Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence plots from
various types machine learning models in R.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.0.4 dated 2016-09-17 and 0.1.0 dated 2016-10-06
DESCRIPTION | 15 +- MD5 | 20 +-- NEWS.md | 15 ++ R/partial.R | 104 +++++++++------- R/plotPartial.R | 272 ++++++++++++++++++++++++++++++------------ R/utils.R | 46 +++++++ README.md | 55 ++++++-- man/partial.Rd | 69 ++++++++-- man/plotPartial.Rd | 52 ++++---- tests/testthat/test-partial.R | 2 tests/testthat/test-utils.R | 28 ++++ 11 files changed, 491 insertions(+), 187 deletions(-)
More information about fragilityindex at CRAN
Permanent link
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal
shaped particles based on the same measured quantities of corresponding planar
vertical section profiles. A single trivariate discretized version of the (stereological)
integral equation in the case of prolate and oblate spheroids is solved
numerically by the EM algorithm. The estimation of diameter distribution of
spheres from planar sections (Wicksell's corpuscle problem) is also implemented.
Further, the package provides routines for the simulation of a Poisson germ-
grain process with either spheroids, spherocylinders or spheres as grains together
with functions for planar sections.
For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.5.8 dated 2016-06-24 and 0.6 dated 2016-10-06
DESCRIPTION | 14 +- MD5 | 59 +++++----- R/cylinder.R | 136 ++++++++++++------------- R/sphere.R | 40 +++---- R/spheroid.R | 216 +++++++++++++++++++++++----------------- R/unfolding.R | 38 +++---- man/drawSpheroidIntersection.Rd |only man/planarSection.Rd | 2 man/simCylinderSystem.Rd | 38 +++---- man/simModel3d.Rd | 7 - man/simSphereSystem.Rd | 14 +- man/simSpheroidSystem.Rd | 29 ++--- man/spheroids3d.Rd | 8 + man/trivarHist.Rd | 2 man/unfold.Rd | 10 - man/updateIntersections.Rd | 2 man/verticalSection.Rd | 4 src/GeometricPrimitives.cpp | 5 src/GeometricPrimitives.h | 26 +++- src/Intersector.cpp | 2 src/SimCylinder.cpp | 51 +++++---- src/SimEllipsoid.cpp | 75 +++++++++---- src/SimEllipsoid.h | 3 src/SimSphere.cpp | 53 ++++++--- src/SimSphere.h | 4 src/Utils.cpp | 11 +- src/Utils.h | 15 +- src/Vector.h | 8 + src/directions.cpp | 2 src/ellipt.cpp | 2 src/unfold.cpp | 4 31 files changed, 508 insertions(+), 372 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.0.2 dated 2016-06-06 and 2.0.3 dated 2016-10-06
DESCRIPTION | 8 +++---- MD5 | 10 ++++---- R/CreateDtm.R | 8 +++++-- R/CreateTcm.R | 10 ++++++-- R/RcppExports.R | 2 - src/RcppExports.cpp | 58 ++++++++++++++++++++++++++-------------------------- 6 files changed, 52 insertions(+), 44 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. Designed to be a generic framework, it leverages the
power of 'Rcpp' to boost the performance, turning DES in R feasible. As a
noteworthy characteristic, 'simmer' exploits the concept of trajectory: a
common path in the simulation model for entities of the same type.
Author: Bart Smeets [aut, cph],
Iñaki Ucar [aut, cph, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.4.3 dated 2016-10-02 and 3.4.4 dated 2016-10-06
simmer-3.4.3/simmer/inst/staticdocs |only simmer-3.4.4/simmer/DESCRIPTION | 6 simmer-3.4.4/simmer/MD5 | 23 +- simmer-3.4.4/simmer/NEWS.md | 94 +++++----- simmer-3.4.4/simmer/inst/doc/A-introduction.html | 74 +++---- simmer-3.4.4/simmer/inst/doc/B-terminology.html | 4 simmer-3.4.4/simmer/inst/doc/C-trajectories.html | 38 ++-- simmer-3.4.4/simmer/inst/doc/D-bank-1.html | 4 simmer-3.4.4/simmer/inst/doc/E-queueing-systems.html | 4 simmer-3.4.4/simmer/inst/doc/F-ctmc.html | 4 simmer-3.4.4/simmer/src/process.cpp | 10 - simmer-3.4.4/simmer/tests/testthat/test-trajectory-seize-release.R | 17 + simmer-3.4.4/simmer/tests/testthat/test-trajectory-select.R | 26 +- 13 files changed, 159 insertions(+), 145 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.4 dated 2016-01-28 and 0.1.5 dated 2016-10-06
DESCRIPTION | 10 MD5 | 76 ++-- NAMESPACE | 2 NEWS | 18 + R/RStoolbox.R | 4 R/RcppExports.R | 2 R/encodeQA.R | 2 R/ggR.R | 2 R/histMatch.R | 5 R/pifMatch.R | 52 +-- R/radCor.R | 410 ++++++++++++------------ R/rasterPCA.R | 74 ++-- R/readMeta.R | 469 ++++++++++++++------------- R/spectralIndices.R | 32 - R/stackMeta.R | 24 + R/superClass.R | 621 +++++++++++++++++++------------------ R/sysdata.rda |binary R/unsuperClass.R | 6 README.md | 2 data/lsat.rda |binary data/rlogo.rda |binary data/srtm.rda |binary inst/external/trainingPolygons.rds |binary man/encodeQA.Rd | 2 man/ggR.Rd | 2 man/pifMatch.Rd | 46 +- man/rasterPCA.Rd | 13 man/spectralIndices.Rd | 2 man/superClass.Rd | 4 man/unsuperClass.Rd | 6 src/RcppExports.cpp | 82 ++-- src/predictKmeans.cpp | 7 src/spectralIndices.cpp | 3 tests/testdata |only tests/testthat/test-normImage.R |only tests/testthat/test-radCor.R | 13 tests/testthat/test-rasterPCA.R |only tests/testthat/test-readMeta.R |only tests/testthat/test-superClass.R | 158 +++++---- tests/testthat/test-unsuperClass.R |only 40 files changed, 1141 insertions(+), 1008 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers and methods to evaluate their performance. The package includes implementations of, among others, Implicitly Constrained Learning, Moment Constrained Learning, the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.6 dated 2016-09-14 and 0.6.1 dated 2016-10-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Plotting.R | 2 +- tests/testthat/test-SVM.R | 8 ++++---- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.
Author: Jason Ge, Xingguo Li, Mengdi Wang, Tong Zhang, Han Liu and Tuo Zhao
Maintainer: Jason Ge <jiange@princeton.edu>
Diff between picasso versions 0.5.0 dated 2015-12-18 and 0.5.4 dated 2016-10-06
picasso-0.5.0/picasso/R/lasso.sc.cov.R |only picasso-0.5.0/picasso/R/lasso.sc.naive.R |only picasso-0.5.0/picasso/R/logit.R |only picasso-0.5.0/picasso/R/picasso.lasso.R |only picasso-0.5.0/picasso/R/picasso.scio.R |only picasso-0.5.0/picasso/R/scio.generator.R |only picasso-0.5.0/picasso/R/scio.plot.R |only picasso-0.5.0/picasso/R/scio.sc.R |only picasso-0.5.0/picasso/man/coef.lasso.Rd |only picasso-0.5.0/picasso/man/plot.lasso.Rd |only picasso-0.5.0/picasso/man/plot.scio.Rd |only picasso-0.5.0/picasso/man/plot.sim.Rd |only picasso-0.5.0/picasso/man/predict.lasso.Rd |only picasso-0.5.0/picasso/man/print.lasso.Rd |only picasso-0.5.0/picasso/man/print.scio.Rd |only picasso-0.5.0/picasso/man/print.sim.Rd |only picasso-0.5.0/picasso/man/scio.generator.Rd |only picasso-0.5.0/picasso/man/scio.plot.Rd |only picasso-0.5.0/picasso/src/Makevars.win |only picasso-0.5.0/picasso/src/SFGen.c |only picasso-0.5.0/picasso/src/euc_proj.c |only picasso-0.5.0/picasso/src/lambda_max.c |only picasso-0.5.0/picasso/src/mathlib.h |only picasso-0.5.0/picasso/src/mymath.h |only picasso-0.5.0/picasso/src/mymath1.c |only picasso-0.5.0/picasso/src/picasso_lasso_sc_cov.c |only picasso-0.5.0/picasso/src/picasso_lasso_sc_naive.c |only picasso-0.5.0/picasso/src/picasso_logit_cyclic.c |only picasso-0.5.0/picasso/src/picasso_logit_greedy.c |only picasso-0.5.0/picasso/src/picasso_logit_prox.c |only picasso-0.5.0/picasso/src/picasso_logit_stoc.c |only picasso-0.5.0/picasso/src/picasso_scio_sc.c |only picasso-0.5.0/picasso/src/standardize_design.c |only picasso-0.5.4/picasso/DESCRIPTION | 14 - picasso-0.5.4/picasso/MD5 | 82 +++----- picasso-0.5.4/picasso/NAMESPACE | 34 +-- picasso-0.5.4/picasso/R/gaussian_solver.R |only picasso-0.5.4/picasso/R/logit_solver.R |only picasso-0.5.4/picasso/R/picasso.R | 73 +++---- picasso-0.5.4/picasso/R/picasso.gaussian.R |only picasso-0.5.4/picasso/R/picasso.logit.R | 117 +++++------ picasso-0.5.4/picasso/R/picasso.poisson.R |only picasso-0.5.4/picasso/R/poisson_solver.R |only picasso-0.5.4/picasso/build/vignette.rds |binary picasso-0.5.4/picasso/inst/doc/PICASSO.pdf |binary picasso-0.5.4/picasso/inst/doc/vignette.pdf |binary picasso-0.5.4/picasso/man/coef.gaussian.Rd |only picasso-0.5.4/picasso/man/coef.logit.Rd | 4 picasso-0.5.4/picasso/man/coef.poisson.Rd |only picasso-0.5.4/picasso/man/picasso-package.Rd | 14 - picasso-0.5.4/picasso/man/picasso.Rd | 213 ++++++++++++++------- picasso-0.5.4/picasso/man/plot.gaussian.Rd |only picasso-0.5.4/picasso/man/plot.logit.Rd | 4 picasso-0.5.4/picasso/man/plot.poisson.Rd |only picasso-0.5.4/picasso/man/predict.gaussian.Rd |only picasso-0.5.4/picasso/man/predict.logit.Rd | 29 -- picasso-0.5.4/picasso/man/predict.poisson.Rd |only picasso-0.5.4/picasso/man/print.gaussian.Rd |only picasso-0.5.4/picasso/man/print.logit.Rd | 4 picasso-0.5.4/picasso/man/print.poisson.Rd |only picasso-0.5.4/picasso/src/IRLS_solver.c |only picasso-0.5.4/picasso/src/IRLS_solver.h |only picasso-0.5.4/picasso/src/mathutils.c |only picasso-0.5.4/picasso/src/mathutils.h |only picasso-0.5.4/picasso/src/picasso_gaussian_cov.c |only picasso-0.5.4/picasso/src/picasso_gaussian_naive.c |only picasso-0.5.4/picasso/src/picasso_logit.c |only picasso-0.5.4/picasso/src/picasso_poisson.c |only picasso-0.5.4/picasso/vignettes/PICASSO.pdf |binary 69 files changed, 300 insertions(+), 288 deletions(-)
Title: Aids in Processing and Plotting Data from a Lemna-Tec
Scananalyzer
Description: Extracts traits from imaging data produced using a Lemna-Tec Scananalyzer
(see <http://www.lemnatec.com/products/hardware-solutions/scanalyzer-3d> for more
information). Growth rates between successive imagings are obtained and those for
a nominated set of intervals can also be calculated. Profile or longitudinal plots
of the traits and growth rates can be produced. These allow one to check for
anomalous data and to explore growth patterns in the data.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between imageData versions 0.1-21 dated 2016-05-16 and 0.1-26 dated 2016-10-06
imageData-0.1-21/imageData/R/data.longi.v2.r |only imageData-0.1-26/imageData/DESCRIPTION | 18 - imageData-0.1-26/imageData/MD5 | 23 - imageData-0.1-26/imageData/NAMESPACE | 1 imageData-0.1-26/imageData/R/PVA.r | 182 ++++++++------- imageData-0.1-26/imageData/R/data.longi.v5.r |only imageData-0.1-26/imageData/build/partial.rdb |binary imageData-0.1-26/imageData/inst/NEWS.Rd | 26 ++ imageData-0.1-26/imageData/inst/doc/imageData-manual.pdf |binary imageData-0.1-26/imageData/man/calcTimes.Rd |only imageData-0.1-26/imageData/man/imageData-pkg.Rd | 7 imageData-0.1-26/imageData/man/imagetimesPlot.Rd | 56 +++- imageData-0.1-26/imageData/man/importExcel.Rd | 62 +++-- imageData-0.1-26/imageData/man/longitudinalPrime.Rd | 12 14 files changed, 245 insertions(+), 142 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 1.2.0 dated 2016-08-01 and 1.2.2 dated 2016-10-06
Cyclops-1.2.0/Cyclops/src/cyclops/SqlModelData.cpp |only Cyclops-1.2.0/Cyclops/src/cyclops/SqlModelData.h |only Cyclops-1.2.2/Cyclops/DESCRIPTION | 6 Cyclops-1.2.2/Cyclops/MD5 | 63 - Cyclops-1.2.2/Cyclops/NAMESPACE | 1 Cyclops-1.2.2/Cyclops/NEWS | 6 Cyclops-1.2.2/Cyclops/R/Abridge.R |only Cyclops-1.2.2/Cyclops/R/DataManagement.R | 2 Cyclops-1.2.2/Cyclops/R/ModelFit.R | 24 Cyclops-1.2.2/Cyclops/R/RcppExports.R | 2 Cyclops-1.2.2/Cyclops/README.md | 6 Cyclops-1.2.2/Cyclops/man/createAbridgePrior.Rd |only Cyclops-1.2.2/Cyclops/man/createCyclopsData.Rd | 6 Cyclops-1.2.2/Cyclops/man/fitCyclopsModel.Rd | 5 Cyclops-1.2.2/Cyclops/src/Makevars | 3 Cyclops-1.2.2/Cyclops/src/RcppExports.cpp | 348 +++++----- Cyclops-1.2.2/Cyclops/src/RcppModelData.cpp | 11 Cyclops-1.2.2/Cyclops/src/RcppModelData.h | 8 Cyclops-1.2.2/Cyclops/src/cyclops/CyclicCoordinateDescent.cpp | 2 Cyclops-1.2.2/Cyclops/src/cyclops/CyclicCoordinateDescent.h | 11 Cyclops-1.2.2/Cyclops/src/cyclops/Iterators.h | 33 Cyclops-1.2.2/Cyclops/src/cyclops/ModelData.cpp | 8 Cyclops-1.2.2/Cyclops/src/cyclops/Types.h | 13 Cyclops-1.2.2/Cyclops/src/cyclops/drivers/AbstractCrossValidationDriver.cpp | 24 Cyclops-1.2.2/Cyclops/src/cyclops/drivers/CrossValidationSelector.cpp | 14 Cyclops-1.2.2/Cyclops/src/cyclops/engine/AbstractModelSpecifics.cpp | 4 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ModelSpecifics.h | 23 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ModelSpecifics.hpp | 23 Cyclops-1.2.2/Cyclops/src/cyclops/engine/ParallelLoops.h | 291 ++++---- Cyclops-1.2.2/Cyclops/src/cyclops/engine/Ranges.h | 16 Cyclops-1.2.2/Cyclops/src/cyclops/engine/Recursions.hpp | 4 Cyclops-1.2.2/Cyclops/src/cyclops/priors/CovariatePrior.cpp | 2 Cyclops-1.2.2/Cyclops/src/utils/HParSearch.cpp | 25 Cyclops-1.2.2/Cyclops/tests/testthat/test-Abridge.R |only Cyclops-1.2.2/Cyclops/tests/testthat/test-smallPoisson.R | 19 35 files changed, 566 insertions(+), 437 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.99.4 dated 2016-08-12 and 0.99.5 dated 2016-10-06
DESCRIPTION | 8 MD5 | 60 +++--- NEWS | 21 ++ R/activityDensity.R | 8 R/activityHistogram.R | 1 R/activityOverlap.R | 4 R/appendSpeciesNames.R | 11 - R/checkSpeciesIdentification.R | 10 - R/detectionHistory.R | 1 R/getSpeciesImages.R | 223 +++++++++++++++----------- R/imageRename.R | 61 ++----- R/recordTable.R | 55 +----- R/recordTableIndividual.R | 57 +----- R/spatialDetectionHistory.R | 1 R/variousOtherHelperFunctions.R | 74 ++++++++ data/recordTableSample.rda |binary inst/doc/DataExploration.html | 14 - inst/doc/DataExtraction.html | 152 +++++++++-------- inst/doc/ImageOrganisation.html | 56 +++--- inst/doc/SpeciesIndividualIdentification.R | 23 ++ inst/doc/SpeciesIndividualIdentification.Rmd | 48 +++++ inst/doc/SpeciesIndividualIdentification.html | 136 +++++++++------ man/activityDensity.Rd | 2 man/activityOverlap.Rd | 2 man/activityRadial.Rd | 2 man/addCopyrightTag.Rd | 4 man/camtrapR-package.Rd | 4 man/getSpeciesImages.Rd | 60 +++++- man/recordTable.Rd | 44 ++++- man/recordTableIndividual.Rd | 10 - vignettes/SpeciesIndividualIdentification.Rmd | 48 +++++ 31 files changed, 737 insertions(+), 463 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.2.1 dated 2016-04-01 and 1.2.2 dated 2016-10-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 16 ++++++++++++++++ R/reportr.R | 5 ++++- 4 files changed, 27 insertions(+), 8 deletions(-)
Title: Multiscale Clustering of Geometrical Network
Description: Co-Expression Network Analysis by adopting network embedding technique.
Author: Won-Min Song, Bin Zhang
Maintainer: Won-Min Song <wonmin1984@gmail.com>
Diff between MEGENA versions 1.3.4-1 dated 2016-07-11 and 1.3.4-6 dated 2016-10-06
MEGENA-1.3.4-1/MEGENA/man/set.parallel.backend.Rd |only MEGENA-1.3.4-6/MEGENA/DESCRIPTION | 12 +- MEGENA-1.3.4-6/MEGENA/MD5 | 26 +++--- MEGENA-1.3.4-6/MEGENA/NAMESPACE | 6 + MEGENA-1.3.4-6/MEGENA/R/ClusteringPackage.R | 20 ++-- MEGENA-1.3.4-6/MEGENA/R/Combined_functions.R | 7 + MEGENA-1.3.4-6/MEGENA/R/Downstream_TableManip.R | 8 - MEGENA-1.3.4-6/MEGENA/R/ModulePlot.R |only MEGENA-1.3.4-6/MEGENA/R/PFN_Computation.R | 95 +++++++++++----------- MEGENA-1.3.4-6/MEGENA/build |only MEGENA-1.3.4-6/MEGENA/inst |only MEGENA-1.3.4-6/MEGENA/man/calculate.PFN.Rd | 7 + MEGENA-1.3.4-6/MEGENA/man/compute.PFN.par.Rd |only MEGENA-1.3.4-6/MEGENA/man/plot_module.Rd |only MEGENA-1.3.4-6/MEGENA/man/plot_subgraph.Rd |only MEGENA-1.3.4-6/MEGENA/src/RcppExports.cpp | 18 +--- MEGENA-1.3.4-6/MEGENA/vignettes |only 17 files changed, 111 insertions(+), 88 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.8.9 dated 2015-05-28 and 1.9.0 dated 2016-10-06
DESCRIPTION | 27 ++--- MD5 | 74 ++++++++------- NAMESPACE | 31 ++++++ R/aalen.r | 18 ++- R/base.r | 96 +++---------------- R/clusterindex-reshape.r | 2 R/comprisk.r | 34 ++++-- R/cox-aalen.r | 23 +++- R/cox.ipw.r | 5 - R/cox.marg.r |only R/event.r | 4 R/event.split.r |only R/ipcw-residualmean.r | 13 +- R/kmplot.r | 9 + R/mgresid.r | 15 +-- R/new.aalen.r | 15 ++- R/new.cox-aalen.r | 24 +++- R/new.dynreg.r | 4 R/plots.r | 4 R/predict-timereg.r | 19 ++- R/prop-odds-subdist.r | 28 +++-- R/qcut.r |only R/residualsTimereg.r |only R/restricted.residual.mean.r | 5 - R/timecox.r | 8 - R/two-stage-reg.r | 99 +++++++++++--------- man/aalen.Rd | 10 +- man/comp.risk.Rd | 8 - man/cox.aalen.Rd | 9 + man/cox.ipw.Rd |only man/event.split.Rd |only man/internal-addreg.Rd | 15 ++- man/predict.timereg.Rd | 14 ++ man/prep.comp.risk.Rd | 4 man/prop.odds.Rd | 11 ++ man/prop.odds.subdist.Rd | 5 - man/res.mean.Rd | 12 +- man/wald.test.Rd | 3 src/aalen.c | 40 ++++++-- src/cox-aalen.c | 210 +++++++++++++++++++++++++++---------------- src/two-stage-reg.c | 11 +- 41 files changed, 550 insertions(+), 359 deletions(-)
Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal
processes. The models may include covariates and can be specified
with familiar formula syntax as in glm().
Author: Tarak Kharrat, Georgi N. Boshnakov
Maintainer: Tarak Kharrat <tarak.kharrat@gmail.com>
Diff between Countr versions 3.2.6 dated 2016-09-14 and 3.2.7 dated 2016-10-06
DESCRIPTION | 15 ++++++++------- MD5 | 28 +++++++++++++++++++--------- NAMESPACE | 1 + NEWS | 4 ++++ R/Countr.R | 10 +++++----- R/Renewal_methods.R | 2 +- build |only inst/doc |only src/conv_all.cpp | 10 +++++++--- src/conv_dePril.cpp | 11 ++++++++--- src/conv_naive.cpp | 10 ++++++---- src/modifiedRenewal.cpp | 12 ++++++++---- vignettes |only 13 files changed, 67 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-31 0.6.0
2016-05-05 0.5.6
2016-01-25 0.5.2
2015-12-02 0.5.0
2015-07-07 0.4.2
2015-06-19 0.4.0
2014-12-20 0.3.3
2014-07-21 0.2.0
2014-03-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-06 1.3.0
2016-06-24 1.2.0
2016-04-20 1.1.4
2016-04-18 1.1.3
2016-04-13 1.1.2
2016-02-16 1.1.1
2016-01-26 1.1.0
2015-08-10 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-31 1.0.3
Title: Convert Spatial Data Using Tidy Tables
Description: Tools to convert from specific formats to more general forms of
spatial data. Using tables to store the actual entities present in spatial
data provides far greater flexibility, and the functions here deliberately
minimize the level of interpretation applied, leaving that for specific
applications. Includes round-trip for 'Spatial' classes and long-form
tables, analogous to 'ggplot2::fortify'.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spbabel versions 0.4.0 dated 2016-08-07 and 0.4.5 dated 2016-10-06
DESCRIPTION | 10 +- MD5 | 43 +++++++---- NAMESPACE | 8 +- NEWS.md | 18 ++++ R/gobbleGeom.r |only R/mtable.r | 74 +++++++++----------- R/raster_geom.r |only R/spFromTable.r | 18 +++- R/sptable.r | 137 ++++++++++++++------------------------ R/trip.r |only R/unique_ids.r | 20 ++--- R/utils.r | 50 +++++-------- README.md | 37 ++++++++++ inst/devignette |only inst/doc/spbabel.Rmd | 2 inst/doc/spbabel.html | 18 ++-- inst/examples |only inst/sf_convert.r |only man/sptable.Rd | 15 ++-- tests/testthat/test-map_table.R | 8 ++ tests/testthat/test-misc.R |only tests/testthat/test-replacement.R |only tests/testthat/test-spFromTable.R | 20 ++++- tests/testthat/test-sptable.R | 5 + tests/testthat/test-trip.R |only tests/testthat/test-utils.R |only vignettes/spbabel.Rmd | 2 27 files changed, 265 insertions(+), 220 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Implement a variety of event-based models, with a focus on
spatially explicit models. These include raster-based, event-based, and
agent-based models. The core simulation components are built upon a discrete
event simulation (DES) framework that facilitates modularity, and easily
enables the user to include additional functionality by running user-built
simulation modules. Included are numerous tools to visualize raster and
other maps. The suggested package 'fastshp' can be installed with
`install.packages("fastshp", repos = "http://rforge.net", type = "source")`.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES versions 1.2.0 dated 2016-06-24 and 1.3.0 dated 2016-10-06
SpaDES-1.2.0/SpaDES/man/nlayers.Rd |only SpaDES-1.2.0/SpaDES/man/simList-accessors-objects.Rd |only SpaDES-1.2.0/SpaDES/man/simList-accessors-params.Rd |only SpaDES-1.3.0/SpaDES/DESCRIPTION | 70 SpaDES-1.3.0/SpaDES/MD5 | 498 SpaDES-1.3.0/SpaDES/NAMESPACE | 1034 - SpaDES-1.3.0/SpaDES/NEWS | 534 SpaDES-1.3.0/SpaDES/R/POM.R |only SpaDES-1.3.0/SpaDES/R/SELES.R | 563 SpaDES-1.3.0/SpaDES/R/agent.R | 176 SpaDES-1.3.0/SpaDES/R/check.R | 545 SpaDES-1.3.0/SpaDES/R/checkpoint.R | 726 - SpaDES-1.3.0/SpaDES/R/copy.R | 78 SpaDES-1.3.0/SpaDES/R/environment.R | 401 SpaDES-1.3.0/SpaDES/R/experiment.R | 1149 - SpaDES-1.3.0/SpaDES/R/helpers.R | 305 SpaDES-1.3.0/SpaDES/R/initialize.R | 710 - SpaDES-1.3.0/SpaDES/R/load.R | 630 - SpaDES-1.3.0/SpaDES/R/mapReduce.R | 167 SpaDES-1.3.0/SpaDES/R/mergeRaster.R | 150 SpaDES-1.3.0/SpaDES/R/misc-methods.R | 1452 +- SpaDES-1.3.0/SpaDES/R/module-dependencies-class.R | 451 SpaDES-1.3.0/SpaDES/R/module-dependencies-methods.R | 541 SpaDES-1.3.0/SpaDES/R/module-repository.R | 957 - SpaDES-1.3.0/SpaDES/R/module-template.R | 1660 +- SpaDES-1.3.0/SpaDES/R/moduleCoverage.R | 300 SpaDES-1.3.0/SpaDES/R/moduleMetadata.R | 213 SpaDES-1.3.0/SpaDES/R/movement.R | 252 SpaDES-1.3.0/SpaDES/R/neighbourhood.R | 1926 +-- SpaDES-1.3.0/SpaDES/R/numerical-comparisons.R | 72 SpaDES-1.3.0/SpaDES/R/plotting-classes.R | 584 SpaDES-1.3.0/SpaDES/R/plotting-colours.R | 1218 + SpaDES-1.3.0/SpaDES/R/plotting-diagrams.R | 719 - SpaDES-1.3.0/SpaDES/R/plotting-helpers.R | 3124 +++-- SpaDES-1.3.0/SpaDES/R/plotting-other.R | 831 - SpaDES-1.3.0/SpaDES/R/plotting.R | 2806 +--- SpaDES-1.3.0/SpaDES/R/priority.R | 86 SpaDES-1.3.0/SpaDES/R/probability.R | 94 SpaDES-1.3.0/SpaDES/R/progress.R | 230 SpaDES-1.3.0/SpaDES/R/rstudio-addins.R |only SpaDES-1.3.0/SpaDES/R/save.R | 326 SpaDES-1.3.0/SpaDES/R/shine.R | 742 - SpaDES-1.3.0/SpaDES/R/simList-accessors.R | 6168 +++++----- SpaDES-1.3.0/SpaDES/R/simList-class.R | 514 SpaDES-1.3.0/SpaDES/R/simulation.R | 2353 ++- SpaDES-1.3.0/SpaDES/R/spades-classes.R | 72 SpaDES-1.3.0/SpaDES/R/spades-package.R | 899 - SpaDES-1.3.0/SpaDES/R/splitRaster.R | 381 SpaDES-1.3.0/SpaDES/R/spread-process.R | 3264 ++--- SpaDES-1.3.0/SpaDES/R/times.R | 938 - SpaDES-1.3.0/SpaDES/R/zzz.R | 62 SpaDES-1.3.0/SpaDES/README.md | 161 SpaDES-1.3.0/SpaDES/build/vignette.rds |binary SpaDES-1.3.0/SpaDES/demo/00Index | 4 SpaDES-1.3.0/SpaDES/demo/spades-simulation.R | 106 SpaDES-1.3.0/SpaDES/inst/doc/i-introduction.R | 91 SpaDES-1.3.0/SpaDES/inst/doc/i-introduction.Rmd | 683 - SpaDES-1.3.0/SpaDES/inst/doc/i-introduction.html | 762 - SpaDES-1.3.0/SpaDES/inst/doc/ii-modules.R | 711 - SpaDES-1.3.0/SpaDES/inst/doc/ii-modules.Rmd | 1630 +- SpaDES-1.3.0/SpaDES/inst/doc/ii-modules.html | 2097 +-- SpaDES-1.3.0/SpaDES/inst/doc/iii-plotting.R | 339 SpaDES-1.3.0/SpaDES/inst/doc/iii-plotting.Rmd | 874 - SpaDES-1.3.0/SpaDES/inst/doc/iii-plotting.html | 813 - SpaDES-1.3.0/SpaDES/inst/examples/example_POM.R |only SpaDES-1.3.0/SpaDES/inst/examples/example_cir.R |only SpaDES-1.3.0/SpaDES/inst/examples/example_experiment.R |only SpaDES-1.3.0/SpaDES/inst/examples/example_splitRaster.R | 116 SpaDES-1.3.0/SpaDES/inst/examples/example_spokes.R |only SpaDES-1.3.0/SpaDES/inst/rstudio |only SpaDES-1.3.0/SpaDES/inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R | 48 SpaDES-1.3.0/SpaDES/inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd | 94 SpaDES-1.3.0/SpaDES/inst/sampleModules/caribouMovement/caribouMovement.R | 311 SpaDES-1.3.0/SpaDES/inst/sampleModules/fireSpread/fireSpread.R | 370 SpaDES-1.3.0/SpaDES/inst/sampleModules/randomLandscapes/randomLandscapes.R | 235 SpaDES-1.3.0/SpaDES/man/POM.Rd |only SpaDES-1.3.0/SpaDES/man/Plot-internal.Rd |only SpaDES-1.3.0/SpaDES/man/Plot.Rd | 694 - SpaDES-1.3.0/SpaDES/man/SELESagentLocation.Rd | 58 SpaDES-1.3.0/SpaDES/man/SELESnumAgents.Rd | 60 SpaDES-1.3.0/SpaDES/man/SELESprobInit.Rd | 86 SpaDES-1.3.0/SpaDES/man/SELEStransitions.Rd | 62 SpaDES-1.3.0/SpaDES/man/SpaDES-package.Rd | 893 - SpaDES-1.3.0/SpaDES/man/addDepends.Rd | 69 SpaDES-1.3.0/SpaDES/man/addin_newModule.Rd |only SpaDES-1.3.0/SpaDES/man/adj.Rd | 208 SpaDES-1.3.0/SpaDES/man/append_attr.Rd | 78 SpaDES-1.3.0/SpaDES/man/arrangeViewports.Rd | 54 SpaDES-1.3.0/SpaDES/man/arrangement-class.Rd | 144 SpaDES-1.3.0/SpaDES/man/assignSpaDES.Rd | 67 SpaDES-1.3.0/SpaDES/man/cache.Rd | 131 SpaDES-1.3.0/SpaDES/man/changeObjEnv.Rd | 124 SpaDES-1.3.0/SpaDES/man/checkModule.Rd | 58 SpaDES-1.3.0/SpaDES/man/checkObject.Rd | 112 SpaDES-1.3.0/SpaDES/man/checkParams.Rd | 72 SpaDES-1.3.0/SpaDES/man/checkPath.Rd | 76 SpaDES-1.3.0/SpaDES/man/checkpoint.Rd | 139 SpaDES-1.3.0/SpaDES/man/checksums.Rd | 118 SpaDES-1.3.0/SpaDES/man/cir.Rd | 412 SpaDES-1.3.0/SpaDES/man/classFilter.Rd | 202 SpaDES-1.3.0/SpaDES/man/clearPlot.Rd | 87 SpaDES-1.3.0/SpaDES/man/clearStubArtifacts.Rd | 58 SpaDES-1.3.0/SpaDES/man/copy.Rd | 58 SpaDES-1.3.0/SpaDES/man/createsOutput.Rd |only SpaDES-1.3.0/SpaDES/man/crw.Rd | 154 SpaDES-1.3.0/SpaDES/man/defineModule.Rd | 232 SpaDES-1.3.0/SpaDES/man/defineParameter.Rd | 108 SpaDES-1.3.0/SpaDES/man/depsEdgeList.Rd | 72 SpaDES-1.3.0/SpaDES/man/depsGraph.Rd | 68 SpaDES-1.3.0/SpaDES/man/depsLoadOrder.Rd | 69 SpaDES-1.3.0/SpaDES/man/depsPruneEdges.Rd | 55 SpaDES-1.3.0/SpaDES/man/dev.Rd | 67 SpaDES-1.3.0/SpaDES/man/digest.Rd | 55 SpaDES-1.3.0/SpaDES/man/directions.Rd | 153 SpaDES-1.3.0/SpaDES/man/distances.Rd | 254 SpaDES-1.3.0/SpaDES/man/divergentColors.Rd | 99 SpaDES-1.3.0/SpaDES/man/doEvent.Rd | 91 SpaDES-1.3.0/SpaDES/man/downloadData.Rd | 75 SpaDES-1.3.0/SpaDES/man/downloadModule.Rd | 124 SpaDES-1.3.0/SpaDES/man/dwrpnorm2.Rd | 88 SpaDES-1.3.0/SpaDES/man/emptyEventList.Rd | 126 SpaDES-1.3.0/SpaDES/man/emptyMetadata.Rd | 48 SpaDES-1.3.0/SpaDES/man/equalExtent.Rd | 44 SpaDES-1.3.0/SpaDES/man/eventDiagram.Rd | 113 SpaDES-1.3.0/SpaDES/man/existsSpaDES.Rd | 53 SpaDES-1.3.0/SpaDES/man/expectsInput.Rd |only SpaDES-1.3.0/SpaDES/man/experiment.Rd | 849 - SpaDES-1.3.0/SpaDES/man/fileEdit.Rd |only SpaDES-1.3.0/SpaDES/man/fileExt.Rd | 42 SpaDES-1.3.0/SpaDES/man/fileName.Rd | 42 SpaDES-1.3.0/SpaDES/man/fileTable.Rd | 75 SpaDES-1.3.0/SpaDES/man/fillInputRows.Rd | 34 SpaDES-1.3.0/SpaDES/man/fillOutputRows.Rd | 34 SpaDES-1.3.0/SpaDES/man/findFactors.Rd | 39 SpaDES-1.3.0/SpaDES/man/findObjects.Rd | 50 SpaDES-1.3.0/SpaDES/man/ganttStatus.Rd | 59 SpaDES-1.3.0/SpaDES/man/gaussmap.Rd | 98 SpaDES-1.3.0/SpaDES/man/getColors.Rd | 76 SpaDES-1.3.0/SpaDES/man/getFileName.Rd | 54 SpaDES-1.3.0/SpaDES/man/getModuleVersion.Rd | 58 SpaDES-1.3.0/SpaDES/man/getSpaDES.Rd | 49 SpaDES-1.3.0/SpaDES/man/globals.Rd |only SpaDES-1.3.0/SpaDES/man/grid-functions.Rd | 46 SpaDES-1.3.0/SpaDES/man/heading.Rd | 128 SpaDES-1.3.0/SpaDES/man/identifyGrobToPlot.Rd | 76 SpaDES-1.3.0/SpaDES/man/inRange.Rd | 60 SpaDES-1.3.0/SpaDES/man/initialize-method.Rd | 34 SpaDES-1.3.0/SpaDES/man/initiateAgents.Rd | 166 SpaDES-1.3.0/SpaDES/man/inputObjects.Rd | 63 SpaDES-1.3.0/SpaDES/man/layerNames.Rd | 78 SpaDES-1.3.0/SpaDES/man/loadFiles.Rd | 176 SpaDES-1.3.0/SpaDES/man/loadPackages.Rd | 102 SpaDES-1.3.0/SpaDES/man/ls-method.Rd | 68 SpaDES-1.3.0/SpaDES/man/ls_str-method.Rd | 68 SpaDES-1.3.0/SpaDES/man/makeColorMatrix.Rd | 115 SpaDES-1.3.0/SpaDES/man/makeDigestible.Rd | 89 SpaDES-1.3.0/SpaDES/man/makeLayout.Rd | 67 SpaDES-1.3.0/SpaDES/man/makeLines.Rd | 118 SpaDES-1.3.0/SpaDES/man/makeList.Rd | 56 SpaDES-1.3.0/SpaDES/man/makeSpadesPlot.Rd | 88 SpaDES-1.3.0/SpaDES/man/makeViewports.Rd | 58 SpaDES-1.3.0/SpaDES/man/maxTimeunit.Rd | 52 SpaDES-1.3.0/SpaDES/man/mergeRaster.Rd | 198 SpaDES-1.3.0/SpaDES/man/minTimeunit.Rd | 57 SpaDES-1.3.0/SpaDES/man/moduleCoverage.Rd | 128 SpaDES-1.3.0/SpaDES/man/moduleDeps-class.Rd | 146 SpaDES-1.3.0/SpaDES/man/moduleDiagram.Rd | 85 SpaDES-1.3.0/SpaDES/man/moduleGraph.Rd |only SpaDES-1.3.0/SpaDES/man/moduleMetadata.Rd | 98 SpaDES-1.3.0/SpaDES/man/namespacing.Rd |only SpaDES-1.3.0/SpaDES/man/newModule.Rd | 194 SpaDES-1.3.0/SpaDES/man/newModuleCode.Rd |only SpaDES-1.3.0/SpaDES/man/newModuleDocumentation.Rd |only SpaDES-1.3.0/SpaDES/man/newModuleTests.Rd |only SpaDES-1.3.0/SpaDES/man/newPlot.Rd | 58 SpaDES-1.3.0/SpaDES/man/newProgressBar.Rd | 50 SpaDES-1.3.0/SpaDES/man/normPath.Rd | 68 SpaDES-1.3.0/SpaDES/man/numLayers.Rd |only SpaDES-1.3.0/SpaDES/man/objectDiagram.Rd | 68 SpaDES-1.3.0/SpaDES/man/objectNames.Rd | 65 SpaDES-1.3.0/SpaDES/man/objects.Rd |only SpaDES-1.3.0/SpaDES/man/openModules.Rd | 106 SpaDES-1.3.0/SpaDES/man/packages.Rd | 60 SpaDES-1.3.0/SpaDES/man/paddedFloatToChar.Rd | 72 SpaDES-1.3.0/SpaDES/man/params.Rd |only SpaDES-1.3.0/SpaDES/man/parseArgs.Rd | 59 SpaDES-1.3.0/SpaDES/man/parseModule.Rd | 84 SpaDES-1.3.0/SpaDES/man/patchSize.Rd | 30 SpaDES-1.3.0/SpaDES/man/paths.Rd |only SpaDES-1.3.0/SpaDES/man/plotGrob.Rd | 221 SpaDES-1.3.0/SpaDES/man/prepareRaster.Rd | 67 SpaDES-1.3.0/SpaDES/man/priority.Rd | 64 SpaDES-1.3.0/SpaDES/man/progress.Rd |only SpaDES-1.3.0/SpaDES/man/randomPolygons.Rd | 103 SpaDES-1.3.0/SpaDES/man/rasterToMemory.Rd | 62 SpaDES-1.3.0/SpaDES/man/rasterizeReduce.Rd | 123 SpaDES-1.3.0/SpaDES/man/rings.Rd | 222 SpaDES-1.3.0/SpaDES/man/rndstr.Rd | 130 SpaDES-1.3.0/SpaDES/man/saveFiles.Rd | 165 SpaDES-1.3.0/SpaDES/man/scheduleEvent.Rd | 132 SpaDES-1.3.0/SpaDES/man/setColors.Rd | 208 SpaDES-1.3.0/SpaDES/man/shine.Rd | 136 SpaDES-1.3.0/SpaDES/man/show-method.Rd | 32 SpaDES-1.3.0/SpaDES/man/sim2gantt.Rd | 73 SpaDES-1.3.0/SpaDES/man/simDeps-class.Rd | 44 SpaDES-1.3.0/SpaDES/man/simInit.Rd | 411 SpaDES-1.3.0/SpaDES/man/simList-accessors-envir.Rd | 98 SpaDES-1.3.0/SpaDES/man/simList-accessors-events.Rd | 193 SpaDES-1.3.0/SpaDES/man/simList-accessors-inout.Rd | 619 - SpaDES-1.3.0/SpaDES/man/simList-accessors-modules.Rd | 157 SpaDES-1.3.0/SpaDES/man/simList-accessors-paths.Rd | 213 SpaDES-1.3.0/SpaDES/man/simList-accessors-times.Rd | 342 SpaDES-1.3.0/SpaDES/man/simList-class.Rd | 222 SpaDES-1.3.0/SpaDES/man/simList_-class.Rd | 47 SpaDES-1.3.0/SpaDES/man/sortDotsFirst.Rd | 49 SpaDES-1.3.0/SpaDES/man/spades-classes.Rd | 90 SpaDES-1.3.0/SpaDES/man/spades.Rd | 280 SpaDES-1.3.0/SpaDES/man/spadesEnv.Rd | 30 SpaDES-1.3.0/SpaDES/man/spadesGrob-class.Rd | 102 SpaDES-1.3.0/SpaDES/man/spadesMaps.Rd | 50 SpaDES-1.3.0/SpaDES/man/spadesMouseClicks.Rd | 136 SpaDES-1.3.0/SpaDES/man/spadesPlot-class.Rd | 96 SpaDES-1.3.0/SpaDES/man/spadesPlotObjects-class.Rd | 44 SpaDES-1.3.0/SpaDES/man/spadesPlottables-class.Rd | 46 SpaDES-1.3.0/SpaDES/man/spadesTime.Rd | 160 SpaDES-1.3.0/SpaDES/man/spatialObjects-class.Rd | 46 SpaDES-1.3.0/SpaDES/man/specnumperpatch-probs.Rd | 119 SpaDES-1.3.0/SpaDES/man/splitRaster.Rd | 289 SpaDES-1.3.0/SpaDES/man/spokes.Rd |only SpaDES-1.3.0/SpaDES/man/spread.Rd | 1029 - SpaDES-1.3.0/SpaDES/man/timeConversion.Rd | 186 SpaDES-1.3.0/SpaDES/man/unittrim.Rd | 45 SpaDES-1.3.0/SpaDES/man/unparsed.Rd | 51 SpaDES-1.3.0/SpaDES/man/updateList.Rd | 104 SpaDES-1.3.0/SpaDES/man/updateSpadesPlot.Rd | 62 SpaDES-1.3.0/SpaDES/man/versionWarning.Rd | 74 SpaDES-1.3.0/SpaDES/man/wrap.Rd | 175 SpaDES-1.3.0/SpaDES/man/zipModule.Rd | 80 SpaDES-1.3.0/SpaDES/tests/test-all.R | 4 SpaDES-1.3.0/SpaDES/tests/testthat/test-Plot.R | 1617 +- SpaDES-1.3.0/SpaDES/tests/testthat/test-adj.R | 725 - SpaDES-1.3.0/SpaDES/tests/testthat/test-checkPath.R | 144 SpaDES-1.3.0/SpaDES/tests/testthat/test-checkpoint.R | 80 SpaDES-1.3.0/SpaDES/tests/testthat/test-downloadModule.R | 202 SpaDES-1.3.0/SpaDES/tests/testthat/test-environment.R | 22 SpaDES-1.3.0/SpaDES/tests/testthat/test-examples.R | 6 SpaDES-1.3.0/SpaDES/tests/testthat/test-experiment.R | 405 SpaDES-1.3.0/SpaDES/tests/testthat/test-inRange.R | 38 SpaDES-1.3.0/SpaDES/tests/testthat/test-load.R | 627 - SpaDES-1.3.0/SpaDES/tests/testthat/test-mapReduce.R | 206 SpaDES-1.3.0/SpaDES/tests/testthat/test-module-deps-methods.R | 367 SpaDES-1.3.0/SpaDES/tests/testthat/test-module-template.R | 94 SpaDES-1.3.0/SpaDES/tests/testthat/test-paths.R | 114 SpaDES-1.3.0/SpaDES/tests/testthat/test-save.R | 201 SpaDES-1.3.0/SpaDES/tests/testthat/test-simList.R | 456 SpaDES-1.3.0/SpaDES/tests/testthat/test-simulation.R | 344 SpaDES-1.3.0/SpaDES/tests/testthat/test-splitRaster.R | 533 SpaDES-1.3.0/SpaDES/tests/testthat/test-spread.R | 2270 +-- SpaDES-1.3.0/SpaDES/tests/testthat/test-timeunits.R | 313 SpaDES-1.3.0/SpaDES/tests/testthat/test-updateList.R | 32 SpaDES-1.3.0/SpaDES/vignettes/bibliography.bib | 270 SpaDES-1.3.0/SpaDES/vignettes/i-introduction.Rmd | 683 - SpaDES-1.3.0/SpaDES/vignettes/ii-modules.Rmd | 1630 +- SpaDES-1.3.0/SpaDES/vignettes/iii-plotting.Rmd | 874 - 264 files changed, 42433 insertions(+), 38828 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Vijay Barve [ctb],
Dan Mcglinn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.4 dated 2016-06-29 and 0.9.5 dated 2016-10-06
DESCRIPTION | 17 MD5 | 94 ++-- NAMESPACE | 2 NEWS.md | 55 ++ R/check_wkt.r | 12 R/dataset_search.r | 5 R/gbif_photos.r | 38 + R/occ_count.r | 111 ++++- R/occ_data.R | 168 ++++---- R/occ_facet.R |only R/occ_search.r | 254 ++++++------- R/occ_spellcheck.R |only R/overload_classes.R |only R/print_gbif.R |only R/zzz.r | 51 ++ README.md | 205 +++++----- inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 286 +++++++------- inst/doc/issues_vignette.html | 286 +++++++------- inst/doc/rgbif_vignette.Rmd | 657 ++++++++++++++++++++++++++++++---- inst/doc/rgbif_vignette.html | 437 +++++++++++----------- inst/doc/taxonomic_names.Rmd | 54 +- inst/doc/taxonomic_names.html | 54 +- inst/singlemaplayout.html | 8 inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 286 +++++++------- inst/vign/rgbif_vignette.md | 435 +++++++++++----------- inst/vign/taxonomic_names.md | 54 +- man/check_wkt.Rd | 3 man/dataset_search.Rd | 6 man/dataset_suggest.Rd | 3 man/gbif_photos.Rd | 12 man/occ_count.Rd | 79 +++- man/occ_data.Rd | 180 ++++++++- man/occ_facet.Rd |only man/occ_search.Rd | 232 +++++++++++- man/occ_spellcheck.Rd |only tests/testthat/test-dataset_search.r | 25 - tests/testthat/test-gbif_names.R | 1 tests/testthat/test-gbif_photos.R | 26 - tests/testthat/test-name_lookup.r | 5 tests/testthat/test-name_suggest.r | 4 tests/testthat/test-nodes.r | 2 tests/testthat/test-occ_count.r | 17 tests/testthat/test-occ_data.R | 25 + tests/testthat/test-occ_facet.R |only tests/testthat/test-occ_metadata.r | 2 tests/testthat/test-occ_search.r | 38 + tests/testthat/test-occ_spellcheck.R |only vignettes/issues_vignette.Rmd | 286 +++++++------- vignettes/rgbif_vignette.Rmd | 435 +++++++++++----------- vignettes/taxonomic_names.Rmd | 54 +- 52 files changed, 3088 insertions(+), 1916 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.4-4 dated 2016-09-26 and 0.4-5 dated 2016-10-06
clusrank-0.4-4/clusrank/data/eye.rda |only clusrank-0.4-5/clusrank/DESCRIPTION | 6 - clusrank-0.4-5/clusrank/MD5 | 16 ++-- clusrank-0.4-5/clusrank/R/RcppExports.R | 2 clusrank-0.4-5/clusrank/R/clusWilcox.R | 8 +- clusrank-0.4-5/clusrank/R/clusranksum.R | 7 +- clusrank-0.4-5/clusrank/R/eye.R | 48 +++++++++----- clusrank-0.4-5/clusrank/data/eye.RData |only clusrank-0.4-5/clusrank/man/eye.Rd | 50 +++++++++------ clusrank-0.4-5/clusrank/src/RcppExports.cpp | 90 ++++++++++++++-------------- 10 files changed, 124 insertions(+), 103 deletions(-)