Title: Who are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation, and other
attributes, such as gender and age. The method utilizes the Bayes' Rule to compute
the posterior probability of each racial category for any given individual.
The package implements methods described in Imai and Khanna (2015) "Improving
Ecological Inference by Predicting Individual Ethnicity from Voter Registration
Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut, cre], Hubert Jin [ctb]
Maintainer: Kabir Khanna <kkhanna@princeton.edu>
Diff between wru versions 0.1-3 dated 2017-04-14 and 0.1-4 dated 2017-05-04
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/merge_surnames.R | 19 ++++++++++++------- man/merge_surnames.Rd | 14 +++++++------- 5 files changed, 28 insertions(+), 22 deletions(-)
Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications
The 'RInside' packages makes it easier to have "R inside" your C++ application
by providing a C++ wrapper class providing the R interpreter.
As R itself is embedded into your application, a shared library build of R
is required. This works on Linux, OS X and even on Windows provided you use
the same tools used to build R itself.
Numerous examples are provided in the eight subdirectories of the examples/
directory of the installed package: standard, mpi (for parallel computing)
qt (showing how to embed 'RInside' inside a Qt GUI application), wt (showing
how to build a "web-application" using the Wt toolkit), armadillo (for
'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with 'RcppEigen').
The example use GNUmakefile(s) with GNU extensions, so a GNU make is required
(and will use the GNUmakefile automatically).
Doxygen-generated documentation of the C++ classes is available at the
'RInside' website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RInside versions 0.2.13 dated 2015-05-20 and 0.2.14 dated 2017-05-04
ChangeLog | 45 ++++++++++++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 23 ++++++------ README.md | 34 +++++++++++++++++- cleanup | 4 +- inst/NEWS.Rd | 42 ++++++++++++++++++---- inst/examples/standard/rinside_interactive0.cpp |only inst/examples/wt/GNUmakefile | 2 - inst/include/RInside.h | 5 +- inst/include/RInsideCommon.h | 4 +- src/Makevars | 2 - src/RInside.cpp | 33 +++++++++-------- src/tools/RInsideEnvVars.r | 4 +- 13 files changed, 160 insertions(+), 46 deletions(-)
Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data,
including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre],
Ian C. Marschner [ths],
Alexandra C. Gillett [ctb] (wrote an initial version of the nplbin
function)
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>
Diff between logbin versions 2.0.2 dated 2017-03-07 and 2.0.3 dated 2017-05-04
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++--------- NEWS.md | 4 +++ R/logbin.cem.r | 21 ++++++++++++++++--- R/logbin.control.r | 6 +++-- R/logbin.em.r | 9 ++++++++ R/logbin.r | 1 R/nplbin.r | 53 ++++++++++++++++++++++++++++++++++++-------------- man/logbin-package.Rd | 4 +-- man/logbin.Rd | 5 +++- man/logbin.control.Rd | 13 +++++++++--- 11 files changed, 105 insertions(+), 39 deletions(-)
Title: Tools for Healthcare Machine Learning
Description: A machine learning toolbox tailored to healthcare data.
Aids in data cleaning, model development, hyperparameter tuning, and model
deployment in a production SQL environment. Algorithms currently supported
are Lasso, Random Forest, and Linear Mixed Model.
Author: Levi Thatcher [aut, cre],
Mike Mastanduno [aut],
Taylor Miller [aut],
Taylor Larsen [aut]
Maintainer: Levi Thatcher <levi.thatcher@healthcatalyst.com>
Diff between healthcareai versions 0.1.11 dated 2017-02-13 and 0.1.12 dated 2017-05-04
healthcareai-0.1.11/healthcareai/R/onLoad.R |only healthcareai-0.1.12/healthcareai/DESCRIPTION | 23 healthcareai-0.1.12/healthcareai/MD5 | 104 +- healthcareai-0.1.12/healthcareai/NAMESPACE | 6 healthcareai-0.1.12/healthcareai/R/common.R | 422 +++++++--- healthcareai-0.1.12/healthcareai/R/feature-availability-profiler.R |only healthcareai-0.1.12/healthcareai/R/healthcareai.R | 39 healthcareai-0.1.12/healthcareai/R/lasso-deployment.R | 203 +++- healthcareai-0.1.12/healthcareai/R/lasso-development.R | 44 - healthcareai-0.1.12/healthcareai/R/linear-mixed-model-deployment.R | 141 ++- healthcareai-0.1.12/healthcareai/R/linear-mixed-model-development.R | 34 healthcareai-0.1.12/healthcareai/R/random-forest-deployment.R | 202 +++- healthcareai-0.1.12/healthcareai/R/random-forest-development.R | 54 - healthcareai-0.1.12/healthcareai/R/risk-adjusted-comparisons.R | 4 healthcareai-0.1.12/healthcareai/R/supervised-model-deployment-params.R | 1 healthcareai-0.1.12/healthcareai/R/supervised-model-deployment.R | 30 healthcareai-0.1.12/healthcareai/R/supervised-model-development.R | 19 healthcareai-0.1.12/healthcareai/R/unsupervised-model.R | 7 healthcareai-0.1.12/healthcareai/README.md | 88 +- healthcareai-0.1.12/healthcareai/inst/docs |only healthcareai-0.1.12/healthcareai/inst/extdata/unit-test.sqlite |only healthcareai-0.1.12/healthcareai/man/LassoDeployment.Rd | 129 ++- healthcareai-0.1.12/healthcareai/man/LassoDevelopment.Rd | 17 healthcareai-0.1.12/healthcareai/man/LinearMixedModelDeployment.Rd | 67 + healthcareai-0.1.12/healthcareai/man/LinearMixedModelDevelopment.Rd | 9 healthcareai-0.1.12/healthcareai/man/RandomForestDeployment.Rd | 123 ++ healthcareai-0.1.12/healthcareai/man/RandomForestDevelopment.Rd | 27 healthcareai-0.1.12/healthcareai/man/calculateHourBins.Rd |only healthcareai-0.1.12/healthcareai/man/countPercentEmpty.Rd | 2 healthcareai-0.1.12/healthcareai/man/featureAvailabilityProfiler.Rd |only healthcareai-0.1.12/healthcareai/man/generateAUC.Rd | 22 healthcareai-0.1.12/healthcareai/man/getCutOffList.Rd |only healthcareai-0.1.12/healthcareai/man/healthcareai.Rd | 41 healthcareai-0.1.12/healthcareai/man/percentDataAvailableInDateRange.Rd |only healthcareai-0.1.12/healthcareai/man/plotProfiler.Rd |only healthcareai-0.1.12/healthcareai/man/returnColsWithMoreThanFiftyCategories.Rd | 10 healthcareai-0.1.12/healthcareai/man/selectData.Rd | 39 healthcareai-0.1.12/healthcareai/man/writeData.Rd | 45 - healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_combined.rda |binary healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_probability.rda |binary healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_var_import.rda |binary healthcareai-0.1.12/healthcareai/tests/testthat/test-calculate-hour-bins.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-count-percent-empty.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-supervised-model.R | 4 healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-to-df.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-to-sql.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-develop-supervised-model.R | 13 healthcareai-0.1.12/healthcareai/tests/testthat/test-feature-availability-profiler.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-generateAUC.r |only healthcareai-0.1.12/healthcareai/tests/testthat/test-order-by-date.r |only healthcareai-0.1.12/healthcareai/tests/testthat/test-percent-data-available-in-date-range.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-remove-cols-with-all-same-value.r | 4 healthcareai-0.1.12/healthcareai/tests/testthat/test-select-data.r | 73 + healthcareai-0.1.12/healthcareai/tests/testthat/test-write-data.r |only 54 files changed, 1483 insertions(+), 563 deletions(-)
Title: Fixed Rank Kriging
Description: Fixed Rank Kriging is a tool for spatial/spatio-temporal modelling
and prediction with large datasets. The approach, discussed in Cressie and
Johannesson (2008) <DOI:10.1111/j.1467-9868.2007.00633.x>, decomposes the field,
and hence the covariance function, using a fixed set of n basis functions,
where n is typically much smaller than the number of data points (or polygons) m.
The method naturally allows for non-stationary, anisotropic covariance functions
and the use of observations with varying support (with known error variance). The
projected field is a key building block of the Spatial Random Effects (SRE) model,
on which this package is based. The package FRK provides helper functions to model,
fit, and predict using an SRE with relative ease.
Author: Andrew Zammit-Mangion [aut, cre],
Timothy Davis [ctb],
Patrick Amestoy [ctb],
Iain Duff [ctb],
John K. Reid [ctb]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
Diff between FRK versions 0.1.2 dated 2017-04-21 and 0.1.3 dated 2017-05-04
DESCRIPTION | 8 ++-- MD5 | 27 ++++++++------ NAMESPACE | 1 R/AllGeneric.R | 19 +++++++++- R/FRK_wrapper.R | 2 - R/geometryfns.R | 73 +++++++++++++++++++++++++++++++++++++++ inst/doc/FRK_intro.R | 14 +++++++ inst/doc/FRK_intro.Rnw | 29 +++++++++++++++ inst/doc/FRK_intro.pdf |binary man/BAUs_from_points.Rd |only tests/testthat/test_BAUs.R | 16 ++++++++ vignettes/FRK_Sections_21_23.tex | 24 ++++++------ vignettes/FRK_bib.bib | 7 +++ vignettes/FRK_intro.Rnw | 29 +++++++++++++++ vignettes/FRK_intro.fdb_latexmk |only vignettes/FRK_intro.fls |only 16 files changed, 219 insertions(+), 30 deletions(-)
Title: Alternative Factor Coding Matrices for Linear Model Formulae
Description: A collection of coding functions as alternatives to the standard
functions in the stats package, which have names starting with 'contr.'. Their
main advantage is that they provide a consistent method for defining marginal
effects in factorial models. In a simple one-way ANOVA model the
intercept term is always the simple average of the class means.
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between codingMatrices versions 0.3.0 dated 2017-04-18 and 0.3.1 dated 2017-05-04
codingMatrices-0.3.0/codingMatrices/vignettes/Chicago.bst |only codingMatrices-0.3.1/codingMatrices/DESCRIPTION | 6 codingMatrices-0.3.1/codingMatrices/MD5 | 16 codingMatrices-0.3.1/codingMatrices/NAMESPACE | 34 - codingMatrices-0.3.1/codingMatrices/build/vignette.rds |binary codingMatrices-0.3.1/codingMatrices/inst/doc/codingMatrices.R | 272 +++++----- codingMatrices-0.3.1/codingMatrices/inst/doc/codingMatrices.pdf |binary codingMatrices-0.3.1/codingMatrices/man/Codings.Rd | 240 ++++---- codingMatrices-0.3.1/codingMatrices/man/mean_contrasts.Rd | 46 - codingMatrices-0.3.1/codingMatrices/vignettes/chicago.bst |only 10 files changed, 307 insertions(+), 307 deletions(-)
More information about codingMatrices at CRAN
Permanent link
Title: Statistical Inference and Sensitivity Analysis for Instrumental
Variables Model
Description: Contains functions for carrying out instrumental variable
estimation of causal effects, including power analysis, sensitivity analysis,
and diagnostics.
Author: Yang Jiang, Hyunseung Kang, and Dylan Small
Maintainer: Hyunseung Kang <hyunseung@stat.wisc.edu>
Diff between ivmodel versions 1.2 dated 2016-05-09 and 1.6 dated 2017-05-04
ivmodel-1.2/ivmodel/R/yang.r |only ivmodel-1.2/ivmodel/man/summary.ivmodel.Rd |only ivmodel-1.6/ivmodel/DESCRIPTION | 10 - ivmodel-1.6/ivmodel/MD5 | 46 +++++---- ivmodel-1.6/ivmodel/NAMESPACE | 4 ivmodel-1.6/ivmodel/R/AR.r |only ivmodel-1.6/ivmodel/R/ARsens.r |only ivmodel-1.6/ivmodel/R/TSLS.r |only ivmodel-1.6/ivmodel/R/fitted.ivmodel.r | 9 + ivmodel-1.6/ivmodel/R/ivmodel.r | 17 +++ ivmodel-1.6/ivmodel/R/ivmodelFormula.r | 8 - ivmodel-1.6/ivmodel/R/ivpower.r |only ivmodel-1.6/ivmodel/R/ivsize.r |only ivmodel-1.6/ivmodel/R/para.r |only ivmodel-1.6/ivmodel/R/print.ivmodel.r | 81 ++++++++++++++-- ivmodel-1.6/ivmodel/R/residuals.ivmodel.r | 7 + ivmodel-1.6/ivmodel/R/summary.ivmodel.r | 141 ---------------------------- ivmodel-1.6/ivmodel/build/partial.rdb |binary ivmodel-1.6/ivmodel/man/AR.size.Rd | 2 ivmodel-1.6/ivmodel/man/ARsens.power.Rd | 2 ivmodel-1.6/ivmodel/man/ARsens.size.Rd | 2 ivmodel-1.6/ivmodel/man/ARsens.test.Rd | 2 ivmodel-1.6/ivmodel/man/IVpower.Rd |only ivmodel-1.6/ivmodel/man/IVsize.Rd |only ivmodel-1.6/ivmodel/man/ivmodel-internal.Rd | 7 - ivmodel-1.6/ivmodel/man/ivmodel-package.Rd | 2 ivmodel-1.6/ivmodel/man/ivmodel.Rd | 5 ivmodel-1.6/ivmodel/man/ivmodelFormula.Rd | 10 - ivmodel-1.6/ivmodel/man/para.Rd | 2 29 files changed, 161 insertions(+), 196 deletions(-)
Title: Education Survey
Description: Read in and analysis functions for education surveys and
assessments data from the National Center for Education Statistics
(NCES) <https://nces.ed.gov/>, including the National Assessment
of Educational Progress (NAEP)
data <https://nces.ed.gov/nationsreportcard/>.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut],
Huade Huo [aut], Michael Lee [aut], Qingshu Xie [aut], Jiao Yu [aut],
Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 1.0.5 dated 2017-04-26 and 1.0.6 dated 2017-05-04
EdSurvey-1.0.5/EdSurvey/inst/doc/AnalysesUsingAchievementLevelsBasedonPlausibleValues.Rnw |only EdSurvey-1.0.5/EdSurvey/inst/doc/AnalysesUsingAchievementLevelsBasedonPlausibleValues.pdf |only EdSurvey-1.0.5/EdSurvey/inst/doc/accommodations.R |only EdSurvey-1.0.5/EdSurvey/inst/doc/accommodations.Rmd |only EdSurvey-1.0.5/EdSurvey/inst/doc/accommodations.pdf |only EdSurvey-1.0.5/EdSurvey/inst/doc/edsurvey.R |only EdSurvey-1.0.5/EdSurvey/inst/doc/edsurvey.Rmd |only EdSurvey-1.0.5/EdSurvey/inst/doc/edsurvey.pdf |only EdSurvey-1.0.5/EdSurvey/inst/doc/getData.R |only EdSurvey-1.0.5/EdSurvey/inst/doc/getData.Rmd |only EdSurvey-1.0.5/EdSurvey/inst/doc/getData.pdf |only EdSurvey-1.0.5/EdSurvey/inst/doc/statistics.Rmd |only EdSurvey-1.0.5/EdSurvey/inst/doc/statistics.pdf |only EdSurvey-1.0.5/EdSurvey/vignettes/AnalysesUsingAchievementLevelsBasedonPlausibleValues.Rnw |only EdSurvey-1.0.5/EdSurvey/vignettes/accommodations.Rmd |only EdSurvey-1.0.5/EdSurvey/vignettes/edsurvey.Rmd |only EdSurvey-1.0.5/EdSurvey/vignettes/getData.Rmd |only EdSurvey-1.0.5/EdSurvey/vignettes/img |only EdSurvey-1.0.5/EdSurvey/vignettes/statistics.Rmd |only EdSurvey-1.0.6/EdSurvey/DESCRIPTION | 16 EdSurvey-1.0.6/EdSurvey/MD5 | 154 ++-- EdSurvey-1.0.6/EdSurvey/R/achievementLevels.R | 11 EdSurvey-1.0.6/EdSurvey/R/cor.sdf.R | 5 EdSurvey-1.0.6/EdSurvey/R/edsurveyTable.R | 11 EdSurvey-1.0.6/EdSurvey/R/getWeightJkReplicates.R | 5 EdSurvey-1.0.6/EdSurvey/R/hasPlausibleValue.R | 5 EdSurvey-1.0.6/EdSurvey/R/isWeight.R | 5 EdSurvey-1.0.6/EdSurvey/R/lm.sdf.R | 7 EdSurvey-1.0.6/EdSurvey/R/readNAEP.r | 87 +- EdSurvey-1.0.6/EdSurvey/R/showPlausibleValues.R | 16 EdSurvey-1.0.6/EdSurvey/R/showWeights.R | 16 EdSurvey-1.0.6/EdSurvey/build/vignette.rds |binary EdSurvey-1.0.6/EdSurvey/inst/NEWS.Rd |only EdSurvey-1.0.6/EdSurvey/inst/doc/v1edsurvey.R |only EdSurvey-1.0.6/EdSurvey/inst/doc/v1edsurvey.Rmd |only EdSurvey-1.0.6/EdSurvey/inst/doc/v1edsurvey.pdf |only EdSurvey-1.0.6/EdSurvey/inst/doc/v2getData.R |only EdSurvey-1.0.6/EdSurvey/inst/doc/v2getData.Rmd |only EdSurvey-1.0.6/EdSurvey/inst/doc/v2getData.pdf |only EdSurvey-1.0.6/EdSurvey/inst/doc/v3accommodations.R |only EdSurvey-1.0.6/EdSurvey/inst/doc/v3accommodations.Rmd |only EdSurvey-1.0.6/EdSurvey/inst/doc/v3accommodations.pdf |only EdSurvey-1.0.6/EdSurvey/inst/doc/v4statistics.Rmd |only EdSurvey-1.0.6/EdSurvey/inst/doc/v4statistics.pdf |only EdSurvey-1.0.6/EdSurvey/inst/doc/v5AchievementLevels.pdf |only EdSurvey-1.0.6/EdSurvey/inst/doc/v5AchievementLevels.pdf.asis |only EdSurvey-1.0.6/EdSurvey/man/achievementLevels.Rd | 67 -- EdSurvey-1.0.6/EdSurvey/man/cor.sdf.Rd | 76 +- EdSurvey-1.0.6/EdSurvey/man/edsurveyTable.Rd | 23 EdSurvey-1.0.6/EdSurvey/man/examples/achievementLevels.R | 66 -- EdSurvey-1.0.6/EdSurvey/man/examples/cor.sdf.R | 76 +- EdSurvey-1.0.6/EdSurvey/man/examples/edsurveyTable.R | 23 EdSurvey-1.0.6/EdSurvey/man/examples/getData.R | 27 EdSurvey-1.0.6/EdSurvey/man/examples/getPlausibleValue.R | 2 EdSurvey-1.0.6/EdSurvey/man/examples/getWeightJkReplicates.R | 2 EdSurvey-1.0.6/EdSurvey/man/examples/hasPlausibleValue.R | 4 EdSurvey-1.0.6/EdSurvey/man/examples/isWeight.R | 4 EdSurvey-1.0.6/EdSurvey/man/examples/levelsSDF.R | 20 EdSurvey-1.0.6/EdSurvey/man/examples/lm.sdf.R | 25 EdSurvey-1.0.6/EdSurvey/man/examples/readNAEP.R | 4 EdSurvey-1.0.6/EdSurvey/man/examples/searchSDF.R | 8 EdSurvey-1.0.6/EdSurvey/man/examples/showCutPoints.R | 2 EdSurvey-1.0.6/EdSurvey/man/examples/showPlausibleValues.R | 2 EdSurvey-1.0.6/EdSurvey/man/examples/showWeights.R | 2 EdSurvey-1.0.6/EdSurvey/man/examples/subset.edsurvey.data.frame.R | 30 EdSurvey-1.0.6/EdSurvey/man/getData.Rd | 27 EdSurvey-1.0.6/EdSurvey/man/getPlausibleValue.Rd | 2 EdSurvey-1.0.6/EdSurvey/man/getWeightJkReplicates.Rd | 6 EdSurvey-1.0.6/EdSurvey/man/hasPlausibleValue.Rd | 8 EdSurvey-1.0.6/EdSurvey/man/isWeight.Rd | 8 EdSurvey-1.0.6/EdSurvey/man/levelsSDF.Rd | 20 EdSurvey-1.0.6/EdSurvey/man/lm.sdf.Rd | 25 EdSurvey-1.0.6/EdSurvey/man/readNAEP.Rd | 4 EdSurvey-1.0.6/EdSurvey/man/searchSDF.Rd | 8 EdSurvey-1.0.6/EdSurvey/man/showCutPoints.Rd | 2 EdSurvey-1.0.6/EdSurvey/man/showPlausibleValues.Rd | 6 EdSurvey-1.0.6/EdSurvey/man/showWeights.Rd | 6 EdSurvey-1.0.6/EdSurvey/man/subset.edsurvey.data.frame.Rd | 30 EdSurvey-1.0.6/EdSurvey/tests/Examples/edsurvey-Ex.Rout.save | 311 ++++------ EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test1.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test2.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test3.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test4.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test5.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test6.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/aLevels_test7.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/es1.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/es2.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/es2b.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/es3.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/es4.rds |binary EdSurvey-1.0.6/EdSurvey/tests/testthat/test-0-main.R | 4 EdSurvey-1.0.6/EdSurvey/vignettes/v1edsurvey.Rmd |only EdSurvey-1.0.6/EdSurvey/vignettes/v2getData.Rmd |only EdSurvey-1.0.6/EdSurvey/vignettes/v3accommodations.Rmd |only EdSurvey-1.0.6/EdSurvey/vignettes/v4statistics.Rmd |only EdSurvey-1.0.6/EdSurvey/vignettes/v5AchievementLevels.pdf.asis |only 97 files changed, 609 insertions(+), 659 deletions(-)
Title: Export Data from R so DataGraph can Read it
Description: Functions to save either '.dtable' or '.dtbin' files that can be read by DataGraph, a graphing and analysis application for macOS. Can save a data frame, collection of data frames and sequences of data frames and individual vectors. For more information see <https://www.visualdatatools.com/DataGraph/Help/DataFiles/R/index.html>.
Author: David Adalsteinsson
Maintainer: David Adalsteinsson <david@visualdatatools.com>
Diff between DataGraph versions 1.0 dated 2017-05-03 and 1.0.1 dated 2017-05-04
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ man/addDTBin.Rd | 2 ++ man/addDTable.Rd | 2 ++ man/closeDTBin.Rd | 2 ++ man/closeDTable.Rd | 2 ++ man/infoDTBin.Rd | 2 ++ man/openDTBin.Rd | 2 ++ man/openDTable.Rd | 2 ++ man/syncDTBin.Rd | 2 ++ man/syncDTable.Rd | 2 ++ man/writeDTable.Rd | 2 ++ src/DTUtilities.h | 2 ++ 13 files changed, 37 insertions(+), 15 deletions(-)
Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for UTF8-encoded Unicode text. The package provides the ability to seamlessly read and process text from large JSON files without holding all of the data in memory simultaneously.
Author: Patrick O. Perry [aut, cre],
Martin Porter and Richard Boulton [ctb, cph] (Snowball),
Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between corpus versions 0.2-0 dated 2017-04-16 and 0.3.0 dated 2017-05-04
corpus-0.2-0/corpus/R/dataset.R |only corpus-0.2-0/corpus/R/json.R |only corpus-0.2-0/corpus/man/read_json.Rd |only corpus-0.2-0/corpus/src/dataset.c |only corpus-0.2-0/corpus/tests/testthat/test-dataset_scalar.R |only corpus-0.2-0/corpus/tests/testthat/test-read_json.R |only corpus-0.3.0/corpus/DESCRIPTION | 12 corpus-0.3.0/corpus/MD5 | 203 ++- corpus-0.3.0/corpus/NAMESPACE | 46 corpus-0.3.0/corpus/R/jsondata.R |only corpus-0.3.0/corpus/R/text-proc.R | 19 corpus-0.3.0/corpus/R/text.R | 170 +- corpus-0.3.0/corpus/man/read_ndjson.Rd |only corpus-0.3.0/corpus/man/segmentation.Rd | 13 corpus-0.3.0/corpus/man/text.Rd | 39 corpus-0.3.0/corpus/man/tokens.Rd | 15 corpus-0.3.0/corpus/src/Makevars | 34 corpus-0.3.0/corpus/src/corpus/Doxyfile | 46 corpus-0.3.0/corpus/src/corpus/LICENSE.Snowball |only corpus-0.3.0/corpus/src/corpus/LICENSE.Unicode |only corpus-0.3.0/corpus/src/corpus/Makefile | 83 + corpus-0.3.0/corpus/src/corpus/NEWS.md | 7 corpus-0.3.0/corpus/src/corpus/README.md | 34 corpus-0.3.0/corpus/src/corpus/TODO.md | 37 corpus-0.3.0/corpus/src/corpus/corpus.xcodeproj/project.pbxproj | 372 +++++ corpus-0.3.0/corpus/src/corpus/lib/libstemmer_c |only corpus-0.3.0/corpus/src/corpus/src/census.c |only corpus-0.3.0/corpus/src/corpus/src/census.h |only corpus-0.3.0/corpus/src/corpus/src/data.c | 29 corpus-0.3.0/corpus/src/corpus/src/data.h | 1 corpus-0.3.0/corpus/src/corpus/src/datatype.c | 2 corpus-0.3.0/corpus/src/corpus/src/datatype.h | 2 corpus-0.3.0/corpus/src/corpus/src/error.h | 4 corpus-0.3.0/corpus/src/corpus/src/filebuf.c | 63 - corpus-0.3.0/corpus/src/corpus/src/main.c | 12 corpus-0.3.0/corpus/src/corpus/src/main_scan.c | 4 corpus-0.3.0/corpus/src/corpus/src/main_sentences.c |only corpus-0.3.0/corpus/src/corpus/src/main_tokens.c | 32 corpus-0.3.0/corpus/src/corpus/src/render.c | 29 corpus-0.3.0/corpus/src/corpus/src/sentscan.c | 14 corpus-0.3.0/corpus/src/corpus/src/sentscan.h | 2 corpus-0.3.0/corpus/src/corpus/src/symtab.c | 6 corpus-0.3.0/corpus/src/corpus/src/symtab.h | 6 corpus-0.3.0/corpus/src/corpus/src/token.c | 97 + corpus-0.3.0/corpus/src/corpus/src/token.h | 33 corpus-0.3.0/corpus/src/corpus/src/unicode.c | 193 +++ corpus-0.3.0/corpus/src/corpus/src/unicode.h | 14 corpus-0.3.0/corpus/src/corpus/src/unicode/compose.h |only corpus-0.3.0/corpus/src/corpus/tests/check_census.c |only corpus-0.3.0/corpus/src/corpus/tests/check_data.c | 35 corpus-0.3.0/corpus/src/corpus/tests/check_sentscan.c | 11 corpus-0.3.0/corpus/src/corpus/tests/check_symtab.c | 2 corpus-0.3.0/corpus/src/corpus/tests/check_token.c | 59 corpus-0.3.0/corpus/src/corpus/tests/check_unicode.c | 126 ++ corpus-0.3.0/corpus/src/corpus/util/gen-compose.py |only corpus-0.3.0/corpus/src/decode.c |only corpus-0.3.0/corpus/src/filebuf.c | 80 + corpus-0.3.0/corpus/src/init.c | 34 corpus-0.3.0/corpus/src/json.c | 113 - corpus-0.3.0/corpus/src/jsondata.c |only corpus-0.3.0/corpus/src/mkchar.c |only corpus-0.3.0/corpus/src/rcorpus.h | 90 + corpus-0.3.0/corpus/src/text.c | 628 ++++++---- corpus-0.3.0/corpus/src/text_filter.c | 22 corpus-0.3.0/corpus/src/text_methods.c |only corpus-0.3.0/corpus/src/text_proc.c | 151 +- corpus-0.3.0/corpus/tests/testthat/test-jsondata_record.R |only corpus-0.3.0/corpus/tests/testthat/test-jsondata_scalar.R |only corpus-0.3.0/corpus/tests/testthat/test-jsondata_serialize.R |only corpus-0.3.0/corpus/tests/testthat/test-read_ndjson.R |only corpus-0.3.0/corpus/tests/testthat/test-sentences.R | 105 + corpus-0.3.0/corpus/tests/testthat/test-text.R |only corpus-0.3.0/corpus/tests/testthat/test-text_names.R | 49 corpus-0.3.0/corpus/tests/testthat/test-tokens.R | 16 74 files changed, 2414 insertions(+), 780 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb],
Andreas Mayr [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between mboost versions 2.7-0 dated 2016-11-23 and 2.8-0 dated 2017-05-04
mboost-2.7-0/mboost/inst/india_fit.R |only mboost-2.8-0/mboost/DESCRIPTION | 17 mboost-2.8-0/mboost/MD5 | 169 mboost-2.8-0/mboost/NAMESPACE | 206 mboost-2.8-0/mboost/R/AAA.R | 58 mboost-2.8-0/mboost/R/bkernel.R |only mboost-2.8-0/mboost/R/bkronecker.R | 550 - mboost-2.8-0/mboost/R/bl.R | 2301 ++--- mboost-2.8-0/mboost/R/bmono.R | 789 - mboost-2.8-0/mboost/R/bmrf.R | 210 mboost-2.8-0/mboost/R/bolscw.R | 248 mboost-2.8-0/mboost/R/brad.R | 326 mboost-2.8-0/mboost/R/btree.R | 226 mboost-2.8-0/mboost/R/buser.R | 202 mboost-2.8-0/mboost/R/confint.R | 652 - mboost-2.8-0/mboost/R/control.R | 28 mboost-2.8-0/mboost/R/crossvalidation.R | 372 mboost-2.8-0/mboost/R/family.R | 2149 ++-- mboost-2.8-0/mboost/R/helpers.R | 565 - mboost-2.8-0/mboost/R/mboost.R | 1656 +-- mboost-2.8-0/mboost/R/mboost_intern.R | 20 mboost-2.8-0/mboost/R/methods.R | 1275 +- mboost-2.8-0/mboost/R/plot.R | 430 mboost-2.8-0/mboost/R/stabsel.R | 174 mboost-2.8-0/mboost/R/survival.R | 202 mboost-2.8-0/mboost/R/varimp.R | 501 - mboost-2.8-0/mboost/README.md | 104 mboost-2.8-0/mboost/build/vignette.rds |binary mboost-2.8-0/mboost/cleanup | 140 mboost-2.8-0/mboost/inst/CITATION | 173 mboost-2.8-0/mboost/inst/India_quantiles.R | 76 mboost-2.8-0/mboost/inst/NEWS.Rd | 1873 ++-- mboost-2.8-0/mboost/inst/birds_Biometrics.R | 196 mboost-2.8-0/mboost/inst/cache/mboost_illustrations_benchmarks.R | 298 mboost-2.8-0/mboost/inst/doc/SurvivalEnsembles.R | 564 - mboost-2.8-0/mboost/inst/doc/SurvivalEnsembles.Rnw | 812 - mboost-2.8-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary mboost-2.8-0/mboost/inst/doc/mboost.R | 344 mboost-2.8-0/mboost/inst/doc/mboost.Rnw | 898 +- mboost-2.8-0/mboost/inst/doc/mboost.pdf |binary mboost-2.8-0/mboost/inst/doc/mboost_illustrations.R | 672 - mboost-2.8-0/mboost/inst/doc/mboost_illustrations.Rnw | 1388 +-- mboost-2.8-0/mboost/inst/doc/mboost_illustrations.pdf |binary mboost-2.8-0/mboost/inst/doc/mboost_tutorial.R | 1198 +- mboost-2.8-0/mboost/inst/doc/mboost_tutorial.Rnw | 4208 ++++----- mboost-2.8-0/mboost/inst/doc/mboost_tutorial.pdf |binary mboost-2.8-0/mboost/inst/india_additive.R | 144 mboost-2.8-0/mboost/inst/india_analysis.R | 298 mboost-2.8-0/mboost/inst/india_blackboost.R | 104 mboost-2.8-0/mboost/inst/india_helpfunc.R | 378 mboost-2.8-0/mboost/inst/india_plots.R | 1212 +- mboost-2.8-0/mboost/inst/india_preproc.R | 550 - mboost-2.8-0/mboost/inst/india_rqss.R | 60 mboost-2.8-0/mboost/inst/india_rqssResults.R | 290 mboost-2.8-0/mboost/inst/india_rqss_lambdaOptFunc.R | 96 mboost-2.8-0/mboost/inst/india_stumps.R | 104 mboost-2.8-0/mboost/inst/india_summary.R | 426 mboost-2.8-0/mboost/inst/india_vcm.R | 180 mboost-2.8-0/mboost/inst/mboost_Bioinf.R | 202 mboost-2.8-0/mboost/inst/readAML_Bullinger.R | 298 mboost-2.8-0/mboost/man/FP.Rd | 136 mboost-2.8-0/mboost/man/Family.Rd | 769 - mboost-2.8-0/mboost/man/IPCweights.Rd | 84 mboost-2.8-0/mboost/man/baselearners.Rd | 1735 +-- mboost-2.8-0/mboost/man/blackboost.Rd | 234 mboost-2.8-0/mboost/man/boost_family-class.Rd | 76 mboost-2.8-0/mboost/man/confint.Rd | 354 mboost-2.8-0/mboost/man/control.Rd | 105 mboost-2.8-0/mboost/man/cvrisk.Rd | 396 mboost-2.8-0/mboost/man/gamboost.Rd | 236 mboost-2.8-0/mboost/man/glmboost.Rd | 298 mboost-2.8-0/mboost/man/mboost.Rd | 286 mboost-2.8-0/mboost/man/mboost_intern.Rd | 46 mboost-2.8-0/mboost/man/mboost_package.Rd | 617 - mboost-2.8-0/mboost/man/methods.Rd | 933 +- mboost-2.8-0/mboost/man/plot.Rd | 412 mboost-2.8-0/mboost/man/stabsel.Rd | 279 mboost-2.8-0/mboost/man/varimp.Rd | 288 mboost-2.8-0/mboost/src/init.c |only mboost-2.8-0/mboost/vignettes/SurvivalEnsembles.Rnw | 812 - mboost-2.8-0/mboost/vignettes/boost.bib | 4478 +++++----- mboost-2.8-0/mboost/vignettes/jmlr2e.sty | 642 - mboost-2.8-0/mboost/vignettes/mboost.Rnw | 898 +- mboost-2.8-0/mboost/vignettes/mboost_illustrations.Rnw | 1388 +-- mboost-2.8-0/mboost/vignettes/mboost_tutorial.Rnw | 4208 ++++----- mboost-2.8-0/mboost/vignettes/mboost_tutorial.bib | 833 - mboost-2.8-0/mboost/vignettes/setup.R | 66 87 files changed, 25778 insertions(+), 25443 deletions(-)
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census Bureau provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and
X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau
offers both source and binary versions -- which this package integrates for
use by other R packages.
Author: Dirk Eddelbuettel and Christoph Sax
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 0.1.2 dated 2016-03-14 and 1.1.39-1 dated 2017-05-04
ChangeLog | 12 +++++++++ DESCRIPTION | 18 +++++++------- LICENSE | 50 ++++++++++++++++++++++----------------- MD5 | 16 ++++++------ R/supportedPlatform.R | 6 ++-- README.md | 14 ++++++++--- configure | 10 ++++--- configure.win | 2 - inst/COPYRIGHT | 63 ++++++++++++++++++++++++++++---------------------- 9 files changed, 114 insertions(+), 77 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3.
Author: Jean-Romain Roussel [aut, cre, cph],
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R),
Florian De Boissieu [ctb] (Enable support of .lax file)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.1.1 dated 2017-03-15 and 1.1.2 dated 2017-05-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/writeLAS.r | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: An integrated set of tools for thermodynamic calculations in compositional
biology and geochemistry. Thermodynamic properties are taken from a database for minerals
and inorganic and organic aqueous species including biomolecules, or from amino acid
group additivity for proteins. High-temperature properties are calculated using the
revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions are
provided to define a system using basis species, automatically balance reactions,
calculate the chemical affinities of reactions for selected species, and plot the results
on potential diagrams or equilibrium activity diagrams. Experimental features are
available to calculate activity coefficients for aqueous species or for multidimensional
optimization of thermodynamic variables using an objective function.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.8 dated 2016-05-28 and 1.1.0 dated 2017-05-04
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CHNOSZ-1.1.0/CHNOSZ/R/add.protein.R |only CHNOSZ-1.1.0/CHNOSZ/R/affinity.R | 7 CHNOSZ-1.1.0/CHNOSZ/R/anim.R | 66 CHNOSZ-1.1.0/CHNOSZ/R/basis.R | 187 - CHNOSZ-1.1.0/CHNOSZ/R/buffer.R | 18 CHNOSZ-1.1.0/CHNOSZ/R/diagram.R | 149 - CHNOSZ-1.1.0/CHNOSZ/R/equilibrate.R | 27 CHNOSZ-1.1.0/CHNOSZ/R/examples.R | 36 CHNOSZ-1.1.0/CHNOSZ/R/findit.R | 10 CHNOSZ-1.1.0/CHNOSZ/R/hkf.R | 2 CHNOSZ-1.1.0/CHNOSZ/R/info.R | 144 CHNOSZ-1.1.0/CHNOSZ/R/makeup.R | 267 - CHNOSZ-1.1.0/CHNOSZ/R/more.aa.R | 4 CHNOSZ-1.1.0/CHNOSZ/R/mosaic.R | 6 CHNOSZ-1.1.0/CHNOSZ/R/nonideal.R | 4 CHNOSZ-1.1.0/CHNOSZ/R/objective.R | 24 CHNOSZ-1.1.0/CHNOSZ/R/palply.R |only CHNOSZ-1.1.0/CHNOSZ/R/protein.info.R | 248 - CHNOSZ-1.1.0/CHNOSZ/R/read.expr.R | 29 CHNOSZ-1.1.0/CHNOSZ/R/revisit.R | 118 CHNOSZ-1.1.0/CHNOSZ/R/species.R | 79 CHNOSZ-1.1.0/CHNOSZ/R/subcrt.R | 37 CHNOSZ-1.1.0/CHNOSZ/R/swap.basis.R | 22 CHNOSZ-1.1.0/CHNOSZ/R/transfer.R | 11 CHNOSZ-1.1.0/CHNOSZ/R/util.affinity.R | 50 CHNOSZ-1.1.0/CHNOSZ/R/util.args.R | 30 CHNOSZ-1.1.0/CHNOSZ/R/util.character.R | 38 CHNOSZ-1.1.0/CHNOSZ/R/util.data.R | 269 + CHNOSZ-1.1.0/CHNOSZ/R/util.expression.R | 82 CHNOSZ-1.1.0/CHNOSZ/R/util.fasta.R | 130 CHNOSZ-1.1.0/CHNOSZ/R/util.formula.R | 55 CHNOSZ-1.1.0/CHNOSZ/R/util.list.R | 3 CHNOSZ-1.1.0/CHNOSZ/R/util.misc.R | 97 CHNOSZ-1.1.0/CHNOSZ/R/util.plot.R | 254 - CHNOSZ-1.1.0/CHNOSZ/R/util.protein.R |only CHNOSZ-1.1.0/CHNOSZ/R/util.units.R | 90 CHNOSZ-1.1.0/CHNOSZ/R/util.water.R | 18 CHNOSZ-1.1.0/CHNOSZ/R/water.R | 20 CHNOSZ-1.1.0/CHNOSZ/R/wjd.R | 10 CHNOSZ-1.1.0/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.1.0/CHNOSZ/data/buffer.csv | 2 CHNOSZ-1.1.0/CHNOSZ/data/protein.csv | 917 +++--- CHNOSZ-1.1.0/CHNOSZ/data/refs.csv | 236 - CHNOSZ-1.1.0/CHNOSZ/data/thermo.R | 48 CHNOSZ-1.1.0/CHNOSZ/demo/00Index | 19 CHNOSZ-1.1.0/CHNOSZ/demo/NaCl.R | 5 CHNOSZ-1.1.0/CHNOSZ/demo/ORP.R | 25 CHNOSZ-1.1.0/CHNOSZ/demo/Shh.R |only CHNOSZ-1.1.0/CHNOSZ/demo/activity_ratios.R |only CHNOSZ-1.1.0/CHNOSZ/demo/affinity.R |only CHNOSZ-1.1.0/CHNOSZ/demo/buffer.R | 77 CHNOSZ-1.1.0/CHNOSZ/demo/bugstab.R |only CHNOSZ-1.1.0/CHNOSZ/demo/copper.R | 8 CHNOSZ-1.1.0/CHNOSZ/demo/dehydration.R | 7 CHNOSZ-1.1.0/CHNOSZ/demo/findit.R | 2 CHNOSZ-1.1.0/CHNOSZ/demo/ionize.R | 2 CHNOSZ-1.1.0/CHNOSZ/demo/mosaic.R | 7 CHNOSZ-1.1.0/CHNOSZ/demo/protbuff.R |only CHNOSZ-1.1.0/CHNOSZ/demo/protein.equil.R |only CHNOSZ-1.1.0/CHNOSZ/demo/revisit.R | 27 CHNOSZ-1.1.0/CHNOSZ/demo/solubility.R | 6 CHNOSZ-1.1.0/CHNOSZ/demo/sources.R | 34 CHNOSZ-1.1.0/CHNOSZ/demo/wjd.R | 36 CHNOSZ-1.1.0/CHNOSZ/demo/yeastgfp.R | 29 CHNOSZ-1.1.0/CHNOSZ/inst/CHECKLIST | 35 CHNOSZ-1.1.0/CHNOSZ/inst/CITATION | 2 CHNOSZ-1.1.0/CHNOSZ/inst/NEWS | 202 + CHNOSZ-1.1.0/CHNOSZ/inst/doc/anintro.R | 2024 +++++++++++--- CHNOSZ-1.1.0/CHNOSZ/inst/doc/anintro.Rmd |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/anintro.html |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/eos-regress.R |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/eos-regress.Rmd |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/eos-regress.html |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/equilibrium.R | 25 CHNOSZ-1.1.0/CHNOSZ/inst/doc/equilibrium.Rnw | 92 CHNOSZ-1.1.0/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.1.0/CHNOSZ/inst/doc/hotspring.R | 6 CHNOSZ-1.1.0/CHNOSZ/inst/doc/hotspring.Rnw | 77 CHNOSZ-1.1.0/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.1.0/CHNOSZ/inst/doc/obigt.R |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/obigt.Rmd |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/obigt.html |only CHNOSZ-1.1.0/CHNOSZ/inst/doc/wjd.R | 114 CHNOSZ-1.1.0/CHNOSZ/inst/doc/wjd.Rnw | 133 CHNOSZ-1.1.0/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.1.0/CHNOSZ/inst/extdata/OBIGT |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/abundance/TBD+05.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/abundance/microbes.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/cpetc/PM90.csv | 32 CHNOSZ-1.1.0/CHNOSZ/inst/extdata/cpetc/SS98_Fig5a.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/cpetc/SS98_Fig5b.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/cpetc/rubisco.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/fasta/rubisco.fasta |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/protein/microbial.aa.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/supcrt |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/thermo/BZA10.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/thermo/Ste01.csv |only CHNOSZ-1.1.0/CHNOSZ/inst/extdata/thermo/obigt_check.csv | 494 +-- CHNOSZ-1.1.0/CHNOSZ/man/CHNOSZ-package.Rd | 111 CHNOSZ-1.1.0/CHNOSZ/man/EOSregress.Rd | 58 CHNOSZ-1.1.0/CHNOSZ/man/IAPWS95.Rd | 19 CHNOSZ-1.1.0/CHNOSZ/man/add.protein.Rd |only CHNOSZ-1.1.0/CHNOSZ/man/affinity.Rd | 214 - 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CHNOSZ-1.1.0/CHNOSZ/vignettes/hotspring.Rnw | 77 CHNOSZ-1.1.0/CHNOSZ/vignettes/hotspring.lyx | 91 CHNOSZ-1.1.0/CHNOSZ/vignettes/obigt.Rmd |only CHNOSZ-1.1.0/CHNOSZ/vignettes/obigt.bib |only CHNOSZ-1.1.0/CHNOSZ/vignettes/obigt.css |only CHNOSZ-1.1.0/CHNOSZ/vignettes/rubisco.svg |only CHNOSZ-1.1.0/CHNOSZ/vignettes/vig.bib | 1140 ++++--- CHNOSZ-1.1.0/CHNOSZ/vignettes/vig.css |only CHNOSZ-1.1.0/CHNOSZ/vignettes/wjd.Rnw | 133 CHNOSZ-1.1.0/CHNOSZ/vignettes/wjd.lyx | 238 + 214 files changed, 7020 insertions(+), 5529 deletions(-)
Title: Similarity and Distance Quantification Between Probability
Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions. These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between philentropy versions 0.0.1 dated 2017-04-25 and 0.0.2 dated 2017-05-04
DESCRIPTION | 8 +++---- MD5 | 15 +++++++------ NEWS.md |only R/dist.diversity.R | 2 - R/distance.R | 10 ++++---- README.md | 16 ++++++++++++-- src/InformationTheory.h | 10 ++++---- src/correlation.h | 26 +++++++++++------------ src/distances.h | 54 ++++++++++++++++++++++++------------------------ 9 files changed, 77 insertions(+), 64 deletions(-)
Title: Protracted Birth-Death Model of Diversification
Description: Conducts maximum likelihood analysis and simulation of the
protracted birth-death model of diversification. See
Etienne, R.S. & J. Rosindell 2012 <doi:10.1093/sysbio/syr091>;
Lambert, A., H. Morlon & R.S. Etienne 2014, <doi:10.1007/s00285-014-0767-x>;
Etienne, R.S., H. Morlon & A. Lambert 2014, <doi:10.1111/evo.12433>.
Author: Rampal S. Etienne
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between PBD versions 1.3 dated 2017-04-29 and 1.4 dated 2017-05-04
PBD-1.3/PBD/R/pbd_simplex.R |only PBD-1.3/PBD/man/PBD-internal.Rd |only PBD-1.3/PBD/tests/testthat/test-test_pbd_sim.R |only PBD-1.4/PBD/DESCRIPTION | 8 - PBD-1.4/PBD/MD5 | 18 +- PBD-1.4/PBD/NAMESPACE | 1 PBD-1.4/PBD/R/pbd_ML.R | 1 PBD-1.4/PBD/R/pbd_durspec_mean.R | 35 +++-- PBD-1.4/PBD/R/pbd_loglik.R | 166 +++++++++++++------------ PBD-1.4/PBD/inst/doc/PBD_ML_demo.html | 4 PBD-1.4/PBD/man/PBD-package.Rd | 7 - PBD-1.4/PBD/tests/testthat/test-test_PBD.R |only 12 files changed, 127 insertions(+), 113 deletions(-)
Title: Stock Assessment Graphs Database Web Services
Description: R interface to access the web services of the ICES Stock Assessment
Graphs database <http://sg.ices.dk>.
Author: Colin Millar [aut, cre],
Scott Large [aut],
Arni Magnusson [aut],
Carlos Pinto [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesSAG versions 1.3-0 dated 2017-04-30 and 1.3-1 dated 2017-05-04
DESCRIPTION | 16 +- MD5 | 30 ++-- NAMESPACE | 1 NEWS | 8 + R/SAGtokens.R | 4 R/SAGxml.R | 284 +++++++++++++++++++++++++++++-------------- R/findAssessmentKey.R | 11 + R/getsetSettingsForAStock.R | 1 R/uploadStock.R | 47 ++++++- R/uploadXMLFile.R | 3 R/utilities.R | 12 - man/findAssessmentKeydocs.Rd | 10 - man/readCreateSAGxml.Rd | 10 - man/stockInfo.Rd | 15 +- man/uploadStock.Rd | 4 tests/testthat/test-test.R | 42 ++++-- 16 files changed, 332 insertions(+), 166 deletions(-)
Title: Generate, Visualise, and Compare Fast and Frugal Decision Trees
Description: Create, visualise, and test fast and frugal decision trees (FFTrees). FFTrees are very simple decision trees for
classifying cases (i.e.; breast cancer patients) into one of two classes (e.g.;
no cancer vs. true cancer) based on a small number of cues (e.g.; test results). FFTrees can be preferable to more complex algorithms because they are easy to communicate, require very little information, and are
robust against overfitting.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Diff between FFTrees versions 1.2.2 dated 2017-04-18 and 1.2.3 dated 2017-05-04
DESCRIPTION | 10 +-- MD5 | 64 ++++++++++++------------ NAMESPACE | 1 R/FFForest.R | 46 ++++++++--------- R/FFTrees.R | 57 ++++++++++++++-------- R/applytree_function.R | 8 +-- R/classtable_function.R | 9 +++ R/comppred_function.R | 3 - R/cuerank_function.R | 14 +++-- R/growFFTrees_function.R | 70 +++++++++------------------ R/helper.R | 2 R/plotFFForest.R | 28 +++++----- R/predictFFTrees_function.R | 38 +++++++++++--- R/printFFForest_function.R | 6 +- R/printFFTrees_function.R | 43 +++++++++++++--- R/zzz.R | 13 ++--- README.md | 6 ++ build/vignette.rds |binary inst/doc/FFTrees_algorithm.html | 8 +-- inst/doc/FFTrees_examples.html | 29 +++++------ inst/doc/FFTrees_function.Rmd | 4 - inst/doc/FFTrees_function.html | 103 ++++++++++++++++++++-------------------- inst/doc/FFTrees_plot.html | 4 - inst/doc/guide.html | 8 +-- man/FFForest.Rd | 6 +- man/FFTrees.Rd | 10 ++- man/apply.tree.Rd | 4 + man/classtable.Rd | 4 + man/comp.pred.Rd | 2 man/cuerank.Rd | 6 +- man/grow.FFTrees.Rd | 12 ++-- man/predict.FFTrees.Rd | 8 +-- vignettes/FFTrees_function.Rmd | 4 - 33 files changed, 353 insertions(+), 277 deletions(-)
Title: Local Polynomial Regression of State Dependent Covariates in
State-Space Models
Description: Facilitates local polynomial regression for state dependent covariates in state-space models. The functionality can also be used from 'C++' based model builder tools such as 'Rcpp'/'inline', 'TMB', or 'JAGS'.
Author: Christoffer Moesgaard Albertsen [aut, cre]
Maintainer: Christoffer Moesgaard Albertsen <cmoe@aqua.dtu.dk>
Diff between covafillr versions 0.4.0 dated 2017-02-16 and 0.4.1 dated 2017-05-04
DESCRIPTION | 11 ++--- LICENSE | 2 MD5 | 41 ++++++++++--------- NAMESPACE | 3 - NEWS | 12 +++++ R/covafill.R | 50 +++++++++++++++--------- R/covatree.R | 35 ++++++++++++---- R/zzz.R.in | 4 - README.md | 35 ++++++++++------ inst/examples/rcode/rtest.R | 2 inst/include/covafill/src/JAGS/covafillJAGS.cpp | 7 ++- man/covafill-class.Rd | 8 ++- man/covatree-class.Rd | 8 ++- man/cxxFlags.Rd | 9 +--- man/kde.Rd | 3 - man/loadJAGSModule.Rd | 9 +--- man/stat_covafill.Rd | 9 +--- man/suggestBandwith.Rd | 3 - src/headers/fill.hpp | 14 ++++++ src/main.cpp | 2 tools |only 21 files changed, 170 insertions(+), 97 deletions(-)
More information about ContourFunctions at CRAN
Permanent link
Title: Graphical User Interface for Seasonal Adjustment
Description: A graphical user interface to the 'seasonal' package and
'X-13ARIMA-SEATS', the U.S. Census Bureau's seasonal adjustment software.
Unifies the code base of <http://www.seasonal.website> and the GUI in the
'seasonal' package.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonalview versions 0.2 dated 2017-02-11 and 0.3 dated 2017-05-04
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NEWS | 16 +++++++++++++++- R/err_to_html.R |only R/fopts.R | 4 +++- R/importable-xts.R | 1 + R/plot_dypraph.R | 2 +- R/series0.R | 6 +++--- inst/app/server.R | 31 +++++-------------------------- inst/app/www/docs.css | 15 +++++++++++---- 10 files changed, 53 insertions(+), 49 deletions(-)
Title: Radiomics Image Analysis Toolbox for Grayscale Images
Description: Radiomics image analysis toolbox for grayscale 2D and 3D images. RIA calculates first-order,
gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics.
Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation
of several thousands of parameters only takes minutes on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@cirg.hu>
Diff between RIA versions 1.0.0 dated 2017-03-19 and 1.0.1 dated 2017-05-04
DESCRIPTION | 8 +- MD5 | 10 +-- R/ZZZ.R | 2 R/glcm_stat.R | 160 +++++++++++++++++++++++++++++++++++++++++++++++++++++ R/glcm_stat_plus.R | 52 ++++++++++------- inst/CITATION | 4 - 6 files changed, 205 insertions(+), 31 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (see <http://www.maxquant.org>).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow <chris.bielow@fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@fu-berlin.de>
Diff between PTXQC versions 0.82.3 dated 2017-04-03 and 0.82.5 dated 2017-05-04
DESCRIPTION | 8 MD5 | 48 - NEWS | 6 R/MQDataReader.R | 5 R/fcn_computeQC.R | 4 R/qcMetric.R | 6 README.md | 39 - build/vignette.rds |binary inst/CITATION | 17 inst/doc/PTXQC-Basic_Guide_for_R_users.R | 7 inst/doc/PTXQC-Basic_Guide_for_R_users.Rmd | 7 inst/doc/PTXQC-Basic_Guide_for_R_users.html | 695 ++++++++++++++++---------- inst/doc/PTXQC-CustomizeReport.html | 96 ++- inst/doc/PTXQC-DragNDrop.html | 96 ++- inst/doc/PTXQC-FAQ.Rmd | 10 inst/doc/PTXQC-FAQ.html | 103 +++ inst/doc/PTXQC-Input_And_Output_Data.Rmd | 4 inst/doc/PTXQC-Input_And_Output_Data.html | 96 ++- inst/dragNdrop/README.md | 16 inst/examples/README.md | 4 inst/reportTemplate/PTXQC_report_template.Rmd | 2 man/MQDataReader-cash-readMQ.Rd | 4 vignettes/PTXQC-Basic_Guide_for_R_users.Rmd | 7 vignettes/PTXQC-FAQ.Rmd | 10 vignettes/PTXQC-Input_And_Output_Data.Rmd | 4 25 files changed, 884 insertions(+), 410 deletions(-)
Title: Bindings for the 'HaveIBeenPwned.com' Data Breach API
Description: Utilising the 'Have I been pwned?' API (see <https://haveibeenpwned.com/API/v2>
for more information), check whether email addresses and/or user names have been present
in a publicly disclosed data breach.
Author: Steph Locke [aut, cre],
Troy Hunt [aut] (HaveIBeenPwned.com)
Maintainer: Steph Locke <stephanie.g.locke@gmail.com>
Diff between HIBPwned versions 0.1.3 dated 2016-09-14 and 0.1.4 dated 2017-05-04
DESCRIPTION | 10 +- MD5 | 32 +++---- NAMESPACE | 4 NEWS.md | 3 R/HIBPwned-package.r | 3 R/utils.R | 8 + README.md | 217 ++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/HIBP.html | 103 +++++++++++----------- man/GETcontent.Rd | 1 man/HIBP_headers.Rd | 1 man/HIBPwned.Rd | 1 man/account_breaches.Rd | 1 man/breached_site.Rd | 1 man/breached_sites.Rd | 1 man/data_classes.Rd | 1 man/pastes.Rd | 1 17 files changed, 228 insertions(+), 160 deletions(-)
Title: An R Interface to Brazilian Central Bank and Sidra APIs and the
IPEA Data
Description: Creates an R interface to the Bacen <http://api.bcb.gov.br/> and Sidra <http://api.sidra.ibge.gov.br> APIs and IPEA data <http://www.ipeadata.gov.br/Default.aspx>.
Author: Fernando Teixeira [aut, cre],
Jonatha Azevedo [aut]
Maintainer: Fernando Teixeira <fernando.teixeira@fgv.br>
Diff between ecoseries versions 0.1.2 dated 2017-04-27 and 0.1.3 dated 2017-05-04
DESCRIPTION | 6 +-- MD5 | 14 +++---- R/series_bacen.R | 2 - R/series_ipeadata.R | 2 - R/series_sidra.R | 93 ++++++++++++++++++++++++++++++++++++++++++------- man/series_bacen.Rd | 2 - man/series_ipeadata.Rd | 2 - man/series_sidra.Rd | 22 ++++++++--- 8 files changed, 112 insertions(+), 31 deletions(-)
Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction
techniques from R packages and provides a common
interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between dimRed versions 0.0.3 dated 2017-01-19 and 0.1.0 dated 2017-05-04
DESCRIPTION | 20 +-- MD5 | 130 +++++++++++----------- NAMESPACE | 8 + NEWS.md |only R/dimRedResult-class.R | 40 ++++++ R/embed.R | 6 - R/fastica.R | 3 R/get_info.R |only R/kpca.R | 2 R/mixColorSpaces.R | 1 R/pca.R | 2 R/quality.R | 78 ++++++++++++- README.md | 8 + man/AUC_lnK_R_NX-dimRedResult-method.Rd | 4 man/DRR-class.Rd | 7 - man/DiffusionMaps-class.Rd | 7 - man/DrL-class.Rd | 7 - man/FastICA-class.Rd | 7 - man/FruchtermanReingold-class.Rd | 7 - man/HLLE-class.Rd | 7 - man/Isomap-class.Rd | 7 - man/KamadaKawai-class.Rd | 7 - man/LCMC-dimRedResult-method.Rd | 4 man/LLE-class.Rd | 7 - man/LaplacianEigenmaps-class.Rd | 7 - man/MDS-class.Rd | 7 - man/PCA-class.Rd | 7 - man/Q_NX-dimRedResult-method.Rd | 4 man/Q_global-dimRedResult-method.Rd | 4 man/Q_local-dimRedResult-method.Rd | 4 man/R_NX-dimRedResult-method.Rd | 4 man/as.data.frame.Rd | 1 man/as.dimRedData.Rd | 1 man/cophenetic_correlation-dimRedResult-method.Rd | 4 man/dataSets.Rd | 3 man/dimRed-package.Rd | 10 + man/dimRedData-class.Rd | 11 + man/dimRedMethod-class.Rd | 2 man/dimRedMethodList.Rd | 1 man/dimRedResult-class.Rd | 36 ++++-- man/distance_correlation-dimRedResult-method.Rd | 4 man/embed.Rd | 6 - man/getData.Rd | 1 man/getDimRedData.Rd | 1 man/getMeta.Rd | 1 man/getOrgData.Rd | 1 man/getPars.Rd | 1 man/getRotationMatrix.Rd |only man/installSuggests.Rd | 1 man/kPCA-class.Rd | 7 - man/makeKNNgraph.Rd | 1 man/maximize_correlation-dimRedResult-method.Rd | 3 man/mean_R_NX-dimRedResult-method.Rd | 4 man/mixColorRamps.Rd | 3 man/nMDS-class.Rd | 7 - man/ndims.Rd | 1 man/plot.Rd | 6 - man/plot_R_NX.Rd | 1 man/print.Rd | 1 man/quality.Rd | 14 +- man/reconstruction_error-dimRedResult-method.Rd |only man/reconstruction_rmse-dimRedResult-method.Rd | 4 man/tSNE-class.Rd | 7 - man/total_correlation-dimRedResult-method.Rd | 4 tests/testthat/test_ICA.R |only tests/testthat/test_PCA.R | 18 +++ tests/testthat/test_dimRedResult.R |only tests/testthat/test_isomap.R | 4 tests/testthat/test_quality.R | 24 ++++ 69 files changed, 404 insertions(+), 196 deletions(-)
Title: Model-Free Covariate Selection in High Dimensions
Description: Model-free selection of covariates in high dimensions under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011) <DOI:10.1093/biomet/asr041> and VanderWeele and Shpitser (2011) <DOI:10.1111/j.1541-0420.2011.01619.x>. Confounder selection can be performed via either Markov/Bayesian networks, random forests or LASSO.
Author: Jenny Häggström
Maintainer: Jenny Häggström <jenny.haggstrom@umu.se>
Diff between CovSelHigh versions 1.0.0 dated 2016-04-26 and 1.1.0 dated 2017-05-04
DESCRIPTION | 8 MD5 | 14 NAMESPACE | 6 R/cov.sel.high.R | 3359 +++++++++++++++++++++++++------------------- R/cov.sel.high.sim.res.R | 233 ++- man/cov.sel.high.Rd | 60 man/cov.sel.high.sim.Rd | 2 man/cov.sel.high.sim.res.Rd | 52 8 files changed, 2197 insertions(+), 1537 deletions(-)
Title: Test for Parallel Regression Assumption
Description: Tests the parallel regression assumption for ordinal logit models generated with the function polr() from the package 'MASS'.
Author: Benjamin Schlegel [aut,cre], Marco Steenbergen [aut]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between brant versions 0.1-0 dated 2017-03-18 and 0.1-3 dated 2017-05-04
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/brant.R | 10 ++++++++-- R/print.testresults.R | 3 ++- man/brant.Rd | 2 +- 5 files changed, 21 insertions(+), 14 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices. Allows for flexible specification of any undirected network
estimation procedure in R, and offers default sets for 'qgraph', 'IsingFit', 'IsingSampler',
'glasso', 'huge' and 'parcor' packages.
Author: Sacha Epskamp and Eiko I. Fried
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 0.4 dated 2017-01-17 and 1.0.0 dated 2017-05-04
DESCRIPTION | 12 +- MD5 | 41 ++++--- NAMESPACE | 19 +++ NEWS | 12 ++ R/bootTable.R | 18 ++- R/bootnet.R | 105 +++++++++++------- R/bootnetResultsMethods.R | 7 - R/checkInput.R | 10 + R/defaultFunctions.R | 266 ++++++++++++++++++++++++++++++++++++++++++---- R/estimateNetwork.R | 30 ++++- R/netSimulator.R |only R/netSimulator_methods.R |only R/parSim.R |only R/plotMethod.R | 53 +++++++-- R/simGraph.R |only R/zzz.R | 3 inst/CITATION | 6 - man/IsingGenerator.Rd |only man/bootnet.Rd | 4 man/estimateNetwork.Rd | 54 ++++++--- man/genGGM.Rd |only man/ggmGenerator.Rd |only man/netSimulator.Rd |only man/plot.bootnet.Rd | 3 man/plot.netSimulator.Rd |only man/plotBootnetResult.Rd | 3 26 files changed, 511 insertions(+), 135 deletions(-)
Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs, weighted multigraphs, and bipartite graphs with different layout options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multigraph versions 0.50 dated 2017-01-24 and 0.60 dated 2017-05-04
DESCRIPTION | 8 - MD5 | 14 +- R/bmgraph.R | 103 +++++++++---------- R/hc.R |only R/multigraph.R | 240 ++++++++++++++++++++++++++++++++++------------ man/bmgraph.Rd | 4 man/hc.Rd |only man/multigraph-package.Rd | 8 - man/multigraph.Rd | 32 ++++-- 9 files changed, 272 insertions(+), 137 deletions(-)
Title: Binary Choice Models with Fixed Effects
Description: Estimates fixed effects binary choice models (logit and probit) with potentially many individual fixed effects and computes average partial effects. Incidental parameter bias can be reduced with a bias-correction proposed by Hahn and Newey (2004) <doi:10.1111/j.1468-0262.2004.00533.x>.
Author: Amrei Stammann [aut, cre],
Daniel Czarnowske [aut],
Florian Heiss [aut],
Daniel McFadden [ctb]
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Diff between bife versions 0.2 dated 2017-03-02 and 0.3 dated 2017-05-04
DESCRIPTION | 10 +- MD5 | 42 +++++---- NAMESPACE | 4 NEWS |only R/apeff_bife.R | 141 ++++++++++++++++--------------- R/bife.R | 57 +++++++----- R/coef_bife.R | 46 +++++----- R/predict_bife.R |only R/print_bife.R | 19 +--- R/print_summary_bife.R | 75 +++++++--------- R/summary_bife.R | 153 +++++++++++++++++----------------- R/vcov_bife.R | 23 ++--- build/partial.rdb |binary build/vignette.rds |binary data/psid.rda |binary inst/CITATION |only inst/doc/bife_introduction.R | 115 +++++++++++++------------ inst/doc/bife_introduction.Rmd | 116 +++++++++++++------------- inst/doc/bife_introduction.html | 79 ++++++++++------- man/apeff_bife.Rd | 37 +++----- man/bife.Rd | 19 ++-- man/predict.bife.Rd |only src/bife.cpp | 178 +++++++++++++++++----------------------- vignettes/bife_introduction.Rmd | 116 +++++++++++++------------- 24 files changed, 615 insertions(+), 615 deletions(-)
Title: Weighted Generalized Estimating Equations and Model Selection
Description: Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
Author: Cong Xu <congxu17@gmail.com>, Zheng Li <zheng.li@outlook.com>,
Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between wgeesel versions 1.1 dated 2017-05-01 and 1.2 dated 2017-05-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cluster_est.R | 3 ++- R/us_matrix.R | 2 +- R/wgee.R | 4 +++- man/data_sim.Rd | 2 +- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Harmonic Analysis of Tides
Description: Implements harmonic analysis of tidal and sea-level data.
Over 400 harmonic tidal constituents can be estimated, all with
daily nodal corrections. Time-varying mean sea-levels can also
be used.
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between TideHarmonics versions 0.1-0 dated 2015-12-25 and 0.1-1 dated 2017-05-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/nodal.R | 6 ++---- R/tidefit.R | 5 ++++- build/vignette.rds |binary inst/doc/Constituent_List.pdf |binary inst/doc/austides.pdf |binary man/ftide.Rd | 2 +- 8 files changed, 18 insertions(+), 17 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.73 dated 2016-11-13 and 0.85 dated 2017-05-04
DESCRIPTION | 8 - MD5 | 105 ++++++++------- NAMESPACE | 5 R/Cosslett.R | 48 ++++--- R/Gosset.R |only R/medde.R | 339 +++++++++++++++------------------------------------ build/vignette.rds |binary data/Gosset.rda |only demo/00Index | 1 demo/Brown.R | 64 +++++++++ demo/Cosslett3.R |only demo/Silverman.R | 5 demo/velo.R | 14 -- inst/ChangeLog | 21 +++ inst/doc/Bdecon.R |only inst/doc/Bdecon.Rnw |only inst/doc/Bdecon.pdf |only inst/doc/medde.R | 26 +-- inst/doc/medde.Rnw | 75 +++++------ inst/doc/medde.pdf |binary inst/doc/rebayes.pdf |binary man/Bmix.Rd | 17 +- man/Cosslett.Rd | 51 +++++-- man/GLmix.Rd | 23 +-- man/GVmix.Rd | 21 +-- man/Gammamix.Rd | 21 +-- man/Gompertzmix.Rd | 23 +-- man/Gosset.Rd |only man/Guvenen.Rd | 3 man/KWDual.Rd | 15 +- man/L1norm.Rd | 5 man/Norberg.Rd | 5 man/Pmix.Rd | 25 +-- man/Rxiv.Rd | 3 man/TLmix.Rd | 19 +- man/Tncpmix.Rd | 25 +-- man/WGLVmix.Rd | 23 +-- man/WGVmix.Rd | 9 - man/WLVmix.Rd | 25 +-- man/WTLVmix.Rd | 25 +-- man/Weibullmix.Rd | 21 +-- man/bball.Rd | 17 +- man/flies.Rd | 11 - man/medde.Rd | 73 +++++----- man/plot.medde.Rd | 9 - man/predict.Bmix.Rd | 3 man/predict.GLmix.Rd | 5 man/predict.Pmix.Rd | 3 man/qmedde.Rd | 5 man/rmedde.Rd | 3 man/tacks.Rd | 13 - man/tannenbaum.Rd | 3 man/traprule.Rd | 3 man/velo.Rd | 15 +- vignettes/Bdecon.Rnw |only vignettes/Bdecon.bib |only vignettes/medde.Rnw | 75 +++++------ vignettes/medde.bib | 38 ++++- 58 files changed, 651 insertions(+), 695 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.23 dated 2017-03-02 and 1.24 dated 2017-05-04
DESCRIPTION | 6 MD5 | 104 +++---- NEWS.md | 29 ++ R/02-item_methods.R | 233 ++++++++--------- R/03-estimation.R | 162 ++++++----- R/DIF.R | 16 - R/DTF.R | 3 R/Discrete-methods.R | 8 R/EMstep.group.R | 143 +++++----- R/EMstep.utils.R | 24 - R/LoadPars.R | 14 - R/M2.R | 35 +- R/MDIFF.R | 12 R/MDISC.R | 5 R/MHRM.group.R | 52 +-- R/MHRM.utils.R | 72 ++--- R/PLCI.mirt.R | 2 R/PrepData.R | 2 R/SE.methods.R | 56 +--- R/SIBTEST.R | 26 + R/SingleGroup-methods.R | 84 +++--- R/bfactor.R | 3 R/calcLogLik.R | 14 - R/expand.table.R | 6 R/fscores.R | 8 R/fscores.internal.R | 116 ++++---- R/imputeMissing.R | 8 R/itemGAM.R | 10 R/itemfit.R | 54 ++- R/itemplot.internal.R | 4 R/mdirt.R | 5 R/mirt.R | 17 - R/mirt.model.R | 2 R/model.elements.R | 46 +-- R/personfit.R | 20 - R/poly2dich.R | 4 R/randef.R | 20 - R/utils.R | 492 ++++++++++++++++++------------------ build/vignette.rds |binary man/M2.Rd | 2 man/MDIFF.Rd | 6 man/MDISC.Rd | 1 man/bfactor.Rd | 3 man/fscores.Rd | 2 man/itemfit.Rd | 5 man/mdirt.Rd | 5 man/mirt.Rd | 17 - man/residuals-method.Rd | 5 tests/tests/test-00-basics.R | 2 tests/tests/test-01-mirtOne.R | 8 tests/tests/test-03-bfactor.R | 4 tests/tests/test-04-multipleGroup.R | 6 tests/tests/test-09-mirt.model.R | 4 53 files changed, 1066 insertions(+), 921 deletions(-)
Title: Detecting Breakpoints and Estimating Segments in Trend
Description: A program for analyzing vegetation time series, with two algorithms: 1) change detection algorithm that detects trend changes, determines their type (abrupt or non-abrupt), and estimates their timing, magnitude, number, and direction; 2) generalization algorithm that simplifies the temporal trend into main features. The user can set the number of major breakpoints or magnitude of greatest changes of interest for detection, and can control the generalization process by setting an additional parameter of generalization-percentage.
Author: Sadegh Jamali, Hristo Tomov
Maintainer: Hristo Tomov <tomov.hristo@gmail.com>
Diff between DBEST versions 1.5 dated 2017-03-31 and 1.6 dated 2017-05-04
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/DETREND_SJ.R | 85 +++++++++++++++++++++++++-------------------------- R/Pvalue_ith_coeff.R | 5 +-- man/DBEST.Rd | 9 ++--- 5 files changed, 58 insertions(+), 57 deletions(-)
Title: Easily Tidy Data with 'spread()' and 'gather()' Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.6.1 dated 2017-01-10 and 0.6.2 dated 2017-05-04
DESCRIPTION | 9 - MD5 | 90 ++++++------ NAMESPACE | 2 NEWS.md | 8 + R/complete.R | 2 R/fill.R | 1 R/separate-rows.R | 1 R/tidyr.R |only R/utils.R | 1 README.md | 4 inst/doc/tidy-data.Rmd | 2 inst/doc/tidy-data.html | 306 +++++++++++++++++++++---------------------- man/complete.Rd | 3 man/complete_.Rd | 1 man/drop_na.Rd | 1 man/drop_na_.Rd | 1 man/expand.Rd | 3 man/expand_.Rd | 1 man/extract.Rd | 1 man/extract_.Rd | 1 man/extract_numeric.Rd | 2 man/figures |only man/fill.Rd | 1 man/fill_.Rd | 1 man/full_seq.Rd | 1 man/gather.Rd | 1 man/gather_.Rd | 1 man/nest.Rd | 1 man/nest_.Rd | 1 man/pipe.Rd | 1 man/replace_na.Rd | 1 man/separate.Rd | 1 man/separate_.Rd | 1 man/separate_rows.Rd | 1 man/separate_rows_.Rd | 2 man/smiths.Rd | 1 man/spread.Rd | 1 man/spread_.Rd | 1 man/table1.Rd | 1 man/tidyr-package.Rd |only man/unite.Rd | 1 man/unite_.Rd | 1 man/unnest.Rd | 1 man/unnest_.Rd | 1 man/who.Rd | 3 src/init.c |only tests/testthat/test-unnest.R | 2 vignettes/tidy-data.Rmd | 2 48 files changed, 222 insertions(+), 247 deletions(-)
Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between REAT versions 1.3.1 dated 2017-03-31 and 1.3.2 dated 2017-05-04
REAT-1.3.1/REAT/R/krugman.specg.R |only REAT-1.3.1/REAT/data/Freiburg1.rda |only REAT-1.3.1/REAT/data/Freiburg2.rda |only REAT-1.3.1/REAT/data/Goettingen.rda |only REAT-1.3.1/REAT/data/datalist |only REAT-1.3.1/REAT/data/gdppc.rda |only REAT-1.3.1/REAT/data/health1.rda |only REAT-1.3.1/REAT/data/health2.rda |only REAT-1.3.1/REAT/data/health3.rda |only REAT-1.3.1/REAT/data/health4.rda |only REAT-1.3.1/REAT/data/health5.rda |only REAT-1.3.1/REAT/man/Freiburg1.Rd |only REAT-1.3.1/REAT/man/Freiburg2.Rd |only REAT-1.3.1/REAT/man/Goettingen.Rd |only REAT-1.3.1/REAT/man/gdppc.Rd |only REAT-1.3.1/REAT/man/health1.Rd |only REAT-1.3.1/REAT/man/health2.Rd |only REAT-1.3.1/REAT/man/health3.Rd |only REAT-1.3.1/REAT/man/health4.Rd |only REAT-1.3.1/REAT/man/health5.Rd |only REAT-1.3.1/REAT/man/krugman.specg.Rd |only REAT-1.3.2/REAT/DESCRIPTION | 9 +- REAT-1.3.2/REAT/MD5 | 109 +++++++++++++++----------------- REAT-1.3.2/REAT/NAMESPACE | 4 - REAT-1.3.2/REAT/R/cv.R | 96 +++++++++++++++------------- REAT-1.3.2/REAT/R/data.dummy.R |only REAT-1.3.2/REAT/R/data.index.R | 9 +- REAT-1.3.2/REAT/R/dist.buf.R | 4 - REAT-1.3.2/REAT/R/dist.calc.R | 3 REAT-1.3.2/REAT/R/dist.mat.R | 1 REAT-1.3.2/REAT/R/gini.R | 5 - REAT-1.3.2/REAT/R/gini.conc.R | 22 +++++- REAT-1.3.2/REAT/R/gini.spec.R | 20 +++++ REAT-1.3.2/REAT/R/hansen.R | 6 - REAT-1.3.2/REAT/R/herf.R | 6 - REAT-1.3.2/REAT/R/hoover.R | 28 +++++--- REAT-1.3.2/REAT/R/huff.R | 5 - REAT-1.3.2/REAT/R/krugman.conc.R |only REAT-1.3.2/REAT/R/krugman.conc2.R |only REAT-1.3.2/REAT/R/krugman.spec2.R |only REAT-1.3.2/REAT/R/lm.beta.R | 5 - REAT-1.3.2/REAT/R/lorenz.R | 102 ++++++++++++++++++----------- REAT-1.3.2/REAT/R/mean2.R |only REAT-1.3.2/REAT/R/portfolio.R | 7 -- REAT-1.3.2/REAT/R/reilly.R | 2 REAT-1.3.2/REAT/R/sd2.R | 82 +++++++++++++----------- REAT-1.3.2/REAT/R/theil.R |only REAT-1.3.2/REAT/data/Freiburg.rda |binary REAT-1.3.2/REAT/data/G.counties.gdp.rda |only REAT-1.3.2/REAT/data/G.regions.emp.rda |only REAT-1.3.2/REAT/man/G.counties.gdp.Rd |only REAT-1.3.2/REAT/man/G.regions.emp.Rd |only REAT-1.3.2/REAT/man/converse.Rd | 4 + REAT-1.3.2/REAT/man/cv.Rd | 4 - REAT-1.3.2/REAT/man/data.dummy.Rd |only REAT-1.3.2/REAT/man/data.index.Rd | 8 +- REAT-1.3.2/REAT/man/disp.Rd | 5 - REAT-1.3.2/REAT/man/dist.buf.Rd | 21 ++---- REAT-1.3.2/REAT/man/dist.mat.Rd | 17 ++-- REAT-1.3.2/REAT/man/gini.conc.Rd | 109 +++++++++++++++++++++++++++++++- REAT-1.3.2/REAT/man/gini.spec.Rd | 75 +++++++++++++++++++++- REAT-1.3.2/REAT/man/hansen.Rd | 51 +++++++------- REAT-1.3.2/REAT/man/hoover.Rd | 10 +- REAT-1.3.2/REAT/man/huff.Rd | 55 ++++++++++++---- REAT-1.3.2/REAT/man/krugman.conc.Rd |only REAT-1.3.2/REAT/man/krugman.conc2.Rd |only REAT-1.3.2/REAT/man/krugman.spec.Rd | 7 +- REAT-1.3.2/REAT/man/krugman.spec2.Rd |only REAT-1.3.2/REAT/man/lorenz.Rd | 10 ++ REAT-1.3.2/REAT/man/mean2.Rd |only REAT-1.3.2/REAT/man/rca.Rd | 8 +- REAT-1.3.2/REAT/man/reilly.Rd | 4 + REAT-1.3.2/REAT/man/sd2.Rd | 6 - REAT-1.3.2/REAT/man/theil.Rd |only 74 files changed, 607 insertions(+), 312 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests (CAT) using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Additionally, optimal test designs (e.g., "shadow testing") are supported
for tests which contain a large number of item selection constraints.
Finally, package contains tools useful for performing Monte Carlo simulations
for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 1.4 dated 2017-03-02 and 1.5 dated 2017-05-04
DESCRIPTION | 8 - MD5 | 49 +++++----- NEWS.md | 15 +++ R/DesignClass.R | 25 ++--- R/PersonClass.R | 11 +- R/ShinyGUIClass.R | 7 + R/TestClass.R | 3 R/findNextCATItem.R | 161 +++++++++++++++++++---------------- R/generate.mirt_object.R | 24 ++--- R/generate_pattern.R | 4 R/mirtCAT.R | 31 ++++-- R/mirtCAT_preamble.R | 34 +++++-- R/run_pattern.R | 7 - R/selection_criteria.R | 11 +- R/server.R | 4 R/util.R | 39 ++++++-- R/zzz-methods.R | 7 - README.md | 6 - build/vignette.rds |binary man/findNextItem.Rd | 69 +++++++++------ man/generate.mirt_object.Rd | 16 +-- man/mirtCAT.Rd | 33 +++++-- tests/GUI-tests/GUI-tests.R | 16 +++ tests/tests/test-mirtCAT_extra.R | 16 +++ vignettes/01-Welcome.jpg |only vignettes/04-Math_stem_Question.jpg |only vignettes/05-Table_stem_question.jpg |only 27 files changed, 375 insertions(+), 221 deletions(-)
Title: Linkage Disequilibrium Corrected by the Structure and the
Relatedness
Description: Four measures of linkage disequilibrium are provided: the usual r^2
measure, the r^2_S measure (r^2 corrected by the structure
sample), the r^2_V (r^2 corrected by the relatedness of
genotyped individuals), the r^2_VS measure (r^2 corrected by
both the relatedness of genotyped individuals and the structure
of the sample).
Author: David Desrousseaux, Florian Sandron, Aurelie Siberchicot,
Christine Cierco-Ayrolles and Brigitte Mangin
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between LDcorSV versions 1.3.1 dated 2013-07-04 and 1.3.2 dated 2017-05-04
DESCRIPTION | 20 - MD5 | 20 - NAMESPACE | 11 - R/Info.Locus.R | 45 ++-- R/Inv.proj.matrix.sdp.R | 21 +- R/LD.Measures.R | 495 ++++++++++++++++++++++++------------------------ R/Measure.R2.R | 47 ++-- R/Measure.R2S.R | 59 ++--- R/Measure.R2V.R | 63 +++--- R/Measure.R2VS.R | 83 ++++---- man/LDcorSV-package.Rd | 5 11 files changed, 442 insertions(+), 427 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.3 dated 2017-03-24 and 1.4 dated 2017-05-04
DESCRIPTION | 8 +++--- MD5 | 8 +++--- R/GSED.R | 65 ++++++++++++++++++++++++++++++++++++---------------- man/GSED-package.Rd | 4 +-- man/max_FI.Rd | 21 +++++++++------- 5 files changed, 67 insertions(+), 39 deletions(-)
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.5-0 dated 2015-11-16 and 1.5-1 dated 2017-05-04
gridSVG-1.5-0/gridSVG/src |only gridSVG-1.5-1/gridSVG/DESCRIPTION | 10 gridSVG-1.5-1/gridSVG/MD5 | 32 +- gridSVG-1.5-1/gridSVG/NAMESPACE | 6 gridSVG-1.5-1/gridSVG/R/animate.R | 319 +++++++++++------------ gridSVG-1.5-1/gridSVG/R/b64.R | 3 gridSVG-1.5-1/gridSVG/R/devsvg.R | 36 ++ gridSVG-1.5-1/gridSVG/R/gradients.R | 4 gridSVG-1.5-1/gridSVG/R/griddev.R | 9 gridSVG-1.5-1/gridSVG/R/gtable.R | 10 gridSVG-1.5-1/gridSVG/R/svg.R | 3 gridSVG-1.5-1/gridSVG/build/vignette.rds |binary gridSVG-1.5-1/gridSVG/inst/NEWS.Rd | 26 + gridSVG-1.5-1/gridSVG/inst/doc/animation.pdf |binary gridSVG-1.5-1/gridSVG/inst/doc/extensibility.pdf |binary gridSVG-1.5-1/gridSVG/inst/doc/gridSVG.pdf |binary 16 files changed, 261 insertions(+), 197 deletions(-)
Title: Complementary Hierarchical Clustering
Description: Performs the complementary hierarchical clustering procedure and returns X' (the expected residual matrix) and a vector of the relative gene importances.
Author: Gen Nowak [aut, cre],
Robert Tibshirani [aut]
Maintainer: Gen Nowak <gen.nowak@gmail.com>
Diff between compHclust versions 1.0-2 dated 2014-01-03 and 1.0-3 dated 2017-05-04
DESCRIPTION | 14 +-- MD5 | 16 +-- NAMESPACE | 6 - NEWS | 33 ++++---- R/A.chc.R | 9 -- R/RGI.chc.R | 8 - R/compHclust.R | 32 +++---- R/compHclust.heatmap.R | 49 +++++------ src/UnNormA.cpp | 202 ++++++++++++++++++++++++++----------------------- 9 files changed, 195 insertions(+), 174 deletions(-)
Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for ultrahigh-dimensional,
multi-gigabyte data sets that cannot be loaded into memory. It's much more
memory- and computation-efficient as compared to existing lasso-fitting packages
like 'glmnet' and 'ncvreg', thus allowing for very powerful big data analysis
even with an ordinary laptop.
Author: Yaohui Zeng [aut,cre], Patrick Breheny [ctb]
Maintainer: Yaohui Zeng <yaohui-zeng@uiowa.edu>
Diff between biglasso versions 1.3-5 dated 2017-04-04 and 1.3-6 dated 2017-05-04
DESCRIPTION | 8 +- MD5 | 19 ++-- NEWS | 6 + R/biglasso-package.R | 2 R/biglasso.R | 23 ++++- man/biglasso-package.Rd | 4 - man/biglasso.Rd | 12 +-- src/binomial_hsr_slores.cpp | 107 ++++++++++++--------------- src/binomial_hsr_slores_nac.cpp |only src/gaussian_hsr_edpp.cpp | 6 - src/init.c | 158 +++++++++++++++++++++------------------- 11 files changed, 182 insertions(+), 163 deletions(-)