Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects and estimation of unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple known relationship matrices and estimate complex unknown covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 3.9.1 dated 2019-03-25 and 3.9.3 dated 2019-04-03
DESCRIPTION | 6 - MD5 | 22 ++--- R/FUN_markers.R | 27 +++--- R/mmer.R | 10 +- inst/doc/sommer.FAQ.R | 2 inst/doc/sommer.FAQ.Rmd | 2 man/spl2D.Rd | 24 ++++- vignettes/sommer.FAQ.Rmd | 2 vignettes/sommer.FAQ.html | 36 ++++---- vignettes/sommer.changes.html | 4 vignettes/sommer.html | 158 ++++++++++++++++++------------------ vignettes/sommer.start.html | 182 +++++++++++++++++++++--------------------- 12 files changed, 248 insertions(+), 227 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.2.3 dated 2018-08-14 and 1.2.5 dated 2019-04-03
rpsftm-1.2.3/rpsftm/man/print.coxph.Rd |only rpsftm-1.2.3/rpsftm/man/print.summary.coxph.Rd |only rpsftm-1.2.3/rpsftm/man/print.summary.survreg.Rd |only rpsftm-1.2.3/rpsftm/man/print.survreg.Rd |only rpsftm-1.2.5/rpsftm/DESCRIPTION | 10 - rpsftm-1.2.5/rpsftm/MD5 | 30 ++-- rpsftm-1.2.5/rpsftm/NEWS.md | 9 + rpsftm-1.2.5/rpsftm/R/extract_z.R | 4 rpsftm-1.2.5/rpsftm/R/print.rpsftm.R | 40 ----- rpsftm-1.2.5/rpsftm/R/rpsftm.R | 2 rpsftm-1.2.5/rpsftm/R/summary.rpsftm.R | 41 +---- rpsftm-1.2.5/rpsftm/R/terms.inner.R | 7 rpsftm-1.2.5/rpsftm/README.md | 9 - rpsftm-1.2.5/rpsftm/inst/doc/rpsftm_vignette.html | 44 ++++- rpsftm-1.2.5/rpsftm/man/print.rpsftm.coxph.Rd |only rpsftm-1.2.5/rpsftm/man/print.rpsftm.summary.coxph.Rd |only rpsftm-1.2.5/rpsftm/man/print.rpsftm.summary.survreg.Rd |only rpsftm-1.2.5/rpsftm/man/print.rpsftm.survreg.Rd |only rpsftm-1.2.5/rpsftm/tests/testthat/test_rpsftm.R | 120 ++++++++++------ rpsftm-1.2.5/rpsftm/tools/README-unnamed-chunk-2-1.png |binary 20 files changed, 174 insertions(+), 142 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines" <doi:10.1214/aos/1176347963>.
(The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 5.0.0 dated 2019-03-21 and 5.1.0 dated 2019-04-03
DESCRIPTION | 8 MD5 | 126 ++++++------ NEWS | 19 + R/earth.R | 9 R/earth.cv.R | 7 R/earth.glm.R | 19 - R/earth.regress.R | 3 build/partial.rdb |binary inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 inst/slowtests/make.bat | 4 inst/slowtests/test.allowedfunc.R |only inst/slowtests/test.allowedfunc.Rout.save |only inst/slowtests/test.allowedfunc.bat |only inst/slowtests/test.big.R | 3 inst/slowtests/test.big.Rout.save | 45 +++- inst/slowtests/test.big.bat | 5 inst/slowtests/test.bpairs.R | 25 ++ inst/slowtests/test.bpairs.Rout.save | 55 ++++- inst/slowtests/test.bpairs.bat | 3 inst/slowtests/test.cv.R | 10 inst/slowtests/test.cv.Rout.save | 44 +++- inst/slowtests/test.cv.bat | 3 inst/slowtests/test.earthc.bat | 31 +-- inst/slowtests/test.earthc.mak | 4 inst/slowtests/test.earthc.out.save | 78 +++---- inst/slowtests/test.earthmain.clang.bat | 6 inst/slowtests/test.earthmain.gcc.bat | 7 inst/slowtests/test.earthmain.gcc64.bat | 15 - inst/slowtests/test.earthmain.vc.bat | 10 inst/slowtests/test.expand.bpairs.bat | 3 inst/slowtests/test.full.R | 159 +-------------- inst/slowtests/test.full.Rout.save | 305 ++---------------------------- inst/slowtests/test.full.bat | 3 inst/slowtests/test.glm.Rout.save | 8 inst/slowtests/test.glm.bat | 3 inst/slowtests/test.incorrect.R | 10 inst/slowtests/test.incorrect.Rout.save | 32 +-- inst/slowtests/test.incorrect.bat | 6 inst/slowtests/test.mem.R |only inst/slowtests/test.mem.Rout.save |only inst/slowtests/test.mem.bat |only inst/slowtests/test.mods.Rout.save | 92 ++++----- inst/slowtests/test.mods.bat | 5 inst/slowtests/test.multresp.bat | 3 inst/slowtests/test.offset.R | 26 +- inst/slowtests/test.offset.Rout.save | 72 +++---- inst/slowtests/test.offset.bat | 3 inst/slowtests/test.plotd.bat | 3 inst/slowtests/test.pmethod.cv.Rout.save | 90 ++++---- inst/slowtests/test.pmethod.cv.bat | 6 inst/slowtests/test.prolog.R | 2 inst/slowtests/test.varmod.bat | 3 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.varmod.mgcv.bat | 3 inst/slowtests/test.weights.R | 8 inst/slowtests/test.weights.Rout.save | 8 inst/slowtests/test.weights.bat | 3 man/earth.Rd | 3 man/expand.bpairs.Rd | 3 src/allowed.c | 22 +- src/earth.c | 183 ++++++++++-------- src/earth.h | 8 src/rentries.c | 4 tests/test.earth.R | 3 tests/test.earth.Rout.save | 12 - 67 files changed, 740 insertions(+), 897 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph] (for source file 'format.perc')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.7.0 dated 2018-08-01 and 2.8.0 dated 2019-04-03
DESCRIPTION | 26 MD5 | 91 NAMESPACE | 16 R/0distrModUtils.R | 312 - R/AllClass.R | 11 R/AllGeneric.R | 3 R/AllPlot.R | 87 R/AllReturnClasses.R | 6 R/AllShow.R | 4 R/Estimator.R | 2 R/Expectation.R | 37 R/L2GroupFamilies.R | 89 R/L2ParamFamily.R | 22 R/MCEstimate.R | 1 R/MCEstimator.R | 14 R/MDEstimator.R | 132 R/MLEstimator.R | 13 R/SimpleL2ParamFamilies.R | 320 - R/asCvMVarianceQtl.R |only R/existsPIC.R | 4 R/internalMleCalc.R | 25 R/mleCalc-methods.R | 183 R/qqplot.R | 62 R/returnlevelplot.R | 91 R/setAs.R | 2 build/vignette.rds |binary inst/NEWS | 118 inst/doc/distrMod.Rnw | 19 inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 91 man/CauchyLocationFamily.Rd |only man/CauchyLocationScaleFamily.Rd | 2 man/InternalReturnClasses-class.Rd | 16 man/L2ParamFamily-class.Rd | 76 man/L2ParamFamily.Rd | 26 man/LogisticLocationScaleFamily.Rd |only man/MCEstimate-class.Rd | 18 man/MCEstimator.Rd | 8 man/MDEstimator.Rd | 136 man/MLEstimator.Rd | 8 man/ParamFamily-class.Rd | 12 man/checkL2deriv.Rd | 13 man/internalmleHelpers.Rd | 4 man/internals.Rd | 45 man/meRes.Rd | 8 man/returnlevelplot.Rd | 9 tests/Examples/distrMod-Ex.Rout.save | 8274 +++++++++++++++++------------------ vignettes/distrMod.Rnw | 19 48 files changed, 5630 insertions(+), 4825 deletions(-)
Title: Plotting Field Plans for Agricultural Experiments
Description: A function for plotting maps of agricultural field experiments that
are laid out in grids.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between desplot versions 1.4 dated 2018-04-03 and 1.5 dated 2019-04-03
DESCRIPTION | 12 - MD5 | 26 +- NAMESPACE | 6 NEWS.md |only R/desplot.R | 374 ++++++++++++++++++--------------- R/geom_tileborder.R |only R/ggdesplot.R |only build/vignette.rds |binary inst/doc/desplot_examples.R | 3 inst/doc/desplot_examples.Rmd | 13 - inst/doc/desplot_examples.html | 463 +++++++++++++++++++++++++---------------- man/desplot.Rd | 118 ++++++---- man/geom_tileborder.Rd |only man/panel.outlinelevelplot.Rd | 4 tests/testthat/test_desplot.R | 17 + vignettes/desplot_examples.Rmd | 13 - 16 files changed, 626 insertions(+), 423 deletions(-)
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. Additionally, 'grouped_' variants
of the generics provides a convenient way to execute functions across
a combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 0.0.1 dated 2019-03-13 and 0.0.2 dated 2019-04-03
DESCRIPTION | 12 ++-- MD5 | 36 ++++++------- NAMESPACE | 1 NEWS.md | 4 + R/augment.R | 4 - R/glance.R | 4 - R/grouped_augment.R | 15 ++++- R/grouped_glance.R | 16 ++++- R/grouped_tidy.R | 15 ++++- R/tidy.R | 4 - README.md | 95 +++++++++++++++++++++++++---------- build/broomExtra.pdf |binary inst/WORDLIST | 3 + inst/doc/available_methods.html | 69 +++++++++++++------------ inst/doc/tests_and_coverage.Rmd | 36 ++++++------- inst/doc/tests_and_coverage.html | 51 +++++++++--------- tests/README.md | 38 +++++++------- tests/testthat/test_grouped_glance.R | 6 +- vignettes/tests_and_coverage.Rmd | 36 ++++++------- 19 files changed, 262 insertions(+), 183 deletions(-)
Title: Multiple Mediation Analysis for Big Data Sets
Description: Used for general multiple mediation analysis with big data sets.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mmabig versions 1.0-0 dated 2018-05-18 and 2.0-0 dated 2019-04-03
DESCRIPTION | 13 + MD5 | 19 +- R/mmabig.r | 183 +++++++++++++++++------- build |only inst |only man/data.org.big.Rd | 6 man/joint.effect.Rd |only man/med.big.Rd | 6 man/mma.big.Rd | 8 - man/mmabig-package.Rd | 368 -------------------------------------------------- vignettes |only 11 files changed, 170 insertions(+), 433 deletions(-)
Title: Shiny Apps on Crunch
Description: To facilitate building custom dashboards on the Crunch data
platform <https://crunch.io/>, the 'crunchy' package provides tools for
working with 'shiny'. These tools include utilities to manage authentication
and authorization automatically and custom stylesheets to help match the
look and feel of the Crunch web application. The package also includes
several gadgets for use in 'RStudio'.
Author: Neal Richardson [aut],
Jonathan Keane [aut, cre],
Gordon Shotwell [aut]
Maintainer: Jonathan Keane <jon.keane@crunch.io>
Diff between crunchy versions 0.2.0 dated 2017-05-05 and 0.3.0 dated 2019-04-03
crunchy-0.2.0/crunchy/tests/testthat/test-shiny-dataset.R |only crunchy-0.3.0/crunchy/DESCRIPTION | 34 ++- crunchy-0.3.0/crunchy/MD5 | 66 ++++++- crunchy-0.3.0/crunchy/NAMESPACE | 58 ++++++ crunchy-0.3.0/crunchy/R/crunch-page.R | 89 ++++++---- crunchy-0.3.0/crunchy/R/crunchy-server.R |only crunchy-0.3.0/crunchy/R/crunchy-ui.R |only crunchy-0.3.0/crunchy/R/crunchy.R |only crunchy-0.3.0/crunchy/R/gadget-list-datasets.R |only crunchy-0.3.0/crunchy/R/gadget-make-array.R |only crunchy-0.3.0/crunchy/R/progress.R |only crunchy-0.3.0/crunchy/R/shiny-dataset.R | 21 +- crunchy-0.3.0/crunchy/R/shiny-user.R |only crunchy-0.3.0/crunchy/build |only crunchy-0.3.0/crunchy/inst/WORDLIST |only crunchy-0.3.0/crunchy/inst/doc |only crunchy-0.3.0/crunchy/inst/example_apps |only crunchy-0.3.0/crunchy/inst/extra.css | 24 ++ crunchy-0.3.0/crunchy/man/crunchPage.Rd | 14 - crunchy-0.3.0/crunchy/man/crunchyBody.Rd |only crunchy-0.3.0/crunchy/man/crunchyPublicBody.Rd |only crunchy-0.3.0/crunchy/man/crunchyServer.Rd |only crunchy-0.3.0/crunchy/man/listDatasetGadget.Rd |only crunchy-0.3.0/crunchy/man/makeArrayGadget.Rd |only crunchy-0.3.0/crunchy/man/setCrunchyAuthorization.Rd |only crunchy-0.3.0/crunchy/man/shinyDataset.Rd | 8 crunchy-0.3.0/crunchy/man/shinyUser.Rd |only crunchy-0.3.0/crunchy/man/withCrunchyProgress.Rd |only crunchy-0.3.0/crunchy/tests/spelling.R |only crunchy-0.3.0/crunchy/tests/testthat/gadgets |only crunchy-0.3.0/crunchy/tests/testthat/helper.R | 2 crunchy-0.3.0/crunchy/tests/testthat/test-crunchy-server.R |only crunchy-0.3.0/crunchy/tests/testthat/test-gadgets.R |only crunchy-0.3.0/crunchy/tests/testthat/test-page.R | 24 ++ crunchy-0.3.0/crunchy/tests/testthat/test-reactive-functions.R |only crunchy-0.3.0/crunchy/vignettes |only 36 files changed, 257 insertions(+), 83 deletions(-)
Title: A 'dplyr' Interface for Crunch
Description: In order to facilitate analysis of datasets hosted on the Crunch
data platform <http://crunch.io/>, the 'crplyr' package implements 'dplyr'
methods on top of the Crunch backend. The usual methods 'select', 'filter',
'group_by', 'summarize', and 'collect' are implemented in such a way as to
perform as much computation on the server and pull as little data locally
as possible.
Author: Neal Richardson [aut],
Jonathan Keane [aut, cre],
Gordon Shotwell [aut]
Maintainer: Jonathan Keane <jon.keane@crunch.io>
Diff between crplyr versions 0.2.0 dated 2018-06-29 and 0.3.0 dated 2019-04-03
crplyr-0.2.0/crplyr/tests/testthat/cubes |only crplyr-0.3.0/crplyr/DESCRIPTION | 27 +- crplyr-0.3.0/crplyr/MD5 | 106 ++++++++-- crplyr-0.3.0/crplyr/NAMESPACE | 67 ++++++ crplyr-0.3.0/crplyr/NEWS.md | 12 + crplyr-0.3.0/crplyr/R/as-tibble.R | 109 ++++++++++- crplyr-0.3.0/crplyr/R/collect.R | 45 +--- crplyr-0.3.0/crplyr/R/crplyr.R | 13 - crplyr-0.3.0/crplyr/R/filter.R | 19 + crplyr-0.3.0/crplyr/R/group-by.R | 75 +++++-- crplyr-0.3.0/crplyr/R/mutate.R |only crplyr-0.3.0/crplyr/R/plotting.R |only crplyr-0.3.0/crplyr/R/select.R | 41 +++- crplyr-0.3.0/crplyr/R/summarize.R | 44 +++- crplyr-0.3.0/crplyr/README.md | 12 - crplyr-0.3.0/crplyr/build |only crplyr-0.3.0/crplyr/inst/WORDLIST | 27 ++ crplyr-0.3.0/crplyr/inst/doc |only crplyr-0.3.0/crplyr/man/autoplot.Rd |only crplyr-0.3.0/crplyr/man/collect.Rd | 15 - crplyr-0.3.0/crplyr/man/filter.Rd |only crplyr-0.3.0/crplyr/man/group_by.Rd |only crplyr-0.3.0/crplyr/man/mutate.Rd |only crplyr-0.3.0/crplyr/man/select.Rd |only crplyr-0.3.0/crplyr/man/summarize.Rd |only crplyr-0.3.0/crplyr/man/theme_crunch.Rd |only crplyr-0.3.0/crplyr/man/unweighted_n.Rd | 2 crplyr-0.3.0/crplyr/tests/figs |only crplyr-0.3.0/crplyr/tests/testthat/cat-cat-cat-catarray.json |only crplyr-0.3.0/crplyr/tests/testthat/helper.R | 7 crplyr-0.3.0/crplyr/tests/testthat/setup.R |only crplyr-0.3.0/crplyr/tests/testthat/tbl_crunch_mocks |only crplyr-0.3.0/crplyr/tests/testthat/test-api.R |only crplyr-0.3.0/crplyr/tests/testthat/test-as-tibble.R | 51 +++++ crplyr-0.3.0/crplyr/tests/testthat/test-collect.R | 73 +++---- crplyr-0.3.0/crplyr/tests/testthat/test-group-by.R | 15 + crplyr-0.3.0/crplyr/tests/testthat/test-mutate.R |only crplyr-0.3.0/crplyr/tests/testthat/test-plots-vdiff.R |only crplyr-0.3.0/crplyr/tests/testthat/test-select.R | 7 crplyr-0.3.0/crplyr/tests/testthat/test-summarize.R | 9 crplyr-0.3.0/crplyr/tests/testthat/test-tbl_crunch_cube.R |only crplyr-0.3.0/crplyr/tests/testthat/test-variable-autoplot.R |only crplyr-0.3.0/crplyr/vignettes |only 43 files changed, 596 insertions(+), 180 deletions(-)
Title: Longitudinal Cascade
Description: Creates a series of set of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Author: Noah Haber [aut, cre]
Maintainer: Noah Haber <noahhaber@gmail.com>
Diff between longitudinalcascade versions 0.1.2.1 dated 2019-03-14 and 0.2.1.1 dated 2019-04-03
DESCRIPTION | 9 MD5 | 8 NAMESPACE | 2 R/longitudinalcascade.R | 1188 ++++++++++++++++++++++++++------------------- man/longitudinalcascade.Rd | 40 + 5 files changed, 735 insertions(+), 512 deletions(-)
More information about longitudinalcascade at CRAN
Permanent link
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and
batch effect correction operations for 'NanoString nCounter' data,
Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various
metrics are used to determine which samples passed or failed QC. Gene
expression should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.1.1 dated 2019-03-25 and 0.1.2 dated 2019-04-03
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- NEWS.md | 10 +++++ R/HKnorm.R | 26 +++++--------- R/NanoStringQC.R | 85 ++++++++++++++++++------------------------------- R/check.R | 37 ++++++++++++--------- data/hld.r.rda |binary data/ovd.r.rda |binary inst/doc/Overview.html | 16 ++++----- 9 files changed, 92 insertions(+), 106 deletions(-)
Title: Estimation of Life Expectancies Using Multi-State Models
Description: Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
Author: Ardo van den Hout and Mei Sum Chan
Maintainer: Ardo van den Hout <Ardo.vandenHout@ucl.ac.uk>
Diff between elect versions 1.1.3 dated 2019-01-06 and 1.2 dated 2019-04-03
elect-1.1.3/elect/R/elect_functions_1.1.3.r |only elect-1.1.3/elect/data/ELECTData.rda |only elect-1.1.3/elect/man/ELECTData.Rd |only elect-1.1.3/elect/man/check.RestrAndConst.elect.Rd |only elect-1.1.3/elect/man/plusmin.elect.Rd |only elect-1.2/elect/DESCRIPTION | 6 ++-- elect-1.2/elect/MD5 | 30 +++++++++++---------- elect-1.2/elect/NEWS | 9 +++++- elect-1.2/elect/R/check.RestrAndConst.r |only elect-1.2/elect/R/elect.r |only elect-1.2/elect/R/explore.r | 6 ++-- elect-1.2/elect/R/hazards.r | 5 ++- elect-1.2/elect/R/plot.elect.r |only elect-1.2/elect/R/plusmin.r |only elect-1.2/elect/R/summary.elect.r |only elect-1.2/elect/data/electData.rda |only elect-1.2/elect/man/check.RestrAndConst.Rd |only elect-1.2/elect/man/elect.Rd | 9 ++---- elect-1.2/elect/man/electData.Rd |only elect-1.2/elect/man/explore.Rd | 2 - elect-1.2/elect/man/hazards.Rd | 6 ++-- elect-1.2/elect/man/plusmin.Rd |only elect-1.2/elect/man/summary.elect.Rd | 2 - 23 files changed, 45 insertions(+), 30 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.5 dated 2018-11-21 and 0.4.6 dated 2019-04-03
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NAMESPACE | 2 ++ NEWS | 9 +++++++++ R/genomic.R | 33 ++++++++++++++++++++++----------- R/global.R | 11 ++++++++++- R/plot.R | 35 +++++++++++++++++++++++++++++++++-- man/CELL_META.rd | 4 ++-- man/circos.genomicLabels.rd | 3 +++ man/circos.genomicText.rd | 3 ++- man/names.CELL_META.rd |only 11 files changed, 98 insertions(+), 31 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>,
'Parameter estimation' vignettes),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb],
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb],
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>
Diff between airGR versions 1.0.15.2 dated 2018-10-10 and 1.2.13.16 dated 2019-04-03
airGR-1.0.15.2/airGR/R/BasinData.R |only airGR-1.0.15.2/airGR/R/plot_OutputsModel.R |only airGR-1.0.15.2/airGR/inst/vignettes_data |only airGR-1.0.15.2/airGR/man/TransfoParam_CemaNeige.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR1A.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR2M.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR4H.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR4J.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR5J.Rd |only airGR-1.0.15.2/airGR/man/TransfoParam_GR6J.Rd |only airGR-1.2.13.16/airGR/DESCRIPTION | 14 airGR-1.2.13.16/airGR/MD5 | 219 - airGR-1.2.13.16/airGR/NAMESPACE | 3 airGR-1.2.13.16/airGR/NEWS | 193 + airGR-1.2.13.16/airGR/R/Calibration.R | 29 airGR-1.2.13.16/airGR/R/Calibration_Michel.R | 157 - airGR-1.2.13.16/airGR/R/CreateCalibOptions.R | 711 +++-- airGR-1.2.13.16/airGR/R/CreateIniStates.R | 97 airGR-1.2.13.16/airGR/R/CreateInputsCrit.R | 389 ++- airGR-1.2.13.16/airGR/R/CreateInputsModel.R | 623 ++--- airGR-1.2.13.16/airGR/R/CreateRunOptions.R | 264 +- airGR-1.2.13.16/airGR/R/DataAltiExtrapolation_Valery.R | 1096 ++++---- airGR-1.2.13.16/airGR/R/ErrorCrit.R | 77 airGR-1.2.13.16/airGR/R/ErrorCrit_KGE.R | 419 +-- airGR-1.2.13.16/airGR/R/ErrorCrit_KGE2.R | 453 +-- airGR-1.2.13.16/airGR/R/ErrorCrit_NSE.R | 289 +- airGR-1.2.13.16/airGR/R/ErrorCrit_RMSE.R | 285 +- airGR-1.2.13.16/airGR/R/PEdaily_Oudin.R | 178 - airGR-1.2.13.16/airGR/R/RunModel.R | 10 airGR-1.2.13.16/airGR/R/RunModel_CemaNeige.R | 246 +- airGR-1.2.13.16/airGR/R/RunModel_CemaNeigeGR4J.R | 140 - airGR-1.2.13.16/airGR/R/RunModel_CemaNeigeGR5J.R | 122 airGR-1.2.13.16/airGR/R/RunModel_CemaNeigeGR6J.R | 104 airGR-1.2.13.16/airGR/R/RunModel_GR1A.R | 182 - airGR-1.2.13.16/airGR/R/RunModel_GR2M.R | 197 - airGR-1.2.13.16/airGR/R/RunModel_GR4H.R | 205 - airGR-1.2.13.16/airGR/R/RunModel_GR4J.R | 18 airGR-1.2.13.16/airGR/R/RunModel_GR5J.R | 206 - airGR-1.2.13.16/airGR/R/RunModel_GR6J.R | 217 - airGR-1.2.13.16/airGR/R/SeriesAggreg.R | 278 +- airGR-1.2.13.16/airGR/R/TransfoParam.R | 1 airGR-1.2.13.16/airGR/R/TransfoParam_CemaNeige.R | 76 airGR-1.2.13.16/airGR/R/TransfoParam_CemaNeigeHyst.R |only airGR-1.2.13.16/airGR/R/TransfoParam_GR1A.R | 32 airGR-1.2.13.16/airGR/R/TransfoParam_GR2M.R | 33 airGR-1.2.13.16/airGR/R/TransfoParam_GR4H.R | 63 airGR-1.2.13.16/airGR/R/TransfoParam_GR4J.R | 64 airGR-1.2.13.16/airGR/R/TransfoParam_GR5J.R | 70 airGR-1.2.13.16/airGR/R/TransfoParam_GR6J.R | 81 airGR-1.2.13.16/airGR/R/Utils.R |only airGR-1.2.13.16/airGR/R/plot.OutputsModel.R | 1349 ++++++----- airGR-1.2.13.16/airGR/build/vignette.rds |binary airGR-1.2.13.16/airGR/data/X0310010.rda |only airGR-1.2.13.16/airGR/inst/CITATION | 8 airGR-1.2.13.16/airGR/inst/doc/V01_get_started.R | 4 airGR-1.2.13.16/airGR/inst/doc/V01_get_started.Rmd | 6 airGR-1.2.13.16/airGR/inst/doc/V01_get_started.html | 66 airGR-1.2.13.16/airGR/inst/doc/V02.1_param_optim.R | 78 airGR-1.2.13.16/airGR/inst/doc/V02.1_param_optim.Rmd | 56 airGR-1.2.13.16/airGR/inst/doc/V02.1_param_optim.html | 87 airGR-1.2.13.16/airGR/inst/doc/V02.2_param_mcmc.R | 81 airGR-1.2.13.16/airGR/inst/doc/V02.2_param_mcmc.Rmd | 66 airGR-1.2.13.16/airGR/inst/doc/V02.2_param_mcmc.html | 87 airGR-1.2.13.16/airGR/inst/doc/V03_param_sets_GR4J.R | 8 airGR-1.2.13.16/airGR/inst/doc/V03_param_sets_GR4J.Rmd | 8 airGR-1.2.13.16/airGR/inst/doc/V03_param_sets_GR4J.html | 31 airGR-1.2.13.16/airGR/inst/doc/V04_cemaneige_hysteresis.R |only airGR-1.2.13.16/airGR/inst/doc/V04_cemaneige_hysteresis.Rmd |only airGR-1.2.13.16/airGR/inst/doc/V04_cemaneige_hysteresis.html |only airGR-1.2.13.16/airGR/inst/vignettesData |only airGR-1.2.13.16/airGR/man/BasinInfo.Rd | 5 airGR-1.2.13.16/airGR/man/BasinObs.Rd | 33 airGR-1.2.13.16/airGR/man/Calibration.Rd | 220 - airGR-1.2.13.16/airGR/man/Calibration_Michel.Rd | 293 +- airGR-1.2.13.16/airGR/man/CreateCalibOptions.Rd | 287 +- airGR-1.2.13.16/airGR/man/CreateIniStates.Rd | 40 airGR-1.2.13.16/airGR/man/CreateInputsCrit.Rd | 157 - airGR-1.2.13.16/airGR/man/CreateInputsModel.Rd | 223 - airGR-1.2.13.16/airGR/man/CreateRunOptions.Rd | 308 +- airGR-1.2.13.16/airGR/man/DataAltiExtrapolation_Valery.Rd | 173 - airGR-1.2.13.16/airGR/man/ErrorCrit.Rd | 222 - airGR-1.2.13.16/airGR/man/ErrorCrit_KGE.Rd | 195 - airGR-1.2.13.16/airGR/man/ErrorCrit_KGE2.Rd | 202 - airGR-1.2.13.16/airGR/man/ErrorCrit_NSE.Rd | 177 - airGR-1.2.13.16/airGR/man/ErrorCrit_RMSE.Rd | 163 - airGR-1.2.13.16/airGR/man/PEdaily_Oudin.Rd | 120 airGR-1.2.13.16/airGR/man/Param_Sets_GR4J.Rd | 212 - airGR-1.2.13.16/airGR/man/RunModel.Rd | 154 - airGR-1.2.13.16/airGR/man/RunModel_CemaNeige.Rd | 244 + airGR-1.2.13.16/airGR/man/RunModel_CemaNeigeGR4J.Rd | 317 +- airGR-1.2.13.16/airGR/man/RunModel_CemaNeigeGR5J.Rd | 151 - airGR-1.2.13.16/airGR/man/RunModel_CemaNeigeGR6J.Rd | 323 +- airGR-1.2.13.16/airGR/man/RunModel_GR1A.Rd | 222 - airGR-1.2.13.16/airGR/man/RunModel_GR2M.Rd | 239 - airGR-1.2.13.16/airGR/man/RunModel_GR4H.Rd | 236 - airGR-1.2.13.16/airGR/man/RunModel_GR4J.Rd | 241 + airGR-1.2.13.16/airGR/man/RunModel_GR5J.Rd | 251 +- airGR-1.2.13.16/airGR/man/RunModel_GR6J.Rd | 249 +- airGR-1.2.13.16/airGR/man/SeriesAggreg.Rd | 143 - airGR-1.2.13.16/airGR/man/TransfoParam.Rd | 152 - airGR-1.2.13.16/airGR/man/airGR.Rd | 125 - airGR-1.2.13.16/airGR/man/figures |only airGR-1.2.13.16/airGR/man/plot.OutputsModel.Rd | 2 airGR-1.2.13.16/airGR/src/airGR.c | 4 airGR-1.2.13.16/airGR/src/frun_CEMANEIGE.f | 111 airGR-1.2.13.16/airGR/src/frun_GR1A.f | 6 airGR-1.2.13.16/airGR/src/frun_GR2M.f | 52 airGR-1.2.13.16/airGR/src/frun_GR4H.f | 78 airGR-1.2.13.16/airGR/src/frun_GR4J.f | 60 airGR-1.2.13.16/airGR/src/frun_GR5J.f | 92 airGR-1.2.13.16/airGR/src/frun_GR6J.f | 120 airGR-1.2.13.16/airGR/vignettes/V00_airgr_ref.bib | 17 airGR-1.2.13.16/airGR/vignettes/V01_get_started.Rmd | 6 airGR-1.2.13.16/airGR/vignettes/V02.1_param_optim.Rmd | 56 airGR-1.2.13.16/airGR/vignettes/V02.2_param_mcmc.Rmd | 66 airGR-1.2.13.16/airGR/vignettes/V03_param_sets_GR4J.Rmd | 8 airGR-1.2.13.16/airGR/vignettes/V04_cemaneige_hysteresis.Rmd |only 117 files changed, 9178 insertions(+), 7353 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 2.4 dated 2019-03-03 and 2.5 dated 2019-04-03
DESCRIPTION | 8 MD5 | 38 ++- NAMESPACE | 2 R/ArAr.R | 66 +----- R/UPb.R | 201 +++++++++++++++++++-- R/age.R | 8 R/commonPb.R | 507 +++++++++++++++++++++++++++++++++++------------------ R/concordia.R | 33 +-- R/discordia.R | 38 --- R/errorellipse.R | 99 +++++++--- R/evolution.R | 10 - R/io.R | 14 - R/isochron.R | 82 +++++--- R/peakfit.R | 4 R/york.R | 39 +--- man/Pb0corr.Rd |only man/age.Rd | 6 man/isochron.Rd | 46 +++- man/peakfit.Rd | 2 man/scatterplot.Rd |only man/york.Rd | 37 +-- 21 files changed, 793 insertions(+), 447 deletions(-)
Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk
under L1 or L2 regularization. Implements the algorithm proposed by Teo et
al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR
2012). The package comes with lot of loss functions for machine learning
which make it powerful for big data analysis. The applications includes:
structured prediction, linear SVM, multi-class SVM, f-beta optimization,
ROC optimization, ordinal regression, quantile regression,
epsilon insensitive regression, least mean square, logistic regression,
least absolute deviation regression (see package examples), etc... all with
L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados <julien.prados@unige.ch>
Diff between bmrm versions 3.7 dated 2018-02-19 and 4.1 dated 2019-04-03
bmrm-3.7/bmrm/man/hclust.fca.Rd |only bmrm-3.7/bmrm/man/tsvmLoss.Rd |only bmrm-4.1/bmrm/DESCRIPTION | 15 bmrm-4.1/bmrm/MD5 | 58 ++- bmrm-4.1/bmrm/NAMESPACE | 32 + bmrm-4.1/bmrm/R/RcppExports.R |only bmrm-4.1/bmrm/R/loss_convex.R | 266 ++++++++++------ bmrm-4.1/bmrm/R/loss_core.R | 5 bmrm-4.1/bmrm/R/loss_non_convex.R | 104 +++++- bmrm-4.1/bmrm/R/misc.R |only bmrm-4.1/bmrm/R/ml_misc.R | 168 ++++++---- bmrm-4.1/bmrm/R/nrbm.R | 2 bmrm-4.1/bmrm/R/wolfe.R | 33 +- bmrm-4.1/bmrm/build/vignette.rds |binary bmrm-4.1/bmrm/inst/doc/bmrm.html | 408 +++++++++++++++---------- bmrm-4.1/bmrm/man/balanced.loss.weights.Rd |only bmrm-4.1/bmrm/man/bhattacharyya.coefficient.Rd |only bmrm-4.1/bmrm/man/binaryClassificationLoss.Rd | 12 bmrm-4.1/bmrm/man/gradient.Rd | 1 bmrm-4.1/bmrm/man/hclust_fca.Rd |only bmrm-4.1/bmrm/man/hellinger.dist.Rd |only bmrm-4.1/bmrm/man/is.convex.Rd | 1 bmrm-4.1/bmrm/man/iterative.hclust.Rd | 19 - bmrm-4.1/bmrm/man/lvalue.Rd | 1 bmrm-4.1/bmrm/man/mmc.Rd | 5 bmrm-4.1/bmrm/man/multivariateHingeLoss.Rd |only bmrm-4.1/bmrm/man/nrbm.Rd | 13 bmrm-4.1/bmrm/man/ontologyLoss.Rd | 3 bmrm-4.1/bmrm/man/preferenceLoss.Rd |only bmrm-4.1/bmrm/man/print.roc.stat.Rd |only bmrm-4.1/bmrm/man/rank.linear.weights.Rd |only bmrm-4.1/bmrm/man/roc.stat.Rd | 4 bmrm-4.1/bmrm/man/rowmean.Rd |only bmrm-4.1/bmrm/man/softMarginVectorLoss.Rd | 5 bmrm-4.1/bmrm/man/softmaxLoss.Rd |only bmrm-4.1/bmrm/man/wolfe.linesearch.Rd | 9 bmrm-4.1/bmrm/src |only 37 files changed, 771 insertions(+), 393 deletions(-)
Title: Load Estimation of River Compounds with Different Methods
Description: Implements several of the most popular load estimation procedures, including averaging methods, ratio estimators and regression methods. The package provides an easy-to-use tool to rapidly calculate the load for various compounds and to compare different methods. The package also supplies additional functions to easily organize and analyze the data.
Author: Veronica Nava [aut, cre], Martina Patelli [ctb], Marco Rotiroti [ctb], Barbara Leoni [ctb]
Maintainer: Veronica Nava <veronicanava245@gmail.com>
Diff between RiverLoad versions 1.0 dated 2019-02-01 and 1.0.1 dated 2019-04-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/CITATION | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Profiling Inference Functions for Various Model Classes
Description: Provides tools that can be used to calculate, evaluate, plot and use for inference the profiles of *arbitrary* inference functions for *arbitrary* 'glm'-like fitted models with linear predictors. More information on the methods that are implemented can be found in Kosmidis (2008) <https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf>.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between profileModel versions 0.5-9 dated 2013-08-17 and 0.6.0 dated 2019-04-03
DESCRIPTION | 21 +++++----- MD5 | 26 ++++++------ NAMESPACE | 10 +++- R/confintModel.R | 26 +++++------- R/objectives.R | 9 +--- R/plot.profileModel.R | 101 +++++++++++++++++++++++-------------------------- R/print.profileModel.R | 20 ++++----- R/profConfint.R | 22 ++++------ R/profSmooth.R | 18 +++----- R/profZoom.R | 42 +++++++++----------- R/profileModel.R | 40 +++++++------------ R/scaleFit.R | 4 - R/signedSquareRoots.R | 20 ++++----- inst/CITATION | 29 +++++++------- 14 files changed, 185 insertions(+), 203 deletions(-)
Title: Class-Agnostic Time Series
Description: Time series toolkit with identical behavior for all
time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo',
'timeSeries', 'tsibble'. Also converts reliably between these classes.
Author: Christoph Sax [aut, cre]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between tsbox versions 0.0.3 dated 2018-06-18 and 0.1.0 dated 2019-04-03
tsbox-0.0.3/tsbox/inst/docs |only tsbox-0.1.0/tsbox/DESCRIPTION | 15 - tsbox-0.1.0/tsbox/MD5 | 140 ++++++----- tsbox-0.1.0/tsbox/NAMESPACE | 3 tsbox-0.1.0/tsbox/NEWS.md | 52 +++- tsbox-0.1.0/tsbox/R/convert_heuristic.R | 65 +++-- tsbox-0.1.0/tsbox/R/data.table_helpers.R | 8 tsbox-0.1.0/tsbox/R/date_helpers.R | 8 tsbox-0.1.0/tsbox/R/date_utils.R | 55 +--- tsbox-0.1.0/tsbox/R/dts_helpers.R | 21 + tsbox-0.1.0/tsbox/R/guess_time_var_value.R | 8 tsbox-0.1.0/tsbox/R/to_from_all.R | 6 tsbox-0.1.0/tsbox/R/to_from_tibble.R | 4 tsbox-0.1.0/tsbox/R/to_from_ts.R | 18 - tsbox-0.1.0/tsbox/R/to_from_tsibble.R | 14 - tsbox-0.1.0/tsbox/R/to_from_tslist.R | 8 tsbox-0.1.0/tsbox/R/ts_.R | 7 tsbox-0.1.0/tsbox/R/ts_apply.R | 24 + tsbox-0.1.0/tsbox/R/ts_default.R |only tsbox-0.1.0/tsbox/R/ts_examples.R | 31 +- tsbox-0.1.0/tsbox/R/ts_frequency.R | 9 tsbox-0.1.0/tsbox/R/ts_ggplot.R | 22 - tsbox-0.1.0/tsbox/R/ts_index.R | 16 - tsbox-0.1.0/tsbox/R/ts_lag.R | 8 tsbox-0.1.0/tsbox/R/ts_long_wide.R | 21 - tsbox-0.1.0/tsbox/R/ts_pc.R | 63 +++-- tsbox-0.1.0/tsbox/R/ts_pick.R | 25 +- tsbox-0.1.0/tsbox/R/ts_plot.R | 27 +- tsbox-0.1.0/tsbox/R/ts_regular.R | 21 + tsbox-0.1.0/tsbox/R/ts_span.R | 162 ++++++++----- tsbox-0.1.0/tsbox/R/ts_summary.R |only tsbox-0.1.0/tsbox/R/tsbox-deprecated.R |only tsbox-0.1.0/tsbox/R/tsbox-package.R |only tsbox-0.1.0/tsbox/README.md | 9 tsbox-0.1.0/tsbox/build/vignette.rds |binary tsbox-0.1.0/tsbox/inst/WORDLIST | 8 tsbox-0.1.0/tsbox/inst/doc/ts-functions.Rmd | 35 +- tsbox-0.1.0/tsbox/inst/doc/ts-functions.html | 34 +- tsbox-0.1.0/tsbox/inst/doc/tsbox.Rmd | 35 +- tsbox-0.1.0/tsbox/inst/doc/tsbox.html | 34 +- tsbox-0.1.0/tsbox/man/ts_.Rd | 5 tsbox-0.1.0/tsbox/man/ts_arithmetic.Rd | 3 tsbox-0.1.0/tsbox/man/ts_bind.Rd | 1 tsbox-0.1.0/tsbox/man/ts_default.Rd |only tsbox-0.1.0/tsbox/man/ts_examples.Rd | 21 - tsbox-0.1.0/tsbox/man/ts_frequency.Rd | 5 tsbox-0.1.0/tsbox/man/ts_ggplot.Rd | 8 tsbox-0.1.0/tsbox/man/ts_index.Rd | 3 tsbox-0.1.0/tsbox/man/ts_lag.Rd | 4 tsbox-0.1.0/tsbox/man/ts_long.Rd | 4 tsbox-0.1.0/tsbox/man/ts_pc.Rd | 22 - tsbox-0.1.0/tsbox/man/ts_pick.Rd | 7 tsbox-0.1.0/tsbox/man/ts_plot.Rd | 14 - tsbox-0.1.0/tsbox/man/ts_regular.Rd | 7 tsbox-0.1.0/tsbox/man/ts_save.Rd | 4 tsbox-0.1.0/tsbox/man/ts_span.Rd | 18 - tsbox-0.1.0/tsbox/man/ts_summary.Rd |only tsbox-0.1.0/tsbox/man/ts_ts.Rd | 13 - tsbox-0.1.0/tsbox/man/tsbox-deprecated.Rd |only tsbox-0.1.0/tsbox/man/tsbox-package.Rd |only tsbox-0.1.0/tsbox/tests/testthat/test_arithmetic.R |only tsbox-0.1.0/tsbox/tests/testthat/test_auto.R | 7 tsbox-0.1.0/tsbox/tests/testthat/test_date_utils.R | 20 + tsbox-0.1.0/tsbox/tests/testthat/test_dirty.R | 34 ++ tsbox-0.1.0/tsbox/tests/testthat/test_nonstandard_cnames.R | 2 tsbox-0.1.0/tsbox/tests/testthat/test_tricky.R | 24 + tsbox-0.1.0/tsbox/tests/testthat/test_ts_.R | 10 tsbox-0.1.0/tsbox/tests/testthat/test_ts_bind.R | 2 tsbox-0.1.0/tsbox/tests/testthat/test_ts_default.R |only tsbox-0.1.0/tsbox/tests/testthat/test_ts_pc.R | 33 ++ tsbox-0.1.0/tsbox/tests/testthat/test_ts_pick.R | 6 tsbox-0.1.0/tsbox/tests/testthat/test_ts_regular.R | 12 tsbox-0.1.0/tsbox/tests/testthat/test_ts_span.R | 61 ++++ tsbox-0.1.0/tsbox/tests/testthat/test_ts_summary.R |only tsbox-0.1.0/tsbox/tests/testthat/test_tsibble.R |only tsbox-0.1.0/tsbox/tests/testthat/test_tslist.R |only tsbox-0.1.0/tsbox/vignettes/ts-functions.Rmd | 35 +- tsbox-0.1.0/tsbox/vignettes/tsbox.Rmd | 35 +- 78 files changed, 912 insertions(+), 524 deletions(-)
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the
'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the
circumstances of car crashes and other incidents on the roads resulting in
casualties in Great Britain from 1979, the types
(including make and model) of vehicles involved and the consequential casualties. The
statistics relate only to personal casualties on public roads that are reported
to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See
the Department for Transportation website
<https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more
information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>),
Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>),
David Ranzolin [rev],
Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 0.2.0 dated 2019-02-15 and 0.2.1 dated 2019-04-03
DESCRIPTION | 14 MD5 | 22 NEWS.md | 6 R/format.R | 2 build/vignette.rds |binary data/stats19_schema.rda |binary inst/doc/blog.R | 85 inst/doc/blog.Rmd | 214 +- inst/doc/blog.html | 5117 ++---------------------------------------------- inst/doc/stats19.html | 39 man/format_vehicles.Rd | 2 vignettes/blog.Rmd | 214 +- 12 files changed, 698 insertions(+), 5017 deletions(-)
Title: Implementation of Random Variables
Description: Implements random variables by means of S4 classes and methods.
Author: Matthias Kohl [cre, cph, aut],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RandVar versions 1.1.0 dated 2018-08-01 and 1.2.0 dated 2019-04-03
DESCRIPTION | 22 - MD5 | 20 - R/EuclRandVariable.R | 8 R/Expectation.R | 577 ++++++++++++++++++++++++++++++------------------ build/vignette.rds |binary inst/NEWS | 18 + inst/doc/RandVar.Rnw | 2 inst/doc/RandVar.pdf |binary man/0RandVar-package.Rd | 94 +++---- tests/tests.Rout.save | 172 +++++++------- vignettes/RandVar.Rnw | 2 11 files changed, 544 insertions(+), 371 deletions(-)
Title: Approximate Bayesian Computations for Phylogenetic Comparative
Methods
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2019) <10.5506/APhysPolBSupp.12.25>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between pcmabc versions 1.0.3 dated 2019-03-18 and 1.0.4 dated 2019-04-03
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 - R/ABCdist.R | 3 --- man/PCM_ABC.Rd | 1 - 5 files changed, 9 insertions(+), 14 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.14 dated 2018-07-21 and 3.15 dated 2019-04-03
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/cindex.CV.R | 2 +- R/uni.selection.R | 6 +++--- man/compound.Cox-package.Rd | 10 +++++----- 5 files changed, 18 insertions(+), 18 deletions(-)
Title: Inferring Dominance Hierarchies and Estimating Uncertainty
Description: Provides: (1) Tools to infer dominance hierarchies based on calculating Elo scores, but with custom functions to improve estimates in animals with relatively stable dominance ranks. (2) Tools to plot the shape of the dominance hierarchy and estimate the uncertainty of a given data set.
Author: Damien R. Farine and Alfredo Sanchez-Tojar
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between aniDom versions 0.1.3 dated 2018-03-11 and 0.1.4 dated 2019-04-03
DESCRIPTION | 8 ++-- MD5 | 12 +++--- NAMESPACE | 2 - R/elo_scores.R | 87 +++++++++++++++++++++++++++-------------------- R/plot_hierarchy_shape.R | 11 +++-- man/aniDom-package.Rd | 4 +- man/elo_scores.Rd | 33 ++++++++++++++++- 7 files changed, 101 insertions(+), 56 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-14 0.1
Title: Compute Sun Position, Sunlight Phases, Moon Position and Lunar
Phase
Description: Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.),
moon position and lunar phase for the given location and time. Most calculations are based on the
formulas given in Astronomy Answers articles about position of the sun and the planets :
<https://www.aa.quae.nl/en/reken/zonpositie.html>.
Author: Benoit Thieurmel [aut, cre] (R interface),
Achraf Elmarhraoui [aut] (R interface)
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between suncalc versions 0.4 dated 2018-02-22 and 0.5.0 dated 2019-04-03
suncalc-0.4/suncalc/inst/suncalc |only suncalc-0.5.0/suncalc/DESCRIPTION | 34 +++++------ suncalc-0.5.0/suncalc/MD5 | 35 +++++------ suncalc-0.5.0/suncalc/NAMESPACE | 7 ++ suncalc-0.5.0/suncalc/NEWS.md | 8 ++ suncalc-0.5.0/suncalc/R/calcFunctions.R |only suncalc-0.5.0/suncalc/R/getMoonIllumination.R | 45 ++++++--------- suncalc-0.5.0/suncalc/R/getMoonPosition.R | 40 +++++-------- suncalc-0.5.0/suncalc/R/getMoonTimes.R | 68 ++++++++--------------- suncalc-0.5.0/suncalc/R/getSunlightPosition.R | 41 +++++-------- suncalc-0.5.0/suncalc/R/getSunlightTimes.R | 65 ++++++++------------- suncalc-0.5.0/suncalc/R/suncalc.R |only suncalc-0.5.0/suncalc/R/utils.R | 18 +++--- suncalc-0.5.0/suncalc/README.md | 48 ++++------------ suncalc-0.5.0/suncalc/inst/dev_tests.R |only suncalc-0.5.0/suncalc/man/getMoonIllumination.Rd | 4 + suncalc-0.5.0/suncalc/man/getMoonTimes.Rd | 4 - suncalc-0.5.0/suncalc/man/getSunlightPosition.Rd | 4 - suncalc-0.5.0/suncalc/man/getSunlightTimes.Rd | 8 +- 19 files changed, 181 insertions(+), 248 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with bibliographic
references. It greatly enhances the 'bibentry' class by providing a class
'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8'
encoding, and can be easily searched by any field, by date ranges, and by
various formats for name lists (author by last names, translator by full names,
etc.). Entries can be updated, combined, sorted, printed in a number of styles,
and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and
converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and
'Zotero' are provided for importing references and references can be created
from locally stored 'PDF' files using 'Poppler'. Includes functions for citing
and generating a bibliography with hyperlinks for documents prepared with
'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre] (<https://orcid.org/0000-0002-7891-9645>)
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 1.2.0 dated 2018-04-25 and 1.2.12 dated 2019-04-03
RefManageR-1.2.0/RefManageR/tests/testthat/file2669698588fe.bib |only RefManageR-1.2.12/RefManageR/DESCRIPTION | 15 RefManageR-1.2.12/RefManageR/LICENSE | 4 RefManageR-1.2.12/RefManageR/MD5 | 247 RefManageR-1.2.12/RefManageR/NAMESPACE | 209 RefManageR-1.2.12/RefManageR/R/02BibOptions.R | 328 RefManageR-1.2.12/RefManageR/R/03BibLaTeX_entry_field_db.R | 308 RefManageR-1.2.12/RefManageR/R/04InternalFunctions.R | 2362 +- RefManageR-1.2.12/RefManageR/R/05makeBibLatex.R | 1654 - RefManageR-1.2.12/RefManageR/R/06BibEntry.R | 390 RefManageR-1.2.12/RefManageR/R/07makeBibLatexAuthoryear.R | 1540 - RefManageR-1.2.12/RefManageR/R/08asBibEntry.R | 242 RefManageR-1.2.12/RefManageR/R/09sort.R | 318 RefManageR-1.2.12/RefManageR/R/BibEntryAddOp.R | 300 RefManageR-1.2.12/RefManageR/R/BibEntryAssignOp.R | 148 RefManageR-1.2.12/RefManageR/R/BibEntryCombineOp.R | 62 RefManageR-1.2.12/RefManageR/R/BibEntryDollarExtract.R | 64 RefManageR-1.2.12/RefManageR/R/BibEntryExtractOp.R | 750 RefManageR-1.2.12/RefManageR/R/BibEntryListExtract.R | 90 RefManageR-1.2.12/RefManageR/R/BibEntryReplaceBibEntry.R | 68 RefManageR-1.2.12/RefManageR/R/BibEntryReplaceOp.R | 270 RefManageR-1.2.12/RefManageR/R/CommonFormatFuns.R | 1240 - RefManageR-1.2.12/RefManageR/R/GetBibEntryWithDOI.R | 124 RefManageR-1.2.12/RefManageR/R/GetDOIs.R | 226 RefManageR-1.2.12/RefManageR/R/NamesAssign.R | 24 RefManageR-1.2.12/RefManageR/R/ReadBib.R | 118 RefManageR-1.2.12/RefManageR/R/ReadCrossRef.R | 650 RefManageR-1.2.12/RefManageR/R/ReadGS.R | 254 RefManageR-1.2.12/RefManageR/R/ReadPDFs.R | 426 RefManageR-1.2.12/RefManageR/R/ReadPDFsSupport.R | 1202 - RefManageR-1.2.12/RefManageR/R/ReadPubMed.R | 1050 - RefManageR-1.2.12/RefManageR/R/ReadZotero.R | 236 RefManageR-1.2.12/RefManageR/R/RefManageR-package.R | 132 RefManageR-1.2.12/RefManageR/R/SearchBib.R | 50 RefManageR-1.2.12/RefManageR/R/UpdateFieldName.R | 50 RefManageR-1.2.12/RefManageR/R/WriteBib.R | 142 RefManageR-1.2.12/RefManageR/R/asdataframe.R | 96 RefManageR-1.2.12/RefManageR/R/format.R | 256 RefManageR-1.2.12/RefManageR/R/head.BibEntry.R | 136 RefManageR-1.2.12/RefManageR/R/levels.R | 60 RefManageR-1.2.12/RefManageR/R/names.R | 40 RefManageR-1.2.12/RefManageR/R/open.BibEntry.R | 174 RefManageR-1.2.12/RefManageR/R/print.R | 190 RefManageR-1.2.12/RefManageR/R/relist.R | 80 RefManageR-1.2.12/RefManageR/R/rmdCite.R | 974 - RefManageR-1.2.12/RefManageR/R/toBiblatex.R | 162 RefManageR-1.2.12/RefManageR/R/toBibtex.R | 306 RefManageR-1.2.12/RefManageR/R/toRd.R | 214 RefManageR-1.2.12/RefManageR/R/unlist.R | 62 RefManageR-1.2.12/RefManageR/README.md | 67 RefManageR-1.2.12/RefManageR/build/vignette.rds |binary RefManageR-1.2.12/RefManageR/inst/Bib/RJC.bib | 9500 +++++----- RefManageR-1.2.12/RefManageR/inst/Bib/badFormat.bib | 52 RefManageR-1.2.12/RefManageR/inst/Bib/biblatexExamples.bib | 3346 +-- RefManageR-1.2.12/RefManageR/inst/Bib/test.bib | 2104 +- RefManageR-1.2.12/RefManageR/inst/CITATION | 20 RefManageR-1.2.12/RefManageR/inst/NEWS.md | 834 RefManageR-1.2.12/RefManageR/inst/Rhtml/TestAuthorYear.Rhtml | 100 RefManageR-1.2.12/RefManageR/inst/Rhtml/TestHtml.Rhtml | 92 RefManageR-1.2.12/RefManageR/inst/Rmd/TestAlphabetic.Rmd | 62 RefManageR-1.2.12/RefManageR/inst/Rmd/TestNumeric.Rmd | 64 RefManageR-1.2.12/RefManageR/inst/Rmd/TestRmd.Rmd | 72 RefManageR-1.2.12/RefManageR/inst/doc/TestAlphabetic.R | 30 RefManageR-1.2.12/RefManageR/inst/doc/TestAlphabetic.Rmd | 68 RefManageR-1.2.12/RefManageR/inst/doc/TestAlphabetic.html | 611 RefManageR-1.2.12/RefManageR/inst/doc/TestHtml.R | 34 RefManageR-1.2.12/RefManageR/inst/doc/TestHtml.Rhtml | 112 RefManageR-1.2.12/RefManageR/inst/doc/TestHtml.html | 416 RefManageR-1.2.12/RefManageR/inst/doc/TestRmd.R | 48 RefManageR-1.2.12/RefManageR/inst/doc/TestRmd.Rmd | 90 RefManageR-1.2.12/RefManageR/inst/doc/TestRmd.html | 610 RefManageR-1.2.12/RefManageR/inst/doc/manual.Rnw | 32 RefManageR-1.2.12/RefManageR/inst/doc/manual.pdf |binary RefManageR-1.2.12/RefManageR/man/BibEntry.Rd | 278 RefManageR-1.2.12/RefManageR/man/BibOptions.Rd | 258 RefManageR-1.2.12/RefManageR/man/Cite.Rd | 267 RefManageR-1.2.12/RefManageR/man/FindBibEntry.Rd | 24 RefManageR-1.2.12/RefManageR/man/GetBibEntryWithDOI.Rd | 80 RefManageR-1.2.12/RefManageR/man/GetDOIs.Rd | 85 RefManageR-1.2.12/RefManageR/man/GetPubMedByID.Rd | 87 RefManageR-1.2.12/RefManageR/man/GetPubMedRelated.Rd | 130 RefManageR-1.2.12/RefManageR/man/LookupPubMedID.Rd | 97 RefManageR-1.2.12/RefManageR/man/ReadBib.Rd | 96 RefManageR-1.2.12/RefManageR/man/ReadCrossRef.Rd | 251 RefManageR-1.2.12/RefManageR/man/ReadGS.Rd | 158 RefManageR-1.2.12/RefManageR/man/ReadPDFs.Rd | 142 RefManageR-1.2.12/RefManageR/man/ReadPubMed.Rd | 133 RefManageR-1.2.12/RefManageR/man/ReadZotero.Rd | 158 RefManageR-1.2.12/RefManageR/man/RefManageR-package.Rd | 156 RefManageR-1.2.12/RefManageR/man/SearchBib.Rd | 262 RefManageR-1.2.12/RefManageR/man/UpdateFieldName.Rd | 64 RefManageR-1.2.12/RefManageR/man/WriteBib.Rd | 128 RefManageR-1.2.12/RefManageR/man/as.BibEntry.Rd | 121 RefManageR-1.2.12/RefManageR/man/as.data.frame.BibEntry.Rd | 71 RefManageR-1.2.12/RefManageR/man/c.BibEntry.Rd | 77 RefManageR-1.2.12/RefManageR/man/cash-.BibEntry.Rd | 71 RefManageR-1.2.12/RefManageR/man/cash-set-.BibEntry.Rd | 91 RefManageR-1.2.12/RefManageR/man/head.BibEntry.Rd | 83 RefManageR-1.2.12/RefManageR/man/levels.BibEntry.Rd | 69 RefManageR-1.2.12/RefManageR/man/macros/macros.Rd | 34 RefManageR-1.2.12/RefManageR/man/merge.BibEntry.Rd | 176 RefManageR-1.2.12/RefManageR/man/names.BibEntry.Rd | 67 RefManageR-1.2.12/RefManageR/man/open.BibEntry.Rd | 100 RefManageR-1.2.12/RefManageR/man/print.BibEntry.Rd | 146 RefManageR-1.2.12/RefManageR/man/sort.BibEntry.Rd | 171 RefManageR-1.2.12/RefManageR/man/sub-sub-.BibEntry.Rd | 99 RefManageR-1.2.12/RefManageR/man/sub-subset-.BibEntry.Rd | 67 RefManageR-1.2.12/RefManageR/man/subset-.BibEntry.Rd | 125 RefManageR-1.2.12/RefManageR/man/toBiblatex.Rd | 173 RefManageR-1.2.12/RefManageR/man/unlist.BibEntry.Rd | 113 RefManageR-1.2.12/RefManageR/tests/test-all.R | 6 RefManageR-1.2.12/RefManageR/tests/testthat/test-BibEntry.R | 54 RefManageR-1.2.12/RefManageR/tests/testthat/test-Read.R | 32 RefManageR-1.2.12/RefManageR/tests/testthat/test-as.R | 34 RefManageR-1.2.12/RefManageR/tests/testthat/test-authors.R | 150 RefManageR-1.2.12/RefManageR/tests/testthat/test-cites.R | 382 RefManageR-1.2.12/RefManageR/tests/testthat/test-crossref.R | 8 RefManageR-1.2.12/RefManageR/tests/testthat/test-methods.R | 26 RefManageR-1.2.12/RefManageR/tests/testthat/test-pubmed.R | 116 RefManageR-1.2.12/RefManageR/tests/testthat/test-search.R | 250 RefManageR-1.2.12/RefManageR/tests/testthat/test-zotero.R | 117 RefManageR-1.2.12/RefManageR/vignettes/TestAlphabetic.Rmd | 68 RefManageR-1.2.12/RefManageR/vignettes/TestHtml.Rhtml | 112 RefManageR-1.2.12/RefManageR/vignettes/TestRmd.Rmd | 90 RefManageR-1.2.12/RefManageR/vignettes/manual.Rnw | 32 125 files changed, 21416 insertions(+), 21176 deletions(-)
Title: Interface to the Fish Tree of Life API
Description: An interface to the Fish Tree of Life API to download taxonomies,
phylogenies, fossil calibrations, and diversification rate information for
ray-finned fishes.
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>),
Michael E Alfaro [ctb],
Daniel L Rabosky [ctb],
Stephen A Smith [ctb]
Maintainer: Jonathan Chang <jonathan.chang@ucla.edu>
Diff between fishtree versions 0.2.0 dated 2019-02-26 and 0.3.0 dated 2019-04-03
DESCRIPTION | 12 +- MD5 | 29 +++---- NAMESPACE | 3 NEWS.md | 14 +++ R/functions.R | 58 +++++++++++++- R/utils.R | 26 +----- README.md | 29 ++++++- build/vignette.rds |binary inst/CITATION | 18 ++++ inst/WORDLIST | 4 inst/doc/community-analysis.R | 74 +++++++++--------- inst/doc/community-analysis.html | 40 ++++++++- inst/doc/comparative-analysis.R | 152 ++++++++++++++++++------------------- inst/doc/comparative-analysis.html | 102 +++++++++++++++++++++--- man/fishtree_complete_phylogeny.Rd |only tests/testthat |only tests/testthat.R |only 17 files changed, 381 insertions(+), 180 deletions(-)