Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.0.0 dated 2015-07-06 and 1.1.0 dated 2015-07-27
DESCRIPTION | 10 +- MD5 | 15 +-- NEWS |only R/WiSEHypothesisTest.R | 17 +-- build/vignette.rds |binary inst/doc/WiSEBoot_Examples_Vignette.R | 154 +++++++++++++++---------------- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 2 inst/doc/WiSEBoot_Examples_Vignette.pdf |binary vignettes/WiSEBoot_Examples_Vignette.Rnw | 2 9 files changed, 100 insertions(+), 100 deletions(-)
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.0.8 dated 2014-11-07 and 1.1.0 dated 2015-07-27
stm-1.0.8/stm/R/STMln.R |only stm-1.1.0/stm/DESCRIPTION | 19 stm-1.1.0/stm/LICENSE | 2 stm-1.1.0/stm/MD5 | 101 ++-- stm-1.1.0/stm/NAMESPACE | 25 - stm-1.1.0/stm/R/RcppExports.R |only stm-1.1.0/stm/R/STMestep.R | 15 stm-1.1.0/stm/R/STMinit.R | 54 +- stm-1.1.0/stm/R/STMlncpp.R |only stm-1.1.0/stm/R/STMmnreg.R | 44 + stm-1.1.0/stm/R/STMmu.R | 86 ++- stm-1.1.0/stm/R/estimateEffect.R | 27 - stm-1.1.0/stm/R/findThoughts.R | 5 stm-1.1.0/stm/R/findTopic.R |only stm-1.1.0/stm/R/heldout.R | 4 stm-1.1.0/stm/R/labelTopics.R | 32 - stm-1.1.0/stm/R/parseFormulas.R | 6 stm-1.1.0/stm/R/plot.STM.R | 5 stm-1.1.0/stm/R/plot.estimateEffect.R | 2 stm-1.1.0/stm/R/plot.searchK.R | 8 stm-1.1.0/stm/R/prepDocuments.R | 4 stm-1.1.0/stm/R/produce_cmatrix.R | 3 stm-1.1.0/stm/R/readCorpus.R | 12 stm-1.1.0/stm/R/spectral.R | 96 +++- stm-1.1.0/stm/R/stm.R | 46 + stm-1.1.0/stm/R/stm.control.R | 4 stm-1.1.0/stm/R/textProcessor.R | 58 +- stm-1.1.0/stm/R/thetaPosterior.R | 8 stm-1.1.0/stm/R/toLDAvis.R |only stm-1.1.0/stm/R/topicLasso.R |only stm-1.1.0/stm/build/vignette.rds |binary stm-1.1.0/stm/data/gadarian.RData |binary stm-1.1.0/stm/data/gadarianFit.RData |binary stm-1.1.0/stm/data/poliblog5k.RData |binary stm-1.1.0/stm/inst/CITATION | 4 stm-1.1.0/stm/inst/NEWS.Rd | 25 + stm-1.1.0/stm/inst/doc/stmVignette.R | 225 +++++---- stm-1.1.0/stm/inst/doc/stmVignette.Rnw | 632 ++++++++++++++++----------- stm-1.1.0/stm/inst/doc/stmVignette.pdf |binary stm-1.1.0/stm/man/estimateEffect.Rd | 9 stm-1.1.0/stm/man/findThoughts.Rd | 12 stm-1.1.0/stm/man/findTopic.Rd |only stm-1.1.0/stm/man/multiSTM.Rd | 4 stm-1.1.0/stm/man/plot.MultimodDiagnostic.Rd | 5 stm-1.1.0/stm/man/plot.estimateEffect.Rd | 3 stm-1.1.0/stm/man/searchK.Rd | 2 stm-1.1.0/stm/man/stm-package.Rd | 4 stm-1.1.0/stm/man/stm.Rd | 23 stm-1.1.0/stm/man/textProcessor.Rd | 14 stm-1.1.0/stm/man/toLDAvis.Rd |only stm-1.1.0/stm/man/topicLasso.Rd |only stm-1.1.0/stm/src |only stm-1.1.0/stm/vignettes/Flowchart.pdf |only stm-1.1.0/stm/vignettes/jsslogo.jpg |only stm-1.1.0/stm/vignettes/stmVignette.Rnw | 632 ++++++++++++++++----------- stm-1.1.0/stm/vignettes/vignetteBib.bib | 415 ++++++++++++----- 56 files changed, 1781 insertions(+), 894 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit
a regression model with possibly right, left or interval
censored observations and with the error distribution
expressed as a mixture of G-splines. Core part
of the computation is done in compiled C++ written
using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between smoothSurv versions 1.5-2 dated 2015-05-21 and 1.6 dated 2015-07-27
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 5 +++++ NEWS | 4 ++++ 4 files changed, 18 insertions(+), 8 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.5 dated 2015-07-15 and 1.3.6 dated 2015-07-27
SciencesPo-1.3.5/SciencesPo/R/add.ellipses.R |only SciencesPo-1.3.5/SciencesPo/R/between.R |only SciencesPo-1.3.5/SciencesPo/R/by.data.frame.R |only SciencesPo-1.3.5/SciencesPo/R/formatPercent.R |only SciencesPo-1.3.5/SciencesPo/R/legendPlotMinimalist.R |only SciencesPo-1.3.5/SciencesPo/R/name.slicer.R |only SciencesPo-1.3.5/SciencesPo/R/posixify.R |only SciencesPo-1.3.5/SciencesPo/R/roman.numeral.R |only SciencesPo-1.3.5/SciencesPo/R/use.R |only SciencesPo-1.3.5/SciencesPo/R/var_order.R |only SciencesPo-1.3.5/SciencesPo/R/weighted.variance.R |only SciencesPo-1.3.5/SciencesPo/man/add.ellipses.Rd |only SciencesPo-1.3.5/SciencesPo/man/as.data.frame.by.Rd |only SciencesPo-1.3.5/SciencesPo/man/bin.Rd |only SciencesPo-1.3.5/SciencesPo/man/formatPercent.Rd |only SciencesPo-1.3.5/SciencesPo/man/legendPlotMinimalist.Rd |only SciencesPo-1.3.5/SciencesPo/man/name.slicer.Rd |only SciencesPo-1.3.5/SciencesPo/man/posixify.Rd |only SciencesPo-1.3.5/SciencesPo/man/roman.numeral.Rd |only SciencesPo-1.3.5/SciencesPo/man/use.Rd |only SciencesPo-1.3.5/SciencesPo/man/varOrder.Rd |only SciencesPo-1.3.5/SciencesPo/man/weighted.variance.Rd |only SciencesPo-1.3.5/SciencesPo/man/zScores.Rd |only SciencesPo-1.3.6/SciencesPo/DESCRIPTION | 14 - SciencesPo-1.3.6/SciencesPo/MD5 | 107 +++++---- SciencesPo-1.3.6/SciencesPo/NAMESPACE | 60 +++-- SciencesPo-1.3.6/SciencesPo/R/DATA.R | 93 ++++---- SciencesPo-1.3.6/SciencesPo/R/MANIPULATION.R | 113 ---------- SciencesPo-1.3.6/SciencesPo/R/Themes.R |only SciencesPo-1.3.6/SciencesPo/R/add.R |only SciencesPo-1.3.6/SciencesPo/R/allocation.R |only SciencesPo-1.3.6/SciencesPo/R/as.percent.R |only SciencesPo-1.3.6/SciencesPo/R/as.roman.R |only SciencesPo-1.3.6/SciencesPo/R/build.R |only SciencesPo-1.3.6/SciencesPo/R/ci.R | 4 SciencesPo-1.3.6/SciencesPo/R/crosstable.R | 135 ++++++++---- SciencesPo-1.3.6/SciencesPo/R/dHondt.R | 30 +- SciencesPo-1.3.6/SciencesPo/R/database.R |only SciencesPo-1.3.6/SciencesPo/R/electoralTool.R | 175 ++++++++++++++++ SciencesPo-1.3.6/SciencesPo/R/ellipses.R |only SciencesPo-1.3.6/SciencesPo/R/footnote.R |only SciencesPo-1.3.6/SciencesPo/R/lookup.R | 3 SciencesPo-1.3.6/SciencesPo/R/mode.R | 4 SciencesPo-1.3.6/SciencesPo/R/normalize.R |only SciencesPo-1.3.6/SciencesPo/R/recode.R |only SciencesPo-1.3.6/SciencesPo/R/rename.R | 105 --------- SciencesPo-1.3.6/SciencesPo/R/svTransform.R |only SciencesPo-1.3.6/SciencesPo/R/tabulate.R |only SciencesPo-1.3.6/SciencesPo/R/utils.R | 11 - SciencesPo-1.3.6/SciencesPo/R/var.order.R |only SciencesPo-1.3.6/SciencesPo/R/weighted.var.R |only SciencesPo-1.3.6/SciencesPo/R/z.scores.R |only SciencesPo-1.3.6/SciencesPo/README.md | 2 SciencesPo-1.3.6/SciencesPo/demo/SciencesPo.R | 52 +++- SciencesPo-1.3.6/SciencesPo/inst/NEWS.Rd | 10 SciencesPo-1.3.6/SciencesPo/man/add-methods.Rd |only SciencesPo-1.3.6/SciencesPo/man/allocation.Rd |only SciencesPo-1.3.6/SciencesPo/man/as.percent.Rd |only SciencesPo-1.3.6/SciencesPo/man/as.roman.Rd |only SciencesPo-1.3.6/SciencesPo/man/build-methods.Rd |only SciencesPo-1.3.6/SciencesPo/man/cox.shugart.Rd |only SciencesPo-1.3.6/SciencesPo/man/dHondt.Rd | 18 + SciencesPo-1.3.6/SciencesPo/man/database.Rd |only SciencesPo-1.3.6/SciencesPo/man/dbTempTable.Rd |only SciencesPo-1.3.6/SciencesPo/man/ellipses.Rd |only SciencesPo-1.3.6/SciencesPo/man/farina.Rd |only SciencesPo-1.3.6/SciencesPo/man/footnote.Rd |only SciencesPo-1.3.6/SciencesPo/man/gallagher.Rd |only SciencesPo-1.3.6/SciencesPo/man/grofman.Rd |only SciencesPo-1.3.6/SciencesPo/man/head.Rd |only SciencesPo-1.3.6/SciencesPo/man/lijphart.Rd |only SciencesPo-1.3.6/SciencesPo/man/lookup.Rd | 3 SciencesPo-1.3.6/SciencesPo/man/normalize.Rd | 2 SciencesPo-1.3.6/SciencesPo/man/recode.Rd |only SciencesPo-1.3.6/SciencesPo/man/rename.Rd | 30 -- SciencesPo-1.3.6/SciencesPo/man/scale_colour_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/scale_fill_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/svTransform.Rd | 2 SciencesPo-1.3.6/SciencesPo/man/tab.Rd | 29 ++ SciencesPo-1.3.6/SciencesPo/man/tabulate.Rd |only SciencesPo-1.3.6/SciencesPo/man/theme_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/var.order.Rd |only SciencesPo-1.3.6/SciencesPo/man/weighted.var.Rd |only SciencesPo-1.3.6/SciencesPo/man/z.scores.Rd |only SciencesPo-1.3.6/SciencesPo/tests/testthat/test-cv.R |only SciencesPo-1.3.6/SciencesPo/tests/testthat/test-se.R | 6 86 files changed, 545 insertions(+), 463 deletions(-)
Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between RcmdrPlugin.NMBU versions 1.8.0.4 dated 2015-03-12 and 1.8.3 dated 2015-07-27
DESCRIPTION | 10 MD5 | 18 NAMESPACE | 15 R/NMBU.GUI.Models.R | 10 R/NMBU.GUI.Statistics.R | 425 ++++++++++------- R/NMBU.RcmdrPlugin.NMBU.R | 2 R/NMBU.Utilities.R | 989 ++++++++++++++++++++++++---------------- R/globals.R | 3 inst/etc/menus.txt | 42 + man/RcmdrPlugin.NMBU-package.Rd | 8 10 files changed, 926 insertions(+), 596 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: An Extension (for Package 'SigTree') of Some of the Classes in
Package 'phylobase'
Description: Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
Author: J. Conrad Stack
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Diff between phyext2 versions 0.0.3 dated 2015-07-17 and 0.0.4 dated 2015-07-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 9 +++++++++ R/phyext2.R | 3 ++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>
Diff between MPTinR versions 1.9.2 dated 2015-06-13 and 1.10.3 dated 2015-07-27
DESCRIPTION | 10 MD5 | 31 NAMESPACE | 3 NEWS | 27 R/fit.mptinr.R | 6 R/get.mpt.fia.R | 316 ++++----- R/select.mpt.R | 10 data/roc6.rda |only data/roc8.rda |only inst/doc/mptinr_introduction.R | 383 ++++++----- inst/doc/mptinr_introduction.Rnw | 1239 +++++++++++++++++++------------------- inst/doc/mptinr_introduction.pdf |binary man/fit.model.Rd | 8 man/rocs.Rd |only man/select.mpt.Rd | 21 src/RcppExports.cpp | 18 vignettes/MPT.bib | 25 vignettes/mptinr_introduction.Rnw | 1239 +++++++++++++++++++------------------- 18 files changed, 1721 insertions(+), 1615 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.0 dated 2015-07-23 and 1.1 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/invert_toeplitz.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Query Team Cymru IP Address, Autonomous System Number (ASN),
Border Gateway Protocol (BGP), Bogon and Malware Hash Data
Services
Description: A toolkit for querying Team Cymru <http://team-cymru.org> IP address,
Autonomous System Number (ASN), Border Gateway Protocol (BGP), Bogon
and Malware Hash Data Services.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between cymruservices versions 0.1.0 dated 2015-07-23 and 0.1.1 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bogons.R | 34 ++++++++++++++++++++++++++++------ man/ipv4_bogons.Rd | 2 +- man/ipv6_bogons.Rd | 2 +- 5 files changed, 37 insertions(+), 15 deletions(-)
Title: Credit Default Swap Functions
Description: One function to bootstrap a credit curve from market quotes (Credit Default Swap spreads) and another function to price Credit Default Swaps from a credit curve.
Author: Bertrand Le Nezet [cre, aut, cph],
Richard Brent [ctb, cph],
John Burkardt [ctb, cph]
Maintainer: Bertrand Le Nezet <bertrand.lenezet@gmail.com>
Diff between credule versions 0.1 dated 2015-07-25 and 0.1.2 dated 2015-07-27
credule-0.1.2/credule/DESCRIPTION | 16 - credule-0.1.2/credule/MD5 | 12 credule-0.1.2/credule/man/bootstrapCDS.Rd | 2 credule-0.1.2/credule/man/credule-package.Rd | 6 credule-0.1.2/credule/man/priceCDS.Rd | 2 credule-0.1.2/credule/src/credule.c | 380 +++++---------------------- credule-0.1.2/credule/src/credule.h |only credule-0.1/credule/R/credule-Ex.R |only 8 files changed, 106 insertions(+), 312 deletions(-)
Title: Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>
Diff between cpm versions 2.1 dated 2015-07-12 and 2.2 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/CITATION | 34 +++++++++++++++++++--------------- man/cpmPackage.Rd | 2 +- 4 files changed, 26 insertions(+), 22 deletions(-)
Title: Bayesian Optimal Interval Design for Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 1.1 dated 2015-02-15 and 1.2 dated 2015-07-27
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/get.boundary.R | 8 ++++++-- R/get.oc.R | 4 ++-- R/select.mtd.R | 8 ++++++-- man/BOIN-package.Rd | 13 +++++++------ man/get.boundary.Rd | 30 +++++++++++++++--------------- man/get.oc.Rd | 30 +++++++++++++++--------------- man/select.mtd.Rd | 23 ++++++++++++++++------- 10 files changed, 83 insertions(+), 63 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Description: Contains Bayesian implementations of Mixed-Effects Accelerated Failure Time (MEAFT) models
for censored data. Those can be not only right-censored but also interval-censored,
doubly-interval-censored or misclassified interval-censored.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between bayesSurv versions 2.4 dated 2015-02-05 and 2.6 dated 2015-07-27
CHANGES | 12 +++++++++++- DESCRIPTION | 13 ++++++++----- MD5 | 14 ++++++++------ NAMESPACE | 15 +++++++++++++++ R/bayessurvreg3.R | 4 ++-- R/bayessurvreg3Para.R |only R/predictive2Para.R |only man/bayessurvreg3.Rd | 26 ++++++++++++++++++++++++++ man/predictive2.Rd | 10 ++++++++++ 9 files changed, 80 insertions(+), 14 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.0.2 dated 2015-04-21 and 1.0.3 dated 2015-07-27
sitar-1.0.2/sitar/R/predict.R |only sitar-1.0.3/sitar/DESCRIPTION | 8 - sitar-1.0.3/sitar/MD5 | 35 +++-- sitar-1.0.3/sitar/NAMESPACE | 33 +++- sitar-1.0.3/sitar/NEWS | 21 +++ sitar-1.0.3/sitar/R/anova.sitar.R |only sitar-1.0.3/sitar/R/ifun.R |only sitar-1.0.3/sitar/R/mplot.R | 10 - sitar-1.0.3/sitar/R/plot.sitar.R | 195 ++++++++++++++++------------ sitar-1.0.3/sitar/R/predict.sitar.R |only sitar-1.0.3/sitar/R/sitar.R | 13 + sitar-1.0.3/sitar/R/sitarlib.R | 33 ---- sitar-1.0.3/sitar/R/xyadj.R |only sitar-1.0.3/sitar/data/heights.rda |binary sitar-1.0.3/sitar/man/anova.sitar.Rd |only sitar-1.0.3/sitar/man/getCovariate.sitar.Rd |only sitar-1.0.3/sitar/man/heights.Rd | 5 sitar-1.0.3/sitar/man/ifun.Rd |only sitar-1.0.3/sitar/man/mplot.Rd | 2 sitar-1.0.3/sitar/man/plot.sitar.Rd | 65 ++++++--- sitar-1.0.3/sitar/man/predict.sitar.Rd | 23 ++- sitar-1.0.3/sitar/man/sitar.Rd | 14 +- sitar-1.0.3/sitar/man/xyadj.Rd |only 23 files changed, 280 insertions(+), 177 deletions(-)
Title: Discrete Laplace Distributions
Description: Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
Author: Alessandro Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo <riccardo.arner@libero.it>
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteLaplace versions 1.0 dated 2012-02-02 and 1.1 dated 2015-07-27
DiscreteLaplace-1.0/DiscreteLaplace/R/pdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/R/qdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/R/rdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/doc |only DiscreteLaplace-1.0/DiscreteLaplace/man/pdlaplace.Rd |only DiscreteLaplace-1.0/DiscreteLaplace/man/qdlaplace.Rd |only DiscreteLaplace-1.0/DiscreteLaplace/man/rdlaplace.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/DESCRIPTION | 20 +-- DiscreteLaplace-1.1/DiscreteLaplace/MD5 | 39 +++-- DiscreteLaplace-1.1/DiscreteLaplace/NAMESPACE | 3 DiscreteLaplace-1.1/DiscreteLaplace/R/Edlaplace.R | 2 DiscreteLaplace-1.1/DiscreteLaplace/R/Edlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/ddlaplace.R | 45 +++++- DiscreteLaplace-1.1/DiscreteLaplace/R/ddlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/dlaplacelike2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/estdlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/iFI.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/iFI2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/ioFI2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/loss.R |only DiscreteLaplace-1.1/DiscreteLaplace/man/DiscreteLaplace-package.Rd | 16 +- DiscreteLaplace-1.1/DiscreteLaplace/man/Edlaplace.Rd | 8 - DiscreteLaplace-1.1/DiscreteLaplace/man/Edlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/ddlaplace.Rd | 66 ++++++++-- DiscreteLaplace-1.1/DiscreteLaplace/man/ddlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/dlaplacelike.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/estdlaplace.Rd | 11 - DiscreteLaplace-1.1/DiscreteLaplace/man/estdlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/iFI.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/iFI2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/ioFI2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/loss.Rd |only 32 files changed, 145 insertions(+), 65 deletions(-)
More information about DiscreteLaplace at CRAN
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Title: An R Package for Changepoint Analysis
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean, cpt.var, cpt.meanvar functions should be your first point of call.
Author: Rebecca Killick [aut, cre],
Kaylea Haynes [aut],
Idris Eckley [aut],
Paul Fearnhead [ctb],
Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between changepoint versions 1.1.5 dated 2014-06-25 and 2.0.1 dated 2015-07-27
changepoint-1.1.5/changepoint/man/PELT.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/PELT.var.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/binseg.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/binseg.var.css.Rd |only changepoint-1.1.5/changepoint/man/binseg.var.norm.Rd |only changepoint-1.1.5/changepoint/man/decision.Rd |only changepoint-1.1.5/changepoint/man/multiple.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/multiple.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/multiple.var.css.Rd |only changepoint-1.1.5/changepoint/man/multiple.var.norm.Rd |only changepoint-1.1.5/changepoint/man/print-methods.Rd |only changepoint-1.1.5/changepoint/man/segneigh.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/segneigh.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/segneigh.var.css.Rd |only changepoint-1.1.5/changepoint/man/segneigh.var.norm.Rd |only changepoint-1.1.5/changepoint/man/single.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/single.mean.cusum.calc.Rd |only changepoint-1.1.5/changepoint/man/single.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/single.mean.norm.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.exp.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.gamma.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.norm.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.poisson.calc.Rd |only changepoint-1.1.5/changepoint/man/single.var.css.Rd |only changepoint-1.1.5/changepoint/man/single.var.css.calc.Rd |only changepoint-1.1.5/changepoint/man/single.var.norm.Rd |only changepoint-1.1.5/changepoint/man/single.var.norm.calc.Rd |only changepoint-1.1.5/changepoint/src/PELT.c |only changepoint-2.0.1/changepoint/DESCRIPTION | 22 changepoint-2.0.1/changepoint/MD5 | 122 changepoint-2.0.1/changepoint/NAMESPACE | 26 changepoint-2.0.1/changepoint/NEWS | 33 changepoint-2.0.1/changepoint/R/BinSeg_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/CROPS.R |only changepoint-2.0.1/changepoint/R/PELT_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/SegNeigh_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/class_input.R |only changepoint-2.0.1/changepoint/R/cpt.R | 364 +- changepoint-2.0.1/changepoint/R/cpt.class.R | 230 + changepoint-2.0.1/changepoint/R/data_input.R |only changepoint-2.0.1/changepoint/R/decision.R | 62 changepoint-2.0.1/changepoint/R/exp.R | 624 ++-- changepoint-2.0.1/changepoint/R/gamma.R | 407 +-- changepoint-2.0.1/changepoint/R/multiple.nonparametric.R | 615 ++-- changepoint-2.0.1/changepoint/R/multiple.norm.R | 1256 +++++----- changepoint-2.0.1/changepoint/R/penalty_decision.R |only changepoint-2.0.1/changepoint/R/poisson.R | 409 +-- changepoint-2.0.1/changepoint/R/range_of_penalties.R |only changepoint-2.0.1/changepoint/R/single.nonparametric.R | 406 +-- changepoint-2.0.1/changepoint/R/single.norm.R | 328 +- changepoint-2.0.1/changepoint/R/zzz.R | 4 changepoint-2.0.1/changepoint/inst/CITATION | 48 changepoint-2.0.1/changepoint/man/changepoint-package.Rd | 4 changepoint-2.0.1/changepoint/man/cpt-class.Rd | 7 changepoint-2.0.1/changepoint/man/cpt.mean.Rd | 29 changepoint-2.0.1/changepoint/man/cpt.meanvar.Rd | 28 changepoint-2.0.1/changepoint/man/cpt.range-class.Rd |only changepoint-2.0.1/changepoint/man/cpt.var.Rd | 26 changepoint-2.0.1/changepoint/man/cpts.full--methods.Rd |only changepoint-2.0.1/changepoint/man/cpts.full-.Rd |only changepoint-2.0.1/changepoint/man/cpts.full-methods.Rd |only changepoint-2.0.1/changepoint/man/cpts.full.Rd |only changepoint-2.0.1/changepoint/man/minseglen--methods.Rd |only changepoint-2.0.1/changepoint/man/minseglen-.Rd |only changepoint-2.0.1/changepoint/man/minseglen-methods.Rd |only changepoint-2.0.1/changepoint/man/minseglen.Rd |only changepoint-2.0.1/changepoint/man/nseg-methods.Rd |only changepoint-2.0.1/changepoint/man/nseg.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full--methods.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full-.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full-methods.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full.Rd |only changepoint-2.0.1/changepoint/man/show-methods.Rd |only changepoint-2.0.1/changepoint/man/summary-methods.Rd | 4 changepoint-2.0.1/changepoint/src/BinSeg_one_func_minseglen.c |only changepoint-2.0.1/changepoint/src/PELT_one_func_minseglen.c |only changepoint-2.0.1/changepoint/src/cost_general_functions.c |only changepoint-2.0.1/changepoint/tests |only 99 files changed, 2888 insertions(+), 2166 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre],
Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>
Diff between alineR versions 1.0 dated 2015-07-10 and 1.1 dated 2015-07-27
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 3 +-- R/ALINE.segments.R | 5 ++++- R/map.R | 2 +- R/optimize.features.R | 12 +++--------- man/aline-package.Rd | 3 +++ man/features.plot.Rd | 2 +- man/optimize.features.Rd | 12 ++---------- 9 files changed, 29 insertions(+), 39 deletions(-)
Title: An R Package for Reading and Writing BAM (Binary Alignment)
Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.12.2 dated 2015-07-16 and 2.12.3 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/data_frame.h | 20 +++++++++++++++++--- 3 files changed, 22 insertions(+), 8 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.4.1 dated 2015-07-09 and 0.4.2 dated 2015-07-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/SES.R | 1 + R/censIndLR.R | 33 +++++++++++++++++---------------- R/testIndLogistic.R | 6 +++++- man/MXM-package.Rd | 4 ++-- 7 files changed, 36 insertions(+), 30 deletions(-)
Title: A Google Analytics API Client
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 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 <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.2 dated 2015-06-14 and 0.2.3 dated 2015-07-27
RGA-0.2.2/RGA/R/first-date.R |only RGA-0.2.3/RGA/DESCRIPTION | 15 +- RGA-0.2.3/RGA/MD5 | 117 +++++++++++------------ RGA-0.2.3/RGA/NAMESPACE | 4 RGA-0.2.3/RGA/R/auth.R | 66 +++++++++--- RGA-0.2.3/RGA/R/convert.R | 21 ++-- RGA-0.2.3/RGA/R/custom-sources.R | 2 RGA-0.2.3/RGA/R/firstdate.R |only RGA-0.2.3/RGA/R/get-data.R | 4 RGA-0.2.3/RGA/R/goals.R | 4 RGA-0.2.3/RGA/R/mgmt.R | 2 RGA-0.2.3/RGA/R/package.R | 3 RGA-0.2.3/RGA/R/profiles.R | 6 - RGA-0.2.3/RGA/R/request.R | 7 + RGA-0.2.3/RGA/R/unsampled.R | 6 - RGA-0.2.3/RGA/R/url.R | 29 +++-- RGA-0.2.3/RGA/R/utils.R | 1 RGA-0.2.3/RGA/R/webproperties.R | 2 RGA-0.2.3/RGA/R/zzz.R | 2 RGA-0.2.3/RGA/README.md | 2 RGA-0.2.3/RGA/build/vignette.rds |binary RGA-0.2.3/RGA/data/ga.rda |binary RGA-0.2.3/RGA/inst/NEWS.Rd | 40 +++++-- RGA-0.2.3/RGA/inst/doc/authorize.R | 2 RGA-0.2.3/RGA/inst/doc/authorize.Rmd | 49 ++++++--- RGA-0.2.3/RGA/inst/doc/authorize.html | 22 +++- RGA-0.2.3/RGA/inst/doc/common-queries.R |only RGA-0.2.3/RGA/inst/doc/common-queries.Rmd |only RGA-0.2.3/RGA/inst/doc/common-queries.html |only RGA-0.2.3/RGA/inst/doc/management-api.R | 2 RGA-0.2.3/RGA/inst/doc/management-api.Rmd | 41 ++++---- RGA-0.2.3/RGA/inst/doc/management-api.html | 42 +++++--- RGA-0.2.3/RGA/inst/doc/metadata-api.R | 2 RGA-0.2.3/RGA/inst/doc/metadata-api.Rmd | 15 ++ RGA-0.2.3/RGA/inst/doc/metadata-api.html | 8 - RGA-0.2.3/RGA/inst/doc/reporting-api.R | 2 RGA-0.2.3/RGA/inst/doc/reporting-api.Rmd | 17 +-- RGA-0.2.3/RGA/inst/doc/reporting-api.html | 15 +- RGA-0.2.3/RGA/man/RGA.Rd | 2 RGA-0.2.3/RGA/man/authorize.Rd | 43 ++++++-- RGA-0.2.3/RGA/man/firstdate.Rd | 5 RGA-0.2.3/RGA/man/get_ga.Rd | 5 RGA-0.2.3/RGA/man/get_goal.Rd | 4 RGA-0.2.3/RGA/man/get_mcf.Rd | 5 RGA-0.2.3/RGA/man/get_profile.Rd | 4 RGA-0.2.3/RGA/man/get_rt.Rd | 5 RGA-0.2.3/RGA/man/get_unsampled_report.Rd | 2 RGA-0.2.3/RGA/man/get_webproperty.Rd | 2 RGA-0.2.3/RGA/man/list_custom_sources.Rd | 2 RGA-0.2.3/RGA/man/list_profiles.Rd | 2 RGA-0.2.3/RGA/man/list_unsampled_reports.Rd | 2 RGA-0.2.3/RGA/tests/testthat/test-auth.R |only RGA-0.2.3/RGA/tests/testthat/test-convert-ga.R | 8 - RGA-0.2.3/RGA/tests/testthat/test-convert-mcf.R | 44 ++++---- RGA-0.2.3/RGA/tests/testthat/test-convert-mgmt.R | 14 +- RGA-0.2.3/RGA/tests/testthat/test-metadata.R | 14 +- RGA-0.2.3/RGA/tests/testthat/test-query.R | 18 ++- RGA-0.2.3/RGA/tests/testthat/test-url.R | 8 - RGA-0.2.3/RGA/vignettes/authorize.Rmd | 49 ++++++--- RGA-0.2.3/RGA/vignettes/common-queries.Rmd |only RGA-0.2.3/RGA/vignettes/management-api.Rmd | 41 ++++---- RGA-0.2.3/RGA/vignettes/metadata-api.Rmd | 15 ++ RGA-0.2.3/RGA/vignettes/reporting-api.Rmd | 17 +-- 63 files changed, 525 insertions(+), 336 deletions(-)
Title: Discrete and Global Optimization Routines
Description:
The R package 'adagio' will provide methods and algorithms for
discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between adagio versions 0.5.9 dated 2013-09-28 and 0.6.1 dated 2015-07-27
adagio-0.5.9/adagio/R/linesearch.R |only adagio-0.5.9/adagio/R/qpspecial.R |only adagio-0.5.9/adagio/man/linesearch.Rd |only adagio-0.5.9/adagio/man/qpspecial.Rd |only adagio-0.6.1/adagio/DESCRIPTION | 14 ++++--- adagio-0.6.1/adagio/MD5 | 28 ++++++--------- adagio-0.6.1/adagio/NAMESPACE | 25 +++++++------ adagio-0.6.1/adagio/NEWS | 9 ++++ adagio-0.6.1/adagio/R/testfunctions.R | 36 +++---------------- adagio-0.6.1/adagio/R/trefethen.R | 7 +-- adagio-0.6.1/adagio/man/maxempty.Rd | 8 ++-- adagio-0.6.1/adagio/man/maxquad.Rd | 3 - adagio-0.6.1/adagio/man/nelmin.Rd | 5 +- adagio-0.6.1/adagio/man/simpleDE.Rd | 2 - adagio-0.6.1/adagio/man/simpleEA.Rd | 2 - adagio-0.6.1/adagio/man/testfunctions.Rd | 57 +++++++++++++++++-------------- adagio-0.6.1/adagio/man/trefethen.Rd | 20 ++++++---- 17 files changed, 103 insertions(+), 113 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.1 dated 2015-07-24 and 1.0.2 dated 2015-07-27
warbleR-1.0.1/warbleR/R/autodetec_1.0.R |only warbleR-1.0.1/warbleR/R/checkwavs_1.0.R |only warbleR-1.0.1/warbleR/R/lspec_1.6.R |only warbleR-1.0.1/warbleR/R/manualoc_1.9.R |only warbleR-1.0.1/warbleR/R/mp32wav_1.0.R |only warbleR-1.0.1/warbleR/R/querxc_1.1.R |only warbleR-1.0.1/warbleR/R/snrspecs_1.4.R |only warbleR-1.0.1/warbleR/R/specan_1.2.R |only warbleR-1.0.1/warbleR/R/specreator_2.4.R |only warbleR-1.0.1/warbleR/R/trackfreqs_1.4.R |only warbleR-1.0.1/warbleR/R/xcmaps_1.2.R |only warbleR-1.0.2/warbleR/DESCRIPTION | 10 +- warbleR-1.0.2/warbleR/MD5 | 82 +++++++++++------------ warbleR-1.0.2/warbleR/R/Arre.aura-data.R | 8 -- warbleR-1.0.2/warbleR/R/Phae.cuvi-data.R | 9 -- warbleR-1.0.2/warbleR/R/Phae.long1-data.R | 10 +- warbleR-1.0.2/warbleR/R/Phae.long2-data.R | 10 -- warbleR-1.0.2/warbleR/R/Phae.long3-data.R | 11 +-- warbleR-1.0.2/warbleR/R/Phae.long4-data.R | 9 -- warbleR-1.0.2/warbleR/R/autodetec.R |only warbleR-1.0.2/warbleR/R/checkwavs.R |only warbleR-1.0.2/warbleR/R/lspec.R |only warbleR-1.0.2/warbleR/R/manualoc.R |only warbleR-1.0.2/warbleR/R/manualoc.df-data.R | 2 warbleR-1.0.2/warbleR/R/mp32wav.R |only warbleR-1.0.2/warbleR/R/querxc.R |only warbleR-1.0.2/warbleR/R/sig2noise.R | 48 ++++++++----- warbleR-1.0.2/warbleR/R/snrspecs.R |only warbleR-1.0.2/warbleR/R/specan.R |only warbleR-1.0.2/warbleR/R/specreator.R |only warbleR-1.0.2/warbleR/R/trackfreqs.R |only warbleR-1.0.2/warbleR/R/warbleR-package.R | 36 +++++----- warbleR-1.0.2/warbleR/R/xcmaps.R |only warbleR-1.0.2/warbleR/man/Arre.aura.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.cuvi.Rd | 10 -- warbleR-1.0.2/warbleR/man/Phae.long1.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long2.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long3.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long4.Rd | 7 - warbleR-1.0.2/warbleR/man/autodetec.Rd | 103 +++++++++++++++-------------- warbleR-1.0.2/warbleR/man/checkwavs.Rd | 16 +++- warbleR-1.0.2/warbleR/man/lspec.Rd | 57 +++++++++------- warbleR-1.0.2/warbleR/man/manualoc.Rd | 89 +++++++++++++------------ warbleR-1.0.2/warbleR/man/manualoc.df.Rd | 2 warbleR-1.0.2/warbleR/man/mp32wav.Rd | 24 +++++- warbleR-1.0.2/warbleR/man/querxc.Rd | 34 ++++++--- warbleR-1.0.2/warbleR/man/sig2noise.Rd | 48 ++++++++----- warbleR-1.0.2/warbleR/man/snrspecs.Rd | 95 +++++++++++++++----------- warbleR-1.0.2/warbleR/man/specan.Rd | 50 ++++++++------ warbleR-1.0.2/warbleR/man/specreator.Rd | 87 ++++++++++++------------ warbleR-1.0.2/warbleR/man/trackfreqs.Rd | 103 ++++++++++++++++------------- warbleR-1.0.2/warbleR/man/warbleR.Rd | 32 +++++---- warbleR-1.0.2/warbleR/man/xcmaps.Rd | 18 ++--- 53 files changed, 574 insertions(+), 464 deletions(-)
Title: Interpolation of Data with Variable Spatial Support
Description: Geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between rtop versions 0.3-45 dated 2014-02-10 and 0.5-5 dated 2015-07-27
rtop-0.3-45/rtop/R/onLoad.r |only rtop-0.5-5/rtop/DESCRIPTION | 17 rtop-0.5-5/rtop/MD5 | 73 ++- rtop-0.5-5/rtop/NAMESPACE | 191 +++++---- rtop-0.5-5/rtop/R/checkVario.R | 5 rtop-0.5-5/rtop/R/discAreas.R | 84 ++-- rtop-0.5-5/rtop/R/estimateParameters.R | 10 rtop-0.5-5/rtop/R/findOverlap.R | 9 rtop-0.5-5/rtop/R/fitVariogram.R | 38 + rtop-0.5-5/rtop/R/gDist.r | 123 ++---- rtop-0.5-5/rtop/R/krige.R |only rtop-0.5-5/rtop/R/riverNetwork.R | 12 rtop-0.5-5/rtop/R/rtop.R | 495 +++++++++++++------------ rtop-0.5-5/rtop/R/rtopCluster.R |only rtop-0.5-5/rtop/R/rtopKrige.R | 184 +++------ rtop-0.5-5/rtop/R/rtopSim.R |only rtop-0.5-5/rtop/R/rtopVario.R | 352 ++++++++++++----- rtop-0.5-5/rtop/R/sceua.R | 481 ++++++++++++------------ rtop-0.5-5/rtop/R/tskrige.R |only rtop-0.5-5/rtop/R/useRtopWithIntamap.R |only rtop-0.5-5/rtop/R/varMat.R | 177 ++++++-- rtop-0.5-5/rtop/R/zzz.R | 25 - rtop-0.5-5/rtop/man/checkVario.Rd | 196 +++++---- rtop-0.5-5/rtop/man/createRtopObject.Rd | 6 rtop-0.5-5/rtop/man/downloadRtopExampleData.rd | 63 +-- rtop-0.5-5/rtop/man/gDist.Rd | 201 +++++----- rtop-0.5-5/rtop/man/getRtopParams.Rd | 35 + rtop-0.5-5/rtop/man/netProp.rd | 143 +++---- rtop-0.5-5/rtop/man/plot.rtopVariogramCloud.Rd | 2 rtop-0.5-5/rtop/man/readAreaInfo.Rd | 87 ++-- rtop-0.5-5/rtop/man/readAreas.Rd | 89 ++-- rtop-0.5-5/rtop/man/rtop-package.Rd | 12 rtop-0.5-5/rtop/man/rtopCluster.Rd |only rtop-0.5-5/rtop/man/rtopFitVariogram.Rd | 207 +++++----- rtop-0.5-5/rtop/man/rtopKrige.Rd | 283 ++++++++------ rtop-0.5-5/rtop/man/rtopSim.Rd |only rtop-0.5-5/rtop/man/rtopVariogram.Rd | 159 ++++---- rtop-0.5-5/rtop/man/sceua.Rd |only rtop-0.5-5/rtop/man/useRtopWithIntamap.Rd | 51 +- rtop-0.5-5/rtop/man/varMat.Rd | 208 +++++----- rtop-0.5-5/rtop/man/variogramModel.Rd | 132 +++--- rtop-0.5-5/rtop/tests/rtop.R | 33 + 42 files changed, 2279 insertions(+), 1904 deletions(-)
Title: Toolbox for WELL Random Number Generators
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky <savicky@cs.cas.cz>.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rngWELL versions 0.10-3 dated 2014-07-25 and 0.10-4 dated 2015-07-27
DESCRIPTION | 13 ++++++------- LICENSE | 2 +- MD5 | 6 +++--- src/config.h | 52 ++++++++++++++++++++++++++++------------------------ 4 files changed, 38 insertions(+), 35 deletions(-)
Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g.,
density estimation or clustering algorithms research and teaching;
providing the widely used Marron-Wand densities. Now fitting to data
by ML (Maximum Likelihood) or EM estimation.
Author: Martin Mächler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between nor1mix versions 1.2-0 dated 2014-09-02 and 1.2-1 dated 2015-07-27
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 10 ++++++---- R/norMixEM.R | 2 +- man/MarronWand.Rd | 5 +++-- 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.4 dated 2015-06-10 and 0.5 dated 2015-07-27
DESCRIPTION | 6 - MD5 | 44 ++++--- NAMESPACE | 1 NEWS | 6 + R/bson.R | 2 R/hacks.R |only R/iter.R |only R/jeroen.R | 7 - R/mongo.R | 13 +- R/object.R | 27 +++- R/stream.R | 9 - build/vignette.rds |binary inst/doc/intro.html | 4 man/mongo.Rd | 8 - src/bson/bson-stdint.h | 2 src/bson/bson-version.h | 6 - src/client.c | 3 src/cursor.c | 6 + src/mongoc/mongoc-cluster-private.h | 2 src/mongoc/mongoc-cluster.c | 207 +++++++++++++++++++++++------------- src/mongoc/mongoc-init.c | 18 --- src/mongoc/mongoc-read-prefs.c | 6 + src/mongoc/mongoc-version.h | 6 - src/mongoc/mongoc-write-command.c | 4 24 files changed, 249 insertions(+), 138 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.2-28 dated 2015-01-21 and 0.2.44 dated 2015-07-27
DESCRIPTION | 14 - MD5 | 35 ++-- NAMESPACE | 8 NEWS | 421 +++++++++++++++++++++------------------------------ R/adj2HPD.R | 2 R/animateHive.R | 19 +- R/drawHiveSpline.R | 10 - R/manipAxis.R | 7 R/plot3dHive.R | 105 +++++++----- R/plotHive.R | 76 ++++++--- R/ranHiveData.R | 10 - R/rcsr.R | 2 R/sumHPD.R | 10 - build/vignette.rds |binary inst/doc/HiveR.pdf |binary man/HidingAnAxis.Rd |only man/HiveR-package.Rd | 12 - man/ranHiveData.Rd | 2 man/rcsr.Rd | 2 19 files changed, 369 insertions(+), 366 deletions(-)
Title: Analysis of Ontologies and Protein Domain Annotations
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dcGOR versions 1.0.5 dated 2015-07-20 and 1.0.6 dated 2015-07-27
DESCRIPTION | 12 ++-- MD5 | 58 +++++++++---------- R/dcAlgo.r | 4 - R/dcAlgoPredict.r | 4 - R/dcAlgoPredictGenome.r | 4 - R/dcAlgoPredictMain.r | 4 - R/dcAlgoPredictPR.r | 4 - R/dcAlgoPropagate.r | 4 - R/dcEnrichment.r | 2 R/dcList2Matrix.r | 2 R/dcNaivePredict.r | 4 - R/dcRDataLoader.r | 135 ++++++++++++++++++++++++++++++++++++--------- R/dcRWRpredict.r | 4 - R/dcSparseMatrix.r | 2 inst/NEWS | 8 ++ inst/staticdocs/README.md | 2 man/dcAlgo.Rd | 17 +---- man/dcAlgoPredict.Rd | 17 +---- man/dcAlgoPredictGenome.Rd | 17 +---- man/dcAlgoPredictMain.Rd | 17 +---- man/dcAlgoPredictPR.Rd | 17 +---- man/dcAlgoPropagate.Rd | 17 +---- man/dcEnrichment.Rd | 14 ---- man/dcList2Matrix.Rd | 2 man/dcNaivePredict.Rd | 17 +---- man/dcRDataLoader.Rd | 24 ++++---- man/dcRWRpredict.Rd | 17 +---- man/dcSparseMatrix.Rd | 4 - man/onto.DO.Rd | 2 man/onto.MP.Rd | 2 30 files changed, 218 insertions(+), 219 deletions(-)
Title: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'
Description: Create interactive heat maps that are usable from the R console, in the
'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the
mouse pointer over a cell to show details, drag a rectangle to zoom, and click
row/column labels to highlight.
Author: Joe Cheng [aut, cre],
Tal Galili [aut],
RStudio, Inc. [cph],
Michael Bostock [ctb, cph] (D3.js library),
Justin Palmer [ctb, cph] (d3.tip library)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between d3heatmap versions 0.6.0 dated 2015-06-23 and 0.6.1 dated 2015-07-27
DESCRIPTION | 10 MD5 | 18 NAMESPACE | 10 NEWS | 7 R/d3heatmap.R | 6 README.md | 12 inst/doc/Introduction.html | 35 - inst/htmlwidgets/lib/d3heatmapcore/heatmap.js | 15 tests/smoketest.R | 4 tests/smoketest.Rout.save | 686 +++++++++++++------------- 10 files changed, 415 insertions(+), 388 deletions(-)