Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Easily implement a variety of simulation models, with a focus on
spatially explicit agent based models. These include raster-based,
event-based, and agent-based models. The core simulation components are
built upon a discrete event simulation 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 1.1.3 dated 2016-04-18 and 1.1.4 dated 2016-04-20
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------- NEWS | 4 +++ R/misc-methods.R | 1 R/simList-accessors.R | 19 +++++++++-------- inst/doc/i-introduction.html | 2 - inst/doc/ii-modules.html | 16 +++++++------- inst/doc/iii-plotting.html | 38 +++++++++++++++++------------------ man/simList-accessors-inout.Rd | 19 +++++++++-------- tests/testthat/test-Plot.R | 18 +++++----------- tests/testthat/test-checkPath.R | 17 ++++++++++----- tests/testthat/test-checkpoint.R | 2 - tests/testthat/test-downloadModule.R | 9 ++------ tests/testthat/test-experiment.R | 8 ++++--- tests/testthat/test-load.R | 11 ++++------ 15 files changed, 101 insertions(+), 99 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.1.2 dated 2015-09-07 and 1.1.4 dated 2016-04-20
SKAT-1.1.2/SKAT/man/Get_EffectiveNumberTest.rd |only SKAT-1.1.4/SKAT/DESCRIPTION | 8 +++--- SKAT-1.1.4/SKAT/MD5 | 30 ++++++++++++------------- SKAT-1.1.4/SKAT/NAMESPACE | 4 +-- SKAT-1.1.4/SKAT/R/Binary_Function.R | 17 +++++++------- SKAT-1.1.4/SKAT/R/Binary_MAIN.R | 29 ++++++++++++++++++++---- SKAT-1.1.4/SKAT/R/Binary_MAIN_ExactBin.R | 3 +- SKAT-1.1.4/SKAT/R/Joint_CommonRare.R | 4 ++- SKAT-1.1.4/SKAT/build/vignette.rds |binary SKAT-1.1.4/SKAT/data/SKAT.example.ChrX.rda |binary SKAT-1.1.4/SKAT/data/SKAT.example.rda |binary SKAT-1.1.4/SKAT/data/SKAT.fam.example.rda |binary SKAT-1.1.4/SKAT/data/SKAT.haplotypes.rda |binary SKAT-1.1.4/SKAT/data/SKATBinary.example.rda |binary SKAT-1.1.4/SKAT/inst/doc/SKAT.pdf |binary SKAT-1.1.4/SKAT/man/Get_ENT.rd |only SKAT-1.1.4/SKAT/man/SKATBinary.rd | 5 ++-- 17 files changed, 62 insertions(+), 38 deletions(-)
Title: Multiscale Bernstein Polynomials for Densities
Description: Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).
Author: Antonio Canale
Maintainer: Antonio Canale <antonio.canale@unito.it>
Diff between msBP versions 1.0-2.1 dated 2015-01-01 and 1.1 dated 2016-04-20
ChangeLog | 1 DESCRIPTION | 10 +- MD5 | 49 +++++++------- NAMESPACE | 2 R/msBP.Gibbs.R | 162 +++++++++++++++++++++++++++++++++++------------ R/msBP.LPML.R |only R/msBP.density.R | 34 +++++++-- R/msBP.leaf.allocation.R | 2 R/msBP.test.R | 6 + R/msBP.test.aux.R | 3 man/msBP-internal.Rd | 1 man/msBP-package.Rd | 6 - man/msBP.Gibbs.Rd | 59 ++++++++++++----- man/msBP.compute.prob.Rd | 4 - man/msBP.density.Rd | 15 ++-- man/msBP.nrvTrees.Rd | 2 man/msBP.postCluster.Rd | 6 - man/msBP.rsample.Rd | 8 -- man/msBP.rtree.Rd | 2 man/msBP.test.Rd | 2 man/msBP.tree.Rd | 4 - src/auxGibbs.cpp | 77 ++-------------------- src/gibbs.cpp | 137 +++++++++++++++++++++++++++++++++++---- src/gibbs.h | 6 - src/msBP.cpp | 25 +++++++ src/msBP.h | 1 26 files changed, 417 insertions(+), 207 deletions(-)
Title: Longitudinal Targeted Maximum Likelihood Estimation
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data.
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab <joshuaschwab@yahoo.com>
Diff between ltmle versions 0.9-7 dated 2016-02-25 and 0.9-8 dated 2016-04-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/ltmle-package.R | 10 +++++++++- man/ltmle-package.Rd | 7 +++++++ 5 files changed, 28 insertions(+), 9 deletions(-)
Title: Support for Linear Models
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course
graduate series in General, Generalized, and Multi-level Linear Models (PSY
610/710).
Author: John Curtin <jjcurtin@wisc.edu>
Maintainer: John Curtin <jjcurtin@wisc.edu>
Diff between lmSupport versions 2.9.2 dated 2015-06-05 and 2.9.4 dated 2016-04-20
DESCRIPTION | 17 ++++++++++------- MD5 | 16 +++++++++------- NAMESPACE | 11 +++++++++++ R/dfMerge.R | 2 +- R/figConfidenceBand.R | 6 +++--- R/modelPredictions.R | 25 +++++++++++++++++++++++++ R/varMarkdown.R |only man/modelAssumptions.Rd | 2 +- man/modelPredictions.Rd | 3 ++- man/varMarkdown.Rd |only 10 files changed, 62 insertions(+), 20 deletions(-)
Title: Geometric Median, k-Median Clustering and Robust Median PCA
Description: Fast algorithms for robust estimation with large samples of multivariate observations. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.
Author: Herve Cardot
Maintainer: Herve Cardot <herve.cardot@u-bourgogne.fr>
Diff between Gmedian versions 1.1 dated 2016-03-28 and 1.2 dated 2016-04-20
Gmedian-1.1/Gmedian/man/Gmedianrowvec_rcpp-internal.Rd |only Gmedian-1.1/Gmedian/man/MedianCovMatRow_rcpp-internal.Rd |only Gmedian-1.1/Gmedian/man/stoKmed_rcpp-internal.Rd |only Gmedian-1.2/Gmedian/DESCRIPTION | 14 +++---- Gmedian-1.2/Gmedian/MD5 | 30 +++++++-------- Gmedian-1.2/Gmedian/NAMESPACE | 4 +- Gmedian-1.2/Gmedian/NEWS | 8 ++++ Gmedian-1.2/Gmedian/R/Gmedian.R | 11 +++++ Gmedian-1.2/Gmedian/R/GmedianCov.R | 22 ++++++++++- Gmedian-1.2/Gmedian/R/RcppExports.R | 8 ++++ Gmedian-1.2/Gmedian/build/partial.rdb |binary Gmedian-1.2/Gmedian/man/Gmedian-package.Rd | 8 +++- Gmedian-1.2/Gmedian/man/Gmedian.Rd | 6 +-- Gmedian-1.2/Gmedian/man/GmedianCov.Rd | 13 +----- Gmedian-1.2/Gmedian/man/Weiszfeld.Rd |only Gmedian-1.2/Gmedian/man/WeiszfeldCov.Rd |only Gmedian-1.2/Gmedian/man/kGmedian.Rd | 2 - Gmedian-1.2/Gmedian/src/RcppExports.cpp | 29 ++++++++++++++ Gmedian-1.2/Gmedian/src/Weiszfeld.cpp |only 19 files changed, 114 insertions(+), 41 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut],
Jordan Read [ctb],
Lindsay Carr [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.5.3 dated 2016-03-28 and 2.5.5 dated 2016-04-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/importRDB1.r | 4 ++-- R/importWaterML1.r | 2 +- README.md | 9 --------- 5 files changed, 11 insertions(+), 20 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Description: A collection of iterators for generating permutations and combinations with or
without replacement; with distinct items or non-distinct items (multiset).
The generated sequences are in lexicographical order (dictionary order). The
algorithms to generate permutations and combinations are memory efficient. These
iterative algorithms enable users to process all sequences without putting all
results in the memory at the same time. The algorithms are written in C/C++ for
faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.2.9 dated 2016-04-09 and 0.2.9-1 dated 2016-04-20
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <http://github.com/obsypy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut, cre],
Rob Casey [aut],
Mary Templeton [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between IRISSeismic versions 1.0.7 dated 2016-01-06 and 1.0.7-1 dated 2016-04-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary src/Makevars.win | 2 +- src/libmseed/Makefile | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution.
It provides the density function, distribution function, and Quantile-Quantile plots.
It implements a variety of estimation methods for the distribution, including diagnostic plots.
Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation.
These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>,
Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.3.2 dated 2016-02-24 and 2.3.3 dated 2016-04-20
Changelog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 4 ++++ R/methods.R | 13 +++++++++---- R/starship.R | 2 ++ man/plot.starship.Rd | 8 ++++++-- 7 files changed, 35 insertions(+), 16 deletions(-)
Title: Multithreaded Fixed Size Subset Sum with Bounded Error in
Multidimensional Real Domain
Description: A novel algorithm for solving the fixed size Subset Sum Problem with bounded error in multidimensional real domain.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 3.1 dated 2014-11-16 and 5.0.1 dated 2016-04-20
FLSSS-3.1/FLSSS/R/FLSSS_20141116.r |only FLSSS-3.1/FLSSS/src/FLSSS_20141115.cpp |only FLSSS-5.0.1/FLSSS/DESCRIPTION | 17 ++--- FLSSS-5.0.1/FLSSS/MD5 | 14 ++-- FLSSS-5.0.1/FLSSS/NAMESPACE | 4 - FLSSS-5.0.1/FLSSS/R/FLSSS_20160323.r |only FLSSS-5.0.1/FLSSS/man/FLSSS-package.Rd | 86 ++++++++++++++------------ FLSSS-5.0.1/FLSSS/man/mFLSSSpar.Rd |only FLSSS-5.0.1/FLSSS/src/FLSSS_20160322.cpp |only FLSSS-5.0.1/FLSSS/src/FLSSSmulti_20160323.cpp |only FLSSS-5.0.1/FLSSS/src/Makevars.win |only FLSSS-5.0.1/FLSSS/src/RcppExports.cpp |only 12 files changed, 68 insertions(+), 53 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.6.1 dated 2016-03-06 and 0.6.2 dated 2016-04-20
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS | 4 ++++ README.md | 2 +- TODO | 6 +----- inst/doc/axis_position.html | 9 +++++---- inst/doc/introduction.html | 10 +++++----- inst/doc/plot_annotations.html | 4 ++-- inst/doc/plot_grid.R | 23 +++++++++++++++++++++++ inst/doc/plot_grid.Rmd | 27 +++++++++++++++++++++++++++ inst/doc/plot_grid.html | 28 ++++++++++++++++++++++++++-- inst/doc/shared_legends.html | 12 ++++++------ vignettes/plot_grid.Rmd | 27 +++++++++++++++++++++++++++ 13 files changed, 142 insertions(+), 40 deletions(-)