Title: Grammatical Evolution for R
Description: A native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian <farzad.noorian@gmail.com>
Diff between gramEvol versions 2.0-2 dated 2015-02-11 and 2.1-2 dated 2015-11-16
gramEvol-2.0-2/gramEvol/ChangeLog |only gramEvol-2.1-2/gramEvol/DESCRIPTION | 14 ++-- gramEvol-2.1-2/gramEvol/MD5 | 34 +++++---- gramEvol-2.1-2/gramEvol/NAMESPACE | 3 gramEvol-2.1-2/gramEvol/NEWS |only gramEvol-2.1-2/gramEvol/R/GERule.R | 5 + gramEvol-2.1-2/gramEvol/R/GERule_Concat.R | 6 + gramEvol-2.1-2/gramEvol/R/SymbolicRuleToListRule.R | 21 +++++- gramEvol-2.1-2/gramEvol/README.md | 37 ++++------ gramEvol-2.1-2/gramEvol/build/vignette.rds |binary gramEvol-2.1-2/gramEvol/inst/CITATION |only gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.R | 72 ++++++++++----------- gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.Rnw | 10 -- gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.pdf |binary gramEvol-2.1-2/gramEvol/man/CreateGrammar.Rd | 16 ++++ gramEvol-2.1-2/gramEvol/man/GeneticAlg.int.Rd | 4 - gramEvol-2.1-2/gramEvol/man/c.GERule.Rd |only gramEvol-2.1-2/gramEvol/tests/grammar_newstyle.R | 5 + gramEvol-2.1-2/gramEvol/vignettes/ge-intro.Rnw | 10 -- gramEvol-2.1-2/gramEvol/vignettes/vig_refs.bib | 12 --- 20 files changed, 137 insertions(+), 112 deletions(-)
Title: Noncentral Dunnett's Test Distribution
Description: Computes the noncentral Dunnett's test distribution (pdf, cdf and quantile) and generates random numbers.
Author: Siomara Cristina Broch, Daniel Furtado Ferreira
Maintainer: Daniel Furtado Ferreira <danielff@dex.ufla.br>
Diff between nCDunnett versions 1.0.0 dated 2013-02-01 and 1.1.0 dated 2015-11-16
nCDunnett-1.0.0/nCDunnett/Rplots.pdf |only nCDunnett-1.1.0/nCDunnett/DESCRIPTION | 14 +++++----- nCDunnett-1.1.0/nCDunnett/MD5 | 17 +++++------- nCDunnett-1.1.0/nCDunnett/NAMESPACE | 1 nCDunnett-1.1.0/nCDunnett/R/dNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/nonCentralDunnett.R | 33 ++++++++++++++---------- nCDunnett-1.1.0/nCDunnett/R/pNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/qNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/rNCDun.R | 4 +- nCDunnett-1.1.0/nCDunnett/man/nCDunnett.Rd | 26 +++++++++--------- 10 files changed, 54 insertions(+), 47 deletions(-)
Title: Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Description: A method for obtain nonparametric estimates of regression models
with or without factor-by-curve interactions using local polynomial
kernel smoothers. Additionally, a parametric model (allometric model)
can be estimated.
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between npregfast versions 1.0 dated 2015-11-09 and 1.0.1 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS |only R/allotest.R | 13 +++++++++---- R/frfast.R | 8 +++++++- R/globaltest.R | 9 +++++++-- R/localtest.R | 7 ++++++- R/predict.frfast.R | 7 ++++++- man/allotest.Rd | 2 +- src/program2.f90 | 11 ++++++----- 10 files changed, 55 insertions(+), 27 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.3-0 dated 2015-07-02 and 4.3-1 dated 2015-11-16
DESCRIPTION | 8 +- MD5 | 34 ++++----- NEWS | 30 ++++++++ R/chkchar.R | 9 +- R/chkclass.R | 5 - R/chklength.R | 5 - R/chklevel.R | 5 - R/chklogical.R | 5 - R/chkmiss.R | 5 - R/chknull.R | 5 - R/chknumeric.R | 6 + R/forest.meta.R | 66 +++++++++++------ R/format.p.R | 7 + R/format.tau.R | 6 - R/paulemandel.R | 11 +- R/setchar.R | 5 - R/settings.meta.R | 201 +++++++++++++++++++++++++++++++++++++----------------- man/forest.Rd | 45 ++++++++---- 18 files changed, 313 insertions(+), 145 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based
on the Clinical Scenario Evaluation (CSE) approach. The package supports a
broad class of data models (including clinical trials with continuous, binary,
survival-type and count-type endpoints as well as multivariate outcomes that are
based on combinations of different endpoints), analysis strategies and commonly
used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0.1 dated 2015-07-26 and 1.0.2 dated 2015-11-16
Mediana-1.0.1/Mediana/R/Mediana.R |only Mediana-1.0.2/Mediana/DESCRIPTION | 18 + Mediana-1.0.2/Mediana/MD5 | 160 ++++++++++++++- Mediana-1.0.2/Mediana/NAMESPACE | 2 Mediana-1.0.2/Mediana/R/AnalysisModel.Interim.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdj.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.Statistic.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.Test.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.default.R |only Mediana-1.0.2/Mediana/R/BinomDist.R |only Mediana-1.0.2/Mediana/R/BonferroniAdj.R |only Mediana-1.0.2/Mediana/R/BonferroniAdj.global.R |only Mediana-1.0.2/Mediana/R/BroadClaimPower.R |only Mediana-1.0.2/Mediana/R/CSE.R |only Mediana-1.0.2/Mediana/R/CSE.default.R |only Mediana-1.0.2/Mediana/R/ChainAdj.R |only Mediana-1.0.2/Mediana/R/ConjunctivePower.R |only Mediana-1.0.2/Mediana/R/CreateAnalysisStructure.R |only Mediana-1.0.2/Mediana/R/CreateDataScenarioEvent.R |only Mediana-1.0.2/Mediana/R/CreateDataScenarioSampleSize.R |only Mediana-1.0.2/Mediana/R/CreateDataSlice.R |only Mediana-1.0.2/Mediana/R/CreateDataStack.R |only Mediana-1.0.2/Mediana/R/CreateDataStructure.R |only Mediana-1.0.2/Mediana/R/CreateEvaluationStructure.R |only Mediana-1.0.2/Mediana/R/CreateReportStructure.R |only Mediana-1.0.2/Mediana/R/CreateSummaryTable.R |only Mediana-1.0.2/Mediana/R/CreateTableDesign.R |only Mediana-1.0.2/Mediana/R/CreateTableOutcome.R |only Mediana-1.0.2/Mediana/R/CreateTableSampleSize.R |only Mediana-1.0.2/Mediana/R/CreateTableStatistic.R |only Mediana-1.0.2/Mediana/R/CreateTableStructure.R |only Mediana-1.0.2/Mediana/R/CreateTableTest.R |only Mediana-1.0.2/Mediana/R/Criterion.R |only Mediana-1.0.2/Mediana/R/CustomLabel.R |only Mediana-1.0.2/Mediana/R/DataModel.Design.R |only Mediana-1.0.2/Mediana/R/DataModel.Event.R |only Mediana-1.0.2/Mediana/R/DataModel.OutcomeDist.R |only Mediana-1.0.2/Mediana/R/DataModel.R |only Mediana-1.0.2/Mediana/R/DataModel.SampleSize.R |only Mediana-1.0.2/Mediana/R/DataModel.default.R |only Mediana-1.0.2/Mediana/R/Design.R |only Mediana-1.0.2/Mediana/R/DiffMeanStat.R |only Mediana-1.0.2/Mediana/R/DiffPropStat.R |only Mediana-1.0.2/Mediana/R/DisjunctivePower.R |only Mediana-1.0.2/Mediana/R/EffectSizeContStat.R |only Mediana-1.0.2/Mediana/R/EffectSizeEventStat.R |only Mediana-1.0.2/Mediana/R/EffectSizePropStat.R |only Mediana-1.0.2/Mediana/R/EnhancedClaimPower.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.Criterion.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.default.R |only Mediana-1.0.2/Mediana/R/Event.R |only Mediana-1.0.2/Mediana/R/EventCountStat.R |only Mediana-1.0.2/Mediana/R/ExpectedRejPower.R |only Mediana-1.0.2/Mediana/R/ExpoDist.R |only Mediana-1.0.2/Mediana/R/FisherTest.R |only Mediana-1.0.2/Mediana/R/GLMNegBinomTest.R |only Mediana-1.0.2/Mediana/R/GLMPoissonTest.R |only Mediana-1.0.2/Mediana/R/GeneratePatients.R |only Mediana-1.0.2/Mediana/R/GenerateReport.R |only Mediana-1.0.2/Mediana/R/GenerateReport.default.R |only Mediana-1.0.2/Mediana/R/HazardRatioStat.R |only Mediana-1.0.2/Mediana/R/HochbergAdj.R |only Mediana-1.0.2/Mediana/R/HochbergAdj.global.R |only Mediana-1.0.2/Mediana/R/HolmAdj.R |only Mediana-1.0.2/Mediana/R/HolmAdj.global.R |only Mediana-1.0.2/Mediana/R/HommelAdj.R |only Mediana-1.0.2/Mediana/R/HommelAdj.global.R |only Mediana-1.0.2/Mediana/R/InfluencePower.R |only Mediana-1.0.2/Mediana/R/InteractionPower.R |only Mediana-1.0.2/Mediana/R/Interim.R |only Mediana-1.0.2/Mediana/R/LogrankTest.R |only Mediana-1.0.2/Mediana/R/MVBinomDist.R |only Mediana-1.0.2/Mediana/R/MVExpoDist.R |only Mediana-1.0.2/Mediana/R/MVExpoPFSOSDist.R |only Mediana-1.0.2/Mediana/R/MVMixedDist.R |only Mediana-1.0.2/Mediana/R/MVNormalDist.R |only Mediana-1.0.2/Mediana/R/MarginalPower.R |only Mediana-1.0.2/Mediana/R/MaxStat.R |only Mediana-1.0.2/Mediana/R/MeanStat.R |only Mediana-1.0.2/Mediana/R/MeanSumm.R |only Mediana-1.0.2/Mediana/R/MedianStat.R |only Mediana-1.0.2/Mediana/R/MedianSumm.R |only Mediana-1.0.2/Mediana/R/MinStat.R |only Mediana-1.0.2/Mediana/R/MultAdj.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdj.MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/MultAdj.R |only Mediana-1.0.2/Mediana/R/MultAdj.default.R |only Mediana-1.0.2/Mediana/R/MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.default.R |only Mediana-1.0.2/Mediana/R/MultipleSequenceGatekeepingAdj.R |only Mediana-1.0.2/Mediana/R/NegBinomDist.R |only Mediana-1.0.2/Mediana/R/NormalDist.R |only Mediana-1.0.2/Mediana/R/NormalParamAdj.R |only Mediana-1.0.2/Mediana/R/NormalParamDist.R |only Mediana-1.0.2/Mediana/R/OutcomeDist.R |only Mediana-1.0.2/Mediana/R/ParallelGatekeepingAdj.R |only Mediana-1.0.2/Mediana/R/PatientCountStat.R |only Mediana-1.0.2/Mediana/R/PerformAnalysis.R |only Mediana-1.0.2/Mediana/R/PoissonDist.R |only Mediana-1.0.2/Mediana/R/PresentationModel.CustomLabel.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Project.R |only Mediana-1.0.2/Mediana/R/PresentationModel.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Section.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Subsection.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Table.R |only Mediana-1.0.2/Mediana/R/PresentationModel.default.R |only Mediana-1.0.2/Mediana/R/Project.R |only Mediana-1.0.2/Mediana/R/PropTest.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizeContStat.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizeEventStat.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizePropStat.R |only Mediana-1.0.2/Mediana/R/RestrictedClaimPower.R |only Mediana-1.0.2/Mediana/R/Sample.R |only Mediana-1.0.2/Mediana/R/SampleSize.R |only Mediana-1.0.2/Mediana/R/SdStat.R |only Mediana-1.0.2/Mediana/R/Section.R |only Mediana-1.0.2/Mediana/R/SimParameters.R |only Mediana-1.0.2/Mediana/R/Statistic.R |only Mediana-1.0.2/Mediana/R/Subsection.R |only Mediana-1.0.2/Mediana/R/TTest.R |only Mediana-1.0.2/Mediana/R/TTestNI.R |only Mediana-1.0.2/Mediana/R/Table.R |only Mediana-1.0.2/Mediana/R/Test.R |only Mediana-1.0.2/Mediana/R/UniformDist.R |only Mediana-1.0.2/Mediana/R/WeightedPower.R |only Mediana-1.0.2/Mediana/R/WilcoxTest.R |only Mediana-1.0.2/Mediana/R/appendList.R |only Mediana-1.0.2/Mediana/R/argmin.R |only Mediana-1.0.2/Mediana/R/capwords.R |only Mediana-1.0.2/Mediana/R/errorfrac.R |only Mediana-1.0.2/Mediana/R/families.R |only Mediana-1.0.2/Mediana/R/is.AnalysisModel.R |only Mediana-1.0.2/Mediana/R/is.DataModel.R |only Mediana-1.0.2/Mediana/R/is.EvaluationModel.R |only Mediana-1.0.2/Mediana/R/is.PresentationModel.R |only Mediana-1.0.2/Mediana/R/mergeOutcomeParameter.R |only Mediana-1.0.2/Mediana/R/parameters.R |only Mediana-1.0.2/Mediana/R/samples.R |only Mediana-1.0.2/Mediana/R/seq_vector.R |only Mediana-1.0.2/Mediana/R/statistics.R |only Mediana-1.0.2/Mediana/R/summary.CSE.R |only Mediana-1.0.2/Mediana/R/tests.R |only Mediana-1.0.2/Mediana/R/z+.AnalysisModel.R |only Mediana-1.0.2/Mediana/R/z+.DataModel.R |only Mediana-1.0.2/Mediana/R/z+.EvaluationModel.R |only Mediana-1.0.2/Mediana/R/z+.PresentationModel.R |only Mediana-1.0.2/Mediana/README.md |only Mediana-1.0.2/Mediana/man/DataModel.Rd | 2 Mediana-1.0.2/Mediana/man/Mediana-package.Rd | 8 Mediana-1.0.2/Mediana/man/OutcomeDist.Rd | 14 + 156 files changed, 184 insertions(+), 20 deletions(-)
Title: Determining and Evaluating High-Risk Zones
Description: Functions for determining and evaluating high-risk zones and
simulating and thinning point process data, as described in 'Determining
high risk zones using point process methodology - Realization by building
an R package' (Seibold, 2012) and 'Determining high-risk zones for
unexploded World War II bombs by using point process methodology' (Mahling
et al., 2013).
Author: Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia Mahling
<monia.mahling@stat.uni-muenchen.de>, Sebastian Linne
<Sebastian.Linne@campus.lmu.de>
Maintainer: Heidi Seibold <Heidi.Seibold@uzh.ch>
Diff between highriskzone versions 1.2 dated 2015-07-22 and 1.3 dated 2015-11-16
DESCRIPTION | 16 +++++++--------- MD5 | 10 +++++----- R/detnsintens_restr.R | 4 ++-- R/simulationbase.R | 2 +- data/craterA.RData |binary data/craterB.RData |binary 6 files changed, 15 insertions(+), 17 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.3.2 dated 2015-08-11 and 0.4.1 dated 2015-11-16
GERGM-0.3.2/GERGM/man/GERGM-package.Rd |only GERGM-0.3.2/GERGM/man/gergm.Rd |only GERGM-0.4.1/GERGM/DESCRIPTION | 23 GERGM-0.4.1/GERGM/MD5 | 58 GERGM-0.4.1/GERGM/NAMESPACE | 10 GERGM-0.4.1/GERGM/R/Create_GERGM_Object_From_Formula.R | 18 GERGM-0.4.1/GERGM/R/Estimate_GERGM.R | 48 GERGM-0.4.1/GERGM/R/Estimate_Plot.R | 23 GERGM-0.4.1/GERGM/R/GERGM_Class.R | 9 GERGM-0.4.1/GERGM/R/GOF.R | 36 GERGM-0.4.1/GERGM/R/Helper_Functions.R | 6 GERGM-0.4.1/GERGM/R/Log_Likelihood_and_MPLE_Objective.R | 38 GERGM-0.4.1/GERGM/R/MCMCMLE.R | 81 GERGM-0.4.1/GERGM/R/Network_Statistic_Calculation_Functions.R | 66 GERGM-0.4.1/GERGM/R/Package_Documentation.R | 15 GERGM-0.4.1/GERGM/R/Parse_Formula_Object.R | 6 GERGM-0.4.1/GERGM/R/Prepare_Covariates.R | 107 GERGM-0.4.1/GERGM/R/RcppExports.R | 4 GERGM-0.4.1/GERGM/R/Simulate_GERGM.R | 17 GERGM-0.4.1/GERGM/R/Trace_Plot.R | 3 GERGM-0.4.1/GERGM/R/Transform_Correlations.R |only GERGM-0.4.1/GERGM/R/gergm.R | 289 ++ GERGM-0.4.1/GERGM/R/plot_network.R |only GERGM-0.4.1/GERGM/R/simulate_networks.R |only GERGM-0.4.1/GERGM/README.md | 21 GERGM-0.4.1/GERGM/man/Estimate_Plot.Rd | 5 GERGM-0.4.1/GERGM/man/GERGM.Rd |only GERGM-0.4.1/GERGM/man/GOF.Rd | 5 GERGM-0.4.1/GERGM/man/Trace_Plot.Rd | 5 GERGM-0.4.1/GERGM/man/plot_network.Rd |only GERGM-0.4.1/GERGM/man/simulate_networks.Rd |only GERGM-0.4.1/GERGM/src/Makevars |only GERGM-0.4.1/GERGM/src/Makevars.win |only GERGM-0.4.1/GERGM/src/Metropolis_Hastings_Sampler.cpp | 1076 +++++----- GERGM-0.4.1/GERGM/src/RcppExports.cpp | 8 35 files changed, 1273 insertions(+), 704 deletions(-)
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Description: The gap encodes the distance between clusters and improves
interpretation of cluster heatmaps. The gaps can be of the same
distance based on a height threshold to cut the dendrogram. Another
option is to vary the size of gaps based on the distance between
clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo.sakai@esat.kuleuven.be>
Diff between gapmap versions 0.0.2 dated 2014-09-29 and 0.0.3 dated 2015-11-16
DESCRIPTION | 14 +++++---- MD5 | 62 ++++++++++++++++++++--------------------- NAMESPACE | 24 +++++++++++++-- R/gap_dendrogram.R | 18 +++++------ R/gap_heatmap.R | 8 ++--- R/gap_label.R | 12 +++---- R/gapmap-package.R | 9 +++-- R/gapmap.R | 36 +++++++++++------------ build/vignette.rds |binary man/as.gapdata.Rd | 7 ++-- man/assign_branch_positions.Rd | 3 + man/assign_positions.Rd | 3 + man/calculate_gap.Rd | 5 +-- man/count_gap.Rd | 3 + man/extract_list.Rd | 3 + man/format_number.Rd | 3 + man/gap_data.Rd | 3 + man/gap_dendrogram.Rd | 3 + man/gap_heatmap.Rd | 3 + man/gap_label.Rd | 3 + man/gapmap-package.Rd | 3 + man/gapmap.Rd | 4 +- man/get_most_left_leaf.Rd | 3 + man/get_most_right_leaf.Rd | 3 + man/get_segment_df.Rd | 3 + man/is.gapdata.Rd | 3 + man/map.Rd | 3 + man/map.exp.Rd | 3 + man/sample_tcga.Rd | 7 ++-- man/set_most_right_leaf.Rd | 3 + man/sum_distance.Rd | 5 +-- vignettes/tcga_example.Rmd | 6 +-- 32 files changed, 155 insertions(+), 113 deletions(-)
Title: Dynamic Slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye <yechao1009@gmail.com>
Diff between dslice versions 1.1.4 dated 2014-11-25 and 1.1.5 dated 2015-11-16
DESCRIPTION | 11 +- MD5 | 62 +++++++------- NAMESPACE | 5 - R/RcppExports.R | 39 ++++----- R/ds_gsa.R | 216 +++++++++++++++++++++++++-------------------------- R/ds_test.R | 140 ++++++++++++++++----------------- R/export_res.R | 154 ++++++++++++++++++------------------ R/load_cls.R | 16 +-- R/load_gct.R | 40 ++++----- R/load_gmt.R | 28 +++--- R/rank_by_s2n.R | 26 +++--- R/relabel.R | 48 +++++------ R/slice_show.R | 53 ++++++------ build |only data/gsa_exp.RData |binary data/gsa_label.RData |binary data/gsa_set.RData |binary inst/CITATION |only inst/doc/dslice.Rnw | 4 inst/doc/dslice.pdf |binary man/ds_eqp_k.Rd | 4 man/ds_gsa.Rd | 2 man/ds_k.Rd | 4 man/ds_test.Rd | 4 src/RcppExports.cpp | 175 +++++++++++++++++++++-------------------- src/ds_1.cpp | 2 src/ds_eqp_1.cpp | 6 - src/ds_eqp_k.cpp | 2 src/ds_k.cpp | 2 src/dslice_eqp_k.cpp | 4 src/dslice_k.cpp | 8 - vignettes/dslice.Rnw | 4 vignettes/dslice.bib | 7 - 33 files changed, 538 insertions(+), 528 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-1 dated 2015-10-26 and 1.1-2 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/MonteCarloDistributions.R | 2 +- R/Transformations.R | 7 ++----- R/helpers.R | 5 +++++ inst/NEWS.Rd | 16 ++++++++++++++++ inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary man/MarginalHomogeneityTests.Rd | 3 ++- tests/Examples/coin-Ex.Rout.save | 11 ++++++----- tests/bugfixes.R | 3 +++ tests/bugfixes.Rout.save | 9 +++++++-- 14 files changed, 59 insertions(+), 31 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.97.1 dated 2015-08-05 and 0.98.0 dated 2015-11-16
camtrapR-0.97.1/camtrapR/R/cameraOperation.r |only camtrapR-0.98.0/camtrapR/DESCRIPTION | 47 - camtrapR-0.98.0/camtrapR/MD5 | 100 ++- camtrapR-0.98.0/camtrapR/NAMESPACE | 6 camtrapR-0.98.0/camtrapR/NEWS | 48 + camtrapR-0.98.0/camtrapR/R/appendSpeciesNames.R | 71 +- camtrapR-0.98.0/camtrapR/R/cameraOperation.R |only camtrapR-0.98.0/camtrapR/R/checkSpeciesFolders.R | 123 +++ camtrapR-0.98.0/camtrapR/R/createSpeciesFolders.R | 8 camtrapR-0.98.0/camtrapR/R/createStationFolders.R |only camtrapR-0.98.0/camtrapR/R/detectionHistory.R | 122 ++- camtrapR-0.98.0/camtrapR/R/detectionMaps.R | 38 + camtrapR-0.98.0/camtrapR/R/exifTagNames.R | 8 camtrapR-0.98.0/camtrapR/R/getSpeciesImages.R | 112 ++- camtrapR-0.98.0/camtrapR/R/imageRename.R | 72 +- camtrapR-0.98.0/camtrapR/R/recordDatabase.R | 309 +++++++--- camtrapR-0.98.0/camtrapR/R/recordDatabaseIndividual.R |only camtrapR-0.98.0/camtrapR/R/spatialDetectionHistory.R |only camtrapR-0.98.0/camtrapR/data/recordDatabaseIndividualSample.rda |only camtrapR-0.98.0/camtrapR/inst/pictures/sample_images_tagged |only camtrapR-0.98.0/camtrapR/man/activityDensity.Rd | 10 camtrapR-0.98.0/camtrapR/man/activityHistogram.Rd | 4 camtrapR-0.98.0/camtrapR/man/activityOverlap.Rd | 22 camtrapR-0.98.0/camtrapR/man/activityRadial.Rd | 18 camtrapR-0.98.0/camtrapR/man/appendSpeciesNames.Rd | 26 camtrapR-0.98.0/camtrapR/man/cameraOperation.Rd | 56 - camtrapR-0.98.0/camtrapR/man/camtrapR-package.Rd | 70 +- camtrapR-0.98.0/camtrapR/man/camtraps.Rd | 6 camtrapR-0.98.0/camtrapR/man/checkSpeciesFolders.Rd | 53 + camtrapR-0.98.0/camtrapR/man/createSpeciesFolders.Rd | 22 camtrapR-0.98.0/camtrapR/man/createStationFolders.Rd |only camtrapR-0.98.0/camtrapR/man/detectionHistory.Rd | 107 +-- camtrapR-0.98.0/camtrapR/man/detectionMaps.Rd | 57 + camtrapR-0.98.0/camtrapR/man/exifTagNames.Rd | 6 camtrapR-0.98.0/camtrapR/man/exiftoolPath.Rd | 6 camtrapR-0.98.0/camtrapR/man/getSpeciesImages.Rd | 18 camtrapR-0.98.0/camtrapR/man/imageRename.Rd | 42 - camtrapR-0.98.0/camtrapR/man/recordDatabase.Rd | 92 +- camtrapR-0.98.0/camtrapR/man/recordDatabaseIndividual.Rd |only camtrapR-0.98.0/camtrapR/man/recordDatabaseIndividualsSample.Rd |only camtrapR-0.98.0/camtrapR/man/spatialDetectionHistory.Rd |only camtrapR-0.98.0/camtrapR/man/surveyReport.Rd | 64 +- camtrapR-0.98.0/camtrapR/man/timeShiftImages.Rd | 34 - camtrapR-0.98.0/camtrapR/man/timeShiftTable.Rd | 2 44 files changed, 1165 insertions(+), 614 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-31 1.4.5
2014-02-01 1.4.3
2013-12-31 1.4.2
2013-10-20 1.4.0
2013-08-04 1.3.0
2013-07-23 1.2.2
Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example datasets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>
Diff between PracTools versions 0.2 dated 2015-05-31 and 0.3 dated 2015-11-16
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 4 ++++ R/NRFUopt.R | 8 ++++---- data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/hospital.RData |binary data/labor.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary man/BW2stagePPS.Rd | 4 ++-- man/BW3stagePPS.Rd | 2 +- man/NRFUopt.Rd | 4 ++-- 16 files changed, 33 insertions(+), 29 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.
2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.7.1 dated 2015-09-09 and 0.7.5 dated 2015-11-16
DESCRIPTION | 17 MD5 | 64 +- NAMESPACE | 32 - NEWS | 163 +++--- R/Qm.R | 34 - R/af.R | 978 ++++++++++++++++++++-------------------- R/bglmnet.R | 616 ++++++++++++------------- R/glmfence.R | 252 +++++----- R/lmfence.R | 300 ++++++------ R/mplot-package.R | 695 ++++++++++++++++------------ R/mplot.R | 556 +++++++++++----------- R/qrange.R | 118 ++-- R/sigMM.R | 50 +- R/vis.R | 1236 +++++++++++++++++++++++++-------------------------- README.md | 140 +++-- data/fev.rda |only data/wallabies.rda |only inst/CITATION | 42 - man/af.Rd | 244 +++++----- man/artificialeg.Rd | 84 +-- man/bglmnet.Rd | 102 ++-- man/bodyfat.Rd | 102 ++-- man/diabetes.Rd | 85 +-- man/fev.Rd |only man/mplot-package.Rd | 22 man/mplot.Rd | 72 +- man/plot.af.Rd | 143 +++-- man/plot.bglmnet.Rd | 171 +++---- man/plot.vis.Rd | 261 +++++----- man/print.af.Rd | 48 - man/print.vis.Rd | 48 - man/summary.af.Rd | 48 - man/txt.fn.Rd | 42 - man/vis.Rd | 160 +++--- man/wallabies.Rd |only 35 files changed, 3532 insertions(+), 3393 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-0 dated 2015-09-15 and 1.1-1 dated 2015-11-16
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/gen.R | 17 ++++++++++++----- man/rmix.Rd | 3 ++- man/rmmix.Rd | 3 ++- 6 files changed, 28 insertions(+), 15 deletions(-)
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.4-3 dated 2015-01-27 and 1.5-0 dated 2015-11-16
DESCRIPTION | 10 MD5 | 39 +-- NAMESPACE | 8 R/attrib.R | 1 R/devsvg.R | 5 R/filters.R | 7 R/griddev.R | 4 R/gridsvg.R | 7 R/svg.R | 541 ++++++++++++++++++++++++++------------------- R/zzz.R |only build/vignette.rds |binary inst/NEWS.Rd | 27 ++ inst/doc/animation.R | 4 inst/doc/animation.Rnw | 4 inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary inst/svg |only man/grid.export.Rd | 12 man/gridsvg.Rd | 4 vignettes/animation.Rnw | 4 21 files changed, 421 insertions(+), 256 deletions(-)
Title: Debugging 'grid' Graphics
Description: Functions for drawing scene trees representing
scenes that have been drawn using grid graphics.
Author: Paul Murrell and Velvet Ly.
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between gridDebug versions 0.4-0 dated 2012-03-31 and 0.5-0 dated 2015-11-16
DESCRIPTION | 16 +++++----- MD5 | 14 ++++----- NAMESPACE | 6 +-- R/svg.R | 32 --------------------- R/tree.R | 77 ++++++++++++++++++++++++++++----------------------- inst/doc/changes.txt | 25 ++++++++++++++++ man/gridTree.Rd | 18 +++++++++++ tests/test.R | 1 8 files changed, 104 insertions(+), 85 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.2 dated 2015-11-13 and 0.3.3 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ src/betaprior.f90 | 5 +---- src/mcsp2.f90 | 12 +++++++++--- 5 files changed, 21 insertions(+), 15 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 1.1 dated 2015-03-10 and 1.3 dated 2015-11-16
forestplot-1.1/forestplot/vignettes/forestplot_files |only forestplot-1.3/forestplot/DESCRIPTION | 24 forestplot-1.3/forestplot/MD5 | 100 +-- forestplot-1.3/forestplot/NAMESPACE | 4 forestplot-1.3/forestplot/NEWS | 14 forestplot-1.3/forestplot/R/forestplot.R | 94 ++- forestplot-1.3/forestplot/R/forestplot_helpers.R | 146 ++++- forestplot-1.3/forestplot/R/private.R | 185 +++++- forestplot-1.3/forestplot/build/vignette.rds |binary forestplot-1.3/forestplot/inst/doc/forestplot.R | 108 +++ forestplot-1.3/forestplot/inst/doc/forestplot.Rmd | 144 ++++ forestplot-1.3/forestplot/inst/doc/forestplot.html | 250 ++++++-- forestplot-1.3/forestplot/man/HRQoL.Rd | 10 forestplot-1.3/forestplot/man/forestplot-package.Rd | 40 - forestplot-1.3/forestplot/man/forestplot.Rd | 378 ++++++------- forestplot-1.3/forestplot/man/fpColors.Rd | 62 -- forestplot-1.3/forestplot/man/fpDrawCI.Rd | 110 ++- forestplot-1.3/forestplot/man/fpLegend.Rd | 71 -- forestplot-1.3/forestplot/man/fpTxtGp.Rd | 42 - forestplot-1.3/forestplot/man/getTicks.Rd | 27 forestplot-1.3/forestplot/man/heightDetails.xaxis.Rd | 9 forestplot-1.3/forestplot/man/prFpConvertMultidimArray.Rd | 4 forestplot-1.3/forestplot/man/prFpDrawLegend.Rd | 76 +- forestplot-1.3/forestplot/man/prFpDrawLine.Rd | 58 + forestplot-1.3/forestplot/man/prFpDrawLines.Rd | 19 forestplot-1.3/forestplot/man/prFpFetchRowLabel.Rd | 36 - forestplot-1.3/forestplot/man/prFpFindWidestGrob.Rd | 11 forestplot-1.3/forestplot/man/prFpGetConfintFnList.Rd | 32 - forestplot-1.3/forestplot/man/prFpGetGraphTicksAndClips.Rd | 76 +- forestplot-1.3/forestplot/man/prFpGetLabels.Rd | 64 -- forestplot-1.3/forestplot/man/prFpGetLayoutVP.Rd | 30 - forestplot-1.3/forestplot/man/prFpGetLegendBoxPosition.Rd | 32 - forestplot-1.3/forestplot/man/prFpGetLegendGrobs.Rd | 20 forestplot-1.3/forestplot/man/prFpGetLines.Rd | 20 forestplot-1.3/forestplot/man/prFpPrepareLegendMarker.Rd | 8 forestplot-1.3/forestplot/man/prFpPrintLabels.Rd | 15 forestplot-1.3/forestplot/man/prFpPrintXaxis.Rd | 15 forestplot-1.3/forestplot/man/prFpValidateLabelList.Rd | 8 forestplot-1.3/forestplot/man/prFpXrange.Rd | 61 -- forestplot-1.3/forestplot/man/prGetTextGrobCex.Rd | 4 forestplot-1.3/forestplot/man/prGparMerge.Rd | 9 forestplot-1.3/forestplot/man/prGridPlotTitle.Rd | 12 forestplot-1.3/forestplot/man/prListRep.Rd | 11 forestplot-1.3/forestplot/man/prPopulateList.Rd |only forestplot-1.3/forestplot/man/prPushMarginViewport.Rd | 16 forestplot-1.3/forestplot/vignettes/forestplot.Rmd | 144 ++++ 46 files changed, 1647 insertions(+), 952 deletions(-)
Title: Elastic Functional Data Analysis
Description: Functions to support functional data analysis using the square root velocity framework.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.4.2 dated 2014-01-29 and 1.5.1 dated 2015-11-16
fdasrvf-1.4.2/fdasrvf/src/DynamicProgrammingQ2.c |only fdasrvf-1.4.2/fdasrvf/src/dp_grid.c |only fdasrvf-1.4.2/fdasrvf/src/dp_grid.h |only fdasrvf-1.4.2/fdasrvf/src/dp_nbhd.h |only fdasrvf-1.5.1/fdasrvf/DESCRIPTION | 26 fdasrvf-1.5.1/fdasrvf/MD5 | 233 ++++- fdasrvf-1.5.1/fdasrvf/NAMESPACE | 24 fdasrvf-1.5.1/fdasrvf/NEWS | 13 fdasrvf-1.5.1/fdasrvf/R/SqrtMean.R | 110 +- fdasrvf-1.5.1/fdasrvf/R/align_fPCA.R | 513 ++++++------ fdasrvf-1.5.1/fdasrvf/R/elastic.distance.R | 36 fdasrvf-1.5.1/fdasrvf/R/elastic_logistic.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_mlogistic.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_prediction.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_regression.R |only fdasrvf-1.5.1/fdasrvf/R/f_to_srvf.R | 20 fdasrvf-1.5.1/fdasrvf/R/fdasrvf-package.r | 75 - fdasrvf-1.5.1/fdasrvf/R/gauss_model.R | 162 +-- fdasrvf-1.5.1/fdasrvf/R/gradient.R | 58 - fdasrvf-1.5.1/fdasrvf/R/horizFPCA.R | 118 +- fdasrvf-1.5.1/fdasrvf/R/optimum.reparam.R | 95 +- fdasrvf-1.5.1/fdasrvf/R/outlier.detection.R | 42 fdasrvf-1.5.1/fdasrvf/R/regression_functions.R |only fdasrvf-1.5.1/fdasrvf/R/rgam.R | 68 - fdasrvf-1.5.1/fdasrvf/R/smooth.data.R | 30 fdasrvf-1.5.1/fdasrvf/R/srsf_to_f.R |only fdasrvf-1.5.1/fdasrvf/R/time_warping.R | 462 +++++----- fdasrvf-1.5.1/fdasrvf/R/utility_functions.R | 971 +++++++++++++++-------- fdasrvf-1.5.1/fdasrvf/R/vertFPCA.R | 146 +-- fdasrvf-1.5.1/fdasrvf/R/warp_f_gamma.R |only fdasrvf-1.5.1/fdasrvf/R/warp_q_gamma.R |only fdasrvf-1.5.1/fdasrvf/README.md | 51 - fdasrvf-1.5.1/fdasrvf/man/SqrtMean.Rd | 30 fdasrvf-1.5.1/fdasrvf/man/align_fPCA.Rd | 58 - fdasrvf-1.5.1/fdasrvf/man/elastic.distance.Rd | 26 fdasrvf-1.5.1/fdasrvf/man/elastic.logistic.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.mlogistic.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.prediction.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.regression.Rd |only fdasrvf-1.5.1/fdasrvf/man/f_to_srvf.Rd | 19 fdasrvf-1.5.1/fdasrvf/man/fdasrvf.Rd | 35 fdasrvf-1.5.1/fdasrvf/man/gauss_model.Rd | 28 fdasrvf-1.5.1/fdasrvf/man/gradient.Rd | 9 fdasrvf-1.5.1/fdasrvf/man/horizFPCA.Rd | 30 fdasrvf-1.5.1/fdasrvf/man/optimum.reparam.Rd | 43 - fdasrvf-1.5.1/fdasrvf/man/outlier.detection.Rd | 31 fdasrvf-1.5.1/fdasrvf/man/rgam.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/simu_data.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/simu_warp.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/smooth.data.Rd | 23 fdasrvf-1.5.1/fdasrvf/man/srsf_to_f.Rd |only fdasrvf-1.5.1/fdasrvf/man/time_warping.Rd | 71 - fdasrvf-1.5.1/fdasrvf/man/toy_data.Rd | 13 fdasrvf-1.5.1/fdasrvf/man/toy_warp.Rd | 13 fdasrvf-1.5.1/fdasrvf/man/vertFPCA.Rd | 41 fdasrvf-1.5.1/fdasrvf/man/warp_f_gamma.Rd |only fdasrvf-1.5.1/fdasrvf/man/warp_q_gamma.Rd |only fdasrvf-1.5.1/fdasrvf/src/Makevars |only fdasrvf-1.5.1/fdasrvf/src/Makevars.win |only fdasrvf-1.5.1/fdasrvf/src/fdasrsf |only fdasrvf-1.5.1/fdasrvf/src/gropt |only fdasrvf-1.5.1/fdasrvf/src/wrapper.cpp |only 62 files changed, 2227 insertions(+), 1559 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.0 dated 2015-11-06 and 0.1.1 dated 2015-11-16
DESCRIPTION | 20 - MD5 | 129 ++++---- NAMESPACE | 13 R/data_prep.R | 56 ++- R/eyetrackingR.R | 22 + R/helpers.R | 220 ++++++++++---- R/time_cluster_data.R | 355 +++++++++++------------ R/time_sequence_data.R | 84 +++-- R/time_spline_data.R | 28 - R/time_window_data.R | 26 + README.md | 16 - data/word_recognition.rda |binary inst/doc/divergence_vignette.R | 26 + inst/doc/divergence_vignette.Rmd | 60 +++ inst/doc/divergence_vignette.html | 96 +++--- inst/doc/growth_curve_analysis_vignette.html | 4 inst/doc/onset_contingent_analysis_vignette.html | 4 inst/doc/preparing_your_data_vignette.R | 2 inst/doc/preparing_your_data_vignette.Rmd | 2 inst/doc/preparing_your_data_vignette.html | 35 +- inst/doc/window_analysis_vignette.Rmd | 2 inst/doc/window_analysis_vignette.html | 19 - man/add_aoi.Rd | 10 man/analyze_boot_splines.Rd | 15 man/analyze_time_bins.Rd | 20 - man/analyze_time_clusters.Rd | 29 + man/clean_by_trackloss.Rd | 17 - man/describe_data.Rd | 7 man/eyetrackingR.Rd | 2 man/filter_.Rd | 18 - man/get_time_clusters.Rd |only man/group_by_.Rd | 18 - man/left_join.Rd | 18 - man/make_boot_splines_data.Rd | 32 +- man/make_eyetrackingr_data.Rd | 27 - man/make_onset_data.Rd | 9 man/make_switch_data.Rd | 19 - man/make_time_cluster_data.Rd | 30 + man/make_time_sequence_data.Rd | 32 +- man/make_time_window_data.Rd | 21 - man/mutate_.Rd | 18 - man/plot.bin_analysis.Rd | 2 man/plot.boot_splines_analysis.Rd | 2 man/plot.boot_splines_data.Rd | 2 man/plot.cluster_analysis.Rd | 2 man/plot.eyetrackingR_data_summary.Rd | 4 man/plot.onset_data.Rd | 2 man/plot.switch_data.Rd | 2 man/plot.time_cluster_data.Rd | 2 man/plot.time_sequence_data.Rd | 12 man/plot.time_window_data.Rd | 9 man/print.cluster_analysis.Rd | 2 man/simulate_eyetrackingr_data.Rd |only man/subset.Rd | 18 - man/subset_by_window.Rd | 35 +- man/summary.bin_analysis.Rd | 2 man/summary.boot_splines_analysis.Rd | 2 man/summary.cluster_analysis.Rd | 2 man/summary.time_cluster_data.Rd | 2 man/trackloss_analysis.Rd | 5 man/ungroup.Rd | 18 - man/word_recognition.Rd | 24 - tests/testthat/test_arbitrary_dv.R |only tests/testthat/test_cluster_analysis.R | 71 +--- vignettes/divergence_vignette.Rmd | 60 +++ vignettes/preparing_your_data_vignette.Rmd | 2 vignettes/window_analysis_vignette.Rmd | 2 67 files changed, 1082 insertions(+), 763 deletions(-)
Title: Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre],
David Welch [aut],
David Hunter [ctb]
Maintainer: Chris Groendyke <cgroendyke@gmail.com>
Diff between epinet versions 2.1.5 dated 2015-11-13 and 2.1.6 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/epi2newick.Rd | 2 +- man/write.epinet.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)