Title: Design and Analysis of Disease Surveillance Activities
Description: A range of functions for the design and
analysis of disease surveillance activities. These functions were
originally developed for animal health surveillance activities but can be
equally applied to aquatic animal, wildlife, plant and human health
surveillance activities. Utilities are included for sample size calculation
and analysis of representative surveys for disease freedom, risk-based
studies for disease freedom and for prevalence estimation.
Author: Evan Sergeant
Maintainer: Evan Sergeant <evan@ausvet.com.au>
Diff between RSurveillance versions 0.1.0 dated 2014-12-08 and 0.2.0 dated 2016-10-03
RSurveillance-0.1.0/RSurveillance/man/sd.tp.Rd |only RSurveillance-0.2.0/RSurveillance/DESCRIPTION | 16 RSurveillance-0.2.0/RSurveillance/MD5 | 131 +++--- RSurveillance-0.2.0/RSurveillance/NAMESPACE | 7 RSurveillance-0.2.0/RSurveillance/R/adj_risk_sim.R |only RSurveillance-0.2.0/RSurveillance/R/freedom_functions_1.R | 205 +++++----- RSurveillance-0.2.0/RSurveillance/R/freedom_functions_2.R | 10 RSurveillance-0.2.0/RSurveillance/R/n_rb2stage.R |only RSurveillance-0.2.0/RSurveillance/R/prevalence_functions.R | 52 -- RSurveillance-0.2.0/RSurveillance/R/risk_based_functions.R | 78 --- RSurveillance-0.2.0/RSurveillance/R/sep_passive.R |only RSurveillance-0.2.0/RSurveillance/R/sse_rb2stage.R |only RSurveillance-0.2.0/RSurveillance/man/adj.risk.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/adj.risk.sim.Rd |only RSurveillance-0.2.0/RSurveillance/man/ap.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/binom.agresti.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/binom.cp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/binom.jeffreys.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/disc.prior.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/epi.calc.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/n.2stage.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.ap.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/n.binom.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.c.freecalc.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/n.c.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.freecalc.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/n.freedom.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.hypergeo.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.pfree.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/n.pooled.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/n.rb.2stage.1.Rd |only RSurveillance-0.2.0/RSurveillance/man/n.rb.2stage.2.Rd |only RSurveillance-0.2.0/RSurveillance/man/n.rb.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/n.rb.varse.Rd | 13 RSurveillance-0.2.0/RSurveillance/man/n.tp.Rd | 5 RSurveillance-0.2.0/RSurveillance/man/pfree.1.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pfree.calc.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pfree.equ.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/pstar.calc.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/se.parallel.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/se.series.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.binom.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.binom.imperfect.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/sep.exact.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sep.freecalc.Rd | 10 RSurveillance-0.2.0/RSurveillance/man/sep.hp.Rd | 9 RSurveillance-0.2.0/RSurveillance/man/sep.hypergeo.Rd | 10 RSurveillance-0.2.0/RSurveillance/man/sep.passive.Rd |only RSurveillance-0.2.0/RSurveillance/man/sep.pfree.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.pooled.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.prior.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.rb.bin.Rd | 11 RSurveillance-0.2.0/RSurveillance/man/sep.rb.bin.varse.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb.hypergeo.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb.hypergeo.varse.Rd | 17 RSurveillance-0.2.0/RSurveillance/man/sep.rb2.binom.Rd | 15 RSurveillance-0.2.0/RSurveillance/man/sep.rb2.hypergeo.Rd | 17 RSurveillance-0.2.0/RSurveillance/man/sep.sys.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sep.var.se.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sp.parallel.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sp.series.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sph.binom.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/sph.hp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/spp.Rd | 3 RSurveillance-0.2.0/RSurveillance/man/sse.combined.Rd | 27 - RSurveillance-0.2.0/RSurveillance/man/sse.rb.2stage.Rd | 39 - RSurveillance-0.2.0/RSurveillance/man/tp.Rd | 7 RSurveillance-0.2.0/RSurveillance/man/tp.normal.Rd | 5 RSurveillance-0.2.0/RSurveillance/tests/RSurveillance.R | 40 + 71 files changed, 482 insertions(+), 475 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.8 dated 2015-12-21 and 1.1.9 dated 2016-10-03
DESCRIPTION | 8 +++--- MD5 | 55 +++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS | 12 +++++++++ R/kdffreq.R | 39 +++++++++++++++++++++--------- R/paleofire-package.R | 4 +-- R/pfAddData.R | 17 ++++++++++--- R/pfCompositeLF.R | 54 ++++++++++++++++++++++++++++++++---------- R/pfGridding.R | 5 +-- R/pfResolution.R | 10 +++++-- R/pfSiteSel.R | 12 +++++++-- R/potveg.R | 42 +++++++++++++++++--------------- R/zzz.R | 2 - README.md | 6 ++-- build/vignette.rds |binary data/countries.rda |binary data/dem.rda |binary inst/doc/paleofire-paper.pdf |binary man/contrib.pfCompositeLF.Rd |only man/kdffreq.Rd | 28 +++++++++++++++------ man/paleofire-internal.Rd | 1 man/paleofire-package.Rd | 2 - man/pfAddData.Rd | 16 +++++++++++- man/pfCompositeLF.Rd | 2 - man/pfGridding.Rd | 1 man/plot.kdffreq.Rd | 9 ++++++- man/plot.pfCompositeLF.Rd | 2 - man/plot.pfGridding.Rd | 4 +-- man/plot.potveg.Rd | 4 ++- 29 files changed, 226 insertions(+), 110 deletions(-)
Title: An R Toolbox for Psychologists, Neuropsychologists and
Neuroscientists
Description: An R package containing free datasets as well as several statistical functions useful in psychology, neuropsychology and neuroscience.
Author: Dominique Makowski [aut, cre],
Phillip Alday [ctb]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between neuropsychology versions 0.1 dated 2016-09-21 and 0.2.4 dated 2016-10-03
neuropsychology-0.1/neuropsychology/tests/testthat/test-basics.R |only neuropsychology-0.2.4/neuropsychology/DESCRIPTION | 26 +- neuropsychology-0.2.4/neuropsychology/MD5 | 58 ++++-- neuropsychology-0.2.4/neuropsychology/NAMESPACE | 13 - neuropsychology-0.2.4/neuropsychology/R/APAze.R | 95 ++++++++-- neuropsychology-0.2.4/neuropsychology/R/Ncolours.R |only neuropsychology-0.2.4/neuropsychology/R/assess.R |only neuropsychology-0.2.4/neuropsychology/R/braincloud.R |only neuropsychology-0.2.4/neuropsychology/R/cortable.R | 62 ++++-- neuropsychology-0.2.4/neuropsychology/R/describe.R | 37 +-- neuropsychology-0.2.4/neuropsychology/R/extract_text.R |only neuropsychology-0.2.4/neuropsychology/R/format_p.R |only neuropsychology-0.2.4/neuropsychology/R/get_factors.R | 13 - neuropsychology-0.2.4/neuropsychology/R/get_numeric.R | 13 - neuropsychology-0.2.4/neuropsychology/README.md | 95 ++++++++-- neuropsychology-0.2.4/neuropsychology/data/masks.rda |only neuropsychology-0.2.4/neuropsychology/inst/CITATION | 6 neuropsychology-0.2.4/neuropsychology/man/APAze.Rd | 28 +- neuropsychology-0.2.4/neuropsychology/man/Ncolours.Rd |only neuropsychology-0.2.4/neuropsychology/man/assess.Rd |only neuropsychology-0.2.4/neuropsychology/man/braincloud.Rd |only neuropsychology-0.2.4/neuropsychology/man/cortable.Rd | 54 ++--- neuropsychology-0.2.4/neuropsychology/man/describe.Rd | 37 +++ neuropsychology-0.2.4/neuropsychology/man/extract_text.Rd |only neuropsychology-0.2.4/neuropsychology/man/format_p.Rd |only neuropsychology-0.2.4/neuropsychology/man/get_factors.Rd | 8 neuropsychology-0.2.4/neuropsychology/man/get_numeric.Rd | 10 - neuropsychology-0.2.4/neuropsychology/man/masks.Rd |only neuropsychology-0.2.4/neuropsychology/man/personality.Rd | 6 neuropsychology-0.2.4/neuropsychology/man/theme_neuropsychology.Rd | 20 -- neuropsychology-0.2.4/neuropsychology/tests/testthat/Lutz2008.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/Sperduti2016a.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/Sperduti2016b.pdf |only neuropsychology-0.2.4/neuropsychology/tests/testthat/assess_plot.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/assess_plot2.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/braincloud.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/cortable_plot.png |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-APAze.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-assess.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-cortable.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-describe.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-extract_text.R |only neuropsychology-0.2.4/neuropsychology/tests/testthat/test-textcloud.R |only 43 files changed, 386 insertions(+), 195 deletions(-)
More information about neuropsychology at CRAN
Permanent link
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.5.3 dated 2016-08-01 and 0.5.4 dated 2016-10-03
DESCRIPTION | 8 - MD5 | 24 +-- R/patch_age.R | 12 + R/range_expansion.R | 8 - inst/doc/MetaLandSim.pdf |binary inst/doc/landscape_simulation.Rnw | 280 ++++++++++++++++++------------------- inst/doc/landscape_simulation.pdf |binary inst/doc/parametrization.pdf |binary inst/doc/range_expansion.pdf |binary man/MetaLandSim-package.Rd | 4 man/range_expansion.Rd | 1 man/range_raster.Rd | 10 - vignettes/landscape_simulation.Rnw | 280 ++++++++++++++++++------------------- 13 files changed, 316 insertions(+), 311 deletions(-)
More information about LabourMarketAreas at CRAN
Permanent link
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.7.0 dated 2016-07-05 and 1.8.0 dated 2016-10-03
strvalidator-1.7.0/strvalidator/R/calculateBalance.r |only strvalidator-1.7.0/strvalidator/R/calculateBalance_gui.r |only strvalidator-1.7.0/strvalidator/R/calculateHeterozygous.r |only strvalidator-1.7.0/strvalidator/R/calculateHeterozygous_gui.r |only strvalidator-1.7.0/strvalidator/man/calculateBalance.Rd |only strvalidator-1.7.0/strvalidator/man/calculateBalance_gui.Rd |only strvalidator-1.7.0/strvalidator/man/calculateHeterozygous.Rd |only strvalidator-1.7.0/strvalidator/man/calculateHeterozygous_gui.Rd |only strvalidator-1.7.0/strvalidator/tests/testthat/test-calculateBalance.r |only strvalidator-1.8.0/strvalidator/DESCRIPTION | 10 strvalidator-1.8.0/strvalidator/MD5 | 129 strvalidator-1.8.0/strvalidator/NAMESPACE | 13 strvalidator-1.8.0/strvalidator/NEWS | 98 strvalidator-1.8.0/strvalidator/R/addColor.r | 8 strvalidator-1.8.0/strvalidator/R/addData.r | 20 strvalidator-1.8.0/strvalidator/R/calculateAT6.r | 25 strvalidator-1.8.0/strvalidator/R/calculateConcordance.r | 53 strvalidator-1.8.0/strvalidator/R/calculateConcordance_gui.r | 41 strvalidator-1.8.0/strvalidator/R/calculateCopies.r |only strvalidator-1.8.0/strvalidator/R/calculateCopies_gui.r |only strvalidator-1.8.0/strvalidator/R/calculateDropout.r | 105 strvalidator-1.8.0/strvalidator/R/calculateDropout_gui.r | 48 strvalidator-1.8.0/strvalidator/R/calculateHb.r |only strvalidator-1.8.0/strvalidator/R/calculateHb_gui.r |only strvalidator-1.8.0/strvalidator/R/calculateHeight.r | 443 +-- strvalidator-1.8.0/strvalidator/R/calculateHeight_gui.r | 172 + strvalidator-1.8.0/strvalidator/R/calculateLb.r | 92 strvalidator-1.8.0/strvalidator/R/calculateLb_gui.r | 53 strvalidator-1.8.0/strvalidator/R/calculateMixture.r | 12 strvalidator-1.8.0/strvalidator/R/calculatePeaks.r | 207 - strvalidator-1.8.0/strvalidator/R/calculatePeaks_gui.r | 55 strvalidator-1.8.0/strvalidator/R/calculateResultType.r | 18 strvalidator-1.8.0/strvalidator/R/calculateResultType_gui.r | 20 strvalidator-1.8.0/strvalidator/R/calculateSlope.r | 2 strvalidator-1.8.0/strvalidator/R/calculateSlope_gui.r | 7 strvalidator-1.8.0/strvalidator/R/calculateSpike.r | 2 strvalidator-1.8.0/strvalidator/R/cropData_gui.r | 2 strvalidator-1.8.0/strvalidator/R/filterProfile.r | 806 +++-- strvalidator-1.8.0/strvalidator/R/filterProfile_gui.r | 129 strvalidator-1.8.0/strvalidator/R/getKit.r | 2 strvalidator-1.8.0/strvalidator/R/globals.R | 7 strvalidator-1.8.0/strvalidator/R/maskAT.r | 13 strvalidator-1.8.0/strvalidator/R/plotContamination_gui.r |only strvalidator-1.8.0/strvalidator/R/plotDistribution_gui.r | 3 strvalidator-1.8.0/strvalidator/R/plotStutter_gui.r | 2 strvalidator-1.8.0/strvalidator/R/strvalidator-package.r | 65 strvalidator-1.8.0/strvalidator/R/strvalidator.r | 44 strvalidator-1.8.0/strvalidator/R/tableBalance.r | 192 - strvalidator-1.8.0/strvalidator/R/tableBalance_gui.r | 26 strvalidator-1.8.0/strvalidator/data/ref61.RData |only strvalidator-1.8.0/strvalidator/data/ref62.RData |only strvalidator-1.8.0/strvalidator/data/ref7.RData |only strvalidator-1.8.0/strvalidator/data/set6.RData |only strvalidator-1.8.0/strvalidator/data/set7.RData |only strvalidator-1.8.0/strvalidator/inst/CITATION |only strvalidator-1.8.0/strvalidator/inst/extdata/set3.txt | 1362 +++++----- strvalidator-1.8.0/strvalidator/man/calculateConcordance.Rd | 5 strvalidator-1.8.0/strvalidator/man/calculateCopies.Rd |only strvalidator-1.8.0/strvalidator/man/calculateCopies_gui.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHb.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHb_gui.Rd |only strvalidator-1.8.0/strvalidator/man/calculateHeight.Rd | 34 strvalidator-1.8.0/strvalidator/man/calculateLb.Rd | 2 strvalidator-1.8.0/strvalidator/man/calculatePeaks.Rd | 30 strvalidator-1.8.0/strvalidator/man/calculateSlope.Rd | 2 strvalidator-1.8.0/strvalidator/man/calculateSpike.Rd | 2 strvalidator-1.8.0/strvalidator/man/filterProfile.Rd | 21 strvalidator-1.8.0/strvalidator/man/getKit.Rd | 2 strvalidator-1.8.0/strvalidator/man/plotContamination_gui.Rd |only strvalidator-1.8.0/strvalidator/man/ref61.Rd |only strvalidator-1.8.0/strvalidator/man/ref62.Rd |only strvalidator-1.8.0/strvalidator/man/ref7.Rd |only strvalidator-1.8.0/strvalidator/man/set6.Rd |only strvalidator-1.8.0/strvalidator/man/set7.Rd |only strvalidator-1.8.0/strvalidator/man/tableBalance.Rd | 15 strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateConcordance.r | 187 + strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateHb.r |only strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateHeight.r | 409 ++- strvalidator-1.8.0/strvalidator/tests/testthat/test-calculateLb.r | 43 strvalidator-1.8.0/strvalidator/tests/testthat/test-filterProfile.r | 370 ++ strvalidator-1.8.0/strvalidator/tests/testthat/test-tableBalance.r | 339 +- 81 files changed, 3579 insertions(+), 2168 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of fitted probabilities and percentiles. A graphical interface for the roulette elicitation
method is also provided. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about population distributions.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.2.0 dated 2016-08-17 and 1.2.1 dated 2016-10-03
SHELF-1.2.0/SHELF/R/SHELF1.2.0-package.R |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.R |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.Rmd |only SHELF-1.2.0/SHELF/inst/doc/Bivariate-copula.pdf |only SHELF-1.2.1/SHELF/DESCRIPTION | 10 - SHELF-1.2.1/SHELF/MD5 | 39 ++-- SHELF-1.2.1/SHELF/R/SHELF-package.R |only SHELF-1.2.1/SHELF/R/elicit.R | 5 SHELF-1.2.1/SHELF/R/expertdensity.R | 3 SHELF-1.2.1/SHELF/R/fitdist.R | 12 + SHELF-1.2.1/SHELF/R/makeLinearPoolPlot.R | 4 SHELF-1.2.1/SHELF/R/plotfit.R | 6 SHELF-1.2.1/SHELF/R/shinyplotgroup.R | 11 - SHELF-1.2.1/SHELF/R/shinyplotsingle.R | 4 SHELF-1.2.1/SHELF/inst/NEWS.md | 21 ++ SHELF-1.2.1/SHELF/inst/doc/Dirichlet-elicitation.pdf |binary SHELF-1.2.1/SHELF/inst/doc/Multivariate-normal-copula.pdf |binary SHELF-1.2.1/SHELF/inst/doc/SHELF-overview.Rmd | 4 SHELF-1.2.1/SHELF/inst/doc/SHELF-overview.pdf |binary SHELF-1.2.1/SHELF/man/SHELF-package.Rd | 10 - SHELF-1.2.1/SHELF/man/fitdist.Rd | 4 SHELF-1.2.1/SHELF/tests/testthat/test-fitting.R | 111 +++++++++++++- SHELF-1.2.1/SHELF/vignettes/SHELF-overview.Rmd | 4 23 files changed, 188 insertions(+), 60 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College Scorecard data
using the public API. It is based on the dplyr model of
piped commands to select and filter data in a single chained function call.
An API key from the U.S. Department of Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <b.skinner@vanderbilt.edu>
Diff between rscorecard versions 0.2.5 dated 2016-05-18 and 0.2.8 dated 2016-10-03
DESCRIPTION | 6 - MD5 | 18 +-- R/get.R | 4 R/rscorecard.R | 2 build/vignette.rds |binary inst/doc/introduction.R | 37 ++++++ inst/doc/introduction.Rmd | 9 + inst/doc/introduction.html | 250 +++++++++++++++++++++++++++++++-------------- man/rscorecard.Rd | 2 vignettes/introduction.Rmd | 9 + 10 files changed, 240 insertions(+), 97 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed. Provides summary and visualization functions for 'randomForest'
results.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 2.1.1 dated 2016-08-04 and 2.1.5 dated 2016-10-03
rfPermute-2.1.1/rfPermute/R/clean.rf.data.R |only rfPermute-2.1.1/rfPermute/R/exptd.err.rate.R |only rfPermute-2.1.1/rfPermute/R/plot.rfPermute.R |only rfPermute-2.1.1/rfPermute/R/proximity.plot.R |only rfPermute-2.1.1/rfPermute/R/rfpNews.R |only rfPermute-2.1.1/rfPermute/man/clean.rf.data.Rd |only rfPermute-2.1.1/rfPermute/man/exptd.err.rate.Rd |only rfPermute-2.1.1/rfPermute/man/plot.rfPermute.Rd |only rfPermute-2.1.1/rfPermute/man/proximity.plot.Rd |only rfPermute-2.1.1/rfPermute/man/rfpNews.Rd |only rfPermute-2.1.5/rfPermute/DESCRIPTION | 9 +- rfPermute-2.1.5/rfPermute/MD5 | 51 +++++++------- rfPermute-2.1.5/rfPermute/NAMESPACE | 22 ++---- rfPermute-2.1.5/rfPermute/R/classConfInt.R | 4 - rfPermute-2.1.5/rfPermute/R/cleanRFdata.R |only rfPermute-2.1.5/rfPermute/R/confusionMatrix.R | 4 - rfPermute-2.1.5/rfPermute/R/dataSets.R |only rfPermute-2.1.5/rfPermute/R/exptdErrRate.R |only rfPermute-2.1.5/rfPermute/R/plot.rp.importance.R | 2 rfPermute-2.1.5/rfPermute/R/plotNull.R |only rfPermute-2.1.5/rfPermute/R/plotVotes.R | 36 ++-------- rfPermute-2.1.5/rfPermute/R/proximityPlot.R |only rfPermute-2.1.5/rfPermute/R/rfPermute.R | 8 +- rfPermute-2.1.5/rfPermute/R/rp.combine.R | 7 +- rfPermute-2.1.5/rfPermute/README.md | 69 ++++++++++++++------ rfPermute-2.1.5/rfPermute/data |only rfPermute-2.1.5/rfPermute/man/classConfInt.Rd | 4 - rfPermute-2.1.5/rfPermute/man/cleanRFdata.Rd |only rfPermute-2.1.5/rfPermute/man/confusionMatrix.Rd | 2 rfPermute-2.1.5/rfPermute/man/exptdErrRate.Rd |only rfPermute-2.1.5/rfPermute/man/plot.rp.importance.Rd | 2 rfPermute-2.1.5/rfPermute/man/plotNull.Rd |only rfPermute-2.1.5/rfPermute/man/plotVotes.Rd | 9 ++ rfPermute-2.1.5/rfPermute/man/proximityPlot.Rd |only rfPermute-2.1.5/rfPermute/man/rfPermute.Rd | 8 +- rfPermute-2.1.5/rfPermute/man/rp.combine.Rd | 5 + rfPermute-2.1.5/rfPermute/man/symb.metab.Rd |only 37 files changed, 130 insertions(+), 112 deletions(-)
Title: Integrate R with 'RDocumentation.org'
Description: Wraps around the default help functionality in R. Instead of plain documentation files, documentation will now show up as it does on 'RDocumentation.org', a platform that shows R documentation from CRAN, GitHub and Bioconductor, together with informative stats to assess the package quality and possibilities to discuss packages.
Author: Jonathan Cornelissen <jonathan@datacamp.com>
Maintainer: Ludovic Vannoorenberghe <ludovic@datacamp.com>
Diff between RDocumentation versions 0.6 dated 2016-09-28 and 0.7.0 dated 2016-10-03
RDocumentation-0.6/RDocumentation/man/makeDefault.Rd |only RDocumentation-0.6/RDocumentation/tests/testthat/test-RProfile.R |only RDocumentation-0.6/RDocumentation/tests/testthat/test-help-search.R |only RDocumentation-0.7.0/RDocumentation/DESCRIPTION | 6 - RDocumentation-0.7.0/RDocumentation/MD5 | 24 ++-- RDocumentation-0.7.0/RDocumentation/NAMESPACE | 4 RDocumentation-0.7.0/RDocumentation/NEWS.md |only RDocumentation-0.7.0/RDocumentation/R/defaults.R |only RDocumentation-0.7.0/RDocumentation/R/overrides.R | 51 +++++----- RDocumentation-0.7.0/RDocumentation/R/utils.R | 13 -- RDocumentation-0.7.0/RDocumentation/R/view_help.R | 5 RDocumentation-0.7.0/RDocumentation/R/zzz.R | 20 ++- RDocumentation-0.7.0/RDocumentation/README.md | 1 RDocumentation-0.7.0/RDocumentation/man/defaults.Rd |only RDocumentation-0.7.0/RDocumentation/tests/testthat/test-defaults.R |only RDocumentation-0.7.0/RDocumentation/tests/testthat/test-help.R | 26 +++-- RDocumentation-0.7.0/RDocumentation/tests/testthat/test-r-profile.R |only 17 files changed, 83 insertions(+), 67 deletions(-)
More information about RDocumentation at CRAN
Permanent link
Title: Occurrence Filtering, Geographic and Taxonomic Standardization
and Generation of Species Range Polygons
Description: Provides tools for filtering occurrence records, generating alpha-hull-derived range polygons and mapping species richness.
Author: Pascal Title
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between rangeBuilder versions 1.2 dated 2016-04-14 and 1.3 dated 2016-10-03
ChangeLog | 13 +++- DESCRIPTION | 11 +-- MD5 | 43 +++++++------ NAMESPACE | 1 R/coordError.R | 140 ++++++++++++++++++++++++++------------------ R/downloadDates.R |only R/getDynamicAlphaHull.R | 12 +-- R/getExtentOfList.R | 9 ++ R/nonSquamates.R | 32 +++++----- R/repDBfunctions.R | 12 +++ R/richnessRaster.R | 11 +-- R/standardizeCountry.R | 77 +++++++++++++++++++----- R/synonymMatch.R | 2 R/sysdata.rda |binary inst |only man/acceptedAndSynonyms.Rd | 8 +- man/downloadDates.Rd |only man/getDynamicAlphaHull.Rd | 16 +++-- man/getExtentOfList.Rd | 2 man/queryGISD.Rd | 7 +- man/rangeBuilder-package.Rd | 8 +- man/richnessRaster.Rd | 20 ++++-- man/standardizeCountry.Rd | 14 +++- man/synonymMatch.Rd | 8 +- 24 files changed, 294 insertions(+), 152 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Matthew Hutchinson <matthewhutchinson15@gmail.com>
Diff between paco versions 0.2.3 dated 2015-11-10 and 0.3.0 dated 2016-10-03
paco-0.2.3/paco/R/residuals.paco.r |only paco-0.2.3/paco/man/coordpcoa.Rd |only paco-0.2.3/paco/man/residuals.paco.Rd |only paco-0.3.0/paco/DESCRIPTION | 13 +++-- paco-0.3.0/paco/MD5 | 37 +++++++-------- paco-0.3.0/paco/NAMESPACE | 2 paco-0.3.0/paco/R/PACo.r | 72 ++++++++++++++++++++++--------- paco-0.3.0/paco/R/add_pcoord.r | 13 +++-- paco-0.3.0/paco/R/coordpcoa.r | 10 ++-- paco-0.3.0/paco/R/paco_data.r | 8 +++ paco-0.3.0/paco/R/paco_links.r | 48 +++++++++++++++----- paco-0.3.0/paco/R/prepare_data.r | 13 +++-- paco-0.3.0/paco/R/residuals_paco.r |only paco-0.3.0/paco/README.md | 2 paco-0.3.0/paco/man/PACo.Rd | 28 +++++++----- paco-0.3.0/paco/man/add_pcoord.Rd | 12 ++--- paco-0.3.0/paco/man/gl_links.Rd | 4 - paco-0.3.0/paco/man/gophertree.Rd | 2 paco-0.3.0/paco/man/licetree.Rd | 2 paco-0.3.0/paco/man/paco_links.Rd | 22 +++++++-- paco-0.3.0/paco/man/prepare_paco_data.Rd | 14 ++---- paco-0.3.0/paco/man/residuals_paco.Rd |only 22 files changed, 196 insertions(+), 106 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.1.16 dated 2016-08-10 and 2.1.17 dated 2016-10-03
DESCRIPTION | 7 MD5 | 44 +-- NEWS | 7 R/create.ddfobj.R | 3 R/ddf.R | 596 ++++++++++++++++++++++++------------------------- R/gof.ds.R | 14 - R/gof.io.R | 180 ++++++++------ R/gof.io.fi.R | 14 - R/gof.trial.R | 175 +++++++------- R/integratepdf.r | 11 R/keyfct.hn.R | 26 +- R/keyfct.hz.R | 24 - R/plot.ds.R | 4 R/predict.ds.R | 2 R/predict.io.fi.R | 4 R/sethazard.R | 38 +-- R/setinitial.ds.R | 11 README.md | 82 +++--- data/book.tee.data.rda |binary man/ddf.Rd | 4 man/integratepdf.Rd | 10 man/plot.ds.Rd | 4 man/setinitial.ds.Rd | 8 23 files changed, 659 insertions(+), 609 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.8 dated 2016-06-28 and 0.9 dated 2016-10-03
DESCRIPTION | 8 - MD5 | 56 +++++---- NAMESPACE | 10 + NEWS | 40 ++++++ R/arx.R | 14 +- R/gets-internal.R | 147 +++---------------------- R/getsm.R | 14 ++ R/getsv.R | 10 + R/iim.R | 2 R/isat.R | 84 +++++++++++--- R/isattest.R | 28 ++-- R/isatvar.R | 252 +++++++++++++++++++++++++++++-------------- R/isvarcor.R |only R/isvareffcor.R |only R/predict.arx.R | 304 ++++++++++++++++++++++++++++++++++++++++++---------- R/predict.gets.R |only R/predict.isat.R |only R/print.arx.R | 14 +- R/print.gets.R | 25 ++-- R/print.isat.R | 26 ++-- R/sim.R | 4 R/tim.R | 2 man/coef.arx.Rd | 297 ++++++++++++++++++++++++++------------------------ man/coef.gets.Rd | 261 ++++++++++++++++++++++++-------------------- man/coef.isat.Rd | 223 +++++++++++++++++++++----------------- man/gets-package.Rd | 4 man/getsm.Rd | 4 man/isat.Rd | 4 man/isattest.Rd | 12 +- man/isatvar.Rd | 15 +- man/isvarcor.Rd |only man/isvareffcor.Rd |only 32 files changed, 1114 insertions(+), 746 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.2.0 dated 2016-09-26 and 2.3.0 dated 2016-10-03
DESCRIPTION | 22 +++++++----- MD5 | 50 ++++++++++++++++------------- NAMESPACE | 34 +++++++++++++++++-- R/DAYMET_FUNCTIONS.R |only R/GHCN_FUNCTIONS.R | 72 +++++++++++++++++++++++++----------------- R/ITRDB_FUNCTIONS.R | 32 +++++++++--------- R/NED_FUNCTIONS.R | 21 +++++------- R/NHD_FUNCTIONS.R | 25 ++++++-------- R/SSURGO_FUNCTIONS.R | 32 +++++++++--------- R/UTILITY_FUNCTIONS.R | 5 +- README.md | 67 +++++++++++++++++++++------------------ data |only inst/CITATION | 4 +- inst/FedDataTester.R | 66 ++++++++++++++++++++++---------------- inst/img/DAYMET.png |only inst/img/NED.png |binary man/FedData-package.Rd | 15 +++++++- man/download_daymet_tile.Rd |only man/get_daymet.Rd |only man/get_daymet_tile.Rd |only man/get_ghcn_daily.Rd | 5 +- man/get_ghcn_daily_station.Rd | 6 ++- man/get_itrdb.Rd | 3 + man/get_ned.Rd | 4 +- man/get_nhd.Rd | 3 + man/get_ssurgo.Rd | 3 + man/tiles.Rd |only tests/testthat/test.DAYMET.R |only tests/testthat/test.NED.R | 8 ++-- tests/testthat/test.NHD.R | 6 +-- 30 files changed, 281 insertions(+), 202 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 2.2.1 dated 2016-09-04 and 2.3.0 dated 2016-10-03
dtwclust-2.2.1/dtwclust/R/all_cent.R |only dtwclust-2.2.1/dtwclust/inst/doc/dtwclust.R |only dtwclust-2.2.1/dtwclust/src/update_lcm.c |only dtwclust-2.2.1/dtwclust/tests/testthat/test_distances.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_pairwise.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_repetitions.R |only dtwclust-2.2.1/dtwclust/tests/testthat/test_tadpole.R |only dtwclust-2.3.0/dtwclust/DESCRIPTION | 23 dtwclust-2.3.0/dtwclust/MD5 | 125 dtwclust-2.3.0/dtwclust/NAMESPACE | 6 dtwclust-2.3.0/dtwclust/R/DBA.R | 460 +- dtwclust-2.3.0/dtwclust/R/NCCc.R | 10 dtwclust-2.3.0/dtwclust/R/SBD.R | 435 +- dtwclust-2.3.0/dtwclust/R/TADPole.R | 643 +-- dtwclust-2.3.0/dtwclust/R/all-cent.R |only dtwclust-2.3.0/dtwclust/R/ddist.R | 378 +- dtwclust-2.3.0/dtwclust/R/dtw-basic.R |only dtwclust-2.3.0/dtwclust/R/dtw-lb.R | 69 dtwclust-2.3.0/dtwclust/R/dtw2.R | 54 dtwclust-2.3.0/dtwclust/R/dtwclust-classes.R | 13 dtwclust-2.3.0/dtwclust/R/dtwclust-methods.R | 1587 ++++----- dtwclust-2.3.0/dtwclust/R/dtwclust.R | 1761 ++++------ dtwclust-2.3.0/dtwclust/R/fuzzy.R | 42 dtwclust-2.3.0/dtwclust/R/lb-improved.R | 18 dtwclust-2.3.0/dtwclust/R/lb-keogh.R | 18 dtwclust-2.3.0/dtwclust/R/partitional.R | 41 dtwclust-2.3.0/dtwclust/R/pkg.R | 91 dtwclust-2.3.0/dtwclust/R/reinterpolate.R | 33 dtwclust-2.3.0/dtwclust/R/shape-extraction.R | 294 - dtwclust-2.3.0/dtwclust/R/utils.R | 148 dtwclust-2.3.0/dtwclust/R/zscore.R | 115 dtwclust-2.3.0/dtwclust/README.md | 53 dtwclust-2.3.0/dtwclust/build/vignette.rds |binary dtwclust-2.3.0/dtwclust/inst/NEWS.Rd | 17 dtwclust-2.3.0/dtwclust/inst/doc/dtwclust.Rnw | 116 dtwclust-2.3.0/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-2.3.0/dtwclust/inst/dtwclust-examples.R | 10 dtwclust-2.3.0/dtwclust/man/DBA.Rd | 25 dtwclust-2.3.0/dtwclust/man/TADPole.Rd | 16 dtwclust-2.3.0/dtwclust/man/dtw2.Rd |only dtwclust-2.3.0/dtwclust/man/dtw_basic.Rd |only dtwclust-2.3.0/dtwclust/man/dtw_lb.Rd | 9 dtwclust-2.3.0/dtwclust/man/dtwclust-class.Rd | 7 dtwclust-2.3.0/dtwclust/man/dtwclust-methods.Rd | 10 dtwclust-2.3.0/dtwclust/man/dtwclust-package.Rd | 51 dtwclust-2.3.0/dtwclust/man/dtwclust.Rd | 66 dtwclust-2.3.0/dtwclust/man/dtwclustControl-class.Rd | 2 dtwclust-2.3.0/dtwclust/man/dtwclustFamily-class.Rd | 2 dtwclust-2.3.0/dtwclust/man/lb_improved.Rd | 4 dtwclust-2.3.0/dtwclust/man/lb_keogh.Rd | 4 dtwclust-2.3.0/dtwclust/man/reinterpolate.Rd | 12 dtwclust-2.3.0/dtwclust/man/shape_extraction.Rd | 8 dtwclust-2.3.0/dtwclust/man/zscore.Rd | 12 dtwclust-2.3.0/dtwclust/src/dtw-basic.c |only dtwclust-2.3.0/dtwclust/src/update-lcm.c |only dtwclust-2.3.0/dtwclust/tests/testthat.R | 14 dtwclust-2.3.0/dtwclust/tests/testthat/helper_all.R | 32 dtwclust-2.3.0/dtwclust/tests/testthat/test_all_distances.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_centroids.R | 468 +- dtwclust-2.3.0/dtwclust/tests/testthat/test_custom_distance.R | 107 dtwclust-2.3.0/dtwclust/tests/testthat/test_cvis.R | 54 dtwclust-2.3.0/dtwclust/tests/testthat/test_dtw_basic.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_fuzzy.R | 97 dtwclust-2.3.0/dtwclust/tests/testthat/test_hierarchical.R | 82 dtwclust-2.3.0/dtwclust/tests/testthat/test_lbs.R | 158 dtwclust-2.3.0/dtwclust/tests/testthat/test_methods.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_partitional.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_types.R | 103 dtwclust-2.3.0/dtwclust/tests/testthat/test_zparallel.R | 26 dtwclust-2.3.0/dtwclust/vignettes/REFERENCES.bib | 73 dtwclust-2.3.0/dtwclust/vignettes/dtwclust-concordance.tex | 4 dtwclust-2.3.0/dtwclust/vignettes/dtwclust.Rnw | 116 72 files changed, 4241 insertions(+), 3881 deletions(-)
Title: Density Surface Modelling of Distance Sampling Data
Description: Density surface modelling of line transect data. A Generalized
Additive Model-based approach is used to calculate spatially-explicit estimates
of animal abundance from distance sampling (also presence/absence and strip
transect) data. Several utility functions are provided for model checking,
plotting and variance estimation.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley.
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dsm versions 2.2.12 dated 2016-08-11 and 2.2.13 dated 2016-10-03
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/dsm.R | 38 ++++++++++++++------------------------ R/dsm.var.gam.R | 29 +++++++++++++++++++++++++++-- R/dsm.var.prop.R | 9 +++++++-- R/print.summary.dsm.var.R | 7 +++++-- R/summary.dsm.var.R | 5 ++++- R/zzz.R | 32 +++++++++++++++++++++++--------- man/dsm.Rd | 2 +- man/dsm.var.gam.Rd | 28 +++++++++++++++++++++++++++- 11 files changed, 127 insertions(+), 56 deletions(-)
Title: Distributed-Lag Structural Equation Modelling with Second-Order
Polynomial Lag Shapes
Description: Estimation and path analysis functionalities for structural equation models with second-order polynomial lag shapes.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.3.2 dated 2016-09-16 and 1.4 dated 2016-10-03
dlsem-1.3.2/dlsem/vignettes/figures/dagsam.png |only dlsem-1.3.2/dlsem/vignettes/figures/polylag.png |only dlsem-1.4/dlsem/DESCRIPTION | 9 dlsem-1.4/dlsem/MD5 | 37 +- dlsem-1.4/dlsem/NAMESPACE | 1 dlsem-1.4/dlsem/build/vignette.rds |binary dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.R | 24 - dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.Rnw | 372 ++++++------------------ dlsem-1.4/dlsem/inst/doc/dlsem_tutorial.pdf |binary dlsem-1.4/dlsem/man/EM.imputation.Rd | 2 dlsem-1.4/dlsem/man/applyDiff.Rd | 2 dlsem-1.4/dlsem/man/dlsem-package.Rd | 6 dlsem-1.4/dlsem/man/dlsem.Rd | 3 dlsem-1.4/dlsem/man/edgeCoeff.Rd | 2 dlsem-1.4/dlsem/man/fitIndices.Rd | 2 dlsem-1.4/dlsem/man/isIndep.Rd | 2 dlsem-1.4/dlsem/man/lagPlot.Rd | 2 dlsem-1.4/dlsem/man/pathAnal.Rd | 2 dlsem-1.4/dlsem/man/unirootTest.Rd | 2 dlsem-1.4/dlsem/vignettes/dlsem_tutorial.Rnw | 372 ++++++------------------ dlsem-1.4/dlsem/vignettes/figures/sampledag.png |only 21 files changed, 261 insertions(+), 579 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from the Bureau of Labor Statistics, which is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 0.4.2 dated 2016-07-29 and 1.0.1 dated 2016-10-03
DESCRIPTION | 6 +- MD5 | 64 +++++++++++++++++++----------- NAMESPACE | 1 NEWS.md | 26 ++++++++++++ R/area_titles.R |only R/get_bls_county.R | 4 - R/maps.R | 2 R/niacs.R |only R/qcew_api.R |only R/size_titles.R |only README.md | 2 build/vignette.rds |binary data/area_titles.rda |only data/niacs.rda |only data/size_titles.rda |only inst/doc/Employment_and_Unemployment.html | 4 - inst/doc/Inflation_and_Prices.Rmd | 2 inst/doc/Inflation_and_Prices.html | 8 +-- inst/doc/Mapping_BLS_Data.R | 2 inst/doc/Mapping_BLS_Data.Rmd | 2 inst/doc/Mapping_BLS_Data.html | 6 +- inst/doc/Pay_and_Benefits.R | 2 inst/doc/Pay_and_Benefits.Rmd | 2 inst/doc/Pay_and_Benefits.html | 6 +- inst/doc/QCEW_API.R |only inst/doc/QCEW_API.Rmd |only inst/doc/QCEW_API.html |only inst/doc/qcew.R |only inst/doc/qcew.Rmd |only inst/doc/qcew.html |only man/area_titles.Rd |only man/bls_map_county.Rd | 2 man/bls_map_state.Rd | 2 man/niacs.Rd |only man/qcew_api.Rd |only man/size_titles.Rd |only tests/testthat/test_bls_csv.R | 2 tests/testthat/test_qcew_api.R |only vignettes/Inflation_and_Prices.Rmd | 2 vignettes/Mapping_BLS_Data.Rmd | 2 vignettes/Pay_and_Benefits.Rmd | 2 vignettes/QCEW_API.Rmd |only vignettes/qcew.Rmd |only 43 files changed, 96 insertions(+), 55 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.4 dated 2016-06-13 and 2.1.5 dated 2016-10-03
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 2 ++ R/BAMMtools-package.R | 1 + R/getJenksBreaks.R | 9 +++++---- R/stepBF.R |only R/traitDependentBAMM.R | 28 ++++++++++++++++++---------- man/getJenksBreaks.Rd | 9 +++++---- man/stepBF.Rd |only man/traitDependentBAMM.Rd | 11 ++++++----- 10 files changed, 50 insertions(+), 34 deletions(-)
Title: Sparse Principal Component Regression
Description: The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano <skawano@uec.ac.jp>
Diff between spcr versions 1.2.1 dated 2014-12-04 and 2.0 dated 2016-10-03
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++++------ NAMESPACE | 8 ++++---- R/SPCRLoG.R |only R/SPCRMultiLoG.R |only R/SPCRPoi.R |only R/cv.spcr.R | 6 +++--- R/cv.spcrglm.R |only R/softthresh.R |only R/spcrglm.R |only man/cv.spcr.Rd | 14 +++++++------- man/cv.spcrglm.Rd |only man/spcr.Rd | 12 ++++++------ man/spcrglm.Rd |only src/SPCR.c | 2 +- 15 files changed, 42 insertions(+), 34 deletions(-)
Title: Simulation of the Forensic DNA Process
Description: Simulate the forensic DNA process: generate random or fixed DNA
profiles, create forensic samples including mixtures of diploid and haploid
cells, simulate DNA extraction, normalization, degradation, amplification
including stutters and inter-locus balance, and capillary electrophoresis.
DNA profiles are visualized as electropherograms and saved in tables.
The command pcrsim() opens up a graphical user interface which allow the user
to create projects, to enter, load, and save parameters required for the simulation.
The simulation is transparent and the parameters used in each step of the simulation
can be viewed in the result tables.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between pcrsim versions 1.0.0 dated 2016-04-21 and 1.0.1 dated 2016-10-03
DESCRIPTION | 8 +- MD5 | 17 +++--- NEWS | 8 ++ R/calibratePCRsim.r | 65 +++++++---------------- R/calibrateScaling.r | 39 +++++++++---- R/getParameter.r | 6 +- R/pcrsim.r | 38 +++++++++---- README.md |only inst/extdata/tutorial_pcrsim_project.RData |binary inst/extdata/tutorial_strvalidator_project.RData |binary 10 files changed, 102 insertions(+), 79 deletions(-)
Title: Pre-Process of Time Series Data Set in R
Description: Pre-process for discrete time series data set which is not continuous at the column
of 'date'. Refilling records of missing 'date' and other columns to the hollow data set so that
final data set is able to be dealt with time series analysis.
Author: Will Kuan <aiien61will@gmail.com>
Maintainer: Will Kuan <aiien61will@gmail.com>
Diff between tigerhitteR versions 1.0.2 dated 2016-07-07 and 1.1.0 dated 2016-10-03
tigerhitteR-1.0.2/tigerhitteR/man/dateRefill.fromsFile.Rd |only tigerhitteR-1.1.0/tigerhitteR/DESCRIPTION | 11 tigerhitteR-1.1.0/tigerhitteR/MD5 | 10 tigerhitteR-1.1.0/tigerhitteR/NAMESPACE | 20 tigerhitteR-1.1.0/tigerhitteR/R/tigerhitteR.R | 443 ++++------ tigerhitteR-1.1.0/tigerhitteR/man/dateRefill.fromData.Rd | 13 tigerhitteR-1.1.0/tigerhitteR/man/dateRefill.fromFileToExcel.Rd |only 7 files changed, 250 insertions(+), 247 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>
Diff between kernlab versions 0.9-24 dated 2016-03-29 and 0.9-25 dated 2016-10-03
DESCRIPTION | 10 - MD5 | 14 +- inst/doc/kernlab.pdf |binary src/esa.cpp | 322 +++++++++++++++++++++++++-------------------------- src/msufsort.cpp | 2 src/msufsort.h | 2 src/stringkernel.cpp | 38 +++--- src/stringkernel.h | 8 - 8 files changed, 199 insertions(+), 197 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.27 dated 2016-04-22 and 2.28 dated 2016-10-03
BDgraph-2.27/BDgraph/src/gcgm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/gcgm_DMH_rj.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_bd.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_bd_multi_update.cpp |only BDgraph-2.27/BDgraph/src/ggm_DMH_rj.cpp |only BDgraph-2.28/BDgraph/DESCRIPTION | 11 - BDgraph-2.28/BDgraph/MD5 | 97 +++++++------ BDgraph-2.28/BDgraph/NAMESPACE | 15 +- BDgraph-2.28/BDgraph/NEWS | 18 +- BDgraph-2.28/BDgraph/R/bdgraph.R | 56 +++---- BDgraph-2.28/BDgraph/R/bdgraph.sim.R | 50 +++--- BDgraph-2.28/BDgraph/R/bdgraph.ts.R |only BDgraph-2.28/BDgraph/R/rcwish.R |only BDgraph-2.28/BDgraph/R/rgcwish.R |only BDgraph-2.28/BDgraph/R/rgwish.R | 21 +- BDgraph-2.28/BDgraph/man/BDgraph-package.Rd | 2 BDgraph-2.28/BDgraph/man/bdgraph.Rd | 9 - BDgraph-2.28/BDgraph/man/bdgraph.npn.Rd | 6 BDgraph-2.28/BDgraph/man/bdgraph.sim.Rd | 8 - BDgraph-2.28/BDgraph/man/bdgraph.ts.Rd |only BDgraph-2.28/BDgraph/man/compare.Rd | 5 BDgraph-2.28/BDgraph/man/geneExpression.Rd | 4 BDgraph-2.28/BDgraph/man/pgraph.Rd | 2 BDgraph-2.28/BDgraph/man/plinks.Rd | 4 BDgraph-2.28/BDgraph/man/plot.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/plot.sim.Rd | 3 BDgraph-2.28/BDgraph/man/plotcoda.Rd | 4 BDgraph-2.28/BDgraph/man/plotroc.Rd | 8 - BDgraph-2.28/BDgraph/man/print.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/rcwish.Rd |only BDgraph-2.28/BDgraph/man/rgcwish.Rd |only BDgraph-2.28/BDgraph/man/rgwish.Rd | 4 BDgraph-2.28/BDgraph/man/rwish.Rd | 4 BDgraph-2.28/BDgraph/man/select.Rd | 4 BDgraph-2.28/BDgraph/man/summary.bdgraph.Rd | 4 BDgraph-2.28/BDgraph/man/surveyData.Rd | 4 BDgraph-2.28/BDgraph/man/traceplot.Rd | 4 BDgraph-2.28/BDgraph/src/Ig.cpp | 2 BDgraph-2.28/BDgraph/src/Makevars | 1 BDgraph-2.28/BDgraph/src/Makevars.win | 1 BDgraph-2.28/BDgraph/src/MyLapack.cpp |only BDgraph-2.28/BDgraph/src/MyLapack.h |only BDgraph-2.28/BDgraph/src/bd_for_ts.cpp |only BDgraph-2.28/BDgraph/src/copula.cpp | 4 BDgraph-2.28/BDgraph/src/gcgm_DMH.cpp |only BDgraph-2.28/BDgraph/src/gcgm_bd.cpp | 24 +-- BDgraph-2.28/BDgraph/src/gcgm_bd_multi_update.cpp | 24 +-- BDgraph-2.28/BDgraph/src/gcgm_rj.cpp | 23 +-- BDgraph-2.28/BDgraph/src/ggm_DMH.cpp |only BDgraph-2.28/BDgraph/src/ggm_bd.cpp | 33 ++-- BDgraph-2.28/BDgraph/src/ggm_bd_multi_update.cpp | 33 ++-- BDgraph-2.28/BDgraph/src/ggm_rj.cpp | 22 +- BDgraph-2.28/BDgraph/src/matrix.cpp | 133 +++++++++++++++++- BDgraph-2.28/BDgraph/src/matrix.h | 15 +- BDgraph-2.28/BDgraph/src/rgcwish.cpp |only BDgraph-2.28/BDgraph/src/rgcwish.h |only BDgraph-2.28/BDgraph/src/rgwish.cpp | 21 -- BDgraph-2.28/BDgraph/src/scaleFree.cpp | 2 59 files changed, 418 insertions(+), 275 deletions(-)
Title: Create and Navigate Large Multi-Panel Visual Displays
Description: An extension of Trellis Display that enables creation,
organization, and interactive viewing of multi-panel displays created
against potentially very large data sets. The dynamic viewer tiles
panels of a display across the screen in a web browser and allows the
user to interactively page through the panels and sort and filter them
based on "cognostic" metrics computed for each panel. Panels can be
created using many of R's plotting capabilities, including base R
graphics, 'lattice', 'ggplot2', and many 'htmlwidgets'. Conditioning is
handled through the 'datadr' package, which enables 'Trelliscope' displays
with potentially millions of panels to be created against terabytes of
data on systems like 'Hadoop'. While designed to scale, 'Trelliscope'
displays can also be very useful for small data sets.
Author: Ryan Hafen [aut, cre],
Jeremiah Rounds [ctb],
Barret Schloerke [ctb],
Landon Sego [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between trelliscope versions 0.9.4 dated 2016-03-25 and 0.9.7 dated 2016-10-03
DESCRIPTION | 14 +++--- MD5 | 44 ++++++++++---------- NAMESPACE | 10 ++++ NEWS.md | 21 ++++++--- R/cognostics.R | 2 R/convert.R |only R/makeDisplay.R | 17 +++++-- R/makeDisplay_internals.R | 11 ++++- R/qtrellis.R | 2 R/state.R | 12 ----- R/trelliscope-package.R | 4 - R/view.R | 6 +- README.md | 16 +++---- inst/trelliscopeViewer/server/_fns.R | 22 ++++++++++ inst/trelliscopeViewer/server/panelTable.R | 11 +++-- inst/trelliscopeViewer/www/assets/custom/custom.css | 3 + inst/trelliscopeViewer/www/assets/custom/main.js | 21 +++++---- inst/trelliscopeViewer/www/index.html | 8 +-- man/cogScagnostics.Rd | 2 man/makeDisplay.Rd | 13 +++-- man/trelliscope-package.Rd | 2 man/vdbConvert.Rd |only man/view.Rd | 5 +- tests/testthat/_init.R | 2 24 files changed, 159 insertions(+), 89 deletions(-)
Title: Streamlined Estimation of Survival for Static, Dynamic and
Stochastic Treatment and Monitoring Regimes
Description: Analysis of longitudinal time-to-event or time-to-failure data.
Estimates the counterfactual discrete survival curve under static, dynamic and
stochastic interventions on treatment (exposure) and monitoring events over time.
Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying
confounding and informative right-censoring. Model fitting can be performed either
with GLM or H2O-3 machine learning libraries, including the ensemble-based
SuperLearner ('h2oEnsemble').
The exposure, monitoring and censoring variables can be coded as either binary,
categorical or continuous. Each can be multivariate (e.g., can use more than one
column of dummy indicators for different censoring events).
The input data needs to be in long format.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between stremr versions 0.1 dated 2016-10-01 and 0.2 dated 2016-10-03
DESCRIPTION | 10 ++++--- MD5 | 30 ++++++++++----------- R/BinomialGLMsClass.R | 4 ++ R/BinomialMLclass.R | 3 -- R/BinomialModelClass.R | 10 +++---- R/reports.R | 10 +++++++ R/zzz.R | 18 ++++++------ README.md | 6 ++-- man/set_all_stremr_options.Rd | 2 - man/survMSM.Rd | 2 + tests/RUnit/RUnit_tests_04a_sims10K_speedglm.R | 15 ++++++---- tests/RUnit/RUnit_tests_04b_sims10K_h2oGLM.R | 5 ++- tests/RUnit/RUnit_tests_04c_sims10K_h2o_ALL_ML.R | 15 ++++++---- tests/RUnit/RUnit_tests_05_stremr_example_SL.R | 5 ++- tests/RUnit/RUnit_tests_06_direct_regression_def.R | 17 +++++++---- tests/examples/4_survMSM_example.R | 2 + 16 files changed, 92 insertions(+), 62 deletions(-)
Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices
The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data
structures and R using concepts from 'Rcpp' which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses 'Rcpp' to connect to another third-party library. The 'autoconf'
script, 'inline' plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGSL versions 0.3.0 dated 2015-08-30 and 0.3.1 dated 2016-10-03
RcppGSL-0.3.0/RcppGSL/R/unit.test.R |only RcppGSL-0.3.0/RcppGSL/inst/unitTests/runTests.R |only RcppGSL-0.3.1/RcppGSL/ChangeLog | 17 ++++ RcppGSL-0.3.1/RcppGSL/DESCRIPTION | 8 +- RcppGSL-0.3.1/RcppGSL/MD5 | 32 +++----- RcppGSL-0.3.1/RcppGSL/README.md | 69 +++++++++++++++++ RcppGSL-0.3.1/RcppGSL/build/vignette.rds |binary RcppGSL-0.3.1/RcppGSL/inst/NEWS.Rd | 14 +++ RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.R | 6 - RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.Rnw | 6 - RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-intro.pdf |binary RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.R | 12 +-- RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.Rnw | 12 +-- RcppGSL-0.3.1/RcppGSL/inst/doc/RcppGSL-unitTests.pdf |binary RcppGSL-0.3.1/RcppGSL/tests/doRUnit.R | 70 ++++++++++-------- RcppGSL-0.3.1/RcppGSL/vignettes/RcppGSL-intro.Rnw | 6 - RcppGSL-0.3.1/RcppGSL/vignettes/RcppGSL-unitTests.Rnw | 12 +-- RcppGSL-0.3.1/RcppGSL/vignettes/buildVignette.R | 2 18 files changed, 182 insertions(+), 84 deletions(-)
Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex, html or xml document. Use
the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between hunspell versions 2.0 dated 2016-09-08 and 2.1 dated 2016-10-03
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS | 7 ++++- R/hunspell.R | 2 - inst/doc/intro.R | 17 +++++++++--- inst/doc/intro.Rmd | 60 ++++++++++++++++++++++++++++----------------- inst/doc/intro.html | 56 +++++++++++++++++------------------------- man/hunspell.Rd | 2 - src/hunspell/suggestmgr.cc | 4 +-- vignettes/intro.Rmd | 34 ++++++++++++------------- 10 files changed, 112 insertions(+), 94 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.1-1 dated 2016-04-14 and 1.2-0 dated 2016-10-03
DESCRIPTION | 10 +++---- MD5 | 31 +++++++++++++---------- NAMESPACE | 21 +++++++--------- NEWS.md |only R/AAAhelpers.R | 5 +++ R/AAAparameter.R | 8 +++--- R/graph.R | 2 - R/groupedmatrix.R | 64 +++++++++++++++++++------------------------------ R/inspectDT.R |only R/iplot.R | 22 ++++++++-------- R/matrix.R | 2 - R/paracoord.R | 2 - R/plotly.R |only R/scatterplot.R | 20 ++++++++------- README.md | 8 +++--- inst/doc/arulesViz.pdf |binary man/inspectDT.Rd |only man/plot.Rd | 53 ++++++++++++++++++++++++++-------------- man/plotly_arules.Rd |only 19 files changed, 130 insertions(+), 118 deletions(-)