Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial
clustering of applications with noise) and OPTICS (ordering points to identify
the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier
factor) algorithm. The implementations use the kd-tree data structure (from
library ANN) for faster k-nearest neighbor search. An R interface to fast kNN
and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-0 dated 2017-03-19 and 1.1-2 dated 2018-05-18
DESCRIPTION | 15 - MD5 | 65 ++--- NEWS.md | 16 + R/AAA_definitions.R |only R/RcppExports.R | 60 ++-- R/hdbscan.R | 41 +-- R/kNN.R | 11 R/optics.R | 5 README.md | 41 +-- build/vignette.rds |binary inst/doc/dbscan.Rnw | 2 inst/doc/dbscan.pdf |binary inst/doc/hdbscan.Rmd | 22 - inst/doc/hdbscan.html | 502 +++++++++++++++++++++++++---------------- man/DS3.Rd | 2 man/NN.Rd | 18 - man/dbscan.Rd | 2 man/fosc.Rd | 4 man/frNN.Rd | 2 man/hdbscan.Rd | 6 man/kNNdist.Rd | 4 man/optics.Rd | 14 - man/reachability.Rd | 4 man/sNN.Rd | 2 src/RcppExports.cpp | 60 ++-- src/buildHDBSCAN.cpp | 7 src/init.c | 128 +++++----- src/kd_split.cpp | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-hdbscan.R | 13 - vignettes/dbscan.Rnw | 2 vignettes/figures/dbscan_a.pdf |binary vignettes/figures/dbscan_b.pdf |binary vignettes/hdbscan.Rmd | 22 - 34 files changed, 627 insertions(+), 453 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.16 dated 2018-03-13 and 0.12.17 dated 2018-05-18
ChangeLog | 73 ++++++++ DESCRIPTION | 18 +- MD5 | 90 +++++----- build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 38 +++- inst/bib/Rcpp.bib | 23 ++ inst/doc/Rcpp-FAQ.Rmd | 79 ++++----- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.Rmd | 10 - inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.R | 12 - inst/doc/Rcpp-introduction.Rmd | 211 ++++++++++++------------- inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.Rnw | 3 inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-modules.Rmd | 6 inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 23 ++ inst/include/Rcpp/Benchmark/Timer.h | 11 - inst/include/Rcpp/String.h | 10 - inst/include/Rcpp/config.h | 5 inst/include/Rcpp/internal/Proxy_Iterator.h | 2 inst/include/Rcpp/sprintf.h | 8 inst/include/Rcpp/stats/random/random.h | 2 inst/include/Rcpp/vector/00_forward_proxy.h | 26 +-- inst/include/Rcpp/vector/Vector.h | 15 - inst/include/Rcpp/vector/const_generic_proxy.h | 10 - inst/include/Rcpp/vector/const_string_proxy.h | 45 ++--- inst/include/Rcpp/vector/generic_proxy.h | 33 ++- inst/include/Rcpp/vector/proxy.h | 102 ++++++------ inst/include/Rcpp/vector/string_proxy.h | 27 ++- inst/include/Rcpp/vector/traits.h | 14 - inst/unitTests/cpp/Vector.cpp | 22 ++ inst/unitTests/runit.Vector.R | 54 ++++-- vignettes/Rcpp-FAQ.Rmd | 79 ++++----- vignettes/Rcpp-attributes.Rmd | 10 - vignettes/Rcpp-introduction.Rmd | 211 ++++++++++++------------- vignettes/Rcpp-jss-2011.Rnw | 3 vignettes/Rcpp-modules.Rmd | 6 vignettes/Rcpp.bib | 23 ++ 46 files changed, 753 insertions(+), 551 deletions(-)
Title: Process Accelerometer Data for Physical Activity Measurement
Description: It provides a function "wearingMarking" for classification of monitor
wear and nonwear time intervals in accelerometer data collected to assess
physical activity. The package also contains functions for making plot for
accelerometer data and obtaining the summary of various information including
daily monitor wear time and the mean monitor wear time during valid days.
The revised package version 0.2-1 improved the functions in the previous version
regarding speed and robustness. In addition, several functions were added:
"markDelivery" can classify days for ActiGraph delivery by mail;
"markPAI" can categorize physical activity intensity level based on user-defined
cut-points of accelerometer counts. It also supports importing ActiGraph AGD files
with "readActigraph" and "queryActigraph" functions. The package also better supports
time zones and daylight saving.
Author: Leena Choi [aut, cre],
Cole Beck [aut],
Zhouwen Liu [aut],
Charles E. Matthews [aut],
Maciej S. Buchowski [aut]
Maintainer: Leena Choi <leena.choi@Vanderbilt.Edu>
Diff between PhysicalActivity versions 0.1-1 dated 2011-11-16 and 0.2-2 dated 2018-05-18
PhysicalActivity-0.1-1/PhysicalActivity/data/.Rhistory |only PhysicalActivity-0.2-2/PhysicalActivity/DESCRIPTION | 40 + PhysicalActivity-0.2-2/PhysicalActivity/MD5 | 63 +- PhysicalActivity-0.2-2/PhysicalActivity/NAMESPACE | 23 PhysicalActivity-0.2-2/PhysicalActivity/R/PhysicalActivity-package.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/dataCollapser.R | 107 ++-- PhysicalActivity-0.2-2/PhysicalActivity/R/dataSec.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/deliveryData.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/markDelivery.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/markPAI.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/marking.R | 224 +++----- PhysicalActivity-0.2-2/PhysicalActivity/R/markingTime.R | 66 +- PhysicalActivity-0.2-2/PhysicalActivity/R/nthOccurance.R | 71 +- PhysicalActivity-0.2-2/PhysicalActivity/R/plotData.R | 153 ++++-- PhysicalActivity-0.2-2/PhysicalActivity/R/queryActigraph.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/readActigraph.R |only PhysicalActivity-0.2-2/PhysicalActivity/R/readCountsData.R | 171 ++++-- PhysicalActivity-0.2-2/PhysicalActivity/R/sumVct.R | 126 ++-- PhysicalActivity-0.2-2/PhysicalActivity/R/summaryData.R | 254 ++++++++-- PhysicalActivity-0.2-2/PhysicalActivity/R/wearingMarking.R | 166 +++++- PhysicalActivity-0.2-2/PhysicalActivity/data/deliveryData.RData |only PhysicalActivity-0.2-2/PhysicalActivity/man/PhysicalActivity-package.Rd | 140 +++-- PhysicalActivity-0.2-2/PhysicalActivity/man/agdMetaKeys.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/agdSettings.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/dataCollapser.Rd | 90 ++- PhysicalActivity-0.2-2/PhysicalActivity/man/dataSec.Rd | 51 +- PhysicalActivity-0.2-2/PhysicalActivity/man/deliveryData.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/deliveryThreshold.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/markDelivery.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/markPAI.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/marking.Rd | 71 +- PhysicalActivity-0.2-2/PhysicalActivity/man/markingTime.Rd | 59 +- PhysicalActivity-0.2-2/PhysicalActivity/man/modeNames.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/nthOccurance.Rd | 52 +- PhysicalActivity-0.2-2/PhysicalActivity/man/plotData.Rd | 151 +++-- PhysicalActivity-0.2-2/PhysicalActivity/man/queryActigraph.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/readActigraph.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/readCountsData.Rd | 64 +- PhysicalActivity-0.2-2/PhysicalActivity/man/sumVct.Rd | 117 ++-- PhysicalActivity-0.2-2/PhysicalActivity/man/summaryData.Rd | 175 ++++-- PhysicalActivity-0.2-2/PhysicalActivity/man/timeFromYear1.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/validWindow.Rd |only PhysicalActivity-0.2-2/PhysicalActivity/man/wearingMarking.Rd | 199 ++++--- 43 files changed, 1672 insertions(+), 961 deletions(-)
More information about PhysicalActivity at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-06 0.0.8
2017-04-10 0.0.4
Title: Generate Random 'WKT' or 'GeoJSON'
Description: Generate random positions (latitude/longitude),
Well-known text ('WKT') points or polygons, or 'GeoJSON' points or
polygons.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>>),
Noam Ross [aut],
Samuel Bosch [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between randgeo versions 0.2.0 dated 2017-02-28 and 0.3.0 dated 2018-05-18
DESCRIPTION | 18 LICENSE | 2 MD5 | 45 - NAMESPACE | 2 NEWS.md | 13 R/geo_linestring.R |only R/geo_point.R | 5 R/geo_polygon.R | 21 R/to_wkt.R | 8 R/wkt_linestring.R |only R/wkt_polygon.R | 2 R/zzz.R | 24 README.md | 138 ++- build/vignette.rds |binary inst/doc/randgeo_vignette.Rmd | 2 inst/doc/randgeo_vignette.html | 1481 ++++++++++++++++++++++++++++++++--- man/geo_linestring.Rd |only man/geo_point.Rd | 3 man/geo_polygon.Rd | 3 man/wkt_linestring.Rd |only man/wkt_polygon.Rd | 4 tests/testthat/test-geo_linestring.R |only tests/testthat/test-geo_point.R | 5 tests/testthat/test-geo_polygon.R | 5 tests/testthat/test-wkt_linestring.R |only tools |only vignettes/randgeo_vignette.Rmd | 2 27 files changed, 1608 insertions(+), 175 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding in Observational
Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding for either an observational study or a meta-analysis of observational studies. For a single observational study, the package reports E-values, defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the treatment and the outcome to fully explain away a specific treatment-outcome association, conditional on the measured covariates. One can use one of the evalues.XX() functions to compute E-values for the relevant outcome types. Outcome types include risk ratios, odds ratio with common or rare outcomes, hazard ratios with common or rare outcomes, and standardized differences in outcomes. Optionally, one can use the bias_plot() function to plot the bias factor as a function of two sensitivity parameters. (See VanderWeele & Ding, 2017 [<http://annals.org/aim/article/2643434>] for details.) For a meta-analysis, use the function confounded_meta to compute point estimates and inference for: (1) the proportion of studies with true causal effect sizes more extreme than a specified threshold of scientific importance; and (2) the minimum bias factor and confounding strength required to reduce to less than a specified threshold the proportion of studies with true effect sizes of scientifically significant size. The functions sens_plot() and sens_table() create plots and tables for visualizing these meta-analysis metrics across a range of bias values, and scrape_meta helps scrape study-level data from a published forest plot or summary table to obtain the needed estimates when these are not reported. (See Mathur & VanderWeele [<https://osf.io/jkhfg/>] for details.) Most of the analyses available in this package can also be conducted using web-based graphical interfaces (for a single observational study: <https://mmathur.shinyapps.io/evalue/>; for a meta-analysis: <https://mmathur.shinyapps.io/meta_gui_2/>).
Author: Maya B. Mathur, Peng Ding, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 1.1.3 dated 2018-04-03 and 1.1.4 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <http://codecov.io> or
'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Müller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyzanowski [ctb],
Markus Wamser [ctb],
Karl Forner [ctb],
Gergely Daróczi [ctb],
Jouni Helske [ctb],
Kun Ren [ctb],
Jeroen Ooms [ctb],
Ken Williams [ctb],
Chris Campbell [ctb],
David Hugh-Jones [ctb],
Qin Wang [ctb]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.0.1 dated 2017-11-07 and 3.1.0 dated 2018-05-18
DESCRIPTION | 11 - MD5 | 82 ++++----- NAMESPACE | 1 NEWS.md | 26 +++ R/cobertura.R | 2 R/codecov.R | 25 +- R/compiled.R | 4 R/coveralls.R | 18 +- R/covr.R | 93 +++++++--- R/display_name.R | 6 R/exclusions.R | 29 ++- R/icc.R | 13 + R/parse_data.R | 15 + R/replace.R | 1 R/summary_functions.R | 22 +- R/system.R | 8 R/trace_calls.R | 6 R/utils.R | 5 R/zzz.R | 2 README.md | 36 +++- build/vignette.rds |binary inst/doc/how_it_works.html | 334 +++++++++++++++++++++++++++++++-------- man/code_coverage.Rd | 6 man/codecov.Rd | 4 man/count.Rd | 2 man/coverage_to_list.Rd |only man/coveralls.Rd | 4 man/covr-package.Rd |only man/exclusions.Rd | 2 man/file_coverage.Rd | 2 man/new_counter.Rd | 2 man/package_coverage.Rd | 10 - man/percent_coverage.Rd | 4 man/report.Rd | 2 man/system_check.Rd | 2 man/system_output.Rd | 2 man/tally_coverage.Rd | 2 man/to_cobertura.Rd | 2 man/trace_calls.Rd | 2 man/zero_coverage.Rd | 6 tests/testthat/test-codecov.R | 18 +- tests/testthat/test-coveralls.R | 38 ++++ tests/testthat/test-exclusions.R | 53 ++++++ 43 files changed, 675 insertions(+), 227 deletions(-)
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa.
Author: Alex Couture-Beil <rjson_pkg@mofo.ca>
Maintainer: Alex Couture-Beil <rjson_pkg@mofo.ca>
Diff between rjson versions 0.2.18 dated 2018-05-06 and 0.2.19 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/json_rpc_server.pdf |binary inst/unittests/test.list.r | 14 ++++++++++++++ src/parser.c | 12 ++++++++++++ 5 files changed, 34 insertions(+), 8 deletions(-)
Title: Calculate Pairwise Distances
Description: A common framework for calculating distance matrices.
Author: Nello Blaser [aut, cre]
Maintainer: Nello Blaser <nello.blaser@uib.no>
Diff between rdist versions 0.0.2 dated 2017-05-12 and 0.0.3 dated 2018-05-18
DESCRIPTION | 10 +- MD5 | 62 ++++++++---- NAMESPACE | 23 ++-- NEWS.md | 63 +++++++------ R/FUN_distances.R |only R/RcppExports.R | 62 ++++++++---- R/correlation_distances.R | 74 +++++++-------- R/distance_functions.r | 179 ++++++++++++++++++++----------------- R/farthest_point_sampling.R |only R/is_metric.R |only R/product_metric.R |only R/rdist-package.r | 69 +++++++------- README.md | 52 +++++----- man/farthest_point_sampling.Rd |only man/is_metric.Rd |only man/product_metric.Rd |only man/rdist.Rd | 99 ++++++++++---------- src/Makevars | 3 src/Makevars.win | 4 src/RcppExports.cpp | 109 ++++++++++++++++++---- src/canberra.h |only src/dist.cpp |only src/dist.h |only src/farthest_point_sampling.cpp |only src/hamming.h |only src/init.c | 98 ++++++++++---------- src/jaccard.h |only src/manhattan.h |only src/maximum.h |only src/minkowski.h |only src/triangle.cpp |only tests/testthat.R | 8 - tests/testthat/test-canberra.R | 33 +++--- tests/testthat/test-correlation.R | 98 ++++++++++---------- tests/testthat/test-euclidean.R | 81 ++++++++-------- tests/testthat/test-hamming.R | 48 ++++----- tests/testthat/test-jaccard.R | 60 ++++++------ tests/testthat/test-manhattan.R | 33 +++--- tests/testthat/test-maximum.R | 33 +++--- tests/testthat/test-minkowski.R | 91 +++++++++--------- tests/testthat/test-user-defined.R |only 41 files changed, 771 insertions(+), 621 deletions(-)
Title: Shiny UI Widgets for Small Screens
Description: Provides UI widget and layout functions for writing Shiny apps
that work well on small screens.
Author: Joe Cheng [cre, aut],
RStudio [cph]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between miniUI versions 0.1.1 dated 2016-01-15 and 0.1.1.1 dated 2018-05-18
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/layout.R | 2 +- README.md | 2 +- tools |only 5 files changed, 9 insertions(+), 8 deletions(-)
Title: Feature Selection and Classification with the Embedded
Validation Procedures for Biomedical Data Analysis
Description: Contains functions for the data analysis with the emphasis on biological data, including several algorithms for feature ranking, feature selection, classification
algorithms with the embedded validation procedures.
The functions can deal with numerical as well as with nominal features. Includes also the functions for calculation
of feature AUC (Area Under the ROC Curve) and HUM (hypervolume under manifold) values and construction 2D- and 3D- ROC curves.
Provides the calculation of Area Above the RCC (AAC) values and construction of Relative Cost Curves
(RCC) to estimate the classifier performance under unequal misclassification costs problem.
There exists the special function to deal with missing values, including different imputing schemes.
Author: Natalia Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn
Maintainer: Natalia Novoselova <novos65@mail.ru>
Diff between Biocomb versions 0.3 dated 2017-03-22 and 0.4 dated 2018-05-18
Biocomb-0.3/Biocomb/src/Biocomb_init.c |only Biocomb-0.4/Biocomb/DESCRIPTION | 8 +++--- Biocomb-0.4/Biocomb/MD5 | 9 +++---- Biocomb-0.4/Biocomb/R/RcppExports.R | 16 ++++++------- Biocomb-0.4/Biocomb/R/select.feature.info.R | 4 +-- Biocomb-0.4/Biocomb/src/RcppExports.cpp | 33 +++++++++++++++++++++------- 6 files changed, 43 insertions(+), 27 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.31 dated 2015-11-06 and 0.4.32 dated 2018-05-18
.Rinstignore |only DESCRIPTION | 8 +-- MD5 | 81 +++++++++++++++++----------------- NAMESPACE | 2 NEWS | 14 +++++ R/00Init.r | 2 R/checkFuncs.r | 2 R/exportHTML.r | 2 R/html.r | 2 R/htmlProtocol.r | 2 R/inspector.r | 2 R/options.r | 2 R/runit.r | 27 ++++++++--- R/testLogger.r | 2 R/textProtocol.r | 2 README.md | 4 - build/RUnit.pdf |binary build/vignette.rds |binary inst/doc/Makefile |only inst/doc/RUnit.pdf |binary inst/examples/correctTestCase.r | 2 inst/examples/runitVirtualClassTest.r | 2 inst/share/R/checkCode.r | 2 inst/share/R/compareRUnitTestData.r | 2 inst/unitTests/runitHTMLProtocol.r | 2 inst/unitTests/runitInspect.r | 2 inst/unitTests/runitPlotConnection.r | 2 inst/unitTests/runitRUnit.r | 44 +++++++----------- inst/unitTests/runitS4.r | 2 inst/unitTests/runitSetUp.r | 2 inst/unitTests/runitTearDown.r | 2 inst/unitTests/runitTestLogger.r | 2 inst/unitTests/runitTextProtocol.r | 2 man/RUnit-internal.Rd | 2 man/RUnit-intro.Rd | 2 man/RUnit-options.Rd | 2 man/checkFuncs.Rd | 2 man/inspect.Rd | 2 man/printHTML.trackinfo.Rd | 2 man/runit.Rd | 19 +++++-- man/testCaseSetUp.Rd | 2 man/textProtocol.Rd | 2 man/tracker.Rd | 2 43 files changed, 144 insertions(+), 115 deletions(-)
Title: Design of Rotatable Central Composite Experiments and Response
Surface Analysis
Description: Produces tables with the level of replication (number of replicates) and the
experimental uncoded values of the quantitative factors to be used for rotatable Central
Composite Design (CCD) experimentation and a 2-D contour plot of the corresponding
variance of the predicted response according to
Mead et al. (2012) <doi:10.1017/CBO9781139020879> design_ccd(), and analyzes
CCD data with response surface methodology ccd_analysis(). A rotatable CCD
provides values of the variance of the predicted response that are concentrically
distributed around the average treatment combination used in the experimentation, which
with uniform precision (implied by the use of several replicates at the average
treatment combination) improves greatly the search and finding of an optimum response.
These properties of a rotatable CCD represent undeniable advantages over the classical
factorial design, as discussed by Panneton et al. (1999) <doi:10.13031/2013.13267> and
Mead et al. (2012) <doi:10.1017/CBO9781139020879.018> among others.
Author: Timothy Schwinghamer [aut, cre],
Dutilleul Pierre [aut, cph]
Maintainer: Timothy Schwinghamer <timothy.schwinghamer@mail.mcgill.ca>
Diff between rsurface versions 1.0.2 dated 2017-09-26 and 1.1.0 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ccd_analysis.R | 4 +++- man/ccd_analysis.Rd | 4 +++- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Classes and Methods to Use Genetic Algorithms for Feature
Selection
Description: Defines classes and methods that can be used
to implement genetic algorithms for feature selection. The idea is
that we want to select a fixed number of features to combine into a
linear classifier that can predict a binary outcome, and can use a
genetic algorithm heuristically to select an optimal set of features.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between GenAlgo versions 2.1.3 dated 2017-07-13 and 2.1.4 dated 2018-05-18
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++++------- NEWS | 10 ++++++++++ R/cp01-genalg.R | 20 ++++++++++---------- build/vignette.rds |binary data/gaTourResults.rda |binary data/tourData09.rda |binary inst/doc/featureSelection.R |only inst/doc/featureSelection.Rmd |only inst/doc/featureSelection.html |only inst/doc/genalg.pdf |binary vignettes/featureSelection.Rmd |only 12 files changed, 39 insertions(+), 24 deletions(-)
Title: Handy File and String Manipulation
Description: Convenient functions for moving files, deleting directories,
and a variety of string operations that facilitate manipulating files
and extracting information from strings.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 2.2.0 dated 2018-04-18 and 2.4.0 dated 2018-05-18
filesstrings-2.2.0/filesstrings/R/RcppExports_deprecated.R |only filesstrings-2.2.0/filesstrings/R/files_deprecated.R |only filesstrings-2.2.0/filesstrings/R/strings_deprecated.R |only filesstrings-2.2.0/filesstrings/R/utils_deprecated.R |only filesstrings-2.2.0/filesstrings/README.md |only filesstrings-2.4.0/filesstrings/DESCRIPTION | 19 - filesstrings-2.4.0/filesstrings/MD5 | 40 +- filesstrings-2.4.0/filesstrings/NAMESPACE | 49 --- filesstrings-2.4.0/filesstrings/NEWS.md | 16 + filesstrings-2.4.0/filesstrings/R/files.R | 69 +++- filesstrings-2.4.0/filesstrings/R/strings.R | 144 +++++++++- filesstrings-2.4.0/filesstrings/R/utils.R | 6 filesstrings-2.4.0/filesstrings/build/partial.rdb |binary filesstrings-2.4.0/filesstrings/build/vignette.rds |binary filesstrings-2.4.0/filesstrings/inst/doc/files.html | 4 filesstrings-2.4.0/filesstrings/inst/doc/strings.html | 8 filesstrings-2.4.0/filesstrings/man/filesstrings-defunct.Rd | 125 -------- filesstrings-2.4.0/filesstrings/man/move_files.Rd | 6 filesstrings-2.4.0/filesstrings/man/nth_number_after_mth.Rd |only filesstrings-2.4.0/filesstrings/man/singleize.Rd | 5 filesstrings-2.4.0/filesstrings/man/str_after_nth.Rd | 4 filesstrings-2.4.0/filesstrings/man/str_nth_instance_indices.Rd | 3 filesstrings-2.4.0/filesstrings/src/strings.cpp | 9 filesstrings-2.4.0/filesstrings/tests/testthat/test_files.R | 24 + 24 files changed, 285 insertions(+), 246 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'FCI' (fast causal inference),
'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.2.0 dated 2018-04-16 and 0.2.2 dated 2018-05-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++------- NAMESPACE | 1 + R/RESIT.R |only R/RESIT_fitting.R |only R/RESIT_indtests.R |only R/checkDependencies.R | 4 ++++ R/checkMode.R | 2 +- R/getParents.R | 5 +++++ R/runRESIT.R |only man/CompareCausalNetworks-package.Rd | 4 ++-- tests/testthat/test_getParents_defaults_all_methods.R | 13 +++++++------ 12 files changed, 36 insertions(+), 21 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: BiCluster Algorithms
Description: The main function biclust() provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0),
spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova,
Martin Sill, Roberto Theron, Luis Quintales, Friedrich
Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser <Sebastian.Kaiser@stat.uni-muenchen.de>
Diff between biclust versions 1.2.0 dated 2015-05-12 and 2.0.0 dated 2018-05-18
DESCRIPTION | 21 +++++++++++---------- MD5 | 43 ++++++++++++++++++++++++------------------- NAMESPACE | 22 +++++++++++++++++++++- NEWS | 8 ++++++++ R/DiagnosticsFunctions.R | 29 ++++++++++++++++++++++------- R/InteractionTest.R |only R/bubbleplot.r | 9 +++------ R/clustmember.r | 16 ++++++++++++++-- R/drawHeatmap.r | 1 - R/iterativekmeans.r | 11 +++-------- README.md |only data/BicatYeast.rda |binary data/EisenYeast.rda |binary data/SyntrenEcoli.rda |binary man/BCPlaid.Rd | 2 +- man/EisenYeast.Rd | 2 +- man/bubbleplot.Rd | 2 +- man/coherence.Rd | 2 +- man/computeObservedFstat.Rd | 4 ++-- man/diagnoseColRow.Rd | 4 ++-- man/diagnosticPlot2.Rd |only man/diagnosticTest.Rd |only man/ensemble.Rd | 12 ++++++++++-- man/plaid.grid.Rd | 2 +- src/biclust_init.c |only 25 files changed, 125 insertions(+), 65 deletions(-)
Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with link to associate outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 1.3.4 dated 2017-07-11 and 1.3.5 dated 2018-05-18
Umpire-1.3.4/Umpire/man/e00-Umpire-package.Rd |only Umpire-1.3.5/Umpire/DESCRIPTION | 8 +++---- Umpire-1.3.5/Umpire/MD5 | 27 ++++++++++++-------------- Umpire-1.3.5/Umpire/R/e00-engine.R | 2 - Umpire-1.3.5/Umpire/R/e01-indNormal.R | 5 +--- Umpire-1.3.5/Umpire/R/e02-indLogNorm.R | 5 +--- Umpire-1.3.5/Umpire/R/e03-mvn.R | 7 ++---- Umpire-1.3.5/Umpire/R/e05-noise.R | 7 ++---- Umpire-1.3.5/Umpire/R/e06-engineAct.R | 6 ++--- Umpire-1.3.5/Umpire/R/e07-1-survModel.R | 11 ++++------ Umpire-1.3.5/Umpire/R/e07-2-cancerModel.R | 15 ++++++-------- Umpire-1.3.5/Umpire/R/e08-cancerEngine.R | 9 +++----- Umpire-1.3.5/Umpire/R/e09-extra.R | 2 - Umpire-1.3.5/Umpire/build/vignette.rds |binary Umpire-1.3.5/Umpire/inst/doc/Umpire.pdf |binary 15 files changed, 48 insertions(+), 56 deletions(-)
Title: STR Decomposition
Description: Methods for decomposing seasonal data: STR (a Seasonal-Trend decomposition procedure based on Regression) and Robust STR. In some ways, STR is similar to Ridge Regression and Robust STR can be related to LASSO. They allow for multiple seasonal components, multiple linear covariates with constant, flexible and seasonal influence. Seasonal patterns (for both seasonal components and seasonal covariates) can be fractional and flexible over time; moreover they can be either strictly periodic or have a more complex topology. The methods provide confidence intervals for the estimated components. The methods can be used for forecasting.
Author: Alexander Dokumentov, Rob J Hyndman
Maintainer: Alexander Dokumentov <alexander.dokumentov@gmail.com>
Diff between stR versions 0.3 dated 2017-01-06 and 0.4 dated 2018-05-18
Changelog | 18 DESCRIPTION | 7 MD5 | 106 - NAMESPACE | 94 - R/RSTR.R | 8 R/STR.R | 24 R/calls.R | 46 R/components.R | 94 - R/electricity.R | 64 - R/grocery.R | 44 R/heuristicSTR.R | 4 R/mstsWrapper.R | 190 +-- R/plot.str.R | 2 R/plotBeta.R | 2 R/seasadj.R | 110 - build/vignette.rds |binary inst/doc/stRvignette.R | 1102 +++++++++--------- inst/doc/stRvignette.html | 1066 +++++++++--------- man/AutoSTR.Rd | 194 +-- man/RSTRmodel.Rd | 314 ++--- man/STR.Rd | 470 ++++---- man/STRmodel.Rd | 314 ++--- man/calls.Rd | 56 man/components.Rd | 58 man/confidence.Rd | 30 man/control.Rd | 26 man/data.Rd | 26 man/electricity.Rd | 72 - man/gapCV.Rd | 28 man/grocery.Rd | 46 man/heuristicSTR.Rd | 560 ++++----- man/lambdas.Rd | 32 man/nFold.Rd | 26 man/nMCIter.Rd | 26 man/pattern.Rd | 30 man/plot.STR.Rd | 128 +- man/plotBeta.Rd | 244 ++-- man/predictors.Rd | 104 - man/reltol.Rd | 28 man/reportDimensionsOnly.Rd | 30 man/robust.Rd | 26 man/seasadj.STR.Rd | 70 - man/solver.Rd | 32 man/strDesign.Rd | 30 man/trace.Rd | 26 tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/test_STR.R | 2048 +++++++++++++++++------------------ vignettes/calls.fit.RDS |binary vignettes/co2.fit.tbats.RDS |binary vignettes/elec.fit.2.forecasting.RDS |binary vignettes/elec.fit.RDS |binary vignettes/elec.fit.forecasting.RDS |binary vignettes/logGrOutl.stR.robust.RDS |binary 54 files changed, 4032 insertions(+), 4031 deletions(-)
Title: Random Forests for Survival, Regression, and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. Now extended to include multivariate and unsupervised forests. Also includes quantile regression forests for univariate and multivariate training/testing settings. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.6.0 dated 2018-05-02 and 2.6.1 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 2 +- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS | 8 +++++++- src/randomForestSRC.c | 7 +++++-- 8 files changed, 35 insertions(+), 26 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Finding the Number of Significant Principal Components
Description: Implements methods to automate the Auer-Gervini graphical
Bayesian approach for determining the number of significant
principal components. Automation uses clustering, change points, or
simple statistical models to distinguish "long" from "short" steps
in a graph showing the posterior number of components as a function
of a prior parameter. See <doi:10.1101/237883>.
Author: Kevin R. Coombes, Min Wang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PCDimension versions 1.1.8 dated 2018-01-09 and 1.1.9 dated 2018-05-18
PCDimension-1.1.8/PCDimension/man/PCDimension-package.Rd |only PCDimension-1.1.9/PCDimension/DESCRIPTION | 8 ++++---- PCDimension-1.1.9/PCDimension/MD5 | 15 +++++++-------- PCDimension-1.1.9/PCDimension/NEWS | 10 ++++++++++ PCDimension-1.1.9/PCDimension/R/00-Auer-Gervini.R | 11 +++++------ PCDimension-1.1.9/PCDimension/build/vignette.rds |binary PCDimension-1.1.9/PCDimension/data/spca.rda |binary PCDimension-1.1.9/PCDimension/inst/doc/PCDimension.pdf |binary PCDimension-1.1.9/PCDimension/man/AuerGervini-class.Rd | 10 +++++++++- 9 files changed, 35 insertions(+), 19 deletions(-)
Title: Normalisation of Psychometric Tests
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided. See Philipps et al (2014) <doi:10.1159/000365637> for details.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between NormPsy versions 1.0.7 dated 2018-03-16 and 1.0.8 dated 2018-05-18
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NAMESPACE | 6 +++--- build |only man/NormPsy-package.Rd | 32 ++++++++++++++++++++------------ man/normMMSE.Rd | 2 +- 6 files changed, 34 insertions(+), 25 deletions(-)
Title: Nested Loop Cross Validation
Description: Nested loop cross validation for classification purposes for misclassification error rate estimation.
The package supports several methodologies for feature selection: random forest, Student t-test, limma,
and provides an interface to the following classification methods in the 'MLInterfaces' package: linear,
quadratic discriminant analyses, random forest, bagging, prediction analysis for microarray, generalized
linear model, support vector machine (svm and ksvm). Visualizations to assess the quality of
the classifier are included: plot of the ranks of the features, scores plot for a specific
classification algorithm and number of features, misclassification rate
for the different number of features and classification algorithms tested and ROC plot.
For further details about the methodology, please check:
Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, and Ulrich Mansmann (2004)
<doi:10.2202/1544-6115.1078>.
Author: Willem Talloen, Tobias Verbeke
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between nlcv versions 0.3.3 dated 2018-05-06 and 0.3.4 dated 2018-05-18
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- inst/NEWS | 2 ++ inst/doc/nlcv.pdf |binary 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods
with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling
conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between inline versions 0.3.14 dated 2015-04-13 and 0.3.15 dated 2018-05-18
DESCRIPTION | 14 ++++++++------ MD5 | 11 ++++++----- R/cfunction.R | 7 ++++--- R/cxxfunction.R | 2 +- build |only inst/NEWS.Rd | 18 ++++++++++++++++-- man/inline-package.Rd | 33 ++++++--------------------------- 7 files changed, 41 insertions(+), 44 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Hector Sanz, Gavin Lucas, Judith Penafiel and David Gimenez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.3.4 dated 2018-04-22 and 3.4.0 dated 2018-05-18
DESCRIPTION | 8 MD5 | 14 R/compareGroups.formula.R | 8 build/vignette.rds |binary inst/doc/changelog | 2 inst/doc/compareGroups_vignette.html | 795 ++++++++++++++--------------------- man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 6 8 files changed, 365 insertions(+), 472 deletions(-)
Title: Adjusting for Optimism in 'glmnet' Regression using
Bootstrapping
Description: Main objective of a predictive model is to provide accurated predictions of a new observations.
Unfortunately we don't know how well the model performs. In addition, at the current era of omic
data where p >> n, is not reasonable applying internal validation using data-splitting. Under this
background a good method to assessing model performance is applying internal bootstrap validation
(Harrell Jr, Frank E (2015) <doi:10.1007/978-1-4757-3462-1>.) This package provides bootstrap validation
for the linear, logistic, multinomial and cox 'glmnet' models.
Author: Antonio Jose Canada Martinez
Maintainer: Antonio Jose Canada Martinez <ancamar2@gmail.com>
Diff between BootValidation versions 0.1.3 dated 2017-11-14 and 0.1.5 dated 2018-05-18
DESCRIPTION | 11 +-- MD5 | 15 ++-- NAMESPACE | 9 ++ R/parallel_vboot.R | 184 +++++++++++++++++++++++++++++++++++++++++++++++---- README.md |only man/vboot.Rd | 14 ++- man/vboot.coxnet.Rd |only man/vboot.elnet.Rd | 3 man/vboot.lognet.Rd | 5 - man/vboot.multnet.Rd |only 10 files changed, 209 insertions(+), 32 deletions(-)
More information about BootValidation at CRAN
Permanent link
More information about uCAREChemSuiteCLI at CRAN
Permanent link
Title: Easily Tidy Data with 'spread()' and 'gather()' Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.8.0 dated 2018-01-29 and 0.8.1 dated 2018-05-18
DESCRIPTION | 8 MD5 | 30 - NEWS.md | 7 R/fill.R | 1 R/replace_na.R | 1 R/separate.R | 5 R/uncount.R | 6 R/unnest.R | 4 README.md | 65 ++- inst/doc/tidy-data.html | 713 +++++++++++++++++++++---------------------- man/fill.Rd | 22 - man/replace_na.Rd | 1 man/separate.Rd | 5 man/uncount.Rd | 6 man/unnest.Rd | 2 tests/testthat/test-unnest.R | 5 16 files changed, 456 insertions(+), 425 deletions(-)
Title: Tools for 'Box Geometry Model' (BGM) Files and Topology for the
Atlantis Ecosystem Model
Description: Facilities for working with Atlantis box-geometry model (BGM)
files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model.
Functions are provided to read from BGM files directly, preserving their
internal topology, as well as helper functions to generate 'Spatial' objects.
This functionality aims to simplify the creation and modification of box
and geometry as well as the ability to integrate with other data sources.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between rbgm versions 0.0.4 dated 2016-07-22 and 0.0.5 dated 2018-05-18
DESCRIPTION | 17 ++---- MD5 | 42 +++++++-------- NAMESPACE | 4 + NEWS.md | 8 ++ R/Spatial.r | 4 + R/bgmfile.r | 32 +++++++---- R/face_parse.R |only R/rbgm.R | 1 README.md | 4 - build/vignette.rds |binary inst/doc/BGM_Spatial.Rmd | 3 - inst/doc/BGM_Spatial.html | 28 +++++----- inst/doc/BGM_examplefiles.R | 30 ++++------ inst/doc/BGM_examplefiles.Rmd | 33 +++++------ inst/doc/BGM_examplefiles.html | 37 +++++++++---- inst/doc/BGMfiles.html | 106 +++++++++++++++++++------------------- man/bgmfile.Rd | 5 + man/build_dz.Rd | 1 man/nodeSpatial.Rd | 1 man/rbgm-Spatial.Rd | 3 - tests/testthat/test-no-names-sp.R |only vignettes/BGM_Spatial.Rmd | 3 - vignettes/BGM_examplefiles.Rmd | 33 +++++------ 23 files changed, 215 insertions(+), 180 deletions(-)
Title: Smoothing of Two-Dimensional Demographic Data, Optionally Taking
into Account Period and Cohort Effects
Description: The implemented method uses for smoothing bivariate thin plate
splines, bivariate lasso-type regularization, and allows for both period
and cohort effects. Thus the mortality rates are modelled as the sum of four
components: a smooth bivariate function of age and time, smooth one-dimensional
cohort effects, smooth one-dimensional period effects and random errors.
Author: Alexander Dokumentov, Rob J Hyndman
Maintainer: Alexander Dokumentov <alexander.dokumentov@gmail.com>
Diff between smoothAPC versions 0.2 dated 2017-09-14 and 0.3 dated 2018-05-18
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/auto.l1tp.smooth.R | 20 ++++++++++---------- R/l1tp.smooth.R | 4 ++-- R/print.R | 2 +- R/show.R | 8 ++++---- man/autoSmoothAPC.Rd | 11 ++++++----- man/plot.matrix.Rd | 3 ++- man/plot.smAPC.Rd | 3 ++- man/plot3d.Rd | 1 + man/plot3d.matrix.Rd | 3 ++- man/plot3d.smAPC.Rd | 3 ++- man/signifAutoSmoothAPC.Rd | 11 ++++++----- man/smoothAPC.Rd | 11 ++++++----- 14 files changed, 62 insertions(+), 54 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.2.6 dated 2018-03-06 and 0.2.7 dated 2018-05-18
SeqFeatR |only 1 file changed
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre],
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb],
Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 0.13 dated 2018-04-14 and 0.15.0 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only R/repr_list.r | 2 ++ tests/testthat/test_repr_htmlwidget.r | 3 +++ 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Relabelling MCMC Outputs of Mixture Models
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between label.switching versions 1.6 dated 2016-05-22 and 1.7 dated 2018-05-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/label.switching-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
More information about label.switching at CRAN
Permanent link
Title: Searching Parsimony Models with Genetic Algorithms
Description: Methodology that combines feature selection, model tuning, and parsimonious model selection with Genetic Algorithms (GA) proposed in {Martinez-de-Pison} (2015) <DOI:10.1016/j.asoc.2015.06.012>. To this objective, a novel GA selection procedure is introduced based on separate cost and complexity evaluations.
Author: F.J. Martinez-de-Pison [aut, cre]
Maintainer: F.J. Martinez-de-Pison <fjmartin@unirioja.es>
Diff between GAparsimony versions 0.9-1 dated 2017-08-03 and 0.9.2 dated 2018-05-18
DESCRIPTION | 8 MD5 | 20 NEWS |only R/ga_parsimony.R | 177 +++++--- R/parsimony_functions.R | 3 R/parsimony_monitor.R | 10 R/startParallel.R | 58 ++ man/GAparsimony-internal.Rd | 1 man/ga_parsimony-class.Rd | 2 man/ga_parsimony.Rd | 938 ++++++++++++++++++++++---------------------- man/matrixNULL-class.Rd |only man/parsimony_rerank.Rd | 111 ++--- 12 files changed, 709 insertions(+), 619 deletions(-)
Title: Analyze Two Choice Reaction Time Data with the D*M Method
Description: A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
Author: Don van den Bergh, Stijn Verdonck, Francis Tuerlinckx
Maintainer: Don van den Bergh <donvdbergh@hotmail.com>
Diff between DstarM versions 0.2.2 dated 2017-04-30 and 0.3.0 dated 2018-05-18
DstarM-0.2.2/DstarM/R/DstarMplot.R |only DstarM-0.2.2/DstarM/R/DstarMprint.R |only DstarM-0.2.2/DstarM/R/DstarMsummary.R |only DstarM-0.2.2/DstarM/man/byParticipant.Rd |only DstarM-0.2.2/DstarM/man/calcIC.Rd |only DstarM-0.3.0/DstarM/DESCRIPTION | 14 DstarM-0.3.0/DstarM/MD5 | 87 + DstarM-0.3.0/DstarM/NAMESPACE | 19 DstarM-0.3.0/DstarM/R/Densities.R | 5 DstarM-0.3.0/DstarM/R/Distances.R | 22 DstarM-0.3.0/DstarM/R/DstarMcoef.R | 12 DstarM-0.3.0/DstarM/R/DstarMmethods.R |only DstarM-0.3.0/DstarM/R/DstarMmethodsDeprecated.R |only DstarM-0.3.0/DstarM/R/RcppExports.R |only DstarM-0.3.0/DstarM/R/byParticipant.R | 214 ++-- DstarM-0.3.0/DstarM/R/calcIC.R | 524 +++++----- DstarM-0.3.0/DstarM/R/chisqFit.R | 144 +- DstarM-0.3.0/DstarM/R/estCdf.R | 17 DstarM-0.3.0/DstarM/R/estDstarM.R | 1200 ++++++++++++------------ DstarM-0.3.0/DstarM/R/estND.R | 555 ++++++----- DstarM-0.3.0/DstarM/R/estObserved.R | 146 +- DstarM-0.3.0/DstarM/R/estQdf.R | 22 DstarM-0.3.0/DstarM/R/getOptim.R | 12 DstarM-0.3.0/DstarM/R/getPdfs.R | 38 DstarM-0.3.0/DstarM/R/getSter.R | 10 DstarM-0.3.0/DstarM/R/getTer.R | 70 - DstarM-0.3.0/DstarM/R/normalize.R |only DstarM-0.3.0/DstarM/R/obsQuantiles.R | 37 DstarM-0.3.0/DstarM/R/plotObserved.R | 269 ++--- DstarM-0.3.0/DstarM/R/rtDescriptives.R | 89 + DstarM-0.3.0/DstarM/R/rtHist.R | 47 DstarM-0.3.0/DstarM/R/simData.R | 108 +- DstarM-0.3.0/DstarM/R/testFun.R | 34 DstarM-0.3.0/DstarM/R/utilities.R |only DstarM-0.3.0/DstarM/man/chisqFit.Rd | 6 DstarM-0.3.0/DstarM/man/estDstarM.Rd | 58 - DstarM-0.3.0/DstarM/man/estND.Rd | 16 DstarM-0.3.0/DstarM/man/estObserved.Rd | 2 DstarM-0.3.0/DstarM/man/getTer.Rd | 6 DstarM-0.3.0/DstarM/man/normalize.Rd |only DstarM-0.3.0/DstarM/man/obsQuantiles.Rd | 6 DstarM-0.3.0/DstarM/man/plotObserved.Rd | 17 DstarM-0.3.0/DstarM/man/rtDescriptives.Rd | 37 DstarM-0.3.0/DstarM/man/upgradeDstarM.Rd |only DstarM-0.3.0/DstarM/src |only DstarM-0.3.0/DstarM/tests |only 46 files changed, 2048 insertions(+), 1795 deletions(-)
Title: Analysis of Circadian Behaviours
Description: Use behavioural variables to compute period, rhythmicity and other circadian parameters.
Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>),
Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>),
and autocorrelation-based periodograms.
Author: Quentin Geissmann [aut, cre],
Luis Garcia [aut]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between zeitgebr versions 0.3.1 dated 2018-05-16 and 0.3.2 dated 2018-05-18
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/find-peaks.R | 1 + R/periodogram.R | 6 ++++++ README.md | 4 ---- man/find_peaks.Rd | 1 + man/periodogram.Rd | 6 ++++++ 7 files changed, 25 insertions(+), 15 deletions(-)
Title: Calculates Business Duration Between Two Dates
Description: Calculates business duration between two dates. This excluding weekends, public holidays and non-business hours.
Author: Gnaneshwar G
Maintainer: Gnaneshwar G <gnaneshwar441@gmail.com>
Diff between BusinessDuration versions 0.1.0 dated 2018-03-13 and 0.2.0 dated 2018-05-18
DESCRIPTION | 6 +- MD5 | 8 +-- NAMESPACE | 1 R/business_duration.R | 100 ++++++++++++++++++++++++------------------------ man/businessDuration.Rd | 77 ++++++++++++++++++++++++++++++++---- 5 files changed, 127 insertions(+), 65 deletions(-)
More information about BusinessDuration at CRAN
Permanent link
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://www.laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] (Enable the support of .lax file and
extra byte attributes),
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.2.1 dated 2018-04-13 and 1.2.3 dated 2018-05-18
DESCRIPTION | 8 - MD5 | 51 ++++++------ NEWS.md | 15 +++ R/RcppExports.R | 8 - R/checkers.r | 24 +++++ R/deprecated.r | 13 --- R/header_tools.r | 40 ++++++++- R/readLAS.r | 106 ++----------------------- README.md | 2 inst/include/lasattributer.hpp | 26 ++++-- inst/include/lasdefinitions.hpp | 2 inst/include/rlasstreamer.h | 15 +++ man/read.las.Rd | 14 +-- man/readlasdata.Rd | 7 - man/readlasheader.Rd | 4 src/LASlib/laswriter.cpp | 5 - src/LASlib/laswriter_bin.cpp | 24 +++-- src/RcppExports.cpp | 44 ++-------- src/deprecated.cpp | 7 + src/point_in_polygon.cpp | 14 +++ src/readLAS.cpp | 42 +--------- src/rlasstreamer.cpp | 155 +++++++++++++++++++++++++++++++++++++ src/writeLAS.cpp | 13 ++- tests/testthat/test-header_tools.R | 117 +++++++++++++++++++++++++++ tests/testthat/test-pnpoly.R |only tests/testthat/test-readlas.R | 16 +-- tests/testthat/test-writelas.R | 6 - 27 files changed, 507 insertions(+), 271 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence
dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting,
decay curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre],
Bo Li [aut],
Jorge More [ctb],
Burton Garbow [ctb],
Kenneth Hillstrom [ctb],
John Burkardt [ctb],
Paul Gilbert [ctb],
Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 2.4 dated 2018-04-25 and 2.5 dated 2018-05-18
DESCRIPTION | 8 - MD5 | 14 +- R/RadialPlotter.R | 4 R/calSARED.R | 335 ++++++++++++++++++++++++++++++++++++++++++-------- R/calSGCED.R | 107 ++++++++++++--- R/fastED.R | 4 R/pickSARdata.R | 232 +++++++++++++++++++++++++++------- man/numOSL-package.Rd | 4 8 files changed, 571 insertions(+), 137 deletions(-)
Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino <toni.giorgino@gmail.com>,
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>
Diff between dtw versions 1.18-1 dated 2015-09-01 and 1.20-1 dated 2018-05-18
DESCRIPTION | 8 +-- MD5 | 54 +++++++++++++----------- NAMESPACE | 6 ++ R/backtrack.R | 4 - R/countPaths.R | 4 - R/dtw-internal.R | 6 +- R/dtw.R | 26 +++++------ R/dtwDist.R | 4 - R/globalCostMatrix.R | 51 ++++++----------------- R/mvm.R | 4 - R/plot.dtw.R | 4 - R/stepPattern.R | 4 - R/triangleFixing.R |only R/warp.R | 4 - R/warpArea.R | 4 - R/window.R | 4 - R/zzz.R | 4 - build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog | 12 +++++ inst/doc/dtw.Rnw | 4 - inst/doc/dtw.pdf |binary man/dtw-package.Rd | 54 +++++++++--------------- man/mvm.Rd | 10 +--- man/stepPattern.Rd | 35 +++++++++------- man/triangleFixing.Rd |only src/computeCM.c | 109 +++++++++++++++++++++++++++++++------------------- src/dtw.h |only src/init.c |only src/triangleFixing.c |only vignettes/dtw.Rnw | 4 - 31 files changed, 217 insertions(+), 202 deletions(-)
Title: R Utilities Accompanying the Software Package BayesX
Description: Functions for exploring and visualising estimation results
obtained with BayesX, a free software for estimating structured additive
regression models (<http://www.BayesX.org>). In addition,
functions that allow to read, write and manipulate map objects that are required in spatial
analyses performed with BayesX.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Nadja Klein [aut],
Felix Heinzl [ctb],
Andreas Brezger [ctb],
Daniel Sabanes Bove [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesX versions 0.2-9 dated 2014-08-18 and 0.3-0 dated 2018-05-18
DESCRIPTION | 37 +- MD5 | 58 ++-- NAMESPACE | 147 ++++++----- R/AAA.R | 35 +- R/add.neighbor.R | 43 +-- R/bnd2gra.R | 230 +++++++---------- R/createxymap.R | 147 +++++------ R/delete.neighbor.R | 43 +-- R/drawmap.R | 441 ++++++++++++++++----------------- R/extractSamples.R | 649 ++++++++++++++++++++----------------------------- R/fuse.R | 177 ++++++------- R/get.centroids.R | 97 +++---- R/get.neighbor.R | 31 +- R/getNumbers.R | 31 -- R/hpd.R | 94 +++---- R/nbAndGraConversion.R | 112 +++----- R/plotautocor.R | 23 - R/plotnonp.R | 119 ++++---- R/plotsample.R | 71 ++--- R/plotsurf.R | 89 +++--- R/read.bnd.R | 253 +++++++++---------- R/read.gra.R | 144 +++++----- R/ringDirxy.R | 153 ++--------- R/round.bnd.R | 25 - R/shp2bnd.R | 392 +++++++++++++---------------- R/spAndBndConversion.R | 351 +++++++++++--------------- R/write.bnd.R | 118 +++----- R/write.gra.R | 63 ++-- man/BayesX-package.Rd | 29 -- man/hpd.Rd | 17 - 30 files changed, 1922 insertions(+), 2297 deletions(-)
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides: 'let()' which
converts non-standard evaluation interfaces to parametric standard
evaluation interface, 'qc()' quoting concatenate, 'DebugFnW()' to
capture function context on error for debugging, dot-pipe, ':='
named map builder, and lambda-abstraction.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.4.0 dated 2018-04-03 and 1.4.1 dated 2018-05-18
DESCRIPTION | 10 +- MD5 | 45 ++++----- NAMESPACE | 6 + NEWS.md | 12 ++ R/bpipe.R | 99 +++++++++----------- R/cf.R | 2 R/match_order.R | 1 R/namedMapBuilder.R | 10 -- R/view.R |only README.md | 193 +++++++++++++++++++++++++++------------ inst/doc/CornerCases.html | 4 inst/doc/DebugFnW.html | 6 - inst/doc/FrameTools.html | 4 inst/doc/Named_Arguments.html | 4 inst/doc/SubstitutionModes.html | 4 inst/doc/dot_pipe.html | 4 inst/doc/lambda.html | 4 inst/doc/let.html | 4 inst/doc/named_map_builder.html | 4 inst/doc/wrapr_applicable.html | 4 man/match_order.Rd | 1 man/named_map_builder.Rd | 1 man/view.Rd |only tests/testthat/test_draw_frame.R |only tests/testthat/test_pipe.R | 6 + 25 files changed, 265 insertions(+), 163 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository 'Xeno-Canto' <http://xeno-canto.org/>, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Diff between warbleR versions 1.1.12 dated 2018-03-14 and 1.1.13 dated 2018-05-18
warbleR-1.1.12/warbleR/R/class.selection.table.R |only warbleR-1.1.12/warbleR/R/contour_tailor.R |only warbleR-1.1.12/warbleR/R/is.selection.table.R |only warbleR-1.1.12/warbleR/R/make.selection.table.R |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase1.R |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase1.Rmd |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase1.html |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase2.R |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase2.Rmd |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase2.html |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase3.R |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase3.Rmd |only warbleR-1.1.12/warbleR/inst/doc/warbleR_workflow_phase3.html |only warbleR-1.1.12/warbleR/man/contour_tailor.Rd |only warbleR-1.1.12/warbleR/man/is.selection.table.Rd |only warbleR-1.1.12/warbleR/vignettes/154161-autodetec.th10.jpg |only warbleR-1.1.12/warbleR/vignettes/Catalog_p1_labels.jpeg |only warbleR-1.1.12/warbleR/vignettes/Catalog_p1_nolabels.jpeg |only warbleR-1.1.12/warbleR/vignettes/Logo_Warble-azul_small_margin.png |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154070.wav-13_badend.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072-p1.jpg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072.wav-104-.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072.wav-104-trackfreqs.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072.wav-148-dfDTW.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072.wav-8-snr.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154072.wav-8-snr2.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154138.wav-33-sp.en.ts.jpeg |only warbleR-1.1.12/warbleR/vignettes/Phaethornis-longirostris-154161.wav-131_badstart.jpeg |only warbleR-1.1.12/warbleR/vignettes/Raven_sels.csv |only warbleR-1.1.12/warbleR/vignettes/Tinamus-major-154191.wav-6-dfDTW.jpeg |only warbleR-1.1.12/warbleR/vignettes/Tinamus-major-154191.wav-6-frange.jpeg |only warbleR-1.1.12/warbleR/vignettes/comp.meth-XCORR-dfDTW-5-12-15-17.jpeg |only warbleR-1.1.12/warbleR/vignettes/manualoc.jpg |only warbleR-1.1.12/warbleR/vignettes/seltailor_output.csv |only warbleR-1.1.12/warbleR/vignettes/song_types_spectros.jpg |only warbleR-1.1.12/warbleR/vignettes/warbleR_workflow_phase1.Rmd |only warbleR-1.1.12/warbleR/vignettes/warbleR_workflow_phase2.Rmd |only warbleR-1.1.12/warbleR/vignettes/warbleR_workflow_phase3.Rmd |only warbleR-1.1.13/warbleR/DESCRIPTION | 17 warbleR-1.1.13/warbleR/MD5 | 306 +++++----- warbleR-1.1.13/warbleR/NAMESPACE | 57 + warbleR-1.1.13/warbleR/NEWS.md | 29 warbleR-1.1.13/warbleR/R/autodetec.R | 50 + warbleR-1.1.13/warbleR/R/catalog.R | 144 ++-- warbleR-1.1.13/warbleR/R/catalog2pdf.R | 29 warbleR-1.1.13/warbleR/R/checksels.R | 149 +++- warbleR-1.1.13/warbleR/R/checkwavs.R | 39 + warbleR-1.1.13/warbleR/R/color.spectro.R | 38 + warbleR-1.1.13/warbleR/R/compare.methods.R | 106 ++- warbleR-1.1.13/warbleR/R/consolidate.R | 35 + warbleR-1.1.13/warbleR/R/coor.graph.R | 31 + warbleR-1.1.13/warbleR/R/coor.test.R | 70 +- warbleR-1.1.13/warbleR/R/cut_sels.R | 54 + warbleR-1.1.13/warbleR/R/dfDTW.R | 44 + warbleR-1.1.13/warbleR/R/dfts.R | 163 +++-- warbleR-1.1.13/warbleR/R/ffDTW.R | 41 + warbleR-1.1.13/warbleR/R/ffts.R | 55 + warbleR-1.1.13/warbleR/R/filtersels.R | 59 + warbleR-1.1.13/warbleR/R/fix_cntr_wrblr_int.R | 37 - warbleR-1.1.13/warbleR/R/fixwavs.R | 34 + warbleR-1.1.13/warbleR/R/frange.R | 54 + warbleR-1.1.13/warbleR/R/frange.detec.R | 34 + warbleR-1.1.13/warbleR/R/frd_plot_wrblr_int.R | 14 warbleR-1.1.13/warbleR/R/inflections.R |only warbleR-1.1.13/warbleR/R/lspec.R | 53 + warbleR-1.1.13/warbleR/R/lspec2pdf.R | 18 warbleR-1.1.13/warbleR/R/manualoc.R | 83 ++ warbleR-1.1.13/warbleR/R/move.imgs.R | 96 ++- warbleR-1.1.13/warbleR/R/mp32wav.R | 27 warbleR-1.1.13/warbleR/R/new_function_names.R |only warbleR-1.1.13/warbleR/R/open_wd.R |only warbleR-1.1.13/warbleR/R/ovlp_sels.R | 30 warbleR-1.1.13/warbleR/R/querxc.R | 39 + warbleR-1.1.13/warbleR/R/read_wave.R |only warbleR-1.1.13/warbleR/R/rm_sil.R | 27 warbleR-1.1.13/warbleR/R/selec.table-data.R | 3 warbleR-1.1.13/warbleR/R/selec_table-data.R |only warbleR-1.1.13/warbleR/R/selection_table.R |only warbleR-1.1.13/warbleR/R/seltailor.R | 117 ++- warbleR-1.1.13/warbleR/R/sig2noise.R | 71 +- warbleR-1.1.13/warbleR/R/sim.coor.sing-data.R | 4 warbleR-1.1.13/warbleR/R/sim_coor_sing-data.R |only warbleR-1.1.13/warbleR/R/sim_songs.R | 33 - warbleR-1.1.13/warbleR/R/snrspecs.R | 114 ++- warbleR-1.1.13/warbleR/R/song_param.R |only warbleR-1.1.13/warbleR/R/sp.en.ts.R | 56 + warbleR-1.1.13/warbleR/R/spec_param.R | 59 + warbleR-1.1.13/warbleR/R/specan.R | 52 + warbleR-1.1.13/warbleR/R/specreator.R | 187 ++++-- warbleR-1.1.13/warbleR/R/spectro_wrblr_int.R | 7 warbleR-1.1.13/warbleR/R/spectro_wrblr_int2.R | 4 warbleR-1.1.13/warbleR/R/track_harm.R | 56 + warbleR-1.1.13/warbleR/R/trackfreqs.R | 111 ++- warbleR-1.1.13/warbleR/R/try_na.R |only warbleR-1.1.13/warbleR/R/warbleR-package.R | 14 warbleR-1.1.13/warbleR/R/warbleR_options.R |only warbleR-1.1.13/warbleR/R/wavdur.R | 36 + warbleR-1.1.13/warbleR/R/xcmaps.R | 36 + warbleR-1.1.13/warbleR/R/xcorr.R | 84 +- warbleR-1.1.13/warbleR/R/xcorr.graph.R | 20 warbleR-1.1.13/warbleR/R/zzz.R | 44 + warbleR-1.1.13/warbleR/build/vignette.rds |binary warbleR-1.1.13/warbleR/data/new_function_names.rda |only warbleR-1.1.13/warbleR/data/selec.table.rda |binary warbleR-1.1.13/warbleR/data/selec_table.rda |only warbleR-1.1.13/warbleR/data/sim.coor.sing.rda |binary warbleR-1.1.13/warbleR/data/sim_coor_sing.rda |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_01.R |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_01.Rmd |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_01.html |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_02.R |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_02.Rmd |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_02.html |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_03.R |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_03.Rmd |only warbleR-1.1.13/warbleR/inst/doc/warbleR_workflow_03.html |only warbleR-1.1.13/warbleR/man/auto_detec.Rd |only warbleR-1.1.13/warbleR/man/autodetec.Rd | 2 warbleR-1.1.13/warbleR/man/catalog.Rd | 16 warbleR-1.1.13/warbleR/man/catalog2pdf.Rd | 2 warbleR-1.1.13/warbleR/man/check_sels.Rd | 20 warbleR-1.1.13/warbleR/man/check_wavs.Rd |only warbleR-1.1.13/warbleR/man/checkwavs.Rd | 2 warbleR-1.1.13/warbleR/man/color_spectro.Rd |only warbleR-1.1.13/warbleR/man/compare.methods.Rd | 6 warbleR-1.1.13/warbleR/man/compare_methods.Rd |only warbleR-1.1.13/warbleR/man/consolidate.Rd | 9 warbleR-1.1.13/warbleR/man/coor.test.Rd | 27 warbleR-1.1.13/warbleR/man/coor_graph.Rd |only warbleR-1.1.13/warbleR/man/coor_test.Rd |only warbleR-1.1.13/warbleR/man/cut_sels.Rd | 2 warbleR-1.1.13/warbleR/man/dfDTW.Rd | 3 warbleR-1.1.13/warbleR/man/df_DTW.Rd |only warbleR-1.1.13/warbleR/man/df_ts.Rd |only warbleR-1.1.13/warbleR/man/dfts.Rd | 21 warbleR-1.1.13/warbleR/man/ffDTW.Rd | 2 warbleR-1.1.13/warbleR/man/ff_DTW.Rd |only warbleR-1.1.13/warbleR/man/ff_ts.Rd |only warbleR-1.1.13/warbleR/man/ffts.Rd | 3 warbleR-1.1.13/warbleR/man/filter_sels.Rd |only warbleR-1.1.13/warbleR/man/filtersels.Rd | 7 warbleR-1.1.13/warbleR/man/fix_extended_selection_table.Rd |only warbleR-1.1.13/warbleR/man/fix_wavs.Rd |only warbleR-1.1.13/warbleR/man/frange.Rd | 2 warbleR-1.1.13/warbleR/man/frange.detec.Rd | 2 warbleR-1.1.13/warbleR/man/freq_range.Rd |only warbleR-1.1.13/warbleR/man/freq_range_detec.Rd |only warbleR-1.1.13/warbleR/man/full_spec.Rd |only warbleR-1.1.13/warbleR/man/full_spec2pdf.Rd |only warbleR-1.1.13/warbleR/man/inflections.Rd |only warbleR-1.1.13/warbleR/man/is_extended_selection_table.Rd |only warbleR-1.1.13/warbleR/man/is_selection_table.Rd |only warbleR-1.1.13/warbleR/man/lspec.Rd | 6 warbleR-1.1.13/warbleR/man/make.selection.table.Rd | 61 - warbleR-1.1.13/warbleR/man/manual_loc.Rd |only warbleR-1.1.13/warbleR/man/manualoc.Rd | 16 warbleR-1.1.13/warbleR/man/move.imgs.Rd | 12 warbleR-1.1.13/warbleR/man/move_imgs.Rd |only warbleR-1.1.13/warbleR/man/new_function_names.Rd |only warbleR-1.1.13/warbleR/man/open_wd.Rd |only warbleR-1.1.13/warbleR/man/ovlp_sels.Rd | 2 warbleR-1.1.13/warbleR/man/print.extended_selection_table.Rd |only warbleR-1.1.13/warbleR/man/print.selection_table.Rd |only warbleR-1.1.13/warbleR/man/quer_xc.Rd |only warbleR-1.1.13/warbleR/man/querxc.Rd | 2 warbleR-1.1.13/warbleR/man/rbind.extended_selection_table.Rd |only warbleR-1.1.13/warbleR/man/rbind.selection_table.Rd |only warbleR-1.1.13/warbleR/man/read_wave.Rd |only warbleR-1.1.13/warbleR/man/se_ts.Rd |only warbleR-1.1.13/warbleR/man/sel_tailor.Rd |only warbleR-1.1.13/warbleR/man/selec.table.Rd | 3 warbleR-1.1.13/warbleR/man/selec_table.Rd |only warbleR-1.1.13/warbleR/man/selection_table.Rd |only warbleR-1.1.13/warbleR/man/seltailor.Rd | 12 warbleR-1.1.13/warbleR/man/sig2noise.Rd | 19 warbleR-1.1.13/warbleR/man/sim.coor.sing.Rd | 4 warbleR-1.1.13/warbleR/man/sim_coor_sing.Rd |only warbleR-1.1.13/warbleR/man/sim_songs.Rd | 4 warbleR-1.1.13/warbleR/man/snr_specs.Rd |only warbleR-1.1.13/warbleR/man/snrspecs.Rd | 11 warbleR-1.1.13/warbleR/man/song_param.Rd |only warbleR-1.1.13/warbleR/man/sp.en.ts.Rd | 5 warbleR-1.1.13/warbleR/man/spec_an.Rd |only warbleR-1.1.13/warbleR/man/spec_param.Rd | 11 warbleR-1.1.13/warbleR/man/specan.Rd | 4 warbleR-1.1.13/warbleR/man/specreator.Rd | 30 warbleR-1.1.13/warbleR/man/spectrograms.Rd |only warbleR-1.1.13/warbleR/man/sub-.extended_selection_table.Rd |only warbleR-1.1.13/warbleR/man/sub-.selection_table.Rd |only warbleR-1.1.13/warbleR/man/track_freqs.Rd |only warbleR-1.1.13/warbleR/man/track_harm.Rd | 8 warbleR-1.1.13/warbleR/man/trackfreqs.Rd | 8 warbleR-1.1.13/warbleR/man/try_na.Rd |only warbleR-1.1.13/warbleR/man/warbleR.Rd | 6 warbleR-1.1.13/warbleR/man/warbleR_options.Rd |only warbleR-1.1.13/warbleR/man/wav_dur.Rd |only warbleR-1.1.13/warbleR/man/x_corr.Rd |only warbleR-1.1.13/warbleR/man/xc_maps.Rd |only warbleR-1.1.13/warbleR/man/xcorr.Rd | 2 warbleR-1.1.13/warbleR/man/xcorr.graph.Rd | 6 warbleR-1.1.13/warbleR/man/xcorr_graph.Rd |only warbleR-1.1.13/warbleR/vignettes/154161-autodetec.th15.jpg |binary warbleR-1.1.13/warbleR/vignettes/Catalog_p1.jpeg |only warbleR-1.1.13/warbleR/vignettes/Phae_hisnr.csv | 52 - warbleR-1.1.13/warbleR/vignettes/Phae_hisnrt.csv |only warbleR-1.1.13/warbleR/vignettes/acoustic_parameters.csv | 46 - warbleR-1.1.13/warbleR/vignettes/logo.png |only warbleR-1.1.13/warbleR/vignettes/warbleR_workflow_01.Rmd |only warbleR-1.1.13/warbleR/vignettes/warbleR_workflow_02.Rmd |only warbleR-1.1.13/warbleR/vignettes/warbleR_workflow_03.Rmd |only warbleR-1.1.13/warbleR/vignettes/xcorr_graph.jpeg |binary 211 files changed, 2657 insertions(+), 969 deletions(-)
Title: Sierpinski Pedal Triangle
Description: A collection of algorithms related to Sierpinski
pedal triangle (SPT).
Author: Bin Wang <bwang@southalabama.edu>.
Maintainer: Bin Wang <bwang@southalabama.edu>
Diff between spt versions 1.13-8-8 dated 2013-08-08 and 2.5.1 dated 2018-05-18
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 14 +++++++++++++- man/chaos.Rd | 1 + man/spt.Rd | 1 + man/st.Rd | 1 + 6 files changed, 27 insertions(+), 11 deletions(-)
Title: Simulate Survival Data
Description: Simulate survival times from standard parametric survival
distributions (exponential, Weibull, Gompertz), 2-component mixture
distributions, or a user-defined hazard, log hazard, cumulative hazard,
or log cumulative hazard function. Baseline covariates can be included
under a proportional hazards assumption.
Time dependent effects (i.e. non-proportional hazards) can be included by
interacting covariates with linear time or a user-defined function of time.
Clustered event times are also accommodated.
The 2-component mixture distributions can allow for a variety of flexible
baseline hazard functions reflecting those seen in practice.
If the user wishes to provide a user-defined
hazard or log hazard function then this is possible, and the resulting
cumulative hazard function does not need to have a closed-form solution.
Note that this package is modelled on the 'survsim' package available in
the 'Stata' software (see Crowther and Lambert (2012)
<http://www.stata-journal.com/sjpdf.html?articlenum=st0275> or
Crowther and Lambert (2013) <doi:10.1002/sim.5823>).
Author: Sam Brilleman [cre, aut, cph],
Alessandro Gasparini [ctb]
Maintainer: Sam Brilleman <sam.brilleman@monash.edu>
Diff between simsurv versions 0.2.0 dated 2018-03-05 and 0.2.2 dated 2018-05-18
DESCRIPTION | 26 +++++++----- MD5 | 14 +++--- R/simsurv.R | 82 +++++++++++++++++++++++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/simsurv_technical.html | 4 - inst/doc/simsurv_usage.html | 20 ++++----- man/simsurv.Rd | 13 +++--- 8 files changed, 91 insertions(+), 68 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M.Draminski, A.Rada-Iglesias, S.Enroth, C.Wadelius, J. Koronacki, J.Komorowski (2008) <doi:10.1093/bioinformatics/btm486>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.2.10 dated 2018-03-27 and 1.2.11 dated 2018-05-18
DESCRIPTION | 8 ++--- MD5 | 25 ++++++++-------- NEWS.md | 6 +++ R/onLoad.R | 6 +-- R/rmcfs.R | 50 +++++++++++++++++++------------- build/vignette.rds |binary inst/doc/jss2621.pdf |binary man/build.idgraph.Rd | 10 +++--- man/mcfs.Rd | 2 - man/plot.idgraph.Rd | 2 - tests/testthat/test-man.build.idgraph.R | 2 - tests/testthat/test-man.mcfs.R | 2 - tests/testthat/test-man.plot.idgraph.R | 2 - vignettes/Figures/topFeatures2.pdf |only 14 files changed, 67 insertions(+), 48 deletions(-)
Title: Classes and Methods for Training and Using Binary Prediction
Models
Description: Defines classes and methods to learn models and use them
to predict binary outcomes. These are generic tools, but we also
include specific examples for many common classifiers.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Modeler versions 3.4.2 dated 2017-07-13 and 3.4.3 dated 2018-05-18
Modeler-3.4.2/Modeler/man/Modeler-package.Rd |only Modeler-3.4.3/Modeler/DESCRIPTION | 8 +++---- Modeler-3.4.3/Modeler/MD5 | 19 ++++++++---------- Modeler-3.4.3/Modeler/NEWS | 26 ++++++++++++++++++++++++- Modeler-3.4.3/Modeler/R/m01-Model.R | 6 ++--- Modeler-3.4.3/Modeler/R/m02-FittedModel.R | 12 +++++------ Modeler-3.4.3/Modeler/build/vignette.rds |binary Modeler-3.4.3/Modeler/inst/doc/Modeler.pdf |binary Modeler-3.4.3/Modeler/man/FittedModel-class.Rd | 3 -- Modeler-3.4.3/Modeler/man/Modeler.Rd | 4 --- Modeler-3.4.3/Modeler/man/learn.Rd | 8 ------- 11 files changed, 47 insertions(+), 39 deletions(-)
Title: Joyplots in 'ggplot2'
Description: Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [cre, aut]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggjoy versions 0.4.0 dated 2017-09-15 and 0.4.1 dated 2018-05-18
ggjoy-0.4.0/ggjoy/inst/doc/gallery.R |only ggjoy-0.4.0/ggjoy/inst/doc/gallery.Rmd |only ggjoy-0.4.0/ggjoy/inst/doc/gallery.html |only ggjoy-0.4.0/ggjoy/inst/doc/introduction.R |only ggjoy-0.4.0/ggjoy/tests |only ggjoy-0.4.0/ggjoy/vignettes/gallery.Rmd |only ggjoy-0.4.1/ggjoy/DESCRIPTION | 21 - ggjoy-0.4.1/ggjoy/MD5 | 49 --- ggjoy-0.4.1/ggjoy/NAMESPACE | 2 ggjoy-0.4.1/ggjoy/NEWS | 5 ggjoy-0.4.1/ggjoy/R/ggjoy.R | 2 ggjoy-0.4.1/ggjoy/README.md | 2 ggjoy-0.4.1/ggjoy/build/vignette.rds |binary ggjoy-0.4.1/ggjoy/inst/doc/introduction.Rmd | 231 --------------- ggjoy-0.4.1/ggjoy/inst/doc/introduction.html | 409 ++++++++++++--------------- ggjoy-0.4.1/ggjoy/vignettes/introduction.Rmd | 231 --------------- 16 files changed, 211 insertions(+), 741 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changes in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 1.3.0 dated 2018-03-15 and 1.3.1 dated 2018-05-18
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 11 insertions(+), 7 deletions(-)