Mon, 26 Nov 2018

Package YPInterimTesting updated to version 1.0.0 with previous version 0.1.0 dated 2017-11-17

Title: Interim Monitoring Using Adaptively Weighted Log-Rank Test in Clinical Trials
Description: For any spending function specified by the user, this package provides corresponding boundaries for interim testing using the adaptively weighted log-rank test developed by Yang and Prentice (2010 <doi:10.1111/j.1541-0420.2009.01243.x>). The package uses a re-sampling method to obtain stopping boundaries at the interim looks.The output consists of stopping boundaries and observed values of the test statistics at the interim looks, along with nominal p-values defined as the probability of the test exceeding the specific observed test statistic value or critical value, regardless of the test behavior at other looks. The asymptotic validity of the stopping boundaries is established in Yang (2018 <doi:10.1002/sim.7958>).
Author: Daewoo Pak and Song Yang
Maintainer: Daewoo Pak <heavyrain.pak@gmail.com>

Diff between YPInterimTesting versions 0.1.0 dated 2017-11-17 and 1.0.0 dated 2018-11-26

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Package spacesXYZ updated to version 1.0-2 with previous version 1.0-1 dated 2018-07-13

Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv. The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included. Compute CCT and the Planckian and daylight loci. Three different standard color difference metrics are included.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>

Diff between spacesXYZ versions 1.0-1 dated 2018-07-13 and 1.0-2 dated 2018-11-26

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 28 files changed, 529 insertions(+), 139 deletions(-)

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Package survival updated to version 2.43-3 with previous version 2.43-1 dated 2018-10-29

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

Diff between survival versions 2.43-1 dated 2018-10-29 and 2.43-3 dated 2018-11-26

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Package SetMethods updated to version 2.4 with previous version 2.3.1 dated 2018-04-25

Title: Functions for Set-Theoretic Multi-Method Research and Advanced QCA
Description: Functions for performing set-theoretic multi-method research, QCA for clustered data, theory evaluation, Enhanced Standard Analysis, indirect calibration, radar visualisations. Additionally it includes data to replicate the examples in the book by C. Q. Schneider and C. Wagemann "Set Theoretic Methods for the Social Sciences", Cambridge University Press and in the online appendix.
Author: Ioana-Elena Oana [aut, cre], Juraj Medzihorsky [aut], Mario Quaranta [aut], Carsten Q. Schneider [aut]
Maintainer: Ioana-Elena Oana <oana_ioana-elena@phd.ceu.edu>

Diff between SetMethods versions 2.3.1 dated 2018-04-25 and 2.4 dated 2018-11-26

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New package Z10 with initial version 0.1.0
Package: Z10
Type: Package
Title: Simple Ecological Statistics from the NEON Network
Version: 0.1.0
Author: Robert Lee <rhlee@colorado.edu>
Maintainer: Robert Lee <rhlee@colorado.edu>
Description: Provides simple statistics from instruments and observations at sites in the NEON network, and acts as a simple interface for v0 of the National Ecological Observatory Network (NEON) API. Statistics are generated for meteorologic and soil-based observations, and are presented for daily, annual, and one-time observations at all available NEON sites. Users can also retrieve any dataset publicly hosted by NEON. Metadata for NEON sites and data products can be returned, as well as information on data product availability by site and date. For more information on NEON, please visit <https://www.neonscience.org>. For detailed data product information, please see the NEON data product catalog at <https://data.neonscience.org/data-product-catalog>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: rjson, stringr, magrittr, lubridate, dplyr
Suggests: RNRCS, metScanR, rnoaa, neonUtilities
NeedsCompilation: no
Packaged: 2018-11-16 20:22:36 UTC; rlee
Repository: CRAN
Date/Publication: 2018-11-26 20:40:07 UTC

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New package TRES with initial version 0.1.0
Package: TRES
Type: Package
Title: Tensor Regression with Envelope Structure and Three Generic Envelope Estimation Approaches
Version: 0.1.0
Author: Wenjing Wang [aut, cre] <wenjing.wang@stat.fsu.edu>, Xin Zhang [aut, cre] <henry@stat.fsu.edu>
Maintainer: Wenjing Wang <wenjing.wang@stat.fsu.edu>
Description: Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0), ManifoldOptim, rTensor, MASS
Imports: pracma, mvtnorm, methods
RcppModules: ManifoldOptim_module
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 18:32:05 UTC; wenja
Repository: CRAN
Date/Publication: 2018-11-26 20:20:06 UTC

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New package SMFilter with initial version 1.0.0
Package: SMFilter
Title: Filtering Algorithms for the State Space Model on the Stiefel Manifold
Version: 1.0.0
Authors@R: person("Yukai", "Yang", email = "yukai.yang@statistik.uu.se",role = c("aut", "cre"))
Description: Provides the filtering algorithms for the state space model on the Stiefel manifold.
Depends: R (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
URL: https://github.com/yukai-yang/SMFilter
BugReports: https://github.com/yukai-yang/SMFilter/issues
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-16 19:59:04 UTC; yyang
Author: Yukai Yang [aut, cre]
Maintainer: Yukai Yang <yukai.yang@statistik.uu.se>
Repository: CRAN
Date/Publication: 2018-11-26 20:40:11 UTC

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Package LLSR updated to version 0.0.2.3 with previous version 0.0.2.2 dated 2018-11-06

Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters and a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>

Diff between LLSR versions 0.0.2.2 dated 2018-11-06 and 0.0.2.3 dated 2018-11-26

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Package ipdw updated to version 0.2-7 with previous version 0.2-6 dated 2017-05-19

Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate geo-referenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>

Diff between ipdw versions 0.2-6 dated 2017-05-19 and 0.2-7 dated 2018-11-26

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New package FSMUMI with initial version 1.0
Package: FSMUMI
Type: Package
Title: Imputation of Time Series Based on Fuzzy Logic
Version: 1.0
Date: 2018-11-16
Author: Thi-Thu-Hong Phan, Andre Bigand, Emilie Poisson-Caillault
Maintainer: Thi Thu Hong Phan <ptthong@vnua.edu.vn>
Description: Filling large gaps in low or uncorrelated multivariate time series uses a new fuzzy weighted similarity measure. It contains all required functions to create large missing consecutive values within time series and then fill these gaps, according to the paper Phan et al. (2018), <DOI:10.1155/2018/9095683>. Performance indicators are also provided to compare similarity between two univariate signals (incomplete signal and imputed signal).
Depends: R (>= 3.0.0)
Imports: FuzzyR, stats, lsa
License: GPL (>= 2)
RoxygenNote: 6.0.1
URL: http://mawenzi.univ-littoral.fr/FSMUMI/
NeedsCompilation: no
Packaged: 2018-11-16 09:45:10 UTC; camille
Repository: CRAN
Date/Publication: 2018-11-26 20:10:06 UTC

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Package capm updated to version 0.13.9 with previous version 0.13.8 dated 2018-11-22

Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population management. Some functions assist survey sampling tasks (calculate sample size for simple and complex designs, select sampling units and estimate population parameters) while others assist the modelling of population dynamics. For demographic characterizations and population management evaluations see: "Baquero, et al." (2018), <doi:10.1016/j.prevetmed.2018.07.006>. For modelling of population dynamics see: "Baquero et al." (2016), <doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076"; "Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre], Marcos Amaku [ctb], Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>

Diff between capm versions 0.13.8 dated 2018-11-22 and 0.13.9 dated 2018-11-26

 DESCRIPTION         |    8 ++++----
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 6 files changed, 23 insertions(+), 18 deletions(-)

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New package bipartiteD3 with initial version 0.1.0
Package: bipartiteD3
Type: Package
Title: Interactive Bipartite Graphs
Version: 0.1.0
Authors@R: person("Chris", "Terry", email = "christerry3@btinternet.com", role = c("aut", "cre"))
Description: Generates interactive bipartite graphs using the D3 library. Designed for use with the 'bipartite' analysis package. Sources open source 'vis-js' library (<http://visjs.org/>). Adapted from examples at <https://bl.ocks.org/NPashaP> (released under GPL-3).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: RColorBrewer (>= 1.1), r2d3 (>= 0.2.2), purrr (>= 0.2.5), dplyr (>= 0.7.5), tidyr (>= 0.8), stringr(>= 1.3), tibble (>= 1.4), bipartite (>= 2.08),
Depends:
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-16 13:31:28 UTC; pemb4504
Author: Chris Terry [aut, cre]
Maintainer: Chris Terry <christerry3@btinternet.com>
Repository: CRAN
Date/Publication: 2018-11-26 20:10:03 UTC

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New package ypr with initial version 0.3.0
Package: ypr
Version: 0.3.0
Title: Yield Per Recruit
Description: An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
Authors@R: person("Joe", "Thorley", email = "joe@poissonconsulting.ca", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7683-4592"))
License: MIT + file LICENSE
URL: https://github.com/poissonconsulting/ypr
BugReports: https://github.com/poissonconsulting/ypr/issues
Depends: R (>= 3.4.0)
Imports: checkr, ggplot2, graphics, scales, stats, tools,
Suggests: covr, testthat, tibble, knitr, rmarkdown, tidyr
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2018-11-16 03:31:41 UTC; joe
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-11-26 20:00:03 UTC

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New package suropt with initial version 0.1.0
Package: suropt
Type: Package
Title: Surrogate-Based Optimization
Version: 0.1.0
Authors@R: c( person("Adriano", "Passos", email="adriano.utfpr@gmail.com", role=c("aut","cre")), person("Marco", "Luersen", email="luersen@utfpr.edu.br", role="ctb"))
Description: Multi-Objective optimization based on surrogate models. Important functions: build_surmodel, train_hego, train_mego, train_sme.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.4.0)
Imports: methods, lhs, ggplot2, dplyr, tidyr, purrr, tibble, DiceKriging, DiceOptim, GPareto, emoa, mco, rgenoud, pso, GenSA
NeedsCompilation: no
Packaged: 2018-11-15 21:28:39 UTC; Adriano
Author: Adriano Passos [aut, cre], Marco Luersen [ctb]
Maintainer: Adriano Passos <adriano.utfpr@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-26 20:00:08 UTC

More information about suropt at CRAN
Permanent link

New package restez with initial version 1.0.0
Package: restez
Type: Package
Title: Create and Query a Local Copy of 'GenBank' in R
Version: 1.0.0
Authors@R: person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com", comment = c(ORCID = "0000-0003-2722-1359"))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
URL: https://github.com/ropensci/restez#readme
BugReports: https://github.com/ropensci/restez/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: utils, rentrez, MonetDBLite (>= 0.6.0), DBI (>= 1.0.0), downloader, RCurl, cli, crayon, callr (>= 3.0.0), devtools
Suggests: testthat, knitr, R.utils, rmarkdown
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-16 09:19:36 UTC; djb208
Author: Dom Bennett [aut, cre] (<https://orcid.org/0000-0003-2722-1359>)
Repository: CRAN
Date/Publication: 2018-11-26 20:00:12 UTC

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New package read.gb with initial version 1.6
Package: read.gb
Type: Package
Title: Open GenBank Files
Version: 1.6
Author: Robin Mercier
Maintainer: Robin Mercier <robin.largon.mercier@hotmail.fr>
Description: Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at <https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Collate: 'CDS.F.R' 'C_region.F.R' 'DNA.treatment.R' 'D_loop.F.R' 'D_segment.F.R' 'F_UTR.F.R' 'variation.F.R' 'V_segment.F.R' 'V_region.F.R' 'unsure.F.R' 'tRNA.F.R' 'transit_peptide.F.R' 'tmRNA.F.R' 'telomere.F.R' 'T_UTR.F.R' 'STS.F.R' 'stem_loop.F.R' 'source.F.R' 'sig_peptide.F.R' 'S_region.F.R' 'rRNA.F.R' 'repeat_region.F.R' 'rep_origin.F.R' 'regulatory.F.R' 'protein_bind.F.R' 'propeptide.F.R' 'primer_bind.F.R' 'prim_transcript.F.R' 'precursor_RNA.F.R' 'polyA_site.F.R' 'oriT.F.R' 'operon.F.R' 'old_sequence.F.R' 'ncRNA.F.R' 'N_region.F.R' 'mRNA.F.R' 'modified_base.F.R' 'mobile_element.F.R' 'misc_structure.F.R' 'misc_RNA.F.R' 'misc_recomb.F.R' 'misc_feature.F.R' 'misc_difference.F.R' 'misc_binding.F.R' 'mat_peptide.F.R' 'J_segment.F.R' 'intron.F.R' 'iDNA.F.R' 'gene.F.R' 'gap.F.R' 'exon.F.R' 'centromere.F.R' 'assembly_gap.F.R' 'Feature.sep.R' 'Reference.sep.R' 'Reorganize.report.R' 'read.gb-internal.R' 'read.gb.R'
NeedsCompilation: no
Packaged: 2018-11-15 13:59:16 UTC; Largon
Repository: CRAN
Date/Publication: 2018-11-26 19:50:03 UTC

More information about read.gb at CRAN
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New package postlogic with initial version 0.1.0
Package: postlogic
Type: Package
Title: Infix and Postfix Logic Operators
Version: 0.1.0
Authors@R: person("Andrew", "Redd", role = c("aut", "cre") , email = "Andrew.Redd@hsc.utah.edu" , comment = c(ORCID = "https://orcid.org/000-0002-6149-2438") )
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Description: Provides adds postfix and infix logic operators for if, then, unless, and otherwise.
Language: en-US
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr
URL: https://github.com/RDocTaskForce/postlogic
BugReports: https://github.com/RDocTaskForce/postlogic/issues
NeedsCompilation: no
Packaged: 2018-11-16 00:30:54 UTC; u0092104
Author: Andrew Redd [aut, cre] (<https://orcid.org/000-0002-6149-2438>)
Repository: CRAN
Date/Publication: 2018-11-26 20:00:23 UTC

More information about postlogic at CRAN
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New package PDShiny with initial version 0.1.0
Package: PDShiny
Type: Package
Title: 'Probability Distribution Shiny'
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive shiny application for working with Probability Distributions. Calculations and Graphs are provided.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.0.3)
Imports: shiny
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 07:14:19 UTC; KARTIKEYA
Repository: CRAN
Date/Publication: 2018-11-26 19:50:06 UTC

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Permanent link

New package coveffectsplot with initial version 0.0.1
Package: coveffectsplot
Title: Produce Forest Plots to Visualize Covariate Effects
Version: 0.0.1
Authors@R: c( person("Samer", "Mouksassi", email = "samermouksassi@gmail.com", role = c("aut", "cre")), person("Dean", "Attali", email = "daattali@gmail.com", role = c("ctb")) )
Description: Produce forest plots to visualize covariate effects using either the command line or an interactive 'Shiny' application.
URL: https://github.com/smouksassi/interactiveforestplot
BugReports: https://github.com/smouksassi/interactiveforestplot/issues
Depends: R (>= 3.1.0)
Imports: colourpicker, dplyr, egg, ggplot2, ggstance, markdown, shiny, shinyjs, stats, tidyr, utils
Suggests: MASS, knitr, rmarkdown, ggridges
License: MIT + file LICENSE
SystemRequirements: pandoc with https support
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-15 13:30:01 UTC; smouksas
Author: Samer Mouksassi [aut, cre], Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-26 19:40:03 UTC

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New package changepoint.mv with initial version 1.0.0
Package: changepoint.mv
Type: Package
Title: Changepoint Analysis for Multivariate Time Series
Version: 1.0.0
Date: 2018-11-15
Author: Lawrence Bardwell <l.bardwell@lancaster.ac.uk> [aut], Idris Eckley <i.eckley@lancaster.ac.uk> [ths,ctb], Paul Fearnhead <p.fearnhead@lancaster.ac.uk> [ths,ctb], Daniel Grose <dan.grose@lancaster.ac.uk> [aut,cre]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Description: Detects the Most Recent Changepoints (mrc) for panel data consisting of many related univariate timeseries.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.12),methods,zoo,tbart,Rdpack,ggplot2,reshape2,assertive
LinkingTo: Rcpp
Suggests: gridExtra
RdMacros: Rdpack
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-15 10:58:50 UTC; grosedj1
Repository: CRAN
Date/Publication: 2018-11-26 19:40:07 UTC

More information about changepoint.mv at CRAN
Permanent link

Package kappaSize updated to version 1.2 with previous version 1.1 dated 2013-03-12

Title: Sample Size Estimation Functions for Studies of Interobserver Agreement
Description: Contains basic tools for sample size estimation in studies of interobserver/interrater agreement (reliability). Includes functions for both the power-based and confidence interval-based methods, with binary or multinomial outcomes and two through six raters.
Author: Michael A Rotondi <mrotondi@yorku.ca>
Maintainer: Michael A Rotondi <mrotondi@yorku.ca>

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Package bioacoustics updated to version 0.1.6 with previous version 0.1.5 dated 2018-08-15

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, Inc. [ctb, cph] (Read WAC files, original C code), WavX Inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

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Package rdwd updated to version 0.11.0 with previous version 0.10.2 dated 2018-05-29

Title: Select and Download Climate Data from 'DWD' (German Weather Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see <https://www.dwd.de/EN/climate_environment/cdc/cdc.html> for more information). Choose files with 'selectDWD()', download and process data sets with 'dataDWD()' and 'readDWD()'.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>

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Package crosswalkr updated to version 0.2.2 with previous version 0.1.1 dated 2017-10-17

Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames using external crosswalk files. It is especially useful when constructing master data sets from multiple smaller data sets that do not name or encode variables consistently across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@virginia.edu>

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Package SAMM updated to version 1.1 with previous version 0.0.1 dated 2016-07-10

Title: Some Algorithms for Mixed Models
Description: This program can be used to fit Gaussian linear mixed models (LMM). Univariate and multivariate response models, multiple variance components, as well as, certain correlation and covariance structures are supported. In many occasions, the user can pick one of the several mixed model fitting algorithms, which are explained further in the details section. Some algorithms are specific to certain types of models (univariate or multivariate, diagonal or non-diagonal residual, one or multiple variance components, etc,...).
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>

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New package GENEAsphere with initial version 1.5.0
Package: GENEAsphere
Type: Package
Title: Visualisation of Raw or Segmented Accelerometer Data
Version: 1.5.0
Date: 2018-11-23
Author: Mango Solutions [aut, cre], Joss Langford [aut, cre], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@Sweetland-solutions.co.uk>
Description: Creates visualisations in two and three dimensions of simulated data based on detected segments or raw accelerometer data.
License: GPL-3 | file LICENSE
LazyData: yes
Depends: ggplot2, rgl, MASS, misc3d, GENEAread
Suggests: knitr, rmarkdown
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-11-26 13:56:21 UTC; CharlesSweetland
Repository: CRAN
Date/Publication: 2018-11-26 14:50:02 UTC

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Package zscorer updated to version 0.2.0 with previous version 0.1.0 dated 2018-02-05

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], Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>

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Package questionr updated to version 0.7.0 with previous version 0.6.3 dated 2018-07-17

Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package npordtests updated to version 1.1 with previous version 1.0 dated 2018-11-19

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 adamethods updated to version 1.1 with previous version 1.0 dated 2018-11-14

Title: Archetypoid Algorithms and Anomaly Detection
Description: Collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect anomalies (outliers).
Author: Guillermo Vinue, Irene Epifanio
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

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Permanent link

Package VarianceGamma updated to version 0.4-0 with previous version 0.3-1 dated 2012-04-13

Title: The Variance Gamma Distribution
Description: Provides functions for the variance gamma distribution. Density, distribution and quantile functions. Functions for random number generation and fitting of the variance gamma to data. Also, functions for computing moments of the variance gamma distribution of any order about any location. In addition, there are functions for checking the validity of parameters and to interchange different sets of parameterizations for the variance gamma distribution.
Author: David Scott <d.scott@auckland.ac.nz> and Christine Yang Dong <c.dong@auckland.ac.nz>
Maintainer: David Scott <d.scott@auckland.ac.nz>

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Package raptr updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-28

Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software package (obtained from <http://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2017) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>

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More information about raptr at CRAN
Permanent link

Package NormalLaplace updated to version 0.3-0 with previous version 0.2-0 dated 2014-04-23

Title: The Normal Laplace Distribution
Description: Functions for the normal Laplace distribution. The package is under development and provides only limited functionality. Density, distribution and quantile functions, random number generation, and moments are provided.
Author: David Scott <d.scott@auckland.ac.nz>, Jason Shicong Fu and Simon Potter
Maintainer: David Scott <d.scott@auckland.ac.nz>

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More information about NormalLaplace at CRAN
Permanent link

Package openCR updated to version 1.3.0 with previous version 1.2.0 dated 2018-05-25

Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between openCR versions 1.2.0 dated 2018-05-25 and 1.3.0 dated 2018-11-26

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Package mixKernel updated to version 0.3 with previous version 0.2 dated 2018-09-11

Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package. Jerome Mariette and Nathalie Villa-Vialaneix (2017) <doi:10.1093/bioinformatics/btx682>.
Author: Jerome Mariette [aut, cre], Nathalie Villa-Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inra.fr>

Diff between mixKernel versions 0.2 dated 2018-09-11 and 0.3 dated 2018-11-26

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More information about mixKernel at CRAN
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Package GSED updated to version 2.0 with previous version 1.10 dated 2018-10-13

Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between GSED versions 1.10 dated 2018-10-13 and 2.0 dated 2018-11-26

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New package FlexParamCurve with initial version 1.5-5
Package: FlexParamCurve
Title: Tools to Fit Flexible Parametric Curves
Version: 1.5-5
Date: 2018-11-19
Authors@R: c(person("Stephen", "Oswald", role = c("aut", "cre"), email = "steve.oswald@psu.edu"))
Author: Stephen Oswald [aut, cre]
Description: Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
License: GPL-2
Encoding: UTF-8
URL: http://pennstate.academia.edu/SteveOswald
Depends: nlme
Imports: stats, utils
LazyData: true
NeedsCompilation: no
RoxygenNote: 6.1.1
Packaged: 2018-11-26 05:24:05 UTC; Admin
Maintainer: Stephen Oswald <steve.oswald@psu.edu>
Repository: CRAN
Date/Publication: 2018-11-26 11:00:14 UTC

More information about FlexParamCurve at CRAN
Permanent link

Package cranlike updated to version 1.0.2 with previous version 1.0.1 dated 2017-08-03

Title: Tools for 'CRAN'-Like Repositories
Description: A set of functions to manage 'CRAN'-like repositories efficiently.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between cranlike versions 1.0.1 dated 2017-08-03 and 1.0.2 dated 2018-11-26

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Package frailtypack updated to version 3.0.1 with previous version 2.13.2 dated 2018-09-25

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction; Evaluation of Failure-Time Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. 10) Joint frailty models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Amadou Diakite, Alexandre Laurent, Myriam Lopez, Agnieszka Krol and Casimir L. Sofeu
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>

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More information about frailtypack at CRAN
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Package MRFcov updated to version 1.0.36 with previous version 1.0.35 dated 2018-08-24

Title: Markov Random Fields with Additional Covariates
Description: Approximate node interaction parameters of Markov Random Fields graphical networks. Models can incorporate additional covariates, allowing users to estimate how interactions between nodes in the graph are predicted to change across covariate gradients. The general methods implemented in this package are described in Clark et al. (2018) <doi:10.1002/ecy.2221>.
Author: Nicholas J Clark [aut, cre], Konstans Wells [aut], Oscar Lindberg [aut]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>

Diff between MRFcov versions 1.0.35 dated 2018-08-24 and 1.0.36 dated 2018-11-26

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Package rio updated to version 0.5.16 with previous version 0.5.15 dated 2018-11-25

Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.
Author: Jason Becker [ctb], Chung-hong Chan [aut], Geoffrey CH Chan [ctb], Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>), Christopher Gandrud [ctb], Andrew MacDonald [ctb], Ista Zahn [ctb], Stanislaus Stadlmann [ctb], Ruaridh Williamson [ctb], Patrick Kennedy [ctb], Ryan Price [ctb], Trevor L Davis [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between rio versions 0.5.15 dated 2018-11-25 and 0.5.16 dated 2018-11-26

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Package readODS updated to version 1.6.7 with previous version 1.6.4 dated 2016-11-27

Title: Read and Write ODS Files
Description: Import ODS (OpenDocument Spreadsheet) into R as a data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten, Chung-hong Chan, Thomas J. Leeper and other contributors
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>

Diff between readODS versions 1.6.4 dated 2016-11-27 and 1.6.7 dated 2018-11-26

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Package hsphase updated to version 2.0.2 with previous version 2.0.1 dated 2015-01-10

Title: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Author: Mohammad Ferdosi <mferdosi@myune.edu.au>, Cedric Gondro <gondroce@msu.edu>
Maintainer: Mohammad Ferdosi <mferdosi@myune.edu.au>

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Package hR updated to version 0.1.4 with previous version 0.1.3 dated 2018-04-11

Title: An HR Analytics Toolkit
Description: Toolkit for leveraging people data.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>

Diff between hR versions 0.1.3 dated 2018-04-11 and 0.1.4 dated 2018-11-26

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Package hmm.discnp updated to version 2.1-5 with previous version 2.1-3 dated 2018-11-11

Title: Hidden Markov Models with Discrete Non-Parametric Observation Distributions
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. The observations may be univariate or bivariate. Simulates data from such models. Finds most probable underlying hidden states, the most probable sequences of such states, and the log likelihood of a collection of observations given the parameters of the model. Auxiliary predictors are accommodated in the univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package fChange updated to version 0.2.0 with previous version 0.1.0 dated 2017-07-29

Title: Change Point Analysis in Functional Data
Description: Change point estimation and detection methods for functional data are implemented using dimension reduction via functional principal component analysis and a fully-functional (norm-based) method. Detecting and dating structural breaks for both dependent and independent functional samples is illustrated along with some basic functional data generating processes.
Author: Ozan Sonmez, Alexander Aue, Gregory Rice
Maintainer: Ozan Sonmez <osonmez@ucdavis.edu>

Diff between fChange versions 0.1.0 dated 2017-07-29 and 0.2.0 dated 2018-11-26

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Package dartR updated to version 1.1.6 with previous version 1.0.5 dated 2018-05-11

Title: Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Lindsay V. Clark [ctb], Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

Diff between dartR versions 1.0.5 dated 2018-05-11 and 1.1.6 dated 2018-11-26

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 dartR-1.1.6/dartR/man/gl.report.repavg.Rd           |    2 
 dartR-1.1.6/dartR/man/gl.report.secondaries.Rd      |    2 
 dartR-1.1.6/dartR/man/gl.sexlinkage.Rd              |    2 
 dartR-1.1.6/dartR/man/gl.sim.ind.Rd                 |only
 dartR-1.1.6/dartR/man/gl.sim.offspring.Rd           |only
 dartR-1.1.6/dartR/man/gl.subsample.loci.Rd          |    2 
 dartR-1.1.6/dartR/man/gl.tree.nj.Rd                 |    2 
 dartR-1.1.6/dartR/man/gl.utils.fdsim.Rd             |    2 
 dartR-1.1.6/dartR/man/gl.write.csv.Rd               |    2 
 dartR-1.1.6/dartR/man/gl2demerelate.Rd              |    2 
 dartR-1.1.6/dartR/man/gl2fasta.Rd                   |    5 
 dartR-1.1.6/dartR/man/gl2faststructure.Rd           |    2 
 dartR-1.1.6/dartR/man/gl2gds.Rd                     |    2 
 dartR-1.1.6/dartR/man/gl2gi.Rd                      |    2 
 dartR-1.1.6/dartR/man/gl2phylip.Rd                  |    5 
 dartR-1.1.6/dartR/man/gl2plink.Rd                   |only
 dartR-1.1.6/dartR/man/gl2sa.Rd                      |only
 dartR-1.1.6/dartR/man/gl2shp.Rd                     |    9 
 dartR-1.1.6/dartR/man/gl2snapp.Rd                   |only
 dartR-1.1.6/dartR/man/gl2svdquartets.Rd             |    8 
 dartR-1.1.6/dartR/man/gl2treemix.Rd                 |only
 dartR-1.1.6/dartR/man/is.fixed.Rd                   |    2 
 dartR-1.1.6/dartR/man/platy.Rd                      |    2 
 dartR-1.1.6/dartR/man/possums.gl.Rd                 |only
 dartR-1.1.6/dartR/man/prob.hwe.Rd                   |    2 
 dartR-1.1.6/dartR/man/testset.gl.Rd                 |    2 
 dartR-1.1.6/dartR/man/testset_SNPs_2Row.Rd          |    2 
 dartR-1.1.6/dartR/man/testset_metadata.Rd           |    2 
 dartR-1.1.6/dartR/man/testset_pop_recode.Rd         |    2 
 dartR-1.1.6/dartR/man/util.outflank.Rd              |    2 
 dartR-1.1.6/dartR/man/util.outflank.plotter.Rd      |    4 
 dartR-1.1.6/dartR/man/utils.hamming.Rd              |    2 
 dartR-1.1.6/dartR/man/utils.hwe.Rd                  |    2 
 dartR-1.1.6/dartR/man/utils.recalc.avgpic.Rd        |    8 
 dartR-1.1.6/dartR/man/utils.recalc.callrate.Rd      |    4 
 dartR-1.1.6/dartR/man/utils.recalc.freqhets.Rd      |    4 
 dartR-1.1.6/dartR/man/utils.recalc.freqhomref.Rd    |    4 
 dartR-1.1.6/dartR/man/utils.recalc.freqhomsnp.Rd    |    4 
 dartR-1.1.6/dartR/man/utils.recalc.maf.Rd           |only
 dartR-1.1.6/dartR/vignettes/IntroTutorial_dartR.Rmd |   28 -
 212 files changed, 1526 insertions(+), 794 deletions(-)

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