Title: Permutation-Based FDR Point and Confidence Interval Estimation
Description: FDR functions for permutation-based estimators, including pi0 as well as FDR
confidence intervals. The confidence intervals account for dependencies between
tests by the incorporation of an overdispersion parameter, which is estimated
from the permuted data. Also included are options for an analog parametric approach.
Author: Joshua Millstein [aut, cre]
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between fdrci versions 2.2 dated 2021-06-11 and 2.3 dated 2022-06-07
DESCRIPTION | 14 ++- MD5 | 24 ++++-- NAMESPACE | 3 R/fdrTbl.R | 66 ++++++++++++++--- R/fdr_od.R | 195 ++++++++++++++++++++++++++++++++++----------------- R/fdrci-package.R | 9 +- R/meff.R |only build |only inst/doc |only man/fdrTbl.Rd | 32 +++++++- man/fdr_od.Rd | 46 +++++++++--- man/fdrci-package.Rd | 9 +- man/meff.jm.Rd |only vignettes |only 14 files changed, 291 insertions(+), 107 deletions(-)
Title: Create a Matrix with Radio Buttons
Description: An input controller for R Shiny: a matrix with radio buttons,
where only one option per row can be selected.
Author: Zsolt Szelepcsenyi [aut, cre],
Zoltan Szelepcsenyi [aut]
Maintainer: Zsolt Szelepcsenyi <szelepcsenyi.zsolt@gmail.com>
Diff between shinyRadioMatrix versions 0.2.0 dated 2021-01-14 and 0.2.1 dated 2022-06-07
DESCRIPTION | 18 ++++--- MD5 | 9 ++- NEWS.md |only R/radioMatrixInput.R | 93 +++++++++++++++++++++++++++---------- inst/inputRadioMatrixBinding.js | 99 +++++++++++++++++++++------------------- man/radioMatrixInput.Rd | 5 ++ 6 files changed, 142 insertions(+), 82 deletions(-)
More information about shinyRadioMatrix at CRAN
Permanent link
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.3.1 dated 2022-05-06 and 1.4.0 dated 2022-06-07
DESCRIPTION | 14 ++-- MD5 | 43 ++++++------ NAMESPACE | 56 +++++++++++++++- NEWS.md | 5 + R/Misc_fun.R | 34 +++++++++- R/RCM_est.R | 124 +++++++++++++++++++++++++++++++++++-- R/RCM_int.R | 7 -- R/RCM_rmd.R | 2 R/define_S4_class_assess_RCMdata.R | 12 ++- R/define_S4_class_project.R | 2 R/define_S4_generic_RCM.R | 12 ++- R/report_auxiliary.R | 6 - build/partial.rdb |binary inst/include/RCM.hpp | 47 ++++++++++++-- inst/include/functions.hpp | 22 ++++++ inst/include/ns/ns_RCM.hpp | 79 +++++++++++++++++++++++ man/HCR_FB.Rd | 90 +++++++++++++------------- man/RCM.Rd | 13 ++- man/SP_production.Rd | 72 ++++++++++----------- man/prof-class.Rd | 60 ++++++++--------- man/projection.Rd | 2 man/userguide.Rd | 4 - src/Makevars |only 23 files changed, 525 insertions(+), 181 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <sebastian.calonico@columbia.edu>, Matias D. Cattaneo <cattaneo@princeton.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@princeton.edu>
Maintainer: Sebastian Calonico <sebastian.calonico@columbia.edu>
Diff between rdrobust versions 2.0.0 dated 2022-06-06 and 2.0.1 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rdrobust.R | 3 ++- man/rdrobust-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.31.1 dated 2022-04-22 and 1.32.0 dated 2022-06-07
parallelly-1.31.1/parallelly/NEWS |only parallelly-1.32.0/parallelly/DESCRIPTION | 8 parallelly-1.32.0/parallelly/MD5 | 41 ++-- parallelly-1.32.0/parallelly/NEWS.md |only parallelly-1.32.0/parallelly/R/availableConnections.R | 2 parallelly-1.32.0/parallelly/R/availableCores.R | 66 +++++- parallelly-1.32.0/parallelly/R/availableWorkers.R | 77 ++++++- parallelly-1.32.0/parallelly/R/makeClusterPSOCK.R | 2 parallelly-1.32.0/parallelly/R/makeNodePSOCK.R | 147 ++++++++------- parallelly-1.32.0/parallelly/R/options.R | 54 ++--- parallelly-1.32.0/parallelly/R/supportsMulticore.R | 4 parallelly-1.32.0/parallelly/R/utils,cluster.R | 7 parallelly-1.32.0/parallelly/R/utils,conditions.R |only parallelly-1.32.0/parallelly/R/utils.R | 12 - parallelly-1.32.0/parallelly/README.md | 2 parallelly-1.32.0/parallelly/man/availableConnections.Rd | 6 parallelly-1.32.0/parallelly/man/availableCores.Rd | 58 ++++- parallelly-1.32.0/parallelly/man/availableWorkers.Rd | 47 +++- parallelly-1.32.0/parallelly/man/makeClusterPSOCK.Rd | 66 ++++-- parallelly-1.32.0/parallelly/man/parallelly.options.Rd | 54 ++--- parallelly-1.32.0/parallelly/man/supportsMulticore.Rd | 4 parallelly-1.32.0/parallelly/tests/availableCores.R | 17 + parallelly-1.32.0/parallelly/tests/availableWorkers.R | 70 +++++++ 23 files changed, 508 insertions(+), 236 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.4.0 dated 2022-01-05 and 3.5.0 dated 2022-06-07
MSEtool-3.4.0/MSEtool/R/Data_documentation.R |only MSEtool-3.5.0/MSEtool/DESCRIPTION | 16 MSEtool-3.5.0/MSEtool/MD5 | 285 +++++---- MSEtool-3.5.0/MSEtool/NAMESPACE | 13 MSEtool-3.5.0/MSEtool/NEWS.md | 18 MSEtool-3.5.0/MSEtool/R/ASAP2OM.R |only MSEtool-3.5.0/MSEtool/R/B_Low_functions.R | 62 +- MSEtool-3.5.0/MSEtool/R/Class_definitions.R | 73 +- MSEtool-3.5.0/MSEtool/R/DFO.R | 107 --- MSEtool-3.5.0/MSEtool/R/Data_Functions.R | 43 - MSEtool-3.5.0/MSEtool/R/Data_Plotting.R | 2 MSEtool-3.5.0/MSEtool/R/Data_documentation.r |only MSEtool-3.5.0/MSEtool/R/Data_fit_index.R |only MSEtool-3.5.0/MSEtool/R/Data_make_update.R | 256 ++------ MSEtool-3.5.0/MSEtool/R/Fease_Functions.R | 4 MSEtool-3.5.0/MSEtool/R/MMSE_Object.r | 1 MSEtool-3.5.0/MSEtool/R/MMSE_plots.R | 13 MSEtool-3.5.0/MSEtool/R/MOM_import.R | 4 MSEtool-3.5.0/MSEtool/R/MOM_object.r | 8 MSEtool-3.5.0/MSEtool/R/MOM_plots.R |only MSEtool-3.5.0/MSEtool/R/MSE_Plotting.R | 6 MSEtool-3.5.0/MSEtool/R/MSE_Plotting_PMs.R | 20 MSEtool-3.5.0/MSEtool/R/MSE_functions.R | 12 MSEtool-3.5.0/MSEtool/R/Misc_Exported.R | 249 ++++++++ MSEtool-3.5.0/MSEtool/R/Misc_Internal.R | 27 MSEtool-3.5.0/MSEtool/R/OM_Plotting.R | 10 MSEtool-3.5.0/MSEtool/R/OM_functions.R | 271 ++++++++- MSEtool-3.5.0/MSEtool/R/OM_import.R | 7 MSEtool-3.5.0/MSEtool/R/OM_init_doc.R | 296 +++++----- MSEtool-3.5.0/MSEtool/R/OM_plots.R | 16 MSEtool-3.5.0/MSEtool/R/PMobjects.R | 2 MSEtool-3.5.0/MSEtool/R/PMtable.R | 10 MSEtool-3.5.0/MSEtool/R/SS2OM.R | 181 +++--- MSEtool-3.5.0/MSEtool/R/SSinternal.R | 49 + MSEtool-3.5.0/MSEtool/R/SampleOM.R | 68 +- MSEtool-3.5.0/MSEtool/R/Sketch_Functions.R | 8 MSEtool-3.5.0/MSEtool/R/Turing.R | 10 MSEtool-3.5.0/MSEtool/R/VPA2OM.R | 240 +++++++- MSEtool-3.5.0/MSEtool/R/WHAM2OM.R |only MSEtool-3.5.0/MSEtool/R/iSCAM2OM.R | 39 - MSEtool-3.5.0/MSEtool/R/multiMSE.R | 214 +++++-- MSEtool-3.5.0/MSEtool/R/multiMSE_internal.R | 25 MSEtool-3.5.0/MSEtool/R/multi_q_estimation.R | 16 MSEtool-3.5.0/MSEtool/R/popdyn.R | 10 MSEtool-3.5.0/MSEtool/R/popdyn_MICE.R | 11 MSEtool-3.5.0/MSEtool/R/runMSE.R | 121 ++-- MSEtool-3.5.0/MSEtool/R/sysdata.rda |binary MSEtool-3.5.0/MSEtool/R/utils.R | 49 + MSEtool-3.5.0/MSEtool/README.md | 2 MSEtool-3.5.0/MSEtool/build/partial.rdb |binary MSEtool-3.5.0/MSEtool/data/Albacore.rda |binary MSEtool-3.5.0/MSEtool/data/Albacore_TwoFleet.rda |binary MSEtool-3.5.0/MSEtool/data/Atlantic_mackerel.rda |binary MSEtool-3.5.0/MSEtool/data/Blue_shark.rda |binary MSEtool-3.5.0/MSEtool/data/Bluefin_tuna.rda |binary MSEtool-3.5.0/MSEtool/data/Bluefin_tuna_WAtl.rda |binary MSEtool-3.5.0/MSEtool/data/Butterfish.rda |binary MSEtool-3.5.0/MSEtool/data/China_rockfish.rda |binary MSEtool-3.5.0/MSEtool/data/Cobia.rda |binary MSEtool-3.5.0/MSEtool/data/DataDescription.rda |binary MSEtool-3.5.0/MSEtool/data/DataSlots.rda |binary MSEtool-3.5.0/MSEtool/data/DecE_Dom.rda |binary MSEtool-3.5.0/MSEtool/data/DecE_HDom.rda |binary MSEtool-3.5.0/MSEtool/data/DecE_NDom.rda |binary MSEtool-3.5.0/MSEtool/data/Example_datafile.rda |binary MSEtool-3.5.0/MSEtool/data/FlatE_Dom.rda |binary MSEtool-3.5.0/MSEtool/data/FlatE_HDom.rda |binary MSEtool-3.5.0/MSEtool/data/FlatE_NDom.rda |binary MSEtool-3.5.0/MSEtool/data/FleetDescription.rda |binary MSEtool-3.5.0/MSEtool/data/Generic_DecE.rda |binary MSEtool-3.5.0/MSEtool/data/Generic_FlatE.rda |binary MSEtool-3.5.0/MSEtool/data/Generic_Fleet.rda |binary MSEtool-3.5.0/MSEtool/data/Generic_IncE.rda |binary MSEtool-3.5.0/MSEtool/data/Generic_Obs.rda |binary MSEtool-3.5.0/MSEtool/data/Gulf_blue_tilefish.rda |binary MSEtool-3.5.0/MSEtool/data/Herring.rda |binary MSEtool-3.5.0/MSEtool/data/HistDescription.rda |binary MSEtool-3.5.0/MSEtool/data/ImpDescription.rda |binary MSEtool-3.5.0/MSEtool/data/Imprecise_Biased.rda |binary MSEtool-3.5.0/MSEtool/data/Imprecise_Unbiased.rda |binary MSEtool-3.5.0/MSEtool/data/IncE_HDom.rda |binary MSEtool-3.5.0/MSEtool/data/IncE_NDom.rda |binary MSEtool-3.5.0/MSEtool/data/LHdatabase.rda |binary MSEtool-3.5.0/MSEtool/data/Low_Effort_Non_Target.rda |binary MSEtool-3.5.0/MSEtool/data/MSEDescription.rda |binary MSEtool-3.5.0/MSEtool/data/Mackerel.rda |binary MSEtool-3.5.0/MSEtool/data/OMDescription.rda |binary MSEtool-3.5.0/MSEtool/data/ObsDescription.rda |binary MSEtool-3.5.0/MSEtool/data/Overages.rda |binary MSEtool-3.5.0/MSEtool/data/Perfect_Imp.rda |binary MSEtool-3.5.0/MSEtool/data/Perfect_Info.rda |binary MSEtool-3.5.0/MSEtool/data/Porgy.rda |binary MSEtool-3.5.0/MSEtool/data/Precise_Biased.rda |binary MSEtool-3.5.0/MSEtool/data/Precise_Unbiased.rda |binary MSEtool-3.5.0/MSEtool/data/Red_snapper.rda |binary MSEtool-3.5.0/MSEtool/data/ReqData.rda |binary MSEtool-3.5.0/MSEtool/data/Rockfish.rda |binary MSEtool-3.5.0/MSEtool/data/SimulatedData.rda |binary MSEtool-3.5.0/MSEtool/data/Simulation_1.rda |binary MSEtool-3.5.0/MSEtool/data/Snapper.rda |binary MSEtool-3.5.0/MSEtool/data/Sole.rda |binary MSEtool-3.5.0/MSEtool/data/StockDescription.rda |binary MSEtool-3.5.0/MSEtool/data/Target_All_Fish.rda |binary MSEtool-3.5.0/MSEtool/data/Targeting_Small_Fish.rda |binary MSEtool-3.5.0/MSEtool/data/Toothfish.rda |binary MSEtool-3.5.0/MSEtool/data/ourReefFish.rda |binary MSEtool-3.5.0/MSEtool/data/testOM.rda |binary MSEtool-3.5.0/MSEtool/inst/Rmd/OM/OM.Rmd | 8 MSEtool-3.5.0/MSEtool/man/ASAP2OM.Rd |only MSEtool-3.5.0/MSEtool/man/Assess2MOM.Rd |only MSEtool-3.5.0/MSEtool/man/Assess2OM.Rd | 14 MSEtool-3.5.0/MSEtool/man/CheckOM.Rd |only MSEtool-3.5.0/MSEtool/man/Data-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/DataDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/DataSlots.Rd | 2 MSEtool-3.5.0/MSEtool/man/Fleet-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/FleetDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/HistDescription.Rd | 4 MSEtool-3.5.0/MSEtool/man/Imp-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/ImpDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/LH2OM.Rd | 10 MSEtool-3.5.0/MSEtool/man/LHdatabase.Rd | 2 MSEtool-3.5.0/MSEtool/man/MOM-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/MSEDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/OM-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/OMDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/Obs-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/Obs-class.Rd | 2 MSEtool-3.5.0/MSEtool/man/ObsDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/ReqData.Rd | 2 MSEtool-3.5.0/MSEtool/man/SimulatedData.Rd | 2 MSEtool-3.5.0/MSEtool/man/Stock-class-objects.Rd | 2 MSEtool-3.5.0/MSEtool/man/StockDescription.Rd | 2 MSEtool-3.5.0/MSEtool/man/SubCpars.Rd | 25 MSEtool-3.5.0/MSEtool/man/WHAM2OM.Rd |only MSEtool-3.5.0/MSEtool/man/XL2OM.Rd | 20 MSEtool-3.5.0/MSEtool/man/getnIVs.Rd |only MSEtool-3.5.0/MSEtool/man/getq_multi_MICE.Rd | 2 MSEtool-3.5.0/MSEtool/man/hconv.Rd |only MSEtool-3.5.0/MSEtool/man/optYield.Rd | 5 MSEtool-3.5.0/MSEtool/man/plot.MOM.Rd |only MSEtool-3.5.0/MSEtool/man/plotRel.Rd |only MSEtool-3.5.0/MSEtool/man/popdynMICE.Rd | 5 MSEtool-3.5.0/MSEtool/man/qestMICE.Rd | 8 MSEtool-3.5.0/MSEtool/man/runMSE.Rd | 11 MSEtool-3.5.0/MSEtool/src/popddynCPP.cpp | 2 MSEtool-3.5.0/MSEtool/tests/manual/run-manual-tests.R | 17 MSEtool-3.5.0/MSEtool/tests/manual/test-code/test-Data_indices.R |only MSEtool-3.5.0/MSEtool/tests/manual/test-code/test-checkPopDynamics.R | 213 ++++++- MSEtool-3.5.0/MSEtool/tests/manual/test-code/test-cpars_realdata.R | 2 MSEtool-3.5.0/MSEtool/tests/manual/test-code/test-runMSE.R | 4 151 files changed, 2108 insertions(+), 1154 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.2.1 dated 2022-06-01 and 1.2.2 dated 2022-06-07
DESCRIPTION | 18 LICENSE | 4 MD5 | 450 - NAMESPACE | 666 +- NEWS.md | 850 +-- R/00_global_variables.R | 30 R/data.R | 218 R/dev-constructor.R | 178 R/dev-model_descriptions.R | 586 +- R/dev-parse_index.R | 216 R/dev-xregs.R | 664 +- R/dials-adam_params.R | 250 - R/dials-arima_params.R | 206 R/dials-ets_params.R | 282 - R/dials-nnetar_params.R | 74 R/dials-prophet_params.R | 318 - R/dials-temporal_hierarchy_params.R | 80 R/dials-ts_params.R | 114 R/helpers-modeltime_residuals.R | 86 R/helpers-modeltime_table.R | 580 +- R/modeltime-accuracy-table.R | 314 - R/modeltime-accuracy.R | 344 - R/modeltime-calibrate.R | 732 +-- R/modeltime-fit-workflowset.R | 646 +- R/modeltime-forecast-plot.R | 562 +- R/modeltime-forecast.R | 2080 ++++----- R/modeltime-recursive.R | 1387 +++--- R/modeltime-refit.R | 992 ++-- R/modeltime-residuals-plot.R | 298 - R/modeltime-residuals-tests.R | 396 - R/modeltime-residuals.R | 206 R/modeltime-table.R | 220 R/nested-modeltime-forecast.R | 828 +-- R/nested-modeltime_data_prep.R | 642 +- R/nested-modeltime_extractors.R | 256 - R/nested-modeltime_fit.R | 1198 ++--- R/nested-modeltime_refit.R | 844 +-- R/nested-modeltime_select_best.R | 410 - R/parsnip-adam.R | 1464 +++--- R/parsnip-adam_data.R | 868 +-- R/parsnip-arima_boost.R | 1618 +++---- R/parsnip-arima_boost_data.R | 742 +-- R/parsnip-arima_reg.R | 1076 ++-- R/parsnip-arima_reg_data.R | 494 +- R/parsnip-exp_smoothing.R | 1802 +++---- R/parsnip-exp_smoothing_data.R | 754 +-- R/parsnip-naive_reg.R | 1010 ++-- R/parsnip-naive_reg_data.R | 308 - R/parsnip-nnetar_reg.R | 778 +-- R/parsnip-nnetar_reg_data.R | 266 - R/parsnip-prophet_boost.R | 1374 ++--- R/parsnip-prophet_boost_data.R | 496 +- R/parsnip-prophet_reg.R | 1158 ++--- R/parsnip-prophet_reg_data.R | 356 - R/parsnip-seasonal_reg.R | 1348 ++--- R/parsnip-seasonal_reg_data.R | 510 +- R/parsnip-temporal_hierarchy.R | 752 +-- R/parsnip-temporal_hierarchy_data.R | 192 R/parsnip-window_reg.R | 1224 ++--- R/parsnip-window_reg_data.R | 344 - R/tibble-type_sum.R | 66 R/utils-checks-validations.R | 804 +-- R/utils-control-par.R | 1094 ++-- R/utils-is_modeltime.R | 132 R/utils-make_grouped_predictions.R | 112 R/utils-parsnip-helpers.R | 346 - R/utils-pipe.R | 22 R/utils-tidy-eval.R | 94 R/utils-xgboost.R | 166 R/yardstick-metric-sets.R | 552 +- R/zzz.R | 86 README.md | 390 - build/vignette.rds |binary inst/doc/getting-started-with-modeltime.R | 282 - inst/doc/getting-started-with-modeltime.Rmd | 818 +-- inst/doc/getting-started-with-modeltime.html | 2303 +++++----- man/Adam_predict_impl.Rd | 38 man/Arima_fit_impl.Rd | 90 man/Arima_predict_impl.Rd | 38 man/Auto_adam_predict_impl.Rd | 38 man/adam_fit_impl.Rd | 160 man/adam_params.Rd | 166 man/adam_reg.Rd | 586 +- man/add_modeltime_model.Rd | 80 man/arima_boost.Rd | 612 +- man/arima_params.Rd | 112 man/arima_reg.Rd | 502 +- man/arima_xgboost_fit_impl.Rd | 250 - man/arima_xgboost_predict_impl.Rd | 38 man/auto_adam_fit_impl.Rd | 160 man/auto_arima_fit_impl.Rd | 90 man/auto_arima_xgboost_fit_impl.Rd | 370 - man/combine_modeltime_tables.Rd | 144 man/control_modeltime.Rd | 200 man/create_model_grid.Rd | 150 man/create_xreg_recipe.Rd | 136 man/croston_fit_impl.Rd | 42 man/croston_predict_impl.Rd | 38 man/dot_prepare_transform.Rd | 42 man/ets_fit_impl.Rd | 98 man/ets_predict_impl.Rd | 38 man/exp_smoothing.Rd | 678 +- man/exp_smoothing_params.Rd | 144 man/get_arima_description.Rd | 60 man/get_model_description.Rd | 84 man/get_tbats_description.Rd | 38 man/is_calibrated.Rd | 32 man/is_modeltime_model.Rd | 32 man/is_modeltime_table.Rd | 30 man/is_residuals.Rd | 30 man/load_namespace.Rd | 40 man/log_extractors.Rd | 98 man/m750.Rd | 60 man/m750_models.Rd | 68 man/m750_splits.Rd | 60 man/m750_training_resamples.Rd | 72 man/maape.Rd | 34 man/maape_vec.Rd | 40 man/make_ts_splits.Rd | 46 man/mdl_time_forecast.Rd | 106 man/mdl_time_refit.Rd | 64 man/modeltime_accuracy.Rd | 182 man/modeltime_calibrate.Rd | 218 man/modeltime_fit_workflowset.Rd | 138 man/modeltime_forecast.Rd | 458 - man/modeltime_nested_fit.Rd | 130 man/modeltime_nested_forecast.Rd | 142 man/modeltime_nested_refit.Rd | 46 man/modeltime_nested_select_best.Rd | 80 man/modeltime_refit.Rd | 198 man/modeltime_residuals.Rd | 134 man/modeltime_residuals_test.Rd | 222 man/modeltime_table.Rd | 174 man/naive_fit_impl.Rd | 46 man/naive_predict_impl.Rd | 34 man/naive_reg.Rd | 306 - man/new_modeltime_bridge.Rd | 102 man/nnetar_fit_impl.Rd | 102 man/nnetar_params.Rd | 80 man/nnetar_predict_impl.Rd | 38 man/nnetar_reg.Rd | 390 - man/panel_tail.Rd | 68 man/parallel_start.Rd | 106 man/parse_index.Rd | 88 man/pipe.Rd | 24 man/plot_modeltime_forecast.Rd | 248 - man/plot_modeltime_residuals.Rd | 204 man/pluck_modeltime_model.Rd | 74 man/prep_nested.Rd | 254 - man/prophet_boost.Rd | 652 +- man/prophet_fit_impl.Rd | 178 man/prophet_params.Rd | 172 man/prophet_predict_impl.Rd | 38 man/prophet_reg.Rd | 504 +- man/prophet_xgboost_fit_impl.Rd | 306 - man/prophet_xgboost_predict_impl.Rd | 38 man/pull_modeltime_residuals.Rd | 36 man/pull_parsnip_preprocessor.Rd | 34 man/recipe_helpers.Rd | 108 man/recursive.Rd | 442 - man/seasonal_reg.Rd | 392 - man/smooth_fit_impl.Rd | 98 man/smooth_predict_impl.Rd | 38 man/snaive_fit_impl.Rd | 46 man/snaive_predict_impl.Rd | 34 man/stlm_arima_fit_impl.Rd | 70 man/stlm_arima_predict_impl.Rd | 38 man/stlm_ets_fit_impl.Rd | 70 man/stlm_ets_predict_impl.Rd | 38 man/summarize_accuracy_metrics.Rd | 84 man/table_modeltime_accuracy.Rd | 242 - man/tbats_fit_impl.Rd | 76 man/tbats_predict_impl.Rd | 38 man/temporal_hier_fit_impl.Rd | 66 man/temporal_hier_predict_impl.Rd | 38 man/temporal_hierarchy.Rd | 298 - man/temporal_hierarchy_params.Rd | 56 man/theta_fit_impl.Rd | 38 man/theta_predict_impl.Rd | 38 man/tidyeval.Rd | 102 man/time_series_params.Rd | 82 man/type_sum.mdl_time_tbl.Rd | 38 man/update_model_description.Rd | 74 man/update_modeltime_model.Rd | 80 man/window_function_fit_impl.Rd | 66 man/window_function_predict_impl.Rd | 34 man/window_reg.Rd | 420 - man/xgboost_impl.Rd | 160 man/xgboost_predict.Rd | 38 tests/testthat.R | 62 tests/testthat/test-algo-adam_reg-Adam.R | 412 - tests/testthat/test-algo-adam_reg-auto_adam.R | 426 - tests/testthat/test-algo-arima_boost-Arima.R | 578 +- tests/testthat/test-algo-arima_boost-auto_arima.R | 548 +- tests/testthat/test-algo-arima_reg-Arima.R | 416 - tests/testthat/test-algo-arima_reg-auto_arima.R | 384 - tests/testthat/test-algo-exp_smoothing-ets.R | 834 +-- tests/testthat/test-algo-nnetar_reg.R | 450 - tests/testthat/test-algo-prophet_boost.R | 770 +-- tests/testthat/test-algo-prophet_reg.R | 658 +- tests/testthat/test-algo-seasonal_decomp_arima.R | 300 - tests/testthat/test-algo-seasonal_decomp_ets.R | 292 - tests/testthat/test-algo-seasonal_reg_tbats.R | 308 - tests/testthat/test-algo-temporal_hierarchy.R | 268 - tests/testthat/test-algo-window_reg.R | 866 +-- tests/testthat/test-conf_by_id.R | 182 tests/testthat/test-default_accuracy_metric_sets.R | 116 tests/testthat/test-developer-tools-constructor.R | 292 - tests/testthat/test-developer-tools-xregs.R | 124 tests/testthat/test-extended_accuracy_metric_set.R | 114 tests/testthat/test-fit_workflowsets.R | 440 - tests/testthat/test-helpers-combine-modeltime-tables.R | 172 tests/testthat/test-helpers-pull_parsnip_preprocessor.R | 132 tests/testthat/test-helpers-update-modeltime-tables.R | 248 - tests/testthat/test-modeltime_residuals.R | 156 tests/testthat/test-modeltime_table-forecast-accuracy-refitting.R | 970 ++-- tests/testthat/test-modeltime_table-no-calib-refit.R | 240 - tests/testthat/test-nested-modeltime.R | 546 +- tests/testthat/test-panel-data.R | 238 - tests/testthat/test-recursive.R | 674 +- tests/testthat/test-refit-parallel.R | 106 tests/testthat/test-results-accuracy-tables.R | 362 - tests/testthat/test-results-forecast-plots.R | 268 - tests/testthat/test-results-residuals-tests.R | 204 tests/testthat/test-tune_workflows.R | 146 vignettes/getting-started-with-modeltime.Rmd | 818 +-- 226 files changed, 37306 insertions(+), 36960 deletions(-)
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly' and 'polyqtlR' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel Gesteira [aut],
Jeekin Lau [ctb],
Guilherme Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Mollinari [aut]
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Diff between viewpoly versions 0.1.1 dated 2022-01-03 and 0.2.0 dated 2022-06-07
viewpoly-0.1.1/viewpoly/R/golem_utils_server.R |only viewpoly-0.1.1/viewpoly/R/golem_utils_ui.R |only viewpoly-0.1.1/viewpoly/man/inputs.Rd |only viewpoly-0.1.1/viewpoly/man/utils.Rd |only viewpoly-0.1.1/viewpoly/man/viewmap.Rd |only viewpoly-0.1.1/viewpoly/man/viewqtl.Rd |only viewpoly-0.2.0/viewpoly/DESCRIPTION | 12 viewpoly-0.2.0/viewpoly/MD5 | 98 viewpoly-0.2.0/viewpoly/NAMESPACE | 7 viewpoly-0.2.0/viewpoly/NEWS.md | 18 viewpoly-0.2.0/viewpoly/R/app_ui.R | 80 viewpoly-0.2.0/viewpoly/R/functions_map.R | 82 viewpoly-0.2.0/viewpoly/R/functions_qtl.R | 1115 +++++----- viewpoly-0.2.0/viewpoly/R/functions_upload.R | 592 ++--- viewpoly-0.2.0/viewpoly/R/mod_genes_view.R | 307 +- viewpoly-0.2.0/viewpoly/R/mod_map_view.R | 330 +- viewpoly-0.2.0/viewpoly/R/mod_qtl_view.R | 418 ++- viewpoly-0.2.0/viewpoly/R/mod_upload.R | 688 +++--- viewpoly-0.2.0/viewpoly/R/utils_helpers.R | 184 + viewpoly-0.2.0/viewpoly/README.md | 5 viewpoly-0.2.0/viewpoly/build/partial.rdb |binary viewpoly-0.2.0/viewpoly/inst/app.R |only viewpoly-0.2.0/viewpoly/inst/ext/functions4tests.R |only viewpoly-0.2.0/viewpoly/inst/ext/viewmap_tetra.rda |binary viewpoly-0.2.0/viewpoly/inst/ext/viewqtl_tetra.rda |binary viewpoly-0.2.0/viewpoly/man/breeding_values.Rd |only viewpoly-0.2.0/viewpoly/man/calc_homologprob.Rd |only viewpoly-0.2.0/viewpoly/man/check_viewmap.Rd |only viewpoly-0.2.0/viewpoly/man/check_viewpoly.Rd |only viewpoly-0.2.0/viewpoly/man/check_viewqtl.Rd |only viewpoly-0.2.0/viewpoly/man/coord_radar.Rd |only viewpoly-0.2.0/viewpoly/man/data_effects.Rd |only viewpoly-0.2.0/viewpoly/man/dist_prob_to_class.Rd |only viewpoly-0.2.0/viewpoly/man/draw_map_shiny.Rd |only viewpoly-0.2.0/viewpoly/man/filter_non_conforming_classes.Rd |only viewpoly-0.2.0/viewpoly/man/get_LOD.Rd |only viewpoly-0.2.0/viewpoly/man/gg_color_hue.Rd |only viewpoly-0.2.0/viewpoly/man/imf_h.Rd |only viewpoly-0.2.0/viewpoly/man/import_data_from_polymapR.Rd |only viewpoly-0.2.0/viewpoly/man/import_phased_maplist_from_polymapR.Rd |only viewpoly-0.2.0/viewpoly/man/is.prob.data.Rd |only viewpoly-0.2.0/viewpoly/man/map_summary.Rd |only viewpoly-0.2.0/viewpoly/man/mf_h.Rd |only viewpoly-0.2.0/viewpoly/man/mrk_chisq_test.Rd |only viewpoly-0.2.0/viewpoly/man/only_plot_profile.Rd |only viewpoly-0.2.0/viewpoly/man/ph_list_to_matrix.Rd |only viewpoly-0.2.0/viewpoly/man/ph_matrix_to_list.Rd |only viewpoly-0.2.0/viewpoly/man/plot.mappoly.homoprob.Rd |only viewpoly-0.2.0/viewpoly/man/plot_cm_mb.Rd |only viewpoly-0.2.0/viewpoly/man/plot_effects.Rd |only viewpoly-0.2.0/viewpoly/man/plot_map_list.Rd |only viewpoly-0.2.0/viewpoly/man/plot_one_map.Rd |only viewpoly-0.2.0/viewpoly/man/plot_profile.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_MAPpoly.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_QTLpoly.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_diaQTL.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_examples.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_map.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_map_custom_files.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_polymapR.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_polyqtlR.Rd |only viewpoly-0.2.0/viewpoly/man/prepare_qtl_custom_files.Rd |only viewpoly-0.2.0/viewpoly/man/segreg_poly.Rd |only viewpoly-0.2.0/viewpoly/man/select_haplo.Rd |only viewpoly-0.2.0/viewpoly/man/summary_maps.Rd |only viewpoly-0.2.0/viewpoly/tests/testthat.R | 1 viewpoly-0.2.0/viewpoly/tests/testthat/_snaps |only viewpoly-0.2.0/viewpoly/tests/testthat/test-MAPpoly.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-QTLpoly.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-custom_files.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-diaQTL.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-golem-recommended.R | 1 viewpoly-0.2.0/viewpoly/tests/testthat/test-polymapR.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-polyqtlR.R |only viewpoly-0.2.0/viewpoly/tests/testthat/test-tetra_example.R |only 75 files changed, 2411 insertions(+), 1527 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <https://spark.apache.org/>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] ,
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut] ,
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] ,
Wil Davis [ctb],
Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr versions 1.7.6 dated 2022-05-26 and 1.7.7 dated 2022-06-07
sparklyr-1.7.6/sparklyr/R/ml_model_aft_survival_regression.R |only sparklyr-1.7.7/sparklyr/DESCRIPTION | 13 sparklyr-1.7.7/sparklyr/MD5 | 33 - sparklyr-1.7.7/sparklyr/NEWS.md | 6 sparklyr-1.7.7/sparklyr/R/dbplyr-compat.R | 7 sparklyr-1.7.7/sparklyr/R/dbplyr_utils.R | 2 sparklyr-1.7.7/sparklyr/R/dplyr_spark_connection.R | 4 sparklyr-1.7.7/sparklyr/R/dplyr_spark_table.R | 4 sparklyr-1.7.7/sparklyr/R/dplyr_sql.R | 2 sparklyr-1.7.7/sparklyr/R/ml_regression_aft_survival_regression.R | 275 ++++------ sparklyr-1.7.7/sparklyr/R/ml_regression_decision_tree_regressor.R | 175 +----- sparklyr-1.7.7/sparklyr/R/ml_regression_gbt_regressor.R | 191 +----- sparklyr-1.7.7/sparklyr/R/ml_regression_generalized_linear_regression.R | 223 ++------ sparklyr-1.7.7/sparklyr/R/ml_regression_isotonic_regression.R | 117 +--- sparklyr-1.7.7/sparklyr/R/ml_regression_linear_regression.R | 158 +---- sparklyr-1.7.7/sparklyr/R/ml_regression_random_forest_regressor.R | 181 +----- sparklyr-1.7.7/sparklyr/R/ml_utils.R | 95 +++ sparklyr-1.7.7/sparklyr/man/ml_aft_survival_regression.Rd | 13 18 files changed, 512 insertions(+), 987 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.8.0 dated 2022-05-11 and 0.8.1 dated 2022-06-07
pdp-0.8.0/pdp/inst/tinytest/test_partial.R |only pdp-0.8.0/pdp/inst/tinytest/test_pkg_gbm.R |only pdp-0.8.1/pdp/DESCRIPTION | 6 ++-- pdp-0.8.1/pdp/MD5 | 28 ++++++++++------------ pdp-0.8.1/pdp/NEWS.md | 15 +++++++++++ pdp-0.8.1/pdp/R/autoplot.R | 2 - pdp-0.8.1/pdp/R/pardep.R | 34 +++++++++++++-------------- pdp-0.8.1/pdp/R/partial.R | 24 ++++++++----------- pdp-0.8.1/pdp/R/plotPartial.R | 2 - pdp-0.8.1/pdp/inst/doc/pdp-approximate.pdf |binary pdp-0.8.1/pdp/inst/doc/pdp-intro.pdf |binary pdp-0.8.1/pdp/inst/doc/pdp-link-function.pdf |binary pdp-0.8.1/pdp/inst/tinytest/test_pkg_MASS.R | 11 +++++++- pdp-0.8.1/pdp/man/autoplot.partial.Rd | 2 - pdp-0.8.1/pdp/man/partial.Rd | 22 +++++++---------- pdp-0.8.1/pdp/man/plotPartial.Rd | 2 - 16 files changed, 83 insertions(+), 65 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Sæboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.1 dated 2022-01-04 and 0.8.2 dated 2022-06-07
multiblock-0.8.1/multiblock/vignettes/vignette_A_basic.R |only multiblock-0.8.1/multiblock/vignettes/vignette_A_basic.html |only multiblock-0.8.1/multiblock/vignettes/vignette_B_unsupervised.R |only multiblock-0.8.1/multiblock/vignettes/vignette_B_unsupervised.html |only multiblock-0.8.1/multiblock/vignettes/vignette_C_asca.R |only multiblock-0.8.1/multiblock/vignettes/vignette_C_asca.html |only multiblock-0.8.1/multiblock/vignettes/vignette_D_supervised.R |only multiblock-0.8.1/multiblock/vignettes/vignette_D_supervised.html |only multiblock-0.8.1/multiblock/vignettes/vignette_E_complex.R |only multiblock-0.8.1/multiblock/vignettes/vignette_E_complex.html |only multiblock-0.8.1/multiblock/vignettes/vignette_asca.R |only multiblock-0.8.1/multiblock/vignettes/vignette_asca.html |only multiblock-0.8.1/multiblock/vignettes/vignette_basic.R |only multiblock-0.8.1/multiblock/vignettes/vignette_basic.html |only multiblock-0.8.1/multiblock/vignettes/vignette_complex.R |only multiblock-0.8.1/multiblock/vignettes/vignette_complex.html |only multiblock-0.8.1/multiblock/vignettes/vignette_supervised.R |only multiblock-0.8.1/multiblock/vignettes/vignette_supervised.html |only multiblock-0.8.1/multiblock/vignettes/vignette_unsupervised.R |only multiblock-0.8.1/multiblock/vignettes/vignette_unsupervised.html |only multiblock-0.8.2/multiblock/DESCRIPTION | 18 multiblock-0.8.2/multiblock/MD5 | 160 multiblock-0.8.2/multiblock/NAMESPACE | 390 - multiblock-0.8.2/multiblock/NEWS | 38 multiblock-0.8.2/multiblock/R/RcppExports.R | 78 multiblock-0.8.2/multiblock/R/asca.R | 432 - multiblock-0.8.2/multiblock/R/asca_plots.R | 276 - multiblock-0.8.2/multiblock/R/asca_results.R | 170 multiblock-0.8.2/multiblock/R/basic.R | 408 - multiblock-0.8.2/multiblock/R/complex.R | 26 multiblock-0.8.2/multiblock/R/crossprodQ.R | 162 multiblock-0.8.2/multiblock/R/datasets.R | 204 multiblock-0.8.2/multiblock/R/direct_export.R | 102 multiblock-0.8.2/multiblock/R/lpls.R | 792 +-- multiblock-0.8.2/multiblock/R/lplsData.R | 96 multiblock-0.8.2/multiblock/R/lpls_results.R | 642 +- multiblock-0.8.2/multiblock/R/maage.R | 302 - multiblock-0.8.2/multiblock/R/multiblock-package.R | 112 multiblock-0.8.2/multiblock/R/multiblock_plots.R | 660 +- multiblock-0.8.2/multiblock/R/multiblock_results.R | 204 multiblock-0.8.2/multiblock/R/popls.R | 380 - multiblock-0.8.2/multiblock/R/rosa.R | 1832 +++---- multiblock-0.8.2/multiblock/R/rosaCV.R | 276 - multiblock-0.8.2/multiblock/R/rosa_plots.R | 216 multiblock-0.8.2/multiblock/R/rosa_results.R | 744 +- multiblock-0.8.2/multiblock/R/sopls.R | 1038 ++-- multiblock-0.8.2/multiblock/R/sopls_crossvalidation.R | 290 - multiblock-0.8.2/multiblock/R/sopls_plots.R | 746 +- multiblock-0.8.2/multiblock/R/sopls_pm.R | 1047 ++-- multiblock-0.8.2/multiblock/R/sopls_results.R | 898 +-- multiblock-0.8.2/multiblock/R/supervised.R | 688 +- multiblock-0.8.2/multiblock/R/unsupervised.R | 1756 +++--- multiblock-0.8.2/multiblock/R/utilities.R | 466 - multiblock-0.8.2/multiblock/README.md | 76 multiblock-0.8.2/multiblock/build/vignette.rds |binary multiblock-0.8.2/multiblock/inst/doc/vignette_A_data.R | 220 multiblock-0.8.2/multiblock/inst/doc/vignette_A_data.Rmd | 330 - multiblock-0.8.2/multiblock/inst/doc/vignette_A_data.html | 1079 ++-- multiblock-0.8.2/multiblock/inst/doc/vignette_B_basic.R | 118 multiblock-0.8.2/multiblock/inst/doc/vignette_B_basic.Rmd | 238 multiblock-0.8.2/multiblock/inst/doc/vignette_B_basic.html | 710 +- multiblock-0.8.2/multiblock/inst/doc/vignette_C_unsupervised.R | 168 multiblock-0.8.2/multiblock/inst/doc/vignette_C_unsupervised.Rmd | 402 - multiblock-0.8.2/multiblock/inst/doc/vignette_C_unsupervised.html | 921 ++- multiblock-0.8.2/multiblock/inst/doc/vignette_D_asca.R | 98 multiblock-0.8.2/multiblock/inst/doc/vignette_D_asca.Rmd | 190 multiblock-0.8.2/multiblock/inst/doc/vignette_D_asca.html | 718 +- multiblock-0.8.2/multiblock/inst/doc/vignette_E_supervised.R | 464 - 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multiblock-0.8.2/multiblock/vignettes/vignette_D_asca.Rmd | 190 multiblock-0.8.2/multiblock/vignettes/vignette_E_supervised.Rmd | 852 +-- multiblock-0.8.2/multiblock/vignettes/vignette_E_supervised.tex | 2532 +++++----- multiblock-0.8.2/multiblock/vignettes/vignette_F_complex.Rmd | 340 - 91 files changed, 16266 insertions(+), 14767 deletions(-)
Title: Maximum Approximate Bernstein/Beta Likelihood Estimation
Description: Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.
Author: Zhong Guan [aut, cre]
Maintainer: Zhong Guan <zguan@iusb.edu>
Diff between mable versions 3.0.1 dated 2021-04-16 and 3.1.0 dated 2022-06-07
mable-3.0.1/mable/vignettes/mable.html |only mable-3.1.0/mable/DESCRIPTION | 13 mable-3.1.0/mable/MD5 | 45 mable-3.1.0/mable/NAMESPACE | 2 mable-3.1.0/mable/R/mable-aft-model.r | 128 +- mable-3.1.0/mable/R/mable-dr.r | 88 + mable-3.1.0/mable/R/mable-multivar.r | 22 mable-3.1.0/mable/R/mable.r | 555 +++++++++-- mable-3.1.0/mable/build/vignette.rds |binary mable-3.1.0/mable/inst/doc/mable.R | 1558 ++++++++++++++++++++++++++++++- mable-3.1.0/mable/inst/doc/mable.Rmd | 1575 +++++++++++++++++++++++++++++++- mable-3.1.0/mable/inst/doc/mable.pdf |binary mable-3.1.0/mable/man/mable.Rd | 12 mable-3.1.0/mable/man/mable.aft.Rd | 10 mable-3.1.0/mable/man/mable.dr.Rd | 10 mable-3.1.0/mable/man/mable.mvar.Rd | 20 mable-3.1.0/mable/man/maple.aft.Rd | 12 mable-3.1.0/mable/man/maple.dr.Rd | 10 mable-3.1.0/mable/man/maple.dr.group.Rd | 2 mable-3.1.0/mable/man/momodem.Rd |only mable-3.1.0/mable/man/optimable.Rd |only mable-3.1.0/mable/man/plot.mable.Rd | 3 mable-3.1.0/mable/src/mable.c | 202 ++-- mable-3.1.0/mable/src/mable_init.c | 29 mable-3.1.0/mable/vignettes/mable.Rmd | 1575 +++++++++++++++++++++++++++++++- 25 files changed, 5428 insertions(+), 443 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Edward Lakatos (1986) <doi:10.1016/0197-2456(86)90047-4> and Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The inverse normal combination method due to Lu Cui, H. M. James Hung, and Sue-Jane Wang (1999) <doi:10.1111/j.0006-341x.1999.00853.x> is used in the simulation study to accommodate the information time not proportional to the total number of events for weighted log-rank tests.
Author: Kaifeng Lu
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.1.3 dated 2022-02-09 and 0.1.4 dated 2022-06-07
DESCRIPTION | 8 MD5 | 51 +- NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 135 +++++- R/print_lrpower.R | 4 README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/fixed_follow-up.html | 255 ++++++++++++- inst/doc/group_sequential_simulation.html | 243 +++++++++++- inst/doc/lakatos_schoenfeld.html | 235 +++++++++++- inst/doc/maxcombo.R | 4 inst/doc/maxcombo.Rmd | 4 inst/doc/maxcombo.html | 319 ++++++++++++++-- inst/doc/non-proportional_hazards.html | 236 +++++++++++- inst/doc/stratified.html | 236 +++++++++++- man/lrsamplesize.Rd | 16 man/lrsim.Rd | 3 man/lrstat.Rd | 11 man/lrstat1.Rd |only man/qtpwexp.Rd | 9 src/RcppExports.cpp | 67 ++- src/lrsim.cpp | 89 ---- src/lrstat.cpp | 582 +++++++++++++++++++----------- src/utilities.cpp | 68 +++ src/utilities.h | 7 vignettes/maxcombo.Rmd | 4 28 files changed, 2097 insertions(+), 490 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'ped suite' collection of packages for pedigree analysis.
A detailed presentation of the 'ped suite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 1.4.0 dated 2021-07-24 and 1.5.0 dated 2022-06-07
DESCRIPTION | 17 - MD5 | 48 ++--- NEWS.md | 17 + R/estimateCoeffs.R | 27 ++- R/genedrop.R | 77 +++++--- R/haploDraw.R | 120 ++++++++++--- R/ibdsim.R | 50 +++-- R/map_constructors.R | 191 +++++++++++++++------- R/map_utils.R | 27 +++ R/meiosis.R | 5 R/profileSimIBD.R | 140 +++++++++------- R/segment_utils.R | 78 ++++++-- R/sysdata.rda |binary R/utils.R | 5 README.md | 22 +- build/partial.rdb |binary man/estimateCoeffs.Rd | 9 - man/figures/README-ibdsim2-example-distplot-1.png |binary man/figures/README-ibdsim2-example-ped-1.png |binary man/haploDraw.Rd | 25 ++ man/ibdsim.Rd | 14 + man/loadMap.Rd | 39 +++- man/profileSimIBD.Rd | 45 +++-- man/uniformMap.Rd | 18 +- tests/testthat/test-maps.R | 16 + 25 files changed, 688 insertions(+), 302 deletions(-)
Title: Bayesian Inference for Neyman-Scott Point Processes
Description: The Bayesian MCMC estimation of parameters for Thomas-type cluster
point process with various inhomogeneities. It allows for inhomogeneity in
(i) distribution of parent points, (ii) mean number of points in a cluster,
(iii) cluster spread. The package also allows for the Bayesian MCMC
algorithm for the homogeneous generalized Thomas process. The cluster size
is allowed to have a variance that is greater or less than the expected
value (cluster sizes are over or under dispersed). Details are described in
Dvořák, Remeš, Beránek & Mrkvička (2022) <arXiv: 10.48550/arXiv.2205.07946>.
Author: Mrkvicka Tomas [aut],
Dvorak Jiri [aut],
Beranek Ladislav [aut],
Remes Radim [aut, cre]
Maintainer: Remes Radim <inrem@jcu.cz>
Diff between binspp versions 0.1.18 dated 2022-05-27 and 0.1.20 dated 2022-06-07
binspp-0.1.18/binspp/inst |only binspp-0.1.20/binspp/DESCRIPTION | 10 +- binspp-0.1.20/binspp/MD5 | 18 ++-- binspp-0.1.20/binspp/R/binspp_auxiliary.R | 14 ++- binspp-0.1.20/binspp/R/rgtp.R | 23 +++--- binspp-0.1.20/binspp/man/estintp.Rd | 14 ++- binspp-0.1.20/binspp/man/rgtp.Rd | 18 ++-- binspp-0.1.20/binspp/src/Binspp_core.cpp | 112 +++++++++++++++--------------- binspp-0.1.20/binspp/src/Makevars |only binspp-0.1.20/binspp/src/par_updates.cpp | 7 - binspp-0.1.20/binspp/src/poit_updates.cpp | 1 11 files changed, 112 insertions(+), 105 deletions(-)
Title: Retrieve Archived Web Pages from the 'Internet Archive'
Description: Scraping content from archived web pages stored in
the 'Internet Archive' (<https://archive.org>) using a systematic
workflow. Get an overview of the mementos available from the
respective homepage, retrieve the Urls and links of the page and
finally scrape the content. The final output is stored in tibbles,
which can be then easily used for further analysis.
Author: Konstantin Gavras [aut] ,
Lukas Isermann [aut, cre]
Maintainer: Lukas Isermann <lukas.isermann@uni-mannheim.de>
Diff between archiveRetriever versions 0.1.1 dated 2022-03-03 and 0.1.2 dated 2022-06-07
DESCRIPTION | 12 ++++----- MD5 | 16 ++++++------ NEWS.md | 9 ++++++ R/retrieve_links.R | 2 - R/scrape_urls.R | 44 ++++++++++++++++++++++++++++------ README.md | 21 ++++++++-------- man/figures/archiveRetriever_logo.png |only man/figures/logo.png |only man/scrape_urls.Rd | 1 tests/testthat/test_scrape_urls.R | 27 ++++++++++++++++++++ 10 files changed, 101 insertions(+), 31 deletions(-)
More information about archiveRetriever at CRAN
Permanent link
Title: Phrase Mining
Description: Functions to extract and handle commonly occurring principal phrases
obtained from collections of texts.
Author: Ellie Small [aut, cre]
Maintainer: Ellie Small <esmall1@drew.edu>
Diff between phm versions 0.1.2 dated 2020-06-24 and 1.1.0 dated 2022-06-07
phm-0.1.2/phm/R/as.matrix.phraseDoc.R |only phm-1.1.0/phm/DESCRIPTION | 15 - phm-1.1.0/phm/MD5 | 47 +++-- phm-1.1.0/phm/NAMESPACE | 20 ++ phm-1.1.0/phm/R/DFSource.R |only phm-1.1.0/phm/R/bestDocs.R |only phm-1.1.0/phm/R/cluster.R |only phm-1.1.0/phm/R/distance.R |only phm-1.1.0/phm/R/freqPhrases.R | 13 - phm-1.1.0/phm/R/getDocs.R | 94 ++++++++-- phm-1.1.0/phm/R/getPubMed.R |only phm-1.1.0/phm/R/phraseDoc.R | 290 +++++++++++++++++++------------ phm-1.1.0/phm/R/removePhrases.R | 14 - phm-1.1.0/phm/build |only phm-1.1.0/phm/inst |only phm-1.1.0/phm/man/DFSource.Rd |only phm-1.1.0/phm/man/as.matrix.phraseDoc.Rd | 14 + phm-1.1.0/phm/man/bestDocs.Rd |only phm-1.1.0/phm/man/canberra.Rd |only phm-1.1.0/phm/man/distMatrix.Rd |only phm-1.1.0/phm/man/getDocs.Rd | 5 phm-1.1.0/phm/man/getElem.DFSource.Rd |only phm-1.1.0/phm/man/getPhrases.Rd |only phm-1.1.0/phm/man/getPubMed.Rd |only phm-1.1.0/phm/man/phm-package.Rd |only phm-1.1.0/phm/man/phraseDoc.Rd | 24 +- phm-1.1.0/phm/man/print.phraseDoc.Rd |only phm-1.1.0/phm/man/print.textCluster.Rd |only phm-1.1.0/phm/man/readDF.Rd |only phm-1.1.0/phm/man/showCluster.Rd |only phm-1.1.0/phm/man/stopEndWords.Rd |only phm-1.1.0/phm/man/stopPhrases.Rd |only phm-1.1.0/phm/man/stopStartWords.Rd |only phm-1.1.0/phm/man/textCluster.Rd |only phm-1.1.0/phm/man/textDist.Rd |only phm-1.1.0/phm/man/textDistMatrix.Rd |only phm-1.1.0/phm/vignettes |only 37 files changed, 377 insertions(+), 159 deletions(-)
Title: Imports Datasets from BCB (Central Bank of Brazil) using Its
Official API
Description: Downloads and organizes datasets using BCB's API <https://www.bcb.gov.br/>. Offers options for caching with the 'memoise' package and
, multicore/multisession with 'furrr' and format of output data (long/wide).
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetBCBData versions 0.6 dated 2021-01-21 and 0.7.0 dated 2022-06-07
GetBCBData-0.6/GetBCBData/man/gbcbd_get_JSON_fct.Rd |only GetBCBData-0.6/GetBCBData/man/gbcbd_get_default_cache_folder.Rd |only GetBCBData-0.6/GetBCBData/man/gbcbd_get_single_series.Rd |only GetBCBData-0.6/GetBCBData/man/gbcbd_message.Rd |only GetBCBData-0.6/GetBCBData/man/gbcbd_test_internet.Rd |only GetBCBData-0.7.0/GetBCBData/DESCRIPTION | 17 GetBCBData-0.7.0/GetBCBData/MD5 | 27 - GetBCBData-0.7.0/GetBCBData/NAMESPACE | 5 GetBCBData-0.7.0/GetBCBData/NEWS.md | 6 GetBCBData-0.7.0/GetBCBData/R/gbcbd_get_series.R | 36 - GetBCBData-0.7.0/GetBCBData/R/gbcbd_utils.R | 34 - GetBCBData-0.7.0/GetBCBData/README.md | 3 GetBCBData-0.7.0/GetBCBData/build/vignette.rds |binary GetBCBData-0.7.0/GetBCBData/inst/doc/GetBCBData-vignette.Rmd | 4 GetBCBData-0.7.0/GetBCBData/inst/doc/GetBCBData-vignette.html | 236 +++++++++- GetBCBData-0.7.0/GetBCBData/tests |only GetBCBData-0.7.0/GetBCBData/vignettes/GetBCBData-vignette.Rmd | 4 17 files changed, 273 insertions(+), 99 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 0.0.17 dated 2022-05-18 and 0.0.18 dated 2022-06-07
DESCRIPTION | 9 MD5 | 30 - NAMESPACE | 2 NEWS | 3 R/di_iterate.R | 105 +++- inst/doc/DI-On-Long-Summarized-Data.html | 25 - inst/doc/Intersectionality.html | 157 +++---- inst/doc/Multi-Ethnicity.Rmd | 4 inst/doc/Multi-Ethnicity.html | 261 +++++------ inst/doc/Scaling-DI-Calculations.R | 44 + inst/doc/Scaling-DI-Calculations.Rmd | 60 ++ inst/doc/Scaling-DI-Calculations.html | 693 ++++++++++++++++--------------- inst/doc/Tutorial.html | 59 +- man/di_iterate.Rd | 11 vignettes/Multi-Ethnicity.Rmd | 4 vignettes/Scaling-DI-Calculations.Rmd | 60 ++ 16 files changed, 904 insertions(+), 623 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.4 dated 2022-05-29 and 0.1.5 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 3 +++ R/chp12.R | 4 ++-- R/chp2.R | 8 +++++--- R/chp3.R | 1 - R/chp5.6.7.R | 44 +++++++++++++++++++++----------------------- R/chp7.power.R | 4 ++-- inst/example/Chapter12.R | 18 ++++++------------ inst/example/LDS_C12.R | 4 +++- inst/example/LDS_C13.R | 3 ++- inst/example/LDS_chp7.R | 20 ++++++++------------ inst/example/LDS_chp8.R | 7 +++---- man/Chapter05to07.Rd | 42 ++++++++++++++++++++---------------------- man/Chapter07_power.Rd | 4 ++-- man/Chapter12.Rd | 22 ++++++++-------------- 16 files changed, 104 insertions(+), 118 deletions(-)
More information about DanielBiostatistics10th at CRAN
Permanent link
Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva [aut, cre]
,
Renato Paiva de Lima [aut]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between soilphysics versions 4.1 dated 2021-11-30 and 5.0 dated 2022-06-07
DESCRIPTION | 10 MD5 | 40 - NAMESPACE | 12 NEWS | 6 R/WRC_App.R |only R/fitsoilwater_App.r | 1480 +++++++++++++++++++------------------- R/maxcurv.R | 56 - inst/doc/vignette.html | 4 man/LLWR_App.Rd | 40 - man/LLWR_LLMPR_App.Rd | 40 - man/PredComp.Rd | 40 - man/WRC_App.Rd |only man/aggreg.stability.Rd | 26 man/aggreg.stability_App.Rd | 40 - man/fitsoilwater_App.Rd | 40 - man/particle.sedimentation_App.Rd | 40 - man/r_App.Rd | 40 - man/sigmaP.Rd | 12 man/simSigmaP.Rd | 15 man/soilDeformation.Rd | 42 - man/soilStrength.Rd | 48 - man/soilphysics-package.Rd | 4 22 files changed, 1045 insertions(+), 990 deletions(-)
Title: Spatial and Spatio-Temporal Semiparametric Regression Models
with Spatial Lags
Description: Estimation and inference of spatial and spatio-temporal
semiparametric models including spatial or spatio-temporal non-parametric
trends, parametric and non-parametric covariates and, possibly, a spatial
lag for the dependent variable and temporal correlation in the noise.
The spatio-temporal trend can be decomposed in ANOVA way including main and
interaction functional terms. Use of SAP algorithm to estimate the spatial
or spatio-temporal trend and non-parametric covariates. The methodology of
these models can be found in next references
Basile, R. et al. (2014), <doi:10.1016/j.jedc.2014.06.011>;
Rodriguez-Alvarez, M.X. et al. (2015) <doi:10.1007/s11222-014-9464-2> and,
particularly referred to the focus of the package, Minguez, R.,
Basile, R. and Durban, M. (2020) <doi:10.1007/s10260-019-00492-8>.
Author: Roman Minguez [aut, cre] ,
Roberto Basile [aut] ,
Maria Durban [aut] ,
Gonzalo Espana-Heredia [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between pspatreg versions 1.0.2 dated 2022-04-28 and 1.0.3 dated 2022-06-07
pspatreg-1.0.2/pspatreg/R/MM_basis.R |only pspatreg-1.0.2/pspatreg/R/buildXZ.R |only pspatreg-1.0.3/pspatreg/DESCRIPTION | 10 pspatreg-1.0.3/pspatreg/MD5 | 128 - pspatreg-1.0.3/pspatreg/NAMESPACE | 6 pspatreg-1.0.3/pspatreg/R/bspline.R | 2 pspatreg-1.0.3/pspatreg/R/build_G.R | 4 pspatreg-1.0.3/pspatreg/R/fit_pspat.R | 197 +- pspatreg-1.0.3/pspatreg/R/fit_terms.R | 316 ++- pspatreg-1.0.3/pspatreg/R/impactsnopar.R | 81 pspatreg-1.0.3/pspatreg/R/impactspar.R | 14 pspatreg-1.0.3/pspatreg/R/llik_reml.R | 28 pspatreg-1.0.3/pspatreg/R/methods_pspatreg.R | 67 pspatreg-1.0.3/pspatreg/R/package-pspatreg.R | 10 pspatreg-1.0.3/pspatreg/R/plot_impactsnopar.R | 62 pspatreg-1.0.3/pspatreg/R/plot_sp2d.R | 48 pspatreg-1.0.3/pspatreg/R/plot_terms.R | 182 +- pspatreg-1.0.3/pspatreg/R/pspatfit.R | 470 ++--- pspatreg-1.0.3/pspatreg/R/pspl_functions.R | 397 ++-- pspatreg-1.0.3/pspatreg/R/summary.pspatreg.R | 35 pspatreg-1.0.3/pspatreg/R/update_tau.R | 52 pspatreg-1.0.3/pspatreg/build/vignette.rds |binary pspatreg-1.0.3/pspatreg/inst/doc/A_pspatregPackage.html | 4 pspatreg-1.0.3/pspatreg/inst/doc/B_Examples_pspatreg_CS_data.Rmd | 846 +++++---- pspatreg-1.0.3/pspatreg/inst/doc/B_Examples_pspatreg_CS_data.html | 858 +++++----- pspatreg-1.0.3/pspatreg/inst/doc/C_Examples_pspatreg_Panel_data.Rmd | 540 ++---- pspatreg-1.0.3/pspatreg/inst/doc/C_Examples_pspatreg_Panel_data.html | 556 ++---- pspatreg-1.0.3/pspatreg/man/fit_terms.Rd | 13 pspatreg-1.0.3/pspatreg/man/impactsnopar.Rd | 57 pspatreg-1.0.3/pspatreg/man/impactspar.Rd | 14 pspatreg-1.0.3/pspatreg/man/map_it.Rd | 48 pspatreg-1.0.3/pspatreg/man/methods_pspatreg.Rd | 67 pspatreg-1.0.3/pspatreg/man/plot_impactsnopar.Rd | 60 pspatreg-1.0.3/pspatreg/man/plot_sp2d.Rd | 36 pspatreg-1.0.3/pspatreg/man/plot_terms.Rd | 75 pspatreg-1.0.3/pspatreg/man/pspatfit.Rd | 346 +--- pspatreg-1.0.3/pspatreg/man/pspatreg.Rd | 2 pspatreg-1.0.3/pspatreg/man/pspl_terms.Rd | 144 + pspatreg-1.0.3/pspatreg/vignettes/B_Examples_pspatreg_CS_data.Rmd | 846 +++++---- pspatreg-1.0.3/pspatreg/vignettes/B_Examples_pspatreg_CS_data.Rmd.orig | 2 pspatreg-1.0.3/pspatreg/vignettes/C_Examples_pspatreg_Panel_data.Rmd | 540 ++---- pspatreg-1.0.3/pspatreg/vignettes/C_Examples_pspatreg_Panel_data.Rmd.orig | 9 pspatreg-1.0.3/pspatreg/vignettes/plot2dpoints_anova_ames-1-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/plot2dpoints_anova_ames-2-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/plot2dpoints_anova_ames-3-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/plot2dpoints_anova_ames-4-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/plot2dpoints_noanova_ames-1-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-19-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-19-2-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-21-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-21-2-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-22-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-22-2-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-22-3-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-23-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-23-2-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-23-3-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-23-4-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-24-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-25-1-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-25-2-vignetteC.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-31-1-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-31-2-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-31-3-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-7-1-vignetteB.png |binary pspatreg-1.0.3/pspatreg/vignettes/unnamed-chunk-7-2-vignetteB.png |binary 66 files changed, 3710 insertions(+), 3462 deletions(-)
Title: Flexible Mixture Modeling
Description: A general framework for finite mixtures of regression
models using the EM algorithm is implemented. The E-step and all
data handling are provided, while the M-step can be supplied by the
user to easily define new models. Existing drivers implement
mixtures of standard linear models, generalized linear models and
model-based clustering.
Author: Bettina Gruen [aut, cre] ,
Friedrich Leisch [aut] ,
Deepayan Sarkar [ctb] ,
Frederic Mortier [ctb],
Nicolas Picard [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexmix versions 2.3-17 dated 2020-10-12 and 2.3-18 dated 2022-06-07
DESCRIPTION | 6 +-- MD5 | 76 +++++++++++++++++++-------------------- R/lmmc.R | 5 +- build/vignette.rds |binary data/BregFix.RData |binary data/Mehta.RData |binary data/NPreg.RData |binary data/Nclus.RData |binary data/NregFix.RData |binary data/betablocker.RData |binary data/bioChemists.RData |binary data/candy.RData |binary data/dmft.RData |binary data/fabricfault.RData |binary data/patent.RData |binary data/seizure.RData |binary data/tribolium.RData |binary data/trypanosome.RData |binary data/whiskey.RData |binary inst/CITATION | 4 -- inst/NEWS.Rd | 11 +++++ inst/doc/bootstrapping.pdf |binary inst/doc/flexmix-intro.pdf |binary inst/doc/mixture-regressions.pdf |binary inst/doc/regression-examples.pdf |binary man/EIC.Rd | 4 +- man/FLXMRcondlogit.Rd | 2 - man/FLXMRlmer.Rd | 3 + man/FLXMRlmmc.Rd | 2 - man/FLXMRmgcv.Rd | 2 - man/FLXMRmultinom.Rd | 2 - man/FLXMRrobglm.Rd | 4 +- man/FLXMRziglm.Rd | 4 +- man/FLXglm.Rd | 4 +- man/FLXglmFix.Rd | 5 +- man/FLXmodel-class.Rd | 11 +++++ man/patent.Rd | 4 +- vignettes/flexmix.bib | 2 - vignettes/mixture.bib | 4 +- 39 files changed, 86 insertions(+), 69 deletions(-)
Title: Observed-Score Linking and Equating
Description: Contains methods for observed-score linking
and equating under the single-group, equivalent-groups,
and nonequivalent-groups with anchor test(s) designs.
Equating types include identity, mean, linear, general
linear, equipercentile, circle-arc, and composites of
these. Equating methods include synthetic, nominal
weights, Tucker, Levine observed score, Levine true
score, Braun/Holland, frequency estimation, and chained
equating. Plotting and summary methods, and methods for
multivariate presmoothing and bootstrap error estimation
are also provided.
Author: Anthony Albano <tony.d.albano@gmail.com>
Maintainer: Anthony Albano <tony.d.albano@gmail.com>
Diff between equate versions 2.0.7 dated 2018-04-08 and 2.0.8 dated 2022-06-07
equate-2.0.7/equate/inst/doc/equate-jss.Rnw |only equate-2.0.7/equate/inst/doc/equate-jss.pdf |only equate-2.0.7/equate/vignettes/equate-jss.Rnw |only equate-2.0.7/equate/vignettes/upgreek.sty |only equate-2.0.8/equate/DESCRIPTION | 13 equate-2.0.8/equate/MD5 | 61 +- equate-2.0.8/equate/NAMESPACE | 1 equate-2.0.8/equate/NEWS | 9 equate-2.0.8/equate/NEWS.md | 265 +++++++----- equate-2.0.8/equate/R/ACTmath.R | 2 equate-2.0.8/equate/R/KBneat.R | 2 equate-2.0.8/equate/R/PISA.R | 9 equate-2.0.8/equate/R/bootstrap.R | 30 - equate-2.0.8/equate/R/equate-package.R | 4 equate-2.0.8/equate/R/equate.R | 2 equate-2.0.8/equate/R/presmoothing.R | 12 equate-2.0.8/equate/R/sample.R |only equate-2.0.8/equate/build/vignette.rds |binary equate-2.0.8/equate/inst/doc/equate-jss.R | 328 ++------------- equate-2.0.8/equate/inst/doc/equate-jss.Rmd |only equate-2.0.8/equate/inst/doc/equate-jss.html |only equate-2.0.8/equate/man/ACTmath.Rd | 8 equate-2.0.8/equate/man/KBneat.Rd | 8 equate-2.0.8/equate/man/PISA.Rd | 15 equate-2.0.8/equate/man/bootstrap.Rd | 14 equate-2.0.8/equate/man/composite.Rd | 6 equate-2.0.8/equate/man/equate-package.Rd | 4 equate-2.0.8/equate/man/equate.Rd | 20 equate-2.0.8/equate/man/freqtab.Rd | 3 equate-2.0.8/equate/man/plot.bootstrap.Rd | 27 + equate-2.0.8/equate/man/plot.equate.Rd | 28 + equate-2.0.8/equate/man/plot.freqtab.Rd | 15 equate-2.0.8/equate/man/presmoothing.Rd | 41 + equate-2.0.8/equate/man/sample.freqtab.Rd |only equate-2.0.8/equate/vignettes/equate-jss.Rmd |only equate-2.0.8/equate/vignettes/equatebibfile.bib | 519 +++++++++++------------- 36 files changed, 690 insertions(+), 756 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.3 dated 2022-03-23 and 2.3.1 dated 2022-06-07
DESCRIPTION | 9 +-- MD5 | 22 ++++---- NEWS.md | 18 ++++--- R/Rdo2Rdf.R | 2 R/bib.R | 16 ++++++ build/partial.rdb |binary inst/REFERENCES.bib | 13 +++++ inst/auto/REFERENCES.el | 3 - inst/doc/Inserting_bibtex_references.pdf |binary inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary man/insert_citeOnly.Rd | 45 +++++++----------- tests/testthat/test-bib.R | 7 ++ 12 files changed, 83 insertions(+), 52 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.
Author: Lampros Mouselimis [aut, cre] ,
Sight Machine [cph] ,
Johannes Buchner [cph] ,
Mohammad Haghighat [cph] ,
Radhakrishna Achanta [cph] )
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.2.1 dated 2022-01-27 and 1.2.2 dated 2022-06-07
DESCRIPTION | 9 +++--- MD5 | 24 ++++++++-------- NEWS.md | 5 +++ R/gabor_feature_extraction.R | 24 ++++++++++++---- README.md | 3 -- inst/doc/Gabor_Feature_Extraction.Rmd | 2 - inst/doc/Gabor_Feature_Extraction.html | 7 ++-- inst/doc/Image_segmentation_superpixels_clustering.html | 5 ++- inst/doc/The_OpenImageR_package.Rmd | 4 +- inst/doc/The_OpenImageR_package.html | 23 ++++++++------- man/GaborFeatureExtract.Rd | 12 +++++++- vignettes/Gabor_Feature_Extraction.Rmd | 2 - vignettes/The_OpenImageR_package.Rmd | 4 +- 13 files changed, 77 insertions(+), 47 deletions(-)
Title: Resampling Tools for Time Series Forecasting
Description: A 'modeltime' extension that implements forecast resampling tools
that assess time-based model performance and stability for a single time series,
panel data, and cross-sectional time series analysis.
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime.resample versions 0.2.0 dated 2021-03-14 and 0.2.1 dated 2022-06-07
DESCRIPTION | 10 MD5 | 21 - NEWS.md | 6 R/modeltime_fit_resamples.R | 7 R/modeltime_resample_accuracy.R | 28 - README.md | 133 ++++--- inst/doc/getting-started.html | 527 ++++++++++++++++++++++------ inst/doc/panel-data.html | 621 ++++++++++++++++++++++++++-------- man/figures/modeltime_ecosystem.jpg |only man/m750_training_resamples_fitted.Rd | 2 man/modeltime_resample_accuracy.Rd | 2 man/plot_modeltime_resamples.Rd | 2 12 files changed, 1010 insertions(+), 349 deletions(-)
More information about modeltime.resample at CRAN
Permanent link
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 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 1.2 dated 2022-05-18 and 1.3 dated 2022-06-07
DESCRIPTION | 8 MD5 | 22 - R/UFA_profile_visualizer_xlsxAnalyzer.R | 40 +- R/UFA_score_function_optimization_xlsxAnalyzer.R | 45 --- R/UFA_workflow.R | 43 +- R/UFA_xlsxAnalyzer.R | 69 +--- R/aligned_molecular_formula_annotator.R | 5 R/isotopic_profile_molecular_formula_feeder.R | 342 ++++++++++++----------- R/molecular_formulas_source_IPDB.R | 6 R/zero_score_function.R | 6 build/partial.rdb |binary inst/extdata/UFA_parameters.xlsx |binary 12 files changed, 295 insertions(+), 291 deletions(-)
Title: Gaussian Graphical Models Using Ridge Penalty Followed by
Thresholding and Reestimation
Description: Estimation of partial correlation matrix using ridge penalty
followed by thresholding and reestimation. Under multivariate Gaussian
assumption, the matrix constitutes an Gaussian graphical model (GGM).
Author: Min Jin Ha [aut, cre], Shannon T. Holloway [ctb]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between GGMridge versions 1.1 dated 2016-02-02 and 1.2 dated 2022-06-07
DESCRIPTION | 16 +++++++------ MD5 | 4 +-- man/GGMridge-package.Rd | 56 ++++++++++++++++++++++++------------------------ 3 files changed, 39 insertions(+), 37 deletions(-)
Title: Force Measurement Analyses
Description: For cleaning and analyses of animal closing force measurements.
'forceR' was initially written and optimized to deal with insect bite force
measurements, but can be used for any time series. Includes a full workflow
to load, plot and crop data, correct amplifier and baseline drifts,
identify individual peak shapes (bites), rescale (normalize) peak curves,
and find best polynomial fits to describe and analyze force curve shapes.
Author: Peter T. Ruehr <peter.ruehr@gmail.com>
Maintainer: Peter T. Ruehr <peter.ruehr@gmail.com>
Diff between forceR versions 1.0.14 dated 2022-05-10 and 1.0.15 dated 2022-06-07
DESCRIPTION | 8 MD5 | 39 - NAMESPACE | 3 NEWS.md | 33 - R/general.R | 1 R/normalization.R | 31 - R/peak_finding.R | 185 +++++- R/plotting.R | 12 R/polynomial.R | 5 R/time_series_manipulations.R | 38 - README.md | 8 inst/CITATION | 4 inst/doc/forceR.R | 29 - inst/doc/forceR.Rmd | 35 - inst/doc/forceR.html | 1110 ++++++++++++++++++++--------------------- man/correct_peak.Rd | 2 man/find_strongest_peaks.Rd | 9 man/peak_duration_max_force.Rd |only man/plot_peaks.Rd | 12 man/y_to_force.Rd | 2 vignettes/forceR.Rmd | 35 - 21 files changed, 897 insertions(+), 704 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and
Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework
allows for elastic analysis of functional data through phase and
amplitude separation.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.9.7 dated 2021-06-21 and 1.9.8 dated 2022-06-07
DESCRIPTION | 18 MD5 | 286 +-- NAMESPACE | 209 +- NEWS | 224 +- R/AmplitudeBoxplot.R | 340 ++-- R/PhaseBoxplot.R | 360 ++-- R/SqrtMean.R | 130 - R/SqrtMedian.R | 158 +- R/align_fPCA.R | 580 +++---- R/bayesian_functions.R | 98 - R/calc_shape_dist.R | 104 - R/curve_functions.R | 1246 +++++++-------- R/curve_geodesic.R | 92 - R/curve_karcher_cov.R | 78 R/curve_karcher_mean.R | 360 ++-- R/curve_pair_align.R | 72 R/curve_principal_directions.R | 150 - R/curve_srvf_align.R | 112 - R/curve_to_q.R | 68 R/elastic.depth.R | 130 - R/elastic.distance.R | 78 R/elastic_logistic.R | 238 +-- R/elastic_lpcr_regression.R | 152 - R/elastic_mlogistic.R | 260 +-- R/elastic_mlpcr_regression.R | 170 +- R/elastic_pcr_regression.R | 162 +- R/elastic_prediction.R | 228 +- R/elastic_regression.R | 304 +-- R/f_to_srvf.R | 52 R/fdasrvf-package.r | 311 +-- R/function_group_warp_bayes.R | 302 +-- R/function_mean_bayes.R | 226 +- R/gauss_model.R | 224 +- R/geometry.R | 276 +-- R/gradient.R | 84 - R/horizFPCA.R | 166 +- R/image_funcs.R | 842 +++++----- R/invertGamma.R | 50 R/joint_gauss_model.R | 142 - R/jointfPCA.R | 306 +-- R/kmeans.R | 462 ++--- R/multiple_align_functions.R | 318 ++-- R/optimum.reparam.R | 208 +- R/outlier.detection.R | 80 - R/pair_align_functions.R | 98 - R/pair_align_functions_bayes.R | 342 ++-- R/pair_align_functions_expomap.R | 1610 ++++++++++---------- R/pair_align_image.R | 194 +- R/plot.ampbox.R | 142 - R/plot.fdakma.R | 58 R/plot.fdawarp.R | 68 R/plot.hfpca.R | 64 R/plot.jfpca.R | 90 - R/plot.phbox.R | 138 - R/plot.vfpca.R | 90 - R/predict.lpcr.R | 292 +-- R/predict.mlpcr.R | 340 ++-- R/predict.pcr.R | 260 +-- R/q_to_curve.R | 58 R/regression_functions.R | 252 +-- R/reparam_curve.R | 284 +-- R/reparam_image.R | 180 +- R/resamplecurve.R | 80 - R/rgam.R | 116 - R/sample_shapes.R | 136 - R/smooth.data.R | 56 R/srvf_to_f.R | 80 - R/summary.fdawarp.R | 28 R/time_warping.R | 549 +++---- R/tolerance.R | 260 +-- R/utility_functions.R | 1644 ++++++++++----------- R/vertFPCA.R | 194 +- R/warp_f_gamma.R | 58 R/warp_q_gamma.R | 68 README.md | 170 +- man/AmplitudeBoxplot.Rd | 84 - man/PhaseBoxplot.Rd | 82 - man/SqrtMean.Rd | 72 man/SqrtMedian.Rd | 72 man/align_fPCA.Rd | 143 - man/beta.Rd | 34 man/bootTB.Rd | 104 - man/calc_shape_dist.Rd | 64 man/curve_geodesic.Rd | 62 man/curve_karcher_cov.Rd | 58 man/curve_karcher_mean.Rd | 112 - man/curve_pair_align.Rd | 62 man/curve_principal_directions.Rd | 86 - man/curve_srvf_align.Rd | 92 - man/curve_to_q.Rd | 52 man/elastic.depth.Rd | 66 man/elastic.distance.Rd | 80 - man/elastic.logistic.Rd | 132 - man/elastic.lpcr.regression.Rd | 108 - man/elastic.mlogistic.Rd | 132 - man/elastic.mlpcr.regression.Rd | 110 - man/elastic.pcr.regression.Rd | 120 - man/elastic.prediction.Rd | 80 - man/elastic.regression.Rd | 138 - man/f_to_srvf.Rd | 68 man/fdasrvf.Rd | 100 - man/function_group_warp_bayes.Rd | 114 - man/function_mean_bayes.Rd | 92 - man/gauss_model.Rd | 68 man/gradient.Rd | 50 man/growth_vel.Rd | 32 man/horizFPCA.Rd | 80 - man/im.Rd | 32 man/invertGamma.Rd | 64 man/jointFPCA.Rd | 124 - man/joint_gauss_model.Rd | 76 man/kmeans_align.Rd | 182 +- man/multiple_align_functions.Rd | 144 - man/optimum.reparam.Rd | 122 - man/outlier.detection.Rd | 84 - man/pair_align_functions.Rd | 128 - man/pair_align_functions_bayes.Rd | 126 - man/pair_align_functions_expomap.Rd | 194 +- man/pair_align_image.Rd | 114 - man/pcaTB.Rd | 96 - man/predict.lpcr.Rd | 70 man/predict.mlpcr.Rd | 72 man/predict.pcr.Rd | 68 man/q_to_curve.Rd | 58 man/reparam_curve.Rd | 106 - man/reparam_image.Rd | 76 man/resamplecurve.Rd | 60 man/rgam.Rd | 72 man/sample_shapes.Rd | 72 man/simu_data.Rd | 44 man/simu_warp.Rd | 44 man/simu_warp_median.Rd | 44 man/smooth.data.Rd | 68 man/srvf_to_f.Rd | 74 man/time_warping.Rd | 155 + man/toy_data.Rd | 38 man/toy_warp.Rd | 38 man/vertFPCA.Rd | 96 - man/warp_f_gamma.Rd | 76 man/warp_q_gamma.Rd | 78 src/gropt/src/DriverElasticCurvesRO.cpp | 3 tests/testthat.R | 16 tests/testthat/test_pair_align_functions_bayes.R | 40 tests/testthat/test_pair_align_functions_expomap.R | 226 +- 144 files changed, 12202 insertions(+), 12182 deletions(-)
Title: Training Set Determination for Genomic Selection
Description: We propose an optimality criterion to determine the required training set, r-score, which is derived directly from Pearson's correlation between the genomic estimated breeding values and phenotypic values of the test set <doi:10.1007/s00122-019-03387-0>. This package provides two main functions to determine a good training set and its size.
Author: Jen-Hsiang Ou [aut, cre] ,
Po-Ya Wu [aut] ,
Chen-Tuo Liao [aut, ths]
Maintainer: Jen-Hsiang Ou <jen-hsiang.ou@imbim.uu.se>
Diff between TSDFGS versions 1.0 dated 2019-03-07 and 2.0 dated 2022-06-07
TSDFGS-1.0/TSDFGS/R/CopyOfRcppExports.R |only TSDFGS-1.0/TSDFGS/R/trainSize.R |only TSDFGS-1.0/TSDFGS/data/datalist |only TSDFGS-1.0/TSDFGS/data/rice44kPCA.RData |only TSDFGS-1.0/TSDFGS/man/rice44k.Rd |only TSDFGS-1.0/TSDFGS/src/functions_cpp.cpp |only TSDFGS-2.0/TSDFGS/DESCRIPTION | 40 + TSDFGS-2.0/TSDFGS/MD5 | 52 + TSDFGS-2.0/TSDFGS/NAMESPACE | 17 TSDFGS-2.0/TSDFGS/R/RcppExports.R | 82 ++- TSDFGS-2.0/TSDFGS/R/SSDFGS.R |only TSDFGS-2.0/TSDFGS/R/TSDFGS-package.R |only TSDFGS-2.0/TSDFGS/R/data.R |only TSDFGS-2.0/TSDFGS/R/optTrain.R | 867 ++++++++++++++++---------------- TSDFGS-2.0/TSDFGS/README.md |only TSDFGS-2.0/TSDFGS/build/partial.rdb |binary TSDFGS-2.0/TSDFGS/data/geno.rda |only TSDFGS-2.0/TSDFGS/data/subpop.rda |only TSDFGS-2.0/TSDFGS/man/FGCM.Rd |only TSDFGS-2.0/TSDFGS/man/SSDFGS.Rd |only TSDFGS-2.0/TSDFGS/man/TSDFGS-package.Rd | 63 +- TSDFGS-2.0/TSDFGS/man/cd_score.Rd | 71 -- TSDFGS-2.0/TSDFGS/man/figures |only TSDFGS-2.0/TSDFGS/man/geno.Rd | 45 - TSDFGS-2.0/TSDFGS/man/nt2r.Rd |only TSDFGS-2.0/TSDFGS/man/optTrain.Rd | 116 +--- TSDFGS-2.0/TSDFGS/man/pev_score.Rd | 73 -- TSDFGS-2.0/TSDFGS/man/r_score.Rd | 71 -- TSDFGS-2.0/TSDFGS/man/subpop.Rd | 45 - TSDFGS-2.0/TSDFGS/src/RcppExports.cpp | 33 - TSDFGS-2.0/TSDFGS/src/cdscore.cpp |only TSDFGS-2.0/TSDFGS/src/pevscore.cpp |only TSDFGS-2.0/TSDFGS/src/rscore.cpp |only 33 files changed, 805 insertions(+), 770 deletions(-)
Title: Whitening and High-Dimensional Canonical Correlation Analysis
Description: Implements the whitening methods (ZCA, PCA, Cholesky,
ZCA-cor, and PCA-cor) discussed in Kessy, Lewin, and Strimmer (2018)
"Optimal whitening and decorrelation", <doi:10.1080/00031305.2016.1277159>,
as well as the whitening approach to canonical correlation analysis allowing
negative canonical correlations described in Jendoubi and Strimmer (2019)
"A whitening approach to probabilistic canonical correlation analysis for omics
data integration", <doi:10.1186/s12859-018-2572-9>. The package also offers
functions to simulate random orthogonal matrices, compute (correlation) loadings
and explained variation. It also contains four example data sets (extended UCI
wine data, TCGA LUSC data, nutrimouse data, extended pitprops data).
Author: Korbinian Strimmer, Takoua Jendoubi, Agnan Kessy, Alex Lewin
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between whitening versions 1.3.0 dated 2021-11-07 and 1.4.0 dated 2022-06-07
whitening-1.3.0/whitening/man/whiteningCrossCov.Rd |only whitening-1.4.0/whitening/DESCRIPTION | 16 ++-- whitening-1.4.0/whitening/MD5 | 42 ++++++---- whitening-1.4.0/whitening/NAMESPACE | 2 whitening-1.4.0/whitening/NEWS | 15 +++ whitening-1.4.0/whitening/R/explainedVariation.R |only whitening-1.4.0/whitening/R/getPhiPsiW.R |only whitening-1.4.0/whitening/R/simOrtho.R | 20 +++-- whitening-1.4.0/whitening/R/whiten.R | 11 ++ whitening-1.4.0/whitening/R/whiteningCrossCov.R | 78 ++------------------ whitening-1.4.0/whitening/R/whiteningLoadings.R |only whitening-1.4.0/whitening/R/whiteningMatrix.R | 71 +----------------- whitening-1.4.0/whitening/data/forina1986.rda |binary whitening-1.4.0/whitening/data/lusc.rda |binary whitening-1.4.0/whitening/data/nutrimouse.rda |binary whitening-1.4.0/whitening/data/pitprops14.rda |only whitening-1.4.0/whitening/man/explainedVariation.Rd |only whitening-1.4.0/whitening/man/forina1986.Rd | 2 whitening-1.4.0/whitening/man/nutrimouse.Rd | 2 whitening-1.4.0/whitening/man/pitprops14.Rd |only whitening-1.4.0/whitening/man/simOrtho.Rd | 5 - whitening-1.4.0/whitening/man/whiten.Rd | 39 ++++------ whitening-1.4.0/whitening/man/whitening-internal.Rd | 2 whitening-1.4.0/whitening/man/whitening.package.Rd | 3 whitening-1.4.0/whitening/man/whiteningLoadings.Rd |only whitening-1.4.0/whitening/man/whiteningMatrix.Rd | 51 +++++-------- 26 files changed, 138 insertions(+), 221 deletions(-)
Title: Ecological and Biogeographical Null Model Tests for Comparing
Rarefaction Curves
Description: Randomization tests for the statistical comparison of i = two or more individual-based, sample-based or coverage-based rarefaction curves. The ecological null hypothesis is that the i samples were all drawn randomly from a single assemblage, with (necessarily) a single underlying species abundance distribution. The biogeographic null hypothesis is that the i samples were all drawn from different assemblages that, nonetheless, share similar species richness and species abundance distributions. Functions are described in L. Cayuela, N.J. Gotelli & R.K. Colwell (2015) <doi:10.1890/14-1261.1>.
Author: Luis Cayuela and Nicholas J. Gotelli
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between rareNMtests versions 1.1 dated 2014-10-18 and 1.2 dated 2022-06-07
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 3 +++ man/BiogTest.individual.Rd | 2 +- man/Chiapas.Rd | 4 ++-- man/EcoTest.individual.Rd | 2 +- 6 files changed, 19 insertions(+), 16 deletions(-)
Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database
from the downloaded images. 'parseRPDR' currently supports txt sources: "mrn", "con", "dem", "enc", "rdt", "lab",
"med", "dia", "rfv", "prc", "phy", "lno", "car", "dis", "end", "hnp", "opn", "pat", "prg", "pul", "rad" and "vis".
All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 0.2.2 dated 2022-05-30 and 0.2.3 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 20 ++++++++++++++++++++ R/convert_notes.R | 2 +- R/create_img_db.R | 9 ++++++--- R/dcm_db.R | 33 +++++++++++++++++++++++++-------- R/load_all.R | 5 ++++- R/load_notes.R | 9 +++++---- README.md | 19 +++++++++++-------- man/convert_notes.Rd | 2 +- man/create_img_db.Rd | 9 ++++++--- man/dcm_db.Rd | 7 +++++-- man/load_all.Rd | 5 ++++- man/load_notes.Rd | 7 +++++-- 14 files changed, 110 insertions(+), 51 deletions(-)
Title: The Multivariate Normal and t Distributions, and Their Truncated
Versions
Description: Functions are provided for computing the density and the
distribution function of d-dimensional normal and "t" random variables,
possibly truncated (on one side or two sides), and for generating random
vectors sampled from these distributions, except sampling from the truncated
"t". Moments of arbitrary order of a multivariate truncated normal are
computed, and converted to cumulants up to order 4.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre],
Alan Genz [aut] ,
Alan Miller [ctb] ,
Michael J. Wichura [ctb] ,
G. W. Hill [ctb] ,
Yihong Ge [ctb] .
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 2.0.2 dated 2020-09-01 and 2.1.0 dated 2022-06-07
mnormt-2.0.2/mnormt/R/sample_mardia.R |only mnormt-2.0.2/mnormt/R/truncNT.R |only mnormt-2.1.0/mnormt/COPYING |only mnormt-2.1.0/mnormt/ChangeLog |only mnormt-2.1.0/mnormt/DESCRIPTION | 9 - mnormt-2.1.0/mnormt/MD5 | 30 +++-- mnormt-2.1.0/mnormt/NAMESPACE | 8 - mnormt-2.1.0/mnormt/NEWS | 35 ++++-- mnormt-2.1.0/mnormt/R/misc_funct.R |only mnormt-2.1.0/mnormt/R/truncNorm.R |only mnormt-2.1.0/mnormt/build |only mnormt-2.1.0/mnormt/inst/notice-Genz |only mnormt-2.1.0/mnormt/man/mnorm.Rd | 36 +++---- mnormt-2.1.0/mnormt/man/mnormt-package.Rd | 2 mnormt-2.1.0/mnormt/man/mt.Rd | 16 +-- mnormt-2.1.0/mnormt/man/mtruncnorm.Rd | 112 ++++++++++++++-------- mnormt-2.1.0/mnormt/man/plot_fxy.Rd |only mnormt-2.1.0/mnormt/man/recintab.Rd | 4 mnormt-2.1.0/mnormt/man/sample_Mardia_measures.Rd | 9 - mnormt-2.1.0/mnormt/src/mnormt_init.c | 12 ++ mnormt-2.1.0/mnormt/src/rtmng.f |only 21 files changed, 168 insertions(+), 105 deletions(-)
Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive
Q-Learning, Q-Learning, weighted learning, and value-search methods based on
Augmented Inverse Probability Weighted Estimators and Inverse Probability
Weighted Estimators. Dynamic Treatment Regimes: Statistical Methods for
Precision Medicine, Tsiatis, A. A., Davidian, M. D., Holloway, S. T., and Laber, E. B.,
Chapman & Hall/CRC Press, 2020, ISBN:978-1-4987-6977-8.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DynTxRegime versions 4.9 dated 2020-11-09 and 4.10 dated 2022-06-07
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/B_TxSubset.R | 20 ++++++++++---------- 3 files changed, 17 insertions(+), 17 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjærde [trl]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 1.0.1 dated 2022-04-21 and 1.0.2 dated 2022-06-07
DESCRIPTION | 8 MD5 | 469 +++--- R/Adjusted_inv_sinh_CI_OR_2x2.R | 92 - R/Adjusted_inv_sinh_CI_ratio_2x2.R | 90 - R/Adjusted_log_CI_2x2.R | 66 R/AgrestiCaffo_CI_2x2.R | 71 R/AgrestiCoull_CI_1x2.R | 95 - R/Arcsine_CI_1x2.R | 104 - R/BaptistaPike_exact_conditional_CI_2x2.R | 131 - R/BaptistaPike_midP_CI_2x2.R | 166 +- R/Blaker_exact_CI_1x2.R | 104 - R/Blaker_exact_test_1x2.R | 96 - R/Blaker_midP_CI_1x2.R | 160 +- R/Blaker_midP_test_1x2.R | 105 - R/Bonferroni_type_CIs_rxc.R | 72 R/Brant_test_2xc.R | 156 +- R/BreslowDay_homogeneity_test_stratified_2x2.R | 2 R/Chacko_test_1xc.R | 95 - R/ClopperPearson_exact_CI_1x2.R | 142 - R/ClopperPearson_midP_CI_1x2.R | 147 - R/CochranArmitage_CI_rx2.R | 72 R/CochranArmitage_MH_tests_rx2.R | 104 - R/CochranArmitage_exact_cond_midP_tests_rx2.R | 85 - R/Cochran_Q_test_stratified_2x2.R | 4 R/Cornfield_exact_conditional_CI_2x2.R | 128 - R/Cornfield_midP_CI_2x2.R | 128 - R/Cumulative_models_for_2xc.R | 340 ++-- R/Cumulative_models_for_rxc.R | 325 ++-- R/Exact_binomial_test_1x2.R | 24 R/Exact_cond_midP_linear_rank_tests_2xc.R | 98 - R/Exact_cond_midP_tests_rxc.R | 472 +++--- R/Exact_cond_midP_unspecific_ordering_rx2.R | 260 +-- R/Exact_multinomial_test_1xc.R | 175 +- R/Exact_unconditional_test_2x2.R | 298 ++-- R/FisherFreemanHalton_asymptotic_test_rxc.R | 106 - R/Fisher_exact_test_2x2.R | 169 +- R/Fisher_midP_test_2x2.R | 158 +- R/Gart_adjusted_logit_CI_2x2.R | 73 R/Gold_Wald_CIs_1xc.R | 56 R/Goodman_Wald_CIs_1xc.R | 57 R/Goodman_Wald_CIs_for_diffs_1xc.R | 106 - R/Goodman_Wilson_score_CIs_1xc.R | 85 - R/Independence_smoothed_logit_CI_2x2.R | 77 - R/Inv_sinh_CI_OR_2x2.R | 83 - R/Inv_sinh_CI_ratio_2x2.R | 81 - R/Jeffreys_CI_1x2.R | 46 R/JonckheereTerpstra_test_rxc.R | 112 - R/Katz_log_CI_2x2.R | 73 R/Kendalls_tau_b_rxc.R | 77 - R/Kendalls_tau_b_rxc_bca.R | 114 - R/Koopman_asymptotic_score_CI_2x2.R | 134 - R/KruskalWallis_asymptotic_test_rxc.R | 96 - R/LR_CI_1x2.R | 132 - R/LR_test_1x2.R | 70 R/LR_test_1xc.R | 62 R/LR_test_2x2.R | 81 - R/MOVER_R_Wilson_CI_OR_2x2.R | 120 - R/MOVER_R_Wilson_CI_ratio_2x2.R | 71 R/MOVER_Wilson_score_CI_paired_2x2.R | 81 - R/MantelHaenszel_test_2xc.R | 62 R/McNemar_exact_cond_test_paired_2x2.R | 8 R/McNemar_exact_unconditional_test_paired_2x2.R | 4 R/Mee_asymptotic_score_CI_2x2.R | 108 - R/MidP_binomial_test_1x2.R | 41 R/MidP_multinomial_test_1xc.R | 180 +- R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R | 123 - R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R | 109 - R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R | 134 - R/Newcombe_hybrid_score_CI_2x2.R | 61 R/Newcombe_square_and_add_CI_paired_2x2.R | 88 - R/Pearson_LR_homogeneity_test_stratified_2x2.R | 2 R/Pearson_LR_test_common_effect_stratified_2x2.R | 2 R/Pearson_LR_tests_cum_OR_2xc.R | 166 +- R/Pearson_LR_tests_rxc.R | 94 - R/Pearson_LR_tests_unspecific_ordering_rx2.R | 155 +- R/Pearson_chi_squared_test_1xc.R | 52 R/Pearson_chi_squared_test_2x2.R | 57 R/Pearson_chi_squared_test_CC_2x2.R | 58 R/Pearson_correlation_coefficient_rxc.R | 95 - R/Pearson_correlation_coefficient_rxc_bca.R | 108 - R/Pearson_residuals_rxc.R | 44 R/PriceBonett_approximate_Bayes_CI_2x2.R | 74 R/QuesenberryHurst_Wilson_score_CIs_1xc.R | 90 - R/RBG_test_and_CI_stratified_2x2.R | 2 R/Scheffe_type_CIs_rxc.R | 74 R/Score_test_1x2.R | 57 R/Score_test_CC_1x2.R | 52 R/Score_test_and_CI_marginal_mean_scores_paired_cxc.R | 4 R/Score_test_for_effect_in_the_probit_model_2xc.R | 322 ++-- R/Spearman_correlation_coefficient_rxc.R | 142 - R/Spearman_correlation_coefficient_rxc_bca.R | 98 - R/Transformed_Blaker_exact_CI_paired_2x2.R | 2 R/Transformed_Clopper_Pearson_exact_CI_paired_2x2.R | 2 R/Transformed_Clopper_Pearson_midP_CI_paired_2x2.R | 2 R/Transformed_Wilson_score_CI_paired_2x2.R | 12 R/Trend_estimate_CI_tests_rx2.R | 172 +- R/Uncorrected_asymptotic_score_CI_2x2.R | 108 - R/Wald_CI_1x2.R | 100 - R/Wald_CI_2x2.R | 77 - R/Wald_CI_CC_1x2.R | 67 R/Wald_CI_CC_2x2.R | 75 - R/Wald_test_1x2.R | 61 R/Wald_test_CC_1x2.R | 71 R/Wald_test_and_CI_common_diff_stratified_2x2.R | 4 R/Wald_test_and_CI_common_ratio_stratified_2x2.R | 4 R/Wald_test_and_CI_marginal_mean_scores_paired_cxc.R | 2 R/Wilson_score_CI_1x2.R | 61 R/Wilson_score_CI_CC_1x2.R | 49 R/Woolf_logit_CI_2x2.R | 58 R/Woolf_test_and_CI_stratified_2x2.R | 2 R/Z_unpooled_test_2x2.R | 40 R/chapters.R | 59 R/gamma_coefficient_rxc.R | 146 - R/gamma_coefficient_rxc_bca.R | 110 - R/generics.R | 894 ++++++------ R/linear_by_linear_test_rxc.R | 71 R/misc.R | 17 R/stratified_2x2_tables.R | 60 R/the_1x2_table_CIs.R | 197 +- R/the_1x2_table_tests.R | 133 - R/the_1xc_table_CIs.R | 83 - R/the_1xc_table_tests.R | 97 - R/the_2x2_table_CIs_OR.R | 150 +- R/the_2x2_table_CIs_difference.R | 49 R/the_2x2_table_CIs_ratio.R | 101 - R/the_2x2_table_tests.R | 121 - R/the_2xc_table.R | 178 +- R/the_paired_2x2_table_CIs_OR.R | 18 R/the_paired_2x2_table_CIs_difference.R | 18 R/the_paired_2x2_table_CIs_ratio.R | 18 R/the_paired_2x2_table_tests.R | 20 R/the_paired_cxc_table_nominal.R | 16 R/the_paired_cxc_table_ordinal.R | 10 R/the_rx2_table.R | 146 - R/the_rxc_table.R | 497 +++--- man/Adjusted_inv_sinh_CI_OR_2x2.Rd | 4 man/Adjusted_inv_sinh_CI_ratio_2x2.Rd | 4 man/Adjusted_log_CI_2x2.Rd | 4 man/AgrestiCaffo_CI_2x2.Rd | 4 man/BaptistaPike_exact_conditional_CI_2x2.Rd | 8 man/BaptistaPike_midP_CI_2x2.Rd | 8 man/Blaker_exact_CI_1x2.Rd | 10 man/Blaker_exact_test_1x2.Rd | 10 man/Blaker_midP_CI_1x2.Rd | 10 man/Blaker_midP_test_1x2.Rd | 10 man/Chacko_test_1xc.Rd | 2 man/ClopperPearson_exact_CI_1x2.Rd | 10 man/ClopperPearson_midP_CI_1x2.Rd | 10 man/CochranArmitage_CI_rx2.Rd | 4 man/CochranArmitage_MH_tests_rx2.Rd | 4 man/CochranArmitage_exact_cond_midP_tests_rx2.Rd | 4 man/Cornfield_exact_conditional_CI_2x2.Rd | 8 man/Cornfield_midP_CI_2x2.Rd | 8 man/Exact_cond_midP_linear_rank_tests_2xc.Rd | 2 man/Exact_cond_midP_tests_rxc.Rd | 4 man/Exact_cond_midP_unspecific_ordering_rx2.Rd | 2 man/Exact_multinomial_test_1xc.Rd | 4 man/Exact_unconditional_test_2x2.Rd | 10 man/Fisher_exact_test_2x2.Rd | 8 man/Fisher_midP_test_2x2.Rd | 8 man/Gart_adjusted_logit_CI_2x2.Rd | 4 man/Gold_Wald_CIs_1xc.Rd | 2 man/Goodman_Wald_CIs_1xc.Rd | 2 man/Goodman_Wald_CIs_for_diffs_1xc.Rd | 2 man/Goodman_Wilson_score_CIs_1xc.Rd | 2 man/Independence_smoothed_logit_CI_2x2.Rd | 4 man/Inv_sinh_CI_OR_2x2.Rd | 4 man/Inv_sinh_CI_ratio_2x2.Rd | 4 man/Jeffreys_CI_1x2.Rd | 10 man/Katz_log_CI_2x2.Rd | 4 man/Kendalls_tau_b_rxc_bca.Rd | 34 man/Koopman_asymptotic_score_CI_2x2.Rd | 4 man/LR_CI_1x2.Rd | 10 man/LR_test_1x2.Rd | 10 man/LR_test_1xc.Rd | 4 man/LR_test_2x2.Rd | 8 man/MOVER_R_Wilson_CI_OR_2x2.Rd | 4 man/MOVER_R_Wilson_CI_ratio_2x2.Rd | 5 man/MOVER_Wilson_score_CI_paired_2x2.Rd | 4 man/Mee_asymptotic_score_CI_2x2.Rd | 4 man/MidP_binomial_test_1x2.Rd | 10 man/MidP_multinomial_test_1xc.Rd | 4 man/MiettinenNurminen_asymptotic_score_CI_OR_2x2.Rd | 4 man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd | 4 man/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.Rd | 4 man/Newcombe_hybrid_score_CI_2x2.Rd | 4 man/Newcombe_square_and_add_CI_paired_2x2.Rd | 4 man/Pearson_LR_tests_rxc.Rd | 18 man/Pearson_LR_tests_unspecific_ordering_rx2.Rd | 13 man/Pearson_chi_squared_test_1xc.Rd | 4 man/Pearson_chi_squared_test_2x2.Rd | 8 man/Pearson_chi_squared_test_CC_2x2.Rd | 8 man/Pearson_correlation_coefficient_rxc.Rd | 4 man/Pearson_correlation_coefficient_rxc_bca.Rd | 4 man/PriceBonett_approximate_Bayes_CI_2x2.Rd | 4 man/QuesenberryHurst_Wilson_score_CIs_1xc.Rd | 2 man/Score_test_1x2.Rd | 10 man/Score_test_CC_1x2.Rd | 10 man/Transformed_Wilson_score_CI_paired_2x2.Rd | 2 man/Trend_estimate_CI_tests_rx2.Rd | 10 man/Uncorrected_asymptotic_score_CI_2x2.Rd | 5 man/Wald_CI_1x2.Rd | 10 man/Wald_CI_2x2.Rd | 4 man/Wald_CI_CC_1x2.Rd | 10 man/Wald_CI_CC_2x2.Rd | 4 man/Wald_test_1x2.Rd | 10 man/Wald_test_CC_1x2.Rd | 10 man/Wilson_score_CI_1x2.Rd | 10 man/Wilson_score_CI_CC_1x2.Rd | 10 man/Woolf_logit_CI_2x2.Rd | 4 man/Z_unpooled_test_2x2.Rd | 8 man/gamma_coefficient_rxc.Rd | 24 man/gamma_coefficient_rxc_bca.Rd | 24 man/linear_by_linear_test_rxc.Rd | 7 man/the_1x2_table_CIs.Rd | 10 man/the_1xc_table_CIs.Rd | 2 man/the_1xc_table_tests.Rd | 6 man/the_2x2_table_CIs_OR.Rd | 8 man/the_2x2_table_CIs_difference.Rd | 4 man/the_2x2_table_CIs_ratio.Rd | 4 man/the_2x2_table_tests.Rd | 8 man/the_rx2_table.Rd | 4 man/the_rxc_table.Rd | 87 - tests/testthat.R | 5 tests/testthat/test-ch10.R | 58 tests/testthat/test-ch2.R | 232 +-- tests/testthat/test-ch3.R | 110 - tests/testthat/test-ch4.R | 332 ++-- tests/testthat/test-ch5.R | 80 - tests/testthat/test-ch6.R | 84 - tests/testthat/test-ch7.R | 185 +- tests/testthat/test-ch8.R | 224 +-- tests/testthat/test-ch9.R | 120 - tests/testthat/test-crossChapterIntegration.R | 32 tests/testthat/test-issue34.R |only tests/testthat/test-outputFormat.R | 805 ++++++---- 236 files changed, 8560 insertions(+), 8444 deletions(-)
More information about contingencytables at CRAN
Permanent link
Title: Vaccine Efficacy Over Time - Variant Aware
Description: Implements methods for inference on potential waning of vaccine efficacy and for estimation of vaccine efficacy at a user-specified time after vaccination based on data from a randomized, double-blind, placebo-controlled vaccine trial in which participants may be unblinded and placebo subjects may be crossed over to the study vaccine. The methods also for variant stratification and allow adjustment for possible confounding via inverse probability weighting through specification of models for the trial entry process, unblinding mechanisms, and the probability an unblinded placebo participant accepts study vaccine.
Author: Marie Davidian [aut],
A.A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between VEwaningVariant versions 1.2 dated 2022-01-17 and 1.3 dated 2022-06-07
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
More information about VEwaningVariant at CRAN
Permanent link
Title: Vaccine Efficacy Over Time
Description: Implements methods for inference on potential waning of vaccine
efficacy and for estimation of vaccine efficacy at a user-specified time
after vaccination based on data from a randomized, double-blind,
placebo-controlled vaccine trial in which participants may be unblinded
and placebo subjects may be crossed over to the study vaccine. The
methods also allow adjustment for possible confounding via inverse
probability weighting through specification of models for the trial
entry process, unblinding mechanisms, and the probability an unblinded
placebo participant accepts study vaccine: Tsiatis, A. A. and Davidian,
M. (2021) <arXiv:2102.13103> .
Author: Marie Davidian [aut],
A.A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between VEwaning versions 1.1 dated 2021-04-08 and 1.2 dated 2022-06-07
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Proportional Odds Model with Censored, Time-Lagged Categorical
Outcome
Description: Implements a semiparametric estimator for the odds ratio model with
censored, time-lagged, ordered categorical outcome in a randomized clinical
trial that incorporates baseline and time-dependent information.
Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut],
A. A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between tLagPropOdds versions 1.7 dated 2022-02-08 and 1.8 dated 2022-06-07
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Stabilising Variable Selection
Description: A stable approach to variable selection through stability selection and the use of a permutation-based objective stability threshold. Lima et al (2021) <doi:10.1038/s41598-020-79317-8>, Meinshausen and Buhlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>.
Author: Robert Hyde [aut, cre] ,
Martin Green [aut],
Eliana Lima [aut]
Maintainer: Robert Hyde <robert.hyde4@nottingham.ac.uk>
Diff between stabiliser versions 1.0.1 dated 2022-04-06 and 1.0.2 dated 2022-06-07
DESCRIPTION | 9 +-- MD5 | 30 +++++++--- NAMESPACE | 25 +++++++++ NEWS.md | 7 -- R/boot_model.R | 10 ++- R/perm_stab.R | 2 R/permute.R | 2 R/prep.R |only R/selection_bias_inner.R |only R/simulate_data_re.R |only R/simulate_selection_bias.R |only R/stabilise.R | 112 +++++++++++++++++++++-------------------- R/stabilise_re.R |only README.md | 4 - inst/doc/stabiliser.html | 85 +++++++++++++++++++++---------- man/selection_bias_inner.Rd |only man/simulate_data_re.Rd |only man/simulate_selection_bias.Rd |only man/stabilise.Rd | 8 ++ man/stabilise_re.Rd |only man/stabiliser_prep.Rd |only 21 files changed, 188 insertions(+), 106 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.0.0 dated 2022-02-04 and 3.0.1 dated 2022-06-07
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 14 +++++++++ R/Args.R | 46 ++++++++++++++++++++---------- R/Layouts.R | 2 - build/vignette.rds |binary inst/doc/Logging.pdf |binary inst/doc/Parallel.pdf |binary tests/testthat/test-saveAndLoadJson.R | 51 ++++++++++++++++++++++++++++++++-- 9 files changed, 107 insertions(+), 32 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: MareFrame DB Querying Library
Description: Creates and manages a PostgreSQL database suitable for storing fisheries data
and aggregating ready for use within a Gadget <https://gadget-framework.github.io/gadget2/> model.
See <https://mareframe.github.io/mfdb/> for more information.
Author: Jamie Lentin [aut, cre, cph],
Bjarki Thor Elvarsson [aut]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between mfdb versions 7.2-0 dated 2021-11-21 and 7.3-0 dated 2022-06-07
ChangeLog | 6 ++++ DESCRIPTION | 8 +++--- MD5 | 28 +++++++++++----------- R/mfdb_import_data.R | 20 ++++++++++++++-- R/mfdb_sql.R | 37 ++++++++++++++++-------------- README.md | 4 +++ inst/doc/import_hydrography_cmems.html | 11 ++++---- inst/doc/population.html | 11 ++++---- inst/doc/tow_data.R | 12 ++++++--- inst/doc/tow_data.Rmd | 12 ++++++--- inst/doc/tow_data.html | 27 +++++++++++---------- inst/doc/trip.html | 11 ++++---- inst/doc/weightmeasurements.html | 11 ++++---- tests/test-mfdb_aggregate_step_interval.R | 2 - vignettes/tow_data.Rmd | 12 ++++++--- 15 files changed, 129 insertions(+), 83 deletions(-)
Title: Durability of Vaccine Efficacy Against SARS-CoV-2 Infection
Description: Implements a nonparametric maximum likelihood method for assessing
potentially time-varying vaccine efficacy (VE) against SARS-CoV-2 infection
under staggered enrollment and time-varying community transmission, allowing
crossover of placebo volunteers to the vaccine arm.
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
Author: Yu Gu [aut],
Shannon T. Holloway [aut, cre],
Dan-Yu Lin [aut]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between iDOVE versions 1.3 dated 2021-09-15 and 1.4 dated 2022-06-07
DESCRIPTION | 16 ++-- MD5 | 8 +- build/vignette.rds |binary inst/doc/iDOVE_vignette.R | 156 ++++++++++++++++++++++---------------------- inst/doc/iDOVE_vignette.pdf |binary 5 files changed, 90 insertions(+), 90 deletions(-)
Title: A Fast Multiple-Kernel Method Based on a Low-Rank Approximation
Description: A computationally efficient and statistically rigorous fast
Kernel Machine method for multi-kernel analysis. The approach is based on
a low-rank approximation to the nuisance effect kernel matrices. The
algorithm is applicable to continuous, binary, and survival traits and
is implemented using the existing single-kernel analysis software 'SKAT'
and 'coxKM'. 'coxKM' can be obtained from
<https://github.com/lin-lab/coxKM>.
Author: Rachel Marceau, Wenbin Lu, Michele M. Sale, Bradford B. Worrall,
Stephen R. Williams, Fang-Chi Hsu, Jung-Ying Tzeng, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between FastKM versions 1.0 dated 2015-11-10 and 1.1 dated 2022-06-07
DESCRIPTION | 21 +++- MD5 | 8 - man/FastKM-package.Rd | 56 ++++++------ man/KITdesign.Rd | 194 ++++++++++++++++++++++---------------------- man/KITkernel.Rd | 216 +++++++++++++++++++++++++------------------------- 5 files changed, 251 insertions(+), 244 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] ,
Chih-Chen Lin [ctb, cph]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-9 dated 2021-09-16 and 1.7-11 dated 2022-06-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/svm.R | 6 +++++- inst/NEWS.Rd | 11 +++++++++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary man/write.svm.Rd | 2 +- 7 files changed, 26 insertions(+), 11 deletions(-)
Title: Dynamic Treatment Regimes for Survival Analysis
Description: Provides methods for estimating multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring. Cho, H., Holloway, S. T., and Kosorok, M. R. (2020) <arXiv:2012.03294>.
Author: Shannon T. Holloway, Hunyong Cho
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between dtrSurv versions 1.3 dated 2022-03-21 and 1.4 dated 2022-06-07
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Durability of Vaccine Efficacy
Description: Implements maximum likelihood methods for
evaluating the durability of vaccine efficacy in a randomized,
placebo-controlled clinical trial with staggered enrollment of participants
and potential crossover of placebo recipients before the end of the trial.
Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab226>
and
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
Author: Danyu Lin [aut],
Yu Gu [aut],
Donglin Zeng [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DOVE versions 1.8 dated 2021-10-12 and 1.9 dated 2022-06-07
DESCRIPTION | 16 +-- MD5 | 8 - build/vignette.rds |binary inst/doc/dove-vignette.R | 234 ++++++++++++++++++++++----------------------- inst/doc/dove-vignette.pdf |binary 5 files changed, 129 insertions(+), 129 deletions(-)
Title: Copy Number Profile Curve-Based Association Test
Description: Implements a kernel-based association test for copy number
variation (CNV) aggregate analysis
in a certain genomic region (e.g., gene set, chromosome, or genome) that is
robust to the within-locus and across-locus etiological heterogeneity, and
bypass the need to define a "locus" unit for CNVs.
Brucker, A., et al. (2020) <doi:10.1101/666875>.
Author: Amanda Brucker, Shannon T. Holloway, Jung-Ying Tzeng
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between CONCUR versions 1.3 dated 2020-08-06 and 1.4 dated 2022-06-07
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: A Portal for Global Governance Data
Description: This is the core package for the many packages universe.
It includes functions to help researchers work with and contribute to
event datasets on global governance.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Bernhard Bieri [ctb] ,
Esther Peev [ctb] ,
Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manydata versions 0.7.3 dated 2022-04-01 and 0.7.5 dated 2022-06-07
DESCRIPTION | 15 - MD5 | 16 - NEWS.md | 16 + build/vignette.rds |binary data/emperors.rda |binary inst/doc/user.html | 532 +++++++++++++++++++++++++++++---------- tests/testthat/test_UNRV.R | 4 tests/testthat/test_britannica.R | 4 tests/testthat/test_wikipedia.R | 4 9 files changed, 445 insertions(+), 146 deletions(-)
Title: Wrappers to Simplify Beautiful 'ggplot2' and 'leaflet'
Visualisation
Description: Wrapper functions around the amazing 'ggplot2' and 'leaflet'
packages that aims to simplify beautiful 'ggplot2' and 'leaflet'
visualisation. Precursor package to the 'ggblanket' package.
Author: David Hodge [aut, cre] ,
Kate Lee [ctb] ,
Xavier Miles [ctb] ,
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 6.2.0 dated 2022-03-03 and 6.3.0 dated 2022-06-07
simplevis-6.2.0/simplevis/R/imports.R |only simplevis-6.2.0/simplevis/R/shiny_demo.R |only simplevis-6.2.0/simplevis/data/datalist |only simplevis-6.2.0/simplevis/inst/shiny |only simplevis-6.2.0/simplevis/man/pal_d3_reorder.Rd |only simplevis-6.2.0/simplevis/man/pal_viridis_reorder.Rd |only simplevis-6.2.0/simplevis/man/shiny_demo.Rd |only simplevis-6.3.0/simplevis/DESCRIPTION | 28 simplevis-6.3.0/simplevis/LICENSE | 2 simplevis-6.3.0/simplevis/MD5 | 305 simplevis-6.3.0/simplevis/NAMESPACE | 173 simplevis-6.3.0/simplevis/NEWS.md | 1560 - simplevis-6.3.0/simplevis/R/data.R | 65 simplevis-6.3.0/simplevis/R/density_max.R | 406 simplevis-6.3.0/simplevis/R/font_size.R | 38 simplevis-6.3.0/simplevis/R/gg_bar.R | 2910 +-- simplevis-6.3.0/simplevis/R/gg_boxplot.R | 2489 +-- simplevis-6.3.0/simplevis/R/gg_density.R | 1717 +- simplevis-6.3.0/simplevis/R/gg_hbar.R | 2937 +-- simplevis-6.3.0/simplevis/R/gg_hboxplot.R | 2502 +-- simplevis-6.3.0/simplevis/R/gg_histogram.R | 1568 - simplevis-6.3.0/simplevis/R/gg_hpointrange.R | 2798 +-- simplevis-6.3.0/simplevis/R/gg_hviolin.R | 2006 +- simplevis-6.3.0/simplevis/R/gg_line.R | 2293 +- simplevis-6.3.0/simplevis/R/gg_point.R | 2536 +-- simplevis-6.3.0/simplevis/R/gg_pointrange.R | 2639 +-- simplevis-6.3.0/simplevis/R/gg_sf.R | 2408 +- simplevis-6.3.0/simplevis/R/gg_smooth.R | 1994 +- simplevis-6.3.0/simplevis/R/gg_stars.R | 837 - simplevis-6.3.0/simplevis/R/gg_theme.R | 532 simplevis-6.3.0/simplevis/R/gg_tile.R | 1459 - simplevis-6.3.0/simplevis/R/gg_violin.R | 1987 +- simplevis-6.3.0/simplevis/R/ggplotly.R | 128 simplevis-6.3.0/simplevis/R/interval_labels.R | 256 simplevis-6.3.0/simplevis/R/leaf_basemap.R | 140 simplevis-6.3.0/simplevis/R/leaf_clear.R | 26 simplevis-6.3.0/simplevis/R/leaf_sf.R | 1282 - simplevis-6.3.0/simplevis/R/leaf_stars.R | 630 simplevis-6.3.0/simplevis/R/logo.R | 74 simplevis-6.3.0/simplevis/R/mutate_text.R | 154 simplevis-6.3.0/simplevis/R/news.R | 8 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| 318 simplevis-6.3.0/simplevis/man/gg_violin_col_facet.Rd | 360 simplevis-6.3.0/simplevis/man/gg_violin_facet.Rd | 302 simplevis-6.3.0/simplevis/man/interval_labels.Rd | 60 simplevis-6.3.0/simplevis/man/leaf_basemap.Rd | 50 simplevis-6.3.0/simplevis/man/leaf_clear.Rd | 34 simplevis-6.3.0/simplevis/man/leaf_sf.Rd | 138 simplevis-6.3.0/simplevis/man/leaf_sf_col.Rd | 266 simplevis-6.3.0/simplevis/man/leaf_stars.Rd | 84 simplevis-6.3.0/simplevis/man/leaf_stars_col.Rd | 160 simplevis-6.3.0/simplevis/man/mutate_text.Rd | 89 simplevis-6.3.0/simplevis/man/pal_d3_mix.Rd |only simplevis-6.3.0/simplevis/man/pal_na.Rd | 40 simplevis-6.3.0/simplevis/man/pal_viridis_mix.Rd |only simplevis-6.3.0/simplevis/man/pipe.Rd | 32 simplevis-6.3.0/simplevis/man/plotly_camera.Rd | 54 simplevis-6.3.0/simplevis/man/plotly_col_legend.Rd | 72 simplevis-6.3.0/simplevis/man/simplevis-package.Rd |only simplevis-6.3.0/simplevis/man/summarise_boxplot_outliers.Rd | 62 simplevis-6.3.0/simplevis/man/summarise_boxplot_stats.Rd | 84 simplevis-6.3.0/simplevis/man/sv_density_max.Rd | 70 simplevis-6.3.0/simplevis/man/sv_density_max_col.Rd | 76 simplevis-6.3.0/simplevis/man/sv_density_max_col_facet.Rd | 110 simplevis-6.3.0/simplevis/man/sv_density_max_facet.Rd | 76 simplevis-6.3.0/simplevis/man/sv_font_size_body.Rd | 30 simplevis-6.3.0/simplevis/man/sv_font_size_title.Rd | 30 simplevis-6.3.0/simplevis/man/sv_interval_labels_chr.Rd | 36 simplevis-6.3.0/simplevis/man/sv_interval_labels_num.Rd | 44 simplevis-6.3.0/simplevis/man/sv_numeric_breaks_h.Rd | 64 simplevis-6.3.0/simplevis/man/sv_numeric_breaks_v.Rd | 58 simplevis-6.3.0/simplevis/man/sv_x_zero_adjust.Rd | 52 simplevis-6.3.0/simplevis/man/sv_y_zero_adjust.Rd | 52 simplevis-6.3.0/simplevis/man/theme_mobile_extra.Rd | 36 simplevis-6.3.0/simplevis/vignettes/simplevis.Rmd | 1277 - 148 files changed, 39624 insertions(+), 36299 deletions(-)
Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between file2meco versions 0.2.4 dated 2022-05-24 and 0.3.0 dated 2022-06-07
DESCRIPTION | 6 +-- MD5 | 12 +++--- R/qiime2meco.R | 24 +++++++----- R/utility.R | 2 - data/MetaCyc_pathway_map.RData |binary inst/extdata/example_PICRUSt2_KEGG_path_abun_unstrat.tsv |only inst/extdata/example_PICRUSt2_MetaCyc_path_abun_unstrat.tsv |only man/qiime2meco.Rd | 13 ++++-- 8 files changed, 33 insertions(+), 24 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2021) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2021) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.4.2 dated 2022-01-24 and 3.4.3 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/uGMARpaper.Rnw | 2 +- inst/doc/uGMARpaper.pdf |binary vignettes/uGMARpaper.Rnw | 2 +- 7 files changed, 16 insertions(+), 12 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] ,
Yi Xiong [aut] ,
Longfei Zhao [aut] ,
Kai Gu [aut] ,
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.7 dated 2022-04-13 and 1.1.8 dated 2022-06-07
DESCRIPTION | 6 MD5 | 291 NAMESPACE | 152 NEWS.md | 122 R/GeomSplitViolin.R | 110 R/analyze_gene_drug_response.R | 908 R/ccle.R | 288 R/data.R | 244 R/ezcor.R | 870 R/get_pancan_value.R | 758 R/get_pcawg_value.R | 254 R/globalVariables.R | 34 R/load_data.R | 204 R/ope_pancan_value.R | 122 R/query_custom_value.R | 20 R/query_toil_value_df.R | 122 R/query_value.R | 400 R/run.R | 50 R/tcga_surv.R | 412 R/utils-pipe.R | 36 R/utils.R | 116 R/vis_analyze_gene_drug_response.R | 224 R/vis_ccle_value.R | 332 R/vis_identifier.R | 748 R/vis_pancan_value.R | 2650 - R/vis_pcawg_value.R | 930 R/xenashiny.R | 18 R/zzz.R | 32 README.md | 577 build/vignette.rds |binary inst/doc/api.R | 108 inst/doc/api.Rmd | 254 inst/doc/api.html | 2195 - inst/extdata/ccle_drug_response_extend.rda |only inst/modules_apps/app.R | 38 inst/modules_apps/simple_module_from_rstudio.R | 66 inst/modules_apps/xx_modules.R | 98 inst/shinyapp/App.R | 678 inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R | 126 inst/shinyapp/modules/home-pancan-search.R | 178 inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R | 352 inst/shinyapp/modules/modules-ccle-gene-drug-target.R | 358 inst/shinyapp/modules/modules-ccle-genecor.R | 516 inst/shinyapp/modules/modules-ccle-search.R | 328 inst/shinyapp/modules/modules-file-upload.R | 238 inst/shinyapp/modules/modules-ga-group-comparison.R | 1496 inst/shinyapp/modules/modules-ga-matrix-correlation.R | 778 inst/shinyapp/modules/modules-ga-scatter-correlation.R | 764 inst/shinyapp/modules/modules-ga-surv-analysis.R | 1440 inst/shinyapp/modules/modules-pancan-anatomy.R | 340 inst/shinyapp/modules/modules-pancan-genecor.R | 498 inst/shinyapp/modules/modules-pancan-immune.R | 352 inst/shinyapp/modules/modules-pancan-radar.R | 403 inst/shinyapp/modules/modules-pancan-search-cancer.R | 380 inst/shinyapp/modules/modules-pancan-search.R | 382 inst/shinyapp/modules/modules-pancan-til.R | 376 inst/shinyapp/modules/modules-pancan-unicox.R | 350 inst/shinyapp/modules/modules-pcawg-genecor.R | 590 inst/shinyapp/modules/modules-pcawg-search.R | 432 inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 736 inst/shinyapp/modules/modules-pcawg-unicox.R | 398 inst/shinyapp/modules/modules-survival-analysis.R | 842 inst/shinyapp/server/general-analysis.R | 384 inst/shinyapp/server/global.R | 32 inst/shinyapp/server/home.R | 170 inst/shinyapp/server/modules.R | 36 inst/shinyapp/server/repository.R | 832 inst/shinyapp/shiny-doc/citation.md | 108 inst/shinyapp/shiny-doc/datasets.md | 38 inst/shinyapp/shiny-doc/terms.md | 324 inst/shinyapp/shiny-doc/usage.md | 324 inst/shinyapp/ui/chooser.R | 94 inst/shinyapp/ui/developers.R | 244 inst/shinyapp/ui/footer.R | 32 inst/shinyapp/ui/general-analysis.R | 188 inst/shinyapp/ui/global.R | 22 inst/shinyapp/ui/help.R | 79 inst/shinyapp/ui/home.R | 284 inst/shinyapp/ui/pancan-analysis.R | 156 inst/shinyapp/ui/repository.R | 238 inst/shinyapp/www/bootstrap4.css | 704 inst/shinyapp/www/chooser-binding.js | 168 inst/shinyapp/www/css/bootstrap-grid.css | 4098 +- inst/shinyapp/www/css/bootstrap-grid.min.css | 12 inst/shinyapp/www/css/bootstrap-reboot.css | 658 inst/shinyapp/www/css/bootstrap-reboot.min.css | 14 inst/shinyapp/www/css/bootstrap.css |17948 +++++----- inst/shinyapp/www/css/bootstrap.min.css | 12 inst/shinyapp/www/js/bootstrap.bundle.js |12656 +++---- inst/shinyapp/www/js/bootstrap.bundle.min.js | 12 inst/shinyapp/www/js/bootstrap.js | 7788 ++-- inst/shinyapp/www/js/bootstrap.min.js | 12 man/TCGA.organ.Rd | 30 man/UCSCXenaShiny.Rd | 18 man/analyze_gene_drug_response_asso.Rd | 74 man/analyze_gene_drug_response_diff.Rd | 130 man/app_run.Rd | 54 man/available_hosts.Rd | 34 man/ccle_absolute.Rd | 36 man/ccle_info.Rd | 36 man/ezcor.Rd | 98 man/ezcor_batch.Rd | 104 man/ezcor_partial_cor.Rd | 98 man/get_pancan_value.Rd | 298 man/keep_cat_cols.Rd | 44 man/load_data.Rd | 122 man/pcawg_info.Rd | 36 man/pcawg_purity.Rd | 36 man/pipe.Rd | 24 man/query_molecule_value.Rd | 76 man/query_pancan_value.Rd | 120 man/query_toil_value_df.Rd | 68 man/tcga_clinical.Rd | 36 man/tcga_genome_instability.Rd | 36 man/tcga_gtex.Rd | 30 man/tcga_purity.Rd | 36 man/tcga_subtypes.Rd | 36 man/tcga_surv.Rd | 36 man/tcga_surv_analysis.Rd | 154 man/tcga_tmb.Rd | 36 man/toil_info.Rd | 36 man/vis_ccle_gene_cor.Rd | 108 man/vis_ccle_tpm.Rd | 44 man/vis_gene_TIL_cor.Rd | 74 man/vis_gene_cor.Rd | 84 man/vis_gene_cor_cancer.Rd | 96 man/vis_gene_drug_response_asso.Rd | 52 man/vis_gene_drug_response_diff.Rd | 70 man/vis_gene_immune_cor.Rd | 72 man/vis_gene_msi_cor.Rd | 66 man/vis_gene_stemness_cor.Rd | 110 man/vis_gene_tmb_cor.Rd | 66 man/vis_identifier_cor.Rd | 136 man/vis_identifier_grp_comparison.Rd | 210 man/vis_identifier_grp_surv.Rd | 144 man/vis_identifier_multi_cor.Rd | 146 man/vis_pancan_anatomy.Rd | 62 man/vis_pcawg_dist.Rd | 102 man/vis_pcawg_gene_cor.Rd | 120 man/vis_pcawg_unicox_tree.Rd | 74 man/vis_toil_TvsN.Rd | 118 man/vis_toil_TvsN_cancer.Rd | 92 man/vis_unicox_tree.Rd | 74 tests/testthat.R | 8 tests/testthat/test-run_app.R | 2 tests/testthat/test-vis_pancan_value.R | 10 vignettes/api.Rmd | 254 147 files changed, 40222 insertions(+), 38931 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 0.5.2 dated 2022-05-18 and 0.5.3 dated 2022-06-07
DESCRIPTION | 6 - MD5 | 35 +++++++---- NAMESPACE | 4 + NEWS.md | 6 + R/data.R | 5 + R/tw_get_cached_item.R | 2 R/tw_get_cached_search.R | 2 R/tw_get_image.R | 4 - R/tw_get_qualifiers.R | 19 +++++- R/tw_get_wikipedia_category_members.R |only R/tw_get_wikipedia_page_links.R | 2 R/tw_get_wikipedia_page_qid.R | 50 +++++++++++----- R/tw_get_wikipedia_page_sections.R | 2 data/tw_empty_wikipedia_category_members.rda |only inst/WORDLIST | 1 man/tw_empty_wikipedia_category_members.Rd |only man/tw_get_cached_wikipedia_category_members.Rd |only man/tw_get_wikipedia_base_api_url.Rd | 16 +++-- man/tw_get_wikipedia_category_members.Rd |only man/tw_get_wikipedia_category_members_single.Rd |only man/tw_reset_wikipedia_category_members_cache.Rd |only man/tw_write_wikipedia_category_members_to_cache.Rd |only tests/testthat/test-tw_get_wikipedia_category_members.R |only 23 files changed, 110 insertions(+), 44 deletions(-)
Title: Fast Region-Based Association Tests on Summary Statistics
Description: An adaptation of classical region/gene-based association analysis
techniques to the use of summary statistics (P values and effect sizes)
and correlations between genetic variants as input. It is a tool to perform
the most popular and efficient gene-based tests using the results of genome-wide
association (meta-)analyses without having the original genotypes and
phenotypes at hand.
See for details:
Svishcheva et al (2019) Gene-based association tests using GWAS summary
statistics. Bioinformatics.
Belonogova et al (2022) SumSTAAR: A flexible framework for gene-based
association studies using GWAS summary statistics. PLOS Comp Biol.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and
Gulnara R. Svishcheva <gulsvi@bionet.nsc.ru>
with contributions from:
Seunggeun Lee ,
Pierre Lafaye de Micheaux ,
Thomas Lumley ,
Minghui Wang, Yiyuan Liu, Shizhong Han ,
Yaowu Liu ,
James O. Ramsay ,
[...truncated...]
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>
Diff between sumFREGAT versions 1.2.4 dated 2022-03-25 and 1.2.5 dated 2022-06-07
ChangeLog | 5 ++++- DESCRIPTION | 11 ++++++++--- MD5 | 8 ++++---- R/sumSTAAR.R | 4 +++- man/sumSTAAR.rd | 5 +++-- 5 files changed, 22 insertions(+), 11 deletions(-)
More information about stortingscrape at CRAN
Permanent link
Title: Sequential Permutation Testing of Random Forest Variable
Importance Measures
Description: Sequential permutation testing for statistical
significance of predictors in random forests. The main function
of the package is rfvimptest(), which allows to test for the
statistical significance of predictors in random forests using different
(sequential) permutation test strategies. The advantage of
sequential over conventional permutation tests is that they
are computationally considerably less intensive, as the sequential
procedure is stopped as soon as there is sufficient evidence
for either the null or the alternative hypothesis.
Author: Alexander Hapfelmeier [aut],
Roman Hornung [aut, cre]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between rfvimptest versions 0.1.1 dated 2022-03-29 and 0.1.2 dated 2022-06-07
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/allinone.R | 2 +- R/rfvimptest.R | 2 +- build/partial.rdb |binary man/allinone.Rd | 2 +- man/rfvimptest.Rd | 2 +- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the 'ped
suite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.6.1 dated 2022-01-05 and 0.7.0 dated 2022-06-07
DESCRIPTION | 10 ++--- MD5 | 26 +++++++------- NEWS.md | 13 +++++++ R/likelihood.R | 18 ++++++---- R/merlin.R | 59 ++++++++++++++++++++-------------- R/reduceAlleles.R | 12 ++++-- R/utils.R | 12 +++++- README.md | 33 +++++++++---------- build/partial.rdb |binary man/likelihood.Rd | 13 +++++-- man/lumpAlleles.Rd | 5 ++ man/merlin.Rd | 48 +++++++++++++++++---------- tests/testthat/test-inbred-founders.R | 6 +-- tests/testthat/test-likelihood-list.R | 12 +++--- 14 files changed, 163 insertions(+), 104 deletions(-)
Title: A Model Object Framework for Regression Analysis
Description: A utility library to facilitate the generalization of statistical methods built on a regression framework. Package developers can use 'modelObj' methods to initiate a regression analysis without concern for the details of the regression model and the method to be used to obtain parameter estimates. The specifics of the regression step are left to the user to define when calling the function. The user of a function developed within the 'modelObj' framework creates as input a 'modelObj' that contains the model and the R methods to be used to obtain parameter estimates and to obtain predictions. In this way, a user can easily go from linear to non-linear models within the same package.
Author: Shannon T. Holloway
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between modelObj versions 4.1 dated 2021-07-16 and 4.2 dated 2022-06-07
DESCRIPTION | 10 +- MD5 | 8 - build/vignette.rds |binary inst/doc/modelObj.R | 208 +++++++++++++++++++++++++------------------------- inst/doc/modelObj.pdf |binary 5 files changed, 113 insertions(+), 113 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 12C/13C 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 1.5 dated 2022-05-18 and 1.6 dated 2022-06-07
DESCRIPTION | 11 -- MD5 | 57 +++++------ R/IPA_CompoundsAnnotation.R | 8 - R/IPA_MSdeconvoluter.R | 4 R/IPA_PeakAlignment.R | 38 ++++--- R/IPA_PeakAnalyzer.R | 40 +++++-- R/IPA_Workflow.R | 152 ++++++++++++++--------------- R/IPA_xlsxAnalyzer.R | 55 +++------- R/XIC.R | 36 +++---- R/carbon_isotopes_explorer.R | 33 ++++-- R/der_5points_stencil.R | 6 - R/fronting_tailing_resolver.R | 2 R/gaussianity_measurement.R | 4 R/islocalminimum.R | 2 R/mz_clustering_xic.R | 98 +++++++++---------- R/peak_Xcol2.R | 3 R/peak_alignment.R | 216 +++++++++++++++++++++++++----------------- R/peak_area.R | 8 - R/peak_sharpness.R | 8 - R/peak_width.R | 8 - R/plot_mz_eic.R | 2 R/plot_simple_tic.R | 2 R/reference_peaks_detector.R | 2 R/sample_rt_corrector.R | 11 -- R/snr_rms.R | 6 - R/snr_xcms.R | 4 R/spectraList_filtering.R | 8 - R/xlsxAnalyzer_EIC.R | 33 +----- build/partial.rdb |binary inst/CITATION |only 30 files changed, 451 insertions(+), 406 deletions(-)
More information about RcmdrPlugin.BWS2 at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-07 0.1.0
Title: Local Pattern Analysis
Description: Describes spatial patterns of categorical raster data for
any defined regular and irregular areas.
Patterns are described quantitatively using built-in signatures
based on co-occurrence matrices but also allows for
any user-defined functions.
It enables spatial analysis such as search, change detection,
and clustering to be performed on spatial patterns (Nowosad (2021) <doi:10.1007/s10980-020-01135-0>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between motif versions 0.5.0 dated 2021-08-23 and 0.5.2 dated 2022-06-07
motif-0.5.0/motif/R/temp.R |only motif-0.5.2/motif/DESCRIPTION | 12 motif-0.5.2/motif/MD5 | 44 +-- motif-0.5.2/motif/NAMESPACE | 2 motif-0.5.2/motif/NEWS.md | 9 motif-0.5.2/motif/R/lsp_add_clusters.R | 10 motif-0.5.2/motif/R/lsp_add_quality.R | 2 motif-0.5.2/motif/R/lsp_add_spatial.R | 19 - motif-0.5.2/motif/R/lsp_compare.R | 18 - motif-0.5.2/motif/R/lsp_extract.R | 2 motif-0.5.2/motif/R/lsp_mosaic.R | 2 motif-0.5.2/motif/R/lsp_search.R | 16 - motif-0.5.2/motif/README.md | 14 - motif-0.5.2/motif/build/partial.rdb |only motif-0.5.2/motif/build/vignette.rds |binary motif-0.5.2/motif/inst/doc/v1_intro.Rmd | 10 motif-0.5.2/motif/inst/doc/v1_intro.html | 372 ++++++------------------------ motif-0.5.2/motif/man/lsp_add_clusters.Rd | 10 motif-0.5.2/motif/man/lsp_add_quality.Rd | 2 motif-0.5.2/motif/man/lsp_add_terra.Rd | 12 motif-0.5.2/motif/man/lsp_compare.Rd | 18 - motif-0.5.2/motif/man/lsp_search.Rd | 19 - motif-0.5.2/motif/man/motif-package.Rd | 12 motif-0.5.2/motif/vignettes/v1_intro.Rmd | 10 24 files changed, 188 insertions(+), 427 deletions(-)
Title: Sample Size Calculations for Microarray Experiments
Description: Functions that calculate appropriate sample sizes for one-sample t-tests, two-sample t-tests, and F-tests for microarray experiments based on desired power while controlling for false discovery rates. For all tests, the standard deviations (variances) among genes can be assumed fixed or random. This is also true for effect sizes among genes in one-sample and two sample experiments. Functions also output a chart of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes.
Author: Megan Orr [aut, cre], Peng Liu [aut]
Maintainer: Megan Orr <megan.orr@ndsu.edu>
Diff between ssize.fdr versions 1.2 dated 2015-02-22 and 1.3 dated 2022-06-07
ssize.fdr-1.2/ssize.fdr/R/ssize.fdr-internal.R |only ssize.fdr-1.3/ssize.fdr/DESCRIPTION | 20 ++----- ssize.fdr-1.3/ssize.fdr/MD5 | 19 +++---- ssize.fdr-1.3/ssize.fdr/NAMESPACE | 3 + ssize.fdr-1.3/ssize.fdr/man/ssize.F.Rd | 24 ++++----- ssize.fdr-1.3/ssize.fdr/man/ssize.Fvary.rd | 26 ++++----- ssize.fdr-1.3/ssize.fdr/man/ssize.fdr-package.Rd | 60 +++++++++++------------ ssize.fdr-1.3/ssize.fdr/man/ssize.oneSamp.Rd | 16 +++--- ssize.fdr-1.3/ssize.fdr/man/ssize.oneSampVary.Rd | 28 +++++----- ssize.fdr-1.3/ssize.fdr/man/ssize.twoSamp.Rd | 22 ++++---- ssize.fdr-1.3/ssize.fdr/man/ssize.twoSampVary.Rd | 32 ++++++------ 11 files changed, 122 insertions(+), 128 deletions(-)
Title: Spatial Analysis of Field Trials with Splines
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
Author: Maria Xose Rodriguez-Alvarez [aut, cre],
Martin Boer [aut],
Paul Eilers [aut],
Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@uvigo.es>
Diff between SpATS versions 1.0-16 dated 2021-11-24 and 1.0-17 dated 2022-06-07
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NEWS | 5 ++++- R/plot.variogram.SpATS.R | 13 ++++++++++++- man/SpATS-package.Rd | 4 ++-- 5 files changed, 27 insertions(+), 14 deletions(-)
Title: Extract Semantic Relations from Text by Querying and Reshaping
Syntax
Description: Various functions for querying and reshaping dependency trees,
as for instance created with the 'spacyr' or 'udpipe' packages.
This enables the automatic extraction of useful semantic relations from texts,
such as quotes (who said what) and clauses (who did what). Method proposed in
Van Atteveldt et al. (2017) <doi:10.1017/pan.2016.12>.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between rsyntax versions 0.1.3 dated 2022-01-24 and 0.1.4 dated 2022-06-07
DESCRIPTION | 11 +-- MD5 | 24 +++--- R/find_nodes.r | 34 ++++----- R/plot_tree.r | 110 +++++++++++++++++++++--------- R/recursive_search.r | 25 ++++-- R/tquery.r | 4 + README.md | 79 ++++++--------------- man/custom_fill.Rd | 4 + man/figures/README-fig1-1.png |only man/figures/README-tree-1.pdf |binary man/figures/README-tree-2.pdf |binary man/figures/README-unnamed-chunk-17-1.png |only man/plot_tree.Rd | 3 tests/testthat/test_find_nodes.r | 1 14 files changed, 167 insertions(+), 128 deletions(-)
Title: Dynamically Pluralize Phrases
Description: Converts English phrases to singular or plural form based on
the length of an associated vector. Contains helper functions to
create natural language lists from vectors and to include the length
of a vector in natural language.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between plu versions 0.2.1 dated 2021-04-07 and 0.2.2 dated 2022-06-07
plu-0.2.1/plu/R/onLoad.R |only plu-0.2.1/plu/R/tosentence.R |only plu-0.2.2/plu/DESCRIPTION | 8 plu-0.2.2/plu/LICENSE | 4 plu-0.2.2/plu/MD5 | 63 +- plu-0.2.2/plu/NAMESPACE | 32 - plu-0.2.2/plu/NEWS.md | 146 +++--- plu-0.2.2/plu/R/errors.R | 78 +-- plu-0.2.2/plu/R/get_fun.R | 96 ++-- plu-0.2.2/plu/R/is_capital.R | 186 +++---- plu-0.2.2/plu/R/plu-package.R | 328 ++++++------- plu-0.2.2/plu/R/plu_more.R | 142 +++--- plu-0.2.2/plu/R/plu_nge.R | 20 plu-0.2.2/plu/R/plu_ral.R | 512 ++++++++++----------- plu-0.2.2/plu/R/plu_ralize.R | 132 ++--- plu-0.2.2/plu/R/plu_split.R | 16 plu-0.2.2/plu/R/plu_stick.R | 165 +++--- plu-0.2.2/plu/R/release_questions.R | 6 plu-0.2.2/plu/R/sysdata.rda |binary plu-0.2.2/plu/R/utils_str.R |only plu-0.2.2/plu/README.md | 198 ++++---- plu-0.2.2/plu/build/plu.pdf |binary plu-0.2.2/plu/inst/COPYRIGHTS | 318 ++++++------- plu-0.2.2/plu/man/capitalize.Rd | 116 ++-- plu-0.2.2/plu/man/figures/weather_blue.svg | 60 +- plu-0.2.2/plu/man/figures/weather_green.svg | 60 +- plu-0.2.2/plu/man/figures/weather_orange.svg | 60 +- plu-0.2.2/plu/tests/testthat.R | 8 plu-0.2.2/plu/tests/testthat/test-get_fun.R | 66 +- plu-0.2.2/plu/tests/testthat/test-is_capital.R | 366 +++++++-------- plu-0.2.2/plu/tests/testthat/test-plu_more.R | 273 +++++------ plu-0.2.2/plu/tests/testthat/test-plu_ral.R | 590 ++++++++++++------------- plu-0.2.2/plu/tests/testthat/test-plu_ralize.R | 140 ++--- plu-0.2.2/plu/tests/testthat/test-plu_stick.R | 134 +++-- 34 files changed, 2168 insertions(+), 2155 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
Pedigree plots are produced by wrapping the plotting functionality of
the 'kinship2' package. A Shiny app for creating pedigrees, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'ped suite', a collection of packages for
pedigree analysis. A detailed presentation of the 'ped suite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 1.2.0 dated 2022-03-30 and 1.3.0 dated 2022-06-07
DESCRIPTION | 8 - MD5 | 65 ++++----- NAMESPACE | 2 NEWS.md | 36 ++++- R/getMap.R | 60 +++++++- R/marker_distribute.R | 6 R/marker_getattr.R | 7 R/marker_properties.R | 44 +++--- R/marker_setattr.R | 47 +++++- R/marker_utils.R | 90 ++++++++++++ R/mergePed.R | 140 +++++++++++++++---- R/ped_basic.R | 61 ++++++-- R/ped_modify.R | 94 +++++++++---- R/readPed.R | 2 R/writePed.R | 59 ++++++++ README.md | 15 +- build/vignette.rds |binary inst/doc/pedtools.R | 30 ++-- inst/doc/pedtools.Rmd | 41 +++-- inst/doc/pedtools.html | 228 ++++++++++++++++---------------- man/addAllele.Rd |only man/figures/README-example-1.png |binary man/getMap.Rd | 5 man/marker_prop.Rd | 28 +-- man/marker_setattr.Rd | 5 man/mergePed.Rd | 81 ++++++++--- man/ped_basic.Rd | 38 ++++- man/ped_modify.Rd | 28 +-- man/readPed.Rd | 2 tests/testthat/test-marker-accessors.R | 15 ++ tests/testthat/test-marker-distribute.R | 12 + tests/testthat/test-ped-modifications.R | 12 + tests/testthat/test-ped-utils.R | 37 +++++ vignettes/pedtools.Rmd | 41 +++-- 34 files changed, 958 insertions(+), 381 deletions(-)
Title: Calculating Linkage Disequilibrium (LD) in Human Population
Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nci.nih.gov/?tab=apiaccess>)
using the R console. This programmatic access facilitates researchers who are
interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393>
data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying
germline variants in human population groups of interest. For more details, please see
Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre] ,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>
Diff between LDlinkR versions 1.2.0 dated 2022-05-11 and 1.2.1 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md | 7 +++++++ R/LDexpress.R | 2 +- R/LDproxy.R | 25 +++---------------------- build/partial.rdb |only inst/WORDLIST | 1 + inst/doc/LDlinkR.html | 6 +++--- man/LDlinkR-package.Rd | 4 ++-- 9 files changed, 29 insertions(+), 39 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.5.6 dated 2022-04-11 and 0.6.0 dated 2022-06-07
DESCRIPTION | 8 MD5 | 52 - NAMESPACE | 4 NEWS | 32 R/correlate.R | 13 R/graphics.R | 11 R/html_eda.R | 15 R/html_transformation.R | 6 R/imputation.R | 30 R/report.R | 24 R/report_tbl_dbi.R | 8 R/stats.R | 47 + R/tbl_dbi.R | 32 R/univariate.R | 3 inst/doc/EDA.R | 24 inst/doc/EDA.Rmd | 10 inst/doc/EDA.html | 1445 +++++++++++++++++++++---------------------- inst/doc/diagonosis.html | 27 inst/doc/introduce.Rmd | 10 inst/doc/introduce.html | 217 +++--- inst/doc/transformation.html | 1179 +++++++++++++++++------------------ man/correlate.data.frame.Rd | 2 man/cramer.Rd |only man/imputate_outlier.Rd | 13 man/plot.correlate.Rd | 1 man/theil.Rd |only vignettes/EDA.Rmd | 10 vignettes/introduce.Rmd | 10 28 files changed, 1722 insertions(+), 1511 deletions(-)
Title: Clinical Trial Registry History
Description: Retrieves historical versions of clinical trial registry
entries.
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Diff between cthist versions 1.0.0 dated 2022-04-08 and 1.2.1 dated 2022-06-07
DESCRIPTION | 10 - MD5 | 22 +-- NEWS.md | 47 ++++++ R/clinicaltrials_gov_dates.R | 50 ++++++- R/clinicaltrials_gov_download.R | 30 ++-- R/clinicaltrials_gov_version.R | 157 ++++++++++++++--------- R/drks_de_dates.R | 19 ++ R/drks_de_download.R | 14 +- R/drks_de_version.R | 6 README.md | 5 man/clinicaltrials_gov_dates.Rd | 5 tests/testthat/test-clinicaltrials_gov_version.R | 2 12 files changed, 265 insertions(+), 102 deletions(-)
Title: Quantile, Composite Quantile Regression and Regularized Versions
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao <jueyu@ualberta.ca>
Diff between cqrReg versions 1.2 dated 2015-04-08 and 1.2.1 dated 2022-06-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Sparse Matrix Format with Data on Disk
Description: Provide a sparse matrix format with data stored on disk, to be
used in both R and C++. This is intended for more efficient use of sparse
data in C++ and also when parallelizing, since data on disk does not need
copying. Only a limited number of features will be implemented. For now,
conversion can be performed from a 'dgCMatrix' or a 'dsCMatrix' from R
package 'Matrix'. A new compact format is also now available.
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigsparser versions 0.6.0 dated 2022-02-22 and 0.6.1 dated 2022-06-07
bigsparser-0.6.0/bigsparser/inst/testdata |only bigsparser-0.6.1/bigsparser/DESCRIPTION | 12 +-- bigsparser-0.6.1/bigsparser/MD5 | 26 ++++---- bigsparser-0.6.1/bigsparser/NAMESPACE | 2 bigsparser-0.6.1/bigsparser/R/RcppExports.R | 8 ++ bigsparser-0.6.1/bigsparser/R/spmat-accessor.R |only bigsparser-0.6.1/bigsparser/README.md | 15 ++++ bigsparser-0.6.1/bigsparser/inst/include/bigsparser/EigenMatrixReplacement.h | 2 bigsparser-0.6.1/bigsparser/inst/include/bigsparser/SFBM.h | 1 bigsparser-0.6.1/bigsparser/man/bigsparser-package.Rd | 2 bigsparser-0.6.1/bigsparser/man/crochet.Rd |only bigsparser-0.6.1/bigsparser/src/RcppExports.cpp | 28 ++++++++ bigsparser-0.6.1/bigsparser/src/spmat-accessor.cpp |only bigsparser-0.6.1/bigsparser/tests/testthat/test-SFBM-compact.R | 32 ++++------ bigsparser-0.6.1/bigsparser/tests/testthat/test-accessor.R |only bigsparser-0.6.1/bigsparser/tests/testthat/testdata |only 16 files changed, 92 insertions(+), 36 deletions(-)