Title: Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre],
Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between fastDummies versions 1.1.0 dated 2018-03-03 and 1.2.0 dated 2018-06-21
DESCRIPTION | 6 +- MD5 | 30 +++++----- NEWS.md | 5 + R/dummy_cols.R | 34 ++++++++++- build/vignette.rds |binary inst/doc/making-dummy-rows.html | 4 - inst/doc/making-dummy-variables.html | 4 - man/dummy_cols.Rd | 9 ++- man/dummy_columns.Rd | 9 ++- tests/testthat/test-columns-dimensions.R | 34 +++++++++++ tests/testthat/test-columns-value-order.R | 21 ++++--- tests/testthat/test-columns-warnings-errors.R | 64 ++++++++++++++++++++++ tests/testthat/test-columns.R | 41 ++++++++++++++ tests/testthat/test-return-type.R | 55 ++++++++++++++----- tests/testthat/test-rows-dimensions.R | 74 ++++++++++++++++---------- tests/testthat/test-rows-warnings-errors.R | 27 ++++++--- 16 files changed, 329 insertions(+), 88 deletions(-)
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic variants or environments, are available <arXiv:1712.04058>.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.2.1 dated 2018-02-07 and 1.2.2 dated 2018-06-21
DESCRIPTION | 10 - MD5 | 17 +- NAMESPACE | 1 R/LEGIT.R | 346 ++++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/GxE_testing.html | 108 ++++++++++--- inst/doc/LEGIT.html | 36 ++-- man/GxE_interaction_test.Rd | 12 - man/nes_var_select.Rd | 12 - man/r1nes_var_select.Rd |only 10 files changed, 451 insertions(+), 91 deletions(-)
Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre] (<https://orcid.org/0000-0002-1256-3375>),
David Firth [aut] (<https://orcid.org/0000-0003-0302-2312>),
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between gnm versions 1.0-8 dated 2015-04-22 and 1.1-0 dated 2018-06-21
gnm-1.0-8/gnm/data/House2001.rda |only gnm-1.0-8/gnm/data/backPain.rda |only gnm-1.0-8/gnm/data/barley.rda |only gnm-1.0-8/gnm/data/barleyHeights.rda |only gnm-1.0-8/gnm/data/cautres.rda |only gnm-1.0-8/gnm/data/erikson.rda |only gnm-1.0-8/gnm/data/friend.rda |only gnm-1.0-8/gnm/data/mentalHealth.rda |only gnm-1.0-8/gnm/data/voting.rda |only gnm-1.0-8/gnm/data/wheat.rda |only gnm-1.0-8/gnm/data/yaish.rda |only gnm-1.0-8/gnm/inst/NEWS |only gnm-1.1-0/gnm/DESCRIPTION | 37 gnm-1.1-0/gnm/MD5 | 141 gnm-1.1-0/gnm/NAMESPACE | 149 gnm-1.1-0/gnm/NEWS.md |only gnm-1.1-0/gnm/R/Diag.R | 72 gnm-1.1-0/gnm/R/Symm.R | 71 gnm-1.1-0/gnm/R/Topo.R | 64 gnm-1.1-0/gnm/R/add1.gnm.R | 295 - gnm-1.1-0/gnm/R/anova.gnm.R | 195 - gnm-1.1-0/gnm/R/checkEstimable.R | 6 gnm-1.1-0/gnm/R/cholInv.R | 190 - gnm-1.1-0/gnm/R/confint.gnm.R | 62 gnm-1.1-0/gnm/R/confint.profile.gnm.R | 88 gnm-1.1-0/gnm/R/drop1.gnm.R | 233 - gnm-1.1-0/gnm/R/getContrasts.R | 276 - gnm-1.1-0/gnm/R/getData.R | 42 gnm-1.1-0/gnm/R/glm.fit.e.R | 344 - gnm-1.1-0/gnm/R/gnm.R | 689 +-- gnm-1.1-0/gnm/R/gnmFit.R | 851 ++-- gnm-1.1-0/gnm/R/gnmTerms.R | 369 +- gnm-1.1-0/gnm/R/gnmTools.R | 513 +- gnm-1.1-0/gnm/R/meanResiduals.R | 158 gnm-1.1-0/gnm/R/nonlinTerms.R | 440 +- gnm-1.1-0/gnm/R/ofInterestReplacement.R | 52 gnm-1.1-0/gnm/R/plot.gnm.R | 542 +-- gnm-1.1-0/gnm/R/plot.profile.gnm.R | 82 gnm-1.1-0/gnm/R/pprod.R | 59 gnm-1.1-0/gnm/R/predict.gnm.R | 334 - gnm-1.1-0/gnm/R/print.meanResiduals.R | 49 gnm-1.1-0/gnm/R/print.profile.gnm.R | 58 gnm-1.1-0/gnm/R/se.R | 170 gnm-1.1-0/gnm/R/summary.gnm.R | 188 - gnm-1.1-0/gnm/R/summary.meanResiduals.R | 82 gnm-1.1-0/gnm/R/unlistOneLevel.R | 70 gnm-1.1-0/gnm/R/vcov.gnm.R | 156 gnm-1.1-0/gnm/R/zzz.R | 11 gnm-1.1-0/gnm/README.md |only gnm-1.1-0/gnm/build/vignette.rds |binary gnm-1.1-0/gnm/data/House2001.R |only gnm-1.1-0/gnm/data/backPain.R |only gnm-1.1-0/gnm/data/barley.R |only gnm-1.1-0/gnm/data/barleyHeights.R |only gnm-1.1-0/gnm/data/cautres.R |only gnm-1.1-0/gnm/data/erikson.R |only gnm-1.1-0/gnm/data/friend.R |only gnm-1.1-0/gnm/data/mentalHealth.R |only gnm-1.1-0/gnm/data/voting.R |only gnm-1.1-0/gnm/data/wheat.R |only gnm-1.1-0/gnm/data/yaish.R |only gnm-1.1-0/gnm/inst/CITATION | 40 gnm-1.1-0/gnm/inst/WORDLIST |only gnm-1.1-0/gnm/inst/doc/gnmOverview.R | 1370 +++---- gnm-1.1-0/gnm/inst/doc/gnmOverview.Rnw | 5739 +++++++++++++++----------------- gnm-1.1-0/gnm/inst/doc/gnmOverview.pdf |binary gnm-1.1-0/gnm/man/Diag.Rd | 75 gnm-1.1-0/gnm/man/Symm.Rd | 56 gnm-1.1-0/gnm/man/Topo.Rd | 2 gnm-1.1-0/gnm/man/checkEstimable.Rd | 116 gnm-1.1-0/gnm/man/confint.gnm.Rd | 212 - gnm-1.1-0/gnm/man/erikson.Rd | 2 gnm-1.1-0/gnm/man/expandCategorical.Rd | 180 - gnm-1.1-0/gnm/man/getContrasts.Rd | 270 - gnm-1.1-0/gnm/man/gnm.Rd | 712 +-- gnm-1.1-0/gnm/man/ofInterest.Rd | 128 gnm-1.1-0/gnm/man/profile.gnm.Rd | 356 - gnm-1.1-0/gnm/man/se.Rd | 88 gnm-1.1-0/gnm/man/se.gnm.Rd |only gnm-1.1-0/gnm/man/summary.gnm.Rd | 242 - gnm-1.1-0/gnm/man/vcov.gnm.Rd | 176 gnm-1.1-0/gnm/src/gnm.c | 42 gnm-1.1-0/gnm/tests/logexcess.R | 52 gnm-1.1-0/gnm/tests/logexcess.Rout.save | 94 gnm-1.1-0/gnm/vignettes/gnmOverview.Rnw | 5739 +++++++++++++++----------------- 85 files changed, 11438 insertions(+), 11391 deletions(-)
Title: Bias and Uncertainty Corrected Sample Size
Description: Implements a method of correcting for publication bias and
uncertainty when planning sample sizes in a future study from an original study. See Anderson, Kelley, & Maxwell (2017; Psychological Science, 28, 1547-1562).
Author: Samantha F. Anderson <samantha.f.anderson@asu.edu>, Ken Kelley <kkelley@nd.edu>
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between BUCSS versions 0.0.2 dated 2017-04-10 and 1.0.0 dated 2018-06-21
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- R/BUCSS.R | 8 ++++---- R/ss.power.ba.R | 11 ++++++----- R/ss.power.ba.general.R | 11 ++++++----- R/ss.power.dt.r | 11 ++++++----- R/ss.power.it.R | 11 ++++++----- R/ss.power.spa.general.R | 11 ++++++----- R/ss.power.spa.r | 11 ++++++----- R/ss.power.wa.general.R | 11 ++++++----- R/ss.power.wa.r | 11 ++++++----- man/BUCSS-package.Rd | 8 ++++---- man/ss.power.ba.Rd | 11 ++++++----- man/ss.power.ba.general.Rd | 11 ++++++----- man/ss.power.dt.Rd | 11 ++++++----- man/ss.power.it.Rd | 11 ++++++----- man/ss.power.spa.Rd | 11 ++++++----- man/ss.power.spa.general.Rd | 11 ++++++----- man/ss.power.wa.Rd | 11 ++++++----- man/ss.power.wa.general.Rd | 11 ++++++----- 20 files changed, 128 insertions(+), 112 deletions(-)
Title: Easily Add Markdown Help Files to 'shiny' App Elements
Description: Creates a lightweight way to add markdown helpfiles to 'shiny' apps,
using modal dialog boxes, with no need to observe each help button separately.
Author: Chris Thom [aut, cre]
Maintainer: Chris Thom <christopher.w.thom@outlook.com>
Diff between shinyhelper versions 0.2.0 dated 2018-06-07 and 0.3.0 dated 2018-06-21
shinyhelper-0.2.0/shinyhelper/R/create-help-files.R |only shinyhelper-0.2.0/shinyhelper/R/for-shiny.R |only shinyhelper-0.2.0/shinyhelper/R/globals.R |only shinyhelper-0.2.0/shinyhelper/R/no-export.R |only shinyhelper-0.2.0/shinyhelper/R/shinyhelper-demo.R |only shinyhelper-0.2.0/shinyhelper/inst/css-helper |only shinyhelper-0.2.0/shinyhelper/man/get_id.Rd |only shinyhelper-0.2.0/shinyhelper/man/shinyhelperDemo.Rd |only shinyhelper-0.2.0/shinyhelper/man/show_help_message.Rd |only shinyhelper-0.2.0/shinyhelper/man/use_shinyhelper.Rd |only shinyhelper-0.3.0/shinyhelper/DESCRIPTION | 10 - shinyhelper-0.3.0/shinyhelper/MD5 | 46 +++--- shinyhelper-0.3.0/shinyhelper/NAMESPACE | 3 shinyhelper-0.3.0/shinyhelper/NEWS.md | 42 +++++ shinyhelper-0.3.0/shinyhelper/R/create_help_files.R |only shinyhelper-0.3.0/shinyhelper/R/helper.R | 98 ++++++++----- shinyhelper-0.3.0/shinyhelper/R/observe_helpers.R |only shinyhelper-0.3.0/shinyhelper/R/shinyhelper-package.r | 14 + shinyhelper-0.3.0/shinyhelper/R/shinyhelper_demo.R |only shinyhelper-0.3.0/shinyhelper/README.md | 121 ++++++++++------- shinyhelper-0.3.0/shinyhelper/inst/assets |only shinyhelper-0.3.0/shinyhelper/inst/example/DESCRIPTION | 2 shinyhelper-0.3.0/shinyhelper/inst/example/Readme.md | 1 shinyhelper-0.3.0/shinyhelper/inst/example/rsconnect |only shinyhelper-0.3.0/shinyhelper/inst/example/server.R | 5 shinyhelper-0.3.0/shinyhelper/inst/example/ui.R | 25 +-- shinyhelper-0.3.0/shinyhelper/man/create_help_files.Rd | 14 + shinyhelper-0.3.0/shinyhelper/man/helper.Rd | 40 +++-- shinyhelper-0.3.0/shinyhelper/man/observe_helpers.Rd | 21 -- shinyhelper-0.3.0/shinyhelper/man/shinyhelper.Rd | 14 + shinyhelper-0.3.0/shinyhelper/man/shinyhelper_demo.Rd |only 31 files changed, 275 insertions(+), 181 deletions(-)
Title: Quantum Entanglement of Bipartite System
Description: It computes the Schmidt decomposition of bipartite quantum systems, discrete or continuous,
and their respective entanglement metrics. See Artur Ekert, Peter L. Knight (1995) <doi:10.1119/1.17904>
for more details.
Author: Kwan-Yuet Ho [aut, cre]
Maintainer: Kwan-Yuet Ho <stephenhky@yahoo.com.hk>
Diff between RQEntangle versions 0.1.0 dated 2018-05-27 and 0.1.1 dated 2018-06-21
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- R/discrete.R | 2 +- README.md | 5 +++++ build/vignette.rds |binary inst/doc/CoupledHarmonics.html | 4 ++-- inst/doc/CoupledHarmonics2.R |only inst/doc/CoupledHarmonics2.Rmd |only inst/doc/CoupledHarmonics2.html |only vignettes/CoupledHarmonics2.Rmd |only 10 files changed, 20 insertions(+), 11 deletions(-)
Title: Recurrent Neural Network
Description: Implementation of a Recurrent Neural Network in R.
Author: Bastiaan Quast [aut, cre],
Dimitri Fichou [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between rnn versions 0.8.0 dated 2016-09-11 and 0.8.1 dated 2018-06-21
DESCRIPTION | 8 MD5 | 86 ++++----- NEWS | 6 R/bin2int.R | 2 R/predictr.R | 9 R/trainr.R | 105 ++++++----- README.md | 3 build/vignette.rds |binary inst/doc/GRU_units.html | 196 ++++++++++++++++++++ inst/doc/LSTM_units.html | 196 ++++++++++++++++++++ inst/doc/rnn.R | 18 + inst/doc/rnn.Rmd | 24 ++ inst/doc/rnn.html | 432 +++++++++++++++++++++++++++++++++++----------- inst/doc/rnn_units.html | 196 ++++++++++++++++++++ inst/doc/sinus.html | 370 ++++++++++++++++++++++++++++++--------- man/backprop_gru.Rd | 1 man/backprop_lstm.Rd | 1 man/backprop_r.Rd | 1 man/backprop_rnn.Rd | 1 man/bin2int.Rd | 2 man/clean_lstm.Rd | 1 man/clean_r.Rd | 1 man/clean_rnn.Rd | 1 man/epoch_annealing.Rd | 1 man/epoch_print.Rd | 1 man/init_gru.Rd | 1 man/init_lstm.Rd | 1 man/init_r.Rd | 1 man/init_rnn.Rd | 1 man/int2bin.Rd | 2 man/loss_L1.Rd | 1 man/predict_gru.Rd | 1 man/predict_lstm.Rd | 1 man/predict_rnn.Rd | 1 man/predictr.Rd | 10 - man/rnn.Rd | 7 man/run.finance_demo.Rd | 1 man/run.rnn_demo.Rd | 1 man/trainr.Rd | 15 - man/update_adagrad.Rd | 1 man/update_r.Rd | 1 man/update_sgd.Rd | 1 tests/testthat/test_rnn.R | 1 vignettes/rnn.Rmd | 24 ++ 44 files changed, 1392 insertions(+), 342 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-4 dated 2018-06-15 and 0.0-5 dated 2018-06-21
DESCRIPTION | 6 MD5 | 4 src/sobol.c | 381 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 196 insertions(+), 195 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository 'Xeno-Canto' <http://xeno-canto.org/>, manipulating sound files, detecting acoustic signals, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Diff between warbleR versions 1.1.13 dated 2018-05-18 and 1.1.14 dated 2018-06-21
warbleR-1.1.13/warbleR/R/selec_table-data.R |only warbleR-1.1.13/warbleR/data/selec_table.rda |only warbleR-1.1.13/warbleR/man/selec_table.Rd |only warbleR-1.1.14/warbleR/DESCRIPTION | 10 warbleR-1.1.14/warbleR/MD5 | 172 +++++++------- warbleR-1.1.14/warbleR/NEWS.md | 11 warbleR-1.1.14/warbleR/R/autodetec.R | 171 +++++++------ warbleR-1.1.14/warbleR/R/boxw_wrblr_int.R | 18 - warbleR-1.1.14/warbleR/R/catalog.R | 2 warbleR-1.1.14/warbleR/R/catalog2pdf.R | 22 - warbleR-1.1.14/warbleR/R/checksels.R | 56 ++-- warbleR-1.1.14/warbleR/R/checkwavs.R | 28 +- warbleR-1.1.14/warbleR/R/color.spectro.R | 44 +-- warbleR-1.1.14/warbleR/R/compare.methods.R | 118 ++++----- warbleR-1.1.14/warbleR/R/consolidate.R | 24 - warbleR-1.1.14/warbleR/R/coor.graph.R | 52 ++-- warbleR-1.1.14/warbleR/R/coor.test.R | 42 +-- warbleR-1.1.14/warbleR/R/cut_sels.R | 30 +- warbleR-1.1.14/warbleR/R/dfDTW.R | 18 - warbleR-1.1.14/warbleR/R/dfts.R | 74 +++--- warbleR-1.1.14/warbleR/R/fade_env_wrblr_int.R | 4 warbleR-1.1.14/warbleR/R/ffDTW.R | 8 warbleR-1.1.14/warbleR/R/ffts.R | 50 ++-- warbleR-1.1.14/warbleR/R/filled_contour_color_wrblr_int.R | 2 warbleR-1.1.14/warbleR/R/filled_contour_wrblr_int.R | 2 warbleR-1.1.14/warbleR/R/filtersels.R | 42 +-- warbleR-1.1.14/warbleR/R/fix_cntr_wrblr_int.R | 8 warbleR-1.1.14/warbleR/R/fixwavs.R | 70 +++-- warbleR-1.1.14/warbleR/R/frange.R | 36 +- warbleR-1.1.14/warbleR/R/frange.detec.R | 4 warbleR-1.1.14/warbleR/R/frd_plot_wrblr_int.R | 12 warbleR-1.1.14/warbleR/R/frd_wrblr_int.R | 16 - warbleR-1.1.14/warbleR/R/inflections.R | 2 warbleR-1.1.14/warbleR/R/lbh_selec_table-data.R |only warbleR-1.1.14/warbleR/R/lspec.R | 82 +++--- warbleR-1.1.14/warbleR/R/lspec2pdf.R | 16 - warbleR-1.1.14/warbleR/R/manualoc.R | 82 +++--- warbleR-1.1.14/warbleR/R/mp32wav.R | 77 ++++-- warbleR-1.1.14/warbleR/R/open_wd.R | 4 warbleR-1.1.14/warbleR/R/ovlp_sels.R | 48 +-- warbleR-1.1.14/warbleR/R/querxc.R | 57 ++-- warbleR-1.1.14/warbleR/R/read_wave.R | 18 - warbleR-1.1.14/warbleR/R/rectw_wrblr_int.R | 14 - warbleR-1.1.14/warbleR/R/rm_sil.R | 32 +- warbleR-1.1.14/warbleR/R/selection_table.R | 30 +- warbleR-1.1.14/warbleR/R/seltailor.R | 120 ++++----- warbleR-1.1.14/warbleR/R/sig2noise.R | 48 +-- warbleR-1.1.14/warbleR/R/sim_songs.R | 6 warbleR-1.1.14/warbleR/R/snrspecs.R | 48 +-- warbleR-1.1.14/warbleR/R/song_param.R | 6 warbleR-1.1.14/warbleR/R/sp.en.ts.R | 48 +-- warbleR-1.1.14/warbleR/R/spec_param.R | 16 - warbleR-1.1.14/warbleR/R/specan.R | 70 ++--- warbleR-1.1.14/warbleR/R/specreator.R | 6 warbleR-1.1.14/warbleR/R/spectro_wrblr_int.R | 18 - warbleR-1.1.14/warbleR/R/spectro_wrblr_int2.R | 18 - warbleR-1.1.14/warbleR/R/track_harm.R | 8 warbleR-1.1.14/warbleR/R/trackfreqs.R | 171 +++++++------ warbleR-1.1.14/warbleR/R/try_na.R | 2 warbleR-1.1.14/warbleR/R/warbleR-package.R | 8 warbleR-1.1.14/warbleR/R/wavdur.R | 8 warbleR-1.1.14/warbleR/R/xcmaps.R | 34 +- warbleR-1.1.14/warbleR/R/xcorr.R | 76 +++--- warbleR-1.1.14/warbleR/R/xcorr.graph.R | 30 +- warbleR-1.1.14/warbleR/build/vignette.rds |binary warbleR-1.1.14/warbleR/data/lbh_selec_table.rda |only warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_01.Rmd | 2 warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_01.html | 38 +-- warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_02.Rmd | 2 warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_02.html | 4 warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_03.Rmd | 2 warbleR-1.1.14/warbleR/inst/doc/warbleR_workflow_03.html | 4 warbleR-1.1.14/warbleR/man/autodetec.Rd | 5 warbleR-1.1.14/warbleR/man/checkwavs.Rd | 2 warbleR-1.1.14/warbleR/man/fix_wavs.Rd | 2 warbleR-1.1.14/warbleR/man/fixwavs.Rd | 12 warbleR-1.1.14/warbleR/man/frange.Rd | 2 warbleR-1.1.14/warbleR/man/lbh_selec_table.Rd |only warbleR-1.1.14/warbleR/man/mp32wav.Rd | 19 + warbleR-1.1.14/warbleR/man/open_wd.Rd | 2 warbleR-1.1.14/warbleR/man/querxc.Rd | 2 warbleR-1.1.14/warbleR/man/sig2noise.Rd | 4 warbleR-1.1.14/warbleR/man/snrspecs.Rd | 4 warbleR-1.1.14/warbleR/man/sp.en.ts.Rd | 2 warbleR-1.1.14/warbleR/man/specreator.Rd | 2 warbleR-1.1.14/warbleR/man/trackfreqs.Rd | 7 warbleR-1.1.14/warbleR/man/warbleR.Rd | 8 warbleR-1.1.14/warbleR/vignettes/warbleR_workflow_01.Rmd | 2 warbleR-1.1.14/warbleR/vignettes/warbleR_workflow_02.Rmd | 2 warbleR-1.1.14/warbleR/vignettes/warbleR_workflow_03.Rmd | 2 90 files changed, 1273 insertions(+), 1207 deletions(-)
Title: Functions for Benchmarking Time Series Prediction
Description: Functions for time series preprocessing, decomposition, prediction and accuracy assessment using automatic linear modelling. The generated linear models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ),
Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles <rebeccapsalles@acm.org>
Diff between TSPred versions 3.0.2 dated 2017-04-05 and 4.0 dated 2018-06-21
DESCRIPTION | 17 +- MD5 | 98 ++++++++----- NAMESPACE | 6 R/BCT.r |only R/DIF.r |only R/LT.r |only R/MAS.r |only R/PCT.r |only R/arimapar.R | 9 - R/arimaparameters.R |only R/data.frame.na.R |only R/detrend.r |only R/fittestArima.r | 114 +++++++++++----- R/fittestArimaKF.r | 318 ++++++++++++++++++++++++++++++--------------- R/fittestEMD.r |only R/fittestLM.r | 47 ++++-- R/fittestMAS.r |only R/fittestPolyR.r | 215 ++++++++++++++++++++++-------- R/fittestPolyRKF.r | 238 ++++++++++++++++++++++++--------- R/fittestWavelet.r |only R/marimapar.R | 5 data/CATS.cont.rda |binary data/CATS.rda |binary data/EUNITE.Loads.cont.rda |binary data/EUNITE.Loads.rda |binary data/EUNITE.Reg.cont.rda |binary data/EUNITE.Reg.rda |binary data/EUNITE.Temp.cont.rda |binary data/EUNITE.Temp.rda |binary data/NN3.A.cont.rda |binary data/NN3.A.rda |binary data/NN5.A.cont.rda |binary data/NN5.A.rda |binary data/SantaFe.A.cont.rda |binary data/SantaFe.A.rda |binary data/SantaFe.D.cont.rda |binary data/SantaFe.D.rda |binary data/ipeadata_d.cont.rda |only data/ipeadata_d.rda |only data/ipeadata_m.cont.rda |only data/ipeadata_m.rda |only man/BCT.Rd |only man/DIF.Rd |only man/LT.Rd |only man/MAS.Rd |only man/PCT.Rd |only man/TSPred-deprecated.Rd |only man/TSPred-internal.Rd | 6 man/TSPred-package.Rd | 95 ++++++++----- man/arimapar.Rd | 4 man/arimaparameters.Rd |only man/arimapred.Rd | 2 man/detrend.Rd |only man/fittestArima.Rd | 25 ++- man/fittestArimaKF.Rd | 64 +++++---- man/fittestEMD.Rd |only man/fittestLM.Rd | 51 +++++-- man/fittestMAS.Rd |only man/fittestPolyR.Rd | 71 ++++++---- man/fittestPolyRKF.Rd | 72 ++++++---- man/fittestWavelet.Rd |only man/ipeadata_d.Rd |only man/ipeadata_m.Rd |only man/marimapar.Rd | 16 +- 64 files changed, 994 insertions(+), 479 deletions(-)
Title: Sigmoid Functions for Machine Learning
Description: Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between sigmoid versions 0.2.1 dated 2017-03-14 and 0.3.0 dated 2018-06-21
sigmoid-0.2.1/sigmoid/man/leakly_relu.Rd |only sigmoid-0.3.0/sigmoid/DESCRIPTION | 6 sigmoid-0.3.0/sigmoid/MD5 | 22 - sigmoid-0.3.0/sigmoid/NAMESPACE | 2 sigmoid-0.3.0/sigmoid/NEWS | 11 sigmoid-0.3.0/sigmoid/R/sigmoid.R | 10 sigmoid-0.3.0/sigmoid/build/vignette.rds |binary sigmoid-0.3.0/sigmoid/inst/doc/sigmoid.R | 7 sigmoid-0.3.0/sigmoid/inst/doc/sigmoid.Rmd | 21 + sigmoid-0.3.0/sigmoid/inst/doc/sigmoid.html | 356 ++++++++++++++++++++++------ sigmoid-0.3.0/sigmoid/man/leakyrelu.Rd |only sigmoid-0.3.0/sigmoid/man/sigmoid.Rd | 4 sigmoid-0.3.0/sigmoid/vignettes/sigmoid.Rmd | 21 + 13 files changed, 371 insertions(+), 89 deletions(-)
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on
'htmlwidgets', it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced but
can easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at <http://datastorm-
open.github.io/introduction_ramcharts/> and <http://www.amcharts.com/> for
more information about the library. The package includes the free version
of 'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate to refer
to this page <http://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Benoit Thieurmel [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Jeffery Petit [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between rAmCharts versions 2.1.7 dated 2018-05-25 and 2.1.8 dated 2018-06-21
rAmCharts-2.1.7/rAmCharts/inst/htmlwidgets/lib/images/logo.png |only rAmCharts-2.1.7/rAmCharts/inst/htmlwidgets/lib/images/style.css |only rAmCharts-2.1.8/rAmCharts/DESCRIPTION | 29 rAmCharts-2.1.8/rAmCharts/MD5 | 380 +++-- rAmCharts-2.1.8/rAmCharts/NAMESPACE | 1 rAmCharts-2.1.8/rAmCharts/R/amChartsAPI.R |only rAmCharts-2.1.8/rAmCharts/R/base_startupMessage.R | 8 rAmCharts-2.1.8/rAmCharts/R/chart_amBarplot.R | 9 rAmCharts-2.1.8/rAmCharts/R/chart_amBoxplot.R | 15 rAmCharts-2.1.8/rAmCharts/R/chart_amBullet.R | 13 rAmCharts-2.1.8/rAmCharts/R/chart_amCandlestick.R | 13 rAmCharts-2.1.8/rAmCharts/R/chart_amDataset.R | 13 rAmCharts-2.1.8/rAmCharts/R/chart_amFloatingBar.R | 13 rAmCharts-2.1.8/rAmCharts/R/chart_amFunnel.R | 16 rAmCharts-2.1.8/rAmCharts/R/chart_amGauge.R | 26 rAmCharts-2.1.8/rAmCharts/R/chart_amHist.R | 16 rAmCharts-2.1.8/rAmCharts/R/chart_amMekko.R | 16 rAmCharts-2.1.8/rAmCharts/R/chart_amOHLC.R | 18 rAmCharts-2.1.8/rAmCharts/R/chart_amPie.R | 18 rAmCharts-2.1.8/rAmCharts/R/chart_amPlot.R | 21 rAmCharts-2.1.8/rAmCharts/R/chart_amRadar.R | 20 rAmCharts-2.1.8/rAmCharts/R/chart_amTimeSeries.R | 23 rAmCharts-2.1.8/rAmCharts/R/chart_amWaterfall.R | 17 rAmCharts-2.1.8/rAmCharts/R/chart_amWind.R | 18 rAmCharts-2.1.8/rAmCharts/R/shiny_modules_timeSeries.R | 36 rAmCharts-2.1.8/rAmCharts/R/utils_amOptions.R | 15 rAmCharts-2.1.8/rAmCharts/inst/api |only rAmCharts-2.1.8/rAmCharts/inst/conf.yaml | 3 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/amcharts.js | 612 ++++---- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/amstock.js | 212 +- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/funnel.js | 68 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/gantt.js | 10 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/gauge.js | 48 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/eraserIcon.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/eraserIcon.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/eraserIconH.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/eraserIconH.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/pencilIcon.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/pencilIcon.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/pencilIconH.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/pencilIconH.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/xIcon.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/xIcon.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/xIconH.gif |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/images/xIconH.png |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/az.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/bg.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/cs.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/de.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/es.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/fi.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/fo.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/fr.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/hr.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/hu.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/id.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/is.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/it.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/lt.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/lv.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/mk.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/mn.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/mt.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/nl.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/no.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/pl.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/pt.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/ro.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/ru.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/rw.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/sk.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/sl.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/so.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/th.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/tr.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/uk.js |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/lang/zh.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/pie.js | 58 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/LICENSE | 402 ++--- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/README.md |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/animate.min.js | 80 - rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/bower.json | 54 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/index.js | 4 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/animate/package.json | 20 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/dataloader/bower.json | 54 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/dataloader/dataloader.min.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/dataloader/index.js | 4 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/dataloader/package.json | 20 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/dataloader/readme.md |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/LICENSE | 404 ++--- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/README.md |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/bower.json | 54 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/export.css | 720 +++++----- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/export.min.js | 3 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/index.js | 4 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/lang/fr.js | 62 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/lang/it.js |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/lang/pt.js | 74 - rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/lang/tr.js |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/lang/zh.js |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/FileSaver.js/FileSaver.min.js | 4 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/blob.js/blob.js | 420 ++--- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/classList.js |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/fabric.js/fabric.min.js | 9 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/jszip/jszip.min.js | 15 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/pdfmake/pdfmake.min.js | 49 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/pdfmake/pdfmake.min.js.map | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/pdfmake/vfs_fonts.js | 8 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/xlsx/LICENSE | 218 ++- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/xlsx/xlsx.min.js | 24 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/libs/xlsx/xlsx.min.map | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/export/package.json | 20 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/bower.json | 54 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/index.js | 4 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/package.json | 20 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/readme.md |only rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/responsive.min.js | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/plugins/responsive/responsive.min.js.map | 2 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/radar.js | 22 rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/serial.js | 191 +- rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/lib/xy.js | 82 - rAmCharts-2.1.8/rAmCharts/inst/htmlwidgets/ramcharts_base.yaml | 2 rAmCharts-2.1.8/rAmCharts/man/amAngularGauge.Rd | 16 rAmCharts-2.1.8/rAmCharts/man/amBarplot.Rd | 9 rAmCharts-2.1.8/rAmCharts/man/amBoxplot.Rd | 11 rAmCharts-2.1.8/rAmCharts/man/amBullet.Rd | 12 rAmCharts-2.1.8/rAmCharts/man/amCandlestick.Rd | 12 rAmCharts-2.1.8/rAmCharts/man/amChartsAPI.Rd |only rAmCharts-2.1.8/rAmCharts/man/amFloatingBar.Rd | 12 rAmCharts-2.1.8/rAmCharts/man/amFunnel.Rd | 12 rAmCharts-2.1.8/rAmCharts/man/amHist.Rd | 14 rAmCharts-2.1.8/rAmCharts/man/amMekko.Rd | 14 rAmCharts-2.1.8/rAmCharts/man/amOHLC.Rd | 16 rAmCharts-2.1.8/rAmCharts/man/amOptions.Rd | 11 rAmCharts-2.1.8/rAmCharts/man/amPie.Rd | 13 rAmCharts-2.1.8/rAmCharts/man/amPlot.Rd | 18 rAmCharts-2.1.8/rAmCharts/man/amRadar.Rd | 17 rAmCharts-2.1.8/rAmCharts/man/amSolidGauge.Rd | 10 rAmCharts-2.1.8/rAmCharts/man/amStockMultiSet.Rd | 13 rAmCharts-2.1.8/rAmCharts/man/amTimeSeries.Rd | 14 rAmCharts-2.1.8/rAmCharts/man/amWaterfall.Rd | 15 rAmCharts-2.1.8/rAmCharts/man/amWind.Rd | 14 142 files changed, 2895 insertions(+), 2296 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) Use of CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.4.2 dated 2018-05-17 and 0.4.3 dated 2018-06-21
NonCompart-0.4.2/NonCompart/inst/doc/validation_0.4.2.pdf |only NonCompart-0.4.3/NonCompart/DESCRIPTION | 8 ++-- NonCompart-0.4.3/NonCompart/MD5 | 10 ++--- NonCompart-0.4.3/NonCompart/R/tblNCA.R | 18 +++++----- NonCompart-0.4.3/NonCompart/inst/NEWS.Rd | 5 ++ NonCompart-0.4.3/NonCompart/inst/doc/NonCompart-manual.pdf |binary NonCompart-0.4.3/NonCompart/inst/doc/NonCompart-validation.pdf |only 7 files changed, 23 insertions(+), 18 deletions(-)
Title: Bayesian Optimization and Model-Based Optimization of Expensive
Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization
('MBO'), also known as Bayesian optimization. It implements the Efficient
Global Optimization Algorithm and is designed for both single- and multi-
objective optimization with mixed continuous, categorical and conditional
parameters. The machine learning toolbox 'mlr' provide dozens of regression
learners to model the performance of the target algorithm with respect to
the parameter settings. It provides many different infill criteria to guide
the search process. Additional features include multi-point batch proposal,
parallel execution as well as visualization and sophisticated logging
mechanisms, which is especially useful for teaching and understanding of
algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that
single components can be easily replaced or adapted by the user for specific
use cases.
Author: Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut, cre] (<https://orcid.org/0000-0003-4481-5554>),
Jakob Bossek [aut] (<https://orcid.org/0000-0002-4121-4668>),
Daniel Horn [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Janek Thomas [aut] (<https://orcid.org/0000-0003-4511-6245>)
Maintainer: Jakob Richter <code@jakob-r.de>
Diff between mlrMBO versions 1.1.1 dated 2018-01-02 and 1.1.2 dated 2018-06-21
mlrMBO-1.1.1/mlrMBO/R/convertOptPathToDf.R |only mlrMBO-1.1.1/mlrMBO/tests/testthat/Rplots.pdf |only mlrMBO-1.1.1/mlrMBO/tests/testthat/test_plotEAF.R |only mlrMBO-1.1.2/mlrMBO/DESCRIPTION | 57 - mlrMBO-1.1.2/mlrMBO/MD5 | 124 +- mlrMBO-1.1.2/mlrMBO/NAMESPACE | 2 mlrMBO-1.1.2/mlrMBO/NEWS.md | 7 mlrMBO-1.1.2/mlrMBO/R/OptState.R | 5 mlrMBO-1.1.2/mlrMBO/R/OptState_getter.R | 11 mlrMBO-1.1.2/mlrMBO/R/OptState_setter.R | 6 mlrMBO-1.1.2/mlrMBO/R/SMBO.R | 2 mlrMBO-1.1.2/mlrMBO/R/checkStuff.R | 2 mlrMBO-1.1.2/mlrMBO/R/convertToDesign.R |only mlrMBO-1.1.2/mlrMBO/R/infillOptCMAES.R | 10 mlrMBO-1.1.2/mlrMBO/R/infillOptEA.R | 6 mlrMBO-1.1.2/mlrMBO/R/infillOptFocus.R | 4 mlrMBO-1.1.2/mlrMBO/R/infillOptNSGA2.R | 14 mlrMBO-1.1.2/mlrMBO/R/infill_crits.R | 62 - mlrMBO-1.1.2/mlrMBO/R/initCrit.R | 9 mlrMBO-1.1.2/mlrMBO/R/makeMBOInfillCrit.R | 4 mlrMBO-1.1.2/mlrMBO/R/makeTaskSingleObj.R | 2 mlrMBO-1.1.2/mlrMBO/R/makeTasks.R | 2 mlrMBO-1.1.2/mlrMBO/R/makeTasksMultiObj.R | 2 mlrMBO-1.1.2/mlrMBO/R/makeTasksParEGO.R | 47 mlrMBO-1.1.2/mlrMBO/R/multiobj_helpers.R | 5 mlrMBO-1.1.2/mlrMBO/R/plot_OptState.R | 14 mlrMBO-1.1.2/mlrMBO/R/proposePointsByInfillOptimization.R | 21 mlrMBO-1.1.2/mlrMBO/R/proposePointsDIB.R | 4 mlrMBO-1.1.2/mlrMBO/R/proposePointsMOIMBO.R | 18 mlrMBO-1.1.2/mlrMBO/R/proposePointsMSPOT.R | 6 mlrMBO-1.1.2/mlrMBO/R/proposePointsParEGO.R | 6 mlrMBO-1.1.2/mlrMBO/R/renderExampleRunPlotMultiObj.R | 43 mlrMBO-1.1.2/mlrMBO/R/renderExampleRunPlotSingleCrit1d.R | 20 mlrMBO-1.1.2/mlrMBO/R/renderExampleRunPlotSingleCrit2d.R | 14 mlrMBO-1.1.2/mlrMBO/R/renderExampleRunPlot_helpers.R | 4 mlrMBO-1.1.2/mlrMBO/R/setMBOControlInfill.R | 2 mlrMBO-1.1.2/mlrMBO/R/setMBOControlTermination.R | 33 mlrMBO-1.1.2/mlrMBO/R/shouldTerminate.R | 9 mlrMBO-1.1.2/mlrMBO/R/term_conds.R | 20 mlrMBO-1.1.2/mlrMBO/build/vignette.rds |binary mlrMBO-1.1.2/mlrMBO/inst/doc/mlrMBO.R | 3 mlrMBO-1.1.2/mlrMBO/inst/doc/mlrMBO.Rmd | 12 mlrMBO-1.1.2/mlrMBO/inst/doc/mlrMBO.html | 515 ++++------ mlrMBO-1.1.2/mlrMBO/man/MBOInfillCrit.Rd | 1 mlrMBO-1.1.2/mlrMBO/man/infillcrits.Rd | 12 mlrMBO-1.1.2/mlrMBO/man/setMBOControlTermination.Rd | 8 mlrMBO-1.1.2/mlrMBO/tests/testthat.R | 7 mlrMBO-1.1.2/mlrMBO/tests/testthat/helper_objects.R | 18 mlrMBO-1.1.2/mlrMBO/tests/testthat/helper_zzz.R | 8 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_adaptive_infillcrits.R |only mlrMBO-1.1.2/mlrMBO/tests/testthat/test_check_design.R | 2 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_infill_opt_ea.R | 10 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_infillcrits.R | 15 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_mboContinue.R | 5 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_mbo_km.R | 6 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_smbo.R | 17 mlrMBO-1.1.2/mlrMBO/tests/testthat/test_termination_criteria.R | 85 - mlrMBO-1.1.2/mlrMBO/vignettes/helpers/animation-.gif |only mlrMBO-1.1.2/mlrMBO/vignettes/mlrMBO.Rmd | 12 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/adaptive_infill_criteria.Rmd |only mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/human_in_the_loop_MBO.Rmd | 13 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/infill_criteria.Rmd | 10 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/machine_learning_with_mlrmbo.Rmd | 11 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/mixed_space_optimization.Rmd | 12 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/mlrmbo_and_the_command_line.rmd |only mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/noisy_optimization.Rmd | 10 mlrMBO-1.1.2/mlrMBO/vignettes/supplementary/parallelization.Rmd | 11 67 files changed, 774 insertions(+), 626 deletions(-)
Title: Independently Interpretable Lasso
Description: Efficient algorithms for fitting linear / logistic regression model with Independently Interpretable Lasso.
Takada, M., Suzuki, T., & Fujisawa, H. (2018). Independently Interpretable Lasso: A New Regularizer for Sparse Regression with Uncorrelated Variables. AISTATS.
<http://proceedings.mlr.press/v84/takada18a/takada18a.pdf>.
Author: Masaaki Takada
Maintainer: Masaaki Takada <tkdmah@gmail.com>
Diff between iilasso versions 0.0.1 dated 2018-04-16 and 0.0.2 dated 2018-06-21
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 ++++- R/cda3.R | 12 ++++++------ R/cross_validator.R | 13 +++++++++---- inst/doc/introduction.R | 2 +- inst/doc/introduction.Rmd | 2 +- inst/doc/introduction.html | 2 +- man/cv_lasso.Rd | 3 +-- src/cda3.cpp | 12 ++++++------ tests/testthat/Rplots.pdf |binary vignettes/introduction.Rmd | 2 +- 12 files changed, 45 insertions(+), 38 deletions(-)
Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs
<https://developers.google.com/apis-explorer/> easily,
with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>),
Jennifer Bryan [ctb],
Johann deBoer [ctb],
Neal Richardson [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAuthR versions 0.6.2 dated 2017-11-14 and 0.6.3 dated 2018-06-21
googleAuthR-0.6.2/googleAuthR/tests/testthat/mock/24a0d02b587bc246 |only googleAuthR-0.6.2/googleAuthR/tests/testthat/mock/54ed4ff2b2693090 |only googleAuthR-0.6.2/googleAuthR/tests/testthat/mock/85460cd6cee1de4a |only googleAuthR-0.6.2/googleAuthR/tests/testthat/mock/90dd9a77247710c6 |only googleAuthR-0.6.3/googleAuthR/DESCRIPTION | 14 googleAuthR-0.6.3/googleAuthR/MD5 | 65 googleAuthR-0.6.3/googleAuthR/NEWS.md | 8 googleAuthR-0.6.3/googleAuthR/R/batch.R | 112 googleAuthR-0.6.3/googleAuthR/R/generator.R | 6 googleAuthR-0.6.3/googleAuthR/R/memoise.R | 6 googleAuthR-0.6.3/googleAuthR/R/set_client.R | 66 googleAuthR-0.6.3/googleAuthR/R/shiny.R | 23 googleAuthR-0.6.3/googleAuthR/README.md | 2 googleAuthR-0.6.3/googleAuthR/build/vignette.rds |binary googleAuthR-0.6.3/googleAuthR/inst/doc/advanced-building.Rmd | 68 googleAuthR-0.6.3/googleAuthR/inst/doc/advanced-building.html | 83 googleAuthR-0.6.3/googleAuthR/inst/doc/building.html | 4 googleAuthR-0.6.3/googleAuthR/inst/doc/google-authentication-types.Rmd | 12 googleAuthR-0.6.3/googleAuthR/inst/doc/google-authentication-types.html | 14 googleAuthR-0.6.3/googleAuthR/inst/doc/setup.html | 4 googleAuthR-0.6.3/googleAuthR/inst/doc/troubleshooting.Rmd | 1 googleAuthR-0.6.3/googleAuthR/inst/doc/troubleshooting.html | 5 googleAuthR-0.6.3/googleAuthR/man/gar_auth_jsUI.Rd | 5 googleAuthR-0.6.3/googleAuthR/man/gar_batch.Rd | 37 googleAuthR-0.6.3/googleAuthR/man/gar_batch_walk.Rd | 55 googleAuthR-0.6.3/googleAuthR/man/gar_set_client.Rd | 16 googleAuthR-0.6.3/googleAuthR/tests/testthat/gdrive.oauth |binary googleAuthR-0.6.3/googleAuthR/tests/testthat/googleAuthR_tests.httr-oauth |binary googleAuthR-0.6.3/googleAuthR/tests/testthat/mock/62e4b253dcc9b5e5 |only googleAuthR-0.6.3/googleAuthR/tests/testthat/test-integration.R | 6 googleAuthR-0.6.3/googleAuthR/tests/www.googleapis.com/discovery/v1/apis.json | 6002 +++++----- googleAuthR-0.6.3/googleAuthR/tests/www.googleapis.com/discovery/v1/apis/acceleratedmobilepageurl/v1/rest.json | 447 googleAuthR-0.6.3/googleAuthR/tests/www.googleapis.com/urlshortener/v1/url-bd4cc3-POST.json | 6 googleAuthR-0.6.3/googleAuthR/vignettes/advanced-building.Rmd | 68 googleAuthR-0.6.3/googleAuthR/vignettes/google-authentication-types.Rmd | 12 googleAuthR-0.6.3/googleAuthR/vignettes/troubleshooting.Rmd | 1 36 files changed, 3800 insertions(+), 3348 deletions(-)
Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators
(ECHO)
Description: Provides a function (echo_find()) designed to find rhythms
from data using extended harmonic oscillators. For more information,
see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> .
Author: Hannah De los Santos [aut, cre],
Emily Collins [aut],
Jonathan Shewchuk [ctb],
E.F. Harding [ctb],
Kristin Bennett [aut],
Jennifer Hurley [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>
Diff between echo.find versions 1.0.1 dated 2018-05-29 and 1.1.1 dated 2018-06-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/echo_utils.R | 18 +++++++++++++++--- inst/CITATION | 4 ++-- inst/doc/echo-vignette.html | 32 ++++++++++++++++---------------- 5 files changed, 40 insertions(+), 28 deletions(-)
Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis,
fixing data errors in numerical, factor and date variables and creating report
tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.3.64 dated 2018-04-21 and 0.4.05 dated 2018-06-21
DESCRIPTION | 9 +- MD5 | 47 +++++----- NAMESPACE | 1 NEWS | 7 + R/descriptive.R | 13 --- R/report_model.R | 186 ++++++++++++++++--------------------------- man/make_table.Rd | 11 -- man/make_word_table.Rd | 12 -- man/report.betareg.Rd | 7 - man/report.brmsfit.Rd | 7 - man/report.clm.Rd | 7 - man/report.clmm.Rd | 7 - man/report.coxph.Rd | 7 - man/report.data.frame.Rd | 10 -- man/report.glm.Rd | 7 - man/report.glmerMod.Rd | 7 - man/report.glmmadmb.Rd | 7 - man/report.glmnet.Rd | 7 - man/report.lm.Rd | 7 - man/report.lmerMod.Rd | 7 - man/report.lqmm.Rd | 7 - man/report.merModLmerTest.Rd | 7 - man/report.rlm.Rd | 7 - man/report.rq.Rd | 7 - man/set_noms.Rd |only 25 files changed, 135 insertions(+), 266 deletions(-)
Title: Create Cartograms with R
Description: Construct continuous and non-contiguous area cartograms.
Author: Sebastian Jeworutzki [aut, cre]
(<https://orcid.org/0000-0002-2671-5253>),
Timothee Giraud [ctb],
Nicolas Lambert [ctb],
Roger Bivand [cph],
Edzer Pebesma [cph],
Jakub Nowosad [ctb] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>
Diff between cartogram versions 0.0.3 dated 2018-05-22 and 0.1.0 dated 2018-06-21
cartogram-0.0.3/cartogram/R/cartogram.R |only cartogram-0.0.3/cartogram/R/nc_cartogram.R |only cartogram-0.1.0/cartogram/DESCRIPTION | 12 - cartogram-0.1.0/cartogram/MD5 | 25 ++- cartogram-0.1.0/cartogram/NAMESPACE | 13 + cartogram-0.1.0/cartogram/NEWS |only cartogram-0.1.0/cartogram/R/cartogram_cont.R |only cartogram-0.1.0/cartogram/R/cartogram_dorling.R |only cartogram-0.1.0/cartogram/R/cartogram_ncont.R |only cartogram-0.1.0/cartogram/README.md | 160 ++++++++++++++------- cartogram-0.1.0/cartogram/man/cartogram.Rd | 74 +-------- cartogram-0.1.0/cartogram/man/cartogram_cont.Rd |only cartogram-0.1.0/cartogram/man/cartogram_dorling.Rd |only cartogram-0.1.0/cartogram/man/cartogram_ncont.Rd |only cartogram-0.1.0/cartogram/man/checkPolygonsGEOS.Rd | 3 cartogram-0.1.0/cartogram/man/figures |only cartogram-0.1.0/cartogram/man/nc_cartogram.Rd | 59 +------ 17 files changed, 168 insertions(+), 178 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889> and Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>,
Ernst Wit [ctb],
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.50 dated 2018-05-20 and 2.51 dated 2018-06-21
DESCRIPTION | 10 ++-- MD5 | 38 ++++++++++------- NEWS | 4 + R/bdgraph.R | 12 ++++- R/bdgraph.mpl.R | 3 - R/bdgraph.npn.R | 9 +++- R/bdgraph.sim.R | 38 +++++++++++------ R/bdgraph.ts.R | 4 + R/plinks.R | 2 R/rgcwish.R | 30 ++++++++----- R/rgwish.R | 27 ++++++------ build |only inst/doc |only man/BDgraph-package.Rd | 4 - man/bdgraph.npn.Rd | 106 ++++++++++++++++++++++++------------------------- man/rgcwish.Rd | 5 +- man/rgwish.Rd | 5 +- src/BDgraph_init.c | 2 src/copula.cpp | 48 +++++++++++----------- vignettes |only 20 files changed, 196 insertions(+), 151 deletions(-)
Title: Bivariate Angular Mixture Models
Description: Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions. Chakraborty and Wong (2017) <arXiv:1708.07804> .
Author: Saptarshi Chakraborty,
Samuel W.K. Wong
Maintainer: Saptarshi Chakraborty <chakra.saptarshi@gmail.com>
Diff between BAMBI versions 1.2.1 dated 2018-04-20 and 2.0.0 dated 2018-06-21
BAMBI-1.2.1/BAMBI/R/all_contour_fns.R |only BAMBI-1.2.1/BAMBI/R/basic_hmc.R |only BAMBI-1.2.1/BAMBI/R/bounded_hmc_modified.r |only BAMBI-1.2.1/BAMBI/R/sysdata.rda |only BAMBI-1.2.1/BAMBI/R/temp_fns.R |only BAMBI-1.2.1/BAMBI/R/utilities.r |only BAMBI-1.2.1/BAMBI/man/WAIC.Rd |only BAMBI-1.2.1/BAMBI/man/densityplot1d.Rd |only BAMBI-1.2.1/BAMBI/man/densityplot2d.Rd |only BAMBI-1.2.1/BAMBI/man/fit_stepwise_bivariate.Rd |only BAMBI-1.2.1/BAMBI/man/fit_stepwise_univariate.Rd |only BAMBI-1.2.1/BAMBI/src/thread_num.h |only BAMBI-2.0.0/BAMBI/DESCRIPTION | 18 BAMBI-2.0.0/BAMBI/MD5 | 154 +- BAMBI-2.0.0/BAMBI/NAMESPACE | 40 BAMBI-2.0.0/BAMBI/R/BAMBI.R | 46 BAMBI-2.0.0/BAMBI/R/RcppExports.R | 168 +- BAMBI-2.0.0/BAMBI/R/all_diagnostics.R | 656 ++++++---- BAMBI-2.0.0/BAMBI/R/all_model_plots.R |only BAMBI-2.0.0/BAMBI/R/all_model_select.R | 506 +++++-- BAMBI-2.0.0/BAMBI/R/all_postprodn_fns.R | 1487 +++++++++++++++++------ BAMBI-2.0.0/BAMBI/R/all_vm_fns.R | 903 +------------ BAMBI-2.0.0/BAMBI/R/all_vmcos_fns.R | 1382 +++++++-------------- BAMBI-2.0.0/BAMBI/R/all_vmsin_fns.R | 1396 ++++++--------------- BAMBI-2.0.0/BAMBI/R/all_wnorm2_fns.R | 1074 ++-------------- BAMBI-2.0.0/BAMBI/R/all_wnorm_fns.R | 906 +------------- BAMBI-2.0.0/BAMBI/R/basic_fns.R | 90 + BAMBI-2.0.0/BAMBI/R/bounded_hmc_biv.R |only BAMBI-2.0.0/BAMBI/R/bounded_rmwh_biv.R |only BAMBI-2.0.0/BAMBI/R/circ_cor.R | 69 - BAMBI-2.0.0/BAMBI/R/data.R | 11 BAMBI-2.0.0/BAMBI/R/fit_mixmodel.R |only BAMBI-2.0.0/BAMBI/R/process_startpar.R |only BAMBI-2.0.0/BAMBI/R/vmstart.R | 22 BAMBI-2.0.0/BAMBI/R/wnormstart.R | 12 BAMBI-2.0.0/BAMBI/R/wrap_angles.R |only BAMBI-2.0.0/BAMBI/data/wind.rda |binary BAMBI-2.0.0/BAMBI/man/AIC.angmcmc.Rd | 22 BAMBI-2.0.0/BAMBI/man/DIC.Rd | 10 BAMBI-2.0.0/BAMBI/man/add_burnin_thin.Rd |only BAMBI-2.0.0/BAMBI/man/as.mcmc.list.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/bestmodel.Rd | 10 BAMBI-2.0.0/BAMBI/man/bridge_sampler.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/circ_cor.Rd | 3 BAMBI-2.0.0/BAMBI/man/circ_varcor_model.Rd | 22 BAMBI-2.0.0/BAMBI/man/contour.angmcmc.Rd | 26 BAMBI-2.0.0/BAMBI/man/contour_model.Rd |only BAMBI-2.0.0/BAMBI/man/d_fitted.Rd | 18 BAMBI-2.0.0/BAMBI/man/densityplot.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/extractsamples.Rd | 21 BAMBI-2.0.0/BAMBI/man/fit_angmix.Rd |only BAMBI-2.0.0/BAMBI/man/fit_incremental_angmix.Rd |only BAMBI-2.0.0/BAMBI/man/fit_vmcosmix.Rd | 68 - BAMBI-2.0.0/BAMBI/man/fit_vmmix.Rd | 66 - BAMBI-2.0.0/BAMBI/man/fit_vmsinmix.Rd | 68 - BAMBI-2.0.0/BAMBI/man/fit_wnorm2mix.Rd | 79 - BAMBI-2.0.0/BAMBI/man/fit_wnormmix.Rd | 71 - BAMBI-2.0.0/BAMBI/man/fix_label.Rd | 26 BAMBI-2.0.0/BAMBI/man/is.angmcmc.Rd | 9 BAMBI-2.0.0/BAMBI/man/latent_allocation.Rd |only BAMBI-2.0.0/BAMBI/man/logLik.angmcmc.Rd | 25 BAMBI-2.0.0/BAMBI/man/loo.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/lpdtrace.Rd | 23 BAMBI-2.0.0/BAMBI/man/paramtrace.Rd | 21 BAMBI-2.0.0/BAMBI/man/plot.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/pointest.Rd | 17 BAMBI-2.0.0/BAMBI/man/quantile.angmcmc.Rd | 13 BAMBI-2.0.0/BAMBI/man/rvm.Rd | 4 BAMBI-2.0.0/BAMBI/man/rvmcos.Rd | 24 BAMBI-2.0.0/BAMBI/man/rvmcosmix.Rd | 10 BAMBI-2.0.0/BAMBI/man/rvmmix.Rd | 4 BAMBI-2.0.0/BAMBI/man/rvmsin.Rd | 21 BAMBI-2.0.0/BAMBI/man/rvmsinmix.Rd | 8 BAMBI-2.0.0/BAMBI/man/rwnorm.Rd | 4 BAMBI-2.0.0/BAMBI/man/rwnorm2.Rd | 10 BAMBI-2.0.0/BAMBI/man/rwnorm2mix.Rd | 8 BAMBI-2.0.0/BAMBI/man/rwnormmix.Rd | 4 BAMBI-2.0.0/BAMBI/man/select_chains.Rd |only BAMBI-2.0.0/BAMBI/man/summary.angmcmc.Rd | 18 BAMBI-2.0.0/BAMBI/man/surface_model.Rd |only BAMBI-2.0.0/BAMBI/man/tim8.Rd | 4 BAMBI-2.0.0/BAMBI/man/waic.angmcmc.Rd |only BAMBI-2.0.0/BAMBI/man/wind.Rd | 7 BAMBI-2.0.0/BAMBI/man/zero_to_2pi.Rd |only BAMBI-2.0.0/BAMBI/src/Makevars | 6 BAMBI-2.0.0/BAMBI/src/Makevars.win | 6 BAMBI-2.0.0/BAMBI/src/RcppExports.cpp | 641 ++++----- BAMBI-2.0.0/BAMBI/src/basic_c_fns.cpp | 26 BAMBI-2.0.0/BAMBI/src/univm_llik_grad.cpp | 205 ++- BAMBI-2.0.0/BAMBI/src/univmgen.h | 78 - BAMBI-2.0.0/BAMBI/src/uniwnorm_llik_grad.cpp | 262 ++-- BAMBI-2.0.0/BAMBI/src/vmcos_llik_grad.cpp | 600 ++++++--- BAMBI-2.0.0/BAMBI/src/vmsin_llik_grad.cpp | 691 ++++++++-- BAMBI-2.0.0/BAMBI/src/wnorm2_llik_grad.cpp | 289 +++- 94 files changed, 5724 insertions(+), 6764 deletions(-)
Title: Read Untidy Excel Files
Description: Imports non-tabular from Excel files into R. Exposes cell content,
position and formatting in a tidy structure for further manipulation.
Tokenizes Excel formulas. Supports '.xlsx' and '.xlsm' via the embedded
'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Does not support
'.xlsb' or '.xls'.
Author: Duncan Garmonsway [aut, cre],
Hadley Wickham [ctb] (Author of included readxl fragments),
Jenny Bryan [ctb] (Author of included readxl fragments),
RStudio [cph] (Copyright holder of included readxl fragments),
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code)
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between tidyxl versions 1.0.1 dated 2018-03-26 and 1.0.3 dated 2018-06-21
DESCRIPTION | 8 +- MD5 | 62 +++++++++-------- NEWS.md | 16 ++++ R/RcppExports.R | 4 - R/tidy_xlsx.R | 2 R/xlsx_cells.R | 12 ++- README.md | 122 +++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/data-validation-rules.html | 24 +++--- inst/doc/smells.html | 6 - inst/doc/tidyxl.html | 72 ++++++++++---------- man/xlsx_cells.Rd | 10 ++ src/RcppExports.cpp | 9 +- src/date.h | 9 ++ src/ref_grammar.h | 40 ++++++++++- src/string.h | 2 src/tidyxl.cpp | 6 + src/xlsxbook.cpp | 33 +++++++-- src/xlsxbook.h | 7 +- src/xlsxcell.cpp | 7 ++ src/xlsxcell.h | 6 + src/xlsxsheet.cpp | 64 +++++++++++++----- src/xlsxsheet.h | 4 - src/xlsxstyles.cpp | 28 +++++--- src/xlsxstyles.h | 2 tests/testthat/formulas.xlsx |binary tests/testthat/phonetic.xlsx |only tests/testthat/test-formats.R | 4 + tests/testthat/test-inline-strings.R | 5 + tests/testthat/test-is_date_format.R | 1 tests/testthat/test-shared-formula.R | 2 tests/testthat/test-xlsx_cells.R | 10 ++ tests/testthat/themes-2016.xlsx |only 33 files changed, 380 insertions(+), 197 deletions(-)
Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre],
Daniel Graeber [aut, ctb],
Stefan Preiner [ctb],
Renata Pinto [ctb],
Nora Maria Zechmeister [ctb],
Christoph Zechmeister [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>
Diff between staRdom versions 1.0.5 dated 2018-05-02 and 1.0.8 dated 2018-06-21
staRdom-1.0.5/staRdom/vignettes/PARAFAC_analysis_of_EEM_files |only staRdom-1.0.8/staRdom/DESCRIPTION | 20 staRdom-1.0.8/staRdom/MD5 | 122 +-- staRdom-1.0.8/staRdom/NAMESPACE | 25 staRdom-1.0.8/staRdom/R/absorption_functions.R | 73 + staRdom-1.0.8/staRdom/R/correction_functions.R | 6 staRdom-1.0.8/staRdom/R/data_check.R |only staRdom-1.0.8/staRdom/R/globals.R | 5 staRdom-1.0.8/staRdom/R/parafac_functions.R | 385 ++++++++-- staRdom-1.0.8/staRdom/R/parafac_plot_functions.R | 100 +- staRdom-1.0.8/staRdom/README | 17 staRdom-1.0.8/staRdom/build/vignette.rds |binary staRdom-1.0.8/staRdom/data/abs_data.rda |binary staRdom-1.0.8/staRdom/data/blank.rda |binary staRdom-1.0.8/staRdom/data/eem_list.rda |binary staRdom-1.0.8/staRdom/data/pfres_comps1.rda |binary staRdom-1.0.8/staRdom/data/pfres_comps2.rda |binary staRdom-1.0.8/staRdom/data/sh.rda |binary staRdom-1.0.8/staRdom/inst/EEM_simple_analysis.Rmd | 196 ++--- staRdom-1.0.8/staRdom/inst/PARAFAC_report.Rmd |only staRdom-1.0.8/staRdom/inst/doc/Basic_analysis_of_DOM_samples.R | 38 staRdom-1.0.8/staRdom/inst/doc/Basic_analysis_of_DOM_samples.Rmd | 42 - staRdom-1.0.8/staRdom/inst/doc/Basic_analysis_of_DOM_samples.html | 16 staRdom-1.0.8/staRdom/inst/doc/PARAFAC_analysis_of_EEM.R | 21 staRdom-1.0.8/staRdom/inst/doc/PARAFAC_analysis_of_EEM.Rmd | 70 + staRdom-1.0.8/staRdom/inst/doc/PARAFAC_analysis_of_EEM.html | 167 +++- staRdom-1.0.8/staRdom/man/A_missing.Rd | 4 staRdom-1.0.8/staRdom/man/abs_parms.Rd | 2 staRdom-1.0.8/staRdom/man/absorbance_read.Rd | 13 staRdom-1.0.8/staRdom/man/eem_absdil.Rd |only staRdom-1.0.8/staRdom/man/eem_checkdata.Rd |only staRdom-1.0.8/staRdom/man/eem_corrections.Rd |only staRdom-1.0.8/staRdom/man/eem_dilcorr.Rd |only staRdom-1.0.8/staRdom/man/eem_duplicates.Rd |only staRdom-1.0.8/staRdom/man/eem_eemdil.Rd |only staRdom-1.0.8/staRdom/man/eem_is.na.Rd |only staRdom-1.0.8/staRdom/man/eem_metatemplate.Rd |only staRdom-1.0.8/staRdom/man/eem_parafac.Rd | 8 staRdom-1.0.8/staRdom/man/eempf4analysis.Rd |only staRdom-1.0.8/staRdom/man/eempf_comp_load_plot.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_comp_mat.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_comps3D.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_corcondia.Rd |only staRdom-1.0.8/staRdom/man/eempf_corplot.Rd | 8 staRdom-1.0.8/staRdom/man/eempf_cortable.Rd | 6 staRdom-1.0.8/staRdom/man/eempf_eemqual.Rd |only staRdom-1.0.8/staRdom/man/eempf_export.Rd |only staRdom-1.0.8/staRdom/man/eempf_leverage.Rd | 8 staRdom-1.0.8/staRdom/man/eempf_load_plot.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_mleverage.Rd |only staRdom-1.0.8/staRdom/man/eempf_openfluor.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_report.Rd |only staRdom-1.0.8/staRdom/man/eempf_rescaleBC.Rd |only staRdom-1.0.8/staRdom/man/eempf_residuals.Rd | 4 staRdom-1.0.8/staRdom/man/eempf_residuals_plot.Rd | 4 staRdom-1.0.8/staRdom/man/maxlines.Rd | 4 staRdom-1.0.8/staRdom/man/norm2A.Rd | 4 staRdom-1.0.8/staRdom/man/splithalf.Rd | 3 staRdom-1.0.8/staRdom/vignettes/Basic_analysis_of_DOM_samples.Rmd | 42 - staRdom-1.0.8/staRdom/vignettes/PARAFAC_analysis_of_EEM.Rmd | 70 + 60 files changed, 1039 insertions(+), 464 deletions(-)
Title: R Source Code Similarity Evaluation
Description: An Implementation of a novel method to determine similarity of R
functions based on program dependence graphs,
see Bartoszuk, Gagolewski (2017) <doi:10.1109/FUZZ-IEEE.2017.8015582>.
Possible use cases include
plagiarism detection among students' homework assignments.
Author: Maciej Bartoszuk [aut, cre],
Marek Gagolewski [aut]
Maintainer: Maciej Bartoszuk <bartoszuk@rexamine.com>
Diff between SimilaR versions 1.0.1 dated 2018-04-12 and 1.0.2 dated 2018-06-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/postprocessingPDG.cpp | 28 +++++++++++++++++++++++++--- 3 files changed, 31 insertions(+), 9 deletions(-)
Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.2.5 dated 2018-06-18 and 1.2.6 dated 2018-06-21
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NEWS.md | 27 +++++++++++++++------------ R/casti.R | 6 ++++-- R/kraje.R | 7 ++++--- R/obce_body.R | 6 ++++-- R/obce_polygony.R | 6 ++++-- R/okresy.R | 7 ++++--- R/orp_polygony.R | 6 ++++-- R/plochy.R | 6 ++++-- R/reky.R | 6 ++++-- R/republika.R | 7 ++++--- build/vignette.rds |binary inst/doc/vignette.html | 8 ++++---- man/casti.Rd | 5 ++++- man/kraje.Rd | 4 +++- man/obce_body.Rd | 5 ++++- man/obce_polygony.Rd | 5 ++++- man/okresy.Rd | 4 +++- man/orp_polygony.Rd | 5 ++++- man/plochy.Rd | 5 ++++- man/reky.Rd | 5 ++++- man/republika.Rd | 4 +++- 23 files changed, 114 insertions(+), 72 deletions(-)
Title: Call Google's 'Natural Language' API, 'Cloud Translation' API,
'Cloud Speech' API and 'Cloud Text-to-Speech' API
Description: Call 'Google Cloud' machine learning APIs for text and speech tasks.
Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection
and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to
analyse text for sentiment, entities or syntax, the 'Cloud Speech' API
<https://cloud.google.com/speech/> to transcribe sound files to text and
the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech/> to turn text
into sound files.
Author: Mark Edmondson [aut, cre],
Neal Richardson [rev] (Neal reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/127>),
Julia Gustavsen [rev] (Julia reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/127>)
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between googleLanguageR versions 0.1.1 dated 2017-11-16 and 0.2.0 dated 2018-06-21
googleLanguageR-0.1.1/googleLanguageR/R/speech.R |only googleLanguageR-0.1.1/googleLanguageR/inst/shiny/capture_speech/transcript_audio20170917235209.wav.rds |only googleLanguageR-0.1.1/googleLanguageR/tests/language.googleapis.com/v1/documents-annotateText-45bb10-POST.json |only googleLanguageR-0.1.1/googleLanguageR/tests/language.googleapis.com/v1/documents-annotateText-89db45-POST.json |only googleLanguageR-0.1.1/googleLanguageR/tests/speech.googleapis.com/v1/operations/2906884386074202099.json |only googleLanguageR-0.1.1/googleLanguageR/tests/speech.googleapis.com/v1/operations/6393897230496725322.json |only googleLanguageR-0.1.1/googleLanguageR/tests/speech.googleapis.com/v1/speech-longrunningrecognize-e400d0-POST.json |only googleLanguageR-0.1.1/googleLanguageR/tests/translation.googleapis.com/language/translate/v2-04272d-POST.json |only googleLanguageR-0.2.0/googleLanguageR/DESCRIPTION | 31 googleLanguageR-0.2.0/googleLanguageR/MD5 | 111 - googleLanguageR-0.2.0/googleLanguageR/NAMESPACE | 7 googleLanguageR-0.2.0/googleLanguageR/NEWS.md | 10 googleLanguageR-0.2.0/googleLanguageR/R/auth.R | 3 googleLanguageR-0.2.0/googleLanguageR/R/natural-language.R | 56 googleLanguageR-0.2.0/googleLanguageR/R/options.R | 6 googleLanguageR-0.2.0/googleLanguageR/R/speech-to-text.R |only googleLanguageR-0.2.0/googleLanguageR/R/text-to-speech.R |only googleLanguageR-0.2.0/googleLanguageR/R/utilities.R | 27 googleLanguageR-0.2.0/googleLanguageR/R/version.R | 10 googleLanguageR-0.2.0/googleLanguageR/README.md | 64 googleLanguageR-0.2.0/googleLanguageR/build/vignette.rds |binary googleLanguageR-0.2.0/googleLanguageR/inst/OSR_us_000_0010_8k.wav |only googleLanguageR-0.2.0/googleLanguageR/inst/doc/nlp.Rmd | 145 + googleLanguageR-0.2.0/googleLanguageR/inst/doc/nlp.html | 144 + googleLanguageR-0.2.0/googleLanguageR/inst/doc/setup.html | 4 googleLanguageR-0.2.0/googleLanguageR/inst/doc/speech.Rmd | 2 googleLanguageR-0.2.0/googleLanguageR/inst/doc/speech.html | 6 googleLanguageR-0.2.0/googleLanguageR/inst/doc/text-to-speech.Rmd |only googleLanguageR-0.2.0/googleLanguageR/inst/doc/text-to-speech.html |only googleLanguageR-0.2.0/googleLanguageR/inst/doc/translation.html | 4 googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/DESCRIPTION |only googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/README.html |only googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/README.md |only googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/babelfish.png |only googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/server.R | 215 ++ googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/ui.R | 74 googleLanguageR-0.2.0/googleLanguageR/inst/shiny/capture_speech/www |only googleLanguageR-0.2.0/googleLanguageR/man/gl_nlp.Rd | 11 googleLanguageR-0.2.0/googleLanguageR/man/gl_speech.Rd | 17 googleLanguageR-0.2.0/googleLanguageR/man/gl_speech_op.Rd | 2 googleLanguageR-0.2.0/googleLanguageR/man/gl_talk.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/gl_talk_languages.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/gl_talk_player.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/gl_talk_shiny.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/gl_talk_shinyUI.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/is.NullOb.Rd |only googleLanguageR-0.2.0/googleLanguageR/man/rmNullObs.Rd |only googleLanguageR-0.2.0/googleLanguageR/tests/language.googleapis.com/v1/documents-annotateText-5215d5-POST.json |only googleLanguageR-0.2.0/googleLanguageR/tests/language.googleapis.com/v1/documents-annotateText-d934c2-POST.json |only googleLanguageR-0.2.0/googleLanguageR/tests/language.googleapis.com/v1beta2 |only googleLanguageR-0.2.0/googleLanguageR/tests/speech.googleapis.com/v1/operations/361795619675526592.json |only googleLanguageR-0.2.0/googleLanguageR/tests/speech.googleapis.com/v1/operations/4349743851081799845.json |only googleLanguageR-0.2.0/googleLanguageR/tests/speech.googleapis.com/v1/operations/7105741293011753800.json |only googleLanguageR-0.2.0/googleLanguageR/tests/speech.googleapis.com/v1/speech-longrunningrecognize-ae1b66-POST.json | 2 googleLanguageR-0.2.0/googleLanguageR/tests/speech.googleapis.com/v1/speech-recognize-e400d0-POST.json | 210 +- googleLanguageR-0.2.0/googleLanguageR/tests/testthat/output.wav |only googleLanguageR-0.2.0/googleLanguageR/tests/testthat/prep_tests.R |only googleLanguageR-0.2.0/googleLanguageR/tests/testthat/test_integration.R | 115 - googleLanguageR-0.2.0/googleLanguageR/tests/testthat/test_unit.R | 151 - googleLanguageR-0.2.0/googleLanguageR/tests/texttospeech.googleapis.com |only googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2-36b63d-POST.json | 16 googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2-a43ef9-POST.json | 16 googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2/detect-b110ba-POST.json | 36 googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2/detect-c6a946-POST.json | 22 googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2/languages-10be03.json | 840 +++++----- googleLanguageR-0.2.0/googleLanguageR/tests/translation.googleapis.com/language/translate/v2/languages-bfb420.json | 840 +++++----- googleLanguageR-0.2.0/googleLanguageR/vignettes/nlp.Rmd | 145 + googleLanguageR-0.2.0/googleLanguageR/vignettes/speech.Rmd | 2 googleLanguageR-0.2.0/googleLanguageR/vignettes/text-to-speech.Rmd |only 69 files changed, 1925 insertions(+), 1419 deletions(-)
More information about googleLanguageR at CRAN
Permanent link
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut],
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.3 dated 2018-04-11 and 8.4 dated 2018-06-21
forecast-8.3/forecast/inst/doc/JSS2008.pdf |only forecast-8.4/forecast/DESCRIPTION | 8 forecast-8.4/forecast/MD5 | 73 ++++---- forecast-8.4/forecast/NAMESPACE | 7 forecast-8.4/forecast/NEWS.md | 6 forecast-8.4/forecast/R/arima.R | 8 forecast-8.4/forecast/R/attach.R | 40 ++++ forecast-8.4/forecast/R/checkresiduals.R | 13 - forecast-8.4/forecast/R/data.R | 5 forecast-8.4/forecast/R/ets.R | 15 + forecast-8.4/forecast/R/ggplot.R | 25 --- forecast-8.4/forecast/R/lm.R | 1 forecast-8.4/forecast/R/modelAR.R |only forecast-8.4/forecast/R/mstl.R | 4 forecast-8.4/forecast/R/newarima2.R | 20 +- forecast-8.4/forecast/R/nnetar.R | 150 +++++++++++------- forecast-8.4/forecast/R/simulate.R | 124 ++++++++++++++ forecast-8.4/forecast/R/unitRoot.R | 2 forecast-8.4/forecast/build/vignette.rds |binary forecast-8.4/forecast/inst/CITATION | 2 forecast-8.4/forecast/inst/doc/JSS2008.html |only forecast-8.4/forecast/man/autolayer.Rd | 10 - forecast-8.4/forecast/man/checkresiduals.Rd | 8 forecast-8.4/forecast/man/ets.Rd | 7 forecast-8.4/forecast/man/fitted.Arima.Rd | 5 forecast-8.4/forecast/man/forecast.modelAR.Rd |only forecast-8.4/forecast/man/forecast.nnetar.Rd | 26 ++- forecast-8.4/forecast/man/geom_forecast.Rd | 2 forecast-8.4/forecast/man/gold.Rd | 3 forecast-8.4/forecast/man/is.ets.Rd | 5 forecast-8.4/forecast/man/modelAR.Rd |only forecast-8.4/forecast/man/reexports.Rd | 6 forecast-8.4/forecast/man/simulate.ets.Rd | 5 forecast-8.4/forecast/man/wineind.Rd | 2 forecast-8.4/forecast/man/woolyrnq.Rd | 2 forecast-8.4/forecast/tests/testthat/Rplots.pdf |only forecast-8.4/forecast/tests/testthat/test-arima.R | 31 +++ forecast-8.4/forecast/tests/testthat/test-modelAR.R |only forecast-8.4/forecast/tests/testthat/test-newarima2.R | 12 + forecast-8.4/forecast/tests/testthat/test-nnetar.R | 18 ++ forecast-8.4/forecast/tests/testthat/test-thetaf.R | 2 41 files changed, 483 insertions(+), 164 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on
the Fisher information. Provides flexible functions for building joint PDFs,
evaluating the Fisher information and finding optimal designs. It includes an
extensible solution to summation and integration called 'nint', functions for
transforming, plotting and comparing designs, as well as a set of tools for
common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.3.4 dated 2018-06-19 and 0.3.5 dated 2018-06-21
DESCRIPTION | 8 ++--- MD5 | 13 ++++---- NAMESPACE | 1 R/base.R | 81 ++++++++++++++++++++++++++++++++++++++++++++-------- R/main.R | 58 ++++++++++++++++++++++++++++++++----- man/grow.grid.Rd |only man/update.param.Rd | 5 ++- src/base.c | 2 - 8 files changed, 137 insertions(+), 31 deletions(-)
Title: Tools for Cleaning Up Messy Files
Description: Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between thinkr versions 0.11 dated 2018-02-20 and 0.13 dated 2018-06-21
thinkr-0.11/thinkr/man/export_xl.Rd |only thinkr-0.13/thinkr/DESCRIPTION | 17 - thinkr-0.13/thinkr/MD5 | 19 - thinkr-0.13/thinkr/NAMESPACE | 12 - thinkr-0.13/thinkr/R/all_ggplot_to_docx.R | 43 ++- thinkr-0.13/thinkr/R/clean_names.R | 1 thinkr-0.13/thinkr/R/efface_test.R | 1 thinkr-0.13/thinkr/R/from_excel_to_posixt.R | 5 thinkr-0.13/thinkr/R/xlsx.plusieurs.R | 214 +++++++++---------- thinkr-0.13/thinkr/man/from_excel_to_posixt.Rd | 4 thinkr-0.13/thinkr/tests/testthat/test-clean_names.R | 1 11 files changed, 165 insertions(+), 152 deletions(-)
Title: Interface for 'GraphFrames'
Description: A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R
interface for 'GraphFrames' <https://graphframes.github.io/>. 'GraphFrames' is a package
for 'Apache Spark' that provides a DataFrame-based API for working with graphs. Functionality
includes motif finding and common graph algorithms, such as PageRank and Breadth-first
search.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>
Diff between graphframes versions 0.1.0 dated 2018-04-06 and 0.1.1 dated 2018-06-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 4 ++-- tests/testthat/output/gf_pagerank.txt | 2 +- tests/testthat/output/gf_triangle_count.txt | 14 +++++++------- 5 files changed, 18 insertions(+), 18 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Stephen Hoover [ctb],
Danning Chen [ctb],
Elizabeth Sander [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.4.0 dated 2018-05-06 and 1.5.0 dated 2018-06-21
DESCRIPTION | 6 MD5 | 819 +-- NAMESPACE | 3 R/civis_future.R | 11 R/generate_client.R | 8 R/generated_client.R | 4698 +++++++++--------- R/io.R | 36 R/sysdata.rda |binary R/zzz.R | 2 man/CivisFuture.Rd | 32 man/apps_delete_instances_projects.Rd | 4 man/apps_get.Rd | 4 man/apps_get_instances.Rd | 4 man/apps_get_releases.Rd | 2 man/apps_list_instances.Rd | 6 man/apps_list_instances_projects.Rd | 8 man/apps_list_instances_shares.Rd | 6 man/apps_list_releases.Rd | 4 man/apps_patch_instances.Rd | 4 man/apps_post_instances.Rd | 4 man/apps_put_instances_archive.Rd | 4 man/apps_put_instances_projects.Rd | 4 man/apps_put_instances_shares_groups.Rd | 6 man/apps_put_instances_shares_users.Rd | 6 man/cancel.Rd | 2 man/clusters_get_kubernetes.Rd | 11 man/clusters_get_kubernetes_partitions.Rd |only man/clusters_list_kubernetes.Rd | 11 man/clusters_list_kubernetes_partitions.Rd |only man/clusters_list_workers_active_jobs.Rd | 8 man/clusters_list_workers_queued_jobs.Rd | 8 man/credentials_get.Rd | 1 man/credentials_list.Rd | 1 man/credentials_list_shares.Rd | 6 man/credentials_post.Rd | 5 man/credentials_post_authenticate.Rd | 3 man/credentials_put.Rd | 6 man/credentials_put_shares_groups.Rd | 6 man/credentials_put_shares_users.Rd | 6 man/databases_list_tables.Rd | 2 man/databases_list_tables_search.Rd | 2 man/enhancements_delete_cass_ncoa_projects.Rd | 4 man/enhancements_delete_person_matching_projects.Rd | 4 man/enhancements_get_cass_ncoa.Rd | 28 man/enhancements_list.Rd | 14 man/enhancements_list_cass_ncoa_projects.Rd | 8 man/enhancements_list_cass_ncoa_runs_outputs.Rd | 6 man/enhancements_list_cass_ncoa_shares.Rd | 6 man/enhancements_list_field_mapping.Rd |only man/enhancements_list_person_matching_projects.Rd | 8 man/enhancements_list_person_matching_shares.Rd | 6 man/enhancements_patch_cass_ncoa.Rd | 50 man/enhancements_post_cass_ncoa.Rd | 50 man/enhancements_put_cass_ncoa.Rd | 50 man/enhancements_put_cass_ncoa_archive.Rd | 28 man/enhancements_put_cass_ncoa_projects.Rd | 4 man/enhancements_put_cass_ncoa_shares_groups.Rd | 6 man/enhancements_put_cass_ncoa_shares_users.Rd | 6 man/enhancements_put_person_matching_archive.Rd | 22 man/enhancements_put_person_matching_projects.Rd | 4 man/enhancements_put_person_matching_shares_groups.Rd | 6 man/enhancements_put_person_matching_shares_users.Rd | 6 man/exports_list.Rd | 8 man/files_delete_projects.Rd | 4 man/files_get.Rd | 4 man/files_list_projects.Rd | 8 man/files_list_shares.Rd | 6 man/files_post.Rd | 4 man/files_post_multipart.Rd | 2 man/files_post_multipart_complete.Rd | 2 man/files_put_projects.Rd | 4 man/files_put_shares_groups.Rd | 6 man/files_put_shares_users.Rd | 6 man/imports_delete_projects.Rd | 4 man/imports_get.Rd | 28 man/imports_get_batches.Rd | 2 man/imports_list.Rd | 26 man/imports_list_batches.Rd | 2 man/imports_list_projects.Rd | 8 man/imports_list_shares.Rd | 6 man/imports_post.Rd | 48 man/imports_post_batches.Rd | 4 man/imports_post_files.Rd | 8 man/imports_post_syncs.Rd | 12 man/imports_put.Rd | 46 man/imports_put_archive.Rd | 28 man/imports_put_projects.Rd | 4 man/imports_put_shares_groups.Rd | 6 man/imports_put_shares_users.Rd | 6 man/imports_put_syncs.Rd | 12 man/imports_put_syncs_archive.Rd | 6 man/jobs_delete_projects.Rd | 4 man/jobs_get.Rd | 18 man/jobs_list.Rd | 24 man/jobs_list_children.Rd | 2 man/jobs_list_parents.Rd | 18 man/jobs_list_projects.Rd | 8 man/jobs_list_shares.Rd | 6 man/jobs_list_workflows.Rd | 18 man/jobs_put_projects.Rd | 4 man/jobs_put_shares_groups.Rd | 6 man/jobs_put_shares_users.Rd | 6 man/media_get_optimizations.Rd | 6 man/media_get_ratecards.Rd | 2 man/media_get_spot_orders.Rd | 2 man/media_list_optimizations.Rd | 6 man/media_list_optimizations_shares.Rd | 6 man/media_list_ratecards.Rd | 4 man/media_list_ratecards_shares.Rd | 6 man/media_list_spot_orders.Rd | 4 man/media_list_spot_orders_shares.Rd | 6 man/media_patch_optimizations.Rd | 8 man/media_patch_ratecards.Rd | 2 man/media_post_optimizations.Rd | 8 man/media_post_optimizations_clone.Rd | 6 man/media_post_ratecards.Rd | 2 man/media_post_spot_orders.Rd | 2 man/media_put_optimizations_archive.Rd | 6 man/media_put_optimizations_shares_groups.Rd | 6 man/media_put_optimizations_shares_users.Rd | 6 man/media_put_ratecards.Rd | 2 man/media_put_ratecards_archive.Rd | 2 man/media_put_ratecards_shares_groups.Rd | 6 man/media_put_ratecards_shares_users.Rd | 6 man/media_put_spot_orders.Rd | 2 man/media_put_spot_orders_archive.Rd | 2 man/media_put_spot_orders_shares_groups.Rd | 6 man/media_put_spot_orders_shares_users.Rd | 6 man/models_delete_projects.Rd | 4 man/models_get.Rd | 26 man/models_list.Rd | 24 man/models_list_projects.Rd | 8 man/models_list_schedules.Rd | 12 man/models_list_shares.Rd | 6 man/models_patch.Rd | 16 man/models_post.Rd | 44 man/models_put_archive.Rd | 26 man/models_put_predictions.Rd | 24 man/models_put_projects.Rd | 4 man/models_put_schedules.Rd | 24 man/models_put_shares_groups.Rd | 6 man/models_put_shares_users.Rd | 6 man/notebooks_delete_projects.Rd | 4 man/notebooks_get.Rd | 12 man/notebooks_get_deployments.Rd | 2 man/notebooks_get_git_commits.Rd | 2 man/notebooks_list.Rd | 10 man/notebooks_list_git.Rd | 4 man/notebooks_list_git_commits.Rd | 2 man/notebooks_list_projects.Rd | 8 man/notebooks_list_shares.Rd | 6 man/notebooks_patch.Rd | 14 man/notebooks_post.Rd | 16 man/notebooks_post_clone.Rd | 12 man/notebooks_post_deployments.Rd | 2 man/notebooks_post_git_commits.Rd | 2 man/notebooks_put.Rd | 14 man/notebooks_put_archive.Rd | 12 man/notebooks_put_git.Rd | 4 man/notebooks_put_projects.Rd | 4 man/notebooks_put_shares_groups.Rd | 6 man/notebooks_put_shares_users.Rd | 6 man/predictions_get.Rd | 14 man/predictions_list.Rd | 2 man/predictions_list_schedules.Rd | 12 man/predictions_patch.Rd | 14 man/predictions_put_schedules.Rd | 24 man/projects_get.Rd | 32 man/projects_list.Rd | 10 man/projects_list_shares.Rd | 6 man/projects_post.Rd | 38 man/projects_put.Rd | 36 man/projects_put_archive.Rd | 32 man/projects_put_shares_groups.Rd | 6 man/projects_put_shares_users.Rd | 6 man/queries_get.Rd | 7 man/queries_list.Rd | 5 man/queries_post.Rd | 7 man/queries_put_scripts.Rd | 7 man/reports_delete_projects.Rd | 4 man/reports_get.Rd | 12 man/reports_get_git_commits.Rd | 2 man/reports_get_services.Rd | 2 man/reports_list.Rd | 12 man/reports_list_git.Rd | 4 man/reports_list_git_commits.Rd | 2 man/reports_list_projects.Rd | 8 man/reports_list_services_shares.Rd | 6 man/reports_list_shares.Rd | 6 man/reports_list_snapshots.Rd | 12 man/reports_patch.Rd | 14 man/reports_patch_services.Rd | 2 man/reports_patch_snapshots.Rd | 24 man/reports_post.Rd | 16 man/reports_post_git_commits.Rd | 2 man/reports_post_grants.Rd | 12 man/reports_post_services.Rd | 2 man/reports_post_snapshots.Rd | 24 man/reports_put_archive.Rd | 12 man/reports_put_git.Rd | 4 man/reports_put_projects.Rd | 4 man/reports_put_services_shares_groups.Rd | 6 man/reports_put_services_shares_users.Rd | 6 man/reports_put_shares_groups.Rd | 6 man/reports_put_shares_users.Rd | 6 man/results_delete_projects.Rd | 4 man/results_get.Rd | 12 man/results_get_git_commits.Rd | 2 man/results_get_services.Rd | 2 man/results_list.Rd | 12 man/results_list_git.Rd | 4 man/results_list_git_commits.Rd | 2 man/results_list_projects.Rd | 8 man/results_list_services_shares.Rd | 6 man/results_list_shares.Rd | 6 man/results_list_snapshots.Rd | 12 man/results_patch.Rd | 14 man/results_patch_services.Rd | 2 man/results_patch_snapshots.Rd | 24 man/results_post.Rd | 16 man/results_post_git_commits.Rd | 2 man/results_post_grants.Rd | 12 man/results_post_services.Rd | 2 man/results_post_snapshots.Rd | 24 man/results_put_archive.Rd | 12 man/results_put_git.Rd | 4 man/results_put_projects.Rd | 4 man/results_put_services_shares_groups.Rd | 6 man/results_put_services_shares_users.Rd | 6 man/results_put_shares_groups.Rd | 6 man/results_put_shares_users.Rd | 6 man/scripts_delete_containers_projects.Rd | 4 man/scripts_delete_custom_projects.Rd | 4 man/scripts_delete_javascript_projects.Rd | 4 man/scripts_delete_python3_projects.Rd | 4 man/scripts_delete_r_projects.Rd | 4 man/scripts_delete_sql_projects.Rd | 4 man/scripts_get.Rd | 30 man/scripts_get_containers.Rd | 31 man/scripts_get_custom.Rd | 26 man/scripts_get_javascript.Rd | 28 man/scripts_get_javascript_git_commits.Rd | 2 man/scripts_get_python3.Rd | 31 man/scripts_get_python3_git_commits.Rd | 2 man/scripts_get_r.Rd | 31 man/scripts_get_r_git_commits.Rd | 2 man/scripts_get_sql.Rd | 32 man/scripts_get_sql_git_commits.Rd | 2 man/scripts_list.Rd | 18 man/scripts_list_containers_projects.Rd | 8 man/scripts_list_containers_runs_outputs.Rd | 6 man/scripts_list_containers_shares.Rd | 6 man/scripts_list_custom.Rd | 14 man/scripts_list_custom_projects.Rd | 8 man/scripts_list_custom_runs_outputs.Rd | 6 man/scripts_list_custom_shares.Rd | 6 man/scripts_list_javascript_git.Rd | 4 man/scripts_list_javascript_git_commits.Rd | 2 man/scripts_list_javascript_projects.Rd | 8 man/scripts_list_javascript_runs_outputs.Rd | 6 man/scripts_list_javascript_shares.Rd | 6 man/scripts_list_python3_git.Rd | 4 man/scripts_list_python3_git_commits.Rd | 2 man/scripts_list_python3_projects.Rd | 8 man/scripts_list_python3_runs_outputs.Rd | 6 man/scripts_list_python3_shares.Rd | 6 man/scripts_list_r_git.Rd | 4 man/scripts_list_r_git_commits.Rd | 2 man/scripts_list_r_projects.Rd | 8 man/scripts_list_r_runs_outputs.Rd | 6 man/scripts_list_r_shares.Rd | 6 man/scripts_list_sql_git.Rd | 4 man/scripts_list_sql_git_commits.Rd | 2 man/scripts_list_sql_projects.Rd | 8 man/scripts_list_sql_runs_outputs.Rd | 6 man/scripts_list_sql_shares.Rd | 6 man/scripts_patch.Rd | 46 man/scripts_patch_containers.Rd | 53 man/scripts_patch_custom.Rd | 42 man/scripts_patch_javascript.Rd | 44 man/scripts_patch_python3.Rd | 55 man/scripts_patch_r.Rd | 55 man/scripts_patch_sql.Rd | 50 man/scripts_post.Rd | 34 man/scripts_post_containers.Rd | 55 man/scripts_post_containers_clone.Rd | 31 man/scripts_post_containers_runs_outputs.Rd | 8 man/scripts_post_custom.Rd | 44 man/scripts_post_custom_clone.Rd | 26 man/scripts_post_custom_runs_outputs.Rd | 8 man/scripts_post_javascript.Rd | 46 man/scripts_post_javascript_clone.Rd | 28 man/scripts_post_javascript_git_commits.Rd | 2 man/scripts_post_javascript_runs_outputs.Rd | 8 man/scripts_post_python3.Rd | 55 man/scripts_post_python3_clone.Rd | 31 man/scripts_post_python3_git_commits.Rd | 2 man/scripts_post_python3_runs_outputs.Rd | 8 man/scripts_post_r.Rd | 55 man/scripts_post_r_clone.Rd | 31 man/scripts_post_r_git_commits.Rd | 2 man/scripts_post_r_runs_outputs.Rd | 8 man/scripts_post_sql.Rd | 52 man/scripts_post_sql_clone.Rd | 32 man/scripts_post_sql_git_commits.Rd | 2 man/scripts_put_containers.Rd | 55 man/scripts_put_containers_archive.Rd | 31 man/scripts_put_containers_projects.Rd | 4 man/scripts_put_containers_shares_groups.Rd | 6 man/scripts_put_containers_shares_users.Rd | 6 man/scripts_put_custom.Rd | 42 man/scripts_put_custom_archive.Rd | 26 man/scripts_put_custom_projects.Rd | 4 man/scripts_put_custom_shares_groups.Rd | 6 man/scripts_put_custom_shares_users.Rd | 6 man/scripts_put_javascript.Rd | 44 man/scripts_put_javascript_archive.Rd | 28 man/scripts_put_javascript_git.Rd | 4 man/scripts_put_javascript_projects.Rd | 4 man/scripts_put_javascript_shares_groups.Rd | 6 man/scripts_put_javascript_shares_users.Rd | 6 man/scripts_put_python3.Rd | 53 man/scripts_put_python3_archive.Rd | 31 man/scripts_put_python3_git.Rd | 4 man/scripts_put_python3_projects.Rd | 4 man/scripts_put_python3_shares_groups.Rd | 6 man/scripts_put_python3_shares_users.Rd | 6 man/scripts_put_r.Rd | 53 man/scripts_put_r_archive.Rd | 31 man/scripts_put_r_git.Rd | 4 man/scripts_put_r_projects.Rd | 4 man/scripts_put_r_shares_groups.Rd | 6 man/scripts_put_r_shares_users.Rd | 6 man/scripts_put_sql.Rd | 50 man/scripts_put_sql_archive.Rd | 32 man/scripts_put_sql_git.Rd | 4 man/scripts_put_sql_projects.Rd | 4 man/scripts_put_sql_shares_groups.Rd | 6 man/scripts_put_sql_shares_users.Rd | 6 man/search_list.Rd | 2 man/services_delete_deployments.Rd | 6 man/services_delete_projects.Rd | 8 man/services_get.Rd | 24 man/services_get_deployments.Rd | 8 man/services_list.Rd | 14 man/services_list_deployments.Rd | 6 man/services_list_projects.Rd | 12 man/services_list_shares.Rd | 6 man/services_patch.Rd | 34 man/services_post.Rd | 36 man/services_post_clone.Rd | 24 man/services_post_deployments.Rd | 8 man/services_post_redeploy.Rd | 8 man/services_put.Rd | 34 man/services_put_archive.Rd | 24 man/services_put_projects.Rd | 8 man/services_put_shares_groups.Rd | 6 man/services_put_shares_users.Rd | 6 man/tables_get.Rd | 4 man/tables_list.Rd | 2 man/tables_list_columns.Rd | 4 man/tables_patch.Rd | 6 man/tables_post_refresh.Rd | 4 man/templates_delete_scripts_projects.Rd | 4 man/templates_get_reports.Rd | 4 man/templates_get_scripts.Rd | 2 man/templates_list_reports.Rd | 4 man/templates_list_reports_shares.Rd | 6 man/templates_list_scripts.Rd | 2 man/templates_list_scripts_projects.Rd | 8 man/templates_list_scripts_shares.Rd | 6 man/templates_patch_reports.Rd | 4 man/templates_patch_scripts.Rd | 2 man/templates_post_reports.Rd | 6 man/templates_post_scripts.Rd | 4 man/templates_put_reports.Rd | 4 man/templates_put_reports_shares_groups.Rd | 6 man/templates_put_reports_shares_users.Rd | 6 man/templates_put_scripts.Rd | 2 man/templates_put_scripts_projects.Rd | 4 man/templates_put_scripts_shares_groups.Rd | 6 man/templates_put_scripts_shares_users.Rd | 6 man/users_list_me.Rd | 4 man/users_patch_me.Rd | 6 man/workflows_delete_projects.Rd | 4 man/workflows_get.Rd | 20 man/workflows_get_executions.Rd | 4 man/workflows_get_git_commits.Rd | 2 man/workflows_list.Rd | 20 man/workflows_list_executions.Rd | 2 man/workflows_list_git.Rd | 4 man/workflows_list_git_commits.Rd | 2 man/workflows_list_projects.Rd | 8 man/workflows_list_shares.Rd | 6 man/workflows_patch.Rd | 34 man/workflows_post.Rd | 36 man/workflows_post_clone.Rd | 20 man/workflows_post_executions.Rd | 6 man/workflows_post_executions_cancel.Rd | 4 man/workflows_post_executions_resume.Rd | 4 man/workflows_post_executions_retry.Rd | 4 man/workflows_post_git_commits.Rd | 2 man/workflows_put.Rd | 34 man/workflows_put_archive.Rd | 20 man/workflows_put_git.Rd | 4 man/workflows_put_projects.Rd | 4 man/workflows_put_shares_groups.Rd | 6 man/workflows_put_shares_users.Rd | 6 tests/testthat/test_autogen.R | 2 tests/testthat/test_civis_ml_plot.R | 5 tests/testthat/test_io.R | 39 tools/generate_default_client.R | 23 412 files changed, 5263 insertions(+), 5039 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>
Diff between choroplethr versions 3.6.1 dated 2017-04-16 and 3.6.2 dated 2018-06-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/choropleth.R | 39 ++++++++++++++------------------------- R/startup_messages.R | 2 +- README.md | 10 +++++++--- 6 files changed, 33 insertions(+), 38 deletions(-)
Title: Chronomics Analysis Toolkit (CAT): Periodicity Analysis
Description: Calculates auto- and cross-correlation functions and plots an actogram and a smoothing function from a time series to identify and visualize periodic components. Tests presence of anticipated rhythm and estimates rhythm parameters; fits model consisting of multiple rhythmic components to data; performs least squares spectral analysis and other cosinor-based analyses, including population-mean cosinor (PMC) and population-mean cosinor parameter tests (PMCtest).
Author: Cathy Lee Gierke, Ruth Helget, Germaine Cornelissen-Guillaume
Maintainer: Cathy Lee Gierke <leegi001@umn.edu>
Diff between CATkit versions 3.2.3 dated 2018-01-03 and 3.3.2 dated 2018-06-21
CATkit-3.2.3/CATkit/R/pmc.R |only CATkit-3.2.3/CATkit/man/pmc.Rd |only CATkit-3.3.2/CATkit/DESCRIPTION | 12 - CATkit-3.3.2/CATkit/MD5 | 26 ++- CATkit-3.3.2/CATkit/NAMESPACE | 5 CATkit-3.3.2/CATkit/R/CATCosinor.R | 184 ++++++++++++++++++---- CATkit-3.3.2/CATkit/R/CATparam.R |only CATkit-3.3.2/CATkit/R/CATpmc.R |only CATkit-3.3.2/CATkit/R/c22f.R |only CATkit-3.3.2/CATkit/R/c23f.R |only CATkit-3.3.2/CATkit/R/c33f.R |only CATkit-3.3.2/CATkit/R/cimf.R |only CATkit-3.3.2/CATkit/R/fvalf.R |only CATkit-3.3.2/CATkit/R/generate_sigma_matrix.R |only CATkit-3.3.2/CATkit/R/phase.R | 19 +- CATkit-3.3.2/CATkit/R/pmc_internal.R | 211 +++++++++++++++----------- CATkit-3.3.2/CATkit/R/pmtest_internal.R |only CATkit-3.3.2/CATkit/R/r_f.R |only CATkit-3.3.2/CATkit/R/writeOutput.R |only CATkit-3.3.2/CATkit/inst/extdata/cos02x03.csv |only CATkit-3.3.2/CATkit/man/CATparam.Rd |only CATkit-3.3.2/CATkit/man/CATpmc.Rd |only 22 files changed, 322 insertions(+), 135 deletions(-)
Title: Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood
Description: Identify peaks in ChIP-seq data with biological replicates using a one-sided quasi-likelihood ratio test in quasi-Poisson or quasi-negative binomial models.
Author: Emily Goren [aut, cre],
Steve Lund [aut] (The author of the QuasiSeq package, from which all
functions were modified to produce this package.),
Long Qu [aut] (The author of the QuasiSeq package, from which all
functions were modified to produce this package.),
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
Daniel Gerhard [aut] (The author of mcprofile::orglm.fit, which was
modified slightly and used under the same name in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Emily Goren <emily.goren@gmail.com>
Diff between BinQuasi versions 0.1-3 dated 2018-04-03 and 0.1-5 dated 2018-06-21
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 1 + R/BQ.R | 9 +++++++-- R/BinQuasi.R | 1 + R/QL.fit.R | 3 +++ R/QL.results.R | 7 ++++++- R/call.peaks.R | 3 +-- R/count.table.R | 10 +++++----- README.md | 2 +- build/vignette.rds |binary inst/doc/BinQuasi.Rmd | 6 +++--- inst/doc/BinQuasi.html | 20 ++++++++++---------- man/BQ.Rd | 5 ++++- man/QL.fit.Rd | 3 +++ man/QL.results.Rd | 3 +++ vignettes/BinQuasi.Rmd | 6 +++--- 17 files changed, 72 insertions(+), 49 deletions(-)