Title: Submit R Calculations to a 'SLURM' Cluster
Description: Functions that simplify the R interface the 'SLURM' cluster workload
manager, and automate the process of dividing a parallel calculation across
cluster nodes.
Author: Philippe Marchand [aut, cre],
Mike Smorul [ctb]
Maintainer: Philippe Marchand <pmarchand@sesync.org>
Diff between rslurm versions 0.3.0 dated 2016-05-27 and 0.3.1 dated 2016-06-18
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 14 +++++++++++++- R/slurm_apply.R | 4 +++- R/slurm_call.R | 4 +++- R/slurm_utils.R | 3 ++- inst/templates/submit_sh.txt | 2 +- inst/templates/submit_single_sh.txt | 2 +- tests/testthat/test_slurm_call.R | 4 +++- 9 files changed, 37 insertions(+), 18 deletions(-)
Title: ROI Plug-in SYMPHONY
Description: Enhances the R Optimization Infrastructure (ROI) package by registering
the SYMPHONY open-source solver from the COIN-OR suite. It allows for
solving mixed integer linear programming (MILP) problems as well as all
variants/combinations of LP, IP.
Author: Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI.plugin.symphony versions 0.0-2 dated 2013-11-28 and 0.2-1 dated 2016-06-18
DESCRIPTION | 21 +++++++++-------- MD5 | 8 +++--- NAMESPACE | 1 R/plugin.R | 71 +++++++++++++++++++++++++++++++++++++++++------------------- R/zzz.R | 20 ++++++++++++---- 5 files changed, 80 insertions(+), 41 deletions(-)
More information about ROI.plugin.symphony at CRAN
Permanent link
Title: ROI Plug-in {quadprog}
Description: Enhances the R Optimization Infrastructure (ROI) package
by registering the quadprog solver. It allows for solving quadratic programming (QP)
problems.
Author: Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI.plugin.quadprog versions 0.0-2 dated 2013-11-28 and 0.2-1 dated 2016-06-18
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- NAMESPACE | 1 + R/plugin.R | 20 ++++++++++---------- R/zzz.R | 19 ++++++++++++++----- 5 files changed, 38 insertions(+), 28 deletions(-)
More information about ROI.plugin.quadprog at CRAN
Permanent link
Title: R Optimization Infrastructure
Description: The R Optimization Infrastructure (ROI) is a
sophisticated framework for handling optimization problems in R.
Author: Kurt Hornik [aut],
David Meyer [aut],
Florian Schwendinger [aut],
Stefan Theussl [aut, cre],
Diethelm Wuertz [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI versions 0.1-0 dated 2013-11-28 and 0.2-1 dated 2016-06-18
ROI-0.1-0/ROI/R/status_codes.R |only ROI-0.1-0/ROI/man/ROI_available_solvers.Rd |only ROI-0.1-0/ROI/man/ROI_installed_solvers.Rd |only ROI-0.1-0/ROI/man/as.F_objective.Rd |only ROI-0.1-0/ROI/man/as.L_constraint.Rd |only ROI-0.1-0/ROI/man/as.L_objective.Rd |only ROI-0.1-0/ROI/man/as.OP.Rd |only ROI-0.1-0/ROI/man/as.Q_constraint.Rd |only ROI-0.1-0/ROI/man/as.Q_objective.Rd |only ROI-0.1-0/ROI/man/as.constraint.Rd |only ROI-0.1-0/ROI/man/as.objective.Rd |only ROI-0.1-0/ROI/man/bounds-replace.Rd |only ROI-0.1-0/ROI/man/bounds.OP.Rd |only ROI-0.1-0/ROI/man/bounds.Rd |only ROI-0.1-0/ROI/man/constraints-replace.Rd |only ROI-0.1-0/ROI/man/constraints.OP.Rd |only ROI-0.1-0/ROI/man/is.L_constraint.Rd |only ROI-0.1-0/ROI/man/is.Q_constraint.Rd |only ROI-0.1-0/ROI/man/length.L_constraint.Rd |only ROI-0.1-0/ROI/man/rbind.L_constraint.Rd |only ROI-0.2-1/ROI/DESCRIPTION | 29 ROI-0.2-1/ROI/MD5 | 128 +- ROI-0.2-1/ROI/NAMESPACE | 210 ++- ROI-0.2-1/ROI/R/OP.R | 181 ++- ROI-0.2-1/ROI/R/bounds.R | 437 ++++++- ROI-0.2-1/ROI/R/constraints.R | 948 ++++++++++++---- ROI-0.2-1/ROI/R/doc_data.R |only ROI-0.2-1/ROI/R/errors.R |only ROI-0.2-1/ROI/R/gradient.R | 73 + ROI-0.2-1/ROI/R/objective.R | 341 +++-- ROI-0.2-1/ROI/R/plugin.R |only ROI-0.2-1/ROI/R/plugin_nlminb.R | 412 ++++++ ROI-0.2-1/ROI/R/roi.R | 372 +++--- ROI-0.2-1/ROI/R/solution.R | 105 + ROI-0.2-1/ROI/R/solver.R | 19 ROI-0.2-1/ROI/R/types.R | 10 ROI-0.2-1/ROI/R/utilities.R | 209 +++ ROI-0.2-1/ROI/R/zzz.R | 68 - ROI-0.2-1/ROI/data |only ROI-0.2-1/ROI/inst |only ROI-0.2-1/ROI/man/Bounds_Accessor_Mutator.Rd |only ROI-0.2-1/ROI/man/C_bound.Rd |only ROI-0.2-1/ROI/man/F_constraint.Rd | 68 - ROI-0.2-1/ROI/man/F_objective.Rd | 37 ROI-0.2-1/ROI/man/G.Rd | 19 ROI-0.2-1/ROI/man/J.Rd |only ROI-0.2-1/ROI/man/L_constraint.Rd | 66 - ROI-0.2-1/ROI/man/L_objective.Rd | 43 ROI-0.2-1/ROI/man/NO_constraint.Rd |only ROI-0.2-1/ROI/man/OP.Rd | 98 + ROI-0.2-1/ROI/man/Q_constraint.Rd | 78 - ROI-0.2-1/ROI/man/Q_objective.Rd | 49 ROI-0.2-1/ROI/man/ROI_applicable_solvers.Rd |only ROI-0.2-1/ROI/man/ROI_bound.Rd |only ROI-0.2-1/ROI/man/ROI_constraint.Rd |only ROI-0.2-1/ROI/man/ROI_options.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_add_status_code_to_db.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_canonicalize_solution.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_get_solver_name.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_make_signature.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_register_solver_control.Rd |only ROI-0.2-1/ROI/man/ROI_plugin_register_solver_method.Rd |only ROI-0.2-1/ROI/man/ROI_registered_solvers.Rd | 26 ROI-0.2-1/ROI/man/ROI_solve.Rd | 71 - ROI-0.2-1/ROI/man/US30.Rd |only ROI-0.2-1/ROI/man/V_bound.Rd | 48 ROI-0.2-1/ROI/man/as.L_term.Rd |only ROI-0.2-1/ROI/man/as.Q_term.Rd |only ROI-0.2-1/ROI/man/constraints.Rd | 27 ROI-0.2-1/ROI/man/equal.Rd |only ROI-0.2-1/ROI/man/nlminb2.Rd |only ROI-0.2-1/ROI/man/objective.Rd | 24 ROI-0.2-1/ROI/man/rbind.constraint.Rd |only ROI-0.2-1/ROI/man/solution.Rd |only ROI-0.2-1/ROI/man/types.Rd | 23 ROI-0.2-1/ROI/man/vech.Rd |only 76 files changed, 3169 insertions(+), 1050 deletions(-)
Title: Algorithm for Pattern Sequence Based Forecasting
Description: Various functions in Pattern Sequence Based Forecasting (PSF) takes
time series data as input and assist to forecast the future value with
the help of Algorithm PSF. This algorithm forecasts the behavior of time series
based on similarity of pattern sequences. Initially, clustering is done with the
labeling of samples from database. The labels associated with samples are then
used for forecasting the future behaviour of time series data. The further
technical details and references regarding PSF are discussed in Vignette.
Author: Neeraj Bokde
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Diff between PSF versions 0.1.1 dated 2016-04-17 and 0.2.1 dated 2016-06-18
DESCRIPTION | 10 ++- MD5 | 12 ++-- R/Mean_Errors.R | 4 - R/pred_for_w_plot.R | 121 +++++++++++++++++++++++---------------------- inst/doc/PSF_vignette.html | 15 ++--- man/mae.Rd | 2 man/rmse.Rd | 2 7 files changed, 86 insertions(+), 80 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between OUwie versions 1.49 dated 2016-02-28 and 1.50 dated 2016-06-18
DESCRIPTION | 14 ++--- MD5 | 36 +++++++------- NAMESPACE | 3 - R/OUwie.R | 135 ++++++++++++++++++++++++++++++++++++----------------- R/OUwie.boot.R | 16 ++++-- R/OUwie.fixed.R | 98 +++++++++++++++++++++----------------- R/OUwie.joint.R | 22 +++++--- R/OUwie.sim.R | 19 +++++-- R/OUwie.slice.R | 118 +++++++++++++++++++++++++++++++--------------- R/expect.trendy.R | 4 - R/hOUwie.R | 9 +-- R/varcov.ou.R | 9 ++- R/weight.mat.R | 6 +- man/OUwie.Rd | 22 ++++++-- man/OUwie.boot.Rd | 5 + man/OUwie.fixed.Rd | 9 ++- man/OUwie.joint.Rd | 13 +++-- man/OUwie.sim.Rd | 5 + man/OUwie.slice.Rd | 20 +++++-- 19 files changed, 361 insertions(+), 202 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between btergm versions 1.7.3 dated 2016-04-21 and 1.7.6 dated 2016-06-18
DESCRIPTION | 18 +- MD5 | 17 +- NAMESPACE | 249 +++++++++++++++++------------------ R/btergm.R | 22 ++- R/interpretation.R | 369 +++++++++++++++++++++++++++++++--------------------- R/mtergm.R | 9 - R/tergmprepare.R | 1 man/btergm-class.Rd | 9 - man/edgeprob.Rd |only man/interpret.Rd | 98 ++++++++++++- 10 files changed, 483 insertions(+), 309 deletions(-)
Title: Parse Data of 'R' Code as an 'XML' Tree
Description: Convert the output of 'utils::getParseData()' to an 'XML'
tree, that is searchable and easier to manipulate in general.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <gcsardi@mango-solutions.com>
Diff between xmlparsedata versions 1.0.0 dated 2016-05-20 and 1.0.1 dated 2016-06-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ R/package.R | 8 +++++++- tests/testthat/test.R | 16 +++++++++++++++- 5 files changed, 38 insertions(+), 9 deletions(-)
Title: Regional Economic Analysis Tools
Description: Collection of analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities, regional specialization and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between REAT versions 1.0.0 dated 2016-04-27 and 1.1.0 dated 2016-06-18
DESCRIPTION | 10 ++-- MD5 | 64 ++++++++++++++++++------------- NAMESPACE | 2 R/converse.R |only R/cv.R | 22 +++++----- R/data.index.R | 14 +++--- R/disp.R | 16 +++---- R/gini.R | 105 ++++++++++++++++++++++++++------------------------- R/gini.conc.R | 42 +++++++++++--------- R/gini.spec.R | 44 ++++++++++++--------- R/hansen.R |only R/herf.R | 24 +++++------ R/herf.eq.R | 6 +- R/huff.R |only R/krugman.spec.R | 20 +++++---- R/locq.R | 14 +++--- R/portfolio.R | 50 +++++++++++++----------- R/reilly.R |only R/reilly.lambda.R |only R/shift.R | 33 +++++++--------- data/Freiburg.rda |binary data/Freiburg1.rda |only data/Freiburg2.rda |only man/Freiburg1.Rd |only man/Freiburg2.Rd |only man/REAT-package.Rd | 5 +- man/converse.Rd |only man/cv.Rd | 2 man/disp.Rd | 4 - man/gini.Rd | 14 +++--- man/hansen.Rd |only man/herf.Rd | 4 - man/herf.eq.Rd | 2 man/huff.Rd |only man/krugman.spec.Rd | 2 man/locq.Rd | 10 ++-- man/portfolio.Rd | 10 ++-- man/reilly.Rd |only man/reilly.lambda.Rd |only man/shift.Rd | 11 ++++- 40 files changed, 291 insertions(+), 239 deletions(-)
Title: Read Spectral Data from Foreign Files
Description: Functions for reading and writing foreign files containing
spectral data from spectrometers and their associated software, and output
from simulation models in common use. As well as functions for exchange
of spectral data with other R packages.
Author: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.4 dated 2016-05-24 and 0.4.5 dated 2016-06-18
DESCRIPTION | 17 MD5 | 35 NAMESPACE | 10 NEWS | 16 R/foreign-conversion.r | 397 +++ R/read-libradtran-vesa.r | 6 R/read-oopi-file.r |only build/vignette.rds |binary inst/doc/user-guide.R | 26 inst/doc/user-guide.Rnw | 40 inst/doc/user-guide.pdf | 3724 +++++++++++++++++++---------------- man/colorSpec2mspct.Rd |only man/hyperSpec2mspct.Rd | 43 man/photobiologyInOut-package.Rd | 3 man/read_oo_pidata.Rd |only man/rspec2mspct.Rd | 58 tests/testthat/data-test/spectrum.pi |only tests/testthat/test-foreign.R |only tests/testthat/test-oo.R | 26 vignettes/user-guide-concordance.tex | 11 vignettes/user-guide.Rnw | 40 21 files changed, 2720 insertions(+), 1732 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Provides new statistics to locate and tag peaks and valleys in 2D
plots, a statistics to add a label with the equation of a polynomial fitted
with lm(), or R^2 or adjusted R^2 or information criteria for any model
fitted with function lm(). Additional statistics give access to functions
in package 'broom'. Provides a function for flexibly converting time
series to data frames suitable for plotting with ggplot(). In addition
provides two statistics and two geometries useful for diagnosing what data
are passed to compute_group() and compute_panel() functions and to
geometries.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.2.8 dated 2016-05-22 and 0.2.9 dated 2016-06-18
DESCRIPTION | 23 +++--- MD5 | 32 ++++----- NEWS | 8 ++ R/geom-debug.R | 11 +-- R/ggpmisc.R | 5 + R/stat-fit-broom.R | 136 ++++++++++++++++++++++++++++++++++------- R/stat-fit-residuals.R | 1 R/stat-poly-eq.R | 61 +++++++++++++----- build/vignette.rds |binary inst/doc/examples.R | 91 ++++++++++++++++++++++++++- inst/doc/examples.Rmd | 112 +++++++++++++++++++++++++++++++--- inst/doc/examples.html | 158 ++++++++++++++++++++++++++++++++++++++---------- man/geom_debug.Rd | 5 - man/ggpmisc-package.Rd | 13 ++- man/stat_fit_augment.Rd | 26 ++++++- man/stat_poly_eq.Rd | 8 +- vignettes/examples.Rmd | 112 +++++++++++++++++++++++++++++++--- 17 files changed, 665 insertions(+), 137 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.7.0 dated 2016-06-13 and 1.7.1 dated 2016-06-18
DESCRIPTION | 9 + MD5 | 106 ++++++++++++----------- NAMESPACE | 6 + NEWS.md | 8 + R/RcppExports.R | 24 +++++ R/beta-binomial-distribution.R | 8 + R/beta-negative-binomial-distribution.R | 8 + R/beta-prime-distribution.R |only R/bivariate-normal-distribution.R | 14 ++- R/bivariate-poisson-distribution.R | 6 + R/categorical-distribution.R | 6 - R/dirichlet-distribution.R | 4 R/dirichlet-multinomial-distribution.R |only R/discrete-weibull-distribution.R | 2 R/gamma-poisson-distribution.R | 6 + R/gev-distribution.R | 4 R/gpd-distribution.R | 4 R/logarithmic-series-distribution.R | 4 R/mixture-of-normal-distributions.R | 2 R/mixture-of-poisson-distributions.R | 2 R/power-distribution.R | 2 R/triangular-distribution.R | 2 R/truncated-normal-distribution.R | 4 R/zero-inflated-negative-binomial-distribution.R | 2 man/BetaBinom.Rd | 8 + man/BetaNegBinom.Rd | 8 + man/BetaPrime.Rd |only man/BivNormal.Rd | 15 ++- man/BivPoiss.Rd | 7 + man/Categorical.Rd | 4 man/DirMnom.Rd |only man/Dirichlet.Rd | 4 man/DiscrWeibull.Rd | 2 man/GEV.Rd | 4 man/GPD.Rd | 4 man/GammaPoiss.Rd | 6 + man/LogSeries.Rd | 4 man/NormalMix.Rd | 2 man/PoissonMix.Rd | 2 man/PowerDist.Rd | 2 man/Triangular.Rd | 2 man/TruncNormal.Rd | 4 man/ZINB.Rd | 2 src/RcppExports.cpp | 88 +++++++++++++++++++ src/beta-binomial-distribution.cpp | 5 - src/beta-negative-binomial-distribution.cpp | 5 - src/beta-prime-distribution.cpp |only src/categorical-distribution.cpp | 4 src/dirichlet-multinomial-distribution.cpp |only src/discrete-uniform-distribution.cpp | 12 -- src/gamma-poisson-distribution.cpp | 5 - src/shared.cpp | 2 tests/testthat/test-inappropriate-parameters.R | 16 +++ tests/testthat/test-infinity.R | 4 tests/testthat/test-multivariate-distributions.R | 14 ++- tests/testthat/test-non-negative.R | 1 tests/testthat/test-quantile-functions.R | 3 57 files changed, 352 insertions(+), 120 deletions(-)
Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling
algorithm and related algorithms. The algorithm implementations aim for
computational efficiency using matrix algebra and covariance data. The
package is designed toward Monte Carlo simulations and includes functions
to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>
Diff between matrixpls versions 1.0.0 dated 2016-06-13 and 1.0.1 dated 2016-06-18
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/matrixpls.boot.R | 79 ++++++++++++++++++++++++++++++++++++++++------------- R/matrixpls.util.R | 2 - R/paramEstimator.R | 3 ++ 5 files changed, 72 insertions(+), 28 deletions(-)
Title: Statistical Analyses of De Novo Genetic Variants
Description: An integrated toolset for the analysis of de novo (sporadic)
genetic sequence variants. denovolyzeR implements a mutational model that
estimates the probability of a de novo genetic variant arising in each human
gene, from which one can infer the expected number of de novo variants in a
given population size. Observed variant frequencies can then be compared against
expectation in a Poisson framework. denovolyzeR provides a suite of functions
to implement these analyses for the interpretation of de novo variation in human
disease.
Author: James Ware [aut, cre],
Jason Homsy [ctb],
Kaitlin Samocha [ctb]
Maintainer: James Ware <j.ware@imperial.ac.uk>
Diff between denovolyzeR versions 0.1.0 dated 2015-04-09 and 0.1.1 dated 2016-06-18
denovolyzeR-0.1.0/denovolyzeR/R/fmrpGenes.doc.R |only denovolyzeR-0.1.1/denovolyzeR/DESCRIPTION | 25 +- denovolyzeR-0.1.1/denovolyzeR/MD5 | 37 ++- denovolyzeR-0.1.1/denovolyzeR/NAMESPACE | 3 denovolyzeR-0.1.1/denovolyzeR/R/FMRPgenes.doc.R |only denovolyzeR-0.1.1/denovolyzeR/R/autismDeNovos.doc.R | 1 denovolyzeR-0.1.1/denovolyzeR/R/denovolyze.R | 9 denovolyzeR-0.1.1/denovolyzeR/build/vignette.rds |binary denovolyzeR-0.1.1/denovolyzeR/inst/CITATION |only denovolyzeR-0.1.1/denovolyzeR/inst/doc/denovolyzeR_intro.R | 9 denovolyzeR-0.1.1/denovolyzeR/inst/doc/denovolyzeR_intro.Rmd | 25 +- denovolyzeR-0.1.1/denovolyzeR/inst/doc/denovolyzeR_intro.html | 93 +++++----- denovolyzeR-0.1.1/denovolyzeR/man/PermuteMultiHits.Rd | 2 denovolyzeR-0.1.1/denovolyzeR/man/autismDeNovos.Rd | 5 denovolyzeR-0.1.1/denovolyzeR/man/denovolyze.Rd | 10 - denovolyzeR-0.1.1/denovolyzeR/man/denovolyzeMultiHits.Rd | 13 - denovolyzeR-0.1.1/denovolyzeR/man/denovolyzeR.Rd | 2 denovolyzeR-0.1.1/denovolyzeR/man/fmrpGenes.Rd | 7 denovolyzeR-0.1.1/denovolyzeR/man/parseInput.Rd | 2 denovolyzeR-0.1.1/denovolyzeR/man/viewProbabilityTable.Rd | 2 denovolyzeR-0.1.1/denovolyzeR/vignettes/denovolyzeR_intro.Rmd | 25 +- 21 files changed, 147 insertions(+), 123 deletions(-)
Title: Common Infrastructure for Extensions of Exponential Random Graph
Models
Description: Datasets and definitions of generic functions used in dependencies of the 'xergm' package.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between xergm.common versions 1.7.3 dated 2016-06-13 and 1.7.4 dated 2016-06-18
DESCRIPTION | 15 ++++--- MD5 | 14 +++---- NAMESPACE | 34 +++++++---------- R/preprocess.R | 99 ++++++++++++++++++++++++++++++++++++++++++++------- data/alliances.RData |binary data/chemnet.rda |binary data/knecht.rda |binary man/adjust.Rd | 43 ++++++++++++++++++++++ 8 files changed, 160 insertions(+), 45 deletions(-)
Title: Analyze System Scalability with the Universal Scalability Law
Description: The Universal Scalability Law is a model to predict hardware and
software scalability. It uses system capacity as a function of load to
forecast the scalability for the system.
Author: Neil J. Gunther [aut],
Stefan Moeding [aut, cre]
Maintainer: Stefan Moeding <stm@moeding.net>
Diff between usl versions 1.5.0 dated 2016-02-25 and 1.6.0 dated 2016-06-18
DESCRIPTION | 10 MD5 | 21 - NEWS | 7 R/confint.R | 11 README.md | 2 build/vignette.rds |binary inst/doc/usl.R | 224 +++++------------- inst/doc/usl.Rnw | 541 +++++++++++++++++++++++++++----------------- inst/doc/usl.pdf |binary man/confint-USL-method.Rd | 5 vignettes/usl-orausl2-1.pdf |only vignettes/usl.Rnw | 541 +++++++++++++++++++++++++++----------------- 12 files changed, 762 insertions(+), 600 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.5-3 dated 2016-03-16 and 0.5-4 dated 2016-06-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/SDMXConceptScheme-methods.R | 2 +- R/SDMXDataStructure-methods.R | 2 +- R/SDMXDataStructures-methods.R | 14 +++++++++----- R/SDMXServiceProvider-methods.R | 25 ++++++++++++++++++++++++- R/readSDMX.R | 37 ++++++++++++++++--------------------- R/rsdmx.R | 4 ++-- README.md | 2 +- inst/doc/quickstart.html | 33 +++++++++++++++------------------ man/rsdmx.Rd | 4 ++-- tests/testthat/test_Main_Helpers.R | 35 +++++++++++++++++++++++++++++++++++ 12 files changed, 121 insertions(+), 67 deletions(-)
Title: Convex Switching Systems
Description: The numerical treatment of optimal switching problems in a finite time setting when the state evolves as a controlled Markov chain consisting of a uncontrolled continuous component following linear dynamics and a controlled Markov chain taking values in a finite set. The reward functions are assumed to be convex and Lipschitz continuous in the continuous state. The action set is finite.
Author: Juri Hinz and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Diff between rcss versions 1.0 dated 2016-05-29 and 1.1 dated 2016-06-18
DESCRIPTION | 10 ++++++---- MD5 | 28 ++++++++++++++-------------- src/accelerated.cpp | 2 ++ src/bellman_accelerated.cpp | 2 ++ src/bellman_optimal.cpp | 2 ++ src/bellman_optimal2.cpp | 2 ++ src/duality.cpp | 1 - src/expected_accelerated.cpp | 2 ++ src/fast.cpp | 2 ++ src/fast_martingale.cpp | 2 ++ src/martingale.cpp | 2 ++ src/path.cpp | 2 ++ src/slow.cpp | 2 ++ src/stochastic_grid.cpp | 2 ++ src/test_policy.cpp | 4 ++-- 15 files changed, 44 insertions(+), 21 deletions(-)
Title: Functional Programming Tools
Description: Make your pure functions purr with the 'purrr' package. This
package completes R's functional programming tools with missing features
present in other programming languages.
Author: Hadley Wickham [aut, cre],
Lionel Henry [ctb],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between purrr versions 0.2.1 dated 2016-02-12 and 0.2.2 dated 2016-06-18
DESCRIPTION | 8 +++--- MD5 | 44 +++++++++++++++++++------------------- NAMESPACE | 2 + NEWS.md | 11 +++++++++ R/invoke.R | 39 +++++++++++++++++++++------------ R/map.R | 6 ++--- R/partial.R | 4 +-- R/reduce.R | 14 ++++++++++-- R/rows.R | 2 - R/set_names.R | 2 - R/transpose.R | 2 - R/utils.R | 42 ++++++++++++++---------------------- R/when.R | 2 - README.md | 2 - man/as_function.Rd | 2 - man/invoke.Rd | 19 ++++++++++------ man/map.Rd | 4 +-- man/partial.Rd | 4 +-- man/transpose.Rd | 2 - man/when.Rd | 2 - src/extract.c |only tests/testthat/test-as-function.R | 36 +++++++++++++++++++++++++++++++ tests/testthat/test-invoke.R | 21 ++++++++++++++++++ tests/testthat/test-reduce.R |only 24 files changed, 180 insertions(+), 90 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.6 dated 2015-08-24 and 1.0.7 dated 2016-06-18
mvMORPH-1.0.6/mvMORPH/src/time_root_mvmorph.c |only mvMORPH-1.0.6/mvMORPH/src/weight-matrix-simmap.c |only mvMORPH-1.0.6/mvMORPH/vignettes/tutorial_mvMORPH.html |only mvMORPH-1.0.7/mvMORPH/DESCRIPTION | 16 mvMORPH-1.0.7/mvMORPH/MD5 | 106 + mvMORPH-1.0.7/mvMORPH/NAMESPACE | 21 mvMORPH-1.0.7/mvMORPH/R/estim.r |only mvMORPH-1.0.7/mvMORPH/R/fun.r | 679 ++++++++++- mvMORPH-1.0.7/mvMORPH/R/mvBM.r | 934 +++++++++++----- mvMORPH-1.0.7/mvMORPH/R/mvBMTS.r |only mvMORPH-1.0.7/mvMORPH/R/mvEB.r | 149 ++ mvMORPH-1.0.7/mvMORPH/R/mvLLIK.r | 8 mvMORPH-1.0.7/mvMORPH/R/mvOU.r | 517 +++++--- mvMORPH-1.0.7/mvMORPH/R/mvOUTS.r |only mvMORPH-1.0.7/mvMORPH/R/mvSHIFT.r | 341 ++++- mvMORPH-1.0.7/mvMORPH/R/mvSIM.r | 328 ++++- mvMORPH-1.0.7/mvMORPH/R/mvmorphPrecalc.r | 15 mvMORPH-1.0.7/mvMORPH/R/testLRT.r | 75 + mvMORPH-1.0.7/mvMORPH/R/utils.r |only mvMORPH-1.0.7/mvMORPH/R/zzz.r |only mvMORPH-1.0.7/mvMORPH/README.md | 38 mvMORPH-1.0.7/mvMORPH/build/vignette.rds |binary mvMORPH-1.0.7/mvMORPH/inst/CITATION | 6 mvMORPH-1.0.7/mvMORPH/inst/doc/How_to_use_mvMORPH.R |only mvMORPH-1.0.7/mvMORPH/inst/doc/How_to_use_mvMORPH.Rmd |only mvMORPH-1.0.7/mvMORPH/inst/doc/How_to_use_mvMORPH.pdf |only mvMORPH-1.0.7/mvMORPH/inst/doc/tutorial_mvMORPH.R | 52 mvMORPH-1.0.7/mvMORPH/inst/doc/tutorial_mvMORPH.Rmd | 65 - mvMORPH-1.0.7/mvMORPH/inst/doc/tutorial_mvMORPH.pdf |binary mvMORPH-1.0.7/mvMORPH/man/LRT.Rd | 2 mvMORPH-1.0.7/mvMORPH/man/aicw.Rd |only mvMORPH-1.0.7/mvMORPH/man/estim.Rd |only mvMORPH-1.0.7/mvMORPH/man/halflife.Rd | 8 mvMORPH-1.0.7/mvMORPH/man/mv.Precalc.Rd | 53 mvMORPH-1.0.7/mvMORPH/man/mvBM.Rd | 104 + mvMORPH-1.0.7/mvMORPH/man/mvEB.Rd | 36 mvMORPH-1.0.7/mvMORPH/man/mvLL.Rd | 45 mvMORPH-1.0.7/mvMORPH/man/mvMORPH-package.Rd | 12 mvMORPH-1.0.7/mvMORPH/man/mvOU.Rd | 130 +- mvMORPH-1.0.7/mvMORPH/man/mvOUTS.Rd |only mvMORPH-1.0.7/mvMORPH/man/mvRWTS.Rd |only mvMORPH-1.0.7/mvMORPH/man/mvSHIFT.Rd | 85 - mvMORPH-1.0.7/mvMORPH/man/mvSIM.Rd | 67 - mvMORPH-1.0.7/mvMORPH/man/stationary.Rd | 12 mvMORPH-1.0.7/mvMORPH/src/chol_rpf_row.c | 43 mvMORPH-1.0.7/mvMORPH/src/chol_rpf_univ.c | 37 mvMORPH-1.0.7/mvMORPH/src/covar-matrix-simmap.c | 148 ++ mvMORPH-1.0.7/mvMORPH/src/covar.h | 4 mvMORPH-1.0.7/mvMORPH/src/functions_complex.h |only mvMORPH-1.0.7/mvMORPH/src/givens.c | 12 mvMORPH-1.0.7/mvMORPH/src/mvmorph-covar-mat.c | 142 ++ mvMORPH-1.0.7/mvMORPH/src/mvmorph-covar-ou-sparse.c | 141 ++ mvMORPH-1.0.7/mvMORPH/src/mvmorph-covar-ou.c | 56 mvMORPH-1.0.7/mvMORPH/src/mvmorph.h | 2 mvMORPH-1.0.7/mvMORPH/src/mvmorph_ou_mat_rpf.c | 105 + mvMORPH-1.0.7/mvMORPH/src/pic_loglik_mvmorph.c | 129 +- mvMORPH-1.0.7/mvMORPH/src/time_serie_expectation.c |only mvMORPH-1.0.7/mvMORPH/src/utils.c |only mvMORPH-1.0.7/mvMORPH/src/weight-matrix-mvmorph.c | 87 + mvMORPH-1.0.7/mvMORPH/tests/tests.r | 335 +++++ mvMORPH-1.0.7/mvMORPH/vignettes/How_to_use_mvMORPH.Rmd |only mvMORPH-1.0.7/mvMORPH/vignettes/How_to_use_mvMORPH.html |only mvMORPH-1.0.7/mvMORPH/vignettes/constraints.png |only mvMORPH-1.0.7/mvMORPH/vignettes/root.png |only mvMORPH-1.0.7/mvMORPH/vignettes/tutorial_mvMORPH.Rmd | 65 - 65 files changed, 4100 insertions(+), 1110 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: Provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm or numerical integration. PACE is useful for the analysis of data that have been generated by a sample of underlying (but usually not fully observed) random trajectories. It does not rely on pre-smoothing of trajectories, which is problematic if functional data are sparsely sampled. PACE provides options for functional regression and correlation, for Longitudinal Data Analysis, the analysis of stochastic processes from samples of realized trajectories, and for the analysis of underlying dynamics. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Xiongtao Dai,
Pantelis Z. Hadjipantelis,
Hao Ji,
Hans-Georg Mueller,
Jane-Ling Wang
Maintainer: Pantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
Diff between fdapace versions 0.1.1 dated 2016-03-14 and 0.2.0 dated 2016-06-18
fdapace-0.1.1/fdapace/R/AdjustBW1.R |only fdapace-0.1.1/fdapace/inst/doc/fdapaceVignette.Rnw |only fdapace-0.1.1/fdapace/inst/doc/fdapaceVignette.pdf |only fdapace-0.1.1/fdapace/man/HandleNumericsAndNAN.Rd |only fdapace-0.1.1/fdapace/vignettes/fdapaceVignette.Rnw |only fdapace-0.2.0/fdapace/DESCRIPTION | 14 fdapace-0.2.0/fdapace/MD5 | 192 ++-- fdapace-0.2.0/fdapace/NAMESPACE | 59 + fdapace-0.2.0/fdapace/NEWS |only fdapace-0.2.0/fdapace/R/BwNN.R |only fdapace-0.2.0/fdapace/R/CheckAndCreateCOPoptions.R |only fdapace-0.2.0/fdapace/R/CheckData.R | 4 fdapace-0.2.0/fdapace/R/CheckOptions.R | 14 fdapace-0.2.0/fdapace/R/CheckSVDOptions.R |only fdapace-0.2.0/fdapace/R/ConvertSupport.R | 27 fdapace-0.2.0/fdapace/R/CreateBWPlot.R | 4 fdapace-0.2.0/fdapace/R/CreateCovPlot.R | 19 fdapace-0.2.0/fdapace/R/CreateDesignPlot.R | 40 fdapace-0.2.0/fdapace/R/CreateDiagnosticsPlot.R | 6 fdapace-0.2.0/fdapace/R/CreateFuncBoxPlot.R | 10 fdapace-0.2.0/fdapace/R/CreateModeOfVarPlot.R | 41 fdapace-0.2.0/fdapace/R/CreateOutliersPlot.R | 378 ++++---- fdapace-0.2.0/fdapace/R/CreatePathPlot.R | 36 fdapace-0.2.0/fdapace/R/CreateScreePlot.R | 6 fdapace-0.2.0/fdapace/R/FCReg.R | 463 +++++++--- fdapace-0.2.0/fdapace/R/FClust.R |only fdapace-0.2.0/fdapace/R/FPCA.R | 94 +- fdapace-0.2.0/fdapace/R/FPCAder.R | 2 fdapace-0.2.0/fdapace/R/FSVD.R |only fdapace-0.2.0/fdapace/R/FVPA.R | 40 fdapace-0.2.0/fdapace/R/GCVLwls2DV2.R | 200 ++-- fdapace-0.2.0/fdapace/R/GenerateFunctionalData.R |only fdapace-0.2.0/fdapace/R/GetBinnedDataset.R | 9 fdapace-0.2.0/fdapace/R/GetCEScores.R | 6 fdapace-0.2.0/fdapace/R/GetCovDense.R | 3 fdapace-0.2.0/fdapace/R/GetCrCovYX.R | 180 ++- fdapace-0.2.0/fdapace/R/GetCrCovYZ.R | 25 fdapace-0.2.0/fdapace/R/GetEigenAnalysisResults.R | 3 fdapace-0.2.0/fdapace/R/GetLogLik.R | 39 fdapace-0.2.0/fdapace/R/GetMeanDense.R | 2 fdapace-0.2.0/fdapace/R/GetMinb.R | 90 - fdapace-0.2.0/fdapace/R/GetNormalisedSample.R | 18 fdapace-0.2.0/fdapace/R/GetRawCov.R | 2 fdapace-0.2.0/fdapace/R/GetRawCrCovFuncFunc.R | 4 fdapace-0.2.0/fdapace/R/GetSmoothedCovarSurface.R | 38 fdapace-0.2.0/fdapace/R/GetSmoothedMeanCurve.R | 5 fdapace-0.2.0/fdapace/R/HandleNumericsAndNAN.R | 34 fdapace-0.2.0/fdapace/R/IsRegular.R | 2 fdapace-0.2.0/fdapace/R/Lwls2D.R | 68 - fdapace-0.2.0/fdapace/R/Lwls2Dv1.R |only fdapace-0.2.0/fdapace/R/MakeFPCAInputs.R | 4 fdapace-0.2.0/fdapace/R/MakeGPFunctionalData.R |only fdapace-0.2.0/fdapace/R/Minb.R | 29 fdapace-0.2.0/fdapace/R/RcppExports.R | 12 fdapace-0.2.0/fdapace/R/SelectK.R | 18 fdapace-0.2.0/fdapace/R/SetOptions.R | 55 - fdapace-0.2.0/fdapace/R/SetSVDOptions.R |only fdapace-0.2.0/fdapace/R/Sparsify.R | 10 fdapace-0.2.0/fdapace/R/TruncateObs.R | 10 fdapace-0.2.0/fdapace/R/Wiener.R | 6 fdapace-0.2.0/fdapace/R/fitted.FPCA.R | 3 fdapace-0.2.0/fdapace/R/kCFC.R |only fdapace-0.2.0/fdapace/R/medfly25.R | 3 fdapace-0.2.0/fdapace/R/oldFCReg.R |only fdapace-0.2.0/fdapace/R/pkgname.R | 10 fdapace-0.2.0/fdapace/R/print.FPCA.R | 4 fdapace-0.2.0/fdapace/R/print.FSVD.R |only fdapace-0.2.0/fdapace/build/vignette.rds |binary fdapace-0.2.0/fdapace/inst/doc/fdapaceVignetteKnitr.R |only fdapace-0.2.0/fdapace/inst/doc/fdapaceVignetteKnitr.Rnw |only fdapace-0.2.0/fdapace/inst/doc/fdapaceVignetteKnitr.pdf |only fdapace-0.2.0/fdapace/man/BwNN.Rd |only fdapace-0.2.0/fdapace/man/ConvertSupport.Rd |only fdapace-0.2.0/fdapace/man/CreateBWPlot.Rd | 2 fdapace-0.2.0/fdapace/man/CreateCovPlot.Rd | 7 fdapace-0.2.0/fdapace/man/CreateDesignPlot.Rd | 6 fdapace-0.2.0/fdapace/man/CreateDiagnosticsPlot.Rd | 2 fdapace-0.2.0/fdapace/man/CreateFuncBoxPlot.Rd | 2 fdapace-0.2.0/fdapace/man/CreateModeOfVarPlot.Rd | 9 fdapace-0.2.0/fdapace/man/CreateOutliersPlot.Rd | 19 fdapace-0.2.0/fdapace/man/CreatePathPlot.Rd | 10 fdapace-0.2.0/fdapace/man/CreateScreePlot.Rd | 2 fdapace-0.2.0/fdapace/man/FCReg.Rd | 66 + fdapace-0.2.0/fdapace/man/FClust.Rd |only fdapace-0.2.0/fdapace/man/FPCA.Rd | 24 fdapace-0.2.0/fdapace/man/FPCAder.Rd | 2 fdapace-0.2.0/fdapace/man/FSVD.Rd |only fdapace-0.2.0/fdapace/man/FVPA.Rd | 17 fdapace-0.2.0/fdapace/man/GetCrCovYX.Rd | 11 fdapace-0.2.0/fdapace/man/GetCrCovYZ.Rd | 12 fdapace-0.2.0/fdapace/man/GetNormalisedSample.Rd | 7 fdapace-0.2.0/fdapace/man/Lwls2D.Rd | 5 fdapace-0.2.0/fdapace/man/Lwls2Dv1.Rd |only fdapace-0.2.0/fdapace/man/MakeFPCAInputs.Rd | 4 fdapace-0.2.0/fdapace/man/MakeGPFunctionalData.Rd |only fdapace-0.2.0/fdapace/man/SelectK.Rd | 8 fdapace-0.2.0/fdapace/man/Sparsify.Rd | 4 fdapace-0.2.0/fdapace/man/fitted.FPCA.Rd | 3 fdapace-0.2.0/fdapace/man/kCFC.Rd |only fdapace-0.2.0/fdapace/man/oldFCReg.Rd |only fdapace-0.2.0/fdapace/man/print.FPCA.Rd | 3 fdapace-0.2.0/fdapace/man/print.FSVD.Rd |only fdapace-0.2.0/fdapace/src/CPPlwls1d.cpp | 2 fdapace-0.2.0/fdapace/src/GetIndCEScoresCPP.cpp | 10 fdapace-0.2.0/fdapace/src/GetIndCEScoresCPPnewInd.cpp | 40 fdapace-0.2.0/fdapace/src/RcppExports.cpp | 49 + fdapace-0.2.0/fdapace/src/Rmullwlsk.cpp | 9 fdapace-0.2.0/fdapace/src/RmullwlskCC.cpp | 7 fdapace-0.2.0/fdapace/src/RmullwlskCCsort2.cpp |only fdapace-0.2.0/fdapace/src/RmullwlskUniversal.cpp |only fdapace-0.2.0/fdapace/src/cumtrapzRcpp.cpp |only fdapace-0.2.0/fdapace/vignettes/Sweavel.sty |only fdapace-0.2.0/fdapace/vignettes/fdapaceVignetteKnitr-concordance.tex |only fdapace-0.2.0/fdapace/vignettes/fdapaceVignetteKnitr.Rnw |only fdapace-0.2.0/fdapace/vignettes/roxygen.bib | 11 115 files changed, 1642 insertions(+), 1052 deletions(-)
Title: Functions for Thermal Comfort Research
Description: Functions to calculate various common and less common thermal comfort indices, convert physical variables, and evaluate the performance of thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>
Diff between comf versions 0.1.3 dated 2016-06-17 and 0.1.4 dated 2016-06-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 7 +++++++ R/ComfortIndices.r | 6 ++++-- R/fct2Node.r | 13 +++++++++---- man/calc2Node.Rd | 8 ++++++++ man/comf-package.Rd | 4 ++-- 7 files changed, 39 insertions(+), 17 deletions(-)