Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, David Bauman, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.2-0 dated 2018-05-23 and 0.3-0 dated 2018-08-31
DESCRIPTION | 12 MD5 | 56 +-- NAMESPACE | 2 R/aem.time.R | 54 +- R/envspace.test.R |only R/listw.candidates.R | 27 - R/listw.select.R | 40 +- R/mem.select.R | 93 +++- R/msr.varipart.R | 60 ++- R/scalogram.R | 8 inst/doc/tutorial.html | 876 +++++++++++++++-------------------------------- inst/listw.explore/app.R | 118 ++++-- man/WRperiodogram.Rd | 5 man/aem.time.Rd | 25 - man/aem.weight.edges.Rd | 5 man/chooseCN.Rd | 6 man/envspace.test.Rd |only man/forward.sel.Rd | 6 man/forward.sel.par.Rd | 3 man/listw.candidates.Rd | 25 - man/listw.select.Rd | 18 man/mem.Rd | 3 man/mem.select.Rd | 34 + man/mfpa.Rd | 2 man/mspa.Rd | 2 man/msr.Rd | 5 man/multispati.Rd | 3 man/orthobasis.poly.Rd | 3 man/scalogram.Rd | 1 man/stimodels.Rd | 1 30 files changed, 652 insertions(+), 841 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-10 dated 2018-04-05 and 1.0-12 dated 2018-08-31
DESCRIPTION | 12 +-- MD5 | 16 ++-- R/ade4-plot.R | 168 ++++++++++++++++++++++++++++----------------- R/ade4-score.R | 47 +++++------- R/multiplot.R | 4 - inst/doc/adegraphics.html | 90 ++++++++++++------------ man/adegraphics-package.Rd | 4 - man/plot.inertia.Rd | 36 +++++---- man/setlimits1D.Rd | 6 - 9 files changed, 214 insertions(+), 169 deletions(-)
Title: Functions to Work with NCBI Accessions and Taxonomy
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
Author: Scott Sherrill-Mix [aut, cre]
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
Diff between taxonomizr versions 0.2.2 dated 2017-03-12 and 0.5.1 dated 2018-08-31
taxonomizr-0.2.2/taxonomizr/src/taxaTrim.h |only taxonomizr-0.5.1/taxonomizr/DESCRIPTION | 11 taxonomizr-0.5.1/taxonomizr/LICENSE |only taxonomizr-0.5.1/taxonomizr/MD5 | 57 taxonomizr-0.5.1/taxonomizr/NAMESPACE | 6 taxonomizr-0.5.1/taxonomizr/R/taxa.R | 640 ++++++++-- taxonomizr-0.5.1/taxonomizr/README.md | 317 ++++ taxonomizr-0.5.1/taxonomizr/build/vignette.rds |binary taxonomizr-0.5.1/taxonomizr/inst/doc/usage.R | 62 taxonomizr-0.5.1/taxonomizr/inst/doc/usage.Rmd | 299 +++- taxonomizr-0.5.1/taxonomizr/inst/doc/usage.html | 530 +++----- taxonomizr-0.5.1/taxonomizr/man/accessionToTaxa.Rd | 8 taxonomizr-0.5.1/taxonomizr/man/condenseTaxa.Rd | 11 taxonomizr-0.5.1/taxonomizr/man/getAccession2taxid.Rd | 6 taxonomizr-0.5.1/taxonomizr/man/getAccessions.Rd |only taxonomizr-0.5.1/taxonomizr/man/getId.Rd | 12 taxonomizr-0.5.1/taxonomizr/man/getId2.Rd |only taxonomizr-0.5.1/taxonomizr/man/getNamesAndNodes.Rd | 4 taxonomizr-0.5.1/taxonomizr/man/getTaxonomy.Rd | 28 taxonomizr-0.5.1/taxonomizr/man/getTaxonomy2.Rd |only taxonomizr-0.5.1/taxonomizr/man/prepareDatabase.Rd |only taxonomizr-0.5.1/taxonomizr/man/read.accession2taxid.Rd | 18 taxonomizr-0.5.1/taxonomizr/man/read.names.Rd | 8 taxonomizr-0.5.1/taxonomizr/man/read.names.sql.Rd |only taxonomizr-0.5.1/taxonomizr/man/read.nodes.Rd | 8 taxonomizr-0.5.1/taxonomizr/man/read.nodes.sql.Rd |only taxonomizr-0.5.1/taxonomizr/man/streamingRead.Rd | 11 taxonomizr-0.5.1/taxonomizr/man/taxonomizr-package.Rd |only taxonomizr-0.5.1/taxonomizr/man/taxonomizrSwitch.Rd |only taxonomizr-0.5.1/taxonomizr/man/trimTaxa.Rd | 4 taxonomizr-0.5.1/taxonomizr/src/taxaTrim.c | 10 taxonomizr-0.5.1/taxonomizr/tests/testthat/fakeNamesNodes.tar.gz |binary taxonomizr-0.5.1/taxonomizr/tests/testthat/test_taxa.R | 465 ++++++- taxonomizr-0.5.1/taxonomizr/vignettes/usage.Rmd | 299 +++- taxonomizr-0.5.1/taxonomizr/vignettes/usage.md |only 35 files changed, 2141 insertions(+), 673 deletions(-)
Title: Foundations and Applications of Statistics Using R (2nd Edition)
Description: Data sets and utilities to accompany the second edition of
"Foundations and Applications of Statistics: an Introduction
using R" (R Pruim, published by AMS, 2017), a text covering
topics from probability and mathematical statistics at an advanced
undergraduate level. R is integrated throughout, and access to all
the R code in the book is provided via the snippet() function.
Author: Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between fastR2 versions 1.1.0 dated 2018-06-27 and 1.2.1 dated 2018-08-31
DESCRIPTION | 24 ++- MD5 | 23 +-- NEWS.md | 15 ++ R/snippet.R | 119 +++++++++++++----- R/sysdata.rda |only R/vaov.R | 2 build/vignette.rds |binary inst/doc/Errata2e.Rmd | 61 +++++---- inst/doc/Errata2e.html | 314 +++++++++++++++++++++++++++++++++++++++---------- man/geolm.Rd | 4 man/snippet.Rd | 31 +++- man/vaov.Rd | 3 vignettes/Errata2e.Rmd | 61 +++++---- 13 files changed, 482 insertions(+), 175 deletions(-)
More information about AgreementInterval at CRAN
Permanent link
Title: Create 'roxygen2' Skeleton with Information from Function Script
Description: Create 'roxygen2' skeleton populated with information scraped from the
within the function script. Also creates field entries for imports in the
'DESCRIPTION' and import in the 'NAMESPACE' files. Can be run from the R
console or through the 'RStudio' 'addin' menu.
Author: Jonathan Sidi [aut, cre] (<https://orcid.org/0000-0002-4222-1819>),
Anton Grishin [ctb],
Lorenzo Busetto [ctb]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>
Diff between sinew versions 0.3.5.1 dated 2017-10-28 and 0.3.8 dated 2018-08-31
sinew-0.3.5.1/sinew/R/defaults.R |only sinew-0.3.5.1/sinew/R/zzz.r |only sinew-0.3.8/sinew/DESCRIPTION | 31 +- sinew-0.3.8/sinew/MD5 | 66 ++-- sinew-0.3.8/sinew/NAMESPACE | 7 sinew-0.3.8/sinew/NEWS.md | 76 +++-- sinew-0.3.8/sinew/R/check_attach.R | 19 - sinew-0.3.8/sinew/R/create_yml.R | 58 +-- sinew-0.3.8/sinew/R/get_oxy.R | 36 +- sinew-0.3.8/sinew/R/importAddin.R | 16 - sinew-0.3.8/sinew/R/interOxyAddIn.R | 440 +++++++++++++++-------------- sinew-0.3.8/sinew/R/ls_param.R | 30 + sinew-0.3.8/sinew/R/makeDictionary.R | 35 +- sinew-0.3.8/sinew/R/makeImport.R | 150 ++++----- sinew-0.3.8/sinew/R/makeOxyFile.R | 137 ++++----- sinew-0.3.8/sinew/R/makeOxygen.R | 209 +++++++------ sinew-0.3.8/sinew/R/makeSeeAlso.R | 24 - sinew-0.3.8/sinew/R/moga.R | 90 ++--- sinew-0.3.8/sinew/R/opts.R |only sinew-0.3.8/sinew/R/opts_complete.R |only sinew-0.3.8/sinew/R/oxygenAddin.R | 12 sinew-0.3.8/sinew/R/pretty_namespace.R | 188 ++++-------- sinew-0.3.8/sinew/R/pretty_utils.R |only sinew-0.3.8/sinew/R/rmOxygen.R | 18 - sinew-0.3.8/sinew/R/rm_oxylines.R | 47 +-- sinew-0.3.8/sinew/R/something.R | 38 +- sinew-0.3.8/sinew/R/tabular.R | 16 - sinew-0.3.8/sinew/R/untangle.R | 110 ++++--- sinew-0.3.8/sinew/R/untangle_examples.R |only sinew-0.3.8/sinew/R/zzz.R |only sinew-0.3.8/sinew/build/sinew.pdf |binary sinew-0.3.8/sinew/man/makeOxyFile.Rd | 4 sinew-0.3.8/sinew/man/makeOxygen.Rd | 9 sinew-0.3.8/sinew/man/moga.Rd | 2 sinew-0.3.8/sinew/man/pretty_namespace.Rd | 18 - sinew-0.3.8/sinew/man/sinew_opts.Rd | 2 sinew-0.3.8/sinew/man/untangle.Rd | 12 sinew-0.3.8/sinew/man/untangle_examples.Rd |only 38 files changed, 991 insertions(+), 909 deletions(-)
Title: Indexing for R
Description: Index structures allow quickly accessing elements from
large collections. While btree are optimized for disk databases
and ttree for ram databases we use hybrid static indexing which
is quite optimal for R.
Author: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between rindex versions 0.12 dated 2012-08-24 and 0.12.1 dated 2018-08-31
DESCRIPTION | 8 +++++--- MD5 | 6 +++--- NAMESPACE | 34 ++++++++++++++++++++++++++++++++++ R/zzz.R | 2 +- 4 files changed, 43 insertions(+), 7 deletions(-)
Title: The Random Subgraph Model
Description: Estimate the parameters, the number of classes and cluster vertices of a random network into groups with homogeneous connection profiles. The clustering is performed for directed graphs with typed edges (edges are assumed to be drawn from multinomial distributions) for which a partition of the vertices is available.
Author: Charles Bouveyron, Yacine Jernite, Pierre Latouche, Laetitia Nouedoui
Maintainer: Pierre Latouche <pierre.latouche@univ-paris1.fr>
Diff between Rambo versions 1.1 dated 2013-11-13 and 1.1.1 dated 2018-08-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 7 ++++++- data/Regions.rda |binary 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Flexible Copula Density Estimation with Penalized Hierarchical
B-Splines
Description: Flexible copula density estimation with penalized hierarchical B-Splines.
Author: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Diff between pencopula versions 0.3.5 dated 2014-02-26 and 0.3.5.1 dated 2018-08-31
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 11 insertions(+), 5 deletions(-)
Title: Routines for Exponential Power Distribution
Description: Collection of utilities referred to Exponential Power distribution,
also known as General Error Distribution (see Mineo, A.M. and Ruggieri, M. (2005), A software Tool for the Exponential Power Distribution: The normalp package. In Journal of Statistical Software, Vol. 12, Issue 4).
Author: Angelo M. Mineo <angelo.mineo@unipa.it>
Maintainer: Angelo M. Mineo <angelo.mineo@unipa.it>
Diff between normalp versions 0.7.0 dated 2014-12-09 and 0.7.0.1 dated 2018-08-31
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 22 ++++++++++++++++++++++ 3 files changed, 29 insertions(+), 7 deletions(-)
Title: Meta-Analysis with Mean Differences
Description: A collection of functions for conducting a meta-analysis with mean differences data. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re & William T. Hoyt
Maintainer: AC Del Re <acdelre@gmail.com>
Diff between MAd versions 0.8-2 dated 2014-12-21 and 0.8-2.1 dated 2018-08-31
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NAMESPACE | 21 ++++++++++++++++++++- data/dat.cooper15.3.rda |binary data/dat.cooperA2.rda |binary data/dat.hoyt.rda |binary data/dat.sim.es.rda |binary data/dat.sim.final.rda |binary data/dat.sim.raw.rda |binary data/dat.sim1.rda |binary data/dat.sim2.rda |binary inst/CITATION | 4 ++-- man/MAd-package.Rd | 14 +++++++------- man/mareg.rd | 6 +++--- 14 files changed, 48 insertions(+), 29 deletions(-)
Title: Meta-Analysis with Correlations
Description: This is an integrated meta-analysis package for conducting
a correlational research synthesis. One of the unique features
of this package is in its integration of user-friendly
functions to facilitate statistical analyses at each stage in a
meta-analysis with correlations. It uses recommended procedures
as described in The Handbook of Research Synthesis and
Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re & William T. Hoyt
Maintainer: AC Del Re <acdelre@gmail.com>
Diff between MAc versions 1.1 dated 2010-07-07 and 1.1.1 dated 2018-08-31
DESCRIPTION | 7 ++++--- MD5 |only NAMESPACE |only man/MAc-package.rd | 14 +++++++------- man/mareg.rd | 6 +++--- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Lan-DeMets Method for Group Sequential Boundaries
Description: Computations related to group sequential boundaries.
Includes calculation of bounds using the Lan-DeMets
alpha spending function approach.
Author: Charlie Casper and Oscar A. Perez. Based on FORTRAN
program ld98.
Maintainer: Charlie Casper <charlie.casper@hsc.utah.edu>
Diff between ldbounds versions 1.1-1 dated 2014-01-19 and 1.1-1.1 dated 2018-08-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 9 +++++++++ 3 files changed, 14 insertions(+), 5 deletions(-)
Title: Elastic-Net for Sparse Estimation and Sparse PCA
Description: Provides functions for fitting the entire
solution path of the Elastic-Net and also provides functions
for estimating sparse Principal Components. The Lasso solution
paths can be computed by the same function. First version:
2005-10.
Author: Hui Zou <hzou@stat.umn.edu> and Trevor Hastie
<hastie@stanford.edu>
Maintainer: Hui Zou <hzou@stat.umn.edu>
Diff between elasticnet versions 1.1 dated 2012-06-28 and 1.1.1 dated 2018-08-31
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 9 +++++++++ data/diabetes.RData |binary data/pitprops.RData |binary man/enet.Rd | 3 ++- man/spca.Rd | 4 +++- 7 files changed, 25 insertions(+), 12 deletions(-)
Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of Bayesian hierarchical models
for faecal egg count data to assess anthelmintic
efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [aut, cre] (<https://orcid.org/0000-0003-1804-2463>),
Michaela Paul [aut],
Tea Isler [ctb],
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>),
Trustees of Columbia University [cph]
Maintainer: Craig Wang <craig.wang@uzh.ch>
Diff between eggCounts versions 2.0 dated 2018-05-02 and 2.1 dated 2018-08-31
eggCounts-2.0/eggCounts/tests/testthat/Rplots.pdf |only eggCounts-2.1/eggCounts/DESCRIPTION | 24 eggCounts-2.1/eggCounts/MD5 | 53 eggCounts-2.1/eggCounts/R/fecr_stan.R | 2 eggCounts-2.1/eggCounts/R/fecr_stanExtra.R | 73 eggCounts-2.1/eggCounts/R/stan2mcmc.R | 2 eggCounts-2.1/eggCounts/build/vignette.rds |binary eggCounts-2.1/eggCounts/cleanup | 1 eggCounts-2.1/eggCounts/cleanup.win | 1 eggCounts-2.1/eggCounts/exec/indefficacy.stan | 6 eggCounts-2.1/eggCounts/exec/nb.stan | 4 eggCounts-2.1/eggCounts/exec/paired.stan | 6 eggCounts-2.1/eggCounts/exec/unpaired.stan | 6 eggCounts-2.1/eggCounts/exec/zipaired.stan | 8 eggCounts-2.1/eggCounts/exec/ziunpaired.stan | 10 eggCounts-2.1/eggCounts/inst/CITATION | 7 eggCounts-2.1/eggCounts/inst/NEWS | 11 eggCounts-2.1/eggCounts/man/eggCounts-package.Rd | 4 eggCounts-2.1/eggCounts/man/fecr_stan.Rd | 8 eggCounts-2.1/eggCounts/man/fecr_stanExtra.Rd | 54 eggCounts-2.1/eggCounts/man/plotCounts.Rd | 4 eggCounts-2.1/eggCounts/man/stan2mcmc.Rd | 2 eggCounts-2.1/eggCounts/src/Makevars | 2 eggCounts-2.1/eggCounts/src/Makevars.win | 2 eggCounts-2.1/eggCounts/src/include/models.hpp | 2391 +++++++++------------- eggCounts-2.1/eggCounts/src/init.cpp | 6 eggCounts-2.1/eggCounts/tests/testthat/test.R | 4 eggCounts-2.1/eggCounts/tools/make_cpp.R | 2 28 files changed, 1251 insertions(+), 1442 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Thomas Nagler [aut, cre],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthias Killiches [ctb],
Harry Joe [ctb],
Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 2.1.6 dated 2018-06-18 and 2.1.7 dated 2018-08-31
DESCRIPTION | 8 +++--- MD5 | 58 ++++++++++++++++++++++---------------------- NEWS.md | 15 +++++++++++ R/BiCopEst.R | 13 ++++++++- R/RVineMLE.R | 4 +-- R/RVineMatrix.R | 5 +++ build/partial.rdb |binary man/BiCopCDF.Rd | 3 +- man/BiCopEst.Rd | 4 +-- man/BiCopEstList.Rd | 3 +- man/BiCopHfunc.Rd | 11 ++++---- man/BiCopHfuncDeriv.Rd | 4 +-- man/BiCopHfuncDeriv2.Rd | 4 +-- man/BiCopHinv.Rd | 11 ++++---- man/BiCopKDE.Rd | 3 +- man/BiCopLambda.Rd | 4 +-- man/BiCopPDF.Rd | 3 +- man/BiCopPar2TailDep.Rd | 3 +- man/BiCopVuongClarke.Rd | 4 +-- man/RVineAIC.Rd | 1 man/RVineCor2pcor.Rd | 1 man/RVineLogLik.Rd | 5 ++- man/RVineMLE.Rd | 4 +-- man/RVineMatrix.Rd | 6 ++-- man/RVineSeqEst.Rd | 4 +-- man/RVineStructureSelect.Rd | 5 ++- man/pairs.copuladata.Rd | 5 ++- man/plot.BiCop.Rd | 1 man/plot.RVineMatrix.Rd | 10 +++---- src/hfunc.c | 17 +++++++++++- 30 files changed, 133 insertions(+), 86 deletions(-)
Title: Utilities for Delaying Function Execution
Description: Executes arbitrary R or C functions some time after the current
time, after the R execution stack has emptied.
Author: Joe Cheng [aut, cre],
RStudio [cph],
Marcus Geelnard [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/),
Evan Nemerson [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between later versions 0.7.3 dated 2018-06-08 and 0.7.4 dated 2018-08-31
later-0.7.3/later/src/Makevars |only later-0.7.3/later/src/tinycthread.c |only later-0.7.3/later/src/tinycthread.h |only later-0.7.4/later/DESCRIPTION | 6 later-0.7.4/later/MD5 | 25 - later-0.7.4/later/NEWS.md | 4 later-0.7.4/later/cleanup |only later-0.7.4/later/configure |only later-0.7.4/later/inst/doc/later-cpp.html | 535 +++++++++++++----------- later-0.7.4/later/src/Makevars.in |only later-0.7.4/later/src/Makevars.win | 5 later-0.7.4/later/src/c11threads.h |only later-0.7.4/later/src/debug.h | 2 later-0.7.4/later/src/threadutils.h | 16 later-0.7.4/later/src/timeconv.h | 2 later-0.7.4/later/src/tinycthread |only later-0.7.4/later/tests/testthat/test-run_now.R | 6 17 files changed, 343 insertions(+), 258 deletions(-)
Title: Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Description: Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation and various plotting functions are included.
Author: Christian Thiele [aut, cre]
Maintainer: Christian Thiele <c.thiele@gmx-topmail.de>
Diff between cutpointr versions 0.7.3 dated 2018-04-13 and 0.7.4 dated 2018-08-31
DESCRIPTION | 16 - MD5 | 133 ++++++------ NAMESPACE | 4 NEWS.md | 8 R/add_metric.R |only R/cutpointr.R | 1 R/metrics.R | 30 ++ R/plot_precision_recall.R | 3 R/plot_sensitivity_specificity.R | 3 R/print.cutpointr.R | 7 inst/doc/cutpointr.R | 24 +- inst/doc/cutpointr.Rmd | 41 ++- inst/doc/cutpointr.html | 399 ++++++++++++++++++------------------ man/F1_score.Rd | 10 man/abs_d_ppv_npv.Rd | 10 man/abs_d_sens_spec.Rd | 10 man/accuracy.Rd | 10 man/add_metric.Rd |only man/cohens_kappa.Rd | 10 man/cutpoint.Rd | 10 man/cutpointr.Rd | 6 man/cutpointr_.Rd | 5 man/false_omission_rate.Rd | 10 man/maximize_boot_metric.Rd | 15 - man/maximize_gam_metric.Rd | 17 - man/maximize_loess_metric.Rd | 1 man/maximize_metric.Rd | 1 man/maximize_spline_metric.Rd | 13 - man/misclassification_cost.Rd | 10 man/multi_cutpointr.Rd | 7 man/npv.Rd | 10 man/oc_manual.Rd | 1 man/oc_mean.Rd | 1 man/oc_median.Rd | 1 man/oc_youden_kernel.Rd | 1 man/oc_youden_normal.Rd | 1 man/odds_ratio.Rd | 9 man/p_chisquared.Rd | 9 man/plot.cutpointr.Rd | 1 man/plot_cut_boot.Rd | 1 man/plot_cutpointr.Rd | 5 man/plot_metric.Rd | 1 man/plot_metric_boot.Rd | 1 man/plot_precision_recall.Rd | 1 man/plot_roc.Rd | 1 man/plot_sensitivity_specificity.Rd | 1 man/plot_x.Rd | 1 man/plr.Rd | 9 man/ppv.Rd | 9 man/precision.Rd | 9 man/predict.cutpointr.Rd | 7 man/print.cutpointr.Rd | 5 man/prod_ppv_npv.Rd | 9 man/prod_sens_spec.Rd | 9 man/recall.Rd | 9 man/risk_ratio.Rd | 9 man/roc.Rd | 9 man/roc01.Rd |only man/sensitivity.Rd | 9 man/specificity.Rd | 9 man/sum_ppv_npv.Rd | 9 man/sum_sens_spec.Rd | 9 man/total_utility.Rd | 13 - man/tp.Rd | 10 man/tpr.Rd | 10 man/youden.Rd | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-cutpointr.R | 50 ++++ vignettes/cutpointr.Rmd | 41 ++- 69 files changed, 676 insertions(+), 438 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-11 dated 2018-04-05 and 1.7-13 dated 2018-08-31
ChangeLog | 90 ++++++++++++++++++++++++++++ DESCRIPTION | 10 +-- MD5 | 42 ++++++------- NAMESPACE | 1 R/dpcoa.R | 2 R/foucart.R | 2 R/inertia.dudi.R | 71 +++++++++++----------- R/orthobasis.R | 2 R/rlq.R | 2 R/varipart.R | 140 ++++++++++++++++++++++++++++++++++----------- inst/CITATION | 110 +++++++++++++++++++---------------- man/ade4.package.Rd | 11 ++- man/bacteria.Rd | 2 man/dist.ktab.Rd | 2 man/inertia.dudi.Rd | 6 + man/maples.Rd | 2 man/mbpcaiv.Rd | 7 +- man/mbpls.Rd | 5 + man/multiblock.Rd | 2 man/randboot.multiblock.Rd | 4 - man/testdim.multiblock.Rd | 7 +- man/varipart.Rd | 24 +++++-- 22 files changed, 375 insertions(+), 169 deletions(-)
Title: Nonparametric Maximum Likelihood Estimation for Random Effect
Models
Description: Nonparametric maximum likelihood estimation or Gaussian
quadrature for overdispersed generalized linear models and
variance component models.
Author: Jochen Einbeck, Ross Darnell and John Hinde
Maintainer: Jochen Einbeck <jochen.einbeck@durham.ac.uk>
Diff between npmlreg versions 0.46-3 dated 2018-04-30 and 0.46-5 dated 2018-08-31
DESCRIPTION | 8 MD5 | 16 R/alldist.R | 27 - R/allvc.R | 1128 ++++++++++++++++++++++++------------------------- build/vignette.rds |binary data/hosp.rda |binary data/irlsuicide.rda |binary data/missouri.rda |binary inst/doc/npmlreg-v.pdf |binary 9 files changed, 593 insertions(+), 586 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb],
Duncan Gormansway [ctb],
Carl Ganz [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.1.8 dated 2018-07-05 and 0.1.9 dated 2018-08-31
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 10 +++++++++- R/area_types.R | 9 +++++++-- R/deprivation_decile.R | 9 +++------ R/enhancements.R | 23 ++++++++++++----------- R/retrieve_data.R | 7 +++++-- build/vignette.rds |binary inst/doc/lifeExpectancy.html | 32 ++++++++++++++++---------------- inst/doc/selectIndicatorsRedRed.html | 2 +- man/deprivation_decile.Rd | 5 +---- tests/testthat/test-deprivation.R | 10 ++-------- tests/testthat/test-enhancements.R | 12 +++++++----- tests/testthat/test-extract.R | 10 +++++----- 14 files changed, 84 insertions(+), 77 deletions(-)
Title: Downscaling Species Occupancy
Description: Downscales species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) doi:10.18637/jss.v086.c03.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 2.0-3 dated 2017-08-25 and 3.0-1 dated 2018-08-31
DESCRIPTION | 15 +++++++-------- MD5 | 32 ++++++++++++++++---------------- NEWS | 10 ++++++++++ build/vignette.rds |binary inst/CITATION | 33 ++++++++++++++++++--------------- inst/doc/Downscaling.Rnw | 10 +++++++--- inst/doc/Downscaling.pdf |binary inst/doc/Upgraining.Rnw | 8 +++++++- inst/doc/Upgraining.pdf |binary man/Downscale-package.Rd | 4 ++++ man/downscale.Rd | 4 ++++ man/ensemble.downscale.Rd | 4 ++++ man/hui.downscale.Rd | 12 ++++-------- man/upgrain.Rd | 4 ++++ man/upgrain.threshold.Rd | 4 ++++ vignettes/Downscaling.Rnw | 10 +++++++--- vignettes/Upgraining.Rnw | 8 +++++++- 17 files changed, 103 insertions(+), 55 deletions(-)
Title: Data Used in the Vignettes Accompanying the CARBayes and
CARBayesST Packages
Description: Spatio-temporal data from Scotland used in the vignettes accompanying the CARBayes (spatial modelling) and CARBayesST (spatio-temporal modelling) packages. All data except for the Scottish lip cancer data relate to the set of 271 Intermediate Geographies (IG, but also known as Intermediate Zones (IZ)) that make up the 2001 definition of the Greater Glasgow and Clyde health board.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesdata versions 2.0 dated 2016-06-13 and 2.1 dated 2018-08-31
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- data/GGHB.IG.rda |binary data/lipdata.rda |binary data/lipdbf.rda |binary data/lipshp.rda |binary data/pollutionhealthdata.rda |binary data/pricedata.rda |binary data/respiratorydata.rda |binary data/salesdata.rda |binary man/CARBayesdata-package.Rd | 16 +++++++--------- man/GGHB.IG.Rd | 15 +++++++++------ man/lipdata.Rd | 16 +++++++--------- man/pollutionhealthdata.Rd | 15 +++++++-------- man/pricedata.Rd | 16 +++++++--------- man/respiratorydata.Rd | 12 ++++++------ man/salesdata.Rd | 4 ++-- 17 files changed, 66 insertions(+), 70 deletions(-)
Title: Bayesian Network Structure Learning from Data with Missing
Values
Description: Bayesian Network Structure Learning from Data with Missing Values.
The package implements the Silander-Myllymaki complete search,
the Max-Min Parents-and-Children, the Hill-Climbing, the
Max-Min Hill-climbing heuristic searches, and the Structural
Expectation-Maximization algorithm. Available scoring functions are
BDeu, AIC, BIC. The package also implements methods for generating and using
bootstrap samples, imputed data, inference.
Author: Francesco Sambo [aut],
Alberto Franzin [aut, cre]
Maintainer: Alberto Franzin <afranzin@ulb.ac.be>
Diff between bnstruct versions 1.0.2 dated 2016-12-13 and 1.0.4 dated 2018-08-31
bnstruct-1.0.2/bnstruct/R/init.R |only bnstruct-1.0.4/bnstruct/DESCRIPTION | 21 - bnstruct-1.0.4/bnstruct/MD5 | 76 ++- bnstruct-1.0.4/bnstruct/NAMESPACE | 7 bnstruct-1.0.4/bnstruct/NEWS |only bnstruct-1.0.4/bnstruct/R/AllGenerics.R | 268 ++++++++------ bnstruct-1.0.4/bnstruct/R/BN-methods.R | 196 ++++++++-- bnstruct-1.0.4/bnstruct/R/BNDataset-methods.R | 20 - bnstruct-1.0.4/bnstruct/R/InferenceEngine-methods.R | 19 bnstruct-1.0.4/bnstruct/R/bnstruct.R |only bnstruct-1.0.4/bnstruct/R/imputation.R | 4 bnstruct-1.0.4/bnstruct/R/learn-methods.R | 175 ++++++--- bnstruct-1.0.4/bnstruct/R/mmhc.R | 150 +++++-- bnstruct-1.0.4/bnstruct/R/sem.R | 16 bnstruct-1.0.4/bnstruct/R/sm.R | 50 +- bnstruct-1.0.4/bnstruct/R/util.R | 4 bnstruct-1.0.4/bnstruct/README.md | 12 bnstruct-1.0.4/bnstruct/build/vignette.rds |binary bnstruct-1.0.4/bnstruct/inst/CITATION |only bnstruct-1.0.4/bnstruct/inst/doc/bnstruct.R | 55 +- bnstruct-1.0.4/bnstruct/inst/doc/bnstruct.Rnw | 103 ++++- bnstruct-1.0.4/bnstruct/inst/doc/bnstruct.pdf |binary bnstruct-1.0.4/bnstruct/man/edge.dir.wpdag.Rd |only bnstruct-1.0.4/bnstruct/man/learn.dynamic.network.Rd | 29 + bnstruct-1.0.4/bnstruct/man/learn.network.Rd | 29 + bnstruct-1.0.4/bnstruct/man/learn.structure.Rd | 30 + bnstruct-1.0.4/bnstruct/man/plot.Rd | 15 bnstruct-1.0.4/bnstruct/man/print.Rd | 33 - bnstruct-1.0.4/bnstruct/man/save.to.eps.Rd | 6 bnstruct-1.0.4/bnstruct/src/bnstruct_init.c |only bnstruct-1.0.4/bnstruct/src/impfast.c | 2 bnstruct-1.0.4/bnstruct/src/impfast.h | 2 bnstruct-1.0.4/bnstruct/src/mmhcfast.c | 6 bnstruct-1.0.4/bnstruct/src/mmhcfast.h | 6 bnstruct-1.0.4/bnstruct/src/smfast.c | 10 bnstruct-1.0.4/bnstruct/src/smfast.h | 8 bnstruct-1.0.4/bnstruct/src/util.c | 17 bnstruct-1.0.4/bnstruct/src/util.h | 8 bnstruct-1.0.4/bnstruct/vignettes/alarm_crosses_1000.pdf |only bnstruct-1.0.4/bnstruct/vignettes/andes_crosses.pdf |only bnstruct-1.0.4/bnstruct/vignettes/bibtex.bib | 11 bnstruct-1.0.4/bnstruct/vignettes/bnstruct.Rnw | 103 ++++- bnstruct-1.0.4/bnstruct/vignettes/child_crosses_1000.pdf |only bnstruct-1.0.4/bnstruct/vignettes/hepar2_crosses_1000.pdf |only 44 files changed, 1039 insertions(+), 452 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.15 dated 2018-08-10 and 0.4.16 dated 2018-08-31
DESCRIPTION | 17 +- MD5 | 79 +++++---- NAMESPACE | 1 NEWS | 17 +- R/read-aster-file.r | 19 +- R/read-avaspec-csv.r | 25 ++- R/read-csi-dat.r | 13 + R/read-fmi-cum.R | 194 ++++++++++++++++++++--- R/read-fred-csv.r | 15 + R/read-libradtran.r | 30 ++- R/read-licor-prn.r | 17 +- R/read-macam-dta.r | 17 +- R/read-oojaz-file.r | 32 ++- R/read-oopi-file.r | 17 +- R/read-ooss-file.r | 26 ++- R/read-tuv-file.r | 61 +++++-- R/read-yoctopuce-csv.r | 10 - README.md | 132 ++++++++++++++-- inst/doc/user-guide.R | 14 + inst/doc/user-guide.Rmd | 54 +++++- inst/doc/user-guide.html | 332 ++++++++++++++++++++++------------------- inst/extdata/2013-05-01.hel |only inst/extdata/garbage.txt |only man/read_ASTER_txt.Rd | 8 man/read_FReD_csv.Rd | 8 man/read_avaspec_csv.Rd | 8 man/read_csi_dat.Rd | 3 man/read_fmi2mspct.Rd |only man/read_fmi_cum.Rd | 41 +++-- man/read_licor_prn.Rd | 8 man/read_macam_dta.Rd | 8 man/read_oo_jazirrad.Rd | 9 - man/read_oo_pidata.Rd | 8 man/read_oo_ssirrad.Rd | 8 man/read_tuv_usrout.Rd | 8 man/read_uvspec_disort.Rd | 8 man/read_uvspec_disort_vesa.Rd | 8 man/read_yoctopuce_csv.Rd | 3 tests/testthat/test-fmi.R | 87 +++++++++- tests/testthat/test-oo.R | 18 +- tests/testthat/test-tuv.R | 16 - vignettes/user-guide.Rmd | 54 +++++- 42 files changed, 1022 insertions(+), 411 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
An elegant function for downloading data from Human Mortality
Database <https://www.mortality.org> is provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
(<https://orcid.org/0000-0002-2568-6489>),
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 1.5.0 dated 2018-07-29 and 1.6.0 dated 2018-08-31
MortalityLaws-1.5.0/MortalityLaws/R/data_and_imports.R |only MortalityLaws-1.5.0/MortalityLaws/inst/doc/Manual.R |only MortalityLaws-1.5.0/MortalityLaws/inst/doc/Manual.Rmd |only MortalityLaws-1.5.0/MortalityLaws/inst/doc/Manual.pdf |only MortalityLaws-1.5.0/MortalityLaws/man/onAttach.Rd |only MortalityLaws-1.5.0/MortalityLaws/vignettes/Manual.Rmd |only MortalityLaws-1.6.0/MortalityLaws/DESCRIPTION | 21 MortalityLaws-1.6.0/MortalityLaws/MD5 | 88 ++- MortalityLaws-1.6.0/MortalityLaws/NAMESPACE | 18 MortalityLaws-1.6.0/MortalityLaws/NEWS | 13 MortalityLaws-1.6.0/MortalityLaws/R/LawTable.R | 78 ++- MortalityLaws-1.6.0/MortalityLaws/R/LifeTable.R | 244 +++++----- MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaw_S3.R | 31 - MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaw_check.R | 20 MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaw_main.R | 243 +++++---- MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaw_models.R | 4 MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaws-data.R |only MortalityLaws-1.6.0/MortalityLaws/R/MortalityLaws-package.R |only MortalityLaws-1.6.0/MortalityLaws/R/availableHMD.R | 2 MortalityLaws-1.6.0/MortalityLaws/R/availableLF.R | 9 MortalityLaws-1.6.0/MortalityLaws/R/availableLaws.R | 70 +- MortalityLaws-1.6.0/MortalityLaws/R/convertFx.R |only MortalityLaws-1.6.0/MortalityLaws/R/graphics.R | 26 - MortalityLaws-1.6.0/MortalityLaws/R/readHMD.R | 69 +- MortalityLaws-1.6.0/MortalityLaws/R/zzz.R |only MortalityLaws-1.6.0/MortalityLaws/build/vignette.rds |binary MortalityLaws-1.6.0/MortalityLaws/inst/doc/Installation.pdf |binary MortalityLaws-1.6.0/MortalityLaws/inst/doc/Intro.R |only MortalityLaws-1.6.0/MortalityLaws/inst/doc/Intro.Rmd |only MortalityLaws-1.6.0/MortalityLaws/inst/doc/Intro.pdf |only MortalityLaws-1.6.0/MortalityLaws/man/LawTable.Rd | 77 ++- MortalityLaws-1.6.0/MortalityLaws/man/LifeTable.Rd | 20 MortalityLaws-1.6.0/MortalityLaws/man/LifeTable.check.Rd | 2 MortalityLaws-1.6.0/MortalityLaws/man/MortalityLaw.Rd | 104 +--- MortalityLaws-1.6.0/MortalityLaws/man/MortalityLaws.Rd |only MortalityLaws-1.6.0/MortalityLaws/man/ReadHMD.Rd | 21 MortalityLaws-1.6.0/MortalityLaws/man/addDetails.Rd |only MortalityLaws-1.6.0/MortalityLaws/man/ahmd.Rd | 8 MortalityLaws-1.6.0/MortalityLaws/man/availableHMD.Rd | 3 MortalityLaws-1.6.0/MortalityLaws/man/availableLF.Rd | 14 MortalityLaws-1.6.0/MortalityLaws/man/availableLaws.Rd | 6 MortalityLaws-1.6.0/MortalityLaws/man/convertFx.Rd |only MortalityLaws-1.6.0/MortalityLaws/man/dx_lx.Rd |only MortalityLaws-1.6.0/MortalityLaws/man/find.my.case.Rd | 8 MortalityLaws-1.6.0/MortalityLaws/man/mx_qx.Rd | 8 MortalityLaws-1.6.0/MortalityLaws/man/plot.MortalityLaw.Rd | 3 MortalityLaws-1.6.0/MortalityLaws/man/predict.MortalityLaw.Rd | 5 MortalityLaws-1.6.0/MortalityLaws/man/uxAbove100.Rd |only MortalityLaws-1.6.0/MortalityLaws/tests/testthat.R | 2 MortalityLaws-1.6.0/MortalityLaws/tests/testthat/test_LawTable.R |only MortalityLaws-1.6.0/MortalityLaws/tests/testthat/test_LifeTable.R | 76 +-- MortalityLaws-1.6.0/MortalityLaws/tests/testthat/test_MortalityLaws.R | 41 + MortalityLaws-1.6.0/MortalityLaws/tests/testthat/test_MortalityLaws2.R |only MortalityLaws-1.6.0/MortalityLaws/tests/testthat/test_convertFx.R |only MortalityLaws-1.6.0/MortalityLaws/vignettes/Intro.Rmd |only MortalityLaws-1.6.0/MortalityLaws/vignettes/Mlaw_Refrences.bib | 11 56 files changed, 776 insertions(+), 569 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Finn Lindgren [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.4.1 dated 2018-07-19 and 2.4.4 dated 2018-08-31
DESCRIPTION | 10 MD5 | 57 ++-- NEWS.md | 15 + R/contourmap.R | 4 R/contourmap.inla.R | 2 R/excursions.R | 2 R/excursions.inla.R | 2 R/gaussint.R | 2 R/geometry.R | 484 ++++++++------------------------------- R/geometry_obsolete.R |only R/interface.mc.R | 4 R/simconf.R | 4 R/simconf.inla.R | 4 R/simconf.mixture.R | 4 inst/CITATION | 41 ++- man/continuous.Rd | 4 man/contourmap.Rd | 4 man/contourmap.inla.Rd | 2 man/contourmap.mc.Rd | 2 man/excursions.Rd | 2 man/excursions.inla.Rd | 2 man/excursions.mc.Rd | 2 man/gaussint.Rd | 2 man/simconf.Rd | 4 man/simconf.inla.Rd | 4 man/simconf.mixture.Rd | 4 man/submesh.mesh.Rd | 2 src/Makevars | 4 src/Makevars.orig |only src/RngStream.c | 20 + tests/testthat/test.continuous.R |only 31 files changed, 248 insertions(+), 445 deletions(-)
Title: Interface to the 'ASSP' Library
Description: A wrapper around Michel Scheffers's 'libassp' (<http://libassp.sourceforge.net/>).
The 'libassp' (Advanced Speech Signal Processor) library aims at providing
functionality for handling speech signal files in most common audio formats
and for performing analyses common in phonetic science/speech science. This
includes the calculation of formants, fundamental frequency, root mean
square, auto correlation, a variety of spectral analyses, zero crossing
rate, filtering etc. This wrapper provides R with a large subset of
'libassp's signal processing functions and provides them to the user in a
(hopefully) user-friendly manner.
Author: Raphael Winkelmann [aut, cre],
Lasse Bombien [aut],
Michel Scheffers [aut]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between wrassp versions 0.1.7 dated 2018-05-07 and 0.1.8 dated 2018-08-31
DESCRIPTION | 8 +++--- MD5 | 46 ++++++++++++++++++++-------------------- NEWS.md | 9 +++++++ build/vignette.rds |binary inst/doc/wrassp_intro.Rmd | 7 ++++++ inst/doc/wrassp_intro.html | 12 ++++++---- man/acfana.Rd | 11 +++++---- man/addTrack.Rd | 3 +- man/afdiff.Rd | 3 +- man/affilter.Rd | 3 +- man/dftSpectrum.Rd | 4 +-- man/forest.Rd | 11 +++++---- man/ksvF0.Rd | 7 +++--- man/mhsF0.Rd | 4 +-- man/rfcana.Rd | 6 ++--- man/rmsana.Rd | 9 ++++--- man/zcrana.Rd | 7 +++--- src/assp/asspfio.c | 3 +- src/assp/filter.c | 3 +- src/assp/headers.c | 46 ++++++++++++++++++++-------------------- src/performAssp.c | 16 ++++++------- src/types.c | 4 +-- tests/testthat/test_dataTypes.R | 12 ++++++---- vignettes/wrassp_intro.Rmd | 7 ++++++ 24 files changed, 141 insertions(+), 100 deletions(-)
Title: Genetic Algorithm for Sequential Symmetric Games
Description: Finds adaptive strategies for sequential symmetric
games using a genetic algorithm. Currently, any symmetric two by two matrix
is allowed, and strategies can remember the history of an opponent's play
from the previous three rounds of moves in iterated interactions between
players. The genetic algorithm returns a list of adaptive strategies given
payoffs, and the mean fitness of strategies in each generation.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between gamesGA versions 1.1.3.2 dated 2017-06-13 and 1.1.3.5 dated 2018-08-31
DESCRIPTION | 16 +++++++++------- MD5 | 6 +++--- R/games_ga_gui.R | 2 +- man/games_ga_gui.Rd | 2 +- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Earthquake Traveltime Calculations for 1-D Earth Models
Description: Evaluates traveltimes and ray paths using predefined Earth
(or other planet) models. Includes phase plotting routines.
The IASP91 (Kennett and Engdahl, 1991 <doi:10.1111/j.1365-246X.1991.tb06724.x>)
and AK135 (Kennett et al., 1995 <doi:10.1111/j.1365-246X.1995.tb03540.x>)
Earth models are included, and most important arrival phases can be
evaluated.
Author: Jake Anderson, Jonathan Lees; largely translated from the TTBOX
Matlab toolbox by Martin Knapmeyer
(http://www.dr-knapmeyer.de/downloads/)
Maintainer: Jake Anderson <ajakef@gmail.com>
Diff between TauP.R versions 1.1 dated 2012-08-13 and 1.5 dated 2018-08-31
DESCRIPTION | 15 ++-- MD5 | 21 +++--- NAMESPACE | 4 + R/DistSummary.R | 2 R/FindRoots.R | 152 +++++++++++++++++++------------------------------- build |only man/DistSummary.Rd | 8 +- man/Rayfan.Rd | 7 +- man/TauP.R-package.Rd | 53 +++++++++-------- man/ak135.Rd | 2 man/iasp91.Rd | 4 - man/model.Rd | 3 12 files changed, 127 insertions(+), 144 deletions(-)
Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data,
including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre],
Ian C. Marschner [ths],
Alexandra C. Gillett [ctb] (wrote an initial version of the nplbin
function)
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>
Diff between logbin versions 2.0.3 dated 2017-05-04 and 2.0.4 dated 2018-08-31
DESCRIPTION | 7 ++--- MD5 | 18 ++++++------- NEWS.md | 4 +++ R/logbin.r | 2 - README.md | 65 ++++++++++++++++++++++++++++++++------------------ inst/CITATION | 24 ++++++++++++++++-- man/B.Iso.Rd | 2 - man/logbin-package.Rd | 7 +++-- man/logbin.Rd | 4 +++ man/logbin.smooth.Rd | 4 +++ 10 files changed, 94 insertions(+), 43 deletions(-)
Title: Likelihood Methods for Mediation Analysis
Description: Implements likelihood based methods for mediation analysis.
Author: Dr. Kai Wang
Maintainer: Kai Wang <kai-wang@uiowa.edu>
Diff between iMediate versions 0.4 dated 2017-09-03 and 0.5 dated 2018-08-31
DESCRIPTION | 14 ++++++----- MD5 | 32 ++++++++++++------------- NAMESPACE | 1 R/delta.lnl.R | 6 +++- R/figure.joint.prob.R | 8 +++--- R/figure.relative.power.R | 8 +++--- R/fimle.lnl.R | 45 ++++++++++++++++++----------------- R/iMediate-package.R | 9 +++---- R/mdn.R | 54 ++++++++++++++++++------------------------- R/print.mdn.R | 26 +++++++------------- R/pwr_mdn.R | 3 +- man/figure.joint.prob.Rd | 8 +++--- man/figure.relative.power.Rd | 8 +++--- man/fimle.lnl.Rd | 5 ++- man/iMediate-package.Rd | 10 +++---- man/mdn.Rd | 5 +-- man/pwr.mdn.Rd | 3 +- 17 files changed, 116 insertions(+), 129 deletions(-)
Title: Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
Description: Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Author: Etienne Becht [cre, aut],
Samuel Granjeaud [ctb]
Maintainer: Etienne Becht <etienne_becht@protonmail.com>
Diff between hypergate versions 0.7 dated 2018-05-14 and 0.8 dated 2018-08-31
DESCRIPTION | 20 - MD5 | 38 ++- NAMESPACE | 4 R/hypergate.R | 438 ++++++++++++++++++++++++++++++--------- README.md |only inst/doc/Hypergate.R | 26 ++ inst/doc/Hypergate.Rmd | 44 +++ inst/doc/Hypergate.html | 97 ++++++++ man/FNTN_matrix.recycle.Rd | 4 man/color_biplot_by_discrete.Rd | 4 man/contract.Rd | 8 man/contract.update.Rd | 3 man/expand.update.Rd | 5 man/hgate_info.Rd |only man/hgate_pheno.Rd |only man/hgate_rule.Rd |only man/hgate_sample.Rd |only man/reoptimize_strategy.Rd | 4 vignettes/Hypergate.Rmd | 44 +++ vignettes/unnamed-chunk-10-1.png |only vignettes/unnamed-chunk-17-1.png |only vignettes/unnamed-chunk-17-2.png |only vignettes/unnamed-chunk-18-1.png |only vignettes/unnamed-chunk-19-1.png |only vignettes/unnamed-chunk-21-1.png |only vignettes/unnamed-chunk-7-1.png |only 26 files changed, 594 insertions(+), 145 deletions(-)
Title: A User-Oriented Statistical Toolkit for Analytical Variance
Estimation
Description: Provides a toolkit for analytical variance estimation in survey sampling. Apart from the implementation of standard variance estimators, its main feature is to help the sampling expert produce easy-to-use variance estimation "wrappers", where systematic operations (linearization, domain estimation) are handled in a consistent and transparent way.
Author: Martin Chevalier [aut, cre, cph]
Maintainer: Martin Chevalier <martin.chevalier@insee.fr>
Diff between gustave versions 0.3.0 dated 2018-06-06 and 0.4.0 dated 2018-08-31
gustave-0.3.0/gustave/R/define_linearization_wrapper.R |only gustave-0.3.0/gustave/R/linearization_wrapper_standard.R |only gustave-0.3.0/gustave/man/add0.Rd |only gustave-0.3.0/gustave/man/define_linearization_wrapper.Rd |only gustave-0.3.0/gustave/man/linearization_wrapper_standard.Rd |only gustave-0.3.0/gustave/man/rescal.Rd |only gustave-0.3.0/gustave/man/sumby.Rd |only gustave-0.3.0/gustave/tests/testthat/test_linearization_wrapper_standard.R |only gustave-0.4.0/gustave/DESCRIPTION | 25 gustave-0.4.0/gustave/MD5 | 72 gustave-0.4.0/gustave/NAMESPACE | 25 gustave-0.4.0/gustave/NEWS.md | 110 - gustave-0.4.0/gustave/R/data.R | 205 +- gustave-0.4.0/gustave/R/define_statistic_wrapper.R |only gustave-0.4.0/gustave/R/define_variance_wrapper.R | 720 ++++--- gustave-0.4.0/gustave/R/qvar.R |only gustave-0.4.0/gustave/R/standard_statistic_wrapper.R |only gustave-0.4.0/gustave/R/utils.R | 599 +++--- gustave-0.4.0/gustave/R/variance_function.R | 955 ++++------ gustave-0.4.0/gustave/README.md | 280 +- gustave-0.4.0/gustave/data/ict_pop.RData |binary gustave-0.4.0/gustave/data/ict_sample.RData |binary gustave-0.4.0/gustave/data/ict_survey.RData |binary gustave-0.4.0/gustave/data/lfs_samp_area.RData |only gustave-0.4.0/gustave/data/lfs_samp_dwel.RData |only gustave-0.4.0/gustave/data/lfs_samp_ind.RData |only gustave-0.4.0/gustave/man/add_zero.Rd |only gustave-0.4.0/gustave/man/define_statistic_wrapper.Rd |only gustave-0.4.0/gustave/man/define_variance_wrapper.Rd | 402 ++-- gustave-0.4.0/gustave/man/ict_pop.Rd | 55 gustave-0.4.0/gustave/man/ict_sample.Rd | 69 gustave-0.4.0/gustave/man/ict_survey.Rd | 63 gustave-0.4.0/gustave/man/lfs_samp_area.Rd |only gustave-0.4.0/gustave/man/lfs_samp_dwel.Rd |only gustave-0.4.0/gustave/man/lfs_samp_ind.Rd |only gustave-0.4.0/gustave/man/qvar.Rd |only gustave-0.4.0/gustave/man/res_cal.Rd |only gustave-0.4.0/gustave/man/standard_statistic_wrapper.Rd |only gustave-0.4.0/gustave/man/sum_by.Rd |only gustave-0.4.0/gustave/man/varDT.Rd | 381 +-- gustave-0.4.0/gustave/man/varSYG.Rd | 135 - gustave-0.4.0/gustave/man/var_pois.Rd | 72 gustave-0.4.0/gustave/tests/testthat.R | 8 gustave-0.4.0/gustave/tests/testthat/test_data.R | 30 gustave-0.4.0/gustave/tests/testthat/test_define_statistic_wrapper.R |only gustave-0.4.0/gustave/tests/testthat/test_define_variance_wrapper.R | 369 ++- gustave-0.4.0/gustave/tests/testthat/test_qvar.R |only gustave-0.4.0/gustave/tests/testthat/test_standard_statistic_wrapper.R |only gustave-0.4.0/gustave/tests/testthat/test_utils.R | 286 +- gustave-0.4.0/gustave/tests/testthat/test_variance_function.R | 118 + 50 files changed, 2845 insertions(+), 2134 deletions(-)
Title: Statistics and Data Sets for Corpus Frequency Data
Description: Utility functions for the statistical analysis of corpus frequency data.
This package is a companion to the open-source course "Statistical Inference:
A Gentle Introduction for Computational Linguists and Similar Creatures" ('SIGIL').
Author: Stefan Evert [http://www.stefan-evert.de/]
Maintainer: Stefan Evert <stefan.evert@fau.de>
Diff between corpora versions 0.4-3 dated 2012-04-04 and 0.5 dated 2018-08-31
corpora-0.4-3/corpora/CHANGES |only corpora-0.4-3/corpora/data/BNCInChargeOf.tab.bz2 |only corpora-0.4-3/corpora/data/BNCcomparison.tab.gz |only corpora-0.4-3/corpora/data/BNCdomains.tab.gz |only corpora-0.4-3/corpora/data/VSS.tab.bz2 |only corpora-0.5/corpora/DESCRIPTION | 24 +++--- corpora-0.5/corpora/MD5 | 76 +++++++++++++------ corpora-0.5/corpora/NAMESPACE | 11 ++ corpora-0.5/corpora/NEWS |only corpora-0.5/corpora/R/corpora_palette.R |only corpora-0.5/corpora/R/fisher_pval.R | 20 +++-- corpora-0.5/corpora/R/prop_cint.R | 21 ++++- corpora-0.5/corpora/R/qw.R |only corpora-0.5/corpora/R/rowColVector.R |only corpora-0.5/corpora/R/simulated_language_course.R |only corpora-0.5/corpora/R/stars_pval.R |only corpora-0.5/corpora/data/BNCInChargeOf.rda |only corpora-0.5/corpora/data/BNCbiber.rda |binary corpora-0.5/corpora/data/BNCcomparison.rda |only corpora-0.5/corpora/data/BNCdomains.rda |only corpora-0.5/corpora/data/BNCmeta.rda |binary corpora-0.5/corpora/data/BNCqueries.rda |only corpora-0.5/corpora/data/BrownBigrams.rda |only corpora-0.5/corpora/data/BrownLOBPassives.rda |only corpora-0.5/corpora/data/BrownPassives.rda |only corpora-0.5/corpora/data/BrownStats.rda |only corpora-0.5/corpora/data/DistFeatBrownFam.rda |only corpora-0.5/corpora/data/KrennPPV.rda |only corpora-0.5/corpora/data/LOBPassives.rda |only corpora-0.5/corpora/data/LOBStats.rda |only corpora-0.5/corpora/data/PassiveBrownFam.rda |only corpora-0.5/corpora/data/VSS.rda |only corpora-0.5/corpora/data/datalist | 10 ++ corpora-0.5/corpora/man/BNCInChargeOf.Rd | 8 +- corpora-0.5/corpora/man/BNCbiber.Rd | 22 +++-- corpora-0.5/corpora/man/BNCcomparison.Rd | 10 +- corpora-0.5/corpora/man/BNCdomains.Rd | 8 +- corpora-0.5/corpora/man/BNCmeta.Rd | 8 +- corpora-0.5/corpora/man/BNCqueries.Rd |only corpora-0.5/corpora/man/BrownBigrams.Rd |only corpora-0.5/corpora/man/BrownLOBPassives.Rd |only corpora-0.5/corpora/man/BrownPassives.Rd |only corpora-0.5/corpora/man/BrownStats.Rd |only corpora-0.5/corpora/man/DistFeatBrownFam.Rd |only corpora-0.5/corpora/man/KrennPPV.Rd |only corpora-0.5/corpora/man/LOBPassives.Rd |only corpora-0.5/corpora/man/LOBStats.Rd |only corpora-0.5/corpora/man/PassiveBrownFam.Rd |only corpora-0.5/corpora/man/VSS.Rd | 29 +++---- corpora-0.5/corpora/man/corpora_package.Rd | 25 +++--- corpora-0.5/corpora/man/corpora_palette.Rd |only corpora-0.5/corpora/man/fisher_pval.Rd | 28 ++++++- corpora-0.5/corpora/man/prop_cint.Rd | 20 +++-- corpora-0.5/corpora/man/qw.Rd |only corpora-0.5/corpora/man/rowColVector.Rd |only corpora-0.5/corpora/man/simulated_census.Rd | 6 - corpora-0.5/corpora/man/simulated_language_course.Rd |only corpora-0.5/corpora/man/simulated_wikipedia.Rd | 4 - corpora-0.5/corpora/man/stars_pval.Rd |only 59 files changed, 219 insertions(+), 111 deletions(-)
Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, and morphing.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.2.1 dated 2018-08-04 and 1.3.0 dated 2018-08-31
DESCRIPTION | 6 MD5 | 105 ++--- NAMESPACE | 1 NEWS | 18 R/analyze.R | 23 - R/matchPars.R | 66 +-- R/morph.R | 76 ++-- R/presets.R | 88 ++-- R/rolloff.R | 73 ++-- R/smoothContours.R | 3 R/soundgen.R | 386 +++++++++++++-------- R/soundgenShiny.R | 2 R/source.R | 169 +++++++-- R/spectrogram.R | 67 +++ R/subharmonics.R | 4 R/utilities_analyze.R | 4 R/utilities_math.R | 29 + R/utilities_soundgen.R | 156 +++++++- data/defaults.rda |binary data/permittedValues.rda |binary data/presets.rda |binary inst/doc/acoustic_analysis.R | 34 + inst/doc/acoustic_analysis.Rmd | 36 + inst/doc/acoustic_analysis.html | 108 +++-- inst/doc/sound_generation.R | 318 +++++++++-------- inst/doc/sound_generation.Rmd | 447 +++++++++++++----------- inst/doc/sound_generation.html | 691 +++++++++++++------------------------- inst/shiny/soundgen_main/server.R | 114 ++++-- inst/shiny/soundgen_main/ui.R | 8 man/addFormants.Rd | 23 - man/analyze.Rd | 12 man/beat.Rd | 26 - man/compareSounds.Rd | 20 - man/crossFade.Rd | 4 man/defaults.Rd | 2 man/fart.Rd | 36 + man/flatEnv.Rd | 8 man/generateHarmonics.Rd | 87 ++-- man/generateNoise.Rd | 26 - man/getMelSpec.Rd | 6 man/getRolloff.Rd | 47 +- man/getSpectralEnvelope.Rd | 18 man/getVocalFry.Rd | 14 man/matchPars.Rd | 12 man/morph.Rd | 23 + man/osc_dB.Rd |only man/soundgen.Rd | 221 ++++++------ man/spectrogram.Rd | 28 + man/spectrogramFolder.Rd | 14 man/wiggleAnchors.Rd | 13 man/wiggleGC.Rd | 2 man/wigglePars.Rd | 4 vignettes/acoustic_analysis.Rmd | 36 + vignettes/sound_generation.Rmd | 447 +++++++++++++----------- 54 files changed, 2340 insertions(+), 1821 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-17 0.2.4
2018-08-16 0.2.3
2017-08-13 0.1.5
2017-05-05 0.1.4
2017-03-16 0.1.2
Title: Stock Market Analysis
Description: Functions for analyzing stocks or other investments. Main features are loading and aligning historical data for ticker symbols, calculating performance metrics for individual funds or portfolios (e.g. annualized growth, maximum drawdown, Sharpe/Sortino ratio), and creating graphs. C++ code is used to improve processing speed where possible.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between stocks versions 1.1.3 dated 2018-05-08 and 1.1.4 dated 2018-08-31
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/stocks.R | 7 +++---- man/stocks.Rd | 4 ++-- 5 files changed, 15 insertions(+), 15 deletions(-)