Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. For more detailed info see: Martinez-Lopez et al. (2015) <doi:10.1016/j.ecolmodel.2014.11.024>.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.1.4 dated 2019-02-20 and 1.1.5 dated 2019-02-26
DESCRIPTION | 12 +++++------- MD5 | 8 ++++---- NAMESPACE | 1 + R/mc_dynmodv2_7_functions.R | 16 ++++++++-------- inst/doc/isem2013_jml.pdf |binary 5 files changed, 18 insertions(+), 19 deletions(-)
Title: Filtering Satellite-Derived Locations
Description: Functions to filter GPS and/or Argos locations. The provided
filters remove temporal and spatial duplicates, fixes located at a given
height from estimated high tide line, and locations with high error as
proposed in Shimada et al. (2012) <doi:10.3354/meps09747> and
Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <taka.shimada@gmail.com>
Diff between SDLfilter versions 1.2.0 dated 2019-02-18 and 1.2.1 dated 2019-02-26
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 3 +++ NEWS.md | 5 +++++ R/plotMap.R | 6 +++--- README.md | 2 +- man/plotMap.Rd | 2 +- 7 files changed, 24 insertions(+), 16 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05>. Also incorporates SV with leverage.
Author: Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>),
Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 2.0.0 dated 2019-02-01 and 2.0.1 dated 2019-02-26
DESCRIPTION | 6 ++-- MD5 | 45 +++++++++++++++--------------- NAMESPACE | 4 ++ NEWS | 6 ++++ R/plotting.R | 69 +++++++++++++++++++++++++++++++++++++++++++++-- R/stochvol-package.R | 4 +- R/utilities_svdraws.R | 40 +++++++++++++-------------- R/wrappers.R | 55 +++++++++++++++++++++++++++++-------- inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary inst/include/stochvol.h | 8 ++--- man/plot.svpredict.Rd |only man/predict.svdraws.Rd | 36 ++++++++++++------------ man/svlsample.Rd | 20 ++++++++++--- man/volplot.Rd | 4 +- src/exports.cpp | 8 ++--- src/sampler.cpp | 9 ++++-- src/sampler.h | 2 - src/theta-sampler.cpp | 5 ++- src/theta-sampler.h | 3 +- src/theta-utils.cpp | 27 +++++------------- src/theta-utils.h | 13 +------- src/update_functions.cpp | 9 ++++-- src/update_functions.h | 3 +- 24 files changed, 243 insertions(+), 133 deletions(-)
Title: Most Probable Number for Serial Dilutions
Description: Calculates the Most Probable Number for serial dilutions to
quantify the concentration (density) of microbes in a laboratory sample
(described in Jarvis (2010) <doi:10.1111/j.1365-2672.2010.04792.x>).
Author: Martine Ferguson [aut] (original R code),
John Ihrie [cre, aut]
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between MPN versions 0.1.0 dated 2018-09-16 and 0.2.0 dated 2019-02-26
DESCRIPTION | 13 +--- MD5 | 25 ++++---- NAMESPACE | 1 NEWS.md |only R/MPN.R | 23 ++++--- R/f_mpn.R | 98 +++++++++++++++++++++++--------- R/helpers.R | 68 ++++++++++++++++++++-- build/vignette.rds |binary inst/doc/MPN-vignette.R | 7 ++ inst/doc/MPN-vignette.Rmd | 50 ++++++++++++---- inst/doc/MPN-vignette.html | 96 ++++++++++++++++++++++++++++--- man/mpn.Rd | 76 +++++++++++++++++-------- tests/testthat/test_mpn.R | 136 +++++++++++++++++++++++++++++++++++++++++++-- vignettes/MPN-vignette.Rmd | 50 ++++++++++++---- 14 files changed, 520 insertions(+), 123 deletions(-)
Title: Statistical Methods for the Item Count Technique and List
Experiment
Description: Allows researchers to conduct multivariate
statistical analyses of survey data with list experiments. This
survey methodology is also known as the item count technique or
the unmatched count technique and is an alternative to the commonly
used randomized response method. The package implements the methods
developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>,
Blair and Imai (2012) <doi:10.1093/pan/mpr048>,
Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>,
Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>,
Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>,
Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and
Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>.
This includes a Bayesian MCMC implementation of regression for the
standard and multiple sensitive item list experiment designs and a
random effects setup, a Bayesian MCMC hierarchical regression model
with up to three hierarchical groups, the combined list experiment
and endorsement experiment regression model, a joint model of the
list experiment that enables the analysis of the list experiment as
a predictor in outcome regression models, a method for combining
list experiments with direct questions, and methods for diagnosing and
adjusting for response error. In addition, the package implements the
statistical test that is designed to detect certain failures of list
experiments, and a placebo test for the list experiment using data from
direct questions.
Author: Graeme Blair [aut, cre],
Winston Chou [aut],
Kosuke Imai [aut],
Bethany Park [ctb],
Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between list versions 9.0 dated 2018-11-06 and 9.1 dated 2019-02-26
ChangeLog | 1 DESCRIPTION | 8 MD5 | 12 - R/ictreg.R | 429 ++++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/combined-list.html | 28 ++ tests/testthat/Rplots.pdf |binary 7 files changed, 393 insertions(+), 85 deletions(-)
Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between DynTxRegime versions 3.2 dated 2018-02-12 and 4.0 dated 2019-02-26
DynTxRegime-3.2/DynTxRegime/R/A00_DynTxRegime.R |only DynTxRegime-3.2/DynTxRegime/R/A01_List.R |only DynTxRegime-3.2/DynTxRegime/R/A02_SubsetList.R |only DynTxRegime-3.2/DynTxRegime/R/A03_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/A04_ModelObjSubset.R |only DynTxRegime-3.2/DynTxRegime/R/A05_ModelObj_SubsetList.R |only DynTxRegime-3.2/DynTxRegime/R/A06_ModelObj_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/A07_ModelObj_SubsetList_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/A08_newModelObjSubset.R |only DynTxRegime-3.2/DynTxRegime/R/AA00_TxInfoBasic.R |only DynTxRegime-3.2/DynTxRegime/R/AA01_TxInfoFactor.R |only DynTxRegime-3.2/DynTxRegime/R/AA02_TxInfoInteger.R |only DynTxRegime-3.2/DynTxRegime/R/AA03_TxInfoNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA04_TxInfoFactorNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA05_TxInfoIntegerNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA06_newTxInfoNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA07_TxInfoWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA08_TxSubset.R |only DynTxRegime-3.2/DynTxRegime/R/AA09_TxInfoFactorWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA10_TxInfoIntegerWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA11_newTxInfoWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AA12_TxInfoList.R |only DynTxRegime-3.2/DynTxRegime/R/AA13_newTxInfo.R |only DynTxRegime-3.2/DynTxRegime/R/AB00_TypedSimpleFit.R |only DynTxRegime-3.2/DynTxRegime/R/AB01_TypedSimpleFitNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AB02_TypedSimpleFitWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AB03_newTypedSimpleFit.R |only DynTxRegime-3.2/DynTxRegime/R/AB04_IterateFit.R |only DynTxRegime-3.2/DynTxRegime/R/AB05_IterateFitNoSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AB06_IterateFitWithSubsets.R |only DynTxRegime-3.2/DynTxRegime/R/AB07_newIterateFit.R |only DynTxRegime-3.2/DynTxRegime/R/AB08_SubsetListFit.R |only DynTxRegime-3.2/DynTxRegime/R/AB09_OutcomeRegression_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/AB10_OutcomeRegression_SubsetList_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/AB11_newOutcomeRegression.R |only DynTxRegime-3.2/DynTxRegime/R/AB12_OutcomeOnly.R |only DynTxRegime-3.2/DynTxRegime/R/AC01_PropensityFit.R |only DynTxRegime-3.2/DynTxRegime/R/AC02_PropensityFit_fSet.R |only DynTxRegime-3.2/DynTxRegime/R/AC03_PropensityFit_SubsetList.R |only DynTxRegime-3.2/DynTxRegime/R/AC04_PropensityFit_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/AC05_PropensityFit_SubsetList_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/AC06_newPropensityRegression.R |only DynTxRegime-3.2/DynTxRegime/R/AC07_PropensityOnly.R |only DynTxRegime-3.2/DynTxRegime/R/AC08_PropensityAndOutcome.R |only DynTxRegime-3.2/DynTxRegime/R/AD01_Regime.R |only DynTxRegime-3.2/DynTxRegime/R/AD02_Regime_DecisionPointList.R |only DynTxRegime-3.2/DynTxRegime/R/AD03_newRegimes.R |only DynTxRegime-3.2/DynTxRegime/R/AE01_CVInfo.R |only DynTxRegime-3.2/DynTxRegime/R/AE02_newCVInfo.R |only DynTxRegime-3.2/DynTxRegime/R/AF01_QLearn.R |only DynTxRegime-3.2/DynTxRegime/R/AF02_newQLearn.R |only DynTxRegime-3.2/DynTxRegime/R/AF03_IQLearnBase.R |only DynTxRegime-3.2/DynTxRegime/R/AF04_IQLearnSS.R |only DynTxRegime-3.2/DynTxRegime/R/AF05_IQLearnFS.R |only DynTxRegime-3.2/DynTxRegime/R/AF06_IQLearnFS_ME.R |only DynTxRegime-3.2/DynTxRegime/R/AF07_IQLearnFS_C.R |only DynTxRegime-3.2/DynTxRegime/R/AF08_IQLearnFS_VHet.R |only DynTxRegime-3.2/DynTxRegime/R/AG00_OptimBasic.R |only DynTxRegime-3.2/DynTxRegime/R/AG01_OptimKernel.R |only DynTxRegime-3.2/DynTxRegime/R/AG02_OWLOptim.R |only DynTxRegime-3.2/DynTxRegime/R/AG03_OWL.R |only DynTxRegime-3.2/DynTxRegime/R/AH01_OptimalClass.R |only DynTxRegime-3.2/DynTxRegime/R/AH02_OptimalClassIPWE.R |only DynTxRegime-3.2/DynTxRegime/R/AH03_OptimalClassAIPWE.R |only DynTxRegime-3.2/DynTxRegime/R/AH04_newOptimalClass.R |only DynTxRegime-3.2/DynTxRegime/R/AI01_OptimalSeq.R |only DynTxRegime-3.2/DynTxRegime/R/AI02_OptimalSeqIPWE_SDP.R |only DynTxRegime-3.2/DynTxRegime/R/AI03_OptimalSeqAIPWE_SDP.R |only DynTxRegime-3.2/DynTxRegime/R/AI04_OptimalSeqIPWE_MDP.R |only DynTxRegime-3.2/DynTxRegime/R/AI05_OptimalSeqAIPWE_MDP.R |only DynTxRegime-3.2/DynTxRegime/R/AI06_newOptimalSeq.R |only DynTxRegime-3.2/DynTxRegime/R/AJ01_EARLOptim.R |only DynTxRegime-3.2/DynTxRegime/R/AJ02_EARL.R |only DynTxRegime-3.2/DynTxRegime/R/AJ03_EARLIPWE.R |only DynTxRegime-3.2/DynTxRegime/R/AJ04_EARLAIPWE.R |only DynTxRegime-3.2/DynTxRegime/R/AJ05_newEARL.R |only DynTxRegime-3.2/DynTxRegime/R/AK01_RWLOptim.R |only DynTxRegime-3.2/DynTxRegime/R/AK02_RWL.R |only DynTxRegime-3.2/DynTxRegime/R/AL01_BOWLBasic.R |only DynTxRegime-3.2/DynTxRegime/R/AL02_BOWLBasic_fSet.R |only DynTxRegime-3.2/DynTxRegime/R/AL03_BOWLWithOneRegime.R |only DynTxRegime-3.2/DynTxRegime/R/AL04_BOWLWithSubsetRegimes.R |only DynTxRegime-3.2/DynTxRegime/R/AL05_BOWL.R |only DynTxRegime-3.2/DynTxRegime/R/AL06_newBOWL.R |only DynTxRegime-3.2/DynTxRegime/R/BOWL.R |only DynTxRegime-3.2/DynTxRegime/R/EARL.R |only DynTxRegime-3.2/DynTxRegime/R/OWL.R |only DynTxRegime-3.2/DynTxRegime/R/RWL.R |only DynTxRegime-3.2/DynTxRegime/R/errors.R |only DynTxRegime-3.2/DynTxRegime/R/getFeasibleTx.R |only DynTxRegime-3.2/DynTxRegime/R/iqLearnFSC.R |only DynTxRegime-3.2/DynTxRegime/R/iqLearnFSM.R |only DynTxRegime-3.2/DynTxRegime/R/iqLearnSS.R |only DynTxRegime-3.2/DynTxRegime/R/iqLearnVar.R |only DynTxRegime-3.2/DynTxRegime/R/kernelFunc.R |only DynTxRegime-3.2/DynTxRegime/R/optimalClass.R |only DynTxRegime-3.2/DynTxRegime/R/optimalSeq.R |only DynTxRegime-3.2/DynTxRegime/R/plugInValue.R |only DynTxRegime-3.2/DynTxRegime/R/qLearn.R |only DynTxRegime-3.2/DynTxRegime/man/BOWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/BOWLBasic_fSet-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/BOWLBinary-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/BOWLWithOneRegime-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/BOWLWithSubsetRegimes-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/CVInfo1Par-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/DynTxRegime-package.Rd |only DynTxRegime-3.2/DynTxRegime/man/EARL.Rd |only DynTxRegime-3.2/DynTxRegime/man/EARLAIPWE-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/EARLIPWE-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/EARLOptim-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/IQLearnBase-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/IterateFit-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/IterateFitNoSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/IterateFitWithSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/ModelObj_SubsetList_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/MultipleDecisionPoint-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/OWLOptim-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalClassAIPWE-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalClassIPWE-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalSeqAIPWE_MDP-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalSeqAIPWE_SDP-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalSeqIPWE_MDP.Rd |only DynTxRegime-3.2/DynTxRegime/man/OptimalSeqIPWE_SDP.Rd |only DynTxRegime-3.2/DynTxRegime/man/OutcomeOnly-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OutcomeRegression-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/OutcomeRegression_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/PropensityAndOutcome-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/PropensityFit_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/PropensityFit_SubsetList_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/PropensityOnly-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/PropensityRegression-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/RWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/RWLOptim-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/RegimeObject-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/Regime_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/SingleDecisionPoint-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/SubsetListFit-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/SubsetListFit_DecisionPointList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/SubsetsModeled-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/SubsetsNotModeled-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TxInfoFactorWithSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TxInfoIntegerWithSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TxInfoList-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TypedSimpleFit-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TypedSimpleFitNoSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/TypedSimpleFitWithSubsets-class.Rd |only DynTxRegime-3.2/DynTxRegime/man/input_fSet.Rd |only DynTxRegime-3.2/DynTxRegime/man/input_iter.Rd |only DynTxRegime-3.2/DynTxRegime/man/input_moPropen.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newBOWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newBOWLBasic.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newBOWLOptimization.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newCVInfo.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newEARL.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newIQLearnFS_C.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newIQLearnFS_ME.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newIQLearnFS_VHet.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newIQLearnSS.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newIterateFit.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newModelObjSubset.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newOWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newOWLOptim.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newOptimalClass.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newOptimalSeq.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newOutcomeRegression.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newPropensityFit.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newQLearn.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newRWL.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newRegime.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newTxInfo.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newTxInfoNoSubsets.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newTxInfoWithSubsets.Rd |only DynTxRegime-3.2/DynTxRegime/man/internal_newTypedSimpleFit.Rd |only DynTxRegime-3.2/DynTxRegime/man/iqLearnFS.Rd |only DynTxRegime-3.2/DynTxRegime/man/iqLearnFSC.Rd |only DynTxRegime-3.2/DynTxRegime/man/iqLearnSS.Rd |only DynTxRegime-3.2/DynTxRegime/man/iqLearnVar.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-Qstep.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-classif.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-coef.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-cvInfo.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-estimator.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-fitObject.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-fittedCont.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-fittedMain.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-genetic.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-optTx.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-optimObj.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-outcome.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-plot.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-propen.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-qqPlot.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-regimeCoef.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-residuals.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-show.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-stdDev.Rd |only DynTxRegime-3.2/DynTxRegime/man/methods-summary.Rd |only DynTxRegime-3.2/DynTxRegime/man/plugInValue.Rd |only DynTxRegime-4.0/DynTxRegime/DESCRIPTION | 47 DynTxRegime-4.0/DynTxRegime/MD5 | 588 +++++---- DynTxRegime-4.0/DynTxRegime/NAMESPACE | 107 - DynTxRegime-4.0/DynTxRegime/R/A_DecisionPointList.R |only DynTxRegime-4.0/DynTxRegime/R/A_DynTxRegime.R |only DynTxRegime-4.0/DynTxRegime/R/A_List.R |only DynTxRegime-4.0/DynTxRegime/R/A_ModelObjSubset.R |only DynTxRegime-4.0/DynTxRegime/R/A_ModelObj_DecisionPointList.R |only DynTxRegime-4.0/DynTxRegime/R/A_ModelObj_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/A_OptimalInfo.R |only DynTxRegime-4.0/DynTxRegime/R/A_OptimalObj.R |only DynTxRegime-4.0/DynTxRegime/R/A_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/A_generics.R |only DynTxRegime-4.0/DynTxRegime/R/A_newModelObjSubset.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoBasic.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoFactor.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoInteger.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoList.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoNoSubsets.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxInfoWithSubsets.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxObj.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxSubset.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxSubsetFactor.R |only DynTxRegime-4.0/DynTxRegime/R/B_TxSubsetInteger.R |only DynTxRegime-4.0/DynTxRegime/R/C_TypedFit.R |only DynTxRegime-4.0/DynTxRegime/R/C_TypedFitObj.R |only DynTxRegime-4.0/DynTxRegime/R/C_TypedFit_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/C_TypedFit_fSet.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeIterateFit.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeNoFit.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeObj.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeSimpleFit.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeSimpleFit_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/D_OutcomeSimpleFit_fSet.R |only DynTxRegime-4.0/DynTxRegime/R/D_newModel.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_IQLearnFS.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_IQLearnFS_C.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_IQLearnFS_ME.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_IQLearnFS_VHet.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_IQLearnSS.R |only DynTxRegime-4.0/DynTxRegime/R/E_class_QLearn.R |only DynTxRegime-4.0/DynTxRegime/R/E_iqLearnFSC.R |only DynTxRegime-4.0/DynTxRegime/R/E_iqLearnFSM.R |only DynTxRegime-4.0/DynTxRegime/R/E_iqLearnFSV.R |only DynTxRegime-4.0/DynTxRegime/R/E_iqLearnSS.R |only DynTxRegime-4.0/DynTxRegime/R/E_qLearn.R |only DynTxRegime-4.0/DynTxRegime/R/F_PropensityFit.R |only DynTxRegime-4.0/DynTxRegime/R/F_PropensityFit_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/F_PropensityFit_fSet.R |only DynTxRegime-4.0/DynTxRegime/R/F_PropensityObj.R |only DynTxRegime-4.0/DynTxRegime/R/G_Regime.R |only DynTxRegime-4.0/DynTxRegime/R/G_RegimeObj.R |only DynTxRegime-4.0/DynTxRegime/R/H_class_OptimalSeq.R |only DynTxRegime-4.0/DynTxRegime/R/H_class_OptimalSeqCoarsened.R |only DynTxRegime-4.0/DynTxRegime/R/H_class_OptimalSeqMissing.R |only DynTxRegime-4.0/DynTxRegime/R/H_optimalSeq.R |only DynTxRegime-4.0/DynTxRegime/R/I_ClassificationFit.R |only DynTxRegime-4.0/DynTxRegime/R/I_ClassificationFit_SubsetList.R |only DynTxRegime-4.0/DynTxRegime/R/I_ClassificationFit_fSet.R |only DynTxRegime-4.0/DynTxRegime/R/I_ClassificationObj.R |only DynTxRegime-4.0/DynTxRegime/R/J_class_OptimalClass.R |only DynTxRegime-4.0/DynTxRegime/R/J_optimalClass.R |only DynTxRegime-4.0/DynTxRegime/R/K_Kernel.R |only DynTxRegime-4.0/DynTxRegime/R/K_KernelObj.R |only DynTxRegime-4.0/DynTxRegime/R/K_LinearKernel.R |only DynTxRegime-4.0/DynTxRegime/R/K_MultiRadialKernel.R |only DynTxRegime-4.0/DynTxRegime/R/K_PolyKernel.R |only DynTxRegime-4.0/DynTxRegime/R/K_RadialKernel.R |only DynTxRegime-4.0/DynTxRegime/R/L_ExpSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_HingeSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_HuberHingeSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_LogitSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_SmoothRampSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_SqHingeSurrogate.R |only DynTxRegime-4.0/DynTxRegime/R/L_Surrogate.R |only DynTxRegime-4.0/DynTxRegime/R/M_MethodObject.R |only DynTxRegime-4.0/DynTxRegime/R/M_OptimBasic.R |only DynTxRegime-4.0/DynTxRegime/R/M_OptimKernel.R |only DynTxRegime-4.0/DynTxRegime/R/M_OptimObj.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVBasic.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVInfo.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVInfo2Par.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVInfoLambda.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVInfoObj.R |only DynTxRegime-4.0/DynTxRegime/R/N_CVInfokParam.R |only DynTxRegime-4.0/DynTxRegime/R/N_OptimStep.R |only DynTxRegime-4.0/DynTxRegime/R/O_Learning.R |only DynTxRegime-4.0/DynTxRegime/R/O_LearningMulti.R |only DynTxRegime-4.0/DynTxRegime/R/O_LearningObject.R |only DynTxRegime-4.0/DynTxRegime/R/P_class_.owl.R |only DynTxRegime-4.0/DynTxRegime/R/P_class_OWL.R |only DynTxRegime-4.0/DynTxRegime/R/P_owl.R |only DynTxRegime-4.0/DynTxRegime/R/Q_class_.rwl.R |only DynTxRegime-4.0/DynTxRegime/R/Q_class_RWL.R |only DynTxRegime-4.0/DynTxRegime/R/Q_rwl.R |only DynTxRegime-4.0/DynTxRegime/R/R_bowl.R |only DynTxRegime-4.0/DynTxRegime/R/R_class_BOWL.R |only DynTxRegime-4.0/DynTxRegime/R/R_class_BOWLBasic.R |only DynTxRegime-4.0/DynTxRegime/R/S_class_.earl.R |only DynTxRegime-4.0/DynTxRegime/R/S_class_EARL.R |only DynTxRegime-4.0/DynTxRegime/R/S_earl.R |only DynTxRegime-4.0/DynTxRegime/R/checkInputs.R | 398 +----- DynTxRegime-4.0/DynTxRegime/R/internalTest.R |only DynTxRegime-4.0/DynTxRegime/R/titleIt.R | 2 DynTxRegime-4.0/DynTxRegime/man/BOWL-class.Rd | 98 - DynTxRegime-4.0/DynTxRegime/man/BOWL-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/BOWLBasic-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/BOWLBasic-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/BOWLObj-class.Rd | 30 DynTxRegime-4.0/DynTxRegime/man/CVBasic-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfo-class.Rd | 55 DynTxRegime-4.0/DynTxRegime/man/CVInfo-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfo2Par-class.Rd | 49 DynTxRegime-4.0/DynTxRegime/man/CVInfo2Par-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfoLambda-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfoLambda-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfoObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfoObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfokParam-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/CVInfokParam-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/Call.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit_SubsetList-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit_SubsetList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit_fSet-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationFit_fSet-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/ClassificationObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/DTRstep.Rd |only DynTxRegime-4.0/DynTxRegime/man/DecisionPointList-class.Rd | 70 - DynTxRegime-4.0/DynTxRegime/man/DecisionPointList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/DynTxRegime-class.Rd | 140 -- DynTxRegime-4.0/DynTxRegime/man/DynTxRegime-internal-api.Rd | 650 +++++++--- DynTxRegime-4.0/DynTxRegime/man/DynTxRegime-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/EARL-class.Rd | 119 - DynTxRegime-4.0/DynTxRegime/man/EARL-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ExpSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/ExpSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/HingeSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/HingeSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/HuberHingeSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/HuberHingeSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/IQLearnFS-class.Rd | 22 DynTxRegime-4.0/DynTxRegime/man/IQLearnFS-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_C-class.Rd | 100 - DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_C-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_ME-class.Rd | 83 - DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_ME-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_VHet-class.Rd | 98 - DynTxRegime-4.0/DynTxRegime/man/IQLearnFS_VHet-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/IQLearnSS-class.Rd | 102 - DynTxRegime-4.0/DynTxRegime/man/IQLearnSS-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/Kernel-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/Kernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/KernelObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/KernelObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/Learning-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/Learning-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/LearningMulti-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/LearningMulti-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/LearningObject-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/LearningObject-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/LinearKernel-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/LinearKernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/List-class.Rd | 50 DynTxRegime-4.0/DynTxRegime/man/LogitSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/LogitSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/MethodObject-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/MethodObject-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ModelObjSubset-class.Rd | 66 - DynTxRegime-4.0/DynTxRegime/man/ModelObjSubset-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/ModelObj_DecisionPointList-class.Rd | 40 DynTxRegime-4.0/DynTxRegime/man/ModelObj_SubsetList-class.Rd | 39 DynTxRegime-4.0/DynTxRegime/man/MultiRadialKernel-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/MultiRadialKernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OWL-class.Rd | 133 +- DynTxRegime-4.0/DynTxRegime/man/OWL-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimBasic-class.Rd | 60 DynTxRegime-4.0/DynTxRegime/man/OptimBasic-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimKernel-class.Rd | 67 - DynTxRegime-4.0/DynTxRegime/man/OptimKernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimStep-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimStep-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimStep.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalClass-class.Rd | 77 - DynTxRegime-4.0/DynTxRegime/man/OptimalClass-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalClassObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalInfo-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalInfo-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalSeq-class.Rd | 84 + DynTxRegime-4.0/DynTxRegime/man/OptimalSeq-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalSeqCoarsened-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalSeqCoarsened-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalSeqMissing-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OptimalSeqMissing-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeIterateFit-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeIterateFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeNoFit-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeNoFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit_SubsetList-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit_SubsetList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit_fSet-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/OutcomeSimpleFit_fSet-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/PolyKernel-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/PolyKernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/PropensityFit-class.Rd | 58 DynTxRegime-4.0/DynTxRegime/man/PropensityFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/PropensityFit_SubsetList-class.Rd | 52 DynTxRegime-4.0/DynTxRegime/man/PropensityFit_SubsetList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/PropensityFit_fSet-class.Rd | 52 DynTxRegime-4.0/DynTxRegime/man/PropensityFit_fSet-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/PropensityObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/PropensityObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/QLearn-class.Rd | 84 - DynTxRegime-4.0/DynTxRegime/man/QLearnObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/RWL-class.Rd | 133 +- DynTxRegime-4.0/DynTxRegime/man/RWL-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/RadialKernel-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/RadialKernel-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/Regime-class.Rd | 96 - DynTxRegime-4.0/DynTxRegime/man/Regime-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/RegimeObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/RegimeObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/SmoothRampSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/SmoothRampSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/SqHingeSurrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/SqHingeSurrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/SubsetList-class.Rd | 72 - DynTxRegime-4.0/DynTxRegime/man/SubsetList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/Surrogate-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/Surrogate-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoBasic-class.Rd | 71 - DynTxRegime-4.0/DynTxRegime/man/TxInfoBasic-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoFactor-class.Rd | 78 - DynTxRegime-4.0/DynTxRegime/man/TxInfoFactor-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoInteger-class.Rd | 77 - DynTxRegime-4.0/DynTxRegime/man/TxInfoInteger-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoList.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoNoSubsets-class.Rd | 55 DynTxRegime-4.0/DynTxRegime/man/TxInfoNoSubsets-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxInfoWithSubsets-class.Rd | 76 - DynTxRegime-4.0/DynTxRegime/man/TxInfoWithSubsets-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxSubset-class.Rd | 78 - DynTxRegime-4.0/DynTxRegime/man/TxSubset-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxSubsetFactor-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxSubsetFactor-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxSubsetInteger-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TxSubsetInteger-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFitObj-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFitObj-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit_SubsetList-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit_SubsetList-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit_fSet-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/TypedFit_fSet-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/bmiData.Rd | 23 DynTxRegime-4.0/DynTxRegime/man/bowl.Rd |only DynTxRegime-4.0/DynTxRegime/man/buildModelObjSubset.Rd | 199 +-- DynTxRegime-4.0/DynTxRegime/man/classif.Rd |only DynTxRegime-4.0/DynTxRegime/man/coef.Rd |only DynTxRegime-4.0/DynTxRegime/man/createearl.Rd |only DynTxRegime-4.0/DynTxRegime/man/createowl.Rd |only DynTxRegime-4.0/DynTxRegime/man/createrwl.Rd |only DynTxRegime-4.0/DynTxRegime/man/cvInfo.Rd |only DynTxRegime-4.0/DynTxRegime/man/cycleList.Rd |only DynTxRegime-4.0/DynTxRegime/man/earl.Rd |only DynTxRegime-4.0/DynTxRegime/man/estimator.Rd |only DynTxRegime-4.0/DynTxRegime/man/fSet.Rd |only DynTxRegime-4.0/DynTxRegime/man/fitObject.Rd |only DynTxRegime-4.0/DynTxRegime/man/fittedCont.Rd |only DynTxRegime-4.0/DynTxRegime/man/fittedMain.Rd |only DynTxRegime-4.0/DynTxRegime/man/genetic.Rd |only DynTxRegime-4.0/DynTxRegime/man/getOutcome.Rd |only DynTxRegime-4.0/DynTxRegime/man/getPrWgt.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-earl-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-earl-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-owl-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-owl-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-rwl-class.Rd |only DynTxRegime-4.0/DynTxRegime/man/internal-rwl-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/iqLearn.Rd |only DynTxRegime-4.0/DynTxRegime/man/iter.Rd |only DynTxRegime-4.0/DynTxRegime/man/moPropen.Rd |only DynTxRegime-4.0/DynTxRegime/man/newBOWL.Rd |only DynTxRegime-4.0/DynTxRegime/man/newBOWLStep.Rd |only DynTxRegime-4.0/DynTxRegime/man/newCVInfo.Rd |only DynTxRegime-4.0/DynTxRegime/man/newCVInfoObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newCVStep.Rd |only DynTxRegime-4.0/DynTxRegime/man/newClassificationFit.Rd |only DynTxRegime-4.0/DynTxRegime/man/newClassificationObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newEARL.Rd |only DynTxRegime-4.0/DynTxRegime/man/newIQLearnFS_C.Rd |only DynTxRegime-4.0/DynTxRegime/man/newIQLearnFS_ME.Rd |only DynTxRegime-4.0/DynTxRegime/man/newIQLearnFS_VHet.Rd |only DynTxRegime-4.0/DynTxRegime/man/newIQLearnSS.Rd |only DynTxRegime-4.0/DynTxRegime/man/newKernelObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newLearning.Rd |only DynTxRegime-4.0/DynTxRegime/man/newModel.Rd |only DynTxRegime-4.0/DynTxRegime/man/newModelObjSubset.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOWL.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOptim.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOptimObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOptimalClass.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOptimalSeq.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOutcomeFit.Rd |only DynTxRegime-4.0/DynTxRegime/man/newOutcomeObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newPropensityFit.Rd |only DynTxRegime-4.0/DynTxRegime/man/newPropensityObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newQLearn.Rd |only DynTxRegime-4.0/DynTxRegime/man/newRWL-methods.Rd |only DynTxRegime-4.0/DynTxRegime/man/newRWL.Rd |only DynTxRegime-4.0/DynTxRegime/man/newRegime.Rd |only DynTxRegime-4.0/DynTxRegime/man/newRegimeObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newTxObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/newTxSubset.Rd |only DynTxRegime-4.0/DynTxRegime/man/newTypedFit.Rd |only DynTxRegime-4.0/DynTxRegime/man/newTypedFitObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/optTx.Rd |only DynTxRegime-4.0/DynTxRegime/man/optimObj.Rd |only DynTxRegime-4.0/DynTxRegime/man/optimalClass.Rd | 464 +++---- DynTxRegime-4.0/DynTxRegime/man/optimalSeq.Rd | 478 +++---- DynTxRegime-4.0/DynTxRegime/man/outcome.Rd |only DynTxRegime-4.0/DynTxRegime/man/owl.Rd |only DynTxRegime-4.0/DynTxRegime/man/plot.Rd |only DynTxRegime-4.0/DynTxRegime/man/propen.Rd |only DynTxRegime-4.0/DynTxRegime/man/qLearn.Rd | 252 +-- DynTxRegime-4.0/DynTxRegime/man/qqplot.Rd |only DynTxRegime-4.0/DynTxRegime/man/regimeCoef.Rd |only DynTxRegime-4.0/DynTxRegime/man/residuals.Rd |only DynTxRegime-4.0/DynTxRegime/man/rwl.Rd |only DynTxRegime-4.0/DynTxRegime/man/sd.Rd |only DynTxRegime-4.0/DynTxRegime/man/seqFunc.Rd |only DynTxRegime-4.0/DynTxRegime/man/summary.Rd |only 545 files changed, 2483 insertions(+), 3289 deletions(-)
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 4.0.0 dated 2015-12-07 and 4.1.0 dated 2019-02-26
DESCRIPTION | 8 MD5 | 79 inst/INSTALL | 16 inst/Perl/Excel/Writer/XLSX.pm | 1027 ++- inst/Perl/Excel/Writer/XLSX/Chart.pm | 1050 +++ inst/Perl/Excel/Writer/XLSX/Chart/Area.pm | 9 inst/Perl/Excel/Writer/XLSX/Chart/Bar.pm | 9 inst/Perl/Excel/Writer/XLSX/Chart/Column.pm | 9 inst/Perl/Excel/Writer/XLSX/Chart/Doughnut.pm | 6 inst/Perl/Excel/Writer/XLSX/Chart/Line.pm | 22 inst/Perl/Excel/Writer/XLSX/Chart/Pie.pm | 34 inst/Perl/Excel/Writer/XLSX/Chart/Radar.pm | 6 inst/Perl/Excel/Writer/XLSX/Chart/Scatter.pm | 54 inst/Perl/Excel/Writer/XLSX/Chart/Stock.pm | 9 inst/Perl/Excel/Writer/XLSX/Chartsheet.pm | 37 inst/Perl/Excel/Writer/XLSX/Drawing.pm | 6 inst/Perl/Excel/Writer/XLSX/Examples.pm | 603 + inst/Perl/Excel/Writer/XLSX/Format.pm | 71 inst/Perl/Excel/Writer/XLSX/Package/App.pm | 24 inst/Perl/Excel/Writer/XLSX/Package/Comments.pm | 44 inst/Perl/Excel/Writer/XLSX/Package/ContentTypes.pm | 21 inst/Perl/Excel/Writer/XLSX/Package/Core.pm | 23 inst/Perl/Excel/Writer/XLSX/Package/Custom.pm |only inst/Perl/Excel/Writer/XLSX/Package/Packager.pm | 67 inst/Perl/Excel/Writer/XLSX/Package/Relationships.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/SharedStrings.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Styles.pm | 120 inst/Perl/Excel/Writer/XLSX/Package/Table.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Theme.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/VML.pm | 8 inst/Perl/Excel/Writer/XLSX/Package/XMLwriter.pm | 9 inst/Perl/Excel/Writer/XLSX/Shape.pm | 8 inst/Perl/Excel/Writer/XLSX/Utility.pm | 6 inst/Perl/Excel/Writer/XLSX/Workbook.pm | 266 inst/Perl/Excel/Writer/XLSX/Worksheet.pm | 1209 +++ inst/Perl/Parse/RecDescent.pm | 424 - inst/Perl/Text/CSV.pm | 2881 +++++++-- inst/Perl/Text/CSV_PP.pm | 5875 +++++++++++++++---- inst/Perl/WriteXLS.pl | 4 inst/Perl/WriteXLSX.pl | 4 man/WriteXLS.Rd | 8 41 files changed, 11196 insertions(+), 2884 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Damiano Oldoni [ctb] (<https://orcid.org/0000-0003-3445-7562>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 1.1.0 dated 2018-10-19 and 1.2.0 dated 2019-02-26
rgbif-1.1.0/rgbif/inst/doc/issues_vignette.Rmd |only rgbif-1.1.0/rgbif/inst/doc/issues_vignette.html |only rgbif-1.1.0/rgbif/inst/doc/rgbif_vignette.Rmd |only rgbif-1.1.0/rgbif/inst/doc/rgbif_vignette.html |only rgbif-1.1.0/rgbif/tests/fixtures/gbif_oai_list_records.yml |only rgbif-1.1.0/rgbif/tools |only rgbif-1.1.0/rgbif/vignettes/issues_vignette.Rmd |only rgbif-1.1.0/rgbif/vignettes/rgbif_vignette.Rmd |only rgbif-1.2.0/rgbif/DESCRIPTION | 35 rgbif-1.2.0/rgbif/LICENSE | 2 rgbif-1.2.0/rgbif/MD5 | 335 rgbif-1.2.0/rgbif/NEWS.md | 23 rgbif-1.2.0/rgbif/R/check_wkt.r | 4 rgbif-1.2.0/rgbif/R/datasets.r | 2 rgbif-1.2.0/rgbif/R/elevation.r | 218 rgbif-1.2.0/rgbif/R/occ_download.R | 24 rgbif-1.2.0/rgbif/R/occ_download_import.R | 4 rgbif-1.2.0/rgbif/R/occ_get.r | 30 rgbif-1.2.0/rgbif/R/occ_issues.r | 80 rgbif-1.2.0/rgbif/R/zzz.r | 133 rgbif-1.2.0/rgbif/README.md | 245 rgbif-1.2.0/rgbif/build/vignette.rds |binary rgbif-1.2.0/rgbif/inst/CITATION | 5 rgbif-1.2.0/rgbif/inst/doc/downloads.Rmd | 13 rgbif-1.2.0/rgbif/inst/doc/downloads.html | 6 rgbif-1.2.0/rgbif/inst/doc/issues.Rmd |only rgbif-1.2.0/rgbif/inst/doc/issues.html |only rgbif-1.2.0/rgbif/inst/doc/rgbif.Rmd |only rgbif-1.2.0/rgbif/inst/doc/rgbif.html |only rgbif-1.2.0/rgbif/inst/doc/taxonomic_names.Rmd | 36 rgbif-1.2.0/rgbif/inst/doc/taxonomic_names.html | 28 rgbif-1.2.0/rgbif/inst/vign/figure/gbifmap1-1.png |binary rgbif-1.2.0/rgbif/inst/vign/issues_vignette.md | 288 rgbif-1.2.0/rgbif/inst/vign/rgbif_vignette.md | 418 rgbif-1.2.0/rgbif/inst/vign/taxonomic_names.md | 18 rgbif-1.2.0/rgbif/man/dataset_search.Rd | 14 rgbif-1.2.0/rgbif/man/dataset_suggest.Rd | 14 rgbif-1.2.0/rgbif/man/elevation.Rd | 105 rgbif-1.2.0/rgbif/man/figures |only rgbif-1.2.0/rgbif/man/occ_data.Rd | 191 rgbif-1.2.0/rgbif/man/occ_download.Rd | 21 rgbif-1.2.0/rgbif/man/occ_get.Rd | 14 rgbif-1.2.0/rgbif/man/occ_issues.Rd | 17 rgbif-1.2.0/rgbif/man/occ_search.Rd | 194 rgbif-1.2.0/rgbif/tests/fixtures/count_facet.yml | 306 rgbif-1.2.0/rgbif/tests/fixtures/dataset_metrics.yml | 62 rgbif-1.2.0/rgbif/tests/fixtures/dataset_metrics_error.yml | 58 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search.yml | 21 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search_keyword.yml | 178 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search_limit.yml | 56 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search_query.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search_repeated_params.yml | 38 rgbif-1.2.0/rgbif/tests/fixtures/dataset_search_return.yml | 21 rgbif-1.2.0/rgbif/tests/fixtures/dataset_suggest.yml | 264 rgbif-1.2.0/rgbif/tests/fixtures/dataset_suggest_description.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/dataset_suggest_limit.yml | 46 rgbif-1.2.0/rgbif/tests/fixtures/dataset_suggest_query.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/dataset_suggest_repeated.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/datasets.yml | 21 rgbif-1.2.0/rgbif/tests/fixtures/datasets_contact.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/datasets_deleted_duplicate.yml | 40 rgbif-1.2.0/rgbif/tests/fixtures/datasets_fails_well.yml | 17 rgbif-1.2.0/rgbif/tests/fixtures/datasets_metadata.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/datasets_single.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/elevation.yml | 1089 rgbif-1.2.0/rgbif/tests/fixtures/elevation_geonames_conn.yml |only rgbif-1.2.0/rgbif/tests/fixtures/elevation_geonames_conn_unauthorized.yml |only rgbif-1.2.0/rgbif/tests/fixtures/elevation_models.yml |only rgbif-1.2.0/rgbif/tests/fixtures/elevation_unauthorized.yml |only rgbif-1.2.0/rgbif/tests/fixtures/enumeration.yml | 93 rgbif-1.2.0/rgbif/tests/fixtures/gbif_oai_get_records.yml | 18 rgbif-1.2.0/rgbif/tests/fixtures/gbif_oai_identify.yml | 18 rgbif-1.2.0/rgbif/tests/fixtures/gbif_oai_list_identifiers.yml | 20 rgbif-1.2.0/rgbif/tests/fixtures/gbif_oai_list_metadataformats.yml | 18 rgbif-1.2.0/rgbif/tests/fixtures/gbif_oai_list_sets.yml | 20 rgbif-1.2.0/rgbif/tests/fixtures/installations.yml | 21 rgbif-1.2.0/rgbif/tests/fixtures/installations_deleted.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/installations_uuid.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/installations_uuid_data.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/name_backbne.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup.yml | 754 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup_habitat.yml | 75 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup_many_inputs.yml | 43 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup_paging1.yml | 26 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup_paging2.yml | 41 rgbif-1.2.0/rgbif/tests/fixtures/name_lookup_paging3.yml | 28 rgbif-1.2.0/rgbif/tests/fixtures/name_suggest.yml | 755 rgbif-1.2.0/rgbif/tests/fixtures/name_suggest_many_args.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/name_usage.yml | 42 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_children.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_descriptions.yml | 58 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_distributions.yml | 153 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_media.yml | 45 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_name.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_parents.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_references.yml | 81 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_related.yml | 198 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_speciesProfiles.yml | 47 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_synonyms.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_typeSpecimens.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_data_vernacularNames.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_fails_well.yml | 13 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_return_data.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/name_usage_return_param.yml | 75 rgbif-1.2.0/rgbif/tests/fixtures/networks.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/nodes.yml | 49 rgbif-1.2.0/rgbif/tests/fixtures/occ_count.yml | 104 rgbif-1.2.0/rgbif/tests/fixtures/occ_count_fails_well.yml | 26 rgbif-1.2.0/rgbif/tests/fixtures/occ_data.yml |12924 ++------- rgbif-1.2.0/rgbif/tests/fixtures/occ_data_args_with_many_inputs.yml | 236 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_catalog_number.yml | 46 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_datasetkey.yml | 1923 - rgbif-1.2.0/rgbif/tests/fixtures/occ_data_depth.yml | 98 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_elevation.yml | 137 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_event_date.yml | 6854 ----- rgbif-1.2.0/rgbif/tests/fixtures/occ_data_fails_well.yml | 32 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_geometry.yml | 429 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_looping.yml | 63 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_scientificname.yml | 167 rgbif-1.2.0/rgbif/tests/fixtures/occ_data_spellcheck.yml | 60 rgbif-1.2.0/rgbif/tests/fixtures/occ_facet.yml | 40 rgbif-1.2.0/rgbif/tests/fixtures/occ_facet_paging.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/occ_facet_unknown_facet_var.yml | 19 rgbif-1.2.0/rgbif/tests/fixtures/occ_get.yml | 295 rgbif-1.2.0/rgbif/tests/fixtures/occ_get_other.yml | 113 rgbif-1.2.0/rgbif/tests/fixtures/occ_issues.yml | 38 rgbif-1.2.0/rgbif/tests/fixtures/occ_issues_type_many.yml |only rgbif-1.2.0/rgbif/tests/fixtures/occ_metadata.yml | 171 rgbif-1.2.0/rgbif/tests/fixtures/occ_search.yml |12954 ++-------- rgbif-1.2.0/rgbif/tests/fixtures/occ_search_catalognumber.yml | 15 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_datasetkey.yml | 1923 - rgbif-1.2.0/rgbif/tests/fixtures/occ_search_depth.yml | 77 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_elevation.yml | 114 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_eventdate.yml | 6862 ----- rgbif-1.2.0/rgbif/tests/fixtures/occ_search_fails_well.yml | 30 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_geometry.yml | 465 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_hierarchy_data.yml | 562 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_looping_works.yml | 63 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_many_inputs.yml | 244 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_scientificname.yml | 177 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_spell_check.yml | 60 rgbif-1.2.0/rgbif/tests/fixtures/occ_search_taxonkey.yml |12321 ++------- rgbif-1.2.0/rgbif/tests/fixtures/occ_spellcheck.yml | 102 rgbif-1.2.0/rgbif/tests/fixtures/parsenames.yml | 41 rgbif-1.2.0/rgbif/tests/fixtures/wkt_large_occ_data.yml | 372 rgbif-1.2.0/rgbif/tests/fixtures/wkt_large_occ_search.yml | 372 rgbif-1.2.0/rgbif/tests/testthat/elevation_test_data.rda |only rgbif-1.2.0/rgbif/tests/testthat/helper-rgbif.R | 15 rgbif-1.2.0/rgbif/tests/testthat/test-count_facet.r | 24 rgbif-1.2.0/rgbif/tests/testthat/test-dataset_metrics.r | 15 rgbif-1.2.0/rgbif/tests/testthat/test-dataset_search.r | 97 rgbif-1.2.0/rgbif/tests/testthat/test-dataset_suggest.r | 49 rgbif-1.2.0/rgbif/tests/testthat/test-datasets.r | 72 rgbif-1.2.0/rgbif/tests/testthat/test-elevation.R | 99 rgbif-1.2.0/rgbif/tests/testthat/test-enumeration.r | 16 rgbif-1.2.0/rgbif/tests/testthat/test-installations.r | 52 rgbif-1.2.0/rgbif/tests/testthat/test-name_backbone.r | 12 rgbif-1.2.0/rgbif/tests/testthat/test-name_lookup.r | 111 rgbif-1.2.0/rgbif/tests/testthat/test-name_suggest.r | 51 rgbif-1.2.0/rgbif/tests/testthat/test-name_usage.r | 261 rgbif-1.2.0/rgbif/tests/testthat/test-networks.r | 11 rgbif-1.2.0/rgbif/tests/testthat/test-nodes.r | 49 rgbif-1.2.0/rgbif/tests/testthat/test-oai.R | 70 rgbif-1.2.0/rgbif/tests/testthat/test-occ_count.r | 39 rgbif-1.2.0/rgbif/tests/testthat/test-occ_data.R | 220 rgbif-1.2.0/rgbif/tests/testthat/test-occ_facet.R | 36 rgbif-1.2.0/rgbif/tests/testthat/test-occ_get.r | 132 rgbif-1.2.0/rgbif/tests/testthat/test-occ_issues.R | 85 rgbif-1.2.0/rgbif/tests/testthat/test-occ_metadata.r | 49 rgbif-1.2.0/rgbif/tests/testthat/test-occ_search.r | 344 rgbif-1.2.0/rgbif/tests/testthat/test-occ_spellcheck.R | 13 rgbif-1.2.0/rgbif/tests/testthat/test-organizations.r | 30 rgbif-1.2.0/rgbif/tests/testthat/test-parsenames.r | 25 rgbif-1.2.0/rgbif/tests/testthat/test-wkt_large.R | 44 rgbif-1.2.0/rgbif/vignettes/downloads.Rmd | 13 rgbif-1.2.0/rgbif/vignettes/issues.Rmd |only rgbif-1.2.0/rgbif/vignettes/rgbif.Rmd |only rgbif-1.2.0/rgbif/vignettes/taxonomic_names.Rmd | 36 178 files changed, 19613 insertions(+), 50870 deletions(-)
Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to kernel methods for enforcing security restrictions.
AppArmor can apply mandatory access control (MAC) policies on a given task
(process) via security profiles with detailed ACL definitions. In addition
this package implements bindings for setting process resource limits (rlimit),
uid, gid, affinity and priority. The high level R function 'eval.secure'
builds on these methods to perform dynamic sandboxing: it evaluates a single
R expression within a temporary fork which acts as a sandbox by enforcing
fine grained restrictions without affecting the main R process. A portable
version of this function is now available in the 'unix' package.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RAppArmor versions 2.0.2 dated 2016-05-17 and 3.0 dated 2019-02-26
RAppArmor-2.0.2/RAppArmor/R/eval.secure.R |only RAppArmor-2.0.2/RAppArmor/R/process.R |only RAppArmor-2.0.2/RAppArmor/R/rlimits.R |only RAppArmor-2.0.2/RAppArmor/R/userinfo.R |only RAppArmor-2.0.2/RAppArmor/man/aa_change_hat.Rd |only RAppArmor-2.0.2/RAppArmor/man/aa_change_profile.Rd |only RAppArmor-2.0.2/RAppArmor/man/aa_find_mountpoint.Rd |only RAppArmor-2.0.2/RAppArmor/man/aa_getcon.Rd |only RAppArmor-2.0.2/RAppArmor/man/aa_is_enabled.Rd |only RAppArmor-2.0.2/RAppArmor/man/eval.secure.Rd |only RAppArmor-2.0.2/RAppArmor/man/process.Rd |only RAppArmor-2.0.2/RAppArmor/man/rlimit.Rd |only RAppArmor-2.0.2/RAppArmor/man/userinfo.Rd |only RAppArmor-2.0.2/RAppArmor/src/process.c |only RAppArmor-2.0.2/RAppArmor/src/rlimits.c |only RAppArmor-3.0/RAppArmor/DESCRIPTION | 43 +-- RAppArmor-3.0/RAppArmor/MD5 | 66 ++---- RAppArmor-3.0/RAppArmor/NAMESPACE | 56 ----- RAppArmor-3.0/RAppArmor/NEWS | 4 RAppArmor-3.0/RAppArmor/R/affinity.R | 70 +++--- RAppArmor-3.0/RAppArmor/R/apparmor.R | 66 ++---- RAppArmor-3.0/RAppArmor/R/eval.R |only RAppArmor-3.0/RAppArmor/R/onAttach.R | 6 RAppArmor-3.0/RAppArmor/R/unittests.R | 4 RAppArmor-3.0/RAppArmor/build/vignette.rds |binary RAppArmor-3.0/RAppArmor/cleanup |only RAppArmor-3.0/RAppArmor/configure | 10 RAppArmor-3.0/RAppArmor/inst/profiles/debian/rapparmor.d/r-user | 3 RAppArmor-3.0/RAppArmor/man/affinity.Rd | 60 ++--- RAppArmor-3.0/RAppArmor/man/apparmor.Rd |only RAppArmor-3.0/RAppArmor/man/sandboxing.Rd |only RAppArmor-3.0/RAppArmor/man/unittests.Rd | 5 RAppArmor-3.0/RAppArmor/src/Makevars.in | 5 RAppArmor-3.0/RAppArmor/src/affinity.c | 63 +++-- RAppArmor-3.0/RAppArmor/src/apparmor.c | 108 +++++----- RAppArmor-3.0/RAppArmor/src/init.c |only RAppArmor-3.0/RAppArmor/tests/testthat/helper-pretest.R | 6 RAppArmor-3.0/RAppArmor/tests/testthat/test-affinity.R | 13 - RAppArmor-3.0/RAppArmor/tests/testthat/test-apparmor.R | 40 +-- RAppArmor-3.0/RAppArmor/tests/testthat/test-priority.R | 18 - RAppArmor-3.0/RAppArmor/tests/testthat/test-rlimit_cpu.R | 14 - RAppArmor-3.0/RAppArmor/tests/testthat/test-rlimit_memory.R | 35 +-- RAppArmor-3.0/RAppArmor/tests/testthat/test-rlimit_nproc.R | 10 RAppArmor-3.0/RAppArmor/tests/testthat/test-root.R | 8 44 files changed, 347 insertions(+), 366 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>),
Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>),
Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>),
Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>),
Jiong Wei Lua [aut],
Patrick O. Perry [aut] (<https://orcid.org/0000-0001-7460-127X>),
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
Benjamin Lauderdale [aut] (<https://orcid.org/0000-0003-3090-0969>),
William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>),
Christian Müller [ctb],
Lori Young [dtc] (Lexicoder Sentiment Dictionary 2015),
Stuart Soroka [dtc] (Lexicoder Sentiment Dictionary 2015),
Ian Fellows [cph] (authored wordcloud C source code (modified)),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 1.4.0 dated 2019-01-30 and 1.4.1 dated 2019-02-26
DESCRIPTION | 6 - MD5 | 66 ++++++++--------- NEWS.md | 128 +++++++++++++++++----------------- R/docvars.R | 73 ++++++++++--------- R/quanteda-documentation.R | 49 ++++++------- R/textplot_network.R | 1 R/textstat_readability.R | 2 R/tokens_compound.R | 88 +++++++++++++---------- R/tokens_replace.R | 5 + R/utils.R | 10 +- inst/WORDLIST | 1 inst/doc/quickstart.html | 62 ++++++++-------- man/corpus_segment.Rd | 5 - man/dfm_select.Rd | 5 - man/kwic.Rd | 5 - man/pattern.Rd | 49 ++++++------- man/pattern2id.Rd | 5 - man/pattern2list.Rd | 5 - man/textplot_network.Rd | 1 man/textstat_readability.Rd | 2 man/textstat_select.Rd | 5 - man/tokens_compound.Rd | 105 +++++++++++++++------------ man/tokens_segment.Rd | 5 - man/tokens_select.Rd | 5 - src/ca_mt.cpp | 37 +++++---- src/fcm_mt.cpp | 6 - src/kwic_mt.cpp | 4 - src/quanteda.h | 6 - src/tokens_chunk_mt.cpp | 2 src/tokens_segment_mt.cpp | 12 +-- tests/testthat/test-docvars.R | 98 +++++++++++++++++++++++++- tests/testthat/test-kwic.R | 11 ++ tests/testthat/test-tokens.R | 14 +-- tests/testthat/test-tokens_compound.R | 34 ++++++--- 34 files changed, 546 insertions(+), 366 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of linear
regression, GLM, and Cox regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/000-0002-0650-1119>),
Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.2-0 dated 2018-09-27 and 3.2-1 dated 2019-02-26
grpreg-3.2-0/grpreg/R/cv.grpsurv.R |only grpreg-3.2-1/grpreg/DESCRIPTION | 10 - grpreg-3.2-1/grpreg/MD5 | 18 +- grpreg-3.2-1/grpreg/NEWS | 8 + grpreg-3.2-1/grpreg/R/G.R | 2 grpreg-3.2-1/grpreg/R/cv-grpreg.R | 25 ++-- grpreg-3.2-1/grpreg/R/cv-grpsurv.R |only grpreg-3.2-1/grpreg/README.md | 4 grpreg-3.2-1/grpreg/build/vignette.rds |binary grpreg-3.2-1/grpreg/inst/doc/getting-started.html | 134 ++++++++++++---------- grpreg-3.2-1/grpreg/inst/tests/cv.R | 32 ++--- 11 files changed, 134 insertions(+), 99 deletions(-)
Title: Translate Integers into English
Description: Allow numbers to be presented in an English language
version, one, two, three, ...
Author: John Fox, Bill Venables, Anthony Damico and Anne Pier Salverda
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between english versions 1.2-0 dated 2019-02-19 and 1.2-1 dated 2019-02-26
english-1.2-0/english/man/as.character.english.Rd |only english-1.2-0/english/man/as.numeric.english.Rd |only english-1.2-0/english/man/print.english.Rd |only english-1.2-0/english/man/sort.english.Rd |only english-1.2-1/english/DESCRIPTION | 8 english-1.2-1/english/MD5 | 28 +-- english-1.2-1/english/NAMESPACE | 42 ++-- english-1.2-1/english/R/english.R | 192 +++++++++++++++------- english-1.2-1/english/R/indefinite.R | 54 +++++- english-1.2-1/english/R/ordinal.R | 64 +++++-- english-1.2-1/english/R/words.R | 18 ++ english-1.2-1/english/man/Ops.english.Rd | 64 ++----- english-1.2-1/english/man/as.english.Rd | 130 ++++++-------- english-1.2-1/english/man/english-package.Rd | 43 ---- english-1.2-1/english/man/indefinite.Rd | 64 +++---- english-1.2-1/english/man/ordinal.Rd | 60 ++---- english-1.2-1/english/man/words.Rd | 54 +----- 17 files changed, 449 insertions(+), 372 deletions(-)
Title: Complexity Measures for Supervised Problems
Description: Provides measures to characterize the complexity of classification
and regression problems based on aspects that quantify the linearity of the
data, the presence of informative feature, the sparsity and dimensionality
of the datasets. This package provides bug fixes, generalizations and
implementations of many state of the art measures. The measures are
described in the papers: Ho and Basu (2002) <doi:10.1109/34.990132> and
Lorena et al. (2018) <doi:10.1007/s10994-017-5681-1>.
Author: Luis Garcia [aut, cre],
Ana Lorena [aut, ctb]
Maintainer: Luis Garcia <lpfgarcia@icmc.usp.br>
Diff between ECoL versions 0.1.0 dated 2018-01-22 and 0.2.0 dated 2019-02-26
ECoL-0.1.0/ECoL/man/linearity.Rd |only ECoL-0.2.0/ECoL/DESCRIPTION | 34 +++--- ECoL-0.2.0/ECoL/LICENSE | 2 ECoL-0.2.0/ECoL/MD5 | 42 ++++--- ECoL-0.2.0/ECoL/NAMESPACE | 15 ++ ECoL-0.2.0/ECoL/R/balance.R | 20 ++- ECoL-0.2.0/ECoL/R/complexity.R | 78 +++++++++----- ECoL-0.2.0/ECoL/R/correlation.R |only ECoL-0.2.0/ECoL/R/dimensionality.R | 40 +++---- ECoL-0.2.0/ECoL/R/internal.R | 80 +++++++++++--- ECoL-0.2.0/ECoL/R/linearity.R | 183 ++++++++++++++++++++++++++------- ECoL-0.2.0/ECoL/R/neighborhood.R | 110 ++++++++----------- ECoL-0.2.0/ECoL/R/network.R | 40 +++---- ECoL-0.2.0/ECoL/R/overlapping.R | 65 ++++++----- ECoL-0.2.0/ECoL/R/smoothness.R |only ECoL-0.2.0/ECoL/README.md |only ECoL-0.2.0/ECoL/man/balance.Rd | 21 ++- ECoL-0.2.0/ECoL/man/complexity.Rd | 48 +++++--- ECoL-0.2.0/ECoL/man/correlation.Rd |only ECoL-0.2.0/ECoL/man/dimensionality.Rd | 31 +++-- ECoL-0.2.0/ECoL/man/linearity.class.Rd |only ECoL-0.2.0/ECoL/man/linearity.regr.Rd |only ECoL-0.2.0/ECoL/man/neighborhood.Rd | 27 ++-- ECoL-0.2.0/ECoL/man/network.Rd | 23 ++-- ECoL-0.2.0/ECoL/man/overlapping.Rd | 18 +-- ECoL-0.2.0/ECoL/man/smoothness.Rd |only 26 files changed, 557 insertions(+), 320 deletions(-)
Title: Computes and Plots Confidence (Compatibility) Intervals,
P-Values, and S-Values to Form Consonance Curves (Functions)
Description: Allows one to compute confidence (compatibility/consonance) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance functions allowing one to see what effect sizes are compatible with the test model at various compatibility levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2012, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2018) <doi:10.7287/peerj.preprints.26857v4>, and Greenland S. (2018) <doi:10.1080/00031305.2018.1529625>.
Author: Zad Chow [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>)
Maintainer: Zad Chow <zad@lesslikely.com>
Diff between concurve versions 1.0.1 dated 2019-01-30 and 1.0.4 dated 2019-02-26
DESCRIPTION | 19 ++++++++++--------- MD5 | 4 ++-- README.md | 48 +++++++++++++++++++++++++++++++++++++++++------- 3 files changed, 53 insertions(+), 18 deletions(-)
Title: Chemical Composition of Differential Protein Expression
Description: Datasets are collected here for differentially (up- and down-)
expressed proteins identified in proteomic studies of cancer and in cell
culture experiments. Tables of amino acid compositions of proteins are
used for calculations of chemical composition, projected into selected
basis species. Plotting functions are used to visualize the compositional
differences and thermodynamic potentials for proteomic transformations.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between canprot versions 0.1.1 dated 2018-01-18 and 0.1.2 dated 2019-02-26
canprot-0.1.1/canprot/data |only canprot-0.1.2/canprot/DESCRIPTION | 10 - canprot-0.1.2/canprot/MD5 | 101 ++++++++--------- canprot-0.1.2/canprot/NAMESPACE | 2 canprot-0.1.2/canprot/R/check_ID.R | 4 canprot-0.1.2/canprot/R/get_comptab.R | 2 canprot-0.1.2/canprot/R/lapply_canprot.R | 18 --- canprot-0.1.2/canprot/R/protcomp.R | 8 - canprot-0.1.2/canprot/R/zzz.R |only canprot-0.1.2/canprot/build/partial.rdb |binary canprot-0.1.2/canprot/build/vignette.rds |binary canprot-0.1.2/canprot/inst/NEWS | 9 + canprot-0.1.2/canprot/inst/doc/basis_comparison.R | 4 canprot-0.1.2/canprot/inst/doc/basis_comparison.Rmd | 6 - canprot-0.1.2/canprot/inst/doc/basis_comparison.html | 32 ++++- canprot-0.1.2/canprot/inst/doc/colorectal.R | 6 - canprot-0.1.2/canprot/inst/doc/colorectal.Rmd | 6 - canprot-0.1.2/canprot/inst/doc/colorectal.html | 38 +++++- canprot-0.1.2/canprot/inst/doc/hyperosmotic.R | 1 canprot-0.1.2/canprot/inst/doc/hyperosmotic.Rmd | 1 canprot-0.1.2/canprot/inst/doc/hyperosmotic.html | 33 ++++- canprot-0.1.2/canprot/inst/doc/hypoxia.R | 1 canprot-0.1.2/canprot/inst/doc/hypoxia.Rmd | 1 canprot-0.1.2/canprot/inst/doc/hypoxia.html | 33 ++++- canprot-0.1.2/canprot/inst/doc/pancreatic.R | 1 canprot-0.1.2/canprot/inst/doc/pancreatic.Rmd | 1 canprot-0.1.2/canprot/inst/doc/pancreatic.html | 33 ++++- canprot-0.1.2/canprot/inst/doc/potential_diagrams.R | 1 canprot-0.1.2/canprot/inst/doc/potential_diagrams.Rmd | 1 canprot-0.1.2/canprot/inst/doc/potential_diagrams.html | 31 ++++- canprot-0.1.2/canprot/inst/extdata/protein |only canprot-0.1.2/canprot/man/Ehplot.Rd | 2 canprot-0.1.2/canprot/man/canprot-package.Rd | 7 - canprot-0.1.2/canprot/man/canprot.Rd | 8 - canprot-0.1.2/canprot/man/check_ID.Rd | 1 canprot-0.1.2/canprot/man/diffplot.Rd | 2 canprot-0.1.2/canprot/man/get_comptab.Rd | 2 canprot-0.1.2/canprot/man/get_pdat.Rd | 2 canprot-0.1.2/canprot/man/groupplots.Rd | 1 canprot-0.1.2/canprot/man/pdat_.Rd | 2 canprot-0.1.2/canprot/man/protcomp.Rd | 4 canprot-0.1.2/canprot/man/rankplot.Rd | 2 canprot-0.1.2/canprot/man/xsummary.Rd | 2 canprot-0.1.2/canprot/vignettes/basis_comparison.Rmd | 6 - canprot-0.1.2/canprot/vignettes/colorectal.Rmd | 6 - canprot-0.1.2/canprot/vignettes/hyperosmotic.Rmd | 1 canprot-0.1.2/canprot/vignettes/hypoxia.Rmd | 1 canprot-0.1.2/canprot/vignettes/pancreatic.Rmd | 1 canprot-0.1.2/canprot/vignettes/potential_diagrams.Rmd | 1 49 files changed, 269 insertions(+), 166 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-31 2.11-4.1
2014-09-10 2.11-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-12 2.16-4
Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between taxotools versions 0.0.7 dated 2019-01-30 and 0.0.9 dated 2019-02-26
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 1 + NEWS | 4 +++- R/BuildCSList.R | 16 ++++++++++++++-- R/MakeCanonical.R |only R/taxotools.R | 1 + man/BuildCSList.Rd | 6 +++++- man/MakeCanonical.Rd |only man/taxotools.Rd | 1 + 10 files changed, 38 insertions(+), 15 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or
better understand data generating processes. The user specifies a set of
relationships between covariates, and generates data based on these
specifications. The final data sets can represent data from randomized
control trials, repeated measure (longitudinal) designs, and cluster
randomized trials. Missingness can be generated using various
mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>
Diff between simstudy versions 0.1.11 dated 2019-02-07 and 0.1.12 dated 2019-02-26
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- NEWS.md | 4 ++ R/addMultiFac.R | 2 - R/genCorFlex.R | 6 +-- inst/doc/simstudy.R | 76 ----------------------------------------- inst/doc/simstudy.Rmd | 90 ------------------------------------------------- inst/doc/simstudy.html | 18 +-------- vignettes/simstudy.Rmd | 90 ------------------------------------------------- 9 files changed, 22 insertions(+), 288 deletions(-)
Title: Facilitates 'PhenoCam' Data Access and Time Series
Post-Processing
Description: Programmatic interface to the 'PhenoCam' web services (<http://phenocam.sr.unh.edu>).
Allows for easy downloading of 'PhenoCam' data directly to your R workspace
or your computer and provides post-processing routines for consistent and easy
timeseries outlier detection, smoothing and estimation of phenological transition dates.
Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.
Author: Hufkens Koen [aut, cre]
Maintainer: Hufkens Koen <koen.hufkens@gmail.com>
Diff between phenocamr versions 1.1.1 dated 2018-08-22 and 1.1.3 dated 2019-02-26
phenocamr-1.1.1/phenocamr/tests/run_tests.r |only phenocamr-1.1.3/phenocamr/DESCRIPTION | 10 phenocamr-1.1.3/phenocamr/MD5 | 39 phenocamr-1.1.3/phenocamr/R/contract_phenocam.r | 10 phenocamr-1.1.3/phenocamr/R/download_phenocam.r | 65 phenocamr-1.1.3/phenocamr/R/list_rois.r | 20 phenocamr-1.1.3/phenocamr/R/list_sites.r | 10 phenocamr-1.1.3/phenocamr/R/read_phenocam.r | 4 phenocamr-1.1.3/phenocamr/R/transition_dates.r | 2 phenocamr-1.1.3/phenocamr/R/truncate_phenocam.r | 2 phenocamr-1.1.3/phenocamr/R/zzz.R |only phenocamr-1.1.3/phenocamr/build/vignette.rds |binary phenocamr-1.1.3/phenocamr/inst/doc/phenocamr-vignette.R | 38 phenocamr-1.1.3/phenocamr/inst/doc/phenocamr-vignette.Rmd | 38 phenocamr-1.1.3/phenocamr/inst/doc/phenocamr-vignette.html | 745 ++++++---- phenocamr-1.1.3/phenocamr/man/contract_phenocam.Rd | 5 phenocamr-1.1.3/phenocamr/man/download_phenocam.Rd | 4 phenocamr-1.1.3/phenocamr/man/truncate_phenocam.Rd | 2 phenocamr-1.1.3/phenocamr/tests/testthat.r |only phenocamr-1.1.3/phenocamr/tests/testthat/test_ancillary_functions.r | 64 phenocamr-1.1.3/phenocamr/tests/testthat/test_download_function.r | 38 phenocamr-1.1.3/phenocamr/vignettes/phenocamr-vignette.Rmd | 38 22 files changed, 696 insertions(+), 438 deletions(-)
Title: Named Capture Regular Expressions
Description: User-friendly wrappers for
named capture regular expressions.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between namedCapture versions 2019.01.14 dated 2019-01-14 and 2019.02.25 dated 2019-02-26
DESCRIPTION | 8 MD5 | 61 - NAMESPACE | 13 NEWS | 154 ++-- R/df.R | 226 +++--- R/engine.R |only R/str_match.R | 501 +++++++------- R/variable.R | 346 +++++----- build/vignette.rds |binary inst/doc/Three_argument_syntax.R | 166 ++-- inst/doc/Three_argument_syntax.Rmd | 314 ++++----- inst/doc/Three_argument_syntax.html | 768 +++++++++------------- inst/doc/Variable_argument_syntax.R | 402 +++++------ inst/doc/Variable_argument_syntax.Rmd | 659 +++++++++---------- inst/doc/Variable_argument_syntax.html | 1129 +++++++++++++-------------------- man/namedCapture.engine.Rd |only man/only_captures.Rd |only man/stop_for_names.Rd |only man/str_match_all_named.Rd | 14 man/str_match_all_variable.Rd | 4 man/str_match_named.Rd | 10 man/str_match_variable.Rd | 6 tests/testthat.R | 4 tests/testthat/test-NA.R | 56 - tests/testthat/test-chr-pos.R | 180 ++--- tests/testthat/test-df.R | 708 ++++++++++---------- tests/testthat/test-dt.R | 145 ++-- tests/testthat/test-engine.R |only tests/testthat/test-errors.R | 317 ++++----- tests/testthat/test-name-value.R | 153 ++-- tests/testthat/test-optional-groups.R | 98 +- tests/testthat/test-variable.R | 602 ++++++++--------- vignettes/Three_argument_syntax.Rmd | 314 ++++----- vignettes/Variable_argument_syntax.Rmd | 659 +++++++++---------- 34 files changed, 3910 insertions(+), 4107 deletions(-)
Title: A Model Object Framework for Regression Analysis
Description: A utility library to facilitate the generalization of statistical methods built on a regression framework. Package developers can use 'modelObj' methods to initiate a regression analysis without concern for the details of the regression model and the method to be used to obtain parameter estimates. The specifics of the regression step are left to the user to define when calling the function. The user of a function developed within the 'modelObj' framework creates as input a 'modelObj' that contains the model and the R methods to be used to obtain parameter estimates and to obtain predictions. In this way, a user can easily go from linear to non-linear models within the same package.
Author: Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between modelObj versions 3.0 dated 2017-05-12 and 4.0 dated 2019-02-26
modelObj-3.0/modelObj/R/A00_generics.R |only modelObj-3.0/modelObj/R/modelObj.R |only modelObj-3.0/modelObj/man/methods-coef.Rd |only modelObj-3.0/modelObj/man/methods-fit.Rd |only modelObj-3.0/modelObj/man/methods-fitObject.Rd |only modelObj-3.0/modelObj/man/methods-model.Rd |only modelObj-3.0/modelObj/man/methods-plot.Rd |only modelObj-3.0/modelObj/man/methods-predict.Rd |only modelObj-3.0/modelObj/man/methods-predictor.Rd |only modelObj-3.0/modelObj/man/methods-predictorArgs.Rd |only modelObj-3.0/modelObj/man/methods-predictorArgs_-.Rd |only modelObj-3.0/modelObj/man/methods-residuals.Rd |only modelObj-3.0/modelObj/man/methods-solver.Rd |only modelObj-3.0/modelObj/man/methods-solverArgs.Rd |only modelObj-3.0/modelObj/man/methods-solverArgs_-.Rd |only modelObj-3.0/modelObj/man/modelObj-class.Rd |only modelObj-3.0/modelObj/man/modelObj-package.Rd |only modelObj-3.0/modelObj/man/modelObjFit-class.Rd |only modelObj-4.0/modelObj/DESCRIPTION | 12 modelObj-4.0/modelObj/MD5 | 81 +-- modelObj-4.0/modelObj/NAMESPACE | 48 - modelObj-4.0/modelObj/R/A01_methodObj.R | 281 ++++++++-- modelObj-4.0/modelObj/R/A02_methodObjPredict.R | 274 ++++------ modelObj-4.0/modelObj/R/A03_methodObjSolver.R | 58 ++ modelObj-4.0/modelObj/R/A04_methodObjSolverFormula.R | 226 +++----- modelObj-4.0/modelObj/R/A05_methodObjSolverXY.R | 257 ++++----- modelObj-4.0/modelObj/R/A06_modelObj.R | 195 +++++-- modelObj-4.0/modelObj/R/A07_modelObjFormula.R | 20 modelObj-4.0/modelObj/R/A08_modelObjXY.R | 17 modelObj-4.0/modelObj/R/A09_modelObjFit.R | 369 ++++++++++---- modelObj-4.0/modelObj/R/buildModelObj.R |only modelObj-4.0/modelObj/R/warnMsg.R | 13 modelObj-4.0/modelObj/build/vignette.rds |binary modelObj-4.0/modelObj/inst/doc/modelObj.R | 2 modelObj-4.0/modelObj/inst/doc/modelObj.Rnw | 4 modelObj-4.0/modelObj/inst/doc/modelObj.pdf |binary modelObj-4.0/modelObj/man/buildModelObj.Rd |only modelObj-4.0/modelObj/man/fit.Rd |only modelObj-4.0/modelObj/man/fitObject.Rd |only modelObj-4.0/modelObj/man/internal-fit.Rd |only modelObj-4.0/modelObj/man/internal-predict.Rd |only modelObj-4.0/modelObj/man/method.Rd |only modelObj-4.0/modelObj/man/methodArgs.Rd |only modelObj-4.0/modelObj/man/methodObj-class.Rd |only modelObj-4.0/modelObj/man/methodObjPredict-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolver-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolverFormula-class.Rd |only modelObj-4.0/modelObj/man/methodObjSolverXY-class.Rd |only modelObj-4.0/modelObj/man/model.Rd |only modelObj-4.0/modelObj/man/modelObj-internal-api.Rd |only modelObj-4.0/modelObj/man/modelObj.Rd | 140 +---- modelObj-4.0/modelObj/man/modelObjFit.Rd |only modelObj-4.0/modelObj/man/newMethodObj.Rd |only modelObj-4.0/modelObj/man/newMethodObjPredict.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolver.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolverFormula.Rd |only modelObj-4.0/modelObj/man/newMethodObjSolverXY.Rd |only modelObj-4.0/modelObj/man/predict.Rd |only modelObj-4.0/modelObj/man/predictor.Rd |only modelObj-4.0/modelObj/man/predictorArgs.Rd |only modelObj-4.0/modelObj/man/solver.Rd |only modelObj-4.0/modelObj/man/solverArgs.Rd |only modelObj-4.0/modelObj/man/warnMsg.Rd |only modelObj-4.0/modelObj/vignettes/modelObj.Rnw | 4 64 files changed, 1164 insertions(+), 837 deletions(-)
Title: Interface to the Fish Tree of Life API
Description: An interface to the Fish Tree of Life API to download taxonomies,
phylogenies, fossil calibrations, and diversification rate information for
ray-finned fishes.
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>),
Michael E Alfaro [ctb],
Daniel L Rabosky [ctb],
Stephen A Smith [ctb]
Maintainer: Jonathan Chang <jonathan.chang@ucla.edu>
Diff between fishtree versions 0.1.0 dated 2018-11-30 and 0.2.0 dated 2019-02-26
DESCRIPTION | 12 +- MD5 | 35 +++--- NAMESPACE | 1 NEWS.md | 15 ++ R/fishtree-package.R |only R/functions.R | 136 ++++++++++++++++------- R/utils.R | 33 ++++- README.md | 53 +++++++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/community-analysis.R |only inst/doc/community-analysis.Rmd |only inst/doc/community-analysis.html |only inst/doc/comparative-analysis.R | 215 ++++++++++++++++++------------------- inst/doc/comparative-analysis.Rmd | 42 +++---- inst/doc/comparative-analysis.html | 134 +++++++---------------- man/fishtree-package.Rd |only man/fishtree_phylogeny.Rd | 21 +++ man/fishtree_rogues.Rd |only man/fishtree_taxonomy.Rd | 19 +-- tests |only vignettes/community-analysis.Rmd |only vignettes/comparative-analysis.Rmd | 42 +++---- 23 files changed, 428 insertions(+), 330 deletions(-)
Title: Animation of Observed Trajectories Using Spline-Based
Interpolation
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf
Maintainer: Henry Scharf <henry.scharf@colostate.edu>
Diff between anipaths versions 0.9.6 dated 2018-06-20 and 0.9.7 dated 2019-02-26
DESCRIPTION | 15 +++--- MD5 | 15 +++--- NEWS |only R/animate_paths.R | 112 +++++++++++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/anipaths.html | 4 - man/animate_paths.Rd | 23 ++++++++- man/get.network.colors.Rd | 4 + man/plot.Rd | 4 - 9 files changed, 115 insertions(+), 62 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 2.3.1 dated 2019-02-15 and 2.3.2 dated 2019-02-26
DESCRIPTION | 12 +-- MD5 | 40 +++++----- NAMESPACE | 10 -- NEWS | 11 ++ R/filters.R | 2 R/heterogeneity.R | 169 +++++++++++++++++++++++++++++-------------- R/ma_d_bb.R | 1 R/ma_generic.R | 82 +++++++++++--------- R/ma_r_bb.R | 1 R/ma_r_ic.R | 3 R/ma_r_order2.R | 15 ++- R/ma_wrappers.R | 34 +++++--- R/metareg.R | 2 R/methods_print.R | 2 R/output.R | 134 +++++++++++++++++++++------------- man/dot-heterogeneity.Rd | 7 + man/heterogeneity.Rd | 13 ++- man/limits_tau.Rd | 24 +++--- man/limits_tau2.Rd | 24 +++--- man/ma_generic.Rd | 7 + man/metabulate_rmd_helper.Rd | 5 - 21 files changed, 377 insertions(+), 221 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb],
Dominik Schneider [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.8.2 dated 2018-04-20 and 0.9.0 dated 2019-02-26
ProjectTemplate-0.8.2/ProjectTemplate/man/arff.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/csv.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/csv2.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/db.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/dbf.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/epiinfo.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/file.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/mp3.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/mtp.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/octave.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/ppm.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/r.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/rdata.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/rds.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/spss.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/sql.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/stata.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/systat.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/tsv.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/url.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/wsv.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/xls.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/xlsx.reader.Rd |only ProjectTemplate-0.8.2/ProjectTemplate/man/xport.reader.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/DESCRIPTION | 50 - ProjectTemplate-0.9.0/ProjectTemplate/LICENSE |only ProjectTemplate-0.9.0/ProjectTemplate/MD5 | 216 +++--- ProjectTemplate-0.9.0/ProjectTemplate/NAMESPACE | 3 ProjectTemplate-0.9.0/ProjectTemplate/NEWS.md | 24 ProjectTemplate-0.9.0/ProjectTemplate/R/add.config.R | 2 ProjectTemplate-0.9.0/ProjectTemplate/R/add.extension.R | 2 ProjectTemplate-0.9.0/ProjectTemplate/R/addins.R |only ProjectTemplate-0.9.0/ProjectTemplate/R/arff.reader.R | 14 ProjectTemplate-0.9.0/ProjectTemplate/R/cache.R | 139 +++- ProjectTemplate-0.9.0/ProjectTemplate/R/cache.name.R | 2 ProjectTemplate-0.9.0/ProjectTemplate/R/clean.variable.name.R | 2 ProjectTemplate-0.9.0/ProjectTemplate/R/clear.R | 54 + ProjectTemplate-0.9.0/ProjectTemplate/R/config.R | 12 ProjectTemplate-0.9.0/ProjectTemplate/R/create.project.R | 110 +++ ProjectTemplate-0.9.0/ProjectTemplate/R/create.template.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/csv.reader.R | 17 ProjectTemplate-0.9.0/ProjectTemplate/R/csv2.reader.R | 26 ProjectTemplate-0.9.0/ProjectTemplate/R/db.reader.R | 26 ProjectTemplate-0.9.0/ProjectTemplate/R/dbf.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/epiinfo.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/feather.reader.R |only ProjectTemplate-0.9.0/ProjectTemplate/R/file.reader.R | 19 ProjectTemplate-0.9.0/ProjectTemplate/R/get.project.R | 26 ProjectTemplate-0.9.0/ProjectTemplate/R/help.R | 5 ProjectTemplate-0.9.0/ProjectTemplate/R/list.data.R | 72 +- ProjectTemplate-0.9.0/ProjectTemplate/R/load.project.R | 163 ++++- ProjectTemplate-0.9.0/ProjectTemplate/R/migrate.project.R | 44 + ProjectTemplate-0.9.0/ProjectTemplate/R/mp3.reader.R | 13 ProjectTemplate-0.9.0/ProjectTemplate/R/mtp.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/octave.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/ppm.reader.R | 17 ProjectTemplate-0.9.0/ProjectTemplate/R/preinstalled.readers.R | 48 - ProjectTemplate-0.9.0/ProjectTemplate/R/project.config.R | 28 ProjectTemplate-0.9.0/ProjectTemplate/R/r.reader.R | 13 ProjectTemplate-0.9.0/ProjectTemplate/R/rdata.reader.R | 13 ProjectTemplate-0.9.0/ProjectTemplate/R/rds.reader.R | 14 ProjectTemplate-0.9.0/ProjectTemplate/R/require.package.R | 35 - ProjectTemplate-0.9.0/ProjectTemplate/R/spss.reader.R | 13 ProjectTemplate-0.9.0/ProjectTemplate/R/sql.reader.R | 34 - ProjectTemplate-0.9.0/ProjectTemplate/R/stata.reader.R | 15 ProjectTemplate-0.9.0/ProjectTemplate/R/stopifnotproject.R | 127 ++- ProjectTemplate-0.9.0/ProjectTemplate/R/systat.reader.R | 15 ProjectTemplate-0.9.0/ProjectTemplate/R/tsv.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/url.reader.R | 17 ProjectTemplate-0.9.0/ProjectTemplate/R/wsv.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/xls.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/xlsx.reader.R | 16 ProjectTemplate-0.9.0/ProjectTemplate/R/xport.reader.R | 15 ProjectTemplate-0.9.0/ProjectTemplate/build/partial.rdb |binary ProjectTemplate-0.9.0/ProjectTemplate/inst/defaults/config/default.dcf | 2 ProjectTemplate-0.9.0/ProjectTemplate/inst/defaults/config/types.dcf | 2 ProjectTemplate-0.9.0/ProjectTemplate/inst/defaults/templates/full/README.md | 2 ProjectTemplate-0.9.0/ProjectTemplate/inst/defaults/templates/full/config/global.dcf | 4 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ProjectTemplate-0.9.0/ProjectTemplate/man/create.project.Rd | 8 ProjectTemplate-0.9.0/ProjectTemplate/man/get.project.Rd | 14 ProjectTemplate-0.9.0/ProjectTemplate/man/internal.attach.or.add.namespace.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.cache.filename.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.cache.hash.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.cache.status.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.cached.variables.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.check.version.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.convert.to.data.table.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.convert.to.tibble.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.create.cache.hash.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.create.project.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.dir.empty.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.evaluate.code.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.get.template.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.has.project.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.init.logger.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.is.ProjectTemplate.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.is.cache.empty.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.is.cached.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.is.dir.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.list.data.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.list.files.and.dirs.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.load.data.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.load.helpers.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.load.libraries.Rd |only 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ProjectTemplate-0.9.0/ProjectTemplate/man/internal.var.diff.from.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/internal.write.cache.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/list.data.Rd | 29 ProjectTemplate-0.9.0/ProjectTemplate/man/loadproject_addin.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/preinstalled.readers.Rd | 322 +++++++++- ProjectTemplate-0.9.0/ProjectTemplate/man/project.config.Rd | 28 ProjectTemplate-0.9.0/ProjectTemplate/man/reloadproject_addin.Rd |only ProjectTemplate-0.9.0/ProjectTemplate/man/require.package.Rd | 3 ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-autogen.R | 2 ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-config.R | 17 ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-create.R | 19 ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-load.R | 64 + ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-migration.R | 88 ++ ProjectTemplate-0.9.0/ProjectTemplate/tests/testthat/test-readers.R | 25 144 files changed, 1633 insertions(+), 725 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox
regression models using lasso or nonconvex penalties, in particular the
minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD)
penalty, with options for additional L2 penalties (the "elastic net" idea).
Utilities for carrying out cross-validation as well as post-fitting
visualization, summarization, inference, and prediction are also provided.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/000-0002-0650-1119>)
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.11-0 dated 2018-09-13 and 3.11-1 dated 2019-02-26
DESCRIPTION | 20 ++++-- MD5 | 28 ++++----- NEWS.md | 8 ++ R/cv.ncvreg.R | 14 +++- R/cv.ncvsurv.R | 15 +++-- R/plot.cv.ncvreg.R | 6 -- README.md | 6 +- build/vignette.rds |binary inst/doc/getting-started.html | 112 ++++++++++++++++++++++---------------- inst/tests/cv.ncvreg.R | 5 + inst/tests/ncvsurv.R | 4 - man/ncvsurv.Rd | 2 vignettes/web/inference-local.rmd | 79 ++++++++++++++++++++++++++ vignettes/web/models.rmd | 7 +- vignettes/web/penalties.rmd | 2 15 files changed, 214 insertions(+), 94 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca> and portions of code contributed by Dan Linden.
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.1-1 dated 2017-06-19 and 2.2-0 dated 2019-02-26
DESCRIPTION | 16 MD5 | 92 +-- NAMESPACE | 90 +++ R/AICc.R | 50 +- R/Nmix.gof.test.R | 46 - R/aictab.R | 257 ++++++++-- R/anovaOD.R |only R/bictab.R | 227 +++++++-- R/c_hat.R | 50 +- R/checkConv.R | 14 R/checkParms.R | 43 + R/countHist.R | 833 +++++++++++++++++---------------- R/covDiag.R | 4 R/detHist.R | 1144 ++++++++++++++++++++++++++++------------------ R/extractX.R | 234 +++++++++ R/importance.R | 326 +++++++++++++ R/mb.gof.test.R | 390 +++++++++++++-- R/modavg.R | 783 +++++++++++++++++++++++++++++++ R/modavg.utility.R | 14 R/modavgEffect.R | 197 ++++++- R/modavgPred.R | 746 ++++++++++++++++++----------- R/modavgShrink.R | 418 ++++++++++++++++ R/multComp.R | 566 ++++++++++++++++++++++ R/summaryOD.R |only R/useBIC.R | 29 + R/xtable.R | 202 ++++++-- inst/NEWS | 30 + man/AICc.Rd | 25 - man/AICcmodavg-package.Rd | 31 - man/Nmix.gof.test.Rd | 6 man/aictab.Rd | 40 + man/anovaOD.Rd |only man/bictab.Rd | 35 - man/c_hat.Rd | 44 - man/checkConv.Rd | 15 man/checkParms.Rd | 3 man/detHist.Rd | 77 ++- man/extractX.Rd | 72 +- man/importance.Rd | 135 ++++- man/mb.gof.test.Rd | 43 + man/modavg.Rd | 62 +- man/modavg.utility.Rd | 32 + man/modavgEffect.Rd | 5 man/modavgPred.Rd | 9 man/modavgShrink.Rd | 61 +- man/multComp.Rd | 91 ++- man/summaryOD.Rd |only man/useBIC.Rd | 17 man/xtable.Rd | 16 49 files changed, 5971 insertions(+), 1649 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 1.0.4 dated 2018-10-26 and 1.0.6 dated 2019-02-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/vis.R | 3 ++- build/vignette.rds |binary inst/doc/set_html.html | 4 ++-- man/plot.Rd | 1 + src/dmvhyper.c | 8 +++++++- src/dmvhyperLog.c | 8 +++++++- src/pmvhyper.c | 10 ++++++++-- 9 files changed, 39 insertions(+), 19 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Tools to Work with the 'Splash' 'JavaScript' Rendering and
Scraping Service
Description: 'Splash' <https://github.com/scrapinghub/splash> is a 'JavaScript' rendering service.
It is a lightweight web browser with an 'HTTP' API, implemented in 'Python' using 'Twisted'
and 'QT' and provides some of the core functionality of the 'RSelenium' or 'seleniumPipes'
R packages in a lightweight footprint. Some of 'Splash' features include the ability to process
multiple web pages in parallel; retrieving 'HTML' results and/or take screen shots; disabling
images or use 'Adblock Plus' rules to make rendering faster; executing custom 'JavaScript' in
page context; getting detailed rendering info in 'HAR' format.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: Bob Rudis <bob@rud.is>
Diff between splashr versions 0.4.1 dated 2018-01-15 and 0.6.0 dated 2019-02-26
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Title: Graphic Presentation of Complex Genomic and Network Data
Analysis
Description: Implements various simple function utilities and flexible pipelines to generate circular images for visualizing complex genomic and network data analysis features.
Author: Minghui Wang, Bin Zhang
Maintainer: Minghui Wang <m.h.wang@live.com>
Diff between NetWeaver versions 0.0.2 dated 2017-01-10 and 0.0.6 dated 2019-02-26
DESCRIPTION | 10 +- MD5 | 91 +++++++++++++---------- NAMESPACE | 12 ++- R/ensemble.rank.R |only R/misc.R |only R/rc.get.coordinates.R | 160 +++++++++++++++++++++++------------------- R/rc.get.params.R | 107 ++++++++++++++-------------- R/rc.initialize.R | 47 ++++++------ R/rc.plot.area.R | 6 + R/rc.plot.barchart.R |only R/rc.plot.heatmap.R | 60 +++++++-------- R/rc.plot.histogram.R | 82 ++++++++++----------- R/rc.plot.ideogram.R | 76 +++++++++++-------- R/rc.plot.line.R | 6 + R/rc.plot.link.R | 9 +- R/rc.plot.mHistogram.R | 94 ++++++++++++------------ R/rc.plot.point.R |only R/rc.plot.sunburst.R |only R/rc.plot.text.R | 5 - R/rc.plot.track.R | 2 R/rc.plot.track.bg.R | 2 R/rc.plot.track.id.R | 6 - R/rc.track.pos.R | 11 ++ build/vignette.rds |binary data/ucsc.hg19.cytoband.RData |only data/ucsc.hg38.cytoband.RData |only inst/doc/netweaver.R | 62 ++++++++-------- inst/doc/netweaver.Rmd | 10 +- inst/doc/netweaver.html | 43 ++++++----- man/cytoband.Rd |only man/ensemblerank.Rd |only man/getrankp.Rd |only man/is.overlap.Rd |only man/rc.get.coordinates.Rd | 13 +-- man/rc.get.params.Rd | 4 - man/rc.initialize.Rd | 51 +++++++++---- man/rc.plot.area.Rd | 2 man/rc.plot.barpchart.Rd |only man/rc.plot.grColLegend.Rd | 4 - man/rc.plot.heatmap.Rd | 5 - man/rc.plot.histogram.Rd | 22 +++-- man/rc.plot.ideogram.Rd | 5 - man/rc.plot.line.Rd | 10 +- man/rc.plot.link.Rd | 7 + man/rc.plot.mHistogram.Rd | 14 ++- man/rc.plot.point.Rd |only man/rc.plot.ribbon.Rd | 2 man/rc.plot.text.Rd | 4 - man/rc.plot.track.Rd | 2 man/rc.plot.track.id.Rd | 2 man/rc.reset.params.Rd | 3 man/rc.track.pos.Rd | 2 vignettes/netweaver.Rmd | 10 +- 53 files changed, 590 insertions(+), 473 deletions(-)
Title: Simply Caching R Objects
Description: Provides intuitive functions for caching R objects, encouraging
reproducible, restartable, and distributed R analysis. The user selects a
location to store caches, and then provides nothing more than a cache name
and instructions (R code) for how to produce the R object. Also
provides some advanced options like environment assignments, recreating or
reloading caches, and cluster compute bindings (using the 'batchtools'
package) making it flexible enough for use in large-scale data analysis
projects.
Author: VP Nagraj [aut],
Nathan Sheffield [aut, cre]
Maintainer: Nathan Sheffield <nathan@code.databio.org>
Diff between simpleCache versions 0.3.1 dated 2017-08-22 and 0.4.1 dated 2019-02-26
simpleCache-0.3.1/simpleCache/NEWS |only simpleCache-0.3.1/simpleCache/man/viewCacheDirs.Rd |only simpleCache-0.4.1/simpleCache/DESCRIPTION | 19 - simpleCache-0.4.1/simpleCache/LICENSE |only simpleCache-0.4.1/simpleCache/MD5 | 68 ++- simpleCache-0.4.1/simpleCache/NAMESPACE | 3 simpleCache-0.4.1/simpleCache/NEWS.md |only simpleCache-0.4.1/simpleCache/R/cacheDirectories.R | 41 +- simpleCache-0.4.1/simpleCache/R/deleteCache.R | 2 simpleCache-0.4.1/simpleCache/R/listCaches.R | 3 simpleCache-0.4.1/simpleCache/R/loadCaches.R | 6 simpleCache-0.4.1/simpleCache/R/sharedCaches.R | 6 simpleCache-0.4.1/simpleCache/R/simpleCache.R | 117 +++--- simpleCache-0.4.1/simpleCache/R/storeCache.R | 14 simpleCache-0.4.1/simpleCache/R/utility.R | 40 +- simpleCache-0.4.1/simpleCache/README.md | 44 +- simpleCache-0.4.1/simpleCache/build/vignette.rds |binary simpleCache-0.4.1/simpleCache/inst/doc/clusterCaches.html | 28 + simpleCache-0.4.1/simpleCache/inst/doc/sharingCaches.html | 30 + simpleCache-0.4.1/simpleCache/inst/doc/simpleCacheIntroduction.Rmd | 2 simpleCache-0.4.1/simpleCache/inst/doc/simpleCacheIntroduction.html | 98 +++-- simpleCache-0.4.1/simpleCache/man/deleteCaches.Rd | 2 simpleCache-0.4.1/simpleCache/man/dot-tooOld.Rd |only simpleCache-0.4.1/simpleCache/man/getCacheDir.Rd |only simpleCache-0.4.1/simpleCache/man/loadCaches.Rd | 4 simpleCache-0.4.1/simpleCache/man/resetCacheSearchEnvironment.Rd | 4 simpleCache-0.4.1/simpleCache/man/setCacheBuildDir.Rd | 2 simpleCache-0.4.1/simpleCache/man/setCacheDir.Rd | 6 simpleCache-0.4.1/simpleCache/man/setSharedCacheDir.Rd | 4 simpleCache-0.4.1/simpleCache/man/simpleCache-package.Rd |only simpleCache-0.4.1/simpleCache/man/simpleCache.Rd | 89 ++--- simpleCache-0.4.1/simpleCache/man/simpleCacheGlobal.Rd | 2 simpleCache-0.4.1/simpleCache/man/simpleCacheOptions.Rd |only simpleCache-0.4.1/simpleCache/man/simpleCacheShared.Rd | 2 simpleCache-0.4.1/simpleCache/man/simpleCacheSharedGlobal.Rd | 2 simpleCache-0.4.1/simpleCache/man/storeCache.Rd | 16 simpleCache-0.4.1/simpleCache/tests/testthat/helper-lifespan.R |only simpleCache-0.4.1/simpleCache/tests/testthat/test_all.R | 177 +++++++++- simpleCache-0.4.1/simpleCache/tests/testthat/test_cache_lifespan.R |only simpleCache-0.4.1/simpleCache/vignettes/simpleCacheIntroduction.Rmd | 2 40 files changed, 547 insertions(+), 286 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>),
Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>),
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 1.0.0 dated 2019-02-18 and 1.0.1 dated 2019-02-26
DESCRIPTION | 22 ++++++++++++---------- MD5 | 6 +++--- R/opal.assign.r | 5 +++-- man/opal.assign.data.Rd | 4 ++-- 4 files changed, 20 insertions(+), 17 deletions(-)
Title: Low-Rank Interactions in Count Data with Covariates
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 2.0.0 dated 2019-02-19 and 2.1.1 dated 2019-02-26
lori-2.0.0/lori/R/lori_MI.R |only lori-2.0.0/lori/R/lori_tools.R |only lori-2.0.0/lori/build |only lori-2.0.0/lori/inst/doc/example.Rmd |only lori-2.0.0/lori/inst/doc/example.html |only lori-2.0.0/lori/man/altmin.Rd |only lori-2.0.0/lori/man/boot.lori.Rd |only lori-2.0.0/lori/man/covmatC.Rd |only lori-2.0.0/lori/man/covmatR.Rd |only lori-2.0.0/lori/man/null_model.Rd |only lori-2.0.0/lori/vignettes |only lori-2.1.1/lori/DESCRIPTION | 12 - lori-2.1.1/lori/MD5 | 40 ++-- lori-2.1.1/lori/NAMESPACE | 5 lori-2.1.1/lori/R/altmin.R |only lori-2.1.1/lori/R/covmat.R |only lori-2.1.1/lori/R/cv.lori.R |only lori-2.1.1/lori/R/grad.R |only lori-2.1.1/lori/R/lori.R | 312 +--------------------------------- lori-2.1.1/lori/R/mi.lori.R |only lori-2.1.1/lori/R/plot.interaction.R |only lori-2.1.1/lori/R/pool.lori.R |only lori-2.1.1/lori/R/qut.R |only lori-2.1.1/lori/inst/doc/example.R | 9 lori-2.1.1/lori/man/covmat.Rd | 16 + lori-2.1.1/lori/man/cv.lori.Rd | 15 + lori-2.1.1/lori/man/lori.Rd | 2 lori-2.1.1/lori/man/mi.lori.Rd | 6 lori-2.1.1/lori/man/plot.Rd |only lori-2.1.1/lori/man/pool.lori.Rd |only lori-2.1.1/lori/man/qut.Rd | 8 31 files changed, 77 insertions(+), 348 deletions(-)
Title: The H-Measure and Other Scalar Classification Performance
Metrics
Description: Classification performance metrics that are derived from the ROC
curve of a classifier. The package includes the H-measure performance metric
as described in <http://link.springer.com/article/10.1007/s10994-009-5119-5>,
which computes the minimum total misclassification cost, integrating over any
uncertainty about the relative misclassification costs, as per a user-defined
prior. It also offers a one-stop-shop for other scalar metrics of performance,
including sensitivity, specificity and many others, and also offers plotting
tools for ROC curves and related statistics.
Author: Christoforos Anagnostopoulos
<christoforos.anagnostopoulos06@imperial.ac.uk> and David J.
Hand <d.j.hand@imperial.ac.uk>
Maintainer: Christoforos Anagnostopoulos
<christoforos.anagnostopoulos06@imperial.ac.uk>
Diff between hmeasure versions 1.0-1 dated 2019-01-02 and 1.0-2 dated 2019-02-26
DESCRIPTION | 8 +++---- LICENSE | 2 - MD5 | 14 ++++++------- NEWS.md | 14 +++---------- inst/doc/hmeasure.R | 52 ++++++++++++++++++++++++------------------------- inst/doc/hmeasure.Rnw | 5 ---- inst/doc/hmeasure.pdf |binary vignettes/hmeasure.Rnw | 5 ---- 8 files changed, 44 insertions(+), 56 deletions(-)
Title: Casting Values into Shape
Description: Helper functions with a consistent interface to coerce and verify
the types and shapes of values for input checking.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>
Diff between forge versions 0.1.0 dated 2018-08-31 and 0.2.0 dated 2019-02-26
forge-0.1.0/forge/R/molds.R |only forge-0.1.0/forge/R/molds_utils.R |only forge-0.1.0/forge/tests/testthat/test-molds.R |only forge-0.2.0/forge/DESCRIPTION | 8 +- forge-0.2.0/forge/MD5 | 21 +++-- forge-0.2.0/forge/NAMESPACE | 9 ++ forge-0.2.0/forge/NEWS.md |only forge-0.2.0/forge/R/cast.R |only forge-0.2.0/forge/R/cast_utils.R |only forge-0.2.0/forge/R/certify.R |only forge-0.2.0/forge/R/imports.R |only forge-0.2.0/forge/R/vctrs.R |only forge-0.2.0/forge/README.md | 60 ++++++++++++--- forge-0.2.0/forge/man/cast.Rd | 93 ++++++++++++++++-------- forge-0.2.0/forge/man/certify.Rd |only forge-0.2.0/forge/man/pipe.Rd |only forge-0.2.0/forge/tests/testthat/test-cast.R |only forge-0.2.0/forge/tests/testthat/test-certify.R |only 18 files changed, 137 insertions(+), 54 deletions(-)
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.0-46 dated 2018-02-21 and 1.0-67 dated 2019-02-26
DESCRIPTION | 13 - MD5 | 48 ++-- NAMESPACE | 15 - R/AAAClasses.R | 36 ++- R/arithm.R |only R/bioclim.R | 18 - R/dismo.R |only R/ensemble.R | 496 +++++++++++++++++++++++++++++++++++++++++- R/installAll.R | 106 ++++++-- R/modelInfo.R |only R/niche.R |only R/plot.R | 281 +++++++++++++++++++++++ R/responseCurve.R |only R/sdm.R | 195 +++------------- R/sdmData.R | 9 R/sdmMethods.R | 27 -- R/subset.R | 39 +-- README.md |only build/vignette.rds |binary inst/external/model.sdm |binary inst/methods/sdm/domain.R |only inst/methods/sdm/glmnet.R | 8 inst/methods/sdm/mahalDismo.R |only inst/methods/sdm/mlp.R |only inst/methods/sdm/rbf.R |only inst/quick_sdm.Rmd |only man/arithm.Rd |only man/ensemble.Rd | 1 man/getModelInfo.Rd | 22 + man/niche.Rd |only man/response.Rd |only man/sdmData.Rd | 2 32 files changed, 1026 insertions(+), 290 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-39 dated 2018-09-10 and 0.4-40 dated 2019-02-26
CHANGELOG | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/attributes.R | 5 +++-- R/control.R | 2 +- R/evaluate.R | 2 +- R/interfaces.R | 2 +- R/readers.R | 14 ++++++++++---- R/utils.R | 2 +- build/vignette.rds |binary inst/doc/RWeka.pdf |binary tests/data_exchange.R | 6 ++++++ tests/data_exchange.Rout.save | 16 ++++++++++++---- 13 files changed, 54 insertions(+), 29 deletions(-)
Title: Memory-Map Character Files
Description: Uses memory-mapping to enable the random access of elements of
a text file of characters separated by characters as if it were a simple
R(cpp) matrix.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between mmapcharr versions 0.1.0 dated 2017-12-12 and 0.3.0 dated 2019-02-26
mmapcharr-0.1.0/mmapcharr/src/Makevars.win |only mmapcharr-0.3.0/mmapcharr/DESCRIPTION | 16 ++-- mmapcharr-0.3.0/mmapcharr/MD5 | 15 +-- mmapcharr-0.3.0/mmapcharr/inst/include/mmapcharr/charsep-acc.h | 38 ++++------ mmapcharr-0.3.0/mmapcharr/man/mmapchar-class.Rd | 2 mmapcharr-0.3.0/mmapcharr/src/Makevars | 1 mmapcharr-0.3.0/mmapcharr/src/RcppExports.cpp | 4 - mmapcharr-0.3.0/mmapcharr/src/charsep-acc-xptr.cpp | 21 ----- mmapcharr-0.3.0/mmapcharr/src/extract.cpp | 4 - 9 files changed, 41 insertions(+), 60 deletions(-)
Title: 32-Bit Floats
Description: R comes with a suite of utilities for linear algebra with "numeric"
(double precision) vectors/matrices. However, sometimes single precision (or
less!) is more than enough for a particular task. This package extends R's
linear algebra facilities to include 32-bit float (single precision) data.
Float vectors/matrices have half the precision of their "numeric"-type
counterparts but are generally faster to numerically operate on, for a
performance vs accuracy trade-off. The internal representation is an S4
class, which allows us to keep the syntax identical to that of base R's.
Interaction between floats and base types for binary operators is generally
possible; in these cases, type promotion always defaults to the higher
precision. The package ships with copies of the single precision 'BLAS' and
'LAPACK', which are automatically built in the event they are not available
on the system.
Author: Drew Schmidt [aut, cre, cph],
Wei-Chen Chen [aut],
Dmitriy Selivanov [ctb] (improvements in external package linking),
ORNL [cph]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between float versions 0.2-1 dated 2018-12-07 and 0.2-2 dated 2019-02-26
ChangeLog | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 18 +++++++++++------- NAMESPACE | 2 ++ R/02-flags.r | 26 +++++++++++++------------- R/sign.r |only README.md | 2 +- man/sign.Rd |only src/Makevars.in | 1 + src/float_native.c | 2 ++ src/sign.c |only tests/sign.r |only 12 files changed, 38 insertions(+), 24 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. The package also provides functions for sample size determination and estimation of diagnostic accuracy measures. It also includes graphical tools.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.6 dated 2017-11-24 and 2.7 dated 2019-02-26
DESCRIPTION | 12 +++--- MD5 | 34 +++++++++---------- R/ThresholdROC-2states.R | 76 +++++++++++++++++++++++++++++++++++++------- R/ThresholdROC-3states.R | 71 ++++++++++++++++++++++++++++++++++------- data/AD.txt.gz |binary man/AD.Rd | 3 - man/ThresholdROC-package.Rd | 4 +- man/chemo.Rd | 2 - man/diagnostic.Rd | 34 +++++++++---------- man/lines-thres2.Rd | 4 +- man/lines-thres3.Rd | 4 +- man/plot-thres2.Rd | 22 ++++++++---- man/plot-thres3.Rd | 21 ++++++++---- man/secondDer2.Rd | 2 - man/thres2.Rd | 8 ++-- man/thres3.Rd | 6 +-- man/thresTH2.Rd | 2 - man/thresTH3.Rd | 2 - 18 files changed, 212 insertions(+), 95 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-44 dated 2018-12-21 and 0.1-45 dated 2019-02-26
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/abind.R | 2 +- R/matrix.R | 8 ++++---- R/reduce.R | 4 ++-- R/rollup.R | 12 ++++++------ R/subassign.R | 2 +- tests/stm.R | 4 ++++ tests/stm.Rout.save | 12 ++++++++---- tests/stm_rollup.Rout.save | 10 +++++----- tests/stm_zeros.R | 5 ++++- tests/stm_zeros.Rout.save | 14 ++++++++++---- 12 files changed, 59 insertions(+), 42 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 0.2.7 dated 2019-01-22 and 1.0.0 dated 2019-02-26
DESCRIPTION | 6 MD5 | 61 ++-- NAMESPACE | 3 NEWS.md | 7 R/XenaHub-class.R | 56 ++-- R/data.R | 6 R/download.R | 127 +++++++-- R/simplify.R | 100 +++---- README.md | 602 +++++++------------------------------------- inst/doc/USCSXenaTools.R | 47 ++- inst/doc/USCSXenaTools.Rmd | 111 +++++--- inst/doc/USCSXenaTools.html | 568 +++++++++++++++++++++++------------------ man/XenaBrowse.Rd |only man/XenaData.Rd | 4 man/XenaDataUpdate.Rd | 2 man/XenaDownload.Rd | 8 man/XenaFilter.Rd | 15 - man/XenaGenerate.Rd | 12 man/XenaHub-class.Rd | 16 - man/XenaHub.Rd | 12 man/XenaPrepare.Rd | 27 + man/XenaQuery.Rd | 4 man/availTCGA.Rd | 2 man/cohorts.Rd | 2 man/datasets.Rd | 2 man/downloadTCGA.Rd | 14 - man/getTCGAdata.Rd | 20 - man/hosts.Rd | 2 man/samples.Rd | 2 man/showTCGA.Rd | 4 man/xena_default_hosts.Rd | 4 vignettes/USCSXenaTools.Rmd | 111 +++++--- 32 files changed, 898 insertions(+), 1059 deletions(-)
Title: Download and Process Data from the Paleobiology Database
Description: Includes 19 functions to wrap each endpoint of
the PaleobioDB API, plus 8 functions to visualize and process the fossil
data. The API documentation for the Paleobiology Database can be found in
<http://paleobiodb.org/data1.1/>.
Author: Sara Varela [aut, cre],
Javier González Hernández [aut],
Luciano Fabris Sgarbi [aut]
Maintainer: Sara Varela <svarela@paleobiogeography.org>
Diff between paleobioDB versions 0.5.0 dated 2016-09-02 and 0.6.0 dated 2019-02-26
paleobioDB-0.5.0/paleobioDB/tests/testthat/test-apitools.R |only paleobioDB-0.5.0/paleobioDB/tests/testthat/test-parse_api_data.R |only paleobioDB-0.5.0/paleobioDB/tests/testthat/test-pbdb_api_query.R |only paleobioDB-0.6.0/paleobioDB/DESCRIPTION | 10 paleobioDB-0.6.0/paleobioDB/MD5 | 29 +- paleobioDB-0.6.0/paleobioDB/R/network.R | 4 paleobioDB-0.6.0/paleobioDB/R/pbdb_querys.R | 3 paleobioDB-0.6.0/paleobioDB/R/pbdb_temporal_functions.R | 137 ++++------ paleobioDB-0.6.0/paleobioDB/README.md | 28 +- paleobioDB-0.6.0/paleobioDB/build |only paleobioDB-0.6.0/paleobioDB/man/figure |only paleobioDB-0.6.0/paleobioDB/tests/testthat/internal |only paleobioDB-0.6.0/paleobioDB/tests/testthat/test-temporal_functions.R | 6 13 files changed, 104 insertions(+), 113 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-31 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-27 0.5.4.1
2018-10-11 0.5.4.0
2018-01-04 0.5.3.1
2017-06-26 0.5.3