Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate.data.frame and ?modify.default.
See ?read_yamlet ?write_yamlet, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.9.8 dated 2022-10-26 and 0.10.0 dated 2022-11-23
DESCRIPTION | 6 - MD5 | 103 +++++++++++-------- NAMESPACE | 9 + R/append_units.R | 62 ++++++++--- R/classified.R | 41 +++++++ R/desolve.R | 34 ++++-- R/drop_title.R |only R/dvec.R | 63 +++++++++++ R/explicit_guide.R | 6 - R/ggplot.R | 6 - R/make_title.R |only R/resolve.R | 23 +++- R/vec_cast.R | 1 R/vec_decorated.R | 19 ++- R/yamlet_options.R |only inst/doc/yamlet-introduction.html | 115 ++++++++++----------- man/alias.data.frame.Rd | 12 ++ man/append_units.Rd | 14 ++ man/append_units.data.frame.Rd | 8 + man/append_units.default.Rd | 19 +++ man/as_dvec.units.Rd | 1 man/as_units.dvec.Rd | 1 man/dd_cast.Rd | 1 man/dd_ptype2.Rd | 1 man/desolve.Rd | 5 man/desolve.classified.Rd | 6 - man/desolve.decorated.Rd | 8 - man/desolve.dvec.Rd | 10 + man/drop_title.Rd |only man/drop_title.decorated.Rd |only man/drop_title.default.Rd |only man/drop_title.dvec.Rd |only man/explicit_guide.data.frame.Rd | 4 man/explicit_guide.dvec.Rd | 2 man/ggplot_build.decorated_ggplot.Rd | 8 - man/make_title.Rd |only man/make_title.decorated.Rd |only man/make_title.default.Rd |only man/make_title.dvec.Rd |only man/print.decorated_ggplot.Rd | 8 - man/resolve.Rd | 4 man/resolve.decorated.Rd | 8 - man/resolve.dvec.Rd | 5 man/sub_units.Rd | 10 + man/vec_cast.data.frame.decorated.Rd | 1 man/vec_cast.decorated.data.frame.Rd | 1 man/vec_cast.decorated.decorated.Rd | 3 man/vec_ptype2.data.frame.decorated.Rd | 5 man/vec_ptype2.decorated.data.frame.Rd | 3 man/vec_ptype2.decorated.decorated.Rd | 3 man/yamlet_options.Rd |only tests/testthat/063.rds |binary tests/testthat/085.rds |binary tests/testthat/108.rds |only tests/testthat/109.rds |only tests/testthat/110.rds |only tests/testthat/111.rds |only tests/testthat/112.rds |only tests/testthat/113.rds |only tests/testthat/114.rds |only tests/testthat/115.rds |only tests/testthat/116.rds |only tests/testthat/test-yamlet.R | 174 ++++++++++++++++++++++++++++++++- 63 files changed, 619 insertions(+), 194 deletions(-)
Title: Display Information About Nested Subsets of a Data Frame
Description: A tool for calculating and drawing "variable trees". Variable trees display information about nested subsets of a data frame.
Author: Nick Barrowman [aut, cre],
Sebastian Gatscha [aut],
Franco Momoli [cph]
Maintainer: Nick Barrowman <nbarrowman@cheo.on.ca>
Diff between vtree versions 5.4.6 dated 2021-10-03 and 5.6.4 dated 2022-11-23
DESCRIPTION | 23 MD5 | 33 NAMESPACE | 2 NEWS.md | 24 R/buildCanopy.R | 67 + R/convertToHTML.R | 4 R/grVizToImageFile.R | 2 R/joinflow.R | 17 R/summaryNodeFunction.R | 30 R/vtree.R | 310 ++++++++ build/vignette.rds |binary inst/doc/vtree.R | 3 inst/doc/vtree.Rmd | 8 inst/doc/vtree.html | 1555 +++++++++++++++++++++++++++++++++----------- man/vtree.Rd | 87 +- tests/testthat/test-vtree.R | 580 ++++++++-------- vignettes/output.txt |only vignettes/vtree.Rmd | 8 18 files changed, 1983 insertions(+), 770 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] ,
Matt Wand [ctb] ,
Jose Chacon [ctb],
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.13.5 dated 2022-04-14 and 1.14.0 dated 2022-11-23
CHANGELOG | 7 DESCRIPTION | 16 MD5 | 158 +-- R/binning.R | 187 ++- R/deconv-kde.R | 26 R/hist.R | 138 +- R/integrate-kde.R | 168 +-- R/kcde.R | 857 ++++++++--------- R/kcopula.R | 379 +++---- R/kda.R | 1286 ++++++++++++------------- R/kdde.R | 1158 +++++++++++----------- R/kde-boundary.R | 913 +++++++++--------- R/kde-test.R | 603 +++++------ R/kde.R | 1764 ++++++++++++++++------------------- R/kdr.R | 28 R/kfe.R | 426 ++++---- R/kfs.R | 20 R/kms.R | 36 R/ksupp.R | 146 +- R/mise.R | 877 ++++++++--------- R/normal.R | 2419 ++++++++++++++++++++++++------------------------ R/prelim.R | 922 +++++++++--------- R/selector.R | 2227 +++++++++++++++++++++----------------------- R/vkde.R | 104 -- build/vignette.rds |binary inst/doc/kde.R | 32 inst/doc/kde.Rnw | 25 inst/doc/kde.pdf |binary man/Hbcv.Rd | 7 man/Hlscv.Rd | 10 man/Hnm.Rd | 5 man/Hns.Rd | 8 man/Hpi.Rd | 7 man/Hscv.Rd | 5 man/air.Rd | 4 man/binning.Rd | 4 man/cardio.Rd | 4 man/contour.Rd | 6 man/grevillea.Rd | 4 man/histde.Rd | 3 man/hsct.Rd | 4 man/ise.mixt.Rd | 5 man/kcde.Rd | 9 man/kcopula.Rd | 18 man/kda.Rd | 7 man/kdcde.Rd | 7 man/kdde.Rd | 4 man/kde.Rd | 22 man/kde.boundary.Rd | 3 man/kde.local.test.Rd | 12 man/kde.test.Rd | 5 man/kde.truncate.Rd | 4 man/kdr.Rd | 4 man/kfe.Rd | 6 man/kfs.Rd | 5 man/kms.Rd | 4 man/kroc.Rd | 5 man/ks-internal.Rd | 2 man/ks-package.Rd | 3 man/ksupp.Rd | 2 man/mixt.Rd | 8 man/plot.histde.Rd | 5 man/plot.kcde.Rd | 4 man/plot.kda.Rd | 5 man/plot.kdde.Rd | 5 man/plot.kde.Rd | 5 man/plot.kde.loctest.Rd | 9 man/plot.kde.part.Rd | 5 man/plot.kfs.Rd | 4 man/plot.kroc.Rd | 9 man/plotmixt.Rd | 7 man/pre.transform.Rd | 7 man/quake.Rd | 6 man/rkde.Rd | 5 man/tempb.Rd | 4 man/unicef.Rd | 4 man/vector.Rd | 4 man/vkde.Rd | 13 man/worldbank.Rd | 4 vignettes/kde.Rnw | 25 80 files changed, 7547 insertions(+), 7711 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.21 dated 2022-08-08 and 3.22 dated 2022-11-23
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 4 +++- R/surv.factorial.R |only man/surv.factorial.Rd |only 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Shiny Apps to Support Capacity Building on Harvest Control Rules
Description: Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management.
'Introduction to HCRs' provides a simple overview to how HCRs work. Users are able to select their own HCR and
step through its performance, year by year. Biological variability and estimation uncertainty are introduced.
'Measuring performance' builds on the previous app and introduces the idea of using performance indicators
to measure HCR performance.
'Comparing performance' allows multiple HCRs to be created and tested, and their performance compared so that the
preferred HCR can be selected.
Author: Finlay Scott [aut, cre] ,
Pacific Community [cph]
Maintainer: Finlay Scott <finlays@spc.int>
Diff between AMPLE versions 1.0.0 dated 2021-11-10 and 1.0.1 dated 2022-11-23
DESCRIPTION | 25 ++++---- MD5 | 50 ++++++++-------- NAMESPACE | 82 +++++++++++++-------------- NEWS.md | 8 ++ R/ample.R | 4 + R/comparing_performance.R | 4 - R/intro_hcr.R | 2 R/measuring_performance.R | 2 R/ui_funcs.R | 3 - README.md | 31 +++++----- build/vignette.rds |binary inst/doc/comparing_performance.Rmd | 52 ++++++++--------- inst/doc/comparing_performance.html | 85 +++++++++++++--------------- inst/doc/intro_hcr.R | 2 inst/doc/intro_hcr.Rmd | 63 +++++++++++---------- inst/doc/intro_hcr.html | 95 +++++++++++++++----------------- inst/doc/measuring_performance.Rmd | 65 +++++++++++---------- inst/doc/measuring_performance.html | 92 +++++++++++++++--------------- inst/introtext/comparing_performance.md | 12 ++-- inst/introtext/intro_hcr.md | 12 ++-- inst/introtext/measuring_performance.md | 12 ++-- man/Stock.Rd | 90 +++++++++++++++--------------- man/ample.Rd | 4 - vignettes/comparing_performance.Rmd | 52 ++++++++--------- vignettes/intro_hcr.Rmd | 63 +++++++++++---------- vignettes/measuring_performance.Rmd | 65 +++++++++++---------- 26 files changed, 498 insertions(+), 477 deletions(-)
Title: Uganda Time Series Database API
Description: An R API providing easy access to a relational database with macroeconomic,
financial and development related time series data for Uganda.
Overall more than 5000 series at varying frequency (daily, monthly,
quarterly, annual in fiscal or calendar years) can be accessed through
the API. The data is provided by the Bank of Uganda,
the Ugandan Ministry of Finance, Planning and Economic Development,
the IMF and the World Bank. The database is being updated once a month.
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between ugatsdb versions 0.2.2 dated 2021-11-25 and 0.2.3 dated 2022-11-23
DESCRIPTION | 10 MD5 | 28 - NAMESPACE | 107 ++-- NEWS.md | 51 + R/accessdb.R | 1299 +++++++++++++++++++++++++------------------------- R/ugatsdb.R | 240 ++++----- man/dot-IDvars.Rd | 64 +- man/expand_date.Rd | 116 ++-- man/get_data.Rd | 168 +++--- man/long2wide.Rd | 92 +-- man/make_date.Rd | 70 +- man/series.Rd | 96 +-- man/transpose_wide.Rd | 54 +- man/wide2excel.Rd | 74 +- man/wide2long.Rd | 100 +-- 15 files changed, 1293 insertions(+), 1276 deletions(-)
Title: Modeling the Kinetics of Carbon Dioxide Production in Alcoholic
Fermentation
Description: Developed to help researchers who need to model the kinetics of carbon dioxide (CO2) production in alcoholic fermentation of wines, beers and other fermented products. The following models are available for modeling the carbon dioxide production curve as a function of time: 5PL, Gompertz and 4PL. This package has different functions, which applied can: perform the modeling of the data obtained in the fermentation and return the coefficients, analyze the model fit and return different statistical metrics, and calculate the kinetic parameters: Maximum production of carbon dioxide; Maximum rate of production of carbon dioxide; Moment in which maximum fermentation rate occurs; Duration of the latency phase for carbon dioxide production; Carbon dioxide produced until maximum fermentation rate occurs. In addition, a function that generates graphs with the observed and predicted data from the models, isolated and combined, is available. Gava, A., Borsato, D., & Ficagna, E. (2020)."Effect [...truncated...]
Author: Angelo Gava [aut, cre]
Maintainer: Angelo Gava <gava.angelogava@gmail.com>
Diff between OenoKPM versions 2.1.1 dated 2022-11-11 and 2.1.3 dated 2022-11-23
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/Coeff.R | 40 ++++++++++++++++++++-------------------- R/kp.R | 53 +++++++++++++++++++++++++++-------------------------- R/metrics.R | 54 +++++++++++++++++++++++++++--------------------------- R/plot_fit.R | 56 ++++++++++++++++++++++++++++---------------------------- man/coeff.Rd | 40 ++++++++++++++++++++-------------------- man/kp.Rd | 52 ++++++++++++++++++++++++++-------------------------- man/metrics.Rd | 54 +++++++++++++++++++++++++++--------------------------- man/plot_fit.Rd | 56 ++++++++++++++++++++++++++++---------------------------- 10 files changed, 217 insertions(+), 216 deletions(-)
Title: Normalised Prediction Distribution Errors for Nonlinear
Mixed-Effect Models
Description: Provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.
Author: Emmanuelle Comets [aut, cre] ,
Karl Brendel [ctb],
Thi Huyen Tram Nguyen [ctb],
Marc Cerou [ctb],
Romain Leroux [ctb],
France Mentre [ctb]
Maintainer: Emmanuelle Comets <emmanuelle.comets@inserm.fr>
Diff between npde versions 3.2 dated 2021-12-20 and 3.3 dated 2022-11-23
CHANGES | 14 +++++ DESCRIPTION | 13 ++-- MD5 | 40 +++++++------- NAMESPACE | 1 R/NpdeData-methods.R | 28 ++++++---- R/NpdeData.R | 4 - R/NpdeObject-methods.R | 19 +++---- R/NpdeRes-methods.R | 20 +++++-- R/aaa_generics.R | 1 R/compute_ploq.R | 3 - R/mainNpde.R | 6 +- R/npde.R | 12 ++-- R/plotNpde-auxDistPlot.R | 33 +++++------- R/plotNpde-auxScatterPlot.R | 114 +++++++++++++++++++++--------------------- R/plotNpde-binningPI.R | 6 +- R/plotNpde-distributionPlot.R | 23 ++++---- R/plotNpde-plotFunctions.R | 21 +++---- man/NpdeData-class.Rd | 4 - man/gof.test.Rd | 4 - man/npde.binning.Rd | 5 - man/npde.cens.method.Rd | 2 21 files changed, 200 insertions(+), 173 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides suite of functions to plot regression model coefficients
("forest plots"). The suite also includes new statistics to compute
proportions, weighted mean and cross-tabulation statistics, as well as new
geometries to add alternative background color to a plot.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.1.0 dated 2022-10-17 and 0.1.1 dated 2022-11-23
DESCRIPTION | 10 +-- MD5 | 28 ++++----- NEWS.md | 4 + R/stat_weighted_mean.R | 32 ---------- README.md | 17 +++-- inst/WORDLIST | 5 + inst/doc/ggcoef_model.Rmd | 2 inst/doc/ggcoef_model.html | 116 +++++++++++++++++++-------------------- inst/doc/stat_cross.html | 111 ++++++++++++++++++------------------- inst/doc/stat_prop.html | 111 ++++++++++++++++++------------------- inst/doc/stat_weighted_mean.html | 111 ++++++++++++++++++------------------- man/ggstats-package.Rd | 46 +++++++-------- man/reexports.Rd | 32 +++++----- man/stat_weighted_mean.Rd | 32 ---------- vignettes/ggcoef_model.Rmd | 2 15 files changed, 301 insertions(+), 358 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services. Data are discovered from
National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] ,
David Blodgett [ctb],
Mike Johnson [aut] ,
Aliesha Krall [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.11 dated 2022-02-18 and 2.7.12 dated 2022-11-23
dataRetrieval-2.7.11/dataRetrieval/R/checkWQPdates.r |only dataRetrieval-2.7.11/dataRetrieval/R/constructNWISURL.r |only dataRetrieval-2.7.11/dataRetrieval/R/importRDB1.r |only dataRetrieval-2.7.11/dataRetrieval/R/importWaterML1.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISdata.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISdv.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISpCode.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISqw.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISsite.r |only dataRetrieval-2.7.11/dataRetrieval/R/readNWISunit.r |only dataRetrieval-2.7.11/dataRetrieval/R/readWQPqw.r |only dataRetrieval-2.7.11/dataRetrieval/R/tabbedDataRetrievals.R |only dataRetrieval-2.7.11/dataRetrieval/R/whatNWISData.r |only dataRetrieval-2.7.11/dataRetrieval/R/zeroPad.r |only dataRetrieval-2.7.11/dataRetrieval/vignettes/stylesSlides.css |only dataRetrieval-2.7.12/dataRetrieval/DESCRIPTION | 35 dataRetrieval-2.7.12/dataRetrieval/MD5 | 191 +- dataRetrieval-2.7.12/dataRetrieval/NAMESPACE | 19 dataRetrieval-2.7.12/dataRetrieval/NEWS | 5 dataRetrieval-2.7.12/dataRetrieval/R/AAA.R | 14 dataRetrieval-2.7.12/dataRetrieval/R/addWaterYear.R | 107 - dataRetrieval-2.7.12/dataRetrieval/R/checkWQPdates.R |only dataRetrieval-2.7.12/dataRetrieval/R/constructNWISURL.R |only dataRetrieval-2.7.12/dataRetrieval/R/dataRetrievals-package.R |only dataRetrieval-2.7.12/dataRetrieval/R/findNLDI.R | 393 ++-- dataRetrieval-2.7.12/dataRetrieval/R/getWebServiceData.R | 131 - dataRetrieval-2.7.12/dataRetrieval/R/importNGWMN_wml2.R | 301 +-- dataRetrieval-2.7.12/dataRetrieval/R/importRDB1.R |only dataRetrieval-2.7.12/dataRetrieval/R/importWQP.R | 432 ++--- dataRetrieval-2.7.12/dataRetrieval/R/importWaterML1.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNGWMNdata.R | 269 +-- dataRetrieval-2.7.12/dataRetrieval/R/readNWISdata.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNWISdv.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNWISpCode.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNWISqw.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNWISsite.R |only dataRetrieval-2.7.12/dataRetrieval/R/readNWISunit.R |only dataRetrieval-2.7.12/dataRetrieval/R/readWQPdata.R | 437 ++--- dataRetrieval-2.7.12/dataRetrieval/R/readWQPdots.R | 88 - dataRetrieval-2.7.12/dataRetrieval/R/readWQPqw.R |only dataRetrieval-2.7.12/dataRetrieval/R/renameColumns.R | 101 - dataRetrieval-2.7.12/dataRetrieval/R/setAccess.R | 130 - dataRetrieval-2.7.12/dataRetrieval/R/whatNWISdata.R |only dataRetrieval-2.7.12/dataRetrieval/R/whatNWISsites.R | 96 - dataRetrieval-2.7.12/dataRetrieval/R/whatWQPdata.R | 313 ++- dataRetrieval-2.7.12/dataRetrieval/R/whatWQPsites.R | 294 ++- dataRetrieval-2.7.12/dataRetrieval/R/zeroPad.R |only dataRetrieval-2.7.12/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.7.12/dataRetrieval/inst/CITATION | 4 dataRetrieval-2.7.12/dataRetrieval/inst/doc/dataRetrieval.R | 505 +++--- dataRetrieval-2.7.12/dataRetrieval/inst/doc/dataRetrieval.Rmd | 531 +++--- dataRetrieval-2.7.12/dataRetrieval/inst/doc/dataRetrieval.html | 831 ++++++---- dataRetrieval-2.7.12/dataRetrieval/inst/doc/qwdata_changes.R | 179 +- dataRetrieval-2.7.12/dataRetrieval/inst/doc/qwdata_changes.Rmd | 179 +- dataRetrieval-2.7.12/dataRetrieval/inst/doc/qwdata_changes.html | 504 +++--- dataRetrieval-2.7.12/dataRetrieval/man/addWaterYear.Rd | 12 dataRetrieval-2.7.12/dataRetrieval/man/calcWaterYear.Rd | 9 dataRetrieval-2.7.12/dataRetrieval/man/checkWQPdates.Rd | 13 dataRetrieval-2.7.12/dataRetrieval/man/constructNWISURL.Rd | 94 - dataRetrieval-2.7.12/dataRetrieval/man/constructUseURL.Rd | 12 dataRetrieval-2.7.12/dataRetrieval/man/constructWQPURL.Rd | 40 dataRetrieval-2.7.12/dataRetrieval/man/convertLists.Rd | 2 dataRetrieval-2.7.12/dataRetrieval/man/countyCd.Rd | 2 dataRetrieval-2.7.12/dataRetrieval/man/countyCdLookup.Rd | 4 dataRetrieval-2.7.12/dataRetrieval/man/dataRetrieval.Rd | 4 dataRetrieval-2.7.12/dataRetrieval/man/figures/hex_logo.png |only dataRetrieval-2.7.12/dataRetrieval/man/figures/logo.png |binary dataRetrieval-2.7.12/dataRetrieval/man/findNLDI.Rd | 35 dataRetrieval-2.7.12/dataRetrieval/man/getWebServiceData.Rd | 8 dataRetrieval-2.7.12/dataRetrieval/man/get_nldi_sources.Rd | 2 dataRetrieval-2.7.12/dataRetrieval/man/importNGWMN.Rd | 22 dataRetrieval-2.7.12/dataRetrieval/man/importRDB1.Rd | 69 dataRetrieval-2.7.12/dataRetrieval/man/importWQP.Rd | 36 dataRetrieval-2.7.12/dataRetrieval/man/importWaterML1.Rd | 79 dataRetrieval-2.7.12/dataRetrieval/man/importWaterML2.Rd | 22 dataRetrieval-2.7.12/dataRetrieval/man/pCodeToName.Rd | 4 dataRetrieval-2.7.12/dataRetrieval/man/parameterCdFile.Rd | 4 dataRetrieval-2.7.12/dataRetrieval/man/readNGWMNdata.Rd | 34 dataRetrieval-2.7.12/dataRetrieval/man/readNGWMNlevels.Rd | 30 dataRetrieval-2.7.12/dataRetrieval/man/readNGWMNsites.Rd | 15 dataRetrieval-2.7.12/dataRetrieval/man/readNWISdata.Rd | 216 +- dataRetrieval-2.7.12/dataRetrieval/man/readNWISdots.Rd | 2 dataRetrieval-2.7.12/dataRetrieval/man/readNWISdv.Rd | 44 dataRetrieval-2.7.12/dataRetrieval/man/readNWISgwl.Rd | 24 dataRetrieval-2.7.12/dataRetrieval/man/readNWISmeas.Rd | 26 dataRetrieval-2.7.12/dataRetrieval/man/readNWISpCode.Rd | 12 dataRetrieval-2.7.12/dataRetrieval/man/readNWISpeak.Rd | 49 dataRetrieval-2.7.12/dataRetrieval/man/readNWISqw.Rd | 68 dataRetrieval-2.7.12/dataRetrieval/man/readNWISrating.Rd | 17 dataRetrieval-2.7.12/dataRetrieval/man/readNWISsite.Rd | 85 - dataRetrieval-2.7.12/dataRetrieval/man/readNWISstat.Rd | 66 dataRetrieval-2.7.12/dataRetrieval/man/readNWISuse.Rd | 63 dataRetrieval-2.7.12/dataRetrieval/man/readNWISuv.Rd | 60 dataRetrieval-2.7.12/dataRetrieval/man/readWQPdata.Rd | 328 ++- dataRetrieval-2.7.12/dataRetrieval/man/readWQPqw.Rd | 211 +- dataRetrieval-2.7.12/dataRetrieval/man/readWQPsummary.Rd | 185 +- dataRetrieval-2.7.12/dataRetrieval/man/renameNWISColumns.Rd | 10 dataRetrieval-2.7.12/dataRetrieval/man/setAccess.Rd | 8 dataRetrieval-2.7.12/dataRetrieval/man/stateCd.Rd | 2 dataRetrieval-2.7.12/dataRetrieval/man/stateCdLookup.Rd | 6 dataRetrieval-2.7.12/dataRetrieval/man/whatNWISdata.Rd | 29 dataRetrieval-2.7.12/dataRetrieval/man/whatNWISsites.Rd | 22 dataRetrieval-2.7.12/dataRetrieval/man/whatWQPdata.Rd | 91 - dataRetrieval-2.7.12/dataRetrieval/man/wqpSpecials.Rd | 151 + dataRetrieval-2.7.12/dataRetrieval/man/zeroPad.Rd | 14 dataRetrieval-2.7.12/dataRetrieval/tests/testthat/tests_general.R | 813 +++++---- dataRetrieval-2.7.12/dataRetrieval/tests/testthat/tests_imports.R | 297 +-- dataRetrieval-2.7.12/dataRetrieval/tests/testthat/tests_nldi.R | 156 + dataRetrieval-2.7.12/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 529 +++--- dataRetrieval-2.7.12/dataRetrieval/vignettes/dataRetrieval.Rmd | 531 +++--- dataRetrieval-2.7.12/dataRetrieval/vignettes/logo.png |only dataRetrieval-2.7.12/dataRetrieval/vignettes/qwdata_changes.Rmd | 179 +- 112 files changed, 6231 insertions(+), 4704 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.3.6 dated 2022-10-12 and 1.3.7 dated 2022-11-23
DESCRIPTION | 24 MD5 | 90 - NEWS.md | 6 R/cross_validate_fn.R | 6 R/cross_validate_list.R | 2 R/evaluate.R | 6 R/helpers.R | 7 R/model_functions.R | 136 +- R/most_challenging.R | 4 R/plot_confusion_matrix.R | 12 R/plot_probabilities.R | 2 R/plot_probabilities_ecdf.R | 2 R/table_of_content_markdown.R | 3 R/update_hyperparameters.R | 16 R/validate_fn.R | 4 README.md | 460 +++++----- build/cvms.pdf |binary inst/doc/Creating_a_confusion_matrix.html | 4 inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.R | 3 inst/doc/cross_validating_custom_functions.Rmd | 3 inst/doc/cross_validating_custom_functions.html | 8 inst/doc/evaluate_by_id.html | 4 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 8 man/cross_validate_fn.Rd | 6 man/evaluate.Rd | 4 man/figures/README-unnamed-chunk-27-1.png |binary man/figures/README-unnamed-chunk-32-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/plot_probabilities.Rd | 2 man/plot_probabilities_ecdf.Rd | 2 man/update_hyperparameters.Rd | 16 man/validate_fn.Rd | 4 tests/testthat.R | 4 tests/testthat/test_baseline.R | 14 tests/testthat/test_compational_grid.R | 6 tests/testthat/test_cross_validate.R | 2 tests/testthat/test_cross_validate_fn.R | 14 tests/testthat/test_evaluate.R | 4 tests/testthat/test_helpers.R | 1 tests/testthat/test_metrics.R | 231 ++--- tests/testthat/test_most_challenging.R | 1 tests/testthat/test_validate_fn.R | 3 vignettes/cross_validating_custom_functions.Rmd | 3 vignettes/man/figures/vignette_pick_k-unnamed-chunk-28-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-32-1.png |binary 46 files changed, 623 insertions(+), 508 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.1.8 dated 2022-10-09 and 0.1.9 dated 2022-11-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/axis.R | 41 ++++++++++++++++++++++++++++++++++++----- R/insertion.R | 2 +- man/plot-insertion.Rd | 2 +- 6 files changed, 53 insertions(+), 17 deletions(-)
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 1.0.0 dated 2022-08-18 and 1.0.1 dated 2022-11-23
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- inst |only src/vistla.h | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Modular Hydrological Model
Description: The HBV hydrological model (Bergström, S. and Lindström, G., (2015) <doi:10.1002/hyp.10510>) has been split in modules to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates routines for clean and debris covered glacier melt simulations.
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Diff between HBV.IANIGLA versions 0.2.1 dated 2021-01-22 and 0.2.6 dated 2022-11-23
DESCRIPTION | 10 MD5 | 32 - NEWS.md | 23 R/alerce_data.R | 3 README.md | 37 - build/vignette.rds |binary inst/CITATION | 29 inst/doc/alerce_mass_balance.html | 961 ++++++++++++++++++-------------- inst/doc/glacio-hydrological_model.html | 445 +++++++------- inst/doc/lumped_basin.html | 762 ++++++++++++++----------- inst/doc/model_overview.html | 158 +++-- inst/doc/semi-distributed_basin.html | 706 +++++++++++++---------- inst/doc/tupungato_river_basin.html | 102 ++- man/alerce_data.Rd | 3 src/RcppExports.cpp | 5 src/Soil_HBV.cpp | 4 vignettes/references.bib | 6 17 files changed, 1895 insertions(+), 1391 deletions(-)
Title: Factor, Bi-Factor, Second-Order and Factor Tree Copula Models
Description: Estimation, model selection and goodness-of-fit of (1) factor copula models for mixed continuous and discrete data in Kadhem and Nikoloulopoulos (2021) <doi:10.1111/bmsp.12231>; (2) bi-factor and second-order copula models for item response data in Kadhem and Nikoloulopoulos (2021) <arXiv:2102.10660>; (3) factor tree copula models for item response data in Kadhem and Nikoloulopoulos (2022) <arXiv:2201.00339>.
Author: Sayed H. Kadhem [aut],
Aristidis K. Nikoloulopoulos [aut, cre]
Maintainer: Aristidis K. Nikoloulopoulos <a.nikoloulopoulos@uea.ac.uk>
Diff between FactorCopula versions 0.8.1 dated 2022-07-14 and 0.9 dated 2022-11-23
DESCRIPTION | 24 ++-- MD5 | 76 ++++++++++--- NAMESPACE | 11 + R/Wrapper-functions_factortree.R |only R/checkGraph.R |only R/copNAMES-factortree.R |only R/copula-selection_12Ftree.R |only R/copula_functions.R | 222 +++++++++++++++++++++++++++++++++++++-- R/cormat.R |only R/getMinimumSpanningTree.R |only R/initial_valuesFactortree.R |only R/isposdef.R |only R/loglikelihood_1factortree.R |only R/loglikelihood_2factortree.R |only R/model-selection_1FTr1.R |only R/model-selection_2FTr1.R |only R/model-selection_vinetree.R |only R/msTreeBoruvka.R |only R/msTreeKruskal.R |only R/msTreePrim.R |only R/ordinal.R |only R/pbnorm.R |only R/pbvncop.R |only R/pbvt.R |only R/removeLoops.R |only R/removeMultiArcs.R |only R/repGraph.R |only R/rfactor-tree.R |only R/searchWalk.R |only R/vuong_factortree.R |only build/partial.rdb |binary data/PTSD.rda |only man/FactorCopula-package.Rd | 25 +++- man/M2.Rd | 1 man/M2_structured.Rd | 1 man/MLE.Rd | 4 man/MLE_factortree.Rd |only man/MLE_structured.Rd | 4 man/PTSD.Rd |only man/mapping.Rd | 1 man/pbnorm.Rd |only man/polychoric0.Rd |only man/rfactor.Rd | 5 man/rfactor_structured.Rd | 3 man/rfactortree.Rd |only man/select.Rd | 1 man/select_factortree.Rd |only man/select_structured.Rd | 1 man/transformation.Rd | 1 man/vuong.Rd | 3 man/vuong_factortree.Rd |only man/vuong_structured.Rd | 3 src |only 53 files changed, 334 insertions(+), 52 deletions(-)
Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of
Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
regression models, partially linear instrumental variable regression models,
interactive regression models and interactive instrumental variable
regression models. 'DoubleML' allows estimation of the nuisance parts in
these models by machine learning methods and computation of the Neyman
orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
the 'R6' package is very flexible.
Author: Philipp Bach [aut, cre],
Victor Chernozhukov [aut],
Malte S. Kurz [aut],
Martin Spindler [aut]
Maintainer: Philipp Bach <philipp.bach@uni-hamburg.de>
Diff between DoubleML versions 0.5.1 dated 2022-08-19 and 0.5.2 dated 2022-11-23
DESCRIPTION | 16 - MD5 | 32 +- R/double_ml.R | 47 +++ R/double_ml_iivm.R | 26 + R/double_ml_irm.R | 17 - R/double_ml_pliv.R | 67 ++-- R/double_ml_plr.R | 24 - R/helper.R | 28 + README.md | 27 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_DoubleML.html | 80 +++-- inst/doc/getstarted.html | 316 +++++++++++---------- inst/doc/install.html | 167 +++++------ tests/testthat/test-double_ml_active_bindings.R | 3 tests/testthat/test-double_ml_irm_binary_outcome.R | 2 tests/testthat/test-double_ml_plr_export_preds.R | 11 17 files changed, 527 insertions(+), 336 deletions(-)
Title: Pediatric Blood Pressure
Description: Data and utilities for estimating pediatric blood pressure
percentiles by sex, age, and optionally height (stature) as described in
Martin et.al. (2022) <doi:10.1001/jamanetworkopen.2022.36918>.
Blood pressure percentiles for children under one year of age come from Gemelli
et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure
percentiles for children at least one year of age are informed by
data from the National Heart, Lung, and Blood Institute (NHLBI) and the
Centers for Disease Control and Prevention (CDC)
<doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013)
<doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing
data source comes from Martin et.al. (2022)
<doi:10.1542/hpeds.2021-005998>.
Author: Peter DeWitt [aut, cre] ,
Blake Martin [ctb] ,
David Albers [ctb] ,
Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedbp versions 1.0.1 dated 2022-10-26 and 1.0.2 dated 2022-11-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/bp_distribution.R | 10 +++++++++- R/lms.R | 14 ++++++++++---- inst/doc/bp-distributions.html | 28 ++++++++++++++-------------- man/bp_distribution.Rd | 10 +++++++++- 7 files changed, 62 insertions(+), 30 deletions(-)
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute and plot adjusted predictions, contrasts, marginal effects, and marginal means for over 70 classes of statistical models in R. Conduct linear and non-linear hypothesis tests using the delta method.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Marcio Augusto Diniz [ctb] ,
Noah Greifer [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.8.0 dated 2022-11-02 and 0.8.1 dated 2022-11-23
marginaleffects-0.8.0/marginaleffects/vignettes/logistic_contrasts.html |only marginaleffects-0.8.0/marginaleffects/vignettes/mcmc_posterior_draws.pickle |only marginaleffects-0.8.0/marginaleffects/vignettes/plot.html |only marginaleffects-0.8.0/marginaleffects/vignettes/predictions.html |only marginaleffects-0.8.0/marginaleffects/vignettes/python.html |only marginaleffects-0.8.0/marginaleffects/vignettes/sandwich.html |only marginaleffects-0.8.0/marginaleffects/vignettes/supported_models.html |only marginaleffects-0.8.0/marginaleffects/vignettes/transformation.html |only marginaleffects-0.8.1/marginaleffects/DESCRIPTION | 46 +-- marginaleffects-0.8.1/marginaleffects/MD5 | 119 ++++------ marginaleffects-0.8.1/marginaleffects/NAMESPACE | 3 marginaleffects-0.8.1/marginaleffects/NEWS.md | 14 + marginaleffects-0.8.1/marginaleffects/R/backtransform.R | 11 marginaleffects-0.8.1/marginaleffects/R/by.R | 2 marginaleffects-0.8.1/marginaleffects/R/comparisons.R | 70 +++-- marginaleffects-0.8.1/marginaleffects/R/datagrid.R | 40 +-- marginaleffects-0.8.1/marginaleffects/R/deltamethod.R | 67 ++++- marginaleffects-0.8.1/marginaleffects/R/get_ci.R | 8 marginaleffects-0.8.1/marginaleffects/R/get_contrasts.R | 26 +- marginaleffects-0.8.1/marginaleffects/R/get_predict.R | 10 marginaleffects-0.8.1/marginaleffects/R/marginaleffects.R | 1 marginaleffects-0.8.1/marginaleffects/R/marginalmeans.R | 19 + marginaleffects-0.8.1/marginaleffects/R/methods_fixest.R | 29 +- marginaleffects-0.8.1/marginaleffects/R/methods_mclogit.R | 2 marginaleffects-0.8.1/marginaleffects/R/methods_mlm.R |only marginaleffects-0.8.1/marginaleffects/R/plot_cap.R | 9 marginaleffects-0.8.1/marginaleffects/R/plot_cco.R | 34 ++ marginaleffects-0.8.1/marginaleffects/R/plot_cme.R | 23 + marginaleffects-0.8.1/marginaleffects/R/posteriordraws.R | 62 +++-- marginaleffects-0.8.1/marginaleffects/R/predictions.R | 25 +- marginaleffects-0.8.1/marginaleffects/R/sanitize_transform_pre.R | 23 + marginaleffects-0.8.1/marginaleffects/R/sanitize_variables.R | 10 marginaleffects-0.8.1/marginaleffects/R/sanity_dots.R | 4 marginaleffects-0.8.1/marginaleffects/R/summary.R | 44 +++ marginaleffects-0.8.1/marginaleffects/R/tidy.R | 9 marginaleffects-0.8.1/marginaleffects/R/tidy.comparisons.R | 30 +- marginaleffects-0.8.1/marginaleffects/R/tidy.predictions.R | 11 marginaleffects-0.8.1/marginaleffects/R/utils.R |only marginaleffects-0.8.1/marginaleffects/README.md | 29 -- marginaleffects-0.8.1/marginaleffects/build/vignette.rds |binary marginaleffects-0.8.1/marginaleffects/inst/WORDLIST | 4 marginaleffects-0.8.1/marginaleffects/inst/tinytest/helpers.R | 3 marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-deltamethod.R | 26 ++ marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-df.R |only marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-nested.R | 24 -- marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-brms.R | 26 ++ marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-fixest.R | 63 +---- marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-lme4.R | 15 - marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-mgcv.R | 5 marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-rms.R | 1 marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-stats.R | 15 + marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-pkg-survival.R | 1 marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-plot_cme.R | 5 marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-posteriordraws.R |only marginaleffects-0.8.1/marginaleffects/inst/tinytest/test-transform_post.R | 7 marginaleffects-0.8.1/marginaleffects/man/comparisons.Rd | 6 marginaleffects-0.8.1/marginaleffects/man/datagridcf.Rd | 24 -- marginaleffects-0.8.1/marginaleffects/man/deltamethod.Rd | 38 ++- marginaleffects-0.8.1/marginaleffects/man/get_coef.Rd | 9 marginaleffects-0.8.1/marginaleffects/man/get_group_names.Rd | 5 marginaleffects-0.8.1/marginaleffects/man/get_predict.Rd | 9 marginaleffects-0.8.1/marginaleffects/man/plot_cco.Rd | 24 +- marginaleffects-0.8.1/marginaleffects/man/plot_cme.Rd | 25 +- marginaleffects-0.8.1/marginaleffects/man/posteriordraws.Rd | 9 marginaleffects-0.8.1/marginaleffects/man/predictions.Rd | 3 marginaleffects-0.8.1/marginaleffects/man/set_coef.Rd | 13 - marginaleffects-0.8.1/marginaleffects/vignettes/gam.html |only 67 files changed, 747 insertions(+), 393 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: End-to-End Automated Machine Learning and Model Evaluation
Description: Single unified interface for end-to-end modelling of regression,
categorical and time-to-event (survival) outcomes. Models created using
familiar are self-containing, and their use does not require additional
information such as baseline survival, feature clustering, or feature
transformation and normalisation parameters. Model performance,
calibration, risk group stratification, (permutation) variable importance,
individual conditional expectation, partial dependence, and more, are
assessed automatically as part of the evaluation process and exported in
tabular format and plotted, and may also be computed manually using export
and plot functions. Where possible, metrics and values obtained during the
evaluation process come with confidence intervals.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
Stefan Leger [ctb],
Iram Shahzadi [ctb],
Asier Rabasco Meneghetti [ctb],
Sebastian Starke [ctb],
Technische Universitaet Dresden [cph],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Diff between familiar versions 1.3.0 dated 2022-10-15 and 1.4.0 dated 2022-11-23
DESCRIPTION | 19 MD5 | 217 - NAMESPACE | 1 NEWS.md | 34 R/DataObject.R | 28 R/FamiliarEnsemble.R | 86 R/FamiliarModel.R | 109 R/FamiliarObjectUpdate.R | 10 R/FamiliarS4Generics.R | 3 R/FamiliarSharedS4Methods.R | 5 R/HyperparameterOptimisation.R | 196 - R/HyperparameterOptimisationMetaLearners.R | 3 R/HyperparameterOptimisationUtilities.R | 246 - R/LearnerMain.R | 10 R/LearnerS4Cox.R | 25 R/LearnerS4GLM.R | 35 R/LearnerS4GLMnet.R | 21 R/LearnerS4KNN.R | 17 R/LearnerS4MBoost.R | 29 R/LearnerS4Naive.R |only R/LearnerS4NaiveBayes.R | 17 R/LearnerS4RFSRC.R | 201 - R/LearnerS4Ranger.R | 21 R/LearnerS4SVM.R | 17 R/LearnerS4SurvivalRegression.R | 25 R/LearnerS4XGBoost.R | 21 R/LearnerSurvivalProbability.R | 31 R/MetricS4.R | 96 R/MetricS4Regression.R | 226 - R/OutcomeInfo.R | 2 R/ParseSettings.R | 122 R/PlotAUCcurves.R | 2 R/PlotCalibration.R | 1614 +++++----- R/PlotConfusionMatrix.R | 9 R/PlotDecisionCurves.R | 2 R/PlotFeatureRanking.R | 8 R/PlotFeatureSimilarity.R | 8 R/PlotICE.R | 304 + R/PlotKaplanMeier.R | 2 R/PlotModelPerformance.R | 8 R/PlotPermutationVariableImportance.R | 2 R/PlotSampleClustering.R | 8 R/PlotUnivariateImportance.R | 2 R/PlotUtilities.R | 213 + R/PredictS4Methods.R | 16 R/StringUtilities.R | 9 R/TestFunctions.R | 173 - R/UtilitiesS4.R | 18 R/VimpMain.R | 11 R/VimpS4OtherMethods.R | 13 inst/config.xml | 4 inst/doc/evaluation_and_explanation_precompiled.Rmd | 8 inst/doc/evaluation_and_explanation_precompiled.html | 181 - inst/doc/feature_selection_precompiled.Rmd | 2 inst/doc/feature_selection_precompiled.html | 36 inst/doc/introduction_precompiled.Rmd | 2 inst/doc/introduction_precompiled.html | 133 inst/doc/learners_precompiled.Rmd | 43 inst/doc/learners_precompiled.html | 88 inst/doc/performance_metrics_precompiled.Rmd | 11 inst/doc/performance_metrics_precompiled.html | 46 inst/doc/prospective_use_precompiled.Rmd | 36 inst/doc/prospective_use_precompiled.html | 157 man/dot-parse_experiment_settings.Rd | 2 man/dot-parse_general_settings.Rd | 19 man/dot-parse_hyperparameter_optimisation_settings.Rd | 19 man/dot-parse_initial_settings.Rd | 2 man/extract_experimental_setup.Rd | 2 man/plotting.check_data_handling.Rd | 4 man/summon_familiar.Rd | 21 man/theme_familiar.Rd |only man/train_familiar.Rd | 19 tests/testthat/test-0_plot_ice_b.R | 5 tests/testthat/test-hyperparameter_optimisation.R | 111 tests/testthat/test-learner_cox_s4.R | 8 tests/testthat/test-learner_mboost_lm_S4.R | 38 tests/testthat/test-learner_ranger_s4.R | 152 tests/testthat/test-naive_model.R |only tests/testthat/test-train_familiar.R | 2 tests/testthat/test-vimp_ranger_S4.R | 76 vignettes/eval_and_explain/auc-pr-curve-bci-1.png |binary vignettes/eval_and_explain/auc-pr-curve-point-1.png |binary vignettes/eval_and_explain/auc-roc-curve-bci-1.png |binary vignettes/eval_and_explain/auc-roc-curve-point-1.png |binary vignettes/eval_and_explain/calibration-data-bci-1.png |binary vignettes/eval_and_explain/calibration-data-point-1.png |binary vignettes/eval_and_explain/confusion-matrix-1.png |binary vignettes/eval_and_explain/decision-curve-bci-1.png |binary vignettes/eval_and_explain/feature-similarity-1.png |binary vignettes/eval_and_explain/ice-2d-1.png |binary vignettes/eval_and_explain/ice-2d-anchored-1.png |binary vignettes/eval_and_explain/ice-2d-survival-1.png |binary vignettes/eval_and_explain/ice-cell-shap-uniformity-1.png |binary vignettes/eval_and_explain/ice-cell-shape-uniformity-anchored-1.png |binary vignettes/eval_and_explain/kaplan-meier-plot-1.png |binary vignettes/eval_and_explain/model-performance-plot-1.png |binary vignettes/eval_and_explain/model-variable-importance-1.png |binary vignettes/eval_and_explain/permutation-variable-importance-bc-1.png |binary vignettes/eval_and_explain/permutation-variable-importance-bc-spearman-1.png |binary vignettes/eval_and_explain/sample-similarity-1.png |binary vignettes/eval_and_explain/sample-similarity-unnormalised-1.png |binary vignettes/evaluation_and_explanation_precompiled.Rmd | 8 vignettes/feature_selection_precompiled.Rmd | 2 vignettes/introduction_precompiled.Rmd | 2 vignettes/learners_precompiled.Rmd | 43 vignettes/performance_metrics_precompiled.Rmd | 11 vignettes/prospective_use/prospective-model-performance-plot-1.png |binary vignettes/prospective_use/prospective-model-performance-plot-ensemble-1.png |binary vignettes/prospective_use/prospective-model-performance-plot-implicit-1.png |binary vignettes/prospective_use/prospective-model-performance-plot-new-directory-1.png |binary vignettes/prospective_use_precompiled.Rmd | 36 111 files changed, 3563 insertions(+), 2061 deletions(-)
Title: Causal Inference Modeling for Estimation of Causal Effects
Description: Provides an array of statistical models common in causal inference such as
standardization, IP weighting, propensity matching, outcome regression, and doubly-robust
estimators. Estimates of the average treatment effects from each model are given with the
standard error and a 95% Wald confidence interval (Hernan, Robins (2020) <https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/>).
Author: Joshua Anderson [aut, cre, cph],
Cyril Rakovski [rev],
Yesha Patel [rev],
Erin Lee [rev]
Maintainer: Joshua Anderson <jwanderson198@gmail.com>
Diff between CausalModels versions 0.1.0 dated 2022-05-30 and 0.2.0 dated 2022-11-23
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++---------- NAMESPACE | 6 ++ NEWS.md | 12 ++++- R/doubly_robust.R | 59 ++++++++++++++------------ R/gestimation.R |only R/helper_funcs.R | 43 ++++++++----------- R/imports.R | 1 R/initialize.R | 63 +++++++++++++++------------- R/ipweighting.R | 80 ++++++++++++++++++----------------- R/iv_est.R | 31 +++++++------ R/outcome_regression.R | 101 ++++++++++++++++++++++++++------------------- R/propensity_matching.R | 94 ++++++++++++++++++++++------------------- R/propensity_scores.R | 31 ++++++++----- R/standardization.R | 84 +++++++++++++++++++++---------------- R/zzz.R | 3 - README.md | 44 +++++++++++++++---- man/doubly_robust.Rd | 28 ++++++++---- man/gestimation.Rd |only man/ipweighting.Rd | 16 ++++--- man/iv_est.Rd | 12 +++-- man/outcome_regression.Rd | 22 ++++++--- man/propensity_matching.Rd | 16 ++++--- man/propensity_scores.Rd | 14 ++++-- man/standardization.Rd | 16 ++++--- 25 files changed, 479 insertions(+), 351 deletions(-)
Title: Shiny Apps for Lateral Flow Assays
Description: Shiny apps for the quantitative analysis of images from lateral flow assays (LFAs). The images are segmented and background corrected and color intensities are extracted. The apps can be used to import and export intensity data and to calibrate LFAs by means of linear, loess, or gam models. The calibration models can further be saved and applied to intensity data from new images for determining concentrations.
Author: Filip Paskali [aut, cre] ,
Weronika Schary [aut] ,
Matthias Kohl [aut]
Maintainer: Filip Paskali <F.Paskali@hs-furtwangen.de>
Diff between LFApp versions 1.3 dated 2021-07-28 and 1.3.1 dated 2022-11-23
DESCRIPTION | 13 MD5 | 40 - NEWS | 5 R/analysis_mobile_server.R | 230 +++---- R/analysis_mobile_ui.R | 35 - R/analysis_server.R | 26 R/cal_mobile_server.R | 218 +++---- R/cal_mobile_ui.R | 26 R/cal_server.R | 26 R/core_mobile_server.R | 102 +-- R/core_mobile_ui.R | 9 R/core_server.R | 6 R/quan_mobile_server.R | 120 ++-- R/quan_mobile_ui.R | 22 R/quan_server.R | 6 R/thresholding_li.R | 2 build/vignette.rds |binary inst/doc/LFApp.html | 801 ++++++++++++++++++--------- inst/markdown/CalibrationAnalysis(gam).Rmd | 6 inst/markdown/CalibrationAnalysis(lm).Rmd | 11 inst/markdown/CalibrationAnalysis(loess).Rmd | 6 21 files changed, 1005 insertions(+), 705 deletions(-)
Title: Linear and Nonlinear Autoregressive Distributed Lag Models:
General-to-Specific Approach
Description: Estimate the linear and nonlinear autoregressive distributed lag (ARDL & NARDL) models and the corresponding error correction models, and test for longrun and short-run asymmetric. The general-to-specific approach is also available in estimating the ARDL and NARDL models. The Pesaran, Shin & Smith (2001) (<doi:10.1002/jae.616>) bounds test for level relationships is also provided. The 'ardl.nardl' package also performs short-run and longrun symmetric restrictions available at Shin et al. (2014) <doi:10.1007/978-1-4899-8008-3_9> and their corresponding tests.
Author: Eric I. Otoakhia [aut, cre]
Maintainer: Eric I. Otoakhia <otoakhiai@gmail.com>
Diff between ardl.nardl versions 1.0.2 dated 2022-11-16 and 1.1.0 dated 2022-11-23
ardl.nardl-1.0.2/ardl.nardl/NEWS |only ardl.nardl-1.1.0/ardl.nardl/DESCRIPTION | 21 ++--- ardl.nardl-1.1.0/ardl.nardl/MD5 | 23 +++--- ardl.nardl-1.1.0/ardl.nardl/NAMESPACE | 12 ++- ardl.nardl-1.1.0/ardl.nardl/R/ARDLM_.R | 36 +++++---- ardl.nardl-1.1.0/ardl.nardl/R/NARDLM_.R | 44 ++++++----- ardl.nardl-1.1.0/ardl.nardl/R/gets_ardl_uecm.R |only ardl.nardl-1.1.0/ardl.nardl/R/gets_nardl_uecm.R |only ardl.nardl-1.1.0/ardl.nardl/data/expectation.rda |only ardl.nardl-1.1.0/ardl.nardl/man/ardl.nardl-package.Rd | 48 ++++++++++--- ardl.nardl-1.1.0/ardl.nardl/man/ardl_uecm.Rd | 37 +++++----- ardl.nardl-1.1.0/ardl.nardl/man/dynamac_pkg_bounds_test.Rd | 2 ardl.nardl-1.1.0/ardl.nardl/man/expectation.Rd |only ardl.nardl-1.1.0/ardl.nardl/man/gets_ardl_uecm.Rd |only ardl.nardl-1.1.0/ardl.nardl/man/gets_nardl_uecm.Rd |only ardl.nardl-1.1.0/ardl.nardl/man/nardl_uecm.Rd | 36 +++++---- 16 files changed, 160 insertions(+), 99 deletions(-)
Title: A System for Planing Analyses
Description: A system to plan analyses within the mental model
where you have one (or more) datasets and want to run either A) the same
function multiple times with different arguments, or B) multiple functions.
This is appropriate when you have multiple strata (e.g. locations, age groups)
that you want to apply the same function to, or you have multiple variables
(e.g. exposures) that you want to apply the same statistical method to, or
when you are creating the output for a report and you need multiple different
tables or graphs.
Author: Richard Aubrey White [aut, cre]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between plnr versions 2022.6.8 dated 2022-06-09 and 2022.11.23 dated 2022-11-23
plnr-2022.11.23/plnr/DESCRIPTION | 17 plnr-2022.11.23/plnr/LICENSE | 2 plnr-2022.11.23/plnr/MD5 | 41 - plnr-2022.11.23/plnr/NAMESPACE | 2 plnr-2022.11.23/plnr/R/3_onAttach.R | 2 plnr-2022.11.23/plnr/R/data.R | 8 plnr-2022.11.23/plnr/R/get_anything.R | 2 plnr-2022.11.23/plnr/R/plan.R | 34 - plnr-2022.11.23/plnr/README.md | 18 plnr-2022.11.23/plnr/data/nor_covid19_cases_by_time_location.rda |only plnr-2022.11.23/plnr/inst/doc/adding_analyses.R | 10 plnr-2022.11.23/plnr/inst/doc/adding_analyses.Rmd | 10 plnr-2022.11.23/plnr/inst/doc/adding_analyses.html | 242 +++++----- plnr-2022.11.23/plnr/inst/doc/plnr.html | 113 ++-- plnr-2022.11.23/plnr/man/Plan.Rd | 62 +- plnr-2022.11.23/plnr/man/example_action_fn.Rd | 2 plnr-2022.11.23/plnr/man/example_data_fn_nor_covid19_cases_by_time_location.Rd |only plnr-2022.11.23/plnr/man/figures/logo.png |binary plnr-2022.11.23/plnr/man/get_anything.Rd | 2 plnr-2022.11.23/plnr/man/nor_covid19_cases_by_time_location.Rd |only plnr-2022.11.23/plnr/vignettes/adding_analyses.Rmd | 10 plnr-2022.6.8/plnr/data/norway_covid19_cases_by_time_location.rda |only plnr-2022.6.8/plnr/man/example_data_fn_norway_covid19_cases_by_time_location.Rd |only plnr-2022.6.8/plnr/man/figures/fhi.png |only plnr-2022.6.8/plnr/man/norway_covid19_cases_by_time_location.Rd |only 25 files changed, 286 insertions(+), 291 deletions(-)
Title: Read Cancer Records in the NAACCR Format
Description: Functions for reading cancer record files which follow a format
defined by the North American Association of Central Cancer Registries
(NAACCR).
Author: Nathan Werth [aut, cre],
Pennsylvania Department of Health [cph],
North American Association of Cancer Registries [cph],
World Health Organization [cph],
United States Centers for Disease Control and Prevention [ctb],
United States Bureau of the Cens [...truncated...]
Maintainer: Nathan Werth <nwerth@pa.gov>
Diff between naaccr versions 1.0.0 dated 2019-12-17 and 2.0.2 dated 2022-11-23
naaccr-1.0.0/naaccr/man/naaccr_format.Rd |only naaccr-2.0.2/naaccr/DESCRIPTION | 10 naaccr-2.0.2/naaccr/MD5 | 97 +- naaccr-2.0.2/naaccr/NAMESPACE | 17 naaccr-2.0.2/naaccr/NEWS | 27 naaccr-2.0.2/naaccr/R/naaccr_factor.R | 2 naaccr-2.0.2/naaccr/R/naaccr_record.R | 5 naaccr-2.0.2/naaccr/R/onLoad.R |only naaccr-2.0.2/naaccr/R/read_naaccr.R | 242 +++++ naaccr-2.0.2/naaccr/R/record_format.R | 199 +++- naaccr-2.0.2/naaccr/R/sysdata.rda |binary naaccr-2.0.2/naaccr/R/write_naaccr.R | 265 +++++- naaccr-2.0.2/naaccr/README.md | 52 - naaccr-2.0.2/naaccr/data/field_levels.RData |binary naaccr-2.0.2/naaccr/man/as.naaccr_record.Rd | 83 - naaccr-2.0.2/naaccr/man/clean_address_city.Rd | 42 naaccr-2.0.2/naaccr/man/clean_address_number_and_street.Rd | 42 naaccr-2.0.2/naaccr/man/clean_age.Rd | 42 naaccr-2.0.2/naaccr/man/clean_census_block.Rd | 42 naaccr-2.0.2/naaccr/man/clean_census_tract.Rd | 42 naaccr-2.0.2/naaccr/man/clean_count.Rd | 48 - naaccr-2.0.2/naaccr/man/clean_county_fips.Rd | 42 naaccr-2.0.2/naaccr/man/clean_facility_id.Rd | 42 naaccr-2.0.2/naaccr/man/clean_icd_9_cm.Rd | 42 naaccr-2.0.2/naaccr/man/clean_icd_code.Rd | 44 - naaccr-2.0.2/naaccr/man/clean_physician_id.Rd | 44 - naaccr-2.0.2/naaccr/man/clean_postal.Rd | 42 naaccr-2.0.2/naaccr/man/clean_ssn.Rd | 44 - naaccr-2.0.2/naaccr/man/clean_telephone.Rd | 44 - naaccr-2.0.2/naaccr/man/clean_text.Rd | 42 naaccr-2.0.2/naaccr/man/field_levels.Rd | 50 - naaccr-2.0.2/naaccr/man/naaccr_boolean.Rd | 56 - naaccr-2.0.2/naaccr/man/naaccr_date.Rd | 50 - naaccr-2.0.2/naaccr/man/naaccr_datetime.Rd | 52 - naaccr-2.0.2/naaccr/man/naaccr_encode.Rd | 82 - naaccr-2.0.2/naaccr/man/naaccr_factor.Rd | 72 - naaccr-2.0.2/naaccr/man/naaccr_formats.Rd |only naaccr-2.0.2/naaccr/man/naaccr_override.Rd | 50 - naaccr-2.0.2/naaccr/man/naaccr_record.Rd | 72 - naaccr-2.0.2/naaccr/man/read_naaccr.Rd | 255 +++-- naaccr-2.0.2/naaccr/man/record_format.Rd | 430 +++++----- naaccr-2.0.2/naaccr/man/split_sentineled.Rd | 70 - naaccr-2.0.2/naaccr/man/split_sequence_number.Rd | 82 - naaccr-2.0.2/naaccr/man/unknown_to_na.Rd | 90 +- naaccr-2.0.2/naaccr/man/write_naaccr.Rd | 53 - naaccr-2.0.2/naaccr/man/write_naaccr_xml.Rd |only naaccr-2.0.2/naaccr/tests/data/custom-incidence-22.xml |only naaccr-2.0.2/naaccr/tests/data/naaccr-xml-sample-v220-incidence-100.xml |only naaccr-2.0.2/naaccr/tests/data/synthetic-naaccr-18-incidence.xml |only naaccr-2.0.2/naaccr/tests/testthat/test-naaccr_factor.R | 7 naaccr-2.0.2/naaccr/tests/testthat/test-naaccr_record.R | 42 naaccr-2.0.2/naaccr/tests/testthat/test-read-xml.R |only naaccr-2.0.2/naaccr/tests/testthat/test-utilities.R |only naaccr-2.0.2/naaccr/tests/testthat/test-write_naaccr.R | 108 ++ 54 files changed, 2048 insertions(+), 1216 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@protonmail.com>
Diff between GenEst versions 1.4.7 dated 2022-11-15 and 1.4.8 dated 2022-11-23
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/splits_functions.R | 4 - build/vignette.rds |binary inst/doc/GenEstGUI.html | 4 - inst/doc/command-line-example.html | 88 ++++++++++++++++++------------------- inst/doc/solar-examples.html | 4 - inst/doc/wind-examples.html | 6 +- 8 files changed, 64 insertions(+), 64 deletions(-)
Title: Coarsened Mixtures of Hierarchical Skew Kernels
Description: Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2020) <arXiv:2001.06451>.
Author: S. Gorsky [aut, cre],
C. Chan [ctb],
L. Ma [ctb]
Maintainer: S. Gorsky <sgorsky@umass.edu>
Diff between COMIX versions 0.1.6 dated 2022-05-12 and 1.0.0 dated 2022-11-23
COMIX-0.1.6/COMIX/inst/doc/COMIX.R |only COMIX-0.1.6/COMIX/inst/doc/COMIX.Rmd |only COMIX-0.1.6/COMIX/inst/doc/COMIX.html |only COMIX-0.1.6/COMIX/vignettes/COMIX.Rmd |only COMIX-1.0.0/COMIX/DESCRIPTION | 15 ++++---- COMIX-1.0.0/COMIX/MD5 | 42 +++++++++++++++-------- COMIX-1.0.0/COMIX/NAMESPACE | 11 +++++- COMIX-1.0.0/COMIX/R/acf_plots.R |only COMIX-1.0.0/COMIX/R/comix.R | 2 + COMIX-1.0.0/COMIX/R/effective_sample_size.R |only COMIX-1.0.0/COMIX/R/geweke.R |only COMIX-1.0.0/COMIX/R/heidelberg_welch.R |only COMIX-1.0.0/COMIX/R/tidy_chain.R |only COMIX-1.0.0/COMIX/R/trace_plot.R |only COMIX-1.0.0/COMIX/R/utilities.R | 8 ++++ COMIX-1.0.0/COMIX/build/vignette.rds |binary COMIX-1.0.0/COMIX/inst/doc/vignette.html |only COMIX-1.0.0/COMIX/inst/doc/vignette.html.asis |only COMIX-1.0.0/COMIX/man/acfParams.Rd |only COMIX-1.0.0/COMIX/man/calibrate.Rd | 2 + COMIX-1.0.0/COMIX/man/calibrateNoDist.Rd | 2 + COMIX-1.0.0/COMIX/man/comix.Rd | 2 + COMIX-1.0.0/COMIX/man/effectiveSampleSize.Rd |only COMIX-1.0.0/COMIX/man/gewekeParams.Rd |only COMIX-1.0.0/COMIX/man/heidelParams.Rd |only COMIX-1.0.0/COMIX/man/plotEffectiveSampleSize.Rd |only COMIX-1.0.0/COMIX/man/plotGewekeParams.Rd |only COMIX-1.0.0/COMIX/man/plotHeidelParams.Rd |only COMIX-1.0.0/COMIX/man/plotTracePlots.Rd |only COMIX-1.0.0/COMIX/man/relabelChain.Rd | 2 + COMIX-1.0.0/COMIX/man/summarizeChain.Rd | 2 + COMIX-1.0.0/COMIX/man/tidyChain.Rd |only COMIX-1.0.0/COMIX/vignettes/vignette.html.asis |only 33 files changed, 66 insertions(+), 22 deletions(-)
Title: Quickly Get Datetime Data Ready for Analysis
Description: Transforms datetime data into a format ready for analysis.
It offers two core functionalities; aggregating data to a higher level interval
(thicken) and imputing records where observations were absent (pad).
Author: Edwin Thoen
Maintainer: Edwin Thoen <edwinthoen@gmail.com>
Diff between padr versions 0.6.1 dated 2022-10-04 and 0.6.2 dated 2022-11-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 +++++- R/formatting_funcs.R | 9 +++++++-- README.md | 11 ++++------- inst/doc/padr.html | 4 ++-- inst/doc/padr_custom.html | 4 ++-- inst/doc/padr_implementation.html | 4 ++-- 8 files changed, 32 insertions(+), 26 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>
Diff between ChannelAttribution versions 2.0.5 dated 2022-02-05 and 2.0.6 dated 2022-11-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/ChannelAttribution-package.Rd | 4 ++-- src/ChannelAttribution.cpp | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unicampania.it>
Diff between CAvariants versions 5.6 dated 2021-02-22 and 5.7 dated 2022-11-23
CAvariants-5.6/CAvariants/R/caplot.R |only CAvariants-5.6/CAvariants/data/asbestos.R |only CAvariants-5.6/CAvariants/data/shopdataM.R |only CAvariants-5.6/CAvariants/man/caplot.Rd |only CAvariants-5.7/CAvariants/DESCRIPTION | 8 - CAvariants-5.7/CAvariants/MD5 | 32 +++--- CAvariants-5.7/CAvariants/NAMESPACE | 24 ++-- CAvariants-5.7/CAvariants/R/CAvariants.R | 115 ++++++++--------------- CAvariants-5.7/CAvariants/R/caRbiplot.R |only CAvariants-5.7/CAvariants/R/plot.CAvariants.R | 75 ++++----------- CAvariants-5.7/CAvariants/R/print.CAvariants.R | 26 +---- CAvariants-5.7/CAvariants/R/summary.CAvariants.R | 4 CAvariants-5.7/CAvariants/R/trendplot.R |only CAvariants-5.7/CAvariants/R/vcaellipse.R | 106 +++++++++++++++++++-- CAvariants-5.7/CAvariants/data/asbestos.rda |only CAvariants-5.7/CAvariants/data/shopdataM.rda |only CAvariants-5.7/CAvariants/man/CAvariants.Rd | 3 CAvariants-5.7/CAvariants/man/caRbiplot.Rd |only CAvariants-5.7/CAvariants/man/emerson.poly.Rd | 8 - CAvariants-5.7/CAvariants/man/plot.CAvariants.Rd | 15 +-- CAvariants-5.7/CAvariants/man/trendplot.Rd |only CAvariants-5.7/CAvariants/man/vcaellipse.Rd | 31 ++++-- 22 files changed, 239 insertions(+), 208 deletions(-)
Title: Harmonizing CN8 and PC8 Product Codes
Description: Several functions are provided to harmonize CN8 (Combined Nomenclature
8 digits) and PC8 (Production Communautaire 8 digits) product codes over
time and the classification systems HS6 and BEC. Harmonization of CN8
codes are possible by default from 1995 to 2022 and of PC8 from 2001 to
2021, respectively.
Author: Christoph Baumgartner [cre, aut]
,
Stjepan Srhoj [aut] ,
Janette Walde [aut]
Maintainer: Christoph Baumgartner <Christoph.Baumgartner@uibk.ac.at>
Diff between harmonizer versions 0.3.0 dated 2022-05-23 and 0.3.1 dated 2022-11-23
harmonizer-0.3.0/harmonizer/inst/extdata/CN8/CN8_concordances_1988_2020.csv |only harmonizer-0.3.1/harmonizer/DESCRIPTION | 8 - harmonizer-0.3.1/harmonizer/MD5 | 43 ++++------ harmonizer-0.3.1/harmonizer/NEWS.md | 4 harmonizer-0.3.1/harmonizer/R/cn8_to_bec.R | 4 harmonizer-0.3.1/harmonizer/R/harmonize_cn8.R | 4 harmonizer-0.3.1/harmonizer/R/harmonize_pc8.R | 4 harmonizer-0.3.1/harmonizer/R/history_matrix_cn8.R | 6 - harmonizer-0.3.1/harmonizer/R/history_matrix_pc8.R | 8 - harmonizer-0.3.1/harmonizer/R/pc8_to_bec.R | 4 harmonizer-0.3.1/harmonizer/inst/doc/harmonizer.R | 2 harmonizer-0.3.1/harmonizer/inst/doc/harmonizer.Rmd | 7 - harmonizer-0.3.1/harmonizer/inst/doc/harmonizer.html | 8 + harmonizer-0.3.1/harmonizer/inst/extdata/CN8/CN8_concordances_1988_2022.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6/HS_1996_to_HS_1992.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6/HS_2002_to_HS_1996.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6/HS_2007_to_HS_2002.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6/HS_2012_to_HS_2007.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6/HS_2017_to_HS_2012.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6toBEC/HS1996toBEC.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6toBEC/HS2012toBEC.csv | 2 harmonizer-0.3.1/harmonizer/inst/extdata/HS6toBEC/HS2017toBEC.csv | 2 harmonizer-0.3.1/harmonizer/vignettes/harmonizer.Rmd | 7 - 23 files changed, 67 insertions(+), 60 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to von Neumann, J. (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9) and Kemeny, J. G., O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.3.1 dated 2022-08-27 and 0.3.2 dated 2022-11-23
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++++---------- NAMESPACE | 2 ++ R/AMSDP.R | 17 +++++++++++++++++ R/DCES.R | 26 ++++++++++++++++++++++++++ R/gemAssetPricing.R |only R/gemSecurityPricing.R | 6 +++--- R/gemTax_5_5.R | 2 +- R/gemTax_QuasilinearPreference_4_4.R |only man/AMSDP.Rd | 17 +++++++++++++++++ man/DCES.Rd | 26 ++++++++++++++++++++++++++ man/gemAssetPricing.Rd |only man/gemSecurityPricing.Rd | 4 ++-- man/gemTax_5_5.Rd | 2 +- man/gemTax_QuasilinearPreference_4_4.Rd |only 15 files changed, 112 insertions(+), 20 deletions(-)
Title: Graph Neural Network-Based Framework for Single Cell Active
Pathways and Gene Modules Analysis
Description: It is a single cell active pathway analysis tool based on the graph neural network (F. Scarselli (2009) <doi:10.1109/TNN.2008.2005605>; Thomas N. Kipf (2017) <arXiv:1609.02907v4>) to construct the gene-cell association network, infer pathway activity scores from different single cell modalities data, integrate multiple modality data on the same cells into one pathway activity score matrix, identify cell phenotype activated gene modules and parse association networks of gene modules under multiple cell phenotype. In addition, abundant visualization programs are provided to display the results.
Author: Xudong Han [aut, cre, cph],
Xujiang Guo [fnd]
Maintainer: Xudong Han <hanxd1217@163.com>
Diff between scapGNN versions 0.1.1 dated 2022-06-26 and 0.1.2 dated 2022-11-23
scapGNN-0.1.1/scapGNN/man/norm1.Rd |only scapGNN-0.1.2/scapGNN/DESCRIPTION | 12 +-- scapGNN-0.1.2/scapGNN/MD5 | 38 +++++----- scapGNN-0.1.2/scapGNN/NAMESPACE | 2 scapGNN-0.1.2/scapGNN/R/ConNetGNN.R | 31 ++++++-- scapGNN-0.1.2/scapGNN/R/cpGModule.R | 8 +- scapGNN-0.1.2/scapGNN/R/plotGANetwork.R | 4 - scapGNN-0.1.2/scapGNN/R/plotMulPhenGM.R | 52 ++++++------- scapGNN-0.1.2/scapGNN/R/scPathway.R | 23 +++--- scapGNN-0.1.2/scapGNN/R/utils.R | 53 +++----------- scapGNN-0.1.2/scapGNN/inst/doc/vignette.Rmd | 4 + scapGNN-0.1.2/scapGNN/inst/doc/vignette.html | 53 +++++++------- scapGNN-0.1.2/scapGNN/inst/extdata/c2.kegg.gmt |only scapGNN-0.1.2/scapGNN/inst/extdata/flow_diagram1.png |binary scapGNN-0.1.2/scapGNN/inst/extdata/flow_diagram2.png |binary scapGNN-0.1.2/scapGNN/inst/python/AutoEncoder_GPU.py |only scapGNN-0.1.2/scapGNN/inst/python/GraphAutoEncoder.py | 18 ++++ scapGNN-0.1.2/scapGNN/inst/python/GraphAutoEncoder_GPU.py |only scapGNN-0.1.2/scapGNN/man/ConNetGNN.Rd | 5 + scapGNN-0.1.2/scapGNN/man/RWR.Rd | 10 -- scapGNN-0.1.2/scapGNN/man/scPathway.Rd | 8 +- scapGNN-0.1.2/scapGNN/vignettes/vignette.Rmd | 4 + 22 files changed, 180 insertions(+), 145 deletions(-)
Title: Assessment Models for Agriculture Soil Conditions and Crop
Suitability
Description: Soil assessment builds information for improved decision in
soil management. It analyzes soil conditions with regard to
agriculture crop suitability requirements [such as those given by FAO
<https://www.fao.org/land-water/databases-and-software/crop-information/en/>]
soil fertility classes, soil erosion, and soil salinity classification
[<doi:10.1002/ldr.4211>]. Suitability requirements are for
crops grouped into cereal crops, nuts, legumes, fruits, vegetables,
industrial crops, and root crops.
Author: Christian Thine Omuto [aut, cre]
Maintainer: Christian Thine Omuto <thineomuto@yahoo.com>
Diff between soilassessment versions 0.2.4 dated 2022-09-03 and 0.2.5 dated 2022-11-23
soilassessment-0.2.4/soilassessment/data/Mod.RData |only soilassessment-0.2.4/soilassessment/man/Mod.Rd |only soilassessment-0.2.5/soilassessment/DESCRIPTION | 8 +- soilassessment-0.2.5/soilassessment/MD5 | 50 ++++++++------- soilassessment-0.2.5/soilassessment/NAMESPACE | 2 soilassessment-0.2.5/soilassessment/R/ECconversion1.R | 15 ++-- soilassessment-0.2.5/soilassessment/R/ECconversion2.R | 2 soilassessment-0.2.5/soilassessment/R/ECconversion4.R | 9 -- soilassessment-0.2.5/soilassessment/R/SASmodels.R |only soilassessment-0.2.5/soilassessment/R/classCode.R | 2 soilassessment-0.2.5/soilassessment/R/conversion.R |only soilassessment-0.2.5/soilassessment/R/featureRep.R | 6 + soilassessment-0.2.5/soilassessment/R/imageIndices.R | 18 +++-- soilassessment-0.2.5/soilassessment/R/predAccuracy.R |only soilassessment-0.2.5/soilassessment/R/saltRating.R | 4 + soilassessment-0.2.5/soilassessment/R/saltSeverity.R | 19 +++++ soilassessment-0.2.5/soilassessment/man/ECSuit.Rd | 2 soilassessment-0.2.5/soilassessment/man/ECconversion1.Rd | 26 +++---- soilassessment-0.2.5/soilassessment/man/ECconversion2.Rd | 13 ++- soilassessment-0.2.5/soilassessment/man/ECconversion4.Rd | 3 soilassessment-0.2.5/soilassessment/man/ME_PHharm.Rd | 2 soilassessment-0.2.5/soilassessment/man/PHConversion.Rd | 2 soilassessment-0.2.5/soilassessment/man/SASmodels.Rd |only soilassessment-0.2.5/soilassessment/man/conversion.Rd |only soilassessment-0.2.5/soilassessment/man/pedoTransfer.Rd | 2 soilassessment-0.2.5/soilassessment/man/predAccuracy.Rd |only soilassessment-0.2.5/soilassessment/man/predUncertain.Rd | 2 soilassessment-0.2.5/soilassessment/man/saltRating.Rd | 2 soilassessment-0.2.5/soilassessment/man/saltSeverity.Rd | 8 +- soilassessment-0.2.5/soilassessment/man/surveyPoints.Rd | 2 30 files changed, 117 insertions(+), 82 deletions(-)
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Title: Cohort Data Analyses
Description: Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Diff between cohorttools versions 0.1.5 dated 2022-11-15 and 0.1.6 dated 2022-11-23
DESCRIPTION | 8 ++-- MD5 | 7 ++- NEWS.md |only R/cohorttools.R | 94 +++++++++++++++++++++++++++++++++++++++++++++------- man/estim.hazard.Rd | 6 +++ 5 files changed, 96 insertions(+), 19 deletions(-)
Title: Tests for Survival Data in General Factorial Designs
Description: Implemented are three Wald-type statistic and respective
permuted versions for null hypotheses formulated in terms of cumulative hazard rate functions, medians and the concordance measure, respectively, in the general framework of survival factorial designs with possibly heterogeneous survival and/or censoring distributions, for crossed designs with an arbitrary number of factors and nested designs with up to three factors.
Ditzhaus, Dobler and Pauly (2020) <doi:10.1177/0962280220980784>
Ditzhaus, Janssen, Pauly (2020) <arXiv: 2004.10818v2>
Dobler and Pauly (2019) <doi:10.1177/0962280219831316>.
Author: Marc Ditzhaus [aut],
Dennis Dobler [aut],
Markus Pauly [aut],
Philipp Steinhauer [aut],
Merle Munko [aut, cre]
Maintainer: Merle Munko <merle.munko@ovgu.de>
Diff between GFDsurv versions 0.1.0 dated 2021-07-14 and 0.1.1 dated 2022-11-23
DESCRIPTION | 16 ++++++++++------ MD5 | 2 +- 2 files changed, 11 insertions(+), 7 deletions(-)
Title: Number-Theoretic Functions
Description: Provides number-theoretic functions for factorization, prime
numbers, twin primes, primitive roots, modular logarithm and
inverses, extended GCD, Farey series and continued fractions.
Includes Legendre and Jacobi symbols, some divisor functions,
Euler's Phi function, etc.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.8-2 dated 2021-05-14 and 0.8-5 dated 2022-11-23
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++++------------- NAMESPACE | 6 ++++-- NEWS | 18 ++++++++++++++++++ R/chinese.R | 3 ++- R/collatz.R | 2 +- R/contFrac.R | 8 +++++--- R/is.R | 29 ++++++++++++++++++++++++++++- R/periodicCF.R |only R/solvePellsEq.R |only build/partial.rdb |binary man/IsIntpower.Rd | 13 +++++++++++-- man/cf2num.Rd | 2 +- man/chinese.Rd | 8 ++++---- man/contFrac.Rd | 44 ++++++++++++++++++++++++-------------------- man/isNatural.Rd | 2 +- man/periodicCF.Rd |only man/solvePellsEq.Rd |only 18 files changed, 122 insertions(+), 55 deletions(-)
Title: Non-Local Prior Based Iterative Variable Selection Tool for
Genome-Wide Association Studies
Description: Performs variable selection with data from Genome-wide association studies (GWAS), or other high-dimensional data with continuous, binary or survival outcomes, combining in an iterative framework the computational efficiency of the structured screen-and-select variable selection strategy based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors (see Sanyal et al., 2019 <DOI:10.1093/bioinformatics/bty472>).
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>
Diff between GWASinlps versions 2.1 dated 2022-09-17 and 2.2 dated 2022-11-23
DESCRIPTION | 14 ++-- MD5 | 16 ++--- NAMESPACE | 3 NEWS | 8 ++ NEWS.md | 8 ++ R/GWASinlps.R | 148 +++++++++++++++++++++++++++++++++++++++++++++-- man/GWASinlps-package.Rd | 11 ++- man/GWASinlps.Rd | 52 +++++++++++----- man/nlps.Rd | 24 +++++-- 9 files changed, 235 insertions(+), 49 deletions(-)
Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for drawing probability-proportional-to-size samples with a given number of units, and is commonly used for price-index surveys. This package gives functions to draw stratified sequential Poisson samples according to the method by Ohlsson (1998, ISSN:0282-423X), and generate appropriate bootstrap replicate weights according to the generalized bootstrap method by Beaumont and Patak (2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <stevemartin041@gmail.com>
Diff between sps versions 0.2.0 dated 2022-10-28 and 0.3.0 dated 2022-11-23
DESCRIPTION | 6 - MD5 | 34 +++++----- NEWS.md | 14 ++++ R/inclusion_prob.R | 38 +++++------ R/prop_allocation.R | 119 ++++++++++++++--------------------- R/sps.R | 72 +++++++++------------ R/sps_repweights.R | 9 +- README.md | 22 +++--- inst/po/en@quot/LC_MESSAGES/R-sps.mo |binary inst/po/fr/LC_MESSAGES/R-sps.mo |binary man/sps.Rd | 91 +++++++++++++++----------- man/sps_repweights.Rd | 15 ++-- po/R-fr.po | 29 ++++---- po/R-sps.pot | 16 ++-- tests/test-allocate.R | 54 +++++++++++---- tests/test-allocate.Rout.save | 88 +++++++++++++++++-------- tests/test-sps.R | 14 ++-- tests/test-sps.Rout.save | 26 +++---- 18 files changed, 348 insertions(+), 299 deletions(-)
Title: PC-Axis with R
Description: Provides a set of functions for reading and writing PC-Axis files, used by different statistical organizations around the globe for data dissemination.
Author: Carlos J. Gil Bellosta [cre, aut],
Francisco J. Viciana [aut],
Oscar Perpinan Lamigueiro [aut],
Emilio Torres Manzanera [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between pxR versions 0.42.4 dated 2020-06-07 and 0.42.7 dated 2022-11-23
DESCRIPTION | 9 - MD5 | 10 - R/read.px.R | 429 ++++++++++++++++++++++++++----------------------- README.md | 4 man/read.px.Rd | 5 man/write.json.stat.Rd | 4 6 files changed, 250 insertions(+), 211 deletions(-)
Title: Grammar of Graphics for Linear Model Diagnostic Plots
Description: Allows for easy creation of diagnostic plots for a variety of model objects using the Grammar of Graphics.
Provides functionality for both individual diagnostic plots and an array of four standard diagnostic plots.
Author: Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between gglm versions 0.1.0 dated 2020-10-08 and 1.0.0 dated 2022-11-23
DESCRIPTION | 26 ++++++---- MD5 | 13 +++-- NAMESPACE | 5 + R/aaa.R |only R/gglm.R | 14 +++++ R/list_model_classes.R |only R/utils.R |only README.md | 118 ++++++++++++++++++++++++++++++++++------------ man/list_model_classes.Rd |only man/reexports.Rd |only 10 files changed, 132 insertions(+), 44 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 0.4.9
2021-03-15 0.4.7
2019-01-25 0.4.6
2018-11-28 0.4.5
2018-03-06 0.4.4
2017-07-08 0.4.3
2017-02-15 0.4.1
2017-01-04 0.4
2016-12-27 0.3
2016-02-07 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-08 1.0.11
2022-04-28 1.0.10
2022-02-17 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-05 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-16 0.9.5
2021-11-02 0.9.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-31 2.7.5