Tue, 11 Oct 2016

Package rbokeh updated to version 0.5.0 with previous version 0.4.2 dated 2016-03-08

Title: R Interface for Bokeh
Description: A native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library <http://bokeh.pydata.org/>.
Author: Ryan Hafen [aut, cre], Kenton Russell [ctb], Jonathan Owen [ctb], Barret Schloerke [ctb], Saptasrhi Guha [ctb], Continuum Analytics, Inc. [aut, cph] (Bokeh library in htmlwidgets/lib, http://bokeh.pydata.org)
Maintainer: Ryan Hafen <rhafen@gmail.com>

Diff between rbokeh versions 0.4.2 dated 2016-03-08 and 0.5.0 dated 2016-10-11

 rbokeh-0.4.2/rbokeh/data/flightFreq.rda                                |only
 rbokeh-0.5.0/rbokeh/DESCRIPTION                                        |   21 
 rbokeh-0.5.0/rbokeh/MD5                                                |  194 +-
 rbokeh-0.5.0/rbokeh/NAMESPACE                                          |    6 
 rbokeh-0.5.0/rbokeh/NEWS.md                                            |   69 +
 rbokeh-0.5.0/rbokeh/R/attr_mapping.R                                   |   60 
 rbokeh-0.5.0/rbokeh/R/bokeh_render_json.R                              |    6 
 rbokeh-0.5.0/rbokeh/R/constants.R                                      |   74 -
 rbokeh-0.5.0/rbokeh/R/fig_axis.R                                       |   43 
 rbokeh-0.5.0/rbokeh/R/fig_callback.R                                   |    8 
 rbokeh-0.5.0/rbokeh/R/fig_gmap.R                                       |   34 
 rbokeh-0.5.0/rbokeh/R/fig_grid.R                                       |  365 +++--
 rbokeh-0.5.0/rbokeh/R/fig_hover.R                                      |   40 
 rbokeh-0.5.0/rbokeh/R/fig_layer.R                                      |   51 
 rbokeh-0.5.0/rbokeh/R/fig_legend.R                                     |    2 
 rbokeh-0.5.0/rbokeh/R/fig_range.R                                      |   22 
 rbokeh-0.5.0/rbokeh/R/fig_tap.R                                        |   24 
 rbokeh-0.5.0/rbokeh/R/fig_title.R                                      |only
 rbokeh-0.5.0/rbokeh/R/fig_tool.R                                       |   37 
 rbokeh-0.5.0/rbokeh/R/figure.R                                         |  130 -
 rbokeh-0.5.0/rbokeh/R/helpers.R                                        |  379 +----
 rbokeh-0.5.0/rbokeh/R/helpers_extra_pars.R                             |   52 
 rbokeh-0.5.0/rbokeh/R/json_helpers.R                                   |    6 
 rbokeh-0.5.0/rbokeh/R/layer__utils.R                                   |   94 -
 rbokeh-0.5.0/rbokeh/R/layer_bar.R                                      |   97 +
 rbokeh-0.5.0/rbokeh/R/layer_glyphs.R                                   |   64 
 rbokeh-0.5.0/rbokeh/R/layer_hexbin.R                                   |   39 
 rbokeh-0.5.0/rbokeh/R/layer_image.R                                    |   90 -
 rbokeh-0.5.0/rbokeh/R/layer_lines.R                                    |  134 +
 rbokeh-0.5.0/rbokeh/R/layer_map.R                                      |    3 
 rbokeh-0.5.0/rbokeh/R/layer_points.R                                   |   25 
 rbokeh-0.5.0/rbokeh/R/layer_shapes.R                                   |   67 
 rbokeh-0.5.0/rbokeh/R/layer_stats.R                                    |  147 +-
 rbokeh-0.5.0/rbokeh/R/layer_text.R                                     |   17 
 rbokeh-0.5.0/rbokeh/R/make_glyph.R                                     |  110 -
 rbokeh-0.5.0/rbokeh/R/misc.R                                           |    7 
 rbokeh-0.5.0/rbokeh/R/output_gist.R                                    |   21 
 rbokeh-0.5.0/rbokeh/R/output_html.R                                    |   60 
 rbokeh-0.5.0/rbokeh/R/output_json.R                                    |    8 
 rbokeh-0.5.0/rbokeh/R/output_prerender.R                               |   11 
 rbokeh-0.5.0/rbokeh/R/output_save.R                                    |   25 
 rbokeh-0.5.0/rbokeh/R/point_types.R                                    |   10 
 rbokeh-0.5.0/rbokeh/R/prepare_figure.R                                 |  236 ++-
 rbokeh-0.5.0/rbokeh/R/rbokeh-package.R                                 |   11 
 rbokeh-0.5.0/rbokeh/R/shiny.R                                          |   12 
 rbokeh-0.5.0/rbokeh/R/theme_axis.R                                     |   57 
 rbokeh-0.5.0/rbokeh/R/theme_grid.R                                     |   44 
 rbokeh-0.5.0/rbokeh/R/theme_legend.R                                   |   21 
 rbokeh-0.5.0/rbokeh/R/theme_palettes.R                                 |  152 ++
 rbokeh-0.5.0/rbokeh/R/theme_plot.R                                     |   41 
 rbokeh-0.5.0/rbokeh/R/theme_title.R                                    |only
 rbokeh-0.5.0/rbokeh/R/themes.R                                         |   36 
 rbokeh-0.5.0/rbokeh/README.md                                          |   19 
 rbokeh-0.5.0/rbokeh/build                                              |only
 rbokeh-0.5.0/rbokeh/data/flightfreq.rda                                |only
 rbokeh-0.5.0/rbokeh/inst/doc                                           |only
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-compiler.min.js |   36 
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.css |   38 
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js  |   98 -
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.css         |    2 
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.js          |  140 +-
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/loader.css            |only
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/rbokeh.js                         |   73 -
 rbokeh-0.5.0/rbokeh/inst/htmlwidgets/rbokeh.yaml                       |    3 
 rbokeh-0.5.0/rbokeh/man/catjitter.Rd                                   |    7 
 rbokeh-0.5.0/rbokeh/man/elements.Rd                                    |    2 
 rbokeh-0.5.0/rbokeh/man/figure.Rd                                      |   10 
 rbokeh-0.5.0/rbokeh/man/gmap.Rd                                        |   19 
 rbokeh-0.5.0/rbokeh/man/gmap_style.Rd                                  |   15 
 rbokeh-0.5.0/rbokeh/man/grid_plot.Rd                                   |   45 
 rbokeh-0.5.0/rbokeh/man/ly_abline.Rd                                   |   16 
 rbokeh-0.5.0/rbokeh/man/ly_annular_wedge.Rd                            |   25 
 rbokeh-0.5.0/rbokeh/man/ly_annulus.Rd                                  |   23 
 rbokeh-0.5.0/rbokeh/man/ly_arc.Rd                                      |   26 
 rbokeh-0.5.0/rbokeh/man/ly_bar.Rd                                      |   39 
 rbokeh-0.5.0/rbokeh/man/ly_boxplot.Rd                                  |   15 
 rbokeh-0.5.0/rbokeh/man/ly_crect.Rd                                    |    2 
 rbokeh-0.5.0/rbokeh/man/ly_density.Rd                                  |    6 
 rbokeh-0.5.0/rbokeh/man/ly_hist.Rd                                     |    6 
 rbokeh-0.5.0/rbokeh/man/ly_image.Rd                                    |    4 
 rbokeh-0.5.0/rbokeh/man/ly_image_url.Rd                                |    2 
 rbokeh-0.5.0/rbokeh/man/ly_quantile.Rd                                 |    4 
 rbokeh-0.5.0/rbokeh/man/ly_text.Rd                                     |    2 
 rbokeh-0.5.0/rbokeh/man/ly_wedge.Rd                                    |   25 
 rbokeh-0.5.0/rbokeh/man/nyctaxihex.Rd                                  |   11 
 rbokeh-0.5.0/rbokeh/man/palettes.Rd                                    |   16 
 rbokeh-0.5.0/rbokeh/man/point_types.Rd                                 |    3 
 rbokeh-0.5.0/rbokeh/man/print_model_json.Rd                            |    2 
 rbokeh-0.5.0/rbokeh/man/set_palette.Rd                                 |only
 rbokeh-0.5.0/rbokeh/man/set_theme.Rd                                   |   31 
 rbokeh-0.5.0/rbokeh/man/sub_names.Rd                                   |    2 
 rbokeh-0.5.0/rbokeh/man/theme_axis.Rd                                  |   10 
 rbokeh-0.5.0/rbokeh/man/theme_grid.Rd                                  |   10 
 rbokeh-0.5.0/rbokeh/man/theme_legend.Rd                                |   25 
 rbokeh-0.5.0/rbokeh/man/theme_plot.Rd                                  |   43 
 rbokeh-0.5.0/rbokeh/man/theme_title.Rd                                 |only
 rbokeh-0.5.0/rbokeh/man/x_axis.Rd                                      |   12 
 rbokeh-0.5.0/rbokeh/man/y_axis.Rd                                      |   12 
 rbokeh-0.5.0/rbokeh/tests/testthat/test-css-svg.R                      |    7 
 rbokeh-0.5.0/rbokeh/tests/testthat/test-figures.R                      |  672 ++++++++--
 rbokeh-0.5.0/rbokeh/vignettes                                          |only
 101 files changed, 2970 insertions(+), 1850 deletions(-)

More information about rbokeh at CRAN
Permanent link

New package PRISMAstatement with initial version 1.0.1
Package: PRISMAstatement
Title: Plot Flow Charts According to the "PRISMA" Statement
Version: 1.0.1
Authors@R: person("Jack O. Wasey", role = c("aut", "cre", "cph"), email = "jack@jackwasey.com")
Description: Plot a PRISMA <http://prisma-statement.org/> flow chart describing the identification, screening, eligibility and inclusion or studies in systematic reviews. PRISMA is an evidence-based minimum set of items for reporting in systematic reviews and meta-analyses. PRISMA focuses on the reporting of reviews evaluating randomized trials, but can also be used as a basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
URL: URL: https://github.com/jackwasey/PRISMAstatement
Imports: DiagrammeR
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
BugReports: https://github.com/jackwasey/PRISMAstatement/issues
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-10-11 18:40:50 UTC; waseyj
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Repository: CRAN
Date/Publication: 2016-10-12 00:41:35

More information about PRISMAstatement at CRAN
Permanent link

Package ODMconverter updated to version 2.2 with previous version 2.1 dated 2015-04-02

Title: Tools to Convert ODM Files
Description: Transformation of 'ODM' (see <http://www.cdisc.org/odm>) files into R format, Microsoft Office format, 'CDA' format and vice versa. 'ODM' format is commonly used in clinical trials. Semantic annotation (such as 'UMLS', 'SNOMED' or 'LOINC' codes) are transformed accordingly.
Author: Martin Dugas
Maintainer: Martin Dugas <dugas@uni-muenster.de>

Diff between ODMconverter versions 2.1 dated 2015-04-02 and 2.2 dated 2016-10-11

 DESCRIPTION  |   10 +++++-----
 MD5          |    8 ++++----
 NAMESPACE    |    1 +
 R/ODM2R.R    |   38 +++++++++++++++++++++++---------------
 man/ODM2R.Rd |    8 +++++++-
 5 files changed, 40 insertions(+), 25 deletions(-)

More information about ODMconverter at CRAN
Permanent link

New package oddsratio with initial version 0.2
Package: oddsratio
Version: 0.2
Title: Odds Ratio Calculation for GAM & GLM
Author: Patrick Schratz
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Description: Simplified odds ratio calculation of GAM(M)s & GLM(M)s. Provides structured output (data frame) of all predictors and their corresponding odds ratios for further analyses. It helps to avoid false references of predictors and increments by specifying these parameters in a list instead of using 'exp(coef(model))' (standard approach of odds ratio calculation for GLMs) which just returns a plain numeric output. For GAM(M)s, odds ratio calculation is highly simplified with this package since it takes care of the multiple 'predict()' calls of the chosen predictor while holding other predictors constant. Also, this package allows odds ratio calculation of percentage steps across the whole predictor distribution range for GAM(M)s.
URL: https://github.com/pat-s/oddsratio
BugReports: https://github.com/pat-s/oddsratio/issues
Imports: mgcv, MASS, stats
License: MIT + file LICENSE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, nlme
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-10-11 18:23:21 UTC; pjs
Repository: CRAN
Date/Publication: 2016-10-12 00:03:07

More information about oddsratio at CRAN
Permanent link

Package nLTT updated to version 1.3.1 with previous version 1.3 dated 2016-10-05

Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
Author: Thijs Janzen [aut, cre], Richel Bilderbeek [aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>

Diff between nLTT versions 1.3 dated 2016-10-05 and 1.3.1 dated 2016-10-11

 nLTT-1.3.1/nLTT/DESCRIPTION                                   |    6 
 nLTT-1.3.1/nLTT/MD5                                           |   44 +-
 nLTT-1.3.1/nLTT/NAMESPACE                                     |    2 
 nLTT-1.3.1/nLTT/R/get_average_nltt_matrix.R                   |   27 -
 nLTT-1.3.1/nLTT/README.md                                     |only
 nLTT-1.3.1/nLTT/build/vignette.rds                            |binary
 nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.R               |    4 
 nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.Rmd             |    4 
 nLTT-1.3.1/nLTT/inst/doc/trees_with_root_edge.html            |   18 -
 nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.R           |  112 +++----
 nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.Rmd         |  127 ++++----
 nLTT-1.3.1/nLTT/inst/doc/vignette_get_nltt_values.html        |  155 +++++-----
 nLTT-1.3.1/nLTT/inst/doc/vignette_nltts_plot.R                |   25 -
 nLTT-1.3.1/nLTT/inst/doc/vignette_nltts_plot.html             |   32 +-
 nLTT-1.3.1/nLTT/inst/doc/vignette_stretch_nltt_matrix.html    |   36 +-
 nLTT-1.3.1/nLTT/inst/doc/walkthrough.R                        |only
 nLTT-1.3.1/nLTT/inst/doc/walkthrough.Rmd                      |only
 nLTT-1.3.1/nLTT/inst/doc/walkthrough.html                     |only
 nLTT-1.3.1/nLTT/man/nLTT-package.Rd                           |   64 ++--
 nLTT-1.3.1/nLTT/tests/testthat/test_get_average_nltt_matrix.R |   41 --
 nLTT-1.3.1/nLTT/vignettes/trees_with_root_edge.Rmd            |    4 
 nLTT-1.3.1/nLTT/vignettes/vignette_get_nltt_values.Rmd        |  102 +++---
 nLTT-1.3.1/nLTT/vignettes/walkthrough.Rmd                     |only
 nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.R            |only
 nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.Rmd          |only
 nLTT-1.3/nLTT/inst/doc/vignette_get_average_nltt.html         |only
 nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_1.Rd           |only
 nLTT-1.3/nLTT/man/get_average_nltt_matrix_impl_2.Rd           |only
 28 files changed, 397 insertions(+), 406 deletions(-)

More information about nLTT at CRAN
Permanent link

New package MethodCompare with initial version 0.1.0
Package: MethodCompare
Type: Package
Title: Bias and Precision Plots to Compare Two Measurements with Possibly Heteroscedastic Measurement Errors
Version: 0.1.0
Date: 2015-11-6
Author: Mingkai Peng, Patrick Taffe, Tyler Williamson
Maintainer: Mingkai Peng <mpeng@ucalgary.ca>
Description: Implementation of the methodology from the paper titled "Effective plots to assess bias and precision in method comparison studies" published in Statistical Methods in Medical Research, P. Taffe (2016) <doi:10.1177/0962280216666667>.
Depends: R (>= 2.10),nlme
Imports: graphics,stats
Repository: CRAN
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-05 19:00:08 UTC; Mingkai
Date/Publication: 2016-10-12 00:37:13

More information about MethodCompare at CRAN
Permanent link

Package ggseas updated to version 0.5.1 with previous version 0.5.0 dated 2016-10-10

Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis [aut, cre], Christophe Sax [ctb]
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>

Diff between ggseas versions 0.5.0 dated 2016-10-10 and 0.5.1 dated 2016-10-11

 DESCRIPTION           |    6 +++---
 MD5                   |   14 ++++++++------
 R/ggseas.R            |only
 R/misc_doc.R          |    2 --
 build/vignette.rds    |binary
 inst/doc/ggsdc.Rmd    |    2 +-
 inst/doc/ggsdc.html   |    4 ++--
 man/ggseas-package.Rd |only
 vignettes/ggsdc.Rmd   |    2 +-
 9 files changed, 15 insertions(+), 15 deletions(-)

More information about ggseas at CRAN
Permanent link

New package GauPro with initial version 0.1.0
Package: GauPro
Type: Package
Title: Gaussian Process Fitting
Version: 0.1.0
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Description: Fits a Gaussian process model to data. Gaussian processes are commonly used in computer experiments to fit an interpolating model. The model is stored as an 'R6' object and can be easily updated with new data. There are options to run in parallel (not for Windows), and 'Rcpp' has been used to speed up calculations. Other R packages that perform similar calculations include 'laGP', 'DiceKriging', 'GPfit', and 'mlegp'.
License: GPL-3
LazyData: TRUE
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, R6, lbfgs
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2016-10-11 20:49:01 UTC; cbe117
Repository: CRAN
Date/Publication: 2016-10-12 00:39:56

More information about GauPro at CRAN
Permanent link

Package fragilityindex updated to version 0.0.7 with previous version 0.0.4 dated 2016-10-06

Title: Fragility Index
Description: Implements and extends the fragility index calculation for dichotomous results as described in Walsh, Srinathan, McAuley, Mrkobrada, Levine, Ribic, Molnar, Dattani, Burke, Guyatt, Thabane, Walter, Pogue, and Devereaux (2014) <DOI:10.1016/j.jclinepi.2013.10.019>.
Author: Kipp Johnson [aut, cre]
Maintainer: Kipp Johnson <kipp.william.johnson@gmail.com>

Diff between fragilityindex versions 0.0.4 dated 2016-10-06 and 0.0.7 dated 2016-10-11

 DESCRIPTION                      |   16 ++++++++--------
 MD5                              |   17 +++++++++++++----
 NAMESPACE                        |   12 ++++++++++++
 R/fragility.index.R              |    9 ++++++---
 R/glmfit2table.R                 |only
 R/logisticfragility.R            |only
 R/logisticfragilityinternal.R    |only
 R/revfragility.index.R           |only
 README.md                        |only
 man/fragility.index.Rd           |    6 ++++--
 man/glmfit2table.Rd              |only
 man/logisticfragility.Rd         |only
 man/logisticfragilityinternal.Rd |only
 man/revfragility.index.Rd        |only
 14 files changed, 43 insertions(+), 17 deletions(-)

More information about fragilityindex at CRAN
Permanent link

Package Fgmutils updated to version 0.9.4 with previous version 0.9.3 dated 2016-09-26

Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga Filho, Ana Paula Simiqueli, Gilson Fernandes da Silva, Miqueias Fernandes, Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>

Diff between Fgmutils versions 0.9.3 dated 2016-09-26 and 0.9.4 dated 2016-10-11

 DESCRIPTION                 |    8 +--
 MD5                         |   22 +++++----
 NAMESPACE                   |    3 +
 NEWS                        |    3 +
 R/avaliaEstimativas.R       |  104 +++++++++++++++++++-------------------------
 R/avaliaVolumeAgeBased.R    |only
 R/avaliaVolumeAvancado.R    |    1 
 R/evalAgeBased.R            |only
 R/projectBaseOriented.R     |only
 R/roundAge.R                |   12 +++--
 R/separaDados.R             |    6 +-
 man/avaliaVolumeAgeBased.Rd |only
 man/evalAgeBased.Rd         |only
 man/projectBaseOriented.Rd  |only
 man/roundAge.Rd             |    4 +
 15 files changed, 85 insertions(+), 78 deletions(-)

More information about Fgmutils at CRAN
Permanent link

Package brms updated to version 1.1.0 with previous version 1.0.1 dated 2016-09-16

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>

Diff between brms versions 1.0.1 dated 2016-09-16 and 1.1.0 dated 2016-10-11

 brms-1.0.1/brms/inst/doc/brms_families.R               |only
 brms-1.0.1/brms/inst/doc/brms_families.html            |only
 brms-1.1.0/brms/DESCRIPTION                            |   10 
 brms-1.1.0/brms/MD5                                    |   73 +-
 brms-1.1.0/brms/R/brm.R                                |    3 
 brms-1.1.0/brms/R/brmsfit-helpers.R                    |  155 ++--
 brms-1.1.0/brms/R/brmsfit-methods.R                    |  104 +--
 brms-1.1.0/brms/R/brmsformula.R                        |   32 
 brms-1.1.0/brms/R/data-helpers.R                       |  125 ++-
 brms-1.1.0/brms/R/extract_draws.R                      |  177 +++--
 brms-1.1.0/brms/R/linear_predictor.R                   |   96 ++
 brms-1.1.0/brms/R/loglik.R                             |    3 
 brms-1.1.0/brms/R/make_stancode.R                      |   75 +-
 brms-1.1.0/brms/R/make_standata.R                      |  124 +--
 brms-1.1.0/brms/R/misc.R                               |   73 +-
 brms-1.1.0/brms/R/plots.R                              |   13 
 brms-1.1.0/brms/R/rename.R                             |  125 ++-
 brms-1.1.0/brms/R/stan-helpers.R                       |  166 +++--
 brms-1.1.0/brms/R/stan-predictor.R                     |  242 ++++---
 brms-1.1.0/brms/R/sysdata.rda                          |binary
 brms-1.1.0/brms/R/validate.R                           |  564 +++++++++++------
 brms-1.1.0/brms/build/vignette.rds                     |binary
 brms-1.1.0/brms/inst/NEWS.Rd                           |   48 +
 brms-1.1.0/brms/inst/chunks/fun_inv_gaussian.stan      |    4 
 brms-1.1.0/brms/inst/chunks/tdataC_inv_gaussian.stan   |only
 brms-1.1.0/brms/inst/chunks/tdataD_inv_gaussian.stan   |only
 brms-1.1.0/brms/inst/doc/brms.pdf                      |binary
 brms-1.1.0/brms/inst/doc/brms_families.Rmd             |   12 
 brms-1.1.0/brms/inst/doc/brms_families.pdf             |only
 brms-1.1.0/brms/man/brmsformula.Rd                     |   32 
 brms-1.1.0/brms/man/residuals.brmsfit.Rd               |   15 
 brms-1.1.0/brms/tests/testthat/tests.brmsfit-helpers.R |   10 
 brms-1.1.0/brms/tests/testthat/tests.brmsfit-methods.R |   24 
 brms-1.1.0/brms/tests/testthat/tests.make_stancode.R   |  107 ++-
 brms-1.1.0/brms/tests/testthat/tests.make_standata.R   |   89 +-
 brms-1.1.0/brms/tests/testthat/tests.plots.R           |    2 
 brms-1.1.0/brms/tests/testthat/tests.rename.R          |   45 +
 brms-1.1.0/brms/tests/testthat/tests.stan-helpers.R    |   35 -
 brms-1.1.0/brms/tests/testthat/tests.validate.R        |   36 -
 brms-1.1.0/brms/vignettes/brms_families.Rmd            |   12 
 40 files changed, 1677 insertions(+), 954 deletions(-)

More information about brms at CRAN
Permanent link

Package bmlm updated to version 1.2.1 with previous version 1.0.0 dated 2016-07-19

Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre]
Maintainer: Matti Vuorre <mv2521@columbia.edu>

Diff between bmlm versions 1.0.0 dated 2016-07-19 and 1.2.1 dated 2016-10-11

 bmlm-1.0.0/bmlm/R/bmlm.R             |only
 bmlm-1.0.0/bmlm/inst/stan            |only
 bmlm-1.0.0/bmlm/man/getpps.Rd        |only
 bmlm-1.2.1/bmlm/DESCRIPTION          |   16 ++-
 bmlm-1.2.1/bmlm/MD5                  |   48 +++++++----
 bmlm-1.2.1/bmlm/NAMESPACE            |    3 
 bmlm-1.2.1/bmlm/NEWS.md              |   28 ++++++
 bmlm-1.2.1/bmlm/R/bmlm-package.R     |only
 bmlm-1.2.1/bmlm/R/mlm.R              |   85 ++++++++++++--------
 bmlm-1.2.1/bmlm/R/mlm_plot.R         |  148 +++++++++++++++++++++++------------
 bmlm-1.2.1/bmlm/R/stanmodels.R       |only
 bmlm-1.2.1/bmlm/R/utils.R            |   53 ++----------
 bmlm-1.2.1/bmlm/R/zzz.R              |only
 bmlm-1.2.1/bmlm/README.md            |   18 ++--
 bmlm-1.2.1/bmlm/cleanup              |only
 bmlm-1.2.1/bmlm/cleanup.win          |only
 bmlm-1.2.1/bmlm/exec                 |only
 bmlm-1.2.1/bmlm/inst/chunks          |only
 bmlm-1.2.1/bmlm/man/bmlm.Rd          |    2 
 bmlm-1.2.1/bmlm/man/mlm.Rd           |   38 ++++----
 bmlm-1.2.1/bmlm/man/mlm_pars_plot.Rd |    6 -
 bmlm-1.2.1/bmlm/man/mlm_path_plot.Rd |   18 +---
 bmlm-1.2.1/bmlm/man/mlm_summary.Rd   |   10 --
 bmlm-1.2.1/bmlm/src                  |only
 bmlm-1.2.1/bmlm/tools                |only
 25 files changed, 276 insertions(+), 197 deletions(-)

More information about bmlm at CRAN
Permanent link

New package bhm with initial version 1.1
Package: bhm
Type: Package
Title: Biomarker Threshold Models
Version: 1.1
Date: 2016-10-11
Author: Bingshu E. Chen
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Depends: coda, survival
Imports: methods
Description: Biomarker threshold models are tools to fit both predictive and prognostic biomarker effects. Both generalized linear models and Cox proportional hazards models can be fitted using either Bayesian method or profile likelihood method.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-10-11 19:03:25 UTC; chenbe
Repository: CRAN
Date/Publication: 2016-10-12 00:37:28

More information about bhm at CRAN
Permanent link

Package aSPU updated to version 1.45 with previous version 1.44 dated 2016-09-22

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single SNP association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.44 dated 2016-09-22 and 1.45 dated 2016-10-11

 DESCRIPTION              |    8 ++++----
 MD5                      |   40 ++++++++++++++++++++--------------------
 R/MTaSPUs.R              |    4 +++-
 R/MTaSPUsSet.R           |    2 +-
 R/MTaSPUsSetScore.R      |    2 +-
 R/aSPUboot.R             |    2 +-
 R/aSPUboot2.R            |    2 +-
 R/aSPUperm.R             |    2 +-
 R/aSPUperm2.R            |    2 +-
 R/aSPUpermC2.R           |    2 +-
 R/aSPUr.R                |    1 +
 R/aSPUs.R                |    3 +--
 R/aSPUsim1.R             |    2 +-
 R/aSPUsim2.R             |    2 +-
 R/aSPUsimC2.R            |    2 +-
 R/aSPUwboot.R            |    4 ++--
 R/aSPUwperm.R            |    2 +-
 R/aSPUwsim.R             |    2 +-
 inst/doc/MTaSPUsSet.Rmd  |    4 ++--
 inst/doc/MTaSPUsSet.html |    4 ++--
 vignettes/MTaSPUsSet.Rmd |    4 ++--
 21 files changed, 49 insertions(+), 47 deletions(-)

More information about aSPU at CRAN
Permanent link

Package stepR updated to version 1.0-5.1 with previous version 1.0-5 dated 2016-10-05

Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut], Thomas Hotz [aut], Hannes Sieling [aut], Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>

Diff between stepR versions 1.0-5 dated 2016-10-05 and 1.0-5.1 dated 2016-10-11

 DESCRIPTION    |    6 +++---
 MD5            |   10 +++++-----
 src/BinTree.h  |    1 +
 src/Bounds.cpp |    1 +
 src/Jump.h     |    2 ++
 src/Step.h     |    1 +
 6 files changed, 13 insertions(+), 8 deletions(-)

More information about stepR at CRAN
Permanent link

Package sinaplot updated to version 1.0.0 with previous version 0.1.5 dated 2016-05-17

Title: An Enhanced Chart for Simple and Truthful Representation of Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting any single variable in a multiclass data set. It is an enhanced jitter strip chart, where the width of the jitter is controlled by the density distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre], Sina Hadi Sohi [aut], Nicolas Rapin [aut], Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>

Diff between sinaplot versions 0.1.5 dated 2016-05-17 and 1.0.0 dated 2016-10-11

 DESCRIPTION            |   15 +-
 MD5                    |   22 +-
 NAMESPACE              |    9 -
 NEWS                   |   58 ++++++-
 R/sinaplot.R           |  367 ++++++++++++++++++++++---------------------------
 README.md              |    1 
 inst/doc/SinaPlot.R    |   19 +-
 inst/doc/SinaPlot.Rmd  |   27 ++-
 inst/doc/SinaPlot.html |  123 ++++++----------
 man/blood.Rd           |    2 
 man/sinaplot.Rd        |   88 +++++------
 vignettes/SinaPlot.Rmd |   27 ++-
 12 files changed, 381 insertions(+), 377 deletions(-)

More information about sinaplot at CRAN
Permanent link

Package regspec updated to version 2.4 with previous version 2.3 dated 2016-08-26

Title: Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Description: Computes linear Bayesian spectral estimates from multirate data for second-order stationary time series. Provides credible intervals and methods for plotting various spectral estimates.
Author: Ben Powell [aut, cre], Guy Nason [aut]
Maintainer: Ben Powell <ben.powell@bristol.ac.uk>

Diff between regspec versions 2.3 dated 2016-08-26 and 2.4 dated 2016-10-11

 DESCRIPTION   |    8 ++++----
 MD5           |    4 ++--
 R/regspec17.R |    4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

More information about regspec at CRAN
Permanent link

Package RandomFieldsUtils updated to version 0.3.3.1 with previous version 0.3.3 dated 2016-09-12

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.3.3 dated 2016-09-12 and 0.3.3.1 dated 2016-10-11

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
 R/zzz.R     |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about RandomFieldsUtils at CRAN
Permanent link

Package RandomFields updated to version 3.1.24.1 with previous version 3.1.24 dated 2016-09-12

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Christoph Berreth [ctr], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.1.24 dated 2016-09-12 and 3.1.24.1 dated 2016-10-11

 DESCRIPTION      |    6 +++---
 MD5              |    6 +++---
 R/zzz.R          |    2 --
 data/weather.rda |binary
 4 files changed, 6 insertions(+), 8 deletions(-)

More information about RandomFields at CRAN
Permanent link

Package piecewiseSEM updated to version 1.2.0 with previous version 1.1.3 dated 2016-07-11

Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>

Diff between piecewiseSEM versions 1.1.3 dated 2016-07-11 and 1.2.0 dated 2016-10-11

 DESCRIPTION                 |    8 +-
 MD5                         |   50 ++++++------
 NAMESPACE                   |    1 
 NEWS.md                     |   13 +++
 R/endogenous.reverse.R      |   44 ++++++++---
 R/filter.exogenous.R        |   51 ++++++++-----
 R/get.basis.set.R           |   21 +++++
 R/get.dag.R                 |   31 +++++--
 R/get.formula.list.R        |    4 -
 R/get.random.formula.R      |   30 ++-----
 R/get.scaled.data.R         |    7 +
 R/get.scaled.model.R        |    2 
 R/get.sort.dag.R            |   44 +++--------
 R/rsquared.R                |only
 R/sem.basis.set.R           |  171 ++++++++++++++++++++++++++------------------
 R/sem.coefs.R               |   69 ++++++++++-------
 R/sem.missing.paths.R       |   51 ++++++++-----
 R/sem.model.fits.R          |   34 +++++---
 R/sem.plot.R                |    3 
 README.md                   |    4 -
 inst/doc/piecewiseSEM.Rmd   |    6 -
 inst/doc/piecewiseSEM.html  |   14 +--
 man/endogenous.reverse.Rd   |    6 +
 man/filter.exogenous.Rd     |   49 +-----------
 man/piecewiseSEM-package.Rd |    6 -
 man/rsquared.Rd             |only
 vignettes/piecewiseSEM.Rmd  |    6 -
 27 files changed, 418 insertions(+), 307 deletions(-)

More information about piecewiseSEM at CRAN
Permanent link

Package nimble updated to version 0.6-1 with previous version 0.6 dated 2016-09-02

Title: Flexible BUGS-Compatible System for Hierarchical Statistical Modeling and Algorithm Development
Description: Flexible application of algorithms to models specified in the BUGS language. Algorithms can be written in the NIMBLE language and made available to any model.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson- Bergman, Duncan Temple Lang
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>

Diff between nimble versions 0.6 dated 2016-09-02 and 0.6-1 dated 2016-10-11

 DESCRIPTION                                 |    6 
 INSTALL                                     |    6 
 MD5                                         |  289 ++---
 NAMESPACE                                   |    3 
 NEWS                                        |   16 
 R/BUGS_model.R                              |    5 
 R/BUGS_modelDef.R                           |   30 
 R/BUGS_testBUGS.R                           |    4 
 R/MCMC_conjugacy.R                          |    5 
 R/MCMC_run.R                                |    2 
 R/RCfunction_compile.R                      |    2 
 R/cppDefs_RCfunction.R                      |   30 
 R/cppDefs_core.R                            |    2 
 R/cppDefs_cppProject.R                      |   77 +
 R/cppInterfaces_modelValues.R               |   46 
 R/cppInterfaces_models.R                    |   58 -
 R/cppInterfaces_nimbleFunctions.R           |  351 ++++--
 R/cppInterfaces_otherTypes.R                |  256 ++--
 R/cppInterfaces_utils.R                     |  140 +-
 R/genCpp_processSpecificCalls.R             |   12 
 R/genCpp_sizeProcessing.R                   |   93 +
 R/nimbleFunction_core.R                     |    4 
 R/nimbleFunction_keywordProcessing.R        |   44 
 R/nimbleFunction_nodeFunction.R             |    3 
 R/nimbleFunction_nodeFunctionNew.R          |    3 
 R/nimbleProject.R                           |  127 ++
 R/options.R                                 |    4 
 R/setNimbleInternalFunctions.R              |    2 
 R/types_nimbleFunctionList.R                |    9 
 R/types_nodeFxnVector.R                     |   40 
 R/types_numericLists.R                      |  252 ++--
 R/types_util.R                              |   23 
 README.md                                   |    8 
 configure                                   |   12 
 configure.ac                                |   12 
 configure.win                               |    5 
 inst/CppCode/GNUmakefile                    |    4 
 inst/CppCode/ModelClassUtils.cpp            |   13 
 inst/CppCode/NamedObjects.cpp               |   20 
 inst/CppCode/RcppNimbleUtils.cpp            |only
 inst/CppCode/RcppUtils.cpp                  | 1456 +++-------------------------
 inst/CppCode/accessorClasses.cpp            |  304 ++---
 inst/CppCode/dists.cpp                      |    1 
 inst/CppCode/dllFinalizer.cpp               |only
 inst/CppCode/nimDists.cpp                   |   13 
 inst/include/nimble/ModelClassUtils.h       |    6 
 inst/include/nimble/NamedObjects.h          |    8 
 inst/include/nimble/NimArr.h                |    7 
 inst/include/nimble/NimArrBase.h            |    4 
 inst/include/nimble/RcppNimbleUtils.h       |only
 inst/include/nimble/RcppUtils.h             |  357 ------
 inst/include/nimble/accessorClasses.h       |   26 
 inst/include/nimble/dllFinalizer.h          |only
 inst/include/nimble/dynamicRegistrations.h  |only
 inst/include/nimble/nodeFun.h               |    1 
 inst/tests/test_utils.R                     |   62 -
 man/BUGSdeclClass-class.Rd                  |    2 
 man/Categorical.Rd                          |    2 
 man/CmodelBaseClass-class.Rd                |    2 
 man/CnimbleFunctionBase-class.Rd            |    2 
 man/Constraint.Rd                           |    2 
 man/Dirichlet.Rd                            |    2 
 man/Exponential.Rd                          |    2 
 man/Interval.Rd                             |    2 
 man/MCMCconf-class.Rd                       |    2 
 man/MCMCsuite.Rd                            |    2 
 man/MCMCsuiteClass-class.Rd                 |    2 
 man/Multinomial.Rd                          |    2 
 man/Multivariate-t.Rd                       |    2 
 man/MultivariateNormal.Rd                   |    2 
 man/Rmatrix2mvOneVar.Rd                     |only
 man/RmodelBaseClass-class.Rd                |    2 
 man/Wishart.Rd                              |    2 
 man/asRow.Rd                                |    2 
 man/autoBlock.Rd                            |    2 
 man/buildAuxiliaryFilter.Rd                 |    2 
 man/buildBootstrapFilter.Rd                 |    2 
 man/buildEnsembleKF.Rd                      |    2 
 man/buildLiuWestFilter.Rd                   |    2 
 man/buildMCEM.Rd                            |    2 
 man/buildMCMC.Rd                            |    2 
 man/checkInterrupt.Rd                       |    2 
 man/codeBlockClass-class.Rd                 |    2 
 man/combine_MCMC_comparison_results.Rd      |    2 
 man/compareMCMCs.Rd                         |    2 
 man/compileNimble.Rd                        |    2 
 man/configureMCMC.Rd                        |    2 
 man/decide.Rd                               |    2 
 man/decideAndJump.Rd                        |    2 
 man/declare.Rd                              |    2 
 man/deregisterDistributions.Rd              |    2 
 man/getBUGSexampleDir.Rd                    |    2 
 man/getDefinition.Rd                        |    2 
 man/getLoadingNamespace.Rd                  |    2 
 man/getNimbleOption.Rd                      |    2 
 man/getParam.Rd                             |    2 
 man/getsize.Rd                              |    2 
 man/identityMatrix.Rd                       |    2 
 man/initializeModel.Rd                      |    2 
 man/is.nf.Rd                                |    2 
 man/makeParamInfo.Rd                        |    2 
 man/make_MCMC_comparison_pages.Rd           |    2 
 man/modelBaseClass-class.Rd                 |    2 
 man/modelDefClass-class.Rd                  |    2 
 man/modelValues.Rd                          |    2 
 man/modelValuesBaseClass-class.Rd           |    2 
 man/modelValuesConf.Rd                      |    2 
 man/nfMethod.Rd                             |    2 
 man/nfVar.Rd                                |    2 
 man/nimArray.Rd                             |    2 
 man/nimCat.Rd                               |    2 
 man/nimCopy.Rd                              |    2 
 man/nimDim.Rd                               |    2 
 man/nimInteger.Rd                           |    2 
 man/nimMatrix.Rd                            |    2 
 man/nimNumeric.Rd                           |    2 
 man/nimPrint.Rd                             |    2 
 man/nimStop.Rd                              |    2 
 man/nimble-internal.Rd                      |    1 
 man/nimbleCode.Rd                           |    2 
 man/nimbleFunction.Rd                       |    2 
 man/nimbleFunctionBase-class.Rd             |    2 
 man/nimbleFunctionList-class.Rd             |only
 man/nimbleFunctionVirtual.Rd                |    2 
 man/nimbleModel.Rd                          |    2 
 man/nimbleOptions.Rd                        |    2 
 man/nodeFunctions.Rd                        |    2 
 man/rankSample.Rd                           |    2 
 man/readBUGSmodel.Rd                        |    2 
 man/registerDistributions.Rd                |    2 
 man/rename_MCMC_comparison_method.Rd        |    2 
 man/reshape_comparison_results.Rd           |    2 
 man/resize.Rd                               |    2 
 man/run.time.Rd                             |    2 
 man/runMCMC.Rd                              |    2 
 man/samplers.Rd                             |    2 
 man/setAndCalculate.Rd                      |    2 
 man/setAndCalculateOne.Rd                   |    2 
 man/setSize.Rd                              |    2 
 man/setupOutputs.Rd                         |    2 
 man/simNodes.Rd                             |    2 
 man/simNodesMV.Rd                           |    2 
 man/singleVarAccessClass-class.Rd           |    2 
 man/t.Rd                                    |    2 
 man/testBUGSmodel.Rd                        |    2 
 man/updateMCMCcomparisonWithHighOrderESS.Rd |    2 
 man/valueInCompiledNimbleFunction.Rd        |    2 
 man/values.Rd                               |    2 
 src/nimble.cpp                              |   56 -
 149 files changed, 1788 insertions(+), 2710 deletions(-)

More information about nimble at CRAN
Permanent link

New package GFA with initial version 1.0.0
Package: GFA
Type: Package
Title: Group Factor Analysis
Version: 1.0.0
Date: 2016-09-09
Authors@R: c(person("Eemeli", "Leppaaho", role = c("aut","cre"), email = "eemeli.leppaaho@aalto.fi"), person("Seppo", "Virtanen", role = c("aut"), email = "s.virtanen@warwick.ac.uk"), person("Muhammad", "Ammad-ud-din", role = "ctb", email = "muhammad.ammad-ud-din@aalto.fi"), person("Suleiman A", "Khan", role = "ctb", email = "suleiman.khan@helsinki.fi"), person("Tommi", "Suvitaival", role = "ctb", email = "tsvv@steno.dk"), person("Inka", "Saarinen", role = "ctb", email = "inka.saarinen@aalto.fi"), person("Samuel", "Kaski", role = "ctb", email = "samuel.kaski@aalto.fi"))
Author: Eemeli Leppaaho [aut, cre], Seppo Virtanen [aut], Muhammad Ammad-ud-din [ctb], Suleiman A Khan [ctb], Tommi Suvitaival [ctb], Inka Saarinen [ctb], Samuel Kaski [ctb]
Maintainer: Eemeli Leppaaho <eemeli.leppaaho@aalto.fi>
Description: Factor analysis implementation for multiple data sources, i.e., for groups of variables. The whole data analysis pipeline is provided, including functions and recommendations for data normalization and model definition, as well as missing value prediction and model visualization. The model group factor analysis (GFA) is inferred with Gibbs sampling.
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2016-10-11 13:01:54 UTC; eleppaah
Repository: CRAN
Date/Publication: 2016-10-11 18:56:42

More information about GFA at CRAN
Permanent link

Package colorspace updated to version 1.2-7 with previous version 1.2-6 dated 2015-03-10

Title: Color Space Manipulation
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut], Paul Murrell [aut], Kurt Hornik [aut], Jason C. Fisher [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

Diff between colorspace versions 1.2-6 dated 2015-03-10 and 1.2-7 dated 2016-10-11

 DESCRIPTION                    |   15 ++++++++-------
 LICENSE                        |    2 +-
 MD5                            |   31 ++++++++++++++++---------------
 NAMESPACE                      |    5 ++++-
 NEWS                           |   10 ++++++++++
 R/choose_palette.R             |   26 ++++++++++++++------------
 R/colorspace.R                 |    2 +-
 build/partial.rdb              |only
 build/vignette.rds             |binary
 data/USSouthPolygon.rda        |binary
 inst/CITATION                  |   28 +++++++++++++++++++++++++---
 inst/doc/hcl-colors.pdf        |binary
 man/USSouthPolygon.Rd          |    2 +-
 man/choose_palette.Rd          |   16 +++++++++++-----
 man/desaturate.Rd              |    2 +-
 man/rainbow_hcl.Rd             |   18 +++++++++++-------
 vignettes/hcl-colors.Rout.save |    4 +---
 17 files changed, 104 insertions(+), 57 deletions(-)

More information about colorspace at CRAN
Permanent link

Package BDgraph updated to version 2.29 with previous version 2.28 dated 2016-10-03

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>

Diff between BDgraph versions 2.28 dated 2016-10-03 and 2.29 dated 2016-10-11

 BDgraph-2.28/BDgraph/src/Ig.cpp                   |only
 BDgraph-2.28/BDgraph/src/gcgm_bd_multi_update.cpp |only
 BDgraph-2.28/BDgraph/src/gcgm_rj.cpp              |only
 BDgraph-2.28/BDgraph/src/ggm_bd_multi_update.cpp  |only
 BDgraph-2.28/BDgraph/src/ggm_rj.cpp               |only
 BDgraph-2.28/BDgraph/src/rgcwish.cpp              |only
 BDgraph-2.28/BDgraph/src/rgcwish.h                |only
 BDgraph-2.28/BDgraph/src/scaleFree.cpp            |only
 BDgraph-2.29/BDgraph/DESCRIPTION                  |    8 
 BDgraph-2.29/BDgraph/MD5                          |   49 --
 BDgraph-2.29/BDgraph/R/bdgraph.sim.R              |    4 
 BDgraph-2.29/BDgraph/man/bdgraph.Rd               |    4 
 BDgraph-2.29/BDgraph/man/bdgraph.sim.Rd           |    4 
 BDgraph-2.29/BDgraph/man/bdgraph.ts.Rd            |    2 
 BDgraph-2.29/BDgraph/man/compare.Rd               |    6 
 BDgraph-2.29/BDgraph/man/gnorm.Rd                 |    4 
 BDgraph-2.29/BDgraph/man/plotroc.Rd               |    6 
 BDgraph-2.29/BDgraph/man/rgwish.Rd                |    2 
 BDgraph-2.29/BDgraph/man/rwish.Rd                 |    2 
 BDgraph-2.29/BDgraph/man/summary.bdgraph.Rd       |    4 
 BDgraph-2.29/BDgraph/src/MyLapack.cpp             |  123 ++---
 BDgraph-2.29/BDgraph/src/MyLapack.h               |   34 -
 BDgraph-2.29/BDgraph/src/bd_for_ts.cpp            |  513 +++++++++++++++++++++-
 BDgraph-2.29/BDgraph/src/gcgm_bd.cpp              |  479 ++++++++++++++++++++
 BDgraph-2.29/BDgraph/src/ggm_bd.cpp               |  458 +++++++++++++++++++
 BDgraph-2.29/BDgraph/src/gm_rj.cpp                |only
 BDgraph-2.29/BDgraph/src/matrix.cpp               |   40 +
 BDgraph-2.29/BDgraph/src/matrix.h                 |    2 
 BDgraph-2.29/BDgraph/src/rgwish.cpp               |  102 ++++
 BDgraph-2.29/BDgraph/src/rgwish.h                 |    4 
 30 files changed, 1693 insertions(+), 157 deletions(-)

More information about BDgraph at CRAN
Permanent link

Package spatialsegregation updated to version 2.43 with previous version 2.42 dated 2016-10-10

Title: Segregation Measures for Multitype Spatial Point Patterns
Description: Summaries for measuring segregation/mingling in multitype spatial point patterns with graph based neighbourhood description. Included indices: Mingling, Shannon, Simpson (also the non-spatial) Included functionals: Mingling, Shannon, Simpson, ISAR, MCI. Included neighbourhoods: Geometric, k- nearest neighbours, Gabriel, Delaunay. Dixon's test.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>

Diff between spatialsegregation versions 2.42 dated 2016-10-10 and 2.43 dated 2016-10-11

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 src/Pp.cpp  |   12 ++++++------
 3 files changed, 12 insertions(+), 12 deletions(-)

More information about spatialsegregation at CRAN
Permanent link

Package prcbench updated to version 0.5.2 with previous version 0.5.0 dated 2016-09-09

Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating precision-recall curves under various conditions.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between prcbench versions 0.5.0 dated 2016-09-09 and 0.5.2 dated 2016-10-11

 DESCRIPTION                   |   22 +++++++++++-----------
 MD5                           |   10 +++++-----
 R/tool_zzz.R                  |   22 +++++++++++++++++++++-
 README.md                     |   30 ++++++++++++++++--------------
 inst/doc/introduction.html    |   28 ++++++++++++++--------------
 tests/testthat/test_tool_pm.R |    4 ++++
 6 files changed, 71 insertions(+), 45 deletions(-)

More information about prcbench at CRAN
Permanent link

Package mixAK updated to version 4.4 with previous version 4.2 dated 2015-08-02

Title: Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between mixAK versions 4.2 dated 2015-08-02 and 4.4 dated 2016-10-11

 DESCRIPTION        |    8 ++++----
 MD5                |   20 ++++++++++----------
 NEWS               |    6 ++++++
 R/cbplot.R         |   23 +++++++++++++----------
 data/Acidity.rda   |binary
 data/Enzyme.rda    |binary
 data/Galaxy.rda    |binary
 man/cbplot.Rd      |   10 ++++++----
 src/AK_LAPACK.h    |    1 +
 src/Dist_MVT.cpp   |    5 +++--
 src/NMix_Utils.cpp |    3 ++-
 11 files changed, 45 insertions(+), 31 deletions(-)

More information about mixAK at CRAN
Permanent link

Package SGCS updated to version 2.5 with previous version 2.4 dated 2016-10-10

Title: Spatial Graph Based Clustering Summaries for Spatial Point Patterns
Description: Graph based clustering summaries for spatial point patterns. Includes Connectivity function, Cumulative connectivity function and clustering function, plus the triangle/triplet intensity function T.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>

Diff between SGCS versions 2.4 dated 2016-10-10 and 2.5 dated 2016-10-11

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 src/Pp.cpp  |   20 ++++++++++----------
 3 files changed, 16 insertions(+), 16 deletions(-)

More information about SGCS at CRAN
Permanent link

New package PTXQC with initial version 0.80.13
Package: PTXQC
Type: Package
Title: Quality Report Generation for MaxQuant Results
Version: 0.80.13
Date: 2016-10-07
Author: Chris Bielow <chris.bielow@mdc-berlin.de>
Maintainer: Chris Bielow <chris.bielow@mdc-berlin.de>
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (see <http://www.maxquant.org>). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Depends: R (>= 3.0.0)
Imports: data.table, ggplot2, ggdendro, graphics, grid, gridExtra, grDevices, gtable, methods, plyr, proto, RColorBrewer, reshape2, rmarkdown, seqinr, stats, utils, yaml
Suggests: knitr (>= 1.10), testthat
VignetteBuilder: knitr
License: GPL-2
RoxygenNote: 5.0.1
URL: https://github.com/cbielow/PTXQC
BugReports: https://github.com/cbielow/PTXQC/issues
Packaged: 2016-10-11 07:35:21 UTC; cbielow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-10-11 12:42:38

More information about PTXQC at CRAN
Permanent link

Package precrec updated to version 0.5.2 with previous version 0.5.0 dated 2016-09-09

Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between precrec versions 0.5.0 dated 2016-09-09 and 0.5.2 dated 2016-10-11

 DESCRIPTION                |   14 ++--
 MD5                        |    6 -
 README.md                  |   20 +++---
 inst/doc/introduction.html |  136 ++++++++++++++++++++++-----------------------
 4 files changed, 89 insertions(+), 87 deletions(-)

More information about precrec at CRAN
Permanent link

Package funModeling updated to version 1.4 with previous version 1.3 dated 2016-10-05

Title: Title: Learn Data Science Through the "Data Science Live Book"
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book <http:// livebook.datascienceheroes.com/> are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>

Diff between funModeling versions 1.3 dated 2016-10-05 and 1.4 dated 2016-10-11

 DESCRIPTION    |    8 ++---
 MD5            |    8 ++---
 R/models_lib.R |    6 ---
 R/numbers.R    |   88 +++++++++++++++++++++++++++++----------------------------
 man/freq.Rd    |    4 +-
 5 files changed, 58 insertions(+), 56 deletions(-)

More information about funModeling at CRAN
Permanent link

New package exp2flux with initial version 0.1
Package: exp2flux
Type: Package
Title: Convert Gene EXPression Data to FBA FLUXes
Version: 0.1
Author: Daniel Osorio[aut,cre], Kelly Botero[aut,cre], Janneth Gonzalez[aut], Andres Pinzon[aut]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Description: For a given metabolic model with well formed Gene-Protein-Reaction (GPR) associations and an expressionSet with their associated gene expression values, this package converts gene expression values to the FBA boundaries for each reaction based in the boolean rules described in its associated GPR.
License: GPL-2
Imports: sybil, gage, igraph
Suggests: Biobase
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-11 02:44:04 UTC; daniel
Repository: CRAN
Date/Publication: 2016-10-11 12:42:48

More information about exp2flux at CRAN
Permanent link

Package evaluate updated to version 0.10 with previous version 0.9 dated 2016-04-29

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Michael Lawrence [ctb], Thomas Kluyver [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between evaluate versions 0.9 dated 2016-04-29 and 0.10 dated 2016-10-11

 DESCRIPTION          |   14 ++++++----
 MD5                  |   16 ++++++------
 NAMESPACE            |    2 +
 NEWS                 |   14 ++++++++++
 R/eval.r             |   66 ++++++++++++++++++++++++++++++++++++++++++++++-----
 R/replay.r           |   34 +++++++++++++++++++++++++-
 R/watcher.r          |   27 +++++++++++++++++---
 man/evaluate.Rd      |    7 ++++-
 man/flush_console.Rd |only
 man/inject_funs.Rd   |only
 10 files changed, 155 insertions(+), 25 deletions(-)

More information about evaluate at CRAN
Permanent link

Package Compositional updated to version 2.0 with previous version 1.8 dated 2016-08-05

Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Compositional versions 1.8 dated 2016-08-05 and 2.0 dated 2016-10-11

 DESCRIPTION                  |    8 +-
 MD5                          |  152 +++++++++++++++++++++----------------------
 NAMESPACE                    |    8 +-
 R/alfa.R                     |   16 ++--
 R/alfa.knn.R                 |   25 +++----
 R/alfa.pcr.R                 |    2 
 R/alfa.profile.R             |    8 +-
 R/alfa.reg.R                 |   23 +++---
 R/alfa.tune.R                |    8 +-
 R/alfainv.R                  |   10 +-
 R/alfaknn.tune.R             |  148 ++++++++++++++++++++---------------------
 R/alfapcr.tune.R             |    8 +-
 R/alfarda.tune.R             |    8 +-
 R/alfareg.tune.R             |   48 +++++++------
 R/alfaridge.tune.R           |    6 -
 R/bic.mixcompnorm.R          |    6 -
 R/bivt.contour.R             |   28 +++----
 R/comp.den.R                 |    6 -
 R/comp.kerncontour.R         |   18 ++---
 R/comp.knn.R                 |   79 +++++++++++-----------
 R/comp.reg.R                 |   10 +-
 R/compknn.tune.R             |   85 ++++++++++++------------
 R/ddiri.R                    |    4 -
 R/diri.contour.R             |   28 +++----
 R/diri.est.R                 |   18 ++---
 R/diri.nr.R                  |   61 ++++-------------
 R/diri.reg.R                 |   28 +++----
 R/diri.reg2.R                |   30 ++++----
 R/dirimean.test.R            |   12 +--
 R/eel.test1.R                |   14 +--
 R/eel.test2.R                |   26 +++----
 R/el.test1.R                 |    6 -
 R/el.test2.R                 |   12 +--
 R/frechet.R                  |   12 +--
 R/glm.pcr.R                  |    7 -
 R/glmpcr.tune.R              |   18 ++---
 R/helm.R                     |    2 
 R/hotel1T2.R                 |   12 +--
 R/hotel2T2.R                 |   18 ++---
 R/james.R                    |   25 +++----
 R/js.compreg.R               |   20 ++---
 R/kl.compreg.R               |   20 ++---
 R/kl.diri.R                  |    2 
 R/maov.R                     |    8 +-
 R/maovjames.R                |   14 +--
 R/mix.compnorm.R             |   16 ++--
 R/mixnorm.contour.R          |   12 +--
 R/mkde.R                     |    6 -
 R/mkde.tune.R                |   14 +--
 R/multivreg.R                |   13 +--
 R/multivt.R                  |    6 -
 R/norm.contour.R             |   19 ++---
 R/ols.compreg.R              |   25 +++----
 R/pcr.R                      |    9 +-
 R/pcr.tune.R                 |   12 +--
 R/rcompnorm.R                |    4 -
 R/rcompsn.R                  |    4 -
 R/rcompt.R                   |    4 -
 R/rda.R                      |   18 ++---
 R/rda.tune.R                 |   25 +++----
 R/rdiri.R                    |    2 
 R/ridge.plot.R               |    6 -
 R/ridge.reg.R                |    5 -
 R/ridge.tune.R               |   12 +--
 R/rmixcomp.R                 |    4 -
 R/rmvnorm.R                  |    5 -
 R/skewnorm.contour.R         |   20 ++---
 R/spat.med.R                 |   16 ++--
 R/spatmed.reg.R              |   22 +++---
 R/sscov.R                    |    6 -
 R/sym.test.R                 |   15 ++--
 R/ternary.R                  |   18 ++---
 man/Compositional-package.Rd |    4 -
 man/comp.knn.Rd              |    2 
 man/diri.nr.Rd               |    4 -
 man/rda.Rd                   |    2 
 man/spat.med.Rd              |    4 -
 77 files changed, 706 insertions(+), 735 deletions(-)

More information about Compositional at CRAN
Permanent link

New package briskaR with initial version 0.1.0
Package: briskaR
Type: Package
Encoding: UTF-8
Title: Biological Risk Assessment
Version: 0.1.0
Date: 2016-10-07
Authors@R: c(person("Emily", "Walker", role = "aut", email = "emily.walker@inra.fr"), person("Jean-Francois", "Rey", role = c("aut","cre"), email = "jean-francois.rey@inra.fr"), person("Melen", "Leclerc", role = "aut", email = "melen.leclerc@inra.fr"), person("Samuel", "Soubeyrand", role = "ctb", email = "samuel.soubeyrand@inra.fr"), person("Marc", "Bourotte", role = "ctb", email = "marc.bourotte@inra.fr"))
Author: Emily Walker [aut], Jean-Francois Rey [aut, cre], Melen Leclerc [aut], Samuel Soubeyrand [ctb], Marc Bourotte [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
Description: A spatio-temporal exposure-hazard model for assessing biological risk and impact. The model is based on stochastic geometry for describing the landscape and the exposed individuals, a dispersal kernel for the dissemination of contaminants and an ecotoxicological equation.
License: GPL (>= 2) | file LICENSE
LazyData: True
BuildVignettes: True
VignetteBuilder: knitr
Depends: methods, grDevices (>= 3.0.0), graphics (>= 3.0.0), R (>= 3.0.0)
Imports: sp (>= 1.0-17), stats (>= 3.0.2), rgeos(>= 0.3), fields(>= 7.1), MASS(>= 7.3.29), deldir(>= 0.1), pracma(>= 1.8.3), raster(>= 2.3.0), fftwtools(>= 0.9.6), mvtnorm(>= 1.0.2), rgdal (>= 0.9)
Suggests: knitr(>= 1.11), rmarkdown(>= 0.8.1)
Collate: '0briskaR.R' 'Class-Individuals.R' 'Class-Landscape.R' 'Individuals-Methods.R' 'simulPrecip.R' 'toxicIntensity.R' 'Landscape-Methods.R' 'Landscape-Individuals-Methods.R' 'briskaR.R' 'pollen-data.R' 'ecoToxic.R' 'demo.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-11 09:28:54 UTC; jfrey
Repository: CRAN
Date/Publication: 2016-10-11 12:42:45

More information about briskaR at CRAN
Permanent link

Package braQCA updated to version 0.9.9.4 with previous version 0.9.9.3 dated 2016-09-30

Title: Bootstrapped Robustness Assessment for Qualitative Comparative Analysis
Description: Test the robustness of a user's Qualitative Comparative Analysis solutions to randomness, using the bootstrapped assessment: baQCA(). This package also includes a function that provides recommendations for improving solutions to reach typical significance levels: brQCA().
Author: C. Ben Gibson [aut, cre], Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>

Diff between braQCA versions 0.9.9.3 dated 2016-09-30 and 0.9.9.4 dated 2016-10-11

 DESCRIPTION |    8 ++++----
 MD5         |    2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

More information about braQCA at CRAN
Permanent link

Package ACEt updated to version 1.7.0 with previous version 1.6.9 dated 2016-09-10

Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>

Diff between ACEt versions 1.6.9 dated 2016-09-10 and 1.7.0 dated 2016-10-11

 DESCRIPTION         |   12 ++++++------
 MD5                 |   18 +++++++++---------
 R/AtCtEtp.R         |   40 +++++++++++++++++++++++++++++++++-------
 R/mcmc_epsp.R       |    9 +++++++++
 man/ACEt-package.Rd |    6 +++---
 man/AtCtEtp.Rd      |    1 +
 src/AtCtEtp.cpp     |    6 +++++-
 src/RInterface.cc   |    8 ++++----
 src/mcmc.cc         |   33 +++++++++++++++++++++++++++++----
 src/mcmc.h          |    2 +-
 10 files changed, 100 insertions(+), 35 deletions(-)

More information about ACEt at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.