Fri, 03 Sep 2021

Package chk updated to version 0.7.0 with previous version 0.6.0 dated 2021-07-04

Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>), Nadine Hussein [ctb] (<https://orcid.org/0000-0003-4470-8361>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

Diff between chk versions 0.6.0 dated 2021-07-04 and 0.7.0 dated 2021-09-03

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Package skewMLRM updated to version 1.1 with previous version 1.0 dated 2021-06-11

Title: Estimation for Scale-Shape Mixtures of Skew-Normal Distributions
Description: Provide data generation and estimation tools for the multivariate scale mixtures of normal presented in Lange and Sinsheimer (1993) <doi:10.2307/1390698>, the multivariate scale mixtures of skew-normal presented in Zeller, Lachos and Vilca (2011) <doi:10.1080/02664760903406504>, the multivariate skew scale mixtures of normal presented in Louredo, Zeller and Ferreira (2021) <doi:10.1007/s13571-021-00257-y> and the multivariate scale mixtures of skew-normal-Cauchy presented in Kahrari et al. (2020) <doi:10.1080/03610918.2020.1804582>.
Author: Clecio Ferreira [aut], Diego Gallardo [aut, cre], Camila Zeller [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>

Diff between skewMLRM versions 1.0 dated 2021-06-11 and 1.1 dated 2021-09-03

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More information about skewMLRM at CRAN
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Package RJcluster updated to version 3.2.2 with previous version 3.2.1 dated 2021-09-02

Title: A Fast Clustering Algorithm for High Dimensional Data Based on the Gram Matrix Decomposition
Description: Clustering algorithm for high dimensional data. Assuming that P feature measurements on N objects are arranged in an N×P matrix X, this package provides clustering based on the left Gram matrix XX^T. To simulate test data, type "help('simulate_HD_data')" and to learn how to use the clustering algorithm, type "help('RJclust')". To cite this package, type 'citation("RJcluster")'.
Author: Shahina Rahman [aut], Valen E. Johnson [aut], Suhasini Subba Rao [aut], Rachael Shudde [aut, cre, trl]
Maintainer: Rachael Shudde <rachael.shudde@gmail.com>

Diff between RJcluster versions 3.2.1 dated 2021-09-02 and 3.2.2 dated 2021-09-03

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Package REndo updated to version 2.4.3 with previous version 2.4.2 dated 2021-02-10

Title: Fitting Linear Models with Endogenous Regressors using Latent Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches. The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized method of moment approach that deals with endogeneity in a multilevel setting. These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed. Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut], Markus Meierer [aut], Rene Algesheimer [aut], Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>

Diff between REndo versions 2.4.2 dated 2021-02-10 and 2.4.3 dated 2021-09-03

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Package rangemap updated to version 0.1.18 with previous version 0.1.17 dated 2021-06-26

Title: Simple Tools for Defining Species Ranges
Description: A collection of tools to create species range maps based on occurrence data, statistics, and spatial objects. Other tools in this collection can be used to analyze the environmental characteristics of the species ranges. Plotting options to represent results in various manners are also available. Results obtained using these tools can be used to explore the distribution of species and define areas of occupancy and extent of occurrence of species. Other packages help to explore species distributions using distinct methods, but options presented in this set of tools (e.g., using trend surface analysis and concave hull polygons) are exclusive. Description of methods, approaches, and comments for some of the tools implemented here can be found in: IUCN (2001) <https://portals.iucn.org/library/node/10315>, Peterson et al. (2011) <https://www.degruyter.com/princetonup/view/title/506966>, and Graham and Hijmans (2006) <doi:10.1111/j.1466-8238.2006.00257.x>.
Author: Marlon E. Cobos [aut, cre] (<https://orcid.org/0000-0002-2611-1767>), Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Narayani Barve [aut] (<https://orcid.org/0000-0002-7893-8774>), Alberto Jimenez-Valverde [aut] (<https://orcid.org/0000-0001-9962-2106>), Claudia Nuñez-Penichet [aut] (<https://orcid.org/0000-0001-7442-8593>)
Maintainer: Marlon E. Cobos <manubio13@gmail.com>

Diff between rangemap versions 0.1.17 dated 2021-06-26 and 0.1.18 dated 2021-09-03

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Package pomp updated to version 3.6 with previous version 3.5 dated 2021-07-28

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Eamon B. O'Dea [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

Diff between pomp versions 3.5 dated 2021-07-28 and 3.6 dated 2021-09-03

 pomp-3.5/pomp/R/measles.R                  |only
 pomp-3.5/pomp/man/measles.Rd               |only
 pomp-3.6/pomp/DESCRIPTION                  |   42 +--
 pomp-3.6/pomp/MD5                          |  356 ++++++++++++++---------------
 pomp-3.6/pomp/R/abc.R                      |   16 -
 pomp-3.6/pomp/R/accumulators.R             |    8 
 pomp-3.6/pomp/R/bake.R                     |   10 
 pomp-3.6/pomp/R/basic_components.R         |   29 +-
 pomp-3.6/pomp/R/basic_probes.R             |   35 --
 pomp-3.6/pomp/R/blowflies.R                |    6 
 pomp-3.6/pomp/R/bsflu.R                    |    6 
 pomp-3.6/pomp/R/bsmc2.R                    |    8 
 pomp-3.6/pomp/R/bsplines.R                 |    2 
 pomp-3.6/pomp/R/builder.R                  |    2 
 pomp-3.6/pomp/R/childhood.R                |only
 pomp-3.6/pomp/R/coef.R                     |    3 
 pomp-3.6/pomp/R/cond_logLik.R              |    3 
 pomp-3.6/pomp/R/covariate_table.R          |   11 
 pomp-3.6/pomp/R/covmat.R                   |    1 
 pomp-3.6/pomp/R/csnippet.R                 |    3 
 pomp-3.6/pomp/R/dacca.R                    |    6 
 pomp-3.6/pomp/R/design.R                   |    2 
 pomp-3.6/pomp/R/distributions.R            |    2 
 pomp-3.6/pomp/R/dmeasure_spec.R            |   16 -
 pomp-3.6/pomp/R/dprocess_spec.R            |   12 
 pomp-3.6/pomp/R/ebola.R                    |    4 
 pomp-3.6/pomp/R/eff_sample_size.R          |    3 
 pomp-3.6/pomp/R/elementary_algorithms.R    |   10 
 pomp-3.6/pomp/R/estimation_algorithms.R    |   16 -
 pomp-3.6/pomp/R/filter_mean.R              |    3 
 pomp-3.6/pomp/R/filter_traj.R              |    3 
 pomp-3.6/pomp/R/flow.R                     |   19 -
 pomp-3.6/pomp/R/forecast.R                 |    1 
 pomp-3.6/pomp/R/gompertz.R                 |    4 
 pomp-3.6/pomp/R/kalman.R                   |    5 
 pomp-3.6/pomp/R/loglik.R                   |    1 
 pomp-3.6/pomp/R/lookup.R                   |    4 
 pomp-3.6/pomp/R/mif2.R                     |    9 
 pomp-3.6/pomp/R/nlf.R                      |   15 -
 pomp-3.6/pomp/R/obs.R                      |   11 
 pomp-3.6/pomp/R/ou2.R                      |    4 
 pomp-3.6/pomp/R/package.R                  |   78 +++---
 pomp-3.6/pomp/R/parameter_trans.R          |   10 
 pomp-3.6/pomp/R/parus.R                    |   32 --
 pomp-3.6/pomp/R/pfilter.R                  |    5 
 pomp-3.6/pomp/R/pmcmc.R                    |   19 +
 pomp-3.6/pomp/R/pomp.R                     |   39 +--
 pomp-3.6/pomp/R/pomp_examp.R               |    7 
 pomp-3.6/pomp/R/pred_mean.R                |    3 
 pomp-3.6/pomp/R/pred_var.R                 |    3 
 pomp-3.6/pomp/R/print.R                    |    2 
 pomp-3.6/pomp/R/prior_spec.R               |   30 +-
 pomp-3.6/pomp/R/probe.R                    |   11 
 pomp-3.6/pomp/R/probe_match.R              |   20 -
 pomp-3.6/pomp/R/proposals.R                |    3 
 pomp-3.6/pomp/R/resample.R                 |    1 
 pomp-3.6/pomp/R/ricker.R                   |    4 
 pomp-3.6/pomp/R/rinit_spec.R               |   11 
 pomp-3.6/pomp/R/rmeasure_spec.R            |   16 -
 pomp-3.6/pomp/R/rprocess_spec.R            |   20 -
 pomp-3.6/pomp/R/rw2.R                      |   17 -
 pomp-3.6/pomp/R/sannbox.R                  |   17 -
 pomp-3.6/pomp/R/saved_states.R             |    3 
 pomp-3.6/pomp/R/simulate.R                 |   23 +
 pomp-3.6/pomp/R/sir.R                      |    6 
 pomp-3.6/pomp/R/skeleton_spec.R            |   10 
 pomp-3.6/pomp/R/spect.R                    |    4 
 pomp-3.6/pomp/R/spect_match.R              |   15 -
 pomp-3.6/pomp/R/spy.R                      |    2 
 pomp-3.6/pomp/R/states.R                   |   12 
 pomp-3.6/pomp/R/summary.R                  |    3 
 pomp-3.6/pomp/R/time.R                     |   16 -
 pomp-3.6/pomp/R/timezero.R                 |    3 
 pomp-3.6/pomp/R/traces.R                   |    3 
 pomp-3.6/pomp/R/traj_match.R               |   47 ++-
 pomp-3.6/pomp/R/trajectory.R               |    4 
 pomp-3.6/pomp/R/transformations.R          |    2 
 pomp-3.6/pomp/R/userdata.R                 |    4 
 pomp-3.6/pomp/R/verhulst.R                 |    2 
 pomp-3.6/pomp/R/workhorses.R               |   45 +--
 pomp-3.6/pomp/R/wpfilter.R                 |    5 
 pomp-3.6/pomp/build/partial.rdb            |binary
 pomp-3.6/pomp/data/LondonYorke.rda         |binary
 pomp-3.6/pomp/data/bsflu.rda               |binary
 pomp-3.6/pomp/data/ebolaWA2014.rda         |binary
 pomp-3.6/pomp/data/ewcitmeas.rda           |binary
 pomp-3.6/pomp/data/ewmeas.rda              |binary
 pomp-3.6/pomp/inst/CITATION                |  102 ++++----
 pomp-3.6/pomp/inst/NEWS                    |   29 ++
 pomp-3.6/pomp/inst/NEWS.Rd                 |   14 +
 pomp-3.6/pomp/inst/doc/index.html          |    5 
 pomp-3.6/pomp/man/abc.Rd                   |   64 +++--
 pomp-3.6/pomp/man/accumulators.Rd          |  156 ++++++------
 pomp-3.6/pomp/man/bake.Rd                  |   11 
 pomp-3.6/pomp/man/basic_components.Rd      |   52 ++--
 pomp-3.6/pomp/man/basic_probes.Rd          |   16 -
 pomp-3.6/pomp/man/blowflies.Rd             |   13 -
 pomp-3.6/pomp/man/bsflu.Rd                 |   14 -
 pomp-3.6/pomp/man/bsmc2.Rd                 |   51 ++--
 pomp-3.6/pomp/man/bsplines.Rd              |    7 
 pomp-3.6/pomp/man/childhood.Rd             |only
 pomp-3.6/pomp/man/coef.Rd                  |   23 +
 pomp-3.6/pomp/man/cond_logLik.Rd           |   24 +
 pomp-3.6/pomp/man/covariate_table.Rd       |   36 +-
 pomp-3.6/pomp/man/covmat.Rd                |   20 +
 pomp-3.6/pomp/man/csnippet.Rd              |   29 +-
 pomp-3.6/pomp/man/dacca.Rd                 |   25 +-
 pomp-3.6/pomp/man/design.Rd                |    2 
 pomp-3.6/pomp/man/distributions.Rd         |   25 +-
 pomp-3.6/pomp/man/dmeasure.Rd              |    5 
 pomp-3.6/pomp/man/dmeasure_spec.Rd         |   64 +++--
 pomp-3.6/pomp/man/dprior.Rd                |   13 -
 pomp-3.6/pomp/man/dprocess.Rd              |    5 
 pomp-3.6/pomp/man/dprocess_spec.Rd         |   33 +-
 pomp-3.6/pomp/man/ebola.Rd                 |   58 ++--
 pomp-3.6/pomp/man/eff_sample_size.Rd       |   24 +
 pomp-3.6/pomp/man/elementary_algorithms.Rd |   13 -
 pomp-3.6/pomp/man/estimation_algorithms.Rd |   27 +-
 pomp-3.6/pomp/man/filter_mean.Rd           |   24 +
 pomp-3.6/pomp/man/filter_traj.Rd           |   24 +
 pomp-3.6/pomp/man/flow.Rd                  |   23 +
 pomp-3.6/pomp/man/forecast.Rd              |   21 +
 pomp-3.6/pomp/man/gompertz.Rd              |    9 
 pomp-3.6/pomp/man/hitch.Rd                 |    2 
 pomp-3.6/pomp/man/kalman.Rd                |   37 +--
 pomp-3.6/pomp/man/loglik.Rd                |   21 +
 pomp-3.6/pomp/man/logmeanexp.Rd            |   14 -
 pomp-3.6/pomp/man/lookup.Rd                |    5 
 pomp-3.6/pomp/man/mif2.Rd                  |   51 ++--
 pomp-3.6/pomp/man/nlf.Rd                   |   52 ++--
 pomp-3.6/pomp/man/obs.Rd                   |   24 +
 pomp-3.6/pomp/man/ou2.Rd                   |    9 
 pomp-3.6/pomp/man/parameter_trans.Rd       |   34 +-
 pomp-3.6/pomp/man/parmat.Rd                |   12 
 pomp-3.6/pomp/man/partrans.Rd              |    3 
 pomp-3.6/pomp/man/parus.Rd                 |   60 ++--
 pomp-3.6/pomp/man/pfilter.Rd               |   31 +-
 pomp-3.6/pomp/man/pmcmc.Rd                 |   69 +++--
 pomp-3.6/pomp/man/pomp-package.Rd          |  132 ++++++----
 pomp-3.6/pomp/man/pomp.Rd                  |   56 +++-
 pomp-3.6/pomp/man/pomp_examp.Rd            |   14 -
 pomp-3.6/pomp/man/pred_mean.Rd             |   24 +
 pomp-3.6/pomp/man/pred_var.Rd              |   24 +
 pomp-3.6/pomp/man/print.Rd                 |    2 
 pomp-3.6/pomp/man/prior_spec.Rd            |  120 +++++++--
 pomp-3.6/pomp/man/probe.Rd                 |   36 +-
 pomp-3.6/pomp/man/probe_match.Rd           |   58 ++--
 pomp-3.6/pomp/man/proposals.Rd             |    5 
 pomp-3.6/pomp/man/resample.Rd              |    1 
 pomp-3.6/pomp/man/ricker.Rd                |    9 
 pomp-3.6/pomp/man/rinit.Rd                 |    5 
 pomp-3.6/pomp/man/rinit_spec.Rd            |   83 +++---
 pomp-3.6/pomp/man/rmeasure.Rd              |    5 
 pomp-3.6/pomp/man/rmeasure_spec.Rd         |   63 +++--
 pomp-3.6/pomp/man/rprior.Rd                |   13 -
 pomp-3.6/pomp/man/rprocess.Rd              |    5 
 pomp-3.6/pomp/man/rprocess_spec.Rd         |   33 +-
 pomp-3.6/pomp/man/rw2.Rd                   |   29 +-
 pomp-3.6/pomp/man/sannbox.Rd               |   17 -
 pomp-3.6/pomp/man/saved_states.Rd          |   24 +
 pomp-3.6/pomp/man/simulate.Rd              |   27 +-
 pomp-3.6/pomp/man/sir.Rd                   |   34 +-
 pomp-3.6/pomp/man/skeleton.Rd              |   12 
 pomp-3.6/pomp/man/skeleton_spec.Rd         |   98 ++++++-
 pomp-3.6/pomp/man/spect.Rd                 |   34 +-
 pomp-3.6/pomp/man/spect_match.Rd           |   55 ++--
 pomp-3.6/pomp/man/spy.Rd                   |   23 +
 pomp-3.6/pomp/man/states.Rd                |   24 +
 pomp-3.6/pomp/man/summary.Rd               |   23 +
 pomp-3.6/pomp/man/time.Rd                  |   25 +-
 pomp-3.6/pomp/man/timezero.Rd              |   23 +
 pomp-3.6/pomp/man/traces.Rd                |   23 +
 pomp-3.6/pomp/man/traj_match.Rd            |   43 ++-
 pomp-3.6/pomp/man/trajectory.Rd            |   23 +
 pomp-3.6/pomp/man/transformations.Rd       |   25 +-
 pomp-3.6/pomp/man/userdata.Rd              |  129 +++++-----
 pomp-3.6/pomp/man/verhulst.Rd              |   24 +
 pomp-3.6/pomp/man/workhorses.Rd            |    9 
 pomp-3.6/pomp/man/wpfilter.Rd              |   31 +-
 pomp-3.6/pomp/src/pomp_decls.h             |    6 
 pomp-3.6/pomp/src/rinit.c                  |    4 
 181 files changed, 2628 insertions(+), 1558 deletions(-)

More information about pomp at CRAN
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Package MIMSunit updated to version 0.11.0 with previous version 0.10.0 dated 2021-04-29

Title: Algorithm to Compute Monitor Independent Movement Summary Unit (MIMS-Unit)
Description: The MIMS-unit algorithm is developed to compute Monitor Independent Movement Summary Unit, a measurement to summarize raw accelerometer data while ensuring harmonized results across different devices. It also includes scripts to reproduce results in the related publication (John, D., Tang. Q., Albinali, F. and Intille, S. (2019) <doi:10.1123/jmpb.2018-0068>).
Author: Qu Tang [aut, cre] (<https://orcid.org/0000-0001-5415-0205>), Dinesh John [aut], Stephen Intille [aut], mHealth Research Group [cph] (https://www.mhealthgroup.org)
Maintainer: Qu Tang <tang.q@northeastern.edu>

Diff between MIMSunit versions 0.10.0 dated 2021-04-29 and 0.11.0 dated 2021-09-03

 DESCRIPTION                             |    8 
 MD5                                     |   19 -
 NEWS.md                                 |   17 +
 R/import_data.R                         |  167 ++++++++-------
 R/mims_unit.R                           |   34 ++-
 data/rest_on_table.rda                  |binary
 inst/extdata/actigraph_no_timestamp.csv |only
 man/custom_mims_unit.Rd                 |  345 ++++++++++++++++----------------
 man/import_actigraph_csv.Rd             |   26 ++
 man/import_actigraph_csv_chunked.Rd     |    4 
 man/mims_unit.Rd                        |  278 +++++++++++++------------
 11 files changed, 500 insertions(+), 398 deletions(-)

More information about MIMSunit at CRAN
Permanent link

Package EpiContactTrace updated to version 0.16.0 with previous version 0.15.0 dated 2020-12-12

Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing and visualisation of network of contacts.
Author: Maria Noremark [aut] (<https://orcid.org/0000-0003-2555-8476>), Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

Diff between EpiContactTrace versions 0.15.0 dated 2020-12-12 and 0.16.0 dated 2021-09-03

 DESCRIPTION                        |    6 +++---
 MD5                                |   16 ++++++++--------
 NEWS.md                            |    7 +++++++
 R/in-degree.R                      |    6 +++---
 R/ingoing-contact-chain.R          |    6 +++---
 R/out-degree.R                     |    6 +++---
 man/InDegree-methods.Rd            |    4 ++--
 man/IngoingContactChain-methods.Rd |    4 ++--
 man/OutDegree-methods.Rd           |    4 ++--
 9 files changed, 33 insertions(+), 26 deletions(-)

More information about EpiContactTrace at CRAN
Permanent link

Package CruzPlot updated to version 1.4.6 with previous version 1.4.5 dated 2021-03-01

Title: Plot Shipboard DAS Data
Description: A utility program oriented to create maps, plot data, and do basic data summaries of 'DAS' data <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> produced by 'WinCruz' from the Southwest Fisheries Science Center. <https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>), Tim Gerrodette [aut]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

Diff between CruzPlot versions 1.4.5 dated 2021-03-01 and 1.4.6 dated 2021-09-03

 CruzPlot-1.4.5/CruzPlot/inst/shiny/server_2_das/cruzDasInteractiveEffort.R |only
 CruzPlot-1.4.5/CruzPlot/inst/shiny/server_2_das/cruzDasInteractiveSight.R  |only
 CruzPlot-1.4.5/CruzPlot/inst/shiny/server_draw_local                       |only
 CruzPlot-1.4.6/CruzPlot/DESCRIPTION                                        |    7 
 CruzPlot-1.4.6/CruzPlot/MD5                                                |   26 -
 CruzPlot-1.4.6/CruzPlot/NEWS.md                                            |    7 
 CruzPlot-1.4.6/CruzPlot/README.md                                          |   16 
 CruzPlot-1.4.6/CruzPlot/inst/shiny/app.R                                   |   30 -
 CruzPlot-1.4.6/CruzPlot/inst/shiny/server_1_map/cruzMapRange.R             |  111 ++---
 CruzPlot-1.4.6/CruzPlot/inst/shiny/server_2_das/cruzDasInteractive.R       |  192 ++++++++++
 CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/drawInteractive.R          |only
 CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/drawStatic.R               |only
 CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/server_render.R            |    6 
 CruzPlot-1.4.6/CruzPlot/inst/shiny/ui_files/ui_createMap.R                 |    2 
 CruzPlot-1.4.6/CruzPlot/inst/shiny/www/CruzPlot_Manual_app.pdf             |binary
 15 files changed, 290 insertions(+), 107 deletions(-)

More information about CruzPlot at CRAN
Permanent link

Package aplot updated to version 0.1.0 with previous version 0.0.7 dated 2021-09-01

Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between aplot versions 0.0.7 dated 2021-09-01 and 0.1.0 dated 2021-09-03

 DESCRIPTION      |    8 -
 MD5              |   26 ++--
 NAMESPACE        |   83 +++++++------
 NEWS.md          |   88 ++++++++------
 R/aplot.R        |  148 ++++++++++++------------
 R/axis.R         |  270 ++++++++++++++++++++++----------------------
 R/insertion.R    |  336 +++++++++++++++++++++++++++----------------------------
 R/plot-list.R    |  117 ++++++++++++++-----
 R/re-export.R    |   14 +-
 R/utilities.R    |   96 +++++++--------
 man/ggrange.Rd   |   46 +++----
 man/is.ggtree.Rd |   40 +++---
 man/plot_list.Rd |   82 ++++++++-----
 man/reexports.Rd |   38 +++---
 14 files changed, 753 insertions(+), 639 deletions(-)

More information about aplot at CRAN
Permanent link

Package netrankr updated to version 1.1.0 with previous version 1.0.0 dated 2021-07-16

Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre], Julian Müller [ctb]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

Diff between netrankr versions 1.0.0 dated 2021-07-16 and 1.1.0 dated 2021-09-03

 DESCRIPTION                              |    8 
 MD5                                      |  170 ++++++-------
 NAMESPACE                                |    6 
 NEWS.md                                  |   15 +
 R/RcppExports.R                          |   12 
 R/aggregate.index.R                      |   84 +++---
 R/approximate.ranks.R                    |  361 +++++++++++++---------------
 R/bradley.terry.R                        |   18 -
 R/check.preservation.R                   |   20 -
 R/comparable.pairs.R                     |   22 +
 R/compare.ranks.R                        |   27 +-
 R/data.R                                 |    4 
 R/distance.index.R                       |   12 
 R/dominance.graph.R                      |   24 +
 R/get.rankings.R                         |   61 ++--
 R/hyperbolic.index.R                     |   70 ++---
 R/index.builder.R                        |  383 +++++++++++++++++-------------
 R/indirect.relations.R                   |  198 ++++++++-------
 R/majorization.gap.R                     |   96 ++++---
 R/mcmc.rank.R                            |  119 +++++----
 R/neighborhood.inclusion.R               |   88 ++++---
 R/netrankr.R                             |   38 +--
 R/plot.rank.intervals.R                  |   27 +-
 R/positional.dominance.R                 |   67 ++---
 R/rank.analysis.R                        |  389 ++++++++++++++++---------------
 R/rank.interval.R                        |   52 ++--
 R/spectral.gap.R                         |   29 +-
 R/threshold.graph.R                      |   52 +---
 R/transform.relations.R                  |   86 +++---
 R/transitive.reduction.R                 |   12 
 R/utils.R                                |  335 ++++++++++++++++++++------
 build/vignette.rds                       |binary
 inst/doc/benchmarks.html                 |    8 
 inst/doc/neighborhood_inclusion.R        |    5 
 inst/doc/neighborhood_inclusion.Rmd      |    6 
 inst/doc/neighborhood_inclusion.html     |    2 
 inst/doc/partial_centrality.R            |   11 
 inst/doc/partial_centrality.Rmd          |   12 
 inst/doc/partial_centrality.html         |   14 -
 inst/doc/probabilistic_cent.R            |    5 
 inst/doc/probabilistic_cent.Rmd          |    8 
 inst/doc/probabilistic_cent.html         |    4 
 inst/doc/threshold_graph.R               |    3 
 inst/doc/threshold_graph.Rmd             |    5 
 inst/doc/use_case.Rmd                    |    2 
 inst/doc/use_case.html                   |    2 
 man/aggregate_positions.Rd               |   40 +--
 man/approx_rank_expected.Rd              |    8 
 man/approx_rank_relative.Rd              |    6 
 man/as.matrix.netrankr_full.Rd           |only
 man/comparable_pairs.Rd                  |    4 
 man/compare_ranks.Rd                     |   10 
 man/dominance_graph.Rd                   |   10 
 man/exact_rank_prob.Rd                   |    6 
 man/get_rankings.Rd                      |    5 
 man/hyperbolic_index.Rd                  |    4 
 man/incomparable_pairs.Rd                |    4 
 man/indirect_relations.Rd                |   16 -
 man/is_preserved.Rd                      |    6 
 man/majorization_gap.Rd                  |   12 
 man/mcmc_rank_prob.Rd                    |    4 
 man/neighborhood_inclusion.Rd            |   14 -
 man/plot.netrankr_interval.Rd            |    4 
 man/plot_rank_intervals.Rd               |   17 -
 man/positional_dominance.Rd              |   13 -
 man/print.netrankr_full.Rd               |    2 
 man/rank_intervals.Rd                    |    2 
 man/spectral_gap.Rd                      |    7 
 man/summary.netrankr_full.Rd             |only
 man/threshold_graph.Rd                   |    8 
 man/transitive_reduction.Rd              |    2 
 src/RcppExports.cpp                      |   34 +-
 src/mcmc_rank.cpp                        |   61 ++++
 src/nialgo.cpp                           |   15 -
 src/pdalgo.cpp                           |    5 
 tests/testthat/test_approximations.R     |   71 ++---
 tests/testthat/test_dominance.R          |  112 ++++----
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Package swfscDAS updated to version 0.6.0 with previous version 0.5.1 dated 2021-05-27

Title: Southwest Fisheries Science Center Shipboard DAS Data Processing
Description: Process and summarize shipboard 'DAS' <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz' <https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>. This package standardizes and streamlines basic DAS data processing, and includes a PDF with the DAS data format requirements.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

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Package AgroR updated to version 1.2.3 with previous version 1.2.2 dated 2021-07-16

Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), Anova of aligned ranks (Wobbrock, JO, Findlater, L., Gergle, D., Higgins , JJ (2011), <doi: 10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi: 10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Rodrigo Yudi Palhaci Marubayashi [aut, ctb] (<https://orcid.org/0000-0003-2778-8654>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>

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Package combinationpvalues updated to version 0.1.4 with previous version 0.1.3 dated 2021-07-05

Title: Combination of Independent P-Values
Description: Provides access to six fundamental statistics that can be used for the purpose of combination p-values. All methods used can referenced here: Heard & Rubin-Delanchy (2017) <arXiv:1707.06897>.
Author: Breya McGlown [cre, aut]
Maintainer: Breya McGlown <bswlker2@memphis.edu>

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Package ssdtools updated to version 0.3.5 with previous version 0.3.4 dated 2021-05-14

Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the log-normal, gamma, log-logistic, log-Gumbel, Gompertz and Weibull. The user can provide custom distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>), Carl Schwarz [aut, ctr], Angeline Tillmanns [ctb], Ali Azizishirazi [ctb], Rebecca Fisher [ctb], David Fox [ctb], Kathleen McTavish [ctb], Heather Thompson [ctb], Andy Teucher [ctb], Emilie Doussantousse [ctb], Stephanie Hazlitt [ctb], Nadine Hussein [ctb], Nan-Hung Hsieh [ctb], Sergio Ibarra Espinosa [ctb], Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package r2dii.data updated to version 0.2.2 with previous version 0.2.1 dated 2021-07-09

Title: Datasets to Measure the Alignment of Corporate Loan Books with Climate Goals
Description: These datasets support the implementation in R of the software 'PACTA' (Paris Agreement Capital Transition Assessment), which is a free tool that calculates the alignment between corporate lending portfolios and climate scenarios (<https://2degrees-investing.org/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals. Because both financial institutions and market data providers keep their data private, this package provides fake, public data to enable the development and use of 'PACTA' in R.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>), Jackson Hoffart [aut, dtc] (<https://orcid.org/0000-0002-8600-5042>), Klaus Hagedorn [aut], 2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>

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Package MultivariateAnalysis updated to version 0.4.1 with previous version 0.4.0 dated 2021-08-05

Title: Pacote Para Analise Multivariada
Description: Package with multivariate analysis methodologies for experiment evaluation. The package estimates dissimilarity measures, builds dendrograms, obtains MANOVA, principal components, canonical variables, etc. (Pacote com metodologias de analise multivariada para avaliação de experimentos. O pacote estima medidas de dissimilaridade, construi de dendogramas, obtem a MANOVA, componentes principais, variáveis canônicas, etc.)
Author: Alcinei Mistico Azevedo [aut, cre] (<https://orcid.org/0000-0001-5196-0851>)
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>

Diff between MultivariateAnalysis versions 0.4.0 dated 2021-08-05 and 0.4.1 dated 2021-09-03

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Package gradeR updated to version 1.0.10 with previous version 1.0.9 dated 2020-09-07

Title: Helps Grade Assignment Submissions that are R Scripts
Description: After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>

Diff between gradeR versions 1.0.9 dated 2020-09-07 and 1.0.10 dated 2021-09-03

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Package FORTLS updated to version 1.0.3 with previous version 1.0.2 dated 2021-04-21

Title: Automatic Processing of TLS Point Cloud Data for Forestry Purposes
Description: Process automation of Terrestrial Laser Scanner (TLS) point cloud data derived from single scans. 'FORTLS' enables (i) detection of trees and estimation of diameter at breast height (dbh), (ii) estimation of some stand variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories (FIs) at stand level and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2020, <doi:10.3390/IECF2020-08003>).
Author: Juan Alberto Molina-Valero [aut, cph, cre], María José Ginzo Villamayor [aut, com], Manuel Antonio Novo Pérez [aut, com], Adela Martínez-Calvo [aut, com], Juan Gabriel Álvarez-González [aut, ths], Fernando Montes [aut], César Pérez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <juanalberto.molina.valero@usc.es>

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Package abess updated to version 0.3.0 with previous version 0.2.0 dated 2021-07-31

Title: Adaptive Best Subset Selection in Polynomial Time
Description: Extremely efficient toolkit for solving the best subset selection problem in linear regression, logistic regression, Poisson regression, Cox proportional hazard model, multiple-response regression, multinomial logistic regression, and (sequential) principal component analysis. It implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times.
Author: Jin Zhu [aut, cre] (<https://orcid.org/0000-0001-8550-5822>), Liyuan Hu [aut], Junhao Huang [aut], Kangkang Jiang [aut], Yanhang Zhang [aut], Shiyun Lin [aut], Junxian Zhu [aut], Canhong Wen [aut], Heping Zhang [aut] (<https://orcid.org/0000-0002-0688-4076>), Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>), spectra contributors [cph] (Spectra implementation)
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>

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Package snahelper updated to version 1.3.0 with previous version 1.2.0 dated 2020-09-13

Title: 'RStudio' Addin for Network Analysis and Visualization
Description: 'RStudio' addin which provides a GUI to visualize and analyse networks. After finishing a session, the code to produce the plot is inserted in the current script. Alternatively, the function SNAhelperGadget() can be used directly from the console. Additional addins include the Netreader() for reading network files, Netbuilder() to create small networks via point and click, and the Componentlayouter() to layout networks with many components manually.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

Diff between snahelper versions 1.2.0 dated 2020-09-13 and 1.3.0 dated 2021-09-03

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Package nat updated to version 1.8.17 with previous version 1.8.16 dated 2020-09-22

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>), James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>

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Package memoiR updated to version 1.1-2 with previous version 1.1-0 dated 2021-07-26

Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

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Package wavemulcor updated to version 3.1.2 with previous version 3.1.0 dated 2020-05-17

Title: Wavelet Routines for Global and Local Multiple Regression and Correlation
Description: Wavelet routines that calculate single sets of wavelet multiple regressions and correlations, and cross-regressions and cross-correlations from a multivariate time series. Dynamic versions of the routines allow the wavelet local multiple (cross-)regressions and (cross-)correlations to evolve over time.
Author: Javier Fernandez-Macho [aut, cre] (<https://orcid.org/0000-0002-5970-4382>)
Maintainer: Javier Fernandez-Macho <javier.fernandezmacho@ehu.es>

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Package RxODE updated to version 1.1.1 with previous version 1.1.0 dated 2021-08-06

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>), Melissa Hallow [aut], Wenping Wang [aut, cre], Zufar Mulyukov [ctb], Alan Hindmarsh [ctb], Awad H. Al-Mohy [ctb], Matt Dowle [ctb], Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Arun Srinivasan [ctb], Ernst Hairer [ctb], Gerhard Wanner [ctb], Goro Fuji [ctb], Hadley Wickham [ctb], Jack Dongarra [ctb], Linda Petzold [ctb], Martin Maechler [ctb], Matteo Fasiolo [ctb], Morwenn [ctb], Nicholas J. Higham [ctb], Roger B. Sidje [ctb], Simon Frost [ctb], Kevin Ushey [ctb], Yu Feng [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>

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Package RRreg updated to version 0.7.3 with previous version 0.7.1 dated 2019-12-04

Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze randomized response (RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A survey technique for eliminating evasive answer bias. Journal of the American Statistical Association, 60, 63–69, <doi:10.2307/2283137>). Besides univariate estimates of true proportions, RR variables can be used for correlations, as dependent variable in a logistic regression (with or without random effects), or as predictors in a linear regression (Heck, D. W., & Moshagen, M. (2018). RRreg: An R package for correlation and regression analyses of randomized response data. Journal of Statistical Software, 85(2), 1–29, <doi:10.18637/jss.v085.i02>). For simulations and the estimation of statistical power, RR data can be generated according to several models. The implemented methods also allow to test the link between continuous covariates and dishonesty in cheating paradigms such as the coin-toss or dice-roll task (Moshagen, M., & Hilbig, B. E. (2017). The statistical analysis of cheating paradigms. Behavior Research Methods, 49, 724–732, <doi:10.3758/s13428-016-0729-x>).
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>), Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>

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Package rlist updated to version 0.4.6.2 with previous version 0.4.6.1 dated 2016-04-04

Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>

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Package RBesT updated to version 1.6-2 with previous version 1.6-1 dated 2020-05-28

Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases). Please refer to Neuenschwander et al. (2010) <doi:10.1177/1740774509356002> and Schmidli et al. (2014) <doi:10.1111/biom.12242> for details on the methodology.
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb], Trustees of Columbia University [cph] (R/stanmodels.R, configure, configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

Diff between RBesT versions 1.6-1 dated 2020-05-28 and 1.6-2 dated 2021-09-03

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New package mvLSW with initial version 1.2.4
Package: mvLSW
Title: Multivariate, Locally Stationary Wavelet Process Estimation
Version: 1.2.4
Date: 2021-09-02
Description: Tools for analysing multivariate time series with wavelets. This includes: simulation of a multivariate locally stationary wavelet (mvLSW) process from a multivariate evolutionary wavelet spectrum (mvEWS); estimation of the mvEWS, local coherence and local partial coherence. See Park, Eckley and Ombao (2014) <doi:10.1109/TSP.2014.2343937> for details.
Depends: R (>= 3.2),fields, wavethresh, xts, zoo
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2021-09-02 09:43:46 UTC; grosedj
Author: Simon Taylor [aut], Tim Park [aut], Idris Eckley [ths], Rebecca Killick [ctb], Daniel Grose [aut, cre]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2021-09-03 12:20:06 UTC

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Package MBmca updated to version 1.0.1-3 with previous version 1.0.1-2 dated 2021-09-02

Title: Nucleic Acid Melting Curve Analysis
Description: Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Author: Stefan Roediger [cre, aut] (<https://orcid.org/0000-0002-1441-6512>), Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>)
Maintainer: Stefan Roediger <stefan_roediger@gmx.de>

Diff between MBmca versions 1.0.1-2 dated 2021-09-02 and 1.0.1-3 dated 2021-09-03

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New package matrixdist with initial version 1.1.3
Package: matrixdist
Title: Statistics for Matrix Distributions
Version: 1.1.3
Date: 2021-08-20
Maintainer: Martin Bladt <martinbladt@gmail.com>
Description: Tools for homogeneous and in-homogeneous phase-type distributions. Methods for functional evaluation, simulation and estimation using the expectation-maximization (EM) algorithm are provided. The methods of this package are based on the following references. Asmussen, S., Nerman, O., & Olsson, M. (1996) <https://www.jstor.org/stable/4616418>, Olsson, M. (1996) <https://www.jstor.org/stable/4616419>. Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60> Albrecher, H., Bladt, M., & Yslas, J. (2020) <doi:10.1111/sjos.12505> Bladt, M., & Yslas, J. (2020) <arXiv:2011.03219>.
Depends: R (>= 3.1.0)
License: GPL-3
Imports: Rcpp, methods
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-08-25 15:17:01 UTC; martinbladt
Author: Martin Bladt [aut, cre], Jorge Yslas [aut]
Repository: CRAN
Date/Publication: 2021-09-03 12:10:02 UTC

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New package ggseg with initial version 1.6.4
Package: ggseg
Title: Plotting Tool for Brain Atlases
Version: 1.6.4
Description: Contains 'ggplot2' geom for plotting brain atlases using simple features. The largest component of the package is the data for the two built-in atlases. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.3)
LazyData: true
LazyDataCompression: xz
Imports: ggplot2 (>= 3.3), dplyr (>= 1.0.0), tidyr (>= 1.0.0), sf (>= 0.9-2), grid, utils, vctrs
Suggests: knitr, here, rmarkdown, freesurfer, covr, vdiffr, testthat (>= 2.1.0), devtools, spelling
VignetteBuilder: knitr
URL: https://github.com/ggseg/ggseg
BugReports: https://github.com/ggseg/ggseg/issues
Language: en-US
NeedsCompilation: no
Packaged: 2021-09-02 08:31:26 UTC; athanasm
Author: Athanasia Mo Mowinckel [aut, cre] (<https://orcid.org/0000-0002-5756-0223>), Didac Vidal-Piñeiro [aut] (<https://orcid.org/0000-0001-9997-9156>)
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Repository: CRAN
Date/Publication: 2021-09-03 12:20:09 UTC

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Package geonetwork updated to version 0.4.1 with previous version 0.3 dated 2019-04-05

Title: Geographic Networks
Description: Provides classes and methods for handling networks or graphs whose nodes are geographical (i.e. locations in the globe). The functionality includes the creation of objects of class geonetwork as a graph with node coordinates, the computation of network measures, the support of spatial operations (projection to different Coordinate Reference Systems, handling of bounding boxes, etc.) and the plotting of the geonetwork object combined with supplementary cartography for spatial representation.
Author: Facundo Muñoz [aut, cre] (<https://orcid.org/0000-0002-5061-4241>)
Maintainer: Facundo Muñoz <facundo.munoz@cirad.fr>

Diff between geonetwork versions 0.3 dated 2019-04-05 and 0.4.1 dated 2021-09-03

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New package geodiv with initial version 1.0.4
Package: geodiv
Title: Methods for Calculating Gradient Surface Metrics
Version: 1.0.4
Author: Annie C. Smith, Phoebe Zarnetske, Kyla Dahlin, Adam Wilson, Andrew Latimer
Maintainer: Annie C. Smith <annie.smith@dnr.wa.gov>
Description: Methods for calculating gradient surface metrics for continuous analysis of landscape features.
URL: https://github.com/bioXgeo/geodiv
BugReports: https://github.com/bioXgeo/geodiv/issues
Depends: R (>= 3.5)
Imports: dplyr (>= 0.7.8), phonTools (>= 0.2-2.1), pracma (>= 2.2.2), raster (>= 2.8-4), rgdal (>= 1.4), spatial (>= 7.3-11), tibble (>= 1.4.2), e1071 (>= 1.7-0), sp (>= 1.3-1), rgeos (>= 0.4-3), parallel (>= 3.5.0), snow (>= 0.4-3), sf (>= 0.7-4), zoo (>= 1.8-5), Rcpp (>= 1.0.1), landscapemetrics(>= 1.5.2)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, ggplot2, rmarkdown, rasterVis, mapdata, maptools, maps, tidyverse, tidyr, ggmap, corrplot, cowplot, gridExtra, factoextra, cluster, knitr, rfigshare
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-09-01 21:46:43 UTC; lsth490
Repository: CRAN
Date/Publication: 2021-09-03 12:20:13 UTC

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Package forestplot updated to version 2.0.1 with previous version 2.0.0 dated 2021-08-10

Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. The aim is to extend the use of forest plots beyond meta-analyses. This is a more general version of the original 'rmeta' package's forestplot() function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre], Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>

Diff between forestplot versions 2.0.0 dated 2021-08-10 and 2.0.1 dated 2021-09-03

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New package expands with initial version 2.1.3
Package: expands
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Version: 2.1.3
Date: 2021-08-23
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (<https://pubmed.ncbi.nlm.nih.gov/24177718/>). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 2.1 include: (i) new parameter ploidy in runExPANdS.R allows specification of non-diploid background ploidies (e.g. for near-triploid cell lines); (ii) parallel computing option is available.
License: GPL-2
URL: https://github.com/noemiandor/expands, https://groups.google.com/d/forum/expands
Depends: R (>= 2.10)
Imports: flexclust, plyr, RColorBrewer, gplots, NbClust, moments (>= 0.13), rJava (>= 0.5-0), flexmix (>= 2.3), matlab (>= 0.8.9), ape (>= 3.2), commonsMath (>= 1.1), parallel
Suggests: phylobase (>= 0.6.8)
SystemRequirements: Java (>= 5.0)
Packaged: 2021-09-03 09:53:05 UTC; 4470246
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2021-09-03 13:00:02 UTC

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Package dockerfiler updated to version 0.1.4 with previous version 0.1.3 dated 2019-03-19

Title: Easy Dockerfile Creation from R
Description: Build a Dockerfile straight from your R session. 'dockerfiler' allows you to create step by step a Dockerfile, and provide convenient tools to wrap R code inside this Dockerfile.
Author: Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>), Vincent Guyader [aut] (<https://orcid.org/0000-0003-0671-9270>)
Maintainer: Colin Fay <contact@colinfay.me>

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Package dataquieR updated to version 1.0.9 with previous version 1.0.8 dated 2021-08-12

Title: Data Quality in Epidemiological Research
Description: A set of functions to assess data quality issues in studies. See 'TMF' <https://www.tmf-ev.de/EnglishSite/Home.aspx> guideline and 'DFG' <https://www.dfg.de/en/index.jsp> project at <https://dataquality.ship-med.uni-greifswald.de>.
Author: University Medicine Greifswald [cph], Adrian Richter [aut], Carsten Oliver Schmidt [aut], Stephan Struckmann [aut, cre]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>

Diff between dataquieR versions 1.0.8 dated 2021-08-12 and 1.0.9 dated 2021-09-03

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Package RRphylo updated to version 2.5.8 with previous version 2.5.7 dated 2021-07-16

Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>

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Package pencal updated to version 1.0.0 with previous version 0.4.2 dated 2021-05-28

Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a statistical method that allows to predict survival from high-dimensional longitudinal predictors. PRC is described in Signorelli et al. (2021, arXiv preprint: <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph] (<https://orcid.org/0000-0002-8102-3356>), Pietro Spitali [ctb], Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

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Package DCLEAR updated to version 1.0.8 with previous version 1.0.0 dated 2021-07-15

Title: Distance Based Cell Lineage Reconstruction
Description: R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020. The challenge paper is Gong et al. (2021) <doi:10.1016/j.cels.2021.05.008>.
Author: Il-Youp Kwak [aut, cre], Wuming Gong [aut]
Maintainer: Il-Youp Kwak <ikwak2@cau.ac.kr>

Diff between DCLEAR versions 1.0.0 dated 2021-07-15 and 1.0.8 dated 2021-09-03

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Package splash updated to version 1.0.1 with previous version 1.0.0 dated 2021-09-02

Title: Simple Process-Led Algorithms for Simulating Habitats
Description: This program calculates bioclimatic indices and fluxes (radiation, evapotranspiration, soil moisture) for use in studies of ecosystem function, species distribution, and vegetation dynamics under changing climate scenarios. Predictions are based on a minimum of required inputs: latitude, precipitation, air temperature, and cloudiness. Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>.
Author: Tyler W. Davis [aut] (<https://orcid.org/0000-0003-4312-919X>), Iain Colin Prentice [aut] (<https://orcid.org/0000-0002-1296-6764>), Benjamin D. Stocker [aut] (<https://orcid.org/0000-0003-2697-9096>), Rebecca T. Thomas [aut], Rhys J. Whitley [aut], Han Wang [aut] (<https://orcid.org/0000-0003-2482-1818>), Bradley J. Evans [aut], Angela V. Gallego-Sala [aut], Martin T. Sykes [aut], Wolfgang Cramer [aut] (<https://orcid.org/0000-0002-9205-5812>), Roberto Villegas-Diaz [cre] (<https://orcid.org/0000-0001-5036-8661>)
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@reading.ac.uk>

Diff between splash versions 1.0.0 dated 2021-09-02 and 1.0.1 dated 2021-09-03

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Package GetFREData updated to version 0.7 with previous version 0.6 dated 2021-04-06

Title: Reading FRE Corporate Data of Public Traded Companies from B3
Description: Reads corporate data such as board composition and compensation for companies traded at B3, the Brazilian exchange <http://www.b3.com.br/>. All data is downloaded and imported from the ftp site <http://dados.cvm.gov.br/dados/CIA_ABERTA/DOC/FRE/>.
Author: Marcelo Perlin [aut, cre], Guilherme Kirch [aut]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetFREData versions 0.6 dated 2021-04-06 and 0.7 dated 2021-09-03

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Package DiscreteFDR updated to version 1.3.6 with previous version 1.3.5 dated 2021-05-25

Title: Multiple Testing Procedures with Adaptation for Discrete Tests
Description: Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
Author: Sebastian Döhler [ctb], Guillermo Durand [aut, ctb], Florian Junge [aut, cre], Etienne Roquain [ctb]
Maintainer: Florian Junge <florian.junge@h-da.de>

Diff between DiscreteFDR versions 1.3.5 dated 2021-05-25 and 1.3.6 dated 2021-09-03

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New package dauphin with initial version 0.2.0
Package: dauphin
Title: Compact Standard for Australian Phone Numbers
Version: 0.2.0
Description: Phone numbers are often represented as strings because there is no obvious and suitable native representation for them. This leads to high memory use and a lack of standard representation. The package provides integer representation of Australian phone numbers with optional raw vector calling code. The package name is an extension of 'au' and 'ph'.
License: GPL-2
Encoding: UTF-8
Suggests: tinytest
Imports: utils
NeedsCompilation: yes
Packaged: 2021-09-01 14:44:13 UTC; hughp
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-03 10:00:02 UTC

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New package bs4cards with initial version 0.1.0
Package: bs4cards
Title: Generate Bootstrap 4 Cards
Version: 0.1.0
Description: Allows the user to generate bootstrap cards within R markdown documents. Intended for use in conjunction with R markdown HTML outputs and other formats that support the bootstrap 4 library.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: htmltools, magrittr, methods, rlang
URL: https://github.com/djnavarro/bs4cards
BugReports: https://github.com/djnavarro/bs4cards/issues
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, tibble, covr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-09-01 11:11:18 UTC; danielle
Author: Danielle Navarro [aut, cre] (<https://orcid.org/0000-0001-7648-6578>)
Maintainer: Danielle Navarro <d.navarro@unsw.edu.au>
Repository: CRAN
Date/Publication: 2021-09-03 09:40:02 UTC

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Package bain updated to version 0.2.6 with previous version 0.2.4 dated 2020-03-09

Title: Bayes Factors for Informative Hypotheses
Description: Computes approximated adjusted fractional Bayes factors for equality, inequality, and about equality constrained hypotheses. S3 methods are available for specific types of lm() models, namely ANOVA, ANCOVA, and multiple regression, and for the t_test(). The statistical underpinnings are described in Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>, Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>.
Author: Xin Gu [aut], Herbert Hoijtink [aut], Joris Mulder [aut], Caspar J van Lissa [aut, cre], Van Zundert Camiel [ctb], Jeff Jones [ctb], Niels Waller [ctb]
Maintainer: Caspar J van Lissa <c.j.vanlissa@uu.nl>

Diff between bain versions 0.2.4 dated 2020-03-09 and 0.2.6 dated 2021-09-03

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More information about bain at CRAN
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Package rgoogleads updated to version 0.3.0 with previous version 0.2.0 dated 2021-08-02

Title: Loading Data from 'Google Ads API'
Description: Interface for loading data from 'Google Ads API', see <https://developers.google.com/google-ads/api/docs/start>. Package provide function for authorization and loading reports.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>), Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>

Diff between rgoogleads versions 0.2.0 dated 2021-08-02 and 0.3.0 dated 2021-09-03

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Package RedditExtractoR updated to version 3.0.3 with previous version 3.0.1 dated 2021-08-23

Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

Diff between RedditExtractoR versions 3.0.1 dated 2021-08-23 and 3.0.3 dated 2021-09-03

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New package REAT with initial version 3.0.3
Package: REAT
Title: Regional Economic Analysis Toolbox
Version: 3.0.3
Date: 2021-08-24
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-09-02 13:45:18 UTC; Thomas
Repository: CRAN
Date/Publication: 2021-09-03 08:00:11 UTC

More information about REAT at CRAN
Permanent link

Package rdacca.hp updated to version 1.0-2 with previous version 1.0-1 dated 2021-08-11

Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <doi:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-Neto
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>

Diff between rdacca.hp versions 1.0-1 dated 2021-08-11 and 1.0-2 dated 2021-09-03

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Package pROC updated to version 1.18.0 with previous version 1.17.0.1 dated 2021-01-13

Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] (<https://orcid.org/0000-0002-6813-3200>), Natacha Turck [aut], Alexandre Hainard [aut], Natalia Tiberti [aut], Frédérique Lisacek [aut], Jean-Charles Sanchez [aut], Markus Müller [aut], Stefan Siegert [ctb] (Fast DeLong code), Matthias Doering [ctb] (Hand & Till Multiclass), Zane Billings [ctb] (DeLong paired test CI)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>

Diff between pROC versions 1.17.0.1 dated 2021-01-13 and 1.18.0 dated 2021-09-03

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 R/roc.utils.R                                                          |   30 +++
 README.md                                                              |    4 
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 man/roc.Rd                                                             |    2 
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Package ggpmisc updated to version 0.4.3 with previous version 0.4.2-1 dated 2021-08-15

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb] (<https://orcid.org/0000-0002-2843-6370>), Samer Mouksassi [ctb] (<https://orcid.org/0000-0002-7152-6654>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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More information about ggpmisc at CRAN
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Package GeodRegr updated to version 0.2.0 with previous version 0.1.0 dated 2020-08-24

Title: Geodesic Regression
Description: Provides a gradient descent algorithm to find a geodesic relationship between real-valued independent variables and a manifold-valued dependent variable (i.e. geodesic regression). Available manifolds are Euclidean space, the sphere, hyperbolic space, and Kendall's 2-dimensional shape space. Besides the standard least-squares loss, the least absolute deviations, Huber, and Tukey biweight loss functions can also be used to perform robust geodesic regression. Functions to help choose appropriate cutoff parameters to maintain high efficiency for the Huber and Tukey biweight estimators are included, as are functions for generating random tangent vectors from the Riemannian normal distributions on the sphere and hyperbolic space. The n-sphere is a n-dimensional manifold: we represent it as a sphere of radius 1 and center 0 embedded in (n+1)-dimensional space. Using the hyperboloid model of hyperbolic space, n-dimensional hyperbolic space is embedded in (n+1)-dimensional Minkowski space as the upper sheet of a hyperboloid of two sheets. Kendall's 2D shape space with K landmarks is of real dimension 2K-4; preshapes are represented as complex K-vectors with mean 0 and magnitude 1. Details are described in Shin, H.-Y. and Oh, H.-S. (2020) <arXiv:2007.04518>. Also see Fletcher, P. T. (2013) <doi:10.1007/s11263-012-0591-y>.
Author: Ha-Young Shin [aut, cre], Hee-Seok Oh [aut]
Maintainer: Ha-Young Shin <hayoung.shin@gmail.com>

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Package finbif updated to version 0.6.2 with previous version 0.6.1 dated 2021-07-26

Title: Interface for the 'Finnish Biodiversity Information Facility' API
Description: A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph], William K. Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>

Diff between finbif versions 0.6.1 dated 2021-07-26 and 0.6.2 dated 2021-09-03

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 finbif-0.6.2/finbif/DESCRIPTION                                                       |    8 
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 finbif-0.6.2/finbif/R/api_get.R                                                       |   14 
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Package bioseq updated to version 0.1.3 with previous version 0.1.2 dated 2020-11-25

Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph] (<https://orcid.org/0000-0002-3323-4167>)
Maintainer: Francois Keck <francois.keck@gmail.com>

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Package AmigaFFH updated to version 0.4.1 with previous version 0.3.1 dated 2019-03-31

Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This package intends to handle many file formats that were native to the antiquated Commodore Amiga machine. This package focuses on file types from the older Amiga operating systems (<= 3.0). It will read and write specific file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

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More information about AmigaFFH at CRAN
Permanent link

Package wdpar updated to version 1.3.1 with previous version 1.0.6 dated 2020-12-18

Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected Areas (WDPA). Data is obtained from Protected Planet <https://www.protectedplanet.net/en>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>

Diff between wdpar versions 1.0.6 dated 2020-12-18 and 1.3.1 dated 2021-09-03

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More information about wdpar at CRAN
Permanent link

Package sigminer updated to version 2.0.5 with previous version 2.0.4 dated 2021-08-03

Title: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>), Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>), Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>), Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>), Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between sigminer versions 2.0.4 dated 2021-08-03 and 2.0.5 dated 2021-09-03

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More information about sigminer at CRAN
Permanent link

Package impactr updated to version 0.2.0 with previous version 0.1.0 dated 2021-07-01

Title: Mechanical Loading Prediction Through Accelerometer Data
Description: Functions to read, process and analyse accelerometer data related to mechanical loading variables. This package is developed and tested for use with raw accelerometer data from triaxial 'ActiGraph' <https://actigraphcorp.com> accelerometers.
Author: Lucas Veras [aut, cre] (<https://orcid.org/0000-0003-0562-5803>)
Maintainer: Lucas Veras <lucasdsveras@gmail.com>

Diff between impactr versions 0.1.0 dated 2021-07-01 and 0.2.0 dated 2021-09-03

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More information about impactr at CRAN
Permanent link

New package hergm with initial version 4.1-8
Package: hergm
Version: 4.1-8
Date: 2021-09-02
Title: Hierarchical Exponential-Family Random Graph Models
Depends: ergm, latentnet, mcgibbsit, network, sna
Imports: methods, mlergm, Rcpp (>= 0.12.7), Matrix, igraph, intergraph, parallel, stringr
Description: Hierarchical exponential-family random graph models with local dependence. See Schweinberger and Luna (2018) <doi:10.18637/jss.v085.i01>.
License: GPL-3
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2021-09-02 20:08:37 UTC; gilgamesh
Author: Michael Schweinberger [cre, aut], Mark S. Handcock [aut], Sergii Babkin [aut], Jonathan Stewart [aut], Duy Vu [aut], Pamela Luna [ctb]
Maintainer: Michael Schweinberger <msq5c@missouri.edu>
Repository: CRAN
Date/Publication: 2021-09-03 07:10:08 UTC

More information about hergm at CRAN
Permanent link

New package helsinki with initial version 1.0.3
Package: helsinki
Title: R Tools for Helsinki Open Data
Version: 1.0.3
Description: Tools for accessing various open data sources in the Helsinki region in Finland. Current data sources include the Real Estate Department (<http://ptp.hel.fi/avoindata/>), Service Map API (<http://api.hel.fi/servicemap/v2/>), Linked Events API (<http://api.hel.fi/linkedevents/v1/>), Helsinki Region Infoshare statistics API (<https://dev.hel.fi/stats/>).
License: BSD_2_clause + file LICENSE
Depends: R (>= 3.1.0)
Imports: jsonlite, sp, httr, purrr, dplyr, xml2, methods, sf, httpcache, curl
Suggests: knitr, rmarkdown, remotes, ggplot2
URL: http://ropengov.github.io/helsinki/, https://github.com/rOpenGov/helsinki
BugReports: https://github.com/ropengov/helsinki/issues
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Encoding: UTF-8
Packaged: 2021-09-02 14:44:32 UTC; juusoparkkinen
Author: Juuso Parkkinen [aut, cre], Joona Lehtomaki [aut], Pyry Kantanen [aut] (<https://orcid.org/0000-0003-2853-2765>), Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>)
Maintainer: Juuso Parkkinen <juuso.parkkinen@iki.fi>
Date/Publication: 2021-09-03 07:20:05 UTC

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Package rym updated to version 1.0.5 with previous version 1.0.3 dated 2020-08-12

Title: R Interface to Yandex Metrica API
Description: Allows work with 'Management API' for load counters, segments, filters, user permissions and goals list from Yandex Metrica, 'Reporting API' allows you to get information about the statistics of site visits and other data without using the web interface, 'Logs API' allows to receive non-aggregated data and 'Compatible with Google Analytics Core Reporting API v3' allows receive information about site traffic and other data using field names from Google Analytics Core API. For more information see official documents <https://yandex.ru/dev/metrika/doc/api2/concept/about-docpage>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>), Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package MINTplates updated to version 1.0.1 with previous version 1.0.0 dated 2021-08-13

Title: Encode "License-Plates" from Sequences and Decode Them Back
Description: It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>.
Author: Shanliang Zhong [aut, cre]
Maintainer: Shanliang Zhong <slzhong@foxmail.com>

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Package fmcmc updated to version 0.5-0 with previous version 0.4-0 dated 2020-09-01

Title: A friendly MCMC framework
Description: Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC) framework for implementing Metropolis-Hastings algorithm in a modular way allowing users to specify automatic convergence checker, personalized transition kernels, and out-of-the-box multiple MCMC chains using parallel computing. Most of the methods implemented in this package can be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5> Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5> Robust Adaptive Metropolis, and Thawornwattana et al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Fabian Scheipl [rev] (JOSS reviewer, <https://orcid.org/0000-0001-8172-3603>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>

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Package eventTrack updated to version 1.0.1 with previous version 1.0.0 dated 2021-05-10

Title: Event Prediction for Time-to-Event Endpoints
Description: Implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>

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 eventTrack-1.0.1/eventTrack/MD5                                                                                     |  114 +++++-----
 eventTrack-1.0.1/eventTrack/NEWS                                                                                    |    4 
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Permanent link

Package BayesXsrc (with last version 3.0-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-04-24 3.0-1
2018-02-22 3.0-0
2013-10-10 2.1-2
2012-05-20 2.1-1

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Package mixl (with last version 1.3.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-08-03 1.3.1
2021-06-15 1.3
2020-10-21 1.2.3
2020-07-13 1.2.2
2020-07-11 1.2.1
2020-07-10 1.2.0
2020-03-21 1.1.2
2019-11-06 1.1

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Package fMRIscrub (with last version 0.8.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-08-20 0.8.2

Permanent link
Package R2BayesX (with last version 1.1-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-12-05 1.1-1
2016-11-17 1.1-0
2015-01-26 1.0-0
2013-08-19 0.3-1
2013-03-19 0.1-2
2012-05-20 0.1-1

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Package tidytable updated to version 0.6.5 with previous version 0.6.4 dated 2021-07-31

Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible, giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre], Abdessabour Moutik [ctb], Matt Carlson [ctb], Ivan Leung [ctb], Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

Diff between tidytable versions 0.6.4 dated 2021-07-31 and 0.6.5 dated 2021-09-03

 DESCRIPTION                         |    6 ++--
 MD5                                 |   29 +++++++++++----------
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Package SMLE updated to version 1.2.3 with previous version 1.1.1 dated 2021-05-09

Title: Joint Feature Screening via Sparse MLE
Description: Feature screening is a powerful tool in processing ultrahigh dimensional data. It attempts to screen out most irrelevant features in preparation for a more elaborate analysis. Xu and Chen (2014)<doi:10.1080/01621459.2013.879531> proposed an effective screening method SMLE, which naturally incorporates the joint effects among features in the screening process. This package provides an efficient implementation of SMLE-screening for high-dimensional linear, logistic, and Poisson models. The package also provides a function for conducting accurate post-screening feature selection based on an iterative hard-thresholding procedure and a user-specified selection criterion.
Author: Qianxiang Zang [aut, cre], Chen Xu [aut], Kelly Burkett [aut],
Maintainer: Qianxiang Zang <qzang023@uottawa.ca>

Diff between SMLE versions 1.1.1 dated 2021-05-09 and 1.2.3 dated 2021-09-03

 DESCRIPTION           |   15 +
 MD5                   |   61 +++---
 NAMESPACE             |  123 +++++++------
 R/Gen_Data.R          |   45 +++--
 R/SMLE.R              |  248 ++++++++++++++-------------
 R/coef.R              |   50 ++++-
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Package stratEst (with last version 1.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-08-18 1.1.0
2020-07-07 1.0.1
2020-06-23 1.0.0
2019-01-25 0.1.2
2018-12-17 0.1.1
2018-10-19 0.1.0

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Package Rpolyhedra (with last version 0.4.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-03-26 0.4.2
2019-02-20 0.4.1

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Package crosstalkr (with last version 0.7.0) was removed from CRAN

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2021-08-16 0.7.0

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Package tci (with last version 0.1.1) was removed from CRAN

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2021-08-15 0.1.1
2021-02-26 0.1.0

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Package NonpModelCheck (with last version 4.0) was removed from CRAN

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2021-08-09 4.0

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Package bcROCsurface (with last version 1.0-4) was removed from CRAN

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2020-02-14 1.0-4
2018-10-16 1.0-3
2017-07-03 1.0-2
2016-11-17 1.0-1

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Package statgenIBD (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-08-16 1.0.0

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Package drugCombo (with last version 1.2.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-29 1.2.1
2021-06-07 1.2.0

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Package CCAMLRGIS (with last version 3.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-08-12 3.1.0
2021-06-18 3.0.7
2020-09-10 3.0.6
2020-07-30 3.0.5
2020-06-07 3.0.4
2020-03-23 3.0.3
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2019-12-18 3.0.0

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Package ubiquity updated to version 2.0.0 with previous version 1.0.5 dated 2021-04-25

Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre] (<https://orcid.org/0000-0003-2052-4373>)
Maintainer: John Harrold <john.m.harrold@gmail.com>

Diff between ubiquity versions 1.0.5 dated 2021-04-25 and 2.0.0 dated 2021-09-03

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Package stringx updated to version 0.2.2 with previous version 0.1.3 dated 2021-08-05

Title: Drop-in Replacements for Base String Functions Powered by 'stringi'
Description: English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>)
Maintainer: Marek Gagolewski <marek@gagolewski.com>

Diff between stringx versions 0.1.3 dated 2021-08-05 and 0.2.2 dated 2021-09-03

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 15 files changed, 546 insertions(+), 87 deletions(-)

More information about stringx at CRAN
Permanent link

Package slurmR updated to version 0.5-1 with previous version 0.4-1 dated 2020-04-22

Title: A Lightweight Wrapper for 'Slurm'
Description: 'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (JOSS reviewer, <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (JOSS reviewer, <https://orcid.org/0000-0001-9754-0393>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>

Diff between slurmR versions 0.4-1 dated 2020-04-22 and 0.5-1 dated 2021-09-03

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More information about slurmR at CRAN
Permanent link

Package rrefine updated to version 1.1.1 with previous version 1.1.0 dated 2020-10-07

Title: r Client for OpenRefine API
Description: 'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Author: VP Nagraj [aut, cre]
Maintainer: VP Nagraj <nagraj@nagraj.net>

Diff between rrefine versions 1.1.0 dated 2020-10-07 and 1.1.1 dated 2021-09-03

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More information about rrefine at CRAN
Permanent link

Package rpanel updated to version 1.1-5 with previous version 1.1-4 dated 2018-05-07

Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple GUI controls for R functions. These are built on the 'tcltk' package. Uses could include changing a parameter on a graph by animating it with a slider or a "doublebutton", up to more sophisticated control panels. Some functions for specific graphical tasks, referred to as 'cartoons', are provided.
Author: Bowman, Bowman, Gibson and Crawford
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>

Diff between rpanel versions 1.1-4 dated 2018-05-07 and 1.1-5 dated 2021-09-03

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More information about rpanel at CRAN
Permanent link

Package pls updated to version 2.8-0 with previous version 2.7-3 dated 2020-08-07

Title: Partial Least Squares and Principal Component Regression
Description: Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Author: Kristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Ron Wehrens [aut], Paul Hiemstra [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between pls versions 2.7-3 dated 2020-08-07 and 2.8-0 dated 2021-09-03

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More information about pls at CRAN
Permanent link

Package paws updated to version 0.1.12 with previous version 0.1.11 dated 2021-03-13

Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws versions 0.1.11 dated 2021-03-13 and 0.1.12 dated 2021-09-03

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More information about paws at CRAN
Permanent link

Package nnTensor updated to version 1.1.5 with previous version 1.1.4 dated 2021-08-17

Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) <doi:10.1002/9780470747278> and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

Diff between nnTensor versions 1.1.4 dated 2021-08-17 and 1.1.5 dated 2021-09-03

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More information about nnTensor at CRAN
Permanent link

Package momentuHMM updated to version 1.5.4 with previous version 1.5.3 dated 2021-07-07

Title: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>

Diff between momentuHMM versions 1.5.3 dated 2021-07-07 and 1.5.4 dated 2021-09-03

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Package matsindf updated to version 0.3.8 with previous version 0.3.6 dated 2020-08-24

Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>

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Package link2GI updated to version 0.4-7 with previous version 0.4-5 dated 2020-12-07

Title: Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
Description: Functions to simplify the linking of open source GIS and remote sensing related command line interfaces.
Author: Chris Reudenbach [cre, aut], Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>

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Package jtools updated to version 2.1.4 with previous version 2.1.3 dated 2021-03-12

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written for the purpose of more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <jacob.long@sc.edu>

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Package interactionR updated to version 0.1.3 with previous version 0.1.2 dated 2021-05-09

Title: Full Reporting of Interaction Analyses
Description: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>]. It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]).
Author: Babatunde Alli
Maintainer: Babatunde Alli <babatunde.alli@mail.mcgill.ca>

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Package glinternet updated to version 1.0.12 with previous version 1.0.11 dated 2020-10-10

Title: Learning Interactions via Hierarchical Group-Lasso Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>

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