Title: Entrez in R
Description: Provides an R interface to the NCBI's EUtils API
allowing users to search databases like GenBank and PubMed, process the
results of those searches and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb],
Han Guangchun [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 1.0.1 dated 2016-02-29 and 1.0.2 dated 2016-04-21
DESCRIPTION | 11 ++++--- MD5 | 60 ++++++++++++++++++++--------------------- NAMESPACE | 2 - NEWS | 8 +++++ R/base.r | 10 ++++-- build/vignette.rds |binary inst/doc/rentrez_tutorial.html | 40 +++++++++++++-------------- man/entrez_citmatch.Rd | 6 ++-- man/entrez_db_links.Rd | 8 ++--- man/entrez_db_searchable.Rd | 10 +++--- man/entrez_db_summary.Rd | 8 ++--- man/entrez_dbs.Rd | 8 ++--- man/entrez_fetch.Rd | 14 +++++---- man/entrez_global_query.Rd | 3 +- man/entrez_info.Rd | 8 ++--- man/entrez_link.Rd | 13 ++++---- man/entrez_post.Rd | 6 ++-- man/entrez_search.Rd | 10 +++--- man/entrez_summary.Rd | 16 +++++----- man/extract_from_esummary.Rd | 2 - man/linkout_urls.Rd | 2 - man/parse_pubmed_xml.Rd | 8 +++-- man/rentrez.Rd | 2 - tests/testthat/test_fetch.r | 8 ++++- tests/testthat/test_info.r | 10 +++--- tests/testthat/test_link.r | 8 ++--- tests/testthat/test_net.r | 2 - tests/testthat/test_parse.r | 6 ++-- tests/testthat/test_post.r | 2 - tests/testthat/test_search.r | 4 +- tests/testthat/test_summary.r | 10 +++--- 31 files changed, 164 insertions(+), 141 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.1.1 dated 2016-04-06 and 0.1.3 dated 2016-04-21
NNS-0.1.1/NNS/man/Co_LPM.Rd |only NNS-0.1.1/NNS/man/Co_UPM.Rd |only NNS-0.1.1/NNS/man/D_LPM.Rd |only NNS-0.1.1/NNS/man/D_UPM.Rd |only NNS-0.1.3/NNS/DESCRIPTION | 6 - NNS-0.1.3/NNS/MD5 | 78 +++++++++++++--------- NNS-0.1.3/NNS/NAMESPACE | 16 +++- NNS-0.1.3/NNS/R/ANOVA.R | 3 NNS-0.1.3/NNS/R/ARMA.R | 106 +++++++++++++++++++------------ NNS-0.1.3/NNS/R/ARMA_Regression.R | 35 +++++++--- NNS-0.1.3/NNS/R/Binary_ANOVA.R | 15 ++-- NNS-0.1.3/NNS/R/Causation.R | 4 + NNS-0.1.3/NNS/R/Correlation.R | 11 ++- NNS-0.1.3/NNS/R/Dependence.R | 21 ++++-- NNS-0.1.3/NNS/R/Dependence_Regression.R |only NNS-0.1.3/NNS/R/FSD.R |only NNS-0.1.3/NNS/R/Normalization.R | 3 NNS-0.1.3/NNS/R/Partial_Moments.R | 40 ++++++++--- NNS-0.1.3/NNS/R/Partition_Map.R | 3 NNS-0.1.3/NNS/R/Regression.R | 76 +++++++++++++++++----- NNS-0.1.3/NNS/R/SD_Efficient_Set.R |only NNS-0.1.3/NNS/R/SSD.R |only NNS-0.1.3/NNS/R/Seasonality_Test.R | 11 ++- NNS-0.1.3/NNS/R/TSD.R |only NNS-0.1.3/NNS/R/Uni_SD_Routines.R |only NNS-0.1.3/NNS/man/Co.LPM.Rd |only NNS-0.1.3/NNS/man/Co.UPM.Rd |only NNS-0.1.3/NNS/man/D.LPM.Rd |only NNS-0.1.3/NNS/man/D.UPM.Rd |only NNS-0.1.3/NNS/man/FSD.Rd |only NNS-0.1.3/NNS/man/LPM.Rd | 7 ++ NNS-0.1.3/NNS/man/LPM.VaR.Rd | 7 ++ NNS-0.1.3/NNS/man/SSD.Rd |only NNS-0.1.3/NNS/man/TSD.Rd |only NNS-0.1.3/NNS/man/UPM.Rd | 7 ++ NNS-0.1.3/NNS/man/Uni.caus.Rd | 3 NNS-0.1.3/NNS/man/VN.ANOVA.Rd | 7 ++ NNS-0.1.3/NNS/man/VN.ARMA.Rd | 7 ++ NNS-0.1.3/NNS/man/VN.ARMA.reg.Rd | 10 ++ NNS-0.1.3/NNS/man/VN.FSD.Rd |only NNS-0.1.3/NNS/man/VN.SD.Efficient.Set.Rd |only NNS-0.1.3/NNS/man/VN.SSD.Rd |only NNS-0.1.3/NNS/man/VN.TSD.Rd |only NNS-0.1.3/NNS/man/VN.caus.Rd | 7 ++ NNS-0.1.3/NNS/man/VN.cor.Rd | 7 ++ NNS-0.1.3/NNS/man/VN.dep.Rd | 10 ++ NNS-0.1.3/NNS/man/VN.dep.reg.Rd |only NNS-0.1.3/NNS/man/VN.norm.Rd | 7 ++ NNS-0.1.3/NNS/man/VN.reg.Rd | 13 +++ NNS-0.1.3/NNS/man/VN.seas.Rd | 7 ++ NNS-0.1.3/NNS/man/partition.map.Rd | 7 ++ 51 files changed, 395 insertions(+), 139 deletions(-)
Title: Individual Conditional Expectation Plot Toolbox
Description: Implements Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. ICE plots refine Friedman's partial dependence plot by graphing the functional relationship between the predicted response and a covariate of interest for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate of interest, suggesting where and to what extent they may exist.
Author: Alex Goldstein, Adam Kapelner, Justin Bleich
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between ICEbox versions 1.0 dated 2014-04-25 and 1.1 dated 2016-04-21
DESCRIPTION | 12 ++--- MD5 | 14 +++--- NAMESPACE | 6 ++ R/ice.R | 121 ++++++++++++++++++++++++++++++++++++++------------------ R/plot.ice.R | 66 ++++++++++++++++++++++-------- inst/CITATION | 10 +++- man/ice.Rd | 12 ++++- man/plot.ice.Rd | 29 ++++++++++--- 8 files changed, 189 insertions(+), 81 deletions(-)
Title: Emoji Fonts for using in R
Description: An implementation of using emoji font in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between emojifont versions 0.3.2 dated 2016-03-09 and 0.3.3 dated 2016-04-21
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS | 8 +++ R/sysdata.rda |binary README.md | 10 ++-- build/vignette.rds |binary inst/doc/emojifont.Rmd | 10 ++++ inst/doc/emojifont.html | 107 +++++++++++++++++++++++++++++------------------- vignettes/emojifont.Rmd | 10 ++++ 9 files changed, 109 insertions(+), 58 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between btergm versions 1.7.0 dated 2016-02-20 and 1.7.3 dated 2016-04-21
DESCRIPTION | 17 +- MD5 | 12 - NAMESPACE | 3 R/gofmethods.R | 402 +++++++++++++++++++++--------------------------------- R/gofstatistics.R | 82 +++++++++-- R/tergmprepare.R | 4 man/gofmethods.Rd | 44 ++--- 7 files changed, 272 insertions(+), 292 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 4.3.15 dated 2016-01-12 and 4.3.18 dated 2016-04-21
RcppParallel-4.3.15/RcppParallel/inst/presentations/rcpp_parallel_talk_jan2015.pdf |only RcppParallel-4.3.15/RcppParallel/inst/presentations/rcpp_parallel_talk_jan2015.tex |only RcppParallel-4.3.15/RcppParallel/man/RcppParallelLibs.Rd |only RcppParallel-4.3.18/RcppParallel/DESCRIPTION | 27 ++++---- RcppParallel-4.3.18/RcppParallel/MD5 | 18 ++--- RcppParallel-4.3.18/RcppParallel/NAMESPACE | 3 RcppParallel-4.3.18/RcppParallel/R/build.R | 31 +++++++--- RcppParallel-4.3.18/RcppParallel/inst/include/RcppParallel/Common.h | 1 RcppParallel-4.3.18/RcppParallel/inst/include/RcppParallel/RVector.h | 1 RcppParallel-4.3.18/RcppParallel/man/RcppParallelFlags.Rd |only RcppParallel-4.3.18/RcppParallel/src/Makevars | 14 ++-- RcppParallel-4.3.18/RcppParallel/src/tbb/build/windows.gcc.inc | 4 - 12 files changed, 62 insertions(+), 37 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 1.0.0 dated 2016-04-14 and 1.0.1 dated 2016-04-21
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 29 +++++++++++++++++++++ R/auto-test.R | 18 ++++++------- R/compare.R | 14 +++++----- R/evaluate-promise.R | 17 ++++++++---- R/expect-output.R | 26 ++++++++++++++++++- R/stack.R | 16 ++++++------ R/traceback.R | 2 - R/utils.R | 10 +++++++ inst/include/testthat/testthat.h | 45 ++++++++++++++++++---------------- man/output-expectations.Rd | 11 +++++++- tests/test-catch.R | 19 ++++++++++---- tests/testthat/test-compare-numeric.R | 4 +-- tests/testthat/test-expect-equality.R | 12 +++++++++ tests/testthat/test-expect-output.R | 26 +++++++++++++++++++ tests/testthat/test-reporter.R | 3 +- 18 files changed, 211 insertions(+), 84 deletions(-)
Title: Test Bench for Missing Data Imputing Models/Methods Comparison
Description: Provides a Test bench for comparison of missing
data imputation models/methods. It compares imputing methods with reference
to RMSE, MAE or MAPE parameters. It allows to add new proposed methods to test
bench and to compare with other methods. The function 'append_method()' allows
to add multiple numbers of methods to the existing methods available in test bench.
Author: Neeraj Bokde
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Diff between imputeTestbench versions 0.1.0 dated 2016-04-17 and 1.1.0 dated 2016-04-21
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ NAMESPACE | 1 + R/append_method.R | 11 ++++++++++- R/impute_errors.R | 20 +++++++++++++++++++- R/remove_method.R |only inst/doc/imputeTestbench-Vignette.html | 4 ++-- man/append_method.Rd | 2 +- man/remove_method.Rd |only 9 files changed, 44 insertions(+), 14 deletions(-)
More information about imputeTestbench at CRAN
Permanent link
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Author: Karl W Broman [aut, cre], Michael Bostock [ctb, cph] (d3.js library
in htmlwidgets/lib, http://d3js.org), Justin Palmer [ctb, cph] (d3.tip library
in htmlwidgets/lib, https://github.com/caged/d3-tip), Cynthia Brewer [cph]
(ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org), Mark Harrower
[cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org),
The Pennsylvania State University [cph] (ColorBrewer library in htmlwidgets/lib,
http://colorbrewer2.org), jQuery Foundation [cph] (jQuery library
in htmlwidgets/lib, http://jquery.com), jQuery contributors [ctb] (jQuery
library in htmlwidgets/lib; see https://github.com/jquery/jquery/blob/master/AUTHORS.txt),
jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib;
see http://jqueryui.com/about)
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtlcharts versions 0.5-25 dated 2015-11-09 and 0.6-6 dated 2016-04-21
qtlcharts-0.5-25/qtlcharts/inst/doc/chartOpts.R |only qtlcharts-0.6-6/qtlcharts/DESCRIPTION | 32 +- qtlcharts-0.6-6/qtlcharts/MD5 | 151 ++++------ qtlcharts-0.6-6/qtlcharts/R/grav-data.R | 2 qtlcharts-0.6-6/qtlcharts/build/vignette.rds |binary qtlcharts-0.6-6/qtlcharts/data/geneExpr.rda |binary qtlcharts-0.6-6/qtlcharts/data/grav.rda |binary qtlcharts-0.6-6/qtlcharts/inst/NEWS.md | 12 qtlcharts-0.6-6/qtlcharts/inst/ReadMe.md | 7 qtlcharts-0.6-6/qtlcharts/inst/doc/userGuide.Rmd | 7 qtlcharts-0.6-6/qtlcharts/inst/doc/userGuide.html | 4 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iboxplot.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iboxplot.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iboxplot.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iheatmap.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iheatmap.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iheatmap.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplot.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplot.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplot.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCorr.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCorr.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCorr.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCurves.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCurves.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotCurves.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMScanone.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMScanone.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMScanone.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMap.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMap.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotMap.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotPXG.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotPXG.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotPXG.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotRF.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotRF.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotRF.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScanone.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScanone.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScanone.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScantwo.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScantwo.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/iplotScantwo.yaml | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/d3panels/d3panels.min.js | 6 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iboxplot.coffee | 3 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iboxplot.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iheatmap.coffee | 4 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iheatmap.js | 11 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplot.coffee | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplot.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCorr.coffee | 5 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCorr.js | 9 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCorr_noscat.coffee | 3 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCorr_noscat.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCurves.coffee | 4 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotCurves.js | 11 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMScanone_eff.coffee | 4 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMScanone_eff.js | 11 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMScanone_noeff.coffee | 4 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMScanone_noeff.js | 11 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMap.coffee | 33 +- qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotMap.js | 38 +- qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotPXG.coffee | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotPXG.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotRF.coffee | 61 ++-- qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotRF.js | 37 +- qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_ci.coffee | 6 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_ci.js | 16 - qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_noeff.coffee | 2 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_noeff.js | 7 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_pxg.coffee | 6 qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScanone_pxg.js | 16 - qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScantwo.coffee | 74 ++-- qtlcharts-0.6-6/qtlcharts/inst/htmlwidgets/lib/qtlcharts/iplotScantwo.js | 69 ++-- qtlcharts-0.6-6/qtlcharts/man/grav.Rd | 2 qtlcharts-0.6-6/qtlcharts/vignettes/userGuide.Rmd | 7 77 files changed, 513 insertions(+), 348 deletions(-)
Title: Koul's Minimum Distance Estimation in Linear Regression and
Autoregression Model
Description: Consider linear regression model and autoregressive model of order p where errors in the linear regression model and innovations in the autoregression model are independent and symmetrically distributed. Hira L. Koul proposed a nonparametric minimum distance estimation method by minimizing L2-type distance between certain weighted residual empirical distribution functions. He also proposed a simpler version of the loss function by using symmetry of the integrating measure in the distance. This package contains two functions: KoulLrMde() and KoulArMde(). KoulLrMde() and KoulArMde() provide minimum distance estimators for linear regression model and autoregression model, respectively, where both are based on Koul's method. These two functions take much less time for the computation than those based on parametric minimum distance estimation methods.
Author: Jiwoong Kim [aut, cre]
Maintainer: Jiwoong Kim <kimjiwo2@stt.msu.edu>
Diff between KoulMde versions 1.0 dated 2015-09-25 and 1.1 dated 2016-04-21
DESCRIPTION | 6 MD5 | 10 - NAMESPACE | 1 R/MdeFunc.R | 345 +++++++++++++++++++++++++++++++++++++++---------------- man/KoulArMde.Rd | 16 +- man/KoulLrMde.Rd | 30 +++- 6 files changed, 282 insertions(+), 126 deletions(-)
Title: Read and Preprocess Fluorescence Excitation-Emission Matrix
(EEM) Data
Description: Read raw EEM data and prepares them for further analysis.
Author: Vipavee Trivittayasil
Maintainer: Vipavee Trivittayasil <vipavee.tri@gmail.com>
Diff between EEM versions 1.0.4 dated 2015-11-05 and 1.1.1 dated 2016-04-21
EEM-1.0.4/EEM/inst/tests/rawdata_F-7000.txt |only EEM-1.0.4/EEM/inst/tests/rawdata_F-7000_Japanese.TXT |only EEM-1.0.4/EEM/inst/tests/rawdata_F-7000_Japanese.xls |only EEM-1.0.4/EEM/inst/tests/rawdata_FP-8500.csv |only EEM-1.0.4/EEM/inst/tests/rawdata_RF-6000.txt |only EEM-1.1.1/EEM/DESCRIPTION | 14 EEM-1.1.1/EEM/MD5 | 100 +++---- EEM-1.1.1/EEM/NAMESPACE | 17 - EEM-1.1.1/EEM/R/EEM-misc.R | 13 EEM-1.1.1/EEM/R/EEM.R | 2 EEM-1.1.1/EEM/R/commonizeEEM.R |only EEM-1.1.1/EEM/R/cutEEM.R | 35 +- EEM-1.1.1/EEM/R/delScattering.R | 6 EEM-1.1.1/EEM/R/delScattering2.R |only EEM-1.1.1/EEM/R/drawEEM.R | 59 +--- EEM-1.1.1/EEM/R/drawEEMgg.R |only EEM-1.1.1/EEM/R/findLocalMax.R | 93 +++--- EEM-1.1.1/EEM/R/fold.R | 32 ++ EEM-1.1.1/EEM/R/plotReg.R | 2 EEM-1.1.1/EEM/R/plotScore.R | 268 +++++++++---------- EEM-1.1.1/EEM/R/plotScorem.R | 4 EEM-1.1.1/EEM/R/printEEM.R | 10 EEM-1.1.1/EEM/R/readEEM.R | 67 ++-- EEM-1.1.1/EEM/R/unfold.R | 77 ++--- EEM-1.1.1/EEM/build/vignette.rds |binary EEM-1.1.1/EEM/inst/doc/file-io.R |only EEM-1.1.1/EEM/inst/doc/file-io.Rmd |only EEM-1.1.1/EEM/inst/doc/file-io.html |only EEM-1.1.1/EEM/inst/doc/vignette.R | 41 ++ EEM-1.1.1/EEM/inst/doc/vignette.Rmd | 96 +++++- EEM-1.1.1/EEM/inst/doc/vignette.html | 153 ++++++++-- EEM-1.1.1/EEM/inst/tests/data_format |only EEM-1.1.1/EEM/inst/tests/test-readEEM.R | 11 EEM-1.1.1/EEM/man/EEM-misc.Rd | 10 EEM-1.1.1/EEM/man/EEM.Rd | 9 EEM-1.1.1/EEM/man/commonizeEEM.Rd |only EEM-1.1.1/EEM/man/cutEEM.Rd | 16 - EEM-1.1.1/EEM/man/delScattering.Rd | 9 EEM-1.1.1/EEM/man/delScattering2.Rd |only EEM-1.1.1/EEM/man/drawEEM.Rd | 26 + EEM-1.1.1/EEM/man/drawEEMgg.Rd |only EEM-1.1.1/EEM/man/extract.Rd | 4 EEM-1.1.1/EEM/man/findLocalMax.Rd | 38 +- EEM-1.1.1/EEM/man/fold.Rd | 20 + EEM-1.1.1/EEM/man/normalize.Rd | 14 EEM-1.1.1/EEM/man/plotLoading.Rd | 5 EEM-1.1.1/EEM/man/plotReg.Rd | 7 EEM-1.1.1/EEM/man/plotScore.Rd | 60 ++-- EEM-1.1.1/EEM/man/plotScorem.Rd | 13 EEM-1.1.1/EEM/man/prcompname.Rd | 5 EEM-1.1.1/EEM/man/print.EEM.Rd | 3 EEM-1.1.1/EEM/man/readEEM.Rd | 9 EEM-1.1.1/EEM/man/sub-.EEM.Rd | 3 EEM-1.1.1/EEM/man/summary.EEM.Rd | 3 EEM-1.1.1/EEM/man/unfold.Rd | 10 EEM-1.1.1/EEM/vignettes/file-io.Rmd |only EEM-1.1.1/EEM/vignettes/vignette.Rmd | 96 +++++- 57 files changed, 903 insertions(+), 557 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 1.4.0 dated 2015-09-30 and 1.5.0 dated 2016-04-21
DESCRIPTION | 12 +- MD5 | 63 ++++++------- NAMESPACE | 6 + R/BAT.R | 226 +++++++++++++++++++++++++++++++---------------- man/accuracy.Rd | 2 man/alpha.Rd | 2 man/alpha.accum.Rd | 7 + man/alpha.estimate.Rd | 2 man/arrabida.Rd | 2 man/beta.Rd | 8 - man/beta.accum.Rd | 13 +- man/beta.multi.Rd | 6 - man/contribution.Rd | 2 man/dispersion.Rd | 2 man/functree.Rd | 2 man/gdm.Rd | 2 man/geres.Rd | 2 man/guadiana.Rd | 2 man/iaor.Rd | 2 man/optim.alpha.Rd | 6 - man/optim.alpha.stats.Rd | 2 man/optim.beta.Rd | 7 + man/optim.beta.stats.Rd | 2 man/optim.spatial.Rd |only man/phylotree.Rd | 2 man/sar.Rd | 2 man/sim.plot.Rd | 8 - man/sim.sad.Rd | 2 man/sim.sample.Rd | 6 + man/sim.spatial.Rd | 2 man/sim.tree.Rd | 6 - man/slope.Rd | 2 man/uniqueness.Rd | 2 33 files changed, 257 insertions(+), 155 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.11.0 dated 2016-04-12 and 1.11.1 dated 2016-04-21
DESCRIPTION | 6 +-- MD5 | 38 ++++++++++++------- NAMESPACE | 1 NEWS.md | 5 ++ R/R.r | 5 +- R/install-version.r | 23 ++++++----- R/rtools.r | 61 +++++++++++++++++++++++++------ R/system.r | 24 +++++++++++- inst/doc/dependencies.html | 6 +-- man/system_check.Rd | 4 +- man/system_output.Rd |only tests/testthat/archive.rds |only tests/testthat/rtools-gcc493 |only tests/testthat/rtools-gcc493-winbuilder |only tests/testthat/test-github-connections.R | 4 +- tests/testthat/test-infrastructure.r | 2 - tests/testthat/test-install-version.R | 28 +++++++++++--- tests/testthat/test-rtools.r | 33 ++++++++++++++-- 18 files changed, 182 insertions(+), 58 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb]
Maintainer: Ben Sherwood <bsherwo2@jhu.edu>
Diff between rqPen versions 1.3 dated 2016-02-08 and 1.4 dated 2016-04-21
rqPen-1.3/rqPen/R/rqPen.R |only rqPen-1.3/rqPen/man/groupQICDMultLambda.Rd |only rqPen-1.4/rqPen/DESCRIPTION | 12 ++-- rqPen-1.4/rqPen/LICENSE | 2 rqPen-1.4/rqPen/MD5 | 34 ++++++++---- rqPen-1.4/rqPen/NAMESPACE | 81 ++++++++++++++++------------- rqPen-1.4/rqPen/NEWS | 10 +++ rqPen-1.4/rqPen/R/Adamsfunc.R |only rqPen-1.4/rqPen/R/mainFunctions.R |only rqPen-1.4/rqPen/R/workHorse.R |only rqPen-1.4/rqPen/man/QICD.Rd |only rqPen-1.4/rqPen/man/cv.rq.group.pen.Rd | 5 + rqPen-1.4/rqPen/man/cv.rq.pen.Rd | 5 + rqPen-1.4/rqPen/man/groupMultLambda.Rd |only rqPen-1.4/rqPen/man/groupQICD.Rd | 3 - rqPen-1.4/rqPen/man/group_derivs.Rd |only rqPen-1.4/rqPen/man/print.cv.rq.pen.Rd |only rqPen-1.4/rqPen/man/print.rq.pen.Rd |only rqPen-1.4/rqPen/man/rq.group.lin.prog.Rd |only rqPen-1.4/rqPen/man/rq.lasso.fit.Rd | 5 + rqPen-1.4/rqPen/man/rq.nc.fit.Rd | 14 +++-- rqPen-1.4/rqPen/src |only 22 files changed, 105 insertions(+), 66 deletions(-)
Title: Client for the HuffPost Pollster API
Description: Client for the HuffPost Pollster API, which provides
access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre],
Thomas J. Leeper [aut],
Drew Linzer [aut]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between pollstR versions 1.2.2 dated 2016-03-04 and 1.3.0 dated 2016-04-21
DESCRIPTION | 8 - MD5 | 28 +-- NEWS | 4 R/charts.R | 41 +++-- build/vignette.rds |binary inst/doc/introduction.Rmd | 145 ++++++++---------- inst/doc/introduction.html | 160 +++++++++----------- inst/vign-src/figures/obama-favorable-chart-1.png |binary inst/vign-src/figures/obama-favorable-chart-2-1.png |binary inst/vign-src/introduction.Rmd | 2 inst/vign-src/introduction.md | 145 ++++++++---------- man/pollstr_charts.Rd | 8 - vignettes/assets/obama-favorable-chart-1.png |binary vignettes/assets/obama-favorable-chart-2-1.png |binary vignettes/introduction.Rmd | 145 ++++++++---------- 15 files changed, 346 insertions(+), 340 deletions(-)
Title: Finding Allele-Specific Copy Number in Next-Generation
Sequencing Data
Description: This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing. Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between falcon versions 0.1 dated 2014-04-24 and 0.2 dated 2016-04-21
falcon-0.1/falcon/man/ReadCounts.Rd |only falcon-0.2/falcon/DESCRIPTION | 10 ++-- falcon-0.2/falcon/MD5 | 22 ++++----- falcon-0.2/falcon/NAMESPACE | 2 falcon-0.2/falcon/R/falcon.r | 69 +++++++++++++++++++++++++++---- falcon-0.2/falcon/R/script_basic.r | 33 -------------- falcon-0.2/falcon/data/Example.rda |binary falcon-0.2/falcon/man/falcon.Rd | 14 ++---- falcon-0.2/falcon/man/getASCN.Rd | 10 +--- falcon-0.2/falcon/man/getChangepoints.Rd | 12 +---- falcon-0.2/falcon/man/readMatrix.Rd |only falcon-0.2/falcon/man/tauhat.Rd | 2 falcon-0.2/falcon/man/view.Rd | 20 +++----- 13 files changed, 101 insertions(+), 93 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.8 dated 2016-03-16 and 1.9 dated 2016-04-21
DESCRIPTION | 10 ++++----- MD5 | 38 ++++++++++++++++++++----------------- NAMESPACE | 4 +-- R/dirknn.tune.R | 29 +++++++++++++++------------- R/f.rbing.R | 3 ++ R/kent.datacontour.R | 37 ++++++++++++++++++++++++------------ R/knn.reg.R | 22 ++++++++++++++------- R/knnreg.tune.R | 11 ++++++++-- R/mediandir.R | 25 +++++++++++++----------- R/mediandir_2.R | 15 ++++++++------ R/rfb.R | 26 ++++++++++++++++--------- R/rkent.R |only R/spher.reg.R | 16 +++++++++------ R/spml.reg.R | 46 ++++++++++++++++++++++----------------------- R/vec.R |only man/Directional-package.Rd | 11 +++++++--- man/kent.datacontour.Rd | 6 ++--- man/rfb.Rd | 12 ++++++++--- man/rkent.Rd |only man/spher.reg.Rd | 9 ++------ man/spml.reg.Rd | 12 +++++------ man/vec.Rd |only 22 files changed, 198 insertions(+), 134 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering.
Author: Taiyun Wei, Viliam Simko
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.76 dated 2016-04-15 and 0.77 dated 2016-04-21
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 19 +++++++++++++------ R/corrplot.R | 4 ++-- README.md | 2 +- inst/doc/corrplot-intro.Rmd | 2 +- inst/doc/corrplot-intro.html | 14 +++++++------- man/corrplot.mixed.Rd | 2 +- vignettes/corrplot-intro.Rmd | 2 +- vignettes/example-corrplot.mixed.R | 2 +- 10 files changed, 39 insertions(+), 32 deletions(-)