Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative
signal is expected to be localized, a series of filters determine which peak
signals are characterized by an implausible spatial distribution. The filters
reduce the dataset dimensionality and increase its information vs noise ratio,
improving the quality of the unsupervised analysis results, reducing data
dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Diff between SPUTNIK versions 1.1.1 dated 2018-10-25 and 1.1.2 dated 2019-04-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 +++++ R/sparseness_funcs.R | 4 ++-- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de> and Matthias Schmid <matthias.schmid@imbie.uni-bonn.de>
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.3.4 dated 2018-08-01 and 1.4.0 dated 2019-04-16
DESCRIPTION | 10 +- MD5 | 23 ++-- NAMESPACE | 1 R/DiscSurvDataTransform.R | 70 ++++++++++++++ R/DiscSurvEvaluation.R | 170 +++++++++++++++++++++++++++--------- man/dataCensoring.Rd | 3 man/dataLongMultiSpell.Rd |only man/devResidShort.Rd | 4 man/discSurv-package.Rd | 4 man/evalCindex.Rd |only man/evalIntPredErr.Rd |only man/intPredErrDisc.Rd | 2 man/predErrDiscShort.Rd | 2 tests/UnitTestsDiscSurvEvaluation.R | 2 14 files changed, 230 insertions(+), 61 deletions(-)
Title: Statistical Visualization Tools
Description: Visualization functions in the applications of translational medicine (TM) and biomarker (BM) development to compare groups by statistically visualizing data and/or results of analyses, such as visualizing data by displaying in one figure different groups' histograms, boxplots, densities, scatter plots, error-bar plots, or trajectory plots, by displaying scatter plots of top principal components or dendrograms with data points colored based on group information, or visualizing volcano plots to check the results of whole genome analyses for gene differential expression.
Author: Wenfei Zhang [aut, cre],
Weiliang Qiu [aut, ctb],
Xuan Lin [aut, ctb],
Donghui Zhang [aut, ctb]
Maintainer: Wenfei Zhang <Wenfei.Zhang@sanofi.com>
Diff between statVisual versions 1.0.5 dated 2019-03-15 and 1.0.9 dated 2019-04-16
DESCRIPTION | 11 MD5 | 26 NAMESPACE | 17 NEWS | 23 R/statVisual.R | 2911 ++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/statVisual.R | 33 inst/doc/statVisual.Rmd | 33 inst/doc/statVisual.html | 66 - man/BiAxisErrBar.Rd | 281 ++-- man/Box.Rd | 4 man/Heat.Rd | 269 ++-- man/PCA_score.Rd | 6 vignettes/statVisual.Rmd | 33 14 files changed, 1944 insertions(+), 1769 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.1.1 dated 2019-03-29 and 0.1.2 dated 2019-04-16
pct-0.1.1/pct/man/figures/README-distance-decay-1.png |only pct-0.1.1/pct/man/figures/README-rnet-1.png |only pct-0.1.1/pct/man/figures/README-routes-vital-1.png |only pct-0.1.1/pct/man/figures/README-unnamed-chunk-4-1.png |only pct-0.1.1/pct/man/figures/README-unnamed-chunk-8-1.png |only pct-0.1.2/pct/DESCRIPTION | 6 - pct-0.1.2/pct/MD5 | 40 +++--- pct-0.1.2/pct/NEWS.md | 7 + pct-0.1.2/pct/R/data.R | 16 ++ pct-0.1.2/pct/R/get_pct.R | 37 ++++-- pct-0.1.2/pct/R/uptake.R | 10 - pct-0.1.2/pct/README.md | 100 ++++++++++++++--- pct-0.1.2/pct/data/santiago_routes_cs.rda |only pct-0.1.2/pct/inst/doc/pct-international.R | 46 +++++++ pct-0.1.2/pct/inst/doc/pct-international.Rmd | 71 +++++++++++- pct-0.1.2/pct/inst/doc/pct-international.html | 67 ++++++++++- pct-0.1.2/pct/inst/doc/pct.html | 29 ++-- pct-0.1.2/pct/man/figures/README-decay-1.png |only pct-0.1.2/pct/man/figures/README-rnetgove-1.png |only pct-0.1.2/pct/man/figures/README-routes_vital-1.png |only pct-0.1.2/pct/man/get_pct.Rd | 9 + pct-0.1.2/pct/man/santiago_routes_cs.Rd |only pct-0.1.2/pct/man/uptake_pct_godutch.Rd | 4 pct-0.1.2/pct/man/uptake_pct_govtarget.Rd | 6 - pct-0.1.2/pct/tests/testthat/test-get-pct.R | 12 -- pct-0.1.2/pct/vignettes/pct-international.Rmd | 71 +++++++++++- 26 files changed, 429 insertions(+), 102 deletions(-)
Title: Tune Random Forest of the 'ranger' Package
Description: Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
Author: Philipp Probst [aut, cre],
Simon Klau [ctb]
Maintainer: Philipp Probst <philipp_probst@gmx.de>
Diff between tuneRanger versions 0.4 dated 2019-01-22 and 0.5 dated 2019-04-16
DESCRIPTION | 10 +++--- MD5 | 19 +++++++----- NAMESPACE | 11 +++++++ R/RLearner_classif_tuneMtryFast.R |only R/RLearner_regr_tuneMtryFast.R |only R/RLearner_surv_tuneMtryFast.R |only R/tuneMtryFast.R |only R/tuneRanger.R | 2 - README.md | 58 ++++++++++++++++++++++++-------------- inst/CITATION | 5 +-- man/tuneMtryFast.Rd |only man/tuneRanger.Rd | 2 - tests/testthat/test_base.R | 22 ++++++++++++++ 13 files changed, 92 insertions(+), 37 deletions(-)
Title: Formatting and Harmonizing Ecological Trait-Data
Description: Assistance for handling ecological trait data and applying the
Ecological Trait-Data Standard terminology (Schneider et al. 2018
<doi:10.1101/328302>). There are two major use cases: (1) preparation of
own trait datasets for upload into public data bases, and (2) harmonizing
trait datasets from different sources by re-formatting them into a unified
format. See 'traitdataform' website for full documentation.
Author: Florian D. Schneider [aut, cre]
(<https://orcid.org/0000-0002-1494-5684>),
Caterina Penone [ctb] (<https://orcid.org/0000-0002-8170-6659>),
Andreas Ostrowski [ctb] (<https://orcid.org/0000-0002-2033-779X>),
Dennis Heimann [ctb],
Felix Neff [ctb],
Markus J. Ankenbrand [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>
Diff between traitdataform versions 0.5.2 dated 2018-12-30 and 0.5.3 dated 2019-04-16
DESCRIPTION | 8 MD5 | 24 NEWS.md | 9 R/data.R | 8 R/glossary.R | 2 R/utils.R | 2 README.md | 16 build/vignette.rds |binary inst/doc/traitdataform.html | 1639 ++++++++++++++++++++++---------------------- man/as.traitdata.Rd | 2 man/heteroptera_raw.Rd | 4 man/mammaldiet.Rd | 4 man/read.service.Rd | 2 13 files changed, 879 insertions(+), 841 deletions(-)
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre],
Flavio Poletti [aut],
Danton Noriega-Goodwin [aut],
Mark Padgham [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.3.8 dated 2019-03-04 and 0.4.0 dated 2019-04-16
tidytransit-0.3.8/tidytransit/data/feedlist_df.rda |only tidytransit-0.3.8/tidytransit/data/route_type_names_df.rda |only tidytransit-0.3.8/tidytransit/inst/doc/GTFS-table-relationships.R |only tidytransit-0.3.8/tidytransit/inst/doc/GTFS-table-relationships.Rmd |only tidytransit-0.3.8/tidytransit/inst/doc/GTFS-table-relationships.html |only tidytransit-0.3.8/tidytransit/man/feedlist_df.Rd |only tidytransit-0.3.8/tidytransit/man/get_date_service_table.Rd |only tidytransit-0.3.8/tidytransit/man/gtfs_set_hms_times.Rd |only tidytransit-0.3.8/tidytransit/man/route_type_names_df.Rd |only tidytransit-0.3.8/tidytransit/vignettes/GTFS-table-relationships.Rmd |only tidytransit-0.4.0/tidytransit/DESCRIPTION | 18 tidytransit-0.4.0/tidytransit/MD5 | 67 +- tidytransit-0.4.0/tidytransit/NAMESPACE | 7 tidytransit-0.4.0/tidytransit/R/data.R | 4 tidytransit-0.4.0/tidytransit/R/frequencies.R | 48 - tidytransit-0.4.0/tidytransit/R/plot.R | 8 tidytransit-0.4.0/tidytransit/R/service.R | 54 + tidytransit-0.4.0/tidytransit/R/spatial.R | 6 tidytransit-0.4.0/tidytransit/R/time.R | 20 tidytransit-0.4.0/tidytransit/R/trips.R |only tidytransit-0.4.0/tidytransit/build/vignette.rds |binary tidytransit-0.4.0/tidytransit/data/feedlist.rda |only tidytransit-0.4.0/tidytransit/data/route_type_names.rda |only tidytransit-0.4.0/tidytransit/inst/doc/frequency.R |only tidytransit-0.4.0/tidytransit/inst/doc/frequency.Rmd |only tidytransit-0.4.0/tidytransit/inst/doc/frequency.html |only tidytransit-0.4.0/tidytransit/inst/doc/introduction.R | 49 + tidytransit-0.4.0/tidytransit/inst/doc/introduction.Rmd | 164 +++-- tidytransit-0.4.0/tidytransit/inst/doc/introduction.html | 293 ++++------ tidytransit-0.4.0/tidytransit/inst/doc/servicepatterns.R |only tidytransit-0.4.0/tidytransit/inst/doc/servicepatterns.Rmd |only tidytransit-0.4.0/tidytransit/inst/doc/servicepatterns.html |only tidytransit-0.4.0/tidytransit/inst/doc/timetable.R |only tidytransit-0.4.0/tidytransit/inst/doc/timetable.Rmd |only tidytransit-0.4.0/tidytransit/inst/doc/timetable.html |only tidytransit-0.4.0/tidytransit/man/feedlist.Rd |only tidytransit-0.4.0/tidytransit/man/get_route_frequency.Rd | 17 tidytransit-0.4.0/tidytransit/man/get_stop_frequency.Rd | 14 tidytransit-0.4.0/tidytransit/man/gtfs_as_sf.Rd | 2 tidytransit-0.4.0/tidytransit/man/route_type_names.Rd |only tidytransit-0.4.0/tidytransit/man/set_date_service_table.Rd |only tidytransit-0.4.0/tidytransit/man/set_hms_times.Rd |only tidytransit-0.4.0/tidytransit/man/set_servicepattern.Rd |only tidytransit-0.4.0/tidytransit/man/set_trippattern.Rd |only tidytransit-0.4.0/tidytransit/tests/testthat/test-headways.R | 6 tidytransit-0.4.0/tidytransit/tests/testthat/test-time.R | 12 tidytransit-0.4.0/tidytransit/vignettes/frequency.Rmd |only tidytransit-0.4.0/tidytransit/vignettes/introduction.Rmd | 164 +++-- tidytransit-0.4.0/tidytransit/vignettes/servicepatterns.Rmd |only tidytransit-0.4.0/tidytransit/vignettes/timetable.Rmd |only 50 files changed, 564 insertions(+), 389 deletions(-)
Title: Client for the Cancer Imaging Archive REST API
Description: A wrapper for The Cancer Imaging Archive's REST API. The Cancer
Imaging Archive (TCIA) hosts de-identified medical images of cancer
available for public download, as well as rich metadata for each image
series. TCIA provides a REST API for programmatic access to the data.
This package provides simple functions to access each API endpoint.
For more information, see <https://github.com/pamelarussell/TCIApathfinder>
and TCIA's website.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@gmail.com>
Diff between TCIApathfinder versions 1.0.4 dated 2019-03-21 and 1.0.5 dated 2019-04-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/introduction.html | 10 +++++----- inst/doc/radiomics.html | 4 ++-- 5 files changed, 20 insertions(+), 16 deletions(-)
More information about TCIApathfinder at CRAN
Permanent link
Title: Utilities for Convenient Extraction of Medical Image Metadata
Description: A collection of utilities for navigating medical image data. The DICOM and NIfTI formats
are supported. Functions provide simple interfaces to the data and metadata contained in these formats.
A particular emphasis on metadata allows simple conversion of image metadata to familiar R data structures
such as lists and data frames. Where possible, generic functions can silently process either DICOM or
NIfTI data. Additionally, image data can be extracted and viewed.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@gmail.com>
Diff between radtools versions 1.0.4 dated 2019-03-13 and 1.0.5 dated 2019-04-16
DESCRIPTION | 10 ++--- MD5 | 14 +++---- NEWS.md | 4 ++ inst/doc/oro_compare.html | 6 +-- inst/doc/radtools_usage.html | 6 +-- tests/testthat/setup-dicomdata.R | 60 ++++++++++++++++++++++++++++--- tests/testthat/test_image_import_nifti.R | 1 tests/testthat/test_metadata_dicom.R | 1 8 files changed, 79 insertions(+), 23 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints
objects are provided. Non-Gaussian models are fit using INLA, and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.7.7 dated 2019-03-06 and 1.7.8 dated 2019-04-16
DESCRIPTION | 12 +++++------ MD5 | 14 ++++++------- build/geostatsp.pdf |binary inst/doc/glgm.pdf |binary inst/doc/lgcp.pdf |binary man/glgm.Rd | 6 +++-- man/matern.Rd | 36 +++++++++++++++++++++-------------- src/matern.c | 53 ++++++++++++++++++++++++++++------------------------ 8 files changed, 68 insertions(+), 53 deletions(-)
Title: Categorical Bayesian Network Inference
Description: Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov <nhbalov@gmail.com>
Diff between catnet versions 1.15.3 dated 2017-10-26 and 1.15.5 dated 2019-04-16
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- R/catnet.joint.prob.R | 4 ++-- README.md |only build/vignette.rds |binary inst/doc/catnet.R | 12 ++++++------ inst/doc/catnet.Rnw | 10 +++++----- inst/doc/catnet.pdf |binary src/catnet_class.h | 4 ++-- src/catnet_rexport.cpp | 40 ++++++++++++++++++++++++---------------- src/rcatnet.cpp | 10 ++++++---- vignettes/catnet.Rnw | 10 +++++----- 12 files changed, 64 insertions(+), 53 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.3 dated 2019-03-28 and 2.4 dated 2019-04-16
DESCRIPTION | 12 +- MD5 | 12 +- NEWS | 4 inst/doc/the-BART-R-package.Rnw | 169 +++++++++++++++++++-------------------- inst/doc/the-BART-R-package.pdf |binary src/Makevars.in | 4 vignettes/the-BART-R-package.Rnw | 169 +++++++++++++++++++-------------------- 7 files changed, 184 insertions(+), 186 deletions(-)
Title: Compute Targeted Minimum Loss-Based Estimates in Right-Censored
Survival Settings
Description: Targeted estimates of marginal cumulative incidence in survival
settings with and without competing risks, including estimators that respect
bounds (Benkeser, Carone, and Gilbert. Statistics in Medicine, 2017.
<doi:10.1002/sim.7337>).
Author: David Benkeser [aut, cre, cph]
(<https://orcid.org/0000-0002-1019-8343>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>)
Maintainer: David Benkeser <benkeser@emory.edu>
Diff between survtmle versions 1.1.0 dated 2018-04-13 and 1.1.1 dated 2019-04-16
DESCRIPTION | 8 MD5 | 62 +-- NAMESPACE | 4 NEWS.md | 3 R/censoring_estimate.R | 5 R/checkInputs.R | 18 R/glm_fast.R | 61 +-- R/hazards_estimate.R | 8 R/iterated_mean_fluctuate.R | 6 R/makeDataList.R | 2 R/makeWideDataList.R | 3 R/printing.R | 3 R/survtmle.R | 4 R/timepoints.R | 3 R/tmle_hazard.R | 13 R/tmle_mean.R | 14 R/treatment_estimate.R | 2 R/updateVariables.R | 19 R/utils.R | 94 ++-- build/vignette.rds |binary inst/doc/survtmle_intro.Rmd | 6 inst/doc/survtmle_intro.html | 756 ++++++++++++++++++++++++-------------- man/checkInputs.Rd | 12 man/estimateHazards.Rd | 4 man/fluctuateHazards.Rd | 4 man/hazard_tmle.Rd | 10 man/mean_tmle.Rd | 13 man/survtmle.Rd | 11 man/updateVariables.Rd | 4 tests/testthat/test-hazard_tmle.R | 2 tests/testthat/test-timepoints.R | 3 vignettes/survtmle_intro.Rmd | 6 32 files changed, 725 insertions(+), 438 deletions(-)
Title: Bayesian Model Selection under Constraints
Description: A Bayesian regression package supporting constrained coefficient estimation and
variable selection using Stan. This includes a robust variable selection
algorithm by a horseshoe prior (<doi:10.1093/biomet/asq017>) that finds the optimal model considering main effects,
interactions as well as powers of given variables under potential parameter constraints.
Author: Marcus Groß [aut, cre],
Ricardo Fernandes [aut],
Mira Celine Klein [ctb]
Maintainer: Marcus Groß <marcus.gross@inwt-statistics.de>
Diff between BMSC versions 0.1.1 dated 2018-10-18 and 0.2.0 dated 2019-04-16
DESCRIPTION | 8 MD5 | 90 +-- NAMESPACE | 88 +-- R/NAMESPACE.R | 28 - R/classes.R | 6 R/createFormula.R | 314 ++++++------- R/estimateModel.R | 649 +++++++++++++++------------- R/method_show.R | 196 ++++---- R/plotModelFit.R | 188 ++++---- R/stanmodels.R | 74 +-- R/zzz.R | 8 inst/include/meta_header.hpp | 2 man/ConstrainedLinReg-class.Rd | 40 - man/addInteractionToVars.Rd | 52 +- man/addPowToVars.Rd | 48 +- man/constrSelEst.Rd | 138 +++-- man/createFormula.Rd | 78 +-- man/createFormulaInternal.Rd | 50 +- man/extractVarname.Rd | 36 - man/getBestModel.Rd | 46 - man/getBetaMatrix.Rd | 38 - man/handleMissingData.Rd | 52 +- man/makeInteractions.Rd | 56 +- man/makePoly.Rd | 48 +- man/plotModelFit.Rd | 50 +- man/plotModels.Rd | 38 - man/predict-ConstrainedLinReg-method.Rd | 46 - man/prepColorVec.Rd | 40 - man/prepDatForPredict.Rd | 52 +- man/prepModelNames.Rd | 32 - man/prepPlotData.Rd | 52 +- man/print.ConstrainedLinReg.Rd | 32 - man/show-ConstrainedLinReg-method.Rd | 32 - man/sortAndPaste.Rd | 34 - man/tryAsFormula.Rd | 34 - src/Makevars | 2 src/Makevars.win | 2 src/stan_files/chunks/license.stan | 28 - src/stan_files/linReg.stan | 68 +- src/stan_files/linRegHorseHoe.stan | 106 ++-- src/stan_files/linRegHorseHoeUnConstr.stan | 104 ++-- src/stan_files/linRegUnConstr.stan | 68 +- src/stan_files/linRegUnConstrXU.stan |only src/stan_files/linRegXU.stan |only tests/testthat.R | 8 tests/testthat/test-predict.R | 159 +++--- tests/testthat/test_missingValuesHandling.R | 117 ++--- 47 files changed, 1767 insertions(+), 1670 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite.
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'.
Author: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 0.92.5 dated 2019-03-15 and 0.92.6 dated 2019-04-16
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ R/fcn_misc.R | 2 +- R/qcMetric_EVD.R | 2 +- R/qcMetric_MSMSScans.R | 2 +- README.md | 1 + inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 ++-- inst/doc/PTXQC-CustomizeReport.html | 4 ++-- inst/doc/PTXQC-DragNDrop.html | 4 ++-- inst/doc/PTXQC-FAQ.html | 4 ++-- inst/doc/PTXQC-Input_And_Output_Data.html | 4 ++-- inst/doc/PTXQC-ListOfMetrics.html | 4 ++-- inst/reportTemplate/PTXQC_report_template.Rmd | 4 ++-- 13 files changed, 36 insertions(+), 35 deletions(-)
Title: Time Series Feature Extraction
Description: Methods for extracting various features from time series data. The features provided are those from Hyndman, Wang and Laptev (2013) <doi:10.1109/ICDMW.2015.104>, Kang, Hyndman and Smith-Miles (2017) <doi:10.1016/j.ijforecast.2016.09.004> and from Fulcher, Little and Jones (2013) <doi:10.1098/rsif.2013.0048>. Features include spectral entropy, autocorrelations, measures of the strength of seasonality and trend, and so on. Users can also define their own feature functions.
Author: Rob Hyndman [aut, cre] (<https://orcid.org/0000-0002-2140-5352>),
Yanfei Kang [aut] (<https://orcid.org/0000-0001-8769-6650>),
Pablo Montero-Manso [aut],
Thiyanga Talagala [aut] (<https://orcid.org/0000-0002-0656-9789>),
Earo Wang [aut] (<https://orcid.org/0000-0001-6448-5260>),
Yangzhuoran Yang [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Souhaib Ben Taieb [ctb],
Cao Hanqing [ctb],
D K Lake [ctb],
Nikolay Laptev [ctb],
J R Moorman [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between tsfeatures versions 1.0.0 dated 2019-02-06 and 1.0.1 dated 2019-04-16
DESCRIPTION | 14 MD5 | 33 NEWS.md |only R/compengine.R | 43 R/featurematrix.R | 5 R/multipleseasonal.R | 3 build/vignette.rds |binary inst/doc/tsfeatures.html | 5451 --------------------------------------- man/autocorr_features.Rd | 2 man/compengine.Rd | 2 man/dist_features.Rd | 2 man/histogram_mode.Rd | 2 man/localsimple_taures.Rd | 3 man/pred_features.Rd | 2 man/scal_features.Rd | 2 man/station_features.Rd | 2 man/std1st_der.Rd | 2 tests/testthat/test-compengine.R | 2 18 files changed, 75 insertions(+), 5495 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.5 dated 2019-01-18 and 8.6 dated 2019-04-16
DESCRIPTION | 6 MD5 | 47 ++--- NAMESPACE | 3 NEWS.md | 10 - R/arima.R | 31 ++- R/attach.R | 20 ++ R/checkresiduals.R | 2 R/clean.R | 22 +- R/dshw.r | 4 R/ggplot.R | 362 ++++++++++++++++++++++---------------------- R/graph.R | 3 R/mforecast.R | 2 R/mstl.R | 10 - R/msts.R | 20 ++ R/naive.R | 4 R/newarima2.R | 21 -- R/simulate.R | 13 - R/unitRoot.R | 17 +- README.md | 1 build/vignette.rds |binary inst/doc/JSS2008.pdf |binary man/auto.arima.Rd | 2 man/na.interp.Rd | 11 - tests/testthat/Rplots.pdf |only tests/testthat/test-arima.R | 4 25 files changed, 340 insertions(+), 275 deletions(-)
Title: Conditional Distance Correlation Based Feature Screening and
Conditional Independence Inference
Description: Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <doi:10.5705/ss.202014.0117>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.
Author: Wenhao Hu, Mian Huang, Wenliang Pan, Xueqin Wang, Canhong Wen, Yuan Tian, Heping Zhang, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between cdcsis versions 2.0.0 dated 2019-01-09 and 2.0.1 dated 2019-04-16
cdcsis-2.0.0/cdcsis/R/cdcor.ada.R |only cdcsis-2.0.1/cdcsis/DESCRIPTION | 10 cdcsis-2.0.1/cdcsis/MD5 | 45 +-- cdcsis-2.0.1/cdcsis/NAMESPACE | 3 cdcsis-2.0.1/cdcsis/NEWS.md | 4 cdcsis-2.0.1/cdcsis/R/cdcov.R | 36 +- cdcsis-2.0.1/cdcsis/R/cdcsis.R | 27 + cdcsis-2.0.1/cdcsis/R/utility.R | 5 cdcsis-2.0.1/cdcsis/man/cdcov.Rd | 14 cdcsis-2.0.1/cdcsis/man/cdcov.test.Rd | 10 cdcsis-2.0.1/cdcsis/man/cdcsis.Rd | 12 cdcsis-2.0.1/cdcsis/src/RcppExports.cpp | 17 - cdcsis-2.0.1/cdcsis/src/cdc_stats.cpp | 96 ++++++ cdcsis-2.0.1/cdcsis/src/cdc_stats.h | 83 +++++ cdcsis-2.0.1/cdcsis/src/cdc_statstics_method.cpp | 44 ++- cdcsis-2.0.1/cdcsis/src/cdc_statstics_method.h | 3 cdcsis-2.0.1/cdcsis/src/cdcsisCpp.cpp | 28 - cdcsis-2.0.1/cdcsis/src/global.h | 4 cdcsis-2.0.1/cdcsis/src/kde.cpp | 96 +++++- cdcsis-2.0.1/cdcsis/src/kde.h | 78 ++++- cdcsis-2.0.1/cdcsis/src/utility.cpp | 297 ++++++++++++++++++++- cdcsis-2.0.1/cdcsis/src/utility.h | 138 +++++++++ cdcsis-2.0.1/cdcsis/tests/testthat/test_cdc_test.R | 4 cdcsis-2.0.1/cdcsis/tests/testthat/test_cdcsis.R | 2 24 files changed, 916 insertions(+), 140 deletions(-)
Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, probabilistic and temporal Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>
Diff between BoolNet versions 2.1.4 dated 2018-06-07 and 2.1.5 dated 2019-04-16
BoolNet-2.1.4/BoolNet/inst/doc/BoolNet_package_vignette.R |only BoolNet-2.1.4/BoolNet/inst/doc/BoolNet_package_vignette.Snw |only BoolNet-2.1.4/BoolNet/inst/doc/BoolNet_package_vignette.pdf |only BoolNet-2.1.4/BoolNet/vignettes/BoolNet_package_vignette.Snw |only BoolNet-2.1.5/BoolNet/DESCRIPTION | 8 BoolNet-2.1.5/BoolNet/MD5 | 20 BoolNet-2.1.5/BoolNet/R/chooseNetwork.R | 2 BoolNet-2.1.5/BoolNet/build/vignette.rds |binary BoolNet-2.1.5/BoolNet/inst/NEWS.Rd | 6 BoolNet-2.1.5/BoolNet/inst/doc/BoolNet_package_vignette.Snw.R |only BoolNet-2.1.5/BoolNet/inst/doc/BoolNet_package_vignette.Snw.Rnw |only BoolNet-2.1.5/BoolNet/inst/doc/BoolNet_package_vignette.Snw.pdf |only BoolNet-2.1.5/BoolNet/src/attractor_search_interface.c | 259 ++++------ BoolNet-2.1.5/BoolNet/src/symbolic_simulator.c | 4 BoolNet-2.1.5/BoolNet/vignettes/BoolNet_package_vignette.Snw.Rnw |only 15 files changed, 151 insertions(+), 148 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
Details for gllvm, see Hui et al. (2015) <doi:10.1111/2041-210X.12236>
and (2017) <doi:10.1080/10618600.2016.1164708> and Niku et al. (2017)
<doi:10.1007/s13253-017-0304-7>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 1.1.2 dated 2019-01-02 and 1.1.3 dated 2019-04-16
DESCRIPTION | 8 ++++---- MD5 | 42 ++++++++++++++++++++++++------------------ NAMESPACE | 12 ++++++++++++ R/TMBtrait.R | 10 ++++++---- R/anova.gllvm.R | 2 +- R/coefplot.gllvm.R | 4 ++-- R/getPredictErr.gllvm.R |only R/getResidualCor.gllvm.R | 30 +++++++++++++----------------- R/getResidualCov.gllvm.R |only R/gllvm.R | 17 +++++++++-------- R/gllvm.VA.R | 16 +++++++++------- R/gllvm.auxiliary.R | 14 ++++++++++++++ R/plot.gllvm.R | 29 +++++++++++++++-------------- R/predict.gllvm.R |only R/residuals.gllvm.R | 5 ++++- man/anova.gllvm.Rd | 2 +- man/coefplot.gllvm.Rd | 4 ++-- man/getPredictErr.gllvm.Rd |only man/getResidualCor.gllvm.Rd | 21 ++++++++------------- man/getResidualCov.gllvm.Rd |only man/gllvm.Rd | 14 +++++++------- man/plot.gllvm.Rd | 12 +++++------- man/predict.gllvm.Rd |only man/residuals.gllvm.Rd | 3 ++- src/gllvm.cpp | 2 ++ 25 files changed, 140 insertions(+), 107 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights; see Kolenikov, 2010;
Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>,
<doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996,
<doi:10.1080/02331889708802523>).
Descriptive statistics, linear and logistic regression,
path models for manifest variables with measurement error
correction and two-level hierarchical regressions for weighted
samples are included. Statistical inference can be conducted for
multiply imputed datasets and nested multiply imputed datasets
and is in particularly suited for the analysis of plausible values
(for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016;
Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham &
Yanagida, 2016; <doi:10.17888/fdb-demo:bistE813I-16a>).
The package development was supported by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [aut, cre],
Konrad Oberwimmer [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 3.1-33 dated 2019-03-20 and 3.2-25 dated 2019-04-16
BIFIEsurvey-3.1-33/BIFIEsurvey/R/BIFIE_lavaan_survey_combine_fit_measures.R |only BIFIEsurvey-3.1-33/BIFIEsurvey/R/bifiesurvey_lavaan_fitMeasures.R |only BIFIEsurvey-3.1-33/BIFIEsurvey/R/bifiesurvey_lavaan_survey_lavaan_survey.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/DESCRIPTION | 16 BIFIEsurvey-3.2-25/BIFIEsurvey/MD5 | 100 +++-- BIFIEsurvey-3.2-25/BIFIEsurvey/NAMESPACE | 34 + BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.BIFIEcdata2BIFIEdata.R | 21 - BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.BIFIEdata2datalist.R | 9 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.bifiedata2bifiecdata.R | 15 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.data.transform.R | 31 - BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.derivedParameters.R | 36 - BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.hist.R | 55 +-- BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.lavaan.survey.R | 60 ++- BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.logistreg.R | 62 +-- BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.pathmodel.R | 5 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.survey.R | 36 + BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE.twolevelreg.R | 11 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_data_transform_process_formula.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_coef.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_fitMeasures.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_lavInspect.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_summary.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_survey_combine_partable.R | 10 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_survey_extract_dataset.R | 4 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_survey_lavaan_survey.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_lavaan_vcov.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIE_mitools_MIcombine.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIEdata.select.R | 19 - BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIEdata2svrepdesign.R | 4 BIFIEsurvey-3.2-25/BIFIEsurvey/R/BIFIEsurvey_print_term_formula.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/RcppExports.R | 10 BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_NMIcombine_results.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_NMIcombine_results_extract_parameters.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_extend_list_length2.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_lavaan_survey_NMIcombine.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_lavaan_survey_combine_fit_measures.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_nmi_error_message.R | 6 BIFIEsurvey-3.2-25/BIFIEsurvey/R/coef.BIFIE.lavaan.survey.R | 4 BIFIEsurvey-3.2-25/BIFIEsurvey/R/summary.BIFIE.lavaan.survey.R | 6 BIFIEsurvey-3.2-25/BIFIEsurvey/R/svrepdesign2BIFIEdata.R | 10 BIFIEsurvey-3.2-25/BIFIEsurvey/R/svrepdesign2datalist.R | 10 BIFIEsurvey-3.2-25/BIFIEsurvey/R/svrepdesign_extract_data.R | 6 BIFIEsurvey-3.2-25/BIFIEsurvey/build/partial.rdb |binary BIFIEsurvey-3.2-25/BIFIEsurvey/inst/CITATION | 8 BIFIEsurvey-3.2-25/BIFIEsurvey/inst/NEWS | 16 BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIE.data.transform.Rd | 35 - BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIE.derivedParameters.Rd | 10 BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIE.lavaan.survey.Rd | 42 +- BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIE.linreg.Rd | 9 BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIE.logistreg.Rd | 5 BIFIEsurvey-3.2-25/BIFIEsurvey/man/BIFIEdata2svrepdesign.Rd | 8 BIFIEsurvey-3.2-25/BIFIEsurvey/man/se.Rd | 6 BIFIEsurvey-3.2-25/BIFIEsurvey/src/RcppExports.cpp | 46 +- BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_helper.cpp | 182 +++------- BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_helper.h | 12 BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_linreg.cpp | 7 BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_logistreg.cpp |only BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_main.cpp | 140 ------- BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_wald_test.cpp | 65 +-- BIFIEsurvey-3.2-25/BIFIEsurvey/src/bifiesurvey_rcpp_wald_test.h | 8 60 files changed, 533 insertions(+), 646 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression
models with missing values in covariates or the dependent
variable using maximum likelihood or Bayesian estimation
(Ibrahim et al., 2005; <doi:10.1198/016214504000001844>).
The regression model can be nonlinear (e.g., interaction
effects, quadratic effects or B-spline functions).
Multilevel models with missing data in predictors are
available for Bayesian estimation. Substantive-model compatible
multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 1.2-4 dated 2019-01-11 and 1.3-18 dated 2019-04-16
DESCRIPTION | 15 ++++++----- MD5 | 44 +++++++++++++++++------------------ NAMESPACE | 8 ++++-- R/RcppExports.R | 2 - R/dbct_scaled.R | 6 +--- R/frm_em_avcov.R | 4 +-- R/frm_fb.R | 3 -- R/frm_fb_initial_parameters.R | 19 +++++++++------ R/frm_fb_sample_parameter_step.R | 2 - R/frm_fb_sample_parameters.R | 4 +-- R/frm_linreg_sample_parameters.R | 5 ++- R/frm_mlreg_create_design_matrices.R | 2 - R/frm_mlreg_sample_parameters.R | 5 ++- R/frm_mlreg_wrapper_ml_mcmc.R | 8 ++++-- R/frm_prepare_models.R | 2 - R/mdmb_ginv.R | 20 +++------------ R/mdmb_regression.R | 5 ++- R/mdmb_regression_loglike_logpost.R | 6 +--- R/remove_NA_data_frame.R | 2 - build/partial.rdb |binary inst/NEWS | 19 +++++++++++++++ man/frm.Rd | 25 +++++++++++++++++++ src/RcppExports.cpp | 2 - 23 files changed, 126 insertions(+), 82 deletions(-)
Title: Extremely Fast Implementation of a Naive Bayes Classifier
Description: This is an extremely fast implementation of a Naive Bayes classifier. This
package is currently the only package that supports a Bernoulli distribution, a Multinomial
distribution, and a Gaussian distribution, making it suitable for both binary features,
frequency counts, and numerical features. Another feature is the support of a mix of
different event models. Only numerical variables are allowed, however, categorical variables
can be transformed into dummies and used with the Bernoulli distribution. This implementation
offers a huge performance gain compared to other implementations in R. The execution times
were compared on a data set of tweets and this package was found to be around 283 to 34,841
times faster for the Bernoulli event models and 17 to 60 times faster for the Multinomial model.
See the vignette for more details. For the Gaussian distribution this package was found to be
between 2.8 and 1679 times faster. The implementation is largely based on the paper
"A comparison of event models for Naive Bayes anti-spam e-mail filtering"
written by K.M. Schneider (2003) <doi:10.3115/1067807>. Any issues can be
submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
Author: Martin Skogholt
Maintainer: Martin Skogholt <m.skogholt@gmail.com>
Diff between fastNaiveBayes versions 1.1.1 dated 2019-03-31 and 1.1.2 dated 2019-04-16
DESCRIPTION | 44 +- MD5 | 75 ++-- NEWS.md | 17 R/data.R |only R/fastNaiveBayes.R | 32 + R/fastNaiveBayes.bernoulli.R | 40 -- R/fastNaiveBayes.bernoulli.default.R | 18 - R/fastNaiveBayes.detect_distribution.R | 34 - R/fastNaiveBayes.gaussian.R | 41 -- R/fastNaiveBayes.gaussian.default.R | 41 +- R/fastNaiveBayes.mixed.R | 98 ----- R/fastNaiveBayes.mixed.default.R | 8 R/fastNaiveBayes.multinomial.R | 37 -- R/fastNaiveBayes.multinomial.default.R | 16 R/predict.fastNaiveBayes.bernoulli.R | 81 ++-- R/predict.fastNaiveBayes.gaussian.R | 98 ++--- R/predict.fastNaiveBayes.mixed.R | 102 +---- R/predict.fastNaiveBayes.multinomial.R | 72 +--- README.md | 106 ++---- data |only inst/doc/fastnaivebayes.R | 185 ++++++++++ inst/doc/fastnaivebayes.Rmd | 270 +++++++++++++-- inst/doc/fastnaivebayes.html | 397 ++++++++++++++++++++--- man/fastNaiveBayes.Rd | 30 + man/fastNaiveBayes.bernoulli.Rd | 40 -- man/fastNaiveBayes.detect_distribution.Rd | 34 - man/fastNaiveBayes.gaussian.Rd | 46 -- man/fastNaiveBayes.mixed.Rd | 99 ----- man/fastNaiveBayes.multinomial.Rd | 37 -- man/predict.fastNaiveBayes.bernoulli.Rd | 52 +-- man/predict.fastNaiveBayes.gaussian.Rd | 47 +- man/predict.fastNaiveBayes.mixed.Rd | 92 ----- man/predict.fastNaiveBayes.multinomial.Rd | 41 +- man/tweets.Rd |only man/tweetsDTM.Rd |only tests/testthat/test-fastnaivebayes_bernoulli.R | 64 ++- tests/testthat/test-fastnaivebayes_gaussian.R | 44 +- tests/testthat/test-fastnaivebayes_mixed.R | 47 +- tests/testthat/test-fastnaivebayes_multinomial.R | 53 +-- vignettes/fastnaivebayes.Rmd | 270 +++++++++++++-- 40 files changed, 1682 insertions(+), 1126 deletions(-)
More information about fastNaiveBayes at CRAN
Permanent link
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/),
Speros Kokenes [aut, cph] (d3-lasso-plugin library,
https://github.com/skokenes/D3-Lasso-Plugin),
Evan Wang [aut, cph] (d3-labeler plugin,
https://github.com/tinker10/D3-Labeler)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.8.2 dated 2018-03-10 and 0.9 dated 2019-04-16
scatterD3-0.8.2/scatterD3/NEWS |only scatterD3-0.8.2/scatterD3/inst/htmlwidgets/lib/d3/d3-4.13.0.min.js |only scatterD3-0.8.2/scatterD3/inst/htmlwidgets/scatterD3-setup.js |only scatterD3-0.9/scatterD3/DESCRIPTION | 20 scatterD3-0.9/scatterD3/MD5 | 60 scatterD3-0.9/scatterD3/NEWS.md |only scatterD3-0.9/scatterD3/R/scatterD3.R | 111 scatterD3-0.9/scatterD3/README.md | 15 scatterD3-0.9/scatterD3/build/vignette.rds |binary scatterD3-0.9/scatterD3/inst/doc/introduction.R | 176 + scatterD3-0.9/scatterD3/inst/doc/introduction.Rmd | 452 ++- scatterD3-0.9/scatterD3/inst/doc/introduction.html | 1157 ++++------ scatterD3-0.9/scatterD3/inst/htmlwidgets/lib/d3-lasso-plugin/lasso.css | 8 scatterD3-0.9/scatterD3/inst/htmlwidgets/lib/d3-lasso-plugin/lasso.js | 30 scatterD3-0.9/scatterD3/inst/htmlwidgets/lib/d3/d3-labeler.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/lib/d3/d3-legend.min.js | 2 scatterD3-0.9/scatterD3/inst/htmlwidgets/lib/d3/d3.v5.min.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-arrows.js | 76 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-axes.js | 34 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-dims.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-dots.js | 117 - scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-ellipses.js | 49 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-exports.js | 27 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-labels.js | 297 ++ scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-lasso.js | 137 - scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-legend.js | 361 ++- scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-lines.js | 126 - scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-menu.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-scales.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-utils.js | 52 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3-zoom.js |only scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3.css | 10 scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3.js | 794 +----- scatterD3-0.9/scatterD3/inst/htmlwidgets/scatterD3.yaml | 12 scatterD3-0.9/scatterD3/man/scatterD3.Rd | 72 scatterD3-0.9/scatterD3/vignettes/introduction.Rmd | 452 ++- 36 files changed, 2678 insertions(+), 1969 deletions(-)
Title: Check Text Files Content at a Glance
Description: Tools to help text files importation. It can return
the number of lines; print the first and last lines; convert
encoding. Operations are made without reading the entire file
before starting, resulting in good performances with large files.
This package provides an alternative to a simple use of the
'head', 'tail', 'wc' and 'iconv' programs that are not always
available on machine where R is installed.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between fpeek versions 0.1.0 dated 2018-07-22 and 0.1.1 dated 2019-04-16
DESCRIPTION | 10 ++++++---- MD5 | 5 +++-- NEWS.md |only tests/testthat/test-iconv.R | 4 +++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-21 dated 2019-03-04 and 0.2-22 dated 2019-04-16
CHANGELOG | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- data/zaki.rda |binary src/similarity.c | 4 ++-- tests/ptree.R | 4 ++++ 6 files changed, 18 insertions(+), 10 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre],
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.1.1 dated 2019-03-04 and 0.1.2 dated 2019-04-16
RJDemetra-0.1.1/RJDemetra/man/regarima_spec_def_tramoseats.Rd |only RJDemetra-0.1.1/RJDemetra/man/regarima_spec_def_x13.Rd |only RJDemetra-0.1.1/RJDemetra/man/tramoseats_spec_def.Rd |only RJDemetra-0.1.1/RJDemetra/man/x13_spec_def.Rd |only RJDemetra-0.1.2/RJDemetra/DESCRIPTION | 13 RJDemetra-0.1.2/RJDemetra/MD5 | 87 + RJDemetra-0.1.2/RJDemetra/NAMESPACE | 31 RJDemetra-0.1.2/RJDemetra/NEWS.md |only RJDemetra-0.1.2/RJDemetra/R/deprecated.R |only RJDemetra-0.1.2/RJDemetra/R/export_workspace.R | 22 RJDemetra-0.1.2/RJDemetra/R/finals.R | 23 RJDemetra-0.1.2/RJDemetra/R/get_jmodel.R |only RJDemetra-0.1.2/RJDemetra/R/import_workspace.R | 59 - RJDemetra-0.1.2/RJDemetra/R/init.R | 8 RJDemetra-0.1.2/RJDemetra/R/jregarima.R |only RJDemetra-0.1.2/RJDemetra/R/jsa2r.R |only RJDemetra-0.1.2/RJDemetra/R/jtramoseats.R |only RJDemetra-0.1.2/RJDemetra/R/jx13.R |only RJDemetra-0.1.2/RJDemetra/R/regarima.R | 138 -- RJDemetra-0.1.2/RJDemetra/R/regarima_rslts.R | 18 RJDemetra-0.1.2/RJDemetra/R/regarima_specTS.R | 317 ++++-- RJDemetra-0.1.2/RJDemetra/R/regarima_specX13.R | 296 +++--- RJDemetra-0.1.2/RJDemetra/R/sa_plot.R | 10 RJDemetra-0.1.2/RJDemetra/R/sa_print.R | 15 RJDemetra-0.1.2/RJDemetra/R/saveSpec.R | 18 RJDemetra-0.1.2/RJDemetra/R/spec.R | 38 RJDemetra-0.1.2/RJDemetra/R/spec_rjd.R | 144 +-- RJDemetra-0.1.2/RJDemetra/R/spec_transform.R | 41 RJDemetra-0.1.2/RJDemetra/R/tramoseats.R | 102 +- RJDemetra-0.1.2/RJDemetra/R/tramoseats_spec.R | 347 ++++--- RJDemetra-0.1.2/RJDemetra/R/user_defined.R | 477 ++++------ RJDemetra-0.1.2/RJDemetra/R/x13.R | 113 +- RJDemetra-0.1.2/RJDemetra/R/x13_spec.R | 359 ++++--- RJDemetra-0.1.2/RJDemetra/README.md | 10 RJDemetra-0.1.2/RJDemetra/man/add_sa_item.Rd | 6 RJDemetra-0.1.2/RJDemetra/man/compute.Rd | 2 RJDemetra-0.1.2/RJDemetra/man/deprecated-RJDemetra.Rd |only RJDemetra-0.1.2/RJDemetra/man/get_model.Rd | 17 RJDemetra-0.1.2/RJDemetra/man/get_name.Rd | 4 RJDemetra-0.1.2/RJDemetra/man/get_object.Rd | 2 RJDemetra-0.1.2/RJDemetra/man/get_ts.Rd | 2 RJDemetra-0.1.2/RJDemetra/man/jSA.Rd |only RJDemetra-0.1.2/RJDemetra/man/plot.Rd | 4 RJDemetra-0.1.2/RJDemetra/man/regarima.Rd | 45 RJDemetra-0.1.2/RJDemetra/man/regarima_spec_tramoseats.Rd |only RJDemetra-0.1.2/RJDemetra/man/regarima_spec_x13.Rd |only RJDemetra-0.1.2/RJDemetra/man/save_spec.Rd | 8 RJDemetra-0.1.2/RJDemetra/man/specification.Rd | 12 RJDemetra-0.1.2/RJDemetra/man/tramoseats.Rd | 34 RJDemetra-0.1.2/RJDemetra/man/tramoseats_spec.Rd |only RJDemetra-0.1.2/RJDemetra/man/user_defined_variables.Rd | 3 RJDemetra-0.1.2/RJDemetra/man/x13.Rd | 34 RJDemetra-0.1.2/RJDemetra/man/x13_spec.Rd |only 53 files changed, 1605 insertions(+), 1254 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Bojanowski Michal [ctb],
Briatte François [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.1.0 dated 2019-02-25 and 2.2.0 dated 2019-04-16
DESCRIPTION | 12 MD5 | 46 +-- NAMESPACE | 13 NEWS.md | 10 R/copy_labels.R | 31 ++ R/labelled.R | 2 R/lookfor.R |only R/retrocompatibility.R | 10 R/tagged_na.R |only R/to_character.R | 2 R/to_factor.R | 4 R/var_label.R | 19 - README.md | 50 ++- build/vignette.rds |binary inst/doc/intro_labelled.R | 5 inst/doc/intro_labelled.Rmd | 9 inst/doc/intro_labelled.html | 617 ++++++++++++++++++++++++++++++------------- man/copy_labels.Rd | 28 + man/labelled.Rd | 2 man/look_for.Rd |only man/recode.haven_labelled.Rd | 13 man/tagged_na.Rd |only man/to_character.Rd | 2 man/to_factor.Rd | 4 man/var_label.Rd | 9 vignettes/intro_labelled.Rmd | 9 26 files changed, 639 insertions(+), 258 deletions(-)
More information about frequentdirections at CRAN
Permanent link
Title: 'DrugBank' Database XML Parser
Description: This tool is for parsing the 'DrugBank' XML database <http://drugbank.ca/>. The parsed
data are then returned in a proper 'R' dataframe with the ability to save
them in a given database.
Author: Mohammed Ali [aut, cre],
Ali Ezzat [aut]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Diff between dbparser versions 1.0.0 dated 2018-12-17 and 1.0.1 dated 2019-04-16
dbparser-1.0.0/dbparser/R/durg_main_node_parser.R |only dbparser-1.0.0/dbparser/man/parse_drug_classifications.Rd |only dbparser-1.0.0/dbparser/tests/testthat/test_durg_all_nodes_parser.R |only dbparser-1.0.0/dbparser/tests/testthat/test_durg_main_node_parser.R |only dbparser-1.0.1/dbparser/DESCRIPTION | 10 dbparser-1.0.1/dbparser/MD5 | 112 - dbparser-1.0.1/dbparser/NAMESPACE | 7 dbparser-1.0.1/dbparser/NEWS.md | 15 dbparser-1.0.1/dbparser/R/drug_all_nodes_parser.R | 752 +++++----- dbparser-1.0.1/dbparser/R/drug_atc_codes_node_parser.R | 2 dbparser-1.0.1/dbparser/R/drug_carrier_node_parser.R | 38 dbparser-1.0.1/dbparser/R/drug_classfication_node_parser.R | 14 dbparser-1.0.1/dbparser/R/drug_common_utilities.R | 65 dbparser-1.0.1/dbparser/R/drug_enzyme_node_parser.R | 48 dbparser-1.0.1/dbparser/R/drug_main_node_parser.R |only dbparser-1.0.1/dbparser/R/drug_manufacturer_node_parser.R | 10 dbparser-1.0.1/dbparser/R/drug_parsers.R | 667 +++++--- dbparser-1.0.1/dbparser/R/drug_pathway_node_parser.R | 21 dbparser-1.0.1/dbparser/R/drug_polypeptide_sub_node_parser.R | 2 dbparser-1.0.1/dbparser/R/drug_price_node_parser.R | 9 dbparser-1.0.1/dbparser/R/drug_reaction_node_parser.R | 8 dbparser-1.0.1/dbparser/R/drug_sequence_node_parser.R | 5 dbparser-1.0.1/dbparser/R/drug_targets_node_parser.R | 58 dbparser-1.0.1/dbparser/R/drug_transporter_node_parser.R | 54 dbparser-1.0.1/dbparser/README.md | 53 dbparser-1.0.1/dbparser/build/vignette.rds |binary dbparser-1.0.1/dbparser/inst/doc/dbparser.R | 169 +- dbparser-1.0.1/dbparser/inst/doc/dbparser.Rmd | 48 dbparser-1.0.1/dbparser/inst/doc/dbparser.html | 453 ++++-- dbparser-1.0.1/dbparser/inst/extdata/drugbank_record.zip |only dbparser-1.0.1/dbparser/man/get_xml_db_rows.Rd | 6 dbparser-1.0.1/dbparser/man/parse_drug.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_affected_organisms.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_ahfs_codes.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_articles.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_books.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_categories.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_classification.Rd |only dbparser-1.0.1/dbparser/man/parse_drug_dosages.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_experimental_properties.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_external_identifiers.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_external_links.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_food_interactions.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_groups.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_interactions.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_international_brands.Rd |only dbparser-1.0.1/dbparser/man/parse_drug_links.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_mixtures.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_packagers.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_patents.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_pdb_entries.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_products.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_salts.Rd |only dbparser-1.0.1/dbparser/man/parse_drug_snp_adverse_drug_reactions.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_snp_effects.Rd | 10 dbparser-1.0.1/dbparser/man/parse_drug_synonyms.Rd | 10 dbparser-1.0.1/dbparser/tests/testthat/test_drug_all_nodes_parser.R |only dbparser-1.0.1/dbparser/tests/testthat/test_drug_main_node_parser.R |only dbparser-1.0.1/dbparser/tests/testthat/test_drug_pathway_node_parser.R | 2 dbparser-1.0.1/dbparser/tests/testthat/test_drug_targets_node_parser.R | 2 dbparser-1.0.1/dbparser/vignettes/dbparser.Rmd | 48 dbparser-1.0.1/dbparser/vignettes/fig1.png |only dbparser-1.0.1/dbparser/vignettes/fig2.png |only dbparser-1.0.1/dbparser/vignettes/fig3.png |only 64 files changed, 1730 insertions(+), 1168 deletions(-)