Sun, 23 Apr 2017

Package SparseM updated to version 1.77 with previous version 1.76 dated 2017-03-12

Title: Sparse Linear Algebra
Description: Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.
Author: Roger Koenker <rkoenker@uiuc.edu> and Pin Ng <Pin.Ng@NAU.EDU>
Maintainer: Roger Koenker <rkoenker@uiuc.edu>

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Package PSF updated to version 0.4 with previous version 0.3 dated 2016-08-19

Title: Forecasting of Univariate Time Series Using the Pattern Sequence-Based Forecasting (PSF) Algorithm
Description: Pattern Sequence Based Forecasting (PSF) takes univariate time series data as input and assist to forecast its future values. This algorithm forecasts the behavior of time series based on similarity of pattern sequences. Initially, clustering is done with the labeling of samples from database. The labels associated with samples are then used for forecasting the future behaviour of time series data. The further technical details and references regarding PSF are discussed in Vignette.
Author: Neeraj Bokde, Gualberto Asencio-Cortes and Francisco Martinez-Alvarez
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>

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Package imputeTS updated to version 2.2 with previous version 2.1 dated 2017-04-18

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

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Package autothresholdr updated to version 0.4.0 with previous version 0.2.0 dated 2017-02-24

Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <http://imagej.net/Auto_Threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl], Luis Alvarez [ctb], Sergi Padilla-Parra [ctb, ths], Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package idem updated to version 2.0 with previous version 1.0 dated 2016-07-05

Title: Inference in Randomized Controlled Trials with Death and Missingness
Description: In randomized studies involving severely ill patients, functional outcomes are often unobserved due to missed clinic visits, premature withdrawal or death. It is well known that if these unobserved functional outcomes are not handled properly, biased treatment comparisons can be produced. In this package, we implement a procedure for comparing treatments that is based on the composite endpoint of both the functional outcome and survival. The procedure was proposed in Wang et al. (2016) <doi:10.1111/biom.12594>. It considers missing data imputation with a sensitivity analysis strategy to handle the unobserved functional outcomes not due to death.
Author: Chenguang Wang [aut, cre], Andrew Leroux [aut, cre], Elizabeth Colantuoni [aut], Daniel O Scharfstein [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>

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Package unpivotr updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-31

Title: Unpivot Complex and Irregular Data Layouts
Description: Tools for converting data from complex or irregular layouts to a columnar structure. For example, tables with multilevel column or row headers, or spreadsheets. Header and data cells are selected by their contents and position, as well as formatting and comments where available, and are associated with one other by their proximity in given directions.
Author: Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>

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Package startupmsg updated to version 0.9.4 with previous version 0.9.3 dated 2016-04-23

Title: Utilities for Start-Up Messages
Description: Provides utilities to create or suppress start-up messages.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

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Package ROptEst updated to version 1.0.1 with previous version 1.0 dated 2016-09-05

Title: Optimally Robust Estimation
Description: Optimally robust estimation in general smoothly parameterized models using S4 classes and methods.
Author: Matthias Kohl [cre, cph], Mykhailo Pupashenko [ctb] (contributed wrapper functions for diagnostic plots), Gerald Kroisandt [ctb] (contributed testing routines), Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package RobAStBase updated to version 1.0.1 with previous version 1.0 dated 2016-09-05

Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.
Author: Matthias Kohl [cre, cph, aut], Peter Ruckdeschel [aut, cph], Mykhailo Pupashenko [ctb] (contributed wrapper functions for diagnostic plots), Gerald Kroisandt [ctb] (contributed testing routines), R Core Team [ctb, cph] (for source file 'format.perc')
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package RandVar updated to version 1.0.1 with previous version 1.0 dated 2016-04-25

Title: Implementation of Random Variables
Description: Implements random variables by means of S4 classes and methods.
Author: Matthias Kohl [cre, cph, aut], Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package npROCRegression updated to version 1.0-5 with previous version 1.0-4 dated 2016-11-15

Title: Kernel-Based Nonparametric ROC Regression Modelling
Description: Implements several nonparametric regression approaches for the inclusion of covariate information on the receiver operating characteristic (ROC) framework.
Author: Maria Xose Rodriguez-Alvarez [aut, cre], Javier Roca-Pardinas [aut]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>

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Package MonteCarlo updated to version 1.0.2 with previous version 1.0.1 dated 2017-04-07

Title: Automatic Parallelized Monte Carlo Simulations
Description: Simplifies Monte Carlo simulation studies by automatically setting up loops to run over parameter grids and parallelising the Monte Carlo repetitions. It also generates LaTeX tables.
Author: Christian Hendrik Leschinski
Maintainer: Christian Hendrik Leschinski <leschinski@statistik.uni-hannover.de>

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Package GGIR updated to version 1.5-1 with previous version 1.4 dated 2017-01-22

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices, .csv-export data from Actigraph devices, and .wav-format data from Axivity. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>

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Package distrEx updated to version 2.6.1 with previous version 2.6 dated 2016-04-24

Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph, aut], Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package plspm updated to version 0.4.9 with previous version 0.4.8 dated 2017-04-21

Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM) analysis for both metric and non-metric data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre], Laura Trinchera [aut], Giorgio Russolillo [aut]
Maintainer: ORPHANED

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Package beanz updated to version 2.0 with previous version 1.7.1 dated 2016-11-14

Title: Bayesian Analysis of Heterogeneous Treatment Effect
Description: It is vital to assess the heterogeneity of treatment effects (HTE) when making health care decisions for an individual patient or a group of patients. Nevertheless, it remains challenging to evaluate HTE based on information collected from clinical studies that are often designed and conducted to evaluate the efficacy of a treatment for the overall population. The Bayesian framework offers a principled and flexible approach to estimate and compare treatment effects across subgroups of patients defined by their characteristics. This package allows users to explore a wide range of Bayesian HTE analysis models, and produce posterior inferences about HTE.
Author: Chenguang Wang [aut, cre], Ravi Varadhan [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>

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Package climextRemes updated to version 0.1.3 with previous version 0.1.2 dated 2016-08-10

Title: Tools for Analyzing Climate Extremes
Description: Functions for fitting GEV and POT (via point process fitting) models for extremes in climate data, providing return values, return probabilities, and return periods for stationary and nonstationary models. Also provides differences in return values and differences in log return probabilities for contrasts of covariate values. Functions for estimating risk ratios for event attribution analyses, including uncertainty. Under the hood, many of the functions use functions from extRemes, including for fitting the statistical models.
Author: Christopher Paciorek [aut, cre]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>

Diff between climextRemes versions 0.1.2 dated 2016-08-10 and 0.1.3 dated 2017-04-23

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Sat, 22 Apr 2017

Package SweaveListingUtils updated to version 0.7.7 with previous version 0.7.5 dated 2016-04-25

Title: Utilities for Sweave Together with TeX 'listings' Package
Description: Provides utilities for defining R / Rd as "language" for TeX-package "listings" and for including R / Rd source file (snippets) copied from R-forge in its most recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

Diff between SweaveListingUtils versions 0.7.5 dated 2016-04-25 and 0.7.7 dated 2017-04-22

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Package scatterplot3d updated to version 0.3-40 with previous version 0.3-39 dated 2017-03-30

Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

Diff between scatterplot3d versions 0.3-39 dated 2017-03-30 and 0.3-40 dated 2017-04-22

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Package readBrukerFlexData updated to version 1.8.5 with previous version 1.8.3 dated 2016-11-30

Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

Diff between readBrukerFlexData versions 1.8.3 dated 2016-11-30 and 1.8.5 dated 2017-04-22

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Package rdlocrand updated to version 0.2 with previous version 0.1 dated 2017-04-07

Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@umich.edu>

Diff between rdlocrand versions 0.1 dated 2017-04-07 and 0.2 dated 2017-04-22

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Package DMMF updated to version 0.3.2.0 with previous version 0.2.8.0 dated 2017-03-12

Title: Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model
Description: Implements the daily based Morgan-Morgan-Finney (DMMF) soil erosion model (Choi et al., 2017 <doi:10.3390/w9040278>) for estimating surface runoff and sediment budgets from a field or a catchment on a daily basis.
Author: Kwanghun Choi [aut, cre], Sebastian Arnhold [dtc, ctb], Bjoern Reineking [ths, ctb]
Maintainer: Kwanghun Choi <kwanghun.choi@yahoo.com>

Diff between DMMF versions 0.2.8.0 dated 2017-03-12 and 0.3.2.0 dated 2017-04-22

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Package BeviMed updated to version 5.0 with previous version 4.0 dated 2017-03-01

Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework.
Author: Daniel Greene, Sylvia Richardson and Ernest Turro
Maintainer: Daniel Greene <dg333@cam.ac.uk>

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Package support.BWS updated to version 0.1-4 with previous version 0.1-3 dated 2015-04-27

Title: Basic Functions for Supporting an Implementation of Best-Worst Scaling
Description: Provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

Diff between support.BWS versions 0.1-3 dated 2015-04-27 and 0.1-4 dated 2017-04-22

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Package RHMS updated to version 1.1 with previous version 1.0 dated 2017-04-21

Title: Hydrologic Modelling System for R Users
Description: Hydrologic modelling system is an object oriented tool which enables R users to simulate and analyze hydrologic events. The package proposes functions and methods for construction, simulation, visualization, and calibration of hydrologic systems.
Author: Rezgar Arabzadeh ; Shahab Araghinejad
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>

Diff between RHMS versions 1.0 dated 2017-04-21 and 1.1 dated 2017-04-22

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Package distr updated to version 2.6.2 with previous version 2.6 dated 2016-04-23

Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase --2005), Matthias Kohl [aut, cph], Peter Ruckdeschel [cre, cph], Thomas Stabla [ctb] (contributed as student in the initial phase --2005), R Core Team [ctb, cph] (for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>

Diff between distr versions 2.6 dated 2016-04-23 and 2.6.2 dated 2017-04-22

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Package deldir updated to version 0.1-14 with previous version 0.1-12 dated 2016-03-06

Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package treatSens updated to version 2.1.2 with previous version 2.1.1 dated 2017-04-20

Title: Sensitivity Analysis for Causal Inference
Description: Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.
Author: Nicole Bohme Carnegie [aut, cre], Masataka Harada [aut], Vincent Dorie [aut], Jennifer Hill [ctb]
Maintainer: Nicole Bohme Carnegie <carnegin@uwm.edu>

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Package HardyWeinberg updated to version 1.5.7 with previous version 1.5.6 dated 2016-03-29

Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>

Diff between HardyWeinberg versions 1.5.6 dated 2016-03-29 and 1.5.7 dated 2017-04-22

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Fri, 21 Apr 2017

Package phylobase updated to version 0.8.4 with previous version 0.8.2 dated 2016-01-22

Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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More information about phylobase at CRAN
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Package metaplot updated to version 0.1.2 with previous version 0.1.1 dated 2017-04-17

Title: Formalized Plots for Self-Describing Data
Description: Creates fully-annotated plots with minimum guidance. Since the data is self-describing, less effort is needed for creating the plot. Generally expects data of class folded (see fold package). If attributes GUIDE and LABEL are present, they will be used to create formal axis labels. Several aesthetics are supported, such as reference lines, unity lines, smooths, and log transformations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package EpiILM updated to version 1.2 with previous version 1.1 dated 2017-04-17

Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar. K. V. and Rob Deardon
Maintainer: Vineetha Warriyar. K. V. <vineethawarriyar.kod@ucalgary.ca>

Diff between EpiILM versions 1.1 dated 2017-04-17 and 1.2 dated 2017-04-21

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Package dtplyr updated to version 0.0.2 with previous version 0.0.1 dated 2016-06-27

Title: Data Table Back-End for 'dplyr'
Description: This implements the data table back-end for 'dplyr' so that you can seamlessly use data table and 'dplyr' together.
Author: Lionel Henry [cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between dtplyr versions 0.0.1 dated 2016-06-27 and 0.0.2 dated 2017-04-21

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Package waterData updated to version 1.0.7 with previous version 1.0.6 dated 2017-02-13

Title: Retrieval, Analysis, and Anomaly Calculation of Daily Hydrologic Time Series Data
Description: Imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services (see <https://waterservices.usgs.gov/> for more information), plots the data, addresses some common data problems, and calculates and plots anomalies.
Author: Karen R. Ryberg and Aldo V. Vecchia
Maintainer: Karen R. Ryberg <kryberg@usgs.gov>

Diff between waterData versions 1.0.6 dated 2017-02-13 and 1.0.7 dated 2017-04-21

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Package SGP updated to version 1.7-0.0 with previous version 1.6-0.0 dated 2017-01-01

Title: Student Growth Percentiles & Percentile Growth Trajectories
Description: Functions to calculate student growth percentiles and percentile growth projections/trajectories for students using large scale, longitudinal assessment data. Functions use quantile regression to estimate the conditional density associated with each student's achievement history. Percentile growth projections/trajectories are calculated using the coefficient matrices derived from the quantile regression analyses and specify what percentile growth is required for students to reach future achievement targets.
Author: Damian W. Betebenner [aut, cre], Adam R. Van Iwaarden [aut], Ben Domingue [aut], Yi Shang [aut], Jonathan Weeks [ctb], John Stewart [ctb], Jinnie Choi [ctb], Xin Wei [ctb], Hi Shin Shim [ctb], Xiaoyuan Tan [ctb] (Arizona Department of Education), Carrie Giovannini [ctb] (Arizona Department of Education), Sarah Polasky [ctb] (Arizona State University), Rebecca Gau [ctb] (Arizona Charter School Association), Jeffrey Dean [ctb] (University of Arkansas), William Bonk [ctb] (Colorado Department of Education), Marie Huchton [ctb] (Colorado Department of Education), Allison Timberlake [ctb] (Georgia Department of Education), Qi Qin [ctb] (Georgia Department of Education), Melissa Fincher [ctb] (Georgia Department of Education), Kiran Athota [ctb] (Georgia Department of Education), Travis Allen [ctb] (Georgia Department of Education), Glenn Hirata [ctb] (Hawaii Department of Education), Glenn Nochi [ctb] (Hawaii Department of Education), Joshua Lee [ctb] (Hawaii Department of Education), Ayaka Nukui [ctb] (Idaho Department of Education), Carissa Miller [ctb] (Idaho Department of Education), Matthew Raimondi [ctb] (Elgin Area School District U46 (Illinois)), Wes Bruce [ctb] (Indiana Department of Education), Robert Hochsegang [ctb] (Indiana Department of Education), Tony Moss [ctb] (Kansas State Department of Education), Xuewen Sheng [ctb] (Kansas State Department of Education), Kathy Flanagan [ctb] (Massachusetts Department of Elementary and Secondary Education), Robert Lee [ctb] (Massachusetts Department of Elementary and Secondary Education), Ji Zeng [ctb] (Michigan Department of Education), Steve Viger [ctb] (Michigan Department of Education), Joe DeCastra [ctb] (Mississippi Department of Education), Ken Thompson [ctb] (Mississippi Department of Education), Soo Yeon Cho [ctb] (Missouri Department of Education), Jeff Halsell [ctb] (Clark County School District, Nevada), Selcuk Ozdemir [ctb] (Washoe County School District, Nevada), Roger Silva [ctb] (Nevada Department of Education), Deb Wiswell [ctb] (New Hampshire Department of Education), Katya Levitan-Reiner [ctb] (New Haven Public Schools), Catherine McCaslin [ctb] (New Haven Public Schools), Joshua Marland [ctb] (New York Education Department), W Joshua Rew [ctb] (Oregon Department of Education), Jason Becker [ctb] (Rhode Island Department of Education), Jessica Bailey [ctb] (Rhode Island Department of Education), Ana Karantonis [ctb] (Rhode Island Department of Education), Deborah Jonas [ctb] (Virginia Department of Education), Juan D'Brot [ctb] (West Virginia Department of Education), Nate Hixson [ctb] (West Virginia Department of Education), Deb Came [ctb] (Washington Office of Superintendent of Public Instruction), Ashley Colburn [ctb] (Washington Office of Superintendent of Public Instruction), Nick Hassell [ctb] (Washington Office of Superintendent of Public Instruction), Krissy Johnson [ctb] (Washington Office of Superintendent of Public Instruction), Daniel Bush [ctb] (Wisconsin Department of Education), Justin Meyer [ctb] (Wisconsin Department of Education), Joseph Newton [ctb] (Wisconsin Department of Education), Nick Stroud [ctb] (Wisconsin Department of Education), John Paul [ctb] (Wyoming Department of Education), Michael Flicek [ctb] (Michael Flicek Projects LLC working with Wyoming Department of Education), Phyllis Clay [ctb] (Albuquerque Public Schools), Peter Kinyua [ctb] (Albuquerque Public Schools), Brendan Houng [ctb] (University of Melbourne, Australia, NAPLAN), Leslie Rosale [ctb] (Ministry of Education, Guatemala), Nathan Wall [ctb] (eMetric working with Nevada Department of Education and South Dakota Department of Education), Narek Sahakyan [ctb] (World Class Instruction and Design (WIDA))
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>

Diff between SGP versions 1.6-0.0 dated 2017-01-01 and 1.7-0.0 dated 2017-04-21

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Package crawl updated to version 2.1.1 with previous version 2.0.1 dated 2016-07-29

Title: Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data
Description: Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>

Diff between crawl versions 2.0.1 dated 2016-07-29 and 2.1.1 dated 2017-04-21

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Package batchtools updated to version 0.9.3 with previous version 0.9.2 dated 2017-02-20

Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>), 'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>), 'TORQUE/PBS' (<http://www.adaptivecomputing.com/products/open-source/torque/>), or 'Docker Swarm' (<https://docs.docker.com/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut], Bernd Bischl [aut], Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between batchtools versions 0.9.2 dated 2017-02-20 and 0.9.3 dated 2017-04-21

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Package SIS updated to version 0.8-4 with previous version 0.8-3 dated 2016-10-12

Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) and all of its variants in generalized linear models and the Cox proportional hazards model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Yang Feng <yang.feng@columbia.edu>

Diff between SIS versions 0.8-3 dated 2016-10-12 and 0.8-4 dated 2017-04-21

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Package sinaplot updated to version 1.1.0 with previous version 1.0.0 dated 2016-10-11

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

Diff between sinaplot versions 1.0.0 dated 2016-10-11 and 1.1.0 dated 2017-04-21

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Package RpeakChrom updated to version 1.1.0 with previous version 0.1.0 dated 2016-12-14

Title: Tools for Chromatographic Column Characterization and Modelling Chromatographic Peak
Description: The quantitative measurement and detection of molecules in HPLC should be carried out by an accurate description of chromatographic peaks. In this package non-linear fitting using a modified Gaussian model with a parabolic variance (PVMG) has been implemented to obtain the retention time and height at the peak maximum. This package also includes the traditional Van Deemter approach and two alternatives approaches to characterize chromatographic column.
Author: Manuel David Peris Diaz, Maria Isabel Alcoriza Balaguer
Maintainer: Manuel David Peris Diaz <madape@alumni.uv.es>

Diff between RpeakChrom versions 0.1.0 dated 2016-12-14 and 1.1.0 dated 2017-04-21

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Package PRROC updated to version 1.3 with previous version 1.1 dated 2015-02-25

Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau <grau@informatik.uni-halle.de>

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Package microPop updated to version 1.2 with previous version 1.1 dated 2017-04-07

Title: Modelling Microbial Populations
Description: Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time.
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>

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Package installr updated to version 0.19.0 with previous version 0.18.0 dated 2016-11-05

Title: Using R to Install Stuff (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Barry Rowlingson [ctb], Boris Hejblum [ctb], Dason [ctb], Felix Schonbrodt [ctb], G. Grothendieck [ctb], GERGELY DAROCZI [ctb], Heuristic Andrew [ctb], James [ctb] (http://stackoverflow.com/users/269476/james), Thomas Leeper [ctb] (http://thomasleeper.com/), VitoshKa [ctb], Yihui Xie [ctb] (http://yihui.name), Michael Friendly [ctb] (http://datavis.ca/), Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/), Dieter Menne [ctb], Tyler Hunt [ctb] (https://github.com/JackStat), Takekatsu Hiramura [ctb] (https://github.com/hiratake55), Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool), Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey), Tom Allard [ctb], ChingChuan Chen [ctb], Jonathan Hill [ctb]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package earth updated to version 4.5.0 with previous version 4.4.9.1 dated 2017-03-21

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>

Diff between earth versions 4.4.9.1 dated 2017-03-21 and 4.5.0 dated 2017-04-21

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Package DMRMark updated to version 1.1.1 with previous version 1.1.0 dated 2017-02-25

Title: DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data
Description: Perform differential analysis for methylation array data. Detect differentially methylated regions (DMRs) from array M-values. The core is a Non-homogeneous Hidden Markov Model for estimating spatial correlation and a novel Constrained Gaussian Mixture Model for modeling the M-value pairs of each individual locus.
Author: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Maintainer: Linghao SHEN <sl013@ie.cuhk.edu.hk>

Diff between DMRMark versions 1.1.0 dated 2017-02-25 and 1.1.1 dated 2017-04-21

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Package tidyjson updated to version 0.2.2 with previous version 0.2.1 dated 2015-05-02

Title: A Grammar for Turning 'JSON' into Tidy Tables
Description: An easy and consistent way to turn 'JSON' into tidy data frames that are natural to work with in 'dplyr', 'ggplot2' and other tools.
Author: Jeremy Stanley <jeremy.stanley@gmail.com>
Maintainer: ORPHANED

Diff between tidyjson versions 0.2.1 dated 2015-05-02 and 0.2.2 dated 2017-04-21

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Package regress updated to version 1.3-15 with previous version 1.3-14 dated 2014-07-14

Title: Gaussian Linear Models with Linear Covariance Structure
Description: Functions to fit Gaussian linear model by maximising the residual log likelihood where the covariance structure can be written as a linear combination of known matrices. Can be used for multivariate models and random effects models. Easy straight forward manner to specify random effects models, including random interactions. Code now optimised to use Sherman Morrison Woodbury identities for matrix inversion in random effects models. We've added the ability to fit models using any kernel as well as a function to return the mean and covariance of random effects conditional on the data (BLUPs).
Author: David Clifford and Peter McCullagh. Additional contributions by HJ Auinger.
Maintainer: ORPHANED

Diff between regress versions 1.3-14 dated 2014-07-14 and 1.3-15 dated 2017-04-21

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Package plspm updated to version 0.4.8 with previous version 0.4.7 dated 2015-05-25

Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM) analysis for both metric and non-metric data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre], Laura Trinchera [aut], Giorgio Russolillo [aut]
Maintainer: ORPHANED

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Package Metrics updated to version 0.1.2 with previous version 0.1.1 dated 2012-06-20

Title: Evaluation Metrics for Machine Learning
Description: Metrics is a set of evaluation metrics that is commonly used in supervised machine learning.
Author: Ben Hamner <ben@benhamner.com>
Maintainer: ORPHANED

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Package synbreed updated to version 0.12-6 with previous version 0.12-5 dated 2017-04-20

Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://www.synbreed.tum.de>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Hans-Juergen Auinger, Valentin Wimmer, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>

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Package rpart updated to version 4.1-11 with previous version 4.1-10 dated 2015-06-29

Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package ratesci updated to version 0.2-0 with previous version 0.1-0 dated 2016-11-12

Title: Confidence Intervals for Comparisons of Binomial or Poisson Rates
Description: Computes confidence intervals for the rate (or risk) difference ("RD") or rate ratio (or relative risk, "RR") for binomial proportions or Poisson rates, or for odds ratio ("OR", binomial only). Also confidence intervals for a single binomial or Poisson rate, and intervals for matched pairs. Includes asymptotic score methods including skewness corrections, which have been developed in Laud (2017, in press) from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart & Nam (1988) <doi:10.2307/2531848>. Also includes MOVER methods (Method Of Variance Estimates Recovery), derived from the Newcombe method but using equal-tailed Jeffreys intervals, and generalised for incorporating prior information. Also methods for stratified calculations (e.g. meta-analysis), either assuming fixed effects or incorporating stratum heterogeneity.
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <p.j.laud@sheffield.ac.uk>

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Package MASS updated to version 7.3-47 with previous version 7.3-45 dated 2015-11-10

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package huxtable updated to version 0.2.0 with previous version 0.1.1 dated 2017-03-14

Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package boot updated to version 1.3-19 with previous version 1.3-18 dated 2016-02-23

Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package KENDL updated to version 1.1 with previous version 1.0 dated 2017-03-21

Title: Kernel-Smoothed Nonparametric Methods for Environmental Exposure Data Subject to Detection Limits
Description: Calculate the kernel-smoothed nonparametric estimator for the exposure distribution in presence of detection limits.
Author: Yuchen Yang <yuchen.y@uky.edu>, Li Chen <lichenuky@uky.edu>
Maintainer: Yuchen Yang <yuchen.y@uky.edu>

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Package FRK updated to version 0.1.2 with previous version 0.1.1 dated 2017-03-07

Title: Fixed Rank Kriging
Description: Fixed Rank Kriging is a tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach, discussed in Cressie and Johannesson (2008) <DOI:10.1111/j.1467-9868.2007.00633.x>, decomposes the field, and hence the covariance function, using a fixed set of n basis functions, where n is typically much smaller than the number of data points (or polygons) m. The method naturally allows for non-stationary, anisotropic covariance functions and the use of observations with varying support (with known error variance). The projected field is a key building block of the Spatial Random Effects (SRE) model, on which this package is based. The package FRK provides helper functions to model, fit, and predict using an SRE with relative ease.
Author: Andrew Zammit-Mangion [aut, cre], Timothy Davis [ctb], Patrick Amestoy [ctb], Iain Duff [ctb], John K. Reid [ctb]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>

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Package vennplot updated to version 0.9.02 with previous version 0.9.01 dated 2017-04-14

Title: Venn Diagrams in 2D and 3D
Description: Calculate and plot Venn diagrams in 2D and 3D.
Author: Zehao Xu [aut, cre], R. Wayne Oldford [ctb], Martin Lysy [ctb]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>

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Package unix updated to version 1.3 with previous version 1.0 dated 2017-04-03

Title: Unix System Utilities
Description: Bindings to system utilities found in most Unix systems such as POSIX functions which are not part of the Standard C Library.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package spocc updated to version 0.7.0 with previous version 0.6.0 dated 2016-12-07

Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Author: Scott Chamberlain [aut, cre], Karthik Ram [ctb], Ted Hart [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package Rgb updated to version 1.5.1 with previous version 1.5.0 dated 2017-03-03

Title: The R Genome Browser
Description: Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as genes or transcripts), and an interactive interface to browse them.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal <maressyl@gmail.com>

Diff between Rgb versions 1.5.0 dated 2017-03-03 and 1.5.1 dated 2017-04-21

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Package RcppCCTZ updated to version 0.2.2 with previous version 0.2.1 dated 2017-02-04

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppCCTZ versions 0.2.1 dated 2017-02-04 and 0.2.2 dated 2017-04-21

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Package rcompanion updated to version 1.5.6 with previous version 1.5.0 dated 2017-03-03

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Education Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

Diff between rcompanion versions 1.5.0 dated 2017-03-03 and 1.5.6 dated 2017-04-21

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Package Morpho updated to version 2.5.1 with previous version 2.5 dated 2017-04-05

Title: Calculations and Visualisations Related to Geometric Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph], Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>

Diff between Morpho versions 2.5 dated 2017-04-05 and 2.5.1 dated 2017-04-21

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Package memoise updated to version 1.1.0 with previous version 1.0.0 dated 2016-01-29

Title: Memoisation of Functions
Description: Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Kirill Müller [aut], Daniel Cook [aut]
Maintainer: Jim Hester <jim.hester@rstudio.com>

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Package Hotelling updated to version 1.0-3 with previous version 1.0-2 dated 2013-11-06

Title: Hotelling's T^2 Test and Variants
Description: A set of R functions which implements Hotelling's T^2 test and some variants of it. Functions are also included for Aitchison's additive log ratio and centred log ratio transformations.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>

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Package gam updated to version 1.14-3 with previous version 1.14 dated 2016-09-10

Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>

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More information about gam at CRAN
Permanent link

Package FREGAT updated to version 1.0.3 with previous version 1.0.2 dated 2016-09-19

Title: Family REGional Association Tests
Description: Fast regional association analysis of quantitative traits for family-based and population studies.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and Gulnara R. Svishcheva <gulsvi@mail.ru>, with contributions from: Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method), Thomas Lumley ('kuonen' method), James O. Ramsay (functional data analysis functions), David Clayton ('read.plink' function) and Brian Ripley ('ginv' function)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>

Diff between FREGAT versions 1.0.2 dated 2016-09-19 and 1.0.3 dated 2017-04-21

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Package depend.truncation updated to version 2.6 with previous version 2.5 dated 2016-04-14

Title: Statistical Inference for Parametric and Semiparametric Models Based on Dependently Truncated Data
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj), subject to Xj<=Yj, for all j=1,...,n, are called truncated data. For truncated data, several different approaches are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between depend.truncation versions 2.5 dated 2016-04-14 and 2.6 dated 2017-04-21

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Package dat updated to version 0.2.0 with previous version 0.1.0 dated 2017-01-06

Title: Tools for Data Manipulation
Description: An implementation of common higher order functions with syntactic sugar for anonymous function. Provides also a link to 'dplyr' for common transformations on data frames to work around non standard evaluation by default.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

Diff between dat versions 0.1.0 dated 2017-01-06 and 0.2.0 dated 2017-04-21

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More information about dat at CRAN
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Package CrossScreening updated to version 0.1.1 with previous version 0.0.1 dated 2017-03-12

Title: Cross-Screening in Observational Studies that Test Many Hypotheses
Description: Cross-screening is a new method that uses both random halves of the sample to screen and test many hypotheses. It generally improves statistical power in observational studies when many hypotheses are tested simultaneously. References: 1. Qingyuan Zhao, Dylan S Small, and Paul R Rosenbaum. Cross-screening in observational studies that test many hypotheses. <arXiv:1703.02078>. 2. Qingyuan Zhao. On sensitivity value of pair-matched observational studies. <arXiv:1702.03442>.
Author: Paul Rosenbaum [aut], Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@wharton.upenn.edu>

Diff between CrossScreening versions 0.0.1 dated 2017-03-12 and 0.1.1 dated 2017-04-21

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Package clifro updated to version 3.1-4 with previous version 3.1-3 dated 2017-03-16

Title: Easily Download and Visualise Climate Data from CliFlo
Description: CliFlo is a web portal to the New Zealand National Climate Database and provides public access (via subscription) to around 6,500 various climate stations (see <https://cliflo.niwa.co.nz/> for more information). Collating and manipulating data from CliFlo (hence clifro) and importing into R for further analysis, exploration and visualisation is now straightforward and coherent. The user is required to have an internet connection, and a current CliFlo subscription (free) if data from stations, other than the public Reefton electronic weather station, is sought.
Author: Blake Seers [aut, cre]
Maintainer: Blake Seers <blake.seers@gmail.com>

Diff between clifro versions 3.1-3 dated 2017-03-16 and 3.1-4 dated 2017-04-21

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Thu, 20 Apr 2017

Package units updated to version 0.4-4 with previous version 0.4-3 dated 2017-03-25

Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors; automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the difftime class. Uses the UNIDATA udunits library and unit database for unit conversion and compatibility checking.
Author: Edzer Pebesma [aut, cre], Thomas Mailund [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between units versions 0.4-3 dated 2017-03-25 and 0.4-4 dated 2017-04-20

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Package rpart.plot updated to version 2.1.2 with previous version 2.1.1 dated 2017-02-17

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

Diff between rpart.plot versions 2.1.1 dated 2017-02-17 and 2.1.2 dated 2017-04-20

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Package gistr updated to version 0.4.0 with previous version 0.3.6 dated 2015-12-23

Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g., <http://en.wikipedia.org/wiki/GitHub#Gist>, <https://help.github.com/articles/about-gists/>). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: <https://gist.github.com/>.
Author: Scott Chamberlain [aut, cre], Ramnath Vaidyanathan [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between gistr versions 0.3.6 dated 2015-12-23 and 0.4.0 dated 2017-04-20

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Package WufooR updated to version 0.6.2 with previous version 0.6.1 dated 2016-03-08

Title: R Wrapper for the 'Wufoo.com' - The Form Building Service
Description: Allows form managers to download entries from their respondents using Wufoo JSON API (<https://www.wufoo.com>). Additionally, the Wufoo reports - when public - can be also acquired programmatically. Note that building new forms within this package is not supported.
Author: John Malc [aut, cre] (@dmpe), Maksim Pecherskiy [ctb] (@MrMaksimize)
Maintainer: John Malc <cincenko@outlook.com>

Diff between WufooR versions 0.6.1 dated 2016-03-08 and 0.6.2 dated 2017-04-20

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Package treatSens updated to version 2.1.1 with previous version 2.1 dated 2017-04-06

Title: Sensitivity Analysis for Causal Inference
Description: Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.
Author: Nicole Bohme Carnegie [aut, cre], Masataka Harada [aut], Vincent Dorie [aut], Jennifer Hill [ctb]
Maintainer: Nicole Bohme Carnegie <carnegin@uwm.edu>

Diff between treatSens versions 2.1 dated 2017-04-06 and 2.1.1 dated 2017-04-20

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Package sys updated to version 1.3 with previous version 1.2 dated 2017-04-01

Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior across platforms. Supports interruption, background tasks, and full control over STDOUT / STDERR binary or text streams. On Unix systems the package also has functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.
Author: Jeroen Ooms [aut, cre], Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between sys versions 1.2 dated 2017-04-01 and 1.3 dated 2017-04-20

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Package LOST updated to version 1.3 with previous version 1.2 dated 2016-06-22

Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric data randomly, with taxonomic bias and with anatomical bias. LOST also includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour, C. Brown
Maintainer: J. Arbour <jarbour@uw.edu>

Diff between LOST versions 1.2 dated 2016-06-22 and 1.3 dated 2017-04-20

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Package synbreed updated to version 0.12-5 with previous version 0.12-4 dated 2017-04-06

Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://www.synbreed.tum.de>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Hans-Juergen Auinger, Valentin Wimmer, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>

Diff between synbreed versions 0.12-4 dated 2017-04-06 and 0.12-5 dated 2017-04-20

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Package stepR updated to version 1.0-7 with previous version 1.0-6 dated 2016-10-17

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

Diff between stepR versions 1.0-6 dated 2016-10-17 and 1.0-7 dated 2017-04-20

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Package Rblpapi updated to version 0.3.6 with previous version 0.3.5 dated 2016-10-25

Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rblpapi versions 0.3.5 dated 2016-10-25 and 0.3.6 dated 2017-04-20

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Package LINselect updated to version 1.1 with previous version 0.0-2 dated 2015-08-26

Title: Selection of Linear Estimators
Description: Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Author: Yannick Baraud, Christophe Giraud, Sylvie Huet
Maintainer: Annie Bouvier <Annie.Bouvier@inra.fr>

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Package ImputeRobust updated to version 1.1-2 with previous version 1.1-1 dated 2017-02-27

Title: Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape
Description: Provides new imputation methods for the 'mice' package based on generalized additive models for location, scale, and shape (GAMLSS) as described in de Jong, van Buuren and Spiess <doi:10.1080/03610918.2014.911894>.
Author: Daniel Salfran [aut, cre], Martin Spiess [aut, ths]
Maintainer: Daniel Salfran <daniel.salfran@uni-hamburg.de>

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Package subniche updated to version 0.9.6 with previous version 0.9.4 dated 2017-03-29

Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays.
Author: Stephane Karasiewicz
Maintainer: Stephane Karasiewicz <stephane.karasiewicz@wanadoo.fr>

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Package prozor updated to version 0.2.3 with previous version 0.1.1 dated 2015-09-05

Title: Minimal Protein Set Explaining Peptide Spectrum Matches
Description: Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating libraries with decoys. Planned is peptide FDR estimation for search results.
Author: Witold Wolski
Maintainer: Witold Wolski <wewolski@gmail.com>

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Package dotwhisker updated to version 0.2.6 with previous version 0.2.5 dated 2017-04-06

Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt [aut], Yue Hu [aut, cre], Oliver Keyes [ctb], Ben Bolker [ctb], Stefan Müller [ctb]
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

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Package validann updated to version 1.2.1 with previous version 1.2.0 dated 2016-11-16

Title: Validation Tools for Artificial Neural Networks
Description: Methods and tools for analysing and validating the outputs and modelled functions of artificial neural networks (ANNs) in terms of predictive, replicative and structural validity. Also provides a method for fitting feed-forward ANNs with a single hidden layer.
Author: Greer B. Humphrey [aut, cre]
Maintainer: Greer B. Humphrey <greer.humphrey@student.adelaide.edu.au>

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Package RCALI updated to version 0.2-18 with previous version 0.2-17 dated 2016-09-21

Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.
Author: Annie Bouvier, Kien Kieu, Kasia Adamczyk, and Herve Monod
Maintainer: Annie Bouvier <Annie.Bouvier@inra.fr>

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Package quanteda updated to version 0.9.9-50 with previous version 0.9.9-24 dated 2017-02-13

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible framework for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre, cph], Kohei Watanabe [ctb], Paul Nulty [ctb], Adam Obeng [ctb], Haiyan Wang [ctb], Benjamin Lauderdale [ctb], Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package prcbench updated to version 0.7.3 with previous version 0.6.2 dated 2016-11-22

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

Diff between prcbench versions 0.6.2 dated 2016-11-22 and 0.7.3 dated 2017-04-20

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Package markdown updated to version 0.8 with previous version 0.7.7 dated 2015-04-22

Title: 'Markdown' Rendering for R
Description: Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.
Author: JJ Allaire [aut], Jeffrey Horner [aut], Henrik Bengtsson [ctb], Jim Hester [ctb], Yixuan Qiu [ctb], Kohske Takahashi [ctb], Adam November [ctb], Nacho Caballero [ctb], Jeroen Ooms [ctb], Thomas Leeper [ctb], Joe Cheng [ctb], Andrzej Oles [ctb], Vicent Marti [aut, cph] (The Sundown library), Natacha Porte [aut, cph] (The Sundown library), RStudio [cph], Yihui Xie [cre, ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package BIOdry updated to version 0.5 with previous version 0.4 dated 2017-01-17

Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>

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Package antaresRead updated to version 1.1.2 with previous version 1.1.1 dated 2017-04-03

Title: Import, Manipulate and Explore the Results of an Antares Simulation
Description: Import, manipulate and explore results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>).
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between antaresRead versions 1.1.1 dated 2017-04-03 and 1.1.2 dated 2017-04-20

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Package antaresProcessing updated to version 0.10.1 with previous version 0.10.0 dated 2017-04-06

Title: Antares Results Processing
Description: Process results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between antaresProcessing versions 0.10.0 dated 2017-04-06 and 0.10.1 dated 2017-04-20

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Package abctools updated to version 1.1.1 with previous version 1.0.4 dated 2016-01-14

Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre], Dennis Prangle [aut], Guilhereme Rodrigues [ctb]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>

Diff between abctools versions 1.0.4 dated 2016-01-14 and 1.1.1 dated 2017-04-20

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Package multivator updated to version 1.1-6 with previous version 1.1-4 dated 2013-12-05

Title: A Multivariate Emulator
Description: A multivariate generalization of the emulator package.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between multivator versions 1.1-4 dated 2013-12-05 and 1.1-6 dated 2017-04-20

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Wed, 19 Apr 2017

Package rfishbase updated to version 2.1.2 with previous version 2.1.1 dated 2016-07-21

Title: R Interface to 'FishBase'
Description: A programmatic interface to <http://www.fishbase.org>, re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to <http://www.sealifebase.org> data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut], Scott Chamberlain [aut], Duncan Temple Lang [aut], Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>

Diff between rfishbase versions 2.1.1 dated 2016-07-21 and 2.1.2 dated 2017-04-19

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Package rarhsmm updated to version 1.0.2 with previous version 1.0.1 dated 2017-04-12

Title: Regularized Autoregressive Hidden Semi Markov Model
Description: Fit Gaussian hidden Markov (or semi-Markov) models with / without autoregressive coefficients and with / without regularization. The fitting algorithm for the hidden Markov model is illustrated by Rabiner (1989) <doi:10.1109/5.18626>. The shrinkage estimation on the covariance matrices is based on the graphical lasso method by Freedman (2007) <doi:10.1093/biostatistics/kxm045>. The shrinkage estimation on the autoregressive coefficients uses the elastic net shrinkage detailed in Zou (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun Xu <zekunxu@gmail.com>

Diff between rarhsmm versions 1.0.1 dated 2017-04-12 and 1.0.2 dated 2017-04-19

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Package paleomorph updated to version 0.1.4 with previous version 0.1.3 dated 2016-09-29

Title: Geometric Morphometric Tools for Paleobiology
Description: Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.
Author: Tim Lucas, Anjali Goswami
Maintainer: Tim Lucas <timcdlucas@gmail.com>

Diff between paleomorph versions 0.1.3 dated 2016-09-29 and 0.1.4 dated 2017-04-19

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