Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Ben Tupper [ctb],
Roy Mendelssohn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.4.2 dated 2017-05-12 and 0.5.0 dated 2019-02-01
DESCRIPTION | 26 +- LICENSE | 2 MD5 | 153 +++++++++------- NAMESPACE | 6 NEWS.md | 20 ++ R/browse.R | 19 +- R/cache_delete.R | 9 R/cache_details.R | 1 R/cache_list.R | 11 + R/cache_paths.R | 76 -------- R/cache_setup.R | 17 + R/convert_time.R | 23 +- R/convert_units.R | 21 +- R/default-url.R | 34 +++ R/fipscounty.R | 13 - R/grid.R | 23 ++ R/info.R | 44 ++-- R/keywords.R | 16 - R/ncdf_helpers.R | 10 + R/on_load.R | 8 R/rerddap-package.r | 41 +++- R/search.R | 11 - R/search_adv.R | 21 +- R/servers.R | 6 R/table.R | 59 +++--- R/utils.R | 1 R/version.R | 14 - R/zzz.r | 47 ++--- README.md | 202 +++++++++++---------- build/vignette.rds |binary inst/doc/Using_rerddap.Rmd | 332 +++++++++++++++++------------------- inst/doc/Using_rerddap.html | 332 +++++++++++++++++------------------- inst/doc/rerddap_vignette.Rmd | 221 ++++++++++------------- inst/doc/rerddap_vignette.html | 221 ++++++++++------------- inst/vign/Using_rerddap.Rmd | 6 inst/vign/Using_rerddap.md | 18 + inst/vign/rerddap_vignette.Rmd | 10 - inst/vign/rerddap_vignette.md | 221 ++++++++++------------- man/browse.Rd | 13 - man/cache_delete.Rd | 10 - man/cache_details.Rd | 1 man/cache_list.Rd | 12 + man/cache_setup.Rd | 14 + man/colors.Rd | 26 +- man/convert_time.Rd | 11 - man/convert_units.Rd | 8 man/ed_search.Rd | 11 - man/ed_search_adv.Rd | 28 +-- man/eurl.Rd | 21 ++ man/fipscounty.Rd | 5 man/griddap.Rd | 96 +++++----- man/info.Rd | 33 +-- man/key_words.Rd | 8 man/rerddap-package.Rd | 37 +++- man/tabledap.Rd | 38 +--- man/version.Rd | 6 tests/test-all.R | 3 tests/testthat/fixtures |only tests/testthat/helper-rerddap.R |only tests/testthat/test-convert_time.R | 11 - tests/testthat/test-convert_units.R | 11 - tests/testthat/test-ed_datasets.R | 21 +- tests/testthat/test-ed_search.R | 28 +-- tests/testthat/test-ed_search_adv.R | 30 +-- tests/testthat/test-griddap.r | 158 ++++++++++------- tests/testthat/test-info.R | 24 +- tests/testthat/test-tabledap.R | 78 +++++--- tests/vcr_cassettes |only vignettes/Using_rerddap.Rmd | 332 +++++++++++++++++------------------- vignettes/rerddap_vignette.Rmd | 221 ++++++++++------------- 70 files changed, 1875 insertions(+), 1715 deletions(-)
Title: Multinomial Logit Models
Description: Maximum Likelihood estimation of random utility discrete choice models (logit and probit).
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 0.4-0 dated 2019-01-31 and 0.4-1 dated 2019-02-01
DESCRIPTION | 12 ++--- MD5 | 34 ++++++++------- NEWS.md | 12 ++++- R/datasets.R | 80 +++++++++++++++++++++++++++++++++++ R/formula.data.R | 25 +++++++++-- R/lnl.mlogit.R | 1 R/mlogit.R | 11 +++- build/partial.rdb |binary data/Car.rda |only data/Catsup.rda |only data/Cracker.rda |only inst/REFERENCES.bib | 83 ++++++++++++++++++++++++++++++++++++ inst/doc/c7.miscmodels.html | 2 inst/doc/e1mlogit.html | 4 - inst/doc/e2nlogit.html | 4 - inst/doc/e3mxlogit.html | 4 - inst/doc/e4mprobit.html | 4 - man/Car.Rd |only man/Catsup.Rd |only man/Cracker.Rd |only tests/AER.R | 99 ++++++++++++++++++++++++++++++++++++++++++-- 21 files changed, 334 insertions(+), 41 deletions(-)
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre],
Zoe Meers [aut],
Jaron Lee [aut]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.2.9 dated 2019-01-14 and 0.3.0 dated 2019-02-01
readabs-0.2.9/readabs/inst/doc/my-vignette.R |only readabs-0.2.9/readabs/inst/doc/my-vignette.Rmd |only readabs-0.2.9/readabs/inst/doc/my-vignette.html |only readabs-0.2.9/readabs/inst/extdata |only readabs-0.2.9/readabs/tests/testdata/5206002_expenditure_volume_measures.xls |only readabs-0.2.9/readabs/tests/testthat/test_read_abs_data.R |only readabs-0.2.9/readabs/vignettes/my-vignette.Rmd |only readabs-0.3.0/readabs/DESCRIPTION | 22 - readabs-0.3.0/readabs/LICENSE | 2 readabs-0.3.0/readabs/MD5 | 52 ++-- readabs-0.3.0/readabs/NAMESPACE | 34 ++ readabs-0.3.0/readabs/NEWS.md | 8 readabs-0.3.0/readabs/R/download_abs.R |only readabs-0.3.0/readabs/R/extract_abs_sheets.R |only readabs-0.3.0/readabs/R/extract_abs_tabletitles.R |only readabs-0.3.0/readabs/R/get_abs_xml_metadata.R |only readabs-0.3.0/readabs/R/get_xml_df.R |only readabs-0.3.0/readabs/R/read_abs.R |only readabs-0.3.0/readabs/R/read_abs_data.R | 34 +- readabs-0.3.0/readabs/R/read_abs_local.R |only readabs-0.3.0/readabs/R/read_abs_sdmx.R | 13 - readabs-0.3.0/readabs/R/tidy_abs.R |only readabs-0.3.0/readabs/R/tidy_abs_list.R |only readabs-0.3.0/readabs/README.md | 121 +++++++++- readabs-0.3.0/readabs/build/vignette.rds |binary readabs-0.3.0/readabs/inst/doc/readabs_vignette.R |only readabs-0.3.0/readabs/inst/doc/readabs_vignette.Rmd |only readabs-0.3.0/readabs/inst/doc/readabs_vignette.html |only readabs-0.3.0/readabs/man/extract_abs_sheets.Rd |only readabs-0.3.0/readabs/man/get_abs.Rd |only readabs-0.3.0/readabs/man/read_abs.Rd |only readabs-0.3.0/readabs/man/read_abs_data.Rd | 16 - readabs-0.3.0/readabs/man/read_abs_local.Rd |only readabs-0.3.0/readabs/man/read_abs_metadata.Rd | 7 readabs-0.3.0/readabs/man/read_abs_sdmx.Rd | 8 readabs-0.3.0/readabs/man/tidy_abs.Rd |only readabs-0.3.0/readabs/man/tidy_abs_list.Rd |only readabs-0.3.0/readabs/tests/testdata/6202021.xls |only readabs-0.3.0/readabs/tests/testthat/test_readabs.R |only readabs-0.3.0/readabs/vignettes/VIGNETTE-6202-screenshot.png |only readabs-0.3.0/readabs/vignettes/VIGNETTE-spreadsheet-screenshot.png |only readabs-0.3.0/readabs/vignettes/readabs_vignette.Rmd |only 42 files changed, 234 insertions(+), 83 deletions(-)
Title: Mitigating the Adverse Impact of Batch Effects in Sample Pattern
Detection
Description: Modifies the distance matrix obtained from data with batch effects, so as to improve the performance of sample pattern detection, such as clustering, dimension reduction, and construction of networks between subjects. The method has been published in Bioinformatics (Fei et al, 2018, <doi:10.1093/bioinformatics/bty117>). Also available on 'GitHub' <https://github.com/tengfei-emory/QuantNorm>.
Author: Teng Fei, Tianwei Yu
Maintainer: Teng Fei <tfei@emory.edu>
Diff between QuantNorm versions 1.0.3 dated 2018-03-06 and 1.0.5 dated 2019-02-01
DESCRIPTION | 12 +++--- MD5 | 11 +++-- R/QuantNorm.R | 26 ++++++++----- R/qnorm1plus.R |only R/qnorm2.R | 69 +++-------------------------------- README.md | 107 ++++++++++++++++++++++++++++++++++++------------------- man/QuantNorm.Rd | 2 - 7 files changed, 106 insertions(+), 121 deletions(-)
Title: Dirichlet Process Weibull Mixture Model for Survival Data
Description: Use Dirichlet process Weibull mixture model and dependent Dirichlet process Weibull mixture model for survival data with and without competing risks. Dirichlet process Weibull mixture model is used for data without covariates and dependent Dirichlet process model is used for regression data. The package is designed to handle exact/right-censored/ interval-censored observations without competing risks and exact/right-censored observations for data with competing risks. Inside each cluster of Dirichlet process, we assume a multiplicative effect of covariates as in Cox model and Fine and Gray model. In addition, we provide a wrapper for DPdensity() function from the R package 'DPpackage'. This wrapper automatically uses Low Information Omnibus prior and can model one and two dimensional data with Dirichlet mixture of Gaussian distributions.
Author: Yushu Shi, Michael Martens
Maintainer: Yushu Shi <shiyushu2006@gmail.com>
Diff between DPWeibull versions 1.2 dated 2018-03-22 and 1.3 dated 2019-02-01
DPWeibull-1.2/DPWeibull/src/arms.cpp |only DPWeibull-1.3/DPWeibull/DESCRIPTION | 11 ++++++----- DPWeibull-1.3/DPWeibull/MD5 | 8 ++++---- DPWeibull-1.3/DPWeibull/NAMESPACE | 1 + DPWeibull-1.3/DPWeibull/src/arms.c |only DPWeibull-1.3/DPWeibull/src/commonfunc.cpp | 2 +- 6 files changed, 12 insertions(+), 10 deletions(-)
Title: Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format
Images
Description: Extracts colors from various image types, returns customized reports and plots treemaps
and 3D scatterplots of image compositions. Color palettes can also be created.
Author: David Zumbach [aut, cre]
Maintainer: David Zumbach <david.zumbach@gfzb.ch>
Diff between colorfindr versions 0.1.3 dated 2018-10-07 and 0.1.4 dated 2019-02-01
DESCRIPTION | 9 +- MD5 | 15 ++-- NAMESPACE | 13 ++++ NEWS | 7 ++ R/make_palette.R |only R/plot_colors.R | 2 R/utils.R | 157 +++++++++++++++++++++++++++++++++++++++++++++++++- inst/extdata/pic6.png |only man/make_palette.Rd |only man/plot_colors.Rd | 2 10 files changed, 190 insertions(+), 15 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for
developing cellular automata, dynamic raster models, and agent based models
in 'SpaDES'.
Included are various methods for spatial spreading, spatial agents, GIS
operations, random map generation, and others.
See '?SpaDES.tools' for an categorized overview of these additional tools.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Jean Marchal [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES.tools versions 0.3.0 dated 2018-07-14 and 0.3.1 dated 2019-02-01
DESCRIPTION | 32 +- MD5 | 65 ++--- NAMESPACE | 16 - NEWS.md | 18 + R/SELES.R | 15 - R/initialize.R | 211 +++++++++++------ R/mapReduce.R | 4 R/mergeRaster.R | 80 ++++-- R/neighbourhood.R | 437 +++++++++++++++++------------------- R/resample.R | 24 + R/spades-tools-deprecated.R | 11 R/spread.R | 2 README.md | 3 inst/WORDLIST | 23 + inst/examples/example_spread.R | 10 man/SpaDES.tools-package.Rd | 4 man/adj.Rd | 12 man/cir.Rd | 8 man/distanceFromEachPoint.Rd | 4 man/gaussmap.Rd | 21 - man/initiateAgents.Rd | 31 +- man/randomPolygons.Rd | 34 ++ man/resample.Rd | 10 man/specnumperpatch-probs.Rd | 3 man/splitRaster.Rd | 23 + man/spokes.Rd | 11 man/spread.Rd | 41 +-- man/spread2-internals.Rd | 5 man/spread2.Rd | 12 man/wrap.Rd | 10 tests/testthat/test-adj.R | 19 - tests/testthat/test-gaussMap.R | 2 tests/testthat/test-mergeRaster.R |only tests/testthat/test-randomPolygon.R | 16 - 34 files changed, 689 insertions(+), 528 deletions(-)
Title: Sensus Analytics
Description: Provides access and analytic functions for Sensus data.
Author: Matthew S. Gerber
Maintainer: Matthew S. Gerber <gerber.matthew@gmail.com>
Diff between SensusR versions 2.3.0 dated 2018-10-02 and 2.3.1 dated 2019-02-01
DESCRIPTION | 12 - MD5 | 62 +++---- NEWS.md | 3 R/SensusR.R | 287 +++++++++++++++++++---------------- man/plot.AccelerometerDatum.Rd | 8 man/plot.AltitudeDatum.Rd | 8 man/plot.BatteryDatum.Rd | 13 - man/plot.CellTowerDatum.Rd | 8 man/plot.CompassDatum.Rd | 8 man/plot.LightDatum.Rd | 8 man/plot.LocationDatum.Rd | 8 man/plot.ScreenDatum.Rd | 8 man/plot.SoundDatum.Rd | 8 man/plot.SpeedDatum.Rd | 8 man/plot.TelephonyDatum.Rd | 8 man/plot.WlanDatum.Rd | 8 man/sensus.decompress.gz.files.Rd | 4 man/sensus.decrypt.bin.files.Rd | 5 man/sensus.get.all.timestamp.lags.Rd | 8 man/sensus.get.timestamp.lags.Rd | 7 man/sensus.get.unique.device.ids.Rd | 2 man/sensus.list.activities.Rd | 3 man/sensus.list.aws.s3.buckets.Rd | 3 man/sensus.plot.lag.cdf.Rd | 8 man/sensus.read.json.files.Rd | 12 - man/sensus.remove.device.id.Rd | 5 man/sensus.sync.from.aws.s3.Rd | 3 man/sensus.write.csv.files.Rd | 8 man/sensus.write.rdata.files.Rd | 8 man/trim.Rd | 3 man/trim.leading.Rd | 3 man/trim.trailing.Rd | 3 32 files changed, 264 insertions(+), 286 deletions(-)
Title: Utilities for Nonlinear Regression and Repeated Measurements
Models
Description: A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey packages such
as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at <http://www.commanster.eu/rcode.html>).
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
CRAN version)
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between rmutil versions 1.1.1 dated 2018-05-27 and 1.1.2 dated 2019-02-01
rmutil-1.1.1/rmutil/COPYING |only rmutil-1.1.2/rmutil/DESCRIPTION | 6 +++--- rmutil-1.1.2/rmutil/MD5 | 7 +++---- rmutil-1.1.2/rmutil/NEWS.md | 9 +++++++++ rmutil-1.1.2/rmutil/R/dist.r | 8 ++++---- 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Easily Install and Load the R Markdown Family
Description: The 'rmd' package manages multiple R markdown packages. These R markdown packages include currently 'rmarkdown', 'knitr', 'bookdown', 'bookdownplus', 'blogdown', 'rticles', 'tinytex', 'xaringan', 'citr', and 'mindr'. They can be installed and loaded in a single step with the 'rmd' package. The conflicts between these packages are evaluated as well.
Author: Peng Zhao [aut, cre]
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between rmd versions 0.1.3 dated 2019-01-09 and 0.1.4 dated 2019-02-01
DESCRIPTION | 21 + LICENSE | 597 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- MD5 | 18 + NAMESPACE | 3 R/addin.R |only R/attach.R | 3 R/utils_addin.R |only inst |only man/rmdAddin.Rd |only 9 files changed, 626 insertions(+), 16 deletions(-)
Title: Unsupervised Photometric Membership Assignment in Stellar
Clusters
Description: An implementation of the UPMASK method for performing membership
assignment in stellar clusters in R. It is prepared to use photometry and
spatial positions, but it can take into account other types of data. The
method is able to take into account arbitrary error models, and it is
unsupervised, data-driven, physical-model-free and relies on as few
assumptions as possible. The approach followed for membership assessment is
based on an iterative process, dimensionality reduction, a clustering
algorithm and a kernel density estimation.
Author: Alberto Krone-Martins [aut, cre],
Andre Moitinho [aut],
Eduardo Bezerra [ctb],
Leonardo Lima [ctb],
Tristan Cantat-Gaudin [ctb]
Maintainer: Alberto Krone-Martins <algol@sim.ul.pt>
Diff between UPMASK versions 1.1 dated 2017-04-03 and 1.2 dated 2019-02-01
ChangeLog | 10 +++- DESCRIPTION | 26 +++++++--- MD5 | 44 ++++++++--------- NAMESPACE | 2 R/UPMASKdata.R | 60 +++++++++++++++--------- R/UPMASKfile.R | 30 +++++++----- R/innerLoop.R | 74 +++++++++++++++++++++++------- R/outerLoop.R | 18 ++++--- man/UPMASK-package.Rd | 4 - man/UPMASKdata.Rd | 54 ++++++++++++--------- man/UPMASKfile.Rd | 36 ++++++++------ man/analyse_randomKde2d.Rd | 9 ++- man/analyse_randomKde2d_AutoCalibrated.Rd | 15 +++--- man/analyse_randomKde2d_smart.Rd | 17 +++--- man/create_randomKde2d.Rd | 19 ++++--- man/create_smartTable.Rd | 11 ++-- man/getStarsAtHighestDensityRegion.Rd | 11 ++-- man/innerLoop.Rd | 39 +++++++++------ man/kde2dForSubset.Rd | 15 +++--- man/meanThreeSigRej.Rd | 13 ++--- man/outerLoop.Rd | 40 +++++++++------- man/performCuts.Rd | 11 ++-- man/takeErrorsIntoAccount.Rd | 25 +++++----- 23 files changed, 358 insertions(+), 225 deletions(-)
Title: Metagenome Coverage Estimation and Projections for 'Nonpareil'
Description: Plot, process, and analyze NPO files produced by
'Nonpareil' <http://enve-omics.ce.gatech.edu/nonpareil>.
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between Nonpareil versions 3.3.3 dated 2018-10-22 and 3.3.4 dated 2019-02-01
Nonpareil-3.3.3/Nonpareil/man/nonpareil-package.Rd |only Nonpareil-3.3.3/Nonpareil/man/z$-methods.Rd |only Nonpareil-3.3.3/Nonpareil/man/z$_--methods.Rd |only Nonpareil-3.3.3/Nonpareil/man/z+-methods.Rd |only Nonpareil-3.3.4/Nonpareil/DESCRIPTION | 7 Nonpareil-3.3.4/Nonpareil/MD5 | 56 Nonpareil-3.3.4/Nonpareil/R/Nonpareil.R | 851 ++++++---- Nonpareil-3.3.4/Nonpareil/man/Nonpareil.Curve-class.Rd | 124 - Nonpareil-3.3.4/Nonpareil/man/Nonpareil.Rd |only Nonpareil-3.3.4/Nonpareil/man/Nonpareil.Set-class.Rd | 43 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.add.curve.Rd | 38 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.antif.Rd | 40 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.col.Rd | 34 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.coverage_factor.Rd | 34 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.curve.Rd | 112 - Nonpareil-3.3.4/Nonpareil/man/Nonpareil.curve.batch.Rd | 75 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.f.Rd | 40 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.fit_model.Rd | 34 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.legend.Rd | 47 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.read_data.Rd | 34 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.read_metadata.Rd | 31 Nonpareil-3.3.4/Nonpareil/man/Nonpareil.set.Rd | 104 - Nonpareil-3.3.4/Nonpareil/man/cash-Nonpareil.Curve-method.Rd |only Nonpareil-3.3.4/Nonpareil/man/cash-Nonpareil.Set-method.Rd |only Nonpareil-3.3.4/Nonpareil/man/cash-set-Nonpareil.Curve-method.Rd |only Nonpareil-3.3.4/Nonpareil/man/cash-set-Nonpareil.Set-method.Rd |only Nonpareil-3.3.4/Nonpareil/man/plot.Nonpareil.Curve.Rd | 144 - Nonpareil-3.3.4/Nonpareil/man/plot.Nonpareil.Set.Rd | 58 Nonpareil-3.3.4/Nonpareil/man/plus-Nonpareil.Set-ANY-method.Rd |only Nonpareil-3.3.4/Nonpareil/man/predict.Nonpareil.Curve.Rd | 40 Nonpareil-3.3.4/Nonpareil/man/print.Nonpareil.Curve.Rd | 40 Nonpareil-3.3.4/Nonpareil/man/print.Nonpareil.Set.Rd | 40 Nonpareil-3.3.4/Nonpareil/man/summary.Nonpareil.Curve.Rd | 70 Nonpareil-3.3.4/Nonpareil/man/summary.Nonpareil.Set.Rd | 40 34 files changed, 1190 insertions(+), 946 deletions(-)
Title: Kernel Semi-Parametric Models
Description: To fit the kernel semi-parametric model and its extensions. It allows multiple kernels and unlimited interactions in the same model. Coefficients are estimated by maximizing a penalized log-likelihood; penalization terms and hyperparameters are estimated by minimizing leave-one-out error. It includes predictions with confidence/prediction intervals, statistical tests for the significance of each kernel, a procedure for variable selection and graphical tools for diagnostics and interpretation of covariate effects. Currently it is implemented for continuous dependent variables.
Author: Catherine Schramm [aut, cre],
Aurelie Labbe [ctb],
Celia M. T. Greenwood [ctb]
Maintainer: Catherine Schramm <cath.schramm@gmail.com>
Diff between KSPM versions 0.1.0 dated 2019-01-09 and 0.1.1 dated 2019-02-01
DESCRIPTION | 6 +++--- MD5 | 10 ++++++++-- R/csm.R |only R/devtools_history.R | 5 +++-- R/energy.R |only data |only man/csm.Rd |only man/energy.Rd |only 8 files changed, 14 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-11 1.0
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MCMCglmm versions 2.26 dated 2018-07-03 and 2.27 dated 2019-02-01
DESCRIPTION | 8 MD5 | 28 NAMESPACE | 7 R/MCMCglmm.R | 156 + R/buildZ.R | 26 R/close.bracket.R | 24 R/me.R |only R/mterms.R | 16 R/predict.MCMCglmm.R | 2 R/simulate.MCMCglmm.R | 7 inst/doc/CourseNotes.pdf |binary inst/doc/Overview.pdf |binary man/me.Rd |only src/MCMCglmm.cc | 4892 ++++++++++++++++++++++++----------------------- src/MCMCglmm.h | 5 src/cs_dense.c |only src/cs_dense0.c |only 17 files changed, 2754 insertions(+), 2417 deletions(-)
Title: Import and Analyse Ego-Centered Network Data
Description: Tools for importing, analyzing and visualizing ego-centered
network data. Supports several data formats, including the export formats of
'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the
intuitive visualization of ego-centered networks is provided. Also included
are procedures for creating and visualizing Clustered Graphs
(Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Author: Till Krenz [aut, cre],
Pavel N. Krivitsky [aut],
Raffaele Vacca [aut],
Michal Bojanowski [aut],
Markus Gamper [ctb],
Andreas Herz [aut],
Christopher McCarty [ctb]
Maintainer: Till Krenz <egor@tillt.net>
Diff between egor versions 0.18.08-02 dated 2018-08-20 and 0.19.1 dated 2019-02-01
DESCRIPTION | 37 +++++++++-------- MD5 | 29 +++++++------ R/conversions.R | 29 +++++++++---- R/create.random.egonet.data.R | 2 R/egor.R | 12 +++-- R/gss2004.R |only R/read.egonet.R | 6 ++ build/vignette.rds |binary data/gss2004.rda |only inst/doc/using_egor.R | 2 inst/doc/using_egor.Rmd | 2 inst/doc/using_egor.html | 76 +++++++++++++++++++++++------------- man/gss2004.Rd |only tests/testthat/test_conversions.R | 2 tests/testthat/test_dplyr_methods.R | 8 ++- tests/testthat/test_egor.R | 11 +++-- vignettes/using_egor.Rmd | 2 17 files changed, 134 insertions(+), 84 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described
by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph]
(<https://orcid.org/0000-0003-4226-6176>),
James Joseph Balamuta [aut, cre]
(<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between dina versions 1.0.2 dated 2017-04-26 and 2.0.0 dated 2019-02-01
dina-1.0.2/dina/R/dina-internal.R |only dina-1.0.2/dina/man/DINAsim.Rd |only dina-1.0.2/dina/man/rDirichlet.Rd |only dina-1.0.2/dina/man/rmultinomial.Rd |only dina-1.0.2/dina/man/update_alpha.Rd |only dina-1.0.2/dina/man/update_sg.Rd |only dina-1.0.2/dina/src/DINAcpp101315.cpp |only dina-1.0.2/dina/src/init.c |only dina-2.0.0/dina/DESCRIPTION | 38 +- dina-2.0.0/dina/MD5 | 35 +- dina-2.0.0/dina/NAMESPACE | 10 dina-2.0.0/dina/NEWS.md | 38 ++ dina-2.0.0/dina/R/RcppExports.R | 323 +++++------------------- dina-2.0.0/dina/R/dina-est.R |only dina-2.0.0/dina/R/dina-package.R |only dina-2.0.0/dina/README.md | 93 ++++++ dina-2.0.0/dina/inst/CITATION | 41 ++- dina-2.0.0/dina/man/DINA_Gibbs.Rd | 146 ---------- dina-2.0.0/dina/man/dina-package.Rd | 15 - dina-2.0.0/dina/man/dina.Rd |only dina-2.0.0/dina/src/Makevars | 9 dina-2.0.0/dina/src/Makevars.win |only dina-2.0.0/dina/src/RcppExports.cpp | 61 +--- dina-2.0.0/dina/src/dina-estimation-routine.cpp |only dina-2.0.0/dina/tests |only 25 files changed, 308 insertions(+), 501 deletions(-)
Title: High Precision Swiss Ephemeris
Description: The Swiss Ephemeris is a high precision ephemeris based upon the
DE431 ephemerides from NASA's JPL. It covers the time range 13201 BC to
AD 17191. This package uses the semi-analytic theory by Steve Moshier.
For faster and more accurate calculations, the compressed Swiss Ephemeris
data is available in the 'swephRdata' package. To access this data package,
run 'install.packages("swephRdata", repos = "https://rstub.github.io/drat/",
type = "source")'. The size of the 'swephRdata' package is approximately
115 MB. The user can also use the original JPL DE431 data.
Author: Ralf Stubner [aut, cre],
Victor Reijs [aut],
Authors and copyright holder of the Swiss Ephemeris [aut, cph] (see
LICENSE for details)
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>
Diff between swephR versions 0.1.3 dated 2019-01-30 and 0.1.4 dated 2019-02-01
DESCRIPTION | 6 MD5 | 31 +- NEWS.md |only inst/doc/swephR.html | 4 src/libswe/swecl.c | 608 +++++++++++++++++++++++++------------------------- src/libswe/swedate.c | 12 src/libswe/swehel.c | 362 ++++++++++++++--------------- src/libswe/swehouse.c | 32 +- src/libswe/swejpl.c | 4 src/libswe/swemmoon.c | 6 src/libswe/swemplan.c | 24 - src/libswe/sweodef.h | 14 + src/libswe/swepcalc.c | 16 - src/libswe/swepdate.c | 6 src/libswe/sweph.c | 354 ++++++++++++++--------------- src/libswe/sweph.h | 2 src/libswe/swephlib.c | 8 17 files changed, 751 insertions(+), 738 deletions(-)
Title: Database Query Interfaces
Description: Facilitates interaction with 'ODBC' data sources.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.6.0 dated 2019-01-31 and 0.6.1 dated 2019-02-01
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/SQRL.R | 8 ++++++-- man/SQRL-package.Rd | 3 ++- 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.0.18 dated 2018-11-01 and 1.0.19 dated 2019-02-01
DESCRIPTION | 13 MD5 | 58 ++-- R/exported_functions.R | 242 +++++++++++----- R/r2_functions.R |only R/r3_functions.R | 460 ++++++++++++++++---------------- R/sysdata.rda |binary inst/doc/Vignette_polymapR.html | 10 man/PCA_progeny.Rd | 3 man/assign_linkage_group.Rd | 4 man/cluster_SN_markers.Rd | 9 man/consensus_LG_assignment.Rd | 4 man/convert_marker_dosages.Rd | 6 man/createMap.Rd | 7 man/create_phased_maplist.Rd | 12 man/define_LG_structure.Rd | 3 man/finish_linkage_analysis.Rd | 8 man/get_markertype_combinations.Rd | 3 man/homologue_lg_assignment.Rd | 9 man/linkage.Rd | 8 man/marker_binning.Rd | 6 man/marker_binning_list.Rd | 3 man/orient_and_merge_maps.Rd | 3 man/phase_SN_diploid.Rd | 4 man/plot_map.Rd | 14 man/plot_phased_maplist.Rd | 3 man/r2_functions.Rd |only man/r3_functions.Rd | 13 man/screen_for_duplicate_individuals.Rd | 4 man/test_prefpairing.Rd | 6 man/write_nested_list.Rd | 4 man/write_pwd_list.Rd | 4 31 files changed, 524 insertions(+), 399 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, particle filtering, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-Bergman, Nick Michaud, Fritz Obermeyer, Claudia Wehrhahn Cortes, Abel Rodriguez, Duncan Temple Lang, and see AUTHORS file for additional contributors.
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6.13 dated 2019-01-25 and 0.7.0 dated 2019-02-01
DESCRIPTION | 8 - INSTALL | 6 MD5 | 12 - R/initializeModel.R | 212 +++++++++++++++++++++------------ inst/CppCode/dists.cpp | 2 inst/CppCode/predefinedNimbleLists.cpp | 32 +++- inst/NEWS | 12 + 7 files changed, 183 insertions(+), 101 deletions(-)
Title: Bootstrapped Confidence Intervals for (Negative) Likelihood
Ratio Tests
Description: Computes appropriate confidence intervals for the likelihood ratio tests commonly used in medicine/epidemiology, using the method of Marill et al. (2015) <doi:10.1177/0962280215592907>. It is particularly useful when the sensitivity or specificity in the sample is 100%. Note that this does not perform the test on nested models--for that, see 'epicalc::lrtest'.
Author: Keith A. Marill and Ari B. Friedman
Maintainer: Ari B. Friedman <abfriedman@gmail.com>
Diff between bootLR versions 1.0 dated 2015-07-12 and 1.0.2 dated 2019-02-01
DESCRIPTION | 13 ++-- MD5 | 28 ++++----- NAMESPACE | 5 + NEWS | 9 ++ R/bootLR.R | 133 ++++++++++++++++++++++++++++++++++++++++++- inst/CITATION | 32 ++++------ man/BayesianLR.test.Rd | 23 +++---- man/bca.Rd | 3 man/confusionStatistics.Rd | 3 man/diagCI.Rd |only man/drawMaxedOut.Rd | 3 man/medianConsistentlyOne.Rd | 3 man/print.diagCI.Rd |only man/print.lrtest.Rd | 3 man/run.BayesianLR.test.Rd | 7 -- man/sequentialGridSearch.Rd | 3 16 files changed, 200 insertions(+), 68 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <http://jmlr.org/papers/v18/15-481.html>; Crispino et al., to appear in Annals of Applied Statistics). Both Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen, Valeria Vitelli, Marta Crispino, Qinghua Liu
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 0.3.0 dated 2019-01-30 and 0.3.1 dated 2019-02-01
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 3 +++ build/partial.rdb |binary inst/doc/BayesMallowsPackage.html | 4 ++-- src/RcppExports.cpp | 2 +- src/misc.cpp | 2 +- src/misc.h | 2 +- src/mixtures.cpp | 2 +- src/pairwise_comparisons.cpp | 12 ++++++------ src/parameterupdates.cpp | 2 +- src/run_mcmc.cpp | 1 - 12 files changed, 30 insertions(+), 28 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for genes with changing
expression and to detect recurrent chromosomal copy number aberrations. This
method may be useful for high-throughput biological data (micro-array, sequencing, ...).
Probabilities are associated with genes or probes in the data set and there is no
problem of multiple tests when using this method. For array-based comparative genomic
hybridization data, segmentation results are obtained by merging the significant
probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.5.6 dated 2018-03-23 and 1.6 dated 2019-02-01
DESCRIPTION | 8 +- MD5 | 100 ++++++++++++++++++---------------- NAMESPACE | 2 R/calcSRmat.R |only R/calcSRmatMod.R |only R/chrSegment.R | 2 R/fcros.R | 141 ++++++++++++++----------------------------------- R/fcros2.R | 6 +- R/fcrosFCmat.R | 14 ++-- R/fcrosMod.R | 63 ++++----------------- R/fcrosTtest.R | 2 R/fcrosWrite.R | 57 +++++-------------- R/histoPlot.R | 7 -- R/pfco.R | 135 ++++++++++++++-------------------------------- R/pfcoMod.R | 61 +++------------------ R/rankReads.R | 127 ++++++++++++++++---------------------------- R/scoreThr.R |only R/tcnReads.R | 5 - data/bott.rda |only data/datalist | 1 man/bott.rd |only man/calcSRmat.rd |only man/calcSRmatMod.rd |only man/cghData.Rd | 6 +- man/cghInfo.Rd | 4 - man/chrMerge.rd | 2 man/chrPlot.rd | 15 ++--- man/chrPlot2.rd | 21 +++---- man/chrSegment.rd | 17 +++-- man/dataSummary.rd | 11 ++- man/fc2Calc.rd | 2 man/fcros-package.Rd | 22 ++++--- man/fcros.Rd | 12 ++-- man/fcros2.Rd | 23 +++++-- man/fcrosFCmat.Rd | 20 ++++-- man/fcrosMod.Rd | 13 ++-- man/fcrosRead.Rd | 2 man/fcrosTopN.Rd | 7 +- man/fcrosTtest.Rd | 8 +- man/fcrosWrite.Rd | 17 +---- man/fdata.Rd | 14 ++-- man/fvalTopN.rd | 10 ++- man/fvalVolcanoPlot.rd | 7 ++ man/histoPlot.rd | 7 ++ man/moyStdCalc.rd | 2 man/pfco.rd | 10 +-- man/pfcoMod.rd | 15 ++--- man/pvalTopN.rd | 7 ++ man/pvalVolcanoPlot.rd | 7 ++ man/rankReads.Rd | 116 ++++++++++++++++++++++------------------ man/rmatCalc.rd | 6 +- man/rmatTrim.rd | 2 man/scoreThr.Rd |only man/tcnReads.Rd | 6 +- man/tprobaCalc.rd | 8 +- 55 files changed, 491 insertions(+), 659 deletions(-)
Title: Bayesian Estimation of (Sparse) Latent Factor Stochastic
Volatility Models
Description: Markov chain Monte Carlo (MCMC) sampler for fully Bayesian
estimation of latent factor stochastic volatility models with
interweaving <doi:10.1080/10618600.2017.1322091>.
Sparsity can be achieved through the usage of Normal-Gamma priors
on the factor loading matrix <doi:10.1016/j.jeconom.2018.11.007>.
Author: Gregor Kastner [aut, cre] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between factorstochvol versions 0.8.3 dated 2016-12-31 and 0.9 dated 2019-02-01
DESCRIPTION | 21 ++++---- MD5 | 99 +++++++++++++++++++++--------------------- NAMESPACE | 2 NEWS | 5 ++ R/factorstochvol-package.R | 25 +++++----- R/imports.R | 2 R/wrappers.R | 24 ++++------ inst/CITATION | 35 ++++++-------- man/comtimeplot.Rd | 2 man/corelement.Rd | 2 man/corimageplot.Rd | 2 man/corplot.Rd | 2 man/cortimeplot.Rd | 2 man/covelement.Rd | 2 man/covmat.Rd | 2 man/covmat.fsvdraws.Rd | 2 man/covmat.fsvsim.Rd | 2 man/expweightcov.Rd | 1 man/facloadcredplot.Rd | 2 man/facloaddensplot.Rd | 2 man/facloadpairplot.Rd | 2 man/facloadpointplot.Rd | 6 +- man/facloadtraceplot.Rd | 2 man/factorstochvol-package.Rd | 29 +++++------- man/findrestrict.Rd | 1 man/fsvsample.Rd | 35 +++++++------- man/fsvsim.Rd | 6 +- man/ledermann.Rd | 1 man/logret.Rd | 4 - man/logvartimeplot.Rd | 2 man/orderident.Rd | 2 man/paratraceplot.Rd | 2 man/plot.fsvdraws.Rd | 2 man/predcond.Rd | 2 man/predcor.Rd | 2 man/predcov.Rd | 2 man/predh.Rd | 2 man/predloglik.Rd | 2 man/predloglikWB.Rd | 2 man/predprecWB.Rd | 2 man/preorder.Rd | 1 man/print.fsvdraws.Rd | 2 man/runningcormat.Rd | 2 man/runningcovmat.Rd | 2 man/signident.Rd | 2 man/voltimeplot.Rd | 2 src/Makevars | 5 +- src/Makevars.win | 7 +- src/register.cpp |only src/sampler.cpp | 28 +++++++++-- src/sampler.h | 2 51 files changed, 208 insertions(+), 189 deletions(-)
More information about factorstochvol at CRAN
Permanent link
Title: Fast and Easy Quality Control of EWAS Results Files
Description: Tools for (automated and manual) quality control of
the results of Epigenome-Wide Association Studies.
Author: Peter J. van der Most,
Leanne K. Kupers,
Ilja Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Diff between QCEWAS versions 1.1-0 dated 2016-12-09 and 1.2-2 dated 2019-02-01
QCEWAS-1.1-0/QCEWAS/R/script_v11-0_package.R |only QCEWAS-1.2-2/QCEWAS/DESCRIPTION | 8 +++---- QCEWAS-1.2-2/QCEWAS/MD5 | 19 ++++++++--------- QCEWAS-1.2-2/QCEWAS/R/script_v12-2_package.R |only QCEWAS-1.2-2/QCEWAS/inst/CITATION | 11 +++++++-- QCEWAS-1.2-2/QCEWAS/inst/doc/QCEWAS_changelog_v122.txt |only QCEWAS-1.2-2/QCEWAS/inst/extdata/sample_map.txt.gz |binary QCEWAS-1.2-2/QCEWAS/man/EWAS_QC.Rd | 6 ++--- QCEWAS-1.2-2/QCEWAS/man/EWAS_plots.Rd | 4 +-- QCEWAS-1.2-2/QCEWAS/man/EWAS_series.Rd | 17 +++++++++++++++ QCEWAS-1.2-2/QCEWAS/man/P_lambda.Rd | 6 ++--- QCEWAS-1.2-2/QCEWAS/man/QCEWAS-package.Rd | 4 +-- 12 files changed, 49 insertions(+), 26 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut],
Manuel Oviedo de la Fuente [aut, cre],
Pedro Galeano [ctb],
Alicia Nieto [ctb],
Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Diff between fda.usc versions 1.4.0 dated 2018-02-14 and 1.5.0 dated 2019-02-01
DESCRIPTION | 10 MD5 | 89 +-- NAMESPACE | 18 NEWS | 30 - R/anova.RPm.R | 62 +- R/anova.RPm.boot.R | 41 + R/auxiliar_VS.R |only R/classif.np.ldata.R | 2 R/depth.FM.r | 31 - R/depth.KFSD.R | 449 +++++++++++----- R/depth.RP.r | 123 +--- R/depth.RPD.r | 113 +--- R/depth.RPp.r | 9 R/depth.RT.r | 94 +-- R/depth.SD.R | 6 R/depth.mode.r | 282 ++++------ R/depth.multivariate.R | 88 +-- R/fda.usc.internal.R | 10 R/fregre.PPC.PPLS.R | 11 R/fregre.basis.cv.R | 47 + R/fregre.basis.cv.old.R |only R/fregre.glm.R | 23 R/fregre.gsam.R | 665 +++++++++++++----------- R/fregre.gsam.cv.R |only R/fregre.gsam.ncomp.R |only R/fregre.gsam.vs.R |only R/fregre.lm.r | 423 ++------------- R/min.np.r | 7 R/plot.depth.R |only R/rp.flm.test2.R |only R/summary.fregre.lm.R |only inst/script/flm_beta_estimation_brownian_data.R | 5 man/DepthFunctional.Rd | 36 - man/LMDC.select.Rd | 4 man/anova.RPm.Rd | 39 - man/classif.DD.Rd | 6 man/fda.usc.internal.Rd | 5 man/fdata.Rd | 4 man/fregre.glm.Rd | 5 man/fregre.gsam.vs.Rd |only man/fregre.pc.Rd | 2 man/fregre.pc.cv.Rd | 4 man/fregre.pls.cv.Rd | 4 man/plot.fdata.Rd | 11 man/r.ou.Rd | 71 +- man/rdir.pc.Rd | 5 man/rp.flm.statistic.Rd | 106 +-- man/rp.flm.test.Rd | 307 ++++------- man/summary.fregre.fd.Rd | 9 src/rp_stat.f90 | 62 +- 50 files changed, 1630 insertions(+), 1688 deletions(-)
Title: Partial Least Squares Regression for Beta Regression Models
Description: Provides Partial least squares Regression for (weighted) beta regression models (Bertrand 2013, <http://journal-sfds.fr/article/view/215>) and k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>)
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between plsRbeta versions 0.2.3 dated 2018-08-28 and 0.2.5 dated 2019-02-01
DESCRIPTION | 22 +- MD5 | 53 +++-- NAMESPACE | 90 +++++----- NEWS | 31 +-- NEWS.md |only R/PLS_beta.R | 100 +++++------ R/PLS_beta_formula.R | 84 ++++----- R/PLS_beta_kfoldcv.R | 354 ++++++++++++++++++++-------------------- R/PLS_beta_kfoldcv_formula.R | 26 +- R/PLS_beta_wvc.R | 74 ++++---- R/bootplsbeta.R | 77 ++++---- R/coefs.plsRbeta.R | 22 +- R/permcoefs.plsRbeta.R | 6 R/plsRbetamodel.default.R | 26 +- R/plsRbetamodel.formula.R | 26 +- R/tilt.bootplsbeta.R | 39 ++-- man/PLS_beta.Rd | 8 man/PLS_beta_formula.Rd | 8 man/PLS_beta_kfoldcv.Rd | 5 man/PLS_beta_kfoldcv_formula.Rd | 5 man/PLS_beta_wvc.Rd | 3 man/bootplsbeta.Rd | 28 +-- man/coefs.plsRbeta.Rd | 42 +--- man/kfolds2Chisq.Rd | 4 man/kfolds2Chisqind.Rd | 4 man/permcoefs.plsRbeta.Rd | 47 ++--- man/plsRbeta.Rd | 10 - man/tilt.bootplsbeta.Rd | 33 +-- 28 files changed, 602 insertions(+), 625 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.10-1 dated 2018-07-14 and 2.11-1 dated 2019-02-01
BiodiversityR-2.10-1/BiodiversityR/inst/etc/Rcmdr.xbm |only BiodiversityR-2.10-1/BiodiversityR/inst/etc/log-exceptions.txt |only BiodiversityR-2.10-1/BiodiversityR/inst/etc/submit.xbm |only BiodiversityR-2.11-1/BiodiversityR/DESCRIPTION | 13 BiodiversityR-2.11-1/BiodiversityR/MD5 | 59 BiodiversityR-2.11-1/BiodiversityR/NAMESPACE | 4 BiodiversityR-2.11-1/BiodiversityR/R/ensemble.VIF.R | 3 BiodiversityR-2.11-1/BiodiversityR/R/ensemble.batch.R | 53 BiodiversityR-2.11-1/BiodiversityR/R/ensemble.calibrate.models.R | 324 ++++- BiodiversityR-2.11-1/BiodiversityR/R/ensemble.calibrate.weights.R | 72 - BiodiversityR-2.11-1/BiodiversityR/R/ensemble.drop1.R | 78 + BiodiversityR-2.11-1/BiodiversityR/R/ensemble.environmentalThin.R |only BiodiversityR-2.11-1/BiodiversityR/R/ensemble.formulae.R | 6 BiodiversityR-2.11-1/BiodiversityR/R/ensemble.outlierThin.R |only BiodiversityR-2.11-1/BiodiversityR/R/ensemble.raster.R | 249 +++- BiodiversityR-2.11-1/BiodiversityR/R/ensemble.spatialThin.R | 79 - BiodiversityR-2.11-1/BiodiversityR/R/ensemble.strategy.R | 11 BiodiversityR-2.11-1/BiodiversityR/R/evaluation.strip.data.R | 88 + BiodiversityR-2.11-1/BiodiversityR/R/evaluation.strip.plot.R | 2 BiodiversityR-2.11-1/BiodiversityR/R/import.from.Excel.R | 46 BiodiversityR-2.11-1/BiodiversityR/inst/CITATION | 2 BiodiversityR-2.11-1/BiodiversityR/inst/ChangeLog | 72 + BiodiversityR-2.11-1/BiodiversityR/inst/etc/BiodiversityGUI.R | 592 ++++++++-- BiodiversityR-2.11-1/BiodiversityR/inst/etc/BiodiversityR-menus.txt | 13 BiodiversityR-2.11-1/BiodiversityR/inst/etc/Rcmdr-menus.txt | 26 BiodiversityR-2.11-1/BiodiversityR/inst/etc/Rcmdr-model-capabilities.txt | 18 BiodiversityR-2.11-1/BiodiversityR/man/ensemble.Rd | 97 + BiodiversityR-2.11-1/BiodiversityR/man/ensemble.batch.Rd | 37 BiodiversityR-2.11-1/BiodiversityR/man/ensemble.raster.Rd | 16 BiodiversityR-2.11-1/BiodiversityR/man/ensemble.red.Rd | 10 BiodiversityR-2.11-1/BiodiversityR/man/ensemble.spatialThin.Rd | 121 +- BiodiversityR-2.11-1/BiodiversityR/man/evaluation.strip.Rd | 6 BiodiversityR-2.11-1/BiodiversityR/man/removeNAcomm.Rd | 21 33 files changed, 1725 insertions(+), 393 deletions(-)
Title: MNREAD Parameters Estimation and Curve Plotting
Description: Allows to analyze the reading data obtained with the MNREAD Acuity
Chart, a continuous-text reading acuity chart for normal and low vision.
Provides the necessary functions to plot the MNREAD curve and estimate
automatically the four MNREAD parameters: Maximum Reading Speed,
Critical Print Size, Reading Acuity and Reading Accessibility Index.
Parameters can be estimated either with the standard method
or with a nonlinear mixed-effects (NLME) modeling.
See Calabrese et al. 2018 for more details <doi.org/10.1167/18.1.8>.
Author: Aurélie Calabrèse [aut, cre],
J. Steve Mansfield [aut],
Gordon E. Legge [aut]
Maintainer: Aurélie Calabrèse <acalabre@umn.edu>
Diff between mnreadR versions 2.1.1 dated 2018-11-14 and 2.1.2 dated 2019-02-01
mnreadR-2.1.1/mnreadR/R/mansfield_algorithm.R |only mnreadR-2.1.2/mnreadR/DESCRIPTION | 8 +++--- mnreadR-2.1.2/mnreadR/MD5 | 16 ++++++------ mnreadR-2.1.2/mnreadR/R/all_mnread_param.R | 16 +++++++----- mnreadR-2.1.2/mnreadR/R/curve_param.R | 22 +++++++++++------ mnreadR-2.1.2/mnreadR/R/mansfield_algorithm_2019.R |only mnreadR-2.1.2/mnreadR/R/mnread_curve.R | 27 +++++++++++++-------- mnreadR-2.1.2/mnreadR/R/zzz.R | 2 - mnreadR-2.1.2/mnreadR/man/curveParam_RS.Rd | 11 ++++++-- mnreadR-2.1.2/mnreadR/man/nlmeModel.Rd | 4 +-- 10 files changed, 65 insertions(+), 41 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05>. Also incorporates SV with leverage.
Author: Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>),
Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 1.3.3 dated 2017-09-19 and 2.0.0 dated 2019-02-01
stochvol-1.3.3/stochvol/inst/include/update.h |only stochvol-2.0.0/stochvol/DESCRIPTION | 21 stochvol-2.0.0/stochvol/MD5 | 105 - stochvol-2.0.0/stochvol/NAMESPACE | 123 - stochvol-2.0.0/stochvol/NEWS | 27 stochvol-2.0.0/stochvol/R/exports.R |only stochvol-2.0.0/stochvol/R/plotting.R | 864 ++++++--- stochvol-2.0.0/stochvol/R/simulation.R | 261 +- stochvol-2.0.0/stochvol/R/stochvol-package.R |only stochvol-2.0.0/stochvol/R/util.R |only stochvol-2.0.0/stochvol/R/utilities_svdraws.R | 622 +++++- stochvol-2.0.0/stochvol/R/wrappers.R | 1613 ++++++++++++++---- stochvol-2.0.0/stochvol/build/vignette.rds |binary stochvol-2.0.0/stochvol/data/exrates.RData |binary stochvol-2.0.0/stochvol/inst/CITATION | 8 stochvol-2.0.0/stochvol/inst/doc/article.Rnw | 2 stochvol-2.0.0/stochvol/inst/doc/article.pdf |binary stochvol-2.0.0/stochvol/inst/doc/heavytails.Rnw | 2 stochvol-2.0.0/stochvol/inst/doc/heavytails.pdf |binary stochvol-2.0.0/stochvol/inst/include/stochvol.h |only stochvol-2.0.0/stochvol/man/arpredict.Rd | 57 stochvol-2.0.0/stochvol/man/exrates.Rd | 29 stochvol-2.0.0/stochvol/man/extractors.Rd | 44 stochvol-2.0.0/stochvol/man/logret.Rd | 24 stochvol-2.0.0/stochvol/man/paradensplot.Rd | 92 - stochvol-2.0.0/stochvol/man/paratraceplot.Rd | 72 stochvol-2.0.0/stochvol/man/plot.svdraws.Rd | 149 - stochvol-2.0.0/stochvol/man/predict.svdraws.Rd | 110 - stochvol-2.0.0/stochvol/man/stochvol-package.Rd | 84 stochvol-2.0.0/stochvol/man/svlsample.Rd |only stochvol-2.0.0/stochvol/man/svlsample2.Rd |only stochvol-2.0.0/stochvol/man/svsample.Rd | 379 ++-- stochvol-2.0.0/stochvol/man/svsample2.Rd | 189 +- stochvol-2.0.0/stochvol/man/svsim.Rd | 157 + stochvol-2.0.0/stochvol/man/updatesummary.Rd | 108 - stochvol-2.0.0/stochvol/man/volplot.Rd | 115 - stochvol-2.0.0/stochvol/src/Makevars | 30 stochvol-2.0.0/stochvol/src/Makevars.win | 7 stochvol-2.0.0/stochvol/src/aug-kalman-filter.cpp |only stochvol-2.0.0/stochvol/src/aug-kalman-filter.h |only stochvol-2.0.0/stochvol/src/auxmix.cpp | 20 stochvol-2.0.0/stochvol/src/auxmix.h | 17 stochvol-2.0.0/stochvol/src/densities.h | 53 stochvol-2.0.0/stochvol/src/exports.cpp |only stochvol-2.0.0/stochvol/src/h-sampler.cpp |only stochvol-2.0.0/stochvol/src/h-sampler.h |only stochvol-2.0.0/stochvol/src/h-utils.cpp |only stochvol-2.0.0/stochvol/src/h-utils.h |only stochvol-2.0.0/stochvol/src/mixture-state-sampler.cpp |only stochvol-2.0.0/stochvol/src/mixture-state-sampler.h |only stochvol-2.0.0/stochvol/src/parameterization.h |only stochvol-2.0.0/stochvol/src/progutils.cpp | 94 - stochvol-2.0.0/stochvol/src/progutils.h | 76 stochvol-2.0.0/stochvol/src/regression.cpp |only stochvol-2.0.0/stochvol/src/regression.h |only stochvol-2.0.0/stochvol/src/sampler.cpp | 1081 +++--------- stochvol-2.0.0/stochvol/src/sampler.h | 96 - stochvol-2.0.0/stochvol/src/simulation-smoother.cpp |only stochvol-2.0.0/stochvol/src/simulation-smoother.h |only stochvol-2.0.0/stochvol/src/theta-sampler.cpp |only stochvol-2.0.0/stochvol/src/theta-sampler.h |only stochvol-2.0.0/stochvol/src/theta-utils.cpp |only stochvol-2.0.0/stochvol/src/theta-utils.h |only stochvol-2.0.0/stochvol/src/update_functions.cpp |only stochvol-2.0.0/stochvol/src/update_functions.h |only stochvol-2.0.0/stochvol/vignettes/article.Rnw | 2 stochvol-2.0.0/stochvol/vignettes/heavytails.Rnw | 2 67 files changed, 4307 insertions(+), 2428 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight and simpler than both), tools
for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.5 dated 2018-11-16 and 0.2.6 dated 2019-02-01
reproducible-0.2.5/reproducible/man/assessDataTypeGDALhelpers.Rd |only reproducible-0.2.5/reproducible/man/makeMemoiseable.Rd |only reproducible-0.2.5/reproducible/man/pipe2.Rd |only reproducible-0.2.5/reproducible/man/reproducible-deprecated.Rd |only reproducible-0.2.5/reproducible/tests/testthat/test-preProcessMessages.R |only reproducible-0.2.6/reproducible/DESCRIPTION | 44 reproducible-0.2.6/reproducible/MD5 | 123 reproducible-0.2.6/reproducible/NAMESPACE | 39 reproducible-0.2.6/reproducible/NEWS.md | 36 reproducible-0.2.6/reproducible/R/cache-helpers.R | 96 reproducible-0.2.6/reproducible/R/cache-internals.R |only reproducible-0.2.6/reproducible/R/cache-tools.R | 123 reproducible-0.2.6/reproducible/R/cache.R | 940 +--- reproducible-0.2.6/reproducible/R/checksums.R | 5 reproducible-0.2.6/reproducible/R/cloud.R |only reproducible-0.2.6/reproducible/R/consistentPaths.R | 17 reproducible-0.2.6/reproducible/R/gis.R | 28 reproducible-0.2.6/reproducible/R/helpers.R | 17 reproducible-0.2.6/reproducible/R/objectSize.R | 3 reproducible-0.2.6/reproducible/R/options.R |only reproducible-0.2.6/reproducible/R/pipe.R | 256 - reproducible-0.2.6/reproducible/R/postProcess.R | 391 - reproducible-0.2.6/reproducible/R/preProcess.R | 233 - reproducible-0.2.6/reproducible/R/prepInputs.R | 367 + reproducible-0.2.6/reproducible/R/reproducible-package.R | 65 reproducible-0.2.6/reproducible/R/robustDigest.R | 172 reproducible-0.2.6/reproducible/R/zzz.R | 23 reproducible-0.2.6/reproducible/README.md | 2 reproducible-0.2.6/reproducible/build/vignette.rds |binary reproducible-0.2.6/reproducible/inst/doc/Intro-to-Cache.R | 31 reproducible-0.2.6/reproducible/inst/doc/Intro-to-Cache.Rmd | 34 reproducible-0.2.6/reproducible/inst/doc/Intro-to-Cache.html | 2180 ++++------ reproducible-0.2.6/reproducible/inst/examples/example_Cache.R | 31 reproducible-0.2.6/reproducible/man/CacheDigest.Rd |only reproducible-0.2.6/reproducible/man/assessDataType.Rd | 16 reproducible-0.2.6/reproducible/man/assessDataTypeGDAL.Rd | 9 reproducible-0.2.6/reproducible/man/basename2.Rd |only reproducible-0.2.6/reproducible/man/cache.Rd | 101 reproducible-0.2.6/reproducible/man/clearStubArtifacts.Rd | 2 reproducible-0.2.6/reproducible/man/cloudCache.Rd |only reproducible-0.2.6/reproducible/man/cloudCheck.Rd |only reproducible-0.2.6/reproducible/man/cloudExtras.Rd |only reproducible-0.2.6/reproducible/man/cloudSyncCache.Rd |only reproducible-0.2.6/reproducible/man/cloudWrite.Rd |only reproducible-0.2.6/reproducible/man/downloadFile.Rd | 2 reproducible-0.2.6/reproducible/man/fastMask.Rd | 7 reproducible-0.2.6/reproducible/man/makeMemoisable.Rd |only reproducible-0.2.6/reproducible/man/pipe.Rd | 77 reproducible-0.2.6/reproducible/man/preProcess.Rd | 4 reproducible-0.2.6/reproducible/man/prepInputs.Rd | 4 reproducible-0.2.6/reproducible/man/projectInputs.Rd | 7 reproducible-0.2.6/reproducible/man/purge.Rd | 2 reproducible-0.2.6/reproducible/man/reproducible-package.Rd | 67 reproducible-0.2.6/reproducible/man/reproducibleOptions.Rd |only reproducible-0.2.6/reproducible/man/robustDigest.Rd | 124 reproducible-0.2.6/reproducible/man/setSubAttrInList.Rd |only reproducible-0.2.6/reproducible/man/testForUnrar.Rd |only reproducible-0.2.6/reproducible/man/unrarExists.Rd |only reproducible-0.2.6/reproducible/man/unrarPath.Rd |only reproducible-0.2.6/reproducible/man/viewCache.Rd | 42 reproducible-0.2.6/reproducible/man/writeFuture.Rd | 2 reproducible-0.2.6/reproducible/tests/testthat/helper-allEqual.R | 3 reproducible-0.2.6/reproducible/tests/testthat/test-cache.R | 311 - reproducible-0.2.6/reproducible/tests/testthat/test-cacheHelpers.R |only reproducible-0.2.6/reproducible/tests/testthat/test-checkPath.R | 3 reproducible-0.2.6/reproducible/tests/testthat/test-devMode.R |only reproducible-0.2.6/reproducible/tests/testthat/test-filesMissingExtension.R |only reproducible-0.2.6/reproducible/tests/testthat/test-multipleCacheRepo.R |only reproducible-0.2.6/reproducible/tests/testthat/test-packages.R | 3 reproducible-0.2.6/reproducible/tests/testthat/test-preProcessDoesntWork.R | 34 reproducible-0.2.6/reproducible/tests/testthat/test-preProcessWorks.R | 243 + reproducible-0.2.6/reproducible/tests/testthat/test-prepInputs.R | 208 reproducible-0.2.6/reproducible/tests/testthat/test-prepInputsInNestedArchives.R |only reproducible-0.2.6/reproducible/tests/testthat/test-reproducibleVerbose.R |only reproducible-0.2.6/reproducible/tests/testthat/test-robustDigest.R | 9 reproducible-0.2.6/reproducible/vignettes/Intro-to-Cache.Rmd | 34 76 files changed, 3588 insertions(+), 2982 deletions(-)
Title: Pam: Prediction Analysis for Microarrays
Description: Some functions for sample classification in microarrays.
Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between pamr versions 1.55 dated 2014-08-27 and 1.56 dated 2019-02-01
pamr-1.55/pamr/R/allknnimp.R |only pamr-1.55/pamr/R/pamr.from.excel.R |only pamr-1.55/pamr/R/pamr.knnimpute.R |only pamr-1.55/pamr/R/pamr.xlfuns.R |only pamr-1.55/pamr/man/pamr.from.excel.Rd |only pamr-1.55/pamr/man/pamr.knnimpute.Rd |only pamr-1.55/pamr/man/pamr.to.excel.Rd |only pamr-1.56/pamr/DESCRIPTION | 10 ++-- pamr-1.56/pamr/MD5 | 13 +---- pamr-1.56/pamr/NAMESPACE | 55 ++++++----------------- pamr-1.56/pamr/man/pamr.internal.Rd | 81 ---------------------------------- 11 files changed, 23 insertions(+), 136 deletions(-)
Title: Import/Export Routines for 'MALDIquant'
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from 'MALDIquant'
objects.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>),
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.11.5 dated 2018-08-14 and 0.12 dated 2019-02-01
DESCRIPTION | 8 ++--- MD5 | 22 ++++++------- NEWS | 13 ++++++++ R/importTab-functions.R | 48 ++++++++++++++++++------------ R/parseMzMl.R | 3 + inst/doc/MALDIquantForeign-intro.pdf |binary inst/exampledata/compressed/csv.tar.gz |binary inst/exampledata/compressed/csv.zip |binary inst/exampledata/compressed/csv1.csv.gz |binary inst/exampledata/csv1.csv | 2 + tests/testthat/test_download-functions.R | 2 - tests/testthat/test_importTab-functions.R | 6 +-- 12 files changed, 66 insertions(+), 38 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-02 0.1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-01 1.1-1
2016-03-11 1.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-15 0.9.2
2017-05-09 0.9.1
2017-04-07 0.9.0
2017-02-10 0.8.0
2016-11-29 0.7.1
2016-11-21 0.7.0
2016-11-11 0.6.0
2016-10-28 0.5.1
2016-10-17 0.5.0
2016-09-16 0.4.0
2016-07-01 0.3.3
2016-06-13 0.3.2
2016-04-04 0.3.1
2016-03-20 0.3.0
2016-02-08 0.2.0
2015-12-23 0.1.0
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 0.2.2 dated 2018-05-18 and 0.2.3 dated 2019-02-01
DESCRIPTION | 15 +- MD5 | 23 +-- NEWS.md |only R/simsurv.R | 248 +++++++++++++++++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/simsurv_technical.Rmd | 4 inst/doc/simsurv_technical.html | 8 - inst/doc/simsurv_usage.Rmd | 2 inst/doc/simsurv_usage.html | 40 +++++- man/simsurv.Rd | 29 +++- vignettes/simsurv_technical.Rmd | 4 vignettes/simsurv_usage.Rmd | 2 13 files changed, 269 insertions(+), 106 deletions(-)
Title: Population Genetics
Description: Classes and methods for handling genetic data. Includes
classes to represent genotypes and haplotypes at single markers
up to multiple markers on multiple chromosomes. Function
include allele frequencies, flagging homo/heterozygotes,
flagging carriers of certain alleles, estimating and testing
for Hardy-Weinberg disequilibrium, estimating and testing for
linkage disequilibrium, ...
Author: Gregory Warnes, with contributions from Gregor Gorjanc,
Friedrich Leisch, and Michael Man.
Maintainer: Gregory Warnes <greg@warnes.net>
Diff between genetics versions 1.3.8.1 dated 2013-09-03 and 1.3.8.1.1 dated 2019-02-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 12 +++++++++++- data/gregorius.rda |binary 4 files changed, 17 insertions(+), 7 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo, ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below. This report has been cited in more than 2,000 scientific articles.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.37 dated 2018-04-05 and 1.38 dated 2019-02-01
DESCRIPTION | 10 MD5 | 18 - NEWS | 8 R/EZR.R | 288 +++++++++++++++++----------- inst/CHANGES | 8 inst/doc/EZR.htm | 4 inst/doc/EZR.pdf |binary inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary man/EZR.Rd | 4 po/R-RcmdrPlugin.EZR.po | 9 10 files changed, 222 insertions(+), 127 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (<http://turfjs.org>) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut],
Morgan Herlocker [cph]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.4.2 dated 2017-10-13 and 0.5.0 dated 2019-02-01
DESCRIPTION | 17 LICENSE | 2 MD5 | 196 ++--- NEWS.md | 9 R/erase.R | 4 R/intersect.R | 10 R/midpoint.R | 4 R/polygonize.R | 248 +++---- R/view.R | 2 README.md | 21 build/vignette.rds |binary inst/doc/lawn_vignette.html | 1393 +++++++++++++++++++++++++++++++++++++++- man/georandom.Rd | 3 man/lawn_along.Rd | 1 man/lawn_area.Rd | 1 man/lawn_average.Rd | 1 man/lawn_bbox.Rd | 1 man/lawn_bbox_polygon.Rd | 1 man/lawn_bearing.Rd | 1 man/lawn_bezier.Rd | 4 man/lawn_boolean_clockwise.Rd | 1 man/lawn_boolean_contains.Rd | 1 man/lawn_boolean_crosses.Rd | 1 man/lawn_boolean_disjoint.Rd | 1 man/lawn_boolean_overlap.Rd | 1 man/lawn_boolean_pointonline.Rd | 1 man/lawn_boolean_within.Rd | 1 man/lawn_buffer.Rd | 1 man/lawn_center.Rd | 1 man/lawn_center_of_mass.Rd | 1 man/lawn_centroid.Rd | 1 man/lawn_circle.Rd | 1 man/lawn_collect.Rd | 1 man/lawn_collectionof.Rd | 1 man/lawn_concave.Rd | 1 man/lawn_convex.Rd | 1 man/lawn_count.Rd | 4 man/lawn_destination.Rd | 1 man/lawn_deviation.Rd | 1 man/lawn_difference.Rd | 5 man/lawn_dissolve.Rd | 1 man/lawn_distance.Rd | 1 man/lawn_envelope.Rd | 1 man/lawn_extent.Rd | 1 man/lawn_feature.Rd | 1 man/lawn_featurecollection.Rd | 1 man/lawn_featureof.Rd | 1 man/lawn_filter.Rd | 1 man/lawn_flatten.Rd | 1 man/lawn_geometrycollection.Rd | 1 man/lawn_geosjontype.Rd | 1 man/lawn_hex_grid.Rd | 1 man/lawn_idw.Rd | 1 man/lawn_inside.Rd | 1 man/lawn_intersect.Rd | 11 man/lawn_isolines.Rd | 1 man/lawn_line_distance.Rd | 1 man/lawn_linestring.Rd | 1 man/lawn_max.Rd | 1 man/lawn_median.Rd | 4 man/lawn_merge.Rd | 1 man/lawn_midpoint.Rd | 5 man/lawn_min.Rd | 1 man/lawn_multilinestring.Rd | 1 man/lawn_multipoint.Rd | 1 man/lawn_multipolygon.Rd | 1 man/lawn_nearest.Rd | 1 man/lawn_planepoint.Rd | 1 man/lawn_point.Rd | 1 man/lawn_point_grid.Rd | 5 man/lawn_point_on_surface.Rd | 1 man/lawn_polygon.Rd | 1 man/lawn_polygonize.Rd | 248 +++---- man/lawn_pt2line_distance.Rd | 5 man/lawn_random.Rd | 5 man/lawn_remove.Rd | 1 man/lawn_sample.Rd | 1 man/lawn_simplify.Rd | 1 man/lawn_square.Rd | 1 man/lawn_square_grid.Rd | 1 man/lawn_sum.Rd | 1 man/lawn_tag.Rd | 1 man/lawn_tesselate.Rd | 1 man/lawn_tin.Rd | 1 man/lawn_triangle_grid.Rd | 1 man/lawn_truncate.Rd | 1 man/lawn_union.Rd | 1 man/lawn_unkinkpolygon.Rd | 1 man/lawn_variance.Rd | 1 man/lawn_within.Rd | 1 man/view.Rd | 2 tests/testthat/test-centroid.R | 3 tests/testthat/test-count.R | 15 tests/testthat/test-intersect.R | 3 tests/testthat/test-max.R | 2 tests/testthat/test-median.R | 23 tests/testthat/test-sum.R | 17 tests/testthat/test-tag.R | 5 tests/testthat/test-variance.R | 2 99 files changed, 1894 insertions(+), 450 deletions(-)