Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
(<https://orcid.org/0000-0001-6519-5265>),
Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.1.3 dated 2019-04-21 and 0.1.4 dated 2019-06-04
DESCRIPTION | 6 +-- MD5 | 29 ++++++++++-------- NAMESPACE | 4 ++ NEWS.md | 8 ++++- R/RcppExports.R | 8 +++++ R/proxy.R | 62 ++++++++++++++++++++++++++++++++++++++- README.md | 35 +++++++++++++++------- man/colSds.Rd |only man/colZeros.Rd |only man/images/unnamed-chunk-4-1.png |binary man/images/unnamed-chunk-5-1.png |binary man/images/unnamed-chunk-6-1.png |binary man/images/unnamed-chunk-7-1.png |only man/simil.Rd | 2 - src/RcppExports.cpp | 24 +++++++++++++++ src/linear.cpp | 21 +++++++++++++ tests/testthat/test-proxy.R | 21 +++++++++++++ 17 files changed, 191 insertions(+), 29 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, a posteriori time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy(), bin_timePaleoPhy(),
cal3TimePaleoPhy() and bin_cal3TimePaleoPhy(), which date cladograms of
fossil taxa using stratigraphic data. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord(), which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord() to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord() into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.
Author: David W. Bapst, Peter J. Wagner
Maintainer: David W. Bapst <dwbapst@gmail.com>
Diff between paleotree versions 3.1.3 dated 2018-10-02 and 3.3.0 dated 2019-06-04
paleotree-3.1.3/paleotree/R/hiddenFunctions.R |only paleotree-3.1.3/paleotree/tests/minBranchLength_check_10-09-15.R |only paleotree-3.1.3/paleotree/tests/testContradiction_tests_05-25-17.R |only paleotree-3.3.0/paleotree/CHANGELOG | 23 paleotree-3.3.0/paleotree/DESCRIPTION | 15 paleotree-3.3.0/paleotree/MD5 | 273 + paleotree-3.3.0/paleotree/NAMESPACE | 16 paleotree-3.3.0/paleotree/R/DiversityCurves.R | 12 paleotree-3.3.0/paleotree/R/RaiaCopesRule.R | 10 paleotree-3.3.0/paleotree/R/SamplingConv.R | 6 paleotree-3.3.0/paleotree/R/SongZhangDicrano.R | 18 paleotree-3.3.0/paleotree/R/binTimeData.R | 125 paleotree-3.3.0/paleotree/R/branchClasses.R | 14 paleotree-3.3.0/paleotree/R/cal3TimePaleoPhy.R | 1434 +++++++--- paleotree-3.3.0/paleotree/R/cladogeneticTraitCont.R | 24 paleotree-3.3.0/paleotree/R/communityEcology.R | 48 paleotree-3.3.0/paleotree/R/compareTimescaling.R | 2 paleotree-3.3.0/paleotree/R/constrainParPaleo.R | 42 paleotree-3.3.0/paleotree/R/createMrBayesConstraints.R | 2 paleotree-3.3.0/paleotree/R/createMrBayesTipDatingNexus.R | 163 - paleotree-3.3.0/paleotree/R/dateNodes.R | 4 paleotree-3.3.0/paleotree/R/dateTaxonTreePBDB.R |only paleotree-3.3.0/paleotree/R/divCurveFossilRecordSim.R | 6 paleotree-3.3.0/paleotree/R/durationFreq.R | 18 paleotree-3.3.0/paleotree/R/equation2function.R | 6 paleotree-3.3.0/paleotree/R/exhaustationFunctions.R | 228 + paleotree-3.3.0/paleotree/R/fixRootTime.R |only paleotree-3.3.0/paleotree/R/footeValues.R | 8 paleotree-3.3.0/paleotree/R/fourDateFunctions.R | 10 paleotree-3.3.0/paleotree/R/freqRat.R | 8 paleotree-3.3.0/paleotree/R/getDataPBDB.R |only paleotree-3.3.0/paleotree/R/getFixedAgesFromNexus.R | 23 paleotree-3.3.0/paleotree/R/graptDisparity.R | 32 paleotree-3.3.0/paleotree/R/graptPBDB.R | 150 - paleotree-3.3.0/paleotree/R/hidden.gettingPhyloPicFunctions.R |only paleotree-3.3.0/paleotree/R/hidden.makePBDBtaxonTree.Functions.R |only paleotree-3.3.0/paleotree/R/hidden.modelExpressionModification.R |only paleotree-3.3.0/paleotree/R/hidden.plotTaxonStratDurations.R |only paleotree-3.3.0/paleotree/R/hidden.plottingPhyloPicFunctions.R |only paleotree-3.3.0/paleotree/R/horizonSampRate.R | 10 paleotree-3.3.0/paleotree/R/inverseSurv.R | 69 paleotree-3.3.0/paleotree/R/kanto.R | 24 paleotree-3.3.0/paleotree/R/macroperforateForam.R | 10 paleotree-3.3.0/paleotree/R/makePBDBtaxonTree.R | 684 ++-- paleotree-3.3.0/paleotree/R/minBranchLength.R | 135 paleotree-3.3.0/paleotree/R/minCharChange.R | 639 ++-- paleotree-3.3.0/paleotree/R/modelMethods.R | 10 paleotree-3.3.0/paleotree/R/modifyTerminalBranches.R | 171 - paleotree-3.3.0/paleotree/R/multiDiv.R | 251 + paleotree-3.3.0/paleotree/R/nearestNeighborDist.R | 6 paleotree-3.3.0/paleotree/R/nodeDates2branchLengths.R | 7 paleotree-3.3.0/paleotree/R/obtainDatedPosteriorTreesMrB.R | 301 +- paleotree-3.3.0/paleotree/R/occData2timeList.R | 106 paleotree-3.3.0/paleotree/R/optimPaleo.R | 4 paleotree-3.3.0/paleotree/R/paleotree-package.R | 22 paleotree-3.3.0/paleotree/R/parentChild2TaxonTree.R | 241 + paleotree-3.3.0/paleotree/R/perCapitaRates.R | 21 paleotree-3.3.0/paleotree/R/perfectParsCharTree.R | 14 paleotree-3.3.0/paleotree/R/plotOccData.R | 13 paleotree-3.3.0/paleotree/R/plotPhyloPicTree.R |only paleotree-3.3.0/paleotree/R/plotTraitgram.R | 2 paleotree-3.3.0/paleotree/R/pqr2Ps.R | 43 paleotree-3.3.0/paleotree/R/probAnc.R | 12 paleotree-3.3.0/paleotree/R/resolveTreeChar.R | 14 paleotree-3.3.0/paleotree/R/retiolitinae.R | 12 paleotree-3.3.0/paleotree/R/sampleRanges.R | 6 paleotree-3.3.0/paleotree/R/seqTimeList.R | 10 paleotree-3.3.0/paleotree/R/setRootAge.R | 2 paleotree-3.3.0/paleotree/R/simFossilRecord.R | 872 ++++-- paleotree-3.3.0/paleotree/R/simFossilRecordMethods.R | 70 paleotree-3.3.0/paleotree/R/taxa2cladogram.R | 8 paleotree-3.3.0/paleotree/R/taxonSortPBDBocc.R | 384 +- paleotree-3.3.0/paleotree/R/taxonTable2TaxonTree.R | 65 paleotree-3.3.0/paleotree/R/termTaxa.R | 174 - paleotree-3.3.0/paleotree/R/testEdgeMat.R | 6 paleotree-3.3.0/paleotree/R/timeLadderTree.R | 6 paleotree-3.3.0/paleotree/R/timePaleoPhy.R | 1024 +++++-- paleotree-3.3.0/paleotree/R/timeSliceTree.R | 2 paleotree-3.3.0/paleotree/R/tipDatingCompatabilitySummaryMrB.R |only paleotree-3.3.0/paleotree/R/treeContradiction.R | 8 paleotree-3.3.0/paleotree/R/twoWayEcologyCluster.R | 80 paleotree-3.3.0/paleotree/README.md | 4 paleotree-3.3.0/paleotree/data/graptPBDB.rdata |binary paleotree-3.3.0/paleotree/man/DiversityCurves.Rd | 8 paleotree-3.3.0/paleotree/man/RaiaCopesRule.Rd | 4 paleotree-3.3.0/paleotree/man/SamplingConv.Rd | 4 paleotree-3.3.0/paleotree/man/SongZhangDicrano.Rd | 4 paleotree-3.3.0/paleotree/man/binTimeData.Rd | 73 paleotree-3.3.0/paleotree/man/branchClasses.Rd | 2 paleotree-3.3.0/paleotree/man/cal3TimePaleoPhy.Rd | 365 +- paleotree-3.3.0/paleotree/man/cladogeneticTraitCont.Rd | 24 paleotree-3.3.0/paleotree/man/communityEcology.Rd | 25 paleotree-3.3.0/paleotree/man/compareTimescaling.Rd | 3 paleotree-3.3.0/paleotree/man/constrainParPaleo.Rd | 2 paleotree-3.3.0/paleotree/man/createMrBayesTipDatingNexus.Rd | 79 paleotree-3.3.0/paleotree/man/dateNodes.Rd | 2 paleotree-3.3.0/paleotree/man/dateTaxonTreePBDB.Rd |only paleotree-3.3.0/paleotree/man/degradeTree.Rd | 4 paleotree-3.3.0/paleotree/man/divCurveFossilRecordSim.Rd | 4 paleotree-3.3.0/paleotree/man/durationFreq.Rd | 3 paleotree-3.3.0/paleotree/man/equation2function.Rd | 3 paleotree-3.3.0/paleotree/man/exhaustionFunctions.Rd | 75 paleotree-3.3.0/paleotree/man/expandTaxonTree.Rd | 4 paleotree-3.3.0/paleotree/man/fixRootTime.Rd |only paleotree-3.3.0/paleotree/man/footeValues.Rd | 4 paleotree-3.3.0/paleotree/man/freqRat.Rd | 2 paleotree-3.3.0/paleotree/man/getDataPBDB.Rd |only paleotree-3.3.0/paleotree/man/graptPBDB.Rd | 144 - paleotree-3.3.0/paleotree/man/horizonSampRate.Rd | 5 paleotree-3.3.0/paleotree/man/inverseSurv.Rd | 30 paleotree-3.3.0/paleotree/man/makePBDBtaxonTree.Rd | 321 +- paleotree-3.3.0/paleotree/man/minBranchLength.Rd | 80 paleotree-3.3.0/paleotree/man/minCharChange.Rd | 432 ++- paleotree-3.3.0/paleotree/man/modelMethods.Rd | 16 paleotree-3.3.0/paleotree/man/modifyTerminalBranches.Rd | 47 paleotree-3.3.0/paleotree/man/multiDiv.Rd | 89 paleotree-3.3.0/paleotree/man/obtainDatedPosteriorTreesMrB.Rd | 187 - paleotree-3.3.0/paleotree/man/occData2timeList.Rd | 68 paleotree-3.3.0/paleotree/man/paleotree-package.Rd | 4 paleotree-3.3.0/paleotree/man/parentChild2taxonTree.Rd | 112 paleotree-3.3.0/paleotree/man/perCapitaRates.Rd | 2 paleotree-3.3.0/paleotree/man/plotOccData.Rd | 6 paleotree-3.3.0/paleotree/man/plotPhyloPicTree.Rd |only paleotree-3.3.0/paleotree/man/pqr2Ps.Rd | 32 paleotree-3.3.0/paleotree/man/probAnc.Rd | 4 paleotree-3.3.0/paleotree/man/resolveTreeChar.Rd | 74 paleotree-3.3.0/paleotree/man/sampleRanges.Rd | 12 paleotree-3.3.0/paleotree/man/seqTimeList.Rd | 2 paleotree-3.3.0/paleotree/man/simFossilRecord.Rd | 788 +++-- paleotree-3.3.0/paleotree/man/simFossilRecordMethods.Rd | 67 paleotree-3.3.0/paleotree/man/taxa2cladogram.Rd | 4 paleotree-3.3.0/paleotree/man/taxonSortPBDBocc.Rd | 241 - paleotree-3.3.0/paleotree/man/taxonTable2taxonTree.Rd | 14 paleotree-3.3.0/paleotree/man/termTaxa.Rd | 88 paleotree-3.3.0/paleotree/man/testEdgeMat.Rd | 7 paleotree-3.3.0/paleotree/man/timeLadderTree.Rd | 2 paleotree-3.3.0/paleotree/man/timePaleoPhy.Rd | 457 ++- paleotree-3.3.0/paleotree/man/timeSliceTree.Rd | 2 paleotree-3.3.0/paleotree/man/tipDatingCompatabilitySummaryMrB.Rd |only paleotree-3.3.0/paleotree/man/twoWayEcologyCluster.Rd | 66 paleotree-3.3.0/paleotree/tests/testthat |only paleotree-3.3.0/paleotree/tests/testthat.R | 6 142 files changed, 8306 insertions(+), 4059 deletions(-)
Title: Miscellaneous Time Series Filters
Description: The mFilter package implements several time series filters useful
for smoothing and extracting trend and cyclical components of a
time series. The routines are commonly used in economics and
finance, however they should also be interest to other areas.
Currently, Christiano-Fitzgerald, Baxter-King,
Hodrick-Prescott, Butterworth, and trigonometric regression
filters are included in the package.
Author: Mehmet Balcilar <mehmet@mbalcilar.net>
Maintainer: Mehmet Balcilar <mehmet@mbalcilar.net>
Diff between mFilter versions 0.1-4 dated 2018-09-23 and 0.1-5 dated 2019-06-04
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/cffilter.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.2-5 dated 2019-05-30 and 1.2-6 dated 2019-06-04
seriation-1.2-5/seriation/src/fprintf.c |only seriation-1.2-6/seriation/DESCRIPTION | 8 ++--- seriation-1.2-6/seriation/MD5 | 21 ++++++-------- seriation-1.2-6/seriation/NEWS.md | 7 ++++ seriation-1.2-6/seriation/R/AAAparameter.R | 3 -- seriation-1.2-6/seriation/R/seriate.array.R | 3 +- seriation-1.2-6/seriation/R/seriate.dist.R | 2 - seriation-1.2-6/seriation/R/seriate_PCA.R | 8 ----- seriation-1.2-6/seriation/inst/doc/seriation.pdf |binary seriation-1.2-6/seriation/src/arsa.f | 25 +++-------------- seriation-1.2-6/seriation/src/bburcg.f | 33 ++++++----------------- seriation-1.2-6/seriation/src/bbwrcg.f | 28 +++++-------------- 12 files changed, 46 insertions(+), 92 deletions(-)
Title: Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
Description: Distance-based parametric bootstrap tests for clustering with
spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus genetical data
for species delimitation, nearest neighbor
based noise detection. Genetic distances between communities.
Tests whether various distance-based regressions
are equal. Try package?prabclus for on overview.
Author: Christian Hennig <christian.hennig@unibo.it>,
Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>
Maintainer: Christian Hennig <christian.hennig@unibo.it>
Diff between prabclus versions 2.2-7.1 dated 2019-05-28 and 2.3-1 dated 2019-06-04
DESCRIPTION | 26 - MD5 | 115 +++--- NAMESPACE | 6 R/abundfunctions.R | 3 R/reg2cluster2dist.R |only data/kykladspecreg.rda |binary data/waterdist.rda |binary man/NNclean.Rd | 4 man/abundtest.Rd | 16 man/allele2zeroone.Rd | 4 man/alleleconvert.Rd | 22 - man/alleledist.Rd | 4 man/alleleinit.Rd | 4 man/allelepaircomp.Rd | 4 man/autoconst.Rd | 4 man/build.charmatrix.Rd | 4 man/build.ext.nblist.Rd | 4 man/build.nblist.Rd | 4 man/cluspop.nb.Rd | 4 man/communities.Rd |only man/communitydist.Rd |only man/comp.test.Rd | 4 man/concomp.Rd | 4 man/conregmat.Rd | 4 man/coord2dist.Rd | 4 man/crmatrix.Rd | 4 man/dicedist.Rd | 4 man/distratio.Rd | 4 man/geco.Rd | 4 man/geo2neighbor.Rd | 4 man/homogen.test.Rd | 4 man/hprabclust.Rd | 4 man/incmatrix.Rd | 4 man/jaccard.Rd | 4 man/kulczynski.Rd | 4 man/lcomponent.Rd | 4 man/lociplots.Rd | 4 man/nastats.Rd | 4 man/nbtest.Rd | 4 man/nn.Rd | 4 man/phipt.Rd |only man/piecewiselin.Rd | 4 man/plotdistreg.Rd |only man/pop.sim.Rd | 4 man/prab.sarestimate.Rd | 24 - man/prabclus-package.Rd | 30 + man/prabclust.Rd | 4 man/prabinit.Rd | 4 man/prabtest.Rd | 4 man/qkulczynski.Rd | 4 man/randpop.nb.Rd | 4 man/regdist.Rd |only man/regdistbetween.Rd |only man/regdistbetweenone.Rd |only man/regdistdiff.Rd |only man/regdistdiffone.Rd |only man/regeqdist.Rd |only man/regpop.sar.Rd | 10 man/specgroups.Rd | 4 man/stressvals.Rd | 4 man/toprab.Rd | 4 man/unbuild.charmatrix.Rd | 4 tests/Examples/prabclus-Ex.Rout.save | 653 ++++++++++++++++++++++++++++++++++- tests/prabclustests.Rout.save | 9 64 files changed, 879 insertions(+), 195 deletions(-)
Title: Nonparametric Estimation and Inference Procedures using
Partitioning-Based Least Squares Regression
Description: Tools for statistical analysis using partitioning-based least squares regression as described in Cattaneo, Farrell and Feng (2019, <arXiv:1804.04916>): lsprobust() for nonparametric point estimation of regression functions and their derivatives and for robust bias-corrected (pointwise and uniform) inference; lspkselect() for data-driven selection of the IMSE-optimal number of knots; lsprobust.plot() for regression plots with robust confidence intervals and confidence bands; lsplincom() for estimation and inference for linear combinations of regression functions from different groups.
Author: Matias D. Cattaneo, Max H. Farrell, Yingjie Feng
Maintainer: Yingjie Feng <yjfeng@umich.edu>
Diff between lspartition versions 0.2 dated 2018-12-03 and 0.3 dated 2019-06-04
DESCRIPTION | 12 +-- MD5 | 26 ++++---- NAMESPACE | 2 R/lspartition-package.R | 24 +++---- R/lspfunctions.R | 140 +++++++++++++++++++++++++++++++++------------ R/lspkselect.R | 103 ++++++++++++++++++++------------- R/lsplincom.R | 19 +++--- R/lsprobust.R | 63 +++++++++----------- R/lsprobust.plot.R | 17 ++--- man/lspartition-package.Rd | 22 +++---- man/lspkselect.Rd | 62 ++++++++++--------- man/lsplincom.Rd | 18 ++--- man/lsprobust.Rd | 54 ++++++++--------- man/lsprobust.plot.Rd | 25 ++++---- 14 files changed, 343 insertions(+), 244 deletions(-)
Title: Interface to the Greek National Data Bank for
Hydrometeorological Information
Description: R interface to the Greek National Data Bank for Hydrological and
Meteorological Information <http://www.hydroscope.gr/>. It covers
Hydroscope's data sources and provides functions to transliterate,
translate and download them into tidy dataframes.
Author: Konstantinos Vantas [aut, cre]
(<https://orcid.org/0000-0001-6387-8791>),
Sharla Gelfand [ctb, rev] (Sharla Gelfand reviewed the package for
rOpenSci, see https://github.com/ropensci/onboarding/issues/185),
Tim Trice [rev] (Tim Trice reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/185)
Maintainer: Konstantinos Vantas <kon.vantas@gmail.com>
Diff between hydroscoper versions 1.1.1 dated 2018-08-25 and 1.2 dated 2019-06-04
DESCRIPTION | 19 LICENSE | 4 MD5 | 94 +-- NAMESPACE | 40 - NEWS.md | 6 R/data.R | 118 +-- R/defunct.R | 44 - R/enhydris_api.R | 240 +++---- R/find_stations.R | 105 +-- R/get_data.R | 114 +-- R/get_tables.R | 437 +++++++------- R/hydro_coords.R | 51 - R/hydro_translate.R | 324 +++++----- R/hydroscoper_package.R | 70 +- R/translit.R | 252 ++++---- R/utils.R | 150 ++-- README.md | 301 ++++----- build/vignette.rds |binary data/stations.rda |binary inst/CITATION | 38 - inst/doc/intro_hydroscoper.R | 100 +-- inst/doc/intro_hydroscoper.Rmd | 308 +++++----- inst/doc/intro_hydroscoper.html | 924 +++++++++++++++--------------- inst/doc/stations_with_data.R | 92 +- inst/doc/stations_with_data.Rmd | 168 ++--- inst/doc/stations_with_data.html | 789 +++++++++++++------------ man/figures/README-plot_time_series-1.png |binary man/find_stations.Rd | 63 +- man/get_data.Rd | 118 +-- man/get_tables.Rd | 309 +++++----- man/greece_borders.Rd | 54 - man/hydro_coords.Rd | 62 +- man/hydro_translate.Rd | 308 +++++----- man/hydroscoper.Rd | 122 +-- man/hydroscoper_defunct.Rd | 48 - man/stations.Rd | 56 - man/timeseries.Rd | 56 - tests/testthat.R | 8 tests/testthat/test_defunct.R | 10 tests/testthat/test_enhydris.R | 278 ++++----- tests/testthat/test_find_stations.R | 38 - tests/testthat/test_get_data.R | 13 tests/testthat/test_get_table.R | 35 - tests/testthat/test_hydro_coords.R | 38 - tests/testthat/test_translit.R | 182 +++-- tests/testthat/test_utils.R | 48 - vignettes/intro_hydroscoper.Rmd | 308 +++++----- vignettes/stations_with_data.Rmd | 168 ++--- 48 files changed, 3602 insertions(+), 3508 deletions(-)
Title: Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Description: Implements a wide variety of one- and two-parameter Bayesian CRM
designs. The program can run interactively, allowing the user to enter outcomes
after each cohort has been recruited, or via simulation to assess operating
characteristics.
Author: Michael Sweeting [aut],
Graham Wheeler [aut, cre]
Maintainer: Graham Wheeler <graham.wheeler@ucl.ac.uk>
Diff between bcrm versions 0.5.2 dated 2019-05-24 and 0.5.3 dated 2019-06-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 +++++ R/bcrm.R | 3 ++- R/nextdose.R | 20 ++++++++++++++------ 5 files changed, 29 insertions(+), 15 deletions(-)
Title: Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, or genotypes sampled from those probabilties, can then be exported
for downstream analysis. 'polyRAD' is described by Clark et al. (2019)
<doi:10.1534/g3.118.200913>.
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polyRAD versions 1.0 dated 2018-11-19 and 1.1 dated 2019-06-04
DESCRIPTION | 12 MD5 | 54 +- NAMESPACE | 16 NEWS | 15 R/RcppExports.R | 4 R/classes_methods.R | 280 +++++++++-- R/data_export.R | 218 +++++++-- R/data_import.R | 45 + R/overdispersion.R | 10 build/vignette.rds |binary inst/CITATION | 3 inst/doc/polyRADtutorial.R | 63 +- inst/doc/polyRADtutorial.Rmd | 135 ++++- inst/doc/polyRADtutorial.html | 857 ++++++++++++++---------------------- inst/extdata/Msi01genes.vcf | 224 ++++----- inst/extdata/Msi01genes.vcf.bgz |binary inst/extdata/Msi01genes.vcf.bgz.tbi |binary inst/extdata/examplePCA.RData |only man/ExportGAPIT.Rd | 107 +++- man/GetWeightedMeanGenotypes.Rd | 16 man/LocusInfo.Rd | 5 man/MergeTaxaDepth.Rd |only man/PipelineMapping2Parents.Rd | 2 man/RADdata.Rd | 19 man/SubsetByLocus.Rd | 25 - man/SubsetByPloidy.Rd |only man/VCF2RADdata.Rd | 6 src/AdjustAlleleFreq.cpp |only src/RcppExports.cpp | 14 vignettes/polyRADtutorial.Rmd | 135 ++++- 30 files changed, 1362 insertions(+), 903 deletions(-)
Title: Dose Titration Algorithm Tuning
Description: DTAT is a methodologic framework allowing dose individualization to be
conceived as a continuous learning process that begins in early-phase
clinical trials and continues throughout drug development, on into
clinical practice. This package includes code that researchers may use
to reproduce or extend key results of the DTAT research programme, plus
tools for trialists to design and simulate a '3+3/PC' dose-finding study.
Please see Norris (2017) <doi:10.12688/f1000research.10624.3> and
Norris (2017) <doi:10.1101/240846>.
Author: David C. Norris [aut, cre]
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between DTAT versions 0.3-1 dated 2019-02-20 and 0.3-2 dated 2019-06-04
DTAT-0.3-1/DTAT/inst/doc/widget_D3-viz.html |only DTAT-0.3-2/DTAT/DESCRIPTION | 8 +- DTAT-0.3-2/DTAT/MD5 | 19 ++---- DTAT-0.3-2/DTAT/R/DTAT-internal.R | 2 DTAT-0.3-2/DTAT/R/DTAT-package.R | 2 DTAT-0.3-2/DTAT/R/Onoue.Friberg.R | 85 +++++++-------------------- DTAT-0.3-2/DTAT/R/titrate.R | 26 ++++++-- DTAT-0.3-2/DTAT/build/vignette.rds |binary DTAT-0.3-2/DTAT/inst/doc/Designing-33PC.html | 11 ++- DTAT-0.3-2/DTAT/man/Onoue.Friberg.Rd | 4 - DTAT-0.3-2/DTAT/man/sim.Rd | 2 11 files changed, 66 insertions(+), 93 deletions(-)
Title: Interface to 'Digital Ocean'
Description: Provides a set of functions for interacting with the 'Digital
Ocean' API at <https://developers.digitalocean.com/documentation/v2>, including
creating images, destroying them, rebooting, getting details on regions, and
available images.
Author: Scott Chamberlain [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
Bob Rudis [ctb],
Bryce Mecum [ctb] (<https://orcid.org/0000-0002-0381-3766>),
RStudio [cph]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between analogsea versions 0.6.0 dated 2018-01-04 and 0.7.0 dated 2019-06-04
analogsea-0.6.0/analogsea/inst/doc/doapi.Rmd |only analogsea-0.6.0/analogsea/inst/doc/doapi.html |only analogsea-0.6.0/analogsea/inst/vign/doapi.Rmd |only analogsea-0.6.0/analogsea/inst/vign/doapi.md |only analogsea-0.6.0/analogsea/tests/testthat/test-space.R |only analogsea-0.6.0/analogsea/vignettes/doapi.Rmd |only analogsea-0.7.0/analogsea/DESCRIPTION | 16 analogsea-0.7.0/analogsea/LICENSE | 2 analogsea-0.7.0/analogsea/MD5 | 103 ++-- analogsea-0.7.0/analogsea/NAMESPACE | 29 + analogsea-0.7.0/analogsea/NEWS.md | 24 + analogsea-0.7.0/analogsea/R/certificates.R |only analogsea-0.7.0/analogsea/R/debian.R | 2 analogsea-0.7.0/analogsea/R/do_options.R | 4 analogsea-0.7.0/analogsea/R/docklet.R | 123 +++-- analogsea-0.7.0/analogsea/R/docklet_ps_data.R | 42 -- analogsea-0.7.0/analogsea/R/docklets_create.R | 5 analogsea-0.7.0/analogsea/R/droplet-actions.R | 10 analogsea-0.7.0/analogsea/R/droplet-ssh.R | 174 ++++---- analogsea-0.7.0/analogsea/R/droplets_create.R | 9 analogsea-0.7.0/analogsea/R/firewalls.R |only analogsea-0.7.0/analogsea/R/info.R |only analogsea-0.7.0/analogsea/R/onload.R | 4 analogsea-0.7.0/analogsea/R/space_create.R |only analogsea-0.7.0/analogsea/R/spaces.R | 210 +++++----- analogsea-0.7.0/analogsea/R/tags.R | 4 analogsea-0.7.0/analogsea/README.md | 8 analogsea-0.7.0/analogsea/build/vignette.rds |binary analogsea-0.7.0/analogsea/inst/doc/analogsea.Rmd |only analogsea-0.7.0/analogsea/inst/doc/analogsea.html |only analogsea-0.7.0/analogsea/inst/ignore/docklet_packrat.R | 2 analogsea-0.7.0/analogsea/inst/vign/analogsea.Rmd |only analogsea-0.7.0/analogsea/inst/vign/analogsea.md |only analogsea-0.7.0/analogsea/man/analogsea-defunct.Rd | 8 analogsea-0.7.0/analogsea/man/as.space.Rd |only analogsea-0.7.0/analogsea/man/certificate_delete.Rd |only analogsea-0.7.0/analogsea/man/certificates.Rd |only analogsea-0.7.0/analogsea/man/cloud_config.Rd | 2 analogsea-0.7.0/analogsea/man/debian.Rd | 2 analogsea-0.7.0/analogsea/man/do_oauth.Rd | 6 analogsea-0.7.0/analogsea/man/do_options.Rd | 5 analogsea-0.7.0/analogsea/man/docklet_create.Rd | 63 ++- analogsea-0.7.0/analogsea/man/docklets_create.Rd | 18 analogsea-0.7.0/analogsea/man/domain_create.Rd | 8 analogsea-0.7.0/analogsea/man/domain_records.Rd | 6 analogsea-0.7.0/analogsea/man/droplet_action.Rd | 17 analogsea-0.7.0/analogsea/man/droplet_create.Rd | 20 analogsea-0.7.0/analogsea/man/droplet_freeze.Rd | 14 analogsea-0.7.0/analogsea/man/droplet_functions.Rd |only analogsea-0.7.0/analogsea/man/droplet_modify.Rd | 6 analogsea-0.7.0/analogsea/man/droplet_snapshot.Rd | 8 analogsea-0.7.0/analogsea/man/droplet_ssh.Rd | 45 +- analogsea-0.7.0/analogsea/man/droplets_create.Rd | 21 - analogsea-0.7.0/analogsea/man/firewall_add_droplets.Rd |only analogsea-0.7.0/analogsea/man/firewall_add_tags.Rd |only analogsea-0.7.0/analogsea/man/firewall_delete.Rd |only analogsea-0.7.0/analogsea/man/firewalls.Rd |only analogsea-0.7.0/analogsea/man/snapshots.Rd | 6 analogsea-0.7.0/analogsea/man/space_create.Rd |only analogsea-0.7.0/analogsea/man/spaces.Rd | 52 -- analogsea-0.7.0/analogsea/man/spaces_GET.Rd |only analogsea-0.7.0/analogsea/man/spaces_info.Rd |only analogsea-0.7.0/analogsea/man/tag_resource_delete.Rd | 4 analogsea-0.7.0/analogsea/man/volumes.Rd | 12 analogsea-0.7.0/analogsea/tests/testthat/test-droplet_create.R |only analogsea-0.7.0/analogsea/vignettes/analogsea.Rmd |only 66 files changed, 633 insertions(+), 461 deletions(-)
Title: The Self-Controlled Case Series Method
Description: Various self-controlled case series models used to investigate
associations between time-varying exposures such as vaccines or
other drugs or non drug exposures and an adverse event can be
fitted. Detailed information on the self-controlled case series
method and its extensions with more examples can be found in
Farrington, P., Whitaker, H., and Ghebremichael Weldeselassie, Y.
(2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies:
A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press)
and <https://sccs-studies.info>.
Author: Yonas Ghebremichael Weldeselassie, Heather Whitaker, Paddy Farrington
Maintainer: "Yonas Ghebremichael-Weldeselassie" <y.weldeselassie@warwick.ac.uk>
Diff between SCCS versions 1.0 dated 2018-05-11 and 1.1 dated 2019-06-04
DESCRIPTION | 10 +++---- MD5 | 10 +++---- R/adrug_matrix.R | 72 +++++++++++++++++++++++++++------------------------- R/formatdata.R | 6 ++-- man/SCCS-package.Rd | 2 - man/standardsccs.Rd | 8 ++--- 6 files changed, 57 insertions(+), 51 deletions(-)
Title: Read 'IPUMS' Extract Files
Description: An easy way to import census, survey and geographic data provided by 'IPUMS'
into R plus tools to help use the associated metadata to make analysis easier. 'IPUMS'
data describing 1.4 billion individuals drawn from over 750 censuses and surveys is
available free of charge from our website <https://ipums.org>.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Minnesota Population Center [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between ipumsr versions 0.4.1 dated 2019-05-15 and 0.4.2 dated 2019-06-04
DESCRIPTION | 6 +-- MD5 | 30 ++++++++-------- NEWS.md | 4 ++ README.md | 2 - inst/doc/ipums-bigdata.html | 4 +- inst/doc/ipums-cps.html | 4 +- inst/doc/ipums-geography.html | 4 +- inst/doc/ipums-nhgis.R | 4 +- inst/doc/ipums-nhgis.html | 6 +-- inst/doc/ipums-terra.html | 8 ++-- inst/doc/ipums.R | 2 - inst/doc/ipums.Rmd | 76 +++++++++++++++++++++--------------------- inst/doc/ipums.html | 59 +++++++++++++++++--------------- inst/doc/value-labels.html | 4 +- man/ipumsr-package.Rd | 2 - vignettes/ipums.Rmd | 76 +++++++++++++++++++++--------------------- 16 files changed, 151 insertions(+), 140 deletions(-)
Title: Adaptive Optimal Two-Stage Designs in R
Description: Optimize one or two-arm, two-stage designs for clinical trials with respect to several
pre-implemented objective criteria or implement custom objectives.
Optimization under uncertainty and conditional (given stage-one outcome) constraints are supported.
Author: Kevin Kunzmann [aut, cre],
Maximilian Pilz [aut]
Maintainer: Kevin Kunzmann <kevin.kunzmann@mrc-bsu.cam.ac.uk>
Diff between adoptr versions 0.1.1 dated 2019-04-01 and 0.2.0 dated 2019-06-04
adoptr-0.1.1/adoptr/R/AffineScoreFunction.R |only adoptr-0.1.1/adoptr/R/boundary_designs.R |only adoptr-0.1.1/adoptr/inst/doc/score-and-constraints-arithmetic.R |only adoptr-0.1.1/adoptr/inst/doc/score-and-constraints-arithmetic.Rmd |only adoptr-0.1.1/adoptr/inst/doc/score-and-constraints-arithmetic.html |only adoptr-0.1.1/adoptr/man/AffineScore-class.Rd |only adoptr-0.1.1/adoptr/man/ConditionalScore-class.Rd |only adoptr-0.1.1/adoptr/man/Constraint-class.Rd |only adoptr-0.1.1/adoptr/man/ConstraintsCollection-class.Rd |only adoptr-0.1.1/adoptr/man/IntegralScore-class.Rd |only adoptr-0.1.1/adoptr/man/UnconditionalScore-class.Rd |only adoptr-0.1.1/adoptr/man/evaluate.Rd |only adoptr-0.1.1/adoptr/man/expected.Rd |only adoptr-0.1.1/adoptr/man/score-arithmetic.Rd |only adoptr-0.1.1/adoptr/tests/testthat/test_AffineScoreFunction.R |only adoptr-0.1.1/adoptr/vignettes/score-and-constraints-arithmetic.Rmd |only adoptr-0.2.0/adoptr/DESCRIPTION | 12 adoptr-0.2.0/adoptr/MD5 | 123 ++-- adoptr-0.2.0/adoptr/NAMESPACE | 14 adoptr-0.2.0/adoptr/NEWS.md | 18 adoptr-0.2.0/adoptr/R/CompositeScore.R |only adoptr-0.2.0/adoptr/R/ConditionalPower.R | 58 + adoptr-0.2.0/adoptr/R/ConditionalSampleSize.R | 47 + adoptr-0.2.0/adoptr/R/Scores.R | 301 ++-------- adoptr-0.2.0/adoptr/R/TwoStageDesign.R | 46 - adoptr-0.2.0/adoptr/R/adoptr.R | 35 - adoptr-0.2.0/adoptr/R/constraints.R | 282 +++------ adoptr-0.2.0/adoptr/R/minimize.R | 189 ++++++ adoptr-0.2.0/adoptr/R/regularization.R | 16 adoptr-0.2.0/adoptr/README.md | 39 - adoptr-0.2.0/adoptr/build/vignette.rds |binary adoptr-0.2.0/adoptr/inst/doc/adoptr.R | 14 adoptr-0.2.0/adoptr/inst/doc/adoptr.Rmd | 37 - adoptr-0.2.0/adoptr/inst/doc/adoptr.html | 59 + adoptr-0.2.0/adoptr/inst/doc/composite-scores.R |only adoptr-0.2.0/adoptr/inst/doc/composite-scores.Rmd |only adoptr-0.2.0/adoptr/inst/doc/composite-scores.html |only adoptr-0.2.0/adoptr/inst/doc/conditional-scores.R |only adoptr-0.2.0/adoptr/inst/doc/conditional-scores.Rmd |only adoptr-0.2.0/adoptr/inst/doc/conditional-scores.html |only adoptr-0.2.0/adoptr/inst/doc/defining-new-scores.R |only adoptr-0.2.0/adoptr/inst/doc/defining-new-scores.Rmd |only adoptr-0.2.0/adoptr/inst/doc/defining-new-scores.html |only adoptr-0.2.0/adoptr/inst/doc/working-with-priors.R | 10 adoptr-0.2.0/adoptr/inst/doc/working-with-priors.Rmd | 12 adoptr-0.2.0/adoptr/inst/doc/working-with-priors.html | 30 adoptr-0.2.0/adoptr/man/AverageN2-class.Rd | 22 adoptr-0.2.0/adoptr/man/ConditionalPower-class.Rd | 34 - adoptr-0.2.0/adoptr/man/ConditionalSampleSize-class.Rd | 37 + adoptr-0.2.0/adoptr/man/Constraints.Rd |only adoptr-0.2.0/adoptr/man/N1-class.Rd | 19 adoptr-0.2.0/adoptr/man/Scores.Rd |only adoptr-0.2.0/adoptr/man/TwoStageDesign-class.Rd | 4 adoptr-0.2.0/adoptr/man/adoptr.Rd | 28 adoptr-0.2.0/adoptr/man/boundary-designs.Rd | 2 adoptr-0.2.0/adoptr/man/composite.Rd |only adoptr-0.2.0/adoptr/man/minimize.Rd | 11 adoptr-0.2.0/adoptr/man/plot-TwoStageDesign-method.Rd | 2 adoptr-0.2.0/adoptr/man/subject_to.Rd | 49 - adoptr-0.2.0/adoptr/tests/testthat/Rplots.pdf |binary adoptr-0.2.0/adoptr/tests/testthat/test_ConditionalScores.R | 113 +-- adoptr-0.2.0/adoptr/tests/testthat/test_ContinuousPrior.R | 120 +-- adoptr-0.2.0/adoptr/tests/testthat/test_DataDistribution.R | 43 - adoptr-0.2.0/adoptr/tests/testthat/test_GaussLegendreIntegration.R | 47 - adoptr-0.2.0/adoptr/tests/testthat/test_GroupSequentialDesign.R | 85 +- adoptr-0.2.0/adoptr/tests/testthat/test_IntegralScores.R | 168 +---- adoptr-0.2.0/adoptr/tests/testthat/test_OneStageDesign.R | 122 +--- adoptr-0.2.0/adoptr/tests/testthat/test_PointMassPrior.R | 88 +- adoptr-0.2.0/adoptr/tests/testthat/test_TwoStageDesign.R | 113 +-- adoptr-0.2.0/adoptr/tests/testthat/test_composite.R |only adoptr-0.2.0/adoptr/tests/testthat/test_constraints.R | 118 +-- adoptr-0.2.0/adoptr/tests/testthat/test_minimize.R | 169 ++--- adoptr-0.2.0/adoptr/tests/testthat/test_regularizer.R | 40 - adoptr-0.2.0/adoptr/tests/testthat/test_tunable.R | 230 ++++--- adoptr-0.2.0/adoptr/vignettes/adoptr.Rmd | 37 - adoptr-0.2.0/adoptr/vignettes/composite-scores.Rmd |only adoptr-0.2.0/adoptr/vignettes/conditional-scores.Rmd |only adoptr-0.2.0/adoptr/vignettes/defining-new-scores.Rmd |only adoptr-0.2.0/adoptr/vignettes/working-with-priors.Rmd | 12 79 files changed, 1508 insertions(+), 1547 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression as described for example
in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>
Diff between sdcTable versions 0.27 dated 2019-02-28 and 0.28 dated 2019-06-04
DESCRIPTION | 12 - MD5 | 107 ++++++++-------- NAMESPACE | 25 +-- NEWS.md | 17 ++ R/0_imports.R | 5 R/classes.R | 16 +- R/contributing_indices.R |only R/createJJFormat.R |only R/defunct.R | 22 ++- R/generics_cutList.r | 8 - R/generics_dataObj.r | 6 R/generics_dimVar.r | 6 R/generics_linProb.r | 6 R/generics_multiple.r | 2 R/generics_problemInstance.r | 2 R/generics_simpleTriplet.r | 6 R/helper_functions.r | 107 +++++++++------- R/makeProblem.R | 188 ++++++++++++++++------------- R/methods_class_dataObj.r | 8 - R/methods_class_sdcProblem.r | 161 +----------------------- R/methods_multiple_classes.r | 71 +++++++--- R/primarySuppression.R | 171 ++++++++++++++++---------- R/utils.R |only R/writeJJFormat.R |only README.md | 11 + build/vignette.rds |binary data/microData1.RData |binary data/microData2.RData |binary data/problem.RData |binary data/problemWithSupps.RData |binary data/protectedData.RData |binary inst/doc/sdcTable.html | 147 +++++++++++----------- man/calc.cutList-method.Rd | 1 man/calc.dimVar-method.Rd | 1 man/calc.linProb-method.Rd | 1 man/calc.multiple-method.Rd | 1 man/calc.problemInstance-method.Rd | 1 man/calc.simpleTriplet-method.Rd | 1 man/contributing_indices.Rd |only man/createJJFormat.Rd |only man/defunct-sdcTable.Rd | 8 - man/get.cutList-method.Rd | 1 man/get.dataObj-method.Rd | 1 man/get.dimVar-method.Rd | 1 man/get.linProb-method.Rd | 1 man/get.simpleTriplet-method.Rd | 1 man/init.cutList-method.Rd | 1 man/init.dataObj-method.Rd | 1 man/init.dimVar-method.Rd | 1 man/init.simpleTriplet-method.Rd | 1 man/makeProblem.Rd | 122 ++++++++++-------- man/primarySuppression.Rd | 108 ++++++++++------ man/set.cutList-method.Rd | 1 man/set.dataObj-method.Rd | 1 man/set.linProb-method.Rd | 1 man/writeJJFormat.Rd |only tests/testthat/test-contributing_indices.r |only tests/testthat/test-jjformat.r |only tests/testthat/test-primarySuppression.r | 79 ++++++++++++ 59 files changed, 784 insertions(+), 655 deletions(-)
Title: Stochastic Complexity-Based Conditional Independence Test for
Discrete Data
Description: An efficient implementation of SCCI using 'Rcpp'. SCCI is short for the Stochastic Complexity-based Conditional Independence criterium (Marx and Vreeken, 2019). SCCI is an asymptotically unbiased and L2 consistent estimator of (conditional) mutual information for discrete data.
Author: Alexander Marx [aut,cre] Jilles Vreeken [aut]
Maintainer: Alexander Marx <amarx@mpi-inf.mpg.de>
Diff between SCCI versions 1.1 dated 2019-05-24 and 1.2 dated 2019-06-04
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NEWS.md |only R/sc.R | 19 ++++++++++++------- man/regret.Rd |only src/sc.cpp | 10 ++++++++++ src/sc.h | 3 +++ 7 files changed, 35 insertions(+), 15 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. 'PINSPlus' supports both single and multiple data types. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust to noise and data perturbation. 'PINSPlus' is fast and it supports parallel computing on Windows, Linux, and Mac OS.
Author: Hung Nguyen, Sangam Shrestha and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>
Diff between PINSPlus versions 1.0.3 dated 2019-01-07 and 2.0.0 dated 2019-06-04
DESCRIPTION | 10 ++--- MD5 | 20 +++++----- R/perturbation-clustering-helpers.R | 71 ++++++++++++++++++++++-------------- R/perturbation-clustering.R | 39 +++++++++++++++---- build/vignette.rds |binary inst/doc/PINSPlus.Rmd | 1 inst/doc/PINSPlus.pdf |binary man/PerturbationClustering.Rd | 6 ++- man/SubtypingOmicsData.Rd | 4 +- vignettes/PINSPlus.Rmd | 1 vignettes/PINSPlus.html | 20 +++++----- 11 files changed, 109 insertions(+), 63 deletions(-)
Title: Annotation of Metabolites from Liquid Chromatography-Mass
Spectrometry Data
Description: Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis.
Author: Manuel David Peris Diaz
Maintainer: Manuel David Peris Diaz <manuel.perisdiaz@uwr.edu.pl>
Diff between MetaboList versions 1.3 dated 2019-03-19 and 1.4 dated 2019-06-04
DESCRIPTION | 9 MD5 | 20 +- NAMESPACE | 4 R/AIF.R | 470 +++++++++++++++++++++++++++------------------------- R/Filter_AIF.R |only R/FullMS.R | 37 ++-- R/PeakGroup.R | 2 R/PeakGroupMS1.R |only R/ScoresDIA.R | 35 +-- man/AIF.rd | 2 man/Filter_AIF.rd |only man/FullMS.rd | 2 man/PeakGroupMS1.rd |only 13 files changed, 313 insertions(+), 268 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' and other model objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models, mixed effects models and Bayesian models. However, some
of the functions also deal with other statistical measures,
like Cronbach's Alpha, Cramer's V, Phi etc.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.17.4 dated 2019-03-15 and 0.17.5 dated 2019-06-04
sjstats-0.17.4/sjstats/R/HDI.R |only sjstats-0.17.4/sjstats/R/colour_tools.R |only sjstats-0.17.4/sjstats/R/compute_variances.R |only sjstats-0.17.4/sjstats/R/converge_ok.R |only sjstats-0.17.4/sjstats/R/credint.R |only sjstats-0.17.4/sjstats/R/equi_test.R |only sjstats-0.17.4/sjstats/R/icc.R |only sjstats-0.17.4/sjstats/R/internal_consistency.R |only sjstats-0.17.4/sjstats/R/link_inverse.R |only sjstats-0.17.4/sjstats/R/mcse.R |only sjstats-0.17.4/sjstats/R/model_family.R |only sjstats-0.17.4/sjstats/R/model_frame.R |only sjstats-0.17.4/sjstats/R/n_eff.R |only sjstats-0.17.4/sjstats/R/pca.R |only sjstats-0.17.4/sjstats/R/pred_vars.R |only sjstats-0.17.4/sjstats/R/predictive_accuracy.R |only sjstats-0.17.4/sjstats/R/r2.R |only sjstats-0.17.4/sjstats/R/re_grp_var.R |only sjstats-0.17.4/sjstats/R/resp_val.R |only sjstats-0.17.4/sjstats/R/resp_var.R |only sjstats-0.17.4/sjstats/R/rmse.R |only sjstats-0.17.4/sjstats/R/rope.R |only sjstats-0.17.4/sjstats/R/var_names.R |only sjstats-0.17.4/sjstats/man/cod.Rd |only sjstats-0.17.4/sjstats/man/converge_ok.Rd |only sjstats-0.17.4/sjstats/man/dot-badlink.Rd |only sjstats-0.17.4/sjstats/man/dot-collapse_cond.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_beta.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_dispersion.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_fixed.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_random.Rd |only sjstats-0.17.4/sjstats/man/dot-get_variance_residual.Rd |only sjstats-0.17.4/sjstats/man/hdi.Rd |only sjstats-0.17.4/sjstats/man/icc.Rd |only sjstats-0.17.4/sjstats/man/pca.Rd |only sjstats-0.17.4/sjstats/man/pred_accuracy.Rd |only sjstats-0.17.4/sjstats/man/pred_vars.Rd |only sjstats-0.17.4/sjstats/man/re_var.Rd |only sjstats-0.17.4/sjstats/man/reliab_test.Rd |only sjstats-0.17.4/sjstats/man/rmse.Rd |only sjstats-0.17.4/sjstats/tests/testthat/test-equi_test.R |only sjstats-0.17.4/sjstats/tests/testthat/test-hdi.R |only sjstats-0.17.4/sjstats/tests/testthat/test-icc_bayes.R |only sjstats-0.17.4/sjstats/tests/testthat/test-icc_r2.R |only sjstats-0.17.4/sjstats/tests/testthat/test-icc_stan.R |only sjstats-0.17.4/sjstats/tests/testthat/test-is_singular.R |only sjstats-0.17.4/sjstats/tests/testthat/test-mcse.R |only sjstats-0.17.4/sjstats/tests/testthat/test-model-information.R |only sjstats-0.17.4/sjstats/tests/testthat/test-model_frame.R |only sjstats-0.17.4/sjstats/tests/testthat/test-neff.R |only sjstats-0.17.4/sjstats/tests/testthat/test-pred_vars.R |only sjstats-0.17.4/sjstats/tests/testthat/test-re_grp_var.R |only sjstats-0.17.4/sjstats/tests/testthat/test-re_var-bayes.R |only sjstats-0.17.4/sjstats/tests/testthat/test-re_var.R |only sjstats-0.17.4/sjstats/tests/testthat/test-resp_val.R |only sjstats-0.17.4/sjstats/tests/testthat/test-resp_val2.R |only sjstats-0.17.4/sjstats/tests/testthat/test-se_icc.R |only sjstats-0.17.4/sjstats/tests/testthat/test-var_names.R |only sjstats-0.17.5/sjstats/DESCRIPTION | 21 sjstats-0.17.5/sjstats/MD5 | 156 - sjstats-0.17.5/sjstats/NAMESPACE | 160 - sjstats-0.17.5/sjstats/NEWS.md | 58 sjstats-0.17.5/sjstats/R/S3-methods.R | 998 ---------- sjstats-0.17.5/sjstats/R/auto_prior.R | 11 sjstats-0.17.5/sjstats/R/boot_ci.R | 6 sjstats-0.17.5/sjstats/R/check_model_assumptions.R | 46 sjstats-0.17.5/sjstats/R/cv.R | 37 sjstats-0.17.5/sjstats/R/cv_error.R | 11 sjstats-0.17.5/sjstats/R/eta_sq.R | 97 sjstats-0.17.5/sjstats/R/gof.R | 93 sjstats-0.17.5/sjstats/R/grpmean.R | 7 sjstats-0.17.5/sjstats/R/helpfunctions.R | 10 sjstats-0.17.5/sjstats/R/is_prime.R | 48 sjstats-0.17.5/sjstats/R/mediation.R | 68 sjstats-0.17.5/sjstats/R/mwu.R | 2 sjstats-0.17.5/sjstats/R/overdisp.R | 287 +- sjstats-0.17.5/sjstats/R/p_value.R | 9 sjstats-0.17.5/sjstats/R/phi.R | 20 sjstats-0.17.5/sjstats/R/prop.R | 2 sjstats-0.17.5/sjstats/R/re-exports.R |only sjstats-0.17.5/sjstats/R/samplesize_lme.R | 17 sjstats-0.17.5/sjstats/R/se.R | 112 - sjstats-0.17.5/sjstats/R/std_b.R | 15 sjstats-0.17.5/sjstats/R/svy_scale_weights.R | 12 sjstats-0.17.5/sjstats/R/tidy_stan.R | 82 sjstats-0.17.5/sjstats/R/xtab_statistics.R | 3 sjstats-0.17.5/sjstats/build/partial.rdb |binary sjstats-0.17.5/sjstats/build/vignette.rds |binary sjstats-0.17.5/sjstats/inst/doc/anova-statistics.html | 37 sjstats-0.17.5/sjstats/inst/doc/bayesian-statistics.R | 79 sjstats-0.17.5/sjstats/inst/doc/bayesian-statistics.Rmd | 149 - sjstats-0.17.5/sjstats/inst/doc/bayesian-statistics.html | 619 +----- sjstats-0.17.5/sjstats/inst/doc/mixedmodels-statistics.R | 41 sjstats-0.17.5/sjstats/inst/doc/mixedmodels-statistics.Rmd | 129 - sjstats-0.17.5/sjstats/inst/doc/mixedmodels-statistics.html | 197 - sjstats-0.17.5/sjstats/man/boot_ci.Rd | 6 sjstats-0.17.5/sjstats/man/check_assumptions.Rd | 35 sjstats-0.17.5/sjstats/man/chisq_gof.Rd |only sjstats-0.17.5/sjstats/man/cv.Rd |only sjstats-0.17.5/sjstats/man/cv_error.Rd | 3 sjstats-0.17.5/sjstats/man/eta_sq.Rd | 30 sjstats-0.17.5/sjstats/man/mediation.Rd |only sjstats-0.17.5/sjstats/man/overdisp.Rd | 128 - sjstats-0.17.5/sjstats/man/reexports.Rd | 17 sjstats-0.17.5/sjstats/man/scale_weights.Rd | 12 sjstats-0.17.5/sjstats/man/se.Rd | 15 sjstats-0.17.5/sjstats/man/tidy_stan.Rd | 10 sjstats-0.17.5/sjstats/man/xtab_statistics.Rd | 17 sjstats-0.17.5/sjstats/vignettes/bayesian-statistics.Rmd | 149 - sjstats-0.17.5/sjstats/vignettes/mixedmodels-statistics.Rmd | 129 - 110 files changed, 1171 insertions(+), 3019 deletions(-)
Title: Predicting Economic Variables using Dynamic Factor Models
Description: It contains the tools to implement dynamic factor models to forecast economic variables. The user will be able to construct pseudo real time vintages, use information criteria for determining the number of factors and shocks, estimate the model, and visualize results among other things.
Author: Daiane Marcolino de Mattos [aut, cre],
Pedro Costa Ferreira [aut],
Serge de Valk [aut],
Guilherme Branco Gomes [aut]
Maintainer: Daiane Marcolino de Mattos <daiane.mattos@fgv.br>
Diff between nowcasting versions 1.1.1 dated 2019-05-02 and 1.1.2 dated 2019-06-04
DESCRIPTION | 8 +- MD5 | 24 +++---- R/Bpanel.R | 4 - R/ICfactors.R | 8 +- R/ICshocks.R | 31 ++++++--- R/method_2s.R | 63 ++++++++----------- R/nowcast.R | 171 +++++++++++++++++++++++++++++----------------------- R/nowcast.plot.R | 65 +++---------------- man/Bpanel.Rd | 6 - man/ICfactors.Rd | 2 man/ICshocks.Rd | 11 +-- man/nowcast.Rd | 53 +++++++--------- man/nowcast.plot.Rd | 30 +++------ 13 files changed, 223 insertions(+), 253 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.
Author: Stéphane Dray, David Bauman, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.3-4 dated 2019-02-27 and 0.3-7 dated 2019-06-04
adespatial-0.3-4/adespatial/src/forward.h |only adespatial-0.3-7/adespatial/DESCRIPTION | 13 adespatial-0.3-7/adespatial/MD5 | 117 +- adespatial-0.3-7/adespatial/R/Cperiodogram.R | 2 adespatial-0.3-7/adespatial/R/WRperiodogram.R | 2 adespatial-0.3-7/adespatial/R/aem.build.binary.R | 2 adespatial-0.3-7/adespatial/R/aem.weight.edges.R | 3 adespatial-0.3-7/adespatial/R/beta.div.R | 23 adespatial-0.3-7/adespatial/R/beta.div.comp.R | 12 adespatial-0.3-7/adespatial/R/dist.ldc.R | 234 ++--- adespatial-0.3-7/adespatial/R/listw.select.R | 2 adespatial-0.3-7/adespatial/R/mem.select.R | 4 adespatial-0.3-7/adespatial/R/mfpa.R | 42 - adespatial-0.3-7/adespatial/R/moran.bounds.R | 2 adespatial-0.3-7/adespatial/R/moran.randtest.R | 2 adespatial-0.3-7/adespatial/R/moranNP.randtest.R | 4 adespatial-0.3-7/adespatial/R/mspa.R | 4 adespatial-0.3-7/adespatial/R/msr.4thcorner.R | 26 adespatial-0.3-7/adespatial/R/msr.R | 2 adespatial-0.3-7/adespatial/R/msr.mantelrtest.R | 39 adespatial-0.3-7/adespatial/R/msr.varipart.R | 26 adespatial-0.3-7/adespatial/R/multispati.R | 5 adespatial-0.3-7/adespatial/R/plot.orthobasisSp.R | 6 adespatial-0.3-7/adespatial/R/scalogram.R | 6 adespatial-0.3-7/adespatial/R/stimodels.R | 2 adespatial-0.3-7/adespatial/build/vignette.rds |binary adespatial-0.3-7/adespatial/inst/doc/tutorial.R | 48 + adespatial-0.3-7/adespatial/inst/doc/tutorial.Rmd | 153 +++ adespatial-0.3-7/adespatial/inst/doc/tutorial.html | 647 ++++++++++++---- adespatial-0.3-7/adespatial/man/Cperiodogram.Rd | 2 adespatial-0.3-7/adespatial/man/WRperiodogram.Rd | 2 adespatial-0.3-7/adespatial/man/aem.build.binary.Rd | 2 adespatial-0.3-7/adespatial/man/beta.div.Rd | 23 adespatial-0.3-7/adespatial/man/beta.div.comp.Rd | 12 adespatial-0.3-7/adespatial/man/dist.ldc.Rd | 198 ++-- adespatial-0.3-7/adespatial/man/listw.select.Rd | 2 adespatial-0.3-7/adespatial/man/mem.select.Rd | 4 adespatial-0.3-7/adespatial/man/mfpa.Rd | 42 - adespatial-0.3-7/adespatial/man/moran.bounds.Rd | 2 adespatial-0.3-7/adespatial/man/moran.randtest.Rd | 2 adespatial-0.3-7/adespatial/man/moranNP.randtest.Rd | 4 adespatial-0.3-7/adespatial/man/mspa.Rd | 4 adespatial-0.3-7/adespatial/man/msr.4thcorner.Rd | 14 adespatial-0.3-7/adespatial/man/msr.Rd | 2 adespatial-0.3-7/adespatial/man/msr.mantelrtest.Rd | 23 adespatial-0.3-7/adespatial/man/msr.varipart.Rd | 12 adespatial-0.3-7/adespatial/man/multispati.Rd | 4 adespatial-0.3-7/adespatial/man/plot.orthobasisSp.Rd | 6 adespatial-0.3-7/adespatial/man/scalogram.Rd | 6 adespatial-0.3-7/adespatial/man/stimodels.Rd | 2 adespatial-0.3-7/adespatial/src/adesub.c |only adespatial-0.3-7/adespatial/src/adesub.h |only adespatial-0.3-7/adespatial/src/betadiv.c | 3 adespatial-0.3-7/adespatial/src/buildbinary.c | 49 - adespatial-0.3-7/adespatial/src/forward.c | 167 ---- adespatial-0.3-7/adespatial/src/init.c | 2 adespatial-0.3-7/adespatial/src/stipermute.c | 9 adespatial-0.3-7/adespatial/src/testsmoran.c | 75 - adespatial-0.3-7/adespatial/vignettes/adespatial.bib | 11 adespatial-0.3-7/adespatial/vignettes/listw_explore.png |binary adespatial-0.3-7/adespatial/vignettes/tutorial.Rmd | 153 +++ 61 files changed, 1327 insertions(+), 938 deletions(-)
Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from
data in Javascript object notation (JSON) format.
This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code
and allows R programmers to read and convert JSON content to R objects.
This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON
and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases.
This package uses methods and is readily extensible by defining methods for different classes,
vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R.
The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional
options to allow customizing the generation and processing of JSON content.
This package uses libjson rather than implementing yet another JSON parser. The aim is to support
other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang [aut, cre] (<https://orcid.org/0000-0003-0159-1546>),
Jonathan Wallace [aut] (aka ninja9578, author of included libjson
sources)
Maintainer: ORPHANED
Diff between RJSONIO versions 1.3-1.1 dated 2018-11-14 and 1.3-1.2 dated 2019-06-04
RJSONIO-1.3-1.1/RJSONIO/configure.in |only RJSONIO-1.3-1.2/RJSONIO/DESCRIPTION | 6 +++--- RJSONIO-1.3-1.2/RJSONIO/MD5 | 8 ++++---- RJSONIO-1.3-1.2/RJSONIO/R/json.R | 2 +- RJSONIO-1.3-1.2/RJSONIO/configure.ac |only RJSONIO-1.3-1.2/RJSONIO/src/init.c | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: ORPHANED
Diff between geiger versions 2.0.6.1 dated 2019-01-16 and 2.0.6.2 dated 2019-06-04
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/TESTING.R | 2 +- R/gbresolve.R | 4 ++-- R/likelihood.R | 2 +- R/proposals.R | 2 +- R/traits.R | 2 +- R/utilities-phylo.R | 2 +- src/init.c | 20 ++++++++++---------- 9 files changed, 28 insertions(+), 28 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the 'stringr'
or 'stringi' packages. The foremost of these is the extraction of numbers
from strings. 'stringr' and 'stringi' make you figure out the regular
expression for yourself; 'strex' takes care of this for you. There are many
other handy functionalities in 'strex'. Contributions to this package are
encouraged: it is intended as a miscellany of string manipulation functions
that cannot be found in 'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.0.2 dated 2019-05-28 and 1.0.3 dated 2019-06-04
DESCRIPTION | 6 - MD5 | 120 ++++++++++++++--------------- NEWS.md | 6 + R/after.R | 5 - R/all-equal.R | 41 +++++++-- R/alphord.R | 4 R/arg-match.R | 21 +++-- R/before.R | 9 +- R/camel-case.R | 5 - R/can-be-num.R | 1 R/currency.R | 12 +- R/elem.R | 13 +-- R/extract-non-nums.R | 14 ++- R/extract-nums.R | 25 ++++-- R/give-ext.R | 5 - R/locate.R | 3 R/num-after.R | 4 R/num-before.R | 4 R/remove.R | 5 - R/singleize.R | 5 - R/split-by-nums.R | 6 - R/to-vec.R | 5 - R/trim.R | 5 - R/utils.R | 27 +++--- build/partial.rdb |binary inst/doc/alphordering-numbers.html | 4 inst/doc/argument-matching.html | 4 inst/doc/before-and-after.html | 4 inst/doc/important-miscellany.html | 4 inst/doc/numbers-in-strings.html | 4 man/before-and-after.Rd | 1 man/str_before_last_dot.Rd | 1 man/str_can_be_numeric.Rd | 1 man/str_elem.Rd | 1 man/str_elems.Rd | 1 man/str_extract_non_numerics.Rd | 1 man/str_extract_numbers.Rd | 1 man/str_give_ext.Rd | 1 man/str_match_arg.Rd | 1 man/str_nth_non_numeric.Rd | 1 man/str_nth_number.Rd | 1 man/str_nth_number_after_mth.Rd | 1 man/str_nth_number_before_mth.Rd | 1 man/str_paste_elems.Rd | 1 man/str_remove_quoted.Rd | 1 man/str_singleize.Rd | 1 man/str_split_by_numbers.Rd | 1 man/str_split_camel_case.Rd | 1 man/str_to_vec.Rd | 1 man/str_trim_anything.Rd | 1 tests/testthat/test-RcppExports.R | 41 ++++++--- tests/testthat/test-after.R | 11 +- tests/testthat/test-arg-match.R | 34 ++++---- tests/testthat/test-before.R | 12 +- tests/testthat/test-currency.R | 64 +++++++++------ tests/testthat/test-elem.R | 25 +++--- tests/testthat/test-extract-non-numerics.R | 95 ++++++++++++++-------- tests/testthat/test-extract-nums.R | 16 ++- tests/testthat/test-locate.R | 95 ++++++++++++++-------- tests/testthat/test-num-after.R | 20 +++- tests/testthat/test-split-by-nums.R | 3 61 files changed, 480 insertions(+), 327 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages. These
include e.g. measures like r-squared, intraclass correlation coefficient
(Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>),
root mean squared error or functions to check models for overdispersion,
singularity or zero-inflation and more. Functions apply to a large variety of
regression models, including generalized linear models, mixed effects models
and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.1.0 dated 2019-04-24 and 0.2.0 dated 2019-06-04
performance-0.1.0/performance/R/error_rate.R |only performance-0.1.0/performance/R/hosmer_lemeshow.R |only performance-0.1.0/performance/R/mse.R |only performance-0.1.0/performance/R/r2_coxnell.R |only performance-0.1.0/performance/R/rmse.R |only performance-0.1.0/performance/R/rse.R |only performance-0.1.0/performance/man/dot-is_empty_object.Rd |only performance-0.1.0/performance/man/dot-obj_has_name.Rd |only performance-0.1.0/performance/man/error_rate.Rd |only performance-0.1.0/performance/man/hosmer_lemeshow.Rd |only performance-0.1.0/performance/man/mse.Rd |only performance-0.1.0/performance/man/r2_coxnell.Rd |only performance-0.1.0/performance/man/rmse.Rd |only performance-0.1.0/performance/man/rse.Rd |only performance-0.2.0/performance/DESCRIPTION | 25 performance-0.2.0/performance/MD5 | 143 +++-- performance-0.2.0/performance/NAMESPACE | 147 +++++ performance-0.2.0/performance/NEWS.md |only performance-0.2.0/performance/R/binned_residuals.R | 4 performance-0.2.0/performance/R/check_autocorrelation.R |only performance-0.2.0/performance/R/check_collinearity.R |only performance-0.2.0/performance/R/check_distribution.R |only performance-0.2.0/performance/R/check_heteroscedasticity.R |only performance-0.2.0/performance/R/check_model.R |only performance-0.2.0/performance/R/check_model_diagnostics.R |only performance-0.2.0/performance/R/check_normality.R |only performance-0.2.0/performance/R/check_outliers.R |only performance-0.2.0/performance/R/check_singularity.R | 6 performance-0.2.0/performance/R/helpers.R | 56 +- performance-0.2.0/performance/R/icc.R | 89 +-- performance-0.2.0/performance/R/logLik.R |only performance-0.2.0/performance/R/looic.R | 2 performance-0.2.0/performance/R/model_performance.R | 54 +- performance-0.2.0/performance/R/model_performance.bayesian.R | 78 +- performance-0.2.0/performance/R/model_performance.lm.R | 95 +++ performance-0.2.0/performance/R/model_performance.mixed.R | 34 + performance-0.2.0/performance/R/performance_accuracy.R |only performance-0.2.0/performance/R/performance_aicc.R |only performance-0.2.0/performance/R/performance_hosmer.R |only performance-0.2.0/performance/R/performance_logloss.R |only performance-0.2.0/performance/R/performance_mse.R |only performance-0.2.0/performance/R/performance_pcp.R |only performance-0.2.0/performance/R/performance_rmse.R |only performance-0.2.0/performance/R/performance_roc.R |only performance-0.2.0/performance/R/performance_rse.R |only performance-0.2.0/performance/R/performance_score.R |only performance-0.2.0/performance/R/plot-methods.R |only performance-0.2.0/performance/R/print-methods.R | 238 ++++++-- performance-0.2.0/performance/R/r2.R | 268 ++++++++-- performance-0.2.0/performance/R/r2_bayes.R | 85 ++- performance-0.2.0/performance/R/r2_coxsnell.R |only performance-0.2.0/performance/R/r2_kl.R | 2 performance-0.2.0/performance/R/r2_loo.R | 4 performance-0.2.0/performance/R/r2_mcfadden.R | 45 + performance-0.2.0/performance/R/r2_mckelvey.R |only performance-0.2.0/performance/R/r2_nagelkerke.R | 41 + performance-0.2.0/performance/R/r2_nakagawa.R | 19 performance-0.2.0/performance/R/r2_tjur.R | 2 performance-0.2.0/performance/R/r2_xu.R |only performance-0.2.0/performance/R/r2_zeroinflated.R |only performance-0.2.0/performance/R/residuals.R |only performance-0.2.0/performance/R/skewness_kurtosis.R |only performance-0.2.0/performance/R/sysdata.rda |only performance-0.2.0/performance/README.md | 44 - performance-0.2.0/performance/build/partial.rdb |binary performance-0.2.0/performance/man/check_autocorrelation.Rd |only performance-0.2.0/performance/man/check_collinearity.Rd |only performance-0.2.0/performance/man/check_distribution.Rd |only performance-0.2.0/performance/man/check_heteroscedasticity.Rd |only performance-0.2.0/performance/man/check_model.Rd |only performance-0.2.0/performance/man/check_normality.Rd |only performance-0.2.0/performance/man/check_outliers.Rd |only performance-0.2.0/performance/man/classify_distribution.Rd |only performance-0.2.0/performance/man/icc.Rd | 29 - performance-0.2.0/performance/man/model_performance.Rd | 23 performance-0.2.0/performance/man/model_performance.lm.Rd | 30 - performance-0.2.0/performance/man/model_performance.merMod.Rd | 10 performance-0.2.0/performance/man/model_performance.stanreg.Rd | 20 performance-0.2.0/performance/man/performance_accuracy.Rd |only performance-0.2.0/performance/man/performance_aicc.Rd |only performance-0.2.0/performance/man/performance_hosmer.Rd |only performance-0.2.0/performance/man/performance_logloss.Rd |only performance-0.2.0/performance/man/performance_mse.Rd |only performance-0.2.0/performance/man/performance_pcp.Rd |only performance-0.2.0/performance/man/performance_rmse.Rd |only performance-0.2.0/performance/man/performance_roc.Rd |only performance-0.2.0/performance/man/performance_rse.Rd |only performance-0.2.0/performance/man/performance_score.Rd |only performance-0.2.0/performance/man/r2.Rd | 8 performance-0.2.0/performance/man/r2_coxsnell.Rd |only performance-0.2.0/performance/man/r2_mcfadden.Rd | 5 performance-0.2.0/performance/man/r2_mckelvey.Rd |only performance-0.2.0/performance/man/r2_xu.Rd |only performance-0.2.0/performance/man/r2_zeroinflated.Rd |only performance-0.2.0/performance/tests/testthat/test-check_convergence.R | 4 performance-0.2.0/performance/tests/testthat/test-check_singularity.R | 2 performance-0.2.0/performance/tests/testthat/test-coxph.R |only performance-0.2.0/performance/tests/testthat/test-icc.R | 42 - performance-0.2.0/performance/tests/testthat/test-model_performance-various.R |only performance-0.2.0/performance/tests/testthat/test-model_performance.bayesian.R | 19 performance-0.2.0/performance/tests/testthat/test-r2_coxsnell.R | 6 performance-0.2.0/performance/tests/testthat/test-r2_mcfadden.R | 19 performance-0.2.0/performance/tests/testthat/test-r2_nagelkerke.R | 12 performance-0.2.0/performance/tests/testthat/test-r2_nakagawa.R | 7 performance-0.2.0/performance/tests/testthat/test-r2_tjur.R | 7 performance-0.2.0/performance/tests/testthat/test-r2_zeroinflated.R |only 106 files changed, 1276 insertions(+), 448 deletions(-)
Title: Interface to 'Azure Resource Manager'
Description: A lightweight but powerful R interface to the 'Azure Resource Manager' REST API. The package exposes classes and methods for 'OAuth' authentication and working with subscriptions and resource groups. It also provides functionality for creating and deleting 'Azure' resources and deploying templates. While 'AzureRMR' can be used to manage any 'Azure' service, it can also be extended by other packages to provide extra functionality for specific services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureRMR versions 2.1.1 dated 2019-05-12 and 2.1.2 dated 2019-06-04
AzureRMR-2.1.1/AzureRMR/tests/testthat/test05_template.R |only AzureRMR-2.1.2/AzureRMR/DESCRIPTION | 12 +- AzureRMR-2.1.2/AzureRMR/MD5 | 24 ++-- AzureRMR-2.1.2/AzureRMR/NAMESPACE | 4 AzureRMR-2.1.2/AzureRMR/NEWS.md | 5 AzureRMR-2.1.2/AzureRMR/R/az_template.R | 51 +++++----- AzureRMR-2.1.2/AzureRMR/R/build_tpl_json.R |only AzureRMR-2.1.2/AzureRMR/README.md | 8 - AzureRMR-2.1.2/AzureRMR/man/az_template.Rd | 4 AzureRMR-2.1.2/AzureRMR/man/build_template.Rd |only AzureRMR-2.1.2/AzureRMR/tests/resources/parameter_values.json |only AzureRMR-2.1.2/AzureRMR/tests/resources/parameters.json |only AzureRMR-2.1.2/AzureRMR/tests/resources/resources.json |only AzureRMR-2.1.2/AzureRMR/tests/resources/template.json | 13 +- AzureRMR-2.1.2/AzureRMR/tests/testthat/test04_resource.R | 2 AzureRMR-2.1.2/AzureRMR/tests/testthat/test05a_template_builders.R |only AzureRMR-2.1.2/AzureRMR/tests/testthat/test05b_template.R |only 17 files changed, 77 insertions(+), 46 deletions(-)
Title: Variable Table
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@fullerton.edu>
Diff between vtable versions 0.4.1 dated 2019-05-30 and 0.5.0 dated 2019-06-04
DESCRIPTION | 8 ++-- MD5 | 22 +++++++------ NAMESPACE | 1 R/labeltable.R |only R/vtable.R | 55 ++++++++++++--------------------- build/vignette.rds |binary inst/doc/vtable.R | 27 +++++++++++++++- inst/doc/vtable.Rmd | 75 ++++++++++++++++++++++++++++++++++++++++++++- inst/doc/vtable.html | 84 +++++++++++++++++++++++++++++++++++++++++++++++---- man/dftoHTML.Rd | 2 - man/labeltable.Rd |only man/vtable.Rd | 6 ++- vignettes/vtable.Rmd | 75 ++++++++++++++++++++++++++++++++++++++++++++- 13 files changed, 291 insertions(+), 64 deletions(-)
Title: Load Data From 'Yandex Direct'
Description: Load data from 'Yandex Direct' API V5
<https://tech.yandex.ru/direct/doc/dg/concepts/about-docpage/> into R.
Provide function for load lists of campaings, ads, keywords and other
objects from 'Yandex Direct' account. Also you can load statistic from
API 'Reports Service' <https://tech.yandex.ru/direct/doc/reports/reports-docpage/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between ryandexdirect versions 3.1.5 dated 2019-04-30 and 3.1.6 dated 2019-06-04
DESCRIPTION | 11 +- MD5 | 29 ++++-- NEWS.md | 7 + R/date_ranges.R |only R/yadirAuth.R | 5 - R/yadirGetAds.R | 2 R/yadirGetReport.R | 217 ++++++++++++-------------------------------------- R/yadirGetReportFun.R |only R/yadirGetToken.R | 2 README.md | 121 +++++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |only inst |only man/yadirGetReport.Rd | 8 + vignettes |only 15 files changed, 176 insertions(+), 226 deletions(-)
Title: Determine the Number of States in Hidden Markov Models via
Marginal Likelihood
Description: Provide functions to make estimate the number of states for a hidden Markov
model (HMM) using marginal likelihood method proposed by the authors.
See the Manual.pdf file a detail description of all functions, and a detail tutorial.
Author: Yang Chen, Cheng-Der Fuh, Chu-Lan Kao, and S. C. Kou.
Maintainer: Chu-Lan Michael Kao <chulankao@gmail.com>
Diff between HMMmlselect versions 0.1.1 dated 2019-05-30 and 0.1.3 dated 2019-06-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/HMMorderselectionfacility.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: The Serial Interface Package
Description: Enables reading and writing binary and ASCII data to
RS232/RS422/RS485 or any other virtual serial interfaces of the
computer.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Diff between serial versions 2.1.3 dated 2019-01-02 and 2.1.4 dated 2019-06-04
DESCRIPTION | 9 +-- MD5 | 32 ++++++------- R/init.R | 3 - R/listPorts.R | 8 +-- R/pkgname.R | 15 ++---- man/close.serialConnection.Rd | 39 +++++++--------- man/flush.serialConnection.Rd | 1 man/isOpen.Rd | 33 ++++++------- man/isOpen.default.Rd | 39 +++++++--------- man/isOpen.serialConnection.Rd | 39 +++++++--------- man/listPorts.Rd | 98 ++++++++++++++++++++--------------------- man/nBytesInQueue.Rd | 1 man/open.serialConnection.Rd | 39 +++++++--------- man/read.serialConnection.Rd | 1 man/serial.Rd | 21 ++------ man/serialConnection.Rd | 2 man/write.serialConnection.Rd | 1 17 files changed, 182 insertions(+), 199 deletions(-)
Title: The Moving Epidemic Method Web Application
Description: The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week. 'memapp' is a web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between memapp versions 2.12 dated 2019-01-29 and 2.13 dated 2019-06-04
DESCRIPTION | 16 MD5 | 22 R/runmemapp.R | 26 inst/shinyapp/helpers.R | 2024 +++---- inst/shinyapp/lang/en_GB.txt | 10 inst/shinyapp/lang/es_ES.txt | 10 inst/shinyapp/lang/fr_FR.txt | 10 inst/shinyapp/lang/ru_RU.txt | 10 inst/shinyapp/lang/translation.bin |binary inst/shinyapp/server.R | 9678 ++++++++++++++++++++----------------- inst/shinyapp/ui.R | 230 man/runmemapp.Rd | 22 12 files changed, 6498 insertions(+), 5560 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David W. Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.8.5 dated 2019-05-16 and 3.8.6 dated 2019-06-04
DESCRIPTION | 8 - MD5 | 91 +++++++++--------- NAMESPACE | 2 NEWS | 51 ++++++++++ R/BarChart.R | 2 R/Read.R | 67 +++++++++---- R/Regression.R | 12 +- R/bc.zmain.R | 48 +++++---- R/dn.zmain.R | 3 R/plt.zmain.R | 6 - R/rd_lbl.R |only R/reg.z3dnResidual.R | 2 R/reg.z5Plot.R | 36 +++---- R/reg.zRmd.R | 239 +++++++++++++++++++++++++++--------------------- R/ss.zfactor.R | 84 ++++++++++++---- R/ss.zreal.R | 135 +++++++++++++++++++-------- R/style.R | 6 - R/xAnd.R | 1 R/xNum.R | 2 R/xP.R | 19 ++- R/xU.R | 1 R/zzz.R | 22 ++-- man/BarChart.Rd | 48 ++++----- man/Histogram.Rd | 4 man/Logit.Rd | 4 man/Merge.Rd | 4 man/Nest.Rd | 4 man/PieChart.Rd | 4 man/Plot.Rd | 8 - man/Read.Rd | 48 +++++---- man/Recode.Rd | 8 - man/Regression.Rd | 14 +- man/Sort.Rd | 4 man/Subset.Rd | 6 - man/SummaryStats.Rd | 2 man/Transform.Rd | 6 - man/corCFA.Rd | 2 man/dataEmployee_lbl.Rd | 4 man/details.Rd | 2 man/factors.Rd | 6 - man/getColors.Rd | 2 man/label.Rd | 2 man/print_out.Rd | 2 man/print_outall.Rd | 2 man/regPlot.Rd | 2 man/style.Rd | 2 man/ttest.Rd | 2 47 files changed, 637 insertions(+), 392 deletions(-)