Title: Evaluate Treatment Selection Biomarkers
Description: Evaluate the performance of markers used to guide treatment selection decisions. Package includes functions to plot risk curves, evaluate marker performance, assess model calibration, and compare markers.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>
Diff between TreatmentSelection versions 1.1.2 dated 2014-06-16 and 1.2.0 dated 2016-01-15
TreatmentSelection-1.1.2/TreatmentSelection/inst/example/tutorial_files |only TreatmentSelection-1.2.0/TreatmentSelection/DESCRIPTION | 10 TreatmentSelection-1.2.0/TreatmentSelection/MD5 | 45 - TreatmentSelection-1.2.0/TreatmentSelection/NAMESPACE | 16 TreatmentSelection-1.2.0/TreatmentSelection/NEWS | 4 TreatmentSelection-1.2.0/TreatmentSelection/R/calibrate.trtsel.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/compare.trtsel.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/eval.trtsel.R | 5 TreatmentSelection-1.2.0/TreatmentSelection/R/get.plot.ci.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/get.plot.ci_disc.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.case.control.R | 6 TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.stratified.case.control.R | 12 TreatmentSelection-1.2.0/TreatmentSelection/R/myplotcompare.trtsel_disc.R | 13 TreatmentSelection-1.2.0/TreatmentSelection/R/plot.trtsel.R | 6 TreatmentSelection-1.2.0/TreatmentSelection/R/predcurvePLOT_gg.R | 4 TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOT_gg_disc.R | 18 TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOTcompare_gg_disc.R | 33 TreatmentSelection-1.2.0/TreatmentSelection/README.md | 2 TreatmentSelection-1.2.0/TreatmentSelection/inst/example/checkSubCohortEstimation.R |only TreatmentSelection-1.2.0/TreatmentSelection/inst/example/tutorial.Rmd | 6 TreatmentSelection-1.2.0/TreatmentSelection/inst/example/tutorial.html | 367 +++++----- TreatmentSelection-1.2.0/TreatmentSelection/man/TreatmentSelection-package.Rd | 4 TreatmentSelection-1.2.0/TreatmentSelection/man/plot.trtsel.Rd | 5 23 files changed, 331 insertions(+), 233 deletions(-)
More information about TreatmentSelection at CRAN
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Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group.
This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package also offers functions to print Q cards and to generate Q distributions for study administration.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.3.1 dated 2015-05-05 and 1.4.0 dated 2016-01-15
DESCRIPTION | 15 +++++++++------ MD5 | 40 ++++++++++++++++++++++++++++++---------- NAMESPACE | 19 +++++++++++++++++-- R/export.pqmethod.R |only R/loa.and.flags.R |only R/make.distribution.R |only R/qbstep.R |only R/qdc.R | 2 +- R/qfcharact.R | 6 +++--- R/qflag.R | 3 ++- R/qfsi.R |only R/qindtest.R |only R/qmb.plot.R |only R/qmb.summary.R |only R/qmboots.R |only R/qmethod.R | 5 ++--- R/qpcrustes.R |only R/qzscores.R | 16 ++++++++-------- man/export.pqmethod.Rd |only man/loa.and.flags.Rd |only man/make.distribution.Rd |only man/qbstep.Rd |only man/qfsi.Rd |only man/qindtest.Rd |only man/qmb.plot.Rd |only man/qmb.summary.Rd |only man/qmboots.Rd |only man/qmethod-package.Rd | 6 ++---- man/qmethod.Rd | 6 ++++-- man/qpcrustes.Rd |only man/qzscores.Rd | 2 +- 31 files changed, 79 insertions(+), 41 deletions(-)
Title: Probability and Statistics with R, Second Edition
Description: Functions and data sets for the text Probability and Statistics
with R, Second Edition.
Author: Alan T. Arnholt
Maintainer: Alan T. Arnholt <arnholtat@appstate.edu>
Diff between PASWR2 versions 1.0 dated 2014-11-21 and 1.0.2 dated 2016-01-15
DESCRIPTION | 15 - MD5 | 218 +++++++++--------- NAMESPACE | 46 +++ R/AgainStart.R | 43 +-- R/binogen.R | 74 +++--- R/checkingplots.R | 6 R/cisim.R | 2 R/ntester.R | 110 ++++----- R/srs.R | 62 ++--- R/wilcoxeTEST.R | 594 +++++++++++++++++++++++++------------------------- README.md | 39 ++- man/AGGRESSION.Rd | 13 - man/APPLE.Rd | 9 man/APTSIZE.Rd | 19 - man/BABERUTH.Rd | 33 +- man/BAC.Rd | 23 + man/BATTERY.Rd | 9 man/BIOMASS.Rd | 13 - man/BODYFAT.Rd | 21 - man/CALCULUS.Rd | 9 man/CARS2004.Rd | 7 man/CHIPS.Rd | 11 man/CIRCUIT.Rd | 19 - man/COSAMA.Rd | 15 - man/COWS.Rd | 11 man/DEPEND.Rd | 9 man/DROSOPHILA.Rd | 17 - man/ENGINEER.Rd | 13 - man/EPIDURAL.Rd | 7 man/EPIDURALF.Rd | 7 man/EURD.Rd | 5 man/FAGUS.Rd | 7 man/FCD.Rd | 5 man/FERTILIZE.Rd | 5 man/FOOD.Rd | 5 man/FORMULA1.Rd | 15 - man/GD.Rd | 9 man/GLUCOSE.Rd | 5 man/GRADES.Rd | 5 man/GROCERY.Rd | 13 - man/HARDWATER.Rd | 9 man/HOUSE.Rd | 5 man/HSWRESTLER.Rd | 10 man/HUBBLE.Rd | 9 man/INSURQUOTES.Rd | 7 man/JANKA.Rd | 5 man/KINDER.Rd | 9 man/LEDDIODE.Rd | 5 man/LOSTR.Rd | 9 man/MILKCARTON.Rd | 9 man/NC2010DMG.Rd | 9 man/PAMTEMP.Rd | 15 - man/PASWR2-package.Rd | 3 man/PHENYL.Rd | 7 man/PHONE.Rd | 7 man/RAT.Rd | 5 man/RATBP.Rd | 11 man/REFRIGERATOR.Rd | 9 man/ROACHEGGS.Rd | 9 man/SALINITY.Rd | 5 man/SATFRUIT.Rd | 7 man/SBIQ.Rd | 5 man/SCHIZO.Rd | 5 man/SCORE.Rd | 5 man/SDS4.Rd | 11 man/SIGN.test.Rd | 14 - man/SIMDATAST.Rd | 5 man/SIMDATAXT.Rd | 5 man/SOCCER.Rd | 5 man/STATTEMPS.Rd | 7 man/STSCHOOL.Rd | 5 man/SUNDIG.Rd | 5 man/SUNFLOWER.Rd | 9 man/SURFACESPAIN.Rd | 11 man/SWIMTIMES.Rd | 7 man/TENNIS.Rd | 5 man/TESTSCORES.Rd | 7 man/TIRE.Rd | 13 - man/TIREWEAR.Rd | 15 - man/TITANIC3.Rd | 9 man/TOE.Rd | 7 man/TOP20.Rd | 11 man/URLADDRESS.Rd | 13 - man/VIT2005.Rd | 9 man/WAIT.Rd | 5 man/WASHER.Rd | 5 man/WATER.Rd | 7 man/WCST.Rd | 7 man/WEIGHTGAIN.Rd | 9 man/WHEATSPAIN.Rd | 13 - man/WHEATUSA2004.Rd | 11 man/WOOL.Rd | 7 man/bino.gen.Rd | 6 man/checking.plots.Rd | 23 + man/cisim.Rd | 10 man/eda.Rd | 4 man/interval.plot.Rd | 4 man/ksdist.Rd | 3 man/ksldist.Rd | 3 man/multiplot.Rd | 4 man/normarea.Rd | 6 man/nsize.Rd | 8 man/ntester.Rd | 14 - man/oneway.plots.Rd | 8 man/srs.Rd | 7 man/tsum.test.Rd | 21 + man/twoway.plots.Rd | 9 man/wilcoxe.test.Rd | 15 - man/z.test.Rd | 42 +-- man/zsum.test.Rd | 49 ++-- 110 files changed, 1189 insertions(+), 1011 deletions(-)
Title: Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMP versions 1.3.1 dated 2013-05-08 and 1.4.2 dated 2016-01-15
DESCRIPTION | 24 +++------ MD5 | 109 +++++++++++++++++++++-------------------- NAMESPACE | 5 + NEWS | 18 ++++++ R/Barchart.data.R | 4 - R/C.alpha.multinomial.R | 5 - R/DM.MoM.R | 6 +- R/Data.filter.R | 9 +-- R/Dirichlet.multinomial.R | 7 +- R/LLDM.R |only R/MC.Xdc.statistics.R | 21 +++---- R/MC.Xmc.statistics.R | 21 +++---- R/MC.Xmcupo.statistics.R | 27 ++++------ R/MC.Xoc.statistics.R | 21 +++---- R/MC.Xsc.statistics.R | 12 +--- R/MC.ZT.statistics.R | 23 +++----- R/Multinomial.R | 7 +- R/T.statistics.R | 4 - R/Xdc.statistics.Hnull.Ha.R | 7 +- R/Xdc.statistics.MoM.R | 7 -- R/Xdc.statistics.R | 4 - R/Xmc.sevsample.R | 18 +++--- R/Xmc.statistics.Hnull.Ha.R | 11 +--- R/Xmc.statistics.R | 24 ++++----- R/Xmcupo.effectsize.R | 2 R/Xmcupo.sevsample.R | 39 +++++++------- R/Xmcupo.statistics.Hnull.Ha.R | 13 ++-- R/Xmcupo.statistics.R | 24 +++------ R/Xoc.statistics.Hnull.Ha.R | 9 +-- R/Xoc.statistics.MoM.R | 9 +-- R/Xoc.statistics.R | 4 - R/Xsc.onesample.R | 2 R/Xsc.statistics.R | 7 +- R/Z.statistics.R | 2 R/formatDataSets.R |only R/kullbackLeiber.R |only R/loglikDM.R | 11 ---- R/pioest.R | 2 R/weirMoM.R | 20 ++----- man/C.alpha.multinomial.Rd | 6 -- man/Data.filter.Rd | 3 - man/Dirichlet.multinomial.Rd | 2 man/HMP-internal.Rd | 1 man/HMP-package.Rd | 3 - man/MC.Xdc.statistics.Rd | 17 +++--- man/MC.Xmc.statistics.Rd | 10 ++- man/MC.Xmcupo.statistics.Rd | 14 ++--- man/MC.Xoc.statistics.Rd | 17 +++--- man/MC.Xsc.statistics.Rd | 12 ++-- man/Xdc.sevsample.Rd | 7 -- man/Xmc.sevsample.Rd | 8 --- man/Xmcupo.effectsize.Rd | 5 + man/Xmcupo.sevsample.Rd | 11 ---- man/Xoc.sevsample.Rd | 6 -- man/Xsc.onesample.Rd | 6 -- man/formatDataSets.Rd |only man/kullbackLeiber.Rd |only man/pioest.Rd | 5 + 58 files changed, 312 insertions(+), 359 deletions(-)
Title: Binary Graph Analysis Tools
Description: Tools to analyze binary graph objects.
Author: Terrence Brooks, Berkley Shands, Skye Buckner-Petty, Patricio S. La Rosa, Elena Deych, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between bingat versions 1.1 dated 2014-06-24 and 1.2.2 dated 2016-01-15
DESCRIPTION | 17 +++++----- MD5 | 68 ++++++++++++++++++++++++------------------ NAMESPACE | 6 ++- NEWS | 24 ++++++++++++++ R/estGStar.R | 4 +- R/estLogLik.R | 2 - R/estMLE.R | 4 +- R/full2lt.R | 2 - R/gaConsensus.R |only R/getGibbsMixture.R | 8 ++-- R/getLoglikeMixture.R | 8 +++- R/glmReg.R | 11 ++---- R/glrtPvalue.R | 76 +++++++++++++++++++++++------------------------ R/glrtReg.R | 6 +-- R/graphNetworkPlot.R | 6 +-- R/lrtPvalue.R |only R/pairedPvalue.R |only R/plotHeatmap.R |only R/plotMDS.R |only R/testGoF.R | 23 +++++++++----- man/BinGAT-package.Rd | 19 +++++++++-- man/braingraphs.Rd | 4 +- man/calcDistance.Rd | 2 - man/estGStar.Rd | 5 +-- man/estLogLik.Rd | 6 +-- man/estMLE.Rd | 7 +--- man/estTau.Rd | 6 +-- man/gaConsensus.Rd |only man/getGibbsMixture.Rd | 13 ++++---- man/getLoglikeMixture.Rd | 5 +-- man/getNumEdges.Rd | 2 - man/getNumNodes.Rd | 4 +- man/glrtPvalue.Rd | 30 ++++++------------ man/graphNetworkPlot.Rd | 2 - man/lrtPvalue.Rd |only man/pairedPvalue.Rd |only man/plotHeatmap.Rd |only man/plotMDS.Rd |only man/rGibbs.Rd | 4 +- man/testGoF.Rd | 13 ++++---- 40 files changed, 218 insertions(+), 169 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.0.5 dated 2015-12-24 and 2.0.7 dated 2016-01-15
DESCRIPTION | 8 - MD5 | 60 ++++---- R/data.utilities.R | 6 R/factor.utilities.R | 2 R/find.interaction.R | 2 R/generic.impute.rfsrc.R | 2 R/generic.predict.rfsrc.R | 314 +++++++++++++++++++++++----------------------- R/impute.rfsrc.R | 2 R/max.subtree.R | 2 R/plot.competing.risk.R | 2 R/plot.rfsrc.R | 2 R/plot.survival.R | 2 R/plot.variable.R | 2 R/predict.rfsrc.R | 2 R/print.rfsrc.R | 2 R/rf2rfz.R | 2 R/rfsrc.R | 268 +++++++++++++++++++-------------------- R/rfsrc.news.R | 2 R/rfsrcSyn.R | 2 R/stat.split.R | 2 R/utilities.R | 2 R/var.select.R | 2 R/vimp.R | 2 R/zzz.R | 2 configure.ac | 2 inst/NEWS | 20 +- inst/doc/rsf-Rnews.pdf |binary man/predict.rfsrc.Rd | 2 man/rfsrc.Rd | 57 +++++--- src/randomForestSRC.c | 143 ++++++++++++-------- src/randomForestSRC.h | 10 - 31 files changed, 484 insertions(+), 444 deletions(-)
More information about randomForestSRC at CRAN
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Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre],
Richard Ellison [aut],
Barry Rowlingson [aut] (Author of overline),
Nick Bearman [aut] (Co-author of gclip)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.0.2 dated 2015-11-02 and 0.1.0 dated 2016-01-15
stplanr-0.0.2/stplanr/R/distance-decay-functions.R |only stplanr-0.0.2/stplanr/R/recat-NTS.R |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.R |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.Rmd |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.html |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.R |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.Rmd |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.html |only stplanr-0.0.2/stplanr/man/age_recat.Rd |only stplanr-0.0.2/stplanr/man/dd_logcub.Rd |only stplanr-0.0.2/stplanr/man/dd_loglin.Rd |only stplanr-0.0.2/stplanr/man/dd_logsqrt.Rd |only stplanr-0.0.2/stplanr/vignettes/cycling-routing-stplanr.Rmd |only stplanr-0.0.2/stplanr/vignettes/flow-data-with-R.Rmd |only stplanr-0.1.0/stplanr/DESCRIPTION | 29 + stplanr-0.1.0/stplanr/LICENSE | 4 stplanr-0.1.0/stplanr/MD5 | 151 +++++----- stplanr-0.1.0/stplanr/NAMESPACE | 68 +++- stplanr-0.1.0/stplanr/NEWS |only stplanr-0.1.0/stplanr/R/RcppExports.R |only stplanr-0.1.0/stplanr/R/SpatialLinesNetwork.R |only stplanr-0.1.0/stplanr/R/catchmentArea.R | 146 +++++++++ stplanr-0.1.0/stplanr/R/crs-funs.R |only stplanr-0.1.0/stplanr/R/data.r | 44 ++ stplanr-0.1.0/stplanr/R/geo-functions.R | 75 ++++ stplanr-0.1.0/stplanr/R/gps.R | 31 -- stplanr-0.1.0/stplanr/R/gtfs.R |only stplanr-0.1.0/stplanr/R/load-stats19.R |only stplanr-0.1.0/stplanr/R/loadABS.R | 22 + stplanr-0.1.0/stplanr/R/od-funs.R | 68 +++- stplanr-0.1.0/stplanr/R/osrmfunctions.R |only stplanr-0.1.0/stplanr/R/overline.R | 1 stplanr-0.1.0/stplanr/R/routes.R | 56 ++- stplanr-0.1.0/stplanr/R/stplanr-package.R | 19 + stplanr-0.1.0/stplanr/R/toptail.R |only stplanr-0.1.0/stplanr/README.md | 96 ++---- stplanr-0.1.0/stplanr/build/vignette.rds |binary stplanr-0.1.0/stplanr/data/cents.rda |binary stplanr-0.1.0/stplanr/data/zones.rda |only stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.R | 6 stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.Rmd | 12 stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.html | 135 +++----- stplanr-0.1.0/stplanr/inst/extdata/beartransit-ca-us.zip |only stplanr-0.1.0/stplanr/inst/extdata/sydroads.zip |only stplanr-0.1.0/stplanr/man/SpatialLinesNetwork-class.Rd |only stplanr-0.1.0/stplanr/man/SpatialLinesNetwork.Rd |only stplanr-0.1.0/stplanr/man/bbox_scale.Rd | 2 stplanr-0.1.0/stplanr/man/buff_geo.Rd |only stplanr-0.1.0/stplanr/man/calc_catchment.Rd | 2 stplanr-0.1.0/stplanr/man/calc_catchment_sum.Rd | 2 stplanr-0.1.0/stplanr/man/calc_moving_catchment.Rd | 2 stplanr-0.1.0/stplanr/man/calc_network_catchment.Rd |only stplanr-0.1.0/stplanr/man/cents.Rd | 13 stplanr-0.1.0/stplanr/man/crs_select_aeq.Rd |only stplanr-0.1.0/stplanr/man/cyclestreet_pat.Rd | 2 stplanr-0.1.0/stplanr/man/decode_gl.Rd |only stplanr-0.1.0/stplanr/man/dl_stats19.Rd |only stplanr-0.1.0/stplanr/man/find_network_nodes.Rd |only stplanr-0.1.0/stplanr/man/flow.Rd | 5 stplanr-0.1.0/stplanr/man/flowlines.Rd | 2 stplanr-0.1.0/stplanr/man/format_stats19_ac.Rd |only stplanr-0.1.0/stplanr/man/format_stats19_ca.Rd |only stplanr-0.1.0/stplanr/man/format_stats19_ve.Rd |only stplanr-0.1.0/stplanr/man/gclip.Rd | 2 stplanr-0.1.0/stplanr/man/graphhopper_pat.Rd | 2 stplanr-0.1.0/stplanr/man/gsection.Rd | 2 stplanr-0.1.0/stplanr/man/gtfs2sldf.Rd |only stplanr-0.1.0/stplanr/man/islines.Rd | 2 stplanr-0.1.0/stplanr/man/line2df.Rd | 4 stplanr-0.1.0/stplanr/man/line2points.Rd |only stplanr-0.1.0/stplanr/man/line2route.Rd | 3 stplanr-0.1.0/stplanr/man/lineLabels.Rd | 2 stplanr-0.1.0/stplanr/man/locate2spdf.Rd |only stplanr-0.1.0/stplanr/man/mapshape.Rd | 55 ++- stplanr-0.1.0/stplanr/man/mapshape_available.Rd |only stplanr-0.1.0/stplanr/man/nearest2spdf.Rd |only stplanr-0.1.0/stplanr/man/od2line.Rd | 2 stplanr-0.1.0/stplanr/man/onewaygeo.Rd | 2 stplanr-0.1.0/stplanr/man/onewayid.Rd | 2 stplanr-0.1.0/stplanr/man/overline.Rd | 2 stplanr-0.1.0/stplanr/man/plot-SpatialLinesNetwork-ANY-method.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ac.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ca.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ve.Rd |only stplanr-0.1.0/stplanr/man/read_table_builder.Rd | 2 stplanr-0.1.0/stplanr/man/route_cyclestreet.Rd | 12 stplanr-0.1.0/stplanr/man/route_graphhopper.Rd | 13 stplanr-0.1.0/stplanr/man/routes_fast.Rd | 2 stplanr-0.1.0/stplanr/man/routes_slow.Rd | 7 stplanr-0.1.0/stplanr/man/stplanr-package.Rd | 2 stplanr-0.1.0/stplanr/man/sum_network_routes.Rd |only stplanr-0.1.0/stplanr/man/summary-SpatialLinesNetwork-method.Rd |only stplanr-0.1.0/stplanr/man/table2matrix.Rd |only stplanr-0.1.0/stplanr/man/toptail.Rd |only stplanr-0.1.0/stplanr/man/toptail_buff.Rd |only stplanr-0.1.0/stplanr/man/toptailgs.Rd |only stplanr-0.1.0/stplanr/man/viaroute.Rd |only stplanr-0.1.0/stplanr/man/viaroute2sldf.Rd |only stplanr-0.1.0/stplanr/man/weightfield.Rd |only stplanr-0.1.0/stplanr/man/writeGeoJSON.Rd | 2 stplanr-0.1.0/stplanr/man/zones.Rd |only stplanr-0.1.0/stplanr/src |only stplanr-0.1.0/stplanr/tests/testthat/test-od2line.R | 2 stplanr-0.1.0/stplanr/vignettes/introducing-stplanr.Rmd | 12 104 files changed, 722 insertions(+), 405 deletions(-)
Title: A Social Media Search and Analytic Tool
Description: Social media search and analytic tool that takes one or multiple URL(s) and returns the information about the popularity and reach of the URL(s) on social media. The function get_socialmedia() retrieves the number of shares, likes, pins, and hits on Facebook (www.facebook.com), Pinterest (www.pinterest.com), StumbleUpon (www.stumbleupon.com), LinkedIn (www.linkedin.com), and Reddit (www.reddit.com). The package also includes dedicated functions for each social network platform and a function to resolve shortened URLs.
Author: Marco Toledo Bastos
Maintainer: Marco Toledo Bastos <marco@toledobastos.com>
Diff between SocialMediaMineR versions 0.1 dated 2014-06-25 and 0.2 dated 2016-01-15
SocialMediaMineR-0.1/SocialMediaMineR/R/get_twitter.R |only SocialMediaMineR-0.1/SocialMediaMineR/man/get_twitter.Rd |only SocialMediaMineR-0.2/SocialMediaMineR/ChangeLog | 5 + SocialMediaMineR-0.2/SocialMediaMineR/DESCRIPTION | 12 +-- SocialMediaMineR-0.2/SocialMediaMineR/MD5 | 38 ++++------ SocialMediaMineR-0.2/SocialMediaMineR/NAMESPACE | 4 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_facebook.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_linkedin.R | 8 +- SocialMediaMineR-0.2/SocialMediaMineR/R/get_pinterest.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_reddit.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_socialmedia.R | 21 ++--- SocialMediaMineR-0.2/SocialMediaMineR/R/get_stumbleupon.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_url.R | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/SocialMediaMineR-package.Rd | 7 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_facebook.Rd | 4 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_linkedin.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_pinterest.Rd | 4 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_reddit.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_socialmedia.Rd | 9 +- SocialMediaMineR-0.2/SocialMediaMineR/man/get_stumbleupon.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_url.Rd | 4 - 21 files changed, 71 insertions(+), 77 deletions(-)
More information about SocialMediaMineR at CRAN
Permanent link
Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.0-6 dated 2015-08-14 and 2.0-7 dated 2016-01-15
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 15 ++++++++------- R/Rcode.r | 8 ++++---- R/rsdiff.r | 28 ++++++++++++++-------------- R/slopop1930_2014.r |only inst |only man/rsdiff.Rd |only man/rssurv.Rd | 2 +- 9 files changed, 39 insertions(+), 35 deletions(-)
Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('pez.shape', 'pez.evenness',
'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation
of Cavender-Bares (2004) correlation of phylogenetic and
ecological matrices ('fingerprint.regression'). Phylogenetic
Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives &
Helmus (2011) and Rafferty & Ives (2013). Simulation of null
assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between pez versions 1.1-0 dated 2015-08-06 and 1.1-1 dated 2016-01-15
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++--------- NEWS | 10 ++++++ R/comparative.comm.R | 2 - R/eco.scape.R | 10 +++++- R/metrics.R | 13 +++++--- R/pglmm.R | 29 ++++++++++++++---- R/scape.R | 55 ++++++++++++++++++----------------- build/vignette.rds |binary inst/CITATION | 6 ++- inst/doc/pez-pglmm-overview.R |only inst/doc/pez-pglmm-overview.Rnw |only inst/doc/pez-pglmm-overview.pdf |only man/eco.scape.Rd | 6 +++ man/pez.metrics.Rd | 10 +++++- man/pglmm.Rd | 18 ++++++++--- man/scape.Rd | 61 +++++++++++++++------------------------ vignettes/pez-pglmm-overview.Rnw |only 18 files changed, 155 insertions(+), 103 deletions(-)
Title: Elastic Functional Data Analysis
Description: Functions to support functional data analysis using the square root velocity framework.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.5.1 dated 2015-11-16 and 1.6.0 dated 2016-01-15
DESCRIPTION | 13 +-- MD5 | 78 ++++++++++++++++----- NAMESPACE | 17 ++++ NEWS | 8 +- R/align_fPCA.R | 6 - R/calc_shape_dist.R |only R/curve_functions.R |only R/curve_geodesic.R |only R/curve_karcher_cov.R |only R/curve_karcher_mean.R |only R/curve_pair_align.R |only R/curve_principal_directions.R |only R/curve_srvf_align.R |only R/curve_to_q.R |only R/f_to_srvf.R | 8 +- R/fdasrvf-package.r | 17 ++++ R/image_funcs.R |only R/optimum.reparam.R | 8 +- R/pair_align_image.R |only R/q_to_curve.R |only R/reparam_curve.R |only R/reparam_image.R |only R/resamplecurve.R |only R/sample_shapes.R |only R/srsf_to_f.R | 8 +- R/time_warping.R | 22 +++--- R/utility_functions.R | 136 +++++++++++++++++++++++++++++++++----- README.md | 4 + data/datalist |only data/mpeg7.RData |only man/align_fPCA.Rd | 6 + man/beta.Rd |only man/calc_shape_dist.Rd |only man/curve_geodesic.Rd |only man/curve_karcher_cov.Rd |only man/curve_karcher_mean.Rd |only man/curve_pair_align.Rd |only man/curve_principal_directions.Rd |only man/curve_srvf_align.Rd |only man/curve_to_q.Rd |only man/f_to_srvf.Rd | 8 +- man/fdasrvf.Rd | 2 man/optimum.reparam.Rd | 8 +- man/pair_align_image.Rd |only man/q_to_curve.Rd |only man/reparam_curve.Rd |only man/reparam_image.Rd |only man/resamplecurve.Rd |only man/sample_shapes.Rd |only man/srsf_to_f.Rd | 8 +- man/time_warping.Rd | 16 ++-- src/Makevars | 6 + src/Makevars.win | 13 ++- src/fdaqmap |only src/gropt/incl/def.h | 17 ---- 55 files changed, 292 insertions(+), 117 deletions(-)
More information about deconstructSigs at CRAN
Permanent link
Title: Actigraphy Data Analysis
Description: Functional linear modeling and analysis for actigraphy data.
Author: William Shannon, Tao Li, Hong Xian, Jia Wang, Elena Deych, Carlos Gonzalez
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between Actigraphy versions 1.2 dated 2012-10-30 and 1.3.2 dated 2016-01-15
DESCRIPTION | 23 +- MD5 | 66 +++--- NAMESPACE | 4 R/Ftest.R | 22 +- R/cat_flm_plot.R | 26 +- R/cont_flm_plot.R | 16 - R/fda.matchid.R | 24 +- R/fda.smoothdata.R | 5 R/flm_cate.R | 7 R/flm_ftest.R | 12 - build |only inst/doc/Categorical-FDA-Tutorial.R |only inst/doc/Categorical-FDA-Tutorial.Rnw | 89 ++++----- inst/doc/Categorical-FDA-Tutorial.pdf |binary inst/doc/Continuous-FDA-Tutorial.R |only inst/doc/Continuous-FDA-Tutorial.Rnw | 90 ++++----- inst/doc/Continuous-FDA-Tutorial.pdf |binary inst/doc/Figures-from-Referenced-Paper.R |only inst/doc/Figures-from-Referenced-Paper.Rnw | 273 +++++++++++++--------------- inst/doc/Figures-from-Referenced-Paper.pdf |binary man/Actigraphy-internal.Rd | 5 man/Actigraphy-package.Rd | 35 +-- man/act_29pt.Rd | 10 - man/act_8pt.Rd | 10 - man/cat_flm_plot.Rd | 69 +++---- man/clinic_29pt_ahi.Rd | 8 man/clinic_29pt_bmi.Rd | 8 man/clinic_8pt.Rd | 8 man/cont_flm_plot.Rd | 59 ++---- man/fda.matchid.Rd | 64 +++--- man/fda.smoothdata.Rd | 45 ++-- man/flm_cate.Rd | 36 +-- man/weekday.Rd | 10 - vignettes/Categorical-FDA-Tutorial.Rnw | 89 ++++----- vignettes/Continuous-FDA-Tutorial.Rnw | 90 ++++----- vignettes/Figures-from-Referenced-Paper.Rnw | 273 +++++++++++++--------------- 36 files changed, 741 insertions(+), 735 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively
adjust alpha in order to maintain the consumer risk in ABEL studies
and adapt the sample size for the loss in power.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-02 dated 2015-12-02 and 1.3-3 dated 2016-01-15
DESCRIPTION | 11 +++++++---- MD5 | 23 ++++++++++++++--------- NAMESPACE | 10 ++++++---- NEWS | 10 ++++++++++ R/power_scABEL2.R |only R/sampleN.scABEL.ad.R |only R/samplesize_RSABE.R | 3 ++- R/samplesize_scABEL.R | 3 ++- R/scABEL.R | 26 ++++++++++++++++++++++++++ R/scABEL.ad.R |only man/sampleN.RSABE.Rd | 12 +++++++----- man/sampleN.scABEL.Rd | 12 +++++++----- man/sampleN.scABEL.ad.Rd |only man/scABEL.Rd | 4 ++-- man/scABEL.ad.Rd |only 15 files changed, 83 insertions(+), 31 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.1.0 dated 2015-11-13 and 1.1.1 dated 2016-01-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/statistics.R | 4 +++- man/PRESS.Rd | 3 +++ 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using gnm, with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre],
Heather Turner [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between logmult versions 0.6.2 dated 2015-04-22 and 0.6.3 dated 2016-01-15
logmult-0.6.2/logmult/R/permn.R |only logmult-0.6.2/logmult/R/regtype.R |only logmult-0.6.2/logmult/tests/lambda.R.rkward_autosave |only logmult-0.6.3/logmult/DESCRIPTION | 21 - logmult-0.6.3/logmult/MD5 | 65 ++-- logmult-0.6.3/logmult/NAMESPACE | 18 + logmult-0.6.3/logmult/NEWS | 16 logmult-0.6.3/logmult/R/hmskew.R | 6 logmult-0.6.3/logmult/R/hmskewL.R | 20 - logmult-0.6.3/logmult/R/jackboot.R | 3 logmult-0.6.3/logmult/R/maor.R | 37 +- logmult-0.6.3/logmult/R/plot.assoc.R | 122 ++----- logmult-0.6.3/logmult/R/ras.R |only logmult-0.6.3/logmult/R/rc.R | 11 logmult-0.6.3/logmult/R/rcL.R | 12 logmult-0.6.3/logmult/R/rcL.trans.R | 8 logmult-0.6.3/logmult/R/summary.assoc.R | 5 logmult-0.6.3/logmult/R/svygnm.R |only logmult-0.6.3/logmult/R/tools.R | 12 logmult-0.6.3/logmult/R/unidiff.R | 7 logmult-0.6.3/logmult/R/yrcskew.R | 82 ++--- logmult-0.6.3/logmult/man/hmskewL.Rd | 6 logmult-0.6.3/logmult/man/maor.Rd | 11 logmult-0.6.3/logmult/man/plot.assoc.Rd | 19 - logmult-0.6.3/logmult/man/ras.Rd |only logmult-0.6.3/logmult/man/rcL.Rd | 2 logmult-0.6.3/logmult/man/summary.assoc.Rd | 4 logmult-0.6.3/logmult/man/summary.unidiff.Rd | 4 logmult-0.6.3/logmult/man/svygnm.Rd |only logmult-0.6.3/logmult/man/unidiff.Rd | 5 logmult-0.6.3/logmult/tests/Clogg-Shihadeh1994.R | 4 logmult-0.6.3/logmult/tests/Rplots.pdf |only logmult-0.6.3/logmult/tests/Wong2010-4.7.R | 4 logmult-0.6.3/logmult/tests/hmskewL.R | 9 logmult-0.6.3/logmult/tests/maor.R | 227 +++++++++++++- logmult-0.6.3/logmult/tests/ras.R |only logmult-0.6.3/logmult/tests/supplementary.R | 2 logmult-0.6.3/logmult/tests/vanderHeijden-Mooijaart1995.R | 5 38 files changed, 523 insertions(+), 224 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download and re-arrange the bi-monthly datasets according to creation time; import downloaded files from native binary (ENVI) format directly into R based on the widely applied 'raster' package; extract accompanying quality flags and perform quality control; calculate monthly value composites (e.g. maximum value composites, MVC) from the bi-monthly input data; and derive long-term monotonous trends from the Mann-Kendall trend test, optionally featuring pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.4.0 dated 2015-12-18 and 0.5.0 dated 2016-01-15
DESCRIPTION | 17 +---- MD5 | 34 +++++----- NEWS | 10 +-- R/downloadGimms.R | 20 ++++-- R/gimmsControls.R | 17 +++++ R/monthlyComposite.R | 26 ++++--- R/monthlyIndices.R | 160 ++++++++++++++++++++++++------------------------ R/rasterizeGimms.R | 55 ++++++++++++---- R/rearrangeFiles.R | 17 ++--- R/significantTau.R | 9 +- R/updateInventory.R | 124 +++++++++++++++++++------------------ man/downloadGimms.Rd | 6 + man/monthlyComposite.Rd | 20 +++--- man/monthlyIndices.Rd | 6 - man/rasterizeGimms.Rd | 42 +++++++----- man/rearrangeFiles.Rd | 17 ++--- man/significantTau.Rd | 9 +- man/updateInventory.Rd | 22 +++--- 18 files changed, 341 insertions(+), 270 deletions(-)
Title: Models and Data Sets for the Study of Species-Area Relationships
Description: Hierarchical models for the analysis of species-area
relationships (SARs) by combining several data sets and covariates;
with a global data set combining individual SAR studies;
as described in Solymos and Lele
(2012, Global Ecology and Biogeography 21, 109-120).
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between sharx versions 1.0-4 dated 2014-05-19 and 1.0-5 dated 2016-01-15
DESCRIPTION | 19 +- MD5 | 20 +- NAMESPACE | 21 +- R/hsarx.R | 422 +++++++++++++++++++++++++-------------------------- R/sie.R | 101 ++++++------ inst/CITATION | 40 ++-- inst/ChangeLog | 39 ++-- man/hsarx.Rd | 164 +++++++++---------- man/sardata.Rd | 108 ++++++------- man/sharx-package.Rd | 50 +++--- man/sie.Rd | 136 ++++++++-------- 11 files changed, 564 insertions(+), 556 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-3 dated 2015-11-10 and 0.0-4 dated 2016-01-15
qrmtools-0.0-3/qrmtools/data |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.R |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.Rmd |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.html |only qrmtools-0.0-3/qrmtools/man/SnP_500.Rd |only qrmtools-0.0-3/qrmtools/vignettes/VaR_ES_estimators.Rmd |only qrmtools-0.0-4/qrmtools/DESCRIPTION | 8 - qrmtools-0.0-4/qrmtools/MD5 | 32 +--- qrmtools-0.0-4/qrmtools/NAMESPACE | 12 + qrmtools-0.0-4/qrmtools/R/VaR_bounds.R | 87 ++++++----- qrmtools-0.0-4/qrmtools/R/zzz.R | 9 - qrmtools-0.0-4/qrmtools/build/vignette.rds |binary qrmtools-0.0-4/qrmtools/inst/doc/ARMA_GARCH_VaR.html | 20 +- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.R | 84 +++++++---- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.Rmd | 90 ++++++++---- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.html | 119 ++++++++++------ qrmtools-0.0-4/qrmtools/man/Black_Scholes.Rd | 4 qrmtools-0.0-4/qrmtools/man/VaR_bounds.Rd | 25 +-- qrmtools-0.0-4/qrmtools/src/VaR_bounds.c | 73 +++++---- qrmtools-0.0-4/qrmtools/vignettes/VaR_bounds.Rmd | 90 ++++++++---- 20 files changed, 407 insertions(+), 246 deletions(-)
Title: Modified Maximum Contrast Method
Description: An implementation of modified maximum contrast methods
and the maximum contrast method: Functions 'mmcm.mvt' and
'mcm.mvt' give P-value by using randomized quasi-Monte Carlo
method with 'pmvt' function of package 'mvtnorm', and
'mmcm.resamp' gives P-value by using a permutation method.
Author: Kengo NAGASHIMA and Yasunori SATO
Maintainer: Kengo NAGASHIMA <nshi@chiba-u.jp>
Diff between mmcm versions 1.2-5 dated 2014-09-10 and 1.2-6 dated 2016-01-15
DESCRIPTION | 18 +++++------ MD5 | 25 ++++++++-------- NAMESPACE | 3 + NEWS | 80 ++++++++++++++++++++-------------------------------- NEWS.md |only R/mcm.mvt.R | 1 R/mmcm.mvt.R | 1 R/mmcm.resamp.R | 14 +++++---- R/print.mmcm.R | 3 + man/mcm.mvt.Rd | 3 + man/mmcm-package.Rd | 3 + man/mmcm.mvt.Rd | 3 + man/mmcm.resamp.Rd | 5 +-- man/print.mmcm.Rd | 3 + 14 files changed, 79 insertions(+), 83 deletions(-)
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 0.10 dated 2012-07-13 and 0.12 dated 2016-01-15
ChangeLog | 7 +++++++ DESCRIPTION | 23 ++++++++++++----------- MD5 | 21 ++++++++++++++++----- NAMESPACE | 2 ++ R/geneticLHS.R | 17 ++++++++++++----- build |only inst/doc/augmentLHS_Example.R |only inst/unitTests |only man/geneticLHS.Rd | 5 +++-- tests |only 10 files changed, 52 insertions(+), 23 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.1 dated 2015-03-04 and 1.3 dated 2016-01-15
DESCRIPTION | 23 - MD5 | 186 ++++++----- NAMESPACE | 23 + NEWS | 15 R/RcppExports.R | 138 ++++---- R/bezierArrowGradient.R | 1 R/bezierArrowSmpl.R | 1 R/bezier_private_functions.R | 42 +- R/descriptionStats.R | 2 R/docx_document.R |only R/figCaptionNo.R | 3 R/getDescriptionStatsBy.R | 59 ++- R/getPval.R | 7 R/getSvdMostInfluential.R | 2 R/mergeDesc.R | 1 R/private_functions.R | 4 R/transitionClass.R | 473 ++++++++++++++++++----------- R/transitionClass_helpers.R | 269 +++++++++++++--- R/transitionPlot.R | 1 R/transitionPlot_helpers.R | 2 build/vignette.rds |binary inst/doc/Descriptives.R | 6 inst/doc/Descriptives.html | 154 +++++---- inst/doc/Transition-class.R | 4 inst/doc/Transition-class.html | 92 +++-- inst/doc/transitionPlot.R | 8 inst/doc/transitionPlot.html | 113 +++--- inst/examples/transitionClass_example.R |only inst/extdata |only inst/rmarkdown |only man/Gmisc-deprecated.Rd | 8 man/Gmisc-package.Rd | 76 ++-- man/Transition-class.Rd | 42 ++ man/bezierArrowGradient.Rd | 101 +++--- man/bezierArrowSmpl.Rd | 79 ++-- man/calculateLinesAndArrow.Rd | 54 +-- man/copyAllNewAttributes.Rd | 21 - man/describeFactors.Rd | 93 ++--- man/describeMean.Rd | 87 ++--- man/describeMedian.Rd | 70 +--- man/describeProp.Rd | 80 ++-- man/docx_document.Rd |only man/fastDoCall.Rd | 47 +- man/figCapNo.Rd | 35 -- man/figCapNoLast.Rd | 15 man/figCapNoNext.Rd | 15 man/getAbsoluteWidth.Rd | 33 -- man/getBezierAdj4Arrw.Rd | 13 man/getDescriptionStatsBy.Rd | 241 ++++++-------- man/getGridVal.Rd | 14 man/getPval.Rd | 53 +-- man/getSvdMostInfluential.Rd | 77 ++-- man/getVectorAngle.Rd | 10 man/gnrlBezierPoints.Rd | 15 man/htmlTable_latex.Rd | 13 man/insertRowAndKeepAttr.Rd | 18 - man/isHorizontal.Rd | 4 man/mergeDesc.Rd | 60 +-- man/mergeLists.Rd | 16 man/mergeLists_internal.Rd | 6 man/prCaptionFix.Rd |only man/prConvertShowMissing.Rd | 12 man/prDescGetAndValidateDefaultRef.Rd | 10 man/prDescGetMissing.Rd | 47 +- man/prFtpHeaderStyle.Rd |only man/prFtpOtherChanges.Rd |only man/prFtpOtherRemoval.Rd |only man/prFtpScriptRemoval.Rd |only man/prGetStatistics.Rd | 77 ++-- man/prGetTextGrobCex.Rd | 4 man/prGridPlotTitle.Rd | 21 - man/prPasteVec.Rd | 8 man/prPushMarginViewport.Rd | 18 - man/prSetMaxWidth.Rd |only man/prTcMatchClr.Rd |only man/prTcPlotArrows.Rd | 33 -- man/prTcPlotBoxColumn.Rd | 17 - man/prTcValidateAndPrepClr.Rd | 20 - man/prTpGetBoxPositions.Rd | 23 - man/prTpGetBoxPropClr.Rd | 14 man/prTpGetBoxSizedTextGrob.Rd | 12 man/prTpGetColors.Rd | 25 - man/prTpPlotArrows.Rd | 38 +- man/prTpPlotBox.Rd | 20 - man/prTpPlotBoxes.Rd | 206 +++++------- man/transitionPlot.Rd | 246 ++++++--------- man/validateAndConvertVectorInputs.Rd | 21 - src/Makevars.win | 2 src/RcppExports.cpp | 46 +- tests/testthat/Rplots.pdf |only tests/testthat/test-bezier.R | 100 ++++-- tests/testthat/test-docx_document.R |only tests/testthat/test-figCapNo.R | 22 - tests/testthat/test-fig_caption.R |only tests/testthat/test-getDescriptionStats.R | 76 +++- tests/testthat/test-transitionClass.R | 209 +++++------- tests/visual_tests/FTP_test |only tests/visual_tests/Full_test_suite.Rmd |only tests/visual_tests/Highlighting_test.Rmd |only tests/visual_tests/MathJax_test.Rmd |only tests/visual_tests/Max_width_test.Rmd |only tests/visual_tests/transitionClass_vtest.R |only 102 files changed, 2361 insertions(+), 1991 deletions(-)
Title: Convert Data from and to 'geoJSON' or 'topoJSON'
Description: Convert data to 'geoJSON' or 'topoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but
rather aims to be a high level client to simplify conversions of data from and
to 'geoJSON' and 'topoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.1.4 dated 2015-08-12 and 0.1.6 dated 2016-01-15
DESCRIPTION | 23 +++--- LICENSE | 2 MD5 | 121 +++++++++++++++++--------------- NAMESPACE | 5 + NEWS | 20 +++++ R/as.json.R | 13 ++- R/as.location.R | 6 - R/construction.R | 4 - R/geojson_json.R | 2 R/geojson_list.R | 5 - R/geojson_sp.R |only R/geojsonio-package.R | 3 R/lint.R | 15 ++- R/mapgist.R | 48 ++++++------ R/mapleaflet.R | 6 - R/pipe.R |only R/startup.R |only R/validate.R | 4 - R/zzz.r | 24 ++---- README.md | 12 +-- build/vignette.rds |binary inst/doc/geojsonio_vignette.Rmd | 5 - inst/doc/geojsonio_vignette.html | 5 - inst/img/unnamed-chunk-18-1.png |binary inst/img/unnamed-chunk-20-1.png |binary inst/vign/figure/unnamed-chunk-17-1.png |binary inst/vign/geojsonio_vignette.Rmd | 3 inst/vign/geojsonio_vignette.md | 5 - man/as.json.Rd | 13 +++ man/as.location.Rd | 2 man/bounds.Rd | 4 - man/canada_cities.Rd | 10 +- man/centroid.Rd | 2 man/file_to_geojson.Rd | 8 +- man/geojson-add.Rd | 10 +- man/geojson_json.Rd | 7 + man/geojson_list.Rd | 2 man/geojson_read.Rd | 8 +- man/geojson_sp.Rd |only man/geojson_style.Rd | 32 ++++---- man/geojson_write.Rd | 4 - man/geojsonio.Rd | 20 ++--- man/lint.Rd | 7 + man/map_gist.Rd | 2 man/map_leaf.Rd | 2 man/pipe.Rd | 4 - man/pretty.Rd | 2 man/projections.Rd | 3 man/states.Rd | 4 - man/topojson_read.Rd | 4 - man/us_cities.Rd | 10 +- man/validate.Rd | 2 tests/testthat/test-as.json.R | 38 ++++++---- tests/testthat/test-as.location.R | 13 +++ tests/testthat/test-file_to_geojson.R | 87 ++++++++++++++--------- tests/testthat/test-geojson_sp.R |only tests/testthat/test-geojson_write.R | 38 ++++++---- tests/testthat/test-lint.R | 115 +++++++++++++++++++++++++++--- tests/testthat/test-map_gist.R | 8 +- tests/testthat/test-mapleaflet.R |only tests/testthat/test-onload.R | 11 ++ tests/testthat/test-pretty.R |only tests/testthat/test-spatial_methods.R |only tests/testthat/test-validate.R |only tests/testthat/us_cities.rds |only tests/testthat/us_citites_two_row.rds |only vignettes/geojsonio_vignette.Rmd | 5 - 67 files changed, 519 insertions(+), 289 deletions(-)
Title: An Interface to the DescribeDisplay GGobi Plugin
Description: Produce publication quality graphics from output of GGobi's
describe display plugin.
Author: Di Cook [aut, cre],
Hadley Wickham [aut],
Andreas Buja [aut],
Barret Schloerke [aut]
Maintainer: Di Cook <dicook@monash.edu>
Diff between DescribeDisplay versions 0.2.4 dated 2013-07-18 and 0.2.5 dated 2016-01-15
DescribeDisplay-0.2.4/DescribeDisplay/R/DescribeDisplay-package.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/axis-geom.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/axis-grob.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/data.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-barchart.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-parcoords.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-scatmat.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-timeseries.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/plots.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/utils.r |only DescribeDisplay-0.2.4/DescribeDisplay/ggobi-xml |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/barchart.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/histogram.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/parcoord.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/plot1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/scatmat.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/timeseries.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour2d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour2x1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/xyplot.r |only DescribeDisplay-0.2.4/DescribeDisplay/load.r |only DescribeDisplay-0.2.4/DescribeDisplay/write-xml.rnw |only DescribeDisplay-0.2.5/DescribeDisplay/DESCRIPTION | 42 ++- DescribeDisplay-0.2.5/DescribeDisplay/LICENSE |only DescribeDisplay-0.2.5/DescribeDisplay/MD5 | 114 +++++----- DescribeDisplay-0.2.5/DescribeDisplay/NAMESPACE | 46 +++- DescribeDisplay-0.2.5/DescribeDisplay/NEWS | 12 + DescribeDisplay-0.2.5/DescribeDisplay/R/DescribeDisplay-package.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/axis-geom.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/axis-grob.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/data.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-barchart.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-parcoords.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-scatmat.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-timeseries.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/plots.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/utils.R |only DescribeDisplay-0.2.5/DescribeDisplay/README.md |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/barchart.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/histogram.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/parcoord.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/plot1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/scatmat.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/timeseries.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour2d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour2x1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/xyplot.R |only DescribeDisplay-0.2.5/DescribeDisplay/man/addbrush.Rd | 31 +- DescribeDisplay-0.2.5/DescribeDisplay/man/axesGrob.Rd | 12 - DescribeDisplay-0.2.5/DescribeDisplay/man/axesViewport.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_pcp.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_scatmat.Rd | 12 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_timeseries.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_clean_plot.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_defaults.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_edges.Rd | 15 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_example.Rd | 9 DescribeDisplay-0.2.5/DescribeDisplay/man/dd_load.Rd | 23 +- DescribeDisplay-0.2.5/DescribeDisplay/man/dd_plot_class.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/dd_points.Rd | 15 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_tour_axes.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/ddpanelGrob.Rd | 22 + DescribeDisplay-0.2.5/DescribeDisplay/man/describedisplayreshape.Rd | 9 DescribeDisplay-0.2.5/DescribeDisplay/man/geom_axis.Rd | 10 DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.barplot.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.dd.Rd | 16 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.ddplot.Rd | 24 +- DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.histogram.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.parcoords.Rd | 25 +- DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.scatmat.Rd | 21 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.timeseries.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/plot.dd.Rd | 44 +-- DescribeDisplay-0.2.5/DescribeDisplay/man/plot.ddplot.Rd | 26 +- DescribeDisplay-0.2.5/DescribeDisplay/man/range01.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/removehiddens.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/zeeThemAll.Rd | 8 DescribeDisplay-0.2.5/DescribeDisplay/tests |only 81 files changed, 406 insertions(+), 299 deletions(-)
More information about DescribeDisplay at CRAN
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Title: Community Dynamics Metrics
Description: A toolbox of ecological community dynamics metrics that are
explicitly temporal. Functions fall into two categories: temporal diversity
indices and community stability metrics. The diversity indices are temporal
analogs to traditional diversity indices such as richness and rank-abundance
curves. Specifically, functions are provided to calculate species turnover, mean
rank shifts, and lags in community similarity between time points. The community
stability metrics calculate overall stability and patterns of species covariance
and synchrony over time.
Author: Lauren Hallett [aut],
Sydney K. Jones [aut],
Andrew A. MacDonald [aut],
Dan F. B. Flynn [aut],
Peter Slaughter [aut],
Julie Ripplinger [aut],
Scott L. Collins [aut],
Corinna Gries [aut],
Matthew B. Jones [aut, cre]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 1.0.0 dated 2015-10-20 and 1.0.1 dated 2016-01-15
DESCRIPTION | 24 +++--- MD5 | 105 +++++++++++++++--------------- NAMESPACE | 2 NEWS | 10 ++ R/rank_shift.R | 1 R/rate_change.R | 2 R/synchrony.R | 4 - R/temporal_torus_translation.R | 2 R/turnover.R | 3 R/utilities.R | 29 +++++++- R/variance_ratio.R | 53 +++++++++++---- README.md | 3 build/vignette.rds |binary inst/CITATION |only inst/doc/Community_Stability_Metrics.html | 52 +++++++------- inst/doc/Temporal_Diversity_Indices.html | 28 ++------ inst/doc/codyn_overview.html | 4 - inst/tests/test_community_stability.R | 10 ++ inst/tests/test_rank_shift.R | 9 ++ inst/tests/test_rate_change.R | 22 ++++++ inst/tests/test_synchrony.R | 13 +++ inst/tests/test_turnover.R | 10 ++ inst/tests/test_utilities.R | 41 +++++++++-- inst/tests/test_variance_ratio.R | 24 ++++++ man/check_multispp.Rd |only man/check_names.Rd | 2 man/check_numeric.Rd | 2 man/check_single.Rd | 2 man/check_single_onerep.Rd | 2 man/check_sppvar.Rd |only man/codyn.Rd | 12 +-- man/collins08.Rd | 4 - man/community_stability.Rd | 4 - man/genRand.Rd | 2 man/get_lag_i.Rd | 2 man/get_lagged_distances.Rd | 4 - man/get_slope.Rd | 2 man/getintersect.Rd | 2 man/getturnover.Rd | 2 man/knz_001d.Rd | 6 - man/mean_rank_shift.Rd | 16 ++-- man/meanrank.Rd | 2 man/rate_change.Rd | 22 +++--- man/rate_change_interval.Rd | 14 ++-- man/stability_onerep.Rd | 2 man/synch_onerep.Rd | 4 - man/synchrony.Rd | 6 - man/temporal_torus_translation.Rd | 6 - man/temporal_torus_translation_CI.Rd | 6 - man/transpose_community.Rd | 2 man/turnover.Rd | 9 +- man/turnover_allyears.Rd | 2 man/variance_ratio.Rd | 66 ++++++++++++------ man/variance_ratio_longformdata.Rd | 2 man/variance_ratio_matrixdata.Rd | 2 55 files changed, 428 insertions(+), 232 deletions(-)