Wed, 20 Jun 2018

Package Gmisc updated to version 1.6.2 with previous version 1.6.1 dated 2018-04-21

Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories, flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>

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Package smicd updated to version 1.0.1 with previous version 1.0.0 dated 2018-06-12

Title: Statistical Methods for Interval Censored Data
Description: Functions that provide statistical methods for interval censored (grouped) data. The package supports the estimation of linear and linear mixed regression models with interval censored dependent variables. Parameter estimates are obtained by a stochastic expectation maximization algorithm. Furthermore, the package enables the direct (without covariates) estimation of statistical indicators from interval censored data via an iterative kernel density algorithm. Survey and Organisation for Economic Co-operation and Development (OECD) weights can be included into the direct estimation (see, Groß, M., U. Rendtel, T. Schmid, S. Schmon, and N. Tzavidis (2017) <doi:10.1111/rssa.12179>).
Author: Paul Walter
Maintainer: Paul Walter <paul.walter@fu-berlin.de>

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Package rEDM updated to version 0.7.1 with previous version 0.6.9 dated 2017-12-04

Title: Applications of Empirical Dynamic Modeling from Time Series
Description: A new implementation of EDM algorithms based on research software previously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) <DOI:10.1126/science.1227079> and multiview embedding as described in Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>.
Author: Hao Ye [aut, cre], Adam Clark [aut], Ethan Deyle [aut], Steve Munch [aut], Jun Cai [ctb], Jane Cowles [ctb], Yair Daon [ctb], Andrew Edwards [ctb], Oliver Keyes [ctb], James Stagge [ctb], Masayuki Ushio [ctb], Ethan White [ctb], George Sugihara [ctb, ccp]
Maintainer: Hao Ye <hao.ye@weecology.org>

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Package VarSelLCM updated to version 2.1.2 with previous version 2.1.1 dated 2018-04-12

Title: Variable Selection for Model-Based Clustering of Mixed-Type Data Set with Missing Values
Description: Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>

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Package modifiedmk updated to version 1.1.0 with previous version 0.1.2 dated 2018-03-03

Title: Modified Mann Kendall Trend Tests
Description: Power of non-parametric Mann-Kendall test is highly influenced by serially correlated data. To address this issue, original time-series may be modified by the following approaches namely Prewhitening (PW), Trend Free Prewhitening (TFPW) and Modified Mann-Kendall tests through variance correction approach by calculating effective sample size. Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>. Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>. Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>. Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>. Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>.
Author: Sandeep Kumar Patakamuri [aut, cre], Nicole O'Brien [ctb]
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>

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Package hsdar updated to version 0.7.1 with previous version 0.7.0 dated 2017-12-14

Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [aut], Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>

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Package mortAAR updated to version 1.0.1 with previous version 1.0.0 dated 2017-10-20

Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality data (on the topic see e.g. Chamberlain 2006 <https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>). It takes demographic data in different formats and displays the result in a standard life table as well as plots the relevant indices (percentage of deaths, survivorship, probability of death, life expectancy, percentage of population).
Author: Nils Mueller-Scheessel [aut, cre, cph], Martin Hinz [aut], Clemens Schmid [aut], Christoph Rinne [aut], Daniel Knitter [aut], Wolfgang Hamer [aut], Dirk Seidensticker [aut], Franziska Faupel [aut], Carolin Tietze [aut], Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>

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Package ggpol updated to version 0.0.2 with previous version 0.0.1 dated 2018-04-26

Title: Visualizing Social Science Data with 'ggplot2'
Description: A 'ggplot2' extension for implementing parliament charts and several other useful visualizations.
Author: Frederik Tiedemann [aut, cre]
Maintainer: Frederik Tiedemann <fj.tiedemann@googlemail.com>

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Package rsimsum updated to version 0.3.3 with previous version 0.3.1 dated 2018-04-04

Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (See White I.R., 2010 <http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>

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Package womblR updated to version 1.0.3 with previous version 1.0.2 dated 2017-09-12

Title: Spatiotemporal Boundary Detection Model for Areal Unit Data
Description: Implements a spatiotemporal boundary detection model with a dissimilarity metric for areal data with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget), probit or Tobit link and spatial correlation is introduced at each time point through a conditional autoregressive (CAR) prior. Temporal correlation is introduced through a hierarchical structure and can be specified as exponential or first-order autoregressive. Full details of the package can be found in the accompanying vignette. Furthermore, the details of the package can be found in the corresponding paper on arXiv by Berchuck et al (2018): "Diagnosing Glaucoma Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method", <arXiv:1805.11636>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>

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New package MetaSubtract with initial version 1.41
Package: MetaSubtract
Type: Package
Title: Subtracting Summary Statistics of One or more Cohorts from Meta-GWAS Results
Version: 1.41
Date: 2018-06-19
Author: Ilja M. Nolte
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Description: If results from a meta-GWAS are used for validation in one of the cohorts that was included in the meta-analysis, this will yield biased (i.e. too optimistic) results. The validation cohort needs to be independent from the meta-Genome-Wide-Association-Study (meta-GWAS) results. 'MetaSubtract' will subtract the results of the respective cohort from the meta-GWAS results analytically without having to redo the meta-GWAS analysis using the leave-one-out methodology. It can handle different meta-analyses methods and takes into account if single or double genomic control correction was applied to the original meta-analysis. It can also handle different meta-analysis methods. It can be used for whole GWAS, but also for a limited set of genetic markers.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2018-06-20 08:32:52 UTC; NolteIM
Repository: CRAN
Date/Publication: 2018-06-20 13:43:02 UTC

More information about MetaSubtract at CRAN
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Package sjmisc updated to version 2.7.3 with previous version 2.7.2 dated 2018-05-06

Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a 'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package fluxweb updated to version 0.1.1 with previous version 0.1.0 dated 2018-03-09

Title: Estimate Energy Fluxes in Food Webs
Description: Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.
Author: Benoit Gauzens
Maintainer: Benoit Gauzens <benoit.gauzens@gmail.com>

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Package projections updated to version 0.3.0 with previous version 0.1.1 dated 2018-05-29

Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R0 in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>.
Author: Thibaut Jombart [aut, cre], Pierre Nouvellet [aut], Sangeeta Bhatia [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

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Package SDLfilter updated to version 1.1.1 with previous version 1.1.0 dated 2018-04-27

Title: Filtering Satellite-Derived Locations
Description: Functions to filter GPS and/or Argos locations. The provided filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as proposed in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <takahiro.shimada@my.jcu.edu.au>

Diff between SDLfilter versions 1.1.0 dated 2018-04-27 and 1.1.1 dated 2018-06-20

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Package imputeTS updated to version 2.7 with previous version 2.6 dated 2018-03-20

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series. Offers several imputation functions and missing data plots. Available imputation algorithms include: 'Mean', 'LOCF', 'Interpolation', 'Moving Average', 'Seasonal Decomposition', 'Kalman Smoothing on Structural Time Series models', 'Kalman Smoothing on ARIMA models'.
Author: Steffen Moritz [aut, cre, cph] (<https://orcid.org/0000-0002-0085-1804>)
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

Diff between imputeTS versions 2.6 dated 2018-03-20 and 2.7 dated 2018-06-20

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 imputeTS-2.7/imputeTS/DESCRIPTION                                                     |   20 +-
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 imputeTS-2.7/imputeTS/NAMESPACE                                                       |    2 
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 imputeTS-2.7/imputeTS/R/na.kalman.R                                                   |    4 
 imputeTS-2.7/imputeTS/R/na.locf.R                                                     |    4 
 imputeTS-2.7/imputeTS/R/na.ma.R                                                       |    4 
 imputeTS-2.7/imputeTS/R/na.mean.R                                                     |    5 
 imputeTS-2.7/imputeTS/R/na.random.R                                                   |    4 
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 imputeTS-2.7/imputeTS/R/na.seadec.R                                                   |    4 
 imputeTS-2.7/imputeTS/R/na.seasplit.R                                                 |    4 
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 imputeTS-2.7/imputeTS/R/plotNA.gapsize.R                                              |    4 
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 imputeTS-2.7/imputeTS/R/statsNA.R                                                     |    4 
 imputeTS-2.7/imputeTS/README.md                                                       |   23 +-
 imputeTS-2.7/imputeTS/inst/CITATION                                                   |    7 
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 imputeTS-2.7/imputeTS/src/locf.cpp                                                    |    4 
 imputeTS-2.7/imputeTS/src/register.c                                                  |    4 
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Package randomizeBE updated to version 0.3-4 with previous version 0.3-3 dated 2017-03-22

Title: Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>

Diff between randomizeBE versions 0.3-3 dated 2017-03-22 and 0.3-4 dated 2018-06-20

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Package MortalityLaws updated to version 1.4.0 with previous version 1.3.0 dated 2018-01-11

Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct full and abridge life tables given various input indices. A mortality law is a parametric function that describes the dying-out process of individuals in a population during a significant portion of their life spans. For a comprehensive review of the most important mortality laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>. An elegant function for downloading data from Human Mortality Database <http://www.mortality.org> is provided as well.
Author: Marius D. Pascariu [aut, cre], Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>

Diff between MortalityLaws versions 1.3.0 dated 2018-01-11 and 1.4.0 dated 2018-06-20

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Package vertexenum updated to version 1.0.2 with previous version 1.0.1 dated 2015-07-17

Title: Vertex Enumeration of Polytopes
Description: When given a description of a polyhedral set by a system of linear inequalities Ax <= b, produce the list of the vertices of the set.
Author: Robert Robere
Maintainer: Robert Robere <robere@cs.toronto.edu>

Diff between vertexenum versions 1.0.1 dated 2015-07-17 and 1.0.2 dated 2018-06-20

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Package emojifont updated to version 0.5.2 with previous version 0.5.1 dated 2017-11-02

Title: Emoji and Font Awesome in Graphics
Description: An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Claus Thorn Ekstrøm [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between emojifont versions 0.5.1 dated 2017-11-02 and 0.5.2 dated 2018-06-20

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Package visualFields updated to version 0.5.4 with previous version 0.4.3 dated 2016-01-16

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <ivan.marin.franch@gmail.com>
Maintainer: Ivan Marin-Franch <ivan.marin.franch@gmail.com>

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Package momentuHMM updated to version 1.4.2 with previous version 1.4.1 dated 2018-05-21

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

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Package mice updated to version 3.1.0 with previous version 3.0.0 dated 2018-05-25

Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Author: Stef van Buuren [aut, cre], Karin Groothuis-Oudshoorn [aut], Alexander Robitzsch [ctb], Gerko Vink [ctb], Lisa Doove [ctb], Shahab Jolani [ctb], Rianne Schouten [ctb], Philipp Gaffert [ctb], Florian Meinfelder [ctb], Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>

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Package docxtools updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-14

Title: Tools for R Markdown to Docx Documents
Description: A set of helper functions for using R Markdown to create documents in docx format, especially documents for use in a classroom or workshop setting.
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>

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Package bfw updated to version 0.1.0 with previous version 0.0.1 dated 2018-06-15

Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>), the present package aim to provide a framework for conducting Bayesian analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>). The initial version include several modules for conducting Bayesian equivalents of chi-squared tests, analysis of variance (ANOVA), multiple (hierarchical) regression, softmax regression, and for fitting data (e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>

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Package anipaths updated to version 0.9.6 with previous version 0.9.3 dated 2018-02-21

Title: Animation of Observed Trajectories Using Spline-Based Interpolation
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf
Maintainer: Henry Scharf <henry.scharf@colostate.edu>

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Package rtweet updated to version 0.6.7 with previous version 0.6.0 dated 2017-11-16

Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

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More information about rtweet at CRAN
Permanent link

Package ncar updated to version 0.4.0 with previous version 0.3.9 dated 2018-05-11

Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method 5) Produce pdf, rtf, text report files. * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

Diff between ncar versions 0.3.9 dated 2018-05-11 and 0.4.0 dated 2018-06-20

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More information about ncar at CRAN
Permanent link

Package future.apply updated to version 1.0.0 with previous version 0.2.0 dated 2018-05-01

Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph], R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future.apply versions 0.2.0 dated 2018-05-01 and 1.0.0 dated 2018-06-20

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Package ecm updated to version 3.1.0 with previous version 3.0.0 dated 2017-12-20

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

Diff between ecm versions 3.0.0 dated 2017-12-20 and 3.1.0 dated 2018-06-20

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More information about ecm at CRAN
Permanent link


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