Title: Implement Tour Methods in R Code
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb],
Di Cook [aut, cre],
Nick Spyrison [ctb],
Ursula Laa [ctb]
Maintainer: Di Cook <dicook@monash.edu>
Diff between tourr versions 0.5.5 dated 2017-08-02 and 0.5.6 dated 2019-02-11
tourr-0.5.5/tourr/inst/tests |only tourr-0.5.5/tourr/man/sphere.Rd |only tourr-0.5.5/tourr/tests |only tourr-0.5.6/tourr/DESCRIPTION | 25 - tourr-0.5.6/tourr/LICENSE | 2 tourr-0.5.6/tourr/MD5 | 82 ++-- tourr-0.5.6/tourr/NAMESPACE | 12 tourr-0.5.6/tourr/NEWS | 7 tourr-0.5.6/tourr/R/animate.r | 5 tourr-0.5.6/tourr/R/display-andrews.r | 24 + tourr-0.5.6/tourr/R/display-density2d.r |only tourr-0.5.6/tourr/R/display-groupxy.r |only tourr-0.5.6/tourr/R/display-xy.r | 10 tourr-0.5.6/tourr/R/history.r | 10 tourr-0.5.6/tourr/R/interesting-indices.r | 464 +++++++++++++------------- tourr-0.5.6/tourr/R/interpolate.r | 7 tourr-0.5.6/tourr/R/linear-algebra.r | 4 tourr-0.5.6/tourr/R/path-dist.r | 4 tourr-0.5.6/tourr/R/path-index.r | 16 tourr-0.5.6/tourr/R/render.r | 6 tourr-0.5.6/tourr/R/search-better.r | 8 tourr-0.5.6/tourr/R/search-geodesic.r | 9 tourr-0.5.6/tourr/R/tour-frozen.r | 2 tourr-0.5.6/tourr/R/tour-guided.r | 37 +- tourr-0.5.6/tourr/R/tour.r | 8 tourr-0.5.6/tourr/R/util.r | 2 tourr-0.5.6/tourr/README.md | 2 tourr-0.5.6/tourr/TODO | 6 tourr-0.5.6/tourr/man/animate.Rd | 4 tourr-0.5.6/tourr/man/cmass.Rd | 5 tourr-0.5.6/tourr/man/display_andrews.Rd | 8 tourr-0.5.6/tourr/man/display_density2d.Rd |only tourr-0.5.6/tourr/man/display_groupxy.Rd |only tourr-0.5.6/tourr/man/display_stereo.Rd | 4 tourr-0.5.6/tourr/man/display_xy.Rd | 2 tourr-0.5.6/tourr/man/frozen_guided_tour.Rd | 2 tourr-0.5.6/tourr/man/guided_tour.Rd | 17 tourr-0.5.6/tourr/man/holes.Rd | 5 tourr-0.5.6/tourr/man/path_dist.Rd | 4 tourr-0.5.6/tourr/man/path_index.Rd | 12 tourr-0.5.6/tourr/man/paths_index.Rd | 4 tourr-0.5.6/tourr/man/save_history.Rd | 6 tourr-0.5.6/tourr/man/search_better.Rd | 2 tourr-0.5.6/tourr/man/search_better_random.Rd | 2 tourr-0.5.6/tourr/man/search_geodesic.Rd | 8 tourr-0.5.6/tourr/man/sphere_data.Rd |only 46 files changed, 470 insertions(+), 367 deletions(-)
Title: Configurable Function for Solving Families of Nonlinear
Equations
Description: This is designed for use with an arbitrary set of equations with
an arbitrary set of unknowns.
The user selects "fixed" values for enough unknowns to leave as many variables as
there are equations, which in most cases means the system is properly
defined and a unique solution exists. The function, the fixed values
and initial values for the remaining unknowns are fed to a nonlinear backsolver.
The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>
Diff between ktsolve versions 1.1 dated 2013-09-23 and 1.1.1 dated 2019-02-11
ChangeLog | 1 + DESCRIPTION | 20 ++++++++++---------- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/ktsolve.R | 12 +++++++++--- 5 files changed, 28 insertions(+), 17 deletions(-)
Title: 'Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)'
Description: Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Author: Rene Locher [aut, cre],
Andreas Ruckstuhl [ctb]
Maintainer: Rene Locher <rene.locher@zhaw.ch>
Diff between IDPmisc versions 1.1.18 dated 2018-10-02 and 1.1.19 dated 2019-02-11
ChangeLog | 5 ++++- DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++++----- NAMESPACE | 13 +++++++------ R/Td.R |only R/Td.aw.R |only R/Tf.ai.R |only R/hr.R |only R/iplot.R | 2 -- R/pw.R |only R/pw.ai.R |only R/pw.aw.R |only man/IDPmisc-package.Rd | 16 ++++------------ man/humidity.Rd |only 14 files changed, 33 insertions(+), 31 deletions(-)
Title: Convenient Functions for Ensemble Time Series Forecasts
Description: Convenient functions for ensemble forecasts in R combining
approaches from the 'forecast' package. Forecasts generated from auto.arima(), ets(),
thetaf(), nnetar(), stlm(), tbats(), and snaive() can be combined with equal weights, weights
based on in-sample errors (introduced by Bates & Granger (1969) <doi:10.1057/jors.1969.103>),
or cross-validated weights. Cross validation for time series data with user-supplied models
and forecasting functions is also supported to evaluate model accuracy.
Author: David Shaub [aut, cre],
Peter Ellis [aut]
Maintainer: David Shaub <davidshaub@gmx.com>
Diff between forecastHybrid versions 4.1.16 dated 2018-12-19 and 4.2.17 dated 2019-02-11
forecastHybrid-4.1.16/forecastHybrid/tests/testthat/test-accuracy.r |only forecastHybrid-4.2.17/forecastHybrid/DESCRIPTION | 22 ++-- forecastHybrid-4.2.17/forecastHybrid/MD5 | 25 ++-- forecastHybrid-4.2.17/forecastHybrid/NAMESPACE | 2 forecastHybrid-4.2.17/forecastHybrid/R/cvts.R | 32 +++-- forecastHybrid-4.2.17/forecastHybrid/R/helper.R | 4 forecastHybrid-4.2.17/forecastHybrid/R/hybridModel.R | 7 + forecastHybrid-4.2.17/forecastHybrid/R/thiefModel.R |only forecastHybrid-4.2.17/forecastHybrid/inst/NEWS.md | 4 forecastHybrid-4.2.17/forecastHybrid/inst/doc/forecastHybrid.html | 54 +++++----- forecastHybrid-4.2.17/forecastHybrid/man/cvts.Rd | 4 forecastHybrid-4.2.17/forecastHybrid/man/thiefModel.Rd |only forecastHybrid-4.2.17/forecastHybrid/tests/testthat/test-accuracy.R |only forecastHybrid-4.2.17/forecastHybrid/tests/testthat/test-forecast.hybridModel.R | 2 forecastHybrid-4.2.17/forecastHybrid/tests/testthat/test-hybridModel.R | 4 forecastHybrid-4.2.17/forecastHybrid/tests/testthat/test-thiefModel.R |only 16 files changed, 89 insertions(+), 71 deletions(-)
More information about forecastHybrid at CRAN
Permanent link
Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker [aut, cre],
Sang Woo Park [ctb],
James Vonesh [dtc],
Jacqueline Wilson [dtc],
Russ Schmitt [dtc],
Sally Holbrook [dtc],
James D. Thomson [dtc],
R. Scot Duncan [dtc]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between emdbook versions 1.3.10 dated 2018-05-19 and 1.3.11 dated 2019-02-11
DESCRIPTION | 28 ++++++++++++++++++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 2 +- R/dists.R | 18 +++++++----------- R/emdbook.R | 18 +++++++++++------- build/partial.rdb |binary inst/NEWS.Rd | 7 +++++++ inst/misc/firfec-batch.R | 31 ++++++++++++++++--------------- inst/misc/firfec-batch.Rout |only man/dbetabinom.Rd | 9 +++++---- tests |only 11 files changed, 79 insertions(+), 52 deletions(-)
Title: Automatic Cognostic Summaries
Description: Automatically calculates cognostic groups for plot objects and list column plot objects. Results are returned in a nested data frame.
Author: Barret Schloerke [aut],
Ryan Hafen [ths, cre]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between autocogs versions 0.1.1 dated 2018-09-21 and 0.1.2 dated 2019-02-11
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
and
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.4 dated 2019-02-08 and 0.5.5 dated 2019-02-11
DESCRIPTION | 10 ++-- MD5 | 30 ++++++------- NEWS.md | 11 +++++ R/select.R | 2 R/summary.ctmm.R | 3 - R/telemetry.R | 2 R/uere.R | 42 ++++++++++++++----- R/units.R | 2 TODO | 1 inst/doc/akde.html | 4 - inst/doc/error.html | 27 +++++------- inst/doc/periodogram.html | 101 +++++++++++++++++++++++++--------------------- inst/doc/variogram.html | 6 +- man/ctmm-package.Rd | 4 - man/ctmm.fit.Rd | 2 man/uere.Rd | 3 - 16 files changed, 147 insertions(+), 103 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>
Diff between cgmanalysis versions 2.1 dated 2018-12-17 and 2.2 dated 2019-02-11
DESCRIPTION | 6 ++-- MD5 | 4 +- R/cgmvariables.R | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 79 insertions(+), 5 deletions(-)
Title: Heritability of Gene Expression for Next-Generation Sequencing
Description: Statistical framework to analyze heritability of gene expression
based on next-generation sequencing data and simulating sequencing reads.
Variance partition coefficients (VPC) are computed using linear mixed effects
and generalized linear mixed effects models. Compound Poisson and negative
binomial models are included. Reference: Rudra, Pratyaydipta, et al. "Model based heritability scores for high-throughput sequencing data." BMC bioinformatics 18.1 (2017): 143.
Author: W. Jenny Shi [aut, cre],
Pamela Russell [aut],
Pratyaydipta Rudra [aut, cre],
Brian Vestal [aut, cre],
Katerina Kechris [aut],
Laura Saba [aut]
Maintainer: W. Jenny Shi <wjennyshi@gmail.com>
Diff between HeritSeq versions 1.0.0 dated 2017-01-04 and 1.0.1 dated 2019-02-11
DESCRIPTION | 12 +++++++----- MD5 | 4 ++-- R/HeriTools.R | 3 ++- 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Dynamical Systems Approach to Immune Response Modeling
Description: A collection of 'shiny' apps that allow for the simulation and
exploration of various within-host immune response scenarios.
The purpose of the package is to help individuals learn
about within-host infection and immune response modeling from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on
what to do with the models. The development of this package was partially supported by NIH grant U19AI117891.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Spencer Hall [ctb],
Sina Solaimanpour [ctb],
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIRM versions 0.5.0 dated 2019-01-17 and 0.5.5 dated 2019-02-11
DSAIRM-0.5.0/DSAIRM/inst/media/dsairm.css |only DSAIRM-0.5.0/DSAIRM/inst/media/references.bib |only DSAIRM-0.5.5/DSAIRM/DESCRIPTION | 14 DSAIRM-0.5.5/DSAIRM/MD5 | 107 +- DSAIRM-0.5.5/DSAIRM/NAMESPACE | 3 DSAIRM-0.5.5/DSAIRM/NEWS.md | 6 DSAIRM-0.5.5/DSAIRM/R/generate_documentation.R | 4 DSAIRM-0.5.5/DSAIRM/R/generate_plots.R | 416 +++++----- DSAIRM-0.5.5/DSAIRM/R/generate_shinyinput.R | 30 DSAIRM-0.5.5/DSAIRM/R/generate_text.R | 13 DSAIRM-0.5.5/DSAIRM/R/run_model.R | 52 + DSAIRM-0.5.5/DSAIRM/inst/DSAIRMshinyappsio |only DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicbacteria_documentation.Rmd | 8 DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicbacteria_documentation.html | 368 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicmodelfit_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicmodelfit_documentation.html | 370 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicvirus_documentation.Rmd | 280 +++--- DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicvirus_documentation.html | 40 DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.html | 368 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/confintfit_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/confintfit_documentation.html | 372 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/drugresistance_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/drugresistance_documentation.html | 368 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelcomparisonfit_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelcomparisonfit_documentation.html | 368 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelexploration_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelexploration_documentation.html | 370 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelvariants_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/modelvariants_documentation.html | 366 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/pkpdmodel_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/pkpdmodel_documentation.html | 366 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/references.bib |only DSAIRM-0.5.5/DSAIRM/inst/appinformation/usanalysis_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/usanalysis_documentation.html | 372 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/virusandir_documentation.Rmd | 289 +++--- DSAIRM-0.5.5/DSAIRM/inst/appinformation/virusandir_documentation.html | 373 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/appinformation/virusandtx_documentation.Rmd | 6 DSAIRM-0.5.5/DSAIRM/inst/appinformation/virusandtx_documentation.html | 368 ++++++++ DSAIRM-0.5.5/DSAIRM/inst/doc/DSAIRM.R | 42 - DSAIRM-0.5.5/DSAIRM/inst/doc/DSAIRM.Rmd | 89 +- DSAIRM-0.5.5/DSAIRM/inst/doc/DSAIRM.html | 120 +- DSAIRM-0.5.5/DSAIRM/inst/docsfordevelopers/documentation.md | 19 DSAIRM-0.5.5/DSAIRM/inst/mainmenu/app.R | 26 DSAIRM-0.5.5/DSAIRM/inst/mainmenu/packagestyle.css |only DSAIRM-0.5.5/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_discrete.R | 30 DSAIRM-0.5.5/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_ode.R | 40 DSAIRM-0.5.5/DSAIRM/inst/simulatorfunctions/simulate_modelexploration.R | 4 DSAIRM-0.5.5/DSAIRM/inst/simulatorfunctions/simulate_usanalysis.R | 4 DSAIRM-0.5.5/DSAIRM/inst/simulatorfunctions/simulatorfunctions.zip |only DSAIRM-0.5.5/DSAIRM/man/generate_plots.Rd | 22 DSAIRM-0.5.5/DSAIRM/man/generate_shinyinput.Rd | 13 DSAIRM-0.5.5/DSAIRM/man/generate_text.Rd | 2 DSAIRM-0.5.5/DSAIRM/man/run_model.Rd | 7 DSAIRM-0.5.5/DSAIRM/tests/testthat/test-generate_documentation.R |only DSAIRM-0.5.5/DSAIRM/tests/testthat/test-generate_shinyinput.R |only DSAIRM-0.5.5/DSAIRM/tests/testthat/test-run_model.R |only DSAIRM-0.5.5/DSAIRM/vignettes/DSAIRM.Rmd | 89 +- 58 files changed, 5332 insertions(+), 926 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tibbletime versions 0.1.1 dated 2018-01-30 and 0.1.2 dated 2019-02-11
tibbletime-0.1.1/tibbletime/R/tibbletime-package.R |only tibbletime-0.1.2/tibbletime/DESCRIPTION | 15 tibbletime-0.1.2/tibbletime/MD5 | 55 tibbletime-0.1.2/tibbletime/NAMESPACE | 1 tibbletime-0.1.2/tibbletime/NEWS.md | 23 tibbletime-0.1.2/tibbletime/R/coercion.R | 4 tibbletime-0.1.2/tibbletime/R/getters.R | 6 tibbletime-0.1.2/tibbletime/R/index-based-generics.R | 17 tibbletime-0.1.2/tibbletime/R/new.R | 15 tibbletime-0.1.2/tibbletime/R/reconstruct.R | 2 tibbletime-0.1.2/tibbletime/R/tibbletime-package.r |only tibbletime-0.1.2/tibbletime/README.md | 199 ++- tibbletime-0.1.2/tibbletime/build/vignette.rds |binary tibbletime-0.1.2/tibbletime/inst/doc/TT-01-time-based-filtering.html | 458 ++++++-- tibbletime-0.1.2/tibbletime/inst/doc/TT-02-changing-time-periods.html | 416 +++++-- tibbletime-0.1.2/tibbletime/inst/doc/TT-03-rollify-for-rolling-analysis.html | 561 +++++++--- tibbletime-0.1.2/tibbletime/inst/doc/TT-04-use-with-dplyr.R | 8 tibbletime-0.1.2/tibbletime/inst/doc/TT-04-use-with-dplyr.Rmd | 10 tibbletime-0.1.2/tibbletime/inst/doc/TT-04-use-with-dplyr.html | 526 ++++++--- tibbletime-0.1.2/tibbletime/inst/include/is_ordered.h | 2 tibbletime-0.1.2/tibbletime/man/as_period.Rd | 4 tibbletime-0.1.2/tibbletime/man/collapse_by.Rd | 4 tibbletime-0.1.2/tibbletime/man/collapse_index.Rd | 4 tibbletime-0.1.2/tibbletime/man/new_tbl_time.Rd |only tibbletime-0.1.2/tibbletime/man/reexports.Rd | 1 tibbletime-0.1.2/tibbletime/man/rollify.Rd | 13 tibbletime-0.1.2/tibbletime/man/tibbletime.Rd | 5 tibbletime-0.1.2/tibbletime/tests/testthat/test_as_period.R | 2 tibbletime-0.1.2/tibbletime/tests/testthat/test_collapse_index.R | 13 tibbletime-0.1.2/tibbletime/vignettes/TT-04-use-with-dplyr.Rmd | 10 30 files changed, 1700 insertions(+), 674 deletions(-)
Title: Biometric Exploratory Analysis Creation House
Description: A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.
Author: Danni Yu [aut, cre],
Michael Man [aut],
ChenChen Yu [com]
Maintainer: Danni Yu <danni.yu@gmail.com>
Diff between BEACH versions 1.2.1 dated 2018-02-22 and 1.3.1 dated 2019-02-11
BEACH-1.2.1/BEACH/inst/app/functions/BridgingAnalysis_configuration.csv |only BEACH-1.2.1/BEACH/inst/app/functions/DataQC_configuration_v2.4.csv |only BEACH-1.2.1/BEACH/inst/app/functions/TrialDesignAnalysis_configuration.csv |only BEACH-1.3.1/BEACH/DESCRIPTION | 21 BEACH-1.3.1/BEACH/MD5 | 24 BEACH-1.3.1/BEACH/build/partial.rdb |binary BEACH-1.3.1/BEACH/inst/app/configuration_empty_dy1.csv | 63 BEACH-1.3.1/BEACH/inst/app/counter_m.Rdata |binary BEACH-1.3.1/BEACH/inst/app/functions/1.DataQC_configuration_v2.4.csv |only BEACH-1.3.1/BEACH/inst/app/functions/2.TrialDesignAnalysis_configuration.csv |only BEACH-1.3.1/BEACH/inst/app/functions/shinyFun.r | 4719 +++++----- BEACH-1.3.1/BEACH/inst/app/functions/users |only BEACH-1.3.1/BEACH/inst/app/server.r | 179 BEACH-1.3.1/BEACH/inst/app/sopHead.txt | 2 BEACH-1.3.1/BEACH/inst/app/ui.r | 36 BEACH-1.3.1/BEACH/man/runBEACH.Rd | 4 16 files changed, 2612 insertions(+), 2436 deletions(-)
Title: Statistical Analysis of Chemistry, Histopathology, and
Reproduction Endpoints Including Repeated Measures and
Multi-Generation Studies
Description: A front end for the statistical analyses involved in the tier II endocrine
disruptor screening program. The analyses available to this package are:
Rao-Scott adjusted Cochran-Armitage test for trend By Slices (RSCABS),
a Standard Cochran-Armitage test for trend By Slices (SCABS),
mixed effects Cox proportional model, Jonckheere-Terpstra step down trend test
Dunn test, one way ANOVA, weighted ANOVA, mixed effects ANOVA, repeated
measures ANOVA, and Dunnett test.
Author: Joe Swintek [aut, cre],
Kevin Flynn [ctb],
Jon Haselman [ctb],
Maki Sakurai [ctb]
Maintainer: Joe Swintek <swintek.joe@epa.gov>
Diff between StatCharrms versions 0.90.91 dated 2018-06-10 and 0.90.92 dated 2019-02-11
DESCRIPTION | 14 ++++++++------ MD5 | 18 +++++++++--------- R/Run.StatCharrms.R | 2 +- R/ShowChangeLog.R | 9 ++++++++- R/StatCharrms-internal.R | 2 +- R/Time2EventMain.R | 1 + R/autoStdAnylsis.R | 3 ++- R/forceStdAnalysis.R | 25 +++++++++++++++---------- R/jonckheereTerpstraTest.R | 35 +++++++++++++++++++++-------------- inst/doc/StatCharrms.pdf |binary 10 files changed, 66 insertions(+), 43 deletions(-)
Title: Statistical Methods for Interval Censored Data
Description: Functions that provide statistical methods for interval censored (grouped) data. The package supports the estimation of linear and linear mixed regression models with interval censored dependent variables. Parameter estimates are obtained by a stochastic expectation maximization algorithm. Furthermore, the package enables the direct (without covariates) estimation of statistical indicators from interval censored data via an iterative kernel density algorithm. Survey and Organisation for Economic Co-operation and Development (OECD) weights can be included into the direct estimation (see, Groß, M., U. Rendtel, T. Schmid, S. Schmon, and N. Tzavidis (2017) <doi:10.1111/rssa.12179>).
Author: Paul Walter
Maintainer: Paul Walter <paul.walter@fu-berlin.de>
Diff between smicd versions 1.0.2 dated 2018-09-10 and 1.0.3 dated 2019-02-11
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/dclassICD.R | 1 - R/indicators.est.R | 14 +++++++++++--- R/kde.algo.R | 2 +- R/standardError.est.R | 39 ++++++++++++++++++++++++++++++++++++--- inst/doc/vignetteSmicd.pdf |binary 8 files changed, 62 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-04 0.4.0
2018-11-30 0.3.0
2018-10-05 0.2.8
2018-10-02 0.2.7
2018-07-10 0.2.6
2018-07-03 0.2.5
2018-03-21 0.2.4
2018-03-17 0.2.3
2018-03-15 0.2.2
2018-03-13 0.2.1
2017-11-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-12 0.29
2015-10-11 0.28
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-01 0.1.0
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changes in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 1.7.0 dated 2018-10-25 and 1.7.1 dated 2019-02-11
DESCRIPTION | 10 +++++----- MD5 | 10 +++++++--- NEWS.md | 3 +++ README.md |only man/figures |only tests/testthat/test-fnsComparison.R | 18 +++++++++--------- 6 files changed, 24 insertions(+), 17 deletions(-)
Title: A Collection of Tools and Helpers Extending the Tidyverse
Description: A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages.
This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of
'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count,
various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks,
saving to PDF and PNG from a pipe and various small utilities.
Author: Marcel Wiesweg [aut, cre]
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>
Diff between tidytidbits versions 0.1.0 dated 2018-08-24 and 0.2.0 dated 2019-02-11
DESCRIPTION | 8 ++-- MD5 | 33 +++++++++------- NAMESPACE | 8 +++- NEWS.md | 8 +++- R/dplyr-like.R | 68 +++++++++++++++++++++++++++++++++++ R/na.R | 42 +++++++++++++++++++++ R/tidytidbits.R | 4 +- README.md | 7 +++ man/add_prop_test.Rd | 5 +- man/count_at.Rd |only man/cross_tabulate.Rd | 3 + man/execute_if.Rd | 2 - man/first_non_nas_at.Rd |only man/first_which_non_na_at.Rd |only man/lookup.Rd | 3 + man/lookup_function_from_dict.Rd | 3 + man/lump.Rd | 4 +- man/lump_rows.Rd | 4 +- man/replace_sequential_duplicates.Rd | 3 + 19 files changed, 168 insertions(+), 37 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.9 dated 2019-02-05 and 2.9.1 dated 2019-02-11
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 8 ++++++++ R/DJL-internal.R |only R/target.spec.dea.R | 2 +- 5 files changed, 17 insertions(+), 8 deletions(-)
Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care
Data and visualization of individual medication histories and adherence
patterns. The package implements a set of S3 classes and
functions consistent with current adherence guidelines and definitions.
It allows the computation of different measures of
adherence (as defined in the literature, but also several original ones),
their publication-quality plotting,
the estimation of event duration and time to initiation,
the interactive exploration of patient medication history and
the real-time estimation of adherence given various parameter settings.
It scales from very small datasets stored in flat CSV files to very large
databases and from single-thread processing on mid-range consumer
laptops to parallel processing on large heterogeneous computing clusters.
It exposes a standardized interface allowing it to be used from other
programming languages and platforms, such as Python.
Author: Dan Dediu [aut, cre],
Alexandra Dima [aut],
Samuel Allemann [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>
Diff between AdhereR versions 0.4 dated 2019-02-10 and 0.4.1 dated 2019-02-11
DESCRIPTION | 6 MD5 | 12 R/adherer.R | 641 ++++++++++++++--------------- inst/doc/AdhereR-overview.html | 4 inst/doc/calling-AdhereR-from-python3.html | 4 inst/interactivePlotShiny/app.R | 104 +++- man/plot.CMA0.Rd | 13 7 files changed, 415 insertions(+), 369 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>),
Andreas Alfons [aut],
Bernd Prantner [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.7.0 dated 2017-04-11 and 4.8.0 dated 2019-02-11
VIM-4.7.0/VIM/README |only VIM-4.7.0/VIM/tests/test_data_frame.R |only VIM-4.7.0/VIM/tests/test_gowerDind.R |only VIM-4.7.0/VIM/tests/test_impNA.R |only VIM-4.7.0/VIM/tests/test_kNN.R |only VIM-4.8.0/VIM/DESCRIPTION | 26 VIM-4.8.0/VIM/MD5 | 113 + VIM-4.8.0/VIM/NAMESPACE | 292 ++-- VIM-4.8.0/VIM/NEWS | 13 VIM-4.8.0/VIM/R/RcppExports.R |only VIM-4.8.0/VIM/R/VIM-package.R | 614 +++++----- VIM-4.8.0/VIM/R/gapMiss.R |only VIM-4.8.0/VIM/R/gower.dist.R | 8 VIM-4.8.0/VIM/R/hotdeck.R | 557 ++++----- VIM-4.8.0/VIM/R/irmi.R | 1880 ++++++++++++++++---------------- VIM-4.8.0/VIM/R/kNNFaster.R | 232 ++- VIM-4.8.0/VIM/R/matchImpute.R |only VIM-4.8.0/VIM/README.md |only VIM-4.8.0/VIM/man/SBS5242.Rd | 61 - VIM-4.8.0/VIM/man/VIM-package.Rd | 103 - VIM-4.8.0/VIM/man/aggr.Rd | 444 +++---- VIM-4.8.0/VIM/man/alphablend.Rd | 65 - VIM-4.8.0/VIM/man/barMiss.Rd | 273 ++-- VIM-4.8.0/VIM/man/bgmap.Rd | 85 - VIM-4.8.0/VIM/man/chorizonDL.Rd | 187 +-- VIM-4.8.0/VIM/man/colSequence.Rd | 149 +- VIM-4.8.0/VIM/man/colormapMiss.Rd | 318 ++--- VIM-4.8.0/VIM/man/countInf.Rd | 57 VIM-4.8.0/VIM/man/gapMiss.Rd |only VIM-4.8.0/VIM/man/growdotMiss.Rd | 275 ++-- VIM-4.8.0/VIM/man/histMiss.Rd | 281 ++-- VIM-4.8.0/VIM/man/hotdeck.Rd | 147 +- VIM-4.8.0/VIM/man/initialise.Rd | 83 - VIM-4.8.0/VIM/man/irmi.Rd | 265 ++-- VIM-4.8.0/VIM/man/kNN.Rd | 206 +-- VIM-4.8.0/VIM/man/kola.background.Rd | 49 VIM-4.8.0/VIM/man/mapMiss.Rd | 177 +-- VIM-4.8.0/VIM/man/marginmatrix.Rd | 155 +- VIM-4.8.0/VIM/man/marginplot.Rd | 267 ++-- VIM-4.8.0/VIM/man/matchImpute.Rd |only VIM-4.8.0/VIM/man/matrixplot.Rd | 242 ++-- VIM-4.8.0/VIM/man/mosaicMiss.Rd | 187 +-- VIM-4.8.0/VIM/man/pairsVIM.Rd | 187 +-- VIM-4.8.0/VIM/man/parcoordMiss.Rd | 297 ++--- VIM-4.8.0/VIM/man/pbox.Rd | 253 ++-- VIM-4.8.0/VIM/man/prepare.Rd | 155 +- VIM-4.8.0/VIM/man/print.summary.aggr.Rd | 61 - VIM-4.8.0/VIM/man/regressionImp.Rd | 117 - VIM-4.8.0/VIM/man/rugNA.Rd | 133 +- VIM-4.8.0/VIM/man/scattJitt.Rd | 209 +-- VIM-4.8.0/VIM/man/scattMiss.Rd | 237 ++-- VIM-4.8.0/VIM/man/scattmatrixMiss.Rd | 245 ++-- VIM-4.8.0/VIM/man/sleep.Rd | 61 - VIM-4.8.0/VIM/man/spineMiss.Rd | 297 ++--- VIM-4.8.0/VIM/man/tao.Rd | 63 - VIM-4.8.0/VIM/man/testdata.Rd | 63 - VIM-4.8.0/VIM/man/vmGUIenvir.Rd | 103 - VIM-4.8.0/VIM/src/RcppExports.cpp |only VIM-4.8.0/VIM/src/gowerD.cpp | 4 VIM-4.8.0/VIM/tests/testthat |only VIM-4.8.0/VIM/tests/testthat.R |only 61 files changed, 5229 insertions(+), 5067 deletions(-)
Title: Test the Homogeneity of Kappa Statistics
Description: Tests the homogeneity of intraclass kappa statistics obtained from independent studies or a stratified study with binary results. It is desired to compare the kappa statistics obtained in multi-center studies or in a single stratified study to give a common or summary kappa using all available information. If the homogeneity test of these kappa statistics is not rejected, then it is possible to make inferences over a single kappa statistic that summarizes all the studies. Muammer Albayrak, Kemal Turhan, Yasemin Yavuz, Zeliha Aydin Kasap (2019) <doi:10.1080/03610918.2018.1538457> Jun-mo Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005) <doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura McSweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner, Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>.
Author: Muammer Albayrak
Maintainer: Muammer Albayrak <m.albayrak@ktu.edu.tr>
Diff between kaphom versions 0.2 dated 2017-10-26 and 0.3 dated 2019-02-11
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Thomas Brand [aut],
Sebastien Galais [cre, ctb]
Maintainer: Sebastien Galais <Sebastien.GALAIS@banque-france.fr>
Diff between rdbnomics versions 0.4.5 dated 2019-01-31 and 0.4.6 dated 2019-02-11
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 4 ++ R/utils.R | 65 ++++++++++++++++++++++++++++++------------------ inst/doc/rdbnomics.html | 48 +++++++++++++++++------------------ 5 files changed, 76 insertions(+), 55 deletions(-)
Title: Versatile Ultra-Fast Spectral Clustering for Single and
Multi-View Data
Description: A versatile ultra-fast spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in dense regions in the graph. For integrating multi-view data and reducing noise we use a recently developed tensor product graph data integration and diffusion system. 'Spectrum' contains two techniques for finding the number of clusters (K); the classical eigengap method and a novel multimodality gap procedure. The multimodality gap analyses the distribution of the eigenvectors of the graph Laplacian to decide K and tune the kernel. 'Spectrum' is suited for clustering a wide range of complex data.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between Spectrum versions 0.1 dated 2019-02-08 and 0.2 dated 2019-02-11
DESCRIPTION | 6 MD5 | 16 - R/spectrum.R | 468 ++++++++++++++++++++-------------------- R/spectrum_functions.R | 2 inst/doc/Spectrum_vignette.R | 10 inst/doc/Spectrum_vignette.Rmd | 12 - inst/doc/Spectrum_vignette.pdf |binary man/Spectrum.Rd | 4 vignettes/Spectrum_vignette.Rmd | 12 - 9 files changed, 267 insertions(+), 263 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Hervé
Maintainer: Maxime Hervé <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-71 dated 2019-01-11 and 0.9-72 dated 2019-02-11
DESCRIPTION | 8 ++-- MD5 | 46 +++++++++++++------------- NEWS | 6 +++ R/MVA.biplot.R | 2 + R/MVA.cmv.R | 18 +++++++++- R/MVA.cor.R | 75 +++++++++++++++++++++++++++++-------------- R/MVA.corplot.R | 2 + R/MVA.cv.R | 18 +++++++++- R/MVA.load.R | 43 +++++++++++++----------- R/MVA.loadplot.R | 2 + R/MVA.pairplot.R | 2 + R/MVA.scoreplot.R | 2 + R/MVA.scores.R | 71 ++++++++++++++++++++++++++++------------ R/MVA.trajplot.R | 2 + R/multtest.gp.R | 3 + R/zzz.R | 2 - man/MVA.cmv.Rd | 1 man/MVA.cor.Rd | 4 +- man/MVA.cv.Rd | 1 man/MVA.load.Rd | 4 +- man/MVA.scores.Rd | 4 +- man/RVAideMemoire-package.Rd | 4 +- man/multtest.gp.Rd | 4 +- man/pairwise.perm.manova.Rd | 4 +- 24 files changed, 220 insertions(+), 108 deletions(-)
Title: Analysis of Matched Case Control Data with a Mismeasured
Exposure that is Accompanied by Instrumental Variables
Description: Applying the methodology from Manuel et al. to estimate parameters using a matched
case control data with a mismeasured exposure variable that is accompanied by
instrumental variables (Submitted).
Author: Chris M Manuel, Samiran Sinha, and Suojin Wang
Maintainer: Chris M Manuel <cmmanuel@stat.tamu.edu>
Diff between mccmeiv versions 2.0 dated 2019-02-06 and 2.1 dated 2019-02-11
DESCRIPTION | 18 +++++++++--------- MD5 | 14 +++++++------- build/partial.rdb |binary man/matcdata.Rd | 2 +- man/matcdatamult.Rd | 2 +- man/mccmeiv-package.Rd | 16 ++++++++-------- man/meivm3.Rd | 14 +++++++------- man/meivm4.Rd | 13 ++++++------- 8 files changed, 39 insertions(+), 40 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables
for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
Kenward-Roger method is also available via the pbkrtest package. Model selection
methods include step, drop1 and anova-like tables for random effects (ranova).
Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths, cre],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between lmerTest versions 3.0-1 dated 2018-04-23 and 3.1-0 dated 2019-02-11
DESCRIPTION | 14 +++++----- MD5 | 55 +++++++++++++++++++++------------------ NAMESPACE | 10 +++++++ NEWS.md | 15 ++++++++++ R/legacy.R |only R/lmer.R | 56 ++++++++++++++++++++++++++++++++++++++++ R/lmerTest.R | 2 - R/lmer_anova.R | 2 - R/ranova.R | 1 R/step.R | 16 +++++++---- inst/testdata/legacy_fits.RData |only man/anova.lmerModLmerTest.Rd | 6 ++-- man/contest.lmerModLmerTest.Rd | 7 ++--- man/legacy.Rd |only man/lmer.Rd | 4 +- man/lmerTest-package.Rd | 2 - man/ls_means.lmerModLmerTest.Rd | 4 +- man/merModLmerTest-class.Rd |only man/nullspace.Rd | 3 +- man/plot.step_list.Rd | 4 +- man/show_tests.Rd | 3 +- man/show_tests.anova.Rd | 3 +- man/show_tests.ls_means.Rd | 3 +- man/step.Rd | 2 - tests/test_anova.R | 8 +++++ tests/test_compare_sas.R | 3 +- tests/test_legacy.R |only tests/test_lmer.R | 11 +++++++ tests/test_lmerTest_paper.R | 11 +++++-- tests/test_ranova_step.R | 24 +++++++++++++++-- tests/test_zerovar.R | 7 +++-- 31 files changed, 208 insertions(+), 68 deletions(-)
Title: Utilities for Delaying Function Execution
Description: Executes arbitrary R or C functions some time after the current
time, after the R execution stack has emptied.
Author: Joe Cheng [aut, cre],
RStudio [cph],
Winston Chang [aut],
Marcus Geelnard [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/),
Evan Nemerson [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between later versions 0.7.5 dated 2018-09-18 and 0.8.0 dated 2019-02-11
later-0.7.5/later/cleanup |only later-0.7.5/later/configure |only later-0.7.5/later/src/Makevars.in |only later-0.7.5/later/src/Makevars.win |only later-0.7.5/later/src/c11threads.h |only later-0.7.5/later/src/tinycthread |only later-0.8.0/later/DESCRIPTION | 8 ++-- later-0.8.0/later/MD5 | 45 +++++++++++------------- later-0.8.0/later/NEWS.md | 10 +++++ later-0.8.0/later/R/RcppExports.R | 4 +- later-0.8.0/later/R/later.R | 9 +++- later-0.8.0/later/build/vignette.rds |binary later-0.8.0/later/inst/doc/later-cpp.html | 38 ++++++++++++++------ later-0.8.0/later/man/run_now.Rd | 6 ++- later-0.8.0/later/src/Makevars |only later-0.8.0/later/src/RcppExports.cpp | 7 ++- later-0.8.0/later/src/badthreads.h |only later-0.8.0/later/src/callback_registry.cpp | 14 +++++-- later-0.8.0/later/src/debug.h | 2 - later-0.8.0/later/src/init.c | 4 +- later-0.8.0/later/src/later.cpp | 6 +-- later-0.8.0/later/src/later.h | 2 - later-0.8.0/later/src/later_posix.cpp | 29 +++++++++------ later-0.8.0/later/src/threadutils.h | 38 ++++++++++---------- later-0.8.0/later/src/timeconv.h | 2 - later-0.8.0/later/src/tinycthread.c |only later-0.8.0/later/src/tinycthread.h |only later-0.8.0/later/tests/testthat/test-run_now.R | 17 +++++++++ 28 files changed, 154 insertions(+), 87 deletions(-)
Title: Robust Tests for Equal Correlation
Description: There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. U are proportion to different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the passage New Statistical Methods for Constructing Robust Differential Correlation Networks (expected to be public).
Author: Danyang Yu, Weiliang Qiu, Zeyu Zhang, Kimberly Glass, Jessica Su, Dawn L. DeMeo, Kelan Tantisira, Scott T. Weiss
Maintainer: Danyang Yu <danyangyu@hnu.edu.cn>
Diff between corTest versions 0.9.6 dated 2018-06-14 and 0.9.7 dated 2019-02-11
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/corTest.R | 7 ++++++- man/fisher_transfer_test.Rd | 13 ++++++++----- man/ghdist.Rd | 4 ++-- man/st1.Rd | 4 ++-- man/st2.Rd | 4 ++-- man/st3.Rd | 4 ++-- man/st4.Rd | 4 ++-- man/st5.Rd | 4 ++-- man/st6.Rd | 4 ++-- 11 files changed, 43 insertions(+), 35 deletions(-)
Title: Generating Various Numerical Representation Schemes for Protein
Sequences
Description: Comprehensive toolkit for generating various numerical
features of protein sequences described in Xiao et al. (2015)
<DOI:10.1093/bioinformatics/btv042>. For full functionality,
the software 'ncbi-blast+' is needed, see
<https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Qing-Song Xu [aut],
Dong-Sheng Cao [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between protr versions 1.5-2 dated 2018-11-22 and 1.6-0 dated 2019-02-11
protr-1.5-2/protr/vignettes/protr.css |only protr-1.6-0/protr/DESCRIPTION | 6 protr-1.6-0/protr/MD5 | 26 +- protr-1.6-0/protr/NEWS.md | 6 protr-1.6-0/protr/R/par-02-parGOSim.R | 352 +++++++++++++++++---------------- protr-1.6-0/protr/R/protr-package.R | 5 protr-1.6-0/protr/build/vignette.rds |binary protr-1.6-0/protr/inst/doc/protr.R | 50 ++-- protr-1.6-0/protr/inst/doc/protr.Rmd | 75 +++---- protr-1.6-0/protr/inst/doc/protr.html | 339 +++++++++++++++++++++++++------ protr-1.6-0/protr/man/parGOSim.Rd | 84 ++++--- protr-1.6-0/protr/man/protr-package.Rd | 6 protr-1.6-0/protr/man/twoGOSim.Rd | 68 +++--- protr-1.6-0/protr/vignettes/custom.css |only protr-1.6-0/protr/vignettes/protr.Rmd | 75 +++---- 15 files changed, 667 insertions(+), 425 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.6.4 dated 2018-09-29 and 1.6.5 dated 2019-02-11
DESCRIPTION | 8 - MD5 | 28 ++--- R/RcppExports.R | 16 ++- R/gibbs.R | 25 ++-- R/gmm.R | 4 R/gwas.R | 28 ++--- R/reml.R | 19 ++- R/snp.R | 2 inst/doc/gwa_description.pdf |binary inst/doc/vignette1.html | 4 inst/doc/vignette2.html | 4 man/Internals.Rd | 17 ++- man/NAM-package.Rd | 4 src/Functions.cpp | 222 +++++++++++++++++++++++++++++++++++++++++-- src/RcppExports.cpp | 55 +++++++++- 15 files changed, 354 insertions(+), 82 deletions(-)