Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers
needed to build R packages on various platforms and ensures the PATH is
configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
RStudio [cph]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgbuild versions 1.0.3 dated 2019-03-20 and 1.0.4 dated 2019-08-05
DESCRIPTION | 14 +++++------ MD5 | 22 +++++++++--------- NEWS.md | 18 ++++++++++++++ R/build-bg.R | 44 +++++++++++++++--------------------- R/build-tools.R | 9 +++++-- R/build.R | 20 +++++++++------- R/compiler.R | 5 ++-- R/rcmd.R | 4 +-- R/rtools-cache.R | 8 ++++++ man/build.Rd | 11 ++++++--- man/has_compiler.Rd | 2 - tests/testthat/test-build-process.r | 19 --------------- 12 files changed, 96 insertions(+), 80 deletions(-)
Title: Spectral Clustering-Based Method for Identifying B Cell Clones
Description: Provides a computational framework for B cell clones identification
from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets.
Three models are included (identical, hierarchical, and spectral)
that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins)
which share the same V gene, J gene and junction length.
Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>.
Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.
Author: Nima Nouri [aut, cre],
Jason Vander Heiden [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Nima Nouri <nima.nouri@yale.edu>
Diff between scoper versions 0.1.0 dated 2018-10-14 and 0.2.0 dated 2019-08-05
scoper-0.1.0/scoper/data/ClonedExampleDb.rda |only scoper-0.1.0/scoper/inst/doc/Scoper-Vignette.html |only scoper-0.1.0/scoper/man/ClonalAnalysis-class.Rd |only scoper-0.1.0/scoper/man/analyzeClones.Rd |only scoper-0.2.0/scoper/DESCRIPTION | 34 scoper-0.2.0/scoper/MD5 | 37 scoper-0.2.0/scoper/NAMESPACE | 45 scoper-0.2.0/scoper/NEWS.md | 31 scoper-0.2.0/scoper/R/Data.R | 13 scoper-0.2.0/scoper/R/Functions.R | 1889 +++++++++++++--------- scoper-0.2.0/scoper/R/RcppExports.R |only scoper-0.2.0/scoper/R/Scoper.R | 51 scoper-0.2.0/scoper/README.md | 13 scoper-0.2.0/scoper/build/vignette.rds |binary scoper-0.2.0/scoper/inst/CITATION |only scoper-0.2.0/scoper/inst/doc/Scoper-Vignette.R | 70 scoper-0.2.0/scoper/inst/doc/Scoper-Vignette.Rmd | 295 +-- scoper-0.2.0/scoper/inst/doc/Scoper-Vignette.pdf |only scoper-0.2.0/scoper/man/ExampleDb.Rd | 5 scoper-0.2.0/scoper/man/defineClonesScoper.Rd | 141 + scoper-0.2.0/scoper/man/scoper.Rd | 17 scoper-0.2.0/scoper/src |only scoper-0.2.0/scoper/vignettes/Scoper-Vignette.Rmd | 295 +-- 23 files changed, 1739 insertions(+), 1197 deletions(-)
Title: Create Pivot Tables in R
Description: Create regular pivot tables with just a few lines of R.
More complex pivot tables can also be created, e.g. pivot tables
with irregular layouts, multiple calculations and/or derived
calculations based on multiple data frames. Pivot tables are
constructed using R only and can be written to a range of
output formats (plain text, 'HTML', 'Latex' and 'Excel'),
including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>
Diff between pivottabler versions 1.2.0 dated 2019-03-20 and 1.2.1 dated 2019-08-05
DESCRIPTION | 6 - MD5 | 38 ++++----- NEWS.md | 10 ++ R/PivotTable.R | 3 build/vignette.rds |binary inst/doc/v01-introduction.html | 106 +++++++++++++------------ inst/doc/v02-datagroups.html | 66 ++++++++------- inst/doc/v03-calculations.html | 86 ++++++++++---------- inst/doc/v04-outputs.html | 22 +++-- inst/doc/v05-latexoutput.html | 14 ++- inst/doc/v06-styling.html | 58 +++++++------ inst/doc/v07-findingandformatting.html | 138 ++++++++++++++++----------------- inst/doc/v08-cellcontext.html | 30 ++++--- inst/doc/v09-irregularlayout.html | 66 ++++++++------- inst/doc/v10-performance.html | 68 ++++++++-------- inst/doc/v11-shiny.html | 10 +- inst/doc/v12-excelexport.html | 14 ++- inst/doc/vA1-appendix.html | 22 +++-- inst/doc/vA2-appendix.html | 82 ++++++++++--------- inst/doc/vA3-appendix.html | 14 ++- 20 files changed, 462 insertions(+), 391 deletions(-)
Title: Machine Learning for S.E.O
Description: Measures different aspects of page content, structure and performance for SEO (Search Engine Optimization).
Aspects covered include HTML tags used in SEO, duplicate and near-duplicate content, structured data, on-site linking structure and popularity transfer, and many other amazing things.
This package can be used to generate a real, full SEO audit report, which serves to detect errors or inefficiencies on a page that can be corrected in order to optimise its performance on search engines.
Author: Vincent Terrasi [aut, cre],
OnCrawl [cph, fnd]
Maintainer: Vincent Terrasi <vincent@data-seo.com>
Diff between oncrawlR versions 0.1.5 dated 2019-06-28 and 0.1.6 dated 2019-08-05
DESCRIPTION | 17 ++- MD5 | 17 ++- NAMESPACE | 12 ++ R/utils-dataviz.R |only R/utils-model.R |only R/utils.R | 169 ---------------------------------- README.md | 198 ++++++++++++++++++++++++++++++++++++++-- man/export_formattableWidget.Rd |only man/oncrawlCreateDashboard.Rd |only man/oncrawlCreateGraph.Rd |only man/oncrawlExplainModel.Rd | 2 man/oncrawlTrainModel.Rd | 2 12 files changed, 228 insertions(+), 189 deletions(-)
Title: Estimating the Number of Essential Genes in a Genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis experiment,
through the use of a Gibbs sampler.
Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between negenes versions 1.0-8 dated 2018-04-02 and 1.0-12 dated 2019-08-05
negenes-1.0-12/negenes/ChangeLog |only negenes-1.0-12/negenes/DESCRIPTION | 26 ++-- negenes-1.0-12/negenes/MD5 | 23 +-- negenes-1.0-12/negenes/NAMESPACE | 13 -- negenes-1.0-12/negenes/R/Mtb80-data.R |only negenes-1.0-12/negenes/R/negenes.R | 193 ++++++++++++++---------------- negenes-1.0-12/negenes/R/sim_mutants.R |only negenes-1.0-12/negenes/README.md | 15 ++ negenes-1.0-12/negenes/data/Mtb80.RData |binary negenes-1.0-12/negenes/inst/CITATION | 6 negenes-1.0-12/negenes/man/Mtb80.Rd | 60 ++++----- negenes-1.0-12/negenes/man/negenes.Rd | 158 ++++++++++++------------ negenes-1.0-12/negenes/man/sim.mutants.Rd | 81 ++++++------ negenes-1.0-8/negenes/inst/INSTALL_ME.txt |only negenes-1.0-8/negenes/inst/STATUS.txt |only 15 files changed, 295 insertions(+), 280 deletions(-)
Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetDictionaries versions 0.1.2 dated 2019-06-19 and 0.1.3 dated 2019-08-05
SemNetDictionaries-0.1.2/SemNetDictionaries/R/fruits.misnomer.R |only SemNetDictionaries-0.1.2/SemNetDictionaries/R/good.misnomer.R |only SemNetDictionaries-0.1.2/SemNetDictionaries/R/hot.misnomer.R |only SemNetDictionaries-0.1.2/SemNetDictionaries/R/jobs.misnomer.R |only SemNetDictionaries-0.1.2/SemNetDictionaries/R/vegetables.misnomer.R |only SemNetDictionaries-0.1.2/SemNetDictionaries/data/fruits.misnomer.RData |only SemNetDictionaries-0.1.2/SemNetDictionaries/data/good.misnomer.RData |only SemNetDictionaries-0.1.2/SemNetDictionaries/data/hot.misnomer.RData |only SemNetDictionaries-0.1.2/SemNetDictionaries/data/jobs.misnomer.RData |only SemNetDictionaries-0.1.2/SemNetDictionaries/data/vegetables.misnomer.RData |only SemNetDictionaries-0.1.2/SemNetDictionaries/man/fruits.misnomer.Rd |only SemNetDictionaries-0.1.2/SemNetDictionaries/man/good.misnomer.Rd |only SemNetDictionaries-0.1.2/SemNetDictionaries/man/hot.misnomer.Rd |only SemNetDictionaries-0.1.2/SemNetDictionaries/man/jobs.misnomer.Rd |only SemNetDictionaries-0.1.2/SemNetDictionaries/man/vegetables.misnomer.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/DESCRIPTION | 13 - SemNetDictionaries-0.1.3/SemNetDictionaries/MD5 | 86 +++++----- SemNetDictionaries-0.1.3/SemNetDictionaries/NAMESPACE | 1 SemNetDictionaries-0.1.3/SemNetDictionaries/NEWS | 12 + SemNetDictionaries-0.1.3/SemNetDictionaries/R/SemNetDictionaries.R | 4 SemNetDictionaries-0.1.3/SemNetDictionaries/R/animals.dictionary.R | 4 SemNetDictionaries-0.1.3/SemNetDictionaries/R/animals.misnomer.R | 8 SemNetDictionaries-0.1.3/SemNetDictionaries/R/animals.moniker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/append.dictionary.R | 51 +++++ SemNetDictionaries-0.1.3/SemNetDictionaries/R/dictionaries.R | 1 SemNetDictionaries-0.1.3/SemNetDictionaries/R/find.dictionaries.R | 79 ++++++--- SemNetDictionaries-0.1.3/SemNetDictionaries/R/fruits.moniker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/general.dictionary.R | 8 SemNetDictionaries-0.1.3/SemNetDictionaries/R/good.moniker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/hot.moinker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/jobs.moniker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/load.dictionaries.R | 19 +- SemNetDictionaries-0.1.3/SemNetDictionaries/R/load.misnomers.R | 6 SemNetDictionaries-0.1.3/SemNetDictionaries/R/load.monikers.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/R/vegetables.moniker.R |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/animals.dictionary.RData |binary SemNetDictionaries-0.1.3/SemNetDictionaries/data/animals.misnomer.RData |binary SemNetDictionaries-0.1.3/SemNetDictionaries/data/animals.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/datalist | 11 - SemNetDictionaries-0.1.3/SemNetDictionaries/data/fruits.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/general.dictionary.RData |binary SemNetDictionaries-0.1.3/SemNetDictionaries/data/good.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/hot.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/jobs.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/data/vegetables.moniker.RData |only SemNetDictionaries-0.1.3/SemNetDictionaries/inst |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/SemNetDictionaries-package.Rd | 4 SemNetDictionaries-0.1.3/SemNetDictionaries/man/animals.dictionary.Rd | 4 SemNetDictionaries-0.1.3/SemNetDictionaries/man/animals.misnomer.Rd | 8 SemNetDictionaries-0.1.3/SemNetDictionaries/man/animals.moniker.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/append.dictionary.Rd | 16 + SemNetDictionaries-0.1.3/SemNetDictionaries/man/dictionaries.Rd | 1 SemNetDictionaries-0.1.3/SemNetDictionaries/man/find.dictionaries.Rd | 23 +- SemNetDictionaries-0.1.3/SemNetDictionaries/man/fruits.moniker.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/general.dictionary.Rd | 8 SemNetDictionaries-0.1.3/SemNetDictionaries/man/good.moniker.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/hot.moniker.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/jobs.moniker.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/load.dictionaries.Rd | 10 - SemNetDictionaries-0.1.3/SemNetDictionaries/man/load.misnomers.Rd | 4 SemNetDictionaries-0.1.3/SemNetDictionaries/man/load.monikers.Rd |only SemNetDictionaries-0.1.3/SemNetDictionaries/man/vegetables.moniker.Rd |only 62 files changed, 242 insertions(+), 139 deletions(-)
More information about SemNetDictionaries at CRAN
Permanent link
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 2.1 dated 2019-07-22 and 2.2 dated 2019-08-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/read.table2.Rd | 7 +++---- man/scan2.Rd | 7 +++---- 4 files changed, 13 insertions(+), 15 deletions(-)
Title: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
Description: Wrapper functions that interface with 'FSL'
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with 'FSL'
completely in R, where you pass R objects of class 'nifti', implemented by
package 'oro.nifti', and the function executes an 'FSL' command and returns an R
object of class 'nifti' if desired.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 2.23.0 dated 2019-07-18 and 2.24.1 dated 2019-08-05
DESCRIPTION | 6 - MD5 | 45 +++++++------- NAMESPACE | 9 ++ NEWS.md | 12 +++ R/convert_xfm.R |only R/face_removal_mask.R | 143 ++++++++++++++++++++++++++++++++++++++++++++- R/fsl_bin_tab.R | 2 R/fsl_dice.R | 2 R/fsl_version.R | 6 + R/fslhd.R | 61 +++++++++++++++---- R/mridefacer.R |only R/readrpi.R | 14 ++++ inst/doc/dti_data.html | 4 - man/check_file.Rd | 3 man/face_removal_mask.Rd | 4 - man/fsl_bin_tab.Rd | 2 man/fsl_dice.Rd | 2 man/fsl_version.Rd | 3 man/fslhd.parse.Rd | 3 man/fslmask.Rd | 22 +++--- man/fslreorient2std.Rd | 10 ++- man/getForms.Rd | 3 man/get_quickshear_mask.Rd |only man/invert_xfm.Rd |only man/mridefacer.Rd |only man/readrpi.Rd | 15 ++++ 26 files changed, 308 insertions(+), 63 deletions(-)
Title: Climate Tools (Series Homogenization and Derived Products)
Description: Functions for the quality control, homogenization and missing data infilling of climatological series and to obtain climatological summaries and grids from the results. Also functions to draw wind-roses and Walter&Lieth climate diagrams.
Author: Jose A. Guijarro <jguijarrop@aemet.es>
Maintainer: Jose A. Guijarro <jguijarrop@aemet.es>
Diff between climatol versions 3.1.1 dated 2018-05-06 and 3.1.2 dated 2019-08-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 2 ++ data/datalist | 2 +- 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between BatchGetSymbols versions 2.5.2 dated 2019-04-24 and 2.5.3 dated 2019-08-05
DESCRIPTION | 10 ++-- MD5 | 20 ++++----- NEWS.md | 5 ++ R/BatchGetSymbols.R | 33 +++++++++------- R/GetSP500Stocks.R | 7 +-- R/Utils.R | 2 R/myGetSymbols.R | 62 +++++++++++++++++++----------- build/vignette.rds |binary inst/doc/BatchGetSymbols-vignette.html | 67 +++++++++++++++++---------------- man/BatchGetSymbols.Rd | 5 +- man/myGetSymbols.Rd | 4 + 11 files changed, 127 insertions(+), 88 deletions(-)
More information about BatchGetSymbols at CRAN
Permanent link
Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions.
Author: Manos Papadakis, Michail Tsagris, Stefanos Fafalios and Marios Dimitriadis.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.0.3 dated 2019-07-28 and 0.0.4 dated 2019-08-05
DESCRIPTION | 8 +++---- MD5 | 22 ++++++++++--------- NAMESPACE | 2 - NEWS.md | 49 +++++++++++++++++++++++++++++++++++++------- R/lm.drop1.R |only man/Rfast2-package.Rd | 4 +-- man/lm.drop1.Rd |only src/Makevars | 2 + src/Makevars.win | 2 + src/apply_funcs_templates.h | 34 +++++++++++++++--------------- src/mmpc2.cpp | 2 - src/reg_lib2.cpp | 1 src/templates.h | 9 ++++---- 13 files changed, 88 insertions(+), 47 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 0.7-9 dated 2016-08-26 and 0.7-10 dated 2019-08-05
DESCRIPTION | 15 +-- MD5 | 15 +-- NEWS |only R/hetcor.R | 5 - R/hetcor.data.frame.R | 215 ++++++++++++++++++++++++---------------------- R/hetcor.default.R | 8 + man/hetcor.Rd | 230 +++++++++++++++++++++++++------------------------- man/polychor.Rd | 190 ++++++++++++++++++++--------------------- man/polyserial.Rd | 184 ++++++++++++++++++++-------------------- 9 files changed, 443 insertions(+), 419 deletions(-)
Title: Query Plane Tickets using the 'Kiwi' API
Description: Query plane tickets, from several airlines, using the 'Kiwi' API
(similar to 'Google Flights').
The API is documented at <https://docs.kiwi.com/>.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Diff between rflights versions 0.1.0 dated 2019-05-16 and 0.1.102 dated 2019-08-05
DESCRIPTION | 9 ++- MD5 | 37 +++++++++++----- NAMESPACE | 1 R/data.R |only R/find-location.R | 9 ++- R/get-flights.R | 12 +++-- README.md | 60 ++++++++++++++------------ build/vignette.rds |binary data |only inst/doc/basic-usage-example.Rmd | 3 - inst/doc/basic-usage-example.html | 82 +++++++++++++++++++++--------------- man/africa.Rd |only man/asia.Rd |only man/country_code.Rd |only man/europe.Rd |only man/north_america.Rd |only man/oceania.Rd |only man/south_america.Rd |only tests/testthat/test-find_location.R | 4 - tests/testthat/test-get_flights.R | 6 +- vignettes/basic-usage-example.Rmd | 3 - 21 files changed, 138 insertions(+), 88 deletions(-)
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary Abrams, Greg Gershkowitz, Anoushka Joglekar,
Chao Liu, Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.2 dated 2019-08-03 and 1.0.4 dated 2019-08-05
DESCRIPTION | 8 MD5 | 12 - inst/doc/newmanomics.html | 388 +++++++++--------------------------------- tests/00-pairedTest.R | 3 tests/00-pairedTest.Rout.save | 6 tests/03-betamix.R | 2 tests/03-betamix.Rout.save | 6 7 files changed, 105 insertions(+), 320 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial
clustering of applications with noise) and OPTICS (ordering points to identify
the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier
factor) algorithm. The implementations use the kd-tree data structure (from
library ANN) for faster k-nearest neighbor search. An R interface to fast kNN
and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-3 dated 2018-11-13 and 1.1-4 dated 2019-08-05
dbscan-1.1-3/dbscan/tests/testthat/Rplots.pdf |only dbscan-1.1-4/dbscan/DESCRIPTION | 11 dbscan-1.1-4/dbscan/MD5 | 52 +- dbscan-1.1-4/dbscan/NAMESPACE | 28 - dbscan-1.1-4/dbscan/NEWS.md | 11 dbscan-1.1-4/dbscan/R/RcppExports.R | 56 +- dbscan-1.1-4/dbscan/R/dbscan.R | 18 dbscan-1.1-4/dbscan/R/frNN.R | 2 dbscan-1.1-4/dbscan/R/hdbscan.R | 6 dbscan-1.1-4/dbscan/R/kNN.R | 4 dbscan-1.1-4/dbscan/R/kNNdist.R | 7 dbscan-1.1-4/dbscan/R/optics.R | 16 dbscan-1.1-4/dbscan/R/predict.R |only dbscan-1.1-4/dbscan/build/vignette.rds |binary dbscan-1.1-4/dbscan/inst/doc/dbscan.Rnw | 8 dbscan-1.1-4/dbscan/inst/doc/dbscan.pdf |binary dbscan-1.1-4/dbscan/inst/doc/hdbscan.R | 2 dbscan-1.1-4/dbscan/inst/doc/hdbscan.Rmd | 2 dbscan-1.1-4/dbscan/inst/doc/hdbscan.html | 509 +++++++++++++--------- dbscan-1.1-4/dbscan/man/frNN.Rd | 2 dbscan-1.1-4/dbscan/man/kNNdist.Rd | 16 dbscan-1.1-4/dbscan/man/optics.Rd | 5 dbscan-1.1-4/dbscan/src/RcppExports.cpp | 218 ++++----- dbscan-1.1-4/dbscan/tests/testthat/test-hdbscan.R | 2 dbscan-1.1-4/dbscan/tests/testthat/test-kNNdist.R | 4 dbscan-1.1-4/dbscan/vignettes/dbscan.Rnw | 8 dbscan-1.1-4/dbscan/vignettes/dbscan.bib | 14 dbscan-1.1-4/dbscan/vignettes/hdbscan.Rmd | 2 28 files changed, 578 insertions(+), 425 deletions(-)
Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, SCORPIUS
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [ctb] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.3 dated 2019-05-27 and 1.0.4 dated 2019-08-05
DESCRIPTION | 14 +- MD5 | 28 ++--- NAMESPACE | 4 R/dummy_proofing.R | 16 +- R/package.R | 2 R/plotting.R | 137 ++++++++++++++++++------- R/trajectory_inference.R | 30 +++-- README.md |only inst/NEWS | 14 ++ inst/doc/ginhoux.html | 4 inst/doc/simulated-data.html | 4 man/draw_trajectory_heatmap.Rd | 23 ++-- man/draw_trajectory_plot.Rd | 20 +++ man/figures/README_infer_trajectory-1.png |binary man/figures/README_reduce_dimensionality-1.png |binary tests/testthat/test-sparse.R |only 16 files changed, 203 insertions(+), 93 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices (PND, PEM, PAND, PET, tauU,
baseline corrected tau), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, truncating,
rank transformation, and smoothing. An exporting function help to generate
html and latex tables in a publication friendly style. More details can be
found at <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre], Timo Lueke [aut]
Maintainer: Juergen Wilbert <jwilbert@uni-potsdam.de>
Diff between scan versions 0.20 dated 2016-10-14 and 0.40 dated 2019-08-05
scan-0.20/scan/R/makeSCDF.R |only scan-0.20/scan/R/makesingleSC.R |only scan-0.20/scan/R/power.test.R |only scan-0.20/scan/man/exampledata.Rd |only scan-0.20/scan/man/makeSCDF.Rd |only scan-0.20/scan/man/plotSC.Rd |only scan-0.20/scan/man/rSC.Rd |only scan-0.40/scan/DESCRIPTION | 35 scan-0.40/scan/MD5 | 158 ++-- scan-0.40/scan/NAMESPACE | 60 + scan-0.40/scan/R/autocorrSC.R | 86 +- scan-0.40/scan/R/corrected_tauSC.R |only scan-0.40/scan/R/deprecated_estimateSC.R |only scan-0.40/scan/R/deprecated_makesingleSC.R |only scan-0.40/scan/R/deprecated_power.testSC.R |only scan-0.40/scan/R/deprecated_rand.test.R |only scan-0.40/scan/R/describeSC.R | 240 +++--- scan-0.40/scan/R/estimate_design.R |only scan-0.40/scan/R/export.R |only scan-0.40/scan/R/fillmissingSC.R | 107 ++ scan-0.40/scan/R/hplm.R | 227 ++++-- scan-0.40/scan/R/inherit_roxygen_descriptions.R |only scan-0.40/scan/R/longSCDF.R |only scan-0.40/scan/R/mplm.R |only scan-0.40/scan/R/nap.R | 107 ++ scan-0.40/scan/R/outlierSC.R | 256 ++++-- scan-0.40/scan/R/overlapSC.R | 125 ++- scan-0.40/scan/R/pand.R | 215 +++-- scan-0.40/scan/R/pem.R | 126 ++- scan-0.40/scan/R/pet.R | 106 +- scan-0.40/scan/R/pkg-package.R |only scan-0.40/scan/R/plm.R | 431 ++++------- scan-0.40/scan/R/plotSC.R | 894 ++++++++++++++++-------- scan-0.40/scan/R/pnd.R | 62 + scan-0.40/scan/R/power_testSC.R |only scan-0.40/scan/R/print.sc.R | 520 ++++++++----- scan-0.40/scan/R/print.scdf.R |only scan-0.40/scan/R/private_SCprepare.R |only scan-0.40/scan/R/private_options.R |only scan-0.40/scan/R/private_regression.R |only scan-0.40/scan/R/private_utilities.R |only scan-0.40/scan/R/rSC.R | 462 ++++++++---- scan-0.40/scan/R/randSC.R | 426 +++++++---- scan-0.40/scan/R/rankSC.R |only scan-0.40/scan/R/rciSC.R | 162 +++- scan-0.40/scan/R/readSC.R | 131 ++- scan-0.40/scan/R/scaleSC.R |only scan-0.40/scan/R/scan-Data.R |only scan-0.40/scan/R/scan.R | 87 -- scan-0.40/scan/R/scdf-functions.R |only scan-0.40/scan/R/scdf.R |only scan-0.40/scan/R/scdf_attr.R |only scan-0.40/scan/R/shiftSC.R |only scan-0.40/scan/R/smoothSC.R | 94 +- scan-0.40/scan/R/style_plotSC.R |only scan-0.40/scan/R/summary.scdf.R |only scan-0.40/scan/R/tauUSC.R | 284 +++++-- scan-0.40/scan/R/trendSC.R | 148 ++- scan-0.40/scan/R/truncateSC.R | 75 +- scan-0.40/scan/R/writeSC.R | 47 + scan-0.40/scan/data/scan-Data.RData |binary scan-0.40/scan/man/Beretvas2008.Rd |only scan-0.40/scan/man/Subsetting.Rd |only scan-0.40/scan/man/as_scdf.Rd |only scan-0.40/scan/man/autocorrSC.Rd | 47 - scan-0.40/scan/man/c.scdf.Rd |only scan-0.40/scan/man/corrected_tauSC.Rd |only scan-0.40/scan/man/describeSC.Rd | 48 - scan-0.40/scan/man/dot-inheritParams.Rd |only scan-0.40/scan/man/estimateSC.Rd |only scan-0.40/scan/man/estimate_design.Rd |only scan-0.40/scan/man/export.Rd |only scan-0.40/scan/man/fillmissingSC.Rd | 71 + scan-0.40/scan/man/hplm.Rd | 121 ++- scan-0.40/scan/man/longSCDF.Rd | 58 + scan-0.40/scan/man/makesingleSC.Rd | 56 - scan-0.40/scan/man/mplm.Rd |only scan-0.40/scan/man/nap.Rd | 70 + scan-0.40/scan/man/outlierSC.Rd | 82 +- scan-0.40/scan/man/overlapSC.Rd | 69 + scan-0.40/scan/man/pand.Rd | 121 ++- scan-0.40/scan/man/pem.Rd | 85 +- scan-0.40/scan/man/pet.Rd | 79 +- scan-0.40/scan/man/plm.Rd | 130 ++- scan-0.40/scan/man/plot.scdf.Rd |only scan-0.40/scan/man/pnd.Rd | 50 - scan-0.40/scan/man/power.testSC.Rd | 188 +++-- scan-0.40/scan/man/power_testSC.Rd |only scan-0.40/scan/man/print.sc.Rd |only scan-0.40/scan/man/print.scdf.Rd |only scan-0.40/scan/man/rand.test.Rd |only scan-0.40/scan/man/randSC.Rd | 158 ++-- scan-0.40/scan/man/random.Rd |only scan-0.40/scan/man/rankSC.Rd |only scan-0.40/scan/man/rciSC.Rd | 97 +- scan-0.40/scan/man/readSC.Rd | 82 +- scan-0.40/scan/man/scaleSC.Rd |only scan-0.40/scan/man/scan-package.Rd | 23 scan-0.40/scan/man/scdf.Rd |only scan-0.40/scan/man/scdf_attr.Rd |only scan-0.40/scan/man/shiftSC.Rd |only scan-0.40/scan/man/smoothSC.Rd | 66 + scan-0.40/scan/man/style_plotSC.Rd |only scan-0.40/scan/man/summary.scdf.Rd |only scan-0.40/scan/man/tauUSC.Rd | 72 + scan-0.40/scan/man/trendSC.Rd | 70 + scan-0.40/scan/man/truncateSC.Rd | 53 - scan-0.40/scan/man/writeSC.Rd | 52 - 108 files changed, 5012 insertions(+), 2607 deletions(-)
Title: R Package for Designing and Analyzing Randomized Experiments
Description: Provides various statistical methods for
designing and analyzing randomized experiments. One functionality
of the package is the implementation of randomized-block and
matched-pair designs based on possibly multivariate pre-treatment
covariates. The package also provides the tools to analyze various
randomized experiments including cluster randomized experiments,
two-stage randomized experiments, randomized experiments with
noncompliance, and randomized experiments with missing data.
Author: Kosuke Imai [aut, cre],
Zhichao Jiang [aut],
Michael Li [aut]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between experiment versions 1.1-4 dated 2018-04-30 and 1.2.0 dated 2019-08-05
DESCRIPTION | 20 +++++++++++--------- MD5 | 20 +++++++++++++------- NAMESPACE | 3 +++ R/ATEnocov.R | 2 +- R/AUPEC.R |only R/PAPD.R |only R/PAPE.R |only man/ATEcluster.Rd | 4 ++-- man/AUPEC.Rd |only man/NoncompLI.Rd | 14 +++++++------- man/PAPD.Rd |only man/PAPE.Rd |only man/randomize.Rd | 5 +++-- man/seguro.Rd | 2 +- 14 files changed, 41 insertions(+), 29 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 2.2.1 dated 2019-06-05 and 2.3.0 dated 2019-08-05
DESCRIPTION | 8 - MD5 | 68 ++++++----- NAMESPACE | 5 NEWS.md | 13 ++ R/data.R | 51 ++++---- R/f_copulacorrection_interface.R | 2 R/f_copulacorrection_linearmodel.R | 22 +++ R/f_latentIV.R | 2 R/f_multilevelIV.R | 2 R/f_s3_multilevel.R | 60 ++++++++++ R/f_s3_rendocopulacorrection.R | 54 +++++++++ R/f_s3_rendoivreg.R | 46 +++++++ R/f_s3_rendolatentIV.R | 46 +++++++ inst/doc/REndo-introduction.pdf |binary man/copulaCorrection.Rd | 2 man/dataCopCont.Rd | 4 man/dataCopCont2.Rd | 4 man/dataCopDis.Rd | 4 man/dataCopDis2.Rd | 4 man/dataCopDisCont.Rd | 4 man/dataHetIV.Rd | 4 man/dataHigherMoments.Rd | 14 +- man/dataLatentIV.Rd | 4 man/dataMultilevelIV.Rd | 2 man/latentIV.Rd | 2 man/multilevelIV.Rd | 2 man/predict.rendo.copula.correction.Rd |only man/predict.rendo.ivreg.Rd |only man/predict.rendo.latent.IV.Rd |only man/predict.rendo.multilevel.Rd |only man/summary.rendo.multilevel.Rd | 2 tests/testthat/test_correctness_copulacorrections.R | 118 ++++++++++++++++++++ tests/testthat/test_correctness_heterrors.R | 51 ++++++++ tests/testthat/test_correctness_highermoments.R | 51 ++++++++ tests/testthat/test_correctness_latentIV.R | 34 +++++ tests/testthat/test_correctness_multilevel.R | 61 ++++++++++ vignettes/REndo-introduction.Rmd | 4 37 files changed, 655 insertions(+), 95 deletions(-)
Title: Multivariate, Locally Stationary Wavelet Process Estimation
Description: Tools for analysing multivariate time series with wavelets. This includes: simulation of a multivariate locally stationary wavelet (mvLSW) process from a multivariate evolutionary wavelet spectrum (mvEWS); estimation of the mvEWS, local coherence and local partial coherence. See Park, Eckley and Ombao (2014) <doi:10.1109/TSP.2014.2343937> for details.
Author: Simon Taylor [aut, cre],
Tim Park [aut],
Idris Eckley [ths],
Rebecca Killick [ctb]
Maintainer: Simon Taylor <s.taylor2@lancaster.ac.uk>
Diff between mvLSW versions 1.2.2 dated 2018-10-24 and 1.2.3 dated 2019-08-05
DESCRIPTION | 8 - MD5 | 30 ++-- NEWS | 42 +++--- R/mvLSW.R | 4 inst/CITATION | 56 ++++++--- man/ApxCI.Rd | 5 man/AutocorrIP.Rd | 5 man/Spectrum2Transfer.Rd | 157 +++++++++++++------------- man/as.mvLSW.Rd | 240 ++++++++++++++++++++------------------- man/coherence.Rd | 173 ++++++++++++++-------------- man/mvEWS.rd | 283 +++++++++++++++++++++++------------------------ man/mvLSW.Rd | 9 + man/plot.mvLSW.Rd | 245 ++++++++++++++++++++-------------------- man/rmvLSW.Rd | 210 +++++++++++++++++----------------- man/summary.mvLSW.Rd | 116 ++++++++++--------- man/varEWS.Rd | 239 ++++++++++++++++++++------------------- 16 files changed, 956 insertions(+), 866 deletions(-)
Title: Pipeline for GWAS Using MLMM
Description: Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjálmsson BJ et al. (2012) <doi:10.1038/ng.2314>. The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC and p-value threshold, estimation of the effects of the SNPs in the selected model and graphical functions.
Author: Fanny Bonnafous [aut], Alexandra Duhnen [aut], Louise Gody [aut], Olivier Guillaume[aut, cre], Brigitte Mangin [aut], Prune Pegot-Espagnet [aut], Vincent Segura [aut], Bjarni J. Vilhjalmsson [aut], Clement Mabire [aut], Timothee Flutre [aut]
Maintainer: Clement Mabire <clement.mabire@inra.fr>
Diff between mlmm.gwas versions 1.0.5 dated 2019-05-22 and 1.0.6 dated 2019-08-05
DESCRIPTION | 10 MD5 | 22 - NEWS | 13 R/eBIC_allmodels_withlmekin_ML.r | 594 +++++++++++++++++++-------------------- R/fromeBICtoEstimation.r | 197 ++++++------ R/mlmm_allmodels_withsommer.r | 2 R/run_entire_gwas_pipeline.R | 6 R/threshold_allmodels.r | 2 build/vignette.rds |binary inst/doc/gwas-manual.html | 152 ++++----- man/eBIC_allmodels.Rd | 4 man/run_entire_gwas_pipeline.Rd | 4 12 files changed, 505 insertions(+), 501 deletions(-)
Title: Creating Groups from Data
Description: Methods for dividing data into groups.
Create balanced partitions and cross-validation folds.
Perform time series windowing and general grouping and splitting of data.
Balance existing groups with up- and downsampling.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between groupdata2 versions 1.1.1 dated 2019-07-05 and 1.1.2 dated 2019-08-05
DESCRIPTION | 8 - MD5 | 76 +++++++------- NAMESPACE | 2 NEWS.md | 11 ++ R/all_groups_identical.R |only R/create_num_col_groups.R | 4 R/differs_from_previous.R | 1 R/find_missing_starts.R | 16 ++ R/fold.R | 48 +++++--- R/helpers.R | 80 +++++++++----- R/primes_remainder.R | 1 R/sampling.R | 64 ++++++++--- R/sampling_methods.R | 48 +++++--- README.md | 75 ++++++++------ inst/doc/automatic_groups_with_groupdata2.html | 10 + inst/doc/cross-validation_with_groupdata2.html | 10 + inst/doc/description_of_groupdata2.html | 10 + inst/doc/introduction_to_groupdata2.html | 8 + inst/doc/time_series_with_groupdata2.html | 10 + man/all_groups_identical.Rd |only man/fold.Rd | 6 - man/group.Rd | 6 - man/group_factor.Rd | 6 - man/partition.Rd | 6 - man/splt.Rd | 6 - tests/testthat/test_all_groups_identical.R |only tests/testthat/test_balance.R | 66 ++++++++---- tests/testthat/test_create_n_primes.R | 2 tests/testthat/test_differs_from_previous.R | 16 ++ tests/testthat/test_find_missing_starts.R |only tests/testthat/test_find_starts.R | 6 - tests/testthat/test_fold.R | 107 ++++++++++++++------ tests/testthat/test_group.R | 14 +- tests/testthat/test_grouping_factor.R | 49 +++++---- tests/testthat/test_numerically_balanced_grouping.R | 69 +++++------- tests/testthat/test_partition.R | 54 +++++----- tests/testthat/test_primes_remainder.R | 1 tests/testthat/test_rearrange.R | 71 +++++++++++++ tests/testthat/test_sampling_methods.R | 46 ++++---- tests/testthat/test_splt.R | 9 + tests/testthat/test_utilities.R | 6 - 41 files changed, 669 insertions(+), 359 deletions(-)
Title: Subtests Using Algorithmic Rummaging Techniques
Description: Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling.
Schultze (2017) <doi:10.17169/refubium-622>.
Author: Martin Schultze [aut, cre]
Maintainer: Martin Schultze <schultze@psych.uni-frankfurt.de>
Diff between stuart versions 0.7.3 dated 2018-09-17 and 0.8.0 dated 2019-08-05
DESCRIPTION | 14 ++-- MD5 | 58 ++++++++-------- R/bf.cycle.R | 3 R/bruteforce.R | 2 R/combinations.R | 1 R/crossvalidate.Mplus.R | 145 ++++++++++++++++++++++-------------------- R/crossvalidate.R | 39 ++--------- R/crossvalidate.lavaan.R | 123 ++++++++++++++++++++++++----------- R/data.prep.R | 2 R/fitness.R | 15 ++++ R/invariance.implementation.R | 69 ++++++++++++++++++- R/mmas.R | 2 R/run.Mplus.R | 124 +++++++++++++++++++++-------------- R/run.lavaan.R | 63 ++++++++++++++---- R/sanitycheck.R | 16 +++- R/stuart.bruteforce.R | 10 ++ R/stuart.gene.R | 10 ++ R/stuart.mmas.R | 15 ++++ R/stuart.randomsamples.R | 10 ++ man/bruteforce.Rd | 16 ++-- man/combinations.Rd | 4 - man/crossvalidate.Rd | 23 ++---- man/fairplayer.Rd | 5 - man/gene.Rd | 22 ++---- man/heuristics.Rd | 4 - man/holdout.Rd | 4 - man/mmas.Rd | 25 +++---- man/randomsamples.Rd | 17 ++-- man/stuart-package.Rd | 2 man/sups.Rd | 5 - 30 files changed, 518 insertions(+), 330 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Also contains two-stage binomial modelling that can do pairwise odds-ratio
dependence modelling based marginal logistic regression models. This is an
alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.2.5 dated 2018-11-20 and 1.2.6 dated 2019-08-05
mets-1.2.5/mets/data/base1cumhaz.txt.gz |only mets-1.2.5/mets/data/base4cumhaz.txt.gz |only mets-1.2.5/mets/data/drcumhaz.txt.gz |only mets-1.2.5/mets/data/migr.txt.gz |only mets-1.2.5/mets/data/multcif.txt.gz |only mets-1.2.5/mets/data/np.txt.gz |only mets-1.2.5/mets/data/twinbmi.txt.gz |only mets-1.2.5/mets/data/twinstut.txt.gz |only mets-1.2.5/mets/inst/doc/index.html |only mets-1.2.5/mets/src/mvt.f |only mets-1.2.5/mets/src/tvpackAux.c |only mets-1.2.6/mets/DESCRIPTION | 16 mets-1.2.6/mets/MD5 | 182 mets-1.2.6/mets/NAMESPACE | 19 mets-1.2.6/mets/NEWS | 14 mets-1.2.6/mets/R/cifreg.R |only mets-1.2.6/mets/R/discrete-survival-haplo.r |only mets-1.2.6/mets/R/dreg.R | 14 mets-1.2.6/mets/R/dsort.R | 25 mets-1.2.6/mets/R/gof-phreg.R | 74 mets-1.2.6/mets/R/mets-package.R | 29 mets-1.2.6/mets/R/mutinomialreg.R |only mets-1.2.6/mets/R/pch.R |only mets-1.2.6/mets/R/phreg.R | 226 mets-1.2.6/mets/R/recurrent.marginal.R | 631 + mets-1.2.6/mets/R/sim.clayton.oakes.R | 31 mets-1.2.6/mets/R/twostage.R | 1858 ++--- mets-1.2.6/mets/R/wild-phreg.R |only mets-1.2.6/mets/build/vignette.rds |binary mets-1.2.6/mets/data/base1cumhaz.txt.xz |only mets-1.2.6/mets/data/base4cumhaz.txt.xz |only mets-1.2.6/mets/data/datalist | 3 mets-1.2.6/mets/data/dermalridges.rda |binary mets-1.2.6/mets/data/dermalridgesMZ.rda |binary mets-1.2.6/mets/data/drcumhaz.txt.xz |only mets-1.2.6/mets/data/hHaplos.rda |only mets-1.2.6/mets/data/hapfreqs.rda |only mets-1.2.6/mets/data/haploX.rda |only mets-1.2.6/mets/data/mena.rda |binary mets-1.2.6/mets/data/migr.txt.xz |only mets-1.2.6/mets/data/multcif.txt.xz |only mets-1.2.6/mets/data/np.txt.xz |only mets-1.2.6/mets/data/prt.rda |binary mets-1.2.6/mets/data/twinbmi.txt.xz |only mets-1.2.6/mets/data/twinstut.txt.xz |only mets-1.2.6/mets/inst/doc/basic-dutils.pdf |binary mets-1.2.6/mets/inst/doc/binomial-case-control-ascertainment.pdf |binary mets-1.2.6/mets/inst/doc/binomial-family.pdf |binary mets-1.2.6/mets/inst/doc/binomial-twin.pdf |binary mets-1.2.6/mets/inst/doc/competing.pdf |binary mets-1.2.6/mets/inst/doc/marginal-cox.pdf |binary mets-1.2.6/mets/inst/doc/quantitative-twin.pdf |binary mets-1.2.6/mets/inst/doc/recurrent-events.pdf |binary mets-1.2.6/mets/inst/doc/twostage-survival-case-control.pdf |binary mets-1.2.6/mets/inst/doc/twostage-survival.pdf |binary mets-1.2.6/mets/inst/include/mets_RcppExports.h | 42 mets-1.2.6/mets/inst/misc/pairwise-twostage.r | 33 mets-1.2.6/mets/man/Bootphreg.Rd |only mets-1.2.6/mets/man/basehazplot.phreg.Rd | 7 mets-1.2.6/mets/man/cifreg.Rd |only mets-1.2.6/mets/man/count.history.Rd | 2 mets-1.2.6/mets/man/dreg.Rd | 5 mets-1.2.6/mets/man/dsort.Rd | 1 mets-1.2.6/mets/man/ghaplos.Rd |only mets-1.2.6/mets/man/gof.phreg.Rd | 2 mets-1.2.6/mets/man/gofG.phreg.Rd | 2 mets-1.2.6/mets/man/gofM.phreg.Rd | 23 mets-1.2.6/mets/man/gofZ.phreg.Rd |only mets-1.2.6/mets/man/hapfreqs.Rd |only mets-1.2.6/mets/man/haplo.surv.discrete.Rd |only mets-1.2.6/mets/man/haploX.Rd |only mets-1.2.6/mets/man/logitSurv.Rd | 2 mets-1.2.6/mets/man/mlogit.Rd |only mets-1.2.6/mets/man/predict.phreg.Rd | 1 mets-1.2.6/mets/man/rpch.Rd |only mets-1.2.6/mets/man/simClaytonOakes.Rd | 1 mets-1.2.6/mets/man/simMultistate.Rd |only mets-1.2.6/mets/man/simRecurrent.Rd | 1 mets-1.2.6/mets/man/simRecurrentII.Rd | 1 mets-1.2.6/mets/man/simRecurrentTS.Rd |only mets-1.2.6/mets/man/survival.twostage.Rd | 22 mets-1.2.6/mets/src/RcppExports.cpp | 76 mets-1.2.6/mets/src/aalenfrailty.cpp | 2 mets-1.2.6/mets/src/binomial-twostage.cpp | 2 mets-1.2.6/mets/src/fastcox.cpp | 3216 +++++----- mets-1.2.6/mets/src/init.c | 12 mets-1.2.6/mets/src/mvn.cpp | 64 mets-1.2.6/mets/src/mvn.h | 22 mets-1.2.6/mets/src/pch.cpp |only mets-1.2.6/mets/src/randomF77.c | 11 mets-1.2.6/mets/src/survival-twostage.cpp | 32 mets-1.2.6/mets/vignettes/basic-dutils.org | 26 mets-1.2.6/mets/vignettes/competing.org | 607 - mets-1.2.6/mets/vignettes/index.html |only mets-1.2.6/mets/vignettes/marginal-cox.org | 160 mets-1.2.6/mets/vignettes/mets.bib | 265 mets-1.2.6/mets/vignettes/quantitative-twin.org | 42 mets-1.2.6/mets/vignettes/rec1.jpg |binary mets-1.2.6/mets/vignettes/rec2.jpg |binary mets-1.2.6/mets/vignettes/rec3.jpg |binary mets-1.2.6/mets/vignettes/rec4.jpg |binary mets-1.2.6/mets/vignettes/rec4Bi.jpg |binary mets-1.2.6/mets/vignettes/rec4MV.jpg |binary mets-1.2.6/mets/vignettes/rec5.jpg |binary mets-1.2.6/mets/vignettes/rec6.jpg |binary mets-1.2.6/mets/vignettes/rec7.jpg |binary mets-1.2.6/mets/vignettes/recurrent-events.org | 429 - mets-1.2.6/mets/vignettes/robcox1.jpg |binary mets-1.2.6/mets/vignettes/robcox2.jpg |binary mets-1.2.6/mets/vignettes/robgofcox1.jpg |binary mets-1.2.6/mets/vignettes/scatter1.jpg |binary mets-1.2.6/mets/vignettes/scatter2.jpg |binary 112 files changed, 4428 insertions(+), 3805 deletions(-)
Title: Tools and GUI for Analyzing Data of Just Finance and
Econometrics
Description: Support the analysis of global assets selection and portfolio backtesting, we also enhance the computation of some performance ratios of 'PerformanceAnalytics'.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between JFE versions 2.1.1 dated 2019-04-09 and 2.1.3 dated 2019-08-05
DESCRIPTION | 14 +++++++------- MD5 | 13 ++++++++----- R/05PortoflioMore.R |only R/PerformanceIndex.R | 4 ++-- man/ActivePremium.Rd | 10 +++++----- man/JFE.Rd | 2 +- man/data-sets.Rd | 8 ++------ man/riskOptimalPortfolio.Rd |only man/riskParityPortfolio.Rd |only 9 files changed, 25 insertions(+), 26 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by
HTTP verbs (GET(), POST(), etc). Configuration functions make it easy
to control additional request components (authenticate(),
add_headers() and so on).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr versions 1.4.0 dated 2018-12-11 and 1.4.1 dated 2019-08-05
DESCRIPTION | 12 MD5 | 30 - NEWS.md | 18 + R/http-post.r | 10 R/request.R | 3 R/response-status.r | 5 R/retry.R | 6 build/vignette.rds |binary demo/oauth2-linkedin.r | 6 inst/doc/api-packages.html | 581 ++++++++++++++++++----------------- inst/doc/quickstart.html | 526 +++++++++++++++++-------------- inst/doc/secrets.html | 173 ++++++---- man/POST.Rd | 8 man/httr-package.Rd | 1 tests/testthat/test-http-condition.R | 4 tests/testthat/test-retry.R | 7 16 files changed, 769 insertions(+), 621 deletions(-)
Title: '2D and 3D plots of linear mathematical programming models'
Description: Make 2D and 3D plots of the polytope of a LP, ILP or MILP problem, including
integer points and iso profit curve. Can also make a plot of the bi-objective
criterion space.
Author: Lars Relund [aut, cre]
Maintainer: Lars Relund <lars@relund.dk>
Diff between gMOIP versions 1.1.0 dated 2017-02-20 and 1.3.0 dated 2019-08-05
gMOIP-1.1.0/gMOIP/inst/examples/examples.R |only gMOIP-1.1.0/gMOIP/man/plotCriterion.Rd |only gMOIP-1.3.0/gMOIP/DESCRIPTION | 22 gMOIP-1.3.0/gMOIP/MD5 | 50 gMOIP-1.3.0/gMOIP/NAMESPACE | 6 gMOIP-1.3.0/gMOIP/NEWS.md |only gMOIP-1.3.0/gMOIP/R/functions.R | 1327 +++++++++++++++----- gMOIP-1.3.0/gMOIP/R/package_doc.R | 11 gMOIP-1.3.0/gMOIP/build |only gMOIP-1.3.0/gMOIP/inst/doc |only gMOIP-1.3.0/gMOIP/inst/examples/3d_interactive.Rmd |only gMOIP-1.3.0/gMOIP/inst/examples/3d_interactive.html |only gMOIP-1.3.0/gMOIP/inst/examples/ex_criterion.R |only gMOIP-1.3.0/gMOIP/inst/examples/ex_polytope.R |only gMOIP-1.3.0/gMOIP/inst/examples/old_examples.R |only gMOIP-1.3.0/gMOIP/man/cornerPoints.Rd | 66 gMOIP-1.3.0/gMOIP/man/cornerPointsCont.Rd |only gMOIP-1.3.0/gMOIP/man/criterionPoints.Rd | 78 - gMOIP-1.3.0/gMOIP/man/df2String.Rd |only gMOIP-1.3.0/gMOIP/man/gMOIP.Rd | 58 gMOIP-1.3.0/gMOIP/man/hullSegment.Rd |only gMOIP-1.3.0/gMOIP/man/inHull.Rd |only gMOIP-1.3.0/gMOIP/man/integerPoints.Rd | 68 - gMOIP-1.3.0/gMOIP/man/loadView.Rd |only gMOIP-1.3.0/gMOIP/man/mergeLists.Rd |only gMOIP-1.3.0/gMOIP/man/plotCriterion2D.Rd |only gMOIP-1.3.0/gMOIP/man/plotPolytope.Rd | 391 +++++ gMOIP-1.3.0/gMOIP/man/plotPolytope2D.Rd |only gMOIP-1.3.0/gMOIP/man/plotPolytope3D.Rd |only gMOIP-1.3.0/gMOIP/man/saveView.Rd |only gMOIP-1.3.0/gMOIP/man/slices.Rd |only gMOIP-1.3.0/gMOIP/vignettes |only 32 files changed, 1482 insertions(+), 595 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression models and get relevant evaluation
metrics in a tidy format. Validate the best model on a test set and compare it to a baseline evaluation.
Currently supports Gaussian and binomial regression.
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Benjamin Hugh Zachariae [aut]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 0.1.1 dated 2019-07-20 and 0.1.2 dated 2019-08-05
cvms-0.1.1/cvms/vignettes/man/figures/README-unnamed-chunk-15-1.png |only cvms-0.1.1/cvms/vignettes/man/figures/README-unnamed-chunk-15-2.png |only cvms-0.1.1/cvms/vignettes/man/figures/README-unnamed-chunk-15-3.png |only cvms-0.1.1/cvms/vignettes/man/figures/README-unnamed-chunk-15-4.png |only cvms-0.1.1/cvms/vignettes/man/figures/README-unnamed-chunk-16-1.png |only cvms-0.1.2/cvms/DESCRIPTION | 12 cvms-0.1.2/cvms/MD5 | 64 +-- cvms-0.1.2/cvms/NEWS.md | 14 cvms-0.1.2/cvms/R/baseline.R | 13 cvms-0.1.2/cvms/R/baseline_binomial.R | 73 ++- cvms-0.1.2/cvms/R/baseline_gaussian.R | 48 +- cvms-0.1.2/cvms/R/basics_cross_validate_list.R | 37 + cvms-0.1.2/cvms/R/basics_fit_model.R | 12 cvms-0.1.2/cvms/R/basics_run_model_fitting.R | 6 cvms-0.1.2/cvms/R/basics_update_model_specifics.R | 4 cvms-0.1.2/cvms/R/basics_validate_list.R | 25 - cvms-0.1.2/cvms/R/binomial_classification_eval.R | 22 - cvms-0.1.2/cvms/R/combine_predictors_prepare_args.R | 6 cvms-0.1.2/cvms/R/cross_validate.R | 2 cvms-0.1.2/cvms/R/helpers.R | 83 ++++ cvms-0.1.2/cvms/R/linear_regression_eval.R | 11 cvms-0.1.2/cvms/README.md | 63 +-- cvms-0.1.2/cvms/inst/doc/Introduction_to_cvms.R | 12 cvms-0.1.2/cvms/inst/doc/Introduction_to_cvms.Rmd | 12 cvms-0.1.2/cvms/inst/doc/Introduction_to_cvms.html | 30 - cvms-0.1.2/cvms/man/cross_validate.Rd | 2 cvms-0.1.2/cvms/man/validate.Rd | 2 cvms-0.1.2/cvms/tests/testthat/test_baseline.R | 107 +++++ cvms-0.1.2/cvms/tests/testthat/test_combine_predictors.R | 67 +++ cvms-0.1.2/cvms/tests/testthat/test_cross_validate.R | 196 +++++++++- cvms-0.1.2/cvms/tests/testthat/test_helpers.R | 6 cvms-0.1.2/cvms/tests/testthat/test_validate.R | 71 +++ cvms-0.1.2/cvms/vignettes/Introduction_to_cvms.Rmd | 12 cvms-0.1.2/cvms/vignettes/man/figures/vignette_intro-unnamed-chunk-15-1.png |only cvms-0.1.2/cvms/vignettes/man/figures/vignette_intro-unnamed-chunk-15-2.png |only cvms-0.1.2/cvms/vignettes/man/figures/vignette_intro-unnamed-chunk-15-3.png |only cvms-0.1.2/cvms/vignettes/man/figures/vignette_intro-unnamed-chunk-15-4.png |only cvms-0.1.2/cvms/vignettes/man/figures/vignette_intro-unnamed-chunk-16-1.png |only 38 files changed, 803 insertions(+), 209 deletions(-)
Title: Working with Car Parking Data for Bath and North East Somerset
Description: Contains functions for importing and working with the BANES car parking
records and other related datasets. For the full version of the package, including
all datasets, see the repo at <https://github.com/owenjonesuob/BANEScarparking>.
The original dataset of parking records can be found at
<https://data.bathhacked.org/Government-and-Society/BANES-Historic-Car-Park-Occupancy/x29s-cczc>.
Author: Owen Jones [aut, cre],
Ryan Kenning [aut, ctb],
Nick Howlett [ctb]
Maintainer: Owen Jones <joneso21164@gmail.com>
Diff between BANEScarparkinglite versions 0.1.2 dated 2018-06-30 and 0.1.3 dated 2019-08-05
DESCRIPTION | 21 +-- MD5 | 12 - NEWS.md | 14 ++ R/add_records.R | 200 +++++++++++++++++--------------- R/web_scraping.R | 6 README.md | 4 inst/tests/testthat/test-web_scraping.R | 23 +-- 7 files changed, 158 insertions(+), 122 deletions(-)
More information about BANEScarparkinglite at CRAN
Permanent link
More information about wyz.code.testthat at CRAN
Permanent link
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages. These
include e.g. measures like r-squared, intraclass correlation coefficient
(Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>),
root mean squared error or functions to check models for overdispersion,
singularity or zero-inflation and more. Functions apply to a large variety of
regression models, including generalized linear models, mixed effects models
and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.2.0 dated 2019-06-04 and 0.3.0 dated 2019-08-05
performance-0.2.0/performance/man/r2_kl.Rd |only performance-0.2.0/performance/tests/testthat/test-r2_kl.R |only performance-0.3.0/performance/DESCRIPTION | 17 - performance-0.3.0/performance/MD5 | 123 +++++----- performance-0.3.0/performance/NAMESPACE | 20 + performance-0.3.0/performance/NEWS.md | 35 ++ performance-0.3.0/performance/R/binned_residuals.R | 36 ++ performance-0.3.0/performance/R/check_autocorrelation.R | 2 performance-0.3.0/performance/R/check_collinearity.R | 44 ++- performance-0.3.0/performance/R/check_convergence.R | 20 + performance-0.3.0/performance/R/check_distribution.R | 104 ++++++-- performance-0.3.0/performance/R/check_heteroscedasticity.R | 11 performance-0.3.0/performance/R/check_homogeneity.R |only performance-0.3.0/performance/R/check_model.R | 25 +- performance-0.3.0/performance/R/check_model_diagnostics.R | 94 ++++++- performance-0.3.0/performance/R/check_normality.R | 31 ++ performance-0.3.0/performance/R/check_outliers.R | 123 ++++++++-- performance-0.3.0/performance/R/check_overdispersion.R | 39 +-- performance-0.3.0/performance/R/check_singularity.R | 2 performance-0.3.0/performance/R/check_zeroinflation.R | 11 performance-0.3.0/performance/R/compare_performance.R |only performance-0.3.0/performance/R/helpers.R | 20 + performance-0.3.0/performance/R/icc.R | 31 +- performance-0.3.0/performance/R/model_performance.R | 55 ---- performance-0.3.0/performance/R/model_performance.bayesian.R | 21 + performance-0.3.0/performance/R/model_performance.lavaan.R |only performance-0.3.0/performance/R/model_performance.lm.R | 27 +- performance-0.3.0/performance/R/performance_accuracy.R | 16 - performance-0.3.0/performance/R/performance_mse.R | 6 performance-0.3.0/performance/R/performance_rmse.R | 2 performance-0.3.0/performance/R/performance_roc.R | 4 performance-0.3.0/performance/R/performance_score.R | 10 performance-0.3.0/performance/R/plot-methods.R | 40 +++ performance-0.3.0/performance/R/print-methods.R | 61 +++- performance-0.3.0/performance/R/r2.R | 12 performance-0.3.0/performance/R/r2_bayes.R | 13 - performance-0.3.0/performance/R/r2_kl.R | 6 performance-0.3.0/performance/R/r2_nakagawa.R | 15 - performance-0.3.0/performance/R/skewness_kurtosis.R | 5 performance-0.3.0/performance/R/sysdata.rda |binary performance-0.3.0/performance/README.md | 100 ++++---- performance-0.3.0/performance/build/partial.rdb |binary performance-0.3.0/performance/man/binned_residuals.Rd | 16 + performance-0.3.0/performance/man/check_collinearity.Rd | 10 performance-0.3.0/performance/man/check_convergence.Rd | 4 performance-0.3.0/performance/man/check_distribution.Rd | 21 + performance-0.3.0/performance/man/check_heteroscedasticity.Rd | 4 performance-0.3.0/performance/man/check_homogeneity.Rd |only performance-0.3.0/performance/man/check_model.Rd | 9 performance-0.3.0/performance/man/check_normality.Rd | 11 performance-0.3.0/performance/man/check_outliers.Rd | 63 ++++- performance-0.3.0/performance/man/check_overdispersion.Rd | 39 +-- performance-0.3.0/performance/man/check_singularity.Rd | 2 performance-0.3.0/performance/man/icc.Rd | 31 +- performance-0.3.0/performance/man/model_performance.Rd | 29 +- performance-0.3.0/performance/man/model_performance.lavaan.Rd |only performance-0.3.0/performance/man/model_performance.stanreg.Rd | 15 + performance-0.3.0/performance/man/performance_accuracy.Rd | 6 performance-0.3.0/performance/man/performance_mse.Rd | 6 performance-0.3.0/performance/man/performance_rmse.Rd | 2 performance-0.3.0/performance/man/r2.Rd | 2 performance-0.3.0/performance/man/r2_bayes.Rd | 7 performance-0.3.0/performance/man/r2_kullback.Rd |only performance-0.3.0/performance/tests/testthat/test-check_singularity.R | 4 performance-0.3.0/performance/tests/testthat/test-coxph.R | 17 - performance-0.3.0/performance/tests/testthat/test-icc.R | 43 --- performance-0.3.0/performance/tests/testthat/test-r2_kullback.R |only 67 files changed, 1035 insertions(+), 487 deletions(-)
Title: Statistical Package for Analysis Related Cleaning Support
Description: To clean and analyze hospital data, and generate sets for statistical modeling.
Author: Wangjian Zhang, Zhicheng Du, Ziqiang Lin, Jijin Yao, Yanan Jin, Wayne R. Lawrence, Yuantao Hao
Maintainer: Wangjian Zhang <wzhang27@albany.edu>
Diff between rSPARCS versions 0.0.4 dated 2019-02-25 and 0.0.5 dated 2019-08-05
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ NAMESPACE | 1 R/DBFgeocode.R | 6 ++--- R/FIPS.name.R | 59 ++++++++++++++++++------------------------------------ R/desc.comp.R | 3 +- man/DBFgeocode.Rd | 20 ++++++++---------- man/FIPS.name.Rd | 44 +++++++++++++++------------------------- 8 files changed, 62 insertions(+), 93 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.4-3 dated 2019-04-24 and 0.5-1 dated 2019-08-05
ChangeLog | 85 +++++++++++++++++++++++++++ DESCRIPTION | 11 +-- MD5 | 32 +++++----- NAMESPACE | 3 R/AAA.R | 13 ++++ R/rgeos_topology.R | 18 +++++ R/rgeos_topology_binary.R | 119 +++++++++++++++++++++++++++++--------- configure | 18 ++--- inst/ChangeLog | 85 +++++++++++++++++++++++++++ inst/SVN_VERSION | 2 man/topo-bin-gDifference.Rd | 4 - man/topo-bin-gIntersection.Rd | 10 +-- man/topo-bin-gSymdifference.Rd | 4 - man/topo-bin-gUnion.Rd | 8 +- man/utility-functions.Rd | 11 ++- src/rgeos_R2geos.c | 2 tests/leak_by_exception.Rout.save | 30 ++++++++- 17 files changed, 374 insertions(+), 81 deletions(-)
Title: A Biomarker Validation Approach for Classification and
Predicting Survival Using Metabolomics Signature
Description: An approach to identifies metabolic biomarker signature for metabolic data by discovering predictive metabolite for predicting survival and classifying patients into risk groups.
Classifiers are constructed as a linear combination of predictive/important metabolites, prognostic factors and treatment effects if necessary.
Several methods were implemented to reduce the metabolomics matrix such as the principle component analysis of Wold Svante et al. (1987) <doi:10.1016/0169-7439(87)80084-9> ,
the LASSO method by Robert Tibshirani (1998) <doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3>, the
elastic net approach by Hui Zou and Trevor Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Sensitivity analysis on the quantile used for the classification can also be accessed to check the deviation of the classification group based on the quantile specified.
Large scale cross validation can be performed in order to investigate the mostly selected predictive metabolites and for internal validation. During the evaluation process, validation is accessed using the hazard ratios (HR) distribution of the test set and inference is mainly based on resampling and permutations technique.
Author: Olajumoke Evangelina Owokotomo [aut, cre],
Ziv Shkedy [aut]
Maintainer: Olajumoke Evangelina Owokotomo <olajumoke.owokotomo@uhasselt.be>
Diff between MetabolicSurv versions 1.0.0 dated 2019-01-30 and 1.1.0 dated 2019-08-05
DESCRIPTION | 6 MD5 | 86 ++++++------ NAMESPACE | 90 ++++++------- NEWS.md | 12 - R/CVPcaPls.R | 2 R/Majorityvotes.R | 2 R/MetFreq.R | 136 ++++++++----------- R/cvle-class.R | 62 ++++----- R/cvmm-class.R | 10 - R/cvmv-class.R | 16 +- R/cvpp-class.R | 7 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/MetabolicSurv.R | 12 - inst/doc/MetabolicSurv.Rmd | 50 +++---- inst/doc/MetabolicSurv.html | 303 +++++++++++++++++++++++++++++++++++--------- man/CVLasoelacox.Rd | 176 ++++++++++++------------- man/CVMajorityvotes.Rd | 134 +++++++++---------- man/CVMetSpecificCoxPh.Rd | 144 ++++++++++---------- man/CVPcaPls.Rd | 148 ++++++++++----------- man/CVSim.Rd | 120 ++++++++--------- man/DataHR.Rd | 58 ++++---- man/DistHR.Rd | 138 ++++++++++---------- man/EstimateHR.Rd | 104 +++++++-------- man/Icvlasoel.Rd | 162 +++++++++++------------ man/Lasoelacox.Rd | 162 +++++++++++------------ man/MSData.Rd | 96 ++++++------- man/MSpecificCoxPh.Rd | 134 +++++++++---------- man/Majorityvotes.Rd | 134 +++++++++---------- man/MetFreq.Rd | 104 +++++++-------- man/MetabolicSurv.Rd | 54 +++---- man/QuantileAnalysis.Rd | 144 ++++++++++---------- man/SIMet.Rd | 142 ++++++++++---------- man/SurvPcaClass.Rd | 152 +++++++++++----------- man/SurvPlsClass.Rd | 152 +++++++++++----------- man/cvle-class.Rd | 162 +++++++++++------------ man/cvmm-class.Rd | 162 +++++++++++------------ man/cvmv-class.Rd | 140 ++++++++++---------- man/cvpp-class.Rd | 140 ++++++++++---------- man/cvsim-class.Rd | 152 +++++++++++----------- man/fcv-class.Rd | 158 +++++++++++----------- man/ms-class.Rd | 148 ++++++++++----------- man/perm-class.Rd | 146 ++++++++++----------- vignettes/MetabolicSurv.Rmd | 50 +++---- 44 files changed, 2336 insertions(+), 2174 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 2.7 dated 2019-06-06 and 3.0 dated 2019-08-05
DESCRIPTION | 8 MD5 | 110 +++--- NAMESPACE | 2 R/UPb.R | 563 ++++++++++++++++---------------- R/age.R | 62 ++- R/agespectrum.R | 45 +- R/cad.R | 29 + R/central.R | 65 +-- R/ci.R | 4 R/commonPb.R | 342 +++++++++++++++---- R/concordia.R | 279 ++++++++------- R/constants.R | 98 ++--- R/discordia.R | 105 +++-- R/diseq.R | 668 ++++++++++++++++++++++++-------------- R/errorellipse.R | 38 +- R/evolution.R | 32 - R/fissiontracks.R | 4 R/helioplot.R | 33 - R/io.R | 278 ++++++++------- R/isochron.R | 257 +++++++++++--- R/kde.R | 26 + R/ludwig.R | 914 ++++++++++++++++++++++++++++++++-------------------- R/mds.R | 2 R/peakfit.R | 44 +- R/radialplot.R | 317 +++++++++--------- R/regression.R | 4 R/titterington.R | 3 R/toolbox.R | 91 +++-- R/weightedmean.R | 59 +-- R/york.R | 204 +++-------- data/examples.rda |binary inst/UPb7.csv | 20 - inst/UPb8.csv | 22 - inst/constants.json | 4 inst/diseq.csv |only man/Pb0corr.Rd | 44 +- man/age.Rd | 44 +- man/agespectrum.Rd | 39 +- man/cad.Rd | 26 + man/central.Rd | 54 +-- man/concordia.Rd | 124 +++---- man/data2york.Rd | 45 +- man/diseq.Rd | 134 ++++--- man/evolution.Rd | 27 - man/helioplot.Rd | 27 - man/isochron.Rd | 148 +++++--- man/kde.Rd | 25 - man/ludwig.Rd | 18 - man/mclean.Rd |only man/peakfit.Rd | 27 + man/radialplot.Rd | 149 ++++---- man/read.data.Rd | 126 +++++-- man/scatterplot.Rd | 36 +- man/settings.Rd | 98 ++--- man/titterington.Rd | 3 man/weightedmean.Rd | 56 +-- man/york.Rd | 2 57 files changed, 3563 insertions(+), 2421 deletions(-)
Title: Create Meme
Description: The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976).
It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity.
The internet memes are captioned photos that are intended to be funny, ridiculous.
Memes behave like infectious viruses and travel from person to person quickly through social media.
The 'meme' package allows users to make custom memes.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between meme versions 0.2.1 dated 2018-09-27 and 0.2.2 dated 2019-08-05
DESCRIPTION | 8 - MD5 | 13 +- build/vignette.rds |binary inst/ash-pikachu.0.0.jpg |only inst/doc/meme.R | 6 - inst/doc/meme.Rmd | 6 - inst/doc/meme.html | 226 ++++++++++++++++++++++++++--------------------- vignettes/meme.Rmd | 6 - 8 files changed, 151 insertions(+), 114 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis.
Author: Gianluca Baio, Andrea Berardi, Anna Heath
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between BCEA versions 2.2-6 dated 2018-07-11 and 2.3-1 dated 2019-08-05
DESCRIPTION | 15 MD5 | 54 +- NAMESPACE | 2 R/BCEA-package.R | 4 R/BCEAweb.R | 2 R/CreateInputs.R | 20 R/ceac.plot.R | 453 +++++++++++++------ R/ceplane.plot.R | 969 ++++++++++++++++++++++++++++-------------- R/eib.plot.R | 444 ++++++++++++++----- R/evi.plot.R | 222 +++++++-- R/evppi.default.R | 17 R/info.rank.R | 195 +++++--- R/make.report.R |only data/datalist | 3 inst/BCEAweb/ui.R | 1196 ++++++++++++++++++++++++++-------------------------- inst/CITATION |only inst/Report |only man/BCEA-package.Rd | 59 +- man/BCEAweb.Rd | 9 man/CreateInputs.Rd | 59 +- man/Vaccine.Rd | 7 man/ceac.plot.Rd | 110 ++-- man/ceplane.plot.Rd | 183 ++++--- man/diag.evppi.Rd | 3 man/eib.plot.Rd | 156 +++--- man/evi.plot.Rd | 76 +-- man/info.rank.Rd | 126 ++--- man/make.report.Rd |only 28 files changed, 2709 insertions(+), 1675 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <http://www.bnlearn.com>.
Author: Marco Scutari [aut, cre], Robert Ness [ctb]
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 4.4.1 dated 2019-03-05 and 4.5 dated 2019-08-05
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