Title: Utility Functions for Working with Random Number Generators
Description: Provides a set of functions for working with
Random Number Generators (RNGs). In particular, a generic
S4 framework is defined for getting/setting the current RNG, or RNG data
that are embedded into objects for reproducibility.
Notably, convenient default methods greatly facilitate the way current
RNG settings can be changed.
Author: Renaud Gaujoux [aut, cre],
Max Kuhn [ctb]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between rngtools versions 1.4 dated 2019-07-01 and 1.5 dated 2020-01-23
DESCRIPTION | 13 ++++++------- MD5 | 15 ++++++++------- NAMESPACE | 2 -- R/format.R | 2 +- R/rngtools-package.r | 2 -- R/utils.R |only tests/testthat/test-RNG.r | 5 +---- tests/testthat/test-RNGseq.r | 3 --- tests/testthat/test-format.R | 4 +--- 9 files changed, 17 insertions(+), 29 deletions(-)
Title: Time-Course Gene Set Analysis
Description: Implementation of Time-course Gene Set Analysis (TcGSA), a method for
analyzing longitudinal gene-expression data at the gene set level. Method is
detailed in: Hejblum, Skinner & Thiebaut (2015) <doi: 10.1371/journal.pcbi.1004310>.
Author: Boris P Hejblum [aut, cre],
Damien Chimits [aut],
Anthony Devaux [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between TcGSA versions 0.12.4 dated 2019-04-30 and 0.12.7 dated 2020-01-23
DESCRIPTION | 23 +- MD5 | 84 +++---- NAMESPACE | 1 NEWS.md | 11 R/MYheatmap.2.R | 2 R/TcGSA-internal.R | 2 R/TcGSA-package.R | 4 R/TcGSA.LR.R | 2 R/TcGSA.LR.parallel.R | 2 R/clustTrend.R | 15 - R/multtest.TcGSA.R | 2 R/plot.TcGSA.R | 7 R/plot1GS.R | 176 +++++++++++---- R/plotFit.GS.R | 2 R/plotPat.1GS.R | 2 R/plotPat.TcGSA.R | 7 R/plotSelect.GS.R | 8 R/pval_simu.R | 2 R/signifLRT.TcGSA.R | 2 R/summary.TcGSA.R | 2 README.md | 8 build/vignette.rds |binary inst/CITATION | 9 inst/doc/TcGSA_userguide.R | 44 +-- inst/doc/TcGSA_userguide.Rmd | 12 - inst/doc/TcGSA_userguide.html | 483 +++++++++++++++++++++--------------------- man/TcGSA-internal.Rd | 2 man/TcGSA-package.Rd | 4 man/TcGSA.LR.Rd | 22 + man/TcGSA.LR.parallel.Rd | 25 +- man/clustTrend.Rd | 36 ++- man/multtest.TcGSA.Rd | 11 man/plot.TcGSA.Rd | 75 ++++-- man/plot1GS.Rd | 82 +++++-- man/plotFit.GS.Rd | 20 + man/plotMultipleGS.Rd | 54 +++- man/plotPat.1GS.Rd | 48 +++- man/plotPat.TcGSA.Rd | 72 ++++-- man/plotSelect.GS.Rd | 57 +++- man/pval_simu.Rd | 2 man/signifLRT.TcGSA.Rd | 15 - man/summary.TcGSA.Rd | 2 vignettes/TcGSA_userguide.Rmd | 12 - 43 files changed, 905 insertions(+), 546 deletions(-)
Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features (i.e. lines and
polygons) to make them more aesthetically pleasing. Smooth curves, fill
holes, and remove small fragments from lines and polygons.
Author: Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>)
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>
Diff between smoothr versions 0.1.1 dated 2018-12-11 and 0.1.2 dated 2020-01-23
DESCRIPTION | 12 - MD5 | 22 +- NAMESPACE | 3 NEWS.md | 4 R/smoothr-package.R |only build/vignette.rds |binary inst/doc/smoothr.R | 46 ++-- inst/doc/smoothr.Rmd | 2 inst/doc/smoothr.html | 525 +++++++++++++++++++++++++++++++++++--------------- man/smooth_chaikin.Rd | 2 man/smooth_ksmooth.Rd | 10 man/smoothr.Rd |only vignettes/smoothr.Rmd | 2 13 files changed, 428 insertions(+), 200 deletions(-)
Title: Visually Assessing the Specificity and Informativeness of Primer
Pairs
Description: Identifies potential target sequences for a given set of primers
and generates phylogenetic trees annotated with the taxonomies of the predicted
amplification products.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between primerTree versions 1.0.4 dated 2018-12-19 and 1.0.5 dated 2020-01-23
DESCRIPTION | 16 ++++++++-------- MD5 | 26 +++++++++++++------------- R/primerTree.R | 7 +++++-- R/search.R | 2 ++ R/sequence.R | 30 ++++++++++++++++++++++++++---- man/clustalo.Rd | 3 +-- man/get_sequence.Rd | 9 ++++++++- man/get_sequences.Rd | 13 +++++++++++-- man/plot_tree.Rd | 13 +++++++++++-- man/plot_tree_ranks.Rd | 14 +++++++++++--- man/primerTree.Rd | 1 - man/primer_search.Rd | 11 +++++++++-- man/search_primer_pair.Rd | 20 ++++++++++++++++---- man/summary.primerTree.Rd | 3 +-- 14 files changed, 122 insertions(+), 46 deletions(-)
Title: Lag Penalized Weighted Correlation for Time Series Clustering
Description: Computes a time series distance measure for clustering based on weighted correlation and introduction of lags. The lags capture delayed responses in a time series dataset. The timepoints must be specified. T. Chandereng, A. Gitter (2020) <doi:10.1186/s12859-019-3324-1>.
Author: Thevaa Chandereng [aut, cre, cph]
(<https://orcid.org/0000-0003-4078-9176>),
Anthony Gitter [aut, cph] (<https://orcid.org/0000-0002-5324-9833>)
Maintainer: Thevaa Chandereng <chandereng@wisc.edu>
Diff between LPWC versions 0.99.5 dated 2019-03-12 and 1.0.0 dated 2020-01-23
DESCRIPTION | 11 +++++---- MD5 | 23 ++++++++++--------- NAMESPACE | 2 - NEWS.md |only R/findC.R | 6 ++--- README.md | 11 ++++++--- build/vignette.rds |binary inst/CITATION | 23 ++++++++++--------- inst/doc/LPWC.R | 2 - inst/doc/LPWC.Rmd | 7 +++--- inst/doc/LPWC.html | 51 +++++++++++++++++++++++++------------------- tests/testthat/test_findC.R | 1 vignettes/LPWC.Rmd | 7 +++--- 13 files changed, 81 insertions(+), 63 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
For details see Niku et al. (2019) <doi:10.1371/journal.pone.0216129>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 1.2.0 dated 2019-12-20 and 1.2.1 dated 2020-01-23
DESCRIPTION | 8 +-- MD5 | 38 ++++++++--------- R/TMBtrait.R | 53 ++++++++++++------------ R/gllvm.R | 20 ++++++--- R/gllvm.TMB.R | 33 +++++++-------- R/gllvm.auxiliary.R | 11 ++++- R/logLik.gllvm.R | 4 + R/ordiplot.gllvm.R | 3 + R/print.gllvm.R | 2 R/randomCoefplot.R | 6 +- inst/doc/vignette1.R | 34 ++++----------- inst/doc/vignette1.Rmd | 46 ++++++-------------- inst/doc/vignette1.html | 90 ++++++++++++++++++----------------------- inst/doc/vignette2.html | 18 ++++---- man/gllvm.Rd | 13 ++++- man/ordiplot.gllvm.Rd | 3 + man/randomCoefplot.gllvm.Rd | 4 - src/gllvm.cpp | 34 +++++---------- tests/testthat/test-fitgllvm.R | 20 ++++----- vignettes/vignette1.Rmd | 46 ++++++-------------- 20 files changed, 227 insertions(+), 259 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay and Charles Reynard.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 1.0-10 dated 2019-11-24 and 1.0-11 dated 2020-01-23
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS | 13 ++++- R/epi.2by2.R | 131 +++++++++++++++++++++++++++---------------------------- man/epi.about.Rd | 1 5 files changed, 83 insertions(+), 78 deletions(-)
Title: Model Butcher
Description: Provides a set of five S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut, cre] (<https://orcid.org/0000-0001-7217-4702>),
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut]
Maintainer: Joyce Cahoon <joyceyu48@gmail.com>
Diff between butcher versions 0.1.1 dated 2020-01-07 and 0.1.2 dated 2020-01-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/c5.R | 5 +++-- build/butcher.pdf |binary inst/doc/butcher.html | 4 ++-- man/axe-C5.0.Rd | 5 +++-- tests/testthat/test-c5.R | 9 +++------ 8 files changed, 27 insertions(+), 22 deletions(-)
Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values.
Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith,
and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>.
Other palettes available in this library have been derived from
'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and
'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between colourvalues versions 0.3.1 dated 2019-11-15 and 0.3.2 dated 2020-01-23
DESCRIPTION | 15 ++-- MD5 | 18 ++--- NEWS.md | 8 ++ R/palettes.R | 15 +++- inst/include/colourvalues/api/api_hex.hpp | 3 man/colour_values.Rd | 97 ++++++++++++++++++++++-------- man/colour_values_rgb.Rd | 97 ++++++++++++++++++++++-------- man/get_palette.Rd | 7 +- tests/testthat/test-colour_values_hex.R | 11 +++ tests/testthat/test-palettes.R | 10 +++ 10 files changed, 211 insertions(+), 70 deletions(-)
Title: Tidy Characterizations of Model Performance
Description: Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).
Author: Max Kuhn [aut],
Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between yardstick versions 0.0.4 dated 2019-08-26 and 0.0.5 dated 2020-01-23
DESCRIPTION | 8 +-- MD5 | 104 ++++++++++++++++++++--------------------- NEWS.md | 8 +++ R/conf_mat.R | 8 +-- R/metrics.R | 2 README.md | 4 + inst/doc/custom-metrics.R | 38 +++++++------- inst/doc/custom-metrics.html | 22 +++++--- inst/doc/metric-types.R | 12 ++-- inst/doc/metric-types.html | 10 ++- inst/doc/multiclass.R | 2 inst/doc/multiclass.html | 8 ++- man/accuracy.Rd | 23 +++++---- man/average_precision.Rd | 16 +++--- man/bal_accuracy.Rd | 26 ++++++---- man/ccc.Rd | 53 ++++++++++++-------- man/conf_mat.Rd | 7 +- man/detection_prevalence.Rd | 36 +++++++++----- man/f_meas.Rd | 37 ++++++++------ man/gain_capture.Rd | 13 ++--- man/gain_curve.Rd | 16 +++--- man/huber_loss.Rd | 43 ++++++++++------ man/huber_loss_pseudo.Rd | 43 ++++++++++------ man/iic.Rd | 40 +++++++++------ man/j_index.Rd | 27 ++++++---- man/kap.Rd | 24 +++++---- man/lift_curve.Rd | 18 +++---- man/mae.Rd | 40 +++++++++------ man/mape.Rd | 40 +++++++++------ man/mase.Rd | 46 ++++++++++-------- man/mcc.Rd | 24 +++++---- man/metric_summarizer.Rd | 15 ++++- man/metric_vec_template.Rd | 13 +++-- man/metrics.Rd | 5 - man/mn_log_loss.Rd | 13 ++--- man/npv.Rd | 55 ++++++++++++++------- man/ppv.Rd | 55 ++++++++++++++------- man/pr_auc.Rd | 13 ++--- man/pr_curve.Rd | 8 +-- man/precision.Rd | 36 ++++++++------ man/recall.Rd | 36 ++++++++------ man/rmse.Rd | 40 +++++++++------ man/roc_auc.Rd | 25 ++++++--- man/roc_curve.Rd | 11 ++-- man/rpd.Rd | 34 ++++++++----- man/rpiq.Rd | 34 ++++++++----- man/rsq.Rd | 34 ++++++++----- man/rsq_trad.Rd | 33 ++++++++----- man/sens.Rd | 37 ++++++++------ man/smape.Rd | 40 +++++++++------ man/spec.Rd | 37 ++++++++------ man/summary.conf_mat.Rd | 5 - tests/testthat/test_autoplot.R | 5 + 53 files changed, 838 insertions(+), 544 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen,
Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>
Diff between SamplingStrata versions 1.4-1 dated 2019-04-22 and 1.5 dated 2020-01-23
SamplingStrata-1.4-1/SamplingStrata/R/aggrStrata_model.r |only SamplingStrata-1.4-1/SamplingStrata/R/buildStrataDF.R |only SamplingStrata-1.4-1/SamplingStrata/R/buildStrataDF_opt2.R |only SamplingStrata-1.4-1/SamplingStrata/R/summaryStrata2.R |only SamplingStrata-1.4-1/SamplingStrata/inst/doc/SamplingStrata.bib |only SamplingStrata-1.4-1/SamplingStrata/man/figures |only SamplingStrata-1.4-1/SamplingStrata/vignettes/output |only SamplingStrata-1.4-1/SamplingStrata/vignettes/simulation |only SamplingStrata-1.4-1/SamplingStrata/vignettes/vignette.RData |only SamplingStrata-1.5/SamplingStrata/DESCRIPTION | 17 SamplingStrata-1.5/SamplingStrata/MD5 | 165 SamplingStrata-1.5/SamplingStrata/NAMESPACE | 8 SamplingStrata-1.5/SamplingStrata/NEWS | 359 - SamplingStrata-1.5/SamplingStrata/R/Bethel.r | 4 SamplingStrata-1.5/SamplingStrata/R/KmeansSolution.R | 1 SamplingStrata-1.5/SamplingStrata/R/KmeansSolution2.R |only SamplingStrata-1.5/SamplingStrata/R/KmeansSolutionSpatial.R |only SamplingStrata-1.5/SamplingStrata/R/aggrStrata.r |only SamplingStrata-1.5/SamplingStrata/R/aggrStrata2.R |only SamplingStrata-1.5/SamplingStrata/R/aggrStrata_spatial.r |only SamplingStrata-1.5/SamplingStrata/R/buildFrameDF.R | 1 SamplingStrata-1.5/SamplingStrata/R/buildFrameSpatial.R |only SamplingStrata-1.5/SamplingStrata/R/buildStrataDFSpatial_4.R |only SamplingStrata-1.5/SamplingStrata/R/buildStrataDF_models_4.R |only SamplingStrata-1.5/SamplingStrata/R/checkInput.R | 12 SamplingStrata-1.5/SamplingStrata/R/computeGamma.R |only SamplingStrata-1.5/SamplingStrata/R/evalSolution.r | 13 SamplingStrata-1.5/SamplingStrata/R/onAttach.R |only SamplingStrata-1.5/SamplingStrata/R/optimStrata.R |only SamplingStrata-1.5/SamplingStrata/R/optimizeStrata.R | 9 SamplingStrata-1.5/SamplingStrata/R/optimizeStrata2.R | 78 SamplingStrata-1.5/SamplingStrata/R/optimizeStrataSpatial.R |only SamplingStrata-1.5/SamplingStrata/R/plotStrata2d_new.R | 17 SamplingStrata-1.5/SamplingStrata/R/prepareSuggestion.R |only SamplingStrata-1.5/SamplingStrata/R/rbga2.R | 11 SamplingStrata-1.5/SamplingStrata/R/rbgaSpatial.R |only SamplingStrata-1.5/SamplingStrata/R/selectSample.R | 7 SamplingStrata-1.5/SamplingStrata/R/selectSampleSytematic.R | 7 SamplingStrata-1.5/SamplingStrata/R/strataGenalg.R | 4 SamplingStrata-1.5/SamplingStrata/R/strataGenalg2.R | 8 SamplingStrata-1.5/SamplingStrata/R/strataGenalgSpatial.R |only SamplingStrata-1.5/SamplingStrata/R/summaryStrata.R |only SamplingStrata-1.5/SamplingStrata/build/vignette.rds |binary SamplingStrata-1.5/SamplingStrata/inst/doc/SamplingStrata.R | 615 -- SamplingStrata-1.5/SamplingStrata/inst/doc/SamplingStrata.Rmd | 1198 +---- SamplingStrata-1.5/SamplingStrata/inst/doc/SamplingStrata.html | 2295 +++------- SamplingStrata-1.5/SamplingStrata/inst/doc/SamplingStrata_cheatsheet.pdf |only SamplingStrata-1.5/SamplingStrata/inst/doc/models.R |only SamplingStrata-1.5/SamplingStrata/inst/doc/models.Rmd |only SamplingStrata-1.5/SamplingStrata/inst/doc/models.html |only SamplingStrata-1.5/SamplingStrata/inst/doc/spatial.R |only SamplingStrata-1.5/SamplingStrata/inst/doc/spatial.Rmd |only SamplingStrata-1.5/SamplingStrata/inst/doc/spatial.html |only SamplingStrata-1.5/SamplingStrata/inst/figures |only SamplingStrata-1.5/SamplingStrata/man/KmeansSolution.Rd | 11 SamplingStrata-1.5/SamplingStrata/man/KmeansSolution2.Rd |only SamplingStrata-1.5/SamplingStrata/man/KmeansSolutionSpatial.Rd |only SamplingStrata-1.5/SamplingStrata/man/aggStrata2.Rd |only SamplingStrata-1.5/SamplingStrata/man/aggStrataSpatial.Rd |only SamplingStrata-1.5/SamplingStrata/man/buildFrameSpatial.Rd |only SamplingStrata-1.5/SamplingStrata/man/buildStrataDF.Rd | 9 SamplingStrata-1.5/SamplingStrata/man/buildStrataDFSpatial.Rd |only SamplingStrata-1.5/SamplingStrata/man/computeGamma.Rd |only SamplingStrata-1.5/SamplingStrata/man/optimStrata.Rd |only SamplingStrata-1.5/SamplingStrata/man/optimizeStrata.Rd | 52 SamplingStrata-1.5/SamplingStrata/man/optimizeStrata2.Rd | 79 SamplingStrata-1.5/SamplingStrata/man/optimizeStrataSpatial.Rd |only SamplingStrata-1.5/SamplingStrata/man/plotStrata2d.Rd | 32 SamplingStrata-1.5/SamplingStrata/man/prepareSuggestion.Rd |only SamplingStrata-1.5/SamplingStrata/vignettes/SamplingStrata.Rmd | 1198 +---- SamplingStrata-1.5/SamplingStrata/vignettes/SamplingStrata.bib | 73 SamplingStrata-1.5/SamplingStrata/vignettes/SamplingStrata_figures |only SamplingStrata-1.5/SamplingStrata/vignettes/SamplingStrata_vignette.RData |only SamplingStrata-1.5/SamplingStrata/vignettes/models.Rmd |only SamplingStrata-1.5/SamplingStrata/vignettes/models_figures |only SamplingStrata-1.5/SamplingStrata/vignettes/models_vignette.RData |only SamplingStrata-1.5/SamplingStrata/vignettes/spatial.Rmd |only SamplingStrata-1.5/SamplingStrata/vignettes/spatial_figures |only SamplingStrata-1.5/SamplingStrata/vignettes/spatial_vignette.RData |only 79 files changed, 2547 insertions(+), 3736 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Interface to 'Altair'
Description: Interface to 'Altair' <https://altair-viz.github.io>, which itself
is a 'Python' interface to 'Vega-Lite' <https://vega.github.io/vega-lite>.
This package uses the 'Reticulate' framework
<https://rstudio.github.io/reticulate> to manage the interface between R
and 'Python'.
Author: Ian Lyttle [aut, cre] (<https://orcid.org/0000-0001-9962-4849>),
Haley Jeppson [aut],
Altair Developers [aut],
Alicia Schep [ctb] (<https://orcid.org/0000-0002-3915-0618>),
Jake Vanderplas [ctb] (Altair library),
Brian Granger [ctb] (Altair library)
Maintainer: Ian Lyttle <ian.lyttle@schneider-electric.com>
Diff between altair versions 3.1.1 dated 2019-07-11 and 4.0.1 dated 2020-01-23
altair-3.1.1/altair/R/utils-vegawidget-altair.vegalite.v3.api.TopLevelMixin.R |only altair-3.1.1/altair/man/repr_text.altair.vegalite.v3.api.Chart.Rd |only altair-3.1.1/altair/man/repr_vegalite3.altair.vegalite.v3.api.Chart.Rd |only altair-4.0.1/altair/DESCRIPTION | 15 ++-- altair-4.0.1/altair/MD5 | 32 +++++----- altair-4.0.1/altair/NAMESPACE | 18 ++--- altair-4.0.1/altair/NEWS.md | 6 + altair-4.0.1/altair/R/concatenation.R | 8 +- altair-4.0.1/altair/R/utils-jupyterlab.R | 6 - altair-4.0.1/altair/R/utils-vegawidget-altair.R |only altair-4.0.1/altair/R/zzz.R | 2 altair-4.0.1/altair/README.md | 9 +- altair-4.0.1/altair/man/altair.Rd | 1 altair-4.0.1/altair/man/altair_concatenation.Rd | 12 +-- altair-4.0.1/altair/man/as_vegaspec.Rd | 10 +-- altair-4.0.1/altair/man/figures/README-example-1.svg | 2 altair-4.0.1/altair/man/install_altair.Rd | 10 ++- altair-4.0.1/altair/man/knit_print.vegaspec.Rd | 11 +-- altair-4.0.1/altair/man/repr_text.altair.vegalite.v4.api.Chart.Rd |only altair-4.0.1/altair/man/repr_vegalite4.altair.vegalite.v4.api.Chart.Rd |only 20 files changed, 71 insertions(+), 71 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey [aut, cre] (<https://orcid.org/0000-0002-7522-3677>)
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.2 dated 2019-12-08 and 1.3 dated 2020-01-23
DESCRIPTION | 16 ++- MD5 | 24 ++--- NEWS | 5 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/compare.R | 97 +++++++++++++++++++- inst/doc/compare.Rnw | 231 ++++++++++++++++++++++++++++++++++++++----------- inst/doc/compare.pdf |binary inst/doc/metap.pdf |binary inst/doc/strength.gv |only inst/doc/struct.gv |only man/meanz.Rd | 7 + vignettes/compare.Rnw | 231 ++++++++++++++++++++++++++++++++++++++----------- vignettes/strength.pdf |only vignettes/struct.pdf |only 15 files changed, 494 insertions(+), 117 deletions(-)
Title: Scoring the EQ-5D Descriptive System
Description: EQ-5D is a standard instrument (<https://euroqol.org/eq-5d-instruments/>) that measures the quality of life
often used in clinical and economic evaluations of health care technologies. Both adult versions of EQ-5D (EQ-5D-3L and EQ-5D-5L)
contain a descriptive system and visual analog scale. The descriptive system measures the patient's health in 5 dimensions:
the 5L versions has 5 levels and 3L version has 3 levels. The descriptive system scores are usually converted to index values
using country specific values sets (that incorporates the country preferences). This package allows the calculation of both descriptive system
scores to the index value scores. The value sets for EQ-5D-3L are from the references mentioned in the website <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/valuation/>
The value sets for EQ-5D-3L for a total of 31 countries are used for the valuation (see the user guide for a complete list of references).
The value sets for EQ-5D-5L are obtained from references mentioned in the <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/valuation-standard-value-sets/> and other sources.
The value sets for EQ-5D-5L for a total of 17 countries are used for the valuation (see the user guide for a complete list of references).
The package can also be used to map 5L scores to 3L index values for 10 countries: Denmark, France, Germany, Japan, Netherlands, Spain, Thailand, UK, USA, and Zimbabwe.
The value set and method for mapping are obtained from Van Hout et al (2012) <doi: 10.1016/j.jval.2012.02.008>.
Author: Sheeja Manchira Krishnan [aut, cre]
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>
Diff between valueEQ5D versions 0.5.0 dated 2019-11-06 and 0.5.1 dated 2020-01-23
DESCRIPTION | 8 MD5 | 13 R/basic_checks.R | 500 ++++++------ R/eq5d.R | 1772 +++++++++++++++++++++++----------------------- R/sysdata.rda |only README.md | 42 - inst/doc/User_Guide.html | 4 tests/testthat/testthat.R | 10 8 files changed, 1175 insertions(+), 1174 deletions(-)
Title: Basic Functions to Check Readability, Consistency, and Content
of an Individual Participant Data File
Description: Basic checks needed with an individual level participant data from randomised controlled trial. This
checks files for existence, read access and individual columns for formats. The checks on format is currently implemented for gender and age formats.
Author: Sheeja Manchira Krishnan
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>
Diff between IPDFileCheck versions 0.6.1 dated 2019-12-04 and 0.6.2 dated 2020-01-23
DESCRIPTION | 6 MD5 | 8 R/IPDFilecheck.R | 44 + inst/doc/User_Guide.html | 54 +- tests/testthat/testthat.R | 1216 +++++++++++++++++++++++----------------------- 5 files changed, 681 insertions(+), 647 deletions(-)
Title: Convolution-Based Nonstationary Spatial Modeling
Description: Fits convolution-based nonstationary
Gaussian process models to point-referenced spatial data. The nonstationary
covariance function allows the user to specify the underlying correlation
structure and which spatial dependence parameters should be allowed to
vary over space: the anisotropy, nugget variance, and process variance.
The parameters are estimated via maximum likelihood, using a local
likelihood approach. Also provided are functions to fit stationary spatial
models for comparison, calculate the Kriging predictor and standard errors,
and create various plots to visualize nonstationarity.
Author: Mark D. Risser [aut, cre]
Maintainer: Mark D. Risser <markdrisser@gmail.com>
Diff between convoSPAT versions 1.2.4 dated 2017-11-03 and 1.2.6 dated 2020-01-23
DESCRIPTION | 13 MD5 | 63 +-- NAMESPACE | 2 R/convoSPAT_fitpred.R | 692 ++++++++++++++++----------------------- R/convoSPAT_paramEst.R | 105 ++++- R/convoSPAT_simulate.R | 11 R/convoSPAT_summplot.R | 4 man/Aniso_fit.Rd | 32 - man/NSconvo_fit.Rd | 33 - man/NSconvo_sim.Rd | 19 - man/US.mc.grids.Rd | 1 man/US.prediction.locs.Rd | 1 man/USprecip97.Rd | 1 man/cov_spatial.Rd |only man/evaluate_CV.Rd | 1 man/f_mc_kernels.Rd | 7 man/kernel_cov.Rd | 1 man/make_global_loglik1.Rd | 1 man/make_global_loglik1_kappa.Rd | 4 man/make_global_loglik2.Rd | 1 man/make_global_loglik2_kappa.Rd | 5 man/make_global_loglik3.Rd | 1 man/make_global_loglik3_kappa.Rd | 1 man/make_global_loglik4_kappa.Rd | 1 man/make_local_lik.Rd | 1 man/mc_N.Rd | 1 man/plot.Aniso.Rd | 5 man/plot.NSconvo.Rd | 1 man/predict.Aniso.Rd | 1 man/predict.NSconvo.Rd | 1 man/simdata.Rd | 1 man/summary.Aniso.Rd | 1 man/summary.NSconvo.Rd | 1 33 files changed, 454 insertions(+), 559 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. The code for Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-7 dated 2019-05-22 and 1.1-8 dated 2020-01-23
DESCRIPTION | 12 ++-- MD5 | 49 ++++++++-------- NAMESPACE | 13 ++-- NEWS.md | 9 ++- R/AAAparameter.R | 2 R/cut_tour.R | 32 ++++++++-- R/insert_dummy.R | 2 R/reformulare_ATSP_as_TSP.R | 2 R/solve_TSP.R | 26 ++++++++ R/tsp_concorde.R | 98 ++++++++++++++------------------ R/write_TSPLIB.R | 66 +++++++++++----------- build/vignette.rds |binary inst/doc/TSP.R | 48 +++++++++------- inst/doc/TSP.Rnw | 76 +++++++++++++------------ inst/doc/TSP.pdf |binary man/Concorde.Rd | 11 ++- man/TSPLIB.Rd | 3 - man/USCA312.Rd | 42 +++++++------- man/cut_tour.Rd | 22 ++++++- man/insert_dummy.Rd | 38 +++++++++--- man/solve_TSP.Rd | 11 +++ src/two_opt.c | 120 ++++++++++++++++++++-------------------- tests/testthat/test-ETSP.R | 2 tests/testthat/test-concorde.R |only tests/testthat/test-solve_TSP.R | 33 ++++++----- vignettes/TSP.Rnw | 76 +++++++++++++------------ 26 files changed, 455 insertions(+), 338 deletions(-)
Title: Maximum Approximate Bernstein/Beta Likelihood Estimation
Description: Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.
Author: Zhong Guan [aut, cre]
Maintainer: Zhong Guan <zguan@iusb.edu>
Diff between mable versions 2.0 dated 2020-01-12 and 2.0.1 dated 2020-01-23
mable-2.0.1/mable/DESCRIPTION | 6 mable-2.0.1/mable/MD5 | 57 ++--- mable-2.0.1/mable/NAMESPACE | 14 + mable-2.0.1/mable/R/mable-aft-model.r | 91 ++++---- mable-2.0.1/mable/R/mable-decon.r | 26 +- mable-2.0.1/mable/R/mable-multivar.r | 213 ++++++++++++++----- mable-2.0.1/mable/R/mable-ph-model.r | 203 ++++++++---------- mable-2.0.1/mable/R/mable.r | 369 ++++++++++++++++++++------------- mable-2.0.1/mable/inst/doc/mable.R | 229 ++++++++++---------- mable-2.0.1/mable/inst/doc/mable.Rmd | 235 ++++++++++----------- mable-2.0.1/mable/inst/doc/mable.pdf |binary mable-2.0.1/mable/man/dmixbeta.Rd |only mable-2.0.1/mable/man/dmixmvbeta.Rd |only mable-2.0.1/mable/man/mable.Rd | 86 +++---- mable-2.0.1/mable/man/mable.aft.Rd | 38 +-- mable-2.0.1/mable/man/mable.decon.Rd | 22 - mable-2.0.1/mable/man/mable.group.Rd | 42 +-- mable-2.0.1/mable/man/mable.ic.Rd | 46 ++-- mable-2.0.1/mable/man/mable.mvar.Rd | 34 +-- mable-2.0.1/mable/man/mable.ph.Rd | 58 ++--- mable-2.0.1/mable/man/mable.reg.Rd | 8 mable-2.0.1/mable/man/maple.aft.Rd | 42 +-- mable-2.0.1/mable/man/maple.ph.Rd | 46 ++-- mable-2.0.1/mable/man/optim.gcp.Rd | 12 - mable-2.0.1/mable/man/plot.mable.Rd | 2 mable-2.0.1/mable/man/summary.mable.Rd | 6 mable-2.0.1/mable/src/mable.c | 84 ++----- mable-2.0.1/mable/vignettes/mable.Rmd | 235 ++++++++++----------- mable-2.0.1/mable/vignettes/mable.html | 241 ++++++++++----------- mable-2.0/mable/man/bern.poly.Rd |only mable-2.0/mable/man/mvbern.poly.Rd |only mable-2.0/mable/man/rmixbeta.Rd |only 32 files changed, 1305 insertions(+), 1140 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 3.1 dated 2019-10-08 and 3.2 dated 2020-01-23
DESCRIPTION | 12 ++--- MD5 | 52 +++++++++++------------ R/IsoplotR.R | 2 R/concordia.R | 44 ++++++++++--------- R/discordia.R | 7 ++- R/diseq.R | 86 ++++++++++++++++++++------------------ R/errorellipse.R | 15 ++++-- R/helioplot.R | 26 +++++------ R/io.R | 46 +++++++++++--------- R/kde.R | 8 +-- R/ludwig.R | 117 +++++++++++++++++++++++++--------------------------- R/mds.R | 38 ++++++---------- R/peakfit.R | 37 +++++++++------- R/radialplot.R | 4 - R/toolbox.R | 79 +++++++---------------------------- R/weightedmean.R | 2 R/york.R | 7 +-- inst/constants.json | 2 man/IsoplotR.Rd | 4 - man/Pb0corr.Rd | 14 +++--- man/helioplot.Rd | 9 ++-- man/kde.Rd | 14 +++--- man/ludwig.Rd | 3 - man/peakfit.Rd | 37 +++++++++------- man/radialplot.Rd | 13 +++-- man/scatterplot.Rd | 7 ++- man/weightedmean.Rd | 14 +++--- 27 files changed, 346 insertions(+), 353 deletions(-)
Title: Event Detection Framework
Description: Detect events in time-series data. Combines multiple well-known R packages like 'forecast' and 'neuralnet' to deliver an easily configurable tool for multivariate event detection.
Author: Margarita Rebolledo [aut],
Sowmya Chandrasekaran [aut, cre],
Frederik Rehbach [aut],
Steffen Moritz [aut] (<https://orcid.org/0000-0002-0085-1804>)
Maintainer: Sowmya Chandrasekaran <sowzz.17@gmail.com>
Diff between EventDetectR versions 0.3.3 dated 2019-08-08 and 0.3.4 dated 2020-01-23
EventDetectR-0.3.3/EventDetectR/man/getDefaultModelControl.Rd |only EventDetectR-0.3.4/EventDetectR/DESCRIPTION | 26 +-- EventDetectR-0.3.4/EventDetectR/MD5 | 49 +++---- EventDetectR-0.3.4/EventDetectR/NAMESPACE | 1 EventDetectR-0.3.4/EventDetectR/NEWS | 2 EventDetectR-0.3.4/EventDetectR/R/EventDetectR-package.R | 3 EventDetectR-0.3.4/EventDetectR/R/bedAlgo.R | 13 + EventDetectR-0.3.4/EventDetectR/R/buildEDModel.R | 69 ++++++++-- EventDetectR-0.3.4/EventDetectR/R/detectEvents.R | 60 ++++++-- EventDetectR-0.3.4/EventDetectR/R/detectionQuality.R | 8 - EventDetectR-0.3.4/EventDetectR/R/eventClassification.R | 19 ++ EventDetectR-0.3.4/EventDetectR/R/getDefaultControlLists.R | 20 ++ EventDetectR-0.3.4/EventDetectR/R/getSupportedMethods.R | 1 EventDetectR-0.3.4/EventDetectR/R/model_NeuralNetwork.R |only EventDetectR-0.3.4/EventDetectR/R/simulateEvents.R | 9 - EventDetectR-0.3.4/EventDetectR/man/EventDetectR-package.Rd | 5 EventDetectR-0.3.4/EventDetectR/man/bedAlgo.Rd | 14 +- EventDetectR-0.3.4/EventDetectR/man/buildEDModel.Rd | 17 +- EventDetectR-0.3.4/EventDetectR/man/detectEvents.Rd | 30 ++-- EventDetectR-0.3.4/EventDetectR/man/getDefaultForecastModelControl.Rd |only EventDetectR-0.3.4/EventDetectR/man/getDefaultNeuralNetModelControl.Rd |only EventDetectR-0.3.4/EventDetectR/man/model_NeuralNetwork.Rd |only EventDetectR-0.3.4/EventDetectR/man/predict.NeuralNetwork.Rd |only EventDetectR-0.3.4/EventDetectR/man/qualityStatistics.Rd | 8 - EventDetectR-0.3.4/EventDetectR/man/simulateEvents.Rd | 9 - EventDetectR-0.3.4/EventDetectR/tests/testthat/Rplots.pdf |only EventDetectR-0.3.4/EventDetectR/tests/testthat/test-buildModel.R | 17 +- EventDetectR-0.3.4/EventDetectR/tests/testthat/test-detectionQuality.R | 11 - EventDetectR-0.3.4/EventDetectR/tests/testthat/test-eventClassification.R | 43 +++++- 29 files changed, 296 insertions(+), 138 deletions(-)
Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression
coefficients can vary over time as random walks.
Gaussian, Poisson, and binomial observations are supported.
The Markov chain Monte Carlo computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, walker uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 0.3.0 dated 2019-09-22 and 0.3.1-1 dated 2020-01-23
walker-0.3.0/walker/cleanup |only walker-0.3.0/walker/cleanup.win |only walker-0.3.0/walker/configure |only walker-0.3.1-1/walker/DESCRIPTION | 8 ++++---- walker-0.3.1-1/walker/MD5 | 13 +++++-------- walker-0.3.1-1/walker/R/plot_fit.R | 8 +++++--- walker-0.3.1-1/walker/R/walker.R | 1 - walker-0.3.1-1/walker/README.md | 4 ++++ walker-0.3.1-1/walker/inst/doc/walker.html | 15 ++++++++------- 9 files changed, 26 insertions(+), 23 deletions(-)
Title: Class-Focused Pattern Metric Comparisons using Simulation
Description: Provides tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps. Current limitation is for binary (classes 1, 2) maps that are 64x64 cells in extent.
Author: Tarmo K. Remmel, (Marie-Josee Fortin, Ferenc Csillag, Sandor Kabos)
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between PatternClass versions 1.7.1 dated 2016-10-28 and 2.0.0 dated 2020-01-23
DESCRIPTION | 12 +++--- MD5 | 44 +++++++++++------------ NAMESPACE | 15 ++++---- R/CARsimu.R | 18 ++++++--- R/build.lut.R | 6 ++- R/buildsurfs.R | 28 ++++++++------- R/doubleplotter.R | 81 ++++++++++++++++++-------------------------- R/findcol.R | 2 - R/imaks.R | 6 ++- R/singlemap.R | 56 +++++++++++++++++------------- R/singleplotter.R | 81 +++++++++++++++++--------------------------- R/surfplot.R | 6 ++- R/wi.R | 14 +++++-- R/wtest.run.R | 6 ++- data/data.rda |binary man/PatternClass-package.Rd | 6 +-- man/buildsurfs.Rd | 10 ++--- man/doubleplotter.Rd | 25 +++++-------- man/findcol.Rd | 2 - man/findrow.Rd | 2 - man/singlemap.Rd | 24 +++++++------ man/singleplotter.Rd | 23 +++++++----- man/wi.Rd | 2 - 23 files changed, 243 insertions(+), 226 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman
Maintainer: Luke Harmon <lukeh@uidaho.edu>
Diff between geiger versions 2.0.6.2 dated 2019-06-04 and 2.0.6.3 dated 2020-01-23
ChangeLog | 10 ++--- DESCRIPTION | 21 +++++------- MD5 | 41 ++++++++++++----------- NAMESPACE | 1 R/TESTING.R | 2 - R/congruify.R | 84 ++++++++++++++++++++++++++++++++++++++++++++----- R/disparity.R | 2 - R/diversitree.R | 1 R/gbresolve.R | 4 +- R/likelihood.R | 2 - R/mecca.R | 4 +- R/medusa.R | 17 ++++++--- R/plotting.R | 2 - R/proposals.R | 2 - R/traits.R | 19 ++--------- R/utilities-misc.R | 11 ++---- R/utilities-phylo.R | 2 - README.md | 3 + inst/CITATION | 17 ++++++++- man/congruify.phylo.Rd | 22 +++++++----- man/r8s.phylo.Rd |only src/init.c | 21 ++++++------ 22 files changed, 181 insertions(+), 107 deletions(-)
Title: Discovery of Motifs in Spatial-Time Series
Description: Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Heraldo Borges [aut, cre] (CEFET/RJ),
Amin Bazaz [aut] (Polytech'Montpellier),
Eduardo Ogasawara [aut] (CEFET/RJ)
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>
Diff between STMotif versions 1.0.3 dated 2019-08-22 and 2.0.0 dated 2020-01-23
STMotif-1.0.3/STMotif/R/test.R |only STMotif-1.0.3/STMotif/README.md |only STMotif-1.0.3/STMotif/data/example_data.RData |only STMotif-1.0.3/STMotif/inst/doc/discovery-motifs.R |only STMotif-1.0.3/STMotif/inst/doc/discovery-motifs.Rmd |only STMotif-1.0.3/STMotif/inst/doc/discovery-motifs.html |only STMotif-1.0.3/STMotif/inst/doc/examples.R |only STMotif-1.0.3/STMotif/inst/doc/examples.Rmd |only STMotif-1.0.3/STMotif/inst/doc/examples.html |only STMotif-1.0.3/STMotif/inst/doc/normalization-and-sax.R |only STMotif-1.0.3/STMotif/inst/doc/normalization-and-sax.Rmd |only STMotif-1.0.3/STMotif/inst/doc/normalization-and-sax.html |only STMotif-1.0.3/STMotif/inst/doc/search-stmotifs.R |only STMotif-1.0.3/STMotif/inst/doc/search-stmotifs.Rmd |only STMotif-1.0.3/STMotif/inst/doc/search-stmotifs.html |only STMotif-1.0.3/STMotif/inst/shiny-visualization |only STMotif-1.0.3/STMotif/man/displayPlotSeries.Rd |only STMotif-1.0.3/STMotif/man/intensityDataset.Rd |only STMotif-1.0.3/STMotif/man/runVisualization.Rd |only STMotif-1.0.3/STMotif/man/top5motifs.Rd |only STMotif-1.0.3/STMotif/vignettes/combineseries.png |only STMotif-1.0.3/STMotif/vignettes/discovery-motifs.Rmd |only STMotif-1.0.3/STMotif/vignettes/examples.Rmd |only STMotif-1.0.3/STMotif/vignettes/normalization-and-sax.Rmd |only STMotif-1.0.3/STMotif/vignettes/partitioningintoblocks.png |only STMotif-1.0.3/STMotif/vignettes/saxencode.png |only STMotif-1.0.3/STMotif/vignettes/search-stmotifs.Rmd |only STMotif-2.0.0/STMotif/DESCRIPTION | 12 - STMotif-2.0.0/STMotif/MD5 | 65 +---- STMotif-2.0.0/STMotif/NAMESPACE | 8 STMotif-2.0.0/STMotif/NEWS.md | 9 STMotif-2.0.0/STMotif/R/STMotif.R | 2 STMotif-2.0.0/STMotif/R/example_dataset.R | 5 STMotif-2.0.0/STMotif/R/mainFunction.R | 19 - STMotif-2.0.0/STMotif/R/visualization.R | 150 ++----------- STMotif-2.0.0/STMotif/build/vignette.rds |binary STMotif-2.0.0/STMotif/data/example_dataset.RData |only STMotif-2.0.0/STMotif/inst/doc/STMotif.R |only STMotif-2.0.0/STMotif/inst/doc/STMotif.Rmd |only STMotif-2.0.0/STMotif/inst/doc/STMotif.html |only STMotif-2.0.0/STMotif/man/CSAMiningProcess.Rd | 7 STMotif-2.0.0/STMotif/man/NormSAX.Rd | 3 STMotif-2.0.0/STMotif/man/RankSTMotifs.Rd | 4 STMotif-2.0.0/STMotif/man/STMotif.Rd | 2 STMotif-2.0.0/STMotif/man/STSADatasetAdjust.Rd | 2 STMotif-2.0.0/STMotif/man/SearchSTMotifs.Rd | 7 STMotif-2.0.0/STMotif/man/display_motifsDataset.Rd |only STMotif-2.0.0/STMotif/man/display_motifsSTSeries.Rd |only STMotif-2.0.0/STMotif/man/example_dataset.Rd | 3 STMotif-2.0.0/STMotif/vignettes/STMotif.Rmd |only 50 files changed, 92 insertions(+), 206 deletions(-)
Title: Expressions with Statistical Details
Description: Statistical processing backend for 'ggstatsplot',
this package creates expressions with details from statistical tests.
Currently, it supports only the most common types of statistical
tests: parametric, nonparametric, robust, and bayesian versions of
t-test/anova, correlation analyses, contingency table analysis, and
meta-analysis.
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>),
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 0.2.0 dated 2020-01-10 and 0.2.1 dated 2020-01-23
DESCRIPTION | 23 - MD5 | 63 ++-- NAMESPACE | 11 NEWS.md | 7 R/global_vars.R | 5 R/helpers_anova_expressions.R | 102 +++---- R/helpers_bf_tests.R | 189 +++++++++++--- R/helpers_corr_test_expressions.R | 3 R/helpers_meta_analysis_expressions.R |only R/helpers_t_test_expressions.R | 21 - R/reexports.R | 6 README.md | 58 +++- inst/WORDLIST | 5 inst/doc/stats_details.html | 48 +-- inst/doc/tests_and_coverage.Rmd | 193 +++++++------- inst/doc/tests_and_coverage.html | 340 ++++++++++++++------------ man/bf_corr_test.Rd | 2 man/bf_meta.Rd |only man/effsize_t_parametric.Rd | 2 man/expr_anova_nonparametric.Rd | 2 man/expr_anova_robust.Rd | 5 man/expr_contingency_tab.Rd | 2 man/expr_corr_test.Rd | 2 man/expr_meta_parametric.Rd |only man/expr_meta_robust.Rd |only man/expr_template.Rd | 2 man/figures/README-example_metaanalysis-1.png |only man/reexports.Rd | 3 man/robcor_ci.Rd | 2 man/t1way_ci.Rd | 2 man/yuend_ci.Rd | 2 tests/README.md | 195 +++++++------- tests/testthat/test-expr_meta_parametric.R |only tests/testthat/test-expr_meta_robust.R |only tests/testthat/test-helpers_bf_tests.R | 99 ++++++- vignettes/tests_and_coverage.Rmd | 193 +++++++------- 36 files changed, 947 insertions(+), 640 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Tilman Davies;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Brown;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
L. Cobo Sanchez;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
H. Heydarian;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
N. Luambua;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
A. Mollie;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
T. Pollington;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
J. Sulavik;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
L. Yates;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.62-2 dated 2019-12-10 and 1.63-0 dated 2020-01-23
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spatstat-1.63-0/spatstat/R/rho2hat.R | 11 - spatstat-1.63-0/spatstat/R/rmh.default.R | 82 ++++---- spatstat-1.63-0/spatstat/R/rmhcontrol.R | 10 - spatstat-1.63-0/spatstat/R/rmhmodel.R | 17 + spatstat-1.63-0/spatstat/R/rmhsnoop.R | 115 ++++++----- spatstat-1.63-0/spatstat/R/smooth.ppp.R | 10 - spatstat-1.63-0/spatstat/R/sparse3Darray.R | 23 +- spatstat-1.63-0/spatstat/R/sparsecommon.R | 33 ++- spatstat-1.63-0/spatstat/R/sparselinalg.R | 3 spatstat-1.63-0/spatstat/R/split.ppp.R | 13 - spatstat-1.63-0/spatstat/R/symbolmap.R | 5 spatstat-1.63-0/spatstat/R/sysdata.rda |binary spatstat-1.63-0/spatstat/R/weights.R | 10 - spatstat-1.63-0/spatstat/build/vignette.rds |binary spatstat-1.63-0/spatstat/inst/doc/Nickname.txt | 2 spatstat-1.63-0/spatstat/inst/doc/bugfixes.Rnw | 64 ++++++ spatstat-1.63-0/spatstat/inst/doc/bugfixes.pdf |binary spatstat-1.63-0/spatstat/inst/doc/datasets.pdf |binary spatstat-1.63-0/spatstat/inst/doc/getstart.pdf |binary spatstat-1.63-0/spatstat/inst/doc/packagesizes.txt | 1 spatstat-1.63-0/spatstat/inst/doc/replicated.pdf |binary spatstat-1.63-0/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.63-0/spatstat/inst/doc/updates.Rnw | 54 ++++- spatstat-1.63-0/spatstat/inst/doc/updates.pdf |binary spatstat-1.63-0/spatstat/man/bw.lppl.Rd | 3 spatstat-1.63-0/spatstat/man/exactMPLEstrauss.Rd | 26 +- spatstat-1.63-0/spatstat/man/lineardisc.Rd | 10 - spatstat-1.63-0/spatstat/man/logLik.kppm.Rd | 39 ++-- spatstat-1.63-0/spatstat/man/maxnndist.Rd | 21 +- spatstat-1.63-0/spatstat/man/nndist.Rd | 15 - spatstat-1.63-0/spatstat/man/plot.owin.Rd | 11 + spatstat-1.63-0/spatstat/man/plot.profilepl.Rd |only spatstat-1.63-0/spatstat/man/profilepl.Rd | 16 + spatstat-1.63-0/spatstat/man/rDGS.Rd | 1 spatstat-1.63-0/spatstat/man/rDiggleGratton.Rd | 1 spatstat-1.63-0/spatstat/man/rHardcore.Rd | 2 spatstat-1.63-0/spatstat/man/rPenttinen.Rd | 6 spatstat-1.63-0/spatstat/man/rStrauss.Rd | 2 spatstat-1.63-0/spatstat/man/rStraussHard.Rd | 1 spatstat-1.63-0/spatstat/man/repairNetwork.Rd | 7 spatstat-1.63-0/spatstat/man/spatstat-deprecated.Rd | 24 -- spatstat-1.63-0/spatstat/man/spatstat-internal.Rd | 22 +- spatstat-1.63-0/spatstat/man/split.ppp.Rd | 2 spatstat-1.63-0/spatstat/src/idw.c | 3 spatstat-1.63-0/spatstat/src/multihard.c | 2 spatstat-1.63-0/spatstat/tests/testsAtoC.R |only spatstat-1.63-0/spatstat/tests/testsD.R |only spatstat-1.63-0/spatstat/tests/testsEtoF.R | 78 +++++++- spatstat-1.63-0/spatstat/tests/testsGtoJ.R |only spatstat-1.63-0/spatstat/tests/testsK.R |only spatstat-1.63-0/spatstat/tests/testsL.R |only spatstat-1.63-0/spatstat/tests/testsM.R |only spatstat-1.63-0/spatstat/tests/testsNtoO.R |only spatstat-1.63-0/spatstat/tests/testsP1.R |only spatstat-1.63-0/spatstat/tests/testsP2.R |only spatstat-1.63-0/spatstat/tests/testsQ.R |only spatstat-1.63-0/spatstat/tests/testsR1.R |only spatstat-1.63-0/spatstat/tests/testsR2.R |only spatstat-1.63-0/spatstat/tests/testsS.R |only spatstat-1.63-0/spatstat/tests/testsT.R |only spatstat-1.63-0/spatstat/tests/testsUtoZ.R |only spatstat-1.63-0/spatstat/vignettes/bugfixes.Rnw | 64 ++++++ spatstat-1.63-0/spatstat/vignettes/updates.Rnw | 54 ++++- 109 files changed, 1246 insertions(+), 574 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>),
Carsten Schwemmer [ctb],
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>),
Amir Djalovski [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.1 dated 2019-12-03 and 2.8.2 dated 2020-01-23
sjPlot-2.8.1/sjPlot/R/Deprecated.R |only sjPlot-2.8.1/sjPlot/R/reexports.R |only sjPlot-2.8.1/sjPlot/R/sjPlotGroupFrequencies.R |only sjPlot-2.8.1/sjPlot/R/sjPlotxtab.R |only sjPlot-2.8.1/sjPlot/R/sjTabItemAnalysis.R |only sjPlot-2.8.1/sjPlot/R/sjTabPropTable.R |only sjPlot-2.8.1/sjPlot/R/sjTabSPSS.R |only sjPlot-2.8.1/sjPlot/R/sjTabStackFrq.R |only sjPlot-2.8.1/sjPlot/man/reexports.Rd |only sjPlot-2.8.1/sjPlot/man/sjc.qclus.Rd |only sjPlot-2.8.1/sjPlot/man/sjt.itemanalysis.Rd |only sjPlot-2.8.1/sjPlot/man/sjt.xtab.Rd |only sjPlot-2.8.1/sjPlot/tests/testthat/test-sjp_grpfrq.R |only sjPlot-2.8.2/sjPlot/DESCRIPTION | 25 +- sjPlot-2.8.2/sjPlot/MD5 | 134 +++++++--------- sjPlot-2.8.2/sjPlot/NAMESPACE | 36 +--- sjPlot-2.8.2/sjPlot/NEWS.md | 17 ++ sjPlot-2.8.2/sjPlot/R/html_print_utils.R | 2 sjPlot-2.8.2/sjPlot/R/plot_diag_linear.R | 8 sjPlot-2.8.2/sjPlot/R/plot_frq.R | 39 ++-- sjPlot-2.8.2/sjPlot/R/plot_grid.R | 53 +++--- sjPlot-2.8.2/sjPlot/R/plot_grpfrq.R |only sjPlot-2.8.2/sjPlot/R/plot_kfold_cv.R | 22 ++ sjPlot-2.8.2/sjPlot/R/plot_likert.R | 7 sjPlot-2.8.2/sjPlot/R/plot_model.R | 12 - sjPlot-2.8.2/sjPlot/R/plot_models.R | 1 sjPlot-2.8.2/sjPlot/R/plot_type_est.R | 1 sjPlot-2.8.2/sjPlot/R/plot_type_ranef.R | 8 sjPlot-2.8.2/sjPlot/R/plot_xtab.R |only sjPlot-2.8.2/sjPlot/R/select_helpers.R | 23 ++ sjPlot-2.8.2/sjPlot/R/sjPlotFA.R | 5 sjPlot-2.8.2/sjPlot/R/sjPlotPCA.R | 5 sjPlot-2.8.2/sjPlot/R/sjPlotPolynomials.R | 13 - sjPlot-2.8.2/sjPlot/R/sjTabCorr.R | 2 sjPlot-2.8.2/sjPlot/R/sjTabFA.R | 12 - sjPlot-2.8.2/sjPlot/R/sjTabPCA.R | 9 - sjPlot-2.8.2/sjPlot/R/sjplot.R | 6 sjPlot-2.8.2/sjPlot/R/tab_itemscale.R |only sjPlot-2.8.2/sjPlot/R/tab_model.R | 38 ++-- sjPlot-2.8.2/sjPlot/R/tab_stackfrq.R |only sjPlot-2.8.2/sjPlot/R/tab_xtab.R |only sjPlot-2.8.2/sjPlot/R/tidiers.R | 71 ++------ sjPlot-2.8.2/sjPlot/R/utils.R | 17 -- sjPlot-2.8.2/sjPlot/R/view_df.R |only sjPlot-2.8.2/sjPlot/build/vignette.rds |binary sjPlot-2.8.2/sjPlot/inst/doc/blackwhitefigures.html | 12 - sjPlot-2.8.2/sjPlot/inst/doc/custplot.html | 12 - sjPlot-2.8.2/sjPlot/inst/doc/plot_interactions.html | 12 - sjPlot-2.8.2/sjPlot/inst/doc/plot_likert_scales.html | 24 +- sjPlot-2.8.2/sjPlot/inst/doc/plot_marginal_effects.html | 12 - sjPlot-2.8.2/sjPlot/inst/doc/plot_model_estimates.html | 14 - sjPlot-2.8.2/sjPlot/inst/doc/sjtitemanalysis.R | 12 + sjPlot-2.8.2/sjPlot/inst/doc/sjtitemanalysis.Rmd | 16 + sjPlot-2.8.2/sjPlot/inst/doc/sjtitemanalysis.html | 68 +++----- sjPlot-2.8.2/sjPlot/inst/doc/tab_bayes.R | 12 + sjPlot-2.8.2/sjPlot/inst/doc/tab_bayes.Rmd | 12 + sjPlot-2.8.2/sjPlot/inst/doc/tab_bayes.html | 44 ++--- sjPlot-2.8.2/sjPlot/inst/doc/tab_mixed.R | 12 + sjPlot-2.8.2/sjPlot/inst/doc/tab_mixed.Rmd | 12 + sjPlot-2.8.2/sjPlot/inst/doc/tab_mixed.html | 47 +---- sjPlot-2.8.2/sjPlot/inst/doc/tab_model_estimates.html | 12 - sjPlot-2.8.2/sjPlot/inst/doc/table_css.html | 12 - sjPlot-2.8.2/sjPlot/man/plot_frq.Rd | 32 ++- sjPlot-2.8.2/sjPlot/man/plot_grid.Rd | 45 ++--- sjPlot-2.8.2/sjPlot/man/plot_grpfrq.Rd | 50 ----- sjPlot-2.8.2/sjPlot/man/plot_model.Rd | 12 - sjPlot-2.8.2/sjPlot/man/plot_xtab.Rd | 44 ----- sjPlot-2.8.2/sjPlot/man/sjplot.Rd | 2 sjPlot-2.8.2/sjPlot/man/sjt.fa.Rd | 1 sjPlot-2.8.2/sjPlot/man/sjt.pca.Rd | 1 sjPlot-2.8.2/sjPlot/man/tab_itemscale.Rd |only sjPlot-2.8.2/sjPlot/man/tab_model.Rd | 16 + sjPlot-2.8.2/sjPlot/man/tab_stackfrq.Rd | 3 sjPlot-2.8.2/sjPlot/man/tab_xtab.Rd |only sjPlot-2.8.2/sjPlot/man/view_df.Rd | 2 sjPlot-2.8.2/sjPlot/tests/testthat/test-plot_grpfrq.R |only sjPlot-2.8.2/sjPlot/vignettes/sjtitemanalysis.Rmd | 16 + sjPlot-2.8.2/sjPlot/vignettes/tab_bayes.Rmd | 12 + sjPlot-2.8.2/sjPlot/vignettes/tab_mixed.Rmd | 12 + 79 files changed, 554 insertions(+), 605 deletions(-)
Title: Maximum Likelihood Shrinkage using Generalized Ridge or Least
Angle Regression Methods
Description: Functions are provided to calculate and display ridge TRACEs for various
shrinkage PATHS. They determine the m-Extent of shrinkage most likely, under
Normal-distribution theory, to produce biased estimates of regression (beta) coefficients
with minimum MSE Risk. An alternative function, correct.signs(), provides beta coefficient
estimates when an ill-conditioned (nearly multicollinear) model yields OLS estimates with
("wrong") numerical signs that disagree with the signs of the observed correlations between
the Y-outcome and the selected X-predictor variables.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between RXshrink versions 1.3 dated 2019-12-09 and 1.3.1 dated 2020-01-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/unr.ridge.R | 28 +++++++++++++++++----------- man/RXshrink-package.Rd | 4 ++-- 4 files changed, 26 insertions(+), 20 deletions(-)
Title: MNREAD Parameters Estimation and Curve Plotting
Description: Allows to analyze the reading data obtained with the MNREAD Acuity
Chart, a continuous-text reading acuity chart for normal and low vision.
Provides the necessary functions to plot the MNREAD curve and estimate
automatically the four MNREAD parameters: Maximum Reading Speed,
Critical Print Size, Reading Acuity and Reading Accessibility Index.
Parameters can be estimated either with the standard method
or with a nonlinear mixed-effects (NLME) modeling.
See Calabrese et al. 2018 for more details <doi:10.1167/18.1.8>.
Author: Aurélie Calabrèse [aut, cre],
J. Steve Mansfield [aut],
Gordon E. Legge [aut]
Maintainer: Aurélie Calabrèse <aurelie.calabrese@inria.fr>
Diff between mnreadR versions 2.1.3 dated 2019-07-19 and 2.1.4 dated 2020-01-23
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 10 ++++++++-- R/mnreadR.R | 4 ++-- R/mnread_curve.R | 6 ++---- R/zzz.R | 4 ++-- 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Generalized Hyperbolic Distribution and Its Special Cases
Description: Detailed functionality for working
with the univariate and multivariate Generalized Hyperbolic
distribution and its special cases (Hyperbolic (hyp), Normal
Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t
and Gaussian distribution). Especially, it contains fitting
procedures, an AIC-based model selection routine, and functions
for the computation of density, quantile, probability, random
variates, expected shortfall and some portfolio optimization
and plotting routines as well as the likelihood ratio test. In
addition, it contains the Generalized Inverse Gaussian
distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts.
Quantitative risk management: Concepts, techniques and tools.
Princeton University Press, Princeton (2005).
Author: David Luethi, Wolfgang Breymann
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between ghyp versions 1.5.7 dated 2016-08-17 and 1.5.8 dated 2020-01-23
ChangeLog | 7 DESCRIPTION | 20 MD5 | 39 NAMESPACE | 4 R/ghypFitting.R | 1120 ++++---- R/ghypGenericMethods.R | 1539 ++++++------ R/ghypInternals.R | 1823 +++++++------- R/ghypMethods.R | 2056 ++++++++-------- build/vignette.rds |binary inst/doc/Generalized_Hyperbolic_Distribution.R | 370 +- inst/doc/Generalized_Hyperbolic_Distribution.Rnw | 2752 +++++++++++---------- inst/doc/Generalized_Hyperbolic_Distribution.pdf |binary man/fit.ghypmv.Rd | 5 man/fit.ghypuv.Rd | 2 man/ghyp-constructors.Rd | 2 man/ghyp-distribution.Rd | 2 man/ghyp-package.Rd | 8 man/pairs-methods.Rd | 8 src/init.c |only src/rgig.c | 5 vignettes/Generalized_Hyperbolic_Distribution.Rnw | 2755 +++++++++++----------- 21 files changed, 6278 insertions(+), 6239 deletions(-)
Title: Scales that Focus Specific Levels in your ggplot()
Description: A 'ggplot2' extension that provides tools for automatically
creating scales to focus on subgroups of the data plotted
without losing other information.
Author: Victor Freguglia [aut, cre]
Maintainer: Victor Freguglia <victorfreguglia@gmail.com>
Diff between ggfocus versions 0.9 dated 2019-01-07 and 1.0.0 dated 2020-01-23
ggfocus-0.9/ggfocus/LICENSE |only ggfocus-0.9/ggfocus/R/gg-focus.R |only ggfocus-0.9/ggfocus/inst/doc/a-quick-guide-to-ggfocus.R |only ggfocus-0.9/ggfocus/inst/doc/a-quick-guide-to-ggfocus.Rmd |only ggfocus-0.9/ggfocus/inst/doc/a-quick-guide-to-ggfocus.html |only ggfocus-0.9/ggfocus/man/figures/README-ex1_create-1.png |only ggfocus-0.9/ggfocus/man/figures/README-unnamed-chunk-2-1.png |only ggfocus-0.9/ggfocus/man/figures/README-unnamed-chunk-3-1.png |only ggfocus-0.9/ggfocus/man/figures/README-unnamed-chunk-4-1.png |only ggfocus-0.9/ggfocus/man/figures/README-unnamed-chunk-6-1.png |only ggfocus-0.9/ggfocus/man/scale_alpha_focus.Rd |only ggfocus-0.9/ggfocus/man/scale_color_focus.Rd |only ggfocus-0.9/ggfocus/man/scale_fill_focus.Rd |only ggfocus-0.9/ggfocus/vignettes/a-quick-guide-to-ggfocus.Rmd |only ggfocus-1.0.0/ggfocus/DESCRIPTION | 24 + ggfocus-1.0.0/ggfocus/MD5 | 47 +-- ggfocus-1.0.0/ggfocus/NAMESPACE | 14 - ggfocus-1.0.0/ggfocus/NEWS.md | 7 ggfocus-1.0.0/ggfocus/R/ggfocus.R |only ggfocus-1.0.0/ggfocus/R/scale_alpha_focus.R | 62 ++-- ggfocus-1.0.0/ggfocus/R/scale_color_focus.R | 87 ++++-- ggfocus-1.0.0/ggfocus/R/scale_fill_focus.R | 70 +++-- ggfocus-1.0.0/ggfocus/R/scale_linetype_focus.R |only ggfocus-1.0.0/ggfocus/R/scale_shape_focus.R |only ggfocus-1.0.0/ggfocus/R/scale_size_focus.R |only ggfocus-1.0.0/ggfocus/R/zzz.R |only ggfocus-1.0.0/ggfocus/README.md | 149 +++++------ ggfocus-1.0.0/ggfocus/build/vignette.rds |binary ggfocus-1.0.0/ggfocus/inst/doc/introduction_to_ggfocus.R |only ggfocus-1.0.0/ggfocus/inst/doc/introduction_to_ggfocus.Rmd |only ggfocus-1.0.0/ggfocus/inst/doc/introduction_to_ggfocus.html |only ggfocus-1.0.0/ggfocus/man/figures/README-example_2-1.png |only ggfocus-1.0.0/ggfocus/man/figures/README-example_map-1.png |only ggfocus-1.0.0/ggfocus/man/figures/logo.png |only ggfocus-1.0.0/ggfocus/man/ggfocus.Rd | 26 + ggfocus-1.0.0/ggfocus/man/reexports.Rd | 2 ggfocus-1.0.0/ggfocus/man/scale_focus.Rd |only ggfocus-1.0.0/ggfocus/vignettes/introduction_to_ggfocus.Rmd |only 38 files changed, 293 insertions(+), 195 deletions(-)
Title: Analysis of Feedback in Time Series
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand <samuel.soubeyrand@inrae.fr>
Diff between FeedbackTS versions 1.4 dated 2016-05-10 and 1.5 dated 2020-01-23
DESCRIPTION | 14 +-- MD5 | 26 ++--- NAMESPACE | 9 + R/KT.output.R | 2 R/feedback.spatial.R | 186 ++++++++++++++++++++--------------------- data/rain.feedback.stats.RData |binary data/rain.site.6008.RData |binary man/FeedbackTS-package.Rd | 24 ++--- man/KDD-class.Rd | 10 +- man/KT.output-class.Rd | 25 ++--- man/krige.Rd | 86 ++++++++++-------- man/krige.test.Rd | 15 +-- man/map.statistic.Rd | 2 man/rain.feedback.stats.Rd | 2 14 files changed, 207 insertions(+), 194 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.1.5 dated 2019-10-18 and 1.1.6 dated 2020-01-23
DESCRIPTION | 8 ++--- MD5 | 72 +++++++++++++++++++++++----------------------- R/dNetPipeline.r | 2 + R/visBoxplotAdv.r | 2 + data/TCGA_mutations.RData |binary data/ig.HPPA.RData |binary data/org.Hs.egHPPA.RData |binary man/TCGA_mutations.Rd | 13 +++++--- man/dContrast.Rd | 6 ++- man/dDAGannotate.Rd | 9 +++-- man/dDAGgeneSim.Rd | 16 +++++++--- man/dDAGinduce.Rd | 7 +++- man/dDAGlevel.Rd | 7 +++- man/dDAGtermSim.Rd | 12 +++++-- man/dEnricher.Rd | 36 +++++++++++++++-------- man/dEnricherView.Rd | 10 ++++-- man/dGSEA.Rd | 37 +++++++++++++++-------- man/dGSEAview.Rd | 12 +++++-- man/dGSEAwrite.Rd | 13 +++++--- man/dNetInduce.Rd | 10 +++++- man/dNetPipeline.Rd | 12 +++++-- man/dNetReorder.Rd | 21 +++++++++---- man/dPvalAggregate.Rd | 9 +++-- man/dRDataLoader.Rd | 71 ++++++++++++++++++++++++++++----------------- man/dRWR.Rd | 14 ++++++-- man/dRWRcontact.Rd | 17 ++++++++-- man/dRWRpipeline.Rd | 19 ++++++++---- man/dSVDsignif.Rd | 14 ++++++-- man/visBoxplotAdv.Rd | 44 +++++++++++++++++++++------- man/visDAG.Rd | 26 ++++++++++++---- man/visGSEA.Rd | 12 +++++-- man/visNet.Rd | 27 ++++++++++++----- man/visNetAnimate.Rd | 34 +++++++++++++++------ man/visNetArc.Rd | 24 +++++++++++---- man/visNetCircle.Rd | 28 ++++++++++++----- man/visNetMul.Rd | 27 ++++++++++++----- man/visNetReorder.Rd | 28 +++++++++++++---- 37 files changed, 483 insertions(+), 216 deletions(-)
Title: Managing, Querying and Analyzing Tokenized Text
Description: Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations).
Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences),
similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages,
and the possibility to reconstruct original text from tokens to facilitate interpretation.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between corpustools versions 0.4.1 dated 2019-11-19 and 0.4.2 dated 2020-01-23
DESCRIPTION | 20 - MD5 | 81 +++--- NAMESPACE | 3 NEWS.md | 5 R/1_tcorpus.r | 75 ------ R/RcppExports.R | 4 R/adjacency_functions.r | 2 R/aggregate.r |only R/collocations.r | 12 - R/compare_corpora.r | 6 R/compare_documents.r | 8 R/create_tcorpus.r | 51 ++-- R/data.r | 8 R/document_term_matrix.r | 3 R/plot_words.r | 4 R/preprocessing.r | 2 R/search_contexts.r | 2 R/search_dictionary.r | 380 ++++++++++++++++++++------------ R/search_features.r | 2 R/search_results.r | 2 R/semnet.r | 7 R/tokenize.r | 3 README.md | 8 build/vignette.rds |binary data/emoticon_dict.rda |only inst/doc/corpustools.R | 37 ++- inst/doc/corpustools.Rmd | 71 +++++ inst/doc/corpustools.html | 101 +++++--- man/agg_tcorpus.Rd |only man/compare_corpus.Rd | 2 man/compare_documents.Rd | 4 man/compare_subset.Rd | 2 man/count_tcorpus.Rd |only man/create_tcorpus.Rd | 40 ++- man/dtm_compare.Rd | 2 man/emoticon_dict.Rd |only man/plot.vocabularyComparison.Rd | 4 man/search_dictionary.Rd | 21 + man/tCorpus-cash-code_dictionary.Rd | 12 - man/tCorpus-cash-replace_dictionary.Rd |only src/RcppExports.cpp | 16 + src/dictionary_lookup.cpp |only tests/testthat/test_dictionary_lookup.r | 7 tests/testthat/test_search_features.r | 4 vignettes/corpustools.Rmd | 71 +++++ 45 files changed, 693 insertions(+), 389 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-15 0.6.10
2018-10-06 0.6.5
2018-08-27 0.6.4
2018-03-15 0.6.2
Title: Data Table Back-End for 'dplyr'
Description: Provides a data.table backend for 'dplyr'. The goal of 'dtplyr'
is to allow you to write 'dplyr' code that is automatically translated to
the equivalent, but usually much faster, data.table code.
Author: Lionel Henry [aut],
Hadley Wickham [cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dtplyr versions 1.0.0 dated 2019-11-12 and 1.0.1 dated 2020-01-23
DESCRIPTION | 10 +-- MD5 | 47 +++++++------- NAMESPACE | 4 + NEWS.md | 22 ++++++ R/step-group.R | 32 ++++++++- R/step-join.R | 55 +++++++++------- R/step-modify.R | 7 -- R/step-mutate.R | 6 - R/step-subset.R | 12 ++- R/step.R | 25 +++++++ R/tidyeval.R | 18 ++++- inst/doc/translation.R | 61 +++++++++--------- inst/doc/translation.Rmd | 8 ++ inst/doc/translation.html | 121 +++++++++++++++++++------------------ man/single_table.Rd |only tests/testthat/helpers-library.R | 1 tests/testthat/test-step-call.R | 2 tests/testthat/test-step-first.R | 8 +- tests/testthat/test-step-group.R | 20 ++++++ tests/testthat/test-step-join.R | 25 ++++++- tests/testthat/test-step-print.txt | 17 +++++ tests/testthat/test-step-subset.R | 4 - tests/testthat/test-step.R | 8 +- tests/testthat/test-tidyeval.R | 13 +++ vignettes/translation.Rmd | 8 ++ 25 files changed, 361 insertions(+), 173 deletions(-)