Title: Integrative Survival Modeling
Description: Contains implementations of
the integrative Cox model with uncertain event times
proposed by Wang, et al. (2020) <doi:10.1214/19-AOAS1287>,
the regularized Cox cure rate model with uncertain event status
proposed by Wang, et al. (2023) <doi:10.1007/s12561-023-09374-w>,
and other survival analysis routines including
the Cox cure rate model proposed by
Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531>
via an EM algorithm proposed by
Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>,
the regularized Cox cure rate model with elastic net penalty following
Masud et al. (2018) <doi:10.1177/0962280216677748>.
Author: Wenjie Wang [aut, cre] ,
Kun Chen [ths] ,
Jun Yan [ths]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between intsurv versions 0.2.2 dated 2021-01-08 and 0.3.0 dated 2025-09-28
intsurv-0.2.2/intsurv/R/intsurv.R |only intsurv-0.2.2/intsurv/inst/examples/cox_cure.R |only intsurv-0.2.2/intsurv/inst/examples/cox_cure_net.R |only intsurv-0.2.2/intsurv/inst/examples/iCoxph.R |only intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_cure.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_cure_uncer.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_reg.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/cross-validation.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/cv_coxph_cure_uncer.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/logistic_reg.h |only intsurv-0.2.2/intsurv/man/intsurv-package.Rd |only intsurv-0.2.2/intsurv/src/Makevars.win |only intsurv-0.2.2/intsurv/src/assessment_export.cpp |only intsurv-0.2.2/intsurv/src/coxph_cure_export.cpp |only intsurv-0.2.2/intsurv/src/coxph_cure_uncer_export.cpp |only intsurv-0.2.2/intsurv/src/coxph_reg_export.cpp |only intsurv-0.2.2/intsurv/src/logistic_reg_export.cpp |only intsurv-0.2.2/intsurv/src/nonparametric_export.cpp |only intsurv-0.2.2/intsurv/src/utils_export.cpp |only intsurv-0.3.0/intsurv/DESCRIPTION | 41 intsurv-0.3.0/intsurv/MD5 | 126 - intsurv-0.3.0/intsurv/NAMESPACE | 3 intsurv-0.3.0/intsurv/NEWS.md | 16 intsurv-0.3.0/intsurv/R/RcppExports.R | 52 intsurv-0.3.0/intsurv/R/Survi.R | 26 intsurv-0.3.0/intsurv/R/assessment.R | 27 intsurv-0.3.0/intsurv/R/bootSe.R | 2 intsurv-0.3.0/intsurv/R/class.R | 2 intsurv-0.3.0/intsurv/R/coef.R | 35 intsurv-0.3.0/intsurv/R/cox_cure.R | 756 +++++---- intsurv-0.3.0/intsurv/R/cox_cure_net.R | 770 ++++------ intsurv-0.3.0/intsurv/R/iCoxph.R | 20 intsurv-0.3.0/intsurv/R/intsurv-package.R |only intsurv-0.3.0/intsurv/R/misc.R | 54 intsurv-0.3.0/intsurv/R/prep_model.R | 35 intsurv-0.3.0/intsurv/R/print.R | 47 intsurv-0.3.0/intsurv/R/show.R | 2 intsurv-0.3.0/intsurv/R/simData4cure.R | 10 intsurv-0.3.0/intsurv/R/simData4iCoxph.R | 2 intsurv-0.3.0/intsurv/R/summary.R | 2 intsurv-0.3.0/intsurv/README.md | 51 intsurv-0.3.0/intsurv/inst/CITATION | 18 intsurv-0.3.0/intsurv/inst/examples/ex-cox_cure.R |only intsurv-0.3.0/intsurv/inst/examples/ex-cox_cure_net.R |only intsurv-0.3.0/intsurv/inst/examples/ex-iCoxph.R |only intsurv-0.3.0/intsurv/inst/include/intsurv.h | 19 intsurv-0.3.0/intsurv/inst/include/intsurv/Control.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/CoxphCure.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/CoxphCureMar.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/CoxphReg.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/CrossValidation.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/LogisticReg.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/assessment.h | 38 intsurv-0.3.0/intsurv/inst/include/intsurv/cv_coxph_cure.h | 364 ---- intsurv-0.3.0/intsurv/inst/include/intsurv/cv_coxph_cure_mar.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/nonparametric.h | 88 - intsurv-0.3.0/intsurv/inst/include/intsurv/subset.h |only intsurv-0.3.0/intsurv/inst/include/intsurv/utils.h | 127 + intsurv-0.3.0/intsurv/inst/rcpp-tests |only intsurv-0.3.0/intsurv/inst/tinytest/test-cox_cure.R | 105 + intsurv-0.3.0/intsurv/inst/tinytest/test-cox_cure_net.R | 33 intsurv-0.3.0/intsurv/inst/tinytest/test-cox_cure_net_uncer.R | 37 intsurv-0.3.0/intsurv/inst/tinytest/test-cox_cure_uncer.R | 23 intsurv-0.3.0/intsurv/man/BIC.cox_cure.Rd | 4 intsurv-0.3.0/intsurv/man/BIC.cox_cure_net.Rd | 4 intsurv-0.3.0/intsurv/man/coef.cox_cure_net.Rd | 8 intsurv-0.3.0/intsurv/man/cox_cure.Rd | 292 +-- intsurv-0.3.0/intsurv/man/cox_cure_net.Rd | 335 +--- intsurv-0.3.0/intsurv/man/iCoxph.Rd | 16 intsurv-0.3.0/intsurv/man/intsurv.Rd |only intsurv-0.3.0/intsurv/man/simData4cure.Rd | 8 intsurv-0.3.0/intsurv/src/Makevars | 5 intsurv-0.3.0/intsurv/src/RcppExports.cpp | 474 +++--- intsurv-0.3.0/intsurv/src/assessment.cpp |only intsurv-0.3.0/intsurv/src/coxph_cure.cpp |only intsurv-0.3.0/intsurv/src/coxph_cure_mar.cpp |only intsurv-0.3.0/intsurv/src/coxph_reg.cpp |only intsurv-0.3.0/intsurv/src/cross-validation.cpp |only intsurv-0.3.0/intsurv/src/logistic_reg.cpp |only intsurv-0.3.0/intsurv/src/nonparametric.cpp |only intsurv-0.3.0/intsurv/src/utils.cpp |only intsurv-0.3.0/intsurv/tests/tinytest.R | 11 82 files changed, 1914 insertions(+), 2174 deletions(-)
Title: Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added. References: Bingham, Melissa A. and Nordman, Dan J. and Vardeman, Steve B. (2009),
Bingham, Melissa A and Vardeman, Stephen B and Nordman, Daniel J (2009),
Bingham, Melissa A and Nordman, Daniel J and Vardeman, Stephen B (2010),
Leon, C.A. and Masse, J.C. and Rivest, L.P. (2006),
Hartley, R and Aftab, K and Trumpf, J. (2011),
Stanfill, Bryan and Genschel, Ulrike and Hofmann, Heike (2013),
Maonton, Jonathan (2004),
Mardia, KV and Jupp, PE (2000, ISBN:9780471953333),
Rancourt, D. and Rivest, L.P. and Asselin, J. (2000),
Chang, Ted and Rivest, Loui [...truncated...]
Author: Bryan Stanfill [aut, cre],
Heike Hofmann [aut],
Ulrike Genschel [aut],
Aymeric Stamm [ctb] ,
Luciano Selzer [ctb]
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.6.5 dated 2023-12-07 and 1.6.6 dated 2025-09-28
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS | 31 +++++++++------ R/data.R | 2 R/help.R | 13 ++---- build/vignette.rds |binary inst/doc/rotations-intro.pdf |binary man/drill.Rd | 2 man/rotations.Rd | 31 +++++++++++++-- src/Makevars | 4 - src/Makevars.win | 5 -- src/RcppExports.cpp | 88 +++++++++++++++++++++---------------------- 12 files changed, 118 insertions(+), 90 deletions(-)
Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
Mark Clements [aut],
R Core Team [ctb]
Maintainer: Devin Incerti <devin.incerti@gmail.com>
Diff between hesim versions 0.5.5 dated 2024-09-18 and 0.5.6 dated 2025-09-28
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Title: Reference on Constants, Units and Uncertainty
Description: CODATA internationally recommended values of the fundamental
physical constants, provided as symbols for direct use within the R language.
Optionally, the values with uncertainties and/or units are also provided if
the 'errors', 'units' and/or 'quantities' packages are installed.
The Committee on Data for Science and Technology (CODATA) is an
interdisciplinary committee of the International Council for Science which
periodically provides the internationally accepted set of values of the
fundamental physical constants. This package contains the "2022 CODATA"
version, published on May 2024:
Eite Tiesinga, Peter J. Mohr, David B. Newell, and Barry N. Taylor (2024)
<https://physics.nist.gov/cuu/Constants/>.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between constants versions 1.0.1 dated 2021-02-25 and 2022.0 dated 2025-09-28
DESCRIPTION | 17 +++++++++-------- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/constants.R | 23 +++++++++++------------ README.md | 24 +++++++++++++----------- data/codata.cor.rda |binary data/codata.rda |binary man/codata.Rd | 12 ++++++------ man/constants-package.Rd | 9 +++++---- 9 files changed, 57 insertions(+), 49 deletions(-)
Title: Shiny Module for Taking Free-Form Notes
Description: An enterprise-targeted scalable and customizable 'shiny' module providing an easy way to incorporate free-form note taking or discussion boards into applications.
The package includes a 'shiny' module that can be included in any 'shiny' application to create a panel containing searchable, editable text broken down by section headers.
Can be used with a local 'SQLite' database, or a compatible remote database of choice.
Author: Daniel Kovtun [cre, aut]
Maintainer: Daniel Kovtun <quantumfusetrader@gmail.com>
Diff between shinyNotes versions 0.0.2 dated 2023-02-19 and 0.0.3 dated 2025-09-28
DESCRIPTION | 8 +- MD5 | 36 ++++++------ NEWS.md | 4 + R/data.R | 10 +-- R/note_crud.R | 4 - R/runExample.R | 2 R/sqlite_db.R | 24 ++++---- build/vignette.rds |binary inst/doc/shinyNotes.R | 18 +++--- inst/doc/shinyNotes.html | 139 ++++++++++++++++++++++++----------------------- man/connect_sqlite.Rd | 8 +- man/create_schema.Rd | 4 - man/db.read_table.Rd | 8 +- man/db.write_table.Rd | 4 - man/demo_notes.Rd | 4 - man/emojis.Rd | 2 man/markdown_notes.Rd | 4 - man/runExample.Rd | 2 man/shinynotes.Rd | 4 - 19 files changed, 148 insertions(+), 137 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.4.2 dated 2025-01-07 and 1.4.3 dated 2025-09-28
DESCRIPTION | 12 +++++------ MD5 | 31 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 8 ++++++- R/lda.R | 6 +++-- R/seededlda.R | 22 ++++++++++++--------- R/utils.R | 23 ++++++++++++++++++++++ inst/WORDLIST | 3 -- man/as.dictionary.textmodel_lda.Rd |only man/print.textmodel_lda.Rd | 4 +-- man/terms.Rd | 10 ++++----- man/textmodel_lda.Rd | 5 ++-- src/Makevars.in | 2 - src/Makevars.win | 2 - tests/testthat/test-textmodel_lda.R | 3 +- tests/testthat/test-textmodel_seededlda.R | 2 - tests/testthat/test-utils.R | 11 ++++++++++ 17 files changed, 97 insertions(+), 48 deletions(-)
Title: Structures for Preference Data
Description: Convenient structures for creating, sourcing, reading, writing
and manipulating ordinal preference data. Methods for writing to/from PrefLib
formats. See Nicholas Mattei and Toby Walsh "PrefLib: A Library of Preference
Data" (2013) <doi:10.1007/978-3-642-41575-3_20>.
Author: Floyd Everest [aut, cre] ,
Heather Turner [aut] ,
Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>
This is a re-admission after prior archival of version 0.1.1 dated 2023-09-07
Diff between prefio versions 0.1.1 dated 2023-09-07 and 0.2.0 dated 2025-09-28
prefio-0.1.1/prefio/R/aggregate.preferences.R |only prefio-0.1.1/prefio/R/choices.R |only prefio-0.1.1/prefio/R/group.preferences.R |only prefio-0.1.1/prefio/R/utils-pipe.R |only prefio-0.1.1/prefio/man/aggregate.preferences.Rd |only prefio-0.1.1/prefio/man/choices.Rd |only prefio-0.1.1/prefio/man/group.Rd |only prefio-0.1.1/prefio/man/pipe.Rd |only prefio-0.1.1/prefio/man/reexports.Rd |only prefio-0.1.1/prefio/tests/testthat/test-aggregated_preferences.R |only prefio-0.1.1/prefio/tests/testthat/test-choices.R |only prefio-0.1.1/prefio/tests/testthat/test-group.R |only prefio-0.2.0/prefio/DESCRIPTION | 21 prefio-0.2.0/prefio/MD5 | 67 prefio-0.2.0/prefio/NAMESPACE | 65 prefio-0.2.0/prefio/NEWS.md | 12 prefio-0.2.0/prefio/R/adjacency.R | 110 prefio-0.2.0/prefio/R/pref_summaries.R |only prefio-0.2.0/prefio/R/pref_tools.R |only prefio-0.2.0/prefio/R/preferences.R | 1573 ++++------ prefio-0.2.0/prefio/R/prefio-package.R | 3 prefio-0.2.0/prefio/R/preflib.R | 152 prefio-0.2.0/prefio/R/ranking_matrix.R |only prefio-0.2.0/prefio/build/partial.rdb |binary prefio-0.2.0/prefio/inst/WORDLIST | 60 prefio-0.2.0/prefio/man/adjacency.Rd | 45 prefio-0.2.0/prefio/man/figures |only prefio-0.2.0/prefio/man/pref_add_unranked.Rd |only prefio-0.2.0/prefio/man/pref_blank.Rd |only prefio-0.2.0/prefio/man/pref_cov.Rd |only prefio-0.2.0/prefio/man/pref_get_items.Rd |only prefio-0.2.0/prefio/man/pref_get_rank.Rd |only prefio-0.2.0/prefio/man/pref_irv.Rd |only prefio-0.2.0/prefio/man/pref_keep.Rd |only prefio-0.2.0/prefio/man/pref_length.Rd |only prefio-0.2.0/prefio/man/pref_omit.Rd |only prefio-0.2.0/prefio/man/pref_pop.Rd |only prefio-0.2.0/prefio/man/pref_rev.Rd |only prefio-0.2.0/prefio/man/pref_trunc.Rd |only prefio-0.2.0/prefio/man/pref_type.Rd |only prefio-0.2.0/prefio/man/preferences.Rd | 319 -- prefio-0.2.0/prefio/man/ranking_matrix.Rd |only prefio-0.2.0/prefio/man/read_preflib.Rd | 24 prefio-0.2.0/prefio/man/write_preflib.Rd | 17 prefio-0.2.0/prefio/tests/data/sydney_2023.tsv |only prefio-0.2.0/prefio/tests/testthat/_snaps |only prefio-0.2.0/prefio/tests/testthat/test-adjacency.R | 49 prefio-0.2.0/prefio/tests/testthat/test-preferences.R | 1046 +++++- prefio-0.2.0/prefio/tests/testthat/test-preflib.R | 48 prefio-0.2.0/prefio/tests/testthat/test-rankingmatrix.R |only prefio-0.2.0/prefio/tests/testthat/test-summaries.R |only prefio-0.2.0/prefio/tests/testthat/test-tools.R |only 52 files changed, 2058 insertions(+), 1553 deletions(-)
Title: Holding the Database for the 'extrafont' Package
Description: It is meant to be used with the 'extrafont' package. The 'extrafont' package contains the code to install and use fonts, while the 'extrafontdb' package contains the font database.
Author: Winston Chang [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between extrafontdb versions 1.0 dated 2012-06-11 and 1.1 dated 2025-09-28
extrafontdb-1.0/extrafontdb/man/extrafontdb.Rd |only extrafontdb-1.1/extrafontdb/DESCRIPTION | 31 ++++++++++++----- extrafontdb-1.1/extrafontdb/MD5 | 17 ++++++--- extrafontdb-1.1/extrafontdb/NAMESPACE | 2 + extrafontdb-1.1/extrafontdb/NEWS |only extrafontdb-1.1/extrafontdb/R/extrafontdb.r | 15 +------- extrafontdb-1.1/extrafontdb/README.md | 24 +++++++++++++ extrafontdb-1.1/extrafontdb/inst/CITATION |only extrafontdb-1.1/extrafontdb/man/extrafontdb-package.Rd |only extrafontdb-1.1/extrafontdb/tests |only 10 files changed, 64 insertions(+), 25 deletions(-)
Title: 'systemPipeShiny' Utility Functions
Description: The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>
Diff between spsUtil versions 0.2.2 dated 2021-10-30 and 0.2.2.1 dated 2025-09-28
DESCRIPTION | 8 ++-- MD5 | 26 ++++++------- R/spsUtil.R | 2 - man/checkNameSpace.Rd | 8 ++-- man/checkUrl.Rd | 2 - man/historyStack.Rd | 94 ++++++++++++++++++++++++-------------------------- man/inc.Rd | 16 ++++---- man/msg.Rd | 43 ++++++++++------------ man/notFalsy.Rd | 23 +++++------- man/quiet.Rd | 8 ++-- man/simepleStack.Rd | 48 ++++++++++++------------- man/spsOption.Rd | 14 +++---- man/strUniquefy.Rd | 2 - man/timeout.Rd | 15 ++++--- 14 files changed, 153 insertions(+), 156 deletions(-)
Title: Sparse Latent Class Model for Cognitive Diagnosis
Description: Perform a Bayesian estimation of the exploratory
Sparse Latent Class Model for Binary Data
described by Chen, Y., Culpepper, S. A., and Liang, F. (2020)
<doi:10.1007/s11336-019-09693-2>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between slcm versions 0.1.0 dated 2023-08-12 and 0.1.1 dated 2025-09-28
DESCRIPTION | 27 ++++++++++++------------ MD5 | 20 +++++++++-------- NAMESPACE | 1 R/slcm-wrapper.R | 38 +++++++++++++++++++++++++++------- R/utils.R |only README.md | 1 build/partial.rdb |binary man/attribute_pattern_table_header.Rd |only man/slcm-package.Rd | 3 -- man/slcm.Rd | 17 ++++++++------- src/Makevars | 3 ++ src/Makevars.win | 3 ++ 12 files changed, 74 insertions(+), 39 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.4.1 dated 2025-01-17 and 1.4.2 dated 2025-09-28
DESCRIPTION | 10 MD5 | 14 NEWS.md | 8 R/nls.R | 4 R/nls_methods.R | 669 ++++++++++++++++++------------------ configure | 18 configure.ac | 2 inst/unit_tests/unit_tests_gslnls.R | 195 +++++----- 8 files changed, 489 insertions(+), 431 deletions(-)
Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.
Author: Juergen Niedballa [aut, cre] ,
Alexandre Courtiol [aut] ,
Rahel Sollmann [aut] ,
John Mathai [ctb],
Seth Timothy Wong [ctb] ,
An The Truong Nguyen [ctb] ,
Azlan bin Mohamed [ctb] ,
Andrew Tilker [ctb] ,
Roshan Guharajan [ctb] ,
Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 2.3.1 dated 2025-09-02 and 3.0.0 dated 2025-09-28
DESCRIPTION | 31 MD5 | 75 NAMESPACE | 141 NEWS.md | 156 R/PPC.residuals.R |only R/aggregateStations.R |only R/cameraOperation.R | 30 R/camtrapR-package.R | 4 R/communityModel.R | 326 R/createCovariates.R |only R/detectionHistory.R | 256 R/detectionMaps.R | 2 R/imageRename.R | 151 R/plot.R | 71 R/predict.R | 738 +- R/readWildlifeInsights.R |only R/readcamtrapDP.R |only R/recordTable.R | 15 R/recordTableIndividual.R | 16 R/speciesAccum.R |only R/surveyDashboard.R |11743 ++++++++++++++++++++++++++++++--- R/variousOtherHelperFunctions.R | 80 R/zzz.R |only README.md | 12 inst/dashboard_help |only inst/doc/camtrapr5.html | 3468 ++++++--- man/PPC.community.Rd |only man/PPC.residuals.Rd |only man/aggregateStations.Rd |only man/camtrapR-package.Rd | 3 man/communityModel.Rd | 24 man/createCovariates.Rd |only man/detectionHistory.Rd | 180 man/imageRename.Rd | 28 man/plot_coef-commOccu-method.Rd | 3 man/plot_effects-commOccu-method.Rd | 3 man/predict-commOccu-method.Rd | 10 man/readWildlifeInsights.Rd |only man/readcamtrapDP.Rd |only man/speciesAccum.Rd |only man/surveyDashboard.Rd | 123 tests/testthat/test_cameraOperation.R | 23 tests/testthat/test_detectionHistory.R | 15 43 files changed, 14859 insertions(+), 2868 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-26 1.0.5
2013-12-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-16 0.3.11
2021-12-08 0.3.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 1.1.1
2020-09-30 1.1.0
2020-05-06 1.0.1
2019-10-11 1.0.0
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.29 dated 2024-11-04 and 2.30 dated 2025-09-28
DESCRIPTION | 28 - MD5 | 47 +- NEWS.md | 14 R/html_document.R | 592 ++++++++++++++++++--------------- R/html_document_base.R | 22 - R/jupyter.R | 4 R/pandoc.R | 23 - R/render.R | 3 R/slidy_presentation.R | 2 R/util.R | 4 build/vignette.rds |binary inst/doc/lua-filters.html | 5 inst/doc/rmarkdown.R | 22 - inst/doc/rmarkdown.Rmd | 2 inst/doc/rmarkdown.html | 4 man/html_document.Rd | 86 ++-- man/html_document_base.Rd | 4 man/html_fragment.Rd | 4 man/html_notebook.Rd | 5 man/html_vignette.Rd | 10 man/ioslides_presentation.Rd | 4 man/slidy_presentation.Rd | 4 tests/testthat/resources/template.html |only tests/testthat/test-pandoc.R | 2 vignettes/rmarkdown.Rmd | 2 25 files changed, 476 insertions(+), 417 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.23 dated 2025-08-18 and 1.1.24 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 7 +++++-- R/lang.aff.R | 9 ++++++++- inst/doc/lingtypology_creating_maps.html | 9 +++++---- inst/doc/lingtypology_db_API.html | 9 +++++---- inst/doc/lingtypology_dplyr.html | 11 ++++++----- inst/doc/lingtypology_glottolog_functions.Rmd | 4 ++-- inst/doc/lingtypology_glottolog_functions.html | 11 ++++++----- inst/doc/lingtypology_intro.html | 9 +++++---- tests/testthat/test-lang-aff.R | 4 ++-- vignettes/lingtypology_glottolog_functions.Rmd | 4 ++-- 12 files changed, 62 insertions(+), 47 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.10.1 dated 2025-08-25 and 2.11.0 dated 2025-09-28
DESCRIPTION | 10 MD5 | 104 NAMESPACE | 25 NEWS.md | 12 R/HPart.R |only R/RcppExports.R | 32 R/VisualizeMatching.R | 10 R/hierarchical_mutual_information.R |only R/spectral_clustering.R | 2 R/tree_distance.R | 15 R/zzz.R | 56 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 22 inst/WORDLIST | 31 inst/doc/Generalized-RF.html | 5 inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.html | 13 inst/doc/compare-treesets.html | 5 inst/doc/different-leaves.html | 5 inst/doc/information.html | 5 inst/doc/landscapes.html | 1954 ---------- inst/doc/treespace.html | 7 inst/doc/using-distances.html | 162 man/GeneralizedRF.Rd | 7 man/HH.Rd |only man/HPart.Rd |only man/HierarchicalMutualInfo.Rd |only man/HierarchicalMutualInformation.Rd |only man/JaccardRobinsonFoulds.Rd | 1 man/KendallColijn.Rd | 1 man/MASTSize.Rd | 161 man/MatchingSplitDistance.Rd | 1 man/NNIDist.Rd | 239 - man/NyeSimilarity.Rd | 1 man/PathDist.Rd | 1 man/Robinson-Foulds.Rd | 1 man/SPRDist.Rd | 1 man/TreeDistance.Rd | 1 man/VisualizeMatching.Rd | 3 man/clone.Rd |only src/RcppExports.cpp | 109 src/day_1985.cpp | 3 src/hmi.cpp |only src/hpart.cpp |only src/hpart.h |only src/hpart_relabel.cpp |only src/ints.h | 8 src/li_diameters.h |only src/nni_distance.cpp | 531 +- src/tree_distances.cpp | 58 src/tree_distances.h | 6 tests/testthat/_snaps/HPart |only tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 20 tests/testthat/test-HPart.R |only tests/testthat/test-hierarchical_mutual_information.R |only tests/testthat/test-hmi.cpp.R |only tests/testthat/test-information.R | 8 tests/testthat/test-spectral_clustering.R | 3 tests/testthat/test-tree_distance.R | 53 tests/testthat/test-tree_distance_nni.R | 73 61 files changed, 1081 insertions(+), 2689 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.4-0 dated 2025-07-25 and 3.4-1 dated 2025-09-28
DESCRIPTION | 18 ++--- MD5 | 38 ++++++----- NEWS | 7 ++ build/vignette.rds |binary inst/doc/NAobjects.R |only inst/doc/NAobjects.Rnw |only inst/doc/NAobjects.pdf |only inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 148 ++++++++++++++++++++++----------------------- inst/doc/datasets.Rnw | 32 ++++----- inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 106 ++++++++++++++++++++++++++++---- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 vignettes/NAobjects.Rnw |only vignettes/datasets.Rnw | 32 ++++----- vignettes/updates.Rnw | 106 ++++++++++++++++++++++++++++---- 22 files changed, 335 insertions(+), 156 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions
by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The
method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Author: Wen-Ting Wang [aut, cre] ,
Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.3.5 dated 2023-11-13 and 1.3.8 dated 2025-09-28
DESCRIPTION | 26 +-- MD5 | 59 ++++---- NAMESPACE | 3 NEWS.md | 13 + R/SpatPCA.R | 86 ++++++----- R/helper.R | 21 +- R/zzz.R | 4 README.md | 102 ++++++++++--- build/vignette.rds |binary inst/doc/demo-one-dim-location.R | 78 ++++++---- inst/doc/demo-one-dim-location.Rmd | 80 ++++++---- inst/doc/demo-one-dim-location.html | 82 ++++++----- inst/doc/demo-two-dim-location.R | 78 +++++----- inst/doc/demo-two-dim-location.Rmd | 81 ++++++----- inst/doc/demo-two-dim-location.html | 145 +++++++++---------- man/plot.spatpca.Rd | 2 man/predict.Rd | 2 man/predictEigenfunction.Rd | 2 man/setCores.Rd | 8 - man/spatpca.Rd | 80 +++++----- src/Makevars | 3 src/Makevars.win | 5 src/RcppExports.cpp | 36 ++-- src/RcppSpatPCA.cpp | 263 ++++++++++++++++++------------------ tests/testthat.R | 1 tests/testthat/test-SpatPCA.R | 8 - tests/testthat/test-helper.R | 12 - tests/testthat/test-zzz.R | 54 +------ tools |only vignettes/demo-one-dim-location.Rmd | 80 ++++++---- vignettes/demo-two-dim-location.Rmd | 81 ++++++----- 31 files changed, 804 insertions(+), 691 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 1.0.1 dated 2025-07-04 and 1.0.2 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/doc/litteR-installation.html | 10 +++++----- inst/doc/litteR-manual.html | 36 ++++++++++++++++++------------------ tests/testthat/test-stats.R | 18 +++++++++--------- 6 files changed, 49 insertions(+), 42 deletions(-)
Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.1 dated 2025-08-27 and 0.1.2 dated 2025-09-28
hdMTD-0.1.1/hdMTD/R/raindata.R |only hdMTD-0.1.1/hdMTD/R/sleepscoring.R |only hdMTD-0.1.1/hdMTD/R/testChains.R |only hdMTD-0.1.1/hdMTD/build |only hdMTD-0.1.1/hdMTD/data/raindata.rda |only hdMTD-0.1.1/hdMTD/data/sleepscoring.rda |only hdMTD-0.1.1/hdMTD/data/testChains.rda |only hdMTD-0.1.1/hdMTD/man/checkSample.Rd |only hdMTD-0.1.1/hdMTD/man/raindata.Rd |only hdMTD-0.1.1/hdMTD/man/sleepscoring.Rd |only hdMTD-0.1.1/hdMTD/man/testChains.Rd |only hdMTD-0.1.2/hdMTD/DESCRIPTION | 6 hdMTD-0.1.2/hdMTD/MD5 | 97 ++--- hdMTD-0.1.2/hdMTD/NAMESPACE | 41 ++ hdMTD-0.1.2/hdMTD/NEWS.md | 31 + hdMTD-0.1.2/hdMTD/R/MTDest-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDest.R | 392 ++++++++++++---------- hdMTD-0.1.2/hdMTD/R/MTDmodel-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDmodel.R | 32 + hdMTD-0.1.2/hdMTD/R/accessors.R |only hdMTD-0.1.2/hdMTD/R/as-MTD.R |only hdMTD-0.1.2/hdMTD/R/checkSample.R | 4 hdMTD-0.1.2/hdMTD/R/countsTab.R | 9 hdMTD-0.1.2/hdMTD/R/dTV_sample.R | 53 ++ hdMTD-0.1.2/hdMTD/R/empirical_probs.R |only hdMTD-0.1.2/hdMTD/R/freqTab.R | 26 + hdMTD-0.1.2/hdMTD/R/hdMTD-methods.R |only hdMTD-0.1.2/hdMTD/R/hdMTD.R | 175 ++++++++- hdMTD-0.1.2/hdMTD/R/hdMTD_BIC.R | 68 +++ hdMTD-0.1.2/hdMTD/R/hdMTD_CUT.R | 23 - hdMTD-0.1.2/hdMTD/R/hdMTD_FS.R | 21 - hdMTD-0.1.2/hdMTD/R/hdMTD_FSC.R | 11 hdMTD-0.1.2/hdMTD/R/oscillation.R | 78 ++-- hdMTD-0.1.2/hdMTD/R/probs.R | 290 ++++++++++++---- hdMTD-0.1.2/hdMTD/R/utils.R | 50 +- hdMTD-0.1.2/hdMTD/R/validation.R | 75 ++-- hdMTD-0.1.2/hdMTD/man/MTD-accessors.Rd |only hdMTD-0.1.2/hdMTD/man/MTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest.Rd | 105 +++-- hdMTD-0.1.2/hdMTD/man/MTDmodel.Rd | 11 hdMTD-0.1.2/hdMTD/man/as.MTD.Rd |only hdMTD-0.1.2/hdMTD/man/countsTab.Rd | 9 hdMTD-0.1.2/hdMTD/man/dTV_sample.Rd | 55 ++- hdMTD-0.1.2/hdMTD/man/empirical_probs.Rd |only hdMTD-0.1.2/hdMTD/man/freqTab.Rd | 18 - hdMTD-0.1.2/hdMTD/man/hdMTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/hdMTD.Rd | 50 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_BIC.Rd | 44 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_CUT.Rd | 19 - hdMTD-0.1.2/hdMTD/man/hdMTD_FS.Rd | 17 hdMTD-0.1.2/hdMTD/man/hdMTD_FSC.Rd | 11 hdMTD-0.1.2/hdMTD/man/oscillation.Rd | 64 ++- hdMTD-0.1.2/hdMTD/man/probs.Rd | 95 +++-- hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDest.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDmodel.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD.R | 46 +- hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_BIC.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_CUT.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_FS.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-probs.R | 4 61 files changed, 1397 insertions(+), 679 deletions(-)
Title: Changepoint Detection via Modified Genetic Algorithm
Description: The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package [...truncated...]
Author: Mo Li [aut, cre],
QiQi Lu [aut]
Maintainer: Mo Li <mo.li@louisiana.edu>
Diff between changepointGA versions 0.1.1 dated 2025-05-22 and 0.1.3 dated 2025-09-28
changepointGA-0.1.1/changepointGA/R/GA.R |only changepointGA-0.1.1/changepointGA/R/IslandGA.R |only changepointGA-0.1.1/changepointGA/R/datasimulation.R |only changepointGA-0.1.1/changepointGA/R/defaultsetting.R |only changepointGA-0.1.1/changepointGA/man/GA.Rd |only changepointGA-0.1.1/changepointGA/man/GA_param.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA_param.Rd |only changepointGA-0.1.1/changepointGA/man/TsPlotCheck.Rd |only changepointGA-0.1.1/changepointGA/man/operators.Rd |only changepointGA-0.1.3/changepointGA/DESCRIPTION | 11 changepointGA-0.1.3/changepointGA/MD5 | 84 changepointGA-0.1.3/changepointGA/NAMESPACE | 18 changepointGA-0.1.3/changepointGA/R/AMOCfunc.R | 57 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.Order.R | 82 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.R | 73 changepointGA-0.1.3/changepointGA/R/GAfunc.R | 164 changepointGA-0.1.3/changepointGA/R/RcppExports.R | 56 changepointGA-0.1.3/changepointGA/R/cptDist.R | 60 changepointGA-0.1.3/changepointGA/R/cptga-class.R |only changepointGA-0.1.3/changepointGA/R/cptga.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl-class.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl.R |only changepointGA-0.1.3/changepointGA/R/ts.sim.R |only changepointGA-0.1.3/changepointGA/R/utils.R |only changepointGA-0.1.3/changepointGA/README.md | 209 changepointGA-0.1.3/changepointGA/build/vignette.rds |binary changepointGA-0.1.3/changepointGA/inst/doc/vignette.R | 223 changepointGA-0.1.3/changepointGA/inst/doc/vignette.Rmd | 271 changepointGA-0.1.3/changepointGA/inst/doc/vignette.html | 6808 +++++++++- changepointGA-0.1.3/changepointGA/man/AMOCcrossover.Rd | 4 changepointGA-0.1.3/changepointGA/man/AMOCmutation.Rd | 8 changepointGA-0.1.3/changepointGA/man/AMOCpopulation.Rd | 12 changepointGA-0.1.3/changepointGA/man/AMOCselection.Rd | 2 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Order.Rd | 23 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Rd | 30 changepointGA-0.1.3/changepointGA/man/changepointGA-package.Rd |only changepointGA-0.1.3/changepointGA/man/cptDist.Rd | 14 changepointGA-0.1.3/changepointGA/man/cptga-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptga.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/mutation.Rd | 18 changepointGA-0.1.3/changepointGA/man/plot.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/plot.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/random_population.Rd | 36 changepointGA-0.1.3/changepointGA/man/selectTau.Rd | 4 changepointGA-0.1.3/changepointGA/man/selection_linearrank.Rd | 2 changepointGA-0.1.3/changepointGA/man/ts.sim.Rd | 118 changepointGA-0.1.3/changepointGA/src/ARIMA_BIC.cpp |only changepointGA-0.1.3/changepointGA/src/Makevars |only changepointGA-0.1.3/changepointGA/src/Makevars.win |only changepointGA-0.1.3/changepointGA/src/PopInitia.cpp | 60 changepointGA-0.1.3/changepointGA/src/RcppExports.cpp | 32 changepointGA-0.1.3/changepointGA/vignettes/vignette.Rmd | 271 57 files changed, 7544 insertions(+), 1206 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.9 dated 2025-06-07 and 1.4.10 dated 2025-09-28
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md |only R/grid.hexagontile.R | 2 +- R/hexDensity.R | 4 ++-- R/hexbinFull.R | 3 ++- R/plotHexDensity.R | 25 +++++++++++++++++++------ R/xy2hcell.R | 2 +- man/hexbinFull.Rd | 2 +- src/hbin.f | 4 ++-- src/hbin_frac.f | 6 ++++-- 11 files changed, 45 insertions(+), 28 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.4-0 dated 2025-07-23 and 3.4-2 dated 2025-09-28
DESCRIPTION | 14 - MD5 | 52 ++--- NEWS | 45 ++++ R/intensity.ppm.R | 383 +++++++++++++++++++++++++---------------- R/kppm.R | 9 R/mppm.R | 50 +++-- R/ppm.R | 4 R/predictmppm.R | 105 ++++++----- R/rmh.ppm.R | 9 R/rmhmodel.ppm.R | 60 +++++- R/simulatekppm.R | 10 - R/slrm.R | 5 R/subfits.R | 28 ++ R/sysdata.rda |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/intensity.ppm.Rd | 17 + man/rmh.ppm.Rd | 28 ++ man/rmhmodel.ppm.Rd | 21 ++ man/simulate.kppm.Rd | 20 +- man/simulate.ppm.Rd | 28 ++ man/spatstat.model-internal.Rd | 14 - tests/testsD.R | 9 tests/testsK.R | 16 + tests/testsM.R | 10 - tests/testsP2.R | 14 + tests/testsR2.R | 20 +- 27 files changed, 684 insertions(+), 291 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre],
Richard Harris [aut],
Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.6-1 dated 2024-11-16 and 0.6-2 dated 2025-09-28
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ NEWS.md | 4 +++ R/hgwr.R | 59 ++++++++++++++++++++++------------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/hgwrr.html | 7 +++--- src/hetero_test.cpp | 6 ++++- 8 files changed, 50 insertions(+), 48 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.6 dated 2025-07-23 and 0.10.7 dated 2025-09-27
sasLM-0.10.6/sasLM/inst/doc/Report-Different-Simplest2410021412.pdf |only sasLM-0.10.6/sasLM/inst/doc/Report-NOT-OKs2410021413.pdf |only sasLM-0.10.6/sasLM/inst/doc/Validation-Report-GLM-2410021413.pdf |only sasLM-0.10.7/sasLM/DESCRIPTION | 6 +- sasLM-0.10.7/sasLM/MD5 | 22 +++++---- sasLM-0.10.7/sasLM/R/CumAlpha.R | 23 +++++----- sasLM-0.10.7/sasLM/R/OBFBound.R |only sasLM-0.10.7/sasLM/R/PocockBound.R | 11 ++-- sasLM-0.10.7/sasLM/inst/NEWS.Rd | 9 +++ sasLM-0.10.7/sasLM/inst/doc/Report-Different-Simplest2509281051.pdf |only sasLM-0.10.7/sasLM/inst/doc/Report-NOT-OKs2509281052.pdf |only sasLM-0.10.7/sasLM/inst/doc/Validation-Report-GLM-2509281053.pdf |only sasLM-0.10.7/sasLM/man/CumAlpha.Rd | 18 ++++--- sasLM-0.10.7/sasLM/man/OBFBound.Rd |only sasLM-0.10.7/sasLM/man/PocockBound.Rd | 6 ++ sasLM-0.10.7/sasLM/man/seqBound.Rd | 6 ++ 16 files changed, 62 insertions(+), 39 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described
by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between dina versions 2.0.0 dated 2019-02-01 and 2.0.2 dated 2025-09-27
DESCRIPTION | 24 ++++++++++++------------ MD5 | 23 ++++++++++++----------- NEWS.md | 24 ++++++++++++++++++++++++ R/dina-est.R | 4 ++-- README.md | 28 ++++++++++------------------ build |only inst/CITATION | 15 ++++++++------- man/dina-package.Rd | 10 ++++------ man/dina.Rd | 4 ++-- src/Makevars | 3 --- src/Makevars.win | 3 --- src/RcppExports.cpp | 5 +++++ src/dina-estimation-routine.cpp | 6 +++--- 13 files changed, 82 insertions(+), 67 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, and push the image to
DockerHub.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.1 dated 2024-12-17 and 0.1.3 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 15 +++++++++++++++ R/create.R | 8 ++++++-- R/dockerfile.R | 10 +++++----- README.md | 4 ++-- man/create.Rd | 6 +++++- tests/testthat/test-build.R | 29 +++++++++++++++++++++++------ tests/testthat/test-create.R | 7 ++++--- 9 files changed, 72 insertions(+), 31 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming
to complement existing R packages. The functionality includes among others
multidimensional compensatory and noncompensatory IRT models
(Reckase, 2009, <doi:10.1007/978-0-387-89976-3>),
MCMC for hierarchical IRT models and testlet models
(Fox, 2010, <doi:10.1007/978-1-4419-0742-4>),
NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>),
Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>;
Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>),
faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011,
<doi:10.1111/j.1745-3984.2011.00143.x>),
ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>),
DETECT statistic (Stout, Habing, Douglas & Kim, 1996,
<doi:10.1177/014662169602000403>), local structural equation modeling
(LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016,
<doi:10.1080/00273171.20 [...truncated...]
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 4.1-15 dated 2024-02-05 and 4.2-133 dated 2025-09-27
DESCRIPTION | 16 MD5 | 539 +++++++++--------- NAMESPACE | 3 R/IRT.anova.sirt.R |only R/IRT.expectedCounts.mirt.R | 8 R/IRT.mle.R | 4 R/RcppExports.R | 26 R/amh_plot.R | 9 R/anova_sirt.R | 42 - R/attach.environment.sirt.R | 18 R/automatic.recode.R | 4 R/brm.irf.R | 4 R/brm.sim.R | 7 R/btm.R | 16 R/categorize.R | 6 R/ccov.np.R | 15 R/ccov_np_compute_ccov_sum_score.R | 4 R/cfa_meas_inv.R | 4 R/class.accuracy.rasch.R | 8 R/conf.detect.R | 4 R/create.ccov.R | 4 R/data.prep.R | 16 R/data.recode.sirt.R | 4 R/data.wide2long.R | 18 R/decategorize.R | 6 R/detect.index.R | 14 R/dexppow.R | 3 R/dif.logisticregression.R | 67 +- R/dif.strata.variance.R | 9 R/dirichlet.simul.R | 4 R/dmlavaan_est_model.R | 5 R/dmlavaan_est_model_bread_matrix_score_derivatives.R | 9 R/dmlavaan_est_model_parameterTable.R | 7 R/dmlavaan_joint_parameterTable.R | 4 R/dmlavaan_se_bootstrap.R | 11 R/dmlavaan_se_sandwich.R | 6 R/eigenvalues.manymatrices.R | 14 R/equating.rasch.jackknife.R | 10 R/expl.detect.R | 22 R/f1d.irt.R | 4 R/fit.adisop.R | 16 R/fit.gradedresponse.R | 23 R/fit.gradedresponse_alg.R | 6 R/gom_em_calc_theta.R | 6 R/gom_em_est_b.R | 10 R/gom_em_est_covariance.R | 4 R/gom_em_est_lambda.R | 14 R/invariance.alignment.R | 150 ++++- R/invariance_alignment_cfa_config.R | 10 R/invariance_alignment_cfa_config_estimate.R | 10 R/invariance_alignment_proc_labels.R | 6 R/invariance_alignment_simulate.R | 18 R/likelihood_adjustment.R | 50 - R/likelihood_adjustment_aux.R | 6 R/linking.haberman.R | 6 R/linking.haberman.lq.R | 87 ++ R/linking.haebara.R | 10 R/linking.robust.R | 4 R/linking_2groups.R |only R/linking_2groups_haebara_fun.R |only R/linking_2groups_haebara_grad.R |only R/linking_2groups_numerical_gradient.R |only R/linking_2groups_power_loss.R |only R/linking_2groups_stocking_lord_fun.R |only R/linking_2groups_stocking_lord_grad.R |only R/linking_2groups_vector_with_names.R |only R/linking_haberman_als.R | 8 R/linking_haberman_als_residual_weights.R | 10 R/linking_haberman_als_vcov.R | 9 R/linking_haberman_compute_lts_mean.R | 8 R/linking_haberman_itempars_prepare.R | 6 R/linking_haberman_lq_pw_create_design.R |only R/linking_haberman_lq_pw_le.R |only R/linking_haberman_lq_pw_le_arrange_Vgamma.R |only R/linking_haberman_lq_pw_le_grad.R |only R/linking_haberman_lq_pw_le_hess_delta.R |only R/linking_haberman_lq_pw_le_hess_gamma.R |only R/linking_haebara_gradient_function_R.R | 6 R/linking_haebara_optim_function_R.R | 9 R/locpolycor.R |only R/locpolycor_est_polycor_itempair.R |only R/locpolycor_est_polycor_opt_fun.R |only R/locpolycor_est_thresh_grad_fun.R |only R/locpolycor_est_thresh_item.R |only R/locpolycor_est_thresh_opt_fun.R |only R/lq_fit.R | 49 + R/lsdm.R | 6 R/lsdm_est_logist_quant.R | 12 R/lsem.MGM.stepfunctions.R | 4 R/lsem.bootstrap.R | 9 R/lsem.estimate.R | 57 + R/lsem.permutationTest.R | 11 R/lsem.test.R | 32 - R/lsem_aggregate_statistics.R |only R/lsem_bootstrap_draw_bootstrap_sample.R | 22 R/lsem_estimate_proc_args.R | 12 R/lsem_fit_initial_model.R | 7 R/lsem_fit_initial_model_sufficient_statistics.R | 36 - R/lsem_fitsem.R | 42 - R/lsem_fitsem_compute_sufficient_statistics.R | 61 +- R/lsem_fitsem_joint_estimation_prepare_partable.R | 14 R/lsem_fitsem_raw_data_define_pseudo_weights.R | 4 R/lsem_group_moderator.R | 32 - R/lsem_local_weights.R | 94 ++- R/lsem_parameter_summary.R | 4 R/lsem_residualize.R | 134 +++- R/m_est.R | 12 R/mcmc.2pno.R | 4 R/mcmc.2pno_alg.R | 5 R/mcmc.2pnoh.R | 64 +- R/mcmc_3pno_testlet_draw_itempars.R | 27 R/mcmc_Rhat.R | 9 R/mcmc_WaldTest.R | 8 R/mcmc_as_formula.R | 6 R/mcmc_confint.R | 11 R/mcmc_derivedPars.R | 6 R/mcmc_plot.R | 9 R/mcmc_rename_define_symbols.R | 6 R/mcmc_rename_helper.R | 8 R/mcmc_rename_parameter_names.R | 6 R/mcmc_rename_undo_parameter_names.R | 4 R/mcmc_summary.R | 21 R/mcmc_summary_print_information_criteria.R | 18 R/mcmclist2coda.R | 4 R/mgsem.R | 4 R/mgsem_bdiag.R | 6 R/mgsem_cd_opt.R | 4 R/mgsem_create_index.R | 6 R/mgsem_duplication_matrix.R | 6 R/mgsem_evaluate_penalties.R | 6 R/mgsem_grad_fun.R | 6 R/mgsem_list_elements_est_total_implied.R | 4 R/mgsem_loglike_suffstat_derivative.R | 16 R/mgsem_opt_fun.R | 4 R/mgsem_output_proc_casewise_likelihood.R | 4 R/mgsem_output_proc_residuals.R | 4 R/mgsem_partable2model.R | 4 R/mgsem_proc_data.R | 4 R/mgsem_proc_model.R | 12 R/mgsem_proc_model_is_B.R | 4 R/mgsem_proc_model_partable_define_index.R | 6 R/mgsem_proc_model_update_penalties_matrix.R | 4 R/mgsem_proc_suffstat.R | 4 R/mgsem_suffstat_covariance_matrix.R | 13 R/mgsem_vcov_me.R | 8 R/mirt.specify.partable.R | 7 R/nedelsky.irf.R | 6 R/nedelsky.sim.R | 6 R/noharm.sirt.R | 4 R/noharm_sirt_efa_rotated_solution.R | 4 R/noharm_sirt_optim_function.R | 19 R/noharm_sirt_optim_function_R.R | 9 R/noharm_sirt_optim_gradient.R | 32 - R/noharm_sirt_optim_gradient_R.R | 11 R/noharm_sirt_optim_gradient_R_der_gamma_item.R | 21 R/noharm_sirt_optim_gradient_R_der_gamma_item_pair.R | 21 R/noharm_sirt_partable_extract_par.R | 4 R/noharm_sirt_partable_include_par.R | 6 R/noharm_sirt_preproc.R | 65 +- R/noharm_sirt_preproc_parameter_table_matrix.R | 9 R/noharm_sirt_preproc_pattern_matrix.R | 4 R/normal2.cw.R | 2 R/package_version_date.R | 6 R/parmsummary_extend.R | 17 R/pbivnorm2.R | 34 - R/rasch.copula3.R | 10 R/rasch.pairwise.itemcluster.R | 11 R/rasch_jml_update_b.R | 7 R/rasch_mirtlc_est_a.R | 11 R/rasch_pairwise_iterations.R | 4 R/rasch_pairwise_optimize.R | 7 R/rasch_pairwise_optimize_opt_fun_terms2.R | 10 R/resp_groupwise.R | 4 R/rexppow.R | 10 R/rm.facets.R | 37 - R/rm_determine_fixed_tau_parameters.R | 4 R/rm_facets_center_value_aggregate.R | 4 R/rm_facets_pp_mle.R | 5 R/rm_facets_pp_mle_calc_ll.R | 5 R/rm_numdiff_index.R | 14 R/rm_pcm_calcprobs.R | 8 R/rm_posterior.R | 4 R/rm_proc_create_pseudoraters.R | 8 R/rm_proc_data.R | 22 R/rm_smooth_distribution.R | 4 R/rm_trim_increments_mstep.R | 5 R/rmvn.R | 4 R/sia.sirt.R | 24 R/sia_sirt_remove_transitive.R | 6 R/sim.rasch.dep.R | 8 R/sim.raschtype.R | 6 R/sirt_EAP.R | 4 R/sirt_MAP.R | 4 R/sirt_add_list_elements.R | 4 R/sirt_logit_to_probs.R | 4 R/sirt_matrix_lower_to_upper.R | 4 R/sirt_max.R |only R/sirt_optimizer.R | 4 R/sirt_pem_collect_parameters.R | 4 R/sirt_pem_create_parameter_index.R | 4 R/sirt_rbind_fill.R | 6 R/sirt_rename_list_entry.R | 6 R/smirt_postproc.R | 33 - R/sqrt_diag.R | 13 R/sqrt_diag_positive.R |only R/summary.gom.em.R | 5 R/summary.lsem.R | 5 R/summary.lsem.permutationTest.R | 4 R/summary_round_helper.R | 4 R/tam2mirt_fix.R | 58 - R/tam2mirt_freed.R | 78 +- R/testlet.marginalized.R | 6 R/tetrachoric2.R | 44 - R/truescore.irt.R | 10 R/truescore_irt_irf.R | 6 R/unidim.csn.R | 8 R/wle.rasch.jackknife.R | 8 R/write.format2.R | 15 R/write.fwf2.R | 10 R/xxirt.R | 76 +- R/xxirt_EAP.R | 8 R/xxirt_classprobs_lca.R | 4 R/xxirt_classprobs_lca_init_par.R | 8 R/xxirt_compute_casewise_likelihood.R | 14 R/xxirt_compute_itemprobs.R | 28 R/xxirt_compute_likelihood.R | 20 R/xxirt_compute_posterior.R | 18 R/xxirt_compute_priorDistribution.R | 7 R/xxirt_compute_prior_Theta_from_x.R | 3 R/xxirt_compute_prob_item_from_x.R | 7 R/xxirt_createDiscItem.R | 11 R/xxirt_createItemList.R | 13 R/xxirt_createParTable.R | 19 R/xxirt_createThetaDistribution.R | 11 R/xxirt_data_proc.R | 10 R/xxirt_em_algorithm.R | 38 - R/xxirt_em_args_extract.R |only R/xxirt_hessian.R | 8 R/xxirt_ic.R | 13 R/xxirt_ic_compute_criteria.R | 16 R/xxirt_irf_lca_init_par.R | 6 R/xxirt_mstep_ThetaParameters.R | 32 - R/xxirt_mstep_itemParameters.R | 63 +- R/xxirt_mstep_itemParameters_evalPrior.R | 4 R/xxirt_newton_raphson.R | 68 +- R/xxirt_nr_grad_fun_R.R | 6 R/xxirt_nr_grad_fun_Rcpp.R | 52 + R/xxirt_nr_grad_fun_numapprox.R | 14 R/xxirt_nr_grad_fun_pml_casewise.R |only R/xxirt_nr_opt_fun_pml_casewise.R |only R/xxirt_nr_optim_fun.R | 27 R/xxirt_nr_pml_grad_fun.R |only R/xxirt_nr_pml_more_arguments.R |only R/xxirt_nr_pml_opt_fun.R |only R/xxirt_nr_pml_opt_fun_R.R |only R/xxirt_nr_pml_preproc_data.R |only R/xxirt_partable_extract_freeParameters.R | 2 R/xxirt_postproc_parameters.R | 16 R/xxirt_prepare_response_data.R | 6 R/xxirt_proc_ParTable.R | 10 R/xxirt_sandwich_pml.R |only R/xxirt_simulate.R | 10 R/xxirt_summary_parts.R | 24 build/partial.rdb |binary data/data.pisa2006Read.rda |only data/datalist | 1 inst/CITATION | 3 inst/NEWS | 40 + man/R2conquest.Rd | 4 man/data.pisa2006Read.Rd |only man/data.pisaMath.Rd | 4 man/invariance.alignment.Rd | 33 + man/linking.haberman.Rd | 48 + man/linking_2groups.Rd |only man/locpolycor.Rd |only man/lq_fit.Rd | 5 man/lsem.estimate.Rd | 15 man/lsem.test.Rd | 8 man/matrixfunctions.sirt.Rd | 5 man/xxirt.Rd | 275 +++++++++ man/xxirt_createParTable.Rd | 5 man/xxirt_createThetaDistribution.Rd | 5 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 123 +++- src/sirt_rcpp_invariance_alignment.cpp | 18 src/sirt_rcpp_polychoric2.cpp | 8 src/sirt_rcpp_rm_sdt.cpp | 27 src/sirt_rcpp_xxirt.cpp | 369 ++++++++++++ 289 files changed, 3292 insertions(+), 1725 deletions(-)
Title: Utility Functions for Forest Inventory and Silviculture
Description: Perform common dendrometry operations such as inventory preparing, and inventory data analysis.
Author: Adrian Cidre Gonzalez [aut, cre],
Aitor Vazquez Veloso [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between silviculture versions 0.1.0 dated 2025-05-29 and 0.2.0 dated 2025-09-27
silviculture-0.1.0/silviculture/R/biomass.R |only silviculture-0.1.0/silviculture/R/dendrometry-summary.R |only silviculture-0.1.0/silviculture/R/dendrometry.R |only silviculture-0.1.0/silviculture/R/globals.R |only silviculture-0.1.0/silviculture/R/inventory.R |only silviculture-0.1.0/silviculture/R/lidar.R |only silviculture-0.1.0/silviculture/R/volume.R |only silviculture-0.1.0/silviculture/man/Inventory.Rd |only silviculture-0.1.0/silviculture/man/SampleSize.Rd |only silviculture-0.1.0/silviculture/man/calc_dominant_height.Rd |only silviculture-0.2.0/silviculture/DESCRIPTION | 27 + silviculture-0.2.0/silviculture/MD5 | 156 +++++++--- silviculture-0.2.0/silviculture/NAMESPACE | 63 ++-- silviculture-0.2.0/silviculture/NEWS.md | 66 ++++ silviculture-0.2.0/silviculture/R/deprecated-funs.R |only silviculture-0.2.0/silviculture/R/inventory-summary.R |only silviculture-0.2.0/silviculture/R/metrics-lidar.R |only silviculture-0.2.0/silviculture/R/metrics-stand-density.R |only silviculture-0.2.0/silviculture/R/metrics-stand-level.R |only silviculture-0.2.0/silviculture/R/metrics-tree-level.R |only silviculture-0.2.0/silviculture/R/predict-biomass.R |only silviculture-0.2.0/silviculture/R/predict-height.R |only silviculture-0.2.0/silviculture/R/sample-size.R |only silviculture-0.2.0/silviculture/R/silviculture-package.R |only silviculture-0.2.0/silviculture/R/sysdata.rda |binary silviculture-0.2.0/silviculture/R/treatment-thinning.R |only silviculture-0.2.0/silviculture/R/utils-not-exported.R | 133 ++++++++ silviculture-0.2.0/silviculture/R/zzz.R | 25 + silviculture-0.2.0/silviculture/README.md | 5 silviculture-0.2.0/silviculture/build/partial.rdb |binary silviculture-0.2.0/silviculture/data/biomass_models.rda |binary silviculture-0.2.0/silviculture/data/inventory_samples.rda |binary silviculture-0.2.0/silviculture/inst |only silviculture-0.2.0/silviculture/man/calc_accumulated_trees.Rd |only silviculture-0.2.0/silviculture/man/calc_dominant_metric.Rd |only silviculture-0.2.0/silviculture/man/calc_n_cost.Rd |only silviculture-0.2.0/silviculture/man/calc_n_optimal.Rd |only silviculture-0.2.0/silviculture/man/calc_n_prop.Rd |only silviculture-0.2.0/silviculture/man/calc_n_simple.Rd | 48 +-- silviculture-0.2.0/silviculture/man/eq_biomass_cudjoe_2024.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_dieguez_aranda_2009.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_manrique_2017.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_menendez_2022.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_montero_2005.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2011.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2012.Rd |only silviculture-0.2.0/silviculture/man/eq_hd_vazquez_veloso_2025.Rd |only silviculture-0.2.0/silviculture/man/figures/lifecycle-deprecated.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-experimental.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-stable.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-superseded.svg |only silviculture-0.2.0/silviculture/man/figures/logo.png |binary silviculture-0.2.0/silviculture/man/lid_fcov.Rd | 66 ++-- silviculture-0.2.0/silviculture/man/lid_lhdi.Rd | 58 +-- silviculture-0.2.0/silviculture/man/plot.Rd | 38 +- silviculture-0.2.0/silviculture/man/silv_basal_area.Rd | 108 +++--- silviculture-0.2.0/silviculture/man/silv_biomass.Rd | 142 ++++----- silviculture-0.2.0/silviculture/man/silv_density_hart.Rd |only silviculture-0.2.0/silviculture/man/silv_density_ntrees_ha.Rd |only silviculture-0.2.0/silviculture/man/silv_density_sdi.Rd |only silviculture-0.2.0/silviculture/man/silv_diametric_class.Rd | 90 ++--- silviculture-0.2.0/silviculture/man/silv_dominant_height.Rd | 118 +++---- silviculture-0.2.0/silviculture/man/silv_lorey_height.Rd | 87 ++--- silviculture-0.2.0/silviculture/man/silv_ntrees_ha.Rd | 85 ++--- silviculture-0.2.0/silviculture/man/silv_predict_biomass.Rd |only silviculture-0.2.0/silviculture/man/silv_predict_height.Rd |only silviculture-0.2.0/silviculture/man/silv_sample_size.Rd | 103 +++--- silviculture-0.2.0/silviculture/man/silv_sample_size_simple.Rd |only silviculture-0.2.0/silviculture/man/silv_sample_size_stratified.Rd |only silviculture-0.2.0/silviculture/man/silv_spacing_index.Rd | 98 +++--- silviculture-0.2.0/silviculture/man/silv_sqrmean_diameter.Rd | 84 ++--- silviculture-0.2.0/silviculture/man/silv_stand_basal_area.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_dominant_diameter.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_dominant_height.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_lorey_height.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_qmean_diameter.Rd |only silviculture-0.2.0/silviculture/man/silv_summary.Rd | 148 ++++----- silviculture-0.2.0/silviculture/man/silv_treatment_thinning.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_basal_area.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_dclass.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_volume.Rd |only silviculture-0.2.0/silviculture/man/silv_volume.Rd | 104 +++--- silviculture-0.2.0/silviculture/man/silviculture-package.Rd |only 83 files changed, 1097 insertions(+), 755 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.8 dated 2025-07-17 and 0.6.9 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/vignette.html | 9 +++++---- src/cwb/cqp/parser.tab.c | 8 ++++---- 6 files changed, 22 insertions(+), 17 deletions(-)
Title: Spectral Data for Light-Emitting-Diodes
Description: Spectral emission data for some frequently used light emitting
diodes available as electronic components. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Shafiuddin Ahmed [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyLEDs versions 0.5.2 dated 2023-11-01 and 0.5.3 dated 2025-09-27
DESCRIPTION | 21 MD5 | 46 - NEWS.md | 10 R/led_brands.r | 5 R/leds-mspct.r | 46 + R/oo-maya-leds.r | 2 README.md | 294 +++-------- build/partial.rdb |binary build/vignette.rds |binary data/COB-dimming-mspct.rda |binary data/COB-reflectors-mspct.rda |binary data/leds-mspct.rda |binary inst/doc/userguide-0-r4p-introduction.Rmd | 158 +++--- inst/doc/userguide-0-r4p-introduction.html | 157 +++--- inst/doc/userguide-1-data-use.R | 12 inst/doc/userguide-1-data-use.Rmd | 50 + inst/doc/userguide-1-data-use.html | 748 ++++++++++++++--------------- man/figures/README-unnamed-chunk-1-1.png |binary man/led_brands.Rd | 12 man/led_colors.Rd | 20 man/leds.mspct.Rd | 47 + man/oo_maya_leds.Rd | 2 vignettes/userguide-0-r4p-introduction.Rmd | 158 +++--- vignettes/userguide-1-data-use.Rmd | 50 + 24 files changed, 936 insertions(+), 902 deletions(-)
More information about photobiologyLEDs at CRAN
Permanent link
Title: Correction of Preprocessed MS Data
Description: An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Author: Allison Mason [aut] ,
Gregory Johnson [aut] ,
Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>
This is a re-admission after prior archival of version 0.3.0 dated 2025-09-07
Diff between mpactr versions 0.3.0 dated 2025-09-07 and 0.3.1 dated 2025-09-27
DESCRIPTION | 9 - MD5 | 106 ++++++++++---------- NAMESPACE | 5 NEWS.md | 10 + R/filter_pactr-accessors.R | 12 ++ R/filters.R | 15 ++ R/import_data.R | 5 R/mpactR-package.R | 4 R/mpactr-accessors.R | 9 + R/peak_table_formatter.R | 20 ++- R/quality_control.R | 3 R/utils.R |only inst/doc/downstream_analyses.R | 3 inst/doc/downstream_analyses.Rmd | 4 inst/doc/downstream_analyses.html | 16 +-- inst/doc/mpactr.R | 10 + inst/doc/mpactr.Rmd | 14 +- inst/doc/mpactr.html | 63 +++--------- inst/doc/reference_semantics.R | 3 inst/doc/reference_semantics.Rmd | 5 man/filter_cv.Rd | 6 - man/filter_group.Rd | 3 man/filter_insource_ions.Rd | 3 man/filter_mispicked_ions.Rd | 3 man/filter_summary.Rd | 3 man/get_cv_data.Rd | 3 man/get_group_averages.Rd | 3 man/get_meta_data.Rd | 3 man/get_peak_table.Rd | 3 man/get_raw_data.Rd | 3 man/get_similar_ions.Rd | 3 man/import_data.Rd | 3 man/limit_cores.Rd |only man/qc_summary.Rd | 3 src/CvFilter.cpp | 18 +-- tests/testthat.R | 1 tests/testthat/exttestdata/cut_ions.csv | 138 +++++++++++++-------------- tests/testthat/test-data.R | 1 tests/testthat/test-filter_pactr-accessors.R | 14 +- tests/testthat/test-filter_pactr-class.R | 113 ++++++++-------------- tests/testthat/test-filter_pactr-methods.R | 101 ++++++++----------- tests/testthat/test-filters.R | 13 +- tests/testthat/test-import_data.R | 21 +--- tests/testthat/test-mpactr-accessors.R | 4 tests/testthat/test-mpactr-class.R | 9 - tests/testthat/test-mpactr-methods.R | 4 tests/testthat/test-pactr-class_cloning.R | 1 tests/testthat/test-peak_table_formatter.R | 9 + tests/testthat/test-qc_graph_pactr-class.R | 10 - tests/testthat/test-quality_control.R | 2 tests/testthat/test-statistics.R | 1 tests/testthat/test-summary-class.R | 1 vignettes/downstream_analyses.Rmd | 4 vignettes/mpactr.Rmd | 14 +- vignettes/reference_semantics.Rmd | 5 55 files changed, 467 insertions(+), 375 deletions(-)
Title: Exploratory Reduced Reparameterized Unified Model Estimation
Description: Perform a Bayesian estimation of the exploratory reduced
reparameterized unified model (ErRUM) described by Culpepper and Chen (2018)
<doi:10.3102/1076998618791306>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph] ,
Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between errum versions 0.0.3 dated 2020-03-20 and 0.0.4 dated 2025-09-27
DESCRIPTION | 25 ++++++++++++------------- MD5 | 17 +++++++++-------- NEWS.md | 12 ++++++++++++ README.md | 10 +++++----- build |only inst/CITATION | 16 ++++++++-------- man/errum-package.Rd | 6 ++---- src/Makevars | 4 +++- src/Makevars.win | 4 +++- src/RcppExports.cpp | 5 +++++ 10 files changed, 59 insertions(+), 40 deletions(-)
Title: DiSTATIS Three Way Metric Multidimensional Scaling
Description: Implement DiSTATIS and CovSTATIS (three-way multidimensional scaling). DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.
Author: Derek Beaton [aut, ctb],
Ju-Chi Yu [aut, ctb],
Vincent Guillemot [aut, ctb],
Herve Abdi [aut, cre]
Maintainer: Herve Abdi <herve@utdallas.edu>
Diff between DistatisR versions 1.1.1 dated 2022-12-05 and 1.1.2 dated 2025-09-27
DistatisR-1.1.1/DistatisR/README.md |only DistatisR-1.1.2/DistatisR/DESCRIPTION | 21 ++- DistatisR-1.1.2/DistatisR/MD5 | 57 ++++------ DistatisR-1.1.2/DistatisR/R/BeersProjectiveMapping.R | 2 DistatisR-1.1.2/DistatisR/R/DistatisR-package.R | 7 - DistatisR-1.1.2/DistatisR/R/GraphDistatisRv.R | 2 DistatisR-1.1.2/DistatisR/R/WinesRankingRawData.R | 2 DistatisR-1.1.2/DistatisR/R/amariSorting.R | 4 DistatisR-1.1.2/DistatisR/R/computePartial4Groups.R | 9 - DistatisR-1.1.2/DistatisR/R/createCubeOfCovDis.R | 4 DistatisR-1.1.2/DistatisR/R/distatis.R | 26 ++++ DistatisR-1.1.2/DistatisR/R/list2CubeOfCov.R | 2 DistatisR-1.1.2/DistatisR/R/multiculturalSortingSpices.R | 2 DistatisR-1.1.2/DistatisR/R/projectVoc.R | 2 DistatisR-1.1.2/DistatisR/R/sortingWines.R | 6 - DistatisR-1.1.2/DistatisR/man/DistatisR-package.Rd | 4 DistatisR-1.1.2/DistatisR/man/GraphDistatisRv.Rd | 2 DistatisR-1.1.2/DistatisR/man/WinesRankingRawData.Rd | 2 DistatisR-1.1.2/DistatisR/man/amariSorting.Rd | 2 DistatisR-1.1.2/DistatisR/man/computePartial4Groups.Rd | 8 - DistatisR-1.1.2/DistatisR/man/createCubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/distatis.Rd | 6 + DistatisR-1.1.2/DistatisR/man/list2CubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.F4voc.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.cubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataAmari.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataSortingSpices.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataSortingWines.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.str_BeersProjectiveMapping.Rd | 2 DistatisR-1.1.2/DistatisR/man/sortingWines.Rd | 4 30 files changed, 110 insertions(+), 80 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.3.0 dated 2025-09-11 and 0.3.1 dated 2025-09-27
DESCRIPTION | 13 - MD5 | 60 +++--- NAMESPACE | 46 ++-- NEWS.md | 9 R/CopernicusMarine-package.r | 4 R/cms_cite_product.r | 48 ++-- R/cms_download_subset.r | 189 +++++++++++-------- R/cms_login.r | 250 ++++++++++++------------- R/cms_products_list.r | 216 ++++++++++----------- R/generics.r | 127 ++++++------ R/import.r | 2 README.md | 396 ++++++++++++++++++++-------------------- man/CopernicusMarine-package.Rd | 52 ++--- man/account.Rd | 88 ++++---- man/cms_cite_product.Rd | 66 +++--- man/cms_download_native.Rd | 166 ++++++++-------- man/cms_download_subset.Rd | 190 ++++++++++--------- man/cms_get_client_info.Rd | 56 ++--- man/cms_login.Rd | 68 +++--- man/cms_product_details.Rd | 70 +++---- man/cms_product_metadata.Rd | 60 +++--- man/cms_product_services.Rd | 74 +++---- man/cms_products_list.Rd | 90 ++++----- man/cms_wmts.Rd | 158 +++++++-------- tests/testthat.R | 10 - tests/testthat/helper.r | 38 +-- tests/testthat/test_dev.r | 52 ++--- tests/testthat/test_login.r | 74 +++---- tests/testthat/test_product.r | 146 +++++++------- tests/testthat/test_subset.r | 3 tests/testthat/test_wmts.r | 112 +++++------ 31 files changed, 1502 insertions(+), 1431 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Bayesian Mode Inference
Description: A two-step Bayesian approach for mode inference following
Cross, Hoogerheide, Labonne and van Dijk (2024) <doi:10.1016/j.econlet.2024.111579>).
First, a mixture distribution is fitted on the data using a sparse finite
mixture (SFM) Markov chain Monte Carlo (MCMC) algorithm. The number of
mixture components does not have to be known; the size of the mixture is
estimated endogenously through the SFM approach. Second, the modes of the
estimated mixture at each MCMC draw are retrieved using algorithms
specifically tailored for mode detection. These estimates are then used to
construct posterior probabilities for the number of modes, their locations
and uncertainties, providing a powerful tool for mode inference.
Author: Nalan Bastuerk [aut],
Jamie Cross [aut],
Peter de Knijff [aut],
Lennart Hoogerheide [aut],
Paul Labonne [aut, cre],
Herman van Dijk [aut]
Maintainer: Paul Labonne <labonnepaul@gmail.com>
Diff between BayesMultiMode versions 0.7.3 dated 2024-10-31 and 0.7.4 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/plot_methods.R | 42 +++++++++++++++++++++++++----------------- build/partial.rdb |binary 5 files changed, 36 insertions(+), 25 deletions(-)
More information about BayesMultiMode at CRAN
Permanent link
Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This
package intends to handle many file formats that were native to the
antiquated Commodore Amiga machine. This package focuses on file types from
the older Amiga operating systems (<= 3.0). It will read and write specific
file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between AmigaFFH versions 0.4.7 dated 2025-01-08 and 0.4.8 dated 2025-09-27
DESCRIPTION | 10 ++-- MD5 | 94 ++++++++++++++++++++--------------------- NAMESPACE | 1 NEWS.md | 5 ++ R/iff.0.r | 1 man/AmigaBasic.Rd | 6 +- man/AmigaBasic.reserved.Rd | 8 +-- man/AmigaBasicBMAP-io.Rd | 12 ++--- man/AmigaBasicBMAP.Rd | 8 +-- man/AmigaBitmapFont.Rd | 4 - man/ExtractBasic.Rd | 8 +-- man/as.AmigaBasic.Rd | 10 ++-- man/as.AmigaBasicBMAP.Rd | 6 +- man/as.character.Rd | 8 +-- man/as.raw.Rd | 4 - man/availableFontSizes.Rd | 4 - man/c.Rd | 4 - man/check.names.AmigaBasic.Rd | 8 +-- man/colourToAmigaRaw.Rd | 4 - man/fontName.Rd | 4 - man/font_example.Rd | 4 - man/getAmigaBitmapFont.Rd | 4 - man/names.AmigaBasic.Rd | 8 +-- man/packBitmap.Rd | 4 - man/rasterToAmigaBitmapFont.Rd | 4 - man/rawToAmigaBasic.Rd | 8 +-- man/rawToAmigaBasicBMAP.Rd | 10 ++-- man/rawToAmigaBasicShape.Rd | 4 - man/rawToAmigaBitmapFont.Rd | 4 - man/rawToAmigaBitmapFontSet.Rd | 4 - man/rawToAmigaIcon.Rd | 4 - man/rawToHWSprite.Rd | 4 - man/rawToIFFChunk.Rd | 4 - man/rawToSysConfig.Rd | 4 - man/read.AmigaBasic.Rd | 10 ++-- man/read.AmigaBasicShape.Rd | 6 +- man/read.AmigaBitmapFont.Rd | 6 +- man/read.AmigaBitmapFontSet.Rd | 6 +- man/read.AmigaIcon.Rd | 6 +- man/read.SysConfig.Rd | 6 +- man/read.iff.Rd | 6 +- man/simpleAmigaIcon.Rd | 4 - man/write.AmigaBasic.Rd | 14 +++--- man/write.AmigaBasicShape.Rd | 4 - man/write.AmigaBitmapFont.Rd | 12 ++--- man/write.AmigaIcon.Rd | 6 +- man/write.SysConfig.Rd | 6 +- man/write.iff.Rd | 6 +- 48 files changed, 192 insertions(+), 185 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.2.4 dated 2025-06-13 and 5.3.0 dated 2025-09-27
secr-5.2.4/secr/R/movemat.R |only secr-5.2.4/secr/R/pxi.R |only secr-5.3.0/secr/DESCRIPTION | 8 secr-5.3.0/secr/MD5 | 226 +- secr-5.3.0/secr/NAMESPACE | 18 secr-5.3.0/secr/NEWS | 41 secr-5.3.0/secr/R/AIC.R | 12 secr-5.3.0/secr/R/CV.R | 6 secr-5.3.0/secr/R/D.designdata.R | 14 secr-5.3.0/secr/R/DENSITY.R | 8 secr-5.3.0/secr/R/Dsurface.R | 350 ++-- secr-5.3.0/secr/R/Enk.R | 17 secr-5.3.0/secr/R/MCgof.R | 60 secr-5.3.0/secr/R/RMarkInput.R | 2 secr-5.3.0/secr/R/RcppExports.R | 4 secr-5.3.0/secr/R/Rsurface.R | 2 secr-5.3.0/secr/R/addSightings.R | 2 secr-5.3.0/secr/R/addTelemetry.R | 6 secr-5.3.0/secr/R/autoini.R | 17 secr-5.3.0/secr/R/circular.R | 16 secr-5.3.0/secr/R/clone.R | 10 secr-5.3.0/secr/R/collate.R | 28 secr-5.3.0/secr/R/confint.secr.R | 111 - secr-5.3.0/secr/R/derivedDcoef.R |only secr-5.3.0/secr/R/derivedDsurface.R | 250 +- secr-5.3.0/secr/R/derivedMS.R | 13 secr-5.3.0/secr/R/detectpar.R | 62 secr-5.3.0/secr/R/deviance.R | 2 secr-5.3.0/secr/R/discretize.R | 4 secr-5.3.0/secr/R/empirical.R | 2 secr-5.3.0/secr/R/esa.R | 75 secr-5.3.0/secr/R/esaPlot.R | 8 secr-5.3.0/secr/R/exportedutility.R | 270 +++ secr-5.3.0/secr/R/fastsecrloglik.R | 85 secr-5.3.0/secr/R/fxi.R | 54 secr-5.3.0/secr/R/generalsecrloglik.R | 175 +- secr-5.3.0/secr/R/homerange.R | 115 + secr-5.3.0/secr/R/join2.R | 30 secr-5.3.0/secr/R/loglikhelperfn.R | 67 secr-5.3.0/secr/R/make.capthist.R | 34 secr-5.3.0/secr/R/make.grid.R | 10 secr-5.3.0/secr/R/make.mask.R | 2 secr-5.3.0/secr/R/makeNewData.R | 18 secr-5.3.0/secr/R/makeStart.R | 53 secr-5.3.0/secr/R/mask.check.R | 13 secr-5.3.0/secr/R/methods.R | 57 secr-5.3.0/secr/R/modelAverage.R | 10 secr-5.3.0/secr/R/par.secr.fit.R | 1 secr-5.3.0/secr/R/pdot.R | 24 secr-5.3.0/secr/R/plot.capthist.r | 33 secr-5.3.0/secr/R/plot.secr.R | 16 secr-5.3.0/secr/R/plot.traps.R | 4 secr-5.3.0/secr/R/pmixProfileLL.R | 6 secr-5.3.0/secr/R/predict.secr.R | 17 secr-5.3.0/secr/R/preparedata.R | 86 - secr-5.3.0/secr/R/reduce.R | 10 secr-5.3.0/secr/R/regionN.R | 166 - secr-5.3.0/secr/R/reparameterize.R | 9 secr-5.3.0/secr/R/score.test.R | 155 + secr-5.3.0/secr/R/secr.design.MS.R | 133 - secr-5.3.0/secr/R/secr.fit.R | 288 ++- secr-5.3.0/secr/R/secr.refit.R | 14 secr-5.3.0/secr/R/sim.capthist.R | 36 secr-5.3.0/secr/R/sim.detect.R | 112 - secr-5.3.0/secr/R/sim.popn.R | 30 secr-5.3.0/secr/R/sim.secr.R | 10 secr-5.3.0/secr/R/simOU.capthist.R |only secr-5.3.0/secr/R/simulate.R | 4 secr-5.3.0/secr/R/snip.R | 2 secr-5.3.0/secr/R/split.capthist.R | 4 secr-5.3.0/secr/R/split.traps.R | 4 secr-5.3.0/secr/R/suggest.buffer.R | 36 secr-5.3.0/secr/R/summary.capthist.R | 8 secr-5.3.0/secr/R/summary.secr.R | 6 secr-5.3.0/secr/R/summary.traps.R | 14 secr-5.3.0/secr/R/telemetry.R | 14 secr-5.3.0/secr/R/trap.builder.R | 120 - secr-5.3.0/secr/R/trend.R | 29 secr-5.3.0/secr/R/utility.R | 1873 ++++++++++------------ secr-5.3.0/secr/R/verify.R | 34 secr-5.3.0/secr/R/write.captures.R | 8 secr-5.3.0/secr/R/write.mask.R | 4 secr-5.3.0/secr/R/write.traps.R | 5 secr-5.3.0/secr/R/xy2CH.R | 2 secr-5.3.0/secr/build/partial.rdb |binary secr-5.3.0/secr/build/vignette.rds |binary secr-5.3.0/secr/inst/doc/secr-datainput.R | 16 secr-5.3.0/secr/inst/doc/secr-datainput.pdf |binary secr-5.3.0/secr/inst/doc/secr-overview.R | 5 secr-5.3.0/secr/inst/doc/secr-overview.Rmd | 753 ++------ secr-5.3.0/secr/inst/doc/secr-overview.pdf |binary secr-5.3.0/secr/man/OVpossum.Rd | 6 secr-5.3.0/secr/man/derivedDsurface.Rd | 31 secr-5.3.0/secr/man/details.Rd | 2 secr-5.3.0/secr/man/detectfn.Rd | 13 secr-5.3.0/secr/man/homerange.Rd | 32 secr-5.3.0/secr/man/make.spcosa.Rd | 4 secr-5.3.0/secr/man/predict.secr.Rd | 4 secr-5.3.0/secr/man/predictDsurface.Rd | 5 secr-5.3.0/secr/man/secr-internal.Rd | 6 secr-5.3.0/secr/man/secr-package.Rd | 34 secr-5.3.0/secr/man/secr.fit.Rd | 10 secr-5.3.0/secr/man/secr.refit.Rd | 10 secr-5.3.0/secr/man/sim.capthist.Rd | 3 secr-5.3.0/secr/man/sim.secr.Rd | 7 secr-5.3.0/secr/man/simOU.capthist.Rd |only secr-5.3.0/secr/man/suggest.buffer.Rd | 10 secr-5.3.0/secr/man/userdist.Rd | 2 secr-5.3.0/secr/src/RcppExports.cpp | 13 secr-5.3.0/secr/src/autils.cpp | 11 secr-5.3.0/secr/tests/testthat.R | 2 secr-5.3.0/secr/tests/testthat/test-derived.R | 4 secr-5.3.0/secr/tests/testthat/test-groups.R |only secr-5.3.0/secr/tests/testthat/test-initial.R | 40 secr-5.3.0/secr/tests/testthat/test-relativeD.R | 2 secr-5.3.0/secr/tests/testthat/test-trapbuilder.R | 6 secr-5.3.0/secr/vignettes/secr-overview.Rmd | 753 ++------ 117 files changed, 3819 insertions(+), 3649 deletions(-)
Title: Target Controlled Infusion (TCI)
Description: Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.
Author: Ryan Jarrett [aut, cre]
Maintainer: Ryan Jarrett <ryantjarrett@gmail.com>
Diff between tci versions 0.2.0 dated 2022-08-15 and 0.2.1 dated 2025-09-27
DESCRIPTION | 15 ++-- MD5 | 29 ++++---- R/poppk_mods.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/custom.R | 2 inst/doc/custom.html | 148 +++++++++++++++++++++++---------------------- inst/doc/overview.R | 14 ++-- inst/doc/overview.html | 154 ++++++++++++++++++++++++----------------------- inst/doc/poppk.R | 12 +-- inst/doc/poppk.html | 150 +++++++++++++++++++++++---------------------- man/eleveld_pd.Rd | 4 - man/eleveld_pk.Rd | 4 - src/Makevars | 18 +++-- src/Makevars.win | 17 ++--- src/pk_cpp_functions.cpp | 2 16 files changed, 297 insertions(+), 274 deletions(-)
Title: Distances and Routes on Geographical Grids
Description: Provides classes and functions to calculate various
distance measures and routes in heterogeneous geographic
spaces represented as grids. The package implements measures
to model dispersal histories first presented by van Etten and
Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost
distances as well as more complex distances based on (constrained)
random walks can be calculated. The distances implemented in
the package are used in geographical genetics, accessibility
indicators, and may also have applications in other fields of
geospatial analysis.
Author: Jacob van Etten [aut] ,
Kaue de Sousa [ctb] ,
Andrew Marx [cre, ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>
Diff between gdistance versions 1.6.4 dated 2023-06-19 and 1.6.5 dated 2025-09-27
DESCRIPTION | 14 - MD5 | 20 +- NEWS.md | 5 R/AAATransition-class.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.R | 10 - inst/doc/Overview.html | 420 ++++++++++++++++++++++++++++------------------ man/Transition-classes.Rd | 2 man/gdistance.Rd | 2 vignettes/gdistance1.bib | 5 11 files changed, 289 insertions(+), 191 deletions(-)
Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov random field model for a network of binary and/or ordinal variables.
Author: Maarten Marsman [aut, cre] ,
Giuseppe Arena [ctb] ,
Karoline Huth [ctb] ,
Nikola Sekulovski [ctb] ,
Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.4.2 dated 2024-12-05 and 0.1.6.0 dated 2025-09-27
bgms-0.1.4.2/bgms/R/print.bgms.R |only bgms-0.1.4.2/bgms/R/utility_functions.R |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.R |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.Rmd |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.html |only bgms-0.1.4.2/bgms/inst/doc/introduction.R |only bgms-0.1.4.2/bgms/inst/doc/introduction.Rmd |only bgms-0.1.4.2/bgms/inst/doc/introduction.html |only bgms-0.1.4.2/bgms/src/gibbs_functions.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions.h |only bgms-0.1.4.2/bgms/src/gibbs_functions_compare.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions_edge_prior.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions_edge_prior.h |only bgms-0.1.4.2/bgms/vignettes/bgmcompare.Rmd |only bgms-0.1.4.2/bgms/vignettes/introduction.Rmd |only bgms-0.1.6.0/bgms/DESCRIPTION | 43 bgms-0.1.6.0/bgms/MD5 | 145 +- bgms-0.1.6.0/bgms/NAMESPACE | 26 bgms-0.1.6.0/bgms/NEWS.md | 82 + bgms-0.1.6.0/bgms/R/RcppExports.R | 28 bgms-0.1.6.0/bgms/R/bgm.R | 1019 +++++++++-------- bgms-0.1.6.0/bgms/R/bgmCompare.R | 1132 ++++++++----------- bgms-0.1.6.0/bgms/R/bgmcompare-methods.r |only bgms-0.1.6.0/bgms/R/bgms-methods.R |only bgms-0.1.6.0/bgms/R/bgms-package.R | 85 - 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Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to
calculate distance matrices for continuous, binary, and multi-dimensional
input matrices, which supports a broad variety of 41 predefined distance
functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user-
defined functions written in C++. For ease of use, the 'parDist' function
extends the signature of the 'dist' function and uses the same parameter
naming conventions as distance methods of existing R packages. The package
is mainly implemented in C++ and leverages the 'RcppParallel' package to
parallelize the distance computations with the help of the 'TinyThread'
library. Furthermore, the 'Armadillo' linear algebra library is used for
optimized matrix operations during distance calculations. The curiously
recurring template pattern (CRTP) technique is applied to avoid virtual
functions, which improves the Dynamic Time Warping calculations while
the implementation stays flexible enough to support differe [...truncated...]
Author: Alexander Eckert [aut, cre],
Lucas Godoy [ctb],
Srikanth KS [ctb]
Maintainer: Alexander Eckert <info@alexandereckert.com>
Diff between parallelDist versions 0.2.6 dated 2022-02-03 and 0.2.7 dated 2025-09-27
DESCRIPTION | 7 +++---- MD5 | 28 ++++++++++++++-------------- R/parDist.R | 2 +- README.md | 38 +++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ inst/doc/parallelDist.R | 2 +- inst/doc/parallelDist.Rnw | 12 ++++++------ inst/doc/parallelDist.pdf |binary man/parDist.Rd | 4 ++-- src/DistanceDTWGeneric.h | 2 +- src/Makevars | 2 -- src/Makevars.win | 2 -- vignettes/parallelDist.Rnw | 12 ++++++------ vignettes/parallelDist.bib | 6 +++--- 15 files changed, 75 insertions(+), 47 deletions(-)
Title: Data for Sunlight Spectra
Description: Data for the extraterrestrial solar spectral irradiance and ground
level solar spectral irradiance and irradiance. In addition data for
shade light under vegetation and irradiance time series from different
broadband sensors. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, trl, cre] ,
T. Matthew Robson [ctb] ,
Saara M. Hartiakinen [ctb] ,
Anders Lindfors [ctb],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySun versions 0.5.0 dated 2024-04-01 and 0.5.1 dated 2025-09-27
DESCRIPTION | 31 +- MD5 | 55 ++-- NEWS.md | 16 + R/example.solar.irrad.data.r | 159 +++++++++++--- R/example.solar.spectra.data.r | 85 +++++++ README.md | 10 build/partial.rdb |binary build/vignette.rds |binary data/broad-band.rda |binary data/gap-mspct.rda |binary data/sun-elevation-spct.rda |only data/sun-hourly-ozone-spct.rda |only data/sun-hourly-spct.rda |binary data/sun-may-morning-spct.rda |binary data/sun-reference-mspct.rda |binary inst/doc/r4p-introduction.Rmd | 162 +++++++------- inst/doc/r4p-introduction.html | 164 +++++++------- inst/doc/user-guide.R | 16 - inst/doc/user-guide.Rmd | 21 + inst/doc/user-guide.html | 342 ++++++++++++++++--------------- man/figures/README-unnamed-chunk-1-1.png |binary man/four_days_1min.data.Rd |only man/gap.mspct.Rd | 7 man/irrad_Kipp.data.Rd | 33 ++ man/photobiologySun-package.Rd | 2 man/ppfd_BF.data.Rd | 40 ++- man/ppfd_LICOR.data.Rd | 37 ++- man/sun_elevation.spct.Rd |only man/sun_hourly_ozone.spct.Rd |only vignettes/r4p-introduction.Rmd | 162 +++++++------- vignettes/user-guide.Rmd | 21 + 31 files changed, 834 insertions(+), 529 deletions(-)
More information about photobiologySun at CRAN
Permanent link
Title: Cone Constrained Convex Problems
Description: Routines for solving convex optimization problems with cone constraints by means of interior-point methods. The implemented algorithms are partially ported from CVXOPT, a Python module for convex optimization (see <https://cvxopt.org> for more information).
Author: Bernhard Pfaff [aut, cre],
Lieven Vandenberghe [cph] ,
Martin Andersen [cph] ,
Joachim Dahl [cph]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between cccp versions 0.3-2 dated 2025-07-30 and 0.3-3 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/DCP.cpp | 2 +- src/DNL.cpp | 2 +- src/GPP.cpp | 2 +- src/RPP.cpp | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Interface with the United Nations Comtrade API
Description: Interface with and extract data from the United Nations 'Comtrade'
API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping
data for a variety of commodities, these functions allow for easy API query
and data returned as a tidy data frame.
Author: Paul Bochtler [aut, cre, cph] ,
Harriet Goers [aut],
Chris Muir [aut],
Alicia Schep [rev] ,
Rafael Hellwig [rev] ,
Ernest Guevarra [rev] ,
Nicholas Potter [rev] ,
Juergen Amann [ctb]
Maintainer: Paul Bochtler <paulbochtler.gh@gmail.com>
Diff between comtradr versions 1.0.3 dated 2024-11-15 and 1.0.4 dated 2025-09-27
DESCRIPTION | 23 +++++---- MD5 | 90 +++++++++++++++++++------------------- NEWS.md | 7 ++ R/data.R | 2 R/utils.R | 11 +++- R/zzz.R | 2 build/vignette.rds |binary data/country_codes.rda |binary data/ct_pretty_cols.rda |binary inst/WORDLIST | 6 ++ inst/doc/bulk_files.html | 5 +- inst/doc/caching.html | 5 +- inst/doc/comtradr.R | 4 - inst/doc/comtradr.Rmd | 4 - inst/doc/comtradr.html | 13 ++--- inst/doc/large_data.html | 5 +- inst/doc/transition.html | 7 +- inst/extdata/cmd_b4.rds |binary inst/extdata/cmd_b5.rds |binary inst/extdata/cmd_eb.rds |binary inst/extdata/cmd_eb02.rds |binary inst/extdata/cmd_eb10.rds |binary inst/extdata/cmd_eb10s.rds |binary inst/extdata/cmd_h0.rds |binary inst/extdata/cmd_h1.rds |binary inst/extdata/cmd_h2.rds |binary inst/extdata/cmd_h3.rds |binary inst/extdata/cmd_h4.rds |binary inst/extdata/cmd_h5.rds |binary inst/extdata/cmd_h6.rds |binary inst/extdata/cmd_hs.rds |binary inst/extdata/cmd_s1.rds |binary inst/extdata/cmd_s2.rds |binary inst/extdata/cmd_s3.rds |binary inst/extdata/cmd_s4.rds |binary inst/extdata/cmd_ss.rds |binary inst/extdata/customs.rds |binary inst/extdata/flow.rds |binary inst/extdata/list_of_datasets.rda |binary inst/extdata/mot.rds |binary inst/extdata/partner.rds |binary inst/extdata/reporter.rds |binary man/country_codes.Rd | 2 tests/testthat/test-.onload.R | 3 + tests/testthat/test-utils.R | 11 ++-- vignettes/comtradr.Rmd | 4 - 46 files changed, 116 insertions(+), 88 deletions(-)
Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers both
distribution-free modeling using Taylor polynomials and parametric modeling
using the beta-binomial and the 'Sinh-Arcsinh' distribution. Originally developed
for achievement tests, it is applicable to a wide range of mental, physical, or
other test scores dependent on continuous or discrete explanatory variables. The
package provides several advantages: It minimizes deviations from representativeness
in subsamples, interpolates between discrete levels of explanatory variables,
and significantly reduces the required sample size compared to conventional
norming per age group. cNORM enables graphical and analytical evaluation of
model fit, accommodates a wide range of scales including those with negative
and descending values, and even supports conventional norming. It generates
norm tables including confidence intervals. It also includes methods f [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.4.1 dated 2025-05-11 and 3.5.0 dated 2025-09-27
DESCRIPTION | 14 +-- MD5 | 62 +++++++++----- NAMESPACE | 20 ++-- NEWS.md | 11 +- R/plot.R | 161 +++++++++++++++++++++++++++++++------- R/predict.R | 4 R/shash.R |only README.md | 25 +++++ build/vignette.rds |binary inst/doc/BetaBinomial.Rmd | 2 inst/doc/BetaBinomial.html | 17 ++-- inst/doc/ShaSh.R |only inst/doc/ShaSh.Rmd |only inst/doc/ShaSh.html |only inst/doc/WeightedRegression.html | 9 +- inst/doc/cNORM-Demo.html | 11 +- man/cnorm.shash.Rd |only man/compare.Rd | 16 ++- man/derivationTable.Rd | 1 man/diagnostics.shash.Rd |only man/dshash.Rd |only man/getNormCurve.Rd | 1 man/log_likelihood_shash.Rd |only man/normTable.Rd | 1 man/normTable.shash.Rd |only man/plot.cnormShaSh.Rd |only man/plotDensity.Rd | 3 man/predict.cnormBetaBinomial.Rd | 1 man/predict.cnormBetaBinomial2.Rd | 1 man/predict.cnormShaSh.Rd |only man/predictCoefficients_shash.Rd |only man/predictNorm.Rd | 1 man/predictRaw.Rd | 1 man/print.cnormShaSh.Rd |only man/pshash.Rd |only man/qshash.Rd |only man/rawTable.Rd | 1 man/rshash.Rd |only man/summary.cnormShaSh.Rd |only vignettes/BetaBinomial.Rmd | 2 vignettes/ShaSh.Rmd |only 41 files changed, 269 insertions(+), 96 deletions(-)
Title: Ordinal Relations
Description: Functions to handle ordinal relations reflected within the feature space. Those function allow to search for ordinal relations in multi-class datasets. One can check whether proposed relations are reflected in a specific feature representation. Furthermore, it provides functions to filter, organize and further analyze those ordinal relations.
Author: L Lausser [aut],
LM Schaefer [aut],
R Szekely [aut],
HA Kestler [aut, cre]
Maintainer: HA Kestler <hans.kestler@uni-ulm.de>
Diff between ORION versions 1.0.3 dated 2022-02-07 and 1.0.4 dated 2025-09-27
DESCRIPTION | 27 - MD5 | 50 - NAMESPACE | 103 ++- R/as.edgedataframe.R | 1 R/conf.R | 4 R/confusionTable.R | 4 R/dropSets.R | 3 R/dropSize.R | 1 R/dropThreshold.R | 2 R/esl_org-data.R | 2 R/groupwise.R | 4 R/keepSets.R | 1 R/keepSize.R | 3 R/keepThreshold.R | 3 R/package.R |only R/plot.R | 7 R/predictionMap.R | 12 R/print.R | 5 R/subcascades.R | 6 R/summary.R | 5 R/tunePareto.occ.R | 11 build/vignette.rds |binary inst/doc/ORION.R | 2 inst/doc/ORION.html | 1322 +++++++++++++++++++++++++++++++++----------------- man/ORION-package.Rd |only man/predictionMap.Rd | 4 man/tunePareto.occ.Rd | 6 27 files changed, 1044 insertions(+), 544 deletions(-)
Title: Detect Population Structure Within Phylogenetic Trees
Description: Algorithms for detecting population structure from the history of
coalescent events recorded in phylogenetic trees. This method classifies each
tip and internal node of a tree into disjoint sets characterized by similar
coalescent patterns.
Author: Erik Volz [aut, cre] ,
Fabricia F. Nascimento [ctb] ,
Vinicius B. Franceschi [ctb]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treestructure versions 0.1.0 dated 2020-02-17 and 0.7.0 dated 2025-09-27
treestructure-0.1.0/treestructure/R/treestructure.R |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.R |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.Rmd |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.html |only treestructure-0.1.0/treestructure/vignettes/structuredCoalescent.Rmd |only treestructure-0.7.0/treestructure/DESCRIPTION | 48 treestructure-0.7.0/treestructure/MD5 | 49 treestructure-0.7.0/treestructure/NAMESPACE | 4 treestructure-0.7.0/treestructure/R/addtips.R |only treestructure-0.7.0/treestructure/R/m13.R | 1067 ++++++---- treestructure-0.7.0/treestructure/R/treestructure-package.R |only treestructure-0.7.0/treestructure/build/vignette.rds |binary treestructure-0.7.0/treestructure/inst/Ebola_down_sampled_tree.rds |only treestructure-0.7.0/treestructure/inst/Makona_1610_genomes_2016-06-23.ml.tree |only treestructure-0.7.0/treestructure/inst/doc/supportValues.R |only treestructure-0.7.0/treestructure/inst/doc/supportValues.Rmd |only treestructure-0.7.0/treestructure/inst/doc/supportValues.html |only treestructure-0.7.0/treestructure/inst/doc/treestructure.R |only treestructure-0.7.0/treestructure/inst/doc/treestructure.Rmd |only treestructure-0.7.0/treestructure/inst/doc/treestructure.html |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.R |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.Rmd |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.html |only treestructure-0.7.0/treestructure/inst/downsampled_tree_struc.rds |only treestructure-0.7.0/treestructure/inst/struc_plot_example.rds |only treestructure-0.7.0/treestructure/inst/treestructure.Rmd | 2 treestructure-0.7.0/treestructure/inst/trestruct_chindex.rds |only treestructure-0.7.0/treestructure/inst/trestruct_res.rds |only treestructure-0.7.0/treestructure/inst/trestruct_res_nobt.rds |only treestructure-0.7.0/treestructure/inst/tscl | 4 treestructure-0.7.0/treestructure/man/addtips.Rd |only treestructure-0.7.0/treestructure/man/plot.TreeStructure.Rd | 14 treestructure-0.7.0/treestructure/man/treestructure-package.Rd | 31 treestructure-0.7.0/treestructure/man/treestructure.test.Rd |only treestructure-0.7.0/treestructure/man/trestruct.Rd | 83 treestructure-0.7.0/treestructure/src/RcppExports.cpp | 5 treestructure-0.7.0/treestructure/vignettes/bib |only treestructure-0.7.0/treestructure/vignettes/supportValues.Rmd |only treestructure-0.7.0/treestructure/vignettes/treestructure.Rmd |only treestructure-0.7.0/treestructure/vignettes/updating_treestructure.Rmd |only 40 files changed, 883 insertions(+), 424 deletions(-)
Title: A Simple Author Handler for Scientific Writing
Description: Handles and formats author information in scientific writing
in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and
flexible tools for inserting author data in 'YAML' as well as
generating author and contribution lists (among others) as strings
from tabular data.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between plume versions 0.2.5 dated 2024-09-02 and 0.3.0 dated 2025-09-27
DESCRIPTION | 13 MD5 | 178 +-- NAMESPACE | 30 NEWS.md | 64 + R/aaa.R | 85 - R/als.R | 19 R/as-lines.R |only R/checkers.R | 335 +++--- R/context-binder.R | 3 R/context-selectors.R | 26 R/credit-roles.R | 31 R/data-encyclopedists.R | 17 R/enumerate.R | 11 R/icon.R | 48 R/name-handler.R | 5 R/plm-symbols.R |only R/plm-template.R | 21 R/plume-handler.R | 195 +-- R/plume-package.R | 24 R/plume-quarto.R | 96 + R/plume.R | 205 ++- R/sequential.R | 10 R/set-default-names.R | 22 R/status-setter.R | 62 - R/utils-doc.R |only R/utils-list.R | 5 R/utils-plm.R | 8 R/utils-tbl.R | 41 R/utils.R | 112 +- R/yaml.R | 26 README.md | 34 inst/doc/comprehensive-affiliation-schema.R | 4 inst/doc/plume-workflow.R | 27 inst/doc/plume-workflow.Rmd | 18 inst/doc/plume-workflow.html | 88 - inst/doc/plume.R | 137 -- inst/doc/plume.Rmd | 163 +-- inst/doc/plume.html | 1289 ++++++++----------------- inst/doc/working-in-other-languages.R | 51 inst/doc/working-in-other-languages.Rmd | 55 - inst/doc/working-in-other-languages.html | 78 - man/Plume.Rd | 102 + man/PlumeHandler.Rd | 45 man/PlumeQuarto.Rd | 50 man/StatusSetter.Rd | 10 man/StatusSetterPlume.Rd | 11 man/StatusSetterPlumeQuarto.Rd | 24 man/as_lines.Rd |only man/credit_roles.Rd | 4 man/encyclopedists.Rd | 6 man/enumerate.Rd | 6 man/everyone.Rd | 17 man/icn_orcid.Rd |only man/orcid.Rd | 11 man/plm_symbols.Rd |only man/plm_template.Rd | 5 man/plume-package.Rd | 2 man/sequential.Rd | 5 man/set_default_names.Rd | 13 tests/testthat/_snaps/as-lines.md |only tests/testthat/_snaps/credit-roles.md | 2 tests/testthat/_snaps/defunct.md |only tests/testthat/_snaps/deprecated.md |only tests/testthat/_snaps/get-author-list.md | 21 tests/testthat/_snaps/get-contact-details.md | 22 tests/testthat/_snaps/get-contributions.md | 48 tests/testthat/_snaps/get-footnotes.md | 28 tests/testthat/_snaps/get-orcids.md | 24 tests/testthat/_snaps/icon.md | 24 tests/testthat/_snaps/initialize.md | 92 - tests/testthat/_snaps/plm-symbols.md |only tests/testthat/_snaps/plm-template.md | 21 tests/testthat/_snaps/sequential.md | 2 tests/testthat/_snaps/set-default-names.md | 69 - tests/testthat/_snaps/set-main-contributors.md | 8 tests/testthat/_snaps/set-status.md | 56 - tests/testthat/_snaps/to-yaml.md | 14 tests/testthat/helper-plume.R | 4 tests/testthat/test-as-lines.R |only tests/testthat/test-defunct.R |only tests/testthat/test-deprecated.R |only tests/testthat/test-get-author-list.R | 31 tests/testthat/test-get-contact-details.R | 4 tests/testthat/test-get-contributions.R | 37 tests/testthat/test-get-footnotes.R | 20 tests/testthat/test-get-orcids.R | 7 tests/testthat/test-icon.R | 18 tests/testthat/test-initialize.R | 124 +- tests/testthat/test-plm-symbols.R |only tests/testthat/test-plm-template.R | 15 tests/testthat/test-sequential.R | 4 tests/testthat/test-set-main-contributors.R | 12 tests/testthat/test-set-status.R | 53 - tests/testthat/test-to-yaml.R | 14 vignettes/plume-workflow.Rmd | 18 vignettes/plume.Rmd | 163 +-- vignettes/working-in-other-languages.Rmd | 55 - 97 files changed, 2283 insertions(+), 2674 deletions(-)
Title: Analysis of Elliptical Tubes Under the Relative Curvature
Condition
Description: Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." Journal of Computational and Graphical Statistics <doi:10.1080/10618600.2025.2535600> and arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition (RCC), computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube. The intrinsic approach relies on the interior path of the original non-convex space, incorporating the RCC, while the no [...truncated...]
Author: Mohsen Taheri Shalmani [aut, cre] ,
Joern Schulz [aut],
Stephen M. Pizer [aut]
Maintainer: Mohsen Taheri Shalmani <MohsenTaheriShalmani@gmail.com>
Diff between ETRep versions 1.2.0 dated 2025-06-05 and 1.2.1 dated 2025-09-27
DESCRIPTION | 12 - MD5 | 29 ++-- NEWS | 15 +- R/ETRep_Display.R |only R/ETRep_Functions.R | 122 ++++++++++++++------ R/OnLoadFile.R |only build/partial.rdb |binary man/create_Elliptical_Tube.Rd | 9 - man/dot-etrep_open3d.Rd |only man/dot-etrep_show3d.Rd |only man/dot-onLoad.Rd |only man/intrinsic_Transformation_Elliptical_Tubes.Rd | 2 man/intrinsic_mean_tube.Rd | 4 man/nonIntrinsic_Transformation_Elliptical_Tubes.Rd | 2 man/nonIntrinsic_mean_tube.Rd | 4 man/plot_Elliptical_Tube.Rd | 5 man/simulate_etube.Rd | 17 +- man/tube_Surface_Mesh.Rd | 11 + 18 files changed, 160 insertions(+), 72 deletions(-)
Title: Multiple Testing for Hypotheses with Hierarchical or Group
Structure
Description: Performs multiple testing corrections that take specific structure
of hypotheses into account, as described in Sankaran & Holmes (2014)
<doi:10.18637/jss.v059.i13>.
Author: Kris Sankaran [aut, cre]
Maintainer: Kris Sankaran <ksankaran@wisc.edu>
This is a re-admission after prior archival of version 1.1.1 dated 2015-05-05
Diff between structSSI versions 1.1.1 dated 2015-05-05 and 1.2.0 dated 2025-09-27
structSSI-1.1.1/structSSI/R/Adaptive.GBH.R |only structSSI-1.1.1/structSSI/R/BuildEdgelist.R |only structSSI-1.1.1/structSSI/R/EstimatedHFDRControl.R |only structSSI-1.1.1/structSSI/R/FindRoot.R |only structSSI-1.1.1/structSSI/R/HypTreeJSON.R |only structSSI-1.1.1/structSSI/R/ListTreePval.R |only structSSI-1.1.1/structSSI/R/Oracle.GBH.R |only structSSI-1.1.1/structSSI/R/PlotHypTree.R |only structSSI-1.1.1/structSSI/R/SignificanceStars.R |only structSSI-1.1.1/structSSI/R/estimate.pi0.R |only structSSI-1.1.1/structSSI/R/gbh_definition.R |only structSSI-1.1.1/structSSI/R/hFDR.adjust.R |only structSSI-1.1.1/structSSI/R/hFDR.internal.R |only structSSI-1.1.1/structSSI/R/pi0.lsl.R |only structSSI-1.1.1/structSSI/R/pi0.tail.p.R |only structSSI-1.1.1/structSSI/R/pi0.tst.R |only structSSI-1.1.1/structSSI/R/stepUp.R |only structSSI-1.1.1/structSSI/R/treePValues.R |only structSSI-1.1.1/structSSI/R/tree_definition.R |only structSSI-1.1.1/structSSI/R/validHypothesesTree.R |only structSSI-1.1.1/structSSI/data/gtemp.txt |only structSSI-1.1.1/structSSI/man/GBH-class.Rd |only structSSI-1.1.1/structSSI/man/hypothesesTree.Rd |only structSSI-1.1.1/structSSI/man/structSSI-internal.Rd |only structSSI-1.1.1/structSSI/tests/testGBHProcedures.R |only structSSI-1.1.1/structSSI/tests/testHierarchicalMethods.R |only structSSI-1.2.0/structSSI/DESCRIPTION | 31 +- structSSI-1.2.0/structSSI/MD5 | 65 +--- structSSI-1.2.0/structSSI/NAMESPACE | 57 +-- structSSI-1.2.0/structSSI/R/chlamydiae.R |only structSSI-1.2.0/structSSI/R/gbh.R |only structSSI-1.2.0/structSSI/R/gbh_class.R |only structSSI-1.2.0/structSSI/R/hfdr.R |only structSSI-1.2.0/structSSI/R/hfdr_class.R |only structSSI-1.2.0/structSSI/R/hfdr_plot.R |only structSSI-1.2.0/structSSI/data/chlamydiae.rda |binary structSSI-1.2.0/structSSI/data/gtemp.txt.gz |only structSSI-1.2.0/structSSI/inst/CITATION | 17 - structSSI-1.2.0/structSSI/man/Adaptive.GBH.Rd | 176 +++++------- structSSI-1.2.0/structSSI/man/EstimatedHFDRControl.Rd | 76 +---- structSSI-1.2.0/structSSI/man/Oracle.GBH.Rd | 175 +++++------- structSSI-1.2.0/structSSI/man/PlotHypTree.Rd |only structSSI-1.2.0/structSSI/man/chlamydiae.Rd | 67 ++-- structSSI-1.2.0/structSSI/man/estimate.pi0.Rd | 201 +++++-------- structSSI-1.2.0/structSSI/man/gbh-class.Rd |only structSSI-1.2.0/structSSI/man/gtemp.Rd | 10 structSSI-1.2.0/structSSI/man/hFDR.adjust.Rd | 204 ++++++-------- structSSI-1.2.0/structSSI/man/hypothesisTree-class.Rd |only structSSI-1.2.0/structSSI/man/structSSI-package.Rd | 4 structSSI-1.2.0/structSSI/man/treePValues.Rd | 74 +---- structSSI-1.2.0/structSSI/tests/testthat |only structSSI-1.2.0/structSSI/tests/testthat.R |only 52 files changed, 506 insertions(+), 651 deletions(-)
More information about spuriouscorrelations at CRAN
Permanent link
Title: Configuration of Jupiter's Four Largest Satellites
Description: Calculate, plot and animate the configuration of Jupiter's four
largest satellites (known as Galilean satellites) for a given date and time
(UTC - Coordinated Universal Time).
The galsat() function returns numerical values of the satellites’ positions.
x – the apparent rectangular coordinate of the satellite with respect to the
center of Jupiter’s disk in the equatorial plane in the units of Jupiter’s
equatorial radius; X is positive toward the west,
y – the apparent rectangular coordinate of the satellite with respect to the
center of Jupiter’s disk from the equatorial plane in the units of Jupiter’s
equatorial radius; Y is positive toward the north.
For more details see Meeus (1988, ISBN 0-943396-22-0) "Astronomical Formulae
for Calculators".
The galsat_animate() function creates an animation of the Galilean
satellites' positions. You provide the starting time, duration, the time
step between frames, and the pause between frames.
The function delta_t() returns the value of delta-T in [...truncated...]
Author: Lech Jaszowski [aut, cre, cph]
Maintainer: Lech Jaszowski <lech.jaszowski@interia.pl>
Diff between galisats versions 2.0.2 dated 2025-09-11 and 2.2.0 dated 2025-09-27
DESCRIPTION | 13 +- MD5 | 27 ++++- NAMESPACE | 1 NEWS.md | 12 ++ R/galilean_satellites.R | 177 ++++++++++++++++++++++++++++++++++++-- README.md | 71 ++++++++++++--- man/figures/README-example-1.png |binary man/figures/README-example-10.png |only man/figures/README-example-11.png |only man/figures/README-example-12.png |only man/figures/README-example-13.png |only man/figures/README-example-2.png |only man/figures/README-example-3.png |only man/figures/README-example-4.png |only man/figures/README-example-5.png |only man/figures/README-example-6.png |only man/figures/README-example-7.png |only man/figures/README-example-8.png |only man/figures/README-example-9.png |only man/galsat.Rd | 20 +++- man/galsat_animate.Rd |only 21 files changed, 282 insertions(+), 39 deletions(-)
Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto-grading check-fields and check-boxes for 'rmarkdown'
or 'quarto' HTML. It can be used in class, when teacher share materials
and tasks, so students can solve some problems and check their work. In
contrast to the 'learnr' package, the 'checkdown' package works serverlessly
without 'shiny'.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between checkdown versions 0.0.12 dated 2023-10-27 and 0.0.13 dated 2025-09-27
DESCRIPTION | 13 - MD5 | 16 - NEWS | 7 R/check_question.R | 18 +- build/vignette.rds |binary inst/doc/start_checkdown.R | 32 +-- inst/doc/start_checkdown.Rmd | 11 - inst/doc/start_checkdown.html | 348 ++++++++++++++++++++++++------------------ vignettes/start_checkdown.Rmd | 11 - 9 files changed, 258 insertions(+), 198 deletions(-)
Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices
within a Bayesian hierarchical framework as described by Culpepper and
Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package
contains the datasets used within the analysis of the paper.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between cIRT versions 1.3.2 dated 2022-02-21 and 1.3.3 dated 2025-09-27
DESCRIPTION | 22 MD5 | 25 - NEWS.md | 14 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/doc/Estimating-the-Model-in-the-Paper.html | 453 +++++++++--------- inst/doc/Package-Overview.html | 66 +- inst/doc/Simulation-Study-with-cIRT.R | 442 ++++++++--------- inst/doc/Simulation-Study-with-cIRT.html | 595 ++++++++++++------------ man/cIRT-package.Rd | 3 src/Makevars | 3 src/Makevars.win | 3 src/project_source.cpp | 6 14 files changed, 862 insertions(+), 778 deletions(-)
Title: Bayesian Estimation of the Reduced Reparameterized Unified Model
with Gibbs Sampling
Description: Implementation of Gibbs sampling algorithm for Bayesian Estimation
of the Reduced Reparameterized Unified Model ('rrum'), described by
Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>.
Author: Steven Andrew Culpepper [aut, cph] ,
Aaron Hudson [aut, cph] ,
James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between rrum versions 0.2.1 dated 2023-11-29 and 0.2.2 dated 2025-09-27
DESCRIPTION | 25 +++++++++++++------------ MD5 | 12 ++++++------ NEWS.md | 18 ++++++++++++------ README.md | 12 ++---------- build/partial.rdb |binary man/rrum-package.Rd | 1 - src/rRUM_Gibbs.cpp | 10 +++++----- 7 files changed, 38 insertions(+), 40 deletions(-)
Title: Ordinal Higher-Order Exploratory General Diagnostic Model for
Polytomous Data
Description: Perform a Bayesian estimation of the ordinal exploratory
Higher-order General Diagnostic Model (OHOEGDM) for Polytomous Data
described by Culpepper, S. A. and Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between ohoegdm versions 0.1.0 dated 2022-02-24 and 0.1.1 dated 2025-09-27
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 15 ++++++++------- NEWS.md | 13 +++++++++++++ README.md | 10 +++++----- build |only inst/CITATION | 4 ++-- man/ohoegdm-package.Rd | 3 +-- src/Makevars | 8 +++++--- src/Makevars.win | 8 +++++--- 9 files changed, 53 insertions(+), 34 deletions(-)
Title: Bayesian Estimation of an Exploratory Deterministic Input, Noisy
and Gate Model
Description: Perform a Bayesian estimation of the exploratory
deterministic input, noisy and gate (EDINA)
cognitive diagnostic model described by Chen et al. (2018)
<doi:10.1007/s11336-017-9579-4>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph] ,
Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between edina versions 0.1.1 dated 2020-03-25 and 0.1.2 dated 2025-09-27
DESCRIPTION | 25 ++++++++++++------------- MD5 | 17 +++++++++-------- NEWS.md | 13 +++++++++++++ README.md | 19 +++++-------------- build |only inst/CITATION | 16 ++++++++-------- man/edina-package.Rd | 7 ++----- src/Makevars | 8 +++++--- src/Makevars.win | 8 +++++--- src/RcppExports.cpp | 5 +++++ 10 files changed, 64 insertions(+), 54 deletions(-)
Title: R Wrapper for 'agena.ai' API
Description: An R wrapper for 'agena.ai' <https://www.agena.ai> which provides users capabilities to work with 'agena.ai' using the R environment. Users can create Bayesian network models from scratch or import existing models in R and export to 'agena.ai' cloud or local API for calculations. Note: running calculations requires a valid 'agena.ai' API license (past the initial trial period of the local API).
Author: Erhan Pisirir [aut],
Eugene Dementiev [aut, cre],
Martin Neil [aut, cph]
Maintainer: Eugene Dementiev <support@agenarisk.com>
Diff between agena.ai versions 1.1.1 dated 2023-09-26 and 1.1.2 dated 2025-09-27
DESCRIPTION | 6 LICENSE | 4 MD5 | 90 NAMESPACE | 46 NEWS.md | 42 R/RAgena.R | 109 - README.md | 2886 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/batch-calculate.Rmd | 132 - inst/doc/batch-calculate.html | 129 - inst/doc/calculate-cloud.Rmd | 148 - inst/doc/calculate-cloud.html | 151 - inst/doc/calculate-local.Rmd | 154 - inst/doc/calculate-local.html | 155 - inst/doc/create-model.html | 203 +- inst/doc/sensitivity-cloud.Rmd | 116 - inst/doc/sensitivity-cloud.html | 139 - inst/doc/sensitivity-local.Rmd | 112 - inst/doc/sensitivity-local.html | 135 - inst/doc/setup-local-calculation.Rmd | 68 inst/doc/setup-local-calculation.html | 121 - man/Dataset-class.Rd | 42 man/Model-class.Rd | 230 +- man/Network-class.Rd | 86 man/Node-class.Rd | 178 - man/calculate.Rd | 52 man/create_batch_cases.Rd | 42 man/create_csv_template.Rd | 36 man/create_sensitivity_config.Rd | 62 man/from_cmpx.Rd | 38 man/generate_cmpx.Rd | 36 man/local_api_activate_license.Rd | 34 man/local_api_batch_calculate.Rd | 34 man/local_api_calculate.Rd | 42 man/local_api_clone.Rd | 28 man/local_api_compile.Rd | 30 man/local_api_sensitivity.Rd | 42 man/login.Rd | 38 man/sensitivity_analysis.Rd | 46 vignettes/CarCosts_DataSet_Modified.csv | 12 vignettes/batch-calculate.Rmd | 132 - vignettes/calculate-cloud.Rmd | 148 - vignettes/calculate-local.Rmd | 154 - vignettes/sensitivity-cloud.Rmd | 116 - vignettes/sensitivity-local.Rmd | 112 - vignettes/setup-local-calculation.Rmd | 68 46 files changed, 3392 insertions(+), 3392 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 geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. 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/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Roger Bivand [ctb] ,
Andrew Brown [ctb] ,
Michael Chirico [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-60 dated 2025-07-21 and 1.8-70 dated 2025-09-26
DESCRIPTION | 8 +-- MD5 | 106 ++++++++++++++++++++--------------------- NEWS.md | 32 +++++++++++- R/SpatVectorCollection.R | 4 + R/aggregate.R | 3 + R/colors.R | 10 +++ R/generics.R | 53 +++++++++++++++++--- R/plot_2rasters.R | 6 +- R/plot_add.R | 1 R/plot_axes.R | 8 +-- R/plot_legend_classes.R | 7 +- R/plot_legend_continuous.R | 20 ++++--- R/plot_vector.R | 13 +++-- R/rast.R | 16 ++++-- R/tapp.R | 11 ++-- R/tiles.R | 13 ++++- R/time.R | 24 +++++---- R/values.R | 49 ++++++++++++++++++ R/vect.R | 19 ++++--- inst/tinytest/test_vect-geom.R | 4 + man/aggregate.Rd | 10 +++ man/all.equal.Rd | 19 +++++-- man/app.Rd | 2 man/colors.Rd | 5 + man/distance.Rd | 4 - man/divide.Rd | 2 man/global.Rd | 2 man/identical.Rd | 16 +++--- man/makeTiles.Rd | 8 +-- man/north.Rd | 2 man/plet.Rd | 2 man/plot.Rd | 7 +- man/resample.Rd | 7 +- man/scatter.Rd | 2 man/terra-package.Rd | 2 man/vect.Rd | 4 - src/RcppModule.cpp | 18 ++++++ src/distValueRaster.cpp | 3 - src/distVector.cpp | 2 src/gdal_algs.cpp | 10 +++ src/gdal_multidimensional.cpp | 32 +++++++++++- src/geos_methods.cpp | 1 src/geos_spat.h | 7 ++ src/geosphere.cpp | 2 src/ncdf.cpp | 1 src/raster_methods.cpp | 25 +++++++++ src/read_ogr.cpp | 91 ++++++++++++++++++++++++++++++++--- src/spatRaster.h | 2 src/spatRasterMultiple.cpp | 2 src/spatVector.cpp | 13 +++-- src/spatVector.h | 2 src/vector_methods.cpp | 2 src/write_gdal.cpp | 2 src/write_ogr.cpp | 9 ++- 54 files changed, 542 insertions(+), 183 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) 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 2.8.12 dated 2025-08-29 and 2.8.13 dated 2025-09-26
DESCRIPTION | 10 - MD5 | 38 ++-- NAMESPACE | 1 NEWS.md | 7 R/SDA-spatial.R | 88 ++++++++--- R/SDA_query.R | 21 +- R/fetchEDIT_tools.R | 6 R/get_OSD.R | 6 R/get_SDA_NASIS_keys.R |only R/get_SDA_property.R | 50 +++--- inst/doc/local-ssurgo.R | 97 +++++------- inst/doc/local-ssurgo.Rmd | 202 +++++++++++++++----------- inst/doc/local-ssurgo.html | 302 +++++++++++++++++++++++---------------- man/SDA_spatialQuery.Rd | 81 +++++++--- man/get_OSD.Rd | 2 man/get_SDA_NASIS_key.Rd |only man/make_EDIT_service_URL.Rd | 6 tests/testthat/test-SDA_query.R | 97 +++++++++++- tests/testthat/test-fetchLDM.R | 2 tests/testthat/test-fetchNASIS.R | 20 +- vignettes/local-ssurgo.Rmd | 202 +++++++++++++++----------- 21 files changed, 764 insertions(+), 474 deletions(-)
Title: Multi-Reader Multi-Case Analysis of Variance
Description: Estimation and comparison of the performances of diagnostic tests
in multi-reader multi-case studies where true case statuses (or ground
truths) are known and one or more readers provide test ratings for multiple
cases. Reader performance metrics are provided for area under and expected
utility of ROC curves, likelihood ratio of positive or negative tests, and
sensitivity and specificity. ROC curves can be estimated empirically or
with binormal or binormal likelihood-ratio models. Statistical comparisons
of diagnostic tests are based on the ANOVA model of Obuchowski-Rockette and
the unified framework of Hillis (2005) <doi:10.1002/sim.2024>. The ANOVA
can be conducted with data from a full factorial, nested, or partially
paired study design; with random or fixed readers or cases; and covariances
estimated with the DeLong method, jackknifing, or an unbiased method. Smith
and Hillis (2020) <doi:10.1117/12.2549075>.
Author: Brian J Smith [aut, cre],
Stephen L Hillis [aut],
Lorenzo L Pesce [ctb]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MRMCaov versions 0.3.0 dated 2023-01-10 and 0.3.1 dated 2025-09-26
DESCRIPTION | 12 MD5 | 34 - NAMESPACE | 2 NEWS.md | 6 R/data.R | 26 R/jackknife.R | 2 R/print.R | 14 R/roc.R | 2 R/summary.R | 19 R/utils.R | 4 README.md | 15 build/partial.rdb |binary build/vignette.rds |binary data/Kundel.RData |binary data/Soh.RData |only inst/CITATION | 2 inst/doc/UserGuide.R | 4 inst/doc/UserGuide.html | 1448 +++++++++++++++++++++++++++++++----------------- man/Soh.Rd |only 19 files changed, 1023 insertions(+), 567 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.21 dated 2025-09-07 and 1.22 dated 2025-09-26
DESCRIPTION | 6 +++--- MD5 | 48 +++++++++++++++++++++++++----------------------- NEWS.md | 4 ++++ data/datalist | 1 + data/drug.RData |only man/adult.Rd | 9 +++------ man/advertising.Rd | 6 ++---- man/bank.Rd | 6 ++---- man/caravan.Rd | 15 +++++++++------ man/cereal.Rd | 17 +++-------------- man/churn.Rd | 16 ++++++++-------- man/churnCredit.Rd | 6 ++---- man/churnTel.Rd | 6 ++---- man/corona.Rd | 6 ++---- man/drug.Rd |only man/fertilizer.Rd | 1 - man/figures/logo.png |binary man/house.Rd | 6 ++---- man/housePrice.Rd | 6 ++---- man/insurance.Rd | 6 ++---- man/kNN.Rd | 3 +-- man/kNN.plot.Rd | 7 ++----- man/marketing.Rd | 6 ++---- man/redWines.Rd | 6 ++---- man/risk.Rd | 1 - man/whiteWines.Rd | 6 ++---- 26 files changed, 81 insertions(+), 113 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, visualise, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. A series of published empirical datasets is included. Documentation about 'archeofrag' is provided by a vignette and by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by the 'archeofrag.gui' R package, a companion GUI application available at <https://analytics.huma-num.fr/Sebast [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 1.2.0 dated 2025-03-27 and 1.2.3 dated 2025-09-26
archeofrag-1.2.0/archeofrag/data/GrandeRivoire.RData |only archeofrag-1.2.0/archeofrag/man/GrandeRivoire.Rd |only archeofrag-1.2.3/archeofrag/DESCRIPTION | 13 archeofrag-1.2.3/archeofrag/MD5 | 54 archeofrag-1.2.3/archeofrag/NEWS.md | 16 archeofrag-1.2.3/archeofrag/R/frag.edges.weighting.R | 2 archeofrag-1.2.3/archeofrag/R/frag.get.parameters.R | 13 archeofrag-1.2.3/archeofrag/R/frag.graph.reduce.R | 16 archeofrag-1.2.3/archeofrag/R/frag.simul.process.R | 1 archeofrag-1.2.3/archeofrag/R/make_frag_object.R | 4 archeofrag-1.2.3/archeofrag/R/utils.R | 24 archeofrag-1.2.3/archeofrag/TODO | 10 archeofrag-1.2.3/archeofrag/build/vignette.rds |binary archeofrag-1.2.3/archeofrag/data/BoutDesVergnes.RData |binary archeofrag-1.2.3/archeofrag/data/Chauzeys.RData |binary archeofrag-1.2.3/archeofrag/data/Fumane.RData |binary archeofrag-1.2.3/archeofrag/data/Geelbek.RData |only archeofrag-1.2.3/archeofrag/data/GrandeRivoire1stMeso.RData |only archeofrag-1.2.3/archeofrag/data/GrandeRivoire2ndMeso.RData |only archeofrag-1.2.3/archeofrag/data/Grotte16.RData |only archeofrag-1.2.3/archeofrag/data/StCesaire1987.RData |only archeofrag-1.2.3/archeofrag/data/StCesaire2024.RData |only archeofrag-1.2.3/archeofrag/inst/doc/archeofrag-vignette.html | 902 ++++------ archeofrag-1.2.3/archeofrag/man/BoutDesVergnes.Rd | 4 archeofrag-1.2.3/archeofrag/man/Chauzeys.Rd | 4 archeofrag-1.2.3/archeofrag/man/Fumane.Rd | 2 archeofrag-1.2.3/archeofrag/man/Geelbek.Rd |only archeofrag-1.2.3/archeofrag/man/GrandeRivoire1stMeso.Rd |only archeofrag-1.2.3/archeofrag/man/GrandeRivoire2ndMeso.Rd |only archeofrag-1.2.3/archeofrag/man/Grotte16.Rd |only archeofrag-1.2.3/archeofrag/man/StCesaire1987.Rd |only archeofrag-1.2.3/archeofrag/man/StCesaire2024.Rd |only archeofrag-1.2.3/archeofrag/man/frag.graph.reduce.Rd | 8 archeofrag-1.2.3/archeofrag/man/frag.simul.process.Rd | 7 archeofrag-1.2.3/archeofrag/tests/testthat/test-frag.simul.compare.R | 1 35 files changed, 475 insertions(+), 606 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
George Stagg [ctb] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 7.0.0 dated 2025-09-01 and 8.0.0 dated 2025-09-26
DESCRIPTION | 8 +++++--- MD5 | 24 +++++++++++++----------- NEWS | 4 ++++ R/wasm.R | 4 ++-- build/partial.rdb |binary configure | 6 ++++++ inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- src/Makevars.win | 2 +- src/V8_types.h | 8 +++++++- src/bindings.cpp | 8 ++++++++ src/emscripten |only tools/winlibs.R | 6 +++--- 13 files changed, 54 insertions(+), 26 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', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.3 dated 2025-08-19 and 1.19.4 dated 2025-09-26
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/csv/replacementPatterns.csv | 5 +++-- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-spark.R | 9 +++++++-- 6 files changed, 27 insertions(+), 14 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models. There is also a function for partial and semipartial
correlations and a function for conducting Cohen's
set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.2.6 dated 2025-06-20 and 0.2.7 dated 2025-09-26
DESCRIPTION | 11 +++--- MD5 | 18 +++++------ NAMESPACE | 2 - R/COUNT_REGRESSION.R | 71 ++++++++++++++++++++++--------------------- R/LOGISTIC_REGRESSION.R | 72 ++++++++++++++++++++++---------------------- R/utilities_boc.R | 4 +- man/COUNT_REGRESSION.Rd | 22 ------------- man/LOGISTIC_REGRESSION.Rd | 21 ------------ man/MODERATED_REGRESSION.Rd | 6 --- man/OLS_REGRESSION.Rd | 6 --- 10 files changed, 89 insertions(+), 144 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: 'ttf2pt1' Program
Description: Contains the program 'ttf2pt1', for use with the
'extrafont' package. This product includes software developed by the 'TTF2PT1'
Project and its contributors.
Author: Winston Chang [aut],
Andrew Weeks [aut],
Frank M. Siegert [aut],
Mark Heath [aut],
Thomas Henlick [aut],
Sergey Babkin [aut],
Turgut Uyar [aut],
Rihardas Hepas [aut],
Szalay Tamas [aut],
Johan Vromans [aut],
Petr Titera [aut],
Lei Wang [aut],
Chen Xi [...truncated...]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Rttf2pt1 versions 1.3.13 dated 2025-09-24 and 1.3.14 dated 2025-09-26
DESCRIPTION | 15 +++++++++------ MD5 | 9 +++++---- NEWS.md | 5 +++++ README.md | 18 ++++++++++++++---- inst |only src/ttf2pt1/t1asm.c | 27 ++++++++++++++++++++++----- 6 files changed, 55 insertions(+), 19 deletions(-)
Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full second- or
third-order polynomial, shifted and rotated squared difference model,
rising ridge surfaces, basic squared difference model, asymmetric or
level-dependent congruence effect models). The package provides plotting
functions for 3d wireframe surfaces, interactive 3d plots, and contour plots.
Calculates many surface parameters (a1 to a5, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schoenbrodt [cre, aut],
Sarah Humberg [aut]
Maintainer: Felix Schoenbrodt <felix@nicebread.de>
Diff between RSA versions 0.10.6 dated 2023-01-12 and 0.10.8 dated 2025-09-26
DESCRIPTION | 12 MD5 | 21 R/RSA.R | 2076 ++++++++++++++++++++++++++++----------------------------- R/RSA.ST.R | 8 R/aictab.R | 2 R/globals.R |only R/plot.RSA.R | 94 +- inst/CITATION | 8 inst/News.Rd | 24 man/RSA.Rd | 6 man/RSA.ST.Rd | 6 man/plotRSA.Rd | 8 12 files changed, 1168 insertions(+), 1097 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] ,
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remify versions 3.2.8 dated 2025-01-29 and 3.2.9 dated 2025-09-26
DESCRIPTION | 11 ++++++----- MD5 | 34 +++++++++++++++++----------------- R/rehshape.R | 6 +++--- R/remify.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rehshape.Rmd | 1 - inst/doc/rehshape.html | 1 - inst/doc/remify.R | 2 +- inst/doc/remify.Rmd | 3 +-- inst/doc/remify.html | 11 +++++------ inst/doc/riskset.R | 17 ++++++++--------- inst/doc/riskset.Rmd | 18 ++++++++---------- inst/doc/riskset.html | 17 ++++++++--------- src/remify.cpp | 16 +++++++++------- vignettes/rehshape.Rmd | 1 - vignettes/remify.Rmd | 3 +-- vignettes/riskset.Rmd | 18 ++++++++---------- 18 files changed, 77 insertions(+), 86 deletions(-)
Title: Prepare American Psychological Association Journal Articles with
R Markdown
Description: Tools to create dynamic, submission-ready manuscripts, which
conform to American Psychological Association manuscript guidelines. We
provide R Markdown document formats for manuscripts (PDF and Word) and
revision letters (PDF). Helper functions facilitate reporting statistical
analyses or create publication-ready tables and plots.
Author: Frederik Aust [aut, cre] ,
Marius Barth [aut] ,
Birk Diedenhofen [ctb],
Christoph Stahl [ctb],
Joseph V. Casillas [ctb],
Rudolf Siegel [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between papaja versions 0.1.3 dated 2024-10-24 and 0.1.4 dated 2025-09-26
papaja-0.1.3/papaja/inst/rmarkdown/templates/apa6/resources/apa6_man__.docx |only papaja-0.1.4/papaja/DESCRIPTION | 19 +++--- papaja-0.1.4/papaja/MD5 | 31 +++++----- papaja-0.1.4/papaja/R/apa_print_emm_lsm.R | 15 +--- papaja-0.1.4/papaja/R/apa_print_glm.R | 10 +-- papaja-0.1.4/papaja/R/cite_r.R | 10 +-- papaja-0.1.4/papaja/R/lookup_tables.R | 2 papaja-0.1.4/papaja/R/mbess-ci-r2.R |only papaja-0.1.4/papaja/R/utils.R | 6 + papaja-0.1.4/papaja/README.md | 12 ++- papaja-0.1.4/papaja/build/partial.rdb |binary papaja-0.1.4/papaja/build/vignette.rds |binary papaja-0.1.4/papaja/inst/NEWS.md | 9 ++ papaja-0.1.4/papaja/inst/WORDLIST | 1 papaja-0.1.4/papaja/inst/doc/extending_apa_print.html | 19 +++--- papaja-0.1.4/papaja/tests/testthat/test_apa_print_emm_lsm.R | 2 papaja-0.1.4/papaja/tests/testthat/test_apa_print_htest.R | 23 ++++++- papaja-0.1.4/papaja/tests/testthat/test_apa_table.log |only 18 files changed, 99 insertions(+), 60 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.34 dated 2025-09-08 and 4.36 dated 2025-09-26
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 219 +++++++++++++++++++++++++++--------------------- R/fuzzyRangeChange.R | 4 R/getRegion.R | 20 ++-- R/gridRecords.R | 4 man/fuzzySim-package.Rd | 4 man/getRegion.Rd | 25 +++-- 8 files changed, 171 insertions(+), 127 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen [aut],
Alain Hauser [aut, cre]
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.3.0 dated 2022-11-09 and 1.4.1 dated 2025-09-26
DESCRIPTION | 25 + MD5 | 32 +- R/impact_analysis.R | 2 R/impact_inference.R | 16 + R/impact_plot.R | 8 README.md | 14 - build/vignette.rds |binary inst/CITATION | 4 inst/doc/CausalImpact.R | 82 +++--- inst/doc/CausalImpact.Rmd | 4 inst/doc/CausalImpact.html | 426 +++++++++++++++++++++++---------- tests/testthat/test-impact-analysis.R | 6 tests/testthat/test-impact-inference.R | 4 tests/testthat/test-impact-misc.R | 10 tests/testthat/test-impact-model.R | 11 tests/testthat/test-impact-plot.R | 57 ++-- vignettes/CausalImpact.Rmd | 4 17 files changed, 462 insertions(+), 243 deletions(-)
Title: Compress and Decompress Data Using the 'BLOSC' Library
Description: Arrays of structured data types can require large volumes of disk
space to store. 'Blosc' is a library that provides a fast and efficient way
to compress such data. It is often applied in storage of n-dimensional
arrays, such as in the case of the geo-spatial 'zarr' file format. This
package can be used to compress and decompress data using 'Blosc'.
Author: Pepijn de Vries [aut, cre] ,
Chris Maiwald [cph],
Alexander Gessler [cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between blosc versions 0.1.1 dated 2025-09-11 and 0.1.2 dated 2025-09-26
DESCRIPTION | 6 MD5 | 34 - NAMESPACE | 16 NEWS.md | 4 R/blosc-package.R | 20 R/r2dtype.R | 174 +++--- README.md | 174 +++--- configure | 911 +++++++++++++++++++++++++++++++++- configure.ac | 71 +- inst/doc/dtypes.Rmd | 342 ++++++------ man/blosc-package.Rd | 64 +- man/blosc.Rd | 122 ++-- man/dtype.Rd | 186 +++--- man/figures/logo.svg | 200 +++---- src/umHalf.inl | 1228 +++++++++++++++++++++++----------------------- tests/testthat.R | 24 tests/testthat/test_dev.R | 50 - vignettes/dtypes.Rmd | 342 ++++++------ 18 files changed, 2432 insertions(+), 1536 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison
methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others.
This version introduces two new procedures: the Jonckheere-Terpstra trend test
and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in
teaching, applied statistical analysis, and reproducible research.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 1.8.5 dated 2025-06-27 and 2.0.0 dated 2025-09-26
DESCRIPTION | 8 - MD5 | 50 +++++----- NAMESPACE | 5 + R/BonferroniTest.R | 173 ++++++++++++++++++++++++++----------- R/DuncanTest.R | 183 +++++++++++++++++++++++++-------------- R/GabrielTest.R | 177 +++++++++++++++++++++++++------------- R/HolmTest.R | 168 ++++++++++++++++++++++++------------ R/LSDTest.R | 163 +++++++++++++++++++++++++---------- R/SNKTest.R | 194 +++++++++++++++++++++++++++--------------- R/ScheffeTest.R | 180 +++++++++++++++++++++++++------------- R/SidakTest.R |only R/TukeyTest.R | 153 ++++++++++++++++++++++++--------- R/plot_comparations.R | 153 ++++++++++++++++++++++----------- R/posthoc_planner.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Analitica-intro.html | 10 +- man/BonferroniTest.Rd | 42 ++++++--- man/DuncanTest.Rd | 44 ++++++--- man/GabrielTest.Rd | 41 ++++++-- man/HolmTest.Rd | 38 +++++--- man/LSDTest.Rd | 34 ++++++- man/Posthoc_planner.Rd |only man/SNKTest.Rd | 40 ++++++-- man/ScheffeTest.Rd | 41 ++++++-- man/SidakTest.Rd |only man/TukeyTest.Rd | 54 +++++++++-- man/plot.comparaciones.Rd | 46 ++++++--- 28 files changed, 1372 insertions(+), 625 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut],
Ken Kellner [cre, aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Lea Pautrel [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between unmarked versions 1.5.0 dated 2025-02-10 and 1.5.1 dated 2025-09-26
unmarked-1.5.0/unmarked/R/classes.R |only unmarked-1.5.0/unmarked/R/deprecated_sim_power.R |only unmarked-1.5.0/unmarked/R/zzz.R |only unmarked-1.5.0/unmarked/inst/shinyPower |only unmarked-1.5.0/unmarked/man/imputeMissing.Rd |only unmarked-1.5.0/unmarked/man/sight2perpdist.Rd |only unmarked-1.5.0/unmarked/src/hmm.c |only unmarked-1.5.0/unmarked/tests/testthat/test_powerAnalysis_deprecated.R |only unmarked-1.5.0/unmarked/tests/testthat/test_simulate_deprecated.R |only unmarked-1.5.1/unmarked/DESCRIPTION | 25 unmarked-1.5.1/unmarked/MD5 | 235 - unmarked-1.5.1/unmarked/NAMESPACE | 8 unmarked-1.5.1/unmarked/NEWS.md | 10 unmarked-1.5.1/unmarked/R/All_classes.R |only unmarked-1.5.1/unmarked/R/All_generics.R |only unmarked-1.5.1/unmarked/R/IDS.R | 176 unmarked-1.5.1/unmarked/R/RcppExports.R | 36 unmarked-1.5.1/unmarked/R/colext.R | 532 +- unmarked-1.5.1/unmarked/R/distsamp.R | 54 unmarked-1.5.1/unmarked/R/distsampOpen.R | 52 unmarked-1.5.1/unmarked/R/fitted.R | 164 unmarked-1.5.1/unmarked/R/gdistremoval.R | 304 - unmarked-1.5.1/unmarked/R/gdistsamp.R | 72 unmarked-1.5.1/unmarked/R/getDesign.R | 1987 +++------- unmarked-1.5.1/unmarked/R/getP.R | 9 unmarked-1.5.1/unmarked/R/gmultmix.R | 50 unmarked-1.5.1/unmarked/R/goccu.R | 117 unmarked-1.5.1/unmarked/R/gpcount.R | 50 unmarked-1.5.1/unmarked/R/mixedModelTools.R | 25 unmarked-1.5.1/unmarked/R/multinomPois.R | 47 unmarked-1.5.1/unmarked/R/multmixOpen.R | 46 unmarked-1.5.1/unmarked/R/nmixTTD.R | 27 unmarked-1.5.1/unmarked/R/nonparboot.R | 10 unmarked-1.5.1/unmarked/R/occu.R | 45 unmarked-1.5.1/unmarked/R/occuCOP.R | 340 - unmarked-1.5.1/unmarked/R/occuComm.R | 133 unmarked-1.5.1/unmarked/R/occuFP.R | 56 unmarked-1.5.1/unmarked/R/occuMS.R | 9 unmarked-1.5.1/unmarked/R/occuMulti.R | 39 unmarked-1.5.1/unmarked/R/occuPEN.R | 92 unmarked-1.5.1/unmarked/R/occuRN.R | 42 unmarked-1.5.1/unmarked/R/occuTTD.R | 46 unmarked-1.5.1/unmarked/R/parboot.R | 14 unmarked-1.5.1/unmarked/R/pcount.R | 41 unmarked-1.5.1/unmarked/R/pcount.spHDS.R | 33 unmarked-1.5.1/unmarked/R/pcountOpen.R | 52 unmarked-1.5.1/unmarked/R/plotEffects.R | 7 unmarked-1.5.1/unmarked/R/posteriorSamples.R | 11 unmarked-1.5.1/unmarked/R/power.R | 15 unmarked-1.5.1/unmarked/R/predict.R | 560 -- unmarked-1.5.1/unmarked/R/ranef.R | 43 unmarked-1.5.1/unmarked/R/removed_functions.R |only unmarked-1.5.1/unmarked/R/residuals.R | 39 unmarked-1.5.1/unmarked/R/simulate.R | 37 unmarked-1.5.1/unmarked/R/square_brackets.R |only unmarked-1.5.1/unmarked/R/unmarkedCrossVal.R | 32 unmarked-1.5.1/unmarked/R/unmarkedEstimate.R | 48 unmarked-1.5.1/unmarked/R/unmarkedFit.R | 233 - unmarked-1.5.1/unmarked/R/unmarkedFitList.R | 54 unmarked-1.5.1/unmarked/R/unmarkedFrame.R | 667 --- unmarked-1.5.1/unmarked/R/unmarkedLinComb.R | 17 unmarked-1.5.1/unmarked/R/update.R | 63 unmarked-1.5.1/unmarked/R/utils.R | 262 - unmarked-1.5.1/unmarked/build/partial.rdb |binary unmarked-1.5.1/unmarked/build/vignette.rds |binary unmarked-1.5.1/unmarked/inst/doc/colext.Rmd | 108 unmarked-1.5.1/unmarked/inst/doc/colext.html | 116 unmarked-1.5.1/unmarked/inst/doc/contributing_to_unmarked.Rmd | 104 unmarked-1.5.1/unmarked/inst/doc/contributing_to_unmarked.html | 139 unmarked-1.5.1/unmarked/inst/doc/distsamp.html | 140 unmarked-1.5.1/unmarked/inst/doc/occuMulti.html | 58 unmarked-1.5.1/unmarked/inst/doc/simulate.html | 144 unmarked-1.5.1/unmarked/inst/doc/spp-dist.html | 40 unmarked-1.5.1/unmarked/inst/doc/unmarked.R | 28 unmarked-1.5.1/unmarked/inst/doc/unmarked.Rmd | 46 unmarked-1.5.1/unmarked/inst/doc/unmarked.html | 188 unmarked-1.5.1/unmarked/man/distsamp.Rd | 2 unmarked-1.5.1/unmarked/man/extract-methods.Rd | 59 unmarked-1.5.1/unmarked/man/unmarkedFrame-class.Rd | 15 unmarked-1.5.1/unmarked/src/RcppExports.cpp | 183 unmarked-1.5.1/unmarked/src/TMB/tmb_colext.hpp |only unmarked-1.5.1/unmarked/src/TMB/tmb_goccu.hpp | 14 unmarked-1.5.1/unmarked/src/TMB/unmarked_TMBExports.cpp | 3 unmarked-1.5.1/unmarked/src/nll_distsampOpen.cpp | 18 unmarked-1.5.1/unmarked/src/nll_gdistremoval.cpp | 16 unmarked-1.5.1/unmarked/src/nll_gdistsamp.cpp | 14 unmarked-1.5.1/unmarked/src/nll_gmultmix.cpp | 45 unmarked-1.5.1/unmarked/src/nll_gpcount.cpp | 16 unmarked-1.5.1/unmarked/src/nll_multmixOpen.cpp | 18 unmarked-1.5.1/unmarked/src/nll_nmixTTD.cpp | 6 unmarked-1.5.1/unmarked/src/nll_occuCOP.cpp | 4 unmarked-1.5.1/unmarked/src/nll_occuTTD.cpp | 10 unmarked-1.5.1/unmarked/src/nll_pcountOpen.cpp | 20 unmarked-1.5.1/unmarked/tests/testthat/data |only unmarked-1.5.1/unmarked/tests/testthat/test_IDS.R | 209 - 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Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight
important informations (differences from totals, comparisons between lines or
columns, contributions to variance, confidence intervals, odds ratios, etc.).
All functions are pipe-friendly and render data frames which can be easily
manipulated. In the same time, time-taking operations are done with 'data.table'
to go faster with big dataframes. Tables can be exported with formats and colors
to 'Excel', plot and html.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between tabxplor versions 1.3.0 dated 2025-03-09 and 1.3.1 dated 2025-09-26
DESCRIPTION | 8 MD5 | 24 NEWS.md | 7 R/jmvtab.b.R | 428 ++-- R/jmvtab.h.R | 67 R/tab.R | 8 R/tab_classes.R | 12 R/utils.R | 90 README.md | 12 build/vignette.rds |binary inst/doc/tabxplor.html | 5144 ++++++++++++++++++------------------------------- inst/i18n/fr.json | 107 - man/jmvtab.Rd | 23 13 files changed, 2392 insertions(+), 3538 deletions(-)
Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
Author: Sergej Potapov [aut],
Werner Adler [aut],
Matthias Schmid [aut],
Frederic Bertrand [cre, aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between survAUC versions 1.3-0 dated 2024-09-09 and 1.4-0 dated 2025-09-26
survAUC-1.3-0/survAUC/R/BaggC.R |only survAUC-1.3-0/survAUC/R/survAUC_Song_Zhou.R |only survAUC-1.3-0/survAUC/man/AUC.ChamDiao.Rd |only survAUC-1.3-0/survAUC/man/AUC.HungChiang.Rd |only survAUC-1.3-0/survAUC/man/AUC.Song_Zhou.Rd |only survAUC-1.3-0/survAUC/man/AUC.uno.Rd |only survAUC-1.3-0/survAUC/man/IntegratedAUC.Rd |only survAUC-1.3-0/survAUC/man/OXS.Rd |only survAUC-1.3-0/survAUC/man/plot.survAUC.Rd |only survAUC-1.3-0/survAUC/man/schemper.Err.Rd |only survAUC-1.4-0/survAUC/DESCRIPTION | 32 ++- survAUC-1.4-0/survAUC/MD5 | 88 +++++---- survAUC-1.4-0/survAUC/NAMESPACE | 39 ++-- survAUC-1.4-0/survAUC/NEWS.md | 10 + survAUC-1.4-0/survAUC/R/BeggC.R |only survAUC-1.4-0/survAUC/R/IntegratedAUC.R | 66 +++++++ survAUC-1.4-0/survAUC/R/UnoC.R | 63 ++++++ survAUC-1.4-0/survAUC/R/plot.survAUC.R | 61 ++++++ survAUC-1.4-0/survAUC/R/schemper.R | 62 ++++++ survAUC-1.4-0/survAUC/R/survAUC-package.R |only survAUC-1.4-0/survAUC/R/survAUC_ChamDiao.R | 61 ++++++ survAUC-1.4-0/survAUC/R/survAUC_HungChiang.R | 61 ++++++ survAUC-1.4-0/survAUC/R/survAUC_SongZhou.R |only survAUC-1.4-0/survAUC/R/survAUC_Uno.R | 79 ++++++++ survAUC-1.4-0/survAUC/R/surv_measures.R | 199 +++++++++++++++++++++- survAUC-1.4-0/survAUC/R/zzz.R | 15 - survAUC-1.4-0/survAUC/README.md |only survAUC-1.4-0/survAUC/inst |only survAUC-1.4-0/survAUC/man/BeggC.Rd | 62 +++--- survAUC-1.4-0/survAUC/man/GHCI.Rd | 79 ++++---- survAUC-1.4-0/survAUC/man/IntAUC.Rd |only survAUC-1.4-0/survAUC/man/R2_type_Coef.Rd |only survAUC-1.4-0/survAUC/man/UnoC.Rd | 88 +++++---- survAUC-1.4-0/survAUC/man/figures |only survAUC-1.4-0/survAUC/man/plot_survAUC_survErr.Rd |only survAUC-1.4-0/survAUC/man/predErr.Rd | 121 +++++++------ survAUC-1.4-0/survAUC/man/schemper.Rd |only survAUC-1.4-0/survAUC/man/survAUC-package.Rd |only survAUC-1.4-0/survAUC/man/survAUC_ChamDiao.Rd |only survAUC-1.4-0/survAUC/man/survAUC_HungChiang.Rd |only survAUC-1.4-0/survAUC/man/survAUC_SongZhou.Rd |only survAUC-1.4-0/survAUC/man/survAUC_Uno.Rd |only survAUC-1.4-0/survAUC/src/R_init_survAUC.c | 2 survAUC-1.4-0/survAUC/src/survAUC_Cham_Diao.c | 2 survAUC-1.4-0/survAUC/src/survAUC_HZ.c | 2 survAUC-1.4-0/survAUC/src/survAUC_Hung_Chiang.c | 2 survAUC-1.4-0/survAUC/src/survAUC_SongZhou.c | 2 survAUC-1.4-0/survAUC/src/survAUC_UNO.c | 2 survAUC-1.4-0/survAUC/src/surv_measures.c | 2 survAUC-1.4-0/survAUC/src/utils.c | 2 survAUC-1.4-0/survAUC/tests |only 51 files changed, 952 insertions(+), 250 deletions(-)
Title: Testing, Monitoring, and Dating Structural Changes: C++ Version
Description: A fast implementation with additional experimental features for
testing, monitoring and dating structural changes in (linear)
regression models. 'strucchangeRcpp' features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g. cumulative/moving
sum, recursive/moving estimates) and F statistics, respectively.
These methods are described in Zeileis et al. (2002)
<doi:10.18637/jss.v007.i02>.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals,
and their magnitude as well as the model fit can be evaluated
using a variety of statistical measures.
Author: Dainius Masiliunas [aut, cre] ,
Achim Zeileis [aut] ,
Marius Appel [aut],
Friedrich Leisch [aut],
Kurt Hornik [aut],
Christian Kleiber [aut],
Andrei Mirt [ctb] ,
Bruce Hansen [ctb],
Edgar C. Merkle [ctb],
Nikolaus Umlauf [ctb]
Maintainer: Dainius Masiliunas <pastas4@gmail.com>
Diff between strucchangeRcpp versions 1.5-4-1.0.0 dated 2024-10-17 and 1.5-4-1.0.1 dated 2025-09-26
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NEWS | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/strucchange-intro.pdf |binary src/recresid.cpp | 4 ++-- 7 files changed, 20 insertions(+), 14 deletions(-)
More information about strucchangeRcpp at CRAN
Permanent link
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.10 dated 2025-03-29 and 1.2.11 dated 2025-09-26
simStateSpace-1.2.10/simStateSpace/R/simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.10/simStateSpace/R/simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.10/simStateSpace/man/LinSDECov.Rd |only simStateSpace-1.2.10/simStateSpace/man/LinSDEMean.Rd |only simStateSpace-1.2.10/simStateSpace/tests/testthat/Rplots.pdf |only simStateSpace-1.2.10/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.10/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.11/simStateSpace/DESCRIPTION | 12 simStateSpace-1.2.11/simStateSpace/MD5 | 142 - simStateSpace-1.2.11/simStateSpace/NAMESPACE | 22 simStateSpace-1.2.11/simStateSpace/NEWS.md | 12 simStateSpace-1.2.11/simStateSpace/R/RcppExports.R | 582 +++++ simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-cov-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-mean-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-long-dot.R | 35 simStateSpace-1.2.11/simStateSpace/R/simStateSpace-methods-simstatespace.R | 33 simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-cov-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-mean-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-wide-dot.R | 9 simStateSpace-1.2.11/simStateSpace/build/partial.rdb |binary simStateSpace-1.2.11/simStateSpace/man/LinSDE2SSM.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/LinSDECovEta.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDECovY.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDEMeanEta.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDEMeanY.Rd |only simStateSpace-1.2.11/simStateSpace/man/ProjectToHurwitz.Rd |only 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simStateSpace-1.2.11/simStateSpace/man/SimSSMLinGrowthIVary.Rd | 42 simStateSpace-1.2.11/simStateSpace/man/SimSSMLinSDEFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMLinSDEIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMOUFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMOUIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMVARFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMVARIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SpectralAbscissa.Rd |only simStateSpace-1.2.11/simStateSpace/man/SpectralRadius.Rd |only simStateSpace-1.2.11/simStateSpace/man/TestPhi.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/TestPhiHurwitz.Rd |only simStateSpace-1.2.11/simStateSpace/man/TestStability.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/TestStationarity.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/as.data.frame.simstatespace.Rd | 9 simStateSpace-1.2.11/simStateSpace/man/as.matrix.simstatespace.Rd | 9 simStateSpace-1.2.11/simStateSpace/man/plot.simstatespace.Rd | 18 simStateSpace-1.2.11/simStateSpace/src/Makevars | 2 simStateSpace-1.2.11/simStateSpace/src/Makevars.win | 2 simStateSpace-1.2.11/simStateSpace/src/RcppExports.cpp | 311 ++ simStateSpace-1.2.11/simStateSpace/src/source.cpp | 1122 +++++++++- simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-project-to-hurwitz.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-project-to-stability.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-alpha-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-beta-n-2.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-beta-n.R | 79 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-cov-diag-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-cov-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-iota-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-nu-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-phi-n-2.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-phi-n.R | 62 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-fixed.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-i-vary.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth-i-vary.R | 27 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth.R | 24 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-fixed.R | 29 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-i-vary.R | 28 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-fixed.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-i-vary.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-fixed.R | 17 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-i-vary.R | 17 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-spectral-abscissa.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-spectral-radius.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-cov-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-mean-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-tests.R | 29 99 files changed, 2926 insertions(+), 205 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.3 dated 2024-09-25 and 1.2.4 dated 2025-09-26
DESCRIPTION | 28 +++---- MD5 | 44 ++++++----- NAMESPACE | 3 NEWS.md | 10 ++ R/export.R | 5 - R/export_methods.R | 6 + R/extensions.R | 6 - R/import.R | 3 R/import_list.R | 21 ++++- R/import_methods.R | 9 ++ R/sysdata.rda |binary R/utils.R | 8 -- README.md | 143 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/labelled.html | 22 ++--- inst/doc/rio.html | 94 ++++++++++++++---------- man/export.Rd | 1 man/import.Rd | 1 man/rio.Rd | 1 tests/testdata/example.xlsm |only tests/testthat/test_extensions.R | 21 +++-- tests/testthat/test_format_qs2.R |only tests/testthat/test_format_xls.R | 27 +++++++ tests/testthat/test_import_list.R | 33 ++++++++ 24 files changed, 305 insertions(+), 181 deletions(-)
Title: Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM), Tenenhaus, Esposito Vinzi, Chatelin, Lauro (2005) <doi:10.1016/j.csda.2004.03.005>,
analysis for both metric and non-metric data, as well as REBUS analysis, Esposito Vinzi, Trinchera, Squillacciotti, and Tenenhaus (2008) <doi:10.1002/asmb.728>.
Author: Gaston Sanchez [aut],
Laura Trinchera [aut],
Giorgio Russolillo [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plspm versions 0.5.2 dated 2025-08-18 and 0.6.0 dated 2025-09-26
DESCRIPTION | 38 +++++++------ MD5 | 53 ++++++++++-------- NAMESPACE | 36 ++++++++---- NEWS | 29 +++++++++- R/check_arguments.R | 6 +- R/check_specifications.R | 4 - R/plot.plspm.R | 3 - R/plspm-package.R | 41 +++++++++----- R/plspm.R | 2 R/plspm.groups.R | 2 R/print.rebus.R | 2 R/rebus.test.R | 2 R/summary_plspm.R | 4 - README.md |only build/partial.rdb |only inst/CITATION |only inst/_pkgdown.yml |only inst/doc/plspm_introduction.R | 50 ++++++++++++++++- inst/doc/plspm_introduction.Rnw | 94 +++++++++++++++++++++++++++++++-- inst/doc/plspm_introduction.pdf |binary man/plspm-package.Rd |only man/plspm.Rd | 1 tests/testthat/test-check-blocks.r | 20 +++---- tests/testthat/test-check-data.r | 20 +++---- tests/testthat/test-check-modes.r | 24 +++----- tests/testthat/test-check-path.r | 8 +- tests/testthat/test-check-scheme.r | 38 ++++++------- tests/testthat/test-get-metric.r | 8 +- tests/testthat/test-manifest-scaling.r | 13 ++-- vignettes/plspm_introduction.Rnw | 94 +++++++++++++++++++++++++++++++-- 30 files changed, 426 insertions(+), 166 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.13.2 dated 2025-07-31 and 0.14.0 dated 2025-09-26
DESCRIPTION | 14 MD5 | 138 ++++----- NAMESPACE | 1 NEWS.md | 39 ++ R/insert.hinges.r | 52 +++ R/interpolate.spectrum.r | 64 ++-- R/make-var-labels.R | 11 R/mspct.quantile.r | 23 + R/mspct.row.funs.r | 2 R/rbindspct.r | 46 +-- R/spct-conversion-qty-unit.R | 434 +++++++++++++--------------- R/spct.classes.r | 11 R/spct.clean.r | 13 R/spct.integrate.r | 46 +-- R/spct.irrad.r | 4 R/spct.metadata.r | 440 +++++++++++++++++++---------- R/spct.new.r | 83 +++++ R/spct.normalize.r | 104 +++++- R/spct.peaks.r | 37 +- R/spct.spikes.R | 32 +- R/spct.summaries.r | 57 ++- R/spct.trim.r | 16 - R/spct.utils.r | 42 +- R/trim.waveband.r | 34 +- R/zmspct.classes.R | 57 +++ README.md | 32 +- data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D50.illuminant.spct.rda |binary data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear_body.spct.rda |binary data/cone_fundamentals10.spct.rda |binary data/filter-cps-mspct.rda |binary data/filter-data.rda |binary data/green_leaf.spct.rda |binary data/r4p-pkgs.rda |binary data/response-data.rda |binary data/solutes.rda |binary data/sun.data.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary inst/doc/userguide-0-r4p-introduction.html | 7 inst/doc/userguide-1-radiation.Rmd | 7 inst/doc/userguide-1-radiation.html | 66 +++- man/add_attr2tb.Rd | 23 + man/as.generic_spct.Rd | 10 man/as.response_spct.Rd | 29 + man/check_wl_stepsize.Rd | 8 man/getWhereMeasured.Rd | 41 +- man/interpolate_spct.Rd | 39 +- man/interpolate_spectrum.Rd | 33 +- man/interpolate_wl.Rd | 46 ++- man/normalize.Rd | 47 +-- man/print.generic_spct.Rd | 19 + man/s_quantile.Rd | 11 man/setWhereMeasured.Rd | 77 ++++- man/spct_metadata.Rd | 9 man/thin_wl.Rd | 60 +-- man/trim_waveband.Rd | 10 man/v_replace_hinges.Rd | 38 ++ vignettes/userguide-1-radiation.Rmd | 7 70 files changed, 1590 insertions(+), 829 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.5 dated 2025-08-20 and 11.6 dated 2025-09-26
NNS-11.5/NNS/R/Internal_Functions.R |only NNS-11.6/NNS/DESCRIPTION | 8 NNS-11.6/NNS/MD5 | 147 +- NNS-11.6/NNS/R/ANOVA.R | 208 ++-- NNS-11.6/NNS/R/ARMA.R | 7 NNS-11.6/NNS/R/ARMA_optim.R | 15 NNS-11.6/NNS/R/Boost.R | 392 +++---- NNS-11.6/NNS/R/Central_tendencies.R | 7 NNS-11.6/NNS/R/Copula.R | 38 NNS-11.6/NNS/R/Dependence.R | 28 NNS-11.6/NNS/R/FSD.R | 2 NNS-11.6/NNS/R/NNS_Distance.R | 104 -- NNS-11.6/NNS/R/NNS_Distance_bulk.R |only NNS-11.6/NNS/R/NNS_VAR.R | 239 +++- NNS-11.6/NNS/R/NNS_meboot.R | 300 ++--- NNS-11.6/NNS/R/Normalization.R | 4 NNS-11.6/NNS/R/Partition_Map.R | 129 -- NNS-11.6/NNS/R/RcppExports.R | 68 + NNS-11.6/NNS/R/Regression.R | 134 +- NNS-11.6/NNS/R/SSD.R | 2 NNS-11.6/NNS/R/Seasonality_Test.R | 2 NNS-11.6/NNS/R/Stack.R | 506 ++++++---- NNS-11.6/NNS/R/TSD.R | 2 NNS-11.6/NNS/R/Uni_Causation.R | 10 NNS-11.6/NNS/R/Uni_SD_Routines.R | 6 NNS-11.6/NNS/R/dy_d_wrt.R | 2 NNS-11.6/NNS/R/dy_dx.R | 2 NNS-11.6/NNS/R/gvload.R | 3 NNS-11.6/NNS/README.md | 4 NNS-11.6/NNS/inst/doc/NNSvignette_Classification.R | 139 +- NNS-11.6/NNS/inst/doc/NNSvignette_Classification.Rmd | 21 NNS-11.6/NNS/inst/doc/NNSvignette_Classification.html | 87 - NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.R | 212 +++- NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 153 ++- NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.html | 318 ++++-- NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.R | 3 NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.Rmd | 3 NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.html | 31 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.R | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.html | 15 NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.R | 174 +-- NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.Rmd | 48 NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.html | 109 +- NNS-11.6/NNS/inst/doc/NNSvignette_Overview.R | 77 - NNS-11.6/NNS/inst/doc/NNSvignette_Overview.Rmd | 68 + NNS-11.6/NNS/inst/doc/NNSvignette_Overview.html | 136 +- NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.R | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.Rmd | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.html | 9 NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.R | 411 ++++---- NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.Rmd | 15 NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.html | 23 NNS-11.6/NNS/man/NNS.boost.Rd | 2 NNS-11.6/NNS/man/NNS.distance.Rd | 2 NNS-11.6/NNS/man/NNS.meboot.Rd | 2 NNS-11.6/NNS/man/NNS.reg.Rd | 372 +++---- NNS-11.6/NNS/man/NNS.stack.Rd | 9 NNS-11.6/NNS/src/NNS_distance.cpp |only NNS-11.6/NNS/src/NNS_part.cpp |only NNS-11.6/NNS/src/RcppExports.cpp | 246 ++++ NNS-11.6/NNS/src/SD.cpp | 43 NNS-11.6/NNS/src/central_tendencies.cpp | 57 - NNS-11.6/NNS/src/fast_lm.cpp | 5 NNS-11.6/NNS/src/internal_functions.cpp |only NNS-11.6/NNS/tests/testthat/Rplots.pdf |binary NNS-11.6/NNS/vignettes/NNSvignette_Classification.Rmd | 21 NNS-11.6/NNS/vignettes/NNSvignette_Clustering_and_Regression.Rmd | 153 ++- NNS-11.6/NNS/vignettes/NNSvignette_Comparing_Distributions.Rmd | 3 NNS-11.6/NNS/vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 5 NNS-11.6/NNS/vignettes/NNSvignette_Forecasting.Rmd | 48 NNS-11.6/NNS/vignettes/NNSvignette_Overview.Rmd | 68 + NNS-11.6/NNS/vignettes/NNSvignette_Partial_Moments.Rmd | 5 NNS-11.6/NNS/vignettes/NNSvignette_Sampling.Rmd | 15 NNS-11.6/NNS/vignettes/images/NNSmc_1_tgt_drift.png |binary NNS-11.6/NNS/vignettes/images/multi_impute.png |only NNS-11.6/NNS/vignettes/images/overview_arma.png |only NNS-11.6/NNS/vignettes/images/overview_reg.png |only NNS-11.6/NNS/vignettes/images/uni_impute.png |only 79 files changed, 3312 insertions(+), 2185 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 3.0.1 dated 2025-08-28 and 3.0.2 dated 2025-09-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 12 ++++++++++++ R/datasetQuery.R | 9 ++++++++- R/stackDataFilesArrow.R | 10 +++++----- README.md | 8 ++++++++ 6 files changed, 42 insertions(+), 15 deletions(-)
Title: A Collection of Graphon Estimation Methods
Description: Provides a not-so-comprehensive list of methods for estimating graphon,
a symmetric measurable function, from a single or multiple of observed networks.
For a detailed introduction on graphon and popular estimation techniques,
see the paper by Orbanz, P. and Roy, D.M.(2014) <doi:10.1109/TPAMI.2014.2334607>.
It also contains several auxiliary functions for generating sample networks
using various network models and graphons.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between graphon versions 0.3.5 dated 2021-08-13 and 0.3.6 dated 2025-09-26
graphon-0.3.5/graphon/man/graphon-package.Rd |only graphon-0.3.6/graphon/DESCRIPTION | 14 +++++++------- graphon-0.3.6/graphon/MD5 | 11 +++++------ graphon-0.3.6/graphon/R/graphon-package.R | 3 +-- graphon-0.3.6/graphon/R/init.R | 2 +- graphon-0.3.6/graphon/README.md | 4 +--- graphon-0.3.6/graphon/build/partial.rdb |binary 7 files changed, 15 insertions(+), 19 deletions(-)
Title: Causal Effect Identification from Multiple Incomplete Data
Sources
Description: Identification of causal effects from arbitrary observational and
experimental probability distributions via do-calculus and standard
probability manipulations using a search-based algorithm by
Tikka, Hyttinen and Karvanen (2021) <doi:10.18637/jss.v099.i05>.
Allows for the presence of mechanisms related to selection bias
(Bareinboim and Tian, 2015) <doi:10.1609/aaai.v29i1.9679>,
transportability (Bareinboim and Pearl, 2014)
<http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>,
missing data (Mohan, Pearl, and Tian, 2013)
<http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations
of these. Also supports identification in the presence of context-specific
independence (CSI) relations through labeled directed acyclic graphs
(LDAG). For details on CSIs see (Corander et al., 2019)
<doi:10.1016/j.apal.2019.04.004>.
Author: Santtu Tikka [aut, cre] ,
Antti Hyttinen [ctb] ,
Juha Karvanen [ctb]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dosearch versions 1.0.11 dated 2024-07-16 and 1.0.12 dated 2025-09-26
dosearch-1.0.11/dosearch/R/srr-stats-standards.R |only dosearch-1.0.12/dosearch/DESCRIPTION | 15 +++-- dosearch-1.0.12/dosearch/MD5 | 35 ++++++------- dosearch-1.0.12/dosearch/NEWS.md | 4 + dosearch-1.0.12/dosearch/R/dosearch-package.R | 38 --------------- dosearch-1.0.12/dosearch/R/dosearch.R | 33 ------------- dosearch-1.0.12/dosearch/R/internal.R | 13 ++--- dosearch-1.0.12/dosearch/R/internal_dag.R | 6 -- dosearch-1.0.12/dosearch/R/internal_ldag.R | 6 -- dosearch-1.0.12/dosearch/build/vignette.rds |binary dosearch-1.0.12/dosearch/inst/CITATION | 29 +++++++---- dosearch-1.0.12/dosearch/inst/doc/dosearch.R | 12 ++-- dosearch-1.0.12/dosearch/inst/doc/dosearch.Rmd | 2 dosearch-1.0.12/dosearch/inst/doc/dosearch.html | 2 dosearch-1.0.12/dosearch/man/dosearch.Rd | 3 - dosearch-1.0.12/dosearch/tests/testthat.R | 20 ------- dosearch-1.0.12/dosearch/tests/testthat/test-errors.R | 2 dosearch-1.0.12/dosearch/tests/testthat/test-interface.R | 4 - dosearch-1.0.12/dosearch/vignettes/dosearch.Rmd | 2 19 files changed, 69 insertions(+), 157 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.6.2 dated 2025-06-10 and 1.7.0 dated 2025-09-26
DESCRIPTION | 10 - MD5 | 75 ++++---- NAMESPACE | 4 NEWS.md | 10 + R/RcppExports.R | 4 R/ability.R | 4 R/database.R | 12 + R/dexter.R | 2 R/dif.R | 19 ++ R/equating.R | 8 R/fit_enorm.R | 19 +- R/individual_differences.R | 25 -- R/interaction_model.R | 10 - R/latent_cor.R | 260 ++++++++++++++++++++++-------- R/misc.R | 34 +++ R/misc_anon.R | 2 R/oplike.R | 74 ++++---- R/plausible_values.R | 7 R/plots.R | 8 R/suf_stats.R | 19 +- R/theta_functions.R | 2 R/tia.R | 33 ++- build/vignette.rds |binary inst/doc/DIF_vignette.html | 15 - inst/doc/Equating.html | 25 +- inst/doc/Plausible_Values.html | 21 +- inst/doc/Test_Individual_differences.html | 19 +- inst/doc/dexter.html | 85 +++++---- inst/doc/profile-plots.html | 20 +- man/coef.latent_cor.Rd |only man/latent_cor.Rd | 21 +- man/start_new_project_from_oplm.Rd | 12 - man/tia_tables.Rd | 7 src/RcppExports.cpp | 13 - src/ability.cpp | 16 + src/data.cpp | 28 ++- src/pv.cpp | 39 +++- tests/testthat/test_database.R | 1 tests/testthat/test_tia.R | 2 39 files changed, 626 insertions(+), 339 deletions(-)
Title: Spatiotemporal Boundary Detection Model for Areal Unit Data
Description: Implements a spatiotemporal boundary detection model with a dissimilarity
metric for areal data with inference in a Bayesian setting using Markov chain
Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget),
probit or Tobit link and spatial correlation is introduced at each time point
through a conditional autoregressive (CAR) prior. Temporal correlation is introduced
through a hierarchical structure and can be specified as exponential or first-order
autoregressive. Full details of the package can be found in the accompanying vignette.
Furthermore, the details of the package can be found in "Diagnosing Glaucoma
Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method",
by Berchuck et al (2019) <doi:10.1080/01621459.2018.1537911>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>
Diff between womblR versions 1.0.5 dated 2022-09-05 and 1.0.6 dated 2025-09-26
DESCRIPTION | 16 +- MD5 | 14 - R/womblR-package.R | 3 build/vignette.rds |binary inst/doc/womblR-example.R | 28 +-- inst/doc/womblR-example.html | 313 +++++++++++++++++++++---------------------- man/womblR.Rd | 1 src/MCMC_Samplers.cpp | 19 +- 8 files changed, 203 insertions(+), 191 deletions(-)
Title: Tools to Create Formal Language Parser
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph],
David M. Beazley [aut, cph],
Yasutaka Tanaka [ctb],
Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.7.4 dated 2022-05-08 and 1.7.7 dated 2025-09-26
DESCRIPTION | 8 MD5 | 26 - R/lex.R | 6 R/logger.R | 4 R/yacc.R | 16 build/vignette.rds |binary inst/doc/intro-to-rly.R | 2 inst/doc/intro-to-rly.html | 938 +++++++++++++++++++++++---------------------- man/LRParser.Rd | 2 man/LexToken.Rd | 2 man/Lexer.Rd | 2 man/NullLogger.Rd | 2 man/RlyLogger.Rd | 2 man/YaccProduction.Rd | 2 14 files changed, 522 insertions(+), 490 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] ,
Maximillian H.K. Hesselbarth [ctb] , get_unique_values, and rcpp_get_coma
functions),
Marco Sciaini [ctb] , get_unique_values, and rcpp_get_coma
functions),
Sebastian Hanss [ctb] , get_unique_values, and rcpp_get_coma
funct [...truncated...]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.9.5 dated 2023-11-28 and 0.9.6 dated 2025-09-26
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/coma.html | 7 ++++--- inst/doc/incoma.html | 9 +++++---- inst/doc/wecoma.html | 9 +++++---- src/create_neighborhood.cpp | 5 +++++ src/rcpp_get_wecoma.cpp | 4 ++-- 10 files changed, 41 insertions(+), 28 deletions(-)
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds
for numerical data, with special functions for thresholding images.
Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R
users. See <https://imagej.net/plugins/auto-threshold> and Landini et
al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] ,
Luis Alvarez [ctb] ,
Sergi Padilla-Parra [ctb, ths] ,
Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.4.2 dated 2023-12-13 and 1.4.3 dated 2025-09-26
DESCRIPTION | 24 ++++++----- MD5 | 18 ++++---- NEWS.md | 6 ++ build/vignette.rds |binary inst/doc/finding-thresholds.R | 2 inst/doc/finding-thresholds.Rmd | 2 inst/doc/finding-thresholds.html | 65 +++++++++++++++----------------- inst/doc/thresholding-image-stacks.html | 36 +++++++---------- inst/doc/thresholding-images.html | 24 +++++------ vignettes/finding-thresholds.Rmd | 2 10 files changed, 90 insertions(+), 89 deletions(-)
More information about autothresholdr at CRAN
Permanent link
Title: Post-Processing of Markov Chain Monte Carlo Simulations for
Chronological Modelling
Description: Statistical analysis of archaeological dates and groups of
dates. This package allows to post-process Markov Chain Monte Carlo
(MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>,
'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal'
<https://bcal.shef.ac.uk/>. It provides functions for the study of
rhythms of the long term from the posterior distribution of a series
of dates (tempo and activity plot). It also allows the estimation and
visualization of time ranges from the posterior distribution of groups
of dates (e.g. duration, transition and hiatus between successive
phases) as described in Philippe and Vibet (2020)
<doi:10.18637/jss.v093.c01>.
Author: Anne Philippe [aut, cre] ,
Marie-Anne Vibet [aut] ,
Nicolas Frerebeau [aut] ,
Thomas S. Dye [ctb] ,
Nantes Universite [fnd] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between ArchaeoPhases versions 2.0 dated 2024-06-16 and 2.1.0 dated 2025-09-26
ArchaeoPhases-2.0/ArchaeoPhases/R/reexport.R |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.R |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.Rmd |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.html |only ArchaeoPhases-2.0/ArchaeoPhases/man/reexports.Rd |only ArchaeoPhases-2.0/ArchaeoPhases/vignettes/bibliography.Rmd |only ArchaeoPhases-2.1.0/ArchaeoPhases/DESCRIPTION | 63 +- ArchaeoPhases-2.1.0/ArchaeoPhases/MD5 | 302 +++++----- ArchaeoPhases-2.1.0/ArchaeoPhases/NAMESPACE | 25 ArchaeoPhases-2.1.0/ArchaeoPhases/NEWS.md | 38 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/AllClasses.R | 66 +- ArchaeoPhases-2.1.0/ArchaeoPhases/R/AllGenerics.R | 105 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/R/ArchaeoPhases-internal.R | 5 ArchaeoPhases-2.1.0/ArchaeoPhases/R/ArchaeoPhases-package.R | 41 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/activity.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/allen-mcmc.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/allen-relations.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/bind.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/boundaries.R | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/R/coerce.R | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/depth.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/R/hiatus.R | 31 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/interval.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/R/occurrence.R | 5 ArchaeoPhases-2.1.0/ArchaeoPhases/R/phases.R | 27 ArchaeoPhases-2.1.0/ArchaeoPhases/R/plot.R | 95 --- ArchaeoPhases-2.1.0/ArchaeoPhases/R/read.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/show.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/summary.R | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/R/transition.R | 18 ArchaeoPhases-2.1.0/ArchaeoPhases/R/validate.R | 25 ArchaeoPhases-2.1.0/ArchaeoPhases/R/zzz.R | 7 ArchaeoPhases-2.1.0/ArchaeoPhases/README.md | 174 +++++ ArchaeoPhases-2.1.0/ArchaeoPhases/build/partial.rdb |binary ArchaeoPhases-2.1.0/ArchaeoPhases/build/vignette.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/CITATION | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/ArchaeoPhases.Rmd | 76 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/ArchaeoPhases.html | 77 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/allen.Rmd | 85 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/allen.html | 101 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/import.Rmd | 59 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/import.html | 104 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-phases.R | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_bcal.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_chronomodel.R | 12 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_oxcal.R | 7 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-tempo.R | 1 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/po |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/events_hiatus.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/occurrence.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_boundaries.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_hiatus.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_transition.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_activity.svg | 28 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_cred.svg | 60 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_decr.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_hdr.svg | 66 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_incr.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_inter.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_occurrence.svg | 48 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_decr.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_hiatus.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_inc.svg | 52 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_succession.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_transition.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_tempo_cred.svg | 34 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_tempo_gauss.svg | 34 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/helpers.R |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_activity.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_allen.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_boundaries.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_events.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_hiatus.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_interval.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_occurrence.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_older.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_phases.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_read.R |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_summary.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_tempo.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_transition.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/man/ActivityEvents-class.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/ArchaeoPhases-package.Rd | 48 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/CumulativeEvents-class.Rd | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/man/EventsMCMC-class.Rd | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/man/MCMC-class.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/OccurrenceEvents-class.Rd | 20 ArchaeoPhases-2.1.0/ArchaeoPhases/man/PhasesMCMC-class.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/TimeRange-class.Rd | 21 ArchaeoPhases-2.1.0/ArchaeoPhases/man/activity.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_analyze.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_analyze_relations.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_complement.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_composition.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_converse.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_count.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_illustrate.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_illustrate_relations.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_intersect.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_joint_concurrency.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_observe.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_observe_frequency.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_plot.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relate_intervals.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relation.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relation_code.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_table.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_union.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/as_events.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/as_phases.Rd | 18 ArchaeoPhases-2.1.0/ArchaeoPhases/man/bury.Rd | 14 ArchaeoPhases-2.1.0/ArchaeoPhases/man/data.frame.Rd | 12 ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-events-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-events-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-phases-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-succession-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-succession-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-tempo-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-tempo-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/interval_credible.Rd | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/man/interval_hdr.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/man/occurrence.Rd | 50 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/phases.Rd | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/man/plot_events.Rd | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/man/plot_phases.Rd | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_bcal.Rd | 32 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_chronomodel.Rd | 49 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_oxcal.Rd | 35 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/summary.Rd | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/man/tempo.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/po |only ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/ArchaeoPhases.Rmd | 76 +- ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/ArchaeoPhases.Rmd.orig | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/allen.Rmd | 85 +- ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/allen.Rmd.orig | 54 - ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/activity-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/analyze_stratigraphy-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/basic_relations-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/bcal-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-autocor-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-autocor-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/event-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/identity_relation-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/illustrate_stratigraphy-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/occurrence-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/oxcal-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/phases-1.png |only ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/phases-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-chronomodel-events-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-chronomodel-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-oxcal-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/relation_and_converse-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/relation_and_converse-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/succession-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/tempo-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/import.Rmd | 59 + ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/import.Rmd.orig | 43 - ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/precompile.R | 4 160 files changed, 1642 insertions(+), 1515 deletions(-)
Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] ,
Remi Barillec [aut],
Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>
Diff between psgp versions 0.3-23 dated 2025-07-17 and 0.3-24 dated 2025-09-26
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/PSGP.cpp | 12 ++++-------- 4 files changed, 14 insertions(+), 15 deletions(-)
Title: A Soil Survey Toolkit
Description: A collection of data processing, visualization, and export functions to support soil survey operations. Many of the functions build on the `SoilProfileCollection` S4 class provided by the aqp package, extending baseline visualization to more elaborate depictions in the context of spatial and taxonomic data. While this package is primarily developed by and for the USDA-NRCS, in support of the National Cooperative Soil Survey, the authors strive for generalization sufficient to support any soil survey operation. Many of the included functions are used by the SoilWeb suite of websites and movile applications. These functions are provided here, with additional documentation, to enable others to replicate high quality versions of these figures for their own purposes.
Author: Dylan Beaudette [cre, aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 2.3.3 dated 2025-04-17 and 2.4 dated 2025-09-26
DESCRIPTION | 6 - MD5 | 34 +++--- NAMESPACE | 2 NEWS.md | 12 ++ R/PLSS2LL.R | 176 +++++++++++++++++++++------------ R/huePositionPlot.R | 20 +-- R/samplingStability.R | 4 R/vizAnnualClimate.R | 4 build/vignette.rds |binary data/OSDexamples.rda |binary data/table5.2.rda |binary man/PLSS2LL.Rd | 10 - man/formatPLSS.Rd | 42 ++++--- man/huePositionPlot.Rd | 20 +-- man/vizAnnualClimate.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-PLSS2LL.R | 66 ++++++++++++ tests/testthat/test-vizAnnualClimate.R | 5 18 files changed, 274 insertions(+), 131 deletions(-)
Title: Analysis of Eye Data
Description: There is no ophthalmic researcher who has not had headaches from
the handling of visual acuity entries. Different notations, untidy entries.
This shall now be a matter of the past. Eye makes it as easy as pie to work
with VA data - easy cleaning, easy conversion between
Snellen, logMAR, ETDRS letters, and qualitative visual acuity
shall never pester you again. The eye
package automates the pesky task to count number of patients and eyes,
and can help to clean data with easy re-coding for right and left eyes.
It also contains functions to help reshaping eye side specific variables
between wide and long format. Visual acuity conversion is based on
Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>,
Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>,
Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and
Bach (2007) <https://michaelbach.de/sci/acuity.html>.
Author: Tjebo Heeren [aut, cre] ,
Antoine Fabri [ctb]
Maintainer: Tjebo Heeren <tjebo@gmx.de>
Diff between eye versions 1.2.1 dated 2021-09-04 and 1.3.0 dated 2025-09-26
eye-1.2.1/eye/build/partial.rdb |only eye-1.3.0/eye/DESCRIPTION | 27 eye-1.3.0/eye/MD5 | 68 - eye-1.3.0/eye/NAMESPACE | 6 eye-1.3.0/eye/NEWS.md | 33 eye-1.3.0/eye/R/eye.R | 2 eye-1.3.0/eye/R/reveal.R | 6 eye-1.3.0/eye/R/str_helper.R | 26 eye-1.3.0/eye/R/va.R | 145 +- eye-1.3.0/eye/R/va_cleaner.R | 64 - eye-1.3.0/eye/R/va_methods.R | 15 eye-1.3.0/eye/README.md | 215 ++- eye-1.3.0/eye/build/vignette.rds |binary eye-1.3.0/eye/inst/CITATION | 6 eye-1.3.0/eye/inst/doc/eye.R | 20 eye-1.3.0/eye/inst/doc/eye.Rmd | 27 eye-1.3.0/eye/inst/doc/eye.html | 1573 ++++++++++++++++++---------- eye-1.3.0/eye/man/VAwrapper.Rd | 2 eye-1.3.0/eye/man/clean_va.Rd | 7 eye-1.3.0/eye/man/convertQuali.Rd | 18 eye-1.3.0/eye/man/eye.Rd | 6 eye-1.3.0/eye/man/eye_codes.Rd | 2 eye-1.3.0/eye/man/plausibility_methods.Rd | 2 eye-1.3.0/eye/man/reveal_methods.Rd | 5 eye-1.3.0/eye/man/reveal_split.Rd | 4 eye-1.3.0/eye/man/set_eye_strings.Rd | 23 eye-1.3.0/eye/man/snellen_steps.Rd | 2 eye-1.3.0/eye/man/va.Rd | 80 - eye-1.3.0/eye/man/va_methods.Rd | 2 eye-1.3.0/eye/man/va_mixed.Rd | 25 eye-1.3.0/eye/man/which_va.Rd | 4 eye-1.3.0/eye/tests/testthat/test-eyes.R | 1 eye-1.3.0/eye/tests/testthat/test-reveal.R | 2 eye-1.3.0/eye/tests/testthat/test-va.R | 54 eye-1.3.0/eye/tests/testthat/test_cleanVA.r |only eye-1.3.0/eye/vignettes/eye.Rmd | 27 36 files changed, 1671 insertions(+), 828 deletions(-)
Title: 'rbi' Helper Functions
Description: Contains a collection of helper functions to use with 'rbi', the R
interface to 'LibBi', described in
Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to
adapt the proposal distribution and number of particles in
particle Markov-Chain Monte Carlo, as well as calculating the
Deviance Information Criterion (DIC) and converting between times in 'LibBi'
results and R time/dates.
Author: Sebastian Funk [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi.helpers versions 0.4.0 dated 2023-08-24 and 0.4.1 dated 2025-09-26
DESCRIPTION | 20 +++++++--- MD5 | 38 ++++++++++---------- NEWS.md | 4 ++ R/acceptance_rate.R | 6 +-- R/adapt_particles.R | 6 +-- R/adapt_proposal.R | 11 +++-- R/get_mvn_params.r | 4 +- R/times.r | 10 ++--- R/update_proposal.r | 6 +-- build/vignette.rds |binary inst/doc/rbi.helpers.R | 76 ++++++++++++++++++++--------------------- inst/doc/rbi.helpers.html | 1 man/acceptance_rate.Rd | 4 +- man/adapt_particles.Rd | 6 +-- man/adapt_proposal.Rd | 6 +-- man/get_mvn_params.Rd | 4 +- man/numeric_to_time.Rd | 2 - man/update_proposal.Rd | 4 +- tests/testthat/test-adapt.r | 4 -- tests/testthat/test-proposal.r | 2 - 20 files changed, 111 insertions(+), 103 deletions(-)
Title: Geographically Weighted Lasso
Description: Performs geographically weighted Lasso regressions. Find optimal bandwidth, fit a geographically weighted lasso or ridge regression, and make predictions.
These methods are specially well suited for ecological inferences. Bandwidth selection algorithm is from A. Comber and P. Harris (2018) <doi:10.1007/s10109-018-0280-7>.
Author: Matthieu Mulot [aut, cre, cph] ,
Sophie Erb [aut]
Maintainer: Matthieu Mulot <matthieu.mulot@gmail.com>
Diff between GWlasso versions 1.0.1 dated 2024-11-22 and 1.0.2 dated 2025-09-26
DESCRIPTION | 14 ++++---- MD5 | 11 +++--- NEWS.md | 6 +++ README.md | 11 +++++- inst/CITATION |only inst/doc/example_analysis.R | 68 ++++++++++++++++++++--------------------- inst/doc/example_analysis.html | 1 7 files changed, 63 insertions(+), 48 deletions(-)
Title: Fast Algorithm for Support Vector Machine
Description: Implements an efficient algorithm for fitting the entire regularization path of support vector machine models with elastic-net penalties using a generalized coordinate descent scheme. The framework also supports SCAD and MCP penalties. It is designed for high-dimensional datasets and emphasizes numerical accuracy and computational efficiency. This package implements the algorithms proposed in Tang, Q., Zhang, Y., & Wang, B. (2022) <https://openreview.net/pdf?id=RvwMTDYTOb>.
Author: Yikai Zhang [aut, cre],
Qian Tang [aut],
Boxiang Wang [aut]
Maintainer: Yikai Zhang <yikai-zhang@uiowa.edu>
Diff between hdsvm versions 1.0.1 dated 2025-02-11 and 1.0.2 dated 2025-09-26
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- R/cv.nc.hdsvm.R | 2 +- inst/CITATION |only inst/doc/hdsvm-vignette.Rmd | 7 ++++++- inst/doc/hdsvm-vignette.html | 9 +++++++-- man/cv.nc.hdsvm.Rd | 2 +- src/hdsvm_cd.f90 | 4 ++-- vignettes/hdsvm-vignette.Rmd | 7 ++++++- 9 files changed, 36 insertions(+), 20 deletions(-)
Title: A Flexible Model for Record Linkage
Description: Implementation of the Stochastic Expectation Maximisation (StEM) approach to Record Linkage described in the paper by K. Robach, S. L. van der Pas, M. A. van de Wiel and M. H. Hof (2024, <doi:10.1093/jrsssc/qlaf016>); see citation("FlexRL") for details. This is a record linkage method, for finding the common set of records among 2 data sources based on Partially Identifying Variables (PIVs) available in both sources. It includes modelling of dynamic Partially Identifying Variables (e.g. postal code) that may evolve over time and registration errors (missing values and mistakes in the registration). Low memory footprint.
Author: Kayane ROBACH [aut, cre, cph] ,
Michel H. HOF [aut, cph]
Maintainer: Kayane ROBACH <k.c.robach@amsterdamumc.nl>
Diff between FlexRL versions 0.1.0 dated 2024-12-09 and 0.1.1 dated 2025-09-26
DESCRIPTION | 20 + MD5 | 18 - NEWS.md | 2 R/FlexRecordLinkage.r | 75 ++++--- README.md | 14 + build/vignette.rds |binary inst/CITATION | 7 inst/doc/FlexRL-vignette.html | 422 ++++++++++++++++++++++++++++++++++++++---- man/loglikSurvival.Rd | 2 man/stEM.Rd | 4 10 files changed, 470 insertions(+), 94 deletions(-)
Title: Taxa Waterbeheer Nederland voor R
Description: The TWN-list (Taxa Waterbeheer Nederland) is the Dutch standard for naming
taxons in Dutch Watermanagement. This package makes it easier to use the
TWN-list for ecological analyses. It consists of two parts. First it makes the
TWN-list itself available in R. Second, it has a few functions that make it
easy to perform some basic and often recurring tasks for checking and consulting
taxonomic data from the TWN-list.
Author: Johan van Tent [aut, cre]
Maintainer: Johan van Tent <tentvanjohan@hotmail.com>
Diff between twn versions 0.2.5 dated 2024-11-11 and 0.2.6 dated 2025-09-26
DESCRIPTION | 10 MD5 | 42 +-- NAMESPACE | 6 NEWS.md | 174 ++++++++------- R/ZZ_package_description.R | 3 R/sysdata.rda |binary R/twn_info.R | 49 +++- R/twn_lijst_doc.R | 8 README.md | 24 +- build/vignette.rds |binary data/twn_lijst.rda |binary data/twn_literatuur.rda |binary data/twn_statuscodes.rda |binary data/twn_taxonlevels.rda |binary inst/doc/krw_beoordeling.R | 450 ++++++++++++++++++++--------------------- inst/doc/krw_beoordeling.html | 62 ++--- man/twn.Rd | 13 + man/twn_info.Rd | 39 ++- man/twn_lijst.Rd | 4 man/twn_literatuur.Rd | 2 man/twn_statuscodes.Rd | 3 tests/testthat/test-twn_info.R | 10 22 files changed, 493 insertions(+), 406 deletions(-)
Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre],
Peter M. Ridland [aut],
David A. Ratkowsky [aut],
Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between IPEC versions 1.1.1 dated 2025-07-23 and 1.1.2 dated 2025-09-26
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/biasIPEC.R | 2 +- R/curvIPEC.R | 2 +- R/parinfo.R | 4 ++-- R/skewIPEC.R | 2 +- build/partial.rdb |binary man/biasIPEC.Rd | 2 +- man/curvIPEC.Rd | 2 +- man/parinfo.Rd | 4 +++- man/skewIPEC.Rd | 2 +- 11 files changed, 25 insertions(+), 23 deletions(-)
Title: Models of Decision Confidence and Measures of Metacognition
Description: Provides fitting functions and other tools for decision confidence
and metacognition researchers, including meta-d'/d', often considered to be
the gold standard to measure metacognitive efficiency, and information-theoretic measures of metacognition.
Also allows to fit and compare several static models of decision making and confidence.
Author: Manuel Rausch [aut, cre] ,
Sascha Meyen [aut] ,
Sebastian Hellmann [aut]
Maintainer: Manuel Rausch <manuel.rausch@ku.de>
Diff between statConfR versions 0.2.0 dated 2025-02-13 and 0.2.1 dated 2025-09-26
DESCRIPTION | 22 ++++--- MD5 | 23 ++++--- R/fitConf.R | 43 ++++++++++++-- R/fitConfModels.R | 40 +++++++++++-- R/int_fitCAS.R |only R/int_fitCEV.R | 5 + R/int_fitRCE.R |only R/int_llCASANDRE.R |only R/plotConfModelFit.R | 140 ++++++++++++++++++++++++++++++++++++++++++++++-- README.md | 25 ++++++-- inst/CITATION | 22 +++---- man/fitConf.Rd | 40 ++++++++++++- man/fitConfModels.Rd | 42 ++++++++++++-- man/plotConfModelFit.Rd | 2 14 files changed, 337 insertions(+), 67 deletions(-)
Title: Learning with Data on Riemannian Manifolds
Description: We provide a variety of algorithms for manifold-valued data, including Fréchet summaries, hypothesis testing, clustering, visualization, and other learning tasks. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> for general exposition to statistics on manifolds.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between Riemann versions 0.1.4 dated 2022-02-28 and 0.1.6 dated 2025-09-26
Riemann-0.1.4/Riemann/build/vignette.rds |only Riemann-0.1.4/Riemann/inst/doc |only Riemann-0.1.4/Riemann/src/functions_07_learning.cpp |only Riemann-0.1.4/Riemann/vignettes |only Riemann-0.1.6/Riemann/DESCRIPTION | 20 +-- Riemann-0.1.6/Riemann/MD5 | 66 +++++----- Riemann-0.1.6/Riemann/NEWS.md | 6 Riemann-0.1.6/Riemann/R/RcppExports.R | 16 ++ Riemann-0.1.6/Riemann/R/auxiliary_checkers.R | 4 Riemann-0.1.6/Riemann/R/dist_splaplace.R | 51 ++++++- Riemann-0.1.6/Riemann/R/future_spd_selection_unsupervised.R |only Riemann-0.1.6/Riemann/R/package-Riemann.R | 5 Riemann-0.1.6/Riemann/R/spatial_GlobalGeary.R |only Riemann-0.1.6/Riemann/R/spatial_GlobalMoran.R |only Riemann-0.1.6/Riemann/R/zzz.R | 2 Riemann-0.1.6/Riemann/README.md | 14 +- Riemann-0.1.6/Riemann/build/partial.rdb |binary Riemann-0.1.6/Riemann/inst/REFERENCES.bib | 6 Riemann-0.1.6/Riemann/src/Makevars | 1 Riemann-0.1.6/Riemann/src/Makevars.win | 1 Riemann-0.1.6/Riemann/src/RcppExports.cpp | 61 +++++++++ Riemann-0.1.6/Riemann/src/auxiliary.cpp | 1 Riemann-0.1.6/Riemann/src/distribution_sphere.cpp | 1 Riemann-0.1.6/Riemann/src/functions_01_basic.cpp | 1 Riemann-0.1.6/Riemann/src/functions_02_inference.cpp | 1 Riemann-0.1.6/Riemann/src/functions_03_clustering.cpp | 1 Riemann-0.1.6/Riemann/src/functions_03_clustering_criteria.cpp | 1 Riemann-0.1.6/Riemann/src/functions_06_curve.cpp | 1 Riemann-0.1.6/Riemann/src/functions_07_spatial.cpp |only Riemann-0.1.6/Riemann/src/functions_08_learning.cpp |only Riemann-0.1.6/Riemann/src/functions_special_others.cpp | 1 Riemann-0.1.6/Riemann/src/functions_special_spd.cpp | 31 ++++ Riemann-0.1.6/Riemann/src/riemann_general.cpp | 1 Riemann-0.1.6/Riemann/src/riemann_general.h | 1 Riemann-0.1.6/Riemann/src/riemann_manifolds.h | 11 - Riemann-0.1.6/Riemann/src/riemann_src.cpp | 2 Riemann-0.1.6/Riemann/src/riemann_src.h | 1 Riemann-0.1.6/Riemann/tests |only 38 files changed, 228 insertions(+), 80 deletions(-)
Title: Discrete Event Simulation in R and C++, with Tools for
Cost-Effectiveness Analysis
Description: Discrete event simulation using both R and C++ (Karlsson et al 2016; <doi:10.1109/eScience.2016.7870915>). The C++ code is adapted from the SSIM library <https://www.inf.usi.ch/carzaniga/ssim/>, allowing for event-oriented simulation. The code includes a SummaryReport class for reporting events and costs by age and other covariates. The C++ code is available as a static library for linking to other packages. A priority queue implementation is given in C++ together with an S3 closure and a reference class implementation. Finally, some tools are provided for cost-effectiveness analysis.
Author: Mark Clements [aut, cre, cph],
Alexandra Jauhiainen [aut],
Andreas Karlsson [aut],
Antonio Carzaniga [cph],
University of Colorado [cph],
Pierre L'Ecuyer [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between microsimulation versions 1.4.4 dated 2024-08-19 and 1.4.5 dated 2025-09-26
DESCRIPTION | 7 +- MD5 | 6 +- inst/include/microsimulation.h | 116 ++++++++++++++++++++++++++++++++++++++--- src/pqueue.cpp | 2 4 files changed, 117 insertions(+), 14 deletions(-)
More information about microsimulation at CRAN
Permanent link
Title: D-Score for Child Development
Description: The D-score summarizes the child's performance on a set of
milestones into a single number. The package implements four Rasch model
keys to convert milestone scores into a D-score. It provides tools to
calculate the D-score and its precision from the child's milestone scores,
to convert the D-score into the Development-for-Age Z-score (DAZ)
using age-conditional references, and to map milestone names into a
generic 9-position item naming convention.
Author: Stef van Buuren [cre, aut],
Iris Eekhout [aut],
Arjan Huizing [aut],
Jonathan Seiden [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between dscore versions 1.10.0 dated 2025-06-05 and 1.11.0 dated 2025-09-26
DESCRIPTION | 11 MD5 | 91 +++--- NAMESPACE | 2 NEWS.md | 42 ++ R/builtin_itemtable.R | 2 R/builtin_keys.R | 2 R/builtin_translate.R |only R/daz.R | 24 + R/decompose_itemnames.R | 4 R/dscore.R | 264 ++++++++++-------- R/get_age_equivalent.R | 26 + R/get_itemnames.R | 42 ++ R/get_itemtable.R | 7 R/get_labels.R | 8 R/get_mu.R | 25 + R/get_reference.R | 36 +- R/get_tau.R | 10 R/gsample.R | 12 R/import.R | 2 R/initialize.R | 4 R/internal.R | 67 +++- R/rename_gcdg_gsed.R | 93 +++++- R/rename_vector.R |only R/set_default.R | 15 - README.md | 9 data/builtin_itembank.rda |binary data/builtin_itemtable.rda |binary data/builtin_keys.rda |binary data/builtin_references.rda |binary data/builtin_translate.rda |only data/gsample.rda |binary data/sample_hf.rda |binary data/sample_lf.rda |binary data/sample_sf.rda |binary inst/doc/custom_priors.html | 5 inst/doc/getting_started.R | 94 ++++-- inst/doc/getting_started.Rmd | 246 +++++++++------- inst/doc/getting_started.html | 613 +++++++++++++++++++++++++++++++++--------- inst/doc/scoring_GSED.html | 317 ++++++++++----------- inst/doc/using_DAZ.html | 5 man/builtin_itemtable.Rd | 2 man/builtin_translate.Rd |only man/gsample.Rd | 5 man/rename_vector.Rd |only man/sample_sf.Rd | 5 src/dscore.cpp | 2 tests/testthat/test-dscore.R | 218 +++++++++++--- tests/testthat/test-prior.R | 2 vignettes/getting_started.Rmd | 246 +++++++++------- 49 files changed, 1719 insertions(+), 839 deletions(-)
Title: Spatial Extreme Value Analysis with the Hierarchical Model of
Reich and Shaby (2012)
Description: Several procedures for the hierarchical kernel extreme value process of Reich and Shaby (2012) <DOI:10.1214/12-AOAS591>, including simulation, estimation and spatial extrapolation. The spatial latent variable model <DOI:10.1214/11-STS376> is also included.
Author: Quentin Sebille [aut],
Leo Belzile [cre]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between hkevp versions 1.1.5 dated 2023-04-18 and 1.1.6 dated 2025-09-26
DESCRIPTION | 21 ++++++++++---- MD5 | 8 ++--- R/hkevp.R | 85 +++++++++++++++++++++------------------------------------- man/hkevp.Rd | 8 +++++ src/hkevp.cpp | 46 +++++++++++++++---------------- 5 files changed, 81 insertions(+), 87 deletions(-)
Title: Inference and Prediction of Toxicokinetic Models
Description: Provides bioaccumulation factors from a toxicokinetic model
fitted to accumulation-depuration data. It is designed to fulfil the requirements
of regulators when examining applications for market authorization of active
substances.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Ophelia Gestin [ctb],
Milena Kaag [aut],
Christelle Lopes [ctb],
Gauthier Multari [ctb],
Alain Pave [ctb],
Aude Ratier [aut],
Aurelie Siberchicot [aut]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
This is a re-admission after prior archival of version 1.2.1 dated 2024-02-26
Diff between rbioacc versions 1.2.1 dated 2024-02-26 and 1.3.1 dated 2025-09-26
rbioacc-1.2.1/rbioacc/README.md |only rbioacc-1.3.1/rbioacc/DESCRIPTION | 17 rbioacc-1.3.1/rbioacc/MD5 | 59 - rbioacc-1.3.1/rbioacc/NAMESPACE | 1 rbioacc-1.3.1/rbioacc/R/bioacc_metric.R | 4 rbioacc-1.3.1/rbioacc/R/plot_PP.R | 8 rbioacc-1.3.1/rbioacc/R/plot_exposure.R | 2 rbioacc-1.3.1/rbioacc/R/plot_fit.R | 6 rbioacc-1.3.1/rbioacc/R/plot_predict.R | 10 rbioacc-1.3.1/rbioacc/R/ppc_fit.R | 16 rbioacc-1.3.1/rbioacc/R/zzz_internals.R | 15 rbioacc-1.3.1/rbioacc/build/vignette.rds |binary rbioacc-1.3.1/rbioacc/inst/WORDLIST |only rbioacc-1.3.1/rbioacc/inst/doc/MWE.R | 20 rbioacc-1.3.1/rbioacc/inst/doc/MWE.html | 1 rbioacc-1.3.1/rbioacc/inst/doc/Tutorial.R | 144 +-- rbioacc-1.3.1/rbioacc/inst/doc/Tutorial.html | 11 rbioacc-1.3.1/rbioacc/man/rmMessWarn.Rd |only rbioacc-1.3.1/rbioacc/src/stanExports_TK.h | 480 +++++----- rbioacc-1.3.1/rbioacc/src/stanExports_odeTK.h | 442 ++++----- rbioacc-1.3.1/rbioacc/tests/testthat/test-PP.R | 22 rbioacc-1.3.1/rbioacc/tests/testthat/test-correlation.R | 49 - rbioacc-1.3.1/rbioacc/tests/testthat/test-elim.R | 52 - rbioacc-1.3.1/rbioacc/tests/testthat/test-mcmcTraces.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-metric.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-ppc.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-predict.R | 159 ++- rbioacc-1.3.1/rbioacc/tests/testthat/test-predict_manual.R | 48 - rbioacc-1.3.1/rbioacc/tests/testthat/test-psrf.R | 8 rbioacc-1.3.1/rbioacc/tests/testthat/test-waic.R | 12 rbioacc-1.3.1/rbioacc/vignettes/Tutorial_files/figure-html/plotMGS-1.png |binary rbioacc-1.3.1/rbioacc/vignettes/Tutorial_files/figure-html/ppcMGS-1.png |binary 32 files changed, 858 insertions(+), 764 deletions(-)
Title: Optimization Frameworks for Tie-Oriented and Actor-Oriented
Relational Event Models
Description: A comprehensive set of tools designed for optimizing likelihood within a tie-oriented (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) or an actor-oriented modelling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>) in relational event networks. The package accommodates both frequentist and Bayesian approaches. The frequentist approaches that the package incorporates are the Maximum Likelihood Optimization (MLE) and the Gradient-based Optimization (GDADAMAX). The Bayesian methodologies included in the package are the Bayesian Sampling Importance Resampling (BSIR) and the Hamiltonian Monte Carlo (HMC). The flexibility of choosing between frequentist and Bayesian optimization approaches allows researchers to select the estimation approach which aligns the most with their analytical preferences.
Author: Giuseppe Arena [aut, cre] ,
Rumana Lakdawala [aut],
Fabio Generoso Vieira [aut],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remstimate versions 2.3.13 dated 2025-01-29 and 2.3.14 dated 2025-09-26
DESCRIPTION | 11 +++++---- MD5 | 16 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/remstimate.R | 8 +++---- inst/doc/remstimate.Rmd | 10 ++++---- inst/doc/remstimate.html | 53 +++++++++++++++++++++-------------------------- src/remstimate.cpp | 4 +-- vignettes/remstimate.Rmd | 10 ++++---- 9 files changed, 54 insertions(+), 58 deletions(-)
Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided. Such as transfer matrix for 1D. Utility functions for exact solutions are provided. Example use cases are as follows: Measuring effective ergodicity and power-laws in so called functional-diffusion.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen <mehmet.suzen@physics.org>
Diff between isingLenzMC versions 0.2.7 dated 2025-09-18 and 0.2.8 dated 2025-09-26
isingLenzMC-0.2.7/isingLenzMC/inst/examples/effectiveErgodicity/README |only isingLenzMC-0.2.8/isingLenzMC/DESCRIPTION | 10 +++--- isingLenzMC-0.2.8/isingLenzMC/MD5 | 16 +++++----- isingLenzMC-0.2.8/isingLenzMC/NEWS | 15 ++++++++- isingLenzMC-0.2.8/isingLenzMC/README.md | 15 +++++++-- isingLenzMC-0.2.8/isingLenzMC/inst/doc/isingLenzMC.Rnw | 6 +-- isingLenzMC-0.2.8/isingLenzMC/inst/doc/isingLenzMC.pdf |binary isingLenzMC-0.2.8/isingLenzMC/inst/examples/effectiveErgodicity/README.md |only isingLenzMC-0.2.8/isingLenzMC/inst/examples/powerLawErgodicity/README.md | 2 - isingLenzMC-0.2.8/isingLenzMC/vignettes/isingLenzMC.Rnw | 6 +-- 10 files changed, 46 insertions(+), 24 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole-model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>).
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 2.1.3 dated 2025-09-09 and 2.2.4 dated 2025-09-26
SVEMnet-2.1.3/SVEMnet/R/svem_random_table.R |only SVEMnet-2.1.3/SVEMnet/man/plot_svem_significance_tests.Rd |only SVEMnet-2.1.3/SVEMnet/man/svem_random_table_from_model.Rd |only SVEMnet-2.2.4/SVEMnet/DESCRIPTION | 24 SVEMnet-2.2.4/SVEMnet/MD5 | 79 ++- SVEMnet-2.2.4/SVEMnet/NAMESPACE | 18 SVEMnet-2.2.4/SVEMnet/NEWS | 3 SVEMnet-2.2.4/SVEMnet/R/SVEMnet-package.R | 42 - SVEMnet-2.2.4/SVEMnet/R/SVEMnet.R | 268 ++++++---- SVEMnet-2.2.4/SVEMnet/R/bigexp.R |only SVEMnet-2.2.4/SVEMnet/R/coef.R | 107 ++-- SVEMnet-2.2.4/SVEMnet/R/glmnet_with_cv.R | 4 SVEMnet-2.2.4/SVEMnet/R/globals.R | 1 SVEMnet-2.2.4/SVEMnet/R/lipid_screen.R |only SVEMnet-2.2.4/SVEMnet/R/plot.svemtest.R | 2 SVEMnet-2.2.4/SVEMnet/R/predict.svem_lasso.R | 171 ++++-- SVEMnet-2.2.4/SVEMnet/R/predict_with_ci.R |only SVEMnet-2.2.4/SVEMnet/R/svem_optimize_random.R |only SVEMnet-2.2.4/SVEMnet/R/svem_random_table_multi.R |only SVEMnet-2.2.4/SVEMnet/R/svem_significance_test.R | 225 ++++++--- SVEMnet-2.2.4/SVEMnet/R/svem_significance_test_parallel.R | 235 ++++++--- SVEMnet-2.2.4/SVEMnet/build/partial.rdb |binary SVEMnet-2.2.4/SVEMnet/build/vignette.rds |binary SVEMnet-2.2.4/SVEMnet/data |only SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.R | 140 +++++ SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 206 ++++++++ SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.html | 275 +++++++++-- SVEMnet-2.2.4/SVEMnet/man/SVEMnet-package.Rd | 33 + SVEMnet-2.2.4/SVEMnet/man/SVEMnet.Rd | 217 +++++--- SVEMnet-2.2.4/SVEMnet/man/bigexp_formula.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_model_matrix.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_prepare.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_terms.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_train.Rd |only SVEMnet-2.2.4/SVEMnet/man/coef.svem_model.Rd | 9 SVEMnet-2.2.4/SVEMnet/man/lipid_screen.Rd |only SVEMnet-2.2.4/SVEMnet/man/plot.svem_significance_test.Rd |only SVEMnet-2.2.4/SVEMnet/man/predict.svem_model.Rd | 54 +- SVEMnet-2.2.4/SVEMnet/man/predict_with_ci.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_optimize_random.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_random_table_multi.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_significance_test.Rd | 69 ++ SVEMnet-2.2.4/SVEMnet/man/svem_significance_test_parallel.Rd | 56 +- SVEMnet-2.2.4/SVEMnet/man/with_bigexp_contrasts.Rd |only SVEMnet-2.2.4/SVEMnet/tests |only SVEMnet-2.2.4/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 206 ++++++++ 46 files changed, 1862 insertions(+), 582 deletions(-)
Title: Partial Least Squares (PLS) Data Analysis Methods
Description: Different methods for PLS analysis of one or two data tables such as Tucker's Inter-Battery, NIPALS, SIMPLS, SIMPLS-CA, PLS Regression, and PLS Canonical Analysis. The main reference for this software is the awesome book (in French) 'La Regression PLS: Theorie et Pratique' by Michel Tenenhaus.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsdepot versions 0.2.0 dated 2023-03-13 and 0.3.0 dated 2025-09-26
plsdepot-0.2.0/plsdepot/NEWS |only plsdepot-0.3.0/plsdepot/DESCRIPTION | 36 ++++++++-------- plsdepot-0.3.0/plsdepot/MD5 | 43 +++++++++++-------- plsdepot-0.3.0/plsdepot/NAMESPACE | 54 +++++++++++++++--------- plsdepot-0.3.0/plsdepot/R/plot.interbat.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.nipals.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsca.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsreg1.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsreg2.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.simpls.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.simplsca.R | 3 - plsdepot-0.3.0/plsdepot/R/plsdepot-package.R |only plsdepot-0.3.0/plsdepot/R/print.interbat.R | 3 - plsdepot-0.3.0/plsdepot/R/print.nipals.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsca.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsreg1.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsreg2.R | 3 - plsdepot-0.3.0/plsdepot/R/print.simpls.R | 3 - plsdepot-0.3.0/plsdepot/R/print.simplsca.R | 3 - plsdepot-0.3.0/plsdepot/inst |only plsdepot-0.3.0/plsdepot/man/plsdepot-package.Rd |only plsdepot-0.3.0/plsdepot/tests |only 22 files changed, 92 insertions(+), 83 deletions(-)
Title: Inferring Causal Network from Mixed Observational Data Using a
Directed Acyclic Graph
Description: Learning a mixed directed acyclic graph based on both continuous and categorical data.
Author: Wujuan Zhong [aut, cre],
Li Dong [aut],
Quefeng Li [aut],
Xiaojing Zheng [aut]
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>
Diff between mDAG versions 1.2.2 dated 2019-08-20 and 1.2.3 dated 2025-09-26
DESCRIPTION | 28 ++++++++++++++++++++++------ MD5 | 10 +++++----- man/mDAG.Rd | 15 ++++++++++++--- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ 6 files changed, 44 insertions(+), 16 deletions(-)
Title: Fast Algorithm for Penalized Quantile Regression
Description: Implements an efficient algorithm for fitting the entire regularization path of quantile regression models with elastic-net penalties using a generalized coordinate descent scheme. The framework also supports SCAD and MCP penalties. It is designed for high-dimensional datasets and emphasizes numerical accuracy and computational efficiency. This package implements the algorithms proposed in Tang, Q., Zhang, Y., & Wang, B. (2022) <https://openreview.net/pdf?id=RvwMTDYTOb>.
Author: Qian Tang [aut, cre],
Yikai Zhang [aut],
Boxiang Wang [aut]
Maintainer: Qian Tang <qian-tang@uiowa.edu>
Diff between hdqr versions 1.0.1 dated 2025-02-12 and 1.0.2 dated 2025-09-26
DESCRIPTION | 10 +++++----- MD5 | 41 +++++++++++++++++++++-------------------- R/cv.nc.hdqr-methods.R | 36 ++++++++++++++++++------------------ R/cv.nc.hdqr.R | 2 +- R/nc.hdqr-methods.R | 36 ++++++++++++++++++------------------ R/nc.hdqr.R | 2 +- R/qr-methods.R | 36 ++++++++++++++++++------------------ R/qr.R | 12 ++++++------ inst/CITATION |only inst/doc/hdqr-vignette.Rmd | 8 ++++++-- inst/doc/hdqr-vignette.html | 10 +++++++--- man/coef.cv.nc.hdqr.Rd | 18 +++++++++--------- man/coef.hdqr.Rd | 22 +++++++++++----------- man/coef.nc.hdqr.Rd | 22 +++++++++++----------- man/cv.nc.hdqr.Rd | 2 +- man/hdqr.Rd | 14 +++++++------- man/nc.hdqr.Rd | 2 +- man/predict.cv.nc.hdqr.Rd | 18 +++++++++--------- man/predict.hdqr.Rd | 14 +++++++------- man/predict.nc.hdqr.Rd | 14 +++++++------- src/lqr_hd.f90 | 7 +++---- vignettes/hdqr-vignette.Rmd | 8 ++++++-- 22 files changed, 173 insertions(+), 161 deletions(-)
Title: Generalized Promotion Time Cure Model with Bayesian Shrinkage
Priors
Description: Generalized promotion time cure model (GPTCM) via Bayesian hierarchical modeling for multiscale data integration (Zhao et al. (2025) <doi:10.48550/arXiv.2509.01001>). The Bayesian GPTCMs are applicable for both low- and high-dimensional data.
Author: Zhi Zhao [aut, cre]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between GPTCM versions 1.1.1 dated 2025-09-16 and 1.1.2 dated 2025-09-26
GPTCM-1.1.1/GPTCM/man/mcmc.Rd |only GPTCM-1.1.2/GPTCM/DESCRIPTION | 6 - GPTCM-1.1.2/GPTCM/MD5 | 60 ++++++------- GPTCM-1.1.2/GPTCM/NEWS.md | 24 ++++- GPTCM-1.1.2/GPTCM/R/GPTCM.R | 5 - GPTCM-1.1.2/GPTCM/R/RcppExports.R | 54 ++++++------ GPTCM-1.1.2/GPTCM/R/plotBrier.R | 25 +++-- GPTCM-1.1.2/GPTCM/R/plotCoeff.R | 5 - GPTCM-1.1.2/GPTCM/R/plotMCMC.R | 3 GPTCM-1.1.2/GPTCM/R/predict.GPTCM.R | 2 GPTCM-1.1.2/GPTCM/R/simData.R | 61 ++++++++----- GPTCM-1.1.2/GPTCM/README.md | 17 +-- GPTCM-1.1.2/GPTCM/configure | 18 ++-- GPTCM-1.1.2/GPTCM/configure.ac | 12 +- GPTCM-1.1.2/GPTCM/inst/CITATION | 5 - GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.R | 31 +++++++ GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.Rmd | 33 +++++++ GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.html | 18 ++-- GPTCM-1.1.2/GPTCM/man/GPTCM.Rd | 6 + GPTCM-1.1.2/GPTCM/man/figures/cran_betas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_brier.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_etas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_gammas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_km.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_zetas.png |binary GPTCM-1.1.2/GPTCM/man/run_mcmc.Rd |only GPTCM-1.1.2/GPTCM/src/BVS.cpp | 114 ++++++++++++++------------ GPTCM-1.1.2/GPTCM/src/BVS.h | 13 ++ GPTCM-1.1.2/GPTCM/src/drive.cpp | 62 +++++++------- GPTCM-1.1.2/GPTCM/src/eval_func.cpp | 4 GPTCM-1.1.2/GPTCM/src/eval_func.h | 4 GPTCM-1.1.2/GPTCM/vignettes/GPTCM.Rmd | 33 +++++++ 32 files changed, 382 insertions(+), 233 deletions(-)
Title: Shrinkage for Effect Estimation
Description: Computes shrinkage estimators for regression problems. Selects penalty parameter by minimizing bias and variance in the effect estimate, where bias and variance are estimated from the posterior predictive distribution. See Keller and Rice (2017) <doi:10.1093/aje/kwx225> for more details.
Author: Kayleigh Keller [aut, cre]
Maintainer: Kayleigh Keller <kayleigh.keller@colostate.edu>
Diff between eshrink versions 0.1.2 dated 2020-09-09 and 0.2.0 dated 2025-09-26
DESCRIPTION | 18 +++++++++--------- MD5 | 28 ++++++++++++++-------------- R/eshrink.R | 1 - R/functions_bayes.R | 2 +- R/functions_ci.R | 4 ++-- R/functions_lasso.R | 2 +- R/functions_ridge.R | 12 ++++++------ man/check_CIbound.Rd | 2 +- man/eshrink-package.Rd | 1 - man/estRidge.Rd | 2 +- man/festRidge.Rd | 2 +- man/mseRidge.Rd | 2 +- man/samplePosterior.Rd | 2 +- man/simLASSO.Rd | 2 +- man/vcovfestRidge.Rd | 2 +- 15 files changed, 40 insertions(+), 42 deletions(-)
Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar K. V. [aut],
Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
This is a re-admission after prior archival of version 1.5.2 dated 2020-09-30
Diff between EpiILM versions 1.5.2 dated 2020-09-30 and 1.5.3 dated 2025-09-26
EpiILM-1.5.2/EpiILM/tests/EpiILM.network.Rout.save |only EpiILM-1.5.2/EpiILM/tests/EpiILM.spatial.Rout.save |only EpiILM-1.5.3/EpiILM/DESCRIPTION | 24 - EpiILM-1.5.3/EpiILM/MD5 | 38 - EpiILM-1.5.3/EpiILM/build/partial.rdb |binary EpiILM-1.5.3/EpiILM/build/vignette.rds |binary EpiILM-1.5.3/EpiILM/inst/doc/Predict.R | 320 +++++++------- EpiILM-1.5.3/EpiILM/inst/doc/Predict.Rnw | 460 ++++++++++----------- EpiILM-1.5.3/EpiILM/inst/doc/Predict.pdf |binary EpiILM-1.5.3/EpiILM/man/EpiILM-package.Rd | 95 ++-- EpiILM-1.5.3/EpiILM/man/as.epidata.Rd | 38 - EpiILM-1.5.3/EpiILM/man/epiBR0.Rd | 201 ++++----- EpiILM-1.5.3/EpiILM/man/epidata.Rd | 366 ++++++++-------- EpiILM-1.5.3/EpiILM/man/epidic.Rd | 138 +++--- EpiILM-1.5.3/EpiILM/man/epilike.Rd | 188 ++++---- EpiILM-1.5.3/EpiILM/man/epimcmc.Rd | 370 ++++++++-------- EpiILM-1.5.3/EpiILM/man/plot.epimcmc.Rd | 100 ++-- EpiILM-1.5.3/EpiILM/man/pred.epi.Rd | 248 +++++------ EpiILM-1.5.3/EpiILM/tests/EpiILM.network.R | 115 ++--- EpiILM-1.5.3/EpiILM/tests/EpiILM.spatial.R | 101 ++-- EpiILM-1.5.3/EpiILM/vignettes/Predict.Rnw | 460 ++++++++++----------- 21 files changed, 1679 insertions(+), 1583 deletions(-)
Title: Parallel and Memory-Efficient Ecological Diversity Metrics
Description: Computes alpha and beta diversity metrics using concurrent 'C' threads.
Metrics include 'UniFrac', Faith's phylogenetic diversity, Bray-Curtis
dissimilarity, Shannon diversity index, and many others.
Also parses newick trees into 'phylo' objects and rarefies feature tables.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between ecodive versions 2.0.0 dated 2025-09-21 and 2.1.0 dated 2025-09-26
DESCRIPTION | 8 ++-- MD5 | 48 ++++++++++++++-------------- NEWS.md | 16 +++++++++ R/alpha_div.r | 55 ++++++++++++++++++++++----------- R/beta_div.r | 68 +++++++++++++++++++++++------------------ R/documentation.r | 10 ++++-- R/utils.r | 3 + R/validate.r | 23 ++++++------- README.md | 13 ++++++- inst/doc/bdiv.Rmd | 4 +- inst/doc/bdiv.html | 6 +-- inst/doc/benchmark.Rmd | 14 ++++---- inst/doc/benchmark.html | 14 ++++---- man/adiv_functions.Rd | 18 +++++++--- man/alpha_div.Rd | 66 ++++++++++++++++++++++++++++++++------- man/bdiv_functions.Rd | 58 +++++++++++++++++++--------------- man/beta_div.Rd | 46 +++++++++++++++++++++++++-- man/documentation.Rd | 10 ++++-- src/beta_div.c | 7 ++++ src/unifrac.c | 45 +++++++++++++++------------ tests/testthat/test-beta_div.r | 24 ++++++++++++++ tests/testthat/test-methods.r | 2 - tests/testthat/test-validate.r | 25 ++++++++++++--- vignettes/bdiv.Rmd | 4 +- vignettes/benchmark.Rmd | 14 ++++---- 25 files changed, 405 insertions(+), 196 deletions(-)
Title: Causal Effect Random Forest of Interaction Trees
Description: Fits a Causal Effect Random Forest of Interaction Tress (CERFIT) which is a modification of the Random Forest algorithm where each split is chosen to maximize subgroup treatment heterogeneity. Doing this allows it to estimate the individualized treatment effect for each observation in either randomized controlled trial (RCT) or observational data. For more information see L. Li, R. A. Levine, and J. Fan (2022) <doi:10.1002/sta4.457>.
Author: Justin Thorp [aut, cre],
Luo Li [aut],
Juanjuan Fan [aut]
Maintainer: Justin Thorp <jjtthorp@gmail.com>
Diff between CERFIT versions 0.1.0 dated 2022-06-01 and 0.1.1 dated 2025-09-26
DESCRIPTION | 12 ++--- MD5 | 20 ++++---- NAMESPACE | 42 +++++++++--------- R/CERFIT.R | 8 ++- R/RcppExports.R | 14 +++--- R/growTree.R | 20 ++++---- R/ordinalize.R | 50 ++++++++++----------- README.md | 128 +++++++++++++++++++++++++++---------------------------- man/CERFIT.Rd | 3 + src/Makevars | 1 src/Makevars.win | 1 11 files changed, 152 insertions(+), 147 deletions(-)
Title: Bayesian Marginal Effects for 'brms' Models
Description: Calculate Bayesian marginal effects, average marginal effects, and marginal coefficients (also called population averaged coefficients) for models fit using the 'brms' package including fixed effects, mixed effects, and location scale models. These are based on marginal predictions that integrate out random effects if necessary (see for example <doi:10.1186/s12874-015-0046-6> and <doi:10.1111/biom.12707>).
Author: Joshua F. Wiley [aut, cre] ,
Donald Hedeker [aut]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between brmsmargins versions 0.2.0 dated 2022-05-18 and 0.2.1 dated 2025-09-26
DESCRIPTION | 13 MD5 | 124 NEWS.md | 67 R/RcppExports.R | 236 R/assert.R | 314 R/averageposterior.R | 74 R/builders.R | 209 R/imp-brms.R | 60 R/marginalcoef.R | 195 R/margins.R | 145 R/prediction.R | 430 - R/rimplementation.R | 110 R/utils.R | 703 - README.md | 364 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/fixed-effects-marginaleffects.Rmd | 1122 +-- inst/doc/fixed-effects-marginaleffects.html | 4874 ++++++------- inst/doc/location-scale-marginaleffects.Rmd | 854 +- inst/doc/location-scale-marginaleffects.html | 4439 ++++++------ inst/doc/mixed-effects-marginaleffects.Rmd | 306 inst/doc/mixed-effects-marginaleffects.html | 6745 +++++++++---------- man/assertall.Rd | 18 man/brmsmargins.Rd | 31 man/bsummary.Rd | 30 man/builders.Rd | 23 man/dot-averagePosterior.Rd | 2 man/dot-extractlink.Rd | 6 man/dot-links.Rd | 15 man/dot-percent.Rd | 2 man/integratemvn.Rd | 4 man/integratere.Rd | 4 man/is.random.Rd | 4 man/marginalcoef.Rd | 24 man/prediction.Rd | 29 man/tab2mat.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 6 src/integratemvn.cpp | 17 src/integratemvn.h | 2 src/integratere.cpp | 30 src/lmcpp.cpp | 15 tests/testthat.R | 12 tests/testthat/test-bsummary.R | 118 tests/testthat/test-builders.R | 32 tests/testthat/test-dot-checktab.R | 22 tests/testthat/test-dot-links.R | 144 tests/testthat/test-dot-percent.R | 98 tests/testthat/test-fixedeffects-bernoulli-margins.R | 120 tests/testthat/test-fixedeffects-beta-margins.R | 140 tests/testthat/test-fixedeffects-gamma-margins.R | 154 tests/testthat/test-integratemvn.R | 90 tests/testthat/test-marginalcoef-mixedlogit.R | 130 tests/testthat/test-marginalcoef-mixedpoisson.R | 126 tests/testthat/test-predict-mixedlogit.R | 342 tests/testthat/test-predict-mixedlogtrans.R | 230 tests/testthat/test-predict-mixedpoisson.R | 222 tests/testthat/test-rowbootmeans.R | 16 tests/testthat/test-tab2mat.R | 10 vignettes/fixed-effects-marginaleffects.Rmd | 1122 +-- vignettes/location-scale-marginaleffects.Rmd | 854 +- vignettes/mixed-effects-marginaleffects.Rmd | 306 63 files changed, 13045 insertions(+), 12897 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-03 3.0.3
2018-01-25 3.0.2
2016-01-09 3.0.1
2015-07-27 3.0.0
Title: Clinical Trial Simulator
Description: Simulate phase II and/or phase III clinical trials. It supports various types of endpoints and adaptive strategies. Tools for carrying out graphical testing procedure and combination test under group sequential design are also provided.
Author: Han Zhang [cre, aut]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between TrialSimulator versions 1.0.0 dated 2025-09-03 and 1.3.0 dated 2025-09-26
TrialSimulator-1.0.0/TrialSimulator/R/Arm.R |only TrialSimulator-1.0.0/TrialSimulator/R/Controller.R |only TrialSimulator-1.0.0/TrialSimulator/R/Endpoint.R |only TrialSimulator-1.0.0/TrialSimulator/R/Listener.R |only TrialSimulator-1.0.0/TrialSimulator/R/Trial.R |only TrialSimulator-1.0.0/TrialSimulator/man/default_action.Rd |only TrialSimulator-1.3.0/TrialSimulator/DESCRIPTION | 6 TrialSimulator-1.3.0/TrialSimulator/MD5 | 209 ++++------ TrialSimulator-1.3.0/TrialSimulator/NEWS.md | 26 + TrialSimulator-1.3.0/TrialSimulator/R/Arms.R | 55 +- TrialSimulator-1.3.0/TrialSimulator/R/Controllers.R | 54 +- TrialSimulator-1.3.0/TrialSimulator/R/CorrelatedPfsAndOs3.R | 34 + TrialSimulator-1.3.0/TrialSimulator/R/CorrelatedPfsAndOs4.R | 43 +- TrialSimulator-1.3.0/TrialSimulator/R/DynamicRNGFunction.R | 41 + TrialSimulator-1.3.0/TrialSimulator/R/Endpoints.R | 115 ++++- TrialSimulator-1.3.0/TrialSimulator/R/EnrollmentCountCondition.R | 15 TrialSimulator-1.3.0/TrialSimulator/R/Listeners.R | 28 + TrialSimulator-1.3.0/TrialSimulator/R/Milestones.R | 69 ++- TrialSimulator-1.3.0/TrialSimulator/R/PiecewiseConstantExponentialRNG.R | 34 + TrialSimulator-1.3.0/TrialSimulator/R/StaggeredRecruiter.R | 25 - TrialSimulator-1.3.0/TrialSimulator/R/Trials.R | 206 +++++++-- TrialSimulator-1.3.0/TrialSimulator/R/arm.R |only TrialSimulator-1.3.0/TrialSimulator/R/calendarTime.R | 17 TrialSimulator-1.3.0/TrialSimulator/R/controller.R |only TrialSimulator-1.3.0/TrialSimulator/R/default_action.R | 12 TrialSimulator-1.3.0/TrialSimulator/R/doNothing.R | 31 + TrialSimulator-1.3.0/TrialSimulator/R/endpoint.R |only TrialSimulator-1.3.0/TrialSimulator/R/enrollment.R | 43 +- TrialSimulator-1.3.0/TrialSimulator/R/eventNumber.R | 24 - TrialSimulator-1.3.0/TrialSimulator/R/fitCoxph.R | 24 - TrialSimulator-1.3.0/TrialSimulator/R/fitFarringtonManning.R | 8 TrialSimulator-1.3.0/TrialSimulator/R/fitLinear.R | 8 TrialSimulator-1.3.0/TrialSimulator/R/fitLogistic.R | 6 TrialSimulator-1.3.0/TrialSimulator/R/fitLogrank.R | 14 TrialSimulator-1.3.0/TrialSimulator/R/listener.R |only TrialSimulator-1.3.0/TrialSimulator/R/milestone.R | 33 + TrialSimulator-1.3.0/TrialSimulator/R/rconst.R | 12 TrialSimulator-1.3.0/TrialSimulator/R/solveMixtureExponentialDistribution.R | 13 TrialSimulator-1.3.0/TrialSimulator/R/solveThreeStateModel.R | 13 TrialSimulator-1.3.0/TrialSimulator/R/summarizeMilestoneTime.R | 16 TrialSimulator-1.3.0/TrialSimulator/R/summarizeTable.R | 9 TrialSimulator-1.3.0/TrialSimulator/R/trial.R |only TrialSimulator-1.3.0/TrialSimulator/R/weibullDropout.R | 11 TrialSimulator-1.3.0/TrialSimulator/README.md | 15 TrialSimulator-1.3.0/TrialSimulator/build/vignette.rds |binary TrialSimulator-1.3.0/TrialSimulator/inst/doc/actionFunctions.Rmd | 60 +- TrialSimulator-1.3.0/TrialSimulator/inst/doc/actionFunctions.html | 113 ++--- TrialSimulator-1.3.0/TrialSimulator/inst/doc/adaptiveDesign.R | 18 TrialSimulator-1.3.0/TrialSimulator/inst/doc/adaptiveDesign.Rmd | 22 - 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TrialSimulator-1.3.0/TrialSimulator/inst/doc/responseAdaptive.html | 23 - TrialSimulator-1.3.0/TrialSimulator/inst/doc/simulatePfsAndOs.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/inst/doc/simulatePfsAndOs.html | 9 TrialSimulator-1.3.0/TrialSimulator/inst/doc/wrappers.html | 5 TrialSimulator-1.3.0/TrialSimulator/man/Arms.Rd | 78 +++ TrialSimulator-1.3.0/TrialSimulator/man/Controllers.Rd | 51 +- TrialSimulator-1.3.0/TrialSimulator/man/CorrelatedPfsAndOs3.Rd | 32 + TrialSimulator-1.3.0/TrialSimulator/man/CorrelatedPfsAndOs4.Rd | 41 + TrialSimulator-1.3.0/TrialSimulator/man/DynamicRNGFunction.Rd | 39 + TrialSimulator-1.3.0/TrialSimulator/man/Endpoints.Rd | 137 +++++- TrialSimulator-1.3.0/TrialSimulator/man/Listeners.Rd | 47 ++ TrialSimulator-1.3.0/TrialSimulator/man/Milestones.Rd | 22 - TrialSimulator-1.3.0/TrialSimulator/man/PiecewiseConstantExponentialRNG.Rd | 33 + TrialSimulator-1.3.0/TrialSimulator/man/StaggeredRecruiter.Rd | 27 - TrialSimulator-1.3.0/TrialSimulator/man/Trials.Rd | 177 ++++++-- TrialSimulator-1.3.0/TrialSimulator/man/arm.Rd | 21 - 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More information about TrialSimulator at CRAN
Permanent link
Title: Precision Agriculture Computational Utilities
Description: Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.
Author: dos Santos Caio [aut, cre],
Miguez Fernando [aut]
Maintainer: dos Santos Caio <clsantos@iastate.edu>
Diff between pacu versions 0.1.63 dated 2025-05-29 and 0.1.72 dated 2025-09-26
DESCRIPTION | 6 MD5 | 45 - NAMESPACE | 4 R/get_rgb.R | 35 R/merge.R |only R/pacu_internal.R | 18 R/plot.R | 82 +- R/print.R | 39 R/trial.R | 279 ++++--- R/yield.R | 16 build/vignette.rds |binary inst/doc/pacu.html | 730 +++++++++--------- inst/doc/pacu_faq.R | 44 - inst/doc/pacu_faq.html | 816 ++++++++++---------- inst/doc/pacu_sat.R | 226 ++--- inst/doc/pacu_sat.html | 1204 +++++++++++++++--------------- inst/doc/pacu_weather.R | 68 - inst/doc/pacu_weather.html | 898 +++++++++++----------- inst/doc/pacu_ym.R | 314 +++---- inst/doc/pacu_ym.html | 1784 ++++++++++++++++++++++----------------------- man/pa_get_rgb.Rd | 12 man/pa_merge.Rd |only man/pa_print.Rd | 3 man/pa_trial.Rd |only man/pa_yield.Rd | 2 25 files changed, 3398 insertions(+), 3227 deletions(-)
Title: Meta-Analytic Effect Size Calculation for Pre-Post Designs with
Correlation Imputation
Description: Tools for the calculation of effect sizes (standardised mean difference) and mean difference in pre-post controlled studies, including robust imputation of missing variances (standard deviation of changes) and correlations (Pearson correlation coefficient). The main function 'metacor_dual()' implements several methods for imputing missing standard deviation of changes or Pearson correlation coefficient, and generates transparent imputation reports. Designed for meta-analyses with incomplete summary statistics. For details on the methods, see Higgins et al. (2023) and Fu et al. (2013).
Author: Iker J. Bautista [aut, cre],
Saul M. Rodriguez [ctb]
Maintainer: Iker J. Bautista <ikerugr@gmail.com>
Diff between metacor versions 1.1.2 dated 2025-07-28 and 1.2.0 dated 2025-09-26
DESCRIPTION | 24 - MD5 | 6 R/metacor_dual.R | 1025 ++++++++++++++++++++++----------------------- inst/doc/introduccion.html | 40 + 4 files changed, 549 insertions(+), 546 deletions(-)
Title: Irish Grid Reference Utilities
Description: Convert between Irish grid references and Irish Grid coordinates. Irish grid
references can also be converted to or from an 'sf' object in any coordinate reference
system. Precisions from 1 m to 100 km including 2 km (tetrads) are supported, as are
datasets with mixed precision. Conversion to 'sf' polygons is precision-aware.
Author: John Kennedy [aut, cre, cph] ,
Digital Nature [fnd]
Maintainer: John Kennedy <john@digitalnature.ie>
Diff between igr versions 1.0.0 dated 2025-01-07 and 1.0.1 dated 2025-09-26
DESCRIPTION | 15 +++-- MD5 | 28 +++++------ NEWS.md | 5 + R/st_irishgridrefs.R | 7 +- R/utils.R | 6 +- README.md | 4 + build/vignette.rds |binary inst/doc/igr.R | 55 ++++++--------------- inst/doc/igr.Rmd | 57 +++++++--------------- inst/doc/igr.html | 66 +++++++++----------------- man/figures/README-example-igr-points-1.png |binary man/figures/README-example-igr-polygons-1.png |binary man/st_irishgridrefs.Rd | 2 tests/testthat/test-st_irishgridrefs.R | 8 +++ vignettes/igr.Rmd | 57 +++++++--------------- 15 files changed, 124 insertions(+), 186 deletions(-)
Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel [aut, cre] ,
Jonathan Gilligan [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.5 dated 2025-03-27 and 0.1.6 dated 2025-09-25
ChangeLog | 9 ++ DESCRIPTION | 14 ++- MD5 | 20 ++--- README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 7 + inst/doc/tintHtmlIntro.html | 38 +++++++--- inst/doc/tintPdfIntro.pdf |binary inst/rmarkdown/templates/tintBook/resources/auto |only inst/rmarkdown/templates/tintBook/resources/tintBook-template.tex | 2 inst/rmarkdown/templates/tintPdf/resources/auto |only inst/rmarkdown/templates/tintPdf/resources/tintPdf-template.tex | 2 12 files changed, 68 insertions(+), 26 deletions(-)
Title: Seasonal to Decadal Verification
Description: An advanced version of package 's2dverification'. Intended for
seasonal to decadal (s2d) climate forecast verification, but also applicable
to other types of forecasts or general climate analysis. This package is
specifically designed for comparing experimental and observational datasets.
It provides functionality for data retrieval, post-processing, skill score
computation against observations, and visualization. Compared to
's2dverification', 's2dv' is more compatible with the package 'startR', able
to use multiple cores for computation and handle multi-dimensional arrays
with a higher flexibility. The Climate Data Operators (CDO) version used in
development is 1.9.8. Implements methods described in Wilks (2011)
<doi:10.1016/B978-0-12-385022-5.00008-7>, DelSole and Tippett
(2016) <doi:10.1175/MWR-D-15-0218.1>, Kharin et al. (2012)
<doi:10.1029/2012GL052647>, Doblas-Reyes et al. (2003)
<doi:10.1007/s00382-003-0350-4>.
Author: BSC-CNS [aut, cph],
An-Chi Ho [aut],
Nuria Perez-Zanon [aut],
Roberto Bilbao [ctb],
Josep Cos [ctb],
Carlos Delgado [ctb],
Llorenc Lledo [ctb],
Andrea Manrique [ctb],
Deborah Verfaillie [ctb],
Eva Rifa [ctb],
Victoria Agudetse [ctb],
Nadia Milders [c [...truncated...]
Maintainer: Ariadna Batalla <ariadna.batalla@bsc.es>
This is a re-admission after prior archival of version 2.1.0 dated 2024-10-13
Diff between s2dv versions 2.1.0 dated 2024-10-13 and 2.2.0 dated 2025-09-25
DESCRIPTION | 34 ++-- MD5 | 279 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 16 +- R/ACC.R | 52 +++--- R/AbsBiasSS.R | 10 - R/AnimateMap.R | 48 ++---- R/Ano.R | 20 +- R/Ano_CrossValid.R | 18 +- R/Bias.R | 10 - R/BrierScore.R | 26 +-- R/CDORemap.R | 271 +++++++++++++++++------------------ R/CRPS.R | 6 R/CRPSS.R | 10 - R/Clim.R | 21 +- R/Cluster.R | 58 +++---- R/ColorBar.R | 11 - R/Composite.R | 76 ++++----- R/ConfigApplyMatchingEntries.R | 43 +++-- R/ConfigEditDefinition.R | 42 ++--- R/ConfigEditEntry.R | 58 +++---- R/ConfigFileOpen.R | 46 +++--- R/ConfigShowSimilarEntries.R | 40 ++--- R/ConfigShowTable.R | 38 ++-- R/Consist_Trend.R | 50 +++--- R/Corr.R | 46 +++--- R/EOF.R | 42 ++--- R/Eno.R | 12 - R/EuroAtlanticTC.R | 13 - R/Filter.R | 30 +-- R/GetProbs.R | 22 +- R/Histo2Hindcast.R | 43 ++--- R/InsertDim.R | 6 R/LeapYear.R | 8 - R/Load.R | 291 +++++++++++++++++--------------------- R/LoadSampleData.R |only R/MSE.R | 36 ++-- R/MSSS.R | 22 +- R/MeanDims.R | 11 - R/NAO.R | 36 ++-- R/Persistence.R | 32 ++-- R/Plot2VarsVsLTime.R | 73 +++++---- R/PlotACC.R | 58 +++---- R/PlotAno.R | 31 ++-- R/PlotBoxWhisker.R | 69 +++------ R/PlotClim.R | 17 +- R/PlotEquiMap.R | 38 +--- R/PlotLayout.R | 41 +---- R/PlotMatrix.R | 8 - R/PlotSection.R | 12 + R/PlotStereoMap.R | 15 + R/PlotVsLTime.R | 55 +++---- R/ProbBins.R | 16 -- R/ProjectField.R | 52 +++--- R/REOF.R | 41 ++--- R/RMS.R | 40 ++--- R/RMSSS.R | 99 ++++++------ R/ROCSS.R | 22 +- R/RPS.R | 86 +++++++---- R/RPSS.R | 192 ++++++++++++++++--------- R/RandomWalkTest.R | 13 + R/RatioPredictableComponents.R | 6 R/RatioRMS.R | 71 ++++----- R/RatioSDRMS.R | 24 +-- R/Regression.R | 16 +- R/Reorder.R | 21 +- R/Season.R | 21 +- R/Smoothing.R | 27 +-- R/Spectrum.R | 30 +-- R/SprErr.R | 10 - R/Spread.R | 74 ++++----- R/StatSeasAtlHurr.R | 18 +- R/ToyModel.R | 91 ++++------- R/Trend.R | 8 - R/UltimateBrier.R | 31 +--- R/Utils.R | 57 ------- R/clim.palette.R | 17 +- build |only data/sampleDepthData.RData |binary data/sampleMap.RData |binary data/sampleTimeSeries.RData |binary man/ACC.Rd | 26 +-- man/AnimateMap.Rd | 43 +---- man/Ano.Rd | 8 - man/Ano_CrossValid.Rd | 12 - man/BrierScore.Rd | 2 man/CDORemap.Rd | 60 ++++--- man/Clim.Rd | 11 - man/Cluster.Rd | 6 man/ColorBar.Rd | 3 man/Composite.Rd | 10 - man/ConfigApplyMatchingEntries.Rd | 13 - man/ConfigEditDefinition.Rd | 12 - man/ConfigEditEntry.Rd | 19 +- man/ConfigFileOpen.Rd | 12 - man/ConfigShowSimilarEntries.Rd | 12 - man/ConfigShowTable.Rd | 10 - man/Consist_Trend.Rd | 18 +- man/Corr.Rd | 12 - man/EOF.Rd | 19 +- man/Eno.Rd | 2 man/Filter.Rd | 16 +- man/GetProbs.Rd | 6 man/Histo2Hindcast.Rd | 25 +-- man/Load.Rd | 65 ++------ man/LoadSampleData.Rd |only man/MSE.Rd | 6 man/MSSS.Rd | 2 man/MeanDims.Rd | 1 man/NAO.Rd | 6 man/Persistence.Rd | 2 man/Plot2VarsVsLTime.Rd | 29 ++- man/PlotACC.Rd | 28 +-- man/PlotAno.Rd | 9 - man/PlotBoxWhisker.Rd | 34 ---- man/PlotClim.Rd | 9 - man/PlotEquiMap.Rd | 34 ---- man/PlotLayout.Rd | 35 ---- man/PlotMatrix.Rd | 3 man/PlotSection.Rd | 6 man/PlotStereoMap.Rd | 5 man/PlotVsLTime.Rd | 21 +- man/ProbBins.Rd | 8 - man/ProjectField.Rd | 39 ++--- man/REOF.Rd | 18 +- man/RMS.Rd | 6 man/RMSSS.Rd | 39 ++--- man/RPS.Rd | 17 +- man/RPSS.Rd | 36 +++- man/RatioRMS.Rd | 23 +-- man/RatioSDRMS.Rd | 10 - man/Regression.Rd | 2 man/Reorder.Rd | 21 +- man/Season.Rd | 1 man/Smoothing.Rd | 9 - man/Spectrum.Rd | 16 +- man/Spread.Rd | 44 ++--- man/ToyModel.Rd | 41 +---- man/Trend.Rd | 2 man/UltimateBrier.Rd | 15 - man/clim.palette.Rd | 5 man/s2dv-package.Rd | 4 142 files changed, 2165 insertions(+), 2277 deletions(-)
Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) <doi:10.1086/676622> to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) <doi:10.1007/BF00275224>, bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices. Further details can be found in Torices & Muñoz-Pajares <doi:10.3732/apps.1400104>.
Author: R. Torices [aut],
A. J. Munoz-Pajares [aut, cre]
Maintainer: A. J. Munoz-Pajares <ajesusmp@ugr.es>
This is a re-admission after prior archival of version 1.3.1 dated 2017-06-02
Diff between PHENIX versions 1.3.1 dated 2017-06-02 and 1.3.2 dated 2025-09-25
PHENIX-1.3.1/PHENIX/NEWS |only PHENIX-1.3.2/PHENIX/DESCRIPTION | 22 +++++++++++++++------- PHENIX-1.3.2/PHENIX/MD5 | 7 +++---- PHENIX-1.3.2/PHENIX/inst/CITATION | 14 +++++--------- PHENIX-1.3.2/PHENIX/man/cor.par.Rd | 1 - 5 files changed, 23 insertions(+), 21 deletions(-)
Title: Computer Modern Font for Use with Extrafont Package
Description: Computer Modern font with Paul Murrell's symbol extensions. Is is to be used with the **extrafont** package. When this font package is installed, the CM fonts will be available for PDF or Postscript output files; however, this will (probably) not make the font available for screen or bitmap output files.
Author: Winston Chang [aut],
Alexej Kryukov [aut],
Paul Murrell [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between fontcm versions 1.1 dated 2014-03-19 and 1.2 dated 2025-09-25
fontcm-1.1/fontcm/man/fontcm.Rd |only fontcm-1.2/fontcm/DESCRIPTION | 37 ++++++++++++++++++++++---------- fontcm-1.2/fontcm/MD5 | 21 ++++++++++++------ fontcm-1.2/fontcm/NAMESPACE | 2 - fontcm-1.2/fontcm/NEWS | 11 +++++++++ fontcm-1.2/fontcm/R/fontcm.r | 18 ++++++--------- fontcm-1.2/fontcm/README.md | 29 +++++++++++++++++++++++-- fontcm-1.2/fontcm/inst/CITATION |only fontcm-1.2/fontcm/man/fontcm-package.Rd |only fontcm-1.2/fontcm/tests |only 10 files changed, 88 insertions(+), 30 deletions(-)
Title: Chronological Bayesian Models Integrating Optically Stimulated
Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and C-14 age
estimates. Bayesian models are based on the following publications:
Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003>
and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This
includes, amongst others, data import, export, application of age
models and palaeodose model.
Author: Claire Christophe [aut],
Anne Philippe [aut, cre] ,
Sebastian Kreutzer [aut] ,
Guillaume Guerin [aut] ,
Frederik Harly Baumgarten [aut] ,
Nicolas Frerebeau [aut] ,
Universite Bordeaux Montaigne [cph, fnd],
CNRS [fnd],
LabEx Sciences archeologiques de [...truncated...]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between BayLum versions 0.3.2 dated 2024-06-16 and 0.3.3 dated 2025-09-25
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Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.5.3 dated 2025-08-28 and 0.5.4 dated 2025-09-25
siera-0.5.3/siera/inst/extdata/ARS_V1_Common_Safety_Displays.json |only siera-0.5.4/siera/DESCRIPTION | 10 siera-0.5.4/siera/MD5 | 59 siera-0.5.4/siera/NEWS.md | 6 siera-0.5.4/siera/R/ARS_example.R | 2 siera-0.5.4/siera/R/readARS.R | 1595 ++-------- siera-0.5.4/siera/README.md | 9 siera-0.5.4/siera/build/vignette.rds |binary siera-0.5.4/siera/inst/doc/ARD_script_structure.R |only siera-0.5.4/siera/inst/doc/ARD_script_structure.Rmd |only siera-0.5.4/siera/inst/doc/ARD_script_structure.html |only siera-0.5.4/siera/inst/doc/Getting_started.R | 56 siera-0.5.4/siera/inst/doc/Getting_started.Rmd | 113 siera-0.5.4/siera/inst/doc/Getting_started.html | 274 - siera-0.5.4/siera/inst/doc/apply-ARD.R |only siera-0.5.4/siera/inst/doc/apply-ARD.Rmd |only siera-0.5.4/siera/inst/doc/apply-ARD.html |only siera-0.5.4/siera/inst/doc/using-cards.R |only siera-0.5.4/siera/inst/doc/using-cards.Rmd |only siera-0.5.4/siera/inst/doc/using-cards.html |only siera-0.5.4/siera/inst/extdata/ADSL.csv | 510 +-- siera-0.5.4/siera/inst/extdata/ADVS.csv |only siera-0.5.4/siera/inst/extdata/ADZSDER.csv |only siera-0.5.4/siera/inst/extdata/Common_Safety_Displays_cards.xlsx |binary siera-0.5.4/siera/inst/extdata/cards_constructs.xlsx |binary siera-0.5.4/siera/inst/extdata/exampleARS_1.json |only siera-0.5.4/siera/inst/extdata/exampleARS_1a.json |only siera-0.5.4/siera/inst/extdata/exampleARS_2.json |only siera-0.5.4/siera/inst/extdata/exampleARS_2.xlsx |only siera-0.5.4/siera/inst/extdata/exampleARS_2a.xlsx |only siera-0.5.4/siera/inst/extdata/exampleARS_3.json |only siera-0.5.4/siera/inst/extdata/test_cards.json |only siera-0.5.4/siera/inst/script/ARD_Out14-1-1.R | 419 +- siera-0.5.4/siera/inst/script/ARD_Out14-3-1-1.R |only siera-0.5.4/siera/man/ARS_example.Rd | 2 siera-0.5.4/siera/man/readARS.Rd | 15 siera-0.5.4/siera/tests/testthat/test-ARD_script_example.R |only siera-0.5.4/siera/tests/testthat/test-ARS_example.R |only siera-0.5.4/siera/tests/testthat/test-readARS.R | 450 ++ siera-0.5.4/siera/vignettes/ARD_script_structure.Rmd |only siera-0.5.4/siera/vignettes/Getting_started.Rmd | 113 siera-0.5.4/siera/vignettes/apply-ARD.Rmd |only siera-0.5.4/siera/vignettes/using-cards.Rmd |only 43 files changed, 1585 insertions(+), 2048 deletions(-)
Title: Null Model Analysis for Ecological Networks
Description: Null models to analyse ecological networks (e.g. food webs,
flower-visitation networks, seed-dispersal networks) and detect resource
preferences or non-random interactions among network nodes. Tools are
provided to run null models, test for and plot preferences, plot and
analyse bipartite networks, and export null model results in a form
compatible with other network analysis packages. The underlying null model
was developed by Agusti et al. (2003) Molecular Ecology
<doi:10.1046/j.1365-294X.2003.02014.x> and the full application to
ecological networks by Vaughan et al. (2018) econullnetr: an R package
using null models to analyse the structure of ecological networks and
identify resource selection. Methods in Ecology & Evolution,
<doi:10.1111/2041-210X.12907>.
Author: Ian Vaughan [aut, cre]
Maintainer: Ian Vaughan <vaughanip@cardiff.ac.uk>
Diff between econullnetr versions 0.2.1 dated 2021-06-02 and 0.2.2 dated 2025-09-25
DESCRIPTION | 35 - MD5 | 54 +- NEWS.md | 5 R/WelshStreams_order.R | 2 R/bipartite_stats.R | 2 R/econullnetr.R | 3 R/generate_edgelist.R | 2 R/plot_bipartite.R | 18 R/plot_preferences.R | 2 R/test_interactions.R | 2 README.md | 1 build/vignette.rds |binary inst/CITATION | 33 - inst/doc/econullnetr-intro.R | 14 inst/doc/econullnetr-intro.Rmd | 2 inst/doc/econullnetr-intro.html | 916 +++++++++++++++++++++++++++++----------- man/WelshStreams.order.Rd | 2 man/econullnetr.Rd | 12 man/plot_bipartite.Rd | 14 tests/testthat/_snaps |only vignettes/econullnetr-intro.Rmd | 2 21 files changed, 801 insertions(+), 320 deletions(-)
Title: Flexible Cutoffs for Model Fit Evaluation in Covariance-Based
Structural Models
Description: A toolbox to derive flexible cutoffs for fit indices in
'Covariance-based Structural Equation Modeling' based on the paper by
'Niemand & Mai (2018)' <doi:10.1007/s11747-018-0602-9>. Flexible
cutoffs are an alternative to fixed cutoffs - rules-of-thumb -
regarding an appropriate cutoff for fit indices such as 'CFI' or
'SRMR'. It has been demonstrated that these flexible cutoffs perform
better than fixed cutoffs in grey areas where misspecification is not
easy to detect. The package provides an alternative to the tool at
<https://flexiblecutoffs.org> as it allows to tailor flexible cutoffs
to a given dataset and model, which is so far not available in the
tool. The package simulates fit indices based on a given dataset and
model and then estimates the flexible cutoffs. Some useful functions,
e.g., to determine the 'GoF-' or 'BoF-nature' of a fit index, are
provided. So far, additional options for a relative use (is a model
better than another?) are provided in an explorat [...truncated...]
Author: Thomas Niemand [aut, cre] ,
Robert Mai [ctb] ,
Nadine Schroeder [ctb] ,
Andreas Falke [ctb]
Maintainer: Thomas Niemand <thomas.niemand@gmail.com>
Diff between FCO versions 0.8.0 dated 2023-03-17 and 2.0.0 dated 2025-09-25
FCO-0.8.0/FCO/man/index_guess.Rd |only FCO-2.0.0/FCO/DESCRIPTION | 65 + FCO-2.0.0/FCO/MD5 | 65 + FCO-2.0.0/FCO/NAMESPACE | 15 FCO-2.0.0/FCO/NEWS.md | 14 FCO-2.0.0/FCO/R/check_std.R | 1 FCO-2.0.0/FCO/R/checker.R |only FCO-2.0.0/FCO/R/constr_mod.R | 1 FCO-2.0.0/FCO/R/flex_co2.R |only FCO-2.0.0/FCO/R/gen_fit.R | 4 FCO-2.0.0/FCO/R/gen_fit2.R |only FCO-2.0.0/FCO/R/gen_nnd.R |only FCO-2.0.0/FCO/R/generator.R | 11 FCO-2.0.0/FCO/R/get_cos.R |only FCO-2.0.0/FCO/R/get_free.R | 1 FCO-2.0.0/FCO/R/get_free_mod.R |only FCO-2.0.0/FCO/R/get_lvo.R |only FCO-2.0.0/FCO/R/globals.R |only FCO-2.0.0/FCO/R/hb_load.R | 1 FCO-2.0.0/FCO/R/index_guess.R | 3 FCO-2.0.0/FCO/R/merge_factors.R | 1 FCO-2.0.0/FCO/R/mini.generator.R |only FCO-2.0.0/FCO/R/mm.misspec.R |only FCO-2.0.0/FCO/R/model.builder.R |only FCO-2.0.0/FCO/R/plot_fit2.R |only FCO-2.0.0/FCO/R/pop_mod.R | 224 +++-- FCO-2.0.0/FCO/R/pop_mod_dv.R | 1 FCO-2.0.0/FCO/R/pop_mod_reg.R |only FCO-2.0.0/FCO/R/power.finder.R |only FCO-2.0.0/FCO/R/recommend.R | 62 + FCO-2.0.0/FCO/R/run_parallel.R |only FCO-2.0.0/FCO/R/rv.misspec.R |only FCO-2.0.0/FCO/R/sm.misspec.R |only FCO-2.0.0/FCO/README.md | 123 +-- FCO-2.0.0/FCO/build/partial.rdb |only FCO-2.0.0/FCO/build/vignette.rds |binary FCO-2.0.0/FCO/inst/doc/FCO.R | 363 ++++----- FCO-2.0.0/FCO/inst/doc/FCO.Rmd | 430 +++++------ FCO-2.0.0/FCO/inst/doc/FCO.html | 1503 ++++++++++++++------------------------- FCO-2.0.0/FCO/man/figures |only FCO-2.0.0/FCO/man/flex_co2.Rd |only FCO-2.0.0/FCO/man/gen_fit2.Rd |only FCO-2.0.0/FCO/man/plot_fit2.Rd |only FCO-2.0.0/FCO/man/pop_mod.Rd | 15 FCO-2.0.0/FCO/vignettes/FCO.Rmd | 430 +++++------ 45 files changed, 1533 insertions(+), 1800 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.10 dated 2025-09-24 and 0.0.11 dated 2025-09-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/gloss_example.R | 3 ++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: R Repository Data
Description: Retrieve metadata about packages from repositories to explore
package dependencies, links between help pages, aliases, package
availability on a given date, and other repository dependent outcome.
This metadata can be used to help package maintainers and users to
navigate changes on dependencies and with reproducibility.
Author: Lluis Revilla Sancho [aut, cre, cph]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between repo.data versions 0.1.4 dated 2025-09-15 and 0.1.5 dated 2025-09-25
DESCRIPTION | 6 - MD5 | 119 +++++++++++++++++------------------ NEWS.md | 5 + R/alias_utils.R | 9 ++ R/base_alias.R | 6 + R/base_help.R | 23 +++++- R/base_xrefs.R | 18 +++++ R/bioconductor.R | 16 ++++ R/cran_actions.R | 8 +- R/cran_alias.R | 4 + R/cran_archive.R | 30 +++++++- R/cran_comments.R | 9 ++ R/cran_doom.R | 6 + R/cran_help.R | 51 ++++++++++++--- R/cran_history.R | 12 +++ R/cran_maintainers.R | 4 + R/cran_snapshot.R | 16 ++-- R/cran_xrefs.R | 36 +++++++++- R/dependencies.R | 25 +++++-- R/package_date.R | 19 ++++- R/repos.R | 7 +- R/utils.R | 50 +++++++++----- R/versions.R |only README.md | 4 - inst/doc/repo.data.R | 36 +++++----- inst/doc/repo.data.Rmd | 37 +++++----- inst/doc/repo.data.html | 113 +++++++++++---------------------- man/base_alias.Rd | 3 man/base_help_cliques.Rd | 7 +- man/base_help_pages_not_linked.Rd | 5 + man/base_help_pages_wo_links.Rd | 2 man/base_links.Rd | 1 man/base_pages_links.Rd | 1 man/base_pkges_links.Rd | 1 man/base_targets_links.Rd | 1 man/bioc_cran_archived.Rd | 1 man/cran_actions.Rd | 1 man/cran_alias.Rd | 1 man/cran_archive.Rd | 11 ++- man/cran_comments.Rd | 1 man/cran_doom.Rd | 3 man/cran_help_cliques.Rd | 1 man/cran_help_pages_links_wo_deps.Rd | 1 man/cran_help_pages_not_linked.Rd | 11 ++- man/cran_help_pages_wo_links.Rd | 11 ++- man/cran_history.Rd | 1 man/cran_links.Rd | 1 man/cran_maintainers.Rd | 1 man/cran_pkges_links.Rd | 1 man/cran_snapshot.Rd | 1 man/duplicated_alias.Rd | 6 + man/package_date.Rd | 1 man/package_dependencies.Rd | 1 man/package_repos.Rd | 1 man/repos_dependencies.Rd | 1 man/update_dependencies.Rd | 3 tests/test-all.R | 7 +- tests/test-cran_doom.R | 3 tests/test-package_date.R | 3 tests/test-update_dependencies.R | 3 vignettes/repo.data.Rmd | 37 +++++----- 61 files changed, 525 insertions(+), 278 deletions(-)
Title: Creation of in-Text Summary Table
Description: Creation of tables of summary statistics or counts for clinical data (for 'TLFs').
These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report
(Word format) or a 'topline' presentation (PowerPoint format),
or as interactive table (with the 'DT' package) to an html document for clinical data review.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
This is a re-admission after prior archival of version 3.3.4 dated 2025-09-03
Diff between inTextSummaryTable versions 3.3.4 dated 2025-09-03 and 3.3.5 dated 2025-09-25
DESCRIPTION | 14 MD5 | 62 - inst/NEWS | 4 inst/doc/inTextSummaryTable-advanced.R | 14 inst/doc/inTextSummaryTable-advanced.Rmd | 14 inst/doc/inTextSummaryTable-advanced.html | 281 +------ inst/doc/inTextSummaryTable-aesthetics.R | 7 inst/doc/inTextSummaryTable-aesthetics.Rmd | 7 inst/doc/inTextSummaryTable-aesthetics.html | 104 +- inst/doc/inTextSummaryTable-createTables.R | 7 inst/doc/inTextSummaryTable-createTables.Rmd | 7 inst/doc/inTextSummaryTable-createTables.html | 236 ++---- inst/doc/inTextSummaryTable-exportTables.R | 13 inst/doc/inTextSummaryTable-exportTables.Rmd | 13 inst/doc/inTextSummaryTable-exportTables.html | 494 ++----------- inst/doc/inTextSummaryTable-introduction.R | 7 inst/doc/inTextSummaryTable-introduction.Rmd | 7 inst/doc/inTextSummaryTable-introduction.html | 88 +- inst/doc/inTextSummaryTable-standardTables.R | 7 inst/doc/inTextSummaryTable-standardTables.Rmd | 7 inst/doc/inTextSummaryTable-standardTables.html | 112 +- inst/doc/inTextSummaryTable-visualization.R | 14 inst/doc/inTextSummaryTable-visualization.Rmd | 14 inst/doc/inTextSummaryTable-visualization.html | 97 +- tests/testthat/test_computeSummaryStatisticsTable-colVar.R | 13 vignettes/inTextSummaryTable-advanced.Rmd | 14 vignettes/inTextSummaryTable-aesthetics.Rmd | 7 vignettes/inTextSummaryTable-createTables.Rmd | 7 vignettes/inTextSummaryTable-exportTables.Rmd | 13 vignettes/inTextSummaryTable-introduction.Rmd | 7 vignettes/inTextSummaryTable-standardTables.Rmd | 7 vignettes/inTextSummaryTable-visualization.Rmd | 14 32 files changed, 540 insertions(+), 1172 deletions(-)
More information about inTextSummaryTable at CRAN
Permanent link
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.2 dated 2025-09-11 and 1.3.3 dated 2025-09-25
fluxible-1.3.2/fluxible/R/flux_plot_exp.R |only fluxible-1.3.2/fluxible/R/flux_plot_lin.R |only fluxible-1.3.2/fluxible/R/flux_plot_quadratic.R |only fluxible-1.3.2/fluxible/man/flux_plot_exp.Rd |only fluxible-1.3.2/fluxible/man/flux_plot_lin.Rd |only fluxible-1.3.2/fluxible/man/flux_plot_quadratic.Rd |only fluxible-1.3.3/fluxible/DESCRIPTION | 8 fluxible-1.3.3/fluxible/MD5 | 54 fluxible-1.3.3/fluxible/NAMESPACE | 2 fluxible-1.3.3/fluxible/NEWS.md | 4 fluxible-1.3.3/fluxible/R/flux_calc.R | 8 fluxible-1.3.3/fluxible/R/flux_fortify.R |only fluxible-1.3.3/fluxible/R/flux_fortify_exp.R |only fluxible-1.3.3/fluxible/R/flux_fortify_lin.R |only fluxible-1.3.3/fluxible/R/flux_fortify_quadratic.R |only fluxible-1.3.3/fluxible/R/flux_plot.R | 224 fluxible-1.3.3/fluxible/R/flux_plot_longpdf.R | 1 fluxible-1.3.3/fluxible/R/flux_plot_pdf.R | 8 fluxible-1.3.3/fluxible/R/flux_print_plot.R | 2 fluxible-1.3.3/fluxible/inst/CITATION | 9 fluxible-1.3.3/fluxible/inst/doc/fluxible.html | 4 fluxible-1.3.3/fluxible/inst/doc/two-gases.html | 4 fluxible-1.3.3/fluxible/man/figures/README-short-example-1.png |binary fluxible-1.3.3/fluxible/man/flux_fortify.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_exp.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_lin.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_quadratic.Rd |only fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/longpdf-and-print.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-hm-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-zhao18-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-kappamax-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-quadratic-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/test-flux_plot.R | 11 35 files changed, 115 insertions(+), 17054 deletions(-)
Title: Single-Cell Meta-Path Based Omic Embedding
Description: Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via 'Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in 'scTenifoldNet'. See <doi:10.1093/bioinformatics/btaf483> for more details.
Author: Yuntong Hou [aut, cre] ,
Yan Zhong [aut, ctb] ,
Yeran Chen [ctb],
Youshi Chang [ctb],
Yongjian Yang [ctb] ,
Xinyue Zheng [ctb],
James Cai [ctb]
Maintainer: Yuntong Hou <houyt223@gmail.com>
Diff between scPOEM versions 0.1.2 dated 2025-08-28 and 0.1.3 dated 2025-09-25
DESCRIPTION | 23 ++++++++++++----------- MD5 | 4 ++-- inst/doc/scPOEM.pdf |binary 3 files changed, 14 insertions(+), 13 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Jonas Lindblad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 1.1.5 dated 2025-08-25 and 1.2.0 dated 2025-09-25
GaussSuppression-1.1.5/GaussSuppression/R/OutputFixRiskyIntervals.R |only GaussSuppression-1.1.5/GaussSuppression/R/OutputIntervalIteration.R |only GaussSuppression-1.1.5/GaussSuppression/R/RangeLimits.R |only GaussSuppression-1.1.5/GaussSuppression/man/RangeLimitsDefault.Rd |only GaussSuppression-1.1.5/GaussSuppression/man/RangeOutputFunction.Rd |only GaussSuppression-1.2.0/GaussSuppression/DESCRIPTION | 12 GaussSuppression-1.2.0/GaussSuppression/MD5 | 50 - GaussSuppression-1.2.0/GaussSuppression/NAMESPACE | 9 GaussSuppression-1.2.0/GaussSuppression/NEWS.md | 39 + GaussSuppression-1.2.0/GaussSuppression/R/FixRiskyIntervals.R | 76 +- GaussSuppression-1.2.0/GaussSuppression/R/GaussSuppressionFromData.R | 248 +++++-- GaussSuppression-1.2.0/GaussSuppression/R/GaussSuppression_with_intervals.R |only GaussSuppression-1.2.0/GaussSuppression/R/IntervalLimits.R |only GaussSuppression-1.2.0/GaussSuppression/R/Intervals.R | 16 GaussSuppression-1.2.0/GaussSuppression/R/MagnitudeRule.R | 68 ++ GaussSuppression-1.2.0/GaussSuppression/R/OutputFunction.R | 63 - GaussSuppression-1.2.0/GaussSuppression/R/PackageSpecs.R | 6 GaussSuppression-1.2.0/GaussSuppression/R/Primary.R | 18 GaussSuppression-1.2.0/GaussSuppression/R/SuppressLinkedTables.R | 7 GaussSuppression-1.2.0/GaussSuppression/R/gaussSuppression_linked.R | 103 +-- GaussSuppression-1.2.0/GaussSuppression/R/interval_suppression.R | 175 ++++- GaussSuppression-1.2.0/GaussSuppression/inst/doc/Linked_table_suppression.html | 338 +++++----- GaussSuppression-1.2.0/GaussSuppression/inst/doc/Small_count_frequency_table_suppression.html | 63 - GaussSuppression-1.2.0/GaussSuppression/man/FixRiskyIntervals.Rd | 4 GaussSuppression-1.2.0/GaussSuppression/man/GaussSuppressionFromData.Rd | 75 +- GaussSuppression-1.2.0/GaussSuppression/man/IntervalLimits.Rd |only GaussSuppression-1.2.0/GaussSuppression/man/MagnitudeRule.Rd | 11 GaussSuppression-1.2.0/GaussSuppression/man/PackageSpecs.Rd | 2 GaussSuppression-1.2.0/GaussSuppression/man/PrimaryDefault.Rd | 17 GaussSuppression-1.2.0/GaussSuppression/tests/testthat/test-FixRiskyIntervals.R | 44 + 30 files changed, 964 insertions(+), 480 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.8 dated 2025-08-25 and 0.3.1 dated 2025-09-25
autoslider.core-0.2.8/autoslider.core/tests/testthat/ft_0.docx |only autoslider.core-0.2.8/autoslider.core/tests/testthat/ft_1.docx |only autoslider.core-0.3.1/autoslider.core/DESCRIPTION | 14 +- autoslider.core-0.3.1/autoslider.core/MD5 | 63 ++++------ autoslider.core-0.3.1/autoslider.core/NAMESPACE | 1 autoslider.core-0.3.1/autoslider.core/NEWS.md | 12 + autoslider.core-0.3.1/autoslider.core/R/package.R | 2 autoslider.core-0.3.1/autoslider.core/R/to_slides.R | 17 +- autoslider.core-0.3.1/autoslider.core/inst/doc/adding_templates.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/autoslideR.html | 8 - autoslider.core-0.3.1/autoslider.core/inst/doc/generate_placeholder_slides.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.R | 13 ++ autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.Rmd | 15 ++ autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/use_LLM.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/using_formats.html | 4 autoslider.core-0.3.1/autoslider.core/man/figure_to_slide.Rd | 3 autoslider.core-0.3.1/autoslider.core/man/format_date.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_eg_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_lb_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_mean_general.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_vs_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_output.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_outputs.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_slides.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/null_report.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/save_outputs.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/slides_from_rds.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/table_to_slide.Rd | 3 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-ft_format.R | 2 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-func_wrapper.R | 2 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-toslide.R |only autoslider.core-0.3.1/autoslider.core/tests/testthat/test_ai.R | 2 autoslider.core-0.3.1/autoslider.core/vignettes/tlg_templates.Rmd | 15 ++ 34 files changed, 144 insertions(+), 70 deletions(-)
More information about autoslider.core at CRAN
Permanent link
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for estimating variants of hidden (latent) Markov models
(HMMs), mixture HMMs, and non-homogeneous HMMs (NHMMs) for social sequence
data and other categorical time series. Special cases include
feedback-augmented NHMMs, Markov models without latent layer, mixture
Markov models, and latent class models. The package supports models for one
or multiple subjects with one or multiple parallel sequences (channels).
External covariates can be added to explain cluster membership in mixture
models as well as initial, transition and emission probabilities in NHMMs.
The package provides functions for evaluating and comparing models, as well
as functions for visualizing of multichannel sequence data and HMMs. For
NHMMs, methods for computing average causal effects and marginal state and
emission probabilities are available. Models are estimated using maximum
likelihood via the EM algorithm or direct numerical maximization with
analytical gradients. Documentation is available via several v [...truncated...]
Author: Jouni Helske [aut, cre] ,
Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 2.0.0 dated 2025-05-16 and 2.1.0 dated 2025-09-25
DESCRIPTION | 16 +- MD5 | 191 +++++++++++++------------- NAMESPACE | 7 NEWS.md | 38 ++++- R/RcppExports.R | 20 +- R/bootstrap.R | 66 ++++++--- R/build_mnhmm.R | 5 R/build_nhmm.R | 6 R/check_build_arguments.R | 7 R/create_base_nhmm.R | 35 +++- R/em_dnm_mnhmm.R | 8 - R/em_dnm_nhmm.R | 8 - R/em_mnhmm.R | 8 - R/em_nhmm.R | 8 - R/estimate_mnhmm.R | 5 R/estimate_nhmm.R | 13 + R/fanhmm_leaves.R | 2 R/fill_time.R | 3 R/fit_mnhmm.R | 27 ++- R/fit_model.R | 8 - R/fit_nhmm.R | 29 ++- R/formulas.R | 3 R/forwardBackward.R | 4 R/get_marginals.R | 17 +- R/get_probs.R | 4 R/logLik.R | 6 R/model_matrix.R | 51 +++--- R/most_probable_cluster.R | 10 - R/mssplot-deprecated.R | 2 R/posterior_probs.R | 12 + R/predict.R | 29 ++- R/print.R | 9 - R/seqHMM-package.R | 2 R/simulate_mnhmm.R | 34 +++- R/simulate_nhmm.R | 39 +++-- R/ssp-deprecated.R | 2 R/ssplot-deprecated.R | 2 R/stacked_sequence_plot.R | 22 ++- R/summary.mhmm.R | 2 R/update.R | 36 +++- R/utilities.R | 24 +-- R/vcov.mhmm.R | 4 README.md | 2 data/leaves.rda |binary inst/doc/seqHMM.Rnw | 2 inst/doc/seqHMM.pdf |binary inst/doc/seqHMM_algorithms.Rnw | 4 inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.Rnw | 2 inst/doc/seqHMM_visualization.pdf |binary man/bootstrap.Rd | 13 + man/estimate_mnhmm.Rd | 8 + man/estimate_nhmm.Rd | 10 + man/fanhmm_leaves.Rd | 2 man/fit_model.Rd | 8 - man/logLik_hmm.Rd | 6 man/mssplot.Rd | 2 man/permute_states.Rd |only man/simulate_mnhmm.Rd | 16 +- man/simulate_nhmm.Rd | 16 +- man/ssp.Rd | 2 man/ssplot.Rd | 2 man/stacked_sequence_plot.Rd | 11 - man/update_nhmm.Rd | 7 man/vcov.mhmm.Rd | 4 src/EM_mnhmm.cpp | 154 +++++++++------------ src/EM_mnhmm.h | 27 +-- src/EM_nhmm.cpp | 163 +++++++++------------- src/EM_nhmm.h | 21 +- src/R_EM_fanhmm.cpp | 5 src/R_EM_mfanhmm.cpp | 5 src/R_EM_mnhmm.cpp | 5 src/R_EM_nhmm.cpp | 5 src/RcppExports.cpp | 48 ++++-- src/backward.h | 19 ++ src/cost_matrix.cpp | 37 +++-- src/fanhmm.cpp | 22 --- src/fanhmm.h | 4 src/forward.h | 41 +++++ src/mfanhmm.cpp | 24 +-- src/mfanhmm.h | 5 src/mnhmm.cpp | 242 ++++++++++++++++----------------- src/mnhmm.h | 39 ++--- src/nhmm.cpp | 203 ++++++++++++++------------- src/nhmm.h | 31 +--- src/pre2-log_EM.cpp | 4 src/softmax.cpp | 6 src/softmax.h | 1 tests/testthat/test-forward_backward.R | 9 - tests/testthat/test-get_probs.R | 6 tests/testthat/test-hidden_paths.R | 8 - tests/testthat/test-posterior_probs.R | 8 - tests/testthat/test-predict.R | 2 vignettes/seqHMM.Rnw | 2 vignettes/seqHMM_algorithms.Rnw | 4 vignettes/seqHMM_visualization.Rnw | 2 97 files changed, 1180 insertions(+), 913 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado [aut, cre] ,
Murilo Dantas Miranda [aut],
Andre Chalom [aut]
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.6.3 dated 2024-01-16 and 0.6.5 dated 2025-09-25
sads-0.6.3/sads/README.md |only sads-0.6.5/sads/DESCRIPTION | 26 sads-0.6.5/sads/MD5 | 47 - sads-0.6.5/sads/NEWS | 6 sads-0.6.5/sads/build/partial.rdb |binary sads-0.6.5/sads/build/vignette.rds |binary sads-0.6.5/sads/inst/doc/sads_intro.Rnw | 35 - sads-0.6.5/sads/inst/doc/sads_intro.pdf |binary sads-0.6.5/sads/man/ICtab.Rd | 2 sads-0.6.5/sads/man/fitrad-class.Rd | 18 sads-0.6.5/sads/man/fitsad-class.Rd | 18 sads-0.6.5/sads/man/fitsadC-class.Rd | 18 sads-0.6.5/sads/man/fitsadC.Rd | 2 sads-0.6.5/sads/vignettes/sads_intro-woven-Biomass-octave-plot.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Octaves-plot.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Plot-of-predicted-values.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Ploting-octaves.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Ploting-profiles.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Rad-plots.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-grasslands_coverpred_plot.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven-grasslands_hist_plot.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven-radplot1.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-radplots.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-rsads-bias-plots.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven.tex | 339 +++++++++- sads-0.6.5/sads/vignettes/sads_intro.Rnw | 35 - 27 files changed, 456 insertions(+), 90 deletions(-)
Title: Result Model Manager
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
Informatics programme. 'ResultModelManager' provides utility functions to allow package
maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Diff between ResultModelManager versions 0.6.0 dated 2025-09-18 and 0.6.1 dated 2025-09-25
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++--------------- NEWS.md | 7 +++++ R/ConnectionHandler.R | 3 +- R/DataMigrationManager.R | 3 +- R/PooledConnectionHandler.R | 2 - inst/doc/CreatingMigrations.pdf |binary inst/doc/PackageDesign.pdf |binary inst/doc/UploadFunctionality.pdf |binary inst/doc/UsingAnExportManager.pdf |binary inst/doc/UsingConnectionHandlers.pdf |binary inst/doc/UsingPythonUploads.pdf |binary inst/doc/UsingQueryNamespaces.pdf |binary man/ResultModelManager-package.Rd | 1 tests/testthat/setup.R | 23 +++++++++++-------- tests/testthat/test-DataMigrationManager.R | 1 tests/testthat/test-QueryNamespace.R | 18 ++++++++++----- tests/testthat/test-ResultExportManager.R | 4 --- 18 files changed, 60 insertions(+), 44 deletions(-)
More information about ResultModelManager at CRAN
Permanent link
Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving
specified levels to front, ordering by first appearance, reversing,
and randomly shuffling), and tools for modifying factor levels
(including collapsing rare levels into other, 'anonymising', and
manually 'recoding').
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between forcats versions 1.0.0 dated 2023-01-29 and 1.0.1 dated 2025-09-25
DESCRIPTION | 19 +- LICENSE | 2 MD5 | 78 +++++----- NEWS.md | 6 R/anon.R | 10 - R/collapse.R | 7 R/compat-obj-type.R | 30 ++-- R/compat-purrr.R | 15 +- R/compat-types-check.R | 236 +++++++++++++++++--------------- R/cross.R | 5 R/expand.R | 6 R/fct.R | 2 R/lump.R | 47 ++++-- R/lvls.R | 21 ++ R/other.R | 1 R/recode.R | 17 +- R/relabel.R | 10 - R/relevel.R | 6 R/reorder.R | 41 +++-- README.md | 33 ++-- build/vignette.rds |binary inst/doc/forcats.R | 32 ++-- inst/doc/forcats.Rmd | 36 ++-- inst/doc/forcats.html | 287 +++++++++++++++++++-------------------- man/fct_anon.Rd | 10 - man/fct_lump.Rd | 20 +- man/fct_relabel.Rd | 10 - man/fct_reorder.Rd | 2 man/figures/logo.png |binary man/forcats-package.Rd | 4 tests/testthat/_snaps/relabel.md | 2 tests/testthat/_snaps/reorder.md | 2 tests/testthat/test-collapse.R | 5 tests/testthat/test-cross.R | 24 ++- tests/testthat/test-fct.R | 4 tests/testthat/test-lump.R | 46 ++++-- tests/testthat/test-lvls.R | 26 +++ tests/testthat/test-recode.R | 5 tests/testthat/test-reorder.R | 34 +++- vignettes/forcats.Rmd | 36 ++-- 40 files changed, 682 insertions(+), 495 deletions(-)
Title: Circular Statistics
Description: Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
Author: Ulric Lund [aut],
Claudio Agostinelli [aut] ,
Hiroyoshi Arai [ctb],
Alessando Gagliardi [ctb],
Eduardo Garcia-Portugues [ctb, cre] ,
Dimitri Giunchi [ctb],
Jean-Olivier Irisson [ctb],
Matthew Pocernich [ctb],
Federico Rotolo [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between circular versions 0.5-1 dated 2024-08-29 and 0.5-2 dated 2025-09-25
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- R/cardioid.R | 2 +- inst/NEWS | 4 ++++ man/cardioid.Rd | 7 +++++++ 5 files changed, 24 insertions(+), 13 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.3.0 dated 2023-09-29 and 1.4.0 dated 2025-09-25
alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.R |only alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.Rmd |only alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.pdf |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.R |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.Rmd |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.pdf |only alakazam-1.3.0/alakazam/vignettes/Lineage-Vignette.Rmd |only alakazam-1.3.0/alakazam/vignettes/Topology-Vignette.Rmd |only alakazam-1.4.0/alakazam/DESCRIPTION | 28 alakazam-1.4.0/alakazam/MD5 | 112 alakazam-1.4.0/alakazam/NEWS.md | 37 alakazam-1.4.0/alakazam/R/Alakazam.R | 5 alakazam-1.4.0/alakazam/R/AminoAcids.R | 12 alakazam-1.4.0/alakazam/R/Classes.R | 12 alakazam-1.4.0/alakazam/R/Core.R | 4 alakazam-1.4.0/alakazam/R/Deprecated.R | 15 alakazam-1.4.0/alakazam/R/Diversity.R | 73 alakazam-1.4.0/alakazam/R/Gene.R | 1705 ++++++++------- alakazam-1.4.0/alakazam/R/Lineage.R | 30 alakazam-1.4.0/alakazam/R/Sequence.R | 14 alakazam-1.4.0/alakazam/R/Topology.R | 20 alakazam-1.4.0/alakazam/README.md | 8 alakazam-1.4.0/alakazam/build/partial.rdb |binary alakazam-1.4.0/alakazam/build/vignette.rds |binary alakazam-1.4.0/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.R | 6 alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.Rmd | 10 alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Fastq-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Files-Vignette.R | 6 alakazam-1.4.0/alakazam/inst/doc/Files-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.R | 8 alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.Rmd | 8 alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.pdf |binary alakazam-1.4.0/alakazam/man/AbundanceCurve-class.Rd | 2 alakazam-1.4.0/alakazam/man/ChangeoClone-class.Rd | 2 alakazam-1.4.0/alakazam/man/DiversityCurve-class.Rd | 6 alakazam-1.4.0/alakazam/man/MRCATest-class.Rd | 2 alakazam-1.4.0/alakazam/man/alakazam-package.Rd | 9 alakazam-1.4.0/alakazam/man/alakazam.Rd | 5 alakazam-1.4.0/alakazam/man/aminoAcidProperties.Rd | 2 alakazam-1.4.0/alakazam/man/buildPhylipLineage.Rd | 6 alakazam-1.4.0/alakazam/man/collapseDuplicates.Rd | 10 alakazam-1.4.0/alakazam/man/combineIgphyml.Rd | 4 alakazam-1.4.0/alakazam/man/countClones.Rd | 4 alakazam-1.4.0/alakazam/man/countGenes.Rd | 80 alakazam-1.4.0/alakazam/man/estimateAbundance.Rd | 4 alakazam-1.4.0/alakazam/man/getSegment.Rd | 72 alakazam-1.4.0/alakazam/man/gridPlot.Rd | 2 alakazam-1.4.0/alakazam/man/groupGenes.Rd | 94 alakazam-1.4.0/alakazam/man/makeChangeoClone.Rd | 6 alakazam-1.4.0/alakazam/man/nonsquareDist.Rd | 4 alakazam-1.4.0/alakazam/man/plotAbundanceCurve.Rd | 2 alakazam-1.4.0/alakazam/man/plotDiversityCurve.Rd | 2 alakazam-1.4.0/alakazam/man/plotDiversityTest.Rd | 2 alakazam-1.4.0/alakazam/man/rarefyDiversity.Rd | 3 alakazam-1.4.0/alakazam/man/readIgphyml.Rd | 4 alakazam-1.4.0/alakazam/man/sortGenes.Rd | 22 alakazam-1.4.0/alakazam/man/testDiversity.Rd | 7 alakazam-1.4.0/alakazam/vignettes/Diversity-Vignette.Rmd | 10 alakazam-1.4.0/alakazam/vignettes/GeneUsage-Vignette.Rmd | 8 61 files changed, 1417 insertions(+), 1070 deletions(-)
Title: Descriptive Statistics and Data Management Tools
Description: Extracts and summarizes metadata from data frames, including variable names, labels, types, and missing values. Computes compact descriptive statistics, frequency tables, and cross-tabulations to assist with efficient data exploration. Facilitates the identification of missing data patterns and structural issues in datasets. Designed to streamline initial data management and exploratory analysis workflows within 'R'.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.1.0 dated 2025-05-05 and 0.2.0 dated 2025-09-25
DESCRIPTION | 13 MD5 | 65 ++- NAMESPACE | 1 NEWS.md | 13 R/copy_clipboard.R | 280 +++++++-------- R/count_n.R | 585 ++++++++++++++++----------------- R/cramer_v.R | 72 ++-- R/cross_tab.R | 28 - R/freq.R | 39 -- R/label_from_names.R |only R/mean_n.R | 9 R/print_spicy.R | 129 +++---- R/spicy-package.R | 66 +-- R/sum_n.R | 9 R/varlist.R | 115 +++--- README.md | 191 +++++++++- inst |only man/count_n.Rd | 408 +++++++++++------------ man/figures/varlist_1.png |only man/figures/varlist_2.png |only man/freq.Rd | 20 - man/label_from_names.Rd |only man/mean_n.Rd | 8 man/print.spicy.Rd | 52 +- man/spicy-package.Rd | 2 man/sum_n.Rd | 8 tests/testthat/test-copy_clipboard.R | 162 ++++----- tests/testthat/test-count_n.R | 273 +++++++-------- tests/testthat/test-cramer_v.R | 54 +-- tests/testthat/test-cross_tab.R | 222 ++++++------ tests/testthat/test-freq.R | 246 ++++++------- tests/testthat/test-label_from_names.R |only tests/testthat/test-mean_n.R | 3 tests/testthat/test-print_spicy.R | 106 ++--- tests/testthat/test-sum_n.R | 3 tests/testthat/test-varlist.R | 81 ++-- 36 files changed, 1708 insertions(+), 1555 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.5.1 dated 2025-02-23 and 0.6.1 dated 2025-09-25
DESCRIPTION | 6 ++-- MD5 | 17 ++++++++----- NAMESPACE | 1 R/alloc_dmd.R |only R/data.R | 43 +++++++++++++++++++++++++++++++++ README.md | 7 +++-- data/alloc_data.rda |only inst/doc/get_started.html | 24 +++++++++--------- inst/doc/user_cases.html | 52 ++++++++++++++++++++-------------------- man/alloc_data.Rd |only man/alloc_dmd.Rd |only tests/testthat/test-alloc_dmd.R |only 12 files changed, 100 insertions(+), 50 deletions(-)
Title: Joint Estimation in Linear Quantile Regression
Description: Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
Author: Surya Tokdar [aut, cre],
Erika Cunningham [aut]
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between qrjoint versions 2.0-9 dated 2023-04-05 and 2.0-11 dated 2025-09-24
DESCRIPTION | 21 +++++++++++++++------ MD5 | 16 ++++++++-------- R/qrjoint.R | 6 +++--- man/qde.Rd | 4 ++-- man/qrjoint-internal.Rd | 2 +- man/qrjoint.Rd | 4 ++-- man/summary.qde.Rd | 2 +- man/summary.qrjoint.Rd | 2 +- src/qrjoint.c | 2 +- 9 files changed, 34 insertions(+), 25 deletions(-)
Title: Estimating Peer Effects Using Partial Network Data
Description: Implements IV-estimator and Bayesian estimator for linear-in-means Spatial Autoregressive (SAR) model (see LeSage, 1997 <doi:10.1177/016001769702000107>; Lee, 2004 <doi:10.1111/j.1468-0262.2004.00558.x>; Bramoullé et al., 2009 <doi:10.1016/j.jeconom.2008.12.021>), while assuming that only a partial information about the network structure is available. Examples are when the adjacency matrix is not fully observed or when only consistent estimation of the network formation model is available (see Boucher and Houndetoungan <doi:10.48550/arXiv.2509.08145>).
Author: Vincent Boucher [aut],
Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between PartialNetwork versions 1.1.0 dated 2025-05-08 and 1.1.1 dated 2025-09-24
PartialNetwork-1.1.0/PartialNetwork/README.md |only PartialNetwork-1.1.1/PartialNetwork/DESCRIPTION | 14 PartialNetwork-1.1.1/PartialNetwork/MD5 | 31 PartialNetwork-1.1.1/PartialNetwork/NEWS.md | 5 PartialNetwork-1.1.1/PartialNetwork/R/PartialNetwork.R | 4 PartialNetwork-1.1.1/PartialNetwork/R/simNetwork.R | 2 PartialNetwork-1.1.1/PartialNetwork/build/partial.rdb |binary PartialNetwork-1.1.1/PartialNetwork/build/vignette.rds |binary PartialNetwork-1.1.1/PartialNetwork/inst/doc/PartialNetwork_vignette.R | 72 - PartialNetwork-1.1.1/PartialNetwork/inst/doc/PartialNetwork_vignette.Rmd | 462 +++++----- PartialNetwork-1.1.1/PartialNetwork/inst/doc/PartialNetwork_vignette.pdf |binary PartialNetwork-1.1.1/PartialNetwork/man/PartialNetwork-package.Rd | 6 PartialNetwork-1.1.1/PartialNetwork/man/sim.network.Rd | 2 PartialNetwork-1.1.1/PartialNetwork/src/Makevars | 14 PartialNetwork-1.1.1/PartialNetwork/src/Makevars.win | 11 PartialNetwork-1.1.1/PartialNetwork/src/mlSAR.cpp | 2 PartialNetwork-1.1.1/PartialNetwork/vignettes/PartialNetwork_vignette.Rmd | 462 +++++----- 17 files changed, 536 insertions(+), 551 deletions(-)
More information about PartialNetwork at CRAN
Permanent link
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.3.1 dated 2025-07-31 and 4.3.2 dated 2025-09-24
OlinkAnalyze-4.3.1/OlinkAnalyze/tests/testthat/Rplots.pdf |only OlinkAnalyze-4.3.1/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-oid40770.svg |only OlinkAnalyze-4.3.1/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-oid40835.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/DESCRIPTION | 16 OlinkAnalyze-4.3.2/OlinkAnalyze/MD5 | 101 - OlinkAnalyze-4.3.2/OlinkAnalyze/NEWS.md | 7 OlinkAnalyze-4.3.2/OlinkAnalyze/R/Olink_heatmap.R | 51 OlinkAnalyze-4.3.2/OlinkAnalyze/R/Olink_theme.R | 117 + OlinkAnalyze-4.3.2/OlinkAnalyze/R/linear_mixed_model.R | 2 OlinkAnalyze-4.3.2/OlinkAnalyze/R/olink_bridgeability_plot.R | 606 +++--- OlinkAnalyze-4.3.2/OlinkAnalyze/R/olink_normalization.R | 4 OlinkAnalyze-4.3.2/OlinkAnalyze/R/utils.R |only OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/LOD.html | 2 OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/OutlierExclusion.html | 4 OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/Vignett.html | 4 OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/bridging_crossproduct.html | 2 OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/bridging_introduction.html | 108 - OlinkAnalyze-4.3.2/OlinkAnalyze/inst/doc/plate_randomizer.html | 14 OlinkAnalyze-4.3.2/OlinkAnalyze/man/is_testing.Rd |only OlinkAnalyze-4.3.2/OlinkAnalyze/man/set_plot_theme.Rd | 4 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot/boxplot-site-10prots.svg | 733 ++++--- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot/boxplot-site-2prots.svg | 311 +-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot/boxplot-time-and-site.svg | 959 +++++----- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot/boxplot-time-with-coloroption.svg | 550 +++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot/boxplot-time.svg | 550 +++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_plate_randomizer/randomized-data.svg | 669 +++--- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Volcano_plot/volcano-plot-with-coloroption.svg | 527 +++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Volcano_plot/volcano-plot.svg | 512 +++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/dist_plot/distribution-plot-col-by-treatment.svg | 488 +++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/dist_plot/distribution-plot.svg | 450 ++-- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/linear_mixed_model/lmer-plot-more-prots-than-space.svg | 191 + OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/linear_mixed_model/lmer-plot.svg | 762 ++++--- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/npxProcessing.md | 130 - OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-counts-oid40770.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-counts-oid40835.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-iqr-oid40770.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-iqr-oid40835.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-ks-oid40770.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-ks-oid40835.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-r2-oid40770.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot/bridgeable-plot-r2-oid40835.svg |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_qc_plot/qc-plot-with-coloroption.svg | 884 +++++---- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_qc_plot/qc-plot.svg | 869 ++++----- OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/data/refResults.RData |binary OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-Olink_boxplot.R | 21 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-Olink_heatmap.R | 9 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-Olink_plate_randomizer.R | 12 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-Volcano_plot.R | 2 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-dist_plot.R | 13 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-linear_mixed_model.R | 10 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-olink_Pathway_Heatmap.R | 3 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-olink_Pathway_Visualization.R | 2 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-olink_bridgeability_plot.R | 239 ++ OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 99 + OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-olink_qc_plot.R | 13 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test-pca_plot.R | 10 OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/test_Olink_wilcox.R | 17 58 files changed, 5948 insertions(+), 4153 deletions(-)
Title: Single Cell Oriented Reconstruction of PANDA Individual
Optimized Networks
Description: Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Author: Daniel Osorio [aut, cre] ,
Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between SCORPION versions 1.1.0 dated 2025-08-25 and 1.2.0 dated 2025-09-24
DESCRIPTION | 6 - MD5 | 24 ++-- R/buildKNN.R | 24 ++-- R/buildKNND.R | 47 +++++---- R/buildNN2.R | 11 +- R/makeSuperCells.R | 63 ++++++------ R/normalizeNetwork.R | 53 +++++----- R/pcNet.R | 18 +-- R/prepResult.R | 12 +- R/runPANDA.R | 238 ++++++++++++++++++++++++------------------------- R/spreadNet.R | 7 - R/tanimotoSimilarity.R | 28 ++--- R/updateDiagonal.R | 8 - 13 files changed, 274 insertions(+), 265 deletions(-)
Title: Analyze High-Dimensional High-Throughput Dataset and Quality
Control Single-Cell RNA-Seq
Description: The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalizati [...truncated...]
Author: Yajing Hao [aut] ,
Shuyang Zhang [ctb] ,
Junhui Li [cre] ,
Guofeng Zhao [ctb],
Xiang-Dong Fu [cph, fnd]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ZetaSuite versions 1.0.1 dated 2022-05-24 and 1.0.2 dated 2025-09-24
DESCRIPTION | 29 LICENSE |only MD5 | 50 - NAMESPACE | 73 ++ R/EventCoverage.R | 59 + R/FDRcutoff.R | 64 + R/QC.R | 45 - R/SVM.R | 41 - R/Zeta.R | 35 - R/ZetaSuitSC.R | 36 - R/ZetaSuiteApp.R |only R/Zscore.R | 27 README.md |only build/vignette.rds |binary inst/doc/ZetaSuite.R | 250 +++++-- inst/doc/ZetaSuite.Rmd | 528 +++++++++++----- inst/doc/ZetaSuite.html | 1549 ++++++++++++++++++++++++++++++++---------------- inst/shiny |only man/EventCoverage.Rd | 51 + man/FDRcutoff.Rd | 56 + man/QC.Rd | 37 - man/SVM.Rd | 38 - man/Zeta.Rd | 34 - man/ZetaSuitSC.Rd | 30 man/ZetaSuiteApp.Rd |only man/Zscore.Rd | 28 vignettes/ZetaSuite.Rmd | 528 +++++++++++----- 27 files changed, 2502 insertions(+), 1086 deletions(-)
Title: Semiparametric Bayesian Density Estimation
Description: Offers Bayesian semiparametric density estimation
and tail-index estimation for heavy tailed data, by
using a parametric, tail-respecting transformation
of the data to the unit interval and then modeling
the transformed data with a purely nonparametric
logistic Gaussian process density prior. Based on
Tokdar et al. (2022) <doi:10.1080/01621459.2022.2104727>.
Author: Surya Tokdar [aut, cre]
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between sbde versions 1.0-1 dated 2024-02-16 and 1.0-2 dated 2025-09-24
DESCRIPTION | 16 ++++++++++------ MD5 | 4 ++-- man/summary.sbde.Rd | 2 +- 3 files changed, 13 insertions(+), 9 deletions(-)
Title: Spectral Transmittance and Spectral Reflectance Data
Description: Spectral 'transmittance' data for frequently used filters and
similar materials. Plastic sheets and films; photography filters;
theatrical gels; machine-vision filters; various types of window glass;
optical glass and some laboratory plastics and glassware. Spectral
reflectance data for frequently encountered materials. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
T. Matthew Robson [ctb] ,
Ricardo Hernandez [ctb] ,
Tania de la Rosa [ctb] ,
Riitta Tegelberg [ctb] ,
Andreas Albert [ctb] ,
SCHOTT AG [ctb] ,
Midwest Optical Systems, Inc. [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyFilters versions 0.6.0 dated 2024-02-27 and 0.6.1 dated 2025-09-24
DESCRIPTION | 19 - MD5 | 68 ++-- NEWS.md | 9 R/bpi-visqueen.r | 2 R/filters-mspct.r | 60 +++ R/glass-windows.r | 4 R/photography-filters.r | 4 R/refractive-index-mspct.r | 2 R/schott.r | 2 R/screens-nets-mspct.R | 6 R/screens_nets.R | 2 README.md | 40 +- build/partial.rdb |binary build/vignette.rds |binary data/filters-UVIVIF-mspct.rda |only data/filters-mspct.rda |binary data/materials-mspct.rda |binary data/metals-mspct.rda |binary data/refractive-index.rda |binary data/screens-nets-mspct.rda |binary inst/doc/r4p-introduction.Rmd | 158 +++++----- inst/doc/r4p-introduction.html | 159 +++++----- inst/doc/user-guide.R | 10 inst/doc/user-guide.Rmd | 14 inst/doc/user-guide.html | 618 +++++++++++++++++++++-------------------- man/bpi_visqueen_filters.Rd | 2 man/filters.mspct.Rd | 17 - man/filters_UVIVIF.mspct.Rd |only man/glass_windows.Rd | 5 man/photography_filters.Rd | 6 man/refractive_index.mspct.Rd | 2 man/schott_filters.Rd | 2 man/screens_nets.mspct.Rd | 6 man/screens_nets_suppliers.Rd | 2 vignettes/r4p-introduction.Rmd | 158 +++++----- vignettes/user-guide.Rmd | 14 36 files changed, 778 insertions(+), 613 deletions(-)
More information about photobiologyFilters at CRAN
Permanent link
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Ben Wilson [aut, cre],
Matei Zaharia [aut],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Ben Wilson <benjamin.wilson@databricks.com>
Diff between mlflow versions 3.3.2 dated 2025-09-04 and 3.4.0 dated 2025-09-24
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Tree Guided Machine Learning for Personalized Prediction and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.1.0 dated 2025-05-02 and 0.2.0 dated 2025-09-24
tgml-0.1.0/tgml/R/03a.rootML_auc.R |only tgml-0.1.0/tgml/R/04a.growTree_auc.R |only tgml-0.1.0/tgml/R/05a.combML_auc.R |only tgml-0.2.0/tgml/DESCRIPTION | 10 +++++----- tgml-0.2.0/tgml/MD5 | 9 +++------ tgml-0.2.0/tgml/R/tgml.R | 31 +++++++++++-------------------- tgml-0.2.0/tgml/man/tgml.Rd | 12 ++++++------ 7 files changed, 25 insertions(+), 37 deletions(-)
Title: Fitting Shared Atoms Nested Models via Markov Chains Monte Carlo
Description: Estimate Bayesian nested mixture models via Markov Chain Monte Carlo methods. Specifically, the package implements the common atoms model (Denti et al., 2023), and hybrid finite-infinite models.
All models use Gaussian mixtures with a normal-inverse-gamma prior distribution on the parameters. Additional functions are provided to help analyzing the results of the fitting procedure.
References:
Denti, Camerlenghi, Guindani, Mira (2023) <doi:10.1080/01621459.2021.1933499>,
D’Angelo, Denti (2024) <doi:10.1214/24-BA1458>.
Author: Francesco Denti [aut, cre] ,
Laura D'Angelo [aut, cph]
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Diff between SANple versions 0.1.1 dated 2024-06-02 and 0.2.0 dated 2025-09-24
SANple-0.1.1/SANple/R/mcmc_CAM_burn.R |only SANple-0.1.1/SANple/R/mcmc_fSAN_burn.R |only SANple-0.1.1/SANple/R/mcmc_fSAN_sparse_burn.R |only SANple-0.1.1/SANple/R/mcmc_fiSAN_burn.R |only SANple-0.1.1/SANple/R/mcmc_fiSAN_sparse_burn.R |only SANple-0.1.1/SANple/man/sample_fSAN_sparsemix.Rd |only SANple-0.1.1/SANple/man/sample_fiSAN_sparsemix.Rd |only SANple-0.1.1/SANple/src/common_functions.cpp |only SANple-0.1.1/SANple/src/common_functions.h |only SANple-0.1.1/SANple/src/funs_cam.cpp |only SANple-0.1.1/SANple/src/funs_cam.h |only SANple-0.1.1/SANple/src/funs_fcam.cpp |only SANple-0.1.1/SANple/src/funs_fcam.h |only SANple-0.1.1/SANple/src/funs_ficam.cpp |only SANple-0.1.1/SANple/src/funs_ficam.h |only SANple-0.1.1/SANple/src/funs_overcam.cpp |only SANple-0.1.1/SANple/src/funs_overcam.h |only SANple-0.1.1/SANple/src/funs_san.cpp |only SANple-0.1.1/SANple/src/funs_san.h |only SANple-0.1.1/SANple/src/main_cam_burn.cpp |only SANple-0.1.1/SANple/src/main_fcam_burn.cpp |only SANple-0.1.1/SANple/src/main_ficam_burn.cpp |only SANple-0.1.1/SANple/src/main_overcam_burn.cpp |only SANple-0.1.1/SANple/src/main_overficam_burn.cpp |only SANple-0.2.0/SANple/DESCRIPTION | 22 ++-- SANple-0.2.0/SANple/MD5 | 75 +++++-------- SANple-0.2.0/SANple/NAMESPACE | 3 SANple-0.2.0/SANple/NEWS.md | 6 + SANple-0.2.0/SANple/R/RcppExports.R | 20 +-- SANple-0.2.0/SANple/R/estimate_clusters.R | 5 SANple-0.2.0/SANple/R/mcmc_CAM.R |only SANple-0.2.0/SANple/R/mcmc_fSAN.R |only SANple-0.2.0/SANple/R/mcmc_fiSAN.R |only SANple-0.2.0/SANple/R/plot.R | 4 SANple-0.2.0/SANple/R/print.R | 5 SANple-0.2.0/SANple/R/traceplot.R | 3 SANple-0.2.0/SANple/README.md | 43 ++------ SANple-0.2.0/SANple/build/partial.rdb |binary SANple-0.2.0/SANple/man/SANple-package.Rd | 2 SANple-0.2.0/SANple/man/estimate_clusters.Rd | 4 SANple-0.2.0/SANple/man/figures/sanple_draft.png |only SANple-0.2.0/SANple/man/plot.SANmcmc.Rd | 4 SANple-0.2.0/SANple/man/print.SANmcmc.Rd | 4 SANple-0.2.0/SANple/man/sample_CAM.Rd | 2 SANple-0.2.0/SANple/man/sample_fSAN.Rd | 70 ++++--------- SANple-0.2.0/SANple/man/sample_fiSAN.Rd | 53 ++++----- SANple-0.2.0/SANple/man/traceplot.Rd | 2 SANple-0.2.0/SANple/src/AUX_FUNS.cpp |only SANple-0.2.0/SANple/src/AUX_FUNS.h |only SANple-0.2.0/SANple/src/CAM_FUNS.cpp |only SANple-0.2.0/SANple/src/CAM_FUNS.h |only SANple-0.2.0/SANple/src/CAM_MAIN.cpp |only SANple-0.2.0/SANple/src/FISAN_MAIN.cpp |only SANple-0.2.0/SANple/src/FSAN_MAIN.cpp |only SANple-0.2.0/SANple/src/RcppExports.cpp | 118 ++-------------------- SANple-0.2.0/SANple/src/SAN_FUNS.cpp |only SANple-0.2.0/SANple/src/SAN_FUNS.h |only 57 files changed, 150 insertions(+), 295 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.30 dated 2025-02-02 and 0.4.32 dated 2025-09-24
DESCRIPTION | 36 +- MD5 | 39 +- NAMESPACE | 1 NEWS.md | 10 R/read-cid-spectravue-csv.r | 49 -- R/read-oojaz-file.r | 61 ++- R/read-ooov-file.r |only R/read-ooss-file.r | 89 +++-- R/read-tuv-file.r | 5 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 26 - inst/doc/user-guide.Rmd | 33 +- inst/doc/user-guide.html | 672 ++++++++++++++++++++--------------------- inst/extdata/spectrum.OVIrrad |only man/read_cid_spectravue_csv.Rd | 54 +-- man/read_oo_jazirrad.Rd | 52 ++- man/read_oo_ovirrad.Rd |only man/read_oo_ssirrad.Rd | 59 ++- tests/testthat/test-oo.R | 4 vignettes/user-guide.Rmd | 33 +- 22 files changed, 650 insertions(+), 575 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Fitting Shared Atoms Nested Models via MCMC or Variational Bayes
Description: An efficient tool for fitting nested mixture models based on a shared set of
atoms via Markov Chain Monte Carlo and variational inference algorithms.
Specifically, the package implements the common atoms model (Denti et al., 2023),
its finite version (similar to D'Angelo et al., 2023), and a hybrid finite-infinite
model (D'Angelo and Denti, 2024). All models implement univariate nested mixtures
with Gaussian kernels equipped with a normal-inverse gamma prior distribution
on the parameters. Additional functions are provided to help analyze the
results of the fitting procedure.
References:
Denti, Camerlenghi, Guindani, Mira (2023) <doi:10.1080/01621459.2021.1933499>,
D’Angelo, Canale, Yu, Guindani (2023) <doi:10.1111/biom.13626>,
D’Angelo, Denti (2024) <doi:10.1214/24-BA1458>.
Author: Francesco Denti [aut, cre, cph] ,
Laura D'Angelo [aut]
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Diff between sanba versions 0.0.2 dated 2025-07-31 and 0.0.3 dated 2025-09-24
DESCRIPTION | 8 +- MD5 | 18 +++--- NEWS.md | 4 + README.md | 6 +- build/partial.rdb |binary man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |binary man/figures/README-example2-1.png |binary man/figures/README-example2-2.png |binary src/CAM_FUNS.cpp | 102 +++++++++++++++++++------------------- 10 files changed, 71 insertions(+), 67 deletions(-)
Title: Likelihood-Based Intrinsic Dimension Estimators
Description: Provides functions to estimate the intrinsic dimension of a dataset
via likelihood-based approaches. Specifically, the package implements the
'TWO-NN' and 'Gride' estimators and the 'Hidalgo' Bayesian mixture model.
In addition, the first reference contains an extended vignette on the usage of
the 'TWO-NN' and 'Hidalgo' models. References:
Denti (2023, <doi:10.18637/jss.v106.i09>);
Allegra et al. (2020, <doi:10.1038/s41598-020-72222-0>);
Denti et al. (2022, <doi:10.1038/s41598-022-20991-1>);
Facco et al. (2017, <doi:10.1038/s41598-017-11873-y>);
Santos-Fernandez et al. (2021, <doi:10.1038/s41598-022-20991-1>).
Author: Francesco Denti [aut, cre, cph] ,
Andrea Gilardi [aut]
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Diff between intRinsic versions 1.1.0 dated 2024-09-12 and 1.1.1 dated 2025-09-24
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NEWS.md | 5 +++++ README.md | 3 +-- build/partial.rdb |binary src/A_AUX.cpp | 2 +- src/B_FULLCOND.cpp | 2 +- 7 files changed, 21 insertions(+), 17 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.16 dated 2025-06-24 and 0.3.17 dated 2025-09-24
DESCRIPTION | 10 MD5 | 93 ++--- NAMESPACE | 360 +++++++++++----------- NEWS.md | 35 ++ R/autoplot-calibration-spct.R | 127 +++++-- R/autoplot-cps-spct.r | 141 ++++++-- R/autoplot-filter-spct.r | 468 +++++++++++++++++++---------- R/autoplot-generic-spct.R | 24 + R/autoplot-raw-spct.r | 145 ++++++-- R/autoplot-response-spct.r | 213 +++++++++---- R/autoplot-source-spct.r | 247 ++++++++++----- R/autoplot-waveband.R | 99 +++--- R/decoration.R | 32 + R/ggplot-methods.R | 428 ++++++++++++++++++-------- R/stat-label-peaks.R | 10 R/stat-peaks.R | 62 +-- R/stat-wb-column.R | 2 R/stat-wb-label.R | 18 + R/stat-wl-strip.R | 46 ++ R/utils-internal.R | 50 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.Rmd | 4 inst/doc/userguide-0-r4p-introduction.html | 12 inst/doc/userguide1-grammar.html | 35 +- inst/doc/userguide2-autoplot-methods.html | 97 +++--- man/apply_normalization.Rd | 36 +- man/autoplot.calibration_spct.Rd | 39 +- man/autoplot.cps_spct.Rd | 39 +- man/autoplot.filter_spct.Rd | 39 +- man/autoplot.generic_spct.Rd | 3 man/autoplot.object_spct.Rd | 56 +-- man/autoplot.raw_spct.Rd | 39 +- man/autoplot.reflector_spct.Rd | 39 +- man/autoplot.response_spct.Rd | 44 +- man/autoplot.source_spct.Rd | 47 +- man/autoplot.waveband.Rd | 47 +- man/figures/README-example0-1.png |binary man/figures/README-example1-1.png |binary man/ggplot.Rd | 180 ++++++++--- man/normalization_label.Rd |only man/set_annotations_default.Rd | 3 man/stat_label_peaks.Rd | 30 - man/stat_peaks.Rd | 75 ++-- man/stat_wb_column.Rd | 2 man/stat_wb_label.Rd | 4 man/stat_wl_strip.Rd | 10 vignettes/userguide-0-r4p-introduction.Rmd | 4 48 files changed, 2249 insertions(+), 1245 deletions(-)
Title: Data Science for Wind Energy
Description: Data science methods used in wind energy applications.
Current functionalities include creating a multi-dimensional power curve model,
performing power curve function comparison, covariate matching, and energy decomposition.
Relevant works for the developed functions are:
funGP() - Prakash et al. (2022) <doi:10.1080/00401706.2021.1905073>,
AMK() - Lee et al. (2015) <doi:10.1080/01621459.2014.977385>,
tempGP() - Prakash et al. (2022) <doi:10.1080/00401706.2022.2069158>,
ComparePCurve() - Ding et al. (2021) <doi:10.1016/j.renene.2021.02.136>,
deltaEnergy() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
syncSize() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
imptPower() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
All other functions - Ding (2019, ISBN:9780429956508).
Author: Nitesh Kumar [aut],
Abhinav Prakash [aut],
Yu Ding [aut, cre],
Effi Latiffianti [ctb, cph],
Ahmadreza Chokhachian [ctb, cph]
Maintainer: Yu Ding <yuding2007@gmail.com>
Diff between DSWE versions 1.8.2 dated 2024-02-17 and 1.8.3 dated 2025-09-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/MatchInternal2.cpp | 5 +++-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Dynamic Factor Models
Description: Efficient estimation of Dynamic Factor Models using the Expectation Maximization (EM) algorithm
or Two-Step (2S) estimation, supporting datasets with missing data. Factors are assumed to follow a stationary VAR
process of order p. The estimation options follow advances in the econometric literature: either running the Kalman
Filter and Smoother once with initial values from PCA - 2S estimation as in Doz, Giannone and Reichlin (2011)
<doi:10.1016/j.jeconom.2011.02.012> - or via iterated Kalman Filtering and Smoothing until EM convergence - following
Doz, Giannone and Reichlin (2012) <doi:10.1162/REST_a_00225> - or using the adapted EM algorithm of Banbura and
Modugno (2014) <doi:10.1002/jae.2306>, allowing arbitrary patterns of missing data. The implementation makes heavy
use of the 'Armadillo' 'C++' library and the 'collapse' package, providing for particularly speedy estimation.
A comprehensive set of methods supports interpretation and visualization of the model as [...truncated...]
Author: Sebastian Krantz [aut, cre],
Rytis Bagdziunas [aut],
Santtu Tikka [rev],
Eli Holmes [rev]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dfms versions 0.3.1 dated 2025-08-20 and 0.3.2 dated 2025-09-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/dynamic_factor_models.pdf |binary inst/doc/introduction.html | 31 ++++++++++++------------------- man/dfms-package.Rd | 24 ++++++++++++++++++++++++ src/KalmanFiltering.cpp | 4 ++-- 7 files changed, 52 insertions(+), 31 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] ,
Eva Cantagallo [aut],
William Anderson [aut],
Julien Peron [ctb],
Johan Verbeeck [ctb]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 3.3.3 dated 2025-07-24 and 3.3.4 dated 2025-09-24
BuyseTest-3.3.3/BuyseTest/inst/doc-paired/paired.synctex.gz |only BuyseTest-3.3.4/BuyseTest/DESCRIPTION | 8 BuyseTest-3.3.4/BuyseTest/MD5 | 371 - BuyseTest-3.3.4/BuyseTest/NAMESPACE | 198 BuyseTest-3.3.4/BuyseTest/NEWS | 612 +- BuyseTest-3.3.4/BuyseTest/R/0-onLoad.R | 22 BuyseTest-3.3.4/BuyseTest/R/1-setGeneric.R | 100 BuyseTest-3.3.4/BuyseTest/R/BuyseMultComp.R | 1036 ++-- BuyseTest-3.3.4/BuyseTest/R/BuyseTTEM.R | 1750 +++---- BuyseTest-3.3.4/BuyseTest/R/BuyseTest-Peron.R | 774 +-- BuyseTest-3.3.4/BuyseTest/R/BuyseTest-check.R | 1190 ++-- BuyseTest-3.3.4/BuyseTest/R/BuyseTest-inference.R | 1064 ++-- BuyseTest-3.3.4/BuyseTest/R/BuyseTest-initialization.R | 2034 ++++---- BuyseTest-3.3.4/BuyseTest/R/BuyseTest-package.R | 142 BuyseTest-3.3.4/BuyseTest/R/BuyseTest-print.R | 366 - BuyseTest-3.3.4/BuyseTest/R/BuyseTest.R | 1599 +++--- BuyseTest-3.3.4/BuyseTest/R/BuyseTest.options.R | 218 BuyseTest-3.3.4/BuyseTest/R/CasinoTest.R | 762 +-- BuyseTest-3.3.4/BuyseTest/R/PairScore.R | 108 BuyseTest-3.3.4/BuyseTest/R/RcppExports.R | 462 - BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower-model.tables.R | 338 - BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower-nobs.R | 96 BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower-print.R | 66 BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower-show.R | 64 BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower-summary.R | 346 - BuyseTest-3.3.4/BuyseTest/R/S4-BuysePower.R | 166 BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-coef.R | 716 +- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-confint.R | 2150 ++++---- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-get.R | 1740 +++---- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-model.tables.R | 558 +- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-nobs.R | 298 - BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-plot.R | 178 BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-print.R | 70 BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-sensitivity.R | 752 +-- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-show.R | 98 BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-summary.R | 952 +-- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest-update.R | 122 BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest.R | 620 +- BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest.options.R | 464 - BuyseTest-3.3.4/BuyseTest/R/S4-BuyseTest.vcov.R | 212 BuyseTest-3.3.4/BuyseTest/R/as.data.table.performance.R | 282 - BuyseTest-3.3.4/BuyseTest/R/auc.R | 792 +-- BuyseTest-3.3.4/BuyseTest/R/autoplot.S4BuyseTest.R | 342 - BuyseTest-3.3.4/BuyseTest/R/brier.R | 604 +- BuyseTest-3.3.4/BuyseTest/R/constStrata.R | 178 BuyseTest-3.3.4/BuyseTest/R/discreteRoot.R | 580 +- BuyseTest-3.3.4/BuyseTest/R/doc-data.R | 246 - BuyseTest-3.3.4/BuyseTest/R/efronlim.R | 242 BuyseTest-3.3.4/BuyseTest/R/iid.S3sensitivity.R | 50 BuyseTest-3.3.4/BuyseTest/R/iid.prodlim.R | 404 - BuyseTest-3.3.4/BuyseTest/R/mover.R | 242 BuyseTest-3.3.4/BuyseTest/R/normexp.R | 424 - BuyseTest-3.3.4/BuyseTest/R/performance.R | 2424 +++++----- BuyseTest-3.3.4/BuyseTest/R/performanceResample.R | 572 +- BuyseTest-3.3.4/BuyseTest/R/plot.S3sensitivity.R | 358 - BuyseTest-3.3.4/BuyseTest/R/powerBuyseTest.R | 1628 +++--- BuyseTest-3.3.4/BuyseTest/R/predict.logit.R | 564 +- BuyseTest-3.3.4/BuyseTest/R/rbind.performanceResample.R | 226 BuyseTest-3.3.4/BuyseTest/R/sim.simBuyseTest.R | 66 BuyseTest-3.3.4/BuyseTest/R/simBuyseTest.R | 1470 +++--- BuyseTest-3.3.4/BuyseTest/R/simCompetingRisks.R | 284 - BuyseTest-3.3.4/BuyseTest/R/summary.performance.R | 228 BuyseTest-3.3.4/BuyseTest/R/valid.R | 960 +-- BuyseTest-3.3.4/BuyseTest/build/vignette.rds |binary BuyseTest-3.3.4/BuyseTest/inst/CITATION | 116 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/bibliography.bib | 58 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired-compress.pdf |binary BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.R | 184 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.aux | 77 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.bbl | 38 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.blg | 94 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.fdb_latexmk | 566 +- BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.fls | 2119 ++------ BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.log | 2005 ++++---- BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.org | 1664 +++--- BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.out | 14 BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.pdf |binary BuyseTest-3.3.4/BuyseTest/inst/doc-paired/paired.tex | 1769 +++---- BuyseTest-3.3.4/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-3.3.4/BuyseTest/inst/doc/overview.pdf.asis | 1178 ++-- BuyseTest-3.3.4/BuyseTest/inst/doc/paired.pdf |binary BuyseTest-3.3.4/BuyseTest/inst/doc/paired.pdf.asis | 305 - BuyseTest-3.3.4/BuyseTest/inst/doc/wilcoxonTest.pdf |binary BuyseTest-3.3.4/BuyseTest/inst/doc/wilcoxonTest.pdf.asis | 210 BuyseTest-3.3.4/BuyseTest/inst/source |only BuyseTest-3.3.4/BuyseTest/man/BuyseMultComp.Rd | 224 BuyseTest-3.3.4/BuyseTest/man/BuyseTTEM.Rd | 158 BuyseTest-3.3.4/BuyseTest/man/BuyseTest-package.Rd | 166 BuyseTest-3.3.4/BuyseTest/man/BuyseTest.Rd | 650 +- BuyseTest-3.3.4/BuyseTest/man/BuyseTest.options-class.Rd | 32 BuyseTest-3.3.4/BuyseTest/man/BuyseTest.options-methods.Rd | 44 BuyseTest-3.3.4/BuyseTest/man/BuyseTest.options.Rd | 66 BuyseTest-3.3.4/BuyseTest/man/CasinoTest.Rd | 236 BuyseTest-3.3.4/BuyseTest/man/GPC_cpp.Rd | 380 - BuyseTest-3.3.4/BuyseTest/man/S4BuysePower-class.Rd | 34 BuyseTest-3.3.4/BuyseTest/man/S4BuysePower-model.tables.Rd | 94 BuyseTest-3.3.4/BuyseTest/man/S4BuysePower-nobs.Rd | 50 BuyseTest-3.3.4/BuyseTest/man/S4BuysePower-print.Rd | 58 BuyseTest-3.3.4/BuyseTest/man/S4BuysePower-summary.Rd | 114 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-class.Rd | 34 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-coef.Rd | 156 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-confint.Rd | 220 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-model.tables.Rd | 132 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-nobs.Rd | 66 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-plot.Rd | 136 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-print.Rd | 52 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-show.Rd | 72 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-summary.Rd | 268 - BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-update.Rd | 50 BuyseTest-3.3.4/BuyseTest/man/S4BuyseTest-vcov.Rd | 96 BuyseTest-3.3.4/BuyseTest/man/as.data.table.performance.Rd | 66 BuyseTest-3.3.4/BuyseTest/man/auc.Rd | 166 BuyseTest-3.3.4/BuyseTest/man/autoplot-S4BuyseTest.Rd | 82 BuyseTest-3.3.4/BuyseTest/man/brier.Rd | 90 BuyseTest-3.3.4/BuyseTest/man/calcIntegralSurv2_cpp.Rd | 94 BuyseTest-3.3.4/BuyseTest/man/coef.BuyseTestAuc.Rd | 38 BuyseTest-3.3.4/BuyseTest/man/coef.BuyseTestBrier.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/confint.BuyseTestAuc.Rd | 38 BuyseTest-3.3.4/BuyseTest/man/confint.BuyseTestBrier.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/constStrata.Rd | 122 BuyseTest-3.3.4/BuyseTest/man/data-CHARM.Rd | 66 BuyseTest-3.3.4/BuyseTest/man/data-EB.Rd | 58 BuyseTest-3.3.4/BuyseTest/man/data-prodige.Rd | 68 BuyseTest-3.3.4/BuyseTest/man/dot-calcIntegralCif_cpp.Rd | 98 BuyseTest-3.3.4/BuyseTest/man/dot-calcIntegralSurv_cpp.Rd | 84 BuyseTest-3.3.4/BuyseTest/man/dot-colCenter_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/dot-colCumSum_cpp.Rd | 36 BuyseTest-3.3.4/BuyseTest/man/dot-colMultiply_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/dot-colScale_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/dot-rowCenter_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/dot-rowCumProd_cpp.Rd | 36 BuyseTest-3.3.4/BuyseTest/man/dot-rowCumSum_cpp.Rd | 36 BuyseTest-3.3.4/BuyseTest/man/dot-rowMultiply_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/dot-rowScale_cpp.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/efronlim.Rd | 104 BuyseTest-3.3.4/BuyseTest/man/getCount.Rd | 52 BuyseTest-3.3.4/BuyseTest/man/getIid.Rd | 136 BuyseTest-3.3.4/BuyseTest/man/getPairScore.Rd | 258 - BuyseTest-3.3.4/BuyseTest/man/getPseudovalue.Rd | 136 BuyseTest-3.3.4/BuyseTest/man/getSurvival.Rd | 98 BuyseTest-3.3.4/BuyseTest/man/iid.BuyseTestAuc.Rd | 38 BuyseTest-3.3.4/BuyseTest/man/iid.BuyseTestBrier.Rd | 40 BuyseTest-3.3.4/BuyseTest/man/iid.prodlim.Rd | 110 BuyseTest-3.3.4/BuyseTest/man/mover.Rd | 76 BuyseTest-3.3.4/BuyseTest/man/performance.Rd | 212 BuyseTest-3.3.4/BuyseTest/man/performanceResample.Rd | 114 BuyseTest-3.3.4/BuyseTest/man/plot-sensitivity.Rd | 118 BuyseTest-3.3.4/BuyseTest/man/powerBuyseTest.Rd | 324 - BuyseTest-3.3.4/BuyseTest/man/predict.BuyseTTEM.Rd | 62 BuyseTest-3.3.4/BuyseTest/man/rbind.performance.Rd | 122 BuyseTest-3.3.4/BuyseTest/man/sensitivity.Rd | 176 BuyseTest-3.3.4/BuyseTest/man/simBuyseTest.Rd | 422 - BuyseTest-3.3.4/BuyseTest/man/simCompetingRisks.Rd | 212 BuyseTest-3.3.4/BuyseTest/man/summary.performance.Rd | 46 BuyseTest-3.3.4/BuyseTest/man/validFCTs.Rd | 312 - BuyseTest-3.3.4/BuyseTest/src/FCT_precompute.cpp | 4 BuyseTest-3.3.4/BuyseTest/tests/testthat.R | 86 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuysePower.R | 400 - BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTTEM.R | 568 +- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 468 - BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R | 240 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 1204 ++-- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 1148 ++-- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 450 - BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-engine.R | 214 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-iid.R | 1604 +++--- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-multcomp.R | 178 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 206 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 202 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 1614 +++--- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 1198 ++-- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-restricted.R | 188 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-sensitivity.R | 196 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-standardization.R | 538 +- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-strata.R | 864 +-- BuyseTest-3.3.4/BuyseTest/tests/testthat/test-BuyseTest-weightObs.R | 130 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-auc.R | 282 - BuyseTest-3.3.4/BuyseTest/tests/testthat/test-initSurvival.R | 438 - BuyseTest-3.3.4/BuyseTest/tests/testthat/test-initThreshold.R | 168 BuyseTest-3.3.4/BuyseTest/tests/testthat/test-otherPackages.R | 394 - BuyseTest-3.3.4/BuyseTest/vignettes/overview.pdf.asis | 1178 ++-- BuyseTest-3.3.4/BuyseTest/vignettes/paired.pdf.asis | 305 - BuyseTest-3.3.4/BuyseTest/vignettes/vignette_CR.Rmd | 146 BuyseTest-3.3.4/BuyseTest/vignettes/wilcoxonTest.pdf.asis | 210 184 files changed, 34118 insertions(+), 35342 deletions(-)
Title: Load Configuration Values
Description: A simple approach to configuring R projects with different
parameter values. Configurations are specified using a reduced subset of base
R and parsed accordingly.
Author: Tim Taylor [aut, cre, cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ronfig versions 0.0.2 dated 2025-09-15 and 0.0.3 dated 2025-09-24
DESCRIPTION | 8 +-- MD5 | 18 +++---- NEWS.md | 17 ++++++- R/load_config.R | 69 +++++++++++++++++++++++----- inst/doc/ronfig.Rmd | 16 +++--- inst/doc/ronfig.html | 15 +++--- man/load_config.Rd | 23 +++++---- tests/testthat/_snaps/load_config.md | 57 ++++++++++++++++++++++- tests/testthat/test-load_config.R | 85 +++++++++++++++++++++++++++++++++-- vignettes/ronfig.Rmd | 16 +++--- 10 files changed, 262 insertions(+), 62 deletions(-)
Title: Response Data for Light Sensors
Description: Spectral response data for broadband ultraviolet and visible
radiation sensors. Angular response data for broadband ultraviolet and visible
radiation sensors and diffusers used as entrance optics. Data obtained from
multiple sources were used: author-supplied data from scientific research
papers, sensor-manufacturer supplied data, and published sensor
specifications. Part of the 'r4photobiology' suite Aphalo P. J. (2015)
<doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySensors versions 0.5.1 dated 2023-10-24 and 0.5.2 dated 2025-09-24
DESCRIPTION | 21 +-- MD5 | 58 ++++----- NEWS.md | 10 + R/KIPP-sensors.r | 8 + R/Skye-sensors.r | 8 - R/SolarLight-sensors.r | 2 R/Solarmeter-sensors.r | 4 R/ams-sensors.r | 32 ++++ R/sensors-mspct.r | 22 ++- R/sglux-sensors.r | 5 R/wavebands.r | 11 + README.md | 97 +++++++++------ build/partial.rdb |binary build/vignette.rds |binary data/diffusers-lst.rda |binary data/sensors.mspct.rda |binary inst/doc/r4p-introduction.Rmd | 163 ++++++++++++------------- inst/doc/r4p-introduction.html | 165 +++++++++++++------------ inst/doc/userguide-1.html | 231 +++++++++++++++++++----------------- man/ams_sensors.Rd | 111 ++++++++++------- man/figures/README-example-07-1.png |binary man/kipp_sensors.Rd | 8 + man/photobiologySensors-package.Rd | 2 man/sensors.mspct.Rd | 22 ++- man/sglux_sensors.Rd | 5 man/skye_sensors.Rd | 8 - man/solarlight_sensors.Rd | 2 man/solarmeter_sensors.Rd | 4 man/uv_sensors.Rd | 26 ++-- vignettes/r4p-introduction.Rmd | 163 ++++++++++++------------- 30 files changed, 668 insertions(+), 520 deletions(-)
More information about photobiologySensors at CRAN
Permanent link
Title: Spectral Irradiance Data for Lamps
Description: Spectral emission data for some frequently used lamps including
bulbs and flashlights based on led emitting diodes (LEDs) but excluding
LEDs available as electronic components. Original spectral irradiance data
for incandescent-, LED- and discharge lamps are included. They are
complemented by data on the effect of temperature on the emission by
fluorescent tubes. Part of the 'r4photobiology' suite, Aphalo P. J. (2015)
<doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Lasse Ylianttila [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyLamps versions 0.5.2 dated 2023-10-24 and 0.5.3 dated 2025-09-24
photobiologyLamps-0.5.2/photobiologyLamps/man/photography_lamps.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/DESCRIPTION | 21 photobiologyLamps-0.5.3/photobiologyLamps/MD5 | 78 photobiologyLamps-0.5.3/photobiologyLamps/NEWS.md | 14 photobiologyLamps-0.5.3/photobiologyLamps/R/amaran-m9-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/andoer-ir49-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/elgato-mkl-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/lamp-brands.r | 25 photobiologyLamps-0.5.3/photobiologyLamps/R/lamp-colors.r | 44 photobiologyLamps-0.5.3/photobiologyLamps/R/lamp-types.r | 28 photobiologyLamps-0.5.3/photobiologyLamps/R/lamp-uses.r | 38 photobiologyLamps-0.5.3/photobiologyLamps/R/ledsavers-mspct.r | 9 photobiologyLamps-0.5.3/photobiologyLamps/R/macam.r | 2 photobiologyLamps-0.5.3/photobiologyLamps/R/nichia-led-recom-dim-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/osram-l-18w-840-temp.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/percival-led-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/R/qp-uvb313-temp.r | 9 photobiologyLamps-0.5.3/photobiologyLamps/R/sunwayfot-fl96-mspct.r |only photobiologyLamps-0.5.3/photobiologyLamps/README.md | 164 + photobiologyLamps-0.5.3/photobiologyLamps/build/partial.rdb |binary photobiologyLamps-0.5.3/photobiologyLamps/build/vignette.rds |binary photobiologyLamps-0.5.3/photobiologyLamps/data/amaran-m9-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/andoer-ir49-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/elgato-klm-cct-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/elgato-klm-dim-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/lamps-mspct.rda |binary photobiologyLamps-0.5.3/photobiologyLamps/data/ledsavers.rda |binary photobiologyLamps-0.5.3/photobiologyLamps/data/nichia-led-recom-dim-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/osram-l-18w-840-temp-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/percival-led-dim-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/data/qp-uvb313-temp-mspct.rda |binary photobiologyLamps-0.5.3/photobiologyLamps/data/qp-uvb313-temp-spct.rda |binary photobiologyLamps-0.5.3/photobiologyLamps/data/sunwayfoto-fl96-mspct.rda |only photobiologyLamps-0.5.3/photobiologyLamps/inst/doc/user-guide.R | 101 - photobiologyLamps-0.5.3/photobiologyLamps/inst/doc/user-guide.Rmd | 411 +++- photobiologyLamps-0.5.3/photobiologyLamps/inst/doc/user-guide.html | 940 ++++++---- photobiologyLamps-0.5.3/photobiologyLamps/man/Nichia_LED_RECOM_dim.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/Osram_L_18W_840_temp.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/Percival_LED_dim.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/amaran_m9.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/andoer_ir49.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/elgato_klm_cct.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/figures/README-example1-1.png |binary photobiologyLamps-0.5.3/photobiologyLamps/man/lamp_brands.Rd | 43 photobiologyLamps-0.5.3/photobiologyLamps/man/lamp_colors.Rd | 64 photobiologyLamps-0.5.3/photobiologyLamps/man/lamp_types.Rd | 43 photobiologyLamps-0.5.3/photobiologyLamps/man/lamp_uses.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/man/ledsavers.mspct.Rd | 10 photobiologyLamps-0.5.3/photobiologyLamps/man/macam_lamps.Rd | 2 photobiologyLamps-0.5.3/photobiologyLamps/man/qp_uvb313_temp.spct.Rd | 6 photobiologyLamps-0.5.3/photobiologyLamps/man/sunwayfoto_fl96.mspct.Rd |only photobiologyLamps-0.5.3/photobiologyLamps/vignettes/user-guide.Rmd | 411 +++- 52 files changed, 1661 insertions(+), 802 deletions(-)
More information about photobiologyLamps at CRAN
Permanent link
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.7.0 dated 2025-07-03 and 0.7.0-1 dated 2025-09-24
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS.md | 5 + R/array.R | 4 + src/array.c | 25 ++++++++ src/array.h | 9 +++ src/flatcc/portable/pstdalign.h | 5 + src/init.c | 2 src/nanoarrow.c | 115 +++++++++++++++++++++++++--------------- src/nanoarrow.h | 103 +++++++++++++++++++++++++---------- tests/testthat/test-array.R | 40 +++++++++++++ 11 files changed, 242 insertions(+), 92 deletions(-)
Title: R Plotting Functions Using 'ggplot2'
Description: Makes it easy to produce everyday 'ggplot2'
charts in a functional way without an extensive "tree"
implementation. The package includes over 15 functions
for the production and arrangement of basic graphing.
Author: Rick Dean [aut, cre, cph]
Maintainer: Rick Dean <deanr3@bardstown.com>
Diff between RplotterPkg versions 0.1.3 dated 2025-03-05 and 0.1.4 dated 2025-09-24
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/create_table.R | 10 +++++++++- README.md | 4 ++++ man/create_table.Rd | 2 +- man/figures/README-unnamed-chunk-2-1.png |binary tests/testthat/_snaps/create_table.md | 2 +- tests/testthat/test-create_table.R | 2 +- 9 files changed, 34 insertions(+), 16 deletions(-)
Title: Bayesian Smoothing of Remote Sensing Image Classification
Description: A Bayesian smoothing method for post-processing of remote
sensing image classification which refines the
labelling in a classified image in order to enhance its classification accuracy.
Combines pixel-based classification methods with a spatial post-processing
method to remove outliers and misclassified pixels.
Author: Gilberto Camara [aut, cre],
Renato Assuncao [aut],
Rolf Simoes [aut],
Felipe Souza [aut]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between bayesEO versions 0.2.1 dated 2024-06-04 and 0.2.2 dated 2025-09-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- inst/extdata/config_colors.yml | 3 +++ src/bayes_smooth.cpp | 4 ++-- src/other_smoothers.cpp | 2 +- tests/testthat/test-bayes.R | 15 +++++---------- 6 files changed, 21 insertions(+), 23 deletions(-)
Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal
clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings.
'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Tatiana Vargas [aut, cre],
Frederic Breant [ctb],
Victor Perrier [ctb],
Baptiste Seguinot [ctb],
Benoit Thieurmel [ctb],
Titouan Robert [ctb],
Jalal-Edine Zawam [ctb],
Etienne Sanchez [ctb],
Janus De Bondt [ctb],
Assil Mansouri [ctb],
Abdallah Mahoud [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresEditObject versions 0.9.0 dated 2025-02-14 and 0.9.2 dated 2025-09-24
antaresEditObject-0.9.0/antaresEditObject/R/createDistrict.R |only antaresEditObject-0.9.0/antaresEditObject/tests/testthat/test-createDistrict.R |only antaresEditObject-0.9.0/antaresEditObject/vignettes/schemas |only antaresEditObject-0.9.2/antaresEditObject/DESCRIPTION | 8 antaresEditObject-0.9.2/antaresEditObject/MD5 | 531 - antaresEditObject-0.9.2/antaresEditObject/NAMESPACE | 340 antaresEditObject-0.9.2/antaresEditObject/NEWS.md | 783 + antaresEditObject-0.9.2/antaresEditObject/R/API-utils.R | 726 - antaresEditObject-0.9.2/antaresEditObject/R/API.R | 688 - antaresEditObject-0.9.2/antaresEditObject/R/RES.R | 196 antaresEditObject-0.9.2/antaresEditObject/R/ST.R | 152 antaresEditObject-0.9.2/antaresEditObject/R/antaresEditObject-package.R | 14 antaresEditObject-0.9.2/antaresEditObject/R/backupStudy.R | 176 antaresEditObject-0.9.2/antaresEditObject/R/checkVersion.R | 78 antaresEditObject-0.9.2/antaresEditObject/R/cleanUpOutput.R | 106 antaresEditObject-0.9.2/antaresEditObject/R/computeTimeStampFromHourly.R | 882 +- antaresEditObject-0.9.2/antaresEditObject/R/computeTimeStepFromHourly.R | 760 - antaresEditObject-0.9.2/antaresEditObject/R/copyOutput.R | 128 antaresEditObject-0.9.2/antaresEditObject/R/createArea.R | 1373 +-- antaresEditObject-0.9.2/antaresEditObject/R/createBindingConstraint.R | 1728 ++-- antaresEditObject-0.9.2/antaresEditObject/R/createCluster.R | 1073 +- antaresEditObject-0.9.2/antaresEditObject/R/createClusterBulk.R | 536 - antaresEditObject-0.9.2/antaresEditObject/R/createClusterST.R | 1162 +- antaresEditObject-0.9.2/antaresEditObject/R/createDSR.R | 1014 +- antaresEditObject-0.9.2/antaresEditObject/R/createLink.R | 662 - antaresEditObject-0.9.2/antaresEditObject/R/createPSP.R | 1074 +- antaresEditObject-0.9.2/antaresEditObject/R/createStudy.R | 497 - antaresEditObject-0.9.2/antaresEditObject/R/district.R |only antaresEditObject-0.9.2/antaresEditObject/R/editArea.R | 486 - antaresEditObject-0.9.2/antaresEditObject/R/editBindingConstraint.R | 860 +- antaresEditObject-0.9.2/antaresEditObject/R/editCluster.R | 559 - antaresEditObject-0.9.2/antaresEditObject/R/editClusterST.R | 832 +- antaresEditObject-0.9.2/antaresEditObject/R/editLink.R | 578 - antaresEditObject-0.9.2/antaresEditObject/R/importStudyAPI.R | 196 antaresEditObject-0.9.2/antaresEditObject/R/playlist.R | 574 - antaresEditObject-0.9.2/antaresEditObject/R/removeArea.R | 454 - antaresEditObject-0.9.2/antaresEditObject/R/removeBindingConstraint.R | 468 - antaresEditObject-0.9.2/antaresEditObject/R/removeCluster.R | 370 antaresEditObject-0.9.2/antaresEditObject/R/removeLink.R | 206 antaresEditObject-0.9.2/antaresEditObject/R/runSimulation.R | 236 antaresEditObject-0.9.2/antaresEditObject/R/runTsGenerator.R | 124 antaresEditObject-0.9.2/antaresEditObject/R/scenarioBuilder.R | 1496 +-- antaresEditObject-0.9.2/antaresEditObject/R/setSolverPath.R | 70 antaresEditObject-0.9.2/antaresEditObject/R/thematic_trimming.R |only antaresEditObject-0.9.2/antaresEditObject/R/tools_aggregate.R | 86 antaresEditObject-0.9.2/antaresEditObject/R/updateAdequacySettings.R | 346 antaresEditObject-0.9.2/antaresEditObject/R/updateGeneralSettings.R | 530 - antaresEditObject-0.9.2/antaresEditObject/R/updateInputSettings.R | 136 antaresEditObject-0.9.2/antaresEditObject/R/updateOptimizationSettings.R | 592 - antaresEditObject-0.9.2/antaresEditObject/R/updateOutputSettings.R | 168 antaresEditObject-0.9.2/antaresEditObject/R/utils.R | 416 - antaresEditObject-0.9.2/antaresEditObject/R/writeAntaresOutput.R | 266 antaresEditObject-0.9.2/antaresEditObject/R/writeEconomicOptions.R | 364 antaresEditObject-0.9.2/antaresEditObject/R/writeHydroValues.R | 1646 ++-- antaresEditObject-0.9.2/antaresEditObject/R/writeIni.R | 316 antaresEditObject-0.9.2/antaresEditObject/R/writeInputTS.R | 616 - antaresEditObject-0.9.2/antaresEditObject/R/writeMiscGen.R | 110 antaresEditObject-0.9.2/antaresEditObject/R/writeOutput.R | 278 antaresEditObject-0.9.2/antaresEditObject/R/writeSeriesPrepro.R | 254 antaresEditObject-0.9.2/antaresEditObject/R/writeWaterValues.R | 158 antaresEditObject-0.9.2/antaresEditObject/README.md | 89 antaresEditObject-0.9.2/antaresEditObject/build/vignette.rds |binary antaresEditObject-0.9.2/antaresEditObject/inst/API/dev-api-offline.R | 258 antaresEditObject-0.9.2/antaresEditObject/inst/API/dev-api-online.R | 380 antaresEditObject-0.9.2/antaresEditObject/inst/API/dev-api-usage.R | 92 antaresEditObject-0.9.2/antaresEditObject/inst/dev/ntc-v820.R | 138 antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v860.R | 388 antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v860.Rmd | 628 - antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v860.html | 3951 ++++------ antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v920.R |only antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v920.Rmd |only antaresEditObject-0.9.2/antaresEditObject/inst/doc/Antares_new_features_v920.html |only antaresEditObject-0.9.2/antaresEditObject/inst/doc/antaresEditObject.R | 22 antaresEditObject-0.9.2/antaresEditObject/inst/doc/antaresEditObject.Rmd | 718 - antaresEditObject-0.9.2/antaresEditObject/inst/doc/antaresEditObject.html | 1268 +-- antaresEditObject-0.9.2/antaresEditObject/inst/doc/api-variant-management.R | 390 antaresEditObject-0.9.2/antaresEditObject/inst/doc/api-variant-management.Rmd | 701 - antaresEditObject-0.9.2/antaresEditObject/inst/doc/api-variant-management.html | 1853 ++-- antaresEditObject-0.9.2/antaresEditObject/inst/doc/renewables-energy-sources.R | 116 antaresEditObject-0.9.2/antaresEditObject/inst/doc/renewables-energy-sources.Rmd | 262 antaresEditObject-0.9.2/antaresEditObject/inst/doc/renewables-energy-sources.html | 864 +- antaresEditObject-0.9.2/antaresEditObject/inst/doc/scenario-builder.R | 256 antaresEditObject-0.9.2/antaresEditObject/inst/doc/scenario-builder.Rmd | 376 antaresEditObject-0.9.2/antaresEditObject/inst/doc/scenario-builder.html | 1106 +- antaresEditObject-0.9.2/antaresEditObject/inst/format_output/digest.csv | 58 antaresEditObject-0.9.2/antaresEditObject/inst/format_output/format.csv | 162 antaresEditObject-0.9.2/antaresEditObject/inst/format_output/tableOutput.csv | 586 - antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/Desktop.ini | 8 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/areas/sets.ini | 12 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/hydro/allocation/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/hydro/common/capacity/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/hydro/prepro/correlation.ini | 6 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/hydro/series/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/links/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/load/prepro/correlation.ini | 6 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/load/series/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/misc-gen/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/reserves/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/solar/prepro/correlation.ini | 6 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/solar/series/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/thermal/areas.ini | 6 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/thermal/clusters/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/thermal/prepro/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/thermal/series/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/wind/prepro/correlation.ini | 6 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/input/wind/series/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/layers/layers.ini | 8 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/logs/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/output/maps/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/settings/comments.txt | 16 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/settings/generaldata.ini | 154 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/settings/scenariobuilder.dat | 4 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/settings/simulations/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/study.antares | 14 antaresEditObject-0.9.2/antaresEditObject/inst/newStudy/user/ANTARESEDITOBJECT_TODELETE.txt | 2 antaresEditObject-0.9.2/antaresEditObject/inst/study_test_generator/generate_template.R | 674 - antaresEditObject-0.9.2/antaresEditObject/inst/study_test_generator/generate_test_study_870.R | 238 antaresEditObject-0.9.2/antaresEditObject/man/activateRES.Rd | 70 antaresEditObject-0.9.2/antaresEditObject/man/activateST.Rd | 66 antaresEditObject-0.9.2/antaresEditObject/man/add_week_number_column_to_ts.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/adequacyOptions.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/antaresEditObject-package.Rd | 84 antaresEditObject-0.9.2/antaresEditObject/man/api_patch.Rd | 104 antaresEditObject-0.9.2/antaresEditObject/man/backupStudy.Rd | 76 antaresEditObject-0.9.2/antaresEditObject/man/check-version.Rd | 64 antaresEditObject-0.9.2/antaresEditObject/man/checkRemovedArea.Rd | 54 antaresEditObject-0.9.2/antaresEditObject/man/check_consistency_reservoir_values.Rd | 36 antaresEditObject-0.9.2/antaresEditObject/man/check_mingen_vs_hydro_storage.Rd | 46 antaresEditObject-0.9.2/antaresEditObject/man/check_mingen_vs_maxpower.Rd | 46 antaresEditObject-0.9.2/antaresEditObject/man/cleanUpOutput.Rd | 32 antaresEditObject-0.9.2/antaresEditObject/man/computeOtherFromHourlyMulti.Rd | 86 antaresEditObject-0.9.2/antaresEditObject/man/computeOtherFromHourlyYear.Rd | 74 antaresEditObject-0.9.2/antaresEditObject/man/computeTimeStampFromHourly.Rd | 86 antaresEditObject-0.9.2/antaresEditObject/man/convertConfigToAdq.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/copyOutput.Rd | 70 antaresEditObject-0.9.2/antaresEditObject/man/copyStudyWeb.Rd | 74 antaresEditObject-0.9.2/antaresEditObject/man/create-study.Rd | 120 antaresEditObject-0.9.2/antaresEditObject/man/createArea.Rd | 118 antaresEditObject-0.9.2/antaresEditObject/man/createBindingConstraint.Rd | 264 antaresEditObject-0.9.2/antaresEditObject/man/createBindingConstraintBulk.Rd | 196 antaresEditObject-0.9.2/antaresEditObject/man/createCluster.Rd | 378 antaresEditObject-0.9.2/antaresEditObject/man/createClusterBulk.Rd | 226 antaresEditObject-0.9.2/antaresEditObject/man/createClusterST.Rd | 349 antaresEditObject-0.9.2/antaresEditObject/man/createDSR.Rd | 178 antaresEditObject-0.9.2/antaresEditObject/man/createDistrict.Rd | 108 antaresEditObject-0.9.2/antaresEditObject/man/createLink.Rd | 176 antaresEditObject-0.9.2/antaresEditObject/man/createPSP.Rd | 202 antaresEditObject-0.9.2/antaresEditObject/man/create_scb_referential_series_type.Rd | 28 antaresEditObject-0.9.2/antaresEditObject/man/deleteStudy.Rd | 36 antaresEditObject-0.9.2/antaresEditObject/man/detect_pattern_in_binding_constraint.Rd | 44 antaresEditObject-0.9.2/antaresEditObject/man/dicoAdequacySettings.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/dicoGeneralSettings.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/dicoOptimizationSettings.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/dicoOutputSettings.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/dot-api_command_execute_edit_area.Rd | 48 antaresEditObject-0.9.2/antaresEditObject/man/dot-api_command_execute_edit_area_ui.Rd |only antaresEditObject-0.9.2/antaresEditObject/man/dot-dailyToWeekly.Rd | 38 antaresEditObject-0.9.2/antaresEditObject/man/dot-format_ini_rhs.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/dot-format_playlist_weights.Rd | 38 antaresEditObject-0.9.2/antaresEditObject/man/dot-format_ui_data_by_mode.Rd |only antaresEditObject-0.9.2/antaresEditObject/man/dot-hourlyToOther.Rd | 38 antaresEditObject-0.9.2/antaresEditObject/man/dot-initializeLinksArea.Rd | 44 antaresEditObject-0.9.2/antaresEditObject/man/dot-initializeRenewablesArea.Rd | 44 antaresEditObject-0.9.2/antaresEditObject/man/dot-initializeThermalArea.Rd | 48 antaresEditObject-0.9.2/antaresEditObject/man/dot-is_version_9.Rd | 36 antaresEditObject-0.9.2/antaresEditObject/man/dot-split_nodalOptimization_by_target.Rd | 28 antaresEditObject-0.9.2/antaresEditObject/man/editArea.Rd | 138 antaresEditObject-0.9.2/antaresEditObject/man/editBindingConstraint.Rd | 244 antaresEditObject-0.9.2/antaresEditObject/man/editCluster.Rd | 164 antaresEditObject-0.9.2/antaresEditObject/man/editClusterST.Rd | 231 antaresEditObject-0.9.2/antaresEditObject/man/editLink.Rd | 144 antaresEditObject-0.9.2/antaresEditObject/man/figures/badge_api_no.svg | 38 antaresEditObject-0.9.2/antaresEditObject/man/figures/badge_api_ok.svg | 38 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-archived.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-defunct.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-deprecated.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-experimental.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-maturing.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-questioning.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-soft-deprecated.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-stable.svg | 58 antaresEditObject-0.9.2/antaresEditObject/man/figures/lifecycle-superseded.svg | 42 antaresEditObject-0.9.2/antaresEditObject/man/fill_empty_hydro_ini_file.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/fill_empty_hydro_ts_file.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/filteringOptions.Rd | 56 antaresEditObject-0.9.2/antaresEditObject/man/getJobLogs.Rd | 68 antaresEditObject-0.9.2/antaresEditObject/man/getJobs.Rd | 54 antaresEditObject-0.9.2/antaresEditObject/man/get_default_hydro_ini_values.Rd | 26 antaresEditObject-0.9.2/antaresEditObject/man/get_type_check_mingen_vs_hydrostorage.Rd | 34 antaresEditObject-0.9.2/antaresEditObject/man/get_type_check_mingen_vs_hydrostorage_to_trigger.Rd | 62 antaresEditObject-0.9.2/antaresEditObject/man/get_type_check_mingen_vs_maxpower_to_trigger.Rd | 64 antaresEditObject-0.9.2/antaresEditObject/man/group_values_meta_check.Rd | 74 antaresEditObject-0.9.2/antaresEditObject/man/importZipStudyWeb.Rd | 70 antaresEditObject-0.9.2/antaresEditObject/man/list_pollutants_values.Rd | 40 antaresEditObject-0.9.2/antaresEditObject/man/mockSimulationAPI.Rd | 62 antaresEditObject-0.9.2/antaresEditObject/man/nodalOptimizationOptions.Rd | 80 antaresEditObject-0.9.2/antaresEditObject/man/playlist.Rd | 122 antaresEditObject-0.9.2/antaresEditObject/man/propertiesLinkOptions.Rd | 96 antaresEditObject-0.9.2/antaresEditObject/man/removeArea.Rd | 60 antaresEditObject-0.9.2/antaresEditObject/man/removeBindingConstraint.Rd | 116 antaresEditObject-0.9.2/antaresEditObject/man/removeCluster.Rd | 128 antaresEditObject-0.9.2/antaresEditObject/man/removeDistrict.Rd |only antaresEditObject-0.9.2/antaresEditObject/man/removeLink.Rd | 56 antaresEditObject-0.9.2/antaresEditObject/man/replicate_missing_ts.Rd | 38 antaresEditObject-0.9.2/antaresEditObject/man/rollback_to_previous_data.Rd | 60 antaresEditObject-0.9.2/antaresEditObject/man/runSimulation.Rd | 102 antaresEditObject-0.9.2/antaresEditObject/man/runTsGenerator.Rd | 80 antaresEditObject-0.9.2/antaresEditObject/man/scenario-builder.Rd | 409 - antaresEditObject-0.9.2/antaresEditObject/man/searchStudy.Rd | 82 antaresEditObject-0.9.2/antaresEditObject/man/setAPImode.Rd | 68 antaresEditObject-0.9.2/antaresEditObject/man/setSolverPath.Rd | 48 antaresEditObject-0.9.2/antaresEditObject/man/setThematicTrimming.Rd |only antaresEditObject-0.9.2/antaresEditObject/man/storage_values_default.Rd | 50 antaresEditObject-0.9.2/antaresEditObject/man/updateAdequacySettings.Rd | 128 antaresEditObject-0.9.2/antaresEditObject/man/updateGeneralSettings.Rd | 278 antaresEditObject-0.9.2/antaresEditObject/man/updateInputSettings.Rd | 60 antaresEditObject-0.9.2/antaresEditObject/man/updateOptimizationSettings.Rd | 180 antaresEditObject-0.9.2/antaresEditObject/man/updateOutputSettings.Rd | 104 antaresEditObject-0.9.2/antaresEditObject/man/update_generaldata_by_section.Rd | 44 antaresEditObject-0.9.2/antaresEditObject/man/variant-commands.Rd | 82 antaresEditObject-0.9.2/antaresEditObject/man/variant.Rd | 64 antaresEditObject-0.9.2/antaresEditObject/man/write-ini.Rd | 94 antaresEditObject-0.9.2/antaresEditObject/man/writeEconomicOptions.Rd | 90 antaresEditObject-0.9.2/antaresEditObject/man/writeHydroValues.Rd | 116 antaresEditObject-0.9.2/antaresEditObject/man/writeIniHydro.Rd | 118 antaresEditObject-0.9.2/antaresEditObject/man/writeInputTS.Rd | 152 antaresEditObject-0.9.2/antaresEditObject/man/writeMiscGen.Rd | 58 antaresEditObject-0.9.2/antaresEditObject/man/writeOutputValues.Rd | 62 antaresEditObject-0.9.2/antaresEditObject/man/writeSeriesPrepro.Rd | 114 antaresEditObject-0.9.2/antaresEditObject/man/writeWaterValues.Rd | 78 antaresEditObject-0.9.2/antaresEditObject/tests/testthat.R | 18 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/helper_init.R | 54 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-RES.R | 208 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-RemoveClusterST.R |only antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-ST.R | 138 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-computeTimeStepFromHourly.R | 178 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-compute_timeStamp_from_hourly.R | 178 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createArea.R | 1121 +- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createBindingConstraint.R | 1892 ++-- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createCluster.R | 572 - antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createClusterBulk.R | 376 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createClusterST.R | 1055 ++ antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createLink.R | 628 - antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-createStudy.R | 220 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-district.R |only antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-editArea.R | 244 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-editBindingConstraint.R | 820 +- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-editCluster.R | 248 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-editClusterST.R | 1230 ++- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-editLink.R | 124 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-playlist.R | 202 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-removeBindingConstraint.R | 476 - antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-scenarioBuilder.R | 1327 +-- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-thematic_trimming.R |only antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateAdequacyPatch.R | 98 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateBindingConstraint.R | 124 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateGeneralSettings.R | 140 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateInputSettings.R | 66 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateOptimizationSettings.R | 96 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-updateOutputSettings.R | 90 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-utils.R | 30 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeEconomicOptions.R | 206 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeHydroValues.R | 2352 ++--- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeInputTS.R | 1412 +-- antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeOutputValues.R | 80 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeSeriesPrepro.R | 138 antaresEditObject-0.9.2/antaresEditObject/tests/testthat/test-writeWaterValues.R | 108 antaresEditObject-0.9.2/antaresEditObject/vignettes/Antares_new_features_v860.Rmd | 628 - antaresEditObject-0.9.2/antaresEditObject/vignettes/Antares_new_features_v920.Rmd |only antaresEditObject-0.9.2/antaresEditObject/vignettes/antaresEditObject.Rmd | 718 - antaresEditObject-0.9.2/antaresEditObject/vignettes/api-variant-management.Rmd | 701 - antaresEditObject-0.9.2/antaresEditObject/vignettes/mingen_draw.png |only antaresEditObject-0.9.2/antaresEditObject/vignettes/mingen_hydro_rules.png |only antaresEditObject-0.9.2/antaresEditObject/vignettes/renewables-energy-sources.Rmd | 262 antaresEditObject-0.9.2/antaresEditObject/vignettes/scenario-builder.Rmd | 376 275 files changed, 37981 insertions(+), 34924 deletions(-)
More information about antaresEditObject at CRAN
Permanent link
Title: Procedures Related to the Zadeh's Extension Principle for Fuzzy
Data
Description: Procedures for calculation, plotting, animation, and approximation of the outputs for fuzzy numbers (see A.I. Ban, L. Coroianu, P. Grzegorzewski "Fuzzy Numbers: Approximations, Ranking and Applications" (2015)) based on the Zadeh's Extension Principle (see de Barros, L.C., Bassanezi, R.C., Lodwick, W.A. (2017) <doi:10.1007/978-3-662-53324-6_2>).
Author: Maciej Romaniuk [cre, aut] ),
Abbas Parchami [aut] ),
Przemyslaw Grzegorzewski [ctb] )
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between ZEP versions 0.2.0 dated 2025-09-18 and 0.2.3 dated 2025-09-24
DESCRIPTION | 12 +++++++----- MD5 | 17 ++++++++++------- NAMESPACE | 1 + R/AnimateZEP.R |only R/AnimateZFunction.R | 11 +++++++++-- R/FuzzyApproximation.R | 1 + R/PlotZFunction.R | 19 ++++++++++--------- man/AnimateZEP.Rd |only man/AnimateZFunction.Rd | 3 +++ man/FuzzyApproximation.Rd | 1 + tests/testthat/test-AnimateZEP.R |only 11 files changed, 42 insertions(+), 23 deletions(-)
Title: A Simple Sky Illuminance Model
Description: A tool to calculate sky illuminance values (in lux) for both sun and moon. The
model is a translation of the Fortran code by Janiczek and DeYoung (1987)
<https://archive.org/details/DTIC_ADA182110>.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between skylight versions 1.2 dated 2023-11-04 and 1.3 dated 2025-09-24
skylight-1.2/skylight/R/subroutines.R |only skylight-1.3/skylight/DESCRIPTION | 22 - skylight-1.3/skylight/MD5 | 24 - skylight-1.3/skylight/NAMESPACE | 6 skylight-1.3/skylight/R/RcppExports.R |only skylight-1.3/skylight/R/skylight.R | 174 ++-------- skylight-1.3/skylight/build/vignette.rds |binary skylight-1.3/skylight/inst/doc/skylight.html | 239 +++++++------- skylight-1.3/skylight/inst/doc/skylight_advanced.R | 62 +-- skylight-1.3/skylight/inst/doc/skylight_advanced.html | 288 +++++++++--------- skylight-1.3/skylight/man/skylight.Rd | 24 + skylight-1.3/skylight/man/skylight_rcpp.Rd |only skylight-1.3/skylight/src |only skylight-1.3/skylight/tests/testthat/test_skylight.R | 24 - 14 files changed, 394 insertions(+), 469 deletions(-)
Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet
(UV) radiation in relation to the photoreceptors Phytochromes,
Cryptochromes, and UVR8 which are present in plants. It also includes data
sets on the optical properties of plants. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyPlants versions 0.6.0 dated 2025-01-12 and 0.6.1 dated 2025-09-24
photobiologyPlants-0.6.0/photobiologyPlants/man/B_G.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/R_FR.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVA1_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVA2_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVA_PAR.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVA_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVAlw_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVAsw_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVB_PAR.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVB_UV.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UVB_UVA.Rd |only photobiologyPlants-0.6.0/photobiologyPlants/man/UV_PAR.Rd |only photobiologyPlants-0.6.1/photobiologyPlants/DESCRIPTION | 21 photobiologyPlants-0.6.1/photobiologyPlants/MD5 | 117 - photobiologyPlants-0.6.1/photobiologyPlants/NAMESPACE | 10 photobiologyPlants-0.6.1/photobiologyPlants/NEWS.md | 22 photobiologyPlants-0.6.1/photobiologyPlants/R/McCree-photosynthesis-mspct.R | 2 photobiologyPlants-0.6.1/photobiologyPlants/R/Pfr-P-ratio.R | 7 photobiologyPlants-0.6.1/photobiologyPlants/R/Pfr-Ptot.R | 42 photobiologyPlants-0.6.1/photobiologyPlants/R/PfrPtot-RFR.R | 3 photobiologyPlants-0.6.1/photobiologyPlants/R/Phy-Sigma-FR.R | 5 photobiologyPlants-0.6.1/photobiologyPlants/R/Phy-Sigma-R.R | 4 photobiologyPlants-0.6.1/photobiologyPlants/R/Phy-Sigma.R | 4 photobiologyPlants-0.6.1/photobiologyPlants/R/carotenoids-mspct.r | 5 photobiologyPlants-0.6.1/photobiologyPlants/R/chlorophylls-fluo-mspct.r | 6 photobiologyPlants-0.6.1/photobiologyPlants/R/chlorophylls-mspct.r | 4 photobiologyPlants-0.6.1/photobiologyPlants/R/phy-reaction-rates.R | 7 photobiologyPlants-0.6.1/photobiologyPlants/R/phytochrome-data.r | 4 photobiologyPlants-0.6.1/photobiologyPlants/R/plant-q-irrads.r |only photobiologyPlants-0.6.1/photobiologyPlants/R/plant-qq-ratios.r | 681 ++++++---- photobiologyPlants-0.6.1/photobiologyPlants/R/water.vapour.R | 1 photobiologyPlants-0.6.1/photobiologyPlants/build/partial.rdb |binary photobiologyPlants-0.6.1/photobiologyPlants/build/vignette.rds |binary photobiologyPlants-0.6.1/photobiologyPlants/data/CRYs.mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/McCree.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/PHOTs.mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/UVR8s.mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/ZTLs.mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/carotenoids-mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/chlorophylls-fluorescence-mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/chlorophylls-mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/leaf-fluorescence-mspct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/leaves.spct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/data/phytochrome.spct.rda |binary photobiologyPlants-0.6.1/photobiologyPlants/inst/doc/r4p-introduction.Rmd | 158 +- photobiologyPlants-0.6.1/photobiologyPlants/inst/doc/r4p-introduction.html | 166 +- photobiologyPlants-0.6.1/photobiologyPlants/inst/doc/user-guide.R | 5 photobiologyPlants-0.6.1/photobiologyPlants/inst/doc/user-guide.Rmd | 22 photobiologyPlants-0.6.1/photobiologyPlants/inst/doc/user-guide.html | 319 ++-- photobiologyPlants-0.6.1/photobiologyPlants/man/ET_ref.Rd | 289 ++-- photobiologyPlants-0.6.1/photobiologyPlants/man/McCree_photosynthesis.mspct.Rd | 7 photobiologyPlants-0.6.1/photobiologyPlants/man/PHYs.mspct.Rd | 13 photobiologyPlants-0.6.1/photobiologyPlants/man/Pfr_Ptot.Rd | 39 photobiologyPlants-0.6.1/photobiologyPlants/man/Pfr_Ptot_R_FR.Rd | 9 photobiologyPlants-0.6.1/photobiologyPlants/man/Phy_Sigma.Rd | 10 photobiologyPlants-0.6.1/photobiologyPlants/man/Phy_Sigma_FR.Rd | 11 photobiologyPlants-0.6.1/photobiologyPlants/man/Phy_Sigma_R.Rd | 11 photobiologyPlants-0.6.1/photobiologyPlants/man/Phy_reaction_rates.Rd | 13 photobiologyPlants-0.6.1/photobiologyPlants/man/carotenoids.mspct.Rd | 4 photobiologyPlants-0.6.1/photobiologyPlants/man/chlorophylls.mspct.Rd | 10 photobiologyPlants-0.6.1/photobiologyPlants/man/chlorophylls_fluorescence.mspct.Rd | 10 photobiologyPlants-0.6.1/photobiologyPlants/man/net_irradiance.Rd | 101 - photobiologyPlants-0.6.1/photobiologyPlants/man/photon-irradiances.Rd |only photobiologyPlants-0.6.1/photobiologyPlants/man/photon-ratios.Rd |only photobiologyPlants-0.6.1/photobiologyPlants/man/water_vp_sat.Rd | 448 +++--- photobiologyPlants-0.6.1/photobiologyPlants/vignettes/r4p-introduction.Rmd | 158 +- photobiologyPlants-0.6.1/photobiologyPlants/vignettes/user-guide.Rmd | 22 67 files changed, 1572 insertions(+), 1198 deletions(-)
More information about photobiologyPlants at CRAN
Permanent link
Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for
economic research and quantitative analysis. The data sources including
NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative
functions for trading strategies based on the 'data.table', 'TTR',
'PerformanceAnalytics' and etc packages.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between pedquant versions 0.2.5 dated 2025-07-26 and 0.2.6 dated 2025-09-24
DESCRIPTION | 6 ++-- MD5 | 15 ++++++----- NAMESPACE | 3 ++ NEWS.md | 4 +++ R/func_helper.R | 9 +++--- R/md_2chinamoney.R | 62 ++++++++++++++++++++++++++++++++++++++++++++---- R/pq_plot2.R | 2 - README.md | 8 +++--- inst/extdata/README.Rmd |only 9 files changed, 85 insertions(+), 24 deletions(-)
Title: Download and Extract Data from US EPA's ECOTOX Database
Description: The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ECOTOXr versions 1.2.2 dated 2025-08-19 and 1.2.4 dated 2025-09-24
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 7 +++++++ R/database_access.r | 2 +- R/init.r | 3 +-- inst/doc/sanitising-ecotox.Rmd | 2 +- inst/doc/sanitising-ecotox.html | 2 +- man/check_ecotox_version.Rd | 2 +- tests/testthat/test_build.r | 11 ++++++++++- tests/testthat/test_online.r | 9 ++++++--- tests/testthat/test_sanitation.r | 2 +- vignettes/sanitising-ecotox.Rmd | 2 +- 12 files changed, 44 insertions(+), 26 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via Markov chain Monte Carlo (MCMC) based on parallel
importance sampling type weighted estimators
(Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>),
particle MCMC, and its delayed acceptance version.
Gaussian, Poisson, binomial, negative binomial, and Gamma
observation densities and basic stochastic volatility models
with linear-Gaussian state dynamics, as well as general non-linear Gaussian
models and discretised diffusion models are supported.
See Helske and Vihola (2021, <doi:10.32614/RJ-2021-103>) for details.
Author: Jouni Helske [aut, cre] ,
Matti Vihola [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 2.0.2 dated 2023-10-27 and 2.0.3 dated 2025-09-24
DESCRIPTION | 11 MD5 | 74 - NEWS.md | 634 ++++---- R/approx.R | 210 +- R/bssm-package.R | 526 +++---- R/ekpf_filter.R | 168 +- R/fitted.R | 242 +-- R/kfilter.R | 378 ++--- R/models.R | 3300 ++++++++++++++++++++++----------------------- R/post_correction.R | 616 ++++---- R/predict.R | 712 ++++----- R/run_mcmc.R | 1714 +++++++++++------------ R/summary.R | 254 +-- README.md | 2 build/vignette.rds |binary inst/doc/bssm.Rmd | 410 ++--- inst/doc/bssm.html | 13 inst/doc/growth_model.Rmd | 444 +++--- inst/doc/growth_model.html | 22 inst/doc/psi_pf.R | 532 +++---- inst/doc/psi_pf.Rmd | 900 ++++++------ inst/doc/psi_pf.html | 3 inst/doc/sde_model.Rmd | 228 +-- inst/doc/sde_model.html | 7 src/R_approx.cpp | 2 src/R_psi.cpp | 2 src/approx_mcmc.cpp | 8 src/mcmc.cpp | 8 src/model_ssm_mng.cpp | 6 src/model_ssm_nlg.cpp | 6 src/model_ssm_sde.cpp | 4 src/model_ssm_ulg.cpp | 40 src/model_ssm_ung.cpp | 22 tests/test_all.R | 8 vignettes/bssm.Rmd | 410 ++--- vignettes/growth_model.Rmd | 444 +++--- vignettes/psi_pf.Rmd | 900 ++++++------ vignettes/sde_model.Rmd | 228 +-- 38 files changed, 6749 insertions(+), 6739 deletions(-)
Title: Create Actuarial Experience Studies: Prepare Data, Summarize
Results, and Create Reports
Description: Experience studies are used by actuaries to explore historical
experience across blocks of business and to inform assumption setting
activities. This package provides functions for preparing data, creating
studies, visualizing results, and beginning assumption development.
Experience study methods, including exposure calculations, are described in:
Atkinson & McGarry (2016) "Experience Study Calculations"
<https://www.soa.org/49378a/globalassets/assets/files/research/experience-study-calculations.pdf>.
The limited fluctuation credibility method used by the 'exp_stats()'
function is described in: Herzog (1999, ISBN:1-56698-374-6)
"Introduction to Credibility Theory".
Author: Matt Heaphy [aut, cre]
Maintainer: Matt Heaphy <mattrmattrs@gmail.com>
Diff between actxps versions 1.6.0 dated 2025-01-07 and 1.6.1 dated 2025-09-24
DESCRIPTION | 8 MD5 | 78 +- NEWS.md | 5 R/add_predictions.R | 6 R/exp_df_helpers.R | 91 ++- R/exp_shiny.R | 811 +++++++++++++++++++------------ R/exp_stats.R | 320 +++++++----- R/expose.R | 203 ++++--- R/expose_split.R | 131 ++--- R/exposed_df_helpers.R | 230 +++++--- R/globals.R | 76 ++ R/plot_special.R | 71 +- R/plot_special_trx.R | 8 R/plot_theme.R | 26 R/plots.R | 210 +++++--- R/pol_yr.R | 8 R/step_expose.R | 79 +-- R/tables.R | 328 +++++++----- R/transactions.R | 49 + R/trx_df_helpers.R | 77 +- R/trx_stats.R | 237 +++++---- build/vignette.rds |binary inst/doc/actxps.html | 7 inst/doc/exp_summary.html | 5 inst/doc/exposures.html | 5 inst/doc/misc.html | 5 inst/doc/transactions.html | 7 man/step_expose.Rd | 26 tests/testthat/test-add_predictions.R | 27 - tests/testthat/test-exp_df_helpers.R | 49 + tests/testthat/test-exp_stats.R | 111 ++-- tests/testthat/test-expose.R | 574 ++++++++++++--------- tests/testthat/test-exposed_df_helpers.R | 238 +++++---- tests/testthat/test-plots.R | 228 +++++--- tests/testthat/test-pol_yr.R | 18 tests/testthat/test-step_expose.R | 11 tests/testthat/test-tables.R | 57 +- tests/testthat/test-transactions.R | 73 +- tests/testthat/test-trx_df_helpers.R | 19 tests/testthat/test-trx_stats.R | 81 +-- 40 files changed, 2813 insertions(+), 1780 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.9 dated 2025-03-05 and 0.0.10 dated 2025-09-24
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ R/add_gloss.R | 7 +++++-- R/gloss_example.R | 32 ++++++++++++++++++-------------- 5 files changed, 38 insertions(+), 26 deletions(-)
Title: Mean Comparison in 'ggplot2'
Description: Add mean comparison annotations to a 'ggplot'.
This package provides an easy way to indicate if two or more groups are significantly different in a 'ggplot'.
Usually you do not need to specify the test method, you only need to tell stat_compare() whether you want to perform a parametric test or a nonparametric test, and stat_compare() will automatically choose the appropriate test method based on your data.
For comparisons between two groups, the p-value is calculated by t-test (parametric) or Wilcoxon rank sum test (nonparametric). For comparisons among more than two groups, the p-value is calculated by One-way ANOVA (parametric) or Kruskal-Wallis test (nonparametric).
Author: Hao Wang [aut, cre]
Maintainer: Hao Wang <wanghao8772@gmail.com>
Diff between ggcompare versions 0.0.4 dated 2025-08-20 and 0.0.5 dated 2025-09-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/GGExtensions.R | 36 +++++++++++++++++++----------------- man/stat_compare.Rd | 4 ++-- 5 files changed, 31 insertions(+), 26 deletions(-)
Title: Phylogenetic ANalyses of DiversificAtion
Description: Implements macroevolutionary analyses on phylogenetic trees. See
Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011)
<DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>,
Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>,
Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>,
Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>,
Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>,
Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>,
Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewi [...truncated...]
Author: Helene Morlon [aut, cre, cph],
Eric Lewitus [aut, cph],
Fabien Condamine [aut, cph],
Marc Manceau [aut, cph],
Julien Clavel [aut, cph],
Jonathan Drury [aut, cph],
Olivier Billaud [aut, cph],
Odile Maliet [aut, cph],
Leandro Aristide [aut, cph],
Benoi [...truncated...]
Maintainer: Helene Morlon <helene.morlon@bio.ens.psl.eu>
Diff between RPANDA versions 2.4 dated 2025-01-14 and 2.5 dated 2025-09-24
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++++----- NAMESPACE | 8 ++++++-- R/fit_t_thresh.R |only R/plot.fit_t_thresh.env.r |only R/plot_BipartiteEvol.R | 2 +- man/fit_t_env_ou.Rd | 8 +++++--- man/fit_t_thresh.Rd |only man/lines.fit_t_env.ou.Rd | 2 +- man/lines.fit_t_thresh.Rd |only man/plot.fit_t_thresh.Rd |only 11 files changed, 27 insertions(+), 16 deletions(-)
Title: Search and Get Data from the I14Y Interoperability Platform of
Switzerland
Description: Search and download Swiss data and metadata from the I14Y
interoperability platform of Switzerland using its public APIs
<https://www.i14y.admin.ch/api/index.html>.
Author: Felix Luginbuhl [aut, cre, cph] ,
Felix Lorenz [ctr]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between I14Y versions 0.1.5 dated 2025-07-14 and 0.1.6 dated 2025-09-24
DESCRIPTION | 6 +- MD5 | 30 +++++++------- NEWS.md | 4 + R/i14y_get_codelist.R | 23 +++++++--- R/i14y_get_concept.R | 14 ++++-- R/i14y_get_concept_all_versions.R | 19 ++++++-- R/i14y_get_content_information.R | 17 ++++++- R/i14y_get_data_service.R | 19 ++++++-- R/i14y_get_data_structure.R | 19 ++++++-- R/i14y_get_dataset_metadata.R | 12 ++++- R/i14y_get_nomenclature_level.R | 44 +++++++++++++------- R/i14y_get_nomenclature_level_multiple.R | 44 +++++++++++++------- R/i14y_search_catalog.R | 48 ++++++++++++++-------- R/i14y_search_concept.R | 66 ++++++++++++++++++++++--------- R/i14y_search_nomenclature.R | 43 ++++++++++++-------- R/validate.R | 23 +--------- 16 files changed, 280 insertions(+), 151 deletions(-)
Title: Tools for Using Fonts
Description: Tools to using fonts other than the standard PostScript fonts.
This package makes it easy to use system TrueType fonts and with PDF or
PostScript output files, and with bitmap output files in Windows. extrafont
can also be used with fonts packaged specifically to be used with, such as
the fontcm package, which has Computer Modern PostScript fonts with math
symbols.
Author: Winston Chang [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
This is a re-admission after prior archival of version 0.19 dated 2023-01-18
Diff between extrafont versions 0.19 dated 2023-01-18 and 0.20 dated 2025-09-24
extrafont-0.19/extrafont/man/extrafont.Rd |only extrafont-0.20/extrafont/DESCRIPTION | 32 +++++++++++++++------- extrafont-0.20/extrafont/MD5 | 22 +++++++++++---- extrafont-0.20/extrafont/NEWS | 8 +++++ extrafont-0.20/extrafont/R/extrafont.r | 16 ++++------- extrafont-0.20/extrafont/README.md | 15 ++++++++-- extrafont-0.20/extrafont/man/extrafont-package.Rd |only extrafont-0.20/extrafont/tests |only 8 files changed, 66 insertions(+), 27 deletions(-)
Title: Clustering with Compositional Data
Description: Cluster analysis with compositional data using the alpha--transformation. Relevant papers include: Tsagris M. and Kontemeniotis N. (2025), <doi:10.48550/arXiv.2509.05945>. Tsagris M.T., Preston S. and Wood A.T.A. (2011), <doi:10.48550/arXiv.1106.1451>. Garcia-Escudero Luis A., Gordaliza Alfonso, Matran Carlos, Mayo-Iscar Agustin. (2008), <doi:10.1214/07-AOS515>.
Author: Michail Tsagris [aut, cre],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalClust versions 1.0 dated 2025-09-18 and 1.1 dated 2025-09-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/index_max.R | 2 ++ R/index_min.R | 2 ++ man/CompositionalClust-package.Rd | 4 ++-- 5 files changed, 14 insertions(+), 10 deletions(-)
More information about CompositionalClust at CRAN
Permanent link
Title: Statistical Analysis to Identify Isotope Incorporating
Metagenomic Features
Description: Statistical analysis as part of a quantitative stable isotope
probing (SIP) metagenomics study to identify isotope incorporating
metagenomic features. Helpful reading and a vignette in bookdown
format is provided on the package site
<https://zielslab.github.io/SIPmg.github.io/>.
Author: Pranav Sampara [aut, cre],
Kate Waring [ctb],
Ryan Ziels [aut],
Alma Garcia Roche [aut]
Maintainer: Pranav Sampara <pranav.sai.4@gmail.com>
This is a re-admission after prior archival of version 1.4.1 dated 2023-02-21
Diff between SIPmg versions 1.4.1 dated 2023-02-21 and 3.0 dated 2025-09-24
DESCRIPTION | 58 MD5 | 36 NAMESPACE | 3 R/DESeq2_l2fc.R | 255 - R/functions_qSIP_MAGs.R | 209 - R/sequin_scaling_lm.R | 92 R/sequin_scaling_rlm.R | 83 build/vignette.rds |binary inst/doc/SIPmg-vignette.R | 635 +-- inst/doc/SIPmg-vignette.Rmd | 1354 +++--- inst/doc/SIPmg-vignette.html | 5741 ++++++++++++++-------------- man/as.Num.Rd |only man/calc_Mheavymax_MAGs.Rd | 2 man/calc_atom_excess_MAGs.Rd | 2 man/phyloseq2df.Rd |only man/phyloseq2table.Rd |only man/qSIP_atom_excess_MAGs.Rd | 2 man/qSIP_bootstrap_fcr.Rd | 15 man/scale_features_lm.Rd | 2 vignettes/SIPmg-vignette.Rmd | 1354 +++--- vignettes/mock_input_data/fractions_15N.csv |only 21 files changed, 5180 insertions(+), 4663 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.2.0 dated 2025-02-05 and 1.2.5 dated 2025-09-24
DESCRIPTION | 10 - MD5 | 29 ++--- NAMESPACE | 3 NEWS.md | 24 ++++ R/PLSrounding.R | 119 +++++++++++++++++++---- R/PLSroundingLoop.R | 10 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_SmallCountRounding.Rmd | 1 inst/doc/Introduction_to_SmallCountRounding.html | 72 ++++++------- man/PLSrounding.Rd | 31 +++++ man/PLSroundingLoop.Rd | 5 man/figures |only tests/testthat/test-PLSrounding.R | 11 +- tests/testthat/test-PLSroundingLoop.R | 6 - vignettes/Introduction_to_SmallCountRounding.Rmd | 1 16 files changed, 234 insertions(+), 88 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: Applied Statistics for Economics and Management with R
Description: Datasets and functions for the book "Statistiques pour l’économie et la gestion", "Théorie et applications en entreprise", F. Bertrand, Ch. Derquenne, G. Dufrénot, F. Jawadi and M. Maumy, C. Borsenberger editor, (2021, ISBN:9782807319448, De Boeck Supérieur, Louvain-la-Neuve).
The first chapter of the book is dedicated to an introduction to statistics and their world.
The second chapter deals with univariate exploratory statistics and graphics.
The third chapter deals with bivariate and multivariate exploratory statistics and graphics.
The fourth chapter is dedicated to data exploration with Principal Component Analysis.
The fifth chapter is dedicated to data exploration with Correspondance Analysis.
The sixth chapter is dedicated to data exploration with Multiple Correspondance Analysis.
The seventh chapter is dedicated to data exploration with automatic clustering.
The eighth chapter is dedicated to an introduction to probability theory and classical probability distributions.
The ni [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Claire Borsenberger [ctb],
Christian Derquenne [ctb],
Gilles Dufrenot [ctb],
Fredj Jawadi [ctb],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between sageR versions 0.6.1 dated 2023-03-23 and 0.7.0 dated 2025-09-24
DESCRIPTION | 28 +++++++++++++------------ MD5 | 41 +++++++++++++++++++++---------------- NEWS.md | 7 ++++++ R/functions.R | 4 +-- README.md | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 ++- inst/_pkgdown.yml |only inst/doc/AllLinksExtVignettes.R | 6 ++--- inst/doc/AllLinksExtVignettes.Rmd | 4 +-- inst/doc/AllLinksExtVignettes.html | 22 +++++++++---------- man/dotchart3.Rd | 2 - man/plotcdf3.Rd | 2 - man/presid_2012.Rd | 4 +-- man/sageR-package.Rd | 4 +-- tests/testthat/Rplots.pdf | 6 ++--- tests/testthat/helper-sageR.R |only tests/testthat/test-data.R |only tests/testthat/test-exports.R |only tests/testthat/test-help.R |only tests/testthat/test-load.R |only tests/testthat/test-todo.R |only tests/testthat/test_plotcdf3.R | 2 - vignettes/AllLinksExtVignettes.Rmd | 4 +-- 25 files changed, 82 insertions(+), 62 deletions(-)
Title: 'ttf2pt1' Program
Description: Contains the program 'ttf2pt1', for use with the
'extrafont' package. This product includes software developed by the 'TTF2PT1'
Project and its contributors.
Author: Winston Chang [aut],
Andrew Weeks [aut],
Frank M. Siegert [aut],
Mark Heath [aut],
Thomas Henlick [aut],
Sergey Babkin [aut],
Turgut Uyar [aut],
Rihardas Hepas [aut],
Szalay Tamas [aut],
Johan Vromans [aut],
Petr Titera [aut],
Lei Wang [aut],
Chen Xi [...truncated...]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
This is a re-admission after prior archival of version 1.3.12 dated 2023-01-22
Diff between Rttf2pt1 versions 1.3.12 dated 2023-01-22 and 1.3.13 dated 2025-09-24
Rttf2pt1-1.3.12/Rttf2pt1/man/Rttf2pt1.Rd |only Rttf2pt1-1.3.13/Rttf2pt1/DESCRIPTION | 99 ++++-- Rttf2pt1-1.3.13/Rttf2pt1/MD5 | 38 +- Rttf2pt1-1.3.13/Rttf2pt1/NEWS.md | 28 + Rttf2pt1-1.3.13/Rttf2pt1/R/Rttf2pt1.r | 13 Rttf2pt1-1.3.13/Rttf2pt1/README.md | 20 - Rttf2pt1-1.3.13/Rttf2pt1/man/Rttf2pt1-package.Rd |only Rttf2pt1-1.3.13/Rttf2pt1/src/Makefile.win | 23 - Rttf2pt1-1.3.13/Rttf2pt1/src/README.md | 2 Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/bdf.c | 33 +- Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/bitmap.c | 197 ++++++------ Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/ft.c | 24 - Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/global.h | 5 Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/pt1.c | 377 +++++++++++++---------- Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/t1asm.c | 49 ++ Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/ttf.c | 90 +++-- Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/ttf.h | 12 Rttf2pt1-1.3.13/Rttf2pt1/src/ttf2pt1/ttf2pt1.c | 313 ++++++++++++------- Rttf2pt1-1.3.13/Rttf2pt1/tests |only 19 files changed, 827 insertions(+), 496 deletions(-)