/helpers.cpp |only robustlmm-3.0-4/robustlmm/src/helpers.h |only robustlmm-3.0-4/robustlmm/src/index.cpp |only robustlmm-3.0-4/robustlmm/src/index.h |only robustlmm-3.0-4/robustlmm/src/rlmerPredDModule.cpp |only robustlmm-3.0-4/robustlmm/src/rlmerPredDModule.h |only robustlmm-3.0-4/robustlmm/src/rlmerRespModule.cpp |only robustlmm-3.0-4/robustlmm/src/rlmerRespModule.h |only robustlmm-3.0-4/robustlmm/src/zeroin.c |only robustlmm-3.0-4/robustlmm/src/zeroin.h |only robustlmm-3.0-4/robustlmm/tests/unitTests.R |only robustlmm-3.1-1/robustlmm/DESCRIPTION | 19 robustlmm-3.1-1/robustlmm/MD5 | 93 robustlmm-3.1-1/robustlmm/NAMESPACE | 10 robustlmm-3.1-1/robustlmm/R/AllClass.R | 406 --- robustlmm-3.1-1/robustlmm/R/DAS-scale.R | 30 robustlmm-3.1-1/robustlmm/R/accessors.R | 32 robustlmm-3.1-1/robustlmm/R/fit.effects.R | 58 robustlmm-3.1-1/robustlmm/R/fromLme4.R | 4 robustlmm-3.1-1/robustlmm/R/helpers.R | 62 robustlmm-3.1-1/robustlmm/R/mutators.R | 12 robustlmm-3.1-1/robustlmm/R/plot.R | 38 robustlmm-3.1-1/robustlmm/R/processFile.R | 2 robustlmm-3.1-1/robustlmm/R/rlmer.R | 44 robustlmm-3.1-1/robustlmm/build/vignette.rds |binary robustlmm-3.1-1/robustlmm/inst/doc/rlmer.pdf |binary robustlmm-3.1-1/robustlmm/inst/doc/simulationStudies.pdf |binary robustlmm-3.1-1/robustlmm/man/plot.rlmerMod.Rd | 4 robustlmm-3.1-1/robustlmm/man/rlmer.Rd | 21 robustlmm-3.1-1/robustlmm/src/Integration.cpp | 1097 ---------- robustlmm-3.1-1/robustlmm/src/Integration.h | 393 --- robustlmm-3.1-1/robustlmm/src/globals.h | 9 robustlmm-3.1-1/robustlmm/src/local_stubs.c |only robustlmm-3.1-1/robustlmm/src/misc.cpp | 74 robustlmm-3.1-1/robustlmm/src/misc.h | 109 robustlmm-3.1-1/robustlmm/src/rlmerMatrixUtils.cpp |only robustlmm-3.1-1/robustlmm/src/rlmerMatrixUtils.h |only robustlmm-3.1-1/robustlmm/src/robustlmm_init.cpp | 11 robustlmm-3.1-1/robustlmm/tests/DAS-scale.R | 92 robustlmm-3.1-1/robustlmm/tests/DASvar-fallback.R | 1 robustlmm-3.1-1/robustlmm/tests/compare-methods.R | 2 robustlmm-3.1-1/robustlmm/tests/compare-methods.Rout.save | 30 robustlmm-3.1-1/robustlmm/tests/getME.Rout.save | 4 robustlmm-3.1-1/robustlmm/tests/multipleGroupingFactorsTestData.R | 14 robustlmm-3.1-1/robustlmm/tests/rlmerMod.R | 40 robustlmm-3.1-1/robustlmm/tests/testMatrices.R | 12 55 files changed, 349 insertions(+), 2374 deletions(-)
Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode
Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new
algorithm, extricate, that performs EEMD in seconds, a linear interpolation
algorithm using the greatest rational common divisor of depth or time,
different algorithms to compute instantaneous amplitude, frequency and
ratios of frequencies, and functions to verify and visualise the outputs.
The functions were developed during the CRASH project (Checking the
Reproducibility of Astrochronology in the Hauterivian). When using for
publication please cite Wouters, S., Da Silva, A.C. Crucifix, M., Sinnesael,
M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019, "Litholog
generation with the 'StratigrapheR' package and signal decomposition for
cyclostratigraphic purposes". Geophysical Research Abstracts Vol. 21,
EGU2019-5520, 2019, EGU General Assembly 2019.
<http://hdl.handle.net/2268/234402>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <wouterseb@gmail.com>
Diff between DecomposeR versions 1.0.4 dated 2021-07-06 and 1.0.5 dated 2022-12-02
DESCRIPTION | 12 ++-- MD5 | 42 ++++++++------ NAMESPACE | 10 ++- NEWS | 9 +++ R/DecomposeR.R | 2 R/HilbertEnvelope.R |only R/HilbertTransform.R |only R/InstantaneousFrequency.R |only R/PrecisionTester.R |only R/as.emd.R | 8 +- R/check.emd.R | 121 ++++++++++++++++++++---------------------- R/inst.pulse.R | 3 - R/pile.down.R | 2 R/plot_hex.R | 28 ++++----- R/plot_hist.R | 6 +- R/plot_ratio.R | 8 +- build/partial.rdb |binary man/DecomposeR.Rd | 2 man/HilbertEnvelope.Rd |only man/HilbertTransform.Rd |only man/InstantaneousFrequency.Rd |only man/PrecisionTester.Rd |only man/inst.pulse.Rd | 2 man/plot_hex.Rd | 2 man/plot_hist.Rd | 2 man/plot_ratio.Rd | 6 +- 26 files changed, 141 insertions(+), 124 deletions(-)
Title: Bivariate Zero-Inflated Count Models Using Copulas
Description: Maximum likelihood estimation of copula-based zero-inflated
(and non-inflated) Poisson and negative binomial count models. Supports Frank
and Gaussian copulas. Allows for mixed margins (e.g., one margin Poisson, the
other zero-inflated negative binomial), and several marginal link functions.
Built-in methods for publication-quality tables using 'texreg', post-estimation
diagnostics using 'DHARMa', and testing for marginal zero-modification
via <doi:10.1177/0962280217749991>. For information on copula regression for count data,
see Genest and Nešlehová (2007) <doi:10.1017/S0515036100014963> as well as
Nikoloulopoulos (2013) <doi:10.1007/978-3-642-35407-6_11>. For information on zero-inflated
count regression generally, see Lambert (1992) <https:www.jstor.org/stable/1269547?origin=crossref>. The author
acknowledges support by NSF DMS-1925119 and DMS-212324.
Author: John Niehaus [aut, cre]
Maintainer: John Niehaus <jniehaus2257@gmail.com>
Diff between bizicount versions 1.2.0 dated 2022-08-14 and 1.3.0 dated 2022-12-02
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------- NEWS.md | 9 ++++++++ R/arg_checks.R | 10 ++++++++- R/bizicount-methods.R | 9 +------- R/bizicount.R | 40 +++++++++++++------------------------ R/utils.R | 34 ------------------------------- R/zi_test.R | 2 - inst/examples/bizicount_ex.R | 2 - inst/examples/make_dharma_ex.R | 4 +-- inst/examples/simulate_zicreg_ex.R | 2 - man/bizicount-class.Rd | 3 -- man/bizicount.Rd | 24 ++++------------------ man/make_DHARMa.Rd | 4 +-- man/simulate.zicreg.Rd | 2 - 15 files changed, 67 insertions(+), 114 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp],
A [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-8 dated 2022-08-09 and 0.7-9 dated 2022-12-02
DESCRIPTION | 11 ++--- MD5 | 38 ++++++++--------- R/aggSEM.R | 18 ++++++-- R/determine.subgroups.R | 3 + R/final.org.R | 80 ++++++++++++++++++++++++++++++++++-- R/get.params.R | 44 +++++++++++++++++--- R/gimme.R | 39 +++++++++++------- R/indSEM.R | 19 +++++++- R/residuals.gimme.R | 65 ++++++++++++++++++++++++++---- R/setup.R | 30 ++++++++++--- R/setupBaseSyntax.R | 15 +++--- R/setupConvolve.R | 18 ++++++-- R/setupPrepPaths.R | 93 +++++++++++++++++++++++++++++++++++++++---- R/setupTransformData.R | 32 +++++++++++--- inst/doc/gimme_vignette.html | 4 - man/aggSEM.Rd | 27 ++++++++---- man/gimmeSEM.Rd | 33 +++++++++------ man/indSEM.Rd | 15 ++++++ man/residuals.gimme.Rd | 12 ++++- man/setupBaseSyntax.Rd | 2 20 files changed, 467 insertions(+), 131 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.5.0 dated 2022-09-30 and 0.5.1 dated 2022-12-02
naijR-0.5.0/naijR/vignettes/img/interactive-2a.png |only naijR-0.5.0/naijR/vignettes/img/interactive-3a.png |only naijR-0.5.0/naijR/vignettes/img/interactive-4a.png |only naijR-0.5.0/naijR/vignettes/img/interactive-5a.png |only naijR-0.5.0/naijR/vignettes/img/interactive-6a.png |only naijR-0.5.1/naijR/DESCRIPTION | 8 naijR-0.5.1/naijR/MD5 | 64 - naijR-0.5.1/naijR/NAMESPACE | 10 naijR-0.5.1/naijR/NEWS.md | 6 naijR-0.5.1/naijR/R/class-regions.R | 51 - naijR-0.5.1/naijR/R/fct.R |only naijR-0.5.1/naijR/R/helpers.R | 8 naijR-0.5.1/naijR/R/isregion.R | 11 naijR-0.5.1/naijR/R/map-helpers.R |only naijR-0.5.1/naijR/R/map_nigeria.R | 902 ------------------ naijR-0.5.1/naijR/R/methods-fix_region.R | 199 +++ naijR-0.5.1/naijR/R/sysdata.rda |binary naijR-0.5.1/naijR/README.md | 118 +- naijR-0.5.1/naijR/build/vignette.rds |binary naijR-0.5.1/naijR/data/lgas_nigeria.rda |binary naijR-0.5.1/naijR/inst/doc/interactive.R | 24 naijR-0.5.1/naijR/inst/doc/interactive.Rmd | 100 + naijR-0.5.1/naijR/inst/doc/interactive.html | 212 ++-- naijR-0.5.1/naijR/inst/doc/nigeria-maps.R | 8 naijR-0.5.1/naijR/inst/doc/nigeria-maps.Rmd | 8 naijR-0.5.1/naijR/inst/doc/nigeria-maps.html | 141 +- naijR-0.5.1/naijR/tests/testthat/test-class-regions.R | 6 naijR-0.5.1/naijR/tests/testthat/test-map_nigeria.R | 21 naijR-0.5.1/naijR/vignettes/img/interactive-1.png |binary naijR-0.5.1/naijR/vignettes/img/interactive-10.png |only naijR-0.5.1/naijR/vignettes/img/interactive-11.png |only naijR-0.5.1/naijR/vignettes/img/interactive-12.png |only naijR-0.5.1/naijR/vignettes/img/interactive-2.png |only naijR-0.5.1/naijR/vignettes/img/interactive-3.png |only naijR-0.5.1/naijR/vignettes/img/interactive-4.png |only naijR-0.5.1/naijR/vignettes/img/interactive-5.png |only naijR-0.5.1/naijR/vignettes/img/interactive-6.png |only naijR-0.5.1/naijR/vignettes/img/interactive-7.png |only naijR-0.5.1/naijR/vignettes/img/interactive-8.png |only naijR-0.5.1/naijR/vignettes/img/interactive-9.png |only naijR-0.5.1/naijR/vignettes/interactive.Rmd | 100 + naijR-0.5.1/naijR/vignettes/nigeria-maps.Rmd | 8 42 files changed, 745 insertions(+), 1260 deletions(-)
Title: A Unifying API for Calling the 'Unity' '3D' Video Game Engine
Description: Functions for the creation and manipulation of scenes and objects
within the 'Unity' '3D' video game engine (<https://unity.com/>). Specific
focuses include the creation and import of terrain data and 'GameObjects' as
well as scene management.
Author: Michael Mahoney [aut, cre] ,
Will Jones [rev] for rOpenSci,
see <https://github.com/ropensci/software-review/issues/521>),
Tan Tran [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/521>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between unifir versions 0.2.2 dated 2022-08-11 and 0.2.3 dated 2022-12-02
DESCRIPTION | 6 - MD5 | 28 +++--- NEWS.md | 12 ++ R/associate_coordinates.R | 15 ++- R/create_project.R | 2 R/instantiate_prefab.R | 3 R/utils.R | 2 build/vignette.rds |binary inst/doc/unifir-asset-guide.html | 111 +++++++++++------------- inst/doc/unifir-dev-guide.html | 129 +++++++++++++--------------- inst/doc/unifir-user-guide.html | 111 +++++++++++------------- tests/testthat/test-add_default_tree.R | 2 tests/testthat/test-add_player.R | 2 tests/testthat/test-associate_coordinates.R | 10 +- tests/testthat/test-instantiate_prefab.R | 2 15 files changed, 225 insertions(+), 210 deletions(-)
Title: Graph Neural Network-Based Framework for Single Cell Active
Pathways and Gene Modules Analysis
Description: It is a single cell active pathway analysis tool based on the graph neural network (F. Scarselli (2009) <doi:10.1109/TNN.2008.2005605>; Thomas N. Kipf (2017) <arXiv:1609.02907v4>) to construct the gene-cell association network, infer pathway activity scores from different single cell modalities data, integrate multiple modality data on the same cells into one pathway activity score matrix, identify cell phenotype activated gene modules and parse association networks of gene modules under multiple cell phenotype. In addition, abundant visualization programs are provided to display the results.
Author: Xudong Han [aut, cre, cph],
Xujiang Guo [fnd]
Maintainer: Xudong Han <hanxd1217@163.com>
Diff between scapGNN versions 0.1.2 dated 2022-11-23 and 0.1.3 dated 2022-12-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/vignette.html | 22 +++++++++++----------- inst/python/GraphAutoEncoder.py | 18 ++---------------- 4 files changed, 20 insertions(+), 34 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.0-3 dated 2022-08-28 and 1.0.1 dated 2022-12-02
DESCRIPTION | 6 MD5 | 30 NEWS.md | 4 R/data.R | 27 data/greek_tractors.rda |only data/refrigeratorSpain.rda |only inst/doc/v01_growth_predictions.html | 725 +++++++++------ inst/doc/v02_growth_fitting.html | 1585 ++++++++++++++++++++------------- inst/doc/v03_growth_uncertainty.html | 611 ++++++++---- inst/doc/v04_model_comparison.html | 538 ++++++----- inst/doc/v21_math_models.html | 481 +++++++--- inst/doc/v22_datasets.html | 221 ++-- inst/doc/v23_units-dilemma.html | 657 +++++++------ inst/doc/v24_publication_figures.html | 285 +++-- inst/doc/v31_secondary_for_static.html | 289 +++--- inst/doc/v99_deprecated.html | 1460 +++++++++++++++++++----------- man/greek_tractors.Rd |only man/refrigeratorSpain.Rd |only 18 files changed, 4302 insertions(+), 2617 deletions(-)
Title: A Collection of DIF Tests for Multistage Tests
Description: A collection of statistical tests for the detection of differential
item functioning (DIF) in multistage tests. Methods entail logistic regression,
an adaptation of the simultaneous item bias test (SIBTEST), and various score-based tests.
The presented tests provide itemwise test for DIF along categorical, ordinal or metric covariates. Methods for uniform and non-uniform
DIF effects are available depending on which method is used.
Author: Rudolf Debelak [aut, cre],
Dries Debeer [aut],
Sebastian Appelbaum [ctb],
Mark J. Gierl [ctb]
Maintainer: Rudolf Debelak <rudolf.debelak@gmail.com>
Diff between mstDIF versions 0.1.6 dated 2020-07-24 and 0.1.7 dated 2022-12-02
DESCRIPTION | 18 MD5 | 53 +- NAMESPACE | 28 - NEWS.md | 4 R/Utils.R | 96 +-- R/Utils_perm_boot.R | 168 +++--- R/bootstrap_sctest.R | 16 R/data.R | 44 - R/get_scores.R | 292 +++++------ R/get_stats.R | 438 ++++++++-------- R/log_reg.R | 18 R/mstDIF-class_methods.R | 2 R/mstDIF-package.R | 20 R/mstDIF.R | 10 R/permutation_sctest.R | 16 build/vignette.rds |binary inst/CITATION |only inst/doc/mstDIF.html | 1215 +++++++++++++++++++++++++--------------------- man/bootstrap_sctest.Rd | 220 ++++---- man/log_reg.Rd | 110 ++-- man/mstDIF-Methods.Rd | 2 man/mstDIF-package.Rd | 22 man/mstDIF.Rd | 16 man/mstSIB.Rd | 124 ++-- man/permutation_sctest.Rd | 220 ++++---- man/toydata.Rd | 66 +- tests/Rsctest.R | 232 ++++---- tests/testthat.R | 8 28 files changed, 1809 insertions(+), 1649 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.28 dated 2021-10-17 and 0.30 dated 2022-12-02
DESCRIPTION | 12 ++-- MD5 | 54 ++++++++++----------- NEWS.md | 39 +++++++++++++++ R/check_cross2.R | 5 + R/genoprob_to_snpprob.R | 4 - R/predict_snpgeno.R | 10 +++ R/read_cross2.R | 5 + R/read_csv.R | 9 +++ R/snpprob_from_cross.R | 4 + README.md | 2 build/partial.rdb |binary data/CCaltcolors.RData |binary data/CCcolors.RData |binary data/CCorigcolors.RData |binary man/basic_summaries.Rd | 48 +++++++++--------- man/n_missing.Rd | 6 +- man/qtl2-internal.Rd | 4 - man/qtl2-package.Rd | 2 man/replace_ids.Rd | 14 ++--- src/cross_dof1.cpp | 87 ++++++++-------------------------- src/cross_hsf1.cpp | 86 ++++++++------------------------- tests/testthat/helper-utils.R | 4 - tests/testthat/test-arrange_genes.R | 2 tests/testthat/test-check_cross.R | 4 + tests/testthat/test-hmmbasic-dof1.R | 31 +++++------- tests/testthat/test-hmmbasic-hsf1.R | 27 +++++----- tests/testthat/test-predict_snpgeno.R | 75 +++++++++++++++++++++++++++++ tests/testthat/test-snpprobs.R | 11 ++++ 28 files changed, 308 insertions(+), 237 deletions(-)
Title: Data to Illustrate OOMPA Algorithms
Description: This is a data-only package to provide example data for
other packages that are part of the "Object-Oriented Microrray and
Proteomics Analysis" suite of packages. These are described in more
detail at the package URL.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaData versions 3.1.2 dated 2022-05-03 and 3.1.3 dated 2022-12-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ data/clinical.info.rda |binary data/expression.data.rda |binary data/gene.info.rda |binary data/lungData.rda |binary man/cd09-1-lungData.Rd | 14 ++++++++------ 7 files changed, 18 insertions(+), 16 deletions(-)
Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for lm() [linear model], glm() [generalised linear model], glm.nb() [negative binomial model],
polr() [ordinal logistic model], multinom() [multinomial model] and tobit() [tobit model],
svyglm() [survey-weighted generalised linear models], lmer() [linear multilevel models] using Monte Carlo simulations or bootstrap. Reference: Bennet A. Zelner (2009) <doi:10.1002/smj.783>.
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 4.1-0 dated 2021-08-16 and 4.2-0 dated 2022-12-02
DESCRIPTION | 15 - MD5 | 20 +- NAMESPACE | 8 R/basepredict.lmerMod.R |only R/dc.lmerMod.R |only R/getValues.R | 51 ++++- R/predicts.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/predicts.html | 444 ++++++++++++++++++++++++++++++++++++--------- man/basepredict.lmerMod.Rd |only man/dc.lmerMod.Rd |only man/predicts.Rd | 13 - 13 files changed, 443 insertions(+), 114 deletions(-)
Title: 'BaseX' Client
Description: 'BaseX' <https://basex.org> is a XML database engine and a compliant 'XQuery 3.1' processor with full support of 'W3C Update Facility'. This package is a full client-implementation of the client/server protocol for 'BaseX' and provides functionalities to create, manipulate and query on XML-data.
Author: Ben Engbers [aut, cre]
Maintainer: Ben Engbers <Ben.Engbers@Be-Logical.nl>
Diff between RBaseX versions 1.1.1 dated 2022-03-10 and 1.1.2 dated 2022-12-02
DESCRIPTION | 13 +-- MD5 | 46 ++++++----- NAMESPACE | 2 R/Execute.R | 2 R/RbaseXClient.R | 33 +++++++- R/Replace.R | 3 R/SocketClass.R | 18 ++-- R/Store.R | 5 + R/UtilFunc.R | 26 ------ R/put.R |only R/putBinary.R |only man/Execute.Rd | 2 man/QueryClass.Rd | 72 +++++++++--------- man/RBaseX.Rd | 140 +++++++++++++++++++++++------------- man/Replace.Rd | 3 man/SocketClass.Rd | 30 +++---- man/Store.Rd | 5 + man/put.Rd |only man/putBinary.Rd |only tests/testthat/helper.R | 2 tests/testthat/test_01_first.R | 4 - tests/testthat/test_02_RbaseX.R | 4 - tests/testthat/test_03_QueryClass.R | 2 tests/testthat/test_04_Utility.R | 8 +- tests/testthat/test_05_Dev.R | 4 - tests/testthat/test_05_Wrappers.R | 23 +++-- 26 files changed, 257 insertions(+), 190 deletions(-)
Title: Server-Side Syntax Highlighting
Description: Prism <https://prismjs.com/> is a lightweight, extensible syntax
highlighter, built with modern web standards in mind. This package provides
server-side rendering in R using 'V8' such that no JavaScript library is
required in the resulting HTML documents. Over 400 languages are supported.
Author: Jeroen Ooms [aut, cre] ,
Lea Verou [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between prismjs versions 1.0.0 dated 2022-11-21 and 1.1.0 dated 2022-12-02
prismjs-1.0.0/prismjs/README.md |only prismjs-1.1.0/prismjs/DESCRIPTION | 12 ++++++------ prismjs-1.1.0/prismjs/MD5 | 6 +++--- prismjs-1.1.0/prismjs/NEWS |only prismjs-1.1.0/prismjs/R/highlight.R | 8 ++++++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Statistical Methodology for Graphical Extreme Value Models
Description: Statistical methodology for sparse multivariate extreme value models. Methods are
provided for exact simulation and statistical inference for multivariate Pareto distributions
on graphical structures as described in the paper 'Graphical Models for Extremes' by
Engelke and Hitz (2020) <doi:10.1111/rssb.12355>.
Author: Sebastian Engelke [aut, cre],
Adrien S. Hitz [aut],
Nicola Gnecco [aut],
Manuel Hentschel [aut]
Maintainer: Sebastian Engelke <sebastian.engelke@unige.ch>
Diff between graphicalExtremes versions 0.1.0 dated 2019-11-08 and 0.2.0 dated 2022-12-02
graphicalExtremes-0.1.0/graphicalExtremes/R/fitting_estimation_functions.R |only graphicalExtremes-0.1.0/graphicalExtremes/R/graphicalExtremes.R |only graphicalExtremes-0.1.0/graphicalExtremes/R/other_helpers.R |only graphicalExtremes-0.1.0/graphicalExtremes/README.md |only graphicalExtremes-0.1.0/graphicalExtremes/man/emp_chi_mat.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/man/fmpareto_HR.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/man/mst_HR.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/man/par2Gamma.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/man/select_edges.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/man/set_graph_parameters.Rd |only graphicalExtremes-0.1.0/graphicalExtremes/tests |only graphicalExtremes-0.2.0/graphicalExtremes/DESCRIPTION | 31 graphicalExtremes-0.2.0/graphicalExtremes/MD5 | 172 +- graphicalExtremes-0.2.0/graphicalExtremes/NAMESPACE | 26 graphicalExtremes-0.2.0/graphicalExtremes/R/data.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/estimation_emtp2.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/estimation_helpers.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/estimation_param.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/estimation_param_MLE.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/estimation_structure.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/flight_plotting.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/generate_examples.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/graphicalExtremes-package.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/graphs_functions.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/graphs_helpers.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/input_checks.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/matrix_completions_general.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/matrix_completions_main.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/options.R |only graphicalExtremes-0.2.0/graphicalExtremes/R/simulation_functions.R | 663 +++++---- graphicalExtremes-0.2.0/graphicalExtremes/R/simulation_helpers.R | 121 - graphicalExtremes-0.2.0/graphicalExtremes/R/transformation_functions.R | 681 +++++----- graphicalExtremes-0.2.0/graphicalExtremes/R/utils.R |only graphicalExtremes-0.2.0/graphicalExtremes/build/partial.rdb |binary graphicalExtremes-0.2.0/graphicalExtremes/build/vignette.rds |only graphicalExtremes-0.2.0/graphicalExtremes/data |only graphicalExtremes-0.2.0/graphicalExtremes/inst/REFERENCES.bib | 131 + graphicalExtremes-0.2.0/graphicalExtremes/inst/doc |only graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2Sigma.Rd | 56 graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2Theta.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2chi.Rd | 8 graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2chi_3D.Rd | 9 graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2graph.Rd | 50 graphicalExtremes-0.2.0/graphicalExtremes/man/Gamma2par.Rd | 7 graphicalExtremes-0.2.0/graphicalExtremes/man/Sigma2Gamma.Rd | 45 graphicalExtremes-0.2.0/graphicalExtremes/man/Theta2Gamma.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/V_HR.Rd | 20 graphicalExtremes-0.2.0/graphicalExtremes/man/Zmatrix.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/censor.Rd | 9 graphicalExtremes-0.2.0/graphicalExtremes/man/check_Gamma_and_graph.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/check_graph.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/check_split_by_sep.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/chi2Gamma.Rd | 10 graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma.Rd | 105 + graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma_decomposable.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma_general.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma_general_demo.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma_general_split.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/complete_Gamma_one_step.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/computeLimits.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/danube.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/data2mpareto.Rd | 26 graphicalExtremes-0.2.0/graphicalExtremes/man/dim_Gamma.Rd | 3 graphicalExtremes-0.2.0/graphicalExtremes/man/eglearn.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/emp_chi.Rd | 42 graphicalExtremes-0.2.0/graphicalExtremes/man/emp_chi_multdim.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/emp_vario.Rd | 24 graphicalExtremes-0.2.0/graphicalExtremes/man/emst.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/emtp2.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fast_diag.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fillFixedParams.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/findVsep.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fitInInterval.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fit_graph_to_Theta.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/flightCountMatrixToConnectionList.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/flights.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fmpareto_HR_MLE.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/fmpareto_graph_HR.Rd | 101 - graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_Gamma.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_cactus.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_chordal_graph.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_connected_graph.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_graphical_Gamma.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_integer_Gamma.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_model.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_spd_matrix.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/generate_random_tree.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/getSubMatrixForSubgraph.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/get_cliques_and_separators.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/get_cliques_and_separators_OLD.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/get_mc_cores.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/get_tol.Rd |only graphicalExtremes-0.2.0/graphicalExtremes/man/graphicalExtremes.Rd | 74 - 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More information about graphicalExtremes at CRAN
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Title: Self-Drive Machine Learning Projects
Description: Implementing some of the pillars of an automated machine learning pipeline such as (i) Automated data preparation, (ii) Feature engineering, (iii) Model building in classification context that includes techniques such as (a) Regularised regression [1], (b) Logistic regression [2], (c) Random Forest [3], (d) Decision tree [4] and (e) Extreme Gradient Boosting (xgboost) [5], and finally, (iv) Model explanation (using lift chart and partial dependency plots). Accomplishes the above tasks by running the function instead of writing lengthy R codes. Also provides some additional features such as generating missing at random (MAR) variables and automated exploratory data analysis. Moreover, function exports the model results with the required plots in an HTML vignette report format that follows the best practices of the industry and the academia. [1] Gonzales G B and De Saeger (2018) <doi:10.1038/s41598-018-21851-7>, [2] Sperandei S (2014) <doi:10.11613/BM.2014.003>, [3] Breiman [...truncated...]
Author: Dayanand Ubrangala [aut, cre],
Sayan Putatunda [aut, ctb],
Kiran R [aut, ctb],
Ravi Prasad Kondapalli [aut, ctb]
Maintainer: Dayanand Ubrangala <daya6489@gmail.com>
Diff between DriveML versions 0.1.4 dated 2021-10-18 and 0.1.5 dated 2022-12-02
DESCRIPTION | 8 LICENSE | 1346 ++++++++++++++-------------- MD5 | 88 - NAMESPACE | 152 +-- NEWS.md | 5 R/ModelMarkdown.R | 3 R/autoDataPrep.R | 2 R/autoFeature.R | 376 +++---- R/autoMAR.R | 310 +++--- R/autoMLModel.R | 476 +++++----- R/caret_help_function.R | 210 ++-- R/data.R | 48 - R/missingPattern.R | 202 ++-- R/model_task.R | 24 R/partialDependence.R | 196 ++-- R/predictDataprep.R | 9 R/predictMAR.R | 2 R/utilis.R | 662 +++++++------- README.md | 340 +++---- build/vignette.rds |binary data/heart.model.rda |binary inst/doc/DriveML.Rmd | 708 +++++++-------- inst/doc/DriveML.html | 1693 ++++++++++++++++++++++++++++++++---- inst/rmd_template/report_tmp.Rmd | 498 +++++----- inst/rmd_template/report_tmp_v1.Rmd | 872 +++++++++--------- man/autoDataprep.Rd | 226 ++-- man/autoMAR.Rd | 70 - man/autoMLReport.Rd | 64 - man/autoMLmodel.Rd | 232 ++-- man/autoPDP.Rd | 122 +- man/generateFeature.Rd | 126 +- man/heart.Rd | 78 - man/heart.model.Rd | 46 man/misspattern.Rd | 56 - man/predictAutoMAR.Rd | 60 - man/predictDataprep.Rd | 64 - tests/testthat.R | 8 tests/testthat/test_autoMAR.R | 32 tests/testthat/test_automodel.R | 42 tests/testthat/test_dataprep.R | 64 - tests/testthat/test_gene_fetures.R | 22 tests/testthat/test_mlreport.R | 24 tests/testthat/test_pdp.R | 34 vignettes/DriveML.Rmd | 708 +++++++-------- vignettes/custom.css | 180 +-- 45 files changed, 5950 insertions(+), 4538 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include standard operations such as intersect and buffer. Raster methods include global, local, zonal, and focal computations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is a replacement for the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.6-41 dated 2022-11-18 and 1.6-47 dated 2022-12-02
terra-1.6-41/terra/man/focalCor.Rd |only terra-1.6-47/terra/DESCRIPTION | 8 terra-1.6-47/terra/MD5 | 159 +++++------ terra-1.6-47/terra/NAMESPACE | 2 terra-1.6-47/terra/NEWS.md | 251 ++++++++++------- terra-1.6-47/terra/R/Agenerics.R | 4 terra-1.6-47/terra/R/Arith_generics.R | 20 - terra-1.6-47/terra/R/RcppExports.R | 8 terra-1.6-47/terra/R/Zdeprecated.R | 22 + terra-1.6-47/terra/R/app.R | 11 terra-1.6-47/terra/R/autocor.R | 4 terra-1.6-47/terra/R/cells.R | 5 terra-1.6-47/terra/R/coerce.R | 2 terra-1.6-47/terra/R/crosstab.R | 11 terra-1.6-47/terra/R/crs.R | 18 + terra-1.6-47/terra/R/dimensions.R | 8 terra-1.6-47/terra/R/extract_single.R | 6 terra-1.6-47/terra/R/focal.R | 309 ++++++++++++++++----- terra-1.6-47/terra/R/generics.R | 46 --- terra-1.6-47/terra/R/geom.R | 9 terra-1.6-47/terra/R/graticule.R | 2 terra-1.6-47/terra/R/levels.R | 29 -- terra-1.6-47/terra/R/lines.R | 22 + terra-1.6-47/terra/R/options.R | 68 +++- terra-1.6-47/terra/R/pack.R | 14 terra-1.6-47/terra/R/plot_let.R | 2 terra-1.6-47/terra/R/plot_vector.R | 5 terra-1.6-47/terra/R/rast.R | 2 terra-1.6-47/terra/R/rasterize.R | 14 terra-1.6-47/terra/R/rasterizeWin.R | 2 terra-1.6-47/terra/R/roll.R |only terra-1.6-47/terra/R/sample.R | 78 ++++- terra-1.6-47/terra/R/show.R | 2 terra-1.6-47/terra/R/spatvec.R | 4 terra-1.6-47/terra/R/tiles.R | 15 - terra-1.6-47/terra/R/time.R | 19 + terra-1.6-47/terra/R/values.R | 4 terra-1.6-47/terra/R/vect.R | 6 terra-1.6-47/terra/man/activeCat.Rd | 5 terra-1.6-47/terra/man/app.Rd | 2 terra-1.6-47/terra/man/buffer.Rd | 2 terra-1.6-47/terra/man/crs.Rd | 5 terra-1.6-47/terra/man/densify.Rd | 5 terra-1.6-47/terra/man/factors.Rd | 4 terra-1.6-47/terra/man/focalPairs.Rd |only terra-1.6-47/terra/man/focalReg.Rd | 20 - terra-1.6-47/terra/man/geomtype.Rd | 6 terra-1.6-47/terra/man/inplace.Rd | 4 terra-1.6-47/terra/man/lines.Rd | 20 + terra-1.6-47/terra/man/makeTiles.Rd | 2 terra-1.6-47/terra/man/math-generics.Rd | 2 terra-1.6-47/terra/man/rangeFill.Rd |only terra-1.6-47/terra/man/roll.Rd |only terra-1.6-47/terra/man/sample.Rd | 6 terra-1.6-47/terra/man/sort.Rd | 2 terra-1.6-47/terra/man/summarize-generics.Rd | 10 terra-1.6-47/terra/man/terra-package.Rd | 4 terra-1.6-47/terra/man/terraOptions.Rd | 11 terra-1.6-47/terra/man/writeRaster.Rd | 13 terra-1.6-47/terra/man/writeVector.Rd | 4 terra-1.6-47/terra/src/RcppExports.cpp | 29 ++ terra-1.6-47/terra/src/RcppFunctions.cpp | 74 +++++ terra-1.6-47/terra/src/RcppModule.cpp | 10 terra-1.6-47/terra/src/arith.cpp | 63 ++++ terra-1.6-47/terra/src/distRaster.cpp | 16 - terra-1.6-47/terra/src/extract.cpp | 6 terra-1.6-47/terra/src/focal.cpp | 3 terra-1.6-47/terra/src/gdal_algs.cpp | 40 ++ terra-1.6-47/terra/src/gdalio.cpp | 29 +- terra-1.6-47/terra/src/geos_methods.cpp | 2 terra-1.6-47/terra/src/geosphere.cpp | 4 terra-1.6-47/terra/src/ncdf.cpp | 4 terra-1.6-47/terra/src/raster_methods.cpp | 381 +++++++++++++++++++++++++-- terra-1.6-47/terra/src/read.cpp | 5 terra-1.6-47/terra/src/read_gdal.cpp | 5 terra-1.6-47/terra/src/read_ogr.cpp | 3 terra-1.6-47/terra/src/spatBase.cpp | 16 - terra-1.6-47/terra/src/spatBase.h | 7 terra-1.6-47/terra/src/spatRaster.cpp | 71 +++-- terra-1.6-47/terra/src/spatRaster.h | 14 terra-1.6-47/terra/src/spatVector.h | 2 terra-1.6-47/terra/src/write.cpp | 7 terra-1.6-47/terra/src/write_gdal.cpp | 113 +++++++- 83 files changed, 1669 insertions(+), 553 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around
the fantastic 'stringi' package. All function and argument names (and
positions) are consistent, all functions deal with "NA"'s and zero
length vectors in the same way, and the output from one function is
easy to feed into the input of another.
Author: Hadley Wickham [aut, cre, cph],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between stringr versions 1.4.1 dated 2022-08-20 and 1.5.0 dated 2022-12-02
stringr-1.4.1/stringr/R/c.r |only stringr-1.4.1/stringr/R/count.r |only stringr-1.4.1/stringr/R/detect.r |only stringr-1.4.1/stringr/R/dup.r |only stringr-1.4.1/stringr/R/extract.r |only stringr-1.4.1/stringr/R/length.r |only stringr-1.4.1/stringr/R/locate.r |only stringr-1.4.1/stringr/R/match.r |only stringr-1.4.1/stringr/R/modifiers.r |only stringr-1.4.1/stringr/R/pad.r |only stringr-1.4.1/stringr/R/remove.r |only stringr-1.4.1/stringr/R/replace.r |only stringr-1.4.1/stringr/R/split.r |only stringr-1.4.1/stringr/R/stringr.R |only stringr-1.4.1/stringr/R/sub.r |only stringr-1.4.1/stringr/R/word.r |only stringr-1.4.1/stringr/R/wrap.r |only stringr-1.4.1/stringr/tests/testthat/test-count.r |only stringr-1.4.1/stringr/tests/testthat/test-detect.r |only stringr-1.4.1/stringr/tests/testthat/test-dup.r |only stringr-1.4.1/stringr/tests/testthat/test-extract.r |only stringr-1.4.1/stringr/tests/testthat/test-interp.r |only stringr-1.4.1/stringr/tests/testthat/test-join.r |only stringr-1.4.1/stringr/tests/testthat/test-length.r |only stringr-1.4.1/stringr/tests/testthat/test-locate.r |only stringr-1.4.1/stringr/tests/testthat/test-match.r |only stringr-1.4.1/stringr/tests/testthat/test-modifiers.r |only stringr-1.4.1/stringr/tests/testthat/test-pad.r |only stringr-1.4.1/stringr/tests/testthat/test-remove.r |only stringr-1.4.1/stringr/tests/testthat/test-replace.r |only stringr-1.4.1/stringr/tests/testthat/test-split.r |only stringr-1.4.1/stringr/tests/testthat/test-sub.r |only stringr-1.4.1/stringr/tests/testthat/test-subset.r |only stringr-1.4.1/stringr/tests/testthat/test-trim.r |only stringr-1.4.1/stringr/tests/testthat/test-trunc.r |only stringr-1.4.1/stringr/tests/testthat/test-word.r |only stringr-1.4.1/stringr/tests/testthat/test-wrap.r |only stringr-1.4.1/stringr/vignettes/releases |only stringr-1.5.0/stringr/DESCRIPTION | 28 stringr-1.5.0/stringr/LICENSE | 341 ----------- stringr-1.5.0/stringr/MD5 | 236 ++++--- stringr-1.5.0/stringr/NAMESPACE | 22 stringr-1.5.0/stringr/NEWS.md | 103 +++ stringr-1.5.0/stringr/R/c.R |only stringr-1.5.0/stringr/R/case.R | 23 stringr-1.5.0/stringr/R/compat-obj-type.R |only stringr-1.5.0/stringr/R/compat-purrr.R |only stringr-1.5.0/stringr/R/compat-types-check.R |only stringr-1.5.0/stringr/R/conv.R | 6 stringr-1.5.0/stringr/R/count.R |only stringr-1.5.0/stringr/R/data.R | 9 stringr-1.5.0/stringr/R/detect.R |only stringr-1.5.0/stringr/R/dup.R |only stringr-1.5.0/stringr/R/equal.R |only stringr-1.5.0/stringr/R/escape.R |only stringr-1.5.0/stringr/R/extract.R |only stringr-1.5.0/stringr/R/flatten.R | 64 +- stringr-1.5.0/stringr/R/glue.R | 14 stringr-1.5.0/stringr/R/interp.R | 11 stringr-1.5.0/stringr/R/length.R |only stringr-1.5.0/stringr/R/locate.R |only stringr-1.5.0/stringr/R/match.R |only stringr-1.5.0/stringr/R/modifiers.R |only stringr-1.5.0/stringr/R/pad.R |only stringr-1.5.0/stringr/R/remove.R |only stringr-1.5.0/stringr/R/replace.R |only stringr-1.5.0/stringr/R/sort.R | 90 ++ stringr-1.5.0/stringr/R/split.R |only stringr-1.5.0/stringr/R/stringr-package.R |only stringr-1.5.0/stringr/R/sub.R |only stringr-1.5.0/stringr/R/subset.R | 44 - stringr-1.5.0/stringr/R/trim.R | 16 stringr-1.5.0/stringr/R/trunc.R | 19 stringr-1.5.0/stringr/R/unique.R |only stringr-1.5.0/stringr/R/utils.R | 18 stringr-1.5.0/stringr/R/view.R | 212 +++++- stringr-1.5.0/stringr/R/word.R |only stringr-1.5.0/stringr/R/wrap.R |only stringr-1.5.0/stringr/README.md | 216 +++--- stringr-1.5.0/stringr/build/vignette.rds |binary stringr-1.5.0/stringr/data/sentences.rda |binary stringr-1.5.0/stringr/inst/doc/from-base.R |only stringr-1.5.0/stringr/inst/doc/from-base.Rmd |only stringr-1.5.0/stringr/inst/doc/from-base.html |only stringr-1.5.0/stringr/inst/doc/regular-expressions.R | 15 stringr-1.5.0/stringr/inst/doc/regular-expressions.Rmd | 21 stringr-1.5.0/stringr/inst/doc/regular-expressions.html | 167 ++--- stringr-1.5.0/stringr/inst/doc/stringr.html | 111 +-- stringr-1.5.0/stringr/inst/htmlwidgets/lib/str_view.css | 11 stringr-1.5.0/stringr/man/case.Rd | 23 stringr-1.5.0/stringr/man/figures/lifecycle-archived.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-defunct.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-deprecated.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-experimental.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-maturing.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-questioning.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-stable.svg |only stringr-1.5.0/stringr/man/figures/lifecycle-superseded.svg |only stringr-1.5.0/stringr/man/invert_match.Rd | 4 stringr-1.5.0/stringr/man/modifiers.Rd | 33 - stringr-1.5.0/stringr/man/str_c.Rd | 58 + stringr-1.5.0/stringr/man/str_conv.Rd | 5 stringr-1.5.0/stringr/man/str_count.Rd | 15 stringr-1.5.0/stringr/man/str_detect.Rd | 20 stringr-1.5.0/stringr/man/str_dup.Rd | 12 stringr-1.5.0/stringr/man/str_equal.Rd |only stringr-1.5.0/stringr/man/str_escape.Rd |only stringr-1.5.0/stringr/man/str_extract.Rd | 35 - stringr-1.5.0/stringr/man/str_flatten.Rd | 40 + stringr-1.5.0/stringr/man/str_glue.Rd | 13 stringr-1.5.0/stringr/man/str_interp.Rd | 6 stringr-1.5.0/stringr/man/str_length.Rd | 47 - stringr-1.5.0/stringr/man/str_like.Rd |only stringr-1.5.0/stringr/man/str_locate.Rd | 30 stringr-1.5.0/stringr/man/str_match.Rd | 34 - stringr-1.5.0/stringr/man/str_order.Rd | 40 - stringr-1.5.0/stringr/man/str_pad.Rd | 23 stringr-1.5.0/stringr/man/str_remove.Rd | 14 stringr-1.5.0/stringr/man/str_replace.Rd | 32 - stringr-1.5.0/stringr/man/str_replace_na.Rd | 2 stringr-1.5.0/stringr/man/str_split.Rd | 62 +- stringr-1.5.0/stringr/man/str_starts.Rd | 15 stringr-1.5.0/stringr/man/str_sub.Rd | 69 +- stringr-1.5.0/stringr/man/str_subset.Rd | 30 stringr-1.5.0/stringr/man/str_trim.Rd | 13 stringr-1.5.0/stringr/man/str_trunc.Rd | 12 stringr-1.5.0/stringr/man/str_unique.Rd |only stringr-1.5.0/stringr/man/str_view.Rd | 83 +- stringr-1.5.0/stringr/man/str_which.Rd |only stringr-1.5.0/stringr/man/str_wrap.Rd | 34 - stringr-1.5.0/stringr/man/stringr-data.Rd | 12 stringr-1.5.0/stringr/man/stringr-package.Rd | 2 stringr-1.5.0/stringr/man/word.Rd | 23 stringr-1.5.0/stringr/tests/testthat/_snaps |only stringr-1.5.0/stringr/tests/testthat/test-c.R |only stringr-1.5.0/stringr/tests/testthat/test-case.R | 7 stringr-1.5.0/stringr/tests/testthat/test-conv.R | 6 stringr-1.5.0/stringr/tests/testthat/test-count.R |only stringr-1.5.0/stringr/tests/testthat/test-detect.R |only stringr-1.5.0/stringr/tests/testthat/test-dup.R |only stringr-1.5.0/stringr/tests/testthat/test-equal.R |only stringr-1.5.0/stringr/tests/testthat/test-escape.R |only stringr-1.5.0/stringr/tests/testthat/test-extract.R |only stringr-1.5.0/stringr/tests/testthat/test-flatten.R | 25 stringr-1.5.0/stringr/tests/testthat/test-glue.R | 2 stringr-1.5.0/stringr/tests/testthat/test-interp.R |only stringr-1.5.0/stringr/tests/testthat/test-length.R |only stringr-1.5.0/stringr/tests/testthat/test-locate.R |only stringr-1.5.0/stringr/tests/testthat/test-match.R |only stringr-1.5.0/stringr/tests/testthat/test-modifiers.R |only stringr-1.5.0/stringr/tests/testthat/test-pad.R |only stringr-1.5.0/stringr/tests/testthat/test-remove.R |only stringr-1.5.0/stringr/tests/testthat/test-replace.R |only stringr-1.5.0/stringr/tests/testthat/test-sort.R | 5 stringr-1.5.0/stringr/tests/testthat/test-split.R |only stringr-1.5.0/stringr/tests/testthat/test-sub.R |only stringr-1.5.0/stringr/tests/testthat/test-subset.R |only stringr-1.5.0/stringr/tests/testthat/test-trim.R |only stringr-1.5.0/stringr/tests/testthat/test-trunc.R |only stringr-1.5.0/stringr/tests/testthat/test-unique.R |only stringr-1.5.0/stringr/tests/testthat/test-view.R | 77 ++ stringr-1.5.0/stringr/tests/testthat/test-word.R |only stringr-1.5.0/stringr/tests/testthat/test-wrap.R |only stringr-1.5.0/stringr/vignettes/from-base.Rmd |only stringr-1.5.0/stringr/vignettes/regular-expressions.Rmd | 21 165 files changed, 1585 insertions(+), 1196 deletions(-)
Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2',
facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre]
,
Baptiste Auguie [ctb] ,
Shaun Jackman [ctb] ,
Hadley Wickham [ctb] ,
Winston Chang [ctb]
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>
Diff between lemon versions 0.4.5 dated 2020-06-08 and 0.4.6 dated 2022-12-02
lemon-0.4.5/lemon/R/coord-cartesian.r |only lemon-0.4.5/lemon/R/scale-expansion.r |only lemon-0.4.5/lemon/R/scale-view.r |only lemon-0.4.5/lemon/man/element_render.Rd |only lemon-0.4.6/lemon/DESCRIPTION | 22 lemon-0.4.6/lemon/MD5 | 169 +- lemon-0.4.6/lemon/NAMESPACE | 123 - lemon-0.4.6/lemon/R/axis-annotation.r | 879 ++++------ lemon-0.4.6/lemon/R/brackets.R | 413 ++--- lemon-0.4.6/lemon/R/coord-capped.r | 410 ++-- lemon-0.4.6/lemon/R/coord-flex.r | 475 ++--- lemon-0.4.6/lemon/R/dot.r | 128 - lemon-0.4.6/lemon/R/facet-rep-lab.r | 327 +-- lemon-0.4.6/lemon/R/facet-wrap.r | 529 +++--- lemon-0.4.6/lemon/R/geom-pointline.r | 913 +++++------ lemon-0.4.6/lemon/R/geom-siderange.r | 576 +++---- lemon-0.4.6/lemon/R/ggplot2.r | 255 +-- lemon-0.4.6/lemon/R/grob_utils.r | 147 - lemon-0.4.6/lemon/R/gtable_show-.r | 289 +-- lemon-0.4.6/lemon/R/guides-axis.r |only lemon-0.4.6/lemon/R/legends.r | 888 +++++----- lemon-0.4.6/lemon/R/lemon-plot.r | 309 +-- lemon-0.4.6/lemon/R/lemon.r | 100 - lemon-0.4.6/lemon/R/lemon_print.r | 256 +-- lemon-0.4.6/lemon/R/scale-symmetric.r | 166 -- lemon-0.4.6/lemon/build/vignette.rds |binary lemon-0.4.6/lemon/inst/doc/capped-axes.R | 180 +- lemon-0.4.6/lemon/inst/doc/capped-axes.Rmd | 565 +++--- lemon-0.4.6/lemon/inst/doc/capped-axes.html | 1151 +++++++------- lemon-0.4.6/lemon/inst/doc/facet-rep-labels.R | 82 lemon-0.4.6/lemon/inst/doc/facet-rep-labels.Rmd | 202 +- lemon-0.4.6/lemon/inst/doc/facet-rep-labels.html | 836 +++++----- lemon-0.4.6/lemon/inst/doc/geoms.R | 38 lemon-0.4.6/lemon/inst/doc/geoms.Rmd | 86 - lemon-0.4.6/lemon/inst/doc/geoms.html | 719 ++++---- lemon-0.4.6/lemon/inst/doc/gtable_show_lemonade.R | 351 ++-- lemon-0.4.6/lemon/inst/doc/gtable_show_lemonade.Rmd | 403 ++-- lemon-0.4.6/lemon/inst/doc/gtable_show_lemonade.html | 1005 ++++++------ lemon-0.4.6/lemon/inst/doc/legends.R | 351 ++-- lemon-0.4.6/lemon/inst/doc/legends.Rmd | 730 ++++---- lemon-0.4.6/lemon/inst/doc/legends.html | 1363 ++++++++-------- lemon-0.4.6/lemon/inst/doc/lemon_print.R | 114 - lemon-0.4.6/lemon/inst/doc/lemon_print.Rmd | 298 +-- lemon-0.4.6/lemon/inst/doc/lemon_print.html | 1397 ++++++++--------- lemon-0.4.6/lemon/inst/examples/axis-annotation-ex.r | 59 lemon-0.4.6/lemon/inst/examples/geom-pointline-ex.r | 84 - lemon-0.4.6/lemon/inst/examples/geom-siderange-ex.r | 44 lemon-0.4.6/lemon/man/annotate_axis.Rd | 21 lemon-0.4.6/lemon/man/coord_flex.Rd | 3 lemon-0.4.6/lemon/man/dot.Rd | 14 lemon-0.4.6/lemon/man/facet_rep.Rd | 2 lemon-0.4.6/lemon/man/geom_pointpath.Rd | 22 lemon-0.4.6/lemon/man/geom_siderange.Rd | 20 lemon-0.4.6/lemon/man/ggplot2-non-exports.Rd | 7 lemon-0.4.6/lemon/man/grid_arrange_shared_legend.Rd | 20 lemon-0.4.6/lemon/man/gtable_show.Rd | 2 lemon-0.4.6/lemon/man/guidebox_as_column.Rd | 3 lemon-0.4.6/lemon/man/lemon-ggproto.Rd | 6 lemon-0.4.6/lemon/man/lemon_print.Rd | 10 lemon-0.4.6/lemon/man/render_gpar.Rd |only lemon-0.4.6/lemon/man/reposition_legend.Rd | 26 lemon-0.4.6/lemon/man/scale_symmetric.Rd | 6 lemon-0.4.6/lemon/tests/testthat.R | 18 lemon-0.4.6/lemon/tests/testthat/_snaps |only lemon-0.4.6/lemon/tests/testthat/test_brackets.R | 166 +- lemon-0.4.6/lemon/tests/testthat/test_caps.R | 69 lemon-0.4.6/lemon/tests/testthat/test_coord_.R | 128 - lemon-0.4.6/lemon/tests/testthat/test_facet.R |only lemon-0.4.6/lemon/tests/testthat/test_facet_aux.R | 115 - lemon-0.4.6/lemon/tests/testthat/test_geom-pointline.r | 90 - lemon-0.4.6/lemon/tests/testthat/test_lemon_plot.r | 50 lemon-0.4.6/lemon/vignettes/capped-axes.Rmd | 565 +++--- lemon-0.4.6/lemon/vignettes/facet-rep-labels.Rmd | 202 +- lemon-0.4.6/lemon/vignettes/facet-rep-labels_files |only lemon-0.4.6/lemon/vignettes/geoms.Rmd | 86 - lemon-0.4.6/lemon/vignettes/gtable_show_lemonade.Rmd | 403 ++-- lemon-0.4.6/lemon/vignettes/gtable_show_lemonade_files |only lemon-0.4.6/lemon/vignettes/legends.Rmd | 730 ++++---- lemon-0.4.6/lemon/vignettes/lemon_print.Rmd | 298 +-- 79 files changed, 10293 insertions(+), 10221 deletions(-)
Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression models
to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. The
package provides functions for model estimation, dispersion testing, and
diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016)
<doi:10.1016/j.csda.2016.01.007> is also supported.
Author: Kimberly Sellers <kfs7@georgetown.edu>
Thomas Lotze <thomas.lotze@thomaslotze.com>
Andrew Raim <andrew.raim@gmail.com>
Maintainer: Andrew Raim <andrew.raim@gmail.com>
Diff between COMPoissonReg versions 0.7.0 dated 2019-11-30 and 0.8.0 dated 2022-12-02
COMPoissonReg-0.7.0/COMPoissonReg/inst/demo-rmd |only COMPoissonReg-0.7.0/COMPoissonReg/inst/examples |only COMPoissonReg-0.7.0/COMPoissonReg/man/nu.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/DESCRIPTION | 13 COMPoissonReg-0.8.0/COMPoissonReg/MD5 | 129 +- COMPoissonReg-0.8.0/COMPoissonReg/NAMESPACE | 83 + COMPoissonReg-0.8.0/COMPoissonReg/R/RcppExports.R | 320 +++++- COMPoissonReg-0.8.0/COMPoissonReg/R/S3methods.R | 9 COMPoissonReg-0.8.0/COMPoissonReg/R/cmp-reg.R | 485 ++++++---- COMPoissonReg-0.8.0/COMPoissonReg/R/cmp.R | 268 +++++ COMPoissonReg-0.8.0/COMPoissonReg/R/fim.R | 4 COMPoissonReg-0.8.0/COMPoissonReg/R/glm.R | 310 ++++-- COMPoissonReg-0.8.0/COMPoissonReg/R/helpers.R |only COMPoissonReg-0.8.0/COMPoissonReg/R/mle.R | 250 ++--- COMPoissonReg-0.8.0/COMPoissonReg/R/package.R | 141 -- COMPoissonReg-0.8.0/COMPoissonReg/R/rqres.R | 8 COMPoissonReg-0.8.0/COMPoissonReg/R/util.R | 27 COMPoissonReg-0.8.0/COMPoissonReg/R/zicmp-reg.R | 447 ++++++--- COMPoissonReg-0.8.0/COMPoissonReg/R/zicmp.R | 95 + COMPoissonReg-0.8.0/COMPoissonReg/R/zip-reg.R | 1 COMPoissonReg-0.8.0/COMPoissonReg/R/zip.R | 71 + COMPoissonReg-0.8.0/COMPoissonReg/build |only COMPoissonReg-0.8.0/COMPoissonReg/inst/doc |only COMPoissonReg-0.8.0/COMPoissonReg/man/CMP-Distribution.Rd | 38 COMPoissonReg-0.8.0/COMPoissonReg/man/COMPoissonReg-deprecated.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/COMPoissonReg-options.Rd | 23 COMPoissonReg-0.8.0/COMPoissonReg/man/COMPoissonReg-package.Rd | 119 -- COMPoissonReg-0.8.0/COMPoissonReg/man/ZICMP-Distribution.Rd | 27 COMPoissonReg-0.8.0/COMPoissonReg/man/ZIP-Distribution.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/couple.Rd | 6 COMPoissonReg-0.8.0/COMPoissonReg/man/equitest.Rd | 14 COMPoissonReg-0.8.0/COMPoissonReg/man/freight.Rd | 6 COMPoissonReg-0.8.0/COMPoissonReg/man/get.control.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.fixed.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.init.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.init.zero.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.modelmatrix.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.offset.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/get.offset.zero.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/glm.cmp-CMP-support.Rd | 82 + COMPoissonReg-0.8.0/COMPoissonReg/man/glm.cmp-ZICMP-support.Rd | 80 + COMPoissonReg-0.8.0/COMPoissonReg/man/glm.cmp-raw.Rd |only COMPoissonReg-0.8.0/COMPoissonReg/man/glm.cmp.Rd | 46 COMPoissonReg-0.8.0/COMPoissonReg/man/parametric.bootstrap.Rd | 3 COMPoissonReg-0.8.0/COMPoissonReg/src/RcppExports.cpp | 261 ++--- COMPoissonReg-0.8.0/COMPoissonReg/src/cmp.cpp | 220 ++-- COMPoissonReg-0.8.0/COMPoissonReg/src/cmp.h | 98 +- COMPoissonReg-0.8.0/COMPoissonReg/src/util.cpp | 90 - COMPoissonReg-0.8.0/COMPoissonReg/src/util.h | 42 COMPoissonReg-0.8.0/COMPoissonReg/src/z-derivs.cpp | 22 COMPoissonReg-0.8.0/COMPoissonReg/src/z-derivs.h |only COMPoissonReg-0.8.0/COMPoissonReg/src/z.cpp | 184 ++- COMPoissonReg-0.8.0/COMPoissonReg/src/z.h |only COMPoissonReg-0.8.0/COMPoissonReg/src/zicmp.cpp | 138 ++ COMPoissonReg-0.8.0/COMPoissonReg/src/zicmp.h |only COMPoissonReg-0.8.0/COMPoissonReg/tests |only COMPoissonReg-0.8.0/COMPoissonReg/vignettes |only 57 files changed, 2584 insertions(+), 1576 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as i [...truncated...]
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.1-4 dated 2019-10-15 and 3.1-5 dated 2022-12-02
DESCRIPTION | 9 MD5 | 136 +- R/rhierMnlRwMixture_rcpp.R | 13 build/vignette.rds |binary inst/doc/Constrained_MNL_Vignette.R | 36 inst/doc/Constrained_MNL_Vignette.html | 765 ++++++++------ inst/doc/bayesm_Overview_Vignette.R | 54 - inst/doc/bayesm_Overview_Vignette.Rmd | 4 inst/doc/bayesm_Overview_Vignette.html | 1729 +++++++++++++++++++++++---------- man/Scotch.Rd | 2 man/bank.Rd | 2 man/breg.Rd | 2 man/camera.Rd | 3 man/cheese.Rd | 2 man/clusterMix.Rd | 2 man/condMom.Rd | 2 man/createX.Rd | 2 man/customerSat.Rd | 2 man/eMixMargDen.Rd | 2 man/ghkvec.Rd | 2 man/llmnl.Rd | 3 man/llmnp.Rd | 2 man/llnhlogit.Rd | 2 man/lndIChisq.Rd | 2 man/lndIWishart.Rd | 2 man/lndMvn.Rd | 2 man/lndMvst.Rd | 2 man/logMargDenNR.Rd | 2 man/margarine.Rd | 2 man/mixDen.Rd | 2 man/mixDenBi.Rd | 2 man/mnlHess.Rd | 2 man/mnpProb.Rd | 2 man/momMix.Rd | 2 man/numEff.Rd | 2 man/orangeJuice.Rd | 2 man/rbayesBLP.Rd | 2 man/rbiNormGibbs.Rd | 2 man/rbprobitGibbs.Rd | 2 man/rdirichlet.Rd | 2 man/rhierBinLogit.Rd | 2 man/rhierLinearMixture.Rd | 2 man/rhierLinearModel.Rd | 2 man/rhierMnlDP.Rd | 2 man/rhierMnlRwMixture.Rd | 2 man/rhierNegbinRw.Rd | 2 man/rivGibbs.Rd | 2 man/rmixGibbs.Rd | 2 man/rmnlIndepMetrop.Rd | 2 man/rmnpGibbs.Rd | 2 man/rmultireg.Rd | 2 man/rmvpGibbs.Rd | 2 man/rmvst.Rd | 2 man/rnegbinRw.Rd | 2 man/rnmixGibbs.Rd | 2 man/rordprobitGibbs.Rd | 2 man/rscaleUsage.Rd | 2 man/rsurGibbs.Rd | 2 man/rtrun.Rd | 2 man/runireg.Rd | 2 man/runiregGibbs.Rd | 2 man/rwishart.Rd | 2 man/simnhlogit.Rd | 2 man/tuna.Rd | 2 src/RcppExports.cpp | 5 src/clusterMix_rcpp_loop.cpp | 8 src/functionTiming.cpp | 7 src/rhierMnlDP_rcpp_loop.cpp | 4 vignettes/bayesm_Overview_Vignette.Rmd | 4 69 files changed, 1851 insertions(+), 1035 deletions(-)
Title: A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical
Behavior Data
Description: A tool to analyse 'ActiGraph' accelerometer data and to implement
the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis
is completed, the app allows to export results to .csv files and to generate
a report of the measurement. All the configured inputs relevant for interpreting
the results are recorded in the report. In addition to the existing 'R' packages
that are fully integrated with the app, the app uses some functions from the
'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Author: Pierre-Yves de Muellenheim [cre, aut]
Maintainer: Pierre-Yves de Muellenheim <pydemull@uco.fr>
Diff between activAnalyzer versions 1.0.5 dated 2022-10-12 and 1.1.0 dated 2022-12-02
DESCRIPTION | 8 LICENCE.note | 2 MD5 | 112 - NAMESPACE | 1 NEWS.md | 285 +-- R/app_server.R | 851 +++++++++ R/app_ui.R | 167 + R/compute_bmr.R | 43 R/compute_mets.R | 22 R/create_fig_mvpa.R | 8 R/create_fig_pal.R | 16 R/create_fig_ratio_mvpa_sed.R | 8 R/create_fig_res_by_day.R | 4 R/create_fig_sed.R | 8 R/create_fig_steps.R | 124 + R/get_pa_period_info.R |only R/globals.R | 3 R/mark_intensity.R | 5 R/mod_control_pa_period_view.R |only R/mod_report_pa_period.R |only R/plot_data.R | 71 R/plot_data_with_intensity.R | 42 R/prepare_dataset.R | 8 R/read_agd.R | 2 R/recap_by_day.R | 4 R/settings.R | 4 README.md | 22 inst/app/www/style.css | 67 inst/doc/activAnalyzer.R | 50 inst/doc/activAnalyzer.Rmd | 50 inst/doc/activAnalyzer.html | 85 inst/extdata/acc.agd |binary inst/guide/user_guide_en.Rmd | 16 inst/guide/user_guide_en.aux | 111 - inst/guide/user_guide_en.pdf |binary inst/guide/user_guide_fr.Rmd | 12 inst/guide/user_guide_fr.log | 2054 ++++++++++-------------- inst/guide/user_guide_fr.pdf |binary inst/report/report_en.Rmd | 4 inst/report/report_fr.Rmd | 6 inst/report/report_fr_cppac.Rmd | 3 man/compute_bmr.Rd | 58 man/compute_mets.Rd | 94 - man/get_pa_period_info.Rd |only man/mark_intensity.Rd | 5 man/plot_data.Rd | 12 man/plot_data_with_intensity.Rd | 12 man/prepare_dataset.Rd | 4 man/recap_by_day.Rd | 2 tests/testthat/test-compute_bmr.R | 17 tests/testthat/test-compute_mets.R | 108 - tests/testthat/test-create_fig_mvpa.R | 12 tests/testthat/test-create_fig_ratio_mvpa_sed.R | 12 tests/testthat/test-create_fig_sed.R | 16 tests/testthat/test-create_fig_steps.R | 12 tests/testthat/test-golem-recommended.R | 1310 ++++++++++----- tests/testthat/test-mark_wear_time.R | 19 tests/testthat/test-plot_data_with_intensity.R | 15 vignettes/activAnalyzer.Rmd | 50 59 files changed, 3735 insertions(+), 2301 deletions(-)
Title: Goodness-of-Fit Test for Weibull Distribution (Weibullness)
Description: Performs a goodness-of-fit test of Weibull distribution (weibullness test) and provides the maximum likelihood estimates of the three-parameter Weibull distribution. Note that the threshold parameter is estimated based on the correlation from the Weibull plot. For more details, see Park (2018) <doi:10.1155/2018/6056975>. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2022R1A2C1091319).
Author: Chanseok Park [aut, cre]
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between weibullness versions 1.19.8 dated 2019-08-19 and 1.22.12 dated 2022-12-02
DESCRIPTION | 12 ++++++------ MD5 | 17 ++++++++++------- NAMESPACE | 2 +- R/weibull.estimate.R | 19 +++++++++++++++++-- build |only inst/CITATION | 13 +++++++++++++ inst/NEWS.Rd |only man/weibull.mle.Rd | 7 ++++--- man/weibull.rm.Rd |only man/weibull.threshold.Rd | 9 +++++---- man/weibull.wp.Rd | 9 ++++----- 11 files changed, 60 insertions(+), 28 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.16.0 dated 2022-10-21 and 0.17.0 dated 2022-12-02
tiledb-0.16.0/tiledb/R/tiledb-package.R |only tiledb-0.16.0/tiledb/R/zzz.R |only tiledb-0.17.0/tiledb/DESCRIPTION | 13 tiledb-0.17.0/tiledb/MD5 | 52 +- tiledb-0.17.0/tiledb/NAMESPACE | 6 tiledb-0.17.0/tiledb/NEWS.md | 39 ++ tiledb-0.17.0/tiledb/R/BatchedQuery.R | 15 tiledb-0.17.0/tiledb/R/Group.R | 13 tiledb-0.17.0/tiledb/R/Init.R |only tiledb-0.17.0/tiledb/R/RcppExports.R | 4 tiledb-0.17.0/tiledb/R/TileDB-Package.R |only tiledb-0.17.0/tiledb/R/TileDBArray.R | 181 ++++++++-- tiledb-0.17.0/tiledb/build/vignette.rds |binary tiledb-0.17.0/tiledb/inst/config.log |only tiledb-0.17.0/tiledb/inst/config.status |only tiledb-0.17.0/tiledb/inst/include/spdlog_r_sink.h |only tiledb-0.17.0/tiledb/inst/tinytest/test_arrayschemaevolution.R | 2 tiledb-0.17.0/tiledb/inst/tinytest/test_dim.R | 168 +++++++++ tiledb-0.17.0/tiledb/inst/tinytest/test_dimsubset.R | 85 +++- tiledb-0.17.0/tiledb/inst/tinytest/test_group.R | 6 tiledb-0.17.0/tiledb/inst/tinytest/test_matrix.R | 5 tiledb-0.17.0/tiledb/inst/tinytest/test_tiledbarray.R | 73 ++-- tiledb-0.17.0/tiledb/man/selected_points-set-tiledb_array-method.Rd |only tiledb-0.17.0/tiledb/man/selected_points-tiledb_array-method.Rd |only tiledb-0.17.0/tiledb/man/tiledb-package.Rd | 2 tiledb-0.17.0/tiledb/man/tiledb_array-class.Rd | 3 tiledb-0.17.0/tiledb/man/tiledb_array.Rd | 6 tiledb-0.17.0/tiledb/man/tiledb_group_is_relative.Rd |only tiledb-0.17.0/tiledb/src/RcppExports.cpp | 19 - tiledb-0.17.0/tiledb/src/libtiledb.cpp | 36 + tiledb-0.17.0/tiledb/src/libtiledb.h | 4 tiledb-0.17.0/tiledb/tools/tiledbVersion.txt | 4 32 files changed, 609 insertions(+), 127 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.10.0 dated 2022-09-20 and 1.11.0 dated 2022-12-02
DESCRIPTION | 14 MD5 | 50 NEWS.md | 52 R/RenderSql.R | 2 build/vignette.rds |binary inst/csv/jarChecksum.txt | 2 inst/csv/replacementPatterns.csv | 98 inst/doc/UsingSqlRender.R | 2 inst/doc/UsingSqlRender.Rmd | 4 inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/org/ohdsi/sql/SqlTranslate.java | 14 java/org/ohdsi/sql/StringUtils.java | 3 java/org/ohdsi/sql/TestSqlRender.java | 16 tests/testthat/test-replacement-patterns-file-format.R |only tests/testthat/test-translate-bigquery.R | 11 tests/testthat/test-translate-duckdb.R | 7 tests/testthat/test-translate-hive.R |only tests/testthat/test-translate-impala.R |only tests/testthat/test-translate-netezza.R |only tests/testthat/test-translate-oracle.R | 55 tests/testthat/test-translate-pdw.R |only tests/testthat/test-translate-postgresql.R |only tests/testthat/test-translate-redshift.R |only tests/testthat/test-translate-snowflake.R |only tests/testthat/test-translate-spark.R | 24 tests/testthat/test-translate-sql_server.R |only tests/testthat/test-translate-sqlite.R | 5 tests/testthat/test-translate-synapse.R |only tests/testthat/test-translateSql.R | 3218 ----------------- vignettes/UsingSqlRender.Rmd | 4 31 files changed, 277 insertions(+), 3304 deletions(-)
Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based
spatial relative risk functions that are estimated using the 'sparr' package.
Details about the 'sparr' package methods can be found in the tutorial: Davies
et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation
can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More
information about relative risk functions using kernel density estimation can
be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Derek W. Brown [aut, cph] ,
Mitchell J. Machiela [ctb] ,
Timothy A. Myers [ctb],
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between sparrpowR versions 0.2.5 dated 2022-02-04 and 0.2.6 dated 2022-12-02
sparrpowR-0.2.5/sparrpowR/man/figures |only sparrpowR-0.2.6/sparrpowR/DESCRIPTION | 20 +++++----- sparrpowR-0.2.6/sparrpowR/MD5 | 33 ++++++---------- sparrpowR-0.2.6/sparrpowR/NEWS.md | 5 ++ sparrpowR-0.2.6/sparrpowR/R/jitter_power.R | 4 +- sparrpowR-0.2.6/sparrpowR/R/package.R | 4 +- sparrpowR-0.2.6/sparrpowR/R/spatial_data.R | 6 +-- sparrpowR-0.2.6/sparrpowR/R/spatial_power.R | 4 +- sparrpowR-0.2.6/sparrpowR/README.md | 42 ++++++++++++++------- sparrpowR-0.2.6/sparrpowR/build/partial.rdb |binary sparrpowR-0.2.6/sparrpowR/build/vignette.rds |binary sparrpowR-0.2.6/sparrpowR/man/jitter_power.Rd | 2 - sparrpowR-0.2.6/sparrpowR/man/sparrpowR-package.Rd | 4 +- sparrpowR-0.2.6/sparrpowR/man/spatial_data.Rd | 2 - sparrpowR-0.2.6/sparrpowR/tests/testthat.R | 1 15 files changed, 71 insertions(+), 56 deletions(-)
Title: Cluster Analysis via Nonparametric Density Estimation
Description: Cluster analysis via nonparametric density
estimation is performed. Operationally, the kernel method is used throughout to estimate
the density. Diagnostics methods for evaluating the quality of the clustering
are available. The package includes also a routine to estimate the
probability density function obtained by the kernel method, given a set of
data with arbitrary dimensions.
Author: Menardi Giovanna [aut, cre],
Azzalini Adelchi [aut],
Rosolin Tiziana [ctb]
Maintainer: Menardi Giovanna <menardi@stat.unipd.it>
Diff between pdfCluster versions 1.0-3 dated 2018-12-04 and 1.0-4 dated 2022-12-02
pdfCluster-1.0-3/pdfCluster/inst/ChangeLog |only pdfCluster-1.0-3/pdfCluster/src/registerDynamicSymbol.c |only pdfCluster-1.0-4/pdfCluster/DESCRIPTION | 22 - pdfCluster-1.0-4/pdfCluster/MD5 | 19 - pdfCluster-1.0-4/pdfCluster/NEWS.md |only pdfCluster-1.0-4/pdfCluster/R/pdfCluster.R | 2 pdfCluster-1.0-4/pdfCluster/R/zzz.R | 2 pdfCluster-1.0-4/pdfCluster/inst/CHANGELOG |only pdfCluster-1.0-4/pdfCluster/inst/CITATION | 4 pdfCluster-1.0-4/pdfCluster/man/adj.rand.index.Rd | 98 ++--- pdfCluster-1.0-4/pdfCluster/man/dbs.Rd | 290 ++++++++-------- pdfCluster-1.0-4/pdfCluster/src/kepdf.c | 7 pdfCluster-1.0-4/pdfCluster/src/pdfCluster_init.c |only 13 files changed, 223 insertions(+), 221 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.6.0 dated 2022-10-24 and 2.7.0 dated 2022-12-02
inlabru-2.6.0/inlabru/man/fm_CRS.Rd |only inlabru-2.6.0/inlabru/man/fm_get_crs.Rd |only inlabru-2.6.0/inlabru/man/stransform.Rd |only inlabru-2.6.0/inlabru/man/vertices.Rd |only inlabru-2.6.0/inlabru/tests/testthat/_snaps/latent_spde1D.md |only inlabru-2.6.0/inlabru/tests/testthat/_snaps/latent_spde2D.md |only inlabru-2.6.0/inlabru/tests/testthat/test_bru_sf.R |only inlabru-2.6.0/inlabru/tests/testthat/test_component.R |only inlabru-2.6.0/inlabru/tests/testthat/test_copy.R |only inlabru-2.6.0/inlabru/tests/testthat/test_data.R |only inlabru-2.6.0/inlabru/tests/testthat/test_fmesher_sf.R |only inlabru-2.6.0/inlabru/tests/testthat/test_fmesher_sp.R |only inlabru-2.6.0/inlabru/tests/testthat/test_globe_mesh.R |only inlabru-2.6.0/inlabru/tests/testthat/test_ipoints.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_ar1.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_clinear.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_factor.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_fixed_effects.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_linear.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_rw2.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_spde1D.R |only inlabru-2.6.0/inlabru/tests/testthat/test_latent_spde2D.R |only inlabru-2.6.0/inlabru/tests/testthat/test_lgcp_1d.R |only inlabru-2.6.0/inlabru/tests/testthat/test_lgcp_1d_nonlinear.R |only inlabru-2.6.0/inlabru/tests/testthat/test_lgcp_2d.R |only inlabru-2.6.0/inlabru/tests/testthat/test_lgcp_2d_covars.R |only inlabru-2.6.0/inlabru/tests/testthat/test_lgcp_2d_plotsample.R |only inlabru-2.6.0/inlabru/tests/testthat/test_linearisation.R |only inlabru-2.6.0/inlabru/tests/testthat/test_mapper.R |only inlabru-2.6.0/inlabru/tests/testthat/test_multi_like.R |only inlabru-2.6.0/inlabru/tests/testthat/test_offset.R |only inlabru-2.6.0/inlabru/tests/testthat/test_predict.R |only inlabru-2.6.0/inlabru/tests/testthat/test_skips.R |only inlabru-2.6.0/inlabru/tests/testthat/test_utils.R |only inlabru-2.7.0/inlabru/DESCRIPTION | 35 inlabru-2.7.0/inlabru/MD5 | 247 - inlabru-2.7.0/inlabru/NAMESPACE | 136 inlabru-2.7.0/inlabru/NEWS.md | 70 inlabru-2.7.0/inlabru/R/bru.gof.R | 3 inlabru-2.7.0/inlabru/R/bru.inference.R | 386 -- inlabru-2.7.0/inlabru/R/bru.integration.R | 65 inlabru-2.7.0/inlabru/R/bru.spatial.R | 45 inlabru-2.7.0/inlabru/R/covariate.R | 21 inlabru-2.7.0/inlabru/R/data.gorillas.R | 1 inlabru-2.7.0/inlabru/R/data.mexdolphin.R | 6 inlabru-2.7.0/inlabru/R/data.seals.R | 5 inlabru-2.7.0/inlabru/R/data.shrimp.R | 1 inlabru-2.7.0/inlabru/R/dsmdata.R | 1 inlabru-2.7.0/inlabru/R/dsmdata.tools.R | 6 inlabru-2.7.0/inlabru/R/effect.R | 367 + inlabru-2.7.0/inlabru/R/environment.R | 75 inlabru-2.7.0/inlabru/R/fmesher_crs.R | 1533 +++++-- inlabru-2.7.0/inlabru/R/fmesher_evaluator.R |only inlabru-2.7.0/inlabru/R/fmesher_sf_mesh.R | 10 inlabru-2.7.0/inlabru/R/fmesher_sp_mesh.R | 3 inlabru-2.7.0/inlabru/R/ggplot.R | 184 inlabru-2.7.0/inlabru/R/integration.R | 202 - inlabru-2.7.0/inlabru/R/local_testthat.R | 10 inlabru-2.7.0/inlabru/R/mappers.R | 1924 +++++++--- inlabru-2.7.0/inlabru/R/mesh.R | 46 inlabru-2.7.0/inlabru/R/model.R | 73 inlabru-2.7.0/inlabru/R/nlinla.R | 31 inlabru-2.7.0/inlabru/R/plotsample.R | 17 inlabru-2.7.0/inlabru/R/prediction.R | 1 inlabru-2.7.0/inlabru/R/rgl.R | 37 inlabru-2.7.0/inlabru/R/sampling.R | 42 inlabru-2.7.0/inlabru/R/sf_utils.R | 9 inlabru-2.7.0/inlabru/R/track_plotting.R | 54 inlabru-2.7.0/inlabru/R/transformation.R | 44 inlabru-2.7.0/inlabru/R/utils.R | 138 inlabru-2.7.0/inlabru/README.md | 33 inlabru-2.7.0/inlabru/build/vignette.rds |binary inlabru-2.7.0/inlabru/inst/doc/bru_mapper.R | 144 inlabru-2.7.0/inlabru/inst/doc/bru_mapper.Rmd | 349 + inlabru-2.7.0/inlabru/inst/doc/bru_mapper.html | 691 ++- inlabru-2.7.0/inlabru/inst/doc/component.R | 2 inlabru-2.7.0/inlabru/inst/doc/component.Rmd | 16 inlabru-2.7.0/inlabru/inst/doc/component.html | 159 inlabru-2.7.0/inlabru/inst/doc/linearapprox.html | 119 inlabru-2.7.0/inlabru/inst/doc/method.html | 14 inlabru-2.7.0/inlabru/inst/doc/prediction_scores.R | 124 inlabru-2.7.0/inlabru/inst/doc/prediction_scores.Rmd | 124 inlabru-2.7.0/inlabru/inst/doc/prediction_scores.html | 255 - inlabru-2.7.0/inlabru/inst/doc/website_examples.R | 1 inlabru-2.7.0/inlabru/inst/doc/website_examples.Rmd | 1 inlabru-2.7.0/inlabru/inst/doc/website_examples.html | 16 inlabru-2.7.0/inlabru/inst/examples/devel.cvmeasure.R | 2 inlabru-2.7.0/inlabru/inst/examples/predict.bru.R | 2 inlabru-2.7.0/inlabru/man/bm_list.Rd |only inlabru-2.7.0/inlabru/man/bru_convergence_plot.Rd |only inlabru-2.7.0/inlabru/man/bru_env_get.Rd | 2 inlabru-2.7.0/inlabru/man/bru_fill_missing.Rd | 9 inlabru-2.7.0/inlabru/man/bru_info.Rd | 8 inlabru-2.7.0/inlabru/man/bru_int_polygon.Rd | 4 inlabru-2.7.0/inlabru/man/bru_mapper.Rd | 173 inlabru-2.7.0/inlabru/man/bru_mapper_generics.Rd |only inlabru-2.7.0/inlabru/man/bru_mapper_methods.Rd | 364 - inlabru-2.7.0/inlabru/man/bru_mapper_summary.Rd |only inlabru-2.7.0/inlabru/man/bru_model.Rd | 12 inlabru-2.7.0/inlabru/man/component.Rd | 8 inlabru-2.7.0/inlabru/man/component_list.Rd | 14 inlabru-2.7.0/inlabru/man/devel.cvmeasure.Rd | 2 inlabru-2.7.0/inlabru/man/figures/README-example-1.png |binary inlabru-2.7.0/inlabru/man/fm_CRS_sp.Rd |only inlabru-2.7.0/inlabru/man/fm_CRSargs.Rd | 2 inlabru-2.7.0/inlabru/man/fm_as.Rd | 8 inlabru-2.7.0/inlabru/man/fm_crs.Rd |only inlabru-2.7.0/inlabru/man/fm_crs_wkt.Rd | 75 inlabru-2.7.0/inlabru/man/fm_evaluate.Rd |only inlabru-2.7.0/inlabru/man/fm_sp_get_crs.Rd | 2 inlabru-2.7.0/inlabru/man/fm_transform.Rd |only inlabru-2.7.0/inlabru/man/gg.RasterLayer.Rd | 1 inlabru-2.7.0/inlabru/man/gg.inla.mesh.1d.Rd | 1 inlabru-2.7.0/inlabru/man/gmap.Rd | 2 inlabru-2.7.0/inlabru/man/inlabru-deprecated.Rd | 69 inlabru-2.7.0/inlabru/man/input_eval.Rd | 2 inlabru-2.7.0/inlabru/man/ipoints.Rd | 3 inlabru-2.7.0/inlabru/man/lgcp.Rd | 1 inlabru-2.7.0/inlabru/man/predict.bru.Rd | 2 inlabru-2.7.0/inlabru/man/spoly.Rd | 7 inlabru-2.7.0/inlabru/man/st_check_dim.Rd | 4 inlabru-2.7.0/inlabru/man/summary.bru.Rd | 9 inlabru-2.7.0/inlabru/man/summary.component.Rd | 13 inlabru-2.7.0/inlabru/man/tsplit.inla.mesh.Rd | 7 inlabru-2.7.0/inlabru/man/vertices.inla.mesh.Rd | 2 inlabru-2.7.0/inlabru/tests/testthat/_snaps/latent_spde_1d.md |only inlabru-2.7.0/inlabru/tests/testthat/_snaps/latent_spde_2d.md |only inlabru-2.7.0/inlabru/tests/testthat/test-aggregate.R |only inlabru-2.7.0/inlabru/tests/testthat/test-bru_sf.R |only inlabru-2.7.0/inlabru/tests/testthat/test-component.R |only inlabru-2.7.0/inlabru/tests/testthat/test-copy.R |only inlabru-2.7.0/inlabru/tests/testthat/test-data.R |only inlabru-2.7.0/inlabru/tests/testthat/test-eval_spatial.R |only inlabru-2.7.0/inlabru/tests/testthat/test-fmesher_sf.R |only inlabru-2.7.0/inlabru/tests/testthat/test-fmesher_sp.R |only inlabru-2.7.0/inlabru/tests/testthat/test-fmesher_transform.R |only inlabru-2.7.0/inlabru/tests/testthat/test-globe_mesh.R |only inlabru-2.7.0/inlabru/tests/testthat/test-integration.R |only inlabru-2.7.0/inlabru/tests/testthat/test-ipoints.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_ar1.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_clinear.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_factor.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_fixed_effects.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_linear.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_rw2.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_spde_1d.R |only inlabru-2.7.0/inlabru/tests/testthat/test-latent_spde_2d.R |only inlabru-2.7.0/inlabru/tests/testthat/test-lgcp_1d.R |only inlabru-2.7.0/inlabru/tests/testthat/test-lgcp_1d_nonlinear.R |only inlabru-2.7.0/inlabru/tests/testthat/test-lgcp_2d.R |only inlabru-2.7.0/inlabru/tests/testthat/test-lgcp_2d_covars.R |only inlabru-2.7.0/inlabru/tests/testthat/test-lgcp_2d_plotsample.R |only inlabru-2.7.0/inlabru/tests/testthat/test-linearisation.R |only inlabru-2.7.0/inlabru/tests/testthat/test-mapper.R |only inlabru-2.7.0/inlabru/tests/testthat/test-multi_like.R |only inlabru-2.7.0/inlabru/tests/testthat/test-offset.R |only inlabru-2.7.0/inlabru/tests/testthat/test-predict.R |only inlabru-2.7.0/inlabru/tests/testthat/test-skips.R |only inlabru-2.7.0/inlabru/tests/testthat/test-utils.R |only inlabru-2.7.0/inlabru/vignettes/bru_mapper.Rmd | 349 + inlabru-2.7.0/inlabru/vignettes/component.Rmd | 16 inlabru-2.7.0/inlabru/vignettes/prediction_scores.Rmd | 124 inlabru-2.7.0/inlabru/vignettes/website_examples.Rmd | 1 163 files changed, 6019 insertions(+), 3157 deletions(-)
Title: R Tools for Helsinki Open Data
Description: Tools for accessing various open data APIs in the Helsinki
region in Finland. Current data sources include the Service Map API,
Linked Events API, and Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen [aut, cre],
Joona Lehtomaki [aut],
Pyry Kantanen [aut] ,
Leo Lahti [aut]
Maintainer: Juuso Parkkinen <juuso.parkkinen@iki.fi>
Diff between helsinki versions 1.0.5 dated 2021-09-29 and 1.0.6 dated 2022-12-02
helsinki-1.0.5/helsinki/man/get_hsy-deprecated.Rd |only helsinki-1.0.6/helsinki/DESCRIPTION | 26 helsinki-1.0.6/helsinki/MD5 | 69 helsinki-1.0.6/helsinki/NAMESPACE | 5 helsinki-1.0.6/helsinki/R/HSY.R | 187 +- helsinki-1.0.6/helsinki/R/firstlib.R | 4 helsinki-1.0.6/helsinki/R/get_city_map.R | 34 helsinki-1.0.6/helsinki/R/get_feature.R | 3 helsinki-1.0.6/helsinki/R/get_feature_list.R | 64 helsinki-1.0.6/helsinki/R/helsinki-package.R | 3 helsinki-1.0.6/helsinki/R/regional_stats.R | 52 helsinki-1.0.6/helsinki/R/services.R | 66 helsinki-1.0.6/helsinki/R/wfs_api.R | 135 + helsinki-1.0.6/helsinki/README.md | 65 helsinki-1.0.6/helsinki/build/vignette.rds |binary helsinki-1.0.6/helsinki/inst/CITATION | 26 helsinki-1.0.6/helsinki/inst/doc/helsinki_tutorial.R | 102 - helsinki-1.0.6/helsinki/inst/doc/helsinki_tutorial.Rmd | 112 - helsinki-1.0.6/helsinki/inst/doc/helsinki_tutorial.html | 1148 +++++++++------ helsinki-1.0.6/helsinki/man/figures |only helsinki-1.0.6/helsinki/man/get_city_map.Rd | 21 helsinki-1.0.6/helsinki/man/get_feature.Rd | 6 helsinki-1.0.6/helsinki/man/get_feature_list.Rd | 12 helsinki-1.0.6/helsinki/man/get_hri_dataset_list.Rd |only helsinki-1.0.6/helsinki/man/get_hri_dataset_metadata.Rd |only helsinki-1.0.6/helsinki/man/get_hri_stats.Rd | 14 helsinki-1.0.6/helsinki/man/get_linkedevents.Rd | 28 helsinki-1.0.6/helsinki/man/get_rakennustietoruudukko.Rd | 27 helsinki-1.0.6/helsinki/man/get_servicemap.Rd | 74 helsinki-1.0.6/helsinki/man/get_vaestotietoruudukko.Rd | 25 helsinki-1.0.6/helsinki/man/gracefully_fail.Rd |only helsinki-1.0.6/helsinki/man/helsinki-deprecated.Rd | 25 helsinki-1.0.6/helsinki/man/helsinki-package.Rd | 7 helsinki-1.0.6/helsinki/man/select_feature.Rd | 4 helsinki-1.0.6/helsinki/man/to_sf.Rd | 2 helsinki-1.0.6/helsinki/man/wfs_api.Rd | 54 helsinki-1.0.6/helsinki/tests/testthat/test_helsinki.R | 17 helsinki-1.0.6/helsinki/vignettes/helsinki_tutorial.Rmd | 112 - 38 files changed, 1553 insertions(+), 976 deletions(-)
Title: Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers
Description: The classical (i.e. Efron's, see Efron and Tibshirani (1994, ISBN:978-0412042317) "An Introduction to the Bootstrap") bootstrap is widely used for both the real (i.e. "crisp") and fuzzy data.
The main aim of the algorithms implemented in this package is to overcome a problem with repetition of a few distinct values and to create fuzzy numbers, which are "similar" (but not the same) to values from the initial sample.
To do this, different characteristics of triangular/trapezoidal numbers are kept (like the value, the ambiguity, etc., see Grzegorzewski et al. <doi:10.2991/eusflat-19.2019.68>, Grzegorzewski et al. (2020) <doi:10.2991/ijcis.d.201012.003>, Grzegorzewski et al. (2020) <doi:10.34768/amcs-2020-0022>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-030-95929-6_3>, Romaniuk and Hryniewicz (2019) <doi:10.1007/s00500-018-3251-5>).
Some additional procedures related to these resampling methods are also provided,
like calculation of the Bertoluz [...truncated...]
Author: Maciej Romaniuk [cre],
Przemyslaw Grzegorzewski [aut],
Olgierd Hryniewicz [aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyResampling versions 0.4.2 dated 2022-03-21 and 0.5.0 dated 2022-12-02
FuzzyResampling-0.4.2/FuzzyResampling/R/EWmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/VAAmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/VAFmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/VAmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/classicalBoostrap.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/dmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/R/wmethod.R |only FuzzyResampling-0.4.2/FuzzyResampling/man/EWmethod.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/VAAmethod.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/VAFmethod.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/VAmethod.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/classicalBootstrap.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/dmethod.Rd |only FuzzyResampling-0.4.2/FuzzyResampling/man/wmethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/DESCRIPTION | 10 FuzzyResampling-0.5.0/FuzzyResampling/MD5 | 91 +++-- FuzzyResampling-0.5.0/FuzzyResampling/NAMESPACE | 29 + FuzzyResampling-0.5.0/FuzzyResampling/NEWS.md | 6 FuzzyResampling-0.5.0/FuzzyResampling/R/BertoluzzaDistance.R | 54 +++ FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateAmbiguity.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateAmbiguityL.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateAmbiguityR.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateExpValue.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateFuzziness.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateValue.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/CalculateWidth.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/ClassicalBoostrap.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/ComparePowerOneSampleCTest.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/ComparisonOneSampleCTest.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/ComparisonSEMean.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/DMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/EWMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/FuzzyResampling-package.R | 26 - FuzzyResampling-0.5.0/FuzzyResampling/R/GeneratorFuzzyNumbers.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/GeneratorNExpUU.R | 55 +-- FuzzyResampling-0.5.0/FuzzyResampling/R/GeneratorNU.R | 55 +-- FuzzyResampling-0.5.0/FuzzyResampling/R/OneSampleCTest.R | 42 ++ FuzzyResampling-0.5.0/FuzzyResampling/R/SEResamplingMean.R | 47 ++ FuzzyResampling-0.5.0/FuzzyResampling/R/TwoSampleCTest.R | 45 +- FuzzyResampling-0.5.0/FuzzyResampling/R/VAAMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/VAFMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/VAMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/WMethod.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/resamplingMethods.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/samplingGenerators.R |only FuzzyResampling-0.5.0/FuzzyResampling/R/utils.R | 160 ++++------ FuzzyResampling-0.5.0/FuzzyResampling/README.md | 142 +++++--- FuzzyResampling-0.5.0/FuzzyResampling/build |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateAmbiguity.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateAmbiguityL.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateAmbiguityR.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateExpValue.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateFuzziness.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateValue.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/CalculateWidth.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/ClassicalBootstrap.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/ComparePowerOneSampleCTest.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/ComparisonOneSampleCTest.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/ComparisonSEMean.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/DMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/EWMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/FuzzyResampling-package.Rd | 27 - FuzzyResampling-0.5.0/FuzzyResampling/man/GeneratorFuzzyNumbers.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/GeneratorNExpUU.Rd | 3 FuzzyResampling-0.5.0/FuzzyResampling/man/GeneratorNU.Rd | 3 FuzzyResampling-0.5.0/FuzzyResampling/man/OneSampleCTest.Rd | 4 FuzzyResampling-0.5.0/FuzzyResampling/man/SEResamplingMean.Rd | 6 FuzzyResampling-0.5.0/FuzzyResampling/man/TwoSampleCTest.Rd | 4 FuzzyResampling-0.5.0/FuzzyResampling/man/VAAMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/VAFMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/VAMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/WMethod.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/resamplingMethods.Rd |only FuzzyResampling-0.5.0/FuzzyResampling/man/samplingGenerators.Rd |only 74 files changed, 464 insertions(+), 345 deletions(-)
More information about FuzzyResampling at CRAN
Permanent link
Title: Adaptive Subgroup Selection in Group Sequential Trials
Description: Clinical trial design for subgroup selection in three-stage group
sequential trial as described in Lai, Lavori and Liao (2014,
<doi:10.1016/j.cct.2014.09.001>). Includes facilities for design,
exploration and analysis of such trials. An implementation of
the initial DEFUSE-3 trial is also provided as a vignette.
Author: Tze Leung Lai [ctb],
Philip Lavori [aut],
Olivia Liao [aut],
Balasubramanian Narasimhan [aut, cre],
Ka Wai Tsang [aut]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ASSISTant versions 1.4.2 dated 2019-05-03 and 1.4.3 dated 2022-12-02
DESCRIPTION | 17 MD5 | 68 - NEWS.md | 5 R/ASSISTDesigns.R | 2304 +++++++++++++++++++++---------------------- R/ASSISTant.R | 74 - R/LLL.SETTINGS.R | 7 R/utilities.R | 118 +- build/partial.rdb |only build/vignette.rds |binary inst/doc/ASSISTant.R | 54 - inst/doc/ASSISTant.Rmd | 3 inst/doc/ASSISTant.html | 2134 +++++++++++++++++++++------------------ inst/doc/Rankin.R | 10 inst/doc/Rankin.Rmd | 3 inst/doc/Rankin.html | 562 ++++++---- inst/doc/defuse3.R | 30 inst/doc/defuse3.Rmd | 3 inst/doc/defuse3.html | 992 +++++++++++------- man/ASSISTDesign.Rd | 294 ++++- man/ASSISTDesignB.Rd | 176 ++- man/ASSISTDesignC.Rd | 177 ++- man/ASSISTant-internal.Rd | 34 man/ASSISTant.Rd | 32 man/DEFUSE3Design.Rd | 224 +++- man/LLL.SETTINGS.Rd | 7 man/computeMHPBoundaries.Rd | 10 man/computeMHPBoundaryITT.Rd | 7 man/conformParameters.Rd |only man/generateDiscreteData.Rd | 6 man/groupSampleSize.Rd | 17 man/mHP.b.Rd | 7 man/mHP.btilde.Rd | 7 man/mHP.c.Rd | 7 vignettes/ASSISTant.Rmd | 3 vignettes/Rankin.Rmd | 3 vignettes/defuse3.Rmd | 3 36 files changed, 4262 insertions(+), 3136 deletions(-)
Title: Semi-Confirmatory Structural Equation Modeling via Penalized
Likelihood or Least Squares
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS). For details, please see Huang (2020) <doi:10.18637/jss.v093.i07>.
Author: Po-Hsien Huang [cre, aut],
Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>
Diff between lslx versions 0.6.10 dated 2020-04-27 and 0.6.11 dated 2022-12-02
DESCRIPTION | 13 MD5 | 26 build/vignette.rds |binary inst/doc/factor-analysis.html | 475 +++++++++----- inst/doc/missing-data-analysis.html | 301 +++++---- inst/doc/multi-group-analysis.html | 369 +++++++---- inst/doc/regression-analysis.html | 326 ++++++--- inst/doc/structural-equation-modeling.html | 297 ++++++--- man/lslx.Rd | 946 +++++++++++++++++++++++++++++ man/plsem.Rd | 24 man/prelslx.Rd | 96 ++ src/RcppExports.cpp | 5 src/compute-moment.cpp | 2 src/lslxOptimizer.cpp | 70 +- 14 files changed, 2274 insertions(+), 676 deletions(-)
Title: Set of Tools to Compute Various Climate Indices
Description: Set of tools to compute metrics and indices for climate analysis.
The package provides functions to compute extreme indices, evaluate the
agreement between models and combine theses models into an ensemble. Multi-model
time series of climate indices can be computed either after averaging the 2-D
fields from different models provided they share a common grid or by combining
time series computed on the model native grid. Indices can be assigned weights
and/or combined to construct new indices.
Author: BSC-CNS [aut, cph],
Nuria Perez-Zanon [aut] ,
An-Chi Ho [cre, ctb],
Nicolau Manubens [ctb],
Alasdair Hunter [aut],
Louis-Philippe Caron [ctb],
Eva Rifa [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>
Diff between ClimProjDiags versions 0.2.0 dated 2022-11-18 and 0.2.1 dated 2022-12-02
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + NEWS.md | 3 +++ R/WeightedCells.R |only man/WeightedCells.Rd |only 6 files changed, 12 insertions(+), 6 deletions(-)
Title: Genetic Linkage Maps in Autopolyploids
Description: Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
For more detail, please see Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.
Author: Marcelo Mollinari [aut, cre] ,
Gabriel Gesteira [aut] ,
Guilhereme Pereira [ctb] ,
Augusto Garcia [ctb] ,
Zhao-Bang Zeng [ctb] ,
Katharine Preedy [ctb, cph] ,
Robert Gentleman [cph] ,
Ross Ihaka [cph] ,
R Foundation [cph] ,
R-core [cph]
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Diff between mappoly versions 0.3.1 dated 2022-07-06 and 0.3.2 dated 2022-12-02
mappoly-0.3.1/mappoly/R/reestimate_map_with_global_genotypic_error.R |only mappoly-0.3.1/mappoly/R/reestimate_map_with_prior_genotypic_probability.R |only mappoly-0.3.1/mappoly/R/rf_snp_filter.R |only mappoly-0.3.1/mappoly/src/quality_lod_hmm.cpp |only mappoly-0.3.2/mappoly/DESCRIPTION | 27 mappoly-0.3.2/mappoly/MD5 | 150 ++-- mappoly-0.3.2/mappoly/NAMESPACE | 11 mappoly-0.3.2/mappoly/NEWS.md | 9 mappoly-0.3.2/mappoly/R/cache_twopts.R | 19 mappoly-0.3.2/mappoly/R/calc_genoprob_dist.R | 32 mappoly-0.3.2/mappoly/R/eliminate_redundant.R | 2 mappoly-0.3.2/mappoly/R/est_map_hmm.R | 25 mappoly-0.3.2/mappoly/R/export_map_list.R | 10 mappoly-0.3.2/mappoly/R/filters.R | 329 +++++---- mappoly-0.3.2/mappoly/R/find_blocks.R |only mappoly-0.3.2/mappoly/R/get_submap.R | 33 mappoly-0.3.2/mappoly/R/haplotype_map_utils.R | 4 mappoly-0.3.2/mappoly/R/homolog_probs.R | 5 mappoly-0.3.2/mappoly/R/import_from_updog.R | 57 + mappoly-0.3.2/mappoly/R/make_seq.R | 26 mappoly-0.3.2/mappoly/R/marker_info.R | 63 + mappoly-0.3.2/mappoly/R/mds.R | 12 mappoly-0.3.2/mappoly/R/one_paprent_single_map_hmm.R | 13 mappoly-0.3.2/mappoly/R/pairwise_rf.R | 49 - mappoly-0.3.2/mappoly/R/plot_genome_vs_map.R | 27 mappoly-0.3.2/mappoly/R/plot_map_list.R | 16 mappoly-0.3.2/mappoly/R/preferential_pairing.R | 4 mappoly-0.3.2/mappoly/R/read_mappoly.R | 36 - mappoly-0.3.2/mappoly/R/read_mappoly_csv.R | 9 mappoly-0.3.2/mappoly/R/read_mappoly_vcf.R | 2 mappoly-0.3.2/mappoly/R/reest_map_error.R |only mappoly-0.3.2/mappoly/R/reestimate_map.R | 2 mappoly-0.3.2/mappoly/R/rf_list_to_matrix.R | 10 mappoly-0.3.2/mappoly/R/split_and_rephase.R | 18 mappoly-0.3.2/mappoly/R/sysdata.rda |binary mappoly-0.3.2/mappoly/R/utils.R | 127 +++ mappoly-0.3.2/mappoly/README.md | 39 - mappoly-0.3.2/mappoly/build/partial.rdb |binary mappoly-0.3.2/mappoly/build/vignette.rds |binary mappoly-0.3.2/mappoly/inst/doc/mappoly_startguide.Rmd | 4 mappoly-0.3.2/mappoly/inst/doc/mappoly_startguide.html | 357 +++------- mappoly-0.3.2/mappoly/man/cache_counts_twopt.Rd | 2 mappoly-0.3.2/mappoly/man/elim_redundant.Rd | 2 mappoly-0.3.2/mappoly/man/est_full_hmm_with_global_error.Rd | 2 mappoly-0.3.2/mappoly/man/est_full_hmm_with_prior_prob.Rd | 7 mappoly-0.3.2/mappoly/man/est_pairwise_rf.Rd | 6 mappoly-0.3.2/mappoly/man/est_rf_hmm_single_one_parent.Rd | 14 mappoly-0.3.2/mappoly/man/filter_individuals.Rd | 2 mappoly-0.3.2/mappoly/man/filter_segregation.Rd | 6 mappoly-0.3.2/mappoly/man/find_blocks.Rd |only mappoly-0.3.2/mappoly/man/generate_all_link_phases_elim_equivalent_haplo.Rd | 2 mappoly-0.3.2/mappoly/man/genotyping_global_error.Rd | 2 mappoly-0.3.2/mappoly/man/get_tab_mrks.Rd | 2 mappoly-0.3.2/mappoly/man/import_from_updog.Rd | 11 mappoly-0.3.2/mappoly/man/make_seq_mappoly.Rd | 2 mappoly-0.3.2/mappoly/man/mds_mappoly.Rd | 5 mappoly-0.3.2/mappoly/man/merge_datasets.Rd | 2 mappoly-0.3.2/mappoly/man/mp_pallet1.Rd |only mappoly-0.3.2/mappoly/man/mp_pallet2.Rd |only mappoly-0.3.2/mappoly/man/mp_pallet3.Rd |only mappoly-0.3.2/mappoly/man/paralell_pairwise_discrete.Rd | 3 mappoly-0.3.2/mappoly/man/paralell_pairwise_probability.Rd | 3 mappoly-0.3.2/mappoly/man/parallel_block.Rd |only mappoly-0.3.2/mappoly/man/plot_genome_vs_map.Rd | 14 mappoly-0.3.2/mappoly/man/plot_map_list.Rd | 5 mappoly-0.3.2/mappoly/man/read_geno_csv.Rd | 2 mappoly-0.3.2/mappoly/man/read_vcf.Rd | 2 mappoly-0.3.2/mappoly/man/reest_rf.Rd | 2 mappoly-0.3.2/mappoly/man/rf_snp_filter.Rd | 23 mappoly-0.3.2/mappoly/man/split_mappoly.Rd |only mappoly-0.3.2/mappoly/man/summary_maps.Rd | 2 mappoly-0.3.2/mappoly/man/update_map.Rd | 2 mappoly-0.3.2/mappoly/src/pairwise_estimation_rcppparallel.cpp | 5 mappoly-0.3.2/mappoly/tests/testthat/test-2pt.R | 7 mappoly-0.3.2/mappoly/tests/testthat/test-cahe_twopts.R | 2 mappoly-0.3.2/mappoly/tests/testthat/test-export_map_list.R | 2 mappoly-0.3.2/mappoly/tests/testthat/test-get_submap.R | 2 mappoly-0.3.2/mappoly/tests/testthat/test-utility_func.R | 5 mappoly-0.3.2/mappoly/vignettes/images/fig1.jpeg |binary mappoly-0.3.2/mappoly/vignettes/images/fig2.jpeg |binary mappoly-0.3.2/mappoly/vignettes/images/fig3.jpeg |binary mappoly-0.3.2/mappoly/vignettes/mappoly_startguide.Rmd | 4 82 files changed, 953 insertions(+), 726 deletions(-)
Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.2.1 dated 2022-08-31 and 1.3.0 dated 2022-12-02
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/spatial_queries.R | 5 +++-- man/sedona_knn_query.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)