Title: Reversible-Jump MCMC Using Post-Processing
Description: Performs reversible-jump Markov chain Monte Carlo (Green, 1995)
<doi:10.2307/2337340>, specifically the restriction introduced by
Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising
a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling
problem. Previously-calculated posterior distributions are used to
quickly estimate posterior model probabilities. Jacobian matrices are
found using automatic differentiation.
Author: Nick Gelling [aut, cre],
Matthew R. Schofield [aut],
Richard J. Barker [aut]
Maintainer: Nick Gelling <nick_gelling@hotmail.com>
Diff between rjmcmc versions 0.4.2 dated 2018-09-29 and 0.4.3 dated 2018-10-04
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- R/defaultpost.R | 26 +++++++++++++------------- R/rjmcmcpost.R | 12 ++++++------ inst/doc/rjmcmcVig.R | 2 +- inst/doc/rjmcmcVig.Rnw | 2 +- inst/doc/rjmcmcVig.pdf |binary man/defaultpost.Rd | 8 ++++---- man/rjmcmcpost.Rd | 8 ++++---- vignettes/fishBert.txt |only vignettes/fishGomp.txt |only vignettes/rjmcmcVig.Rnw | 2 +- 12 files changed, 45 insertions(+), 43 deletions(-)
Title: Pathway Enrichment Analysis Utilizing Active Subnetworks
Description: Pathway enrichment analysis enables researchers to uncover mechanisms
underlying the phenotype. pathfindR is a tool for pathway enrichment analysis
utilizing active subnetworks. It identifies active subnetworks in a
protein-protein interaction network using user-provided a list of genes.
It performs pathway enrichment analyses on the identified subnetworks.
pathfindR also offers functionalities to cluster enriched pathways and identify
representative pathways and to score the pathways per sample. The method is
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R
Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv.
<doi:10.1101/272450>.
Author: Ege Ulgen, Ozan Ozisik
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.2.1 dated 2018-08-17 and 1.2.2 dated 2018-10-04
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/pathmap.R | 1 + R/pwd.R | 35 +++++++++++++++++++++++++---------- R/wrapper.R | 27 +++++++++++++++++++-------- inst/doc/pathfindr_vignette.html | 13 +++++++------ inst/rmd/clustering.Rmd | 16 +++++++++++++--- man/calculate_pwd.Rd | 15 ++++++++++++--- man/choose_clusters.Rd | 12 ++++++++++-- 11 files changed, 110 insertions(+), 47 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional kernel term and sampling techniques as described
by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.5.5 dated 2018-09-16 and 1.5.6 dated 2018-10-04
bWGR-1.5.5/bWGR/README.md |only bWGR-1.5.6/bWGR/DESCRIPTION | 11 ++- bWGR-1.5.6/bWGR/MD5 | 21 +++---- bWGR-1.5.6/bWGR/R/RcppExports.R | 4 + bWGR-1.5.6/bWGR/R/cv.R | 102 ++++++++++++++++++++++++++++++------ bWGR-1.5.6/bWGR/R/mix.R | 12 ++-- bWGR-1.5.6/bWGR/man/bWGR.Rd | 7 +- bWGR-1.5.6/bWGR/man/em.Rd | 11 +++ bWGR-1.5.6/bWGR/man/mix.Rd | 11 ++- bWGR-1.5.6/bWGR/man/wgr.Rd | 6 +- bWGR-1.5.6/bWGR/src/RcppExports.cpp | 14 ++++ bWGR-1.5.6/bWGR/src/wgr20180916.cpp | 73 +++++++++++++++++++++++-- 12 files changed, 219 insertions(+), 53 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Paul Blanche [ctb],
Ulla Brasch Mogensen [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2018.04.21 dated 2018-04-19 and 2018.10.03 dated 2018-10-04
riskRegression-2018.04.21/riskRegression/R/print.InfluenceCoxTest.R |only riskRegression-2018.04.21/riskRegression/man/coxDesign.Rd |only riskRegression-2018.04.21/riskRegression/man/coxSpecialStrata.Rd |only riskRegression-2018.04.21/riskRegression/man/extractStrata.Rd |only riskRegression-2018.04.21/riskRegression/man/influenceCoxTest.Rd |only riskRegression-2018.04.21/riskRegression/man/print.influenceCoxTest.Rd |only riskRegression-2018.04.21/riskRegression/tests/test-predictCox.R |only riskRegression-2018.04.21/riskRegression/tests/test-predictCox_vs_timereg.R |only riskRegression-2018.10.03/riskRegression/DESCRIPTION | 12 riskRegression-2018.10.03/riskRegression/MD5 | 226 +- riskRegression-2018.10.03/riskRegression/NAMESPACE | 49 riskRegression-2018.10.03/riskRegression/NEWS | 8 riskRegression-2018.10.03/riskRegression/R/0onload.R |only riskRegression-2018.10.03/riskRegression/R/CSC.R | 9 riskRegression-2018.10.03/riskRegression/R/RcppExports.R | 139 - riskRegression-2018.10.03/riskRegression/R/Score.R | 619 +++--- riskRegression-2018.10.03/riskRegression/R/as.data.table.ate.R |only riskRegression-2018.10.03/riskRegression/R/as.data.table.ateRobust.R |only riskRegression-2018.10.03/riskRegression/R/as.data.table.influenceTest.R |only riskRegression-2018.10.03/riskRegression/R/as.data.table.predictCSC.R | 85 riskRegression-2018.10.03/riskRegression/R/as.data.table.predictCox.R | 138 + riskRegression-2018.10.03/riskRegression/R/ate.R | 377 ++-- riskRegression-2018.10.03/riskRegression/R/ateRobust.R |only riskRegression-2018.10.03/riskRegression/R/autoplot.Score.R |only riskRegression-2018.10.03/riskRegression/R/autoplot.ate.R | 96 - riskRegression-2018.10.03/riskRegression/R/autoplot.predictCSC.R | 117 - riskRegression-2018.10.03/riskRegression/R/autoplot.predictCox.R | 338 ++- riskRegression-2018.10.03/riskRegression/R/calcBootATE.R | 279 --- riskRegression-2018.10.03/riskRegression/R/calcSeATE.R | 305 +-- riskRegression-2018.10.03/riskRegression/R/calcSeCSC.R | 304 +-- riskRegression-2018.10.03/riskRegression/R/calcSeCox.R | 278 +-- riskRegression-2018.10.03/riskRegression/R/confBandCox.R | 8 riskRegression-2018.10.03/riskRegression/R/confint.ate.R |only riskRegression-2018.10.03/riskRegression/R/confint.ateRobust.R |only riskRegression-2018.10.03/riskRegression/R/confint.influenceTest.R |only riskRegression-2018.10.03/riskRegression/R/confint.predictCSC.R |only riskRegression-2018.10.03/riskRegression/R/confint.predictCox.R |only riskRegression-2018.10.03/riskRegression/R/getCensoringWeights.R | 5 riskRegression-2018.10.03/riskRegression/R/getComparisons.R | 15 riskRegression-2018.10.03/riskRegression/R/getCoxInfo.R | 688 ++++--- riskRegression-2018.10.03/riskRegression/R/getResponse.R | 36 riskRegression-2018.10.03/riskRegression/R/getVcov.R | 10 riskRegression-2018.10.03/riskRegression/R/iid.R |only riskRegression-2018.10.03/riskRegression/R/iidCox.R | 128 - riskRegression-2018.10.03/riskRegression/R/influenceTest.R | 336 +-- riskRegression-2018.10.03/riskRegression/R/plotAUC.R | 201 +- riskRegression-2018.10.03/riskRegression/R/plotBrier.R | 6 riskRegression-2018.10.03/riskRegression/R/plotCalibration.R | 23 riskRegression-2018.10.03/riskRegression/R/predict.CauseSpecificCox.R | 437 +--- riskRegression-2018.10.03/riskRegression/R/predictCox.R | 917 +++++----- riskRegression-2018.10.03/riskRegression/R/predictCoxPL.R | 260 +- riskRegression-2018.10.03/riskRegression/R/predictRisk.R | 29 riskRegression-2018.10.03/riskRegression/R/print.Score.R | 8 riskRegression-2018.10.03/riskRegression/R/print.ate.R | 256 ++ riskRegression-2018.10.03/riskRegression/R/print.ateRobust.R |only riskRegression-2018.10.03/riskRegression/R/print.influenceTest.R |only riskRegression-2018.10.03/riskRegression/R/print.predictCSC.R | 57 riskRegression-2018.10.03/riskRegression/R/print.predictCox.R | 60 riskRegression-2018.10.03/riskRegression/R/riskRegression-package.R | 5 riskRegression-2018.10.03/riskRegression/R/transform.R |only riskRegression-2018.10.03/riskRegression/man/CSC.Rd | 7 riskRegression-2018.10.03/riskRegression/man/Melanoma.Rd | 3 riskRegression-2018.10.03/riskRegression/man/Score.list.Rd | 13 riskRegression-2018.10.03/riskRegression/man/as.data.table.ate.Rd |only riskRegression-2018.10.03/riskRegression/man/as.data.table.ateRobust.Rd |only riskRegression-2018.10.03/riskRegression/man/as.data.table.influenceTest.Rd |only riskRegression-2018.10.03/riskRegression/man/as.data.table.predictCSC.Rd | 9 riskRegression-2018.10.03/riskRegression/man/as.data.table.predictCox.Rd | 13 riskRegression-2018.10.03/riskRegression/man/ate.Rd | 118 - riskRegression-2018.10.03/riskRegression/man/ateRobust.Rd |only riskRegression-2018.10.03/riskRegression/man/autoplot.Score.Rd |only riskRegression-2018.10.03/riskRegression/man/autoplot.ate.Rd | 37 riskRegression-2018.10.03/riskRegression/man/autoplot.predictCSC.Rd | 43 riskRegression-2018.10.03/riskRegression/man/autoplot.predictCox.Rd | 75 riskRegression-2018.10.03/riskRegression/man/boxplot.Score.Rd | 7 riskRegression-2018.10.03/riskRegression/man/calcSeCSC.Rd | 8 riskRegression-2018.10.03/riskRegression/man/calcSeCox.Rd | 26 riskRegression-2018.10.03/riskRegression/man/colCenter_cpp.Rd | 1 riskRegression-2018.10.03/riskRegression/man/colMultiply_cpp.Rd | 1 riskRegression-2018.10.03/riskRegression/man/colScale_cpp.Rd | 1 riskRegression-2018.10.03/riskRegression/man/confint.ate.Rd |only riskRegression-2018.10.03/riskRegression/man/confint.ateRobust.Rd |only riskRegression-2018.10.03/riskRegression/man/confint.influenceTest.Rd |only riskRegression-2018.10.03/riskRegression/man/confint.predictCSC.Rd |only riskRegression-2018.10.03/riskRegression/man/confint.predictCox.Rd |only riskRegression-2018.10.03/riskRegression/man/coxModelFrame.Rd |only riskRegression-2018.10.03/riskRegression/man/coxSpecial.Rd |only riskRegression-2018.10.03/riskRegression/man/coxStrata.Rd | 15 riskRegression-2018.10.03/riskRegression/man/coxStrataLevel.Rd |only riskRegression-2018.10.03/riskRegression/man/coxVariableName.Rd | 5 riskRegression-2018.10.03/riskRegression/man/iidCox.Rd | 4 riskRegression-2018.10.03/riskRegression/man/influenceTest.Rd |only riskRegression-2018.10.03/riskRegression/man/model.matrix.cph.Rd |only riskRegression-2018.10.03/riskRegression/man/plotAUC.Rd | 45 riskRegression-2018.10.03/riskRegression/man/plotBrier.Rd | 4 riskRegression-2018.10.03/riskRegression/man/plotCalibration.Rd | 14 riskRegression-2018.10.03/riskRegression/man/plotEffects.Rd | 4 riskRegression-2018.10.03/riskRegression/man/plotROC.Rd | 6 riskRegression-2018.10.03/riskRegression/man/plotRisk.Rd | 4 riskRegression-2018.10.03/riskRegression/man/predict.CauseSpecificCox.Rd | 110 - riskRegression-2018.10.03/riskRegression/man/predictCox.Rd | 114 - riskRegression-2018.10.03/riskRegression/man/predictCoxPL.Rd | 80 riskRegression-2018.10.03/riskRegression/man/predictRisk.Rd | 2 riskRegression-2018.10.03/riskRegression/man/predictSurv.Rd |only riskRegression-2018.10.03/riskRegression/man/print.ate.Rd | 23 riskRegression-2018.10.03/riskRegression/man/print.ateRobust.Rd |only riskRegression-2018.10.03/riskRegression/man/print.influenceTest.Rd |only riskRegression-2018.10.03/riskRegression/man/print.predictCSC.Rd | 32 riskRegression-2018.10.03/riskRegression/man/print.predictCox.Rd | 47 riskRegression-2018.10.03/riskRegression/man/rowCenter_cpp.Rd | 1 riskRegression-2018.10.03/riskRegression/man/rowScale_cpp.Rd | 1 riskRegression-2018.10.03/riskRegression/man/sliceMultiply_cpp.Rd | 4 riskRegression-2018.10.03/riskRegression/man/sliceScale_cpp.Rd | 4 riskRegression-2018.10.03/riskRegression/man/subjectWeights.Rd | 4 riskRegression-2018.10.03/riskRegression/man/terms.phreg.Rd |only riskRegression-2018.10.03/riskRegression/man/transformCI.Rd |only riskRegression-2018.10.03/riskRegression/man/transformCIBP.Rd |only riskRegression-2018.10.03/riskRegression/man/transformIID.Rd |only riskRegression-2018.10.03/riskRegression/man/transformP.Rd |only riskRegression-2018.10.03/riskRegression/man/transformSE.Rd |only riskRegression-2018.10.03/riskRegression/src/RcppExports.cpp | 135 + riskRegression-2018.10.03/riskRegression/src/baseHaz.cpp | 2 riskRegression-2018.10.03/riskRegression/src/calcSeHazardCif.cpp | 630 ++++++ riskRegression-2018.10.03/riskRegression/src/rowSumsCrossprod.cpp | 1 riskRegression-2018.10.03/riskRegression/src/sweepCenterScale.cpp | 83 riskRegression-2018.10.03/riskRegression/tests/test-BrierScore.R | 52 riskRegression-2018.10.03/riskRegression/tests/test-FineGrayRegression.R | 2 riskRegression-2018.10.03/riskRegression/tests/test-ate.R | 260 +- riskRegression-2018.10.03/riskRegression/tests/test-ateRobust.R |only riskRegression-2018.10.03/riskRegression/tests/test-confidenceBand_vs_timereg.R | 240 +- riskRegression-2018.10.03/riskRegression/tests/test-iidCox.R | 335 ++- riskRegression-2018.10.03/riskRegression/tests/test-phreg.R | 163 + riskRegression-2018.10.03/riskRegression/tests/test-predictCSC_vs_mstate.R | 388 +--- riskRegression-2018.10.03/riskRegression/tests/test-predictCox-CSC.R | 244 -- riskRegression-2018.10.03/riskRegression/tests/test-predictCox-SEconfint.R |only riskRegression-2018.10.03/riskRegression/tests/test-predictCoxPL.R |only riskRegression-2018.10.03/riskRegression/tests/test-predictCox_vs_basehaz.R | 226 +- riskRegression-2018.10.03/riskRegression/tests/test-predictSurv.R |only riskRegression-2018.10.03/riskRegression/tests/test-score-bootstrap.R |only riskRegression-2018.10.03/riskRegression/tests/test-score.R | 317 +-- 140 files changed, 6173 insertions(+), 4654 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Measure of Agreement Between Two Raters
Description: Measure of agreement delta was originally by MartÃn & Femia (2004) <DOI:10.1348/000711004849268>.
Since then has been considered as agreement measure for different
fields, since their behavior is usually better than the usual kappa index
by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta
is that can not be computed by hand contrary to kappa. The current algorithm
is based on the Version 5 of the delta windows program that can be found on
<https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
Author: Antonio Rodriguez [aut, cre],
Pedro Femia [cph, ctb],
Antonio Martin [cph, ctb]
Maintainer: Antonio Rodriguez <tonirodriguezcontesti@gmail.com>
Diff between Delta versions 0.2.0.1 dated 2018-10-03 and 0.2.0.2 dated 2018-10-04
DESCRIPTION | 16 ++++++++++------ MD5 | 2 +- 2 files changed, 11 insertions(+), 7 deletions(-)
Title: Conduct RISE Analysis
Description: Implements techniques for educational resource inspection, selection, and evaluation (RISE) described in Bodily, Nyland, and Wiley (2017)
<doi:10.19173/irrodl.v18i2.2952>. Automates the process of identifying learning materials that are not effectively supporting student learning in
technology-mediated courses by synthesizing information about access to course content and performance on assessments.
Author: David Wiley [aut, cre],
Lumen Learning [cph]
Maintainer: David Wiley <david.wiley@gmail.com>
Diff between rise versions 1.0.3 dated 2018-07-29 and 1.0.4 dated 2018-10-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 3 ++- R/rise.R | 42 +++++++++++++++++++++++++++--------------- README.md | 33 +++++++++++++++++++++++---------- tests/testthat/test-rise.R | 8 ++++++-- 6 files changed, 67 insertions(+), 37 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response.
Author: Jean-Eudes Dazard [aut, cre],
Michael Choe [ctb],
Michael LeBlanc [ctb],
Alberto Santana [ctb],
J. Sunil Rao [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between PRIMsrc versions 0.8.1 dated 2018-09-10 and 0.8.2 dated 2018-10-04
PRIMsrc-0.8.1/PRIMsrc/inst/doc/PRIMsrc_0.8.1.pdf |only PRIMsrc-0.8.2/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.8.2/PRIMsrc/MD5 | 20 PRIMsrc-0.8.2/PRIMsrc/R/PRIMsrc.internal.r | 455 +++++++-- PRIMsrc-0.8.2/PRIMsrc/R/PRIMsrc.r | 1083 ++++++++++++----------- PRIMsrc-0.8.2/PRIMsrc/README.md | 14 PRIMsrc-0.8.2/PRIMsrc/inst/NEWS | 92 + PRIMsrc-0.8.2/PRIMsrc/inst/doc/PRIMsrc_0.8.2.pdf |only PRIMsrc-0.8.2/PRIMsrc/man/plot.sbh.Rd | 28 PRIMsrc-0.8.2/PRIMsrc/man/plot_km.Rd | 5 PRIMsrc-0.8.2/PRIMsrc/man/predict.sbh.Rd | 19 PRIMsrc-0.8.2/PRIMsrc/man/sbh.Rd | 125 +- 12 files changed, 1144 insertions(+), 705 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the Oceanographic
literature.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>),
Clark Richards [aut] (<https://orcid.org/0000-0002-7833-206X>),
Chantelle Layton [ctb] (<https://orcid.org/0000-0002-3199-5763>, curl()
coauthor),
British Geological Survey [ctb, cph] (magnetic-field subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 0.9-23 dated 2018-01-28 and 1.0-1 dated 2018-10-04
oce-0.9-23/oce/NEWS |only oce-0.9-23/oce/data/colors.rda |only oce-0.9-23/oce/inst/extdata/CTD_BCD2014666_008_1_DN.ODF |only oce-0.9-23/oce/man/colors.Rd |only oce-0.9-23/oce/man/makeSection.Rd |only oce-0.9-23/oce/man/oce.colorsGebco.Rd |only oce-0.9-23/oce/man/oce.colorsTwo.Rd |only oce-0.9-23/oce/src/adv_vector_time.c |only oce-0.9-23/oce/src/amsr.c |only oce-0.9-23/oce/src/approx.c |only oce-0.9-23/oce/src/curl.c |only oce-0.9-23/oce/src/echosounder.c |only oce-0.9-23/oce/src/fillgap.c |only oce-0.9-23/oce/src/geod.c |only oce-0.9-23/oce/src/get_bit.c |only oce-0.9-23/oce/src/gradient.c |only oce-0.9-23/oce/src/interp_barnes.c |only oce-0.9-23/oce/src/landsat.c |only oce-0.9-23/oce/src/latlon_trim.c |only oce-0.9-23/oce/src/ldc_ad2cp_in_file.c |only oce-0.9-23/oce/src/ldc_rdi_in_file.c |only oce-0.9-23/oce/src/matrix_smooth.c |only oce-0.9-23/oce/src/oce_approx.c |only oce-0.9-23/oce/src/oce_convolve.c |only oce-0.9-23/oce/src/oce_filter.c |only oce-0.9-23/oce/src/run.c |only oce-0.9-23/oce/src/sfm_enu.c |only oce-0.9-23/oce/src/sontek_adp.c |only oce-0.9-23/oce/src/topo_interpolate.c |only oce-0.9-23/oce/src/trap.c |only oce-0.9-23/oce/src/trim.c |only oce-0.9-23/oce/tests/testthat/test_local_echosounder.R |only oce-1.0-1/oce/DESCRIPTION | 28 oce-1.0-1/oce/MD5 | 1085 +++++----- oce-1.0-1/oce/NAMESPACE | 44 oce-1.0-1/oce/NEWS.md |only oce-1.0-1/oce/R/AllClass.R | 482 ++++ oce-1.0-1/oce/R/RcppExports.R |only oce-1.0-1/oce/R/accessors.R | 50 oce-1.0-1/oce/R/adp.R | 303 +- oce-1.0-1/oce/R/adp.nortek.R | 14 oce-1.0-1/oce/R/adp.rdi.R | 350 ++- oce-1.0-1/oce/R/adp.sontek.R | 22 oce-1.0-1/oce/R/adv.R | 132 - oce-1.0-1/oce/R/adv.nortek.R | 4 oce-1.0-1/oce/R/adv.sontek.R | 10 oce-1.0-1/oce/R/air.R | 10 oce-1.0-1/oce/R/amsr.R | 64 oce-1.0-1/oce/R/argo.R | 263 +- oce-1.0-1/oce/R/bremen.R | 27 oce-1.0-1/oce/R/cm.R | 24 oce-1.0-1/oce/R/coastline.R | 46 oce-1.0-1/oce/R/colors.R | 183 - oce-1.0-1/oce/R/ctd.R | 765 +++---- oce-1.0-1/oce/R/ctd.itp.R | 2 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oce-1.0-1/oce/man/read.adp.nortek.Rd | 19 oce-1.0-1/oce/man/read.adp.rdi.Rd | 154 + oce-1.0-1/oce/man/read.adp.sontek.Rd | 14 oce-1.0-1/oce/man/read.adp.sontek.serial.Rd | 18 oce-1.0-1/oce/man/read.adv.Rd | 9 oce-1.0-1/oce/man/read.adv.nortek.Rd | 7 oce-1.0-1/oce/man/read.adv.sontek.adr.Rd | 11 oce-1.0-1/oce/man/read.adv.sontek.serial.Rd | 10 oce-1.0-1/oce/man/read.adv.sontek.text.Rd | 11 oce-1.0-1/oce/man/read.amsr.Rd | 5 oce-1.0-1/oce/man/read.aquadopp.Rd | 18 oce-1.0-1/oce/man/read.aquadoppHR.Rd | 14 oce-1.0-1/oce/man/read.aquadoppProfiler.Rd | 21 oce-1.0-1/oce/man/read.argo.Rd | 3 oce-1.0-1/oce/man/read.bremen.Rd | 1 oce-1.0-1/oce/man/read.cm.Rd | 5 oce-1.0-1/oce/man/read.coastline.openstreetmap.Rd | 6 oce-1.0-1/oce/man/read.coastline.shapefile.Rd | 5 oce-1.0-1/oce/man/read.ctd.Rd | 9 oce-1.0-1/oce/man/read.ctd.itp.Rd | 4 oce-1.0-1/oce/man/read.ctd.odf.Rd | 11 oce-1.0-1/oce/man/read.ctd.sbe.Rd | 42 oce-1.0-1/oce/man/read.ctd.woce.Rd | 7 oce-1.0-1/oce/man/read.ctd.woce.other.Rd | 7 oce-1.0-1/oce/man/read.echosounder.Rd | 6 oce-1.0-1/oce/man/read.g1sst.Rd | 1 oce-1.0-1/oce/man/read.gps.Rd | 4 oce-1.0-1/oce/man/read.index.Rd | 6 oce-1.0-1/oce/man/read.landsat.Rd | 6 oce-1.0-1/oce/man/read.lisst.Rd | 4 oce-1.0-1/oce/man/read.met.Rd | 3 oce-1.0-1/oce/man/read.odf.Rd | 85 oce-1.0-1/oce/man/read.rsk.Rd | 6 oce-1.0-1/oce/man/read.sealevel.Rd | 1 oce-1.0-1/oce/man/read.section.Rd | 2 oce-1.0-1/oce/man/read.topo.Rd | 1 oce-1.0-1/oce/man/read.woa.Rd |only oce-1.0-1/oce/man/rescale.Rd | 4 oce-1.0-1/oce/man/resizableLabel.Rd | 6 oce-1.0-1/oce/man/rotateAboutZ.Rd |only oce-1.0-1/oce/man/rsk-class.Rd | 61 oce-1.0-1/oce/man/rsk.Rd | 13 oce-1.0-1/oce/man/rsk2ctd.Rd | 6 oce-1.0-1/oce/man/rskPatm.Rd | 1 oce-1.0-1/oce/man/rskToc.Rd | 1 oce-1.0-1/oce/man/satellite-class.Rd | 7 oce-1.0-1/oce/man/sealevel-class.Rd | 61 oce-1.0-1/oce/man/sealevel.Rd | 12 oce-1.0-1/oce/man/sealevelTuktoyaktuk.Rd | 12 oce-1.0-1/oce/man/secondsToCtime.Rd | 1 oce-1.0-1/oce/man/section-class.Rd | 107 oce-1.0-1/oce/man/section.Rd | 21 oce-1.0-1/oce/man/sectionAddStation.Rd | 2 oce-1.0-1/oce/man/sectionGrid.Rd | 6 oce-1.0-1/oce/man/sectionSmooth.Rd | 6 oce-1.0-1/oce/man/sectionSort.Rd | 2 oce-1.0-1/oce/man/setFlags-adp-method.Rd |only oce-1.0-1/oce/man/setFlags-ctd-method.Rd |only oce-1.0-1/oce/man/setFlags-oce-method.Rd |only oce-1.0-1/oce/man/setFlags.Rd |only oce-1.0-1/oce/man/shiftLongitude.Rd | 1 oce-1.0-1/oce/man/showMetadataItem.Rd | 4 oce-1.0-1/oce/man/siderealTime.Rd | 3 oce-1.0-1/oce/man/sub-sub-adp-method.Rd | 50 oce-1.0-1/oce/man/sub-sub-adv-method.Rd | 62 oce-1.0-1/oce/man/sub-sub-amsr-method.Rd | 23 oce-1.0-1/oce/man/sub-sub-argo-method.Rd | 46 oce-1.0-1/oce/man/sub-sub-bremen-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-cm-method.Rd | 24 oce-1.0-1/oce/man/sub-sub-coastline-method.Rd | 28 oce-1.0-1/oce/man/sub-sub-ctd-method.Rd | 44 oce-1.0-1/oce/man/sub-sub-echosounder-method.Rd | 24 oce-1.0-1/oce/man/sub-sub-g1sst-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-gps-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-ladp-method.Rd | 27 oce-1.0-1/oce/man/sub-sub-landsat-method.Rd | 104 oce-1.0-1/oce/man/sub-sub-lisst-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-lobo-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-met-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-oce-method.Rd | 9 oce-1.0-1/oce/man/sub-sub-odf-method.Rd | 22 oce-1.0-1/oce/man/sub-sub-rsk-method.Rd | 24 oce-1.0-1/oce/man/sub-sub-sealevel-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-section-method.Rd | 63 oce-1.0-1/oce/man/sub-sub-tidem-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-topo-method.Rd | 21 oce-1.0-1/oce/man/sub-sub-windrose-method.Rd | 21 oce-1.0-1/oce/man/sub-subset-adp-method.Rd | 13 oce-1.0-1/oce/man/sub-subset-adv-method.Rd | 27 oce-1.0-1/oce/man/sub-subset-amsr-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-argo-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-bremen-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-cm-method.Rd | 7 oce-1.0-1/oce/man/sub-subset-coastline-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-ctd-method.Rd | 7 oce-1.0-1/oce/man/sub-subset-echosounder-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-g1sst-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-gps-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-ladp-method.Rd |only oce-1.0-1/oce/man/sub-subset-landsat-method.Rd |only oce-1.0-1/oce/man/sub-subset-lisst-method.Rd | 6 oce-1.0-1/oce/man/sub-subset-lobo-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-met-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-oce-method.Rd | 3 oce-1.0-1/oce/man/sub-subset-odf-method.Rd | 5 oce-1.0-1/oce/man/sub-subset-rsk-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-sealevel-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-section-method.Rd | 5 oce-1.0-1/oce/man/sub-subset-tidem-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-topo-method.Rd | 4 oce-1.0-1/oce/man/sub-subset-windrose-method.Rd | 4 oce-1.0-1/oce/man/subset-adp-method.Rd | 11 oce-1.0-1/oce/man/subset-adv-method.Rd | 8 oce-1.0-1/oce/man/subset-amsr-method.Rd | 2 oce-1.0-1/oce/man/subset-argo-method.Rd | 20 oce-1.0-1/oce/man/subset-cm-method.Rd | 3 oce-1.0-1/oce/man/subset-coastline-method.Rd | 2 oce-1.0-1/oce/man/subset-ctd-method.Rd | 5 oce-1.0-1/oce/man/subset-echosounder-method.Rd | 2 oce-1.0-1/oce/man/subset-lobo-method.Rd | 2 oce-1.0-1/oce/man/subset-met-method.Rd | 2 oce-1.0-1/oce/man/subset-oce-method.Rd | 3 oce-1.0-1/oce/man/subset-odf-method.Rd | 8 oce-1.0-1/oce/man/subset-rsk-method.Rd | 2 oce-1.0-1/oce/man/subset-sealevel-method.Rd | 2 oce-1.0-1/oce/man/subset-section-method.Rd | 32 oce-1.0-1/oce/man/subset-topo-method.Rd | 2 oce-1.0-1/oce/man/summary-adp-method.Rd | 10 oce-1.0-1/oce/man/summary-adv-method.Rd | 7 oce-1.0-1/oce/man/summary-amsr-method.Rd | 5 oce-1.0-1/oce/man/summary-argo-method.Rd | 1 oce-1.0-1/oce/man/summary-bremen-method.Rd | 1 oce-1.0-1/oce/man/summary-cm-method.Rd | 2 oce-1.0-1/oce/man/summary-coastline-method.Rd | 1 oce-1.0-1/oce/man/summary-ctd-method.Rd | 4 oce-1.0-1/oce/man/summary-echosounder-method.Rd | 1 oce-1.0-1/oce/man/summary-gps-method.Rd | 1 oce-1.0-1/oce/man/summary-ladp-method.Rd | 5 oce-1.0-1/oce/man/summary-landsat-method.Rd | 6 oce-1.0-1/oce/man/summary-lisst-method.Rd | 1 oce-1.0-1/oce/man/summary-lobo-method.Rd | 1 oce-1.0-1/oce/man/summary-met-method.Rd | 1 oce-1.0-1/oce/man/summary-odf-method.Rd | 2 oce-1.0-1/oce/man/summary-rsk-method.Rd | 1 oce-1.0-1/oce/man/summary-satellite-method.Rd | 5 oce-1.0-1/oce/man/summary-sealevel-method.Rd | 1 oce-1.0-1/oce/man/summary-section-method.Rd | 2 oce-1.0-1/oce/man/summary-tidem-method.Rd | 1 oce-1.0-1/oce/man/summary-topo-method.Rd | 1 oce-1.0-1/oce/man/summary-windrose-method.Rd | 1 oce-1.0-1/oce/man/sunAngle.Rd | 5 oce-1.0-1/oce/man/swAbsoluteSalinity.Rd | 1 oce-1.0-1/oce/man/swAlpha.Rd | 1 oce-1.0-1/oce/man/swAlphaOverBeta.Rd | 5 oce-1.0-1/oce/man/swBeta.Rd | 1 oce-1.0-1/oce/man/swCSTp.Rd | 5 oce-1.0-1/oce/man/swConservativeTemperature.Rd | 5 oce-1.0-1/oce/man/swDepth.Rd | 4 oce-1.0-1/oce/man/swDynamicHeight.Rd | 5 oce-1.0-1/oce/man/swLapseRate.Rd | 5 oce-1.0-1/oce/man/swN2.Rd | 11 oce-1.0-1/oce/man/swPressure.Rd | 4 oce-1.0-1/oce/man/swRho.Rd | 6 oce-1.0-1/oce/man/swRrho.Rd | 1 oce-1.0-1/oce/man/swSCTp.Rd | 5 oce-1.0-1/oce/man/swSTrho.Rd | 5 oce-1.0-1/oce/man/swSigma.Rd | 6 oce-1.0-1/oce/man/swSigma0.Rd | 6 oce-1.0-1/oce/man/swSigma1.Rd | 6 oce-1.0-1/oce/man/swSigma2.Rd | 6 oce-1.0-1/oce/man/swSigma3.Rd | 6 oce-1.0-1/oce/man/swSigma4.Rd | 6 oce-1.0-1/oce/man/swSigmaT.Rd | 6 oce-1.0-1/oce/man/swSigmaTheta.Rd | 1 oce-1.0-1/oce/man/swSoundAbsorption.Rd | 1 oce-1.0-1/oce/man/swSoundSpeed.Rd | 5 oce-1.0-1/oce/man/swSpecificHeat.Rd | 5 oce-1.0-1/oce/man/swSpice.Rd | 3 oce-1.0-1/oce/man/swTFreeze.Rd | 1 oce-1.0-1/oce/man/swTSrho.Rd | 1 oce-1.0-1/oce/man/swThermalConductivity.Rd | 1 oce-1.0-1/oce/man/swTheta.Rd | 1 oce-1.0-1/oce/man/swViscosity.Rd | 1 oce-1.0-1/oce/man/swZ.Rd | 4 oce-1.0-1/oce/man/tail.oce.Rd | 30 oce-1.0-1/oce/man/tidedata.Rd | 1 oce-1.0-1/oce/man/tidem-class.Rd | 53 oce-1.0-1/oce/man/tidem.Rd | 3 oce-1.0-1/oce/man/tidemAstron.Rd | 1 oce-1.0-1/oce/man/tidemVuf.Rd | 1 oce-1.0-1/oce/man/toEnu.Rd | 14 oce-1.0-1/oce/man/toEnuAdp.Rd | 12 oce-1.0-1/oce/man/toEnuAdv.Rd | 6 oce-1.0-1/oce/man/topo-class.Rd | 61 oce-1.0-1/oce/man/topoInterpolate.Rd | 1 oce-1.0-1/oce/man/topoWorld.Rd | 12 oce-1.0-1/oce/man/unabbreviateYear.Rd | 1 oce-1.0-1/oce/man/unduplicateNames.Rd | 26 oce-1.0-1/oce/man/unitFromString.Rd | 1 oce-1.0-1/oce/man/unitFromStringRsk.Rd | 1 oce-1.0-1/oce/man/usrLonLat.Rd | 1 oce-1.0-1/oce/man/utm2lonlat.Rd | 1 oce-1.0-1/oce/man/velocityStatistics.Rd | 14 oce-1.0-1/oce/man/webtide.Rd | 4 oce-1.0-1/oce/man/wind.Rd | 11 oce-1.0-1/oce/man/windrose-class.Rd | 51 oce-1.0-1/oce/man/woceNames2oceNames.Rd | 5 oce-1.0-1/oce/man/woceUnit2oceUnit.Rd | 5 oce-1.0-1/oce/man/write.ctd.Rd | 7 oce-1.0-1/oce/man/xyzToEnu.Rd | 14 oce-1.0-1/oce/man/xyzToEnuAdp.Rd | 10 oce-1.0-1/oce/man/xyzToEnuAdv.Rd | 6 oce-1.0-1/oce/src/RcppExports.cpp |only oce-1.0-1/oce/src/adv_vector_time.cpp |only oce-1.0-1/oce/src/amsr.cpp |only oce-1.0-1/oce/src/approx.cpp |only oce-1.0-1/oce/src/bilinear_interp.cpp |only oce-1.0-1/oce/src/bitwise.c | 224 -- oce-1.0-1/oce/src/curl.cpp |only oce-1.0-1/oce/src/echosounder.cpp |only oce-1.0-1/oce/src/fillgap.cpp |only oce-1.0-1/oce/src/geod.cpp |only oce-1.0-1/oce/src/get_bit.cpp |only oce-1.0-1/oce/src/gradient.cpp |only oce-1.0-1/oce/src/interp_barnes.cpp |only oce-1.0-1/oce/src/landsat.cpp |only oce-1.0-1/oce/src/ldc_ad2cp_in_file.cpp |only oce-1.0-1/oce/src/ldc_rdi_in_file.cpp |only oce-1.0-1/oce/src/matrix_smooth.cpp |only oce-1.0-1/oce/src/oce_approx.cpp |only oce-1.0-1/oce/src/oce_convolve.cpp |only oce-1.0-1/oce/src/oce_filter.cpp |only oce-1.0-1/oce/src/registerDynamicSymbol.c | 67 oce-1.0-1/oce/src/run.cpp |only oce-1.0-1/oce/src/sfm_enu.cpp |only oce-1.0-1/oce/src/sontek_adp.cpp |only oce-1.0-1/oce/src/time.cpp |only oce-1.0-1/oce/src/trap.cpp |only oce-1.0-1/oce/src/trim.cpp |only oce-1.0-1/oce/tests/testthat/CTD_BCD2014666_008_1_DN_altered.ODF.gz |only oce-1.0-1/oce/tests/testthat/test_ad2cp.R |only oce-1.0-1/oce/tests/testthat/test_adp.R | 144 + oce-1.0-1/oce/tests/testthat/test_adv.R | 46 oce-1.0-1/oce/tests/testthat/test_amsr.R |only oce-1.0-1/oce/tests/testthat/test_argo.R | 27 oce-1.0-1/oce/tests/testthat/test_colormap.R | 2 oce-1.0-1/oce/tests/testthat/test_ctd.R | 130 - oce-1.0-1/oce/tests/testthat/test_curl.R | 2 oce-1.0-1/oce/tests/testthat/test_datasets.R | 4 oce-1.0-1/oce/tests/testthat/test_deprecation.R |only oce-1.0-1/oce/tests/testthat/test_echosounder.R |only oce-1.0-1/oce/tests/testthat/test_flags.R | 216 + oce-1.0-1/oce/tests/testthat/test_geod.R | 19 oce-1.0-1/oce/tests/testthat/test_landsat.R | 14 oce-1.0-1/oce/tests/testthat/test_local_adp.R | 59 oce-1.0-1/oce/tests/testthat/test_local_odf.R | 5 oce-1.0-1/oce/tests/testthat/test_map.R | 14 oce-1.0-1/oce/tests/testthat/test_met.R | 3 oce-1.0-1/oce/tests/testthat/test_misc.R | 427 ++- oce-1.0-1/oce/tests/testthat/test_oce.R | 425 +++ oce-1.0-1/oce/tests/testthat/test_odf.R |only oce-1.0-1/oce/tests/testthat/test_section.R | 30 oce-1.0-1/oce/tests/testthat/test_topo.R |only oce-1.0-1/oce/tests/tide.R | 2 oce-1.0-1/oce/vignettes/adp.Rmd |only oce-1.0-1/oce/vignettes/flags.Rmd |only oce-1.0-1/oce/vignettes/oce.Rmd | 132 - 604 files changed, 10458 insertions(+), 5345 deletions(-)
Title: Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in
reference classes. Compared to reference classes, R6 classes are simpler
and lighter-weight, and they are not built on S4 classes so they do not
require the methods package. These classes allow public and private
members, and they support inheritance, even when the classes are defined in
different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.2.2 dated 2017-06-17 and 2.3.0 dated 2018-10-04
R6-2.2.2/R6/build |only R6-2.2.2/R6/inst |only R6-2.2.2/R6/vignettes |only R6-2.3.0/R6/DESCRIPTION | 24 - R6-2.3.0/R6/MD5 | 38 -- R6-2.3.0/R6/NEWS.md | 28 + R6-2.3.0/R6/R/clone.R | 395 +++++++++++++++++----------- R6-2.3.0/R6/R/generator_funs.R | 8 R6-2.3.0/R6/R/new.R | 12 R6-2.3.0/R6/R/print.R | 10 R6-2.3.0/R6/README.md | 36 +- R6-2.3.0/R6/tests/testthat/test-clone.R | 302 +++++++++++++++++---- R6-2.3.0/R6/tests/testthat/test-finalizer.R | 33 ++ R6-2.3.0/R6/tests/testthat/test-set.R | 12 14 files changed, 639 insertions(+), 259 deletions(-)
Title: Voronoi Diagrams and Heatmaps with 'ggplot2'
Description: Easy creation and manipulation of Voronoi diagrams using 'deldir' with visualization in 'ggplot2'.
Author: Robert C. Garrett [aut, cre],
Austin Nar [aut],
Thomas J. Fisher [aut],
Karsten Maurer [ctb]
Maintainer: Robert C. Garrett <garretrc@miamioh.edu>
Diff between ggvoronoi versions 0.8.0 dated 2018-07-20 and 0.8.1 dated 2018-10-04
DESCRIPTION | 14 ++++++++------ MD5 | 20 +++++++++++--------- R/data.R | 8 ++++++++ R/geom_voronoi.R | 5 +++++ R/stat_voronoi.R | 7 ++++++- README.md | 4 ++++ data/oxford_map.rda |only inst/doc/ggvoronoi.R | 23 +++++++++++++---------- inst/doc/ggvoronoi.Rmd | 28 +++++++++++++++++----------- inst/doc/ggvoronoi.html | 20 ++++++++++---------- man/oxford_map.Rd |only vignettes/ggvoronoi.Rmd | 28 +++++++++++++++++----------- 12 files changed, 99 insertions(+), 58 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from eBird
(<http://ebird.org>), an online tool for recording bird observations.
Public access to the full eBird database is via the eBird Basic Dataset
(EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable
text file. This package is an interface to AWK for extracting data from the
EBD based on taxonomic, spatial, or temporal filters, to produce a
manageable file size that can be imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.2.2 dated 2018-07-23 and 0.3.0 dated 2018-10-04
auk-0.2.2/auk/R/auk-extent.r |only auk-0.2.2/auk/R/auk-getpath.r |only auk-0.2.2/auk/R/auk-version-date.r |only auk-0.2.2/auk/inst/extdata/ebd-sample_messy.txt |only auk-0.2.2/auk/man/auk_getpath.Rd |only auk-0.2.2/auk/man/auk_version_date.Rd |only auk-0.2.2/auk/tests/testthat/test_auk-clean.r |only auk-0.3.0/auk/DESCRIPTION | 14 auk-0.3.0/auk/MD5 | 170 + auk-0.3.0/auk/NAMESPACE | 22 auk-0.3.0/auk/NEWS.md | 25 auk-0.3.0/auk/R/auk-bbox.r |only auk-0.3.0/auk/R/auk-bcr.r |only auk-0.3.0/auk/R/auk-breeding.r | 5 auk-0.3.0/auk/R/auk-clean.r | 41 auk-0.3.0/auk/R/auk-country.r | 3 auk-0.3.0/auk/R/auk-ebd-version.r |only auk-0.3.0/auk/R/auk-ebd.r | 84 auk-0.3.0/auk/R/auk-filter.r | 47 auk-0.3.0/auk/R/auk-get-awk-path.r |only auk-0.3.0/auk/R/auk-get-ebd-path.r |only auk-0.3.0/auk/R/auk-last-edited.r | 9 auk-0.3.0/auk/R/auk-package.r | 2 auk-0.3.0/auk/R/auk-project.r | 8 auk-0.3.0/auk/R/auk-protocol.r | 9 auk-0.3.0/auk/R/auk-rollup.r | 47 auk-0.3.0/auk/R/auk-sampling.r | 31 auk-0.3.0/auk/R/auk-select.r | 6 auk-0.3.0/auk/R/auk-set-awk-path.r |only auk-0.3.0/auk/R/auk-set-ebd-path.r |only auk-0.3.0/auk/R/auk-species.r | 45 auk-0.3.0/auk/R/auk-split.r | 23 auk-0.3.0/auk/R/auk-state.r | 2 auk-0.3.0/auk/R/auk-unique.r | 2 auk-0.3.0/auk/R/auk-version.r |only auk-0.3.0/auk/R/auk-zerofill.r | 91 auk-0.3.0/auk/R/data.r | 41 auk-0.3.0/auk/R/ebird-species.r | 41 auk-0.3.0/auk/R/filter-repeat-visits.r |only auk-0.3.0/auk/R/format-unmarked-occu.r |only auk-0.3.0/auk/R/get-ebird-taxonomy.r |only auk-0.3.0/auk/R/read.r | 6 auk-0.3.0/auk/R/utils.r | 17 auk-0.3.0/auk/R/zzz.r | 18 auk-0.3.0/auk/data/bcr_codes.rda |only auk-0.3.0/auk/data/ebird_taxonomy.rda |binary auk-0.3.0/auk/inst/CITATION | 8 auk-0.3.0/auk/inst/doc/auk.R | 24 auk-0.3.0/auk/inst/doc/auk.Rmd | 38 auk-0.3.0/auk/inst/doc/auk.html | 707 +++---- auk-0.3.0/auk/inst/extdata/ebd-rollup-ex.txt | 42 auk-0.3.0/auk/inst/extdata/ebd-sample.txt | 1000 +++++----- auk-0.3.0/auk/inst/extdata/zerofill-ex_ebd.txt | 503 ++--- auk-0.3.0/auk/inst/extdata/zerofill-ex_sampling.txt | 1610 +++++------------ auk-0.3.0/auk/man/auk.Rd | 2 auk-0.3.0/auk/man/auk_bbox.Rd |only auk-0.3.0/auk/man/auk_bcr.Rd |only auk-0.3.0/auk/man/auk_breeding.Rd | 3 auk-0.3.0/auk/man/auk_clean.Rd | 33 auk-0.3.0/auk/man/auk_complete.Rd | 3 auk-0.3.0/auk/man/auk_country.Rd | 3 auk-0.3.0/auk/man/auk_date.Rd | 3 auk-0.3.0/auk/man/auk_distance.Rd | 3 auk-0.3.0/auk/man/auk_duration.Rd | 3 auk-0.3.0/auk/man/auk_ebd.Rd | 7 auk-0.3.0/auk/man/auk_ebd_version.Rd |only auk-0.3.0/auk/man/auk_extent.Rd | 22 auk-0.3.0/auk/man/auk_filter.Rd | 11 auk-0.3.0/auk/man/auk_get_awk_path.Rd |only auk-0.3.0/auk/man/auk_get_ebd_path.Rd |only auk-0.3.0/auk/man/auk_last_edited.Rd | 3 auk-0.3.0/auk/man/auk_project.Rd | 3 auk-0.3.0/auk/man/auk_protocol.Rd | 10 auk-0.3.0/auk/man/auk_rollup.Rd | 19 auk-0.3.0/auk/man/auk_set_awk_path.Rd |only auk-0.3.0/auk/man/auk_set_ebd_path.Rd |only auk-0.3.0/auk/man/auk_species.Rd | 19 auk-0.3.0/auk/man/auk_split.Rd | 20 auk-0.3.0/auk/man/auk_state.Rd | 5 auk-0.3.0/auk/man/auk_time.Rd | 3 auk-0.3.0/auk/man/auk_version.Rd |only auk-0.3.0/auk/man/auk_zerofill.Rd | 47 auk-0.3.0/auk/man/bcr_codes.Rd |only auk-0.3.0/auk/man/ebird_species.Rd | 23 auk-0.3.0/auk/man/ebird_states.Rd | 3 auk-0.3.0/auk/man/ebird_taxonomy.Rd | 17 auk-0.3.0/auk/man/filter_repeat_visits.Rd |only auk-0.3.0/auk/man/format_unmarked_occu.Rd |only auk-0.3.0/auk/man/get_ebird_taxonomy.Rd |only auk-0.3.0/auk/tests/testthat/test_auk-ebd-version.r |only auk-0.3.0/auk/tests/testthat/test_auk-ebd.r | 4 auk-0.3.0/auk/tests/testthat/test_auk-filter.r | 22 auk-0.3.0/auk/tests/testthat/test_auk-keep-drop.r | 8 auk-0.3.0/auk/tests/testthat/test_auk-rollup.r | 18 auk-0.3.0/auk/tests/testthat/test_auk-select.r | 2 auk-0.3.0/auk/tests/testthat/test_auk-split.r | 3 auk-0.3.0/auk/tests/testthat/test_auk-zerofill.r | 10 auk-0.3.0/auk/tests/testthat/test_ebird-species.r | 8 auk-0.3.0/auk/tests/testthat/test_filters.r | 54 auk-0.3.0/auk/tests/testthat/test_filters_sampling.r | 26 auk-0.3.0/auk/tests/testthat/test_get-ebird-taxonomy.r |only auk-0.3.0/auk/tests/testthat/test_unmarked.r |only auk-0.3.0/auk/vignettes/auk.Rmd | 38 103 files changed, 2528 insertions(+), 2671 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 0.9-0 dated 2018-08-04 and 0.10-1 dated 2018-10-04
Rdpack-0.10-1/Rdpack/DESCRIPTION | 16 Rdpack-0.10-1/Rdpack/MD5 | 66 - Rdpack-0.10-1/Rdpack/NAMESPACE | 3 Rdpack-0.10-1/Rdpack/NEWS.md | 453 +++++----- Rdpack-0.10-1/Rdpack/R/bib.R | 123 ++ Rdpack-0.10-1/Rdpack/R/f_usage.R | 21 Rdpack-0.10-1/Rdpack/R/inspect.R | 12 Rdpack-0.10-1/Rdpack/R/runexamples.R | 12 Rdpack-0.10-1/Rdpack/R/slots.R | 6 Rdpack-0.10-1/Rdpack/README.md | 127 +- Rdpack-0.10-1/Rdpack/build/partial.rdb |binary Rdpack-0.10-1/Rdpack/inst/REFERENCES.bib | 4 Rdpack-0.10-1/Rdpack/inst/doc/Inserting_bibtex_references.Rnw | 46 - Rdpack-0.10-1/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-0.10-1/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-0.10-1/Rdpack/inst/examples/RdpackTester |only Rdpack-0.10-1/Rdpack/inst/examples/RdpackTester.pdf |only Rdpack-0.10-1/Rdpack/man/Rdo_which.Rd | 27 Rdpack-0.10-1/Rdpack/man/Rdpack-package.Rd | 40 Rdpack-0.10-1/Rdpack/man/S4formals.Rd | 14 Rdpack-0.10-1/Rdpack/man/deparse_usage.Rd | 66 - Rdpack-0.10-1/Rdpack/man/get_sig_text.Rd | 2 Rdpack-0.10-1/Rdpack/man/insert_all_ref.Rd | 7 Rdpack-0.10-1/Rdpack/man/insert_ref.Rd | 4 Rdpack-0.10-1/Rdpack/man/macros/refmacros.Rd | 8 Rdpack-0.10-1/Rdpack/man/parse_Rdpiece.Rd | 4 Rdpack-0.10-1/Rdpack/man/parse_pairlist.Rd | 84 + Rdpack-0.10-1/Rdpack/man/predefined.Rd | 22 Rdpack-0.10-1/Rdpack/man/promptUsage.Rd | 116 ++ Rdpack-0.10-1/Rdpack/vignettes/Inserting_bibtex_references.Rnw | 46 - Rdpack-0.10-1/Rdpack/vignettes/Inserting_bibtex_references.org | 21 Rdpack-0.10-1/Rdpack/vignettes/auto/Inserting_bibtex_references.el | 37 Rdpack-0.9-0/Rdpack/man/macros/refmacros.RdSav |only 33 files changed, 895 insertions(+), 492 deletions(-)
Title: Pseudo-Ranks
Description: Efficient calculation of pseudo-ranks and (pseudo)-rank based test statistics. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Georg Zimmermann [aut],
Arne C. Bathke [aut],
Edgar Brunner [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between pseudorank versions 0.3.0 dated 2018-08-22 and 0.3.7 dated 2018-10-04
pseudorank-0.3.0/pseudorank/man/psrank.Rd |only pseudorank-0.3.7/pseudorank/DESCRIPTION | 10 pseudorank-0.3.7/pseudorank/MD5 | 38 ++- pseudorank-0.3.7/pseudorank/NAMESPACE | 10 pseudorank-0.3.7/pseudorank/NEWS.md | 4 pseudorank-0.3.7/pseudorank/R/S3method.R | 109 ++++++++-- pseudorank-0.3.7/pseudorank/R/data.R |only pseudorank-0.3.7/pseudorank/R/hettmansperger.R | 8 pseudorank-0.3.7/pseudorank/R/kepner_robinson.R |only pseudorank-0.3.7/pseudorank/R/kruskal_wallis.R | 10 pseudorank-0.3.7/pseudorank/README.md | 33 +-- pseudorank-0.3.7/pseudorank/data |only pseudorank-0.3.7/pseudorank/man/ParadoxicalRanks.Rd |only pseudorank-0.3.7/pseudorank/man/hettmansperger_norton_test.Rd | 4 pseudorank-0.3.7/pseudorank/man/hettmansperger_norton_test_internal.Rd | 4 pseudorank-0.3.7/pseudorank/man/kepner_robinson_test.Rd |only pseudorank-0.3.7/pseudorank/man/kepner_robinson_test_internal.Rd |only pseudorank-0.3.7/pseudorank/man/kruskal_wallis_internal.Rd | 4 pseudorank-0.3.7/pseudorank/man/kruskal_wallis_test.Rd | 6 pseudorank-0.3.7/pseudorank/man/pseudorank-package.Rd |only pseudorank-0.3.7/pseudorank/man/pseudorank.Rd | 59 ++++- pseudorank-0.3.7/pseudorank/man/psrank-deprecated.Rd |only pseudorank-0.3.7/pseudorank/tests/testthat/test.R | 82 +++---- pseudorank-0.3.7/pseudorank/tests/testthat/test_kepner_robinson.R |only pseudorank-0.3.7/pseudorank/tests/testthat/test_min_max.R | 28 +- 25 files changed, 272 insertions(+), 137 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.4 dated 2018-08-24 and 0.3.5 dated 2018-10-04
ChangeLog | 25 DESCRIPTION | 8 MD5 | 17 configure | 18 configure.ac | 2 inst/NEWS.Rd | 21 inst/doc/littler-examples.html | 1275 ++++++++++++++++++++++++++++++++++++++++- inst/examples/rcc.r | 6 inst/examples/rchk.r |only inst/examples/roxy.r | 6 10 files changed, 1343 insertions(+), 35 deletions(-)
Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between REAT versions 2.0.1 dated 2018-08-24 and 2.0.2 dated 2018-10-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/growth.R | 2 +- data/EU28.emp.rda |binary data/Freiburg.rda |binary data/G.counties.gdp.rda |binary data/G.regions.emp.rda |binary 7 files changed, 11 insertions(+), 11 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case study, see Happ (2018) <arXiv:1707.02129>.
Author: Clara Happ [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>
Diff between MFPCA versions 1.3 dated 2018-08-13 and 1.3-1 dated 2018-10-04
DESCRIPTION | 10 +++--- MD5 | 38 ++++++++++++------------- NEWS.md | 8 +++++ R/FCP_TPA.R | 2 - R/MFPCA_calculation.R | 62 ++++++++++++++++++++--------------------- R/MFPCAfit_methods.R | 18 +++++------ R/UMPCA.R | 26 ++++++++--------- R/bootstrap.R | 2 - R/multivExpansions.R | 2 - R/univDecomp.R | 38 ++++++++++++------------- R/univPCA.R | 8 ++--- R/univariateExpansions.R | 12 +++---- build/partial.rdb |binary configure | 18 +++++------ configure.ac | 2 - man/MFPCA.Rd | 2 - man/fpcaBasis.Rd | 2 - man/plot.MFPCAfit.Rd | 2 - tests/testthat/Rplots.pdf | 4 +- tests/testthat/test_MFPCAfit.R | 6 +++ 20 files changed, 137 insertions(+), 125 deletions(-)
Title: Generalized Graded Unfolding Model
Description: An implementation of the generalized graded unfolding model (GGUM) in R, see Roberts, Donoghue, and Laughlin (2000) <doi:10.1177/01466216000241001>). It allows to simulate data sets based on the GGUM. It fits the GGUM and the GUM, and it retrieves item and person parameter estimates. Several plotting functions are available (item and test information functions; item and test characteristic curves; item category response curves). Additionally, there are some functions that facilitate the communication between R and 'GGUM2004'. Finally, a model-fit checking utility, MODFIT(), is also available.
Author: Jorge N. Tendeiro [aut, cre],
Sebastian Castro-Alvarez [aut]
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>
Diff between GGUM versions 0.3.2 dated 2018-07-04 and 0.3.3 dated 2018-10-04
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- R/GGUM2004.R | 1 + R/MODFIT.R | 4 ++-- build/partial.rdb |binary inst/REFERENCES.bib | 18 ++++++++++++++++++ man/GGUM.Rd | 4 ++-- man/GUM.Rd | 4 ++-- man/MODFIT.Rd | 4 ++-- 9 files changed, 40 insertions(+), 20 deletions(-)
Title: n-Gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix <lmiratrix@stat.harvard.edu>
Diff between textreg versions 0.1.4 dated 2017-03-17 and 0.1.5 dated 2018-10-04
textreg-0.1.4/textreg/inst/doc/bathtub-vignette.R |only textreg-0.1.4/textreg/inst/doc/bathtub-vignette.Rmd |only textreg-0.1.4/textreg/inst/doc/bathtub-vignette.html |only textreg-0.1.4/textreg/vignettes/bathtub-vignette.Rmd |only textreg-0.1.5/textreg/DESCRIPTION | 12 textreg-0.1.5/textreg/LICENSE |only textreg-0.1.5/textreg/MD5 | 91 - textreg-0.1.5/textreg/NAMESPACE | 2 textreg-0.1.5/textreg/R/cross_validation_code.R | 2 textreg-0.1.5/textreg/R/package_and_data_documentation.R | 5 textreg-0.1.5/textreg/R/textreg.R | 7 textreg-0.1.5/textreg/README.md |only textreg-0.1.5/textreg/build/vignette.rds |binary textreg-0.1.5/textreg/inst/doc/bathtub_vignette.R |only textreg-0.1.5/textreg/inst/doc/bathtub_vignette.Rmd |only textreg-0.1.5/textreg/inst/doc/bathtub_vignette.pdf |only textreg-0.1.5/textreg/man/bathtub.Rd | 1 textreg-0.1.5/textreg/man/cluster.phrases.Rd | 1 textreg-0.1.5/textreg/man/dirtyBathtub.Rd | 1 textreg-0.1.5/textreg/man/find.CV.C.Rd | 4 textreg-0.1.5/textreg/man/find.threshold.C.Rd | 7 textreg-0.1.5/textreg/man/grab.fragments.Rd | 4 textreg-0.1.5/textreg/man/is.fragment.sample.Rd | 1 textreg-0.1.5/textreg/man/is.textreg.corpus.Rd | 1 textreg-0.1.5/textreg/man/is.textreg.result.Rd | 1 textreg-0.1.5/textreg/man/make.appearance.matrix.Rd | 1 textreg-0.1.5/textreg/man/make.count.table.Rd | 1 textreg-0.1.5/textreg/man/make.path.matrix.Rd | 1 textreg-0.1.5/textreg/man/make.phrase.correlation.chart.Rd | 1 textreg-0.1.5/textreg/man/make.phrase.matrix.Rd | 1 textreg-0.1.5/textreg/man/make.similarity.matrix.Rd | 1 textreg-0.1.5/textreg/man/path.matrix.chart.Rd | 5 textreg-0.1.5/textreg/man/phrase.count.Rd | 1 textreg-0.1.5/textreg/man/phrases.Rd | 1 textreg-0.1.5/textreg/man/plot.textreg.result.Rd | 1 textreg-0.1.5/textreg/man/print.fragment.sample.Rd | 1 textreg-0.1.5/textreg/man/print.textreg.corpus.Rd | 1 textreg-0.1.5/textreg/man/print.textreg.result.Rd | 1 textreg-0.1.5/textreg/man/reformat.textreg.model.Rd | 1 textreg-0.1.5/textreg/man/sample.fragments.Rd | 1 textreg-0.1.5/textreg/man/textreg-package.Rd | 2 textreg-0.1.5/textreg/man/textreg.Rd | 13 textreg-0.1.5/textreg/src/textreg.cpp | 868 ++++------ textreg-0.1.5/textreg/src/textreg_init.c |only textreg-0.1.5/textreg/tests/testthat/Rplots.pdf |binary textreg-0.1.5/textreg/tests/testthat/test-make-word-lists.R | 28 textreg-0.1.5/textreg/tests/testthat/test-ngram-call-basics.R | 3 textreg-0.1.5/textreg/tests/testthat/test-positive_feature_rescaling.R | 2 textreg-0.1.5/textreg/tests/testthat/test-text-searching.R | 8 textreg-0.1.5/textreg/tests/testthat/test-tm-compatability.R | 67 textreg-0.1.5/textreg/tests/testthat/test-zero-labeling-and-text-files.R | 3 textreg-0.1.5/textreg/vignettes/bathtub_vignette.Rmd |only 52 files changed, 609 insertions(+), 544 deletions(-)
Title: Implements Measures for the Comparison of Two Partitions
Description: Provides several measures ((dis)similarity, distance/metric,
correlation, entropy) for comparing two partitions of the same set of
objects. The different measures can be assigned to three different
classes: Pair comparison (containing the famous Jaccard and Rand
indices), set based, and information theory based.
Many of the implemented measures can be found in
Albatineh AN, Niewiadomska-Bugaj M and Mihalko D (2006)
<doi:10.1007/s00357-006-0017-z> and
Meila M (2007) <doi:10.1016/j.jmva.2006.11.013>.
Partitions are represented by vectors of class labels which allow a
straightforward integration with existing clustering algorithms
(e.g. kmeans()). The package is mostly based on the S4 object system.
Author: Fabian Ball [aut, cre, cph, ctb],
Andreas Geyer-Schulz [cph]
Maintainer: Fabian Ball <fabian.ball@kit.edu>
Diff between partitionComparison versions 0.2.3 dated 2017-12-19 and 0.2.4 dated 2018-10-04
DESCRIPTION | 11 ++-- MD5 | 6 +- build/partial.rdb |binary inst/REFERENCES.bib | 143 +++++++++++++--------------------------------------- 4 files changed, 46 insertions(+), 114 deletions(-)
More information about partitionComparison at CRAN
Permanent link
Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal
processes. The models may include covariates and can be specified
with familiar formula syntax as in glm() and package 'flexsurv'.
The methodology is described in a forthcoming paper in the Journal
of Statistical Software (included as vignette 'Countr_guide').
Author: Tarak Kharrat [aut, cre],
Georgi N. Boshnakov [aut]
Maintainer: Tarak Kharrat <Tarak.Kharrat@liverpool.ac.uk>
Diff between Countr versions 3.4.1 dated 2017-11-20 and 3.5.2 dated 2018-10-04
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Countr-3.5.2/Countr/inst/include/Countr_types.h | 26 Countr-3.5.2/Countr/inst/include/built_in_distributions.h | 26 Countr-3.5.2/Countr/inst/include/dePril_conv.h | 30 Countr-3.5.2/Countr/inst/include/series_weibull.h | 96 Countr-3.5.2/Countr/inst/include/utils.h | 16 Countr-3.5.2/Countr/man/Countr.Rd | 70 Countr-3.5.2/Countr/man/CountrFormula.Rd |only Countr-3.5.2/Countr/man/addBootSampleObject.Rd | 64 Countr-3.5.2/Countr/man/alphagen.Rd | 72 Countr-3.5.2/Countr/man/chiSq_gof.Rd | 90 Countr-3.5.2/Countr/man/chiSq_pearson.Rd | 80 Countr-3.5.2/Countr/man/compareToGLM.Rd | 76 Countr-3.5.2/Countr/man/count_table.Rd | 62 Countr-3.5.2/Countr/man/dCount_allProbs_bi.Rd | 112 Countr-3.5.2/Countr/man/dCount_conv_bi.Rd | 216 Countr-3.5.2/Countr/man/dCount_conv_loglik_bi.Rd | 192 Countr-3.5.2/Countr/man/dCount_dePril_bi.Rd | 80 Countr-3.5.2/Countr/man/dCount_naive_bi.Rd | 84 Countr-3.5.2/Countr/man/dWeibullCount.Rd | 176 Countr-3.5.2/Countr/man/dWeibullCount_mat.Rd | 120 Countr-3.5.2/Countr/man/dWeibullgammaCount.Rd | 228 Countr-3.5.2/Countr/man/dWeibullgammaCount_mat.Rd | 32 Countr-3.5.2/Countr/man/dWeibullgammaCount_mat_Covariates.Rd | 52 Countr-3.5.2/Countr/man/dmodifiedCount_bi.Rd | 126 Countr-3.5.2/Countr/man/evCount_conv_bi.Rd | 188 Countr-3.5.2/Countr/man/fertility.Rd | 70 Countr-3.5.2/Countr/man/football.Rd | 52 Countr-3.5.2/Countr/man/frequency_plot.Rd | 58 Countr-3.5.2/Countr/man/getParNames.Rd | 38 Countr-3.5.2/Countr/man/predict.renewal.Rd | 128 Countr-3.5.2/Countr/man/renewal.Rd | 34 Countr-3.5.2/Countr/man/renewal.control.Rd | 78 Countr-3.5.2/Countr/man/renewal.convPars.Rd | 44 Countr-3.5.2/Countr/man/renewal.seriesPars.Rd | 50 Countr-3.5.2/Countr/man/renewal.weiMethod.Rd | 36 Countr-3.5.2/Countr/man/renewalCoef.Rd | 98 Countr-3.5.2/Countr/man/renewalCoefList.Rd | 50 Countr-3.5.2/Countr/man/renewalCount.Rd | 442 - 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Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.3.0 dated 2018-08-31 and 1.3.1 dated 2018-10-04
DESCRIPTION | 12 MD5 | 179 +++++------ NAMESPACE | 1 NEWS | 23 + R/SSM.R | 65 ++-- R/analyze.R | 180 +++++++---- R/data.R | 12 R/formants.R | 160 +++++++--- R/loudness.R |only R/matchPars.R | 4 R/morph.R | 16 - R/optimize.R | 19 - R/postprocessing.R |only R/rolloff.R | 21 - R/segment.R | 10 R/soundgen.R | 19 - R/source.R | 186 ++++++----- R/spectrogram.R | 154 ++++++++- R/sysdata.rda |binary R/utilities_analyze.R | 40 +- R/utilities_loudness.R |only R/utilities_math.R | 99 +++++- R/utilities_postprocessing.R |only R/utilities_soundgen.R | 606 -------------------------------------- README.md | 4 inst/CITATION | 2 inst/doc/acoustic_analysis.R | 53 ++- inst/doc/acoustic_analysis.Rmd | 105 ++++-- inst/doc/acoustic_analysis.html | 225 +++++++------- inst/doc/sound_generation.Rmd | 49 +-- inst/doc/sound_generation.html | 113 +++---- inst/shiny/soundgen_main/server.R | 112 ++++--- man/HzToSemitones.Rd | 8 man/addFormants.Rd | 58 +++ man/analyze.Rd | 91 +++-- man/analyzeFolder.Rd | 69 ++-- man/analyzeFrame.Rd | 11 man/beat.Rd | 17 - man/compareSounds.Rd | 5 man/crossFade.Rd | 20 - man/drawContour.Rd | 4 man/estimateVTL.Rd | 6 man/evaluatePars.Rd | 10 man/fade.Rd | 2 man/fart.Rd | 33 +- man/findVoicedSegments.Rd | 4 man/flatEnv.Rd | 32 +- man/generateGC.Rd | 3 man/generateHarmonics.Rd | 14 man/generateNoise.Rd | 102 +++--- man/getBandwidth.Rd | 3 man/getCheckerboardKernel.Rd | 3 man/getDiscreteContour.Rd | 8 man/getEntropy.Rd | 8 man/getEnv.Rd | 2 man/getFrameBank.Rd | 4 man/getIntegerRandomWalk.Rd | 4 man/getLoudness.Rd |only man/getLoudnessPerFrame.Rd |only man/getNovelty.Rd | 2 man/getPitchSpec.Rd | 3 man/getRandomWalk.Rd | 5 man/getRolloff.Rd | 21 - man/getSmoothContour.Rd | 4 man/getSpectralEnvelope.Rd | 15 man/getVocalFry_per_epoch.Rd | 4 man/interpolMatrix.Rd |only man/iso226.Rd |only man/killDC.Rd | 4 man/matchPars.Rd | 4 man/morph.Rd | 16 - man/notesDict.Rd | 5 man/optimizePars.Rd | 28 + man/osc_dB.Rd | 4 man/pathfinder.Rd | 8 man/phon2sone.Rd |only man/pitchManual.Rd | 2 man/playme.Rd | 2 man/sampleModif.Rd | 2 man/scaleSPL.Rd |only man/schwa.Rd | 7 man/segment.Rd | 9 man/segmentFolder.Rd | 17 - man/segmentManual.Rd | 2 man/selfsim.Rd | 2 man/semitonesToHz.Rd | 3 man/soundgen.Rd | 51 +-- man/spectrogram.Rd | 46 +- man/spectrogramFolder.Rd | 21 - man/spreadSpec.Rd |only man/ssm.Rd | 26 + man/wiggleAnchors.Rd | 4 man/wiggleGC.Rd | 1 man/zeroOne.Rd | 4 vignettes/acoustic_analysis.Rmd | 105 ++++-- vignettes/sound_generation.Rmd | 49 +-- 96 files changed, 1801 insertions(+), 1665 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.47-1 dated 2017-11-30 and 0.47-2 dated 2018-10-04
DESCRIPTION | 15 - INDEX | 159 +++++++++++---------- MD5 | 30 +-- R/cluster.Sim.r | 3 R/reszta.r | 93 +++++------- data/data_binary.rda |binary data/data_interval.rda |binary data/data_mixed.rda |binary data/data_nominal.rda |binary data/data_ordinal.rda |binary data/data_ratio.rda |binary data/data_symbolic_interval_polish_voivodships.rda |binary man/HINoV.Mod.rd | 2 man/HINoV.Symbolic.rd | 2 man/dist.BC.rd | 2 man/index.KL.rd | 1 16 files changed, 159 insertions(+), 148 deletions(-)
Title: Datasets for 'spatstat'
Description: Contains all the datasets for the 'spatstat' package.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 1.3-1 dated 2018-06-11 and 1.4-0 dated 2018-10-04
DESCRIPTION | 8 +-- MD5 | 118 +++++++++++++++++++++++----------------------- data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/doc/packagesizes.txt | 9 +++ man/nbfires.Rd | 37 ++++++++++++-- 60 files changed, 103 insertions(+), 69 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-18 0.1
2018-04-13 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-19 1.1.9.0
2018-08-24 1.1.8.0
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 3.1.6 dated 2018-05-14 and 3.1.7 dated 2018-10-04
secr-3.1.6/secr/inst/doc/secr-manual.pdf |only secr-3.1.7/secr/DESCRIPTION | 8 +- secr-3.1.7/secr/MD5 | 50 +++++++------- secr-3.1.7/secr/NEWS | 22 ++++++ secr-3.1.7/secr/R/addTelemetry.R | 26 ++++++- secr-3.1.7/secr/R/join.R |only secr-3.1.7/secr/R/join2.R | 1 secr-3.1.7/secr/R/methods.R | 17 +++-- secr-3.1.7/secr/R/pdot.R | 73 +++++++++++++++++---- secr-3.1.7/secr/R/reduce.R | 10 +- secr-3.1.7/secr/R/regionN.R | 73 ++++++++++++--------- secr-3.1.7/secr/R/sim.popn.R | 91 +++++++++++++++++++++++++++ secr-3.1.7/secr/R/trap.builder.R | 36 +++++----- secr-3.1.7/secr/R/write.traps.R | 4 - secr-3.1.7/secr/data/OVpossum.RData |binary secr-3.1.7/secr/inst/doc/index.html | 13 +-- secr-3.1.7/secr/inst/doc/secr-datainput.R | 7 -- secr-3.1.7/secr/inst/doc/secr-datainput.Rmd | 17 ++--- secr-3.1.7/secr/inst/doc/secr-datainput.pdf |binary secr-3.1.7/secr/inst/doc/secr-overview.pdf |binary secr-3.1.7/secr/inst/extdata/stoat.xlsx |binary secr-3.1.7/secr/man/esaplot.Rd | 18 +++-- secr-3.1.7/secr/man/esaplotsecr.Rd | 10 ++ secr-3.1.7/secr/man/region.N.Rd | 8 +- secr-3.1.7/secr/man/secr-package.Rd | 4 - secr-3.1.7/secr/man/turnover.Rd | 9 +- secr-3.1.7/secr/vignettes/secr-datainput.Rmd | 17 ++--- 27 files changed, 366 insertions(+), 148 deletions(-)
Title: Tile Manager
Description: Tools for creating and detecting tiling schemes for raster data sets.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between TileManager versions 0.2.0 dated 2017-09-07 and 0.3.0 dated 2018-10-04
TileManager-0.2.0/TileManager/R/TileHandlers.R |only TileManager-0.2.0/TileManager/R/temp_TilePlot.R |only TileManager-0.2.0/TileManager/R/tileScheme-methods.R |only TileManager-0.2.0/TileManager/man/TempTiles.Rd |only TileManager-0.2.0/TileManager/man/TileApply.Rd |only TileManager-0.2.0/TileManager/man/TileInput.Rd |only TileManager-0.2.0/TileManager/man/removeTempTiles.Rd |only TileManager-0.3.0/TileManager/DESCRIPTION | 10 TileManager-0.3.0/TileManager/MD5 | 17 TileManager-0.3.0/TileManager/NEWS.md | 6 TileManager-0.3.0/TileManager/R/TileDetector.R | 16 TileManager-0.3.0/TileManager/R/TileScheme.R | 480 +++++----- TileManager-0.3.0/TileManager/tests/testthat/test_TileScheme.R | 2 13 files changed, 268 insertions(+), 263 deletions(-)
Title: Bayesian Modeling via Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>
Diff between BayesGOF versions 4.2 dated 2018-08-15 and 5.0 dated 2018-10-04
DESCRIPTION | 8 +++---- MD5 | 44 ++++++++++++++++++++++------------------ NAMESPACE | 4 ++- R/DS.Finite.Bayes.R |only R/DS.entropy.R |only R/DS.micro.inf.nnu.R | 4 +-- R/DS.micro.inf.pge.R | 4 +-- R/DS.prior.nnu.R | 2 - R/gMLE.nn.R | 12 ++++++++++ R/plot.DS_FB_obj.R |only R/print.DS_FB_obj.R |only build/partial.rdb |binary inst/doc/vignette_BayesGOF.R | 10 ++++++++- inst/doc/vignette_BayesGOF.Rmd | 15 ++++++++++++- inst/doc/vignette_BayesGOF.html | 43 ++++++++++++++++++++++++++++----------- man/BayesGOF-package.Rd | 2 - man/DS.Finite.Bayes.Rd |only man/DS.entropy.Rd |only man/DS.macro.inf.Rd | 2 - man/DS.micro.inf.Rd | 2 - man/DS.posterior.reduce.Rd | 2 - man/DS.prior.Rd | 3 +- man/DS.sampler.Rd | 3 +- man/gLP.basis.Rd | 3 +- man/gMLE.nn.Rd | 6 +++-- vignettes/vignette_BayesGOF.Rmd | 15 ++++++++++++- 26 files changed, 130 insertions(+), 54 deletions(-)