Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette <dylan.beaudette@ca.usda.gov>
Diff between soilDB versions 1.5-4 dated 2015-04-23 and 1.6.6 dated 2015-12-04
soilDB-1.5-4/soilDB/R/MUKEYS_by_ll_bbox.R |only soilDB-1.5-4/soilDB/man/MUKEYS_by_ll_bbox.Rd |only soilDB-1.6.6/soilDB/DESCRIPTION | 18 - soilDB-1.6.6/soilDB/MD5 | 60 +-- soilDB-1.6.6/soilDB/NAMESPACE | 23 - soilDB-1.6.6/soilDB/NEWS | 29 + soilDB-1.6.6/soilDB/R/SDA_query.R | 226 +++++++++---- soilDB-1.6.6/soilDB/R/SSURGO_spatial_query.R | 2 soilDB-1.6.6/soilDB/R/fetchHenry.R | 276 +++++++++++++++- soilDB-1.6.6/soilDB/R/fetchKSSL.R | 45 ++ soilDB-1.6.6/soilDB/R/fetchNASIS.R | 8 soilDB-1.6.6/soilDB/R/fetchNASISLabData.R | 2 soilDB-1.6.6/soilDB/R/fetchOSD.R | 2 soilDB-1.6.6/soilDB/R/fetchRaCA.R | 5 soilDB-1.6.6/soilDB/R/fetchSCAN.R | 98 +++++ soilDB-1.6.6/soilDB/R/get_extended_data_from_NASIS_db.R | 17 soilDB-1.6.6/soilDB/R/get_site_data_from_NASIS_db.R | 5 soilDB-1.6.6/soilDB/R/get_vegplot_data_from_NASIS_db.R |only soilDB-1.6.6/soilDB/R/get_vegplot_from_NASIS_db.R |only soilDB-1.6.6/soilDB/R/mapunit_geom_by_ll_bbox.R | 2 soilDB-1.6.6/soilDB/R/utils.R | 23 + soilDB-1.6.6/soilDB/data/andic.subset.rda |binary soilDB-1.6.6/soilDB/data/cisne.rda |binary soilDB-1.6.6/soilDB/data/gSSURGO.chunk.rda |binary soilDB-1.6.6/soilDB/data/gopheridge.rda |binary soilDB-1.6.6/soilDB/data/loafercreek.rda |binary soilDB-1.6.6/soilDB/man/SDA_query.Rd | 66 +-- soilDB-1.6.6/soilDB/man/SDA_query_features.Rd |only soilDB-1.6.6/soilDB/man/SSURGO_spatial_query.Rd | 14 soilDB-1.6.6/soilDB/man/fetchHenry.Rd |only soilDB-1.6.6/soilDB/man/fetchKSSL.Rd | 13 soilDB-1.6.6/soilDB/man/fetchNASIS.Rd | 1 soilDB-1.6.6/soilDB/man/fetchSCAN.Rd | 3 soilDB-1.6.6/soilDB/man/mapunit_geom_by_ll_bbox.Rd | 2 34 files changed, 740 insertions(+), 200 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.2 dated 2015-09-01 and 2.3 dated 2015-12-04
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++----------- R/BayesID.R | 91 +++++++++++++++++++++--------------------- R/BayesSurv.R | 24 +++-------- R/FreqID.R | 45 ++++++++++++++++---- R/internalFunc.R | 62 ++++++++++++++++++++++++++++ R/methods.R | 27 +++++++++--- man/BayesID.Rd | 2 man/FreqID.Rd | 9 ++-- man/SemiCompRisks-package.Rd | 4 - man/simID.Rd | 4 - src/BpeDpCorScr.c | 2 src/BpeDpCorScrSM.c | 4 - src/BpeDpCorScrSM_Updates.c | 3 - src/BpeDpCorScr_Updates.c | 2 src/BpeDpCorSurv.c | 2 src/BpeDpCorSurv_Updates.c | 2 src/BweibDpCorScr.c | 2 src/BweibDpCorScrSM.c | 2 src/BweibDpCorScrSM_Updates.c | 6 +- src/BweibDpCorScr_Updates.c | 4 + src/BweibDpCorSurv.c | 2 src/BweibDpCorSurv_Updates.c | 2 src/Utilities.c | 8 +-- 24 files changed, 234 insertions(+), 129 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.20-23 dated 2015-10-10 and 2.21 dated 2015-12-04
DESCRIPTION | 10 ++++---- MD5 | 54 +++++++++++++++++++++++---------------------- NAMESPACE | 23 +++++++++++++++---- R/MCMC-support.R | 4 +-- R/countreg-support.R |only R/helpers.R | 34 ++++++++++++++++++++-------- R/lsmeans.R | 26 +++++++++++---------- R/lsmip.R | 8 +++--- R/multinom-support.R | 2 - R/nonlin-support.R | 2 - R/ordinal-support.R | 6 ++--- R/pmmeans.R |only R/rbind.R | 11 +-------- R/ref.grid.R | 38 ++++++++++++++++++++++--------- R/summary.R | 8 ++++++ inst/NEWS | 15 ++++++++++++ inst/doc/extending.R | 18 +++++---------- inst/doc/extending.pdf |binary inst/doc/extending.rnw | 33 +++++++++++++++++++++++---- inst/doc/using-lsmeans.pdf |binary man/extending.Rd | 23 ++++++++----------- man/glht.Rd | 4 ++- man/lsmeans.Rd | 26 +++++++++++++++------ man/lsmip.Rd | 9 +++++-- man/models.Rd | 21 ++++++++++++++++- man/summary.Rd | 2 - man/update.Rd | 7 +++++ tests/tests1.Rout.save | 29 ++++++++++-------------- vignettes/extending.rnw | 33 +++++++++++++++++++++++---- 29 files changed, 293 insertions(+), 153 deletions(-)
Title: Hierarchical Inference Testing
Description: Hierarchical inference testing (HIT) for (generalized) linear
models with correlated covariates applicable to high-dimensional settings.
Author: Jonas Klasen [aut, cre]
Maintainer: Jonas Klasen <qtcat@gmx.de>
Diff between hit versions 0.1-0 dated 2015-10-21 and 0.2-0 dated 2015-12-04
DESCRIPTION | 13 +- MD5 | 43 +++---- NAMESPACE | 14 ++ NEWS.md |only R/anova.R | 116 ++++++++++++++++++-- R/hit.R | 266 ++++++++++++++++++++++++++++++---------------- R/hitPackage.R | 4 README.md | 8 - man/as.hierarchy.Rd | 13 +- man/dend2hier.Rd | 6 - man/fast.anova.Rd | 25 ++-- man/fast.glmanova.Rd |only man/fast.lmanova.Rd |only man/heightDendrogram.Rd | 2 man/heightHierarchy.Rd | 2 man/hit-package.Rd | 6 - man/hit.Rd | 83 ++++++++------ man/names.hierarchy.Rd | 2 man/reorder.hierarchy.Rd | 4 man/samp1.lasso.Rd | 31 +++-- man/samp2.sigHierarchy.Rd | 34 +++-- man/samp2.sigNode.Rd | 11 + man/summary.hit.Rd | 2 tests/testthat/test_hit.R | 6 - 24 files changed, 474 insertions(+), 217 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette <debeaudette@ucdavis.edu>, Pierre Roudier <roudierp@landcareresearch.co.nz>
Maintainer: Dylan Beaudette <debeaudette@ucdavis.edu>
Diff between aqp versions 1.8-6 dated 2015-04-23 and 1.9.2 dated 2015-12-04
DESCRIPTION | 20 +- MD5 | 49 ++--- NAMESPACE | 20 ++ NEWS | 15 + R/aggregateColor.R |only R/get.ml.hz.R | 4 R/getSoilDepthClass.R | 4 R/guessGenHzLevels.R |only R/profile_plot.R | 79 +++++++- data/amarillo.rda |binary data/ca630.rda |binary data/munsell.rda |binary data/rruff.sample.rda |binary data/sp1.rda |binary data/sp2.rda |binary data/sp3.rda |binary data/sp4.rda |binary data/sp5.rda |binary man/SPC-plotting.Rd | 4 man/aggregateColor.Rd |only man/groupedProfilePlot.Rd |only man/guessGenHzLevels.Rd |only man/munsell2rgb.Rd | 3 man/plotMultipleSPC.Rd | 6 man/profileApply-methods.Rd | 99 +++++----- man/profile_compare-methods.Rd | 372 ++++++++++++++++++++--------------------- man/sp2.Rd | 4 man/sp3.Rd | 25 +- 28 files changed, 413 insertions(+), 291 deletions(-)
Title: Spatial Position Models
Description: Computes spatial position models: Stewart potentials, Reilly
catchment areas, Huff catchment areas.
Author: Timothée Giraud [cre, aut],
Hadrien Commenges [aut],
Joël Boulier [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between SpatialPosition versions 0.9 dated 2015-05-06 and 1.0 dated 2015-12-04
DESCRIPTION | 28 +++++---- MD5 | 64 ++++++++++++---------- NAMESPACE | 4 + NEWS |only R/contourStewart.R |only R/gridandmat.R | 7 +- R/huff.R | 2 R/package.R | 10 ++- R/reilly.R | 5 + R/stewart.R | 122 +++++++----------------------------------- README.md | 40 ++++++++++++- build/vignette.rds |binary inst/doc/SpatialPosition.R | 6 +- inst/doc/SpatialPosition.Rmd | 2 inst/doc/SpatialPosition.html | 10 +-- inst/doc/StewartExample.R |only inst/doc/StewartExample.Rmd |only inst/doc/StewartExample.html |only man/CreateDistMatrix.Rd | 16 ++--- man/CreateGrid.Rd | 8 +- man/SpatialPosition.Rd | 18 ++++-- man/contourStewart.Rd | 90 ++++++++++++++++++++++-------- man/huff.Rd | 42 +++++++------- man/plotHuff.Rd | 2 man/plotReilly.Rd | 2 man/plotStewart.Rd | 4 - man/rasterHuff.Rd | 4 - man/rasterReilly.Rd | 6 +- man/rasterStewart.Rd | 4 - man/reilly.Rd | 42 +++++++------- man/spatMask.Rd | 2 man/spatPts.Rd | 4 - man/spatUnits.Rd | 2 man/stewart.Rd | 40 ++++++------- vignettes/SpatialPosition.Rmd | 2 vignettes/StewartExample.Rmd |only 36 files changed, 304 insertions(+), 284 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 8.0-0.0 dated 2014-01-20 and 12.0-0.0 dated 2015-12-04
SGPdata-12.0-0.0/SGPdata/DESCRIPTION | 20 ++++----- SGPdata-12.0-0.0/SGPdata/MD5 | 26 ++++++------ SGPdata-12.0-0.0/SGPdata/NAMESPACE | 1 SGPdata-12.0-0.0/SGPdata/R/zzz.R |only SGPdata-12.0-0.0/SGPdata/data/datalist | 1 SGPdata-12.0-0.0/SGPdata/data/sgpData.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgpData_INSTRUCTOR_NUMBER.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgpData_LONG.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgptData_LONG.rda |only SGPdata-12.0-0.0/SGPdata/inst/CITATION | 12 ++--- SGPdata-12.0-0.0/SGPdata/inst/NEWS | 18 +++++++- SGPdata-12.0-0.0/SGPdata/man/SGPdata-package.Rd | 11 ++--- SGPdata-12.0-0.0/SGPdata/man/sgpData.Rd | 20 ++++----- SGPdata-12.0-0.0/SGPdata/man/sgpData_LONG.Rd | 6 +- SGPdata-12.0-0.0/SGPdata/man/sgptData_LONG.Rd |only SGPdata-8.0-0.0/SGPdata/R/dummy.R |only 16 files changed, 68 insertions(+), 47 deletions(-)
Title: Thurstonian Models for Sensory Discrimination
Description: Provides methods for sensory discrimination methods;
duotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-different,
2-AC and degree-of-difference.
This enables the calculation of d-primes, standard errors of
d-primes, sample size and power computations, and
comparisons of different d-primes. Methods for profile likelihood
confidence intervals and plotting are included.
Author: Rune Haubo Bojesen Christensen [aut],
Per Bruun Brockhoff [aut, cre]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between sensR versions 1.4-5 dated 2015-01-21 and 1.4-6 dated 2015-12-04
DESCRIPTION | 23 +++++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 10 ++++++++++ NEWS | 15 ++++++++++++++- R/discrim.R | 3 ++- R/discrimR.R | 2 +- build/vignette.rds |binary inst/doc/methodology.pdf |binary inst/doc/twoACexamples.pdf |binary 9 files changed, 48 insertions(+), 21 deletions(-)
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, Rmpfr interfaces to
the LGPL'ed MPFR (Multiple Precision Floating-Point Reliable) Library
which itself is based on the GMP (GNU Multiple Precision) Library.
Author: Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.5-7 dated 2014-11-27 and 0.6-0 dated 2015-12-04
ChangeLog | 32 ++++ DESCRIPTION | 17 +- MD5 | 98 +++++++------- NAMESPACE | 110 ++++++++------- R/Arith.R | 4 R/Consts.R | 5 R/Math.R | 28 ++-- R/Summary.R | 38 +++++ R/array.R | 50 ++++++- R/as.R | 117 ++++++++++------ R/formatHex.R |only R/hjk.R | 31 ++-- R/mpfr.R | 103 +++++++++++--- R/special-fun.R | 174 +++++++++++------------- TODO | 38 ++--- build/vignette.rds |binary configure | 237 ++++++++++++++++++++-------------- configure.ac | 6 inst/NEWS.Rd |only inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.R | 99 ++++++++++++-- inst/doc/Rmpfr-pkg.Rnw | 112 ++++++++++++++-- inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.Rnw | 5 inst/doc/log1mexp-note.pdf |binary man/Bessel_mpfr.Rd | 10 + man/chooseMpfr.Rd | 6 man/factorialMpfr.Rd | 5 man/formatHex.Rd |only man/formatMpfr.Rd | 51 ++++++- man/mpfr-class.Rd | 66 ++++++++- man/mpfr.Rd | 49 +++++-- man/mpfrMatrix-class.Rd | 13 + man/pbetaI.Rd | 4 man/roundMpfr.Rd | 6 man/str.mpfr.Rd | 28 +++- man/utils.Rd | 72 +++------- src/Rmpfr_utils.h | 38 ++--- src/Syms.h | 6 src/convert.c | 11 - src/init.c | 50 +++---- src/utils.c | 95 ++++++------- tests/arith-ex.R | 13 + tests/bit-repr.R | 3 tests/bit-repr.Rout.save | 74 +++++----- tests/create.R | 17 +- tests/lowlevel.R | 13 + tests/matrix-ex.R | 12 + tests/special-fun-ex.R | 2 tests/tstHexBin.R |only vignettes/Rmpfr-pkg.Rnw | 112 ++++++++++++++-- vignettes/log1mexp-note.Rnw | 5 52 files changed, 1366 insertions(+), 699 deletions(-)
Title: Search and Extract Data from the OECD
Description: Search and extract data from the OECD.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between OECD versions 0.1 dated 2015-09-21 and 0.2.0 dated 2015-12-04
OECD-0.1/OECD/vignettes/figuresplot-1.pdf |only OECD-0.2.0/OECD/DESCRIPTION | 23 ++-- OECD-0.2.0/OECD/MD5 | 23 ++-- OECD-0.2.0/OECD/NAMESPACE | 4 OECD-0.2.0/OECD/R/main.R | 123 +++++++++++------------ OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.R | 63 ++++++----- OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.Rmd | 109 +++++++++++--------- OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.pdf |binary OECD-0.2.0/OECD/man/browse_metadata.Rd | 4 OECD-0.2.0/OECD/man/get_dataset.Rd | 5 OECD-0.2.0/OECD/man/get_datasets.Rd | 10 + OECD-0.2.0/OECD/man/search_dataset.Rd | 5 OECD-0.2.0/OECD/vignettes/oecd_vignette_main.Rmd | 109 +++++++++++--------- 13 files changed, 262 insertions(+), 216 deletions(-)
Title: Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Description: Returns nonparametric aligned rank tests for the interaction in two-way factorial designs, on R data sets with repeated measures in 'wide' format. Five ANOVAs tables are reported. A PARAMETRIC one on the original data, one for a CHECK upon the interaction alignments, and three aligned rank tests: one on the aligned REGULAR, one on the FRIEDMAN, and one on the KOCH ranks. In these rank tests, only the resulting values for the interaction are relevant.
Author: Jos Feys
Maintainer: Jos Feys <jos.feys@faber.kuleuven.be>
Diff between npIntFactRep versions 1.4 dated 2015-11-11 and 1.5 dated 2015-12-04
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut],
Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.6 dated 2015-11-26 and 2.7 dated 2015-12-04
mlr-2.6/mlr/R/generateBenchmarkSummary.R |only mlr-2.6/mlr/R/generateRankMatrixAsBar.R |only mlr-2.6/mlr/R/plotBenchmarkResult.R |only mlr-2.6/mlr/man/generateBenchmarkSummaryData.Rd |only mlr-2.6/mlr/man/generateRankMatrixAsBarData.Rd |only mlr-2.6/mlr/man/plotBenchmarkResult.Rd |only mlr-2.6/mlr/man/plotBenchmarkSummary.Rd |only mlr-2.6/mlr/man/plotRankMatrixAsBar.Rd |only mlr-2.6/mlr/tests/testthat/test_base_plotBenchmarkResult.R |only mlr-2.6/mlr/tests/testthat/test_base_plotBenchmarkSummary.R |only mlr-2.7/mlr/DESCRIPTION | 6 mlr-2.7/mlr/MD5 | 124 +++++----- mlr-2.7/mlr/NAMESPACE | 8 mlr-2.7/mlr/NEWS | 9 mlr-2.7/mlr/R/BenchmarkResultOrderLevels.R | 37 +- mlr-2.7/mlr/R/benchmark.R | 46 ++- mlr-2.7/mlr/R/checkBMRMeasure.R |only mlr-2.7/mlr/R/convertBMRToRankMatrix.R | 61 ++-- mlr-2.7/mlr/R/generateCritDifferences.R | 81 +++--- mlr-2.7/mlr/R/helpers.R | 4 mlr-2.7/mlr/R/plotBMRBoxplots.R |only mlr-2.7/mlr/R/plotBMRRanksAsBarChart.R |only mlr-2.7/mlr/R/plotBMRSummary.R |only mlr-2.7/mlr/inst/doc/mlr.html | 2 mlr-2.7/mlr/man/BenchmarkResult.Rd | 10 mlr-2.7/mlr/man/benchmark.Rd | 28 +- mlr-2.7/mlr/man/convertBMRToRankMatrix.Rd | 24 - mlr-2.7/mlr/man/friedmanPostHocTestBMR.Rd | 10 mlr-2.7/mlr/man/friedmanTestBMR.Rd | 10 mlr-2.7/mlr/man/generateCalibrationData.Rd | 4 mlr-2.7/mlr/man/generateCritDifferencesData.Rd | 14 - mlr-2.7/mlr/man/generateFilterValuesData.Rd | 4 mlr-2.7/mlr/man/generateLearningCurveData.Rd | 4 mlr-2.7/mlr/man/generatePartialPredictionData.Rd | 4 mlr-2.7/mlr/man/generateROCRCurvesData.Rd | 4 mlr-2.7/mlr/man/generateThreshVsPerfData.Rd | 4 mlr-2.7/mlr/man/getBMRAggrPerformances.Rd | 10 mlr-2.7/mlr/man/getBMRFeatSelResults.Rd | 10 mlr-2.7/mlr/man/getBMRFilteredFeatures.Rd | 10 mlr-2.7/mlr/man/getBMRLearnerIds.Rd | 10 mlr-2.7/mlr/man/getBMRLearners.Rd | 10 mlr-2.7/mlr/man/getBMRMeasureIds.Rd | 10 mlr-2.7/mlr/man/getBMRMeasures.Rd | 10 mlr-2.7/mlr/man/getBMRPerformances.Rd | 10 mlr-2.7/mlr/man/getBMRPredictions.Rd | 10 mlr-2.7/mlr/man/getBMRTaskIds.Rd | 10 mlr-2.7/mlr/man/getBMRTuneResults.Rd | 10 mlr-2.7/mlr/man/getFilterValues.Rd | 4 mlr-2.7/mlr/man/plotBMRBoxplots.Rd |only mlr-2.7/mlr/man/plotBMRRanksAsBarChart.Rd |only mlr-2.7/mlr/man/plotBMRSummary.Rd |only mlr-2.7/mlr/man/plotCalibration.Rd | 6 mlr-2.7/mlr/man/plotCritDifferences.Rd | 16 - mlr-2.7/mlr/man/plotFilterValues.Rd | 6 mlr-2.7/mlr/man/plotFilterValuesGGVIS.Rd | 6 mlr-2.7/mlr/man/plotLearningCurve.Rd | 6 mlr-2.7/mlr/man/plotLearningCurveGGVIS.Rd | 6 mlr-2.7/mlr/man/plotPartialPrediction.Rd | 6 mlr-2.7/mlr/man/plotPartialPredictionGGVIS.Rd | 6 mlr-2.7/mlr/man/plotROCCurves.Rd | 6 mlr-2.7/mlr/man/plotROCRCurves.Rd | 6 mlr-2.7/mlr/man/plotROCRCurvesGGVIS.Rd | 6 mlr-2.7/mlr/man/plotThreshVsPerf.Rd | 6 mlr-2.7/mlr/man/plotThreshVsPerfGGVIS.Rd | 6 mlr-2.7/mlr/tests/testthat/Rplots.pdf |binary mlr-2.7/mlr/tests/testthat/helper_helpers.R | 6 mlr-2.7/mlr/tests/testthat/test_base_benchmark.R | 20 + mlr-2.7/mlr/tests/testthat/test_base_convertBMRToRankMatrix.R |only mlr-2.7/mlr/tests/testthat/test_base_plotBMRBoxplots.R |only mlr-2.7/mlr/tests/testthat/test_base_plotBMRSummary.R |only mlr-2.7/mlr/tests/testthat/test_base_plotCritDifferences.R | 24 + mlr-2.7/mlr/tests/testthat/test_base_plotRankMatrixAsBar.R | 47 --- mlr-2.7/mlr/tests/testthat/test_base_plotViperCharts.R | 33 +- 73 files changed, 393 insertions(+), 437 deletions(-)
Title: Estimation and Tests of Hierarchical F-Statistics
Description: Allows the estimation of hierarchical F-statistics from haploid or diploid genetic data
with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956;
<DOI:10.2307/2411227>. Functions are also given to test via randomisations the significance of each F and variance components,
using the likelihood-ratio statistics G.
Author: Jerome Goudet [aut, cre],
Thibaut Jombart [aut]
Maintainer: Jerome Goudet <jerome.goudet@unil.ch>
Diff between hierfstat versions 0.04-14 dated 2014-09-29 and 0.04-22 dated 2015-12-04
hierfstat-0.04-14/hierfstat/R/beta.R |only hierfstat-0.04-14/hierfstat/data/exhier.txt.gz |only hierfstat-0.04-14/hierfstat/data/yangex.txt.gz |only hierfstat-0.04-14/hierfstat/inst/doc/hierfstat.pdf |only hierfstat-0.04-14/hierfstat/man/betai.rd |only hierfstat-0.04-14/hierfstat/man/cfe.dist.rd |only hierfstat-0.04-14/hierfstat/man/da.dist.rd |only hierfstat-0.04-14/hierfstat/man/nei.dist.rd |only hierfstat-0.04-14/hierfstat/man/prepdata.Rd |only hierfstat-0.04-22/hierfstat/CHANGES | 33 + hierfstat-0.04-22/hierfstat/DESCRIPTION | 30 - hierfstat-0.04-22/hierfstat/MD5 | 77 ++- hierfstat-0.04-22/hierfstat/NAMESPACE | 32 + hierfstat-0.04-22/hierfstat/R/betas.R |only hierfstat-0.04-22/hierfstat/R/fstat.from.adegenet.R |only hierfstat-0.04-22/hierfstat/R/genetdist.R |only hierfstat-0.04-22/hierfstat/R/genind2hierfstat.R |only hierfstat-0.04-22/hierfstat/R/gstat.randtest.R |only hierfstat-0.04-22/hierfstat/R/hierana.r | 11 hierfstat-0.04-22/hierfstat/R/indpca.R | 5 hierfstat-0.04-22/hierfstat/R/misc.R | 210 ++-------- hierfstat-0.04-22/hierfstat/R/nwc.R | 21 - hierfstat-0.04-22/hierfstat/R/pairwise.fst.R |only hierfstat-0.04-22/hierfstat/R/readQN.R |only hierfstat-0.04-22/hierfstat/R/sexbiaseddisp.R |only hierfstat-0.04-22/hierfstat/R/simgenot_new.R |only hierfstat-0.04-22/hierfstat/R/w2c.R |only hierfstat-0.04-22/hierfstat/R/writebayescan.R |only hierfstat-0.04-22/hierfstat/R/writeped.R | 30 + hierfstat-0.04-22/hierfstat/build |only hierfstat-0.04-22/hierfstat/data/crocrussula.rda |only hierfstat-0.04-22/hierfstat/data/exhier.txt |only hierfstat-0.04-22/hierfstat/data/gtrunchier.rda |binary hierfstat-0.04-22/hierfstat/data/yangex.txt |only hierfstat-0.04-22/hierfstat/inst/doc/demeeusgoudet_ige_tut_2007.pdf |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.R |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.Rmd |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.html |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat_note.pdf |only hierfstat-0.04-22/hierfstat/inst/extdata/qn2_sex.dat |only hierfstat-0.04-22/hierfstat/man/AIc.Rd |only hierfstat-0.04-22/hierfstat/man/basic.stats.rd | 6 hierfstat-0.04-22/hierfstat/man/betas.Rd |only hierfstat-0.04-22/hierfstat/man/crocrussula.Rd |only hierfstat-0.04-22/hierfstat/man/eucl.dist.rd | 2 hierfstat-0.04-22/hierfstat/man/fstat.from.adegenet.Rd |only hierfstat-0.04-22/hierfstat/man/genet.dist.Rd |only hierfstat-0.04-22/hierfstat/man/genind2hierfstat.Rd |only hierfstat-0.04-22/hierfstat/man/gstat.randtest.Rd |only hierfstat-0.04-22/hierfstat/man/hierfstat.Rd | 6 hierfstat-0.04-22/hierfstat/man/pairwise.WCfst.Rd |only hierfstat-0.04-22/hierfstat/man/pairwise.neifst.Rd |only hierfstat-0.04-22/hierfstat/man/pcoa.rd | 2 hierfstat-0.04-22/hierfstat/man/ppfst.rd | 8 hierfstat-0.04-22/hierfstat/man/qn2.read.fstat.Rd |only hierfstat-0.04-22/hierfstat/man/sexbias.test.Rd |only hierfstat-0.04-22/hierfstat/man/sim.genot.rd | 2 hierfstat-0.04-22/hierfstat/man/sim.genot.t.Rd |only hierfstat-0.04-22/hierfstat/man/wc.rd | 2 hierfstat-0.04-22/hierfstat/man/write.bayescan.Rd |only hierfstat-0.04-22/hierfstat/man/write.ped.Rd |only hierfstat-0.04-22/hierfstat/vignettes |only 62 files changed, 245 insertions(+), 232 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-11 dated 2015-10-03 and 0.2-12 dated 2015-12-04
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/03rules.R | 11 ++++++----- R/05read_write.R | 3 ++- R/10timed.R | 2 ++ man/sequencerules-class.Rd | 3 ++- 7 files changed, 26 insertions(+), 17 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Assessment and Evaluation of Formations in United
Description: United is a software tool which can be downloaded at the following
website <http://www.schroepl.net/pbm/software/united/>. In general, it is
a virtual manager game for football teams. This package contains helpful
functions for determining an optimal formation for a virtual match in
United. E.g. knowing that the opponent has a strong defensive it is
advisable to beat him in the midfield. Furthermore, this package contains
functions for computing the optimal usage of hardness in a game.
Author: David Schindler [aut, cre]
Maintainer: David Schindler <dv.schindler@gmail.com>
Diff between unitedR versions 0.1 dated 2015-10-13 and 0.2 dated 2015-12-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/unitedRPackage.R | 2 +- R/unitedSimOne.R | 4 ++-- inst/doc/unitedR.pdf |binary man/unitedR-package.Rd | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.0 dated 2015-03-09 and 0.1.1 dated 2015-12-04
GetoptLong-0.1.0/GetoptLong/R/global.R |only GetoptLong-0.1.1/GetoptLong/DESCRIPTION | 12 GetoptLong-0.1.1/GetoptLong/MD5 | 55 GetoptLong-0.1.1/GetoptLong/NAMESPACE | 24 GetoptLong-0.1.1/GetoptLong/NEWS | 133 GetoptLong-0.1.1/GetoptLong/R/0_global.R |only GetoptLong-0.1.1/GetoptLong/R/GetoptLong.R | 1559 +++++----- GetoptLong-0.1.1/GetoptLong/R/qq.R | 400 +- GetoptLong-0.1.1/GetoptLong/README | 8 GetoptLong-0.1.1/GetoptLong/build/vignette.rds |binary GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.R | 159 - GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.Rnw | 597 +-- GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.pdf |binary GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.R | 316 +- GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.Rnw | 582 +-- GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.pdf |binary GetoptLong-0.1.1/GetoptLong/inst/tests/test.R | 2 GetoptLong-0.1.1/GetoptLong/inst/tests/test_GetoptLong.R | 518 +-- GetoptLong-0.1.1/GetoptLong/inst/tests/test_qq.R | 222 - GetoptLong-0.1.1/GetoptLong/man/GetOptions.rd | 45 GetoptLong-0.1.1/GetoptLong/man/GetoptLong.options.rd | 60 GetoptLong-0.1.1/GetoptLong/man/GetoptLong.rd | 98 GetoptLong-0.1.1/GetoptLong/man/get_scriptname.rd | 34 GetoptLong-0.1.1/GetoptLong/man/qq.options.rd | 60 GetoptLong-0.1.1/GetoptLong/man/qq.rd | 62 GetoptLong-0.1.1/GetoptLong/man/qqcat.rd | 99 GetoptLong-0.1.1/GetoptLong/man/source.rd |only GetoptLong-0.1.1/GetoptLong/tests/test-all.R | 28 GetoptLong-0.1.1/GetoptLong/vignettes/GetoptLong.Rnw | 597 +-- GetoptLong-0.1.1/GetoptLong/vignettes/variable_interpolation.Rnw | 582 +-- 30 files changed, 3132 insertions(+), 3120 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002), seq-gen (Rambaut and Grassly 1997),
Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for
simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-15 dated 2013-12-14 and 0.1-16 dated 2015-12-04
phyclust-0.1-15/phyclust/vignettes/phyclust-include/jss.bst |only phyclust-0.1-15/phyclust/vignettes/phyclust-include/jss.cls |only phyclust-0.1-16/phyclust/ChangeLog | 28 ++++ phyclust-0.1-16/phyclust/DESCRIPTION | 13 +- phyclust-0.1-16/phyclust/MD5 | 41 +++--- phyclust-0.1-16/phyclust/NAMESPACE | 29 ++++ phyclust-0.1-16/phyclust/R/000_globalVariables.r |only phyclust-0.1-16/phyclust/R/p_ms.r | 42 +++++-- phyclust-0.1-16/phyclust/demo/00Index | 1 phyclust-0.1-16/phyclust/demo/simu_ms_tbs.r |only phyclust-0.1-16/phyclust/inst/doc/phyclust-guide.Rnw | 60 +++++----- phyclust-0.1-16/phyclust/inst/doc/phyclust-guide.pdf |binary phyclust-0.1-16/phyclust/man/ms.Rd | 40 ++++-- phyclust-0.1-16/phyclust/man/seqgen.Rd | 25 ++-- phyclust-0.1-16/phyclust/src/R_phyclust.c | 2 phyclust-0.1-16/phyclust/src/R_phyclust_em_step.c | 9 + phyclust-0.1-16/phyclust/src/msdir/ms.c | 12 +- phyclust-0.1-16/phyclust/src/msdir/ms_main.c | 2 phyclust-0.1-16/phyclust/src/phyclust/phyclust_em_step.c | 46 ++++++- phyclust-0.1-16/phyclust/src/phyclust/phyclust_qmatrix_array.c | 4 phyclust-0.1-16/phyclust/vignettes/build_pdf.sh | 15 ++ phyclust-0.1-16/phyclust/vignettes/phyclust-guide.Rnw | 60 +++++----- phyclust-0.1-16/phyclust/vignettes/phyclust-include/01-introduction.tex | 21 ++- phyclust-0.1-16/phyclust/vignettes/phyclust-include/my_jss.cls |only 24 files changed, 311 insertions(+), 139 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to
data files written using Unidata's
netCDF library (version 4 or earlier), which are binary data files that are portable
across platforms and include metadata information in addition to the data sets.
Using this package, netCDF files (either version 4
or "classic" version 3) can be opened and data sets read in easily.
It is also easy to create new netCDF dimensions, variables, and files,
in either version 3 or 4 format, and manipulate existing netCDF files.
This package replaces the former ncdf package, which only worked with
netcdf version 3 files. For various reasons the names of the functions
have had to be changed from the names in the ncdf package. The old ncdf package is still
available at the URL given below, if you need to have backward compatibility.
It should be possible to have both the ncdf and ncdf4 packages installed
simultaneously without a problem.
However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.14 dated 2015-11-10 and 1.15 dated 2015-12-04
ncdf4-1.14/ncdf4/tools/autom4te.cache |only ncdf4-1.15/ncdf4/DESCRIPTION | 8 ++++---- ncdf4-1.15/ncdf4/MD5 | 15 +++------------ ncdf4-1.15/ncdf4/R/ncdf4.R | 2 +- ncdf4-1.15/ncdf4/src/Makevars.win | 2 +- 5 files changed, 9 insertions(+), 18 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0-2 dated 2015-10-02 and 3.0.1 dated 2015-12-04
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/db.r | 35 +++++++++++++++++++---------------- inst/NEWS.Rd | 8 ++++++++ man/legacy_world.Rd | 2 +- man/map.Rd | 4 ++-- man/match.map.Rd | 2 +- man/world.Rd | 2 +- man/world2.Rd | 2 +- src/world.name | 8 ++++---- 10 files changed, 50 insertions(+), 39 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 0.3 dated 2015-11-05 and 0.4 dated 2015-12-04
imputeTS-0.3/imputeTS/R/vis.differences.R |only imputeTS-0.3/imputeTS/man/vis.differences.Rd |only imputeTS-0.4/imputeTS/DESCRIPTION | 8 ++++---- imputeTS-0.4/imputeTS/MD5 | 18 +++++++++++------- imputeTS-0.4/imputeTS/NAMESPACE | 7 ++++++- imputeTS-0.4/imputeTS/NEWS | 15 ++++++++++++++- imputeTS-0.4/imputeTS/R/na.interpolation.R | 22 +++++++++++++++------- imputeTS-0.4/imputeTS/R/vis.barMissing.R |only imputeTS-0.4/imputeTS/R/vis.imputations.R |only imputeTS-0.4/imputeTS/R/vis.missing.R |only imputeTS-0.4/imputeTS/man/na.interpolation.Rd | 9 ++++++--- imputeTS-0.4/imputeTS/man/vis.barMissing.Rd |only imputeTS-0.4/imputeTS/man/vis.imputations.Rd |only imputeTS-0.4/imputeTS/man/vis.missing.Rd |only 14 files changed, 56 insertions(+), 23 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.4.2 dated 2015-11-17 and 0.5.1 dated 2015-12-04
DESCRIPTION | 13 +++-- MD5 | 42 ++++++++++--------- NAMESPACE | 1 R/Create_GERGM_Object.R | 15 +++++- R/Create_GERGM_Object_From_Formula.R | 4 + R/Estimate_GERGM.R | 4 - R/Estimate_Plot.R | 5 +- R/GERGM_Class.R | 3 - R/GOF.R | 2 R/Helper_Functions.R | 39 ++++++++++++++--- R/MCMCMLE.R | 50 ++++++++-------------- R/Network_Statistic_Calculation_Functions.R | 32 ++++++++++++++ R/Package_Documentation.R | 3 + R/Parse_Formula_Object.R | 13 +++++ R/Parse_Undirected_Structural_Terms.R |only R/Prepare_Covariates.R | 11 ++--- R/Simulate_GERGM.R | 10 ++-- R/Trace_Plot.R | 8 ++- R/gergm.R | 61 +++++++++++++++------------- README.md | 12 +++-- man/GERGM.Rd | 13 +---- tests |only 22 files changed, 209 insertions(+), 132 deletions(-)