Sat, 27 May 2017

Package BEST updated to version 0.5.0 with previous version 0.4.0 dated 2015-12-28

Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates for group means and standard deviations and their differences and effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>

Diff between BEST versions 0.4.0 dated 2015-12-28 and 0.5.0 dated 2017-05-27

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Package tsoutliers updated to version 0.6-6 with previous version 0.6-5 dated 2016-12-08

Title: Detection of Outliers in Time Series
Description: Detection of outliers in time series following the Chen and Liu (1993) <DOI:10.2307/2290724> procedure. Innovational outliers, additive outliers, level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>

Diff between tsoutliers versions 0.6-5 dated 2016-12-08 and 0.6-6 dated 2017-05-27

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Package timedelay updated to version 1.0.7 with previous version 1.0.6 dated 2017-03-23

Title: Time Delay Estimation for Stochastic Time Series of Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>

Diff between timedelay versions 1.0.6 dated 2017-03-23 and 1.0.7 dated 2017-05-27

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Package respirometry updated to version 0.4.0 with previous version 0.3.1 dated 2016-12-31

Title: Tools for Conducting Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct respirometry experiments. Strong emphasis is on aquatic respirometry. Tools focus on helping the researcher setup and conduct experiments. Analysis of the resulting data is not a focus since analyses are often specific to a particular setup, and thus are better created by the researcher individually. This package provides tools for intermittent, flow-through, and closed respirometry techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>

Diff between respirometry versions 0.3.1 dated 2016-12-31 and 0.4.0 dated 2017-05-27

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Package tablaxlsx updated to version 1.2.2 with previous version 1.2.0 dated 2016-06-13

Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>

Diff between tablaxlsx versions 1.2.0 dated 2016-06-13 and 1.2.2 dated 2017-05-27

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Package rust updated to version 1.2.0 with previous version 1.1.0 dated 2016-11-18

Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalised ratio-of-uniforms (RU) method to simulate from univariate and (low-dimensional) multivariate continuous distributions. The user specifies the log-density, up to an additive constant. The RU algorithm is applied after relocation of mode of the density to zero, and the user can choose a tuning parameter r. For details see Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random variates via the ratio-of-uniforms method, Statistics and Computing (1991) 1, 129-133. A Box-Cox variable transformation can be used to make the input density suitable for the RU method and to improve efficiency. In the multivariate case rotation of axes can also be used to improve efficiency. From version 1.2.0 the 'Rcpp' package <https://cran.r-project.org/package=Rcpp> can be used to improve efficiency. See the rust website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>

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Package overlap updated to version 0.3.0 with previous version 0.2.7 dated 2017-03-01

Title: Estimates of Coefficient of Overlapping for Animal Activity Patterns
Description: Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Author: Mike Meredith and Martin Ridout
Maintainer: Mike Meredith <mmeredith@wcs.org>

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Package MIICD updated to version 2.4 with previous version 2.3 dated 2016-11-28

Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression with interval censored data or proportional sub-distribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the 'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>

Diff between MIICD versions 2.3 dated 2016-11-28 and 2.4 dated 2017-05-27

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Package heatmaply updated to version 0.10.1 with previous version 0.9.1 dated 2017-04-14

Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Jonathan Sidi [ctb] (https://github.com/yonicd), Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package googleCloudStorageR updated to version 0.3.0 with previous version 0.2.0 dated 2016-09-11

Title: R Interface with Google Cloud Storage
Description: Interact with Google Cloud Storage API in R. Part of the 'cloudyr' project.
Author: Mark Edmondson [aut, cre]
Maintainer: Mark Edmondson <r@sunholo.com>

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Package cleanNLP updated to version 1.9.0 with previous version 1.5.2 dated 2017-04-12

Title: A Tidy Data Model for Natural Language Processing
Description: Provides a set of fast tools for converting a textual corpus into a set of normalized tables. Users may make use of a Python back end with 'spaCy' <https://spacy.io> or the Java back end 'CoreNLP' <http://stanfordnlp.github.io/CoreNLP/>. A minimal back end with no external dependencies is also provided. Exposed annotation tasks include tokenization, part of speech tagging, named entity recognition, entity linking, sentiment analysis, dependency parsing, coreference resolution, and word embeddings. Summary statistics regarding token unigram, part of speech tag, and dependency type frequencies are also included to assist with analyses.
Author: Taylor B. Arnold [aut, cre]
Maintainer: Taylor B. Arnold <taylor.arnold@acm.org>

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 cleanNLP-1.9.0/cleanNLP/R/backend_tokenizers.R                                                       |    5 
 cleanNLP-1.9.0/cleanNLP/R/data.R                                                                     |    8 
 cleanNLP-1.9.0/cleanNLP/R/download.R                                                                 |  125 +-
 cleanNLP-1.9.0/cleanNLP/R/onLoad.R                                                                   |    5 
 cleanNLP-1.9.0/cleanNLP/R/pkg.R                                                                      |   38 
 cleanNLP-1.9.0/cleanNLP/R/tools.R                                                                    |  142 +-
 cleanNLP-1.9.0/cleanNLP/build/vignette.rds                                                           |binary
 cleanNLP-1.9.0/cleanNLP/data/obama.rda                                                               |binary
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 cleanNLP-1.9.0/cleanNLP/inst/doc/schema.html                                                         |    2 
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 cleanNLP-1.9.0/cleanNLP/inst/extdata/cleanNLP-0.1.jar                                                |binary
 cleanNLP-1.9.0/cleanNLP/inst/py/load_spacy.py                                                        |   47 
 cleanNLP-1.9.0/cleanNLP/java/pom.xml                                                                 |    4 
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 cleanNLP-1.9.0/cleanNLP/java/target                                                                  |only
 cleanNLP-1.9.0/cleanNLP/man/cleanNLP-package.Rd                                                      |   33 
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 cleanNLP-1.9.0/cleanNLP/man/doc_id_reset.Rd                                                          |    9 
 cleanNLP-1.9.0/cleanNLP/man/download_core_nlp.Rd                                                     |   43 
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 cleanNLP-1.9.0/cleanNLP/man/get_document.Rd                                                          |   26 
 cleanNLP-1.9.0/cleanNLP/man/get_entity.Rd                                                            |   28 
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 cleanNLP-1.9.0/cleanNLP/man/obama.Rd                                                                 |    3 
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 cleanNLP-1.9.0/cleanNLP/man/write_annotation.Rd                                                      |    9 
 cleanNLP-1.9.0/cleanNLP/tests/testthat.R                                                             |    2 
 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-annotation_utils.R                                       |   17 
 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-java.R                                                   |   57 
 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-python.R                                                 |   34 
 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-tokenizers.R                                             |   30 
 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-tools.R                                                  |    6 
 cleanNLP-1.9.0/cleanNLP/vignettes/case_study.Rmd                                                     |    2 
 66 files changed, 1540 insertions(+), 1295 deletions(-)

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Package BayesianTools updated to version 0.1.2 with previous version 0.1.1 dated 2017-04-05

Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre], Francesco Minunno [aut], Stefan Paul [aut], David Cameron [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

Diff between BayesianTools versions 0.1.1 dated 2017-04-05 and 0.1.2 dated 2017-05-27

 BayesianTools-0.1.1/BayesianTools/inst/examples/createUniformPrior.R        |only
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 BayesianTools-0.1.2/BayesianTools/NEWS                                      |   16 
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 BayesianTools-0.1.2/BayesianTools/R/mcmcDREAM.R                             |    2 
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 95 files changed, 561 insertions(+), 223 deletions(-)

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New package survidm with initial version 0.1.0
Package: survidm
Type: Package
Title: Inference and Prediction in an Illness-Death Model
Version: 0.1.0
Date: 2017-05-24
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Description: Newly developed methods for the estimation of several probabilities in an illness-death model. The package can be used to obtain nonparametric and semiparametric estimates for: transition probabilities, occupation probabilities, cumulative incidence function and the sojourn time distributions. Several auxiliary functions are also provided which can be used for marginal estimation of the survival functions.
Depends: R (>= 3.0.0)
Encoding: UTF-8
License: GPL-3
LazyData: true
Imports: KernSmooth, np, survival, doParallel, parallel, doRNG, foreach
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-05-27 12:26:46 UTC; Sestelo
Repository: CRAN
Date/Publication: 2017-05-27 14:05:27 UTC

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New package stratvns with initial version 1.0
Package: stratvns
Type: Package
Title: Optimal Stratification in Stratified Sampling Optimization Algorithm
Version: 1.0
Author: Breno Oliveira, Leonardo Lima and Jose Brito
Maintainer: Jose Brito <jambrito@gmail.com>
Description: An Optimization Algorithm Applied to stratification Problem. It is aims to delimit the population strata and defining the allocation of sample,considering the following objective: minimize the sample size given a fixed precision level. Exhaustive enumeration method is applied in small problems, while in problems with greater complexity the algorithm is based on metaheuristic Variable Neighborhood Decomposition Search with Path Relink.
Depends: Rglpk,snowfall,stratification, sampling, MultAlloc
Encoding: UTF-8
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-27 01:32:32 UTC; AMANDOCA_AMD
Repository: CRAN
Date/Publication: 2017-05-27 14:07:58 UTC

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New package SeerMapper with initial version 1.2.0
Package: SeerMapper
Type: Package
Version: 1.2.0
Date: 2017-05-26
Title: A Quick Way to Map U.S. Rates and Data of U. S. States, Counties, Census Tracts, or Seer Registries using 2000 and 2010 U. S. Census Boundaries
Author: "Jim Pearson" <jpearson@statnetconsulting.com>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Imports: graphics, maptools, RColorBrewer, rgdal, sp, stats, stringr, SeerMapperRegs, SeerMapperEast, SeerMapperWest, SeerMapper2010Regs, SeerMapper2010East, SeerMapper2010West
Depends: R (>= 3.2.0)
Suggests:
Description: Provides an easy way to map seer registry area rate data on a U. S, map. The U. S. data may be mapped at the state, U. S. NCI Seer Register, state/county or census tract level. The function can categorize the data into "n" quantiles, where "n" is 3 to 11 or the caller can specify a cut point list for the categorizes. The caller can also provide the data and the comparison operation to request hatching over any areas. The default operation and value are > 0.05 (p-values). The location id provided in the data determines the geographic level of the mapping. If states, state/counties or census tracts are being mapped, the location ids used must be the U.S. FIPS codes for states (2 digits), state/counties (5 digits) or state/county/census tracts (11 digits). If the location id references the U.S. Seer Registry areas, the Seer Registry area identifier used to link the data to the geographical areas, then the location id is the Seer Registry name or abbreviation. Additional parameters are used to provide control over the drawing of the boundaries at the data's boundary level and higher levels. The package uses modified boundary data from the 2000 and 2010 U. S. Census to reduce the storage requirements and improve drawing speed. The 'SeerMapper' package contains the U. S. Census 2000 and 2010 boundary data for the regional, state, Seer Registry, and county levels. Six supplement packages contain the census tract boundary data (see manual for more details.)
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-05-27 00:31:45 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-05-27 14:09:10 UTC

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New package polypoly with initial version 0.0.2
Package: polypoly
Title: Helper Functions for Orthogonal Polynomials
Version: 0.0.2
Authors@R: person("Tristan", "Mahr", email = "tristan.mahr@gmail.com", role = c("aut", "cre"))
Description: Tools for reshaping, plotting, and manipulating matrices of orthogonal polynomials.
Depends: R (>= 3.3.3)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/tjmahr/polypoly
BugReports: https://github.com/tjmahr/polypoly/issues
Imports: tibble, reshape2, ggplot2, rlang, stats
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, lme4, splines
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-05-26 18:22:42 UTC; mahr
Author: Tristan Mahr [aut, cre]
Maintainer: Tristan Mahr <tristan.mahr@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-27 14:12:20 UTC

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Package phrasemachine updated to version 1.1.1 with previous version 1.0.0 dated 2016-10-24

Title: Simple Phrase Extraction
Description: Simple noun phrase extraction using part-of-speech information. Takes a collection of un-processed documents as input and returns a set of noun phrases associated with those documents.
Author: Matthew J. Denny, Abram Handler, Brendan O'Connor
Maintainer: Matthew J. Denny <mdenny@psu.edu>

Diff between phrasemachine versions 1.0.0 dated 2016-10-24 and 1.1.1 dated 2017-05-27

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 vignettes/getting_started_with_phrasemachine.Rmd |    7 +-
 20 files changed, 220 insertions(+), 104 deletions(-)

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Package nauf updated to version 1.0.1 with previous version 1.0.0 dated 2017-05-09

Title: Regression with NA Values in Unordered Factors
Description: Fits regressions where unordered factors can be set to NA in subsets of the data where they are not applicable or otherwise not contrastive by using sum contrasts and setting NA values to zero.
Author: Christopher D. Eager [aut, cre]
Maintainer: Christopher D. Eager <eagerstats@gmail.com>

Diff between nauf versions 1.0.0 dated 2017-05-09 and 1.0.1 dated 2017-05-27

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 9 files changed, 103 insertions(+), 94 deletions(-)

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New package KarsTS with initial version 1.0
Package: KarsTS
Type: Package
Title: An Interface for Karstic Time Series
Version: 1.0
Date: 2017-05-23
Authors@R: c(person("Marina", "Saez", email = "marinasaez_andreu@hotmail.com",role = c("aut", "cre")),person("David", "Benavente", role = c("ths")),person("Soledad", "Cuezva", role = c("ths")),person("Concepcion", "Pla", role = c("ctb")))
Author: Marina Saez [aut, cre], David Benavente [ths], Soledad Cuezva [ths], Concepcion Pla [ctb]
Maintainer: Marina Saez <marinasaez_andreu@hotmail.com>
Description: An R graphical user interface for karstic time series, based on the 'tcltk' package. Karstic research typically includes CO2 and Rn concentrations and microclimatic measurements. Many of these time series have a strong non-linear behavior. Gaps are often a significant problem because caves are aggressive environments for the apparels. 'KarsTS' provides linear and non-linear analysis and filling methods, as well as tools to manipulate easily time series and gap sets.
License: GPL (>= 2)
Note: Please, cite this package as: Marina Saez (2017). KarsTS: An Interface For Karstic Time Series. R package version 1.0.
RoxygenNote: 6.0.1
Imports: circular, BaylorEdPsych, MVN, tcltk, tcltk2, tkrplot, tseriesChaos, stlplus, tseries, forecast, stinepack, missForest, nonlinearTseries, stats, graphics, utils, zoo, grDevices, rgl, mgcv
NeedsCompilation: no
Packaged: 2017-05-26 13:41:01 UTC; rs
Repository: CRAN
Date/Publication: 2017-05-27 14:26:52 UTC

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New package didrooRFM with initial version 1.0.0
Package: didrooRFM
Title: Compute Recency Frequency Monetary Scores for your Customer Data
Version: 1.0.0
Authors@R: person("Satish", "Hariharan", email = "satish181990@gmail.com", role = c("aut", "cre"))
Description: This hosts the findRFM function which generates RFM scores on a 1-5 point scale for customer transaction data. The function consumes a data frame with Transaction Number, Customer ID, Date of Purchase (in date format) and Amount of Purchase as the attributes. The function returns a data frame with RFM data for the sales information.
Depends: R (>= 3.3.3)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: dplyr
BugReports: https://goo.gl/forms/BU7rb8HmgTSeWZE02
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-27 13:49:57 UTC; didroo
Author: Satish Hariharan [aut, cre]
Maintainer: Satish Hariharan <satish181990@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-27 14:29:07 UTC

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