Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau Guillerme and Smith (2017) <doi:10.1101/209775>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph],
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martins@gmail.com>
Diff between TreeSearch versions 0.1.0 dated 2018-03-14 and 0.1.2 dated 2018-03-19
TreeSearch-0.1.0/TreeSearch/data/inapplicable.datasets.RData |only TreeSearch-0.1.0/TreeSearch/inst/extdata |only TreeSearch-0.1.2/TreeSearch/DESCRIPTION | 8 TreeSearch-0.1.2/TreeSearch/MD5 | 89 TreeSearch-0.1.2/TreeSearch/NEWS.md | 8 TreeSearch-0.1.2/TreeSearch/R/helper_functions.R | 4 TreeSearch-0.1.2/TreeSearch/R/zzz.R | 11 TreeSearch-0.1.2/TreeSearch/README.md | 6 TreeSearch-0.1.2/TreeSearch/build/partial.rdb |binary TreeSearch-0.1.2/TreeSearch/data/inapplicable.citations.R |only TreeSearch-0.1.2/TreeSearch/data/inapplicable.datasets.rda |only TreeSearch-0.1.2/TreeSearch/data/inapplicable.phyData.rda |only TreeSearch-0.1.2/TreeSearch/inst/apa-old-doi-prefix.csl |only TreeSearch-0.1.2/TreeSearch/inst/doc/getting-started.Rmd | 2 TreeSearch-0.1.2/TreeSearch/inst/doc/getting-started.html | 4 TreeSearch-0.1.2/TreeSearch/inst/doc/inapplicable.Rmd | 2 TreeSearch-0.1.2/TreeSearch/inst/doc/inapplicable.html | 4 TreeSearch-0.1.2/TreeSearch/inst/doc/load-data.Rmd | 4 TreeSearch-0.1.2/TreeSearch/inst/doc/load-data.html | 6 TreeSearch-0.1.2/TreeSearch/inst/doc/profile-scores.R | 44 TreeSearch-0.1.2/TreeSearch/inst/doc/profile-scores.Rmd | 11 TreeSearch-0.1.2/TreeSearch/inst/doc/profile-scores.html | 113 TreeSearch-0.1.2/TreeSearch/inst/doc/profile.Rmd | 2 TreeSearch-0.1.2/TreeSearch/inst/doc/profile.html | 22 TreeSearch-0.1.2/TreeSearch/man/ListToMatrix.Rd | 4 TreeSearch-0.1.2/TreeSearch/src/fitch.c | 1867 +++++------ TreeSearch-0.1.2/TreeSearch/src/morphydefs.h | 334 - TreeSearch-0.1.2/TreeSearch/src/statedata.c | 2 TreeSearch-0.1.2/TreeSearch/vignettes/getting-started.Rmd | 2 TreeSearch-0.1.2/TreeSearch/vignettes/inapplicable.Rmd | 2 TreeSearch-0.1.2/TreeSearch/vignettes/load-data.Rmd | 4 TreeSearch-0.1.2/TreeSearch/vignettes/profile-scores.Rmd | 11 TreeSearch-0.1.2/TreeSearch/vignettes/profile.Rmd | 2 33 files changed, 1237 insertions(+), 1331 deletions(-)
Title: Non-Supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications
of the Regional Frequency Analysis methods in hydrology.
The package refers to the index-value method and, more precisely, helps the
hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions
with similar growth curves; (3) fit distribution functions to the
empirical regional growth curves.
Author: Alberto Viglione [aut, cre],
Jonathan R. M. Hosking [ctb],
Francesco Laio [ctb],
Alan Miller [ctb],
Eric Gaume [ctb],
Olivier Payrastre [ctb],
Jose Luis Salinas [ctb],
Chi Cong N'guyen [ctb],
Karine Halbert [ctb]
Maintainer: Alberto Viglione <viglione@hydro.tuwien.ac.at>
Diff between nsRFA versions 0.7-12 dated 2014-08-30 and 0.7-13 dated 2018-03-19
DESCRIPTION | 13 ++++++------- MD5 | 27 ++++++++++++++------------- NAMESPACE | 16 ++++++++++++++++ R/BayesianMCMC.R | 8 ++++---- R/BayesianMCMCreg.R | 17 ----------------- R/DISTPLOTS.R | 4 ++-- R/HOMTESTS.R | 4 ++-- build/vignette.rds |binary inst/doc/BayesianMCMC_reg.pdf |binary inst/doc/Fig11GriffisStedinger.pdf |binary inst/doc/Fig1ElamirSeheult.pdf |binary inst/doc/MSClaio2008.pdf |binary inst/doc/nsRFA_ex01.pdf |binary inst/doc/nsRFA_ex02.pdf |binary src/registerDynamicSymbol.c |only 15 files changed, 44 insertions(+), 45 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between magick versions 1.7 dated 2018-02-26 and 1.8 dated 2018-03-19
DESCRIPTION | 15 +-- MD5 | 46 ++++----- NAMESPACE | 6 + NEWS | 7 + R/RcppExports.R | 8 - R/analysis.R | 28 +++-- R/edit.R | 94 +++++++++++++------ R/ggplot2.R |only R/ocr.R | 16 ++- R/utils.R | 2 build/vignette.rds |binary configure | 14 +- inst/WORDLIST | 1 inst/doc/intro.R | 18 +-- inst/doc/intro.Rmd | 22 +--- inst/doc/intro.html | 237 ++++++++++++++++++++++++++---------------------- man/analysis.Rd | 23 +++- man/editing.Rd | 63 ++++++++---- man/image_ggplot.Rd |only man/ocr.Rd | 4 src/RcppExports.cpp | 18 ++- src/base.cpp | 4 src/edit.cpp | 4 src/transformations.cpp | 18 ++- vignettes/intro.Rmd | 22 +--- 25 files changed, 391 insertions(+), 279 deletions(-)
Title: 'GeoJSON' Topology Calculations and Operations
Description: Tools for doing calculations and manipulations on 'GeoJSON',
a 'geospatial' data interchange format (<https://tools.ietf.org/html/rfc7946>).
'GeoJSON' is also valid 'JSON'.
Author: Scott Chamberlain [aut, cre],
Niels Lohmann [cph]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between geoops versions 0.1.2 dated 2017-10-17 and 0.1.8 dated 2018-03-19
DESCRIPTION | 10 LICENSE | 2 MD5 | 28 NEWS.md | 9 README.md | 56 build/vignette.rds |binary inst/doc/geoops_vignette.R | 2 inst/doc/geoops_vignette.Rmd | 2 inst/doc/geoops_vignette.html | 1305 +++++++ src/json.h | 7085 ++++++++++++++++++++++++++------------- tools/img/unnamed-chunk-18-1.png |binary tools/img/unnamed-chunk-19-1.png |binary tools/img/unnamed-chunk-20-1.png |binary tools/img/unnamed-chunk-21-1.png |only tools/img/unnamed-chunk-22-1.png |only vignettes/geoops_vignette.Rmd | 2 16 files changed, 6132 insertions(+), 2369 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss amounts and loss
frequency: 19 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities.
Author: Vincent Goulet [cre, aut],
Sébastien Auclair [ctb],
Christophe Dutang [aut],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Alexandre Parent [ctb],
Mathieu Pigeon [aut],
Louis-Philippe Pouliot [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 2.3-0 dated 2018-02-07 and 2.3-1 dated 2018-03-19
DESCRIPTION | 8 - MD5 | 65 +++++----- R/bayes.R | 4 R/bstraub.R | 10 - inst/NEWS.Rd | 24 +++ inst/doc/actuar.R | 4 inst/doc/actuar.Rnw | 5 inst/doc/actuar.pdf |binary inst/doc/coverage.R | 24 +-- inst/doc/coverage.Rnw | 5 inst/doc/coverage.pdf |binary inst/doc/credibility.R | 29 ++-- inst/doc/credibility.Rnw | 275 +++++++++++++++++++++++++++++++++++++++++++- inst/doc/credibility.pdf |binary inst/doc/distributions.Rnw | 5 inst/doc/distributions.pdf |binary inst/doc/modeling.R | 74 +++++------ inst/doc/modeling.Rnw | 5 inst/doc/modeling.pdf |binary inst/doc/risk.R | 50 ++++---- inst/doc/risk.Rnw | 3 inst/doc/risk.pdf |binary inst/doc/simulation.R | 38 +++--- inst/doc/simulation.Rnw | 5 inst/doc/simulation.pdf |binary man/cm.Rd | 4 vignettes/actuar.Rnw | 5 vignettes/auto |only vignettes/coverage.Rnw | 5 vignettes/credibility.Rnw | 275 +++++++++++++++++++++++++++++++++++++++++++- vignettes/distributions.Rnw | 5 vignettes/modeling.Rnw | 5 vignettes/risk.Rnw | 3 vignettes/simulation.Rnw | 5 34 files changed, 759 insertions(+), 181 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-02 1.0.1
2014-03-24 1.0.0
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.4-1 dated 2018-01-05 and 1.4-3 dated 2018-03-19
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 22 ++++++++++++++++++++++ R/functions.syn.r | 22 ++++++++++++++++++---- R/methods.syn.r | 8 ++++---- R/padModel.syn.r | 9 +++++---- R/utility.syn.r | 2 +- build/partial.rdb |binary inst/doc/inference.pdf |binary inst/doc/synthpop.pdf |binary man/syn.Rd | 2 ++ man/syn.polyreg.Rd | 9 +++++++-- man/synthpop-package.Rd | 4 ++-- 13 files changed, 77 insertions(+), 33 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.7.9 dated 2017-11-30 and 0.8.0 dated 2018-03-19
nonmemica-0.7.9/nonmemica/man/fold.character.Rd |only nonmemica-0.7.9/nonmemica/man/fold.numeric.Rd |only nonmemica-0.7.9/nonmemica/man/fold_character.Rd |only nonmemica-0.7.9/nonmemica/man/unfold.character.Rd |only nonmemica-0.7.9/nonmemica/man/unfold.numeric.Rd |only nonmemica-0.8.0/nonmemica/DESCRIPTION | 10 nonmemica-0.8.0/nonmemica/MD5 | 35 +- nonmemica-0.8.0/nonmemica/NAMESPACE | 5 nonmemica-0.8.0/nonmemica/R/nonmemica.R | 9 nonmemica-0.8.0/nonmemica/R/path.R | 4 nonmemica-0.8.0/nonmemica/R/superset.R | 235 ++-------------- nonmemica-0.8.0/nonmemica/build/vignette.rds |binary nonmemica-0.8.0/nonmemica/inst/doc/parameter-table.html | 38 +- nonmemica-0.8.0/nonmemica/man/datafile.character.Rd | 2 nonmemica-0.8.0/nonmemica/man/meta.character.Rd | 2 nonmemica-0.8.0/nonmemica/man/metaplot.character.Rd | 18 - nonmemica-0.8.0/nonmemica/man/metaplot_character.Rd | 20 - nonmemica-0.8.0/nonmemica/man/metasuperset.Rd | 8 nonmemica-0.8.0/nonmemica/man/nonmemica.Rd | 9 nonmemica-0.8.0/nonmemica/man/specfile.character.Rd | 2 nonmemica-0.8.0/nonmemica/man/superset.character.Rd | 2 21 files changed, 102 insertions(+), 297 deletions(-)
Title: Consistant Cotrend Rank Selection
Description: Implements cointegration/cotrending rank selection
algorithm in Guo and Shintani (2013) "Consistant
cotrending rank selection when both stochastic and nonlinear
deterministic trends are present".
The Econometrics Journal 16: 473-483
<doi:10.1111/j.1368-423X.2012.00392.x>.
Numbered examples correspond to Feb 2011 preprint
<http://www.fas.nus.edu.sg/ecs/events/seminar/seminar-papers/05Apr11.pdf>.
Author: A. Christian Silva
Maintainer: A. Christian Silva <a.christian.silva@gmail.com>
Diff between cotrend versions 1.0 dated 2011-11-03 and 1.0.1 dated 2018-03-19
DESCRIPTION | 21 +++- MD5 | 5 - NAMESPACE |only R/cotrend.R | 279 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 158 insertions(+), 147 deletions(-)
Title: Wrapper Algorithm for All Relevant Feature Selection
Description: An all relevant feature selection wrapper algorithm.
It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).
Author: Miron Bartosz Kursa [aut, cre]
(<https://orcid.org/0000-0001-7672-648X>),
Witold Remigiusz Rudnicki [aut]
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Diff between Boruta versions 5.2.0 dated 2017-01-27 and 5.3.0 dated 2018-03-19
DESCRIPTION | 35 ++-- MD5 | 37 ++-- NAMESPACE | 1 R/Boruta.R | 360 ++++++++++++++++++++--------------------- R/importance.R | 208 +++++++++++++----------- R/tools.R | 372 +++++++++++++++++++++---------------------- inst/NEWS | 149 ++++++++--------- man/Boruta.Rd | 53 +++--- man/TentativeRoughFix.Rd | 1 man/attStats.Rd | 13 - man/getFormulae.Rd | 1 man/getImpFerns.Rd | 1 man/getImpLegacyRf.Rd | 13 - man/getImpRf.Rd | 3 man/getImpXgboost.Rd |only man/getSelectedAttributes.Rd | 9 - man/plot.Boruta.Rd | 11 - man/plotImpHistory.Rd | 9 - man/print.Boruta.Rd | 1 tests |only 20 files changed, 652 insertions(+), 625 deletions(-)
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' to learn more.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 2.0.2 dated 2018-02-13 and 2.4.0 dated 2018-03-19
DESCRIPTION | 12 - MD5 | 112 +++++++------ NEWS | 23 ++ R/build_run_modify.r | 115 ++++++++------ R/datasets.R | 8 R/deprecated.r | 2 R/fit_and_reporting.r | 284 ++++++++++++++++++----------------- R/misc_and_utility.r | 151 +++++++++++------- R/model_builders.r | 71 ++++++-- R/tmx.r | 10 - R/umxACEcov_fixed.R | 4 R/umxACEv.R | 189 +++++++++++++---------- R/umxGxE_biv.R | 11 - R/umxSexLim.R | 13 + R/xmu.r | 4 inst/CITATION | 2 inst/WORDLIST | 83 ++++++++-- man/GFF.Rd | 15 - man/figures/ACEv.png |only man/figures/umx_help_figures |only man/figures/umx_help_figures.graffle |binary man/install.OpenMx.Rd | 25 +-- man/reliability.Rd | 2 man/umx.Rd | 3 man/umxACE.Rd | 26 +-- man/umxACE_cov_fixed.Rd | 2 man/umxACEv.Rd | 90 ++++++----- man/umxAPA.Rd | 34 +--- man/umxBrownie.Rd | 18 +- man/umxCP.Rd | 15 - man/umxCompare.Rd | 12 - man/umxEFA.Rd | 40 +++- man/umxFactorScores.Rd | 3 man/umxGetParameters.Rd | 2 man/umxIP.Rd | 32 ++- man/umxPath.Rd | 50 +++--- man/umxPlotACE.Rd | 6 man/umxPlotACEv.Rd | 2 man/umxPlotCP.Rd | 5 man/umxPlotIP.Rd | 5 man/umxSexLim.Rd | 2 man/umxSummaryACE.Rd | 2 man/umxSummaryCP.Rd | 6 man/umxSummaryGxE_biv.Rd | 4 man/umxSummaryIP.Rd | 11 - man/umxTwoStage.Rd | 2 man/umxUnexplainedCausalNexus.Rd | 8 man/umx_check_model.Rd | 6 man/umx_explode_twin_names.Rd | 3 man/umx_make.Rd | 8 man/umx_make_TwinData.Rd | 7 man/umx_names.Rd | 18 -- man/umx_rename_file.Rd | 2 man/umx_scale_wide_twin_data.Rd | 2 man/umx_standardize_IP.Rd | 2 man/umx_standardize_RAM.Rd | 2 man/us_skinfold_data.Rd | 3 man/xmuLabel_Matrix.Rd | 2 58 files changed, 929 insertions(+), 642 deletions(-)
Title: Estimating and Testing Direct Effects in Directed Acyclic Graphs
using Estimating Equations
Description: In many studies across different disciplines, detailed measures of the variables of interest are available. If assumptions can be made regarding the direction of effects between the assessed variables, this has to be considered in the analysis. The functions in this package implement the novel approach CIEE (causal inference using estimating equations; Konigorski et al., 2018, <DOI:10.1002/gepi.22107>) for estimating and testing the direct effect of an exposure variable on a primary outcome, while adjusting for indirect effects of the exposure on the primary outcome through a secondary intermediate outcome and potential factors influencing the secondary outcome. The underlying directed acyclic graph (DAG) of this considered model is described in the vignette. CIEE can be applied to studies in many different fields, and it is implemented here for the analysis of a continuous primary outcome and a time-to-event primary outcome subject to censoring. CIEE uses estimating equations to obtain estimates of the direct effect and robust sandwich standard error estimates. Then, a large-sample Wald-type test statistic is computed for testing the absence of the direct effect. Additionally, standard multiple regression, regression of residuals, and the structural equation modeling approach are implemented for comparison.
Author: Stefan Konigorski [aut, cre],
Yildiz E. Yilmaz [ctb]
Maintainer: Stefan Konigorski <stefan.konigorski@gmail.com>
Diff between CIEE versions 0.1.0 dated 2017-11-16 and 0.1.1 dated 2018-03-19
CIEE-0.1.0/CIEE/vignettes/Figure1.tiff |only CIEE-0.1.1/CIEE/DESCRIPTION | 8 ++++---- CIEE-0.1.1/CIEE/MD5 | 14 +++++++------- CIEE-0.1.1/CIEE/build/vignette.rds |binary CIEE-0.1.1/CIEE/inst/CITATION | 10 ++++++---- CIEE-0.1.1/CIEE/inst/doc/ciee.Rmd | 10 +++++----- CIEE-0.1.1/CIEE/inst/doc/ciee.pdf |binary CIEE-0.1.1/CIEE/vignettes/Figure1.pdf |only CIEE-0.1.1/CIEE/vignettes/ciee.Rmd | 10 +++++----- 9 files changed, 27 insertions(+), 25 deletions(-)
Title: Learn Foreign Language Vocabulary
Description: Use the R console as an interactive learning environment to memorize any two columns dataset.
Author: Félix Luginbuhl [aut, cre]
Maintainer: Félix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between polyglot versions 0.1.1 dated 2018-03-19 and 0.1.2 dated 2018-03-19
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- README.md | 2 +- inst/doc/Introduction-to-polyglot.Rmd | 2 +- inst/doc/Introduction-to-polyglot.html | 6 +++--- vignettes/Introduction-to-polyglot.Rmd | 2 +- 6 files changed, 15 insertions(+), 14 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 0.5 dated 2017-05-09 and 0.6 dated 2018-03-19
DESCRIPTION | 14 - MD5 | 41 ++-- R/bmixnorm.R | 436 ++++++++++++++++++++++------------------------- R/bmixnorm_bdmcmc.R |only man/bmixgamma.Rd | 2 man/bmixnorm.Rd | 11 + man/bmixt.Rd | 2 man/bmixture-internal.Rd | 2 man/bmixture-package.Rd | 6 man/mixgamma.Rd | 2 man/mixnorm.Rd | 2 man/mixt.Rd | 2 man/plot.bmixgamma.Rd | 2 man/plot.bmixnorm.Rd | 2 man/plot.bmixt.Rd | 2 man/print.bmixgamma.Rd | 2 man/print.bmixnorm.Rd | 2 man/print.bmixt.Rd | 2 man/rdirichlet.Rd | 2 man/summary.bmixgamma.Rd | 2 man/summary.bmixnorm.Rd | 2 man/summary.bmixt.Rd | 2 22 files changed, 267 insertions(+), 273 deletions(-)
Title: Classification and Visualization
Description: Miscellaneous functions for classification and visualization,
e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes,
an interface to 'svmlight' and stepclass() wrapper variable selection
for supervised classification, partimat() visualization of classification rules
and shardsplot() of cluster results as well as kmodes() clustering for categorical data,
corclust() variable clustering, variable extraction from different variable clustering models
and weight of evidence preprocessing.
Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero Szepannek, Marc Zentgraf
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between klaR versions 0.6-13 dated 2018-03-14 and 0.6-14 dated 2018-03-19
DESCRIPTION | 8 MD5 | 22 NAMESPACE | 4 NEWS | 8 man/corclust.Rd | 7 man/cvtree.Rd |only man/xtractvars.Rd |only tests/EDAM.R | 6 tests/EDAM.Rout.save | 15 tests/EDAM.ps.save | 4330 - tests/testklaR.ps.save |136828 +++++++++++++++++++++++----------------------- tests/testsklaR.R | 8 tests/testsklaR.Rout.save | 25 13 files changed, 70699 insertions(+), 70562 deletions(-)
Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scatterpie versions 0.0.8 dated 2017-12-04 and 0.0.9 dated 2018-03-19
DESCRIPTION | 8 - MD5 | 10 +- R/geom_scatterpie.R | 1 README.md | 29 +++--- build/vignette.rds |binary inst/doc/scatterpie.html | 203 ++++++++++++++++++++--------------------------- 6 files changed, 115 insertions(+), 136 deletions(-)
Title: Estimation Methods for Stochastic Differential Mixed Effects
Models
Description: Inference on stochastic differential models Ornstein-Uhlenbeck or
Cox-Ingersoll-Ross, with one or two random effects in the drift function.
S. Hermann, K. Ickstadt and C. Mueller (2016) <doi:10.1002/asmb.2175>
M. Delattre, V. Genon-Catalot and A. Samson (2012) <doi:10.1111/j.1467-9469.2012.00813.x>
F. Comte, V. Genon-Catalot and A. Samson (2013) <doi:10.1016/j.spa.2013.04.009>
V. Genon-Catalot and C. Laredo (2014) <doi:10.1080/02331888.2016.1141910>
C. Dion and V. Genon-Catalot (2015) <doi:10.1007/s11203-015-9122-0>.
Author: Charlotte Dion [aut, cre],
Adeline Sansom [aut], Simone Hermann [aut]
Maintainer: Charlotte Dion <charlotte.dion@upmc.fr>
Diff between mixedsde versions 3.0 dated 2017-08-04 and 4.0 dated 2018-03-19
DESCRIPTION | 11 +-- MD5 | 78 +++++++++++----------- R/mixedsde.fit.R | 3 README.md | 1 man/Bayes.fit-class.Rd | 2 man/Bayes.pred-class.Rd | 2 man/BayesianNormal.Rd | 5 - man/EstParamNormal.Rd | 3 man/Freq.fit-class.Rd | 2 man/UV.Rd | 5 - man/ad.propSd.Rd | 3 man/ad.propSd_random.Rd | 3 man/bx.Rd | 3 man/chain2samples.Rd | 3 man/dcCIR2.Rd | 3 man/diagnostic.Rd | 3 man/discr.Rd | 3 man/eigenvaluesV.Rd | 3 man/likelihoodNormal.Rd | 3 man/likelihoodNormalestimfix.Rd | 3 man/mixedsde.fit.Rd | 120 +++++++++++++++++----------------- man/mixedsde.sim.Rd | 33 ++++----- man/mixture.sim.Rd | 13 +-- man/out.Rd | 3 man/plot-Bayes.fit-ANY-method.Rd | 10 +- man/plot-Bayes.pred-ANY-method.Rd | 3 man/plot-Freq.fit-ANY-method.Rd | 3 man/plot2compare-Bayes.fit-method.Rd | 3 man/plot2compare-Bayes.pred-method.Rd | 7 - man/plot2compare.Rd | 3 man/pred-Bayes.fit-method.Rd | 3 man/pred-Freq.fit-method.Rd | 3 man/pred.Rd | 3 man/print-Bayes.fit-method.Rd | 3 man/print-Freq.fit-method.Rd | 3 man/summary-Bayes.fit-method.Rd | 3 man/summary-Freq.fit-method.Rd | 3 man/valid-Bayes.fit-method.Rd | 3 man/valid-Freq.fit-method.Rd | 3 man/valid.Rd | 3 40 files changed, 170 insertions(+), 200 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 3.0 dated 2017-11-22 and 3.1 dated 2018-03-19
DESCRIPTION | 8 ++-- MD5 | 42 +++++++++++------------ NAMESPACE | 2 - R/bic.mixvmf.R | 4 +- R/f.rbing.R | 58 ++++++++++++++++++-------------- R/fishkent.R | 4 +- R/mix.vmf.R | 21 +++-------- R/rbingham.R | 80 +++++++++++++++++++++++++-------------------- R/rvmf.R | 43 ++++++++++++++++++++++++ R/rvonmises.R | 20 +++++++++++ R/spher.reg.R | 2 - R/spml.mle.R | 2 - R/tang.conc.R | 1 R/vmf.kde.R | 2 - man/Directional-package.Rd | 4 +- man/ESAGdensity.Rd | 3 + man/ESAGmle.Rd | 6 ++- man/ESAGsim.Rd | 12 +++--- man/bic.mixvmf.Rd | 5 ++ man/f.rbing.Rd | 8 +++- man/mix.vmf.Rd | 13 ++++--- man/spml.mle.Rd | 6 ++- 22 files changed, 216 insertions(+), 130 deletions(-)
Title: Calculate the RR for the GAM
Description: To calculate the relative risk (RR) for the generalized additive model.
Author: Zhicheng Du,Wangjian Zhang, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between gamRR versions 0.3.0 dated 2017-11-22 and 0.4.0 dated 2018-03-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/gamRR.R | 42 +++++++++++++++++++++++++++++++++++++----- R/gamRR.boot.R | 2 ++ man/gamRR.Rd | 9 +++++++-- man/gamRR.boot.Rd | 6 +++++- 6 files changed, 59 insertions(+), 16 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>.
Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M).
Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre],
Gabriel Lang [aut],
Stephane Traissac [aut],
Florence Puech [aut]
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between dbmss versions 2.5-1 dated 2017-11-28 and 2.6-3 dated 2018-03-19
dbmss-2.5-1/dbmss/NEWS |only dbmss-2.5-1/dbmss/inst/doc/dbmss.R |only dbmss-2.5-1/dbmss/inst/doc/dbmss.Rnw |only dbmss-2.5-1/dbmss/inst/doc/dbmss.pdf |only dbmss-2.5-1/dbmss/src/init.c |only dbmss-2.5-1/dbmss/vignettes/KdFig.pdf |only dbmss-2.5-1/dbmss/vignettes/dbmss.Rnw |only dbmss-2.6-3/dbmss/DESCRIPTION | 17 +-- dbmss-2.6-3/dbmss/MD5 | 123 +++++++++++----------- dbmss-2.6-3/dbmss/NAMESPACE | 6 - dbmss-2.6-3/dbmss/NEWS.md |only dbmss-2.6-3/dbmss/R/CheckdbmssArguments.R | 16 ++ dbmss-2.6-3/dbmss/R/wmppp.R | 36 ++++-- dbmss-2.6-3/dbmss/README.md | 9 + dbmss-2.6-3/dbmss/build/vignette.rds |binary dbmss-2.6-3/dbmss/inst/doc/docs.Rmd |only dbmss-2.6-3/dbmss/inst/doc/docs.html |only dbmss-2.6-3/dbmss/inst/doc/rd.Rmd |only dbmss-2.6-3/dbmss/inst/doc/rd.html |only dbmss-2.6-3/dbmss/man/DEnvelope.Rd | 16 +- dbmss-2.6-3/dbmss/man/Dhat.Rd | 13 +- dbmss-2.6-3/dbmss/man/Dtable.Rd | 6 - dbmss-2.6-3/dbmss/man/FillEnvelope.Rd | 6 - dbmss-2.6-3/dbmss/man/GlobalEnvelope.Rd | 4 dbmss-2.6-3/dbmss/man/GoFtest.Rd | 6 - dbmss-2.6-3/dbmss/man/KEnvelope.Rd | 24 +--- dbmss-2.6-3/dbmss/man/KdEnvelope.Rd | 43 +++---- dbmss-2.6-3/dbmss/man/Kdhat.Rd | 31 ++--- dbmss-2.6-3/dbmss/man/Khat.Rd | 11 - dbmss-2.6-3/dbmss/man/KinhomEnvelope.Rd | 17 +-- dbmss-2.6-3/dbmss/man/Kinhomhat.Rd | 12 -- dbmss-2.6-3/dbmss/man/KmmEnvelope.Rd | 12 -- dbmss-2.6-3/dbmss/man/Kmmhat.Rd | 8 - dbmss-2.6-3/dbmss/man/Ktest.Rd | 6 - dbmss-2.6-3/dbmss/man/LEnvelope.Rd | 17 +-- dbmss-2.6-3/dbmss/man/Lhat.Rd | 12 -- dbmss-2.6-3/dbmss/man/LmmEnvelope.Rd | 12 -- dbmss-2.6-3/dbmss/man/Lmmhat.Rd | 10 - dbmss-2.6-3/dbmss/man/MEnvelope.Rd | 25 ++-- dbmss-2.6-3/dbmss/man/Mhat.Rd | 15 +- dbmss-2.6-3/dbmss/man/Rcpp.Rd | 34 +++--- dbmss-2.6-3/dbmss/man/as.Dtable.Rd | 5 dbmss-2.6-3/dbmss/man/as.wmppp.Rd | 9 - dbmss-2.6-3/dbmss/man/envelope.Dtable.Rd | 24 ++-- dbmss-2.6-3/dbmss/man/gEnvelope.Rd | 17 +-- dbmss-2.6-3/dbmss/man/generic.spatstat.Rd | 12 +- dbmss-2.6-3/dbmss/man/ghat.Rd | 11 - dbmss-2.6-3/dbmss/man/is.wmppp.Rd | 2 dbmss-2.6-3/dbmss/man/m_Envelope.Rd | 37 +++--- dbmss-2.6-3/dbmss/man/m_hat.Rd | 31 ++--- dbmss-2.6-3/dbmss/man/paracou16.Rd | 1 dbmss-2.6-3/dbmss/man/print.dbmssEnvelope.Rd | 6 - dbmss-2.6-3/dbmss/man/rPopulationIndependenceK.Rd | 9 - dbmss-2.6-3/dbmss/man/rPopulationIndependenceM.Rd | 9 - dbmss-2.6-3/dbmss/man/rRandomLabeling.Rd | 8 - dbmss-2.6-3/dbmss/man/rRandomLabelingM.Rd | 8 - dbmss-2.6-3/dbmss/man/rRandomLocation.Rd | 7 - dbmss-2.6-3/dbmss/man/rRandomPositionK.Rd | 5 dbmss-2.6-3/dbmss/man/summary.dbmssEnvelope.Rd | 5 dbmss-2.6-3/dbmss/man/wmppp.Rd | 8 - dbmss-2.6-3/dbmss/man/wmppp.object.Rd | 6 - dbmss-2.6-3/dbmss/src/RcppExports.cpp | 16 ++ dbmss-2.6-3/dbmss/tests/testthat.R | 2 dbmss-2.6-3/dbmss/tests/testthat/testDtable.R |only dbmss-2.6-3/dbmss/tests/testthat/testKd.R | 34 ++++-- dbmss-2.6-3/dbmss/tests/testthat/testM.R | 12 +- dbmss-2.6-3/dbmss/tests/testthat/testwmppp.R |only dbmss-2.6-3/dbmss/vignettes/dbmss.bib | 6 - dbmss-2.6-3/dbmss/vignettes/docs.Rmd |only dbmss-2.6-3/dbmss/vignettes/rd.Rmd |only dbmss-2.6-3/dbmss/vignettes/rd_index.yaml |only 71 files changed, 436 insertions(+), 401 deletions(-)
Title: Variable Selection for Model-Based Clustering of Mixed-Type Data
Set with Missing Values
Description: Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering<doi:10.1007/s11222-016-9670-1>. Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 2.0.1 dated 2017-10-16 and 2.1.0 dated 2018-03-19
VarSelLCM-2.0.1/VarSelLCM/R/DataCstr.R |only VarSelLCM-2.0.1/VarSelLCM/R/VSLCMGrlClasses.R |only VarSelLCM-2.0.1/VarSelLCM/man/VSLCMdataContinous-class.Rd |only VarSelLCM-2.0.1/VarSelLCM/man/VSLCMdataMixed-class.Rd |only VarSelLCM-2.0.1/VarSelLCM/man/VSLCMparamMixed-class.Rd |only VarSelLCM-2.0.1/VarSelLCM/man/VSLCMresultsMixed-class.Rd |only VarSelLCM-2.1.0/VarSelLCM/DESCRIPTION | 36 - VarSelLCM-2.1.0/VarSelLCM/MD5 | 84 +- VarSelLCM-2.1.0/VarSelLCM/NAMESPACE | 18 VarSelLCM-2.1.0/VarSelLCM/R/ARI.R |only VarSelLCM-2.1.0/VarSelLCM/R/DesignOutput.R | 3 VarSelLCM-2.1.0/VarSelLCM/R/ICLexact.R | 54 + VarSelLCM-2.1.0/VarSelLCM/R/Imputation.R | 91 +- VarSelLCM-2.1.0/VarSelLCM/R/Plot.R | 314 +++++----- VarSelLCM-2.1.0/VarSelLCM/R/Print.R | 108 --- VarSelLCM-2.1.0/VarSelLCM/R/Summary.R | 164 ----- VarSelLCM-2.1.0/VarSelLCM/R/VarSelConvert.R |only VarSelLCM-2.1.0/VarSelLCM/R/VarSelLCM.R | 211 +++++- VarSelLCM-2.1.0/VarSelLCM/R/VarSelShiny.R |only VarSelLCM-2.1.0/VarSelLCM/R/data.R |only VarSelLCM-2.1.0/VarSelLCM/R/model.R |only VarSelLCM-2.1.0/VarSelLCM/R/param.R |only VarSelLCM-2.1.0/VarSelLCM/R/results.R |only VarSelLCM-2.1.0/VarSelLCM/R/withoutmixture.R | 2 VarSelLCM-2.1.0/VarSelLCM/build |only VarSelLCM-2.1.0/VarSelLCM/inst/CITATION |only VarSelLCM-2.1.0/VarSelLCM/inst/NEWS |only VarSelLCM-2.1.0/VarSelLCM/inst/doc |only VarSelLCM-2.1.0/VarSelLCM/inst/shinyApp |only VarSelLCM-2.1.0/VarSelLCM/man/ARI.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VSLCMcriteria-class.Rd | 5 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMdata-class.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VSLCMdataCategorical-class.Rd | 16 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMdataContinuous-class.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VSLCMdataInteger-class.Rd | 18 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMmodel-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMparam-class.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VSLCMparamCategorical-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMparamContinuous-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMparamInteger-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMpartitions-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMresults-class.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VSLCMresultsCategorical-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMresultsContinuous-class.Rd | 6 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMresultsInteger-class.Rd | 6 VarSelLCM-2.1.0/VarSelLCM/man/VSLCMstrategy-class.Rd | 4 VarSelLCM-2.1.0/VarSelLCM/man/VarSelCluster.Rd | 74 +- VarSelLCM-2.1.0/VarSelLCM/man/VarSelConvert.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VarSelImputation.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/VarSelLCM-package.Rd | 49 + VarSelLCM-2.1.0/VarSelLCM/man/VarSelShiny.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/heart.Rd | 35 - VarSelLCM-2.1.0/VarSelLCM/man/plot-methods.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/print-methods.Rd |only VarSelLCM-2.1.0/VarSelLCM/man/summary-methods.Rd | 20 VarSelLCM-2.1.0/VarSelLCM/vignettes |only 56 files changed, 687 insertions(+), 655 deletions(-)
Title: Ecological Drift under the UNTB
Description: A collection of utilities for biodiversity data.
Includes the simulation of ecological drift under Hubbell's Unified
Neutral Theory of Biodiversity, and the calculation of various
diagnostics such as Preston curves. Now includes functionality
provided by Francois Munoz and Andrea Manica.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between untb versions 1.7-2 dated 2013-12-12 and 1.7-3 dated 2018-03-19
DESCRIPTION | 13 ++++++------- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 17 +++++++++++++++++ R/sysdata.rda |binary build/vignette.rds |binary data/butterflies.rda |binary data/caruso.rda |binary data/copepod.rda |binary data/ghats.rda |binary data/ostracod.rda |binary data/sahfos.rda |binary data/saunders.rda |binary data/spitale.rda |binary inst/CITATION | 5 ++--- inst/doc/untbpaper.pdf |binary man/bci.Rd | 11 ++--------- man/butterflies.Rd | 3 --- man/caruso.Rd | 5 ++++- man/optimal.params.sloss.Rd | 3 +++ man/sahfos.Rd | 7 +------ 20 files changed, 54 insertions(+), 48 deletions(-)
Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R that records plots
in a LaTeX-friendly format. The device transforms plotting
commands issued by R functions into LaTeX code blocks. When
included in a LaTeX document, these blocks are interpreted with
the help of 'TikZ'---a graphics package for TeX and friends
written by Till Tantau. Using the 'tikzDevice', the text of R
plots can contain LaTeX commands such as mathematical formula.
The device also allows arbitrary LaTeX code to be inserted into
the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb, cre],
Yihui Xie [ctb]
Maintainer: ORPHANED
Diff between tikzDevice versions 0.10-1.1 dated 2018-02-14 and 0.11 dated 2018-03-19
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tikzDevice-0.11/tikzDevice/tests/testthat/test_graphics.R | 726 +++++----- tikzDevice-0.11/tikzDevice/tests/testthat/test_metrics_dict.R | 48 tikzDevice-0.11/tikzDevice/tests/testthat/test_pointsize.R | 27 tikzDevice-0.11/tikzDevice/vignettes/figs/annotation.tex | 80 - tikzDevice-0.11/tikzDevice/vignettes/figs/latexEx.tex | 82 - tikzDevice-0.11/tikzDevice/vignettes/figs/pdf-example.pdf |binary tikzDevice-0.11/tikzDevice/vignettes/figs/simpleEx.tex | 2 tikzDevice-0.11/tikzDevice/vignettes/figs/tikz-example.tex | 2 tikzDevice-0.11/tikzDevice/vignettes/figs/titlePlot.tex | 2 tikzDevice-0.11/tikzDevice/vignettes/figs/westCoast.tex | 2 tikzDevice-0.11/tikzDevice/vignettes/tikzCodeBlock.sty | 12 tikzDevice-0.11/tikzDevice/vignettes/tikzDevice-concordance.tex | 2 tikzDevice-0.11/tikzDevice/vignettes/tikzDevice.Rnw | 3 82 files changed, 1762 insertions(+), 1720 deletions(-)
Title: Fit Rank-Ordered Logit (RO-Logit) Model
Description: Implements the rank-ordered logit (RO-logit) model for stratified
analysis of continuous outcomes introduced by
Tan et al. (2017) <doi:10.1177/0962280217747309>. Model diagnostics based on
the heuristic residuals and estimates in linear scales are available from
the package, and outcomes with ties are supported.
Author: Tan Chuen Seng, Ning Yilin
Maintainer: Ning Yilin <ningyilinnyl@gmail.com>
Diff between ROlogit versions 0.1.1 dated 2018-02-05 and 0.1.2 dated 2018-03-19
DESCRIPTION | 6 MD5 | 8 R/ROlogit.R | 686 ++++++++++++++++++++++++++-------------------------- data/inpat_bg.RData |binary inst/CITATION | 31 -- 5 files changed, 359 insertions(+), 372 deletions(-)
Title: Arrays with Arbitrary Offsets
Description: Generalise the starting point of the array index.
Author: Jonathan Rougier <j.c.rougier@bristol.ac.uk>
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between Oarray versions 1.4-5 dated 2013-01-21 and 1.4-7 dated 2018-03-19
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/Oarray.R | 11 +++-------- man/Oarray.Rd | 2 +- man/internal.Rd | 15 +++++++-------- 6 files changed, 26 insertions(+), 29 deletions(-)
Title: Simulation and Estimation of the Neyman-Scott Type Spatial
Cluster Models
Description: Simulation and estimation for Neyman-Scott spatial cluster point
process models and their extensions, based on the methodology in Tanaka, Ogata,
and Stoyan (2008) <doi:10.1002/bimj.200610339>. For estimating parameters by
the simplex method, parallel computation using 'OpenMP' application programming
interface is available.
Author: Ushio Tanaka [aut] (Fortran original),
Junji Nakano [aut],
Masami Saga [aut, cre]
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between NScluster versions 1.1.1 dated 2016-12-15 and 1.2.0 dated 2018-03-19
NScluster-1.1.1/NScluster/inst/AUTHORS |only NScluster-1.1.1/NScluster/man/SimplexIP.Rd |only NScluster-1.1.1/NScluster/man/SimplexThomas.Rd |only NScluster-1.1.1/NScluster/man/SimplexTypeA.Rd |only NScluster-1.1.1/NScluster/man/SimplexTypeB.Rd |only NScluster-1.1.1/NScluster/man/SimplexTypeC.Rd |only NScluster-1.1.1/NScluster/src/IP-Simulate.c |only NScluster-1.1.1/NScluster/src/IP-Simulatef.f |only NScluster-1.1.1/NScluster/src/Simplex-IPfp.f |only NScluster-1.1.1/NScluster/src/Simplex-Thomasfp.f |only NScluster-1.1.1/NScluster/src/Simplex-TypeAfp.f |only NScluster-1.1.1/NScluster/src/Simplex-TypeBfp.f |only NScluster-1.1.1/NScluster/src/Simplex-TypeCfp.f |only NScluster-1.1.1/NScluster/src/Thomas-Simulate.c |only NScluster-1.1.1/NScluster/src/Thomas-Simulatef.f |only NScluster-1.1.1/NScluster/src/TypeA-Simulate.c |only NScluster-1.1.1/NScluster/src/TypeA-Simulatef.f |only NScluster-1.1.1/NScluster/src/TypeB-Simulate.c |only NScluster-1.1.1/NScluster/src/TypeB-Simulatef.f |only NScluster-1.1.1/NScluster/src/TypeC-Simulate.c |only NScluster-1.1.1/NScluster/src/TypeC-Simulatef.f |only NScluster-1.2.0/NScluster/DESCRIPTION | 26 NScluster-1.2.0/NScluster/MD5 | 103 NScluster-1.2.0/NScluster/NAMESPACE | 10 NScluster-1.2.0/NScluster/R/NScluster.R | 2016 ++++++++++------- NScluster-1.2.0/NScluster/inst/COPYRIGHTS |only NScluster-1.2.0/NScluster/inst/doc/NScluster-guide.pdf |binary NScluster-1.2.0/NScluster/man/EstimateIP.Rd |only NScluster-1.2.0/NScluster/man/EstimateThomas.Rd |only NScluster-1.2.0/NScluster/man/EstimateTypeA.Rd |only NScluster-1.2.0/NScluster/man/EstimateTypeB.Rd |only NScluster-1.2.0/NScluster/man/EstimateTypeC.Rd |only NScluster-1.2.0/NScluster/man/NScluster-package.Rd | 17 NScluster-1.2.0/NScluster/man/PalmIP.Rd | 74 NScluster-1.2.0/NScluster/man/PalmThomas.Rd | 70 NScluster-1.2.0/NScluster/man/PalmTypeA.Rd | 74 NScluster-1.2.0/NScluster/man/PalmTypeB.Rd | 71 NScluster-1.2.0/NScluster/man/PalmTypeC.Rd | 75 NScluster-1.2.0/NScluster/man/SimulateIP.Rd | 76 NScluster-1.2.0/NScluster/man/SimulateThomas.Rd | 67 NScluster-1.2.0/NScluster/man/SimulateTypeA.Rd | 70 NScluster-1.2.0/NScluster/man/SimulateTypeB.Rd | 77 NScluster-1.2.0/NScluster/man/SimulateTypeC.Rd | 83 NScluster-1.2.0/NScluster/src/Makevars | 2 NScluster-1.2.0/NScluster/src/Palm-IP.c | 7 NScluster-1.2.0/NScluster/src/Palm-Thomas.c | 6 NScluster-1.2.0/NScluster/src/Palm-Thomasf.f | 2 NScluster-1.2.0/NScluster/src/Palm-TypeA.c | 7 NScluster-1.2.0/NScluster/src/Palm-TypeB.c | 6 NScluster-1.2.0/NScluster/src/Palm-TypeBf.f | 3 NScluster-1.2.0/NScluster/src/Palm-TypeC.c | 6 NScluster-1.2.0/NScluster/src/Simplex-IP.c | 13 NScluster-1.2.0/NScluster/src/Simplex-IPf.f |only NScluster-1.2.0/NScluster/src/Simplex-Thomas.c | 13 NScluster-1.2.0/NScluster/src/Simplex-Thomasf.f |only NScluster-1.2.0/NScluster/src/Simplex-TypeA.c | 13 NScluster-1.2.0/NScluster/src/Simplex-TypeAf.f |only NScluster-1.2.0/NScluster/src/Simplex-TypeB.c | 13 NScluster-1.2.0/NScluster/src/Simplex-TypeBf.f |only NScluster-1.2.0/NScluster/src/Simplex-TypeC.c | 23 NScluster-1.2.0/NScluster/src/Simplex-TypeCf.f |only NScluster-1.2.0/NScluster/src/Simulate-IP.c |only NScluster-1.2.0/NScluster/src/Simulate-IPf.f |only NScluster-1.2.0/NScluster/src/Simulate-Thomas.c |only NScluster-1.2.0/NScluster/src/Simulate-Thomasf.f |only NScluster-1.2.0/NScluster/src/Simulate-TypeA.c |only NScluster-1.2.0/NScluster/src/Simulate-TypeAf.f |only NScluster-1.2.0/NScluster/src/Simulate-TypeB.c |only NScluster-1.2.0/NScluster/src/Simulate-TypeBf.f |only NScluster-1.2.0/NScluster/src/Simulate-TypeC.c |only NScluster-1.2.0/NScluster/src/Simulate-TypeCf.f |only NScluster-1.2.0/NScluster/src/comsub.f | 42 NScluster-1.2.0/NScluster/src/init.c |only NScluster-1.2.0/NScluster/src/mt19937-64.c |only NScluster-1.2.0/NScluster/src/mt64.h |only 75 files changed, 1864 insertions(+), 1201 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Mikael Dubik (lart and glouvain functions). The package uses functions from dlib, Eigen, Spectra and eclat libraries, whose code has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 1.1.1 dated 2017-08-28 and 1.1.2 dated 2018-03-19
multinet-1.1.1/multinet/src/eclat/apriori/src/makefile |only multinet-1.1.1/multinet/src/eclat/eclat/src/makefile |only multinet-1.1.1/multinet/src/eclat/math/src/makefile |only multinet-1.1.1/multinet/src/eclat/tract/src/makefile |only multinet-1.1.1/multinet/src/eclat/util/src/makefile |only multinet-1.1.1/multinet/src/lib/dlib/CMakeLists.txt |only multinet-1.1.1/multinet/src/lib/dlib/LICENSE.txt |only multinet-1.1.1/multinet/src/lib/dlib/all |only multinet-1.1.1/multinet/src/lib/dlib/all_console.cpp |only multinet-1.1.1/multinet/src/lib/dlib/all_gui.cpp |only multinet-1.1.1/multinet/src/lib/dlib/base64 |only multinet-1.1.1/multinet/src/lib/dlib/base64.h |only multinet-1.1.1/multinet/src/lib/dlib/bayes_utils |only multinet-1.1.1/multinet/src/lib/dlib/bayes_utils.h |only multinet-1.1.1/multinet/src/lib/dlib/bigint |only multinet-1.1.1/multinet/src/lib/dlib/bigint.h |only multinet-1.1.1/multinet/src/lib/dlib/bit_stream |only multinet-1.1.1/multinet/src/lib/dlib/bit_stream.h |only 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multinet-1.1.2/multinet/src/multinet/measures/layer_similarity.cpp |only multinet-1.1.2/multinet/src/multinet/utils/CSVReader.cpp | 4 192 files changed, 448 insertions(+), 1162 deletions(-)
Title: Stock Data Analysis Functions
Description: Analysis of stock data ups and downs trend, the stock technical analysis indicators function have trend line, reversal pattern and market trend.
Author: Chun-Yu Liu [aut,cph],
Shu-Nung Yao [rev,ths]
Maintainer: Chun-Yu Liu <john401528@gmail.com>
Diff between lcyanalysis versions 1.0.1 dated 2018-03-18 and 1.0.2 dated 2018-03-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/bearpower.R | 13 +++++++------ R/bullpower.R | 13 +++++++------ man/bearpower.Rd | 6 ++++-- man/bullpower.Rd | 6 ++++-- 6 files changed, 31 insertions(+), 25 deletions(-)
Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.1.0 dated 2017-12-05 and 0.1.2 dated 2018-03-19
ggimage-0.1.0/ggimage/NEWS |only ggimage-0.1.2/ggimage/DESCRIPTION | 13 ++++++----- ggimage-0.1.2/ggimage/MD5 | 18 ++++++++-------- ggimage-0.1.2/ggimage/NAMESPACE | 4 +-- ggimage-0.1.2/ggimage/NEWS.md |only ggimage-0.1.2/ggimage/R/geom_image.R | 15 +++++++++---- ggimage-0.1.2/ggimage/R/geom_subview.R | 17 ++++++--------- ggimage-0.1.2/ggimage/README.md | 31 ++++++++++++++-------------- ggimage-0.1.2/ggimage/build/vignette.rds |binary ggimage-0.1.2/ggimage/inst/doc/ggimage.html | 26 +++++++++++------------ ggimage-0.1.2/ggimage/man/geom_image.Rd | 4 ++- 11 files changed, 67 insertions(+), 61 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Andreas Alfons, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Kamil Barton, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Romain Francois, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Christopher Jackson, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Henric Nilsson, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Nathan Russell, Nick Sabbe, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Alec Stephenson, Mark Stevenson, Matthias Templ, Terry Therneau, Yves Tille, Adrian Trapletti, Joshua Ulrich, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Hadley Wickham, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.23 dated 2017-12-11 and 0.99.24 dated 2018-03-19
DescTools-0.99.23/DescTools/man/InsRow.Rd |only DescTools-0.99.23/DescTools/man/PlotMatrix.Rd |only DescTools-0.99.24/DescTools/DESCRIPTION | 12 DescTools-0.99.24/DescTools/MD5 | 94 + DescTools-0.99.24/DescTools/NAMESPACE | 21 DescTools-0.99.24/DescTools/NEWS | 50 DescTools-0.99.24/DescTools/R/Desc.R | 14 DescTools-0.99.24/DescTools/R/DescTools.r | 1025 ++++++++++--------- DescTools-0.99.24/DescTools/R/Dialogs.r | 41 DescTools-0.99.24/DescTools/R/Distributions.R |only DescTools-0.99.24/DescTools/R/RcppExports.R | 12 DescTools-0.99.24/DescTools/R/SpecialPlots.r | 343 +++--- DescTools-0.99.24/DescTools/R/StatsAndCIs.r | 38 DescTools-0.99.24/DescTools/R/Tables.r | 46 DescTools-0.99.24/DescTools/R/Tests.r | 9 DescTools-0.99.24/DescTools/man/Append.Rd |only DescTools-0.99.24/DescTools/man/CohenKappa.Rd | 36 DescTools-0.99.24/DescTools/man/CountCompCases.Rd |only DescTools-0.99.24/DescTools/man/CramerV.Rd | 4 DescTools-0.99.24/DescTools/man/DenseRank.Rd | 9 DescTools-0.99.24/DescTools/man/Desc.Rd | 12 DescTools-0.99.24/DescTools/man/DescTools-package.Rd | 134 +- DescTools-0.99.24/DescTools/man/ErrBars.Rd | 13 DescTools-0.99.24/DescTools/man/ExtrVal.Rd |only DescTools-0.99.24/DescTools/man/Frechet.Rd |only DescTools-0.99.24/DescTools/man/GenExtrVal.Rd |only DescTools-0.99.24/DescTools/man/GenPareto.Rd |only DescTools-0.99.24/DescTools/man/Gompertz.Rd |only DescTools-0.99.24/DescTools/man/Gumbel.Rd |only DescTools-0.99.24/DescTools/man/KendallW.Rd | 26 DescTools-0.99.24/DescTools/man/Lc.Rd | 3 DescTools-0.99.24/DescTools/man/Order.Rd |only DescTools-0.99.24/DescTools/man/PlotCorr.Rd | 24 DescTools-0.99.24/DescTools/man/PlotFaces.Rd | 32 DescTools-0.99.24/DescTools/man/PlotFun.Rd | 13 DescTools-0.99.24/DescTools/man/PlotMarDens.Rd | 2 DescTools-0.99.24/DescTools/man/Recode.Rd | 21 DescTools-0.99.24/DescTools/man/Rename.Rd | 3 DescTools-0.99.24/DescTools/man/RevWeibull.Rd |only DescTools-0.99.24/DescTools/man/RgbToCol.Rd | 6 DescTools-0.99.24/DescTools/man/RunsTest.Rd | 12 DescTools-0.99.24/DescTools/man/SelectVarDlg.Rd | 29 DescTools-0.99.24/DescTools/man/SetNames.Rd | 4 DescTools-0.99.24/DescTools/man/Shade.Rd | 18 DescTools-0.99.24/DescTools/man/SplitAt.Rd |only DescTools-0.99.24/DescTools/man/StrVal.Rd | 14 DescTools-0.99.24/DescTools/man/TOne.Rd | 23 DescTools-0.99.24/DescTools/man/ToWrd.Rd | 13 DescTools-0.99.24/DescTools/man/XLGetRange.Rd | 4 DescTools-0.99.24/DescTools/man/as.matrix.Rd | 4 DescTools-0.99.24/DescTools/man/d.whisky.Rd | 18 DescTools-0.99.24/DescTools/man/figures/ModelDlg.png |only DescTools-0.99.24/DescTools/src/RcppExports.cpp | 38 DescTools-0.99.24/DescTools/src/distribution.h |only DescTools-0.99.24/DescTools/src/gompertz.cpp |only DescTools-0.99.24/DescTools/src/init.c | 8 DescTools-0.99.24/DescTools/src/rep_len.h |only 57 files changed, 1410 insertions(+), 818 deletions(-)
Title: Time Series Regression
Description: Time series regression. The dyn class interfaces ts,
irts(), zoo() and zooreg() time series classes to lm(), glm(),
loess(), quantreg::rq(), MASS::rlm(), MCMCpack::MCMCregress(),
quantreg::rq(), randomForest::randomForest() and other regression
functions allowing those functions to be used with time series
including specifications that may contain lags, diffs and
missing values.
Author: G. Grothendieck
Maintainer: M. Leeds <markleeds2@gmail.com>
Diff between dyn versions 0.2-9.3 dated 2017-02-08 and 0.2-9.6 dated 2018-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 5 +---- NEWS | 33 ++++++++++++++++++++++++++++++++- 4 files changed, 40 insertions(+), 12 deletions(-)
Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy data form.
Author: Earo Wang [aut, cre]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between rwalkr versions 0.3.2 dated 2017-11-11 and 0.3.3 dated 2018-03-19
DESCRIPTION | 6 +-- MD5 | 18 ++++----- NEWS.md | 10 +++++ R/scrape.R | 37 +++++++++---------- R/shiny.R | 70 ++++++++++++++++++++----------------- R/sysdata.rda |binary README.md | 93 ++++++++++++++++++++++++++++++-------------------- man/figure/plot-1.png |binary man/shine_melb.Rd | 5 +- man/walk_melb.Rd | 5 -- 10 files changed, 136 insertions(+), 108 deletions(-)
Title: RNA Secondary Structure Module Mining, Comparison and Plotting
Description: Provides function for RNA secondary structure plotting, comparison and module mining. Given a RNA secondary structure, you can obtain stem regions, hairpin loops, internal loops, bulge loops and multibranch loops of this RNA structure using this program. They are the basic modules of RNA secondary structure. For each module you get, you can use this program to label the RNA structure with a specific color. You can also use this program to compare two RNA secondary structures to get a score that represents similarity. Reference: Reuter JS, Mathews DH (2010) <doi:10.1186/1471-2105-11-129>.
Author: Zheng HeWei
Maintainer: Zheng HeWei<zhenghw@hrbmu.edu.cn>
Diff between RNAsmc versions 0.2.0 dated 2018-03-12 and 0.3.0 dated 2018-03-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/stem.R | 9 +++++++++ 3 files changed, 14 insertions(+), 5 deletions(-)