Title: Interface to 'LMDB'
Description: Key-value store, implemented as a wrapper around 'LMDB';
the "lightning memory-mapped database" <https://symas.com/lmdb/>.
'LMDB' is a transactional key value store that uses a memory map
for efficient access. This package wraps the entire 'LMDB'
interface (except duplicated keys), and provides objects for
transactions and cursors.
Author: Rich FitzJohn [aut, cre],
Howard Chu [aut, cph],
Symas Corporation [cph],
Martin Hedenfalk [aut, cph],
The OpenLDAP Foundation [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between thor versions 1.1.0 dated 2019-03-14 and 1.1.1 dated 2020-01-16
DESCRIPTION | 14 MD5 | 11 build/vignette.rds |binary inst/doc/thor.html | 1292 ++++++++++++++++++++++++++----------------- src/lmdb/mdb.c | 161 ----- src/lmdb/mdb.patch |only tests/testthat/test-cursor.R | 16 7 files changed, 817 insertions(+), 677 deletions(-)
Title: Statistical Modeling of Animal Movements
Description: Animal movement models including moving-resting process
with embedded Brownian motion according to
Yan et al. (2014) <doi:10.1007/s10144-013-0428-8>,
Pozdnyakov et al. (2017) <doi:10.1007/s11009-017-9547-6>,
Brownian motion with measurement error according to
Pozdnyakov et al. (2014) <doi:10.1890/13-0532.1>,
and moving-resting-handling process with embedded Brownian motion,
Pozdnyakov et al. (2018) <arXiv:1806.00849>.
Author: Chaoran Hu [aut, cre],
Vladimir Pozdnyakov [aut],
Jun Yan [aut]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>
Diff between smam versions 0.5.1 dated 2020-01-15 and 0.5.2 dated 2020-01-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ configure | 18 +++++++++--------- configure.ac | 2 +- inst/CITATION | 4 ++-- src/MRME.cpp | 2 +- 7 files changed, 31 insertions(+), 23 deletions(-)
Title: Robust Methods for Multiway Data Analysis, Applicable also for
Compositional Data
Description: Provides methods for multiway data analysis by means of Parafac
and Tucker 3 models. Robust versions (Engelen and Hubert (2011) <doi:10.1016/j.aca.2011.04.043>) and versions
for compositional data are also provided (Gallo (2015) <doi:10.1080/03610926.2013.798664>, Di Palma et al. (2018) <doi:10.1080/02664763.2017.1381669>.
Author: Valentin Todorov <valentin.todorov@chello.at>, Maria Anna Di Palma <madipalma@unior.it> and Michele Gallo \email{mgallo@unior.it}
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between rrcov3way versions 0.1-10 dated 2017-06-22 and 0.1-18 dated 2020-01-16
rrcov3way-0.1-10/rrcov3way/R/als.R |only rrcov3way-0.1-10/rrcov3way/R/congruence.R |only rrcov3way-0.1-10/rrcov3way/R/krp.R |only rrcov3way-0.1-10/rrcov3way/R/pinv.R |only rrcov3way-0.1-18/rrcov3way/ChangeLog | 25 rrcov3way-0.1-18/rrcov3way/DESCRIPTION | 16 rrcov3way-0.1-18/rrcov3way/MD5 | 64 - rrcov3way-0.1-18/rrcov3way/NAMESPACE | 27 rrcov3way-0.1-18/rrcov3way/R/Parafac.R | 213 ++-- rrcov3way-0.1-18/rrcov3way/R/Tucker3.R | 57 - rrcov3way-0.1-18/rrcov3way/R/cp_als.R |only rrcov3way-0.1-18/rrcov3way/R/datadoc.R |only rrcov3way-0.1-18/rrcov3way/R/mtx-utils.R |only rrcov3way-0.1-18/rrcov3way/R/plot-utils.R | 18 rrcov3way-0.1-18/rrcov3way/R/t3_als.R |only rrcov3way-0.1-18/rrcov3way/R/utils.R | 166 ++- rrcov3way-0.1-18/rrcov3way/R/varimcoco.R |only rrcov3way-0.1-18/rrcov3way/data/amino.rda |only rrcov3way-0.1-18/rrcov3way/data/va3way.rda |binary rrcov3way-0.1-18/rrcov3way/man/Arno.Rd | 4 rrcov3way-0.1-18/rrcov3way/man/Parafac.Rd | 40 rrcov3way-0.1-18/rrcov3way/man/Tucker3.Rd | 58 - rrcov3way-0.1-18/rrcov3way/man/amino.Rd |only rrcov3way-0.1-18/rrcov3way/man/congruence.Rd | 89 - rrcov3way-0.1-18/rrcov3way/man/cp_als.Rd |only rrcov3way-0.1-18/rrcov3way/man/do3Rotate.Rd |only rrcov3way-0.1-18/rrcov3way/man/do3Scale.Rd | 3 rrcov3way-0.1-18/rrcov3way/man/elind.Rd | 4 rrcov3way-0.1-18/rrcov3way/man/krp.Rd | 82 - rrcov3way-0.1-18/rrcov3way/man/mtrace.Rd |only rrcov3way-0.1-18/rrcov3way/man/orth.Rd |only rrcov3way-0.1-18/rrcov3way/man/orthmax2.Rd |only rrcov3way-0.1-18/rrcov3way/man/plot-methods.Rd | 54 - rrcov3way-0.1-18/rrcov3way/man/ulabor.Rd | 12 rrcov3way-0.1-18/rrcov3way/man/utils.Rd | 2 rrcov3way-0.1-18/rrcov3way/man/va3way.Rd | 4 rrcov3way-0.1-18/rrcov3way/man/waterquality.Rd | 6 rrcov3way-0.1-18/rrcov3way/tests/tparafac.R | 24 rrcov3way-0.1-18/rrcov3way/tests/tparafac.Rout.save | 770 ++++++++------- rrcov3way-0.1-18/rrcov3way/tests/ttucker3.R | 27 rrcov3way-0.1-18/rrcov3way/tests/ttucker3.Rout.save | 991 ++++++++++---------- 41 files changed, 1517 insertions(+), 1239 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao Alexandra
J. White (2019) A quantile-based g-computation approach to addressing
the effects of exposure mixtures; <arXiv:1902.04200> [stat.ME].
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 1.3.0 dated 2019-12-11 and 2.0.0 dated 2020-01-16
DESCRIPTION | 12 +- MD5 | 47 +++++----- NAMESPACE | 2 NEWS.md | 9 + R/base.R | 191 ++++++++++++++++++++++++++---------------- R/base_surv.R | 28 +++--- R/base_zi.R |only R/utility.R | 60 +++++++++++++ inst/doc/qgcomp-vignette.R | 2 inst/doc/qgcomp-vignette.html | 72 +++++++-------- man/coxmsm.fit.Rd | 13 ++ man/msm.fit.Rd | 14 ++- man/plot.qgcompfit.Rd | 19 +++- man/predict.qgcompfit.Rd | 3 man/qgcomp.boot.Rd | 41 ++++++--- man/qgcomp.cox.boot.Rd | 34 +++++-- man/qgcomp.cox.noboot.Rd | 16 ++- man/qgcomp.noboot.Rd | 15 ++- man/qgcomp.zi.noboot.Rd |only tests/test_asis.R | 2 tests/test_bayesqgcomp.R | 3 tests/test_boot_ints.R | 2 tests/test_boot_vs_noboot.R | 1 tests/test_bootchooser.R | 1 tests/test_cox_msmtest.R | 1 tests/test_zi.R |only 26 files changed, 399 insertions(+), 189 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut],
Hua Zhou [aut],
Nicole Doudican [aut],
John Carucci [aut],
Adriana Heguy [aut],
Boris Reizis [aut],
Aristotelis Tsirigos [aut] (<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.2.7 dated 2019-12-04 and 1.2.9 dated 2020-01-16
DESCRIPTION | 40 ++-- MD5 | 90 +++++----- NAMESPACE | 2 R/F002.data.aggregation.R | 1 R/F008.norm.data.R | 2 R/F012.run.pca.R | 34 --- R/F018.run.umap.R | 389 +++++++++++++++++++++++++++++++++++++++++---- R/F019.run.diffusion.map.R | 27 ++- R/F023.cell.gating.R | 2 R/F027.clust.stats.plot.R | 14 + R/F031.gene.plot.R | 16 + R/F035.volcano.ma.plot.R | 2 R/F044.myclass.R | 22 +- R/globalVariables.R | 1 R/k.pseudotime.R | 4 man/cell.filter.Rd | 17 + man/cell.gating.Rd | 2 man/cell.type.pred.Rd | 10 - man/change.clust.Rd | 3 man/clono.plot.Rd | 17 + man/clust.cond.info.Rd | 8 man/clust.stats.plot.Rd | 22 +- man/cluster.plot.Rd | 22 +- man/data.aggregation.Rd | 1 man/findMarkers.Rd | 11 + man/gene.plot.Rd | 34 ++- man/gg.cor.Rd | 14 + man/heatmap.gg.plot.Rd | 20 +- man/make.gene.model.Rd | 25 ++ man/norm.data.Rd | 11 - man/pseudotime.tree.Rd | 15 + man/qc.stats.Rd | 10 - man/run.anchor.Rd | 35 +++- man/run.cca.Rd | 15 + man/run.clustering.Rd | 12 + man/run.diff.exp.Rd | 10 - man/run.diffusion.map.Rd | 38 +++- man/run.impute.Rd | 23 ++ man/run.mnn.Rd | 28 ++- man/run.pc.tsne.Rd | 30 ++- man/run.pca.Rd | 12 + man/run.tsne.Rd | 29 ++- man/run.umap.Rd | 361 +++++++++++++++++++++++++++++++++++++++++ man/stats.plot.Rd | 16 + man/top.markers.Rd | 9 - man/volcano.ma.plot.Rd | 22 +- 46 files changed, 1254 insertions(+), 274 deletions(-)
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Description: Comfortable ways to work with hyperspectral data sets.
I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f (wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites [aut, cre, dtc],
Valter Sergo [aut],
Alois Bonifacio [ctb, dtc],
Marcel Dahms [ctb],
Björn Egert [ctb],
Simon Fuller [ctb],
Vilmantas Gegzna [ctb],
Rustam Guliev [ctb],
Bryan Hanson [ctb],
Michael Hermes [ctb],
Martin Kammer [dtc],
Roman Kiselev [ctb],
Sebastian Mellor [ctb]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
Diff between hyperSpec versions 0.99-20180627 dated 2018-06-28 and 0.99-20200115 dated 2020-01-16
hyperSpec-0.99-20180627/hyperSpec/tests/unittests.Rout |only hyperSpec-0.99-20200115/hyperSpec/DESCRIPTION | 47 - hyperSpec-0.99-20200115/hyperSpec/MD5 | 222 ++--- hyperSpec-0.99-20200115/hyperSpec/NAMESPACE | 7 hyperSpec-0.99-20200115/hyperSpec/R/Arith.R | 12 hyperSpec-0.99-20200115/hyperSpec/R/Summary.R | 99 ++ hyperSpec-0.99-20200115/hyperSpec/R/aggregate.R | 185 ++-- hyperSpec-0.99-20200115/hyperSpec/R/as.data.frame.R | 46 - hyperSpec-0.99-20200115/hyperSpec/R/barbiturates.R | 2 hyperSpec-0.99-20200115/hyperSpec/R/colMeans.R | 6 hyperSpec-0.99-20200115/hyperSpec/R/collapse.R | 419 +++++++++- hyperSpec-0.99-20200115/hyperSpec/R/decomposition.R | 1 hyperSpec-0.99-20200115/hyperSpec/R/droplevels.R | 33 hyperSpec-0.99-20200115/hyperSpec/R/extract.R | 103 +- hyperSpec-0.99-20200115/hyperSpec/R/initialize.R | 163 +++ hyperSpec-0.99-20200115/hyperSpec/R/merge.R | 4 hyperSpec-0.99-20200115/hyperSpec/R/plotspc.R | 32 hyperSpec-0.99-20200115/hyperSpec/R/qplotmixmap.R | 1 hyperSpec-0.99-20200115/hyperSpec/R/read.ENVI.HySpex.R |only hyperSpec-0.99-20200115/hyperSpec/R/read.ENVI.Nicolet.R | 1 hyperSpec-0.99-20200115/hyperSpec/R/read.ENVI.R | 170 +++- hyperSpec-0.99-20200115/hyperSpec/R/read.asc.Andor.R | 32 hyperSpec-0.99-20200115/hyperSpec/R/read.asc.PerkinElmer.R |only hyperSpec-0.99-20200115/hyperSpec/R/read.jdx.R | 112 ++ hyperSpec-0.99-20200115/hyperSpec/R/read.spc.R | 162 +++ hyperSpec-0.99-20200115/hyperSpec/R/read.txt.Witec.R | 197 ++++ hyperSpec-0.99-20200115/hyperSpec/R/read.txt.long.R | 60 - hyperSpec-0.99-20200115/hyperSpec/R/sample.R | 131 ++- hyperSpec-0.99-20200115/hyperSpec/R/spc.rubberband.R | 42 - hyperSpec-0.99-20200115/hyperSpec/R/sysdata.rda |binary hyperSpec-0.99-20200115/hyperSpec/R/vandermonde.R | 10 hyperSpec-0.99-20200115/hyperSpec/R/wc.R | 40 hyperSpec-0.99-20200115/hyperSpec/build/vignette.rds |binary hyperSpec-0.99-20200115/hyperSpec/data/barbiturates.rda |binary hyperSpec-0.99-20200115/hyperSpec/data/flu.rda |binary hyperSpec-0.99-20200115/hyperSpec/data/laser.rda |binary hyperSpec-0.99-20200115/hyperSpec/data/paracetamol.rda |binary hyperSpec-0.99-20200115/hyperSpec/inst/CITATION | 6 hyperSpec-0.99-20200115/hyperSpec/inst/doc/baseline.R | 10 hyperSpec-0.99-20200115/hyperSpec/inst/doc/baseline.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/chondro.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/chondro.pdf.asis | 2 hyperSpec-0.99-20200115/hyperSpec/inst/doc/fileio.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/fileio.pdf.asis | 70 - hyperSpec-0.99-20200115/hyperSpec/inst/doc/flu.R | 10 hyperSpec-0.99-20200115/hyperSpec/inst/doc/flu.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/hyperspec.R | 41 hyperSpec-0.99-20200115/hyperSpec/inst/doc/hyperspec.Rnw | 25 hyperSpec-0.99-20200115/hyperSpec/inst/doc/hyperspec.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/laser.R | 10 hyperSpec-0.99-20200115/hyperSpec/inst/doc/laser.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/plotting.R | 10 hyperSpec-0.99-20200115/hyperSpec/inst/doc/plotting.pdf |binary hyperSpec-0.99-20200115/hyperSpec/inst/doc/vignettes.defs | 17 hyperSpec-0.99-20200115/hyperSpec/man/Arith.Rd | 30 hyperSpec-0.99-20200115/hyperSpec/man/Comparison.Rd | 18 hyperSpec-0.99-20200115/hyperSpec/man/aggregate.Rd | 20 hyperSpec-0.99-20200115/hyperSpec/man/apply.Rd | 11 hyperSpec-0.99-20200115/hyperSpec/man/as.hyperSpec.Rd | 22 hyperSpec-0.99-20200115/hyperSpec/man/asdataframe.Rd | 22 hyperSpec-0.99-20200115/hyperSpec/man/barbiturates.Rd | 2 hyperSpec-0.99-20200115/hyperSpec/man/baselines.Rd | 31 hyperSpec-0.99-20200115/hyperSpec/man/bind.Rd | 20 hyperSpec-0.99-20200115/hyperSpec/man/colSums.Rd | 1 hyperSpec-0.99-20200115/hyperSpec/man/collapse.Rd | 34 hyperSpec-0.99-20200115/hyperSpec/man/cov.Rd | 9 hyperSpec-0.99-20200115/hyperSpec/man/decomposition.Rd | 12 hyperSpec-0.99-20200115/hyperSpec/man/dim.Rd | 11 hyperSpec-0.99-20200115/hyperSpec/man/dot-cluster.wavelengths.Rd |only hyperSpec-0.99-20200115/hyperSpec/man/dot-collapse.equal.Rd |only hyperSpec-0.99-20200115/hyperSpec/man/droplevels-hyperSpec-method.Rd | 12 hyperSpec-0.99-20200115/hyperSpec/man/initialize.Rd | 11 hyperSpec-0.99-20200115/hyperSpec/man/labels.Rd | 3 hyperSpec-0.99-20200115/hyperSpec/man/levelplot.Rd | 33 hyperSpec-0.99-20200115/hyperSpec/man/mark.dendrogram.Rd | 17 hyperSpec-0.99-20200115/hyperSpec/man/markpeak.Rd | 4 hyperSpec-0.99-20200115/hyperSpec/man/math.Rd | 3 hyperSpec-0.99-20200115/hyperSpec/man/mean_sd.Rd | 4 hyperSpec-0.99-20200115/hyperSpec/man/normalize01.Rd | 1 hyperSpec-0.99-20200115/hyperSpec/man/plot.Rd | 1 hyperSpec-0.99-20200115/hyperSpec/man/plotc.Rd | 10 hyperSpec-0.99-20200115/hyperSpec/man/plotmat.Rd | 10 hyperSpec-0.99-20200115/hyperSpec/man/plotspc.Rd | 46 - hyperSpec-0.99-20200115/hyperSpec/man/qplotc.Rd | 10 hyperSpec-0.99-20200115/hyperSpec/man/qplotmap.Rd | 10 hyperSpec-0.99-20200115/hyperSpec/man/qplotmix.Rd | 45 - hyperSpec-0.99-20200115/hyperSpec/man/qplotspc.Rd | 12 hyperSpec-0.99-20200115/hyperSpec/man/rbind.fill.Rd | 7 hyperSpec-0.99-20200115/hyperSpec/man/read-ini.Rd | 7 hyperSpec-0.99-20200115/hyperSpec/man/read-spc-Kaiser.Rd | 15 hyperSpec-0.99-20200115/hyperSpec/man/read-spc.Rd | 15 hyperSpec-0.99-20200115/hyperSpec/man/read.ENVI.Rd | 107 +- hyperSpec-0.99-20200115/hyperSpec/man/read.asc.Andor.Rd | 9 hyperSpec-0.99-20200115/hyperSpec/man/read.asc.PerkinElmer.Rd |only hyperSpec-0.99-20200115/hyperSpec/man/read.jdx.Rd | 27 hyperSpec-0.99-20200115/hyperSpec/man/read.spe.Rd | 11 hyperSpec-0.99-20200115/hyperSpec/man/read.txt.Horiba.Rd | 24 hyperSpec-0.99-20200115/hyperSpec/man/read.txt.Renishaw.Rd | 16 hyperSpec-0.99-20200115/hyperSpec/man/read.txt.Witec.Rd | 54 - hyperSpec-0.99-20200115/hyperSpec/man/rmmvnorm.Rd | 1 hyperSpec-0.99-20200115/hyperSpec/man/sample.Rd | 9 hyperSpec-0.99-20200115/hyperSpec/man/show.Rd | 14 hyperSpec-0.99-20200115/hyperSpec/man/spc-identify.Rd | 25 hyperSpec-0.99-20200115/hyperSpec/man/spc.NA.approx.Rd | 10 hyperSpec-0.99-20200115/hyperSpec/man/summary.Rd | 15 hyperSpec-0.99-20200115/hyperSpec/man/sweep.Rd | 3 hyperSpec-0.99-20200115/hyperSpec/man/textio.Rd | 98 +- hyperSpec-0.99-20200115/hyperSpec/man/vanderMonde.Rd | 1 hyperSpec-0.99-20200115/hyperSpec/tests/unittests.R | 3 hyperSpec-0.99-20200115/hyperSpec/vignettes/chondro.pdf.asis | 2 hyperSpec-0.99-20200115/hyperSpec/vignettes/fileio.pdf.asis | 70 - hyperSpec-0.99-20200115/hyperSpec/vignettes/hyperspec.Rnw | 25 hyperSpec-0.99-20200115/hyperSpec/vignettes/hyperspec.bib | 10 hyperSpec-0.99-20200115/hyperSpec/vignettes/strukturhyperspec.pdf |binary hyperSpec-0.99-20200115/hyperSpec/vignettes/vignettes.defs | 17 115 files changed, 2560 insertions(+), 1050 deletions(-)
Title: Solve Delay Differential Equations
Description: Solves ordinary and delay differential equations, where
the objective function is written in either R or C. Suitable only
for non-stiff equations, the solver uses a 'Dormand-Prince' method
that allows interpolation of the solution at any point. This
approach is as described by Hairer, Norsett and Wanner (1993)
<ISBN:3540604529>. Support is also included for iterating
difference equations.
Author: Rich FitzJohn [aut, cre],
Wes Hinsley [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between dde versions 1.0.0 dated 2019-05-16 and 1.0.1 dated 2020-01-16
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 README.md | 2 build/vignette.rds |binary inst/doc/dde.html | 1321 ++++++++++++++++++++++++++++------------------------- src/dopri.c | 13 src/r_difeq.c | 6 src/r_dopri.c | 11 9 files changed, 746 insertions(+), 633 deletions(-)
Title: Generalized Framework for Cross-Validation
Description: A general framework for the application of cross-validation schemes
to particular functions. By allowing arbitrary lists of results, origami
accommodates a range of cross-validation applications.
Author: Jeremy Coyle [aut, cre, cph] (<https://orcid.org/0000-0002-9874-6649>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Ivana Malenica [ctb] (<https://orcid.org/0000-0002-7404-8088>),
Rachael Phillips [ctb] (<https://orcid.org/0000-0002-8474-591X>)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Diff between origami versions 1.0.1 dated 2019-05-01 and 1.0.3 dated 2020-01-16
DESCRIPTION | 35 + MD5 | 54 +-- NAMESPACE | 5 R/Fold.R | 10 R/combine_results.R | 28 - R/cross_validate.R | 43 +- R/fold_funs.R | 231 +++++++++++- R/make_folds.R | 23 - R/utils.R | 29 - R/zzz.R | 9 build/vignette.rds |binary inst/doc/generalizedCV.R | 24 - inst/doc/generalizedCV.Rmd | 4 inst/doc/generalizedCV.html | 556 +++++++++++++++++++++---------- man/Combiners.Rd | 2 man/combine_results.Rd | 16 man/cross_validate.Rd | 45 +- man/fold_from_foldvec.Rd | 14 man/fold_funs.Rd | 96 +++-- man/folds2foldvec.Rd | 16 man/guess_combiner.Rd | 2 man/id_folds_to_folds.Rd | 6 man/make_fold.Rd | 8 man/make_folds.Rd | 22 - man/make_repeated_folds.Rd | 16 tests/testthat/test-cvfun_arg_X.R | 2 tests/testthat/test-overall_timeseries.R | 195 ++++++---- vignettes/generalizedCV.Rmd | 4 28 files changed, 1006 insertions(+), 489 deletions(-)
Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut],
Yuxing Liao [aut, cre],
Eric Jaehnig [ctb],
Zhiao Shi [ctb],
Quanhu Sheng [ctb]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>
Diff between WebGestaltR versions 0.4.2 dated 2019-09-17 and 0.4.3 dated 2020-01-16
DESCRIPTION | 14 +++--- MD5 | 58 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 2 R/WebGestaltR.R | 15 +++++- R/WebGestaltRBatch.R | 2 R/WebGestaltRGsea.R | 6 +- R/createReport.R | 7 +-- R/gseaEnrichment.R | 64 ++++++++++++++++++++-------- R/listArchiveURL.R | 1 R/loadGeneSet.R | 6 +- R/summaryDescription.R | 14 +++--- inst/templates/summaryGsea.mustache | 3 + inst/templates/summaryOra.mustache | 6 ++ man/WebGestaltR.Rd | 80 +++++++++++++++++++++++++++--------- man/createNtaReport.Rd | 14 +++++- man/createReport.Rd | 50 +++++++++++++++++----- man/enrichResultSection.Rd | 11 ++++ man/formatCheck.Rd | 3 - man/goSlimSummary.Rd | 12 ++++- man/idMapping.Rd | 35 +++++++++++---- man/linkModification.Rd | 3 - man/listGeneSet.Rd | 7 ++- man/listIdType.Rd | 7 ++- man/listReferenceSet.Rd | 7 ++- man/loadGeneSet.Rd | 13 ++++- man/specificParameterSummaryGsea.Rd | 18 ++++++-- man/specificParameterSummaryOra.Rd | 25 +++++++++-- man/summaryDescription.Rd | 39 ++++++++++++++--- man/swGsea.Rd | 22 +++++++-- 30 files changed, 392 insertions(+), 153 deletions(-)
Title: Estimate Univariate Gaussian or Student's t Mixture
Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.2.1 dated 2019-12-11 and 3.2.2 dated 2020-01-16
DESCRIPTION | 10 MD5 | 211 +++++++------- NAMESPACE | 1 NEWS.md | 12 R/GSMARconstructor.R | 83 ++--- R/MAINest.R | 147 +++++----- R/argumentChecks.R | 116 ++++--- R/diagnosticPlot.R | 199 ++++++++++++- R/geneticAlgorithm.R | 385 ++++++++++++++------------ R/getOmega.R | 9 R/loglikelihood.R | 308 ++++++++++++--------- R/misc3methods.R | 2 R/numericalDifferentiation.R | 31 +- R/parameterReforms.R | 72 ++-- R/pickAndChangeParams.R | 55 ++- R/plotMethods.R | 42 +- R/predictMethod.R | 49 +-- R/printMethods.R | 91 +++--- R/quantileResidualTests.R | 179 +++++------- R/quantileResiduals.R | 407 ++++++---------------------- R/simulateGSMAR.R | 127 +++----- R/standardErrors.R | 12 R/uGMAR.R | 14 R/uncondMoments.R | 43 +- README.md | 1 build/vignette.rds |binary inst/doc/intro-to-uGMAR.Rmd | 2 inst/doc/intro-to-uGMAR.html | 6 man/GAfit.Rd | 65 ++-- man/GSMAR.Rd | 66 ++-- man/add_data.Rd | 20 - man/add_dfs.Rd | 6 man/all_pos_ints.Rd | 4 man/alt_gsmar.Rd | 21 - man/calc_gradient.Rd | 21 - man/changeRegime.Rd | 24 - man/change_parametrization.Rd | 30 +- man/checkAndCorrectData.Rd | 12 man/checkConstraintMat.Rd | 12 man/checkPM.Rd | 14 man/check_data.Rd | 4 man/check_gsmar.Rd | 4 man/check_model.Rd | 10 man/check_params_length.Rd | 28 - man/condMoments.Rd | 30 +- man/diagnosticPlot.Rd | 22 - man/extractRegime.Rd | 32 +- man/fitGSMAR.Rd | 85 +++-- man/format_valuef.Rd | 4 man/getOmega.Rd | 28 - man/get_IC.Rd | 4 man/get_ar_roots.Rd | 6 man/get_minval.Rd |only man/get_regime_autocovs.Rd | 6 man/get_regime_means.Rd | 8 man/get_regime_vars.Rd | 6 man/get_varying_h.Rd | 30 +- man/isStationary.Rd | 34 +- man/isStationary_int.Rd | 39 +- man/iterate_more.Rd | 29 + man/loglikelihood.Rd | 38 +- man/loglikelihood_int.Rd | 68 ++-- man/mixingWeights.Rd | 31 +- man/mixingWeights_int.Rd | 42 +- man/nParams.Rd | 14 man/parameterChecks.Rd | 20 - man/pick_alphas.Rd | 29 + man/pick_dfs.Rd | 27 - man/pick_pars.Rd | 33 +- man/pick_phi0.Rd | 24 - man/plot.gsmarpred.Rd | 12 man/predict.gsmar.Rd | 34 +- man/print.gsmarpred.Rd | 10 man/print.gsmarsum.Rd | 11 man/profile_logliks.Rd |only man/quantileResidualPlot.Rd | 10 man/quantileResidualTests.Rd | 38 +- man/quantileResiduals.Rd | 37 +- man/quantileResiduals_int.Rd | 39 +- man/randomIndividual.Rd | 50 +-- man/randomIndividual_int.Rd | 48 +-- man/random_arcoefs.Rd | 8 man/random_regime.Rd | 19 - man/reformConstrainedPars.Rd | 24 - man/reformParameters.Rd | 30 +- man/reformRestrictedPars.Rd | 20 - man/regime_distance.Rd | 6 man/removeAllConstraints.Rd | 26 - man/simulateGSMAR.Rd | 32 -- man/sortComponents.Rd | 34 +- man/standardErrors.Rd | 34 +- man/stmar_to_gstmar.Rd | 38 +- man/stmarpars_to_gstmar.Rd | 29 + man/swap_parametrization.Rd | 36 +- man/uGMAR.Rd | 14 man/uncondMoments.Rd | 6 man/uncondMoments_int.Rd | 35 +- man/warn_dfs.Rd | 29 - tests/testthat/test_GAfunctions.R | 9 tests/testthat/test_MAINest.R |only tests/testthat/test_argumentChecks.R | 13 tests/testthat/test_getOmega.R | 269 +++++++++--------- tests/testthat/test_loglikelihood.R | 4 tests/testthat/test_quantileResidualTests.R | 170 +++++------ tests/testthat/test_quantileResiduals.R | 51 +-- tests/testthat/test_simulateGSMAR.R | 18 - tests/testthat/test_standardErrors.R | 15 - vignettes/intro-to-uGMAR.Rmd | 2 108 files changed, 2504 insertions(+), 2400 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-24 0.15.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-06 0.0.2
Title: Wavelet Variance
Description: Provides a series of tools to compute and plot quantities related to classical and robust wavelet variance for time series and regular lattices. More details can be found, for example, in Serroukh, A., Walden, A.T., & Percival, D.B. (2000) <doi:10.2307/2669537> and Guerrier, S. & Molinari, R. (2016) <arXiv:1607.05858>.
Author: Stéphane Guerrier [aut, cre],
James Balamuta [aut],
Justin Lee [aut],
Roberto Molinari [aut],
Yuming Zhang [aut],
Nathanael Claussen [ctb],
Haotian Xu [ctb],
Lionel Voirol [ctb]
Maintainer: Stéphane Guerrier <stef.guerrier@gmail.com>
Diff between wv versions 0.1.0 dated 2019-08-30 and 0.1.1 dated 2020-01-16
DESCRIPTION | 19 - MD5 | 59 ++-- NAMESPACE | 4 NEWS.md | 12 R/data.R |only R/wvar.R | 390 ++++++++++++++++++++++++++---- README.md | 86 +++--- data |only man/adis_wv.Rd |only man/batch_modwt_wvar_cpp.Rd | 12 man/ci_wave_variance.Rd | 10 man/compare_wvar.Rd | 24 + man/create_wvar.Rd | 16 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/imar_wv.Rd |only man/kvh1750_wv.Rd |only man/ln200_wv.Rd |only man/modwt_wvar_cpp.Rd | 12 man/navchip_wv.Rd |only man/plot.auto_corr.Rd | 3 man/plot.imu_wvar.Rd |only man/plot.wccv_pair.Rd | 16 + man/plot.wvar.Rd | 22 + man/robust_eda.Rd | 17 + man/unitConversion.Rd |only man/wv.Rd | 1 man/wvar.Rd | 93 +++++-- 33 files changed, 624 insertions(+), 172 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Provides two approaches of comparison; the univariate and the multivariate analysis in two or more populations. Since the main obstacle of performing systematic comparisons in anthropological studies is the absence of raw data, the current package offer a solution for this problem by allowing the use of published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [ctb, dtc] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bas12@fayoum.edu.eg>
Diff between TestDimorph versions 0.2.1 dated 2019-11-11 and 0.2.9 dated 2020-01-16
TestDimorph-0.2.1/TestDimorph/man/pMatrix.Rd |only TestDimorph-0.2.9/TestDimorph/DESCRIPTION | 14 TestDimorph-0.2.9/TestDimorph/MD5 | 68 - TestDimorph-0.2.9/TestDimorph/NAMESPACE | 37 TestDimorph-0.2.9/TestDimorph/NEWS.md | 15 TestDimorph-0.2.9/TestDimorph/R/AccuModel.R | 298 ++++-- TestDimorph-0.2.9/TestDimorph/R/RawGen.R | 547 +++++++----- TestDimorph-0.2.9/TestDimorph/R/TestDimorph-deprecated.R |only TestDimorph-0.2.9/TestDimorph/R/Tg.R | 441 +++++++-- TestDimorph-0.2.9/TestDimorph/R/anova_es.R |only TestDimorph-0.2.9/TestDimorph/R/aovSS.R | 224 +++- TestDimorph-0.2.9/TestDimorph/R/cbind_fill.R |only TestDimorph-0.2.9/TestDimorph/R/extract_sum.R | 273 +++-- TestDimorph-0.2.9/TestDimorph/R/multivariate.R | 483 ++++++---- TestDimorph-0.2.9/TestDimorph/R/pMatrix.R | 193 ++-- TestDimorph-0.2.9/TestDimorph/R/padjust_n.R |only TestDimorph-0.2.9/TestDimorph/R/univariate.R | 231 +++-- TestDimorph-0.2.9/TestDimorph/README.md | 48 - TestDimorph-0.2.9/TestDimorph/build/partial.rdb |binary TestDimorph-0.2.9/TestDimorph/data/baboon.parms_df.rda |binary TestDimorph-0.2.9/TestDimorph/man/AccuModel.Rd | 147 ++- TestDimorph-0.2.9/TestDimorph/man/Howells.Rd | 64 - TestDimorph-0.2.9/TestDimorph/man/R.Rd | 26 TestDimorph-0.2.9/TestDimorph/man/RawGen.Rd | 121 +- TestDimorph-0.2.9/TestDimorph/man/TestDimorph-deprecated.Rd |only TestDimorph-0.2.9/TestDimorph/man/Tg.Rd | 267 +++-- TestDimorph-0.2.9/TestDimorph/man/anova_es.Rd |only TestDimorph-0.2.9/TestDimorph/man/aovSS.Rd | 141 +-- TestDimorph-0.2.9/TestDimorph/man/baboon.parms_df.Rd | 70 - TestDimorph-0.2.9/TestDimorph/man/baboon.parms_list.Rd | 70 - TestDimorph-0.2.9/TestDimorph/man/cbind_fill.Rd |only TestDimorph-0.2.9/TestDimorph/man/extract_sum.Rd | 113 +- TestDimorph-0.2.9/TestDimorph/man/multivariate.Rd | 136 +- TestDimorph-0.2.9/TestDimorph/man/pMatrix-deprecated.Rd |only TestDimorph-0.2.9/TestDimorph/man/padjust_n.Rd |only TestDimorph-0.2.9/TestDimorph/man/univariate.Rd | 164 +-- TestDimorph-0.2.9/TestDimorph/tests |only 37 files changed, 2619 insertions(+), 1572 deletions(-)
Title: Insert Proper Minus Signs
Description: Provides convenience functions to replace hyphen-minuses (ASCII 45)
with proper minus signs (Unicode character 2212). The true minus matches
the plus symbol in width, line thickness, and height above the baseline.
It was designed for mathematics, looks better in presentation,
and is understood properly by screen readers.
Author: Benjamin E. Wolfe [aut, cre] (<https://orcid.org/0000-0002-4339-9328>)
Maintainer: Benjamin E. Wolfe <benjamin.e.wolfe@gmail.com>
Diff between signs versions 0.1.1 dated 2019-11-25 and 0.1.2 dated 2020-01-16
DESCRIPTION | 11 LICENSE | 4 MD5 | 36 - NAMESPACE | 10 NEWS.md | 32 - R/globals.R | 2 R/signs.R | 332 +++++----- R/utils.R | 62 +- R/zzz.R | 26 README.md | 310 +++++----- TODO | 2 build/vignette.rds |binary inst/doc/signs.R | 410 ++++++------- inst/doc/signs.Rmd | 606 ++++++++++---------- inst/doc/signs.html | 1117 ++++++++++++++++++------------------- tests/testthat.R | 8 tests/testthat/test-signs-format.R | 278 ++++----- tests/testthat/test-signs.R | 288 ++++----- vignettes/signs.Rmd | 606 ++++++++++---------- 19 files changed, 2081 insertions(+), 2059 deletions(-)
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point:
principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>),
linear and quadratic discriminant analysis (Todorov and Pires (2007)),
multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>),
outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).
See also Todorov and Filzmoser (2009) <ISBN-13:978-3838108148>,
Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and
Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Author: Valentin Todorov <valentin.todorov@chello.at>
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between rrcov versions 1.4-9 dated 2019-11-25 and 1.5-2 dated 2020-01-16
rrcov-1.4-9/rrcov/inst/bm |only rrcov-1.5-2/rrcov/ChangeLog | 29 +++++- rrcov-1.5-2/rrcov/DESCRIPTION | 14 +-- rrcov-1.5-2/rrcov/MD5 | 52 +++++------ rrcov-1.5-2/rrcov/NAMESPACE | 4 rrcov-1.5-2/rrcov/R/AllClasses.R | 4 rrcov-1.5-2/rrcov/R/CovMrcd.R | 11 +- rrcov-1.5-2/rrcov/R/Lda.R | 2 rrcov-1.5-2/rrcov/R/LdaClassic.R | 4 rrcov-1.5-2/rrcov/R/Linda.R | 37 ++++++-- rrcov-1.5-2/rrcov/R/detmrcd.R | 146 ++++++++++++++++---------------- rrcov-1.5-2/rrcov/R/plot-utils.R | 109 ++++++++++++++--------- rrcov-1.5-2/rrcov/R/utils.R | 12 ++ rrcov-1.5-2/rrcov/inst/NEWS.Rd | 21 ++++ rrcov-1.5-2/rrcov/inst/doc/rrcov.pdf |binary rrcov-1.5-2/rrcov/inst/examples |only rrcov-1.5-2/rrcov/man/CovMrcd.Rd | 8 + rrcov-1.5-2/rrcov/man/Lda-class.Rd | 7 + rrcov-1.5-2/rrcov/man/Linda.Rd | 6 - rrcov-1.5-2/rrcov/man/getEllipse.Rd |only rrcov-1.5-2/rrcov/man/pottery.Rd | 6 - rrcov-1.5-2/rrcov/tests/tlda.R | 34 +++++-- rrcov-1.5-2/rrcov/tests/tlda.Rout.save | 108 +++++++++++++---------- rrcov-1.5-2/rrcov/tests/togk4.R | 9 + rrcov-1.5-2/rrcov/tests/togk4.Rout.save | 17 ++- 25 files changed, 395 insertions(+), 245 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.26 dated 2019-11-12 and 1.27 dated 2020-01-16
DESCRIPTION | 12 - MD5 | 178 ++++++++++++------------- R/block.R | 11 + R/cache.R | 6 R/citation.R | 2 R/defaults.R | 8 - R/engine.R | 9 - R/hooks-extra.R | 4 R/hooks-latex.R | 6 R/hooks-md.R | 15 +- R/hooks.R | 6 R/output.R | 11 - R/package.R | 6 R/pandoc.R | 3 R/parser.R | 15 +- R/pattern.R | 6 R/plot.R | 72 +++++----- R/spin.R | 2 R/utils-conversion.R | 2 R/utils-rd2html.R | 2 R/utils-sweave.R | 2 R/utils-upload.R | 2 R/utils-vignettes.R | 5 R/utils.R | 11 - README.md | 12 - build/vignette.rds |binary inst/doc/docco-classic.html | 4 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 inst/doc/knit_print.R | 2 inst/doc/knit_print.Rmd | 2 inst/doc/knit_print.html | 272 ++++++++++++++++++++------------------- inst/doc/knitr-intro.Rmd | 6 inst/doc/knitr-intro.html | 83 ++++++----- inst/doc/knitr-markdown.html | 2 inst/doc/knitr-refcard.Rmd | 6 inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-beamer.Rnw | 2 inst/examples/knitr-beamer.lyx | 2 inst/examples/knitr-listings.Rnw | 2 inst/examples/knitr-listings.lyx | 2 inst/examples/knitr-manual.Rnw | 30 ++-- inst/examples/knitr-manual.bib | 2 inst/examples/knitr-manual.lyx | 30 ++-- inst/examples/knitr-minimal.Rmd | 2 inst/examples/knitr-packages.bib | 2 inst/misc/docco-classic.html | 4 inst/misc/docco-template.html | 2 man/Sweave2knitr.Rd | 9 - man/all_labels.Rd | 11 + man/all_patterns.Rd | 2 man/chunk_hook.Rd | 4 man/combine_words.Rd | 3 man/dep_auto.Rd | 2 man/dep_prev.Rd | 2 man/fig_chunk.Rd | 3 man/hook_document.Rd | 2 man/hook_plot.Rd | 2 man/imgur_upload.Rd | 2 man/include_graphics.Rd | 7 - man/kable.Rd | 18 ++ man/knit.Rd | 17 +- man/knit2html.Rd | 12 + man/knit2pandoc.Rd | 15 +- man/knit2pdf.Rd | 10 + man/knit2wp.Rd | 15 +- man/knit_child.Rd | 9 - man/knit_engines.Rd | 4 man/knit_hooks.Rd | 4 man/knit_patterns.Rd | 4 man/knit_print.Rd | 2 man/knitr-package.Rd | 6 man/load_cache.Rd | 9 + man/opts_chunk.Rd | 4 man/opts_hooks.Rd | 2 man/opts_knit.Rd | 4 man/output_hooks.Rd | 5 man/pandoc.Rd | 2 man/plot_crop.Rd | 20 +- man/rand_seed.Rd | 2 man/read_chunk.Rd | 15 +- man/set_parent.Rd | 4 man/spin.Rd | 19 +- man/stitch.Rd | 10 + man/vignette_engines.Rd | 2 man/write_bib.Rd | 9 + tests/testit/test-utils.R | 19 +- vignettes/knit_print.Rmd | 2 vignettes/knitr-intro.Rmd | 6 vignettes/knitr-refcard.Rmd | 6 90 files changed, 651 insertions(+), 525 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.5.0 dated 2020-01-08 and 1.5.1 dated 2020-01-16
DESCRIPTION | 16 +-- MD5 | 81 ++++++++-------- NAMESPACE | 3 NEWS.md | 7 + R/ft.R | 142 +++++++++++++++++++++++++---- R/mult_class.R | 65 ++++++++----- R/rquery_treatment.R | 3 R/utils.R | 25 +++-- R/vtreat.R | 15 ++- R/vtreat_pipes.R | 4 R/zzz.R | 4 README.md | 53 ++++++---- inst/doc/MultiClassVtreat.html | 4 inst/doc/SavingTreamentPlans.html | 4 inst/doc/VariableImportance.html | 10 +- inst/doc/vtreat.html | 86 ++++++++++------- inst/doc/vtreatCrossFrames.html | 173 ++++++++++++++++++----------------- inst/doc/vtreatGrouping.html | 4 inst/doc/vtreatOverfit.html | 174 ++++++++++++++++++------------------ inst/doc/vtreatRareLevels.html | 54 ++++++----- inst/doc/vtreatScaleMode.html | 154 +++++++++++++++++-------------- inst/doc/vtreatSignificance.html | 40 ++++---- inst/doc/vtreatSplitting.html | 4 inst/doc/vtreatVariableTypes.html | 106 +++++++++++---------- inst/unit_tests/test_BO.R | 12 +- inst/unit_tests/test_Car.R | 2 inst/unit_tests/test_NoY.R | 4 inst/unit_tests/test_Parallel.R | 11 +- inst/unit_tests/test_Scale.R | 4 inst/unit_tests/test_UniqValue.R | 12 +- inst/unit_tests/test_W1.R | 8 - inst/unit_tests/test_ZW.R | 12 +- inst/unit_tests/test_bind_frames.R |only inst/unit_tests/test_col_dups.R | 2 inst/unit_tests/test_ft.R | 125 +++++++++++++++++++++++++ inst/unit_tests/test_level_clash.R | 4 inst/unit_tests/test_multiclass.R | 2 inst/unit_tests/test_name_munging.R | 2 inst/unit_tests/test_rquery.R | 6 - man/mkCrossFrameMExperiment.Rd | 12 +- man/prepare.multinomial_plan.Rd | 5 - man/prepare.treatmentplan.Rd | 5 - 42 files changed, 899 insertions(+), 560 deletions(-)
Title: Add CSS Loading Animations to 'shiny' Outputs
Description: Automatically show loader animations while a Shiny output is (re)calculating. This is mostly a wrapper around the css-loaders created by Luke Hass <https://github.com/lukehaas/css-loaders>.
Author: Andras Sali [aut] (Original creator of shinycssloaders package),
Luke Hass [ctb, cph] (Author of included CSS loader code),
Dean Attali [aut, cre] (Creator of Shiny-wrapper code)
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinycssloaders versions 0.2.0 dated 2017-05-12 and 0.3 dated 2020-01-16
DESCRIPTION | 26 ++- MD5 | 90 ++++++------ NAMESPACE | 6 NEWS.md | 38 +++-- R/globals.R | 8 - R/shinycssloaders-package.r | 24 +-- R/withSpinner.R | 270 ++++++++++++++++++------------------ README.md | 152 ++++++++++---------- inst/assets/spinner.css | 42 ++--- inst/assets/spinner.js | 70 +++++++-- inst/css-loaders/Gruntfile.js | 110 +++++++------- inst/css-loaders/LICENSE | 38 ++--- inst/css-loaders/README.md | 82 +++++----- inst/css-loaders/bower.json | 50 +++--- inst/css-loaders/css/fallback.css | 44 ++--- inst/css-loaders/css/load1.css | 118 +++++++-------- inst/css-loaders/css/load2.css | 134 ++++++++--------- inst/css-loaders/css/load3.css | 126 ++++++++-------- inst/css-loaders/css/load4.css | 138 +++++++++--------- inst/css-loaders/css/load5.css | 136 +++++++++--------- inst/css-loaders/css/load6.css | 136 +++++++++--------- inst/css-loaders/css/load7.css | 114 +++++++-------- inst/css-loaders/css/load8.css | 82 +++++----- inst/css-loaders/less/fallback.less | 68 ++++----- inst/css-loaders/less/load1.less | 132 ++++++++--------- inst/css-loaders/less/load2.less | 152 ++++++++++---------- inst/css-loaders/less/load3.less | 134 ++++++++--------- inst/css-loaders/less/load4.less | 232 +++++++++++++++--------------- inst/css-loaders/less/load5.less | 230 +++++++++++++++--------------- inst/css-loaders/less/load6.less | 176 +++++++++++------------ inst/css-loaders/less/load7.less | 130 ++++++++--------- inst/css-loaders/less/load8.less | 90 ++++++------ inst/css-loaders/package.json | 36 ++-- inst/css-loaders/sass/fallback.scss | 68 ++++----- inst/css-loaders/sass/load1.scss | 126 ++++++++-------- inst/css-loaders/sass/load2.scss | 152 ++++++++++---------- inst/css-loaders/sass/load3.scss | 134 ++++++++--------- inst/css-loaders/sass/load4.scss | 234 +++++++++++++++---------------- inst/css-loaders/sass/load5.scss | 232 +++++++++++++++--------------- inst/css-loaders/sass/load6.scss | 178 +++++++++++------------ inst/css-loaders/sass/load7.scss | 130 ++++++++--------- inst/css-loaders/sass/load8.scss | 90 ++++++------ inst/examples |only man/shinycssloaders.Rd | 33 ++-- man/withSpinner.Rd | 69 ++++----- 45 files changed, 2461 insertions(+), 2399 deletions(-)
More information about shinycssloaders at CRAN
Permanent link
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20200108.1025 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 0.4-1 dated 2020-01-09 and 0.4-2 dated 2020-01-16
DESCRIPTION | 8 +-- MD5 | 56 +++++++++++------------ R/getMatches.R | 3 + R/labbcatCredentials.R | 17 +++--- R/nzilbb.labbcat.R | 12 ++-- build/partial.rdb |binary man/labbcatCredentials.Rd | 7 +- tests/testthat/test-countAnnotations.R | 3 - tests/testthat/test-getAnchors.R | 3 - tests/testthat/test-getAnnotationLabels.R | 3 - tests/testthat/test-getAnnotations.R | 3 - tests/testthat/test-getAvailableMedia.R | 3 - tests/testthat/test-getCorpusIds.R | 3 - tests/testthat/test-getDictionaries.R | 3 - tests/testthat/test-getDictionaryEntries.R | 3 - tests/testthat/test-getFragments.R | 3 - tests/testthat/test-getGraphIds.R | 3 - tests/testthat/test-getGraphIdsInCorpus.R | 3 - tests/testthat/test-getGraphIdsWithParticipant.R | 3 - tests/testthat/test-getId.R | 3 - tests/testthat/test-getLayer.R | 3 - tests/testthat/test-getLayerIds.R | 3 - tests/testthat/test-getLayers.R | 3 - tests/testthat/test-getMatches.R | 17 +++++- tests/testthat/test-getMatchingGraphIds.R | 3 - tests/testthat/test-getMedia.R | 3 - tests/testthat/test-getMediaTracks.R | 3 - tests/testthat/test-getParticipantIds.R | 3 - tests/testthat/test-getSoundFragments.R | 3 - 29 files changed, 108 insertions(+), 75 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Regression Subset Selection
Description: Regression subset selection, including exhaustive search.
Author: Thomas Lumley based on Fortran code by Alan Miller
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between leaps versions 3.0 dated 2017-01-09 and 3.1 dated 2020-01-16
DESCRIPTION | 6 MD5 | 8 NEWS | 4 R/leaps.R | 2 src/leaps.f | 830 +++++++++++++++++++++++++++++------------------------------- 5 files changed, 426 insertions(+), 424 deletions(-)
Title: Graph/Network Visualization
Description: Build graph/network structures using functions for stepwise addition and
deletion of nodes and edges. Work with data available in tables for bulk
addition of nodes, edges, and associated metadata. Use graph selections
and traversals to apply changes to specific nodes or edges. A wide
selection of graph algorithms allow for the analysis of graphs. Visualize
the graphs and take advantage of any aesthetic properties assigned to
nodes and edges.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 1.0.1 dated 2019-04-22 and 1.0.5 dated 2020-01-16
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| 31 DiagrammeR-1.0.5/DiagrammeR/R/add_graph_to_graph_series.R | 23 DiagrammeR-1.0.5/DiagrammeR/R/add_grid_2d.R | 91 DiagrammeR-1.0.5/DiagrammeR/R/add_grid_3d.R | 89 DiagrammeR-1.0.5/DiagrammeR/R/add_growing_graph.R | 99 DiagrammeR-1.0.5/DiagrammeR/R/add_islands_graph.R | 97 DiagrammeR-1.0.5/DiagrammeR/R/add_n_node_clones.R | 45 DiagrammeR-1.0.5/DiagrammeR/R/add_n_nodes.R | 48 DiagrammeR-1.0.5/DiagrammeR/R/add_n_nodes_ws.R | 140 DiagrammeR-1.0.5/DiagrammeR/R/add_node.R | 80 DiagrammeR-1.0.5/DiagrammeR/R/add_node_clones_ws.R | 75 DiagrammeR-1.0.5/DiagrammeR/R/add_node_df.R | 29 DiagrammeR-1.0.5/DiagrammeR/R/add_nodes_from_df_cols.R | 61 DiagrammeR-1.0.5/DiagrammeR/R/add_nodes_from_table.R | 59 DiagrammeR-1.0.5/DiagrammeR/R/add_pa_graph.R | 154 - DiagrammeR-1.0.5/DiagrammeR/R/add_path.R | 74 DiagrammeR-1.0.5/DiagrammeR/R/add_prism.R | 82 DiagrammeR-1.0.5/DiagrammeR/R/add_reverse_edges_ws.R | 90 DiagrammeR-1.0.5/DiagrammeR/R/add_smallworld_graph.R | 110 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DiagrammeR-1.0.5/DiagrammeR/R/get_constraint.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/get_coreness.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/get_degree_distribution.R | 33 DiagrammeR-1.0.5/DiagrammeR/R/get_degree_histogram.R | 31 DiagrammeR-1.0.5/DiagrammeR/R/get_degree_in.R | 29 DiagrammeR-1.0.5/DiagrammeR/R/get_degree_out.R | 30 DiagrammeR-1.0.5/DiagrammeR/R/get_degree_total.R | 30 DiagrammeR-1.0.5/DiagrammeR/R/get_dice_similarity.R | 43 DiagrammeR-1.0.5/DiagrammeR/R/get_eccentricity.R | 36 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_attrs.R | 42 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_attrs_ws.R | 47 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_count_w_multiedge.R | 34 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_df.R | 19 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_df_ws.R | 35 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_ids.R | 40 DiagrammeR-1.0.5/DiagrammeR/R/get_edge_info.R | 29 DiagrammeR-1.0.5/DiagrammeR/R/get_edges.R | 70 DiagrammeR-1.0.5/DiagrammeR/R/get_eigen_centrality.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/get_girth.R | 29 DiagrammeR-1.0.5/DiagrammeR/R/get_global_graph_attr_info.R | 19 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_actions.R | 25 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_from_graph_series.R | 15 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_info.R | 17 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_log.R | 23 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_name.R | 23 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_series_info.R | 21 DiagrammeR-1.0.5/DiagrammeR/R/get_graph_time.R | 20 DiagrammeR-1.0.5/DiagrammeR/R/get_jaccard_similarity.R | 44 DiagrammeR-1.0.5/DiagrammeR/R/get_last_edges_created.R | 37 DiagrammeR-1.0.5/DiagrammeR/R/get_last_nodes_created.R | 40 DiagrammeR-1.0.5/DiagrammeR/R/get_leverage_centrality.R | 36 DiagrammeR-1.0.5/DiagrammeR/R/get_max_eccentricity.R | 23 DiagrammeR-1.0.5/DiagrammeR/R/get_mean_distance.R | 22 DiagrammeR-1.0.5/DiagrammeR/R/get_min_cut_between.R | 29 DiagrammeR-1.0.5/DiagrammeR/R/get_min_eccentricity.R | 32 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DiagrammeR-1.0.5/DiagrammeR/R/join_node_attrs.R | 54 DiagrammeR-1.0.5/DiagrammeR/R/layout_nodes_w_string.R | 78 DiagrammeR-1.0.5/DiagrammeR/R/mermaid.R | 215 - DiagrammeR-1.0.5/DiagrammeR/R/mutate_edge_attrs.R | 47 DiagrammeR-1.0.5/DiagrammeR/R/mutate_edge_attrs_ws.R | 66 DiagrammeR-1.0.5/DiagrammeR/R/mutate_node_attrs.R | 47 DiagrammeR-1.0.5/DiagrammeR/R/mutate_node_attrs_ws.R | 68 DiagrammeR-1.0.5/DiagrammeR/R/node_aes.R | 244 - DiagrammeR-1.0.5/DiagrammeR/R/node_data.R | 19 DiagrammeR-1.0.5/DiagrammeR/R/nudge_node_positions_ws.R | 62 DiagrammeR-1.0.5/DiagrammeR/R/open_graph.R | 31 DiagrammeR-1.0.5/DiagrammeR/R/pipe.R | 6 DiagrammeR-1.0.5/DiagrammeR/R/print.R | 9 DiagrammeR-1.0.5/DiagrammeR/R/recode_edge_attrs.R | 53 DiagrammeR-1.0.5/DiagrammeR/R/recode_node_attrs.R | 56 DiagrammeR-1.0.5/DiagrammeR/R/remove_graph_from_graph_series.R | 27 DiagrammeR-1.0.5/DiagrammeR/R/rename_edge_attrs.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/rename_node_attrs.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/render_graph.R | 244 + DiagrammeR-1.0.5/DiagrammeR/R/render_graph_from_graph_series.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/reorder_graph_actions.R | 46 DiagrammeR-1.0.5/DiagrammeR/R/rescale_edge_attrs.R | 68 DiagrammeR-1.0.5/DiagrammeR/R/rescale_node_attrs.R | 71 DiagrammeR-1.0.5/DiagrammeR/R/rev_edge_dir.R | 23 DiagrammeR-1.0.5/DiagrammeR/R/rev_edge_dir_ws.R | 43 DiagrammeR-1.0.5/DiagrammeR/R/save_graph.R | 32 DiagrammeR-1.0.5/DiagrammeR/R/select_edges.R | 116 DiagrammeR-1.0.5/DiagrammeR/R/select_edges_by_edge_id.R | 92 DiagrammeR-1.0.5/DiagrammeR/R/select_edges_by_node_id.R | 95 DiagrammeR-1.0.5/DiagrammeR/R/select_last_edges_created.R | 38 DiagrammeR-1.0.5/DiagrammeR/R/select_last_nodes_created.R | 38 DiagrammeR-1.0.5/DiagrammeR/R/select_nodes.R | 106 DiagrammeR-1.0.5/DiagrammeR/R/select_nodes_by_degree.R | 110 DiagrammeR-1.0.5/DiagrammeR/R/select_nodes_by_id.R | 92 DiagrammeR-1.0.5/DiagrammeR/R/select_nodes_in_neighborhood.R | 101 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DiagrammeR-1.0.5/DiagrammeR/man/grVizOutput.Rd | 34 DiagrammeR-1.0.5/DiagrammeR/man/import_graph.Rd | 85 DiagrammeR-1.0.5/DiagrammeR/man/invert_selection.Rd | 20 DiagrammeR-1.0.5/DiagrammeR/man/is_edge_loop.Rd | 20 DiagrammeR-1.0.5/DiagrammeR/man/is_edge_multiple.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/is_edge_mutual.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/is_edge_present.Rd | 39 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_connected.Rd | 9 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_dag.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_directed.Rd | 17 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_empty.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_simple.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_undirected.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/is_graph_weighted.Rd | 20 DiagrammeR-1.0.5/DiagrammeR/man/is_node_present.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/is_property_graph.Rd | 31 DiagrammeR-1.0.5/DiagrammeR/man/join_edge_attrs.Rd | 41 DiagrammeR-1.0.5/DiagrammeR/man/join_node_attrs.Rd | 45 DiagrammeR-1.0.5/DiagrammeR/man/layout_nodes_w_string.Rd | 83 DiagrammeR-1.0.5/DiagrammeR/man/mermaid.Rd | 199 - DiagrammeR-1.0.5/DiagrammeR/man/mutate_edge_attrs.Rd | 35 DiagrammeR-1.0.5/DiagrammeR/man/mutate_edge_attrs_ws.Rd | 53 DiagrammeR-1.0.5/DiagrammeR/man/mutate_node_attrs.Rd | 35 DiagrammeR-1.0.5/DiagrammeR/man/mutate_node_attrs_ws.Rd | 55 DiagrammeR-1.0.5/DiagrammeR/man/node_aes.Rd | 300 -- DiagrammeR-1.0.5/DiagrammeR/man/node_data.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/node_edge_aes_data.Rd |only DiagrammeR-1.0.5/DiagrammeR/man/node_list_1.Rd | 4 DiagrammeR-1.0.5/DiagrammeR/man/node_list_2.Rd | 10 DiagrammeR-1.0.5/DiagrammeR/man/nudge_node_positions_ws.Rd | 54 DiagrammeR-1.0.5/DiagrammeR/man/open_graph.Rd | 26 DiagrammeR-1.0.5/DiagrammeR/man/pipe.Rd | 5 DiagrammeR-1.0.5/DiagrammeR/man/print.dgr_graph.Rd | 6 DiagrammeR-1.0.5/DiagrammeR/man/recode_edge_attrs.Rd | 53 DiagrammeR-1.0.5/DiagrammeR/man/recode_node_attrs.Rd | 56 DiagrammeR-1.0.5/DiagrammeR/man/remove_graph_from_graph_series.Rd | 18 DiagrammeR-1.0.5/DiagrammeR/man/rename_edge_attrs.Rd | 23 DiagrammeR-1.0.5/DiagrammeR/man/rename_node_attrs.Rd | 23 DiagrammeR-1.0.5/DiagrammeR/man/renderDiagrammeR.Rd | 8 DiagrammeR-1.0.5/DiagrammeR/man/renderGrViz.Rd | 2 DiagrammeR-1.0.5/DiagrammeR/man/render_graph.Rd | 49 DiagrammeR-1.0.5/DiagrammeR/man/render_graph_from_graph_series.Rd | 36 DiagrammeR-1.0.5/DiagrammeR/man/reorder_graph_actions.Rd | 33 DiagrammeR-1.0.5/DiagrammeR/man/replace_in_spec.Rd | 6 DiagrammeR-1.0.5/DiagrammeR/man/rescale_edge_attrs.Rd | 73 DiagrammeR-1.0.5/DiagrammeR/man/rescale_node_attrs.Rd | 73 DiagrammeR-1.0.5/DiagrammeR/man/rev_edge_dir.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/rev_edge_dir_ws.Rd | 31 DiagrammeR-1.0.5/DiagrammeR/man/save_graph.Rd | 27 DiagrammeR-1.0.5/DiagrammeR/man/select_edges.Rd | 58 DiagrammeR-1.0.5/DiagrammeR/man/select_edges_by_edge_id.Rd | 29 DiagrammeR-1.0.5/DiagrammeR/man/select_edges_by_node_id.Rd | 32 DiagrammeR-1.0.5/DiagrammeR/man/select_last_edges_created.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/select_last_nodes_created.Rd | 16 DiagrammeR-1.0.5/DiagrammeR/man/select_nodes.Rd | 36 DiagrammeR-1.0.5/DiagrammeR/man/select_nodes_by_degree.Rd | 49 DiagrammeR-1.0.5/DiagrammeR/man/select_nodes_by_id.Rd | 33 DiagrammeR-1.0.5/DiagrammeR/man/select_nodes_in_neighborhood.Rd | 44 DiagrammeR-1.0.5/DiagrammeR/man/set_cache.Rd | 46 DiagrammeR-1.0.5/DiagrammeR/man/set_df_as_edge_attr.Rd | 26 DiagrammeR-1.0.5/DiagrammeR/man/set_df_as_node_attr.Rd | 24 DiagrammeR-1.0.5/DiagrammeR/man/set_edge_attr_to_display.Rd | 59 DiagrammeR-1.0.5/DiagrammeR/man/set_edge_attrs.Rd | 39 DiagrammeR-1.0.5/DiagrammeR/man/set_edge_attrs_ws.Rd | 38 DiagrammeR-1.0.5/DiagrammeR/man/set_graph_directed.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/set_graph_name.Rd | 11 DiagrammeR-1.0.5/DiagrammeR/man/set_graph_time.Rd | 19 DiagrammeR-1.0.5/DiagrammeR/man/set_graph_undirected.Rd | 14 DiagrammeR-1.0.5/DiagrammeR/man/set_node_attr_to_display.Rd | 59 DiagrammeR-1.0.5/DiagrammeR/man/set_node_attr_w_fcn.Rd | 66 DiagrammeR-1.0.5/DiagrammeR/man/set_node_attrs.Rd | 34 DiagrammeR-1.0.5/DiagrammeR/man/set_node_attrs_ws.Rd | 49 DiagrammeR-1.0.5/DiagrammeR/man/set_node_position.Rd | 43 DiagrammeR-1.0.5/DiagrammeR/man/to_igraph.Rd | 9 DiagrammeR-1.0.5/DiagrammeR/man/transform_to_complement_graph.Rd | 25 DiagrammeR-1.0.5/DiagrammeR/man/transform_to_min_spanning_tree.Rd | 10 DiagrammeR-1.0.5/DiagrammeR/man/transform_to_subgraph_ws.Rd | 74 DiagrammeR-1.0.5/DiagrammeR/man/trav_both.Rd | 108 DiagrammeR-1.0.5/DiagrammeR/man/trav_both_edge.Rd | 97 DiagrammeR-1.0.5/DiagrammeR/man/trav_in.Rd | 108 DiagrammeR-1.0.5/DiagrammeR/man/trav_in_edge.Rd | 80 DiagrammeR-1.0.5/DiagrammeR/man/trav_in_node.Rd | 100 DiagrammeR-1.0.5/DiagrammeR/man/trav_in_until.Rd | 92 DiagrammeR-1.0.5/DiagrammeR/man/trav_out.Rd | 108 DiagrammeR-1.0.5/DiagrammeR/man/trav_out_edge.Rd | 77 DiagrammeR-1.0.5/DiagrammeR/man/trav_out_node.Rd | 100 DiagrammeR-1.0.5/DiagrammeR/man/trav_out_until.Rd | 92 DiagrammeR-1.0.5/DiagrammeR/man/trav_reverse_edge.Rd | 51 DiagrammeR-1.0.5/DiagrammeR/man/trigger_graph_actions.Rd | 28 DiagrammeR-1.0.5/DiagrammeR/man/usd_exchange_rates.Rd | 6 DiagrammeR-1.0.5/DiagrammeR/man/visnetwork.Rd | 18 DiagrammeR-1.0.5/DiagrammeR/man/x11_hex.Rd | 5 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-add_graphs.R | 1 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-generate_dot.R |only DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-get_graph_metrics.R | 1 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-get_node_calculations.R | 73 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-get_nodes_edges.R | 2 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-join_attrs.R | 2 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-metagraph.R | 6 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-node_edge_data_aes.R |only DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-node_edge_info.R | 2 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-predecessors_successors.R | 1 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-print.R | 2 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-set_get_graph_attrs.R | 2 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-spectools.R | 9 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-transform_graph.R | 22 DiagrammeR-1.0.5/DiagrammeR/tests/testthat/test-write_graph_backup.R | 520 ++- DiagrammeR-1.0.5/DiagrammeR/vignettes |only 532 files changed, 12129 insertions(+), 15484 deletions(-)
Title: Effects of Changing Deposition Rates
Description: Reverse and model the effects of changing deposition rates on geological data and rates. Based on Hohmann (2018) <doi:10.13140/RG.2.2.23372.51841> .
Author: Niklas Hohmann
Maintainer: Niklas Hohmann <Niklas.Hohmann@fau.de>
Diff between DAIME versions 2.1 dated 2020-01-09 and 2.1.1 dated 2020-01-16
DESCRIPTION | 8 +-- MD5 | 10 ++-- build/partial.rdb |binary inst/doc/DAIME.Rmd | 92 ++++++++++++++++++++++++++++++++++----------- inst/doc/DAIME.html | 105 +++++++++++++++++++++++++++++++++++++++++----------- vignettes/DAIME.Rmd | 92 ++++++++++++++++++++++++++++++++++----------- 6 files changed, 233 insertions(+), 74 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.4 dated 2019-09-12 and 0.3.5 dated 2020-01-16
DESCRIPTION | 16 MD5 | 190 ++--- NAMESPACE | 2 NEWS | 8 R/build-plot-title.R | 2 R/geom-spct.R | 2 R/ggplot-methods.R | 119 ++- R/multiplot.R | 1 R/si-prefixes.R | 2 R/title-utils.R | 39 - README.md | 4 build/vignette.rds |binary inst/doc/userguide1-grammar.R | 213 +++-- inst/doc/userguide1-grammar.Rmd | 3 inst/doc/userguide1-grammar.html | 1068 +++++++++++++++--------------- inst/doc/userguide2-autoplot-methods.R | 104 +- inst/doc/userguide2-autoplot-methods.html | 185 ++--- inst/doc/userguide3-data-manip.R |only inst/doc/userguide3-data-manip.Rmd |only inst/doc/userguide3-data-manip.html |only man/A_internal_label.Rd | 90 +- man/A_plot.Rd | 119 +-- man/Afr_plot.Rd | 116 +-- man/O_plot.Rd | 112 +-- man/R_plot.Rd | 124 +-- man/Rfr_specular_label.Rd | 94 +- man/SI_pl_format.Rd | 74 +- man/SI_tg_format.Rd | 86 +- man/T_plot.Rd | 124 +-- man/Tfr_internal_label.Rd | 94 +- man/autoplot.calibration_spct.Rd | 201 +++-- man/autoplot.cps_spct.Rd | 178 ++--- man/autoplot.filter_spct.Rd | 223 +++--- man/autoplot.generic_spct.Rd | 38 - man/autoplot.object_spct.Rd | 208 +++-- man/autoplot.raw_spct.Rd | 180 ++--- man/autoplot.reflector_spct.Rd | 213 +++-- man/autoplot.response_spct.Rd | 216 +++--- man/autoplot.source_spct.Rd | 202 ++--- man/autoplot.waveband.Rd | 191 ++--- man/autotitle.Rd | 144 ++-- man/black_or_white.Rd | 48 - man/cal_plot.Rd | 135 ++- man/color_chart.Rd | 83 +- man/counts_label.Rd | 62 - man/cps_label.Rd | 66 - man/cps_plot.Rd | 131 ++- man/decode_annotations.Rd | 34 man/decoration.Rd | 100 +- man/duration2character.Rd | 42 - man/e_plot.Rd | 119 +-- man/e_rsp_plot.Rd | 127 +-- man/exponent2prefix.Rd | 130 +-- man/find_idfactor.Rd | 64 - man/geom_spct.Rd | 137 ++- man/gg2spectra-ggproto.Rd | 180 ++--- man/ggplot.Rd | 296 ++++---- man/ggspectra-package.Rd | 198 ++--- man/multiplot.Rd | 128 +-- man/plot.Rd | 112 +-- man/q_plot.Rd | 119 +-- man/q_rsp_plot.Rd | 127 +-- man/raw_plot.Rd | 137 ++- man/s.e.irrad_label.Rd | 72 +- man/s.e.response_label.Rd | 72 +- man/scale_x_wl_continuous.Rd | 103 +- man/scale_y_A_internal_continuous.Rd | 94 +- man/scale_y_Rfr_specular_continuous.Rd | 114 +-- man/scale_y_Tfr_internal_continuous.Rd | 114 +-- man/scale_y_counts_continuous.Rd | 104 +- man/scale_y_cps_continuous.Rd | 81 +- man/scale_y_s.e.irrad_continuous.Rd | 152 ++-- man/scale_y_s.e.response_continuous.Rd | 94 +- man/sec_axis_w_number.Rd | 92 +- man/set_annotations_default.Rd | 133 +-- man/stat_color.Rd | 206 +++-- man/stat_find_qtys.Rd | 292 ++++---- man/stat_find_wls.Rd | 286 ++++---- man/stat_label_peaks.Rd | 382 +++++----- man/stat_peaks.Rd | 341 +++++---- man/stat_wb_box.Rd | 276 ++++--- man/stat_wb_column.Rd | 274 ++++--- man/stat_wb_contribution.Rd | 325 ++++----- man/stat_wb_hbar.Rd | 288 ++++---- man/stat_wb_irrad.Rd | 378 +++++----- man/stat_wb_label.Rd | 274 ++++--- man/stat_wb_mean.Rd | 323 ++++----- man/stat_wb_relative.Rd | 327 ++++----- man/stat_wb_sirrad.Rd | 380 +++++----- man/stat_wb_total.Rd | 312 ++++---- man/stat_wl_strip.Rd | 277 ++++--- man/stat_wl_summary.Rd | 243 +++--- man/subtitle_spct.generic_spct.Rd | 52 - man/title_spct.Rd | 40 - man/w_length_label.Rd | 90 +- man/w_number.Rd | 48 - vignettes/userguide1-grammar.Rmd | 3 vignettes/userguide3-data-manip.Rmd |only 98 files changed, 7511 insertions(+), 6691 deletions(-)
Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2. See Song et al. (2019) <doi:10.1371/journal.pcbi.1007565> for a detailed presentation of the method.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>
Diff between EBPRS versions 1.2.2 dated 2019-11-07 and 2.0.1 dated 2020-01-16
EBPRS-1.2.2/EBPRS/R/bedNA0.R |only EBPRS-1.2.2/EBPRS/R/getEffectSize.R |only EBPRS-1.2.2/EBPRS/R/getpara.R |only EBPRS-1.2.2/EBPRS/man/extractInfo.Rd |only EBPRS-1.2.2/EBPRS/man/findPara.Rd |only EBPRS-1.2.2/EBPRS/man/generateScore.Rd |only EBPRS-1.2.2/EBPRS/man/getEffectSize.Rd |only EBPRS-2.0.1/EBPRS/DESCRIPTION | 8 +- EBPRS-2.0.1/EBPRS/MD5 | 34 +++----- EBPRS-2.0.1/EBPRS/NAMESPACE | 5 - EBPRS-2.0.1/EBPRS/R/exdata.R | 5 - EBPRS-2.0.1/EBPRS/R/extractInfo.R | 115 ++++++++++------------------- EBPRS-2.0.1/EBPRS/R/findPara.R | 127 +++++++++++++++++++++------------ EBPRS-2.0.1/EBPRS/R/findpara_ltdr.R |only EBPRS-2.0.1/EBPRS/R/generateScore.R | 39 ++-------- EBPRS-2.0.1/EBPRS/R/packageEBPRS.R | 49 ++++++++---- EBPRS-2.0.1/EBPRS/R/snpEM.R | 48 +++++++++++- EBPRS-2.0.1/EBPRS/R/snpEMrobust.R |only EBPRS-2.0.1/EBPRS/R/validate.R | 44 +++++++---- EBPRS-2.0.1/EBPRS/man/EBPRS.Rd |only EBPRS-2.0.1/EBPRS/man/EBPRSpackage.Rd | 48 +++++++----- EBPRS-2.0.1/EBPRS/man/traindat.Rd | 5 - EBPRS-2.0.1/EBPRS/man/validate.Rd | 16 +--- 23 files changed, 292 insertions(+), 251 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-16 0.2-2
2019-02-18 0.1-97
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-17 2.2-39
2019-02-22 2.2-32
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-14 0.1.5
2014-06-12 0.1.4
2013-03-07 0.1.1
2012-10-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-16 0.1.3
2012-09-07 0.1.2
2012-08-23 0.1.1
2011-10-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-17 1.0
Title: Learn R, in R
Description: Use the R console as an interactive learning
environment. Users receive immediate feedback as they are guided through
self-paced lessons in data science and R programming.
Author: Sean Kross [aut, cre],
Nick Carchedi [aut],
Bill Bauer [aut],
Gina Grdina [aut],
Filip Schouwenaars [ctb],
Wush Wu [ctb]
Maintainer: Sean Kross <sean@seankross.com>
Diff between swirl versions 2.4.4 dated 2019-05-03 and 2.4.5 dated 2020-01-16
DESCRIPTION | 8 ++--- MD5 | 58 ++++++++++++++++++------------------- NEWS.md | 5 +++ R/menu.R | 2 - man/AnswerTests.Rd | 20 +++++++----- man/InstallCourses.Rd | 22 +++++++------- man/any_of_exprs.Rd | 20 +++++++----- man/calculates_same_value.Rd | 20 +++++++----- man/expr_creates_var.Rd | 20 +++++++----- man/expr_identical_to.Rd | 20 +++++++----- man/expr_is_a.Rd | 21 +++++++------ man/expr_uses_func.Rd | 20 +++++++----- man/func_of_newvar_equals.Rd | 20 +++++++----- man/install_course.Rd | 22 +++++++------- man/install_course_directory.Rd | 22 +++++++------- man/install_course_dropbox.Rd | 22 +++++++------- man/install_course_github.Rd | 30 +++++++++++-------- man/install_course_google_drive.Rd | 22 +++++++------- man/install_course_url.Rd | 22 +++++++------- man/install_course_zip.Rd | 22 +++++++------- man/install_from_swirl.Rd | 22 +++++++------- man/omnitest.Rd | 29 +++++++++++------- man/swirl.Rd | 2 - man/uninstall_all_courses.Rd | 22 +++++++------- man/uninstall_course.Rd | 23 +++++++------- man/val_has_length.Rd | 21 +++++++------ man/val_matches.Rd | 21 +++++++------ man/var_is_a.Rd | 21 +++++++------ man/zip_course.Rd | 23 +++++++------- tests/testthat/test-rmatch_calls.R | 2 - 30 files changed, 341 insertions(+), 263 deletions(-)
Title: Detecting Structural Change with Heteroskedasticity
Description: Calculates the sup MZ value to detect the unknown structural break points under Heteroskedasticity as given in Ahmed et al. (2017) (<DOI: 10.1080/03610926.2016.1235200>).
Author: Muhammad Yaseen [aut, cre],
Sami Ullah [aut, ctb],
Gulfam Haider [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between SupMZ versions 0.1.0 dated 2019-05-24 and 0.2.0 dated 2020-01-16
DESCRIPTION | 8 +++---- MD5 | 10 ++++----- NAMESPACE | 3 ++ NEWS.md | 6 +++++ R/supmz.R | 61 +++++++++++++++++++++++++++++++++++++++++++++-------------- man/supmz.Rd | 22 +++++++++++++-------- 6 files changed, 79 insertions(+), 31 deletions(-)
Title: Separation Plots
Description: Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.
Author: Brian D. Greenhill, Michael D. Ward and Audrey Sacks
Maintainer: Brian Greenhill <bgreenhill@albany.edu>
Diff between separationplot versions 1.2 dated 2020-01-10 and 1.3 dated 2020-01-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/separationplot.Rd | 8 +++----- man/sp.categorical.Rd | 8 +++----- 4 files changed, 13 insertions(+), 17 deletions(-)
More information about separationplot at CRAN
Permanent link
Title: Translate 'SQL' Queries into 'R' Expressions
Description: Translate 'SQL' 'SELECT' statements into lists of 'R' expressions.
Author: Ian Cook [aut, cre],
Cloudera [cph]
Maintainer: Ian Cook <ian@cloudera.com>
Diff between queryparser versions 0.1.1 dated 2019-09-04 and 0.2.0 dated 2020-01-16
DESCRIPTION | 20 +- MD5 | 71 +++++---- NAMESPACE | 2 NEWS.md | 11 + R/agg_scalar.R | 2 R/check_expressions.R | 2 R/column_references.R |only R/common.R | 91 +++++++++-- R/compat.R | 4 R/extract_alias.R | 11 + R/parse_clauses.R | 65 ++------ R/parse_expression.R | 32 ++-- R/parse_join.R |only R/parse_query.R | 31 ++-- R/parse_table_reference.R |only R/process_translations.R | 2 R/replace.R | 138 ++++++++++++++++- R/secure.R | 11 - R/split_query.R | 15 - R/squish_sql.R | 50 +++++- R/translate.R | 5 R/translations.R | 161 +++++++++++++++++++- R/unpipe.R | 2 R/unqualify.R |only R/wrap_bangs.R | 2 README.md | 66 +++++--- man/column_references.Rd |only man/extract_alias.Rd | 3 man/parse_expression.Rd | 12 - man/parse_query.Rd | 11 - man/split_query.Rd | 8 - man/squish_sql.Rd | 7 man/unqualify_query.Rd |only tests/testthat/test-column_references.R |only tests/testthat/test-extract_alias.R | 28 +++ tests/testthat/test-parse_expression.R | 247 ++++++++++++++++++++++++++++++-- tests/testthat/test-parse_join.R |only tests/testthat/test-parse_query.R | 236 ++++++++++++++++++++++++++++++ tests/testthat/test-secure.R | 7 tests/testthat/test-split_query.R |only tests/testthat/test-squish_sql.R |only tests/testthat/test-unqualify_query.R |only 42 files changed, 1110 insertions(+), 243 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 2.0.1.14 dated 2018-04-22 and 2.0.3 dated 2020-01-16
DESCRIPTION | 12 ++++--- MD5 | 73 ++++++++++++++++++++++---------------------- R/gdal_chooseInstallation.R | 4 +- R/gdal_cmd_builder.R | 69 ++++++++++++++++++++++++++++++++++------- R/gdal_rasterize.R | 7 ++-- R/gdal_setInstallation.R | 16 +++++---- R/gdal_translate.R | 27 ++++++++++------ R/gdaldem.R | 7 ++-- R/gdalinfo.R | 7 ++-- R/gdallocationinfo.R | 16 +++++++-- R/gdalwarp.R | 3 + R/mosaic_rasters.R | 7 ++-- README.md |only man/align_rasters.Rd | 12 ++++++- man/batch_gdal_translate.Rd | 11 +++++- man/gdal_cmd_builder.Rd | 20 +++++++++--- man/gdal_contour.Rd | 23 ++++++++++++- man/gdal_grid.Rd | 44 ++++++++++++++++++++------ man/gdal_rasterize.Rd | 34 ++++++++++++++++++-- man/gdal_setInstallation.Rd | 8 +++- man/gdal_translate.Rd | 53 ++++++++++++++++++++++++++----- man/gdaladdo.Rd | 13 ++++++- man/gdalbuildvrt.Rd | 29 +++++++++++++++-- man/gdaldem.Rd | 37 ++++++++++++++++++---- man/gdalinfo.Rd | 32 +++++++++++++++++-- man/gdallocationinfo.Rd | 21 ++++++++++-- man/gdalmanage.Rd | 12 ++++++- man/gdalsrsinfo.Rd | 11 +++++- man/gdaltindex.Rd | 18 +++++++++- man/gdaltransform.Rd | 19 ++++++++++- man/gdalwarp.Rd | 55 +++++++++++++++++++++++++++++---- man/get_subdatasets.Rd | 8 +++- man/mosaic_rasters.Rd | 22 +++++++++---- man/nearblack.Rd | 20 ++++++++++-- man/ogr2ogr.Rd | 73 ++++++++++++++++++++++++++++++++++++++------ man/ogrinfo.Rd | 28 +++++++++++++++- man/ogrlineref.Rd | 35 +++++++++++++++++++-- man/ogrtindex.Rd | 17 ++++++++-- 38 files changed, 718 insertions(+), 185 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.15.1 dated 2019-11-25 and 1.16.0 dated 2020-01-16
DESCRIPTION | 12 - MD5 | 211 +++++++++++++++-------------- NAMESPACE | 4 NEWS | 60 ++++++++ R/ClusterFuture-class.R | 230 ++++++++++++++++++++++++++----- R/ConstantFuture-class.R | 2 R/Future-class.R | 268 ++++++++++++++++++++----------------- R/FutureCondition-class.R | 12 - R/FutureGlobals-class.R | 4 R/FutureResult-class.R | 33 ++-- R/MulticoreFuture-class.R | 31 +++- R/MultiprocessFuture-class.R | 6 R/MultisessionFuture-class.R | 4 R/UniprocessFuture-class.R | 7 R/as.cluster.R | 6 R/availableCores.R | 50 +++--- R/availableWorkers.R | 24 +-- R/cluster.R | 10 - R/conditions_OP.R | 4 R/connections.R | 4 R/future.R | 84 +++++------ R/futureAssign.R | 14 - R/futureCall.R | 10 - R/futureOf.R | 10 - R/futures.R | 6 R/globals.R | 8 - R/globals_OP.R | 2 R/label_OP.R | 2 R/lazy_OP.R | 2 R/makeClusterMPI.R | 20 +- R/makeClusterPSOCK.R | 172 +++++++++++------------ R/mandelbrot.R | 16 +- R/multicore.R | 22 +-- R/multiprocess.R | 20 +- R/multisession.R | 22 +-- R/nbrOfWorkers.R | 4 R/options.R | 74 ++++++---- R/plan_OP.R | 6 R/remote.R | 12 - R/resolve.R | 20 +- R/resolved.R | 4 R/rng.R |only R/seed_OP.R | 2 R/sequential.R | 6 R/sessionDetails.R | 4 R/signalConditions.R | 8 - R/stdout_OP.R | 4 R/sticky_globals.R |only R/supportsMulticore.R | 16 +- R/tweak.R | 2 R/tweak_OP.R | 2 R/utils.R | 78 ++++++---- R/values.R | 8 - R/zzz.plan.R | 56 +++---- build/vignette.rds |binary inst/WORDLIST | 2 man/ClusterFuture-class.Rd | 6 man/ConstantFuture-class.Rd | 2 man/Future-class.Rd | 24 ++- man/FutureCondition.Rd | 2 man/FutureResult.Rd | 7 man/MulticoreFuture-class.Rd | 6 man/MultiprocessFuture-class.Rd | 4 man/UniprocessFuture-class.Rd | 8 - man/availableCores.Rd | 76 +++++----- man/availableWorkers.Rd | 42 ++--- man/cluster.Rd | 22 ++- man/clusterExportSticky.Rd |only man/future.Rd | 33 +++- man/future.options.Rd | 76 ++++++---- man/futureOf.Rd | 2 man/futures.Rd | 2 man/getExpression.Rd | 12 - man/grapes-conditions-grapes.Rd | 2 man/grapes-globals-grapes.Rd | 4 man/grapes-label-grapes.Rd | 2 man/grapes-lazy-grapes.Rd | 4 man/grapes-plan-grapes.Rd | 6 man/grapes-seed-grapes.Rd | 16 +- man/grapes-stdout-grapes.Rd | 2 man/grapes-tweak-grapes.Rd | 2 man/makeClusterMPI.Rd | 12 - man/makeClusterPSOCK.Rd | 22 +-- man/make_rng_seeds.Rd |only man/mandelbrot.Rd | 4 man/multicore.Rd | 28 ++- man/multiprocess.Rd | 22 ++- man/multisession.Rd | 28 ++- man/nbrOfWorkers.Rd | 2 man/nullcon.Rd | 2 man/pid_exists.Rd | 20 +- man/plan.Rd | 68 ++++----- man/remote.Rd | 20 ++ man/requestCore.Rd | 2 man/resetWorkers.Rd | 1 man/resolve.Rd | 4 man/sequential.Rd | 20 ++ man/sticky_globals.Rd |only man/supportsMulticore.Rd | 2 man/tweak.Rd | 2 tests/futureCall.R | 4 tests/immediateCondition.R | 42 ++++- tests/incl/start,load-only.R | 3 tests/invalid-owner.R | 5 tests/multicore,multithreading.R |only tests/objectSize.R | 3 tests/plan.R | 14 - tests/reserved-keyword-functions.R |only tests/rng.R | 94 +++++++++--- tests/utils.R | 2 110 files changed, 1505 insertions(+), 983 deletions(-)
Title: A Basis for Modular Model Creation
Description: Create modular models. Quickly prototype models whose input includes (multiple) time series data. Create pieces of model use cases separately, and swap out particular models as desired. Create modeling competitions, data processing pipelines, and re-useable models.
Author: Joshua Kaminsky [aut, cre],
Justin Lessler [aut],
Nicholas Reich [aut]
Maintainer: Joshua Kaminsky <jkaminsky@jhu.edu>
Diff between ForecastFramework versions 0.10.2 dated 2019-11-03 and 0.10.3 dated 2020-01-16
DESCRIPTION | 12 MD5 | 45 +-- NEWS.md | 2 README.md | 4 build/vignette.rds |binary data |only exec/writeClassDiagram.pl | 31 -- inst/doc/ClassDiagram.Rnw |only inst/doc/ClassDiagram.pdf |only inst/doc/DataPolymorphism.R | 2 inst/doc/DataPolymorphism.Rmd | 2 inst/doc/DataPolymorphism.html | 431 ++++++++++++++++---------------- inst/doc/Forecasting.R | 2 inst/doc/Forecasting.Rmd | 2 inst/doc/Forecasting.html | 524 ++++++++++++++++++++-------------------- inst/doc/SpatialPrediction.R | 2 inst/doc/SpatialPrediction.Rmd | 2 inst/doc/SpatialPrediction.html | 523 +++++++++++++++++++-------------------- man/IncidenceForecast.Rd | 23 + man/ObservationList.Rd | 2 man/SimulatedForecast.Rd | 23 + man/bomregions.Rd |only vignettes/ClassDiagram.Rnw |only vignettes/DataPolymorphism.Rmd | 2 vignettes/Forecasting.Rmd | 2 vignettes/SpatialPrediction.Rmd | 2 26 files changed, 803 insertions(+), 835 deletions(-)
More information about ForecastFramework at CRAN
Permanent link
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson [aut, cre],
Gerhard Krennrich [aut]
Maintainer: John Lawson <lawson@byu.edu>
Diff between daewr versions 1.1-7 dated 2016-10-12 and 1.1-8 dated 2020-01-16
DESCRIPTION | 20 ++++---- MD5 | 128 ++++++++++++++++++++++++++-------------------------- NAMESPACE | 49 ++++++++++--------- R/stepforward.R |only data/Apo.rda |binary data/BPmonitor.rda |binary data/Bdish.rda |binary data/Bff.rda |binary data/BoxM.rda |binary data/COdata.rda |binary data/MPV.rda |binary data/Naph.rda |binary data/SPMPV.rda |binary data/Smotor.rda |binary data/Tet.rda |binary data/Treb.rda |binary data/antifungal.rda |binary data/apple.rda |binary data/arso.rda |binary data/augm.rda |binary data/bha.rda |binary data/bioequiv.rda |binary data/bioeqv.rda |binary data/blood.rda |binary data/bread.rda |binary data/cake.rda |binary data/cement.rda |binary data/chem.rda |binary data/chipman.rda |binary data/cont.rda |binary data/cpipe.rda |binary data/culture.rda |binary data/dairy.rda |binary data/drug.rda |binary data/eptaxr.rda |binary data/eptaxs2.rda |binary data/eptaxyb.rda |binary data/gagerr.rda |binary data/gear.rda |binary data/hardwood.rda |binary data/inject.rda |binary data/pastry.rda |binary data/pest.rda |binary data/pesticide.rda |binary data/plasma.rda |binary data/polvdat.rda |binary data/polymer.rda |binary data/prodstd.rda |binary data/qsar.rda |binary data/rcb.rda |binary data/residue.rda |binary data/rubber.rda |binary data/sausage.rda |binary data/soup.rda |binary data/soupmx.rda |binary data/splitPdes.rda |binary data/strung.rda |binary data/strungtile.rda |binary data/sugarbeet.rda |binary data/taste.rda |binary data/teach.rda |binary data/tile.rda |binary data/virus.rda |binary data/volt.rda |binary data/web.rda |binary man/stepforward.Rd |only 66 files changed, 104 insertions(+), 93 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-19 3.0.2
2018-05-16 3.0.1
2017-09-06 3.0.0
2015-10-19 2.3
2015-04-13 2.2.1
2015-03-23 2.2
2014-08-19 2.1
2014-07-22 2.0
2014-03-19 1.3
2013-09-18 1.2.1
2012-11-07 1.2
2012-06-15 1.1
2012-05-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-05 0.0.5
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC)
as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations,
and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring.
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints to estimate the probability that a random observation drawn from
one group performs better than a random observation drawn from the other group.
The net benefit and win ratio statistics,
i.e. the difference and ratio between the probabilities relative to the intervention and control groups,
can then be estimated. Confidence intervals and p-values are obtained using permutations, a non-parametric bootstrap, or the asymptotic theory.
The software enables the use of thresholds of minimal importance difference,
stratification, non-prioritized endpoints (O'Brien test), and corrections to deal with missing values.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 1.8 dated 2019-11-13 and 1.8.3 dated 2020-01-16
BuyseTest-1.8.3/BuyseTest/DESCRIPTION | 35 BuyseTest-1.8.3/BuyseTest/MD5 | 205 ++-- BuyseTest-1.8.3/BuyseTest/NAMESPACE | 7 BuyseTest-1.8.3/BuyseTest/NEWS | 39 BuyseTest-1.8.3/BuyseTest/R/1-setGeneric.R | 2 BuyseTest-1.8.3/BuyseTest/R/BuyseRes-coef.R | 5 BuyseTest-1.8.3/BuyseTest/R/BuyseRes-confint.R | 5 BuyseTest-1.8.3/BuyseTest/R/BuyseRes-iid.R | 29 BuyseTest-1.8.3/BuyseTest/R/BuyseRes-object.R | 2 BuyseTest-1.8.3/BuyseTest/R/BuyseRes-summary.R | 27 BuyseTest-1.8.3/BuyseTest/R/BuyseRes_get.R | 6 BuyseTest-1.8.3/BuyseTest/R/BuyseRes_show.R | 1 BuyseTest-1.8.3/BuyseTest/R/BuyseSim-object.R | 2 BuyseTest-1.8.3/BuyseTest/R/BuyseSim-summary.R | 1 BuyseTest-1.8.3/BuyseTest/R/BuyseSim_show.R | 1 BuyseTest-1.8.3/BuyseTest/R/BuyseTest-check.R | 76 + BuyseTest-1.8.3/BuyseTest/R/BuyseTest-inference.R | 5 BuyseTest-1.8.3/BuyseTest/R/BuyseTest-initialization.R | 182 ++-- BuyseTest-1.8.3/BuyseTest/R/BuyseTest-print.R | 30 BuyseTest-1.8.3/BuyseTest/R/BuyseTest.R | 166 ++- BuyseTest-1.8.3/BuyseTest/R/BuyseTest.options-object.R | 1 BuyseTest-1.8.3/BuyseTest/R/RcppExports.R | 43 - BuyseTest-1.8.3/BuyseTest/R/auc.R |only BuyseTest-1.8.3/BuyseTest/R/constStrata.R | 1 BuyseTest-1.8.3/BuyseTest/R/discreteRoot.R | 6 BuyseTest-1.8.3/BuyseTest/R/powerBuyseTest.R | 16 BuyseTest-1.8.3/BuyseTest/R/prodlim-iid.R | 6 BuyseTest-1.8.3/BuyseTest/R/simBuyseTest.R | 14 BuyseTest-1.8.3/BuyseTest/build/vignette.rds |binary BuyseTest-1.8.3/BuyseTest/inst/CITATION | 4 BuyseTest-1.8.3/BuyseTest/inst/article |only BuyseTest-1.8.3/BuyseTest/inst/doc-software |only BuyseTest-1.8.3/BuyseTest/inst/doc-theory |only BuyseTest-1.8.3/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-1.8.3/BuyseTest/inst/doc/overview.pdf.asis |only BuyseTest-1.8.3/BuyseTest/man/BuyseRes-class.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-coef.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-confint.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-getCount.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-getPairScore.Rd | 6 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-getSurvival.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-iid.Rd | 11 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-show.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseRes-summary.Rd | 14 BuyseTest-1.8.3/BuyseTest/man/BuyseSim-class.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseSim-show.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseSim-summary.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/BuyseTest.Rd | 36 BuyseTest-1.8.3/BuyseTest/man/BuyseTest.options-class.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/GPC_cpp.Rd | 21 BuyseTest-1.8.3/BuyseTest/man/auc.Rd |only BuyseTest-1.8.3/BuyseTest/man/calcIntegralCif_cpp.Rd |only BuyseTest-1.8.3/BuyseTest/man/calcIntegralSurv_cpp.Rd |only BuyseTest-1.8.3/BuyseTest/man/coef.BuyseTestAuc.Rd |only BuyseTest-1.8.3/BuyseTest/man/confint.BuyseTestAuc.Rd |only BuyseTest-1.8.3/BuyseTest/man/constStrata.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/discreteRoot.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/iidProdlim.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/internal-initialization.Rd | 28 BuyseTest-1.8.3/BuyseTest/man/internal-print.Rd | 7 BuyseTest-1.8.3/BuyseTest/man/powerBuyseTest.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/simulation.Rd | 3 BuyseTest-1.8.3/BuyseTest/man/testArgs.Rd | 12 BuyseTest-1.8.3/BuyseTest/src/FCT_buyseTest.cpp | 31 BuyseTest-1.8.3/BuyseTest/src/FCT_calcAllPairs.h | 98 +- BuyseTest-1.8.3/BuyseTest/src/FCT_calcOnePair.h | 418 ++++++++-- BuyseTest-1.8.3/BuyseTest/src/RcppExports.cpp | 37 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 234 +++++ BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 46 - BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 33 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 18 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-iid.R | 41 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 47 - BuyseTest-1.8.3/BuyseTest/tests/testthat/test-auc.R |only BuyseTest-1.8.3/BuyseTest/tests/testthat/test-initSurvival.R | 4 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-initThreshold.R | 6 BuyseTest-1.8.3/BuyseTest/tests/testthat/test-otherPackages.R | 6 BuyseTest-1.8.3/BuyseTest/vignettes/overview.pdf.asis |only BuyseTest-1.8.3/BuyseTest/vignettes/vignette_CR.Rmd |only BuyseTest-1.8/BuyseTest/inst/Documentation |only BuyseTest-1.8/BuyseTest/inst/doc/overview.ltx |only BuyseTest-1.8/BuyseTest/man/calcIntegralScore_cpp.Rd |only BuyseTest-1.8/BuyseTest/vignettes/changes.sty |only BuyseTest-1.8/BuyseTest/vignettes/overview.ltx |only BuyseTest-1.8/BuyseTest/vignettes/overview.org |only 85 files changed, 1534 insertions(+), 582 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-25 2.1.1
2019-04-22 2.1.0
2017-06-30 2.0.1
2016-09-02 2.0.0
2016-02-12 1.3.2
2015-10-21 1.3.1
2015-07-28 1.3.0
2015-06-23 1.2.0
2015-05-05 1.1.4
2015-04-16 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-09 1.5-0
2012-12-02 1.4-2
2012-03-22 1.4-1
2011-08-09 1.4-0
2009-06-09 1.3-2
2006-09-08 1.3-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-12 0.2-8
2019-02-01 0.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-16 2.0.7
2019-01-08 2.0.6
2018-12-12 2.0.5
2018-11-30 2.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-17 0.2-5
2016-06-20 0.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-31 1.3-3
2017-01-31 1.3-2
2015-09-01 1.3-1
2015-01-06 1.3-0
2011-04-26 1.2-2
2010-08-11 1.2-1
2009-02-25 1.2-0
2009-01-11 1.1-6
2008-01-26 1.1-5
2006-10-02 1.1-3.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-26 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-25 0.7.3
2018-12-10 0.7.2
2018-06-20 0.7.1
2017-12-04 0.6.9
2017-11-07 0.6.5
2016-11-15 0.5.4
2016-10-22 0.5.3
2016-03-10 0.4.7
2016-03-07 0.4.5
2016-03-05 0.4.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-09 1.0.2
2013-08-02 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-31 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-27 0.1-1
2019-11-13 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-12 1.1.6
2019-10-23 1.1.5
2019-09-29 1.1.4
2019-09-13 1.1.3
2019-09-02 1.1.2
2019-07-18 1.1.1
2019-05-18 1.1.0
2019-04-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-02 1.1.4
2019-05-31 1.1.2
2019-03-12 1.1.1
2018-10-23 1.1.0
2018-09-18 1.0.0
2018-04-16 0.8.0
2018-02-19 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-09 1.0-7
2014-05-27 1.0-4
2012-12-21 1.0-2
2012-04-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-09 0.3.1
2019-04-13 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-19 0.2
2013-04-18 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-14 1.5
2013-01-27 1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-31 0.3.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-29 2.0
2017-06-24 1.0
Title: Analysis, Seriation and Visualization of Archaeological Count
Data
Description: An easy way to examine archaeological count data. This package
provides a convenient and reproducible toolkit for relative and absolute
dating and analysis of (chronological) patterns. It includes functions for
matrix seriation (reciprocal ranking, CA-based seriation), chronological
modeling and dating of archaeological assemblages and/or objects.
Beyond these, the package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.),
turnover and similarity (Brainerd-Robinson, etc.).
The package make it easy to visualize count data and statistical thresholds:
rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>),
Matthew Peeples [ctb] (<https://orcid.org/0000-0003-4496-623X>),
Ben Marwick [ctb] (<https://orcid.org/0000-0001-7879-4531>),
Anne Philippe [ctb],
Jean-Baptiste Fourvel [ctb] (<https://orcid.org/0000-0002-1061-4642>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 1.3.0 dated 2019-09-20 and 1.5.0 dated 2020-01-16
tabula-1.3.0/tabula/R/check.R |only tabula-1.3.0/tabula/R/predicates.R |only tabula-1.3.0/tabula/inst/doc/matrix.R |only tabula-1.3.0/tabula/inst/doc/matrix.Rmd |only tabula-1.3.0/tabula/inst/doc/matrix.html |only tabula-1.3.0/tabula/inst/examples/ex-abundance-class.R |only tabula-1.3.0/tabula/inst/examples/ex-coerce.R |only tabula-1.3.0/tabula/inst/examples/ex-geography.R |only tabula-1.3.0/tabula/inst/examples/ex-logical-class.R |only tabula-1.3.0/tabula/man/CountMatrix-class.Rd |only tabula-1.3.0/tabula/man/FrequencyMatrix-class.Rd |only tabula-1.3.0/tabula/man/IncidenceMatrix-class.Rd |only tabula-1.3.0/tabula/man/LogicalMatrix-class.Rd |only tabula-1.3.0/tabula/man/Matrix-class.Rd |only tabula-1.3.0/tabula/man/NumericMatrix-class.Rd |only tabula-1.3.0/tabula/man/OccurrenceMatrix-class.Rd |only tabula-1.3.0/tabula/man/SimilarityMatrix-class.Rd |only tabula-1.3.0/tabula/man/SpaceTime-class.Rd |only tabula-1.3.0/tabula/man/coerce.Rd |only tabula-1.3.0/tabula/man/diversity.Rd |only tabula-1.3.0/tabula/man/geography.Rd |only tabula-1.3.0/tabula/man/richness.Rd |only tabula-1.3.0/tabula/man/turnover-method.Rd |only tabula-1.3.0/tabula/tests/testthat/test-check.R |only tabula-1.3.0/tabula/tests/testthat/test-class-matrix.R |only tabula-1.3.0/tabula/tests/testthat/test-coerce.R |only tabula-1.3.0/tabula/tests/testthat/test-predicates.R |only tabula-1.3.0/tabula/vignettes/classes.svg |only tabula-1.3.0/tabula/vignettes/matrix.Rmd |only tabula-1.5.0/tabula/DESCRIPTION | 24 tabula-1.5.0/tabula/MD5 | 210 +-- tabula-1.5.0/tabula/NAMESPACE | 47 tabula-1.5.0/tabula/NEWS.md | 208 +-- tabula-1.5.0/tabula/R/AllClasses.R | 629 +++-------- tabula-1.5.0/tabula/R/AllGenerics.R | 386 ++----- tabula-1.5.0/tabula/R/coerce.R | 260 ---- tabula-1.5.0/tabula/R/data.R | 10 tabula-1.5.0/tabula/R/date.R | 25 tabula-1.5.0/tabula/R/deprecate.R | 129 ++ tabula-1.5.0/tabula/R/extract.R | 311 ----- tabula-1.5.0/tabula/R/index-diversity.R | 354 +----- tabula-1.5.0/tabula/R/index-heterogeneity.R |only tabula-1.5.0/tabula/R/index-rarefaction.R | 8 tabula-1.5.0/tabula/R/index-richness.R | 160 +-- tabula-1.5.0/tabula/R/index-similarity.R | 28 tabula-1.5.0/tabula/R/index-turnover.R | 4 tabula-1.5.0/tabula/R/plot-date.R | 7 tabula-1.5.0/tabula/R/plot-diversity.R |only tabula-1.5.0/tabula/R/plot-matrix.R | 4 tabula-1.5.0/tabula/R/plot-prepare.R | 3 tabula-1.5.0/tabula/R/plot-rank.R | 6 tabula-1.5.0/tabula/R/plot-spot.R | 11 tabula-1.5.0/tabula/R/plot-time.R | 4 tabula-1.5.0/tabula/R/refine.R | 10 tabula-1.5.0/tabula/R/seriate.R | 14 tabula-1.5.0/tabula/R/seriation.R | 4 tabula-1.5.0/tabula/R/show.R | 107 -- tabula-1.5.0/tabula/R/statistics.R | 99 - 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Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre],
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.5.1 dated 2017-08-14 and 1.6.0 dated 2020-01-16
smoof-1.5.1/smoof/src/benchmarksdeclare.c |only smoof-1.5.1/smoof/src/init.c |only smoof-1.6.0/smoof/DESCRIPTION | 16 smoof-1.6.0/smoof/LICENSE | 2 smoof-1.6.0/smoof/MD5 | 130 +++--- smoof-1.6.0/smoof/NAMESPACE | 15 smoof-1.6.0/smoof/NEWS | 10 smoof-1.6.0/smoof/NEWS.md | 13 smoof-1.6.0/smoof/R/RcppExports.R | 62 ++- smoof-1.6.0/smoof/R/addCountingWrapper.R | 2 smoof-1.6.0/smoof/R/addLoggingWrapper.R | 2 smoof-1.6.0/smoof/R/makeBBOBFunction.R | 26 - smoof-1.6.0/smoof/R/makeBiObjBBOBFunction.R |only smoof-1.6.0/smoof/R/makeUFFunction.R | 2 smoof-1.6.0/smoof/R/mof.ED1.R |only smoof-1.6.0/smoof/R/mof.ED2.R |only smoof-1.6.0/smoof/R/mof.MOP3.R | 2 smoof-1.6.0/smoof/R/mof.MOP4.R | 2 smoof-1.6.0/smoof/R/mof.MOP6.R | 2 smoof-1.6.0/smoof/R/mof.WFG1.R |only smoof-1.6.0/smoof/R/mof.WFG2.R |only smoof-1.6.0/smoof/R/mof.WFG3.R |only smoof-1.6.0/smoof/R/mof.WFG4.R |only smoof-1.6.0/smoof/R/mof.WFG5.R |only smoof-1.6.0/smoof/R/mof.WFG6.R |only smoof-1.6.0/smoof/R/mof.WFG7.R |only smoof-1.6.0/smoof/R/mof.WFG8.R |only smoof-1.6.0/smoof/R/mof.WFG9.R |only smoof-1.6.0/smoof/R/mof.kursawe.R |only smoof-1.6.0/smoof/R/mof.zdt1.R | 2 smoof-1.6.0/smoof/R/mof.zdt2.R | 2 smoof-1.6.0/smoof/R/mof.zdt3.R | 2 smoof-1.6.0/smoof/R/mof.zdt4.R | 2 smoof-1.6.0/smoof/R/mof.zdt6.R | 2 smoof-1.6.0/smoof/R/plot.autoplot.R | 2 smoof-1.6.0/smoof/R/sof.michalewicz.R | 6 smoof-1.6.0/smoof/R/sof.mpm2.R | 6 smoof-1.6.0/smoof/R/sof.rosenbrock.R | 4 smoof-1.6.0/smoof/R/sof.shekel.R | 10 smoof-1.6.0/smoof/R/zzz.R | 2 smoof-1.6.0/smoof/inst/mpm2.py | 33 + smoof-1.6.0/smoof/man/addCountingWrapper.Rd | 2 smoof-1.6.0/smoof/man/addLoggingWrapper.Rd | 2 smoof-1.6.0/smoof/man/makeBBOBFunction.Rd | 6 smoof-1.6.0/smoof/man/makeBiObjBBOBFunction.Rd |only smoof-1.6.0/smoof/man/makeED1Function.Rd |only smoof-1.6.0/smoof/man/makeED2Function.Rd |only smoof-1.6.0/smoof/man/makeKursaweFunction.Rd |only smoof-1.6.0/smoof/man/makeMPM2Function.Rd | 4 smoof-1.6.0/smoof/man/makeMultiObjectiveFunction.Rd | 9 smoof-1.6.0/smoof/man/makeSingleObjectiveFunction.Rd | 9 smoof-1.6.0/smoof/man/makeWFG1Function.Rd |only smoof-1.6.0/smoof/man/makeWFG2Function.Rd |only smoof-1.6.0/smoof/man/makeWFG3Function.Rd |only smoof-1.6.0/smoof/man/makeWFG4Function.Rd |only smoof-1.6.0/smoof/man/makeWFG5Function.Rd |only smoof-1.6.0/smoof/man/makeWFG6Function.Rd |only smoof-1.6.0/smoof/man/makeWFG7Function.Rd |only smoof-1.6.0/smoof/man/makeWFG8Function.Rd |only smoof-1.6.0/smoof/man/makeWFG9Function.Rd |only smoof-1.6.0/smoof/man/mnof.Rd | 8 smoof-1.6.0/smoof/man/plot2DNumeric.Rd | 3 smoof-1.6.0/smoof/man/snof.Rd | 8 smoof-1.6.0/smoof/src/Makevars |only smoof-1.6.0/smoof/src/RcppExports.cpp | 223 ++++++++++- smoof-1.6.0/smoof/src/bbob_r_to_c_interface.c | 9 smoof-1.6.0/smoof/src/benchmarks.c | 7 smoof-1.6.0/smoof/src/benchmarksdeclare.h | 13 smoof-1.6.0/smoof/src/mof.ED.cpp |only smoof-1.6.0/smoof/src/mof.MOP1.c | 2 smoof-1.6.0/smoof/src/mof.MOP2.c | 2 smoof-1.6.0/smoof/src/mof.MOP3.c | 2 smoof-1.6.0/smoof/src/mof.MOP4.c | 2 smoof-1.6.0/smoof/src/mof.MOP5.c | 2 smoof-1.6.0/smoof/src/mof.MOP6.c | 2 smoof-1.6.0/smoof/src/mof.MOP7.c | 4 smoof-1.6.0/smoof/src/mof.kursawe.cpp |only smoof-1.6.0/smoof/src/mof.wfg.cpp |only smoof-1.6.0/smoof/tests/testthat/Rplots.pdf |binary smoof-1.6.0/smoof/tests/testthat/test_counting_evaluations.R | 2 smoof-1.6.0/smoof/tests/testthat/test_logging.R | 12 smoof-1.6.0/smoof/tests/testthat/test_soofuns.R | 16 82 files changed, 536 insertions(+), 172 deletions(-)
Title: The Generalized Semi-Supervised Elastic-Net
Description: Implements the generalized semi-supervised elastic-net. This method extends the supervised elastic-net problem, and thus it is a practical solution to the problem of feature selection in semi-supervised contexts. Its mathematical formulation is presented from a general perspective, covering a wide range of models. We focus on linear and logistic responses, but the implementation could be easily extended to other losses in generalized linear models. We develop a flexible and fast implementation, written in 'C++' using 'RcppArmadillo' and integrated into R via 'Rcpp' modules. See Culp, M. 2013 <doi:10.1080/10618600.2012.657139> for references on the Joint Trained Elastic-Net.
Author: Juan C. Laria [aut, cre] (<https://orcid.org/0000-0001-7734-9647>),
Line H. Clemmensen [aut]
Maintainer: Juan C. Laria <juank.laria@gmail.com>
Diff between s2net versions 1.0 dated 2020-01-13 and 1.0.1 dated 2020-01-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- README.md | 4 ++-- build/partial.rdb |binary inst/doc/supervised.Rmd | 2 +- inst/doc/supervised.html | 2 +- src/losses.h | 8 ++++---- src/nExtJT.cpp | 12 ++++++------ vignettes/supervised.Rmd | 2 +- 9 files changed, 26 insertions(+), 26 deletions(-)
Title: Scalable Robust Estimators with High Breakdown Point for
Incomplete Data
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point for Incomplete
Data (missing values) (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).
Author: Valentin Todorov <valentin.todorov@chello.at>
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between rrcovNA versions 0.4-13 dated 2019-10-22 and 0.4-15 dated 2020-01-16
ChangeLog | 15 ++ DESCRIPTION | 12 +- MD5 | 14 +- NAMESPACE | 23 +++- R/covNAMcd3.R | 5 src/emncov.f | 71 ++++++++----- src/fmcd.f | 280 ++++++++++++++++++++++++++++------------------------- src/rrcovna_init.c | 8 + 8 files changed, 246 insertions(+), 182 deletions(-)
Title: Regularized Generalized Linear Models with Interaction Effects
Description: Provides an efficient procedure for fitting the entire solution
path for high-dimensional regularized quadratic generalized linear models with
interactions effects under the strong or weak heredity constraint.
Author: Yang Feng [aut, cre],
Ning Hao [aut],
Hao Helen Zhang [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>
Diff between RAMP versions 2.0.1 dated 2017-05-24 and 2.0.2 dated 2020-01-16
DESCRIPTION | 20 +++++++++++++------- MD5 | 10 +++++----- R/RAMP.R | 3 +++ man/predict.RAMP.Rd | 4 ++-- src/cd_general_bin.f | 2 +- src/cd_general_lin.f | 2 +- 6 files changed, 25 insertions(+), 16 deletions(-)
Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis,
and sparse canonical correlation analysis, described in
Witten, Tibshirani and Hastie (2009)
<doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani
(2009) Extensions of sparse canonical correlation analysis,
with applications to genomic data
<doi:10.2202/1544-6115.1470>.
Author: Daniela Witten and Rob Tibshirani
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between PMA versions 1.1 dated 2019-01-29 and 1.2 dated 2020-01-16
PMA-1.1/PMA/man/PMA-internal.Rd |only PMA-1.1/PMA/src/init.cc |only PMA-1.2/PMA/DESCRIPTION | 38 +- PMA-1.2/PMA/MD5 | 49 +-- PMA-1.2/PMA/NAMESPACE | 64 ++-- PMA-1.2/PMA/R/CCA.R | 364 +++++++++++++++++++++++- PMA-1.2/PMA/R/MultiCCA.R | 194 +++++++++++++ PMA-1.2/PMA/R/PMA-package.R |only PMA-1.2/PMA/R/PMD.R | 526 ++++++++++++++++++++++++++++++++++-- PMA-1.2/PMA/R/PlotFusedLasso.R | 47 +++ PMA-1.2/PMA/R/zzz.R | 8 PMA-1.2/PMA/README.md |only PMA-1.2/PMA/build |only PMA-1.2/PMA/inst |only PMA-1.2/PMA/man/CCA.Rd | 305 +++++++++++--------- PMA-1.2/PMA/man/CCA.permute.Rd | 321 +++++++++++---------- PMA-1.2/PMA/man/MultiCCA.Rd | 125 ++++---- PMA-1.2/PMA/man/MultiCCA.permute.Rd | 199 ++++++------- PMA-1.2/PMA/man/PMA-package.Rd | 60 +--- PMA-1.2/PMA/man/PMD.Rd | 236 +++++++++------- PMA-1.2/PMA/man/PMD.cv.Rd | 222 ++++++++------- PMA-1.2/PMA/man/PlotCGH.Rd | 76 ++--- PMA-1.2/PMA/man/SPC.Rd | 176 ++++++------ PMA-1.2/PMA/man/SPC.cv.Rd | 158 +++++----- PMA-1.2/PMA/man/breastdata.Rd | 78 +---- PMA-1.2/PMA/src/Groups.cc | 2 PMA-1.2/PMA/src/MaxFlowGraph.cc | 2 PMA-1.2/PMA/src/PenaltyGraph.cc | 2 PMA-1.2/PMA/src/flsa_init.c |only 29 files changed, 2221 insertions(+), 1031 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
(<https://orcid.org/0000-0002-2568-6489>),
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 1.8.2 dated 2019-11-26 and 1.8.3 dated 2020-01-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/Installation.pdf |binary inst/doc/Intro.pdf |binary tests/testthat/test_LifeTable.R | 7 +++---- 5 files changed, 10 insertions(+), 11 deletions(-)
Title: Non-Uniform Memory Access ('NUMA') Optimized, Parallel K-Means
Description: The k-means 'NUMA' Optimized Routine library or 'knor' is a highly optimized and fast library for computing k-means in parallel with accelerations for Non-Uniform Memory Access ('NUMA') architectures. Disa Mhembere, Da Zheng, Carey E. Priebe, Joshua T. Vogelstein, Randal Burns (2017) <arXiv:1606.08905>.
Author: Disa Mhembere [aut, cre],
Neurodata (https://neurodata.io) [cph]
Maintainer: Disa Mhembere <disa@cs.jhu.edu>
Diff between knor versions 0.0-6 dated 2018-09-13 and 0.0-7 dated 2020-01-16
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++------------ R/knor.R | 27 ++++++++++----------------- man/Kmeans.Rd | 21 ++++++++++++--------- src/Makevars.win | 6 +++--- src/cknor/binding/knori.hpp | 5 +---- src/cknor/libman/kmeans_coordinator.hpp | 7 ++++--- src/cknor/libman/kmeans_task_coordinator.hpp | 20 +++++++++----------- src/cknor/libman/kmeans_task_thread.hpp | 6 +++--- src/cknor/libman/kmeans_thread.hpp | 2 ++ src/package_init.c | 12 ++++++------ src/rinterface.cpp | 5 ++--- tests/testthat/test-knori.R | 24 ------------------------ 13 files changed, 72 insertions(+), 103 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction; Evaluation of Failure-Time Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
10) Joint frailty models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints
11) Two-part joint model for longitudinal semicontinuous data and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Moreover, the package can be used with its shiny application, in a local mode or by following the link below.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite, Alexandre Laurent, Myriam Lopez,
Agnieszka Krol, Casimir L. Sofeu, Julien Dumerc, Denis Rustand
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 3.0.3.2.1 dated 2019-10-30 and 3.1.0 dated 2020-01-16
DESCRIPTION | 19 MD5 | 188 NAMESPACE | 2 NEWS | 12 R/dataHelp.R | 33 R/frailtyPenal.R | 66 R/frailtypack-package.R | 2 R/longiPenal.R | 1692 ++++++-- R/plot.additivePenal.R |only R/plot.nestedPenal.additivePenal.R | 24 R/print.jointNestedPenal.R | 10 R/print.jointPenal.R | 8 R/print.longiPenal.R | 106 R/print.nestedPenal.R | 2 R/print.trivPenalNL.R | 34 R/runShiny.R |only R/summary.longiPenal.R | 43 R/trivPenal.R | 42 R/trivPenalNL.R | 167 data/longDat.rda |only data/survDat.rda |only inst/doc/Package_summary.Rmd | 27 inst/doc/Package_summary.html | 832 ++-- inst/shiny_frailtypack |only man/figures/trivNLmodel1.png |binary man/figures/trivNLmodel2.png |binary man/frailtyPenal.Rd | 8 man/frailtypack-package.Rd | 2 man/jointSurrSimul.Rd | 4 man/longDat.Rd |only man/longiPenal.Rd | 109 man/plot.additivePenal.Rd |only man/plot.nestedPenal.Rd | 22 man/runShiny.Rd |only man/survDat.Rd |only man/trivPenalNL.Rd | 6 src/Adonnees.f90 | 6276 +++++++++++++++++++++++++++++++++ src/Aparameters.f90 | 31 src/Integrale_mult_scl.f90 | 134 src/Integrant_scl.f90 | 110 src/Makevars | 7 src/Pour_Adaptative.f90 | 8 src/aaOptim.f90 | 2 src/aaOptim_New_scl.f90 | 12 src/aaOptim_New_scl2.f90 | 10 src/aaOptim_SCL_0.f90 | 12 src/autres_fonctions.f90 | 638 +-- src/frailtypack.f90 | 90 src/frailtypack.h | 87 src/funcpaG_tps.f90 | 4 src/funcpaGcpm.f90 | 4 src/funcpaGcpm_intcens.f90 | 6 src/funcpaGcpm_log.f90 | 10 src/funcpaGsplines.f90 | 4 src/funcpaGsplines_intcens.f90 | 6 src/funcpaGsplines_log.f90 | 10 src/funcpaGweib.f90 | 4 src/funcpaGweib_intcens.f90 | 6 src/funcpaGweib_log.f90 | 10 src/funcpa_adaptative.f90 | 20 src/funcpa_laplace.f90 | 10 src/funcpaj_tps.f90 | 4 src/funcpajcpm.f90 | 4 src/funcpajcpm_log.f90 | 4 src/funcpajgeneral.f90 | 8 src/funcpajlongisplines.f90 | 377 + src/funcpajlongisplines_nl.f90 | 34 src/funcpajlongiweib.f90 | 6 src/funcpajlongiweib_nl.f90 | 36 src/funcpajsplines.f90 | 4 src/funcpajsplinesIndiv.f90 | 4 src/funcpajsplines_fam.f90 | 4 src/funcpajsplines_intcens.f90 | 6 src/funcpajsplines_log.f90 | 4 src/funcpajsplines_logIndiv.f90 | 4 src/funcpajsplines_surrogate_scl_1.f90 | 6 src/funcpajsplines_surrogate_scl_2.f90 | 14 src/funcpajweib.f90 | 4 src/funcpajweib_fam.f90 | 6 src/funcpajweib_intcens.f90 | 6 src/funcpajweib_log.f90 | 4 src/funcpalongi_uni.f90 | 32 src/funcpancpm.f90 | 8 src/funcpansplines.f90 | 9 src/funcpanweib.f90 | 8 src/funcpascpm_log.f90 | 8 src/funcpassplines_log.f90 | 10 src/funcpasweib_log.f90 | 8 src/init.c | 8 src/joint.f90 | 211 - src/jointSurrogate.f90 | 109 src/joint_longi.f90 | 2124 +++++++++-- src/joint_longi_nl.f90 | 208 - src/joint_surrogate.f90 | 12 src/longi_uni_nl.f90 | 228 - src/multiveJoint.f90 | 10 src/nested.f90 | 51 src/survival.f90 | 2 vignettes/Package_summary.Rmd | 27 99 files changed, 12010 insertions(+), 2573 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass Functions, Negative Log Likelihood value, parameter estimation and modeling data using Binomial Mixture Distributions (BMD) (Manoj et al (2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>), also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] (<https://orcid.org/0000-0002-0643-9052>),
Pushpakanthie Wijekoon [aut, ctb]
(<https://orcid.org/0000-0003-4242-1017>)
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.4.1 dated 2019-07-02 and 1.4.1-1 dated 2020-01-16
DESCRIPTION | 8 - MD5 | 208 +++++++++++++++++----------------- NAMESPACE | 2 man/Alcohol_data.Rd | 76 ++++++------ man/BODextract.Rd | 64 +++++----- man/Chromosome_data.Rd | 66 +++++------ man/Course_data.Rd | 68 +++++------ man/Epidemic_Cold.Rd | 96 ++++++++-------- man/EstMGFBetaBin.Rd | 158 +++++++++++++------------- man/EstMLEAddBin.Rd | 140 +++++++++++------------ man/EstMLEBetaBin.Rd | 134 +++++++++++----------- man/EstMLEBetaCorrBin.Rd | 118 +++++++++---------- man/EstMLECOMPBin.Rd | 110 +++++++++--------- man/EstMLECorrBin.Rd | 130 ++++++++++----------- man/EstMLEGHGBB.Rd | 128 ++++++++++----------- man/EstMLEGammaBin.Rd | 102 ++++++++--------- man/EstMLEGrassiaIIBin.Rd | 102 ++++++++--------- man/EstMLEKumBin.Rd | 116 +++++++++---------- man/EstMLELMBin.Rd | 106 ++++++++--------- man/EstMLEMcGBB.Rd | 136 +++++++++++----------- man/EstMLEMultiBin.Rd | 120 ++++++++++---------- man/EstMLETriBin.Rd | 144 ++++++++++++------------ man/Exam_data.Rd | 80 ++++++------- man/Male_Children.Rd | 70 +++++------ man/NegLLAddBin.Rd | 102 ++++++++--------- man/NegLLBetaBin.Rd | 108 +++++++++--------- man/NegLLBetaCorrBin.Rd | 96 ++++++++-------- man/NegLLCOMPBin.Rd | 94 +++++++-------- man/NegLLCorrBin.Rd | 108 +++++++++--------- man/NegLLGHGBB.Rd | 102 ++++++++--------- man/NegLLGammaBin.Rd | 88 +++++++------- man/NegLLGrassiaIIBin.Rd | 88 +++++++------- man/NegLLKumBin.Rd | 100 ++++++++-------- man/NegLLLMBin.Rd | 84 +++++++------- man/NegLLMcGBB.Rd | 106 ++++++++--------- man/NegLLMultiBin.Rd | 98 ++++++++-------- man/NegLLTriBin.Rd | 104 ++++++++--------- man/Overdispersion.Rd | 86 +++++++------- man/Plant_DiseaseData.Rd | 82 ++++++------- man/Terror_data_ARG.Rd | 62 +++++----- man/Terror_data_USA.Rd | 62 +++++----- man/dAddBin.Rd | 196 ++++++++++++++++---------------- man/dBETA.Rd | 200 ++++++++++++++++----------------- man/dBetaBin.Rd | 190 +++++++++++++++---------------- man/dBetaCorrBin.Rd | 216 ++++++++++++++++++------------------ man/dCOMPBin.Rd | 170 ++++++++++++++-------------- man/dCorrBin.Rd | 222 ++++++++++++++++++------------------- man/dGAMMA.Rd | 184 +++++++++++++++--------------- man/dGBeta1.Rd | 182 +++++++++++++++--------------- man/dGHGBB.Rd | 204 +++++++++++++++++----------------- man/dGHGBeta.Rd | 208 +++++++++++++++++----------------- man/dGammaBin.Rd | 170 ++++++++++++++-------------- man/dGrassiaIIBin.Rd | 168 ++++++++++++++-------------- man/dKUM.Rd | 196 ++++++++++++++++---------------- man/dKumBin.Rd | 196 ++++++++++++++++---------------- man/dLMBin.Rd | 178 ++++++++++++++--------------- man/dMcGBB.Rd | 196 ++++++++++++++++---------------- man/dMultiBin.Rd | 188 +++++++++++++++---------------- man/dTRI.Rd | 216 ++++++++++++++++++------------------ man/dTriBin.Rd | 198 ++++++++++++++++----------------- man/dUNI.Rd | 160 +++++++++++++------------- man/dUniBin.Rd | 152 ++++++++++++------------- man/fitAddBin.Rd | 194 ++++++++++++++++---------------- man/fitBetaBin.Rd | 226 +++++++++++++++++++------------------- man/fitBetaCorrBin.Rd | 194 ++++++++++++++++---------------- man/fitBin.Rd | 120 ++++++++++---------- man/fitCOMPBin.Rd | 182 +++++++++++++++--------------- man/fitCorrBin.Rd | 192 ++++++++++++++++---------------- man/fitGHGBB.Rd | 212 +++++++++++++++++------------------ man/fitGammaBin.Rd | 180 +++++++++++++++--------------- man/fitGrassiaIIBin.Rd | 178 ++++++++++++++--------------- man/fitKumBin.Rd | 204 +++++++++++++++++----------------- man/fitLMBin.Rd | 180 +++++++++++++++--------------- man/fitMcGBB.Rd | 220 ++++++++++++++++++------------------ man/fitMultiBin.Rd | 194 ++++++++++++++++---------------- man/fitTriBin.Rd | 186 +++++++++++++++---------------- man/mazBETA.Rd | 188 +++++++++++++++---------------- man/mazGAMMA.Rd | 172 ++++++++++++++-------------- man/mazGBeta1.Rd | 170 ++++++++++++++-------------- man/mazGHGBeta.Rd | 198 ++++++++++++++++----------------- man/mazKUM.Rd | 182 +++++++++++++++--------------- man/mazTRI.Rd | 204 +++++++++++++++++----------------- man/mazUNI.Rd | 148 ++++++++++++------------ man/pAddBin.Rd | 184 +++++++++++++++--------------- man/pBETA.Rd | 188 +++++++++++++++---------------- man/pBetaBin.Rd | 178 ++++++++++++++--------------- man/pBetaCorrBin.Rd | 192 ++++++++++++++++---------------- man/pCOMPBin.Rd | 158 +++++++++++++------------- man/pCorrBin.Rd | 198 ++++++++++++++++----------------- man/pGAMMA.Rd | 172 ++++++++++++++-------------- man/pGBeta1.Rd | 170 ++++++++++++++-------------- man/pGHGBB.Rd | 186 +++++++++++++++---------------- man/pGHGBeta.Rd | 198 ++++++++++++++++----------------- man/pGammaBin.Rd | 154 ++++++++++++------------- man/pGrassiaIIBin.Rd | 152 ++++++++++++------------- man/pKUM.Rd | 184 +++++++++++++++--------------- man/pKumBin.Rd | 180 +++++++++++++++--------------- man/pLMBin.Rd | 164 +++++++++++++-------------- man/pMcGBB.Rd | 180 +++++++++++++++--------------- man/pMultiBin.Rd | 174 ++++++++++++++--------------- man/pTRI.Rd | 204 +++++++++++++++++----------------- man/pTriBin.Rd | 182 +++++++++++++++--------------- man/pUNI.Rd | 148 ++++++++++++------------ man/pUniBin.Rd | 136 +++++++++++----------- tests/testthat/test-EstMLEGHGBB.R | 8 - 105 files changed, 7828 insertions(+), 7828 deletions(-)
Title: High Performance Colour Space Manipulation
Description: The encoding of colour can be handled in many different ways, using
different colour spaces. As different colour spaces have different uses,
efficient conversion between these representations are important. The
'farver' package provides a set of functions that gives access to very fast
colour space conversion and comparisons implemented in C++, and offers
speed improvements over the 'convertColor' function in the 'grDevices'
package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Berendea Nicolae [aut] (Author of the ColorSpace C++ library),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between farver versions 2.0.2 dated 2020-01-09 and 2.0.3 dated 2020-01-16
DESCRIPTION | 8 - MD5 | 36 +++---- NEWS.md | 12 ++ R/aaa.R | 19 +++- R/decode.R | 10 +- R/modify.R | 36 ++++--- R/sysdata.rda |binary R/zzz.R | 35 +++++++ man/compare_colour.Rd | 11 +- man/convert_colour.Rd | 3 man/decode_colour.Rd | 10 +- man/encode_colour.Rd | 7 - man/farver-package.Rd | 6 - man/manip_channel.Rd | 65 +++++++++++-- src/Comparison.cpp | 2 src/encode.cpp | 182 ++++++++++++++++++++++++++------------- src/encode.h | 5 - src/init.cpp | 4 tests/testthat/test-comparison.R | 7 + 19 files changed, 319 insertions(+), 139 deletions(-)
Title: Extremal Dependence Models
Description: A set of procedures for modelling parametrically and non-parametrically the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. Adapts the methodologies derived in Beranger et al. (2019) <arxiv:1904.08251>, Beranger et al. (2017) <doi:10.1111/sjos.12240>, Beranger and Padoan (2015) <arxiv:1508.05561>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Marcon et al. (2016) <doi:10.1214/16-EJS1162>. It also refers to the works of Bortot (2010) <https://pdfs.semanticscholar.org/b0dc/1cb608d35bf515c76e39aacc14b4de82e281.pdf>, Padoan (2011) <doi:10.1016/j.jmva.2011.01.014>, Cooley et al. (2010) <doi:10.1016/j.jmva.2010.04.007>, Husler and Reiss (1989) <doi:10.1016/0167-7152(89)90106-5>, Engelke et al. (2015) <doi:10.1111/rssb.12074>, Coles and Tawn (1991) <doi:10.1111/j.2517-6161.1991.tb01830.x>, Nikoloulopoulos et al. (2011) <doi:10.1007/s10687-008-0072-4>, Opitz (2013) <doi:10.1016/j.jmva.2013.08.008>, Tawn (1990) <doi:10.2307/2336802>, Azzalini (1985) <https://www.jstor.org/stable/pdf/4615982.pdf>, Azzalini and Capitanio (2014) <doi:10.1017/CBO9781139248891>, Azzalini (2003) <doi:10.1111/1467-9469.00322>, Azzalini and Capitanio (1999) <doi:10.1111/1467-9868.00194>, Azzalini and Dalla Valle (1996) <doi:10.1093/biomet/83.4.715>, Einmahl et al. (2013) <doi:10.1007/s10687-012-0156-z>, Naveau et al (2009) <doi:10.1093/biomet/asp001> and Heffernan and Tawn (2004) <doi:10.1111/j.1467-9868.2004.02050.x>.
Author: Boris Beranger [aut],
Simone Padoan [cre, aut],
Giulia Marcon [aut],
Steven G. Johnson [ctb] (Author of included cubature fragments)
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremalDep versions 0.0.3-1 dated 2019-08-29 and 0.0.3-3 dated 2020-01-16
DESCRIPTION | 13 +++++----- MD5 | 12 ++++----- data/MilanPollution.rda |binary data/Wind.rda |binary data/pollution.rda |binary src/dependence.c | 9 +++++++ src/distributions.c | 60 ++++++++++++++++++++++++++++++++---------------- 7 files changed, 63 insertions(+), 31 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-11 dated 2019-03-14 and 0.9-13 dated 2020-01-16
diversitree-0.9-11/diversitree/man/geosse.phy.Rd |only diversitree-0.9-13/diversitree/DESCRIPTION | 21 ++++--- diversitree-0.9-13/diversitree/MD5 | 27 ++++----- diversitree-0.9-13/diversitree/build/partial.rdb |binary diversitree-0.9-13/diversitree/configure | 15 ++++- diversitree-0.9-13/diversitree/configure.ac | 1 diversitree-0.9-13/diversitree/inst/tests/helper-diversitree.R | 1 diversitree-0.9-13/diversitree/inst/tests/test-bm.R | 6 +- diversitree-0.9-13/diversitree/inst/tests/test-eb.R | 3 - diversitree-0.9-13/diversitree/inst/tests/test-lambda.R | 6 +- diversitree-0.9-13/diversitree/inst/tests/test-ou.R | 8 +- diversitree-0.9-13/diversitree/src/dnchbv.f | 6 +- diversitree-0.9-13/diversitree/src/util-matrix.c | 13 +++- diversitree-0.9-13/diversitree/src/util.c | 14 +++- diversitree-0.9-13/diversitree/src/zzz.c | 30 +++++----- 15 files changed, 93 insertions(+), 58 deletions(-)
Title: Bridge Sampling for Marginal Likelihoods and Bayes Factors
Description: Provides functions for estimating marginal likelihoods, Bayes
factors, posterior model probabilities, and normalizing constants in general,
via different versions of bridge sampling (Meng & Wong, 1996,
<http://www3.stat.sinica.edu.tw/statistica/j6n4/j6n43/j6n43.htm>).
Author: Quentin F. Gronau [aut, cre] (<https://orcid.org/0000-0001-5510-6943>),
Henrik Singmann [aut] (<https://orcid.org/0000-0002-4842-3657>),
Jonathan J. Forster [ctb],
Eric-Jan Wagenmakers [ths],
The JASP Team [ctb],
Jiqiang Guo [ctb],
Jonah Gabry [ctb],
Ben Goodrich [ctb],
Kees Mulder [ctb],
Perry de Valpine [ctb]
Maintainer: Quentin F. Gronau <Quentin.F.Gronau@gmail.com>
Diff between bridgesampling versions 0.7-2 dated 2019-07-21 and 0.8-1 dated 2020-01-16
DESCRIPTION | 10 - MD5 | 56 ++--- NAMESPACE | 2 NEWS | 21 ++ R/bridge_sampler.R | 8 R/bridge_sampler_internals.R | 8 R/bridge_sampler_normal.R | 11 - R/bridge_sampler_warp3.R | 15 - build/vignette.rds |binary inst/doc/bridgesampling_example_jags.R | 26 +- inst/doc/bridgesampling_example_jags.html | 13 - inst/doc/bridgesampling_example_nimble.R | 24 +- inst/doc/bridgesampling_example_nimble.html | 13 - inst/doc/bridgesampling_example_stan.R | 24 +- inst/doc/bridgesampling_example_stan.html | 13 - inst/doc/bridgesampling_paper.pdf |binary inst/doc/bridgesampling_paper_extended.pdf |binary inst/doc/bridgesampling_stan_ttest.R | 38 +-- inst/doc/bridgesampling_stan_ttest.html | 13 - inst/doc/bridgesampling_tutorial.pdf |binary man/bridge_sampler.Rd | 199 ++++++++++++++------ man/post_prob.Rd | 9 tests/testthat/test-bf.R | 4 tests/testthat/test-bridge_sampler.R | 8 tests/testthat/test-bridge_sampler_Rcpp.R | 6 tests/testthat/test-bridge_sampler_Rcpp_parallel.R | 6 tests/testthat/test-bridge_sampler_parallel.R | 6 tests/testthat/test-bridge_sampler_print_method.R | 4 tests/testthat/test-bridge_sampler_summary_method.R | 4 29 files changed, 333 insertions(+), 208 deletions(-)
More information about bridgesampling at CRAN
Permanent link
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis' (included as a fallback) with
'MsgPack' encoding provided via 'RcppMsgPack' headers.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.9 dated 2018-10-27 and 0.1.10 dated 2020-01-16
RcppRedis-0.1.10/RcppRedis/ChangeLog | 17 +++++++++++++ RcppRedis-0.1.10/RcppRedis/DESCRIPTION | 12 ++++----- RcppRedis-0.1.10/RcppRedis/MD5 | 32 ++++++++++++------------- RcppRedis-0.1.10/RcppRedis/configure | 20 +++++++-------- RcppRedis-0.1.10/RcppRedis/configure.ac | 6 ++-- RcppRedis-0.1.10/RcppRedis/inst/NEWS.Rd | 6 ++++ RcppRedis-0.1.10/RcppRedis/inst/tinytest |only RcppRedis-0.1.10/RcppRedis/src/Makevars.in | 6 ++-- RcppRedis-0.1.10/RcppRedis/tests/tinytest.R |only RcppRedis-0.1.9/RcppRedis/inst/tests |only RcppRedis-0.1.9/RcppRedis/tests/runUnitTests.R |only 11 files changed, 61 insertions(+), 38 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: LUOMUS - Finnish Museum of Natural History [cph],
William Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William Morris <willi@mmorris.email>
Diff between finbif versions 0.1.0 dated 2019-11-19 and 0.2.0 dated 2020-01-16
finbif-0.1.0/finbif/inst/vign/cache/admin-status_d3dc7b58b00b45f65d21c1602c409bc5.RData |only finbif-0.1.0/finbif/inst/vign/cache/admin-status_d3dc7b58b00b45f65d21c1602c409bc5.rdb |only finbif-0.1.0/finbif/inst/vign/cache/admin-status_d3dc7b58b00b45f65d21c1602c409bc5.rdx |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type-specific_7d3f5b4184bdbae0ede08a15b452a4fe.RData |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type-specific_7d3f5b4184bdbae0ede08a15b452a4fe.rdb |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type-specific_7d3f5b4184bdbae0ede08a15b452a4fe.rdx |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type_1664fa4a388c5981ae919e6f0091a63d.RData |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type_1664fa4a388c5981ae919e6f0091a63d.rdb |only finbif-0.1.0/finbif/inst/vign/cache/habitat-type_1664fa4a388c5981ae919e6f0091a63d.rdx |only finbif-0.1.0/finbif/inst/vign/cache/informal-groups_502606bd446e41703932596b2fc7f8c2.RData |only finbif-0.1.0/finbif/inst/vign/cache/informal-groups_502606bd446e41703932596b2fc7f8c2.rdb |only finbif-0.1.0/finbif/inst/vign/cache/informal-groups_502606bd446e41703932596b2fc7f8c2.rdx |only finbif-0.1.0/finbif/inst/vign/cache/jays_2cedb03811d34998e357f43bad471eb2.RData |only finbif-0.1.0/finbif/inst/vign/cache/jays_2cedb03811d34998e357f43bad471eb2.rdb |only finbif-0.1.0/finbif/inst/vign/cache/jays_2cedb03811d34998e357f43bad471eb2.rdx |only finbif-0.1.0/finbif/inst/vign/cache/occurrence2_19e01eb534a3eb0cfdd2bab1d31dc864.RData |only finbif-0.1.0/finbif/inst/vign/cache/occurrence2_19e01eb534a3eb0cfdd2bab1d31dc864.rdb |only finbif-0.1.0/finbif/inst/vign/cache/occurrence2_19e01eb534a3eb0cfdd2bab1d31dc864.rdx |only finbif-0.1.0/finbif/inst/vign/cache/occurrence_273929d73c2e62654b9f82d614fba2a3.RData |only finbif-0.1.0/finbif/inst/vign/cache/occurrence_273929d73c2e62654b9f82d614fba2a3.rdb |only finbif-0.1.0/finbif/inst/vign/cache/occurrence_273929d73c2e62654b9f82d614fba2a3.rdx |only finbif-0.1.0/finbif/inst/vign/cache/plot-occurrences_55b3774b3315967ff282f12e8ecdd154.RData |only finbif-0.1.0/finbif/inst/vign/cache/plot-occurrences_55b3774b3315967ff282f12e8ecdd154.rdb |only finbif-0.1.0/finbif/inst/vign/cache/plot-occurrences_55b3774b3315967ff282f12e8ecdd154.rdx |only finbif-0.1.0/finbif/inst/vign/cache/red-list-status_fa96c98cf0b785ea36067863070e03dc.RData |only finbif-0.1.0/finbif/inst/vign/cache/red-list-status_fa96c98cf0b785ea36067863070e03dc.rdb |only finbif-0.1.0/finbif/inst/vign/cache/red-list-status_fa96c98cf0b785ea36067863070e03dc.rdx |only finbif-0.1.0/finbif/inst/vign/cache/taxon-check_9144e7fdbcd68cf47a6174909364b99e.RData |only finbif-0.1.0/finbif/inst/vign/cache/taxon-check_9144e7fdbcd68cf47a6174909364b99e.rdb |only finbif-0.1.0/finbif/inst/vign/cache/taxon-check_9144e7fdbcd68cf47a6174909364b99e.rdx |only finbif-0.1.0/finbif/inst/vign/cache/taxon-not-found_2327853875d7474af31aff6ed03530fa.RData |only 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finbif-0.2.0/finbif/vignettes/finbif.Rmd | 305 + finbif-0.2.0/finbif/vignettes/v02_filtering.Rmd | 545 +- 167 files changed, 6449 insertions(+), 2696 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-11 2.16.17
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2013-10-10 0.7-4
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2013-02-07 0.6-2
2011-11-10 0.4-1
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2011-10-15 0.1-3
2011-10-14 0.1-2
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.0.3 dated 2019-02-25 and 2.4.0 dated 2020-01-16
RRphylo-2.0.3/RRphylo/R/RBC.R |only RRphylo-2.0.3/RRphylo/man/RBC.Rd |only RRphylo-2.4.0/RRphylo/DESCRIPTION | 18 RRphylo-2.4.0/RRphylo/MD5 | 77 + RRphylo-2.4.0/RRphylo/NAMESPACE | 21 RRphylo-2.4.0/RRphylo/R/DataCetaceans.R | 8 RRphylo-2.4.0/RRphylo/R/DataOrnithodirans.R | 2 RRphylo-2.4.0/RRphylo/R/PGLS_fossil.R | 90 +- RRphylo-2.4.0/RRphylo/R/RRphylo.R | 539 +++++++++---- RRphylo-2.4.0/RRphylo/R/StableTraitsR.R |only RRphylo-2.4.0/RRphylo/R/angle.matrix.R | 980 ++++++++++++------------- RRphylo-2.4.0/RRphylo/R/overfitRR.R |only RRphylo-2.4.0/RRphylo/R/phyloclust.R |only RRphylo-2.4.0/RRphylo/R/plotRates.R | 156 +-- RRphylo-2.4.0/RRphylo/R/retrieve.angles.R | 472 ++++++------ RRphylo-2.4.0/RRphylo/R/scaleTree.R |only RRphylo-2.4.0/RRphylo/R/search.conv.R | 776 ++++++++++++------- RRphylo-2.4.0/RRphylo/R/search.shift.R | 418 ++++++---- RRphylo-2.4.0/RRphylo/R/search.trend.R | 905 +++++++++++++++-------- RRphylo-2.4.0/RRphylo/R/setBM.R | 2 RRphylo-2.4.0/RRphylo/R/sizedsubtree.R | 98 +- RRphylo-2.4.0/RRphylo/R/swap.phylo.R | 207 ++--- RRphylo-2.4.0/RRphylo/R/swapONE.R | 104 ++ RRphylo-2.4.0/RRphylo/data/DataCetaceans.rda |binary RRphylo-2.4.0/RRphylo/data/DataFelids.rda |binary RRphylo-2.4.0/RRphylo/data/DataUng.rda |binary RRphylo-2.4.0/RRphylo/inst |only RRphylo-2.4.0/RRphylo/man/DataCetaceans.Rd | 10 RRphylo-2.4.0/RRphylo/man/DataOrnithodirans.Rd | 2 RRphylo-2.4.0/RRphylo/man/PGLS_fossil.Rd | 44 - RRphylo-2.4.0/RRphylo/man/RRphylo.Rd | 48 - RRphylo-2.4.0/RRphylo/man/StableTraitsR.Rd |only RRphylo-2.4.0/RRphylo/man/angle.matrix.Rd | 6 RRphylo-2.4.0/RRphylo/man/overfitRR.Rd |only RRphylo-2.4.0/RRphylo/man/phyloclust.Rd |only RRphylo-2.4.0/RRphylo/man/plotRates.Rd | 4 RRphylo-2.4.0/RRphylo/man/retrieve.angles.Rd | 4 RRphylo-2.4.0/RRphylo/man/scaleTree.Rd |only RRphylo-2.4.0/RRphylo/man/search.conv.Rd | 52 - RRphylo-2.4.0/RRphylo/man/search.shift.Rd | 76 - RRphylo-2.4.0/RRphylo/man/search.trend.Rd | 92 +- RRphylo-2.4.0/RRphylo/man/setBM.Rd | 2 RRphylo-2.4.0/RRphylo/man/sizedsubtree.Rd | 2 RRphylo-2.4.0/RRphylo/man/swap.phylo.Rd | 6 RRphylo-2.4.0/RRphylo/man/swapONE.Rd | 17 45 files changed, 3110 insertions(+), 2128 deletions(-)
Title: Bayesian Variable Selection for SNP Data using Normal-Gamma
Description: Posterior distribution of case-control fine-mapping. Specifically, Bayesian variable selection for single-nucleotide polymorphism (SNP) data using the normal-gamma prior. Alenazi A.A., Cox A., Juarez M,. Lin W-Y. and Walters, K. (2019) Bayesian variable selection using partially observed categorical prior information in fine-mapping association studies, Genetic Epidemiology. <doi:10.1002/gepi.22213>.
Author: Abdulaziz Alenazi [aut, cre]
Maintainer: Abdulaziz Alenazi <a.alenazi@nbu.edu.sa>
Diff between NGBVS versions 0.1.0 dated 2019-11-04 and 0.2.0 dated 2020-01-16
DESCRIPTION | 10 - MD5 | 24 +-- NAMESPACE | 16 +- R/asym_m_ng.R | 397 +++++++++++++++++++++++++------------------------- R/asym_s_ng.R | 236 +++++++++++++++--------------- R/m_ng.R | 422 +++++++++++++++++++++++++++--------------------------- R/rgig.R |only R/s_ng.R | 2 man/NG-package.Rd | 4 man/asym_m_ng.Rd | 2 man/asym_s_ng.Rd | 2 man/m_ng.Rd | 2 man/rgig.Rd |only man/s_ng.Rd | 2 14 files changed, 560 insertions(+), 559 deletions(-)
Title: Analyse Text Documents Using Ecological Tools
Description: A set of functions to analyse and compare texts, using classical
text mining functions, as well as those from theoretical ecology.
Author: Rebaudo Francois (IRD, UMR EGCE, IRD, CNRS, Univ. ParisSaclay)
Maintainer: Rebaudo Francois <francois.rebaudo@ird.fr>
Diff between inpdfr versions 0.1.8 dated 2018-10-24 and 0.1.11 dated 2020-01-16
inpdfr-0.1.11/inpdfr/DESCRIPTION | 12 - inpdfr-0.1.11/inpdfr/MD5 | 101 +++++----- inpdfr-0.1.11/inpdfr/NAMESPACE | 3 inpdfr-0.1.11/inpdfr/NEWS.md | 13 + inpdfr-0.1.11/inpdfr/R/inpdfr_ALL_quickFunctions.R | 31 --- inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_ECO_entropart.R | 20 - inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_ECO_metacom.R | 30 -- inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_barplot.R | 26 -- inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_cluster.R | 57 +---- inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_correspAnalysis.R | 111 ++++------ inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_freqWordCor.R | 78 +------ inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_hist.R | 61 ++---- inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_occur.R | 8 inpdfr-0.1.11/inpdfr/R/inpdfr_ANA_wordcloud.R | 8 inpdfr-0.1.11/inpdfr/R/inpdfr_PRO_extractTxt.R | 2 inpdfr-0.1.11/inpdfr/R/inpdfr_PRO_manageFiles.R | 4 inpdfr-0.1.11/inpdfr/R/inpdfr_PRO_processDF.R | 2 inpdfr-0.1.11/inpdfr/R/inpdfr_PRO_processTxt.R | 8 inpdfr-0.1.11/inpdfr/R/inpdfr_dataset_docu.R | 14 + inpdfr-0.1.11/inpdfr/build/vignette.rds |binary inpdfr-0.1.11/inpdfr/data/wordOccuDF.RData |only inpdfr-0.1.11/inpdfr/inst/doc/inpdfr-vignette.html | 202 +++++++++++++++++++- inpdfr-0.1.11/inpdfr/man/IdentifyStructure.Rd | 64 +++--- inpdfr-0.1.11/inpdfr/man/doCluster.Rd | 105 ++++------ inpdfr-0.1.11/inpdfr/man/doKmeansClust.Rd | 103 ++++------ inpdfr-0.1.11/inpdfr/man/doMetacomEntropart.Rd | 109 +++++----- inpdfr-0.1.11/inpdfr/man/doMetacomMetacom.Rd | 99 ++++----- inpdfr-0.1.11/inpdfr/man/excludeStopWords.Rd | 50 ++-- inpdfr-0.1.11/inpdfr/man/exclusionList_FR.Rd | 36 +-- inpdfr-0.1.11/inpdfr/man/exclusionList_SP.Rd | 36 +-- inpdfr-0.1.11/inpdfr/man/exclusionList_UK.Rd | 32 +-- inpdfr-0.1.11/inpdfr/man/getAllAnalysis.Rd | 92 +++------ inpdfr-0.1.11/inpdfr/man/getListFiles.Rd | 42 ++-- inpdfr-0.1.11/inpdfr/man/getMostFreqWord.Rd | 86 +++----- inpdfr-0.1.11/inpdfr/man/getMostFreqWordCor.Rd | 104 ++++------ inpdfr-0.1.11/inpdfr/man/getPDF.Rd | 91 ++++----- inpdfr-0.1.11/inpdfr/man/getStopWords.Rd | 32 +-- inpdfr-0.1.11/inpdfr/man/getSummaryStatsBARPLOT.Rd | 86 +++----- inpdfr-0.1.11/inpdfr/man/getSummaryStatsHISTO.Rd | 78 +++---- inpdfr-0.1.11/inpdfr/man/getSummaryStatsOCCUR.Rd | 67 +++--- inpdfr-0.1.11/inpdfr/man/getTXT.Rd | 76 +++---- inpdfr-0.1.11/inpdfr/man/getXFreqWord.Rd | 62 ++---- inpdfr-0.1.11/inpdfr/man/getwordOccuDF.Rd | 82 ++++---- inpdfr-0.1.11/inpdfr/man/inpdfr.Rd | 33 +-- inpdfr-0.1.11/inpdfr/man/loremIpsum.Rd | 32 +-- inpdfr-0.1.11/inpdfr/man/makeWordcloud.Rd | 90 ++++---- inpdfr-0.1.11/inpdfr/man/mergeWordFreq.Rd | 76 +++---- inpdfr-0.1.11/inpdfr/man/postProcTxt.Rd | 60 ++--- inpdfr-0.1.11/inpdfr/man/preProcTxt.Rd | 62 +++--- inpdfr-0.1.11/inpdfr/man/quitSpaceFromChars.Rd | 46 ++-- inpdfr-0.1.11/inpdfr/man/truncNumWords.Rd | 48 ++-- inpdfr-0.1.11/inpdfr/man/wordOccuDF.Rd |only inpdfr-0.1.8/inpdfr/man/doCA.Rd |only 53 files changed, 1381 insertions(+), 1389 deletions(-)
Title: Deep Learning with Metaheuristic
Description: Fits from simple regression to highly customizable deep neural networks
either with gradient descent or metaheuristic, using automatic hyper parameters
tuning and custom cost function.
A mix inspired by the common tricks on Deep Learning and Particle Swarm Optimization.
Author: Alex Boulangé [aut, cre]
Maintainer: Alex Boulangé <aboul@free.fr>
Diff between automl versions 1.3.1 dated 2020-01-09 and 1.3.2 dated 2020-01-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/automl.R | 25 +++++++++++++------------ inst/doc/howto_automl.pdf |binary man/hpar.Rd | 2 +- vignettes/automl.Rmd | 2 +- 7 files changed, 32 insertions(+), 23 deletions(-)
Title: Spatial Influence of Landscape
Description: Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.
Author: Carpentier F. and Martin O.
Maintainer: Martin Olivier <olivier.martin@inra.fr>
Diff between siland versions 1.4.5 dated 2019-12-13 and 1.4.6 dated 2020-01-16
siland-1.4.5/siland/R/landtorasterold.R |only siland-1.4.6/siland/DESCRIPTION | 8 ++++---- siland-1.4.6/siland/MD5 | 7 +++---- siland-1.4.6/siland/R/Bsiland.R | 2 +- siland-1.4.6/siland/build/partial.rdb |binary 5 files changed, 8 insertions(+), 9 deletions(-)
Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre],
Samuel Blanck [ctb],
Alain Celisse [ths],
Guillemette Marot [ths],
Yi Yang [ctb],
Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between MLGL versions 0.6 dated 2019-12-10 and 0.6.1 dated 2020-01-16
DESCRIPTION | 15 +++++++++------ MD5 | 8 ++++---- R/hierarchicalFDR.R | 2 +- R/hierarchicalFWER.R | 1 - R/stability.R | 2 +- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between RCurl versions 1.95-4.12 dated 2019-03-04 and 1.95-4.13 dated 2020-01-16
RCurl-1.95-4.12/RCurl/Changes.html |only RCurl-1.95-4.12/RCurl/CodeGeneration |only RCurl-1.95-4.12/RCurl/README.windows |only RCurl-1.95-4.12/RCurl/Todo.html |only RCurl-1.95-4.12/RCurl/dynGC.R |only RCurl-1.95-4.12/RCurl/encoding.R |only RCurl-1.95-4.12/RCurl/exampleCode |only RCurl-1.95-4.12/RCurl/getURL.html |only RCurl-1.95-4.12/RCurl/libcurlLicense |only RCurl-1.95-4.12/RCurl/post.R |only RCurl-1.95-4.12/RCurl/postForm.html |only RCurl-1.95-4.13/RCurl/DESCRIPTION | 21 ++------- RCurl-1.95-4.13/RCurl/LICENSE |only RCurl-1.95-4.13/RCurl/MD5 | 53 ++++++++--------------- RCurl-1.95-4.13/RCurl/inst/doc/Changes.html |only RCurl-1.95-4.13/RCurl/inst/doc/FAQ.html | 6 +- RCurl-1.95-4.13/RCurl/inst/doc/getURL.html |only RCurl-1.95-4.13/RCurl/inst/doc/philosophy.html | 15 +++--- RCurl-1.95-4.13/RCurl/inst/doc/withCookies.html | 10 ++-- RCurl-1.95-4.13/RCurl/man/basicHeaderGatherer.Rd | 4 - RCurl-1.95-4.13/RCurl/man/basicTextGatherer.Rd | 13 +++-- RCurl-1.95-4.13/RCurl/man/binaryBuffer.Rd | 4 - RCurl-1.95-4.13/RCurl/man/complete.Rd | 3 - RCurl-1.95-4.13/RCurl/man/curlPerform.Rd | 13 +++-- RCurl-1.95-4.13/RCurl/man/dynCurlReader.Rd | 12 ++--- RCurl-1.95-4.13/RCurl/man/getBinaryURL.Rd | 17 +++---- RCurl-1.95-4.13/RCurl/man/getCurlInfo.Rd | 4 - RCurl-1.95-4.13/RCurl/man/getFormParams.Rd | 4 - RCurl-1.95-4.13/RCurl/man/getURL.Rd | 12 ++--- RCurl-1.95-4.13/RCurl/man/postForm.Rd | 8 +-- RCurl-1.95-4.13/RCurl/man/scp.Rd | 4 - 31 files changed, 93 insertions(+), 110 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-09 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-20 0.5.1
2018-02-05 0.5.0
2010-08-23 0.4.9
2009-10-28 0.4.7
2007-04-04 0.4.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-11 1.1.1
2015-10-09 1.1
2014-01-23 1.0.4
2014-01-17 1.0.3
2013-08-25 1.0.2
2013-06-28 1.0.1
2013-06-14 1.0
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),
Mattan S. Ben-Shachar [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between afex versions 0.25-1 dated 2019-08-27 and 0.26-0 dated 2020-01-16
DESCRIPTION | 14 +- MD5 | 44 +++--- NEWS | 23 +++ R/afex_plot.R | 12 + R/afex_plot_utils.R | 92 +++++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/afex_anova_example.html | 45 +++--- inst/doc/afex_mixed_example.html | 14 +- inst/doc/afex_plot_introduction.Rmd | 3 inst/doc/afex_plot_introduction.html | 28 ++-- inst/doc/afex_plot_supported_models.html | 9 - man/afex-package.Rd | 4 man/afex_aov-methods.Rd | 25 ++- man/afex_plot.Rd | 213 +++++++++++++++++++++++-------- man/all_fit.Rd | 13 + man/aov_car.Rd | 60 ++++++-- man/mixed.Rd | 25 ++- man/nice.Rd | 28 ++-- man/sk2011.1.Rd | 2 tests/testthat/test-afex_plot-basics.R | 65 +++++++++ tests/testthat/test-aov_car-bugs.R | 4 vignettes/afex_plot_introduction.Rmd | 3 23 files changed, 540 insertions(+), 186 deletions(-)