Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.
Author: Matthias Kohl [cre, cph, aut],
Peter Ruckdeschel [aut, cph],
Mykhailo Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
R Core Team [ctb, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobAStBase versions 1.2.2 dated 2022-08-22 and 1.2.3 dated 2022-11-15
DESCRIPTION | 16 - MD5 | 8 inst/NEWS | 9 man/0RobAStBase-package.Rd | 6 man/internal_plots.Rd | 447 ++++++++++++++++++++++----------------------- 5 files changed, 246 insertions(+), 240 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Supports several parallel processing backends.
Author: Peter Solymos [aut, cre] , Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.5-0 dated 2021-09-16 and 1.6-0 dated 2022-11-15
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++++------ NAMESPACE | 2 +- R/pbmapply.R | 23 +++++++++++++++++++++++ R/pbwalk.R |only inst |only man/pbapply.Rd | 41 +++++++++++++++++++++++++++++++++++------ man/pboptions.Rd | 4 ++-- tests/file-1.csv |only tests/file-2.csv |only tests/file-3.csv |only tests/tests.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 12 files changed, 123 insertions(+), 20 deletions(-)
Title: Create and Investigate Magic Squares
Description: A collection of functions for the manipulation and
analysis of arbitrarily dimensioned arrays. The original motivation
for the package was the development of efficient, vectorized
algorithms for the creation and investigation of magic squares and
high-dimensional magic hypercubes.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between magic versions 1.6-0 dated 2022-02-08 and 1.6-1 dated 2022-11-15
DESCRIPTION | 6 ++-- MD5 | 34 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary data/Frankenstein.rda |binary data/Ollerenshaw.rda |binary data/cube2.rda |binary data/hendricks.rda |binary data/magiccubes.rda |binary data/perfectcube5.rda |binary data/perfectcube6.rda |binary inst/doc/magic.R | 12 ++++----- inst/doc/magic.Rnw | 62 ++++++++++++++++++++++++-------------------------- inst/doc/magic.pdf |binary man/cilleruelo.Rd | 6 +--- man/is.magic.Rd | 2 - vignettes/magic.Rnw | 62 ++++++++++++++++++++++++-------------------------- vignettes/magic.bib | 2 - 18 files changed, 90 insertions(+), 96 deletions(-)
Title: High Dimensional Geometry, Set Operations, Projection, and
Inference Using Kernel Density Estimation, Support Vector
Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder, with contributions from Cecina Babich Morrow, David J. Harris, Stuart Brown, Gregoire Butruille, Alex Laini, and Dan Chen
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between hypervolume versions 3.0.4 dated 2022-05-28 and 3.1.0 dated 2022-11-15
DESCRIPTION | 8 MD5 | 59 +++- NAMESPACE | 20 + R/bootstrap_n_hypervolume.R |only R/find_optimal_occupancy_thin.R |only R/get_centroid.R | 35 +- R/get_centroid_weighted.R | 60 +--- R/get_occupancy_intersection_bootstrap.R |only R/get_occupancy_stats.R |only R/get_occupancy_stats_bootstrap.R |only R/get_occupancy_unshared_bootstrap.R |only R/get_occupancy_volume_bootstrap.R |only R/get_relative_volume.R |only R/hypervolume_n_occupancy.R | 377 ---------------------------- R/hypervolume_n_occupancy_bootstrap.R |only R/hypervolume_n_occupancy_permute.R | 301 ++++++++++++---------- R/hypervolume_n_occupancy_test.R | 70 +++-- R/hypervolume_n_resample.R |only R/hypervolume_plot.R | 27 +- R/hypervolume_to_data_frame.R |only R/n_occupancy_function.R |only R/occupancy_bootstrap_gof.R |only R/occupancy_filter.R |only R/occupancy_to_intersection.R |only R/occupancy_to_union.R |only R/occupancy_to_unshared.R |only R/progress_bar_foreach.R |only build/partial.rdb |binary inst/doc/Hypervolume-Resampling.html | 13 man/find_optimal_occupancy_thin.Rd |only man/get_centroid_weighted.Rd | 19 + man/get_occupancy_intersection_bootstrap.Rd |only man/get_occupancy_stats.Rd |only man/get_occupancy_unshared_bootstrap.Rd |only man/get_occupancy_volume_bootstrap.Rd |only man/get_relative_volume.Rd |only man/hypervolume_n_occupancy.Rd | 115 ++++++-- man/hypervolume_n_occupancy_permute.Rd | 66 ++-- man/hypervolume_n_occupancy_test.Rd | 57 ++-- man/hypervolume_n_resample.Rd |only man/hypervolume_to_data_frame.Rd |only man/occupancy_bootstrap_gof.Rd |only man/occupancy_filter.Rd |only man/occupancy_to_intersection.Rd |only man/occupancy_to_union.Rd |only man/occupancy_to_unshared.Rd |only 46 files changed, 527 insertions(+), 700 deletions(-)
Title: Detect and Characterize Sub-Daily Flow Fluctuations
Description: An important environmental impact on running water ecosystems
is caused by hydropeaking - the discontinuous release of turbine water
because of peaks of energy demand. An event-based algorithm is implemented
to detect flow fluctuations referring to increase events (IC) and decrease
events (DC). For each event, a set of parameters related to the fluctuation
intensity is calculated. The framework is introduced in Greimel et al. (2016)
"A method to detect and characterize sub-daily flow fluctuations"
<doi:10.1002/hyp.10773> and can be used to identify different fluctuation
types according to the potential source: e.g., sub-daily flow fluctuations
caused by hydropeaking, rainfall, or snow and glacier melt.
This is a companion to the package 'hydroroute', which is used to detect and
follow hydropower plant-specific hydropeaking waves at the sub-catchment
scale and to describe how hydropeaking flow parameters change along the
longitudinal flow path as proposed and validated in Greimel [...truncated...]
Author: Bettina Gruen [cre, ctb] ,
Julia Haider [aut],
Franz Greimel [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between hydropeak versions 0.1.1 dated 2022-03-11 and 0.1.2 dated 2022-11-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/class-flow.R | 19 ++++++++++--------- build/vignette.rds |binary inst/CITATION | 2 -- inst/NEWS.Rd | 10 +++++++++- inst/doc/hydropeak-intro.html | 14 +++++++++++--- 7 files changed, 39 insertions(+), 24 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 1.4.6 dated 2021-06-17 and 1.4.7 dated 2022-11-15
DESCRIPTION | 15 ++-- MD5 | 18 ++--- R/app_utilities.R | 2 R/searcher_efficiency_figure_functions.R | 4 - R/utility_functions.R | 7 +- build/vignette.rds |binary inst/doc/GenEstGUI.html | 5 - inst/doc/command-line-example.html | 104 ++++++++++++++++--------------- inst/doc/solar-examples.html | 34 ++++++---- inst/doc/wind-examples.html | 24 ++++--- 10 files changed, 119 insertions(+), 94 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.8.5 dated 2022-06-14 and 2.9.0 dated 2022-11-15
DESCRIPTION | 10 ++--- MD5 | 26 +++++++------- NAMESPACE | 5 +- R/SimpleL2ParamFamilies.R | 7 +++ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 9 ++++ inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 6 +-- man/CauchyLocationScaleFamily.Rd | 2 + man/LogisticLocationScaleFamily.Rd | 2 + man/MDEstimator.Rd | 2 + man/NormLocationScaleFamily.Rd | 2 + tests/Examples/distrMod-Ex.Rout.save | 65 +++++++++++++++-------------------- 14 files changed, 76 insertions(+), 60 deletions(-)
Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is
an open source distributed SQL query engine for running interactive
analytic queries against data sources of all sizes ranging from
gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut],
Sergey Goder [aut],
Jarod G.R. Meng [aut, cre],
Thomas J. Leeper [ctb],
John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>
Diff between RPresto versions 1.4.0 dated 2022-09-27 and 1.4.1 dated 2022-11-15
DESCRIPTION | 30 +-- MD5 | 79 +++++----- NAMESPACE | 6 NEWS.md | 13 + R/PrestoSession.R | 4 R/chunk.R |only R/create.dummy.tables.R | 33 ++-- R/cte.R | 8 - R/dbAppendTable.R |only R/dbDataType.R | 171 ++++----------------- R/dbListFields.R | 7 R/dbQuoteLiteral.R |only R/dbWriteTable.R | 178 +++++++++++++++++++--- R/dbplyr-db.R | 3 R/presto.field.R | 5 R/presto.field_utilities.R | 4 R/sqlCreateTable.R | 2 inst/doc/common-table-expressions.html | 2 inst/doc/complex-types.Rmd | 2 inst/doc/complex-types.html | 237 +++++++++++++++--------------- inst/doc/primitive-types.R | 8 + inst/doc/primitive-types.Rmd | 19 ++ inst/doc/primitive-types.html | 233 ++++++++++++++++------------- man/PrestoConnection-class.Rd | 52 ++++-- man/add_chunk.Rd |only man/dbDataType.Rd | 27 +-- man/dbplyr-db.Rd | 3 man/dummy_tables.Rd | 21 +- tests/testthat/test-add_chunk.R |only tests/testthat/test-copy_to.src_presto.R | 19 -- tests/testthat/test-cte.R | 41 +++++ tests/testthat/test-dbAppendTable.R |only tests/testthat/test-dbDataType.R | 103 ++++++++----- tests/testthat/test-dbFetch.R | 8 - tests/testthat/test-dbListFields.R | 18 ++ tests/testthat/test-dbQuoteLiteral.R |only tests/testthat/test-dbWriteTable.R | 58 ++++--- tests/testthat/test-presto_field.R | 90 ++++++++++- tests/testthat/test-response.to.content.R | 4 tests/testthat/test-tbl.src_presto.R | 33 ++++ tests/testthat/test-translate_sql.R | 17 -- tests/testthat/utilities.R | 31 ++- vignettes/complex-types.Rmd | 2 vignettes/primitive-types.Rmd | 19 ++ 44 files changed, 995 insertions(+), 595 deletions(-)
Title: A Tool for Processing and Analyzing Dendrometer Data
Description: There are various functions for managing and cleaning data before the application of different approaches. This includes identifying and erasing sudden jumps in dendrometer data not related to environmental change, identifying the time gaps of recordings, and changing the temporal resolution of data to different frequencies. Furthermore, the package calculates daily statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water. In addition, it identifies periods of consecutive days with user-defined climatic conditions in daily meteorological data, then check what trees are doing during that period.
Author: Sugam Aryal [aut, cre, dtc],
Martin Haeusser [aut],
Jussi Grießinger [aut],
Ze-Xin Fan [aut],
Achim Braeuning [aut, dgs]
Maintainer: Sugam Aryal <sugam.aryal@fau.de>
Diff between dendRoAnalyst versions 0.1.3 dated 2021-10-06 and 0.1.4 dated 2022-11-15
DESCRIPTION | 10 - MD5 | 30 ++- NAMESPACE | 1 R/daily.data.R | 4 R/dendro.resample.R | 6 R/i.jump.locator.R |only R/jump.locator.R | 110 +++++++------- R/phase.sc.R | 12 - R/phase.zg.R | 48 +++--- R/spline.interpolation.R | 12 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/dendRoAnalyst_vignettes.html | 258 +++++++++++++++++++++++++++++++--- man/dendro.resample.Rd | 2 man/i.jump.locator.Rd |only man/jump.locator.Rd | 10 - man/phase.zg.Rd | 3 17 files changed, 369 insertions(+), 137 deletions(-)
Title: Download Data from the Bank for International Settlements (BIS)
Description: Functions for downloading data from the Bank for
International Settlements (BIS; <https://www.bis.org/>) in
Basel. Supported are only full datasets in (typically) CSV
format. The package is lightweight and without dependencies;
suggested packages are used only if data is to be transformed
into particular data structures, for instance into 'zoo'
objects. Downloaded data can optionally be cached, to avoid
repeated downloads of the same files.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between BISdata versions 0.2-0 dated 2022-10-06 and 0.2-1 dated 2022-11-15
DESCRIPTION | 11 ++++++----- MD5 | 9 +++++---- NEWS | 12 ++++++++++++ R/functions.R | 45 +++++++++++++++++++++++++++++++++++---------- README.md |only man/BISdata.Rd | 14 +++++++++++++- 6 files changed, 71 insertions(+), 20 deletions(-)
Title: Risk Tool Library - Trading, Risk, 'Analytics' for Commodities
Description: A toolkit for Commodities 'analytics', risk management and
trading professionals. Includes functions for API calls to
'Morningstar Commodities' and 'Genscape'.
Author: Philippe Cote [aut, cre],
Nima Safaian [aut]
Maintainer: Philippe Cote <pcote@ualberta.ca>
Diff between RTL versions 1.3.0 dated 2022-11-07 and 1.3.1 dated 2022-11-15
RTL-1.3.0/RTL/data/CLc1.rda |only RTL-1.3.0/RTL/data/CLc1c2.rda |only RTL-1.3.0/RTL/data/CLc2.rda |only RTL-1.3.0/RTL/data/cancrudeassays.rda |only RTL-1.3.0/RTL/data/cancrudeprices.rda |only RTL-1.3.0/RTL/data/crudeassaysBP.rda |only RTL-1.3.0/RTL/data/crudeassaysXOM.rda |only RTL-1.3.0/RTL/data/crudes.rda |only RTL-1.3.0/RTL/data/futuresMonths.rda |only RTL-1.3.0/RTL/data/futuresSpecs.rda |only RTL-1.3.0/RTL/data/ref.opt.inputs.rda |only RTL-1.3.0/RTL/data/ref.opt.outputs.rda |only RTL-1.3.0/RTL/data/ry.rda |only RTL-1.3.0/RTL/data/spy.rda |only RTL-1.3.0/RTL/data/uso.rda |only RTL-1.3.0/RTL/man/CLc1.Rd |only RTL-1.3.0/RTL/man/CLc1c2.Rd |only RTL-1.3.0/RTL/man/CLc2.Rd |only RTL-1.3.0/RTL/man/cancrudeassays.Rd |only RTL-1.3.0/RTL/man/cancrudeprices.Rd |only RTL-1.3.0/RTL/man/crudeassaysBP.Rd |only RTL-1.3.0/RTL/man/crudeassaysXOM.Rd |only RTL-1.3.0/RTL/man/crudes.Rd |only RTL-1.3.0/RTL/man/futuresMonths.Rd |only RTL-1.3.0/RTL/man/futuresSpecs.Rd |only RTL-1.3.0/RTL/man/ref.opt.inputs.Rd |only RTL-1.3.0/RTL/man/ref.opt.outputs.Rd |only RTL-1.3.0/RTL/man/ry.Rd |only RTL-1.3.0/RTL/man/spy.Rd |only RTL-1.3.0/RTL/man/uso.Rd |only RTL-1.3.1/RTL/DESCRIPTION | 8 - RTL-1.3.1/RTL/MD5 | 156 ++++++++++++--------------- RTL-1.3.1/RTL/NAMESPACE | 2 RTL-1.3.1/RTL/NEWS.md | 19 +-- RTL-1.3.1/RTL/R/chart_eia_sd.R | 126 +++++++++++----------- RTL-1.3.1/RTL/R/chart_eia_steo.R | 10 - RTL-1.3.1/RTL/R/chart_spreads.R | 176 ++++++++++++++++--------------- RTL-1.3.1/RTL/R/data.R | 141 +++++++----------------- RTL-1.3.1/RTL/R/eia2tidy.R | 15 -- RTL-1.3.1/RTL/R/eia2tidy_all.R |only RTL-1.3.1/RTL/R/globals.R | 1 RTL-1.3.1/RTL/R/promptBeta.R | 156 +++++++++++++-------------- RTL-1.3.1/RTL/R/refineryLP.R | 4 RTL-1.3.1/RTL/R/simMultivariates.R | 2 RTL-1.3.1/RTL/R/tradeStats.R | 2 RTL-1.3.1/RTL/R/tradeStrategyDY.R | 6 - RTL-1.3.1/RTL/R/tradeStrategySMA.R | 6 - RTL-1.3.1/RTL/README.md | 137 +++++++++++------------- RTL-1.3.1/RTL/data/crudeOil.rda |only RTL-1.3.1/RTL/data/cushing.rda |only RTL-1.3.1/RTL/data/dflong.rda |binary RTL-1.3.1/RTL/data/dfwide.rda |binary RTL-1.3.1/RTL/data/eiaStocks.rda |binary RTL-1.3.1/RTL/data/futuresRef.rda |only RTL-1.3.1/RTL/data/ohlc.rda |binary RTL-1.3.1/RTL/data/refineryLPdata.rda |only RTL-1.3.1/RTL/data/spot2futCurve.rda |binary RTL-1.3.1/RTL/data/steo.rda |binary RTL-1.3.1/RTL/data/stocks.rda |only RTL-1.3.1/RTL/data/tsQuotes.rda |binary RTL-1.3.1/RTL/data/usSwapCurves.rda |binary RTL-1.3.1/RTL/data/usSwapCurvesPar.rda |binary RTL-1.3.1/RTL/inst/WORDLIST | 16 +- RTL-1.3.1/RTL/man/chart_eia_sd.Rd | 2 RTL-1.3.1/RTL/man/chart_spreads.Rd | 9 - RTL-1.3.1/RTL/man/crudeOil.Rd |only RTL-1.3.1/RTL/man/cushing.Rd |only RTL-1.3.1/RTL/man/dflong.Rd | 2 RTL-1.3.1/RTL/man/dfwide.Rd | 2 RTL-1.3.1/RTL/man/eia2tidy.Rd | 13 -- RTL-1.3.1/RTL/man/eia2tidy_all.Rd |only RTL-1.3.1/RTL/man/eiaStocks.Rd | 2 RTL-1.3.1/RTL/man/eiaStorageCap.Rd | 2 RTL-1.3.1/RTL/man/eurodollar.Rd | 2 RTL-1.3.1/RTL/man/expiry_table.Rd | 2 RTL-1.3.1/RTL/man/fizdiffs.Rd | 2 RTL-1.3.1/RTL/man/futuresRef.Rd |only RTL-1.3.1/RTL/man/fxfwd.Rd | 2 RTL-1.3.1/RTL/man/holidaysOil.Rd | 2 RTL-1.3.1/RTL/man/ohlc.Rd | 2 RTL-1.3.1/RTL/man/planets.Rd | 2 RTL-1.3.1/RTL/man/promptBeta.Rd | 18 +-- RTL-1.3.1/RTL/man/refineryLP.Rd | 7 - RTL-1.3.1/RTL/man/refineryLPdata.Rd |only RTL-1.3.1/RTL/man/simMultivariates.Rd | 2 RTL-1.3.1/RTL/man/spot2futConvergence.Rd | 2 RTL-1.3.1/RTL/man/spot2futCurve.Rd | 2 RTL-1.3.1/RTL/man/steo.Rd | 2 RTL-1.3.1/RTL/man/stocks.Rd |only RTL-1.3.1/RTL/man/tickers_eia.Rd | 2 RTL-1.3.1/RTL/man/tradeCycle.Rd | 2 RTL-1.3.1/RTL/man/tradeHubs.Rd | 2 RTL-1.3.1/RTL/man/tradeStats.Rd | 2 RTL-1.3.1/RTL/man/tradeStrategyDY.Rd | 6 - RTL-1.3.1/RTL/man/tradeStrategySMA.Rd | 6 - RTL-1.3.1/RTL/man/tradeprocess.Rd | 2 RTL-1.3.1/RTL/man/tsQuotes.Rd | 2 RTL-1.3.1/RTL/man/usSwapCurves.Rd | 2 RTL-1.3.1/RTL/man/usSwapCurvesPar.Rd | 2 RTL-1.3.1/RTL/man/wtiSwap.Rd | 2 100 files changed, 500 insertions(+), 592 deletions(-)
Title: Conditional Manifold Learning
Description: Find a low-dimensional embedding of high-dimensional data, conditioning on auxiliary manifold information. The current version supports conditional MDS and conditional ISOMAP.
Author: Anh Tuan Bui [aut, cre]
Maintainer: Anh Tuan Bui <atbui@u.northwestern.edu>
Diff between cml versions 0.0.5 dated 2022-05-05 and 0.1.0 dated 2022-11-15
cml-0.0.5/cml/R/condSmacof_matrix.R |only cml-0.0.5/cml/R/condSmacof_vector.R |only cml-0.1.0/cml/DESCRIPTION | 8 ++--- cml-0.1.0/cml/MD5 | 31 +++++++++++++--------- cml-0.1.0/cml/NAMESPACE | 3 -- cml-0.1.0/cml/R/condIsomap.R | 9 ++---- cml-0.1.0/cml/R/condMDS.R | 28 +++++--------------- cml-0.1.0/cml/R/condMDSeigen.R |only cml-0.1.0/cml/R/condSmacof.R |only cml-0.1.0/cml/R/cz.R |only cml-0.1.0/cml/R/mpinv.R |only cml-0.1.0/cml/inst/CITATION | 18 +++++++++++-- cml-0.1.0/cml/man/ccor.Rd | 20 +++++++++----- cml-0.1.0/cml/man/cml-package.Rd | 49 +++++++++++++++++++++++++----------- cml-0.1.0/cml/man/condDist.Rd | 4 +- cml-0.1.0/cml/man/condIsomap.Rd | 28 ++++++++++---------- cml-0.1.0/cml/man/condMDS.Rd | 31 +++++++++++----------- cml-0.1.0/cml/man/condMDSeigen.Rd |only cml-0.1.0/cml/man/condSmacof.Rd | 38 +++++++++++++-------------- cml-0.1.0/cml/man/cz.Rd |only cml-0.1.0/cml/man/mpinv.Rd |only 21 files changed, 149 insertions(+), 118 deletions(-)
Title: Statistical Inference for Box-Cox Based Receiver Operating
Characteristic Curves
Description: Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018) <doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021) <doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.
Author: Leonidas Bantis [aut],
Benjamin Brewer [cre, ctb],
Christos Nakas [ctb],
Benjamin Reiser [ctb]
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>
Diff between rocbc versions 0.1.1 dated 2022-09-27 and 0.2.0 dated 2022-11-15
DESCRIPTION | 6 MD5 | 24 R/checkboxcox.R | 12 R/comparebcAUC.R | 37 R/comparebcJ.R | 37 R/comparebcSens.R | 34 R/comparebcSpec.R | 18 R/rocboxcox.R | 36 R/rocboxcoxCI.R | 18 inst/doc/documentation_rocbc.R | 4374 +++++++++++++++++++------------------ inst/doc/documentation_rocbc.Rmd | 4376 +++++++++++++++++++------------------- inst/doc/documentation_rocbc.html | 24 vignettes/documentation_rocbc.Rmd | 4376 +++++++++++++++++++------------------- 13 files changed, 6863 insertions(+), 6509 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
NPX Manager or MyData. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Kristian Hoden [ctb] ,
Per Eriksson [ctb] ,
Klev Diamant [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 3.2.0 dated 2022-10-31 and 3.2.2 dated 2022-11-15
DESCRIPTION | 6 MD5 | 48 - NEWS.md | 10 R/Olink_theme.R | 2 R/Read_NPX_data.R | 5 inst/doc/Vignett.Rmd | 18 inst/doc/Vignett.html | 42 - tests/testthat/_snaps/Olink_boxplot/boxplot-site-10prots.svg | 140 +-- tests/testthat/_snaps/Olink_boxplot/boxplot-site-2prots.svg | 80 +- tests/testthat/_snaps/Olink_boxplot/boxplot-time-and-site.svg | 280 +++---- tests/testthat/_snaps/Olink_boxplot/boxplot-time-with-coloroption.svg | 96 +- tests/testthat/_snaps/Olink_boxplot/boxplot-time.svg | 96 +- tests/testthat/_snaps/Read_NPX_data.md | 30 tests/testthat/_snaps/dist_plot/distribution-plot-col-by-treatment.svg | 88 +- tests/testthat/_snaps/dist_plot/distribution-plot.svg | 80 +- tests/testthat/_snaps/linear_mixed_model/lmer-plot-more-prots-than-space.svg | 16 tests/testthat/_snaps/linear_mixed_model/lmer-plot.svg | 76 +- tests/testthat/_snaps/olink_Pathway_Heatmap/gsea-heatmap.svg | 356 +++++----- tests/testthat/_snaps/olink_Pathway_Heatmap/ora-heatmap-with-keyword.svg | 104 +- tests/testthat/_snaps/olink_Pathway_Visualization/gsea-vis-with-keyword.svg | 4 tests/testthat/_snaps/olink_Pathway_Visualization/gsea-visualization.svg | 14 tests/testthat/_snaps/olink_Pathway_Visualization/ora-vis-with-keyword.svg | 4 tests/testthat/_snaps/olink_Pathway_Visualization/ora-vis-with-terms.svg | 10 tests/testthat/_snaps/pca_plot.md | 260 +++---- vignettes/Vignett.Rmd | 18 25 files changed, 946 insertions(+), 937 deletions(-)
Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components:
horizontal versions of 'Stats' and 'Geoms', and vertical versions
of 'Positions'. This package is now superseded by 'ggplot2' itself
which now has full native support for horizontal layouts. It
remains available for backward compatibility.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between ggstance versions 0.3.5 dated 2020-12-17 and 0.3.6 dated 2022-11-15
ggstance-0.3.5/ggstance/tests/figs |only ggstance-0.3.6/ggstance/DESCRIPTION | 14 +-- ggstance-0.3.6/ggstance/MD5 | 71 ++++++++---------- ggstance-0.3.6/ggstance/NEWS.md | 7 + ggstance-0.3.6/ggstance/R/ggstance.R | 4 + ggstance-0.3.6/ggstance/README.md | 4 - ggstance-0.3.6/ggstance/tests/testthat/_snaps |only ggstance-0.3.6/ggstance/tests/testthat/helper-utils.R | 36 ++++----- ggstance-0.3.6/ggstance/tests/testthat/test-flip.R | 10 ++ 9 files changed, 81 insertions(+), 65 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.8.3 dated 2022-08-19 and 0.8.4 dated 2022-11-15
ggiraph-0.8.3/ggiraph/inst/htmlwidgets/lib/ggiraphjs-0.4.2 |only ggiraph-0.8.3/ggiraph/man/ipar.Rd |only ggiraph-0.8.4/ggiraph/DESCRIPTION | 64 - ggiraph-0.8.4/ggiraph/MD5 | 371 +++++----- ggiraph-0.8.4/ggiraph/NAMESPACE | 23 ggiraph-0.8.4/ggiraph/NEWS.md | 33 ggiraph-0.8.4/ggiraph/R/RcppExports.R | 4 ggiraph-0.8.4/ggiraph/R/annotate_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/annotation_raster_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/default.R |only ggiraph-0.8.4/ggiraph/R/dsvg.R | 43 + ggiraph-0.8.4/ggiraph/R/dsvg_view.R | 4 ggiraph-0.8.4/ggiraph/R/element_interactive.R | 10 ggiraph-0.8.4/ggiraph/R/facet_interactive.R |only ggiraph-0.8.4/ggiraph/R/fonts.R | 4 ggiraph-0.8.4/ggiraph/R/geom_abline_interactive.R | 6 ggiraph-0.8.4/ggiraph/R/geom_bar_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_bin_2d_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_boxplot_interactive.R | 194 ++++- ggiraph-0.8.4/ggiraph/R/geom_contour_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_count_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_crossbar_interactive.R | 97 -- ggiraph-0.8.4/ggiraph/R/geom_density_2d_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_density_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_dotplot_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_errorbar_interactive.R | 63 - ggiraph-0.8.4/ggiraph/R/geom_errorbarh_interactive.R | 58 - ggiraph-0.8.4/ggiraph/R/geom_hex_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_histogram_interactive.R | 4 ggiraph-0.8.4/ggiraph/R/geom_jitter_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_linerange_interactive.R | 5 ggiraph-0.8.4/ggiraph/R/geom_map_interactive.R | 11 ggiraph-0.8.4/ggiraph/R/geom_path_interactive.R | 8 ggiraph-0.8.4/ggiraph/R/geom_point_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_polygon_interactive.R | 20 ggiraph-0.8.4/ggiraph/R/geom_quantile_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_raster_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_rect_interactive.R | 21 ggiraph-0.8.4/ggiraph/R/geom_ribbon_interactive.R | 14 ggiraph-0.8.4/ggiraph/R/geom_segment_interactive.R | 10 ggiraph-0.8.4/ggiraph/R/geom_sf_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_smooth_interactive.R | 7 ggiraph-0.8.4/ggiraph/R/geom_spoke_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_text_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_text_repel_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/geom_tile_interactive.R | 4 ggiraph-0.8.4/ggiraph/R/geom_violin_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/ggiraph.R | 8 ggiraph-0.8.4/ggiraph/R/girafe.R | 60 + ggiraph-0.8.4/ggiraph/R/girafe_options.R | 317 ++++++-- ggiraph-0.8.4/ggiraph/R/guide_bins_interactive.R | 9 ggiraph-0.8.4/ggiraph/R/guide_colourbar_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/guide_coloursteps_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/guide_interactive.R | 23 ggiraph-0.8.4/ggiraph/R/guide_legend_interactive.R | 9 ggiraph-0.8.4/ggiraph/R/interactive_circle_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_curve_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_path_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_points_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_polygon_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_polyline_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_raster_grob.R | 4 ggiraph-0.8.4/ggiraph/R/interactive_rect_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_roundrect_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_segments_grob.R | 2 ggiraph-0.8.4/ggiraph/R/interactive_text_grob.R | 2 ggiraph-0.8.4/ggiraph/R/ipar.R | 20 ggiraph-0.8.4/ggiraph/R/labeller_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/layer_interactive.R | 8 ggiraph-0.8.4/ggiraph/R/scale_alpha_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_brewer_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_colour_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_gradient_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_linetype_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_manual_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_shape_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_size_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_steps_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/scale_viridis_interactive.R | 2 ggiraph-0.8.4/ggiraph/R/tracers.R | 4 ggiraph-0.8.4/ggiraph/R/utils.R | 23 ggiraph-0.8.4/ggiraph/R/utils_css.R | 66 + ggiraph-0.8.4/ggiraph/R/utils_ggplot2.R | 21 ggiraph-0.8.4/ggiraph/build/vignette.rds |binary ggiraph-0.8.4/ggiraph/inst/COPYRIGHTS | 22 ggiraph-0.8.4/ggiraph/inst/examples/shiny/crimes/server.R | 3 ggiraph-0.8.4/ggiraph/inst/examples/shiny/gender/server.R | 1 ggiraph-0.8.4/ggiraph/inst/examples/shiny/gender/ui.R | 8 ggiraph-0.8.4/ggiraph/inst/htmlwidgets/girafe.yaml | 8 ggiraph-0.8.4/ggiraph/inst/htmlwidgets/lib/flatbush-4.0.0 |only ggiraph-0.8.4/ggiraph/inst/htmlwidgets/lib/ggiraphjs-0.4.6 |only ggiraph-0.8.4/ggiraph/inst/htmlwidgets/lib/save-svg-as-png-1.4.17/save-svg-as-png.min.js | 2 ggiraph-0.8.4/ggiraph/inst/tinytest/setup.R | 4 ggiraph-0.8.4/ggiraph/inst/tinytest/test-dsvg.R | 42 + ggiraph-0.8.4/ggiraph/inst/tinytest/test-dsvg_text.R | 10 ggiraph-0.8.4/ggiraph/inst/tinytest/test-geom_point_interactive.R | 11 ggiraph-0.8.4/ggiraph/inst/tinytest/test-ggiraph.R | 14 ggiraph-0.8.4/ggiraph/inst/tinytest/test-girafe.R | 14 ggiraph-0.8.4/ggiraph/inst/tinytest/test-girafe_options.R | 159 ++++ ggiraph-0.8.4/ggiraph/inst/tinytest/test-guide_bins_interactive.R | 2 ggiraph-0.8.4/ggiraph/inst/tinytest/test-guide_legend_interactive.R | 2 ggiraph-0.8.4/ggiraph/inst/tinytest/test-labeller_interactive.R | 79 ++ ggiraph-0.8.4/ggiraph/inst/tinytest/test-tracers.R | 7 ggiraph-0.8.4/ggiraph/inst/tinytest/test-zz-dom.R | 3 ggiraph-0.8.4/ggiraph/man/annotate_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/annotation_raster_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/dsvg.Rd | 10 ggiraph-0.8.4/ggiraph/man/dsvg_view.Rd | 2 ggiraph-0.8.4/ggiraph/man/element_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/facet_grid_interactive.Rd |only ggiraph-0.8.4/ggiraph/man/facet_wrap_interactive.Rd |only ggiraph-0.8.4/ggiraph/man/geom_abline_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_bar_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_bin_2d_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_boxplot_interactive.Rd | 68 + ggiraph-0.8.4/ggiraph/man/geom_contour_interactive.Rd | 12 ggiraph-0.8.4/ggiraph/man/geom_count_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_crossbar_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_density_2d_interactive.Rd | 4 ggiraph-0.8.4/ggiraph/man/geom_density_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_dotplot_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_errorbarh_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_hex_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_histogram_interactive.Rd | 6 ggiraph-0.8.4/ggiraph/man/geom_jitter_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_map_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_path_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_point_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_polygon_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_quantile_interactive.Rd | 8 ggiraph-0.8.4/ggiraph/man/geom_raster_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_rect_interactive.Rd | 4 ggiraph-0.8.4/ggiraph/man/geom_ribbon_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_segment_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_sf_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_smooth_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_spoke_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_text_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_text_repel_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/geom_violin_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/ggiraph-ggproto.Rd | 39 - ggiraph-0.8.4/ggiraph/man/ggiraph.Rd | 10 ggiraph-0.8.4/ggiraph/man/girafe.Rd | 18 ggiraph-0.8.4/ggiraph/man/girafe_css.Rd | 3 ggiraph-0.8.4/ggiraph/man/girafe_css_bicolor.Rd |only ggiraph-0.8.4/ggiraph/man/girafe_defaults.Rd |only ggiraph-0.8.4/ggiraph/man/girafe_options.Rd | 7 ggiraph-0.8.4/ggiraph/man/guide_bins_interactive.Rd | 4 ggiraph-0.8.4/ggiraph/man/guide_colourbar_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/guide_coloursteps_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/guide_legend_interactive.Rd | 6 ggiraph-0.8.4/ggiraph/man/init_girafe_defaults.Rd |only ggiraph-0.8.4/ggiraph/man/interactive_circle_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_curve_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_parameters.Rd |only ggiraph-0.8.4/ggiraph/man/interactive_path_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_points_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_polygon_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_polyline_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_raster_grob.Rd | 4 ggiraph-0.8.4/ggiraph/man/interactive_rect_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_roundrect_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_segments_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/interactive_text_grob.Rd | 2 ggiraph-0.8.4/ggiraph/man/label_interactive.Rd | 4 ggiraph-0.8.4/ggiraph/man/labeller_interactive.Rd | 14 ggiraph-0.8.4/ggiraph/man/opts_hover.Rd | 19 ggiraph-0.8.4/ggiraph/man/opts_selection.Rd | 24 ggiraph-0.8.4/ggiraph/man/opts_sizing.Rd | 5 ggiraph-0.8.4/ggiraph/man/opts_toolbar.Rd | 48 + ggiraph-0.8.4/ggiraph/man/opts_tooltip.Rd | 7 ggiraph-0.8.4/ggiraph/man/opts_zoom.Rd | 9 ggiraph-0.8.4/ggiraph/man/renderggiraph.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_alpha_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_colour_brewer_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_colour_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_colour_steps_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_gradient_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_linetype_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_manual_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_shape_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_size_interactive.Rd | 2 ggiraph-0.8.4/ggiraph/man/scale_viridis_interactive.Rd | 6 ggiraph-0.8.4/ggiraph/man/set_girafe_defaults.Rd |only ggiraph-0.8.4/ggiraph/src/RcppExports.cpp | 10 ggiraph-0.8.4/ggiraph/src/a_color.cpp | 13 ggiraph-0.8.4/ggiraph/src/a_color.h | 2 ggiraph-0.8.4/ggiraph/src/dsvg.cpp | 24 ggiraph-0.8.4/ggiraph/src/dsvg_dev.cpp | 30 ggiraph-0.8.4/ggiraph/src/dsvg_dev.h | 7 ggiraph-0.8.4/ggiraph/src/interactive.cpp | 19 ggiraph-0.8.4/ggiraph/src/svg.cpp | 13 192 files changed, 1835 insertions(+), 845 deletions(-)
Title: Delete or Merge Regressors Algorithms for Linear and Logistic
Model Selection and High-Dimensional Data
Description: Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka Sołtys, Michał Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831–863. <doi:10.1111/sjos.12546>.
Author: Agnieszka Prochenka-Soltys [aut] ,
Piotr Pokarowski [aut],
Szymon Nowakowski [aut, cre]
Maintainer: Szymon Nowakowski <s.nowakowski@mimuw.edu.pl>
Diff between DMRnet versions 0.3.2 dated 2022-10-07 and 0.3.3 dated 2022-11-15
DESCRIPTION | 6 - MD5 | 70 +++++++++------- NEWS.md | 15 +++ R/DMR4glm.R | 106 +++++++------------------ R/DMR4glm_help.R | 7 - R/DMR4lm.R | 91 +++++---------------- R/DMR4lm_help.R | 4 R/DMRnet4glm.R | 143 ++++----------------------------- R/DMRnet4lm.R | 142 ++++----------------------------- R/SOSnet4glm.R | 85 ++++++-------------- R/SOSnet4lm.R | 71 +++++----------- R/clusters_4glm_help.R | 7 - R/clusters_4lm_help.R | 10 +- R/coef.cv.DMR.R | 6 - R/constants.R |only R/cv.DMRnet.R | 6 - R/cv_GIC_indexed.R | 38 ++++++-- R/cv_MD_indexed.R | 13 ++- R/gic.DMR.R | 5 - R/glamer_4glm.R | 165 ++++----------------------------------- R/glamer_4lm.R | 151 ++++------------------------------- R/glamer_4lm_help.R | 2 R/plot.cv.DMR.R | 19 ++-- R/postlasso_O_step_preparation.R |only R/postlasso_common.R |only R/postlasso_fac.R |only R/postlasso_glamer.R |only R/predict.DMR.R | 2 R/predict.cv.DMR.R | 8 - R/predict.gic.DMR.R | 2 R/prelasso_binomial.R |only R/prelasso_common.R |only R/prelasso_cont_columns.R |only R/wrap_up_binomial.R |only R/wrap_up_gaussian.R |only inst/doc/getting-started.html | 4 man/cv.DMRnet.Rd | 6 - man/gic.DMR.Rd | 6 + man/predict.DMR.Rd | 2 man/predict.cv.DMR.Rd | 2 man/predict.gic.DMR.Rd | 2 41 files changed, 337 insertions(+), 859 deletions(-)
Title: Adds Functionality to the R Markdown + Shiny Bootstrap Framework
Description: The Bootstrap framework lets you add some JavaScript functionality to your web site by
adding attributes to your HTML tags - Bootstrap takes care of the JavaScript
<https://getbootstrap.com/docs/3.3/javascript/>. If you are using R Markdown or Shiny, you can
use these functions to create collapsible sections, accordion panels, modals, tooltips,
popovers, and an accordion sidebar framework (not described at Bootstrap site).
Please note this package was designed for Bootstrap 3.3.
Author: Ian Lyttle [aut, cre] ,
Alex Shum [ctb],
Emerson Berry [ctb]
Maintainer: Ian Lyttle <ijlyttle@me.com>
Diff between bsplus versions 0.1.3 dated 2021-10-05 and 0.1.4 dated 2022-11-15
DESCRIPTION | 22 ++++++++++------------ LICENSE | 4 ++-- MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/tidyverse.R | 1 + R/utils.R | 5 +++++ README.md | 3 ++- man/pipe.Rd | 1 + tests/testthat/test-shiny.R | 2 +- 9 files changed, 38 insertions(+), 24 deletions(-)
More information about LakeMetabolizer at CRAN
Permanent link
Title: Access to 'Google Ads' via the 'Windsor.ai' API
Description: Collect marketing data from 'Google Ads' using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
Author: Pablo Sanchez [aut, cre],
Windsor.ai [cph]
Maintainer: Pablo Sanchez <pablosama@outlook.es>
Diff between googleadsR versions 0.1.2 dated 2022-10-17 and 1.0.0 dated 2022-11-15
googleadsR-0.1.2/googleadsR/R/windsor_fetch_googleAds.R |only googleadsR-0.1.2/googleadsR/man/windsor_fetch_googleAds.Rd |only googleadsR-1.0.0/googleadsR/DESCRIPTION | 10 +- googleadsR-1.0.0/googleadsR/MD5 | 22 ++--- googleadsR-1.0.0/googleadsR/NAMESPACE | 6 - googleadsR-1.0.0/googleadsR/NEWS.md | 9 +- googleadsR-1.0.0/googleadsR/R/fetch_googleads.R |only googleadsR-1.0.0/googleadsR/R/my_data_googleads.R | 6 - googleadsR-1.0.0/googleadsR/README.md | 17 +-- googleadsR-1.0.0/googleadsR/inst/doc/basics.R | 7 - googleadsR-1.0.0/googleadsR/inst/doc/basics.Rmd | 11 -- googleadsR-1.0.0/googleadsR/inst/doc/basics.html | 57 ++++++------- googleadsR-1.0.0/googleadsR/man/fetch_googleads.Rd |only googleadsR-1.0.0/googleadsR/vignettes/basics.Rmd | 11 -- 14 files changed, 72 insertions(+), 84 deletions(-)
Title: Microsoft Finance Time Series Forecasting Framework
Description: Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time
Series Forecasting Framework, aka Finn, can be used to forecast any component of the income
statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time,
Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn want built
to meet the needs of financial analysts to better forecast their businesses within a company, and has
a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!
Author: Mike Tokic [aut, cre] ,
Aadharsh Kannan [aut]
Maintainer: Mike Tokic <mftokic@gmail.com>
Diff between finnts versions 0.2.0 dated 2022-07-14 and 0.2.1 dated 2022-11-15
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 28 +++++++++++++++++++--------- R/forecast_models.R | 19 +++++++++++++------ R/forecast_time_series.R | 8 ++++---- R/multivariate_data_prep.R | 12 +++++++----- R/utility.R | 2 +- inst/doc/models-used-in-finnts.html | 4 ++-- inst/doc/parallel-processing.Rmd | 2 +- inst/doc/parallel-processing.html | 2 +- vignettes/parallel-processing.Rmd | 2 +- 11 files changed, 62 insertions(+), 43 deletions(-)
Title: A Suite of High-Performance Packages for Statistics and Data
Manipulation
Description: Easy installation, loading and management, of high-performance packages
for statistical computing and data manipulation in R.
The core 'fastverse' consists of 4 packages: 'data.table', 'collapse',
'kit' and 'magrittr', that jointly only depend on 'Rcpp'.
The 'fastverse' can be freely and permanently extended with
additional packages, both globally or for individual projects.
Separate package verses can also be created. Fast packages
for many common tasks such as time series, dates and times, strings,
spatial data, statistics, data serialization, larger-than-memory
processing, and compilation of R code are listed in the README file:
<https://github.com/fastverse/fastverse#suggested-extensions>.
Author: Sebastian Krantz [aut, cre],
Hadley Wickham [ctb]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between fastverse versions 0.2.4 dated 2022-05-31 and 0.3.0 dated 2022-11-15
DESCRIPTION | 39 +- MD5 | 46 +- NAMESPACE | 1 NEWS.md | 13 R/attach.R | 34 - R/children.R | 2 R/conflicts.R | 10 R/fastverse.R | 43 +- R/update.R | 71 ++- R/utils.R | 14 README.md | 153 +++++--- inst/doc/fastverse_intro.R | 14 inst/doc/fastverse_intro.Rmd | 43 +- inst/doc/fastverse_intro.html | 799 +++++++++++++++++++++++++++++++----------- man/fastverse.Rd | 43 +- man/fastverse_child.Rd | 2 man/fastverse_conflicts.Rd | 7 man/fastverse_deps.Rd | 9 man/fastverse_detach.Rd | 4 man/fastverse_extend.Rd | 29 - man/fastverse_install.Rd | 12 man/fastverse_packages.Rd | 2 man/fastverse_update.Rd | 15 vignettes/fastverse_intro.Rmd | 43 +- 24 files changed, 990 insertions(+), 458 deletions(-)
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 0.1.4 dated 2020-12-03 and 0.1.5 dated 2022-11-15
DESCRIPTION | 9 +--- MD5 | 6 +- R/cohorttools.R | 112 ++++++++++++++++++++++++++++++++++++---------------- man/estim.hazard.Rd | 10 ++++ 4 files changed, 95 insertions(+), 42 deletions(-)
Title: Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator
Description: This is a port of Jonathan Shewchuk's Triangle library to
R. From his description: "Triangle generates exact Delaunay
triangulations, constrained Delaunay triangulations, conforming
Delaunay triangulations, Voronoi diagrams, and high-quality
triangular meshes. The latter can be generated with no small or
large angles, and are thus suitable for finite element analysis."
Author: Jonathan Richard Shewchuk [ctb, cph],
David C. Sterratt [cph, aut, cre],
Elias Pipping [ctb],
Michael Sumner [ctb]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between RTriangle versions 1.6-0.10 dated 2018-01-31 and 1.6-0.11 dated 2022-11-15
DESCRIPTION | 18 +++++++++------ MD5 | 21 +++++++++-------- NEWS | 24 +++++++++++++++++++- R/triangle.R | 45 ++++++++++++++++++++------------------ inst/extdata/inf-steiner.RData |only man/triangulate.Rd | 27 ++++++++++++---------- src/Makevars | 7 +++++ src/interface.c | 25 ++++++++++++++++----- src/triangle.c | 12 ++++++++++ tests/attributes.Rout.save | 20 ++++++++++++++-- tests/basic.Rout.save | 15 ++++++++---- tests/testthat/test-triangulate.R | 26 +++++++++++++++++++++ 12 files changed, 174 insertions(+), 66 deletions(-)
Title: Helper Functions for Point Pattern Analysis
Description: Growing collection of helper functions for point pattern analysis. Most functions
are designed to work with the 'spatstat' (<http://spatstat.org>) package. The focus of
most functions are either null models or summary functions for spatial point patterns.
For a detailed description of all null models and summary functions, see
Wiegand and Moloney (2014, ISBN:9781420082548).
Author: Maximilian H.K. Hesselbarth [aut, cre]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between onpoint versions 1.0.2 dated 2022-02-02 and 1.0.3 dated 2022-11-15
DESCRIPTION | 17 ++++---- MD5 | 62 +++++++++++++++---------------- NEWS.md | 6 +++ R/center_l_function.R | 8 ++-- R/estimate_o_ring.R | 6 +-- R/estimate_pcf_fast.R | 4 +- R/plot.env_summarized.R | 2 - R/plot_quantums.R | 6 +-- R/print.env_summarized.R | 2 - R/simulate_antecedent_conditions.R | 9 ++-- R/simulate_heterogenous_pattern.R | 10 ++--- R/summarize_envelope.R | 4 +- man/center_l_function.Rd | 4 +- man/estimate_o_ring.Rd | 2 - man/figures/README-plot_antecedent-1.png |binary man/figures/README-plot_hetero-1.png |binary man/figures/README-plot_lfun-1.png |binary man/figures/README-plot_oring-1.png |binary man/figures/README-plot_quantums-1.png |binary man/onpoint.Rd | 2 - man/plot.env_summarized.Rd | 2 - man/plot_quantums.Rd | 4 +- man/print.env_summarized.Rd | 2 - man/simulate_antecedent_conditions.Rd | 7 ++- man/simulate_heterogenous_pattern.Rd | 6 +-- man/summarize_envelope.Rd | 2 - tests/testthat.R | 2 - tests/testthat/test-center_l_function.R | 2 - tests/testthat/test-plot.R | 6 +-- tests/testthat/test-plot_quantums.R | 16 ++++---- tests/testthat/test-print.R | 2 - tests/testthat/test-summarize_envelope.R | 20 ++++++++-- 32 files changed, 119 insertions(+), 96 deletions(-)
Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between nnTensor versions 1.1.8 dated 2022-07-14 and 1.1.10 dated 2022-11-15
nnTensor-1.1.10/nnTensor/DESCRIPTION | 10 nnTensor-1.1.10/nnTensor/LICENSE |only nnTensor-1.1.10/nnTensor/MD5 | 28 +- nnTensor-1.1.10/nnTensor/NAMESPACE | 1 nnTensor-1.1.10/nnTensor/R/NMF.R | 256 ++++++++++----------- nnTensor-1.1.10/nnTensor/R/NMTF.R | 113 ++++++--- nnTensor-1.1.10/nnTensor/R/NTD.R | 5 nnTensor-1.1.10/nnTensor/R/NTF.R | 21 + nnTensor-1.1.10/nnTensor/R/nnTensor-internal.R | 26 +- nnTensor-1.1.10/nnTensor/build/partial.rdb |binary nnTensor-1.1.10/nnTensor/inst/NEWS | 10 nnTensor-1.1.10/nnTensor/man/NMF.Rd | 4 nnTensor-1.1.10/nnTensor/man/NMTF.Rd | 14 + nnTensor-1.1.10/nnTensor/man/NTD.Rd | 10 nnTensor-1.1.10/nnTensor/tests/testthat/test_NMF.R | 18 - nnTensor-1.1.8/nnTensor/README.md |only 16 files changed, 297 insertions(+), 219 deletions(-)
Title: Spatio-Temporal Adaptive Kernel Estimators for Intensities
Description: Adaptive estimation of the first-order intensity function of a spatio-temporal point process using kernels and variable bandwidths. The methodology used for estimation is presented in González and Moraga (2022). <arXiv:2208.12026>.
Author: Jonatan A Gonzalez [aut, cre] ,
Paula Moraga [aut]
Maintainer: Jonatan A Gonzalez <jonathan.gonzalez@kaust.edu.sa>
Diff between kernstadapt versions 0.0.1 dated 2022-09-20 and 0.0.2 dated 2022-11-15
DESCRIPTION | 12 ++++++------ MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 6 +++--- NEWS.md |only R/dens.direct.R | 4 ++-- R/dens.direct.sep.R | 2 +- R/dens.par.R | 2 +- R/dens.par.sep.R | 4 ++-- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/intensity_with_simulation.pdf |binary inst/doc/spatiotemporal_intensity.pdf |binary inst/doc/temp_intensity.pdf |binary man/dens.direct.Rd | 2 +- man/dens.direct.sep.Rd | 2 +- man/dens.par.Rd | 2 +- man/dens.par.sep.Rd | 2 +- 17 files changed, 39 insertions(+), 38 deletions(-)
Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Charles Karney [ctb] ,
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geosphere versions 1.5-14 dated 2021-10-13 and 1.5-18 dated 2022-11-15
geosphere-1.5-14/geosphere/src/dist.c |only geosphere-1.5-14/geosphere/src/geodesic.c |only geosphere-1.5-14/geosphere/src/geodesic.h |only geosphere-1.5-14/geosphere/src/geolib.c |only geosphere-1.5-14/geosphere/src/geosphere_init.c |only geosphere-1.5-14/geosphere/src/pointInPolygon.cpp |only geosphere-1.5-14/geosphere/src/util.c |only geosphere-1.5-14/geosphere/src/util.h |only geosphere-1.5-18/geosphere/DESCRIPTION | 11 +- geosphere-1.5-18/geosphere/MD5 | 75 ++++++++++++------ geosphere-1.5-18/geosphere/NAMESPACE | 3 geosphere-1.5-18/geosphere/R/RcppExports.R |only geosphere-1.5-18/geosphere/R/antipodal.R | 2 geosphere-1.5-18/geosphere/R/areaPolygon.R | 2 geosphere-1.5-18/geosphere/R/bearing.R | 2 geosphere-1.5-18/geosphere/R/daylength.R | 4 geosphere-1.5-18/geosphere/R/destPoint.R | 2 geosphere-1.5-18/geosphere/R/distGeo.R | 2 geosphere-1.5-18/geosphere/R/finalBearing.R | 2 geosphere-1.5-18/geosphere/R/gcIntermediate.R | 37 ++++++++ geosphere-1.5-18/geosphere/R/geodesic.R | 4 geosphere-1.5-18/geosphere/R/perimeter.R | 7 - geosphere-1.5-18/geosphere/build/partial.rdb |binary geosphere-1.5-18/geosphere/build/vignette.rds |binary geosphere-1.5-18/geosphere/inst/doc/geosphere.pdf |binary geosphere-1.5-18/geosphere/man/daylength.Rd | 2 geosphere-1.5-18/geosphere/src/Accumulator.cpp |only geosphere-1.5-18/geosphere/src/Accumulator.h |only geosphere-1.5-18/geosphere/src/AlbersEqualArea.cpp |only geosphere-1.5-18/geosphere/src/AlbersEqualArea.h |only geosphere-1.5-18/geosphere/src/Config.h |only geosphere-1.5-18/geosphere/src/Constants.h |only geosphere-1.5-18/geosphere/src/DST.cpp |only geosphere-1.5-18/geosphere/src/DST.h |only geosphere-1.5-18/geosphere/src/Ellipsoid.cpp |only geosphere-1.5-18/geosphere/src/Ellipsoid.h |only geosphere-1.5-18/geosphere/src/EllipticFunction.cpp |only geosphere-1.5-18/geosphere/src/EllipticFunction.h |only geosphere-1.5-18/geosphere/src/Geodesic.cpp |only geosphere-1.5-18/geosphere/src/Geodesic.h |only geosphere-1.5-18/geosphere/src/GeodesicExact.cpp |only geosphere-1.5-18/geosphere/src/GeodesicExact.h |only geosphere-1.5-18/geosphere/src/GeodesicLine.cpp |only geosphere-1.5-18/geosphere/src/GeodesicLine.h |only geosphere-1.5-18/geosphere/src/GeodesicLineExact.cpp |only geosphere-1.5-18/geosphere/src/GeodesicLineExact.h |only geosphere-1.5-18/geosphere/src/Math.cpp |only geosphere-1.5-18/geosphere/src/Math.h |only geosphere-1.5-18/geosphere/src/PolygonArea.cpp |only geosphere-1.5-18/geosphere/src/PolygonArea.h |only geosphere-1.5-18/geosphere/src/RcppExports.cpp |only geosphere-1.5-18/geosphere/src/Rhumb.cpp |only geosphere-1.5-18/geosphere/src/Rhumb.h |only geosphere-1.5-18/geosphere/src/TransverseMercator.cpp |only geosphere-1.5-18/geosphere/src/TransverseMercator.h |only geosphere-1.5-18/geosphere/src/a_dist.c |only geosphere-1.5-18/geosphere/src/a_geodesic.cpp |only geosphere-1.5-18/geosphere/src/a_util.c |only geosphere-1.5-18/geosphere/src/a_util.h |only geosphere-1.5-18/geosphere/src/kissfft.h |only 60 files changed, 111 insertions(+), 44 deletions(-)
Title: Breaks Single Page Applications from 'flexdashboard' in Multiple
Files
Description: A drop-in replacement for 'flexdashboard' 'Rmd' documents, which
implements an after-knit-hook to split the generated single page application
in one document per main section to reduce rendering load in the web browser
displaying the document. Put all 'JavaScript' stuff needed in all sections
before the first headline featuring navigation menu attributes. This package
is experimental and maybe replaced by a solution inside 'flexdashboard'.
Author: University Medicine Greifswald [cph],
Stephan Struckmann [aut, cre]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between flexsiteboard versions 0.0.6 dated 2022-09-07 and 0.0.7 dated 2022-11-15
DESCRIPTION | 11 +++++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/pandoc_read.R | 3 ++- R/pandoc_write.R | 1 + 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided. See
Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
methods and <https://examples.distancesampling.org/> for example analyses.
Author: David Lawrence Miller, T.J. Clark-Wolf
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between Distance versions 1.0.6 dated 2022-08-20 and 1.0.7 dated 2022-11-15
Distance-1.0.6/Distance/data/minke.rda |only Distance-1.0.7/Distance/DESCRIPTION | 12 Distance-1.0.7/Distance/MD5 | 241 - Distance-1.0.7/Distance/NAMESPACE | 146 Distance-1.0.7/Distance/NEWS | 405 - Distance-1.0.7/Distance/R/AIC.dsmodel.R | 86 Distance-1.0.7/Distance/R/Distance-package.R | 288 - Distance-1.0.7/Distance/R/ER_var_f.R | 226 - Distance-1.0.7/Distance/R/QAIC.R | 340 - Distance-1.0.7/Distance/R/add_df_covar_line.R | 84 Distance-1.0.7/Distance/R/bootdht.R | 658 +- Distance-1.0.7/Distance/R/bootdht_Dhat_summarize.R | 48 Distance-1.0.7/Distance/R/bootdht_Nhat_summarize.R | 48 Distance-1.0.7/Distance/R/bootdht_bootit.R | 216 Distance-1.0.7/Distance/R/bootdht_resample_data.R | 142 Distance-1.0.7/Distance/R/checkdata.R | 318 - Distance-1.0.7/Distance/R/compute_df.R | 61 Distance-1.0.7/Distance/R/convert_units.R | 130 Distance-1.0.7/Distance/R/create.bins.R | 30 Distance-1.0.7/Distance/R/create_bins.R | 96 Distance-1.0.7/Distance/R/deprecated_args.R | 32 Distance-1.0.7/Distance/R/dht2.R | 2236 +++++----- Distance-1.0.7/Distance/R/dht2_checkdata.R | 144 Distance-1.0.7/Distance/R/dht2_misc.R | 81 Distance-1.0.7/Distance/R/dht2_multipliers.R | 198 Distance-1.0.7/Distance/R/dht2_process_ddf.R |only Distance-1.0.7/Distance/R/ds.R | 1519 +++--- Distance-1.0.7/Distance/R/dsdata.R | 1088 ++-- Distance-1.0.7/Distance/R/dummy_ddf.R |only Distance-1.0.7/Distance/R/get_adj_orders.R | 43 Distance-1.0.7/Distance/R/get_truncation.R | 116 Distance-1.0.7/Distance/R/gof_ds.R | 156 Distance-1.0.7/Distance/R/logLik.dsmodel.R | 60 Distance-1.0.7/Distance/R/make_activity_fn.R | 104 Distance-1.0.7/Distance/R/model.description.R | 54 Distance-1.0.7/Distance/R/p_dist_table.R | 46 Distance-1.0.7/Distance/R/plot.dsmodel.R | 40 Distance-1.0.7/Distance/R/print.dht_result.R | 246 - Distance-1.0.7/Distance/R/print.dsmodel.R | 44 Distance-1.0.7/Distance/R/print.summary.dht_bootstrap.R | 28 Distance-1.0.7/Distance/R/safe_factorize.R | 52 Distance-1.0.7/Distance/R/safetruncate.R | 83 Distance-1.0.7/Distance/R/summarize_ds_models.R | 320 - Distance-1.0.7/Distance/R/summary.dht_bootstrap.R | 106 Distance-1.0.7/Distance/R/unflatten.R | 118 Distance-1.0.7/Distance/R/units_table.R | 194 Distance-1.0.7/Distance/R/varNhat.R | 137 Distance-1.0.7/Distance/R/variance_contributions.R | 68 Distance-1.0.7/Distance/README.md | 56 Distance-1.0.7/Distance/build/partial.rdb |binary Distance-1.0.7/Distance/data/DuikerCameraTraps.RData |binary Distance-1.0.7/Distance/data/minke.RData |only Distance-1.0.7/Distance/man/AIC.dsmodel.Rd | 64 Distance-1.0.7/Distance/man/ClusterExercise.Rd | 75 Distance-1.0.7/Distance/man/CueCountingExample.Rd | 90 Distance-1.0.7/Distance/man/Distance-package.Rd | 92 Distance-1.0.7/Distance/man/DuikerCameraTraps.Rd | 73 Distance-1.0.7/Distance/man/ETP_Dolphin.Rd | 100 Distance-1.0.7/Distance/man/LTExercise.Rd | 66 Distance-1.0.7/Distance/man/PTExercise.Rd | 58 Distance-1.0.7/Distance/man/QAIC.Rd | 214 Distance-1.0.7/Distance/man/Savannah_sparrow_1980.Rd | 88 Distance-1.0.7/Distance/man/Stratify_example.Rd | 68 Distance-1.0.7/Distance/man/Systematic_variance_1.Rd | 74 Distance-1.0.7/Distance/man/add_df_covar_line.Rd | 156 Distance-1.0.7/Distance/man/amakihi.Rd | 78 Distance-1.0.7/Distance/man/bootdht.Rd | 344 - Distance-1.0.7/Distance/man/bootdht_Dhat_summarize.Rd | 68 Distance-1.0.7/Distance/man/bootdht_Nhat_summarize.Rd | 68 Distance-1.0.7/Distance/man/capercaillie.Rd | 52 Distance-1.0.7/Distance/man/checkdata.Rd | 72 Distance-1.0.7/Distance/man/convert_units.Rd | 92 Distance-1.0.7/Distance/man/create.bins.Rd | 46 Distance-1.0.7/Distance/man/create_bins.Rd | 64 Distance-1.0.7/Distance/man/dht2.Rd | 616 +- Distance-1.0.7/Distance/man/ds.Rd | 800 +-- Distance-1.0.7/Distance/man/ds.gof.Rd | 68 Distance-1.0.7/Distance/man/ducknest.Rd | 78 Distance-1.0.7/Distance/man/dummy_ddf.Rd |only Distance-1.0.7/Distance/man/flatfile.Rd | 168 Distance-1.0.7/Distance/man/gof_ds.Rd | 186 Distance-1.0.7/Distance/man/golftees.Rd | 128 Distance-1.0.7/Distance/man/logLik.dsmodel.Rd | 66 Distance-1.0.7/Distance/man/make_activity_fn.Rd | 62 Distance-1.0.7/Distance/man/minke.Rd | 91 Distance-1.0.7/Distance/man/p_dist_table.Rd | 122 Distance-1.0.7/Distance/man/plot.dsmodel.Rd | 56 Distance-1.0.7/Distance/man/predict.dsmodel.Rd | 136 Distance-1.0.7/Distance/man/predict.fake_ddf.Rd |only Distance-1.0.7/Distance/man/print.dht_result.Rd | 40 Distance-1.0.7/Distance/man/print.dsmodel.Rd | 40 Distance-1.0.7/Distance/man/print.summary.dsmodel.Rd | 56 Distance-1.0.7/Distance/man/sikadeer.Rd | 78 Distance-1.0.7/Distance/man/summarize_ds_models.Rd | 86 Distance-1.0.7/Distance/man/summary.dht_bootstrap.Rd | 56 Distance-1.0.7/Distance/man/summary.dsmodel.Rd | 58 Distance-1.0.7/Distance/man/unflatten.Rd | 48 Distance-1.0.7/Distance/man/unimak.Rd | 72 Distance-1.0.7/Distance/man/units_table.Rd | 30 Distance-1.0.7/Distance/man/wren.Rd | 166 Distance-1.0.7/Distance/tests/testthat.R | 8 Distance-1.0.7/Distance/tests/testthat/test_adjustments.R | 271 - Distance-1.0.7/Distance/tests/testthat/test_bootdht.R | 168 Distance-1.0.7/Distance/tests/testthat/test_cluster.R | 178 Distance-1.0.7/Distance/tests/testthat/test_cuecounts.R | 294 - Distance-1.0.7/Distance/tests/testthat/test_dht.R | 138 Distance-1.0.7/Distance/tests/testthat/test_dht2.R | 466 +- Distance-1.0.7/Distance/tests/testthat/test_ds.R | 506 +- Distance-1.0.7/Distance/tests/testthat/test_golftees.R | 184 Distance-1.0.7/Distance/tests/testthat/test_inputs.R | 178 Distance-1.0.7/Distance/tests/testthat/test_minke.R | 651 +- Distance-1.0.7/Distance/tests/testthat/test_multipliers.R | 68 Distance-1.0.7/Distance/tests/testthat/test_pt.R | 158 Distance-1.0.7/Distance/tests/testthat/test_ptexercise.R | 126 Distance-1.0.7/Distance/tests/testthat/test_replicate.R | 158 Distance-1.0.7/Distance/tests/testthat/test_samplefraction.R | 136 Distance-1.0.7/Distance/tests/testthat/test_satterthwaite.R | 292 - Distance-1.0.7/Distance/tests/testthat/test_sika.R | 172 Distance-1.0.7/Distance/tests/testthat/test_simpletable.R | 140 Distance-1.0.7/Distance/tests/testthat/test_summarize.R | 138 Distance-1.0.7/Distance/tests/testthat/test_systematic_var2.R | 190 Distance-1.0.7/Distance/tests/testthat/test_truncation.R | 104 Distance-1.0.7/Distance/tests/testthat/test_unif.R |only Distance-1.0.7/Distance/tests/testthat/test_variance.R | 130 Distance-1.0.7/Distance/tests/testthat/test_wrens.R | 209 125 files changed, 10818 insertions(+), 10598 deletions(-)
Title: Analyze Big Files Without Loading Them in Memory
Description: A simple set of wrapper functions for data.table::fread() that allows subsetting or
filtering rows and selecting columns of table-formatted files too large for the available RAM.
'b stands for 'big files'.
bread makes heavy use of Unix commands like 'grep', 'sed', 'wc', 'awk' and 'cut'. They are available
by default in all Unix environments.
For Windows, you need to install those commands externally in order to simulate a
Unix environment and make sure that the executables are in the Windows PATH variable.
To my knowledge, the simplest ways are to install 'RTools', 'Git' or 'Cygwin'. If they have been
correctly installed (with the expected registry entries), they should be detected on loading
the package and the correct directories will be added automatically to the PATH.
Author: Vincent Guegan [aut, cre]
Maintainer: Vincent Guegan <vincent.guegan@banque-france.fr>
Diff between bread versions 0.2.3 dated 2022-08-08 and 0.3.1 dated 2022-11-15
DESCRIPTION | 9 MD5 | 26 +- NAMESPACE | 1 R/bcolnames.R | 75 ++--- R/bfile_split.R | 656 ++++++++++++++++++++++++++------------------------- R/bfilter.R | 11 R/bnrow.R | 65 ++--- R/bnumrange.R | 7 R/bread.R | 17 + R/bselect.R | 5 R/bsep.R | 107 ++++---- R/bsubset.R | 6 R/helper_functions.R | 31 +- man/bfile_split.Rd | 4 14 files changed, 529 insertions(+), 491 deletions(-)
Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome
association studies are implemented. These analyses include descriptive
statistics and exploratory analysis of missing values, calculation of
Hardy-Weinberg equilibrium, analysis of association based on generalized
linear models (either for quantitative or binary traits), and analysis
of multiple SNPs (haplotype and epistasis analysis). Permutation test
and related tests (sum statistic and truncated product) are also
implemented. Max-statistic and genetic risk-allele score exact
distributions are also possible to be estimated. The methods are
described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Author: Victor Moreno [aut],
Juan R Gonzalez [aut],
Dolors Pelegri [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri@isglobal.org>
Diff between SNPassoc versions 2.0-17 dated 2022-10-04 and 2.0-18 dated 2022-11-15
DESCRIPTION | 35 +++-- MD5 | 10 - NAMESPACE | 7 - R/getGeneSymbol.R | 127 ++++++++++++------- build/vignette.rds |binary inst/doc/SNPassoc.html | 322 +++++++++++++++---------------------------------- 6 files changed, 216 insertions(+), 285 deletions(-)
Title: Generation and Tracking of Super-Resolution Filamentous Datasets
Description: A pair of functions that allow for the generation and tracking of coordinate data clouds without a time dimension,
primarily for use in super-resolution plant micro-tubule image segmentation.
Author: Andrew Buist [aut, cre]
Maintainer: Andrew Buist <andrew.buist99@outlook.com>
Diff between smlmkalman versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2022-11-15
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/crescent_kf.R | 6 ++++-- R/generate_filaments.R | 8 ++++---- man/crescent_kf.Rd | 5 ++++- 6 files changed, 26 insertions(+), 17 deletions(-)
Title: Simulation-Based Landscape Construction for Dynamical Systems
Description: A toolbox for constructing potential landscapes for dynamical
systems using Monte Carlo simulation. The method is based on the
potential landscape definition by Wang et al. (2008)
<doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016
<doi:10.1063/1.4943096> for further mathematical discussions) and can
be used for a large variety of models.
Author: Jingmeng Cui [aut, cre]
Maintainer: Jingmeng Cui <jingmeng.cui@outlook.com>
Diff between simlandr versions 0.2.1 dated 2022-08-24 and 0.3.0 dated 2022-11-15
simlandr-0.2.1/simlandr/R/batch_simulation_deprecated.R |only simlandr-0.2.1/simlandr/R/landscape_plot.R |only simlandr-0.2.1/simlandr/R/undefined_global.R |only simlandr-0.2.1/simlandr/man/calculate_barrier_2d.Rd |only simlandr-0.2.1/simlandr/man/calculate_barrier_2d_batch.Rd |only simlandr-0.2.1/simlandr/man/calculate_barrier_3d.Rd |only simlandr-0.2.1/simlandr/man/calculate_barrier_3d_batch.Rd |only simlandr-0.2.1/simlandr/man/figures/README-example-1.png |only simlandr-0.2.1/simlandr/man/figures/README-example-10.png |only simlandr-0.2.1/simlandr/man/figures/README-example-11.png |only simlandr-0.2.1/simlandr/man/figures/README-example-12.png |only simlandr-0.2.1/simlandr/man/figures/README-example-13.png |only simlandr-0.2.1/simlandr/man/figures/README-example-14.png |only simlandr-0.2.1/simlandr/man/figures/README-example-2.png |only simlandr-0.2.1/simlandr/man/figures/README-example-3.png |only simlandr-0.2.1/simlandr/man/figures/README-example-4.png |only simlandr-0.2.1/simlandr/man/figures/README-example-5.png |only simlandr-0.2.1/simlandr/man/figures/README-example-6.png |only simlandr-0.2.1/simlandr/man/figures/README-example-7.png |only simlandr-0.2.1/simlandr/man/figures/README-example-8.png |only simlandr-0.2.1/simlandr/man/figures/README-example-9.png |only simlandr-0.2.1/simlandr/man/figures/README-example-l2.png |only simlandr-0.2.1/simlandr/man/figures/README-example-l3.png |only simlandr-0.2.1/simlandr/man/find_local_min_2d.Rd |only simlandr-0.2.1/simlandr/man/find_local_min_3d.Rd |only simlandr-0.2.1/simlandr/man/hash_big.matrix-class.Rd |only simlandr-0.2.1/simlandr/man/make_2d_density.Rd |only simlandr-0.2.1/simlandr/man/make_2d_kernel_dist.Rd |only simlandr-0.2.1/simlandr/man/make_3d_kernel_dist.Rd |only simlandr-0.2.1/simlandr/man/make_3d_tidy_dist.Rd |only simlandr-0.2.1/simlandr/man/make_arg_grid.Rd |only simlandr-0.2.1/simlandr/man/make_var_grid.Rd |only simlandr-0.2.1/simlandr/man/narg.Rd |only simlandr-0.2.1/simlandr/man/nele.Rd |only simlandr-0.2.1/simlandr/man/new_arg_set.Rd |only simlandr-0.2.1/simlandr/man/new_var_set.Rd |only simlandr-0.2.1/simlandr/man/npar.Rd |only simlandr-0.2.1/simlandr/man/nvar.Rd |only simlandr-0.2.1/simlandr/man/plot.barrier.Rd |only simlandr-0.2.1/simlandr/man/print.arg_grid.Rd |only simlandr-0.2.1/simlandr/man/print.arg_set.Rd |only simlandr-0.2.1/simlandr/man/print.batch_simulation.Rd |only simlandr-0.2.1/simlandr/man/print.check_conv.Rd |only simlandr-0.2.1/simlandr/man/print.var_grid.Rd |only simlandr-0.2.1/simlandr/man/print.var_set.Rd |only simlandr-0.2.1/simlandr/man/reverselog_trans.Rd |only simlandr-0.3.0/simlandr/DESCRIPTION | 35 + simlandr-0.3.0/simlandr/MD5 | 136 ++----- simlandr-0.3.0/simlandr/NAMESPACE | 43 -- simlandr-0.3.0/simlandr/NEWS.md | 42 +- simlandr-0.3.0/simlandr/R/barrier.R | 198 ++++------ simlandr-0.3.0/simlandr/R/barrier_batch.R | 143 ++----- simlandr-0.3.0/simlandr/R/batch_simulation.R | 81 ++-- simlandr-0.3.0/simlandr/R/check_conv.R | 22 - simlandr-0.3.0/simlandr/R/hash_big.R | 24 - simlandr-0.3.0/simlandr/R/kernel_api.R |only simlandr-0.3.0/simlandr/R/methods_landscape.R | 55 ++ simlandr-0.3.0/simlandr/R/multiple_simulation_landscape.R | 251 ++++++------- simlandr-0.3.0/simlandr/R/simlandr-package.R | 16 simlandr-0.3.0/simlandr/R/single_simulation_landscape.R | 263 ++------------ simlandr-0.3.0/simlandr/R/test_function.R | 3 simlandr-0.3.0/simlandr/R/utils-autolayer.R |only simlandr-0.3.0/simlandr/README.md | 164 ++++++-- simlandr-0.3.0/simlandr/inst/doc/simlandr.pdf |binary simlandr-0.3.0/simlandr/man/arg_set-class.Rd |only simlandr-0.3.0/simlandr/man/attach_all_matrices.Rd | 38 +- simlandr-0.3.0/simlandr/man/autolayer.Rd |only simlandr-0.3.0/simlandr/man/autolayer.barrier.Rd |only simlandr-0.3.0/simlandr/man/batch_simulation.Rd | 120 +++--- simlandr-0.3.0/simlandr/man/calculate_barrier.Rd | 137 ++++--- simlandr-0.3.0/simlandr/man/check_conv.Rd | 60 +-- simlandr-0.3.0/simlandr/man/figures/README-example2-1.png |only simlandr-0.3.0/simlandr/man/figures/README-example2-2.png |only simlandr-0.3.0/simlandr/man/figures/README-example2-3.png |only simlandr-0.3.0/simlandr/man/figures/README-example2-4.png |only simlandr-0.3.0/simlandr/man/figures/README-example2-5.png |only simlandr-0.3.0/simlandr/man/figures/README-example3-1.png |only simlandr-0.3.0/simlandr/man/figures/README-example3-2.png |only simlandr-0.3.0/simlandr/man/figures/README-example3-3.png |only simlandr-0.3.0/simlandr/man/figures/README-example3-4.png |only simlandr-0.3.0/simlandr/man/fill_in_struct.Rd | 45 +- simlandr-0.3.0/simlandr/man/get_barrier_height.Rd | 13 simlandr-0.3.0/simlandr/man/get_dist.Rd | 38 +- simlandr-0.3.0/simlandr/man/get_geom.Rd | 15 simlandr-0.3.0/simlandr/man/hash_big_matrix-class.Rd |only simlandr-0.3.0/simlandr/man/make_2d_matrix.Rd | 33 + simlandr-0.3.0/simlandr/man/make_2d_static.Rd | 33 + simlandr-0.3.0/simlandr/man/make_2d_tidy_dist.Rd | 43 +- simlandr-0.3.0/simlandr/man/make_3d_animation.Rd | 36 + simlandr-0.3.0/simlandr/man/make_3d_matrix.Rd | 86 ++-- simlandr-0.3.0/simlandr/man/make_3d_static.Rd | 86 ++-- simlandr-0.3.0/simlandr/man/make_4d_static.Rd | 88 ++-- simlandr-0.3.0/simlandr/man/make_barrier_grid_2d.Rd | 62 +-- simlandr-0.3.0/simlandr/man/make_barrier_grid_3d.Rd | 62 +-- simlandr-0.3.0/simlandr/man/make_kernel_dist.Rd |only simlandr-0.3.0/simlandr/man/modified_simulation.Rd |only simlandr-0.3.0/simlandr/man/plot.landscape.Rd | 46 +- simlandr-0.3.0/simlandr/man/save_landscape.Rd | 48 +- simlandr-0.3.0/simlandr/man/sim_fun_test.Rd | 47 +- simlandr-0.3.0/simlandr/man/summary.barrier.Rd |only simlandr-0.3.0/simlandr/vignettes/simlandr_manuscript.pdf |binary 101 files changed, 1354 insertions(+), 1258 deletions(-)
Title: Efficient Bayesian Inference for Dynamic Survival Models with
Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully
Bayesian estimation of dynamic survival models with shrinkage priors.
Details on the algorithms used are provided in Wagner (2011) <doi:10.1007/s11222-009-9164-5>,
Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and
Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.
Author: Daniel Winkler [aut, cre],
Peter Knaus [aut]
Maintainer: Daniel Winkler <daniel.winkler@wu.ac.at>
Diff between shrinkDSM versions 0.1.0 dated 2021-09-06 and 0.2.0 dated 2022-11-15
DESCRIPTION | 8 MD5 | 27 NAMESPACE | 1 R/RcppExports.R | 18 R/predict_shrinkDSM.R | 8 R/shrinkDSM.R | 1349 +++++++++++++++++++++++++----------------------- R/utilities_shrinkDSM.R | 670 ++++++++++++++--------- man/prep_tvinput.Rd |only man/shrinkDSM.Rd | 39 + src/Makevars | 4 src/Makevars.win | 2 src/RcppExports.cpp | 29 - src/do_shrinkDSM.cpp | 512 +++++++++++++----- src/init.cpp | 95 ++- src/init.h | 4 15 files changed, 1695 insertions(+), 1071 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package. M.Ballin, G.Barcar [...truncated...]
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen,
Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>
Diff between SamplingStrata versions 1.5-3 dated 2022-08-28 and 1.5-4 dated 2022-11-15
SamplingStrata-1.5-3/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-10-1.jpg |only SamplingStrata-1.5-4/SamplingStrata/DESCRIPTION | 8 SamplingStrata-1.5-4/SamplingStrata/MD5 | 34 SamplingStrata-1.5-4/SamplingStrata/NEWS | 5 SamplingStrata-1.5-4/SamplingStrata/R/aggrStrata2.R | 4 SamplingStrata-1.5-4/SamplingStrata/build/vignette.rds |binary SamplingStrata-1.5-4/SamplingStrata/inst/doc/SamplingStrata.html | 699 +-- SamplingStrata-1.5-4/SamplingStrata/inst/doc/models.html | 289 - SamplingStrata-1.5-4/SamplingStrata/inst/doc/spatial.R | 6 SamplingStrata-1.5-4/SamplingStrata/inst/doc/spatial.Rmd | 24 SamplingStrata-1.5-4/SamplingStrata/inst/doc/spatial.html | 1981 +--------- SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial.Rmd | 24 SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-10-1.jpeg |only SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-2-1.png |binary SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-3-1.png |binary SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-3-2.png |binary SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-7-1.png |binary SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-8-1.png |binary SamplingStrata-1.5-4/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-9-1.png |binary 19 files changed, 892 insertions(+), 2182 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Computationally Efficient Queue Simulation
Description: Implementation of a computationally efficient method for
simulating queues with arbitrary arrival and service times.
Please see Ebert, Wu, Mengersen & Ruggeri (2020, <doi:10.18637/jss.v095.i05>)
for further details.
Author: Anthony Ebert [aut, cre] ,
Kerrie Mengersen [ths],
Paul Wu [ths],
Fabrizio Ruggeri [ths]
Maintainer: Anthony Ebert <anthonyebert+CRAN@gmail.com>
Diff between queuecomputer versions 1.1.0 dated 2021-04-09 and 1.2.0 dated 2022-11-15
DESCRIPTION | 8 LICENSE | 678 +++++++++++----------- MD5 | 84 +- NAMESPACE | 40 - NEWS.md | 112 +-- R/RcppExports.R | 22 R/core_queuefunctions.R | 688 +++++++++++----------- R/dplyr_plugins.R | 318 +++++----- R/globals.R | 2 R/plot_functions.R | 419 ++++++------- R/post_analysis.R | 356 +++++------ R/util_stepfun.R | 266 ++++---- R/utils.R | 470 +++++++-------- R/zzz.R | 18 README.md | 428 ++++++++------ build/vignette.rds |binary inst/COPYRIGHTS | 6 inst/doc/Howto.R | 154 ++--- inst/doc/Howto.Rmd | 232 +++---- inst/doc/Howto.html | 813 +++++++++++++++++---------- inst/doc/MMk_queues.R | 414 ++++++------- inst/doc/MMk_queues.Rmd | 516 ++++++++--------- inst/doc/MMk_queues.html | 1083 +++++++++++++++++++++--------------- man/as.server.list.Rd | 56 - man/as.server.stepfun.Rd | 78 +- man/average_queue.Rd | 50 - man/depart.Rd | 50 - man/lag_step.Rd | 70 +- man/plot.queue_list.Rd | 115 +-- man/print.summary_queue_list.Rd | 82 +- man/ql_summary.Rd | 50 - man/queue.Rd | 88 +- man/queue_lengths.Rd | 152 ++--- man/queue_step.Rd | 139 ++-- man/summary.queue_list.Rd | 32 - man/wait_step.Rd | 126 ++-- src/RcppExports.cpp | 5 src/loops.cpp | 2 tests/testthat.R | 10 tests/testthat/test_addons.R | 96 +-- tests/testthat/test_deterministic.R | 474 +++++++-------- vignettes/Howto.Rmd | 232 +++---- vignettes/MMk_queues.Rmd | 516 ++++++++--------- 43 files changed, 5047 insertions(+), 4503 deletions(-)
Title: Analyse Biological Time-Series Data
Description: Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007&g [...truncated...]
Author: Lakshman Abhilash [aut, cre]
Maintainer: Lakshman Abhilash <labhilash@gc.cuny.edu>
Diff between phase versions 1.2.6 dated 2022-11-05 and 1.2.7 dated 2022-11-15
DESCRIPTION | 6 +-- MD5 | 6 +-- R/indSomnogram.R | 102 +++++++++++++++++++++++----------------------------- man/indSomnogram.Rd | 2 - 4 files changed, 52 insertions(+), 64 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
Author: Matteo Magnani [aut, cre],
Luca Rossi [aut] ,
Davide Vega [aut] ,
Obaida Hanteer [ctb]
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 4.1 dated 2022-09-12 and 4.1.1 dated 2022-11-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ src/src/core/attributes/Value.hpp | 12 ++++++------ 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Lightweight parallel code execution, local or distributed across
the network. Designed for simplicity, a 'mirai' evaluates an arbitrary
expression asynchronously, resolving automatically upon completion.
Built on 'nanonext' and 'NNG' (Nanomsg Next Gen) scalability protocols,
defaults to the optimal choice of abstract sockets, Unix domain sockets or
named pipes in addition to TCP/IP.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.7.0 dated 2022-10-19 and 0.7.1 dated 2022-11-15
DESCRIPTION | 19 ++- MD5 | 37 +++---- NAMESPACE | 2 NEWS.md | 7 + R/mirai-package.R | 29 +++-- R/mirai.R | 236 ++++++++++++++++++++++++++++------------------ R/pipe.R | 4 README.md | 86 ++++++++++------ man/call_mirai.Rd | 28 +++-- man/daemons.Rd | 51 +++++---- man/eval_mirai.Rd | 48 ++++----- man/is_error_value.Rd | 8 - man/is_mirai.Rd | 4 man/is_mirai_error.Rd | 4 man/is_mirai_interrupt.Rd |only man/mirai-package.Rd | 22 +++- man/server.Rd | 7 - man/stop_mirai.Rd | 10 - man/unresolved.Rd | 18 +-- tests/tests.R | 20 ++- 20 files changed, 392 insertions(+), 248 deletions(-)
Title: Some 'MASS' Enhancements
Description: Some enhancements, extensions and additions
to the facilities of the recommended 'MASS' package
that are useful mainly for teaching purposes, with
more convenient default settings and user interfaces.
Key functions from 'MASS' are imported and re-exported
to avoid masking conflicts. In addition we provide
some additional functions mainly used to illustrate
coding paradigms and techniques, such as Gramm-Schmidt
orthogonalisation and generalised eigenvalue problems.
Author: Bill Venables
Maintainer: Bill Venables <bill.venables@gmail.com>
Diff between MASSExtra versions 1.1.2 dated 2021-05-02 and 1.2.0 dated 2022-11-15
DESCRIPTION | 8 - MD5 | 14 +- NAMESPACE | 13 ++ R/avoid.R |only build/vignette.rds |binary inst/doc/rationale.html | 251 +++++++++++++++++++++++++++--------------------- man/as_complex.Rd |only man/avoid.Rd |only man/unitChange.Rd |only man/usr2in.Rd |only man/xy-class.Rd |only 11 files changed, 173 insertions(+), 113 deletions(-)
Title: K-Medians
Description: Online, Semi-online, and Offline K-medians algorithms are
given. For both methods, the algorithms can be initialized
randomly or with the help of a robust hierarchical
clustering. The number of clusters can be selected with the
help of a penalized criterion. We provide functions to provide
robust clustering. Function gen_K() enables to generate a sample
of data following a contaminated Gaussian mixture.
Functions Kmedians() and Kmeans() consists in a K-median and a
K-means algorithms while Kplot() enables to produce graph for both
methods.
Cardot, H., Cenac, P. and Zitt, P-A. (2013). "Efficient and fast estimation of the geometric median in Hilbert spaces with an averaged stochastic gradient algorithm". Bernoulli, 19, 18-43. <doi:10.3150/11-BEJ390>.
Cardot, H. and Godichon-Baggioni, A. (2017). "Fast Estimation of the Median Covariation Matrix with Application to Online Robust Principal Components Analysis". Test, 26(3), 461-480 <doi:10.1007/s11749-016-0519-x>.
Godichon-Bagg [...truncated...]
Author: Antoine Godichon-Baggioni [aut, cre, cph],
Sobihan Surendran [aut]
Maintainer: Antoine Godichon-Baggioni <antoine.godichon_baggioni@upmc.fr>
Diff between Kmedians versions 0.2.0 dated 2022-09-15 and 1.2.0 dated 2022-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Final.R | 4 ++-- build/partial.rdb |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Efficient Sequential and Batch Estimation of Univariate and
Bivariate Probability Density Functions and Cumulative
Distribution Functions along with Quantiles (Univariate) and
Nonparametric Correlation (Bivariate)
Description: Facilitates estimation of full univariate and bivariate
probability density functions and cumulative distribution functions along with
full quantile functions (univariate) and nonparametric correlation
(bivariate) using Hermite series based estimators. These estimators are
particularly useful in the sequential setting (both stationary and
non-stationary) and one-pass batch estimation setting for large data sets.
Based on: Stephanou, Michael, Varughese, Melvin and Macdonald, Iain. "Sequential quantiles via Hermite series density estimation." Electronic Journal of Statistics 11.1 (2017): 570-607 <doi:10.1214/17-EJS1245>,
Stephanou, Michael and Varughese, Melvin. "On the properties of Hermite series based distribution function estimators." Metrika (2020) <doi:10.1007/s00184-020-00785-z> and Stephanou, Michael and Varughese, Melvin. "Sequential estimation of Spearman rank correlation using Hermite series estimators." Journal of Multivariate Analysis (2021) <doi:10.1016/j.jmv [...truncated...]
Author: Michael Stephanou [aut, cre],
Melvin Varughese [ctb]
Maintainer: Michael Stephanou <michael.stephanou@gmail.com>
Diff between hermiter versions 2.1.0 dated 2021-11-16 and 2.2.0 dated 2022-11-15
hermiter-2.1.0/hermiter/man/hermite_function_sum.Rd |only hermiter-2.1.0/hermiter/man/update_batch.Rd |only hermiter-2.1.0/hermiter/man/update_batch.hermite_estimator_bivar.Rd |only hermiter-2.1.0/hermiter/man/update_batch.hermite_estimator_univar.Rd |only hermiter-2.2.0/hermiter/DESCRIPTION | 16 hermiter-2.2.0/hermiter/MD5 | 118 hermiter-2.2.0/hermiter/NAMESPACE | 26 hermiter-2.2.0/hermiter/NEWS.md | 27 hermiter-2.2.0/hermiter/R/RcppExports.R | 19 hermiter-2.2.0/hermiter/R/hermite_estimator.R | 244 hermiter-2.2.0/hermiter/R/hermite_estimator_bivar.R | 428 - hermiter-2.2.0/hermiter/R/hermite_estimator_univar.R | 396 hermiter-2.2.0/hermiter/R/sysdata.rda |binary hermiter-2.2.0/hermiter/R/utils.R | 113 hermiter-2.2.0/hermiter/README.md | 136 hermiter-2.2.0/hermiter/build/partial.rdb |binary hermiter-2.2.0/hermiter/build/vignette.rds |binary hermiter-2.2.0/hermiter/inst/CITATION |only hermiter-2.2.0/hermiter/inst/doc/hermiter.R | 55 hermiter-2.2.0/hermiter/inst/doc/hermiter.Rmd | 68 hermiter-2.2.0/hermiter/inst/doc/hermiter.html | 4175 ++++++++-- hermiter-2.2.0/hermiter/man/cum_prob.Rd | 13 hermiter-2.2.0/hermiter/man/cum_prob.hermite_estimator_bivar.Rd | 13 hermiter-2.2.0/hermiter/man/cum_prob.hermite_estimator_univar.Rd | 11 hermiter-2.2.0/hermiter/man/dens.Rd | 13 hermiter-2.2.0/hermiter/man/dens.hermite_estimator_bivar.Rd | 13 hermiter-2.2.0/hermiter/man/dens.hermite_estimator_univar.Rd | 11 hermiter-2.2.0/hermiter/man/hermite_estimator.Rd | 34 hermiter-2.2.0/hermiter/man/hermite_estimator_bivar.Rd | 20 hermiter-2.2.0/hermiter/man/hermite_estimator_univar.Rd | 19 hermiter-2.2.0/hermiter/man/hermite_function.Rd | 5 hermiter-2.2.0/hermiter/man/hermite_function_N.Rd | 5 hermiter-2.2.0/hermiter/man/hermite_function_sum_N.Rd | 5 hermiter-2.2.0/hermiter/man/hermite_function_sum_serial.Rd |only hermiter-2.2.0/hermiter/man/hermite_int_lower.Rd | 10 hermiter-2.2.0/hermiter/man/hermite_int_upper.Rd | 10 hermiter-2.2.0/hermiter/man/hermite_normalization.Rd | 3 hermiter-2.2.0/hermiter/man/hermite_normalization_N.Rd | 5 hermiter-2.2.0/hermiter/man/initialize_batch_bivar.Rd |only hermiter-2.2.0/hermiter/man/initialize_batch_univar.Rd |only hermiter-2.2.0/hermiter/man/kendall.Rd | 9 hermiter-2.2.0/hermiter/man/kendall.hermite_estimator_bivar.Rd | 12 hermiter-2.2.0/hermiter/man/merge_hermite.Rd | 12 hermiter-2.2.0/hermiter/man/merge_hermite_univar.Rd | 7 hermiter-2.2.0/hermiter/man/merge_pair.Rd | 17 hermiter-2.2.0/hermiter/man/merge_pair.hermite_estimator_bivar.Rd | 6 hermiter-2.2.0/hermiter/man/merge_pair.hermite_estimator_univar.Rd | 13 hermiter-2.2.0/hermiter/man/print.hermite_estimator_bivar.Rd | 4 hermiter-2.2.0/hermiter/man/print.hermite_estimator_univar.Rd | 4 hermiter-2.2.0/hermiter/man/quant.Rd | 17 hermiter-2.2.0/hermiter/man/quant.hermite_estimator_univar.Rd | 9 hermiter-2.2.0/hermiter/man/spearmans.Rd | 18 hermiter-2.2.0/hermiter/man/spearmans.hermite_estimator_bivar.Rd | 12 hermiter-2.2.0/hermiter/man/summary.hermite_estimator_bivar.Rd | 6 hermiter-2.2.0/hermiter/man/summary.hermite_estimator_univar.Rd | 5 hermiter-2.2.0/hermiter/man/update_sequential.Rd | 7 hermiter-2.2.0/hermiter/man/update_sequential.hermite_estimator_bivar.Rd | 8 hermiter-2.2.0/hermiter/man/update_sequential.hermite_estimator_univar.Rd | 8 hermiter-2.2.0/hermiter/src/Makevars |only hermiter-2.2.0/hermiter/src/Makevars.win |only hermiter-2.2.0/hermiter/src/RcppExports.cpp | 33 hermiter-2.2.0/hermiter/src/hermite_utils.cpp | 67 hermiter-2.2.0/hermiter/tests/testthat/test_hermite_estimator.R | 180 hermiter-2.2.0/hermiter/tests/testthat/test_hermite_estimator_bivar.R | 187 hermiter-2.2.0/hermiter/vignettes/hermiter.Rmd | 68 65 files changed, 4782 insertions(+), 1938 deletions(-)
Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between distrEx versions 2.8.0 dated 2019-03-29 and 2.9.0 dated 2022-11-15
distrEx-2.8.0/distrEx/tests |only distrEx-2.9.0/distrEx/DESCRIPTION | 16 - distrEx-2.9.0/distrEx/MD5 | 30 +- distrEx-2.9.0/distrEx/R/Expectation.R | 209 ++++++++++------ distrEx-2.9.0/distrEx/R/Functionals.R | 326 ++++++++++++++++++-------- distrEx-2.9.0/distrEx/R/KolmogorovDist.R | 18 - distrEx-2.9.0/distrEx/R/Kurtosis.R | 112 +++++--- distrEx-2.9.0/distrEx/R/Skewness.R | 104 +++++--- distrEx-2.9.0/distrEx/R/distrExOptions.R | 3 distrEx-2.9.0/distrEx/R/sysdata.rda |binary distrEx-2.9.0/distrEx/inst/NEWS | 17 + distrEx-2.9.0/distrEx/man/0distrEx-package.Rd | 48 --- distrEx-2.9.0/distrEx/man/E.Rd | 68 +++-- distrEx-2.9.0/distrEx/man/KolmogorovDist.Rd | 14 - distrEx-2.9.0/distrEx/man/Var.Rd | 136 +++++----- distrEx-2.9.0/distrEx/man/distrExOptions.Rd | 4 16 files changed, 691 insertions(+), 414 deletions(-)
Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Jens Oehlschlaegel [aut, cre], Brian Ripley [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 4.0.4 dated 2020-08-04 and 4.0.5 dated 2022-11-15
bit-4.0.4/bit/inst/doc/bit-demo.html |only bit-4.0.4/bit/inst/doc/bit-performance.html |only bit-4.0.4/bit/inst/doc/bit-usage.html |only bit-4.0.5/bit/DESCRIPTION | 10 +- bit-4.0.5/bit/MD5 | 22 ++--- bit-4.0.5/bit/NEWS | 11 ++ bit-4.0.5/bit/R/bit-package.R | 37 ++++++--- bit-4.0.5/bit/R/clone.R | 1 bit-4.0.5/bit/build/vignette.rds |binary bit-4.0.5/bit/inst/doc/bit-demo.pdf |only bit-4.0.5/bit/inst/doc/bit-performance.pdf |only bit-4.0.5/bit/inst/doc/bit-usage.pdf |only bit-4.0.5/bit/src/bit.c | 115 ++++++++++++++++++++++------ bit-4.0.5/bit/src/chunkutil.c | 2 bit-4.0.5/bit/src/init.c | 2 15 files changed, 149 insertions(+), 51 deletions(-)
Title: Partition/Decomposition of Breeding Values by Paths of
Information
Description: A software that implements a method for partitioning genetic trends to
quantify the sources of genetic gain in breeding programmes.
The partitioning method is described in Garcia-Cortes et al.
(2008) <doi:10.1017/S175173110800205X>. The package includes the
main function AlphaPart for partitioning breeding values and auxiliary
functions for manipulating data and summarizing, visualizing, and saving
results.
Author: Gregor Gorjanc [aut, cre] ,
Jana Obsteter [aut] ,
Thiago de Paula Oliveira [aut]
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>
Diff between AlphaPart versions 0.9.7 dated 2022-09-23 and 0.9.8 dated 2022-11-15
DESCRIPTION | 8 +++--- MD5 | 24 +++++++++---------- R/AlphaPart.R | 45 +++++++++++++++++++++---------------- R/dataMethods.R | 3 +- R/methods.R | 17 ++++++++------ R/write.csv.R | 22 ++++++++++-------- build/partial.rdb |binary inst/doc/alphapart-variance.html | 6 +++- inst/doc/alphapart-vignette.html | 4 +-- man/AlphaPart.Rd | 47 ++++++++++++++++++++++++--------------- man/mapLevels.Rd | 3 +- man/summary.AlphaPart.Rd | 18 +++++++++----- man/write.csv.Rd | 22 +++++++++++------- 13 files changed, 129 insertions(+), 90 deletions(-)
Title: Manage Data from Cardiopulmonary Exercise Testing
Description: Import, process, summarize and visualize raw data from
metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Author: Simon Nolte [aut, cre] ,
Manuel Ramon [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>),
James Hunter [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>)
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>
Diff between spiro versions 0.1.1 dated 2022-08-26 and 0.1.2 dated 2022-11-15
DESCRIPTION | 6 MD5 | 62 NEWS.md | 23 R/add_bodymass.R | 10 R/add_heartrate.R | 1 R/add_protocol.R | 48 R/spiro_import.R | 46 R/spiro_interpolate.R | 2 R/spiro_max.R | 5 R/spiro_plot.R | 196 R/spiro_smooth.R | 3 R/spiro_summary.R | 2 README.md | 18 inst/CITATION | 4 inst/WORDLIST | 2 inst/doc/import_processing.Rmd | 2 inst/doc/import_processing.html | 77 inst/doc/summarizing_plotting.html | 19 man/add_bodymass.Rd | 4 man/figures/README-example-1.png |binary man/set_protocol.Rd | 14 man/spiro_import.Rd | 2 tests/testthat/_snaps/add_hr.md | 110 tests/testthat/_snaps/add_protocol.md | 120 tests/testthat/_snaps/spiro.md | 3422 +-- tests/testthat/_snaps/spiro_import.md | 4146 ++-- tests/testthat/_snaps/spiro_max.md | 50 tests/testthat/_snaps/spiro_plot.md | 32 tests/testthat/_snaps/spiro_smooth.md |34120 ++++++++++++++++----------------- tests/testthat/_snaps/spiro_summary.md | 314 tests/testthat/test-add_protocol.R | 10 vignettes/import_processing.Rmd | 2 32 files changed, 21482 insertions(+), 21390 deletions(-)
Title: Microbiome Regression-Based Analysis Tests
Description: Test for overall association between microbiome composition data
and phenotypes via phylogenetic kernels. The phenotype can be univariate
continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>),
survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>),
multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and
structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>).
The package can also use robust regression (unpublished work) and
integrated quantile regression (Wang et al. (2021) <doi:10.1093/bioinformatics/btab668>).
In each case, the microbiome community effect is modeled nonparametrically
through a kernel function, which can incorporate phylogenetic tree information.
Author: Anna Plantinga [aut, cre],
Nehemiah Wilson [aut, ctb],
Haotian Zheng [aut, ctb],
Tianying Wang [aut, ctb],
Xiang Zhan [aut, ctb],
Michael Wu [aut],
Ni Zhao [aut, ctb],
Jun Chen [aut]
Maintainer: Anna Plantinga <amp9@williams.edu>
Diff between MiRKAT versions 1.2.1 dated 2021-09-24 and 1.2.2 dated 2022-11-15
DESCRIPTION | 11 MD5 | 44 +- R/GLMMMiRKAT.R | 25 - R/KRV.R | 19 R/MMiRKAT.R | 10 R/MiRKAT.R | 10 R/MiRKATS.R | 12 R/MiRKAT_Q.R | 10 R/MiRKAT_R.R | 10 R/MiRKAT_iQ.R | 10 build/vignette.rds |binary inst/doc/MiRKAT_Vignette.R | 37 + inst/doc/MiRKAT_Vignette.Rmd | 45 +- inst/doc/MiRKAT_Vignette.html | 848 ++++++++++++++++++++++++++++++++++++------ man/GLMMMiRKAT.Rd | 25 - man/KRV.Rd | 19 man/MMiRKAT.Rd | 10 man/MiRKAT.Q.Rd | 10 man/MiRKAT.R.Rd | 10 man/MiRKAT.Rd | 10 man/MiRKAT.iQ.Rd | 10 man/MiRKATS.Rd | 12 vignettes/MiRKAT_Vignette.Rmd | 45 +- 23 files changed, 989 insertions(+), 253 deletions(-)
Title: Thematic Plots for Mazama Spatial Datasets
Description: A suite of convenience functions for generating US state and county
thematic maps using datasets from the MazamaSpatialUtils package.
Author: Jonathan Callahan [aut, cre],
Rachel Carroll [aut],
Eli Grosman [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialPlots versions 0.1.2 dated 2021-09-16 and 0.2.0 dated 2022-11-15
MazamaSpatialPlots-0.1.2/MazamaSpatialPlots/man/validateLonLat.Rd |only MazamaSpatialPlots-0.1.2/MazamaSpatialPlots/man/validateLonsLats.Rd |only MazamaSpatialPlots-0.1.2/MazamaSpatialPlots/vignettes/articles/Creating_State_Maps_files |only MazamaSpatialPlots-0.1.2/MazamaSpatialPlots/vignettes/articles/Opportunity_Insights_files |only MazamaSpatialPlots-0.1.2/MazamaSpatialPlots/vignettes/articles/Working_with_Locations.Rmd |only MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/DESCRIPTION | 13 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/MD5 | 52 +- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/NAMESPACE | 5 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/NEWS.md | 6 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/R/countyMap.R | 128 +++--- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/R/data.R | 32 - MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/R/stateMap.R | 82 ++-- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/R/utils-validation.R | 78 ---- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/build/vignette.rds |binary MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/data/USCensusCounties_02.rda |binary MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/data/USCensusStates_02.rda |binary MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/data/example_US_countyCovid.rda |binary MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/data/example_US_stateObesity.rda |binary MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/inst/doc/MazamaSpatialPlots.Rmd | 4 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/inst/doc/MazamaSpatialPlots.html | 184 ++++++---- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/man/USCensusCounties_02.Rd | 16 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/man/USCensusStates_02.Rd | 16 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/man/countyMap.Rd | 12 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/man/stateMap.Rd | 4 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/tests/testthat/test-countyMap.R | 43 +- MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/tests/testthat/test-stateMap.R | 34 - MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/vignettes/MazamaSpatialPlots.Rmd | 4 MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/vignettes/articles/Creating_County_Maps.Rmd | 20 - MazamaSpatialPlots-0.2.0/MazamaSpatialPlots/vignettes/articles/Creating_State_Maps.Rmd | 14 29 files changed, 360 insertions(+), 387 deletions(-)
More information about MazamaSpatialPlots at CRAN
Permanent link
Title: Download Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut], Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geodata versions 0.4-11 dated 2022-10-02 and 0.4-13 dated 2022-11-15
geodata-0.4-11/geodata/inst/ex/oldcountries.rds |only geodata-0.4-11/geodata/man/crop_calendar_Sachs.Rd |only geodata-0.4-13/geodata/DESCRIPTION | 8 - geodata-0.4-13/geodata/MD5 | 39 ++++---- geodata-0.4-13/geodata/R/crop_sacks.R | 20 +++- geodata-0.4-13/geodata/R/crops_monfreda.R | 98 +++++++++++++++++----- geodata-0.4-13/geodata/R/helper-functions.R | 2 geodata-0.4-13/geodata/R/landuse.R | 24 +++++ geodata-0.4-13/geodata/R/occurrence.R | 91 +++++++++++++++++--- geodata-0.4-13/geodata/R/worldclim.R | 53 +++++++++-- geodata-0.4-13/geodata/R/zzz.R | 2 geodata-0.4-13/geodata/build/partial.rdb |binary geodata-0.4-13/geodata/inst/ex/countries.rds |binary geodata-0.4-13/geodata/inst/ex/tiles.rds |only geodata-0.4-13/geodata/man/crop_calendar_Sacks.Rd |only geodata-0.4-13/geodata/man/crop_monfreda.Rd | 13 +- geodata-0.4-13/geodata/man/cropland.Rd | 2 geodata-0.4-13/geodata/man/elevation.Rd | 2 geodata-0.4-13/geodata/man/footprint.Rd |only geodata-0.4-13/geodata/man/geodata-package.Rd | 1 geodata-0.4-13/geodata/man/landcover.Rd | 6 - geodata-0.4-13/geodata/man/sp_occurrence.Rd | 19 +++- geodata-0.4-13/geodata/man/worldclim.Rd | 27 ++++-- 23 files changed, 313 insertions(+), 94 deletions(-)
Title: Discrete Multivariate Probability Distributions
Description: Provides an object class for dealing with many multivariate
probability distributions at once, useful for simulation.
Author: Robin Evans [aut, cre]
Maintainer: Robin Evans <evans@stats.ox.ac.uk>
Diff between contingency versions 0.0.6 dated 2021-01-29 and 0.0.9 dated 2022-11-15
DESCRIPTION | 9 -- MD5 | 21 ++--- NAMESPACE | 5 + R/capply.R | 22 +++++ R/entropy.R | 59 ++++++++++++++ R/probMat.R | 11 ++ build/vignette.rds |binary inst/doc/tables.html | 176 ++++++++++++++++++++++++++----------------- man/multiInf.Rd |only man/repTables.Rd |only man/tables.Rd |only tests/testthat/test_capply.R | 10 ++ tests/testthat/test_kl.R | 11 ++ 13 files changed, 241 insertions(+), 83 deletions(-)
Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb] ,
Dianne Cook [aut, cre] ,
Nick Spyrison [ctb],
Ursula Laa [ctb] ,
H. Sherry Zhang [ctb],
Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between tourr versions 0.6.1 dated 2022-08-25 and 0.6.2 dated 2022-11-15
DESCRIPTION | 12 +++--- MD5 | 73 ++++++++++++++++++++----------------- NAMESPACE | 2 + NEWS.md | 15 +++++++ R/animate.r | 2 - R/data.r | 16 ++++++++ R/display-slice.r | 87 ++++++++++++++++++++++++++++++++++++++++----- R/geodesic.r | 4 +- R/history.r | 13 +++--- R/interesting-indices.r | 15 ++++--- R/linear-algebra.r | 19 ++++++++- R/manual_slice.r |only R/path-andrews.r | 4 +- R/path-dist.r | 23 ++++++----- R/path-index.r | 14 +++---- R/render.r | 9 +++- R/search_polish.r | 13 +++--- R/tour-guided-section.r | 2 - R/tour-guided.r | 2 - R/tour.r | 2 - data/t1.rda |only inst/doc/edges.html | 6 +-- inst/doc/tourr.html | 22 +++++------ man/animate.Rd | 2 - man/display_slice.Rd | 9 +++- man/draw_slice_center.Rd |only man/geodesic_path.Rd | 2 - man/guided_section_tour.Rd | 2 - man/guided_tour.Rd | 2 - man/manual_slice.Rd |only man/orthonormalise_by.Rd | 3 + man/path_curves.Rd | 4 +- man/path_dist.Rd | 23 ++++++----- man/path_index.Rd | 6 +-- man/paths_index.Rd | 8 ++-- man/render.Rd | 2 - man/save_history.Rd | 13 +++--- man/search_polish.Rd | 13 +++--- man/t1.Rd |only man/tourr-package.Rd | 2 - 40 files changed, 288 insertions(+), 158 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] ,
Jakub Nowosad [aut, cre] ,
Robin Lovelace [aut] ,
Angelos Mimis [ctb],
Mark Monmonier [ctb] ,
Greg Snow [ctb]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 2.2.0 dated 2022-08-31 and 2.2.1 dated 2022-11-15
DESCRIPTION | 8 +++++--- MD5 | 10 ++++++++-- R/depmunic.R |only R/properties.R |only README.md | 6 ++++-- data/depmunic.rda |only data/properties.rda |only man/depmunic.Rd |only man/properties.Rd |only 9 files changed, 17 insertions(+), 7 deletions(-)
Title: r Client for OpenRefine API
Description: 'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Author: VP Nagraj [aut, cre]
Maintainer: VP Nagraj <nagraj@nagraj.net>
Diff between rrefine versions 2.0.0 dated 2021-11-14 and 2.1.0 dated 2022-11-15
DESCRIPTION | 8 ++--- MD5 | 13 ++++---- NAMESPACE | 1 NEWS.md | 12 ++++++++ R/utils.R | 61 +++++++++++++++++++++++++++++++++++++++++ README.md | 1 inst/doc/rrefine-vignette.html | 4 +- man/refine_project_summary.Rd |only 8 files changed, 88 insertions(+), 12 deletions(-)
Title: Analyze Dependency Heaviness of R Packages
Description: A new metric named 'dependency heaviness' is proposed that measures the number
of additional dependency packages that a parent package brings to its child package
and are unique to the dependency packages imported by all other parents.
The dependency heaviness analysis is visualized by a customized heatmap.
The package is described in <doi:10.1093/bioinformatics/btac449>. We have also performed
the dependency heaviness analysis on the CRAN/Bioconductor package ecosystem and the results
are implemented as a web-based database which provides comprehensive tools for
querying dependencies of individual R packages.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between pkgndep versions 1.2.0 dated 2022-08-30 and 1.2.1 dated 2022-11-15
DESCRIPTION | 8 +- MD5 | 68 ++++++++++---------- NAMESPACE | 6 + NEWS | 9 ++ R/load_data.R | 10 +- R/pkgndep.R | 31 ++++++++- R/plot.R | 21 +++++- R/stat.R | 23 +++++- R/version.R |only R/website.R | 22 ++++++ inst/doc/co_heaviness.R | 2 inst/doc/co_heaviness.Rmd | 2 inst/doc/co_heaviness.html | 2 inst/doc/database.Rmd | 2 inst/doc/database.html | 2 inst/doc/pkgndep.R | 10 +- inst/doc/pkgndep.Rmd | 16 ++-- inst/doc/pkgndep.html | 30 ++++---- inst/extdata/analysis.R | 35 ++++++++++ inst/website/dependency_diagram.svg | 2 inst/website/lib.R | 2 inst/website/template/downstream_dependency.html | 15 +++- inst/website/template/upstream_dependency.html | 2 man/dependency_database.Rd |only man/dependency_heatmap.Rd |only man/get_all_functions_imported_to_children.Rd |only man/heaviness_db.Rd |only man/heaviness_on_downstream.Rd | 3 man/load_all_pkg_dep.Rd | 2 man/load_pkg_db.Rd | 4 - man/load_pkg_downstream_dependency_path_snapshot.Rd | 2 man/load_pkg_stat_snapshot.Rd | 2 man/pkgndep.Rd | 2 man/plot.pkgndep.Rd | 24 +------ man/print.heaviness_db_info.Rd |only vignettes/co_heaviness.Rmd | 2 vignettes/database.Rmd | 2 vignettes/pkgndep.Rmd | 16 ++-- 38 files changed, 253 insertions(+), 126 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.12.0 dated 2022-10-04 and 0.13.0 dated 2022-11-15
DESCRIPTION | 6 - MD5 | 24 ++--- R/trans_abund.R | 19 ++-- R/trans_alpha.R | 124 ++++++++++++++++++----------- R/trans_beta.R | 222 ++++++++++++++++++++++++++++------------------------- R/trans_diff.R | 121 +++++++++++++++++----------- R/trans_env.R | 99 ++++++++++++++--------- R/trans_network.R | 17 ++-- man/trans_abund.Rd | 4 man/trans_alpha.Rd | 17 ++-- man/trans_beta.Rd | 91 ++++++++++++--------- man/trans_diff.Rd | 21 +++-- man/trans_env.Rd | 24 ++--- 13 files changed, 455 insertions(+), 334 deletions(-)
Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for
Gaussian finite mixture modeling by including:
density estimation for data with bounded support
(Scrucca, 2019 <doi:10.1002/bimj.201800174>);
modal clustering using MEM algorithm for Gaussian mixtures
(Scrucca, 2021 <doi:10.1002/sam.11527>);
entropy estimation via Gaussian mixture modeling
(Robin & Scrucca, 2023 <doi:10.1016/j.csda.2022.107582>).
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclustAddons versions 0.6 dated 2021-12-17 and 0.7 dated 2022-11-15
DESCRIPTION | 14 + MD5 | 34 ++-- NAMESPACE | 17 ++ NEWS.md | 7 R/EntropyGMM.R |only R/ModalEM.R | 11 - R/RcppExports.R | 8 + R/densityMclustBounded.R | 34 ++-- R/util.R | 23 ++- R/zzz.R |only build/vignette.rds |binary inst/doc/mclustAddons.R | 34 ++++ inst/doc/mclustAddons.Rmd | 59 +++++++ inst/doc/mclustAddons.html | 331 ++++++++++++++++++++++++++++---------------- man/EntropyGMM.Rd |only man/logsumexp.Rd |only man/mclustAddons-package.Rd |only src/RcppExports.cpp | 24 +++ src/init.c | 4 src/logsumexp.cpp |only vignettes/mclustAddons.Rmd | 59 +++++++ 21 files changed, 498 insertions(+), 161 deletions(-)
Title: "A Practical Guide to Ecological Modelling - Using R as a
Simulation Platform"
Description: Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer.
All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11.
The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter.
Solutions to model projects are in the same subdirectories.
Author: Karline Soetaert <karline.soetaert@nioz.nl>, Peter MJ Herman <peter.herman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between ecolMod versions 1.2.6.3 dated 2022-09-04 and 1.2.6.4 dated 2022-11-15
ecolMod-1.2.6.3/ecolMod/inst/doc/examples |only ecolMod-1.2.6.3/ecolMod/inst/examples/examples.zip |only ecolMod-1.2.6.4/ecolMod/DESCRIPTION | 8 +-- ecolMod-1.2.6.4/ecolMod/MD5 | 53 --------------------- ecolMod-1.2.6.4/ecolMod/inst/doc/ecolMod.pdf |binary 5 files changed, 6 insertions(+), 55 deletions(-)
Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <wei.liu@duke-nus.edu.sg>
Diff between DR.SC versions 2.9 dated 2022-05-27 and 3.0 dated 2022-11-15
DR.SC-2.9/DR.SC/inst/doc/DR.SC.HCC1.R |only DR.SC-2.9/DR.SC/inst/doc/DR.SC.HCC1.Rmd |only DR.SC-2.9/DR.SC/inst/doc/DR.SC.HCC1.html |only DR.SC-2.9/DR.SC/vignettes/DR.SC.HCC1.Rmd |only DR.SC-3.0/DR.SC/DESCRIPTION | 16 +- DR.SC-3.0/DR.SC/MD5 | 36 ++--- DR.SC-3.0/DR.SC/NAMESPACE | 4 DR.SC-3.0/DR.SC/R/main.R | 85 +++++++++---- DR.SC-3.0/DR.SC/README.md | 59 ++++++++- DR.SC-3.0/DR.SC/build/vignette.rds |binary DR.SC-3.0/DR.SC/inst/doc/DR-SC.html | 74 ++++------- DR.SC-3.0/DR.SC/inst/doc/DR.SC.DLPFC.R |only DR.SC-3.0/DR.SC/inst/doc/DR.SC.DLPFC.Rmd |only DR.SC-3.0/DR.SC/inst/doc/DR.SC.DLPFC.html |only DR.SC-3.0/DR.SC/inst/doc/DR.SC.Simu.R | 5 DR.SC-3.0/DR.SC/inst/doc/DR.SC.Simu.Rmd | 21 ++- DR.SC-3.0/DR.SC/inst/doc/DR.SC.Simu.html | 187 +++++++++++++----------------- DR.SC-3.0/DR.SC/man/DR.SC.Rd | 16 +- DR.SC-3.0/DR.SC/man/DR.SC.fit.Rd | 4 DR.SC-3.0/DR.SC/man/getAdj.Rd | 10 - DR.SC-3.0/DR.SC/man/getAdj_auto.Rd | 4 DR.SC-3.0/DR.SC/vignettes/DR.SC.DLPFC.Rmd |only DR.SC-3.0/DR.SC/vignettes/DR.SC.Simu.Rmd | 21 ++- 23 files changed, 305 insertions(+), 237 deletions(-)
Title: Interface to the 'ASSP' Library
Description: A wrapper around Michel Scheffers's 'libassp' (<https://libassp.sourceforge.net/>).
The 'libassp' (Advanced Speech Signal Processor) library aims at providing
functionality for handling speech signal files in most common audio formats
and for performing analyses common in phonetic science/speech science. This
includes the calculation of formants, fundamental frequency, root mean
square, auto correlation, a variety of spectral analyses, zero crossing
rate, filtering etc. This wrapper provides R with a large subset of
'libassp's signal processing functions and provides them to the user in a
(hopefully) user-friendly manner.
Author: Markus Jochim [cre],
Raphael Winkelmann [aut],
Lasse Bombien [aut],
Michel Scheffers [aut]
Maintainer: Markus Jochim <markusjochim@phonetik.uni-muenchen.de>
Diff between wrassp versions 1.0.1 dated 2021-05-19 and 1.0.2 dated 2022-11-15
DESCRIPTION | 16 - MD5 | 30 +-- NEWS.md | 7 R/AsspDataObj.R | 6 README.md | 50 +++-- build/vignette.rds |binary inst/doc/wrassp_intro.Rmd | 2 inst/doc/wrassp_intro.html | 429 ++++++++++++++++++++++++++++++++++++--------- src/assp/asspfio.c | 31 --- src/assp/freqconv.c | 2 src/assp/ksv.h | 2 src/assp/math.c | 2 src/types.c | 6 src/wrassp.h | 2 src/wrassp_init.c | 6 vignettes/wrassp_intro.Rmd | 2 16 files changed, 431 insertions(+), 162 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.0-2 dated 2022-11-09 and 3.0-3 dated 2022-11-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 15 +++++++++++++++ R/pairdistlpp.R | 4 ++-- inst/doc/packagesizes.txt | 1 + src/proto.h | 2 +- 6 files changed, 28 insertions(+), 12 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] . We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genom [...truncated...]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 8.4 dated 2022-02-07 and 8.5 dated 2022-11-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/bam_endian.h | 2 +- src/bcf.h | 2 +- src/bcfutils.c | 2 +- src/bgzf.c | 2 +- src/khash.h | 2 +- src/tabix_index.c | 7 ++++--- 8 files changed, 20 insertions(+), 19 deletions(-)
Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian and weather data
<https://data.melbourne.vic.gov.au> in tidy data form.
Author: Earo Wang [aut, cre] ,
Stuart Lee [aut]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between rwalkr versions 0.5.6 dated 2021-08-16 and 0.5.7 dated 2022-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/soda.R | 7 +++---- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] ),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.9 dated 2022-08-15 and 2.2.10 dated 2022-11-15
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ build/partial.rdb |binary man/bibConvert.Rd | 6 ++++-- src/bib2be.c | 2 +- src/bibtexdirectin.c | 2 +- src/charsets.c | 2 +- src/charsets.h | 2 +- 9 files changed, 25 insertions(+), 17 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <htt [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodrìguez [aut] ,
Duncan Temple Lang [aut] ,
Sally Paganin [aut [...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.12.2 dated 2022-02-24 and 0.13.0 dated 2022-11-15
nimble-0.12.2/nimble/inst/NEWS |only nimble-0.12.2/nimble/tests/testthat/test-refactorCompilationSteps.R |only nimble-0.13.0/nimble/DESCRIPTION | 10 nimble-0.13.0/nimble/MD5 | 106 +- nimble-0.13.0/nimble/NAMESPACE | 1 nimble-0.13.0/nimble/R/BUGS_BUGSdecl.R | 4 nimble-0.13.0/nimble/R/BUGS_model.R | 125 ++- nimble-0.13.0/nimble/R/BUGS_modelDef.R | 23 nimble-0.13.0/nimble/R/BUGS_utils.R | 5 nimble-0.13.0/nimble/R/MCMC_WAIC.R | 14 nimble-0.13.0/nimble/R/MCMC_build.R | 48 + nimble-0.13.0/nimble/R/MCMC_configuration.R | 400 +++++++--- nimble-0.13.0/nimble/R/MCMC_conjugacy.R | 19 nimble-0.13.0/nimble/R/MCMC_run.R | 20 nimble-0.13.0/nimble/R/MCMC_samplers.R | 268 ++---- nimble-0.13.0/nimble/R/MCMC_utils.R | 89 +- nimble-0.13.0/nimble/R/all_utils.R | 2 nimble-0.13.0/nimble/R/cppDefs_BUGSmodel.R | 6 nimble-0.13.0/nimble/R/cppDefs_nimbleList.R | 4 nimble-0.13.0/nimble/R/cppInterfaces_nimbleFunctions.R | 8 nimble-0.13.0/nimble/R/crossValidation.R | 3 nimble-0.13.0/nimble/R/distributions_implementations.R | 9 nimble-0.13.0/nimble/R/nimbleList_core.R | 1 nimble-0.13.0/nimble/R/options.R | 7 nimble-0.13.0/nimble/R/zzz.R | 7 nimble-0.13.0/nimble/inst/CppCode/RcppNimbleUtils.cpp | 24 nimble-0.13.0/nimble/inst/CppCode/RcppUtils.cpp | 6 nimble-0.13.0/nimble/inst/CppCode/accessorClasses.cpp | 4 nimble-0.13.0/nimble/inst/CppCode/dists.cpp | 4 nimble-0.13.0/nimble/inst/CppCode/nimDists.cpp | 16 nimble-0.13.0/nimble/inst/CppCode/nimbleGraph.cpp | 16 nimble-0.13.0/nimble/inst/CppCode/predefinedNimbleLists.cpp | 11 nimble-0.13.0/nimble/inst/NEWS.md |only nimble-0.13.0/nimble/inst/include/nimble/EigenTypedefs.h | 2 nimble-0.13.0/nimble/inst/include/nimble/dynamicRegistrations.h | 16 nimble-0.13.0/nimble/inst/include/nimble/predefinedNimbleLists.h | 1 nimble-0.13.0/nimble/man/MCMCconf-class.Rd | 71 + nimble-0.13.0/nimble/man/configureMCMC.Rd | 3 nimble-0.13.0/nimble/man/getConditionallyIndependentSets.Rd | 2 nimble-0.13.0/nimble/man/modelBaseClass-class.Rd | 14 nimble-0.13.0/nimble/man/nimbleFunction.Rd | 3 nimble-0.13.0/nimble/man/nimbleFunctionVirtual.Rd | 3 nimble-0.13.0/nimble/man/samplers.Rd | 14 nimble-0.13.0/nimble/man/waic.Rd | 6 nimble-0.13.0/nimble/tests/testthat/mcemTestLog_Correct.Rout | 16 nimble-0.13.0/nimble/tests/testthat/mcmcTestLog.Rout | 46 + nimble-0.13.0/nimble/tests/testthat/mcmcTestLog_Correct.Rout | 20 nimble-0.13.0/nimble/tests/testthat/test-bnp.R | 10 nimble-0.13.0/nimble/tests/testthat/test-car.R | 9 nimble-0.13.0/nimble/tests/testthat/test-dynamicIndexing.R | 4 nimble-0.13.0/nimble/tests/testthat/test-getDependencies.R | 57 + nimble-0.13.0/nimble/tests/testthat/test-mcem.R | 3 nimble-0.13.0/nimble/tests/testthat/test-mcmc.R | 399 +++++++-- nimble-0.13.0/nimble/tests/testthat/test-nimbleList.R | 1 nimble-0.13.0/nimble/tests/testthat/test-waic.R | 29 nimble-0.13.0/nimble/tests/testthat/userTestLog.Rout |only 56 files changed, 1382 insertions(+), 607 deletions(-)
Title: Non-Additive Measure and Integral Manipulation Functions
Description: S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation in a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known M<f6>bius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach based on parametric entropies. The functions contained in Kappal [...truncated...]
Author: Michel Grabisch, Ivan Kojadinovic, Patrick Meyer.
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between kappalab versions 0.4-7 dated 2015-07-18 and 0.4-8 dated 2022-11-15
DESCRIPTION | 8 +++---- MD5 | 44 +++++++++++++++++++++---------------------- man/Mobius.set.func-class.Rd | 2 - man/card.set.func-class.Rd | 2 - man/set.func-class.Rd | 2 - man/to.data.frame-methods.Rd | 2 - src/Mobius.bounds.c | 10 ++++----- src/Mobius.bounds.h | 2 - src/cdf.Choquet.c | 2 - src/cdf.Choquet.h | 2 - src/constraints.c | 30 +++++++++++++---------------- src/constraints.h | 2 - src/core.c | 6 ++--- src/core.h | 2 - src/heuristic.ls.c | 16 +++++++-------- src/least.squares.c | 10 ++++----- src/least.squares.h | 2 - src/min.dist.c | 2 - src/min.dist.h | 2 - src/min.var.c | 2 - src/min.var.h | 2 - src/moments.Choquet.c | 2 - src/moments.Choquet.h | 2 - 23 files changed, 77 insertions(+), 79 deletions(-)
Title: Interpreting High Resolution Mass Spectra
Description: High resolution mass spectrometry yields often large data sets of spectra from
compounds which are not present in available libraries. These spectra need to be annotated
and interpreted.'InterpretMSSpectrum' provides a set of functions to perform such tasks
for Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived data
in positive and negative ionization mode.
Author: Jan Lisec [aut, cre] ,
Jaeger Carsten [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between InterpretMSSpectrum versions 1.2 dated 2018-05-06 and 1.3.3 dated 2022-11-15
InterpretMSSpectrum-1.2/InterpretMSSpectrum/data/neutral_losses.rda |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/data/test_spectrum.rda |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/DetermineIsomainPeaks.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/GetIsotopeDistribution.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/RestrictByTypicalLosses.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/ScoreFormulaCombination.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/findiso.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/getRuleFromIonSymbol.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/is.subformula.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/neutral_losses.Rd |only InterpretMSSpectrum-1.2/InterpretMSSpectrum/man/test_spectrum.Rd |only InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/DESCRIPTION | 50 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/MD5 | 91 - InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/NAMESPACE | 11 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/CountChemicalElements.R | 19 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/DetermineIsomainPeaks.R | 57 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/GenerateMetaboliteSQLiteDB.R | 102 - InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/GetGroupFactor.R | 2 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/GetIsotopeDistribution.R | 32 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/IMS_parallel.R | 53 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/InterpretMSSpectrum.R | 306 ++- InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/PlausibleFormula.R | 2 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/PlotSpec.R | 4 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/RestrictByTypicalLosses.R | 26 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/ScoreFormulaCombination.R | 39 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/data.R |only InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/findMAIN.r | 833 +++++----- InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/findiso.R | 23 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/getRuleFromIonSymbol.R | 17 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/is.subformula.R | 26 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/mScore.R | 2 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/R/sendToMSF.r | 41 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/data/param.default.RData |only InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/inst |only InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/Adducts.Rd | 41 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/CountChemicalElements.Rd | 6 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/GenerateMetaboliteSQLiteDB.Rd | 35 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/GetGroupFactor.Rd | 2 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/IMS_parallel.Rd | 16 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/InterpretMSSpectrum.Rd | 110 - InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/OrbiMS1.Rd | 41 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/PlausibleFormula.Rd | 2 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/PlotSpec.Rd | 23 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/apci_spectrum.Rd | 44 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/chemical_elements.Rd | 43 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/esi_spectrum.Rd | 44 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/findMAIN.Rd | 30 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/mScore.Rd | 13 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/neutral_losses_APCI.Rd | 71 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/neutral_losses_ESI.Rd | 71 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/param.default.Rd |only InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/sendToMSF.Rd | 25 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/man/writeMSF.Rd | 17 InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/tests |only 54 files changed, 1291 insertions(+), 1079 deletions(-)
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Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 1.0-34 dated 2021-10-14 and 2.1.16 dated 2022-11-15
growthPheno-1.0-34/growthPheno/R/data2LevOp_v1.r |only growthPheno-1.0-34/growthPheno/R/dataCart_v2.r |only growthPheno-1.0-34/growthPheno/man/probeDF.Rd |only growthPheno-1.0-34/growthPheno/tests/testthat/TestSplines.r |only growthPheno-1.0-34/growthPheno/tests/testthat/testProbeDF.r |only growthPheno-1.0-34/growthPheno/tests/testthat/testProbeSmooth.r |only growthPheno-1.0-34/growthPheno/tests/testthat/testexamplaData.r |only growthPheno-2.1.16/growthPheno/DESCRIPTION | 50 growthPheno-2.1.16/growthPheno/MD5 | 179 growthPheno-2.1.16/growthPheno/NAMESPACE | 47 growthPheno-2.1.16/growthPheno/R/PVA.v3.r | 25 growthPheno-2.1.16/growthPheno/R/S3methodsDeprecations.r | 21 growthPheno-2.1.16/growthPheno/R/byIndv.r |only growthPheno-2.1.16/growthPheno/R/byIndv4Intvl.r |only growthPheno-2.1.16/growthPheno/R/byIndv4Times.r |only growthPheno-2.1.16/growthPheno/R/calcs.r |only growthPheno-2.1.16/growthPheno/R/dataLongi_v9.r | 1876 +--------- growthPheno-2.1.16/growthPheno/R/growthPhenoUtilities.r | 68 growthPheno-2.1.16/growthPheno/R/softDeprec.r |only growthPheno-2.1.16/growthPheno/R/traitExtract.r |only growthPheno-2.1.16/growthPheno/R/traitSmooth.r |only growthPheno-2.1.16/growthPheno/R/traitUtilities.r |only growthPheno-2.1.16/growthPheno/build/partial.rdb |binary growthPheno-2.1.16/growthPheno/build/vignette.rds |binary growthPheno-2.1.16/growthPheno/data/RicePrepped.dat.rda |only growthPheno-2.1.16/growthPheno/data/RiceRaw.dat.rda |binary growthPheno-2.1.16/growthPheno/data/cart.dat.rda |binary growthPheno-2.1.16/growthPheno/data/datalist |only growthPheno-2.1.16/growthPheno/data/exampleData.rda |binary growthPheno-2.1.16/growthPheno/data/tomato.dat.rda |binary growthPheno-2.1.16/growthPheno/inst/News.Rd | 158 growthPheno-2.1.16/growthPheno/inst/doc/Rice.pdf |binary growthPheno-2.1.16/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-2.1.16/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-2.1.16/growthPheno/man/GrowthRates.Rd | 7 growthPheno-2.1.16/growthPheno/man/PVA.data.frame.Rd | 13 growthPheno-2.1.16/growthPheno/man/PVA.matrix.Rd | 13 growthPheno-2.1.16/growthPheno/man/RicePrepped.dat.Rd |only growthPheno-2.1.16/growthPheno/man/RiceRaw.dat.Rd | 4 growthPheno-2.1.16/growthPheno/man/WUI.Rd | 6 growthPheno-2.1.16/growthPheno/man/anom.Rd | 2 growthPheno-2.1.16/growthPheno/man/args4chosen_plot.Rd |only growthPheno-2.1.16/growthPheno/man/args4chosen_smooth.Rd |only growthPheno-2.1.16/growthPheno/man/args4devnboxes_plot.Rd |only growthPheno-2.1.16/growthPheno/man/args4meddevn_plot.Rd |only growthPheno-2.1.16/growthPheno/man/args4profile_plot.Rd |only growthPheno-2.1.16/growthPheno/man/args4smoothing.Rd |only growthPheno-2.1.16/growthPheno/man/as.smooths.frame.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Intvl_GRsAvg.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Intvl_GRsDiff.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Intvl_ValueCalc.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Intvl_WaterUse.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Times_GRsDiff.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv4Times_SplinesGRs.Rd |only growthPheno-2.1.16/growthPheno/man/byIndv_ValueCalc.Rd |only growthPheno-2.1.16/growthPheno/man/calcLagged.Rd | 2 growthPheno-2.1.16/growthPheno/man/calcTimes.Rd | 2 growthPheno-2.1.16/growthPheno/man/cumulate.Rd | 7 growthPheno-2.1.16/growthPheno/man/designFactors.Rd | 62 growthPheno-2.1.16/growthPheno/man/exampleData.Rd | 10 growthPheno-2.1.16/growthPheno/man/fitSpline.Rd | 184 growthPheno-2.1.16/growthPheno/man/getTimesSubset.Rd | 45 growthPheno-2.1.16/growthPheno/man/growthPheno-deprecated.Rd | 9 growthPheno-2.1.16/growthPheno/man/growthPheno-pkg.Rd | 231 - growthPheno-2.1.16/growthPheno/man/intervalGRaverage.Rd | 62 growthPheno-2.1.16/growthPheno/man/intervalGRdiff.Rd | 76 growthPheno-2.1.16/growthPheno/man/intervalPVA.data.frame.Rd | 31 growthPheno-2.1.16/growthPheno/man/intervalValueCalculate.Rd | 47 growthPheno-2.1.16/growthPheno/man/intervalWUI.Rd | 62 growthPheno-2.1.16/growthPheno/man/is.smooths.frame.Rd |only growthPheno-2.1.16/growthPheno/man/longitudinalPrime.Rd | 21 growthPheno-2.1.16/growthPheno/man/plotAnom.Rd | 62 growthPheno-2.1.16/growthPheno/man/plotCorrmatrix.Rd | 13 growthPheno-2.1.16/growthPheno/man/plotDeviationsBoxes.Rd | 28 growthPheno-2.1.16/growthPheno/man/plotImagetimes.Rd | 2 growthPheno-2.1.16/growthPheno/man/plotLongitudinal.Rd | 39 growthPheno-2.1.16/growthPheno/man/plotMedianDeviations.Rd | 67 growthPheno-2.1.16/growthPheno/man/plotProfiles.Rd |only growthPheno-2.1.16/growthPheno/man/plotSmoothsComparison.Rd |only growthPheno-2.1.16/growthPheno/man/plotSmoothsDevnBoxplots.Rd |only growthPheno-2.1.16/growthPheno/man/plotSmoothsMedianDevns.Rd |only growthPheno-2.1.16/growthPheno/man/prepImageData.Rd |only growthPheno-2.1.16/growthPheno/man/probeSmoothing.Rd | 64 growthPheno-2.1.16/growthPheno/man/probeSmooths.Rd |only growthPheno-2.1.16/growthPheno/man/rcontrib.data.frame.Rd | 15 growthPheno-2.1.16/growthPheno/man/rcontrib.matrix.Rd | 15 growthPheno-2.1.16/growthPheno/man/smoothSpline.Rd |only growthPheno-2.1.16/growthPheno/man/smooths.frame.Rd |only growthPheno-2.1.16/growthPheno/man/splitContGRdiff.Rd | 95 growthPheno-2.1.16/growthPheno/man/splitSplines.Rd | 180 growthPheno-2.1.16/growthPheno/man/splitValueCalculate.Rd | 26 growthPheno-2.1.16/growthPheno/man/tomato.dat.Rd | 17 growthPheno-2.1.16/growthPheno/man/traitExtractFeatures.Rd |only growthPheno-2.1.16/growthPheno/man/traitSmooth.Rd |only growthPheno-2.1.16/growthPheno/man/twoLevelOpcreate.Rd | 29 growthPheno-2.1.16/growthPheno/man/validSmoothsFrame.Rd |only growthPheno-2.1.16/growthPheno/tests/testthat/Rplots.pdf |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/area.dat.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/chkpeadat.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/dat1.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/raw.19.dat.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/raw.RGB.dat.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/raw.fluo.dat.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/data/testSpline.rda |binary growthPheno-2.1.16/growthPheno/tests/testthat/testContGRdiff.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testCorrPlot.r | 19 growthPheno-2.1.16/growthPheno/tests/testthat/testGRsDiff.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testPVA.r | 21 growthPheno-2.1.16/growthPheno/tests/testthat/testProbeSmoothing.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testProbeSmooths.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testRiceNoPlots.r | 238 - growthPheno-2.1.16/growthPheno/tests/testthat/testSplines.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testTomatovignette.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testTraitWrappers.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testbyIndv4Intvl.R |only growthPheno-2.1.16/growthPheno/tests/testthat/testbyIndv4Times.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testexampleData.r |only growthPheno-2.1.16/growthPheno/tests/testthat/testsmoothSpline.R |only 118 files changed, 1869 insertions(+), 2381 deletions(-)
Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between file2meco versions 0.4.0 dated 2022-08-07 and 0.5.0 dated 2022-11-15
DESCRIPTION | 10 +++---- MD5 | 28 ++++++++++----------- R/humann2meco.R | 46 ++++++++++++++++++++--------------- R/mpa2meco.R | 26 +++++++++++-------- R/ncyc2meco.R | 29 ++++++++++++---------- R/physeq2meco.R | 15 +++++++++-- R/qiime1meco.R | 49 ++++++++++++++++++++++++------------- R/qiime2meco.R | 60 ++++++++++++++++++++++++++-------------------- R/utility.R | 45 +++++++++++++++++++++++----------- man/check_sample_table.Rd | 4 +-- man/humann2meco.Rd | 38 +++++++++++++++++------------ man/mpa2meco.Rd | 20 +++++++++------ man/ncyc2meco.Rd | 19 ++++++++------ man/qiime1meco.Rd | 33 +++++++++++++++++-------- man/qiime2meco.Rd | 40 +++++++++++++++++------------- 15 files changed, 279 insertions(+), 183 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages
part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.2.2 dated 2021-01-05 and 3.3.0 dated 2022-11-15
aroma.core-3.2.2/aroma.core/NEWS |only aroma.core-3.2.2/aroma.core/R/999.DEPRECATED.R |only aroma.core-3.3.0/aroma.core/DESCRIPTION | 10 +- aroma.core-3.3.0/aroma.core/MD5 | 44 +++++----- aroma.core-3.3.0/aroma.core/NAMESPACE | 1 aroma.core-3.3.0/aroma.core/NEWS.md |only aroma.core-3.3.0/aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R | 1 aroma.core-3.3.0/aroma.core/R/AromaUnitTabularBinaryFile.writeDataFrame.R | 1 aroma.core-3.3.0/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R | 5 + aroma.core-3.3.0/aroma.core/README.md |only aroma.core-3.3.0/aroma.core/man/AbstractCNData.Rd | 2 aroma.core-3.3.0/aroma.core/man/AbstractPSCNData.Rd | 2 aroma.core-3.3.0/aroma.core/man/NonPairedPSCNData.Rd | 2 aroma.core-3.3.0/aroma.core/man/PairedPSCNData.Rd | 2 aroma.core-3.3.0/aroma.core/man/RawAlleleBFractions.Rd | 2 aroma.core-3.3.0/aroma.core/man/RawCopyNumbers.Rd | 2 aroma.core-3.3.0/aroma.core/man/RawGenomicSignals.Rd | 2 aroma.core-3.3.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2 aroma.core-3.3.0/aroma.core/man/RawSequenceReads.Rd | 2 aroma.core-3.3.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 2 aroma.core-3.3.0/aroma.core/man/SegmentedCopyNumbers.Rd | 2 aroma.core-3.3.0/aroma.core/man/segmentByMPCBS.RawGenomicSignals.Rd | 20 ++-- aroma.core-3.3.0/aroma.core/man/writeDataFrame.AromaUnitSignalBinaryFile.Rd | 1 aroma.core-3.3.0/aroma.core/man/writeDataFrame.AromaUnitTabularBinaryFile.Rd | 1 aroma.core-3.3.0/aroma.core/tests/RawGenomicSignals.SEG,MP.R | 15 +-- 25 files changed, 58 insertions(+), 63 deletions(-)