Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-24 0.2.0
2019-09-17 0.1.3
2019-05-14 0.1.2
2019-02-22 0.1.0
Title: Structurally Guided Sampling
Description: Structurally guided sampling (SGS) approaches for airborne laser scanning (ALS; LIDAR). Primary functions provide means
to generate data-driven stratifications & methods for allocating samples. Intermediate functions for calculating and extracting important information
about input covariates and samples are also included. Processing outcomes are intended to help forest and environmental management
practitioners better optimize field sample placement as well as assess and augment existing sample networks in the context of data
distributions and conditions. ALS data is the primary intended use case, however any rasterized remote sensing data can be used,
enabling data-driven stratifications and sampling approaches.
Author: Tristan RH Goodbody [aut, cre, cph]
,
Nicholas C Coops [aut] ,
Martin Queinnec [aut]
Maintainer: Tristan RH Goodbody <goodbody.t@gmail.com>
Diff between sgsR versions 1.3.3 dated 2023-01-17 and 1.3.4 dated 2023-01-27
DESCRIPTION | 6 MD5 | 47 +- NAMESPACE | 1 NEWS.md | 24 - R/sample_existing.R | 2 R/sample_srs.R | 5 R/sample_strat.R | 7 R/sample_systematic.R | 89 ++-- R/strat_map.R | 14 R/strat_poly.R | 2 R/utils-plot.R | 88 +++ inst/doc/calculating.html | 22 inst/doc/sampling.R | 40 - inst/doc/sampling.Rmd | 6 inst/doc/sampling.html | 712 +++++++++++++++++--------------- inst/doc/sgsR.html | 4 inst/doc/stratification.html | 9 man/plot.Rd | 12 man/sample_existing.Rd | 2 man/sample_systematic.Rd | 5 tests/testthat/test-sample_strat.R | 11 tests/testthat/test-sample_systematic.R | 12 tests/testthat/test-strat_map.R | 2 tests/testthat/test-utils-plot.R |only vignettes/sampling.Rmd | 6 25 files changed, 664 insertions(+), 464 deletions(-)
Title: Recurrent Event Regression
Description: A comprehensive collection of practical and easy-to-use tools for regression analysis of recurrent events, with or without the presence of a (possibly) informative terminal event described in Chiou et al. (2023) <doi:10.18637/jss.v105.i05>. The modeling framework is based on a joint frailty scale-change model, that includes models described in Wang et al. (2001) <doi:10.1198/016214501753209031>, Huang and Wang (2004) <doi:10.1198/016214504000001033>, Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, and Xu et al. (2019) <doi:10.5705/SS.202018.0224> as special cases. The implemented estimating procedure does not require any parametric assumption on the frailty distribution. The package also allows the users to specify different model forms for both the recurrent event process and the terminal event.
Author: Sy Han Chiou [aut, cre],
Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.4.4 dated 2022-06-15 and 1.4.5 dated 2023-01-27
DESCRIPTION | 12 MD5 | 35 - NEWS.md | 23 R/data.R | 2 R/plot.R | 1166 ++++++++++++++++++++++++---------------------- R/reReg.R | 8 R/reReg_pkg.R | 4 R/regGeneral.R | 41 + R/simu.R | 240 ++++----- inst |only man/plotEvents.control.Rd | 17 man/reReg-package.Rd | 5 man/reReg.Rd | 5 man/reReg.control.Rd | 4 man/reexports.Rd | 2 man/simDat.Rd | 2 man/simGSC.Rd | 2 src/RcppExports.cpp | 2 src/regRec.cpp | 134 ++++- 19 files changed, 933 insertions(+), 771 deletions(-)
Title: Data Analysis for Censored Environmental Data
Description: Contains methods described by Dennis Helsel in
his book "Statistics for Censored Environmental Data
using Minitab and R" (2011) and courses and videos at
<https://practicalstats.com>. This package adds new functions to
the `NADA` Package.
Author: Paul Julian [aut, cre],
Dennis Helsel [aut, cph]
Maintainer: Paul Julian <pauljulianphd@gmail.com>
Diff between NADA2 versions 1.1.1 dated 2023-01-19 and 1.1.2 dated 2023-01-27
DESCRIPTION | 8 MD5 | 10 NEWS.md | 4 R/cencorreg.R | 24 +- build/partial.rdb |binary inst/doc/DataAnalysis.html | 506 ++++++++++++++++++++++----------------------- 6 files changed, 279 insertions(+), 273 deletions(-)
Title: Fit Interpretable Machine Learning Models
Description: Package for training interpretable machine learning models. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.28 dated 2023-01-26 and 0.1.33 dated 2023-01-27
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- src/Makevars | 2 +- src/ebm_native/ApplyTermUpdate.cpp | 2 ++ src/ebm_native/BoosterShell.cpp | 2 ++ src/ebm_native/Transpose.hpp |only src/ebm_native/include_ordering.txt | 1 + 7 files changed, 17 insertions(+), 11 deletions(-)
Title: State Space Modelling in 'R'
Description: A tool that makes estimating models in state space form
a breeze. See "Time Series Analysis by State Space Methods" by
Durbin and Koopman (2012, ISBN: 978-0-19-964117-8) for details
about the algorithms implemented.
Author: Dylan Beijers [aut, cre]
Maintainer: Dylan Beijers <dylanbeijers@gmail.com>
Diff between statespacer versions 0.4.1 dated 2022-05-10 and 0.5.0 dated 2023-01-27
DESCRIPTION | 10 MD5 | 44 +- NEWS.md | 10 R/Cholesky.R | 3 R/predict.R | 550 +++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/boxjenkins.R | 3 inst/doc/boxjenkins.Rmd | 3 inst/doc/boxjenkins.html | 412 +++++++++++++++------------ inst/doc/dictionary.html | 303 +++++++++++++++----- inst/doc/intro.html | 318 ++++++++++++--------- inst/doc/seatbelt.html | 677 ++++++++++++++++++++++++--------------------- inst/doc/selfspec.R | 3 inst/doc/selfspec.Rmd | 3 inst/doc/selfspec.html | 558 +++++++++++++++++++++---------------- man/FedYieldCurve.Rd | 92 +++--- man/predict.statespacer.Rd | 28 + src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 vignettes/boxjenkins.Rmd | 3 vignettes/selfspec.Rmd | 3 23 files changed, 1983 insertions(+), 1049 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.1.3 dated 2023-01-15 and 9.1.4 dated 2023-01-27
DESCRIPTION | 8 MD5 | 218 +++++----- NEWS.md | 4 README.md | 16 src/Makevars | 8 src/swipl-devel/CMakeLists.txt | 6 src/swipl-devel/VERSION | 2 src/swipl-devel/boot/init.pl | 8 src/swipl-devel/boot/messages.pl | 44 +- src/swipl-devel/cmake/EmscriptenTargets.cmake | 21 src/swipl-devel/cmake/GCCBuiltins.cmake | 12 src/swipl-devel/doc/Testing.md | 20 src/swipl-devel/library/ansi_term.pl | 44 +- src/swipl-devel/library/build/tools.pl | 2 src/swipl-devel/library/check.pl | 7 src/swipl-devel/library/csv.pl | 2 src/swipl-devel/library/debug.pl | 125 ++++- src/swipl-devel/library/prolog_colour.pl | 75 +++ src/swipl-devel/library/prolog_config.pl | 3 src/swipl-devel/library/prolog_debug.pl | 11 src/swipl-devel/library/prolog_stack.pl | 2 src/swipl-devel/library/prolog_trace.pl | 54 +- src/swipl-devel/library/prolog_xref.pl | 6 src/swipl-devel/library/shlib.pl | 15 src/swipl-devel/library/streams.pl | 5 src/swipl-devel/packages/archive/archive4pl.c | 11 src/swipl-devel/packages/clib/nonblockio.c | 12 src/swipl-devel/packages/clib/process.c | 2 src/swipl-devel/packages/clib/streaminfo.c | 2 src/swipl-devel/packages/clib/test_uri.pl | 5 src/swipl-devel/packages/clib/time.c | 4 src/swipl-devel/packages/clib/unix.c | 11 src/swipl-devel/packages/clib/uri.c | 16 src/swipl-devel/packages/cmake/PrologPackage.cmake | 2 src/swipl-devel/packages/http/cgi_stream.c | 2 src/swipl-devel/packages/http/graphql.pl | 2 src/swipl-devel/packages/http/http_chunked.c | 2 src/swipl-devel/packages/http/http_error.pl | 15 src/swipl-devel/packages/http/http_path.pl | 29 - src/swipl-devel/packages/http/http_redis_plugin.pl | 80 ++- src/swipl-devel/packages/http/http_unix_daemon.pl | 5 src/swipl-devel/packages/http/http_wrapper.pl | 2 src/swipl-devel/packages/http/hub.pl | 4 src/swipl-devel/packages/http/term_html.pl | 2 src/swipl-devel/packages/sgml/CMakeLists.txt | 1 src/swipl-devel/packages/sgml/config.h.cmake | 2 src/swipl-devel/packages/sgml/parser.c | 5 src/swipl-devel/packages/sgml/parser.h | 1 src/swipl-devel/packages/sgml/quote.c | 77 ++- src/swipl-devel/packages/sgml/sgml.doc | 3 src/swipl-devel/packages/sgml/sgml.pl | 2 src/swipl-devel/packages/sgml/sgml2pl.c | 29 - src/swipl-devel/packages/sgml/utf8.c | 5 src/swipl-devel/packages/sgml/utf8.h | 117 +++++ src/swipl-devel/packages/sgml/util.c | 49 +- src/swipl-devel/packages/ssl/http_ssl_plugin.pl | 6 src/swipl-devel/src/CMakeLists.txt | 10 src/swipl-devel/src/SWI-Prolog.h | 2 src/swipl-devel/src/Tests/core/test_arith.pl | 16 src/swipl-devel/src/Tests/core/test_dcg.pl | 4 src/swipl-devel/src/Tests/core/test_unicode.pl | 14 src/swipl-devel/src/Tests/files/test_files.pl | 2 src/swipl-devel/src/Tests/files/test_pipe.pl | 39 - src/swipl-devel/src/Tests/library/test_aggregate.pl | 4 src/swipl-devel/src/Tests/library/test_prolog_colour.pl |only src/swipl-devel/src/Tests/tabling/test_reeval.pl | 3 src/swipl-devel/src/Tests/tabling/test_wfs.pl | 3 src/swipl-devel/src/Tests/thread_wait/test_thread_signals.pl | 2 src/swipl-devel/src/Tests/thread_wait/test_thread_wait.pl | 39 + src/swipl-devel/src/Tests/transaction/test_transaction_deadlock.pl |only src/swipl-devel/src/Tests/xsb/nonmt_tests/cmu_sei_0050.P | 4 src/swipl-devel/src/Tests/xsb/ptq/ptq.P | 12 src/swipl-devel/src/Tests/xsb/ptq/ptqlred.P | 12 src/swipl-devel/src/config.h.cmake | 2 src/swipl-devel/src/libbf/bf_gmp.h | 64 ++ src/swipl-devel/src/os/SWI-Stream.h | 23 - src/swipl-devel/src/os/pl-cstack.c | 16 src/swipl-devel/src/os/pl-prologflag.c | 3 src/swipl-devel/src/os/pl-stream.c | 76 +++ src/swipl-devel/src/pl-arith.c | 14 src/swipl-devel/src/pl-assert.c | 6 src/swipl-devel/src/pl-comp.c | 7 src/swipl-devel/src/pl-dde.c | 2 src/swipl-devel/src/pl-debug.c | 1 src/swipl-devel/src/pl-debug.h | 1 src/swipl-devel/src/pl-ext.c | 12 src/swipl-devel/src/pl-fli.c | 4 src/swipl-devel/src/pl-gmp.c | 127 ++--- src/swipl-devel/src/pl-init.c | 4 src/swipl-devel/src/pl-nt.c | 7 src/swipl-devel/src/pl-prims.c | 46 +- src/swipl-devel/src/pl-proc.c | 5 src/swipl-devel/src/pl-read.c | 12 src/swipl-devel/src/pl-setup.c | 6 src/swipl-devel/src/pl-srcfile.c | 2 src/swipl-devel/src/pl-termhash.c | 17 src/swipl-devel/src/pl-thread.c | 7 src/swipl-devel/src/pl-trace.c | 2 src/swipl-devel/src/pl-transaction.c | 19 src/swipl-devel/src/pl-util.c | 10 src/swipl-devel/src/pl-vmi.c | 53 ++ src/swipl-devel/src/pl-write.c | 2 src/swipl-devel/src/test.pl | 8 src/swipl-devel/src/wasm/cbg.html | 2 src/swipl-devel/src/wasm/chat80.html | 2 src/swipl-devel/src/wasm/pl-wasm.c | 2 src/swipl-devel/src/wasm/pre.js | 10 src/swipl-devel/src/wasm/prolog.js | 10 src/swipl-devel/src/wasm/server.pl | 3 src/swipl-devel/src/wasm/shell.html | 5 src/swipl-devel/src/wasm/test.html | 2 111 files changed, 1355 insertions(+), 628 deletions(-)
Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <https://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'. The vignette provides an update of the original paper <doi:10.18637/jss.v092.i04>.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 3.2.19 dated 2020-04-05 and 3.2.21 dated 2023-01-27
rscala-3.2.19/rscala/vignettes/rscala-concordance.tex |only rscala-3.2.21/rscala/DESCRIPTION | 12 ++--- rscala-3.2.21/rscala/MD5 | 27 ++++++------- rscala-3.2.21/rscala/NEWS | 3 + rscala-3.2.21/rscala/R/scala.R | 14 +++--- rscala-3.2.21/rscala/R/scalaConfig.R | 34 ++++++---------- rscala-3.2.21/rscala/R/sysdata.rda |binary rscala-3.2.21/rscala/README.md | 27 ++++++++----- rscala-3.2.21/rscala/build/vignette.rds |binary rscala-3.2.21/rscala/inst/data-raw/urls.txt | 37 ++++++------------ rscala-3.2.21/rscala/inst/doc/rscala.pdf |binary rscala-3.2.21/rscala/inst/java/scala-2.11/rscala.jar |binary rscala-3.2.21/rscala/inst/java/scala-2.12/rscala.jar |binary rscala-3.2.21/rscala/inst/java/scala-2.13/rscala.jar |binary rscala-3.2.21/rscala/java/rscala-source.jar |binary 15 files changed, 73 insertions(+), 81 deletions(-)
Title: 'Mangal' Client
Description: An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
Author: Steve Vissault [aut, ctb] ,
Kevin Cazelles [aut, cre] ,
Gabriel Bergeron [aut, ctb],
Benjamin Mercier [aut, ctb],
Clement Violet [aut, ctb],
Dominique Gravel [aut],
Timothee Poisot [aut],
Thomas Lin Pedersen [rev] ,
Anna Willoughby [rev]
Maintainer: Kevin Cazelles <kevin.cazelles@gmail.com>
Diff between rmangal versions 2.1.1 dated 2022-05-15 and 2.1.2 dated 2023-01-27
rmangal-2.1.1/rmangal/tests/fixtures/get_404.yml |only rmangal-2.1.1/rmangal/tests/fixtures/get_citation.yml |only rmangal-2.1.1/rmangal/tests/fixtures/get_collection_id.yml |only rmangal-2.1.1/rmangal/tests/fixtures/mg100.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_datasets_default.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_datasets_empty.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_datasets_list.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_interactions_default.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_interactions_id100.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_interactions_type.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_networks_def.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_networks_spat.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_nodes_default.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_nodes_id926.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_references_default.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_references_list.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_taxonomy_default.yml |only rmangal-2.1.1/rmangal/tests/fixtures/search_taxonomy_taxid.yml |only rmangal-2.1.2/rmangal/DESCRIPTION | 8 - rmangal-2.1.2/rmangal/MD5 | 66 +++++----- rmangal-2.1.2/rmangal/NEWS.md | 11 - rmangal-2.1.2/rmangal/README.md | 6 rmangal-2.1.2/rmangal/build/vignette.rds |binary rmangal-2.1.2/rmangal/inst/bib/main.bib | 1 rmangal-2.1.2/rmangal/inst/doc/rmangal.Rmd | 4 rmangal-2.1.2/rmangal/inst/doc/rmangal.html | 17 +- rmangal-2.1.2/rmangal/man/as.igraph.Rd | 6 rmangal-2.1.2/rmangal/man/get_citation.Rd | 6 rmangal-2.1.2/rmangal/man/get_collection.Rd | 16 +- rmangal-2.1.2/rmangal/man/get_network_by_id.Rd | 4 rmangal-2.1.2/rmangal/man/search_networks.Rd | 4 rmangal-2.1.2/rmangal/tests/fixtures/get_404.json |only rmangal-2.1.2/rmangal/tests/fixtures/get_citation.json |only rmangal-2.1.2/rmangal/tests/fixtures/get_collection_id.json |only rmangal-2.1.2/rmangal/tests/fixtures/mg100.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_datasets_default.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_datasets_empty.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_datasets_list.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_interactions_default.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_interactions_id100.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_interactions_type.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_networks_def.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_networks_spat.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_nodes_default.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_nodes_id926.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_references_default.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_references_list.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_taxonomy_default.json |only rmangal-2.1.2/rmangal/tests/fixtures/search_taxonomy_taxid.json |only rmangal-2.1.2/rmangal/tests/testthat/setup-rmangal.R | 6 rmangal-2.1.2/rmangal/vignettes/rmangal.Rmd | 4 rmangal-2.1.2/rmangal/vignettes/rmangal.Rmd.orig | 2 52 files changed, 86 insertions(+), 75 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@rstudio.com>
Diff between reticulate versions 1.27 dated 2023-01-07 and 1.28 dated 2023-01-27
DESCRIPTION | 6 MD5 | 32 NEWS.md | 12 R/config.R | 17 R/miniconda.R | 4 R/utils.R | 6 build/vignette.rds |binary inst/doc/arrays.html | 1076 +++++++++++++++------------ inst/doc/calling_python.html | 660 ++++++++++------- inst/doc/package.html | 471 +++++++----- inst/doc/python_dependencies.html | 289 ++++--- inst/doc/python_packages.html | 304 ++++--- inst/doc/python_primer.html | 1466 ++++++++++++++++++++++---------------- inst/doc/r_markdown.html | 82 +- inst/doc/versions.html | 256 ++++-- inst/python/rpytools/call.py | 50 - src/python.cpp | 33 17 files changed, 2904 insertions(+), 1860 deletions(-)
Title: Pretty Colour Palettes
Description: Defines aesthetically pleasing colour palettes.
Author: Nicola Rennie [aut, cre]
Maintainer: Nicola Rennie <nrennie35@gmail.com>
Diff between PrettyCols versions 1.0.0 dated 2022-08-31 and 1.0.1 dated 2023-01-27
DESCRIPTION | 8 MD5 | 89 +++++----- NAMESPACE | 2 NEWS.md | 10 + R/PrettyColsPalettes.R | 129 +++++++++++--- R/colorblind_friendly.R |only R/colourblind_friendly.R |only R/prettycols.R | 4 R/print_palette.R | 4 R/scale_color_pretty_c.R | 12 + R/scale_color_pretty_d.R | 18 +- R/scale_colour_pretty_c.R | 1 R/scale_colour_pretty_d.R | 1 R/scale_fill_pretty_c.R | 14 + R/scale_fill_pretty_d.R | 19 +- R/view_all_palettes.R | 35 ++- README.md | 11 - build/vignette.rds |binary inst/doc/available-palettes.R | 40 ++++ inst/doc/available-palettes.Rmd | 71 +++++++ inst/doc/available-palettes.html | 249 +++++++++++++++++----------- inst/doc/colourblind-friendly-palettes.R |only inst/doc/colourblind-friendly-palettes.Rmd |only inst/doc/colourblind-friendly-palettes.html |only inst/doc/using-with-ggplot2.R | 9 - inst/doc/using-with-ggplot2.Rmd | 16 + inst/doc/using-with-ggplot2.html | 132 +++++++------- inst/doc/using-with-python.R |only inst/doc/using-with-python.Rmd |only inst/doc/using-with-python.html |only inst/doc/viewing-palettes.R | 2 inst/doc/viewing-palettes.Rmd | 8 inst/doc/viewing-palettes.html | 136 +++++++-------- man/PrettyColsPalettes.Rd | 2 man/colorblind_friendly.Rd |only man/colourblind_friendly.Rd |only man/figures/logo.png |binary man/scale_color_pretty_c.Rd | 4 man/scale_color_pretty_d.Rd | 4 man/scale_colour_pretty_c.Rd | 4 man/scale_colour_pretty_d.Rd | 4 man/scale_fill_pretty_c.Rd | 4 man/scale_fill_pretty_d.Rd | 4 man/view_all_palettes.Rd | 9 - tests/testthat/test-display.R | 10 + tests/testthat/test-scales.R | 44 ++++ vignettes/available-palettes.Rmd | 71 +++++++ vignettes/colourblind-friendly-palettes.Rmd |only vignettes/matplotlib-bright.png |only vignettes/using-with-ggplot2.Rmd | 16 + vignettes/using-with-python.Rmd |only vignettes/viewing-palettes.Rmd | 8 52 files changed, 839 insertions(+), 365 deletions(-)
Title: Density Goodness-of-Fit Test
Description: Provides functions for the implementation of a density goodness-of-fit test, based on piecewise approximation of the L2 distance.
Author: Dimitrios Bagkavos [aut, cre]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between L2DensityGoFtest versions 0.5.0 dated 2022-05-15 and 0.6.0 dated 2023-01-27
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- NAMESPACE | 1 + R/S.nd.R |only man/S.nd.Rd |only 5 files changed, 9 insertions(+), 6 deletions(-)
More information about L2DensityGoFtest at CRAN
Permanent link
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>
Diff between distances versions 0.1.8 dated 2019-09-18 and 0.1.9 dated 2023-01-27
DESCRIPTION | 13 ++++++------- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ README.md | 7 ++----- man/distances.Rd | 9 +++++++-- man/max_distance_search.Rd | 3 +-- man/nearest_neighbor_search.Rd | 9 +++++++-- src/internal.c | 4 ++-- 8 files changed, 40 insertions(+), 27 deletions(-)
Title: Delaunay and Voronoï Tessellations
Description: Delaunay and Voronoï tessellations, with emphasis on the
two-dimensional and the three-dimensional cases (the package provides
functions to plot the tessellations for these cases). Delaunay
tessellations are computed in C with the help of the 'Qhull' library
<http://www.qhull.org/>.
Author: Stephane Laurent [aut, cre],
C. B. Barber [cph] ,
The Geometry Center [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between tessellation versions 2.1.0 dated 2022-04-05 and 2.1.1 dated 2023-01-27
DESCRIPTION | 30 +++++++++++------- MD5 | 12 +++---- NEWS.md | 39 +++++++++++++----------- README.md | 90 ++++++++++++++++++++++++++++---------------------------- src/delaunay.c | 4 +- src/global_r.c | 6 +-- src/rboxlib_r.c | 2 - 7 files changed, 97 insertions(+), 86 deletions(-)
Title: Sparse Group Lasso
Description: Efficient implementation of sparse group lasso with optional
bound constraints on the coefficients. It supports the use of a sparse
design matrix as well as returning coefficient estimates in a sparse
matrix. Furthermore, it correctly calculates the degrees of freedom to
allow for information criteria rather than cross-validation with very
large data. Finally, the interface to compiled code avoids unnecessary
copies and allows for the use of long integers.
Author: Daniel J. McDonald [aut, cre],
Xiaoxuan Liang [aut],
Anibal Solon Heinsfeld [aut],
Aaron Cohen [aut],
Yi Yang [ctb],
Hui Zou [ctb],
Jerome Friedman [ctb],
Trevor Hastie [ctb],
Rob Tibshirani [ctb],
Balasubramanian Narasimhan [ctb],
Kenneth Tay [ctb], [...truncated...]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between sparsegl versions 1.0.0 dated 2022-11-28 and 1.0.1 dated 2023-01-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- data/trust_experts.rda |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Description: Functions to simplify the linking of open source GIS and remote sensing related command line interfaces.
Author: Chris Reudenbach [cre, aut],
Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Diff between link2GI versions 0.5-0 dated 2022-08-29 and 0.5-2 dated 2023-01-27
DESCRIPTION | 16 +- MD5 | 94 ++++++------- NEWS | 19 ++ NEWS.md | 19 ++ R/gdalControls.R | 16 +- R/grassControl.R | 16 +- R/link2GI-package.R | 4 R/link2giKarim.R | 110 +++++++++------ R/linkGRASS.R | 247 ++++++++++++++++++++--------------- R/linkOTB.R | 3 R/otbControls.R | 8 - R/parseOTB.R | 133 ++++++++++++------- README.md | 8 - build/vignette.rds |binary data/rgb.rda |binary inst/doc/link2GI1.Rmd | 4 inst/doc/link2GI1.html | 266 ++++++++------------------------------ inst/doc/link2GI2.R | 6 inst/doc/link2GI2.Rmd | 8 - inst/doc/link2GI2.html | 339 ++++++++++++------------------------------------- inst/doc/link2GI3.R | 16 -- inst/doc/link2GI3.Rmd | 23 +-- inst/doc/link2GI3.html | 303 +++++++++++-------------------------------- inst/doc/link2GI4.R | 4 inst/doc/link2GI4.Rmd | 4 inst/doc/link2GI4.html | 238 ++++++++-------------------------- inst/doc/link2GI5.html | 181 ++++++-------------------- inst/doc/link2GI6.Rmd | 4 inst/doc/link2GI6.html | 313 ++++++++++++--------------------------------- man/findGDAL.Rd | 4 man/getSpatialClass.Rd | 2 man/gvec2sf.Rd | 35 ++--- man/linkAll.Rd | 9 - man/linkGRASS.Rd | 46 +++--- man/linkGRASS7.Rd | 24 +-- man/paramGRASSw.Rd | 8 - man/paramGRASSx.Rd | 4 man/rgb.Rd | 4 man/runOTB.Rd | 30 ++-- man/searchGDALW.Rd | 4 man/searchGDALX.Rd | 4 man/setenvGDAL.Rd | 4 man/sf2gvec.Rd | 43 +++--- vignettes/link2GI1.Rmd | 4 vignettes/link2GI2.Rmd | 8 - vignettes/link2GI3.Rmd | 23 +-- vignettes/link2GI4.Rmd | 4 vignettes/link2GI6.Rmd | 4 48 files changed, 1018 insertions(+), 1648 deletions(-)
Title: Convex Hull
Description: Computes the convex hull in arbitrary dimension, based on the
Qhull library (<http://www.qhull.org>). The package provides a
complete description of the convex hull: edges, ridges, facets,
adjacencies. Triangulation is optional.
Author: C. B. Barber [cph] ,
The Geometry Center [cph],
Stephane Laurent [cph, aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between cxhull versions 0.7.0 dated 2022-10-25 and 0.7.1 dated 2023-01-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ src/convexhull.c | 2 +- src/global_r.c | 6 +++--- 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.28.8 dated 2022-10-27 and 0.29.4 dated 2023-01-27
rayrender-0.28.8/rayrender/src/test_windows.cpp |only rayrender-0.29.4/rayrender/DESCRIPTION | 12 rayrender-0.29.4/rayrender/MD5 | 27 rayrender-0.29.4/rayrender/R/generate_camera_motion.R | 86 rayrender-0.29.4/rayrender/R/objects.R | 2 rayrender-0.29.4/rayrender/configure | 2511 ++++++++++----- rayrender-0.29.4/rayrender/configure.ac | 9 rayrender-0.29.4/rayrender/man/generate_camera_motion.Rd | 10 rayrender-0.29.4/rayrender/src/buildscene.cpp | 2 rayrender-0.29.4/rayrender/src/distributions.cpp | 2 rayrender-0.29.4/rayrender/src/integrator.cpp | 12 rayrender-0.29.4/rayrender/src/mathinline.h | 1 rayrender-0.29.4/rayrender/src/mesh3d.cpp | 10 rayrender-0.29.4/rayrender/src/render_scene_rcpp.cpp | 10 rayrender-0.29.4/rayrender/src/trianglemesh.cpp | 12 15 files changed, 1852 insertions(+), 854 deletions(-)
Title: Analysis of Graph-Structured Data with a Focus on
Protein-Protein Interaction Networks
Description: Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.
Author: Davis Weaver [aut, cre]
Maintainer: Davis Weaver <davis.weaver@case.edu>
Diff between crosstalkr versions 0.9.0 dated 2022-11-16 and 1.0.0 dated 2023-01-27
crosstalkr-0.9.0/crosstalkr/R/compute_crosstalk.R |only crosstalkr-0.9.0/crosstalkr/tests/testthat/test-compute_crosstalk.R |only crosstalkr-1.0.0/crosstalkr/DESCRIPTION | 23 crosstalkr-1.0.0/crosstalkr/MD5 | 80 - crosstalkr-1.0.0/crosstalkr/NAMESPACE | 23 crosstalkr-1.0.0/crosstalkr/R/RcppExports.R |only crosstalkr-1.0.0/crosstalkr/R/calc_np.R |only crosstalkr-1.0.0/crosstalkr/R/create_null.R | 186 +++ crosstalkr-1.0.0/crosstalkr/R/crosstalkr-package.R | 15 crosstalkr-1.0.0/crosstalkr/R/filter.R |only crosstalkr-1.0.0/crosstalkr/R/node_suppression.R |only crosstalkr-1.0.0/crosstalkr/R/np_pipeline.R |only crosstalkr-1.0.0/crosstalkr/R/plot.R | 16 crosstalkr-1.0.0/crosstalkr/R/ppi_ingest.R | 44 crosstalkr-1.0.0/crosstalkr/R/utils.R | 56 crosstalkr-1.0.0/crosstalkr/README.md | 42 crosstalkr-1.0.0/crosstalkr/inst/doc/crosstalkr_vignette.R | 60 - crosstalkr-1.0.0/crosstalkr/inst/doc/crosstalkr_vignette.Rmd | 151 ++ crosstalkr-1.0.0/crosstalkr/inst/doc/crosstalkr_vignette.html | 594 ++++++++-- crosstalkr-1.0.0/crosstalkr/man/add_expression.Rd |only crosstalkr-1.0.0/crosstalkr/man/add_value.Rd |only crosstalkr-1.0.0/crosstalkr/man/bootstrap_null.Rd | 122 +- crosstalkr-1.0.0/crosstalkr/man/calc_dnp_i.Rd |only crosstalkr-1.0.0/crosstalkr/man/calc_np.Rd |only crosstalkr-1.0.0/crosstalkr/man/calc_np_all.Rd |only crosstalkr-1.0.0/crosstalkr/man/calc_np_all_legacy.Rd |only crosstalkr-1.0.0/crosstalkr/man/calc_np_i.Rd |only crosstalkr-1.0.0/crosstalkr/man/combine_null.Rd |only crosstalkr-1.0.0/crosstalkr/man/compute_crosstalk.Rd | 206 +-- crosstalkr-1.0.0/crosstalkr/man/compute_dnp.Rd |only crosstalkr-1.0.0/crosstalkr/man/compute_np.Rd |only crosstalkr-1.0.0/crosstalkr/man/compute_null_dnp.Rd |only crosstalkr-1.0.0/crosstalkr/man/crosstalk_subgraph.Rd | 58 crosstalkr-1.0.0/crosstalkr/man/dist_calc.Rd | 42 crosstalkr-1.0.0/crosstalkr/man/experiment_breakout.Rd |only crosstalkr-1.0.0/crosstalkr/man/fcalc_np_all.Rd |only crosstalkr-1.0.0/crosstalkr/man/final_combine.Rd |only crosstalkr-1.0.0/crosstalkr/man/final_dist_calc.Rd | 34 crosstalkr-1.0.0/crosstalkr/man/get_neighbors.Rd |only crosstalkr-1.0.0/crosstalkr/man/get_random_graph.Rd |only crosstalkr-1.0.0/crosstalkr/man/get_topn.Rd |only crosstalkr-1.0.0/crosstalkr/man/gfilter.Rd |only crosstalkr-1.0.0/crosstalkr/man/gfilter.ct.Rd |only crosstalkr-1.0.0/crosstalkr/man/gfilter.igraph_method.Rd |only crosstalkr-1.0.0/crosstalkr/man/gfilter.np.Rd |only crosstalkr-1.0.0/crosstalkr/man/gfilter.value.Rd |only crosstalkr-1.0.0/crosstalkr/man/load_ppi.Rd |only crosstalkr-1.0.0/crosstalkr/man/node_repression.Rd |only crosstalkr-1.0.0/crosstalkr/man/ppi_intersection.Rd | 46 crosstalkr-1.0.0/crosstalkr/man/prep_stringdb.Rd | 7 crosstalkr-1.0.0/crosstalkr/man/tidy_expression.Rd |only crosstalkr-1.0.0/crosstalkr/src |only crosstalkr-1.0.0/crosstalkr/tests/testthat/test-calc_np.R |only crosstalkr-1.0.0/crosstalkr/tests/testthat/test-create_null.R | 2 crosstalkr-1.0.0/crosstalkr/tests/testthat/test-filter.R |only crosstalkr-1.0.0/crosstalkr/tests/testthat/test-node_suppression.R |only crosstalkr-1.0.0/crosstalkr/tests/testthat/test-ppi_ingest.R | 3 crosstalkr-1.0.0/crosstalkr/vignettes/crosstalkr_vignette.Rmd | 151 ++ crosstalkr-1.0.0/crosstalkr/vignettes/rsconnect |only 59 files changed, 1576 insertions(+), 385 deletions(-)
More information about RationalMatrix at CRAN
Permanent link
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks
(walk, bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks engine
<https://github.com/conveyal/r5>. The package allows users to generate
detailed routing analysis or calculate travel time matrices using
seamless parallel computing on top of the R5 Java machine. While R5
is developed by Conveyal, the package r5r is independently developed
by a team at the Institute for Applied Economic Research (Ipea) with
contributions from collaborators. Apart from the documentation in this
package, users will find additional information on R5 documentation at
<https://docs.conveyal.com/>. Although we try to keep new releases of
r5r in synchrony with R5, the development of R5 follows Conveyal's
independent update process. Hence, users should confirm the R5 version
implied by the Conveyal user manual (see
<https://docs.conveyal.com/changelog>) corresponds with the R5 ver [...truncated...]
Author: Marcus Saraiva [aut] ,
Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Carlos Kaue Vieira Braga [aut]
,
Matthew Wigginton Conway [aut]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 0.7.1 dated 2022-07-05 and 1.0.0 dated 2023-01-27
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Title: Owen Q-Function
Description: Evaluates the Owen Q-function for an integer value of the
degrees of freedom, by applying Owen's algorithm (1965)
<doi:10.1093/biomet/52.3-4.437>. It is useful for the calculation of
the power of equivalence tests.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between OwenQ versions 1.0.5 dated 2022-01-05 and 1.0.6 dated 2023-01-27
DESCRIPTION | 26 MD5 | 22 NEWS.md | 50 R/RcppExports.R | 126 - README.md | 5 build/vignette.rds |binary inst/doc/OwenQ.R | 164 +- inst/doc/OwenQ.html | 1045 ++++++++----- inst/doc/Validation.R | 784 +++++----- inst/doc/Validation.html | 3547 +++++++++++++++++++++++++---------------------- src/Makevars | 2 src/Makevars.win | 4 12 files changed, 3217 insertions(+), 2558 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package
development. This can retrieve all dependencies that are used in ".R"
files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and
in 'roxygen2' documentation of functions. There is a function to
update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package.
All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can
be used independently of a package development.
Author: Sebastien Rochette [cre, aut] ,
Vincent Guyader [aut] ,
ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between attachment versions 0.3.0 dated 2022-09-19 and 0.3.1 dated 2023-01-27
DESCRIPTION | 9 MD5 | 56 ++-- NEWS.md | 12 R/att_from_namespace.R | 6 R/att_to_description.R | 29 +- R/create_dependencies_file.R | 6 R/create_renv.R | 23 + R/set_remotes.R | 17 + README.md | 56 +++- inst/doc/a-fill-pkg-description.R | 22 + inst/doc/a-fill-pkg-description.Rmd | 39 ++- inst/doc/a-fill-pkg-description.html | 227 +++++++++-------- inst/doc/b-bookdown-and-scripts.html | 115 ++++---- inst/doc/use_renv.html | 111 ++++---- inst/dummypackage/man/my_mean.Rd | 28 +- man/att_amend_desc.Rd | 16 - man/att_from_namespace.Rd | 6 man/att_to_desc_from_is.Rd | 10 man/create_dependencies_file.Rd | 6 man/create_renv_for_dev.Rd | 4 man/set_remotes_to_desc.Rd | 7 tests/testthat/test-amend-description.R | 110 ++++++-- tests/testthat/test-att_from_namespace.R | 13 - tests/testthat/test-create_dependencies_file.R | 6 tests/testthat/test-install_from_description.R | 5 tests/testthat/test-renv_create.R | 322 +++++++++++++++++++++++-- tests/testthat/test-rscript.R | 4 tests/testthat/test-set-remotes.R | 44 +++ vignettes/a-fill-pkg-description.Rmd | 39 ++- 29 files changed, 982 insertions(+), 366 deletions(-)
Title: Download and Manage Open Data from INEGI
Description: Download and manage data sets of statistical projects and geographic data created by Instituto Nacional de Estadistica y Geografia (INEGI). See <https://www.inegi.org.mx/>.
Author: Cesar Renteria [aut, cre]
Maintainer: Cesar Renteria <cesar.renteria@cide.edu>
Diff between importinegi versions 1.1.3 dated 2021-01-13 and 1.2.0 dated 2023-01-27
DESCRIPTION | 9 - MD5 | 18 +- R/catalogo_inegi.R | 4 R/enoe.R | 74 +++------- README.md | 5 build/vignette.rds |binary inst/doc/importinegi.R | 10 - inst/doc/importinegi.Rmd | 10 - inst/doc/importinegi.html | 318 ++++++++++------------------------------------ vignettes/importinegi.Rmd | 10 - 10 files changed, 135 insertions(+), 323 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stephane Dray <stephane.dray@univ-lyon1.fr> and Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferriere.
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-16 dated 2021-09-16 and 1.0-17 dated 2023-01-27
DESCRIPTION | 8 MD5 | 40 +- R/ADEg.C1.R | 2 R/ADEg.S2.R | 18 - R/ADEgS.R | 6 R/S2.arrow.R | 2 R/S2.class.R | 2 R/S2.corcircle.R | 2 R/S2.density.R | 2 R/S2.distri.R | 2 R/S2.image.R | 2 R/S2.label.R | 2 R/S2.logo.R | 2 R/S2.match.R | 2 R/S2.traject.R | 2 R/S2.value.R | 2 R/Tr.match.R | 2 R/utils.R | 4 build/vignette.rds |binary inst/doc/adegraphics.html | 679 ++++++++++++++++++++++++---------------------- man/adeg.panel.label.Rd | 4 21 files changed, 415 insertions(+), 370 deletions(-)
Title: Parametric Ordinary Differential Equations Model of Growth,
Death, and Respiration of Macroinvertebrate and Algae Taxa
Description: Numerically solve and plot solutions of a parametric ordinary
differential equations model of growth, death, and respiration of
macroinvertebrate and algae taxa dependent on pre-defined environmental
factors. The model (version 1.0) is introduced in Schuwirth, N. and
Reichert, P., (2013) <DOI:10.1890/12-0591.1>. This package includes
model extensions and the core functions introduced and used in
Schuwirth, N. et al. (2016) <DOI:10.1111/1365-2435.12605>,
Kattwinkel, M. et al. (2016) <DOI:10.1021/acs.est.5b04068>,
Mondy, C. P., and Schuwirth, N. (2017) <DOI:10.1002/eap.1530>,
and Paillex, A. et al. (2017) <DOI:10.1111/fwb.12927>.
Author: Nele Schuwirth, Peter Reichert, Mikolaj Rybinski
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between streambugs versions 1.2 dated 2020-10-20 and 1.3 dated 2023-01-27
DESCRIPTION | 10 MD5 | 78 NAMESPACE | 56 R/streambugs-package.r | 14 R/streambugs.r | 1162 R/streambugs_aux.r | 3202 R/streambugs_aux_indval_vec.R | 776 R/streambugs_aux_proc.r | 982 R/streambugs_c.r | 498 R/streambugs_examples.r | 628 R/streambugs_plot.r | 1024 inst/extdata/extended_example-pars.tsv | 5052 - inst/extdata/extended_example-vars_sourcepooltaxa.tsv | 74 man/construct.statevariables.Rd | 88 man/count.feeding.links.Rd | 60 man/decode.statevarnames.Rd | 70 man/foodweb.plot.Rd | 162 man/plot.streambugs.Rd | 60 man/run.streambugs.Rd | 208 man/streambugs-package.Rd | 42 man/streambugs.example.model.extended.Rd | 68 man/streambugs.example.model.toy.Rd | 78 man/streambugs.get.sys.def.Rd | 82 man/streambugs.write.sys.def.Rd | 52 src/streambugs_init.c | 24 src/streambugs_rhs.c | 53 tests/benchmarks/run_for_toy.R | 348 tests/testthat.R | 8 tests/testthat/extended_example_res_C.csv | 404 tests/testthat/extended_example_sysdef.dat |41028 +++++----- tests/testthat/get_inpind_parval_envcond_habitat-minimum_example.json | 296 tests/testthat/helper_test_example.R | 172 tests/testthat/minimum_example_res_C.csv | 404 tests/testthat/minimum_example_res_R.csv | 404 tests/testthat/minimum_example_sysdef.dat | 4420 - tests/testthat/run_extended_example.R | 86 tests/testthat/run_minimum_example.R | 210 tests/testthat/test_aux.R | 688 tests/testthat/test_extended_example.R | 82 tests/testthat/test_minimum_example.R | 112 40 files changed, 31633 insertions(+), 31632 deletions(-)
Title: MST-kNN Clustering Algorithm
Description: Implements the MST-kNN clustering algorithm which was proposed by Inostroza-Ponta, M. (2008) <https://trove.nla.gov.au/work/28729389?selectedversion=NBD44634158>.
Author: Jorge Parraga-Alava [aut, cre],
Pablo Moscato [aut],
Mario Inostroza-Ponta [aut]
Maintainer: Jorge Parraga-Alava <jorge.parraga@usach.cl>
Diff between mstknnclust versions 0.3.1 dated 2020-09-17 and 0.3.2 dated 2023-01-27
DESCRIPTION | 8 MD5 | 18 R/dsyeastexpression.R | 34 build/vignette.rds |binary inst/doc/guide.R | 64 inst/doc/guide.Rmd | 232 +- inst/doc/guide.html | 1329 ++++++++-------- man/dsyeastexpression.Rd | 2 vignettes/guide.Rmd | 232 +- vignettes/guide_files/figure-html/unnamed-chunk-6-1.png |binary 10 files changed, 1020 insertions(+), 899 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.3.2 dated 2022-11-24 and 4.4.0 dated 2023-01-27
ergm-4.3.2/ergm/man/as.rlebdm.ergm.Rd |only ergm-4.4.0/ergm/DESCRIPTION | 40 ergm-4.4.0/ergm/LICENSE | 2 ergm-4.4.0/ergm/MD5 | 678 +++++----- ergm-4.4.0/ergm/NAMESPACE | 5 ergm-4.4.0/ergm/R/InitErgmConstraint.R | 2 ergm-4.4.0/ergm/R/InitErgmConstraint.blockdiag.R | 4 ergm-4.4.0/ergm/R/InitErgmConstraint.hints.R | 2 ergm-4.4.0/ergm/R/InitErgmProposal.R | 2 ergm-4.4.0/ergm/R/InitErgmProposal.dyadnoise.R | 2 ergm-4.4.0/ergm/R/InitErgmReference.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.auxnet.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.bipartite.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.bipartite.degree.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.blockop.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.coincidence.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.dgw_sp.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.extra.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.indices.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.interaction.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.operator.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.spcache.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.test.R | 2 ergm-4.4.0/ergm/R/InitErgmTerm.transitiveties.R | 2 ergm-4.4.0/ergm/R/InitWtErgmProposal.R | 2 ergm-4.4.0/ergm/R/InitWtErgmTerm.R | 2 ergm-4.4.0/ergm/R/InitWtErgmTerm.operator.R | 2 ergm-4.4.0/ergm/R/InitWtErgmTerm.test.R | 2 ergm-4.4.0/ergm/R/anova.ergm.R | 2 ergm-4.4.0/ergm/R/anova.ergmlist.R | 2 ergm-4.4.0/ergm/R/approx.hotelling.diff.test.R | 2 ergm-4.4.0/ergm/R/as.network.numeric.R | 2 ergm-4.4.0/ergm/R/build_term_index.R | 2 ergm-4.4.0/ergm/R/check.ErgmTerm.R | 2 ergm-4.4.0/ergm/R/control.ergm.R | 18 ergm-4.4.0/ergm/R/control.ergm.bridge.R | 2 ergm-4.4.0/ergm/R/control.gof.R | 2 ergm-4.4.0/ergm/R/control.logLik.ergm.R | 2 ergm-4.4.0/ergm/R/control.san.R | 2 ergm-4.4.0/ergm/R/control.simulate.R | 2 ergm-4.4.0/ergm/R/data.R | 2 ergm-4.4.0/ergm/R/ergm-defunct.R | 2 ergm-4.4.0/ergm/R/ergm-deprecated.R | 2 ergm-4.4.0/ergm/R/ergm-internal.R | 2 ergm-4.4.0/ergm/R/ergm-options.R | 2 ergm-4.4.0/ergm/R/ergm-package.R | 10 ergm-4.4.0/ergm/R/ergm-terms-index.R | 2 ergm-4.4.0/ergm/R/ergm.CD.fixed.R | 2 ergm-4.4.0/ergm/R/ergm.Cprepare.R | 2 ergm-4.4.0/ergm/R/ergm.MCMCse.R | 2 ergm-4.4.0/ergm/R/ergm.MCMLE.R | 2 ergm-4.4.0/ergm/R/ergm.R | 87 - ergm-4.4.0/ergm/R/ergm.allstats.R | 2 ergm-4.4.0/ergm/R/ergm.auxstorage.R | 2 ergm-4.4.0/ergm/R/ergm.bounddeg.R | 2 ergm-4.4.0/ergm/R/ergm.bridge.R | 2 ergm-4.4.0/ergm/R/ergm.design.R | 2 ergm-4.4.0/ergm/R/ergm.errors.R | 2 ergm-4.4.0/ergm/R/ergm.estimate.R | 2 ergm-4.4.0/ergm/R/ergm.eta.R | 2 ergm-4.4.0/ergm/R/ergm.etagrad.R | 2 ergm-4.4.0/ergm/R/ergm.etagradmult.R | 2 ergm-4.4.0/ergm/R/ergm.etamap.R | 2 ergm-4.4.0/ergm/R/ergm.geodistn.R | 2 ergm-4.4.0/ergm/R/ergm.getCDsample.R | 2 ergm-4.4.0/ergm/R/ergm.getMCMCsample.R | 2 ergm-4.4.0/ergm/R/ergm.getnetwork.R | 2 ergm-4.4.0/ergm/R/ergm.initialfit.R | 2 ergm-4.4.0/ergm/R/ergm.llik.R | 2 ergm-4.4.0/ergm/R/ergm.llik.obs.R | 2 ergm-4.4.0/ergm/R/ergm.logitreg.R | 2 ergm-4.4.0/ergm/R/ergm.mple.R | 21 ergm-4.4.0/ergm/R/ergm.pen.glm.R | 2 ergm-4.4.0/ergm/R/ergm.phase12.R | 2 ergm-4.4.0/ergm/R/ergm.pl.R | 2 ergm-4.4.0/ergm/R/ergm.san.R | 3 ergm-4.4.0/ergm/R/ergm.stepping.R | 2 ergm-4.4.0/ergm/R/ergm.stocapprox.R | 2 ergm-4.4.0/ergm/R/ergm.utility.R | 6 ergm-4.4.0/ergm/R/ergmMPLE.R | 3 ergm-4.4.0/ergm/R/ergm_estfun.R | 2 ergm-4.4.0/ergm/R/ergm_keyword.R | 2 ergm-4.4.0/ergm/R/ergm_model.R | 2 ergm-4.4.0/ergm/R/ergm_model.utils.R | 2 ergm-4.4.0/ergm/R/ergm_proposal.R | 2 ergm-4.4.0/ergm/R/ergm_response.R | 2 ergm-4.4.0/ergm/R/ergm_state.R | 2 ergm-4.4.0/ergm/R/ergmlhs.R | 2 ergm-4.4.0/ergm/R/formula.utils.R | 2 ergm-4.4.0/ergm/R/get.node.attr.R | 2 ergm-4.4.0/ergm/R/godfather.R | 2 ergm-4.4.0/ergm/R/gof.ergm.R | 6 ergm-4.4.0/ergm/R/is.curved.R | 2 ergm-4.4.0/ergm/R/is.dyad.independent.R | 20 ergm-4.4.0/ergm/R/is.inCH.R | 2 ergm-4.4.0/ergm/R/is.na.ergm.R |only ergm-4.4.0/ergm/R/is.valued.R | 5 ergm-4.4.0/ergm/R/logLik.ergm.R | 29 ergm-4.4.0/ergm/R/mcmc.diagnostics.ergm.R | 73 - ergm-4.4.0/ergm/R/network.list.R | 2 ergm-4.4.0/ergm/R/network.update.R | 2 ergm-4.4.0/ergm/R/nonidentifiability.R | 2 ergm-4.4.0/ergm/R/nparam.R | 2 ergm-4.4.0/ergm/R/obs.constraints.R | 2 ergm-4.4.0/ergm/R/parallel.utils.R | 2 ergm-4.4.0/ergm/R/param_names.R | 2 ergm-4.4.0/ergm/R/predict.ergm.R | 2 ergm-4.4.0/ergm/R/print.ergm.R | 17 ergm-4.4.0/ergm/R/print.network.list.R | 2 ergm-4.4.0/ergm/R/print.summary.ergm.R | 2 ergm-4.4.0/ergm/R/rank_test.ergm.R | 2 ergm-4.4.0/ergm/R/rlebdm.R | 19 ergm-4.4.0/ergm/R/simulate.ergm.R | 21 ergm-4.4.0/ergm/R/simulate.formula.R | 2 ergm-4.4.0/ergm/R/summary.ergm.R | 8 ergm-4.4.0/ergm/R/summary.ergm_model.R | 2 ergm-4.4.0/ergm/R/summary.network.list.R | 2 ergm-4.4.0/ergm/R/summary.statistics.network.R | 2 ergm-4.4.0/ergm/R/to_ergm_Cdouble.R | 2 ergm-4.4.0/ergm/R/vcov.ergm.R | 2 ergm-4.4.0/ergm/R/wtd.median.R | 2 ergm-4.4.0/ergm/R/zzz.R | 3 ergm-4.4.0/ergm/build/ergm.pdf |binary ergm-4.4.0/ergm/build/partial.rdb |only ergm-4.4.0/ergm/inst/CITATION | 31 ergm-4.4.0/ergm/inst/NEWS.Rd | 59 ergm-4.4.0/ergm/inst/REFERENCES.bib |only ergm-4.4.0/ergm/inst/doc/ergm-term-crossRef.html | 30 ergm-4.4.0/ergm/inst/doc/ergm.pdf |binary ergm-4.4.0/ergm/inst/doc/nodal_attributes.html | 4 ergm-4.4.0/ergm/inst/include/MHproposal.h | 2 ergm-4.4.0/ergm/inst/include/changestat.h | 2 ergm-4.4.0/ergm/inst/include/edgelist.h | 2 ergm-4.4.0/ergm/inst/include/edgetree.h | 2 ergm-4.4.0/ergm/inst/include/ergm_BDNodeLists.h | 2 ergm-4.4.0/ergm/inst/include/ergm_BDStratBlocks.h | 2 ergm-4.4.0/ergm/inst/include/ergm_BDStrat_proposals.h | 2 ergm-4.4.0/ergm/inst/include/ergm_MHproposal.h | 2 ergm-4.4.0/ergm/inst/include/ergm_MHproposal_bd.h | 2 ergm-4.4.0/ergm/inst/include/ergm_MHstorage.h | 2 ergm-4.4.0/ergm/inst/include/ergm_Rutil.h | 2 ergm-4.4.0/ergm/inst/include/ergm_block.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestat.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestat_auxnet.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestat_common.do_not_include_directly.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestat_operator.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestats_auxnet.h | 2 ergm-4.4.0/ergm/inst/include/ergm_changestats_operator.h | 2 ergm-4.4.0/ergm/inst/include/ergm_constants.h | 2 ergm-4.4.0/ergm/inst/include/ergm_dyad_hashmap.h | 2 ergm-4.4.0/ergm/inst/include/ergm_dyad_hashmap_utils.h | 2 ergm-4.4.0/ergm/inst/include/ergm_dyadgen.h | 2 ergm-4.4.0/ergm/inst/include/ergm_edgelist.h | 2 ergm-4.4.0/ergm/inst/include/ergm_edgetree.h | 2 ergm-4.4.0/ergm/inst/include/ergm_edgetree_common.do_not_include_directly.h | 2 ergm-4.4.0/ergm/inst/include/ergm_edgetree_inline.do_not_include_directly.h | 2 ergm-4.4.0/ergm/inst/include/ergm_edgetree_types.h | 2 ergm-4.4.0/ergm/inst/include/ergm_etamap.h | 2 ergm-4.4.0/ergm/inst/include/ergm_hash_edgelist.h | 2 ergm-4.4.0/ergm/inst/include/ergm_khash.h | 2 ergm-4.4.0/ergm/inst/include/ergm_model.h | 2 ergm-4.4.0/ergm/inst/include/ergm_nodelist.h | 2 ergm-4.4.0/ergm/inst/include/ergm_rlebdm.h | 2 ergm-4.4.0/ergm/inst/include/ergm_state.h | 2 ergm-4.4.0/ergm/inst/include/ergm_storage.h | 2 ergm-4.4.0/ergm/inst/include/ergm_stubs.c | 2 ergm-4.4.0/ergm/inst/include/ergm_unsorted_edgelist.h | 2 ergm-4.4.0/ergm/inst/include/ergm_util.h | 2 ergm-4.4.0/ergm/inst/include/ergm_weighted_population.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtMHproposal.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtchangestat.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtchangestat_operator.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtchangestats_operator.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtedgetree.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtmodel.h | 2 ergm-4.4.0/ergm/inst/include/ergm_wtstate.h | 2 ergm-4.4.0/ergm/inst/include/model.h | 2 ergm-4.4.0/ergm/inst/include/wtMHproposal.h | 2 ergm-4.4.0/ergm/inst/include/wtchangestat.h | 2 ergm-4.4.0/ergm/inst/include/wtedgetree.h | 2 ergm-4.4.0/ergm/inst/include/wtmodel.h | 2 ergm-4.4.0/ergm/man/control.ergm.Rd | 11 ergm-4.4.0/ergm/man/ergm-package.Rd | 6 ergm-4.4.0/ergm/man/ergm.Rd | 55 ergm-4.4.0/ergm/man/ergm.mple.Rd | 19 ergm-4.4.0/ergm/man/is.dyad.independent.Rd | 6 ergm-4.4.0/ergm/man/logLik.ergm.Rd | 9 ergm-4.4.0/ergm/man/macros/ergm-spec.Rd | 2 ergm-4.4.0/ergm/man/macros/ergmCSS.Rd | 2 ergm-4.4.0/ergm/man/macros/uid-algo.Rd | 2 ergm-4.4.0/ergm/man/mcmc.diagnostics.Rd | 7 ergm-4.4.0/ergm/man/simulate.ergm.Rd | 7 ergm-4.4.0/ergm/man/summary.ergm.Rd | 2 ergm-4.4.0/ergm/src/CD.c | 2 ergm-4.4.0/ergm/src/CD.c.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/CD.h | 2 ergm-4.4.0/ergm/src/CD.h.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/MCMC.c | 2 ergm-4.4.0/ergm/src/MCMC.c.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/MCMC.h | 2 ergm-4.4.0/ergm/src/MCMC.h.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/MHproposal.c | 2 ergm-4.4.0/ergm/src/MHproposal_bd.c | 2 ergm-4.4.0/ergm/src/MHproposals.c | 2 ergm-4.4.0/ergm/src/MHproposals.h | 2 ergm-4.4.0/ergm/src/MHproposals_bipartite.c | 2 ergm-4.4.0/ergm/src/MHproposals_degree.c | 2 ergm-4.4.0/ergm/src/MHproposals_dyadnoise.c | 2 ergm-4.4.0/ergm/src/MPLE.c | 2 ergm-4.4.0/ergm/src/MPLE.h | 2 ergm-4.4.0/ergm/src/SAN.c | 2 ergm-4.4.0/ergm/src/SAN.c.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/SAN.h | 2 ergm-4.4.0/ergm/src/SAN.h.template.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/allstatistics.c | 2 ergm-4.4.0/ergm/src/changestat.c | 2 ergm-4.4.0/ergm/src/changestats.c | 2 ergm-4.4.0/ergm/src/changestats.h | 2 ergm-4.4.0/ergm/src/changestats_auxnet.c | 2 ergm-4.4.0/ergm/src/changestats_auxnetalike.c | 2 ergm-4.4.0/ergm/src/changestats_coincidence.c | 2 ergm-4.4.0/ergm/src/changestats_concurrentties.c | 2 ergm-4.4.0/ergm/src/changestats_dgw_sp.c | 2 ergm-4.4.0/ergm/src/changestats_dgw_sp.h | 2 ergm-4.4.0/ergm/src/changestats_experimental.c | 2 ergm-4.4.0/ergm/src/changestats_experimental.h | 2 ergm-4.4.0/ergm/src/changestats_homoproportion.c | 2 ergm-4.4.0/ergm/src/changestats_indices.c | 2 ergm-4.4.0/ergm/src/changestats_interaction.c | 2 ergm-4.4.0/ergm/src/changestats_internal.c | 2 ergm-4.4.0/ergm/src/changestats_operator.c | 2 ergm-4.4.0/ergm/src/changestats_spcache.c | 2 ergm-4.4.0/ergm/src/changestats_test.c | 2 ergm-4.4.0/ergm/src/edgetree.c | 2 ergm-4.4.0/ergm/src/edgetree_inline.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/ergm_dyad_hashmap_utils.c | 2 ergm-4.4.0/ergm/src/ergm_dyadgen.c | 2 ergm-4.4.0/ergm/src/ergm_omp.c | 2 ergm-4.4.0/ergm/src/ergm_omp.h | 2 ergm-4.4.0/ergm/src/ergm_rlebdm.c | 2 ergm-4.4.0/ergm/src/ergm_state.c | 2 ergm-4.4.0/ergm/src/ergm_type_defs_common.h | 2 ergm-4.4.0/ergm/src/ergm_wtstate.c | 2 ergm-4.4.0/ergm/src/ergm_wttype_defs_common.h | 2 ergm-4.4.0/ergm/src/etamap.c | 2 ergm-4.4.0/ergm/src/geodist.c | 2 ergm-4.4.0/ergm/src/geodist.h | 2 ergm-4.4.0/ergm/src/godfather.c | 2 ergm-4.4.0/ergm/src/init.c | 2 ergm-4.4.0/ergm/src/model.c | 2 ergm-4.4.0/ergm/src/netstats.c | 2 ergm-4.4.0/ergm/src/test_weighted_population.c | 2 ergm-4.4.0/ergm/src/wtCD.c | 2 ergm-4.4.0/ergm/src/wtCD.h | 2 ergm-4.4.0/ergm/src/wtMCMC.c | 2 ergm-4.4.0/ergm/src/wtMCMC.h | 2 ergm-4.4.0/ergm/src/wtMHproposal.c | 2 ergm-4.4.0/ergm/src/wtMHproposals.c | 2 ergm-4.4.0/ergm/src/wtSAN.c | 2 ergm-4.4.0/ergm/src/wtSAN.h | 2 ergm-4.4.0/ergm/src/wtchangestats.c | 2 ergm-4.4.0/ergm/src/wtchangestats.h | 2 ergm-4.4.0/ergm/src/wtchangestats_operator.c | 2 ergm-4.4.0/ergm/src/wtchangestats_operator.h | 2 ergm-4.4.0/ergm/src/wtchangestats_test.c | 2 ergm-4.4.0/ergm/src/wtedgetree.c | 2 ergm-4.4.0/ergm/src/wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.4.0/ergm/src/wtgodfather.c | 2 ergm-4.4.0/ergm/src/wtmodel.c | 2 ergm-4.4.0/ergm/src/wtnetstats.c | 2 ergm-4.4.0/ergm/tests/requireNamespaceTest.R | 2 ergm-4.4.0/ergm/tests/testthat.R | 2 ergm-4.4.0/ergm/tests/testthat/helper-edges-MLE.R | 2 ergm-4.4.0/ergm/tests/testthat/test-C-curved.R | 2 ergm-4.4.0/ergm/tests/testthat/test-Sum.R | 2 ergm-4.4.0/ergm/tests/testthat/test-bd.R | 2 ergm-4.4.0/ergm/tests/testthat/test-bipartite-missing-data.R | 2 ergm-4.4.0/ergm/tests/testthat/test-bridge-target.stats.R | 2 ergm-4.4.0/ergm/tests/testthat/test-c-ergm_model.R | 2 ergm-4.4.0/ergm/tests/testthat/test-checkpointing.R | 2 ergm-4.4.0/ergm/tests/testthat/test-constrain-blockdiag.R | 2 ergm-4.4.0/ergm/tests/testthat/test-constrain-degrees-edges.R | 12 ergm-4.4.0/ergm/tests/testthat/test-constrain-dind.R | 15 ergm-4.4.0/ergm/tests/testthat/test-constrain-egocentric.R | 2 ergm-4.4.0/ergm/tests/testthat/test-constraints.R | 2 ergm-4.4.0/ergm/tests/testthat/test-drop.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergm-godfather.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergm-proposal-unload.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergm-san.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergm-term-doc.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergm.bridge.llr.R | 2 ergm-4.4.0/ergm/tests/testthat/test-ergmMPLE.R | 2 ergm-4.4.0/ergm/tests/testthat/test-fix.curved.R | 2 ergm-4.4.0/ergm/tests/testthat/test-gflomiss.R | 2 ergm-4.4.0/ergm/tests/testthat/test-gmonkmiss.R | 2 ergm-4.4.0/ergm/tests/testthat/test-gof.R | 2 ergm-4.4.0/ergm/tests/testthat/test-gw-sp.R | 2 ergm-4.4.0/ergm/tests/testthat/test-metrics.R | 2 ergm-4.4.0/ergm/tests/testthat/test-miss.CD.R | 2 ergm-4.4.0/ergm/tests/testthat/test-miss.R | 8 ergm-4.4.0/ergm/tests/testthat/test-mple-largenetwork.R | 2 ergm-4.4.0/ergm/tests/testthat/test-mple-offset.R | 2 ergm-4.4.0/ergm/tests/testthat/test-mple-target.R | 2 ergm-4.4.0/ergm/tests/testthat/test-nodemix.R | 2 ergm-4.4.0/ergm/tests/testthat/test-nodrop.R | 2 ergm-4.4.0/ergm/tests/testthat/test-nonident-test.R | 2 ergm-4.4.0/ergm/tests/testthat/test-nonunique-names.R | 2 ergm-4.4.0/ergm/tests/testthat/test-offsets.R | 2 ergm-4.4.0/ergm/tests/testthat/test-operators.R | 2 ergm-4.4.0/ergm/tests/testthat/test-parallel.R | 2 ergm-4.4.0/ergm/tests/testthat/test-predict.ergm.R | 2 ergm-4.4.0/ergm/tests/testthat/test-proposal-bdstrattnt.R | 2 ergm-4.4.0/ergm/tests/testthat/test-runtime-diags.R | 2 ergm-4.4.0/ergm/tests/testthat/test-scoping.R | 2 ergm-4.4.0/ergm/tests/testthat/test-shrink-into-CH.R | 2 ergm-4.4.0/ergm/tests/testthat/test-simple.R | 2 ergm-4.4.0/ergm/tests/testthat/test-simulate-batch.R | 13 ergm-4.4.0/ergm/tests/testthat/test-snctrl.R | 2 ergm-4.4.0/ergm/tests/testthat/test-stocapprox.R | 2 ergm-4.4.0/ergm/tests/testthat/test-target-offset.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-For.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-Offset.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-attrcov.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-b12factor.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-b12nodematch.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-bipartite.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-directed.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-edgecov.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-errors.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-flexible.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-hamming.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-mm.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-options.R | 10 ergm-4.4.0/ergm/tests/testthat/test-term-undirected.R | 2 ergm-4.4.0/ergm/tests/testthat/test-term-valued.R | 2 ergm-4.4.0/ergm/tests/testthat/test-u-function.R | 2 ergm-4.4.0/ergm/tests/testthat/test-update.network.R | 2 ergm-4.4.0/ergm/tests/testthat/test-valued-sim.R | 2 ergm-4.4.0/ergm/tests/testthat/test-valued-terms.R | 2 ergm-4.4.0/ergm/tests/testthat/test-weighted-population.R | 2 342 files changed, 1085 insertions(+), 889 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
Fragpipe(da Veiga et al 2020, <doi:10.1038/s41592-020-0912-y>), MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), MassChroq (Valot et al 2011] <doi:10.1002/pmic.201100120>), ProteomeDiscoverer,
OpenMS (<doi:10.1038/nmeth.3959>) and Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>). Meta-data provided in sdrf format can be integrated to the analysis.
Quantitative proteomics measurements frequently contain multiple NA values, due to [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.7.0.1 dated 2022-11-24 and 1.7.1 dated 2023-01-27
wrProteo-1.7.0.1/wrProteo/inst/extdata/pxd001819f_PL.xlsx |only wrProteo-1.7.1/wrProteo/DESCRIPTION | 8 wrProteo-1.7.1/wrProteo/MD5 | 67 wrProteo-1.7.1/wrProteo/NAMESPACE | 1 wrProteo-1.7.1/wrProteo/R/cleanListCoNames.R | 27 wrProteo-1.7.1/wrProteo/R/combineMultFilterNAimput.R | 10 wrProteo-1.7.1/wrProteo/R/corColumnOrder.R | 37 wrProteo-1.7.1/wrProteo/R/readFragpipeFile.R | 163 wrProteo-1.7.1/wrProteo/R/readMassChroQFile.R | 6 wrProteo-1.7.1/wrProteo/R/readMaxQuantFile.R | 557 -- wrProteo-1.7.1/wrProteo/R/readProlineFile.R | 112 wrProteo-1.7.1/wrProteo/R/readProtDiscovFile.R | 166 wrProteo-1.7.1/wrProteo/R/readSampleMetaData.R | 237 wrProteo-1.7.1/wrProteo/R/readSdrf.R | 77 wrProteo-1.7.1/wrProteo/R/summarizeForROC.R | 6 wrProteo-1.7.1/wrProteo/R/testRobustToNAimputation.R | 2 wrProteo-1.7.1/wrProteo/build/vignette.rds |binary wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignette1.R | 47 wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignette1.Rmd | 215 wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignette1.html | 1223 ++-- wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignetteUPS1.R | 280 - wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignetteUPS1.Rmd | 485 - wrProteo-1.7.1/wrProteo/inst/doc/wrProteoVignetteUPS1.html | 3619 ++++++------- wrProteo-1.7.1/wrProteo/man/cleanListCoNames.Rd | 6 wrProteo-1.7.1/wrProteo/man/combineMultFilterNAimput.Rd | 2 wrProteo-1.7.1/wrProteo/man/corColumnOrder.Rd | 9 wrProteo-1.7.1/wrProteo/man/readFragpipeFile.Rd | 21 wrProteo-1.7.1/wrProteo/man/readMassChroQFile.Rd | 4 wrProteo-1.7.1/wrProteo/man/readMaxQuantFile.Rd | 17 wrProteo-1.7.1/wrProteo/man/readProlineFile.Rd | 10 wrProteo-1.7.1/wrProteo/man/readProtDiscovFile.Rd | 26 wrProteo-1.7.1/wrProteo/man/readSampleMetaData.Rd | 9 wrProteo-1.7.1/wrProteo/man/readSdrf.Rd | 8 wrProteo-1.7.1/wrProteo/vignettes/wrProteoVignette1.Rmd | 215 wrProteo-1.7.1/wrProteo/vignettes/wrProteoVignetteUPS1.Rmd | 485 - 35 files changed, 4039 insertions(+), 4118 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes
several measures for structural balance as introduced by Cartwright
and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms
from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various
centrality indices, and projections of signed two-mode networks
introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between signnet versions 1.0.0 dated 2022-12-22 and 1.0.1 dated 2023-01-27
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/signed_triangles.R | 2 +- README.md | 11 +++++++---- inst/CITATION | 19 ++++++++++++------- inst/doc/signed_2mode.html | 8 ++++---- inst/doc/signed_networks.html | 4 ++-- man/figures/README-block_example-1.png |binary man/figures/README-general_example-1.png |binary man/triad_census_signed.Rd | 2 +- 11 files changed, 44 insertions(+), 32 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.20.1 dated 2023-01-11 and 0.20.2 dated 2023-01-27
DESCRIPTION | 8 MD5 | 120 ++--- NAMESPACE | 1 NEWS.md | 20 R/1_model_parameters.R | 14 R/bootstrap_model.R | 10 R/compare_parameters.R | 8 R/dof_kenward.R | 90 ---- R/dof_ml1.R | 4 R/extract_parameters.R | 41 + R/extract_parameters_anova.R | 2 R/extract_random_variances.R | 8 R/format.R | 74 +-- R/format_p_adjust.R | 6 R/methods_BayesFactor.R | 7 R/methods_DirichletReg.R | 2 R/methods_aov.R | 85 ++-- R/methods_cplm.R | 16 R/methods_emmeans.R | 94 ++++ R/methods_gam.R | 52 +- R/methods_glmmTMB.R | 6 R/methods_hclust.R | 6 R/methods_htest.R | 12 R/methods_lme4.R | 25 - R/methods_logistf.R | 2 R/methods_mmrm.R | 9 R/methods_multcomp.R | 4 R/methods_other.R | 8 R/n_clusters.R | 2 R/n_clusters_easystats.R | 24 - R/n_factors.R | 21 R/principal_components.R | 1 R/utils_clustering.R | 6 R/utils_model_parameters.R | 65 +-- R/utils_pca_efa.R | 9 inst/WORDLIST |only inst/doc/overview_of_vignettes.html | 14 man/compare_parameters.Rd | 8 man/model_parameters.aov.Rd | 25 - man/model_parameters.averaging.Rd | 9 man/model_parameters.befa.Rd | 2 man/model_parameters.cgam.Rd | 8 man/model_parameters.default.Rd | 5 man/model_parameters.htest.Rd | 4 man/model_parameters.kmeans.Rd | 2 man/model_parameters.merMod.Rd | 12 man/principal_components.Rd | 11 tests/testthat/_snaps/glmmTMB.md |only tests/testthat/_snaps/printing-stan.md | 18 tests/testthat/_snaps/printing.md | 486 +++++++++++------------ tests/testthat/test-Hmisc.R | 12 tests/testthat/test-bootstrap_emmeans.R | 24 + tests/testthat/test-format_parameters.R | 156 +++---- tests/testthat/test-mmrm.R | 70 +-- tests/testthat/test-model_parameters.anova.R | 10 tests/testthat/test-model_parameters.aov.R | 2 tests/testthat/test-model_parameters.aov_es_ci.R | 48 +- tests/testthat/test-model_parameters.cgam.R | 4 tests/testthat/test-model_parameters.fixest.R | 6 tests/testthat/test-printing-stan.r | 97 +--- tests/testthat/test-printing.r | 2 tests/testthat/test-printing2.r | 2 62 files changed, 981 insertions(+), 918 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <https://curl.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between RCurl versions 1.98-1.9 dated 2022-10-03 and 1.98-1.10 dated 2023-01-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- configure | 9 +++++++++ configure.ac | 9 +++++++++ src/Makevars.in | 2 +- 5 files changed, 26 insertions(+), 8 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.10 dated 2022-09-09 and 2.11 dated 2023-01-27
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 10 +++++----- R/Morpho-package.R | 6 +++--- R/check.lm.r | 4 ++-- R/crossp.r | 5 +++-- R/fiducials.r | 29 ++++++++++++++++++++++++++--- R/find.outliers.r | 12 ++++++------ R/meshDist.r | 8 ++++---- R/meshDistMatrix.r | 4 ++-- R/tanplan.r | 1 + R/updateNormals.r | 2 +- R/vertex.r | 2 +- R/warpmovie.matrix.r | 6 +++--- R/warpmovie.r | 6 +++--- inst/NEWS.Rd | 17 +++++++++++++++++ man/Morpho-package.Rd | 4 ++-- man/meshDist.Rd | 2 +- man/render.Rd | 2 +- man/tangentPlane.Rd | 4 +++- man/updateNormals.Rd | 2 +- man/vertex.Rd | 2 +- src/Makevars | 1 - 23 files changed, 112 insertions(+), 69 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 5.4-10 dated 2022-11-18 and 5.4-12 dated 2023-01-27
gamlss-5.4-10/gamlss/R/gamlssVGD.R |only gamlss-5.4-12/gamlss/DESCRIPTION | 8 - gamlss-5.4-12/gamlss/MD5 | 19 +-- gamlss-5.4-12/gamlss/NAMESPACE | 2 gamlss-5.4-12/gamlss/R/Formulae2data.R | 43 +++++--- gamlss-5.4-12/gamlss/R/gamlss-5.R | 16 +-- gamlss-5.4-12/gamlss/R/gamlssVGD_23_12_21.R | 2 gamlss-5.4-12/gamlss/R/hatvalues.R | 148 +++++++++++++++------------- gamlss-5.4-12/gamlss/R/pb.R | 2 gamlss-5.4-12/gamlss/build/partial.rdb |binary gamlss-5.4-12/gamlss/inst/doc/NEWS.txt | 20 +++ 11 files changed, 161 insertions(+), 99 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.0-3 dated 2022-11-15 and 3.0-4 dated 2023-01-27
DESCRIPTION | 14 +++---- MD5 | 22 ++++++------ NAMESPACE | 2 + NEWS | 20 +++++++++++ R/linim.R | 23 +++++++++++-- R/relrisk.lpp.R | 81 ++++++++++++++++++++++++++++------------------ inst/CITATION | 16 ++++----- inst/doc/packagesizes.txt | 2 - man/macros/defns.Rd | 2 + man/mean.linim.Rd | 14 +++++++ man/relrisk.lpp.Rd | 12 +++--- tests/testsAtoK.R | 2 - 12 files changed, 142 insertions(+), 68 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to 'SWI'-'Prolog', <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to 'prolog' ('consult', 'query'/'submit', 'once', 'findall').
Author: Matthias Gondan [aut, com, cre]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rolog versions 0.9.10 dated 2023-01-12 and 0.9.11 dated 2023-01-27
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 4 ++ build/vignette.rds |binary inst/doc/rolog.R | 10 +++--- inst/doc/rolog.Rmd | 31 ++++++++++-------- inst/doc/rolog.html | 70 ++++++++++++++++++++++++------------------ src/rolog.cpp | 16 ++++----- vignettes/bibliography.bibtex | 10 +++++- vignettes/rolog.Rmd | 31 ++++++++++-------- 10 files changed, 115 insertions(+), 83 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
The package does not require any installation of Microsoft products to be able to write Microsoft
files.
Author: David Gohel [aut, cre],
ArData [cph],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Stefan Moog [ctb] ,
Greg Leleu [ctb] ,
Hong [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.5.1 dated 2023-01-06 and 0.5.2 dated 2023-01-27
DESCRIPTION | 8 +- MD5 | 35 +++++----- NEWS.md | 19 +++++ R/custom_properties.R | 30 ++++++-- R/docx_add.R | 15 +++- R/docx_part.R | 7 -- R/docx_section.R | 17 +++- R/ooxml_run_objects.R | 45 ++++++++++-- R/openxml_document.R | 1 R/post-proc.R | 22 ++++++ R/read_docx.R | 136 +++++++++++++++++++-------------------- R/utils.R | 16 ++++ man/external_img.Rd | 18 ++++- man/prop_section.Rd | 3 tests/testthat/test-docx-add.R | 1 tests/testthat/test-fpar.R | 20 +++-- tests/testthat/test-pptx-add.R | 6 - tests/testthat/test-sections.R | 6 + tests/testthat/test-wml-chunks.R |only 19 files changed, 267 insertions(+), 138 deletions(-)
Title: Mast Inference and Forecasting
Description: Analyzes production and dispersal of seeds dispersed from trees and recovered in seed traps. Motivated by long-term inventory plots where seed collections are used to infer seed production by each individual plant.
Author: James S. Clark
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between mastif versions 1.0.1 dated 2020-10-25 and 2.0 dated 2023-01-27
DESCRIPTION | 12 MD5 | 36 NAMESPACE | 21 R/mastifFunctions.R |22286 +++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/mastifVignette.R | 559 - inst/doc/mastifVignette.Rmd | 894 + inst/doc/mastifVignette.html | 2121 ++-- man/mastClimate.Rd | 11 man/mastFillCensus.Rd | 4 man/mastMap.Rd | 3 man/mastPlot.Rd | 4 man/mastPriors.Rd | 3 man/mastSim.Rd | 7 man/mastSpectralDensity.Rd |only man/mastVolatility.Rd |only man/mastif-package.Rd | 4 man/mastif.Rd | 36 src/RcppExports.cpp | 5 vignettes/mastifVignette.Rmd | 894 + 20 files changed, 15125 insertions(+), 11775 deletions(-)