Title: Joint Estimation in Linear Quantile Regression
Description: Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
Author: Surya Tokdar <surya.tokdar@duke.edu> and Erika Cunningham <erika.ball@duke.edu>
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between qrjoint versions 2.0-3 dated 2019-01-25 and 2.0-6 dated 2022-05-18
DESCRIPTION | 12 +- MD5 | 10 - NAMESPACE | 2 R/qrjoint.R | 10 - man/predict.qrjoint.Rd | 5 src/qrjoint.c | 248 +++++++++++++++++++++++++------------------------ 6 files changed, 145 insertions(+), 142 deletions(-)
Title: Risk Tool Library - Trading, Risk, 'Analytics' for Commodities
Description: A toolkit for Commodities 'analytics', risk management and
trading professionals. Includes functions for API calls to
'Morningstar Commodities' and 'Genscape'.
Author: Philippe Cote [aut, cre],
Nima Safaian [aut]
Maintainer: Philippe Cote <pcote@ualberta.ca>
Diff between RTL versions 1.0.0 dated 2022-02-11 and 1.1.0 dated 2022-05-18
RTL-1.0.0/RTL/R/ir_df_us.R |only RTL-1.0.0/RTL/data/usSwapIR.rda |only RTL-1.0.0/RTL/data/usSwapIRdef.rda |only RTL-1.0.0/RTL/man/getIRswapCurve.Rd |only RTL-1.0.0/RTL/man/ir_df_us.Rd |only RTL-1.0.0/RTL/man/usSwapIR.Rd |only RTL-1.0.0/RTL/man/usSwapIRdef.Rd |only RTL-1.1.0/RTL/DESCRIPTION | 22 +- RTL-1.1.0/RTL/MD5 | 100 ++++----- RTL-1.1.0/RTL/NAMESPACE | 6 RTL-1.1.0/RTL/NEWS.md | 28 ++ RTL-1.1.0/RTL/R/RTL-package.R | 2 RTL-1.1.0/RTL/R/RcppExports.R |only RTL-1.1.0/RTL/R/chart_zscore.R | 11 - RTL-1.1.0/RTL/R/data.R | 318 ++++++++++++++--------------- RTL-1.1.0/RTL/R/morningstar.R | 48 ---- RTL-1.1.0/RTL/R/npv.R | 79 +++---- RTL-1.1.0/RTL/R/promptBeta.R | 155 +++++++------- RTL-1.1.0/RTL/R/simGBM.R | 27 +- RTL-1.1.0/RTL/R/simOU.R | 38 ++- RTL-1.1.0/RTL/R/simOUJ.R | 63 ++++- RTL-1.1.0/RTL/R/simOUt.R |only RTL-1.1.0/RTL/R/tradeStats.R | 11 - RTL-1.1.0/RTL/README.md | 10 RTL-1.1.0/RTL/data/cancrudeassays.rda |binary RTL-1.1.0/RTL/data/cancrudeassayssum.rda |binary RTL-1.1.0/RTL/data/crudeassaysBP.rda |binary RTL-1.1.0/RTL/data/crudeassaysXOM.rda |binary RTL-1.1.0/RTL/data/crudes.rda |binary RTL-1.1.0/RTL/data/dflong.rda |binary RTL-1.1.0/RTL/data/dfwide.rda |binary RTL-1.1.0/RTL/data/eiaStocks.rda |binary RTL-1.1.0/RTL/data/eiaStorageCap.rda |binary RTL-1.1.0/RTL/data/eurodollar.rda |binary RTL-1.1.0/RTL/data/expiry_table.rda |binary RTL-1.1.0/RTL/data/fizdiffs.rda |binary RTL-1.1.0/RTL/data/fxfwd.rda |binary RTL-1.1.0/RTL/data/planets.rda |binary RTL-1.1.0/RTL/data/spot2futConvergence.rda |binary RTL-1.1.0/RTL/data/spot2futCurve.rda |binary RTL-1.1.0/RTL/data/spy.rda |only RTL-1.1.0/RTL/data/tradeHubs.rda |only RTL-1.1.0/RTL/data/tsQuotes.rda |only RTL-1.1.0/RTL/data/usSwapCurves.rda |binary RTL-1.1.0/RTL/data/usSwapCurvesPar.rda |binary RTL-1.1.0/RTL/data/wtiSwap.rda |binary RTL-1.1.0/RTL/inst |only RTL-1.1.0/RTL/man/eiaStorageCap.Rd | 32 +- RTL-1.1.0/RTL/man/npv.Rd | 7 RTL-1.1.0/RTL/man/simGBM.Rd | 18 + RTL-1.1.0/RTL/man/simOU.Rd | 6 RTL-1.1.0/RTL/man/simOUJ.Rd | 5 RTL-1.1.0/RTL/man/simOUt.Rd |only RTL-1.1.0/RTL/man/spy.Rd |only RTL-1.1.0/RTL/man/tradeHubs.Rd |only RTL-1.1.0/RTL/man/tradeStats.Rd | 6 RTL-1.1.0/RTL/man/tsQuotes.Rd |only RTL-1.1.0/RTL/src |only 58 files changed, 527 insertions(+), 465 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.6.15 dated 2022-04-14 and 2.7.0 dated 2022-05-18
soilDB-2.6.15/soilDB/R/SDA_coecoclass.R |only soilDB-2.6.15/soilDB/R/SDA_hydric.R |only soilDB-2.6.15/soilDB/R/SDA_interpretations.R |only soilDB-2.6.15/soilDB/R/SDA_muaggatt.R |only soilDB-2.6.15/soilDB/R/SDA_pmgroupname.R |only soilDB-2.6.15/soilDB/R/SDA_properties.R |only soilDB-2.6.15/soilDB/R/mapunit_geom_by_ll_bbox.R |only soilDB-2.6.15/soilDB/man/mapunit_geom_by_ll_bbox.Rd |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_coecoclass.R |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_hydric.R |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_interpretations.R |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_muaggatt.R |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_pmgroupname.R |only soilDB-2.6.15/soilDB/tests/testthat/test-SDA_properties.R |only soilDB-2.7.0/soilDB/DESCRIPTION | 13 soilDB-2.7.0/soilDB/MD5 | 398 +- soilDB-2.7.0/soilDB/NAMESPACE | 27 soilDB-2.7.0/soilDB/NEWS.md | 29 soilDB-2.7.0/soilDB/R/AAAA.R | 50 soilDB-2.7.0/soilDB/R/ISSR800.R | 370 + soilDB-2.7.0/soilDB/R/KSSL_VG_model.R | 232 - soilDB-2.7.0/soilDB/R/OSDquery.R | 296 - soilDB-2.7.0/soilDB/R/ROSETTA.R | 490 +- soilDB-2.7.0/soilDB/R/SDA-spatial.R | 934 ++-- soilDB-2.7.0/soilDB/R/SDA_query.R | 632 +-- soilDB-2.7.0/soilDB/R/SDA_utils.R | 66 soilDB-2.7.0/soilDB/R/SSURGO_spatial_query.R | 170 soilDB-2.7.0/soilDB/R/SoilDataViewer.R | 236 - soilDB-2.7.0/soilDB/R/WCS-utils.R | 1050 ++--- soilDB-2.7.0/soilDB/R/createSSURGO.R |only soilDB-2.7.0/soilDB/R/createStaticNASIS.R | 354 - soilDB-2.7.0/soilDB/R/dbQueryNASIS.R | 158 soilDB-2.7.0/soilDB/R/estimateColorMixture.R | 142 soilDB-2.7.0/soilDB/R/fetchEDIT_tools.R | 326 - soilDB-2.7.0/soilDB/R/fetchHenry.R | 902 ++-- soilDB-2.7.0/soilDB/R/fetchKSSL.R | 912 ++-- soilDB-2.7.0/soilDB/R/fetchLDM.R | 17 soilDB-2.7.0/soilDB/R/fetchNASIS.R | 262 - soilDB-2.7.0/soilDB/R/fetchNASISLabData.R | 146 soilDB-2.7.0/soilDB/R/fetchNASISWebReport.R | 809 ++-- soilDB-2.7.0/soilDB/R/fetchNASIS_components.R | 39 soilDB-2.7.0/soilDB/R/fetchNASIS_pedons.R | 2 soilDB-2.7.0/soilDB/R/fetchNASIS_report.R | 720 +-- soilDB-2.7.0/soilDB/R/fetchNOAA.R | 264 - soilDB-2.7.0/soilDB/R/fetchOSD.R | 796 ++-- soilDB-2.7.0/soilDB/R/fetchPedonPC.R | 232 - soilDB-2.7.0/soilDB/R/fetchRaCA.R | 402 -- soilDB-2.7.0/soilDB/R/fetchSCAN.R | 2 soilDB-2.7.0/soilDB/R/fetchSDA_spatial.R | 574 +- soilDB-2.7.0/soilDB/R/fetchSoilGrids.R | 400 +- soilDB-2.7.0/soilDB/R/fetchVegdata.R | 122 soilDB-2.7.0/soilDB/R/getHzErrorsNASIS.R | 90 soilDB-2.7.0/soilDB/R/getHzErrorsPedonPC.R | 44 soilDB-2.7.0/soilDB/R/get_NASIS_table_key_by_name.R | 124 soilDB-2.7.0/soilDB/R/get_NASIS_table_name_by_purpose.R | 460 +- soilDB-2.7.0/soilDB/R/get_OSD.R | 444 +- soilDB-2.7.0/soilDB/R/get_SDA_coecoclass.R |only soilDB-2.7.0/soilDB/R/get_SDA_cosurfmorph.R |only soilDB-2.7.0/soilDB/R/get_SDA_hydric.R |only soilDB-2.7.0/soilDB/R/get_SDA_interpretation.R |only soilDB-2.7.0/soilDB/R/get_SDA_muaggatt.R |only soilDB-2.7.0/soilDB/R/get_SDA_pmgroupname.R |only soilDB-2.7.0/soilDB/R/get_SDA_property.R |only soilDB-2.7.0/soilDB/R/get_SSURGO_utils.R |only soilDB-2.7.0/soilDB/R/get_colors_from_pedon_db.R | 202 - soilDB-2.7.0/soilDB/R/get_component_from_GDB.R | 1126 ++--- soilDB-2.7.0/soilDB/R/get_component_from_SDA.R | 1774 ++++----- soilDB-2.7.0/soilDB/R/get_concentrations_from_NASIS_db.R | 108 soilDB-2.7.0/soilDB/R/get_cosoilmoist_from_LIMS.R | 4 soilDB-2.7.0/soilDB/R/get_cosoilmoist_from_NASIS.R | 158 soilDB-2.7.0/soilDB/R/get_cosoilmoist_from_SDA.R | 84 soilDB-2.7.0/soilDB/R/get_extended_data_from_NASIS_db.R | 27 soilDB-2.7.0/soilDB/R/get_extended_data_from_pedon_db.R | 296 - soilDB-2.7.0/soilDB/R/get_hz_data_from_NASIS_db.R | 182 soilDB-2.7.0/soilDB/R/get_hz_data_from_pedon_db.R | 178 soilDB-2.7.0/soilDB/R/get_lablayer_data_from_NASIS_db.R | 122 soilDB-2.7.0/soilDB/R/get_labpedon_data_from_NASIS_db.R | 82 soilDB-2.7.0/soilDB/R/get_mapunit_from_NASIS.R | 443 +- soilDB-2.7.0/soilDB/R/get_phfmp_from_NASIS_db.R | 66 soilDB-2.7.0/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 236 - soilDB-2.7.0/soilDB/R/get_projectmapunit_from_NASIS.R | 100 soilDB-2.7.0/soilDB/R/get_site_data_from_NASIS_db.R | 362 - soilDB-2.7.0/soilDB/R/get_site_data_from_pedon_db.R | 198 - soilDB-2.7.0/soilDB/R/get_soilseries_from_NASIS.R | 203 - soilDB-2.7.0/soilDB/R/get_text_notes_from_NASIS_db.R | 366 - soilDB-2.7.0/soilDB/R/get_veg_data_from_NASIS_db.R | 188 soilDB-2.7.0/soilDB/R/get_veg_from_AK_Site.R | 88 soilDB-2.7.0/soilDB/R/get_veg_from_MT_veg_db.R | 84 soilDB-2.7.0/soilDB/R/get_veg_from_NPS_PLOTS_db.R | 78 soilDB-2.7.0/soilDB/R/get_veg_other_from_MT_veg_db.R | 84 soilDB-2.7.0/soilDB/R/get_veg_species_from_MT_veg_db.R | 80 soilDB-2.7.0/soilDB/R/get_vegplot_data_from_NASIS_db.R | 925 ++-- soilDB-2.7.0/soilDB/R/mix_and_clean_colors.R | 166 soilDB-2.7.0/soilDB/R/mukey-WCS.R | 380 + soilDB-2.7.0/soilDB/R/openNASISchannel.R | 166 soilDB-2.7.0/soilDB/R/parseWebReport.R | 192 soilDB-2.7.0/soilDB/R/seriesExtent.R | 299 - soilDB-2.7.0/soilDB/R/siblings.R | 264 - soilDB-2.7.0/soilDB/R/simplfyFragmentData.R | 541 +- soilDB-2.7.0/soilDB/R/simplifyArtifactData.R | 328 - soilDB-2.7.0/soilDB/R/simplifyColorData.R | 394 +- soilDB-2.7.0/soilDB/R/soilDB-package.R | 260 - soilDB-2.7.0/soilDB/R/taxaExtent.R | 612 +-- soilDB-2.7.0/soilDB/R/uncode.R | 54 soilDB-2.7.0/soilDB/R/utils.R | 1966 +++++----- soilDB-2.7.0/soilDB/R/waterDayYear.R | 118 soilDB-2.7.0/soilDB/build/partial.rdb |binary soilDB-2.7.0/soilDB/data/gopheridge.rda |binary soilDB-2.7.0/soilDB/data/loafercreek.rda |binary soilDB-2.7.0/soilDB/data/mineralKing.rda |binary soilDB-2.7.0/soilDB/data/us_ss_timeline.rda |binary soilDB-2.7.0/soilDB/inst/CITATION | 4 soilDB-2.7.0/soilDB/inst/WORDLIST | 1244 +++--- soilDB-2.7.0/soilDB/man/ISSR800.wcs.Rd | 95 soilDB-2.7.0/soilDB/man/KSSL_VG_model.Rd | 122 soilDB-2.7.0/soilDB/man/NASISDomainsAsFactor.Rd | 44 soilDB-2.7.0/soilDB/man/OSDquery.Rd | 204 - soilDB-2.7.0/soilDB/man/ROSETTA.Rd | 188 soilDB-2.7.0/soilDB/man/SCAN_SNOTEL_metadata.Rd | 48 soilDB-2.7.0/soilDB/man/SDA_query.Rd | 170 soilDB-2.7.0/soilDB/man/SDA_spatialQuery.Rd | 373 - soilDB-2.7.0/soilDB/man/SoilWeb_spatial_query.Rd | 118 soilDB-2.7.0/soilDB/man/createSSURGO.Rd |only soilDB-2.7.0/soilDB/man/createStaticNASIS.Rd | 72 soilDB-2.7.0/soilDB/man/dbConnectNASIS.Rd | 44 soilDB-2.7.0/soilDB/man/dbQueryNASIS.Rd | 46 soilDB-2.7.0/soilDB/man/downloadSSURGO.Rd |only soilDB-2.7.0/soilDB/man/fetchGDB.Rd | 156 soilDB-2.7.0/soilDB/man/fetchHenry.Rd | 182 soilDB-2.7.0/soilDB/man/fetchKSSL.Rd | 286 - soilDB-2.7.0/soilDB/man/fetchNASIS.Rd | 196 soilDB-2.7.0/soilDB/man/fetchNASISLabData.Rd | 66 soilDB-2.7.0/soilDB/man/fetchNASISWebReport.Rd | 224 - soilDB-2.7.0/soilDB/man/fetchOSD.Rd | 270 - soilDB-2.7.0/soilDB/man/fetchPedonPC.Rd | 70 soilDB-2.7.0/soilDB/man/fetchRaCA.Rd | 148 soilDB-2.7.0/soilDB/man/fetchSDA.Rd | 240 - soilDB-2.7.0/soilDB/man/fetchSDA_spatial.Rd | 151 soilDB-2.7.0/soilDB/man/fetchSoilGrids.Rd | 158 soilDB-2.7.0/soilDB/man/fetchVegdata.Rd | 162 soilDB-2.7.0/soilDB/man/getHzErrorsNASIS.Rd | 50 soilDB-2.7.0/soilDB/man/get_EDIT_ecoclass_by_geoUnit.Rd | 54 soilDB-2.7.0/soilDB/man/get_NASIS_table_key_by_name.Rd | 60 soilDB-2.7.0/soilDB/man/get_NASIS_table_name_by_purpose.Rd | 82 soilDB-2.7.0/soilDB/man/get_NOAA_GHCND.Rd | 76 soilDB-2.7.0/soilDB/man/get_NOAA_stations_nearXY.Rd | 70 soilDB-2.7.0/soilDB/man/get_OSD.Rd | 86 soilDB-2.7.0/soilDB/man/get_SDA_coecoclass.Rd | 84 soilDB-2.7.0/soilDB/man/get_SDA_cosurfmorph.Rd |only soilDB-2.7.0/soilDB/man/get_SDA_hydric.Rd | 96 soilDB-2.7.0/soilDB/man/get_SDA_interpretation.Rd | 1376 +++--- soilDB-2.7.0/soilDB/man/get_SDA_muaggatt.Rd | 58 soilDB-2.7.0/soilDB/man/get_SDA_pmgroupname.Rd | 80 soilDB-2.7.0/soilDB/man/get_SDA_property.Rd | 310 - soilDB-2.7.0/soilDB/man/get_SDV_legend_elements.Rd | 56 soilDB-2.7.0/soilDB/man/get_colors_from_pedon_db.Rd | 50 soilDB-2.7.0/soilDB/man/get_comonth_from_NASIS_db.Rd | 102 soilDB-2.7.0/soilDB/man/get_component_data_from_NASIS_db.Rd | 210 - soilDB-2.7.0/soilDB/man/get_cosoilmoist_from_NASIS.Rd | 122 soilDB-2.7.0/soilDB/man/get_extended_data_from_NASIS_db.Rd | 108 soilDB-2.7.0/soilDB/man/get_extended_data_from_pedon_db.Rd | 50 soilDB-2.7.0/soilDB/man/get_hz_data_from_NASIS_db.Rd | 78 soilDB-2.7.0/soilDB/man/get_hz_data_from_pedon_db.Rd | 58 soilDB-2.7.0/soilDB/man/get_lablayer_data_from_NASIS_db.Rd | 64 soilDB-2.7.0/soilDB/man/get_labpedon_data_from_NASIS_db.Rd | 72 soilDB-2.7.0/soilDB/man/get_mapunit_from_NASIS.Rd | 92 soilDB-2.7.0/soilDB/man/get_site_data_from_NASIS_db.Rd | 82 soilDB-2.7.0/soilDB/man/get_site_data_from_pedon_db.Rd | 50 soilDB-2.7.0/soilDB/man/get_soilseries_from_NASIS.Rd | 66 soilDB-2.7.0/soilDB/man/get_text_notes_from_NASIS_db.Rd | 110 soilDB-2.7.0/soilDB/man/get_veg_data_from_NASIS_db.Rd | 76 soilDB-2.7.0/soilDB/man/get_veg_from_AK_Site.Rd | 50 soilDB-2.7.0/soilDB/man/get_veg_from_MT_veg_db.Rd | 52 soilDB-2.7.0/soilDB/man/get_veg_from_NPS_PLOTS_db.Rd | 54 soilDB-2.7.0/soilDB/man/get_veg_other_from_MT_veg_db.Rd | 52 soilDB-2.7.0/soilDB/man/get_veg_species_from_MT_veg_db.Rd | 52 soilDB-2.7.0/soilDB/man/make_EDIT_service_URL.Rd | 192 soilDB-2.7.0/soilDB/man/mukey.wcs.Rd | 111 soilDB-2.7.0/soilDB/man/processSDA_WKT.Rd | 80 soilDB-2.7.0/soilDB/man/seriesExtent.Rd | 131 soilDB-2.7.0/soilDB/man/siblings.Rd | 132 soilDB-2.7.0/soilDB/man/simplifyFragmentData.Rd | 134 soilDB-2.7.0/soilDB/man/soilDB-package.Rd | 46 soilDB-2.7.0/soilDB/man/taxaExtent.Rd | 449 +- soilDB-2.7.0/soilDB/man/uncode.Rd | 2 soilDB-2.7.0/soilDB/man/waterDayYear.Rd | 86 soilDB-2.7.0/soilDB/tests/testthat/test-ISSR800.R | 157 soilDB-2.7.0/soilDB/tests/testthat/test-OSDquery.R | 74 soilDB-2.7.0/soilDB/tests/testthat/test-ROSETTA.R | 253 - soilDB-2.7.0/soilDB/tests/testthat/test-SDA_query.R | 397 +- soilDB-2.7.0/soilDB/tests/testthat/test-SoilDataViewer.R | 52 soilDB-2.7.0/soilDB/tests/testthat/test-fetchEDIT_tools.R | 98 soilDB-2.7.0/soilDB/tests/testthat/test-fetchHenry.R | 452 +- soilDB-2.7.0/soilDB/tests/testthat/test-fetchKSSL.R | 296 - soilDB-2.7.0/soilDB/tests/testthat/test-fetchNASIS.R | 308 - soilDB-2.7.0/soilDB/tests/testthat/test-fetchNASISLabData.R | 88 soilDB-2.7.0/soilDB/tests/testthat/test-fetchNASISWebReport.R | 145 soilDB-2.7.0/soilDB/tests/testthat/test-fetchOSD.R | 212 - soilDB-2.7.0/soilDB/tests/testthat/test-fetchSCAN.R | 70 soilDB-2.7.0/soilDB/tests/testthat/test-fetchSDA_component.R | 116 soilDB-2.7.0/soilDB/tests/testthat/test-fetchSDA_spatial.R | 154 soilDB-2.7.0/soilDB/tests/testthat/test-fetchSoilGrids.R | 119 soilDB-2.7.0/soilDB/tests/testthat/test-get_OSD.R | 116 soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_coecoclass.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_cosurfmorph.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_hydric.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_interpretation.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_muaggatt.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_pmgroupname.R |only soilDB-2.7.0/soilDB/tests/testthat/test-get_SDA_property.R |only soilDB-2.7.0/soilDB/tests/testthat/test-mukey-WCS.R | 76 soilDB-2.7.0/soilDB/tests/testthat/test-multi-row-simplification.R | 118 soilDB-2.7.0/soilDB/tests/testthat/test-seriesExtent.R |only soilDB-2.7.0/soilDB/tests/testthat/test-siblings.R | 114 soilDB-2.7.0/soilDB/tests/testthat/test-simplifyArtifactData.R | 392 - soilDB-2.7.0/soilDB/tests/testthat/test-simplifyFragmentData.R | 984 ++--- soilDB-2.7.0/soilDB/tests/testthat/test-waterDayYear.R | 106 217 files changed, 21535 insertions(+), 21314 deletions(-)
Title: Plotting Linkage and Association Results
Description: Provides routines for plotting
linkage and association results along a chromosome,
with marker names displayed along the top border.
There are also routines for generating BED and BedGraph
custom tracks for viewing in the UCSC genome browser.
The data reformatting program Mega2 uses this
package to plot output from a variety of
programs.
Author: Robert V Baron <rvb5@pitt.edu>, Nandita Mukhopadhyay,
Xinyu Tang, Daniel E. Weeks <weeks@pitt.edu>
Maintainer: Daniel E. Weeks <weeks@pitt.edu>
Diff between nplplot versions 4.5 dated 2014-05-01 and 4.6 dated 2022-05-18
nplplot-4.5/nplplot/INDEX |only nplplot-4.6/nplplot/DESCRIPTION | 17 +++++++++-------- nplplot-4.6/nplplot/MD5 | 7 +++---- nplplot-4.6/nplplot/NAMESPACE | 7 +++++++ nplplot-4.6/nplplot/R/prepareplot.R | 9 +++++---- 5 files changed, 24 insertions(+), 16 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] ,
Kosuke Imai [aut] ,
Gary King [aut] ,
Elizabeth Stuart [aut] ,
Alex Whitworth [ctb],
Noah Greifer [ctb, cre, aut]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.3.4 dated 2022-03-08 and 4.4.0 dated 2022-05-18
MatchIt-4.3.4/MatchIt/build/partial.rdb |only MatchIt-4.3.4/MatchIt/inst/figures |only MatchIt-4.4.0/MatchIt/DESCRIPTION | 19 MatchIt-4.4.0/MatchIt/MD5 | 82 +- MatchIt-4.4.0/MatchIt/NAMESPACE | 8 MatchIt-4.4.0/MatchIt/NEWS.md | 28 MatchIt-4.4.0/MatchIt/R/RcppExports.R | 8 MatchIt-4.4.0/MatchIt/R/aux_functions.R | 289 +++++++--- MatchIt-4.4.0/MatchIt/R/cem_matchit.R | 54 + MatchIt-4.4.0/MatchIt/R/class_functions.R | 14 MatchIt-4.4.0/MatchIt/R/dist_functions.R |only MatchIt-4.4.0/MatchIt/R/distance2_methods.R | 59 -- MatchIt-4.4.0/MatchIt/R/matchit.R | 87 --- MatchIt-4.4.0/MatchIt/R/matchit2_methods.R | 282 +++++---- MatchIt-4.4.0/MatchIt/build/MatchIt.pdf |binary MatchIt-4.4.0/MatchIt/build/vignette.rds |binary MatchIt-4.4.0/MatchIt/inst/doc/MatchIt.html | 51 - MatchIt-4.4.0/MatchIt/inst/doc/assessing-balance.html | 47 - MatchIt-4.4.0/MatchIt/inst/doc/estimating-effects.Rmd | 4 MatchIt-4.4.0/MatchIt/inst/doc/estimating-effects.html | 43 - MatchIt-4.4.0/MatchIt/inst/doc/matching-methods.Rmd | 12 MatchIt-4.4.0/MatchIt/inst/doc/matching-methods.html | 105 ++- MatchIt-4.4.0/MatchIt/inst/doc/sampling-weights.html | 57 + MatchIt-4.4.0/MatchIt/man/distance.Rd | 44 + MatchIt-4.4.0/MatchIt/man/euclidean_dist.Rd |only MatchIt-4.4.0/MatchIt/man/figures/README-unnamed-chunk-5-1.png |binary MatchIt-4.4.0/MatchIt/man/figures/logo.png |binary MatchIt-4.4.0/MatchIt/man/matchit.Rd | 32 - MatchIt-4.4.0/MatchIt/man/method_cardinality.Rd | 10 MatchIt-4.4.0/MatchIt/man/method_cem.Rd | 6 MatchIt-4.4.0/MatchIt/man/method_full.Rd | 24 MatchIt-4.4.0/MatchIt/man/method_genetic.Rd | 18 MatchIt-4.4.0/MatchIt/man/method_nearest.Rd | 19 MatchIt-4.4.0/MatchIt/man/method_optimal.Rd | 25 MatchIt-4.4.0/MatchIt/man/summary.matchit.Rd | 8 MatchIt-4.4.0/MatchIt/src/RcppExports.cpp | 20 MatchIt-4.4.0/MatchIt/src/dist_to_matrix.cpp |only MatchIt-4.4.0/MatchIt/src/internal.cpp | 10 MatchIt-4.4.0/MatchIt/src/internal.h | 2 MatchIt-4.4.0/MatchIt/src/nn_matchC.cpp | 49 + MatchIt-4.4.0/MatchIt/vignettes/estimating-effects.Rmd | 4 MatchIt-4.4.0/MatchIt/vignettes/matching-methods.Rmd | 12 MatchIt-4.4.0/MatchIt/vignettes/references.bib | 59 ++ 43 files changed, 943 insertions(+), 648 deletions(-)
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition using following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.1 dated 2022-03-22 and 1.2 dated 2022-05-18
IDSL.UFAx-1.1/IDSL.UFAx/data |only IDSL.UFAx-1.1/IDSL.UFAx/man/UFAx_null.Rd |only IDSL.UFAx-1.2/IDSL.UFAx/DESCRIPTION | 14 ++--- IDSL.UFAx-1.2/IDSL.UFAx/MD5 | 12 +--- IDSL.UFAx-1.2/IDSL.UFAx/NAMESPACE | 3 - IDSL.UFAx-1.2/IDSL.UFAx/R/UFAx_molecular_formula_library_search.R | 8 +- IDSL.UFAx-1.2/IDSL.UFAx/R/UFAx_score_coefficient_corrector.R | 6 +- IDSL.UFAx-1.2/IDSL.UFAx/R/UFAx_workflow.R | 28 +++++----- 8 files changed, 35 insertions(+), 36 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths]
,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between GerminaR versions 2.1.3 dated 2021-10-10 and 2.1.4 dated 2022-05-18
DESCRIPTION | 24 MD5 | 34 - NEWS.md | 7 README.md | 8 build/vignette.rds |binary inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 6 inst/GerminaQuant/server.R | 5 inst/GerminaQuant/ui.R | 4 inst/doc/GerminaQuant.Rmd | 6 inst/doc/GerminaQuant.html | 290 ++++++++- inst/doc/GerminaR.Rmd | 6 inst/doc/GerminaR.html | 278 ++++++++- inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 306 +++++++++- man/figures/logo.png |binary vignettes/GerminaQuant.Rmd | 6 vignettes/GerminaR.Rmd | 6 vignettes/introduction.Rmd | 2 18 files changed, 873 insertions(+), 117 deletions(-)
Title: Bayesian Marginal Effects for 'brms' Models
Description: Calculate Bayesian marginal effects, average marginal effects, and marginal coefficients (also called population averaged coefficients) for models fit using the 'brms' package including fixed effects, mixed effects, and location scale models. These are based on marginal predictions that integrate out random effects if necessary (see for example <doi:10.1186/s12874-015-0046-6> and <doi:10.1111/biom.12707>).
Author: Joshua F. Wiley [aut, cre] ,
Donald Hedeker [aut]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between brmsmargins versions 0.1.1 dated 2021-12-16 and 0.2.0 dated 2022-05-18
brmsmargins-0.1.1/brmsmargins/vignettes/fixed-effects-marginaleffects.Rmd.orig |only brmsmargins-0.1.1/brmsmargins/vignettes/location-scale-marginaleffects.Rmd.orig |only brmsmargins-0.1.1/brmsmargins/vignettes/mixed-effects-marginaleffects.Rmd.orig |only brmsmargins-0.1.1/brmsmargins/vignettes/precompile.R |only brmsmargins-0.2.0/brmsmargins/DESCRIPTION | 28 brmsmargins-0.2.0/brmsmargins/MD5 | 71 brmsmargins-0.2.0/brmsmargins/NAMESPACE | 6 brmsmargins-0.2.0/brmsmargins/NEWS.md | 22 brmsmargins-0.2.0/brmsmargins/R/RcppExports.R | 20 brmsmargins-0.2.0/brmsmargins/R/marginalcoef.R |only brmsmargins-0.2.0/brmsmargins/R/margins.R | 816 ++-- brmsmargins-0.2.0/brmsmargins/R/prediction.R | 122 brmsmargins-0.2.0/brmsmargins/R/utils.R | 96 brmsmargins-0.2.0/brmsmargins/README.md | 27 brmsmargins-0.2.0/brmsmargins/build/partial.rdb |binary brmsmargins-0.2.0/brmsmargins/build/vignette.rds |binary brmsmargins-0.2.0/brmsmargins/inst/doc/fixed-effects-marginaleffects.Rmd | 82 brmsmargins-0.2.0/brmsmargins/inst/doc/fixed-effects-marginaleffects.html | 408 +- brmsmargins-0.2.0/brmsmargins/inst/doc/location-scale-marginaleffects.Rmd | 103 brmsmargins-0.2.0/brmsmargins/inst/doc/location-scale-marginaleffects.html | 317 + brmsmargins-0.2.0/brmsmargins/inst/doc/mixed-effects-marginaleffects.Rmd | 1724 ++++++---- brmsmargins-0.2.0/brmsmargins/inst/doc/mixed-effects-marginaleffects.html | 1411 +++++++- brmsmargins-0.2.0/brmsmargins/man/brmsmargins.Rd | 86 brmsmargins-0.2.0/brmsmargins/man/dot-links.Rd | 5 brmsmargins-0.2.0/brmsmargins/man/integratere.Rd | 4 brmsmargins-0.2.0/brmsmargins/man/lmcpp.Rd |only brmsmargins-0.2.0/brmsmargins/man/marginalcoef.Rd |only brmsmargins-0.2.0/brmsmargins/man/prediction.Rd | 90 brmsmargins-0.2.0/brmsmargins/src/RcppExports.cpp | 13 brmsmargins-0.2.0/brmsmargins/src/integratere.cpp | 6 brmsmargins-0.2.0/brmsmargins/src/lmcpp.cpp |only brmsmargins-0.2.0/brmsmargins/src/lmcpp.h |only brmsmargins-0.2.0/brmsmargins/tests/testthat/test-dot-links.R | 21 brmsmargins-0.2.0/brmsmargins/tests/testthat/test-fixedeffects-bernoulli-margins.R | 1 brmsmargins-0.2.0/brmsmargins/tests/testthat/test-marginalcoef-mixedlogit.R |only brmsmargins-0.2.0/brmsmargins/tests/testthat/test-marginalcoef-mixedpoisson.R |only brmsmargins-0.2.0/brmsmargins/tests/testthat/test-predict-mixedlogit.R | 4 brmsmargins-0.2.0/brmsmargins/tests/testthat/test-predict-mixedlogtrans.R | 4 brmsmargins-0.2.0/brmsmargins/tests/testthat/test-predict-mixedpoisson.R | 4 brmsmargins-0.2.0/brmsmargins/vignettes/fixed-effects-marginaleffects.Rmd | 82 brmsmargins-0.2.0/brmsmargins/vignettes/location-scale-marginaleffects.Rmd | 103 brmsmargins-0.2.0/brmsmargins/vignettes/mixed-effects-marginaleffects.Rmd | 1724 ++++++---- 42 files changed, 5240 insertions(+), 2160 deletions(-)
Title: Depth Importance in Precision Medicine (DIPM) Method
Description: An implementation of the Depth Importance in Precision Medicine (DIPM) method
in Chen and Zhang (2022) <doi:10.1093/biostatistics/kxaa021> and Chen and
Zhang (2020) <doi:10.1007/978-3-030-46161-4_16>. The DIPM method is a classification
tree that searches for subgroups with especially poor or strong performance in a given treatment group.
Author: Cai Li [aut, cre],
Victoria Chen [aut],
Heping Zhang [aut]
Maintainer: Cai Li <cli9@ncsu.edu>
Diff between dipm versions 1.6 dated 2022-03-10 and 1.7 dated 2022-05-18
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/dipm.R | 54 +++++++++++++++++++++++++++--------------------------- R/ini_node.R | 2 +- R/pmprune.R | 2 +- R/spmtree.R | 56 ++++++++++++++++++++++++++++---------------------------- man/dipm.Rd | 40 ++++++++++++++++++++-------------------- man/spmtree.Rd | 42 +++++++++++++++++++++--------------------- 8 files changed, 110 insertions(+), 110 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] ,
Marcel Ramos [ctb, cre]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.17 dated 2022-04-21 and 1.30.18 dated 2022-05-18
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS | 10 +++ R/version.R | 53 +++++++++++++++++---- build/vignette.rds |binary inst/doc/BiocManager.Rmd | 34 +++++++++++++ inst/doc/BiocManager.html | 50 +++++++++++++++---- tests/testthat/test_version.R | 106 ++++++++++++++++++++++++++++++++++++++++-- vignettes/BiocManager.Rmd | 34 +++++++++++++ 9 files changed, 274 insertions(+), 35 deletions(-)
More information about TSdisaggregation at CRAN
Permanent link
Title: Helper Package for Installing OpenCV with R
Description: Installs 'OpenCV' for use by other packages. 'OpenCV' <https://opencv.org/>
is library of programming functions mainly aimed at real-time computer
vision. This 'Lite' version contains the stable base version of 'OpenCV' and
does not contain any of its externally contributed modules.
Author: Simon Garnier [aut, cre] ,
Muschelli John [ctb]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between ROpenCVLite versions 4.55.0 dated 2022-04-13 and 4.55.2 dated 2022-05-18
DESCRIPTION | 10 +- MD5 | 23 +++-- NAMESPACE | 2 NEWS.md | 45 ++++++++--- R/opencv.R | 191 ++++++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/path |only man/OpenCVPath.Rd |only man/defaultOpenCVPath.Rd |only man/installOpenCV.Rd | 20 ++-- man/isCmakeInstalled.Rd | 4 man/isOpenCVInstalled.Rd | 7 - man/opencvConfig.Rd | 8 - man/opencvVersion.Rd | 8 - 14 files changed, 214 insertions(+), 104 deletions(-)
Title: Create Visual Citations for Presentation Slides
Description: Provides 'visual citations' containing the metadata of a scientific paper and a 'QR' code.
A 'visual citation' is a banner containing title, authors, journal and year of a publication.
This package can create such banners based on 'BibTeX' and 'BibLaTeX' references
and includes a QR code pointing to the 'DOI'.
The resulting HTML object or PNG image can be included in a presentation to point the audience to good resources for further reading.
Styling is possible via predefined designs or via custom 'CSS'.
This package is not intended as replacement for proper reference manager packages,
but a tool to enrich scientific presentation slides.
Author: Christian A. Gebhard [aut, cre]
Maintainer: Christian A. Gebhard <christian.gebhard@posteo.de>
Diff between namedropR versions 2.3.2 dated 2022-05-09 and 2.3.3 dated 2022-05-18
DESCRIPTION | 12 +- MD5 | 30 ++--- NAMESPACE | 1 NEWS.md | 7 + R/drop_html.R | 17 +- R/drop_name.R | 26 +++- R/write_vc.R | 51 ++++++-- inst/doc/use_rmarkdown.R | 2 inst/doc/use_rmarkdown.Rmd | 2 inst/doc/use_rmarkdown.html | 2 man/drop_name.Rd | 20 ++- tests/testthat/aesthetic_tests.R | 26 ++-- tests/testthat/test-drop_html.R | 40 ------ tests/testthat/test-drop_name.R | 211 ++++++++++++++++++++++++------------ tests/testthat/test-write_vc.R | 226 ++++++++++++++++++++++++++------------- vignettes/use_rmarkdown.Rmd | 2 16 files changed, 426 insertions(+), 249 deletions(-)
More information about ThomasJeffersonUniv at CRAN
Permanent link
More information about ScaleSpikeSlab at CRAN
Permanent link
Title: Reference Based Multiple Imputation
Description: Implements reference based multiple imputation allowing for the imputation of longitudinal datasets using predefined strategies.
Author: Craig Gower-Page [aut, cre],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Roche [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@roche.com>
Diff between rbmi versions 1.1.3 dated 2022-03-21 and 1.1.4 dated 2022-05-18
DESCRIPTION | 6 MD5 | 59 ++++--- NEWS.md |only R/delta.R | 2 R/draws.R | 14 - R/longData.R | 85 +++++++---- R/simulate_data.R | 19 +- R/stanmodels.R | 2 README.md | 4 build/vignette.rds |binary inst/doc/advanced.html | 28 +-- inst/doc/quickstart.html | 58 +++---- inst/doc/stat_specs.html | 104 +++++++------- man/draws.Rd | 14 - man/simulate_data.Rd | 15 +- src/Makevars | 3 src/Makevars.win | 3 src/stanExports_MMRM.cc | 2 tests/testthat/helper-misc.R | 4 tests/testthat/test-delta.R | 13 + tests/testthat/test-draws.R | 2 tests/testthat/test-fullusage.R | 16 +- tests/testthat/test-longData.R | 252 ++++++++++++++++++++++++++++++++++ tests/testthat/test-mcmc.R | 4 tests/testthat/test-mmrm.R | 6 tests/testthat/test-parallel.R | 2 tests/testthat/test-reproducibility.R | 2 tests/testthat/test-simulate_data.R | 7 vignettes/build.R | 2 vignettes/quickstart.Rmd | 2 vignettes/references.bib | 4 31 files changed, 516 insertions(+), 218 deletions(-)
Title: Calculates Disproportionate Impact When Binary Success Data are
Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index.
California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>.
California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between DisImpact versions 0.0.16 dated 2022-02-18 and 0.0.17 dated 2022-05-18
DESCRIPTION | 8 MD5 | 24 NEWS | 2 R/di_iterate_on_long.R | 85 +- inst/doc/DI-On-Long-Summarized-Data.R | 19 inst/doc/DI-On-Long-Summarized-Data.Rmd | 26 inst/doc/DI-On-Long-Summarized-Data.html | 556 +++++++++++----- inst/doc/Intersectionality.html | 335 +++++----- inst/doc/Multi-Ethnicity.html | 466 ++++++++------ inst/doc/Scaling-DI-Calculations.html | 1029 +++++++++++++++++-------------- inst/doc/Tutorial.html | 484 ++++++++------ man/di_iterate_on_long.Rd | 3 vignettes/DI-On-Long-Summarized-Data.Rmd | 26 13 files changed, 1868 insertions(+), 1195 deletions(-)
Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate
time-dependent true/false positive rates and AUC curves from a
set of censored survival data.
Author: Sergej Potapov, Werner Adler and Matthias Schmid.
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between survAUC versions 1.0-5 dated 2012-09-04 and 1.1-0 dated 2022-05-18
DESCRIPTION | 19 +++++----- MD5 | 84 +++++++++++++++++++++++----------------------- NAMESPACE | 4 ++ NEWS.md |only R/BaggC.R | 14 ++++--- R/IntegratedAUC.R | 9 ++-- R/UnoC.R | 7 ++- R/plot.survAUC.R | 4 +- R/schemper.R | 12 +++--- R/survAUC_ChamDiao.R | 7 ++- R/survAUC_HZ.R | 21 ++++++----- R/survAUC_HungChiang.R | 7 ++- R/survAUC_Song_Zhou.R | 21 ++++++----- R/survAUC_Uno.R | 21 ++++++----- R/survFitCox.R | 21 ++++++----- R/surv_measures.R | 21 ++++++----- R/utils.R | 7 ++- R/zzz.R | 9 ++++ man/AUC.ChamDiao.Rd | 10 ++--- man/AUC.HungChiang.Rd | 10 ++--- man/AUC.Song_Zhou.Rd | 8 ++-- man/AUC.uno.Rd | 8 ++-- man/BeggC.Rd | 10 ++--- man/GHCI.Rd | 4 +- man/OXS.Rd | 10 ++--- man/UnoC.Rd | 10 ++--- man/plot.survAUC.Rd | 7 ++- man/predErr.Rd | 8 ++-- man/schemper.Err.Rd | 5 +- src/R_init_survAUC.c |only src/survAUC_Cham_Diao.c | 6 +-- src/survAUC_Cham_Diao.h | 2 - src/survAUC_HZ.c | 2 - src/survAUC_HZ.h | 2 - src/survAUC_Hung_Chiang.c | 10 ++--- src/survAUC_Hung_Chiang.h | 2 - src/survAUC_SongZhou.c | 14 +++---- src/survAUC_SongZhou.h | 6 +-- src/survAUC_UNO.c | 16 ++++---- src/survAUC_UNO.h | 8 ++-- src/surv_measures.c | 28 +++++++-------- src/surv_measures.h | 15 ++++---- src/utils.c | 16 ++++---- src/utils.h | 8 ++-- 44 files changed, 275 insertions(+), 238 deletions(-)
Title: Metabolomics-Based Models for Imputing Risk
Description: Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Author: Daniele Bizzarri [aut, cre] ,
Marcel Reinders [aut, ths] ,
Marian Beekman [aut] ,
Pieternella Eline Slagboom [aut, ths]
,
Erik van den Akker [aut, ths]
Maintainer: Daniele Bizzarri <d.bizzarri@lumc.nl>
Diff between MiMIR versions 1.2 dated 2022-04-15 and 1.3 dated 2022-05-18
MiMIR-1.2/MiMIR/inst/shinyApp/example_metabolic_dataset.csv |only MiMIR-1.2/MiMIR/inst/shinyApp/example_phenotypic_dataset.csv |only MiMIR-1.2/MiMIR/man/impute.miss.Rd |only MiMIR-1.3/MiMIR/DESCRIPTION | 17 MiMIR-1.3/MiMIR/MD5 | 132 +- MiMIR-1.3/MiMIR/NAMESPACE | 8 MiMIR-1.3/MiMIR/R/datasets.R |only MiMIR-1.3/MiMIR/R/predictors_functions.R | 66 - MiMIR-1.3/MiMIR/R/utils.R | 162 ++- MiMIR-1.3/MiMIR/README.md | 65 - MiMIR-1.3/MiMIR/inst/shinyApp/lib/libraries.R | 1 MiMIR-1.3/MiMIR/inst/shinyApp/markdown/Rshiny_markdown.Rmd | 10 MiMIR-1.3/MiMIR/inst/shinyApp/markdown/Rshiny_markdown_no_pheno.Rmd | 11 MiMIR-1.3/MiMIR/inst/shinyApp/rsconnect |only MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_about/server_about.R | 2 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_about/ui_about.R | 2 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_accuracy_scores/server_accuracy_scores.R | 11 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_calibration/ui_calibration.R | 5 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_download/server_download.R | 51 - MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_metabolites/ui_metabolites.R | 2 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_qc/server_qc.R | 75 + MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_scores_tables/server_scores_tables.R | 114 +- MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_surro_tables/server_surro_tables.R | 41 MiMIR-1.3/MiMIR/inst/shinyApp/tabs/tab_upload/server_upload.R | 114 -- MiMIR-1.3/MiMIR/inst/shinyApp/ui.R | 31 MiMIR-1.3/MiMIR/inst/shinyApp/www/App_mimir_logo.pdf |only MiMIR-1.3/MiMIR/inst/shinyApp/www/app_mimir_logo.png |only MiMIR-1.3/MiMIR/man/Ahola_Olli_betas.Rd | 34 MiMIR-1.3/MiMIR/man/BBMRI_hist.Rd | 480 ---------- MiMIR-1.3/MiMIR/man/BBMRI_hist_plot.Rd | 10 MiMIR-1.3/MiMIR/man/BBMRI_hist_scaled.Rd | 480 ---------- MiMIR-1.3/MiMIR/man/BMI_LDL_eGFR.Rd | 6 MiMIR-1.3/MiMIR/man/CVD_score_betas.Rd | 34 MiMIR-1.3/MiMIR/man/LOBOV_accuracies.Rd | 2 MiMIR-1.3/MiMIR/man/MOLEPI_LCBC_header.Rd |only MiMIR-1.3/MiMIR/man/MetaboWAS.Rd | 2 MiMIR-1.3/MiMIR/man/PARAM_metaboAge.Rd | 44 MiMIR-1.3/MiMIR/man/PARAM_surrogates.Rd | 152 --- MiMIR-1.3/MiMIR/man/QCprep.Rd | 2 MiMIR-1.3/MiMIR/man/QCprep_surrogates.Rd | 2 MiMIR-1.3/MiMIR/man/acc_LOBOV.Rd | 31 MiMIR-1.3/MiMIR/man/activateButtn.Rd |only MiMIR-1.3/MiMIR/man/apply.fit.Rd | 4 MiMIR-1.3/MiMIR/man/apply.fit_surro.Rd | 2 MiMIR-1.3/MiMIR/man/apply.scale.Rd | 4 MiMIR-1.3/MiMIR/man/binarize_all_pheno.Rd | 2 MiMIR-1.3/MiMIR/man/c21.Rd | 26 MiMIR-1.3/MiMIR/man/calculate_surrogate_scores.Rd | 2 MiMIR-1.3/MiMIR/man/comp.CVD_score.Rd | 4 MiMIR-1.3/MiMIR/man/comp.T2D_Ahola_Olli.Rd | 2 MiMIR-1.3/MiMIR/man/comp.mort_score.Rd | 2 MiMIR-1.3/MiMIR/man/comp_covid_score.Rd | 2 MiMIR-1.3/MiMIR/man/covid_betas.Rd | 34 MiMIR-1.3/MiMIR/man/getvol.Rd |only MiMIR-1.3/MiMIR/man/impute_miss.Rd |only MiMIR-1.3/MiMIR/man/loading.Rd |only MiMIR-1.3/MiMIR/man/loading_spin.Rd |only MiMIR-1.3/MiMIR/man/metabo_names_translator.Rd | 52 - MiMIR-1.3/MiMIR/man/metabolites_subsets.Rd | 39 MiMIR-1.3/MiMIR/man/mort_betas.Rd | 33 MiMIR-1.3/MiMIR/man/pheno_barplots.Rd | 2 MiMIR-1.3/MiMIR/man/phenotypes_names.Rd | 28 MiMIR-1.3/MiMIR/man/predictions_surrogates.Rd | 2 MiMIR-1.3/MiMIR/man/prep_data_COVID_score.Rd | 2 MiMIR-1.3/MiMIR/man/prep_met_for_scores.Rd | 6 MiMIR-1.3/MiMIR/man/rendertable.Rd |only MiMIR-1.3/MiMIR/man/report.dim.Rd | 4 MiMIR-1.3/MiMIR/man/subset_metabolites_overlap.Rd | 4 MiMIR-1.3/MiMIR/man/subset_samples_miss.Rd | 4 MiMIR-1.3/MiMIR/man/subset_samples_sd.Rd | 4 MiMIR-1.3/MiMIR/man/subset_samples_sd_surrogates.Rd | 2 MiMIR-1.3/MiMIR/man/subset_samples_zero.Rd | 4 MiMIR-1.3/MiMIR/man/synthetic_metabolic_dataset.Rd | 30 MiMIR-1.3/MiMIR/man/synthetic_phenotypic_dataset.Rd | 26 74 files changed, 800 insertions(+), 1725 deletions(-)
Title: United Formula Annotation (UFA) for HRMS Data Processing
Description: A pipeline to annotate peaklists from the IDSL.IPA package with molecular formula using an isotopic profile matching approach. The IDSL.UFA pipeline is especially beneficial when MS/MS data channels are not available. The IDSL.UFA package has functions to process user-defined adduct formulas.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFA versions 1.1 dated 2022-03-22 and 1.2 dated 2022-05-18
DESCRIPTION | 15 MD5 | 54 +-- NAMESPACE | 5 R/UFA_enumerated_chemical_space.R | 38 +- R/UFA_enumerated_chemical_space_xlsxAnalyzer.R | 6 R/UFA_profile_visualizer.R | 6 R/UFA_profile_visualizer_xlsxAnalyzer.R | 21 - R/UFA_score_coefficient_corrector.R | 6 R/UFA_score_function_optimization_xlsxAnalyzer.R | 14 R/UFA_workflow.R | 13 R/UFA_xlsxAnalyzer.R | 22 - R/aligned_molecular_formula_annotator.R | 393 +++++++++++++++-------- R/detect_formula_sets.R | 12 R/element_sorter.R | 2 R/formula_vector_generator.R | 4 R/hill_molecular_formula_printer.R | 6 R/isotopic_profile_molecular_formula_feeder.R | 10 R/molecular_formula_annotator.R | 6 R/molecular_formulas_source_IPDB.R | 1 R/monoisotopic_mass_calculator.R | 2 R/zero_score_function.R | 12 build/partial.rdb |binary data/IUPAC_Isotopes.rda |binary inst/extdata/UFA_parameters.xlsx |binary man/IUPAC_Isotopes.Rd | 6 man/identification_score.Rd | 2 man/isotopic_profile_calculator.Rd | 2 man/isotopic_profile_molecular_formula_feeder.Rd | 2 28 files changed, 399 insertions(+), 261 deletions(-)
Title: Epidemiological Data Display Package
Description: Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at '<https://medipe.psu.ac.th/epicalc/>'.
Author: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Maintainer: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Diff between epiDisplay versions 3.5.0.1 dated 2018-05-10 and 3.5.0.2 dated 2022-05-18
DESCRIPTION | 10 - MD5 | 104 +++++----- R/epiDisplay.R | 22 +- man/aggregate.numeric.rd | 2 man/aggregate.plot.rd | 214 +++++++++++----------- man/alpha.rd | 164 ++++++++--------- man/cc.rd | 2 man/ci.rd | 202 ++++++++++----------- man/codebook.rd | 2 man/des.rd | 2 man/dotplot.rd | 158 ++++++++-------- man/followup.plot.rd | 174 +++++++++--------- man/kap.rd | 2 man/lookup.rd | 4 man/lrtest.rd | 2 man/lsNoFunction.rd | 54 ++--- man/matchTab.rd | 2 man/mhor.rd | 2 man/poisgof.rd | 2 man/power.for.2means.rd | 2 man/power.rd | 76 +++---- man/print.alpha.rd | 2 man/print.cci.rd | 2 man/print.des.rd | 2 man/print.kap.ByCategory.rd | 2 man/print.kap.table.rd | 2 man/print.lrtest.rd | 2 man/print.matchTab.rd | 2 man/print.n.for.2means.rd | 2 man/print.n.for.2p.rd | 2 man/print.n.for.cluster.2means.rd | 2 man/print.n.for.cluster.2p.rd | 2 man/print.n.for.equi.2p.rd | 2 man/print.n.for.lqas.rd | 2 man/print.n.for.noninferior.2p.rd | 2 man/print.n.for.survey.rd | 2 man/print.power.for.2p.rd | 2 man/print.statStack.rd | 2 man/print.summ.data.frame.rd | 2 man/print.summ.default.rd | 2 man/print.tableStack.rd | 2 man/pyramid.rd | 4 man/risk.display.rd | 2 man/roc.rd | 2 man/sampsize.rd | 362 +++++++++++++++++++------------------- man/setTitle.rd | 70 +++---- man/shapiro.qqnorm.rd | 2 man/statStack.rd | 94 ++++----- man/summ.rd | 2 man/tab1.rd | 4 man/tableStack.rd | 2 man/tabpct.rd | 4 man/titleString.rd | 134 +++++++------- 53 files changed, 962 insertions(+), 962 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022, <arxiv:1910.09219>).
Multivariate conditional transformation models (Klein et al, 2022, <DOI:10.1111/sjos.12501>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.7-0 dated 2022-04-01 and 0.7-1 dated 2022-05-18
tram-0.7-0/tram/inst/doc/mtram.R |only tram-0.7-0/tram/vignettes/mtram-CAO-plot-1.pdf |only tram-0.7-0/tram/vignettes/mtram-neck_Colr_distr-1.pdf |only tram-0.7-0/tram/vignettes/mtram-neck_plot-1.pdf |only tram-0.7-0/tram/vignettes/mtram-sleep-plot-1.pdf |only tram-0.7-0/tram/vignettes/mtram-sleep_BoxCoxPlot-1.pdf |only tram-0.7-0/tram/vignettes/mtram-sleep_marginal-1.pdf |only tram-0.7-0/tram/vignettes/mtram-toenail-plot-1.pdf |only tram-0.7-0/tram/vignettes/mtram-toenail_OR_2-1.png |only tram-0.7-0/tram/vignettes/mtram-toenail_probplot-1.pdf |only tram-0.7-1/tram/DESCRIPTION | 14 tram-0.7-1/tram/MD5 | 49 tram-0.7-1/tram/NAMESPACE | 6 tram-0.7-1/tram/R/methods.R | 76 tram-0.7-1/tram/R/mmlt.R | 16 tram-0.7-1/tram/R/mtram.R | 184 tram-0.7-1/tram/build/partial.rdb |binary tram-0.7-1/tram/build/vignette.rds |binary tram-0.7-1/tram/demo/mtram.R | 6473 ++++++++++++++++- tram-0.7-1/tram/inst/NEWS.Rd | 8 tram-0.7-1/tram/inst/doc/mtram.Rnw | 2026 ----- tram-0.7-1/tram/inst/doc/mtram.pdf |binary tram-0.7-1/tram/inst/doc/tram.Rnw | 3 tram-0.7-1/tram/inst/doc/tram.pdf |binary tram-0.7-1/tram/man/mtram.Rd | 17 tram-0.7-1/tram/man/tram-methods.Rd | 10 tram-0.7-1/tram/tests/stram-Ex.R | 13 tram-0.7-1/tram/tests/stram-Ex.Rout.save | 17 tram-0.7-1/tram/vignettes/mtram-rendered.pdf |only tram-0.7-1/tram/vignettes/mtram.Rnw | 2026 ----- tram-0.7-1/tram/vignettes/tram.Rnw | 3 31 files changed, 6632 insertions(+), 4309 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] ,
EDJNet [fnd]
Maintainer: Giorgio Comai <giorgio.comai@cci.tn.it>
Diff between tidywikidatar versions 0.5.1 dated 2022-03-11 and 0.5.2 dated 2022-05-18
DESCRIPTION | 16 - MD5 | 94 ++++---- NAMESPACE | 16 - NEWS.md | 17 + R/tw_cache_indexing.R |only R/tw_check_qid.R | 41 +++ R/tw_connect_to_cache.R | 6 R/tw_extract.R | 3 R/tw_filter.R | 32 ++ R/tw_get.R | 17 - R/tw_get_cached_item.R | 12 - R/tw_get_cached_search.R | 3 R/tw_get_field.R | 8 R/tw_get_image.R | 13 - R/tw_get_others.R | 108 ++++++++- R/tw_get_p_wide.R |only R/tw_get_property.R | 102 ++++++--- R/tw_get_property_label_description.R | 3 R/tw_get_property_with_details.R | 3 R/tw_get_qualifiers.R | 10 R/tw_get_wikipedia_page_links.R | 5 R/tw_get_wikipedia_page_qid.R | 9 R/tw_get_wikipedia_page_sections.R | 7 R/tw_search.R | 3 R/tw_write_item_to_cache.R | 14 - R/tw_write_search_to_cache.R | 4 R/utils-tidy-eval.R | 4 README.md | 324 ++++++++++++++++------------- build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/caching.R | 20 + inst/doc/caching.Rmd | 26 ++ inst/doc/caching.html | 20 + man/tw_check_cache_index.Rd |only man/tw_check_qid.Rd | 18 + man/tw_connect_to_cache.Rd | 2 man/tw_extract_single.Rd | 2 man/tw_get_cache_table_name.Rd | 7 man/tw_get_description.Rd | 2 man/tw_get_p1.Rd |only man/tw_get_p_wide.Rd |only man/tw_get_property_label_single.Rd | 2 man/tw_get_property_same_length.Rd | 6 man/tw_get_property_with_details_single.Rd | 2 man/tw_get_qualifiers_single.Rd | 2 man/tw_get_single.Rd | 2 man/tw_get_wikipedia.Rd | 5 man/tw_index_cache_item.Rd |only man/tw_index_cache_search.Rd |only man/tw_search_single.Rd | 2 tests/testthat/test-tw_get_p_wide.R |only vignettes/caching.Rmd | 26 ++ 52 files changed, 705 insertions(+), 316 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre]
,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] ,
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.7.0 dated 2022-05-09 and 0.7.1 dated 2022-05-18
DESCRIPTION | 8 ++--- MD5 | 6 ++-- NEWS.md | 4 ++ tests/testthat/test-conversions.R | 56 +++++++++++++++++++------------------- 4 files changed, 39 insertions(+), 35 deletions(-)
More information about rdataretriever at CRAN
Permanent link
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary Abrams, Greg Gershkowitz, Anoushka Joglekar,
Chao Liu, Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.9 dated 2022-05-03 and 1.0.10 dated 2022-05-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/newmanomics.html | 42 +++++++++++++++++++++--------------------- tests/03-betamix.R | 7 ++++--- tests/03-betamix.Rout.save | 11 +++++------ 5 files changed, 38 insertions(+), 38 deletions(-)
Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs, compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary [aut, cre] ,
Gilles Vuidel [ctb] ,
Tyler Rudolph [ctb]
Maintainer: Paul Savary <psavary@protonmail.com>
Diff between graph4lg versions 1.4.0 dated 2022-03-08 and 1.6.0 dated 2022-05-18
DESCRIPTION | 6 MD5 | 48 NEWS.md | 239 ++-- R/get_graphab.R | 14 R/graph_plot_compar.R | 354 +++--- R/graph_to_shp.R | 2 R/graphab_metric.R | 8 R/graphab_project.R | 468 ++++---- R/mat_cost_dist.R | 3 R/pop_rare_gen_index.R | 396 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/genetic_graph_2.R | 428 ++++---- inst/doc/genetic_graph_2.html | 1798 ++++++++++++++++++++++----------- inst/doc/graph_comparisons_4.R | 290 ++--- inst/doc/graph_comparisons_4.html | 1315 ++++++++++++++++-------- inst/doc/input_data_processing_1.R | 292 ++--- inst/doc/input_data_processing_1.html | 1801 +++++++++++++++++++++------------- inst/doc/landscape_graph_3.R | 288 ++--- inst/doc/landscape_graph_3.html | 1691 ++++++++++++++++++++----------- man/graph_to_shp.Rd | 2 man/graphab_metric.Rd | 7 man/graphab_project.Rd | 4 man/mat_cost_dist.Rd | 2 man/pop_rare_gen_index.Rd | 7 25 files changed, 5695 insertions(+), 3768 deletions(-)
Title: Dimension Reduction for Outlier Detection
Description: A dimension reduction technique for outlier detection. DOBIN: a Distance
based Outlier BasIs using Neighbours, constructs a set of basis vectors for outlier
detection. This is not an outlier detection method; rather it is a pre-processing
method for outlier detection. It brings outliers to the fore-front using fewer basis
vectors (Kandanaarachchi, Hyndman 2020) <doi:10.1080/10618600.2020.1807353>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between dobin versions 1.0.2 dated 2020-02-24 and 1.0.3 dated 2022-05-18
DESCRIPTION | 15 +- MD5 | 31 +++--- NAMESPACE | 9 + R/autoplot_dobin.R |only R/dobin-package.R |only R/dobin.R | 44 ++++++-- R/print.R |only R/y_space.R | 4 build/vignette.rds |binary inst/doc/dobin.R | 34 +++--- inst/doc/dobin.Rmd | 16 +-- inst/doc/dobin.html | 232 +++++++++++++++++++++++++++++++-------------- man/autoplot.dobin.Rd |only man/dobin-package.Rd |only man/dobin.Rd | 10 - man/figures/bimodal-1.png |binary man/figures/plotting-1.png |only man/reexports.Rd |only vignettes/bibliography.bib | 25 +++- vignettes/dobin.Rmd | 16 +-- 20 files changed, 292 insertions(+), 144 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages like
'ggplot2' and 'lattice' to help facilitate the plotting of data over long time
intervals, including, but not limited to, geological, evolutionary, and ecological
data. The primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to assist
with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 0.2.1 dated 2022-01-10 and 0.2.2 dated 2022-05-18
DESCRIPTION | 6 - MD5 | 28 +++--- NAMESPACE | 1 NEWS.md | 5 - R/coord_geo.R | 42 ++++++--- man/coord_geo.Rd | 18 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/coord_geo/custom-discrete-scale.svg | 24 ++--- tests/testthat/_snaps/coord_geo/scale-on-discrete-axis.svg | 24 ++--- tests/testthat/setup-data.R | 56 +++++++------ tests/testthat/test-coord_geo.R | 50 +++++++---- tests/testthat/test-disparity_through_time.R | 5 - tests/testthat/test-ggarrange2.R | 8 + tests/testthat/test-gggeo_scale.R | 7 + tests/testthat/test-gggeo_scale_old.R | 6 + 15 files changed, 175 insertions(+), 105 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-22 1.1.9
2015-04-01 1.1.8
2015-03-14 1.1.7
2012-04-13 1.0-15
2011-12-11 1.0-13
2011-12-09 1.0-12
2011-11-30 1.0-11
2011-01-30 1.0-1
2011-01-21 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-06 0.2.3
2022-03-25 0.2.2
2022-01-06 0.2.1
2021-11-16 0.2.0
2021-09-09 0.1.0
Title: The 'Monaco' Editor as a HTML Widget
Description: A HTML widget rendering the 'Monaco' editor. The 'Monaco' editor is the code editor which powers 'VS Code'. It is particularly well developed for 'JavaScript'. In addition to the built-in features of the 'Monaco' editor, the widget allows to prettify multiple languages, to view the 'HTML' rendering of 'Markdown' code, and to view and resize 'SVG' images.
Author: Stephane Laurent [aut, cre],
Microsoft Corporation [ctb, cph] ,
James Long and contributors [ctb, cph] ,
Rich Harris [ctb, cph] ,
Lionel Tzatzkin [ctb, cph] ,
Andrei Kashcha [ctb, cph] ,
Vitaly Puzrin [ctb, cph] ,
Alex Kocharin [ctb, cph] ,
John Schl [...truncated...]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between monaco versions 0.2.1 dated 2021-03-06 and 0.2.2 dated 2022-05-18
DESCRIPTION | 7 LICENSE.note | 568 MD5 | 86 NAMESPACE | 38 NEWS.md | 32 R/getMonacoX.R | 48 R/internal.R | 830 - R/monaco.R | 660 - R/zzz.R | 14 README.md | 70 inst/exampleFiles/JavaScript.js | 42 inst/exampleFiles/Markdown.md | 184 inst/exampleFiles/react.svg | 12 inst/htmlwidgets/MW/MW.css | 482 inst/htmlwidgets/MW/MW.js | 2056 +-- inst/htmlwidgets/customRangeInput/customRangeInput.css | 210 inst/htmlwidgets/customRangeInput/customRangeInput.scss | 288 inst/htmlwidgets/github-markdown-css/github-markdown.css | 2000 +-- inst/htmlwidgets/jQuery/jquery.min.js | 4 inst/htmlwidgets/jQueryModal/jquery.modal.min.js | 10 inst/htmlwidgets/markdown-it/markdown-it.min.js | 6 inst/htmlwidgets/monaco-editor/monaco.min.js | 22 inst/htmlwidgets/monaco.js | 222 inst/htmlwidgets/monaco.yaml | 126 inst/htmlwidgets/panzoom/panzoom.min.js | 2 inst/htmlwidgets/prettier/parser-babel.js | 2 inst/htmlwidgets/prettier/parser-html.js | 226 inst/htmlwidgets/prettier/parser-markdown.js | 38 inst/htmlwidgets/prettier/parser-typescript.js | 2 inst/htmlwidgets/prettier/parser-yaml.js | 30 inst/htmlwidgets/prettier/standalone.js | 110 inst/htmlwidgets/scale-that-svg/scale-that-svg-bundle.js | 9454 +++++++-------- inst/htmlwidgets/svg-parser/svg-parser-bundle.js | 598 inst/htmlwidgets/word-wrap/word-wrap-bundle.js | 108 inst/monaco-bundle/dist/index.html | 50 inst/monaco-bundle/index.js | 34 inst/monaco-bundle/loaders/blobUrl.js | 12 inst/monaco-bundle/loaders/compile.js | 174 inst/monaco-bundle/package.json | 30 inst/monaco-bundle/webpack.config.js | 72 man/getMonacoLanguages.Rd | 22 man/getMonacoThemes.Rd | 24 man/monaco-shiny.Rd | 240 man/monaco.Rd | 232 44 files changed, 9740 insertions(+), 9737 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 5.1.0 dated 2022-04-03 and 5.2.0 dated 2022-05-18
lefko3-5.1.0/lefko3/vignettes/Ch2.20-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch2.29-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch2.40-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch5.16-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch5.21-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch5.26-1.png |only lefko3-5.1.0/lefko3/vignettes/Ch5.29-1.png |only lefko3-5.2.0/lefko3/DESCRIPTION | 10 lefko3-5.2.0/lefko3/MD5 | 136 +- lefko3-5.2.0/lefko3/NAMESPACE | 2 lefko3-5.2.0/lefko3/NEWS | 48 lefko3-5.2.0/lefko3/R/RcppExports.R | 245 +++- lefko3-5.2.0/lefko3/R/datamanag.R | 20 lefko3-5.2.0/lefko3/R/errorchecks.R | 108 ++ lefko3-5.2.0/lefko3/R/matrixcreation.R | 123 +- lefko3-5.2.0/lefko3/R/modelselection.R | 35 lefko3-5.2.0/lefko3/R/popchar.R | 326 ++++++ lefko3-5.2.0/lefko3/R/popdyn.R | 90 + lefko3-5.2.0/lefko3/build/vignette.rds |binary lefko3-5.2.0/lefko3/inst/doc/Chapter1.Rmd | 36 lefko3-5.2.0/lefko3/inst/doc/Chapter1.html | 125 +- lefko3-5.2.0/lefko3/inst/doc/Chapter2.Rmd | 146 +- lefko3-5.2.0/lefko3/inst/doc/Chapter2.html | 988 +++++++++---------- lefko3-5.2.0/lefko3/inst/doc/Chapter5.Rmd | 45 lefko3-5.2.0/lefko3/inst/doc/Chapter5.html | 610 ++++++------ lefko3-5.2.0/lefko3/inst/doc/Chapter6.Rmd | 9 lefko3-5.2.0/lefko3/inst/doc/Chapter6.html | 10 lefko3-5.2.0/lefko3/inst/doc/Chapter8.Rmd | 51 - lefko3-5.2.0/lefko3/inst/doc/Chapter8.html | 67 - lefko3-5.2.0/lefko3/man/aflefko2.Rd | 28 lefko3-5.2.0/lefko3/man/density_input.Rd | 22 lefko3-5.2.0/lefko3/man/density_vr.Rd |only lefko3-5.2.0/lefko3/man/f_projection3.Rd | 49 lefko3-5.2.0/lefko3/man/flefko2.Rd | 28 lefko3-5.2.0/lefko3/man/flefko3.Rd | 28 lefko3-5.2.0/lefko3/man/fleslie.Rd | 8 lefko3-5.2.0/lefko3/man/modelsearch.Rd | 26 lefko3-5.2.0/lefko3/man/projection3.Rd | 7 lefko3-5.2.0/lefko3/man/summary.lefkoProj.Rd | 41 lefko3-5.2.0/lefko3/man/summary_hfv.Rd |only lefko3-5.2.0/lefko3/man/verticalize3.Rd | 10 lefko3-5.2.0/lefko3/src/DataManagement.cpp | 286 +++-- lefko3-5.2.0/lefko3/src/RcppExports.cpp | 61 - lefko3-5.2.0/lefko3/src/matsndyn.cpp | 1168 ++++++++++++++++++----- lefko3-5.2.0/lefko3/vignettes/Ch2.18-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch2.19-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch2.26-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch2.27-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch2.28-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch2.38-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch2.39-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch5.14-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch5.15-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch5.18-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch5.19-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch5.20-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch5.24-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch5.25-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch5.28-1.png |only lefko3-5.2.0/lefko3/vignettes/Ch8.15-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.16-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.17-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.2-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.20-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.21-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.25-1.png |binary lefko3-5.2.0/lefko3/vignettes/Ch8.26-1.png |binary lefko3-5.2.0/lefko3/vignettes/Chapter1.Rmd | 36 lefko3-5.2.0/lefko3/vignettes/Chapter2.Rmd | 146 +- lefko3-5.2.0/lefko3/vignettes/Chapter2.Rmd.orig | 128 +- lefko3-5.2.0/lefko3/vignettes/Chapter5.Rmd | 45 lefko3-5.2.0/lefko3/vignettes/Chapter5.Rmd.orig | 56 - lefko3-5.2.0/lefko3/vignettes/Chapter6.Rmd | 9 lefko3-5.2.0/lefko3/vignettes/Chapter6.Rmd.orig | 4 lefko3-5.2.0/lefko3/vignettes/Chapter8.Rmd | 51 - lefko3-5.2.0/lefko3/vignettes/Chapter8.Rmd.orig | 4 lefko3-5.2.0/lefko3/vignettes/Lefko3Tutorial.bib | 14 77 files changed, 3609 insertions(+), 1876 deletions(-)
Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract
signals of organic compounds. The package performs isotope pairing, peak
detection, alignment, RT correction, gap filling, peak annotation and
visualization of extracted ion chromatograms and total ion chromatograms.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 1.4 dated 2022-03-22 and 1.5 dated 2022-05-18
DESCRIPTION | 19 ++--- MD5 | 38 +++++----- NAMESPACE | 3 R/IPA_GapFiller.R | 12 +-- R/IPA_MSdeconvoluter.R | 10 +- R/IPA_PeakAlignment.R | 6 - R/IPA_PeakAnalyzer.R | 10 +- R/IPA_PeaklistAnnotation.R | 11 +- R/IPA_TargetedAnalysis.R | 15 +-- R/IPA_Workflow.R | 148 ++++++++++++++++++++------------------- R/IPA_xlsxAnalyzer.R | 4 - R/global.R | 2 R/peak_alignment.R | 6 - R/plot_mz_eic.R | 10 +- R/plot_simple_tic.R | 10 +- R/xlsxAnalyzer_EIC.R | 14 +-- build/partial.rdb |binary inst/extdata/IPA_parameters.xlsx |binary man/IPA_TargetedAnalysis.Rd | 2 man/gaussianity_measurement.Rd | 2 20 files changed, 162 insertions(+), 160 deletions(-)
Title: Big Data Preprocessing Architecture
Description: Provide a tool to easily build customized data flows to pre-process large volumes
of information from different sources. To this end, 'bdpar' allows to (i) easily use and
create new functionalities and (ii) develop new data source extractors according to the
user needs. Additionally, the package provides by default a predefined data flow
to extract and pre-process the most relevant information (tokens, dates, ... ) from some textual
sources (SMS, Email, tweets, YouTube comments).
Author: Miguel Ferreiro-Diaz [aut, cre],
David Ruano-Ordas [aut, ctr],
Tomas R. Cotos-Yanez [aut, ctr],
Jose Ramon Mendez Reboredo [aut, ctr],
University of Vigo [cph]
Maintainer: Miguel Ferreiro-Diaz <miguel.ferreiro.diaz@gmail.com>
Diff between bdpar versions 3.0.1 dated 2021-06-24 and 3.0.2 dated 2022-05-18
DESCRIPTION | 14 MD5 | 177 +++++------ NEWS.md | 4 R/AbbreviationPipe.R | 4 R/Bdpar.R | 2 R/BdparOptions.R | 2 R/Connections.R | 2 R/ContractionPipe.R | 6 R/DefaultPipeline.R | 2 R/DynamicPipeline.R | 2 R/ExtractorEml.R | 2 R/ExtractorFactory.R | 2 R/ExtractorSms.R | 2 R/ExtractorTwtid.R | 2 R/ExtractorYtbid.R | 2 R/File2Pipe.R | 2 R/FindEmojiPipe.R | 10 R/FindEmoticonPipe.R | 2 R/FindHashtagPipe.R | 2 R/FindUrlPipe.R | 2 R/FindUserNamePipe.R | 2 R/GenericPipe.R | 6 R/GenericPipeline.R | 2 R/GuessDatePipe.R | 2 R/GuessLanguagePipe.R | 2 R/Instance.R | 2 R/InterjectionPipe.R | 4 R/MeasureLengthPipe.R | 2 R/ResourceHandler.R | 2 R/SlangPipe.R | 5 R/StopWordPipe.R | 4 R/StoreFileExtPipe.R | 2 R/TargetAssigningPipe.R | 2 R/TeeCSVPipe.R | 2 R/ToLowerCasePipe.R | 2 R/bdpar.Options.R | 2 R/bdpar.log.R | 2 R/bdparData.R | 2 R/eml.R | 6 R/emojisData.R |only R/operator-pipe.R | 2 R/runPipeline.R | 2 R/wrapper.R | 2 build/vignette.rds |binary data/emojisData.rda |only exec/parse.py | 2 inst/doc/bdpar.html | 501 +++++++++++++++++++++++++++++---- inst/doc/bdparExample.html | 223 ++++++++++++++ inst/doc/bdparExampleImage.html | 231 ++++++++++++++- man/AbbreviationPipe.Rd | 78 ++--- man/Bdpar.Rd | 18 - man/Connections.Rd | 54 +-- man/ContractionPipe.Rd | 78 ++--- man/DefaultPipeline.Rd | 52 +-- man/DynamicPipeline.Rd | 76 ++--- man/ExtractorEml.Rd | 100 +++--- man/ExtractorFactory.Rd | 72 ++-- man/ExtractorSms.Rd | 88 ++--- man/ExtractorTwtid.Rd | 100 +++--- man/ExtractorYtbid.Rd | 100 +++--- man/File2Pipe.Rd | 48 +-- man/FindEmojiPipe.Rd | 62 ++-- man/FindEmoticonPipe.Rd | 60 +-- man/FindHashtagPipe.Rd | 60 +-- man/FindUrlPipe.Rd | 90 ++--- man/FindUserNamePipe.Rd | 60 +-- man/GenericPipe.Rd | 60 +-- man/GenericPipeline.Rd | 30 - man/GuessDatePipe.Rd | 48 +-- man/GuessLanguagePipe.Rd | 54 +-- man/Instance.Rd | 156 +++++----- man/InterjectionPipe.Rd | 78 ++--- man/MeasureLengthPipe.Rd | 54 +-- man/ResourceHandler.Rd | 36 +- man/SlangPipe.Rd | 78 ++--- man/StopWordPipe.Rd | 78 ++--- man/StoreFileExtPipe.Rd | 54 +-- man/TargetAssigningPipe.Rd | 66 ++-- man/TeeCSVPipe.Rd | 48 +-- man/ToLowerCasePipe.Rd | 54 +-- man/emojisData.Rd |only tests/testthat/test_AbbreviationPipe.R | 2 tests/testthat/test_Bdpar.R | 8 tests/testthat/test_ContractionPipe.R | 2 tests/testthat/test_DefaultPipeline.R | 1 tests/testthat/test_DynamicPipeline.R | 1 tests/testthat/test_FindEmojiPipe.R | 15 tests/testthat/test_InterjectionPipe.R | 2 tests/testthat/test_SlangPipe.R | 2 tests/testthat/test_StopWordPipe.R | 2 tests/testthat/test_runPipeline.R | 1 91 files changed, 2083 insertions(+), 1302 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.2.7 dated 2022-02-22 and 2.2.8 dated 2022-05-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 4 ++++ R/userlib.R | 14 ++++++++++++-- build/vignette.rds |binary inst/doc/opencpu-paper.pdf |binary 6 files changed, 24 insertions(+), 10 deletions(-)
Title: Complex Matrix Algebra with 'Eigen'
Description: Matrix algebra using the 'Eigen' C++ library: determinant, rank, inverse, pseudo-inverse, kernel and image, QR decomposition, Cholesky decomposition, linear least-squares problems. Also provides matrix functions such as exponential, logarithm, power, sine and cosine. Complex matrices are supported.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between EigenR versions 1.2.2 dated 2022-01-22 and 1.2.3 dated 2022-05-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/EigenR.R | 5 ++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package development
infrastructure inside the data integration centers ('DIZ') to
standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.0.15 dated 2022-02-28 and 0.1.0 dated 2022-05-18
DESCRIPTION | 9 - MD5 | 38 ++-- NAMESPACE | 20 +- R/check_if_table_exists.R | 126 +++++++-------- R/close_connection.R | 90 +++++------ R/combine_stats.R | 316 +++++++++++++++++++-------------------- R/db_connection.R | 73 +++++---- R/get_config_env.R | 344 +++++++++++++++++++++---------------------- R/get_db_systems.R | 66 ++++---- R/query_database.R | 188 ++++++++++++----------- README.md | 185 +++++++++++------------ man/check_if_table_exists.Rd | 54 +++--- man/close_connection.Rd | 64 ++++---- man/combine_stats.Rd | 62 +++---- man/db_connection.Rd | 156 +++++++++---------- man/get_config_env.Rd | 112 +++++++------- man/get_db_systems.Rd | 44 ++--- man/query_database.Rd | 118 +++++++------- man/xml_2_json.Rd | 34 ++-- tests/testthat/test-lints.R | 66 ++++---- 20 files changed, 1100 insertions(+), 1065 deletions(-)
Title: Core Functionality of the 'spatstat' Family
Description: Functionality for data analysis and modelling of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Chiara Fend [ctb],
Julian Gilbey [ctb],
Yongtao G [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.core versions 2.4-2 dated 2022-03-31 and 2.4-4 dated 2022-05-18
DESCRIPTION | 25 ++- MD5 | 132 +++++++++--------- NAMESPACE | 11 + NEWS | 51 +++++++ R/FGmultiInhom.R | 10 - R/GJfox.R | 13 + R/Jinhom.R | 23 ++- R/Kest.R | 2 R/Kinhom.R | 6 R/Kmulti.R | 3 R/Kscaled.R | 2 R/anova.mppm.R | 7 - R/bw.pcf.R | 2 R/cdf.test.mppm.R | 2 R/clarkevans.R | 2 R/density.ppp.R | 6 R/density.psp.R | 2 R/densityAdaptiveKernel.R | 4 R/densityfun.R | 2 R/digestCovariates.R | 27 ++- R/edgeTrans.R | 4 R/envelope.R | 15 +- R/evalcovar.R | 292 ++++++++++++++++++++++++++++++++++++++++-- R/fii.R | 2 R/fv.R | 35 +++-- R/hackglmm.R | 12 + R/hopskel.R | 2 R/kernel2d.R | 5 R/kmrs.R | 18 +- R/kppm.R | 21 ++- R/localKcross.R | 4 R/lohboot.R | 2 R/measures.R | 4 R/mppm.R | 2 R/pcfinhom.R | 4 R/pcfmulti.inhom.R | 4 R/pool.R | 4 R/ppmclass.R | 2 R/predictmppm.R | 4 R/rat.R | 4 R/rhohat.R | 28 ++-- R/rmh.ppm.R | 12 + R/rose.R | 2 R/scanstat.R | 5 R/segtest.R | 4 R/simulate.detPPF.R | 12 + R/simulatekppm.R | 12 - R/slrm.R | 8 - R/smooth.ppp.R | 21 +-- R/smoothfun.R | 2 R/ssf.R | 2 R/sysdata.rda |binary R/thresholding.R | 9 - R/twostage.R | 14 +- R/vblogistic.R | 2 R/vcov.ppm.R | 2 R/zgibbsmodel.R | 3 inst/doc/packagesizes.txt | 2 man/Jinhom.Rd | 8 + man/envelopeArray.Rd | 3 man/macros/defns.Rd | 4 man/spatstat.core-internal.Rd | 18 +- tests/testsD.R | 29 +++- tests/testsEtoF.R | 9 + tests/testsGtoJ.R | 13 + tests/testsK.R | 4 tests/testsS.R | 4 67 files changed, 734 insertions(+), 270 deletions(-)
Title: Estimating and Testing the Number of Interesting Components in
Linear Dimension Reduction
Description: For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.
Author: Klaus Nordhausen [aut, cre] ,
Hannu Oja [aut] ,
David E. Tyler [aut],
Joni Virta [aut]
Maintainer: Klaus Nordhausen <klaus.k.nordhausen@jyu.fi>
Diff between ICtest versions 0.3-4 dated 2021-03-20 and 0.3-5 dated 2022-05-18
DESCRIPTION | 10 MD5 | 36 +- NAMESPACE | 4 R/FOBIboot.R | 4 R/ICSboot.R |only R/PCAaug.R |only R/PCAboot.R | 6 build/vignette.rds |binary inst/ChangeLog | 6 inst/doc/ICA.html | 647 +++++++++++++++++++++++------------------------------ inst/doc/PCA.html | 512 +++++++++++++++++++---------------------- inst/doc/SIR.html | 459 ++++++++++++++++++------------------- man/FOBIasymp.Rd | 2 man/FOBIboot.Rd | 2 man/ICSboot.Rd |only man/PCAasymp.Rd | 2 man/PCAaug.Rd |only man/PCAboot.Rd | 2 man/SIRasymp.Rd | 2 man/SIRboot.Rd | 2 man/covSIR.Rd | 2 21 files changed, 800 insertions(+), 898 deletions(-)
Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression
models, with the support of reproducible survival model building,
validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Miao-Zhu Li [aut],
Frank Harrell [ctb] ,
Sergej Potapov [ctb] ,
Werner Adler [ctb] ,
Matthias Schmid [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 6.0.0 dated 2019-06-23 and 6.0.1 dated 2022-05-18
DESCRIPTION | 29 MD5 | 124 +- NAMESPACE | 6 NEWS.md | 11 R/3_2_validate_utils.R | 3 R/3_5_validate_external_utils.R | 3 R/hdnom.R | 3 R/survAUC_ChamDiao.R |only R/survAUC_Song_Zhou.R |only R/survAUC_Uno.R |only R/survAUC_utils.R |only README.md | 62 - build/vignette.rds |binary inst/CITATION | 4 inst/doc/hdnom.R | 40 inst/doc/hdnom.Rmd | 47 inst/doc/hdnom.html | 1169 +++++++++++---------- inst/logo |only man/as_nomogram.Rd | 11 man/calibrate.Rd | 26 man/calibrate_external.Rd | 13 man/calibrate_external_surv_prob_true.Rd | 10 man/compare_by_calibrate.Rd | 18 man/compare_by_validate.Rd | 20 man/figures |only man/fit_aenet.Rd | 12 man/fit_alasso.Rd | 9 man/fit_enet.Rd | 12 man/fit_flasso.Rd | 16 man/fit_lasso.Rd | 3 man/fit_mcp.Rd | 14 man/fit_mnet.Rd | 15 man/fit_scad.Rd | 14 man/fit_snet.Rd | 15 man/glmnet_calibrate_surv_prob_pred.Rd | 11 man/glmnet_validate_external_tauc.Rd | 11 man/glmnet_validate_tauc.Rd | 13 man/hdnom-package.Rd | 14 man/kmplot.Rd | 8 man/kmplot_raw.Rd | 9 man/ncvreg_calibrate_surv_prob_pred.Rd | 12 man/ncvreg_validate_external_tauc.Rd | 11 man/ncvreg_validate_tauc.Rd | 14 man/penalized_basesurv.Rd | 3 man/penalized_calibrate_external_surv_prob_pred.Rd | 3 man/penalized_calibrate_surv_prob_pred.Rd | 3 man/penalized_validate_external_tauc.Rd | 11 man/penalized_validate_tauc.Rd | 12 man/plot.hdnom.calibrate.Rd | 9 man/plot.hdnom.calibrate.external.Rd | 9 man/plot.hdnom.compare.calibrate.Rd | 9 man/plot.hdnom.compare.validate.Rd | 9 man/plot.hdnom.validate.Rd | 3 man/plot.hdnom.validate.external.Rd | 3 man/smart.Rd | 6 man/smarto.Rd | 6 man/validate.Rd | 27 man/validate_external.Rd | 13 src |only vignettes/hdnom.Rmd | 47 60 files changed, 1209 insertions(+), 776 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 0.0.4 dated 2022-03-03 and 0.0.5 dated 2022-05-18
DESCRIPTION | 10 ++++----- MD5 | 20 +++++++++++-------- NAMESPACE | 3 ++ R/check_if_unique_rows.R |only R/close_all_connections.R | 2 + R/feedback.R | 42 ++++++++++++++++++++++++++++++++++++----- R/is.empty.R | 26 +++++++++++++++++++------ README.md | 11 +++++----- man/check_if_unique_rows.Rd |only man/is.empty.Rd | 15 +++++++++----- man/log_get_current_options.Rd |only tests/testthat/test-feedback.R | 35 ++++++++++++++++------------------ tests/testthat/test-is.empty.R |only 13 files changed, 112 insertions(+), 52 deletions(-)
Title: A Light-Weight, Portable Tool for Reviewing Individual Patient
Records
Description: A portable Shiny tool to explore patient-level electronic health record data
and perform chart review in a single integrated framework. This tool supports
browsing clinical data in many different formats including multiple versions
of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In
addition, chart review information is captured and stored securely via the
Shiny interface in a 'REDCap' (Research Electronic Data Capture) project
using the 'REDCap' API. See the 'ReviewR' website for additional information,
documentation, and examples.
Author: Laura Wiley [aut] ,
Luke Rasmussen [aut] ,
David Mayer [cre, aut] ,
The Wiley Lab [cph, fnd]
Maintainer: David Mayer <david.mayer@cuanschutz.edu>
Diff between ReviewR versions 2.3.7 dated 2021-09-02 and 2.3.8 dated 2022-05-18
DESCRIPTION | 18 MD5 | 41 NEWS.md | 13 R/mod_REDCap.R | 2 R/mod_layout_chartreview.R | 2 R/reviewr_dev.R | 41 README.md | 6 build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 1 inst/doc/customize_support_new_data_model.html | 3227 ++++++++++++++++++++++++- inst/doc/customize_support_new_rdbms.html | 368 ++ inst/doc/deploy_bigquery.html | 250 + inst/doc/deploy_docker.html | 365 ++ inst/doc/deploy_local.html | 207 + inst/doc/deploy_server.html | 377 ++ inst/doc/usage_connect_to_record_database.html | 261 +- inst/doc/usage_connect_to_redcap.html | 453 +++ inst/doc/usage_perform_chart_review.html | 315 ++ inst/golem-config.yml | 2 man/dev_add_data_model.Rd | 24 man/mod_layout_chartreview.Rd | 2 22 files changed, 5607 insertions(+), 368 deletions(-)
Title: Bayesian Change-Point Detection and Time Series Decomposition
Description: Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications include its use to identify regime shifts in ecological data, map forest disturbance and land degradation from satellite imagery, detect market trends in economic data, pinpoint anomaly and extreme events in climate data, and unravel system dynamics in biological data. Details on BEAST are reported in Zhao et al. (2019) <doi:10.1016/j.rse.2019.04.034>.
Author: Kaiguang Zhao [aut, cre],
Tongxi Hu [aut],
Yang Li [aut],
Jack Dongarra [ctb],
Cleve Moler [ctb]
Maintainer: Kaiguang Zhao <zhao.1423@osu.edu>
Diff between Rbeast versions 0.9.3 dated 2022-03-04 and 0.9.4 dated 2022-05-18
Rbeast-0.9.3/Rbeast/src/abc_ioFlush.cpp |only Rbeast-0.9.3/Rbeast/src/beastv2_io_out_print.c |only Rbeast-0.9.4/Rbeast/DESCRIPTION | 9 Rbeast-0.9.4/Rbeast/MD5 | 137 + Rbeast-0.9.4/Rbeast/NAMESPACE | 6 Rbeast-0.9.4/Rbeast/NEWS | 5 Rbeast-0.9.4/Rbeast/R/beast.R | 39 Rbeast-0.9.4/Rbeast/R/beast.irreg.R | 17 Rbeast-0.9.4/Rbeast/R/beast123.R | 3 Rbeast-0.9.4/Rbeast/R/plot.beast.R | 158 +- Rbeast-0.9.4/Rbeast/R/plot.interactive.R | 187 +- Rbeast-0.9.4/Rbeast/R/plot.mrbeast.R |only Rbeast-0.9.4/Rbeast/R/print.beast.R | 40 Rbeast-0.9.4/Rbeast/R/tsextract.R |only Rbeast-0.9.4/Rbeast/R/util.R | 127 - Rbeast-0.9.4/Rbeast/data/datalist | 3 Rbeast-0.9.4/Rbeast/data/googletrend_beach.RData |only Rbeast-0.9.4/Rbeast/man/CNAchrom11.Rd | 5 Rbeast-0.9.4/Rbeast/man/beast.Rd | 133 + Rbeast-0.9.4/Rbeast/man/beast.irreg.Rd | 83 - Rbeast-0.9.4/Rbeast/man/beast123.Rd | 93 - Rbeast-0.9.4/Rbeast/man/covid19.Rd | 7 Rbeast-0.9.4/Rbeast/man/geeLandsat.Rd | 6 Rbeast-0.9.4/Rbeast/man/googletrend_beach.Rd |only Rbeast-0.9.4/Rbeast/man/minesweeper.Rd | 6 Rbeast-0.9.4/Rbeast/man/ohio.Rd | 18 Rbeast-0.9.4/Rbeast/man/plot.beast.Rd | 16 Rbeast-0.9.4/Rbeast/man/print.beast.Rd | 2 Rbeast-0.9.4/Rbeast/man/simdata.Rd | 2 Rbeast-0.9.4/Rbeast/man/tetris.Rd | 2 Rbeast-0.9.4/Rbeast/man/tsextract.Rd | 2 Rbeast-0.9.4/Rbeast/src/abc_000_macro.h | 32 Rbeast-0.9.4/Rbeast/src/abc_001_config.h | 16 Rbeast-0.9.4/Rbeast/src/abc_common.c | 42 Rbeast-0.9.4/Rbeast/src/abc_common.h | 6 Rbeast-0.9.4/Rbeast/src/abc_ide_util.c | 104 - Rbeast-0.9.4/Rbeast/src/abc_ide_util.h | 3 Rbeast-0.9.4/Rbeast/src/abc_ioFlush.c |only Rbeast-0.9.4/Rbeast/src/abc_mat.c | 79 + Rbeast-0.9.4/Rbeast/src/abc_mat.h | 10 Rbeast-0.9.4/Rbeast/src/abc_mcmc.c | 41 Rbeast-0.9.4/Rbeast/src/abc_mcmc.h | 4 Rbeast-0.9.4/Rbeast/src/abc_mem.c | 9 Rbeast-0.9.4/Rbeast/src/abc_pthread.h | 4 Rbeast-0.9.4/Rbeast/src/abc_ts_func.c | 18 Rbeast-0.9.4/Rbeast/src/abc_ts_func.h | 4 Rbeast-0.9.4/Rbeast/src/abc_vec.c | 14 Rbeast-0.9.4/Rbeast/src/abc_vec.h | 7 Rbeast-0.9.4/Rbeast/src/abc_vec_avx2.c | 114 + Rbeast-0.9.4/Rbeast/src/abc_vec_avx512.c | 120 + Rbeast-0.9.4/Rbeast/src/abc_vec_generic.c | 79 + Rbeast-0.9.4/Rbeast/src/beastv2_COREV4.c | 266 ++- Rbeast-0.9.4/Rbeast/src/beastv2_COREV4_gui.c | 272 ++- Rbeast-0.9.4/Rbeast/src/beastv2_COREV4_mthrd.c | 270 ++- Rbeast-0.9.4/Rbeast/src/beastv2_basis_computexy_q.c | 18 Rbeast-0.9.4/Rbeast/src/beastv2_basis_cvtKnotsToBinVec.c | 9 Rbeast-0.9.4/Rbeast/src/beastv2_basis_gensegment.c | 132 - Rbeast-0.9.4/Rbeast/src/beastv2_basis_proposeNew_q.c | 246 ++- Rbeast-0.9.4/Rbeast/src/beastv2_basis_updategoodvec.c | 6 Rbeast-0.9.4/Rbeast/src/beastv2_func.h | 4 Rbeast-0.9.4/Rbeast/src/beastv2_func_q.c | 28 Rbeast-0.9.4/Rbeast/src/beastv2_header.h | 56 Rbeast-0.9.4/Rbeast/src/beastv2_header_solaris.h | 91 - Rbeast-0.9.4/Rbeast/src/beastv2_io.h | 1 Rbeast-0.9.4/Rbeast/src/beastv2_io_in_args.c | 177 +- Rbeast-0.9.4/Rbeast/src/beastv2_io_out_allocmem_q.c | 1049 ++++----------- Rbeast-0.9.4/Rbeast/src/beastv2_io_out_printargs.c |only Rbeast-0.9.4/Rbeast/src/beastv2_io_out_tsextractprint.c |only Rbeast-0.9.4/Rbeast/src/beastv2_io_out_write_q.c | 234 --- Rbeast-0.9.4/Rbeast/src/beastv2_model_allocinit_q.c | 9 Rbeast-0.9.4/Rbeast/src/beastv2_prior_model.c | 25 Rbeast-0.9.4/Rbeast/src/beastv2_prior_precfunc.c | 148 -- Rbeast-0.9.4/Rbeast/src/beastv2_prior_precfunc.h | 2 Rbeast-0.9.4/Rbeast/src/glue_code.c | 32 74 files changed, 2532 insertions(+), 2355 deletions(-)
Title: Multiple Administrations Adaptive Testing
Description: Provides an extension of the shadow-test approach to computerized adaptive
testing (CAT) implemented in the 'TestDesign' package for the assessment framework
involving multiple tests administered periodically throughout the year. This framework
is referred to as the Multiple Administrations Adaptive Testing (MAAT) and supports
multiple item pools vertically scaled and multiple phases (stages) of CAT within each test.
Between phases and tests, transitioning from one item pool (and associated constraints)
to another is allowed as deemed necessary to enhance the quality of measurement.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut] ,
Luping Niu [aut] ,
Sooyong Lee [aut] ,
M. Christina Schneider [ctb],
Jay Lee [ctb],
Garron Gianopulos [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between maat versions 1.0.2 dated 2021-07-09 and 1.1.0 dated 2022-05-18
DESCRIPTION | 27 MD5 | 68 +- NAMESPACE | 2 NEWS.md | 11 R/examinee_class.R | 23 R/examinee_updaters.R | 6 R/import.R | 2 R/module_functions.R | 60 + R/module_structure_operators.R | 35 - R/plot_functions.R | 78 +- R/routing_functions.R | 142 +++- R/sim_functions.R | 124 +++ R/validators.r |only build/vignette.rds |binary data/assessment_structure_math.rda |binary data/cut_scores_math.rda |binary data/examinee_list_math.rda |binary data/module_list_math.rda |binary inst/doc/maat.R | 16 inst/doc/maat.Rmd | 176 +++-- inst/doc/maat.html | 349 ++++++++--- inst/extdata/constraints_MATH4_T1P1.csv |only inst/extdata/constraints_MATH4_T1P2.csv |only inst/extdata/constraints_MATH4_T2P1.csv |only inst/extdata/constraints_MATH4_T2P2.csv |only inst/extdata/constraints_MATH4_T3P1.csv |only inst/extdata/constraints_MATH4_T3P2.csv |only inst/extdata/datasets.r | 2 inst/extdata/module_definition_MATH_normal_N500_flexible.csv |only man/examinee-class.Rd | 22 man/loadModules.Rd | 8 man/maat.Rd | 21 man/output_maat-class.Rd | 2 man/plot-methods.Rd | 7 man/simExaminees.Rd | 10 man/updateAssessmentLevelTheta.Rd |only tests/testthat/test_routing_functions.r |only tests/testthat/test_simulation_functions.R | 30 vignettes/bibliography.bib | 31 vignettes/maat.Rmd | 176 +++-- 40 files changed, 974 insertions(+), 454 deletions(-)
Title: Relevance-Integrated Statistical Inference Engine
Description: Provide methods to perform customized inference at individual level by taking
contextual covariates into account. Three main functions are provided
in this package: (i) LASER(): it generates specially-designed artificial relevant
samples for a given case; (ii) g2l.proc(): computes customized fdr(z|x); and (iii)
rEB.proc(): performs empirical Bayes inference based on LASERs. The details can be
found in Mukhopadhyay, S., and Wang, K (2021, <arXiv:2004.09588>).
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kaijunwang.19@gmail.com>
Diff between LPRelevance versions 3.2 dated 2021-04-22 and 3.3 dated 2022-05-18
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/partial.rdb |binary man/g2l.proc.Rd | 30 +++++++++++++++--------------- man/rEB.Finite.Bayes.Rd | 6 +++--- man/rEB.proc.Rd | 4 ++-- 6 files changed, 30 insertions(+), 30 deletions(-)
Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry
Data)
Description: A tiny parser to extract mass spectra data and metadata table of MS acquisition properties from mzML, mzXML and netCDF mass spectrometry files.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.MXP versions 1.1 dated 2022-03-22 and 1.2 dated 2022-05-18
IDSL.MXP-1.1/IDSL.MXP/R/getPeakTable.R |only IDSL.MXP-1.1/IDSL.MXP/man/getPeakTable.Rd |only IDSL.MXP-1.2/IDSL.MXP/DESCRIPTION | 14 ++++++++------ IDSL.MXP-1.2/IDSL.MXP/MD5 | 14 ++++++++------ IDSL.MXP-1.2/IDSL.MXP/NAMESPACE | 3 ++- IDSL.MXP-1.2/IDSL.MXP/R/getNetCDF.R |only IDSL.MXP-1.2/IDSL.MXP/R/getScanTable.R |only IDSL.MXP-1.2/IDSL.MXP/R/peak2list.R | 14 +++++++++----- IDSL.MXP-1.2/IDSL.MXP/man/getNetCDF.Rd |only IDSL.MXP-1.2/IDSL.MXP/man/getScanTable.Rd |only IDSL.MXP-1.2/IDSL.MXP/man/peak2list.Rd | 5 ++++- 11 files changed, 31 insertions(+), 19 deletions(-)
Title: Reweighted Marginal Hypothesis Tests for Clustered Data
Description: A collection of reweighted marginal hypothesis tests for clustered data, based
on reweighting methods of Williamson, J., Datta, S., and Satten, G. (2003) <doi:10.1111/1541-0420.00005>.
The tests in this collection are clustered analogs to well-known hypothesis tests
in the classical setting, and are appropriate for data with cluster- and/or group-size
informativeness. The syntax and output of functions are modeled after common,
recognizable functions native to R. Methods used in the package refer to
Gregg, M., Datta, S., and Lorenz, D. (2020) <doi:10.1177/0962280220928572>,
Nevalainen, J., Oja, H., and Datta, S. (2017) <doi:10.1002/sim.7288>
Dutta, S. and Datta, S. (2015) <doi:10.1111/biom.12447>,
Lorenz, D., Datta, S., and Harkema, S. (2011) <doi:10.1002/sim.4368>,
Datta, S. and Satten, G. (2008) <doi:10.1111/j.1541-0420.2007.00923.x>,
Datta, S. and Satten, G. (2005) <doi:10.1198/016214504000001583>.
Author: Mary Gregg [aut, cre] ,
Somnath Datta [aut] ,
Doug Lorenz [aut]
Maintainer: Mary Gregg <megregg07@gmail.com>
Diff between htestClust versions 0.2.1 dated 2022-02-13 and 0.2.2 dated 2022-05-18
DESCRIPTION | 8 - MD5 | 12 + R/proptestClust.R | 320 ++++++++++++++++++++++++++------------------------- build |only inst |only man/proptestClust.Rd | 8 + vignettes |only 7 files changed, 186 insertions(+), 162 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-30 0.1.9.5
2020-03-16 0.1.9.4
2020-02-08 0.1.9.3
2019-11-07 0.1.9.2
2019-05-19 0.1.9.1
2019-04-19 0.1.9
2019-01-28 0.1.8
2018-08-11 0.1.7
2018-04-22 0.1.4
2018-04-19 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-21 0.1.0