Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes
are commonly used in computer experiments to fit an interpolating model.
The model is stored as an 'R6' object and can be easily updated with new
data. There are options to run in parallel (not for Windows), and 'Rcpp'
has been used to speed up calculations. Other R packages that perform
similar calculations include 'laGP', 'DiceKriging', 'GPfit', and 'mlegp'.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between GauPro versions 0.1.0 dated 2016-10-11 and 0.2.0 dated 2017-08-16
GauPro-0.1.0/GauPro/R/GauPro.R |only GauPro-0.2.0/GauPro/DESCRIPTION | 11 GauPro-0.2.0/GauPro/MD5 | 106 ++++++++- GauPro-0.2.0/GauPro/NAMESPACE | 25 ++ GauPro-0.2.0/GauPro/NEWS.md | 6 GauPro-0.2.0/GauPro/R/GauPro_Gauss.R |only GauPro-0.2.0/GauPro/R/GauPro_S3.R |only GauPro-0.2.0/GauPro/R/GauPro_base.R |only GauPro-0.2.0/GauPro/R/GauPro_selector.R |only GauPro-0.2.0/GauPro/R/Gaussian_deviance.R |only GauPro-0.2.0/GauPro/R/Gaussian_hessian.R |only GauPro-0.2.0/GauPro/R/RcppExports.R | 92 ++++++-- GauPro-0.2.0/GauPro/R/corr.R | 2 GauPro-0.2.0/GauPro/R/kernel_Exponential.R |only GauPro-0.2.0/GauPro/R/kernel_Gaussian.R |only GauPro-0.2.0/GauPro/R/kernel_Matern32.R |only GauPro-0.2.0/GauPro/R/kernel_Matern52.R |only GauPro-0.2.0/GauPro/R/kernel_RatQuad.R |only GauPro-0.2.0/GauPro/R/kernel_base.R |only GauPro-0.2.0/GauPro/R/kernel_beta.R |only GauPro-0.2.0/GauPro/R/kernel_model.R |only GauPro-0.2.0/GauPro/R/kernel_periodic.R |only GauPro-0.2.0/GauPro/R/kernel_product.R |only GauPro-0.2.0/GauPro/R/kernel_sum.R |only GauPro-0.2.0/GauPro/R/transformations.R |only GauPro-0.2.0/GauPro/R/trend_0.R |only GauPro-0.2.0/GauPro/R/trend_LM.R |only GauPro-0.2.0/GauPro/R/trend_base.R |only GauPro-0.2.0/GauPro/R/trend_constant.R |only GauPro-0.2.0/GauPro/README.md | 31 ++ GauPro-0.2.0/GauPro/build |only GauPro-0.2.0/GauPro/inst |only GauPro-0.2.0/GauPro/man/Exponential.Rd |only GauPro-0.2.0/GauPro/man/GauPro.Rd | 71 +----- GauPro-0.2.0/GauPro/man/GauPro_Gauss.Rd |only GauPro-0.2.0/GauPro/man/GauPro_base.Rd |only GauPro-0.2.0/GauPro/man/GauPro_kernel.Rd |only GauPro-0.2.0/GauPro/man/GauPro_kernel_beta.Rd |only GauPro-0.2.0/GauPro/man/GauPro_kernel_model.Rd |only GauPro-0.2.0/GauPro/man/GauPro_trend.Rd |only GauPro-0.2.0/GauPro/man/Gaussian.Rd |only GauPro-0.2.0/GauPro/man/Gaussian_devianceC.Rd |only GauPro-0.2.0/GauPro/man/Gaussian_hessianC.Rd |only GauPro-0.2.0/GauPro/man/Gaussian_hessianCC.Rd |only GauPro-0.2.0/GauPro/man/Gaussian_hessianR.Rd |only GauPro-0.2.0/GauPro/man/Matern32.Rd |only GauPro-0.2.0/GauPro/man/Matern52.Rd |only GauPro-0.2.0/GauPro/man/Periodic.Rd |only GauPro-0.2.0/GauPro/man/RatQuad.Rd |only GauPro-0.2.0/GauPro/man/corr_gauss_matrix.Rd | 5 GauPro-0.2.0/GauPro/man/corr_gauss_matrix_symC.Rd |only GauPro-0.2.0/GauPro/man/corr_gauss_matrix_sym_armaC.Rd |only GauPro-0.2.0/GauPro/man/kernel_product.Rd |only GauPro-0.2.0/GauPro/man/kernel_sum.Rd |only GauPro-0.2.0/GauPro/man/plot.GauPro.Rd |only GauPro-0.2.0/GauPro/man/plus-.GauPro_kernel.Rd |only GauPro-0.2.0/GauPro/man/predict.GauPro.Rd |only GauPro-0.2.0/GauPro/man/times-.GauPro_kernel.Rd |only GauPro-0.2.0/GauPro/man/trend_0.Rd |only GauPro-0.2.0/GauPro/man/trend_LM.Rd |only GauPro-0.2.0/GauPro/man/trend_c.Rd |only GauPro-0.2.0/GauPro/src/GauPro_init.c |only GauPro-0.2.0/GauPro/src/Gaussian_deviance.cpp |only GauPro-0.2.0/GauPro/src/Gaussian_hessian.cpp |only GauPro-0.2.0/GauPro/src/RcppExports.cpp | 124 +++++++++-- GauPro-0.2.0/GauPro/src/corr.h |only GauPro-0.2.0/GauPro/src/corr_gauss_matrix.cpp | 67 +++++ GauPro-0.2.0/GauPro/src/deviance.cpp | 2 GauPro-0.2.0/GauPro/src/pred_mean.cpp | 8 GauPro-0.2.0/GauPro/tests/testthat/test_1D.R | 2 GauPro-0.2.0/GauPro/tests/testthat/test_kernel_model.R |only GauPro-0.2.0/GauPro/tests/testthat/test_kernel_model_grad.R |only GauPro-0.2.0/GauPro/tests/testthat/test_kernel_model_trend.R |only GauPro-0.2.0/GauPro/tests/testthat/test_kernels_right_type.R |only GauPro-0.2.0/GauPro/tools |only GauPro-0.2.0/GauPro/vignettes |only 76 files changed, 424 insertions(+), 128 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 1.0 dated 2017-01-16 and 1.1 dated 2017-08-16
multinet-1.0/multinet/src/Attribute.cpp |only multinet-1.0/multinet/src/AttributeStore.cpp |only multinet-1.0/multinet/src/BAEvolutionModel.cpp |only multinet-1.0/multinet/src/CSVReader.cpp |only multinet-1.0/multinet/src/DuplicateElementException.cpp |only multinet-1.0/multinet/src/ElementNotFoundException.cpp |only multinet-1.0/multinet/src/EvolutionModel.cpp |only multinet-1.0/multinet/src/FileNotFoundException.cpp |only multinet-1.0/multinet/src/MLNetwork.cpp |only multinet-1.0/multinet/src/Makevars.bk |only multinet-1.0/multinet/src/OperationNotSupportedException.cpp |only multinet-1.0/multinet/src/UniformEvolutionModel.cpp |only multinet-1.0/multinet/src/WrongFormatException.cpp |only multinet-1.0/multinet/src/WrongParameterException.cpp |only multinet-1.0/multinet/src/actor.cpp |only multinet-1.0/multinet/src/actor_sets.cpp |only multinet-1.0/multinet/src/basic.cpp |only multinet-1.0/multinet/src/clique.cpp |only multinet-1.0/multinet/src/community.h |only multinet-1.0/multinet/src/contagion.cpp |only multinet-1.0/multinet/src/correlation.cpp |only multinet-1.0/multinet/src/datastructures.cpp |only multinet-1.0/multinet/src/datastructures.h |only multinet-1.0/multinet/src/degree.cpp |only multinet-1.0/multinet/src/distance_based.cpp |only multinet-1.0/multinet/src/dynamics.h |only multinet-1.0/multinet/src/edge.cpp |only multinet-1.0/multinet/src/evolution.cpp |only multinet-1.0/multinet/src/evolution_strategies.cpp |only multinet-1.0/multinet/src/exceptions.h |only multinet-1.0/multinet/src/flattening.cpp |only multinet-1.0/multinet/src/generation.h |only multinet-1.0/multinet/src/graphml.cpp |only multinet-1.0/multinet/src/io.h |only multinet-1.0/multinet/src/layer.cpp |only multinet-1.0/multinet/src/layout.h |only multinet-1.0/multinet/src/math.cpp |only multinet-1.0/multinet/src/measures.h |only multinet-1.0/multinet/src/mlcpm.cpp |only multinet-1.0/multinet/src/mlnetwork.h |only multinet-1.0/multinet/src/modularity.cpp |only multinet-1.0/multinet/src/multiforce.cpp |only multinet-1.0/multinet/src/multilayer.cpp |only multinet-1.0/multinet/src/neighborhood.cpp |only multinet-1.0/multinet/src/node.cpp |only multinet-1.0/multinet/src/paths.cpp |only multinet-1.0/multinet/src/projection.cpp |only multinet-1.0/multinet/src/random.cpp |only multinet-1.0/multinet/src/randomwalk_measures.cpp |only multinet-1.0/multinet/src/randomwalks.cpp |only multinet-1.0/multinet/src/randomwalks.h |only multinet-1.0/multinet/src/relevance.cpp |only multinet-1.0/multinet/src/state_dynamics.cpp |only multinet-1.0/multinet/src/threshold.cpp |only multinet-1.0/multinet/src/transformation.h |only multinet-1.0/multinet/src/transformation_utility_functions.cpp |only multinet-1.0/multinet/src/utils |only multinet-1.0/multinet/src/utils.h |only multinet-1.1/multinet/DESCRIPTION | 14 multinet-1.1/multinet/MD5 | 2239 +++++++++ multinet-1.1/multinet/NAMESPACE | 9 multinet-1.1/multinet/R/functions.R | 145 multinet-1.1/multinet/inst/extdata/aucs.mpx | 68 multinet-1.1/multinet/man/ActorMeasures.Rd | 12 multinet-1.1/multinet/man/Attributes.Rd | 24 multinet-1.1/multinet/man/Communities.Rd | 48 multinet-1.1/multinet/man/Conversion.Rd | 16 multinet-1.1/multinet/man/Directionality.Rd | 20 multinet-1.1/multinet/man/DistanceMeasures.Rd | 11 multinet-1.1/multinet/man/Generation.Rd | 6 multinet-1.1/multinet/man/IO.Rd | 30 multinet-1.1/multinet/man/LayerMeasures.Rd | 87 multinet-1.1/multinet/man/Layout.Rd |only multinet-1.1/multinet/man/Manipulation.Rd | 55 multinet-1.1/multinet/man/Navigation.Rd | 2 multinet-1.1/multinet/man/Plot.Rd | 75 multinet-1.1/multinet/man/Predefined.Rd | 4 multinet-1.1/multinet/man/Properties.Rd | 13 multinet-1.1/multinet/man/RandomWalkMeasures.Rd | 4 multinet-1.1/multinet/man/Transformation.Rd | 2 multinet-1.1/multinet/man/multinet-package.Rd | 10 multinet-1.1/multinet/src/Makevars | 4 multinet-1.1/multinet/src/Makevars.win | 5 multinet-1.1/multinet/src/RcppExports.cpp |only multinet-1.1/multinet/src/eclat |only multinet-1.1/multinet/src/include |only multinet-1.1/multinet/src/lib |only multinet-1.1/multinet/src/multinet |only multinet-1.1/multinet/src/r_functions.cpp | 2255 +++++----- multinet-1.1/multinet/src/r_functions.h | 60 multinet-1.1/multinet/src/rcpp_module_definition.cpp | 29 multinet-1.1/multinet/src/rcpp_utils.cpp | 93 multinet-1.1/multinet/src/rcpp_utils.h | 9 93 files changed, 3889 insertions(+), 1460 deletions(-)
Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk
under L1 or L2 regularization. Implements the algorithm proposed by Teo et
al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR
2012). The package comes with lot of loss functions for machine learning
which make it powerful for big data analysis. The applications includes:
structured prediction, linear SVM, multi-class SVM, f-beta optimization,
ROC optimization, ordinal regression, quantile regression,
epsilon insensitive regression, least mean square, logistic regression,
least absolute deviation regression (see package examples), etc... all with
L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados <julien.prados@unige.ch>
Diff between bmrm versions 3.3 dated 2017-05-19 and 3.4 dated 2017-08-16
bmrm-3.3/bmrm/R/bmrm.R |only bmrm-3.3/bmrm/R/core_loss.R |only bmrm-3.3/bmrm/R/loss.R |only bmrm-3.3/bmrm/R/misc_ML.R |only bmrm-3.3/bmrm/man/binaryClassificationLosses.Rd |only bmrm-3.3/bmrm/man/bmrm.Rd |only bmrm-3.3/bmrm/man/regressionLosses.Rd |only bmrm-3.4/bmrm/DESCRIPTION | 8 bmrm-3.4/bmrm/MD5 | 62 ++--- bmrm-3.4/bmrm/NAMESPACE | 24 +- bmrm-3.4/bmrm/NEWS | 10 bmrm-3.4/bmrm/R/loss_convex.R |only bmrm-3.4/bmrm/R/loss_core.R |only bmrm-3.4/bmrm/R/loss_non_convex.R |only bmrm-3.4/bmrm/R/ml_misc.R |only bmrm-3.4/bmrm/R/mmc.R |only bmrm-3.4/bmrm/R/nrbm.R | 286 ++++++++++++++++-------- bmrm-3.4/bmrm/R/svmLP.R | 32 +- bmrm-3.4/bmrm/R/wolfe.R | 79 +++--- bmrm-3.4/bmrm/build/vignette.rds |binary bmrm-3.4/bmrm/inst/doc/bmrm.R | 5 bmrm-3.4/bmrm/inst/doc/bmrm.Rmd | 42 +-- bmrm-3.4/bmrm/inst/doc/bmrm.html | 23 - bmrm-3.4/bmrm/man/balanced.cv.fold.Rd | 2 bmrm-3.4/bmrm/man/binaryClassificationLoss.Rd |only bmrm-3.4/bmrm/man/costMatrix.Rd | 4 bmrm-3.4/bmrm/man/gradient.Rd | 4 bmrm-3.4/bmrm/man/is.convex.Rd |only bmrm-3.4/bmrm/man/linearRegressionLoss.Rd |only bmrm-3.4/bmrm/man/lpSVM.Rd | 13 - bmrm-3.4/bmrm/man/lvalue.Rd |only bmrm-3.4/bmrm/man/mmc.Rd |only bmrm-3.4/bmrm/man/mmcLoss.Rd |only bmrm-3.4/bmrm/man/nrbm.Rd | 51 +++- bmrm-3.4/bmrm/man/ontologyLoss.Rd | 6 bmrm-3.4/bmrm/man/ordinalRegressionLoss.Rd | 8 bmrm-3.4/bmrm/man/predict.mmc.Rd |only bmrm-3.4/bmrm/man/roc.stat.Rd | 9 bmrm-3.4/bmrm/man/softMarginVectorLoss.Rd | 20 - bmrm-3.4/bmrm/man/tsvmLoss.Rd |only bmrm-3.4/bmrm/man/wolfe.linesearch.Rd | 12 - bmrm-3.4/bmrm/vignettes/bmrm.Rmd | 42 +-- 42 files changed, 472 insertions(+), 270 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith' plots). Constructs total Pb-U, Pb-Pb, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 0.15 dated 2017-07-11 and 0.16 dated 2017-08-16
DESCRIPTION | 12 - MD5 | 74 +++++----- NAMESPACE | 10 - R/UPb.R | 292 +++++++++++++++++++++++++++++++++++++++--- R/UThHe.R | 2 R/age.R | 26 +++ R/agespectrum.R | 5 R/cad.R | 20 ++ R/central.R | 13 - R/concordia.R | 109 +++++++++------ R/discordia.R | 218 +++++++++++++++++++++++-------- R/errorellipse.R | 29 ++-- R/evolution.R | 15 +- R/helioplot.R | 164 ++++++++++++----------- R/internals.R |only R/io.R | 91 ++++++++++++- R/isochron.R | 219 +++++++++++++++++-------------- R/kde.R | 32 +++- R/ludwig.R | 357 +++++++++++++++++++++++++++++++++++++++++++++++++--- R/peakfit.R | 36 ++--- R/radialplot.R | 34 +++- R/regression.R |only R/titterington.R | 4 R/toolbox.R | 2 R/weightedmean.R | 57 +++++--- R/york.R | 13 - README.md |only inst/UPb4.csv | 16 +- inst/UPb5.csv |only inst/UPb6.csv |only inst/constants.json | 3 man/age.Rd | 14 +- man/cad.Rd | 14 +- man/concordia.Rd | 23 ++- man/evolution.Rd | 1 man/isochron.Rd | 34 +++- man/kde.Rd | 14 +- man/ludwig.Rd |only man/radialplot.Rd | 14 +- man/read.data.Rd | 5 man/weightedmean.Rd | 14 +- 41 files changed, 1494 insertions(+), 492 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) a bivariate Egger's test for detecting publication bias.
Author: Yong Chen [aut, cre],
Chuan Hong [aut],
Haitao Chu [ctb],
Yulun Liu [ctb]
Maintainer: Yong Chen <ychen123@upenn.edu>
Diff between xmeta versions 1.1-3 dated 2017-02-06 and 1.1-4 dated 2017-08-16
DESCRIPTION | 8 MD5 | 8 R/mmeta.R | 1352 +++++++++++++++++++++++++-------------------------- man/mmeta.Rd | 6 man/xmeta-package.Rd | 2 5 files changed, 690 insertions(+), 686 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) Use of CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.3.2 dated 2017-07-20 and 0.3.3 dated 2017-08-16
NonCompart-0.3.2/NonCompart/R/tabNCA.R |only NonCompart-0.3.2/NonCompart/man/tabNCA.Rd |only NonCompart-0.3.3/NonCompart/DESCRIPTION | 8 - NonCompart-0.3.3/NonCompart/MD5 | 42 ++++---- NonCompart-0.3.3/NonCompart/R/AUC.R | 33 ++++-- NonCompart-0.3.3/NonCompart/R/BestSlope.R | 44 +++++--- NonCompart-0.3.3/NonCompart/R/IntAUC.R | 37 +++++-- NonCompart-0.3.3/NonCompart/R/Interpol.R | 42 ++++++-- NonCompart-0.3.3/NonCompart/R/LinAUC.R | 19 ++- NonCompart-0.3.3/NonCompart/R/LogAUC.R | 17 ++- NonCompart-0.3.3/NonCompart/R/Slope.R | 26 ++--- NonCompart-0.3.3/NonCompart/R/UT.R |only NonCompart-0.3.3/NonCompart/R/Unit.R | 33 ++++-- NonCompart-0.3.3/NonCompart/R/UnitUrine.R |only NonCompart-0.3.3/NonCompart/R/sNCA.R | 66 ++++++++----- NonCompart-0.3.3/NonCompart/R/tblNCA.R |only NonCompart-0.3.3/NonCompart/inst/NEWS.Rd | 6 + NonCompart-0.3.3/NonCompart/inst/doc/NonCompart-manual.pdf |binary NonCompart-0.3.3/NonCompart/man/BestSlope.Rd | 6 - NonCompart-0.3.3/NonCompart/man/NonCompart-package.Rd | 16 +-- NonCompart-0.3.3/NonCompart/man/UT.Rd |only NonCompart-0.3.3/NonCompart/man/UnitUrine.Rd |only NonCompart-0.3.3/NonCompart/man/sNCA.Rd | 30 +---- NonCompart-0.3.3/NonCompart/man/tblNCA.Rd |only NonCompart-0.3.3/NonCompart/tests/BE-Conc.csv |only NonCompart-0.3.3/NonCompart/tests/BE-NCA.csv |only NonCompart-0.3.3/NonCompart/tests/Test.R | 16 +-- 27 files changed, 279 insertions(+), 162 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Peter Li [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.8-1 dated 2017-01-09 and 0.8-2 dated 2017-08-16
DESCRIPTION | 20 +- MD5 | 102 ++++++------ NEWS | 6 build/vignette.rds |binary data/Arbuthnot.RData |binary data/Armada.RData |binary data/Bowley.RData |binary data/Cavendish.RData |binary data/ChestSizes.RData |binary data/Cholera.RData |binary data/CushnyPeebles.RData |binary data/CushnyPeeblesN.RData |binary data/Dactyl.RData |binary data/DrinksWages.RData |binary data/Fingerprints.RData |binary data/Galton.RData |binary data/GaltonFamilies.RData |binary data/Guerry.RData |binary data/HalleyLifeTable.RData |binary data/Jevons.RData |binary data/Langren.all.RData |binary data/Langren1644.RData |binary data/Macdonell.RData |binary data/MacdonellDF.RData |binary data/Michelson.RData |binary data/MichelsonSets.RData |binary data/Minard.cities.RData |binary data/Minard.temp.RData |binary data/Minard.troops.RData |binary data/Nightingale.RData |binary data/OldMaps.RData |binary data/PearsonLee.RData |binary data/PolioTrials.RData |binary data/Prostitutes.RData |binary data/Pyx.RData |binary data/Quarrels.RData |binary data/Snow.dates.RData |binary data/Snow.deaths.RData |binary data/Snow.deaths2.RData |binary data/Snow.polygons.RData |binary data/Snow.pumps.RData |binary data/Snow.streets.RData |binary data/Virginis.RData |only data/Virginis.interp.RData |only data/Wheat.RData |binary data/Wheat.monarchs.RData |binary data/Yeast.RData |binary data/YeastD.mat.RData |binary data/ZeaMays.RData |binary inst/doc/Snow_deaths-duplicates.R |only inst/doc/Snow_deaths-duplicates.html | 276 ++++++++++++++++++----------------- man/HistData-package.Rd | 11 + man/Minard.Rd | 59 +++++-- man/Virginis.Rd |only 54 files changed, 265 insertions(+), 209 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
('Springer', 2009).
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.8.0 dated 2017-01-04 and 0.9.0 dated 2017-08-16
DESCRIPTION | 12 ++-- MD5 | 76 +++++++++++++------------ NAMESPACE | 1 NEWS.md | 10 +++ R/confounders.R | 2 R/confounders.emm.R | 2 R/confounders.poly.R | 2 R/misclassification.R | 123 ++++++++++++++++++----------------------- R/misclassification_cov.R |only R/multidimBias.R | 4 - R/print.episensr.booted.R | 4 - R/probsens.R | 4 - R/probsens.conf.R | 4 - R/probsens.irr.R | 4 - R/probsens.irr.conf.R | 2 R/probsens.sel.R | 2 R/selection.R | 11 --- build/vignette.rds |binary inst/doc/episensr.html | 9 ++- man/boot.bias.Rd | 1 man/confounders.Rd | 3 - man/confounders.emm.Rd | 3 - man/confounders.limit.Rd | 1 man/confounders.poly.Rd | 3 - man/mbias.Rd | 1 man/misclassification.Rd | 41 ++++++++----- man/misclassification_cov.Rd |only man/multidimBias.Rd | 5 - man/plot.episensr.booted.Rd | 1 man/plot.mbias.Rd | 1 man/print.episensr.Rd | 1 man/print.episensr.booted.Rd | 5 - man/print.mbias.Rd | 1 man/probsens.Rd | 5 - man/probsens.conf.Rd | 5 - man/probsens.irr.Rd | 5 - man/probsens.irr.conf.Rd | 3 - man/probsens.sel.Rd | 3 - man/selection.Rd | 9 +-- tests/testthat/test-misclass.R | 9 +++ 40 files changed, 186 insertions(+), 192 deletions(-)
Title: Compare Baseline Characteristics Between Groups
Description: Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.
Author: Zhongheng Zhang,
Sir Run-Run Shaw hospital,
Zhejiang university school of medicine
Maintainer: Zhongheng Zhang <zh_zhang1984@zju.edu.cn>
Diff between CBCgrps versions 2.0 dated 2017-08-15 and 2.1 dated 2017-08-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/multigrps.R | 13 ++++++------- R/twogrps.R | 12 +++++------- man/multigrps.Rd | 6 +++--- man/twogrps.Rd | 6 +++--- 6 files changed, 26 insertions(+), 29 deletions(-)
Title: Detection and Correction of Spatial Bias in HTS Screens
Description: Allows to correct bias in high-throughput screening (HTS) assays. It (1) Detects plate-specific spatial bias by identifying rows and columns of all plates of the assay affected by this bias (following the results of the Mann-Whitney U test) as well as assay-specific spatial bias by identifying well locations (i.e., well positions scanned across all plates of a given assay) affected by this bias (also following the results of the Mann-Whitney U test); (2) Allows one to correct plate-specific spatial bias using either of the three additive or either of the three multiplicative PMP (Partial Mean Polish) methods (the most appropriate spatial bias model can be either specified by the user or determined by the program following the results of the Kolmogorov-Smirnov, Anderson-Darling or Cramer-von-Mises two-sample test) to correct the assay measurements as well as to correct assay-specific spatial bias by carrying out robust Z-scores within each plate of the assay and then traditional Z-scores across well locations.
Author: Bogdan Mazoure (McGill University, Department of Mathematics and Statistics), Iurie Caraus (UQAM, Departement d'Informatique), Robert Nadon (McGill University, Department of Human Genetics and Genome Quebec Innovation Center) and Vladimir Makarenkov (UQAM, Departement d'Informatique)
Maintainer: Bogdan Mazoure <bogdan.mazoure@gmail.com>
Diff between AssayCorrector versions 1.1.3 dated 2016-12-28 and 2.0.0 dated 2017-08-16
DESCRIPTION | 17 +++--- MD5 | 22 ++++---- NAMESPACE | 5 ++ R/AssayCorrector.R | 128 ++++++++++++++++++++++++++++++++++------------------ data/plate7.rda |binary man/correct_bias.Rd | 3 - man/create_assay.Rd | 7 ++ man/detect_bias.Rd | 7 +- man/m.Rd | 1 man/plate7.Rd | 3 - man/plot.assay.Rd | 1 man/print.assay.Rd | 1 12 files changed, 121 insertions(+), 74 deletions(-)
More information about AssayCorrector at CRAN
Permanent link
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.0 dated 2017-05-15 and 0.4.1 dated 2017-08-16
TraMineRextras-0.4.0/TraMineRextras/R/STS_to_SPELL.R |only TraMineRextras-0.4.0/TraMineRextras/man/STS_to_SPELL.Rd |only TraMineRextras-0.4.1/TraMineRextras/DESCRIPTION | 13 TraMineRextras-0.4.1/TraMineRextras/MD5 | 23 TraMineRextras-0.4.1/TraMineRextras/NAMESPACE | 112 +- TraMineRextras-0.4.1/TraMineRextras/R/seqauto.R | 56 - TraMineRextras-0.4.1/TraMineRextras/R/seqeformat.R | 544 +++++----- TraMineRextras-0.4.1/TraMineRextras/R/seqrep-grp.R | 72 - TraMineRextras-0.4.1/TraMineRextras/inst/NEWS | 22 TraMineRextras-0.4.1/TraMineRextras/inst/NEWS.Rd | 279 ++--- TraMineRextras-0.4.1/TraMineRextras/man/TraMineRextras-package.Rd | 2 TraMineRextras-0.4.1/TraMineRextras/man/seqrep-grp.Rd | 149 +- TraMineRextras-0.4.1/TraMineRextras/src/init.c |only TraMineRextras-0.4.1/TraMineRextras/src/seqstart.cpp | 22 14 files changed, 664 insertions(+), 630 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Easily Tidy Data with 'spread()' and 'gather()' Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.6.3 dated 2017-05-15 and 0.7.0 dated 2017-08-16
tidyr-0.6.3/tidyr/R/drop_na.r |only tidyr-0.6.3/tidyr/man/complete_.Rd |only tidyr-0.6.3/tidyr/man/drop_na_.Rd |only tidyr-0.6.3/tidyr/man/expand_.Rd |only tidyr-0.6.3/tidyr/man/extract_.Rd |only tidyr-0.6.3/tidyr/man/fill_.Rd |only tidyr-0.6.3/tidyr/man/gather_.Rd |only tidyr-0.6.3/tidyr/man/nest_.Rd |only tidyr-0.6.3/tidyr/man/separate_.Rd |only tidyr-0.6.3/tidyr/man/separate_rows_.Rd |only tidyr-0.6.3/tidyr/man/spread_.Rd |only tidyr-0.6.3/tidyr/man/unite_.Rd |only tidyr-0.6.3/tidyr/man/unnest_.Rd |only tidyr-0.6.3/tidyr/src/init.c |only tidyr-0.7.0/tidyr/DESCRIPTION | 11 - tidyr-0.7.0/tidyr/MD5 | 126 +++++------- tidyr-0.7.0/tidyr/NAMESPACE | 85 +++++--- tidyr-0.7.0/tidyr/NEWS.md | 150 ++++++++++++++ tidyr-0.7.0/tidyr/R/RcppExports.R | 8 tidyr-0.7.0/tidyr/R/compat-lazyeval.R |only tidyr-0.7.0/tidyr/R/complete.R | 56 ++--- tidyr-0.7.0/tidyr/R/data.R | 21 +- tidyr-0.7.0/tidyr/R/drop-na.R |only tidyr-0.7.0/tidyr/R/expand.R | 142 ++++++------- tidyr-0.7.0/tidyr/R/extract.R | 109 +++++----- tidyr-0.7.0/tidyr/R/fill.R | 53 ++--- tidyr-0.7.0/tidyr/R/gather.R | 209 ++++++++++++-------- tidyr-0.7.0/tidyr/R/id.R | 9 tidyr-0.7.0/tidyr/R/nest.R | 110 +++++----- tidyr-0.7.0/tidyr/R/replace_na.R | 14 - tidyr-0.7.0/tidyr/R/separate-rows.R | 61 ++--- tidyr-0.7.0/tidyr/R/separate.R | 196 +++++++++--------- tidyr-0.7.0/tidyr/R/seq.R | 4 tidyr-0.7.0/tidyr/R/spread.R | 167 +++++++-------- tidyr-0.7.0/tidyr/R/tidyr.R | 34 +++ tidyr-0.7.0/tidyr/R/unite.R | 78 +++---- tidyr-0.7.0/tidyr/R/unnest.R | 162 +++++++-------- tidyr-0.7.0/tidyr/R/utils.R | 46 ++-- tidyr-0.7.0/tidyr/build/vignette.rds |binary tidyr-0.7.0/tidyr/inst/doc/tidy-data.Rmd | 4 tidyr-0.7.0/tidyr/inst/doc/tidy-data.html | 160 ++++++--------- tidyr-0.7.0/tidyr/man/complete.Rd | 40 +-- tidyr-0.7.0/tidyr/man/deprecated-se.Rd |only tidyr-0.7.0/tidyr/man/drop_na.Rd | 45 +++- tidyr-0.7.0/tidyr/man/expand.Rd | 51 +--- tidyr-0.7.0/tidyr/man/extract.Rd | 15 - tidyr-0.7.0/tidyr/man/fill.Rd | 24 +- tidyr-0.7.0/tidyr/man/gather.Rd | 58 ++++- tidyr-0.7.0/tidyr/man/nest.Rd | 56 ++++- tidyr-0.7.0/tidyr/man/replace_na.Rd | 2 tidyr-0.7.0/tidyr/man/separate.Rd | 56 ++--- tidyr-0.7.0/tidyr/man/separate_rows.Rd | 42 +++- tidyr-0.7.0/tidyr/man/spread.Rd | 17 - tidyr-0.7.0/tidyr/man/tidyr-package.Rd | 7 tidyr-0.7.0/tidyr/man/unite.Rd | 50 ++++ tidyr-0.7.0/tidyr/man/unnest.Rd | 28 +- tidyr-0.7.0/tidyr/man/who.Rd | 27 +- tidyr-0.7.0/tidyr/src/RcppExports.cpp | 21 +- tidyr-0.7.0/tidyr/tests/testthat/test-complete.R | 8 tidyr-0.7.0/tidyr/tests/testthat/test-drop_na.R | 46 +--- tidyr-0.7.0/tidyr/tests/testthat/test-expand.R | 29 -- tidyr-0.7.0/tidyr/tests/testthat/test-extract.R | 6 tidyr-0.7.0/tidyr/tests/testthat/test-fill.R | 20 - tidyr-0.7.0/tidyr/tests/testthat/test-gather.R | 21 -- tidyr-0.7.0/tidyr/tests/testthat/test-id.R | 1 tidyr-0.7.0/tidyr/tests/testthat/test-nest.R | 22 -- tidyr-0.7.0/tidyr/tests/testthat/test-replace_na.R | 6 tidyr-0.7.0/tidyr/tests/testthat/test-separate.R | 31 +- tidyr-0.7.0/tidyr/tests/testthat/test-spread.R | 43 ++-- tidyr-0.7.0/tidyr/tests/testthat/test-underscored.R |only tidyr-0.7.0/tidyr/tests/testthat/test-unite.R | 14 - tidyr-0.7.0/tidyr/tests/testthat/test-unnest.R | 63 +++--- tidyr-0.7.0/tidyr/vignettes/tidy-data.Rmd | 4 73 files changed, 1612 insertions(+), 1256 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.6-5 dated 2017-05-10 and 3.6-6 dated 2017-08-16
DESCRIPTION | 8 - MD5 | 30 +++--- NAMESPACE | 2 NEWS | 8 + R/color2D.matplot.R | 5 - R/draw.circle.R | 32 ++++--- R/fan.plot.R | 13 +-- R/gantt.R | 13 +-- R/radial.plot.R | 5 - R/violin_plot.R | 212 +++++++++++++++++++++++++++++-------------------- data/soils.rda |binary demo/plotrix.R | 113 +++++++++++++++----------- man/draw.circle.Rd | 13 ++- man/fan.plot.Rd | 4 man/plotrix-package.Rd | 9 +- man/violin_plot.Rd | 78 ++++++++++-------- 16 files changed, 326 insertions(+), 219 deletions(-)
Title: Green Finance and Environmental Risk
Description: Focuses on data collecting, analyzing and visualization in green finance and environmental
risk research and analysis. Main function includes environmental data collecting from
official websites such as MEP (Ministry of Environmental Protection of China, <http://www.mep.gov.cn>), water
related projects identification and environmental data visualization.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>
Diff between gfer versions 0.1.7 dated 2017-07-03 and 0.1.8 dated 2017-08-16
gfer-0.1.7/gfer/R/rstatscn.R |only gfer-0.1.8/gfer/DESCRIPTION | 16 ++++--- gfer-0.1.8/gfer/MD5 | 53 +++++++++++++++---------- gfer-0.1.8/gfer/NAMESPACE | 17 +++++++- gfer-0.1.8/gfer/NEWS | 11 ++++- gfer-0.1.8/gfer/R/data.R |only gfer-0.1.8/gfer/R/getIndex.R | 3 - gfer-0.1.8/gfer/R/getNBS.R |only gfer-0.1.8/gfer/R/getPPPList.R | 8 +-- gfer-0.1.8/gfer/R/plotChord.R |only gfer-0.1.8/gfer/R/plotScatterPie.R |only gfer-0.1.8/gfer/README.md | 1 gfer-0.1.8/gfer/build/vignette.rds |binary gfer-0.1.8/gfer/data |only gfer-0.1.8/gfer/inst/doc/gfer.pdf |binary gfer-0.1.8/gfer/man/GDPmix.Rd |only gfer-0.1.8/gfer/man/checkHttpStatus.Rd | 2 gfer-0.1.8/gfer/man/cm.Rd |only gfer-0.1.8/gfer/man/dataJson2df.Rd | 2 gfer-0.1.8/gfer/man/genDfwds.Rd | 2 gfer-0.1.8/gfer/man/getIndex.Rd | 3 - gfer-0.1.8/gfer/man/getNBS.Rd |only gfer-0.1.8/gfer/man/getWaternomicsData_NBS.Rd |only gfer-0.1.8/gfer/man/getWaternomicsData_goog.Rd |only gfer-0.1.8/gfer/man/milSec.Rd | 2 gfer-0.1.8/gfer/man/plotChord.Rd |only gfer-0.1.8/gfer/man/plotScatterPie.Rd |only gfer-0.1.8/gfer/man/statscnDbs.Rd | 2 gfer-0.1.8/gfer/man/statscnQueryData.Rd | 2 gfer-0.1.8/gfer/man/statscnQueryLastN.Rd | 2 gfer-0.1.8/gfer/man/statscnQueryZb.Rd | 2 gfer-0.1.8/gfer/man/statscnRegions.Rd | 2 gfer-0.1.8/gfer/man/statscnRowNamePrefix.Rd | 2 gfer-0.1.8/gfer/man/updateNBS.Rd |only 34 files changed, 86 insertions(+), 46 deletions(-)
Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis
using the log-ratio approach introduced by John Aitchison in 1982. Main functions
have been implemented in c++ for better performance.
Author: Marc Comas-Cufí [aut, cre]
Maintainer: Marc Comas-Cufí <mcomas@imae.udg.edu>
Diff between coda.base versions 0.1.4 dated 2017-07-27 and 0.1.6 dated 2017-08-16
DESCRIPTION | 10 ++++---- MD5 | 22 +++++++++++------- NAMESPACE | 2 + R/RcppExports.R | 8 ++++++ R/coordinates.R | 54 +++++++++++++++++++++++++++++++++++++++++++-- man/pb_basis.Rd |only man/variation_array.Rd |only src/Makevars | 2 - src/Makevars.win | 2 - src/RcppExports.cpp | 26 +++++++++++++++++++++ src/coda.cpp | 34 ++++++++++++++++++++++------ src/principal_balances.cpp |only src/principal_balances.h |only src/sbp.cpp |only src/sbp.h |only 15 files changed, 134 insertions(+), 26 deletions(-)
Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for
mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means
Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining
and Knowledge Discovery 2, 283-304, <DOI:10.1023/A:1009769707641>.
Author: Gero Szepannek
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between clustMixType versions 0.1-22 dated 2017-07-27 and 0.1-25 dated 2017-08-16
DESCRIPTION | 8 +-- MD5 | 11 ++-- NAMESPACE | 2 R/kprototypes.R | 119 +++++++++++++++++++++++++++++++++++++++++++++----- man/kproto.Rd | 6 +- man/lambdaest.Rd | 13 +++-- man/summary.kproto.Rd |only 7 files changed, 133 insertions(+), 26 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between statnet.common versions 3.3.0 dated 2015-10-24 and 4.0.0 dated 2017-08-16
DESCRIPTION | 14 +- LICENSE | 2 MD5 | 67 ++++++---- NAMESPACE | 99 ++++++++++++++- NEWS | 27 +++- R/cite.utilities.R | 43 ++++++ R/control.utilities.R | 114 +++++++++++++++++ R/formula.utilities.R | 112 ++++++++++++++--- R/logspace.utils.R |only R/misc.utilities.R | 274 +++++++++++++++++++++++++++++++++++++++++-- R/rle_utils.R |only R/startup.utilities.R | 61 +++++++++ R/string.utilities.R | 37 +++++ R/wmatrix.R |only R/zzz.R |only README.md |only build |only inst/CITATION | 2 man/ERRVL.Rd | 34 ++--- man/NVL.Rd | 63 +++++---- man/all_identical.Rd |only man/check.control.class.Rd | 55 +++----- man/compress.data.frame.Rd | 53 +++++--- man/compress_rows.Rd |only man/control.list.accessor.Rd | 52 ++------ man/control.remap.Rd |only man/formula.utilities.Rd | 120 ++++++++++-------- man/logspace.utils.Rd |only man/opttest.Rd | 60 ++++----- man/paste.and.Rd | 42 ++---- man/print.control.list.Rd | 26 +--- man/rle.utils.Rd |only man/set.control.class.Rd | 38 ++--- man/sort.data.frame.Rd | 68 ++++++---- man/statnet.cite.Rd | 50 +++---- man/statnetStartupMessage.Rd | 97 +++++++-------- man/sweep_cols.matrix.Rd |only man/vector.namesmatch.Rd | 39 ++---- man/wmatrix.Rd |only man/wmatrix_weights.Rd |only src |only 41 files changed, 1185 insertions(+), 464 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
K. Colyvas;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.51-0 dated 2017-05-08 and 1.52-1 dated 2017-08-16
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| 2 spatstat-1.52-1/spatstat/R/closepairs.R | 2 spatstat-1.52-1/spatstat/R/clusterinfo.R | 8 spatstat-1.52-1/spatstat/R/compileK.R | 27 spatstat-1.52-1/spatstat/R/connected.R | 21 spatstat-1.52-1/spatstat/R/crossdistlpp.R | 24 spatstat-1.52-1/spatstat/R/daogenton.R | 2 spatstat-1.52-1/spatstat/R/deldir.R | 2 spatstat-1.52-1/spatstat/R/density.lpp.R | 12 spatstat-1.52-1/spatstat/R/density.ppp.R | 8 spatstat-1.52-1/spatstat/R/density.psp.R | 2 spatstat-1.52-1/spatstat/R/dg.R | 2 spatstat-1.52-1/spatstat/R/dgs.R | 2 spatstat-1.52-1/spatstat/R/discarea.R | 2 spatstat-1.52-1/spatstat/R/dist2dpath.R | 2 spatstat-1.52-1/spatstat/R/distan3D.R | 2 spatstat-1.52-1/spatstat/R/distances.R | 2 spatstat-1.52-1/spatstat/R/distanxD.R | 2 spatstat-1.52-1/spatstat/R/distfun.R | 6 spatstat-1.52-1/spatstat/R/distmap.R | 2 spatstat-1.52-1/spatstat/R/dppm.R | 9 spatstat-1.52-1/spatstat/R/edgeRipley.R | 2 spatstat-1.52-1/spatstat/R/edges2triangles.R | 2 spatstat-1.52-1/spatstat/R/effectfun.R | 41 - 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spatstat-1.52-1/spatstat/R/linearpcf.R | 58 + spatstat-1.52-1/spatstat/R/linearpcfmulti.R | 4 spatstat-1.52-1/spatstat/R/linequad.R | 2 spatstat-1.52-1/spatstat/R/linfun.R | 2 spatstat-1.52-1/spatstat/R/linim.R | 96 ++ spatstat-1.52-1/spatstat/R/linnet.R | 12 spatstat-1.52-1/spatstat/R/linnetsurgery.R | 2 spatstat-1.52-1/spatstat/R/lintess.R | 2 spatstat-1.52-1/spatstat/R/lixellate.R | 2 spatstat-1.52-1/spatstat/R/localpcf.R | 2 spatstat-1.52-1/spatstat/R/lpp.R | 67 + spatstat-1.52-1/spatstat/R/lppm.R | 11 spatstat-1.52-1/spatstat/R/measures.R | 116 +++ spatstat-1.52-1/spatstat/R/mincontrast.R | 27 spatstat-1.52-1/spatstat/R/minkowski.R | 2 spatstat-1.52-1/spatstat/R/minnndist.R | 2 spatstat-1.52-1/spatstat/R/mpl.R | 19 spatstat-1.52-1/spatstat/R/nncross.R | 2 spatstat-1.52-1/spatstat/R/nncross3D.R | 2 spatstat-1.52-1/spatstat/R/nndist.R | 2 spatstat-1.52-1/spatstat/R/nndistlpp.R | 5 spatstat-1.52-1/spatstat/R/nnmap.R | 2 spatstat-1.52-1/spatstat/R/options.R | 8 spatstat-1.52-1/spatstat/R/otherpackages.R | 2 spatstat-1.52-1/spatstat/R/pairdistlpp.R | 2 spatstat-1.52-1/spatstat/R/pcf.R | 2 spatstat-1.52-1/spatstat/R/pcfinhom.R | 2 spatstat-1.52-1/spatstat/R/pixellate.R | 2 spatstat-1.52-1/spatstat/R/plot.anylist.R | 5 spatstat-1.52-1/spatstat/R/plot.im.R | 1 spatstat-1.52-1/spatstat/R/plot.ppp.R | 3 spatstat-1.52-1/spatstat/R/polygood.R | 2 spatstat-1.52-1/spatstat/R/pool.R | 61 - spatstat-1.52-1/spatstat/R/ppm.R | 3 spatstat-1.52-1/spatstat/R/ppmclass.R | 74 +- spatstat-1.52-1/spatstat/R/ppp.R | 7 spatstat-1.52-1/spatstat/R/pppmatch.R | 2 spatstat-1.52-1/spatstat/R/ppx.R | 4 spatstat-1.52-1/spatstat/R/profilepl.R | 5 spatstat-1.52-1/spatstat/R/psp.R | 11 spatstat-1.52-1/spatstat/R/psp2pix.R | 2 spatstat-1.52-1/spatstat/R/pspcross.R | 2 spatstat-1.52-1/spatstat/R/quasirandom.R | 2 spatstat-1.52-1/spatstat/R/rPerfect.R | 2 spatstat-1.52-1/spatstat/R/random.R | 2 spatstat-1.52-1/spatstat/R/rat.R | 208 +++-- spatstat-1.52-1/spatstat/R/rho2hat.R | 2 spatstat-1.52-1/spatstat/R/rhohat.R | 17 spatstat-1.52-1/spatstat/R/rmh.default.R | 2 spatstat-1.52-1/spatstat/R/rmhmodel.R | 2 spatstat-1.52-1/spatstat/R/rmhmodel.ppm.R | 2 spatstat-1.52-1/spatstat/R/rppm.R | 5 spatstat-1.52-1/spatstat/R/scanstat.R | 2 spatstat-1.52-1/spatstat/R/setcov.R | 2 spatstat-1.52-1/spatstat/R/smooth.ppp.R | 97 ++ spatstat-1.52-1/spatstat/R/solist.R | 2 spatstat-1.52-1/spatstat/R/sparse3Darray.R | 3 spatstat-1.52-1/spatstat/R/sparsecommon.R | 2 spatstat-1.52-1/spatstat/R/sparselinalg.R | 2 spatstat-1.52-1/spatstat/R/strauss.R | 2 spatstat-1.52-1/spatstat/R/sysdata.rda |binary spatstat-1.52-1/spatstat/R/timed.R | 8 spatstat-1.52-1/spatstat/R/util.R | 18 spatstat-1.52-1/spatstat/R/vcov.ppm.R | 2 spatstat-1.52-1/spatstat/R/weightedStats.R | 2 spatstat-1.52-1/spatstat/R/wingeom.R | 2 spatstat-1.52-1/spatstat/build/vignette.rds |binary spatstat-1.52-1/spatstat/data/Kovesi.rda |binary spatstat-1.52-1/spatstat/data/amacrine.rda |binary 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spatstat-1.52-1/spatstat/man/rat.Rd | 5 spatstat-1.52-1/spatstat/man/spatstat-internal.Rd | 53 + spatstat-1.52-1/spatstat/man/spatstat-package.Rd | 5 spatstat-1.52-1/spatstat/src/denspt.c | 2 spatstat-1.52-1/spatstat/src/hasclose.h | 2 spatstat-1.52-1/spatstat/src/init.c | 3 spatstat-1.52-1/spatstat/src/proto.h | 415 +++++------ spatstat-1.52-1/spatstat/tests/testsAtoF.R | 76 ++ spatstat-1.52-1/spatstat/tests/testsGtoK.R | 46 + spatstat-1.52-1/spatstat/tests/testsNtoP.R | 48 - spatstat-1.52-1/spatstat/vignettes/datasets.Rnw | 8 spatstat-1.52-1/spatstat/vignettes/shapefiles.Rnw | 14 spatstat-1.52-1/spatstat/vignettes/updates.Rnw | 187 ++++- 270 files changed, 3556 insertions(+), 1417 deletions(-)
Title: Functions for Plotting Graphical Shapes, Colors
Description: Functions for plotting graphical shapes
such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between shape versions 1.4.2 dated 2014-11-05 and 1.4.3 dated 2017-08-16
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NAMESPACE | 11 +++++++++-- R/Arrows.R | 6 +++++- build/vignette.rds |binary inst/doc/shape.pdf |binary 6 files changed, 27 insertions(+), 16 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.6 dated 2017-05-03 and 2.7 dated 2017-08-16
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- R/as.signed.R | 12 ++++++++- R/comps.R | 21 ++++++++++------- R/perm.R | 33 ++++++++++++++++++--------- R/transf.R | 57 ++++++++++++++++++++++++++++------------------- R/trnf.R | 4 ++- R/zbind.R | 31 ++++++++++++++++--------- inst/CHANGELOG | 9 +++++++ man/multiplex-package.Rd | 4 +-- man/perm.Rd | 5 +++- man/transf.Rd | 14 +++++------ 12 files changed, 140 insertions(+), 80 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav
Yalamanchi [aut], Mildenberger Thoralf [ctb], Deepak Yadav [ctb], Nacho Cordón
Castillo [ctb], Vandit Jain [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.6.9.6 dated 2017-07-09 and 0.6.9.8-1 dated 2017-08-16
markovchain-0.6.9.6/markovchain/inst/doc/GSoC-2017_additions.html |only markovchain-0.6.9.6/markovchain/src/init.c |only markovchain-0.6.9.8-1/markovchain/ChangeLog | 3 markovchain-0.6.9.8-1/markovchain/DESCRIPTION | 10 markovchain-0.6.9.8-1/markovchain/MD5 | 80 ++-- markovchain-0.6.9.8-1/markovchain/NAMESPACE | 6 markovchain-0.6.9.8-1/markovchain/NEWS | 6 markovchain-0.6.9.8-1/markovchain/R/0_classesAndMethods.R | 103 +++-- markovchain-0.6.9.8-1/markovchain/R/0_ctmcClassesAndMethodsSAI.R | 32 - markovchain-0.6.9.8-1/markovchain/R/0_higherOrder.R | 29 - markovchain-0.6.9.8-1/markovchain/R/0_hommc.R | 132 ++++++- markovchain-0.6.9.8-1/markovchain/R/1_ctmcProbabilisticSAI.R | 183 ++++++++-- markovchain-0.6.9.8-1/markovchain/R/1_functions4Fitting.R | 21 + markovchain-0.6.9.8-1/markovchain/R/2_probabilistic.R | 135 +++++++ markovchain-0.6.9.8-1/markovchain/R/5_statisticalTests.R | 165 ++++----- markovchain-0.6.9.8-1/markovchain/R/RcppExports.R | 76 ++-- markovchain-0.6.9.8-1/markovchain/README.md | 3 markovchain-0.6.9.8-1/markovchain/build/vignette.rds |binary markovchain-0.6.9.8-1/markovchain/inst/CITATION | 12 markovchain-0.6.9.8-1/markovchain/inst/doc/GSoC-2017_additions.R | 48 ++ markovchain-0.6.9.8-1/markovchain/inst/doc/GSoC-2017_additions.Rmd | 132 ++++++- markovchain-0.6.9.8-1/markovchain/inst/doc/GSoC-2017_additions.pdf |only markovchain-0.6.9.8-1/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 106 +++-- markovchain-0.6.9.8-1/markovchain/inst/doc/an_introduction_to_markovchain_package.Rnw | 26 + markovchain-0.6.9.8-1/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary markovchain-0.6.9.8-1/markovchain/inst/doc/complicateSteadyStates.pdf |binary markovchain-0.6.9.8-1/markovchain/inst/doc/higher_order_markov_chains.pdf |binary markovchain-0.6.9.8-1/markovchain/inst/doc/markovchainCrashIntro.pdf |binary markovchain-0.6.9.8-1/markovchain/man/expectedRewards.Rd |only markovchain-0.6.9.8-1/markovchain/man/expectedRewardsforA.Rd |only markovchain-0.6.9.8-1/markovchain/man/firstPassageMultiple.Rd | 10 markovchain-0.6.9.8-1/markovchain/man/is.CTMCirreducible.Rd |only markovchain-0.6.9.8-1/markovchain/man/is.TimeReversible.Rd |only markovchain-0.6.9.8-1/markovchain/man/kullback.Rd | 10 markovchain-0.6.9.8-1/markovchain/man/predictHommc.Rd |only markovchain-0.6.9.8-1/markovchain/src/1_ctmcProbabilistic.cpp | 15 markovchain-0.6.9.8-1/markovchain/src/1_functions4Fitting.cpp | 8 markovchain-0.6.9.8-1/markovchain/src/2_probabilistic.cpp | 60 +++ markovchain-0.6.9.8-1/markovchain/src/RcppExports.cpp | 140 +++++-- markovchain-0.6.9.8-1/markovchain/tests/testthat/testBasic1.R | 56 +++ markovchain-0.6.9.8-1/markovchain/tests/testthat/testFits.R | 15 markovchain-0.6.9.8-1/markovchain/tests/testthat/testctmc.R | 50 ++ markovchain-0.6.9.8-1/markovchain/vignettes/GSoC-2017_additions.Rmd | 132 ++++++- markovchain-0.6.9.8-1/markovchain/vignettes/an_introduction_to_markovchain_package.Rnw | 26 + markovchain-0.6.9.8-1/markovchain/vignettes/markovchainBiblio.bib | 41 +- 45 files changed, 1463 insertions(+), 408 deletions(-)
Title: Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagrams
Description: Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams,
visualising webs, electrical networks, etc.
Support for the book "A practical guide to ecological modelling -
using R as a simulation platform"
by Karline Soetaert and Peter M.J. Herman (2009), Springer.
and the book "Solving Differential Equations in R"
by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer.
Includes demo(flowchart), demo(plotmat), demo(plotweb).
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between diagram versions 1.6.3 dated 2014-11-06 and 1.6.4 dated 2017-08-16
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 18 +++++++++--------- NAMESPACE | 16 ++++++++++------ R/plotmat.R | 14 +++++++++++--- build/vignette.rds |binary data/Teasel.rda |binary data/rigaweb.rda |binary data/takapotoweb.rda |binary inst/doc/diagram.pdf |binary man/plotmat.Rd | 17 ++++++++++++++--- 10 files changed, 58 insertions(+), 35 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.6.4 dated 2017-04-29 and 1.6.8 dated 2017-08-16
DESCRIPTION | 6 - MD5 | 30 ++++---- NAMESPACE | 5 - R/CarmaNoise.R | 139 +++++++++++++++++++------------------ R/DiagnosticCogarch.R | 4 + R/PseudoLogLikCOGARCH.R | 30 ++++---- R/RcppExports.R | 82 +++++++++++---------- R/qmle.R | 41 +++++++++- R/setHawkes.R | 24 ++++++ R/simulateForPpr.R | 9 ++ inst/CITATION | 30 +++++++- man/setCogarch.Rd | 6 + man/setHawkes.Rd | 68 +++++++++++------- man/yuima-class.Rd | 180 ++++++++++++++++++++++++------------------------ src/RcppExports.cpp | 68 ++++++++++++------ src/yuima_init.c | 80 ++++++++++----------- 16 files changed, 480 insertions(+), 322 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Müller [aut],
Reto Bürgin [aut],
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.0-6 dated 2017-06-17 and 2.0-7 dated 2017-08-16
DESCRIPTION | 8 ++--- MD5 | 54 +++++++++++++++++------------------ NEWS | 44 +++++++++++++++++++++++++++- R/alphabet.R | 14 +++++++-- R/implicativestat.R | 6 ++- R/seqdecomp.R | 8 ++--- R/seqdef.R | 4 ++ R/seqecreate.R | 13 ++++++-- R/seqetm.R | 8 +++++ R/seqformat-SPS_to_STS.R | 2 - R/seqformat-STS_to_TSE.R | 4 -- R/seqformat.R | 17 ++++++----- R/seqpcplot.R | 2 - R/seqtrate.R | 23 +++++++++++--- build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/NEWS.Rd | 43 +++++++++++++++++++++++++++ inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 - man/alphabet.Rd | 25 ++++++++++------ man/seqdef.Rd | 2 - man/seqdist.Rd | 2 - man/seqecreate.Rd | 19 +++++++++++- man/seqefsub.Rd | 4 +- man/seqformat.Rd | 49 +++++++++++++++++++++++++------ man/seqtrate.Rd | 18 +++++++---- 28 files changed, 279 insertions(+), 92 deletions(-)
Title: Power and Reversal Power Distributions
Description: Density, distribution function, quantile function and random generation for the family of power and reversal power distributions.
Author: Susan Anyosa [aut, cre],
Jorge Luis Bazán [aut]
Maintainer: Susan Anyosa <susanaliciach@gmail.com>
Diff between powdist versions 0.1.2 dated 2017-08-05 and 0.1.3 dated 2017-08-16
DESCRIPTION | 10 ++--- MD5 | 102 ++++++++++++++++++++++++++++---------------------------- R/dpc.R | 14 ++++++- R/dpgmav.R | 13 ++++++- R/dpgmiv.R | 16 +++++++- R/dpl.R | 15 +++++++- R/dpn.R | 13 ++++++- R/drpc.R | 13 ++++++- R/drpgmav.R | 13 ++++++- R/drpgmiv.R | 13 ++++++- R/drpl.R | 12 ++++++ R/drpn.R | 13 ++++++- R/ppc.R | 12 ++++-- R/ppgmav.R | 12 ++++-- R/ppgmiv.R | 12 ++++-- R/ppl.R | 14 +++++-- R/ppn.R | 12 ++++-- R/prpc.R | 12 ++++-- R/prpgmav.R | 13 ++++--- R/prpgmiv.R | 12 ++++-- R/prpl.R | 12 ++++-- R/prpn.R | 12 ++++-- R/qpc.R | 10 ++++- R/qpgmav.R | 10 ++++- R/qpgmiv.R | 12 +++++- R/qpl.R | 12 ++++-- R/qpn.R | 10 ++++- R/qrpc.R | 10 ++++- R/qrpgmav.R | 10 ++++- R/qrpgmiv.R | 10 ++++- R/qrpl.R | 10 ++++- R/qrpn.R | 10 ++++- R/rpc.R | 2 - R/rpgmav.R | 2 - R/rpgmiv.R | 2 - R/rpl.R | 4 +- R/rpn.R | 2 - R/rrpc.R | 2 - R/rrpgmav.R | 2 - R/rrpgmiv.R | 2 - R/rrpl.R | 2 - R/rrpn.R | 2 - man/pc.Rd | 21 +++++++++-- man/pgmav.Rd | 21 +++++++++-- man/pgmiv.Rd | 21 +++++++++-- man/pl.Rd | 21 +++++++++-- man/pn.Rd | 21 +++++++++-- man/revpc.Rd | 21 +++++++++-- man/revpgmav.Rd | 21 +++++++++-- man/revpgmiv.Rd | 21 +++++++++-- man/revpl.Rd | 20 ++++++++-- man/revpn.Rd | 21 +++++++++-- 52 files changed, 531 insertions(+), 174 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-10 dated 2017-04-28 and 1.2-11 dated 2017-08-16
Matrix-1.2-10/Matrix/vignettes/fullpage.sty |only Matrix-1.2-11/Matrix/DESCRIPTION | 8 +- Matrix-1.2-11/Matrix/MD5 | 85 +++++++++++------------- Matrix-1.2-11/Matrix/NAMESPACE | 6 - Matrix-1.2-11/Matrix/R/Auxiliaries.R | 8 +- Matrix-1.2-11/Matrix/R/Matrix.R | 24 +++++- Matrix-1.2-11/Matrix/R/Tsparse.R | 2 Matrix-1.2-11/Matrix/R/denseMatrix.R | 8 ++ Matrix-1.2-11/Matrix/R/diagMatrix.R | 11 +-- Matrix-1.2-11/Matrix/R/dppMatrix.R | 2 Matrix-1.2-11/Matrix/R/dtCMatrix.R | 2 Matrix-1.2-11/Matrix/R/eigen.R | 25 ++++--- Matrix-1.2-11/Matrix/R/products.R | 4 - Matrix-1.2-11/Matrix/R/rankMatrix.R | 21 +++-- Matrix-1.2-11/Matrix/R/spModels.R | 1 Matrix-1.2-11/Matrix/R/sparseMatrix.R | 37 ++++++++++ Matrix-1.2-11/Matrix/R/sparseQR.R | 9 +- Matrix-1.2-11/Matrix/R/zzz.R | 13 +++ Matrix-1.2-11/Matrix/TODO | 29 +++++++- Matrix-1.2-11/Matrix/build/vignette.rds |binary Matrix-1.2-11/Matrix/inst/NEWS.Rd | 25 +++++++ Matrix-1.2-11/Matrix/inst/doc/Comparisons.pdf |binary Matrix-1.2-11/Matrix/inst/doc/Design-issues.pdf |binary Matrix-1.2-11/Matrix/inst/doc/Intro2Matrix.pdf |binary Matrix-1.2-11/Matrix/inst/doc/Introduction.pdf |binary Matrix-1.2-11/Matrix/inst/doc/sparseModels.pdf |binary Matrix-1.2-11/Matrix/inst/test-tools-Matrix.R | 8 ++ Matrix-1.2-11/Matrix/man/Diagonal.Rd | 23 ++++-- Matrix-1.2-11/Matrix/man/Matrix-class.Rd | 3 Matrix-1.2-11/Matrix/man/dgeMatrix-class.Rd | 2 Matrix-1.2-11/Matrix/man/index-class.Rd | 2 Matrix-1.2-11/Matrix/man/norm.Rd | 2 Matrix-1.2-11/Matrix/man/qr-methods.Rd | 70 +++++++++---------- Matrix-1.2-11/Matrix/man/rankMatrix.Rd | 7 + Matrix-1.2-11/Matrix/man/replValue-class.Rd | 2 Matrix-1.2-11/Matrix/man/sparseQR-class.Rd | 47 +++++++++---- Matrix-1.2-11/Matrix/src/sparseQR.c | 23 ++++-- Matrix-1.2-11/Matrix/tests/Simple.R | 58 ++++++++-------- Matrix-1.2-11/Matrix/tests/bind.R | 11 +-- Matrix-1.2-11/Matrix/tests/bind.Rout.save | 28 +++---- Matrix-1.2-11/Matrix/tests/dpo-test.R | 7 + Matrix-1.2-11/Matrix/tests/factorizing.R | 40 +++++++---- Matrix-1.2-11/Matrix/tests/indexing.R | 46 ++++++------ Matrix-1.2-11/Matrix/tests/indexing.Rout.save | 76 +++++++++++---------- 44 files changed, 492 insertions(+), 283 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr versions 1.2.1 dated 2016-07-03 and 1.3.0 dated 2017-08-16
httr-1.2.1/httr/R/safe-callback.R |only httr-1.2.1/httr/man/httr.Rd |only httr-1.2.1/httr/man/safe_callback.Rd |only httr-1.3.0/httr/DESCRIPTION | 13 httr-1.3.0/httr/MD5 | 223 ++-- httr-1.3.0/httr/NAMESPACE | 9 httr-1.3.0/httr/NEWS.md | 91 + httr-1.3.0/httr/R/body.R | 18 httr-1.3.0/httr/R/callback.R |only httr-1.3.0/httr/R/http-browse.r | 8 httr-1.3.0/httr/R/httr.r | 5 httr-1.3.0/httr/R/oauth-app.r | 19 httr-1.3.0/httr/R/oauth-cache.R | 19 httr-1.3.0/httr/R/oauth-endpoint.r | 3 httr-1.3.0/httr/R/oauth-exchanger.r | 18 httr-1.3.0/httr/R/oauth-init.R | 181 ++- httr-1.3.0/httr/R/oauth-listener.r | 6 httr-1.3.0/httr/R/oauth-server-side.R | 72 - httr-1.3.0/httr/R/oauth-signature.r | 61 - httr-1.3.0/httr/R/oauth-token.r | 73 + httr-1.3.0/httr/R/progress.R | 22 httr-1.3.0/httr/R/request.R | 13 httr-1.3.0/httr/R/retry.R | 70 + httr-1.3.0/httr/R/url.r | 16 httr-1.3.0/httr/R/utils.r | 10 httr-1.3.0/httr/R/verbose.r | 14 httr-1.3.0/httr/R/write-function.R | 3 httr-1.3.0/httr/README.md | 8 httr-1.3.0/httr/build/vignette.rds |binary httr-1.3.0/httr/demo/00Index | 1 httr-1.3.0/httr/demo/oauth2-facebook.r | 3 httr-1.3.0/httr/demo/oauth2-linkedin.r | 2 httr-1.3.0/httr/demo/oauth2-reddit.R | 9 httr-1.3.0/httr/demo/oauth2-yelp.R |only httr-1.3.0/httr/inst/doc/api-packages.R | 4 httr-1.3.0/httr/inst/doc/api-packages.Rmd | 90 - httr-1.3.0/httr/inst/doc/api-packages.html | 195 +-- httr-1.3.0/httr/inst/doc/quickstart.Rmd | 22 httr-1.3.0/httr/inst/doc/quickstart.html | 862 ++++++---------- httr-1.3.0/httr/inst/doc/secrets.R |only httr-1.3.0/httr/inst/doc/secrets.Rmd |only httr-1.3.0/httr/inst/doc/secrets.html |only httr-1.3.0/httr/man/BROWSE.Rd | 1 httr-1.3.0/httr/man/DELETE.Rd | 2 httr-1.3.0/httr/man/GET.Rd | 2 httr-1.3.0/httr/man/HEAD.Rd | 2 httr-1.3.0/httr/man/PATCH.Rd | 1 httr-1.3.0/httr/man/POST.Rd | 1 httr-1.3.0/httr/man/PUT.Rd | 1 httr-1.3.0/httr/man/RETRY.Rd | 27 httr-1.3.0/httr/man/Token-class.Rd | 4 httr-1.3.0/httr/man/VERB.Rd | 1 httr-1.3.0/httr/man/add_headers.Rd | 1 httr-1.3.0/httr/man/authenticate.Rd | 1 httr-1.3.0/httr/man/cache_info.Rd | 1 httr-1.3.0/httr/man/config.Rd | 1 httr-1.3.0/httr/man/content.Rd | 4 httr-1.3.0/httr/man/content_type.Rd | 7 httr-1.3.0/httr/man/cookies.Rd | 1 httr-1.3.0/httr/man/get_callback.Rd |only httr-1.3.0/httr/man/guess_media.Rd | 1 httr-1.3.0/httr/man/handle.Rd | 1 httr-1.3.0/httr/man/handle_pool.Rd | 3 httr-1.3.0/httr/man/has_content.Rd | 1 httr-1.3.0/httr/man/headers.Rd | 1 httr-1.3.0/httr/man/hmac_sha1.Rd | 1 httr-1.3.0/httr/man/http_condition.Rd | 1 httr-1.3.0/httr/man/http_error.Rd | 3 httr-1.3.0/httr/man/http_status.Rd | 1 httr-1.3.0/httr/man/http_type.Rd | 1 httr-1.3.0/httr/man/httr-package.Rd |only httr-1.3.0/httr/man/httr_dr.Rd | 1 httr-1.3.0/httr/man/httr_options.Rd | 3 httr-1.3.0/httr/man/init_oauth1.0.Rd | 3 httr-1.3.0/httr/man/init_oauth2.0.Rd | 22 httr-1.3.0/httr/man/insensitive.Rd | 1 httr-1.3.0/httr/man/jwt_signature.Rd | 24 httr-1.3.0/httr/man/modify_url.Rd | 1 httr-1.3.0/httr/man/oauth1.0_token.Rd | 1 httr-1.3.0/httr/man/oauth2.0_token.Rd | 14 httr-1.3.0/httr/man/oauth_app.Rd | 7 httr-1.3.0/httr/man/oauth_callback.Rd | 1 httr-1.3.0/httr/man/oauth_endpoint.Rd | 4 httr-1.3.0/httr/man/oauth_endpoints.Rd | 1 httr-1.3.0/httr/man/oauth_exchanger.Rd | 10 httr-1.3.0/httr/man/oauth_listener.Rd | 3 httr-1.3.0/httr/man/oauth_service_token.Rd | 6 httr-1.3.0/httr/man/oauth_signature.Rd | 3 httr-1.3.0/httr/man/parse_http_date.Rd | 3 httr-1.3.0/httr/man/parse_media.Rd | 1 httr-1.3.0/httr/man/parse_url.Rd | 13 httr-1.3.0/httr/man/progress.Rd | 7 httr-1.3.0/httr/man/response.Rd | 1 httr-1.3.0/httr/man/revoke_all.Rd | 1 httr-1.3.0/httr/man/set_config.Rd | 3 httr-1.3.0/httr/man/set_cookies.Rd | 1 httr-1.3.0/httr/man/sha1_hash.Rd | 1 httr-1.3.0/httr/man/sign_oauth.Rd | 1 httr-1.3.0/httr/man/status_code.Rd | 1 httr-1.3.0/httr/man/stop_for_status.Rd | 3 httr-1.3.0/httr/man/timeout.Rd | 1 httr-1.3.0/httr/man/upload_file.Rd | 1 httr-1.3.0/httr/man/use_proxy.Rd | 1 httr-1.3.0/httr/man/user_agent.Rd | 1 httr-1.3.0/httr/man/verbose.Rd | 2 httr-1.3.0/httr/man/with_config.Rd | 1 httr-1.3.0/httr/man/write_disk.Rd | 1 httr-1.3.0/httr/man/write_function.Rd | 1 httr-1.3.0/httr/man/write_stream.Rd | 3 httr-1.3.0/httr/tests/testthat/test-callback.R |only httr-1.3.0/httr/tests/testthat/test-config.r | 2 httr-1.3.0/httr/tests/testthat/test-oauth-cache.R | 42 httr-1.3.0/httr/tests/testthat/test-oauth-server-side.R | 12 httr-1.3.0/httr/tests/testthat/test-oauth.R | 30 httr-1.3.0/httr/tests/testthat/test-oauth_signature.R |only httr-1.3.0/httr/tests/testthat/test-url.r | 7 httr-1.3.0/httr/vignettes/api-packages.Rmd | 90 - httr-1.3.0/httr/vignettes/quickstart.Rmd | 22 httr-1.3.0/httr/vignettes/secrets.Rmd |only 119 files changed, 1350 insertions(+), 1243 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in R. The
framework is unopinionated when it comes to how HTTP requests and WebSocket
messages are handled and supports all levels of app complexity; from serving
static content to full-blown dynamic web-apps. Fiery does not hold your hand
as much as e.g. the shiny package does, but instead sets you free to create
your web app the way you want.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 0.2.3 dated 2017-06-26 and 1.0.0 dated 2017-08-16
DESCRIPTION | 15 - LICENSE |only MD5 | 34 +-- NAMESPACE | 5 NEWS.md | 39 +++ R/Fire.R | 374 ++++++++++++++++++++++++++----------- R/HandlerStack.R | 1 R/aaa.R | 10 R/event_doc.R |only R/fake_request.R | 23 +- R/fiery-package.R | 26 +- R/plugin_doc.R |only README.md | 42 +--- man/Fire.Rd | 108 ++++++---- man/event_doc.Rd |only man/fake_request.Rd | 16 - man/fiery-package.Rd | 37 ++- man/figures |only man/plugin_doc.Rd |only tests/testthat/test-Fire.R | 217 +++++++++++++++------ tests/testthat/test-fake_request.R | 2 21 files changed, 657 insertions(+), 292 deletions(-)
Title: Process and Visualise Output from Atlantis Models
Description: Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (<http://atlantis.cmar.csiro.au>). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) <DOI:10.18637/jss.v059.i10>. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.
Author: Alexander Keth [aut, cre]
Maintainer: Alexander Keth <alexander.keth@uni-hamburg.de>
Diff between atlantistools versions 0.4.2 dated 2017-05-18 and 0.4.3 dated 2017-08-16
atlantistools-0.4.2/atlantistools/inst/extdata/setas-model-new-trunk/shrink-output-trunk.R |only atlantistools-0.4.3/atlantistools/DESCRIPTION | 8 atlantistools-0.4.3/atlantistools/MD5 | 110 - atlantistools-0.4.3/atlantistools/NAMESPACE | 4 atlantistools-0.4.3/atlantistools/R/get-diet-fishbase.R |only atlantistools-0.4.3/atlantistools/R/get-growth-fishbase.R | 8 atlantistools-0.4.3/atlantistools/R/get-ids-fishbase.R | 17 atlantistools-0.4.3/atlantistools/R/get-maturity-fishbase.R |only atlantistools-0.4.3/atlantistools/R/get-ref-fishbase.R | 41 atlantistools-0.4.3/atlantistools/R/load-nc-physics.R | 21 atlantistools-0.4.3/atlantistools/R/load-nc.R | 7 atlantistools-0.4.3/atlantistools/R/plot-consumed-biomass.R | 4 atlantistools-0.4.3/atlantistools/R/ref_to_bibkey.R |only atlantistools-0.4.3/atlantistools/R/scan-reference-fishbase.R |only atlantistools-0.4.3/atlantistools/R/utils.R | 46 atlantistools-0.4.3/atlantistools/README.md | 23 atlantistools-0.4.3/atlantistools/data/ref_agemat.rda |binary atlantistools-0.4.3/atlantistools/data/ref_bio_cons.rda |binary atlantistools-0.4.3/atlantistools/data/ref_bio_sp.rda |binary atlantistools-0.4.3/atlantistools/data/ref_dietmatrix.rda |binary atlantistools-0.4.3/atlantistools/data/ref_dm.rda |binary atlantistools-0.4.3/atlantistools/data/ref_eat.rda |binary atlantistools-0.4.3/atlantistools/data/ref_grazing.rda |binary atlantistools-0.4.3/atlantistools/data/ref_growth.rda |binary atlantistools-0.4.3/atlantistools/data/ref_n.rda |binary atlantistools-0.4.3/atlantistools/data/ref_nums.rda |binary atlantistools-0.4.3/atlantistools/data/ref_physics.rda |binary atlantistools-0.4.3/atlantistools/data/ref_resn.rda |binary atlantistools-0.4.3/atlantistools/data/ref_structn.rda |binary atlantistools-0.4.3/atlantistools/data/ref_vol.rda |binary atlantistools-0.4.3/atlantistools/data/ref_vol_dz.rda |binary atlantistools-0.4.3/atlantistools/inst/doc/model-calibration-species.pdf |binary atlantistools-0.4.3/atlantistools/inst/doc/model-calibration.pdf |binary atlantistools-0.4.3/atlantistools/inst/doc/model-comparison.pdf |binary atlantistools-0.4.3/atlantistools/inst/doc/model-preprocess.html | 10 atlantistools-0.4.3/atlantistools/inst/doc/package-demo.html | 63 atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/INIT_VMPA_Jan2015.nc |binary atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/README.txt | 10 atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/VMPA_setas_run_fishing_F_Trunk.prm | 8 atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETAS.nc |binary atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASDietCheck.txt | 462 +---- atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASPROD.nc |binary atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASSSB.txt | 28 atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASSpecificMort.txt | 8 atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASSpecificPredMort.txt | 848 +--------- atlantistools-0.4.3/atlantistools/inst/extdata/setas-model-new-trunk/outputSETASYOY.txt | 28 atlantistools-0.4.3/atlantistools/man/get_diet_fishbase.Rd |only atlantistools-0.4.3/atlantistools/man/get_maturity_fishbase.Rd |only atlantistools-0.4.3/atlantistools/man/get_ref_fishbase.Rd | 17 atlantistools-0.4.3/atlantistools/man/load_nc_physics.Rd | 2 atlantistools-0.4.3/atlantistools/man/plot_consumed_biomass.Rd | 4 atlantistools-0.4.3/atlantistools/man/ref_to_bibkey.Rd |only atlantistools-0.4.3/atlantistools/man/scan_reference_fishbase.Rd |only atlantistools-0.4.3/atlantistools/tests/testthat/Rplots.pdf |binary atlantistools-0.4.3/atlantistools/tests/testthat/test-convert-time.R | 2 atlantistools-0.4.3/atlantistools/tests/testthat/test-diet-fishbase.R |only atlantistools-0.4.3/atlantistools/tests/testthat/test-growth-fishbase.R | 10 atlantistools-0.4.3/atlantistools/tests/testthat/test-load-dietcheck.R | 10 atlantistools-0.4.3/atlantistools/tests/testthat/test-load-rec.R | 2 atlantistools-0.4.3/atlantistools/tests/testthat/test-load-spec-mort.R | 6 atlantistools-0.4.3/atlantistools/tests/testthat/test-sc-init.R | 1 61 files changed, 482 insertions(+), 1326 deletions(-)
Title: A Shiny GUI for Smith's Mean Measure of Divergence (MMD)
Description: Offers a Shiny user interface for Mean Measure of Divergence with facilities for trait selection and graphical representations.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 2.1.0 dated 2017-08-09 and 2.2.0 dated 2017-08-16
DESCRIPTION | 14 ++++----- MD5 | 15 +++++----- inst/AnthropMMDShinyApp/calcMMD.R | 3 +- inst/AnthropMMDShinyApp/fisherTestTab.R |only inst/AnthropMMDShinyApp/selectVars.R | 7 ++++ inst/AnthropMMDShinyApp/server.R | 48 ++++++++++++++++++++++---------- inst/AnthropMMDShinyApp/ui.R | 25 ++++++++-------- man/AnthropMMD-package.Rd | 16 ++++++---- man/StartMMD.Rd | 47 ++++++++++++++++++++----------- 9 files changed, 110 insertions(+), 65 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-16 0.2.0
2016-06-29 0.1.0
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://ropensci.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and others.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.5 dated 2017-06-21 and 1.0.6 dated 2017-08-16
DESCRIPTION | 8 +- MD5 | 92 ++++++++++++++++----------- NAMESPACE | 7 ++ NEWS | 13 +++ R/abvd.R |only R/abvd.feature.R |only R/afbo.feature.R |only R/autotyp.feature.R | 34 ++++++---- R/glottolog.modified.R | 22 ++---- R/glottolog.original.R | 22 ++---- R/gltc.iso.R | 1 R/iso.gltc.R | 1 R/lang.country.R | 41 +++++++++--- R/lang.gltc.R | 1 R/lang.iso.R | 1 R/map.feature.R | 5 - R/phoible.feature.R |only R/sails.feature.R |only R/wals.R |only R/wals.feature.R |only build/vignette.rds |binary data/abvd.RData |only data/autotyp.RData |binary data/circassian.RData |binary data/countries.RData |binary data/datalist | 2 data/ejective_and_n_consonants.RData |binary data/glottolog.modified.RData |binary data/glottolog.original.RData |binary data/wals.RData |only inst/doc/lingtypology.R | 52 +++++++++++++++ inst/doc/lingtypology.Rmd | 91 ++++++++++++++++++++++++++- inst/doc/lingtypology.html | 111 +++++++++++++++++++++++++++------ inst/doc/manual/lingtypology.pdf |binary man/abvd.Rd |only man/abvd.feature.Rd |only man/afbo.feature.Rd |only man/autotyp.feature.Rd | 9 +- man/glottolog.modified.Rd | 22 ++---- man/glottolog.original.Rd | 22 ++---- man/lang.country.Rd | 7 +- man/phoible.feature.Rd |only man/sails.feature.Rd |only man/wals.Rd |only man/wals.feature.Rd |only tests/testthat/test-abvd-feature.R |only tests/testthat/test-afbo-feature.R |only tests/testthat/test-autotyp-feature.R |only tests/testthat/test-gltc-iso.R | 2 tests/testthat/test-iso-gltc.R | 2 tests/testthat/test-lang-aff.R | 32 +++++---- tests/testthat/test-lang-country.R | 14 +++- tests/testthat/test-lang-gltc.R | 2 tests/testthat/test-lang-iso.R | 2 tests/testthat/test-phoible-features.R |only tests/testthat/test-sails-feature.R |only tests/testthat/test-wals-feature.R |only vignettes/lingtypology.Rmd | 91 ++++++++++++++++++++++++++- 58 files changed, 544 insertions(+), 165 deletions(-)
Title: Apply Statistical Post-Processing to Improve Sea Ice Predictions
Description: Tools for modeling and correcting biases in sea ice predictions obtained from dynamical models. This package depends on the 'ncdf4' and 'rgeos' R packages. These packages respectively require installing externally from R Unidata's 'NetCDF' library and Geometry Engine - Open Source ('GEOS'). (See the 'rgeos' and 'ncdf4' packages for details.) References, Bivand and Rundel (2017) <https://CRAN.R-project.org/package=rgeos>, Open Source Geospatial Foundation (2017) <https://trac.osgeo.org/geos>, Pierce (2017) <https://CRAN.R-project.org/package=ncdf4>, Unidata (2017) <https://www.unidata.ucar.edu/software/netcdf/>.
Author: Hannah M. Director, Adrian E. Raftery, and Cecilia M. Bitz
Maintainer: Hannah M. Director <direch@uw.edu>
Diff between IceCast versions 1.1.0 dated 2017-06-23 and 1.2.0 dated 2017-08-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/geodesicAreas.R | 2 +- inst/doc/biasCorrectDemo.R | 20 ++++++++++++-------- inst/doc/biasCorrectDemo.Rmd | 20 ++++++++++++-------- inst/doc/biasCorrectDemo.html | 22 +++++++++++++--------- man/mapxy.Rd | 2 +- vignettes/biasCorrectDemo.Rmd | 20 ++++++++++++-------- 8 files changed, 62 insertions(+), 46 deletions(-)
Title: Partition-Assisted Clustering and Multiple Alignments of
Networks
Description: Implements Partition-Assisted Clustering and Multiple Alignments of Networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set.
Author: Ye Henry Li, Dangna Li
Maintainer: Ye Henry Li <ywli@stanford.edu>
Diff between PAC versions 1.0.8 dated 2017-04-30 and 1.0.9 dated 2017-08-16
DESCRIPTION | 11 +++++---- MD5 | 38 +++++++++++++++++++++----------- NAMESPACE | 18 ++++++++++----- R/MINetworkPlot_topEdges.R | 12 +++++----- R/MINetwork_matrix_topEdges.R | 2 - R/MINetwork_simpliefied_topEdges.R | 2 - R/aggregateData.R | 4 +-- R/constellationPlot.R |only R/getAverageSpreadOf2SubpopClades.R |only R/getExtraneousCladeSubpopulations.R |only R/recordWithinClusterSpread.R |only R/renamePrunedSubpopulations.R |only R/runElbowPointAnalysis.R |only inst/doc/intro.md | 2 - man/MINetworkPlot_topEdges.Rd | 4 +-- man/MINetwork_matrix_topEdges.Rd | 2 - man/MINetwork_simplified_topEdges.Rd | 2 - man/PAC.Rd | 4 +-- man/aggregateData.Rd | 4 +-- man/constellationPlot.Rd |only man/getAverageSpreadOf2SubpopClades.Rd |only man/getExtraneousCladeSubpopulations.Rd |only man/recordWithinClusterSpread.Rd |only man/renamePrunedSubpopulations.Rd |only man/runElbowPointAnalysis.Rd |only vignettes/intro.md | 2 - 26 files changed, 65 insertions(+), 42 deletions(-)