Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut],
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
Norbert Mercier [ctb] (<https://orcid.org/0000-0002-6375-9108>),
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>),
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [ctb],
Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>),
Svenja Riedesel [ctb] (<https://orcid.org/0000-0003-2936-8776>),
Martin Autzen [ctb],
Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>),
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.9.3 dated 2019-07-31 and 0.9.4 dated 2019-09-19
Luminescence-0.9.3/Luminescence/src/src_find_first_larger_value.cpp |only Luminescence-0.9.4/Luminescence/DESCRIPTION | 18 Luminescence-0.9.4/Luminescence/MD5 | 325 ++++------ Luminescence-0.9.4/Luminescence/NEWS.md | 99 ++- Luminescence-0.9.4/Luminescence/R/Luminescence-package.R | 24 Luminescence-0.9.4/Luminescence/R/RcppExports.R | 4 Luminescence-0.9.4/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 53 - Luminescence-0.9.4/Luminescence/R/analyse_SAR.CWOSL.R | 20 Luminescence-0.9.4/Luminescence/R/analyse_pIRIRSequence.R | 9 Luminescence-0.9.4/Luminescence/R/calc_CentralDose.R | 70 +- Luminescence-0.9.4/Luminescence/R/calc_MaxDose.R | 100 +-- Luminescence-0.9.4/Luminescence/R/calc_MinDose.R | 90 ++ Luminescence-0.9.4/Luminescence/R/fit_OSLLifeTimes.R | 2 Luminescence-0.9.4/Luminescence/R/install_DevelopmentVersion.R | 58 - Luminescence-0.9.4/Luminescence/R/internals_RLum.R | 15 Luminescence-0.9.4/Luminescence/R/plot_DetPlot.R | 18 Luminescence-0.9.4/Luminescence/R/plot_GrowthCurve.R | 52 - Luminescence-0.9.4/Luminescence/R/plot_KDE.R | 8 Luminescence-0.9.4/Luminescence/R/plot_RLum.Results.R | 64 + Luminescence-0.9.4/Luminescence/README.md | 33 - Luminescence-0.9.4/Luminescence/build/partial.rdb |binary Luminescence-0.9.4/Luminescence/build/vignette.rds |binary Luminescence-0.9.4/Luminescence/data/ExampleData.DeValues.rda |binary Luminescence-0.9.4/Luminescence/data/datalist | 35 - Luminescence-0.9.4/Luminescence/inst/doc/HowTo_analyse_Al2O3.html | 160 ++-- Luminescence-0.9.4/Luminescence/inst/doc/HowTo_analyse_pIRIRMeasurements.html | 72 +- Luminescence-0.9.4/Luminescence/inst/rstudio/addins.dcf | 2 Luminescence-0.9.4/Luminescence/man/Analyse_SAR.OSLdata.Rd | 2 Luminescence-0.9.4/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd | 3 Luminescence-0.9.4/Luminescence/man/CW2pHMi.Rd | 2 Luminescence-0.9.4/Luminescence/man/CW2pLM.Rd | 2 Luminescence-0.9.4/Luminescence/man/CW2pLMi.Rd | 2 Luminescence-0.9.4/Luminescence/man/CW2pPMi.Rd | 2 Luminescence-0.9.4/Luminescence/man/ExampleData.Al2O3C.Rd | 2 Luminescence-0.9.4/Luminescence/man/ExampleData.BINfileData.Rd | 3 Luminescence-0.9.4/Luminescence/man/ExampleData.CW_OSL_Curve.Rd | 1 Luminescence-0.9.4/Luminescence/man/ExampleData.FittingLM.Rd | 2 Luminescence-0.9.4/Luminescence/man/ExampleData.LxTxData.Rd | 1 Luminescence-0.9.4/Luminescence/man/ExampleData.LxTxOSLData.Rd | 2 Luminescence-0.9.4/Luminescence/man/ExampleData.RLum.Analysis.Rd | 1 Luminescence-0.9.4/Luminescence/man/ExampleData.XSYG.Rd | 2 Luminescence-0.9.4/Luminescence/man/GitHub-API.Rd | 2 Luminescence-0.9.4/Luminescence/man/Luminescence-package.Rd | 1 Luminescence-0.9.4/Luminescence/man/PSL2Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum.Analysis-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum.Data.Curve-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/RLum.Results-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-0.9.4/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 2 Luminescence-0.9.4/Luminescence/man/Second2Gray.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_Al2O3C_ITC.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_FadingMeasurement.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_IRSAR.RF.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_SAR.CWOSL.Rd | 6 Luminescence-0.9.4/Luminescence/man/analyse_SAR.TL.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_baSAR.Rd | 2 Luminescence-0.9.4/Luminescence/man/analyse_pIRIRSequence.Rd | 11 Luminescence-0.9.4/Luminescence/man/analyse_portableOSL.Rd | 2 Luminescence-0.9.4/Luminescence/man/app_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-0.9.4/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-0.9.4/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_AverageDose.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_CentralDose.Rd | 9 Luminescence-0.9.4/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_Huntley2006.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_IEU.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_Kars2008.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_MaxDose.Rd | 4 Luminescence-0.9.4/Luminescence/man/calc_MinDose.Rd | 21 Luminescence-0.9.4/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_SourceDoseRate.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-0.9.4/Luminescence/man/calc_gSGC.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-0.9.4/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-0.9.4/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-0.9.4/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-0.9.4/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-0.9.4/Luminescence/man/fit_OSLLifeTimes.Rd | 4 Luminescence-0.9.4/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-0.9.4/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-0.9.4/Luminescence/man/get_Layout.Rd | 2 Luminescence-0.9.4/Luminescence/man/get_Quote.Rd | 2 Luminescence-0.9.4/Luminescence/man/get_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/get_Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-0.9.4/Luminescence/man/install_DevelopmentVersion.Rd | 2 Luminescence-0.9.4/Luminescence/man/length_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-0.9.4/Luminescence/man/merge_RLum.Data.Curve.Rd | 2 Luminescence-0.9.4/Luminescence/man/merge_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-0.9.4/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/names_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_AbanicoPlot.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_DRCSummary.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_DRTResults.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_DetPlot.Rd | 11 Luminescence-0.9.4/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_GrowthCurve.Rd | 4 Luminescence-0.9.4/Luminescence/man/plot_Histogram.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_KDE.Rd | 6 Luminescence-0.9.4/Luminescence/man/plot_NRt.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Analysis.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_RadialPlot.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/plot_ViolinPlot.Rd | 2 Luminescence-0.9.4/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-0.9.4/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-0.9.4/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-0.9.4/Luminescence/man/read_SPE2R.Rd | 2 Luminescence-0.9.4/Luminescence/man/read_XSYG2R.Rd | 2 Luminescence-0.9.4/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/report_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/sTeve.Rd | 2 Luminescence-0.9.4/Luminescence/man/scale_GammaDose.Rd | 2 Luminescence-0.9.4/Luminescence/man/set_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-0.9.4/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/structure_RLum.Rd | 2 Luminescence-0.9.4/Luminescence/man/template_DRAC.Rd | 2 Luminescence-0.9.4/Luminescence/man/tune_Data.Rd | 2 Luminescence-0.9.4/Luminescence/man/use_DRAC.Rd | 2 Luminescence-0.9.4/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-0.9.4/Luminescence/man/write_R2BIN.Rd | 2 Luminescence-0.9.4/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-0.9.4/Luminescence/src/RcppExports.cpp | 23 Luminescence-0.9.4/Luminescence/src/src_create_RLumDataCurve_matrix.cpp | 61 - Luminescence-0.9.4/Luminescence/tests/testthat/test_analyse_SARCWOSL.R | 8 Luminescence-0.9.4/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 4 Luminescence-0.9.4/Luminescence/tests/testthat/test_calc_CentralDose.R | 26 Luminescence-0.9.4/Luminescence/tests/testthat/test_calc_MaxDose.R | 2 Luminescence-0.9.4/Luminescence/tests/testthat/test_calc_MinDose.R | 2 Luminescence-0.9.4/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 6 Luminescence-0.9.4/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 1 Luminescence-0.9.4/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 16 Luminescence-0.9.4/Luminescence/tests/testthat/test_read_BIN2R.R | 5 164 files changed, 1008 insertions(+), 785 deletions(-)
Title: Summarize Data for Publication
Description: A variety of tools for preparing and summarizing data for publication purposes. Function verbs include 'tabulate' for creating usable tabulated data from models, 'paste' for generating human-readable statistics from a variety of summarizable data types, 'calc' for reliably calculating differences between data points, and 'test' for conducting simple statistical tests which return human-readable results.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>
Diff between utile.tools versions 0.2.0 dated 2019-07-01 and 0.2.1 dated 2019-09-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/calc.R | 12 ++++++++++-- README.md | 36 ++++++++++++++++++------------------ man/calc_duration.Rd | 5 +++++ 6 files changed, 44 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-19 0.1.7
Title: Build Tables for Publication
Description: A collection of functions to make building customized ready-to-export tables for publication purposes easier or expedite summarization of a large dataset for review. Includes methods for automatically building a table from data or building the table row-by-row. Key functions include build_row() & build_table() for summarizing columns of data overall or by stratum with appropriate testing and build_event_row() & build_event_table() for creating tables that summarize time-to-event model (Cox Parametric Hazard) parameters, supporting both univariate and multivariate methods.
Author: Eric Finnesgard [aut, cre],
Jennifer Grauberger [aut]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>
Diff between utile.tables versions 0.1.5 dated 2019-07-01 and 0.1.6 dated 2019-09-19
DESCRIPTION | 13 ++++++------- MD5 | 8 ++++---- NEWS.md | 8 +++++--- R/build_event_row.R | 9 +++++++-- README.md | 18 +++++++++--------- 5 files changed, 31 insertions(+), 25 deletions(-)
Title: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices.
The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use,
3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>
Diff between matrixTests versions 0.1.5 dated 2019-07-09 and 0.1.6 dated 2019-09-19
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++++----- NAMESPACE | 4 +++ NEWS | 8 ++++++ R/levene.R |only inst/benchmarks/row_brownforsythe.R |only inst/benchmarks/row_levene.R |only man/levene.Rd |only tests/testthat/test-col-versions.R | 8 ++++++ tests/testthat/test-correct-brownforsythe.R |only tests/testthat/test-correct-levene.R |only tests/testthat/test-parameters-main-errors.R | 26 ++++++++++++++++++++ tests/testthat/test-parameters-special-cases.R | 32 +++++++++++++++++++++++++ tests/testthat/test-result-rownames.R | 10 +++++++ 14 files changed, 105 insertions(+), 11 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.57.0 dated 2018-11-13 and 0.61.3 dated 2019-09-19
DESCRIPTION | 11 MD5 | 88 +++---- NEWS | 81 ++++++ R/RcppExports.R | 24 - R/calc_interaction_degrees.R |only R/calculate_degrees_of_freedom.R |only R/calculate_split_columns.R |only R/calculatepower.R | 6 R/convert_blockcolumn_rownames.R | 36 ++ R/convert_rownames_to_covariance.R |only R/effectpower.R | 14 - R/effectpowermc.R | 22 + R/eval_design.R | 424 +++++++++++++++++----------------- R/eval_design_custom_mc.R | 52 ++-- R/eval_design_mc.R | 267 +++++++++++++++------ R/eval_design_survival_mc.R | 50 ++-- R/extractPvalues.R | 9 R/gen_anticoef.R | 24 + R/gen_binomial_anticoef.R | 4 R/gen_design.R | 59 +++- R/is_intralayer_interaction.R |only R/parameterpower.R | 21 + R/plot_correlations.R | 10 R/plot_fds.R | 10 R/rearrange_formula_by_order.R | 18 + R/skprGUI.R | 13 - R/skprGUIbrowser.R | 3 R/skprGUIserver.R | 13 - README.md | 4 inst/shiny/skprGUI/server.R | 10 man/calc_interaction_degrees.Rd |only man/calculate_degrees_of_freedom.Rd |only man/calculate_split_columns.Rd |only man/calculatepower.Rd | 4 man/convert_blockcolumn_rownames.Rd | 4 man/convert_rownames_to_covariance.Rd |only man/effectpower.Rd | 3 man/eval_design.Rd | 61 +++- man/eval_design_mc.Rd | 3 man/gen_anticoef.Rd | 6 man/gen_design.Rd | 5 man/is_intralayer_interaction.Rd |only man/parameterpower.Rd | 9 man/plot_fds.Rd | 6 man/skprGUI.Rd | 3 man/skprGUIbrowser.Rd | 3 man/skprGUIserver.Rd | 3 src/RcppExports.cpp | 78 +++--- tests/testthat/Rplots.pdf |binary tests/testthat/testExampleCode.R | 14 - 50 files changed, 927 insertions(+), 548 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.14.0 dated 2019-05-28 and 0.15.0 dated 2019-09-19
spant-0.14.0/spant/man/plot_fit_slice.Rd |only spant-0.14.0/spant/man/plot_fit_slice_inter.Rd |only spant-0.15.0/spant/DESCRIPTION | 9 spant-0.15.0/spant/MD5 | 83 ++++---- spant-0.15.0/spant/NAMESPACE | 21 +- spant-0.15.0/spant/NEWS.md | 11 - spant-0.15.0/spant/R/basis_set.R | 12 - spant-0.15.0/spant/R/fit_display.R | 49 +++- spant-0.15.0/spant/R/fitting.R | 41 +++- spant-0.15.0/spant/R/image_reg.R | 180 +++++++++++++++++ spant-0.15.0/spant/R/interactive_plotting.R | 32 ++- spant-0.15.0/spant/R/mrs_data_display.R | 48 ++-- spant-0.15.0/spant/R/mrs_data_proc.R | 243 ++++++++++++++++-------- spant-0.15.0/spant/R/mrs_read_rda.R | 29 ++ spant-0.15.0/spant/R/pulse_sequences.R | 3 spant-0.15.0/spant/R/qm_simulation.R | 2 spant-0.15.0/spant/R/utils.R | 46 ++++ spant-0.15.0/spant/build/vignette.rds |binary spant-0.15.0/spant/inst/doc/spant-intro.html | 70 +++--- spant-0.15.0/spant/man/Ncoils.Rd |only spant-0.15.0/spant/man/Ndyns.Rd |only spant-0.15.0/spant/man/Npts.Rd |only spant-0.15.0/spant/man/Nx.Rd |only spant-0.15.0/spant/man/Ny.Rd |only spant-0.15.0/spant/man/Nz.Rd |only spant-0.15.0/spant/man/auto_phase.Rd | 5 spant-0.15.0/spant/man/calc_peak_info_vec.Rd |only spant-0.15.0/spant/man/calc_spec_snr.Rd | 2 spant-0.15.0/spant/man/collapse_to_dyns.Rd | 12 - spant-0.15.0/spant/man/comb_fits.Rd |only spant-0.15.0/spant/man/crop_xy.Rd |only spant-0.15.0/spant/man/ecc.Rd | 2 spant-0.15.0/spant/man/fit_amps.Rd | 6 spant-0.15.0/spant/man/get_2d_psf.Rd |only spant-0.15.0/spant/man/get_mrsi_voi.Rd |only spant-0.15.0/spant/man/get_mrsi_voxel.Rd |only spant-0.15.0/spant/man/get_mrsi_voxel_xy_psf.Rd |only spant-0.15.0/spant/man/get_voi_seg_psf.Rd |only spant-0.15.0/spant/man/image.mrs_data.Rd | 2 spant-0.15.0/spant/man/int_spec.Rd | 2 spant-0.15.0/spant/man/nifti_flip_lr.Rd |only spant-0.15.0/spant/man/plot.fit_result.Rd | 25 +- spant-0.15.0/spant/man/plot.mrs_data.Rd | 30 +- spant-0.15.0/spant/man/plot_slice_fit.Rd |only spant-0.15.0/spant/man/plot_slice_fit_inter.Rd |only spant-0.15.0/spant/man/plot_slice_map_inter.Rd | 9 spant-0.15.0/spant/man/plot_voi_overlay.Rd | 4 spant-0.15.0/spant/man/plot_voi_overlay_seg.Rd | 4 spant-0.15.0/spant/man/print.mrs_data.Rd | 4 spant-0.15.0/spant/man/read_tqn_result.Rd | 2 spant-0.15.0/spant/man/seq_slaser_ideal.Rd | 4 spant-0.15.0/spant/man/stackplot.fit_result.Rd | 7 52 files changed, 726 insertions(+), 273 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre] (<https://orcid.org/0000-0002-4791-442X>),
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
Rishi Kumar Tyagi [aut],
ICAR-NBGPR [cph] (www.nbpgr.ernet.in),
Maurice Aubrey [ctb] (Double Metaphone),
Kevin Atkinson [ctb] (Double Metaphone),
Lawrence Philips [ctb] (Double Metaphone)
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.3.3 dated 2018-01-13 and 0.2.3.4 dated 2019-09-19
PGRdup-0.2.3.3/PGRdup/vignettes/imgs |only PGRdup-0.2.3.4/PGRdup/DESCRIPTION | 74 +++--- PGRdup-0.2.3.4/PGRdup/MD5 | 50 ++-- PGRdup-0.2.3.4/PGRdup/NEWS.md | 8 PGRdup-0.2.3.4/PGRdup/R/DataClean.R | 2 PGRdup-0.2.3.4/PGRdup/R/DoubleMetaphone.R | 2 PGRdup-0.2.3.4/PGRdup/R/KWIC.R | 79 +++---- PGRdup-0.2.3.4/PGRdup/R/MergeKW.R | 6 PGRdup-0.2.3.4/PGRdup/R/MergeProbDup.R | 2 PGRdup-0.2.3.4/PGRdup/R/ProbDup.R | 2 PGRdup-0.2.3.4/PGRdup/R/SplitProbDup.R | 2 PGRdup-0.2.3.4/PGRdup/R/read.genesys.R | 2 PGRdup-0.2.3.4/PGRdup/README.md | 256 ++++++++++++++--------- PGRdup-0.2.3.4/PGRdup/build/vignette.rds |binary PGRdup-0.2.3.4/PGRdup/inst/CITATION | 37 +-- PGRdup-0.2.3.4/PGRdup/inst/doc/Introduction.Rmd | 145 +++++++++---- PGRdup-0.2.3.4/PGRdup/inst/doc/Introduction.pdf |binary PGRdup-0.2.3.4/PGRdup/inst/extdata/PGRdup_v2.png |only PGRdup-0.2.3.4/PGRdup/man/DataClean.Rd | 2 PGRdup-0.2.3.4/PGRdup/man/DoubleMetaphone.Rd | 2 PGRdup-0.2.3.4/PGRdup/man/KWIC.Rd | 49 ++-- PGRdup-0.2.3.4/PGRdup/man/MergeProbDup.Rd | 2 PGRdup-0.2.3.4/PGRdup/man/ProbDup.Rd | 8 PGRdup-0.2.3.4/PGRdup/man/ReviewProbDup.Rd | 4 PGRdup-0.2.3.4/PGRdup/man/SplitProbDup.Rd | 2 PGRdup-0.2.3.4/PGRdup/src/fdouble_metaphone.c | 16 + PGRdup-0.2.3.4/PGRdup/vignettes/Introduction.Rmd | 145 +++++++++---- 27 files changed, 557 insertions(+), 340 deletions(-)
Title: Simulation-Based Inference Methods for Infectious Disease Models
Description: Provides some code to run simulations of state-space models, and then
use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC)
algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle
filter based particle Markov chain Monte Carlo (PMCMC) algorithm
(Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>).
Also provides functions to plot and summarise the outputs.
Author: Trevelyan J. McKinley [aut, cre],
Stefan Widgren [aut] (Author of 'R/mparse.R'),
Pavol Bauer [cph] (R/mparse.R),
Robin Eriksson [cph] (R/mparse.R),
Stefan Engblom [cph] (R/mparse.R)
Maintainer: Trevelyan J. McKinley <t.mckinley@exeter.ac.uk>
Diff between SimBIID versions 0.1.1 dated 2019-08-24 and 0.1.2 dated 2019-09-19
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- NEWS.md | 5 ++ R/Rcpp_mparse.R | 78 +++++++++++++++++++++++++++++++----------- inst/simFunction.R | 2 - tests/testthat/mparse | 2 - tests/testthat/mparseinc | 2 - tests/testthat/mparseinctspan | 2 - tests/testthat/mparsetspan | 2 - tests/testthat/test-run.R | 17 +++++++++ 10 files changed, 99 insertions(+), 37 deletions(-)
Title: Import 'Epidata' XML Files '.epx'
Description: Import data from 'Epidata' XML files '.epx' and convert it to R data structures.
Author: Jean Pierre Decorps [aut, cre],
David Whiting [aut],
Bruno Granouillac [ctb],
Laura March [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between epxToR versions 0.3-0 dated 2017-11-07 and 0.4-0 dated 2019-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/read-epx.R | 35 +++++++++++++++++++---------------- README.md | 4 ++++ man/abstract.Rd | 3 +-- man/as.data.frame.Rd | 3 +-- man/read.epx.Rd | 3 +-- 7 files changed, 36 insertions(+), 32 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 0.29 dated 2019-08-31 and 0.30 dated 2019-09-19
DESCRIPTION | 8 +- MD5 | 27 ++++----- NEWS.md | 8 ++ R/createJJFormat.R | 2 R/makeProblem.R | 58 +++++++++----------- R/methods_class_dataObj.r | 96 +++++++++++++++++++--------------- R/methods_class_sdcProblem.r | 6 +- R/methods_multiple_classes.r | 73 +++++++++++++------------ R/sdcProb2df.R | 51 +++++++++--------- R/writeJJFormat.R | 2 inst/doc/sdcTable.html | 12 ++-- man/makeProblem.Rd | 7 +- man/sdcProb2df.Rd | 80 ++++++++++++++++++++++++---- tests/testthat/test-jjformat.r | 4 - tests/testthat/test-samplingweights.r |only 15 files changed, 261 insertions(+), 173 deletions(-)
Title: Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses
Description: Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.
Author: Gabriel Margarido [aut],
Marcelo Mollinari [aut],
Karl Broman [ctb],
Rodrigo Amadeu [ctb],
Cristiane Taniguti [ctb, cre],
Augusto Garcia [aut, ctb],
Getulio Ferreira [ctb]
Maintainer: Cristiane Taniguti <chtaniguti@usp.br>
Diff between onemap versions 2.1.1 dated 2017-10-18 and 2.1.2 dated 2019-09-19
onemap-2.1.1/onemap/data/example_out.RData |only onemap-2.1.1/onemap/inst/extdata/example_bc.raw |only onemap-2.1.1/onemap/inst/extdata/example_out.raw |only onemap-2.1.1/onemap/man/example_out.Rd |only onemap-2.1.1/onemap/src/onemap_init.c |only onemap-2.1.2/onemap/DESCRIPTION | 33 onemap-2.1.2/onemap/MD5 | 236 onemap-2.1.2/onemap/NAMESPACE | 117 onemap-2.1.2/onemap/R/add_marker.R | 4 onemap-2.1.2/onemap/R/combine_onemap.R | 2 onemap-2.1.2/onemap/R/compare.R | 21 onemap-2.1.2/onemap/R/cpp_utils.R | 22 onemap-2.1.2/onemap/R/create_dataset_bins.R | 2 onemap-2.1.2/onemap/R/draw_map.R | 7 onemap-2.1.2/onemap/R/draw_map2.R |only onemap-2.1.2/onemap/R/drop_marker.R | 4 onemap-2.1.2/onemap/R/find_bins.R | 4 onemap-2.1.2/onemap/R/get_info_2pt.R | 2 onemap-2.1.2/onemap/R/group.R | 6 onemap-2.1.2/onemap/R/group_seq.R | 15 onemap-2.1.2/onemap/R/make_seq.R | 11 onemap-2.1.2/onemap/R/map.R | 221 onemap-2.1.2/onemap/R/map_func.R | 11 onemap-2.1.2/onemap/R/marker_type.R | 6 onemap-2.1.2/onemap/R/mds_onemap.R |only onemap-2.1.2/onemap/R/onemap_read_vcfR.R |only onemap-2.1.2/onemap/R/order_seq.R | 12 onemap-2.1.2/onemap/R/plot_raw_data.R | 42 onemap-2.1.2/onemap/R/rcd.R | 6 onemap-2.1.2/onemap/R/read_mapmaker.R | 12 onemap-2.1.2/onemap/R/read_onemap.R | 4 onemap-2.1.2/onemap/R/record.R | 6 onemap-2.1.2/onemap/R/rf_2pts.R | 9 onemap-2.1.2/onemap/R/rf_graph_table.R | 584 - onemap-2.1.2/onemap/R/ripple_seq.R | 14 onemap-2.1.2/onemap/R/seriation.R | 6 onemap-2.1.2/onemap/R/suggest_lod.R | 4 onemap-2.1.2/onemap/R/test_segregation.R | 171 onemap-2.1.2/onemap/R/try_seq.R | 22 onemap-2.1.2/onemap/R/ug.R | 6 onemap-2.1.2/onemap/R/vcf2raw.R | 67 onemap-2.1.2/onemap/R/write_map.R | 2 onemap-2.1.2/onemap/build/vignette.rds |binary onemap-2.1.2/onemap/data/mapmaker_example_bc.RData |binary onemap-2.1.2/onemap/data/mapmaker_example_f2.RData |binary onemap-2.1.2/onemap/data/onemap_example_bc.RData |only onemap-2.1.2/onemap/data/onemap_example_f2.RData |binary onemap-2.1.2/onemap/data/onemap_example_out.RData |only onemap-2.1.2/onemap/data/onemap_example_riself.RData |only onemap-2.1.2/onemap/data/vcf_example_bc.RData |only onemap-2.1.2/onemap/data/vcf_example_f2.RData |binary onemap-2.1.2/onemap/data/vcf_example_out.RData |binary onemap-2.1.2/onemap/data/vcf_example_riself.RData |only onemap-2.1.2/onemap/inst/CITATION | 31 onemap-2.1.2/onemap/inst/doc/Inbred_Based_Populations.R | 83 onemap-2.1.2/onemap/inst/doc/Inbred_Based_Populations.Rmd | 235 onemap-2.1.2/onemap/inst/doc/Inbred_Based_Populations.html | 4414 +++++----- onemap-2.1.2/onemap/inst/doc/Introduction_R.html | 479 - onemap-2.1.2/onemap/inst/doc/Outcrossing_Populations.R | 231 onemap-2.1.2/onemap/inst/doc/Outcrossing_Populations.Rmd | 390 onemap-2.1.2/onemap/inst/doc/Outcrossing_Populations.html | 4191 +++++---- onemap-2.1.2/onemap/inst/doc/Overview.Rmd | 2 onemap-2.1.2/onemap/inst/doc/Overview.html | 201 onemap-2.1.2/onemap/inst/extdata/mapmaker_example_bc.raw |only onemap-2.1.2/onemap/inst/extdata/onemap_example_bc.raw |only onemap-2.1.2/onemap/inst/extdata/onemap_example_f2.raw | 1 onemap-2.1.2/onemap/inst/extdata/onemap_example_out.raw |only onemap-2.1.2/onemap/inst/extdata/onemap_example_riself.raw |only onemap-2.1.2/onemap/inst/extdata/vcf_example_bc.raw |only onemap-2.1.2/onemap/inst/extdata/vcf_example_bc.vcf |only onemap-2.1.2/onemap/inst/extdata/vcf_example_bc.vcf.gz |only onemap-2.1.2/onemap/inst/extdata/vcf_example_bc.vcf.gz.tbi |only onemap-2.1.2/onemap/inst/extdata/vcf_example_riself.raw |only onemap-2.1.2/onemap/inst/extdata/vcf_example_riself.vcf |only onemap-2.1.2/onemap/inst/extdata/vcf_example_riself.vcf.gz |only onemap-2.1.2/onemap/inst/extdata/vcf_example_riself.vcf.gz.tbi |only onemap-2.1.2/onemap/man/Bonferroni_alpha.Rd | 4 onemap-2.1.2/onemap/man/add_marker.Rd | 4 onemap-2.1.2/onemap/man/combine_onemap.Rd | 1 onemap-2.1.2/onemap/man/compare.Rd | 5 onemap-2.1.2/onemap/man/create_data_bins.Rd | 1 onemap-2.1.2/onemap/man/draw_map.Rd | 5 onemap-2.1.2/onemap/man/draw_map2.Rd |only onemap-2.1.2/onemap/man/drop_marker.Rd | 4 onemap-2.1.2/onemap/man/find_bins.Rd | 1 onemap-2.1.2/onemap/man/group.Rd | 5 onemap-2.1.2/onemap/man/group_seq.Rd | 11 onemap-2.1.2/onemap/man/make_seq.Rd | 5 onemap-2.1.2/onemap/man/map.Rd | 15 onemap-2.1.2/onemap/man/mapmaker_example_bc.Rd | 19 onemap-2.1.2/onemap/man/mapmaker_example_f2.Rd | 39 onemap-2.1.2/onemap/man/marker_type.Rd | 5 onemap-2.1.2/onemap/man/mds_onemap.Rd |only onemap-2.1.2/onemap/man/onemap-internal.Rd | 2 onemap-2.1.2/onemap/man/onemap_example_bc.Rd |only onemap-2.1.2/onemap/man/onemap_example_f2.Rd | 39 onemap-2.1.2/onemap/man/onemap_example_out.Rd |only onemap-2.1.2/onemap/man/onemap_example_riself.Rd |only onemap-2.1.2/onemap/man/onemap_read_vcfR.Rd |only onemap-2.1.2/onemap/man/order_seq.Rd | 9 onemap-2.1.2/onemap/man/plot.onemap.Rd | 15 onemap-2.1.2/onemap/man/plot.onemap_segreg_test.Rd | 12 onemap-2.1.2/onemap/man/plot_by_segreg_type.Rd | 14 onemap-2.1.2/onemap/man/print.onemap_segreg_test.Rd | 4 onemap-2.1.2/onemap/man/rcd.Rd | 5 onemap-2.1.2/onemap/man/read_mapmaker.Rd | 1 onemap-2.1.2/onemap/man/read_onemap.Rd | 1 onemap-2.1.2/onemap/man/record.Rd | 5 onemap-2.1.2/onemap/man/rf_2pts.Rd | 5 onemap-2.1.2/onemap/man/rf_graph_table.Rd | 62 onemap-2.1.2/onemap/man/ripple_seq.Rd | 5 onemap-2.1.2/onemap/man/select_segreg.Rd | 9 onemap-2.1.2/onemap/man/seriation.Rd | 5 onemap-2.1.2/onemap/man/suggest_lod.Rd | 4 onemap-2.1.2/onemap/man/test_segregation.Rd | 4 onemap-2.1.2/onemap/man/test_segregation_of_a_marker.Rd | 8 onemap-2.1.2/onemap/man/try_seq.Rd | 5 onemap-2.1.2/onemap/man/ug.Rd | 5 onemap-2.1.2/onemap/man/vcf2raw.Rd | 2 onemap-2.1.2/onemap/man/vcf_example_bc.Rd |only onemap-2.1.2/onemap/man/vcf_example_f2.Rd | 2 onemap-2.1.2/onemap/man/vcf_example_out.Rd | 2 onemap-2.1.2/onemap/man/vcf_example_riself.Rd |only onemap-2.1.2/onemap/man/write_map.Rd | 1 onemap-2.1.2/onemap/man/write_onemap_raw.Rd |only onemap-2.1.2/onemap/src/Makevars.win |only onemap-2.1.2/onemap/src/f2_est.cpp | 601 - onemap-2.1.2/onemap/src/out_est.cpp | 34 onemap-2.1.2/onemap/src/twopts_bc.cpp | 1 onemap-2.1.2/onemap/src/twopts_f2.cpp | 4 onemap-2.1.2/onemap/src/twopts_f2.h | 2 onemap-2.1.2/onemap/src/twopts_out.cpp | 4 onemap-2.1.2/onemap/src/twopts_out.h | 2 onemap-2.1.2/onemap/vignettes/Inbred_Based_Populations.Rmd | 235 onemap-2.1.2/onemap/vignettes/Outcrossing_Populations.Rmd | 390 onemap-2.1.2/onemap/vignettes/Overview.Rmd | 2 onemap-2.1.2/onemap/vignettes/test.txt |only 137 files changed, 7545 insertions(+), 6029 deletions(-)
Title: Boltzmann Entropy of a Landscape Gradient
Description: Calculates the Boltzmann entropy of a landscape gradient.
This package uses the analytical method created by Gao, P., Zhang, H.
and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019
(<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by
allowing calculations on data with missing values.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between belg versions 0.2.3 dated 2018-06-17 and 1.0.0 dated 2019-09-19
DESCRIPTION | 17 +++--- MD5 | 51 ++++++++++++-------- NEWS.md | 5 ++ R/RcppExports.R | 4 + R/datasets.R | 16 +++++- R/get_boltzmann.R | 44 +++++++++++++---- README.md | 64 ++++++++++++++++--------- build/vignette.rds |binary data/complex_land.rda |binary data/land_gradient1.rda |only data/land_gradient2.rda |only data/simple_land.rda |binary inst/CITATION |only inst/doc/belg1.R | 11 +++- inst/doc/belg1.Rmd | 11 +++- inst/doc/belg1.html | 77 ++++++++++++++++++++----------- man/belg-package.Rd | 11 ++-- man/complex_land.Rd | 6 +- man/figures/README-unnamed-chunk-1-1.png |binary man/get_boltzmann.Rd | 38 ++++++++++----- man/land_gradient1.Rd |only man/land_gradient2.Rd |only man/simple_land.Rd | 6 +- src/RcppExports.cpp | 14 +++++ src/get_boltzmann.cpp | 52 -------------------- src/get_boltzmann_aggregation.cpp |only src/utils.cpp |only src/utils.h |only tests/testthat/test-aggregation.R |only tests/testthat/test-raster.R | 6 +- vignettes/belg1.Rmd | 11 +++- 31 files changed, 272 insertions(+), 172 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.0 dated 2019-01-07 and 0.3.2 dated 2019-09-19
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/afcon.R | 2 +- R/boston.R | 28 ++++++++++++++++------------ R/cycle_hire.R | 2 +- R/getisord.R | 12 ++++++------ R/nz.R | 4 ++-- R/used.cars.R | 27 +++++++++++++++------------ data/datalist | 2 +- data/getisord.rda |binary data/world.rda |binary inst/shapes/world.dbf |binary inst/shapes/world.gpkg |binary man/afcon.Rd | 2 +- man/boston.Rd | 28 ++++++++++++++++------------ man/cycle_hire.Rd | 2 +- man/getisord.Rd | 16 ++++++++-------- man/nz.Rd | 4 ++-- man/used.cars.Rd | 27 +++++++++++++++------------ 19 files changed, 108 insertions(+), 94 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces two main verbs. describe() to describe a variable or table, explore() to graphically explore a variable or table.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 0.4.4 dated 2019-08-27 and 0.5.0 dated 2019-09-19
DESCRIPTION | 6 MD5 | 51 ++- NAMESPACE | 2 NEWS.md |only R/explore.R | 356 +++++++++++++++++--------- README.md | 79 ++++- inst/doc/explore.R | 33 +- inst/doc/explore.Rmd | 61 +++- inst/doc/explore.html | 60 +++- inst/doc/explore_mtcars.R | 13 inst/doc/explore_mtcars.Rmd | 39 +- inst/doc/explore_mtcars.html | 86 ++++-- inst/extdata/template_report_target_pct.Rmd | 10 inst/extdata/template_report_target_split.Rmd | 10 inst/extdata/template_report_variable.Rmd | 10 man/explain_tree.Rd | 6 man/explore_cor.Rd | 4 man/explore_density.Rd | 7 man/figures |only man/format_num_auto.Rd |only man/format_num_kMB.Rd | 2 man/format_num_space.Rd | 2 man/get_nrow.Rd | 4 man/total_fig_height.Rd |only vignettes/explore.Rmd | 61 +++- vignettes/explore_mtcars.Rmd | 39 +- 26 files changed, 600 insertions(+), 341 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.18 dated 2019-07-04 and 3.19 dated 2019-09-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/dependCox.reg.R | 16 +++++++++++++++- man/compound.Cox-package.Rd | 4 ++-- man/dependCox.reg.Rd | 3 ++- 5 files changed, 27 insertions(+), 12 deletions(-)
Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, and Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059> methods for the detection of anomalies in time series data.
Author: Alex Fisch [aut],
Daniel Grose [aut, cre],
Lawrence Bardwell [ctb],
Idris Eckley [ths],
Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 2.0.1 dated 2019-09-11 and 2.0.2 dated 2019-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary src/pass.cpp | 7 ++++--- src/populate.cpp | 17 ++++++++++++++--- src/populate_mean.cpp | 13 ++++++++++++- src/sequential_quantiles.cpp | 2 +- 7 files changed, 41 insertions(+), 18 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>) and generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [ctb]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 1.2.0 dated 2019-07-26 and 1.2.2 dated 2019-09-19
DESCRIPTION | 12 ++-- MD5 | 42 +++++++-------- NAMESPACE | 2 NEWS.md | 49 +++++++++++++++++ R/cNORM.R | 15 ++--- R/modelling.R | 131 ++++++++++++++++++++--------------------------- R/plot.R | 60 ++++++++++++++++----- R/preparation.R | 86 +++++++++++++++--------------- README.md | 26 +++++++-- inst/CITATION |only inst/doc/cNORM-Demo.Rmd | 17 ++++-- inst/doc/cNORM-Demo.html | 25 +++++--- inst/shiny/server.R | 6 +- inst/shiny/ui.R | 5 + man/bestModel.Rd | 4 + man/cNORM.Rd | 15 ++--- man/cnorm.cv.Rd | 4 - man/computePowers.Rd | 4 + man/plotPercentiles.Rd | 2 man/plotSubset.Rd | 4 + man/prepareData.Rd | 4 + vignettes/cNORM-Demo.Rmd | 17 ++++-- vignettes/plos.png |only 23 files changed, 324 insertions(+), 206 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses (resource and step-selection functions), and simulation of space-use from fitted step-selection functions.
Author: Johannes Signer [aut, cre],
Bjoern Reineking [ctb],
Ulrike Schlaegel [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.0.6 dated 2019-03-19 and 0.0.7 dated 2019-09-19
DESCRIPTION | 11 - MD5 | 64 ++++---- NAMESPACE | 14 + NEWS.md | 15 + R/amt.R | 21 -- R/as_track.R | 10 + R/coercion.R | 1 R/crs.R | 3 R/eda_sampling_rate.R | 15 + R/fit_clogit.R | 5 R/fit_distr.R | 4 R/hr_documentation.R | 21 +- R/hr_isopleths.R | 12 - R/hr_kde.R | 139 +++++++++++++++++ R/hr_locoh.R | 55 ++++++ R/hr_mcp.R | 33 +--- R/random_points.R | 14 + R/random_steps.R | 6 R/steps.R | 9 + R/track.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/p1_getting_started.R | 22 +- inst/doc/p1_getting_started.Rmd | 22 +- inst/doc/p1_getting_started.html | 210 ++++++++++++++++---------- inst/doc/p4_SSF.html | 312 ++++++++++++++++++++------------------- man/as_track.Rd | 3 man/fit_sl_dist.Rd | 2 man/fit_ta_dist.Rd | 2 man/hr.Rd | 62 +++++-- man/random_points.Rd | 3 man/summarize_sampling_rate.Rd | 9 + vignettes/p1_getting_started.Rmd | 22 +- 33 files changed, 731 insertions(+), 396 deletions(-)
Title: Parametric Ordinary Differential Equations Model of Growth,
Death, and Respiration of Macroinvertebrate and Algae Taxa
Description: Numerically solve and plot solutions of a parametric ordinary
differential equations model of growth, death, and respiration of
macroinvertebrate and algae taxa dependent on pre-defined environmental
factors. The model (version 1.0) is introduced in Schuwirth, N. and
Reichert, P., (2013) <DOI:10.1890/12-0591.1>. This package includes
model extensions and the core functions introduced and used in
Schuwirth, N. et al. (2016) <DOI:10.1111/1365-2435.12605>,
Kattwinkel, M. et al. (2016) <DOI:10.1021/acs.est.5b04068>,
Mondy, C. P., and Schuwirth, N. (2017) <DOI:10.1002/eap.1530>,
and Paillex, A. et al. (2017) <DOI:10.1111/fwb.12927>.
Author: Nele Schuwirth, Peter Reichert, Mikolaj Rybinski
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between streambugs versions 1.0 dated 2017-11-29 and 1.1 dated 2019-09-19
streambugs-1.0/streambugs/R/streambugs-package.R |only streambugs-1.0/streambugs/R/streambugs_examples.R |only streambugs-1.0/streambugs/inst/doc |only streambugs-1.0/streambugs/tests/testthat/test_streambugs.R |only streambugs-1.1/streambugs/DESCRIPTION | 16 - streambugs-1.1/streambugs/MD5 | 42 +- streambugs-1.1/streambugs/NAMESPACE | 12 streambugs-1.1/streambugs/R/streambugs-package.r |only streambugs-1.1/streambugs/R/streambugs.r | 7 streambugs-1.1/streambugs/R/streambugs_aux.r | 150 ++-------- streambugs-1.1/streambugs/R/streambugs_examples.r |only streambugs-1.1/streambugs/R/streambugs_plot.r |only streambugs-1.1/streambugs/README.md | 7 streambugs-1.1/streambugs/inst/docs |only streambugs-1.1/streambugs/inst/extdata |only streambugs-1.1/streambugs/man/count.feeding.links.Rd |only streambugs-1.1/streambugs/man/foodweb.plot.Rd |only streambugs-1.1/streambugs/man/plot.streambugs.Rd | 8 streambugs-1.1/streambugs/man/run.streambugs.Rd | 12 streambugs-1.1/streambugs/man/streambugs-package.Rd | 2 streambugs-1.1/streambugs/man/streambugs.example.model.extended.Rd |only streambugs-1.1/streambugs/man/streambugs.example.model.toy.Rd | 12 streambugs-1.1/streambugs/tests/benchmarks |only streambugs-1.1/streambugs/tests/testthat/extended_example_foodweb.pdf |only streambugs-1.1/streambugs/tests/testthat/extended_example_res.pdf |only streambugs-1.1/streambugs/tests/testthat/extended_example_res_C.csv |only streambugs-1.1/streambugs/tests/testthat/extended_example_sysdef.dat |only streambugs-1.1/streambugs/tests/testthat/helper_test_example.R |only streambugs-1.1/streambugs/tests/testthat/minimum_example_foodweb-points.pdf |only streambugs-1.1/streambugs/tests/testthat/minimum_example_foodweb-texts.pdf |only streambugs-1.1/streambugs/tests/testthat/run_extended_example.R |only streambugs-1.1/streambugs/tests/testthat/test_extended_example.R |only streambugs-1.1/streambugs/tests/testthat/test_minimum_example.R |only 33 files changed, 124 insertions(+), 144 deletions(-)
Title: Open Trade Statistics API Wrapper and Utility Program
Description: Access 'Open Trade Statistics' API from R to download international trade data.
Author: Mauricio Vargas [aut, cre, cph]
(<https://orcid.org/0000-0003-1017-7574>),
Joshua Kunst [ctb] (contributed to different parts of the pre-release
code),
Emily Riederer [rev] (reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/274),
Mark Padgham [rev] (reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/274),
Amanda Dobbyn [rev] (reviewed an archived package that evolved into the
current package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/217),
Jorge Cimentada [rev] (reviewed an archived package that evolved into
the current package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/217),
UN Comtrade [dtc],
The World Bank [dtc],
Center for International Development at Harvard University [dtc],
The Observatory of Economic Complexity [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between tradestatistics versions 0.2.4 dated 2019-09-17 and 0.2.5 dated 2019-09-19
DESCRIPTION | 6 MD5 | 78 - NAMESPACE | 66 - NEWS.md | 76 - R/ots_country_code.R | 172 +- R/ots_create_tidy_data.R | 826 ++++++------- R/ots_inflation_adjustment.R | 196 +-- R/ots_product_code.R | 216 +-- R/ots_read_from_api.R | 236 +-- R/tradestatistics-package.R | 4 build/vignette.rds |binary data/ots_inflation.rda |binary inst/doc/basic-usage.R | 168 +- inst/doc/basic-usage.Rmd | 411 +++--- inst/doc/basic-usage.html | 1544 ++++++++++++-------------- inst/doc/creating-datasets.R | 195 +-- inst/doc/creating-datasets.Rmd | 257 ++-- inst/doc/creating-datasets.html | 853 +++++++------- inst/references.bib | 194 +-- man/ots_communities.Rd | 44 man/ots_countries.Rd | 54 man/ots_country_code.Rd | 56 man/ots_create_tidy_data.Rd | 144 +- man/ots_inflation.Rd | 50 man/ots_inflation_adjustment.Rd | 62 - man/ots_product_code.Rd | 62 - man/ots_product_shortnames.Rd | 40 man/ots_products.Rd | 50 man/ots_read_from_api.Rd | 110 - man/ots_tables.Rd | 44 man/tradestatistics-package.Rd | 72 - tests/fixtures/vcr_cassettes/chl_arg_1962.yml | 920 ++++++++------- tests/testthat.R | 8 tests/testthat/helper-tradestatistics.R | 4 tests/testthat/test-ots_country_code.R | 64 - tests/testthat/test-ots_create_tidy_data.R | 133 +- tests/testthat/test-ots_product_code.R | 124 +- vignettes/basic-usage.Rmd | 411 +++--- vignettes/creating-datasets.Rmd | 257 ++-- vignettes/creating-datasets.md | 194 +-- 40 files changed, 4249 insertions(+), 4152 deletions(-)
More information about tradestatistics at CRAN
Permanent link
Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data,
with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 1.0.1 dated 2019-07-15 and 1.1 dated 2019-09-19
DESCRIPTION | 6 - MD5 | 30 +++++-- NAMESPACE | 4 + NEWS | 1 R/cepp.sim.R |only R/cepp.test.R |only R/cepp.weights.R |only R/dweights.R | 3 R/flex.zones.R | 13 --- R/nnpop.R | 114 ++++++++++++++---------------- R/preamble.R | 13 +-- R/rflex.zones.R | 2 man/arg_check_cepp_test.Rd |only man/cepp.sim.Rd |only man/cepp.test.Rd |only man/cepp.weights.Rd |only man/scan.nn.Rd | 10 +- tests/testthat/test-cepp.test.R |only tests/testthat/test-rflex.test-binomial.R | 92 ++++++++++++------------ tests/testthat/test-rflex.test-poisson.R | 90 +++++++++++------------ 20 files changed, 187 insertions(+), 191 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://www.laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] (Enable the support of .lax file and
extra byte attributes),
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R),
Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.3.3 dated 2019-08-30 and 1.3.4 dated 2019-09-19
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS.md | 5 ++ R/RcppExports.R | 4 - R/deprecated.r | 2 R/header_tools.r | 4 - R/las_specifications.r | 2 src/LASlib/lasfilter.cpp | 4 - src/LASlib/lasreader_ply.cpp | 8 +-- src/LASlib/lasreader_txt.cpp | 8 +-- src/LASzip/laswriteitemcompressed_v3.cpp | 68 +++++++++++++++---------------- src/LASzip/laswriteitemcompressed_v4.cpp | 68 +++++++++++++++---------------- src/RcppExports.cpp | 13 ----- src/fast.cpp | 14 ------ 14 files changed, 102 insertions(+), 132 deletions(-)
Title: Global Sensitivity Analysis in Physiologically Based Kinetic
Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters.
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>),
Brad Reisfeld [aut],
Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>
Diff between pksensi versions 1.1.3 dated 2019-08-20 and 1.1.4 dated 2019-09-19
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------------ NEWS.md | 5 ++++ R/check.R | 39 ++++++++++++++++++------------------ R/compile.R | 36 ++++++++++++--------------------- R/data.R | 16 +++++++------- R/install.R | 30 ++++++++++++++------------- R/models.R | 19 +++++++++-------- R/package.R | 16 ++++++++------ R/pksim.R | 10 ++++----- R/rfast99.R | 20 ++++++++++-------- R/solve_fun.R | 23 +++++++++------------ R/solve_mcsim.R | 18 ++++++++-------- R/tell2.R | 2 - inst/doc/pbpk_apap.html | 4 +-- inst/doc/pbtk1cpt.html | 4 +-- man/APAP.Rd | 16 +++++++------- man/about-pksensi.Rd | 15 +++++++------ man/check.Rd | 33 +++++++++++++++--------------- man/compile_model.Rd | 27 ++++++++++++------------ man/mcsim.Rd | 30 ++++++++++++++------------- man/models.Rd | 19 +++++++++-------- man/pksim.Rd | 10 ++++----- man/rfast99.Rd | 20 ++++++++++-------- man/solve_fun.Rd | 22 +++++++++----------- man/solve_mcsim.Rd | 18 ++++++++-------- man/tell2.Rd | 2 - 27 files changed, 261 insertions(+), 255 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.4 dated 2019-07-07 and 5.5.5 dated 2019-09-19
DESCRIPTION | 8 MD5 | 47 +- R/CENTROIDS-dba.R | 3 R/CLUSTERING-tadpole.R | 3 R/DISTANCES-dtw-basic.R | 25 - R/DISTANCES-dtw-lb.R | 3 inst/CITATION |only inst/NEWS.Rd | 37 - inst/doc/dtwclust.Rnw | 9 inst/doc/dtwclust.pdf |binary inst/doc/parallelization-considerations.html | 6 inst/doc/timing-experiments.html | 44 +- inst/include/dtwclust.h | 6 man/dtw_basic.Rd | 13 src/centroids/dba.cpp | 4 src/distances/R-gateways.cpp | 7 src/distances/R-gateways.h | 2 src/distances/calculators.cpp | 3 src/distances/calculators.h | 1 src/distances/details.h | 5 src/distances/dtw-basic.cpp | 6 src/init.cpp | 2 tests/testthat/unit/distances.R | 567 +++++++++++++-------------- vignettes/REFERENCES.bib | 8 vignettes/dtwclust.Rnw | 9 25 files changed, 441 insertions(+), 377 deletions(-)
Title: Computes and Plots Consonance (Confidence) Intervals, P-Values,
and S-Values to Form Consonance and Surprisal Functions
Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019) <arXiv:1909.08579>, and Greenland S, Chow ZR. (2019) <arXiv:1909.08583>.
Author: Zad R. Chow [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew D. Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>)
Maintainer: Zad R. Chow <zad@lesslikely.com>
Diff between concurve versions 2.0 dated 2019-07-10 and 2.1.0 dated 2019-09-19
DESCRIPTION | 10 +-- MD5 | 40 ++++++------- NEWS.md | 13 ++++ R/curve_rev.R | 4 - R/ggconcurve.R | 61 ++++++++++----------- R/plot_concurve.R | 113 +++++++++++++++++++++++++++------------ README.md | 10 ++- inst/doc/examples.Rmd | 4 - inst/doc/examples.html | 24 ++++---- inst/doc/stata.html | 6 +- man/curve_rev.Rd | 9 ++- man/ggconcurve.Rd | 30 +++------- man/plot_concurve.Rd | 20 +++++- vignettes/examples.Rmd | 4 - vignettes/figures/function1.png |binary vignettes/figures/function2.png |binary vignettes/figures/function3.png |binary vignettes/figures/function4.png |binary vignettes/figures/function5.png |binary vignettes/figures/function6.png |binary vignettes/figures/likelihood.png |binary 21 files changed, 218 insertions(+), 130 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] (<https://orcid.org/0000-0003-1676-0197>),
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.1.0 dated 2019-05-27 and 4.2.0 dated 2019-09-19
DESCRIPTION | 20 MD5 | 57 +- NAMESPACE | 4 NEWS.md | 12 R/compare.i.R | 4 R/compareGroups.R | 31 - R/compareGroups.fit.R | 7 R/descrTable.R | 2 R/descripSurv.R | 7 R/export2md.R | 41 + R/export2mdcbind.R | 6 R/export2mdword.R | 236 ++++++++-- R/export2mdwordcbind.R |only R/export2word.R | 15 R/norm.plot.R | 5 R/report.R | 6 build/vignette.rds |binary inst/app/global.R | 3 inst/app/server.R | 778 +++++++++++++++++------------------ inst/app/ui.R | 15 inst/doc/compareGroups_vignette.Rmd | 2 inst/doc/compareGroups_vignette.html | 181 ++++---- man/cGroupsGUI.Rd | 2 man/cGroupsWUI.Rd | 2 man/compareGroups-internal.Rd | 13 man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 4 man/descrTable.Rd | 4 man/report.Rd | 4 vignettes/compareGroups_vignette.Rmd | 2 30 files changed, 831 insertions(+), 636 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-27 0.0.2
2017-09-28 0.0.1
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("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 2.10.0 dated 2019-04-25 and 3.0.0 dated 2019-09-19
umx-2.10.0/umx/R/deprecated_old_twin_versions.R |only umx-2.10.0/umx/R/umxACEnew.R |only umx-2.10.0/umx/man/umxACEold.Rd |only umx-2.10.0/umx/man/umxCPold.Rd |only umx-2.10.0/umx/man/umxCovData.Rd |only umx-2.10.0/umx/man/umxDescribeDataWLS.Rd |only umx-2.10.0/umx/man/umxEval.Rd |only umx-2.10.0/umx/man/umxIPold.Rd |only umx-2.10.0/umx/man/umxLatent.Rd |only umx-2.10.0/umx/man/umxPadAndPruneForDefVars.Rd |only umx-2.10.0/umx/man/umxPlotCPold.Rd |only umx-2.10.0/umx/man/umxRAM2.Rd |only umx-2.10.0/umx/man/umxTwoStage.Rd |only umx-2.10.0/umx/man/umx_cell_is_on.Rd |only umx-2.10.0/umx/man/umx_cov2raw.Rd |only umx-2.10.0/umx/man/umx_default_option.Rd |only umx-2.10.0/umx/man/umx_dot_define_shapes.Rd |only umx-2.10.0/umx/man/umx_dot_mat2dot.Rd |only umx-2.10.0/umx/man/umx_dot_rank.Rd |only umx-2.10.0/umx/man/umx_drop_ok.Rd |only umx-2.10.0/umx/man/umx_make_bin_cont_pair_data.Rd |only umx-2.10.0/umx/man/umx_merge_CIs.Rd |only umx-2.10.0/umx/man/umx_parameters.Rd |only umx-2.10.0/umx/man/umx_set_optimization_options.Rd |only umx-2.10.0/umx/man/umx_show_fit_or_comparison.Rd |only umx-2.10.0/umx/man/umx_standardize_ACE.Rd |only umx-2.10.0/umx/man/umx_standardize_ACEcov.Rd |only umx-2.10.0/umx/man/umx_standardize_ACEv.Rd |only umx-2.10.0/umx/man/umx_standardize_CP.Rd |only umx-2.10.0/umx/man/umx_standardize_IP.Rd |only umx-2.10.0/umx/man/umx_standardize_RAM.Rd |only umx-2.10.0/umx/man/umx_standardize_SexLim.Rd |only umx-2.10.0/umx/man/umx_standardize_Simplex.Rd |only umx-2.10.0/umx/man/umx_stash_CIs.Rd |only umx-2.10.0/umx/man/umx_swap_a_block.Rd |only umx-2.10.0/umx/man/xmu_model_needs_means.Rd |only umx-2.10.0/umx/tests/testthat/test_umx_default_option.r |only umx-3.0.0/umx/DESCRIPTION | 10 umx-3.0.0/umx/MD5 | 559 ++-- umx-3.0.0/umx/NAMESPACE | 80 umx-3.0.0/umx/NEWS.md | 208 + umx-3.0.0/umx/R/TRHG_code.R | 16 umx-3.0.0/umx/R/build_run_modify.R | 1667 +++++++----- umx-3.0.0/umx/R/datasets.R | 47 umx-3.0.0/umx/R/deprecated.R | 65 umx-3.0.0/umx/R/fit_and_reporting.R | 1548 ++++++----- umx-3.0.0/umx/R/lavanify2ram.R | 340 +- umx-3.0.0/umx/R/misc_and_utility.R | 2100 +++++++++------- umx-3.0.0/umx/R/tmx.R | 9 umx-3.0.0/umx/R/umxIPnew.R | 29 umx-3.0.0/umx/R/umxPower.R |only umx-3.0.0/umx/R/umx_build_high_level_models.R | 175 - umx-3.0.0/umx/R/umx_build_umxACEcov_fixed.R | 17 umx-3.0.0/umx/R/umx_build_umxACEv.R | 119 umx-3.0.0/umx/R/umx_build_umxGxEbiv.R | 88 umx-3.0.0/umx/R/umx_build_umxSexLim.R | 143 - umx-3.0.0/umx/R/umx_build_umxSimplex.R | 75 umx-3.0.0/umx/R/umx_fit_stash_CIs.R | 24 umx-3.0.0/umx/R/umx_fit_umxFitIndices.R | 19 umx-3.0.0/umx/R/umx_nice_data.R |only umx-3.0.0/umx/R/xmu.R | 390 ++ umx-3.0.0/umx/R/xmu_make_top_twin_models.R | 50 umx-3.0.0/umx/README.md | 32 umx-3.0.0/umx/inst/WORDLIST | 48 umx-3.0.0/umx/man/FishersMethod.Rd |only umx-3.0.0/umx/man/RMSEA.MxModel.Rd | 45 umx-3.0.0/umx/man/RMSEA.Rd | 32 umx-3.0.0/umx/man/RMSEA.summary.mxmodel.Rd | 44 umx-3.0.0/umx/man/SE_from_p.Rd |only umx-3.0.0/umx/man/deg2rad.Rd |only umx-3.0.0/umx/man/dl_from_dropbox.Rd | 10 umx-3.0.0/umx/man/extractAIC.MxModel.Rd | 45 umx-3.0.0/umx/man/figures/TSLS.pdf |only umx-3.0.0/umx/man/figures/TSLS.png |only umx-3.0.0/umx/man/figures/power.pdf |only umx-3.0.0/umx/man/figures/power.png |only umx-3.0.0/umx/man/figures/umx_help_figures.graffle |binary umx-3.0.0/umx/man/install.OpenMx.Rd | 52 umx-3.0.0/umx/man/loadings.MxModel.Rd | 37 umx-3.0.0/umx/man/loadings.Rd | 36 umx-3.0.0/umx/man/oddsratio.Rd |only umx-3.0.0/umx/man/plot.MxLISRELModel.Rd | 60 umx-3.0.0/umx/man/plot.MxModel.Rd | 65 umx-3.0.0/umx/man/power.ACE.test.Rd |only umx-3.0.0/umx/man/print.oddsratio.Rd |only umx-3.0.0/umx/man/print.reliability.Rd |only umx-3.0.0/umx/man/qm.Rd | 23 umx-3.0.0/umx/man/rad2deg.Rd |only umx-3.0.0/umx/man/reliability.Rd | 20 umx-3.0.0/umx/man/residuals.MxModel.Rd | 43 umx-3.0.0/umx/man/tmx_genotypic_effect.Rd | 4 umx-3.0.0/umx/man/tmx_is.identified.Rd | 38 umx-3.0.0/umx/man/tmx_show.Rd | 46 umx-3.0.0/umx/man/umx-deprecated.Rd | 66 umx-3.0.0/umx/man/umx.Rd | 407 +-- umx-3.0.0/umx/man/umxACE.Rd | 88 umx-3.0.0/umx/man/umxACE_cov_fixed.Rd | 44 umx-3.0.0/umx/man/umxACEcov.Rd | 41 umx-3.0.0/umx/man/umxACEv.Rd | 97 umx-3.0.0/umx/man/umxAPA.Rd | 88 umx-3.0.0/umx/man/umxAdd1.Rd | 16 umx-3.0.0/umx/man/umxAlgebra.Rd | 18 umx-3.0.0/umx/man/umxBrownie.Rd | 25 umx-3.0.0/umx/man/umxCI.Rd | 58 umx-3.0.0/umx/man/umxCI_boot.Rd | 47 umx-3.0.0/umx/man/umxCP.Rd | 61 umx-3.0.0/umx/man/umxCompare.Rd | 73 umx-3.0.0/umx/man/umxConfint.Rd | 61 umx-3.0.0/umx/man/umxCov2cor.Rd | 22 umx-3.0.0/umx/man/umxDiagnose.Rd | 31 umx-3.0.0/umx/man/umxDrop1.Rd | 20 umx-3.0.0/umx/man/umxEFA.Rd | 75 umx-3.0.0/umx/man/umxEquate.Rd | 41 umx-3.0.0/umx/man/umxExamples.Rd | 16 umx-3.0.0/umx/man/umxExpCov.Rd | 53 umx-3.0.0/umx/man/umxExpMeans.Rd | 46 umx-3.0.0/umx/man/umxFactor.Rd | 49 umx-3.0.0/umx/man/umxFactorScores.Rd | 38 umx-3.0.0/umx/man/umxFitIndices.Rd | 52 umx-3.0.0/umx/man/umxFixAll.Rd | 28 umx-3.0.0/umx/man/umxGetParameters.Rd | 49 umx-3.0.0/umx/man/umxGxE.Rd | 72 umx-3.0.0/umx/man/umxGxE_window.Rd | 24 umx-3.0.0/umx/man/umxGxEbiv.Rd | 55 umx-3.0.0/umx/man/umxHetCor.Rd | 64 umx-3.0.0/umx/man/umxIP.Rd | 57 umx-3.0.0/umx/man/umxJiggle.Rd | 26 umx-3.0.0/umx/man/umxLabel.Rd | 39 umx-3.0.0/umx/man/umxLav2RAM.Rd | 127 umx-3.0.0/umx/man/umxMI.Rd | 41 umx-3.0.0/umx/man/umxMatrix.Rd | 22 umx-3.0.0/umx/man/umxMendelianRandomization.Rd |only umx-3.0.0/umx/man/umxModel.Rd | 87 umx-3.0.0/umx/man/umxModify.Rd | 58 umx-3.0.0/umx/man/umxParameters.Rd |only umx-3.0.0/umx/man/umxPath.Rd | 70 umx-3.0.0/umx/man/umxPlotACE.Rd | 39 umx-3.0.0/umx/man/umxPlotACEcov.Rd | 32 umx-3.0.0/umx/man/umxPlotACEv.Rd | 53 umx-3.0.0/umx/man/umxPlotCP.Rd | 67 umx-3.0.0/umx/man/umxPlotGxE.Rd | 41 umx-3.0.0/umx/man/umxPlotGxEbiv.Rd | 30 umx-3.0.0/umx/man/umxPlotIP.Rd | 33 umx-3.0.0/umx/man/umxPlotSexLim.Rd | 37 umx-3.0.0/umx/man/umxPlotSimplex.Rd | 29 umx-3.0.0/umx/man/umxPower.Rd |only umx-3.0.0/umx/man/umxRAM.Rd | 106 umx-3.0.0/umx/man/umxRAM2Ordinal.Rd | 24 umx-3.0.0/umx/man/umxReduce.Rd | 67 umx-3.0.0/umx/man/umxReduceACE.Rd | 22 umx-3.0.0/umx/man/umxReduceGxE.Rd | 33 umx-3.0.0/umx/man/umxRotate.MxModelCP.Rd |only umx-3.0.0/umx/man/umxRotate.Rd |only umx-3.0.0/umx/man/umxRun.Rd | 29 umx-3.0.0/umx/man/umxSetParameters.Rd | 59 umx-3.0.0/umx/man/umxSexLim.Rd | 61 umx-3.0.0/umx/man/umxSimplex.Rd | 31 umx-3.0.0/umx/man/umxSummarizeTwinData.Rd | 32 umx-3.0.0/umx/man/umxSummary.MxModel.Rd | 78 umx-3.0.0/umx/man/umxSummary.Rd | 34 umx-3.0.0/umx/man/umxSummaryACE.Rd | 86 umx-3.0.0/umx/man/umxSummaryACEcov.Rd | 66 umx-3.0.0/umx/man/umxSummaryACEv.Rd | 70 umx-3.0.0/umx/man/umxSummaryCP.Rd | 50 umx-3.0.0/umx/man/umxSummaryGxE.Rd | 65 umx-3.0.0/umx/man/umxSummaryGxEbiv.Rd | 64 umx-3.0.0/umx/man/umxSummaryIP.Rd | 49 umx-3.0.0/umx/man/umxSummarySexLim.Rd | 72 umx-3.0.0/umx/man/umxSummarySimplex.Rd | 66 umx-3.0.0/umx/man/umxSuperModel.Rd | 49 umx-3.0.0/umx/man/umxThresholdMatrix.Rd | 16 umx-3.0.0/umx/man/umxUnexplainedCausalNexus.Rd | 18 umx-3.0.0/umx/man/umxValues.Rd | 48 umx-3.0.0/umx/man/umxVersion.Rd | 35 umx-3.0.0/umx/man/umxWeightedAIC.Rd | 36 umx-3.0.0/umx/man/umx_APA_pval.Rd | 34 umx-3.0.0/umx/man/umx_aggregate.Rd | 42 umx-3.0.0/umx/man/umx_apply.Rd | 30 umx-3.0.0/umx/man/umx_array_shift.Rd | 27 umx-3.0.0/umx/man/umx_as_numeric.Rd | 46 umx-3.0.0/umx/man/umx_check.Rd | 30 umx-3.0.0/umx/man/umx_check_OS.Rd | 34 umx-3.0.0/umx/man/umx_check_model.Rd | 43 umx-3.0.0/umx/man/umx_check_names.Rd | 35 umx-3.0.0/umx/man/umx_check_parallel.Rd | 42 umx-3.0.0/umx/man/umx_cont_2_quantiles.Rd | 35 umx-3.0.0/umx/man/umx_cor.Rd | 33 umx-3.0.0/umx/man/umx_explode.Rd | 24 umx-3.0.0/umx/man/umx_explode_twin_names.Rd | 12 umx-3.0.0/umx/man/umx_find_object.Rd | 23 umx-3.0.0/umx/man/umx_fix_first_loadings.Rd | 22 umx-3.0.0/umx/man/umx_fix_latents.Rd | 39 umx-3.0.0/umx/man/umx_fun_mean_sd.Rd | 26 umx-3.0.0/umx/man/umx_get_bracket_addresses.Rd | 35 umx-3.0.0/umx/man/umx_get_checkpoint.Rd | 48 umx-3.0.0/umx/man/umx_get_options.Rd | 28 umx-3.0.0/umx/man/umx_grep.Rd | 46 umx-3.0.0/umx/man/umx_has_CIs.Rd | 41 umx-3.0.0/umx/man/umx_has_been_run.Rd | 46 umx-3.0.0/umx/man/umx_has_means.Rd | 48 umx-3.0.0/umx/man/umx_has_square_brackets.Rd | 33 umx-3.0.0/umx/man/umx_is_MxData.Rd | 28 umx-3.0.0/umx/man/umx_is_MxMatrix.Rd | 36 umx-3.0.0/umx/man/umx_is_MxModel.Rd | 36 umx-3.0.0/umx/man/umx_is_RAM.Rd | 47 umx-3.0.0/umx/man/umx_is_class.Rd | 22 umx-3.0.0/umx/man/umx_is_cov.Rd | 29 umx-3.0.0/umx/man/umx_is_endogenous.Rd | 33 umx-3.0.0/umx/man/umx_is_exogenous.Rd | 32 umx-3.0.0/umx/man/umx_is_numeric.Rd | 21 umx-3.0.0/umx/man/umx_is_ordered.Rd | 36 umx-3.0.0/umx/man/umx_long2wide.Rd | 11 umx-3.0.0/umx/man/umx_lower2full.Rd | 37 umx-3.0.0/umx/man/umx_make.Rd | 34 umx-3.0.0/umx/man/umx_make_MR_data.Rd | 29 umx-3.0.0/umx/man/umx_make_TwinData.Rd | 194 - umx-3.0.0/umx/man/umx_make_fake_data.Rd | 31 umx-3.0.0/umx/man/umx_make_raw_from_cov.Rd |only umx-3.0.0/umx/man/umx_make_sql_from_excel.Rd | 21 umx-3.0.0/umx/man/umx_means.Rd | 14 umx-3.0.0/umx/man/umx_move_file.Rd | 24 umx-3.0.0/umx/man/umx_msg.Rd | 38 umx-3.0.0/umx/man/umx_names.Rd | 44 umx-3.0.0/umx/man/umx_nice_data.Rd |only umx-3.0.0/umx/man/umx_object_as_str.Rd | 22 umx-3.0.0/umx/man/umx_open.Rd | 22 umx-3.0.0/umx/man/umx_open_CRAN_page.Rd | 25 umx-3.0.0/umx/man/umx_pad.Rd | 23 umx-3.0.0/umx/man/umx_paste_names.Rd | 17 umx-3.0.0/umx/man/umx_pb_note.Rd | 37 umx-3.0.0/umx/man/umx_polychoric.Rd | 29 umx-3.0.0/umx/man/umx_polypairwise.Rd | 29 umx-3.0.0/umx/man/umx_polytriowise.Rd | 29 umx-3.0.0/umx/man/umx_print.Rd | 55 umx-3.0.0/umx/man/umx_r_test.Rd | 28 umx-3.0.0/umx/man/umx_read_lower.Rd | 39 umx-3.0.0/umx/man/umx_rename.Rd | 85 umx-3.0.0/umx/man/umx_rename_file.Rd | 22 umx-3.0.0/umx/man/umx_reorder.Rd | 33 umx-3.0.0/umx/man/umx_residualize.Rd | 21 umx-3.0.0/umx/man/umx_rot.Rd | 24 umx-3.0.0/umx/man/umx_round.Rd | 22 umx-3.0.0/umx/man/umx_scale.Rd | 23 umx-3.0.0/umx/man/umx_scale_wide_twin_data.Rd | 29 umx-3.0.0/umx/man/umx_score_scale.Rd | 29 umx-3.0.0/umx/man/umx_select_valid.Rd |only umx-3.0.0/umx/man/umx_set_auto_plot.Rd | 41 umx-3.0.0/umx/man/umx_set_auto_run.Rd | 36 umx-3.0.0/umx/man/umx_set_checkpoint.Rd | 48 umx-3.0.0/umx/man/umx_set_condensed_slots.Rd | 36 umx-3.0.0/umx/man/umx_set_cores.Rd | 36 umx-3.0.0/umx/man/umx_set_data_variance_check.Rd | 28 umx-3.0.0/umx/man/umx_set_mvn_optimization_options.Rd |only umx-3.0.0/umx/man/umx_set_optimizer.Rd | 40 umx-3.0.0/umx/man/umx_set_plot_file_suffix.Rd | 36 umx-3.0.0/umx/man/umx_set_plot_format.Rd | 36 umx-3.0.0/umx/man/umx_set_separator.Rd |only umx-3.0.0/umx/man/umx_set_silent.Rd |only umx-3.0.0/umx/man/umx_set_table_format.Rd | 38 umx-3.0.0/umx/man/umx_stack.Rd | 36 umx-3.0.0/umx/man/umx_standardize.Rd | 55 umx-3.0.0/umx/man/umx_string_to_algebra.Rd | 30 umx-3.0.0/umx/man/umx_time.Rd | 47 umx-3.0.0/umx/man/umx_trim.Rd | 22 umx-3.0.0/umx/man/umx_var.Rd | 60 umx-3.0.0/umx/man/umx_wide2long.Rd | 10 umx-3.0.0/umx/man/umx_write_to_clipboard.Rd | 21 umx-3.0.0/umx/man/us_skinfold_data.Rd | 44 umx-3.0.0/umx/man/xmuHasSquareBrackets.Rd | 78 umx-3.0.0/umx/man/xmuLabel_MATRIX_Model.Rd | 86 umx-3.0.0/umx/man/xmuLabel_Matrix.Rd | 82 umx-3.0.0/umx/man/xmuLabel_RAM_Model.Rd | 83 umx-3.0.0/umx/man/xmuMI.Rd | 79 umx-3.0.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 74 umx-3.0.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 78 umx-3.0.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 78 umx-3.0.0/umx/man/xmuMaxLevels.Rd | 79 umx-3.0.0/umx/man/xmuMinLevels.Rd | 79 umx-3.0.0/umx/man/xmuPropagateLabels.Rd | 89 umx-3.0.0/umx/man/xmu_CI_merge.Rd |only umx-3.0.0/umx/man/xmu_CI_stash.Rd |only umx-3.0.0/umx/man/xmu_DF_to_mxData_TypeCov.Rd |only umx-3.0.0/umx/man/xmu_PadAndPruneForDefVars.Rd |only umx-3.0.0/umx/man/xmu_assemble_twin_supermodel.Rd | 78 umx-3.0.0/umx/man/xmu_cell_is_on.Rd |only umx-3.0.0/umx/man/xmu_check_levels_identical.Rd | 76 umx-3.0.0/umx/man/xmu_check_needs_means.Rd |only umx-3.0.0/umx/man/xmu_check_variance.Rd | 67 umx-3.0.0/umx/man/xmu_clean_label.Rd | 82 umx-3.0.0/umx/man/xmu_data_swap_a_block.Rd |only umx-3.0.0/umx/man/xmu_describe_data_WLS.Rd |only umx-3.0.0/umx/man/xmu_dot_define_shapes.Rd |only umx-3.0.0/umx/man/xmu_dot_make_paths.Rd | 92 umx-3.0.0/umx/man/xmu_dot_make_residuals.Rd | 84 umx-3.0.0/umx/man/xmu_dot_maker.Rd | 90 umx-3.0.0/umx/man/xmu_dot_mat2dot.Rd |only umx-3.0.0/umx/man/xmu_dot_move_ranks.Rd | 101 umx-3.0.0/umx/man/xmu_dot_rank.Rd |only umx-3.0.0/umx/man/xmu_dot_rank_str.Rd | 80 umx-3.0.0/umx/man/xmu_get_CI.Rd | 84 umx-3.0.0/umx/man/xmu_lavaan_process_group.Rd | 84 umx-3.0.0/umx/man/xmu_make_bin_cont_pair_data.Rd |only umx-3.0.0/umx/man/xmu_make_mxData.Rd | 92 umx-3.0.0/umx/man/xmu_make_top_twin.Rd | 95 umx-3.0.0/umx/man/xmu_match.arg.Rd |only umx-3.0.0/umx/man/xmu_name_from_lavaan_str.Rd |only umx-3.0.0/umx/man/xmu_safe_run_summary.Rd | 112 umx-3.0.0/umx/man/xmu_set_sep_from_suffix.Rd | 74 umx-3.0.0/umx/man/xmu_show_fit_or_comparison.Rd |only umx-3.0.0/umx/man/xmu_simplex_corner.Rd | 84 umx-3.0.0/umx/man/xmu_standardize_ACE.Rd |only umx-3.0.0/umx/man/xmu_standardize_ACEcov.Rd |only umx-3.0.0/umx/man/xmu_standardize_ACEv.Rd |only umx-3.0.0/umx/man/xmu_standardize_CP.Rd |only umx-3.0.0/umx/man/xmu_standardize_IP.Rd |only umx-3.0.0/umx/man/xmu_standardize_RAM.Rd |only umx-3.0.0/umx/man/xmu_standardize_SexLim.Rd |only umx-3.0.0/umx/man/xmu_standardize_Simplex.Rd |only umx-3.0.0/umx/man/xmu_start_value_list.Rd | 78 umx-3.0.0/umx/man/xmu_starts.Rd | 98 umx-3.0.0/umx/man/xmu_twin_check.Rd | 75 umx-3.0.0/umx/tests/testthat/test_residuals.MxModel.r | 5 umx-3.0.0/umx/tests/testthat/test_umx_ACE_etc.r |only umx-3.0.0/umx/tests/testthat/test_xmu_match.arg.r |only 324 files changed, 10607 insertions(+), 7588 deletions(-)
Title: Regression Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Author: Oldemar Rodriguez R. [aut, cre],
Andres Navarro D. [ctb, prg],
Diego Jimenez A. [ctb, prg]
Maintainer: Oldemar Rodriguez R. <oldemar.rodriguez@ucr.ac.cr>
Diff between regressoR versions 1.1.7 dated 2019-06-11 and 1.1.8 dated 2019-09-19
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/code_generate.R | 2 +- README.md |only inst/application/server.R | 9 ++++----- inst/application/ui.R | 7 ++++--- inst/application/www/style_regressor.css | 4 ---- 7 files changed, 18 insertions(+), 21 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters). It specifies basic functions that allow many visual field tests to be constructed. As of October 2017 it is fully implemented on the Octopus 900 and partially on the Heidelberg Edge Perimeter, the Kowa AP 7000, the CrewT imo and the Centervue Compass. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph],
David Lawson [ctb, cph],
Matthias Muller [ctb],
Jonathan Dennis [ctb, cph],
Astrid Zeman [ctb],
Ivan Marin-Franch [ctb]
Maintainer: Andrew Turpin <aturpin@unimelb.edu.au>
Diff between OPI versions 2.7 dated 2017-10-25 and 2.9 dated 2019-09-19
OPI-2.7/OPI/ChangeLog |only OPI-2.9/OPI/DESCRIPTION | 24 +++- OPI-2.9/OPI/MD5 | 54 +++++----- OPI-2.9/OPI/NAMESPACE | 13 +- OPI-2.9/OPI/NEWS.md |only OPI-2.9/OPI/R/compassClient.r | 124 ++++++++++++----------- OPI-2.9/OPI/R/daydreamClient.r |only OPI-2.9/OPI/R/imoClient.r | 134 ++++++++++++------------- OPI-2.9/OPI/R/kowaAP7000Client.r | 169 +++++++++++++++---------------- OPI-2.9/OPI/R/mocs.r | 78 ++++++++++---- OPI-2.9/OPI/R/octopus600.r | 52 ++++----- OPI-2.9/OPI/R/octopus900Client.r | 185 +++++++++++++---------------------- OPI-2.9/OPI/R/opi.r | 31 +++-- OPI-2.9/OPI/R/pix2deg.r |only OPI-2.9/OPI/R/simDisplay.r | 45 ++++---- OPI-2.9/OPI/R/simG.r | 14 +- OPI-2.9/OPI/R/simH.r | 51 ++++----- OPI-2.9/OPI/R/simH_RT.r | 60 +++++------ OPI-2.9/OPI/R/zest.r | 50 +++++++-- OPI-2.9/OPI/README.md |only OPI-2.9/OPI/man/MOCS.Rd | 34 ++++-- OPI-2.9/OPI/man/OPI-package.Rd | 5 OPI-2.9/OPI/man/ZEST.Rd | 27 ++++- OPI-2.9/OPI/man/degTopix.Rd |only OPI-2.9/OPI/man/opiClose.Rd | 6 + OPI-2.9/OPI/man/opiInitialize.Rd | 26 +++- OPI-2.9/OPI/man/opiPresent.Rd | 27 ++--- OPI-2.9/OPI/man/opiQueryDevice.Rd | 5 OPI-2.9/OPI/man/opiSetBackground.Rd | 13 ++ OPI-2.9/OPI/man/opiStaticStimulus.Rd | 6 - OPI-2.9/OPI/man/pixTodeg.Rd |only OPI-2.9/OPI/tests/k_test.r |only 32 files changed, 680 insertions(+), 553 deletions(-)
Title: Integer Calibration
Description: Specific functions are provided for rounding real weights to integers and performing an integer programming algorithm for calibration problems. They are useful for census-weights adjustments, or for performing linear regression with integer parameters. This research was supported in part by the U.S. Department of Agriculture, National Agriculture Statistics Service. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA, or US Government determination or policy.
Author: Luca Sartore <luca.sartore@usda.gov> and Kelly Toppin <kelly.toppin@nass.usda.gov>
Maintainer: Luca Sartore <drwolf85@gmail.com>
Diff between inca versions 0.0.3 dated 2018-02-12 and 0.0.4 dated 2019-09-19
ChangeLog | 109 ++++++++++++++++++++++++++++++++++++---------------- DESCRIPTION | 17 ++++---- MD5 | 34 ++++++++-------- NAMESPACE | 4 - R/inca.R | 35 ++++++++++------ R/intcalibrate.R | 2 R/roundWeights.R | 2 README.md | 20 +++++---- inst/INSTALL.md | 12 ++--- man/inca-package.Rd | 30 ++++++++------ src/Losses/L1.h | 2 src/Losses/LB1.h | 2 src/Losses/aL1.h | 2 src/Losses/rB1.h | 2 src/Losses/rL1.h | 2 src/bestRound.h | 4 - src/inca.cpp | 95 +++++++++++++++++++++++++++++++++++++++++++-- src/intCalib.h | 8 +-- 18 files changed, 266 insertions(+), 116 deletions(-)