Title: Strategic Selection Estimator
Description: Provides functions to estimate a strategic selection estimator. A strategic selection estimator is an agent error model in which the two random components are not assumed to be orthogonal. In addition this package provides generic functions to print and plot objects of its class as well as the necessary functions to create tables for LaTeX. There is also a function to create dyadic data sets.
Author: Lucas Leemann
Maintainer: Lucas Leemann <lleemann@gmail.com>
Diff between StratSel versions 1.2 dated 2016-05-10 and 1.3 dated 2018-05-26
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics
from satellite nightlight rasters downloaded from the United States
National Oceanic and Atmospheric Administration (<http://www.noaa.gov>)
free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly
nightlight raster data are supported. Satellite nightlight raster tiles are
downloaded and cropped to the country boundaries using shapefiles from the GADM
database of Global Administrative Areas (<http://gadm.org>). Zonal statistics
are then calculated at the lowest administrative boundary for the selected
country and cached locally for future retrieval. Finally, a simple data
explorer/browser is included that allows one to visualize the cached data e.g.
graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>
Diff between Rnightlights versions 0.2.0 dated 2018-04-22 and 0.2.1 dated 2018-05-26
DESCRIPTION | 8 - MD5 | 29 ++-- R/ctrynldata.R | 11 + R/downloadnltiles.R | 6 R/polygons.R | 34 ++++ R/upgrade.R | 60 +++++--- inst/application/server.R | 257 ++++++++++++++++++++---------------- inst/application/ui.R | 8 - man/getCtryShpLyrNames.Rd | 5 tests/testthat.R | 17 +- tests/testthat/helper.R | 2 tests/testthat/helper_ctrynltiles.R | 49 +++--- tests/testthat/helper_masq.R | 68 +++++---- tests/testthat/test-admlevels.R |only tests/testthat/test-ctrynltiles.R | 57 ++++--- tests/testthat/test-masq.R | 15 +- 16 files changed, 371 insertions(+), 255 deletions(-)
Title: Import 'Stata' Data Files
Description: Function to read and write the 'Stata' file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre]
(<https://orcid.org/0000-0002-2671-5253>),
R Core Team [cph],
Magnus Thor Torfason [ctb],
Luke M. Olson [ctb],
Giovanni Righi [ctb],
Kevin Jin [ctb]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.9.1 dated 2018-05-25 and 0.9.2 dated 2018-05-26
DESCRIPTION | 6 +- MD5 | 9 ++- NEWS | 3 + README.md | 108 +++++++++++++++++++++++------------------------ inst/extdata/test.zip |only inst/include/readstata.h | 5 ++ 6 files changed, 69 insertions(+), 62 deletions(-)
Title: Protocol Inspection and State Machine Analysis
Description: Loads and processes huge text
corpora processed with the sally toolbox (<http://www.mlsec.org/sally/>).
sally acts as a very fast preprocessor which splits the text files into
tokens or n-grams. These output files can then be read with the PRISMA
package which applies testing-based token selection and has some
replicate-aware, highly tuned non-negative matrix factorization and
principal component analysis implementation which allows the processing of
very big data sets even on desktop machines.
Author: Tammo Krueger, Nicole Kraemer
Maintainer: Tammo Krueger <tammokrueger@googlemail.com>
Diff between PRISMA versions 0.2-6 dated 2017-02-27 and 0.2-7 dated 2018-05-26
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ build/partial.rdb |only build/vignette.rds |binary data/asap.rda |binary data/thesis.rda |binary inst/doc/PRISMA.pdf |binary man/PRISMA-package.Rd | 27 ++++++++------------------- 8 files changed, 19 insertions(+), 29 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/LaTeX.
Author: Max Gordon [aut, cre],
Stephen Gragg [aut],
Peter Konings [aut]
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.11.2 dated 2018-01-20 and 1.12 dated 2018-05-26
htmlTable-1.11.2/htmlTable/tests/visual_tests/word_test.html |only htmlTable-1.12/htmlTable/DESCRIPTION | 10 htmlTable-1.12/htmlTable/MD5 | 184 htmlTable-1.12/htmlTable/NAMESPACE | 101 htmlTable-1.12/htmlTable/NEWS | 252 htmlTable-1.12/htmlTable/R/concatHtmlTables.R | 70 htmlTable-1.12/htmlTable/R/data-SCB.R | 28 htmlTable-1.12/htmlTable/R/deprecated.R | 78 htmlTable-1.12/htmlTable/R/htmlTable.R | 2405 - htmlTable-1.12/htmlTable/R/htmlTableWidget.R | 140 htmlTable-1.12/htmlTable/R/htmlTable_helpers.R | 1979 htmlTable-1.12/htmlTable/R/htmlTable_render.R | 512 htmlTable-1.12/htmlTable/R/interactiveTable.R | 474 htmlTable-1.12/htmlTable/R/tidyHtmlTable.R | 920 htmlTable-1.12/htmlTable/R/txtFrmt.R | 751 htmlTable-1.12/htmlTable/README.md | 2362 - htmlTable-1.12/htmlTable/build/vignette.rds |binary htmlTable-1.12/htmlTable/inst/doc/general.R | 384 htmlTable-1.12/htmlTable/inst/doc/general.Rmd | 688 htmlTable-1.12/htmlTable/inst/doc/general.html | 8738 ++-- htmlTable-1.12/htmlTable/inst/doc/tables.R | 450 htmlTable-1.12/htmlTable/inst/doc/tables.Rmd | 830 htmlTable-1.12/htmlTable/inst/doc/tables.html |20423 +++++----- htmlTable-1.12/htmlTable/inst/doc/tidyHtmlTable.R | 82 htmlTable-1.12/htmlTable/inst/doc/tidyHtmlTable.Rmd | 170 htmlTable-1.12/htmlTable/inst/doc/tidyHtmlTable.html | 2190 - htmlTable-1.12/htmlTable/inst/examples/data-SCB_example.R | 60 htmlTable-1.12/htmlTable/inst/examples/htmlTable_example.R | 160 htmlTable-1.12/htmlTable/inst/examples/interactiveTable_example.R | 38 htmlTable-1.12/htmlTable/inst/html_components/button.html | 4 htmlTable-1.12/htmlTable/inst/htmlwidgets/htmlTableWidget.js | 78 htmlTable-1.12/htmlTable/inst/htmlwidgets/htmlTableWidget.yaml | 20 htmlTable-1.12/htmlTable/inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt | 434 htmlTable-1.12/htmlTable/inst/htmlwidgets/lib/jquery/jquery.min.js | 8 htmlTable-1.12/htmlTable/inst/htmlwidgets/lib/table_pagination/table_pagination.css | 200 htmlTable-1.12/htmlTable/inst/htmlwidgets/lib/table_pagination/table_pagination.js | 288 htmlTable-1.12/htmlTable/inst/javascript/button.js | 48 htmlTable-1.12/htmlTable/inst/javascript/toggler.js | 80 htmlTable-1.12/htmlTable/man/SCB.Rd | 102 htmlTable-1.12/htmlTable/man/concatHtmlTables.Rd | 206 htmlTable-1.12/htmlTable/man/htmlTable.Rd | 890 htmlTable-1.12/htmlTable/man/htmlTableWidget-shiny.Rd | 76 htmlTable-1.12/htmlTable/man/htmlTableWidget.Rd | 72 htmlTable-1.12/htmlTable/man/interactiveTable.Rd | 150 htmlTable-1.12/htmlTable/man/outputInt.Rd | 38 htmlTable-1.12/htmlTable/man/prAddCells.Rd | 103 htmlTable-1.12/htmlTable/man/prAddSemicolon2StrEnd.Rd | 55 htmlTable-1.12/htmlTable/man/prAttr4RgroupAdd.Rd | 44 htmlTable-1.12/htmlTable/man/prConvertDfFactors.Rd | 36 htmlTable-1.12/htmlTable/man/prEscapeHtml.Rd |only htmlTable-1.12/htmlTable/man/prGetAlign.Rd | 44 htmlTable-1.12/htmlTable/man/prGetCgroupHeader.Rd | 139 htmlTable-1.12/htmlTable/man/prGetRgroupLine.Rd | 106 htmlTable-1.12/htmlTable/man/prGetRowlabelPos.Rd | 75 htmlTable-1.12/htmlTable/man/prGetScriptString.Rd | 38 htmlTable-1.12/htmlTable/man/prGetStyle.Rd | 67 htmlTable-1.12/htmlTable/man/prGetThead.Rd | 178 htmlTable-1.12/htmlTable/man/prIsNotebook.Rd | 28 htmlTable-1.12/htmlTable/man/prMergeClr.Rd | 44 htmlTable-1.12/htmlTable/man/prPrepareAlign.Rd | 85 htmlTable-1.12/htmlTable/man/prPrepareCgroup.Rd | 89 htmlTable-1.12/htmlTable/man/prPrepareColors.Rd | 48 htmlTable-1.12/htmlTable/man/prPrepareCss.Rd | 66 htmlTable-1.12/htmlTable/man/prSkipRownames.Rd | 38 htmlTable-1.12/htmlTable/man/prTblNo.Rd | 63 htmlTable-1.12/htmlTable/man/pvalueFormatter.Rd | 36 htmlTable-1.12/htmlTable/man/splitLines4Table.Rd | 36 htmlTable-1.12/htmlTable/man/tblNoLast.Rd | 50 htmlTable-1.12/htmlTable/man/tblNoNext.Rd | 50 htmlTable-1.12/htmlTable/man/tidyHtmlTable.Rd | 280 htmlTable-1.12/htmlTable/man/txtInt.Rd | 70 htmlTable-1.12/htmlTable/man/txtMergeLines.Rd | 76 htmlTable-1.12/htmlTable/man/txtPval.Rd | 96 htmlTable-1.12/htmlTable/man/txtRound.Rd | 127 htmlTable-1.12/htmlTable/tests/testInteractive.R | 54 htmlTable-1.12/htmlTable/tests/testthat.R | 6 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable-dimnames.R | 128 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable-input_checks.R | 24 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable.R | 842 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable_cgroup.R | 250 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable_dates.R | 92 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable_rgroup_tspanner.R | 484 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable_styles.R | 96 htmlTable-1.12/htmlTable/tests/testthat/test-htmlTable_total.R | 148 htmlTable-1.12/htmlTable/tests/testthat/test-interactiveTable.R | 632 htmlTable-1.12/htmlTable/tests/testthat/test-txtFrmt.R | 382 htmlTable-1.12/htmlTable/tests/testthat/test-txtMergeLines.R | 48 htmlTable-1.12/htmlTable/tests/visual_tests/htmlTable_vtests.R | 230 htmlTable-1.12/htmlTable/tests/visual_tests/pandoc_test.Rmd | 58 htmlTable-1.12/htmlTable/tests/visual_tests/word_test.Rmd | 84 htmlTable-1.12/htmlTable/vignettes/custom.css | 324 htmlTable-1.12/htmlTable/vignettes/general.Rmd | 688 htmlTable-1.12/htmlTable/vignettes/tables.Rmd | 830 htmlTable-1.12/htmlTable/vignettes/tidyHtmlTable.Rmd | 170 94 files changed, 27495 insertions(+), 27415 deletions(-)
Title: Hierarchical Latent Space Network Model
Description: Implements Hierarchical Latent Space Network Model (HLSM) for ensemble of networks as described in Sweet et. al. (2012). <DOI:10.3102/1076998612458702>.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari <asam.cmu@gmail.com>
Diff between HLSM versions 0.7 dated 2016-11-25 and 0.8 dated 2018-05-26
DESCRIPTION | 8 +-- MD5 | 11 ++-- NAMESPACE | 2 R/HLSM_C.R | 139 ++++++++++++++++++++++++++++------------------------- R/HLSM_C_fixedEf.R | 139 ++++++++++++++++++++++++++++------------------------- R/adjust.my.tune.R | 113 ++++++++++++++++++++++--------------------- src/init.c |only 7 files changed, 219 insertions(+), 193 deletions(-)
Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.5-2 dated 2017-10-04 and 0.9.6 dated 2018-05-26
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS |only R/matchtools.R | 2 +- R/memtools.R | 23 +++++++++++++++-------- build/vignette.rds |binary inst/doc/introduction.pdf |binary man/match.ga.Rd | 19 +++++++++++++------ man/mem.powersimu.Rd | 8 ++++---- 9 files changed, 45 insertions(+), 30 deletions(-)
Title: Testing Goodness-of-Fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on a kernel smoothing of the data.
Author: Jose M. Pavia
Maintainer: Jose M. Pavia <Jose.M.Pavia@uv.es>
Diff between GoFKernel versions 2.1-0 dated 2016-01-04 and 2.1-1 dated 2018-05-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/GoFKernel-package.Rd | 4 ++-- man/dgeometric.test.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Fast Cross-Validation via Sequential Testing
Description: The fast cross-validation via sequential testing (CVST) procedure is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. By eliminating under-performing candidates quickly and keeping promising candidates as long as possible, the method speeds up the computation while preserving the capability of a full cross-validation. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.
Author: Tammo Krueger, Mikio Braun
Maintainer: Tammo Krueger <tammokrueger@googlemail.com>
Diff between CVST versions 0.2-1 dated 2013-12-10 and 0.2-2 dated 2018-05-26
DESCRIPTION | 10 ++++----- MD5 | 15 +++++++------- NAMESPACE | 4 +++ build |only man/CVST-package.Rd | 43 ++++++++++------------------------------- man/constructCVSTModel.Rd | 10 +-------- man/constructSequentialTest.Rd | 10 +-------- man/fastCV.Rd | 10 +-------- man/noisySine.Rd | 10 +-------- 9 files changed, 36 insertions(+), 76 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, Can Candan, and Tyler Hunt.
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-79 dated 2018-03-29 and 6.0-80 dated 2018-05-26
DESCRIPTION | 8 ++--- MD5 | 33 +++++++++++---------- NAMESPACE | 3 + R/createDataPartition.R | 2 - R/prec_rec.R | 2 - R/recipes.R | 9 +++-- R/resamples.R | 65 +++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/NEWS.Rd | 14 ++++++++- inst/doc/caret.Rmd | 2 - inst/doc/caret.html | 4 +- inst/models/models.RData |binary inst/models/sampling.RData |binary man/createDataPartition.Rd | 3 + man/recall.Rd | 2 - man/xyplot.resamples.Rd | 15 +++++++-- tests/testthat/test_tibble.R |only vignettes/caret.Rmd | 2 - 18 files changed, 125 insertions(+), 39 deletions(-)
Title: Stylometric Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.6 dated 2018-04-13 and 0.6.7 dated 2018-05-26
stylo-0.6.6/stylo/NEWS |only stylo-0.6.7/stylo/DESCRIPTION | 8 +-- stylo-0.6.7/stylo/MD5 | 18 +++++--- stylo-0.6.7/stylo/NAMESPACE | 2 stylo-0.6.7/stylo/NEWS.md |only stylo-0.6.7/stylo/R/dist.wurzburg.R | 3 + stylo-0.6.7/stylo/R/imposters.R |only stylo-0.6.7/stylo/R/imposters.optimize.R |only stylo-0.6.7/stylo/R/parse.pos.tags.R | 57 +++++++++++++++++++++++++++- stylo-0.6.7/stylo/man/imposters.Rd |only stylo-0.6.7/stylo/man/imposters.optimize.Rd |only stylo-0.6.7/stylo/man/parse.pos.tags.Rd | 7 +-- stylo-0.6.7/stylo/man/perform.impostors.Rd | 8 ++- 13 files changed, 85 insertions(+), 18 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joeseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <mail@richard-schuster.com>
Diff between prioritizr versions 3.0.4 dated 2018-03-25 and 4.0.1 dated 2018-05-26
prioritizr-3.0.4/prioritizr/R/add_connected_constraints.R |only prioritizr-3.0.4/prioritizr/R/add_corridor_constraints.R |only prioritizr-3.0.4/prioritizr/inst/doc/prioritizr_basics.Rmd |only prioritizr-3.0.4/prioritizr/inst/doc/prioritizr_basics.html |only prioritizr-3.0.4/prioritizr/inst/doc/quick_start.Rmd |only prioritizr-3.0.4/prioritizr/inst/doc/quick_start.html |only prioritizr-3.0.4/prioritizr/man/add_connected_constraints.Rd |only prioritizr-3.0.4/prioritizr/man/add_corridor_constraints.Rd |only prioritizr-3.0.4/prioritizr/man/figures/README-unnamed-chunk-10-1.png |only prioritizr-3.0.4/prioritizr/man/figures/README-unnamed-chunk-6-1.png |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_asymmetric_boundary_constraints.cpp |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_connected_constraints.cpp |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_corridor_constraints.cpp |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_locked_in_constraints.cpp |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_locked_out_constraints.cpp |only prioritizr-3.0.4/prioritizr/src/rcpp_apply_symmetric_boundary_constraints.cpp |only prioritizr-3.0.4/prioritizr/tests/testthat/test_add_connected_constraints.R |only prioritizr-3.0.4/prioritizr/tests/testthat/test_add_corridor_constraints.R |only prioritizr-3.0.4/prioritizr/vignettes/prioritizr_basics.Rmd |only prioritizr-3.0.4/prioritizr/vignettes/quick_start.Rmd |only prioritizr-4.0.1/prioritizr/DESCRIPTION | 66 prioritizr-4.0.1/prioritizr/MD5 | 553 +++--- prioritizr-4.0.1/prioritizr/NAMESPACE | 314 +-- prioritizr-4.0.1/prioritizr/R/ArrayParameter-proto.R | 9 prioritizr-4.0.1/prioritizr/R/Collection-proto.R | 3 prioritizr-4.0.1/prioritizr/R/ConservationModifier-proto.R | 5 prioritizr-4.0.1/prioritizr/R/ConservationProblem-proto.R | 194 +- prioritizr-4.0.1/prioritizr/R/Constraint-proto.R | 3 prioritizr-4.0.1/prioritizr/R/Decision-proto.R | 3 prioritizr-4.0.1/prioritizr/R/Id.R | 2 prioritizr-4.0.1/prioritizr/R/MiscParameter-proto.R |only prioritizr-4.0.1/prioritizr/R/Objective-proto.R | 3 prioritizr-4.0.1/prioritizr/R/OptimizationProblem-methods.R | 191 -- prioritizr-4.0.1/prioritizr/R/OptimizationProblem-proto.R | 11 prioritizr-4.0.1/prioritizr/R/Parameter-proto.R | 5 prioritizr-4.0.1/prioritizr/R/Parameters-proto.R | 3 prioritizr-4.0.1/prioritizr/R/Penalty-proto.R | 3 prioritizr-4.0.1/prioritizr/R/Portfolio-proto.R | 7 prioritizr-4.0.1/prioritizr/R/RcppExports.R | 342 +-- prioritizr-4.0.1/prioritizr/R/ScalarParameter-proto.R | 7 prioritizr-4.0.1/prioritizr/R/Solver-proto.R | 3 prioritizr-4.0.1/prioritizr/R/Target-proto.R | 3 prioritizr-4.0.1/prioritizr/R/add_absolute_targets.R | 223 +- prioritizr-4.0.1/prioritizr/R/add_binary_decisions.R | 72 prioritizr-4.0.1/prioritizr/R/add_boundary_penalties.R | 369 ++-- prioritizr-4.0.1/prioritizr/R/add_connectivity_penalties.R | 606 +++++- prioritizr-4.0.1/prioritizr/R/add_contiguity_constraints.R |only prioritizr-4.0.1/prioritizr/R/add_cuts_portfolio.R | 127 + prioritizr-4.0.1/prioritizr/R/add_default_decisions.R | 2 prioritizr-4.0.1/prioritizr/R/add_default_portfolio.R | 5 prioritizr-4.0.1/prioritizr/R/add_default_solver.R | 11 prioritizr-4.0.1/prioritizr/R/add_feature_contiguity_constraints.R |only prioritizr-4.0.1/prioritizr/R/add_feature_weights.R | 317 ++- prioritizr-4.0.1/prioritizr/R/add_gurobi_solver.R | 64 prioritizr-4.0.1/prioritizr/R/add_locked_in_constraints.R | 313 ++- prioritizr-4.0.1/prioritizr/R/add_locked_out_constraints.R | 283 ++- prioritizr-4.0.1/prioritizr/R/add_loglinear_targets.R | 132 - 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Title: North Temperate Lakes - Microbial Observatory 16S Time Series
Data and Functions
Description: Analyses of OTU tables produced by 16S rRNA gene amplicon sequencing, as well as example data. It contains the data and scripts used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes," <doi: 10.1128/mSphere.00169-17>.
Author: Alexandra Linz
Maintainer: Alexandra Linz <amlinz16@gmail.com>
Diff between OTUtable versions 1.1.1 dated 2017-06-29 and 1.1.2 dated 2018-05-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/OTUtable-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a high
level interface to writing, styling and editing worksheets. Through the use of
'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages
with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker <Alexander.Walker1989@gmail.com>
Diff between openxlsx versions 4.0.17 dated 2017-03-23 and 4.1.0 dated 2018-05-26
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Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex
programming (DCP). It allows the user to formulate convex optimization problems
in a natural way following mathematical convention and DCP rules. The system
analyzes the problem, verifies its convexity, converts it into a canonical form,
and hands it off to an appropriate solver to obtain the solution.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 0.95 dated 2018-02-20 and 0.99 dated 2018-05-26
CVXR-0.95/CVXR/tests/manual/test_constant_atoms.R |only CVXR-0.95/CVXR/tests/manual/test_examples.R |only CVXR-0.95/CVXR/tests/manual/test_ls.R |only CVXR-0.95/CVXR/tests/manual/test_scs.R |only CVXR-0.95/CVXR/tests/manual/test_vignette.R |only CVXR-0.95/CVXR/tests/testthat.R |only CVXR-0.95/CVXR/tests/testthat/test_atoms.R |only CVXR-0.95/CVXR/tests/testthat/test_constraints.R |only CVXR-0.95/CVXR/tests/testthat/test_convolution.R |only CVXR-0.95/CVXR/tests/testthat/test_curvature.R |only CVXR-0.95/CVXR/tests/testthat/test_domain.R |only CVXR-0.95/CVXR/tests/testthat/test_expressions.R |only CVXR-0.95/CVXR/tests/testthat/test_grad.R |only CVXR-0.95/CVXR/tests/testthat/test_lin_ops.R |only CVXR-0.95/CVXR/tests/testthat/test_matrices.R |only CVXR-0.95/CVXR/tests/testthat/test_mip_vars.R |only CVXR-0.95/CVXR/tests/testthat/test_monotonicity.R |only CVXR-0.95/CVXR/tests/testthat/test_non_optimal.R |only CVXR-0.95/CVXR/tests/testthat/test_nonlinear_atoms.R |only CVXR-0.95/CVXR/tests/testthat/test_objectives.R |only CVXR-0.95/CVXR/tests/testthat/test_problem.R |only CVXR-0.95/CVXR/tests/testthat/test_quad_form.R |only CVXR-0.95/CVXR/tests/testthat/test_quadratic.R |only CVXR-0.95/CVXR/tests/testthat/test_semidefinite_vars.R |only CVXR-0.95/CVXR/tests/testthat/test_shape.R |only CVXR-0.95/CVXR/tests/testthat/test_sign.R |only CVXR-0.95/CVXR/tests/testthat/test_unpack_results.R |only CVXR-0.99/CVXR/DESCRIPTION | 20 CVXR-0.99/CVXR/MD5 | 105 +- CVXR-0.99/CVXR/NAMESPACE | 8 CVXR-0.99/CVXR/NEWS.md |only CVXR-0.99/CVXR/R/affine.R | 17 CVXR-0.99/CVXR/R/constraints.R | 3 CVXR-0.99/CVXR/R/globals.R | 82 + CVXR-0.99/CVXR/R/glpk_solver.R |only CVXR-0.99/CVXR/R/gurobi-solver.R |only CVXR-0.99/CVXR/R/interface.R | 6 CVXR-0.99/CVXR/R/lpsolve_solver.R |only CVXR-0.99/CVXR/R/mosek-solver.R |only CVXR-0.99/CVXR/R/problem_data.R | 87 + CVXR-0.99/CVXR/R/solver.R | 352 ------- CVXR-0.99/CVXR/R/solver_utilities.R |only CVXR-0.99/CVXR/R/utilities.R | 149 +- CVXR-0.99/CVXR/README.md | 58 - CVXR-0.99/CVXR/build/vignette.rds |binary CVXR-0.99/CVXR/inst/doc/cvxr_intro.html | 652 ++++--------- CVXR-0.99/CVXR/inst/python |only CVXR-0.99/CVXR/man/GLPK-class.Rd |only CVXR-0.99/CVXR/man/GLPK-status_map.Rd |only CVXR-0.99/CVXR/man/GUROBI-class.Rd |only CVXR-0.99/CVXR/man/GUROBI-status_map.Rd |only CVXR-0.99/CVXR/man/LPSOLVE-class.Rd |only CVXR-0.99/CVXR/man/LPSOLVE-status_map.Rd |only CVXR-0.99/CVXR/man/MOSEK-class.Rd |only CVXR-0.99/CVXR/man/MOSEK-status_map.Rd |only CVXR-0.99/CVXR/man/get_gurobiglue.Rd |only CVXR-0.99/CVXR/man/get_mosekglue.Rd |only CVXR-0.99/CVXR/man/get_np.Rd |only CVXR-0.99/CVXR/man/get_sp.Rd |only CVXR-0.99/CVXR/man/installed_solvers.Rd | 2 CVXR-0.99/CVXR/tests/group01.R |only CVXR-0.99/CVXR/tests/group02.R |only CVXR-0.99/CVXR/tests/group03.R |only CVXR-0.99/CVXR/tests/group04.R |only CVXR-0.99/CVXR/tests/manual/test-constant_atoms.R |only CVXR-0.99/CVXR/tests/manual/test-examples.R |only CVXR-0.99/CVXR/tests/manual/test-vignette.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-atoms.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-constraints.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-convolution.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-curvature.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-domain.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-expressions.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-grad.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-lin_ops.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-matrices.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-mip_vars.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-monotonicity.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-non_optimal.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-nonlinear_atoms.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-objectives.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-problem.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-quad_form.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-quadratic.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-semidefinite_vars.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-shape.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-sign.R |only CVXR-0.99/CVXR/tests/testthat/test-g01-unpack_results.R |only CVXR-0.99/CVXR/tests/testthat/test-g02-examples.R |only CVXR-0.99/CVXR/tests/testthat/test-g03-test_ls.R |only CVXR-0.99/CVXR/tests/testthat/test-g04-scs.R |only 91 files changed, 607 insertions(+), 934 deletions(-)
Title: Structural Equation Multidimensional Scaling
Description: Fits a structural equation multidimensional scaling (SEMDS) model for asymmetric and three-way input dissimilarities. It assumes that the dissimilarities are measured with errors. The latent dissimilarities are estimated as factor scores within an SEM framework while the objects are represented in a low-dimensional space as in MDS.
Author: Patrick Mair [aut, cre],
Jose Fernando Vera [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between semds versions 0.9-2 dated 2016-06-14 and 0.9-3 dated 2018-05-26
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Title: Modern Psychometrics with R
Description: Supplementary materials and datasets for the book "Modern Psychometrics With R" (Mair, 2018, Springer useR! series).
Author: Patrick Mair [aut, cre]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between MPsychoR versions 0.10-6 dated 2018-03-11 and 0.10-7 dated 2018-05-26
DESCRIPTION | 13 ++---- MD5 | 86 +++++++++++++++++++++++---------------------- data/ASTI.rda |binary data/AvalanchePrep.rda |binary data/BSSS.rda |binary data/Bergh.rda |binary data/BrainIQ.rda |binary data/CEAQ.rda |binary data/FamilyIQ.rda |binary data/HRB.rda |binary data/HarvardPsych.rda |binary data/KoreanSpeech.rda |binary data/Lakes.rda |binary data/NeuralActivity.rda |binary data/NeuralHM.rda |binary data/NeuralScales.rda |binary data/NeuralScanner.rda |binary data/Pashkam.rda |binary data/Paskvan.rda |binary data/Privacy.rda |binary data/RWDQ.rda |binary data/Rmotivation.rda |binary data/Rmotivation2.rda |binary data/Rogers.rda |binary data/Rogers_Adolescent.rda |only data/SDOwave.rda |binary data/Wenchuan.rda |binary data/WilPat.rda |binary data/Wilmer.rda |binary data/YouthDep.rda |binary data/ageiat.rda |binary data/bandpref.rda |binary data/chile.rda |binary data/condom.rda |binary data/datalist | 1 data/granularity.rda |binary data/iatfaces.rda |binary data/learnemo.rda |binary data/storcap.rda |binary data/tension.rda |binary data/yaass.rda |binary data/zareki.rda |binary man/Rogers.Rd | 2 - man/Rogers_Adolescent.Rd |only man/Wenchuan.Rd | 2 - 45 files changed, 52 insertions(+), 52 deletions(-)
Title: Gifi Methods for Optimal Scaling
Description: Performs a homogeneity analysis (multiple correspondence analysis) and various extensions. Rank restrictions on the category quantifications can be imposed (nonlinear PCA). The categories are transformed by means of optimal scaling with options for nominal, ordinal, and numerical scale levels (for rank-1 restrictions). Variables can be grouped into sets, in order to emulate regression analysis and canonical correlation analysis.
Author: Patrick Mair [aut, cre],
Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between homals versions 1.0-6 dated 2015-07-23 and 1.0-8 dated 2018-05-26
homals-1.0-6/homals/man/homals-package.Rd |only homals-1.0-8/homals/DESCRIPTION | 11 ++++++----- homals-1.0-8/homals/MD5 | 3 +-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Extended Rasch Modeling
Description: Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices.
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Thomas Rusch [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between eRm versions 0.16-0 dated 2018-03-11 and 0.16-1 dated 2018-05-26
eRm-0.16-0/eRm/build/partial.rdb |only eRm-0.16-0/eRm/inst/NEWSRd2txt.R |only eRm-0.16-0/eRm/man/eRm-package.Rd |only eRm-0.16-0/eRm/vignettes/UCML.svg |only eRm-0.16-1/eRm/.Rinstignore |only eRm-0.16-1/eRm/DESCRIPTION | 8 ++++---- eRm-0.16-1/eRm/MD5 | 10 +++------- eRm-0.16-1/eRm/build/vignette.rds |binary eRm-0.16-1/eRm/inst/doc/eRm.pdf |binary 9 files changed, 7 insertions(+), 11 deletions(-)
Title: A General Framework for Multivariate Analysis with Optimal
Scaling
Description: Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
Author: Patrick Mair [cre, aut],
Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between aspect versions 1.0-4 dated 2015-07-24 and 1.0-5 dated 2018-05-26
aspect-1.0-4/aspect/man/aspect-package.Rd |only aspect-1.0-5/aspect/DESCRIPTION | 8 +-- aspect-1.0-5/aspect/MD5 | 7 +- aspect-1.0-5/aspect/man/plot.aspect.Rd | 9 --- aspect-1.0-5/aspect/man/wurzer.Rd | 71 ++++++++++++++---------------- 5 files changed, 43 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-27 1.0.0
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2.2 dated 2015-12-03 and 1.2.3 dated 2018-05-26
ChangeLog | 2 ++ DESCRIPTION | 12 ++++++------ MD5 | 16 +++++++++------- NAMESPACE | 6 ++++-- R/klcv.R | 2 +- R/sglasso.fit.R | 8 ++++---- inst/CITATION | 2 +- man/sglasso-package.Rd | 4 ++-- src/init.c |only src/sglasso.h |only 10 files changed, 29 insertions(+), 23 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias GreniƩ [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.4 dated 2018-04-18 and 0.4.5 dated 2018-05-26
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++-------- NEWS.md | 4 ++ inst/doc/basics.html | 38 ++++++++++++------------ inst/doc/plot_dist.html | 10 +++--- inst/doc/plot_lm.html | 16 +++++----- inst/doc/plot_map.html | 14 ++++---- inst/doc/plot_pca.html | 42 +++++++++++++------------- inst/doc/plot_surv.html | 12 +++---- inst/doc/plot_ts.html | 64 ++++++++++++++++++++--------------------- man/ggmultiplot-class.Rd | 3 - tests/testthat/Rplots.pdf |binary tests/testthat/test-plotlib.R | 24 +++++++-------- tests/testthat/test-stats-lm.R | 13 +++----- 14 files changed, 138 insertions(+), 136 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: Provides a 'ggplot2' geom and helper functions for drawing gene
arrow maps.
Author: David Wilkins [aut, cre]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.2.0 dated 2017-08-24 and 0.3.0 dated 2018-05-26
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Title: Probability Functions and Generalized Regression Models for
Stable Distributions
Description: Density, distribution, quantile and hazard functions of a
stable variate; generalized regression models for the parameters
of a stable distribution. See the README for how to make equivalent calls
to those of 'stabledist'. See github for Journal article.
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
CRAN version),
Philippe Lambert [aut]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between stable versions 1.1.2 dated 2016-12-16 and 1.1.3 dated 2018-05-26
DESCRIPTION | 11 +- MD5 | 17 ++-- NAMESPACE | 6 + NEWS.md | 11 ++ R/pm1_to_pm0_and_pm0_to_pm1.R |only R/sd2s_and_s2sd.R |only R/stable.r | 14 +-- README.md | 114 ++++++++++++++++++++++++++++-- man/Parameter_Conversion.Rd |only man/Parameter_Conversion_Nolan_pm1_pm0.Rd |only src/stable.c | 4 - src/stable_init.c |only 12 files changed, 149 insertions(+), 28 deletions(-)
Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 1.1-1 dated 2017-12-18 and 1.2-0 dated 2018-05-26
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/LC.R | 11 +++++------ 4 files changed, 18 insertions(+), 13 deletions(-)
Title: Metagenomics Longitudinal Differential Abundance Method
Description: Identify time intervals of differentially abundant metagenomics features in longitudinal studies.
Author: Ahmed Metwally, Yang Dai, Patricia Finn, David Perkins
Maintainer: Ahmed Metwally <ametwa2@uic.edu>
Diff between MetaLonDA versions 1.0.9 dated 2018-01-21 and 1.1.0 dated 2018-05-26
DESCRIPTION | 15 +++++++++------ LICENSE | 2 +- MD5 | 21 +++++++++++++-------- R/CurveFitting.R | 4 ++-- R/Metalonda.R | 19 ++++++++++++------- build |only inst/CITATION | 7 ------- inst/doc |only man/curveFitting.Rd | 2 +- man/metalonda.Rd | 2 +- man/metalondaAll.Rd | 2 +- vignettes |only 12 files changed, 40 insertions(+), 34 deletions(-)
Title: Statistical Significance of the Markowitz Portfolio
Description: A collection of tools for analyzing significance of
Markowitz portfolios.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between MarkowitzR versions 0.9900.0 dated 2016-09-17 and 1.0.1 dated 2018-05-26
MarkowitzR-0.9900.0/MarkowitzR/inst/doc/AsymptoticMarkowitz.R |only MarkowitzR-0.9900.0/MarkowitzR/inst/doc/MarkowitzR.R |only MarkowitzR-1.0.1/MarkowitzR/ChangeLog |only MarkowitzR-1.0.1/MarkowitzR/DESCRIPTION | 20 +++--- MarkowitzR-1.0.1/MarkowitzR/MD5 | 26 ++++---- MarkowitzR-1.0.1/MarkowitzR/R/MarkowitzR.r | 5 + MarkowitzR-1.0.1/MarkowitzR/README.md | 31 +++++----- MarkowitzR-1.0.1/MarkowitzR/build/vignette.rds |binary MarkowitzR-1.0.1/MarkowitzR/inst/doc/AsymptoticMarkowitz.pdf |binary MarkowitzR-1.0.1/MarkowitzR/inst/doc/MarkowitzR.pdf |binary MarkowitzR-1.0.1/MarkowitzR/man/MarkowitzR.Rd | 10 +-- MarkowitzR-1.0.1/MarkowitzR/man/NEWS.Rd | 7 ++ MarkowitzR-1.0.1/MarkowitzR/man/figures |only MarkowitzR-1.0.1/MarkowitzR/man/itheta_vcov.Rd | 9 +- MarkowitzR-1.0.1/MarkowitzR/man/mp_vcov.Rd | 9 +- MarkowitzR-1.0.1/MarkowitzR/man/theta_vcov.Rd | 9 +- 16 files changed, 71 insertions(+), 55 deletions(-)