Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <http://www.iconplc.com/innovation/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Sebastian Ueckert [aut, cph],
Mike K. Smith [ctb],
Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.6 dated 2020-01-12 and 0.4.7 dated 2020-02-04
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++--------- NEWS.md | 3 ++ R/vpc_data.R | 1 inst/doc/access_xpdb_data.html | 46 +++++++++++------------------------- inst/doc/customize_plots.html | 46 +++++++++++------------------------- inst/doc/import_model_outputs.html | 46 +++++++++++------------------------- inst/doc/introduction.html | 46 +++++++++++------------------------- inst/doc/multiple_pages.html | 46 +++++++++++------------------------- inst/doc/vpc.html | 46 +++++++++++------------------------- man/vpc_data.Rd | 2 - tests/testthat/test-model-summary.R | 2 + 12 files changed, 109 insertions(+), 203 deletions(-)
Title: Airborne LiDAR Filtering Method Based on Cloth Simulation
Description: Cloth Simulation Filter (CSF) is an airborne LiDAR (Light Detection and Ranging) ground
points filtering algorithm which is based on cloth simulation. It tries to simulate the interactions
between the cloth nodes and the corresponding LiDAR points, the locations of the cloth nodes can be
determined to generate an approximation of the ground surface <https://www.mdpi.com/2072-4292/8/6/501/htm>.
Author: Jean-Romain Roussel [aut, cre, cph],
Jianbo Qi [aut, cph],
Wuming Zhang [cph],
Peng Wan [cph],
Hongtao Wang [cph],
State Key Laboratory of Remote Sensing Science, Institute of Remote
Sensing Science and Engineering, Beijing Normal University [cph]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between RCSF versions 1.0.1 dated 2018-11-14 and 1.0.2 dated 2020-02-04
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NEWS.md |only README.md | 33 ++++----------------------------- man/CSF.Rd | 12 +++++++++--- tests/testthat/test-CSF.R | 3 +-- 6 files changed, 25 insertions(+), 44 deletions(-)
Title: Bayesian Projected Normal Regression Models for Circular Data
Description: Fitting Bayesian multiple and mixed-effect regression models for
circular data based on the projected normal distribution. Both continuous
and categorical predictors can be included. Sampling from the posterior is
performed via an MCMC algorithm. Posterior descriptives of all parameters,
model fit statistics and Bayes factors for hypothesis tests for inequality
constrained hypotheses are provided. See Cremers, Mulder & Klugkist (2018)
<doi:10.1111/bmsp.12108> and Nuñez-Antonio & Guttiérez-Peña (2014)
<doi:10.1016/j.csda.2012.07.025>.
Author: Jolien Cremers [aut, cre]
Maintainer: Jolien Cremers <joliencremers@gmail.com>
Diff between bpnreg versions 1.0.2 dated 2019-12-08 and 1.0.3 dated 2020-02-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/bpnreg.R | 14 +++++++++----- R/classfunctions.R | 1 - man/BFc.Rd | 2 -- man/bpnreg.Rd | 13 ++++++++----- 7 files changed, 31 insertions(+), 22 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. Users can collect open-access avian recordings or enter their own data into a workflow that facilitates spectrographic visualization and measurement of acoustic parameters. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
(<https://orcid.org/0000-0003-3594-619X>),
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.1.20 dated 2020-01-11 and 1.1.21 dated 2020-02-04
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++------------- NEWS.md | 8 ++++++ R/catalog2pdf.R | 15 ++++++----- R/find_annotations.R | 48 +++++++++++++++++++++++++++++++----- R/find_peaks.R | 4 +-- R/lspec2pdf.R | 4 +-- R/selection_table.R | 42 +++++++++++++++++++++++++++---- R/warbleR-package.R | 4 +++ R/xcorr.R | 16 +++++++----- inst/doc/Intro_to_warbleR.html | 50 ++++++++++++++++++++++++-------------- inst/doc/warbleR_workflow_01.html | 2 - inst/doc/warbleR_workflow_02.html | 4 +-- inst/doc/warbleR_workflow_03.html | 6 ++-- man/catalog2pdf.Rd | 2 - man/find_annotations.Rd | 4 ++- man/find_peaks.Rd | 2 - man/warbleR.Rd | 4 +++ 18 files changed, 180 insertions(+), 77 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
RStudio, Inc. [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.7 dated 2019-12-19 and 0.8 dated 2020-02-04
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 10 +++ R/chrome.R | 109 ++++++++++++++++++++++++++---------------- inst/resources/css/resume.css | 4 + tests/test-travis.R | 5 + 6 files changed, 93 insertions(+), 51 deletions(-)
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jeffrey Horner [ctb],
Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.8 dated 2019-12-19 and 0.9 dated 2020-02-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/mime.R | 1 + 4 files changed, 13 insertions(+), 6 deletions(-)
Title: Methods for Calculating 'EQ-5D' Utility Index Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://www.euroqol.org>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://www.euroqol.org/eq-5d-instruments/eq-5d-3l-about>) or a five-level
(EQ-5D-5L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-5l-about>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension scores. 25 TTO and 11 VAS EQ-5D-3L value
sets including those for countries in Szende et al (2007)
<doi:10.1007/1-4020-5511-0> and Szende et al (2014)
<doi:10.1007/978-94-007-7596-1>, 20 EQ-5D-5L EQ-VT value sets from the EuroQol
website, and the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012)
<doi:10.1016/j.jval.2012.02.008> are included. Additionally, a shiny web tool is
included to enable the calculation, visualisation and automated statistical
analysis of EQ-5D index values via a web browser using EQ-5D dimension scores
stored in CSV or Excel files.
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.5.0 dated 2019-12-15 and 0.6.0 dated 2020-02-04
DESCRIPTION | 11 ++++++----- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/data.R | 5 +++-- R/shiny.R | 2 +- README.md | 4 ++-- data/vt.RData |binary inst/doc/eq5d.html | 8 ++++---- man/VT.Rd | 7 ++++--- man/eq5d-package.Rd | 2 +- tests/testthat/test-eq5d3l.R | 4 ++-- tests/testthat/test-eq5d5l.R | 9 +++++++++ 12 files changed, 51 insertions(+), 31 deletions(-)
Title: BiCluster Algorithms
Description: The main function biclust() provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0),
spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova,
Martin Sill, Roberto Theron, Luis Quintales, Friedrich
Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser <dr.sebastian.kaiser@gmail.com>
Diff between biclust versions 2.0.1 dated 2018-06-09 and 2.0.2 dated 2020-02-04
COPYING | 680 +++++++++++++++++++++---------------------- DESCRIPTION | 21 - MD5 | 40 +- NEWS | 14 R/aaa-biclust.r | 378 +++++++++++------------ R/biclustbarchart.r | 276 ++++++++--------- R/predict.r | 44 +- R/questmetmotif.r | 182 +++++------ R/questordmotif.r | 176 +++++------ README.md | 7 data/datalist | 6 man/BCBimax.rd | 114 +++---- man/BCCC.rd | 92 ++--- man/BCQuest.rd | 126 +++---- man/BCXmotifs.rd | 116 +++---- man/Biclust.rd | 92 ++--- man/BiclustMethod.rd | 46 +- man/biclust-method.rd | 90 ++--- man/isoverlapp.rd | 70 ++-- man/predict.rd | 60 +-- man/writeBiclusterResults.Rd | 3 21 files changed, 1316 insertions(+), 1317 deletions(-)
Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the
survey responses, but also the survey metadata, e.g. the original survey
questions and the answer options. The 'surveydata' package makes it easy to
keep track of this metadata, and to easily extract columns with
specific questions.
Author: Andrie de Vries [aut, cre, cph],
Evan Odell [ctb]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between surveydata versions 0.2.3 dated 2019-01-23 and 0.2.4 dated 2020-02-04
DESCRIPTION | 29 ++- MD5 | 120 +++++++-------- NAMESPACE | 8 - NEWS | 14 + R/cleandata.R | 13 + R/dplyr_verbs.R | 10 - R/encoding.R | 2 R/extract.R | 4 R/opentext.R | 2 R/pattern.R | 3 R/plots.R | 2 R/questions.R | 29 --- R/strings.R | 2 R/surveydata-deprecated.R | 40 +++++ R/surveydata-package.R | 2 R/surveydata.R | 1 R/varlabels.R | 9 - build/vignette.rds |binary inst/doc/surveydata.R | 30 +-- inst/doc/surveydata.html | 190 ++++++++++++++---------- inst/vignette_child/child.Rmd | 6 man/Extract.Rd | 125 ++++++++-------- man/as.data.frame.surveydata.Rd | 44 ++--- man/as.surveydata.Rd | 227 +++++++++++++++-------------- man/as_opentext_datatable.Rd | 47 +++--- man/cbind.surveydata.Rd | 30 +-- man/dplyr-surveydata.Rd | 97 ++++++------ man/dropout.Rd | 44 ++--- man/encToInt.Rd | 70 ++++----- man/fix_common_encoding_problems.Rd | 56 +++---- man/fix_levels_01.Rd | 68 ++++---- man/has_dont_know.Rd | 62 ++++---- man/intToEnc.Rd | 70 ++++----- man/is.surveydata.Rd | 32 ++-- man/lapply_names.Rd | 49 +++--- man/leveltest.Rd | 60 ++++--- man/membersurvey.Rd | 26 +-- man/merge.Rd | 36 ++-- man/merge_varlabels.Rd | 38 ++-- man/names.Rd | 41 ++--- man/pattern.Rd | 100 ++++++------ man/print_opentext.Rd | 51 +++--- man/question_order.Rd | 35 ++-- man/question_text.Rd | 112 +++++++------- man/question_text_common.Rd | 113 +++++++------- man/question_text_unique.Rd | 113 +++++++------- man/questions.Rd | 116 +++++++-------- man/remove_all_dont_know.Rd | 69 ++++---- man/remove_dont_know.Rd | 62 ++++---- man/rm.attrs.Rd | 28 +-- man/rm.pattern.Rd | 28 +-- man/split_common_unique.Rd | 50 +++--- man/strCommonUnique.Rd | 50 +++--- man/survey_plot_question.Rd | 59 +++---- man/survey_plot_satisfaction.Rd | 63 ++++---- man/survey_plot_title.Rd | 36 ++-- man/survey_plot_yes_no.Rd | 59 +++---- man/surveydata-deprecated.Rd | 133 ++++++++--------- man/surveydata-package.Rd | 278 ++++++++++++++++++------------------ man/varlabels.Rd | 95 ++++++------ man/which.q.Rd | 114 +++++++------- 61 files changed, 1805 insertions(+), 1697 deletions(-)
Title: Graphical Toolbox for Clustering and Classification of Data
Frames
Description: Graphical toolbox for clustering and classification of data frames.
It proposes a graphical interface to process clustering and classification methods on features
data-frames, and to view initial data as well as resulted cluster or classes. According to the
level of available labels, different approaches are proposed: unsupervised clustering,
semi-supervised clustering and supervised classification.
To assess the processed clusters or classes, the toolbox can import and show some supplementary
data formats: either profile/time series, or images.
These added information can help the expert to label clusters (clustering), or to constrain data
frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by
Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by
Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.
Author: Guillaume Wacquet [aut],
Pierre-Alexandre Hebert [aut, cre],
Emilie Poisson [aut],
Pierre Talon [aut]
Maintainer: Pierre-Alexandre Hebert <hebert@univ-littoral.fr>
Diff between RclusTool versions 0.91.2 dated 2020-01-09 and 0.91.3 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 15 +++++++++------ R/sampleClustering.R | 12 +++++++----- R/semisupTab.R | 5 +++-- R/supTab.R | 4 +++- R/unsupTab.R | 4 +++- inst/images/create.png |only inst/images/large_line.png |only inst/images/small_line.png |only man/RclusTool-package.Rd | 4 ++-- 10 files changed, 31 insertions(+), 21 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Standardisation of cluster validation statistics by random clusterings and
comparison between many clustering methods and numbers of clusters based on
this.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig <christian.hennig@unibo.it>
Maintainer: Christian Hennig <christian.hennig@unibo.it>
Diff between fpc versions 2.2-4 dated 2020-01-17 and 2.2-5 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/clusterboot.Rd | 18 +++++++++--------- man/kmeansCBI.Rd | 17 ++++++++--------- tests/Examples/fpc-Ex.Rout.save | 10 +++++----- 5 files changed, 30 insertions(+), 31 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 10.2 dated 2020-02-02 and 10.3 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/sim.rf.Rd | 3 --- 3 files changed, 6 insertions(+), 9 deletions(-)
Title: Automatic Description of Factorial Analysis
Description: Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Author: Simon Thuleau, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between FactoInvestigate versions 1.5 dated 2019-11-16 and 1.6 dated 2020-02-04
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/Investigate.R | 2 +- build/partial.rdb |binary 4 files changed, 9 insertions(+), 9 deletions(-)
More information about FactoInvestigate at CRAN
Permanent link
Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>
Diff between arrayhelpers versions 1.0-20160527 dated 2016-05-27 and 1.1-0 dated 2020-02-04
arrayhelpers-1.0-20160527/arrayhelpers/tests/tests.Rout.save |only arrayhelpers-1.1-0/arrayhelpers/DESCRIPTION | 11 +-- arrayhelpers-1.1-0/arrayhelpers/MD5 | 39 +++++------ arrayhelpers-1.1-0/arrayhelpers/R/ndim.R | 4 - arrayhelpers-1.1-0/arrayhelpers/man/array2df.Rd | 16 ++-- arrayhelpers-1.1-0/arrayhelpers/man/array2vec.Rd | 7 - arrayhelpers-1.1-0/arrayhelpers/man/arrayhelpers-package.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/arrayhelpers.unittest.Rd | 7 - arrayhelpers-1.1-0/arrayhelpers/man/colSums.Rd | 23 +++--- arrayhelpers-1.1-0/arrayhelpers/man/countrows.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/delold.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/dropdimnames.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/ensuredim.Rd | 3 arrayhelpers-1.1-0/arrayhelpers/man/groupsum.Rd | 18 +++-- arrayhelpers-1.1-0/arrayhelpers/man/makeNd.Rd | 12 ++- arrayhelpers-1.1-0/arrayhelpers/man/ndim.Rd | 4 - arrayhelpers-1.1-0/arrayhelpers/man/numericindex.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/rowsum.Rd | 7 - arrayhelpers-1.1-0/arrayhelpers/man/slice.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/stack.Rd | 1 arrayhelpers-1.1-0/arrayhelpers/man/ta.Rd | 7 - 21 files changed, 81 insertions(+), 84 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). This is a
reimplementation of the method suggested by Nuske et al. (2009)
<doi:10.1016/j.foreco.2009.09.050> using the libraries 'GEOS' and 'GDAL'
directly instead of through 'PostGIS'.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.1.3 dated 2019-06-13 and 0.1.4 dated 2020-02-04
DESCRIPTION | 10 - MD5 | 30 ++-- NEWS.md | 3 R/apcf-package.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary configure | 29 +++- configure.ac | 27 ++- inst/doc/intro.R | 10 - inst/doc/intro.html | 375 ++++++++++++++++++++++++++++++++++++++++------------ man/apcf-package.Rd | 2 man/dists2pcf.Rd | 3 man/pat2dists.Rd | 11 + man/plot.fv_pcf.Rd | 20 ++ man/sim_patterns.Rd | 16 +- 16 files changed, 401 insertions(+), 139 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau
(<https://www.census.gov/geo/maps-data/data/tiger-line.html>) and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tigris versions 0.9.1 dated 2020-01-13 and 0.9.2 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/national.R | 2 +- man/nation.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Reproducible Research with a Table of R Codes
Description: Makes documents containing plots and tables from a table of R codes.
Can make "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents with or without R code.
In the package, modularized 'shiny' app codes are provided. These modules are intended for reuse across applications.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between rrtable versions 0.1.6 dated 2020-01-29 and 0.1.7 dated 2020-02-04
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++----------- NEWS.md | 8 ++++++++ R/add_2plots.R | 8 +++++--- R/flextable2ztable.R | 4 ++-- R/plot2pptx.R | 27 +++++++++++++++++++++------ inst/doc/rrtable.html | 6 +++--- inst/pptxList/app.R | 2 +- inst/pptxList/rsconnect |only man/add_2plots.Rd | 3 +++ man/add_anyplot.Rd | 3 +++ man/flextable2ztable.Rd | 2 +- man/plot2office.Rd | 3 +++ 13 files changed, 65 insertions(+), 30 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] (Enable the support of .lax file and
extra byte attributes),
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R),
Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.3.4 dated 2019-09-19 and 1.3.5 dated 2020-02-04
rlas-1.3.4/rlas/R/deprecated.r |only rlas-1.3.4/rlas/man/deprecated.Rd |only rlas-1.3.5/rlas/DESCRIPTION | 14 ++--- rlas-1.3.5/rlas/MD5 | 43 +++++++--------- rlas-1.3.5/rlas/NAMESPACE | 4 - rlas-1.3.5/rlas/NEWS.md | 6 ++ rlas-1.3.5/rlas/R/check_content.r | 34 ++++++++++++ rlas-1.3.5/rlas/R/header_tools.r | 4 - rlas-1.3.5/rlas/R/las_specifications.r | 25 ++++++++- rlas-1.3.5/rlas/R/readLAS.r | 4 - rlas-1.3.5/rlas/R/writeLAS.r | 2 rlas-1.3.5/rlas/R/zzz.r | 2 rlas-1.3.5/rlas/README.md | 6 +- rlas-1.3.5/rlas/inst/include/rlasstreamer.h | 3 - rlas-1.3.5/rlas/man/check.Rd | 7 -- rlas-1.3.5/rlas/man/crs_tools.Rd | 7 +- rlas-1.3.5/rlas/man/extra_bytes_attribute_tools.Rd | 20 +++++-- rlas-1.3.5/rlas/man/las_specification_tools.Rd | 15 +++-- rlas-1.3.5/rlas/man/public_header_block_tools.Rd | 5 + rlas-1.3.5/rlas/man/read.las.Rd | 2 rlas-1.3.5/rlas/man/read.lasheader.Rd | 5 + rlas-1.3.5/rlas/man/write.las.Rd | 5 + rlas-1.3.5/rlas/src/rlasstreamer.cpp | 35 ++----------- rlas-1.3.5/rlas/tests/testthat/test-las-specification.R |only 24 files changed, 148 insertions(+), 100 deletions(-)
Title: Download and Manage Open Data from INEGI
Description: Download and manage data sets of statistical projects and geographic data created by Instituto Nacional de Estadistica y Geografia (INEGI). See <https://www.inegi.org.mx/>.
Author: Cesar Renteria [aut, cre]
Maintainer: Cesar Renteria <crenteria@albany.edu>
Diff between importinegi versions 1.0.0 dated 2019-08-05 and 1.1.0 dated 2020-02-04
importinegi-1.0.0/importinegi/inst/doc/my-vignette.R |only importinegi-1.0.0/importinegi/inst/doc/my-vignette.Rmd |only importinegi-1.0.0/importinegi/inst/doc/my-vignette.html |only importinegi-1.0.0/importinegi/vignettes/my-vignette.Rmd |only importinegi-1.1.0/importinegi/DESCRIPTION | 8 importinegi-1.1.0/importinegi/MD5 | 52 +-- importinegi-1.1.0/importinegi/NAMESPACE | 2 importinegi-1.1.0/importinegi/R/catalogo_inegi.R | 2 importinegi-1.1.0/importinegi/R/censo_municipal.R | 10 importinegi-1.1.0/importinegi/R/enigh_nuevaconstruccion.R | 155 +++++------ importinegi-1.1.0/importinegi/R/sig_caminos_descarga.R | 27 + importinegi-1.1.0/importinegi/R/sig_caminos_extrae.R | 24 - importinegi-1.1.0/importinegi/R/sig_marcogeo.R | 9 importinegi-1.1.0/importinegi/README.md | 15 - importinegi-1.1.0/importinegi/build/vignette.rds |binary importinegi-1.1.0/importinegi/inst/doc/importinegi.R |only importinegi-1.1.0/importinegi/inst/doc/importinegi.Rmd |only importinegi-1.1.0/importinegi/inst/doc/importinegi.html |only importinegi-1.1.0/importinegi/man/catalogo_inegi.Rd | 56 ++- importinegi-1.1.0/importinegi/man/censo_municipal.Rd | 64 ++-- importinegi-1.1.0/importinegi/man/censo_poblacion_ageb.Rd | 90 +++--- importinegi-1.1.0/importinegi/man/censo_poblacion_iter.Rd | 79 ++--- importinegi-1.1.0/importinegi/man/censo_poblacion_muestra.Rd | 58 ++-- importinegi-1.1.0/importinegi/man/censo_poblacion_rural.Rd | 54 +-- importinegi-1.1.0/importinegi/man/censo_poblacion_urbano.Rd | 60 ++-- importinegi-1.1.0/importinegi/man/enigh_nuevaconstruccion.Rd | 70 +--- importinegi-1.1.0/importinegi/man/enoe.Rd | 64 ++-- importinegi-1.1.0/importinegi/man/sig_caminos_descarga.Rd | 50 +-- importinegi-1.1.0/importinegi/man/sig_caminos_extrae.Rd | 62 ++-- importinegi-1.1.0/importinegi/man/sig_marcogeo.Rd | 64 ++-- importinegi-1.1.0/importinegi/vignettes/importinegi.Rmd |only 31 files changed, 540 insertions(+), 535 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages
part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.2.0 dated 2019-06-17 and 3.2.1 dated 2020-02-04
DESCRIPTION | 19 ++---- MD5 | 74 ++++++++++++------------ NAMESPACE | 3 NEWS | 17 +++++ R/008.BioC.R | 10 +-- R/AromaCellSequenceFile.R | 4 - R/AromaCellSequenceFile.REPEATS.R | 2 R/AromaCellSequenceFile.SNPs.R | 4 - R/AromaUnitCallFile.R | 4 - R/AromaUnitGenotypeCallFile.R | 10 +-- R/AromaUnitPscnBinarySet.R | 4 - R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R | 2 R/AromaUnitTotalCnBinarySet.R | 4 - R/BinnedScatter.R | 1 R/CopyNumberChromosomalModel.R | 4 - R/CopyNumberRegions.EXT.R | 4 - R/GLAD.EXTS.R | 5 + R/PairedPSCNData.R | 2 R/ProbePositionEffects.R | 2 R/RawGenomicSignals.R | 12 +-- R/RawGenomicSignals.segmentByCBS.R | 2 R/RawGenomicSignals.segmentByGLAD.R | 2 R/RawGenomicSignals.segmentByHaarSeg.R | 2 R/RawGenomicSignals.segmentByMPCBS.R | 2 R/SegmentedGenomicSignalsInterface.COLS.R | 2 R/SegmentedGenomicSignalsInterface.R | 4 - R/colBinnedSmoothing.R | 6 - R/colGaussianSmoothing.R | 2 R/colKernelSmoothing.R | 2 R/matrixBlockPolish.matrix.R | 4 - R/processTime.R | 2 R/profileCGH.plotProfile2.R | 5 + R/profileCGH.plotRawCNs.R | 5 + R/smoothWRMA.matrix.R | 2 R/smoothWSA.matrix.R | 2 man/BinnedScatter.Rd | 1 man/segmentByMPCBS.RawGenomicSignals.Rd | 10 ++- tests/RawGenomicSignals.SEG,MP.R | 10 ++- 38 files changed, 145 insertions(+), 107 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 2.0 dated 2018-12-18 and 3.0 dated 2020-02-04
fuzzySim-2.0/fuzzySim/R/fuzzySim-internal.R |only fuzzySim-2.0/fuzzySim/R/onAttach.R |only fuzzySim-3.0/fuzzySim/DESCRIPTION | 20 ++- fuzzySim-3.0/fuzzySim/MD5 | 87 +++++++++------- fuzzySim-3.0/fuzzySim/NAMESPACE | 11 +- fuzzySim-3.0/fuzzySim/NEWS | 129 ++++++++++++++++++++++++- fuzzySim-3.0/fuzzySim/R/Fav.R | 8 + fuzzySim-3.0/fuzzySim/R/bioThreat.R |only fuzzySim-3.0/fuzzySim/R/favClass.R |only fuzzySim-3.0/fuzzySim/R/getPreds.R | 20 +-- fuzzySim-3.0/fuzzySim/R/gridRecords.R |only fuzzySim-3.0/fuzzySim/R/modOverlap.R | 6 - fuzzySim-3.0/fuzzySim/R/multGLM.R | 63 ++++++++---- fuzzySim-3.0/fuzzySim/R/rangemapSim.R | 2 fuzzySim-3.0/fuzzySim/R/sharedFav.R |only fuzzySim-3.0/fuzzySim/data/rotif.env.rda |binary fuzzySim-3.0/fuzzySim/data/rotifers.rda |binary fuzzySim-3.0/fuzzySim/inst |only fuzzySim-3.0/fuzzySim/man/FDR.Rd | 16 +-- fuzzySim-3.0/fuzzySim/man/Fav.Rd | 16 +-- fuzzySim-3.0/fuzzySim/man/bioThreat.Rd |only fuzzySim-3.0/fuzzySim/man/corSelect.Rd | 18 +-- fuzzySim-3.0/fuzzySim/man/distPres.Rd | 7 - fuzzySim-3.0/fuzzySim/man/favClass.Rd |only fuzzySim-3.0/fuzzySim/man/fuzSim.Rd | 8 - fuzzySim-3.0/fuzzySim/man/fuzzyOverlay.Rd | 8 - fuzzySim-3.0/fuzzySim/man/fuzzyRangeChange.Rd | 20 +-- fuzzySim-3.0/fuzzySim/man/fuzzySim-package.Rd | 8 - fuzzySim-3.0/fuzzySim/man/getPreds.Rd | 6 - fuzzySim-3.0/fuzzySim/man/gridRecords.Rd |only fuzzySim-3.0/fuzzySim/man/integerCols.Rd | 10 - fuzzySim-3.0/fuzzySim/man/modOverlap.Rd | 6 - fuzzySim-3.0/fuzzySim/man/modelTrim.Rd | 2 fuzzySim-3.0/fuzzySim/man/multConvert.Rd | 11 -- fuzzySim-3.0/fuzzySim/man/multGLM.Rd | 68 +++++++------ fuzzySim-3.0/fuzzySim/man/multTSA.Rd | 12 +- fuzzySim-3.0/fuzzySim/man/multicol.Rd | 2 fuzzySim-3.0/fuzzySim/man/pairwiseRangemaps.Rd | 10 - fuzzySim-3.0/fuzzySim/man/percentTestData.Rd | 2 fuzzySim-3.0/fuzzySim/man/rangemapSim.Rd | 2 fuzzySim-3.0/fuzzySim/man/rotif.env.Rd | 2 fuzzySim-3.0/fuzzySim/man/rotifers.Rd | 2 fuzzySim-3.0/fuzzySim/man/sharedFav.Rd |only fuzzySim-3.0/fuzzySim/man/simFromSetOps.Rd | 6 - fuzzySim-3.0/fuzzySim/man/simMat.Rd | 4 fuzzySim-3.0/fuzzySim/man/spCodes.Rd | 7 - fuzzySim-3.0/fuzzySim/man/splist2presabs.Rd | 12 +- fuzzySim-3.0/fuzzySim/man/stepByStep.Rd | 6 - fuzzySim-3.0/fuzzySim/man/timer.Rd | 2 fuzzySim-3.0/fuzzySim/man/transpose.Rd | 6 - 50 files changed, 398 insertions(+), 227 deletions(-)
Title: Matrix Completion, Imputation, and Inpainting Methods
Description: Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between filling versions 0.2.0 dated 2018-09-16 and 0.2.1 dated 2020-02-04
DESCRIPTION | 15 ++++++++------- MD5 | 31 ++++++++++++++++--------------- NEWS.md |only R/RcppExports.R | 8 ++++---- R/fill_OptSpace.R | 2 ++ R/fill_SVDimpute.R | 2 ++ R/fill_SVT.R | 2 ++ R/fill_nuclear.R | 13 +++++++++++-- R/zzz.R | 12 +++++++++--- build/partial.rdb |binary man/fill_HardImpute.Rd | 9 +++++++-- man/fill_OptSpace.Rd | 2 ++ man/fill_SVDimpute.Rd | 2 ++ man/fill_SVT.Rd | 2 ++ man/fill_SoftImpute.Rd | 3 +-- src/RcppExports.cpp | 26 +++++++++++++------------- src/cppfill_SVT.cpp | 1 - 17 files changed, 81 insertions(+), 49 deletions(-)
Title: Download Data from the FAOSTAT Database of the Food and
Agricultural Organization (FAO) of the United Nations
Description: A list of functions to download statistics from FAOSTAT (database of the Food and Agricultural Organization of the United Nations) and WDI (database of the World Bank), and to perform some harmonization operations.
Author: Michael C. J. Kao <michael.kao@fao.org>, Markus Gesmann, Filippo Gheri
Maintainer: Paul Rougieux <paul.rougieux@gmail.com>
Diff between FAOSTAT versions 2.0 dated 2015-06-01 and 2.1.1 dated 2020-02-04
DESCRIPTION | 21 - MD5 | 126 +++--- NAMESPACE | 81 ++-- R/Aggregation.R | 395 ++++++++++---------- R/FAOSTAT-package.R | 1 R/FAOsearch.R | 212 +++++------ R/chConstruct.R | 66 +-- R/chgr.R | 90 ++-- R/constructSYB.R | 192 +++++----- R/faostat_bulk_download.R |only R/fillCountryCode.R | 68 +-- R/geogr.R | 80 ++-- R/getFAO.R | 6 R/getWDI.R | 110 ++--- R/getWDImetaData.R | 150 +++---- R/grConstruct.R | 128 +++--- R/indConstruct.R | 84 ++-- R/lsgr.R | 148 +++---- R/mergeSYB.R | 84 ++-- R/printLab.R | 58 +-- R/scaleUnit.R | 114 ++--- R/shConstruct.R | 134 +++--- R/translateCountryCode.R | 122 +++--- R/translateUnit.R | 96 ++--- build/vignette.rds |binary data/FAOcountryProfile.RData |binary data/FAOmetaTable.RData |binary data/FAOregionProfile.RData |binary demo/00Index | 2 inst/doc/FAOSTAT.R | 252 ++++++------- inst/doc/FAOSTAT.Rnw | 728 +++++++++++++++++++------------------- inst/doc/FAOSTAT.pdf |binary man/Aggregation.Rd | 144 +++---- man/CHMT.Rd | 54 +- man/FAOSTAT-package.Rd | 34 - man/FAOcheck.Rd | 77 ++-- man/FAOcountryProfile.Rd | 20 - man/FAOmetaTable.Rd | 22 - man/FAOregionProfile.Rd | 22 - man/FAOsearch.Rd | 26 - man/chConstruct.Rd | 68 +-- man/chgr.Rd | 68 +-- man/constructSYB.Rd | 103 ++--- man/download_faostat_bulk.Rd |only man/ebind.Rd | 44 +- man/fillCountryCode.Rd | 40 +- man/geogr.Rd | 68 +-- man/getFAO.Rd | 116 +++--- man/getFAOtoSYB.Rd | 121 +++--- man/getWDI.Rd | 90 ++-- man/getWDImetaData.Rd | 59 +-- man/getWDItoSYB.Rd | 113 +++-- man/grConstruct.Rd | 75 +-- man/indConstruct.Rd | 61 +-- man/lsgr.Rd | 87 ++-- man/mergeSYB.Rd | 56 +- man/overlap.Rd | 52 +- man/printLab.Rd | 46 +- man/read_faostat_bulk.Rd |only man/scaleUnit.Rd | 69 +-- man/shConstruct.Rd | 88 ++-- man/translateCountryCode.Rd | 42 +- man/translateUnit.Rd | 51 +- tests |only vignettes/FAOSTAT-concordance.tex |only vignettes/FAOSTAT.Rnw | 728 +++++++++++++++++++------------------- 66 files changed, 3144 insertions(+), 3048 deletions(-)
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 5.0.1 dated 2019-11-26 and 6.0.0 dated 2020-02-04
cgraph-5.0.1/cgraph/R/math.R |only cgraph-5.0.1/cgraph/man/cg_graph_gradients.Rd |only cgraph-5.0.1/cgraph/man/cg_graph_run.Rd |only cgraph-5.0.1/cgraph/src/math.c |only cgraph-5.0.1/cgraph/src/math.h |only cgraph-6.0.0/cgraph/DESCRIPTION | 8 cgraph-6.0.0/cgraph/MD5 | 182 +++--- cgraph-6.0.0/cgraph/NAMESPACE | 11 cgraph-6.0.0/cgraph/NEWS.md | 117 +--- cgraph-6.0.0/cgraph/R/array.R | 273 ++++----- cgraph-6.0.0/cgraph/R/function.R | 6 cgraph-6.0.0/cgraph/R/graph.R | 121 +--- cgraph-6.0.0/cgraph/R/internal.R | 47 + cgraph-6.0.0/cgraph/R/node.R | 22 cgraph-6.0.0/cgraph/R/session.R | 16 cgraph-6.0.0/cgraph/R/subset.R |only cgraph-6.0.0/cgraph/R/vector.R |only cgraph-6.0.0/cgraph/R/zzz.R | 2 cgraph-6.0.0/cgraph/man/approx_gradient.Rd | 12 cgraph-6.0.0/cgraph/man/bsum.Rd | 6 cgraph-6.0.0/cgraph/man/cg_abs.Rd | 6 cgraph-6.0.0/cgraph/man/cg_acos.Rd | 6 cgraph-6.0.0/cgraph/man/cg_acosh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_add.Rd | 8 cgraph-6.0.0/cgraph/man/cg_as_double.Rd | 10 cgraph-6.0.0/cgraph/man/cg_as_numeric.Rd | 10 cgraph-6.0.0/cgraph/man/cg_asin.Rd | 6 cgraph-6.0.0/cgraph/man/cg_asinh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_atan.Rd | 6 cgraph-6.0.0/cgraph/man/cg_atanh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_colsums.Rd | 6 cgraph-6.0.0/cgraph/man/cg_constant.Rd | 2 cgraph-6.0.0/cgraph/man/cg_cos.Rd | 6 cgraph-6.0.0/cgraph/man/cg_cosh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_crossprod.Rd | 8 cgraph-6.0.0/cgraph/man/cg_dim.Rd |only cgraph-6.0.0/cgraph/man/cg_div.Rd | 8 cgraph-6.0.0/cgraph/man/cg_exp.Rd | 6 cgraph-6.0.0/cgraph/man/cg_function.Rd | 4 cgraph-6.0.0/cgraph/man/cg_graph.Rd | 7 cgraph-6.0.0/cgraph/man/cg_graph_backward.Rd | 8 cgraph-6.0.0/cgraph/man/cg_graph_forward.Rd | 6 cgraph-6.0.0/cgraph/man/cg_graph_get.Rd |only cgraph-6.0.0/cgraph/man/cg_length.Rd |only cgraph-6.0.0/cgraph/man/cg_linear.Rd | 8 cgraph-6.0.0/cgraph/man/cg_ln.Rd | 6 cgraph-6.0.0/cgraph/man/cg_log10.Rd | 6 cgraph-6.0.0/cgraph/man/cg_log2.Rd | 6 cgraph-6.0.0/cgraph/man/cg_matmul.Rd | 6 cgraph-6.0.0/cgraph/man/cg_max.Rd | 4 cgraph-6.0.0/cgraph/man/cg_mean.Rd | 4 cgraph-6.0.0/cgraph/man/cg_min.Rd | 4 cgraph-6.0.0/cgraph/man/cg_mul.Rd | 8 cgraph-6.0.0/cgraph/man/cg_ncol.Rd |only cgraph-6.0.0/cgraph/man/cg_neg.Rd | 6 cgraph-6.0.0/cgraph/man/cg_nrow.Rd |only cgraph-6.0.0/cgraph/man/cg_operator.Rd | 4 cgraph-6.0.0/cgraph/man/cg_parameter.Rd | 2 cgraph-6.0.0/cgraph/man/cg_pmax.Rd | 6 cgraph-6.0.0/cgraph/man/cg_pmin.Rd | 6 cgraph-6.0.0/cgraph/man/cg_pos.Rd | 6 cgraph-6.0.0/cgraph/man/cg_pow.Rd | 8 cgraph-6.0.0/cgraph/man/cg_prod.Rd | 4 cgraph-6.0.0/cgraph/man/cg_rowsums.Rd | 4 cgraph-6.0.0/cgraph/man/cg_session_graph.Rd | 2 cgraph-6.0.0/cgraph/man/cg_sigmoid.Rd | 6 cgraph-6.0.0/cgraph/man/cg_sin.Rd | 6 cgraph-6.0.0/cgraph/man/cg_sinh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_sqrt.Rd | 6 cgraph-6.0.0/cgraph/man/cg_square.Rd | 6 cgraph-6.0.0/cgraph/man/cg_sub.Rd | 8 cgraph-6.0.0/cgraph/man/cg_subset1.Rd |only cgraph-6.0.0/cgraph/man/cg_subset2.Rd |only cgraph-6.0.0/cgraph/man/cg_sum.Rd | 4 cgraph-6.0.0/cgraph/man/cg_t.Rd | 6 cgraph-6.0.0/cgraph/man/cg_tan.Rd | 6 cgraph-6.0.0/cgraph/man/cg_tanh.Rd | 6 cgraph-6.0.0/cgraph/man/cg_tcrossprod.Rd | 8 cgraph-6.0.0/cgraph/man/dots.Rd |only cgraph-6.0.0/cgraph/src/class.c | 18 cgraph-6.0.0/cgraph/src/class.h | 27 cgraph-6.0.0/cgraph/src/function.c | 47 - cgraph-6.0.0/cgraph/src/function.h | 2 cgraph-6.0.0/cgraph/src/graph.c | 650 ++++------------------- cgraph-6.0.0/cgraph/src/graph.h | 16 cgraph-6.0.0/cgraph/src/init.c | 53 + cgraph-6.0.0/cgraph/src/internal.c | 107 +++ cgraph-6.0.0/cgraph/src/internal.h | 4 cgraph-6.0.0/cgraph/src/node.c | 439 +++++---------- cgraph-6.0.0/cgraph/src/node.h | 26 cgraph-6.0.0/cgraph/src/session.c | 15 cgraph-6.0.0/cgraph/src/session.h | 2 cgraph-6.0.0/cgraph/src/stack.c | 2 cgraph-6.0.0/cgraph/src/stack.h | 2 cgraph-6.0.0/cgraph/src/vector.c |only cgraph-6.0.0/cgraph/src/vector.h |only cgraph-6.0.0/cgraph/tests/testthat.R | 16 cgraph-6.0.0/cgraph/tests/testthat/test_array.R | 44 - cgraph-6.0.0/cgraph/tests/testthat/test_graph.R | 52 - cgraph-6.0.0/cgraph/tests/testthat/test_math.R | 59 -- cgraph-6.0.0/cgraph/tests/testthat/test_subset.R |only 101 files changed, 1185 insertions(+), 1524 deletions(-)
Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms
using adequate sample sizes for power and accuracy. Implements the
methodology originally presented in Campelo and Takahashi (2019)
<doi:10.1007/s10732-018-9396-7>
for the comparison of two algorithms, and later generalised in
Campelo and Wanner (Submitted, 2019) <arxiv:1908.01720>.
Author: Felipe Campelo [aut, cre],
Fernanda Takahashi [ctb],
Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <f.campelo@aston.ac.uk>
Diff between CAISEr versions 1.0.15 dated 2019-08-19 and 1.0.16 dated 2020-02-04
DESCRIPTION | 12 ++++----- MD5 | 36 ++++++++++++++-------------- NEWS.md | 4 +++ R/onAttach.R | 2 - R/se_boot.R | 5 ++- README.md | 3 +- build/vignette.rds |binary inst/doc/Adapting_Algorithm_for_CAISEr.R | 22 ++++++++--------- inst/doc/Adapting_Algorithm_for_CAISEr.html | 25 ++++++++----------- man/calc_instances.Rd | 17 +++++++++---- man/calc_nreps.Rd | 24 ++++++++++++++---- man/calc_se.Rd | 9 +++++-- man/dummyalgo.Rd | 8 +++--- man/plot.CAISEr.Rd | 12 +++++++-- man/plot.nreps.Rd | 14 ++++++++-- man/print.CAISEr.Rd | 3 -- man/run_experiment.Rd | 36 ++++++++++++++++++++-------- man/se_boot.Rd | 4 +-- man/summary.CAISEr.Rd | 3 -- 19 files changed, 149 insertions(+), 90 deletions(-)
Title: A Client for the 'MTurk' Requester API
Description: Provides access to the latest 'Amazon Mechanical Turk' ('MTurk') <https://www.mturk.com> Requester API (version '2017–01–17'), replacing the now deprecated 'MTurkR' package.
Author: Tyler Burleigh [aut, cre] (https://twitter.com/tylerburleigh),
Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>),
Solomon Messing [ctb],
Sean Murphy [ctb],
Jonathan Chang [ctb],
Andrew Brown [ctb]
Maintainer: Tyler Burleigh <tylerburleigh@gmail.com>
Diff between pyMTurkR versions 1.1 dated 2019-09-05 and 1.1.4 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/AssignQualification.R | 5 +++++ R/CreateHIT.R | 9 ++++++--- R/GenerateHITsFromTemplate.R | 1 - R/GetAssignment.R | 1 + R/GetClient.R | 11 ++++------- R/GrantBonus.R | 2 +- R/ToDataFrame.R | 12 ++++++++++++ README.md | 15 +++++++++++---- man/CreateHIT.Rd | 4 ++-- man/GenerateHITsFromTemplate.Rd | 2 -- man/GetClient.Rd | 6 +----- 13 files changed, 59 insertions(+), 41 deletions(-)
Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.20 dated 2019-12-12 and 0.21 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ inst/doc/pritikin-schmidt.R | 12 ++++++++---- inst/doc/pritikin-schmidt.Rnw | 21 ++++++++++++++------- inst/doc/pritikin-schmidt.pdf |binary tools/rox | 2 +- tools/vignetter |only vignettes/pritikin-schmidt.Rnw | 21 ++++++++++++++------- 8 files changed, 48 insertions(+), 29 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes several measures for structural balance as introduced by Cartwright and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various centrality indices, and projections of signed two-mode networks introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between signnet versions 0.5.0 dated 2020-01-24 and 0.5.1 dated 2020-02-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ inst/doc/signed_2mode.html | 8 ++++---- inst/doc/signed_networks.html | 4 ++-- src/circArc.cpp | 2 +- tests/testthat/test-centrality_indices.R | 8 ++++---- 7 files changed, 25 insertions(+), 20 deletions(-)
Title: Polynomials in R
Description: Implements univariate polynomial operations in R, including
polynomial arithmetic, finding zeros, plotting, and some operations on
lists of polynomials.
Author: Bill Venables, with contribution by Kurt Hornik and Georgi Boshnakov
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between PolynomF versions 2.0-2 dated 2019-06-18 and 2.0-3 dated 2020-02-04
PolynomF-2.0-2/PolynomF/man/defunct.Rd |only PolynomF-2.0-3/PolynomF/DESCRIPTION | 10 PolynomF-2.0-3/PolynomF/MD5 | 58 - PolynomF-2.0-3/PolynomF/NAMESPACE | 10 PolynomF-2.0-3/PolynomF/R/Orthogonal_polynomials.R | 386 ++++------ PolynomF-2.0-3/PolynomF/R/PolynomF.R | 130 +-- PolynomF-2.0-3/PolynomF/build/vignette.rds |binary PolynomF-2.0-3/PolynomF/inst/doc/polynomials.R | 16 PolynomF-2.0-3/PolynomF/inst/doc/polynomials.pdf |binary PolynomF-2.0-3/PolynomF/man/Ops.polynom.Rd | 2 PolynomF-2.0-3/PolynomF/man/as.character.polynom.Rd | 3 PolynomF-2.0-3/PolynomF/man/plot.polynom.Rd | 41 - PolynomF-2.0-3/PolynomF/man/poly_calc.Rd | 9 PolynomF-2.0-3/PolynomF/man/poly_orth.Rd | 5 PolynomF-2.0-3/PolynomF/man/print.polynom.Rd | 3 PolynomF-2.0-3/PolynomF/man/zap.Rd | 2 PolynomF-2.0-3/PolynomF/src/poly_mult.c |only PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-10-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-10-2.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-11-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-11-2.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-2-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-3-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-4-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-7-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-7-2.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-8-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-8-2.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-9-1.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-9-2.pdf |binary PolynomF-2.0-3/PolynomF/vignettes/polynomials_files/figure-latex/unnamed-chunk-9-3.pdf |binary 31 files changed, 337 insertions(+), 338 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between set6 versions 0.1.0 dated 2019-12-23 and 0.1.1 dated 2020-02-04
set6-0.1.0/set6/man/absComplement.Rd |only set6-0.1.1/set6/DESCRIPTION | 24 - set6-0.1.1/set6/MD5 | 157 ++++----- set6-0.1.1/set6/NAMESPACE | 2 set6-0.1.1/set6/NEWS.md | 19 + set6-0.1.1/set6/R/Properties.R | 4 set6-0.1.1/set6/R/Set.R | 133 ++++---- set6-0.1.1/set6/R/SetWrapper.R | 18 - set6-0.1.1/set6/R/SetWrapper_ComplementSet.R | 6 set6-0.1.1/set6/R/SetWrapper_ExponentSet.R | 2 set6-0.1.1/set6/R/SetWrapper_PowersetSet.R | 2 set6-0.1.1/set6/R/SetWrapper_ProductSet.R | 2 set6-0.1.1/set6/R/SetWrapper_UnionSet.R | 2 set6-0.1.1/set6/R/Set_ConditionalSet.R | 10 set6-0.1.1/set6/R/Set_FuzzySet.R | 25 - set6-0.1.1/set6/R/Set_FuzzySet_FuzzyTuple.R | 19 - set6-0.1.1/set6/R/Set_Interval.R | 53 +-- set6-0.1.1/set6/R/Set_Interval_SpecialSet.R | 39 +- set6-0.1.1/set6/R/Set_Tuple.R | 36 +- set6-0.1.1/set6/R/Set_UniversalSet.R |only set6-0.1.1/set6/R/helpers.R | 20 - set6-0.1.1/set6/R/operation_cleaner.R | 5 set6-0.1.1/set6/R/operation_powerset.R | 34 +- set6-0.1.1/set6/R/operation_setcomplement.R | 42 +- set6-0.1.1/set6/R/operation_setintersect.R | 18 - set6-0.1.1/set6/R/operation_setpower.R | 3 set6-0.1.1/set6/R/operation_setunion.R | 19 + set6-0.1.1/set6/R/set6-deprecated.R |only set6-0.1.1/set6/R/setSymbol.R | 29 - set6-0.1.1/set6/R/zzz.R | 4 set6-0.1.1/set6/README.md | 163 +++++++--- set6-0.1.1/set6/build/vignette.rds |binary set6-0.1.1/set6/inst/doc/set6.R | 24 - set6-0.1.1/set6/inst/doc/set6.html | 21 - set6-0.1.1/set6/man/ComplementSet.Rd | 3 set6-0.1.1/set6/man/Complex.Rd | 3 set6-0.1.1/set6/man/ConditionalSet.Rd | 8 set6-0.1.1/set6/man/ExponentSet.Rd | 3 set6-0.1.1/set6/man/ExtendedReals.Rd | 3 set6-0.1.1/set6/man/FuzzySet.Rd | 11 set6-0.1.1/set6/man/FuzzyTuple.Rd | 11 set6-0.1.1/set6/man/Integers.Rd | 3 set6-0.1.1/set6/man/Interval.Rd | 12 set6-0.1.1/set6/man/Naturals.Rd | 3 set6-0.1.1/set6/man/NegIntegers.Rd | 3 set6-0.1.1/set6/man/NegRationals.Rd | 3 set6-0.1.1/set6/man/NegReals.Rd | 3 set6-0.1.1/set6/man/PosIntegers.Rd | 3 set6-0.1.1/set6/man/PosNaturals.Rd | 3 set6-0.1.1/set6/man/PosRationals.Rd | 3 set6-0.1.1/set6/man/PosReals.Rd | 3 set6-0.1.1/set6/man/PowersetSet.Rd | 3 set6-0.1.1/set6/man/ProductSet.Rd | 3 set6-0.1.1/set6/man/Rationals.Rd | 3 set6-0.1.1/set6/man/Reals.Rd | 3 set6-0.1.1/set6/man/Set.Rd | 14 set6-0.1.1/set6/man/Tuple.Rd | 14 set6-0.1.1/set6/man/UnionSet.Rd | 3 set6-0.1.1/set6/man/UniversalSet.Rd |only set6-0.1.1/set6/man/absComplement-deprecated.Rd |only set6-0.1.1/set6/man/contains.Rd | 1 set6-0.1.1/set6/man/equals.Rd | 1 set6-0.1.1/set6/man/isSubset.Rd | 1 set6-0.1.1/set6/man/set6-deprecated.Rd |only set6-0.1.1/set6/man/setcomplement.Rd | 11 set6-0.1.1/set6/man/universe.Rd | 4 set6-0.1.1/set6/tests/testthat/test_misc_helpers.R | 10 set6-0.1.1/set6/tests/testthat/test_operation_powerset.R | 5 set6-0.1.1/set6/tests/testthat/test_operations_setcomplement.R | 6 set6-0.1.1/set6/tests/testthat/test_operations_setpower.R | 6 set6-0.1.1/set6/tests/testthat/test_operations_setproduct.R | 16 set6-0.1.1/set6/tests/testthat/test_operations_setunion.R | 2 set6-0.1.1/set6/tests/testthat/test_set.R | 55 +-- set6-0.1.1/set6/tests/testthat/test_set_conditionalset.R | 6 set6-0.1.1/set6/tests/testthat/test_set_fuzzyset.R | 48 +- set6-0.1.1/set6/tests/testthat/test_set_fuzzyset_fuzzytuple.R | 48 +- set6-0.1.1/set6/tests/testthat/test_set_interval.R | 16 set6-0.1.1/set6/tests/testthat/test_set_tuple.R | 32 - set6-0.1.1/set6/tests/testthat/test_set_universalset.R |only set6-0.1.1/set6/tests/testthat/test_setwrapper.R | 10 set6-0.1.1/set6/tests/testthat/test_setwrapper_complementset.R | 18 - set6-0.1.1/set6/tests/testthat/test_setwrapper_productset.R | 14 set6-0.1.1/set6/tests/testthat/test_setwrapper_unionset.R | 2 83 files changed, 741 insertions(+), 630 deletions(-)
Title: Relationship Between Species and Groups of Sites
Description: Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].
Author: Miquel De Cáceres [aut, cre],
Florian Jansen [aut],
Noah Dell [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between indicspecies versions 1.7.8 dated 2019-11-05 and 1.7.9 dated 2020-02-04
DESCRIPTION | 14 +++++----- MD5 | 22 ++++++++-------- NEWS.md | 3 ++ R/indicators.r | 5 ++- R/multipatt.r | 51 +++++++++++++++++++++++--------------- R/signassoc.r | 19 +++++++++++--- build/vignette.rds |binary inst/doc/PigeonExample.pdf |binary inst/doc/indicspeciesTutorial.pdf |binary man/indicators.Rd | 5 ++- man/multipatt.Rd | 7 +++-- man/signassoc.Rd | 7 +++-- 12 files changed, 85 insertions(+), 48 deletions(-)
Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut],
Jose Luis Aznarte [ctb],
Matthieu Stigler [aut],
Ho Tsung-wu [cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between tsDyn versions 10-1.1 dated 2020-01-10 and 10-1.2 dated 2020-02-04
tsDyn-10-1.1/tsDyn/inst |only tsDyn-10-1.2/tsDyn/DESCRIPTION | 8 tsDyn-10-1.2/tsDyn/MD5 | 15 tsDyn-10-1.2/tsDyn/R/setar.sim.R | 552 ++++++++++++++++---------------- tsDyn-10-1.2/tsDyn/man/setar.Rd | 1 tsDyn-10-1.2/tsDyn/man/setar.sim.Rd | 178 +++++----- tsDyn-10-1.2/tsDyn/man/setarTest.Rd | 148 ++++---- tsDyn-10-1.2/tsDyn/man/toLatex.setar.Rd | 68 +-- 8 files changed, 482 insertions(+), 488 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.8 dated 2019-03-08 and 0.9.1 dated 2020-02-04
DESCRIPTION | 8 +- MD5 | 104 ++++++++++++++++----------------- R/CrossValidation.R | 20 +++--- R/EMLeastSquaresClassifier.R | 1 R/Generics.R | 1 R/HelperFunctions.R | 2 R/ICLeastSquaresClassifier.R | 3 R/KernelLeastSquaresClassifier.R | 4 - R/LearningCurve.R | 17 ++--- R/LeastSquaresClassifier.R | 10 --- R/LinearDiscriminantClassifier.R | 2 R/LinearSVM.R | 2 R/LogisticLossClassifier.R | 2 R/LogisticRegression.R | 28 +++++++- R/MCNearestMeanClassifier.R | 4 - R/MCPLDA.R | 6 - R/MajorityClassClassifier.R | 2 R/NearestMeanClassifier.R | 4 - R/NormalBasedClassifier.R | 2 R/Plotting.R | 2 R/QuadraticDiscriminantClassifier.R | 2 R/SelfLearning.R | 2 R/TSVM.R | 2 R/USMLeastSquaresClassifier.R | 8 -- R/WellSVM.R | 8 +- R/svmlin.R | 2 README.md | 53 +++++++++------- man/CrossValidationSSL.Rd | 2 man/EMLeastSquaresClassifier.Rd | 2 man/ICLeastSquaresClassifier.Rd | 4 - man/KernelLeastSquaresClassifier.Rd | 2 man/LeastSquaresClassifier.Rd | 2 man/LinearDiscriminantClassifier.Rd | 2 man/MCNearestMeanClassifier.Rd | 6 - man/NearestMeanClassifier.Rd | 4 - man/QuadraticDiscriminantClassifier.Rd | 2 man/TSVM.Rd | 2 man/clapply.Rd | 2 man/find_a_violated_label.Rd | 2 man/gaussian_kernel.Rd | 6 - man/minimaxlda.Rd | 2 man/posterior-methods.Rd | 6 + man/rssl-predict.Rd | 27 +++----- man/stat_classifier.Rd | 2 man/svdinvsqrtm.Rd | 4 - man/wlda.Rd | 2 src/ssl.cpp | 5 + src/ssl.h | 2 src/svm.cpp | 2 src/utils.cpp | 6 - tests/testthat.R | 1 tests/testthat/test-LearningCurves.R | 1 tools/example-1.png |binary 53 files changed, 199 insertions(+), 200 deletions(-)
Title: Mixture and Composite Distributions
Description: A flexible computational framework for mixture distributions with the focus on the composite models.
Author: Lukas Sablica [aut, cre] (<https://orcid.org/0000-0001-9166-4563>),
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between mistr versions 0.0.2 dated 2019-07-25 and 0.0.3 dated 2020-02-04
DESCRIPTION | 11 ++++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/fit_risk.R | 4 ++++ R/mixdist.R | 1 - R/standist.R | 38 ++++++++++++++++++++++++++++++++++++++ inst/CITATION |only inst/doc/mistr-extensions.pdf |binary inst/doc/mistr-introduction.pdf |binary man/q_approxfun.Rd |only man/qlim_mixdist.Rd | 2 -- 12 files changed, 72 insertions(+), 17 deletions(-)
Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct
social-ecological models that simulate the management of populations and
stakeholder actions. These models build off of a previously developed
management strategy evaluation (MSE) framework to simulate all aspects of
management: population dynamics, manager observation of populations, manager
decision making, and stakeholder responses to management decisions. The
newly developed generalised management strategy evaluation (GMSE)
framework uses genetic algorithms to mimic the decision-making process of
managers and stakeholders under conditions of change, uncertainty, and
conflict. Simulations can be run using gmse(), gmse_apply(), and
gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>),
Nils Bunnefeld [ctb, fnd] (<https://orcid.org/0000-0002-1349-4463>),
Jeremy Cusack [ctb] (<https://orcid.org/0000-0003-3004-1586>),
Isabel Jones [ctb] (<https://orcid.org/0000-0002-8361-1370>),
Jeroen Minderman [ctb] (<https://orcid.org/0000-0002-8451-5540>),
Erlend Nilsen [ctb] (<https://orcid.org/0000-0002-5119-8331>),
Rocio Pozo [ctb] (<https://orcid.org/0000-0002-7546-8076>),
Sarobidy Rakotonarivo [ctb] (<https://orcid.org/0000-0002-8032-1431>),
Bram Van Moorter [ctb] (<https://orcid.org/0000-0002-3196-1993>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between GMSE versions 0.4.0.11 dated 2019-03-18 and 0.4.0.13 dated 2020-02-04
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/manager.R | 1 - R/observation.R | 1 - R/user.R | 1 - README.md | 2 +- build/vignette.rds |binary man/manager.Rd | 2 -- man/observation.Rd | 2 -- man/user.Rd | 2 -- 10 files changed, 13 insertions(+), 22 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [aut, ctb, cph],
Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 0.1-17 dated 2019-10-14 and 0.1-18 dated 2020-02-04
DESCRIPTION | 10 MD5 | 58 - NAMESPACE | 9 R/get_membership.R | 2 R/get_model.R | 8 R/get_transformed_data.R | 2 R/make_mcmc.R | 21 R/make_models.R | 11 R/print_RTMPT.R | 6 R/set_params.R | 3 R/set_resps.R | 3 R/simulate_rtmpt.R | 77 ++ R/simulate_rtmpt_SBC.R | 67 -- build/vignette.rds |binary inst/doc/rtmpt_intro.R | 364 +++++------ inst/doc/rtmpt_intro.Rmd | 720 +++++++++++------------ inst/doc/rtmpt_intro.html | 1423 +++++++++++++++++++++++++--------------------- man/SimData.Rd | 110 +-- man/fit_rtmpt.Rd | 309 +++++---- man/fit_rtmpt_SBC.Rd | 305 +++++---- man/set_params.Rd | 154 ++-- man/set_resps.Rd | 114 +-- man/sim_rtmpt_data.Rd | 288 ++++----- man/sim_rtmpt_data_SBC.Rd | 212 +++--- man/to_rtmpt_data.Rd | 112 +-- man/to_rtmpt_model.Rd | 216 +++--- src/additions.cpp | 1 src/diagnosis.cpp | 2 src/invtri.c | 1 vignettes/rtmpt_intro.Rmd | 720 +++++++++++------------ 30 files changed, 2774 insertions(+), 2554 deletions(-)
Title: Project Multidimensional Data in 2D Space
Description: An implementation of the radviz projection in R. It enables the visualization of
multidimensional data while maintaining the relation to the original dimensions.
This package provides functions to create and plot radviz projections, and a number of summary
plots that enable comparison and analysis. For reference see
Ankerst *et al.* (1996) (<http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation,
see Di Caro *et al* 2012 (<http://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>) for the original method for dimensional
anchor arrangements.
Author: Yann Abraham [aut, cre]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
Diff between Radviz versions 0.8.1 dated 2020-01-10 and 0.8.2 dated 2020-02-04
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 5 + R/do.L.R | 17 ++-- R/do.radviz.R | 13 ++- R/smoothRadviz.R | 1 inst/doc/single_cell_projections.R | 13 ++- inst/doc/single_cell_projections.Rmd | 13 ++- inst/doc/single_cell_projections.html | 140 ++++++++++++++++++---------------- man/do.L.Rd | 4 man/smoothRadviz.Rd | 2 vignettes/single_cell_projections.Rmd | 13 ++- 12 files changed, 147 insertions(+), 102 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.4.4-5.1 dated 2019-01-31 and 0.4.4-7 dated 2020-02-04
pairwise-0.4.4-5.1/pairwise/R/summary.pair.S.R |only pairwise-0.4.4-5.1/pairwise/R/summary.pairwise.item.fit.R |only pairwise-0.4.4-5.1/pairwise/R/summary.pairwise.person.fit.R |only pairwise-0.4.4-5.1/pairwise/man/summary.pair.S.Rd |only pairwise-0.4.4-5.1/pairwise/man/summary.pairwise.item.fit.Rd |only pairwise-0.4.4-5.1/pairwise/man/summary.pairwise.person.fit.Rd |only pairwise-0.4.4-7/pairwise/DESCRIPTION | 9 pairwise-0.4.4-7/pairwise/MD5 | 127 +-- pairwise-0.4.4-7/pairwise/NAMESPACE | 29 pairwise-0.4.4-7/pairwise/NEWS | 16 pairwise-0.4.4-7/pairwise/R/ftab.R | 8 pairwise-0.4.4-7/pairwise/R/grm.R | 276 +++---- pairwise-0.4.4-7/pairwise/R/i.pvx.super.R | 2 pairwise-0.4.4-7/pairwise/R/logLik.pers.R | 132 +-- pairwise-0.4.4-7/pairwise/R/pairSE.R | 214 +++--- pairwise-0.4.4-7/pairwise/R/pairwise-package.r | 132 +-- pairwise-0.4.4-7/pairwise/R/pairwise.S.R | 7 pairwise-0.4.4-7/pairwise/R/pairwise.item.fit.R | 6 pairwise-0.4.4-7/pairwise/R/pairwise.person.fit.R | 6 pairwise-0.4.4-7/pairwise/R/plot.grm.R | 140 ++-- pairwise-0.4.4-7/pairwise/R/plot.pair.R | 144 ++-- pairwise-0.4.4-7/pairwise/R/plot.pairSE.R | 180 ++--- pairwise-0.4.4-7/pairwise/R/plot.pers.R | 168 ++-- pairwise-0.4.4-7/pairwise/R/plot.rfa.R | 92 +- pairwise-0.4.4-7/pairwise/R/summary.grm.R | 52 - pairwise-0.4.4-7/pairwise/R/summary.pair.R | 44 - pairwise-0.4.4-7/pairwise/R/summary.pairS.R |only pairwise-0.4.4-7/pairwise/R/summary.pairSE.R | 62 - pairwise-0.4.4-7/pairwise/R/summary.pers.R | 66 - pairwise-0.4.4-7/pairwise/R/summary.pifit.R |only pairwise-0.4.4-7/pairwise/R/summary.ppfit.R |only pairwise-0.4.4-7/pairwise/R/summary.rfa.R | 74 +- pairwise-0.4.4-7/pairwise/build/vignette.rds |binary pairwise-0.4.4-7/pairwise/data/DEU_PISA2012.RData |binary pairwise-0.4.4-7/pairwise/data/Neoffi5.RData |binary pairwise-0.4.4-7/pairwise/data/bfiN.RData |binary pairwise-0.4.4-7/pairwise/data/bfiN_miss.RData |binary pairwise-0.4.4-7/pairwise/data/bfi_cov.RData |binary pairwise-0.4.4-7/pairwise/data/cog.RData |binary pairwise-0.4.4-7/pairwise/data/cogBOOKLET.RData |binary pairwise-0.4.4-7/pairwise/data/kft5.RData |binary pairwise-0.4.4-7/pairwise/data/sim200x3.RData |binary pairwise-0.4.4-7/pairwise/inst/CITATION |only pairwise-0.4.4-7/pairwise/inst/doc/DEU_PISA2012_description.R | 346 +++++----- pairwise-0.4.4-7/pairwise/inst/doc/DEU_PISA2012_description.pdf |binary pairwise-0.4.4-7/pairwise/man/andersentest.pers.Rd | 9 pairwise-0.4.4-7/pairwise/man/esc.Rd | 3 pairwise-0.4.4-7/pairwise/man/gif.Rd | 3 pairwise-0.4.4-7/pairwise/man/grm.Rd | 19 pairwise-0.4.4-7/pairwise/man/iff.Rd | 12 pairwise-0.4.4-7/pairwise/man/pair.Rd | 3 pairwise-0.4.4-7/pairwise/man/pairSE.Rd | 15 pairwise-0.4.4-7/pairwise/man/pairwise-package.Rd | 2 pairwise-0.4.4-7/pairwise/man/pairwise.S.Rd | 12 pairwise-0.4.4-7/pairwise/man/pairwise.item.fit.Rd | 2 pairwise-0.4.4-7/pairwise/man/pairwise.person.fit.Rd | 2 pairwise-0.4.4-7/pairwise/man/pers.Rd | 12 pairwise-0.4.4-7/pairwise/man/plot.grm.Rd | 26 pairwise-0.4.4-7/pairwise/man/plot.pair.Rd | 18 pairwise-0.4.4-7/pairwise/man/plot.pairSE.Rd | 24 pairwise-0.4.4-7/pairwise/man/plot.pers.Rd | 19 pairwise-0.4.4-7/pairwise/man/plot.rfa.Rd | 17 pairwise-0.4.4-7/pairwise/man/q3.Rd | 9 pairwise-0.4.4-7/pairwise/man/rfa.Rd | 11 pairwise-0.4.4-7/pairwise/man/simra.Rd | 10 pairwise-0.4.4-7/pairwise/man/summary.grm.Rd | 4 pairwise-0.4.4-7/pairwise/man/summary.pairS.Rd |only pairwise-0.4.4-7/pairwise/man/summary.pairSE.Rd | 4 pairwise-0.4.4-7/pairwise/man/summary.pifit.Rd |only pairwise-0.4.4-7/pairwise/man/summary.ppfit.Rd |only pairwise-0.4.4-7/pairwise/man/tff.Rd | 14 71 files changed, 1348 insertions(+), 1234 deletions(-)
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.2.1 dated 2019-11-12 and 1.3.0 dated 2020-02-04
sen2r-1.2.1/sen2r/R/gdal_formats_db.R |only sen2r-1.2.1/sen2r/man/gdal_formats_db.Rd |only sen2r-1.3.0/sen2r/DESCRIPTION | 16 sen2r-1.3.0/sen2r/MD5 | 228 +-- sen2r-1.3.0/sen2r/NAMESPACE | 21 sen2r-1.3.0/sen2r/NEWS.md | 57 sen2r-1.3.0/sen2r/R/abs2rel.R | 16 sen2r-1.3.0/sen2r/R/build_example_param_file.R | 2 sen2r-1.3.0/sen2r/R/check_gdal.R | 78 + sen2r-1.3.0/sen2r/R/check_param_list.R | 160 +- sen2r-1.3.0/sen2r/R/check_sen2r_deps.R | 141 +- sen2r-1.3.0/sen2r/R/compute_s2_paths.R | 611 ++++---- sen2r-1.3.0/sen2r/R/comsub.R | 9 sen2r-1.3.0/sen2r/R/create_indices_db.R | 55 sen2r-1.3.0/sen2r/R/expand_path.R | 17 sen2r-1.3.0/sen2r/R/fix_envi_format.R | 2 sen2r-1.3.0/sen2r/R/gdal_abs2rel.R | 18 sen2r-1.3.0/sen2r/R/gdal_warp.R | 143 +- sen2r-1.3.0/sen2r/R/gdalwarp_grid.R | 67 sen2r-1.3.0/sen2r/R/geograbber_process.R | 6 sen2r-1.3.0/sen2r/R/gipp.R |only sen2r-1.3.0/sen2r/R/helpers_extent.R | 23 sen2r-1.3.0/sen2r/R/init_python.R | 119 - sen2r-1.3.0/sen2r/R/install_sen2cor.R | 97 - sen2r-1.3.0/sen2r/R/load_binpaths.R | 10 sen2r-1.3.0/sen2r/R/mountpoint.R | 9 sen2r-1.3.0/sen2r/R/print_message.R | 59 sen2r-1.3.0/sen2r/R/projpar.R | 95 - sen2r-1.3.0/sen2r/R/raster_metadata.R | 31 sen2r-1.3.0/sen2r/R/s2_calcindices.R | 218 ++- sen2r-1.3.0/sen2r/R/s2_download.R | 64 sen2r-1.3.0/sen2r/R/s2_gui.R | 681 ++++++---- sen2r-1.3.0/sen2r/R/s2_list.R | 134 + sen2r-1.3.0/sen2r/R/s2_mask.R | 140 +- sen2r-1.3.0/sen2r/R/s2_merge.R | 61 sen2r-1.3.0/sen2r/R/s2_order.R | 134 + sen2r-1.3.0/sen2r/R/s2_rgb.R | 10 sen2r-1.3.0/sen2r/R/s2_thumbnails.R | 14 sen2r-1.3.0/sen2r/R/s2_translate.R | 28 sen2r-1.3.0/sen2r/R/safe_getMetadata.R | 192 +- sen2r-1.3.0/sen2r/R/safe_is_online.R | 42 sen2r-1.3.0/sen2r/R/safelist-class.R | 101 - sen2r-1.3.0/sen2r/R/scihub_login.R | 16 sen2r-1.3.0/sen2r/R/sen2cor.R | 130 + sen2r-1.3.0/sen2r/R/sen2r.R | 576 +++++--- sen2r-1.3.0/sen2r/R/sen2r_process_report.R |only sen2r-1.3.0/sen2r/R/smooth_mask.R | 84 + sen2r-1.3.0/sen2r/R/st_as_text_2.R |only sen2r-1.3.0/sen2r/R/st_crs2.R | 173 ++ sen2r-1.3.0/sen2r/R/suppress_warnings.R |only sen2r-1.3.0/sen2r/R/trace_functions.R | 15 sen2r-1.3.0/sen2r/build/vignette.rds |binary sen2r-1.3.0/sen2r/inst/CITATION | 8 sen2r-1.3.0/sen2r/inst/WORDLIST | 50 sen2r-1.3.0/sen2r/inst/doc/docker.R | 4 sen2r-1.3.0/sen2r/inst/doc/installation.R | 34 sen2r-1.3.0/sen2r/inst/extdata/settings/indices.json | 22 sen2r-1.3.0/sen2r/man/build_example_param_file.Rd | 6 sen2r-1.3.0/sen2r/man/check_gdal.Rd | 9 sen2r-1.3.0/sen2r/man/check_param_list.Rd | 3 sen2r-1.3.0/sen2r/man/compute_s2_paths.Rd | 90 + sen2r-1.3.0/sen2r/man/comsub.Rd | 2 sen2r-1.3.0/sen2r/man/create_indices_db.Rd | 2 sen2r-1.3.0/sen2r/man/editModPoly.Rd | 12 sen2r-1.3.0/sen2r/man/expand_path.Rd | 2 sen2r-1.3.0/sen2r/man/fix_envi_format.Rd | 2 sen2r-1.3.0/sen2r/man/gdal_warp.Rd | 33 sen2r-1.3.0/sen2r/man/gdalwarp_grid.Rd | 9 sen2r-1.3.0/sen2r/man/geograbber_process.Rd | 16 sen2r-1.3.0/sen2r/man/gipp.Rd |only sen2r-1.3.0/sen2r/man/gipp_init.Rd |only sen2r-1.3.0/sen2r/man/init_python.Rd | 11 sen2r-1.3.0/sen2r/man/install_sen2cor.Rd | 11 sen2r-1.3.0/sen2r/man/normalize_path.Rd | 2 sen2r-1.3.0/sen2r/man/print_message.Rd | 37 sen2r-1.3.0/sen2r/man/projpar.Rd | 35 sen2r-1.3.0/sen2r/man/raster2rgb.Rd | 15 sen2r-1.3.0/sen2r/man/s2_calcindices.Rd | 62 sen2r-1.3.0/sen2r/man/s2_dop.Rd | 3 sen2r-1.3.0/sen2r/man/s2_download.Rd | 18 sen2r-1.3.0/sen2r/man/s2_list.Rd | 34 sen2r-1.3.0/sen2r/man/s2_mask.Rd | 75 - sen2r-1.3.0/sen2r/man/s2_merge.Rd | 26 sen2r-1.3.0/sen2r/man/s2_order.Rd | 33 sen2r-1.3.0/sen2r/man/s2_rgb.Rd | 25 sen2r-1.3.0/sen2r/man/s2_thumbnails.Rd | 14 sen2r-1.3.0/sen2r/man/s2_translate.Rd | 28 sen2r-1.3.0/sen2r/man/safe_getMetadata.Rd | 16 sen2r-1.3.0/sen2r/man/safe_is_online.Rd | 7 sen2r-1.3.0/sen2r/man/safe_shortname.Rd | 19 sen2r-1.3.0/sen2r/man/safelist-class.Rd | 11 sen2r-1.3.0/sen2r/man/scihub_login.Rd | 16 sen2r-1.3.0/sen2r/man/sen2cor.Rd | 91 + sen2r-1.3.0/sen2r/man/sen2r.Rd | 148 +- sen2r-1.3.0/sen2r/man/sen2r_process_report.Rd |only sen2r-1.3.0/sen2r/man/smooth_mask.Rd | 14 sen2r-1.3.0/sen2r/man/st_as_text_2.Rd |only sen2r-1.3.0/sen2r/man/st_crs2.Rd | 70 - sen2r-1.3.0/sen2r/man/stack2rgb.Rd | 17 sen2r-1.3.0/sen2r/man/suppress_warnings.Rd |only sen2r-1.3.0/sen2r/man/tiles_intersects.Rd | 3 sen2r-1.3.0/sen2r/tests/testthat/test-t05_load_binpaths.R | 31 sen2r-1.3.0/sen2r/tests/testthat/test-t06_scihub_login.R | 10 sen2r-1.3.0/sen2r/tests/testthat/test-t07_s2_dop.R | 25 sen2r-1.3.0/sen2r/tests/testthat/test-t08_build_example_param_file.R | 3 sen2r-1.3.0/sen2r/tests/testthat/test-t10_s2_list.R | 88 - sen2r-1.3.0/sen2r/tests/testthat/test-t11_s2_classes.R | 40 sen2r-1.3.0/sen2r/tests/testthat/test-t12_s2_download.R | 74 - sen2r-1.3.0/sen2r/tests/testthat/test-t13_install_sen2cor.R | 112 + sen2r-1.3.0/sen2r/tests/testthat/test-t14_sen2cor.R | 123 + sen2r-1.3.0/sen2r/tests/testthat/test-t15_s2_order.R | 43 sen2r-1.3.0/sen2r/tests/testthat/test-t20_s2_merge.R | 15 sen2r-1.3.0/sen2r/tests/testthat/test-t21_s2_warp.R | 172 +- sen2r-1.3.0/sen2r/tests/testthat/test-t22_s2_mask.R | 21 sen2r-1.3.0/sen2r/tests/testthat/test-t23_s2_indices.R | 12 sen2r-1.3.0/sen2r/tests/testthat/test-t24_s2_rgb.R | 10 sen2r-1.3.0/sen2r/tests/testthat/test-t31_abs2rel.R | 7 sen2r-1.3.0/sen2r/tests/testthat/test-t34_st_crs2.R | 73 - sen2r-1.3.0/sen2r/tests/testthat/test-t35_create_indices_db.R | 4 sen2r-1.3.0/sen2r/tests/testthat/test-t36_mountpoint.R | 35 sen2r-1.3.0/sen2r/tests/testthat/test-t37_projpar.R |only 121 files changed, 4570 insertions(+), 2376 deletions(-)
Title: Tools for Binning Data
Description: Manually bin data using weight of evidence and information value. Includes other binning
methods such as equal length, quantile and winsorized. Options for combining levels of categorical
data are also available. Dummy variables can be generated based on the bins created using any of
the available binning methods. References: Siddiqi, N. (2006) <doi:10.1002/9781119201731.biblio>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between rbin versions 0.1.1 dated 2019-01-04 and 0.1.2 dated 2020-02-04
DESCRIPTION | 11 MD5 | 63 ++--- NAMESPACE | 1 NEWS.md | 4 R/rbin-equal-length.R | 17 - R/rbin-factor.R | 24 +- R/rbin-manual.R | 32 +- R/rbin-print.R | 36 +-- R/rbin-quantile.R | 28 +- R/rbin-winsorize.R | 45 ++- R/rbin.R | 1 R/zzz.R |only README.md | 24 -- build/vignette.rds |binary inst/doc/introduction.html | 429 +++++++++++++++++++------------------- man/rbin_equal_length.Rd | 4 man/rbin_factor.Rd | 4 man/rbin_manual.Rd | 6 man/rbin_quantiles.Rd | 4 man/rbin_winsorize.Rd | 4 tests/figs/deps.txt | 8 tests/figs/test-plots/el-plot.svg | 71 ++++++ tests/figs/test-plots/fl-plot.svg | 55 ++++ tests/figs/test-plots/ml-plot.svg | 69 ++++++ tests/figs/test-plots/ql-plot.svg | 69 ++++++ tests/figs/test-plots/wl-plot.svg | 73 ++++++ tests/testthat/test-bins.R | 40 +-- tests/testthat/test-plots.R | 10 tools/README-equal_length-1.png |binary tools/README-factor-1.png |binary tools/README-manual-1.png |binary tools/README-quantile-1.png |binary tools/README-winsorize-1.png |binary 33 files changed, 763 insertions(+), 369 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo and parallel importance sampling type weighted
Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>).
Gaussian, Poisson, binomial, or negative binomial
observation densities and basic stochastic volatility models with Gaussian state
dynamics, as well as general non-linear Gaussian models and discretised diffusion models
are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.9 dated 2020-01-28 and 0.1.10 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 ++++++- R/print_mcmc.R | 1 - inst/doc/bssm.html | 26 ++++++++++++-------------- inst/doc/growth_model.html | 17 ++++++++--------- man/expand_sample.Rd | 2 -- src/ung_amcmc.cpp | 1 + 8 files changed, 38 insertions(+), 38 deletions(-)
Title: Easily Tidy Gapminder Datasets
Description: A toolset that allows you to easily import and tidy data sheets retrieved
from Gapminder data web tools. It will therefore contribute to reduce the time
used in data cleaning of Gapminder indicator data sheets as they are very messy.
Author: Anicet Ebou [aut, cre] (<https://orcid.org/0000-0003-4005-177X>)
Maintainer: Anicet Ebou <anicet.ebou@gmail.com>
Diff between tidygapminder versions 0.1.0 dated 2019-12-06 and 0.1.1 dated 2020-02-04
tidygapminder-0.1.0/tidygapminder/inst/extdata/children_per_woman_total_fertility.xlsx |only tidygapminder-0.1.0/tidygapminder/inst/extdata/gapminder |only tidygapminder-0.1.1/tidygapminder/DESCRIPTION | 8 tidygapminder-0.1.1/tidygapminder/MD5 | 32 tidygapminder-0.1.1/tidygapminder/NEWS.md | 5 tidygapminder-0.1.1/tidygapminder/R/tidy_bunch.R | 26 tidygapminder-0.1.1/tidygapminder/R/tidy_indice.R | 3 tidygapminder-0.1.1/tidygapminder/README.md | 792 +++++++++- tidygapminder-0.1.1/tidygapminder/build/vignette.rds |binary tidygapminder-0.1.1/tidygapminder/inst/doc/tidygapminder.R | 16 tidygapminder-0.1.1/tidygapminder/inst/doc/tidygapminder.Rmd | 18 tidygapminder-0.1.1/tidygapminder/inst/doc/tidygapminder.html | 486 ++---- tidygapminder-0.1.1/tidygapminder/inst/extdata/agriculture_land.xlsx |only tidygapminder-0.1.1/tidygapminder/man/tidy_bunch.Rd | 8 tidygapminder-0.1.1/tidygapminder/man/tidy_indice.Rd | 8 tidygapminder-0.1.1/tidygapminder/tests/testthat/test-tidy_bunch.R | 2 tidygapminder-0.1.1/tidygapminder/tests/testthat/test-tidy_indice.R | 4 tidygapminder-0.1.1/tidygapminder/vignettes/tidygapminder.Rmd | 18 18 files changed, 1001 insertions(+), 425 deletions(-)
Title: R Interface to the 'UNU.RAN' Random Variate Generators
Description: Interface to the 'UNU.RAN' library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold [aut, cre],
Wolfgang H"ormann [aut]
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.27 dated 2019-03-14 and 0.28 dated 2020-02-04
DESCRIPTION | 8 MD5 | 683 +++++++-------- NEWS | 10 build/vignette.rds |binary configure | 20 configure.ac | 6 inst/doc/Runuran.pdf |binary inst/include/unuran.h | 2 man/Runuran-package.Rd | 4 src/Makevars.in | 2 src/init.c | 6 src/unuran-src/distr/cemp.c | 2 src/unuran-src/distr/cemp.h | 2 src/unuran-src/distr/condi.c | 2 src/unuran-src/distr/condi.h | 2 src/unuran-src/distr/cont.c | 2 src/unuran-src/distr/cont.h | 2 src/unuran-src/distr/corder.c | 2 src/unuran-src/distr/corder.h | 2 src/unuran-src/distr/cvec.c | 2 src/unuran-src/distr/cvec.h | 2 src/unuran-src/distr/cvemp.c | 2 src/unuran-src/distr/cvemp.h | 2 src/unuran-src/distr/cxtrans.c | 2 src/unuran-src/distr/cxtrans.h | 2 src/unuran-src/distr/deprecated_distr.h | 2 src/unuran-src/distr/discr.c | 2 src/unuran-src/distr/discr.h | 2 src/unuran-src/distr/distr.c | 2 src/unuran-src/distr/distr.h | 2 src/unuran-src/distr/distr_info.c | 2 src/unuran-src/distr/distr_source.h | 2 src/unuran-src/distr/distr_struct.h | 2 src/unuran-src/distr/matr.c | 2 src/unuran-src/distr/matr.h | 2 src/unuran-src/distributions/c_F.c | 2 src/unuran-src/distributions/c_beta.c | 2 src/unuran-src/distributions/c_beta_gen.c | 2 src/unuran-src/distributions/c_burr.c | 4 src/unuran-src/distributions/c_cauchy.c | 4 src/unuran-src/distributions/c_chi.c | 2 src/unuran-src/distributions/c_chi_gen.c | 2 src/unuran-src/distributions/c_chisquare.c | 2 src/unuran-src/distributions/c_exponential.c | 4 src/unuran-src/distributions/c_exponential_gen.c | 2 src/unuran-src/distributions/c_extremeI.c | 4 src/unuran-src/distributions/c_extremeII.c | 4 src/unuran-src/distributions/c_gamma.c | 4 src/unuran-src/distributions/c_gamma_gen.c | 2 src/unuran-src/distributions/c_ghyp.c | 2 src/unuran-src/distributions/c_gig.c | 2 src/unuran-src/distributions/c_gig2.c | 2 src/unuran-src/distributions/c_gig_gen.c | 2 src/unuran-src/distributions/c_hyperbolic.c | 2 src/unuran-src/distributions/c_ig.c | 2 src/unuran-src/distributions/c_laplace.c | 4 src/unuran-src/distributions/c_logistic.c | 4 src/unuran-src/distributions/c_lognormal.c | 2 src/unuran-src/distributions/c_lomax.c | 2 src/unuran-src/distributions/c_meixner.c | 2 src/unuran-src/distributions/c_normal.c | 4 src/unuran-src/distributions/c_normal_gen.c | 2 src/unuran-src/distributions/c_pareto.c | 2 src/unuran-src/distributions/c_powerexponential.c | 2 src/unuran-src/distributions/c_powerexponential_gen.c | 2 src/unuran-src/distributions/c_rayleigh.c | 2 src/unuran-src/distributions/c_slash.c | 2 src/unuran-src/distributions/c_slash_gen.c | 2 src/unuran-src/distributions/c_student.c | 2 src/unuran-src/distributions/c_student_gen.c | 2 src/unuran-src/distributions/c_triangular.c | 2 src/unuran-src/distributions/c_uniform.c | 2 src/unuran-src/distributions/c_vg.c | 2 src/unuran-src/distributions/c_weibull.c | 4 src/unuran-src/distributions/d_binomial.c | 2 src/unuran-src/distributions/d_binomial_gen.c | 2 src/unuran-src/distributions/d_geometric.c | 2 src/unuran-src/distributions/d_hypergeometric.c | 2 src/unuran-src/distributions/d_hypergeometric_gen.c | 2 src/unuran-src/distributions/d_logarithmic.c | 2 src/unuran-src/distributions/d_logarithmic_gen.c | 2 src/unuran-src/distributions/d_negativebinomial.c | 2 src/unuran-src/distributions/d_poisson.c | 2 src/unuran-src/distributions/d_poisson_gen.c | 2 src/unuran-src/distributions/d_zipf.c | 2 src/unuran-src/distributions/d_zipf_gen.c | 2 src/unuran-src/distributions/m_correlation.c | 2 src/unuran-src/distributions/unur_distributions.h | 2 src/unuran-src/distributions/unur_distributions_source.h | 2 src/unuran-src/distributions/unur_stddistr.h | 2 src/unuran-src/distributions/vc_copula.c | 2 src/unuran-src/distributions/vc_multicauchy.c | 2 src/unuran-src/distributions/vc_multiexponential.c | 2 src/unuran-src/distributions/vc_multinormal.c | 2 src/unuran-src/distributions/vc_multinormal_gen.c | 2 src/unuran-src/distributions/vc_multistudent.c | 2 src/unuran-src/methods/arou.c | 2 src/unuran-src/methods/arou.h | 2 src/unuran-src/methods/arou_struct.h | 2 src/unuran-src/methods/ars.c | 2 src/unuran-src/methods/ars.h | 2 src/unuran-src/methods/ars_struct.h | 2 src/unuran-src/methods/auto.c | 2 src/unuran-src/methods/auto.h | 2 src/unuran-src/methods/auto_struct.h | 2 src/unuran-src/methods/cext.c | 2 src/unuran-src/methods/cext.h | 2 src/unuran-src/methods/cext_struct.h | 2 src/unuran-src/methods/cstd.c | 3 src/unuran-src/methods/cstd.h | 2 src/unuran-src/methods/cstd_struct.h | 2 src/unuran-src/methods/dari.c | 2 src/unuran-src/methods/dari.h | 2 src/unuran-src/methods/dari_struct.h | 2 src/unuran-src/methods/dau.c | 2 src/unuran-src/methods/dau.h | 2 src/unuran-src/methods/dau_struct.h | 2 src/unuran-src/methods/deprecated_methods.h | 2 src/unuran-src/methods/deprecated_tdrgw.h | 2 src/unuran-src/methods/deprecated_vmt.h | 2 src/unuran-src/methods/deprecated_vmt_struct.h | 2 src/unuran-src/methods/dext.c | 2 src/unuran-src/methods/dext.h | 2 src/unuran-src/methods/dext_struct.h | 2 src/unuran-src/methods/dgt.c | 2 src/unuran-src/methods/dgt.h | 2 src/unuran-src/methods/dgt_struct.h | 2 src/unuran-src/methods/dsrou.c | 2 src/unuran-src/methods/dsrou.h | 2 src/unuran-src/methods/dsrou_struct.h | 2 src/unuran-src/methods/dss.c | 2 src/unuran-src/methods/dss.h | 2 src/unuran-src/methods/dss_struct.h | 2 src/unuran-src/methods/dstd.c | 3 src/unuran-src/methods/dstd.h | 2 src/unuran-src/methods/dstd_struct.h | 2 src/unuran-src/methods/empk.c | 2 src/unuran-src/methods/empk.h | 2 src/unuran-src/methods/empk_struct.h | 2 src/unuran-src/methods/empl.c | 2 src/unuran-src/methods/empl.h | 2 src/unuran-src/methods/empl_struct.h | 2 src/unuran-src/methods/gibbs.c | 2 src/unuran-src/methods/gibbs.h | 2 src/unuran-src/methods/gibbs_struct.h | 2 src/unuran-src/methods/hinv.c | 6 src/unuran-src/methods/hinv.h | 2 src/unuran-src/methods/hinv_struct.h | 2 src/unuran-src/methods/hist.c | 2 src/unuran-src/methods/hist.h | 2 src/unuran-src/methods/hist_struct.h | 2 src/unuran-src/methods/hitro.c | 2 src/unuran-src/methods/hitro.h | 2 src/unuran-src/methods/hitro_struct.h | 2 src/unuran-src/methods/hrb.c | 2 src/unuran-src/methods/hrb.h | 2 src/unuran-src/methods/hrb_struct.h | 2 src/unuran-src/methods/hrd.c | 2 src/unuran-src/methods/hrd.h | 2 src/unuran-src/methods/hrd_struct.h | 2 src/unuran-src/methods/hri.c | 2 src/unuran-src/methods/hri.h | 2 src/unuran-src/methods/hri_struct.h | 2 src/unuran-src/methods/itdr.c | 2 src/unuran-src/methods/itdr.h | 2 src/unuran-src/methods/itdr_struct.h | 2 src/unuran-src/methods/mcorr.c | 2 src/unuran-src/methods/mcorr.h | 2 src/unuran-src/methods/mcorr_struct.h | 2 src/unuran-src/methods/mixt.c | 2 src/unuran-src/methods/mixt.h | 2 src/unuran-src/methods/mixt_struct.h | 2 src/unuran-src/methods/mvstd.c | 2 src/unuran-src/methods/mvstd.h | 2 src/unuran-src/methods/mvstd_struct.h | 2 src/unuran-src/methods/mvtdr.c | 2 src/unuran-src/methods/mvtdr.h | 2 src/unuran-src/methods/mvtdr_debug.ch | 2 src/unuran-src/methods/mvtdr_info.ch | 2 src/unuran-src/methods/mvtdr_init.ch | 2 src/unuran-src/methods/mvtdr_newset.ch | 2 src/unuran-src/methods/mvtdr_sample.ch | 2 src/unuran-src/methods/mvtdr_struct.h | 2 src/unuran-src/methods/ninv.c | 2 src/unuran-src/methods/ninv.h | 2 src/unuran-src/methods/ninv_debug.ch | 2 src/unuran-src/methods/ninv_info.ch | 2 src/unuran-src/methods/ninv_init.ch | 2 src/unuran-src/methods/ninv_newset.ch | 2 src/unuran-src/methods/ninv_newton.ch | 2 src/unuran-src/methods/ninv_regula.ch | 2 src/unuran-src/methods/ninv_sample.ch | 2 src/unuran-src/methods/ninv_struct.h | 2 src/unuran-src/methods/norta.c | 2 src/unuran-src/methods/norta.h | 2 src/unuran-src/methods/norta_struct.h | 2 src/unuran-src/methods/nrou.c | 2 src/unuran-src/methods/nrou.h | 2 src/unuran-src/methods/nrou_struct.h | 2 src/unuran-src/methods/pinv.c | 2 src/unuran-src/methods/pinv.h | 2 src/unuran-src/methods/pinv_debug.ch | 2 src/unuran-src/methods/pinv_info.ch | 2 src/unuran-src/methods/pinv_init.ch | 2 src/unuran-src/methods/pinv_newset.ch | 2 src/unuran-src/methods/pinv_newton.ch | 5 src/unuran-src/methods/pinv_prep.ch | 2 src/unuran-src/methods/pinv_sample.ch | 2 src/unuran-src/methods/pinv_struct.h | 2 src/unuran-src/methods/srou.c | 2 src/unuran-src/methods/srou.h | 2 src/unuran-src/methods/srou_struct.h | 2 src/unuran-src/methods/ssr.c | 2 src/unuran-src/methods/ssr.h | 2 src/unuran-src/methods/ssr_struct.h | 2 src/unuran-src/methods/tabl.c | 2 src/unuran-src/methods/tabl.h | 2 src/unuran-src/methods/tabl_debug.ch | 2 src/unuran-src/methods/tabl_info.ch | 2 src/unuran-src/methods/tabl_init.ch | 2 src/unuran-src/methods/tabl_newset.ch | 2 src/unuran-src/methods/tabl_sample.ch | 2 src/unuran-src/methods/tabl_struct.h | 2 src/unuran-src/methods/tdr.c | 2 src/unuran-src/methods/tdr.h | 2 src/unuran-src/methods/tdr_debug.ch | 2 src/unuran-src/methods/tdr_gw_debug.ch | 2 src/unuran-src/methods/tdr_gw_init.ch | 2 src/unuran-src/methods/tdr_gw_sample.ch | 2 src/unuran-src/methods/tdr_ia_sample.ch | 2 src/unuran-src/methods/tdr_info.ch | 2 src/unuran-src/methods/tdr_init.ch | 2 src/unuran-src/methods/tdr_newset.ch | 2 src/unuran-src/methods/tdr_ps_debug.ch | 2 src/unuran-src/methods/tdr_ps_init.ch | 2 src/unuran-src/methods/tdr_ps_sample.ch | 2 src/unuran-src/methods/tdr_sample.ch | 2 src/unuran-src/methods/tdr_struct.h | 2 src/unuran-src/methods/unif.c | 2 src/unuran-src/methods/unif.h | 2 src/unuran-src/methods/unif_struct.h | 2 src/unuran-src/methods/unur_methods.h | 2 src/unuran-src/methods/unur_methods_source.h | 2 src/unuran-src/methods/utdr.c | 2 src/unuran-src/methods/utdr.h | 2 src/unuran-src/methods/utdr_struct.h | 2 src/unuran-src/methods/vempk.c | 2 src/unuran-src/methods/vempk.h | 2 src/unuran-src/methods/vempk_struct.h | 2 src/unuran-src/methods/vnrou.c | 2 src/unuran-src/methods/vnrou.h | 2 src/unuran-src/methods/vnrou_struct.h | 2 src/unuran-src/methods/x_gen.c | 2 src/unuran-src/methods/x_gen.h | 2 src/unuran-src/methods/x_gen_source.h | 2 src/unuran-src/methods/x_gen_struct.h | 2 src/unuran-src/parser/functparser.c | 2 src/unuran-src/parser/functparser_debug.ch | 2 src/unuran-src/parser/functparser_deriv.ch | 2 src/unuran-src/parser/functparser_eval.ch | 2 src/unuran-src/parser/functparser_init.ch | 2 src/unuran-src/parser/functparser_parser.ch | 2 src/unuran-src/parser/functparser_scanner.ch | 2 src/unuran-src/parser/functparser_source.h | 2 src/unuran-src/parser/functparser_stringgen.ch | 2 src/unuran-src/parser/functparser_struct.h | 2 src/unuran-src/parser/functparser_symbols.h | 2 src/unuran-src/parser/parser.c | 2 src/unuran-src/parser/parser.h | 2 src/unuran-src/parser/parser_source.h | 2 src/unuran-src/parser/stringparser.c | 2 src/unuran-src/parser/stringparser_lists.ch | 2 src/unuran-src/specfunct/bessel_asympt.c | 2 src/unuran-src/specfunct/cgamma.c | 2 src/unuran-src/specfunct/hypot.c | 2 src/unuran-src/specfunct/log1p.c | 2 src/unuran-src/specfunct/unur_specfunct_source.h | 2 src/unuran-src/tests/countpdf.c | 2 src/unuran-src/tests/counturn.c | 2 src/unuran-src/tests/inverror.c | 2 src/unuran-src/tests/unuran_tests.h | 2 src/unuran-src/uniform/mrg31k3p.c | 2 src/unuran-src/uniform/urng_builtin.h | 2 src/unuran-src/uniform/urng_fvoid.h | 2 src/unuran-src/uniform/urng_gsl.h | 2 src/unuran-src/uniform/urng_gslqrng.h | 2 src/unuran-src/uniform/urng_prng.h | 2 src/unuran-src/uniform/urng_randomshift.h | 2 src/unuran-src/uniform/urng_rngstreams.h | 2 src/unuran-src/unur_cookies.h | 2 src/unuran-src/unur_source.h | 2 src/unuran-src/unur_struct.h | 2 src/unuran-src/unur_typedefs.h | 2 src/unuran-src/unuran.h | 2 src/unuran-src/urng/urng.c | 2 src/unuran-src/urng/urng.h | 2 src/unuran-src/urng/urng_default.c | 2 src/unuran-src/urng/urng_set.c | 2 src/unuran-src/urng/urng_source.h | 2 src/unuran-src/urng/urng_struct.h | 2 src/unuran-src/urng/urng_unuran.c | 2 src/unuran-src/utils/debug.c | 2 src/unuran-src/utils/debug.h | 2 src/unuran-src/utils/debug_source.h | 2 src/unuran-src/utils/eigensystem.c | 2 src/unuran-src/utils/error.c | 2 src/unuran-src/utils/error.h | 2 src/unuran-src/utils/error_source.h | 2 src/unuran-src/utils/fmax.c | 2 src/unuran-src/utils/fmax_source.h | 2 src/unuran-src/utils/hooke.c | 2 src/unuran-src/utils/hooke_source.h | 2 src/unuran-src/utils/lobatto.c | 2 src/unuran-src/utils/lobatto_source.h | 2 src/unuran-src/utils/lobatto_struct.h | 2 src/unuran-src/utils/matrix.c | 2 src/unuran-src/utils/matrix_source.h | 2 src/unuran-src/utils/mrou_rectangle.c | 2 src/unuran-src/utils/mrou_rectangle_source.h | 2 src/unuran-src/utils/mrou_rectangle_struct.h | 2 src/unuran-src/utils/slist.c | 2 src/unuran-src/utils/slist.h | 2 src/unuran-src/utils/slist_struct.h | 2 src/unuran-src/utils/stream.c | 2 src/unuran-src/utils/stream.h | 2 src/unuran-src/utils/stream_source.h | 2 src/unuran-src/utils/string.c | 2 src/unuran-src/utils/string_source.h | 2 src/unuran-src/utils/string_struct.h | 2 src/unuran-src/utils/umalloc.c | 2 src/unuran-src/utils/umalloc_source.h | 2 src/unuran-src/utils/umath.c | 2 src/unuran-src/utils/umath.h | 2 src/unuran-src/utils/umath_source.h | 2 src/unuran-src/utils/unur_errno.h | 2 src/unuran-src/utils/unur_fp.c | 2 src/unuran-src/utils/unur_fp_const_source.h | 2 src/unuran-src/utils/unur_fp_source.h | 2 src/unuran-src/utils/unur_math_source.h | 2 src/unuran-src/utils/vector.c | 2 src/unuran-src/utils/vector_source.h | 2 tests/test_details.Rout.save |only vignettes/inputs/version.tex | 2 343 files changed, 738 insertions(+), 694 deletions(-)
Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Author: Alexandre Almeida [aut],
Adam Loy [aut, cre],
Heike Hofmann [aut]
Maintainer: Adam Loy <loyad01@gmail.com>
Diff between qqplotr versions 0.0.3 dated 2018-07-18 and 0.0.4 dated 2020-02-04
DESCRIPTION | 20 MD5 | 88 +- NAMESPACE | 46 - NEWS.md | 7 R/geom_qq_band.R | 42 - R/stat_pp_band.R | 30 R/stat_pp_line.R | 22 R/stat_pp_point.R | 24 R/stat_qq_band.R | 912 +++++++++++++-------------- R/stat_qq_line.R | 32 R/stat_qq_point.R | 30 README.md | 566 +++++++--------- build/vignette.rds |binary inst/CITATION | 20 inst/doc/introduction.R | 224 +++--- inst/doc/introduction.html | 1001 +++++++++++++++--------------- inst/image |only man/GeomQqBand.Rd | 22 man/StatPpBand.Rd | 22 man/StatPpLine.Rd | 22 man/StatPpPoint.Rd | 22 man/StatQqBand.Rd | 22 man/StatQqLine.Rd | 22 man/StatQqPoint.Rd | 22 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |only man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/figures/devBadge.svg |only man/iowa.Rd | 44 - man/longjump.Rd | 46 - man/qqplotr.Rd | 44 - man/runShinyExample.Rd | 18 man/stat_pp_band.Rd | 257 +++---- man/stat_pp_line.Rd | 193 ++--- man/stat_pp_point.Rd | 223 +++--- man/stat_qq_band.Rd | 405 ++++++------ man/stat_qq_line.Rd | 263 +++---- man/stat_qq_point.Rd | 239 +++---- 47 files changed, 2465 insertions(+), 2485 deletions(-)
Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R.
Enables clustering using the leiden algorithm for partition a graph into communities.
See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg>
Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl],
Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>
Diff between leiden versions 0.3.2 dated 2020-01-18 and 0.3.3 dated 2020-02-04
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/leiden.R | 1 - build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/run_igraph.html | 26 +++++++++++++------------- inst/doc/run_leiden.html | 26 +++++++++++++------------- man/leiden.Rd | 2 -- 9 files changed, 46 insertions(+), 43 deletions(-)
Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory
(IRT) models. The current implementation includes IRT models for binary and ordinal
responses, along with dynamic and hierarchical IRT models with binary responses. The
latter two models are derived and implemented using variational EM. Subsequent edits
also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <lojames@usc.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <lojames@usc.edu>
Diff between emIRT versions 0.0.9 dated 2019-12-13 and 0.0.11 dated 2020-02-04
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/binIRT.R | 3 ++- src/getEx.cpp | 7 ++++++- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Description: The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lectures and computer labs) at <https://nwfsc-timeseries.github.io/> See the NEWS file for update information.
Author: Eli Holmes, Eric Ward, Mark Scheuerell, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>
Diff between MARSS versions 3.10.10 dated 2018-11-02 and 3.10.12 dated 2020-02-04
MARSS-3.10.10/MARSS/NEWS |only MARSS-3.10.10/MARSS/R/MARSSFisherI.R |only MARSS-3.10.10/MARSS/R/MARSS_dfa.R |only MARSS-3.10.10/MARSS/R/MARSSkf.R |only MARSS-3.10.10/MARSS/R/MARSSkfas.R |only MARSS-3.10.10/MARSS/R/checkMARSSInputs.R |only MARSS-3.10.10/MARSS/R/checkModelList.R |only MARSS-3.10.10/MARSS/R/fitted_marssMLE.R |only MARSS-3.10.10/MARSS/R/print_marssMLE.R |only MARSS-3.10.12/MARSS/DESCRIPTION | 12 MARSS-3.10.12/MARSS/MD5 | 249 +- MARSS-3.10.12/MARSS/NAMESPACE | 3 MARSS-3.10.12/MARSS/NEWS.md |only MARSS-3.10.12/MARSS/R/CSEGriskfigure.R | 343 +- MARSS-3.10.12/MARSS/R/CSEGtmufigure.R | 155 - MARSS-3.10.12/MARSS/R/MARSS.R | 353 +- MARSS-3.10.12/MARSS/R/MARSSFisherI.r |only MARSS-3.10.12/MARSS/R/MARSS_dfa.r |only MARSS-3.10.12/MARSS/R/MARSS_marss.R | 1077 ++++----- MARSS-3.10.12/MARSS/R/MARSS_marxss.R | 2141 +++++++++--------- MARSS-3.10.12/MARSS/R/MARSSaic.R | 133 - MARSS-3.10.12/MARSS/R/MARSSapplynames.R | 44 MARSS-3.10.12/MARSS/R/MARSSboot.R | 278 +- MARSS-3.10.12/MARSS/R/MARSSharveyobsFI.R | 408 +-- MARSS-3.10.12/MARSS/R/MARSShatyt.r | 231 + MARSS-3.10.12/MARSS/R/MARSShessian.R | 63 MARSS-3.10.12/MARSS/R/MARSShessian_numerical.R | 44 MARSS-3.10.12/MARSS/R/MARSSinfo.R | 553 ++-- MARSS-3.10.12/MARSS/R/MARSSinits.R | 210 - MARSS-3.10.12/MARSS/R/MARSSinnovationsboot.R | 175 - MARSS-3.10.12/MARSS/R/MARSSkem.r | 2070 +++++++++-------- MARSS-3.10.12/MARSS/R/MARSSkemcheck.r | 525 ++-- MARSS-3.10.12/MARSS/R/MARSSkf.r |only MARSS-3.10.12/MARSS/R/MARSSkfas.r |only MARSS-3.10.12/MARSS/R/MARSSkfss.R | 777 +++--- MARSS-3.10.12/MARSS/R/MARSSoptim.r | 338 +- MARSS-3.10.12/MARSS/R/MARSSparamCIs.R | 114 MARSS-3.10.12/MARSS/R/MARSSresiduals.tT.R |only MARSS-3.10.12/MARSS/R/MARSSresiduals_tt1.R |only MARSS-3.10.12/MARSS/R/MARSSsimulate.R | 309 +- MARSS-3.10.12/MARSS/R/MARSSvectorizeparam.R | 124 - MARSS-3.10.12/MARSS/R/augment_marssMLE.R | 145 - MARSS-3.10.12/MARSS/R/autoplot_marssMLE.R | 432 ++- MARSS-3.10.12/MARSS/R/checkMARSSInputs.r |only MARSS-3.10.12/MARSS/R/checkModelList.r |only MARSS-3.10.12/MARSS/R/coef_marssMLE.r | 153 - MARSS-3.10.12/MARSS/R/describe_marssMODEL.R | 26 MARSS-3.10.12/MARSS/R/fitted_marssMLE.r |only MARSS-3.10.12/MARSS/R/glance_marssMLE.R | 18 MARSS-3.10.12/MARSS/R/is_marssMLE.r | 283 +- MARSS-3.10.12/MARSS/R/is_marssMODEL.R | 335 +- MARSS-3.10.12/MARSS/R/logLik_marssMLE.R | 14 MARSS-3.10.12/MARSS/R/model_frame_marssMODEL.R | 54 MARSS-3.10.12/MARSS/R/onLoad.R | 58 MARSS-3.10.12/MARSS/R/plot.marssMLE.R | 388 +-- MARSS-3.10.12/MARSS/R/print_marssMLE.r |only MARSS-3.10.12/MARSS/R/print_marssMODEL.R | 47 MARSS-3.10.12/MARSS/R/progressBar.R | 48 MARSS-3.10.12/MARSS/R/residuals_marssMLE.R | 199 - MARSS-3.10.12/MARSS/R/summary_marssMLE.R | 18 MARSS-3.10.12/MARSS/R/summary_marssMODEL.R | 60 MARSS-3.10.12/MARSS/R/tidy_marssMLE.R | 240 +- MARSS-3.10.12/MARSS/R/toLatex_marssMODEL.R |only MARSS-3.10.12/MARSS/R/utility_functions.R | 1284 ++++++---- MARSS-3.10.12/MARSS/build/vignette.rds |binary MARSS-3.10.12/MARSS/inst/doc/Chapter_AnimalTracking.R | 15 MARSS-3.10.12/MARSS/inst/doc/Chapter_Covariates.R | 8 MARSS-3.10.12/MARSS/inst/doc/Chapter_DFA.R | 3 MARSS-3.10.12/MARSS/inst/doc/Chapter_MARp.R | 4 MARSS-3.10.12/MARSS/inst/doc/EMDerivation.Rnw | 39 MARSS-3.10.12/MARSS/inst/doc/EMDerivation.pdf |binary MARSS-3.10.12/MARSS/inst/doc/Quick_Start.Rnw | 73 MARSS-3.10.12/MARSS/inst/doc/Quick_Start.pdf |binary MARSS-3.10.12/MARSS/inst/doc/Residuals.Rnw | 621 +++-- MARSS-3.10.12/MARSS/inst/doc/Residuals.pdf |binary MARSS-3.10.12/MARSS/inst/doc/UserGuide.pdf |binary MARSS-3.10.12/MARSS/inst/doc/versiontest.R | 135 - MARSS-3.10.12/MARSS/man/CSEGriskfigure.Rd | 6 MARSS-3.10.12/MARSS/man/CSEGtmufigure.Rd | 2 MARSS-3.10.12/MARSS/man/MARSS-package.Rd | 100 MARSS-3.10.12/MARSS/man/MARSS.Rd | 205 - MARSS-3.10.12/MARSS/man/MARSSFisherI.Rd |only MARSS-3.10.12/MARSS/man/MARSS_dfa.Rd | 28 MARSS-3.10.12/MARSS/man/MARSS_marss.Rd | 25 MARSS-3.10.12/MARSS/man/MARSS_marxss.Rd | 20 MARSS-3.10.12/MARSS/man/MARSS_vectorized.Rd |only MARSS-3.10.12/MARSS/man/MARSSaic.Rd | 16 MARSS-3.10.12/MARSS/man/MARSSapplynames.Rd | 6 MARSS-3.10.12/MARSS/man/MARSSboot.Rd | 32 MARSS-3.10.12/MARSS/man/MARSSharveyobsFI.Rd | 28 MARSS-3.10.12/MARSS/man/MARSShatyt.Rd | 38 MARSS-3.10.12/MARSS/man/MARSShessian.Rd | 54 MARSS-3.10.12/MARSS/man/MARSShessian_numerical.Rd | 17 MARSS-3.10.12/MARSS/man/MARSSinfo.Rd | 6 MARSS-3.10.12/MARSS/man/MARSSinits.Rd | 16 MARSS-3.10.12/MARSS/man/MARSSinnovationsboot.Rd | 16 MARSS-3.10.12/MARSS/man/MARSSkem.Rd | 25 MARSS-3.10.12/MARSS/man/MARSSkemcheck.Rd | 4 MARSS-3.10.12/MARSS/man/MARSSkf.Rd | 48 MARSS-3.10.12/MARSS/man/MARSSoptim.Rd | 28 MARSS-3.10.12/MARSS/man/MARSSparamCIs.Rd | 22 MARSS-3.10.12/MARSS/man/MARSSresiduals_tT.Rd |only MARSS-3.10.12/MARSS/man/MARSSresiduals_tt1.Rd |only MARSS-3.10.12/MARSS/man/MARSSsimulate.Rd | 27 MARSS-3.10.12/MARSS/man/MARSSvectorizeparam.Rd | 14 MARSS-3.10.12/MARSS/man/SalmonSurvCUI.Rd | 4 MARSS-3.10.12/MARSS/man/allowed.Rd | 6 MARSS-3.10.12/MARSS/man/as_marssMODEL.Rd | 2 MARSS-3.10.12/MARSS/man/augment_marssMLE.Rd | 90 MARSS-3.10.12/MARSS/man/checkMARSSInputs.Rd | 12 MARSS-3.10.12/MARSS/man/checkModelList.Rd | 8 MARSS-3.10.12/MARSS/man/coef_marssMLE.Rd | 30 MARSS-3.10.12/MARSS/man/datasets.Rd |only MARSS-3.10.12/MARSS/man/describe_marssMODEL.Rd |only MARSS-3.10.12/MARSS/man/fitted_marssMLE.Rd | 81 MARSS-3.10.12/MARSS/man/glance_marssMLE.Rd | 21 MARSS-3.10.12/MARSS/man/graywhales.Rd | 7 MARSS-3.10.12/MARSS/man/harborSeal.Rd | 2 MARSS-3.10.12/MARSS/man/is_marssMLE.Rd | 26 MARSS-3.10.12/MARSS/man/is_marssMODEL.Rd | 8 MARSS-3.10.12/MARSS/man/isleRoyal.Rd | 5 MARSS-3.10.12/MARSS/man/logLik_marssMLE.Rd |only MARSS-3.10.12/MARSS/man/loggerhead.Rd | 3 MARSS-3.10.12/MARSS/man/marssMLE-class.Rd | 29 MARSS-3.10.12/MARSS/man/marssMODEL-class.Rd | 27 MARSS-3.10.12/MARSS/man/model_frame_marssMODEL.Rd | 10 MARSS-3.10.12/MARSS/man/plankton.Rd | 17 MARSS-3.10.12/MARSS/man/plot_marssMLE.Rd | 44 MARSS-3.10.12/MARSS/man/print_marssMLE.Rd | 13 MARSS-3.10.12/MARSS/man/print_marssMODEL.Rd | 18 MARSS-3.10.12/MARSS/man/residuals_marssMLE.Rd | 139 - MARSS-3.10.12/MARSS/man/stdInnov.Rd | 4 MARSS-3.10.12/MARSS/man/tidy_marssMLE.Rd | 148 + MARSS-3.10.12/MARSS/man/toLatex_marssMLE.Rd |only MARSS-3.10.12/MARSS/man/utility_functions.Rd | 48 MARSS-3.10.12/MARSS/man/zscore.Rd | 10 MARSS-3.10.12/MARSS/vignettes/EMDerivation.Rnw | 39 MARSS-3.10.12/MARSS/vignettes/EMDerivation.bib | 20 MARSS-3.10.12/MARSS/vignettes/Quick_Start.Rnw | 73 MARSS-3.10.12/MARSS/vignettes/Residuals.Rnw | 621 +++-- 140 files changed, 9891 insertions(+), 7886 deletions(-)