Title: Accurate Numerical Derivatives
Description: Methods for calculating (usually) accurate
numerical first and second order derivatives. Accurate calculations
are done using 'Richardson''s' extrapolation or, when applicable, a
complex step derivative is available. A simple difference
method is also provided. Simple difference is (usually) less accurate
but is much quicker than 'Richardson''s' extrapolation and provides a
useful cross-check.
Methods are provided for real scalar and vector valued functions.
Author: Paul Gilbert and Ravi Varadhan
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between numDeriv versions 2014.2-1 dated 2015-05-04 and 2016.8-1 dated 2016-08-26
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NEWS | 11 +++++++++++ R/num2Deriv.R | 10 +++++++--- build/vignette.rds |binary inst/doc/Guide.pdf |binary man/hessian.Rd | 6 +++++- 7 files changed, 36 insertions(+), 17 deletions(-)
Title: Polychoric and Polyserial Correlations
Description: Computes polychoric and polyserial correlations by quick "two-step" methods or ML,
optionally with standard errors; tetrachoric and biserial correlations are special cases.
Author: John Fox [aut, cre]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between polycor versions 0.7-8 dated 2010-04-03 and 0.7-9 dated 2016-08-26
DESCRIPTION | 29 ++++--- MD5 |only NAMESPACE | 6 + R/hetcor.data.frame.R | 186 +++++++++++++++++++++++++----------------------- R/polychor.R | 191 +++++++++++++++++++++++++------------------------- R/polyserial.R | 37 ++++----- R/utilities.R | 2 inst/CHANGES | 3 man/hetcor.Rd | 42 ++++++---- man/polychor.Rd | 39 +++++++--- man/polyserial.Rd | 36 +++++++-- man/print.polycor.Rd | 20 +++-- 12 files changed, 331 insertions(+), 260 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class that offers better checking and
printing capabilities than traditional data frames.
Author: Hadley Wickham [aut],
Romain Francois [aut],
Kirill Müller [aut, cre],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 1.1 dated 2016-07-04 and 1.2 dated 2016-08-26
tibble-1.1/tibble/R/frame-data.R |only tibble-1.1/tibble/man/frame_data.Rd |only tibble-1.1/tibble/tests/testthat/test-data_frame.R |only tibble-1.1/tibble/tests/testthat/test-frame-data.R |only tibble-1.1/tibble/tests/testthat/test-matrixToDataFrame.R |only tibble-1.2/tibble/DESCRIPTION | 10 tibble-1.2/tibble/MD5 | 109 ++++----- tibble-1.2/tibble/NAMESPACE | 11 tibble-1.2/tibble/NEWS.md | 33 ++ tibble-1.2/tibble/R/add.R |only tibble-1.2/tibble/R/all-equal.r | 4 tibble-1.2/tibble/R/check-names.R | 32 ++ tibble-1.2/tibble/R/dataframe.R | 56 ---- tibble-1.2/tibble/R/glimpse.R | 12 tibble-1.2/tibble/R/tbl-df.r | 4 tibble-1.2/tibble/R/tibble.R | 2 tibble-1.2/tibble/R/tribble.R |only tibble-1.2/tibble/R/type-sum.r | 8 tibble-1.2/tibble/R/utils-format.r | 47 +++ tibble-1.2/tibble/R/utils.r | 10 tibble-1.2/tibble/README.md | 27 +- tibble-1.2/tibble/build/vignette.rds |binary tibble-1.2/tibble/inst/doc/formatting.R |only tibble-1.2/tibble/inst/doc/formatting.Rmd |only tibble-1.2/tibble/inst/doc/formatting.html |only tibble-1.2/tibble/inst/doc/tibble.Rmd | 6 tibble-1.2/tibble/inst/doc/tibble.html | 29 +- tibble-1.2/tibble/man/add_column.Rd |only tibble-1.2/tibble/man/add_row.Rd | 19 + tibble-1.2/tibble/man/formatting.Rd | 12 tibble-1.2/tibble/man/glimpse.Rd | 9 tibble-1.2/tibble/man/tibble-package.Rd | 2 tibble-1.2/tibble/man/tribble.Rd |only tibble-1.2/tibble/src/RcppExports.cpp | 4 tibble-1.2/tibble/src/matrixToDataFrame.cpp | 121 +++++++--- tibble-1.2/tibble/tests/testthat/output/glimpse/all-35.txt | 2 tibble-1.2/tibble/tests/testthat/output/glimpse/all-50.txt | 2 tibble-1.2/tibble/tests/testthat/output/glimpse/all-70.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/POSIXlt-8-60.txt | 4 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all--30.txt | 4 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all--300.txt | 4 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all-1-30-0.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all-1-30-2.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all-knit-120.txt | 4 tibble-1.2/tibble/tests/testthat/output/trunc_mat/all-knit-60.txt | 4 tibble-1.2/tibble/tests/testthat/output/trunc_mat/iris--70.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/iris-3-5.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/iris-5-30.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/long-5-30.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/mtcars-8-30.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/mtcars-knit-60.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/wide-8-60.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/zero-rows_unk-5-30.txt |only tibble-1.2/tibble/tests/testthat/output/trunc_mat/zero_cols-5-30.txt | 2 tibble-1.2/tibble/tests/testthat/output/trunc_mat/zero_rows--30.txt | 2 tibble-1.2/tibble/tests/testthat/test-add.R |only tibble-1.2/tibble/tests/testthat/test-data-frame.R |only tibble-1.2/tibble/tests/testthat/test-equality.R | 5 tibble-1.2/tibble/tests/testthat/test-matrix.R | 25 +- tibble-1.2/tibble/tests/testthat/test-nibble.R |only tibble-1.2/tibble/tests/testthat/test-obj-sum.R | 12 tibble-1.2/tibble/tests/testthat/test-trunc-mat.R | 27 ++ tibble-1.2/tibble/vignettes/formatting.Rmd |only tibble-1.2/tibble/vignettes/tibble.Rmd | 6 64 files changed, 448 insertions(+), 242 deletions(-)
Title: Exploring Genomic Relations for Precision Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.2 dated 2016-06-26 and 1.0.3 dated 2016-08-26
DESCRIPTION | 8 +++--- MD5 | 21 ++++++++------- R/xGRviaGenomicAnno.r | 54 ++++++++++++++++++++++++++++++++--------- R/xGRviaGenomicAnnoAdv.r | 4 --- R/xRDataLoader.r | 15 +++++++---- data/JKscience_TS2A.RData |binary inst/CITATION |only inst/NEWS | 10 +++++++ inst/xGRviaGenomicAnno.html | 26 +++++++++++++------ inst/xGRviaGenomicAnnoAdv.html | 7 +---- man/xGRviaGenomicAnno.Rd | 24 ++++++++++++------ man/xGRviaGenomicAnnoAdv.Rd | 7 +---- 12 files changed, 117 insertions(+), 59 deletions(-)
Title: 'TSdbi' Extension to Connect with 'SDMX'
Description: Methods to
retrieve data in the Statistical Data and Metadata Exchange ('SDMX') format
from several database. (For example,
'EuroStat', the European Central Bank, the Organisation for Economic
Co-operation and Development, the 'Unesco' Institute for Statistics,
and the International Labor Organization.)
This is a wrapper for package 'RJSDMX'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSsdmx versions 2015.12-1 dated 2015-12-16 and 2016.8-1 dated 2016-08-26
DESCRIPTION | 12 +++---- MD5 | 20 +++++------ NEWS | 5 ++ build/vignette.rds |binary inst/testWithInternet/0serviceCheck_EuroStat.R | 4 +- inst/testWithInternet/0serviceCheck_INEGI.R | 9 +++++ inst/testWithInternet/0serviceCheck_OECD.R | 42 ++++++++++++++++++------- inst/testWithInternet/ecb.R | 6 ++- inst/testWithInternet/eurostat.R | 16 ++++++++- inst/testWithInternet/ilo.R | 4 +- inst/testWithInternet/oecd.R | 27 ++++++++-------- 11 files changed, 100 insertions(+), 45 deletions(-)
Title: 'TSdbi' Extensions to Wrap Miscellaneous Data Sources
Description: Methods to
retrieve data from several different sources. This include historical
quote data from 'Yahoo' and 'Oanda', economic data from 'FRED', and
'xls' and 'csv' data from different sources.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSmisc versions 2015.1-3 dated 2015-05-02 and 2016.8-1 dated 2016-08-26
DESCRIPTION | 16 ++++++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 13 +++++++++---- NEWS | 15 +++++++++++++++ R/TSdbiMethods.R | 2 +- build/vignette.rds |binary inst/testWithInternet/getSymbol-tfOnePlotPNG.R | 2 +- inst/testWithInternet/histQuote-tfOnePlotPNG.R | 19 +++++++++++++------ inst/testWithInternet/histQuote.R | 9 ++++++--- man/TSdbiMethods.Rd | 7 ++++--- 10 files changed, 66 insertions(+), 35 deletions(-)
Title: 'TSdbi' Illustration
Description: Illustrates the various 'TSdbi' packages with a vignette using time series
data from several sources. The vignette also illustrates some simple time series
manipulation and plotting using packages 'tframe' and 'tfplot'.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSdata versions 2015.4-2 dated 2015-05-22 and 2016.8-1 dated 2016-08-26
TSdata-2015.4-2/TSdata/inst/doc/Guide.bib |only TSdata-2016.8-1/TSdata/DESCRIPTION | 12 TSdata-2016.8-1/TSdata/MD5 | 26 TSdata-2016.8-1/TSdata/NEWS | 7 TSdata-2016.8-1/TSdata/build/vignette.rds |binary TSdata-2016.8-1/TSdata/inst/doc/Guide.Stex | 899 +++----------------- TSdata-2016.8-1/TSdata/inst/doc/Guide.pdf |binary TSdata-2016.8-1/TSdata/inst/doc/GuideAppendix.Stex | 2 TSdata-2016.8-1/TSdata/inst/doc/GuideAppendix.pdf |binary TSdata-2016.8-1/TSdata/inst/doc/GuideDevel.Stex | 11 TSdata-2016.8-1/TSdata/inst/doc/GuideDevel.pdf |binary TSdata-2016.8-1/TSdata/man |only TSdata-2016.8-1/TSdata/vignettes/Guide.Stex | 58 - TSdata-2016.8-1/TSdata/vignettes/GuideAppendix.Stex | 2 TSdata-2016.8-1/TSdata/vignettes/GuideDevel.Stex | 11 15 files changed, 230 insertions(+), 798 deletions(-)
Title: Time Frame Coding Kernel Extensions
Description: Extensions and additional 'tframe' utilities.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between tframePlus versions 2015.1-2 dated 2015-04-27 and 2016.7-1 dated 2016-08-26
tframePlus-2015.1-2/tframePlus/R/its.R |only tframePlus-2015.1-2/tframePlus/man/its.Rd |only tframePlus-2015.1-2/tframePlus/tests/its.R |only tframePlus-2016.7-1/tframePlus/DESCRIPTION | 14 ++++++------- tframePlus-2016.7-1/tframePlus/MD5 | 11 +++------- tframePlus-2016.7-1/tframePlus/NAMESPACE | 23 +++------------------- tframePlus-2016.7-1/tframePlus/NEWS | 8 +++++++ tframePlus-2016.7-1/tframePlus/build/vignette.rds |binary 8 files changed, 23 insertions(+), 33 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
F<c3><b6>retagsplatsen [ctb, cph] (Numbro.js library),
Draper Adam [ctb, cph] (Numeral.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library),
Russell Kent [ctb, cph] (Sparkline.js library),
Rohan Jon [ctb, cph] (ZeroClipboard library),
Greene James [ctb, cph] (ZeroClipboard library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.3.2 dated 2016-07-07 and 0.3.3 dated 2016-08-26
rhandsontable-0.3.2/rhandsontable/inst/htmlwidgets/lib/numeral |only rhandsontable-0.3.3/rhandsontable/DESCRIPTION | 12 rhandsontable-0.3.3/rhandsontable/LICENSE | 2 rhandsontable-0.3.3/rhandsontable/MD5 | 32 +- rhandsontable-0.3.3/rhandsontable/NEWS | 11 rhandsontable-0.3.3/rhandsontable/R/misc.R | 21 + rhandsontable-0.3.3/rhandsontable/R/rhandsontable.R | 11 rhandsontable-0.3.3/rhandsontable/inst/doc/intro_rhandsontable.R | 11 rhandsontable-0.3.3/rhandsontable/inst/doc/intro_rhandsontable.Rmd | 24 + rhandsontable-0.3.3/rhandsontable/inst/doc/intro_rhandsontable.html | 141 +++++----- rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.css | 2 rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.js | 48 +-- rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/lib/numbro |only rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/lib/sparkline/jquery.sparkline.min.js | 9 rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/rhandsontable.js | 69 +++- rhandsontable-0.3.3/rhandsontable/inst/htmlwidgets/rhandsontable.yaml | 10 rhandsontable-0.3.3/rhandsontable/man/hot_col.Rd | 6 rhandsontable-0.3.3/rhandsontable/vignettes/intro_rhandsontable.Rmd | 24 + 18 files changed, 265 insertions(+), 168 deletions(-)
Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of
JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>
Diff between rtson versions 1.2 dated 2016-06-24 and 1.3 dated 2016-08-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/deserializer.R | 32 +++++++++++++++++--------------- R/serializer.R | 3 ++- README.md | 6 ++++-- 5 files changed, 30 insertions(+), 25 deletions(-)
Title: Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Description: Computes linear Bayesian spectral estimates from multirate
data for second-order stationary time series. Provides credible
intervals and methods for plotting various spectral estimates.
Author: Ben Powell [aut, cre],
Guy Nason [aut]
Maintainer: Ben Powell <ben.powell@bristol.ac.uk>
Diff between regspec versions 2.1 dated 2016-05-04 and 2.3 dated 2016-08-26
regspec-2.1/regspec/R/regspec15.R |only regspec-2.3/regspec/DESCRIPTION | 8 ++++---- regspec-2.3/regspec/MD5 | 6 +++--- regspec-2.3/regspec/R/regspec17.R |only regspec-2.3/regspec/man/regspec.Rd | 11 ++++------- 5 files changed, 11 insertions(+), 14 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with -std=c++11 which is the default starting
with release 0.2.3 following the release of R 3.1.0, and available on all
platforms following the release of R 3.3.0 with the updated 'Rtools'.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.4 dated 2015-01-06 and 0.2.5 dated 2016-08-26
ChangeLog | 17 +++++++ DESCRIPTION | 21 ++++----- MD5 | 20 ++++---- README.md | 22 ++++++++- build/vignette.rds |binary inst/NEWS.Rd | 8 +++ inst/doc/RcppCNPy-intro.R | 10 ++-- inst/doc/RcppCNPy-intro.Rnw | 96 +++++++++++++++++++++---------------------- inst/doc/RcppCNPy-intro.pdf |binary src/cnpy.cpp | 10 ++-- vignettes/RcppCNPy-intro.Rnw | 96 +++++++++++++++++++++---------------------- 11 files changed, 173 insertions(+), 127 deletions(-)
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.2.0 dated 2016-05-24 and 0.2.1 dated 2016-08-26
DESCRIPTION | 12 ++++----- MD5 | 56 +++++++++++++++++++++--------------------- NAMESPACE | 4 --- R/dataVAR1.r | 15 +++++++++-- R/impulseResponseVAR1.r | 42 ++++++------------------------- R/mutualInfoVAR1.r | 55 ++++++++++++----------------------------- R/nodeStatsVAR1.r | 10 +++---- R/sparsifyVAR1.r | 33 +++++++++++++++--------- inst/CITATION | 6 ++-- inst/NEWS.Rd | 10 +++++++ man/CIGofVAR1.Rd | 6 ++-- man/createA.Rd | 2 - man/dataVAR1.Rd | 11 +++++--- man/graphVAR1.Rd | 2 - man/hpvP35.Rd | 2 - man/impulseResponseVAR1.Rd | 13 ++++----- man/loglikLOOCVVAR1.Rd | 2 - man/loglikLOOCVcontourVAR1.Rd | 2 - man/mutualInfoVAR1.Rd | 23 +++++++++-------- man/nodeStatsVAR1.Rd | 4 +-- man/optPenaltyPchordal.Rd | 8 +++--- man/optPenaltyVAR1.Rd | 2 - man/ragt2ridges-package.Rd | 4 +-- man/ridgePchordal.Rd | 8 +++--- man/ridgeVAR1.Rd | 2 - man/sparsifyVAR1.Rd | 37 +++++++++++++++++---------- src/Makevars | 6 +--- src/Makevars.win | 6 ---- src/ragt2ridges.cpp | 18 ++++++------- 29 files changed, 192 insertions(+), 209 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.1.4 dated 2015-07-30 and 3.1.5 dated 2016-08-26
plotmo-3.1.4/plotmo/inst/slowtests/Rplots.ps |only plotmo-3.1.4/plotmo/inst/slowtests/test.plotmo.Rout |only plotmo-3.1.5/plotmo/DESCRIPTION | 6 plotmo-3.1.5/plotmo/MD5 | 80 ++++----- plotmo-3.1.5/plotmo/NAMESPACE | 4 plotmo-3.1.5/plotmo/NEWS | 17 ++ plotmo-3.1.5/plotmo/R/dot.R | 4 plotmo-3.1.5/plotmo/R/dotlib.R | 1 plotmo-3.1.5/plotmo/R/elegend.R | 2 plotmo-3.1.5/plotmo/R/lib.R | 91 +++++++---- plotmo-3.1.5/plotmo/R/meta.R | 5 plotmo-3.1.5/plotmo/R/plot.glmnetx.R | 88 ++++++---- plotmo-3.1.5/plotmo/R/plotqq.R | 5 plotmo-3.1.5/plotmo/R/w1.R | 6 plotmo-3.1.5/plotmo/inst/doc/modguide.pdf |binary plotmo-3.1.5/plotmo/inst/doc/plotmo-notes.pdf |binary plotmo-3.1.5/plotmo/inst/doc/plotres-notes.pdf |binary plotmo-3.1.5/plotmo/inst/slowtests/make.bat | 6 plotmo-3.1.5/plotmo/inst/slowtests/test.center.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.dots.R | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.dots.Rout.save | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.dots.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.emma.Rout.save | 10 - plotmo-3.1.5/plotmo/inst/slowtests/test.emma.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.fac.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.glmnet.R | 18 +- plotmo-3.1.5/plotmo/inst/slowtests/test.glmnet.Rout.save | 59 +++---- plotmo-3.1.5/plotmo/inst/slowtests/test.glmnet.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.ltut.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.non.earth.R | 12 + plotmo-3.1.5/plotmo/inst/slowtests/test.non.earth.Rout.save | 99 +++++++----- plotmo-3.1.5/plotmo/inst/slowtests/test.non.earth.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo.Rout.save | 28 +-- plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo.args.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo.dots.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo.x.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo3.Rout.save | 6 plotmo-3.1.5/plotmo/inst/slowtests/test.plotmo3.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotres.Rout.save | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.plotres.bat | 2 plotmo-3.1.5/plotmo/inst/slowtests/test.printcall.bat | 2 42 files changed, 352 insertions(+), 229 deletions(-)
Title: Rapid Calculation of Model Metrics
Description: Collection of metrics for evaluating models written in C++ using 'Rcpp'.
Author: Tyler Hunt [aut, cre]
Maintainer: Tyler Hunt <thunt@snapfinance.com>
Diff between ModelMetrics versions 1.0.0 dated 2016-08-16 and 1.1.0 dated 2016-08-26
DESCRIPTION | 6 +- MD5 | 29 ++++++---- NAMESPACE | 4 + NEWS.md |only R/ModelMetrics.R | 99 +++++++++++++++++++++++++++++++++++-- R/RcppExports.R | 20 +++---- README.md | 52 +++++++++++++++++-- man/mauc.Rd |only man/mcc.Rd |only man/mlogLoss.Rd | 2 man/tnr.Rd |only src/RcppExports.cpp | 55 +++++++++++--------- src/auc_.cpp | 17 ------ src/confusionMatrix_.cpp | 32 +++++++++++ tests/testthat/test_auc.R | 28 ++++++++++ tests/testthat/test_calculations.R | 18 ++++++ tests/testthat/test_errors.R |only tests/testthat/test_logloss.R | 50 +++++++++++++++++- 18 files changed, 335 insertions(+), 77 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sb [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.1.3 dated 2016-05-12 and 1.1.4 dated 2016-08-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/statistics.R | 16 +++++++++------- 3 files changed, 15 insertions(+), 13 deletions(-)
Title: Utilities for Official Spanish Microdata
Description: Provides utilities for reading and processing microdata from Spanish official statistics with R.
Author: Carlos J. Gil Bellosta [aut, cre],
Carlos Neira [ctb],
Diego Paniagua Sánchez [ctb],
José Luis Cañadas Reche [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between MicroDatosEs versions 0.8.01 dated 2016-08-09 and 0.8.2 dated 2016-08-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/read.fwf.microdata.R | 42 ++++++++++++++++++++++++++---------------- 3 files changed, 32 insertions(+), 22 deletions(-)
Title: Alternative Implementations of Base R Functions
Description: Alternative implementations of some base R functions, including sort, order, and match. Functions are simplified but can be faster or have other advantages.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between grr versions 0.9.2 dated 2016-02-29 and 0.9.5 dated 2016-08-26
DESCRIPTION | 6 +- MD5 | 10 ++-- NAMESPACE | 2 R/grr.R | 115 ++++++++++++++++++++++++++++++++++++++++++++++++++++- man/convertBase.Rd |only man/sample2.Rd |only src/grr.cpp | 3 - 7 files changed, 125 insertions(+), 11 deletions(-)
Title: Gower's Distance
Description: Compute Gower's distance (or similarity) coefficient between records. Compute
the top-n matches between records. Core algorithms are executed in parallel on systems
supporting OpenMP.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between gower versions 0.1.0 dated 2016-08-10 and 0.1.1 dated 2016-08-26
DESCRIPTION | 10 ++++---- MD5 | 19 ++++++++-------- NEWS |only R/gower.R | 19 ++++++++++++---- inst/doc/intro.Rmd | 2 - inst/doc/intro.html | 6 ++--- man/gower_dist.Rd | 2 - man/gower_topn.Rd | 2 - src/gower.c | 50 ++++++++++++++++++++++++++++++++++++-------- tests/testthat/test_gower.R | 15 +++++++++++++ vignettes/intro.Rmd | 2 - 11 files changed, 92 insertions(+), 35 deletions(-)
Title: Advanced Fire History Analysis in R
Description: Basic tools to analyze forest fire history data (e.g. FHX2) in R.
Author: Steven Malevich [aut, cre],
Christopher Guiterman [ctb],
Ellis Margolis [ctb]
Maintainer: Steven Malevich <malevich@email.arizona.edu>
Diff between burnr versions 0.1.0 dated 2016-07-10 and 0.1.1 dated 2016-08-26
DESCRIPTION | 12 ++-- MD5 | 18 +++--- NEWS.md | 10 +++ R/stats.R | 120 +++++++++++++++++++++++++++++++++++---------- R/utils.R | 26 ++++++--- README.md | 4 - inst/doc/introduction.html | 4 - man/run_sea.Rd | 76 +++++++++++++++++++++++++--- man/series_stats.Rd | 4 - man/sort.fhx.Rd | 10 ++- 10 files changed, 218 insertions(+), 66 deletions(-)
Title: Improved False Positive Control of Gene-Permuting GSEA with
Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Diff between AbsFilterGSEA versions 1.2.1 dated 2016-04-04 and 1.5 dated 2016-08-26
AbsFilterGSEA-1.2.1/AbsFilterGSEA/vignettes |only AbsFilterGSEA-1.5/AbsFilterGSEA/DESCRIPTION | 14 AbsFilterGSEA-1.5/AbsFilterGSEA/MD5 | 12 AbsFilterGSEA-1.5/AbsFilterGSEA/R/GenePermGSEA.R | 478 ++++++++++---------- AbsFilterGSEA-1.5/AbsFilterGSEA/data/example.rda |binary AbsFilterGSEA-1.5/AbsFilterGSEA/man/GenePermGSEA.Rd | 174 +++---- AbsFilterGSEA-1.5/AbsFilterGSEA/man/example.Rd | 60 +- 7 files changed, 370 insertions(+), 368 deletions(-)
Title: Graphical Analysis of Structural Causal Models
Description: A port of the web-based software 'DAGitty', available at
<http://dagitty.net>, for analyzing structural causal models
(also known as directed acyclic graphs or DAGs).
This package computes covariate adjustment sets for estimating causal
effects, enumerates instrumental variables, derives testable
implications (d-separation and vanishing tetrads), generates equivalent
models, and includes a simple facility for data simulation.
Author: Johannes Textor, Benito van der Zander
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between dagitty versions 0.1-10 dated 2016-03-26 and 0.2-2 dated 2016-08-26
DESCRIPTION | 8 MD5 | 26 - NAMESPACE | 4 NEWS |only R/dagitty.r | 269 +++++++++++----- R/internal.r | 63 +++ build/vignette.rds |binary inst/doc/dagitty4semusers.html | 20 - inst/js/RUtil.js | 12 inst/js/dagitty-alg.js | 507 ++++++++++++++++++++------------ man/exogenousVariables.Rd |only man/impliedConditionalIndependencies.Rd | 2 man/localTests.Rd | 36 +- man/plotLocalTestResults.Rd | 14 man/simulateSEM.Rd | 21 - 15 files changed, 675 insertions(+), 307 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows
various cartographic representations such as proportional symbols, chroropleth,
typology, flows or discontinuities. In addition, it also proposes some useful
features like cartographic palettes, layout (scale, north arrow, title...), labels,
legends or access to cartographic API to ease the graphic presentation of maps.
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between cartography versions 1.3.0 dated 2016-06-13 and 1.4.0 dated 2016-08-26
cartography-1.3.0/cartography/R/discretization.R |only cartography-1.3.0/cartography/man/discretization.Rd |only cartography-1.4.0/cartography/DESCRIPTION | 13 cartography-1.4.0/cartography/MD5 | 89 +-- cartography-1.4.0/cartography/NAMESPACE | 4 cartography-1.4.0/cartography/NEWS | 25 - cartography-1.4.0/cartography/R/choro.R | 28 - cartography-1.4.0/cartography/R/choroLayer.R | 48 + cartography-1.4.0/cartography/R/circles.R | 10 cartography-1.4.0/cartography/R/discLayer.R | 8 cartography-1.4.0/cartography/R/dotDensityLayer.R | 10 cartography-1.4.0/cartography/R/getBorders.R | 14 cartography-1.4.0/cartography/R/getBreaks.R |only cartography-1.4.0/cartography/R/getOuterBorders.R |only cartography-1.4.0/cartography/R/gradLinkLayer.R | 4 cartography-1.4.0/cartography/R/gradLinkTypoLayer.R | 18 cartography-1.4.0/cartography/R/labelLayer.R | 4 cartography-1.4.0/cartography/R/layoutLayer.R | 43 + cartography-1.4.0/cartography/R/legends.R | 180 +++++++ cartography-1.4.0/cartography/R/palettes.R | 89 +++ cartography-1.4.0/cartography/R/propSymbolsChoroLayer.R | 265 +++++----- cartography-1.4.0/cartography/R/propSymbolsLayer.R | 227 ++++----- cartography-1.4.0/cartography/R/propSymbolsTypoLayer.R | 295 +++++------- cartography-1.4.0/cartography/R/propTrianglesLayer.R | 4 cartography-1.4.0/cartography/R/smoothLayer.R | 18 cartography-1.4.0/cartography/R/typo.R | 9 cartography-1.4.0/cartography/R/typoLayer.R | 42 + cartography-1.4.0/cartography/README.md | 63 +- cartography-1.4.0/cartography/data/cartography.colors.RData |binary cartography-1.4.0/cartography/man/carto.pal.Rd | 37 + cartography-1.4.0/cartography/man/carto.pal.info.Rd |only cartography-1.4.0/cartography/man/choroLayer.Rd | 36 - cartography-1.4.0/cartography/man/discLayer.Rd | 6 cartography-1.4.0/cartography/man/display.carto.all.Rd | 2 cartography-1.4.0/cartography/man/display.carto.pal.Rd | 26 - cartography-1.4.0/cartography/man/dotDensityLayer.Rd | 6 cartography-1.4.0/cartography/man/getBorders.Rd | 11 cartography-1.4.0/cartography/man/getBreaks.Rd |only cartography-1.4.0/cartography/man/getOuterBorders.Rd |only cartography-1.4.0/cartography/man/gradLinkLayer.Rd | 2 cartography-1.4.0/cartography/man/gradLinkTypoLayer.Rd | 6 cartography-1.4.0/cartography/man/labelLayer.Rd | 3 cartography-1.4.0/cartography/man/layoutLayer.Rd | 18 cartography-1.4.0/cartography/man/propSymbolsChoroLayer.Rd | 21 cartography-1.4.0/cartography/man/propSymbolsLayer.Rd | 3 cartography-1.4.0/cartography/man/propSymbolsTypoLayer.Rd | 31 - cartography-1.4.0/cartography/man/propTrianglesLayer.Rd | 3 cartography-1.4.0/cartography/man/smoothLayer.Rd | 3 cartography-1.4.0/cartography/man/typoLayer.Rd | 30 - 49 files changed, 1108 insertions(+), 646 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.3.0 dated 2016-07-30 and 0.4.0 dated 2016-08-26
DESCRIPTION | 15 +- MD5 | 34 +++--- NAMESPACE | 203 +++++++++++++++++++----------------- NEWS | 66 ++++++----- NEWS.md | 39 ++++--- R/S3-methods.R | 68 ++++++++++++ R/boot_ci.R | 270 +++++++++++++++++++++++++++---------------------- R/bootstrap.R | 118 +++++++++++---------- R/cv.R | 190 ++++++++++++++++------------------ R/helpfunctions.R | 1 R/inequ_trends.R |only R/mwu.R | 1 R/pred_vars.R | 6 - R/pseudo_r2.R | 1 R/rmse.R | 194 +++++++++++++++++------------------ build/partial.rdb |binary man/boot_ci.Rd | 31 +++-- man/inequ_trend.Rd |only man/sjstats-package.Rd | 74 ++++++------- 19 files changed, 731 insertions(+), 580 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.9 dated 2016-07-15 and 3.10 dated 2016-08-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 36 +++++++++++++++++++++++++++++++++++- R/randomCAT.R | 1 + R/startItems.R | 52 ++++++++++++++++++++++++---------------------------- 5 files changed, 68 insertions(+), 37 deletions(-)
Title: Point and Figure Package
Description: A set of functions to analyze and print the development of a
commodity using the Point and Figure (P&F) approach. A P&F processor can be used
to calculate daily statistics for the time series. These statistics can be used
for deeper investigations as well as to create plots. Plots can be generated as
well known X/O Plots in plain text format, and additionally in a more graphical
format.
Author: Sascha Herrmann
Maintainer: Sascha Herrmann <sascha.herrmann.consulting@gmail.com>
Diff between rpnf versions 1.0.4 dated 2015-10-12 and 1.0.5 dated 2016-08-26
rpnf-1.0.4/rpnf/tests/testthat/test-boxutils.R |only rpnf-1.0.5/rpnf/DESCRIPTION | 25 -- rpnf-1.0.5/rpnf/MD5 | 106 ++++++--- rpnf-1.0.5/rpnf/NAMESPACE | 2 rpnf-1.0.5/rpnf/R/box2lower.R | 29 -- rpnf-1.0.5/rpnf/R/box2upper.R | 29 -- rpnf-1.0.5/rpnf/R/nextBox.R | 60 ++--- rpnf-1.0.5/rpnf/R/nextReversal.R | 40 +-- rpnf-1.0.5/rpnf/R/quote2box.R | 74 +++--- rpnf-1.0.5/rpnf/R/quoteToBoxnumber.R |only rpnf-1.0.5/rpnf/R/quoteToScale.R |only rpnf-1.0.5/rpnf/R/scaleToQuote.R |only rpnf-1.0.5/rpnf/R/xo.processor.R | 190 +++++++++-------- rpnf-1.0.5/rpnf/inst/examples/rpnf-example2.R | 73 +++--- rpnf-1.0.5/rpnf/man/DOW.Rd | 12 - rpnf-1.0.5/rpnf/man/box2lower.Rd | 2 rpnf-1.0.5/rpnf/man/box2upper.Rd | 2 rpnf-1.0.5/rpnf/man/bp.signalprocessor.Rd | 2 rpnf-1.0.5/rpnf/man/currentVPOBreakoutMethod.Rd | 6 rpnf-1.0.5/rpnf/man/currentVPOReversalMethod.Rd | 6 rpnf-1.0.5/rpnf/man/doubleBottom.Rd | 2 rpnf-1.0.5/rpnf/man/doubleTop.Rd | 2 rpnf-1.0.5/rpnf/man/fallingBottom.Rd | 2 rpnf-1.0.5/rpnf/man/fallingTop.Rd | 2 rpnf-1.0.5/rpnf/man/getLogBoxsize.Rd | 2 rpnf-1.0.5/rpnf/man/maxBox.Rd | 2 rpnf-1.0.5/rpnf/man/minBox.Rd | 2 rpnf-1.0.5/rpnf/man/nextBox.Rd | 6 rpnf-1.0.5/rpnf/man/nextReversal.Rd | 2 rpnf-1.0.5/rpnf/man/pnfplot.Rd | 4 rpnf-1.0.5/rpnf/man/pnfplottxt.Rd | 4 rpnf-1.0.5/rpnf/man/pnfprocessor.Rd | 4 rpnf-1.0.5/rpnf/man/quote2box.Rd | 2 rpnf-1.0.5/rpnf/man/quoteToBoxnumber.Rd |only rpnf-1.0.5/rpnf/man/quoteToScale.Rd |only rpnf-1.0.5/rpnf/man/raisingBottom.Rd | 2 rpnf-1.0.5/rpnf/man/raisingTop.Rd | 2 rpnf-1.0.5/rpnf/man/rpnf-package.Rd | 22 - rpnf-1.0.5/rpnf/man/rs.signal.processor.Rd | 2 rpnf-1.0.5/rpnf/man/scaleToQuote.Rd |only rpnf-1.0.5/rpnf/man/signalanalyzer.Rd | 2 rpnf-1.0.5/rpnf/man/xo.priceobjective.processor.Rd | 6 rpnf-1.0.5/rpnf/man/xo.processor.Rd | 10 rpnf-1.0.5/rpnf/man/xo.signalprocessor.Rd | 2 rpnf-1.0.5/rpnf/tests/testthat/test-getLogBoxsize.R |only rpnf-1.0.5/rpnf/tests/testthat/test-nextBox.R |only rpnf-1.0.5/rpnf/tests/testthat/test-nextReversal.R |only rpnf-1.0.5/rpnf/tests/testthat/test-signalprocessors.R | 166 +++++++------- rpnf-1.0.5/rpnf/tests/testthat/test-xoProcessor.R |only rpnf-1.0.5/rpnf/tests/testthat/testdata |only 50 files changed, 470 insertions(+), 438 deletions(-)
Title: 'rgl' in 'htmlwidgets' Framework
Description: The contents of this package have
been merged into rgl, so it is no longer needed.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rglwidget versions 0.2 dated 2016-08-25 and 0.2.1 dated 2016-08-26
DESCRIPTION | 7 ++++--- MD5 | 6 ++++-- NAMESPACE | 12 +++++++++++- build |only man |only 5 files changed, 19 insertions(+), 6 deletions(-)
Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 0.15.11 dated 2015-11-03 and 0.16.8.19 dated 2016-08-26
QuantumClone-0.15.11/QuantumClone/README.md |only QuantumClone-0.15.11/QuantumClone/man/ThreeD_plot.Rd |only QuantumClone-0.16.8.19/QuantumClone/DESCRIPTION | 26 QuantumClone-0.16.8.19/QuantumClone/MD5 | 105 - QuantumClone-0.16.8.19/QuantumClone/NAMESPACE | 8 QuantumClone-0.16.8.19/QuantumClone/R/EM.R | 351 ++- QuantumClone-0.16.8.19/QuantumClone/R/Phylogeny_tree.R |only QuantumClone-0.16.8.19/QuantumClone/R/QuantumCat.R | 166 - QuantumClone-0.16.8.19/QuantumClone/R/QuantumClone.R | 886 ++++------ QuantumClone-0.16.8.19/QuantumClone/R/data.R | 2 QuantumClone-0.16.8.19/QuantumClone/R/plots.R | 208 +- QuantumClone-0.16.8.19/QuantumClone/inst/doc/Release.Rmd | 33 QuantumClone-0.16.8.19/QuantumClone/inst/doc/Release.html | 96 - QuantumClone-0.16.8.19/QuantumClone/inst/doc/Use_case.html | 26 QuantumClone-0.16.8.19/QuantumClone/man/BIC_criterion.Rd | 6 QuantumClone-0.16.8.19/QuantumClone/man/CellularitiesFromFreq.Rd | 6 QuantumClone-0.16.8.19/QuantumClone/man/Cluster_plot_from_cell.Rd | 18 QuantumClone-0.16.8.19/QuantumClone/man/Compute_NMI.Rd |only QuantumClone-0.16.8.19/QuantumClone/man/EM.algo.Rd | 6 QuantumClone-0.16.8.19/QuantumClone/man/EM_clustering.Rd | 12 QuantumClone-0.16.8.19/QuantumClone/man/From_freq_to_cell.Rd | 9 QuantumClone-0.16.8.19/QuantumClone/man/FullEM.Rd | 8 QuantumClone-0.16.8.19/QuantumClone/man/Input_Example.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/Multitest.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/One_D_plot.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/One_step_clustering.Rd | 24 QuantumClone-0.16.8.19/QuantumClone/man/Patient_schrodinger_cellularities.Rd | 7 QuantumClone-0.16.8.19/QuantumClone/man/Probability.to.belong.to.clone.Rd | 3 QuantumClone-0.16.8.19/QuantumClone/man/QC_output.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/QuantumCat.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/QuantumClone.Rd | 21 QuantumClone-0.16.8.19/QuantumClone/man/Tidy_output.Rd |only QuantumClone-0.16.8.19/QuantumClone/man/Tree.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/Tree_generation.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/add_leaf_list.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/create_priors.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/e.step.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/evolution_plot.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/filter_on_fik.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/find_x_position.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/hard.clustering.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/is_included.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/list_prod.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/longueur.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/m.step.Rd | 6 QuantumClone-0.16.8.19/QuantumClone/man/manual_plot_trees.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/multiplot_trees.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/parallelEM.Rd | 11 QuantumClone-0.16.8.19/QuantumClone/man/phylo_tree_generation.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/plot_QC_out.Rd | 5 QuantumClone-0.16.8.19/QuantumClone/man/plot_cell_from_Return_out.Rd | 4 QuantumClone-0.16.8.19/QuantumClone/man/plot_with_margins_densities.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/statistics_on_Multitest.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/man/strcount.Rd | 2 QuantumClone-0.16.8.19/QuantumClone/vignettes/Release.Rmd | 78 QuantumClone-0.16.8.19/QuantumClone/vignettes/Use_case.Rmd | 8 56 files changed, 1267 insertions(+), 934 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.2-1 dated 2016-04-19 and 1.2-2 dated 2016-08-26
pbapply-1.2-1/pbapply/inst |only pbapply-1.2-2/pbapply/DESCRIPTION | 10 +++++----- pbapply-1.2-2/pbapply/MD5 | 9 ++++----- pbapply-1.2-2/pbapply/R/timerProgressBar.R | 4 ++-- pbapply-1.2-2/pbapply/R/zzz.R | 7 +++++-- pbapply-1.2-2/pbapply/man/pboptions.Rd | 3 ++- 6 files changed, 18 insertions(+), 15 deletions(-)
Title: Inference and Analysis for Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic diffusion processes for both scalar and bivariate diffusion systems. For scalar diffusions, a module is provided for solving first passage time problems for both time-homogeneous and time-inhomogeneous GQDs.
Author: Etienne A.D. Pienaar [aut, cre],
Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>
Diff between DiffusionRgqd versions 0.1.2 dated 2016-01-20 and 0.1.3 dated 2016-08-26
DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_1_Introduction.R |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_1_Introduction.Rmd |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_2_Transition_Densities.R |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_2_Transition_Densities.Rmd |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_4_First_Passage_Times.R |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst/doc/Part_4_First_Passage_Times.Rmd |only DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes/Part_1_Introduction.Rmd |only DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes/Part_2_Transition_Densities.Rmd |only DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes/Part_3_Performing_Inference_files |only DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes/Part_4_First_Passage_Times.Rmd |only DiffusionRgqd-0.1.3/DiffusionRgqd/DESCRIPTION | 6 DiffusionRgqd-0.1.3/DiffusionRgqd/MD5 | 66 DiffusionRgqd-0.1.3/DiffusionRgqd/NAMESPACE | 2 DiffusionRgqd-0.1.3/DiffusionRgqd/NEWS.md | 7 DiffusionRgqd-0.1.3/DiffusionRgqd/R/BiGQD.mcmc.R | 12 DiffusionRgqd-0.1.3/DiffusionRgqd/R/GQD.TIpassage.R | 538 +++--- DiffusionRgqd-0.1.3/DiffusionRgqd/R/GQD.estimates.R | 11 DiffusionRgqd-0.1.3/DiffusionRgqd/R/GQD.mcmc.R | 12 DiffusionRgqd-0.1.3/DiffusionRgqd/R/GQD.plot.R | 31 DiffusionRgqd-0.1.3/DiffusionRgqd/README.md | 10 DiffusionRgqd-0.1.3/DiffusionRgqd/build/vignette.rds |binary DiffusionRgqd-0.1.3/DiffusionRgqd/data/SDEsim6.RData |only DiffusionRgqd-0.1.3/DiffusionRgqd/inst/CITATION | 4 DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/DiffusionRgqd_Paper.pdf |binary DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/DiffusionRgqd_RepMaterials.html | 881 +++++----- DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_1_Introduction.html | 238 +- DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_1_Introduction.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_2_Transition_Densities.html | 362 ++-- DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_2_Transition_Densities.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_3_Performing_Inference.html | 396 ++-- DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_4_First_Passage_Times.html | 326 ++- DiffusionRgqd-0.1.3/DiffusionRgqd/inst/doc/Part_4_First_Passage_Times.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/man/BiGQD.mcmc.Rd | 3 DiffusionRgqd-0.1.3/DiffusionRgqd/man/GQD.estimates.Rd | 27 DiffusionRgqd-0.1.3/DiffusionRgqd/man/GQD.mcmc.Rd | 4 DiffusionRgqd-0.1.3/DiffusionRgqd/man/GQD.plot.Rd | 3 DiffusionRgqd-0.1.3/DiffusionRgqd/man/SDEsim6.Rd |only DiffusionRgqd-0.1.3/DiffusionRgqd/man/fpt.sim.times.Rd |only DiffusionRgqd-0.1.3/DiffusionRgqd/vignettes/Part_1_Introduction.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/vignettes/Part_2_Transition_Densities.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/vignettes/Part_4_First_Passage_Times.html.asis |only DiffusionRgqd-0.1.3/DiffusionRgqd/vignettes/bibliography.bib |only 42 files changed, 1723 insertions(+), 1216 deletions(-)
Title: Client for Various 'CrossRef' APIs
Description: Client for various 'CrossRef' APIs, including 'metadata' search
with their old and newer search APIs, get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Ted Hart [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.5.4 dated 2016-07-20 and 0.5.8 dated 2016-08-26
DESCRIPTION | 21 +++--- MD5 | 104 +++++++++++++++++---------------- NAMESPACE | 26 +++++++- NEWS.md | 23 +++++++ R/crAddins.R |only R/cr_abstract.R |only R/cr_agency.r | 11 ++- R/cr_citation_count.r | 6 + R/cr_cn.r | 53 ++++++++++++----- R/cr_ft_links.R | 29 +++++++-- R/cr_ft_text.R | 117 ++++++++++++++++++++++++-------------- R/cr_fundref.r | 55 +++++++++++------ R/cr_journals.r | 86 ++++++++++++++++++++------- R/cr_licenses.R | 23 ++++--- R/cr_members.r | 47 +++++++++------ R/cr_prefixes.r | 78 +++++++++++++++++-------- R/cr_r.r | 3 R/cr_search.r | 29 ++++++--- R/cr_search2.r | 9 +- R/cr_search_free.r | 26 +++++--- R/cr_types.R | 56 ++++++++++++------ R/cr_works.R | 73 +++++++++++++++-------- R/crosscite.R | 32 ++++++---- R/deprecated_defunct.R | 26 ++++---- R/extract_pdf.R | 35 +---------- R/filters.R | 2 R/id_converter.R | 3 R/pmid2doi.R | 3 R/rcrossref-package.R | 80 +++++++++++++++---------- R/requestor.R | 19 +++--- R/tdmurl.R | 18 ++++- R/zzz.R | 6 - inst/rstudio |only man/as.tdmurl.Rd | 6 + man/cr_abstract.Rd |only man/cr_agency.Rd | 3 man/cr_cn.Rd | 8 ++ man/cr_ft_text.Rd | 74 +++++++++++++----------- man/cr_fundref.Rd | 6 + man/cr_journals.Rd | 15 +++- man/cr_licenses.Rd | 17 ++--- man/cr_members.Rd | 12 ++- man/cr_prefixes.Rd | 31 +++++----- man/cr_r.Rd | 3 man/cr_search.Rd | 7 +- man/cr_search_free.Rd | 19 +++--- man/cr_types.Rd | 3 man/cr_works.Rd | 19 +++--- man/crosscite.Rd | 11 +-- man/extract_xpdf.Rd | 3 man/rcrossref-defunct.Rd | 12 ++- man/rcrossref-deprecated.Rd | 14 ++-- man/rcrossref-package.Rd | 63 ++++++++++++-------- tests/testthat/test_cr_cn.R | 14 ++++ tests/testthat/test_cr_journals.R | 8 +- 55 files changed, 922 insertions(+), 525 deletions(-)
Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-level treatments and individual-level outcomes using a network optimization algorithm. Functions for checking balance at the cluster and individual levels are also provided, as are methods for permutation-inference-based outcome analysis.
Author: Luke Keele and Sam Pimentel
Maintainer: Sam Pimentel <spi@wharton.upenn.edu>
Diff between matchMulti versions 1.1.4 dated 2016-08-13 and 1.1.5 dated 2016-08-26
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 5 ++--- R/buildCaliper.R |only R/matchMulti-internal.R | 19 +++++++++++++++---- R/matchMulti.R | 13 +++++++++---- build/partial.rdb |binary inst/doc/multiMatch_vignette.pdf |binary man/buildCaliper.Rd |only man/matchMulti.Rd | 9 ++++++--- man/matchStudents.Rd | 13 +++++++++++-- 11 files changed, 57 insertions(+), 28 deletions(-)
Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac <hlavac@fas.harvard.edu>
Maintainer: Marek Hlavac <hlavac@fas.harvard.edu>
Diff between ExtremeBounds versions 0.1.5.1 dated 2015-08-10 and 0.1.5.2 dated 2016-08-26
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 9 R/ExtremeBounds-internal.R | 4 build/vignette.rds |binary inst/CITATION | 29 - inst/ChangeLog | 3 inst/doc/ExtremeBounds.pdf |binary man/ExtremeBounds.Rd | 3 man/eba.Rd | 5 man/hist.eba.Rd | 3 man/print.eba.Rd | 3 vignettes/ExtremeBounds.bib | 1038 ++++++++++++++++++++++---------------------- 13 files changed, 571 insertions(+), 558 deletions(-)
Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference,
including distance correlation, one-sample, two-sample, and multi-sample tests for
comparing multivariate distributions, are implemented. Measuring and testing
multivariate independence based on distance correlation, partial distance correlation,
multivariate goodness-of-fit tests, clustering based on energy distance, testing for
multivariate normality, distance components (disco) for non-parametric analysis of
structured data, and other energy statistics/methods are implemented.
Author: Maria L. Rizzo and Gabor J. Szekely
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>
Diff between energy versions 1.6.2 dated 2014-10-28 and 1.7-0 dated 2016-08-26
energy-1.6.2/energy/man/mvnorm.etest.Rd |only energy-1.7-0/energy/DESCRIPTION | 28 + energy-1.7-0/energy/MD5 | 67 ++-- energy-1.7-0/energy/NAMESPACE | 53 ++- energy-1.7-0/energy/NEWS | 55 ++- energy-1.7-0/energy/R/Ecluster.R | 120 +------- energy-1.7-0/energy/R/Eeqdist.R | 50 +-- energy-1.7-0/energy/R/Eindep.R | 95 +++--- energy-1.7-0/energy/R/Emvnorm.R | 111 +++---- energy-1.7-0/energy/R/Epoisson.R | 22 - energy-1.7-0/energy/R/RcppExports.R |only energy-1.7-0/energy/R/centering.R |only energy-1.7-0/energy/R/dcorT.R | 6 energy-1.7-0/energy/R/dcov.R | 58 ++-- energy-1.7-0/energy/R/dcovu.R |only energy-1.7-0/energy/R/disco.R | 390 +++++++++++++-------------- energy-1.7-0/energy/R/edist.R |only energy-1.7-0/energy/R/pdcor.R |only energy-1.7-0/energy/R/pdcov-test.R |only energy-1.7-0/energy/man/U_product.Rd |only energy-1.7-0/energy/man/centering.Rd |only energy-1.7-0/energy/man/dcor.ttest.Rd | 47 +-- energy-1.7-0/energy/man/dcov.Rd | 76 ++--- energy-1.7-0/energy/man/dcov.test.Rd | 74 ++--- energy-1.7-0/energy/man/dcovu.Rd |only energy-1.7-0/energy/man/disco.Rd | 248 ++++++++--------- energy-1.7-0/energy/man/edist.Rd | 70 ++-- energy-1.7-0/energy/man/energy-deprecated.Rd | 26 - energy-1.7-0/energy/man/energy-package.Rd | 14 energy-1.7-0/energy/man/energy.hclust.Rd | 61 ++-- energy-1.7-0/energy/man/eqdist.etest.Rd | 90 +++--- energy-1.7-0/energy/man/indep.test.Rd | 66 ++-- energy-1.7-0/energy/man/mvI.test.Rd | 36 +- energy-1.7-0/energy/man/mvnorm-etest.Rd |only energy-1.7-0/energy/man/pdcor.Rd |only energy-1.7-0/energy/man/poisson.mtest.Rd | 24 - energy-1.7-0/energy/src/RcppExports.cpp |only energy-1.7-0/energy/src/U-product.cpp |only energy-1.7-0/energy/src/centering.cpp |only energy-1.7-0/energy/src/dcovU.cpp |only energy-1.7-0/energy/src/energy.c | 70 ---- energy-1.7-0/energy/src/mvnorm.cpp |only energy-1.7-0/energy/src/partial-dcor.cpp |only energy-1.7-0/energy/src/projection.cpp |only 44 files changed, 926 insertions(+), 1031 deletions(-)