Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-9 dated 2018-01-15 and 0.2-10 dated 2018-01-31
ChangeLog | 6 ++++++ DESCRIPTION | 21 +++++++++++++++------ MD5 | 16 ++++++++-------- man/11_d.EMControl.Rd | 4 ++-- man/23_emgroup.Rd | 4 ++-- man/30_assign.class.Rd | 4 ++-- man/31_em.ic.Rd | 4 ++-- man/91_mvn.Rd | 4 ++-- src/Makevars | 2 +- 9 files changed, 40 insertions(+), 25 deletions(-)
Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful
and 'ready-to-publish' survival curves with the 'number at risk' table
and 'censoring count plot'. Other functions are also available to plot
adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre],
Marcin Kosinski [aut],
Przemyslaw Biecek [ctb],
Scheipl Fabian [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between survminer versions 0.4.1 dated 2017-11-17 and 0.4.2 dated 2018-01-31
DESCRIPTION | 12 +-- MD5 | 46 +++++++------- NEWS.md | 12 +++ R/ggadjustedcurves.R | 27 ++++---- R/ggflexsurvplot.R | 10 ++- R/ggsurvplot.R | 2 R/ggsurvplot_combine.R | 2 R/ggurvplot_arguments.R | 6 + R/utilities.R | 19 +++++ inst/doc/Informative_Survival_Plots.html | 2 inst/doc/Playing_with_fonts_and_texts.html | 12 +-- inst/doc/Specifiying_weights_in_log-rank_comparisons.R | 18 ++--- inst/doc/Specifiying_weights_in_log-rank_comparisons.Rmd | 18 ++--- inst/doc/Specifiying_weights_in_log-rank_comparisons.html | 32 ++++----- man/ggadjustedcurves.Rd | 8 +- man/ggflexsurvplot.Rd | 6 + man/ggsurvplot.Rd | 6 + man/ggsurvplot_arguments.Rd | 6 + man/ggsurvplot_combine.Rd | 2 man/ggsurvplot_df.Rd | 4 - man/ggsurvplot_facet.Rd | 4 - man/ggsurvtable.Rd | 6 + tools/README-ggplot2-basic-survival-plot-1.png |binary vignettes/Specifiying_weights_in_log-rank_comparisons.Rmd | 18 ++--- 24 files changed, 166 insertions(+), 112 deletions(-)
Title: Paired Response Curve
Description: Estimation, prediction and testing for analyzing serial dilution assay data (Fong and Yu 2015 <DOI:10.1080/19466315.2015.1093019>) using paired response curve, which is a model of the nonlinear functional relationship between experimental outcomes measured at two different dilutions.
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between prc versions 2015.6-24 dated 2015-06-24 and 2018.1-31 dated 2018-01-31
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- NAMESPACE | 9 ++++++++- R/prc.R | 12 ++++++++---- data/mtct.eg.rda |binary man/mtct.eg.Rd | 2 +- man/prc.Rd | 3 ++- src/computeA.c | 5 +++-- src/registerDynamicSymbol.c |only tests/doRUnit.R | 4 ++-- 10 files changed, 39 insertions(+), 25 deletions(-)
Title: Optimistic Optimization in R
Description: Implementation of optimistic optimization methods for global optimization of deterministic or stochastic functions. The algorithms feature guarantees of the convergence to a global optimum. They require minimal assumptions on the (only local) smoothness, where the smoothness parameter does not need to be known. They are expected to be useful for the most difficult functions when we have no information on smoothness and the gradients are unknown or do not exist. Due to the weak assumptions, however, they can be mostly effective only in small dimensions, for example, for hyperparameter tuning.
Author: M. Binois [cre, aut, trl] (R port),
A. Carpentier [aut] (Matlab original),
J.-B. Grill [aut] (Python original),
R. Munos [aut] (Python and Matlab original),
M. Valko [aut, ctb] (Python and Matlab original)
Maintainer: M. Binois <mbinois@mcs.anl.gov>
Diff between OOR versions 0.1.1 dated 2017-02-03 and 0.1.2 dated 2018-01-31
DESCRIPTION | 14 +++++++------- MD5 | 7 ++++--- NEWS |only R/StoSOO.R | 2 +- man/StoSOO.Rd | 2 +- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Functions for Nonlinear Least Squares Solutions
Description: Provides tools for working with nonlinear least squares problems.
It is intended to eventually supersede the 'nls()' function in the R
distribution. For example, 'nls()' specifically does NOT deal with small
or zero residual problems as its Gauss-Newton method frequently stops with
'singular gradient' messages. 'nlsr' is based on the now-deprecated package
'nlmrt', and has refactored functions and R-language symbolic derivative
features.
Author: John C Nash [aut, cre],
Duncan Murdoch [aut]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between nlsr versions 2017.10.4 dated 2017-10-05 and 2018.1.28 dated 2018-01-31
DESCRIPTION | 19 - MD5 | 26 - NEWS | 20 + R/derivs.R | 10 build/vignette.rds |binary inst/doc/FixedParameters.html | 28 +- inst/doc/nlsr-derivs.html | 576 ++++++++++++++++++++---------------------- inst/doc/nlsr-devdoc.html | 416 +++++++++++++++--------------- man/Simplify.Rd | 5 man/nlfb.Rd | 1 man/nlsr-package.Rd | 10 man/nlxb.Rd | 3 tests/derivs.R | 5 tests/derivs.Rout.save | 14 - 14 files changed, 577 insertions(+), 556 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015)<doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016)<doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016)<arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016)<arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016)<arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Amos Donald D. [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 2.1 dated 2017-01-06 and 2.2 dated 2018-01-31
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- man/MGHFA.Rd | 3 ++- man/cMSGHD.Rd | 3 ++- src/Makevars | 2 +- src/registerDynamicSymbol.c |only 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. Kriging models, are
applied to global multi-objective optimization of black-box functions.
Multi-objective Expected Improvement and Step-wise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mbinois@mcs.anl.gov>
Diff between GPareto versions 1.1.0 dated 2017-06-29 and 1.1.1 dated 2018-01-31
GPareto-1.1.0/GPareto/src/init.c |only GPareto-1.1.1/GPareto/DESCRIPTION | 22 - GPareto-1.1.1/GPareto/MD5 | 33 - GPareto-1.1.1/GPareto/NAMESPACE | 3 GPareto-1.1.1/GPareto/NEWS | 7 GPareto-1.1.1/GPareto/R/RcppExports.R | 6 GPareto-1.1.1/GPareto/R/checkPredict.R | 12 GPareto-1.1.1/GPareto/R/plotGPareto.R | 149 ++++--- GPareto-1.1.1/GPareto/R/plotParetoEmp.R | 173 ++++++--- GPareto-1.1.1/GPareto/R/predictkms.R | 6 GPareto-1.1.1/GPareto/build/vignette.rds |binary GPareto-1.1.1/GPareto/inst/doc/GPareto_vignette.R | 218 ++++++----- GPareto-1.1.1/GPareto/inst/doc/GPareto_vignette.Rnw | 355 +++++++++++-------- GPareto-1.1.1/GPareto/inst/doc/GPareto_vignette.pdf |binary GPareto-1.1.1/GPareto/man/plotGPareto.Rd | 34 + GPareto-1.1.1/GPareto/man/plotParetoEmp.Rd | 21 + GPareto-1.1.1/GPareto/src/RcppExports.cpp | 18 GPareto-1.1.1/GPareto/vignettes/GPareto_vignette.Rnw | 355 +++++++++++-------- 18 files changed, 875 insertions(+), 537 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the 'evd' package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott, Yang Hu and Alfadino Akbar, University of Canterbury
Maintainer: Carl Scarrott <carl.scarrott@canterbury.ac.nz>
Diff between evmix versions 2.7 dated 2017-04-03 and 2.8 dated 2018-01-31
DESCRIPTION | 10 +++---- MD5 | 70 +++++++++++++++++++++++++-------------------------- R/dbckden.r | 6 ++-- R/dbckdengpd.r | 2 - R/dbckdengpdcon.r | 2 - R/dgkg.r | 2 - R/dgkgcon.r | 2 - R/dkden.r | 4 +- R/dkdengpd.r | 2 - R/dkdengpdcon.r | 2 - R/dpsden.r | 2 - R/evmix-package.r | 6 ++-- R/fbckdengpd.r | 5 ++- R/fbckdengpdcon.r | 5 ++- R/fgkg.r | 4 +- R/fgkgcon.r | 4 +- R/fkdengpd.r | 4 +- R/fkdengpdcon.r | 4 +- inst/CITATION | 8 ++--- inst/doc/Rd2.pdf |binary man/bckden.Rd | 6 ++-- man/bckdengpd.Rd | 2 - man/bckdengpdcon.Rd | 2 - man/evmix-package.Rd | 6 ++-- man/fbckdengpd.Rd | 4 +- man/fbckdengpdcon.Rd | 4 +- man/fgkg.Rd | 4 +- man/fgkgcon.Rd | 4 +- man/fkdengpd.Rd | 4 +- man/fkdengpdcon.Rd | 4 +- man/gkg.Rd | 2 - man/gkgcon.Rd | 2 - man/kden.Rd | 4 +- man/kdengpd.Rd | 2 - man/kdengpdcon.Rd | 2 - man/psden.Rd | 2 - 36 files changed, 100 insertions(+), 98 deletions(-)
Title: Statistical Tools for Filebacked Big Matrices
Description: Easy-to-use, efficient, flexible and scalable statistical tools.
Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping.
It provides for instance matrix operations, Principal Component Analysis,
sparse linear supervised models, utility functions and more.
Preprint: Privé et al. (2017) <doi:10.1101/190926>.
Author: Florian Privé [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigstatsr versions 0.2.3 dated 2017-11-30 and 0.2.4 dated 2018-01-31
bigstatsr-0.2.3/bigstatsr/R/CMSA.R |only bigstatsr-0.2.3/bigstatsr/R/sparseSVM.R |only bigstatsr-0.2.3/bigstatsr/inst/include/bigstatsr/SubIntMatCovAcc.h |only bigstatsr-0.2.3/bigstatsr/man/COPY_biglasso.Rd |only bigstatsr-0.2.3/bigstatsr/man/COPY_sparseSVM.Rd |only bigstatsr-0.2.3/bigstatsr/man/big_CMSA.Rd |only bigstatsr-0.2.3/bigstatsr/man/big_spSVM.Rd |only bigstatsr-0.2.3/bigstatsr/man/predict.big_CMSA.Rd |only bigstatsr-0.2.3/bigstatsr/src/sparseSVM.cpp |only bigstatsr-0.2.3/bigstatsr/tests/testthat/test-CMSA.R |only bigstatsr-0.2.3/bigstatsr/tests/testthat/test-spSVM.R |only bigstatsr-0.2.4/bigstatsr/DESCRIPTION | 29 bigstatsr-0.2.4/bigstatsr/MD5 | 242 +-- bigstatsr-0.2.4/bigstatsr/NAMESPACE | 120 - bigstatsr-0.2.4/bigstatsr/NEWS.md | 28 bigstatsr-0.2.4/bigstatsr/R/AUC.R | 217 +- bigstatsr-0.2.4/bigstatsr/R/FBM-attach.R | 76 - bigstatsr-0.2.4/bigstatsr/R/FBM-code256.R | 306 ++-- bigstatsr-0.2.4/bigstatsr/R/FBM-copy.R | 138 - bigstatsr-0.2.4/bigstatsr/R/FBM.R | 446 +++--- bigstatsr-0.2.4/bigstatsr/R/RcppExports.R | 246 +-- bigstatsr-0.2.4/bigstatsr/R/SVD.R | 222 +-- bigstatsr-0.2.4/bigstatsr/R/apply-parallelize.R | 326 ++-- bigstatsr-0.2.4/bigstatsr/R/biglasso.R | 731 +++++----- bigstatsr-0.2.4/bigstatsr/R/bigstatsr.R | 98 - bigstatsr-0.2.4/bigstatsr/R/colstats.R | 52 bigstatsr-0.2.4/bigstatsr/R/counts.R | 90 - bigstatsr-0.2.4/bigstatsr/R/crochet.R | 304 ++-- bigstatsr-0.2.4/bigstatsr/R/crossprodSelf.R | 188 +- bigstatsr-0.2.4/bigstatsr/R/plot.R | 474 +++--- bigstatsr-0.2.4/bigstatsr/R/predict.R | 345 ++-- bigstatsr-0.2.4/bigstatsr/R/randomSVD.R | 404 ++--- bigstatsr-0.2.4/bigstatsr/R/read.R | 228 +-- bigstatsr-0.2.4/bigstatsr/R/scaling.R | 122 - bigstatsr-0.2.4/bigstatsr/R/tcrossprodSelf.R | 102 - bigstatsr-0.2.4/bigstatsr/R/transpose.R | 82 - bigstatsr-0.2.4/bigstatsr/R/univLinReg.R | 145 - bigstatsr-0.2.4/bigstatsr/R/univLogReg.R | 220 +-- bigstatsr-0.2.4/bigstatsr/R/utils-assert.R | 382 ++--- bigstatsr-0.2.4/bigstatsr/R/utils-mult.R | 362 ++-- bigstatsr-0.2.4/bigstatsr/R/utils.R | 230 +-- bigstatsr-0.2.4/bigstatsr/R/zzz.R | 46 bigstatsr-0.2.4/bigstatsr/README.md | 99 - bigstatsr-0.2.4/bigstatsr/inst/CITATION | 24 bigstatsr-0.2.4/bigstatsr/inst/WORDLIST | 181 +- bigstatsr-0.2.4/bigstatsr/inst/extdata/example.ped | 20 bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/BMAcc.h | 234 +-- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/BMCodeAcc.h | 126 - bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/FBM.h | 58 bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/SubMatCovAcc.h | 258 +-- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/biglasso/linear.hpp | 373 ++--- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/biglasso/logistic.hpp | 534 +++---- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/biglasso/utils.hpp | 295 +--- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/colstats.hpp | 86 - bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/prodMatVec.hpp | 142 - bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/types.h | 42 bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/univLinReg.hpp | 137 - bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/univLogReg.hpp | 175 +- bigstatsr-0.2.4/bigstatsr/inst/include/bigstatsr/utils.h | 38 bigstatsr-0.2.4/bigstatsr/man/AUC.Rd | 133 - bigstatsr-0.2.4/bigstatsr/man/COPY_biglasso_main.Rd |only bigstatsr-0.2.4/bigstatsr/man/COPY_biglasso_part.Rd |only bigstatsr-0.2.4/bigstatsr/man/Extract.Rd | 70 bigstatsr-0.2.4/bigstatsr/man/FBM-class.Rd | 136 - bigstatsr-0.2.4/bigstatsr/man/FBM-methods.Rd | 98 - bigstatsr-0.2.4/bigstatsr/man/FBM.code256-class.Rd | 148 +- bigstatsr-0.2.4/bigstatsr/man/FBM.code256-methods.Rd | 60 bigstatsr-0.2.4/bigstatsr/man/Replace.Rd | 74 - bigstatsr-0.2.4/bigstatsr/man/asPlotlyText.Rd | 62 bigstatsr-0.2.4/bigstatsr/man/big_SVD.Rd | 204 +- bigstatsr-0.2.4/bigstatsr/man/big_apply.Rd | 170 +- bigstatsr-0.2.4/bigstatsr/man/big_attach.Rd | 60 bigstatsr-0.2.4/bigstatsr/man/big_colstats.Rd | 110 - bigstatsr-0.2.4/bigstatsr/man/big_copy.Rd | 130 - bigstatsr-0.2.4/bigstatsr/man/big_cor.Rd | 124 - bigstatsr-0.2.4/bigstatsr/man/big_counts.Rd | 122 - bigstatsr-0.2.4/bigstatsr/man/big_cprodMat.Rd | 108 - bigstatsr-0.2.4/bigstatsr/man/big_cprodVec.Rd | 94 - bigstatsr-0.2.4/bigstatsr/man/big_crossprodSelf.Rd | 140 - bigstatsr-0.2.4/bigstatsr/man/big_parallelize.Rd | 182 +- bigstatsr-0.2.4/bigstatsr/man/big_prodMat.Rd | 108 - bigstatsr-0.2.4/bigstatsr/man/big_prodVec.Rd | 94 - bigstatsr-0.2.4/bigstatsr/man/big_randomSVD.Rd | 210 +- bigstatsr-0.2.4/bigstatsr/man/big_read.Rd | 116 - bigstatsr-0.2.4/bigstatsr/man/big_scale.Rd | 96 - bigstatsr-0.2.4/bigstatsr/man/big_spLinReg.Rd | 284 +-- bigstatsr-0.2.4/bigstatsr/man/big_spLogReg.Rd | 287 +-- bigstatsr-0.2.4/bigstatsr/man/big_tcrossprodSelf.Rd | 136 - bigstatsr-0.2.4/bigstatsr/man/big_transpose.Rd | 86 - bigstatsr-0.2.4/bigstatsr/man/big_univLinReg.Rd | 168 +- bigstatsr-0.2.4/bigstatsr/man/big_univLogReg.Rd | 198 +- bigstatsr-0.2.4/bigstatsr/man/bigstatsr-package.Rd | 156 +- bigstatsr-0.2.4/bigstatsr/man/block_size.Rd | 52 bigstatsr-0.2.4/bigstatsr/man/get_beta.Rd |only bigstatsr-0.2.4/bigstatsr/man/nb_cores.Rd | 58 bigstatsr-0.2.4/bigstatsr/man/pasteLoc.Rd | 62 bigstatsr-0.2.4/bigstatsr/man/plot.big_SVD.Rd | 162 +- bigstatsr-0.2.4/bigstatsr/man/plot.mhtest.Rd | 104 - bigstatsr-0.2.4/bigstatsr/man/predict.big_SVD.Rd | 156 +- bigstatsr-0.2.4/bigstatsr/man/predict.big_sp.Rd | 91 - bigstatsr-0.2.4/bigstatsr/man/predict.big_sp_best_list.Rd |only bigstatsr-0.2.4/bigstatsr/man/predict.mhtest.Rd | 56 bigstatsr-0.2.4/bigstatsr/man/seq-dim.Rd | 50 bigstatsr-0.2.4/bigstatsr/src/RcppExports.cpp | 95 - bigstatsr-0.2.4/bigstatsr/src/biglassoLin.cpp | 29 bigstatsr-0.2.4/bigstatsr/src/biglassoLog.cpp | 28 bigstatsr-0.2.4/bigstatsr/src/biglassoUtils.cpp |only bigstatsr-0.2.4/bigstatsr/src/extract.cpp | 2 bigstatsr-0.2.4/bigstatsr/tests/spelling.R | 2 bigstatsr-0.2.4/bigstatsr/tests/testthat.R | 8 bigstatsr-0.2.4/bigstatsr/tests/testthat/helper-init.R | 96 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-AUC.R | 100 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-FBM-accessors.R | 202 +- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-SVD.R | 222 +-- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-apply.R | 96 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-checkArgs.R | 260 +-- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-colstats.R | 54 bigstatsr-0.2.4/bigstatsr/tests/testthat/test-copy.R | 164 +- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-cor.R | 94 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-counts.R | 130 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-crossprodSelf.R | 140 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-prodVec.R | 84 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-randomSVD.R | 214 +- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-readBM.R | 164 +- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-spLinReg.R | 152 +- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-spLogReg.R | 154 -- bigstatsr-0.2.4/bigstatsr/tests/testthat/test-tcrossprodSelf.R | 140 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-transpose.R | 38 bigstatsr-0.2.4/bigstatsr/tests/testthat/test-univLinReg.R | 128 - bigstatsr-0.2.4/bigstatsr/tests/testthat/test-univLogReg.R | 152 +- 130 files changed, 8854 insertions(+), 8872 deletions(-)
Title: Call 'EPANET' Functions to Simulate Pipe Networks
Description: Enables simulation of water piping networks using 'EPANET'.
The package provides functions from the 'EPANET' programmer's toolkit as R
functions so that basic or customized simulations can be carried out from R.
The package uses 'EPANET' version 2.1 from Open Water Analytics
<https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.1>.
Author: Ernesto Arandia [aut],
Bradley Eck [aut, cre],
Lew Rossman [aut],
Michael Tryby [ctb],
Feng Shang [ctb],
James Uber [ctb],
Tom Taxon [ctb],
Sam Hatchett [ctb],
Hyoungmin Woo [ctb],
Jinduan Chen [ctb],
Yunier Soad [ctb],
Mike Kane [ctb],
Demetrios Eliades [ctb],
Will Furnass [ctb],
Steffen Macke [ctb],
Mariosmsk [ctb],
Elad Salomons [ctb],
Maurizio Cingi [ctb],
Bryant McDonnell [ctb],
IBM Corp. [cph],
Open Water Analytics [cph]
Maintainer: Bradley Eck <brad@bradeck.net>
Diff between epanet2toolkit versions 0.1.3 dated 2017-10-20 and 0.2.1 dated 2018-01-31
DESCRIPTION | 10 LICENSE | 4 MD5 | 212 +++---- NAMESPACE | 214 +++---- R/Rtoolkit.R | 484 ++++++++-------- R/codes.r | 100 +-- R/controls.r | 302 +++++----- R/coords.r | 166 ++--- R/epanet.r | 152 ++--- R/epanet2toolkit.r | 36 - R/hydraulics.r | 522 ++++++++--------- R/links.r | 704 ++++++++++++------------ R/nodes.r | 648 +++++++++++----------- R/options.r | 252 ++++---- R/patterns.r | 566 +++++++++---------- R/quality.r | 510 ++++++++--------- R/report.r | 50 - R/times.r | 296 +++++----- R/util.r | 136 ++-- README.md | 179 +++--- inst/COPYRIGHTS | 48 - inst/extdata/Net1.inp | 358 ++++++------ man/ENclose.Rd | 50 - man/ENcloseH.Rd | 38 - man/ENcloseQ.Rd | 34 - man/ENepanet.Rd | 54 - man/ENgetcontrol.Rd | 64 +- man/ENgetcoord.Rd | 48 - man/ENgetcount.Rd | 84 +- man/ENgetflowunits.Rd | 88 +-- man/ENgetlinkid.Rd | 62 +- man/ENgetlinkindex.Rd | 60 +- man/ENgetlinknodes.Rd | 68 +- man/ENgetlinktype.Rd | 86 +- man/ENgetlinkvalue.Rd | 128 ++-- man/ENgetnodeid.Rd | 66 +- man/ENgetnodeindex.Rd | 64 +- man/ENgetnodetype.Rd | 80 +- man/ENgetnodevalue.Rd | 134 ++-- man/ENgetoption.Rd | 72 +- man/ENgetpatternid.Rd | 60 +- man/ENgetpatternindex.Rd | 60 +- man/ENgetpatternlen.Rd | 54 - man/ENgetpatternvalue.Rd | 70 +- man/ENgetqualinfo.Rd | 48 - man/ENgetqualtype.Rd | 100 +-- man/ENgettimeparam.Rd | 92 +-- man/ENgetversion.Rd | 42 - man/ENinitH.Rd | 92 +-- man/ENinitQ.Rd | 70 +- man/ENnextH.Rd | 104 +-- man/ENnextQ.Rd | 60 +- man/ENopen.Rd | 82 +- man/ENopenH.Rd | 62 +- man/ENopenQ.Rd | 56 - man/ENreport.Rd | 40 - man/ENrunH.Rd | 72 +- man/ENrunQ.Rd | 62 +- man/ENsaveH.Rd | 38 - man/ENsaveinpfile.Rd | 36 - man/ENsetcontrol.Rd | 138 ++-- man/ENsetcoord.Rd | 60 +- man/ENsetlinkvalue.Rd | 122 ++-- man/ENsetnodevalue.Rd | 126 ++-- man/ENsetoption.Rd | 72 +- man/ENsetpattern.Rd | 70 +- man/ENsetpatternvalue.Rd | 60 +- man/ENsetqualtype.Rd | 98 +-- man/ENsettimeparam.Rd | 96 +-- man/ENsolveH.Rd | 40 - man/ENsolveQ.Rd | 50 - man/ENstepQ.Rd | 34 - man/epanet2toolkit.Rd | 30 - man/getOpenHflag.Rd | 46 - man/getOpenflag.Rd | 44 - src/epanet.c | 5 tests/testthat.r | 28 tests/testthat/Net1-ld.rpt | 24 tests/testthat/Net1-longduration.inp | 358 ++++++------ tests/testthat/Net1.bin |binary tests/testthat/Net1.inp | 358 ++++++------ tests/testthat/Net1.rpt |binary tests/testthat/Net2.inp | 618 ++++++++++----------- tests/testthat/Net2.rpt | 24 tests/testthat/Net3.bin |binary tests/testthat/Net3.inp | 962 ++++++++++++++++----------------- tests/testthat/n1.rpt | 24 tests/testthat/net3.rpt | 24 tests/testthat/test_ENclose.r | 73 +- tests/testthat/test_ENopen.r | 78 +- tests/testthat/test_Rtoolkit.r | 244 ++++---- tests/testthat/test_call.r | 152 ++--- tests/testthat/test_codes.r | 73 +- tests/testthat/test_controls.R | 114 +-- tests/testthat/test_coords.r | 112 +-- tests/testthat/test_epanet.r | 234 +++----- tests/testthat/test_epanet_example_2.r | 90 +-- tests/testthat/test_epanet_example_3.r | 129 ++-- tests/testthat/test_hydraulics.r | 314 +++++----- tests/testthat/test_links.r | 322 +++++------ tests/testthat/test_nodes.r | 282 ++++----- tests/testthat/test_options.r | 228 ++++--- tests/testthat/test_patterns.r | 352 ++++++------ tests/testthat/test_quality.r | 420 +++++++------- tests/testthat/test_report.r | 54 - tests/testthat/test_times.r | 192 +++--- tests/testthat/test_util.r | 98 +-- 107 files changed, 7808 insertions(+), 7793 deletions(-)
More information about epanet2toolkit at CRAN
Permanent link
Title: Integer Sequence Generator
Description: Generates well-known integer sequences. 'Rmpfr' package is adopted for computing with arbitrarily large numbers with user-specified bit precision. Every function has hyperlink to its corresponding item in OEIS (The On-Line Encyclopedia of Integer Sequences) in the function help page. For interested readers, see Sloane and Plouffe (1995, ISBN:978-0125586306).
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between Zseq versions 0.1.1 dated 2017-10-27 and 0.1.2 dated 2018-01-31
DESCRIPTION | 17 ++++++++--------- MD5 | 6 +++--- R/Fibonacci.R | 4 ++-- man/A000045.Rd | 2 +- 4 files changed, 14 insertions(+), 15 deletions(-)
Title: Simple Matrix Construction
Description: Constructing matrices for quick prototyping can be a nuisance,
requiring the user to think about how to fill the matrix with values using
the matrix() function. The %<-% operator solves that issue by allowing the
user to construct matrices using code that shows the actual matrices.
Author: Erik-Jan van Kesteren
Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
Diff between Massign versions 1.0.0 dated 2017-11-15 and 1.1.0 dated 2018-01-31
DESCRIPTION | 7 ++-- MD5 | 12 ++++++-- NAMESPACE | 1 R/Massign.R | 80 +++++++++++------------------------------------------- R/Multiplipe.R |only man/Multiplipe.Rd |only tests |only 7 files changed, 31 insertions(+), 69 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and
the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many
geographies.
Author: Kyle Walker [aut, cre],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tidycensus versions 0.4 dated 2018-01-02 and 0.4.1 dated 2018-01-31
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/acs.R | 20 +++++++++++++++----- R/helpers.R | 4 ++++ R/tidycensus-package.R | 1 + 6 files changed, 31 insertions(+), 15 deletions(-)
Title: Pacific Decadal Oscillation Index Data
Description: Monthly Pacific Decadal Oscillation (PDO) index
values from January 1900 to December 2017.
Includes pdo_download() to scrape the latest values from
<http://research.jisao.washington.edu/pdo/PDO.latest>.
Author: Joe Thorley [aut, cre],
Nathan Mantua [aut, dtc],
Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rpdo versions 0.2.2 dated 2017-04-12 and 0.2.3 dated 2018-01-31
rpdo-0.2.2/rpdo/R/download-pdo.R |only rpdo-0.2.2/rpdo/man/download_pdo.Rd |only rpdo-0.2.2/rpdo/tests/testthat/test-download-pdo.R |only rpdo-0.2.3/rpdo/DESCRIPTION | 22 ++--- rpdo-0.2.3/rpdo/MD5 | 26 +++--- rpdo-0.2.3/rpdo/NAMESPACE | 7 + rpdo-0.2.3/rpdo/NEWS.md | 19 ++-- rpdo-0.2.3/rpdo/R/namespace.R |only rpdo-0.2.3/rpdo/R/package.R | 12 ++ rpdo-0.2.3/rpdo/R/pdo-download.R |only rpdo-0.2.3/rpdo/README.md | 86 ++++++++++++++------- rpdo-0.2.3/rpdo/data/pdo.rda |binary rpdo-0.2.3/rpdo/man/pdo_download.Rd |only rpdo-0.2.3/rpdo/man/rpdo-package.Rd |only rpdo-0.2.3/rpdo/tests/testthat.R | 1 rpdo-0.2.3/rpdo/tests/testthat/test-data.R | 2 rpdo-0.2.3/rpdo/tests/testthat/test-pdo-download.R |only rpdo-0.2.3/rpdo/tools/README-unnamed-chunk-2-1.png |binary 18 files changed, 114 insertions(+), 61 deletions(-)
Title: Differential Expression Analysis Using a Bottom-Up Model
Description: Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of a bottom-up model for PCR amplification. This model is developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.
Author: Gershom Buri [aut, cre],
Wilfred Ndifon [aut]
Maintainer: Gershom Buri <buri@aims.edu.gh>
Diff between denoiSeq versions 0.1.0 dated 2017-07-18 and 0.1.1 dated 2018-01-31
denoiSeq-0.1.0/denoiSeq/inst/doc/denoiSeq-vignette.pdf |only denoiSeq-0.1.0/denoiSeq/man/setInitValues-readsData-method.Rd |only denoiSeq-0.1.0/denoiSeq/man/setOutput-readsData-method.Rd |only denoiSeq-0.1.0/denoiSeq/man/setReplicates-readsData-method.Rd |only denoiSeq-0.1.0/denoiSeq/man/setStepSizes-readsData-method.Rd |only denoiSeq-0.1.1/denoiSeq/DESCRIPTION | 10 denoiSeq-0.1.1/denoiSeq/MD5 | 58 +-- denoiSeq-0.1.1/denoiSeq/NAMESPACE | 6 denoiSeq-0.1.1/denoiSeq/NEWS.md |only denoiSeq-0.1.1/denoiSeq/R/Class_denoiSeq.R | 160 +++++----- denoiSeq-0.1.1/denoiSeq/R/DE_analysis.R | 48 +-- denoiSeq-0.1.1/denoiSeq/R/Gibbs_samplers.R | 24 + denoiSeq-0.1.1/denoiSeq/R/Metrapolis_Hast_samplers.R | 3 denoiSeq-0.1.1/denoiSeq/R/ercc.R | 6 denoiSeq-0.1.1/denoiSeq/R/full_conditionals.R | 21 - denoiSeq-0.1.1/denoiSeq/R/n_step_sampler.R | 69 ++-- denoiSeq-0.1.1/denoiSeq/R/output_functions.R | 31 + denoiSeq-0.1.1/denoiSeq/R/simulated.R | 14 denoiSeq-0.1.1/denoiSeq/build/vignette.rds |binary denoiSeq-0.1.1/denoiSeq/inst/doc/denoiSeq-vignette.R | 24 - denoiSeq-0.1.1/denoiSeq/inst/doc/denoiSeq-vignette.Rmd | 50 +-- denoiSeq-0.1.1/denoiSeq/inst/doc/denoiSeq-vignette.html |only denoiSeq-0.1.1/denoiSeq/man/ERCC.Rd | 6 denoiSeq-0.1.1/denoiSeq/man/denoiseq.Rd | 55 ++- denoiSeq-0.1.1/denoiSeq/man/getSamplesOf.Rd | 20 - denoiSeq-0.1.1/denoiSeq/man/readsData.Rd | 35 +- denoiSeq-0.1.1/denoiSeq/man/results.Rd | 45 +- denoiSeq-0.1.1/denoiSeq/man/setInitValues.Rd | 26 + denoiSeq-0.1.1/denoiSeq/man/setOutput.Rd |only denoiSeq-0.1.1/denoiSeq/man/setReplicates.Rd | 25 + denoiSeq-0.1.1/denoiSeq/man/setStepSizes.Rd | 26 + denoiSeq-0.1.1/denoiSeq/man/simdat.Rd | 14 denoiSeq-0.1.1/denoiSeq/man/tunedStepSize.Rd | 9 denoiSeq-0.1.1/denoiSeq/vignettes/denoiSeq-vignette.Rmd | 50 +-- 34 files changed, 481 insertions(+), 354 deletions(-)
Title: Extrema-Weighted Feature Extraction
Description: Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in Van den Boom et al. (2017) <arXiv:1709.10467>.
Author: Willem van den Boom [aut, cre]
Maintainer: Willem van den Boom <willem@wvdboom.nl>
Diff between xwf versions 0.2-0 dated 2018-01-03 and 0.2-1 dated 2018-01-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/xwfGridsearch.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.6 dated 2018-01-11 and 1.0.7 dated 2018-01-31
DESCRIPTION | 10 - MD5 | 32 ++-- NEWS.md | 145 ++++++++++---------- R/add_labels.R | 7 - R/as_factor.R | 287 ++++++++++++++++++++--------------------- R/convert_case.R | 123 +++++++++-------- inst/doc/intro_sjlabelled.html | 66 ++++----- inst/doc/labelleddata.html | 4 man/add_labels.Rd | 3 man/as_factor.Rd | 3 man/as_label.Rd | 3 man/as_numeric.Rd | 3 man/convert_case.Rd | 10 - man/set_labels.Rd | 3 man/tidy_labels.Rd | 3 man/zap_labels.Rd | 3 man/zap_na_tags.Rd | 3 17 files changed, 362 insertions(+), 346 deletions(-)
Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here [Thrun/Ultsch,2017] <DOI:10.13140/RG.2.2.13124.53124>. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The visualization of the topographic map is derived from the generalized U*-matrix. Thus, it can be used to define the clusters of high-dimensional data automatically. The whole system is a generalization of the book "Projection-Based Clustering through Self-Organization and Swarm Intelligence" <DOI:10.1007/978-3-658-20540-9>. Choosing a correct projection method will result in a visualization where mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre, cph],
Florian Lerch [aut],
Felix Pape [aut],
Kristian Nybo [cph],
Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ProjectionBasedClustering versions 1.0.5 dated 2017-11-17 and 1.0.6 dated 2018-01-31
ProjectionBasedClustering-1.0.5/ProjectionBasedClustering/R/DefaultColorSequence.R |only ProjectionBasedClustering-1.0.5/ProjectionBasedClustering/R/ShepardDiagram.R |only ProjectionBasedClustering-1.0.5/ProjectionBasedClustering/man/ShepardDiagram.Rd |only ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/DESCRIPTION | 18 ++-- ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/MD5 | 39 ++++------ ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/NAMESPACE | 1 ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/R/interactiveGeneralizedUmatrixIsland.R |only ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/CCA.Rd | 6 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/Delaunay4Points.Rd | 2 ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/ICA.Rd | 7 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/Isomap.Rd | 7 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/KruskalStress.Rd | 3 ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/MDS.Rd | 7 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/NeRV.rd | 7 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/PCA.Rd | 5 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/ProjectionBasedClustering-package.Rd | 18 ++++ ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/ProjectionBasedClustering.Rd | 6 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/ProjectionPursuit.Rd | 8 ++ ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/SammonsMapping.Rd | 7 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/ShortestGraphPathsC.Rd | 6 - ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/interactiveClustering.Rd | 5 + ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/interactiveGeneralizedUmatrixIsland.Rd |only ProjectionBasedClustering-1.0.6/ProjectionBasedClustering/man/tSNE.Rd | 6 + 23 files changed, 112 insertions(+), 46 deletions(-)
More information about ProjectionBasedClustering at CRAN
Permanent link
Title: Fast Multivariate Normal and Student's t Methods
Description: Provides computationally efficient tools related to
the multivariate normal and Student's t distributions. The main functionalities are:
simulating multivariate random vectors, evaluating multivariate
normal or Student's t densities and Mahalanobis distances. These tools are very efficient
thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo [aut, cre],
Thijs van den Berg [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mvnfast versions 0.2.4 dated 2018-01-04 and 0.2.5 dated 2018-01-31
DESCRIPTION | 8 +- MD5 | 18 +++--- R/dmvn.R | 5 + R/maha.R | 5 + inst/doc/mvnfast.R | 52 +++++++++++-------- inst/doc/mvnfast.Rmd | 57 ++++++++++++--------- inst/doc/mvnfast.html | 134 ++++++++++++++++++++++++++------------------------ man/dmvn.Rd | 5 + man/maha.Rd | 5 + vignettes/mvnfast.Rmd | 57 ++++++++++++--------- 10 files changed, 198 insertions(+), 148 deletions(-)
Title: An R Package for Facilitating Large-Scale Latent Variable
Analyses in Mplus
Description: Leverages the R language to automate latent variable model estimation
and interpretation using 'Mplus', a powerful latent variable modeling program
developed by Muthen and Muthen (<http://www.statmodel.com>). Specifically, this package
provides routines for creating related groups of models, running batches of
models, and extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist [aut, cre],
Joshua Wiley [aut]
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>
Diff between MplusAutomation versions 0.7 dated 2017-07-14 and 0.7-1 dated 2018-01-31
DESCRIPTION | 11 - MD5 | 42 +++--- NAMESPACE | 1 NEWS | 16 ++ R/MplusAutomation.R | 29 +++- R/extractIndirect.R |only R/extractParameters.R | 169 +++++-------------------- R/mplus.R | 80 ++++++++++- R/parseOutput.R | 330 ++++++------------------------------------------- R/readModels.R |only R/runModels.R | 6 R/trainlgmm.R | 7 - R/utilityFunctions.R | 206 ++++++++++++++++-------------- build/vignette.rds |binary inst/CITATION |only inst/doc/Vignette.Rnw | 2 inst/doc/Vignette.pdf |binary man/MplusAutomation.Rd | 4 man/extractIndirect.Rd |only man/getSection.Rd | 4 man/mplusModeler.Rd | 80 ++++++++++- man/readModels.Rd | 49 ++++--- man/runModels.Rd | 6 vignettes/Vignette.Rnw | 2 24 files changed, 458 insertions(+), 586 deletions(-)
More information about MplusAutomation at CRAN
Permanent link
Title: An Interface for Karstic Time Series
Description: An R graphical user interface for karstic time series, based on the 'tcltk' package. Karstic research typically includes CO2 and 222Rn concentrations and microclimatic measurements. Many of these time series have a strong non-linear behavior. Gaps are often a significant problem because caves are aggressive environments for the measuring devices. 'KarsTS' provides linear and non-linear analysis (Marwan et al. (2007) <10.1016/j.physrep.2006.11.001>) and filling methods (Moffat et al. (2007) <doi:10.1016/j.agrformet.2007.08.011>), as well as tools to manipulate easily time series and gap sets.
Author: Marina Saez [aut, cre],
David Benavente [ths],
Soledad Cuezva [ths],
Concepcion Pla [ctb]
Maintainer: Marina Saez <marinasaez_andreu@hotmail.com>
Diff between KarsTS versions 1.1 dated 2017-06-02 and 2.0 dated 2018-01-31
KarsTS-1.1/KarsTS/R/createJointRMPlot.R |only KarsTS-2.0/KarsTS/DESCRIPTION | 20 KarsTS-2.0/KarsTS/MD5 | 101 KarsTS-2.0/KarsTS/R/KarsTS.R | 4 KarsTS-2.0/KarsTS/R/RPKTS.R |only KarsTS-2.0/KarsTS/R/aggregateKTS.R | 5 KarsTS-2.0/KarsTS/R/applyTheiler.R |only KarsTS-2.0/KarsTS/R/buttons1.R | 24 KarsTS-2.0/KarsTS/R/buttons3.R | 9 KarsTS-2.0/KarsTS/R/buttons4.R | 12 KarsTS-2.0/KarsTS/R/cleanEnvir.R | 67 KarsTS-2.0/KarsTS/R/composeKTS.R | 597 +++- KarsTS-2.0/KarsTS/R/createChbEntry.R | 9 KarsTS-2.0/KarsTS/R/createCrossRMPlot.R | 765 +++++- KarsTS-2.0/KarsTS/R/createDistMatrix.R |only KarsTS-2.0/KarsTS/R/createSimpleRM.R | 8 KarsTS-2.0/KarsTS/R/createSimpleRMPlot.R | 763 +++++- KarsTS-2.0/KarsTS/R/determinismKTS.R | 133 - KarsTS-2.0/KarsTS/R/functToExport.R | 3 KarsTS-2.0/KarsTS/R/gapForSelMethod.R | 4 KarsTS-2.0/KarsTS/R/genRmExample.R | 3 KarsTS-2.0/KarsTS/R/getCRP.R |only KarsTS-2.0/KarsTS/R/getCoordsKTS.R | 8 KarsTS-2.0/KarsTS/R/getProTaos.R |only KarsTS-2.0/KarsTS/R/getRecurrencePoints.R | 2 KarsTS-2.0/KarsTS/R/getScreenSize.R | 5 KarsTS-2.0/KarsTS/R/globalV.R | 14 KarsTS-2.0/KarsTS/R/histKTS.R | 15 KarsTS-2.0/KarsTS/R/loadAllTypes.R | 16 KarsTS-2.0/KarsTS/R/loadKarsTSFonts.R | 18 KarsTS-2.0/KarsTS/R/mainScreen.R | 370 +-- KarsTS-2.0/KarsTS/R/meanValue.R | 415 +-- KarsTS-2.0/KarsTS/R/mutInf.R |only KarsTS-2.0/KarsTS/R/packagesToImport.R | 11 KarsTS-2.0/KarsTS/R/plotTimeSeries.R | 1324 +++++++---- KarsTS-2.0/KarsTS/R/removePoints.R | 14 KarsTS-2.0/KarsTS/R/roundKTS.R | 4 KarsTS-2.0/KarsTS/R/scattTimeSeries.R | 568 +++- KarsTS-2.0/KarsTS/R/selectionGaps.R | 7 KarsTS-2.0/KarsTS/R/stationarityKTS.R | 2 KarsTS-2.0/KarsTS/R/stinemannKTS.R | 317 +- KarsTS-2.0/KarsTS/R/stlplusKTS.R | 28 KarsTS-2.0/KarsTS/R/theilerKTS.R |only KarsTS-2.0/KarsTS/R/welcomeScreen.R | 15 KarsTS-2.0/KarsTS/build/partial.rdb |binary KarsTS-2.0/KarsTS/inst/extdata/KarsTS-manual.pdf |binary KarsTS-2.0/KarsTS/inst/extdata/KarsTSUserGuide.pdf |binary KarsTS-2.0/KarsTS/inst/extdata/aboutKTS.txt | 4 KarsTS-2.0/KarsTS/inst/extdata/wombeyan_caves_formations.gif |binary KarsTS-2.0/KarsTS/man/KarsTS-package.Rd | 4 KarsTS-2.0/KarsTS/man/RPKTS.Rd |only KarsTS-2.0/KarsTS/man/applyTheiler.Rd |only KarsTS-2.0/KarsTS/man/createChbEntry.Rd | 8 KarsTS-2.0/KarsTS/man/createDistMatrix.Rd |only KarsTS-2.0/KarsTS/man/getCRP.Rd |only KarsTS-2.0/KarsTS/man/getProTaos.Rd |only KarsTS-2.0/KarsTS/man/mutInf.Rd |only KarsTS-2.0/KarsTS/man/scaleKTS.Rd | 4 KarsTS-2.0/KarsTS/man/theilerKTS.Rd |only 59 files changed, 3999 insertions(+), 1701 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018]. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 0.9.5 dated 2017-08-20 and 1.0.0 dated 2018-01-31
GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/R/DefaultColorSequence.R |only GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/R/interactiveGeneralizedUmatrixIsland.R |only GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/R/setdiffMatrix.R |only GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/man/addRowWiseC.Rd |only GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/man/interactiveGeneralizedUmatrixIsland.Rd |only GeneralizedUmatrix-0.9.5/GeneralizedUmatrix/src/addRowWiseC.cpp |only GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/DESCRIPTION | 22 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/MD5 | 38 - GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/NAMESPACE | 15 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/R/GeneralizedUmatrix.R | 278 +++++----- GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/R/RcppExports.R | 4 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/R/plotTopographicMap.R | 20 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/data/DefaultColorSequence.rda |only GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/data/Lsun3D.rda |binary GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/DefaultColorSequence.Rd |only GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/Delta3DWeightsC.Rd | 7 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/GeneralizedUmatrix-package.Rd | 26 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/GeneralizedUmatrix.Rd | 32 - GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/Lsun3D.Rd | 7 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/XYcoords2LinesColumns.Rd | 8 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/plotTopographicMap.Rd | 9 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/sESOM4BMUs.Rd | 10 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/man/trainstepC.Rd | 12 GeneralizedUmatrix-1.0.0/GeneralizedUmatrix/src/RcppExports.cpp | 13 24 files changed, 272 insertions(+), 229 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called databionic swarm (DBS) is introduced. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DatabionicSwarm versions 0.9.8 dated 2017-09-28 and 1.0.0 dated 2018-01-31
DESCRIPTION | 18 ++++++----- MD5 | 47 +++++++++++++++++-------------- NAMESPACE | 2 - R/RobustNormalization.R |only R/getUmatrix4Projection.R |only data/Lsun3D.rda |binary man/DBSclustering.Rd | 8 ++--- man/DatabionicSwarm-package.Rd | 25 ++++++++++++---- man/Delaunay4Points.Rd | 2 - man/Delta3DWeightsC.Rd | 3 - man/GeneratePswarmVisualization.Rd | 7 +--- man/Lsun3D.Rd | 5 ++- man/ProjectedPoints2Grid.Rd | 6 ++- man/Pswarm.Rd | 2 - man/PswarmCurrentRadiusC2botsPositive.Rd | 6 +++ man/RobustNormalization.Rd |only man/ShortestGraphPathsC.Rd | 4 +- man/findPossiblePositionsCsingle.Rd | 7 +++- man/getCartesianCoordinates.Rd | 7 ++++ man/getUmatrix4Projection.Rd |only man/rDistanceToroidCsingle.Rd | 9 +++++ man/sESOM4BMUs.Rd | 6 ++- man/setGridSize.Rd | 4 +- man/setPolarGrid.Rd | 7 ++++ man/setRmin.Rd | 6 +-- man/setdiffMatrix.Rd |only man/trainstepC.Rd | 10 +++++- 27 files changed, 128 insertions(+), 63 deletions(-)
More information about DatabionicSwarm at CRAN
Permanent link
Title: Easy Condition Handling
Description: A friendlier condition handler, inspired by 'purrr' mappers and
based on 'rlang'.'attempt' extends and facilitates condition handling by
providing a consistent grammar, and provides a set of easy to use functions
for common tests and conditions. 'attempt' only depends on 'rlang', and
focuses on speed, so it can be easily integrated in other functions and
used in data analysis.
Author: Colin Fay [aut, cre]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between attempt versions 0.1.0 dated 2018-01-03 and 0.2.0 dated 2018-01-31
attempt-0.1.0/attempt/inst/doc/attempt.R |only attempt-0.1.0/attempt/inst/doc/attempt.Rmd |only attempt-0.1.0/attempt/inst/doc/attempt.html |only attempt-0.1.0/attempt/man/if.Rd |only attempt-0.1.0/attempt/man/if_else.Rd |only attempt-0.1.0/attempt/man/if_then.Rd |only attempt-0.1.0/attempt/vignettes/attempt.Rmd |only attempt-0.2.0/attempt/DESCRIPTION | 17 - attempt-0.2.0/attempt/MD5 | 73 ++++-- attempt-0.2.0/attempt/NAMESPACE | 8 attempt-0.2.0/attempt/NEWS.md | 11 attempt-0.2.0/attempt/R/adverbs.R |only attempt-0.2.0/attempt/R/attempt-package.R | 10 attempt-0.2.0/attempt/R/if.R | 87 +++---- attempt-0.2.0/attempt/R/try_catch.R | 140 +----------- attempt-0.2.0/attempt/R/utils.R | 2 attempt-0.2.0/attempt/R/warn_if.R | 94 ++------ attempt-0.2.0/attempt/README.md | 211 +++++++++++++------ attempt-0.2.0/attempt/build/vignette.rds |binary attempt-0.2.0/attempt/inst/doc/a_intro_attempt.R |only attempt-0.2.0/attempt/inst/doc/a_intro_attempt.Rmd |only attempt-0.2.0/attempt/inst/doc/a_intro_attempt.html |only attempt-0.2.0/attempt/inst/doc/b_try_catch.R |only attempt-0.2.0/attempt/inst/doc/b_try_catch.Rmd |only attempt-0.2.0/attempt/inst/doc/b_try_catch.html |only attempt-0.2.0/attempt/inst/doc/c_adverbs.R |only attempt-0.2.0/attempt/inst/doc/c_adverbs.Rmd |only attempt-0.2.0/attempt/inst/doc/c_adverbs.html |only attempt-0.2.0/attempt/inst/doc/d_if.R |only attempt-0.2.0/attempt/inst/doc/d_if.Rmd |only attempt-0.2.0/attempt/inst/doc/d_if.html |only attempt-0.2.0/attempt/inst/doc/e_conditions.R |only attempt-0.2.0/attempt/inst/doc/e_conditions.Rmd |only attempt-0.2.0/attempt/inst/doc/e_conditions.html |only attempt-0.2.0/attempt/man/attempt-package.Rd | 6 attempt-0.2.0/attempt/man/attempt.Rd | 7 attempt-0.2.0/attempt/man/ifthenelse.Rd |only attempt-0.2.0/attempt/man/messagefunctions.Rd |only attempt-0.2.0/attempt/man/messagehandler.Rd | 8 attempt-0.2.0/attempt/man/scopedif.Rd |only attempt-0.2.0/attempt/man/silent_attempt.Rd | 2 attempt-0.2.0/attempt/man/silently.Rd | 2 attempt-0.2.0/attempt/man/surely.Rd | 2 attempt-0.2.0/attempt/man/try_catch.Rd | 4 attempt-0.2.0/attempt/tests/testthat/test-if.R | 20 + attempt-0.2.0/attempt/tests/testthat/test-trycatch.R | 13 + attempt-0.2.0/attempt/tests/testthat/test-utils.R | 9 attempt-0.2.0/attempt/tests/testthat/test-warn.R | 15 - attempt-0.2.0/attempt/vignettes/a_intro_attempt.Rmd |only attempt-0.2.0/attempt/vignettes/b_try_catch.Rmd |only attempt-0.2.0/attempt/vignettes/c_adverbs.Rmd |only attempt-0.2.0/attempt/vignettes/d_if.Rmd |only attempt-0.2.0/attempt/vignettes/e_conditions.Rmd |only 53 files changed, 348 insertions(+), 393 deletions(-)
Title: Relational Query Generator for Data Manipulation
Description: A query generator based on Edgar F. Codd's relational
algebra and operator names (plus experience using 'SQL' at big data
scale). The design represents an attempt to make 'SQL' more teachable by
denoting composition a sequential pipeline notation instead of nested
queries or functions. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible modeling step, and convenience methods for applying query
trees to in-memory 'data.frame's.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 0.2.0 dated 2018-01-24 and 0.3.0 dated 2018-01-31
DESCRIPTION | 10 ++-- MD5 | 42 ++++++++++---------- NEWS.md | 6 ++ R/ex_data_frame.R | 18 ++++---- R/extend.R | 76 ++++++++++++++++++++++--------------- R/order_by.R | 37 +++++++++++------- R/pre_sql.R | 12 ++--- R/relop.R | 18 ++++++++ R/rename.R | 2 R/utils.R | 8 ++- README.md | 13 ++---- inst/doc/AdHocQueries.R | 15 +++++++ inst/doc/AdHocQueries.Rmd | 21 ++++++++-- inst/doc/AdHocQueries.html | 31 ++++++++++----- inst/doc/AssigmentPartitioner.html | 4 - inst/doc/QueryGeneration.html | 4 - man/execute_data_frame.Rd | 9 ++-- man/extend_nse.Rd | 12 ++--- man/extend_se.Rd | 10 +--- man/orderby.Rd | 8 +-- man/rquery_apply_to_data_frame.Rd | 9 ++-- vignettes/AdHocQueries.Rmd | 21 ++++++++-- 22 files changed, 246 insertions(+), 140 deletions(-)
Title: Simulating Multistate Movements in River/Heterogeneous
Landscapes
Description: Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers,
heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on
resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to
linear habitats/dendritic ecological networks (e.g. river networks), the simulation algorithm is built to be
highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the
landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in
homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using
the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input
parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as
mechanistic null models (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology'
hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources,
infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk,
dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as
those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species
spread, and population dynamics.
Author: Lorenzo Quaglietta [aut],
Miguel Porto [aut, cre],
Erida Gjini [ctb]
Maintainer: Miguel Porto <mpbertolo@gmail.com>
Diff between SiMRiv versions 1.0.2 dated 2017-11-07 and 1.0.3 dated 2018-01-31
DESCRIPTION | 8 - MD5 | 20 +- NAMESPACE | 1 R/estimation.r | 277 +++++++++++++++++++++++++------------- R/internal.r | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/SiMRiv.pdf |binary man/adjustModel.Rd | 19 +- man/state.Rd | 6 tests/testthat/test-simulations.R | 10 - 11 files changed, 225 insertions(+), 130 deletions(-)
Title: Programming with Big Data -- Interface to 'ZeroMQ'
Description: 'ZeroMQ' is a well-known library for high-performance
asynchronous messaging in scalable, distributed applications. This
package provides high level R wrapper functions to easily utilize
'ZeroMQ'. We mainly focus on interactive client/server programming
frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2)
is shipped with 'pbdZMQ', which can be used if no system installation
of 'ZeroMQ' is available. A few wrapper functions compatible with
'rzmq' are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Christian Heckendorf [aut] (file transfer),
George Ostrouchov [aut] (Mac OSX),
Whit Armstrong [ctb] (some functions are modified from the rzmq package
for backwards compatibility),
Brian Ripley [ctb] (C code of shellexec, and Solaris),
R Core team [ctb] (some functions are modified from the R source code),
Philipp A. [ctb] (Fedora),
Elliott Sales de Andrade [ctb] (sprintf),
Spencer Aiello [ctb] (windows conf)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.3-1 dated 2018-01-11 and 0.3-2 dated 2018-01-31
ChangeLog | 8 +++++ DESCRIPTION | 14 ++++----- INSTALL | 27 ++++++++++++++++-- MD5 | 13 +++++--- NAMESPACE | 1 R/overwrite_shpkg.r |only R/zzz.r.in | 67 +++++++++++++++++++++++++++++++++++++--------- man/zz_overwrite_shpkg.Rd |only src/pkg.m4 |only 9 files changed, 102 insertions(+), 28 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented lassnags)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 1.4.0 dated 2018-01-24 and 1.4.1 dated 2018-01-31
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NEWS.md | 10 ++++++++ R/catalog_makecluster.r | 50 +++++++++++++++++++++++------------------ R/grid_catalog.r | 10 +++++--- R/grid_metrics.r | 3 -- R/lastrees.r | 5 ---- README.md | 2 - man/lastrees.Rd | 5 ---- tests/testthat/Rplots.pdf |binary tests/testthat/test-lastrees.R | 16 +++++-------- 11 files changed, 69 insertions(+), 60 deletions(-)
Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2',
facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre]
(<https://orcid.org/0000-0002-4628-8148>),
Baptiste Auguie [ctb] (For g_legend and grid_arrange_shared_legend),
Shaun Jackman [ctb] (For grid_arrange_shared_legend),
Hadley Wickham [ctb] (ggplot2 functions),
Winston Chang [ctb] (ggplot2 functions)
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>
Diff between lemon versions 0.3.1 dated 2017-09-12 and 0.3.3 dated 2018-01-31
DESCRIPTION | 25 ++++--- MD5 | 71 +++++++++++++--------- NAMESPACE | 6 + R/brackets.R | 117 ++++++++++++++++++++++++------------- R/coord-capped.r | 39 ++++++++---- R/coord-flex.r | 49 ++++++++++++--- R/facet-rep-lab.r | 45 +++++++++++--- R/facet-wrap.r | 15 ++-- R/geom-pointline.r |only R/legends.r | 61 +++++++++++++++---- R/lemon.r | 4 - R/lemon_print.r | 19 +++++- build/vignette.rds |binary inst/doc/capped-axes.R | 14 ++-- inst/doc/capped-axes.Rmd | 22 +++--- inst/doc/capped-axes.html | 46 +++++++------- inst/doc/facet-rep-labels.R |only inst/doc/facet-rep-labels.Rmd |only inst/doc/facet-rep-labels.html |only inst/doc/gtable_show_lemonade.html | 12 +-- inst/doc/legends.R | 21 ++++++ inst/doc/legends.Rmd | 58 +++++++++++++++--- inst/doc/legends.html | 95 +++++++++++++++++++----------- inst/doc/lemon_print.html | 4 - inst/examples |only man/brackets.Rd | 21 +++--- man/coord_capped.Rd | 11 +-- man/coord_flex.Rd | 18 ++--- man/facet_rep.Rd | 14 +++- man/geom_pointpath.Rd |only man/grid_arrange_shared_legend.Rd | 31 +++++++-- man/lemon-ggproto.Rd | 4 - man/lemon.Rd | 4 - man/reposition_legend.Rd | 6 + tests |only vignettes/capped-axes.Rmd | 22 +++--- vignettes/facet-rep-labels.Rmd |only vignettes/legends.Rmd | 58 +++++++++++++++--- 38 files changed, 634 insertions(+), 278 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.6.0 dated 2017-10-25 and 0.7.0 dated 2018-01-31
spant-0.6.0/spant/man/combine_metab_ref.Rd |only spant-0.7.0/spant/DESCRIPTION | 8 spant-0.7.0/spant/MD5 | 46 ++ spant-0.7.0/spant/NAMESPACE | 12 spant-0.7.0/spant/NEWS.md | 7 spant-0.7.0/spant/R/fit_display.R | 7 spant-0.7.0/spant/R/fitting.R | 4 spant-0.7.0/spant/R/fp_corr_td.R |only spant-0.7.0/spant/R/image_reg.R | 72 ++++ spant-0.7.0/spant/R/mrs_data_display.R | 13 spant-0.7.0/spant/R/mrs_data_io.R | 427 --------------------------- spant-0.7.0/spant/R/mrs_data_proc.R | 72 ++++ spant-0.7.0/spant/R/mrs_read_ima.R |only spant-0.7.0/spant/R/mrs_read_list_data.R |only spant-0.7.0/spant/R/mrs_read_paravis.R |only spant-0.7.0/spant/R/mrs_read_pfile.R |only spant-0.7.0/spant/R/mrs_read_rda.R |only spant-0.7.0/spant/R/mrs_read_spar_sdat.R |only spant-0.7.0/spant/R/mrs_read_twix.R |only spant-0.7.0/spant/R/utils.R | 54 +++ spant-0.7.0/spant/inst/doc/spant-intro.html | 4 spant-0.7.0/spant/man/apply_axes.Rd |only spant-0.7.0/spant/man/apply_mrs.Rd |only spant-0.7.0/spant/man/calc_spec_diff.Rd |only spant-0.7.0/spant/man/comb_metab_ref.Rd |only spant-0.7.0/spant/man/fp_corr_td.Rd |only spant-0.7.0/spant/man/get_fh_dyns.Rd |only spant-0.7.0/spant/man/get_sh_dyns.Rd |only spant-0.7.0/spant/man/get_voi_seg.Rd | 6 spant-0.7.0/spant/man/interleave_dyns.Rd |only spant-0.7.0/spant/man/is_fd.Rd |only spant-0.7.0/spant/man/median_dyns.Rd |only spant-0.7.0/spant/man/read_mrs.Rd | 3 spant-0.7.0/spant/man/spm_pve2categorical.Rd |only 34 files changed, 283 insertions(+), 452 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-31 0.0-4
Title: Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator
Description: This is a port of Jonathan Shewchuk's Triangle library to
R. From his description: "Triangle generates exact Delaunay
triangulations, constrained Delaunay triangulations, conforming
Delaunay triangulations, Voronoi diagrams, and high-quality
triangular meshes. The latter can be generated with no small or
large angles, and are thus suitable for finite element analysis."
Author: Jonathan Richard Shewchuk [ctb, cph],
David C. Sterratt [cph, aut, cre],
Elias Pipping [ctb]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between RTriangle versions 1.6-0.9 dated 2017-07-13 and 1.6-0.10 dated 2018-01-31
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 9 ++++++++- src/triangle.c | 16 ++++++++++++---- 4 files changed, 28 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-12 1.2
2013-01-07 1.1
2012-03-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-22 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-29 0.17
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>
Diff between wallace versions 1.0.2 dated 2017-12-15 and 1.0.3 dated 2018-01-31
DESCRIPTION | 18 +++++++++--------- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ README.md | 4 ++-- inst/Rmd/gtext_comp3_userEnvs.Rmd | 18 ++++++++++++++++++ inst/Rmd/text_intro.Rmd | 4 ++-- inst/Rmd/text_intro_tab.Rmd | 5 +++-- inst/Rmd/userReport.Rmd | 2 +- inst/shiny/modules/mod_c3_userEnvs.R | 11 ++++++++++- inst/shiny/modules/mod_c7_mapPreds.R | 10 ++++++++++ inst/shiny/modules/mod_c7_mapPredsMaxent.R | 10 ++++++++++ inst/shiny/server.R | 4 +++- 12 files changed, 84 insertions(+), 29 deletions(-)
Title: R Wrappers for EXPOKIT; Other Matrix Functions
Description: Wraps some of the matrix exponentiation
utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>),
a FORTRAN library that is widely recommended for matrix
exponentiation (Sidje RB, 1998. "Expokit: A Software Package
for Computing Matrix Exponentials." ACM Trans. Math. Softw.
24(1): 130-156). EXPOKIT includes functions for
exponentiating both small, dense matrices, and large, sparse
matrices (in sparse matrices, most of the cells have value 0).
Rapid matrix exponentiation is useful in phylogenetics when we
have a large number of states (as we do when we are inferring
the history of transitions between the possible geographic
ranges of a species), but is probably useful in other ways as
well.
Author: Nicholas J. Matzke [aut, cre, cph],
Roger B. Sidje [aut, cph],
Drew Schmidt [aut]
Maintainer: ORPHANED
Diff between rexpokit versions 0.26.1 dated 2017-08-15 and 0.26.2 dated 2018-01-31
DESCRIPTION | 12 +++++--- MD5 | 6 ++-- src/lapack/blas_mod.f | 26 ++++++++--------- src/lapack/lapack.f | 74 +++++++++++++++++++++++++------------------------- 4 files changed, 61 insertions(+), 57 deletions(-)
Title: Likelihood Based Optimal Partitioning and Indicator Species
Analysis
Description: Likelihood based optimal partitioning and indicator
species analysis. Finding the best binary partition for each species
based on model selection, with the possibility to take into account
modifying/confounding variables as described
in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>.
The package implements binary and multi-level response models,
various measures of uncertainty, Lorenz-curve based thresholding,
with native support for parallel computations.
Author: Peter Solymos [cre, aut], Ermias T. Azeria [ctb]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between opticut versions 0.1-0 dated 2016-12-17 and 0.1-1 dated 2018-01-31
opticut-0.1-0/opticut/R/sindex.R |only opticut-0.1-0/opticut/R/wrsi.R |only opticut-0.1-0/opticut/R/wrsidot.R |only opticut-0.1-0/opticut/man/sindex.Rd |only opticut-0.1-1/opticut/DESCRIPTION | 25 +- opticut-0.1-1/opticut/MD5 | 120 +++++++----- opticut-0.1-1/opticut/NAMESPACE | 48 +++- opticut-0.1-1/opticut/R/as.data.frame.multicut.R |only opticut-0.1-1/opticut/R/as.data.frame.summary.multicut.R |only opticut-0.1-1/opticut/R/bestmodel.multicut.R |only opticut-0.1-1/opticut/R/bestpart.multicut.R |only opticut-0.1-1/opticut/R/bestpart.uncertainty1.R | 4 opticut-0.1-1/opticut/R/bsmooth.uncertainty.R | 2 opticut-0.1-1/opticut/R/bsmooth.uncertainty1.R | 12 - opticut-0.1-1/opticut/R/extractOpticutdot.R | 28 ++ opticut-0.1-1/opticut/R/fitted.multicut.R |only opticut-0.1-1/opticut/R/fitted.opticut.R |only opticut-0.1-1/opticut/R/fix_levels.R | 3 opticut-0.1-1/opticut/R/getMLE.multicut.R |only opticut-0.1-1/opticut/R/getMLE.opticut.R | 48 +++- opticut-0.1-1/opticut/R/get_linkinvdot.R |only opticut-0.1-1/opticut/R/iquantile.R |only opticut-0.1-1/opticut/R/iquantile.lorenz.R |only opticut-0.1-1/opticut/R/lc_cutdot.R |only opticut-0.1-1/opticut/R/lcplot.R |only opticut-0.1-1/opticut/R/lcplot.multicut1.R |only opticut-0.1-1/opticut/R/lorenz.R | 23 +- opticut-0.1-1/opticut/R/multicut.R |only opticut-0.1-1/opticut/R/multicut.default.R |only opticut-0.1-1/opticut/R/multicut.formula.R |only opticut-0.1-1/opticut/R/multicut1.R |only opticut-0.1-1/opticut/R/opticut.default.R | 23 +- opticut-0.1-1/opticut/R/opticut.formula.R | 12 - opticut-0.1-1/opticut/R/opticut1.R | 19 + opticut-0.1-1/opticut/R/opticut1dot.R | 83 +++----- opticut-0.1-1/opticut/R/opticut_distdot.R |only opticut-0.1-1/opticut/R/optilevels.R | 20 ++ opticut-0.1-1/opticut/R/optilevelsdot.R | 11 - opticut-0.1-1/opticut/R/plot.lorenz.R | 2 opticut-0.1-1/opticut/R/plot.multicut.R |only opticut-0.1-1/opticut/R/plot.multicut1.R |only opticut-0.1-1/opticut/R/predict.multicut.R |only opticut-0.1-1/opticut/R/predict.opticut.R |only opticut-0.1-1/opticut/R/predict_distdot.R |only opticut-0.1-1/opticut/R/print.multicut.R |only opticut-0.1-1/opticut/R/print.multicut1.R |only opticut-0.1-1/opticut/R/print.summary.multicut.R |only opticut-0.1-1/opticut/R/print.summary.opticut.R | 2 opticut-0.1-1/opticut/R/print.summary.uncertainty.R | 6 opticut-0.1-1/opticut/R/print.uncertainty.R | 6 opticut-0.1-1/opticut/R/print.uncertainty1.R | 6 opticut-0.1-1/opticut/R/quantile.lorenz.R | 5 opticut-0.1-1/opticut/R/strata.multicut.R |only opticut-0.1-1/opticut/R/strata.uncertainty.R | 5 opticut-0.1-1/opticut/R/subset.multicut.R |only opticut-0.1-1/opticut/R/subset.opticut.R |only opticut-0.1-1/opticut/R/subset.uncertainty.R |only opticut-0.1-1/opticut/R/summary.multicut.R |only opticut-0.1-1/opticut/R/summary_opticutdot.R | 12 - opticut-0.1-1/opticut/R/uncertainty.multicut.R |only opticut-0.1-1/opticut/R/uncertainty.opticut.R | 12 - opticut-0.1-1/opticut/R/uncertaintyMulticut1dot.R |only opticut-0.1-1/opticut/R/uncertaintyOpticut1dot.R | 57 +---- opticut-0.1-1/opticut/R/wplot.opticut1.R | 7 opticut-0.1-1/opticut/R/zzz.R | 3 opticut-0.1-1/opticut/build/partial.rdb |binary opticut-0.1-1/opticut/data/birdrec.rda |only opticut-0.1-1/opticut/man/allComb.Rd | 17 - opticut-0.1-1/opticut/man/bestmodel.Rd | 8 opticut-0.1-1/opticut/man/beta2i.Rd | 7 opticut-0.1-1/opticut/man/birdrec.Rd |only opticut-0.1-1/opticut/man/dolina.Rd | 8 opticut-0.1-1/opticut/man/lorenz.Rd | 81 ++++++-- opticut-0.1-1/opticut/man/multicut.Rd |only opticut-0.1-1/opticut/man/occolors.Rd | 38 ++- opticut-0.1-1/opticut/man/ocoptions.Rd | 26 +- opticut-0.1-1/opticut/man/opticut-package.Rd | 13 - opticut-0.1-1/opticut/man/opticut.Rd | 146 ++++++++++----- opticut-0.1-1/opticut/man/optilevels.Rd | 55 ++--- opticut-0.1-1/opticut/man/rankComb.Rd | 4 opticut-0.1-1/opticut/man/uncertainty.Rd | 140 +++++++++++--- 81 files changed, 726 insertions(+), 421 deletions(-)
Title: Analyzing Wildlife Data with Detection Error
Description: Models for analyzing site occupancy and count data models
with detection error, including single-visit based models,
conditional distance sampling and time-removal models.
Package development was supported by the
Alberta Biodiversity Monitoring Institute (www.abmi.ca)
and the Boreal Avian Modelling Project (borealbirds.ca).
Author: Peter Solymos [cre, aut], Monica Moreno [aut], Subhash R. Lele [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between detect versions 0.4-0 dated 2016-03-03 and 0.4-1 dated 2018-01-31
detect-0.4-0/detect/inst |only detect-0.4-1/detect/DESCRIPTION | 9 +- detect-0.4-1/detect/MD5 | 57 +++++++------- detect-0.4-1/detect/NAMESPACE | 5 + detect-0.4-1/detect/R/cmulti.R | 5 - detect-0.4-1/detect/R/cmulti.fit.R | 103 +++++++++++++++++---------- detect-0.4-1/detect/R/cmulti.fit0.R | 19 ++-- detect-0.4-1/detect/R/cmulti2.fit.R | 10 +- detect-0.4-1/detect/R/extractMLE.svocc.R | 4 - detect-0.4-1/detect/R/fitted.cmulti.R | 4 - detect-0.4-1/detect/R/model.frame.cmulti.R |only detect-0.4-1/detect/R/model.matrix.cmulti.R |only detect-0.4-1/detect/R/predict.cmulti.R |only detect-0.4-1/detect/R/predictMCMC.svabu.R | 2 detect-0.4-1/detect/R/print.cmulti.R | 2 detect-0.4-1/detect/R/print.summary.cmulti.R | 6 + detect-0.4-1/detect/R/solveneardot.R |only detect-0.4-1/detect/R/svabu.fit.R | 4 - detect-0.4-1/detect/R/svabu_nb.fit.R | 22 ++--- detect-0.4-1/detect/R/svocc.fit.R | 4 - detect-0.4-1/detect/R/vcov.svabu.R | 4 - detect-0.4-1/detect/R/vcov.svocc.R | 2 detect-0.4-1/detect/man/cmulti.Rd | 96 ++++++++++++++++++------- detect-0.4-1/detect/man/convertEDR.Rd | 18 ++-- detect-0.4-1/detect/man/databu.Rd | 1 detect-0.4-1/detect/man/datocc.Rd | 7 + detect-0.4-1/detect/man/detect-package.Rd | 27 ++++--- detect-0.4-1/detect/man/internals.Rd | 10 +- detect-0.4-1/detect/man/load_BAM_QPAD.Rd | 9 +- detect-0.4-1/detect/man/oven.Rd | 9 +- detect-0.4-1/detect/man/svabu.Rd | 9 ++ detect-0.4-1/detect/man/svocc.Rd | 3 32 files changed, 287 insertions(+), 164 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-12 2.0-2
2017-11-28 2.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-11 2.0.1
2016-05-05 2.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-11 0.38