Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-01 1.2
2009-10-14 1.01
2008-12-23 1.0
Title: Robust data-driven statistical inference in
Regression-Discontinuity designs
Diff between rdrobust versions 0.5 dated 2014-06-08 and 0.6 dated 2014-06-17
Description: Regression-discontinuity (RD) designs are quasi-experimental
research designs popular in social, behavioral and natural sciences.
The RD design is usually employed to study the (local) causal effect
of a treatment, intervention or policy. This package provides tools
for data-driven graphical and analytical statistical inference in RD
designs: rdrobust to construct local-polynomial point estimators
and robust confidence intervals for average treatment effects at the
cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform
bandwidth selection for the different procedures implemented, and
rdbinselect to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico
Maintainer: Sebastian Calonico
DESCRIPTION | 8 -
MD5 | 14 +-
R/functions.R | 1
R/rdbinselect.R | 1
R/rdbwselect.R | 237 ++++++++++++++++++++++++------------------------
R/rdrobust.R | 15 +--
man/rdrobust-package.Rd | 4
man/rdrobust.Rd | 10 +-
8 files changed, 153 insertions(+), 137 deletions(-)
Title: Parameter space exploration with Latin Hypercubes
Diff between pse versions 0.3.3 dated 2014-03-23 and 0.3.4 dated 2014-06-17
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom
Changelog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
R/plotcv.R | 9 ---------
R/plotecdf.R | 8 +++++---
R/plotprcc.R | 11 ++++++-----
R/plotscatter.R | 13 ++++++++++---
inst/doc/multiple.pdf |binary
inst/doc/pse_tutorial.Rnw | 4 ++--
inst/doc/pse_tutorial.pdf |binary
man/plotecdf.Rd | 13 +++++++++++--
man/plotscatter.Rd | 10 +++++++++-
vignettes/pse_tutorial.Rnw | 4 ++--
13 files changed, 64 insertions(+), 43 deletions(-)
Title: R Code for mark-recapture analysis
Diff between marked versions 1.1.3 dated 2013-11-23 and 1.1.6 dated 2014-06-17
Description: This package provides a framework for handling
data and analysis for mark-recapture.
Author: Jeff Laake
Maintainer: Jeff Laake
marked-1.1.3/marked/R/probitMsCJS.R |only
marked-1.1.3/marked/inst/doc/marked.pdf |only
marked-1.1.3/marked/man/probitMsCJS.Rd |only
marked-1.1.3/marked/vignettes/marked.Rnw |only
marked-1.1.6/marked/DESCRIPTION | 32
marked-1.1.6/marked/MD5 | 177 +--
marked-1.1.6/marked/NAMESPACE | 7
marked-1.1.6/marked/NEWS | 44
marked-1.1.6/marked/R/HMMLikelihood.r | 41
marked-1.1.6/marked/R/Observation_functions.r | 46
marked-1.1.6/marked/R/Transition_functions.r | 61 +
marked-1.1.6/marked/R/cjs.R | 702 ++++++-------
marked-1.1.6/marked/R/cjs.accumulate.R | 186 +--
marked-1.1.6/marked/R/cjs.initial.R | 82 -
marked-1.1.6/marked/R/compute.real.R | 344 ++++--
marked-1.1.6/marked/R/compute_matrices.r |only
marked-1.1.6/marked/R/create.dm.R | 32
marked-1.1.6/marked/R/create.dmdf.R | 5
marked-1.1.6/marked/R/crm.R | 865 ++++++++--------
marked-1.1.6/marked/R/crm.wrapper.R | 31
marked-1.1.6/marked/R/make.design.data.R | 13
marked-1.1.6/marked/R/marked-package.R | 129 ++
marked-1.1.6/marked/R/mixed.model.r | 5
marked-1.1.6/marked/R/omega.r |only
marked-1.1.6/marked/R/predict.crm.r | 33
marked-1.1.6/marked/R/print.crm.r | 2
marked-1.1.6/marked/R/probitCJS.R | 304 ++++-
marked-1.1.6/marked/R/proc.formula.r | 58 -
marked-1.1.6/marked/R/process.data.R | 1093 ++++++++++-----------
marked-1.1.6/marked/R/set.fixed.R | 6
marked-1.1.6/marked/R/set_mvms.r |only
marked-1.1.6/marked/R/setup.model.R | 29
marked-1.1.6/marked/R/setup.parameters.R | 10
marked-1.1.6/marked/R/simHMM.r | 2
marked-1.1.6/marked/R/zzz.R | 58 -
marked-1.1.6/marked/build |only
marked-1.1.6/marked/data/dipper.rda |binary
marked-1.1.6/marked/data/tagloss.rda |only
marked-1.1.6/marked/inst/doc/markedVignette.R |only
marked-1.1.6/marked/inst/doc/markedVignette.Rnw |only
marked-1.1.6/marked/inst/doc/markedVignette.pdf |only
marked-1.1.6/marked/inst/models.txt | 30
marked-1.1.6/marked/inst/parameters.txt | 77 -
marked-1.1.6/marked/man/HMMLikelihood.Rd | 100 -
marked-1.1.6/marked/man/Phi.mean.Rd | 20
marked-1.1.6/marked/man/R_HMMLikelihood.Rd | 32
marked-1.1.6/marked/man/cjs.Rd | 76 -
marked-1.1.6/marked/man/cjs.accumulate.Rd | 20
marked-1.1.6/marked/man/cjs.hessian.Rd | 14
marked-1.1.6/marked/man/cjs.initial.Rd | 14
marked-1.1.6/marked/man/cjs.lnl.Rd | 36
marked-1.1.6/marked/man/cjs_delta.Rd | 21
marked-1.1.6/marked/man/cjs_dmat.Rd | 24
marked-1.1.6/marked/man/cjs_gamma.Rd | 18
marked-1.1.6/marked/man/compute.real.Rd | 55 -
marked-1.1.6/marked/man/compute_matrices.Rd |only
marked-1.1.6/marked/man/convert.link.to.real.Rd | 31
marked-1.1.6/marked/man/create.dm.Rd | 42
marked-1.1.6/marked/man/create.dmdf.Rd | 472 ++++-----
marked-1.1.6/marked/man/create.fixed.matrix.Rd | 8
marked-1.1.6/marked/man/create.links.Rd | 19
marked-1.1.6/marked/man/crm.Rd | 397 +++----
marked-1.1.6/marked/man/crm.wrapper.Rd | 66 -
marked-1.1.6/marked/man/deriv_inverse.link.Rd | 36
marked-1.1.6/marked/man/dipper.Rd | 99 -
marked-1.1.6/marked/man/fix.parameters.Rd | 14
marked-1.1.6/marked/man/function.wrapper.Rd | 26
marked-1.1.6/marked/man/hmmDemo.Rd | 20
marked-1.1.6/marked/man/inverse.link.Rd | 61 -
marked-1.1.6/marked/man/js.Rd | 73 -
marked-1.1.6/marked/man/js.accumulate.Rd | 20
marked-1.1.6/marked/man/js.hessian.Rd | 14
marked-1.1.6/marked/man/js.lnl.Rd | 32
marked-1.1.6/marked/man/make.design.data.Rd | 110 +-
marked-1.1.6/marked/man/merge_design.covariates.Rd | 74 -
marked-1.1.6/marked/man/mixed.model.admb.Rd | 67 -
marked-1.1.6/marked/man/mscjs.Rd | 60 -
marked-1.1.6/marked/man/omega.Rd |only
marked-1.1.6/marked/man/predict.crm.Rd | 23
marked-1.1.6/marked/man/print.crm.Rd | 22
marked-1.1.6/marked/man/probitCJS.Rd | 34
marked-1.1.6/marked/man/proc.form.Rd | 20
marked-1.1.6/marked/man/process.ch.Rd | 31
marked-1.1.6/marked/man/process.data.Rd | 305 ++---
marked-1.1.6/marked/man/resight.matrix.Rd | 38
marked-1.1.6/marked/man/set.fixed.Rd | 14
marked-1.1.6/marked/man/set.initial.Rd | 8
marked-1.1.6/marked/man/set.scale.Rd | 20
marked-1.1.6/marked/man/set_mvms.Rd |only
marked-1.1.6/marked/man/setup.model.Rd | 65 -
marked-1.1.6/marked/man/setup.parameters.Rd | 101 -
marked-1.1.6/marked/man/simHMM.Rd | 45
marked-1.1.6/marked/man/splitCH.Rd | 31
marked-1.1.6/marked/man/tagloss.Rd |only
marked-1.1.6/marked/man/valid.parameters.Rd | 14
marked-1.1.6/marked/src/cjs1tldmat.f |only
marked-1.1.6/marked/src/cjs1tlgam.f |only
marked-1.1.6/marked/src/cjs2tldmat.f |only
marked-1.1.6/marked/src/cjs2tlgam.f |only
marked-1.1.6/marked/vignettes/markedVignette.Rnw |only
100 files changed, 4032 insertions(+), 3414 deletions(-)
Title: Subdistribution Analysis of Competing Risks
Diff between cmprsk versions 2.2-6 dated 2013-04-17 and 2.2-7 dated 2014-06-17
Description: Estimation, testing and regression modeling of
subdistribution functions in competing risks, as described in Gray
(1988), A class of K-sample tests for comparing the cumulative
incidence of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and
Gray RJ (1999), A proportional hazards model for the subdistribution
of a competing risk, JASA, 94:496-509.
Author: Bob Gray
Maintainer: Bob Gray
DESCRIPTION | 19 +++++++++----------
MD5 | 8 ++++----
NAMESPACE | 8 ++++----
R/cmprsk.R | 14 +++++++-------
man/crr.Rd | 6 +++---
5 files changed, 27 insertions(+), 28 deletions(-)
Title: Nonparametric Item Response Theory
Diff between KernSmoothIRT versions 6.0 dated 2013-09-16 and 6.1 dated 2014-06-17
Description: This package fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools.
Author: Angelo Mazza, Antonio Punzo, Brian McGuire
Maintainer: Brian McGuire
DESCRIPTION | 10 +++++-----
MD5 | 13 +++++++------
NAMESPACE | 31 +++++++++++++++++--------------
R/ksIRT.R | 4 +++-
inst |only
man/KernSmoothIRT-package.Rd | 3 +++
man/ksIRT.Rd | 12 +++++++++---
man/plot.ksIRT.Rd | 6 +++++-
8 files changed, 49 insertions(+), 30 deletions(-)
Title: Sorting and reordering dendrogram nodes.
Diff between dendsort versions 0.2.0 dated 2014-03-14 and 0.2.1 dated 2014-06-17
Description: This package includes functions to optimize ordering of nodes in a dendrogram,
without affecting the meaning of the dendrogram. A dendrogram can be sorted based
on the average distance of subtrees, or based on the smallest distance value.
These sorting methods improve readability and interpretability of tree structure,
especially for tasks such as comparison of different distance measures or linkage
types and identification of tight clusters and outliers. As a result, it also
introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/dendsort.R | 9 +++++----
man/cal_length.Rd | 25 ++++++++++++-------------
man/cal_node_limit.Rd | 15 +++++++--------
man/cal_total_length.Rd | 10 +++++-----
man/dendsort.Rd | 23 +++++++++++------------
man/sort_average.Rd | 14 ++++++++------
man/sort_average_r.Rd | 15 ++++++++-------
man/sort_smallest.Rd | 13 +++++++------
man/sort_smallest_r.Rd | 11 ++++++-----
11 files changed, 83 insertions(+), 80 deletions(-)
Title: Bayesian network structure learning, parameter learning and
inference
Diff between bnlearn versions 3.5 dated 2014-01-23 and 3.6 dated 2014-06-17
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for both discrete and Gaussian networks, along with many score functions
and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari
bnlearn-3.5/bnlearn/R/discretize.R |only
bnlearn-3.5/bnlearn/man/discretize.Rd |only
bnlearn-3.5/bnlearn/src/monte.carlo.c |only
bnlearn-3.6/bnlearn/Changelog | 26
bnlearn-3.6/bnlearn/DESCRIPTION | 8
bnlearn-3.6/bnlearn/MD5 | 213 ++++----
bnlearn-3.6/bnlearn/NAMESPACE | 2
bnlearn-3.6/bnlearn/R/arc.strength.R | 2
bnlearn-3.6/bnlearn/R/backend-indep.R | 57 --
bnlearn-3.6/bnlearn/R/choose.direction.R | 4
bnlearn-3.6/bnlearn/R/ci.test.R | 43 -
bnlearn-3.6/bnlearn/R/cpq.R | 42 -
bnlearn-3.6/bnlearn/R/cv.R | 2
bnlearn-3.6/bnlearn/R/data.preprocessing.R |only
bnlearn-3.6/bnlearn/R/fast-iamb.R | 13
bnlearn-3.6/bnlearn/R/fit.R | 7
bnlearn-3.6/bnlearn/R/foreign-write.R | 65 ++
bnlearn-3.6/bnlearn/R/formula.R | 3
bnlearn-3.6/bnlearn/R/frontend-bn.R | 8
bnlearn-3.6/bnlearn/R/frontend-bootstrap.R | 14
bnlearn-3.6/bnlearn/R/frontend-data.R | 53 +-
bnlearn-3.6/bnlearn/R/frontend-fit.R | 11
bnlearn-3.6/bnlearn/R/frontend-foreign.R | 16
bnlearn-3.6/bnlearn/R/frontend-packages.R | 6
bnlearn-3.6/bnlearn/R/frontend-predict.R | 54 +-
bnlearn-3.6/bnlearn/R/frontend-score.R | 15
bnlearn-3.6/bnlearn/R/frontend-simulation.R | 14
bnlearn-3.6/bnlearn/R/globals.R | 22
bnlearn-3.6/bnlearn/R/graphviz.R | 8
bnlearn-3.6/bnlearn/R/grow-shrink.R | 4
bnlearn-3.6/bnlearn/R/hill-climbing.R | 4
bnlearn-3.6/bnlearn/R/hiton-pc.R | 38 -
bnlearn-3.6/bnlearn/R/incremental-association.R | 13
bnlearn-3.6/bnlearn/R/init.R | 14
bnlearn-3.6/bnlearn/R/inter-iamb.R | 12
bnlearn-3.6/bnlearn/R/learning-algorithms.R | 4
bnlearn-3.6/bnlearn/R/maxmin-pc.R | 2
bnlearn-3.6/bnlearn/R/predict.R | 20
bnlearn-3.6/bnlearn/R/relevant.R | 6
bnlearn-3.6/bnlearn/R/tabu.R | 1
bnlearn-3.6/bnlearn/R/test.R | 606 +----------------------
bnlearn-3.6/bnlearn/R/utils-misc.R | 2
bnlearn-3.6/bnlearn/R/utils-sanitization.R | 297 +++++++----
bnlearn-3.6/bnlearn/R/utils-tests.R | 2
bnlearn-3.6/bnlearn/man/bn.fit.methods.Rd | 28 -
bnlearn-3.6/bnlearn/man/bnlearn-package.Rd | 16
bnlearn-3.6/bnlearn/man/cpdag.Rd | 13
bnlearn-3.6/bnlearn/man/cpquery.Rd | 27 -
bnlearn-3.6/bnlearn/man/foreign.Rd | 33 -
bnlearn-3.6/bnlearn/man/gRain.Rd | 3
bnlearn-3.6/bnlearn/man/graphviz.plot.Rd | 2
bnlearn-3.6/bnlearn/man/naive.bayes.Rd | 14
bnlearn-3.6/bnlearn/man/preprocessing.Rd |only
bnlearn-3.6/bnlearn/man/strength.plot.Rd | 2
bnlearn-3.6/bnlearn/src/acyclic.c | 49 -
bnlearn-3.6/bnlearn/src/all.monte.carlo.c |only
bnlearn-3.6/bnlearn/src/allocations.c | 13
bnlearn-3.6/bnlearn/src/allsubs.test.c |only
bnlearn-3.6/bnlearn/src/arcs2elist.c | 69 +-
bnlearn-3.6/bnlearn/src/bayesian.network.c | 124 +---
bnlearn-3.6/bnlearn/src/bn.recovery.c | 39 -
bnlearn-3.6/bnlearn/src/bootstrap.c | 18
bnlearn-3.6/bnlearn/src/cache.structure.c | 34 -
bnlearn-3.6/bnlearn/src/common.c | 193 -------
bnlearn-3.6/bnlearn/src/common.h | 167 ++++--
bnlearn-3.6/bnlearn/src/configurations.c | 70 ++
bnlearn-3.6/bnlearn/src/covariance.c |only
bnlearn-3.6/bnlearn/src/cpdag.c | 86 +--
bnlearn-3.6/bnlearn/src/cpdist.c |only
bnlearn-3.6/bnlearn/src/data.frame.c |only
bnlearn-3.6/bnlearn/src/dedup.c |only
bnlearn-3.6/bnlearn/src/df.adjust.c |only
bnlearn-3.6/bnlearn/src/dirichlet.posterior.c | 4
bnlearn-3.6/bnlearn/src/discrete.loglikelihood.c | 27 -
bnlearn-3.6/bnlearn/src/discrete.monte.carlo.c |only
bnlearn-3.6/bnlearn/src/fitted.c | 39 -
bnlearn-3.6/bnlearn/src/gaussian.likelihood.c | 2
bnlearn-3.6/bnlearn/src/gaussian.monte.carlo.c |only
bnlearn-3.6/bnlearn/src/globals.c | 21
bnlearn-3.6/bnlearn/src/graph.generation.c | 191 ++-----
bnlearn-3.6/bnlearn/src/graph.priors.c | 15
bnlearn-3.6/bnlearn/src/hash.c | 30 -
bnlearn-3.6/bnlearn/src/hc.cache.lookup.c | 118 +---
bnlearn-3.6/bnlearn/src/htest.c |only
bnlearn-3.6/bnlearn/src/indep.test.c |only
bnlearn-3.6/bnlearn/src/is.dag.c | 27 -
bnlearn-3.6/bnlearn/src/is.row.equal.c | 33 -
bnlearn-3.6/bnlearn/src/jonckheere.c | 82 +--
bnlearn-3.6/bnlearn/src/likelihood.weighting.c | 28 -
bnlearn-3.6/bnlearn/src/linear.algebra.c | 45 -
bnlearn-3.6/bnlearn/src/linear.correlation.c | 256 +--------
bnlearn-3.6/bnlearn/src/loss.c | 87 +--
bnlearn-3.6/bnlearn/src/map.lw.c |only
bnlearn-3.6/bnlearn/src/mi.matrix.c | 42 -
bnlearn-3.6/bnlearn/src/mutual.information.c | 140 ++---
bnlearn-3.6/bnlearn/src/mvber.c | 30 -
bnlearn-3.6/bnlearn/src/parse.c | 8
bnlearn-3.6/bnlearn/src/path.c | 9
bnlearn-3.6/bnlearn/src/pdag2dag.c | 4
bnlearn-3.6/bnlearn/src/pearson.x2.c | 94 +--
bnlearn-3.6/bnlearn/src/per.node.score.c | 6
bnlearn-3.6/bnlearn/src/predict.c | 88 +--
bnlearn-3.6/bnlearn/src/rbn.c |only
bnlearn-3.6/bnlearn/src/rcont2.c | 3
bnlearn-3.6/bnlearn/src/sampling.c | 370 --------------
bnlearn-3.6/bnlearn/src/sanitization.c |only
bnlearn-3.6/bnlearn/src/score.delta.c | 80 +--
bnlearn-3.6/bnlearn/src/shd.c | 19
bnlearn-3.6/bnlearn/src/shrinkage.c | 195 ++-----
bnlearn-3.6/bnlearn/src/simulation.c | 12
bnlearn-3.6/bnlearn/src/strings.c |only
bnlearn-3.6/bnlearn/src/subsets.c | 18
bnlearn-3.6/bnlearn/src/symmetric.c | 62 --
bnlearn-3.6/bnlearn/src/tabu.c | 65 +-
bnlearn-3.6/bnlearn/src/test.counter.c | 8
bnlearn-3.6/bnlearn/src/tiers.c | 6
bnlearn-3.6/bnlearn/src/which.max.c |only
bnlearn-3.6/bnlearn/src/wishart.posterior.c | 69 +-
118 files changed, 1938 insertions(+), 3128 deletions(-)
Title: Sparse principal component regression
Diff between spcr versions 1.1 dated 2014-04-18 and 1.2 dated 2014-06-17
Description: This package computes the sparse principal component regression. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano
DESCRIPTION | 8 +++----
MD5 | 10 ++++-----
R/cv.spcr.R | 59 +++++++++++++++++++++++++++++++++++++++++++--------------
R/spcr.R | 11 +++++-----
man/cv.spcr.Rd | 16 +++++++++++----
man/spcr.Rd | 15 ++++++++------
6 files changed, 81 insertions(+), 38 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.7-0 dated 2013-11-19 and 1.8-0 dated 2014-06-17
Description: A package implementing statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g. discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for
surveillance data, or continuous-space point process data such as the
occurrence of disease or earthquakes. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of infectious diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently the package contains implementations of typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Hoehle and Paul (2008). Furthermore, inference
methods for the retrospective infectious disease model in Held
et al (2005), Held et al (2006), Paul et al (2008) and Paul
and Held (2011) are provided. A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ("twinSIR", discrete
space) and Meyer et al (2012) ("twinstim", continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: The suggested package INLA is unfortunately not available from
any mainstream repository - in case one wants to use the 'boda'
algorithm one needs to manually install the INLA package
as specified at http://www.r-inla.org/download.
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
surveillance-1.7-0/surveillance/R/hhh4_weights.R |only
surveillance-1.7-0/surveillance/R/twinstim_epidata.R |only
surveillance-1.7-0/surveillance/R/twinstim_epidata_methods.R |only
surveillance-1.7-0/surveillance/R/twinstim_glm.R |only
surveillance-1.7-0/surveillance/R/twinstim_siaf_lomax.R |only
surveillance-1.7-0/surveillance/inst/unitTests |only
surveillance-1.7-0/surveillance/man/powerlaw.Rd |only
surveillance-1.7-0/surveillance/man/simulate.ah4.Rd |only
surveillance-1.7-0/surveillance/man/stsDisp.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_epidataCS.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_epidataCS_aggregate.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_epidataCS_animate.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_epidataCS_plot.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_epidataCS_update.Rd |only
surveillance-1.7-0/surveillance/man/twinstim_intensityplot.Rd |only
surveillance-1.7-0/surveillance/tests/createSTS-objects.R |only
surveillance-1.7-0/surveillance/tests/doRUnit.R |only
surveillance-1.7-0/surveillance/tests/flu_ByBw.txt |only
surveillance-1.7-0/surveillance/tests/neighourhood_ByBw.txt |only
surveillance-1.7-0/surveillance/tests/population_2001-12-31_ByBw.txt |only
surveillance-1.7-0/surveillance/tests/test-nbOrder.R |only
surveillance-1.7-0/surveillance/tests/test-siafs.R |only
surveillance-1.7-0/surveillance/vignettes/map-weserems.eps |only
surveillance-1.7-0/surveillance/vignettes/map-weserems.pdf |only
surveillance-1.8-0/surveillance/DESCRIPTION | 107
surveillance-1.8-0/surveillance/MD5 | 301 +-
surveillance-1.8-0/surveillance/NAMESPACE | 802 +++----
surveillance-1.8-0/surveillance/R/AllClass.R | 12
surveillance-1.8-0/surveillance/R/AllGeneric.R | 67
surveillance-1.8-0/surveillance/R/LRCUSUM.runlength.R | 2
surveillance-1.8-0/surveillance/R/algo_bayes.R | 2
surveillance-1.8-0/surveillance/R/algo_glrnb.R | 8
surveillance-1.8-0/surveillance/R/boda.R |only
surveillance-1.8-0/surveillance/R/catCUSUM.R | 430 +--
surveillance-1.8-0/surveillance/R/checkDerivatives.R | 2
surveillance-1.8-0/surveillance/R/epidataCS.R |only
surveillance-1.8-0/surveillance/R/epidataCS_aggregate.R |only
surveillance-1.8-0/surveillance/R/epidataCS_animate.R |only
surveillance-1.8-0/surveillance/R/epidataCS_methods.R |only
surveillance-1.8-0/surveillance/R/epidataCS_plot.R |only
surveillance-1.8-0/surveillance/R/farringtonFlexible.r | 191 -
surveillance-1.8-0/surveillance/R/gd.R |only
surveillance-1.8-0/surveillance/R/glm_epidataCS.R |only
surveillance-1.8-0/surveillance/R/gpc.poly-methods.R | 2
surveillance-1.8-0/surveillance/R/graphs.R | 2
surveillance-1.8-0/surveillance/R/hhh4.R | 353 +--
surveillance-1.8-0/surveillance/R/hhh4_W.R |only
surveillance-1.8-0/surveillance/R/hhh4_W_np.R |only
surveillance-1.8-0/surveillance/R/hhh4_W_powerlaw.R |only
surveillance-1.8-0/surveillance/R/hhh4_methods.R | 547 ++--
surveillance-1.8-0/surveillance/R/hhh4_oneStepAhead.R | 187 +
surveillance-1.8-0/surveillance/R/hhh4_plot.R |only
surveillance-1.8-0/surveillance/R/hhh4_simulate.R | 53
surveillance-1.8-0/surveillance/R/intersectPolyCircle.R | 8
surveillance-1.8-0/surveillance/R/isoWeekYear.R | 64
surveillance-1.8-0/surveillance/R/modifyListcall.R | 2
surveillance-1.8-0/surveillance/R/nowcast.R | 1145 +++++++---
surveillance-1.8-0/surveillance/R/options.R | 217 -
surveillance-1.8-0/surveillance/R/permutationTest.R |only
surveillance-1.8-0/surveillance/R/pit.R |only
surveillance-1.8-0/surveillance/R/qlomax.R |only
surveillance-1.8-0/surveillance/R/scores.R | 116 -
surveillance-1.8-0/surveillance/R/spatial_tools.R | 34
surveillance-1.8-0/surveillance/R/sts.R | 811 +------
surveillance-1.8-0/surveillance/R/stsNC.R |only
surveillance-1.8-0/surveillance/R/sts_animate.R |only
surveillance-1.8-0/surveillance/R/sts_coerce.R |only
surveillance-1.8-0/surveillance/R/stsplot_space.R |only
surveillance-1.8-0/surveillance/R/stsplot_spacetime.R |only
surveillance-1.8-0/surveillance/R/stsplot_time.R |only
surveillance-1.8-0/surveillance/R/sysdata.rda |binary
surveillance-1.8-0/surveillance/R/twinSIR_epidata.R | 26
surveillance-1.8-0/surveillance/R/twinstim.R | 192 -
surveillance-1.8-0/surveillance/R/twinstim_helper.R | 49
surveillance-1.8-0/surveillance/R/twinstim_iafplot.R |only
surveillance-1.8-0/surveillance/R/twinstim_intensity.R |only
surveillance-1.8-0/surveillance/R/twinstim_methods.R | 533 ----
surveillance-1.8-0/surveillance/R/twinstim_siaf.R | 264 +-
surveillance-1.8-0/surveillance/R/twinstim_siaf_gaussian.R | 21
surveillance-1.8-0/surveillance/R/twinstim_siaf_powerlaw.R | 188 -
surveillance-1.8-0/surveillance/R/twinstim_siaf_powerlawL.R | 174 -
surveillance-1.8-0/surveillance/R/twinstim_siaf_step.R |only
surveillance-1.8-0/surveillance/R/twinstim_siaf_student.R |only
surveillance-1.8-0/surveillance/R/twinstim_simulation.R | 258 +-
surveillance-1.8-0/surveillance/R/twinstim_step.R | 2
surveillance-1.8-0/surveillance/R/twinstim_tiaf.R | 111
surveillance-1.8-0/surveillance/R/twinstim_tiaf_exponential.R |only
surveillance-1.8-0/surveillance/R/twinstim_tiaf_step.R |only
surveillance-1.8-0/surveillance/R/untie.R | 8
surveillance-1.8-0/surveillance/R/wrap_univariate.R | 8
surveillance-1.8-0/surveillance/R/zzz.R | 52
surveillance-1.8-0/surveillance/build/partial.rdb |only
surveillance-1.8-0/surveillance/build/vignette.rds |binary
surveillance-1.8-0/surveillance/data/campyDE.RData |only
surveillance-1.8-0/surveillance/data/husO104Hosp.RData |only
surveillance-1.8-0/surveillance/data/imdepi.RData |binary
surveillance-1.8-0/surveillance/data/imdepifit.RData |binary
surveillance-1.8-0/surveillance/data/measlesWeserEms.RData |only
surveillance-1.8-0/surveillance/data/rotaBB.RData |only
surveillance-1.8-0/surveillance/data/salmHospitalized.RData |only
surveillance-1.8-0/surveillance/data/salmNewport.RData |only
surveillance-1.8-0/surveillance/demo/biosurvbook.R | 409 +--
surveillance-1.8-0/surveillance/demo/cost.R | 3
surveillance-1.8-0/surveillance/inst/CITATION | 258 +-
surveillance-1.8-0/surveillance/inst/NEWS.Rd | 291 ++
surveillance-1.8-0/surveillance/inst/THANKS |only
surveillance-1.8-0/surveillance/inst/doc/glrnb.R | 46
surveillance-1.8-0/surveillance/inst/doc/glrnb.Rnw | 6
surveillance-1.8-0/surveillance/inst/doc/glrnb.pdf |binary
surveillance-1.8-0/surveillance/inst/doc/hhh4-cache.RData |binary
surveillance-1.8-0/surveillance/inst/doc/hhh4.R | 77
surveillance-1.8-0/surveillance/inst/doc/hhh4.Rnw | 86
surveillance-1.8-0/surveillance/inst/doc/hhh4.pdf |binary
surveillance-1.8-0/surveillance/inst/doc/surveillance.R | 60
surveillance-1.8-0/surveillance/inst/doc/surveillance.Rnw | 12
surveillance-1.8-0/surveillance/inst/doc/surveillance.pdf |binary
surveillance-1.8-0/surveillance/inst/jags |only
surveillance-1.8-0/surveillance/inst/shapes/districtsD.RData |binary
surveillance-1.8-0/surveillance/man/LRCUSUM.runlength.Rd | 24
surveillance-1.8-0/surveillance/man/algo.bayes.Rd | 37
surveillance-1.8-0/surveillance/man/algo.call.Rd | 15
surveillance-1.8-0/surveillance/man/algo.cdc.Rd | 7
surveillance-1.8-0/surveillance/man/algo.compare.Rd | 4
surveillance-1.8-0/surveillance/man/algo.cusum.Rd | 10
surveillance-1.8-0/surveillance/man/algo.farrington.Rd | 19
surveillance-1.8-0/surveillance/man/algo.farrington.fitGLM.Rd | 13
surveillance-1.8-0/surveillance/man/algo.glrnb.Rd | 8
surveillance-1.8-0/surveillance/man/algo.twins.Rd | 15
surveillance-1.8-0/surveillance/man/backprojNP.Rd | 6
surveillance-1.8-0/surveillance/man/boda.Rd |only
surveillance-1.8-0/surveillance/man/campyDE.Rd |only
surveillance-1.8-0/surveillance/man/categoricalCUSUM.Rd | 2
surveillance-1.8-0/surveillance/man/deleval.Rd | 84
surveillance-1.8-0/surveillance/man/epidataCS.Rd |only
surveillance-1.8-0/surveillance/man/epidataCS_aggregate.Rd |only
surveillance-1.8-0/surveillance/man/epidataCS_animate.Rd |only
surveillance-1.8-0/surveillance/man/epidataCS_plot.Rd |only
surveillance-1.8-0/surveillance/man/epidataCS_update.Rd |only
surveillance-1.8-0/surveillance/man/farringtonFlexible.Rd | 5
surveillance-1.8-0/surveillance/man/glm_epidataCS.Rd |only
surveillance-1.8-0/surveillance/man/hhh4.Rd | 156 -
surveillance-1.8-0/surveillance/man/hhh4_W.Rd |only
surveillance-1.8-0/surveillance/man/hhh4_formula.Rd | 18
surveillance-1.8-0/surveillance/man/hhh4_methods.Rd | 129 -
surveillance-1.8-0/surveillance/man/hhh4_plot.Rd |only
surveillance-1.8-0/surveillance/man/hhh4_predict.Rd | 12
surveillance-1.8-0/surveillance/man/hhh4_simulate.Rd |only
surveillance-1.8-0/surveillance/man/hhh4_validation.Rd | 72
surveillance-1.8-0/surveillance/man/husO104Hosp.Rd |only
surveillance-1.8-0/surveillance/man/imdepi.Rd | 108
surveillance-1.8-0/surveillance/man/isoWeekYear.Rd | 6
surveillance-1.8-0/surveillance/man/linelist2sts.Rd | 5
surveillance-1.8-0/surveillance/man/measles.weser.Rd | 131 -
surveillance-1.8-0/surveillance/man/multiplicity.Rd | 57
surveillance-1.8-0/surveillance/man/nowcast.Rd | 273 +-
surveillance-1.8-0/surveillance/man/pairedbinCUSUM.Rd | 4
surveillance-1.8-0/surveillance/man/permutationTest.Rd |only
surveillance-1.8-0/surveillance/man/pit.Rd |only
surveillance-1.8-0/surveillance/man/polyAtBorder.Rd | 1
surveillance-1.8-0/surveillance/man/rotaBB.Rd |only
surveillance-1.8-0/surveillance/man/runifdisc.Rd | 5
surveillance-1.8-0/surveillance/man/salmHospitalized.Rd |only
surveillance-1.8-0/surveillance/man/salmNewport.Rd |only
surveillance-1.8-0/surveillance/man/sts-class.Rd | 21
surveillance-1.8-0/surveillance/man/stsAggregate.Rd | 10
surveillance-1.8-0/surveillance/man/stsNC-class.Rd |only
surveillance-1.8-0/surveillance/man/sts_animate.Rd |only
surveillance-1.8-0/surveillance/man/stsplot.Rd |only
surveillance-1.8-0/surveillance/man/stsplot_space.Rd |only
surveillance-1.8-0/surveillance/man/stsplot_spacetime.Rd |only
surveillance-1.8-0/surveillance/man/stsplot_time.Rd |only
surveillance-1.8-0/surveillance/man/surveillance-package.Rd | 81
surveillance-1.8-0/surveillance/man/toLatex.sts.Rd |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata_intersperse.Rd | 11
surveillance-1.8-0/surveillance/man/twinstim.Rd | 126 -
surveillance-1.8-0/surveillance/man/twinstim_iaf.Rd | 288 +-
surveillance-1.8-0/surveillance/man/twinstim_iafplot.Rd | 140 -
surveillance-1.8-0/surveillance/man/twinstim_intensity.Rd |only
surveillance-1.8-0/surveillance/man/twinstim_methods.Rd | 66
surveillance-1.8-0/surveillance/man/twinstim_profile.Rd | 8
surveillance-1.8-0/surveillance/man/twinstim_siaf.Rd |only
surveillance-1.8-0/surveillance/man/twinstim_simulation.Rd | 23
surveillance-1.8-0/surveillance/man/twinstim_step.Rd | 3
surveillance-1.8-0/surveillance/man/twinstim_tiaf.Rd |only
surveillance-1.8-0/surveillance/man/twinstim_update.Rd | 24
surveillance-1.8-0/surveillance/man/untie.Rd | 3
surveillance-1.8-0/surveillance/man/zetaweights.Rd | 4
surveillance-1.8-0/surveillance/tests/test-all.R |only
surveillance-1.8-0/surveillance/tests/testthat |only
surveillance-1.8-0/surveillance/vignettes/glrnb.Rnw | 6
surveillance-1.8-0/surveillance/vignettes/hhh4-cache.RData |binary
surveillance-1.8-0/surveillance/vignettes/hhh4.Rnw | 86
surveillance-1.8-0/surveillance/vignettes/surveillance.Rnw | 12
193 files changed, 5755 insertions(+), 4982 deletions(-)
Title: stream - Interface to MOA Algorithms
Diff between streamMOA versions 0.1-0 dated 2014-05-25 and 0.1-1 dated 2014-06-17
Description: This package provides an interface to algorithms implemented in the MOA (Massive Online Analysis) framework for data stream mining.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler
streamMOA-0.1-0/streamMOA/R/cluster.R |only
streamMOA-0.1-1/streamMOA/DESCRIPTION | 17 ++-
streamMOA-0.1-1/streamMOA/MD5 | 30 ++++--
streamMOA-0.1-1/streamMOA/NAMESPACE | 6 +
streamMOA-0.1-1/streamMOA/R/AAA.R |only
streamMOA-0.1-1/streamMOA/R/DSC_CluStream.R | 22 +---
streamMOA-0.1-1/streamMOA/R/DSC_DenStream.R | 32 ++-----
streamMOA-0.1-1/streamMOA/R/DSC_MOA.R | 111 +++++++++++++++++++++++++
streamMOA-0.1-1/streamMOA/R/DSD_MOA.R | 35 -------
streamMOA-0.1-1/streamMOA/R/ellipse.R |only
streamMOA-0.1-1/streamMOA/build |only
streamMOA-0.1-1/streamMOA/inst/NEWS | 7 +
streamMOA-0.1-1/streamMOA/inst/doc |only
streamMOA-0.1-1/streamMOA/man/DSC_CluStream.Rd | 6 -
streamMOA-0.1-1/streamMOA/man/DSC_ClusTree.Rd | 4
streamMOA-0.1-1/streamMOA/man/DSC_DenStream.Rd | 29 +++---
streamMOA-0.1-1/streamMOA/vignettes |only
17 files changed, 189 insertions(+), 110 deletions(-)
Title: Lasso method for RCON(V,E) models
Diff between sglasso versions 1.0-0 dated 2014-04-23 and 1.0-1 dated 2014-06-17
Description: RCON(V, E) models (Hojsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Augugliaro et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) algorithm and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/loglik.R | 2 +-
man/sglasso-package.Rd | 4 ++--
5 files changed, 11 insertions(+), 10 deletions(-)
Title: Generate Physical Random Numbers on Intel CPUs with the RdRand
instruction
Diff between Rrdrand versions 0.1-7 dated 2014-06-16 and 0.1-8 dated 2014-06-17
Description: Make use of the physical random number accessed by the RdRand
instruction in recent Intel CPUs (Ivy Bridge and later).
Author: Eiji Nakama
Maintainer: Eiji Nakama
Changelog | 1 +
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
configure | 2 +-
configure.ac | 2 +-
src/Rrdrand.c | 5 ++---
6 files changed, 13 insertions(+), 13 deletions(-)
Title: Import, plot and analyze bathymetric and topographic data
Diff between marmap versions 0.7 dated 2013-10-11 and 0.8 dated 2014-06-17
Description: Import, plot and analyze bathymetric and topographic data
Author: Eric Pante and Benoit Simon-Bouhet
Maintainer: Eric Pante
DESCRIPTION | 13 ++--
MD5 | 79 ++++++++++++++++-----------
NAMESPACE | 2
R/add.nas.R |only
R/antimeridian.box.R |only
R/as.bathy.R | 21 ++++---
R/collate.bathy.R |only
R/get.depth.R | 102 +++++++++++++++++++++++++++++++-----
R/get.sample.R | 7 +-
R/get.transect.R | 2
R/getNOAA.bathy.R | 72 ++++++++++++++++++-------
R/palette.bathy.R |only
R/plot.bathy.R | 25 ++++----
R/read.bathy.R | 32 +++++------
R/scaleBathy.R | 4 -
R/space.pies.R |only
R/subsetBathy.R |only
R/summary.bathy.R | 11 +++
build/vignette.rds |binary
data/aleutians.rda |only
data/celt.rda |binary
data/datalist | 1
data/florida.rda |binary
data/hawaii.rda |binary
data/hawaii.sites.rda |binary
data/metallo.rda |binary
data/nw.atlantic.coast.rda |binary
data/nw.atlantic.rda |binary
inst/doc/marmap.R | 55 +++++++++----------
inst/doc/marmap.Rnw | 127 +++++++++++++++------------------------------
inst/doc/marmap.pdf |binary
man/add.nas.Rd |only
man/aleutians.Rd |only
man/antimeridian.box.Rd |only
man/collate.bathy.Rd |only
man/get.depth.Rd | 47 ++++++++++++----
man/get.sample.Rd | 11 +--
man/get.transect.Rd | 4 -
man/getNOAA.bathy.Rd | 11 ++-
man/marmap.Rd | 4 -
man/palette.bathy.Rd |only
man/plot.bathy.Rd | 48 ++++++++++++-----
man/scaleBathy.Rd | 6 +-
man/space.pies.Rd |only
man/subsetBathy.Rd |only
man/summary.bathy.Rd | 2
vignettes/aleu.pdf |only
vignettes/marmap.Rnw | 127 +++++++++++++++------------------------------
48 files changed, 464 insertions(+), 349 deletions(-)
Title: Parse command-line arguments and variable interpolation
Diff between GetoptLong versions 0.0.3 dated 2013-12-10 and 0.0.4 dated 2014-06-17
Description: Parsing command-line arguments by Perl module Getopt::Long.
It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 10 ++--
MD5 | 31 +++++++------
NEWS | 6 ++
R/GetoptLong.R | 2
R/qq.R | 18 ++++++-
build |only
inst/doc/GetoptLong.R | 23 +++++++---
inst/doc/GetoptLong.Rnw | 30 ++++++++-----
inst/doc/GetoptLong.pdf |binary
inst/doc/variable_interpolation.R | 80 ++++++++++++++++++++++-------------
inst/doc/variable_interpolation.Rnw | 53 ++++++++++++++---------
inst/doc/variable_interpolation.pdf |binary
inst/tests/test_qq.R | 8 +++
man/qqcat.rd | 8 +++
tests/test-all.R | 14 ++++--
vignettes/GetoptLong.Rnw | 30 ++++++++-----
vignettes/variable_interpolation.Rnw | 53 ++++++++++++++---------
17 files changed, 240 insertions(+), 126 deletions(-)
Title: Density surface modelling of distance sampling data
Diff between dsm versions 2.2.3 dated 2014-04-23 and 2.2.4 dated 2014-06-17
Description: This library implements density surface modelling of line
transect data, based on the methods of Hedley et al. (2004). Some
recent developments in the literature have also be incorporated.
Outputs are point and interval estimates of population abundance
and density.
Please note that this version of dsm WILL NOT work with the Windows
package DISTANCE earlier than version 6.2. For a version that works with
DISTANCE 6.1, please go to:
https://github.com/DistanceDevelopment/dsm-distance-6.1
For the latest version of dsm, please use the github version at the URL
listed below.
Miller, D. L., M. L. Burt, E. Rexstad and L. Thomas. 2013. Spatial
models for distance sampling data: recent developments and future
directions. Methods in Ecology and Evolution
Hedley, S.L., S.T. Buckland and D.L. Borchers. 2004. "Spatial
distance sampling methods" pp 48-70 in Advanced Distance Sampling,
Buckland, S.T. et al. (eds). Oxford University Press.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley.
Maintainer: David Lawrence Miller
DESCRIPTION | 8 -
MD5 | 60 ++++++-------
NAMESPACE | 2
NEWS | 3
R/make.data.R | 4
man/block.info.per.su.Rd | 26 +++--
man/check.cols.Rd | 18 +--
man/dsm-data.Rd | 33 +++----
man/dsm-package.Rd | 1
man/dsm.Rd | 188 ++++++++++++-----------------------------
man/dsm.cor.Rd | 62 +++----------
man/dsm.var.gam.Rd | 55 ++++++-----
man/dsm.var.movblk.Rd | 79 +++++++----------
man/dsm.var.prop.Rd | 90 +++++++++----------
man/generate.ds.uncertainty.Rd | 20 ++--
man/generate.mb.sample.Rd | 19 +---
man/latlong2km.Rd | 25 ++---
man/make.soapgrid.Rd | 24 ++---
man/matrixnotposdef.handler.Rd | 16 +--
man/mexdolphins.Rd | 27 +----
man/offsets.Rd | 1
man/plot.dsm.Rd | 6 -
man/plot.dsm.var.Rd | 69 ++++++---------
man/predict.dsm.Rd | 26 ++---
man/print.dsm.Rd | 11 +-
man/print.dsm.var.Rd | 6 -
man/print.summary.dsm.var.Rd | 6 -
man/rqgam.check.Rd | 16 +--
man/summary.dsm.Rd | 6 -
man/summary.dsm.var.Rd | 23 ++---
man/trim.var.Rd | 17 +--
31 files changed, 402 insertions(+), 545 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Diff between arules versions 1.1-2 dated 2014-02-21 and 1.1-3 dated 2014-06-17
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 20 -
MD5 | 74 ++---
R/AAADefs.R | 2
R/AllClasses.R | 3
R/associations.R | 89 +++---
R/interestMeasures.R | 563 ++++++++++++++++++++++---------------------
R/pmml.R | 29 +-
R/random.transactions.R | 4
R/rules.R | 18 +
R/support.R | 2
build/vignette.rds |binary
data/Adult.rda |binary
data/AdultUCI.rda |binary
data/Epub.rda |binary
data/Groceries.rda |binary
data/Income.rda |binary
data/IncomeESL.rda |binary
inst/NEWS | 8
inst/doc/arules.Rnw | 2
inst/doc/arules.pdf |binary
man/APappearance-class.Rd | 39 ++
man/AScontrol-class.Rd | 5
man/ASparameter-class.Rd | 5
man/apriori.Rd | 2
man/associations-class.Rd | 1
man/discretize.Rd | 28 +-
man/eclat.Rd | 2
man/interestMeasure.Rd | 22 +
man/itemsets-class.Rd | 3
man/pmml.Rd | 2
man/rules-class.Rd | 2
man/tidLists-class.Rd | 1
man/transactions-class.Rd | 1
tests/associations.R | 21 +
tests/associations.Rout.save | 40 ++-
tests/matrix.Rout.save | 8
tests/measures.Rout.save | 174 ++++++-------
vignettes/arules.Rnw | 2
38 files changed, 669 insertions(+), 503 deletions(-)
Title: RbioRXN - process Rhea, KEGG, MetaCyc, Unipathway biochemical
reaction data
Diff between RbioRXN versions 1.2 dated 2014-05-14 and 1.3 dated 2014-06-17
Description: RbioRXN is an R package that facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min
RbioRXN-1.2/RbioRXN/R/BioCyc.instantiate.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc.is.generic.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc.massBal.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc2ChEBI.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc2KEGG.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc2PubChem.R |only
RbioRXN-1.2/RbioRXN/R/BioCyc2cName.R |only
RbioRXN-1.2/RbioRXN/R/Rhea.buildHash.class.R |only
RbioRXN-1.2/RbioRXN/R/Rhea.instantiate.R |only
RbioRXN-1.2/RbioRXN/R/Rhea.is.generic.R |only
RbioRXN-1.2/RbioRXN/R/Rhea.massBal.R |only
RbioRXN-1.2/RbioRXN/R/Rhea2KEGG.R |only
RbioRXN-1.2/RbioRXN/R/Rhea2cName.R |only
RbioRXN-1.2/RbioRXN/R/addBiopax.compound.R |only
RbioRXN-1.2/RbioRXN/R/conv.R |only
RbioRXN-1.2/RbioRXN/R/get.ChEBI.R |only
RbioRXN-1.2/RbioRXN/R/get.Rhea.R |only
RbioRXN-1.2/RbioRXN/R/mass.bal.R |only
RbioRXN-1.2/RbioRXN/R/parse.ChEBI.R |only
RbioRXN-1.2/RbioRXN/R/parse.MetaCyc.c.R |only
RbioRXN-1.2/RbioRXN/R/parse.MetaCyc.r.R |only
RbioRXN-1.2/RbioRXN/R/parse.Rhea.R |only
RbioRXN-1.2/RbioRXN/man/BioCyc.instantiate.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc.is.generic.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc.massBal.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc2ChEBI.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc2KEGG.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc2PubChem.Rd |only
RbioRXN-1.2/RbioRXN/man/BioCyc2cName.Rd |only
RbioRXN-1.2/RbioRXN/man/Rhea.instantiate.Rd |only
RbioRXN-1.2/RbioRXN/man/Rhea.is.generic.Rd |only
RbioRXN-1.2/RbioRXN/man/Rhea.massBal.Rd |only
RbioRXN-1.2/RbioRXN/man/Rhea2KEGG.Rd |only
RbioRXN-1.2/RbioRXN/man/Rhea2cName.Rd |only
RbioRXN-1.2/RbioRXN/man/get.ChEBI.Rd |only
RbioRXN-1.2/RbioRXN/man/get.Rhea.Rd |only
RbioRXN-1.2/RbioRXN/man/parse.ChEBI.Rd |only
RbioRXN-1.2/RbioRXN/man/parse.MetaCyc.c.Rd |only
RbioRXN-1.2/RbioRXN/man/parse.MetaCyc.r.Rd |only
RbioRXN-1.2/RbioRXN/man/parse.Rhea.Rd |only
RbioRXN-1.3/RbioRXN/DESCRIPTION | 17
RbioRXN-1.3/RbioRXN/MD5 | 88 -
RbioRXN-1.3/RbioRXN/NAMESPACE | 4
RbioRXN-1.3/RbioRXN/R/RbioRXN-internal.R | 1281 +++++++++++++++++--
RbioRXN-1.3/RbioRXN/R/build.subtable.R |only
RbioRXN-1.3/RbioRXN/R/check.mass.balance.R |only
RbioRXN-1.3/RbioRXN/R/get.chebi.all.R |only
RbioRXN-1.3/RbioRXN/R/get.kegg.all.R |only
RbioRXN-1.3/RbioRXN/R/get.kegg.byId.R |only
RbioRXN-1.3/RbioRXN/R/get.metacyc.all.R |only
RbioRXN-1.3/RbioRXN/R/get.metacyc.reaction.byId.R |only
RbioRXN-1.3/RbioRXN/R/get.rhea.all.R |only
RbioRXN-1.3/RbioRXN/R/get.rhea.byCompound.R |only
RbioRXN-1.3/RbioRXN/R/get.rhea.byId.R |only
RbioRXN-1.3/RbioRXN/R/get.unipathway.all.R |only
RbioRXN-1.3/RbioRXN/R/instantiate.R | 429 +++---
RbioRXN-1.3/RbioRXN/R/instantiate.metacyc.R |only
RbioRXN-1.3/RbioRXN/R/instantiate.rhea.R |only
RbioRXN-1.3/RbioRXN/R/is.generic.metacyc.R |only
RbioRXN-1.3/RbioRXN/R/is.generic.rhea.R |only
RbioRXN-1.3/RbioRXN/R/parse.metacyc.compound.R |only
RbioRXN-1.3/RbioRXN/R/parse.metacyc.reaction.R |only
RbioRXN-1.3/RbioRXN/data/example.rda |binary
RbioRXN-1.3/RbioRXN/man/RbioRXN-package.Rd | 110 -
RbioRXN-1.3/RbioRXN/man/build.subtable.Rd |only
RbioRXN-1.3/RbioRXN/man/check.mass.balance.Rd |only
RbioRXN-1.3/RbioRXN/man/example.Rd | 8
RbioRXN-1.3/RbioRXN/man/get.chebi.all.Rd |only
RbioRXN-1.3/RbioRXN/man/get.kegg.all.Rd |only
RbioRXN-1.3/RbioRXN/man/get.kegg.byId.Rd |only
RbioRXN-1.3/RbioRXN/man/get.metacyc.all.Rd |only
RbioRXN-1.3/RbioRXN/man/get.metacyc.reaction.byId.Rd |only
RbioRXN-1.3/RbioRXN/man/get.rhea.all.Rd |only
RbioRXN-1.3/RbioRXN/man/get.rhea.byCompound.Rd |only
RbioRXN-1.3/RbioRXN/man/get.rhea.byId.Rd |only
RbioRXN-1.3/RbioRXN/man/get.unipathway.all.Rd |only
RbioRXN-1.3/RbioRXN/man/instantiate.metacyc.Rd |only
RbioRXN-1.3/RbioRXN/man/instantiate.rhea.Rd |only
RbioRXN-1.3/RbioRXN/man/is.generic.metacyc.Rd |only
RbioRXN-1.3/RbioRXN/man/is.generic.rhea.Rd |only
RbioRXN-1.3/RbioRXN/man/parse.metacyc.compound.Rd |only
RbioRXN-1.3/RbioRXN/man/parse.metacyc.reaction.Rd |only
82 files changed, 1475 insertions(+), 462 deletions(-)
Title: Transforms input data from a PMML perspective
Diff between pmmlTransformations versions 1.2.1 dated 2013-10-22 and 1.2.2 dated 2014-06-17
More information about pmmlTransformations at CRAN
Description: Allows for data to be transformed before using
it to construct models. Builds structures to allow functions in
the PMML package to output transformation details in
addition to the model in the resulting PMML file.
Author: Tridivesh Jena, Wen Ching Lin (Zementis, Inc.)
Maintainer: Tridivesh Jena
DESCRIPTION | 8
MD5 | 26 +-
NAMESPACE | 2
R/DiscretizeXform.R | 202 +++++++++++++---------
R/MapXform.R | 261 +++++++++++++++++++----------
R/MinMaxXform.R | 11 +
R/NormDiscreteXform.R | 7
R/RenameVar.R | 15 +
R/WrapData.R | 10 -
R/ZScoreXform.R | 6
man/pmmlTransformations.DiscretizeXform.Rd | 72 +++++++-
man/pmmlTransformations.MapXform.Rd | 63 +++++--
man/pmmlTransformations.MinMaxXform.Rd | 1
man/pmmlTransformations.WrapData.Rd | 11 -
14 files changed, 478 insertions(+), 217 deletions(-)
Permanent link
Title: Generate PMML for various models
Diff between pmml versions 1.4.1 dated 2013-10-24 and 1.4.2 dated 2014-06-17
Description:
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org.
The generated PMML can be imported into any PMML consuming application,
such as the Zementis ADAPA and UPPI scoring engines which allow for
predictive models built in R to be deployed and executed on site, in
the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza, Pivotal,
Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler (arules),
Zementis Inc, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Maintainer: Tridivesh Jena
DESCRIPTION | 13 +-
MD5 | 84 ++++++++-------
NAMESPACE | 3
R/addLT.R |only
R/addMSAttributes.R |only
R/pmml.R | 29 +++--
R/pmml.ada.R | 7 -
R/pmml.coxph.R | 15 ++
R/pmml.cv.glmnet.R | 9 -
R/pmml.glm.R | 7 -
R/pmml.hclust.R | 5
R/pmml.itemsets.R | 3
R/pmml.kmeans.R | 8 -
R/pmml.ksvm.R | 5
R/pmml.lm.R | 5
R/pmml.miningschema.R | 84 +++++++++++----
R/pmml.multinom.R | 5
R/pmml.naiveBayes.R | 5
R/pmml.nnet.R | 5
R/pmml.randomForest.R | 257 +++++++++++++++++++++++++++++++----------------
R/pmml.rfsrc.R | 9 -
R/pmml.rpart.R | 10 +
R/pmml.rules.R | 2
R/pmml.survreg.R | 5
R/pmml.svm.R | 7 -
man/addLT.Rd |only
man/addMSAttributes.Rd |only
man/fileToXMLNode.Rd | 21 ++-
man/pmml.Rd | 7 -
man/pmml.ada.Rd | 11 +-
man/pmml.arules.Rd | 6 -
man/pmml.coxph.Rd | 5
man/pmml.cv.glmnet.Rd | 4
man/pmml.glm.Rd | 4
man/pmml.hclust.Rd | 28 ++++-
man/pmml.kmeans.Rd | 5
man/pmml.ksvm.Rd | 7 +
man/pmml.lm.Rd | 8 +
man/pmml.multinom.Rd | 6 -
man/pmml.naiveBayes.Rd | 8 +
man/pmml.nnet.Rd | 11 +-
man/pmml.randomForest.Rd | 9 +
man/pmml.rfsrc.Rd | 6 -
man/pmml.rpart.Rd | 8 +
man/pmml.svm.Rd | 7 +
45 files changed, 499 insertions(+), 244 deletions(-)
Title: Fitting exact conditional logistic regression with lasso and
elastic net penalties.
Diff between clogitL1 versions 1.3 dated 2014-04-18 and 1.4 dated 2014-06-17
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid and Robert Tibshirani
Maintainer: Stephen Reid
DESCRIPTION | 6 +++---
MD5 | 19 ++++++++++---------
inst |only
man/clogitL1-package.Rd | 7 ++++++-
man/clogitL1.Rd | 4 ++++
man/cv.clogitL1.Rd | 4 ++++
man/plot.clogitL1.Rd | 4 ++++
man/plot.cv.clogitL1.Rd | 5 +++++
man/print.clogitL1.Rd | 4 ++++
man/summary.clogitL1.Rd | 4 ++++
man/summary.cv.clogitL1.Rd | 4 ++++
11 files changed, 48 insertions(+), 13 deletions(-)