Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the packages uses NRFA peak flow dataset version 9. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the ‘extreme rank plot’ for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>.
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.1.0 dated 2020-11-23 and 0.1.1 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/All.R | 26 +++++++++++++------------- man/AMextract.Rd | 2 +- man/DesHydro.Rd | 2 +- man/EncProb.Rd | 4 ++-- man/HydroPlot.Rd | 2 +- man/ImportCDs.Rd | 6 +++--- man/POTextract.Rd | 2 +- man/TrendTest.Rd | 2 +- man/Uncertainty.Rd | 2 +- 11 files changed, 37 insertions(+), 37 deletions(-)
Title: Scatterplots with More Points
Description: C-based conversion of large scatterplot data to rasters. Speeds up
plotting of data with millions of points.
Author: Mirek Kratochvil [aut, cre] (<https://orcid.org/0000-0001-7356-4075>)
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between scattermore versions 0.6 dated 2020-03-06 and 0.7 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 15 +++++++++++++++ R/scattermore.R | 39 ++++++++++++++++++++++++++++++--------- man/geom_scattermore.Rd | 19 ++++++++++++++----- man/geom_scattermost.Rd | 11 ++++++++--- man/scattermore.Rd | 12 +++++++++--- man/scattermoreplot.Rd | 19 ++++++++++++++++--- src/scattermore.c | 8 ++++---- 9 files changed, 109 insertions(+), 40 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity statistics, beta diversity statistics, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis.
Author: Chi Liu [aut, cre],
Minjie Yao [aut],
Xiangzhen Li [aut],
Paul J. McMurdie [ctb],
Yang Cao [ctb],
James Robert White [ctb],
Stilianos Louca [cph],
Nhu H. Nguyen [cph]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.3.0 dated 2020-11-15 and 0.3.1 dated 2020-11-24
DESCRIPTION | 14 +++--- MD5 | 46 +++++++++++----------- R/microtable.R | 21 +++------- R/trans_abund.R | 23 +++++++---- R/trans_alpha.R | 9 +++- R/trans_beta.R | 4 + R/trans_diff.R | 4 - R/trans_func.R | 8 --- R/trans_network.R | 41 -------------------- R/trans_nullmodel.R | 4 + R/trans_venn.R | 4 + data/fungi_func.RData |binary data/otu_table_16S.RData |binary data/taxonomy_table_16S.RData |binary inst/CITATION | 2 man/microtable.Rd | 80 +++++++++------------------------------ man/trans_abund.Rd | 44 +++++++++++++++------ man/trans_alpha.Rd | 22 +++++++--- man/trans_beta.Rd | 12 ++++- man/trans_diff.Rd | 8 +-- man/trans_func.Rd | 36 ----------------- man/trans_network.Rd | 86 ------------------------------------------ man/trans_nullmodel.Rd | 12 ++++- man/trans_venn.Rd | 12 ++++- 24 files changed, 177 insertions(+), 315 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.4-4 dated 2020-09-04 and 1.4-6 dated 2020-11-24
maxLik-1.4-4/maxLik/R/head....R |only maxLik-1.4-6/maxLik/DESCRIPTION | 8 maxLik-1.4-6/maxLik/MD5 | 53 ++--- maxLik-1.4-6/maxLik/NEWS | 13 + maxLik-1.4-6/maxLik/R/10-MaxControl_class.R | 16 - maxLik-1.4-6/maxLik/R/compareDerivatives.R | 12 - maxLik-1.4-6/maxLik/R/headDots.R |only maxLik-1.4-6/maxLik/R/maxBFGSRCompute.R | 2 maxLik-1.4-6/maxLik/R/maxNRCompute.R | 30 -- maxLik-1.4-6/maxLik/R/maxSGACompute.R | 4 maxLik-1.4-6/maxLik/R/maximMessage.R | 10 maxLik-1.4-6/maxLik/R/returnCode.R | 7 maxLik-1.4-6/maxLik/build/vignette.rds |binary maxLik-1.4-6/maxLik/inst/doc/stochastic-gradient-maxLik.Rnw | 2 maxLik-1.4-6/maxLik/inst/doc/stochastic-gradient-maxLik.pdf |binary maxLik-1.4-6/maxLik/man/activePar.Rd | 24 +- maxLik-1.4-6/maxLik/man/compareDerivatives.Rd | 18 + maxLik-1.4-6/maxLik/man/maxLik-methods.Rd | 13 - maxLik-1.4-6/maxLik/man/maxLik-package.Rd | 77 +++---- maxLik-1.4-6/maxLik/man/maxLik.Rd | 65 ++++-- maxLik-1.4-6/maxLik/man/maxNR.Rd | 47 ++-- maxLik-1.4-6/maxLik/man/returnCode.Rd | 2 maxLik-1.4-6/maxLik/tests/finalHessian.Rout.save | 32 +-- maxLik-1.4-6/maxLik/tests/fitNormalDist_privateTest.Rout.save | 105 +++++----- maxLik-1.4-6/maxLik/tests/maxControl_privateTest.Rout.save | 6 maxLik-1.4-6/maxLik/tests/maxSG_privateTest.Rout.save | 6 maxLik-1.4-6/maxLik/tests/parameters_privateTest.Rout.save | 75 +------ maxLik-1.4-6/maxLik/vignettes/auto |only maxLik-1.4-6/maxLik/vignettes/stochastic-gradient-maxLik.Rnw | 2 29 files changed, 318 insertions(+), 311 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
Aimee Teo Broman [ctb] (<https://orcid.org/0000-0003-3783-2807>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.70-4 dated 2020-05-22 and 0.71-6 dated 2020-11-24
DESCRIPTION | 10 ++++----- MD5 | 52 +++++++++++++++++++++++++-------------------------- NAMESPACE | 1 NEWS | 26 ++++++++++++++++++++++++- R/brocolors.R | 2 - R/ciplot.R | 8 ++++--- R/dotplot.R | 46 +++++++++++++++++++++++++++------------------ R/excel_fig.R | 2 - R/grayplot.R | 15 +++++--------- R/grayplot_na.R | 4 +-- R/holmans_triangle.R | 4 +-- R/jiggle.R | 13 ++++++++++-- R/mypairs.R | 2 - man/dotplot.Rd | 6 +++-- man/grayplot.Rd | 4 +-- man/grayplot_na.Rd | 2 - man/jiggle.Rd | 12 ++++++++++- man/mypairs.Rd | 2 - man/myround.Rd | 2 - man/objectsizes.Rd | 2 - man/paste..Rd | 2 - man/paste00.Rd | 2 - man/qqline2.Rd | 6 ++--- man/revrainbow.Rd | 6 ++--- man/rmvn.Rd | 2 - man/triplot.Rd | 2 - man/twocolorpal.Rd | 2 - 27 files changed, 145 insertions(+), 92 deletions(-)
Title: Taxonomic Uncertainty on Multivariate Analyses of Ecological
Data
Description: Permutational method to incorporate taxonomic uncertainty and some functions to assess its effects on parameters of some widely used multivariate methods in ecology, as explained in Cayuela et al. (2011) <doi:10.1111/j.1600-0587.2009.05899.x>.
Author: Luis Cayuela and Marcelino de la Cruz
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between betaper versions 1.1-1 dated 2020-03-02 and 1.1-2 dated 2020-11-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/pertables.p2.R | 3 ++- man/adonis_pertables.Rd | 5 ++--- man/cca_pertables.Rd | 5 ++--- man/mantel_pertables.Rd | 5 ++--- man/pertables.Rd | 8 +++++--- man/rda_pertables.Rd | 5 ++--- 9 files changed, 28 insertions(+), 29 deletions(-)
Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs
from text using a variety of sentiment dictionaries conveniently
packaged for consumption by R users. Implemented dictionaries include
"syuzhet" (default) developed in the Nebraska Literary Lab
"afinn" developed by Finn Årup Nielsen, "bing" developed by Minqing Hu
and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D.
Applicable references are available in README.md and in the documentation
for the "get_sentiment" function. The package also provides a hack for
implementing Stanford's coreNLP sentiment parser. The package provides
several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>
Diff between syuzhet versions 1.0.4 dated 2017-12-14 and 1.0.6 dated 2020-11-24
DESCRIPTION | 21 MD5 | 37 - NAMESPACE | 2 R/sysdata.rda |binary R/syuzhet.R | 119 ++++- README.md | 2 build/vignette.rds |binary inst/doc/syuzhet-vignette.R | 102 ++-- inst/doc/syuzhet-vignette.Rmd | 65 ++- inst/doc/syuzhet-vignette.html | 854 ++++++++++++++++++++++++++-------------- inst/extdata/quijote.txt | 573 -------------------------- man/get_dct_transform.Rd | 9 man/get_nrc_sentiment.Rd | 4 man/get_sentiment.Rd | 18 man/get_sentiment_dictionary.Rd | 6 man/get_tokens.Rd | 4 man/get_transformed_values.Rd | 10 man/mixed_messages.Rd |only man/simple_plot.Rd | 9 vignettes/syuzhet-vignette.Rmd | 65 ++- 20 files changed, 907 insertions(+), 993 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) 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> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05> and the package vignette.
Author: Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>),
Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 3.0.2 dated 2020-11-17 and 3.0.3 dated 2020-11-24
DESCRIPTION | 9 ++++----- MD5 | 34 +++++++++++++++++----------------- NEWS | 3 +++ R/util.R | 8 ++++---- R/wrappers.R | 8 ++++---- inst/doc/article2.R | 12 +++--------- inst/doc/article2.Rnw | 35 +++++++++++++++-------------------- inst/doc/article2.pdf |binary inst/examples/svsample.R | 4 ++-- inst/include/stochvol.h | 2 +- man/svsample.Rd | 4 ++-- src/sampling_latent_states.cc | 6 +++--- src/sampling_main.cc | 16 ++++++++-------- src/utils_main.h | 3 +++ tests/testthat/test-samplers.R | 9 +++------ tests/testthat/test-wrappers.R | 4 ++++ vignettes/article2.Rnw | 35 +++++++++++++++-------------------- vignettes/ref.bib | 9 ++++++++- 18 files changed, 99 insertions(+), 102 deletions(-)
More information about SpatialRegimes at CRAN
Permanent link
Title: Robust Bootstrap Forecast Densities for GARCH Models
Description: Bootstrap forecast densities for GARCH (Generalized Autoregressive Conditional Heteroskedastic) returns and volatilities using the robust residual-based bootstrap procedure of Trucios, Hotta and Ruiz (2017) <DOI:10.1080/00949655.2017.1359601>.
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Diff between RobGARCHBoot versions 1.0.1 dated 2020-05-13 and 1.1.0 dated 2020-11-24
DESCRIPTION | 14 +++++++------- MD5 | 25 ++++++++++++++----------- NAMESPACE | 8 ++++++++ R/ROBUSTGARCH.R | 6 ++---- R/RcppExports.R | 1 + R/RobGARCHBoot.R | 17 +++++++++++++---- R/RobGARCHBootParallel.R |only R/bootstrap_replication.R |only README.md | 9 +++++++-- man/ROBUSTGARCH.Rd | 3 +-- man/RobGARCHBoot-package.Rd | 11 ++++++----- man/RobGARCHBoot.Rd | 9 ++++++--- man/RobGARCHBootParallel.Rd |only man/fitted_Vol.Rd | 2 +- src/ROBUSTGARCH.cpp | 2 +- 15 files changed, 67 insertions(+), 40 deletions(-)
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between jti versions 0.5.1 dated 2020-11-19 and 0.5.2 dated 2020-11-24
DESCRIPTION | 8 ++-- MD5 | 12 +++---- NEWS.md | 4 ++ R/api_compile.R | 2 - R/helper_charge.R | 2 - R/helper_jt.R | 91 +++++++++++++++++++++++++----------------------------- R/sandbox.R | 59 ++++++++++++++++++++++++----------- 7 files changed, 100 insertions(+), 78 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.4.1 dated 2020-11-01 and 0.4.2 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 40 ++++----- NEWS.md | 4 R/jskm.R | 26 +++++- R/svyjskm.R | 20 ++++ README.md | 14 ++- build/vignette.rds |binary inst/doc/jskm.R | 10 +- inst/doc/jskm.Rmd | 12 +- inst/doc/jskm.html | 130 ++++++++++++------------------- man/figures/README-unnamed-chunk-1-2.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-4-3.png |binary man/figures/README-unnamed-chunk-5-3.png |binary man/jskm.Rd | 5 - man/svyjskm.Rd | 5 - tests/testthat/test-km.R | 10 +- vignettes/jskm.Rmd | 12 +- 21 files changed, 162 insertions(+), 134 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations.
It makes it possible to easily perform routine tasks when
exploring correlation matrices such as ignoring the diagonal,
focusing on the correlations of certain variables against others,
or rearranging and visualizing the matrix in terms of the
strength of the correlations.
Author: Max Kuhn [aut, cre],
Simon Jackson [aut],
Jorge Cimentada [aut]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between corrr versions 0.4.2 dated 2020-03-22 and 0.4.3 dated 2020-11-24
corrr-0.4.2/corrr/tests/testthat/stretch.txt |only corrr-0.4.2/corrr/tools |only corrr-0.4.3/corrr/DESCRIPTION | 19 - corrr-0.4.3/corrr/MD5 | 94 ++++---- corrr-0.4.3/corrr/NAMESPACE | 2 corrr-0.4.3/corrr/NEWS.md | 21 + corrr-0.4.3/corrr/R/colpair.R |only corrr-0.4.3/corrr/R/cor_df.R | 172 +++++++++------ corrr-0.4.3/corrr/R/correlate.R | 77 +++--- corrr-0.4.3/corrr/R/dataframe.R | 4 corrr-0.4.3/corrr/R/internal.R | 12 - corrr-0.4.3/corrr/R/matrix.R | 4 corrr-0.4.3/corrr/R/output.R | 74 +++--- corrr-0.4.3/corrr/R/reshape.R | 56 ++--- corrr-0.4.3/corrr/R/utility.R | 48 ++-- corrr-0.4.3/corrr/README.md | 73 +++--- corrr-0.4.3/corrr/build/vignette.rds |binary corrr-0.4.3/corrr/inst/doc/databases.Rmd | 2 corrr-0.4.3/corrr/inst/doc/databases.html | 96 +++++++- corrr-0.4.3/corrr/inst/doc/using-corrr.R | 8 corrr-0.4.3/corrr/inst/doc/using-corrr.Rmd | 12 - corrr-0.4.3/corrr/inst/doc/using-corrr.html | 188 +++++++++++------ corrr-0.4.3/corrr/man/as_cordf.Rd | 2 corrr-0.4.3/corrr/man/as_matrix.Rd | 2 corrr-0.4.3/corrr/man/colpair_map.Rd |only corrr-0.4.3/corrr/man/correlate.Rd | 25 +- corrr-0.4.3/corrr/man/corrr-package.Rd | 1 corrr-0.4.3/corrr/man/fashion.Rd | 2 corrr-0.4.3/corrr/man/figures/README-combination-1.png |only corrr-0.4.3/corrr/man/figures/README-combination-2.png |only corrr-0.4.3/corrr/man/figures/logo.png |binary corrr-0.4.3/corrr/man/figures/to-cor-df.png |only corrr-0.4.3/corrr/man/first_col.Rd | 6 corrr-0.4.3/corrr/man/focus.Rd | 8 corrr-0.4.3/corrr/man/network_plot.Rd | 5 corrr-0.4.3/corrr/man/rplot.Rd | 20 + corrr-0.4.3/corrr/man/stretch.Rd | 4 corrr-0.4.3/corrr/tests/testthat/test-as_cordf.R | 16 - corrr-0.4.3/corrr/tests/testthat/test-as_matrix.R | 56 ++--- corrr-0.4.3/corrr/tests/testthat/test-colpair.R |only corrr-0.4.3/corrr/tests/testthat/test-correlate.R | 15 + corrr-0.4.3/corrr/tests/testthat/test-dataframe.R | 2 corrr-0.4.3/corrr/tests/testthat/test-fashion.R | 2 corrr-0.4.3/corrr/tests/testthat/test-focus.R | 18 - corrr-0.4.3/corrr/tests/testthat/test-focus_.R | 14 - corrr-0.4.3/corrr/tests/testthat/test-plots.R | 28 +- corrr-0.4.3/corrr/tests/testthat/test-rearrange.R | 2 corrr-0.4.3/corrr/tests/testthat/test-stretch.R | 29 ++ corrr-0.4.3/corrr/tests/testthat/test-utilities.R | 6 corrr-0.4.3/corrr/vignettes/databases.Rmd | 2 corrr-0.4.3/corrr/vignettes/using-corrr.Rmd | 12 - 51 files changed, 762 insertions(+), 477 deletions(-)
Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Jeffrey Oliver [aut],
James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>
Diff between corHMM versions 2.4 dated 2020-10-01 and 2.5 dated 2020-11-24
DESCRIPTION | 8 MD5 | 31 +-- R/ancRECON.R | 176 +++++++++++++++++++ R/corHMM.R | 4 R/makeSimmap.R | 330 ++++++++++++++++++++++--------------- R/rate.mat.maker.R | 15 - R/rayDISC.R | 4 inst/doc/corHMMv2.1-vignette.R | 23 +- inst/doc/corHMMv2.1-vignette.Rmd | 24 +- inst/doc/corHMMv2.1-vignette.pdf |binary man/ancRECON.Rd | 4 man/corHMM.Rd | 6 man/makeSimmap.Rd | 20 -- man/rayDISC.Rd | 4 vignettes/corHMMResults.Rsave |only vignettes/corHMMv2.1-vignette.Rmd | 24 +- vignettes/corHMMv2.1-vignette.html | 262 ++++++++++------------------- 17 files changed, 539 insertions(+), 396 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A file-based
mechanism for documenting datasets. It reads and writes
YAML-formatted metadata and applies it as data
item attributes. Data and metadata are stored independently
but can be coordinated by using similar file paths with
different extensions. The 'yamlet' dialect is valid 'YAML',
but some conventions are chosen to improve readability.
Defaults and conventions can be over-ridden by the user.
See ?yamlet and ?decorate.data.frame.
See ?read_yamlet ?write_yamlet, and ?io_csv.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.4.8 dated 2020-06-18 and 0.5.1 dated 2020-11-24
yamlet-0.4.8/yamlet/R/agplot.R |only yamlet-0.4.8/yamlet/man/print.decorated.Rd |only yamlet-0.4.8/yamlet/man/print.dg.Rd |only yamlet-0.4.8/yamlet/man/resolve.data.frame.Rd |only yamlet-0.5.1/yamlet/DESCRIPTION | 12 yamlet-0.5.1/yamlet/MD5 | 273 +++++----- yamlet-0.5.1/yamlet/NAMESPACE | 29 + yamlet-0.5.1/yamlet/R/alias.R | 21 yamlet-0.5.1/yamlet/R/append_units.R | 26 - yamlet-0.5.1/yamlet/R/classified.R | 2 yamlet-0.5.1/yamlet/R/conditionalize.R | 2 yamlet-0.5.1/yamlet/R/decorate.R |only yamlet-0.5.1/yamlet/R/explicit_guide.R | 52 +- yamlet-0.5.1/yamlet/R/factorize_codelist.R | 12 yamlet-0.5.1/yamlet/R/ggplot.R |only yamlet-0.5.1/yamlet/R/ggplot_ggready.R |only yamlet-0.5.1/yamlet/R/ggready.R | 143 ++++- yamlet-0.5.1/yamlet/R/io_res.R |only yamlet-0.5.1/yamlet/R/modify.R |only yamlet-0.5.1/yamlet/R/named.R |only yamlet-0.5.1/yamlet/R/parseable.R | 1 yamlet-0.5.1/yamlet/R/resolve.R | 18 yamlet-0.5.1/yamlet/R/selected.R |only yamlet-0.5.1/yamlet/R/singularity.R |only yamlet-0.5.1/yamlet/R/sub_units.R | 11 yamlet-0.5.1/yamlet/R/xtable.R | 63 +- yamlet-0.5.1/yamlet/R/yamlet.R | 376 +-------------- yamlet-0.5.1/yamlet/build/vignette.rds |binary yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.R | 4 yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.Rmd | 4 yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.html | 363 ++++++++------ yamlet-0.5.1/yamlet/man/alias.data.frame.Rd | 79 +-- yamlet-0.5.1/yamlet/man/anti_join.decorated.Rd | 128 ++--- yamlet-0.5.1/yamlet/man/append_units.Rd | 73 +- yamlet-0.5.1/yamlet/man/append_units.data.frame.Rd | 73 +- yamlet-0.5.1/yamlet/man/append_units.default.Rd | 124 ++-- yamlet-0.5.1/yamlet/man/arrange.decorated.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as.character.yam.Rd | 82 +-- yamlet-0.5.1/yamlet/man/as.character.yamlet.Rd | 89 +-- yamlet-0.5.1/yamlet/man/as_classified.Rd | 60 +- yamlet-0.5.1/yamlet/man/as_classified.factor.Rd | 77 +-- yamlet-0.5.1/yamlet/man/as_decorated.Rd | 93 ++- yamlet-0.5.1/yamlet/man/as_decorated.default.Rd |only yamlet-0.5.1/yamlet/man/as_spork.symbolic_units.Rd | 86 +-- yamlet-0.5.1/yamlet/man/as_spork.unit_string.Rd | 70 +- yamlet-0.5.1/yamlet/man/as_spork.units.Rd | 72 +- yamlet-0.5.1/yamlet/man/as_unit_string.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as_unit_string.character.Rd | 68 +- yamlet-0.5.1/yamlet/man/as_unit_string.factor.Rd | 70 +- yamlet-0.5.1/yamlet/man/as_unit_string.symbolic_units.Rd | 94 +-- yamlet-0.5.1/yamlet/man/as_unit_string.units.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as_yam.Rd | 56 +- yamlet-0.5.1/yamlet/man/as_yam.character.Rd | 90 +-- yamlet-0.5.1/yamlet/man/as_yam.yamlet.Rd | 90 +-- yamlet-0.5.1/yamlet/man/as_yamlet.Rd | 74 +- yamlet-0.5.1/yamlet/man/as_yamlet.character.Rd | 116 ++-- yamlet-0.5.1/yamlet/man/as_yamlet.data.frame.Rd | 67 +- yamlet-0.5.1/yamlet/man/as_yamlet.list.Rd |only yamlet-0.5.1/yamlet/man/as_yamlet.yam.Rd | 82 +-- yamlet-0.5.1/yamlet/man/as_yamlet.yamlet.Rd | 65 +- yamlet-0.5.1/yamlet/man/conditionalize.Rd | 58 +- yamlet-0.5.1/yamlet/man/conditionalize.data.frame.Rd | 163 ++---- yamlet-0.5.1/yamlet/man/decorate.Rd | 83 +-- yamlet-0.5.1/yamlet/man/decorate.character.Rd | 226 ++++----- yamlet-0.5.1/yamlet/man/decorate.data.frame.Rd | 140 ++--- yamlet-0.5.1/yamlet/man/decorate.list.Rd | 100 ++- yamlet-0.5.1/yamlet/man/decorations.Rd | 77 +-- yamlet-0.5.1/yamlet/man/decorations.data.frame.Rd | 114 ++-- yamlet-0.5.1/yamlet/man/encode.yamlet.Rd | 71 +- yamlet-0.5.1/yamlet/man/explicit_guide.Rd | 59 +- yamlet-0.5.1/yamlet/man/explicit_guide.data.frame.Rd | 118 ++-- yamlet-0.5.1/yamlet/man/explicit_guide.yamlet.Rd | 124 ++-- yamlet-0.5.1/yamlet/man/factorize_codelist.Rd | 61 +- yamlet-0.5.1/yamlet/man/factorize_codelist.character.Rd | 66 +- yamlet-0.5.1/yamlet/man/factorize_codelist.data.frame.Rd | 71 +- yamlet-0.5.1/yamlet/man/factorize_codelist.default.Rd | 56 +- yamlet-0.5.1/yamlet/man/factorize_codelist.factor.Rd | 58 +- yamlet-0.5.1/yamlet/man/filter.decorated.Rd | 123 +++- yamlet-0.5.1/yamlet/man/footnote.decorated.Rd | 89 +-- yamlet-0.5.1/yamlet/man/full_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/ggplot.decorated.Rd | 199 +++++-- yamlet-0.5.1/yamlet/man/ggplot.ggready.Rd |only yamlet-0.5.1/yamlet/man/ggplot_build.decorated_ggplot.Rd |only yamlet-0.5.1/yamlet/man/ggplot_build.ggready_ggplot.Rd |only yamlet-0.5.1/yamlet/man/ggready.Rd | 101 ++-- yamlet-0.5.1/yamlet/man/ggready.data.frame.Rd | 104 +--- yamlet-0.5.1/yamlet/man/ggready.decorated.Rd |only yamlet-0.5.1/yamlet/man/ggready.resolved.Rd |only yamlet-0.5.1/yamlet/man/group_by.decorated.Rd | 99 +-- yamlet-0.5.1/yamlet/man/inner_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/io_csv.Rd | 90 +-- yamlet-0.5.1/yamlet/man/io_csv.character.Rd | 121 ++-- yamlet-0.5.1/yamlet/man/io_csv.data.frame.Rd | 157 +++--- yamlet-0.5.1/yamlet/man/io_res.Rd |only yamlet-0.5.1/yamlet/man/io_res.character.Rd |only yamlet-0.5.1/yamlet/man/io_table.Rd | 92 +-- yamlet-0.5.1/yamlet/man/io_table.character.Rd | 121 ++-- yamlet-0.5.1/yamlet/man/io_table.data.frame.Rd | 155 +++--- yamlet-0.5.1/yamlet/man/io_yamlet.Rd | 90 +-- yamlet-0.5.1/yamlet/man/io_yamlet.character.Rd | 131 ++--- yamlet-0.5.1/yamlet/man/io_yamlet.data.frame.Rd | 163 +++--- yamlet-0.5.1/yamlet/man/io_yamlet.yamlet.Rd | 126 ++--- yamlet-0.5.1/yamlet/man/isConditional.default.Rd | 52 +- yamlet-0.5.1/yamlet/man/isConditional.list.Rd | 64 +- yamlet-0.5.1/yamlet/man/isLevels.character.Rd | 62 +- yamlet-0.5.1/yamlet/man/isLevels.default.Rd | 52 +- yamlet-0.5.1/yamlet/man/is_parseable.Rd | 58 +- yamlet-0.5.1/yamlet/man/is_parseable.default.Rd | 110 ++-- yamlet-0.5.1/yamlet/man/left_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/list2encoding.Rd | 64 +- yamlet-0.5.1/yamlet/man/modify.Rd |only yamlet-0.5.1/yamlet/man/modify.default.Rd |only yamlet-0.5.1/yamlet/man/mutate.decorated.Rd | 94 +-- yamlet-0.5.1/yamlet/man/named.Rd |only yamlet-0.5.1/yamlet/man/print.decorated_ggplot.Rd |only yamlet-0.5.1/yamlet/man/print.decorated_xtable.Rd |only yamlet-0.5.1/yamlet/man/print.decorations.Rd |only yamlet-0.5.1/yamlet/man/print.ggready_ggplot.Rd |only yamlet-0.5.1/yamlet/man/print.yamlet.Rd | 60 +- yamlet-0.5.1/yamlet/man/promote.Rd |only yamlet-0.5.1/yamlet/man/promote.default.Rd |only yamlet-0.5.1/yamlet/man/read_yamlet.Rd | 115 ++-- yamlet-0.5.1/yamlet/man/redecorate.Rd | 89 +-- yamlet-0.5.1/yamlet/man/reexports.Rd | 48 - yamlet-0.5.1/yamlet/man/resolve.Rd | 60 +- yamlet-0.5.1/yamlet/man/resolve.decorated.Rd |only yamlet-0.5.1/yamlet/man/right_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/select.decorated.Rd | 80 +-- yamlet-0.5.1/yamlet/man/selected.Rd |only yamlet-0.5.1/yamlet/man/selected.default.Rd |only yamlet-0.5.1/yamlet/man/semi_join.decorated.Rd | 128 ++--- yamlet-0.5.1/yamlet/man/singularity.Rd | 117 ++-- yamlet-0.5.1/yamlet/man/slice.decorated.Rd | 96 +-- yamlet-0.5.1/yamlet/man/sub-.classified.Rd | 64 +- yamlet-0.5.1/yamlet/man/sub-.decorated.Rd |only yamlet-0.5.1/yamlet/man/sub-.unit_string.Rd | 80 +-- yamlet-0.5.1/yamlet/man/sub-.yamlet.Rd | 67 +- yamlet-0.5.1/yamlet/man/sub-sub-.unit_string.Rd | 80 +-- yamlet-0.5.1/yamlet/man/sub_units.Rd | 147 ++--- yamlet-0.5.1/yamlet/man/summarise.decorated.Rd | 90 +-- yamlet-0.5.1/yamlet/man/summarize.decorated.Rd | 90 +-- yamlet-0.5.1/yamlet/man/to_yamlet.NULL.Rd | 62 +- yamlet-0.5.1/yamlet/man/to_yamlet.Rd | 60 +- yamlet-0.5.1/yamlet/man/to_yamlet.character.Rd | 68 +- yamlet-0.5.1/yamlet/man/to_yamlet.default.Rd | 68 +- yamlet-0.5.1/yamlet/man/to_yamlet.list.Rd | 66 +- yamlet-0.5.1/yamlet/man/unnest.Rd | 72 +- yamlet-0.5.1/yamlet/man/unnest.default.Rd | 54 +- yamlet-0.5.1/yamlet/man/unnest.list.Rd | 76 +-- yamlet-0.5.1/yamlet/man/write_yamlet.Rd | 143 ++--- yamlet-0.5.1/yamlet/man/xtable.decorated.Rd | 80 +-- yamlet-0.5.1/yamlet/man/yamlet.Rd | 192 +++---- yamlet-0.5.1/yamlet/tests/testthat/Rplots.pdf |only yamlet-0.5.1/yamlet/tests/testthat/test-yamlet.R | 349 +++++++++++++ yamlet-0.5.1/yamlet/vignettes/yamlet-introduction.Rmd | 4 155 files changed, 5757 insertions(+), 5272 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.6.0 dated 2020-11-09 and 0.6.1 dated 2020-11-24
DESCRIPTION | 10 +-- MD5 | 20 +++--- NEWS.md | 4 + R/RcppExports.R | 8 +- R/api_sparta.R | 12 +-- R/helpers_sparta.R | 52 ++++++++++------- R/sparta-package.R | 2 README.md | 1 man/sparta-package.Rd | 2 src/RcppExports.cpp | 26 ++++++-- src/marginalize.cpp | 152 +++++++++++++++++++++++++++++++++++++++++++------- 11 files changed, 218 insertions(+), 71 deletions(-)
Title: Media News Extraction for Text Analysis
Description: Extract textual data from different media channels
through its source, based on users choice of keywords.
These data can be used to perform text analysis to
identify patterns in respective media reporting.
The media channels used in this package are print media
from India. The data (or news) used are publicly
available to consumers.
Author: Vatsal Aima
Maintainer: Vatsal Aima <vaima75@hotmail.com>
Diff between MediaNews versions 0.1.0 dated 2020-02-09 and 0.2.0 dated 2020-11-24
DESCRIPTION | 14 +++++------ MD5 | 14 +++++------ NAMESPACE | 3 -- R/ClearText.R | 2 - R/TOI_News_Articles.R | 55 ++++++++++++++++++++++++----------------------- R/TOI_News_Dataset.R | 10 +++----- README.md | 7 ++--- man/TOI_News_Articles.Rd | 21 +++++------------ 8 files changed, 59 insertions(+), 67 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.10.0 dated 2020-10-22 and 0.11.0 dated 2020-11-24
insight-0.10.0/insight/man/format_table.Rd |only insight-0.11.0/insight/DESCRIPTION | 15 insight-0.11.0/insight/MD5 | 272 ++--- insight-0.11.0/insight/NAMESPACE | 49 + insight-0.11.0/insight/NEWS.md | 480 ++++++++-- insight-0.11.0/insight/R/clean_parameters.R | 10 insight-0.11.0/insight/R/colour_tools.R | 5 insight-0.11.0/insight/R/display.R |only insight-0.11.0/insight/R/export_table.R |only insight-0.11.0/insight/R/find_algorithm.R | 3 insight-0.11.0/insight/R/find_formula.R | 113 +- insight-0.11.0/insight/R/find_offset.R |only insight-0.11.0/insight/R/find_parameters.R | 107 ++ insight-0.11.0/insight/R/find_response.R | 11 insight-0.11.0/insight/R/find_statistic.R | 19 insight-0.11.0/insight/R/find_terms.R | 7 insight-0.11.0/insight/R/find_variables.R | 49 - insight-0.11.0/insight/R/format_bf.R | 26 insight-0.11.0/insight/R/format_ci.R | 27 insight-0.11.0/insight/R/format_table.R | 448 ++++++++- insight-0.11.0/insight/R/format_value.R | 4 insight-0.11.0/insight/R/get_data.R | 70 + insight-0.11.0/insight/R/get_parameters.R | 158 ++- insight-0.11.0/insight/R/get_priors.R | 68 + insight-0.11.0/insight/R/get_response.R | 4 insight-0.11.0/insight/R/get_statistic.R | 20 insight-0.11.0/insight/R/get_varcov.R | 7 insight-0.11.0/insight/R/get_variances.R | 36 insight-0.11.0/insight/R/helper_functions.R | 193 +++- insight-0.11.0/insight/R/is_model.R | 9 insight-0.11.0/insight/R/is_model_supported.R | 8 insight-0.11.0/insight/R/model_info.R | 15 insight-0.11.0/insight/R/n_obs.R | 12 insight-0.11.0/insight/R/null_model.R | 6 insight-0.11.0/insight/R/print_parameters.R | 60 + insight-0.11.0/insight/R/standardize_names.R | 164 ++- insight-0.11.0/insight/R/utils_get_data.R | 26 insight-0.11.0/insight/R/utils_model_info.R | 78 + insight-0.11.0/insight/README.md | 63 - insight-0.11.0/insight/build/partial.rdb |binary insight-0.11.0/insight/inst/WORDLIST | 65 - insight-0.11.0/insight/inst/doc/insight.html | 100 -- insight-0.11.0/insight/man/display.Rd |only insight-0.11.0/insight/man/export_table.Rd |only insight-0.11.0/insight/man/find_offset.Rd |only insight-0.11.0/insight/man/find_response.Rd | 3 insight-0.11.0/insight/man/find_terms.Rd | 2 insight-0.11.0/insight/man/find_variables.Rd | 49 - insight-0.11.0/insight/man/format_bf.Rd | 1 insight-0.11.0/insight/man/format_ci.Rd | 3 insight-0.11.0/insight/man/format_value.Rd | 127 +- insight-0.11.0/insight/man/get_parameters.Rd | 19 insight-0.11.0/insight/man/get_priors.Rd | 5 insight-0.11.0/insight/man/get_variance.Rd | 16 insight-0.11.0/insight/man/model_info.Rd | 6 insight-0.11.0/insight/man/parameters_table.Rd |only insight-0.11.0/insight/man/print_parameters.Rd | 15 insight-0.11.0/insight/man/standardize_names.Rd | 26 insight-0.11.0/insight/tests/spelling.R | 9 insight-0.11.0/insight/tests/testthat/test-BayesFactorBF.R | 85 + insight-0.11.0/insight/tests/testthat/test-GLMMadaptive.R | 4 insight-0.11.0/insight/tests/testthat/test-Gam2.R | 6 insight-0.11.0/insight/tests/testthat/test-LORgee.R | 6 insight-0.11.0/insight/tests/testthat/test-MCMCglmm.R | 20 insight-0.11.0/insight/tests/testthat/test-aovlist.R | 6 insight-0.11.0/insight/tests/testthat/test-backticks.R | 1 insight-0.11.0/insight/tests/testthat/test-betabin.R | 8 insight-0.11.0/insight/tests/testthat/test-betareg.R | 7 insight-0.11.0/insight/tests/testthat/test-bigglm.R | 5 insight-0.11.0/insight/tests/testthat/test-blmer.R | 10 insight-0.11.0/insight/tests/testthat/test-brms.R | 8 insight-0.11.0/insight/tests/testthat/test-censReg.R | 6 insight-0.11.0/insight/tests/testthat/test-cgam.R | 11 insight-0.11.0/insight/tests/testthat/test-clean_names.R | 1 insight-0.11.0/insight/tests/testthat/test-clm.R | 5 insight-0.11.0/insight/tests/testthat/test-clm2.R | 5 insight-0.11.0/insight/tests/testthat/test-clmm.R | 8 insight-0.11.0/insight/tests/testthat/test-coxme.R | 8 insight-0.11.0/insight/tests/testthat/test-coxph.R | 14 insight-0.11.0/insight/tests/testthat/test-cpglmm.R | 7 insight-0.11.0/insight/tests/testthat/test-crch.R | 6 insight-0.11.0/insight/tests/testthat/test-crq.R | 5 insight-0.11.0/insight/tests/testthat/test-data.frame.R | 2 insight-0.11.0/insight/tests/testthat/test-feis.R | 5 insight-0.11.0/insight/tests/testthat/test-felm.R | 3 insight-0.11.0/insight/tests/testthat/test-find_predictor_nested_re.R | 2 insight-0.11.0/insight/tests/testthat/test-fixest.R | 8 insight-0.11.0/insight/tests/testthat/test-format.R | 18 insight-0.11.0/insight/tests/testthat/test-gam.R | 9 insight-0.11.0/insight/tests/testthat/test-gamlss.R | 5 insight-0.11.0/insight/tests/testthat/test-gamm.R | 4 insight-0.11.0/insight/tests/testthat/test-gamm4.R | 3 insight-0.11.0/insight/tests/testthat/test-gbm.R | 3 insight-0.11.0/insight/tests/testthat/test-gee.R | 5 insight-0.11.0/insight/tests/testthat/test-geeglm.R | 5 insight-0.11.0/insight/tests/testthat/test-get_data.R | 11 insight-0.11.0/insight/tests/testthat/test-glm.R | 8 insight-0.11.0/insight/tests/testthat/test-glmmTMB.R | 10 insight-0.11.0/insight/tests/testthat/test-glmrob_base.R | 6 insight-0.11.0/insight/tests/testthat/test-gls.R | 3 insight-0.11.0/insight/tests/testthat/test-has_intercept.R | 2 insight-0.11.0/insight/tests/testthat/test-hurdle.R | 6 insight-0.11.0/insight/tests/testthat/test-is_nullmodel.R | 2 insight-0.11.0/insight/tests/testthat/test-iv_robust.R | 3 insight-0.11.0/insight/tests/testthat/test-ivreg.R | 39 insight-0.11.0/insight/tests/testthat/test-ivreg_AER.R |only insight-0.11.0/insight/tests/testthat/test-lm.R | 8 insight-0.11.0/insight/tests/testthat/test-lm_robust.R | 5 insight-0.11.0/insight/tests/testthat/test-lme.R | 8 insight-0.11.0/insight/tests/testthat/test-lmer.R | 26 insight-0.11.0/insight/tests/testthat/test-lmrob_base.R | 5 insight-0.11.0/insight/tests/testthat/test-logistf.R | 6 insight-0.11.0/insight/tests/testthat/test-mixed.R | 6 insight-0.11.0/insight/tests/testthat/test-mlogit.R | 1 insight-0.11.0/insight/tests/testthat/test-model_data.R | 2 insight-0.11.0/insight/tests/testthat/test-model_info.R |only insight-0.11.0/insight/tests/testthat/test-multinom.R | 6 insight-0.11.0/insight/tests/testthat/test-mvrstanarm.R | 2 insight-0.11.0/insight/tests/testthat/test-namespace.R | 3 insight-0.11.0/insight/tests/testthat/test-negbin.R | 10 insight-0.11.0/insight/tests/testthat/test-nlmer.R | 8 insight-0.11.0/insight/tests/testthat/test-offset.R |only insight-0.11.0/insight/tests/testthat/test-ols.R | 5 insight-0.11.0/insight/tests/testthat/test-plm.R | 5 insight-0.11.0/insight/tests/testthat/test-polr.R | 5 insight-0.11.0/insight/tests/testthat/test-psm.R | 9 insight-0.11.0/insight/tests/testthat/test-rlmer.R | 8 insight-0.11.0/insight/tests/testthat/test-rms.R | 6 insight-0.11.0/insight/tests/testthat/test-rq.R | 3 insight-0.11.0/insight/tests/testthat/test-rqss.R | 5 insight-0.11.0/insight/tests/testthat/test-rstanarm.R | 12 insight-0.11.0/insight/tests/testthat/test-spatial.R | 3 insight-0.11.0/insight/tests/testthat/test-speedglm.R | 6 insight-0.11.0/insight/tests/testthat/test-speedlm.R | 8 insight-0.11.0/insight/tests/testthat/test-standardize_names.R |only insight-0.11.0/insight/tests/testthat/test-survey.R | 5 insight-0.11.0/insight/tests/testthat/test-survfit.R | 4 insight-0.11.0/insight/tests/testthat/test-survreg.R | 38 insight-0.11.0/insight/tests/testthat/test-tobit.R | 9 insight-0.11.0/insight/tests/testthat/test-truncreg.R | 5 insight-0.11.0/insight/tests/testthat/test-vgam.R | 8 insight-0.11.0/insight/tests/testthat/test-vglm.R | 6 insight-0.11.0/insight/tests/testthat/test-zeroinfl.R | 4 143 files changed, 2702 insertions(+), 1040 deletions(-)
Title: Handling HL7 FHIR Resources in R
Description: Useful tools for conveniently downloading FHIR resources in xml format
and converting them to R data frames. The package uses FHIR-search to download bundles
from a FHIR server, provides functions to save and read xml-files containing such bundles
and allows flattening the bundles to data.frames using XPath expressions.
Author: Thomas Peschel [aut, cre],
Julia Gantner [aut] (<https://orcid.org/0000-0003-1568-5893>),
Jens Przybilla [aut],
Frank Meineke [aut] (<https://orcid.org/0000-0002-9256-7543>)
Maintainer: Thomas Peschel <tpeschel@imise.uni-leipzig.de>
Diff between fhircrackr versions 0.2.0 dated 2020-10-19 and 0.2.1 dated 2020-11-24
DESCRIPTION | 10 - MD5 | 14 +- NEWS.md | 14 ++ R/design.R | 12 +- R/fhircrack.R | 51 +++++---- R/helpers.R | 2 man/fhir_melt.Rd | 2 vignettes/fhircrackr.html | 246 +++++++++++++++++++++++++++------------------- 8 files changed, 209 insertions(+), 142 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-14 dated 2020-09-04 and 0.9-15 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary configure | 1 + configure.ac | 1 + 5 files changed, 9 insertions(+), 7 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [ctb],
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.3.5 dated 2020-08-10 and 2.3.7 dated 2020-11-24
clam-2.3.5/clam/inst/extdata/IntCal20.14C |only clam-2.3.5/clam/inst/extdata/Marine20.14C |only clam-2.3.5/clam/inst/extdata/SHCal20.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH1.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH2.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH3.14C |only clam-2.3.5/clam/inst/extdata/postbomb_SH1-2.14C |only clam-2.3.5/clam/inst/extdata/postbomb_SH3.14C |only clam-2.3.5/clam/man/age.pMC.Rd |only clam-2.3.5/clam/man/copyCalibrationCurve.Rd |only clam-2.3.5/clam/man/pMC.age.Rd |only clam-2.3.7/clam/DESCRIPTION | 10 - clam-2.3.7/clam/MD5 | 35 +---- clam-2.3.7/clam/NAMESPACE | 7 - clam-2.3.7/clam/NEWS.md | 9 + clam-2.3.7/clam/R/calibrate.R | 158 ++++++------------------ clam-2.3.7/clam/R/clam.R | 71 +++++----- clam-2.3.7/clam/R/models.R | 60 ++++----- clam-2.3.7/clam/R/readwrite.R | 50 +++---- clam-2.3.7/clam/man/calBP.14C.Rd | 11 + clam-2.3.7/clam/man/calibrate.Rd | 17 +- clam-2.3.7/clam/man/clam.Rd | 31 +--- clam-2.3.7/clam/man/mix.calibrationcurves.Rd | 9 - clam-2.3.7/clam/man/student.t.Rd | 5 24 files changed, 202 insertions(+), 271 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of
elements into groups (i.e., anticlusters) in such a way that the
between-group similarity is maximized and -- at the same time -- the
within-group heterogeneity is maximized. This reverses the logic of
cluster analysis that strives for high within-group homogeneity and
low similarity of the different groups. Computationally,
anticlustering is accomplished by maximizing instead of minimizing a
clustering objective function, such as the intra-cluster variance
(used in k-means clustering) or the sum of pairwise distances within
clusters. The function anticlustering() implements exact and
heuristic anticlustering algorithms as described in Papenberg and Klau
(2020; <doi:10.1037/met0000301>). The exact approach requires that the
GNU linear programming kit
(<https://www.gnu.org/software/glpk/glpk.html>) is available and the R
package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is
installed. Some other functions are available to solve classical
clustering problems. The function balanced_clustering() applies a
cluster analysis under size constraints, i.e., creates equal-sized
clusters. The function matching() can be used for (unrestricted,
bipartite, or K-partite) matching. The function wce() can be used
optimally solve the (weighted) cluster editing problem, also known as
correlation clustering, clique partitioning problem or transitivity
clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>),
Meik Michalke [ctb] (centroid based clustering algorithm),
Gunnar W. Klau [ths],
Juliane V. Tkotz [ctb] (package logo)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.5.3 dated 2020-09-25 and 0.5.6 dated 2020-11-24
DESCRIPTION | 10 +-- MD5 | 42 ++++++++++----- NAMESPACE | 3 + R/anticlust.R |only R/c-anticlustering.R |only R/input-validation.R | 63 ++++++++++++++-------- R/plotting.R | 17 ++++-- R/repeated-exchange.R | 8 +- R/sample-by-category.R | 76 +++++++++++++++++++++++---- R/wrapper-anticlustering.R | 91 +++++++++++++++++---------------- build/vignette.rds |binary inst/doc/stimulus-selection.html | 42 +++++++-------- man/anticlust.Rd |only man/anticlustering.Rd | 32 +++++++---- man/categorical_sampling.Rd | 4 + src |only tests/testthat/test-c-implementation.R |only tests/testthat/test-distance-input.R | 46 +++++++++------- tests/testthat/test-kplus-criterion.R | 17 ++++++ tests/testthat/test-preclustering.R |only tests/testthat/test-standardize.R |only 21 files changed, 295 insertions(+), 156 deletions(-)
Title: Robust Econometric Inference
Description: Drawing statistical inference on the coefficients
of a short- or long-horizon predictive regression with persistent
regressors by using the IVX method of Magdalinos and Phillips (2009)
<doi:10.1017/S0266466608090154> and Kostakis, Magdalinos and
Stamatogiannis (2015) <doi:10.1093/rfs/hhu139>.
Author: Kostas Vasilopoulos [cre, aut],
Efthymios Pavlidis [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between ivx versions 1.0.0 dated 2019-05-04 and 1.1.0 dated 2020-11-24
ivx-1.0.0/ivx/R/utils-pipe.R |only ivx-1.0.0/ivx/man/pipe.Rd |only ivx-1.0.0/ivx/tests/testthat/test-ivx_fit.R |only ivx-1.1.0/ivx/DESCRIPTION | 16 ivx-1.1.0/ivx/MD5 | 64 ++- ivx-1.1.0/ivx/NAMESPACE | 54 ++- ivx-1.1.0/ivx/NEWS.md |only ivx-1.1.0/ivx/R/ac_test.R |only ivx-1.1.0/ivx/R/auto-ar.R |only ivx-1.1.0/ivx/R/data.R | 36 +- ivx-1.1.0/ivx/R/extract-texreg-methods.R |only ivx-1.1.0/ivx/R/ivx-package.R | 9 ivx-1.1.0/ivx/R/ivx.R | 468 ++++++++++++++++++-------- ivx-1.1.0/ivx/R/ivx_ar.R |only ivx-1.1.0/ivx/R/methods.R |only ivx-1.1.0/ivx/R/step-methods.R |only ivx-1.1.0/ivx/R/utils.R |only ivx-1.1.0/ivx/README.md | 85 +++- ivx-1.1.0/ivx/build |only ivx-1.1.0/ivx/data/kms.rda |only ivx-1.1.0/ivx/data/kms_quarterly.rda |only ivx-1.1.0/ivx/data/ylpc.rda |only ivx-1.1.0/ivx/inst/WORDLIST | 24 + ivx-1.1.0/ivx/man/ac_test.Rd |only ivx-1.1.0/ivx/man/ac_test_.Rd |only ivx-1.1.0/ivx/man/delta.Rd | 2 ivx-1.1.0/ivx/man/extract.ivx.Rd |only ivx-1.1.0/ivx/man/figures |only ivx-1.1.0/ivx/man/ivx-package.Rd | 9 ivx-1.1.0/ivx/man/ivx.Rd | 95 +++-- ivx-1.1.0/ivx/man/ivx_ar.Rd |only ivx-1.1.0/ivx/man/ivx_ar_fit.Rd |only ivx-1.1.0/ivx/man/ivx_fit.Rd | 13 ivx-1.1.0/ivx/man/kms.Rd |only ivx-1.1.0/ivx/man/kms_quarterly.Rd |only ivx-1.1.0/ivx/man/monthly.Rd | 25 - ivx-1.1.0/ivx/man/quarterly.Rd | 25 - ivx-1.1.0/ivx/man/summary.ivx.Rd | 8 ivx-1.1.0/ivx/man/summary.ivx_ar.Rd |only ivx-1.1.0/ivx/man/vcov.ivx.Rd | 2 ivx-1.1.0/ivx/man/ylpc.Rd |only ivx-1.1.0/ivx/src/ivx_fit_cpp.cpp | 11 ivx-1.1.0/ivx/tests/testthat/test-ac_test.R |only ivx-1.1.0/ivx/tests/testthat/test-ivx-ar.R |only ivx-1.1.0/ivx/tests/testthat/test-ivx.R |only ivx-1.1.0/ivx/tests/testthat/test-methods.R | 28 + ivx-1.1.0/ivx/tests/testthat/test-warn-stop.R | 16 47 files changed, 687 insertions(+), 303 deletions(-)
Title: 'Compressive' Hierarchical Kernel Clustering Toolbox
Description: Routines for efficient cluster analysis of large scale data. This package implements the 'CHICKN'
clustering algorithm (see 'Permiakova' 'et' 'al.' (2020) "'CHICKN': Extraction of 'peptide' 'chromatographic'
'elution' profiles from large scale mass 'spectrometry' data by means of 'Wasserstein' 'compressive' hierarchical
cluster analysis"). Functions for data compression, hierarchical clustering and post processing are provided.
Author: Olga Permiakova [aut, cre],
Romain Guibert [aut],
Thomas Burger [aut]
Maintainer: Olga Permiakova <olga.permiakova@gmail.com>
Diff between chickn versions 1.2.2 dated 2020-11-12 and 1.2.3 dated 2020-11-24
chickn-1.2.2/chickn/README.md |only chickn-1.2.3/chickn/DESCRIPTION | 21 ++++++++++----------- chickn-1.2.3/chickn/MD5 | 23 +++++++++++------------ chickn-1.2.3/chickn/R/CHICKN_W1.R | 7 +++++-- chickn-1.2.3/chickn/R/DB_funR.R | 12 ++++++++++++ chickn-1.2.3/chickn/R/DrawFreq.R | 12 ++++++++++++ chickn-1.2.3/chickn/R/HCC_parallel.R | 6 ++++++ chickn-1.2.3/chickn/R/Sketch.R | 6 ++++++ chickn-1.2.3/chickn/R/zzz.R | 16 ++++++++++------ chickn-1.2.3/chickn/build/partial.rdb |binary chickn-1.2.3/chickn/inst/REFERENCES.bib | 1 - chickn-1.2.3/chickn/man/CHICKN_W1.Rd | 5 +++-- chickn-1.2.3/chickn/man/chickn.Rd | 14 ++++++++------ 13 files changed, 83 insertions(+), 40 deletions(-)
Title: Parallel Use of Statistical Packages in Teaching
Description: When teaching statistics, it can often be desirable to
uncouple the content from specific software packages. To ease such
efforts, the Rosetta Stats website (<https://rosettastats.com>) allows
comparing analyses in different packages. This package is the companion
to the Rosetta Stats website, aiming to provide functions that produce
output that is similar to output from other statistical packages, thereby
facilitating 'software-agnostic' teaching of statistics.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Ron Pat-El [ctb] (<https://orcid.org/0000-0002-4742-0163>),
Peter Verboon [ctb] (<https://orcid.org/0000-0001-8656-0890>),
Melissa Gordon Wolf [ctb] (<https://orcid.org/0000-0001-7677-0659>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between rosetta versions 0.3.0 dated 2020-11-12 and 0.3.1 dated 2020-11-24
DESCRIPTION | 20 ++-- MD5 | 34 ++++--- NAMESPACE | 6 + R/dataReduction.R | 110 ++++++++++++++++++------ R/descr.R |only R/factoranalysisjmv.b.R |only R/factoranalysisjmv.h.R |only R/histogram.R | 31 ++++++ R/logRegr.R | 30 ++++++ R/opts.R | 2 R/regr.R | 17 +-- inst/partials/_rosettaDataReduction_partial.Rmd | 32 ++++++ inst/partials/_rosettaDescr_partial.Rmd |only inst/partials/_rosettaLogRegr_partial.Rmd | 40 ++++++-- inst/partials/_rosettaRegr_partial.Rmd | 28 ++---- man/factorAnalysisjmv.Rd |only man/histogram.Rd |only man/rosettaDataReduction.Rd | 18 ++- man/rosettaDescr.Rd |only man/rosettaLogRegr.Rd | 4 tests |only 21 files changed, 282 insertions(+), 90 deletions(-)
Title: Perform Monothetic Clustering with Extensions to Circular Data
Description: Implementation of the Monothetic Clustering
algorithm (Chavent, 1998 <doi:10.1016/S0167-8655(98)00087-7>) on
continuous data sets. A lot of extensions are included in the package,
including applying Monothetic clustering on data sets with circular
variables, visualizations with the results, and permutation and
cross-validation based tests to support the decision on the number of
clusters.
Author: Tan Tran [aut, cre] (<https://orcid.org/0000-0001-9881-6339>),
Brian McGuire [aut],
Mark Greenwood [aut] (<https://orcid.org/0000-0001-6933-1201>)
Maintainer: Tan Tran <vinhtantran@gmail.com>
Diff between monoClust versions 1.1.0 dated 2020-11-17 and 1.2.0 dated 2020-11-24
monoClust-1.1.0/monoClust/R/mono_utils.R |only monoClust-1.1.0/monoClust/R/plot_utils.R |only monoClust-1.2.0/monoClust/DESCRIPTION | 17 ++- monoClust-1.2.0/monoClust/MD5 | 91 +++++++++++---------- monoClust-1.2.0/monoClust/NAMESPACE | 20 +++- monoClust-1.2.0/monoClust/NEWS.md | 22 ++++- monoClust-1.2.0/monoClust/R/MonoClust.R | 47 ++++------ monoClust-1.2.0/monoClust/R/MonoClust.object.R |only monoClust-1.2.0/monoClust/R/as_MonoClust.R |only monoClust-1.2.0/monoClust/R/circ_arith.R |only monoClust-1.2.0/monoClust/R/circ_dist.R | 5 - monoClust-1.2.0/monoClust/R/cv.test.R | 14 +-- monoClust-1.2.0/monoClust/R/ggcv.R | 9 +- monoClust-1.2.0/monoClust/R/ggpcp.R | 15 +-- monoClust-1.2.0/monoClust/R/inertia_calc.R |only monoClust-1.2.0/monoClust/R/is_MonoClust.R |only monoClust-1.2.0/monoClust/R/medoid.R |only monoClust-1.2.0/monoClust/R/perm.test.R | 12 +- monoClust-1.2.0/monoClust/R/plot.MonoClust.R | 19 ++-- monoClust-1.2.0/monoClust/R/plot.cv.MonoClust.R | 12 +- monoClust-1.2.0/monoClust/R/predict.MonoClust.R | 11 -- monoClust-1.2.0/monoClust/R/print.MonoClust.R | 66 +-------------- monoClust-1.2.0/monoClust/R/utils.R |only monoClust-1.2.0/monoClust/README.md | 5 - monoClust-1.2.0/monoClust/build/partial.rdb |binary monoClust-1.2.0/monoClust/inst/doc/monoclust.R | 1 monoClust-1.2.0/monoClust/inst/doc/monoclust.Rmd | 1 monoClust-1.2.0/monoClust/inst/doc/monoclust.html | 45 +++++----- monoClust-1.2.0/monoClust/man/MonoClust.object.Rd | 6 - monoClust-1.2.0/monoClust/man/as_MonoClust.Rd |only monoClust-1.2.0/monoClust/man/centroid.Rd | 2 monoClust-1.2.0/monoClust/man/circ_arith.Rd | 2 monoClust-1.2.0/monoClust/man/create_labels.Rd | 2 monoClust-1.2.0/monoClust/man/cv.test.Rd | 4 monoClust-1.2.0/monoClust/man/error_bar.Rd | 56 ++++++------ monoClust-1.2.0/monoClust/man/find_closest.Rd | 2 monoClust-1.2.0/monoClust/man/find_split.Rd | 14 --- monoClust-1.2.0/monoClust/man/ggcv.Rd | 3 monoClust-1.2.0/monoClust/man/inertia_calc.Rd | 20 +++- monoClust-1.2.0/monoClust/man/is_MonoClust.Rd |only monoClust-1.2.0/monoClust/man/medoid.Rd | 19 +++- monoClust-1.2.0/monoClust/man/monoClust-package.Rd | 1 monoClust-1.2.0/monoClust/man/new_node.Rd | 2 monoClust-1.2.0/monoClust/man/plot.MonoClust.Rd | 4 monoClust-1.2.0/monoClust/man/plot_prep_branch.Rd | 2 monoClust-1.2.0/monoClust/man/plot_prep_node.Rd | 2 monoClust-1.2.0/monoClust/man/plot_tree.Rd | 2 monoClust-1.2.0/monoClust/man/predict.MonoClust.Rd | 3 monoClust-1.2.0/monoClust/man/text_tree.Rd | 4 monoClust-1.2.0/monoClust/man/tree_depth.Rd | 10 +- monoClust-1.2.0/monoClust/man/tree_walk.Rd | 42 ++++----- monoClust-1.2.0/monoClust/vignettes/monoclust.Rmd | 1 52 files changed, 306 insertions(+), 309 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Author: Fabio Demarqui [aut, cre],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between covid19br versions 0.1.0 dated 2020-09-29 and 0.1.1 dated 2020-11-24
DESCRIPTION | 9 -- MD5 | 11 +- NAMESPACE | 1 NEWS.md |only R/covid19br.R | 1 R/downloadData.R | 233 +++++++++++++++++++++++++++++++------------------------ README.md |only inst |only 8 files changed, 146 insertions(+), 109 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees or functional kernel n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.3.0 dated 2020-10-28 and 2.4.0 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 8 + NAMESPACE | 2 R/BAT.R | 173 ++++++++++++++++++++++++++++++++---- man/evenness.contribution.Rd |only man/kernel.evenness.contribution.Rd |only 6 files changed, 168 insertions(+), 23 deletions(-)
Title: Data and Tools for Analyzing the Pali Canon
Description: Provides access to the complete Pali Canon, or
Tipitaka, the canonical scripture for Theravadin Buddhists
worldwide. Based on the Chattha Sangayana Tipitaka version
4 (Vipassana Research Institute, 1990).
Author: Dan Zigmond [aut, cre]
Maintainer: Dan Zigmond <djz@shmonk.com>
Diff between tipitaka versions 0.1.0 dated 2020-09-22 and 0.1.1 dated 2020-11-24
DESCRIPTION | 17 ++-- MD5 | 44 ++++++----- NAMESPACE | 1 NEWS.md | 4 + R/cpp11.R |only R/pali-sort.R | 136 +++++++++++++++--------------------- R/tipitaka-docs.R | 2 R/tipitaka-package.R |only README.md | 50 ++++++++++++- data/abhidhamma_pitaka.rda |binary data/pali_alphabet.rda |binary data/sati_sutta_long.rda |binary data/sati_sutta_raw.rda |binary data/sutta_pitaka.rda |binary data/tipitaka_long.rda |binary data/tipitaka_names.rda |binary data/tipitaka_raw.rda |binary data/tipitaka_wide.rda |binary data/vinaya_pitaka.rda |binary man/figures/README-kmeans-1.png |binary man/figures/README-wordclouds-1.png |binary man/pali_lt.Rd | 1 man/pali_sort.Rd | 12 +-- src |only 24 files changed, 152 insertions(+), 115 deletions(-)
Title: Stacked Elastic Net
Description: Implements stacked elastic net regression (Rauschenberger 2020, <doi:10.1093/bioinformatics/btaa535>). The elastic net generalises ridge and lasso regularisation (Zou 2005, <doi:10.1111/j.1467-9868.2005.00503.x>). Instead of fixing or tuning the mixing parameter alpha, we combine multiple alpha by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between starnet versions 0.0.5 dated 2020-11-09 and 0.0.6 dated 2020-11-24
DESCRIPTION | 6 ++-- MD5 | 28 +++++++++++------------ R/functions.R | 59 +++++++++++++++++++++++++++++++++++++++++++------ R/pkgname.R | 31 ++++++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/script.html | 4 +-- man/coef.starnet.Rd | 11 ++++++++- man/cv.starnet.Rd | 5 ++-- man/predict.starnet.Rd | 11 ++++++++- man/print.starnet.Rd | 11 ++++++++- man/starnet-package.Rd | 29 ------------------------ man/starnet.Rd | 10 +++++++- man/weights.starnet.Rd | 11 ++++++++- tests/testthat/test.R | 2 + 15 files changed, 152 insertions(+), 66 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.2 dated 2020-10-02 and 1.1.3 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NEWS.md | 3 +++ R/SDMmodel2MaxEnt.R | 2 +- R/maxentTh.R | 2 +- R/maxentVarImp.R | 2 +- R/reduceVar.R | 2 +- R/train.R | 2 +- R/varSel.R | 2 +- man/SDMmodel2MaxEnt.Rd | 2 +- man/maxentTh.Rd | 2 +- man/maxentVarImp.Rd | 2 +- man/reduceVar.Rd | 2 +- man/train.Rd | 2 +- man/varSel.Rd | 2 +- 15 files changed, 34 insertions(+), 31 deletions(-)
Title: Robust Model-Based Clustering
Description: Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2016) <doi:10.1080/01621459.2015.1100996>, and Coretto and Hennig (2017) <https://jmlr.org/papers/v18/16-382.html>.
Author: Pietro Coretto [aut, cre],
Christian Hennig [aut]
Maintainer: Pietro Coretto <pcoretto@unisa.it>
Diff between otrimle versions 1.3 dated 2019-09-24 and 1.6 dated 2020-11-24
otrimle-1.3/otrimle/ChangeLog |only otrimle-1.6/otrimle/DESCRIPTION | 17 ++--- otrimle-1.6/otrimle/MD5 | 28 ++++---- otrimle-1.6/otrimle/NEWS |only otrimle-1.6/otrimle/R/ecm.R | 26 ++++--- otrimle-1.6/otrimle/R/init.R | 88 +++++++++++++++++++++++++- otrimle-1.6/otrimle/R/otrimle.R | 105 ++++++++++++++++++++------------ otrimle-1.6/otrimle/R/plotting.R | 97 +++++++++++++++++++---------- otrimle-1.6/otrimle/R/printers.R | 8 ++ otrimle-1.6/otrimle/R/rimle.R | 57 +++++++++++------ otrimle-1.6/otrimle/inst/CITATION | 2 otrimle-1.6/otrimle/man/InitClust.Rd | 18 +++-- otrimle-1.6/otrimle/man/otrimle.Rd | 81 ++++++++++++++++++++---- otrimle-1.6/otrimle/man/plot.otrimle.Rd | 5 - otrimle-1.6/otrimle/man/plot.rimle.Rd | 3 otrimle-1.6/otrimle/man/rimle.Rd | 51 ++++++++++----- 16 files changed, 415 insertions(+), 171 deletions(-)
Title: Bayesian Calculation of Region-Specific Fixation Index to Detect
Local Adaptation
Description: An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer <bastianxpfeifer@gmail.com>
Diff between BlockFeST versions 1.6 dated 2018-05-06 and 1.8 dated 2020-11-24
DESCRIPTION | 10 ++++------ MD5 | 15 +++++++++------ NEWS |only R/slim.R | 11 +++++++---- R/update_slim.R | 29 +++++++++++++++++++++++++++-- README.md |only build/vignette.rds |binary inst/CITATION |only inst/doc/Input_format.pdf |binary src/update_group_C.c | 16 ++++++++++------ 10 files changed, 57 insertions(+), 24 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.6 dated 2020-05-16 and 1.0.7 dated 2020-11-24
DESCRIPTION | 12 - MD5 | 16 - R/Penalty_weights.R | 13 + R/plot_lambda.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 16 + inst/doc/smurf.html | 54 ++++- man/glmsmurf.Rd | 540 +++++++++++++++++++++++++-------------------------- man/smurf-package.Rd | 56 ++--- 9 files changed, 390 insertions(+), 319 deletions(-)
Title: A Data Cube 'dplyr' Backend
Description: An implementation of a data cube extracted out of
'dplyr' for backward compatibility.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between cubelyr versions 1.0.0 dated 2020-02-29 and 1.0.1 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 2 ++ NEWS.md |only R/cube.R | 7 +++++++ README.md | 1 + man/nasa.Rd | 4 +++- 7 files changed, 24 insertions(+), 11 deletions(-)
Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between survParamSim versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 24 +-- NEWS.md | 10 + README.md | 2 build/vignette.rds |binary inst/doc/survParamSim.html | 74 +++++++++- tests/figs/deps.txt | 2 tests/figs/test-calc-km-pi/km-plot-with-sex-and-ph-ecog-as-group.svg | 14 - tests/figs/test-calc-km-pi/km-plot-with-sex-as-trt.svg | 4 tests/figs/test-calc-km-pi/long-sim-time-not-truncating-with-censor.svg | 4 tests/figs/test-calc-km-pi/long-sim-time-truncating-with-censor.svg | 4 tests/figs/test-calc-km-pi/no-observed-km-curves.svg | 4 tests/testthat.R | 2 13 files changed, 112 insertions(+), 40 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <DOI:10.1126/science.1132939>).
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.2 dated 2020-09-24 and 0.1.3 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/plotDScoreHeatmap.R | 30 ++++++++++++++++++++++++------ R/plotDSpwHeatmap.R | 33 +++++++++++++++++++++++++++------ inst/doc/vignette.html | 8 ++++---- man/plotDScoreHeatmap.Rd | 18 ++++++++++++++++++ man/plotDSpwHeatmap.Rd | 15 +++++++++++++++ 7 files changed, 97 insertions(+), 25 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: LUOMUS - Finnish Museum of Natural History [cph],
William Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William Morris <willi@mmorris.email>
Diff between finbif versions 0.3.0 dated 2020-04-23 and 0.3.1 dated 2020-11-24
finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.RData |only finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.rdb |only finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.rdx |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.RData |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.rdb |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.rdx |only finbif-0.3.1/finbif/DESCRIPTION | 14 finbif-0.3.1/finbif/MD5 | 58 finbif-0.3.1/finbif/NEWS.md | 18 finbif-0.3.1/finbif/R/filters.R | 6 finbif-0.3.1/finbif/R/sysdata.rda |binary finbif-0.3.1/finbif/R/variables.R | 6 finbif-0.3.1/finbif/README.md | 22 finbif-0.3.1/finbif/build/vignette.rds |binary finbif-0.3.1/finbif/data/finland_map.rda |binary finbif-0.3.1/finbif/inst/NEWS.Rd | 19 finbif-0.3.1/finbif/inst/doc/finbif.html | 568 +++++---- finbif-0.3.1/finbif/inst/doc/v02_occurrence_data.html | 462 ++++--- finbif-0.3.1/finbif/inst/doc/v03_selecting_variables.html | 316 +++-- finbif-0.3.1/finbif/inst/doc/v04_metadata.html | 550 ++++---- finbif-0.3.1/finbif/inst/doc/v05_filtering.Rmd | 23 finbif-0.3.1/finbif/inst/doc/v05_filtering.html | 625 +++++----- finbif-0.3.1/finbif/inst/doc/v06_plotting.html | 184 ++ finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.RData |only finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.rdb |only finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.rdx |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.RData |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.rdb |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.rdx |only finbif-0.3.1/finbif/inst/vign/v05_filtering.Rmd | 14 finbif-0.3.1/finbif/inst/vign/v05_filtering.md | 23 finbif-0.3.1/finbif/man/filters.Rd | 6 finbif-0.3.1/finbif/man/finbif-package.Rd | 2 finbif-0.3.1/finbif/man/variables.Rd | 6 finbif-0.3.1/finbif/tests/testthat/test-finbif_occurrence.R | 14 finbif-0.3.1/finbif/vignettes/v05_filtering.Rmd | 23 36 files changed, 1705 insertions(+), 1254 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1>.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.7 dated 2020-09-01 and 0.7-1 dated 2020-11-24
COPYING |only DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- R/Gbeta.R | 18 +++++++++++++----- 4 files changed, 22 insertions(+), 13 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R)
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between rstanemax versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-24
rstanemax-0.1.2/rstanemax/tests/testthat/Rplots.pdf |only rstanemax-0.1.3/rstanemax/DESCRIPTION | 8 rstanemax-0.1.3/rstanemax/MD5 | 19 rstanemax-0.1.3/rstanemax/NEWS.md | 12 rstanemax-0.1.3/rstanemax/R/stanemax-methods.R | 6 rstanemax-0.1.3/rstanemax/build/vignette.rds |binary rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.R | 3 rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.Rmd | 8 rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.html | 401 +++++++++++--------- rstanemax-0.1.3/rstanemax/tests/testthat.R | 2 rstanemax-0.1.3/rstanemax/vignettes/emaxmodel.Rmd | 8 11 files changed, 274 insertions(+), 193 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <https://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>),
Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>),
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>),
Matthew E Watts [aut],
Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>),
Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>),
Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 5.0.2 dated 2020-07-30 and 5.0.3 dated 2020-11-24
DESCRIPTION | 32 MD5 | 645 NAMESPACE | 409 R/ArrayParameter-proto.R | 288 R/Collection-proto.R | 334 R/ConservationModifier-proto.R | 362 R/ConservationProblem-proto.R | 1230 R/Constraint-proto.R | 48 R/Decision-proto.R | 50 R/Id.R | 114 R/MiscParameter-proto.R | 208 R/Objective-proto.R | 44 R/OptimizationProblem-methods.R | 622 R/OptimizationProblem-proto.R | 402 R/Parameter-proto.R | 152 R/Parameters-proto.R | 330 R/Penalty-proto.R | 50 R/Portfolio-proto.R | 188 R/RcppExports.R | 382 R/ScalarParameter-proto.R | 258 R/Solver-proto.R | 296 R/Target-proto.R | 48 R/add_absolute_targets.R | 432 R/add_binary_decisions.R | 160 R/add_boundary_penalties.R | 658 R/add_connectivity_penalties.R | 1080 R/add_contiguity_constraints.R | 616 R/add_cplex_solver.R |only R/add_cuts_portfolio.R | 252 R/add_default_decisions.R | 34 R/add_default_objective.R | 18 R/add_default_portfolio.R | 32 R/add_default_solver.R | 103 R/add_default_targets.R | 18 R/add_extra_portfolio.R | 208 R/add_feature_contiguity_constraints.R | 748 R/add_feature_weights.R | 564 R/add_gap_portfolio.R | 268 R/add_gurobi_solver.R | 407 R/add_linear_penalties.R | 712 R/add_locked_in_constraints.R | 732 R/add_locked_out_constraints.R | 610 R/add_loglinear_targets.R | 313 R/add_lpsymphony_solver.R | 309 R/add_mandatory_allocation_constraints.R | 198 R/add_manual_bounded_constraints.R | 472 R/add_manual_locked_constraints.R | 492 R/add_manual_targets.R | 636 R/add_max_cover_objective.R | 362 R/add_max_features_objective.R | 314 R/add_max_phylo_div_objective.R | 558 R/add_max_phylo_end_objective.R | 586 R/add_max_utility_objective.R | 292 R/add_min_set_objective.R | 216 R/add_min_shortfall_objective.R | 290 R/add_neighbor_contraints.R | 694 R/add_proportion_decisions.R | 144 R/add_relative_targets.R | 332 R/add_rsymphony_solver.R | 328 R/add_semicontinuous_decisions.R | 168 R/add_shuffle_portfolio.R | 306 R/add_top_portfolio.R | 222 R/adjacency_matrix.R | 346 R/binary_stack.R | 102 R/boundary_matrix.R | 414 R/branch_matrix.R | 114 R/category_layer.R | 104 R/category_vector.R | 156 R/compile.R | 274 R/connectivity_matrix.R | 594 R/constraints.R | 188 R/data.R | 364 R/decisions.R | 160 R/deprecated.R | 154 R/distribute_load.R | 164 R/fast_extract.R | 318 R/feature_abundances.R | 324 R/feature_names.R | 134 R/feature_representation.R | 806 R/ferrier_score.R | 641 R/internal.R | 543 R/intersecting_units.R | 448 R/irreplaceability.R | 226 R/loglinear_interpolation.R | 154 R/magrittr-operators.R | 160 R/marxan_boundary_data_to_matrix.R | 314 R/marxan_problem.R | 728 R/misc.R | 84 R/new_optimization_problem.R | 42 R/number_of_features.R | 152 R/number_of_planning_units.R | 116 R/number_of_total_units.R | 128 R/number_of_zones.R | 154 R/objectives.R | 192 R/package.R | 170 R/parameters.R | 996 R/penalties.R | 176 R/portfolios.R | 216 R/pproto.R | 150 R/predefined_optimization_problem.R | 198 R/presolve_check.R | 578 R/print.R | 216 R/problem.R | 2010 R/proximity_matrix.R | 346 R/rarity_weighted_richness.R | 866 R/replacement_cost.R | 1164 R/rij_matrix.R | 274 R/run_calculations.R | 164 R/sf.R | 12 R/show.R | 140 R/simulate.R | 262 R/solve.R | 770 R/solvers.R | 228 R/targets.R | 150 R/tbl_df.R | 148 R/waiver.R | 62 R/zone_names.R | 140 R/zones.R | 362 R/zzz.R | 62 README.md | 1020 build/vignette.rds |binary inst/doc/gurobi_installation.Rmd | 382 inst/doc/gurobi_installation.html | 1063 inst/doc/prioritizr.Rmd | 1667 inst/doc/prioritizr.html | 3413 - inst/doc/publication_record.Rmd | 104 inst/doc/publication_record.html | 632 inst/doc/saltspring.Rmd | 475 inst/doc/saltspring.html | 1132 inst/doc/tasmania.Rmd | 451 inst/doc/tasmania.html |28490 ------------- inst/doc/zones.Rmd | 646 inst/doc/zones.html | 2171 inst/extdata/input.dat | 110 inst/extdata/simulate_data.R | 356 man/ArrayParameter-class.Rd | 200 man/Collection-class.Rd | 194 man/ConservationModifier-class.Rd | 256 man/ConservationProblem-class.Rd | 594 man/Constraint-class.Rd | 32 man/Decision-class.Rd | 34 man/MiscParameter-class.Rd | 166 man/Objective-class.Rd | 26 man/OptimizationProblem-class.Rd | 248 man/OptimizationProblem-methods.Rd | 288 man/Parameter-class.Rd | 118 man/Parameters-class.Rd | 180 man/Penalty-class.Rd | 34 man/Portfolio-class.Rd | 132 man/ScalarParameter-class.Rd | 182 man/Solver-class.Rd | 198 man/Target-class.Rd | 32 man/add_absolute_targets.Rd | 312 man/add_binary_decisions.Rd | 140 man/add_boundary_penalties.Rd | 496 man/add_connectivity_penalties.Rd | 834 man/add_contiguity_constraints.Rd | 420 man/add_cplex_solver.Rd |only man/add_cuts_portfolio.Rd | 180 man/add_default_decisions.Rd | 38 man/add_default_solver.Rd | 56 man/add_extra_portfolio.Rd | 150 man/add_feature_contiguity_constraints.Rd | 460 man/add_feature_weights.Rd | 426 man/add_gap_portfolio.Rd | 182 man/add_gurobi_solver.Rd | 206 man/add_linear_penalties.Rd | 422 man/add_locked_in_constraints.Rd | 476 man/add_locked_out_constraints.Rd | 472 man/add_loglinear_targets.Rd | 245 man/add_lsymphony_solver.Rd | 176 man/add_mandatory_allocation_constraints.Rd | 148 man/add_manual_bounded_constraints.Rd | 282 man/add_manual_locked_constraints.Rd | 280 man/add_manual_targets.Rd | 410 man/add_max_cover_objective.Rd | 314 man/add_max_features_objective.Rd | 254 man/add_max_phylo_div_objective.Rd | 460 man/add_max_phylo_end_objective.Rd | 464 man/add_max_utility_objective.Rd | 242 man/add_min_set_objective.Rd | 194 man/add_min_shortfall_objective.Rd | 244 man/add_neighbor_constraints.Rd | 384 man/add_proportion_decisions.Rd | 144 man/add_relative_targets.Rd | 306 man/add_rsymphony_solver.Rd | 164 man/add_semicontinuous_decisions.Rd | 160 man/add_shuffle_portfolio.Rd | 176 man/add_top_portfolio.Rd | 154 man/adjacency_matrix.Rd | 230 man/array_parameters.Rd | 270 man/as.Rd | 58 man/as.list.Rd | 38 man/binary_stack.Rd | 84 man/boundary_matrix.Rd | 228 man/branch_matrix.Rd | 92 man/category_layer.Rd | 90 man/category_vector.Rd | 108 man/compile.Rd | 116 man/connectivity_matrix.Rd | 428 man/constraints.Rd | 192 man/decisions.Rd | 164 man/distribute_load.Rd | 138 man/fast_extract.Rd | 138 man/feature_abundances.Rd | 290 man/feature_names.Rd | 80 man/feature_representation.Rd | 478 man/ferrier_score.Rd | 243 man/intersecting_units.Rd | 190 man/irreplaceability.Rd | 228 man/is.Rd | 42 man/loglinear_interpolation.Rd | 144 man/marxan_boundary_data_to_matrix.Rd | 114 man/marxan_problem.Rd | 388 man/matrix_parameters.Rd | 138 man/misc_parameter.Rd | 122 man/new_id.Rd | 70 man/new_optimization_problem.Rd | 48 man/new_waiver.Rd | 64 man/number_of_features.Rd | 86 man/number_of_planning_units.Rd | 74 man/number_of_total_units.Rd | 98 man/number_of_zones.Rd | 90 man/objectives.Rd | 194 man/parameters.Rd | 66 man/penalties.Rd | 180 man/pipe.Rd | 68 man/portfolios.Rd | 216 man/pproto.Rd | 88 man/predefined_optimization_problem.Rd | 142 man/presolve_check.Rd | 368 man/print.Rd | 108 man/prioritizr-deprecated.Rd | 144 man/prioritizr.Rd | 156 man/problem.Rd | 900 man/proximity_matrix.Rd | 224 man/rarity_weighted_richness.Rd | 304 man/replacement_cost.Rd | 446 man/rij_matrix.Rd | 144 man/run_calculations.Rd | 154 man/scalar_parameters.Rd | 244 man/show.Rd | 72 man/sim_data.Rd | 386 man/simulate_cost.Rd | 108 man/simulate_data.Rd | 94 man/simulate_species.Rd | 106 man/solve.Rd | 484 man/solvers.Rd | 230 man/targets.Rd | 140 man/tee.Rd | 80 man/tibble-methods.Rd | 104 man/zone_names.Rd | 84 man/zones.Rd | 204 tests/testthat.R | 36 tests/testthat/test_Id.R | 26 tests/testthat/test_OptimizationProblem.R | 246 tests/testthat/test_Waiver.R | 22 tests/testthat/test_add_absolute_targets.R | 452 tests/testthat/test_add_boundary_penalties.R | 842 tests/testthat/test_add_connectivity_penalties.R | 648 tests/testthat/test_add_contiguity_constraints.R | 542 tests/testthat/test_add_cuts_portfolio.R | 408 tests/testthat/test_add_extra_portfolio.R | 432 tests/testthat/test_add_feature_contiguity_constraints.R | 937 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Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.9.6 dated 2020-10-21 and 0.9.7 dated 2020-11-24
DESCRIPTION | 6 +- MD5 | 16 ++--- R/model.R | 7 +- R/runrecord.R | 6 +- R/safejoin.R | 2 build/vignette.rds |binary inst/doc/parameter-table.html | 125 +++++++++++++++++++++++++++++------------- man/as.model.Rd | 2 man/safe_join.data.frame.Rd | 2 9 files changed, 110 insertions(+), 56 deletions(-)
Title: Extreme Value Analysis
Description: General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between extRemes versions 2.0-12 dated 2020-05-03 and 2.1 dated 2020-11-24
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ man/CarcasonneHeat.Rd | 2 +- man/hwmi.Rd | 2 +- man/hwmid.Rd | 2 +- man/xbooter.Rd | 5 +++++ man/xtibber.Rd | 6 ++++++ 7 files changed, 26 insertions(+), 15 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression
model 'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel D. Sjoberg [aut] (<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.0.0 dated 2020-09-18 and 1.1.0 dated 2020-11-24
DESCRIPTION | 24 MD5 | 129 +- NAMESPACE | 61 + NEWS.md | 61 + R/broom.helpers-package.R | 38 R/helpers.R |only R/model_get_coefficients_type.R |only R/model_get_model.R |only R/model_get_nlevels.R |only R/model_identify_variables.R | 95 + R/model_list_contrasts.R | 16 R/model_list_terms_levels.R | 149 +- R/model_list_variables.R | 90 + R/reexport.R |only R/select_helpers.R |only R/select_utilities.R |only R/tidy_add_coefficients_type.R |only R/tidy_add_contrasts.R | 12 R/tidy_add_estimate_to_reference_rows.R | 97 + R/tidy_add_header_rows.R | 38 R/tidy_add_reference_rows.R | 44 R/tidy_add_term_labels.R | 33 R/tidy_add_variable_labels.R | 51 R/tidy_and_attach.R | 68 + R/tidy_identify_variables.R | 49 R/tidy_plus_plus.R | 58 - R/tidy_remove_intercept.R | 5 R/tidy_select_variables.R |only README.md | 230 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/tidy.R | 49 inst/doc/tidy.Rmd | 59 - inst/doc/tidy.html | 1085 +++++++++++++++++-- man/dot-clean_backticks.Rd |only man/dot-escape_regex.Rd |only man/dot-formula_list_to_named_list.Rd |only man/dot-generic_selector.Rd |only man/dot-select_to_varnames.Rd |only man/model_get_coefficients_type.Rd |only man/model_get_contrasts.Rd | 3 man/model_get_model.Rd |only man/model_get_model_frame.Rd | 3 man/model_get_model_matrix.Rd | 3 man/model_get_nlevels.Rd |only man/model_get_xlevels.Rd | 3 man/model_identify_variables.Rd | 16 man/model_list_contrasts.Rd | 7 man/model_list_terms_levels.Rd | 40 man/model_list_variables.Rd | 17 man/reexports.Rd | 43 man/select_helpers.Rd |only man/tidy_add_coefficients_type.Rd |only man/tidy_add_contrasts.Rd | 98 - man/tidy_add_estimate_to_reference_rows.Rd | 10 man/tidy_add_header_rows.Rd | 17 man/tidy_add_reference_rows.Rd | 26 man/tidy_add_term_labels.Rd | 25 man/tidy_add_variable_labels.Rd | 12 man/tidy_attach_model.Rd | 14 man/tidy_identify_variables.Rd | 26 man/tidy_plus_plus.Rd | 42 man/tidy_remove_intercept.Rd | 4 man/tidy_select_variables.Rd |only tests/spelling.R |only tests/testthat/test-add_coefficients_type.R |only tests/testthat/test-add_contrasts.R | 41 tests/testthat/test-add_estimate_to_reference_rows.R | 56 tests/testthat/test-add_header_rows.R | 75 - tests/testthat/test-add_reference_rows.R | 42 tests/testthat/test-add_term_labels.R | 19 tests/testthat/test-add_variable_labels.R | 11 tests/testthat/test-attach_and_detach.R | 22 tests/testthat/test-identify_variables.R | 173 ++- tests/testthat/test-select_helpers.R |only tests/testthat/test-select_variables.R |only tests/testthat/test-tidy_plus_plus.R | 290 +++++ vignettes/tidy.Rmd | 59 - 78 files changed, 3088 insertions(+), 650 deletions(-)
Title: Boosted Multivariate Trees for Longitudinal Data
Description: Implements Friedman's gradient descent boosting algorithm for modeling longitudinal response using multivariate tree base learners. Longitudinal response could be continuous, binary, nominal or ordinal. A time-covariate interaction effect is modeled using penalized B-splines (P-splines) with estimated adaptive smoothing parameter. Although the package is design for longitudinal data, it can handle cross-sectional data as well. Implementation details are provided in Pande et al. (2017), Mach Learn <DOI:10.1007/s10994-016-5597-1>.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Amol Pande <amoljpande@gmail.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between boostmtree versions 1.4.1 dated 2019-11-21 and 1.5.0 dated 2020-11-24
DESCRIPTION | 12 MD5 | 52 +-- NAMESPACE | 2 R/boostmtree.R | 576 ++++++++++++++++++++++++++++++++--------- R/boostmtree.news.R | 2 R/generic.predict.boostmtree.R | 424 ++++++++++++++++++++++++++---- R/marginalPlot.R | 81 ++++- R/partialPlot.R | 94 +++++- R/plot.boostmtree.R | 167 ++++++++--- R/predict.boostmtree.R | 4 R/print.boostmtree.R | 68 ++++ R/simLong.R | 2 R/utilities.R | 86 +++++- R/vimp.boostmtree.R | 408 +++++++++++++++++++++-------- R/vimpPlot.R | 53 ++- R/zzz.R | 2 data/AF.RData |binary data/spirometry.RData |binary inst/NEWS | 14 man/AF.Rd | 2 man/boostmtree.Rd | 40 ++ man/boostmtree_package.Rd | 3 man/marginalPlot.Rd | 35 +- man/partialPlot.Rd | 33 +- man/plot.boostmtree.Rd | 4 man/predict.boostmtree.Rd | 17 - man/vimpPlot.Rd | 10 27 files changed, 1705 insertions(+), 486 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 1.2.1 dated 2020-03-31 and 2.0.2 dated 2020-11-24
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Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.2-3571 dated 2020-10-10 and 0.3 dated 2020-11-24
fastmatrix-0.2-3571/fastmatrix/src/cpy_triangle.f |only fastmatrix-0.2-3571/fastmatrix/src/stats.c |only fastmatrix-0.3/fastmatrix/ChangeLog | 72 ++-- fastmatrix-0.3/fastmatrix/DESCRIPTION | 8 fastmatrix-0.3/fastmatrix/MD5 | 54 +-- fastmatrix-0.3/fastmatrix/NAMESPACE | 10 fastmatrix-0.3/fastmatrix/R/cholesky.R |only fastmatrix-0.3/fastmatrix/R/cov.R | 4 fastmatrix-0.3/fastmatrix/R/lu.R | 8 fastmatrix-0.3/fastmatrix/R/mahalanobis.R |only fastmatrix-0.3/fastmatrix/R/mardia.R |only fastmatrix-0.3/fastmatrix/R/norms.R | 4 fastmatrix-0.3/fastmatrix/R/ols.R | 6 fastmatrix-0.3/fastmatrix/R/sherman_morrison.R | 11 fastmatrix-0.3/fastmatrix/R/tri_mat.R |only fastmatrix-0.3/fastmatrix/inst/CITATION | 4 fastmatrix-0.3/fastmatrix/inst/include/fastmatrix.h | 34 + fastmatrix-0.3/fastmatrix/inst/include/fastmatrix_API.h | 188 ++++++++++ fastmatrix-0.3/fastmatrix/man/Mahalanobis.Rd |only fastmatrix-0.3/fastmatrix/man/cov.MSSD.Rd | 6 fastmatrix-0.3/fastmatrix/man/cov.weighted.Rd | 12 fastmatrix-0.3/fastmatrix/man/is.lower.tri.Rd |only fastmatrix-0.3/fastmatrix/man/kurtosis.Rd |only fastmatrix-0.3/fastmatrix/src/R_init_fastmatrix.c | 213 ++++++------ fastmatrix-0.3/fastmatrix/src/distance_API.c |only fastmatrix-0.3/fastmatrix/src/fastmatrix.h | 44 ++ fastmatrix-0.3/fastmatrix/src/ls_API.c |only fastmatrix-0.3/fastmatrix/src/mahalanobis.c |only fastmatrix-0.3/fastmatrix/src/mardia.c |only fastmatrix-0.3/fastmatrix/src/matrix_API.c | 284 +++++++++++++++- fastmatrix-0.3/fastmatrix/src/ols.c | 2 fastmatrix-0.3/fastmatrix/src/power_method.c | 6 fastmatrix-0.3/fastmatrix/src/sherman_morrison.c | 35 + fastmatrix-0.3/fastmatrix/src/stats_API.c |only fastmatrix-0.3/fastmatrix/src/utils.c | 24 - 35 files changed, 791 insertions(+), 238 deletions(-)
Title: Gaussian Process Models for Scalar and Functional Inputs
Description: Construction and smart selection of Gaussian process models
with emphasis on treatment of functional inputs. This package
offers: (i) flexible modeling of functional-input regression
problems through the fairly general Gaussian process model; (ii)
built-in dimension reduction for functional inputs; (iii)
heuristic optimization of the structural parameters of the model
(e.g., active inputs, kernel function, type of distance).
Metamodeling background is provided in
Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>.
The algorithm for structural parameter optimization is described
in <https://hal.archives-ouvertes.fr/hal-02532713>.
Author: Jose Betancourt [cre, aut],
François Bachoc [aut],
Thierry Klein [aut],
Deborah Idier [ctb],
Jeremy Rohmer [ctb]
Maintainer: Jose Betancourt <djbetancourt@uninorte.edu.co>
Diff between funGp versions 0.2.0 dated 2020-11-17 and 0.2.1 dated 2020-11-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 9 +++++++-- R/3_ant_admin.R | 3 +-- man/get_active_in.Rd | 3 +-- 5 files changed, 17 insertions(+), 14 deletions(-)