Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>). The package contains R wrappers to the UK NRFA data temporary-API. There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information. The package is fully described in Vitolo et al (2016) "rnrfa: An R package to Retrieve, Filter and Visualize Data from the UK National River Flow Archive" <https://journal.r-project.org/archive/2016/RJ-2016-036/RJ-2016-036.pdf>.
Author: Ilaria Prosdocimi [ctb, cre] ,
Claudia Vitolo [aut] ,
Matthew Fry [ctb] ,
Wouter Buytaert [ctb] ,
Michael Spencer [ctb] ,
Tobias Gauster [ctb]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between rnrfa versions 2.1.0 dated 2022-09-08 and 2.1.0.5 dated 2024-02-14
rnrfa-2.1.0.5/rnrfa/DESCRIPTION | 27 rnrfa-2.1.0.5/rnrfa/MD5 | 27 rnrfa-2.1.0.5/rnrfa/NEWS.md | 13 rnrfa-2.1.0.5/rnrfa/R/catalogue.R | 15 rnrfa-2.1.0.5/rnrfa/R/plot_trend.R | 57 rnrfa-2.1.0.5/rnrfa/README.md | 5 rnrfa-2.1.0.5/rnrfa/build/vignette.rds |binary rnrfa-2.1.0.5/rnrfa/inst/CITATION | 44 rnrfa-2.1.0.5/rnrfa/inst/doc/rnrfa-vignette.R | 227 rnrfa-2.1.0.5/rnrfa/inst/doc/rnrfa-vignette.Rmd | 131 rnrfa-2.1.0.5/rnrfa/inst/doc/rnrfa-vignette.html |10936 +++++++++++++++++++++- rnrfa-2.1.0.5/rnrfa/man/catalogue.Rd | 2 rnrfa-2.1.0.5/rnrfa/man/plot_trend.Rd | 14 rnrfa-2.1.0.5/rnrfa/vignettes/rnrfa-vignette.Rmd | 131 rnrfa-2.1.0/rnrfa/vignettes/file219c155919c3.html |only 15 files changed, 11146 insertions(+), 483 deletions(-)
Title: Probabilistic Latent Feature Analysis
Description: Functions for estimating probabilistic latent feature models with a disjunctive, conjunctive or additive mapping rule on (aggregated) binary three-way data.
Author: Michel Meulders [aut, cre],
Philippe De Bruecker [ctb]
Maintainer: Michel Meulders <michel.meulders@kuleuven.be>
Diff between plfm versions 2.2.5 dated 2022-03-30 and 2.2.6 dated 2024-02-14
DESCRIPTION | 9 MD5 | 6 man/plfm-package.Rd | 10 src/main.cpp | 616 ++++++++++++++++++++++++++-------------------------- 4 files changed, 316 insertions(+), 325 deletions(-)
Title: Create Codebooks from Data Frames
Description: Quickly and easily create codebooks (i.e. data dictionaries) directly from a data frame.
Author: Brad Cannell [aut, cre, cph]
Maintainer: Brad Cannell <brad.cannell@gmail.com>
Diff between codebookr versions 0.1.6 dated 2023-03-16 and 0.1.7 dated 2024-02-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/cb_add_col_attributes.R | 17 ++++++----------- R/cb_get_col_attributes.R | 2 +- R/cb_summary_stats_few_cats.R | 2 +- R/cb_summary_stats_numeric.R | 4 ++-- README.md | 2 +- man/cb_add_col_attributes.Rd | 17 ++++++----------- 9 files changed, 36 insertions(+), 39 deletions(-)
Title: Calculates Conditional Mahalanobis Distances
Description: Calculates a Mahalanobis distance for every row of a set of
outcome variables (Mahalanobis, 1936
<doi:10.1007/s13171-019-00164-5>). The conditional Mahalanobis
distance is calculated using a conditional covariance matrix (i.e., a
covariance matrix of the outcome variables after controlling for a set
of predictors). Plotting the output of the cond_maha() function can
help identify which elements of a profile are unusual after
controlling for the predictors.
Author: W. Joel Schneider [aut, cre] ,
Feng Ji [aut]
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between unusualprofile versions 0.1.2 dated 2022-12-13 and 0.1.4 dated 2024-02-14
unusualprofile-0.1.2/unusualprofile/man/unusualprofile.Rd |only unusualprofile-0.1.4/unusualprofile/DESCRIPTION | 11 unusualprofile-0.1.4/unusualprofile/MD5 | 25 - unusualprofile-0.1.4/unusualprofile/NEWS.md | 10 unusualprofile-0.1.4/unusualprofile/R/main.R | 20 unusualprofile-0.1.4/unusualprofile/R/unusualprofile-package.R | 18 unusualprofile-0.1.4/unusualprofile/README.md | 26 + unusualprofile-0.1.4/unusualprofile/build/partial.rdb |only unusualprofile-0.1.4/unusualprofile/build/vignette.rds |binary unusualprofile-0.1.4/unusualprofile/inst/WORDLIST | 3 unusualprofile-0.1.4/unusualprofile/inst/doc/unusualprofile_calculations.R | 2 unusualprofile-0.1.4/unusualprofile/inst/doc/unusualprofile_calculations.html | 224 +++++----- unusualprofile-0.1.4/unusualprofile/man/cond_maha.Rd | 2 unusualprofile-0.1.4/unusualprofile/man/unusualprofile-package.Rd |only unusualprofile-0.1.4/unusualprofile/tests/testthat/test-main.R | 4 15 files changed, 189 insertions(+), 156 deletions(-)
More information about unusualprofile at CRAN
Permanent link
Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles
of species distribution model (SDM) predictions.
Functionality is offered through R functions or a GUI (R Shiny app).
This tool can assist users in identifying spatial uncertainties and
making informed conservation and management decisions. The package is
further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between eSDM versions 0.4.0 dated 2023-10-24 and 0.4.1 dated 2024-02-14
DESCRIPTION | 12 ++++---- MD5 | 14 +++++----- NEWS.md | 5 +++ R/eSDM-package.R | 1 build/vignette.rds |binary inst/doc/example-analysis.html | 6 ++-- inst/shiny/app.R | 55 +++++++++++++++++++++++++++++------------ man/eSDM-package.Rd | 1 8 files changed, 61 insertions(+), 33 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.36.0 dated 2023-05-26 and 1.37.0 dated 2024-02-14
parallelly-1.36.0/parallelly/man/canPortBeUsed.Rd |only parallelly-1.36.0/parallelly/man/getOption2.Rd |only parallelly-1.37.0/parallelly/DESCRIPTION | 18 - parallelly-1.37.0/parallelly/MD5 | 54 +-- parallelly-1.37.0/parallelly/NAMESPACE | 1 parallelly-1.37.0/parallelly/NEWS.md | 32 ++ parallelly-1.37.0/parallelly/R/000.import.R | 6 parallelly-1.37.0/parallelly/R/availableConnections.R | 11 parallelly-1.37.0/parallelly/R/availableCores.R | 99 ++++++ parallelly-1.37.0/parallelly/R/getOptionOrEnvVar.R | 18 - parallelly-1.37.0/parallelly/R/isConnectionValid.R | 4 parallelly-1.37.0/parallelly/R/killNode.R | 2 parallelly-1.37.0/parallelly/R/makeClusterPSOCK.R | 48 ++- parallelly-1.37.0/parallelly/R/makeNodePSOCK.R | 4 parallelly-1.37.0/parallelly/R/options.R | 5 parallelly-1.37.0/parallelly/R/parallelly_disable_parallel_setup_if_needed.R | 32 -- parallelly-1.37.0/parallelly/R/ports.R | 150 ++++++---- parallelly-1.37.0/parallelly/R/zzz.R | 6 parallelly-1.37.0/parallelly/README.md | 6 parallelly-1.37.0/parallelly/inst/WORDLIST | 1 parallelly-1.37.0/parallelly/man/availableConnections.Rd | 10 parallelly-1.37.0/parallelly/man/freePort.Rd | 8 parallelly-1.37.0/parallelly/man/isConnectionValid.Rd | 4 parallelly-1.37.0/parallelly/man/killNode.Rd | 2 parallelly-1.37.0/parallelly/man/makeClusterPSOCK.Rd | 100 +++++- parallelly-1.37.0/parallelly/man/parallelly.options.Rd | 2 parallelly-1.37.0/parallelly/src |only parallelly-1.37.0/parallelly/tests/r_bug18119.R | 24 - 28 files changed, 446 insertions(+), 201 deletions(-)
Title: Monthly Climate Data for Germany, Usable for Heating and Cooling
Calculations
Description: This data package contains monthly climate data in Germany, it can be used for heating and
cooling calculations (external temperature, heating / cooling days, solar radiation).
Author: Tobias Loga [aut] ,
Guillaume Behem [aut],
Jens Calisti [cre]
Maintainer: Jens Calisti <jens@tangled.de>
Diff between clidamonger versions 1.0.0 dated 2023-02-09 and 1.1.0 dated 2024-02-14
clidamonger-1.0.0/clidamonger/data/list.stationta.rda |only clidamonger-1.1.0/clidamonger/DESCRIPTION | 9 +++-- clidamonger-1.1.0/clidamonger/MD5 | 20 ++++++------ clidamonger-1.1.0/clidamonger/NEWS.md | 6 +++ clidamonger-1.1.0/clidamonger/README.md | 3 + clidamonger-1.1.0/clidamonger/data/data.sol.rda |binary clidamonger-1.1.0/clidamonger/data/data.ta.hd.rda |binary clidamonger-1.1.0/clidamonger/data/list.station.ta.rda |only clidamonger-1.1.0/clidamonger/data/tab.estim.sol.orient.rda |binary clidamonger-1.1.0/clidamonger/data/tab.stationmapping.rda |binary clidamonger-1.1.0/clidamonger/man/data.ta.hd.Rd | 2 - clidamonger-1.1.0/clidamonger/man/list.station.ta.Rd | 2 - 12 files changed, 25 insertions(+), 17 deletions(-)
Title: A Traceability Focused Grammar of Clinical Data Summary
Description: A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Author: Eli Miller [aut] ,
Mike Stackhouse [aut, cre] ,
Ashley Tarasiewicz [aut],
Nathan Kosiba [ctb] ,
Sadchla Mascary [ctb],
Andrew Bates [ctb],
Shiyu Chen [ctb],
Oleksii Mikryukov [ctb],
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 1.1.0 dated 2023-01-10 and 1.2.0 dated 2024-02-14
Tplyr-1.1.0/Tplyr/vignettes/adae.Rdata |only Tplyr-1.1.0/Tplyr/vignettes/adas.Rdata |only Tplyr-1.1.0/Tplyr/vignettes/adlb.Rdata |only Tplyr-1.1.0/Tplyr/vignettes/adsl.Rdata |only Tplyr-1.2.0/Tplyr/DESCRIPTION | 24 Tplyr-1.2.0/Tplyr/MD5 | 238 +- Tplyr-1.2.0/Tplyr/NAMESPACE | 23 Tplyr-1.2.0/Tplyr/NEWS.md | 15 Tplyr-1.2.0/Tplyr/R/apply_conditional_format.R | 8 Tplyr-1.2.0/Tplyr/R/apply_formats.R | 4 Tplyr-1.2.0/Tplyr/R/assertions.R | 53 Tplyr-1.2.0/Tplyr/R/call_standardise.R |only Tplyr-1.2.0/Tplyr/R/collapse_row_labels.R |only Tplyr-1.2.0/Tplyr/R/count.R | 317 ++- Tplyr-1.2.0/Tplyr/R/count_bindings.R | 83 Tplyr-1.2.0/Tplyr/R/data.R |only Tplyr-1.2.0/Tplyr/R/denom.R | 29 Tplyr-1.2.0/Tplyr/R/desc.R | 17 Tplyr-1.2.0/Tplyr/R/format.R | 2 Tplyr-1.2.0/Tplyr/R/layer.R | 10 Tplyr-1.2.0/Tplyr/R/layer_templates.R | 2 Tplyr-1.2.0/Tplyr/R/layering.R | 8 Tplyr-1.2.0/Tplyr/R/meta-builders.R | 6 Tplyr-1.2.0/Tplyr/R/nested.R | 30 Tplyr-1.2.0/Tplyr/R/pop_data.R | 42 Tplyr-1.2.0/Tplyr/R/replace_leading_whitespace.R |only Tplyr-1.2.0/Tplyr/R/riskdiff.R | 8 Tplyr-1.2.0/Tplyr/R/set_format_strings.R | 5 Tplyr-1.2.0/Tplyr/R/set_limit_data_by.R |only Tplyr-1.2.0/Tplyr/R/shift.R | 5 Tplyr-1.2.0/Tplyr/R/sort.R | 181 +- Tplyr-1.2.0/Tplyr/R/table.R | 9 Tplyr-1.2.0/Tplyr/R/table_bindings.R | 11 Tplyr-1.2.0/Tplyr/R/utils.R | 51 Tplyr-1.2.0/Tplyr/R/zzz.R | 31 Tplyr-1.2.0/Tplyr/README.md | 85 Tplyr-1.2.0/Tplyr/build/vignette.rds |binary Tplyr-1.2.0/Tplyr/data |only Tplyr-1.2.0/Tplyr/inst/doc/Tplyr.R | 39 Tplyr-1.2.0/Tplyr/inst/doc/Tplyr.Rmd | 39 Tplyr-1.2.0/Tplyr/inst/doc/Tplyr.html | 334 +-- Tplyr-1.2.0/Tplyr/inst/doc/count.R | 13 Tplyr-1.2.0/Tplyr/inst/doc/count.Rmd | 13 Tplyr-1.2.0/Tplyr/inst/doc/count.html | 120 - Tplyr-1.2.0/Tplyr/inst/doc/custom-metadata.R | 8 Tplyr-1.2.0/Tplyr/inst/doc/custom-metadata.Rmd | 8 Tplyr-1.2.0/Tplyr/inst/doc/custom-metadata.html | 156 - Tplyr-1.2.0/Tplyr/inst/doc/denom.R | 58 Tplyr-1.2.0/Tplyr/inst/doc/denom.Rmd | 67 Tplyr-1.2.0/Tplyr/inst/doc/denom.html | 810 +++++---- Tplyr-1.2.0/Tplyr/inst/doc/desc.R | 14 Tplyr-1.2.0/Tplyr/inst/doc/desc.Rmd | 18 Tplyr-1.2.0/Tplyr/inst/doc/desc.html | 146 - Tplyr-1.2.0/Tplyr/inst/doc/desc_layer_formatting.R | 37 Tplyr-1.2.0/Tplyr/inst/doc/desc_layer_formatting.Rmd | 37 Tplyr-1.2.0/Tplyr/inst/doc/desc_layer_formatting.html | 366 ++-- Tplyr-1.2.0/Tplyr/inst/doc/general_string_formatting.R | 19 Tplyr-1.2.0/Tplyr/inst/doc/general_string_formatting.Rmd | 19 Tplyr-1.2.0/Tplyr/inst/doc/general_string_formatting.html | 272 +-- Tplyr-1.2.0/Tplyr/inst/doc/layer_templates.R | 7 Tplyr-1.2.0/Tplyr/inst/doc/layer_templates.Rmd | 7 Tplyr-1.2.0/Tplyr/inst/doc/layer_templates.html | 148 - Tplyr-1.2.0/Tplyr/inst/doc/metadata.R | 9 Tplyr-1.2.0/Tplyr/inst/doc/metadata.Rmd | 11 Tplyr-1.2.0/Tplyr/inst/doc/metadata.html | 78 Tplyr-1.2.0/Tplyr/inst/doc/options.R | 17 Tplyr-1.2.0/Tplyr/inst/doc/options.Rmd | 17 Tplyr-1.2.0/Tplyr/inst/doc/options.html | 276 +-- Tplyr-1.2.0/Tplyr/inst/doc/post_processing.R | 63 Tplyr-1.2.0/Tplyr/inst/doc/post_processing.Rmd | 88 - Tplyr-1.2.0/Tplyr/inst/doc/post_processing.html | 873 ++++++++-- Tplyr-1.2.0/Tplyr/inst/doc/shift.R | 11 Tplyr-1.2.0/Tplyr/inst/doc/shift.Rmd | 11 Tplyr-1.2.0/Tplyr/inst/doc/shift.html | 154 + Tplyr-1.2.0/Tplyr/inst/doc/table.R | 47 Tplyr-1.2.0/Tplyr/inst/doc/table.Rmd | 66 Tplyr-1.2.0/Tplyr/inst/doc/table.html | 517 +++++ Tplyr-1.2.0/Tplyr/man/Tplyr.Rd | 3 Tplyr-1.2.0/Tplyr/man/add_missing_subjects_row.Rd |only Tplyr-1.2.0/Tplyr/man/add_total_row.Rd | 4 Tplyr-1.2.0/Tplyr/man/collapse_row_labels.Rd |only Tplyr-1.2.0/Tplyr/man/get_data_labels.Rd |only Tplyr-1.2.0/Tplyr/man/layer_templates.Rd | 2 Tplyr-1.2.0/Tplyr/man/pop_data.Rd | 2 Tplyr-1.2.0/Tplyr/man/replace_leading_whitespace.Rd |only Tplyr-1.2.0/Tplyr/man/set_limit_data_by.Rd |only Tplyr-1.2.0/Tplyr/man/set_missing_subjects_row_label.Rd |only Tplyr-1.2.0/Tplyr/man/tplyr_adae.Rd |only Tplyr-1.2.0/Tplyr/man/tplyr_adas.Rd |only Tplyr-1.2.0/Tplyr/man/tplyr_adlb.Rd |only Tplyr-1.2.0/Tplyr/man/tplyr_adpe.Rd |only Tplyr-1.2.0/Tplyr/man/tplyr_adsl.Rd |only Tplyr-1.2.0/Tplyr/man/treat_grps.Rd | 36 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/apply_formats.md | 2 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/count.md | 636 ++++--- Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/data.md |only Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/desc.md | 24 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/functional.md | 2 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/layer.md | 2 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/layering.md | 2 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/meta.md | 36 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/precision.md | 64 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/shift.md | 4 Tplyr-1.2.0/Tplyr/tests/testthat/_snaps/table.md | 8 Tplyr-1.2.0/Tplyr/tests/testthat/test-apply_conditional_format.R | 10 Tplyr-1.2.0/Tplyr/tests/testthat/test-collapse_row_labels.R |only Tplyr-1.2.0/Tplyr/tests/testthat/test-count.R | 275 ++- Tplyr-1.2.0/Tplyr/tests/testthat/test-data.R |only Tplyr-1.2.0/Tplyr/tests/testthat/test-denom.R | 21 Tplyr-1.2.0/Tplyr/tests/testthat/test-desc.R | 27 Tplyr-1.2.0/Tplyr/tests/testthat/test-format.R | 22 Tplyr-1.2.0/Tplyr/tests/testthat/test-layering.R | 18 Tplyr-1.2.0/Tplyr/tests/testthat/test-meta.R | 4 Tplyr-1.2.0/Tplyr/tests/testthat/test-precision.R | 6 Tplyr-1.2.0/Tplyr/tests/testthat/test-replace_leading_whitespace.R |only Tplyr-1.2.0/Tplyr/tests/testthat/test-set_limit_data_by.R |only Tplyr-1.2.0/Tplyr/tests/testthat/test-sort.R | 36 Tplyr-1.2.0/Tplyr/tests/testthat/test-table.R | 6 Tplyr-1.2.0/Tplyr/vignettes/Tplyr.Rmd | 39 Tplyr-1.2.0/Tplyr/vignettes/count.Rmd | 13 Tplyr-1.2.0/Tplyr/vignettes/custom-metadata.Rmd | 8 Tplyr-1.2.0/Tplyr/vignettes/denom.Rmd | 67 Tplyr-1.2.0/Tplyr/vignettes/desc.Rmd | 18 Tplyr-1.2.0/Tplyr/vignettes/desc_layer_formatting.Rmd | 37 Tplyr-1.2.0/Tplyr/vignettes/general_string_formatting.Rmd | 19 Tplyr-1.2.0/Tplyr/vignettes/layer_templates.Rmd | 7 Tplyr-1.2.0/Tplyr/vignettes/metadata.Rmd | 11 Tplyr-1.2.0/Tplyr/vignettes/options.Rmd | 17 Tplyr-1.2.0/Tplyr/vignettes/post_processing.Rmd | 88 - Tplyr-1.2.0/Tplyr/vignettes/shift.Rmd | 11 Tplyr-1.2.0/Tplyr/vignettes/table.Rmd | 66 131 files changed, 5237 insertions(+), 2706 deletions(-)
Title: Client Library for SpatioTemporal Asset Catalog
Description: Provides functions to access, search and download spacetime earth
observation data via SpatioTemporal Asset Catalog (STAC). This package
supports the version 1.0.0 (and older) of the STAC specification
(<https://github.com/radiantearth/stac-spec>).
For further details see Simoes et al. (2021) <doi:10.1109/IGARSS47720.2021.9553518>.
Author: Rolf Simoes [aut],
Felipe Carvalho [aut, cre],
Brazil Data Cube Team [aut],
National Institute for Space Research [cph]
Maintainer: Felipe Carvalho <lipecaso@gmail.com>
Diff between rstac versions 0.9.2-5 dated 2024-02-11 and 1.0.0 dated 2024-02-14
rstac-0.9.2-5/rstac/R/document-funs.R |only rstac-0.9.2-5/rstac/R/stac_search.R |only rstac-0.9.2-5/rstac/R/stac_version.R |only rstac-0.9.2-5/rstac/build/vignette.rds |only rstac-0.9.2-5/rstac/inst/doc |only rstac-0.9.2-5/rstac/man/RSTACDocument.Rd |only rstac-0.9.2-5/rstac/man/assets_filter.Rd |only rstac-0.9.2-5/rstac/man/doc_query.Rd |only rstac-0.9.2-5/rstac/man/sign_bdc.Rd |only rstac-0.9.2-5/rstac/man/sign_planetary_computer.Rd |only rstac-0.9.2-5/rstac/man/stac_version.Rd |only rstac-0.9.2-5/rstac/vignettes |only rstac-1.0.0/rstac/DESCRIPTION | 27 rstac-1.0.0/rstac/MD5 | 138 +-- rstac-1.0.0/rstac/NAMESPACE | 158 +-- rstac-1.0.0/rstac/NEWS.md | 16 rstac-1.0.0/rstac/R/assets-funs.R | 146 +-- rstac-1.0.0/rstac/R/assets-utils.R | 20 rstac-1.0.0/rstac/R/check-utils.R | 66 - rstac-1.0.0/rstac/R/collections-query.R | 66 - rstac-1.0.0/rstac/R/conformance-query.R | 36 rstac-1.0.0/rstac/R/cql2-adv_comp.R | 9 rstac-1.0.0/rstac/R/cql2-funs.R | 4 rstac-1.0.0/rstac/R/cql2-text.R | 2 rstac-1.0.0/rstac/R/cql2-types.R | 62 + rstac-1.0.0/rstac/R/deprec-funs.R | 160 --- rstac-1.0.0/rstac/R/doc-funs.R |only rstac-1.0.0/rstac/R/ext_filter.R | 60 - rstac-1.0.0/rstac/R/ext_query.R | 64 - rstac-1.0.0/rstac/R/extensions.R | 104 +- rstac-1.0.0/rstac/R/geom-funs.R |only rstac-1.0.0/rstac/R/items-funs.R | 666 +++++++-------- rstac-1.0.0/rstac/R/items-query.R | 105 -- rstac-1.0.0/rstac/R/items-utils.R | 87 - rstac-1.0.0/rstac/R/parse-utils.R | 91 -- rstac-1.0.0/rstac/R/preview-utils.R | 2 rstac-1.0.0/rstac/R/print.R | 142 ++- rstac-1.0.0/rstac/R/query-funs.R | 75 - rstac-1.0.0/rstac/R/queryables-query.R | 57 - rstac-1.0.0/rstac/R/request.R | 121 -- rstac-1.0.0/rstac/R/rstac-funs.R |only rstac-1.0.0/rstac/R/rstac.R | 18 rstac-1.0.0/rstac/R/search-query.R |only rstac-1.0.0/rstac/R/signatures.R | 174 ++- rstac-1.0.0/rstac/R/stac-funs.R |only rstac-1.0.0/rstac/R/stac-query.R | 38 rstac-1.0.0/rstac/R/static-funs.R |only rstac-1.0.0/rstac/R/url-utils.R | 149 ++- rstac-1.0.0/rstac/README.md | 89 +- rstac-1.0.0/rstac/build/partial.rdb |binary rstac-1.0.0/rstac/man/assets_functions.Rd | 75 - rstac-1.0.0/rstac/man/collections.Rd | 4 rstac-1.0.0/rstac/man/conformance.Rd | 6 rstac-1.0.0/rstac/man/ext_filter.Rd | 11 rstac-1.0.0/rstac/man/ext_query.Rd | 8 rstac-1.0.0/rstac/man/extensions.Rd | 75 - rstac-1.0.0/rstac/man/items.Rd | 4 rstac-1.0.0/rstac/man/items_functions.Rd | 255 +++-- rstac-1.0.0/rstac/man/items_sign_bdc.Rd |only rstac-1.0.0/rstac/man/items_sign_planetary_computer.Rd |only rstac-1.0.0/rstac/man/print.Rd | 66 - rstac-1.0.0/rstac/man/queryables.Rd | 16 rstac-1.0.0/rstac/man/request.Rd | 6 rstac-1.0.0/rstac/man/rstac.Rd | 8 rstac-1.0.0/rstac/man/stac.Rd | 2 rstac-1.0.0/rstac/man/stac_functions.Rd |only rstac-1.0.0/rstac/man/stac_search.Rd | 12 rstac-1.0.0/rstac/man/static_functions.Rd |only rstac-1.0.0/rstac/tests/testthat.R | 2 rstac-1.0.0/rstac/tests/testthat/test-assets_functions.R | 122 -- rstac-1.0.0/rstac/tests/testthat/test-examples.R | 80 - rstac-1.0.0/rstac/tests/testthat/test-ext_filter.R | 55 - rstac-1.0.0/rstac/tests/testthat/test-internals.R | 18 rstac-1.0.0/rstac/tests/testthat/test-items_functions.R | 78 - rstac-1.0.0/rstac/tests/testthat/test-rstac_objs.R | 278 ++---- rstac-1.0.0/rstac/tests/testthat/test-signatures.R | 8 76 files changed, 1845 insertions(+), 2296 deletions(-)
Title: Kalman Filter
Description: 'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations. There is also a function to handle time varying parameters.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kalmanfilter versions 2.0.2 dated 2023-09-25 and 2.1.0 dated 2024-02-14
DESCRIPTION | 10 MD5 | 30 +- NEWS.md | 8 R/RcppExports.R | 9 R/kalman_filter.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/kalmanfilter_vignette.R | 18 + inst/doc/kalmanfilter_vignette.Rmd | 21 + inst/doc/kalmanfilter_vignette.html | 435 ++++++++++++++++++------------------ man/kalman_filter.Rd | 107 +++++--- man/kalman_filter_cpp.Rd |only man/kalmanfilter-package.Rd | 2 src/RcppExports.cpp | 27 +- src/kalmanfilter.cpp | 173 ++++++++++++++ tests/testthat.R | 2 vignettes/kalmanfilter_vignette.Rmd | 21 + 17 files changed, 588 insertions(+), 275 deletions(-)
Title: Individual Based Models in R
Description: Implementation of some Individual Based Models (IBMs, sensu Grimm and Railsback 2005)
and methods to create new ones, particularly for population dynamics models (reproduction,
mortality and movement). The basic operations for the simulations are implemented in Rcpp for speed.
Author: Ricardo Oliveros-Ramos [aut, cre]
Maintainer: Ricardo Oliveros-Ramos <ricardo.oliveros@gmail.com>
Diff between ibm versions 0.1.0 dated 2016-06-13 and 0.3.0 dated 2024-02-14
DESCRIPTION | 18 ++++++------- MD5 | 27 ++++++++++--------- NAMESPACE | 2 - R/aaa-.R | 2 - R/ibm-auxiliar.R | 2 - R/ibm-main.R | 1 R/model-localLotkaVolterra.R | 59 +++++++++++++++++++++++++++++++++---------- README.md | 25 ++++++++++++++++-- man/boundaries.Rd | 1 man/diffusion.Rd | 1 man/ibm-package.Rd | 9 ------ man/localLotkaVolterra.Rd | 31 ++++++++++++++++------ man/mortality.Rd | 1 man/reproduction.Rd | 1 src/registerDynamicSymbol.c |only 15 files changed, 118 insertions(+), 62 deletions(-)
Title: High-Dimensional Metrics
Description: Implementation of selected high-dimensional statistical and
econometric methods for estimation and inference. Efficient estimators and
uniformly valid confidence intervals for various low-dimensional causal/
structural parameters are provided which appear in high-dimensional
approximately sparse models. Including functions for fitting heteroscedastic
robust Lasso regressions with non-Gaussian errors and for instrumental variable
(IV) and treatment effect estimation in a high-dimensional setting. Moreover,
the methods enable valid post-selection inference and rely on a theoretically
grounded, data-driven choice of the penalty.
Chernozhukov, Hansen, Spindler (2016) <arXiv:1603.01700>.
Author: Martin Spindler [cre, aut],
Victor Chernozhukov [aut],
Christian Hansen [aut],
Philipp Bach [ctb]
Maintainer: Martin Spindler <martin.spindler@gmx.de>
Diff between hdm versions 0.3.1 dated 2019-01-18 and 0.3.2 dated 2024-02-14
hdm-0.3.1/hdm/inst/doc/hdm.Rnw |only hdm-0.3.1/hdm/inst/doc/hdm.pdf |only hdm-0.3.1/hdm/vignettes/hdm.Rnw |only hdm-0.3.2/hdm/DESCRIPTION | 25 hdm-0.3.2/hdm/MD5 | 118 - hdm-0.3.2/hdm/NAMESPACE | 3 hdm-0.3.2/hdm/R/help_functions.R | 4 hdm-0.3.2/hdm/R/p_adjust.R | 3 hdm-0.3.2/hdm/R/pkg-package.R | 8 hdm-0.3.2/hdm/R/rlasso.R | 49 hdm-0.3.2/hdm/R/rlassoEffects.R | 64 hdm-0.3.2/hdm/R/rlassoIV.R | 120 + hdm-0.3.2/hdm/R/rlassoIVselectX.R | 83 hdm-0.3.2/hdm/R/rlassoIVselectZ.R | 79 hdm-0.3.2/hdm/R/rlassologit.R | 7 hdm-0.3.2/hdm/R/rlassologitEffect.R | 6 hdm-0.3.2/hdm/R/rlassotreatment.R | 2 hdm-0.3.2/hdm/README.md |only hdm-0.3.2/hdm/build/vignette.rds |binary hdm-0.3.2/hdm/data/AJR.rda |binary hdm-0.3.2/hdm/data/BLP.rda |binary hdm-0.3.2/hdm/data/EminentDomain.rda |binary hdm-0.3.2/hdm/data/GrowthData.rda |binary hdm-0.3.2/hdm/data/cps2012.rda |binary hdm-0.3.2/hdm/data/pension.rda |binary hdm-0.3.2/hdm/inst/CITATION | 14 hdm-0.3.2/hdm/inst/doc/hdm.R |only hdm-0.3.2/hdm/inst/doc/hdm.Rmd |only hdm-0.3.2/hdm/inst/doc/hdm.html |only hdm-0.3.2/hdm/man/AJR.Rd | 8 hdm-0.3.2/hdm/man/BLP.Rd | 6 hdm-0.3.2/hdm/man/EminentDomain.Rd | 8 hdm-0.3.2/hdm/man/Growth-Data.Rd | 10 hdm-0.3.2/hdm/man/LassoShooting.fit.Rd | 12 hdm-0.3.2/hdm/man/TE.Rd | 66 hdm-0.3.2/hdm/man/coef.rlassoEffects.Rd | 36 hdm-0.3.2/hdm/man/coef.rlassoIV.Rd |only hdm-0.3.2/hdm/man/coef.rlassoIVselectX.Rd |only hdm-0.3.2/hdm/man/coef.rlassoIVselectZ.Rd |only hdm-0.3.2/hdm/man/cps2012.Rd | 6 hdm-0.3.2/hdm/man/hdm-package.Rd | 24 hdm-0.3.2/hdm/man/lambdaCalculation.Rd | 18 hdm-0.3.2/hdm/man/methods.rlasso.Rd | 8 hdm-0.3.2/hdm/man/methods.rlassoEffects.Rd | 20 hdm-0.3.2/hdm/man/methods.rlassoIV.Rd | 4 hdm-0.3.2/hdm/man/methods.rlassoIVselectX.Rd | 7 hdm-0.3.2/hdm/man/methods.rlassoIVselectZ.Rd | 7 hdm-0.3.2/hdm/man/methods.rlassoTE.Rd | 4 hdm-0.3.2/hdm/man/methods.rlassologit.Rd | 12 hdm-0.3.2/hdm/man/methods.rlassologitEffects.Rd | 11 hdm-0.3.2/hdm/man/methods.tsls.Rd | 4 hdm-0.3.2/hdm/man/p_adjust.Rd | 8 hdm-0.3.2/hdm/man/pension.Rd | 6 hdm-0.3.2/hdm/man/print_coef.Rd | 29 hdm-0.3.2/hdm/man/rlasso.Rd | 90 hdm-0.3.2/hdm/man/rlassoEffects.Rd | 29 hdm-0.3.2/hdm/man/rlassoIV.Rd | 7 hdm-0.3.2/hdm/man/rlassoIVselectZ.Rd | 8 hdm-0.3.2/hdm/man/rlassologit.Rd | 39 hdm-0.3.2/hdm/man/rlassologitEffects.Rd | 6 hdm-0.3.2/hdm/man/summary.rlassoEffects.Rd | 3 hdm-0.3.2/hdm/man/tsls.Rd | 6 hdm-0.3.2/hdm/vignettes/econometrica.bst | 2584 ++++++++++++------------ hdm-0.3.2/hdm/vignettes/hdm.Rmd |only hdm-0.3.2/hdm/vignettes/mybib.bib | 34 hdm-0.3.2/hdm/vignettes/preamble.tex |only 66 files changed, 2073 insertions(+), 1632 deletions(-)
More information about genetic.algo.optimizeR at CRAN
Permanent link
Title: Automated Parameter Estimation for Complex Models
Description: General optimisation and specific tools for the parameter estimation (i.e. calibration) of complex models, including stochastic ones. It implements generic functions that can be used for fitting any type of models, especially those with non-differentiable objective functions, with the same syntax as base::optim.
It supports multiple phases estimation (sequential parameter masking), constrained optimization (bounding box restrictions) and automatic parallel computation of numerical gradients.
Some common maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs is provided.
See <https://roliveros-ramos.github.io/calibrar/> for more details.
Author: Ricardo Oliveros-Ramos [aut, cre]
Maintainer: Ricardo Oliveros-Ramos <ricardo.oliveros@gmail.com>
Diff between calibrar versions 0.2.0 dated 2016-02-17 and 0.9.0 dated 2024-02-14
calibrar-0.2.0/calibrar/R/calibraR-main.R |only calibrar-0.2.0/calibrar/R/calibrar-demoLV.R |only calibrar-0.2.0/calibrar/R/calibrar-demoPoisson.R |only calibrar-0.2.0/calibrar/R/calibrar-optimWrapper.R |only calibrar-0.2.0/calibrar/man/SphereN.Rd |only calibrar-0.2.0/calibrar/man/calibrarDemo.Rd |only calibrar-0.2.0/calibrar/man/createObjectiveFunction.Rd |only calibrar-0.2.0/calibrar/man/getCalibrationInfo.Rd |only calibrar-0.2.0/calibrar/man/getObservedData.Rd |only calibrar-0.2.0/calibrar/man/optimES.Rd |only calibrar-0.9.0/calibrar/DESCRIPTION | 34 calibrar-0.9.0/calibrar/MD5 | 99 +- calibrar-0.9.0/calibrar/NAMESPACE | 57 + calibrar-0.9.0/calibrar/R/aaa-.R | 13 calibrar-0.9.0/calibrar/R/calibrar-AHR_ES.R | 374 +++++++-- calibrar-0.9.0/calibrar/R/calibrar-DEPRECATED.R |only calibrar-0.9.0/calibrar/R/calibrar-auxiliar.R | 301 ++++++- calibrar-0.9.0/calibrar/R/calibrar-class.R | 115 ++ calibrar-0.9.0/calibrar/R/calibrar-core-calibrar.R |only calibrar-0.9.0/calibrar/R/calibrar-core-optim2.R |only calibrar-0.9.0/calibrar/R/calibrar-demo-IBM_LV.R |only calibrar-0.9.0/calibrar/R/calibrar-demo-IBM_logistic.R |only calibrar-0.9.0/calibrar/R/calibrar-demo-LV.R |only calibrar-0.9.0/calibrar/R/calibrar-demo-Poisson.R |only calibrar-0.9.0/calibrar/R/calibrar-demo-SIR.R |only calibrar-0.9.0/calibrar/R/calibrar-fitness.R | 84 +- calibrar-0.9.0/calibrar/R/calibrar-gradient.R |only calibrar-0.9.0/calibrar/R/calibrar-internal.R | 411 ++++++++-- calibrar-0.9.0/calibrar/R/calibrar-main.R |only calibrar-0.9.0/calibrar/R/calibrar-random.R | 119 +- calibrar-0.9.0/calibrar/R/calibrar-restart.R | 57 - calibrar-0.9.0/calibrar/R/calibrar-splines.R |only calibrar-0.9.0/calibrar/R/calibrar-stopping.R |only calibrar-0.9.0/calibrar/R/calibrar-test_functions.R | 13 calibrar-0.9.0/calibrar/R/calibrar-wrapper.R |only calibrar-0.9.0/calibrar/R/calibrar-wrapper_dfoptim.R |only calibrar-0.9.0/calibrar/R/calibrar-wrapper_optimh.R |only calibrar-0.9.0/calibrar/R/calibrar-wrapper_optimr.R |only calibrar-0.9.0/calibrar/R/calibrar-wrapper_stats.R |only calibrar-0.9.0/calibrar/R/external-Rvmmin.R |only calibrar-0.9.0/calibrar/R/external-Rvmminb.R |only calibrar-0.9.0/calibrar/R/external-Rvmminu.R |only calibrar-0.9.0/calibrar/R/external-minqa.R |only calibrar-0.9.0/calibrar/R/external-soma.R |only calibrar-0.9.0/calibrar/R/external-utils.R |only calibrar-0.9.0/calibrar/README.md | 78 + calibrar-0.9.0/calibrar/build |only calibrar-0.9.0/calibrar/inst/CITATION | 4 calibrar-0.9.0/calibrar/inst/doc |only calibrar-0.9.0/calibrar/man/ahres.Rd |only calibrar-0.9.0/calibrar/man/calibrar-defunct.Rd |only calibrar-0.9.0/calibrar/man/calibrar-package.Rd | 45 - calibrar-0.9.0/calibrar/man/calibrar_demo.Rd |only calibrar-0.9.0/calibrar/man/calibrate.Rd | 98 +- calibrar-0.9.0/calibrar/man/calibration_data.Rd |only calibrar-0.9.0/calibrar/man/calibration_objFn.Rd |only calibrar-0.9.0/calibrar/man/calibration_setup.Rd |only calibrar-0.9.0/calibrar/man/createObjectiveFunction-defunct.Rd |only calibrar-0.9.0/calibrar/man/dot-get_command_argument.Rd |only calibrar-0.9.0/calibrar/man/dot-read_configuration.Rd |only calibrar-0.9.0/calibrar/man/figures |only calibrar-0.9.0/calibrar/man/gaussian_kernel.Rd |only calibrar-0.9.0/calibrar/man/getCalibrationInfo-defunct.Rd |only calibrar-0.9.0/calibrar/man/getObservedData-defunct.Rd |only calibrar-0.9.0/calibrar/man/gradient.Rd |only calibrar-0.9.0/calibrar/man/objFn.Rd |only calibrar-0.9.0/calibrar/man/optim2.Rd |only calibrar-0.9.0/calibrar/man/optimh.Rd |only calibrar-0.9.0/calibrar/man/sphereN.Rd |only calibrar-0.9.0/calibrar/man/spline_par.Rd |only calibrar-0.9.0/calibrar/man/summary.calibrar.results.Rd |only calibrar-0.9.0/calibrar/tests |only calibrar-0.9.0/calibrar/vignettes |only 73 files changed, 1502 insertions(+), 400 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. [...truncated...]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund versions 0.1-34 dated 2023-12-07 and 0.1-35 dated 2024-02-14
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- R/mfpca.face.R | 2 +- R/pfr.R | 2 +- man/mfpca.face.Rd | 2 +- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Chris Wudel [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb] ,
Janosch Heinermann [ctb]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 2.2.1 dated 2024-01-09 and 2.3 dated 2024-02-14
shar-2.2.1/shar/man/energy_fun.Rd |only shar-2.3/shar/DESCRIPTION | 8 shar-2.3/shar/MD5 | 78 +++--- shar-2.3/shar/NEWS.md | 7 shar-2.3/shar/R/fit_point_process.R | 47 +++- shar-2.3/shar/R/list_to_randomized.R | 9 shar-2.3/shar/R/plot_energy.R | 2 shar-2.3/shar/R/print.rd_mar.R | 6 shar-2.3/shar/R/print.rd_pat.R | 6 shar-2.3/shar/R/print.rd_ras.R | 2 shar-2.3/shar/R/randomize_raster.R | 2 shar-2.3/shar/R/reconstruct_algorithm.R | 36 +-- shar-2.3/shar/R/reconstruct_pattern.R | 21 - shar-2.3/shar/R/reconstruct_pattern_marks.R | 23 -- shar-2.3/shar/R/translate_raster.R | 2 shar-2.3/shar/inst/doc/get_started.html | 4 shar-2.3/shar/man/Energy_fun.Rd |only shar-2.3/shar/man/fit_point_process.Rd | 113 +++++---- shar-2.3/shar/man/reconstruct_pattern.Rd | 2 shar-2.3/shar/man/shar.Rd | 2 shar-2.3/shar/tests/testthat/Rplots.pdf |binary shar-2.3/shar/tests/testthat/test-calculate_energy.R | 45 ++- shar-2.3/shar/tests/testthat/test-classify_habitats.R | 18 - shar-2.3/shar/tests/testthat/test-classint_to_vector.R | 7 shar-2.3/shar/tests/testthat/test-create_neighbourhood.R | 23 +- shar-2.3/shar/tests/testthat/test-extract_points.R | 13 - shar-2.3/shar/tests/testthat/test-fit-point_process.R | 102 +++++--- shar-2.3/shar/tests/testthat/test-list_to_randomized.R | 46 +--- shar-2.3/shar/tests/testthat/test-pack-unpack.R | 20 - shar-2.3/shar/tests/testthat/test-plot_energy.R | 23 +- shar-2.3/shar/tests/testthat/test-plot_rd_multi.R | 8 shar-2.3/shar/tests/testthat/test-plot_rd_pat.R | 30 +- shar-2.3/shar/tests/testthat/test-plot_rd_ras.R | 32 +- shar-2.3/shar/tests/testthat/test-print.R | 19 - shar-2.3/shar/tests/testthat/test-randomize_raster.R | 63 ++--- shar-2.3/shar/tests/testthat/test-reconstruct_pattern.R | 80 +++---- shar-2.3/shar/tests/testthat/test-reconstruct_pattern_marks.R | 114 ++++------ shar-2.3/shar/tests/testthat/test-reconstruct_pattern_multi.R | 30 +- shar-2.3/shar/tests/testthat/test-results_habitat_association.R | 114 +++++----- shar-2.3/shar/tests/testthat/test-sample_randomized.R | 10 shar-2.3/shar/tests/testthat/test-translate_raster.R | 50 ++-- 41 files changed, 642 insertions(+), 575 deletions(-)
Title: Object Pooling
Description: Enables the creation of object pools, which make it less
computationally expensive to fetch a new object. Currently the only
supported pooled objects are 'DBI' connections.
Author: Joe Cheng [aut],
Barbara Borges [aut],
Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between pool versions 1.0.2 dated 2024-01-18 and 1.0.3 dated 2024-02-14
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/dbplyr.R | 15 +++++++++++++++ R/pool-methods.R | 5 +++++ R/pool-package.R | 5 +++++ man/Pool-class.Rd | 5 +++++ tests/testthat/_snaps/dbplyr.md | 9 +++++++++ tests/testthat/test-dbplyr.R | 13 +++++++++++++ 10 files changed, 73 insertions(+), 15 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre] ,
Edward L. Ionides [aut] ,
Carles Breto [aut] ,
Stephen P. Ellner [ctb] ,
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb] ,
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb] ,
Michael Lavine [ctb],
Dao Nguyen [ctb] ,
Eamon B. O [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 5.5 dated 2023-12-02 and 5.6 dated 2024-02-14
DESCRIPTION | 10 - MD5 | 100 +++++------ R/blowflies.R | 2 R/bsmc2.R | 7 R/logmeanexp.R | 10 - R/objfun.R | 3 R/package.R | 28 +-- R/transformations.R | 7 inst/NEWS | 9 + inst/NEWS.Rd | 7 inst/doc/index.html | 414 +++++++++++++++++++++++++++++++++++++++++++++++- inst/include/pomp.h | 6 man/abc.Rd | 6 man/basic_probes.Rd | 6 man/blowflies.Rd | 2 man/bsmc2.Rd | 6 man/coef.Rd | 2 man/cond_logLik.Rd | 2 man/covmat.Rd | 2 man/eff_sample_size.Rd | 2 man/filter_mean.Rd | 2 man/filter_traj.Rd | 2 man/flow.Rd | 2 man/forecast.Rd | 2 man/loglik.Rd | 2 man/logmeanexp.Rd | 10 - man/macros/citations.Rd | 12 - man/nlf.Rd | 6 man/obs.Rd | 2 man/parameter_trans.Rd | 4 man/pomp-package.Rd | 7 man/pomp_fun.Rd | 2 man/pred_mean.Rd | 2 man/pred_var.Rd | 2 man/probe.Rd | 4 man/probe_match.Rd | 4 man/saved_states.Rd | 2 man/spect.Rd | 2 man/spect_match.Rd | 2 man/spy.Rd | 2 man/states.Rd | 2 man/summary.Rd | 2 man/traces.Rd | 4 man/traj_match.Rd | 2 man/trajectory.Rd | 2 man/transformations.Rd | 7 src/bspline.c | 5 src/decls.h | 2 src/init.c | 4 src/pomp.h | 6 src/userdata.c | 6 51 files changed, 572 insertions(+), 174 deletions(-)
Title: Fuzzy and Non-Fuzzy Classifiers
Description: It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
Author: Jodavid Ferreira [aut, cre] ,
Ronei Moraes [ctb] ,
Arthur Ricardo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Diff between FuzzyClass versions 0.1.5 dated 2023-08-17 and 0.1.6 dated 2024-02-14
DESCRIPTION | 8 - MD5 | 57 +++++----- NAMESPACE | 14 ++ NEWS.md | 8 + R/DWFuzzyGammaNaiveBayes.R | 15 +- R/FuzzyBayesRule.R | 15 +- R/FuzzyBetaNaiveBayes.R | 14 +- R/FuzzyBinomialNaiveBayes.R | 34 ++---- R/FuzzyExponentialNaiveBayes.R | 14 +- R/FuzzyGammaNaiveBayes.R | 14 +- R/FuzzyGaussianNaiveBayes.R | 105 +++---------------- R/FuzzyGeoNaiveBayes.R | 28 +---- R/FuzzyNaiveBayes.R | 1 R/FuzzyPoissonNaiveBayes.R | 35 ++---- R/FuzzyRuleBasedSystem.R |only R/FuzzyTrapeNaiveBayes.R | 184 ++++++++++++---------------------- R/FuzzyTriangNaiveBayes.R | 14 +- R/functions.R | 220 ++++++++++++++++++++++++++++++++++++++++- README.md | 29 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/REFERENCES.bib | 8 + inst/doc/FuzzyClass.R | 2 inst/doc/FuzzyClass.html | 8 - inst/doc/index.R | 2 inst/doc/index.html | 8 - man/FuzzyGeoNaiveBayes.Rd | 4 man/HouseVotes84.Rd | 5 man/hidden_functions.Rd |only tests/test_type.R | 12 ++ 31 files changed, 498 insertions(+), 360 deletions(-)
Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with
utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description
of the package functionalities and its interplay with the MFPCA package for
multivariate functional principal component analysis
<https://CRAN.R-project.org/package=MFPCA>.
Author: Clara Happ-Kurz [aut, cre]
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between funData versions 1.3-8 dated 2021-10-17 and 1.3-9 dated 2024-02-14
funData-1.3-8/funData/man/funData-constructor.Rd |only funData-1.3-8/funData/man/irregFunData-constructor.Rd |only funData-1.3-8/funData/man/multiFunData-constructor.Rd |only funData-1.3-9/funData/DESCRIPTION | 10 ++-- funData-1.3-9/funData/MD5 | 28 ++++++------- funData-1.3-9/funData/NEWS.md | 7 +++ funData-1.3-9/funData/R/funDataClass.R | 25 +---------- funData-1.3-9/funData/R/plotMethods.R | 6 ++ funData-1.3-9/funData/README.md | 3 - funData-1.3-9/funData/man/extractObs.Rd | 4 - funData-1.3-9/funData/man/funData-class.Rd | 21 ++++++--- funData-1.3-9/funData/man/irregFunData-class.Rd | 19 ++++++-- funData-1.3-9/funData/man/multiFunData-class.Rd | 17 +++++-- funData-1.3-9/funData/man/plot.funData.Rd | 2 funData-1.3-9/funData/man/plot.irregFunData.Rd | 2 funData-1.3-9/funData/man/plot.multiFunData.Rd | 2 funData-1.3-9/funData/tests/testthat/testthat-problems.rds |only 17 files changed, 79 insertions(+), 67 deletions(-)
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to research Bayesian Vector heterogeneous autoregressive (VHAR) model,
referring to Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph]
,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>
Diff between bvhar versions 1.2.0 dated 2024-01-09 and 2.0.0 dated 2024-02-14
bvhar-1.2.0/bvhar/inst/include/bvharprob.h |only bvhar-1.2.0/bvhar/src/bvhardraw.h |only bvhar-1.2.0/bvhar/src/bvharinterrupt.cpp |only bvhar-1.2.0/bvhar/src/bvharinterrupt.h |only bvhar-1.2.0/bvhar/src/bvharmisc.h |only bvhar-1.2.0/bvhar/src/bvharomp.h |only bvhar-1.2.0/bvhar/src/bvharprogress.cpp |only bvhar-1.2.0/bvhar/src/bvharprogress.h |only bvhar-1.2.0/bvhar/src/design.cpp |only bvhar-1.2.0/bvhar/src/fitvar.h |only bvhar-1.2.0/bvhar/src/forecast-expand.cpp |only bvhar-1.2.0/bvhar/src/forecast-roll.cpp |only bvhar-1.2.0/bvhar/src/generate-distn.cpp |only bvhar-1.2.0/bvhar/src/mcmc-draw.cpp |only bvhar-1.2.0/bvhar/src/misc-eigen.cpp |only bvhar-1.2.0/bvhar/src/randsim.h |only bvhar-2.0.0/bvhar/DESCRIPTION | 13 bvhar-2.0.0/bvhar/MD5 | 159 +- bvhar-2.0.0/bvhar/NAMESPACE | 13 bvhar-2.0.0/bvhar/NEWS.md | 27 bvhar-2.0.0/bvhar/R/RcppExports.R | 1114 +++++------------- bvhar-2.0.0/bvhar/R/bvar-flat.R | 2 bvhar-2.0.0/bvhar/R/bvar-hierarchical.R | 6 bvhar-2.0.0/bvhar/R/bvar-horseshoe.R | 175 +- bvhar-2.0.0/bvhar/R/bvar-minnesota.R | 88 - bvhar-2.0.0/bvhar/R/bvar-ssvs.R | 445 +++---- bvhar-2.0.0/bvhar/R/bvar-sv.R | 515 ++++---- bvhar-2.0.0/bvhar/R/bvhar-horseshoe.R | 182 +- bvhar-2.0.0/bvhar/R/bvhar-minnesota.R | 134 -- bvhar-2.0.0/bvhar/R/bvhar-ssvs.R | 463 +++---- bvhar-2.0.0/bvhar/R/bvhar-sv.R | 567 ++++----- bvhar-2.0.0/bvhar/R/forecast.R | 186 ++- bvhar-2.0.0/bvhar/R/hyperparam.R | 148 +- bvhar-2.0.0/bvhar/R/member.R | 12 bvhar-2.0.0/bvhar/R/misc-r.R | 45 bvhar-2.0.0/bvhar/R/plot.R | 29 bvhar-2.0.0/bvhar/R/print-bvharsp.R | 18 bvhar-2.0.0/bvhar/R/print-bvharspec.R | 102 + bvhar-2.0.0/bvhar/R/simulate-param.R | 10 bvhar-2.0.0/bvhar/R/tuning.R | 24 bvhar-2.0.0/bvhar/R/varlse.R | 54 bvhar-2.0.0/bvhar/R/vharlse.R | 55 bvhar-2.0.0/bvhar/R/zzz.R |only bvhar-2.0.0/bvhar/README.md | 7 bvhar-2.0.0/bvhar/build/vignette.rds |binary bvhar-2.0.0/bvhar/inst/doc/bvhar.html | 82 - bvhar-2.0.0/bvhar/inst/doc/empirical-bayes.html | 18 bvhar-2.0.0/bvhar/inst/doc/forecasting.html | 2 bvhar-2.0.0/bvhar/inst/doc/linking.R |only bvhar-2.0.0/bvhar/inst/doc/linking.Rmd |only bvhar-2.0.0/bvhar/inst/doc/linking.html |only bvhar-2.0.0/bvhar/inst/doc/shrinkage.R | 26 bvhar-2.0.0/bvhar/inst/doc/shrinkage.Rmd | 51 bvhar-2.0.0/bvhar/inst/doc/shrinkage.html | 313 ++--- bvhar-2.0.0/bvhar/inst/include/bvharcommon.h |only bvhar-2.0.0/bvhar/inst/include/bvhardesign.h |only bvhar-2.0.0/bvhar/inst/include/bvhardraw.h |only bvhar-2.0.0/bvhar/inst/include/bvharinterrupt.h |only bvhar-2.0.0/bvhar/inst/include/bvharomp.h |only bvhar-2.0.0/bvhar/inst/include/bvharprogress.h |only bvhar-2.0.0/bvhar/inst/include/bvharsim.h |only bvhar-2.0.0/bvhar/inst/include/mcmchs.h |only bvhar-2.0.0/bvhar/inst/include/mcmcssvs.h |only bvhar-2.0.0/bvhar/inst/include/mcmcsv.h |only bvhar-2.0.0/bvhar/inst/include/minnesota.h |only bvhar-2.0.0/bvhar/inst/include/ols.h |only bvhar-2.0.0/bvhar/man/bvar_horseshoe.Rd | 10 bvhar-2.0.0/bvhar/man/bvar_ssvs.Rd | 10 bvhar-2.0.0/bvhar/man/bvar_sv.Rd | 62 - bvhar-2.0.0/bvhar/man/bvhar_horseshoe.Rd | 10 bvhar-2.0.0/bvhar/man/bvhar_ssvs.Rd | 10 bvhar-2.0.0/bvhar/man/bvhar_sv.Rd | 33 bvhar-2.0.0/bvhar/man/figures/README-predfig-1.png |binary bvhar-2.0.0/bvhar/man/is.varlse.Rd | 6 bvhar-2.0.0/bvhar/man/set_intercept.Rd |only bvhar-2.0.0/bvhar/man/set_ssvs.Rd | 14 bvhar-2.0.0/bvhar/man/set_sv.Rd |only bvhar-2.0.0/bvhar/src/Makevars | 4 bvhar-2.0.0/bvhar/src/Makevars.win | 4 bvhar-2.0.0/bvhar/src/RcppExports.cpp | 1294 ++++++--------------- bvhar-2.0.0/bvhar/src/bvhardesign.cpp |only bvhar-2.0.0/bvhar/src/bvharomp.cpp |only bvhar-2.0.0/bvhar/src/bvharsim.cpp |only bvhar-2.0.0/bvhar/src/estimate-bvar.cpp | 89 - bvhar-2.0.0/bvhar/src/estimate-hierarchical.cpp | 24 bvhar-2.0.0/bvhar/src/estimate-horseshoe.cpp | 181 +- bvhar-2.0.0/bvhar/src/estimate-ssvs.cpp | 223 +-- bvhar-2.0.0/bvhar/src/estimate-sv.cpp | 477 +------ bvhar-2.0.0/bvhar/src/estimate-var.cpp | 26 bvhar-2.0.0/bvhar/src/estimate-vhar.cpp | 72 - bvhar-2.0.0/bvhar/src/forecast-bvar.cpp | 522 ++++++-- bvhar-2.0.0/bvhar/src/forecast-bvhar.cpp | 438 ++++--- bvhar-2.0.0/bvhar/src/forecast-var.cpp | 78 + bvhar-2.0.0/bvhar/src/forecast-vhar.cpp | 78 + bvhar-2.0.0/bvhar/src/simulate-data.cpp | 9 bvhar-2.0.0/bvhar/src/tuning-models.cpp | 59 bvhar-2.0.0/bvhar/tests/testthat/test-bvar-sv.R |only bvhar-2.0.0/bvhar/tests/testthat/test-bvhar-sv.R |only bvhar-2.0.0/bvhar/tests/testthat/test-zzz.R |only bvhar-2.0.0/bvhar/vignettes/linking.Rmd |only bvhar-2.0.0/bvhar/vignettes/shrinkage.Rmd | 51 101 files changed, 4092 insertions(+), 4777 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):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe(da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>), AlphaPept (prepri [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.10.1 dated 2023-08-18 and 1.11.0.1 dated 2024-02-14
wrProteo-1.10.1/wrProteo/R/readProtDiscovererPeptides.R |only wrProteo-1.10.1/wrProteo/build/partial.rdb |only wrProteo-1.11.0.1/wrProteo/DESCRIPTION | 16 wrProteo-1.11.0.1/wrProteo/MD5 | 87 wrProteo-1.11.0.1/wrProteo/NAMESPACE | 3 wrProteo-1.11.0.1/wrProteo/R/fuseProteomicsProjects.R |only wrProteo-1.11.0.1/wrProteo/R/getUPS1acc.R | 6 wrProteo-1.11.0.1/wrProteo/R/matrixNAneighbourImpute.R | 2 wrProteo-1.11.0.1/wrProteo/R/readAlphaPeptFile.R |only wrProteo-1.11.0.1/wrProteo/R/readDiaNNFile.R | 27 wrProteo-1.11.0.1/wrProteo/R/readDiaNNPeptides.R | 10 wrProteo-1.11.0.1/wrProteo/R/readFragpipeFile.R | 4 wrProteo-1.11.0.1/wrProteo/R/readMassChroQFile.R | 12 wrProteo-1.11.0.1/wrProteo/R/readMaxQuantFile.R | 17 wrProteo-1.11.0.1/wrProteo/R/readMaxQuantPeptides.R | 10 wrProteo-1.11.0.1/wrProteo/R/readOpenMSFile.R | 5 wrProteo-1.11.0.1/wrProteo/R/readProlineFile.R | 6 wrProteo-1.11.0.1/wrProteo/R/readProtDiscovFile.R | 6 wrProteo-1.11.0.1/wrProteo/R/readProtDiscovPeptides.R | 7 wrProteo-1.11.0.1/wrProteo/R/readProteomeDiscovererFile.R | 203 +- wrProteo-1.11.0.1/wrProteo/R/readProteomeDiscovererPeptides.R |only wrProteo-1.11.0.1/wrProteo/R/readSampleMetaData.R | 5 wrProteo-1.11.0.1/wrProteo/R/readUCSCtable.R | 4 wrProteo-1.11.0.1/wrProteo/R/readUniProtExport.R | 8 wrProteo-1.11.0.1/wrProteo/R/readWombatNormFile.R | 3 wrProteo-1.11.0.1/wrProteo/build/vignette.rds |binary wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignette1.R | 25 wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignette1.Rmd | 129 + wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignette1.html | 875 +++++--- wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.R | 8 wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.Rmd | 7 wrProteo-1.11.0.1/wrProteo/inst/doc/wrProteoVignetteUPS1.html | 1001 +++++----- wrProteo-1.11.0.1/wrProteo/inst/extdata/tinyAlpaPeptide.csv.gz |only wrProteo-1.11.0.1/wrProteo/man/dot-plotQuantDistr.Rd | 13 wrProteo-1.11.0.1/wrProteo/man/fuseProteomicsProjects.Rd |only wrProteo-1.11.0.1/wrProteo/man/getUPS1acc.Rd | 6 wrProteo-1.11.0.1/wrProteo/man/readAlphaPeptFile.Rd |only wrProteo-1.11.0.1/wrProteo/man/readDiaNNFile.Rd | 12 wrProteo-1.11.0.1/wrProteo/man/readDiaNNPeptides.Rd | 4 wrProteo-1.11.0.1/wrProteo/man/readProtDiscovFile.Rd | 2 wrProteo-1.11.0.1/wrProteo/man/readProtDiscovPeptides.Rd | 2 wrProteo-1.11.0.1/wrProteo/man/readProtDiscovererPeptides.Rd | 100 wrProteo-1.11.0.1/wrProteo/man/readProteomeDiscovererFile.Rd | 17 wrProteo-1.11.0.1/wrProteo/man/readProteomeDiscovererPeptides.Rd |only wrProteo-1.11.0.1/wrProteo/man/readUCSCtable.Rd | 2 wrProteo-1.11.0.1/wrProteo/man/readUniProtExport.Rd | 6 wrProteo-1.11.0.1/wrProteo/man/readWombatNormFile.Rd | 1 wrProteo-1.11.0.1/wrProteo/vignettes/wrProteoVignette1.Rmd | 129 + wrProteo-1.11.0.1/wrProteo/vignettes/wrProteoVignetteUPS1.Rmd | 7 49 files changed, 1573 insertions(+), 1214 deletions(-)
Title: Network-Based Clustering
Description: Network-based clustering using a Bayesian network mixture model with optional covariate adjustment.
Author: Fritz Bayer [aut, cre, cph],
Jack Kuipers [ctb]
Maintainer: Fritz Bayer <frbayer@ethz.ch>
Diff between clustNet versions 1.1.0 dated 2023-09-27 and 1.2.0 dated 2024-02-14
DESCRIPTION | 6 - MD5 | 15 ++-- NEWS.md | 4 + README.md | 13 +++ build/vignette.rds |binary inst/doc/clustNet.R |only inst/doc/clustNet.Rmd | 57 ++++++++++++++++- inst/doc/clustNet.html | 163 ++++++++++++++++++++++++++++++++++++++++++++++++- vignettes/clustNet.Rmd | 57 ++++++++++++++++- 9 files changed, 299 insertions(+), 16 deletions(-)
Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Description: Provides plotting utilities supporting packages in the 'easystats'
ecosystem (<https://github.com/easystats/easystats>) and some extra themes,
geoms, and scales for 'ggplot2'. Color scales are based on
<https://materialui.co/colors>.
References: Lüdecke et al. (2021) <doi:10.21105/joss.03393>.
Author: Daniel Luedecke [aut, ctb] ,
Dominique Makowski [aut, inv] ,
Indrajeet Patil [aut, cre] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Jeffrey R. Stevens [ctb] ,
Matthew Smith [rev] ,
Jakob Bossek [re [...truncated...]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between see versions 0.8.1 dated 2023-11-03 and 0.8.2 dated 2024-02-14
DESCRIPTION | 12 MD5 | 36 - NEWS.md | 10 R/data_plot.R | 5 R/geom_binomdensity.R | 238 +++++------ R/geom_from_list.R | 516 ++++++++++++------------ R/plot.check_collinearity.R | 374 ++++++++--------- R/plot.check_heteroscedasticity.R | 166 +++---- R/plot.check_model.R | 518 ++++++++++++------------ R/plot.check_normality.R | 799 +++++++++++++++++++------------------- R/plot.check_outliers.R | 377 ++++++++--------- R/plot.n_factors.R | 100 +++- R/plot.parameters_brms_meta.R | 64 +-- R/utils.R | 8 R/utils_add_prior_layer.R | 310 +++++++------- build/partial.rdb |binary inst/WORDLIST | 1 man/plot.see_n_factors.Rd | 3 man/see-package.Rd | 1 19 files changed, 1806 insertions(+), 1732 deletions(-)
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.1.2 dated 2024-02-07 and 2.2.0 dated 2024-02-14
DESCRIPTION | 6 MD5 | 96 +++++++-------- NAMESPACE | 1 NEWS.md | 13 +- R/fbam.R | 19 +-- R/get_est.R | 33 +++-- R/get_plot_data.R | 3 R/hbam.R | 38 +++--- R/hbam_cv.R | 16 +- R/inits.R | 3 R/plot_by_group.R |only R/plot_over_self.R | 32 +++-- R/plot_respondents.R | 4 R/plot_stimuli.R | 2 R/prep_data.R | 77 ++++++++++-- R/prep_data_cv.R | 4 inst/doc/hbamr.R | 14 +- inst/doc/hbamr.Rmd | 34 ++--- inst/doc/hbamr.html | 155 ++++++++++++------------ inst/stan/BAM.stan | 13 +- inst/stan/FBAM_MINI.stan | 2 inst/stan/FBAM_MULTI.stan | 2 inst/stan/FBAM_MULTI_NF.stan | 2 inst/stan/HBAM.stan | 2 inst/stan/HBAM_MINI.stan | 2 inst/stan/HBAM_MULTI.stan | 2 inst/stan/HBAM_MULTI_NF.stan | 2 inst/stan/HBAM_NF.stan | 2 man/fbam.Rd | 18 +- man/get_est.Rd | 13 +- man/get_plot_data.Rd | 2 man/hbam.Rd | 27 ++-- man/hbam_cv.Rd | 16 +- man/plot_by_group.Rd |only man/plot_over_self.Rd | 17 +- man/plot_respondents.Rd | 2 man/plot_stimuli.Rd | 2 man/prep_data.Rd | 14 +- man/prep_data_cv.Rd | 4 src/stanExports_BAM.h | 250 ++++++++++++++++++++++++---------------- src/stanExports_FBAM_MINI.h | 29 +++- src/stanExports_FBAM_MULTI.h | 29 +++- src/stanExports_FBAM_MULTI_NF.h | 29 +++- src/stanExports_HBAM.h | 29 +++- src/stanExports_HBAM_MINI.h | 29 +++- src/stanExports_HBAM_MULTI.h | 29 +++- src/stanExports_HBAM_MULTI_NF.h | 29 +++- src/stanExports_HBAM_NF.h | 29 +++- vignettes/data.rda |binary vignettes/hbamr.Rmd | 34 ++--- 50 files changed, 738 insertions(+), 472 deletions(-)
Title: Staged Event Trees
Description: Creates and fits staged event tree probability models,
which are probabilistic graphical models capable of representing
asymmetric conditional independence statements
for categorical variables.
Includes functions to create, plot and fit staged
event trees from data, as well as many efficient structure
learning algorithms.
References:
Carli F, Leonelli M, Riccomagno E, Varando G (2022).
<doi: 10.18637/jss.v102.i06>.
Collazo R. A., Görgen C. and Smith J. Q.
(2018, ISBN:9781498729604).
Görgen C., Bigatti A., Riccomagno E. and Smith J. Q. (2018)
<arXiv:1705.09457>.
Thwaites P. A., Smith, J. Q. (2017) <arXiv:1510.00186>.
Barclay L. M., Hutton J. L. and Smith J. Q. (2013)
<doi:10.1016/j.ijar.2013.05.006>.
Smith J. Q. and Anderson P. E. (2008)
<doi:10.1016/j.artint.2007.05.004>.
Author: Gherardo Varando [aut, cre] ,
Federico Carli [aut],
Manuele Leonelli [aut] ,
Eva Riccomagno [aut]
Maintainer: Gherardo Varando <gherardo.varando@gmail.com>
Diff between stagedtrees versions 2.2.1 dated 2022-04-28 and 2.3.0 dated 2024-02-14
stagedtrees-2.2.1/stagedtrees/R/0-util-functions.R |only stagedtrees-2.2.1/stagedtrees/R/1-base-model-function.R |only stagedtrees-2.2.1/stagedtrees/R/10-comparison-functions.R |only stagedtrees-2.2.1/stagedtrees/R/1b-base-model-function.R |only stagedtrees-2.2.1/stagedtrees/R/2-plot-functions.R |only stagedtrees-2.2.1/stagedtrees/R/3-inference-functions.R |only stagedtrees-2.2.1/stagedtrees/R/4-model-selection.R |only stagedtrees-2.2.1/stagedtrees/R/5-classifier-model-functions.R |only stagedtrees-2.2.1/stagedtrees/R/6-sampling-functions.R |only stagedtrees-2.2.1/stagedtrees/R/7-ceg-functions.R |only stagedtrees-2.2.1/stagedtrees/R/8-conversion-functions.R |only stagedtrees-2.2.1/stagedtrees/R/9-search-order.R |only stagedtrees-2.2.1/stagedtrees/man/ceg2adjmat.Rd |only stagedtrees-2.2.1/stagedtrees/man/check_sevt_prob.Rd |only stagedtrees-2.2.1/stagedtrees/man/has_ctables.Rd |only stagedtrees-2.2.1/stagedtrees/man/has_prob.Rd |only stagedtrees-2.2.1/stagedtrees/man/is_fitted_sevt.Rd |only stagedtrees-2.2.1/stagedtrees/man/set_stage.Rd |only stagedtrees-2.2.1/stagedtrees/man/simple_clustering.Rd |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_ceg.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_cid.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_compare.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_confint.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_conversions.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_explore.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_inference.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_info_functions.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_model_selection.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_order_search.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_plot.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_predict.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_sampling.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_staged_ev_tree.R |only stagedtrees-2.2.1/stagedtrees/tests/testthat/test_util_functions.R |only stagedtrees-2.3.0/stagedtrees/DESCRIPTION | 44 - stagedtrees-2.3.0/stagedtrees/MD5 | 303 ++++--- stagedtrees-2.3.0/stagedtrees/NAMESPACE | 37 stagedtrees-2.3.0/stagedtrees/NEWS.md | 149 ++- stagedtrees-2.3.0/stagedtrees/R/as_adj_matrix.R |only stagedtrees-2.3.0/stagedtrees/R/as_bn.R |only stagedtrees-2.3.0/stagedtrees/R/as_sevt.R |only stagedtrees-2.3.0/stagedtrees/R/barplot.R |only stagedtrees-2.3.0/stagedtrees/R/ceg.R |only stagedtrees-2.3.0/stagedtrees/R/checks.R |only stagedtrees-2.3.0/stagedtrees/R/ci_matrices.R |only stagedtrees-2.3.0/stagedtrees/R/cid.R |only stagedtrees-2.3.0/stagedtrees/R/compare.R |only stagedtrees-2.3.0/stagedtrees/R/confint.R |only stagedtrees-2.3.0/stagedtrees/R/data-doc.R | 60 + stagedtrees-2.3.0/stagedtrees/R/erase_fit.R |only stagedtrees-2.3.0/stagedtrees/R/expand_prob.R |only stagedtrees-2.3.0/stagedtrees/R/full_indep.R |only stagedtrees-2.3.0/stagedtrees/R/generate_toy_data.R |only stagedtrees-2.3.0/stagedtrees/R/get_paths_stages.R |only stagedtrees-2.3.0/stagedtrees/R/igraph_conversion.R |only stagedtrees-2.3.0/stagedtrees/R/inclusions_stages.R |only stagedtrees-2.3.0/stagedtrees/R/join_positions.R |only stagedtrees-2.3.0/stagedtrees/R/join_stages.R |only stagedtrees-2.3.0/stagedtrees/R/join_unobserved.R |only stagedtrees-2.3.0/stagedtrees/R/loglikelihood.R |only stagedtrees-2.3.0/stagedtrees/R/lr_test.R |only stagedtrees-2.3.0/stagedtrees/R/make_ctables.R |only stagedtrees-2.3.0/stagedtrees/R/model_info.R |only stagedtrees-2.3.0/stagedtrees/R/parentslist.R |only stagedtrees-2.3.0/stagedtrees/R/plot.R |only stagedtrees-2.3.0/stagedtrees/R/plot_ceg.R |only stagedtrees-2.3.0/stagedtrees/R/predict.R |only stagedtrees-2.3.0/stagedtrees/R/print.R |only stagedtrees-2.3.0/stagedtrees/R/print_util.R |only stagedtrees-2.3.0/stagedtrees/R/probability.R |only stagedtrees-2.3.0/stagedtrees/R/probdist.R |only stagedtrees-2.3.0/stagedtrees/R/random_parentslist.R |only stagedtrees-2.3.0/stagedtrees/R/random_sevt.R |only stagedtrees-2.3.0/stagedtrees/R/sample_from.R |only stagedtrees-2.3.0/stagedtrees/R/search_best.R |only stagedtrees-2.3.0/stagedtrees/R/search_greedy.R |only stagedtrees-2.3.0/stagedtrees/R/sevt.R |only stagedtrees-2.3.0/stagedtrees/R/sevt_add.R |only stagedtrees-2.3.0/stagedtrees/R/sevt_fit.R |only stagedtrees-2.3.0/stagedtrees/R/sevt_simplify.R |only stagedtrees-2.3.0/stagedtrees/R/stage_operations.R |only stagedtrees-2.3.0/stagedtrees/R/stagedtrees.R | 6 stagedtrees-2.3.0/stagedtrees/R/stages.R |only stagedtrees-2.3.0/stagedtrees/R/stages_bhc.R |only stagedtrees-2.3.0/stagedtrees/R/stages_bhcr.R |only stagedtrees-2.3.0/stagedtrees/R/stages_bj.R |only stagedtrees-2.3.0/stagedtrees/R/stages_csbhc.R |only stagedtrees-2.3.0/stagedtrees/R/stages_fbhc.R |only stagedtrees-2.3.0/stagedtrees/R/stages_hc.R |only stagedtrees-2.3.0/stagedtrees/R/stages_hclust.R |only stagedtrees-2.3.0/stagedtrees/R/stages_kmeans.R |only stagedtrees-2.3.0/stagedtrees/R/stages_simplebhc.R |only stagedtrees-2.3.0/stagedtrees/R/stndnaming.R |only stagedtrees-2.3.0/stagedtrees/R/subtrees.R |only stagedtrees-2.3.0/stagedtrees/R/summary.R |only stagedtrees-2.3.0/stagedtrees/R/tree_indexing.R |only stagedtrees-2.3.0/stagedtrees/R/util_functions.R |only stagedtrees-2.3.0/stagedtrees/R/write_tikz.R |only stagedtrees-2.3.0/stagedtrees/README.md | 428 ---------- stagedtrees-2.3.0/stagedtrees/data/covid_patients.rda |only stagedtrees-2.3.0/stagedtrees/data/trajectories.rda |only stagedtrees-2.3.0/stagedtrees/man/as_adj_matrix.Rd | 17 stagedtrees-2.3.0/stagedtrees/man/as_bn.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/as_parentslist.Rd | 10 stagedtrees-2.3.0/stagedtrees/man/as_sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/barplot.sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/ceg.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/check_sevt.Rd | 104 ++ stagedtrees-2.3.0/stagedtrees/man/ci_matrices.Rd |only stagedtrees-2.3.0/stagedtrees/man/cid.Rd | 12 stagedtrees-2.3.0/stagedtrees/man/compare_stages.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/confint.sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/covid_patients.Rd |only stagedtrees-2.3.0/stagedtrees/man/depsubtree.Rd |only stagedtrees-2.3.0/stagedtrees/man/distance_mat_stages.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/edge.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/erase_fit.Rd |only stagedtrees-2.3.0/stagedtrees/man/expand_prob.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/figures/README-unnamed-chunk-3-1.png |only stagedtrees-2.3.0/stagedtrees/man/find_stage.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/full_indep.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/generate_linear_dataset.Rd | 16 stagedtrees-2.3.0/stagedtrees/man/generate_random_dataset.Rd | 10 stagedtrees-2.3.0/stagedtrees/man/generate_xor_dataset.Rd | 10 stagedtrees-2.3.0/stagedtrees/man/get_stage.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/igraph-conversion.Rd |only stagedtrees-2.3.0/stagedtrees/man/inclusions_stages.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/join_positions.Rd |only stagedtrees-2.3.0/stagedtrees/man/join_stages.Rd | 17 stagedtrees-2.3.0/stagedtrees/man/join_unobserved.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/logLik.sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/lr_test.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/make_ctables.Rd | 7 stagedtrees-2.3.0/stagedtrees/man/new_label.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/node.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/noisy_xor.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/path_probability.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/plot.ceg.Rd | 7 stagedtrees-2.3.0/stagedtrees/man/plot.sevt.Rd | 28 stagedtrees-2.3.0/stagedtrees/man/predict.sevt.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/print.parentslist.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/print.sevt.Rd | 8 stagedtrees-2.3.0/stagedtrees/man/prob.Rd | 13 stagedtrees-2.3.0/stagedtrees/man/probdist.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/random_parentslist.Rd |only stagedtrees-2.3.0/stagedtrees/man/random_sevt.Rd |only stagedtrees-2.3.0/stagedtrees/man/rename_stage.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/sample_from.Rd | 10 stagedtrees-2.3.0/stagedtrees/man/search_best.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/search_greedy.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/sevt.Rd | 6 stagedtrees-2.3.0/stagedtrees/man/sevt_add.Rd | 7 stagedtrees-2.3.0/stagedtrees/man/sevt_df.Rd | 3 stagedtrees-2.3.0/stagedtrees/man/sevt_fit.Rd | 42 stagedtrees-2.3.0/stagedtrees/man/sevt_nvar.Rd | 3 stagedtrees-2.3.0/stagedtrees/man/sevt_simplify.Rd |only stagedtrees-2.3.0/stagedtrees/man/sevt_varnames.Rd | 3 stagedtrees-2.3.0/stagedtrees/man/split_stage_random.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/stagedtrees.Rd | 22 stagedtrees-2.3.0/stagedtrees/man/stages.Rd | 108 ++ stagedtrees-2.3.0/stagedtrees/man/stages_bhc.Rd | 8 stagedtrees-2.3.0/stagedtrees/man/stages_bhcr.Rd | 8 stagedtrees-2.3.0/stagedtrees/man/stages_bj.Rd | 6 stagedtrees-2.3.0/stagedtrees/man/stages_csbhc.Rd |only stagedtrees-2.3.0/stagedtrees/man/stages_fbhc.Rd | 10 stagedtrees-2.3.0/stagedtrees/man/stages_hc.Rd | 8 stagedtrees-2.3.0/stagedtrees/man/stages_hclust.Rd | 28 stagedtrees-2.3.0/stagedtrees/man/stages_kmeans.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/stages_simplebhc.Rd |only stagedtrees-2.3.0/stagedtrees/man/stndnaming.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/subtree.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/summary.sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/text.sevt.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/trajectories.Rd |only stagedtrees-2.3.0/stagedtrees/man/tree_idx.Rd | 2 stagedtrees-2.3.0/stagedtrees/man/tree_string.Rd |only stagedtrees-2.3.0/stagedtrees/man/uni_idx.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/which_class.Rd | 4 stagedtrees-2.3.0/stagedtrees/man/write_tikz.Rd |only stagedtrees-2.3.0/stagedtrees/tests/testthat/Rplots.pdf |binary stagedtrees-2.3.0/stagedtrees/tests/testthat/test-as_adj_matrix.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-as_bn.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-as_sevt.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-barplot.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-ceg.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-checks.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-cid.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-compare.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-confint.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-erase_fit.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-full.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-generate_toy_data.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-igraph_conversion.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-inclusion_stages.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-indep.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-join_stages.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-join_unobserved.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-likelihood.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-lr_test.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-model_info.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-parentslist.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-plot.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-plot_ceg.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-predict.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-print.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-print_util.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-probability.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-probdist.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-random_parentslist.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-random_sevt.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-sample_from.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-search_best.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-search_greedy.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-sevt.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-sevt_add.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-sevt_fit.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-sevt_simplify.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stage_operations.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_bhc.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_bhcr.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_bj.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_csbhc.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_fbhc.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_hc.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_kmeans.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_simplebhc.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-stages_stages_hclust.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-subtrees.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-summary.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-tree_indexing.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-util_functions.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test-write_tikz.R |only stagedtrees-2.3.0/stagedtrees/tests/testthat/test_simple.R |only 234 files changed, 888 insertions(+), 754 deletions(-)
Title: Geometries to Plot Networks with 'ggplot2'
Description: Geometries to plot network objects with 'ggplot2'.
Author: Francois Briatte [aut, cre] ,
Michal Bojanowski [ctb] ,
Mickael Canouil [ctb] ,
Zachary Charlop-Powers [ctb] ,
Jacob C. Fisher [ctb] ,
Kipp Johnson [ctb] ,
Tyler Rinker [ctb]
Maintainer: Francois Briatte <f.briatte@gmail.com>
Diff between ggnetwork versions 0.5.12 dated 2023-03-06 and 0.5.13 dated 2024-02-14
DESCRIPTION | 10 ++-- MD5 | 16 +++---- NEWS.md | 7 +++ R/fortify-igraph.R | 2 build/vignette.rds |binary inst/doc/ggnetwork.R | 24 +++++----- inst/doc/ggnetwork.html | 109 +++++++++++++++++++++++------------------------- man/geom_edgetext.Rd | 2 man/geom_nodetext.Rd | 2 9 files changed, 88 insertions(+), 84 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.3 dated 2023-03-28 and 1.1.5 dated 2024-02-14
DESCRIPTION | 8 - MD5 | 68 +++++------ NAMESPACE | 1 NEWS | 8 + R/confrontation.R | 2 R/expressionset.R | 8 - R/rule.R | 2 R/utils.R | 2 R/validate_pkg.R | 8 - build/vignette.rds |binary inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.R | 60 +++++----- inst/doc/cookbook.Rmd | 114 +++++++++---------- inst/doc/cookbook.html | 179 +++++++++++++----------------- man/as.data.frame-confrontation-method.Rd | 2 man/created.Rd | 2 man/description.Rd | 2 man/errors.Rd | 2 man/event.Rd | 4 man/keyset.Rd | 2 man/label.Rd | 2 man/length.Rd | 2 man/meta.Rd | 2 man/names.Rd | 2 man/origin.Rd | 2 man/plot-validator-method.Rd | 2 man/satisfying.Rd | 3 man/select.Rd | 2 man/validate-summary.Rd | 2 man/validate.Rd | 23 +++ man/validate_extend.Rd | 3 man/values.Rd | 2 man/variables.Rd | 4 man/voptions.Rd | 4 vignettes/cookbook.Rmd | 114 +++++++++---------- 35 files changed, 327 insertions(+), 316 deletions(-)
Title: CCR, Advanced Correlation & Beta Estimates, Betting Strategies
Description: Contains performance analysis metrics of track records including entropy-based
correlation and dynamic beta based on the Kalman filter. The normalized sample entropy method
has been implemented which produces accurate entropy estimation even on smaller datasets while for
the dynamic beta calculation the Kalman filter methodology has been utilized.
On a separate stream, trades from the five major assets classes and also
functionality to use pricing curves, rating tables, CSAs and add-on tables. The
implementation follows an object oriented logic whereby each trade inherits from
more abstract classes while also the curves/tables are objects. Furthermore, odds calculators
and P&L back-testing functionality has been implemented for the most widely used betting/trading
strategies including martingale, DAlembert, Labouchere and Fibonacci. Back-testing has also been included for the EuroMillions and EuroJackpot lotteries.
Furthermore, some basic functionality about climate risk has been i [...truncated...]
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between Trading versions 2.5 dated 2022-08-26 and 3.0 dated 2024-02-14
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 25 +++++++++++++++++++++++-- NAMESPACE | 14 +++++++++++++- R/CalcEuroLotteryPnL.R |only R/EuroJackpotResults.R |only R/EuroLotteryAllCombinations.R |only R/EuroLotteryBacktesting.R |only R/EuroMillionsResults.R |only R/OuterJoinMerge.R |only R/eurojackpotExample.R |only R/euromillionsExample.R |only R/globals.R |only R/top5.R |only inst/extdata/eurojackpot_results.csv |only inst/extdata/euromillions_results.csv |only man/CalcEuroLotteryPnL.Rd |only man/EuroJackpotExample.Rd |only man/EuroJackpotResults.Rd |only man/EuroLotteryAllCombinations.Rd |only man/EuroLotteryBacktesting.Rd |only man/EuroMillionsExample.Rd |only man/EuroMillionsResults.Rd |only man/OuterJoinMerge.Rd |only man/top5.Rd |only 24 files changed, 51 insertions(+), 13 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.5-7 dated 2023-08-14 and 3.5-8 dated 2024-02-14
DESCRIPTION | 8 +-- MD5 | 86 +++++++++++++++++------------------ NAMESPACE | 5 +- R/clogit.R | 4 - R/plot.cox.zph.R | 6 ++ R/quantile.survfit.R | 3 + R/survcondense.R | 9 +-- R/xtras.R | 10 ++++ data/cancer.rda |binary inst/NEWS.Rd | 10 ++++ inst/doc/adjcurve.pdf |binary inst/doc/approximate.pdf |binary inst/doc/compete.pdf |binary inst/doc/concordance.pdf |binary inst/doc/discrim.pdf |binary inst/doc/matrix.pdf |binary inst/doc/multi.pdf |binary inst/doc/other.pdf |binary inst/doc/population.pdf |binary inst/doc/redistribute.pdf |binary inst/doc/splines.pdf |binary inst/doc/survival.R | 3 - inst/doc/survival.Rnw | 4 - inst/doc/survival.pdf |binary inst/doc/tiedtimes.pdf |binary inst/doc/timedep.pdf |binary inst/doc/validate.pdf |binary man/hoel.Rd | 2 man/myeloid.Rd | 18 +++++-- man/pbc.Rd | 3 - man/plot.cox.zph.Rd | 4 + man/royston.Rd | 4 - man/summary.coxph.Rd | 6 +- man/survSplit.Rd | 18 ++++++- man/survcheck.Rd | 51 ++++++++++++-------- man/survfit.Rd | 2 man/survival-internal.Rd | 3 + man/tmerge.Rd | 10 ++-- noweb/coxsurv3.Rnw | 2 tests/Examples/survival-Ex.Rout.save | 36 ++++++++++---- tests/pyear.R | 9 --- tests/pyear.Rout.save | 17 ++---- vignettes/refer.bib | 8 +++ vignettes/survival.Rnw | 4 - 44 files changed, 215 insertions(+), 130 deletions(-)
Title: R Bindings for the 'prqlc' Rust Library
Description: Provides a function to convert 'PRQL' strings to 'SQL' strings.
Combined with other R functions that take 'SQL' as an argument,
'PRQL' can be used on R.
Author: Tatsuya Shima [aut, cre],
Authors of the dependency Rust crates [aut]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between prqlr versions 0.7.0 dated 2024-01-08 and 0.8.0 dated 2024-02-14
prqlr-0.7.0/prqlr/R/extendr-wrappers.R |only prqlr-0.7.0/prqlr/src/entrypoint.c |only prqlr-0.7.0/prqlr/src/prqlr-win.def |only prqlr-0.7.0/prqlr/src/rust/src/utils.rs |only prqlr-0.8.0/prqlr/DESCRIPTION | 19 - prqlr-0.8.0/prqlr/LICENSE.note | 124 +++++++---- prqlr-0.8.0/prqlr/MD5 | 59 ++--- prqlr-0.8.0/prqlr/NEWS.md | 17 + prqlr-0.8.0/prqlr/R/compile.R | 17 - prqlr-0.8.0/prqlr/R/utils.R | 49 ---- prqlr-0.8.0/prqlr/R/wrappers.R |only prqlr-0.8.0/prqlr/README.md | 21 - prqlr-0.8.0/prqlr/configure | 33 ++- prqlr-0.8.0/prqlr/inst/AUTHORS | 16 - prqlr-0.8.0/prqlr/inst/doc/knitr.html | 8 prqlr-0.8.0/prqlr/inst/doc/prqlr.html | 2 prqlr-0.8.0/prqlr/man/prql_compile.Rd | 10 prqlr-0.8.0/prqlr/man/prql_get_targets.Rd | 2 prqlr-0.8.0/prqlr/man/prql_version.Rd | 6 prqlr-0.8.0/prqlr/man/prqlr-package.Rd | 8 prqlr-0.8.0/prqlr/src/Makevars.in | 14 + prqlr-0.8.0/prqlr/src/Makevars.win | 10 prqlr-0.8.0/prqlr/src/init.c |only prqlr-0.8.0/prqlr/src/rust/Cargo.lock | 171 ++++++++++------ prqlr-0.8.0/prqlr/src/rust/Cargo.toml | 10 prqlr-0.8.0/prqlr/src/rust/api.h |only prqlr-0.8.0/prqlr/src/rust/src/lib.rs | 105 ++++----- prqlr-0.8.0/prqlr/src/rust/vendor-config.toml | 4 prqlr-0.8.0/prqlr/src/rust/vendor.tar.xz |binary prqlr-0.8.0/prqlr/tests/testthat/_snaps/compile.md | 20 - prqlr-0.8.0/prqlr/tests/testthat/_snaps/knitr-engine.md | 4 prqlr-0.8.0/prqlr/tests/testthat/test-compile.R | 19 + prqlr-0.8.0/prqlr/tools/lib-sums.tsv | 10 prqlr-0.8.0/prqlr/tools/prep-lib.R | 8 34 files changed, 429 insertions(+), 337 deletions(-)
Title: Selection Response Analysis
Description: Artificial selection through selective breeding is an efficient way to induce changes in traits of interest in experimental populations. This package (sra) provides a set of tools to analyse artificial-selection response datasets. The data typically feature for several generations the average value of a trait in a population, the variance of the trait, the population size and the average value of the parents that were chosen to breed. Sra implements two families of models aiming at describing the dynamics of the genetic architecture of the trait during the selection response. The first family relies on purely descriptive (phenomenological) models, based on an autoregressive framework. The second family provides different mechanistic models, accounting e.g. for inbreeding, mutations, genetic and environmental canalization, or epistasis. The parameters underlying the dynamics of the time series are estimated by maximum likelihood. The sra package thus provides (i) a wrapper for the R fun [...truncated...]
Author: Arnaud Le Rouzic
Maintainer: Arnaud Le Rouzic <arnaud.le-rouzic@universite-paris-saclay.fr>
Diff between sra versions 0.1.4 dated 2023-03-08 and 0.1.4.1 dated 2024-02-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/sraAutoregTimeseries.Rd | 1 - 3 files changed, 6 insertions(+), 7 deletions(-)
Title: Estimation of Fuzzy Poverty Measures
Description: Estimates fuzzy measures of poverty and deprivation. It also estimates the sampling variance of these measures using bootstrap or jackknife repeated replications.
Author: Federico Crescenzi [aut, cre] ,
Lorenzo Mori [aut] ,
Gianni Betti [ctb]
Maintainer: Federico Crescenzi <federico.crescenzi@unitus.it>
Diff between FuzzyPovertyR versions 2.0.0 dated 2024-02-12 and 2.0.1 dated 2024-02-14
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/fs_plot.R | 6 ++++-- R/plot_method.R | 23 ++++++++++++----------- inst/doc/FuzzyPovertyR.html | 13 +++++++------ man/FN.Rd | 4 ++-- man/MemberhsipGradesMatrix.Rd | 2 +- man/fm_construct.Rd | 2 +- man/fs_var.Rd | 6 +++--- man/ub1.Rd | 2 +- man/ub2.Rd | 2 +- man/z_fun.Rd | 2 +- 12 files changed, 47 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-19 1.2.0
2022-10-27 1.1.8
2021-11-03 1.1.7
2021-06-18 1.1.6
2021-04-02 1.1.5
2021-02-17 1.1.4
2021-01-18 1.1.3
2020-12-08 1.1.2
2020-10-29 1.1.1
2020-09-25 1.1.0
2020-02-17 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-12 0.4.1
2020-01-11 0.4.0
2019-09-15 0.3.4
2019-05-30 0.3.3
2019-03-22 0.3.1
2019-01-07 0.3.0
2017-09-23 0.2.1
2017-08-10 0.2.0
2017-07-15 0.1.0
Title: Wavelet Deconvolution
Description: Makes available code necessary to reproduce figures and
tables in papers on the WaveD method for wavelet deconvolution
of noisy signals as presented in The WaveD Transform in R,
Journal of Statistical Software Volume 21, No. 3, 2007.
Author: Marc Raimondo <marcr@maths.usyd.edu.au> and Michael Stewart
<michael.stewart@sydney.edu.au>
Maintainer: Michael Stewart <michael.stewart@sydney.edu.au>
Diff between waved versions 1.2 dated 2018-05-29 and 1.3 dated 2024-02-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/WaveDjF.Rd | 4 ++-- man/dyad.Rd | 4 ++-- man/dyadjk.Rd | 4 ++-- man/maxithresh.Rd | 13 +++++-------- 6 files changed, 20 insertions(+), 23 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Ethan B. Smith [ctb],
Wouter Thielen [ctb],
Paul Teetor [ctb],
Steve Bronder [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4.25 dated 2023-08-22 and 0.4.26 dated 2024-02-14
DESCRIPTION | 9 ++-- MD5 | 42 +++++++++---------- NAMESPACE | 1 R/chart_Series.R | 103 +++++++++++++++++++++++++++++++++++++++++++++-- R/getOptionChain.R | 22 ++++++---- R/getQuote.R | 2 R/periodReturn.R | 10 ++-- man/TA.Rd | 84 ++++++++++++++++++-------------------- man/attachSymbols.Rd | 2 man/buildModel.Rd | 4 - man/chartSeries.Rd | 8 +-- man/chartTheme.Rd | 37 ++++++++-------- man/chart_Series.Rd | 1 man/getModelData.Rd | 2 man/getQuote.Rd | 2 man/getSymbols.Rd | 2 man/getSymbols.SQLite.Rd | 2 man/periodReturn.Rd | 10 ++-- man/quantmod-defunct.Rd | 2 man/setSymbolLookup.Rd | 10 ++-- man/specifyModel.Rd | 4 - man/tradeModel.Rd | 2 22 files changed, 233 insertions(+), 128 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut],
Yoonkyoung Jeon [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.4.4 dated 2023-12-06 and 1.5.0 dated 2024-02-14
DESCRIPTION | 18 ++++++++++-------- MD5 | 18 ++++++++++++------ NAMESPACE | 15 +++++++++++++++ NEWS.md | 7 +++++++ R/forestcox.R |only R/forestglm.R |only R/jsBasicGadget.R | 5 +++++ R/line.R | 3 +-- inst/doc/jsmodule.html | 4 ++-- man/forestcoxServer.Rd |only man/forestcoxUI.Rd |only man/forestglmServer.Rd |only man/forestglmUI.Rd |only 13 files changed, 52 insertions(+), 18 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 2.2.1 dated 2024-02-07 and 2.2.2 dated 2024-02-14
DESCRIPTION | 6 MD5 | 10 NEWS.md | 78 +-- R/runSearch.R | 11 inst/doc/a03_Options_for_CodelistGenerator.html | 30 - tests/testthat/test-getCandidateCodes.R | 610 ++++++++++++------------ 6 files changed, 383 insertions(+), 362 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 0.2.0 dated 2022-09-19 and 0.3.0 dated 2024-02-14
brulee-0.2.0/brulee/tests/testthat/_snaps/logistic_reg-fit.md |only brulee-0.2.0/brulee/tests/testthat/_snaps/mlp-binary.md |only brulee-0.2.0/brulee/tests/testthat/_snaps/mlp-multinomial.md |only brulee-0.2.0/brulee/tests/testthat/_snaps/multinomial_reg-fit.md |only brulee-0.3.0/brulee/DESCRIPTION | 22 brulee-0.3.0/brulee/LICENSE | 4 brulee-0.3.0/brulee/MD5 | 65 brulee-0.3.0/brulee/NAMESPACE | 1 brulee-0.3.0/brulee/NEWS.md | 8 brulee-0.3.0/brulee/R/activation.R |only brulee-0.3.0/brulee/R/checks.R | 35 brulee-0.3.0/brulee/R/coef.R | 6 brulee-0.3.0/brulee/R/convert_data.R | 2 brulee-0.3.0/brulee/R/linear_reg-fit.R | 41 brulee-0.3.0/brulee/R/linear_reg-predict.R | 4 brulee-0.3.0/brulee/R/logistic_reg-fit.R | 42 brulee-0.3.0/brulee/R/logistic_reg-predict.R | 4 brulee-0.3.0/brulee/R/mlp-fit.R | 93 - brulee-0.3.0/brulee/R/mlp-predict.R | 10 brulee-0.3.0/brulee/R/multinomial_reg-fit.R | 42 brulee-0.3.0/brulee/R/multinomial_reg-predict.R | 4 brulee-0.3.0/brulee/R/schedulers.R | 2 brulee-0.3.0/brulee/README.md | 18 brulee-0.3.0/brulee/inst/WORDLIST | 23 brulee-0.3.0/brulee/man/brulee-package.Rd | 8 brulee-0.3.0/brulee/man/brulee_activations.Rd |only brulee-0.3.0/brulee/man/brulee_mlp.Rd | 11 brulee-0.3.0/brulee/tests/testthat/_snaps/class-weight.md |only brulee-0.3.0/brulee/tests/testthat/_snaps/mlp-regression.md | 270 +++- brulee-0.3.0/brulee/tests/testthat/test-class-weight.R |only brulee-0.3.0/brulee/tests/testthat/test-linear_reg-fit.R | 171 ++ brulee-0.3.0/brulee/tests/testthat/test-logistic_reg-fit.R | 276 +++- brulee-0.3.0/brulee/tests/testthat/test-mlp-activations.R |only brulee-0.3.0/brulee/tests/testthat/test-mlp-binary.R | 342 +++-- brulee-0.3.0/brulee/tests/testthat/test-mlp-multinomial.R | 268 +++- brulee-0.3.0/brulee/tests/testthat/test-mlp-regression.R | 668 +++++----- brulee-0.3.0/brulee/tests/testthat/test-multinomial_reg-fit.R | 263 ++- brulee-0.3.0/brulee/tests/testthat/test-schedulers.R | 1 38 files changed, 1777 insertions(+), 927 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre, cph]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.1.0 dated 2023-12-04 and 1.2.0 dated 2024-02-14
vaccine-1.1.0/vaccine/vignettes/basic.Rmd.orig |only vaccine-1.1.0/vaccine/vignettes/unnamed-chunk-6-1.png |only vaccine-1.1.0/vaccine/vignettes/unnamed-chunk-7-1.png |only vaccine-1.2.0/vaccine/DESCRIPTION | 12 vaccine-1.2.0/vaccine/MD5 | 31 - vaccine-1.2.0/vaccine/NAMESPACE | 2 vaccine-1.2.0/vaccine/NEWS.md | 11 vaccine-1.2.0/vaccine/R/nuisance_estimators.R | 22 - vaccine-1.2.0/vaccine/R/plots.R | 315 ++++++++++++++--- vaccine-1.2.0/vaccine/build/partial.rdb |binary vaccine-1.2.0/vaccine/build/vignette.rds |binary vaccine-1.2.0/vaccine/inst/doc/basic.Rmd | 72 +++ vaccine-1.2.0/vaccine/inst/doc/basic.html | 83 +++- vaccine-1.2.0/vaccine/man/as_table.Rd |only vaccine-1.2.0/vaccine/man/plot_ce.Rd | 35 + vaccine-1.2.0/vaccine/man/trim.Rd |only vaccine-1.2.0/vaccine/vignettes/basic.Rmd | 72 +++ vaccine-1.2.0/vaccine/vignettes/cr_curves.png |only vaccine-1.2.0/vaccine/vignettes/cr_curves_styled.png |only vaccine-1.2.0/vaccine/vignettes/cr_curves_trimmed.png |only vaccine-1.2.0/vaccine/vignettes/cr_curves_with_kde.png |only 21 files changed, 530 insertions(+), 125 deletions(-)
Title: Multiblock Sparse Multivariable Analysis
Description: Several functions can be used to analyze multiblock multivariable data. If the input is a single matrix, then principal components analysis (PCA) is implemented. If the input is a list of matrices, then multiblock PCA is implemented. If the input is two matrices, for exploratory and objective variables, then partial least squares (PLS) analysis is implemented. If the input is two lists of matrices, for exploratory and objective variables, then multiblock PLS analysis is implemented. Additionally, if an extra outcome variable is specified, then a supervised version of the methods above is implemented. For each method, sparse modeling is also incorporated. Functions for selecting the number of components and regularized parameters are also provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between msma versions 3.0 dated 2023-08-25 and 3.1 dated 2024-02-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/msma.R | 4 ++-- inst/doc/msma.html | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)