Wed, 09 Oct 2019

Package coveffectsplot updated to version 0.0.4 with previous version 0.0.3 dated 2019-02-25

Title: Produce Forest Plots to Visualize Covariate Effects
Description: Produce forest plots to visualize covariate effects using either the command line or an interactive 'Shiny' application.
Author: Samer Mouksassi [aut, cre] (<>), Dean Attali [ctb]
Maintainer: Samer Mouksassi <>

Diff between coveffectsplot versions 0.0.3 dated 2019-02-25 and 0.0.4 dated 2019-10-09

 DESCRIPTION                                  |    6 
 MD5                                          |   24                                      |    6 
 R/forest_plot.R                              |   25                                    |    2 
 build/vignette.rds                           |binary
 inst/doc/introduction_to_coveffectsplot.R    |   11 
 inst/doc/introduction_to_coveffectsplot.Rmd  |   13 
 inst/doc/introduction_to_coveffectsplot.html | 2673 ++++++++++++++++++++++++---
 inst/shiny/server.R                          |    3 
 inst/shiny/ui.R                              |   13 
 man/forest_plot.Rd                           |   22 
 vignettes/introduction_to_coveffectsplot.Rmd |   13 
 13 files changed, 2472 insertions(+), 339 deletions(-)

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Package sensitivity updated to version 1.16.2 with previous version 1.16.1 dated 2019-06-30

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Sebastien Da Veiga, Thibault Delage, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <>

Diff between sensitivity versions 1.16.1 dated 2019-06-30 and 1.16.2 dated 2019-10-09

 DESCRIPTION                |    8 
 MD5                        |   44 +-
 NAMESPACE                  |    2 
 NEWS                       |   10 
 R/nodeggplot.R             |  284 +++++++--------
 R/sb.R                     |    2 
 R/sensiFdiv.R              |    5 
 R/sensiHSIC.R              |  824 ++++++++++++++++++++++++++++++---------------
 R/sobolMultOut.R           |  232 ++++++------
 man/PoincareConstant.Rd    |    3 
 man/PoincareOptimal.Rd     |    3 
 man/sensiHSIC.Rd           |   76 +++-
 man/sensitivity-package.Rd |    8 
 man/shapleyPermEx.Rd       |    4 
 man/shapleyPermRand.Rd     |    4 
 man/shapleySubsetMc.Rd     |    2 
 man/sobol.Rd               |    6 
 man/sobolSmthSpl.Rd        |    6 
 man/sobolmara.Rd           |    2 
 man/sobolmartinez.Rd       |    3 
 man/sobolowen.Rd           |    2 
 man/soboltouati.Rd         |    3 
 man/support.Rd             |    4 
 23 files changed, 942 insertions(+), 595 deletions(-)

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New package intePareto with initial version 0.0.1
Package: intePareto
Type: Package
Title: Integrative Analysis of RNA-Seq and ChIP-Seq Data
Version: 0.0.1
Date: 2019-10-08
Authors@R: person(given = "Yingying", family = "Cao", role = c("aut", "cre"), email = "")
Description: Integrative analysis of gene expression (RNA-Seq data), and histone modification data for user-defined sets of histone marks (ChIP-Seq data) to discover consistent changes in genes between biological conditions. Additionally, Pareto optimization is used to prioritize genes based on the level of consistent changes in both RNA-Seq and ChIP-Seq data.
License: GPL (>= 2)
Depends: R (>= 3.6.0)
Imports: GenomicRanges, GenomeInfoDb, IRanges, GenomicAlignments, biomaRt, Rsamtools, rPref, DESeq2, apeglm
Suggests: knitr, rmarkdown
LazyLoad: yes
NeedsCompilation: no
ByteCompile: true
Encoding: UTF-8
Packaged: 2019-10-08 18:20:45 UTC; yingying
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Author: Yingying Cao [aut, cre]
Maintainer: Yingying Cao <>
Repository: CRAN
Date/Publication: 2019-10-09 16:10:02 UTC

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New package DAFOT with initial version 0.0.1
Package: DAFOT
Title: Detector of Active Flow on a Tree
Version: 0.0.1
Date: 2019-10-7
Author: Shulei Wang, T. Tony Cai and Hongzhe Li
Maintainer: Shulei Wang <>
Description: Quantitative comparison of microbial composition from different populations is a fundamental task in various microbiome studies. The main goal of this package is to provide a new method for two-sample testing for microbial compositional data by leveraging the phylogenetic tree information. Empirical evidence from real data sets suggests that the phylogenetic microbial composition difference between two populations is usually sparse. Motivated by this observation, this package implements a new maximum type test, Detector of Active Flow on a Tree (DAFOT). It is shown that DAFOT is particularly powerful against sparse phylogenetic composition difference and enjoys certain optimality. Chen, J., Bittinger, K., Charlson, E. S., Hoffmann, C., Lewis, J., Wu, G. D., Collman, R. G., Bushman, F. D., Li, H. (2012) <doi:10.1093/bioinformatics/bts342>.
Imports: tidytree, stats, methods, gtools, tibble, ape
Suggests: metagenomeFeatures
License: MIT+file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2019-10-09 14:54:15 UTC; shuleiwang
Repository: CRAN
Date/Publication: 2019-10-09 16:20:02 UTC

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New package YPPE with initial version 1.0.0
Package: YPPE
Title: Yang and Prentice Model with Piecewise Exponential Baseline Distribution
Version: 1.0.0
Authors@R: person(given = "Fabio", family = "Demarqui", email = "", role = c("aut", "cre"))
Description: Semiparametric modeling of lifetime data with crossing survival curves via Yang and Prentice model with piecewise exponential baseline distribution curves. Details about the model can be found in Demarqui and Mayrink (2019) <arXiv:1910.02406>. Model fitting carried out via likelihood-based and Bayesian approaches. The package also provides point and interval estimation for the crossing survival times.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.4.0), survival
Imports: methods, Formula, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.0.0)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>=, rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2019-10-08 12:27:58 UTC; fndemarqui
Author: Fabio Demarqui [aut, cre]
Maintainer: Fabio Demarqui <>
Repository: CRAN
Date/Publication: 2019-10-09 15:20:05 UTC

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New package VARshrink with initial version 0.3.1
Package: VARshrink
Title: Shrinkage Estimation Methods for Vector Autoregressive Models
Version: 0.3.1
Authors@R: c( person("Namgil", "Lee", role = c("aut", "cre"), email = "", comment = c(ORCID = "0000-0003-0593-9028")), person("Heon Young", "Yang", role = c("ctb"), email = ""), person("Sung-Ho", "Kim", role = c("aut"), email = "") )
Description: Vector autoregressive (VAR) model is a fundamental and effective approach for multivariate time series analysis. Shrinkage estimation methods can be applied to high-dimensional VAR models with dimensionality greater than the number of observations, contrary to the standard ordinary least squares method. This package is an integrative package delivering nonparametric, parametric, and semiparametric methods in a unified and consistent manner, such as the multivariate ridge regression in Golub, Heath, and Wahba (1979) <doi:10.2307/1268518>, a James-Stein type nonparametric shrinkage method in Opgen-Rhein and Strimmer (2007) <doi:10.1186/1471-2105-8-S2-S3>, and Bayesian estimation methods using noninformative and informative priors in Lee, Choi, and S.-H. Kim (2016) <doi:10.1016/j.csda.2016.03.007> and Ni and Sun (2005) <doi:10.1198/073500104000000622>.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: vars (>= 1.5.3), ars (>= 0.6), corpcor (>= 1.6.9), strucchange, stats, MASS, mvtnorm
Suggests: knitr, rmarkdown, rticles, kableExtra
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-07 13:31:17 UTC; namgi
Author: Namgil Lee [aut, cre] (<>), Heon Young Yang [ctb], Sung-Ho Kim [aut]
Maintainer: Namgil Lee <>
Repository: CRAN
Date/Publication: 2019-10-09 15:10:03 UTC

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New package rayrender with initial version 0.4.0
Package: rayrender
Type: Package
Title: Build and Raytrace 3D Scenes
Version: 0.4.0
Authors@R: c(person("Tyler", "Morgan-Wall", email = "", role = c("aut", "cph", "cre"), comment = c(ORCID = "0000-0002-3131-3814")), person("Syoyo", "Fujita", role=c("ctb", "cph")), person("Melissa", "O'Neill", email = "", role = c("ctb", "cph")))
Maintainer: Tyler Morgan-Wall <>
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <>.
License: GPL-3
Copyright: file inst/COPYRIGHTS
Imports: Rcpp (>= 1.0.0), parallel, assertthat, tibble, magrittr, purrr, png, raster
LinkingTo: Rcpp, RcppThread, progress
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-08 01:49:10 UTC; tyler
Author: Tyler Morgan-Wall [aut, cph, cre] (<>), Syoyo Fujita [ctb, cph], Melissa O'Neill [ctb, cph]
Repository: CRAN
Date/Publication: 2019-10-09 15:30:02 UTC

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New package gwsem with initial version 0.1.2
Package: gwsem
Type: Package
Title: Genome-Wide Structural Equation Modeling
Version: 0.1.2
Authors@R: c(person(c("Joshua", "N."), "Pritikin", email="", role=c("aut", 'cre')), person("Bradley", "Verhulst", role="cph", email=""), person("Gavin", "Band", role="cph"), person("Yann", "Collet", role="cph"), person("Facebook, Inc.", role="cph"), person("Yuta", "Mori", role="cph"), person("Shaun", "Purcell", role="cph"), person("Christopher", "Chang", role="cph"), person("Wojciech", "Mula", role="cph"), person("Kim", "Walisch", role="cph"))
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.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Language: en-US
LinkingTo: BH (>= 1.69.0-1)
Depends: R (>= 3.5), OpenMx (>= 2.14)
Imports: data.table, methods
Suggests: testthat (>= 2.1.0), MASS, covr, knitr, rmarkdown, qqman
RoxygenNote: 6.1.1
SystemRequirements: GNU make
NeedsCompilation: yes
VignetteBuilder: knitr
Packaged: 2019-10-09 14:28:13 UTC; joshua
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 <>
Repository: CRAN
Date/Publication: 2019-10-09 15:20:02 UTC

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New package forecastML with initial version 0.5.0
Package: forecastML
Type: Package
Title: Time Series Forecasting with Machine Learning Methods
Version: 0.5.0
Author: Nickalus Redell
Maintainer: Nickalus Redell <>
Description: The purpose of 'forecastML' is to simplify the process of multi-step-ahead direct forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: tidyr (>= 0.8.1), dplyr (>= 0.7.8), rlang (>= 0.4.0), magrittr (>= 1.5), stringr (>= 1.4.0), lubridate (>= 1.7.4), ggplot2 (>= 3.1.0), future.apply (>= 1.3.0), methods, purrr (>= 0.3.2)
RoxygenNote: 6.1.1
Collate: 'fill_gaps.R' 'create_windows.R' 'lagged_df.R' 'return_error.R' 'return_hyper.R' 'train_model.R' 'data_seatbelts.R' 'data_buoy.R' 'data_buoy_gaps.R'
Depends: R (>= 3.4.0)
Suggests: glmnet (>= 2.0.16), DT (>= 0.5), knitr (>= 1.22), rmarkdown (>= 1.12.6), xgboost (>= 0.82.1), randomForest (>= 4.6.14), testthat (>= 2.2.1), covr (>= 3.3.1)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-08 06:29:23 UTC; REDELLN
Repository: CRAN
Date/Publication: 2019-10-09 15:30:05 UTC

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New package ushr with initial version 0.1.0
Package: ushr
Type: Package
Title: Understanding Suppression of HIV
Version: 0.1.0
Date: 2019-09-26
Authors@R: c(person("Sinead E.", "Morris", role = c("aut", "cre"), email = "", comment = c(ORCID = "0000-0001-8626-1698")), person("Luise", "Dziobek-Garrett", role = "ctb"), person("Andrew", "Yates", role = "ctb"))
Maintainer: Sinead E. Morris <>
Description: Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: dplyr (>=, tidyr (>= 0.8.3), ggplot2 (>= 3.1.1), stats
Suggests: knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 2.2.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-08 01:42:18 UTC; sineadmorris
Author: Sinead E. Morris [aut, cre] (<>), Luise Dziobek-Garrett [ctb], Andrew Yates [ctb]
Repository: CRAN
Date/Publication: 2019-10-09 15:00:02 UTC

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Package tsBSS updated to version 0.5.4 with previous version 0.5.3 dated 2019-09-03

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 <>

Diff between tsBSS versions 0.5.3 dated 2019-09-03 and 0.5.4 dated 2019-10-09

 DESCRIPTION          |    8 ++++----
 MD5                  |    8 ++++----
 R/gSOBI.R            |   31 +++++++++++--------------------
 inst/ChangeLog       |    3 +++
 man/tsBSS-package.Rd |    8 ++++----
 5 files changed, 26 insertions(+), 32 deletions(-)

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New package tfautograph with initial version 0.1.0
Package: tfautograph
Title: Autograph R for 'Tensorflow'
Version: 0.1.0
Authors@R: person("Tomasz", "Kalinowski", email = "", role = c("aut", "cre"))
Description: Translate R control flow expressions into 'Tensorflow' graphs.
SystemRequirements: TensorFlow (
Depends: R (>= 3.5.0)
Imports: tensorflow, reticulate,
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: rlang, spelling, testthat (>= 2.1.0), knitr, tfdatasets, magrittr, rmarkdown, keras
Language: en-US
NeedsCompilation: no
Packaged: 2019-10-07 22:22:24 UTC; tomasz
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <>
Repository: CRAN
Date/Publication: 2019-10-09 14:40:02 UTC

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New package simsl with initial version 0.1.0
Package: simsl
Type: Package
Title: Single-Index Models with a Surface-Link
Version: 0.1.0
Author: Park, H., Petkova, E., Tarpey, T., Ogden, R.T.
Maintainer: Hyung Park <>
Description: An implementation of a single-index regression for optimizing individualized dose rules from an observational study. To model interaction effects between baseline covariates and a treatment variable defined on a continuum, we employ two-dimensional penalized spline regression on an index-treatment domain, where the index is defined as a linear combination of the covariates (a single-index). An unspecified main effect for the covariates is allowed. A unique contribution of this work is in the parsimonious single-index parametrization specifically defined for the interaction effect term. We refer to Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1016/j.jspi.2019.05.008> (for the case of a discrete treatment) and Park, Petkova, Tarpey, and Ogden (2019) "A single-index model with a surface-link for optimizing individualized dose rules" (pre-print) for detail of the method. The main function of this package is simsl().
License: GPL-3
Imports: mgcv, stats
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-08 01:04:28 UTC; parkh15
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2019-10-09 14:50:06 UTC

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New package posterdown with initial version 1.0
Package: posterdown
Title: Generate PDF Conference Posters Using R Markdown
Version: 1.0
Authors@R: c(person(given = "Brent", family = "Thorne", role = c("aut", "cre"), email = "", comment = c(ORCID = "0000-0002-1099-3857")), person(given = "Peter", family = "Higgins", role = "ctb"), person(given = "Shea", family = "Connell", role = "ctb"), person(given = "Luke", family = "Johnston", role = "ctb"))
Description: Use 'rmarkdown' and 'pagedown' to generate HTML and PDF conference posters.
License: MIT + file LICENSE
Imports: pagedown, rmarkdown, yaml
Suggests: knitr
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-09 13:53:33 UTC; thornux
Author: Brent Thorne [aut, cre] (<>), Peter Higgins [ctb], Shea Connell [ctb], Luke Johnston [ctb]
Maintainer: Brent Thorne <>
Repository: CRAN
Date/Publication: 2019-10-09 14:30:02 UTC

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Package politeness updated to version 0.4.0 with previous version 0.3.3 dated 2019-10-01

Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness (Brown & Levinson, 1987 <>; Danescu-Niculescu-Mizil et al., 2013 <arXiv:1306.6078>; Voigt et al., 2017 <doi:10.1073/pnas.1702413114>). We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <>

Diff between politeness versions 0.3.3 dated 2019-10-01 and 0.4.0 dated 2019-10-09

 DESCRIPTION              |    6 +++---
 MD5                      |   20 ++++++++++++--------
 NAMESPACE                |    1 +
 R/data.R                 |   22 ++++++++++++++++++++--
 R/politeness.R           |    2 +-
 R/receptiveness.R        |only
 data/receptTrain.rdata   |only
 inst/doc/politeness.html |   10 +++++-----
 man/bowl_offers.Rd       |    2 +-
 man/phone_offers.Rd      |    2 +-
 man/politeness.Rd        |    2 +-
 man/receptTrain.Rd       |only
 man/receptiveness.Rd     |only
 13 files changed, 45 insertions(+), 22 deletions(-)

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New package mniw with initial version 1.0
Package: mniw
Type: Package
Title: The Matrix-Normal Inverse-Wishart Distribution
Version: 1.0
Date: 2019-10-06
Authors@R: c(person("Martin", "Lysy", role = c("aut", "cre"), email = ""), person("Bryan", "Yates", role = "aut"))
Description: Density evaluation and random number generation for the Matrix-Normal Inverse-Wishart (MNIW) distribution, as well as the the Matrix-Normal, Matrix-T, Wishart, and Inverse-Wishart distributions. Core calculations are implemented in a portable (header-only) C++ library, with matrix manipulations using the 'Eigen' library for linear algebra. Also provided is a Gibbs sampler for Bayesian inference on a random-effects model with multivariate normal observations.
License: GPL-3
Depends: R (>= 2.10)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppEigen
LazyData: true
Suggests: testthat, knitr, rmarkdown
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-10-09 13:43:27 UTC; mlysy
Author: Martin Lysy [aut, cre], Bryan Yates [aut]
Maintainer: Martin Lysy <>
Repository: CRAN
Date/Publication: 2019-10-09 14:20:02 UTC

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Package geomorph updated to version 3.1.3 with previous version 3.1.2 dated 2019-05-20

Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Author: Dean Adams [aut, cre], Michael Collyer [aut], Antigoni Kaliontzopoulou [aut]
Maintainer: Dean Adams <>

Diff between geomorph versions 3.1.2 dated 2019-05-20 and 3.1.3 dated 2019-10-09

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 NAMESPACE                         |    1                           | 1187 ++++++++++++-------------
 R/build.template.r                |    3 
 R/compare.CR.R                    |only
 R/compare.pls.r                   |   16 
 R/define.sliders.r                |    4 
 R/digit.fixed.r                   |    3 
 R/digitsurface.r                  |    3 
 R/fixed.angle.r                   |    5 
 R/         |   36 
 R/geomorph.utils.r                | 1766 +++++++++++++++++++-------------------
 R/plotRefToTarget.r               |    2 
 R/plotspec.r                      |    3 
 R/read.ply.r                      |    4 
 R/           |    5 
 R/warpRefMesh.r                   |    5 
 build/vignette.rds                |binary
 inst/doc/geomorph.assistance.html |   36 
 inst/doc/geomorph.digitize3D.html |   10 
 inst/doc/geomorph.functions.html  |    8 
 man/compare.CR.Rd                 |only
 man/compare.pls.Rd                |    7 
 man/define.sliders.Rd             |    4 
 man/mshape.Rd                     |    2 
 man/read.ply.Rd                   |    4 
 27 files changed, 1629 insertions(+), 1563 deletions(-)

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New package fpp3 with initial version 0.1
Package: fpp3
Title: Data for "Forecasting: Principles and Practice" (3rd Edition)
Version: 0.1
Authors@R: c(person(given = "Rob", family = "Hyndman", role = c("aut", "cre", "cph"), email = "", comment = c(ORCID = "0000-0002-2140-5352")), person(given = "George", family = "Athanasopoulos", role = "ctb"), person(given = "Mitchell", family = "O'Hara-Wild", role = "ctb"), person(given = "RStudio", role = c("cph")))
Description: All data sets required for the examples and exercises in the book "Forecasting: principles and practice" by Rob J Hyndman and George Athanasopoulos <>. All packages required to run the examples are also loaded.
License: GPL-3
Depends: R (>= 3.2)
Imports: cli (>= 1.0.0), crayon (>= 1.3.4), dplyr (>= 0.7.4), fable (>= 0.1.0), fabletools (>= 0.1.0), feasts (>=, ggplot2 (>= 3.1.1), lubridate (>= 1.7.4), magrittr (>= 1.5), purrr (>= 0.2.4), rstudioapi (>= 0.7), tibble (>= 1.4.2), tidyr (>= 0.8.3), tsibble (>= 0.8.2), tsibbledata (>= 0.1.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-08 01:20:20 UTC; hyndman
Author: Rob Hyndman [aut, cre, cph] (<>), George Athanasopoulos [ctb], Mitchell O'Hara-Wild [ctb], RStudio [cph]
Maintainer: Rob Hyndman <>
Repository: CRAN
Date/Publication: 2019-10-09 15:00:05 UTC

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New package details with initial version 0.1.0
Package: details
Title: Create Details HTML Tag for Markdown and Package Documentation
Version: 0.1.0
Authors@R: person(given = "Jonathan", family = "Sidi", role = c("aut", "cre"), email = "")
Description: Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Depends: R (>= 3.2.0)
Imports: utils, clipr, magrittr, withr, xml2, httr, png
Suggests: sessioninfo, tibble, knitr, testthat, rmarkdown, covr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-07 22:54:47 UTC; yonis
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <>
Repository: CRAN
Date/Publication: 2019-10-09 14:50:13 UTC

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Package cmprsk updated to version 2.2-9 with previous version 2.2-8 dated 2019-05-27

Title: Subdistribution Analysis of Competing Risks
Description: Estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154 <DOI:10.1214/aos/1176350951>, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509, <DOI:10.1080/01621459.1999.10474144>.
Author: Bob Gray <>
Maintainer: Bob Gray <>

Diff between cmprsk versions 2.2-8 dated 2019-05-27 and 2.2-9 dated 2019-10-09

 DESCRIPTION          |   10 +++++-----
 MD5                  |    8 ++++----
 R/cmprsk.R           |    5 ++++-
 tests/test.R         |    6 ++++--
 tests/ |   15 ++++++---------
 5 files changed, 23 insertions(+), 21 deletions(-)

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New package Ryacas0 with initial version 0.4.2
Package: Ryacas0
Version: 0.4.2
Title: Legacy 'Ryacas' (Interface to 'Yacas' Computer Algebra System)
Authors@R: c( person(given = "Mikkel Meyer", family = "Andersen", email = "", role = c("aut", "cre", "cph")), person(given = "Rob", family = "Goedman", email = "", role = c("aut", "cph")), person(given = "Gabor", family = "Grothendieck", email = "", role = c("aut", "cph")), person(given = "Søren", family = "Højsgaard", email = "", role = c("aut", "cph")), person(given = "Grzegorz", family = "Mazur", email = "", role = c("aut", "cph")), person(given = "Ayal", family = "Pinkus", email = "", role = c("aut", "cph")), person(given = "Nemanja", family = "Trifunovic", role = c("cph"), comment = "UTF-8 part of yacas (src/yacas/include/yacas/utf8*)") )
Maintainer: Mikkel Meyer Andersen <>
Encoding: UTF-8
Description: A legacy version of 'Ryacas', an interface to the 'yacas' computer algebra system (<>).
Depends: R (>= 3.3.0)
Imports: methods, Rcpp (>= 0.12.0), stats, settings, xml2
LinkingTo: Rcpp
Suggests: devtools, exams, knitr, Matrix, pkgload, rmarkdown, igraph, testthat
License: GPL-2
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-10-07 20:06:49 UTC; mikl
Author: Mikkel Meyer Andersen [aut, cre, cph], Rob Goedman [aut, cph], Gabor Grothendieck [aut, cph], Søren Højsgaard [aut, cph], Grzegorz Mazur [aut, cph], Ayal Pinkus [aut, cph], Nemanja Trifunovic [cph] (UTF-8 part of yacas (src/yacas/include/yacas/utf8*))
Repository: CRAN
Date/Publication: 2019-10-09 13:40:02 UTC

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Package RcppArmadillo updated to version 0.9.800.1.0 with previous version 0.9.700.2.0 dated 2019-09-02

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <>

Diff between RcppArmadillo versions 0.9.700.2.0 dated 2019-09-02 and 0.9.800.1.0 dated 2019-10-09

 RcppArmadillo-0.9.700.2.0/RcppArmadillo/R/unit.test.R                                             |only
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 RcppArmadillo-0.9.800.1.0/RcppArmadillo/DESCRIPTION                                               |   12 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/MD5                                                       |  125 -
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/R/RcppExports.R                                           |    8 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/                                                 |   25 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/configure                                                 |   12 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/                                              |   12 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/NEWS.Rd                                              |   20 
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 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf                   |binary
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/RcppArmadilloSugar.h                         |   11 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo                                    |    1 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/Base_bones.hpp                |   19 
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 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp                 |    2 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp                  |   14 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp                 |    2 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp                  |   14 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp              |   19 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_meat.hpp               |   76 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp              |    2 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp              |    6 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp              |   70 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp               |  988 ++++++++--
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/band_helper.hpp               |    6 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp            |    1 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp                     |    4 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/def_lapack.hpp                |  232 ++
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/fn_solve.hpp                  |   92 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/fn_spsolve.hpp                |   25 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/glue_polyfit_meat.hpp         |    2 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp          |   45 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp           |  237 ++
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/op_cond_meat.hpp              |   23 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/strip.hpp                     |   44 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_slices_bones.hpp |    6 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_slices_meat.hpp  |   63 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/sympd_helper.hpp              |    4 
 RcppArmadillo-0.9.800.1.0/RcppArmadillo/inst/include/armadillo_bits/translate_lapack.hpp          |  241 ++
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 46 files changed, 2199 insertions(+), 501 deletions(-)

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Package pkgbuild updated to version 1.0.6 with previous version 1.0.5 dated 2019-08-26

Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], RStudio [cph]
Maintainer: Jim Hester <>

Diff between pkgbuild versions 1.0.5 dated 2019-08-26 and 1.0.6 dated 2019-10-09

 DESCRIPTION              |    6 +-
 MD5                      |   44 ++++++++---------
 NAMESPACE                |   78 +++++++++++++++---------------                  |    7 ++
 R/rtools-config.R        |    3 -
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 man/clean_dll.Rd         |   34 ++++++-------
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 man/compiler_flags.Rd    |   60 +++++++++++------------
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 man/has_compiler.Rd      |   64 ++++++++++++-------------
 man/has_latex.Rd         |   28 +++++-----
 man/has_rtools.Rd        |   90 +++++++++++++++++------------------
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 man/pkg_has_src.Rd       |   28 +++++-----
 man/pkg_links_to_rcpp.Rd |   30 +++++------
 man/pkgbuild_process.Rd  |   92 ++++++++++++++++++------------------
 man/rcmd_build_tools.Rd  |   70 +++++++++++++--------------
 man/with_debug.Rd        |   78 +++++++++++++++---------------
 man/without_compiler.Rd  |   38 +++++++-------
 23 files changed, 598 insertions(+), 565 deletions(-)

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Package pingr updated to version 1.2.0 with previous version 1.1.2 dated 2017-03-02

Title: Check if a Remote Computer is Up
Description: Check if a remote computer is up. It can either just call the system ping command, or check a specified TCP port.
Author: Gábor Csárdi [aut, cre]
Maintainer: Gábor Csárdi <>

Diff between pingr versions 1.1.2 dated 2017-03-02 and 1.2.0 dated 2019-10-09

 DESCRIPTION                |   15 +++----
 MD5                        |   21 +++++----
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 tests/testthat/test-icmp.r |    2 
 tests/testthat/test-tcp.r  |    4 -
 12 files changed, 131 insertions(+), 78 deletions(-)

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New package macs with initial version 1.0
Package: macs
Type: Package
Title: Recursive Partitioning Based Multivariate Adaptive Regression Models, Classification Trees, Survival Trees
Version: 1.0
Author: Heping Zhang, Yihao Lu, Haixu Ma, Mingliang Ma, Yidong Zhou, Qi Yu
Maintainer: Qi Yu <>
Description: Implements recursive partitioning based, nonparametric methods for high dimensional regression and classification. Depending on the aims of data analysis as well as the structures of the data, macs provides three major functions: multivariate adaptive regression models, classification trees and survival trees. A list of references for this package is, Zhang, H. (1997) <doi:10.1080/10618600.1997.10474728>, Zhang, H. et al. (1999) <ISBN:978-1-4757-3027-2>, Zhang, H. et al. (2014) <doi:10.1002/gepi.21843>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-07 19:49:45 UTC; Frederick Yu
Repository: CRAN
Date/Publication: 2019-10-09 13:30:03 UTC

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New package ltsspca with initial version 0.1.0
Package: ltsspca
Type: Package
Title: Sparse Principal Component Based on Least Trimmed Squares
Version: 0.1.0
Date: 2019-09-13
Authors@R: c( person(given="Yixin",family="Wang", role = c("aut","cre"), email=""), person(given="Stefan",family="Van Aelst", role = c("aut"), email=""), person(given="Holger",family="Cevallos Valdiviezo",role=c("ctb"), comment = "Original R code for the LTS-PCA algorithm"), person(given="Tom",family="Reynkens",role=c("ctb"), comment = "Original R code for angle in the rospca package") )
Depends: R (>= 3.2.0)
Maintainer: Yixin Wang <>
Description: Implementation of robust and sparse PCA algorithm of Wang and Van Aelst (2019) <DOI:10.1080/00401706.2019.1671234>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: yes
VignetteBuilder: knitr
Suggests: robustbase, rrcov, stats, mvtnorm, graphics, knitr, rmarkdown, testthat
Imports: Rcpp (>= 1.0.1),pracma
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-07 19:44:19 UTC; wangy
Author: Yixin Wang [aut, cre], Stefan Van Aelst [aut], Holger Cevallos Valdiviezo [ctb] (Original R code for the LTS-PCA algorithm), Tom Reynkens [ctb] (Original R code for angle in the rospca package)
Repository: CRAN
Date/Publication: 2019-10-09 13:20:02 UTC

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Package GADMTools updated to version 3.7-2 with previous version 3.7-1 dated 2019-06-26

Title: Easy Use of 'GADM' Maps
Description: Manipulate, assemble, export <> maps. Create 'choropleth', 'isopleth', dots plot, proportional dots, dot-density and more.
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <>

Diff between GADMTools versions 3.7-1 dated 2019-06-26 and 3.7-2 dated 2019-10-09

 DESCRIPTION                                     |    8 +--
 MD5                                             |   25 +++++-----
 NAMESPACE                                       |    1 
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 R/20_gadm_sf_core.R                             |   41 +++++++++++++++++
 build/vignette.rds                              |binary
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 14 files changed, 189 insertions(+), 27 deletions(-)

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New package miscIC with initial version 0.1.0
Package: miscIC
Type: Package
Title: Misclassified Interval Censored Time-to-Event Data
Version: 0.1.0
Authors@R: person("Andrew", "Titman", role=c("aut", "cre"), email = "")
Description: Estimation of the survivor function for interval censored time-to-event data subject to misclassification using nonparametric maximum likelihood estimation, implementing the methods of Titman (2017) <doi:10.1007/s11222-016-9705-7>. Misclassification probabilities can either be specified as fixed or estimated. Models with time dependent misclassification may also be fitted.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: stats, nnls
NeedsCompilation: no
Packaged: 2019-10-07 16:57:20 UTC; andre
Author: Andrew Titman [aut, cre]
Maintainer: Andrew Titman <>
Repository: CRAN
Date/Publication: 2019-10-09 13:00:02 UTC

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Package bigQueryR updated to version 0.5.0 with previous version 0.4.0 dated 2018-06-08

Title: Interface with Google BigQuery with Shiny Compatibility
Description: Interface with 'Google BigQuery', see <> for more information. This package uses 'googleAuthR' so is compatible with similar packages, including 'Google Cloud Storage' (<>) for result extracts.
Author: Mark Edmondson [aut, cre], Hadley Wickham [ctb]
Maintainer: Mark Edmondson <>

Diff between bigQueryR versions 0.4.0 dated 2018-06-08 and 0.5.0 dated 2019-10-09

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 bigQueryR-0.5.0/bigQueryR/man/bqr_wait_for_job.Rd         |    1 
 bigQueryR-0.5.0/bigQueryR/tests/testthat/test_query.R     |   12 
 bigQueryR-0.5.0/bigQueryR/vignettes/bigQueryR.Rmd         |   19 
 55 files changed, 1059 insertions(+), 497 deletions(-)

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New package silicate with initial version 0.2.0
Package: silicate
Title: Common Forms for Complex Hierarchical and Relational Data Structures
Version: 0.2.0
Authors@R: c(person("Michael D.","Sumner", role = c("aut", "cre"), email = ""), person("John", "Corbett", role = "ctb", comment = "the original inspiration"), person("Simon", "Wotherspoon", role = "ctb"), person("Kent", "Johnson", role = "dtc"), person("Mark", "Padgham", role = "aut") )
Description: Generate common data forms for complex data suitable for conversions and transmission by decomposition as paths or primitives. Paths are sequentially-linked records, primitives are basic atomic elements and both can model many forms and be grouped into hierarchical structures. The universal models 'SC0' (structural) and 'SC' (labelled, relational) are composed of edges and can represent any hierarchical form. Specialist models 'PATH', 'ARC' and 'TRI' provide the most common intermediate forms used for converting from one form to another. The methods are inspired by the simplicial complex <> and provide intermediate forms that relate spatial data structures to this mathematical construct.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: covr, knitr, rmarkdown, sp, testthat, trip, vdiffr
RoxygenNote: 6.1.1
Imports: dplyr, gibble (>= 0.2.0), methods, purrr, rlang, decido, tibble, unjoin (>= 0.0.3), geometry, tidyr (>= 1.0.0), grDevices, graphics, stats, magrittr, gridBase
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-07 14:27:46 UTC; mdsumner
Author: Michael D. Sumner [aut, cre], John Corbett [ctb] (the original inspiration), Simon Wotherspoon [ctb], Kent Johnson [dtc], Mark Padgham [aut]
Maintainer: Michael D. Sumner <>
Repository: CRAN
Date/Publication: 2019-10-09 11:30:02 UTC

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New package MUACz with initial version 1.0.0
Package: MUACz
Type: Package
Title: Generate MUAC z-Scores for School Children Aged 5-19 Years Old
Version: 1.0.0
Authors@R: c( person("Lazarus", "Mramba", email = "", role = c("aut", "cre")), person("James", "Berkley", email = "", role = "aut"))
Maintainer: Lazarus Mramba <>
Description: Generates mid upper arm circumference (MUAC) for age z-scores for children and adolescents aged 5 to 19 years that can be used to assess nutritional and health status and define risk of adverse health events. The standard growth reference constructed by Mramba et. al (2017) (<doi:10.1136/bmj.j3423>) smoothly join the WHO (2005) standards at age 5 years (<>) and has been validated against mortality risk among children and adolescents in Kenya, Uganda and Zimbabwe.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: epiDisplay, ggplot2, dplyr
SystemRequirements: GNU make
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-09 10:48:52 UTC; lmramba
Author: Lazarus Mramba [aut, cre], James Berkley [aut]
Repository: CRAN
Date/Publication: 2019-10-09 11:30:09 UTC

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New package lazyraster with initial version 0.5.0
Package: lazyraster
Version: 0.5.0
Title: Generate Raster Data Lazily from 'GDAL'
Description: Read raster data at a specified resolution on-demand via 'GDAL' (the Geospatial Data Abstraction Library <>). Augments the 'raster' package by never reading data from a raster source until necessary for generating an in-memory 'raster' object. A 'lazyraster' object may be cropped and converted to 'raster' object, and by default will only read a small amount of data sufficient for an overall summary. The amount of data read can be controlled by specifying the output dimensions.
Authors@R: person("Michael", "Sumner", email = "", role = c("aut", "cre"))
License: GPL-3
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.1
Imports: graphics, raster, vapour (>= 0.4.0), methods, quadmesh (>= 0.4.0)
Suggests: palr, testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2019-10-07 11:57:45 UTC; mdsumner
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <>
Repository: CRAN
Date/Publication: 2019-10-09 11:10:02 UTC

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New package hypr with initial version 0.1.2
Package: hypr
Type: Package
Title: Hypothesis Matrix Translation
Version: 0.1.2
Authors@R: c( person(given = "Maximilian M.", family = "Rabe", email = "", role = c("aut","cre")), person(given = "Shravan", family = "Vasishth", role = c("aut")), person(given = "Sven", family = "Hohenstein", role = c("aut")), person(given = "Reinhold", family = "Kliegl", email = "", role = c("aut")), person(given = "Daniel J.", family = "Schad", email = "", role = c("aut")))
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) <arXiv:1807.10451>.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: MASS, Matrix, pracma, methods, stats, rlang
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Collate: 'equations.R' 'hello.R' 'hypr.R'
NeedsCompilation: no
Packaged: 2019-10-07 13:32:52 UTC; max
Author: Maximilian M. Rabe [aut, cre], Shravan Vasishth [aut], Sven Hohenstein [aut], Reinhold Kliegl [aut], Daniel J. Schad [aut]
Maintainer: Maximilian M. Rabe <>
Repository: CRAN
Date/Publication: 2019-10-09 11:20:02 UTC

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New package ggVennDiagram with initial version 0.3
Package: ggVennDiagram
Type: Package
Title: A 'ggplot2' Implement of Venn Diagram
Version: 0.3
Authors@R: c( person("Chun-Hui","Gao",email="",role=c("aut","cre"), comment=c(ORCID = "0000-0002-1445-7939")), person("Guangchuang", "Yu", email = "", role = c("ctb"), comment = c(ORCID = "0000-0002-6485-8781")) )
Maintainer: Chun-Hui Gao <>
Description: Easy-to-use functions to generate 2-4 sets Venn plot in publication quality. 'ggVennDiagram' is the first software that can automatically fill different colors to each part of a Venn diagram.
Depends: R (>= 3.5.0)
Imports: VennDiagram, sf, ggplot2, dplyr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2019-10-07 01:34:38 UTC; gaosp
Author: Chun-Hui Gao [aut, cre] (<>), Guangchuang Yu [ctb] (<>)
Repository: CRAN
Date/Publication: 2019-10-09 11:40:02 UTC

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Package dglars updated to version 2.1.3 with previous version 2.1.2 dated 2019-06-14

Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <>

Diff between dglars versions 2.1.2 dated 2019-06-14 and 2.1.3 dated 2019-10-09

 ChangeLog             |    3 +++
 DESCRIPTION           |    8 ++++----
 MD5                   |    8 ++++----
 man/dglars-package.Rd |    4 ++--
 src/pc_cvdglars.f90   |    2 +-
 5 files changed, 14 insertions(+), 11 deletions(-)

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New package coil with initial version 1.0.0
Package: coil
Type: Package
Title: Contextualization and Evaluation of COI-5P Barcode Data
Version: 1.0.0
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <>
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.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R(>= 3.0.0)
Imports: ape, aphid, seqinr
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-07 12:58:25 UTC; cnuge
Repository: CRAN
Date/Publication: 2019-10-09 11:20:05 UTC

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New package PosteriorBootstrap with initial version 0.1.0
Package: PosteriorBootstrap
Title: Non-Parametric Sampling with Parallel Monte Carlo
Version: 0.1.0
Authors@R: c( person(given = "Simon", family = "Lyddon", role = c("aut"), email = ""), person(given = "Miguel", family = "Morin", role = c("aut"), email = ""), person(given = "James", family = "Robinson", role = c("aut", "cre"), email = ""), person("The Alan Turing Institute", role=c("cph"), email = ""))
Description: An implementation of a non-parametric statistical model using a parallelised Monte Carlo sampling scheme. The method implemented in this package allows non-parametric inference to be regularized for small sample sizes, while also being more accurate than approximations such as variational Bayes. The concentration parameter is an effective sample size parameter, determining the faith we have in the model versus the data. When the concentration is low, the samples are close to the exact Bayesian logistic regression method; when the concentration is high, the samples are close to the simplified variational Bayes logistic regression. The method is described in full in the paper Lyddon, Walker, and Holmes (2018), "Nonparametric learning from Bayesian models with randomized objective functions" <arXiv:1806.11544>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr (>= 0.7.4), e1071 (>= 1.7.1), ggplot2 (>= 3.1.1), gridExtra (>= 2.3), MASS (>=, Rcpp (>= 1.0.1), rstan (>= 2.18.2), utils (>= 3.4.3), StanHeaders (>= 2.18.1), tibble (>= 2.1.1)
Suggests: knitr (>= 1.21), lintr (>= 1.0.3), rmarkdown (>= 1.11), testthat (>= 2.0.1)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-09 10:13:58 UTC; jrobinson
Author: Simon Lyddon [aut], Miguel Morin [aut], James Robinson [aut, cre], The Alan Turing Institute [cph]
Maintainer: James Robinson <>
Repository: CRAN
Date/Publication: 2019-10-09 11:00:02 UTC

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New package klassR with initial version 0.1.2
Package: klassR
Type: Package
Title: Classifications and Codelists for Statistics Norway
Version: 0.1.2
Author: Susie Jentoft, Lisa Li, Diana-Cristina Iancu
Maintainer: Susie Jentoft <>
Description: Functions to search, retrieve and apply classifications and codelists using Statistics Norway's API <> from the system 'KLASS'. Retrieves classifications by date with options to choose language, hierarchical level and formatting.
Imports: tm, httr, jsonlite
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-01 12:37:59 UTC; coo
Repository: CRAN
Date/Publication: 2019-10-09 09:50:02 UTC

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New package CKAT with initial version 0.1.0
Package: CKAT
Type: Package
Title: Composite Kernel Association Test for Pharmacogenetics Studies
Version: 0.1.0
Author: Hong Zhang and Judong Shen
Maintainer: Hong Zhang <>
Description: Composite Kernel Association Test (CKAT) is a flexible and robust kernel machine based approach to jointly test the genetic main effect and gene-treatment interaction effect for a set of single-nucleotide polymorphisms (SNPs) in pharmacogenetics (PGx) assessments embedded within randomized clinical trials.
License: GPL-2
Imports: stats, CompQuadForm
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2019-10-07 01:39:20 UTC; consi
Repository: CRAN
Date/Publication: 2019-10-09 09:20:02 UTC

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New package optimCheck with initial version 1.0
Package: optimCheck
Type: Package
Title: Graphical and Numerical Checks for Mode-Finding Routines
Version: 1.0
Date: 2019-10-06
Author: Martin Lysy
Maintainer: Martin Lysy <>
Description: Tools for checking that the output of an optimization algorithm is indeed at a local mode of the objective function. This is accomplished graphically by calculating all one-dimensional "projection plots" of the objective function, i.e., varying each input variable one at a time with all other elements of the potential solution being fixed. The numerical values in these plots can be readily extracted for the purpose of automated and systematic unit-testing of optimization routines.
License: GPL-3
Imports: stats, graphics
RoxygenNote: 6.1.1
Encoding: UTF-8
Suggests: testthat, quantreg, mclust, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-06 18:18:06 UTC; mlysy
Repository: CRAN
Date/Publication: 2019-10-09 08:40:02 UTC

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New package nimbleEcology with initial version 0.1.0
Package: nimbleEcology
Type: Package
Title: Distributions for Ecological Models in 'nimble'
Version: 0.1.0
Maintainer: Benjamin R. Goldstein <>
Authors@R: c(person("Benjamin R.", "Goldstein", role = c("aut", "cre"), email = ""), person("Daniel", "Turek", role = "aut"), person("Lauren", "Ponisio", role = "aut"), person("Perry", "de Valpine", role = "aut"))
Date: 2019-09-24
Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, and dynamic hidden Markov models. (Jolly (1965) <doi:10.2307/2333826>, Seber (1965) <10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
License: GPL-3
Copyright: Copyright (c) 2019, Perry de Valpine, Ben Goldstein, Daniel Turek, Lauren Ponisio
Depends: R (>= 3.4.0), nimble
Encoding: UTF-8
LazyData: true
Collate: dDynOcc.R dCJS.R dDHMM.R dHMM.R dOcc.R zzz.R
RoxygenNote: 6.1.1
Suggests: rmarkdown, testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2019-10-03 18:11:34 UTC; Ben
Author: Benjamin R. Goldstein [aut, cre], Daniel Turek [aut], Lauren Ponisio [aut], Perry de Valpine [aut]
Repository: CRAN
Date/Publication: 2019-10-09 08:40:07 UTC

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New package ipwCoxCSV with initial version 1.0
Package: ipwCoxCSV
Type: Package
Title: Inverse Probability Weighted Cox Model with Corrected Sandwich Variance
Version: 1.0
Date: 2019-09-16
Author: Di Shu <>, Rui Wang <>
Maintainer: Di Shu <>
Description: An implementation of corrected sandwich variance (CSV) estimation method for making inference of marginal hazard ratios (HR) in inverse probability weighted (IPW) Cox model without and with clustered data, proposed by Shu, Young, Toh, and Wang (2019) in their paper under revision for Biometrics. Both conventional inverse probability weights and stabilized weights are implemented. Logistic regression model is assumed for propensity score model.
License: GPL (>= 2)
Imports: survival, stats
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2019-10-06 18:39:09 UTC; dishu
Repository: CRAN
Date/Publication: 2019-10-09 08:50:03 UTC

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New package intdag with initial version 1.0.1
Package: intdag
Type: Package
Title: Reconstruction of a Directed Acyclic Graph with Interventions
Version: 1.0.1
Author: Si Peng, Xiaotong Shen, Wei Pan
Maintainer: Si Peng <>
Depends: R (>= 3.4.0)
Description: Provides intdag() for a constrained maximum likelihood estimate of a directed acyclic graph with intervention data. Also available is obsdag() for an estimate with observation data only, based on the method in the paper by Yuan, Shen and Pan (2018) <doi:10.1093/biomet/asy057>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-08 13:26:19 UTC; si
Repository: CRAN
Date/Publication: 2019-10-09 08:40:10 UTC

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New package gscaLCA with initial version 0.0.2
Package: gscaLCA
Type: Package
Title: Generalized Structure Component Analysis- Latent Class Analysis
Version: 0.0.2
Authors@R: c( person("Jihoon", "Ryoo", role = c("aut")), person("Seohee", "Park", email = "", role = c("aut", "cre")), person("Seoungeun", "Kim", role = c("aut")), person("heungsun", "Hwaung", role = c("aut")))
Description: Execute Latent Class Analysis (LCA) by using Generalized Structured Component Analysis (GSCA). This is explained in Ryoo, Park, and Kim (2009) <doi:10.1007/s41237-019-00084-6>. It estimates the parameters of latent class prevalence and item response probability in LCA with a single line comment. It also provide graphs of item response probabilities.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: gridExtra, ggplot2, stringr, progress, psych, fastDummies, fclust, MASS, devtools, foreach, doSNOW
Suggests: knitr, rmarkdown, R.rsp
NeedsCompilation: no
Packaged: 2019-10-06 21:38:27 UTC; Spenser
Author: Jihoon Ryoo [aut], Seohee Park [aut, cre], Seoungeun Kim [aut], heungsun Hwaung [aut]
Maintainer: Seohee Park <>
Repository: CRAN
Date/Publication: 2019-10-09 09:00:02 UTC

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Package FunnelPlotR updated to version 0.2.1 with previous version 0.2.0 dated 2019-09-04

Title: Funnel Plots for Indirectly-Standardised Ratios
Description: An implementation of the Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for reporting standardised ratios, with overdispersion adjustment.
Author: Chris Mainey [aut, cre] (<>), Matthew Bass [ctb]
Maintainer: Chris Mainey <>

Diff between FunnelPlotR versions 0.2.0 dated 2019-09-04 and 0.2.1 dated 2019-10-09

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Package HypergeoMat updated to version 2.0.0 with previous version 1.0.1 dated 2019-09-29

Title: Hypergeometric Function of a Matrix Argument
Description: Evaluates the hypergeometric functions of a matrix argument, which appear in random matrix theory. This is an implementation of Koev & Edelman's algorithm (2006) <doi:10.1090/S0025-5718-06-01824-2>.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <>

Diff between HypergeoMat versions 1.0.1 dated 2019-09-29 and 2.0.0 dated 2019-10-09

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 tests/testthat/test-3F2.R    |    9 +++++
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 20 files changed, 186 insertions(+), 34 deletions(-)

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Package UCSCXenaTools updated to version 1.2.7 with previous version 1.2.6 dated 2019-09-07

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<>), Xue-Song Liu [aut] (<>), Martin Morgan [ctb], Christine Stawitz [rev] (Christine reviewed the package for ropensci, see <>), Carl Ganz [rev] (Carl reviewed the package for ropensci, see <>)
Maintainer: Shixiang Wang <>

Diff between UCSCXenaTools versions 1.2.6 dated 2019-09-07 and 1.2.7 dated 2019-10-09

 DESCRIPTION                      |    8 -
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 tests/testthat/test-full-tests.R |    2 
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 14 files changed, 232 insertions(+), 158 deletions(-)

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Package matahari updated to version 0.1.1 with previous version 0.1.0 dated 2019-05-17

Title: Spy on Your R Session
Description: Conveniently log everything you type into the R console. Logs are are stored as tidy data frames which can then be analyzed using 'tidyverse' style tools.
Author: Sean Kross [aut, cre] (<>), Lucy D'Agostino McGowan [aut] (<>), Jeff Leek [ldr] (<>)
Maintainer: Sean Kross <>

Diff between matahari versions 0.1.0 dated 2019-05-17 and 0.1.1 dated 2019-10-09

 DESCRIPTION            |    6 +--
 MD5                    |   14 ++++----
 NAMESPACE              |    1                |    5 +++
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Package funModeling updated to version 1.9.3 with previous version 1.9.2 dated 2019-09-08

Title: Exploratory Data Analysis and Data Preparation Tool-Box
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas [aut, cre]
Maintainer: Pablo Casas <>

Diff between funModeling versions 1.9.2 dated 2019-09-08 and 1.9.3 dated 2019-10-09

 DESCRIPTION                 |    8 +--
 MD5                         |    9 ++-
 NAMESPACE                   |    3 +
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Package caMST updated to version 0.1.2 with previous version 0.1.0 dated 2018-09-16

Title: Mixed Computerized Adaptive Multistage Testing
Description: Provides functions to more easily analyze computerized adaptive tests. Currently, functions for computerized adaptive tests (CAT), computer adaptive multistage tests (CMT), and mixed computer adaptive multistage tests (McaMST) utilizing CAT item-level adaptation for the initial stage and traditional MST module-level adaptation for the subsequent stages have been created, and a variation of Hybrid computer adaptive MST is planned as well. For an in-depth look at CAT and MST, see Weiss & Kingsbury (1984) <doi:10.1111/j.1745-3984.1984.tb01040.x> and Luecht & Nungester (2000) <doi:10.1007/0-306-47531-6_6> respectively.
Author: Anthony Raborn [aut, cre]
Maintainer: Anthony Raborn <>

Diff between caMST versions 0.1.0 dated 2018-09-16 and 0.1.2 dated 2019-10-09

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More information about caMST at CRAN
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Package airportr updated to version 0.1.3 with previous version 0.1.2 dated 2018-10-06

Title: Convenience Tools for Working with Airport Data
Description: Retrieves open source airport data and provides tools to look up information, translate names into codes and vice-verse, as well as some basic calculation functions for measuring distances. Data is licensed under the Open Database License.
Author: Dmitry Shkolnik [cre, aut]
Maintainer: Dmitry Shkolnik <>

Diff between airportr versions 0.1.2 dated 2018-10-06 and 0.1.3 dated 2019-10-09

 airportr-0.1.2/airportr/R/data.R                               |only
 airportr-0.1.3/airportr/DESCRIPTION                            |   13 -
 airportr-0.1.3/airportr/LICENSE                                |    2 
 airportr-0.1.3/airportr/MD5                                    |   29 +-
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 airportr-0.1.3/airportr/R/airport_lookups.R                    |   55 ++--
 airportr-0.1.3/airportr/R/airportr.R                           |    2 
 airportr-0.1.3/airportr/R/data-airports.R                      |only
 airportr-0.1.3/airportr/R/utils.R                              |only
 airportr-0.1.3/airportr/                              |    6 
 airportr-0.1.3/airportr/build/vignette.rds                     |binary
 airportr-0.1.3/airportr/data/airports.rda                      |binary
 airportr-0.1.3/airportr/inst/doc/Introduction_to_Airportr.Rmd  |    2 
 airportr-0.1.3/airportr/inst/doc/Introduction_to_Airportr.html |  115 ++++++----
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 airportr-0.1.3/airportr/man/airports.Rd                        |    9 
 airportr-0.1.3/airportr/man/city_airports.Rd                   |    7 
 airportr-0.1.3/airportr/vignettes/Introduction_to_Airportr.Rmd |    2 
 18 files changed, 147 insertions(+), 95 deletions(-)

More information about airportr at CRAN
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Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.