Sun, 20 Oct 2019

Package scrobbler updated to version 0.2.12 with previous version 0.1.0 dated 2019-01-08

Title: Download 'Scrobbles' from 'Last.fm'
Description: 'Last.fm'<https://www.last.fm> is a music platform focussed on building a detailed profile of a users listening habits. It does this by 'scrobbling' (recording) every track you listen to on other platforms ('spotify', 'youtube', 'soundcloud' etc) and transferring them to your 'Last.fm' database. This allows 'Last.fm' to act as a complete record of your entire listening history. 'scrobbler' provides helper functions to download and analyse your listening history in R.
Author: Conor Neilson
Maintainer: Conor Neilson <condwanaland@gmail.com>

Diff between scrobbler versions 0.1.0 dated 2019-01-08 and 0.2.12 dated 2019-10-20

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Package NMOF updated to version 2.0-1 with previous version 1.6-0 dated 2019-04-01

Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and the second edition of "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2019, ISBN:978-0128150658). The package provides implementations of optimisation heuristics (Differential Evolution, Genetic Algorithms, Particle Swarm Optimisation, Simulated Annealing and Threshold Accepting), and other optimisation tools, such as grid search and greedy search. There are also functions for the valuation of financial instruments, such as bonds and options, and functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>

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Package idiogramFISH updated to version 1.7.1 with previous version 1.6.3 dated 2019-10-13

Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>

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Package nadiv updated to version 2.16.2.0 with previous version 2.16.0.0 dated 2018-05-10

Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml>).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>

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Package comorbidity updated to version 0.5.2 with previous version 0.5.1 dated 2019-10-16

Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Hojjat Salmasian [ctb] (ICD-9-CM scores), Jonathan Williman [ctb] (<https://orcid.org/0000-0001-5080-4435>)
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

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Package RcppGSL updated to version 0.3.7 with previous version 0.3.6 dated 2018-06-10

Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses 'Rcpp' to connect to another third-party library. The 'autoconf' script, 'inline' plugin and example package can all be used as a stanza to write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package RNetCDF updated to version 2.1-1 with previous version 2.0-3 dated 2019-10-08

Title: Interface to 'NetCDF' Datasets
Description: An interface to the 'NetCDF' file formats designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Most capabilities of 'NetCDF' version 4 are supported. Optional conversions of time units are enabled by 'UDUNITS' version 2, also from Unidata.
Author: Pavel Michna [aut], Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>

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Permanent link

Package heavy updated to version 0.38.196 with previous version 0.38.19 dated 2018-02-13

Title: Robust Estimation Using Heavy-Tailed Distributions
Description: Functions to perform robust estimation considering heavy-tailed distributions. Currently, the package includes routines for linear regression, linear mixed-effect models, Grubbs' model, multivariate location and scatter estimation, multivariate regression, penalized splines, random variate generation and some support functions.
Author: Felipe Osorio
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>

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Package DTSg updated to version 0.2.1 with previous version 0.2.0 dated 2019-10-14

Title: A Class for Working with Time Series Based on 'data.table' and 'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing values, application of arbitrary aggregation as well as rolling window functions and automatic detection of periodicity. As it is mainly based on 'data.table', it is fast and - in combination with the 'R6' package - offers reference semantics. In addition to its native R6 interface, it provides an S3 interface inclusive an S3 wrapper method generator for those who prefer the latter.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>

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Package dragon updated to version 0.2.1 with previous version 0.2.0 dated 2019-09-13

Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Visualization and manipulation of the mineral-chemistry network across deep time on earth.
Author: Stephanie J. Spielman [aut, cre]
Maintainer: Stephanie J. Spielman <spielman@rowan.edu>

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Package bayestestR updated to version 0.4.0 with previous version 0.3.0 dated 2019-09-22

Title: Understand and Describe Bayesian Models and Posterior Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>), Paul-Christian Bürkner [rev], Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package bayesLife updated to version 4.1-0 with previous version 4.0-2 dated 2019-06-14

Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>.
Author: Hana Sevcikova, Adrian Raftery, Jennifer Chunn
Maintainer: Hana Sevcikova <hanas@uw.edu>

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 bayesLife-4.1-0/bayesLife/man/bayesLife-package.Rd                                        |    7 
 bayesLife-4.1-0/bayesLife/man/include.Rd                                                  |    4 
 bayesLife-4.1-0/bayesLife/man/run.e0.mcmc.Rd                                              |   10 
 bayesLife-4.1-0/bayesLife/tests/run_tests.R                                               |    3 
 bayesLife-4.1-0/bayesLife/tests/test_functions.R                                          |   51 
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More information about bayesLife at CRAN
Permanent link

Package paws.storage updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Storage APIs
Description: Interface to Amazon Web Services storage APIs, including 'Simple Storage Service' ('S3') and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.storage versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-20

 DESCRIPTION                   |   13 --
 MD5                           |   52 ++++----
 NAMESPACE                     |    2 
 R/backup_operations.R         |  131 +++++++++++++-------
 R/backup_service.R            |   34 ++++-
 R/dlm_operations.R            |   17 +-
 R/dlm_service.R               |   34 ++++-
 R/efs_operations.R            |   44 ++++--
 R/efs_service.R               |   34 ++++-
 R/fsx_operations.R            |   35 +++--
 R/fsx_service.R               |   34 ++++-
 R/glacier_operations.R        |  101 ++++++++++-----
 R/glacier_service.R           |   34 ++++-
 R/s3_operations.R             |  266 +++++++++++++++++++++++++++---------------
 R/s3_service.R                |   34 ++++-
 R/s3control_operations.R      |   26 ++--
 R/s3control_service.R         |   34 ++++-
 R/storagegateway_operations.R |  221 +++++++++++++++++++++++-----------
 R/storagegateway_service.R    |   34 ++++-
 man/backup.Rd                 |   23 +++
 man/dlm.Rd                    |   23 +++
 man/efs.Rd                    |   23 +++
 man/fsx.Rd                    |   23 +++
 man/glacier.Rd                |   23 +++
 man/s3.Rd                     |   23 +++
 man/s3control.Rd              |   23 +++
 man/storagegateway.Rd         |   23 +++
 27 files changed, 1000 insertions(+), 364 deletions(-)

More information about paws.storage at CRAN
Permanent link

Package paws.security.identity updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Security, Identity, & Compliance APIs
Description: Interface to Amazon Web Services security, identity, and compliance APIs, including the 'Identity & Access Management' ('IAM') service for managing access to services and resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.security.identity versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-20

 DESCRIPTION                                            |   16 
 MD5                                                    |  140 ++---
 NAMESPACE                                              |    2 
 R/acm_operations.R                                     |   41 +
 R/acm_service.R                                        |   34 +
 R/acmpca_operations.R                                  |   62 +-
 R/acmpca_service.R                                     |   34 +
 R/clouddirectory_operations.R                          |  200 +++++--
 R/clouddirectory_service.R                             |   34 +
 R/cloudhsm_operations.R                                |   62 +-
 R/cloudhsm_service.R                                   |   34 +
 R/cloudhsmv2_operations.R                              |   41 +
 R/cloudhsmv2_service.R                                 |   34 +
 R/cognitoidentity_operations.R                         |   65 +-
 R/cognitoidentity_service.R                            |   34 +
 R/cognitoidentityprovider_operations.R                 |  305 +++++++----
 R/cognitoidentityprovider_service.R                    |   34 +
 R/cognitosync_operations.R                             |   53 +-
 R/cognitosync_service.R                                |   34 +
 R/directoryservice_operations.R                        |  152 +++--
 R/directoryservice_service.R                           |   34 +
 R/fms_operations.R                                     |   44 +
 R/fms_service.R                                        |   34 +
 R/guardduty_operations.R                               |  137 +++--
 R/guardduty_service.R                                  |   34 +
 R/iam_operations.R                                     |  433 +++++++++++------
 R/iam_service.R                                        |   34 +
 R/inspector_operations.R                               |  113 ++--
 R/inspector_service.R                                  |   34 +
 R/kms_operations.R                                     |  125 +++-
 R/kms_service.R                                        |   34 +
 R/macie_operations.R                                   |   23 
 R/macie_service.R                                      |   34 +
 R/ram_operations.R                                     |   50 +
 R/ram_service.R                                        |   34 +
 R/secretsmanager_operations.R                          |   56 +-
 R/secretsmanager_service.R                             |   34 +
 R/securityhub_operations.R                             |  116 +++-
 R/securityhub_service.R                                |   34 +
 R/shield_operations.R                                  |   56 +-
 R/shield_service.R                                     |   34 +
 R/sts_operations.R                                     |   23 
 R/sts_service.R                                        |   34 +
 R/waf_operations.R                                     |  230 ++++++---
 R/waf_service.R                                        |   34 +
 R/wafregional_operations.R                             |  242 ++++++---
 R/wafregional_service.R                                |   34 +
 man/acm.Rd                                             |   23 
 man/acmpca.Rd                                          |   23 
 man/clouddirectory.Rd                                  |   23 
 man/cloudhsm.Rd                                        |   23 
 man/cloudhsmv2.Rd                                      |   23 
 man/cognitoidentity.Rd                                 |   23 
 man/cognitoidentityprovider.Rd                         |   23 
 man/cognitoidentityprovider_create_user_pool_client.Rd |    2 
 man/cognitosync.Rd                                     |   23 
 man/directoryservice.Rd                                |   23 
 man/fms.Rd                                             |   23 
 man/guardduty.Rd                                       |   23 
 man/iam.Rd                                             |   23 
 man/iam_get_policy_version.Rd                          |   10 
 man/inspector.Rd                                       |   23 
 man/kms.Rd                                             |   23 
 man/macie.Rd                                           |   23 
 man/ram.Rd                                             |   23 
 man/secretsmanager.Rd                                  |   23 
 man/securityhub.Rd                                     |   23 
 man/shield.Rd                                          |   23 
 man/sts.Rd                                             |   23 
 man/waf.Rd                                             |   23 
 man/wafregional.Rd                                     |   23 
 71 files changed, 2950 insertions(+), 1103 deletions(-)

More information about paws.security.identity at CRAN
Permanent link

Package paws.networking updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Networking & Content Delivery APIs
Description: Interface to Amazon Web Services networking and content delivery APIs, including 'Route 53' Domain Name System service, 'CloudFront' content delivery, load balancing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.networking versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-20

 DESCRIPTION                            |   14 -
 MD5                                    |   82 +++----
 NAMESPACE                              |    2 
 R/apigateway_operations.R              |  362 +++++++++++++++++++++------------
 R/apigateway_service.R                 |   34 ++-
 R/apigatewaymanagementapi_operations.R |    5 
 R/apigatewaymanagementapi_service.R    |   34 ++-
 R/apigatewayv2_operations.R            |  179 ++++++++++------
 R/apigatewayv2_service.R               |   34 ++-
 R/appmesh_operations.R                 |   86 +++++--
 R/appmesh_service.R                    |   34 ++-
 R/cloudfront_operations.R              |  137 ++++++++----
 R/cloudfront_service.R                 |   34 ++-
 R/directconnect_operations.R           |  161 +++++++++-----
 R/directconnect_service.R              |   34 ++-
 R/elb_operations.R                     |   89 +++++---
 R/elb_service.R                        |   34 ++-
 R/elbv2_operations.R                   |  104 ++++++---
 R/elbv2_service.R                      |   34 ++-
 R/globalaccelerator_operations.R       |   53 +++-
 R/globalaccelerator_service.R          |   34 ++-
 R/route53_operations.R                 |  170 ++++++++++-----
 R/route53_service.R                    |   34 ++-
 R/route53domains_operations.R          |   74 ++++--
 R/route53domains_service.R             |   34 ++-
 R/route53resolver_operations.R         |   68 ++++--
 R/route53resolver_service.R            |   34 ++-
 R/servicediscovery_operations.R        |   62 +++--
 R/servicediscovery_service.R           |   34 ++-
 man/apigateway.Rd                      |   23 ++
 man/apigatewaymanagementapi.Rd         |   23 ++
 man/apigatewayv2.Rd                    |   23 ++
 man/appmesh.Rd                         |   23 ++
 man/cloudfront.Rd                      |   23 ++
 man/directconnect.Rd                   |   23 ++
 man/elb.Rd                             |   23 ++
 man/elbv2.Rd                           |   23 ++
 man/globalaccelerator.Rd               |   23 ++
 man/route53.Rd                         |   23 ++
 man/route53domains.Rd                  |   23 ++
 man/route53resolver.Rd                 |   23 ++
 man/servicediscovery.Rd                |   23 ++
 42 files changed, 1742 insertions(+), 647 deletions(-)

More information about paws.networking at CRAN
Permanent link

Package paws.management updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Management & Governance APIs
Description: Interface to Amazon Web Services management and governance APIs, including 'CloudWatch' application and infrastructure monitoring, 'Auto Scaling' for automatically scaling resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.management versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-20

 DESCRIPTION                             |   12 -
 MD5                                     |  136 ++++++------
 NAMESPACE                               |    2 
 R/applicationautoscaling_operations.R   |   32 +-
 R/applicationautoscaling_service.R      |   34 ++-
 R/applicationinsights_operations.R      |   50 ++--
 R/applicationinsights_service.R         |   34 ++-
 R/autoscaling_operations.R              |  164 +++++++++-----
 R/autoscaling_service.R                 |   34 ++-
 R/autoscalingplans_operations.R         |   20 +
 R/autoscalingplans_service.R            |   34 ++-
 R/cloudformation_operations.R           |  137 ++++++++----
 R/cloudformation_service.R              |   34 ++-
 R/cloudtrail_operations.R               |   44 ++-
 R/cloudtrail_service.R                  |   34 ++-
 R/cloudwatch_operations.R               |   71 ++++--
 R/cloudwatch_service.R                  |   34 ++-
 R/cloudwatchevents_operations.R         |   95 +++++---
 R/cloudwatchevents_service.R            |   34 ++-
 R/cloudwatchlogs_operations.R           |  119 ++++++----
 R/cloudwatchlogs_service.R              |   34 ++-
 R/configservice_operations.R            |  185 ++++++++++------
 R/configservice_service.R               |   34 ++-
 R/health_operations.R                   |   20 +
 R/health_service.R                      |   34 ++-
 R/licensemanager_operations.R           |   47 ++--
 R/licensemanager_service.R              |   34 ++-
 R/opsworks_operations.R                 |  224 +++++++++++++------
 R/opsworks_service.R                    |   34 ++-
 R/opsworkscm_operations.R               |   50 ++--
 R/opsworkscm_service.R                  |   34 ++-
 R/organizations_operations.R            |  140 ++++++++----
 R/organizations_service.R               |   34 ++-
 R/pi_operations.R                       |    8 
 R/pi_service.R                          |   34 ++-
 R/resourcegroups_operations.R           |   38 ++-
 R/resourcegroups_service.R              |   34 ++-
 R/resourcegroupstaggingapi_operations.R |   17 -
 R/resourcegroupstaggingapi_service.R    |   34 ++-
 R/servicecatalog_operations.R           |  251 ++++++++++++++--------
 R/servicecatalog_service.R              |   34 ++-
 R/servicequotas_operations.R            |   50 ++--
 R/servicequotas_service.R               |   34 ++-
 R/ssm_operations.R                      |  362 +++++++++++++++++++++-----------
 R/ssm_service.R                         |   34 ++-
 R/support_operations.R                  |   44 ++-
 R/support_service.R                     |   34 ++-
 man/applicationautoscaling.Rd           |   23 +-
 man/applicationinsights.Rd              |   23 +-
 man/autoscaling.Rd                      |   23 +-
 man/autoscalingplans.Rd                 |   23 +-
 man/cloudformation.Rd                   |   23 +-
 man/cloudtrail.Rd                       |   23 +-
 man/cloudwatch.Rd                       |   23 +-
 man/cloudwatchevents.Rd                 |   23 +-
 man/cloudwatchlogs.Rd                   |   23 +-
 man/configservice.Rd                    |   23 +-
 man/health.Rd                           |   23 +-
 man/licensemanager.Rd                   |   23 +-
 man/opsworks.Rd                         |   23 +-
 man/opsworkscm.Rd                       |   23 +-
 man/organizations.Rd                    |   23 +-
 man/pi.Rd                               |   23 +-
 man/resourcegroups.Rd                   |   23 +-
 man/resourcegroupstaggingapi.Rd         |   23 +-
 man/servicecatalog.Rd                   |   23 +-
 man/servicequotas.Rd                    |   23 +-
 man/ssm.Rd                              |   23 +-
 man/support.Rd                          |   23 +-
 69 files changed, 2636 insertions(+), 936 deletions(-)

More information about paws.management at CRAN
Permanent link

Sat, 19 Oct 2019

Package telegram.bot updated to version 2.4.0 with previous version 2.3.1 dated 2019-04-28

Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>

Diff between telegram.bot versions 2.3.1 dated 2019-04-28 and 2.4.0 dated 2019-10-19

 DESCRIPTION                                     |    6 
 MD5                                             |   52 +++----
 NEWS.md                                         |    6 
 R/base.R                                        |    8 -
 R/basefilter.R                                  |    4 
 R/bot.R                                         |  178 +++++++++++++++++++++---
 R/commandhandler.R                              |    6 
 R/dispatcher.R                                  |    4 
 R/errorhandler.R                                |    4 
 R/filters.R                                     |    2 
 R/handler.R                                     |    8 -
 R/inlinequeryresult.R                           |    2 
 R/messagehandler.R                              |    2 
 R/replymarkup.R                                 |   18 +-
 R/telegram.bot-package.R                        |    6 
 R/updater.R                                     |   51 +++---
 R/utils.R                                       |    4 
 build/vignette.rds                              |binary
 inst/doc/telegrambot-advanced-filters.html      |   10 -
 inst/doc/telegrambot-basic-functionalities.html |   10 -
 inst/doc/telegrambot-building-a-bot.html        |   10 -
 inst/doc/telegrambot-introduction.html          |   10 -
 inst/doc/telegrambot-set-a-proxy.html           |   10 -
 inst/doc/telegrambot-the-add-operator.html      |   10 -
 man/Bot.Rd                                      |    2 
 man/editMessageCaption.Rd                       |only
 man/editMessageText.Rd                          |only
 man/getUpdates.Rd                               |    3 
 28 files changed, 302 insertions(+), 124 deletions(-)

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Package paws.machine.learning updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Machine Learning APIs
Description: Interface to Amazon Web Services machine learning APIs, including 'SageMaker' managed machine learning service, natural language processing, speech recognition, translation, and more <https://aws.amazon.com/machine-learning/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.machine.learning versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                            |   12 -
 MD5                                    |   94 ++++++-------
 NAMESPACE                              |    2 
 R/comprehend_operations.R              |  137 +++++++++++++------
 R/comprehend_service.R                 |   34 ++++
 R/comprehendmedical_operations.R       |    8 -
 R/comprehendmedical_service.R          |   34 ++++
 R/lexmodelbuildingservice_operations.R |  110 ++++++++++-----
 R/lexmodelbuildingservice_service.R    |   34 ++++
 R/lexruntimeservice_operations.R       |    8 -
 R/lexruntimeservice_service.R          |   34 ++++
 R/machinelearning_operations.R         |   86 ++++++++----
 R/machinelearning_service.R            |   34 ++++
 R/personalize_operations.R             |  110 ++++++++++-----
 R/personalize_service.R                |   34 ++++
 R/personalizeevents_operations.R       |    5 
 R/personalizeevents_service.R          |   34 ++++
 R/personalizeruntime_operations.R      |    8 -
 R/personalizeruntime_service.R         |   34 ++++
 R/polly_operations.R                   |   29 ++--
 R/polly_service.R                      |   34 ++++
 R/rekognition_operations.R             |  104 ++++++++++-----
 R/rekognition_service.R                |   34 ++++
 R/sagemaker_operations.R               |  227 +++++++++++++++++++++------------
 R/sagemaker_service.R                  |   34 ++++
 R/sagemakerruntime_operations.R        |    5 
 R/sagemakerruntime_service.R           |   34 ++++
 R/textract_operations.R                |   20 +-
 R/textract_service.R                   |   34 ++++
 R/transcribeservice_operations.R       |   29 ++--
 R/transcribeservice_service.R          |   34 ++++
 R/translate_operations.R               |   17 +-
 R/translate_service.R                  |   34 ++++
 man/comprehend.Rd                      |   23 +++
 man/comprehendmedical.Rd               |   23 +++
 man/lexmodelbuildingservice.Rd         |   23 +++
 man/lexruntimeservice.Rd               |   23 +++
 man/machinelearning.Rd                 |   23 +++
 man/personalize.Rd                     |   23 +++
 man/personalizeevents.Rd               |   23 +++
 man/personalizeruntime.Rd              |   23 +++
 man/polly.Rd                           |   23 +++
 man/rekognition.Rd                     |   23 +++
 man/sagemaker.Rd                       |   23 +++
 man/sagemakerruntime.Rd                |   23 +++
 man/textract.Rd                        |   23 +++
 man/transcribeservice.Rd               |   23 +++
 man/translate.Rd                       |   23 +++
 48 files changed, 1417 insertions(+), 449 deletions(-)

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Permanent link

Package paws.database updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Database APIs
Description: Interface to Amazon Web Services database APIs, including 'Relational Database Service' ('RDS'), 'DynamoDB' 'NoSQL' database, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.database versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                    |   14 -
 MD5                            |   64 +++----
 NAMESPACE                      |    2 
 R/dax_operations.R             |   65 +++++--
 R/dax_service.R                |   34 +++-
 R/docdb_operations.R           |  125 ++++++++++-----
 R/docdb_service.R              |   34 +++-
 R/dynamodb_operations.R        |  110 ++++++++-----
 R/dynamodb_service.R           |   34 +++-
 R/dynamodbstreams_operations.R |   14 +
 R/dynamodbstreams_service.R    |   34 +++-
 R/elasticache_operations.R     |  140 +++++++++++------
 R/elasticache_service.R        |   34 +++-
 R/neptune_operations.R         |  173 ++++++++++++++-------
 R/neptune_service.R            |   34 +++-
 R/rds_operations.R             |  335 +++++++++++++++++++++++++++--------------
 R/rds_service.R                |   34 +++-
 R/rdsdataservice_operations.R  |   20 +-
 R/rdsdataservice_service.R     |   34 +++-
 R/redshift_operations.R        |  245 +++++++++++++++++++----------
 R/redshift_service.R           |   34 +++-
 R/simpledb_operations.R        |   32 ++-
 R/simpledb_service.R           |   34 +++-
 man/dax.Rd                     |   23 ++
 man/docdb.Rd                   |   23 ++
 man/dynamodb.Rd                |   23 ++
 man/dynamodbstreams.Rd         |   23 ++
 man/elasticache.Rd             |   23 ++
 man/neptune.Rd                 |   23 ++
 man/rds.Rd                     |   23 ++
 man/rdsdataservice.Rd          |   23 ++
 man/redshift.Rd                |   23 ++
 man/simpledb.Rd                |   23 ++
 33 files changed, 1387 insertions(+), 522 deletions(-)

More information about paws.database at CRAN
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Package paws.customer.engagement updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Customer Engagement APIs
Description: Interface to Amazon Web Services customer engagement APIs, including 'Simple Email Service', 'Connect' contact center service, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.customer.engagement versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                     |   14 +-
 MD5                             |   34 ++---
 NAMESPACE                       |    2 
 R/connect_operations.R          |   65 +++++++----
 R/connect_service.R             |   34 ++++-
 R/pinpoint_operations.R         |  233 ++++++++++++++++++++++++++--------------
 R/pinpoint_service.R            |   34 ++++-
 R/pinpointemail_operations.R    |  128 ++++++++++++++-------
 R/pinpointemail_service.R       |   34 ++++-
 R/pinpointsmsvoice_operations.R |   26 ++--
 R/pinpointsmsvoice_service.R    |   34 ++++-
 R/ses_operations.R              |  215 ++++++++++++++++++++++++------------
 R/ses_service.R                 |   34 ++++-
 man/connect.Rd                  |   23 +++
 man/pinpoint.Rd                 |   23 +++
 man/pinpointemail.Rd            |   23 +++
 man/pinpointsmsvoice.Rd         |   23 +++
 man/ses.Rd                      |   23 +++
 18 files changed, 724 insertions(+), 278 deletions(-)

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Package paws.cost.management updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Cost Management APIs
Description: Interface to Amazon Web Services cost management APIs, including cost and usage reports, budgets, pricing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.cost.management versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                                  |   12 +++----
 MD5                                          |   46 +++++++++++++--------------
 NAMESPACE                                    |    2 +
 R/budgets_operations.R                       |   44 +++++++++++++++++--------
 R/budgets_service.R                          |   34 +++++++++++++++++--
 R/costandusagereportservice_operations.R     |   11 ++++--
 R/costandusagereportservice_service.R        |   34 +++++++++++++++++--
 R/costexplorer_operations.R                  |   26 +++++++++------
 R/costexplorer_service.R                     |   34 +++++++++++++++++--
 R/marketplacecommerceanalytics_operations.R  |    8 ++--
 R/marketplacecommerceanalytics_service.R     |   34 +++++++++++++++++--
 R/marketplaceentitlementservice_operations.R |    5 +-
 R/marketplaceentitlementservice_service.R    |   34 +++++++++++++++++--
 R/marketplacemetering_operations.R           |   14 +++++---
 R/marketplacemetering_service.R              |   34 +++++++++++++++++--
 R/pricing_operations.R                       |   11 ++++--
 R/pricing_service.R                          |   34 +++++++++++++++++--
 man/budgets.Rd                               |   23 ++++++++++++-
 man/costandusagereportservice.Rd             |   23 ++++++++++++-
 man/costexplorer.Rd                          |   23 ++++++++++++-
 man/marketplacecommerceanalytics.Rd          |   23 ++++++++++++-
 man/marketplaceentitlementservice.Rd         |   23 ++++++++++++-
 man/marketplacemetering.Rd                   |   23 ++++++++++++-
 man/pricing.Rd                               |   23 ++++++++++++-
 24 files changed, 465 insertions(+), 113 deletions(-)

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Package paws.compute updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Compute APIs
Description: Interface to Amazon Web Services compute APIs, including 'Elastic Compute Cloud' ('EC2'), 'Lambda' functions-as-a-service, containers, batch processing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.compute versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                                    |   15 
 MD5                                            |   66 -
 NAMESPACE                                      |    2 
 R/batch_operations.R                           |   50 -
 R/batch_service.R                              |   34 
 R/ec2_operations.R                             | 1063 ++++++++++++++++---------
 R/ec2_service.R                                |   34 
 R/ec2instanceconnect_operations.R              |    5 
 R/ec2instanceconnect_service.R                 |   34 
 R/ecr_operations.R                             |   77 +
 R/ecr_service.R                                |   34 
 R/ecs_operations.R                             |  134 ++-
 R/ecs_service.R                                |   34 
 R/eks_operations.R                             |   26 
 R/eks_service.R                                |   34 
 R/elasticbeanstalk_operations.R                |  134 ++-
 R/elasticbeanstalk_service.R                   |   34 
 R/lambda_operations.R                          |  119 +-
 R/lambda_service.R                             |   34 
 R/lightsail_operations.R                       |  305 ++++---
 R/lightsail_service.R                          |   34 
 R/serverlessapplicationrepository_operations.R |   41 
 R/serverlessapplicationrepository_service.R    |   34 
 man/batch.Rd                                   |   23 
 man/ec2.Rd                                     |   23 
 man/ec2_create_traffic_mirror_session.Rd       |    5 
 man/ec2instanceconnect.Rd                      |   23 
 man/ecr.Rd                                     |   23 
 man/ecs.Rd                                     |   23 
 man/eks.Rd                                     |   23 
 man/elasticbeanstalk.Rd                        |   23 
 man/lambda.Rd                                  |   23 
 man/lightsail.Rd                               |   23 
 man/serverlessapplicationrepository.Rd         |   23 
 34 files changed, 1852 insertions(+), 760 deletions(-)

More information about paws.compute at CRAN
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Package paws.application.integration updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Application Integration APIs
Description: Interface to Amazon Web Services application integration APIs, including 'Simple Queue Service' ('SQS') message queue, 'Simple Notification Service' ('SNS') publish/subscribe messaging, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.application.integration versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                |   16 +++---
 MD5                        |   40 +++++++--------
 NAMESPACE                  |    2 
 R/eventbridge_operations.R |   95 +++++++++++++++++++++++++------------
 R/eventbridge_service.R    |   34 +++++++++++--
 R/mq_operations.R          |   68 +++++++++++++++++----------
 R/mq_service.R             |   34 +++++++++++--
 R/sfn_operations.R         |   68 +++++++++++++++++----------
 R/sfn_service.R            |   34 +++++++++++--
 R/sns_operations.R         |  101 ++++++++++++++++++++++++++--------------
 R/sns_service.R            |   34 +++++++++++--
 R/sqs_operations.R         |   62 ++++++++++++++++--------
 R/sqs_service.R            |   34 +++++++++++--
 R/swf_operations.R         |  113 +++++++++++++++++++++++++++++----------------
 R/swf_service.R            |   34 +++++++++++--
 man/eventbridge.Rd         |   23 ++++++++-
 man/mq.Rd                  |   23 ++++++++-
 man/sfn.Rd                 |   23 ++++++++-
 man/sns.Rd                 |   23 ++++++++-
 man/sqs.Rd                 |   23 ++++++++-
 man/swf.Rd                 |   23 ++++++++-
 21 files changed, 672 insertions(+), 235 deletions(-)

More information about paws.application.integration at CRAN
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Package paws.analytics updated to version 0.1.5 with previous version 0.1.4 dated 2019-08-21

Title: Amazon Web Services Analytics APIs
Description: Interface to Amazon Web Services analytics APIs, including 'Elastic MapReduce' 'Hadoop' and 'Spark' big data service, 'Elasticsearch' search engine, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.analytics versions 0.1.4 dated 2019-08-21 and 0.1.5 dated 2019-10-19

 DESCRIPTION                         |   12 -
 MD5                                 |   88 ++++-----
 NAMESPACE                           |    2 
 R/athena_operations.R               |   59 ++++--
 R/athena_service.R                  |   34 +++
 R/cloudsearch_operations.R          |   74 +++++---
 R/cloudsearch_service.R             |   34 +++
 R/cloudsearchdomain_operations.R    |   11 -
 R/cloudsearchdomain_service.R       |   34 +++
 R/datapipeline_operations.R         |   59 ++++--
 R/datapipeline_service.R            |   34 +++
 R/elasticsearchservice_operations.R |   71 +++++--
 R/elasticsearchservice_service.R    |   34 +++
 R/emr_operations.R                  |   83 ++++++---
 R/emr_service.R                     |   34 +++
 R/firehose_operations.R             |   38 ++--
 R/firehose_service.R                |   34 +++
 R/glue_operations.R                 |  329 +++++++++++++++++++++++-------------
 R/glue_service.R                    |   34 +++
 R/kafka_operations.R                |   56 ++++--
 R/kafka_service.R                   |   34 +++
 R/kinesis_operations.R              |   83 ++++++---
 R/kinesis_service.R                 |   34 +++
 R/kinesisanalytics_operations.R     |   62 ++++--
 R/kinesisanalytics_service.R        |   34 +++
 R/kinesisanalyticsv2_operations.R   |   74 +++++---
 R/kinesisanalyticsv2_service.R      |   34 +++
 R/mturk_operations.R                |  119 ++++++++-----
 R/mturk_service.R                   |   34 +++
 R/quicksight_operations.R           |   50 +++--
 R/quicksight_service.R              |   34 +++
 man/athena.Rd                       |   23 ++
 man/cloudsearch.Rd                  |   23 ++
 man/cloudsearchdomain.Rd            |   23 ++
 man/datapipeline.Rd                 |   23 ++
 man/elasticsearchservice.Rd         |   23 ++
 man/emr.Rd                          |   23 ++
 man/firehose.Rd                     |   23 ++
 man/glue.Rd                         |   23 ++
 man/kafka.Rd                        |   23 ++
 man/kinesis.Rd                      |   23 ++
 man/kinesisanalytics.Rd             |   23 ++
 man/kinesisanalyticsv2.Rd           |   23 ++
 man/mturk.Rd                        |   23 ++
 man/quicksight.Rd                   |   23 ++
 45 files changed, 1540 insertions(+), 528 deletions(-)

More information about paws.analytics at CRAN
Permanent link

Package utile.tools updated to version 0.2.2 with previous version 0.2.1 dated 2019-09-19

Title: Summarize Data for Publication
Description: A variety of tools for preparing and summarizing data for publication purposes. Function verbs include 'tabulate' for creating usable tabulated data from models, 'paste' for generating human-readable statistics from a variety of summarizable data types, 'calc' for reliably calculating differences between data points, and 'test' for conducting simple statistical tests which return human-readable results.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>

Diff between utile.tools versions 0.2.1 dated 2019-09-19 and 0.2.2 dated 2019-10-19

 DESCRIPTION                 |    8 ++++--
 MD5                         |   23 +++++++++++--------
 NAMESPACE                   |    2 +
 NEWS.md                     |   10 ++++++--
 R/calc.R                    |   52 ++++++++++++++++++++++++++++++++++----------
 R/chunk.R                   |only
 R/paste.R                   |   16 +++++++------
 R/tabulate.R                |   14 +++++------
 R/utils.R                   |   24 +++++++++++++-------
 README.md                   |    4 +++
 man/calc_chunks.Rd          |only
 man/chunk_data_.Rd          |only
 man/paste_freq.Rd           |    8 +++---
 man/tabulate_model.coxph.Rd |   14 +++++------
 14 files changed, 116 insertions(+), 59 deletions(-)

More information about utile.tools at CRAN
Permanent link

Package utile.tables updated to version 0.1.7 with previous version 0.1.6 dated 2019-09-19

Title: Build Tables for Publication
Description: A collection of functions to make building customized ready-to-export tables for publication purposes easier or expedite summarization of a large dataset for review. Includes methods for automatically building a table from data or building the table row-by-row. Key functions include build_row() & build_table() for summarizing columns of data overall or by stratum with appropriate testing and build_event_row() & build_event_table() for creating tables that summarize time-to-event model (Cox Parametric Hazard) parameters, supporting both univariate and multivariate methods.
Author: Eric Finnesgard [aut, cre], Jennifer Grauberger [aut]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>

Diff between utile.tables versions 0.1.6 dated 2019-09-19 and 0.1.7 dated 2019-10-19

 utile.tables-0.1.6/utile.tables/tests               |only
 utile.tables-0.1.7/utile.tables/DESCRIPTION         |    9 +++++----
 utile.tables-0.1.7/utile.tables/MD5                 |   10 ++++------
 utile.tables-0.1.7/utile.tables/NEWS.md             |    4 ++++
 utile.tables-0.1.7/utile.tables/R/build_event_row.R |   11 +++++++++--
 utile.tables-0.1.7/utile.tables/R/utils.R           |   14 ++++++++++----
 6 files changed, 32 insertions(+), 16 deletions(-)

More information about utile.tables at CRAN
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Package RWekajars updated to version 3.9.3-2 with previous version 3.9.3-1 dated 2018-09-10

Title: R/Weka Interface Jars
Description: External jars required for package 'RWeka'.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between RWekajars versions 3.9.3-1 dated 2018-09-10 and 3.9.3-2 dated 2019-10-19

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
 configure   |    3 ++-
 3 files changed, 7 insertions(+), 6 deletions(-)

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Package RWeka updated to version 0.4-41 with previous version 0.4-40 dated 2019-02-26

Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package 'RWeka' contains the interface code, the Weka jar is in a separate package 'RWekajars'. For more information on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Christian Buchta [ctb], Torsten Hothorn [ctb], Alexandros Karatzoglou [ctb], David Meyer [ctb], Achim Zeileis [ctb] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package RKEAjars updated to version 5.0-4 with previous version 5.0-3 dated 2017-11-12

Title: R/KEA Interface Jars
Description: External jars required for package RKEA.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Eibe Frank [ctb, cph] (KEA Java library), Olena Medelyan [ctb, cph] (KEA Java library), The Apache Software Foundation [ctb, cph] (Apache Commons Logging and Apache Jena Java libraries), International Business Machines Corporation and others [ctb, cph] (International Components for Unicode for Java (ICU4J)), Martin Porter [ctb, cph] (Snowball base), Richard Boulton [ctb, cph] (Snowball Java library), University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package matrixTests updated to version 0.1.7 with previous version 0.1.6 dated 2019-09-19

Title: Fast Statistical Hypothesis Tests on Rows and Columns of Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices. The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use, 3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>

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Package bimets updated to version 1.4.2 with previous version 1.4.1 dated 2019-09-03

Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization.
Author: Andrea Luciani [aut, cre], Roberto Stok [aut], Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>

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Package zscorer updated to version 0.3.1 with previous version 0.3.0 dated 2019-09-28

Title: Child Anthropometry z-Score Calculator
Description: A tool for calculating z-scores and centiles for weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age, head circumference-for-age, age circumference-for-age, subscapular skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth Standards.
Author: Mark Myatt [aut, cph] (<https://orcid.org/0000-0003-1119-1474>), Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>

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Package tm.plugin.lexisnexis updated to version 1.4.1 with previous version 1.4.0 dated 2018-06-05

Title: Import Articles from 'LexisNexis' Using the 'tm' Text Mining Framework
Description: Provides a 'tm' Source to create corpora from articles exported from the 'LexisNexis' content provider as HTML files. It is able to read both text content and meta-data information (including source, date, title, author and pages). Note that the file format is highly unstable: there is no warranty that this package will work for your corpus, and you may have to adjust the code to adapt it to your particular format.
Author: Milan Bouchet-Valat [aut, cre], Tom Nicholls [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

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Package tm.plugin.factiva updated to version 1.8 with previous version 1.7 dated 2017-11-20

Title: Import Articles from 'Factiva' Using the 'tm' Text Mining Framework
Description: Provides a 'tm' Source to create corpora from articles exported from the Dow Jones 'Factiva' content provider as XML or HTML files. It is able to read both text content and meta-data information (including source, date, title, author, subject, geographical coverage, company, industry, and various provider-specific fields).
Author: Milan Bouchet-Valat [aut, cre], Grigorij Ljubownikow [ctb], Juliane Krueger [ctb], Tom Nicholls [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

Diff between tm.plugin.factiva versions 1.7 dated 2017-11-20 and 1.8 dated 2019-10-19

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Package RcppThread updated to version 0.5.4 with previous version 0.5.3 dated 2018-11-23

Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>

Diff between RcppThread versions 0.5.3 dated 2018-11-23 and 0.5.4 dated 2019-10-19

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Package plinkQC updated to version 0.3.0 with previous version 0.2.3 dated 2019-09-25

Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>

Diff between plinkQC versions 0.2.3 dated 2019-09-25 and 0.3.0 dated 2019-10-19

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Package paws.common updated to version 0.2.4 with previous version 0.2.3 dated 2019-10-15

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.common versions 0.2.3 dated 2019-10-15 and 0.2.4 dated 2019-10-19

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Package BMA updated to version 3.18.10 with previous version 3.18.9 dated 2018-09-14

Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression).
Author: Adrian Raftery <raftery@uw.edu>, Jennifer Hoeting, Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between BMA versions 3.18.9 dated 2018-09-14 and 3.18.10 dated 2019-10-19

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Package openblender updated to version 0.2.2 with previous version 0.2.0 dated 2019-09-03

Title: Request <https://openblender.io> API Services
Description: Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.
Author: Open Blender Inc. [cph], Daniel V. Pinacho [aut, cre]
Maintainer: Daniel V. Pinacho <danielvpinacho@gmail.com>

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Package CorBin updated to version 0.3.3 with previous version 0.3.1 dated 2019-08-08

Title: Generate High-Dimensional Binary Data with Correlation Structures
Description: We design algorithms with linear time complexity with respect to the dimension for three commonly studied correlation structures, including exchangeable, decaying-product and K-dependent correlation structures, and extend the algorithms to generate binary data of general non-negative correlation matrices with quadratic time complexity. Jiang, W., Song, S., Hou, L. and Zhao, H. "A set of efficient methods to generate high-dimensional binary data with correlation structures." Submitted.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>

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Fri, 18 Oct 2019

Package spatialrisk updated to version 0.6.3 with previous version 0.6.2 dated 2019-07-29

Title: Calculating Concentration Risk under Solvency II
Description: Methods for determining spatial risk, in particular calculating the maximum value of insured fire risk policies of all buildings that are partly or fully located within circle of a radius of 200m.
Author: Martin Haringa
Maintainer: Martin Haringa <mtharinga@gmail.com>

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Package dnet updated to version 1.1.5 with previous version 1.1.4 dated 2018-08-10

Title: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology
Description: The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

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Package data.table updated to version 1.12.6 with previous version 1.12.4 dated 2019-10-03

Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre], Arun Srinivasan [aut], Jan Gorecki [ctb], Michael Chirico [ctb], Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>

Diff between data.table versions 1.12.4 dated 2019-10-03 and 1.12.6 dated 2019-10-18

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More information about data.table at CRAN
Permanent link

Package bayesTFR updated to version 6.4-0 with previous version 6.3-1 dated 2019-06-11

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between bayesTFR versions 6.3-1 dated 2019-06-11 and 6.4-0 dated 2019-10-18

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Permanent link

Package threeBrain updated to version 0.1.4 with previous version 0.1.3 dated 2019-09-10

Title: 3D Brain Visualization
Description: In neuroscience, 'AFNI/SUMA' is a great tool to visualize 3D brain. However, it takes efforts to interact and share the viewer to others. In addition, 'AFNI/SUMA' doesn't support Windows platform. In the 'EEG/iEEG' field, it's hard to have multiple cortical electrodes mapped to a template brain for group analysis. Therefore this package is written aimed at providing a fast, stable, interactive and easy to share tool based on 'Three.js', a 'WebGL' engine to render 3D objects in the web browser such that we can display brain surfaces on webpage interactively. This package translates R objects to JavaScript objects via 'JSON' format, and provides 'R-Shiny' interface to manipulate geometries interactively. The visualizations can also serve as standalone widgets that can be easily shared across different platforms. Along with 'rave', another package developed by Beauchamp's lab at Baylor College Medicine, this package provides solutions to easily map surface electrodes from multiple subjects to one template 141 brain.
Author: Zhengjia Wang [aut, cre, cph], John Magnotti [aut], Brian Metzger [aut], Elizabeth Nesbitt [res], Michael Beauchamp [aut, dtc, fnd]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>

Diff between threeBrain versions 0.1.3 dated 2019-09-10 and 0.1.4 dated 2019-10-18

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Permanent link

Package geonapi updated to version 0.2-2 with previous version 0.2-1 dated 2019-05-26

Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and exposte it to OGC CSW.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Diff between geonapi versions 0.2-1 dated 2019-05-26 and 0.2-2 dated 2019-10-18

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Permanent link

Package dosearch updated to version 1.0.3 with previous version 1.0.2 dated 2019-02-28

Title: Causal Effect Identification from Multiple Incomplete Data Sources
Description: Identification of causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations using a search-based algorithm. Allows for the presence of mechanisms related to selection bias (Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>), transportability (Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>), missing data (Mohan, K. and Pearl, J. and Tian., J. (2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these. Also supports identification in the presence of context-specific independence (CSI) relations through labeled directed acyclic graphs (LDAG). For details on CSIs see Corander et al. (2019) <doi:10.1016/j.apal.2019.04.004>. For further information on the search-based approach see Tikka et al. (2019) <arXiv:1902.01073>.
Author: Santtu Tikka [aut, cre] (<https://orcid.org/0000-0003-4039-4342>), Antti Hyttinen [ctb] (<https://orcid.org/0000-0002-6649-3229>), Juha Karvanen [ctb] (<https://orcid.org/0000-0001-5530-769X>)
Maintainer: Santtu Tikka <santtuth@gmail.com>

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Package colocalized updated to version 0.2.0 with previous version 0.1.0 dated 2019-09-19

Title: Clusters of Colocalized Sequences
Description: Also abbreviates to "CCSeq". Finds clusters of colocalized sequences in .bed annotation files up to a specified cut-off distance. Two sequences are colocalized if they are within the cut-off distance of each other, and clusters are sets of sequences where each sequence is colocalized to at least one other sequence in the cluster. For a set of .bed annotation tables provided in a list along with a cut-off distance, the program will output a file containing the locations of each cluster. Annotated .bed files are from the 'pwmscan' application at <https://ccg.epfl.ch/pwmtools/pwmscan.php>. Personal machines might crash or take excessively long depending on the number of annotated sequences in each file and whether chromsearch() or gensearch() is used.
Author: Stefan Golas [cre, aut]
Maintainer: Stefan Golas <stefanmgolas@gmail.com>

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Package adiv updated to version 1.3 with previous version 1.2 dated 2018-08-24

Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>

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Package RPresto updated to version 1.3.4 with previous version 1.3.3 dated 2019-05-03

Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is an open source distributed SQL query engine for running interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut, cre], Sergey Goder [aut], John Myles White [ctb]
Maintainer: Onur Ismail Filiz <onur@fb.com>

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Package DTDA.cif updated to version 1.0.1 with previous version 1.0 dated 2019-08-02

Title: Doubly Truncated Data Analysis, Cumulative Incidence Functions
Description: Nonparametric estimator of the cumulative incidences of competing risks under double truncation. The estimator generalizes the Efron-Petrosian NPMLE (Non-Parametric Maximun Likelihood Estimator) to the competing risks setting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>.
Author: Jacobo de Uña Álvarez [aut], José Carlos Soage González [cre]
Maintainer: José Carlos Soage González <jsoage@uvigo.es>

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Package BLPestimatoR updated to version 0.3.0 with previous version 0.2.9 dated 2019-05-14

Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>

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Package rMVP updated to version 0.99.17 with previous version 0.99.16 dated 2019-09-24

Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can (1) effectively process large data, (2) rapidly evaluate population structure, (3) efficiently estimate variance components several algorithms, (4) implement parallel-accelerated association tests of markers three methods, (5) globally efficient design on GWAS process computing, (6) enhance visualization of related information. 'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>) and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX (Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>, R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and 'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression (Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).
Author: Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [aut], Jingya Xu [aut], Dong Yin [aut], Zhiwu Zhang [aut], Xiaohui Yuan [aut], Mengjin Zhu [aut], Shuhong Zhao [aut], Xinyun Li [aut], Qishan Wang [ctb], Feng Tian [ctb], Hyunmin Kang [ctb], Xiang Zhou [ctb], Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>

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Package purrr updated to version 0.3.3 with previous version 0.3.2 dated 2019-03-15

Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package WARN updated to version 1.2-4 with previous version 1.2-3 dated 2017-12-08

Title: Weaning Age Reconstruction with Nitrogen Isotope Analysis
Description: This estimates precise weaning ages for a given skeletal population by analyzing the stable nitrogen isotope ratios of them. Bone collagen turnover rates estimated anew and the approximate Bayesian computation (ABC) were adopted in this package.
Author: Takumi Tsutaya
Maintainer: Takumi Tsutaya <tsutayatakumi@gmail.com>

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Package hypr updated to version 0.1.3 with previous version 0.1.2 dated 2019-10-09

Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038>.
Author: Maximilian M. Rabe [aut, cre], Shravan Vasishth [aut], Sven Hohenstein [aut], Reinhold Kliegl [aut], Daniel J. Schad [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>

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Permanent link

Package dLagM updated to version 1.0.18 with previous version 1.0.17 dated 2019-08-24

Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>

Diff between dLagM versions 1.0.17 dated 2019-08-24 and 1.0.18 dated 2019-10-18

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Package MAVE updated to version 1.3.10 with previous version 1.3.9 dated 2019-05-08

Title: Methods for Dimension Reduction
Description: Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included. Xia (2002) <doi:10.1111/1467-9868.03411>; Xia (2007) <doi:10.1214/009053607000000352>; Wang (2008) <doi:10.1198/016214508000000418>.
Author: Hang Weiqiang<E0010758@u.nus.edu>, Xia Yingcun<staxyc@nus.edu.sg>
Maintainer: Hang Weiqiang<E0010758@u.nus.edu>

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Package r4ss updated to version 1.36.1 with previous version 1.24.0 dated 2015-12-23

Title: R Code for Stock Synthesis
Description: A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks.
Author: Ian G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison, Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson, Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz, Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet, Sean C. Anderson, Gwladys I. Lambert, Megan M. Stachura, Andrew B. Cooper, Andi Stephens, Neil L. Klaer, Carey R. McGilliard, Iago Mosqueira, Watal M. Iwasaki, Kathryn Doering, and Andrea M. Havron
Maintainer: Ian G. Taylor <Ian.Taylor@noaa.gov>

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Package bigreadr updated to version 0.2.0 with previous version 0.1.11 dated 2019-10-16

Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files. Package 'bigreadr' also provides some convenient wrappers around fread() and fwrite() from package 'data.table'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

Diff between bigreadr versions 0.1.11 dated 2019-10-16 and 0.2.0 dated 2019-10-18

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Package BB updated to version 2019.10-1 with previous version 2014.10-1 dated 2014-11-07

Title: Solving and Optimizing Large-Scale Nonlinear Systems
Description: Barzilai-Borwein spectral methods for solving nonlinear system of equations, and for optimizing nonlinear objective functions subject to simple constraints. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("BB").
Author: Ravi Varadhan [aut, cph, trl], Paul Gilbert [aut, cre], Marcos Raydan [ctb] (with co-authors, wrote original algorithms in fortran. These provided some guidance for implementing R code in the BB package.), JM Martinez [ctb] (with co-authors, wrote original algorithms in fortran. These provided some guidance for implementing R code in the BB package.), EG Birgin [ctb] (with co-authors, wrote original algorithms in fortran. These provided some guidance for implementing R code in the BB package.), W LaCruz [ctb] (with co-authors, wrote original algorithms in fortran. These provided some guidance for implementing R code in the BB package.)
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>

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Thu, 17 Oct 2019

Package SmallCountRounding updated to version 0.4.0 with previous version 0.3.0 dated 2019-02-28

Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398>.
Author: Øyvind Langsrud [aut, cre], Johan Heldal [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>

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Package phuse updated to version 0.2.0 with previous version 0.1.8 dated 2019-06-18

Title: Web Application Framework for 'PhUSE' Scripts
Description: Make it easy to review, download and execute scripts stored in Github 'phuse-scripts' repository <https://github.com/phuse-org/phuse-scripts>. Some examples included show the web application framework using the script metadata. The 'PhUSE' is Pharmaceutical Users Software Exchange <http://www.phuse.eu>.
Author: Hanming Tu [aut, cre]
Maintainer: Hanming Tu <hanming.tu@gmail.com>

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Package nhdplusTools updated to version 0.3.10 with previous version 0.3.9 dated 2019-10-16

Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre], Mike Johnson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package MBHdesign updated to version 2.1.5 with previous version 1.0.79 dated 2017-10-30

Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region for point-based and for transect-based surveys. Accommodates, without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>

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Package jackalope updated to version 0.1.3 with previous version 0.1.2 dated 2019-07-11

Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Description: Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written to standard file formats.
Author: Lucas A. Nell [cph, aut, cre] (<https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucas@lucasnell.com>

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Package eSDM updated to version 0.3.1 with previous version 0.3.0 dated 2019-08-19

Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles of species distribution model (SDM) predictions. Functionality is offered through R functions or a GUI (R Shiny app). This tool can assist users in identifying spatial uncertainties and making informed conservation and management decisions. The package is further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

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Package BMTME updated to version 1.0.12 with previous version 1.0.11 dated 2019-10-01

Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis
Description: Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions that help to create regression models for some genomic models proposed by Montesinos-López, et al. (2016) <doi:10.1534/g3.116.032359> also in Montesinos-López et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-López et al. (2018) <doi:10.2134/agronj2018.06.0362>.
Author: Francisco Javier Luna-Vazquez [aut, cre] (<https://orcid.org/0000-0002-5370-7152>), Fernando H. Toledo [aut], Osval Antonio Montesinos-Lopez [aut] (<https://orcid.org/0000-0002-3973-6547>), Abelardo Montesinos-Lopez [aut], Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>

Diff between BMTME versions 1.0.11 dated 2019-10-01 and 1.0.12 dated 2019-10-17

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Package trackdem updated to version 0.5 with previous version 0.4.3 dated 2019-03-19

Title: Particle Tracking and Demography
Description: Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in evolutionary and ecological studies.
Author: Marjolein Bruijning, Marco D. Visser, Caspar A. Hallmann, Eelke Jongejans
Maintainer: Marjolein Bruijning <mbruijning@princeton.edu>

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Package taxize updated to version 0.9.9 with previous version 0.9.8 dated 2019-06-28

Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Eduard Szoecs [aut], Zachary Foster [aut], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between taxize versions 0.9.8 dated 2019-06-28 and 0.9.9 dated 2019-10-17

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Package styler updated to version 1.2.0 with previous version 1.1.1 dated 2019-05-06

Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting intent.
Author: Kirill Müller [aut], Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>

Diff between styler versions 1.1.1 dated 2019-05-06 and 1.2.0 dated 2019-10-17

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Package permutations updated to version 1.0-5 with previous version 1.0-4 dated 2019-04-11

Title: The Symmetric Group: Permutations of a Finite Set
Description: Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between permutations versions 1.0-4 dated 2019-04-11 and 1.0-5 dated 2019-10-17

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Package LDlinkR updated to version 1.0.1 with previous version 1.0.0 dated 2019-08-01

Title: An R Package for Calculating Linkage Disequilibrium
Description: Provides access to the LDlink API (<https://ldlink.nci.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project data using LDlink.
Author: Timothy A. Myers [aut, cre], Stephen J. Chanock [aut], Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>

Diff between LDlinkR versions 1.0.0 dated 2019-08-01 and 1.0.1 dated 2019-10-17

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Permanent link

Package insight updated to version 0.6.0 with previous version 0.5.0 dated 2019-09-07

Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>), Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between insight versions 0.5.0 dated 2019-09-07 and 0.6.0 dated 2019-10-17

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Package xgxr updated to version 1.0.5 with previous version 1.0.4 dated 2019-10-10

Title: Exploratory Graphics for Pharmacometrics
Description: Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Author: Andrew Stein [aut, cre], Alison Margolskee [aut], Fariba Khanshan [aut], Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>), Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>), Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>

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Package MLML2R updated to version 0.3.3 with previous version 0.3.2 dated 2019-04-06

Title: Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2019) <doi:10.1515/sagmb-2018-0031>.
Author: Samara Kiihl [aut, cre], Maria Jose Martinez-Garrido [aut], Arce Domingo-Relloso [aut], Jose Bermudez [aut], Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>

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Package scorecard updated to version 0.2.7 with previous version 0.2.6 dated 2019-09-01

Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard easier and efficient by providing functions for some common tasks, such as data partition, variable selection, woe binning, scorecard scaling, performance evaluation and report generation. These functions can also used in the development of machine learning models. The references including: 1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS. 2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards. Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>

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Package classInt updated to version 0.4-2 with previous version 0.4-1 dated 2019-08-06

Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre] (<https://orcid.org/0000-0003-2392-6140>), Hisaji Ono [ctb], Richard Dunlap [ctb], Matthieu Stigler [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>)
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package bibliometrix updated to version 2.3.0 with previous version 2.2.1 dated 2019-06-27

Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics. It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>), Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Dimensions (<https://www.dimensions.ai/>), Cochrane Library (<http://www.cochranelibrary.com/>) and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut], Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>

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Package basetheme updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-18

Title: Themes for Base Graphics Plots
Description: Functions to create and select graphical themes for the base plotting system. Contains: 1) several custom pre-made themes 2) mechanism for creating new themes by making persistent changes to the graphical parameters of base plots.
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>

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Package DTRreg updated to version 1.5 with previous version 1.4 dated 2019-08-21

Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv).
Author: Michael Wallace, Erica E M Moodie, David A Stephens and Gabrielle Simoneau
Maintainer: Michael Wallace <michael.wallace@uwaterloo.ca>

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Package CircMLE updated to version 0.2.2 with previous version 0.2.1 dated 2018-02-20

Title: Maximum Likelihood Analysis of Circular Data
Description: A series of wrapper functions to implement the 10 maximum likelihood models of animal orientation described by Schnute and Groot (1992) <DOI:10.1016/S0003-3472(05)80068-5>. The functions also include the ability to use different optimizer methods and calculate various model selection metrics (i.e., AIC, AICc, BIC).
Author: Robert Fitak [aut, cre], Sönke Johnsen [aut]
Maintainer: Robert Fitak <rfitak9@gmail.com>

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Package AzureContainers updated to version 1.1.1 with previous version 1.1.0 dated 2019-07-15

Title: Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'
Description: An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/overview/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'kubectl' and 'helm' commandline tools are provided. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Bill Liang [ctb] (Assistance debugging MMLS on Kubernetes), Ramkumar Chandrasekaran [ctb] (Original blog article on Dockerising MMLS), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package ashr updated to version 2.2-39 with previous version 2.2-32 dated 2019-02-22

Title: Methods for Adaptive Shrinkage, using Empirical Bayes
Description: The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accomodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).
Author: Matthew Stephens [aut], Peter Carbonetto [aut, cre], Chaoxing Dai [ctb], David Gerard [aut], Mengyin Lu [aut], Lei Sun [aut], Jason Willwerscheid [aut], Nan Xiao [aut], Mazon Zeng [ctb]
Maintainer: Peter Carbonetto <pcarbo@uchicago.edu>

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Package sabre updated to version 0.3.2 with previous version 0.3.1 dated 2019-07-18

Title: Spatial Association Between Regionalizations
Description: Calculates a degree of spatial association between regionalizations or categorical maps using the information-theoretical V-measure (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>). It also offers an R implementation of the MapCurve method (Hargrove et al. (2006) <doi:10.1007/s10109-006-0025-x>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>), Tomasz Stepinski [aut], Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package rAmCharts updated to version 2.1.12 with previous version 2.1.11 dated 2019-08-28

Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <http://datastorm- open.github.io/introduction_ramcharts/> and <http://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <http://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Benoit Thieurmel [aut, cre], Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/), Jeffery Petit [aut, ctb], Elena Salette [aut, ctb], Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>

Diff between rAmCharts versions 2.1.11 dated 2019-08-28 and 2.1.12 dated 2019-10-17

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Package s2dverification updated to version 2.8.6 with previous version 2.8.5 dated 2019-03-19

Title: Set of Common Tools for Forecast Verification
Description: Set of tools to verify forecasts through the computation of typical prediction scores against one or more observational datasets or reanalyses (a reanalysis being a physical extrapolation of observations that relies on the equations from a model, not a pure observational dataset). Intended for seasonal to decadal climate forecasts although can be useful to verify other kinds of forecasts. The package can be helpful in climate sciences for other purposes than forecasting.
Author: BSC-CNS [aut, cph], Virginie Guemas [aut], Nicolau Manubens [aut], An-Chi Ho [ctb, cre], Nuria Perez-Zanon [ctb], Javier Garcia-Serrano [aut], Neven Fuckar [aut], Louis-Philippe Caron [aut], Omar Bellprat [aut], Luis Rodrigues [aut], Veronica Torralba [aut], Alasdair Hunter [aut], Chloe Prodhomme [aut], Martin Menegoz [aut], Domingo Manubens [ctb], Constantin Ardilouze [ctb], Lauriane Batte [ctb], Fabian Lienert [ctb], Julia Giner [ctb], Jean-Philippe Baudouin [ctb], Nube Gonzalez [ctb], Ludovic Auger [ctb], Nicola Cortesi [ctb], Eleftheria Exarchou [ctb], Ruben Cruz [ctb], Isabel Andreu-Burillo [ctb], Ramiro Saurral [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>

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More information about s2dverification at CRAN
Permanent link

Package R.rsp updated to version 0.43.2 with previous version 0.43.1 dated 2019-02-05

Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.rsp versions 0.43.1 dated 2019-02-05 and 0.43.2 dated 2019-10-17

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 NAMESPACE                                                               |    5 
 NEWS                                                                    |   16 
 R/RspDocument.R                                                         |    5 
 R/RspResponse.R                                                         |    5 
 build/vignette.rds                                                      |binary
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 inst/rsp_examples/favicon.md.rsp                                        |   40 
 inst/rsp_tests/R-vignette.tex.rsp                                       |   36 
 inst/rsp_tests/birth.txt.rsp                                            |    4 
 inst/rsp_tests/comments.txt.rsp                                         |   28 
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 inst/rsp_tests/example.md.rsp                                           |   14 
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 inst/rsp_tests/trimming-3.txt.rsp                                       |   12 
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 man/R.rsp-package.Rd                                                    |    2 
 man/rargs.Rd                                                            |    7 
 man/rfile.Rd                                                            |   10 
 tests/rargs.R                                                           |    4 
 tests/rfile.R                                                           |    1 
 vignettes/Dynamic_document_creation_using_RSP.tex.rsp                   | 2550 +++++-----
 vignettes/RSP_refcard.tex.rsp                                           |  596 +-
 vignettes/R_packages-RSP_vignettes.md.rsp                               |  142 
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 79 files changed, 6097 insertions(+), 6094 deletions(-)

More information about R.rsp at CRAN
Permanent link

Package ncodeR updated to version 0.2.0.0 with previous version 0.1.3.0 dated 2019-05-03

Title: Techniques for Automated Classifiers
Description: A set of techniques that can be used to develop, validate, and implement automated classifiers. A powerful tool for transforming raw data into meaningful information, 'ncodeR' (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is designed specifically for working with big data: large document collections, logfiles, and other text data.
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>), Zachari Swiecki [aut], Brendan Eagan [aut], David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>

Diff between ncodeR versions 0.1.3.0 dated 2019-05-03 and 0.2.0.0 dated 2019-10-17

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 ncodeR-0.2.0.0/ncodeR/R/RegexCode.R                   |  118 +++++----
 ncodeR-0.2.0.0/ncodeR/R/Test.R                        |  231 ++++++++++++++----
 ncodeR-0.2.0.0/ncodeR/R/differences.R                 |   60 ++--
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More information about ncodeR at CRAN
Permanent link

Package mRpostman updated to version 0.3.0 with previous version 0.2.0 dated 2019-08-22

Title: IMAP Toolkit
Description: IMAP4rev1 (Internet Message Access Protocol, Version 4rev1) functionalities based on the RFC 3501 manual (Crispin, 2003, <doi:10.17487/RFC3501>), its updates, and other related documents. 'mRpostman' makes extensive use of 'curl' and 'libcurl' capabilities, providing functions for mailboxes and electronic messages manipulation, such as moving, deleting, and searching messages using specific criteria, setting and clearing flags, selective fetching of message attributes and more.
Author: Allan Quadros [aut, cre]
Maintainer: Allan Quadros <allanvcq@gmail.com>

Diff between mRpostman versions 0.2.0 dated 2019-08-22 and 0.3.0 dated 2019-10-17

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Package litteR updated to version 0.6.4 with previous version 0.6.2 dated 2019-10-07

Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain litter, floating litter, and seafloor litter are rapidly growing. This package offers a simple user interface to analyse these litter data in a consistent and reproducible way. It also provides functions to facilitate several kinds of litter analysis, e.g., trend analysis, power analysis, and baseline analysis. Under the hood, these functions are also used by the user interface. See Schulz et al. (2019) <doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph], Willem van Loon [aut, cph], Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>

Diff between litteR versions 0.6.2 dated 2019-10-07 and 0.6.4 dated 2019-10-17

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Package ggimage updated to version 0.2.4 with previous version 0.2.3 dated 2019-09-23

Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggimage versions 0.2.3 dated 2019-09-23 and 0.2.4 dated 2019-10-17

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Package DynTxRegime updated to version 4.2 with previous version 4.1 dated 2019-03-21

Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

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Package irtplay updated to version 1.2.0 with previous version 1.1.0 dated 2019-09-18

Title: Evaluation of Model-Data Fit in Item Response Theory (IRT) and Useful Functions Related to IRT
Description: Examine the IRT model-data fit on item-level in different ways as well as provide useful functions related to unidimensional item response theory (IRT). In terms of assessing the IRT model-data fit, one of distinguished features of this package is that it gives not only well-known item fit statistics (e.g., chi-square (X2), likelihood ratio chi-square (G2), infit and oufit statistics (Ames & Penfield (2015) <doi:10.1111/emip.12067>)) but also graphical displays to look at residuals between between the observed data and model-based predictions (Hambleton, Swaminathan, & Rogers (1991, ISBN:9780803936478)). More evaluation methods will be included in the future updated version. In addition to the evaluation of IRT model-data fit, there are several useful functions such as estimating proficiency parameters, calibrating item parameters given the fixed effects (aka. ability values) (Baker & Kim (2004, ISBN:9780824758257)), computing asymptotic variance-covariance matrices of item parameter estimates (Li & Lissitz (2004) <doi:10.1111/j.1745-3984.2004.tb01109.x>), importing item and/or ability parameters from popular IRT software, generating simulated data, computing the conditional distribution of observed scores using the Lord-Wingersky recursion formula (Lord & Wingersky (1984) <doi:10.1207/s15324818ame1002_1>), computing the loglikelihood of individual items, computing item and test information functions, computing item and test characteristic curve functions, and plotting item and test characteristic curves and item and test information functions.
Author: Hwanggyu Lim [aut, cre], Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>

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Package childesr updated to version 0.1.2 with previous version 0.1.1 dated 2019-04-25

Title: Accessing the 'CHILDES' Database
Description: Tools for connecting to 'CHILDES', an open repository for transcripts of parent-child interaction. For more information on the underlying data, see <http://childes-db.stanford.edu>.
Author: Mika Braginsky [aut, cre], Alessandro Sanchez [aut, ctb], Daniel Yurovsky [aut], Kyle MacDonald [ctb], Stephan Meylan [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>

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Wed, 16 Oct 2019

Package mixsqp updated to version 0.2-2 with previous version 0.1-97 dated 2019-02-18

Title: Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
Description: Provides optimization algorithms based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithms are expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly in large data sets. The algorithms are described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2018) <arXiv:1806.01412>.
Author: Youngseok Kim [aut], Peter Carbonetto [aut, cre], Mihai Anitescu [aut], Matthew Stephens [aut], Jason Willwerscheid [ctb], Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>

Diff between mixsqp versions 0.1-97 dated 2019-02-18 and 0.2-2 dated 2019-10-16

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Package metScanR updated to version 1.2.3 with previous version 1.2.2 dated 2019-02-02

Title: Find, Map, and Gather Environmental Data and Metadata
Description: A tool for locating, mapping, and gathering environmental data and metadata, worldwide. Users can search for and filter metadata from > 157,000 environmental monitoring stations among 219 countries/territories and >20 networks/organizations via elevation, location, active dates, elements measured (e.g., temperature, precipitation), country, network, and/or known identifier. Future updates to the package will allow the user to obtain datasets from stations within the database.
Author: Josh Roberti [aut, cre], Cody Flagg [aut], Lee Stanish [aut], Robert Lee [aut]
Maintainer: Josh Roberti <jaroberti87@gmail.com>

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Package dlsem updated to version 2.4.4 with previous version 2.4.3 dated 2019-08-20

Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models where each factor of the joint probability distribution is a distributed-lag linear regression (Magrini, 2018 <doi:10.2478/bile-2018-0012>; Magrini et al., 2019 <doi:10.1007/s11135-019-00855-z>). DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>

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Package DChaos updated to version 0.1-3 with previous version 0.1-2 dated 2019-05-29

Title: Chaotic Time Series Analysis
Description: Provides several algorithms for the purpose of detecting chaotic signals inside univariate time series. We focus on methods derived from chaos theory which estimate the complexity of a dataset through exploring the structure of the attractor. We have taken into account the Lyapunov exponents as an ergodic measure. We have implemented the Jacobian method by a fit through neural networks in order to estimate both the largest and the spectrum of Lyapunov exponents. We have considered the full sample and three different methods of subsampling by blocks (non-overlapping, equally spaced and bootstrap) to estimate them. In addition, it is possible to make inference about them and know if the estimated Lyapunov exponents values are or not statistically significant. This library can be used with time series whose time-lapse is fixed or variable. That is, it considers time series whose observations are sampled at fixed or variable time intervals. For a review see David Ruelle and Floris Takens (1971) <doi:10.1007/BF01646553>, Ramazan Gencay and W. Davis Dechert (1992) <doi:10.1016/0167-2789(92)90210-E>, Jean-Pierre Eckmann and David Ruelle (1995) <doi:10.1103/RevModPhys.57.617>, Mototsugu Shintani and Oliver Linton (2004) <doi:10.1016/S0304-4076(03)00205-7>, Jeremy P. Huke and David S. Broomhead (2007) <doi:10.1088/0951-7715/20/9/011>.
Author: Julio E. Sandubete [aut, cre], Lorenzo Escot [aut]
Maintainer: Julio E. Sandubete <jsandube@ucm.es>

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Package ctrdata updated to version 1.0 with previous version 0.18.2 dated 2019-05-01

Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analysing protocol- and results-related information on clinical trials from two public registers, the European Union Clinical Trials Register (EUCTR, <https://www.clinicaltrialsregister.eu/>) and ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The information is transformed and then stored in a database (mongo). Functions are provided for accessing and analysing the locally stored information on the clinical trials, as well as for identifying duplicate records. The package is motivated by the need for aggregating and trend-analysing the design, conduct and outcomes across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

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Package covr updated to version 3.3.2 with previous version 3.3.1 dated 2019-08-23

Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
Author: Jim Hester [aut, cre], Willem Ligtenberg [ctb], Kirill Müller [ctb], Henrik Bengtsson [ctb], Steve Peak [ctb], Kirill Sevastyanenko [ctb], Jon Clayden [ctb], Robert Flight [ctb], Eric Brown [ctb], Brodie Gaslam [ctb], Will Beasley [ctb], Robert Krzyzanowski [ctb], Markus Wamser [ctb], Karl Forner [ctb], Gergely Daróczi [ctb], Jouni Helske [ctb], Kun Ren [ctb], Jeroen Ooms [ctb], Ken Williams [ctb], Chris Campbell [ctb], David Hugh-Jones [ctb], Qin Wang [ctb], Ivan Sagalaev [ctb, cph] (highlight.js library), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library)
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Package decisionSupport updated to version 1.105.2 with previous version 1.103.8 dated 2018-10-15

Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based decision making processes using Monte Carlo simulations. Decision support is given on two levels: (i) The actual decision level is to choose between two alternatives under probabilistic uncertainty. This package calculates the optimal decision based on maximizing expected welfare. (ii) The meta decision level is to allocate resources to reduce the uncertainty in the underlying decision problem, i.e to increase the current information to improve the actual decision making process. This problem is dealt with using the Value of Information Analysis. The Expected Value of Information for arbitrary prospective estimates can be calculated as well as Individual Expected Value of Perfect Information. The probabilistic calculations are done via Monte Carlo simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (University of Bonn), Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting), Katja Schiffers [aut] (University of Bonn)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package coil updated to version 1.0.1 with previous version 1.0.0 dated 2019-10-09

Title: Contextualization and Evaluation of COI-5P Barcode Data
Description: Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data.
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <nugentc@uoguelph.ca>

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Package simstudy updated to version 0.1.15 with previous version 0.1.14 dated 2019-08-09

Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>

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Package nhdplusTools updated to version 0.3.9 with previous version 0.3.8 dated 2019-08-27

Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre], Michael Johnson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package exact2x2 updated to version 1.6.3.1 with previous version 1.6.3 dated 2018-07-27

Title: Exact Tests and Confidence Intervals for 2x2 Tables
Description: Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case. Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail.
Author: Michael P. Fay, Sally A. Hunsberger, Martha Nason, Erin Gabriel
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>

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Package bigreadr updated to version 0.1.11 with previous version 0.1.10 dated 2019-09-17

Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files. Package 'bigreadr' also provides some convenient wrappers around fread() and fwrite() from package 'data.table'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

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Package logNormReg updated to version 0.3-0 with previous version 0.2-0 dated 2018-10-16

Title: log Normal Linear Regression
Description: Functions to fits simple linear regression models with log normal errors and identity link (taking the responses on the original scale). See Muggeo (2018) <doi:10.13140/RG.2.2.18118.16965>.
Author: Vito M. R. Muggeo [aut, cre] (<https://orcid.org/0000-0002-3386-4054>)
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>

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Package details updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-09

Title: Create Details HTML Tag for Markdown and Package Documentation
Description: Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>

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Package hutilscpp updated to version 0.3.0 with previous version 0.2.0 dated 2019-08-20

Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for 'reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package 'hutils' by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

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Package comorbidity updated to version 0.5.1 with previous version 0.5.0 dated 2019-08-20

Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Hojjat Salmasian [ctb] (ICD-9-CM scores), Jonathan Williman [ctb] (<https://orcid.org/0000-0001-5080-4435>)
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

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Package npordtests updated to version 1.2 with previous version 1.1 dated 2018-11-26

Title: Nonparametric Tests for Equality of Location Against Ordered Alternatives
Description: Performs nonparametric tests for equality of location against ordered alternatives.
Author: Bulent Altunkaynak [aut, cre], Hamza Gamgam [aut]
Maintainer: Bulent Altunkaynak <bulenta@gazi.edu.tr>

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Package MTA updated to version 0.2.0 with previous version 0.1.2 dated 2018-05-14

Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut], Nicolas Lambert [aut], Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>

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Package WeightIt updated to version 0.7.0 with previous version 0.6.0 dated 2019-09-05

Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>

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Package StepReg updated to version 1.3.0 with previous version 1.2.1 dated 2019-09-20

Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward', 'backward' and 'bidirection' steps. Besides, best subset selection is included in this package. Procedure can use Akaike information criterion, corrected Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, corrected Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria. Multicollinearity detection in regression model are performed by checking tolerance value. Continuous variables nested within class effect and weighted stepwise regression are also considered.
Author: Junhui Li,Xiaohuan Lu,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>

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Package loon updated to version 1.2.3 with previous version 1.2.2 dated 2019-03-23

Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut], R. Wayne Oldford [aut, cre, ths], Zehao Xu [ctb], Martin Gauch [ctb]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>

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Package BiocManager updated to version 1.30.8 with previous version 1.30.7 dated 2019-10-07

Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>

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Tue, 15 Oct 2019

Package RiemBase updated to version 0.2.3 with previous version 0.2.2 dated 2019-02-05

Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>

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Package pmpp updated to version 0.1.1 with previous version 0.1.0 dated 2018-10-12

Title: Posterior Mean Panel Predictor
Description: Dynamic panel modelling framework based on an empirical-Bayes approach. Contains tools for computing point forecasts and bootstrapping prediction intervals. Reference: Liu et al. (2016) <doi:10.2139/ssrn.2889000>.
Author: Michal Oleszak [aut, cre]
Maintainer: Michal Oleszak <oleszak.michal@gmail.com>

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Package gwsem updated to version 0.1.5 with previous version 0.1.2 dated 2019-10-09

Title: Genome-Wide Structural Equation Modeling
Description: Melds genome-wide association tests with structural equation modeling (SEM) using 'OpenMx'. This package contains low-level C/C++ code to rapidly read genetic data encoded in U.K. Biobank or 'plink' formats. Prebuilt modeling options include one and two factor models. Alternately, analyses may utilize arbitrary, user-provided SEMs. See Verhulst, Maes, & Neale (2017) <doi:10.1007/s10519-017-9842-6> for details. An updated manuscript is in preparation.
Author: Joshua N. Pritikin [aut, cre], Bradley Verhulst [cph], Gavin Band [cph], Yann Collet [cph], Facebook, Inc. [cph], Yuta Mori [cph], Shaun Purcell [cph], Christopher Chang [cph], Wojciech Mula [cph], Kim Walisch [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

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Package gdalcubes updated to version 0.2.2 with previous version 0.2.1 dated 2019-08-21

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Niels Lohmann [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

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Package CRFCSD updated to version 2.0 with previous version 1.0 dated 2019-04-04

Title: Mixture Cure Generalized Odds Ratio Frailty Models for Clustered Current Status Data
Description: A methodology to estimate the parameters for the cure rate frailty models with clustered current status data.
Author: Tong Wang, Kejun He, Wei Ma, Dipankar Bandyopadhyay, Samiran Sinha
Maintainer: Tong Wang<tong@stat.tamu.edu>

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Package cansim updated to version 0.3.3 with previous version 0.3.2 dated 2019-08-26

Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for bilingual English or French language data retrieval, and bundles convenience functions to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre], Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>

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Package stats19 updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-28

Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979, the types (including make and model) of vehicles involved and the consequential casualties. The statistics relate only to personal casualties on public roads that are reported to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See the Department for Transportation website <https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>), Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>), David Ranzolin [rev], Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>), RAC Foundation [fnd]
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package IPDFileCheck updated to version 0.4.0 with previous version 0.3.0 dated 2019-10-07

Title: Basic Functions to Check the Readability, Consistency, and Content of an Individual Participant/Patient Data File from a Randomised Controlled Trial
Description: Checks files for existence, read access and checks individual columns for formats. Currently implemented for gender and age formats.
Author: Sheeja Manchira Krishnan
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>

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Package freesurferformats updated to version 0.1.3 with previous version 0.1.2 dated 2019-10-02

Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>

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Package Rd2roxygen updated to version 1.9 with previous version 1.8 dated 2019-03-05

Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an Rd file to a list, create the 'roxygen' documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities that can help developers build packages using 'roxygen' more easily. The 'formatR' package can be used to reformat the R code in the examples sections so that the code will be more readable.
Author: Hadley Wickham [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package lidR updated to version 2.1.4 with previous version 2.1.3 dated 2019-09-10

Title: Airborne LiDAR Data Manipulation and Visualization for Forestry Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph], David Auty [aut, ctb] (Reviews the documentation), Florian De Boissieu [ctb] (Fixed bugs and improved catalog features), Andrew Sánchez Meador [ctb] (Implemented lassnags)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

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Package AzureGraph updated to version 1.0.5 with previous version 1.0.4 dated 2019-09-20

Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package expSBM updated to version 1.3.5 with previous version 1.1 dated 2019-03-12

Title: An Exponential Stochastic Block Model for Interaction Lengths
Description: Given a continuous-time dynamic network, this package allows one to fit a stochastic blockmodel where nodes belonging to the same group create interactions and non-interactions of similar lengths. This package implements the methodology described by R. Rastelli and M. Fop (2019) <arXiv:1901.09828>.
Author: Riccardo Rastelli [aut, cre] (<https://orcid.org/0000-0003-0982-2935>), Michael Fop [aut] (<https://orcid.org/0000-0003-3936-2757>)
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>

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Package datapack updated to version 1.3.2 with previous version 1.3.1 dated 2017-08-29

Title: A Flexible Container to Transport and Manipulate Data and Associated Resources
Description: Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>

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Package rerddapXtracto updated to version 0.4.5 with previous version 0.4.4 dated 2019-09-25

Title: Extracts Environmental Data from 'ERDDAP' Web Services
Description: Contains three functions that access environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts data along a trajectory for a given "radius" around the point. The rxtracto_3D() function extracts data in a box. The rxtractogon() function extracts data in a polygon. All of those three function use the 'rerddap' package to extract the data, and should work with any 'ERDDAP' server. There are also two functions, plotBBox() and plotTrack() that use the 'plotdap' package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>

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Package tmle updated to version 1.4.0.1 with previous version 1.4.0 dated 2019-10-13

Title: Targeted Maximum Likelihood Estimation
Description: Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Author: Susan Gruber [aut, cre], Mark van der Laan [aut], Chris Kennedy [ctr]
Maintainer: Susan Gruber <sgruber@cal.berkeley.edu>

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Package rstpm2 updated to version 1.5.0 with previous version 1.4.5 dated 2019-01-17

Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb], Lasse Hjort Jakobsen [ctb], Alessandro Gasparini [ctb], Gordon Smyth [cph], Patrick Alken [cph], Simon Wood [cph], Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>

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Package plotdap updated to version 0.0.4 with previous version 0.0.3 dated 2019-07-26

Title: Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap' Package
Description: Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.
Author: Carson Sievert [aut], Roy Mendelssohn [aut, ctb, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>

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Package ercv updated to version 1.0.1 with previous version 1.0.0 dated 2017-07-17

Title: Fitting Tails by the Empirical Residual Coefficient of Variation
Description: Provides a methodology simple and trustworthy for the analysis of extreme values and multiple threshold tests for a generalized Pareto distribution, together with an automatic threshold selection algorithm. See del Castillo, J, Daoudi, J and Lockhart, R (2014) <doi:10.1111/sjos.12037>.
Author: Joan del Castillo, David Moriña Soler and Isabel Serra
Maintainer: Isabel Serra <iserra@crm.cat>

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Package AzureKeyVault updated to version 1.0.2 with previous version 1.0.1 dated 2019-07-18

Title: Key and Secret Management in 'Azure'
Description: Manage keys, certificates, secrets, and storage accounts in Microsoft's 'Key Vault' service: <https://azure.microsoft.com/services/key-vault>. Provides facilities to store and retrieve secrets, use keys to encrypt, decrypt, sign and verify data, and manage certificates. Integrates with the 'AzureAuth' package to enable authentication with a certificate, and with the 'openssl' package for importing and exporting cryptographic objects. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package rblt updated to version 0.2.4.4 with previous version 0.2.4.3 dated 2019-06-27

Title: Bio-Logging Toolbox
Description: An R-shiny application to plot datalogger time series at a microsecond precision as Acceleration, Temperature, Pressure, Light intensity from CATS, AXY-TREK LUL and WACU bio-loggers. It is possible to link behavioral labels extracted from 'BORIS' software <http://www.boris.unito.it> or manually written in a csv file. CATS bio-logger are manufactured by <http://www.cats.is>, AXY-TREK are manufactured by <http://www.technosmart.eu> and LUL and WACU are manufactured by <http://www.iphc.cnrs.fr/-MIBE-.html>.
Author: Sebastien Geiger [aut, cre]
Maintainer: Sebastien Geiger <sebastien.geiger@iphc.cnrs.fr>

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Package netgwas updated to version 1.11 with previous version 1.10 dated 2019-04-12

Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical models for accomplishing the three interrelated goals in genetics and genomics in an unified way: (1) linkage map construction, (2) constructing linkage disequilibrium networks, and (3) exploring high-dimensional genotype-phenotype network and genotype- phenotype-environment interactions networks. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is considerably larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>. NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>

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Package ihpdr updated to version 1.1.0 with previous version 1.0.0 dated 2019-08-20

Title: Download Data from the International House Price Database
Description: Web scraping the <https://www.dallasfed.org> for up-to-date data on international house prices and exuberance indicators. Download data in tidy format.
Author: Kostas Vasilopoulos [aut, cre]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>

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Package drugCombo updated to version 1.1.1 with previous version 1.1.0 dated 2019-06-18

Title: Drug Interaction Modeling Based on Loewe Additivity Following Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based on the Loewe additivity model, following Harbron's approach (Statistics in Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling of the drug interaction index and supports "2-stage" estimation in addition to "1-stage" estimation, including bootstrap-based confidence intervals. The method requires data on the monotherapy responses and the package accommodates both checkerboard and ray designs. Functions are available for graphical exploration of model goodness-of-fit and diagnostics, as well as for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>

Diff between drugCombo versions 1.1.0 dated 2019-06-18 and 1.1.1 dated 2019-10-15

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More information about drugCombo at CRAN
Permanent link

Package AMR updated to version 0.8.0 with previous version 0.7.1 dated 2019-06-23

Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) <doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alex W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between AMR versions 0.7.1 dated 2019-06-23 and 0.8.0 dated 2019-10-15

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More information about AMR at CRAN
Permanent link

Package mrgsolve updated to version 0.10.0 with previous version 0.9.2 dated 2019-07-13

Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>), Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Dilawar Singh [ctb], Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>

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Package KernSmooth updated to version 2.23-16 with previous version 2.23-15 dated 2015-06-29

Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src), Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package essurvey updated to version 1.0.3 with previous version 1.0.2 dated 2018-08-23

Title: Download Data from the European Social Survey on the Fly
Description: Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
Author: Jorge Cimentada [aut, cre], Thomas Leeper [rev] (Thomas reviewed the package for rOpensci,see https://github.com/ropensci/onboarding/issues/201), Nujcharee Haswell [rev] (Nujcharee reviewed the package for rOpensci, see https://github.com/ropensci/onboarding/issues/201), Jorge Lopez [ctb], François Briatte [ctb]
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>

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Package dextergui updated to version 0.2.1 with previous version 0.2.0 dated 2019-08-26

Title: A Graphical User Interface for Dexter
Description: Classical Test and Item analysis, Item Response analysis and data management for educational and psychological tests.
Author: jesse koops [aut, cre], Eva de Schipper [aut], Ivailo Partchev [aut, ctb], Gunter Maris [aut, ctb], Timo Bechger [aut, ctb], Gareth Watts [aut, cph] (author of jquery.sparkline), Hakim El Hattab [aut, cph] (author of zoom.js)
Maintainer: jesse koops <jesse.koops@cito.nl>

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Package mosum updated to version 1.2.2 with previous version 1.2.1 dated 2019-05-10

Title: Moving Sum Based Procedures for Changes in the Mean
Description: Implementations of MOSUM-based statistical procedures and algorithms for detecting multiple changes in the mean. This comprises the MOSUM procedure for estimating multiple mean changes from Eichinger and Kirch (2018) <doi:10.3150/16-BEJ887> and the multiscale algorithmic extensions from Cho and Kirch (2019+).
Author: Alexander Meier [aut], Haeran Cho [aut, cre], Claudia Kirch [aut]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>

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Package OECD updated to version 0.2.4 with previous version 0.2.3.999 dated 2018-06-30

Title: Search and Extract Data from the OECD
Description: Search and extract data from the Organization for Economic Cooperation and Development (OECD).
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>

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Package glmmEP updated to version 1.0-3.1 with previous version 1.0-3 dated 2019-10-13

Title: Generalized Linear Mixed Model Analysis via Expectation Propagation
Description: Approximate frequentist inference for generalized linear mixed model analysis with expectation propagation used to circumvent the need for multivariate integration. In this version, the random effects can be any reasonable dimension. However, only probit mixed models with one level of nesting are supported. The methodology is described in Hall, Johnstone, Ormerod, Wand and Yu (2018) <arXiv:1805.08423v1>.
Author: Matt P. Wand [aut, cre], James C.F. Yu [aut]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>

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Package drake updated to version 7.7.0 with previous version 7.6.2 dated 2019-09-14

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>), Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>), Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>), Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>), Ellis Hughes [ctb], Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package bayesm updated to version 3.1-4 with previous version 3.1-3 dated 2019-07-29

Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>

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Package ohenery updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-06

Title: Modeling of Ordinal Random Variables via Softmax Regression
Description: Supports the modeling of ordinal random variables, like the outcomes of races, via Softmax regression, under the Harville <doi:10.1080/01621459.1973.10482425> and Henery <doi:10.1111/j.2517-6161.1981.tb01153.x> models.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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Package lslx updated to version 0.6.9 with previous version 0.6.8 dated 2019-07-24

Title: Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS).
Author: Po-Hsien Huang [cre, aut], Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>

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Package txtq updated to version 0.2.0 with previous version 0.1.6 dated 2019-09-15

Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets parallel processes send and receive messages, and it can help coordinate the work of complicated parallel tasks. Processes can push new messages to the queue, pop old messages, and obtain a log of all the messages ever pushed. File locking preserves the integrity of the data even when multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Ian E. Fellows [ctb], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package paws.common updated to version 0.2.3 with previous version 0.2.2 dated 2019-10-03

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

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Package iCellR updated to version 1.2.0 with previous version 1.1.4 dated 2019-09-26

Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis.
Author: Alireza Khodadadi-Jamayran, Joseph Pucella, Hua Zhou, Nicole Doudican, John Carucci, Adriana Heguy, Boris Reizis, Aristotelis Tsirigos
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>

Diff between iCellR versions 1.1.4 dated 2019-09-26 and 1.2.0 dated 2019-10-15

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Mon, 14 Oct 2019

Package LHD updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-07

Title: Latin Hypercube Designs (LHDs) Algorithms
Description: Contains functions for finding space-filling Latin Hypercube Designs (LHDs), e.g. maximin distance LHDs. Unlike other packages, our package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, it is very useful in design of computer experiments. One advantage of our package is its comprehensiveness. It contains a variety of heuristic algorithms (and their modifications) for searching maximin distance LHDs. In addition to that, it also contains other useful tools for developing and constructing maximin distance LHDs. In the future, algebraic construction methods will be added. Please refer to the function documentations for the detailed references of each function. Among all the references we used, one reference should be highlighted here, which is Ruichen Jin, Wei Chen, Agus Sudjianto (2005) <doi:10.1016/j.jspi.2004.02.014>. They provided a new form of phi_p criterion, which does not lose the space-filling property and simultaneously reduces the computational complexity when evaluating (or re-evaluating) an LHD. Their new phi_p criterion is a fundamental component of our many functions. Besides, the computation nature of the new phi_p criterion enables our functions to have less CPU time.
Author: Hongzhi Wang, Qian Xiao, Abhyuday Mandal
Maintainer: Hongzhi Wang <hw34508@uga.edu>

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Package DTSg updated to version 0.2.0 with previous version 0.1.3 dated 2019-08-29

Title: A Class for Working with Time Series Based on 'data.table' and 'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing values, application of arbitrary aggregation as well as rolling window functions and automatic detection of periodicity. As it is mainly based on 'data.table', it is fast and - in combination with the 'R6' package - offers reference semantics. In addition to its native R6 interface, it provides an S3 interface inclusive an S3 wrapper method generator for those who prefer the latter.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>

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Package vtree updated to version 3.0.0 with previous version 2.0.0 dated 2019-05-15

Title: Display Information About Nested Subsets of a Data Frame
Description: A tool for calculating and drawing "variable trees". Variable trees display information about hierarchical subsets of a data frame defined by values of categorical variables.
Author: Nick Barrowman
Maintainer: Nick Barrowman <nbarrowman@cheo.on.ca>

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Package pkgfilecache updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-07

Title: Download and Manage Optional Package Data
Description: Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>

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Package gdtools updated to version 0.2.1 with previous version 0.2.0 dated 2019-09-03

Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre], Hadley Wickham [aut], Lionel Henry [aut], Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>), Yixuan Qiu [ctb], R Core Team [cph] (Cairo code from X11 device), RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between gdtools versions 0.2.0 dated 2019-09-03 and 0.2.1 dated 2019-10-14

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Package fungible updated to version 1.92 with previous version 1.91 dated 2019-10-07

Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications: Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>. Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights. Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>. Waller, N. G. (2016). Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>. Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF) covariance matrix of standardized regression coefficients: theoretical extensions and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>. Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre], Jeff Jones [ctb], Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>

Diff between fungible versions 1.91 dated 2019-10-07 and 1.92 dated 2019-10-14

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Package enrichwith updated to version 0.3 with previous version 0.2 dated 2019-01-11

Title: Methods to Enrich R Objects with Extra Components
Description: Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm', 'glm' and 'betareg'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package coxmeg updated to version 1.0.8 with previous version 1.0.7 dated 2019-09-16

Title: Cox Mixed-Effects Model for Genome-Wide Association Studies
Description: Fast algorithms for fitting a Cox mixed-effects model for e.g., genome-wide association studies. See Liang He and Alexander Kulminski (2019) <doi:10.1101/729285>.
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>

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Package rtmpt updated to version 0.1-17 with previous version 0.1-16 dated 2019-10-08

Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it to estimate process completion times and encoding plus motor execution times next to the process probabilities of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre], Karl C. Klauer [cph, aut, ctb, ths], Henrik Singmann [aut, ctb, cph], Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>

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Package NFP updated to version 0.99.3 with previous version 0.99.2 dated 2016-11-21

Title: Network Fingerprint Framework in R
Description: An implementation of the network fingerprint framework that introduced in paper "Network fingerprint: a knowledge-based characterization of biomedical networks" (Cui, 2015) <doi:10.1038/srep13286>. This method worked by making systematic comparisons to a set of well-studied "basic networks", measuring both the functional and topological similarity. A biological could be characterized as a spectrum-like vector consisting of similarities to basic networks. It shows great potential in biological network study.
Author: Yang Cao [aut, cre], Fei Li [aut]
Maintainer: Yang Cao <yiluheihei@gmail.com>

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Package KSPM updated to version 0.2.0 with previous version 0.1.2 dated 2019-04-07

Title: Kernel Semi-Parametric Models
Description: To fit the kernel semi-parametric model and its extensions. It allows multiple kernels and unlimited interactions in the same model. Coefficients are estimated by maximizing a penalized log-likelihood; penalization terms and hyperparameters are estimated by minimizing leave-one-out error. It includes predictions with confidence/prediction intervals, statistical tests for the significance of each kernel, a procedure for variable selection and graphical tools for diagnostics and interpretation of covariate effects. Currently it is implemented for continuous dependent variables. The package is based on the paper of Liu et al. (2007), <doi:10.1111/j.1541-0420.2007.00799.x>.
Author: Catherine Schramm [aut, cre], Aurelie Labbe [ctb], Celia M. T. Greenwood [ctb]
Maintainer: Catherine Schramm <cath.schramm@gmail.com>

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Package tsBSS updated to version 0.5.5 with previous version 0.5.4 dated 2019-10-09

Title: Blind Source Separation and Supervised Dimension Reduction for Time Series
Description: Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>

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Package rasterImage updated to version 0.4.0 with previous version 0.3.0 dated 2016-09-09

Title: An Improved Wrapper of image()
Description: This is a wrapper function for image(), which makes reasonable raster plots with nice axis and other useful features.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>

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Package interep updated to version 0.3.0 with previous version 0.2.0 dated 2018-11-10

Title: Interaction Analysis of Repeated Measure Data
Description: Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Fei Zhou, Jie Ren, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Fei Zhou <feiz@ksu.edu>

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Package dynamichazard updated to version 0.6.6 with previous version 0.6.5 dated 2019-04-05

Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using state space models. The first implemented model is described in Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994) <doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the Extended Kalman filter is replaced by an unscented Kalman filter and other options including particle filters. The implemented particle filters support more general state space models.
Author: Benjamin Christoffersen [cre, aut], Alan Miller [cph], Anthony Williams [cph], Boost developers [cph], R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

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 NAMESPACE                                                                      |    1 
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 R/ddhazard.R                                                                   |    3 
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 src/BLAS_LAPACK/dchur.f                                                        |   29 
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 src/Makevars.win                                                               |    1 
 src/PF.cpp                                                                     |   46 
 src/PF/PF_data.h                                                               |   12 
 src/PF/PF_logger.cpp                                                           |   40 
 src/PF/PF_score_n_Hess.cpp                                                     |  502 +++++-----
 src/PF/PF_utils.cpp                                                            |   16 
 src/PF/PF_utils.h                                                              |   28 
 src/PF/PFs.cpp                                                                 |   42 
 src/PF/cond_approx.cpp                                                         |  159 +--
 src/PF/cond_approx.h                                                           |   23 
 src/PF/covarmat.cpp                                                            |    3 
 src/PF/dists.cpp                                                               |   16 
 src/PF/est_params.h                                                            |    4 
 src/PF/est_params_dens.cpp                                                     |   32 
 src/PF/importance_samplers.cpp                                                 |   27 
 src/PF/particles.h                                                             |    2 
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 src/PF/resamplers.cpp                                                          |    4 
 src/PF/smoother_output.cpp                                                     |    2 
 src/PF_fixed_effects.cpp                                                       |   31 
 src/R_BLAS_LAPACK.h                                                            |    3 
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 src/arma_n_rcpp.h                                                              |    9 
 src/ddhazard_fit.cpp                                                           |    2 
 src/family.h                                                                   |    6 
 src/parallel_glm.cpp                                                           |    4 
 tests/testthat.R                                                               |    4 
 tests/testthat/helper.R                                                        |   12 
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Package tidytransit updated to version 0.6 with previous version 0.5.2 dated 2019-08-25

Title: Read, Validate, Analyze, and Map Files in the General Transit Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Flavio Poletti [aut], Tom Buckley [aut, cre], Danton Noriega-Goodwin [aut], Mark Padgham [aut], Angela Li [ctb], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], Kearey Smith [ctb], Dave Vautin [ctb], Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>

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Package ConR updated to version 1.2.4 with previous version 1.2.3 dated 2019-05-07

Title: Computation of Parameters Used in Preliminary Assessment of Conservation Status
Description: Multi-species estimation of geographical range parameters for preliminary assessment of conservation status following Criterion B of the International Union for Conservation of Nature (IUCN, see <http://www.iucnredlist.org>).
Author: Gilles Dauby
Maintainer: Gilles Dauby <gildauby@gmail.com>

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Package Exact updated to version 2.0 with previous version 1.7 dated 2016-10-22

Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables.
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

Diff between Exact versions 1.7 dated 2016-10-22 and 2.0 dated 2019-10-14

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Package CNVScope updated to version 2.7.7 with previous version 2.7.2.5 dated 2019-09-22

Title: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>

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Sun, 13 Oct 2019

Package StratifiedMedicine updated to version 0.2.0 with previous version 0.1.3 dated 2019-09-04

Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine. Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate models (counterfactual patient-level quantities, for example the individual treatment effect), (3) subgroup identification models (find subsets of patients with similar treatment effects), and (4) parameter estimation and inference (for the overall population and discovered subgroups). These tools can directly feed into stratified medicine algorithms including PRISM (patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019 (in progress)). PRISM is a flexible and general framework which accepts user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>

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Package cgam updated to version 1.15 with previous version 1.14 dated 2019-05-01

Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Liao X, Meyer MC (2019)<doi: 10.18637/jss.v089.i05> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>

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Package EpiILMCT updated to version 1.1.4 with previous version 1.1.3 dated 2019-04-17

Title: Continuous Time Distance-Based and Network-Based Individual Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry [aut, cre], Rob Deardon [aut, ths], Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>

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Package idiogramFISH updated to version 1.6.3 with previous version 1.6.1 dated 2019-10-04

Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>

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Package wrapr updated to version 1.9.2 with previous version 1.9.1 dated 2019-10-06

Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), and more.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package fields updated to version 9.9 with previous version 9.8-6 dated 2019-08-19

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research. See the Fields URL for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut], Florian Gerber [aut], Matthew Iverson [aut], University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>

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Package raceland updated to version 1.0.3 with previous version 1.0.0 dated 2019-09-04

Title: Pattern-Based Zoneless Method for Analysis and Visualization of Racial Topography
Description: Implements a computational framework for a pattern-based, zoneless analysis, and visualization of (ethno)racial topography. It is a reimagined approach for analyzing residential segregation and racial diversity based on the concept of 'landscape’ used in the domain of landscape ecology.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>), Anna Dmowska [aut], Tomasz Stepinski [aut]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package noweb updated to version 1.1-2 with previous version 1.0-4 dated 2013-03-27

Title: The 'noweb' System for R
Description: The noweb system for source code, implemented in R.
Author: Terry Therneau
Maintainer: Terry Therneau <terry.therneau@mayo.edu>

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Package glmmEP updated to version 1.0-3 with previous version 1.0-2 dated 2019-09-16

Title: Generalized Linear Mixed Model Analysis via Expectation Propagation
Description: Approximate frequentist inference for generalized linear mixed model analysis with expectation propagation used to circumvent the need for multivariate integration. In this version, the random effects can be any reasonable dimension. However, only probit mixed models with one level of nesting are supported. The methodology is described in Hall, Johnstone, Ormerod, Wand and Yu (2018) <arXiv:1805.08423v1>.
Author: Matt P. Wand [aut, cre], James C.F. Yu [aut]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>

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Package redland updated to version 1.0.17-11 with previous version 1.0.17-10 dated 2018-07-20

Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Jeroen Ooms [aut], Carl Boettiger [aut], Scott Chamberlain [aut], David Beckett [cph], University of Bristol [cph], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>

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Package interpret updated to version 0.1.22 with previous version 0.1.21 dated 2019-10-10

Title: Fit Interpretable Models and Explain Blackbox Machine Learning
Description: Machine Learning package for training interpretable models and explaining blackbox systems. Historically, the most intelligible models were not very accurate, and the most accurate models were not intelligible. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and intelligibility. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>

Diff between interpret versions 0.1.21 dated 2019-10-10 and 0.1.22 dated 2019-10-13

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Package clues updated to version 0.6.1 with previous version 0.5.9 dated 2016-10-14

Title: Clustering Method Based on Local
Description: We developed the clues R package to provide functions for automatically estimating the number of clusters and getting the final cluster partition without any input parameter except the stopping rule for convergence. The package also provides functions to evaluate and compare the performances of partitions of a data set both numerically and graphically.
Author: Fang Chang [aut, ctb], Weiliang Qiu [aut, cre], Vincent Carey [aut, ctb], Ruben H. Zamar [aut, ctb], Ross Lazarus [aut, ctb], Xiaogang Wang [aut, ctb]
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>

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Package tmle updated to version 1.4.0 with previous version 1.3.0-2 dated 2019-02-20

Title: Targeted Maximum Likelihood Estimation
Description: Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Author: Susan Gruber [aut, cre], Mark van der Laan [aut], Chris Kennedy [ctr]
Maintainer: Susan Gruber <sgruber@cal.berkeley.edu>

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Package BNSP updated to version 2.1.1 with previous version 2.1.0 dated 2019-05-24

Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for multivariate (and univariate) regression, with nonparametric models for the means, the variances and the correlation matrix.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>

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Package wyz.code.testthat updated to version 1.1.9 with previous version 1.1.6 dated 2019-08-28

Title: Wizardry Code Offensive Programming Test Generation
Description: Allows to generate automatically 'testthat' code files from offensive programming test cases. Generated test files are complete and ready to run. Using 'wyz.code.testthat' you will earn a lot of time, reduce the number of errors in test case production, be able to test immediately generated files without any need to view or modify them, and enter a zero time latency between code implementation and industrial testing. As with 'testthat', you may complete provided test cases according to your needs to push testing further, but this need is nearly void when using 'wyz.code.offensiveProgramming'. Refer to chapter 9 of Offensive Programming Book, Fabien GELINEAU (2019, ISBN:979-10-699-4075-8), to learn about details and get value from this package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>

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Package stplanr updated to version 0.4.0 with previous version 0.3.1 dated 2019-09-17

Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. Enables common transport planning tasks including: downloading and cleaning transport datasets; creating geographic "desire lines" from origin-destination (OD) data; route assignment, locally and via interfaces to routing services such as <http://cyclestreets.net/>; calculation of route segment attributes such as bearing and aggregate flow; and 'travel watershed' analysis. See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Richard Ellison [aut], Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Barry Rowlingson [ctb] (Author of overline), Nick Bearman [ctb] (Co-author of gclip), Nikolai Berkoff [ctb] (Co-author of line2route), Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10), Mark Padgham [ctb], Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

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Package flashlight updated to version 0.3.0 with previous version 0.2.0 dated 2019-09-18

Title: Shed Light on Black Box Machine Learning Models
Description: Shed light on black box machine learning models by the help of model performance, permutation variable importance (Fisher et al. (2018) <arxiv:1801.01489>), ICE profiles, partial dependence (Friedman J. H. (2001) <doi:10.1214/aos/1013203451>), accumulated local effects (Apley D. W. (2016) <arXiv:1612.08468>), further effects plots, and variable contribution breakdown for single observations (Gosiewska and Biecek (2019) <arxiv:1903.11420>). All tools are implemented to work with case weights and allow for stratified analysis. Furthermore, multiple flashlights can be combined and analyzed together.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package economiccomplexity updated to version 0.2.3 with previous version 0.2.2 dated 2019-09-17

Title: Methods Used in the Economic Complexity Literature
Description: A wrapper of different indices and networks commonly used in Economic Complexity to explore bipartite relations such as countries and their exported products. These methods are also useful for different kind of relations such as countries and their spoken languages. The functions within this package correspond to code implementations of the equations described in Hausmann, et al. (2005) <doi:10.3386/w11905>, Hausmann, et al. (2014) <doi:10.7551/mitpress/9647.001.0001>, and Mariani, et al. (2015) <doi:10.1140/epjb/e2015-60298-7>.
Author: Mauricio Vargas [aut, cre, cph] (<https://orcid.org/0000-0003-1017-7574>), Carlo Bottai [ctb] (improved the eigenvalues calculation), Diego Kozlowski [ctb] (provided initial RCA and proximity functions he used for his thesis), Mark Padgham [rev] (compared PRODY equations from different articles), Nico Pintar [rev] (suggested improvements to special cases in eigenvalues calculation), The World Bank [dtc], Open Trade Statistics [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>

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Package metacom updated to version 1.5.2 with previous version 1.5.1 dated 2018-08-17

Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas [aut, cre], Tom Pulliam [ctb]
Maintainer: Tad Dallas <tad.a.dallas@gmail.com>

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Sat, 12 Oct 2019

Package WVPlots updated to version 1.2.1 with previous version 1.2.0 dated 2019-10-04

Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'. Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package strucchange updated to version 1.5-2 with previous version 1.5-1 dated 2015-06-06

Title: Testing, Monitoring, and Dating Structural Changes
Description: Testing, monitoring and dating structural changes in (linear) regression models. strucchange features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>), Friedrich Leisch [aut], Kurt Hornik [aut], Christian Kleiber [aut], Bruce Hansen [ctb], Edgar C. Merkle [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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More information about strucchange at CRAN
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Package shinyglide updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-10

Title: Glide Component for Shiny Applications
Description: Insert Glide JavaScript component into Shiny applications for carousel or assistant-like user interfaces.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

Diff between shinyglide versions 0.1.1 dated 2019-07-10 and 0.1.2 dated 2019-10-12

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More information about shinyglide at CRAN
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Package BatchGetSymbols updated to version 2.5.4 with previous version 2.5.3 dated 2019-08-05

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between BatchGetSymbols versions 2.5.3 dated 2019-08-05 and 2.5.4 dated 2019-10-12

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 7 files changed, 29 insertions(+), 25 deletions(-)

More information about BatchGetSymbols at CRAN
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Package CollessLike updated to version 2.0 with previous version 1.0 dated 2018-04-03

Title: Distribution and Percentile of Sackin, Cophenetic and Colless-Like Balance Indices of Phylogenetic Trees
Description: Computation of Colless-Like, Sackin and cophenetic balance indices of a phylogenetic tree and study of the distribution of these balance indices under the alpha-gamma model. For more details see A. Mir, F. Rossello, L. Rotger (2013) <doi:10.1016/j.mbs.2012.10.005> and (2018) <doi:10.1371/journal.pone.0203401>, M. J. Sackin (1972) <doi:10.1093/sysbio/21.2.225>, D. H. Colless (1982) <doi:10.2307/2413420>.
Author: Arnau Mir, Francesc Rossello, Lucia Rotger
Maintainer: Lucia Rotger <lucia.rotger@uib.es>

Diff between CollessLike versions 1.0 dated 2018-04-03 and 2.0 dated 2019-10-12

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Package fusedest updated to version 1.3.1 with previous version 1.3 dated 2019-09-20

Title: Block Splitting Algorithm for Estimation with Fused Penalty Functions
Description: Provides methods fusedest_normal() and fusedest_logit() for carrying out block splitting algorithms for fused penalty estimation. For details, please see Tso-Jung Yen (2019) <doi.10618600.2019.1660178>.
Author: Tso-Jung Yen
Maintainer: Tso-Jung Yen <tjyen@stat.sinica.edu.tw>

Diff between fusedest versions 1.3 dated 2019-09-20 and 1.3.1 dated 2019-10-12

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 src/Rcpp_MaxEigenXTXrhoGTG.cpp   |    2 +-
 6 files changed, 13 insertions(+), 13 deletions(-)

More information about fusedest at CRAN
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