Title: Lex and Yacc
Description: R implementation of the common parsing tools lex and yacc.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.0.3 dated 2016-11-26 and 1.1.0 dated 2016-12-04
rly-1.0.3/rly/tests/testthat/parser.out |only rly-1.1.0/rly/DESCRIPTION | 8 rly-1.1.0/rly/MD5 | 16 - rly-1.1.0/rly/NEWS.md | 15 + rly-1.1.0/rly/R/lex.R | 13 - rly-1.1.0/rly/R/yacc.R | 225 +++++++++++++++++----- rly-1.1.0/rly/README.md | 86 ++++++++ rly-1.1.0/rly/tests/testthat/test.calclex2.R |only rly-1.1.0/rly/tests/testthat/test.lex_state_try.R | 2 rly-1.1.0/rly/tests/testthat/test.yacc_error5.R | 106 +++++----- 10 files changed, 361 insertions(+), 110 deletions(-)
Title: Censored Spatial Models
Description: Fits linear regression models for censored spatial data. Provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. Also offers graphical tools for assessing the fitted model.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between CensSpatial versions 1.1 dated 2016-10-17 and 1.2 dated 2016-12-04
DESCRIPTION | 10 +++++----- MD5 | 13 ++++++++----- NAMESPACE | 2 +- R/atypicalfin.R |only R/atypicalprin.R |only R/derivQfunprin.R | 1 + R/localinfmeasprin.R | 7 +++++-- R/predgraphicsfin.R | 2 +- man/atypical.Rd |only 9 files changed, 21 insertions(+), 14 deletions(-)
Title: Covariance Matrix Adaptation Evolution Strategy
Description: Pure R implementation of the Covariance Matrix Adaptation -
Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between cmaesr versions 1.0.2 dated 2016-08-04 and 1.0.3 dated 2016-12-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 +++- R/cmaes.R | 2 -- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.10.3 dated 2016-05-13 and 2.10.4 dated 2016-12-04
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++------------------- NAMESPACE | 1 NEWS | 22 +++++++++++ R/clone.R | 12 +++--- R/derivedMS.R | 27 +++++++------ R/empirical.R | 84 +++++++++++++++++++++++++++++++++++++++++++ R/esa.R | 50 +++++++++++++++++++------ R/make.capthist.R | 8 +++- R/make.grid.R | 3 + R/make.mask.R | 3 + R/mash.r | 4 +- R/methods.R | 14 ++++++- R/model.average.R | 6 +++ R/par.secr.fit.R | 12 ++++-- R/secr.design.MS.R | 73 +++++++++++++++++++++++-------------- R/secr.fit.R | 27 ------------- R/secrloglik.R | 1 R/sim.popn.R | 65 +++++++++++++++++++-------------- R/utility.R | 29 ++++++++------ inst/CITATION | 2 - inst/doc/secr-datainput.Rmd | 7 ++- inst/doc/secr-datainput.pdf |binary inst/doc/secr-manual.pdf |binary inst/doc/secr-overview.Rmd | 61 +++++++++++++++---------------- inst/doc/secr-overview.pdf |binary man/make.traps.Rd | 2 - man/par.secr.fit.Rd | 2 - man/randomHabitat.Rd | 2 - man/read.traps.Rd | 17 +++++++- man/secr-package.Rd | 8 ++-- man/sim.popn.Rd | 7 ++- man/smooths.Rd | 4 +- man/utility.Rd | 2 - src/secr.c | 3 + src/sighting.c | 14 +++---- vignettes/secr-datainput.Rmd | 7 ++- vignettes/secr-overview.Rmd | 61 +++++++++++++++---------------- 38 files changed, 459 insertions(+), 263 deletions(-)
Title: Proportional Habitat Use Assessment
Description: Assessment of habitat selection by means of the permutation-based combination of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>). To exemplify the application of this procedure, habitat selection is assessed for a population of European Brown Hares settled in central Italy.
Author: Caterina Pisani [aut, cre]
Lorenzo Fattorini [aut]
Francesco Riga [aut]
Marco Zaccaroni [aut]
Maintainer: Caterina Pisani <caterina.pisani@unisi.it>
Diff between phuassess versions 1.0 dated 2016-10-22 and 1.1 dated 2016-12-04
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/phuassess.Rd | 28 ++++++++++++++++++---------- 3 files changed, 24 insertions(+), 16 deletions(-)
Title: Monitor the Total and Peak RAM Used by an Expression or Function
Description: When working with big datasets, RAM conservation is critically
important. However, it is not always enough to just monitor the
size of the objects created. So-called "copy-on-modify" behavior,
characteristic of R, means that some expressions or functions may
require an unexpectedly large amount of RAM overhead. For example,
replacing a single value in a matrix duplicates that matrix in the
backend, making this task require twice as much RAM as that used
by the matrix itself. This package makes it easy to monitor the total
and peak RAM used so that developers can quickly identify and
eliminate RAM hungry code.
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between peakRAM versions 1.0.0 dated 2016-07-29 and 1.0.1 dated 2016-12-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/peakRAM.R | 2 +- build/vignette.rds |binary inst/doc/peakRAM.html | 14 +++++++------- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Data Preparation, Estimation and Prediction in Multi-State
Models
Description: Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco, with contributions by
Ronald Geskus
Maintainer: Hein Putter <H.Putter@lumc.nl>
Diff between mstate versions 0.2.9 dated 2016-02-28 and 0.2.10 dated 2016-12-04
ChangeLog | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/cuminc.R | 38 ++++++++++++++++++++++---------------- R/misc.R | 3 ++- R/msfit.R | 2 +- build/vignette.rds |binary inst/doc/Tutorial.pdf |binary man/mstate-package.Rd | 6 ++---- 9 files changed, 45 insertions(+), 36 deletions(-)
Title: A LazyData Facility
Description: Supplies a LazyData facility for packages which have data
sets but do not provide LazyData: true. A single function is
is included, requireData, which is a drop-in replacement for
base::require, but carrying the additional
functionality. By default, it suppresses package
startup messages as well. See argument 'reallyQuitely'.
Author: Bill Venables
Maintainer: Bill Venables <bill.venables@gmail.com>
Diff between lazyData versions 1.0.3 dated 2014-01-29 and 1.1.0 dated 2016-12-04
DESCRIPTION | 10 +-- MD5 | 6 - R/requireData.R | 152 ++++++++++++++++++++++++------------------------ man/lazyData-package.Rd | 11 +-- 4 files changed, 91 insertions(+), 88 deletions(-)
Title: Visualizing Asymmetric Data
Description: Models and methods for the visualization for asymmetric data. A matrix is asymmetric if the number of rows equals the number of columns, and these rows and columns refer to the same set of objects. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. The slide-vector model, a heat map, and the decomposition of asymmetry are provided for the analysis of these tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 1.1.2 dated 2016-11-11 and 1.1.3 dated 2016-12-04
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- R/decomposition.R | 10 ++++++---- R/slidevector.R | 4 ++-- build/partial.rdb |binary inst/doc/asymmetry.R | 5 ++++- inst/doc/asymmetry.Rmd | 14 +++++++++----- inst/doc/asymmetry.html | 29 +++++++++++++++++------------ inst/java/asymmetry.jar |binary man/decomposition.Rd | 6 +++--- man/plot.slidevector.Rd | 2 +- man/print.slidevector.Rd | 10 +--------- man/slidevector.Rd | 7 ++++--- man/summary.decomposition.Rd | 2 +- man/summary.slidevector.Rd | 2 +- vignettes/asymmetry.Rmd | 14 +++++++++----- 16 files changed, 78 insertions(+), 67 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Leonardo de Oliveira Martins [aut],
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.0.4 dated 2016-06-21 and 2.1.1 dated 2016-12-04
DESCRIPTION | 22 + MD5 | 124 ++++----- NAMESPACE | 26 + NEWS | 36 ++ R/Densi.R | 231 ----------------- R/RcppExports.R |only R/ancestral_pml.R | 32 +- R/bootstrap.R | 55 ++-- R/distSeq.R | 97 ------- R/distTree.R | 104 +++---- R/fitch.R | 3 R/networx.R | 120 ++++++-- R/parsimony.R | 46 ++- R/phyDat.R | 390 ++++++++++++++--------------- R/phylo.R | 36 +- R/sankoff.R | 2 R/simSeq.R | 17 + R/superTree.R |only R/treeManipulation.R | 65 +++- R/treedist.R | 154 ++++++++++- R/zzz.R | 5 README.md | 6 build/vignette.rds |binary inst/doc/Ancestral.pdf |binary inst/doc/IntertwiningTreesAndNetworks.html | 6 inst/doc/Networx.Rmd | 2 inst/doc/Networx.html | 16 - inst/doc/Trees.pdf |binary inst/doc/phangorn-specials.pdf |binary man/SOWH.test.Rd | 2 man/ancestral.pml.Rd | 2 man/as.splits.Rd | 9 man/densiTree.Rd | 7 man/dist.p.Rd | 2 man/hadamard.Rd | 14 - man/maxCladeCred.Rd | 2 man/midpoint.Rd | 2 man/modelTest.Rd | 4 man/nni.Rd | 2 man/parsimony.Rd | 5 man/phyDat.Rd | 19 + man/plot.networx.Rd | 2 man/pml.Rd | 4 man/pml.fit.Rd | 31 -- man/simSeq.Rd | 5 man/superTree.Rd | 22 + man/treedist.Rd | 20 + src/RcppExports.cpp |only src/dist.c | 9 src/fitch.c | 18 - src/ml.c | 51 ++- src/phangorn.c | 25 + src/phangorn_help.cpp |only src/sankoff.c | 11 src/sprdist.c |only tests/testthat/test_dist_tree.R |only tests/testthat/test_distances.R | 22 + tests/testthat/test_hadamard.R |only tests/testthat/test_parsimony.R | 34 ++ tests/testthat/test_phyDat.R | 78 +++++ tests/testthat/test_pml.R | 93 ++++++ tests/testthat/test_splits.R | 39 ++ tests/testthat/test_superTree.R |only tests/testthat/test_treeManipulation.R | 31 ++ tests/testthat/test_treedist.R | 27 ++ vignettes/Networx.Rmd | 2 vignettes/phangorn.bib | 79 +++++ 67 files changed, 1342 insertions(+), 926 deletions(-)