Fri, 19 Dec 2014

Package GPLTR updated to version 1.1 with previous version 0.95 dated 2014-05-27

Title: Generalized Partially Linear Tree-based Regression Model
Description: Combining a generalized linear model with an additional tree part on the same scale. A four-step procedure is proposed to fit the model and test the joint effect of the selected tree part while adjusting on confounding factors. We also proposed an ensemble procedure based on the bagging to improve prediction accuracy and computed several scores of importance for variable selection.
Author: Cyprien Mbogning and Wilson Toussile
Maintainer: Cyprien Mbogning

Diff between GPLTR versions 0.95 dated 2014-05-27 and 1.1 dated 2014-12-19

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Package sBF updated to version 1.1.1 with previous version 1.1 dated 2012-08-01

Title: Smooth Backfitting
Description: Smooth Backfitting for additive models using Nadaraya-Watson estimator
Author: A. Arcagni, L. Bagnato
Maintainer: Alberto Arcagni

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Package RGA updated to version 0.1.4 with previous version 0.1.3 dated 2014-10-27

Title: A Google Analytics API client for R
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also the RGA package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov

Diff between RGA versions 0.1.3 dated 2014-10-27 and 0.1.4 dated 2014-12-19

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Package penalized updated to version 0.9-45 with previous version 0.9-42 dated 2012-11-06

Title: L1 (lasso and fused lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model
Description: A package for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman

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Package geonames updated to version 0.998 with previous version 0.997 dated 2014-10-19

Title: Interface to www.geonames.org web service
Description: Code for querying the web service at www.geonames.org
Author: Barry Rowlingson
Maintainer: Barry Rowlingson

Diff between geonames versions 0.997 dated 2014-10-19 and 0.998 dated 2014-12-19

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Package vardpoor updated to version 0.2.1 with previous version 0.2.0.14 dated 2014-11-04

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks

Diff between vardpoor versions 0.2.0.14 dated 2014-11-04 and 0.2.1 dated 2014-12-19

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Package cgdsr updated to version 1.1.32 with previous version 1.1.31 dated 2014-12-12

Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS).
Description: The package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen Skanderup
Maintainer: Anders Jacobsen Skanderup

Diff between cgdsr versions 1.1.31 dated 2014-12-12 and 1.1.32 dated 2014-12-19

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New package biogram with initial version 1.0
Package: biogram
Type: Package
Title: N-Gram Analysis of Biological Sequences
Version: 1.0
LazyData: true
Date: 2014-12-19
Authors@R: c( person("Michal", "Burdukiewicz", email = "michalburdukiewicz@gmail.com", role = c("cre", "aut")), person("Piotr", "Sobczyk", role = "aut"), person("Chris", "Lauber", role = "aut"))
Description: Tools for extraction and analysis of various n-grams (sequences of n items) derived from biological sequences (proteins or nucleic acids). To deal with the dimensionality of the n-gram data, biogram uses QuiPT (quick permutation test) for fast feature-filtering.
License: GPL-3
URL: https://github.com/michbur/biogram
Depends: R (>= 3.0.0), slam
Imports: bit
Suggests: testthat
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-12-19 11:17:38 UTC; michal
Author: Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Chris Lauber [aut]
Maintainer: Michal Burdukiewicz
Date/Publication: 2014-12-19 15:58:01

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Package bgmm updated to version 1.7 with previous version 1.6 dated 2013-11-19

Title: Gaussian Mixture Modeling Algorithms And The Belief-based Mixture Modeling
Description: Two partially supervised mixture modeling methods: soft-label and belief-based modeling are implemented. For completeness, we equipped the package also with the functionality of unsupervised, semi- and fully supervised mixture modeling. The package can be applied also to selection of the best-fitting from a set of models with different component numbers or constraints on their structures. For detailed introduction see: Przemyslaw Biecek, Ewa Szczurek, Martin Vingron, Jerzy Tiuryn (2012), The R Package bgmm: Mixture Modeling with Uncertain Knowledge, Journal of Statistical Software.
Author: Przemyslaw Biecek \& Ewa Szczurek
Maintainer: Przemyslaw Biecek

Diff between bgmm versions 1.6 dated 2013-11-19 and 1.7 dated 2014-12-19

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Package rcicr updated to version 0.2.6 with previous version 0.2.5 dated 2014-11-17

Title: Reverse correlation image classification toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch

Diff between rcicr versions 0.2.5 dated 2014-11-17 and 0.2.6 dated 2014-12-19

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New package nlsem with initial version 0.1
Package: nlsem
Version: 0.1
Date: 2014-12-19
Title: Fitting Structural Equation Mixture Models
Authors@R: c(person("Nora", "Umbach", role = c("aut", "cre"), email = "nora.umbach@web.de"), person("Katharina", "Naumann", role = "aut"), person("David", "Hoppe", role = "aut"), person("Holger", "Brandt", role = "aut"), person("Augustin", "Kelava", role="ctb"), person("Bernhard", "Schmitz", role="ctb"))
Depends: R (>= 3.1.0), gaussquad, mvtnorm, nlme
Description: Estimation of structural equation models with nonlinear effects and underlying nonnormal distributions.
License: GPL (>= 2)
Packaged: 2014-12-19 09:42:10 UTC; noraumbach
Author: Nora Umbach [aut, cre], Katharina Naumann [aut], David Hoppe [aut], Holger Brandt [aut], Augustin Kelava [ctb], Bernhard Schmitz [ctb]
Maintainer: Nora Umbach
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-19 12:07:02

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Package aoos updated to version 0.1.0 with previous version 0.0.3 dated 2014-11-14

Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. Has reference semantics and is build around S4.
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz

Diff between aoos versions 0.0.3 dated 2014-11-14 and 0.1.0 dated 2014-12-19

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Package PowerTOST updated to version 1.2-04 with previous version 1.2-03 dated 2014-11-13

Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits based on simulations. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / samplesize estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut]
Maintainer: Detlew Labes

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Package helsinki updated to version 0.9.22 with previous version 0.9.20 dated 2014-06-09

Title: Helsinki open data R tools
Description: Tools for accessing various open data sources in the Helsinki region in Finland. Current data sources include the Real Estate Department (district maps), the Environmental Services Authority, Service Map API, Linked Events API and Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen

Diff between helsinki versions 0.9.20 dated 2014-06-09 and 0.9.22 dated 2014-12-19

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Package ztable updated to version 0.1.1 with previous version 0.1.0 dated 2014-12-15

Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"

Diff between ztable versions 0.1.0 dated 2014-12-15 and 0.1.1 dated 2014-12-19

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More information about ztable at CRAN
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Package taxize updated to version 0.5.2 with previous version 0.4.0 dated 2014-09-09

Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package interacts with a suite of web APIs for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Zachary Foster [aut], Carl Boettiger [aut], Karthik Ram [aut], Ignasi Bartomeus [aut], John Baumgartner [aut]
Maintainer: Scott Chamberlain

Diff between taxize versions 0.4.0 dated 2014-09-09 and 0.5.2 dated 2014-12-19

 taxize-0.4.0/taxize/R/deprecated.R                                                 |only
 taxize-0.4.0/taxize/R/eol_ping.R                                                   |only
 taxize-0.4.0/taxize/R/itis_ping.R                                                  |only
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 taxize-0.4.0/taxize/R/startup.R                                                    |only
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 taxize-0.4.0/taxize/tests/testthat/test-ubio_synonyms.R                            |only
 taxize-0.5.2/taxize/DESCRIPTION                                                    |   16 
 taxize-0.5.2/taxize/MD5                                                            |  600 ++--
 taxize-0.5.2/taxize/NAMESPACE                                                      |  111 
 taxize-0.5.2/taxize/NEWS                                                           |   50 
 taxize-0.5.2/taxize/R/apg_lookup.R                                                 |   11 
 taxize-0.5.2/taxize/R/bold_search.R                                                |   25 
 taxize-0.5.2/taxize/R/children.R                                                   |   77 
 taxize-0.5.2/taxize/R/class2tree.R                                                 |   46 
 taxize-0.5.2/taxize/R/classification.R                                             |  430 +-
 taxize-0.5.2/taxize/R/col_children.R                                               |   58 
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 taxize-0.5.2/taxize/R/col_downstream.R                                             |  110 
 taxize-0.5.2/taxize/R/col_search.R                                                 |   38 
 taxize-0.5.2/taxize/R/comm2sci.R                                                   |   24 
 taxize-0.5.2/taxize/R/downstream.R                                                 |  126 
 taxize-0.5.2/taxize/R/eol_dataobjects.R                                            |   14 
 taxize-0.5.2/taxize/R/eol_hierarchy.R                                              |only
 taxize-0.5.2/taxize/R/eol_invasive.R                                               |   55 
 taxize-0.5.2/taxize/R/eol_pages.R                                                  |   42 
 taxize-0.5.2/taxize/R/eol_search.R                                                 |   28 
 taxize-0.5.2/taxize/R/gbif_parse.R                                                 |   14 
 taxize-0.5.2/taxize/R/genbank2uid.R                                                |only
 taxize-0.5.2/taxize/R/get_boldid.R                                                 |  152 -
 taxize-0.5.2/taxize/R/get_colid.R                                                  |  182 -
 taxize-0.5.2/taxize/R/get_eolid.R                                                  |  210 +
 taxize-0.5.2/taxize/R/get_gbifid.R                                                 |  133 
 taxize-0.5.2/taxize/R/get_ids.R                                                    |   58 
 taxize-0.5.2/taxize/R/get_nbnid.R                                                  |only
 taxize-0.5.2/taxize/R/get_tpsid.R                                                  |  166 -
 taxize-0.5.2/taxize/R/get_tsn.R                                                    |  176 -
 taxize-0.5.2/taxize/R/get_ubioid.R                                                 |  126 
 taxize-0.5.2/taxize/R/get_uid.R                                                    |  186 -
 taxize-0.5.2/taxize/R/gisd_isinvasive.R                                            |   63 
 taxize-0.5.2/taxize/R/gni_details.R                                                |   18 
 taxize-0.5.2/taxize/R/gni_parse.R                                                  |   16 
 taxize-0.5.2/taxize/R/gni_search.R                                                 |   35 
 taxize-0.5.2/taxize/R/gnr_datasources.R                                            |   24 
 taxize-0.5.2/taxize/R/gnr_resolve.R                                                |   28 
 taxize-0.5.2/taxize/R/iplant_resolve.R                                             |   10 
 taxize-0.5.2/taxize/R/ipni_search.R                                                |   39 
 taxize-0.5.2/taxize/R/itis-api.R                                                   |only
 taxize-0.5.2/taxize/R/itis.R                                                       | 1477 +++-------
 taxize-0.5.2/taxize/R/itis_acceptname.R                                            |    6 
 taxize-0.5.2/taxize/R/itis_downstream.R                                            |   80 
 taxize-0.5.2/taxize/R/itis_getrecord.R                                             |   18 
 taxize-0.5.2/taxize/R/itis_hierarchy.R                                             |   23 
 taxize-0.5.2/taxize/R/itis_kingdomnames.R                                          |   10 
 taxize-0.5.2/taxize/R/itis_lsid.R                                                  |   19 
 taxize-0.5.2/taxize/R/itis_name.R                                                  |    2 
 taxize-0.5.2/taxize/R/itis_native.R                                                |   16 
 taxize-0.5.2/taxize/R/itis_refs.R                                                  |    8 
 taxize-0.5.2/taxize/R/itis_taxrank.R                                               |   14 
 taxize-0.5.2/taxize/R/itis_terms.R                                                 |   18 
 taxize-0.5.2/taxize/R/iucn_getname.R                                               |    6 
 taxize-0.5.2/taxize/R/iucn_summary.R                                               |   54 
 taxize-0.5.2/taxize/R/names_list.r                                                 |   14 
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 taxize-0.5.2/taxize/R/ncbi_getbyid.R                                               |   11 
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 taxize-0.5.2/taxize/R/phylomatic_format.R                                          |   16 
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 taxize-0.5.2/taxize/R/plantminer.R                                                 |   22 
 taxize-0.5.2/taxize/R/rankagg.R                                                    |   14 
 taxize-0.5.2/taxize/R/resolve.R                                                    |   30 
 taxize-0.5.2/taxize/R/sci2comm.R                                                   |  116 
 taxize-0.5.2/taxize/R/scrapenames.r                                                |   56 
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 taxize-0.5.2/taxize/R/synonyms.R                                                   |  109 
 taxize-0.5.2/taxize/R/tax_agg.R                                                    |   70 
 taxize-0.5.2/taxize/R/tax_name.R                                                   |  161 -
 taxize-0.5.2/taxize/R/tax_rank.R                                                   |   44 
 taxize-0.5.2/taxize/R/taxize-package.R                                             |   65 
 taxize-0.5.2/taxize/R/tnrs.R                                                       |    2 
 taxize-0.5.2/taxize/R/tnrs_sources.r                                               |    8 
 taxize-0.5.2/taxize/R/tp_accnames.R                                                |    2 
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 taxize-0.5.2/taxize/R/tp_dist.R                                                    |    6 
 taxize-0.5.2/taxize/R/tp_refs.R                                                    |    4 
 taxize-0.5.2/taxize/R/tp_search.R                                                  |   10 
 taxize-0.5.2/taxize/R/tp_summary.R                                                 |   16 
 taxize-0.5.2/taxize/R/tp_synonyms.R                                                |    4 
 taxize-0.5.2/taxize/R/tpl_families.r                                               |   16 
 taxize-0.5.2/taxize/R/tpl_get.r                                                    |   34 
 taxize-0.5.2/taxize/R/tpl_search.r                                                 |    8 
 taxize-0.5.2/taxize/R/ubio_classification.R                                        |   32 
 taxize-0.5.2/taxize/R/ubio_classification_search.R                                 |   22 
 taxize-0.5.2/taxize/R/ubio_id.R                                                    |   36 
 taxize-0.5.2/taxize/R/ubio_search.R                                                |   18 
 taxize-0.5.2/taxize/R/ubio_synonyms.R                                              |   12 
 taxize-0.5.2/taxize/R/upstream.R                                                   |only
 taxize-0.5.2/taxize/R/vascan_search.r                                              |   20 
 taxize-0.5.2/taxize/R/zzz.R                                                        |   86 
 taxize-0.5.2/taxize/README.md                                                      |  519 ++-
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 taxize-0.5.2/taxize/man/apg_families.Rd                                            |    3 
 taxize-0.5.2/taxize/man/apg_genera.Rd                                              |    3 
 taxize-0.5.2/taxize/man/apg_lookup.Rd                                              |    5 
 taxize-0.5.2/taxize/man/apg_orders.Rd                                              |    3 
 taxize-0.5.2/taxize/man/bold_search.Rd                                             |   25 
 taxize-0.5.2/taxize/man/children.Rd                                                |   22 
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 taxize-0.5.2/taxize/man/get_seqs-deprecated.Rd                                     |    3 
 taxize-0.5.2/taxize/man/get_tpsid.Rd                                               |   74 
 taxize-0.5.2/taxize/man/get_tsn.Rd                                                 |   76 
 taxize-0.5.2/taxize/man/get_ubioid.Rd                                              |   74 
 taxize-0.5.2/taxize/man/get_uid.Rd                                                 |   82 
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 taxize-0.5.2/taxize/man/getanymatchcount.Rd                                        |   19 
 taxize-0.5.2/taxize/man/getcommentdetailfromtsn.Rd                                 |   15 
 taxize-0.5.2/taxize/man/getcommonnamesfromtsn.Rd                                   |   14 
 taxize-0.5.2/taxize/man/getcoremetadatafromtsn.Rd                                  |   17 
 taxize-0.5.2/taxize/man/getcoveragefromtsn.Rd                                      |   16 
 taxize-0.5.2/taxize/man/getcredibilityratingfromtsn.Rd                             |   15 
 taxize-0.5.2/taxize/man/getcredibilityratings.Rd                                   |   12 
 taxize-0.5.2/taxize/man/getcurrencyfromtsn.Rd                                      |   16 
 taxize-0.5.2/taxize/man/getdatedatafromtsn.Rd                                      |   14 
 taxize-0.5.2/taxize/man/getdescription.Rd                                          |   12 
 taxize-0.5.2/taxize/man/getexpertsfromtsn.Rd                                       |   14 
 taxize-0.5.2/taxize/man/getfullhierarchyfromtsn.Rd                                 |   19 
 taxize-0.5.2/taxize/man/getfullrecordfromlsid.Rd                                   |   19 
 taxize-0.5.2/taxize/man/getfullrecordfromtsn.Rd                                    |   22 
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 taxize-0.5.2/taxize/man/gethierarchyupfromtsn.Rd                                   |   17 
 taxize-0.5.2/taxize/man/getitisterms.Rd                                            |   17 
 taxize-0.5.2/taxize/man/getitistermsfromcommonname.Rd                              |   18 
 taxize-0.5.2/taxize/man/getitistermsfromscientificname.Rd                          |   19 
 taxize-0.5.2/taxize/man/getjurisdictionaloriginfromtsn.Rd                          |   17 
 taxize-0.5.2/taxize/man/getjurisdictionoriginvalues.Rd                             |   12 
 taxize-0.5.2/taxize/man/getjurisdictionvalues.Rd                                   |   12 
 taxize-0.5.2/taxize/man/getkey.Rd                                                  |    5 
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 taxize-0.5.2/taxize/man/getkingdomnames.Rd                                         |   12 
 taxize-0.5.2/taxize/man/getlastchangedate.Rd                                       |   12 
 taxize-0.5.2/taxize/man/getlsidfromtsn.Rd                                          |   14 
 taxize-0.5.2/taxize/man/getothersourcesfromtsn.Rd                                  |   15 
 taxize-0.5.2/taxize/man/getparenttsnfromtsn.Rd                                     |   14 
 taxize-0.5.2/taxize/man/getpublicationsfromtsn.Rd                                  |   17 
 taxize-0.5.2/taxize/man/getranknames.Rd                                            |   12 
 taxize-0.5.2/taxize/man/getrecordfromlsid.Rd                                       |   18 
 taxize-0.5.2/taxize/man/getreviewyearfromtsn.Rd                                    |   14 
 taxize-0.5.2/taxize/man/getscientificnamefromtsn.Rd                                |   15 
 taxize-0.5.2/taxize/man/getsynonymnamesfromtsn.Rd                                  |   19 
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 taxize-0.5.2/taxize/man/gettaxonomicranknamefromtsn.Rd                             |   17 
 taxize-0.5.2/taxize/man/gettaxonomicusagefromtsn.Rd                                |   17 
 taxize-0.5.2/taxize/man/gettsnbyvernacularlanguage.Rd                              |   19 
 taxize-0.5.2/taxize/man/gettsnfromlsid.Rd                                          |   21 
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 taxize-0.5.2/taxize/man/gni_details.Rd                                             |    5 
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 taxize-0.5.2/taxize/man/itis_lsid.Rd                                               |    8 
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 taxize-0.5.2/taxize/man/itis_terms.Rd                                              |    5 
 taxize-0.5.2/taxize/man/iucn_getname.Rd                                            |    5 
 taxize-0.5.2/taxize/man/iucn_status.Rd                                             |    5 
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 taxize-0.5.2/taxize/tests/testthat/test-comm2sci.R                                 |    8 
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 taxize-0.5.2/taxize/tests/testthat/test-eol_invasive.R                             |    4 
 taxize-0.5.2/taxize/tests/testthat/test-eol_ping.R                                 |    8 
 taxize-0.5.2/taxize/tests/testthat/test-eol_search.R                               |    6 
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 taxize-0.5.2/taxize/tests/testthat/test-itis.R                                     |    4 
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 taxize-0.5.2/taxize/tests/testthat/test-itis_hierarchy.R                           |    5 
 taxize-0.5.2/taxize/tests/testthat/test-itis_kingdomnames.R                        |    7 
 taxize-0.5.2/taxize/tests/testthat/test-itis_lsid.R                                |    4 
 taxize-0.5.2/taxize/tests/testthat/test-itis_native.R                              |    5 
 taxize-0.5.2/taxize/tests/testthat/test-itis_phymat_format.R                       |    4 
 taxize-0.5.2/taxize/tests/testthat/test-itis_ping.R                                |    9 
 taxize-0.5.2/taxize/tests/testthat/test-itis_refs.R                                |    4 
 taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyname.R                           |    9 
 taxize-0.5.2/taxize/tests/testthat/test-ncbi_search.R                              |    4 
 taxize-0.5.2/taxize/tests/testthat/test-sci2comm.R                                 |    6 
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 taxize-0.5.2/taxize/tests/testthat/test-tax_name.R                                 |   40 
 taxize-0.5.2/taxize/tests/testthat/test-tp_accnames.R                              |    4 
 taxize-0.5.2/taxize/tests/testthat/test-tp_summary.R                               |    4 
 taxize-0.5.2/taxize/tests/testthat/test-vascan_search.r                            |   12 
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Package streamMOA updated to version 1.0-0 with previous version 0.1-1 dated 2014-06-17

Title: stream - Interface to MOA Algorithms
Description: This package provides an interface to algorithms implemented in the MOA (Massive Online Analysis) framework for data stream mining.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler

Diff between streamMOA versions 0.1-1 dated 2014-06-17 and 1.0-0 dated 2014-12-19

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 NAMESPACE                           |    2 
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 build/vignette.rds                  |binary
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 man/DSC_ClusTree.Rd                 |   26 ++--
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 19 files changed, 301 insertions(+), 571 deletions(-)

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Package spBayesSurv updated to version 1.0.2 with previous version 1.0.1 dated 2014-10-25

Title: Bayesian Modeling and Analysis of Spatially Correlated Survival Data
Description: This package provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, and generalized accelerated failure time frailty models.
Author: Haiming Zhou and Tim Hanson
Maintainer: Haiming Zhou

Diff between spBayesSurv versions 1.0.1 dated 2014-10-25 and 1.0.2 dated 2014-12-19

 DESCRIPTION                    |    6 
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Package RJDBC updated to version 0.2-5 with previous version 0.2-4 dated 2014-06-26

Title: Provides access to databases through the JDBC interface
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between RJDBC versions 0.2-4 dated 2014-06-26 and 0.2-5 dated 2014-12-19

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Package R2SWF updated to version 0.8-2 with previous version 0.8-1 dated 2014-12-10

Title: Convert R Graphics to Flash Animations
Description: This package uses the Ming library (http://www.libming.org/) to create Flash animations. Users can either use the SWF device swf() to generate SWF file directly through plotting functions like plot() and lines(), or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between R2SWF versions 0.8-1 dated 2014-12-10 and 0.8-2 dated 2014-12-19

 DESCRIPTION              |    8 ++++----
 MD5                      |    6 +++---
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 4 files changed, 19 insertions(+), 9 deletions(-)

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Package lpme updated to version 1.0.1 with previous version 1.0.0 dated 2014-11-05

Title: Local Polynomial Estimator in Measurement Error Models
Description: Two local polynomial estimators for solving the errors-in-variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both estimators.
Author: Haiming Zhou and Xianzheng Huang
Maintainer: Haiming Zhou

Diff between lpme versions 1.0.0 dated 2014-11-05 and 1.0.1 dated 2014-12-19

 DESCRIPTION         |    6 +++---
 MD5                 |    4 ++--
 src/lpme_common.cpp |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about lpme at CRAN
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Package io updated to version 0.2.1 with previous version 0.2 dated 2014-12-11

Title: A Unified Framework for Input-Output Operations in R
Description: One function to read files. One function to write files. One function to direct plots to screen or file. Automatic file format inference and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih

Diff between io versions 0.2 dated 2014-12-11 and 0.2.1 dated 2014-12-19

 DESCRIPTION             |    8 ++++----
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 R/hdf5.R                |    6 ++++--
 R/internal.R            |    8 ++++++++
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 R/xml.R                 |    6 ++++--
 R/yaml.R                |    4 ++--
 tests/testthat/helper.R |   11 ++++++++++-
 8 files changed, 41 insertions(+), 20 deletions(-)

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Package interpretR updated to version 0.2.0 with previous version 0.1.0 dated 2014-11-21

Title: Binary Classifier Interpretation Functions
Description: Compute permutation- based performance measures and create partial dependence plots for binary (cross-validated) classification models. Currently only binary classification models estimated with the packages randomForest and ada are supported.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings

Diff between interpretR versions 0.1.0 dated 2014-11-21 and 0.2.0 dated 2014-12-19

 DESCRIPTION               |   19 +++---
 MD5                       |   14 ++--
 NAMESPACE                 |    2 
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Package hypervolume updated to version 1.1.1 with previous version 1.1 dated 2014-12-04

Title: High-dimensional Kernel Density Estimation and Geometry Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

Diff between hypervolume versions 1.1 dated 2014-12-04 and 1.1.1 dated 2014-12-19

 DESCRIPTION    |   14 +++++++-------
 MD5            |    6 +++---
 demo/finch.R   |    4 ++--
 demo/quercus.R |   15 ++++++---------
 4 files changed, 18 insertions(+), 21 deletions(-)

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Package BDgraph updated to version 2.14 with previous version 2.13 dated 2014-11-17

Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: This package provides a Bayesian methodology for structure learning in undirected graphical models. Our Bayesian methodology is based on birth-death Markov chain Monte Carlo (BDMCMC) algorithm which is the main function with the name 'bdgraph'. The main target of this package is high-dimensional data analysis wherein usually p >> n. The computation is memory-optimized using the sparse matrix output.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

Diff between BDgraph versions 2.13 dated 2014-11-17 and 2.14 dated 2014-12-19

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 BDgraph-2.14/BDgraph/man/bdgraph.Rd         |  126 +++++++++++++------------
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 BDgraph-2.14/BDgraph/man/compare.Rd         |   30 +++---
 BDgraph-2.14/BDgraph/man/phat.Rd            |   14 +-
 BDgraph-2.14/BDgraph/man/plot.bdgraph.Rd    |   18 +--
 BDgraph-2.14/BDgraph/man/plot.simulate.Rd   |   10 +-
 BDgraph-2.14/BDgraph/man/plotcoda.Rd        |   28 ++---
 BDgraph-2.14/BDgraph/man/plotroc.Rd         |   20 ++--
 BDgraph-2.14/BDgraph/man/print.bdgraph.Rd   |   18 +--
 BDgraph-2.14/BDgraph/man/print.simulate.Rd  |   10 +-
 BDgraph-2.14/BDgraph/man/prob.Rd            |   22 ++--
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 BDgraph-2.14/BDgraph/man/summary.bdgraph.Rd |   18 +--
 BDgraph-2.14/BDgraph/man/traceplot.Rd       |   20 ++--
 BDgraph-2.14/BDgraph/src/bdmcmc.cpp         |    8 -
 38 files changed, 260 insertions(+), 349 deletions(-)

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

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

2014-12-10 0.1

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Package WhopGenome (with last version 0.9.0) was removed from CRAN

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

2014-09-12 0.9.0
2014-08-27 0.8.9
2013-12-03 0.8.2
2013-11-19 0.8.1

Permanent link
Package hddtools (with last version 0.2.2) was removed from CRAN

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

2014-09-24 0.2.2
2014-08-13 0.1.1

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