Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day ('GSOD') weather data
from the from the USA National Centers for Environmental Information
('NCEI') for use in R. Units are converted from from United States
Customary System ('USCS') units to International System of Units ('SI').
Stations may be individually checked for number of missing days defined by
the user, where stations with too many missing observations are omitted.
Only stations with valid reported latitude and longitude values are
permitted in the final data. Additional useful elements, saturation vapour
pressure ('es'), actual vapour pressure ('ea') and relative humidity are
calculated from the original data and included in the final data set. The
resulting data include station identification information, state, country,
latitude, longitude, elevation, weather observations and associated flags.
Additional data are included with this R package: a list of elevation values
for stations between -60 and 60 degrees latitude derived from the Shuttle
Radar Topography Measuring Mission ('SRTM'). For information on the 'GSOD'
data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from,
<http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>),
Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>),
Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>),
Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>),
Gwenael Giboire [ctb] (Several bug reports in early versions and
testing feedback),
Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation),
Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing
'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 1.3.1 dated 2018-12-19 and 1.3.2 dated 2019-01-18
DESCRIPTION | 6 MD5 | 22 NEWS.md | 25 R/get_GSOD.R | 4 build/vignette.rds |binary inst/doc/GSODR.html | 1405 +++++++++----------- inst/doc/Working_with_spatial_and_climate_data.html | 679 +++++---- inst/doc/use_case_1.html | 702 ++++++--- inst/extdata/country_list.rda |binary inst/extdata/isd_history.rda |binary man/figures/logo.png |binary tests/testthat/test-get_GSOD.R | 17 12 files changed, 1578 insertions(+), 1282 deletions(-)
Title: Split Plot
Description: Automates common plotting tasks to ease data exploration.
Makes density plots (potentially overlaid on histograms),
scatter plots with prediction lines, or bar or line plots with error bars.
For each type, y, or x and y variables can be plotted at levels of other variables,
all with minimal specification.
Author: Micah Iserman
Maintainer: Micah Iserman <micah.iserman@ttu.edu>
Diff between splot versions 0.4.0 dated 2018-06-24 and 0.4.1 dated 2019-01-18
DESCRIPTION | 10 +++--- MD5 | 14 ++++----- R/splot.R | 77 +++++++++++++++++++++++++++++++++-------------------- R/utils.R | 62 +++++++++++++++++++++++++++++++++++++----- inst/NEWS.Rd | 17 +++++++++++ man/splot.Rd | 32 +++++++++++----------- man/splot.bench.Rd | 46 ++++++++++++++++++++++++++++--- man/splot.color.Rd | 5 ++- 8 files changed, 193 insertions(+), 70 deletions(-)
Title: High-Dimensional Metrics
Description: Implementation of selected high-dimensional statistical and
econometric methods for estimation and inference. Efficient estimators and
uniformly valid confidence intervals for various low-dimensional causal/
structural parameters are provided which appear in high-dimensional
approximately sparse models. Including functions for fitting heteroscedastic
robust Lasso regressions with non-Gaussian errors and for instrumental variable
(IV) and treatment effect estimation in a high-dimensional setting. Moreover,
the methods enable valid post-selection inference and rely on a theoretically
grounded, data-driven choice of the penalty.
Chernozhukov, Hansen, Spindler (2016) <arXiv:1603.01700>.
Author: Martin Spindler [cre, aut],
Victor Chernozhukov [aut],
Christian Hansen [aut],
Philipp Bach [ctb]
Maintainer: Martin Spindler <martin.spindler@gmx.de>
Diff between hdm versions 0.2.3 dated 2018-01-23 and 0.3.1 dated 2019-01-18
hdm-0.2.3/hdm/inst/doc/hdm_introduction.Rnw |only hdm-0.2.3/hdm/inst/doc/hdm_introduction.pdf |only hdm-0.2.3/hdm/tests/testthat/no_test_LassoShooting.fit.R |only hdm-0.2.3/hdm/tests/testthat/no_test_rlasso.R |only hdm-0.2.3/hdm/tests/testthat/no_test_rlasso_MS.R |only hdm-0.2.3/hdm/tests/testthat/no_test_rlasso_predict_MS.R |only hdm-0.2.3/hdm/tests/testthat/no_test_rlassologit_MS.R |only hdm-0.2.3/hdm/vignettes/hdm_introduction.Rnw |only hdm-0.3.1/hdm/DESCRIPTION | 21 - hdm-0.3.1/hdm/MD5 | 107 ++++---- hdm-0.3.1/hdm/NAMESPACE | 6 hdm-0.3.1/hdm/R/p_adjust.R |only hdm-0.3.1/hdm/R/rlasso.R | 84 +++++- hdm-0.3.1/hdm/R/rlassoEffects.R | 190 +++++++++++++-- hdm-0.3.1/hdm/R/rlassoIV.R | 14 - hdm-0.3.1/hdm/R/rlassoIVselectZ.R | 33 +- hdm-0.3.1/hdm/R/rlassologitEffect.R | 13 - hdm-0.3.1/hdm/R/rlassotreatment.R | 124 ++++++++- hdm-0.3.1/hdm/build/vignette.rds |binary hdm-0.3.1/hdm/data/AJR.rda |binary hdm-0.3.1/hdm/data/BLP.rda |binary hdm-0.3.1/hdm/data/EminentDomain.rda |binary hdm-0.3.1/hdm/data/GrowthData.rda |binary hdm-0.3.1/hdm/data/cps2012.rda |binary hdm-0.3.1/hdm/data/pension.rda |binary hdm-0.3.1/hdm/inst/CITATION | 2 hdm-0.3.1/hdm/inst/doc/hdm.Rnw |only hdm-0.3.1/hdm/inst/doc/hdm.pdf |only hdm-0.3.1/hdm/man/AJR.Rd | 1 hdm-0.3.1/hdm/man/BLP.Rd | 1 hdm-0.3.1/hdm/man/EminentDomain.Rd | 1 hdm-0.3.1/hdm/man/Growth-Data.Rd | 7 hdm-0.3.1/hdm/man/LassoShooting.fit.Rd | 1 hdm-0.3.1/hdm/man/TE.Rd | 32 +- hdm-0.3.1/hdm/man/coef.rlassoEffects.Rd |only hdm-0.3.1/hdm/man/cps2012.Rd | 1 hdm-0.3.1/hdm/man/hdm-package.Rd | 11 hdm-0.3.1/hdm/man/lambdaCalculation.Rd | 1 hdm-0.3.1/hdm/man/methods.rlasso.Rd | 7 hdm-0.3.1/hdm/man/methods.rlassoEffects.Rd | 7 hdm-0.3.1/hdm/man/methods.rlassoIV.Rd | 6 hdm-0.3.1/hdm/man/methods.rlassoIVselectX.Rd | 6 hdm-0.3.1/hdm/man/methods.rlassoIVselectZ.Rd | 6 hdm-0.3.1/hdm/man/methods.rlassoTE.Rd | 6 hdm-0.3.1/hdm/man/methods.rlassologit.Rd | 6 hdm-0.3.1/hdm/man/methods.rlassologitEffects.Rd | 7 hdm-0.3.1/hdm/man/methods.tsls.Rd | 4 hdm-0.3.1/hdm/man/p_adjust.Rd |only hdm-0.3.1/hdm/man/pension.Rd | 5 hdm-0.3.1/hdm/man/print_coef.Rd |only hdm-0.3.1/hdm/man/rlasso.Rd | 3 hdm-0.3.1/hdm/man/rlassoEffects.Rd | 7 hdm-0.3.1/hdm/man/rlassoIV.Rd | 6 hdm-0.3.1/hdm/man/rlassoIVselectX.Rd | 5 hdm-0.3.1/hdm/man/rlassoIVselectZ.Rd | 7 hdm-0.3.1/hdm/man/rlassologit.Rd | 3 hdm-0.3.1/hdm/man/rlassologitEffects.Rd | 9 hdm-0.3.1/hdm/man/summary.rlassoEffects.Rd | 3 hdm-0.3.1/hdm/man/tsls.Rd | 1 hdm-0.3.1/hdm/tests/testthat/test_rlasso.R | 30 +- hdm-0.3.1/hdm/vignettes/hdm.Rnw |only hdm-0.3.1/hdm/vignettes/mybib.bib | 23 + 62 files changed, 557 insertions(+), 250 deletions(-)
More information about ClinicalTrialSummary at CRAN
Permanent link
Title: Classes for 'GeoJSON'
Description: Classes for 'GeoJSON' to make working with 'GeoJSON' easier.
Includes S3 classes for 'GeoJSON' classes with brief summary output,
and a few methods such as extracting and adding bounding boxes,
properties, and coordinate reference systems; working with
newline delimited 'GeoJSON'; linting through the 'geojsonlint'
package; and serializing to/from 'Geobuf' binary 'GeoJSON'
format.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Jeroen Ooms [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojson versions 0.2.0 dated 2017-11-08 and 0.3.0 dated 2019-01-18
DESCRIPTION | 33 - LICENSE | 2 MD5 | 88 +-- NAMESPACE | 5 NEWS.md | 21 R/as.geojson.R | 80 ++- R/feature.R | 2 R/featurecollection.R | 5 R/geo_bbox.R | 6 R/geo_write.R | 4 R/linestring.R | 2 R/multilinestring.R | 9 R/multipoint.R | 2 R/multipolygon.R | 2 R/ndgeojson.R |only R/onLoad.R | 6 R/point.R | 2 R/polygon.R | 2 R/sp_to_geojson.R | 1 R/stream_in_geojson.R |only R/zzz.R | 9 README.md | 60 ++ build/vignette.rds |binary inst/doc/geojson-operations.html | 770 ++++++++++++++++++++------------ inst/doc/geojson.html | 490 ++++++++++++++------ inst/examples/ndgeojson1.json |only inst/examples/ndgeojson2.json |only inst/examples/ndgeojson3.json |only man/as.geojson.Rd | 7 man/crs.Rd | 1 man/feature.Rd | 18 man/featurecollection.Rd | 2 man/geo_bbox.Rd | 4 man/geo_write.Rd | 2 man/geojson-package.Rd | 53 +- man/geojson_data.Rd | 26 - man/linestring.Rd | 2 man/linting_opts.Rd | 6 man/multilinestring.Rd | 9 man/multipoint.Rd | 2 man/multipolygon.Rd | 2 man/ndgeo.Rd |only man/point.Rd | 2 man/polygon.Rd | 2 tests/testthat/test-as.geojson.R | 15 tests/testthat/test-geo_bbox.R | 11 tests/testthat/test-ndgeo.R |only tests/testthat/test-stream_in_geojson.R |only tests/testthat/test-tibbles.R | 2 49 files changed, 1192 insertions(+), 575 deletions(-)
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),
Christian Che-Castaldo [ctb],
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.12.0 dated 2019-01-02 and 0.12.1 dated 2019-01-18
DESCRIPTION | 6 +-- MD5 | 14 ++++----- NEWS.md | 9 ++++- R/MCMCplot.R | 76 ++++++++++++++++++++++++++++++++++++++++++++++++++ R/MCMCtrace.R | 11 +------ build/vignette.rds |binary inst/doc/MCMCvis.html | 12 +++---- man/MCMCplot.Rd | 25 ++++++++++++++-- 8 files changed, 123 insertions(+), 30 deletions(-)
Title: All of Your Chuck Norris Needs
Description: Utility functions for the lovely 'ICNDB' API, <http://www.icndb.com/api/>, which allows users to retrieve Chuck Norris jokes either randomly or by joke number.
Author: Chris Cardillo [aut, cre]
Maintainer: Chris Cardillo <CFCardillo23@gmail.com>
Diff between norris versions 0.1.0 dated 2018-06-12 and 0.1.1 dated 2019-01-18
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 6 +++--- README.md | 6 ++++-- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and file.show(system.file("NEWS", package="umx")) for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 2.9.0 dated 2018-12-19 and 2.9.9 dated 2019-01-18
umx-2.9.0/umx/R/build_run_modify.R |only umx-2.9.0/umx/R/fit_and_reporting.R |only umx-2.9.0/umx/R/xmu.R |only umx-2.9.9/umx/DESCRIPTION | 10 umx-2.9.9/umx/MD5 | 207 ++++++++-------- umx-2.9.9/umx/NAMESPACE | 2 umx-2.9.9/umx/NEWS.md | 14 + umx-2.9.9/umx/R/build_run_modify.r |only umx-2.9.9/umx/R/datasets.R | 2 umx-2.9.9/umx/R/fit_and_reporting.r |only umx-2.9.9/umx/R/misc_and_utility.R | 16 - umx-2.9.9/umx/R/umxACEnew.R | 12 umx-2.9.9/umx/R/umx_build_umxSexLim.R | 10 umx-2.9.9/umx/R/xmu.r |only umx-2.9.9/umx/man/GFF.Rd | 2 umx-2.9.9/umx/man/RMSEA.MxModel.Rd | 2 umx-2.9.9/umx/man/RMSEA.Rd | 2 umx-2.9.9/umx/man/RMSEA.summary.mxmodel.Rd | 2 umx-2.9.9/umx/man/extractAIC.MxModel.Rd | 2 umx-2.9.9/umx/man/loadings.MxModel.Rd | 2 umx-2.9.9/umx/man/loadings.Rd | 2 umx-2.9.9/umx/man/plot.MxModel.Rd | 23 - umx-2.9.9/umx/man/residuals.MxModel.Rd | 2 umx-2.9.9/umx/man/umx.Rd | 5 umx-2.9.9/umx/man/umxACE.Rd | 21 + umx-2.9.9/umx/man/umxACEcov.Rd | 2 umx-2.9.9/umx/man/umxACEnew.Rd | 12 umx-2.9.9/umx/man/umxAPA.Rd | 2 umx-2.9.9/umx/man/umxAdd1.Rd | 2 umx-2.9.9/umx/man/umxAlgebra.Rd | 2 umx-2.9.9/umx/man/umxCI.Rd | 2 umx-2.9.9/umx/man/umxCI_boot.Rd | 2 umx-2.9.9/umx/man/umxCP.Rd | 2 umx-2.9.9/umx/man/umxCompare.Rd | 2 umx-2.9.9/umx/man/umxConfint.Rd | 2 umx-2.9.9/umx/man/umxDiagnose.Rd | 2 umx-2.9.9/umx/man/umxDrop1.Rd | 2 umx-2.9.9/umx/man/umxEquate.Rd | 2 umx-2.9.9/umx/man/umxExpCov.Rd | 2 umx-2.9.9/umx/man/umxExpMeans.Rd | 2 umx-2.9.9/umx/man/umxFixAll.Rd | 2 umx-2.9.9/umx/man/umxGetParameters.Rd | 2 umx-2.9.9/umx/man/umxGxE.Rd | 2 umx-2.9.9/umx/man/umxGxE_window.Rd | 2 umx-2.9.9/umx/man/umxIP.Rd | 2 umx-2.9.9/umx/man/umxLabel.Rd | 2 umx-2.9.9/umx/man/umxLatent.Rd | 2 umx-2.9.9/umx/man/umxMI.Rd | 2 umx-2.9.9/umx/man/umxMatrix.Rd | 2 umx-2.9.9/umx/man/umxModel.Rd | 2 umx-2.9.9/umx/man/umxModify.Rd | 2 umx-2.9.9/umx/man/umxPath.Rd | 2 umx-2.9.9/umx/man/umxPlotACE.Rd | 2 umx-2.9.9/umx/man/umxPlotACEcov.Rd | 2 umx-2.9.9/umx/man/umxPlotCP.Rd | 2 umx-2.9.9/umx/man/umxPlotGxE.Rd | 2 umx-2.9.9/umx/man/umxPlotIP.Rd | 2 umx-2.9.9/umx/man/umxRAM.Rd | 2 umx-2.9.9/umx/man/umxRAM2Ordinal.Rd | 2 umx-2.9.9/umx/man/umxReduce.Rd | 5 umx-2.9.9/umx/man/umxReduceACE.Rd | 5 umx-2.9.9/umx/man/umxReduceGxE.Rd | 5 umx-2.9.9/umx/man/umxRun.Rd | 2 umx-2.9.9/umx/man/umxSetParameters.Rd | 2 umx-2.9.9/umx/man/umxSexLim.Rd | 11 umx-2.9.9/umx/man/umxSummarizeTwinData.Rd |only umx-2.9.9/umx/man/umxSummary.MxModel.Rd | 2 umx-2.9.9/umx/man/umxSummary.Rd | 2 umx-2.9.9/umx/man/umxSummaryACE.Rd | 2 umx-2.9.9/umx/man/umxSummaryACEcov.Rd | 2 umx-2.9.9/umx/man/umxSummaryCP.Rd | 2 umx-2.9.9/umx/man/umxSummaryGxE.Rd | 2 umx-2.9.9/umx/man/umxSummaryIP.Rd | 4 umx-2.9.9/umx/man/umxSuperModel.Rd | 2 umx-2.9.9/umx/man/umxThresholdMatrix.Rd | 2 umx-2.9.9/umx/man/umxUnexplainedCausalNexus.Rd | 2 umx-2.9.9/umx/man/umxValues.Rd | 2 umx-2.9.9/umx/man/umxWeightedAIC.Rd | 2 umx-2.9.9/umx/man/umx_APA_model_CI.Rd | 2 umx-2.9.9/umx/man/umx_APA_pval.Rd | 2 umx-2.9.9/umx/man/umx_aggregate.Rd | 2 umx-2.9.9/umx/man/umx_fun_mean_sd.Rd | 2 umx-2.9.9/umx/man/umx_is_MxData.Rd | 1 umx-2.9.9/umx/man/umx_names.Rd | 2 umx-2.9.9/umx/man/umx_parameters.Rd | 2 umx-2.9.9/umx/man/umx_r_test.Rd | 2 umx-2.9.9/umx/man/umx_scale_wide_twin_data.Rd | 6 umx-2.9.9/umx/man/xmuHasSquareBrackets.Rd | 2 umx-2.9.9/umx/man/xmuLabel_MATRIX_Model.Rd | 2 umx-2.9.9/umx/man/xmuLabel_Matrix.Rd | 2 umx-2.9.9/umx/man/xmuLabel_RAM_Model.Rd | 2 umx-2.9.9/umx/man/xmuMI.Rd | 2 umx-2.9.9/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 2 umx-2.9.9/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 2 umx-2.9.9/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 2 umx-2.9.9/umx/man/xmuMaxLevels.Rd | 2 umx-2.9.9/umx/man/xmuMinLevels.Rd | 2 umx-2.9.9/umx/man/xmuPropagateLabels.Rd | 2 umx-2.9.9/umx/man/xmu_check_levels_identical.Rd | 2 umx-2.9.9/umx/man/xmu_dot_make_paths.Rd | 2 umx-2.9.9/umx/man/xmu_dot_make_residuals.Rd | 2 umx-2.9.9/umx/man/xmu_dot_maker.Rd | 2 umx-2.9.9/umx/man/xmu_make_mxData.Rd | 2 umx-2.9.9/umx/man/xmu_safe_run_summary.Rd | 2 umx-2.9.9/umx/man/xmu_set_sep_from_suffix.Rd | 2 umx-2.9.9/umx/man/xmu_simplex_corner.Rd | 2 umx-2.9.9/umx/man/xmu_start_value_list.Rd | 2 umx-2.9.9/umx/man/xmu_twin_check.Rd | 2 108 files changed, 292 insertions(+), 243 deletions(-)
Title: Draws Overview of Outliers (O3) Plots
Description: Potential outliers are identified for all combinations of a dataset's variables. The available methods are HDoutliers() from the package 'HDoutliers', FastPCS() from the package 'FastPCS', mvBACON() from 'robustX', adjOutlyingness() from 'robustbase', DectectDeviatingCells() from 'cellWise', covMcd() from 'robustbase'.
Author: Antony Unwin
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>
Diff between OutliersO3 versions 0.5.4 dated 2018-02-08 and 0.6 dated 2019-01-18
OutliersO3-0.5.4/OutliersO3/inst/doc/O3-alphas-vignette.R |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-alphas-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-alphas-vignette.html |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-newMethod-vignette.R |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-newMethod-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-newMethod-vignette.html |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-pcps-vignette.R |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-pcps-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-pcps-vignette.html |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-vignette.R |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/inst/doc/O3-vignette.html |only OutliersO3-0.5.4/OutliersO3/vignettes/O3-alphas-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/vignettes/O3-newMethod-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/vignettes/O3-pcps-vignette.Rmd |only OutliersO3-0.5.4/OutliersO3/vignettes/O3-vignette.Rmd |only OutliersO3-0.6/OutliersO3/DESCRIPTION | 8 - OutliersO3-0.6/OutliersO3/MD5 | 62 ++++---- OutliersO3-0.6/OutliersO3/NEWS | 17 ++ OutliersO3-0.6/OutliersO3/R/O3a.R | 51 ++++-- OutliersO3-0.6/OutliersO3/R/O3plotM.R | 77 ++++++---- OutliersO3-0.6/OutliersO3/R/O3plotT.R | 71 ++++----- OutliersO3-0.6/OutliersO3/R/O3prep.R | 14 + OutliersO3-0.6/OutliersO3/R/sortO3.R | 12 - OutliersO3-0.6/OutliersO3/README.md | 6 OutliersO3-0.6/OutliersO3/build/vignette.rds |binary OutliersO3-0.6/OutliersO3/inst/doc/DrawingO3plots.R |only OutliersO3-0.6/OutliersO3/inst/doc/DrawingO3plots.Rmd |only OutliersO3-0.6/OutliersO3/inst/doc/DrawingO3plots.html |only OutliersO3-0.6/OutliersO3/inst/doc/MultTolLevels.R |only OutliersO3-0.6/OutliersO3/inst/doc/MultTolLevels.Rmd |only OutliersO3-0.6/OutliersO3/inst/doc/MultTolLevels.html |only OutliersO3-0.6/OutliersO3/inst/doc/PCPsO3.R |only OutliersO3-0.6/OutliersO3/inst/doc/PCPsO3.Rmd |only OutliersO3-0.6/OutliersO3/inst/doc/PCPsO3.html |only OutliersO3-0.6/OutliersO3/inst/doc/xtraO3methods.R |only OutliersO3-0.6/OutliersO3/inst/doc/xtraO3methods.Rmd |only OutliersO3-0.6/OutliersO3/inst/doc/xtraO3methods.html |only OutliersO3-0.6/OutliersO3/man/O3plotM.Rd | 14 + OutliersO3-0.6/OutliersO3/man/O3plotT.Rd | 12 + OutliersO3-0.6/OutliersO3/man/O3prep.Rd | 8 - OutliersO3-0.6/OutliersO3/man/OutliersO3.Rd | 2 OutliersO3-0.6/OutliersO3/man/figures/README-unnamed-chunk-3-1.png |binary OutliersO3-0.6/OutliersO3/man/figures/README-unnamed-chunk-4-1.png |binary OutliersO3-0.6/OutliersO3/vignettes/DrawingO3plots.Rmd |only OutliersO3-0.6/OutliersO3/vignettes/MultTolLevels.Rmd |only OutliersO3-0.6/OutliersO3/vignettes/PCPsO3.Rmd |only OutliersO3-0.6/OutliersO3/vignettes/xtraO3methods.Rmd |only 48 files changed, 213 insertions(+), 141 deletions(-)
Title: The R Version of WebGestalt
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut],
Yuxing Liao [aut, cre]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>
Diff between WebGestaltR versions 0.1.1 dated 2017-05-11 and 0.3.0 dated 2019-01-18
WebGestaltR-0.1.1/WebGestaltR/R/GOSlimSummary.R |only WebGestaltR-0.1.1/WebGestaltR/R/IDMapping.R |only WebGestaltR-0.1.1/WebGestaltR/R/WebGestaltR_batch.R |only WebGestaltR-0.1.1/WebGestaltR/R/listIDType.R |only WebGestaltR-0.1.1/WebGestaltR/R/readGMT.R |only WebGestaltR-0.1.1/WebGestaltR/R/zzz.R |only WebGestaltR-0.1.1/WebGestaltR/build |only WebGestaltR-0.1.1/WebGestaltR/inst/doc |only WebGestaltR-0.1.1/WebGestaltR/man/GOSlimSummary.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/IDMapping.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/WebGestaltR-package.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/WebGestaltR_batch.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/listArchiveURL.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/listIDType.Rd |only WebGestaltR-0.1.1/WebGestaltR/man/readGMT.Rd |only WebGestaltR-0.1.1/WebGestaltR/vignettes |only WebGestaltR-0.3.0/WebGestaltR/DESCRIPTION | 34 WebGestaltR-0.3.0/WebGestaltR/MD5 | 114 WebGestaltR-0.3.0/WebGestaltR/NAMESPACE | 79 WebGestaltR-0.3.0/WebGestaltR/NEWS.md | 4 WebGestaltR-0.3.0/WebGestaltR/R/RcppExports.R |only WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltR-package.R |only WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltR.R | 1970 ---------- WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltRBatch.R |only WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltRGsea.R |only WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltRNta.R |only WebGestaltR-0.3.0/WebGestaltR/R/WebGestaltROra.R |only WebGestaltR-0.3.0/WebGestaltR/R/affinityPropagation.R |only WebGestaltR-0.3.0/WebGestaltR/R/createNtaReport.R |only WebGestaltR-0.3.0/WebGestaltR/R/createReport.R |only WebGestaltR-0.3.0/WebGestaltR/R/dagUtils.R |only WebGestaltR-0.3.0/WebGestaltR/R/enrichResultSection.R |only WebGestaltR-0.3.0/WebGestaltR/R/errorMessage.R |only WebGestaltR-0.3.0/WebGestaltR/R/formatCheck.R | 190 WebGestaltR-0.3.0/WebGestaltR/R/goSlimReport.R |only WebGestaltR-0.3.0/WebGestaltR/R/goSlimSummary.R |only WebGestaltR-0.3.0/WebGestaltR/R/gseaEnrichment.R |only WebGestaltR-0.3.0/WebGestaltR/R/idMapping.R |only WebGestaltR-0.3.0/WebGestaltR/R/idMappingGene.R |only WebGestaltR-0.3.0/WebGestaltR/R/idMappingPhosphosite.R |only WebGestaltR-0.3.0/WebGestaltR/R/idMappingUtils.R |only WebGestaltR-0.3.0/WebGestaltR/R/idToSymbol.R |only WebGestaltR-0.3.0/WebGestaltR/R/linkModification.R |only WebGestaltR-0.3.0/WebGestaltR/R/listArchiveURL.R | 28 WebGestaltR-0.3.0/WebGestaltR/R/listGeneSet.R | 54 WebGestaltR-0.3.0/WebGestaltR/R/listIdType.R |only WebGestaltR-0.3.0/WebGestaltR/R/listOrganism.R | 23 WebGestaltR-0.3.0/WebGestaltR/R/listReferenceSet.R | 25 WebGestaltR-0.3.0/WebGestaltR/R/loadGeneList.R |only WebGestaltR-0.3.0/WebGestaltR/R/loadGeneSet.R |only WebGestaltR-0.3.0/WebGestaltR/R/mergeDuplicate.R |only WebGestaltR-0.3.0/WebGestaltR/R/oraEnrichment.R |only WebGestaltR-0.3.0/WebGestaltR/R/randomWalkEnrichment.R |only WebGestaltR-0.3.0/WebGestaltR/R/readGmt.R |only WebGestaltR-0.3.0/WebGestaltR/R/reportUtils.R |only WebGestaltR-0.3.0/WebGestaltR/R/summaryDescription.R |only WebGestaltR-0.3.0/WebGestaltR/R/swGsea.R |only WebGestaltR-0.3.0/WebGestaltR/R/weightedSetCover.R |only WebGestaltR-0.3.0/WebGestaltR/README.md | 4 WebGestaltR-0.3.0/WebGestaltR/inst/templates |only WebGestaltR-0.3.0/WebGestaltR/man/WebGestaltR.Rd | 450 +- WebGestaltR-0.3.0/WebGestaltR/man/affinityPropagation.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/createNtaReport.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/createReport.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/enrichResultSection.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/expandDag.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/fillInputDataFrame.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/formatCheck.Rd | 57 WebGestaltR-0.3.0/WebGestaltR/man/goSlimSummary.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/gseaPermutation.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/idMapping.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/jaccardSim.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/linkModification.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/listArchiveUrl.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/listGeneSet.Rd | 46 WebGestaltR-0.3.0/WebGestaltR/man/listIdType.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/listOrganism.Rd | 35 WebGestaltR-0.3.0/WebGestaltR/man/listReferenceSet.Rd | 47 WebGestaltR-0.3.0/WebGestaltR/man/prepareGseaInput.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/prepareInputMatrixGsea.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/readGmt.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/specificParameterSummaryGsea.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/specificParameterSummaryOra.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/summaryDescription.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/swGsea.Rd |only WebGestaltR-0.3.0/WebGestaltR/man/weightedSetCover.Rd |only WebGestaltR-0.3.0/WebGestaltR/src |only 87 files changed, 837 insertions(+), 2323 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
For a pedagogical introduction to the package refer to
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>.
Author: Phil Chalmers [aut, cre],
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 1.11 dated 2018-07-17 and 1.13 dated 2019-01-18
DESCRIPTION | 11 +++++----- MD5 | 44 +++++++++++++++++++++--------------------- R/SimFunctions.R | 11 +++++++++- R/analysis.R | 12 +++++------ R/functions.R | 15 ++++++++++++-- R/runSimulation.R | 10 +++++++-- R/summary_functions.R | 23 ++++++++++++++++----- R/zzz.R | 5 ++-- build/partial.rdb |binary inst/doc/Catch_errors.Rmd | 6 +++-- inst/doc/Catch_errors.html | 24 ++++++++++++---------- inst/doc/Fixed_obj_fun.html | 6 ++--- inst/doc/Saving-results.html | 23 +++++++++++---------- inst/doc/SimDesign-intro.html | 32 +++++++++++++++--------------- man/SimFunctions.Rd | 6 ++++- man/add_missing.Rd | 3 +- man/bias.Rd | 10 ++++++++- man/boot_predict.Rd | 5 ++-- man/rHeadrick.Rd | 5 ++-- man/rValeMaurelli.Rd | 5 ++-- man/runSimulation.Rd | 28 ++++++++++++++++---------- tests/tests/test-SimDesign.R | 15 +++++++++++--- vignettes/Catch_errors.Rmd | 6 +++-- 23 files changed, 191 insertions(+), 114 deletions(-)
Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization
facilities of MOSEK available from the R-language. The interface supports
large-scale optimization of many kinds: Mixed-integer and continuous linear,
second-order cone, exponential cone and power cone optimization, as well as
continuous semidefinite optimization. Rmosek and the R-language are
open-source projects. MOSEK is a proprietary product, but
unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>
Diff between Rmosek versions 1.2.5.1 dated 2014-02-21 and 1.3.0 dated 2019-01-18
Rmosek-1.2.5.1/Rmosek/COPYING.LGPL |only Rmosek-1.2.5.1/Rmosek/R/main.R |only Rmosek-1.2.5.1/Rmosek/R/obtain_sparsematrix.R |only Rmosek-1.2.5.1/Rmosek/R/transformations.R |only Rmosek-1.2.5.1/Rmosek/configure |only Rmosek-1.2.5.1/Rmosek/configure.win |only Rmosek-1.2.5.1/Rmosek/configure_script.R |only Rmosek-1.2.5.1/Rmosek/inst |only Rmosek-1.2.5.1/Rmosek/man/mosek.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_clean.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_lptoprob.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_qptoprob.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_read.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_version.Rd |only Rmosek-1.2.5.1/Rmosek/man/mosek_write.Rd |only Rmosek-1.2.5.1/Rmosek/src |only Rmosek-1.3.0/Rmosek/COPYING | 64 ++++++++++----------- Rmosek-1.3.0/Rmosek/DESCRIPTION | 38 ++++++------- Rmosek-1.3.0/Rmosek/MD5 | 73 ++----------------------- Rmosek-1.3.0/Rmosek/NAMESPACE | 16 +---- Rmosek-1.3.0/Rmosek/NEWS | 13 +++- Rmosek-1.3.0/Rmosek/R/builder.R |only Rmosek-1.3.0/Rmosek/man/mosek_attachbuilder.Rd |only 23 files changed, 69 insertions(+), 135 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Description: Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can in
general be programmed on. A useful OptPath object (archive) to log function
evaluations is also provided.
Author: Bernd Bischl [aut],
Michel Lang [aut],
Jakob Richter [aut, cre],
Jakob Bossek [aut],
Daniel Horn [aut],
Karin Schork [ctb],
Pascal Kerschke [aut]
Maintainer: Jakob Richter <code@jakob-r.de>
Diff between ParamHelpers versions 1.11 dated 2018-06-25 and 1.12 dated 2019-01-18
DESCRIPTION | 8 +- MD5 | 84 +++++++++++++-------------- NAMESPACE | 3 NEWS | 4 + R/ParamSet.R | 6 - R/aParam.R | 8 -- R/isFeasible.R | 5 - R/zzz.R | 7 +- man/LearnerParam.Rd | 18 ++--- man/OptPath.Rd | 1 man/Param.Rd | 31 ++++----- man/addOptPathEl.Rd | 1 man/as.data.frame.OptPathDF.Rd | 6 - man/filterParams.Rd | 4 - man/generateDesign.Rd | 4 - man/getOptPathBestIndex.Rd | 1 man/getOptPathCol.Rd | 1 man/getOptPathCols.Rd | 1 man/getOptPathDOB.Rd | 1 man/getOptPathEOL.Rd | 1 man/getOptPathEl.Rd | 1 man/getOptPathErrorMessages.Rd | 1 man/getOptPathExecTimes.Rd | 1 man/getOptPathLength.Rd | 1 man/getOptPathParetoFront.Rd | 1 man/getOptPathX.Rd | 1 man/getOptPathY.Rd | 1 man/isFeasible.Rd | 5 - man/isRequiresOk.Rd | 3 man/makeParamSet.Rd | 2 man/renderOptPathPlot.Rd | 11 +-- man/sampleValue.Rd | 2 man/sampleValues.Rd | 2 man/setOptPathElDOB.Rd | 1 man/setOptPathElEOL.Rd | 1 src/c_dfRowsToList.c | 13 +++- src/c_generateDesign.c | 4 - tests/testthat/Rplots.pdf |binary tests/testthat/test_convertParamSetToIrace.R | 1 tests/testthat/test_dfRowToList.R | 4 - tests/testthat/test_generateDesign.R | 42 ++++++------- tests/testthat/test_generateRandomDesign.R | 10 +-- tests/testthat/test_sample.R | 2 43 files changed, 168 insertions(+), 137 deletions(-)
Title: GPL Palettes Copied from 'Gimp' and 'Inkscape'
Description: A set of palettes imported from 'Gimp' distributed
under GPL3 (<https://www.gimp.org/about/COPYING>), and 'Inkscape'
distributed under GPL2 (<https://inkscape.org/about/license/>).
Author: Francois Rebaudo [aut, cre],
Gimp [cph] (copyright holder for palettes imported from Gimp),
Inkscape [cph] (copyright holder for palettes imported from Inkscape)
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>
Diff between palettesForR versions 0.1.1 dated 2019-01-17 and 0.1.2 dated 2019-01-18
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others. MacOS users can download the most up-to-date
package binaries from <http://openmx.ssri.psu.edu>.
See Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.11.5 dated 2018-10-05 and 2.12.1 dated 2019-01-18
OpenMx-2.11.5/OpenMx/src/nloptcpp.cpp |only OpenMx-2.11.5/OpenMx/src/nloptcpp.h |only OpenMx-2.12.1/OpenMx/CHANGES | 4 OpenMx-2.12.1/OpenMx/DESCRIPTION | 15 OpenMx-2.12.1/OpenMx/MD5 | 536 +- OpenMx-2.12.1/OpenMx/NAMESPACE | 3 OpenMx-2.12.1/OpenMx/NEWS | 3 OpenMx-2.12.1/OpenMx/R/0ClassUnion.R | 6 OpenMx-2.12.1/OpenMx/R/DefinitionVars.R | 5 OpenMx-2.12.1/OpenMx/R/MxAlgebraFunctions.R | 7 OpenMx-2.12.1/OpenMx/R/MxAutoStart.R | 56 OpenMx-2.12.1/OpenMx/R/MxAvailableOptimizers.R | 1 OpenMx-2.12.1/OpenMx/R/MxBaseNamed.R | 2 OpenMx-2.12.1/OpenMx/R/MxCompare.R | 2 OpenMx-2.12.1/OpenMx/R/MxCompute.R | 182 OpenMx-2.12.1/OpenMx/R/MxData.R | 153 OpenMx-2.12.1/OpenMx/R/MxDataWLS.R | 282 + OpenMx-2.12.1/OpenMx/R/MxEval.R | 2 OpenMx-2.12.1/OpenMx/R/MxExpectation.R | 5 OpenMx-2.12.1/OpenMx/R/MxExpectationBA81.R | 11 OpenMx-2.12.1/OpenMx/R/MxExpectationLISREL.R | 27 OpenMx-2.12.1/OpenMx/R/MxExpectationNormal.R | 50 OpenMx-2.12.1/OpenMx/R/MxExpectationRAM.R | 26 OpenMx-2.12.1/OpenMx/R/MxExpectationStateSpace.R | 4 OpenMx-2.12.1/OpenMx/R/MxFactorScores.R | 5 OpenMx-2.12.1/OpenMx/R/MxFitFunction.R | 4 OpenMx-2.12.1/OpenMx/R/MxFitFunctionML.R | 7 OpenMx-2.12.1/OpenMx/R/MxFitFunctionMultigroup.R | 4 OpenMx-2.12.1/OpenMx/R/MxFitFunctionR.R | 4 OpenMx-2.12.1/OpenMx/R/MxFitFunctionWLS.R | 116 OpenMx-2.12.1/OpenMx/R/MxInterval.R | 2 OpenMx-2.12.1/OpenMx/R/MxLISRELModel.R | 6 OpenMx-2.12.1/OpenMx/R/MxMatrix.R | 4 OpenMx-2.12.1/OpenMx/R/MxModelFunctions.R | 10 OpenMx-2.12.1/OpenMx/R/MxModelParameters.R | 2 OpenMx-2.12.1/OpenMx/R/MxMultiModel.R | 4 OpenMx-2.12.1/OpenMx/R/MxNamespace.R | 2 OpenMx-2.12.1/OpenMx/R/MxOptions.R | 2 OpenMx-2.12.1/OpenMx/R/MxPath.R | 2 OpenMx-2.12.1/OpenMx/R/MxRAMModel.R | 15 OpenMx-2.12.1/OpenMx/R/MxRObjective.R | 4 OpenMx-2.12.1/OpenMx/R/MxRename.R | 2 OpenMx-2.12.1/OpenMx/R/MxRetro.R | 4 OpenMx-2.12.1/OpenMx/R/MxRobustSE.R | 8 OpenMx-2.12.1/OpenMx/R/MxRun.R | 2 OpenMx-2.12.1/OpenMx/R/MxSE.R | 8 OpenMx-2.12.1/OpenMx/R/MxSaturatedModel.R | 21 OpenMx-2.12.1/OpenMx/R/MxSummary.R | 13 OpenMx-2.12.1/OpenMx/R/MxThreshold.R | 6 OpenMx-2.12.1/OpenMx/R/MxTryHard.R | 40 OpenMx-2.12.1/OpenMx/R/MxVersion.R | 6 OpenMx-2.12.1/OpenMx/R/MxVersion.R.in | 4 OpenMx-2.12.1/OpenMx/R/omxBrownie.R | 58 OpenMx-2.12.1/OpenMx/R/sysdata.rda |binary OpenMx-2.12.1/OpenMx/R/zzz.R | 2 OpenMx-2.12.1/OpenMx/configure | 5 OpenMx-2.12.1/OpenMx/demo/AlternativeApproaches.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateHeterogeneity_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateHeterogeneity_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated_MatrixCovCholesky.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/BivariateSaturated_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/GrowthMixtureModel_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/GrowthMixtureModel_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/LatentGrowthCurveModel_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/LatentGrowthCurveModel_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/LatentGrowthCurveModel_PathRaw_ModelRec.R | 2 OpenMx-2.12.1/OpenMx/demo/LatentGrowthCurveModel_PathRaw_ObjectAdd.R | 2 OpenMx-2.12.1/OpenMx/demo/MultipleRegression_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/MultipleRegression_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/MultipleRegression_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/MultipleRegression_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/MultivariateRegression_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/MultivariateRegression_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/MultivariateRegression_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/MultivariateRegression_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/OneFactorModel_LikelihoodVector.R | 2 OpenMx-2.12.1/OpenMx/demo/OneFactorModel_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/OneFactorModel_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/OneFactorModel_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/OneFactorModel_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/RObjectiveLISRELFactorRegression.R | 2 OpenMx-2.12.1/OpenMx/demo/RowObjectiveSimpleExamples.R | 2 OpenMx-2.12.1/OpenMx/demo/SimpleRegression_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/SimpleRegression_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/SimpleRegression_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/SimpleRegression_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/TwoFactorModel_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/TwoFactorModel_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/TwoFactorModel_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/TwoFactorModel_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/UnivariateSaturated.R | 2 OpenMx-2.12.1/OpenMx/demo/UnivariateSaturated_MatrixCov.R | 2 OpenMx-2.12.1/OpenMx/demo/UnivariateSaturated_MatrixRaw.R | 2 OpenMx-2.12.1/OpenMx/demo/UnivariateSaturated_PathCov.R | 2 OpenMx-2.12.1/OpenMx/demo/UnivariateSaturated_PathRaw.R | 2 OpenMx-2.12.1/OpenMx/inst/CITATION | 8 OpenMx-2.12.1/OpenMx/inst/WORDLIST |only OpenMx-2.12.1/OpenMx/inst/models/codeRed/fail_on_re-run_entity_already_exists.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/FactorScores.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/GREML_monophenotype_1GRM.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/GREML_monophenotype_1GRM_GradDesc.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/GrowthMixtureModelRandomStarts.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/InvalidComparisonDetection.R | 5 OpenMx-2.12.1/OpenMx/inst/models/nightly/JointWLS.R | 17 OpenMx-2.12.1/OpenMx/inst/models/nightly/LegacyContinuousOnlyWLSTest.R |only OpenMx-2.12.1/OpenMx/inst/models/nightly/LegacyMultipleGroupWLS.R |only OpenMx-2.12.1/OpenMx/inst/models/nightly/LegacyWLS+CI.R |only OpenMx-2.12.1/OpenMx/inst/models/nightly/MultigroupWLS.R | 15 OpenMx-2.12.1/OpenMx/inst/models/nightly/NelderMeadUnitTesting.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/ParamBoot2.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/data/jointdata.txt |only OpenMx-2.12.1/OpenMx/inst/models/nightly/mplus-ex9.23.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/mxSE-defvar.R |only OpenMx-2.12.1/OpenMx/inst/models/nightly/npdWarningWLS.R |only OpenMx-2.12.1/OpenMx/inst/models/nightly/thresholdModel1Factor3Variate.R | 2 OpenMx-2.12.1/OpenMx/inst/models/nightly/thresholdModel1Factor5VariateWLS.R | 28 OpenMx-2.12.1/OpenMx/inst/models/passing/AlgebraComputePassing.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/ContinuousOnlyWLSTest.R | 35 OpenMx-2.12.1/OpenMx/inst/models/passing/GREML--minimal_test_model.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/GREML--testStarterFunctionWithMissingData.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/GREML_intercept_check.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/IntroSEM-OneFactorCov.R | 26 OpenMx-2.12.1/OpenMx/inst/models/passing/IntroSEM-OneFactorRaw.R | 6 OpenMx-2.12.1/OpenMx/inst/models/passing/IntroSEM-UnivariateRaw.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/InvalidWLS.R |only OpenMx-2.12.1/OpenMx/inst/models/passing/MultipleGroupWLS.R | 8 OpenMx-2.12.1/OpenMx/inst/models/passing/NA-defvar.R | 4 OpenMx-2.12.1/OpenMx/inst/models/passing/NelderMeadErrorTesting.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/OrdinalPathTest.R | 3 OpenMx-2.12.1/OpenMx/inst/models/passing/SaturatedWLSTest.R | 37 OpenMx-2.12.1/OpenMx/inst/models/passing/SimpleAlgebraCIs.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/StateSpaceAlg.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/StateSpaceInputs.R | 4 OpenMx-2.12.1/OpenMx/inst/models/passing/TestUseOptimizer.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/UselessConstraint.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/WLS+CI.R | 5 OpenMx-2.12.1/OpenMx/inst/models/passing/WeightedWLS.R |only OpenMx-2.12.1/OpenMx/inst/models/passing/checkStandardizedLoadingsEtcetera.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/exoPredWLS.R |only OpenMx-2.12.1/OpenMx/inst/models/passing/ifa-drm1.R | 1 OpenMx-2.12.1/OpenMx/inst/models/passing/ifa-grm1.R | 7 OpenMx-2.12.1/OpenMx/inst/models/passing/ifa-lmp.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/jointFactorWls.R | 44 OpenMx-2.12.1/OpenMx/inst/models/passing/loadData.R |only OpenMx-2.12.1/OpenMx/inst/models/passing/loadMatrix.R | 6 OpenMx-2.12.1/OpenMx/inst/models/passing/mxSE_test.R | 2 OpenMx-2.12.1/OpenMx/inst/models/passing/mxVersion.R | 4 OpenMx-2.12.1/OpenMx/inst/models/passing/nonlinearDefinitionTest.R | 4 OpenMx-2.12.1/OpenMx/inst/models/passing/oneLocusLikelihood.R | 4 OpenMx-2.12.1/OpenMx/inst/models/passing/tangleF.R | 82 OpenMx-2.12.1/OpenMx/inst/tools/testModels.R | 35 OpenMx-2.12.1/OpenMx/inst/tools/updateCopyright.sh | 11 OpenMx-2.12.1/OpenMx/man/Bollen_data.Rd | 2 OpenMx-2.12.1/OpenMx/man/MxData-class.Rd | 4 OpenMx-2.12.1/OpenMx/man/MxMMI.Rd | 2 OpenMx-2.12.1/OpenMx/man/MxMatrix-class.Rd | 4 OpenMx-2.12.1/OpenMx/man/MxOptionalDataFrame-class.Rd |only OpenMx-2.12.1/OpenMx/man/as.statusCode.Rd | 4 OpenMx-2.12.1/OpenMx/man/factorScaleExample2_data.Rd | 2 OpenMx-2.12.1/OpenMx/man/imxConDecMatrixSlots.Rd | 2 OpenMx-2.12.1/OpenMx/man/imxDataTypes.Rd | 2 OpenMx-2.12.1/OpenMx/man/imxFlattenModel.Rd | 4 OpenMx-2.12.1/OpenMx/man/imxGenericModelBuilder.Rd | 4 OpenMx-2.12.1/OpenMx/man/imxGetSlotDisplayNames.Rd | 4 OpenMx-2.12.1/OpenMx/man/imxModelBuilder.Rd | 4 OpenMx-2.12.1/OpenMx/man/imxPPML.Test.Battery.Rd | 4 OpenMx-2.12.1/OpenMx/man/imxWlsChiSquare.Rd | 6 OpenMx-2.12.1/OpenMx/man/imxWlsStandardErrors.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxAlgebra.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxAutoStart.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxBootstrap.Rd | 10 OpenMx-2.12.1/OpenMx/man/mxBootstrapStdizeRAMpaths.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxCI.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxCompare.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxComputeCheckpoint.Rd | 3 OpenMx-2.12.1/OpenMx/man/mxComputeConfidenceInterval.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxComputeEM.Rd | 18 OpenMx-2.12.1/OpenMx/man/mxComputeGradientDescent.Rd | 5 OpenMx-2.12.1/OpenMx/man/mxComputeIterate.Rd | 3 OpenMx-2.12.1/OpenMx/man/mxComputeJacobian.Rd | 7 OpenMx-2.12.1/OpenMx/man/mxComputeLoadData.Rd |only OpenMx-2.12.1/OpenMx/man/mxComputeLoadMatrix.Rd | 12 OpenMx-2.12.1/OpenMx/man/mxComputeNelderMead.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxComputeNewtonRaphson.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxComputeOnce.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxComputeSetOriginalStarts.Rd |only OpenMx-2.12.1/OpenMx/man/mxComputeStandardError.Rd | 3 OpenMx-2.12.1/OpenMx/man/mxComputeTryHard.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxConstraint.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxData.Rd | 31 OpenMx-2.12.1/OpenMx/man/mxDataWLS.Rd | 22 OpenMx-2.12.1/OpenMx/man/mxEvaluateOnGrid.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxExpectationBA81.Rd | 16 OpenMx-2.12.1/OpenMx/man/mxExpectationHiddenMarkov.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxExpectationLISREL.Rd | 8 OpenMx-2.12.1/OpenMx/man/mxExpectationMixture.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxExpectationStateSpace.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxExpectationStateSpaceContinuousTime.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxFitFunctionR.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxFitFunctionWLS.Rd | 30 OpenMx-2.12.1/OpenMx/man/mxGREMLDataHandler.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxGenerateData.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxGetExpected.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxKalmanScores.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxLISRELObjective.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxMatrix.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxModel.Rd | 32 OpenMx-2.12.1/OpenMx/man/mxOption.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxPath.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxPower.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxRObjective.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxRestore.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxRetro.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxRun.Rd | 2 OpenMx-2.12.1/OpenMx/man/mxSE.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxSave.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxThreshold.Rd | 6 OpenMx-2.12.1/OpenMx/man/mxTryHard.Rd | 4 OpenMx-2.12.1/OpenMx/man/mxVersion.Rd | 4 OpenMx-2.12.1/OpenMx/man/myRegDataRaw_data.Rd | 2 OpenMx-2.12.1/OpenMx/man/myRegData_data.Rd | 2 OpenMx-2.12.1/OpenMx/man/omxAugmentDataWithWLSSummary.Rd |only OpenMx-2.12.1/OpenMx/man/omxBrownie.Rd | 31 OpenMx-2.12.1/OpenMx/man/omxGetParameters.Rd | 4 OpenMx-2.12.1/OpenMx/man/omxGraphviz.Rd | 4 OpenMx-2.12.1/OpenMx/man/omxParallelCI.Rd | 2 OpenMx-2.12.1/OpenMx/man/omxRMSEA.Rd | 4 OpenMx-2.12.1/OpenMx/man/omxSaturatedModel.Rd | 6 OpenMx-2.12.1/OpenMx/man/summary.MxModel.Rd | 6 OpenMx-2.12.1/OpenMx/man/twinData.Rd | 6 OpenMx-2.12.1/OpenMx/man/vechs.Rd | 3 OpenMx-2.12.1/OpenMx/src/AlgebraFunctions.h | 2 OpenMx-2.12.1/OpenMx/src/Compute.cpp | 491 +- OpenMx-2.12.1/OpenMx/src/Compute.h | 29 OpenMx-2.12.1/OpenMx/src/ComputeGD.cpp | 9 OpenMx-2.12.1/OpenMx/src/ComputeGD.h | 2 OpenMx-2.12.1/OpenMx/src/ComputeNM.cpp | 4 OpenMx-2.12.1/OpenMx/src/ComputeNR.cpp | 491 +- OpenMx-2.12.1/OpenMx/src/MarkovExpectation.cpp | 2 OpenMx-2.12.1/OpenMx/src/RAMInternal.h | 49 OpenMx-2.12.1/OpenMx/src/finiteDifferences.h | 5 OpenMx-2.12.1/OpenMx/src/glue.cpp | 39 OpenMx-2.12.1/OpenMx/src/glue.h | 4 OpenMx-2.12.1/OpenMx/src/mvbvn.f |only OpenMx-2.12.1/OpenMx/src/nr.h |only OpenMx-2.12.1/OpenMx/src/omxBVN.h |only OpenMx-2.12.1/OpenMx/src/omxData.cpp | 2106 ++++++++-- OpenMx-2.12.1/OpenMx/src/omxData.h | 145 OpenMx-2.12.1/OpenMx/src/omxDefines.h | 93 OpenMx-2.12.1/OpenMx/src/omxExpectation.cpp | 111 OpenMx-2.12.1/OpenMx/src/omxExpectation.h | 13 OpenMx-2.12.1/OpenMx/src/omxExpectationBA81.cpp | 3 OpenMx-2.12.1/OpenMx/src/omxExportBackendState.cpp | 8 OpenMx-2.12.1/OpenMx/src/omxFIMLFitFunction.cpp | 16 OpenMx-2.12.1/OpenMx/src/omxFIMLFitFunction.h | 2 OpenMx-2.12.1/OpenMx/src/omxFitFunction.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxFitFunction.h | 2 OpenMx-2.12.1/OpenMx/src/omxGREMLExpectation.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxGREMLfitfunction.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxHessianCalculation.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxImportFrontendState.cpp | 38 OpenMx-2.12.1/OpenMx/src/omxLISRELExpectation.cpp | 131 OpenMx-2.12.1/OpenMx/src/omxLISRELExpectation.h | 31 OpenMx-2.12.1/OpenMx/src/omxMLFitFunction.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxMatrix.cpp | 90 OpenMx-2.12.1/OpenMx/src/omxMatrix.h | 32 OpenMx-2.12.1/OpenMx/src/omxNLopt.cpp |only OpenMx-2.12.1/OpenMx/src/omxNLopt.h |only OpenMx-2.12.1/OpenMx/src/omxNPSOLSpecific.cpp | 4 OpenMx-2.12.1/OpenMx/src/omxNormalExpectation.cpp | 2 OpenMx-2.12.1/OpenMx/src/omxRAMExpectation.cpp | 610 +- OpenMx-2.12.1/OpenMx/src/omxState.cpp | 19 OpenMx-2.12.1/OpenMx/src/omxState.h | 6 OpenMx-2.12.1/OpenMx/src/omxStateSpaceExpectation.cpp | 4 OpenMx-2.12.1/OpenMx/src/omxWLSFitFunction.cpp | 195 OpenMx-2.12.1/OpenMx/src/ssMLFit.cpp | 2 280 files changed, 5180 insertions(+), 2363 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.5 dated 2017-04-27 and 0.6 dated 2019-01-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/NlcOptim.R | 18 ++++++++++++------ 3 files changed, 17 insertions(+), 11 deletions(-)
Title: Importing and Manipulating Symmetric Input-Output Tables
Description: Pre-processing and basic analytical tasks related to working with Eurostat's symmetric input-output
tables and provide basic input-output economics calculations. The package is
a part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre] (<https://orcid.org/0000-0001-7513-6760>)
Maintainer: Daniel Antal <daniel.antal@ceemid.eu>
Diff between iotables versions 0.4.1 dated 2019-01-17 and 0.4.2 dated 2019-01-18
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 1 - NEWS.md | 4 +++- R/create_knitr_table.R | 16 +++++----------- inst/doc/germany_1990.html | 4 ++-- inst/doc/united_kingdom_2010.html | 6 +++--- inst/doc/working_with_eurostat.html | 4 ++-- man/create_knitr_table.Rd | 5 +++-- 9 files changed, 29 insertions(+), 33 deletions(-)
Title: Change Point Detection in Genomic Sequences
Description: Estimation of number and location of change points in
mean-shift (piecewise constant) models. Particularly useful to
model genomic sequences of continuous measurements.
Author: Vito M.R. Muggeo
Maintainer: Vito M.R. Muggeo <vito.muggeo@unipa.it>
Diff between cumSeg versions 1.1 dated 2011-10-17 and 1.2 dated 2019-01-18
DESCRIPTION | 11 ++++++----- MD5 | 15 ++++++++------- NAMESPACE |only R/jumpoints.R | 17 +++++++++-------- R/plot.aCGHsegmented.R | 2 +- man/cumSeg-package.Rd | 16 ++++++++-------- man/fibroblast.Rd | 4 ++-- man/jumpoints.Rd | 7 ++++--- man/sel.control.Rd | 2 +- 9 files changed, 39 insertions(+), 35 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression as described for example
in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>
Diff between sdcTable versions 0.25 dated 2018-11-14 and 0.26 dated 2019-01-18
DESCRIPTION | 8 ++--- MD5 | 29 +++++++++++---------- NAMESPACE | 1 R/classes.r | 1 R/createArgusInput.R | 5 ++- R/export_functions.r | 2 - R/methods_class_sdcProblem.r | 58 +++++++++++++++++++++++++++++++------------ README.md |only build/vignette.rds |binary data/microData1.RData |binary data/microData2.RData |binary data/problem.RData |binary data/problemWithSupps.RData |binary data/protectedData.RData |binary inst/doc/sdcTable.html | 34 ++++++++++++++++++++----- man/protectTable.Rd | 2 - 16 files changed, 97 insertions(+), 43 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Bojanowski Michal [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.0.1 dated 2018-11-25 and 2.0.2 dated 2019-01-18
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 4 +++ R/to_factor.R | 2 - build/vignette.rds |binary inst/doc/intro_labelled.Rmd | 2 - inst/doc/intro_labelled.html | 46 ++++++++++++++++++++++++++++++----------- tests/testthat/test-labelled.r | 16 ++++++++++++++ vignettes/intro_labelled.Rmd | 2 - 9 files changed, 68 insertions(+), 26 deletions(-)
Title: Using KEEL in R Code
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks.
This package takes the advantages of 'KEEL' and R, allowing to use 'KEEL' algorithms in simple R code.
The implemented R code layer between R and 'KEEL' makes easy both using 'KEEL' algorithms in R as implementing new algorithms for 'RKEEL' in a very simple way.
It includes more than 100 algorithms for classification, regression, preprocess, association rules and imbalance learning, which allows a more complete experimentation process.
For more information about KEEL, see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre],
Luciano Sanchez [aut],
Oliver Sanchez [ctb],
Jesus Alcala-Fernandez [ctb]
Maintainer: Jose M. Moyano <jmoyano@uco.es>
Diff between RKEEL versions 1.2.5 dated 2018-12-19 and 1.2.7 dated 2019-01-18
DESCRIPTION | 18 ++++--- MD5 | 24 +++++----- R/AssociationRulesAlgorithm.R | 35 ++------------- R/ClassificationAlgorithm.R | 62 +++------------------------ R/ImbalancedClassificationAlgorithm.R | 32 +------------ R/KeelAlgorithm.R | 53 +++++++++++++++++++---- R/PreprocessAlgorithm.R | 34 +------------- R/RegressionAlgorithm.R | 34 +------------- man/AdaBoost-I.Rd | 10 ++-- man/C45-C.Rd | 72 +++++++++++++++---------------- man/runCV.Rd | 62 +++++++++++++-------------- man/runParallel.Rd | 78 +++++++++++++++++----------------- man/runSequential.Rd | 76 ++++++++++++++++----------------- 13 files changed, 241 insertions(+), 349 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.4 dated 2018-06-21 and 8.5 dated 2019-01-18
forecast-8.4/forecast/inst/doc/JSS2008.html |only forecast-8.4/forecast/tests/testthat/Rplots.pdf |only forecast-8.5/forecast/DESCRIPTION | 18 - forecast-8.5/forecast/MD5 | 165 ++++----- forecast-8.5/forecast/NAMESPACE | 8 forecast-8.5/forecast/NEWS.md | 8 forecast-8.5/forecast/R/HoltWintersNew.R | 2 forecast-8.5/forecast/R/acf.R | 7 forecast-8.5/forecast/R/arima.R | 53 ++- forecast-8.5/forecast/R/baggedModel.R | 15 forecast-8.5/forecast/R/bats.R | 2 forecast-8.5/forecast/R/checkresiduals.R | 60 ++- forecast-8.5/forecast/R/clean.R | 2 forecast-8.5/forecast/R/dshw.r | 23 - forecast-8.5/forecast/R/forecast2.R | 4 forecast-8.5/forecast/R/getResponse.R | 10 forecast-8.5/forecast/R/ggplot.R | 61 ++- forecast-8.5/forecast/R/lm.R | 17 - forecast-8.5/forecast/R/mstl.R | 35 +- forecast-8.5/forecast/R/naive.R | 217 +++++++++--- forecast-8.5/forecast/R/newarima2.R | 337 +++++++++++++------- forecast-8.5/forecast/R/nnetar.R | 3 forecast-8.5/forecast/R/residuals.R | 9 forecast-8.5/forecast/R/season.R | 13 forecast-8.5/forecast/R/simulate.R | 74 ++++ forecast-8.5/forecast/R/tbats.R | 2 forecast-8.5/forecast/R/theta.R | 6 forecast-8.5/forecast/R/tscv.R | 80 +++- forecast-8.5/forecast/R/unitRoot.R | 66 ++- forecast-8.5/forecast/build/vignette.rds |binary forecast-8.5/forecast/inst/doc/JSS2008.Rmd | 4 forecast-8.5/forecast/inst/doc/JSS2008.pdf |only forecast-8.5/forecast/man/Acf.Rd | 5 forecast-8.5/forecast/man/Arima.Rd | 4 forecast-8.5/forecast/man/BoxCox.lambda.Rd | 3 forecast-8.5/forecast/man/CVar.Rd | 2 forecast-8.5/forecast/man/accuracy.Rd | 3 forecast-8.5/forecast/man/auto.arima.Rd | 38 +- forecast-8.5/forecast/man/autoplot.acf.Rd | 5 forecast-8.5/forecast/man/autoplot.seas.Rd | 7 forecast-8.5/forecast/man/autoplot.ts.Rd | 13 forecast-8.5/forecast/man/baggedModel.Rd | 6 forecast-8.5/forecast/man/bats.Rd | 9 forecast-8.5/forecast/man/bizdays.Rd | 3 forecast-8.5/forecast/man/dshw.Rd | 7 forecast-8.5/forecast/man/ets.Rd | 12 forecast-8.5/forecast/man/forecast.Arima.Rd | 5 forecast-8.5/forecast/man/forecast.HoltWinters.Rd | 6 forecast-8.5/forecast/man/forecast.Rd | 7 forecast-8.5/forecast/man/forecast.StructTS.Rd | 6 forecast-8.5/forecast/man/forecast.baggedModel.Rd | 4 forecast-8.5/forecast/man/forecast.ets.Rd | 7 forecast-8.5/forecast/man/forecast.lm.Rd | 3 forecast-8.5/forecast/man/forecast.mlm.Rd | 3 forecast-8.5/forecast/man/forecast.modelAR.Rd | 4 forecast-8.5/forecast/man/forecast.mts.Rd | 6 forecast-8.5/forecast/man/forecast.nnetar.Rd | 4 forecast-8.5/forecast/man/forecast.stl.Rd | 20 - forecast-8.5/forecast/man/fourier.Rd | 3 forecast-8.5/forecast/man/geom_forecast.Rd | 3 forecast-8.5/forecast/man/gghistogram.Rd | 4 forecast-8.5/forecast/man/gglagplot.Rd | 3 forecast-8.5/forecast/man/ggmonthplot.Rd | 3 forecast-8.5/forecast/man/msts.Rd | 3 forecast-8.5/forecast/man/naive.Rd | 17 - forecast-8.5/forecast/man/ndiffs.Rd | 6 forecast-8.5/forecast/man/nsdiffs.Rd | 7 forecast-8.5/forecast/man/plot.Arima.Rd | 4 forecast-8.5/forecast/man/plot.forecast.Rd | 10 forecast-8.5/forecast/man/plot.mforecast.Rd | 4 forecast-8.5/forecast/man/reexports.Rd | 1 forecast-8.5/forecast/man/residuals.forecast.Rd | 21 - forecast-8.5/forecast/man/seasonplot.Rd | 8 forecast-8.5/forecast/man/ses.Rd | 18 - forecast-8.5/forecast/man/simulate.ets.Rd | 11 forecast-8.5/forecast/man/subset.ts.Rd | 3 forecast-8.5/forecast/man/tbats.Rd | 9 forecast-8.5/forecast/man/thetaf.Rd | 4 forecast-8.5/forecast/man/tsCV.Rd | 7 forecast-8.5/forecast/man/tsdisplay.Rd | 10 forecast-8.5/forecast/tests/testthat/test-arima.R | 4 forecast-8.5/forecast/tests/testthat/test-modelAR.R | 5 forecast-8.5/forecast/tests/testthat/test-nnetar.R | 6 forecast-8.5/forecast/tests/testthat/test-tslm.R | 10 forecast-8.5/forecast/vignettes/JSS2008.Rmd | 4 85 files changed, 1085 insertions(+), 596 deletions(-)
Title: Forecasting Mortality, Fertility, Migration and Population Data
Description: Functions for demographic analysis including lifetable
calculations; Lee-Carter modelling; functional data analysis of
mortality rates, fertility rates, net migration numbers; and
stochastic population forecasting.
Author: Rob J Hyndman with contributions from Heather Booth, Leonie Tickle and John Maindonald.
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between demography versions 1.20 dated 2017-04-25 and 1.21 dated 2019-01-18
ChangeLog | 4 ++ DESCRIPTION | 10 ++--- MD5 | 22 ++++++------ R/attach.R | 10 +++-- R/fdm.R | 21 ++++++----- R/hmd.R | 8 ++-- R/lca.R | 6 +-- R/netmigration.R | 100 +++++++++++++++++++++++++++++-------------------------- README.md | 2 - man/hmd.Rd | 1 man/migration.Rd | 9 ++-- man/monotonic.Rd | 3 - 12 files changed, 105 insertions(+), 91 deletions(-)
Title: Converts Spatial Data to Javascript Object Notation (JSON) for
Use in Htmlwidgets
Description: Many packages use 'htmlwidgets' <https://CRAN.R-project.org/package=htmlwidgets>
for interactive plotting of spatial data.
This package provides functions for converting R objects, such as simple features,
into structures suitable for use in 'htmlwidgets' mapping libraries.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between spatialwidget versions 0.1 dated 2018-12-23 and 0.2 dated 2019-01-18
spatialwidget-0.1/spatialwidget/R/todo.R |only spatialwidget-0.1/spatialwidget/inst/include/spatialwidget/geojson/geometrycollection.hpp |only spatialwidget-0.1/spatialwidget/inst/include/spatialwidget/geojson/write_geojson.hpp |only spatialwidget-0.2/spatialwidget/DESCRIPTION | 14 spatialwidget-0.2/spatialwidget/MD5 | 55 - spatialwidget-0.2/spatialwidget/NEWS.md |only spatialwidget-0.2/spatialwidget/R/RcppExports.R | 24 spatialwidget-0.2/spatialwidget/R/spatial_widget.R | 24 spatialwidget-0.2/spatialwidget/README.md | 8 spatialwidget-0.2/spatialwidget/inst/doc/spatialwidget.R | 8 spatialwidget-0.2/spatialwidget/inst/doc/spatialwidget.Rmd | 28 spatialwidget-0.2/spatialwidget/inst/doc/spatialwidget.html | 53 - spatialwidget-0.2/spatialwidget/inst/include/spatialwidget/colour/colour.hpp | 81 ++ spatialwidget-0.2/spatialwidget/inst/include/spatialwidget/geojson/geojson.hpp | 304 +++------- spatialwidget-0.2/spatialwidget/inst/include/spatialwidget/palette/palette.hpp | 44 - spatialwidget-0.2/spatialwidget/inst/include/spatialwidget/parameters/parameters.hpp | 7 spatialwidget-0.2/spatialwidget/inst/include/spatialwidget/spatialwidget.hpp | 65 +- spatialwidget-0.2/spatialwidget/man/widget_line.Rd | 2 spatialwidget-0.2/spatialwidget/man/widget_od.Rd | 2 spatialwidget-0.2/spatialwidget/man/widget_point.Rd | 2 spatialwidget-0.2/spatialwidget/man/widget_polygon.Rd | 2 spatialwidget-0.2/spatialwidget/src/RcppExports.cpp | 54 - spatialwidget-0.2/spatialwidget/src/geojson.cpp | 12 spatialwidget-0.2/spatialwidget/src/palette.cpp | 10 spatialwidget-0.2/spatialwidget/src/widget_line.cpp | 2 spatialwidget-0.2/spatialwidget/src/widget_point.cpp | 4 spatialwidget-0.2/spatialwidget/src/widget_polygon.cpp | 2 spatialwidget-0.2/spatialwidget/tests/testthat/test-data_construction.R | 23 spatialwidget-0.2/spatialwidget/tests/testthat/test-legends.R |only spatialwidget-0.2/spatialwidget/tests/testthat/test-palette.R | 4 spatialwidget-0.2/spatialwidget/vignettes/spatialwidget.Rmd | 28 31 files changed, 392 insertions(+), 470 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm that results in a
minimal causal combination that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.3 dated 2018-07-11 and 3.4 dated 2019-01-18
QCA-3.3/QCA/R/getNoflevels.R |only QCA-3.3/QCA/R/sop.R |only QCA-3.3/QCA/src/findSubsets.c |only QCA-3.4/QCA/DESCRIPTION | 8 QCA-3.4/QCA/MD5 | 200 +-- QCA-3.4/QCA/NAMESPACE | 19 QCA-3.4/QCA/R/Electron.R |only QCA-3.4/QCA/R/XYplot.R | 2 QCA-3.4/QCA/R/Xplot.R | 2 QCA-3.4/QCA/R/allExpressions.R | 2 QCA-3.4/QCA/R/calibrate.R | 14 QCA-3.4/QCA/R/causalChain.R | 2 QCA-3.4/QCA/R/combinations.R | 4 QCA-3.4/QCA/R/compute.R | 2 QCA-3.4/QCA/R/createMatrix.R | 4 QCA-3.4/QCA/R/dimnames.R | 8 QCA-3.4/QCA/R/export.R | 2 QCA-3.4/QCA/R/factorize.R | 4 QCA-3.4/QCA/R/findRows.R | 17 QCA-3.4/QCA/R/findSubsets.R | 4 QCA-3.4/QCA/R/findSupersets.R | 2 QCA-3.4/QCA/R/findTh.R | 2 QCA-3.4/QCA/R/findmin.R | 4 QCA-3.4/QCA/R/fuzzyand.R | 6 QCA-3.4/QCA/R/fuzzyor.R | 6 QCA-3.4/QCA/R/getInfo.R | 4 QCA-3.4/QCA/R/getLevels.R |only QCA-3.4/QCA/R/getRow.R | 4 QCA-3.4/QCA/R/getSolution.R | 25 QCA-3.4/QCA/R/intersection.R | 4 QCA-3.4/QCA/R/makeChart.R | 16 QCA-3.4/QCA/R/minimize.R | 199 +-- QCA-3.4/QCA/R/modelFit.R | 2 QCA-3.4/QCA/R/negate.R | 6 QCA-3.4/QCA/R/numeric.R | 2 QCA-3.4/QCA/R/onAttach.R | 2 QCA-3.4/QCA/R/panel.R | 2 QCA-3.4/QCA/R/pof.R | 61 QCA-3.4/QCA/R/pofind.R | 26 QCA-3.4/QCA/R/prettyString.R | 10 QCA-3.4/QCA/R/prettyTable.R | 2 QCA-3.4/QCA/R/print.R | 102 - QCA-3.4/QCA/R/recode.R | 2 QCA-3.4/QCA/R/removeRedundants.R | 4 QCA-3.4/QCA/R/retention.R | 2 QCA-3.4/QCA/R/rowDominance.R | 2 QCA-3.4/QCA/R/runGUI.R | 2 QCA-3.4/QCA/R/simplify.R |only QCA-3.4/QCA/R/solveChart.R | 10 QCA-3.4/QCA/R/sortExpressions.R |only QCA-3.4/QCA/R/sortMatrix.R | 2 QCA-3.4/QCA/R/sortVector.R | 2 QCA-3.4/QCA/R/string.R | 38 QCA-3.4/QCA/R/superSubset.R | 14 QCA-3.4/QCA/R/translate.R | 54 QCA-3.4/QCA/R/truthTable.R | 30 QCA-3.4/QCA/R/uninstall.R | 2 QCA-3.4/QCA/R/validateNames.R | 2 QCA-3.4/QCA/R/verifyQCA.R | 126 + QCA-3.4/QCA/R/writePrimeimp.R | 2 QCA-3.4/QCA/R/writeSolution.R | 2 QCA-3.4/QCA/inst/CITATION | 2 QCA-3.4/QCA/inst/ChangeLog | 37 QCA-3.4/QCA/inst/gui/server.R | 38 QCA-3.4/QCA/inst/gui/www/js/maincode.js | 14 QCA-3.4/QCA/inst/gui/www/js/utils.js | 17 QCA-3.4/QCA/inst/staticdocs/CV.html | 4 QCA-3.4/QCA/inst/staticdocs/LegacyDatasets.html | 4 QCA-3.4/QCA/inst/staticdocs/Lipset.html | 4 QCA-3.4/QCA/inst/staticdocs/QCA.package.html | 8 QCA-3.4/QCA/inst/staticdocs/RS.html | 4 QCA-3.4/QCA/inst/staticdocs/SOPexpression.html | 51 QCA-3.4/QCA/inst/staticdocs/XYplot.html | 4 QCA-3.4/QCA/inst/staticdocs/Xplot.html | 4 QCA-3.4/QCA/inst/staticdocs/calibrate.html | 4 QCA-3.4/QCA/inst/staticdocs/causalChain.html | 4 QCA-3.4/QCA/inst/staticdocs/chartFunctions.html | 4 QCA-3.4/QCA/inst/staticdocs/export.html | 4 QCA-3.4/QCA/inst/staticdocs/factorize.html | 14 QCA-3.4/QCA/inst/staticdocs/findRows.html | 30 QCA-3.4/QCA/inst/staticdocs/findTh.html | 4 QCA-3.4/QCA/inst/staticdocs/fuzzyops.html | 4 QCA-3.4/QCA/inst/staticdocs/implicantMatrixFunctions.html | 4 QCA-3.4/QCA/inst/staticdocs/index.html | 6 QCA-3.4/QCA/inst/staticdocs/intersection.html | 8 QCA-3.4/QCA/inst/staticdocs/minimize.html | 93 - QCA-3.4/QCA/inst/staticdocs/modelFit.html | 4 QCA-3.4/QCA/inst/staticdocs/negate.html | 4 QCA-3.4/QCA/inst/staticdocs/pof.html | 4 QCA-3.4/QCA/inst/staticdocs/recode.html | 4 QCA-3.4/QCA/inst/staticdocs/retention.html | 4 QCA-3.4/QCA/inst/staticdocs/runGUI.html | 4 QCA-3.4/QCA/inst/staticdocs/subsetsAndSupersets.html | 4 QCA-3.4/QCA/inst/staticdocs/truthTable.html | 4 QCA-3.4/QCA/man/QCA-internal.Rd | 16 QCA-3.4/QCA/man/QCA.package.Rd | 4 QCA-3.4/QCA/man/SOPexpression.Rd | 46 QCA-3.4/QCA/man/findRows.Rd | 26 QCA-3.4/QCA/man/intersection.Rd | 4 QCA-3.4/QCA/man/minimize.Rd | 24 QCA-3.4/QCA/man/truthTable.Rd | 11 QCA-3.4/QCA/src/Makevars |only QCA-3.4/QCA/src/QCA.c | 894 +++++++++----- QCA-3.4/QCA/src/registerDynamicSymbol.c | 5 QCA-3.4/QCA/src/truthTable.c | 4 105 files changed, 1487 insertions(+), 1026 deletions(-)
Title: Query 'HaploReg', 'RegulomeDB', 'LDlink'
Description: A set of utilities for querying
'HaploReg' <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>,
'RegulomeDB' <http://www.regulomedb.org>, and LDlink <https://analysistools.nci.nih.gov/LDlink>
web-based tools. The package connects to
'HaploReg', 'RegulomeDB' and 'LDlink', searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.
Author: Ilya Y. Zhbannikov [aut, cre],
Konstantin G. Arbeev [aut],
Anatoliy I. Yashin [aut]
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between haploR versions 2.0.6 dated 2018-08-17 and 2.0.7 dated 2019-01-18
DESCRIPTION | 10 +-- MD5 | 14 ++-- R/LDlink.R | 6 -- inst/NEWS | 4 - inst/doc/haplor-vignette.html | 103 +++++++++++++++++++++++++++++------- inst/unitTests/test_queryHaploreg.R | 15 +++-- man/haploR-makeStylishLDmatrix.Rd | 9 --- man/haploR-queryHaploreg.Rd | 9 +-- 8 files changed, 115 insertions(+), 55 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff
Algorithm)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.1.11.1 dated 2019-01-13 and 0.2.1 dated 2019-01-18
DESCRIPTION | 21 +- MD5 | 199 ++++++++++++---------- NAMESPACE | 2 NEWS.md | 28 +++ R/capt.R | 40 ++-- R/check.R | 98 ++++++++--- R/core.R | 51 ++++- R/diff.R | 96 ++++++++-- R/finalizer.R | 5 R/get.R | 2 R/guides.R | 35 ++-- R/html.R | 12 - R/hunks.R | 18 +- R/layout.R | 9 - R/misc.R | 58 +++++- R/myerssimple.R | 2 R/options.R |only R/pager.R | 210 +++++++++++++++--------- R/rdiff.R | 2 R/rds.R | 2 R/s4.R | 34 ++- R/set.R | 2 R/styles.R | 108 ++++++------ R/subset.R | 2 R/summmary.R | 57 ++++-- R/system.R | 78 -------- R/text.R | 134 +++++++-------- R/tochar.R | 56 ++++-- R/trim.R | 57 +++--- R/word.R | 2 README.md | 7 build/vignette.rds |binary inst/COPYRIGHTS | 2 inst/css/diffobj.css | 108 ++++++------ inst/doc/diffobj.R | 4 inst/doc/diffobj.Rmd | 10 - inst/doc/diffobj.html | 179 ++++++++++---------- inst/doc/embed.R | 29 +++ inst/doc/embed.Rmd | 92 ++++++++-- inst/doc/embed.html | 297 +++++++++++++++++++--------------- inst/doc/metacomp.Rmd | 7 inst/doc/metacomp.html | 147 +++++++++------- man/Pager.Rd | 135 +++++++++------ man/Rdiff_chr.Rd | 6 man/Style.Rd | 4 man/diffChr.Rd | 83 +++++++-- man/diffCsv.Rd | 83 +++++++-- man/diffDeparse.Rd | 83 +++++++-- man/diffFile.Rd | 83 +++++++-- man/diffPrint.Rd | 87 +++++++-- man/diffStr.Rd | 83 +++++++-- man/diffobj_set_def_opts.Rd | 2 man/gdo.Rd | 2 man/guides.Rd | 1 man/make_blocking.Rd | 9 - man/nchar_html.Rd | 4 man/strip_hz_control.Rd | 17 + man/summary-Diff-method.Rd | 4 man/tag_f.Rd | 3 man/trim.Rd | 1 man/webfiles.Rd | 1 src/diff.c | 13 - src/diff.h | 2 src/diffobj.c | 2 src/diffobj.h | 2 src/init.c | 2 tests/run.R | 86 +++++---- tests/testthat/helper/context/100.txt |only tests/testthat/helper/context/200.txt |only tests/testthat/helper/diffChr/100.txt |only tests/testthat/helper/diffChr/200.txt |only tests/testthat/helper/diffChr/300.txt |only tests/testthat/helper/diffChr/400.txt |only tests/testthat/helper/diffChr/800.rds |binary tests/testthat/helper/diffStr/100.txt |only tests/testthat/helper/html/100.rds |binary tests/testthat/helper/html/200.rds |binary tests/testthat/helper/html/300.rds |binary tests/testthat/helper/html/350.rds |binary tests/testthat/helper/html/400.rds |binary tests/testthat/helper/pager |only tests/testthat/helper/summary/100.txt |only tests/testthat/helper/summary/900.rds |binary tests/testthat/helper/trim/100.rds |binary tests/testthat/testthat.capture.R | 54 ++++++ tests/testthat/testthat.context.R | 23 ++ tests/testthat/testthat.diffChr.R | 19 ++ tests/testthat/testthat.diffObj.R | 9 - tests/testthat/testthat.diffStr.R | 14 + tests/testthat/testthat.guide.R | 38 ++++ tests/testthat/testthat.misc.R | 15 + tests/testthat/testthat.pager.R | 193 ++++++++++++++++++++-- tests/testthat/testthat.rrdiff.R | 5 tests/testthat/testthat.ses.R | 5 tests/testthat/testthat.style.R | 14 + tests/testthat/testthat.summary.R | 12 + tests/testthat/testthat.text.R | 57 ++++-- tests/testthat/testthat.trim.R | 27 ++- tests/valgrind |only vignettes/diffobj.Rmd | 10 - vignettes/embed.Rmd | 92 ++++++++-- vignettes/metacomp.Rmd | 7 vignettes/styles.css | 4 103 files changed, 2460 insertions(+), 1238 deletions(-)