Title: Implement Material Design in Shiny Applications
Description: Allows shiny developers to incorporate UI elements based on Google's Material design. See <https://material.io/guidelines/> for more information.
Author: Eric Anderson [aut, cre],
Alvin Wang [ctb, cph] (Materialize CSS library),
Alan Chang [ctb, cph] (Materialize CSS library),
Alex Mark [ctb, cph] (Materialize CSS library),
Kevin Louie [ctb, cph] (Materialize CSS library)
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinymaterial versions 0.5.0 dated 2017-12-17 and 0.5.1 dated 2018-01-13
DESCRIPTION | 6 +-- MD5 | 15 ++++--- R/update-shiny-material-radio-button.R | 5 ++ inst/doc/shinymaterial.pdf |binary inst/js/shiny-material-side-nav-tabs.js | 2 - tests/app.R | 6 +-- tests/issues |only tests/side_nav_tabs.R | 64 ++++++++++++++++---------------- tests/testUpdateDropdown/app.R | 18 +++++---- 9 files changed, 63 insertions(+), 53 deletions(-)
Title: Calculation of the OPTICS Cordillera
Description: Functions for calculating the OPTICS Cordillera. The OPTICS Cordillera measures the amount of 'clusteredness' in a numeric data matrix within a distance-density based framework for a given minimum number of points comprising a cluster, as described in Rusch, Hornik, Mair (2017) <doi:10.1080/10618600.2017.1349664>. There is an R native version and a version that uses 'ELKI', with methods for printing, summarizing, and plotting the result. There also is an interface to the reference implementation of OPTICS in 'ELKI'.
Author: Thomas Rusch [aut, cre], Patrick Mair [ctb], Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between cordillera versions 0.7-0 dated 2017-07-24 and 0.8-0 dated 2018-01-13
DESCRIPTION | 8 ++-- MD5 | 26 ++++++------- NAMESPACE | 1 NEWS | 16 +++++++- R/CAClimateIndicatorsCountyMedian-data.R | 7 +++ R/cordillera-package.R | 25 ++++++------ R/cordillera.R | 60 ++++++++++++++++++------------- R/optics.R | 3 + inst/CITATION | 2 - man/CAClimateIndicatorsCountyMedian.Rd | 6 ++- man/cordillera-package.Rd | 25 ++++++------ man/cordillera.Rd | 38 ++++++++++--------- man/e_cordillera.Rd | 8 ++-- man/print.summary.opticse.Rd | 4 -- 14 files changed, 134 insertions(+), 95 deletions(-)
Title: Ensemble Clustering using K Means and Hierarchical Clustering
Description: Implements an ensemble algorithm for clustering combining a k-means and a hierarchical clustering approach.
Author: Kaloyan Stoyanov [aut],
Henrik Nordmark [aut],
Aris Perperoglou [aut],
Rolando Medellin [aut],
Ilan Fridman Rojas [cre],
Berthold Lausen [aut]
Maintainer: Ilan Fridman Rojas <ilanf@profusion.com>
Diff between hkclustering versions 1.0 dated 2016-09-15 and 1.0.1 dated 2018-01-13
DESCRIPTION | 25 +++++++-- MD5 | 4 - man/hkclusplus.Rd | 146 +++++++++++++++++++++++++++--------------------------- 3 files changed, 94 insertions(+), 81 deletions(-)
Title: Management and Exploratory Analysis of Spatial Data in Landscape
Genetics
Description: Management and exploratory analysis of spatial data in landscape genetics. Easy integration of information from multiple sources with "ecogen" objects.
Author: Leandro Roser [aut, cre],
Juan Vilardi [aut],
Beatriz Saidman [aut],
Laura Ferreyra [aut],
Thibaut Jombart [ctb] (author of included adegenet code),
Winston Chang [ctb] (author of the multiplot function included under
the name grf.multiplot)
Maintainer: Leandro Roser <learoser@gmail.com>
Diff between EcoGenetics versions 1.2.1-3 dated 2018-01-12 and 1.2.1-4 dated 2018-01-13
DESCRIPTION | 15 +++++++++------ MD5 | 10 +++++----- NEWS | 9 ++++++++- R/int.order.R | 24 ++++++++++-------------- man/EcoGenetics-package.Rd | 4 ++-- man/int.order.Rd | 14 -------------- 6 files changed, 34 insertions(+), 42 deletions(-)
Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation
comments for one of your functions that was not part of one of your
packages (yet)?
This is exactly what this package is about: running 'roxygen2' on
(chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between document versions 2.2.0 dated 2017-12-09 and 2.2.1 dated 2018-01-13
DESCRIPTION | 6 MD5 | 12 NAMESPACE | 1 NEWS.md | 5 R/file_parsing.R | 4 build/vignette.rds |binary inst/doc/Introduction_to_document.html | 442 +++++++++++++++++++++++---------- 7 files changed, 332 insertions(+), 138 deletions(-)
Title: Wamser Misc: Reading Files by Tokens, Stateful Computations,
Utility Functions
Description: A tokenizer to read a text file token by token with a very lightweight API, a framework for stateful computations with finite state machines and a few string utility functions.
Author: Markus S. Wamser [aut, cre]
Maintainer: Markus S. Wamser <r-wmisc@devel.wamser.eu>
Diff between Wmisc versions 0.3.3 dated 2017-10-03 and 0.3.4 dated 2018-01-13
DESCRIPTION | 8 +- MD5 | 14 ++--- build/vignette.rds |binary inst/doc/Automat.html | 139 ++++++++++++++++++++++++-------------------------- inst/doc/Strings.R | 19 ++++-- inst/doc/Strings.Rmd | 22 +++++-- inst/doc/Strings.html | 50 ++++++++--------- vignettes/Strings.Rmd | 22 +++++-- 8 files changed, 146 insertions(+), 128 deletions(-)
Title: Conventional Tukey Test
Description: Perform the conventional Tukey test from formula, lm, aov, aovlist and lmer objects.
Author: José Cláudio Faria <joseclaudio.faria@gmail.com>,
Enio G. Jelihovschi <eniojelihovs@gmail.com>,
Ivan Bezerra Allaman <ivanalaman@gmail.com>
Maintainer: José Cláudio Faria <joseclaudio.faria@gmail.com>
Diff between TukeyC versions 1.1-5 dated 2014-08-18 and 1.3-0 dated 2018-01-13
TukeyC-1.1-5/TukeyC/R/TukeyC.aov.R |only TukeyC-1.1-5/TukeyC/R/TukeyC.nest.R |only TukeyC-1.1-5/TukeyC/R/TukeyC.nest.aov.R |only TukeyC-1.1-5/TukeyC/R/TukeyC.nest.default.R |only TukeyC-1.1-5/TukeyC/R/m.inf.1a.R |only TukeyC-1.1-5/TukeyC/R/m.inf.1b.R |only TukeyC-1.1-5/TukeyC/R/m.inf.2a.R |only TukeyC-1.1-5/TukeyC/R/m.inf.2b.R |only TukeyC-1.1-5/TukeyC/R/m.inf.3a.R |only TukeyC-1.1-5/TukeyC/R/m.inf.3b.R |only TukeyC-1.1-5/TukeyC/demo/SPE.r |only TukeyC-1.1-5/TukeyC/demo/SPET.r |only TukeyC-1.1-5/TukeyC/demo/SSPE.r |only TukeyC-1.1-5/TukeyC/man/TukeyC.nest.Rd |only TukeyC-1.1-5/TukeyC/man/m.inf.Rd |only TukeyC-1.3-0/TukeyC/ChangeLog | 141 +++--- TukeyC-1.3-0/TukeyC/DESCRIPTION | 19 TukeyC-1.3-0/TukeyC/MD5 | 79 ++- TukeyC-1.3-0/TukeyC/NAMESPACE | 26 + TukeyC-1.3-0/TukeyC/R/TukeyC.R | 10 TukeyC-1.3-0/TukeyC/R/TukeyC.aovlist.R | 225 +++++++++-- TukeyC-1.3-0/TukeyC/R/TukeyC.default.R | 60 -- TukeyC-1.3-0/TukeyC/R/TukeyC.formula.R |only TukeyC-1.3-0/TukeyC/R/TukeyC.lm.R |only TukeyC-1.3-0/TukeyC/R/TukeyC.lmerMod.R |only TukeyC-1.3-0/TukeyC/R/TukeyC.nest.aovlist.R | 551 +++------------------------ TukeyC-1.3-0/TukeyC/R/TukeyC.nest.lm.R |only TukeyC-1.3-0/TukeyC/R/TukeyC.nest.lmerMod.R |only TukeyC-1.3-0/TukeyC/R/cv.R | 2 TukeyC-1.3-0/TukeyC/R/m.infos.aovlist.R |only TukeyC-1.3-0/TukeyC/R/m.infos.lm.R |only TukeyC-1.3-0/TukeyC/R/m.infos.lmerMod.R |only TukeyC-1.3-0/TukeyC/R/m.infos.nest.aovlist.R |only TukeyC-1.3-0/TukeyC/R/m.infos.nest.lm.R |only TukeyC-1.3-0/TukeyC/R/m.infos.nest.lmerMod.R |only TukeyC-1.3-0/TukeyC/R/make.TukeyC.groups.R | 6 TukeyC-1.3-0/TukeyC/R/make.TukeyC.test.R | 179 ++++---- TukeyC-1.3-0/TukeyC/R/plot.TukeyC.R | 341 +++++++++------- TukeyC-1.3-0/TukeyC/R/print.TukeyC.R |only TukeyC-1.3-0/TukeyC/R/summary.TukeyC.R | 60 +- TukeyC-1.3-0/TukeyC/README.md |only TukeyC-1.3-0/TukeyC/demo/CRD.R | 188 ++------- TukeyC-1.3-0/TukeyC/demo/FE.R | 297 +++----------- TukeyC-1.3-0/TukeyC/demo/LSD.R | 38 - TukeyC-1.3-0/TukeyC/demo/RCBD.R | 40 - TukeyC-1.3-0/TukeyC/demo/SPE.R |only TukeyC-1.3-0/TukeyC/demo/SPET.R |only TukeyC-1.3-0/TukeyC/demo/SSPE.R |only TukeyC-1.3-0/TukeyC/inst/CITATION | 44 +- TukeyC-1.3-0/TukeyC/man/TukeyC-internal.Rd |only TukeyC-1.3-0/TukeyC/man/TukeyC-package.Rd | 442 +++------------------ TukeyC-1.3-0/TukeyC/man/TukeyC.Rd | 545 ++++++++++++++++++-------- TukeyC-1.3-0/TukeyC/man/cv.Rd | 1 TukeyC-1.3-0/TukeyC/man/make.TukeyC.test.Rd | 26 - TukeyC-1.3-0/TukeyC/man/plot.TukeyC.Rd | 147 +++---- TukeyC-1.3-0/TukeyC/man/print.TukeyC.Rd |only TukeyC-1.3-0/TukeyC/man/summary.Rd | 182 ++++---- 57 files changed, 1530 insertions(+), 2119 deletions(-)
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and
in forecasting. Currently the package includes exponential smoothing models and
SARIMA in state-space form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 2.3.0 dated 2017-12-23 and 2.3.1 dated 2018-01-13
DESCRIPTION | 8 MD5 | 55 - NAMESPACE | 1 NEWS | 14 R/autoces.R | 3 R/autossarima.R | 2 R/ces.R | 43 - R/error-measures.R | 85 + R/es.R | 72 + R/ges.R | 45 - R/iss.R | 5 R/sma.R | 16 R/ssarima.R | 49 - R/ssfunctions.R | 182 ++-- R/stepwise.R | 10 R/viss.R | 5 R/vmethods.R | 17 inst/doc/ces.html | 28 inst/doc/es.html | 2104 +++++++++++++++++++++++++++++++++++++++++++++++-- inst/doc/ges.html | 12 inst/doc/simulate.html | 74 - inst/doc/sma.html | 8 inst/doc/smooth.Rmd | 29 inst/doc/smooth.html | 33 inst/doc/ssarima.html | 37 inst/doc/ves.html | 6 man/Accuracy.Rd |only man/error-measures.Rd | 3 vignettes/smooth.Rmd | 29 29 files changed, 2576 insertions(+), 399 deletions(-)
More information about simpleroptions at CRAN
Permanent link
Title: Build and Grade Multiple Choice Exams with Randomized Content
Description: Using as input a 'LaTeX' file with a multiple choice exam, this package will produce several versions with randomized contents of the same exam. Functions for grading and testing for cheating are also available.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between RndTexExams versions 1.4 dated 2016-06-05 and 1.4.1 dated 2018-01-13
DESCRIPTION | 10 MD5 | 46 - NEWS.md | 80 +-- R/rte_Utils.R | 457 +++++++++--------- R/rte_build_rdn_test.R | 574 +++++++++++------------ build/vignette.rds |binary inst/doc/rte-vignette_creating_exams.R | 204 ++++---- inst/doc/rte-vignette_creating_exams.html | 690 ++++++++++++++-------------- inst/doc/rte-vignette_testing_cheating.R | 72 +- inst/doc/rte-vignette_testing_cheating.html | 576 +++++++++++------------ man/engine.analyze.class.exam.Rd | 51 +- man/engine.analyze.class.examdesign.Rd | 51 +- man/rte.The.Randomizer.Rd | 65 +- man/rte.analyze.tex.file.Rd | 99 +--- man/rte.build.rdn.test.Rd | 5 man/rte.check.latex.flavor.Rd | 1 man/rte.check.my.os.Rd | 1 man/rte.check.pdflatex.Rd | 1 man/rte.compile.latex.Rd | 1 man/rte.get.classes.def.Rd | 43 - man/rte.get.n.cases.Rd | 1 man/rte.grade.exams.Rd | 163 +++--- man/rte.test.cheating.Rd | 1 tests/testthat/test_rte.R | 163 +++--- 24 files changed, 1671 insertions(+), 1684 deletions(-)
Title: Point Density for Geospatial Data
Description: The function pointdensity returns a density count and the temporal average for
every point in the original list. The dataframe returned includes four
columns: lat, lon, count, and date_avg. The "lat" column is the original
latitude data; the "lon" column is the original longitude data; the "count"
is the density count of the number of points within a radius of
radius*grid_size (the neighborhood); and the date_avg column includes the
average date of each point in the neighborhood.
Author: "Paul Evangelista <paul.evangelista@usma.edu> and Dave Beskow
<david.beskow@usma.edu>"
Maintainer: Paul Evangelista <paul.evangelista@usma.edu>
Diff between pointdensityP versions 0.2.1 dated 2015-06-03 and 0.3.2 dated 2018-01-13
pointdensityP-0.2.1/pointdensityP/R/pointdensity2.R |only pointdensityP-0.3.2/pointdensityP/DESCRIPTION | 26 +++++++++------ pointdensityP-0.3.2/pointdensityP/LICENSE | 2 - pointdensityP-0.3.2/pointdensityP/MD5 | 18 +++++----- pointdensityP-0.3.2/pointdensityP/NAMESPACE | 3 + pointdensityP-0.3.2/pointdensityP/R/pointdensity_0.3.2.R |only pointdensityP-0.3.2/pointdensityP/data/Arigon.rda |binary pointdensityP-0.3.2/pointdensityP/data/clean_crime.rda |binary pointdensityP-0.3.2/pointdensityP/man/Arigon.Rd | 4 +- pointdensityP-0.3.2/pointdensityP/man/clean_crime.Rd | 10 ++--- pointdensityP-0.3.2/pointdensityP/man/pointdensity.Rd | 14 ++++---- 11 files changed, 42 insertions(+), 35 deletions(-)
Title: Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype
and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and
separate treatment of local (cis) and distant (trans) eQTLs.
Author: Andrey A Shabalin [aut, cre] (0000-0003-0309-6821)
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between MatrixEQTL versions 2.1.1 dated 2015-02-03 and 2.2 dated 2018-01-13
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA5.r |only MatrixEQTL-2.1.1/MatrixEQTL/demo/e.interaction.r |only MatrixEQTL-2.2/MatrixEQTL/DESCRIPTION | 37 MatrixEQTL-2.2/MatrixEQTL/MD5 | 58 MatrixEQTL-2.2/MatrixEQTL/NAMESPACE | 26 MatrixEQTL-2.2/MatrixEQTL/R/Matrix_eQTL_engine.R | 4021 +++++++++---------- MatrixEQTL-2.2/MatrixEQTL/data/Covariates.txt | 6 MatrixEQTL-2.2/MatrixEQTL/demo/00Index | 4 MatrixEQTL-2.2/MatrixEQTL/demo/a.nocvrt.r | 32 MatrixEQTL-2.2/MatrixEQTL/demo/b.cvrt.r | 34 MatrixEQTL-2.2/MatrixEQTL/demo/c.weights.r | 34 MatrixEQTL-2.2/MatrixEQTL/demo/d.ANOVA.r | 34 MatrixEQTL-2.2/MatrixEQTL/demo/e.ANOVA5.r |only MatrixEQTL-2.2/MatrixEQTL/demo/f.interaction.r |only MatrixEQTL-2.2/MatrixEQTL/demo/p.hist.r | 21 MatrixEQTL-2.2/MatrixEQTL/demo/q.qqplot.r | 21 MatrixEQTL-2.2/MatrixEQTL/demo/sample.all.r | 38 MatrixEQTL-2.2/MatrixEQTL/demo/sample.cis.r | 62 MatrixEQTL-2.2/MatrixEQTL/inst/CITATION | 25 MatrixEQTL-2.2/MatrixEQTL/man/Covariates.Rd | 26 MatrixEQTL-2.2/MatrixEQTL/man/GE.Rd | 27 MatrixEQTL-2.2/MatrixEQTL/man/MatrixEQTL-package.Rd | 46 MatrixEQTL-2.2/MatrixEQTL/man/MatrixEQTL_cis_code.Rd | 20 MatrixEQTL-2.2/MatrixEQTL/man/Matrix_eQTL_main.Rd | 441 +- MatrixEQTL-2.2/MatrixEQTL/man/SNP.Rd | 28 MatrixEQTL-2.2/MatrixEQTL/man/SlicedData-class.Rd | 257 - MatrixEQTL-2.2/MatrixEQTL/man/geneloc.Rd | 47 MatrixEQTL-2.2/MatrixEQTL/man/modelANOVA.Rd | 76 MatrixEQTL-2.2/MatrixEQTL/man/modelLINEAR.Rd | 55 MatrixEQTL-2.2/MatrixEQTL/man/modelLINEAR_CROSS.Rd | 59 MatrixEQTL-2.2/MatrixEQTL/man/plot.MatrixEQTL.Rd | 103 MatrixEQTL-2.2/MatrixEQTL/man/snpsloc.Rd | 43 32 files changed, 3095 insertions(+), 2586 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 0.6.3 dated 2017-12-11 and 0.7.4 dated 2018-01-13
DESCRIPTION | 16 ++++---- MD5 | 62 +++++++++++++++++++-------------- NAMESPACE | 3 + NEWS | 32 +++++++++++++++-- R/available_data.R | 18 +++++---- R/enable_word_list.R |only R/grady_augmented.R | 2 - R/hash_grady_pos.R | 42 +++++++++++++++++++--- R/hash_internet_slang.R |only R/hash_sentiment_jockers_rinker.R | 2 - R/hash_sentiment_slangsd.R |only R/hash_sentiment_socal_google.R |only R/hash_valence_shifters.R | 2 - R/lexicon-package.R | 2 - R/pos_action_verb.R | 6 +-- R/pos_adverb.R | 6 +-- README.md | 38 ++++++++++++++++---- data/datalist | 4 ++ data/emojis_sentiment.rda |binary data/enable_word_list.rda |only data/hash_emojis.rda |binary data/hash_grady_pos.rda |binary data/hash_internet_slang.rda |only data/hash_sentiment_jockers_rinker.rda |binary data/hash_sentiment_slangsd.rda |only data/hash_sentiment_socal_google.rda |only data/hash_valence_shifters.rda |binary inst/CITATION | 8 ++-- man/enable_word_list.Rd |only man/grady_augmented.Rd | 2 - man/hash_grady_pos.Rd | 22 ++++++++--- man/hash_internet_slang.Rd |only man/hash_sentiment_jockers_rinker.Rd | 2 - man/hash_sentiment_slangsd.Rd |only man/hash_sentiment_socal_google.Rd |only man/hash_valence_shifters.Rd | 2 - man/pos_action_verb.Rd | 6 +-- man/pos_adverb.Rd | 6 +-- 38 files changed, 197 insertions(+), 86 deletions(-)
Title: File-Backed Matrix Class with Convenient Read and Write Access
Description: Interface for working with large matrices stored in files,
not in computer memory. Supports multiple non-character
data types (double, integer, logical and raw) of
various sizes (e.g. 8 and 4 byte real values).
Access to parts of the matrix is done by indexing,
exactly as with usual R matrices.
Supports very large matrices.
Tested on multi-terabyte matrices.
Allows for more than 2^32 rows or columns.
Allows for quick addition of extra columns to a filematrix.
Cross-platform as the package has R code only.
Author: Andrey A Shabalin [aut, cre] (0000-0003-0309-6821)
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between filematrix versions 1.1.0 dated 2016-05-23 and 1.2 dated 2018-01-13
filematrix-1.1.0/filematrix/inst/doc/Best_Prectices.R |only filematrix-1.1.0/filematrix/inst/doc/Best_Prectices.Rmd |only filematrix-1.1.0/filematrix/inst/doc/Best_Prectices.html |only filematrix-1.1.0/filematrix/inst/doc/UsingFilematrices.R |only filematrix-1.1.0/filematrix/inst/doc/UsingFilematrices.Rmd |only filematrix-1.1.0/filematrix/inst/doc/UsingFilematrices.html |only filematrix-1.1.0/filematrix/inst/doc/filematrix_vs_bigmemory.R |only filematrix-1.1.0/filematrix/inst/doc/filematrix_vs_bigmemory.Rmd |only filematrix-1.1.0/filematrix/inst/doc/filematrix_vs_bigmemory.html |only filematrix-1.1.0/filematrix/vignettes/Best_Prectices.Rmd |only filematrix-1.1.0/filematrix/vignettes/UsingFilematrices.Rmd |only filematrix-1.1.0/filematrix/vignettes/filematrix_vs_bigmemory.Rmd |only filematrix-1.2/filematrix/DESCRIPTION | 40 filematrix-1.2/filematrix/MD5 | 40 filematrix-1.2/filematrix/NAMESPACE | 16 filematrix-1.2/filematrix/R/filematrix.R | 1675 +++++----- filematrix-1.2/filematrix/build/vignette.rds |binary filematrix-1.2/filematrix/inst/doc/FM1_UsingFilematrices.R |only filematrix-1.2/filematrix/inst/doc/FM1_UsingFilematrices.Rmd |only filematrix-1.2/filematrix/inst/doc/FM1_UsingFilematrices.html |only filematrix-1.2/filematrix/inst/doc/FM2_Best_Practices.R |only filematrix-1.2/filematrix/inst/doc/FM2_Best_Practices.Rmd |only filematrix-1.2/filematrix/inst/doc/FM2_Best_Practices.html |only filematrix-1.2/filematrix/inst/doc/FM3_filematrix_vs_bigmemory.R |only filematrix-1.2/filematrix/inst/doc/FM3_filematrix_vs_bigmemory.Rmd |only filematrix-1.2/filematrix/inst/doc/FM3_filematrix_vs_bigmemory.html |only filematrix-1.2/filematrix/man/filematrix-class.Rd | 160 filematrix-1.2/filematrix/man/filematrix-package.Rd | 65 filematrix-1.2/filematrix/man/fm.create.Rd | 214 - filematrix-1.2/filematrix/tests/random_write_test.R | 103 filematrix-1.2/filematrix/vignettes/FM1_UsingFilematrices.Rmd |only filematrix-1.2/filematrix/vignettes/FM2_Best_Practices.Rmd |only filematrix-1.2/filematrix/vignettes/FM3_filematrix_vs_bigmemory.Rmd |only 33 files changed, 1294 insertions(+), 1019 deletions(-)
Title: Estimation of Interpretable eQTL Effect Sizes Using a Log of
Linear Model
Description: We use a non-linear model, termed ACME,
that reflects a parsimonious biological model for
allelic contributions of cis-acting eQTLs.
With non-linear least-squares algorithm we
estimate maximum likelihood parameters. The ACME model
provides interpretable effect size estimates and
p-values with well controlled Type-I error.
Includes both R and (much faster) C implementations.
For more details see Palowitch et al. (2017) <doi:10.1111/biom.12810>.
Author: Andrey A Shabalin [aut, cre] (0000-0003-0309-6821),
John Palowitch [aut] (0000-0002-1419-3056)
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between ACMEeqtl versions 1.4 dated 2017-03-12 and 1.5 dated 2018-01-13
ACMEeqtl-1.4/ACMEeqtl/R/estimate_multiSNP.R |only ACMEeqtl-1.5/ACMEeqtl/DESCRIPTION | 35 - ACMEeqtl-1.5/ACMEeqtl/MD5 | 37 - ACMEeqtl-1.5/ACMEeqtl/NAMESPACE | 14 ACMEeqtl-1.5/ACMEeqtl/R/ACMEeqtl.r | 227 +++---- ACMEeqtl-1.5/ACMEeqtl/R/make_eQTL_data.r | 367 ++++++----- ACMEeqtl-1.5/ACMEeqtl/R/multiSNP.r |only ACMEeqtl-1.5/ACMEeqtl/R/parallel_process.r | 405 ++++++------ ACMEeqtl-1.5/ACMEeqtl/build/vignette.rds |binary ACMEeqtl-1.5/ACMEeqtl/inst/CITATION | 21 ACMEeqtl-1.5/ACMEeqtl/inst/doc/ACMEeqtl.R | 66 -- ACMEeqtl-1.5/ACMEeqtl/inst/doc/ACMEeqtl.Rmd | 84 +- ACMEeqtl-1.5/ACMEeqtl/inst/doc/ACMEeqtl.html | 554 +++++++++-------- ACMEeqtl-1.5/ACMEeqtl/man/ACMEeqtl-package.Rd | 38 - ACMEeqtl-1.5/ACMEeqtl/man/create_artificial_data.Rd | 99 +-- ACMEeqtl-1.5/ACMEeqtl/man/effectSizeEstimation.Rd | 82 +- ACMEeqtl-1.5/ACMEeqtl/man/multisnpACME.Rd | 211 +++--- ACMEeqtl-1.5/ACMEeqtl/man/multithreadACME.Rd | 188 +++-- ACMEeqtl-1.5/ACMEeqtl/src/c_code.c | 645 ++++++++++---------- ACMEeqtl-1.5/ACMEeqtl/vignettes/ACMEeqtl.Rmd | 84 +- ACMEeqtl-1.5/ACMEeqtl/vignettes/bib.bib |only 21 files changed, 1729 insertions(+), 1428 deletions(-)
Title: Sequential Rank Agreement
Description: Tools for analysing the agreement of two or more rankings of the same items. Examples are importance rankings of predictor variables and risk predictions of subjects. Benchmarks for agreement are computed based on random permutation and bootstrap.
Author: Claus Thorn Ekstrøm and Thomas Alexander Gerds
Maintainer: Claus Thorn Ekstrøm <ekstrom@sund.ku.dk>
Diff between SuperRanker versions 1.0.1 dated 2016-07-18 and 1.1.0 dated 2018-01-13
SuperRanker-1.0.1/SuperRanker/README.md |only SuperRanker-1.1.0/SuperRanker/DESCRIPTION | 12 - SuperRanker-1.1.0/SuperRanker/MD5 | 30 ++-- SuperRanker-1.1.0/SuperRanker/R/RcppExports.R | 26 ++- SuperRanker-1.1.0/SuperRanker/R/sra.R | 50 ++++-- SuperRanker-1.1.0/SuperRanker/man/SuperRanker.Rd | 1 SuperRanker-1.1.0/SuperRanker/man/average_overlap.Rd | 1 SuperRanker-1.1.0/SuperRanker/man/overlap.Rd | 1 SuperRanker-1.1.0/SuperRanker/man/plot.sra.Rd | 1 SuperRanker-1.1.0/SuperRanker/man/random_list_sra.Rd | 5 SuperRanker-1.1.0/SuperRanker/man/smooth_sra.Rd | 1 SuperRanker-1.1.0/SuperRanker/man/sra.Rd | 18 +- SuperRanker-1.1.0/SuperRanker/man/sracpp.Rd |only SuperRanker-1.1.0/SuperRanker/man/sracppfull.Rd | 6 SuperRanker-1.1.0/SuperRanker/man/test_sra.Rd | 1 SuperRanker-1.1.0/SuperRanker/src/RcppExports.cpp | 53 +++++-- SuperRanker-1.1.0/SuperRanker/src/sra.cpp | 140 ++++++++++++------- 17 files changed, 230 insertions(+), 116 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' and
'lavaan' packages. It also implements the two-stage SEM approach
to conduct meta-analytic structural equation modeling on
correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 0.9.16 dated 2017-09-29 and 1.0.0 dated 2018-01-13
metaSEM-0.9.16/metaSEM/R/bootMASEM.R |only metaSEM-0.9.16/metaSEM/man/bootMASEM1.Rd |only metaSEM-0.9.16/metaSEM/man/bootMASEM2.Rd |only metaSEM-1.0.0/metaSEM/DESCRIPTION | 22 - metaSEM-1.0.0/metaSEM/MD5 | 143 ++++----- metaSEM-1.0.0/metaSEM/NAMESPACE | 7 metaSEM-1.0.0/metaSEM/NEWS | 15 metaSEM-1.0.0/metaSEM/R/as.mxMatrix.R | 10 metaSEM-1.0.0/metaSEM/R/asyCov.R | 10 metaSEM-1.0.0/metaSEM/R/bootuniR.R |only metaSEM-1.0.0/metaSEM/R/lavaan2RAM.R | 16 - metaSEM-1.0.0/metaSEM/R/smd.R | 8 metaSEM-1.0.0/metaSEM/R/summary.R | 28 + metaSEM-1.0.0/metaSEM/R/tssem.R | 164 ++++++++++ metaSEM-1.0.0/metaSEM/R/uniR.R | 7 metaSEM-1.0.0/metaSEM/build/vignette.rds |binary metaSEM-1.0.0/metaSEM/data/Aloe14.rda |binary metaSEM-1.0.0/metaSEM/data/BCG.rda |binary metaSEM-1.0.0/metaSEM/data/Becker09.rda |binary metaSEM-1.0.0/metaSEM/data/Becker83.rda |binary metaSEM-1.0.0/metaSEM/data/Becker92.rda |binary metaSEM-1.0.0/metaSEM/data/Becker94.rda |binary metaSEM-1.0.0/metaSEM/data/Berkey98.rda |binary metaSEM-1.0.0/metaSEM/data/Boer16.rda |binary metaSEM-1.0.0/metaSEM/data/Bornmann07.rda |binary metaSEM-1.0.0/metaSEM/data/Cheung00.rda |binary metaSEM-1.0.0/metaSEM/data/Cheung09.rda |binary metaSEM-1.0.0/metaSEM/data/Cooke16.rda |binary metaSEM-1.0.0/metaSEM/data/Cooper03.rda |binary metaSEM-1.0.0/metaSEM/data/Digman97.rda |binary metaSEM-1.0.0/metaSEM/data/HedgesOlkin85.rda |binary metaSEM-1.0.0/metaSEM/data/Hox02.rda |binary metaSEM-1.0.0/metaSEM/data/Hunter83.rda |binary metaSEM-1.0.0/metaSEM/data/Jaramillo05.rda |binary metaSEM-1.0.0/metaSEM/data/Mak09.rda |binary metaSEM-1.0.0/metaSEM/data/Nohe15A1.rda |binary metaSEM-1.0.0/metaSEM/data/Nohe15A2.rda |binary metaSEM-1.0.0/metaSEM/data/Norton13.rda |binary metaSEM-1.0.0/metaSEM/data/Roorda11.rda |binary metaSEM-1.0.0/metaSEM/data/issp05.rda |binary metaSEM-1.0.0/metaSEM/data/issp89.rda |binary metaSEM-1.0.0/metaSEM/data/wvs94a.rda |binary metaSEM-1.0.0/metaSEM/data/wvs94b.rda |binary metaSEM-1.0.0/metaSEM/inst/doc/Examples.html | 422 +++++++++++++-------------- metaSEM-1.0.0/metaSEM/inst/doc/metaSEM.pdf |binary metaSEM-1.0.0/metaSEM/man/Aloe14.Rd | 3 metaSEM-1.0.0/metaSEM/man/Becker09.Rd | 2 metaSEM-1.0.0/metaSEM/man/Berkey98.Rd | 2 metaSEM-1.0.0/metaSEM/man/Boer16.Rd | 2 metaSEM-1.0.0/metaSEM/man/Cheung00.Rd | 2 metaSEM-1.0.0/metaSEM/man/Cheung09.Rd | 2 metaSEM-1.0.0/metaSEM/man/Cooke16.Rd | 2 metaSEM-1.0.0/metaSEM/man/Diag.Rd | 6 metaSEM-1.0.0/metaSEM/man/Hunter83.Rd | 6 metaSEM-1.0.0/metaSEM/man/Nohe15.Rd | 12 metaSEM-1.0.0/metaSEM/man/as.mxMatrix.Rd | 4 metaSEM-1.0.0/metaSEM/man/asyCov.Rd | 4 metaSEM-1.0.0/metaSEM/man/bootuniR1.Rd |only metaSEM-1.0.0/metaSEM/man/bootuniR2.Rd |only metaSEM-1.0.0/metaSEM/man/create.mxMatrix.Rd | 4 metaSEM-1.0.0/metaSEM/man/impliedR.Rd | 2 metaSEM-1.0.0/metaSEM/man/meta.Rd | 2 metaSEM-1.0.0/metaSEM/man/meta3.Rd | 2 metaSEM-1.0.0/metaSEM/man/metaSEM-package.Rd | 8 metaSEM-1.0.0/metaSEM/man/reml.Rd | 4 metaSEM-1.0.0/metaSEM/man/reml3.Rd | 4 metaSEM-1.0.0/metaSEM/man/smdMES.Rd | 12 metaSEM-1.0.0/metaSEM/man/smdMTS.Rd | 7 metaSEM-1.0.0/metaSEM/man/summary.Rd | 12 metaSEM-1.0.0/metaSEM/man/tssem1.Rd | 33 +- metaSEM-1.0.0/metaSEM/man/tssemParaVar.Rd |only metaSEM-1.0.0/metaSEM/man/uniR2.Rd | 5 metaSEM-1.0.0/metaSEM/man/vec2symMat.Rd | 3 metaSEM-1.0.0/metaSEM/man/wls.Rd | 4 metaSEM-1.0.0/metaSEM/man/wvs94a.Rd | 2 metaSEM-1.0.0/metaSEM/tests |only 76 files changed, 613 insertions(+), 390 deletions(-)
Title: Incremental Calculation of Dynamic Time Warping
Description: Implements incremental calculation of the DTW (Dynamic Time Warping) distance of two vectors, which is specifically useful for life data streams. Further the calculation of the global cost matrix is implemented in C++ to be faster. The Sakoe Chiba band is also implemented. The calculation of DTW is less functional then the one of dtw(), however much faster. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>. Any feedback is highly appreciated!
Author: Maximilian Leodolter
Maintainer: Maximilian Leodolter <maximilian.leodolter@gmail.com>
Diff between IncDTW versions 1.0.0 dated 2017-10-10 and 1.0.1 dated 2018-01-13
DESCRIPTION | 8 - MD5 | 18 +-- R/Rfunctions.R | 138 ++++++++++++++++------- inst/doc/Incremental_Dynamic_Time_Warping.R | 75 +++++++----- inst/doc/Incremental_Dynamic_Time_Warping.Rmd | 86 +++++++++----- inst/doc/Incremental_Dynamic_Time_Warping.html | 149 ++++++++++++++++--------- man/dtw.Rd | 13 ++ man/idtw.Rd | 58 +++++++-- man/plot_idtw.Rd | 6 - vignettes/Incremental_Dynamic_Time_Warping.Rmd | 86 +++++++++----- 10 files changed, 422 insertions(+), 215 deletions(-)
Title: Stubbing Framework for R
Description: Create stubs of functions for use while testing.
Author: Sainath Adapa [aut, cre],
Nitin Madasu [aut]
Maintainer: Sainath Adapa <adapasainath@gmail.com>
Diff between stubthat versions 1.2.0 dated 2017-05-03 and 1.2.1 dated 2018-01-13
DESCRIPTION | 8 MD5 | 16 NEWS.md | 3 build/vignette.rds |binary inst/doc/stubthat.R | 62 +-- inst/doc/stubthat.Rmd | 16 inst/doc/stubthat.html | 694 ++++++++++++++++++++-------------------- tests/testthat/test-with-mock.r | 14 vignettes/stubthat.Rmd | 16 9 files changed, 422 insertions(+), 407 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre] (0000-0002-4791-442X),
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut],
ICAR-NBGPR [cph],
Maurice Aubrey [ctb] (Double Metaphone),
Kevin Atkinson [ctb] (Double Metaphone),
Lawrence Philips [ctb] (Double Metaphone)
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.3.2 dated 2017-08-04 and 0.2.3.3 dated 2018-01-13
DESCRIPTION | 29 +++++--- MD5 | 30 ++++---- NEWS.md | 148 +++++++++++++++++++++--------------------- R/DoubleMetaphone.R | 6 + R/KWIC.R | 24 +++--- R/ProbDup.R | 18 ++--- README.md | 24 +++--- build/vignette.rds |binary inst/CITATION | 7 + inst/doc/Introduction.Rmd | 124 +++++++++++++++++++++-------------- inst/doc/Introduction.pdf |binary man/DoubleMetaphone.Rd | 6 + man/KWIC.Rd | 21 +++-- man/ProbDup.Rd | 18 ++--- vignettes/Introduction.Rmd | 124 +++++++++++++++++++++-------------- vignettes/bibliography.bibtex | 72 +++++++++++--------- 16 files changed, 374 insertions(+), 277 deletions(-)
Title: Computation and Visualization of Empirical Joint Distribution
(Empirical Joint CDF)
Description: Computes and visualizes empirical joint distribution of multivariate data with optimized algorithms and multi-thread computation. There is a faster algorithm using dynamic programming to compute the whole empirical joint distribution of a bivariate data. There are optimized algorithms for computing empirical joint CDF function values for other multivariate data. Visualization is focused on bivariate data. Levelplots and wireframes are included.
Author: En-shuo Hsu, Jeffrey C. Miecznikowski
Maintainer: En-shuo Hsu <daviden1013@gmail.com>
Diff between Emcdf versions 0.1.0 dated 2017-06-02 and 0.1.2 dated 2018-01-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/RcppExports.R | 4 ++-- R/emcdf.R | 2 +- src/Matrix.h | 2 +- src/RcppExports.cpp | 35 +++++++++++++++++++++++++++++++---- src/emcdf_single.cpp | 16 ++++++++-------- 7 files changed, 52 insertions(+), 25 deletions(-)