Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also given.
Set partitions and now compositions and riffle shuffles are
included.
Author: Robin K. S. Hankin [aut, cre] ,
Paul Egeler [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.10-4 dated 2021-10-23 and 1.10-7 dated 2022-07-20
DESCRIPTION | 15 ++--- MD5 | 51 ++++++++--------- NAMESPACE | 3 + R/partitions.R | 21 ++++++- README.md | 87 ++++++++++++++++++++++++----- build/partial.rdb |binary build/partitions.pdf |binary build/vignette.rds |binary inst/doc/partitionspaper.R | 10 +-- inst/doc/partitionspaper.Rnw | 9 +-- inst/doc/partitionspaper.pdf |binary inst/doc/scrabble.R | 4 - inst/doc/scrabble.Rnw | 5 + inst/doc/scrabble.pdf |binary inst/doc/setpartitions.R | 14 ++-- inst/doc/setpartitions.Rnw | 6 +- inst/doc/setpartitions.pdf |binary man/conjugate.Rd | 12 ++-- man/partitions.package.Rd | 2 man/parts.Rd | 125 +++++++++--------------------------------- man/perms.Rd | 7 -- man/riffle.Rd |only man/setparts.Rd | 24 ++++++-- man/summary.partition.Rd | 2 vignettes/partitionspaper.Rnw | 9 +-- vignettes/scrabble.Rnw | 5 + vignettes/setpartitions.Rnw | 6 +- 27 files changed, 227 insertions(+), 190 deletions(-)
Title: Facilitates 'PhenoCam' Data Access and Time Series
Post-Processing
Description: Programmatic interface to the 'PhenoCam' web services (<https://phenocam.nau.edu/webcam>).
Allows for easy downloading of 'PhenoCam' data directly to your R workspace
or your computer and provides post-processing routines for consistent and easy
timeseries outlier detection, smoothing and estimation of phenological transition dates.
Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between phenocamr versions 1.1.4 dated 2020-03-22 and 1.1.5 dated 2022-07-20
DESCRIPTION | 32 - MD5 | 52 +- NAMESPACE | 2 R/contract_phenocam.r | 2 R/detect_outliers.r | 2 R/expand_phenocam.r | 2 R/grvi.r | 2 R/list_rois.r | 2 R/list_sites.r | 4 R/merge_daymet.r | 2 R/merge_modis.R | 2 R/phenophases.r | 2 R/smooth_ts.r | 2 R/transition_dates.r | 2 R/truncate_phenocam.r | 2 R/write_phenocam.r | 2 R/zzz.R | 10 build/vignette.rds |binary inst/CITATION | 2 inst/doc/phenocamr-vignette.R | 2 inst/doc/phenocamr-vignette.Rmd | 12 inst/doc/phenocamr-vignette.html | 614 +++++++++++++++++------------- inst/shiny/phenocam_explorer/server.R | 12 inst/shiny/phenocam_explorer/ui.R | 38 + tests/testthat/test_ancillary_functions.r | 17 tests/testthat/test_download_function.r | 231 ++++++----- vignettes/phenocamr-vignette.Rmd | 12 27 files changed, 616 insertions(+), 448 deletions(-)
Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, eight different methods for smoothing parameter selection, and flexible tools for prediction and inference.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between npreg versions 1.0-8 dated 2022-03-31 and 1.0-9 dated 2022-07-20
npreg-1.0-8/npreg/R/resid.R |only npreg-1.0-8/npreg/man/resid.Rd |only npreg-1.0-9/npreg/ChangeLog | 52 ++++++++++++++ npreg-1.0-9/npreg/DESCRIPTION | 8 +- npreg-1.0-9/npreg/MD5 | 74 +++++++++++++-------- npreg-1.0-9/npreg/NAMESPACE | 57 +++++++++++----- npreg-1.0-9/npreg/R/boot.gsm.R | 11 +-- npreg-1.0-9/npreg/R/boot.sm.R | 12 +-- npreg-1.0-9/npreg/R/boot.ss.R | 50 ++++++++++---- npreg-1.0-9/npreg/R/coef.R |only npreg-1.0-9/npreg/R/cooks.distance.R |only npreg-1.0-9/npreg/R/cov.ratio.R |only npreg-1.0-9/npreg/R/deviance.R |only npreg-1.0-9/npreg/R/dfbeta.R |only npreg-1.0-9/npreg/R/dfbetas.R |only npreg-1.0-9/npreg/R/diagnostic.plots.R |only npreg-1.0-9/npreg/R/fit_gsm.R | 7 + npreg-1.0-9/npreg/R/fit_sm.R | 4 - npreg-1.0-9/npreg/R/fit_ssi.R |only npreg-1.0-9/npreg/R/fitted.R | 18 ----- npreg-1.0-9/npreg/R/gsm.R | 5 + npreg-1.0-9/npreg/R/hatvalues.R |only npreg-1.0-9/npreg/R/model.matrix.R | 9 +- npreg-1.0-9/npreg/R/residuals.R |only npreg-1.0-9/npreg/R/rstandard.R |only npreg-1.0-9/npreg/R/rstudent.R |only npreg-1.0-9/npreg/R/smooth.influence.R |only npreg-1.0-9/npreg/R/smooth.influence.measures.R |only npreg-1.0-9/npreg/R/ss.R | 31 +++++++- npreg-1.0-9/npreg/R/summary.gsm.R | 9 -- npreg-1.0-9/npreg/R/summary.sm.R | 15 +--- npreg-1.0-9/npreg/R/varimp.R | 8 +- npreg-1.0-9/npreg/R/varinf.R |only npreg-1.0-9/npreg/R/vcov.R |only npreg-1.0-9/npreg/R/weights.R |only npreg-1.0-9/npreg/build/partial.rdb |binary npreg-1.0-9/npreg/man/coef.Rd |only npreg-1.0-9/npreg/man/deviance.Rd |only npreg-1.0-9/npreg/man/diagnostic.plots.Rd |only npreg-1.0-9/npreg/man/fitted.Rd | 12 --- npreg-1.0-9/npreg/man/gsm.Rd | 65 +++++++++++++++--- npreg-1.0-9/npreg/man/npreg-internals.Rd | 5 - npreg-1.0-9/npreg/man/residuals.Rd |only npreg-1.0-9/npreg/man/sm.Rd | 61 +++++++++++++---- npreg-1.0-9/npreg/man/smooth.influence.Rd |only npreg-1.0-9/npreg/man/smooth.influence.measures.Rd |only npreg-1.0-9/npreg/man/ss.Rd | 74 ++++++++++++++++----- npreg-1.0-9/npreg/man/summary.Rd | 2 npreg-1.0-9/npreg/man/varimp.Rd | 7 + npreg-1.0-9/npreg/man/varinf.Rd |only npreg-1.0-9/npreg/man/vcov.Rd |only npreg-1.0-9/npreg/man/weights.Rd |only 52 files changed, 422 insertions(+), 174 deletions(-)
Title: Create ToxPi Prioritization Models
Description: Enables users to build 'ToxPi' prioritization models and provides
functionality within the grid framework for plotting ToxPi graphs.
'toxpiR' allows for more customization than the 'ToxPi GUI'
(<https://toxpi.org>) and integration into existing workflows for greater
ease-of-use, reproducibility, and transparency.
toxpiR package behaves nearly identically to the GUI; the package
documentation includes notes about all differences.
The vignettes download example files from
<https://github.com/ToxPi/ToxPi-example-files>.
Author: Dayne L Filer [aut, cre, fnd] ,
Dillon T Lloyd [aut],
Preethi Thunga [aut] ,
Skylar W Marvel [aut],
Alison A Motsinger-Reif [fnd] ,
David M Reif [aut, fnd]
Maintainer: Dayne L Filer <dayne.filer@gmail.com>
Diff between toxpiR versions 1.0.3 dated 2022-02-18 and 1.2.1 dated 2022-07-20
DESCRIPTION | 8 MD5 | 64 ++-- NAMESPACE | 6 NEWS.md |only R/allClasses.R | 13 R/allGenerics.R | 5 R/methods-TxpModel.R | 18 + R/methods-TxpModelList.R | 6 R/methods-TxpResult.R | 17 - R/methods-TxpResultParam.R |only R/methods-TxpTransFuncList.R | 2 R/txpCalculateScores.R | 84 ++---- R/txpExportGui.R |only R/txpImportGui.R | 15 - R/utils.R | 41 ++ build/vignette.rds |binary inst/doc/exportToGui.R |only inst/doc/exportToGui.html |only inst/doc/exportToGui.rmd |only inst/doc/importFromGui.R | 2 inst/doc/importFromGui.Rmd | 4 inst/doc/importFromGui.html | 229 +++++++++++++++- inst/doc/introduction.Rmd | 46 +-- inst/doc/introduction.html | 371 ++++++++++++++++++++++++--- man/TxpModel-class.Rd | 8 man/TxpResult-class.Rd | 7 man/TxpResultParam-class.Rd |only man/txpCalculateScores.Rd | 15 - man/txpExportGui.Rd |only man/txpGenerics.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/guiFiles/gui_test_data.csv |only tests/testthat/guiFiles/gui_test_results.csv |only tests/testthat/test-TxpModel.R | 3 tests/testthat/test-txpExportGui.R |only tests/testthat/test-vsGuiResults.R |only vignettes/embeddedFigures/txp_explain.png |only vignettes/exportToGui.rmd |only vignettes/importFromGui.Rmd | 4 vignettes/introduction.Rmd | 46 +-- 40 files changed, 823 insertions(+), 194 deletions(-)
Title: Post-Process 'ggplot2' Plots with 'TikZ' Code Using Plot
Coordinates
Description: Annotation of 'ggplot2' plots with arbitrary 'TikZ' code, using absolute data or relative plot coordinates.
Author: Oliver Thomas [aut, cre]
Maintainer: Oliver Thomas <oliver.thomas@sgbm.uni-freiburg.de>
Diff between ggtikz versions 0.1.0 dated 2021-11-04 and 0.1.1 dated 2022-07-20
ggtikz-0.1.0/ggtikz/tests/visualtests |only ggtikz-0.1.1/ggtikz/DESCRIPTION | 12 ++--- ggtikz-0.1.1/ggtikz/MD5 | 28 ++++++------- ggtikz-0.1.1/ggtikz/NEWS.md | 5 ++ ggtikz-0.1.1/ggtikz/R/ggtikzTransform.R | 13 ------ ggtikz-0.1.1/ggtikz/R/ggtikzUninfinite.R | 3 - ggtikz-0.1.1/ggtikz/R/padding.R | 4 + ggtikz-0.1.1/ggtikz/R/unclip.R | 22 +++++++++- ggtikz-0.1.1/ggtikz/build/vignette.rds |binary ggtikz-0.1.1/ggtikz/inst/doc/examples.pdf |binary ggtikz-0.1.1/ggtikz/inst/testdata |only ggtikz-0.1.1/ggtikz/man/tikz_exts_pattern.Rd |only ggtikz-0.1.1/ggtikz/tests/testthat/helpers.R | 14 +++--- ggtikz-0.1.1/ggtikz/tests/testthat/test-ggtikzTransform.R | 27 ------------ ggtikz-0.1.1/ggtikz/tests/testthat/test-ggtikzUninfinite.R | 20 --------- ggtikz-0.1.1/ggtikz/tests/testthat/test-unclip.R | 21 +++++++++ 16 files changed, 78 insertions(+), 91 deletions(-)
Title: Efficient Implementation of Binary Segmentation
Description: Standard template library
containers are used to implement an efficient binary segmentation
algorithm, which is log-linear on average and quadratic in the
worst case.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between binsegRcpp versions 2022.1.24 dated 2022-01-26 and 2022.7.19 dated 2022-07-20
binsegRcpp-2022.1.24/binsegRcpp/man/binsegRcpp-package.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/coef.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/plot.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/print.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/src/binseg_normal.cpp |only binsegRcpp-2022.1.24/binsegRcpp/src/binseg_normal.h |only binsegRcpp-2022.1.24/binsegRcpp/tests/testthat/test-CRAN-binseg.R |only binsegRcpp-2022.7.19/binsegRcpp/DESCRIPTION | 11 binsegRcpp-2022.7.19/binsegRcpp/MD5 | 78 + binsegRcpp-2022.7.19/binsegRcpp/NAMESPACE | 18 binsegRcpp-2022.7.19/binsegRcpp/NEWS | 117 +- binsegRcpp-2022.7.19/binsegRcpp/R/RcppExports.R | 36 binsegRcpp-2022.7.19/binsegRcpp/R/binseg.R |only binsegRcpp-2022.7.19/binsegRcpp/R/binseg_normal.R | 96 -- binsegRcpp-2022.7.19/binsegRcpp/R/binseg_normal_cv.R | 2 binsegRcpp-2022.7.19/binsegRcpp/R/complexity.R | 475 ++++++++-- binsegRcpp-2022.7.19/binsegRcpp/R/cum_median.R |only binsegRcpp-2022.7.19/binsegRcpp/build/vignette.rds |binary binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.R |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.Rmd |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.html |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.R | 214 ++-- binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.Rmd | 214 ++-- binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.html | 240 ++--- binsegRcpp-2022.7.19/binsegRcpp/man/binseg.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/binseg_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/binseg_normal.Rd | 20 binsegRcpp-2022.7.19/binsegRcpp/man/check_sizes.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/coef.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/cum_median.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/cum_median_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/depth_first_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity.Rd | 130 ++ binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_heuristic_equal_breadth_full.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_heuristic_equal_depth_full.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_cost.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_splits.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_tree.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_empirical.Rd | 9 binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_extreme.Rd | 8 binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_worst.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_distribution_info.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_tree_empirical.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/plot.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/print.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/qp.x.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/size_to_splits.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/tree_layout.Rd |only binsegRcpp-2022.7.19/binsegRcpp/src/PiecewiseFunction.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/PiecewiseFunction.h |only binsegRcpp-2022.7.19/binsegRcpp/src/RcppExports.cpp | 53 - binsegRcpp-2022.7.19/binsegRcpp/src/binseg.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/binseg.h |only binsegRcpp-2022.7.19/binsegRcpp/src/cum_median.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/cum_median.h |only binsegRcpp-2022.7.19/binsegRcpp/src/depth_first.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/depth_first.h |only binsegRcpp-2022.7.19/binsegRcpp/src/interface.cpp | 179 +++ binsegRcpp-2022.7.19/binsegRcpp/tests/testthat/test-CRAN.R |only binsegRcpp-2022.7.19/binsegRcpp/vignettes/comparisons.Rmd |only binsegRcpp-2022.7.19/binsegRcpp/vignettes/cross-validation.Rmd | 214 ++-- 61 files changed, 1384 insertions(+), 730 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.4.10 dated 2021-11-11 and 0.4.12 dated 2022-07-20
DESCRIPTION | 6 - MD5 | 32 +++++----- NEWS.md | 11 +++ R/errorHandling.R | 124 ++++++++++++++++++++++++++++------------- R/html_getLinks.R | 8 +- R/html_getTables.R | 14 ++-- R/initializeLogging.R | 12 +-- R/loadDataFile.R | 13 ---- R/timeStamp.R | 8 -- inst/doc/cache-management.html | 1 inst/doc/date-parsing.html | 1 inst/doc/error-handling.html | 56 +++++++++--------- inst/doc/logging.html | 58 +++++++++---------- man/html_getLinks.Rd | 2 man/html_getTables.Rd | 2 man/stopOnError.Rd | 99 ++++++++++++++++++++++++-------- man/timeStamp.Rd | 8 -- 17 files changed, 281 insertions(+), 174 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.6.1 dated 2015-10-27 and 1.7.0 dated 2022-07-20
aroma.cn-1.6.1/aroma.cn/NEWS |only aroma.cn-1.7.0/aroma.cn/DESCRIPTION | 17 aroma.cn-1.7.0/aroma.cn/MD5 | 195 aroma.cn-1.7.0/aroma.cn/NAMESPACE | 12 aroma.cn-1.7.0/aroma.cn/NEWS.md |only aroma.cn-1.7.0/aroma.cn/R/000.R | 10 aroma.cn-1.7.0/aroma.cn/R/006.fixVarArgs.R | 8 aroma.cn-1.7.0/aroma.cn/R/009.setup.R | 13 aroma.cn-1.7.0/aroma.cn/R/021.dynamic_imports.R | 2 aroma.cn-1.7.0/aroma.cn/R/999.DEPRECATED.R | 44 aroma.cn-1.7.0/aroma.cn/R/999.NonDocumentedObjects.R | 6 aroma.cn-1.7.0/aroma.cn/R/AbstractCurveNormalization.R | 1243 ++-- aroma.cn-1.7.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R | 585 - aroma.cn-1.7.0/aroma.cn/R/C1C2.R | 46 aroma.cn-1.7.0/aroma.cn/R/CBS.findAtomicAberrations.R | 174 aroma.cn-1.7.0/aroma.cn/R/CartesianSnpData.R | 205 aroma.cn-1.7.0/aroma.cn/R/CopyNumberRegions.findAtomicAberrations.R | 115 aroma.cn-1.7.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R | 2962 ++++------ aroma.cn-1.7.0/aroma.cn/R/MultiSourceCopyNumberNormalization.XTRAS.R | 273 aroma.cn-1.7.0/aroma.cn/R/NaiveFracBGenotyping.R | 539 - aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.BOOT.R | 1286 ++-- aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.CALL2.R | 544 - aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.NORM.R | 600 +- aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.PLOT3.R | 63 aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.backgroundCorrect.R | 566 - aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.findAtomicAberrations.R | 194 aroma.cn-1.7.0/aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R | 120 aroma.cn-1.7.0/aroma.cn/R/PairedPSCBSFile.R | 46 aroma.cn-1.7.0/aroma.cn/R/PairedPSCBSFileSet.R | 212 aroma.cn-1.7.0/aroma.cn/R/PairedPscbsCaller.R | 397 - aroma.cn-1.7.0/aroma.cn/R/PairedPscbsModel.R | 1190 +--- aroma.cn-1.7.0/aroma.cn/R/PeaksAndValleys.EXTS.R | 304 - aroma.cn-1.7.0/aroma.cn/R/PolarSnpData.R | 46 aroma.cn-1.7.0/aroma.cn/R/PrincipalCurve.XTRAS.R | 131 aroma.cn-1.7.0/aroma.cn/R/PrincipalCurveNormalization.R | 33 aroma.cn-1.7.0/aroma.cn/R/PruneCNA.EXTS.R | 57 aroma.cn-1.7.0/aroma.cn/R/PruneCNA.PLOT.R | 305 - aroma.cn-1.7.0/aroma.cn/R/RawAlleleBFractions.XTRAS.R | 49 aroma.cn-1.7.0/aroma.cn/R/RawGenotypeCalls.R | 49 aroma.cn-1.7.0/aroma.cn/R/SnpData.R | 22 aroma.cn-1.7.0/aroma.cn/R/TotalCnBinnedSmoothing.R | 71 aroma.cn-1.7.0/aroma.cn/R/TotalCnKernelSmoothing.R | 91 aroma.cn-1.7.0/aroma.cn/R/TotalCnSmoothing.R | 850 +- aroma.cn-1.7.0/aroma.cn/R/TotalFracBSnpData.R | 108 aroma.cn-1.7.0/aroma.cn/R/TumorBoostNormalization.R | 1021 +-- aroma.cn-1.7.0/aroma.cn/R/XYCurveNormalization.R | 14 aroma.cn-1.7.0/aroma.cn/R/calculatePairedPSCNByGenotype.R | 224 aroma.cn-1.7.0/aroma.cn/R/callXXorXY.numeric.R | 67 aroma.cn-1.7.0/aroma.cn/R/cnr.R | 40 aroma.cn-1.7.0/aroma.cn/R/fitLoessKD.matrix.R | 166 aroma.cn-1.7.0/aroma.cn/R/normalizeMirroredBAFsByRegions.R | 110 aroma.cn-1.7.0/aroma.cn/R/normalizePrincipalCurve.matrix.R | 175 aroma.cn-1.7.0/aroma.cn/R/principal.curve.pairs2.R | 44 aroma.cn-1.7.0/aroma.cn/R/pruneCNA.R | 338 - aroma.cn-1.7.0/aroma.cn/R/segmentByPruneCBS.R | 799 +- aroma.cn-1.7.0/aroma.cn/R/testAllelicBalanceByBAFs.R | 376 - aroma.cn-1.7.0/aroma.cn/R/testEquality.R | 359 - aroma.cn-1.7.0/aroma.cn/R/utils.R |only aroma.cn-1.7.0/aroma.cn/R/zzz.R | 22 aroma.cn-1.7.0/aroma.cn/inst/CITATION | 208 aroma.cn-1.7.0/aroma.cn/inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R | 350 - aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01a.downloadAllAnnotationData.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01b.downloadAllRawDataSet.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01c.installAllPackages.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/99a.cleanupRootDirectories.R | 100 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex | 22 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex | 6 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex | 6 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/segmentation/20091110,CBS.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/tracks/20091010,TCGA,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/tracks/utils.R | 2 aroma.cn-1.7.0/aroma.cn/man/AbstractCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 10 aroma.cn-1.7.0/aroma.cn/man/PairedPscbsModel.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/PrincipalCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnKernelSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TumorBoostNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/XYCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/aroma.cn-package.Rd | 4 aroma.cn-1.7.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd | 6 100 files changed, 8957 insertions(+), 9533 deletions(-)
Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Steve Lianoglou [ctb],
Jim Nikelski [ctb],
Kirill Mueller [ctb],
Peter Humburg [ctb],
Rich FitzJohn [ctb],
Gyu Jin Choi [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between optparse versions 1.7.1 dated 2021-10-08 and 1.7.3 dated 2022-07-20
DESCRIPTION | 16 ++-- MD5 | 20 +++--- NEWS.md | 11 +++ R/optparse.R | 132 +++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/COPYRIGHTS | 6 - inst/doc/optparse.R | 23 +++---- inst/doc/optparse.Rrst | 23 +++---- inst/doc/optparse.html | 51 +++++++-------- tests/testthat/test-optparse.R | 2 vignettes/optparse.Rrst | 23 +++---- 11 files changed, 180 insertions(+), 127 deletions(-)
Title: Flexible Segment Geoms with Arrows for 'ggplot2'
Description: Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.
Author: Matthew Hall [aut, cre]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Diff between ggarchery versions 0.2.0 dated 2022-02-25 and 0.3.0 dated 2022-07-20
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 8 ++++++-- R/geom-arrowsegment.R | 8 ++++++-- R/position-attractsegment.R | 11 ++++++++--- README.md | 19 +++++++++++++------ man/geom_arrowsegment.Rd | 5 ++++- man/position_attractsegment.Rd | 5 ++++- 8 files changed, 53 insertions(+), 27 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Winston Chang [aut],
Jennifer Bryan [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between devtools versions 2.4.3 dated 2021-11-30 and 2.4.4 dated 2022-07-20
devtools-2.4.3/devtools/man/devtools.Rd |only devtools-2.4.4/devtools/DESCRIPTION | 62 +- devtools-2.4.4/devtools/MD5 | 133 +++-- devtools-2.4.4/devtools/NAMESPACE | 4 devtools-2.4.4/devtools/NEWS.md | 20 devtools-2.4.4/devtools/R/active.R | 19 devtools-2.4.4/devtools/R/build-manual.R | 2 devtools-2.4.4/devtools/R/build-readme.R | 11 devtools-2.4.4/devtools/R/check-devtools.R | 4 devtools-2.4.4/devtools/R/check-doc.R | 6 devtools-2.4.4/devtools/R/check-mac.R | 19 devtools-2.4.4/devtools/R/check-win.R | 45 + devtools-2.4.4/devtools/R/check.R | 47 - devtools-2.4.4/devtools/R/dev-mode.R | 14 devtools-2.4.4/devtools/R/devtools-package.R |only devtools-2.4.4/devtools/R/document.R | 2 devtools-2.4.4/devtools/R/install.R | 10 devtools-2.4.4/devtools/R/lint.R | 20 devtools-2.4.4/devtools/R/package.R | 49 - devtools-2.4.4/devtools/R/pkgbuild.R | 2 devtools-2.4.4/devtools/R/r-hub.R | 2 devtools-2.4.4/devtools/R/release.R | 115 +--- devtools-2.4.4/devtools/R/reload.R | 4 devtools-2.4.4/devtools/R/run-examples.R | 16 devtools-2.4.4/devtools/R/run-source.R | 44 + devtools-2.4.4/devtools/R/show-news.R | 2 devtools-2.4.4/devtools/R/sitrep.R | 32 + devtools-2.4.4/devtools/R/test.R | 24 devtools-2.4.4/devtools/R/uninstall.R | 16 devtools-2.4.4/devtools/R/usethis.R | 2 devtools-2.4.4/devtools/R/utils.R | 8 devtools-2.4.4/devtools/R/vignette-r.R | 6 devtools-2.4.4/devtools/R/vignettes.R | 47 - devtools-2.4.4/devtools/R/wd.R | 4 devtools-2.4.4/devtools/R/zzz.R | 35 - devtools-2.4.4/devtools/README.md | 5 devtools-2.4.4/devtools/inst/WORDLIST | 32 - devtools-2.4.4/devtools/inst/doc/dependencies.html | 247 +++++++++- devtools-2.4.4/devtools/man/as.package.Rd | 6 devtools-2.4.4/devtools/man/build.Rd | 5 devtools-2.4.4/devtools/man/build_vignettes.Rd | 2 devtools-2.4.4/devtools/man/check.Rd | 4 devtools-2.4.4/devtools/man/check_mac_release.Rd | 5 devtools-2.4.4/devtools/man/check_man.Rd | 1 devtools-2.4.4/devtools/man/check_win.Rd | 11 devtools-2.4.4/devtools/man/devtools-package.Rd |only devtools-2.4.4/devtools/man/figures/lifecycle-archived.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-defunct.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-deprecated.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-experimental.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-maturing.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-questioning.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-stable.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-superseded.svg |only devtools-2.4.4/devtools/man/lint.Rd | 20 devtools-2.4.4/devtools/man/load_all.Rd | 48 + devtools-2.4.4/devtools/man/run_examples.Rd | 13 devtools-2.4.4/devtools/man/uninstall.Rd | 14 devtools-2.4.4/devtools/tests/testthat/_snaps |only devtools-2.4.4/devtools/tests/testthat/helper.R | 26 - devtools-2.4.4/devtools/tests/testthat/test-active.R | 10 devtools-2.4.4/devtools/tests/testthat/test-build-readme.R | 61 +- devtools-2.4.4/devtools/tests/testthat/test-check-doc.R | 4 devtools-2.4.4/devtools/tests/testthat/test-check-win.R |only devtools-2.4.4/devtools/tests/testthat/test-install.R | 21 devtools-2.4.4/devtools/tests/testthat/test-package.R |only devtools-2.4.4/devtools/tests/testthat/test-reload.R | 5 devtools-2.4.4/devtools/tests/testthat/test-run-source.R | 41 - devtools-2.4.4/devtools/tests/testthat/test-sitrep.R | 52 +- devtools-2.4.4/devtools/tests/testthat/test-vignettes.R | 85 --- devtools-2.4.4/devtools/tests/testthat/testError/R/error.R | 2 devtools-2.4.4/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-warn.R | 2 72 files changed, 885 insertions(+), 663 deletions(-)
Title: Interpretable Bivariate Density Visualization with 'ggplot2'
Description: The 'ggplot2' package provides simple functions for visualizing contours
of 2-d kernel density estimates. 'ggdensity' implements several additional density estimators
as well as more interpretable visualizations based on highest density regions instead of
the traditional height of the estimated density surface.
Author: James Otto [aut, cre] ,
David Kahle [aut]
Maintainer: James Otto <jamesotto852@gmail.com>
Diff between ggdensity versions 0.0.1 dated 2022-02-15 and 0.1.0 dated 2022-07-20
ggdensity-0.0.1/ggdensity/man/figures |only ggdensity-0.1.0/ggdensity/DESCRIPTION | 14 +- ggdensity-0.1.0/ggdensity/MD5 | 48 +++------ ggdensity-0.1.0/ggdensity/NAMESPACE | 10 + ggdensity-0.1.0/ggdensity/NEWS.md |only ggdensity-0.1.0/ggdensity/R/hdr.R | 12 +- ggdensity-0.1.0/ggdensity/R/hdr_fun.R | 12 +- ggdensity-0.1.0/ggdensity/R/hdr_lines.R | 1 ggdensity-0.1.0/ggdensity/R/hdr_lines_fun.R | 1 ggdensity-0.1.0/ggdensity/R/hdr_points.R |only ggdensity-0.1.0/ggdensity/R/hdr_points_fun.R |only ggdensity-0.1.0/ggdensity/R/hdr_rug.R |only ggdensity-0.1.0/ggdensity/R/iso.R | 100 +++++++++++++++++-- ggdensity-0.1.0/ggdensity/R/marginals.R |only ggdensity-0.1.0/ggdensity/man/geom_hdr.Rd | 9 - ggdensity-0.1.0/ggdensity/man/geom_hdr_fun.Rd | 13 +- ggdensity-0.1.0/ggdensity/man/geom_hdr_points.Rd |only ggdensity-0.1.0/ggdensity/man/geom_hdr_points_fun.Rd |only ggdensity-0.1.0/ggdensity/man/geom_hdr_rug.Rd |only 19 files changed, 157 insertions(+), 63 deletions(-)
Title: Fast Simulation of Simple Temporal Exponential Random Graph
Models
Description: Provides functions for the computationally efficient simulation of
dynamic networks estimated with the statistical framework of temporal
exponential random graph models, implemented in the 'tergm' package.
Author: Samuel M. Jenness [aut, cre],
Chad Klumb [aut]
Maintainer: Samuel M. Jenness <samuel.m.jenness@emory.edu>
Diff between tergmLite versions 2.5.5 dated 2021-11-11 and 2.6.1 dated 2022-07-20
DESCRIPTION | 10 MD5 | 18 - NEWS.md | 2 R/network.R | 6 R/tergmLite-package.r | 4 man/get_vertex_attribute.Rd | 2 man/network_initialize.Rd | 2 man/set_vertex_attribute.Rd | 2 man/tergmLite-package.Rd | 4 tests/testthat/test-networkLite.R | 404 +++++++++++++++++++------------------- 10 files changed, 239 insertions(+), 215 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super
Imposition by Translation And Rotation) growth curve models. SITAR is
a shape-invariant model with a regression B-spline mean curve and
subject-specific random effects on both the measurement and age
scales. The model was first described by Lindstrom (1995)
<doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole
et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole [aut, cre]
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.2.0 dated 2021-04-22 and 1.3.0 dated 2022-07-20
DESCRIPTION | 8 MD5 | 77 +- NAMESPACE | 16 NEWS | 12 R/BICadj.R | 2 R/LMS2z.R | 7 R/LMSfit.R | 4 R/berkeley.R | 1 R/deren.R | 13 R/dfpower.R | 2 R/dfset.R | 2 R/functions.R |only R/getData.sitar.R | 2 R/getPeakTrough.R | 2 R/ifun.R | 2 R/mplot.R | 2 R/ob_convertr.R | 671 +++++++++++++++-------- R/optimal_design.R | 2 R/pdLMS.R | 2 R/plot.sitar.R | 36 - R/plotclean.R | 16 R/predict.sitar.R | 110 +-- R/sitar.R | 41 - R/sitarlib.R | 16 R/timegap.R | 2 R/who0607.R | 2 R/xyadj.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/berkeley.rda |binary data/deren.rda |binary inst/doc/Fitting_models_with_SITAR.html | 316 +++++++++- inst/doc/Optimal_design_for_centile_studies.html | 360 ++++++++++-- man/berkeley.Rd | 1 man/deren.Rd | 13 man/ob_convertr.Rd | 209 +++++-- man/plot.sitar.Rd | 29 man/predict.sitar.Rd | 4 man/sitar.Rd | 12 man/who0607.Rd | 2 40 files changed, 1484 insertions(+), 514 deletions(-)
Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre],
Mark Fredrickson [aut],
Ben Hansen [aut],
Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.1-18 dated 2022-02-28 and 0.3-0 dated 2022-07-20
RItools-0.1-18/RItools/R/data.R |only RItools-0.1-18/RItools/R/xBalance.make.stratwts.R |only RItools-0.1-18/RItools/man/xBalance.make.stratwts.Rd |only RItools-0.1-18/RItools/man/xBalance.makeMM.Rd |only RItools-0.1-18/RItools/man/xBalanceEngine.Rd |only RItools-0.3-0/RItools/DESCRIPTION | 14 RItools-0.3-0/RItools/MD5 | 112 ++-- RItools-0.3-0/RItools/NAMESPACE | 15 RItools-0.3-0/RItools/NEWS.md | 91 ++- RItools-0.3-0/RItools/R/Design.R |only RItools-0.3-0/RItools/R/balanceTest.R |only RItools-0.3-0/RItools/R/balanceTest.make.stratwts.R |only RItools-0.3-0/RItools/R/balanceTestEngine.R |only RItools-0.3-0/RItools/R/harmonic.R | 49 + RItools-0.3-0/RItools/R/naImpute.R | 33 - RItools-0.3-0/RItools/R/nuclearplants.R |only RItools-0.3-0/RItools/R/plot.balancetest.R |only RItools-0.3-0/RItools/R/plot.xbal.R | 44 + RItools-0.3-0/RItools/R/print.xbal.R | 256 +++++++--- RItools-0.3-0/RItools/R/utils.R | 172 ++++++ RItools-0.3-0/RItools/R/xBalance.R | 59 -- RItools-0.3-0/RItools/R/xBalance.find.goodstrats.R | 1 RItools-0.3-0/RItools/R/xBalance.make.stratwts.old.R |only RItools-0.3-0/RItools/R/xBalance.makeMM.R | 6 RItools-0.3-0/RItools/R/xBalance.makepooledsd.R | 19 RItools-0.3-0/RItools/R/xBalanceEngine.R | 52 -- RItools-0.3-0/RItools/R/xbal_tidiers.R |only RItools-0.3-0/RItools/R/xtable.xbal.R | 21 RItools-0.3-0/RItools/R/ym_long.R |only RItools-0.3-0/RItools/R/ym_short.R |only RItools-0.3-0/RItools/README.md | 72 +- RItools-0.3-0/RItools/data/ym_long.rda |only RItools-0.3-0/RItools/data/ym_short.rda |only RItools-0.3-0/RItools/inst/CITATION | 6 RItools-0.3-0/RItools/inst/examples/plot.xbal.R | 9 RItools-0.3-0/RItools/inst/extdata |only RItools-0.3-0/RItools/man/CovsAlignedToADesign-class.Rd |only RItools-0.3-0/RItools/man/DesignOptions-class.Rd |only RItools-0.3-0/RItools/man/DesignWeights.Rd |only RItools-0.3-0/RItools/man/HB08.Rd |only RItools-0.3-0/RItools/man/HB08_2016.Rd |only RItools-0.3-0/RItools/man/ModelMatrixPlus-class.Rd |only RItools-0.3-0/RItools/man/StratumWeightedDesignOptions-class.Rd |only RItools-0.3-0/RItools/man/aggregateDesigns.Rd |only RItools-0.3-0/RItools/man/alignDesignsByStrata.Rd |only RItools-0.3-0/RItools/man/balanceTest.Rd |only RItools-0.3-0/RItools/man/balanceTest.make.stratwts.Rd |only RItools-0.3-0/RItools/man/balanceTestEngine.Rd |only RItools-0.3-0/RItools/man/balanceplot.Rd | 17 RItools-0.3-0/RItools/man/designToDescriptives.Rd |only RItools-0.3-0/RItools/man/effectOfTreatmentOnTreated.Rd |only RItools-0.3-0/RItools/man/formula.xbal.Rd | 1 RItools-0.3-0/RItools/man/harmonic.Rd | 3 RItools-0.3-0/RItools/man/harmonic_times_mean_weight.Rd |only RItools-0.3-0/RItools/man/identify_NM_vars.Rd |only RItools-0.3-0/RItools/man/makeDesigns.Rd |only RItools-0.3-0/RItools/man/model_matrix.Rd |only RItools-0.3-0/RItools/man/naImpute.Rd | 6 RItools-0.3-0/RItools/man/nuclearplants.Rd | 2 RItools-0.3-0/RItools/man/original_units_var_formatter.Rd |only RItools-0.3-0/RItools/man/plot.balancetest.Rd |only RItools-0.3-0/RItools/man/plot.xbal.Rd | 12 RItools-0.3-0/RItools/man/print.xbal.Rd | 39 - RItools-0.3-0/RItools/man/sparseToVec.Rd |only RItools-0.3-0/RItools/man/subset.xbal.Rd | 5 RItools-0.3-0/RItools/man/tidy.xbal.Rd |only RItools-0.3-0/RItools/man/xBalance.Rd | 15 RItools-0.3-0/RItools/man/xBalance.find.goodstrats.Rd | 1 RItools-0.3-0/RItools/man/xBalance.makepooledsd.Rd | 1 RItools-0.3-0/RItools/man/xtable.xbal.Rd | 18 RItools-0.3-0/RItools/man/ym_long.Rd |only RItools-0.3-0/RItools/man/ym_short.Rd |only RItools-0.3-0/RItools/tests/testthat/test.Design.R |only RItools-0.3-0/RItools/tests/testthat/test.balanceTest.R |only RItools-0.3-0/RItools/tests/testthat/test.clusters.R |only RItools-0.3-0/RItools/tests/testthat/test.plot.balancetest.R |only RItools-0.3-0/RItools/tests/testthat/test.plot.xbal.R | 9 RItools-0.3-0/RItools/tests/testthat/test.utils.R | 192 ++++++- RItools-0.3-0/RItools/tests/testthat/test.xBalance.R | 93 +-- RItools-0.3-0/RItools/tests/xBalanceTests2.Rout.save | 10 80 files changed, 996 insertions(+), 459 deletions(-)
Title: R Client for the Daisi Microservice Platform
Description: Connect, execute, and parse results from the Daisi Microservice Platform <https://www.daisi.io/>. The rdaisi client
includes a set of functionality that allows remote execution of microservices directly from R.
Daisis allow R users to access a wide variety of Python functionality and interact with them natively.
Author: Daisi Technology, Inc. [aut],
Jean-Marie Laigle [aut],
Eric Hare [aut, cre]
Maintainer: Eric Hare <eric.hare@daisi.io>
Diff between rdaisi versions 0.1.2 dated 2022-07-05 and 0.1.3 dated 2022-07-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/rdaisi.R | 2 +- README.md | 5 ++--- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Retrieve Records from the Urban Institute's Education Data
Portal API
Description: Allows R users to retrieve and parse data from the Urban
Institute's Education Data API <https://educationdata.urban.org/> into a
'data.frame' for analysis.
Author: Erika Tyagi [cre],
Kyle Ueyama [aut],
The Urban Institute [cph]
Maintainer: Erika Tyagi <etyagi@urban.org>
Diff between educationdata versions 0.1.1 dated 2021-05-31 and 0.1.2 dated 2022-07-20
DESCRIPTION | 18 - MD5 | 20 - NEWS.md | 8 R/construct-url.R | 8 R/validate-args.R | 9 README.md | 330 +++++++++++++------------- build/vignette.rds |binary inst/doc/introducing-educationdata.Rmd | 4 inst/doc/introducing-educationdata.html | 397 ++++++++++++++++++++++++++------ tests/testthat/test-validation.R | 4 vignettes/introducing-educationdata.Rmd | 4 11 files changed, 535 insertions(+), 267 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre]
,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.9 dated 2022-07-16 and 0.1.10 dated 2022-07-20
DESCRIPTION | 8 MD5 | 85 - R/check_installation.R | 98 + R/github.R | 15 R/worcs_checklist.R | 1 R/worcs_project.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/setup-docker.html | 13 inst/doc/setup.Rmd | 21 inst/doc/setup.html | 31 inst/doc/workflow.Rmd | 4 inst/doc/workflow.html | 7 inst/rstudio/addins.dcf | 6 inst/rstudio/templates/project/licenses/cc_by-nc-nd_4.0.txt | 806 +++++------ inst/rstudio/templates/project/licenses/cc_by-nc-sa_4.0.txt | 876 ++++++------ inst/rstudio/templates/project/licenses/cc_by-nc_4.0.txt | 816 +++++------ inst/rstudio/templates/project/licenses/cc_by-nd_4.0.txt | 782 +++++----- inst/rstudio/templates/project/licenses/cc_by-sa_4.0.txt | 856 +++++------ inst/rstudio/templates/project/licenses/cc_by_4.0.txt | 792 +++++----- man/add_manuscript.Rd | 196 +- man/add_preregistration.Rd | 124 - man/check_worcs.Rd | 60 man/check_worcs_installation.Rd | 102 - man/cite_all.Rd | 78 - man/cite_essential.Rd | 78 - man/codebook.Rd | 140 - man/data_label.Rd | 76 - man/data_unlabel.Rd | 54 man/descriptives.Rd | 44 man/export_project.Rd | 70 man/git_user.Rd | 72 man/has_git_user.Rd | 42 man/load_data.Rd | 144 - man/load_entrypoint.Rd | 84 - man/open_data.Rd | 156 +- man/skew_kurtosis.Rd | 60 man/worcs_badge.Rd | 82 - man/worcs_checklist.Rd | 72 man/worcs_project.Rd | 154 +- tests/testthat/test-check_worcs_installation.R |only tests/testthat/test-worcsfile.R | 78 - vignettes/setup.Rmd | 21 vignettes/workflow.Rmd | 4 44 files changed, 3656 insertions(+), 3564 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.7.2 dated 2022-05-24 and 1.7.3 dated 2022-07-20
DESCRIPTION | 12 MD5 | 65 ++--- NEWS.md | 9 R/Splits.R | 9 R/Support.R | 1 R/TreeNumber.R | 66 ++--- R/parse_files.R | 346 ++++++++++++++-------------- R/zzz.R | 3 build/partial.rdb |binary inst/REFERENCES.bib | 5 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.html | 4 inst/doc/load-trees.html | 4 inst/extdata/tests/tnt-bare-tree.tnt |only inst/extdata/tests/tnt-tree.tre | 2 inst/extdata/tests/tnt-trees-and-matrix.tnt | 5 man/ApeTime.Rd | 6 man/DoubleFactorial.Rd | 10 man/DropTip.Rd | 8 man/ExtractTaxa.Rd | 18 - man/ImposeConstraint.Rd | 4 man/ListAncestors.Rd | 4 man/MatrixToPhyDat.Rd | 12 man/NRooted.Rd | 20 - man/PhyToString.Rd | 6 man/ReadCharacters.Rd | 29 -- man/ReadTntTree.Rd | 22 - man/Reorder.Rd | 10 man/SplitFrequency.Rd | 8 man/match.Splits.Rd | 2 src/int_to_tree.cpp | 23 + tests/testthat/test-SplitFunctions.R | 24 - tests/testthat/test-TreeNumber.R | 9 tests/testthat/test-parsers.R | 229 ++++++++++-------- 34 files changed, 519 insertions(+), 460 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.4.0 dated 2022-03-23 and 2.4.1 dated 2022-07-20
TreeDist-2.4.0/TreeDist/R/ClusterTable.R |only TreeDist-2.4.0/TreeDist/build/TreeDist.pdf |only TreeDist-2.4.0/TreeDist/man/ClusterTable-methods.Rd |only TreeDist-2.4.0/TreeDist/man/ClusterTable.Rd |only TreeDist-2.4.0/TreeDist/tests/testthat/test-ClusterTable.R |only TreeDist-2.4.1/TreeDist/DESCRIPTION | 15 TreeDist-2.4.1/TreeDist/MD5 | 134 +- TreeDist-2.4.1/TreeDist/NAMESPACE | 8 TreeDist-2.4.1/TreeDist/NEWS.md | 16 TreeDist-2.4.1/TreeDist/R/Information.R | 38 TreeDist-2.4.1/TreeDist/R/RcppExports.R | 12 TreeDist-2.4.1/TreeDist/R/lap.R | 14 TreeDist-2.4.1/TreeDist/R/plot.R | 1 TreeDist-2.4.1/TreeDist/R/tree_distance.R | 18 TreeDist-2.4.1/TreeDist/R/tree_distance_info.R | 35 TreeDist-2.4.1/TreeDist/R/tree_distance_kendall-colijn.R | 82 - TreeDist-2.4.1/TreeDist/R/tree_distance_mast.R | 12 TreeDist-2.4.1/TreeDist/R/tree_distance_msd.R | 11 TreeDist-2.4.1/TreeDist/R/tree_distance_nni.R | 16 TreeDist-2.4.1/TreeDist/R/tree_distance_nye.R | 17 TreeDist-2.4.1/TreeDist/R/tree_distance_path.R | 37 TreeDist-2.4.1/TreeDist/R/tree_distance_rf.R | 21 TreeDist-2.4.1/TreeDist/build/partial.rdb |only TreeDist-2.4.1/TreeDist/build/vignette.rds |binary TreeDist-2.4.1/TreeDist/inst/CITATION | 10 TreeDist-2.4.1/TreeDist/inst/REFERENCES.bib | 9 TreeDist-2.4.1/TreeDist/inst/WORDLIST | 1 TreeDist-2.4.1/TreeDist/inst/doc/Generalized-RF.html | 375 ++++++- TreeDist-2.4.1/TreeDist/inst/doc/Robinson-Foulds.html | 370 ++++++- TreeDist-2.4.1/TreeDist/inst/doc/Using-TreeDist.html | 276 ++++- TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.R |only TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.Rmd |only TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.html |only TreeDist-2.4.1/TreeDist/inst/doc/information.html | 459 +++++++- TreeDist-2.4.1/TreeDist/inst/doc/treespace.R | 64 - TreeDist-2.4.1/TreeDist/inst/doc/treespace.Rmd | 85 - TreeDist-2.4.1/TreeDist/inst/doc/treespace.html | 495 +++++++-- TreeDist-2.4.1/TreeDist/inst/doc/using-distances.html | 469 +++++++-- TreeDist-2.4.1/TreeDist/inst/treespace/app.R | 516 +++++----- TreeDist-2.4.1/TreeDist/man/AllSplitPairings.Rd | 10 TreeDist-2.4.1/TreeDist/man/CalculateTreeDistance.Rd | 7 TreeDist-2.4.1/TreeDist/man/GeneralizedRF.Rd | 16 TreeDist-2.4.1/TreeDist/man/JaccardRobinsonFoulds.Rd | 27 TreeDist-2.4.1/TreeDist/man/KendallColijn.Rd | 64 - TreeDist-2.4.1/TreeDist/man/LAPJV.Rd | 9 TreeDist-2.4.1/TreeDist/man/MASTSize.Rd | 11 TreeDist-2.4.1/TreeDist/man/MSTSegments.Rd | 8 TreeDist-2.4.1/TreeDist/man/MapTrees.Rd | 1 TreeDist-2.4.1/TreeDist/man/MappingQuality.Rd | 1 TreeDist-2.4.1/TreeDist/man/MatchingSplitDistance.Rd | 21 TreeDist-2.4.1/TreeDist/man/MeilaVariationOfInformation.Rd | 9 TreeDist-2.4.1/TreeDist/man/NNIDist.Rd | 16 TreeDist-2.4.1/TreeDist/man/NyeSimilarity.Rd | 19 TreeDist-2.4.1/TreeDist/man/PathDist.Rd | 36 TreeDist-2.4.1/TreeDist/man/Robinson-Foulds.Rd | 36 TreeDist-2.4.1/TreeDist/man/SpectralEigens.Rd | 1 TreeDist-2.4.1/TreeDist/man/SplitEntropy.Rd | 7 TreeDist-2.4.1/TreeDist/man/SplitSharedInformation.Rd | 19 TreeDist-2.4.1/TreeDist/man/TreeDist-package.Rd | 4 TreeDist-2.4.1/TreeDist/man/TreeDistance.Rd | 35 TreeDist-2.4.1/TreeDist/man/median.multiPhylo.Rd | 1 TreeDist-2.4.1/TreeDist/src/RcppExports.cpp | 36 TreeDist-2.4.1/TreeDist/src/day_1985.cpp | 26 TreeDist-2.4.1/TreeDist/src/mast.cpp | 4 TreeDist-2.4.1/TreeDist/src/nni_distance.cpp | 4 TreeDist-2.4.1/TreeDist/src/tree_distances.cpp | 14 TreeDist-2.4.1/TreeDist/tests/testthat/_snaps/plot/mst-example-plot.svg | 8 TreeDist-2.4.1/TreeDist/tests/testthat/test-day_1985.cpp.r | 8 TreeDist-2.4.1/TreeDist/tests/testthat/test-plot.R | 3 TreeDist-2.4.1/TreeDist/tests/testthat/test-tree_distance_kc.R | 18 TreeDist-2.4.1/TreeDist/vignettes/Batch1.svg |only TreeDist-2.4.1/TreeDist/vignettes/Batch2.svg |only TreeDist-2.4.1/TreeDist/vignettes/compare-treesets.Rmd |only TreeDist-2.4.1/TreeDist/vignettes/treespace.Rmd | 85 - 74 files changed, 2923 insertions(+), 1257 deletions(-)
Title: Solve for Leaf Temperature Using Energy Balance
Description: Implements models of leaf temperature using energy balance. It uses units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately as in Foster and Smith (1986) <doi:10.1111/j.1365-3040.1986.tb02108.x>. It's straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind. It can also model leaf temperature over trait gradients such as leaf size or stomatal conductance. Other references are Monteith and Unsworth (2013, ISBN:9780123869104), Nobel (2009, ISBN:9780123741431), and Okajima et al. (2012) <doi:10.1007/s11284-011-0905-5>.
Author: Chris Muir [aut, cre]
Maintainer: Chris Muir <cdmuir@hawaii.edu>
Diff between tealeaves versions 1.0.5 dated 2020-06-18 and 1.0.6 dated 2022-07-20
DESCRIPTION | 12 - MD5 | 26 +- NEWS.md | 8 R/tleaves.R | 2 README.md | 50 ++--- build/vignette.rds |binary inst/CITATION | 4 inst/doc/parameter-functions.html | 142 ++++++++++----- inst/doc/tealeaves-intermediate.html | 142 ++++++++++----- inst/doc/tealeaves-introduction.R | 67 +++---- inst/doc/tealeaves-introduction.Rmd | 3 inst/doc/tealeaves-introduction.html | 325 ++++++++++++++++++++++------------- man/dot-get_Sr.Rd | 2 vignettes/tealeaves-introduction.Rmd | 3 14 files changed, 490 insertions(+), 296 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.3.1 dated 2022-06-07 and 2.4 dated 2022-07-20
DESCRIPTION | 6 - MD5 | 26 +++-- NEWS.md | 19 ++++ R/bib.R | 24 ++++- README.md | 81 +++++++++--------- build/partial.rdb |binary inst/REFERENCES.bib | 6 - inst/doc/Inserting_bibtex_references.pdf |binary inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary man/insert_all_ref.Rd | 5 - man/macros/refmacros.Rd | 2 tests/testthat/dummyArticle.rds |only tests/testthat/test-bib.R | 39 ++++++++ vignettes/Inserting_bibtex_references.md |only vignettes/Inserting_bibtex_references.org | 11 ++ 15 files changed, 157 insertions(+), 62 deletions(-)
Title: A 'pkgdown' Template
Description: This is an accessible template for 'pkgdown'. It uses two
bootstrap themes, Flatly and Darkly and utilizes the
'prefers-color-scheme' CSS variable to automatically serve either of
the two based on user’s operating system setting, or allowing them to
manually toggle between them.
Author: Amir Masoud Abdol [aut, cre]
Maintainer: Amir Masoud Abdol <i@amirmasoudabdol.name>
Diff between preferably versions 0.4 dated 2021-12-02 and 0.4.1 dated 2022-07-20
DESCRIPTION | 11 - MD5 | 22 +- NAMESPACE | 2 NEWS.md | 8 + R/preferably-package.R | 3 README.md | 8 - build/vignette.rds |binary inst/doc/in-the-wild.Rmd | 3 inst/doc/in-the-wild.html | 264 ++++++++++++++++++++++++++++++--- inst/pkgdown/BS5/assets/preferably.css | 28 +++ inst/pkgdown/BS5/templates/navbar.html | 2 vignettes/in-the-wild.Rmd | 3 12 files changed, 311 insertions(+), 43 deletions(-)
Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a
statistical method that allows to predict survival from
high-dimensional longitudinal predictors. PRC is described in
Signorelli et al. (2021, <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 1.2.1 dated 2022-06-22 and 1.2.2 dated 2022-07-20
DESCRIPTION | 6 MD5 | 24 - R/fit_lmms.R | 8 R/fit_mlpmms.R | 6 R/fit_prclmm.R | 6 R/summarize_lmms.R | 45 ++ inst/NEWS.md | 10 inst/doc/pencal-vignette.R | 12 inst/doc/pencal-vignette.Rmd | 644 ++++++++++++++++++++---------------------- inst/doc/pencal-vignette.html | 83 ++--- man/fit_lmms.Rd | 6 man/fit_mlpmms.Rd | 6 vignettes/pencal-vignette.Rmd | 644 ++++++++++++++++++++---------------------- 13 files changed, 769 insertions(+), 731 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.4 dated 2022-07-19 and 0.5.5 dated 2022-07-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS.md | 5 +++++ R/boundary_datasets.R | 17 +++++++++++++++++ inst/doc/advanced_network.html | 2 +- man/get_boundaries.Rd |only 7 files changed, 33 insertions(+), 9 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between netassoc versions 0.6.3 dated 2017-06-05 and 0.7.0 dated 2022-07-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/plot.R | 2 +- man/plot_netassoc_network.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Estimation and Plotting of IDF Curves
Description: Intensity-duration-frequency (IDF) curves are a widely used analysis-tool
in hydrology to assess extreme values of precipitation
[e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>].
The package 'IDF' provides functions to estimate IDF parameters for given
precipitation time series on the basis of a duration-dependent
generalized extreme value distribution
[Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].
Author: Felix S. Fauer [aut, cre],
Jana Ulrich [aut],
Laura Mack [ctb],
Oscar E. Jurado [ctb],
Christoph Ritschel [aut],
Carola Detring [ctb],
Sarah Joedicke [ctb]
Maintainer: Felix S. Fauer <felix.fauer@met.fu-berlin.de>
Diff between IDF versions 2.1.1 dated 2022-03-03 and 2.1.2 dated 2022-07-20
DESCRIPTION | 24 ++++++++++++------------ MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 19 insertions(+), 14 deletions(-)
Title: Side Grammar Graphics
Description: The grammar of graphics as shown in 'ggplot2' has provided
an expressive API for users to build plots. 'ggside' extends 'ggplot2'
by allowing users to add graphical information about one of the main panel's
axis using a familiar 'ggplot2' style API with tidy data. This package is
particularly useful for visualizing metadata on a discrete axis, or summary
graphics on a continuous axis such as a boxplot or a density distribution.
Author: Justin Landis [aut, cre]
Maintainer: Justin Landis <jtlandis314@gmail.com>
Diff between ggside versions 0.2.0 dated 2021-12-11 and 0.2.1 dated 2022-07-20
DESCRIPTION | 19 MD5 | 95 +- NAMESPACE | 12 NEWS.md | 24 R/Layer.r | 426 ---------- R/aab-other_utils.r | 4 R/geom-sidebar.r | 1 R/geom-sideboxplot.r | 1 R/geom-sidefreqpoly.r | 1 R/geom-sidefunction.r |only R/geom-sidehistogram.r | 1 R/geom-sidelabel.r |only R/geom-sidepath.r | 2 R/ggside.R | 9 R/plot-construction.R | 52 - R/scales-sides-.R | 7 R/sideCoord--utils.R | 3 R/sideFacet--utils.R | 95 +- R/sideFacet-Grid.R | 54 + R/sideFacet-Null.R | 17 R/sideFacet-Wrap.R | 34 R/sideLayer.R | 13 README.md | 15 build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/ggside_aes_mapping.html | 268 +++++- inst/doc/ggside_basic_usage.R | 2 inst/doc/ggside_basic_usage.Rmd | 2 inst/doc/ggside_basic_usage.html | 388 ++++++++- man/figures/README-example-1.png |binary man/figures/README-example-mix-scales-1.png |binary man/figures/README-example-side-themes-1.png |binary man/geom_xsidebar.Rd | 4 man/geom_xsideboxplot.Rd | 78 - man/geom_xsidefreqpoly.Rd | 4 man/geom_xsidefunction.Rd |only man/geom_xsidehistogram.Rd | 4 man/geom_xsidelabel.Rd |only man/geom_xsidetext.Rd | 6 man/ggside-ggproto-facets.Rd | 13 man/ggside-ggproto-geoms.Rd | 11 man/ggside.Rd | 6 tests/testthat/_snaps/ggside_axis_polts/xyside-strip-main.svg |only tests/testthat/_snaps/vdiff_irisScatter/collapsed-histo.svg | 174 ---- tests/testthat/_snaps/vdiff_irisScatter/facetgrid-collapsed-density.svg | 30 tests/testthat/_snaps/vdiff_irisScatter/stacked-side-density.svg | 32 tests/testthat/_snaps/vdiff_irisScatter/yside-histo.svg | 177 ---- tests/testthat/test_FacetGrid_ggside_themes.R | 1 tests/testthat/test_ggside_axis_polts.R | 6 tests/testthat/test_ggside_scales.R | 27 vignettes/ggside_basic_usage.Rmd | 2 51 files changed, 1093 insertions(+), 1029 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.6 dated 2021-12-10 and 1.6.7 dated 2022-07-20
geoknife-1.6.6/geoknife/R/algorithmVersion-webprocess.R |only geoknife-1.6.6/geoknife/R/bufferPoint.R |only geoknife-1.6.6/geoknife/R/check.R |only geoknife-1.6.6/geoknife/R/dodsReplace.R |only geoknife-1.6.6/geoknife/R/geoknife-generic.R |only geoknife-1.6.6/geoknife/R/geoknifeUtils.R |only geoknife-1.6.6/geoknife/R/initializeProcessInputs.R |only geoknife-1.6.6/geoknife/R/parseCategorical.R |only geoknife-1.6.6/geoknife/R/parseTimeseries.R |only geoknife-1.6.6/geoknife/R/query-webdata.R |only geoknife-1.6.6/geoknife/R/query-webgeom.R |only geoknife-1.6.6/geoknife/R/query-webprocess.R |only geoknife-1.6.6/geoknife/R/setJobState.R |only geoknife-1.6.6/geoknife/R/setProcessInputs.R |only geoknife-1.6.6/geoknife/R/show-datagroup.R |only geoknife-1.6.6/geoknife/R/show-geojob.R |only geoknife-1.6.6/geoknife/R/show-simplegeom.R |only geoknife-1.6.6/geoknife/R/show-webdata.R |only geoknife-1.6.6/geoknife/R/show-webgeom.R |only geoknife-1.6.6/geoknife/R/show-webprocess.R |only geoknife-1.6.6/geoknife/R/successful.R |only geoknife-1.6.6/geoknife/R/waitUntilFinished.R |only geoknife-1.6.6/geoknife/inst/extdata/nasa_data.zip |only geoknife-1.6.7/geoknife/DESCRIPTION | 16 geoknife-1.6.7/geoknife/MD5 | 130 - geoknife-1.6.7/geoknife/NAMESPACE | 14 geoknife-1.6.7/geoknife/NEWS.md | 11 geoknife-1.6.7/geoknife/R/00-gconfig.R | 50 geoknife-1.6.7/geoknife/R/02-webgeom-obj.R | 3 geoknife-1.6.7/geoknife/R/03-webdata-obj.R | 38 geoknife-1.6.7/geoknife/R/04-webprocess-obj.R | 10 geoknife-1.6.7/geoknife/R/06-simplegeom-obj.R | 119 + geoknife-1.6.7/geoknife/R/08-geoknife-function.R |only geoknife-1.6.7/geoknife/R/cancel-geojob.R | 2 geoknife-1.6.7/geoknife/R/check-geojob.R |only geoknife-1.6.7/geoknife/R/processInputsToXML.R | 8 geoknife-1.6.7/geoknife/R/query.R |only geoknife-1.6.7/geoknife/R/show.R |only geoknife-1.6.7/geoknife/R/util-bufferPoint.R |only geoknife-1.6.7/geoknife/R/util-geoknife.R |only geoknife-1.6.7/geoknife/R/util-initializeProcessInputs.R |only geoknife-1.6.7/geoknife/R/util-parseCategorical.R |only geoknife-1.6.7/geoknife/R/util-parseTimeseries.R |only geoknife-1.6.7/geoknife/R/util-setJobState.R |only geoknife-1.6.7/geoknife/R/util-setProcessInputs.R |only geoknife-1.6.7/geoknife/R/wait-geojob.R |only geoknife-1.6.7/geoknife/build/vignette.rds |binary geoknife-1.6.7/geoknife/inst/doc/custom_data_sources.R | 66 geoknife-1.6.7/geoknife/inst/doc/custom_data_sources.html | 292 +++ geoknife-1.6.7/geoknife/inst/doc/geoknife.Rmd | 14 geoknife-1.6.7/geoknife/inst/doc/geoknife.html | 769 +++++++--- geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.R | 74 geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.Rmd | 52 geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.html | 296 +++ geoknife-1.6.7/geoknife/inst/unnamed-chunk-6-1.png |only geoknife-1.6.7/geoknife/man/bufferPoint.Rd | 2 geoknife-1.6.7/geoknife/man/canStart.Rd | 2 geoknife-1.6.7/geoknife/man/cancel-methods.Rd | 2 geoknife-1.6.7/geoknife/man/check-geojob.Rd | 2 geoknife-1.6.7/geoknife/man/datagroup-methods.Rd | 4 geoknife-1.6.7/geoknife/man/defaultProcessInputs.Rd | 2 geoknife-1.6.7/geoknife/man/gconfig.Rd | 1 geoknife-1.6.7/geoknife/man/gcontent.Rd | 2 geoknife-1.6.7/geoknife/man/geoknife-methods.Rd | 6 geoknife-1.6.7/geoknife/man/getJobState.Rd | 2 geoknife-1.6.7/geoknife/man/parseCategorical.Rd | 2 geoknife-1.6.7/geoknife/man/parseTimeseries.Rd | 2 geoknife-1.6.7/geoknife/man/query.Rd | 11 geoknife-1.6.7/geoknife/man/retryVERB.Rd | 2 geoknife-1.6.7/geoknife/man/setJobState.Rd | 2 geoknife-1.6.7/geoknife/man/simplegeom-class.Rd | 65 geoknife-1.6.7/geoknife/man/simplegeom-methods.Rd | 24 geoknife-1.6.7/geoknife/man/successful-methods.Rd | 2 geoknife-1.6.7/geoknife/man/wait.Rd | 35 geoknife-1.6.7/geoknife/man/webdata-class.Rd | 2 geoknife-1.6.7/geoknife/man/webgeom-methods.Rd | 3 geoknife-1.6.7/geoknife/man/webprocess-class.Rd | 4 geoknife-1.6.7/geoknife/tests/testthat/data/test_simplegeom_two_points.rds |binary geoknife-1.6.7/geoknife/tests/testthat/test-geoknife_setters.R | 17 geoknife-1.6.7/geoknife/tests/testthat/test-parseCategorical.R | 3 geoknife-1.6.7/geoknife/tests/testthat/test-waitUntilFinished.R | 7 geoknife-1.6.7/geoknife/tests/testthat/test-webprocess_input.R | 2 geoknife-1.6.7/geoknife/vignettes/geoknife.Rmd | 14 geoknife-1.6.7/geoknife/vignettes/plot_geotiff.Rmd | 52 84 files changed, 1584 insertions(+), 654 deletions(-)
Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown'
documents and 'Shiny' apps. These icons can be inserted into HTML content
through inline 'SVG' tags or 'i' tags. There is also a utility function for
exporting 'Font Awesome' icons as 'PNG' images for those situations where
raster graphics are needed.
Author: Richard Iannone [aut, cre] ,
Christophe Dervieux [ctb] ,
Winston Chang [ctb],
Dave Gandy [ctb, cph] ,
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between fontawesome versions 0.2.2 dated 2021-07-02 and 0.3.0 dated 2022-07-20
fontawesome-0.2.2/fontawesome/R/fa_tbl.R |only fontawesome-0.2.2/fontawesome/R/fa_v4_v5.R |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-brands-400.woff |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-regular-400.woff |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-solid-900.woff |only fontawesome-0.3.0/fontawesome/DESCRIPTION | 15 fontawesome-0.3.0/fontawesome/MD5 | 56 fontawesome-0.3.0/fontawesome/NEWS.md | 8 fontawesome-0.3.0/fontawesome/R/fa.R | 247 fontawesome-0.3.0/fontawesome/R/fa_brands.R | 461 fontawesome-0.3.0/fontawesome/R/fa_i.R | 73 fontawesome-0.3.0/fontawesome/R/fa_metadata.R | 9 fontawesome-0.3.0/fontawesome/R/fa_version.R | 2 fontawesome-0.3.0/fontawesome/R/knit_print.R | 10 fontawesome-0.3.0/fontawesome/R/staticimports.R |only fontawesome-0.3.0/fontawesome/R/sysdata.rda |only fontawesome-0.3.0/fontawesome/R/utils.R | 7 fontawesome-0.3.0/fontawesome/R/zzz.R | 26 fontawesome-0.3.0/fontawesome/README.md | 2 fontawesome-0.3.0/fontawesome/inst/apps/138-icon-fontawesome/app.R | 18 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/all.css | 8411 ++++++---- fontawesome-0.3.0/fontawesome/inst/fontawesome/css/all.min.css | 5 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/v4-shims.css | 808 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/v4-shims.min.css | 5 fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-brands-400.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-brands-400.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-regular-400.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-regular-400.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-solid-900.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-solid-900.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-v4compatibility.ttf |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-v4compatibility.woff2 |only fontawesome-0.3.0/fontawesome/man/fa_html_dependency.Rd | 6 fontawesome-0.3.0/fontawesome/man/fa_i.Rd | 10 fontawesome-0.3.0/fontawesome/tests/testthat/test-fa_icon.R | 133 35 files changed, 6549 insertions(+), 3763 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.0 dated 2022-01-13 and 2.1.1 dated 2022-07-20
DESCRIPTION | 10 - MD5 | 44 ++-- NEWS.md | 5 R/Rogue-package.R | 8 R/RogueTaxa.R | 4 R/SPIC.R | 10 - R/stability.R | 44 ++-- R/utilities.R | 2 R/zz_RogueNaRok.R | 6 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Bayesian.R | 36 +-- inst/doc/Bayesian.Rmd | 41 +--- inst/doc/Bayesian.html | 383 +++++++++++++++++++++++++++++++-------- man/Rogue-package.Rd | 8 man/RogueTaxa.Rd | 8 man/TipInstability.Rd | 4 tests/testthat/test-RogueNaRok.R | 2 tests/testthat/test-spic.R | 3 tests/testthat/test-stability.R | 10 - tests/testthat/test-utilities.R | 4 vignettes/Bayesian.Rmd | 41 +--- 23 files changed, 440 insertions(+), 235 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.7-3 dated 2021-11-10 and 0.3.7-4 dated 2022-07-20
DESCRIPTION | 12 MD5 | 36 NEWS | 2 R/inverter.R | 2 build/vignette.rds |binary inst/doc/a_1_getting_started.html | 1306 +++++++++++--------------- inst/doc/a_2_mlrCPO_core.R | 8 inst/doc/a_2_mlrCPO_core.Rmd | 8 inst/doc/a_2_mlrCPO_core.html | 1476 ++++++++++++----------------- inst/doc/a_3_all_CPOs.html | 1290 ++++++++++--------------- inst/doc/a_4_custom_CPOs.html | 1594 +++++++++++++------------------- inst/doc/z_1_getting_started_terse.html | 488 ++------- inst/doc/z_2_mlrCPO_core_terse.R | 8 inst/doc/z_2_mlrCPO_core_terse.html | 568 +++-------- inst/doc/z_3_all_CPOs_terse.html | 434 ++------ inst/doc/z_4_custom_CPOs_terse.html | 898 ++++++------------ man/cpoFilterPermutationImportance.Rd | 4 tests/testthat/test_core_targetop.R | 4 vignettes/a_2_mlrCPO_core.Rmd | 8 19 files changed, 3251 insertions(+), 4895 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen [aut, cre]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.4.0 dated 2022-07-03 and 0.5.0 dated 2022-07-20
DESCRIPTION | 6 ++-- MD5 | 22 +++++++-------- NEWS.md | 6 ++++ R/corrected_lasso.R | 4 +- R/corrected_lasso_glm.R | 6 ++-- R/project_gradient.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/hdme.html | 44 +++++++++++++++---------------- man/corrected_lasso.Rd | 4 +- tests/testthat/test_corrected_lasso.R | 18 +++++++++++- tests/testthat/test_cv_corrected_lasso.R | 8 ++--- 12 files changed, 71 insertions(+), 49 deletions(-)
Title: Process Map Token Replay Animation
Description: Provides animated process maps based on the 'procesmapR' package.
Cases stored in event logs created with with 'bupaR' S3 class eventlog() are
rendered as tokens (SVG shapes) and animated according to their occurrence
times on top of the process map. For rendering SVG animations ('SMIL') and the
'htmlwidget' package are used.
Author: Felix Mannhardt [aut, cre],
Gert Janssenswillen [ctb]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>
Diff between processanimateR versions 1.0.4 dated 2021-10-11 and 1.0.5 dated 2022-07-20
DESCRIPTION | 9 MD5 | 28 NEWS.md | 4 R/processanimateR.R | 7 R/renderer.R | 2 README.md | 2 build/vignette.rds |binary data/example_log.rda |binary inst/doc/use-external-data-to-change-tokens.html | 4517 ++++++++++++++++++ inst/doc/use-shiny-selections.html | 209 inst/doc/use-timestamp-change-token-aes.html | 4543 ++++++++++++++++++- inst/doc/use-token_scales.html | 4517 ++++++++++++++++++ inst/doc/use-with-shiny.html | 208 man/renderer_graphviz.Rd | 6 vignettes/use-external-data-to-change-activites.R |only vignettes/use-external-data-to-change-activites.html |only 16 files changed, 13932 insertions(+), 120 deletions(-)
More information about processanimateR at CRAN
Permanent link
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://serpstat.com/api/>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.1.0 dated 2021-01-10 and 0.2.0 dated 2022-07-20
DESCRIPTION | 9 +- MD5 | 41 +++++------ NAMESPACE | 2 NEWS.md | 9 ++ R/backlinks.R |only R/rank_tracker.R | 133 +++++++++++++++++++++--------------- R/search_analytics.R | 147 +++++++++++++++++++++------------------- R/utility_functions.R | 2 README.md | 18 ++++ man/sst_bl_domain_summary.Rd |only man/sst_bl_referring_domains.Rd |only man/sst_call_api_method.Rd | 2 man/sst_rt_competitors.Rd | 24 ++++-- man/sst_rt_positions_history.Rd | 29 ++++--- man/sst_rt_project_regions.Rd | 5 + man/sst_rt_serp_history.Rd | 27 ++++--- man/sst_sa_database_info.Rd | 7 + man/sst_sa_domain_keywords.Rd | 26 +++---- man/sst_sa_domains_info.Rd | 11 +- man/sst_sa_keyword_top.Rd | 11 +- man/sst_sa_keywords.Rd | 26 +++---- man/sst_sa_keywords_info.Rd | 11 +- man/sst_sa_stats.Rd | 2 23 files changed, 320 insertions(+), 222 deletions(-)
Title: Extending Base R List
Description: Extends the functionality of base R list and
provides specialized data structures deque,
set, dict, and 'dict.table', the latter to extend the 'data.table'
package.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between container versions 1.0.1 dated 2022-02-19 and 1.0.2 dated 2022-07-20
container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.rdx |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.rdx |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.rdx |only container-1.0.2/container/DESCRIPTION | 10 +- container-1.0.2/container/MD5 | 40 +++++----- container-1.0.2/container/NEWS.md | 17 ++-- container-1.0.2/container/build/vignette.rds |binary container-1.0.2/container/inst/doc/code-development.html | 1 container-1.0.2/container/inst/doc/container.html | 1 container-1.0.2/container/inst/doc/deque-set-dict.html | 1 container-1.0.2/container/inst/doc/manage-data-columns.html | 12 +-- container-1.0.2/container/inst/doc/parameter-list.html | 1 container-1.0.2/container/inst/doc/reference-semantics.html | 1 container-1.0.2/container/inst/tinytest/test_Ops-extract.R | 1 container-1.0.2/container/vignettes/manage-data-columns_cache/html/__packages | 1 container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.rdx |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.rdx |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.rdx |only 30 files changed, 49 insertions(+), 37 deletions(-)
Title: Hyperbolic Geometry
Description: Hyperbolic geometry in the Minkowski model and the Poincaré
model. The methods are based on the gyrovector space theory developed
by A. A. Ungar that can be found in the book 'Analytic Hyperbolic
Geometry: Mathematical Foundations And Applications'
<doi:10.1142/5914>. The package provides functions to plot
three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings
of the Poincaré disk.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between gyro versions 1.0.1 dated 2022-06-13 and 1.1.0 dated 2022-07-20
DESCRIPTION | 30 +- MD5 | 45 ++-- NAMESPACE | 85 ++++---- NEWS.md | 7 R/RcppExports.R | 8 R/aaa.R | 2 R/examples.R |only R/gyro.R | 516 ++++---------------------------------------------- R/gyro_operations.R |only R/gyrocentroid.R |only R/gyromidpoint.R |only R/gyrosegment.R |only R/gyrosubdiv.R |only R/hdelaunay.R |only R/internal.R | 3 R/isomorphisms.R |only R/misc.R |only R/plot.R |only README.md | 2 build/vignette.rds |binary man/changesOfSign.Rd | 2 man/gyroABt.Rd | 60 ++--- man/gyrocentroid.Rd |only man/gyrodemos.Rd | 2 man/gyrosegment.Rd | 160 +++++++-------- man/gyrotriangle.Rd | 190 +++++++++--------- man/gyrotube.Rd | 108 +++++----- man/hdelaunay.Rd |only man/plotGyrohull3d.Rd | 360 +++++++++++++++++----------------- man/plotHdelaunay.Rd |only 30 files changed, 601 insertions(+), 979 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models for conditional quantile functions:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press,
<doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression,
CRC Press, <doi:10.1201/9781315120256>.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] ,
Pin Tian Ng [ctb] ,
Blaise Melly [ctb] ,
Achim Zeileis [ctb] ,
Philip Grosjean [ctb] ,
Cleve Moler [ctb] ,
Yousef Saad [ctb] ,
Victor Chernozhukov [ctb] ,
Ivan Fernandez-Val [ctb] ,
Brian D Ripley [tr [...truncated...]
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.93 dated 2022-05-02 and 5.94 dated 2022-07-20
DESCRIPTION | 17 ++- MD5 | 28 +++--- R/crq.R | 1 R/dynrq.R | 68 +++++++-------- R/quantreg.R | 89 ++++++++++--------- R/rqss.R | 232 ++++++++++++++++++++++++++-------------------------- demo/cobar.R | 2 demo/hinged.R | 4 inst/ChangeLog | 28 ++++++ man/plot.rqss.Rd | 5 - man/predict.rqss.Rd | 4 man/qss.Rd | 2 man/rqss.Rd | 2 man/rqss.object.Rd | 2 man/summary.crq.Rd | 4 15 files changed, 260 insertions(+), 228 deletions(-)
Title: Rmetrics - Nonlinear and Chaotic Time Series Modelling
Description: Provides a collection of functions for testing various aspects of
univariate time series including independence and neglected
nonlinearities. Further provides functions to investigate the chaotic
behavior of time series processes and to simulate different types of chaotic
time series maps.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [aut],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fNonlinear versions 3042.79 dated 2017-11-16 and 4021.80 dated 2022-07-20
ChangeLog | 6 +++ DESCRIPTION | 23 +++++++------ MD5 | 11 +++--- R/NonLinStatistics.R | 20 ++++++------ R/NonLinTests.R | 10 +++--- src/Tisean.c | 84 +++++++++++++++++++++++++-------------------------- src/init.c |only 7 files changed, 83 insertions(+), 71 deletions(-)
Title: Rmetrics - Bivariate Dependence Structures with Copulae
Description: Provides a collection of functions to
manage, to investigate and to analyze bivariate financial returns by
Copulae. Included are the families of Archemedean, Elliptical,
Extreme Value, and Empirical Copulae.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [ctb],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fCopulae versions 3042.82.1 dated 2020-03-07 and 4021.84 dated 2022-07-20
fCopulae-3042.82.1/fCopulae/inst/obsolete |only fCopulae-4021.84/fCopulae/ChangeLog | 9 +++++++++ fCopulae-4021.84/fCopulae/DESCRIPTION | 21 ++++++++++++--------- fCopulae-4021.84/fCopulae/MD5 | 19 +++---------------- fCopulae-4021.84/fCopulae/R/EllipticalCopulae.R | 8 +++++--- 5 files changed, 29 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 1.1.0
2020-06-29 1.0.4
2020-04-21 1.0.3