Title: Toolkit for the plotting and analysis of stratigraphic and
palaeontological data
Diff between stratigraph versions 0.64 dated 2011-08-03 and 0.66 dated 2015-01-13
Description: A collection of tools for plotting and analyzing paleontological and geological data distributed through through time in stratigraphic cores or sections. Includes some miscellaneous functions for handling other kinds of palaeontological and paleoecological data.
Author: Walton A. Green
Maintainer: Walton A. Green
stratigraph-0.64/stratigraph/data/.Rapp.history |only
stratigraph-0.66/stratigraph/DESCRIPTION | 15 ++---
stratigraph-0.66/stratigraph/MD5 |only
stratigraph-0.66/stratigraph/NAMESPACE |only
stratigraph-0.66/stratigraph/R/plot.strat.column.R | 44 ++++++++--------
stratigraph-0.66/stratigraph/data/cerrejon.rda |binary
stratigraph-0.66/stratigraph/data/corneta.rda |binary
stratigraph-0.66/stratigraph/data/mohawk.rda |binary
stratigraph-0.66/stratigraph/data/plain.rda |binary
stratigraph-0.66/stratigraph/data/rogerslk.rda |binary
stratigraph-0.66/stratigraph/data/sI.rda |binary
stratigraph-0.66/stratigraph/data/sII.rda |binary
stratigraph-0.66/stratigraph/data/sIII.rda |binary
stratigraph-0.66/stratigraph/data/sIV.rda |binary
stratigraph-0.66/stratigraph/data/sV.rda |binary
stratigraph-0.66/stratigraph/data/sVI.rda |binary
stratigraph-0.66/stratigraph/data/stippled.rda |binary
stratigraph-0.66/stratigraph/data/striped.rda |binary
stratigraph-0.66/stratigraph/man/a.datums.Rd | 2
stratigraph-0.66/stratigraph/man/compress2matrix.Rd | 14 +----
stratigraph-0.66/stratigraph/man/corneta.Rd | 2
stratigraph-0.66/stratigraph/man/dloc.Rd | 7 +-
stratigraph-0.66/stratigraph/man/fill.ranges.Rd | 7 +-
stratigraph-0.66/stratigraph/man/gluesheets.Rd | 4 -
stratigraph-0.66/stratigraph/man/grid.prop.plot.Rd | 14 ++---
stratigraph-0.66/stratigraph/man/mohawk.Rd | 3 -
stratigraph-0.66/stratigraph/man/nonuser.Rd | 14 ++---
stratigraph-0.66/stratigraph/man/oe.rates.Rd | 3 -
stratigraph-0.66/stratigraph/man/plain.Rd | 6 +-
stratigraph-0.66/stratigraph/man/plot.strat.column.Rd | 3 -
stratigraph-0.66/stratigraph/man/rangechart.Rd | 6 +-
stratigraph-0.66/stratigraph/man/readGPDascii.Rd | 5 +
stratigraph-0.66/stratigraph/man/rogerslk.Rd | 3 -
stratigraph-0.66/stratigraph/man/sI.Rd | 4 -
stratigraph-0.66/stratigraph/man/strat.column.Rd | 10 +--
stratigraph-0.66/stratigraph/man/stratigraph.package.Rd | 6 +-
stratigraph-0.66/stratigraph/man/writeCONOP.Rd | 10 +--
stratigraph-0.66/stratigraph/man/writeGPDascii.Rd | 5 +
38 files changed, 93 insertions(+), 94 deletions(-)
Title: Robust Mixture Discriminant Analysis
Diff between robustDA versions 1.0 dated 2014-09-29 and 1.1 dated 2015-01-13
Description: Robust mixture discriminant analysis (RMDA, Bouveyron & Girard, 2009) allows to build a robust supervised classifier from learning data with label noise. The idea of the proposed method is to confront an unsupervised modeling of the data with the supervised information carried by the labels of the learning data in order to detect inconsistencies. The method is able afterward to build a robust classifier taking into account the detected inconsistencies into the labels.
Author: Charles Bouveyron & Stephane Girard
Maintainer: Charles Bouveyron
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/rmda.R | 26 +++++++++++++-------------
R/robustDA-internal.R | 2 +-
4 files changed, 20 insertions(+), 20 deletions(-)
Title: Multi-Resolution Estimation of the Hazard Rate
Diff between MRH versions 1.1 dated 2014-10-23 and 2.0 dated 2015-01-13
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times. Can accommodate covariates under the proportional and non-proportional hazards setting, and is ideal for analysis of survival data with long-term follow-up.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar
MRH-1.1/MRH/R/MRHCovNPHBA.r |only
MRH-1.1/MRH/R/MRHCovPH.r |only
MRH-2.0/MRH/DESCRIPTION | 10 -
MRH-2.0/MRH/MD5 | 52 +++--
MRH-2.0/MRH/R/FunctionsNotforUser_Assorted.r | 228 +++++++++++++-----------
MRH-2.0/MRH/R/FunctionsNotforUser_CheckChains.r |only
MRH-2.0/MRH/R/FunctionsNotforUser_Convergence.r | 7
MRH-2.0/MRH/R/FunctionsNotforUser_Posteriors.r | 27 ++
MRH-2.0/MRH/R/FunctionsforUser.r | 127 ++++++++-----
MRH-2.0/MRH/R/NPHBA_samplegamma.r |only
MRH-2.0/MRH/R/NPHBA_samplek.r |only
MRH-2.0/MRH/R/NPHBA_samplekandgamma.r |only
MRH-2.0/MRH/R/NPHBA_samplesimple.r |only
MRH-2.0/MRH/R/NPHBA_shell.r |only
MRH-2.0/MRH/R/PH_samplegamma.r |only
MRH-2.0/MRH/R/PH_samplek.r |only
MRH-2.0/MRH/R/PH_samplekandgamma.r |only
MRH-2.0/MRH/R/PH_samplesimple.r |only
MRH-2.0/MRH/R/PH_shell.r |only
MRH-2.0/MRH/R/S3functions.r | 103 ++++++++++
MRH-2.0/MRH/R/S3functions_BA.r | 62 ------
MRH-2.0/MRH/R/S3functions_PH.r | 106 +----------
MRH-2.0/MRH/R/estimateMRH.r | 187 +++++++++++++++++--
MRH-2.0/MRH/build/vignette.rds |binary
MRH-2.0/MRH/inst/doc/MRH.pdf |binary
MRH-2.0/MRH/man/AnalyzeMultiple.Rd | 23 +-
MRH-2.0/MRH/man/CalcFunction.Rd | 12 -
MRH-2.0/MRH/man/DIC.Rd | 17 +
MRH-2.0/MRH/man/MRH.Rd | 15 +
MRH-2.0/MRH/man/estimateMRH.Rd | 72 +++++--
MRH-2.0/MRH/man/nph.Rd | 3
MRH-2.0/MRH/man/plot.MRH.Rd | 23 +-
MRH-2.0/MRH/man/summary.MRH.Rd |only
MRH-2.0/MRH/src/arms-R.c | 4
34 files changed, 662 insertions(+), 416 deletions(-)
Title: A Utility to Send Emails from R
Diff between mailR versions 0.4 dated 2015-01-11 and 0.4.1 dated 2015-01-13
Description: Interface to Apache Commons Email to send emails
from R.
Author: Rahul Premraj
Maintainer: Rahul Premraj
mailR-0.4.1/mailR/DESCRIPTION | 8
mailR-0.4.1/mailR/MD5 | 577 ------------------------------------------
mailR-0.4.1/mailR/R/mailR.R | 2
mailR-0.4.1/mailR/java/README |only
mailR-0.4/mailR/java/email |only
mailR-0.4/mailR/java/javamail |only
6 files changed, 8 insertions(+), 579 deletions(-)
Title: Hive Plots of R Package Function Calls
Diff between FuncMap versions 1.0-2 dated 2013-03-29 and 1.0-3 dated 2015-01-13
Description: FuncMap analyzes the function calls in an R package and creates a hive plot of the calls, dividing them among functions that only make outgoing calls (sources), functions that have only incoming calls (sinks), and those that have both incoming calls and make outgoing calls (managers). Function calls can be mapped by their absolute numbers, their normalized absolute numbers, or their rank. FuncMap should be useful for comparing packages at a high level for their overall design. Plus, it's just plain fun. The hive plot concept was developed by Martin Krzywinski (www.hiveplot.com) and inspired this package.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
DESCRIPTION | 19 +++++--------------
MD5 | 8 ++++----
NEWS | 7 +++++++
inst/CITATION | 5 ++---
man/FuncMap-package.Rd | 4 ++--
5 files changed, 20 insertions(+), 23 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Diff between ExomeDepth versions 1.0.7 dated 2014-07-20 and 1.1.1 dated 2015-01-13
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
ExomeDepth-1.0.7/ExomeDepth/man/plot-methods.Rd |only
ExomeDepth-1.1.1/ExomeDepth/DESCRIPTION | 19
ExomeDepth-1.1.1/ExomeDepth/MD5 | 40 -
ExomeDepth-1.1.1/ExomeDepth/NAMESPACE | 12
ExomeDepth-1.1.1/ExomeDepth/R/class_definition.R | 18
ExomeDepth-1.1.1/ExomeDepth/R/countBamInGranges.R | 129 ++---
ExomeDepth-1.1.1/ExomeDepth/R/plot_CNVs_method.R | 22
ExomeDepth-1.1.1/ExomeDepth/R/tools.R | 8
ExomeDepth-1.1.1/ExomeDepth/build/vignette.rds |binary
ExomeDepth-1.1.1/ExomeDepth/data/Conrad.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/ExomeCount.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/exons.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/exons.hg19.X.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/genes.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.R | 249 +++-------
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw | 48 +
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary
ExomeDepth-1.1.1/ExomeDepth/man/plot.ExomeDepth.Rd |only
ExomeDepth-1.1.1/ExomeDepth/src/CNV_estimate.cpp | 2
ExomeDepth-1.1.1/ExomeDepth/src/VP_gamma.c | 2
ExomeDepth-1.1.1/ExomeDepth/src/hmm.cpp | 3
ExomeDepth-1.1.1/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw | 48 +
22 files changed, 295 insertions(+), 305 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Diff between bnlearn versions 3.6 dated 2014-06-17 and 3.7 dated 2015-01-13
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 discrete, Gaussian and conditional 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-3.6/bnlearn/src/gaussian.likelihood.c |only
bnlearn-3.6/bnlearn/src/mutual.information.c |only
bnlearn-3.7/bnlearn/Changelog | 29
bnlearn-3.7/bnlearn/DESCRIPTION | 16
bnlearn-3.7/bnlearn/MD5 | 213 +--
bnlearn-3.7/bnlearn/NAMESPACE | 11
bnlearn-3.7/bnlearn/R/arc.operations.R | 2
bnlearn-3.7/bnlearn/R/arc.strength.R | 2
bnlearn-3.7/bnlearn/R/backend-indep.R | 111 -
bnlearn-3.7/bnlearn/R/backend-s4.R | 6
bnlearn-3.7/bnlearn/R/backend-score.R | 2
bnlearn-3.7/bnlearn/R/bootstrap.R | 32
bnlearn-3.7/bnlearn/R/choose.direction.R | 437 ++----
bnlearn-3.7/bnlearn/R/ci.test.R | 192 --
bnlearn-3.7/bnlearn/R/cpq.R | 6
bnlearn-3.7/bnlearn/R/custom.fit.R |only
bnlearn-3.7/bnlearn/R/cv.R | 18
bnlearn-3.7/bnlearn/R/fast-iamb.R | 49
bnlearn-3.7/bnlearn/R/fit.R | 289 ++--
bnlearn-3.7/bnlearn/R/fitted.assignment.R |only
bnlearn-3.7/bnlearn/R/foreign-read.R | 60
bnlearn-3.7/bnlearn/R/frontend-bn.R | 16
bnlearn-3.7/bnlearn/R/frontend-bootstrap.R | 8
bnlearn-3.7/bnlearn/R/frontend-data.R | 16
bnlearn-3.7/bnlearn/R/frontend-fit.R | 207 --
bnlearn-3.7/bnlearn/R/frontend-foreign.R | 6
bnlearn-3.7/bnlearn/R/frontend-learning.R | 11
bnlearn-3.7/bnlearn/R/frontend-mvber.R | 2
bnlearn-3.7/bnlearn/R/frontend-nodes.R | 8
bnlearn-3.7/bnlearn/R/frontend-packages.R | 41
bnlearn-3.7/bnlearn/R/frontend-plot.R | 4
bnlearn-3.7/bnlearn/R/frontend-predict.R | 33
bnlearn-3.7/bnlearn/R/frontend-print.R | 31
bnlearn-3.7/bnlearn/R/frontend-score.R | 18
bnlearn-3.7/bnlearn/R/frontend-simulation.R | 18
bnlearn-3.7/bnlearn/R/globals.R | 54
bnlearn-3.7/bnlearn/R/graphviz.R | 60
bnlearn-3.7/bnlearn/R/grow-shrink.R | 41
bnlearn-3.7/bnlearn/R/hiton-pc.R | 48
bnlearn-3.7/bnlearn/R/incremental-association.R | 39
bnlearn-3.7/bnlearn/R/init.R | 4
bnlearn-3.7/bnlearn/R/inter-iamb.R | 43
bnlearn-3.7/bnlearn/R/lattice.R | 164 +-
bnlearn-3.7/bnlearn/R/learning-algorithms.R | 181 +-
bnlearn-3.7/bnlearn/R/loss.R | 4
bnlearn-3.7/bnlearn/R/maxmin-pc.R | 86 -
bnlearn-3.7/bnlearn/R/nparams.R |only
bnlearn-3.7/bnlearn/R/predict.R | 31
bnlearn-3.7/bnlearn/R/test.R | 11
bnlearn-3.7/bnlearn/R/utils-arcs.R | 14
bnlearn-3.7/bnlearn/R/utils-cluster.R | 21
bnlearn-3.7/bnlearn/R/utils-graph.R | 54
bnlearn-3.7/bnlearn/R/utils-misc.R | 96 -
bnlearn-3.7/bnlearn/R/utils-sanitization.R | 506 ++++---
bnlearn-3.7/bnlearn/data/clgaussian.test.rda |only
bnlearn-3.7/bnlearn/inst/network.scripts/clgaussian.test.R |only
bnlearn-3.7/bnlearn/man/arc.strength.Rd | 8
bnlearn-3.7/bnlearn/man/bn.cv.Rd | 2
bnlearn-3.7/bnlearn/man/bn.fit.Rd | 45
bnlearn-3.7/bnlearn/man/bn.fit.class.Rd | 83 -
bnlearn-3.7/bnlearn/man/bn.fit.methods.Rd | 8
bnlearn-3.7/bnlearn/man/bnlearn-package.Rd | 31
bnlearn-3.7/bnlearn/man/ci.test.Rd | 12
bnlearn-3.7/bnlearn/man/clgaussian-test.Rd |only
bnlearn-3.7/bnlearn/man/cpdag.Rd | 12
bnlearn-3.7/bnlearn/man/cpquery.Rd | 2
bnlearn-3.7/bnlearn/man/foreign.Rd | 4
bnlearn-3.7/bnlearn/man/gRain.Rd | 2
bnlearn-3.7/bnlearn/man/learn.Rd | 6
bnlearn-3.7/bnlearn/man/naive.bayes.Rd | 12
bnlearn-3.7/bnlearn/man/score.Rd | 13
bnlearn-3.7/bnlearn/src/allocations.c | 23
bnlearn-3.7/bnlearn/src/allsubs.test.c | 907 ++++++++-----
bnlearn-3.7/bnlearn/src/bayesian.network.c | 142 --
bnlearn-3.7/bnlearn/src/bind.c | 6
bnlearn-3.7/bnlearn/src/cache.structure.c | 2
bnlearn-3.7/bnlearn/src/cg.assumptions.c |only
bnlearn-3.7/bnlearn/src/cg.loglikelihood.c |only
bnlearn-3.7/bnlearn/src/cg.mutual.information.c |only
bnlearn-3.7/bnlearn/src/common.c | 21
bnlearn-3.7/bnlearn/src/common.h | 51
bnlearn-3.7/bnlearn/src/configurations.c | 93 -
bnlearn-3.7/bnlearn/src/ctest.c |only
bnlearn-3.7/bnlearn/src/data.frame.c | 3
bnlearn-3.7/bnlearn/src/dedup.c | 4
bnlearn-3.7/bnlearn/src/dirichlet.posterior.c | 7
bnlearn-3.7/bnlearn/src/discrete.loglikelihood.c | 10
bnlearn-3.7/bnlearn/src/discrete.monte.carlo.c | 2
bnlearn-3.7/bnlearn/src/discrete.mutual.information.c |only
bnlearn-3.7/bnlearn/src/filter.arcs.c | 2
bnlearn-3.7/bnlearn/src/fitted.c | 48
bnlearn-3.7/bnlearn/src/gaussian.loglikelihood.c |only
bnlearn-3.7/bnlearn/src/gaussian.monte.carlo.c | 5
bnlearn-3.7/bnlearn/src/gaussian.mutual.information.c |only
bnlearn-3.7/bnlearn/src/globals.c | 1
bnlearn-3.7/bnlearn/src/graph.generation.c | 2
bnlearn-3.7/bnlearn/src/graph.priors.c | 2
bnlearn-3.7/bnlearn/src/indep.test.c | 765 ----------
bnlearn-3.7/bnlearn/src/jonckheere.c | 2
bnlearn-3.7/bnlearn/src/likelihood.weighting.c | 4
bnlearn-3.7/bnlearn/src/linear.algebra.c | 36
bnlearn-3.7/bnlearn/src/linear.correlation.c | 2
bnlearn-3.7/bnlearn/src/loss.c | 224 ++-
bnlearn-3.7/bnlearn/src/map.lw.c | 5
bnlearn-3.7/bnlearn/src/nparams.c |only
bnlearn-3.7/bnlearn/src/pearson.x2.c | 1
bnlearn-3.7/bnlearn/src/per.node.score.c | 110 +
bnlearn-3.7/bnlearn/src/predict.c | 57
bnlearn-3.7/bnlearn/src/rbn.c | 176 +-
bnlearn-3.7/bnlearn/src/sanitization.c | 88 +
bnlearn-3.7/bnlearn/src/score.delta.c | 11
bnlearn-3.7/bnlearn/src/shrinkage.c | 16
bnlearn-3.7/bnlearn/src/subsets.c | 38
bnlearn-3.7/bnlearn/src/tiers.c | 15
bnlearn-3.7/bnlearn/src/utest.c |only
bnlearn-3.7/bnlearn/src/wishart.posterior.c | 7
116 files changed, 3068 insertions(+), 3411 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Diff between BCEA versions 2.0-2 dated 2013-12-02 and 2.1-0 dated 2015-01-13
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, BCEA computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis
Author: Gianluca Baio, Andrea Berardi
Maintainer: Gianluca Baio
BCEA-2.0-2/BCEA/man/MCMCvaccine.Rd |only
BCEA-2.0-2/BCEA/man/N.Rd |only
BCEA-2.0-2/BCEA/man/N.outcomes.Rd |only
BCEA-2.0-2/BCEA/man/N.resources.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.adv.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.death.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.hosp.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.inf.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.pne.Rd |only
BCEA-2.0-2/BCEA/man/c.Rd |only
BCEA-2.0-2/BCEA/man/cost.GP.Rd |only
BCEA-2.0-2/BCEA/man/cost.hosp.Rd |only
BCEA-2.0-2/BCEA/man/cost.otc.Rd |only
BCEA-2.0-2/BCEA/man/cost.time.off.Rd |only
BCEA-2.0-2/BCEA/man/cost.time.vac.Rd |only
BCEA-2.0-2/BCEA/man/cost.travel.Rd |only
BCEA-2.0-2/BCEA/man/cost.trt1.Rd |only
BCEA-2.0-2/BCEA/man/cost.trt2.Rd |only
BCEA-2.0-2/BCEA/man/cost.vac.Rd |only
BCEA-2.0-2/BCEA/man/e.Rd |only
BCEA-2.0-2/BCEA/man/treats.Rd |only
BCEA-2.1-0/BCEA/DESCRIPTION | 11
BCEA-2.1-0/BCEA/MD5 | 85 -
BCEA-2.1-0/BCEA/R/bcea.R | 2413 ++++++++++++++++++++-------------
BCEA-2.1-0/BCEA/data/Smoking.RData |only
BCEA-2.1-0/BCEA/data/Vaccine.RData |binary
BCEA-2.1-0/BCEA/data/datalist |only
BCEA-2.1-0/BCEA/man/BCEA-package.Rd | 4
BCEA-2.1-0/BCEA/man/CEriskav.Rd | 26
BCEA-2.1-0/BCEA/man/CreateInputs.Rd | 16
BCEA-2.1-0/BCEA/man/Smoking.Rd |only
BCEA-2.1-0/BCEA/man/Vaccine.Rd | 52
BCEA-2.1-0/BCEA/man/bcea.Rd | 52
BCEA-2.1-0/BCEA/man/ceac.plot.Rd | 14
BCEA-2.1-0/BCEA/man/ceaf.plot.Rd | 14
BCEA-2.1-0/BCEA/man/ceef.plot.Rd |only
BCEA-2.1-0/BCEA/man/ceplane.plot.Rd | 29
BCEA-2.1-0/BCEA/man/contour.bcea.Rd | 20
BCEA-2.1-0/BCEA/man/contour2.Rd | 32
BCEA-2.1-0/BCEA/man/diag.evppi.Rd | 45
BCEA-2.1-0/BCEA/man/eib.plot.Rd | 24
BCEA-2.1-0/BCEA/man/evi.plot.Rd | 15
BCEA-2.1-0/BCEA/man/evppi.Rd | 17
BCEA-2.1-0/BCEA/man/ib.plot.Rd | 22
BCEA-2.1-0/BCEA/man/mce.plot.Rd | 6
BCEA-2.1-0/BCEA/man/mixedAn.Rd | 11
BCEA-2.1-0/BCEA/man/multi.ce.Rd | 10
BCEA-2.1-0/BCEA/man/multi.evppi.Rd | 56
BCEA-2.1-0/BCEA/man/plot.CEriskav.Rd | 3
BCEA-2.1-0/BCEA/man/plot.bcea.Rd | 22
BCEA-2.1-0/BCEA/man/plot.evppi.Rd | 4
BCEA-2.1-0/BCEA/man/plot.mixedAn.Rd | 4
BCEA-2.1-0/BCEA/man/sim.table.Rd | 6
BCEA-2.1-0/BCEA/man/struct.psa.Rd | 87 -
BCEA-2.1-0/BCEA/man/summary.bcea.Rd | 10
BCEA-2.1-0/BCEA/man/summary.mixedAn.Rd | 10
56 files changed, 1808 insertions(+), 1312 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Diff between blocksdesign versions 1.3 dated 2014-12-01 and 1.4 dated 2015-01-13
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks strata are optimized hierarchically with each set of
nested blocks optimized within the levels of the preceding set. Block sizes
are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson
DESCRIPTION | 8
MD5 | 10
R/blocks.r | 689 +++++++++++++++++++++++++---------------------------
R/pairwise_effics.r | 6
R/upper_bounds.r | 7
man/blocks.Rd | 145 ++++++----
6 files changed, 431 insertions(+), 434 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Diff between logmult versions 0.6 dated 2014-03-15 and 0.6.1 dated 2015-01-13
Description: Functions to fit log-multiplicative models using gnm, with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
DESCRIPTION | 12 +--
MD5 | 38 +++++-----
NEWS | 12 +++
R/jackboot.R | 7 -
R/jackknife.R | 2
R/maor.R | 83 ++++++++++++++++++-----
R/plot.assoc.R | 182 +++++++++++++++++++++++++++++++++++++++++----------
R/prepareTable.R | 2
R/survey.R | 2
R/unidiff.R | 7 +
man/HMSkew-nonlin.Rd | 2
man/hmskew.Rd | 2
man/hmskewL.Rd | 4 -
man/maor.Rd | 46 ++++++++----
man/plot.assoc.Rd | 34 +++++----
man/plot.unidiff.Rd | 5 -
man/rc.Rd | 4 -
man/rcL.Rd | 8 +-
man/rcL.trans.Rd | 4 -
tests/maor.R | 58 +++++++++++-----
20 files changed, 367 insertions(+), 147 deletions(-)
Title: Calculation of the Integrated Flow of Particles between Polygons
Diff between RCALI versions 0.2-6 dated 2013-01-22 and 0.2-15 dated 2015-01-13
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.
Author: Annie Bouvier, Kien Kieu, Kasia Adamczyk, and Herve Monod
Maintainer: Annie Bouvier
RCALI-0.2-15/RCALI/DESCRIPTION | 20 +++++-------
RCALI-0.2-15/RCALI/LICENSE |only
RCALI-0.2-15/RCALI/MD5 | 42 ++++++++++----------------
RCALI-0.2-15/RCALI/NAMESPACE | 14 ++++----
RCALI-0.2-15/RCALI/NEWS | 42 ++++++++++++++++++++++++++
RCALI-0.2-15/RCALI/R/califlopp.R | 6 +--
RCALI-0.2-15/RCALI/R/listpoly-methods.R | 1
RCALI-0.2-15/RCALI/R/poly-methods.R | 12 +++----
RCALI-0.2-15/RCALI/inst/CITATION | 7 +---
RCALI-0.2-15/RCALI/inst/doc/RCALIvignette.pdf |binary
RCALI-0.2-15/RCALI/src/caliconfig.h | 2 -
RCALI-0.2-15/RCALI/src/fluxsd.cc | 11 +++---
RCALI-0.2-15/RCALI/src/methodAdapt.cc | 1
RCALI-0.2-15/RCALI/src/read1Poly.cc | 3 +
RCALI-0.2-15/RCALI/src/readPoly.cc | 10 ++++--
RCALI-0.2-15/RCALI/tests/paysage.R | 2 -
RCALI-0.2-15/RCALI/tests/paysage.cubres | 9 +++--
RCALI-0.2-15/RCALI/tests/paysage.grid1.1res | 2 -
RCALI-0.2-6/RCALI/COPYING |only
RCALI-0.2-6/RCALI/Makevars |only
RCALI-0.2-6/RCALI/RCALI-Ex.R |only
RCALI-0.2-6/RCALI/tests/data |only
RCALI-0.2-6/RCALI/tests/data.R |only
RCALI-0.2-6/RCALI/tests/data.Rout.save |only
RCALI-0.2-6/RCALI/tests/data.txt |only
RCALI-0.2-6/RCALI/tests/data2 |only
RCALI-0.2-6/RCALI/tests/gridresult |only
27 files changed, 115 insertions(+), 69 deletions(-)
Title: Principal Coordinates of Phylogenetic Structure
Diff between PCPS versions 1.0.1 dated 2014-05-13 and 1.0.2 dated 2015-01-13
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/pcps.curve.R | 2 +-
R/pcps.sig.R | 53 ++++++++++++++++++++++++++++++-----------------------
R/plot.pcps.R | 16 +++++++++++++---
man/pcps.Rd | 6 +++---
man/pcps.sig.Rd | 9 ++++++---
7 files changed, 64 insertions(+), 44 deletions(-)
Title: Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R
Diff between MBmca versions 0.0.3-4 dated 2014-08-26 and 0.0.3-5 dated 2015-01-13
Description: The MBmca package provides data sets and lightweight utilities for
nucleic acid melting curve analysis and presentation on microbead surfaces
but also for reactions in solution (e.g., qPCR).
Author: Stefan Roediger [aut, cre],
Michal Burdukiewicz [ctb]
Maintainer: Stefan Roediger
CHANGELOG | 10
DESCRIPTION | 22 +-
MD5 | 46 ++--
NAMESPACE | 21 -
R/MBmca-package.R |only
R/MFIerror.R | 72 ++++++
R/datasets.R |only
R/diffQ.R | 529 +++++++++++++++++++++++++++++++++++++------------
R/diffQ2.R | 425 +++++++++++++++++++++++++++++++++------
R/mcaPeaks.R | 91 ++++++++
R/mcaSmoother.R | 238 +++++++++++++++++++++-
R/print.diffQ2object.R |only
R/print.diffQobject.R |only
README.md |only
data/DMP.rda |binary
data/DualHyb.rda |binary
data/MultiMelt.rda |binary
inst |only
man/DMP.Rd | 107 ++++-----
man/DualHyb.Rd | 109 ++++------
man/MBmca-package.Rd | 74 ++----
man/MFIerror.Rd | 123 +++++------
man/MultiMelt.Rd | 154 ++++++--------
man/diffQ.Rd | 375 ++++++++++++++++------------------
man/diffQ2.Rd | 413 +++++++++++++++++++-------------------
man/mcaPeaks.Rd | 88 +++-----
man/mcaSmoother.Rd | 266 ++++++++++++------------
27 files changed, 2047 insertions(+), 1116 deletions(-)
Title: A graphical user interface for calculating power and sample size
for hierarchical data
Diff between HierO versions 0.1 dated 2014-10-10 and 0.2 dated 2015-01-13
Description: HierO is a graphical user interface (GUI) tool for calculating optimal statistical power and sample size for hierarchical data structure. HierO constructs a user defined sample size optimization problem to GAMS (General Algebraic Modeling System)form and uses Rneos package to send the problem to NEOS server for solving.
Author: Kari Tokola
Maintainer: Kari Tokola
DESCRIPTION | 11 ++++++-----
MD5 | 4 ++--
NAMESPACE | 1 -
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Spatial point patterns analysis
Diff between ads versions 1.5-2.1 dated 2014-04-22 and 1.5-2.2 dated 2015-01-13
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function, for univariate,
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
statistical significance based on Monte Carlo simulations.
Author: R. Pelissier and F. Goreaud
Maintainer: Raphael Pelissier
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
inst |only
src/adssub.c | 4 ++--
src/adssub.h | 2 +-
src/triangulate.c | 24 +++++++++++++++++++++++-
6 files changed, 35 insertions(+), 12 deletions(-)
Title: Package for ttf2pt1 program
Description: This package contains the program ttf2pt1, for use with the
extrafont package. This product includes software developed by the TTF2PT1
Project and its contributors.
Author: Winston Chang,
Andrew Weeks,
Frank M. Siegert,
Mark Heath,
Thomas Henlick,
Sergey Babkin,
Turgut Uyar,
Rihardas Hepas,
Szalay Tamas,
Johan Vromans,
Petr Titera,
Lei Wang,
Chen Xiangyang,
Zvezdan Petkovic,
Rigel,
I. Lee Hetherington
Maintainer: ORPHANED
Diff between Rttf2pt1 versions 1.3.2 dated 2014-08-15 and 1.3.3 dated 2015-01-13
DESCRIPTION | 8 +++++--- MD5 | 6 +++--- src/ttf2pt1/bitmap.c | 10 +++++----- src/ttf2pt1/pt1.c | 4 ++-- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Reading Machine Learning Benchmark Data Sets in Different
Formats
Diff between readMLData versions 0.9-6 dated 2012-02-08 and 0.9-7 dated 2015-01-13
Description: Functions for reading data sets in different formats
for testing machine learning tools are provided. This allows to run
a loop over several data sets in their original form, for example
if they are downloaded from UCI Machine Learning Repository.
The data are not part of the package and have to be downloaded
separately.
Author: Petr Savicky
Maintainer: Petr Savicky
ChangeLog | 2 ++
DESCRIPTION | 30 +++++++++++++++---------------
MD5 | 8 ++++----
NAMESPACE | 2 ++
man/dsRead.Rd | 3 ++-
5 files changed, 25 insertions(+), 20 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.0.1 dated 2014-10-22 and 1.1 dated 2015-01-13
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 12 -
MD5 | 15 +-
NAMESPACE | 7 +
R/BAT.R | 354 +++++++++++++++++++++++++++++++++++++++++++++--------
man/alpha.accum.Rd | 11 +
man/beta.accum.Rd | 4
man/sim.plot.Rd |only
man/sim.sad.Rd |only
man/sim.sample.Rd |only
man/sim.spatial.Rd |only
man/sim.tree.Rd |only
11 files changed, 333 insertions(+), 70 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-04 1.0.4
2012-04-26 1.0
Title: Trajectory Analysis
Diff between traj versions 1.1 dated 2014-12-01 and 1.2 dated 2015-01-13
Description: Implements the three-step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
inst/CITATION | 5 ++---
inst/doc/Measurement_Equations.pdf |binary
man/traj-package.Rd | 2 +-
5 files changed, 10 insertions(+), 11 deletions(-)
Title: Quantification of the effect of geographic versus environmental
isolation on genetic differentiation
Diff between Sunder versions 0.0.3 dated 2014-08-26 and 0.0.4 dated 2015-01-13
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Casper Eriksen, Gilles Guillot
Maintainer: Filippo Botta
ChangeLog | 24 ++++++++----------------
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/MCMCCV.R | 6 +++---
inst/CITATION | 10 +++++++---
man/Sunder-package.Rd | 4 ++--
6 files changed, 29 insertions(+), 33 deletions(-)
Title: Functions for University of Auckland course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-10 dated 2013-01-14 and 3.1-11 dated 2015-01-13
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
s20x-3.1-10/s20x/data/airpass.df.txt.gz |only
s20x-3.1-10/s20x/data/apples.df.txt.gz |only
s20x-3.1-10/s20x/data/arousal.df.txt.gz |only
s20x-3.1-10/s20x/data/beer.df.txt.gz |only
s20x-3.1-10/s20x/data/body.df.txt.gz |only
s20x-3.1-10/s20x/data/books.df.txt.gz |only
s20x-3.1-10/s20x/data/bursary.df.txt.gz |only
s20x-3.1-10/s20x/data/butterfat.df.txt.gz |only
s20x-3.1-10/s20x/data/camplake.df.txt.gz |only
s20x-3.1-10/s20x/data/chalk.df.txt.gz |only
s20x-3.1-10/s20x/data/computer.df.txt.gz |only
s20x-3.1-10/s20x/data/course.df.txt.gz |only
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s20x-3.1-10/s20x/data/fruitfly.df.txt.gz |only
s20x-3.1-10/s20x/data/house.df.txt.gz |only
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s20x-3.1-10/s20x/data/mozart.df.txt.gz |only
s20x-3.1-10/s20x/data/nail.df.txt.gz |only
s20x-3.1-10/s20x/data/oysters.df.txt.gz |only
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s20x-3.1-10/s20x/data/rain.df.txt.gz |only
s20x-3.1-10/s20x/data/seeds.df.txt.gz |only
s20x-3.1-10/s20x/data/sheep.df.txt.gz |only
s20x-3.1-10/s20x/data/skulls.df.txt.gz |only
s20x-3.1-10/s20x/data/soyabean.df.txt.gz |only
s20x-3.1-10/s20x/data/teach.df.txt.gz |only
s20x-3.1-10/s20x/data/technitron.df.txt.gz |only
s20x-3.1-10/s20x/data/thyroid.df.txt.gz |only
s20x-3.1-10/s20x/data/toothpaste.df.txt.gz |only
s20x-3.1-10/s20x/data/zoo.df.txt.gz |only
s20x-3.1-10/s20x/tests |only
s20x-3.1-11/s20x/DESCRIPTION | 21 -
s20x-3.1-11/s20x/LICENSE |only
s20x-3.1-11/s20x/MD5 | 231 ++++++------
s20x-3.1-11/s20x/NAMESPACE | 94 ++--
s20x-3.1-11/s20x/R/boxqq.r | 106 ++---
s20x-3.1-11/s20x/R/ciReg.R | 46 +-
s20x-3.1-11/s20x/R/cooks20x.R | 22 -
s20x-3.1-11/s20x/R/crossFactors.R | 56 +-
s20x-3.1-11/s20x/R/crosstabs.R | 98 ++---
s20x-3.1-11/s20x/R/eovcheck.R | 290 +++++++--------
s20x-3.1-11/s20x/R/estimateContrasts.R | 18
s20x-3.1-11/s20x/R/estimateContrasts1.R | 90 ++--
s20x-3.1-11/s20x/R/estimateContrasts2.R | 104 ++---
s20x-3.1-11/s20x/R/interactionPlots.R | 306 +++++++--------
s20x-3.1-11/s20x/R/multipleComp.R | 58 +--
s20x-3.1-11/s20x/R/normcheck.R | 114 +++--
s20x-3.1-11/s20x/R/onewayPlot.R | 466 ++++++++++++------------
s20x-3.1-11/s20x/R/pairs20x.R | 54 +-
s20x-3.1-11/s20x/R/predict20x.R | 98 ++---
s20x-3.1-11/s20x/R/propslsd.new.R | 49 +-
s20x-3.1-11/s20x/R/residPlot.R | 84 ++--
s20x-3.1-11/s20x/R/rowdistr.r | 410 +++++++++++----------
s20x-3.1-11/s20x/R/rr.r | 12
s20x-3.1-11/s20x/R/stripqq.r | 106 ++---
s20x-3.1-11/s20x/R/summary1way.R | 150 +++----
s20x-3.1-11/s20x/R/summary2way.R | 558 ++++++++++++++---------------
s20x-3.1-11/s20x/R/summaryStats.R | 82 ++--
s20x-3.1-11/s20x/R/trendscatter.R | 100 +++--
s20x-3.1-11/s20x/README.md |only
s20x-3.1-11/s20x/data/airpass.df.txt |only
s20x-3.1-11/s20x/data/apples.df.txt |only
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s20x-3.1-11/s20x/data/lakemary.df.txt |only
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s20x-3.1-11/s20x/data/seeds.df.txt |only
s20x-3.1-11/s20x/data/sheep.df.txt |only
s20x-3.1-11/s20x/data/skulls.df.txt |only
s20x-3.1-11/s20x/data/soyabean.df.txt |only
s20x-3.1-11/s20x/data/teach.df.txt |only
s20x-3.1-11/s20x/data/technitron.df.txt |only
s20x-3.1-11/s20x/data/thyroid.df.txt |only
s20x-3.1-11/s20x/data/toothpaste.df.txt |only
s20x-3.1-11/s20x/data/zoo.df.txt |only
s20x-3.1-11/s20x/demo/00Index | 88 ++--
s20x-3.1-11/s20x/demo/cs1.r | 16
s20x-3.1-11/s20x/demo/cs10.r | 14
s20x-3.1-11/s20x/demo/cs11.r | 16
s20x-3.1-11/s20x/demo/cs12.r | 26 -
s20x-3.1-11/s20x/demo/cs13.r | 40 +-
s20x-3.1-11/s20x/demo/cs14.r | 24 -
s20x-3.1-11/s20x/demo/cs15.r | 30 -
s20x-3.1-11/s20x/demo/cs16.r | 44 +-
s20x-3.1-11/s20x/demo/cs17.r | 32 -
s20x-3.1-11/s20x/demo/cs18.r | 24 -
s20x-3.1-11/s20x/demo/cs19.r | 30 -
s20x-3.1-11/s20x/demo/cs2.r | 14
s20x-3.1-11/s20x/demo/cs20.r | 36 -
s20x-3.1-11/s20x/demo/cs21.r | 42 +-
s20x-3.1-11/s20x/demo/cs22.r | 22 -
s20x-3.1-11/s20x/demo/cs23.r | 66 +--
s20x-3.1-11/s20x/demo/cs24.r | 36 -
s20x-3.1-11/s20x/demo/cs25.r | 90 ++--
s20x-3.1-11/s20x/demo/cs26.r | 38 -
s20x-3.1-11/s20x/demo/cs27.r | 36 -
s20x-3.1-11/s20x/demo/cs28.r | 18
s20x-3.1-11/s20x/demo/cs29.r | 22 -
s20x-3.1-11/s20x/demo/cs3.r | 10
s20x-3.1-11/s20x/demo/cs30.r | 20 -
s20x-3.1-11/s20x/demo/cs31.r | 18
s20x-3.1-11/s20x/demo/cs32.r | 22 -
s20x-3.1-11/s20x/demo/cs33.r | 20 -
s20x-3.1-11/s20x/demo/cs34.r | 28 -
s20x-3.1-11/s20x/demo/cs35.r | 16
s20x-3.1-11/s20x/demo/cs36.r | 26 -
s20x-3.1-11/s20x/demo/cs37.r | 24 -
s20x-3.1-11/s20x/demo/cs38.r | 30 -
s20x-3.1-11/s20x/demo/cs39.r | 30 -
s20x-3.1-11/s20x/demo/cs4.r | 10
s20x-3.1-11/s20x/demo/cs40.r | 20 -
s20x-3.1-11/s20x/demo/cs41.r | 24 -
s20x-3.1-11/s20x/demo/cs42.r | 22 -
s20x-3.1-11/s20x/demo/cs43.r | 20 -
s20x-3.1-11/s20x/demo/cs5.r | 12
s20x-3.1-11/s20x/demo/cs6.r | 18
s20x-3.1-11/s20x/demo/cs7.r | 24 -
s20x-3.1-11/s20x/demo/cs8.r | 34 -
s20x-3.1-11/s20x/demo/cs9.r | 14
s20x-3.1-11/s20x/inst |only
s20x-3.1-11/s20x/man/eovcheck.Rd | 155 ++++----
s20x-3.1-11/s20x/man/interactionPlots.Rd | 145 ++++---
s20x-3.1-11/s20x/man/normcheck.Rd | 105 ++---
s20x-3.1-11/s20x/man/rowdistr.Rd | 79 ++--
s20x-3.1-11/s20x/man/trendscatter.Rd | 110 ++---
154 files changed, 2885 insertions(+), 2778 deletions(-)
Title: R Transcription Factor Binding Site identification tool
Diff between rtfbs versions 0.3.2 dated 2013-12-06 and 0.3.3 dated 2015-01-13
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
rtfbs-0.3.2/rtfbs/configure.win |only
rtfbs-0.3.2/rtfbs/src/pcre |only
rtfbs-0.3.2/rtfbs/tests/input.fas |only
rtfbs-0.3.2/rtfbs/tests/pwm.meme |only
rtfbs-0.3.3/rtfbs/ChangeLog | 1
rtfbs-0.3.3/rtfbs/DESCRIPTION | 15
rtfbs-0.3.3/rtfbs/LICENSE | 2
rtfbs-0.3.3/rtfbs/MD5 | 143 -
rtfbs-0.3.3/rtfbs/NAMESPACE | 16
rtfbs-0.3.3/rtfbs/build/vignette.rds |binary
rtfbs-0.3.3/rtfbs/configure | 2749 ++-----------------------------
rtfbs-0.3.3/rtfbs/configure.ac | 508 -----
rtfbs-0.3.3/rtfbs/inst/doc/vignette.pdf |binary
rtfbs-0.3.3/rtfbs/man/as.pointer.ms.Rd | 30
rtfbs-0.3.3/rtfbs/man/build.mm.Rd | 35
rtfbs-0.3.3/rtfbs/man/calc.fdr.Rd | 54
rtfbs-0.3.3/rtfbs/man/concat.ms.Rd | 10
rtfbs-0.3.3/rtfbs/man/from.pointer.ms.Rd | 35
rtfbs-0.3.3/rtfbs/man/gcContent.ms.Rd | 13
rtfbs-0.3.3/rtfbs/man/groupByGC.ms.Rd | 18
rtfbs-0.3.3/rtfbs/man/is.pointer.ms.Rd | 19
rtfbs-0.3.3/rtfbs/man/label.matrix.Rd | 28
rtfbs-0.3.3/rtfbs/man/length.ms.Rd | 11
rtfbs-0.3.3/rtfbs/man/lengths.ms.Rd | 13
rtfbs-0.3.3/rtfbs/man/makeFdrPlot.Rd | 39
rtfbs-0.3.3/rtfbs/man/ms.Rd | 89 -
rtfbs-0.3.3/rtfbs/man/names.ms.Rd | 15
rtfbs-0.3.3/rtfbs/man/offsets.ms.Rd | 14
rtfbs-0.3.3/rtfbs/man/open-brace.ms.Rd | 31
rtfbs-0.3.3/rtfbs/man/output.sites.Rd | 40
rtfbs-0.3.3/rtfbs/man/print.ms.Rd | 18
rtfbs-0.3.3/rtfbs/man/read.mm.Rd | 13
rtfbs-0.3.3/rtfbs/man/read.ms.Rd | 26
rtfbs-0.3.3/rtfbs/man/read.pwm.Rd | 29
rtfbs-0.3.3/rtfbs/man/rtfbs-package.Rd | 18
rtfbs-0.3.3/rtfbs/man/score.ms.Rd | 81
rtfbs-0.3.3/rtfbs/man/sequences.ms.Rd | 11
rtfbs-0.3.3/rtfbs/man/simulate.ms.Rd | 36
rtfbs-0.3.3/rtfbs/man/split.ms.Rd | 34
rtfbs-0.3.3/rtfbs/man/summary.ms.Rd | 25
rtfbs-0.3.3/rtfbs/man/write.mm.Rd | 15
rtfbs-0.3.3/rtfbs/man/write.ms.Rd | 14
rtfbs-0.3.3/rtfbs/src/Makevars.in | 125 -
rtfbs-0.3.3/rtfbs/src/Makevars.win | 125 -
rtfbs-0.3.3/rtfbs/src/complex_matrix.c | 34
rtfbs-0.3.3/rtfbs/src/fit_column.c | 454 ++---
rtfbs-0.3.3/rtfbs/src/fit_column.h | 74
rtfbs-0.3.3/rtfbs/src/fit_feature.c | 2
rtfbs-0.3.3/rtfbs/src/lists.h | 9
rtfbs-0.3.3/rtfbs/src/maf.c | 274 +--
rtfbs-0.3.3/rtfbs/src/markov_matrix.c | 98 -
rtfbs-0.3.3/rtfbs/src/matrix.c | 38
rtfbs-0.3.3/rtfbs/src/misc.c | 4
rtfbs-0.3.3/rtfbs/src/misc.h | 159 -
rtfbs-0.3.3/rtfbs/src/phylo_fit.c | 60
rtfbs-0.3.3/rtfbs/src/phylo_p_print.c | 207 +-
rtfbs-0.3.3/rtfbs/src/prob_matrix.c | 6
rtfbs-0.3.3/rtfbs/src/subst_mods.c | 635 +++----
58 files changed, 1838 insertions(+), 4714 deletions(-)
Title: Functions for clustering of presence-absence, abundance and
multilocus genetic data
Diff between prabclus versions 2.2-4 dated 2012-08-25 and 2.2-5 dated 2015-01-13
Description: Distance-based parametric bootstrap tests for clustering
with spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus
genetical data for species delimitation, nearest neighbor based
noise detection. Try package?prabclus for on overview.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 7 ++++---
MD5 | 4 ++--
R/abundfunctions.R | 1 +
3 files changed, 7 insertions(+), 5 deletions(-)
Title: Robust Meta-analysis and Meta-regression
Diff between metaplus versions 0.7-0 dated 2015-01-11 and 0.7-1 dated 2015-01-13
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Author: Ken Beath
Maintainer: Ken Beath
DESCRIPTION | 8
MD5 | 14
NAMESPACE | 2
R/makestart.profilemix.metaplus.R | 360 ++++++++++++------------
R/profilemix.metaplus.R | 298 ++++++++++----------
R/profilemix.profile.R | 556 +++++++++++++++++++-------------------
R/profilet.metaplus.R | 2
inst/NEWS | 44 +--
8 files changed, 671 insertions(+), 613 deletions(-)
Title: Various Options and Add-ins for Lattice
Diff between loa versions 0.2.15 dated 2014-01-15 and 0.2.21 dated 2015-01-13
Description: This package, Lattice Options and Add-ins (or loa), contains various plots and
functions that make use of the lattice/trellis plotting framework. The plots (which include
loaPlot, GoogleMap and trianglePlot) use panelPal, a function that extends lattice and hexbin
package methods to automate plot subscripting and panel-to-panel and panel-to key
synchronization. See ?loa for further details.
Author: Karl Ropkins
Maintainer: Karl Ropkins
DESCRIPTION | 20
MD5 | 32 -
NAMESPACE | 29 -
NEWS | 52 ++
R/formulaHandler.R | 467 +++++++++++-------
R/key.handlers.R | 22
R/lims.and.scales.handlers.R | 18
R/loaPlot.R | 24
R/panelPal.R | 26 -
R/trianglePlot.R | 941 ++++++++++++++++---------------------
data/lat.lon.meuse.RData |binary
data/roadmap.meuse.RData |binary
man/1.1.loaPlot.Rd | 3
man/1.2.googleMap.Rd | 2
man/1.3.trianglePlot.Rd | 359 ++++++--------
man/4.2.plot.structure.handlers.Rd | 18
man/loa-package.Rd | 4
17 files changed, 1077 insertions(+), 940 deletions(-)
Title: Linear regression based on linear structure between covariates
Diff between CorReg versions 0.15.8 dated 2014-11-04 and 1.0 dated 2015-01-13
Description: Linear regression based on a recursive structural equation model
(explicit correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elasticnet, etc.). It also provides some graphical tools for basic
statistics.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY
DESCRIPTION | 25 +--
MD5 | 90 ++++++-------
NAMESPACE | 4
R/A_clere.R | 2
R/CorReg-package.R | 9 -
R/WhoIs.R | 2
R/correg.R | 311 +++++-----------------------------------------
R/density_estimation.R | 5
R/fillmiss.R | 26 +--
R/meilleur_lars.R | 6
man/BicZ.Rd | 3
man/BicZcurve.Rd | 3
man/CVMSE.Rd | 3
man/CorReg-package.Rd | 11 -
man/Estep.Rd | 3
man/MSEZ.Rd | 3
man/MSE_loc.Rd | 3
man/OLS.Rd | 3
man/ProbaZ.Rd | 3
man/R2Z.Rd | 3
man/Terminator.Rd | 3
man/WhoIs.Rd | 5
man/Winitial.Rd | 3
man/Y_generator.Rd | 3
man/cleanYtest.Rd | 3
man/cleanZ.Rd | 3
man/cleanZR2.Rd | 3
man/cleancolZ.Rd | 3
man/compare_beta.Rd | 3
man/compare_sign.Rd | 3
man/compare_struct.Rd | 3
man/compare_zero.Rd | 3
man/confint_coef.Rd | 3
man/correg.Rd | 28 +---
man/density_estimation.Rd | 3
man/fillmiss.Rd | 8 -
man/hatB.Rd | 3
man/matplot_zone.Rd | 3
man/mixture_generator.Rd | 3
man/readY.Rd | 3
man/readZ.Rd | 3
man/recursive_tree.Rd | 3
man/rforge.Rd | 3
man/searchZ_sparse.Rd | 3
man/showdata.Rd | 3
man/structureFinder.Rd | 3
46 files changed, 213 insertions(+), 415 deletions(-)