Thu, 04 Oct 2018

New package simode with initial version 1.1.0
Package: simode
Type: Package
Title: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching
Version: 1.1.0
Authors@R: c( person("Itai", "Dattner", email = "idattner@stat.haifa.ac.il", role = "aut"), person("Rami", "Yaari", email = "ramiyaari@gmail.com", role = c("aut", "cre")))
Description: Implements statistical inference for systems of ordinary differential equations, that uses the integral-matching criterion and takes advantage of the separability of parameters, in order to obtain initial parameter estimates for nonlinear least squares optimization. Dattner & Yaari (2018) <arXiv:1807.04202>. Dattner et al. (2017) <doi:10.1098/rsif.2016.0525>. Dattner & Klaassen (2015) <doi:10.1214/15-EJS1053>.
Depends: R (>= 3.4.0)
Imports: deSolve, pracma, quadprog
Suggests: parallel, Rcgmin, Rvmmin, R.rsp
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2018-10-04 12:28:02 UTC; ramiy
Author: Itai Dattner [aut], Rami Yaari [aut, cre]
Maintainer: Rami Yaari <ramiyaari@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-04 22:50:02 UTC

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Package rjmcmc updated to version 0.4.3 with previous version 0.4.2 dated 2018-09-29

Title: Reversible-Jump MCMC Using Post-Processing
Description: Performs reversible-jump Markov chain Monte Carlo (Green, 1995) <doi:10.2307/2337340>, specifically the restriction introduced by Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling problem. Previously-calculated posterior distributions are used to quickly estimate posterior model probabilities. Jacobian matrices are found using automatic differentiation.
Author: Nick Gelling [aut, cre], Matthew R. Schofield [aut], Richard J. Barker [aut]
Maintainer: Nick Gelling <nick_gelling@hotmail.com>

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Package pathfindR updated to version 1.2.2 with previous version 1.2.1 dated 2018-08-17

Title: Pathway Enrichment Analysis Utilizing Active Subnetworks
Description: Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. <doi:10.1101/272450>.
Author: Ege Ulgen, Ozan Ozisik
Maintainer: Ege Ulgen <egeulgen@gmail.com>

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Package bWGR updated to version 1.5.6 with previous version 1.5.5 dated 2018-09-16

Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM or Gibbs sampling, with optional kernel term and sampling techniques as described by Xavier (2017) <doi:10.1186/s12859-017-1582-3>.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

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Package riskRegression updated to version 2018.10.03 with previous version 2018.04.21 dated 2018-04-19

Title: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre], Paul Blanche [ctb], Ulla Brasch Mogensen [ctb], Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>

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Package Delta updated to version 0.2.0.2 with previous version 0.2.0.1 dated 2018-10-03

Title: Measure of Agreement Between Two Raters
Description: Measure of agreement delta was originally by Martín & Femia (2004) <DOI:10.1348/000711004849268>. Since then has been considered as agreement measure for different fields, since their behavior is usually better than the usual kappa index by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta is that can not be computed by hand contrary to kappa. The current algorithm is based on the Version 5 of the delta windows program that can be found on <https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
Author: Antonio Rodriguez [aut, cre], Pedro Femia [cph, ctb], Antonio Martin [cph, ctb]
Maintainer: Antonio Rodriguez <tonirodriguezcontesti@gmail.com>

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Package rise updated to version 1.0.4 with previous version 1.0.3 dated 2018-07-29

Title: Conduct RISE Analysis
Description: Implements techniques for educational resource inspection, selection, and evaluation (RISE) described in Bodily, Nyland, and Wiley (2017) <doi:10.19173/irrodl.v18i2.2952>. Automates the process of identifying learning materials that are not effectively supporting student learning in technology-mediated courses by synthesizing information about access to course content and performance on assessments.
Author: David Wiley [aut, cre], Lumen Learning [cph]
Maintainer: David Wiley <david.wiley@gmail.com>

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Package PRIMsrc updated to version 0.8.2 with previous version 0.8.1 dated 2018-09-10

Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb], J. Sunil Rao [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>

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Package oce updated to version 1.0-1 with previous version 0.9-23 dated 2018-01-28

Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>), Clark Richards [aut] (<https://orcid.org/0000-0002-7833-206X>), Chantelle Layton [ctb] (<https://orcid.org/0000-0002-3199-5763>, curl() coauthor), British Geological Survey [ctb, cph] (magnetic-field subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>

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Package R6 updated to version 2.3.0 with previous version 2.2.2 dated 2017-06-17

Title: Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>

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Package ggvoronoi updated to version 0.8.1 with previous version 0.8.0 dated 2018-07-20

Title: Voronoi Diagrams and Heatmaps with 'ggplot2'
Description: Easy creation and manipulation of Voronoi diagrams using 'deldir' with visualization in 'ggplot2'.
Author: Robert C. Garrett [aut, cre], Austin Nar [aut], Thomas J. Fisher [aut], Karsten Maurer [ctb]
Maintainer: Robert C. Garrett <garretrc@miamioh.edu>

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Package auk updated to version 0.3.0 with previous version 0.2.2 dated 2018-07-23

Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from eBird (<http://ebird.org>), an online tool for recording bird observations. Public access to the full eBird database is via the eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable text file. This package is an interface to AWK for extracting data from the EBD based on taxonomic, spatial, or temporal filters, to produce a manageable file size that can be imported into R.
Author: Matthew Strimas-Mackey [aut, cre] (<https://orcid.org/0000-0001-8929-7776>), Eliot Miller [aut], Wesley Hochachka [aut], Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>

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Package Rdpack updated to version 0.10-1 with previous version 0.9-0 dated 2018-08-04

Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.
Author: Georgi N. Boshnakov [aut, cre], Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between Rdpack versions 0.9-0 dated 2018-08-04 and 0.10-1 dated 2018-10-04

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Package pseudorank updated to version 0.3.7 with previous version 0.3.0 dated 2018-08-22

Title: Pseudo-Ranks
Description: Efficient calculation of pseudo-ranks and (pseudo)-rank based test statistics. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>), Georg Zimmermann [aut], Arne C. Bathke [aut], Edgar Brunner [aut]
Maintainer: Martin Happ <martin.happ@aon.at>

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Package littler updated to version 0.3.5 with previous version 0.3.4 dated 2018-08-24

Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package REAT updated to version 2.0.2 with previous version 2.0.1 dated 2018-08-24

Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>

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Package MFPCA updated to version 1.3-1 with previous version 1.3 dated 2018-08-13

Title: Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis for data observed on different dimensional domains. The estimation algorithm relies on univariate basis expansions for each element of the multivariate functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are represented by S4 classes for this type of data implemented in the package 'funData'. For more details on the general concepts of both packages and a case study, see Happ (2018) <arXiv:1707.02129>.
Author: Clara Happ [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>

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Package GGUM updated to version 0.3.3 with previous version 0.3.2 dated 2018-07-04

Title: Generalized Graded Unfolding Model
Description: An implementation of the generalized graded unfolding model (GGUM) in R, see Roberts, Donoghue, and Laughlin (2000) <doi:10.1177/01466216000241001>). It allows to simulate data sets based on the GGUM. It fits the GGUM and the GUM, and it retrieves item and person parameter estimates. Several plotting functions are available (item and test information functions; item and test characteristic curves; item category response curves). Additionally, there are some functions that facilitate the communication between R and 'GGUM2004'. Finally, a model-fit checking utility, MODFIT(), is also available.
Author: Jorge N. Tendeiro [aut, cre], Sebastian Castro-Alvarez [aut]
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>

Diff between GGUM versions 0.3.2 dated 2018-07-04 and 0.3.3 dated 2018-10-04

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Package textreg updated to version 0.1.5 with previous version 0.1.4 dated 2017-03-17

Title: n-Gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix <lmiratrix@stat.harvard.edu>

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Package partitionComparison updated to version 0.2.4 with previous version 0.2.3 dated 2017-12-19

Title: Implements Measures for the Comparison of Two Partitions
Description: Provides several measures ((dis)similarity, distance/metric, correlation, entropy) for comparing two partitions of the same set of objects. The different measures can be assigned to three different classes: Pair comparison (containing the famous Jaccard and Rand indices), set based, and information theory based. Many of the implemented measures can be found in Albatineh AN, Niewiadomska-Bugaj M and Mihalko D (2006) <doi:10.1007/s00357-006-0017-z> and Meila M (2007) <doi:10.1016/j.jmva.2006.11.013>. Partitions are represented by vectors of class labels which allow a straightforward integration with existing clustering algorithms (e.g. kmeans()). The package is mostly based on the S4 object system.
Author: Fabian Ball [aut, cre, cph, ctb], Andreas Geyer-Schulz [cph]
Maintainer: Fabian Ball <fabian.ball@kit.edu>

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Package Countr updated to version 3.5.2 with previous version 3.4.1 dated 2017-11-20

Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal processes. The models may include covariates and can be specified with familiar formula syntax as in glm() and package 'flexsurv'. The methodology is described in a forthcoming paper in the Journal of Statistical Software (included as vignette 'Countr_guide').
Author: Tarak Kharrat [aut, cre], Georgi N. Boshnakov [aut]
Maintainer: Tarak Kharrat <Tarak.Kharrat@liverpool.ac.uk>

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Package soundgen updated to version 1.3.1 with previous version 1.3.0 dated 2018-08-31

Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis. Performs parametric synthesis of sounds with harmonic and noise components such as animal vocalizations or human voice. Also includes tools for spectral analysis, pitch tracking, audio segmentation, self-similarity matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>

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Package clusterSim updated to version 0.47-2 with previous version 0.47-1 dated 2017-11-30

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

Diff between clusterSim versions 0.47-1 dated 2017-11-30 and 0.47-2 dated 2018-10-04

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Package spatstat.data updated to version 1.4-0 with previous version 1.3-1 dated 2018-06-11

Title: Datasets for 'spatstat'
Description: Contains all the datasets for the 'spatstat' package.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.data versions 1.3-1 dated 2018-06-11 and 1.4-0 dated 2018-10-04

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Package mlvocab (with last version 0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-09-18 0.1
2018-04-13 0.0.1

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Package RTest (with last version 1.1.9.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-09-19 1.1.9.0
2018-08-24 1.1.8.0

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Package secr updated to version 3.1.7 with previous version 3.1.6 dated 2018-05-14

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Package TileManager updated to version 0.3.0 with previous version 0.2.0 dated 2017-09-07

Title: Tile Manager
Description: Tools for creating and detecting tiling schemes for raster data sets.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

Diff between TileManager versions 0.2.0 dated 2017-09-07 and 0.3.0 dated 2018-10-04

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Package BayesGOF updated to version 5.0 with previous version 4.2 dated 2018-08-15

Title: Bayesian Modeling via Goodness-of-Fit
Description: A Bayesian data modeling scheme that performs four interconnected tasks: (i) characterizes the uncertainty of the elicited parametric prior; (ii) provides exploratory diagnostic for checking prior-data conflict; (iii) computes the final statistical prior density estimate; and (iv) executes macro- and micro-inference. Primary reference is Mukhopadhyay, S. and Fletcher, D. 2018 paper "Generalized Empirical Bayes via Frequentist Goodness of Fit" (<https://www.nature.com/articles/s41598-018-28130-5 >).
Author: Subhadeep Mukhopadhyay, Douglas Fletcher
Maintainer: Doug Fletcher <tug25070@temple.edu>

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